From 9f4090952a6a0550844868afc9c07f01761e2d30 Mon Sep 17 00:00:00 2001 From: Alan Garny Date: Wed, 14 Jan 2026 16:30:53 +1300 Subject: [PATCH] Generator: have our `computedConstants()` method use `algebraicVariables` rather than `algebraic`. --- src/generatorprofile.cpp | 20 +- src/generatorprofilesha1values.h | 4 +- .../bindings/python/test_generator_profile.py | 10 +- tests/generator/generatorprofile.cpp | 10 +- tests/resources/coverage/generator/model.c | 4 +- tests/resources/coverage/generator/model.h | 2 +- .../generator/model.implementation.out | 2 +- .../coverage/generator/model.interface.out | 2 +- .../generator/model.modified.profile.c | 4 +- .../generator/model.modified.profile.h | 2 +- .../generator/model.modified.profile.py | 26 +- .../coverage/generator/model.no.tracking.c | 4 +- .../coverage/generator/model.no.tracking.h | 2 +- tests/resources/coverage/generator/model.out | 2 +- tests/resources/coverage/generator/model.py | 26 +- .../algebraic_eqn_computed_var_on_rhs/model.c | 4 +- .../model.external.c | 4 +- .../model.external.h | 2 +- .../model.external.py | 8 +- .../algebraic_eqn_computed_var_on_rhs/model.h | 2 +- .../model.py | 4 +- .../algebraic_eqn_const_var_on_rhs/model.c | 4 +- .../algebraic_eqn_const_var_on_rhs/model.h | 2 +- .../algebraic_eqn_const_var_on_rhs/model.py | 4 +- .../algebraic_eqn_constant_on_rhs/model.c | 4 +- .../algebraic_eqn_constant_on_rhs/model.h | 2 +- .../algebraic_eqn_constant_on_rhs/model.py | 4 +- .../algebraic_eqn_derivative_on_rhs/model.c | 4 +- .../algebraic_eqn_derivative_on_rhs/model.h | 2 +- .../algebraic_eqn_derivative_on_rhs/model.py | 6 +- .../model.c | 4 +- .../model.h | 2 +- .../model.py | 6 +- .../algebraic_eqn_state_var_on_rhs/model.c | 4 +- .../algebraic_eqn_state_var_on_rhs/model.h | 2 +- .../algebraic_eqn_state_var_on_rhs/model.py | 6 +- .../model.c | 4 +- .../model.h | 2 +- .../model.py | 6 +- .../model.c | 4 +- .../model.external.c | 4 +- .../model.external.h | 2 +- .../model.external.py | 16 +- .../model.h | 2 +- .../model.py | 14 +- .../model.c | 4 +- .../model.external.c | 4 +- .../model.external.h | 2 +- .../model.external.py | 10 +- .../model.h | 2 +- .../model.py | 34 +- .../model.not.ordered.c | 4 +- .../model.not.ordered.h | 2 +- .../model.not.ordered.py | 26 +- .../model.ordered.c | 4 +- .../model.ordered.h | 2 +- .../model.ordered.py | 26 +- .../algebraic_unknown_var_on_rhs/model.c | 4 +- .../algebraic_unknown_var_on_rhs/model.h | 2 +- .../algebraic_unknown_var_on_rhs/model.py | 4 +- .../generator/cell_geometry_model/model.c | 4 +- .../cell_geometry_model/model.external.c | 4 +- .../cell_geometry_model/model.external.h | 2 +- .../cell_geometry_model/model.external.py | 12 +- .../generator/cell_geometry_model/model.h | 2 +- .../generator/cell_geometry_model/model.py | 4 +- .../model.c | 4 +- .../model.h | 2 +- .../model.py | 8 +- .../generator/cellml_slc_example/model.py | 4 +- .../model.c | 4 +- .../model.h | 2 +- .../model.py | 4 +- .../cellml_unit_scaling_constant/model.c | 4 +- .../cellml_unit_scaling_constant/model.h | 2 +- .../cellml_unit_scaling_constant/model.py | 4 +- .../cellml_unit_scaling_rate/model.c | 4 +- .../cellml_unit_scaling_rate/model.h | 2 +- .../cellml_unit_scaling_rate/model.py | 8 +- .../cellml_unit_scaling_state/model.c | 4 +- .../cellml_unit_scaling_state/model.h | 2 +- .../cellml_unit_scaling_state/model.py | 8 +- .../model.c | 4 +- .../model.h | 2 +- .../model.py | 4 +- .../model.c | 4 +- .../model.h | 2 +- .../model.py | 4 +- .../cellml_unit_scaling_voi_direct/model.c | 4 +- .../cellml_unit_scaling_voi_direct/model.h | 2 +- .../cellml_unit_scaling_voi_direct/model.py | 4 +- .../cellml_unit_scaling_voi_indirect/model.c | 4 +- .../cellml_unit_scaling_voi_indirect/model.h | 2 +- .../cellml_unit_scaling_voi_indirect/model.py | 4 +- .../generator/dae_cellml_1_1_model/model.c | 4 +- .../generator/dae_cellml_1_1_model/model.h | 2 +- .../generator/dae_cellml_1_1_model/model.py | 40 +- .../generator/dependent_eqns/model.c | 4 +- .../generator/dependent_eqns/model.h | 2 +- .../generator/dependent_eqns/model.py | 8 +- .../model.c | 4 +- .../model.h | 2 +- .../model.py | 462 +++++++++--------- .../model.c | 4 +- .../model.h | 2 +- .../model.py | 242 ++++----- .../model.algebraic.c | 4 +- .../model.algebraic.h | 2 +- .../model.algebraic.py | 52 +- .../model.c | 4 +- .../model.computed.constant.c | 4 +- .../model.computed.constant.h | 2 +- .../model.computed.constant.py | 54 +- .../model.constant.c | 4 +- .../model.constant.h | 2 +- .../model.constant.py | 54 +- .../model.dae.c | 4 +- .../model.dae.external.c | 4 +- .../model.dae.external.h | 2 +- .../model.dae.external.py | 134 ++--- .../model.dae.for.tracking.control.c | 4 +- .../model.dae.for.tracking.control.h | 2 +- .../model.dae.for.tracking.control.py | 130 ++--- ....dae.for.tracking.control.with.externals.c | 4 +- ....dae.for.tracking.control.with.externals.h | 2 +- ...dae.for.tracking.control.with.externals.py | 124 ++--- ...r.tracking.untracked.algebraic.variables.c | 4 +- ...r.tracking.untracked.algebraic.variables.h | 2 +- ....tracking.untracked.algebraic.variables.py | 126 ++--- ...acked.algebraic.variables.with.externals.c | 4 +- ...acked.algebraic.variables.with.externals.h | 2 +- ...cked.algebraic.variables.with.externals.py | 124 ++--- ...or.tracking.untracked.computed.constants.c | 4 +- ...or.tracking.untracked.computed.constants.h | 2 +- ...r.tracking.untracked.computed.constants.py | 130 ++--- ...racked.computed.constants.with.externals.c | 4 +- ...racked.computed.constants.with.externals.h | 2 +- ...acked.computed.constants.with.externals.py | 124 ++--- ...del.dae.for.tracking.untracked.constants.c | 4 +- ...del.dae.for.tracking.untracked.constants.h | 2 +- ...el.dae.for.tracking.untracked.constants.py | 130 ++--- ...cking.untracked.constants.with.externals.c | 4 +- ...cking.untracked.constants.with.externals.h | 2 +- ...king.untracked.constants.with.externals.py | 124 ++--- ...del.dae.for.tracking.untracked.variables.c | 4 +- ...del.dae.for.tracking.untracked.variables.h | 2 +- ...el.dae.for.tracking.untracked.variables.py | 126 ++--- ...cking.untracked.variables.with.externals.c | 4 +- ...cking.untracked.variables.with.externals.h | 2 +- ...king.untracked.variables.with.externals.py | 124 ++--- .../model.dae.h | 2 +- .../model.dae.py | 146 +++--- .../model.dependent.algebraic.c | 4 +- .../model.dependent.algebraic.h | 2 +- .../model.dependent.algebraic.py | 52 +- .../model.dependent.computed.constant.c | 4 +- .../model.dependent.computed.constant.h | 2 +- .../model.dependent.computed.constant.py | 66 +-- .../model.dependent.constant.c | 4 +- .../model.dependent.constant.h | 2 +- .../model.dependent.constant.py | 58 +-- .../model.dependent.state.c | 4 +- .../model.dependent.state.h | 2 +- .../model.dependent.state.py | 34 +- .../model.external.c | 4 +- .../model.external.h | 2 +- .../model.external.py | 36 +- .../model.h | 2 +- .../model.py | 50 +- .../model.state.c | 4 +- .../model.state.h | 2 +- .../model.state.py | 48 +- .../model.untracked.algebraic.variables.c | 4 +- .../model.untracked.algebraic.variables.h | 2 +- .../model.untracked.algebraic.variables.py | 4 +- ...acked.algebraic.variables.with.externals.c | 4 +- ...acked.algebraic.variables.with.externals.h | 2 +- ...cked.algebraic.variables.with.externals.py | 16 +- .../model.untracked.computed.constants.c | 4 +- .../model.untracked.computed.constants.h | 2 +- .../model.untracked.computed.constants.py | 50 +- ...racked.computed.constants.with.externals.c | 4 +- ...racked.computed.constants.with.externals.h | 2 +- ...acked.computed.constants.with.externals.py | 50 +- .../model.untracked.constants.c | 4 +- .../model.untracked.constants.h | 2 +- .../model.untracked.constants.py | 50 +- ...model.untracked.constants.with.externals.c | 4 +- ...model.untracked.constants.with.externals.h | 2 +- ...odel.untracked.constants.with.externals.py | 50 +- .../model.untracked.variables.c | 4 +- .../model.untracked.variables.h | 2 +- .../model.untracked.variables.py | 4 +- ...model.untracked.variables.with.externals.c | 4 +- ...model.untracked.variables.with.externals.h | 2 +- ...odel.untracked.variables.with.externals.py | 16 +- .../generator/noble_model_1962/model.c | 4 +- .../generator/noble_model_1962/model.h | 2 +- .../generator/noble_model_1962/model.py | 60 +-- .../generator/ode_computed_var_on_rhs/model.c | 4 +- .../generator/ode_computed_var_on_rhs/model.h | 2 +- .../ode_computed_var_on_rhs/model.py | 4 +- .../model.c | 4 +- .../model.h | 2 +- .../model.py | 4 +- .../generator/ode_const_var_on_rhs/model.c | 4 +- .../generator/ode_const_var_on_rhs/model.h | 2 +- .../generator/ode_const_var_on_rhs/model.py | 4 +- .../model.c | 4 +- .../model.h | 2 +- .../model.py | 4 +- .../generator/ode_constant_on_rhs/model.c | 4 +- .../generator/ode_constant_on_rhs/model.h | 2 +- .../generator/ode_constant_on_rhs/model.py | 4 +- .../ode_constant_on_rhs_one_component/model.c | 4 +- .../ode_constant_on_rhs_one_component/model.h | 2 +- .../model.py | 4 +- .../ode_multiple_dependent_odes/model.c | 4 +- .../ode_multiple_dependent_odes/model.h | 2 +- .../ode_multiple_dependent_odes/model.py | 4 +- .../model.c | 4 +- .../model.h | 2 +- .../model.py | 4 +- .../ode_multiple_odes_with_same_name/model.c | 4 +- .../ode_multiple_odes_with_same_name/model.h | 2 +- .../ode_multiple_odes_with_same_name/model.py | 4 +- .../generator/ode_unknown_var_on_rhs/model.c | 4 +- .../generator/ode_unknown_var_on_rhs/model.h | 2 +- .../generator/ode_unknown_var_on_rhs/model.py | 4 +- .../robertson_model_1966/model.dae.c | 4 +- .../robertson_model_1966/model.dae.h | 2 +- .../robertson_model_1966/model.dae.py | 20 +- .../robertson_model_1966/model.ode.c | 4 +- .../robertson_model_1966/model.ode.h | 2 +- .../robertson_model_1966/model.ode.py | 6 +- .../generator/sine_model_imports/model.c | 4 +- .../generator/sine_model_imports/model.h | 2 +- .../generator/sine_model_imports/model.py | 10 +- .../model.c | 4 +- .../model.h | 2 +- .../model.py | 8 +- .../model.c | 4 +- .../model.h | 2 +- .../model.py | 242 ++++----- 244 files changed, 2121 insertions(+), 2121 deletions(-) diff --git a/src/generatorprofile.cpp b/src/generatorprofile.cpp index ed7f3f847..649f40ced 100644 --- a/src/generatorprofile.cpp +++ b/src/generatorprofile.cpp @@ -225,7 +225,7 @@ void GeneratorProfile::GeneratorProfileImpl::loadProfile(GeneratorProfile::Profi "#include \n"; mInterfaceVersionString = "extern const char VERSION[];\n"; - mImplementationVersionString = "const char VERSION[] = \"0.7.0\";\n"; + mImplementationVersionString = "const char VERSION[] = \"0.8.0\";\n"; mInterfaceLibcellmlVersionString = "extern const char LIBCELLML_VERSION[];\n"; mImplementationLibcellmlVersionString = "const char LIBCELLML_VERSION[] = \"[LIBCELLML_VERSION]\";\n"; @@ -489,14 +489,14 @@ void GeneratorProfile::GeneratorProfileImpl::loadProfile(GeneratorProfile::Profi "[CODE]" "}\n"; - mInterfaceComputeComputedConstantsMethodNonDiffString = "void computeComputedConstants(double *constants, double *computedConstants, double *algebraic);\n"; - mImplementationComputeComputedConstantsMethodNonDiffString = "void computeComputedConstants(double *constants, double *computedConstants, double *algebraic)\n" + mInterfaceComputeComputedConstantsMethodNonDiffString = "void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables);\n"; + mImplementationComputeComputedConstantsMethodNonDiffString = "void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables)\n" "{\n" "[CODE]" "}\n"; - mInterfaceComputeComputedConstantsMethodDiffString = "void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic);\n"; - mImplementationComputeComputedConstantsMethodDiffString = "void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic)\n" + mInterfaceComputeComputedConstantsMethodDiffString = "void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables);\n"; + mImplementationComputeComputedConstantsMethodDiffString = "void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables)\n" "{\n" "[CODE]" "}\n"; @@ -741,7 +741,7 @@ void GeneratorProfile::GeneratorProfileImpl::loadProfile(GeneratorProfile::Profi "\n"; mInterfaceVersionString = ""; - mImplementationVersionString = "__version__ = \"0.6.0\"\n"; + mImplementationVersionString = "__version__ = \"0.8.0\"\n"; mInterfaceLibcellmlVersionString = ""; mImplementationLibcellmlVersionString = "LIBCELLML_VERSION = \"[LIBCELLML_VERSION]\"\n"; @@ -799,8 +799,8 @@ void GeneratorProfile::GeneratorProfileImpl::loadProfile(GeneratorProfile::Profi mRatesArrayString = "rates"; mConstantsArrayString = "constants"; mComputedConstantsArrayString = "computed_constants"; - mAlgebraicVariablesArrayString = "algebraicVariables"; - mExternalVariablesArrayString = "externalVariables"; + mAlgebraicVariablesArrayString = "algebraic_variables"; + mExternalVariablesArrayString = "external_variables"; mExternalVariableMethodTypeDefinitionNonDiffString = ""; mExternalVariableMethodTypeDefinitionDiffString = ""; @@ -928,12 +928,12 @@ void GeneratorProfile::GeneratorProfileImpl::loadProfile(GeneratorProfile::Profi mInterfaceComputeComputedConstantsMethodNonDiffString = ""; mImplementationComputeComputedConstantsMethodNonDiffString = "\n" - "def compute_computed_constants(constants, computed_constants, algebraic):\n" + "def compute_computed_constants(constants, computed_constants, algebraic_variables):\n" "[CODE]"; mInterfaceComputeComputedConstantsMethodDiffString = ""; mImplementationComputeComputedConstantsMethodDiffString = "\n" - "def compute_computed_constants(states, rates, constants, computed_constants, algebraic):\n" + "def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ):\n" "[CODE]"; mInterfaceComputeRatesMethodWoevString = ""; diff --git a/src/generatorprofilesha1values.h b/src/generatorprofilesha1values.h index c21e4fcfe..2de1cb57d 100644 --- a/src/generatorprofilesha1values.h +++ b/src/generatorprofilesha1values.h @@ -24,7 +24,7 @@ namespace libcellml { * The content of this file is generated, do not edit this file directly. * See docs/dev_utilities.rst for further information. */ -static const char C_GENERATOR_PROFILE_SHA1[] = "24b7a2f82510d2f79aeaee509a1b1b04ea1d749b"; -static const char PYTHON_GENERATOR_PROFILE_SHA1[] = "b117a2500aae147f477127f0bfb0e2c9e242c6c8"; +static const char C_GENERATOR_PROFILE_SHA1[] = "4270b05a372c6224e650ca4efd193fb0f0838b14"; +static const char PYTHON_GENERATOR_PROFILE_SHA1[] = "143e1fe4a300b1b447fb8a2eda5144e7aca27e5e"; } // namespace libcellml diff --git a/tests/bindings/python/test_generator_profile.py b/tests/bindings/python/test_generator_profile.py index a5d27226c..40e086e93 100644 --- a/tests/bindings/python/test_generator_profile.py +++ b/tests/bindings/python/test_generator_profile.py @@ -698,12 +698,12 @@ def test_implementation_compute_computed_constants_method_string(self): g = GeneratorProfile() - self.assertEqual('void computeComputedConstants(double *constants, double *computedConstants, double *algebraic)\n{\n[CODE]}\n', + self.assertEqual('void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables)\n{\n[CODE]}\n', g.implementationComputeComputedConstantsMethodString(False)) g.setImplementationComputeComputedConstantsMethodString(False, GeneratorProfileTestCase.VALUE) self.assertEqual(GeneratorProfileTestCase.VALUE, g.implementationComputeComputedConstantsMethodString(False)) - self.assertEqual('void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic)\n{\n[CODE]}\n', + self.assertEqual('void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables)\n{\n[CODE]}\n', g.implementationComputeComputedConstantsMethodString(True)) g.setImplementationComputeComputedConstantsMethodString(True, GeneratorProfileTestCase.VALUE) self.assertEqual(GeneratorProfileTestCase.VALUE, g.implementationComputeComputedConstantsMethodString(True)) @@ -949,7 +949,7 @@ def test_implementation_version_string(self): g = GeneratorProfile() - self.assertEqual('const char VERSION[] = "0.7.0";\n', g.implementationVersionString()) + self.assertEqual('const char VERSION[] = "0.8.0";\n', g.implementationVersionString()) g.setImplementationVersionString(GeneratorProfileTestCase.VALUE) self.assertEqual(GeneratorProfileTestCase.VALUE, g.implementationVersionString()) @@ -985,12 +985,12 @@ def test_interface_compute_computed_constants_method_string(self): g = GeneratorProfile() - self.assertEqual('void computeComputedConstants(double *constants, double *computedConstants, double *algebraic);\n', + self.assertEqual('void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables);\n', g.interfaceComputeComputedConstantsMethodString(False)) g.setInterfaceComputeComputedConstantsMethodString(False, GeneratorProfileTestCase.VALUE) self.assertEqual(GeneratorProfileTestCase.VALUE, g.interfaceComputeComputedConstantsMethodString(False)) - self.assertEqual('void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic);\n', + self.assertEqual('void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables);\n', g.interfaceComputeComputedConstantsMethodString(True)) g.setInterfaceComputeComputedConstantsMethodString(True, GeneratorProfileTestCase.VALUE) self.assertEqual(GeneratorProfileTestCase.VALUE, g.interfaceComputeComputedConstantsMethodString(True)) diff --git a/tests/generator/generatorprofile.cpp b/tests/generator/generatorprofile.cpp index 683a9692b..5dc60248f 100644 --- a/tests/generator/generatorprofile.cpp +++ b/tests/generator/generatorprofile.cpp @@ -271,7 +271,7 @@ TEST(GeneratorProfile, defaultMiscellaneousValues) generatorProfile->implementationHeaderString()); EXPECT_EQ("extern const char VERSION[];\n", generatorProfile->interfaceVersionString()); - EXPECT_EQ("const char VERSION[] = \"0.7.0\";\n", generatorProfile->implementationVersionString()); + EXPECT_EQ("const char VERSION[] = \"0.8.0\";\n", generatorProfile->implementationVersionString()); EXPECT_EQ("extern const char LIBCELLML_VERSION[];\n", generatorProfile->interfaceLibcellmlVersionString()); EXPECT_EQ("const char LIBCELLML_VERSION[] = \"[LIBCELLML_VERSION]\";\n", generatorProfile->implementationLibcellmlVersionString()); @@ -574,17 +574,17 @@ TEST(GeneratorProfile, defaultMiscellaneousValues) "}\n", generatorProfile->implementationInitialiseArraysMethodString(true)); - EXPECT_EQ("void computeComputedConstants(double *constants, double *computedConstants, double *algebraic);\n", + EXPECT_EQ("void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables);\n", generatorProfile->interfaceComputeComputedConstantsMethodString(false)); - EXPECT_EQ("void computeComputedConstants(double *constants, double *computedConstants, double *algebraic)\n" + EXPECT_EQ("void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables)\n" "{\n" "[CODE]" "}\n", generatorProfile->implementationComputeComputedConstantsMethodString(false)); - EXPECT_EQ("void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic);\n", + EXPECT_EQ("void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables);\n", generatorProfile->interfaceComputeComputedConstantsMethodString(true)); - EXPECT_EQ("void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic)\n" + EXPECT_EQ("void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables)\n" "{\n" "[CODE]" "}\n", diff --git a/tests/resources/coverage/generator/model.c b/tests/resources/coverage/generator/model.c index fd5521da4..88304ddc6 100644 --- a/tests/resources/coverage/generator/model.c +++ b/tests/resources/coverage/generator/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 1; @@ -452,7 +452,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * algebraicVariables[1] = 1.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { computedConstants[0] = constants[1] == constants[0]; computedConstants[1] = constants[1]/(constants[0] == constants[0]); diff --git a/tests/resources/coverage/generator/model.h b/tests/resources/coverage/generator/model.h index 9568a7de8..efde37441 100644 --- a/tests/resources/coverage/generator/model.h +++ b/tests/resources/coverage/generator/model.h @@ -37,6 +37,6 @@ void deleteArray(double *array); typedef double (* ExternalVariable)(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, size_t index); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); diff --git a/tests/resources/coverage/generator/model.implementation.out b/tests/resources/coverage/generator/model.implementation.out index 014dd8939..b2f8e6a7a 100644 --- a/tests/resources/coverage/generator/model.implementation.out +++ b/tests/resources/coverage/generator/model.implementation.out @@ -211,7 +211,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * algebraicVariables[1] = 1.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { computedConstants[0] = eq(constants[1], constants[0]); computedConstants[1] = constants[1]/eq(constants[0], constants[0]); diff --git a/tests/resources/coverage/generator/model.interface.out b/tests/resources/coverage/generator/model.interface.out index f7f199098..350b99ec6 100644 --- a/tests/resources/coverage/generator/model.interface.out +++ b/tests/resources/coverage/generator/model.interface.out @@ -15,6 +15,6 @@ void deleteArray(double *array); typedef double (* ExternalVariable)(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, size_t index); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); diff --git a/tests/resources/coverage/generator/model.modified.profile.c b/tests/resources/coverage/generator/model.modified.profile.c index 825cc7760..72c3a055e 100644 --- a/tests/resources/coverage/generator/model.modified.profile.c +++ b/tests/resources/coverage/generator/model.modified.profile.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0.post0"; +const char VERSION[] = "0.8.0.post0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 1; @@ -452,7 +452,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * algebraicVariables[1] = 1.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { computedConstants[0] = constants[1] == constants[0]; computedConstants[1] = constants[1]/(constants[0] == constants[0]); diff --git a/tests/resources/coverage/generator/model.modified.profile.h b/tests/resources/coverage/generator/model.modified.profile.h index 0a608f783..30db9705e 100644 --- a/tests/resources/coverage/generator/model.modified.profile.h +++ b/tests/resources/coverage/generator/model.modified.profile.h @@ -37,6 +37,6 @@ void deleteArray(double *array); typedef double (* ExternalVariable)(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, size_t index); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); diff --git a/tests/resources/coverage/generator/model.modified.profile.py b/tests/resources/coverage/generator/model.modified.profile.py index 76e84d822..3d4fe1e3d 100644 --- a/tests/resources/coverage/generator/model.modified.profile.py +++ b/tests/resources/coverage/generator/model.modified.profile.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0.post0" +__version__ = "0.8.0.post0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 1 @@ -375,23 +375,23 @@ def objective_function_0(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[0] = u[0] - algebraicVariables[1] = u[1] + algebraic_variables[0] = u[0] + algebraic_variables[1] = u[1] - f[0] = algebraicVariables[1]+algebraicVariables[0]+states[0]-0.0 - f[1] = algebraicVariables[1]-algebraicVariables[0]-(computed_constants[198]+computed_constants[197]) + f[0] = algebraic_variables[1]+algebraic_variables[0]+states[0]-0.0 + f[1] = algebraic_variables[1]-algebraic_variables[0]-(computed_constants[198]+computed_constants[197]) def find_root_0(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*2 - u[0] = algebraicVariables[0] - u[1] = algebraicVariables[1] + u[0] = algebraic_variables[0] + u[1] = algebraic_variables[1] u = nla_solve(objective_function_0, u, 2, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[0] = u[0] - algebraicVariables[1] = u[1] + algebraic_variables[0] = u[0] + algebraic_variables[1] = u[1] def initialise_arrays(states, rates, constants, computed_constants, algebraic_variables): @@ -415,11 +415,11 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va computed_constants[186] = nan computed_constants[198] = 1.0 computed_constants[197] = 3.0 - algebraicVariables[0] = 2.0 - algebraicVariables[1] = 1.0 + algebraic_variables[0] = 2.0 + algebraic_variables[1] = 1.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): computed_constants[0] = eq_func(constants[1], constants[0]) computed_constants[1] = constants[1]/eq_func(constants[0], constants[0]) computed_constants[2] = neq_func(constants[1], constants[0]) @@ -614,5 +614,5 @@ def compute_rates(voi, states, rates, constants, computed_constants, algebraic_v def compute_variables(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, external_variable): - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) find_root_0(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) diff --git a/tests/resources/coverage/generator/model.no.tracking.c b/tests/resources/coverage/generator/model.no.tracking.c index b5665cbcb..043bc124c 100644 --- a/tests/resources/coverage/generator/model.no.tracking.c +++ b/tests/resources/coverage/generator/model.no.tracking.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 1; @@ -221,7 +221,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * algebraicVariables[1] = 1.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/coverage/generator/model.no.tracking.h b/tests/resources/coverage/generator/model.no.tracking.h index 86c60ae92..c2e75a66e 100644 --- a/tests/resources/coverage/generator/model.no.tracking.h +++ b/tests/resources/coverage/generator/model.no.tracking.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/coverage/generator/model.out b/tests/resources/coverage/generator/model.out index f705cd845..08e9fc330 100644 --- a/tests/resources/coverage/generator/model.out +++ b/tests/resources/coverage/generator/model.out @@ -122,7 +122,7 @@ void findRoot0(double voi, double *states, double *rates, double *constants, dou algebraicVariables[1] = u[1]; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { computedConstants[0] = constants[1] == constants[0]; computedConstants[1] = constants[1]/(constants[0] == constants[0]); diff --git a/tests/resources/coverage/generator/model.py b/tests/resources/coverage/generator/model.py index 2176333de..fe0b04cbe 100644 --- a/tests/resources/coverage/generator/model.py +++ b/tests/resources/coverage/generator/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 1 @@ -375,23 +375,23 @@ def objective_function_0(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[0] = u[0] - algebraicVariables[1] = u[1] + algebraic_variables[0] = u[0] + algebraic_variables[1] = u[1] - f[0] = algebraicVariables[1]+algebraicVariables[0]+states[0]-0.0 - f[1] = algebraicVariables[1]-algebraicVariables[0]-(computed_constants[198]+computed_constants[197]) + f[0] = algebraic_variables[1]+algebraic_variables[0]+states[0]-0.0 + f[1] = algebraic_variables[1]-algebraic_variables[0]-(computed_constants[198]+computed_constants[197]) def find_root_0(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*2 - u[0] = algebraicVariables[0] - u[1] = algebraicVariables[1] + u[0] = algebraic_variables[0] + u[1] = algebraic_variables[1] u = nla_solve(objective_function_0, u, 2, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[0] = u[0] - algebraicVariables[1] = u[1] + algebraic_variables[0] = u[0] + algebraic_variables[1] = u[1] def initialise_arrays(states, rates, constants, computed_constants, algebraic_variables): @@ -415,11 +415,11 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va computed_constants[186] = nan computed_constants[198] = 1.0 computed_constants[197] = 3.0 - algebraicVariables[0] = 2.0 - algebraicVariables[1] = 1.0 + algebraic_variables[0] = 2.0 + algebraic_variables[1] = 1.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): computed_constants[0] = eq_func(constants[1], constants[0]) computed_constants[1] = constants[1]/eq_func(constants[0], constants[0]) computed_constants[2] = neq_func(constants[1], constants[0]) @@ -614,5 +614,5 @@ def compute_rates(voi, states, rates, constants, computed_constants, algebraic_v def compute_variables(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, external_variable): - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) find_root_0(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) diff --git a/tests/resources/generator/algebraic_eqn_computed_var_on_rhs/model.c b/tests/resources/generator/algebraic_eqn_computed_var_on_rhs/model.c index 8bf4f961e..f6f5fd553 100644 --- a/tests/resources/generator/algebraic_eqn_computed_var_on_rhs/model.c +++ b/tests/resources/generator/algebraic_eqn_computed_var_on_rhs/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t CONSTANT_COUNT = 0; @@ -66,7 +66,7 @@ void initialiseArrays(double *constants, double *computedConstants, double *alge computedConstants[0] = 1.0; } -void computeComputedConstants(double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables) { computedConstants[1] = computedConstants[0]; } diff --git a/tests/resources/generator/algebraic_eqn_computed_var_on_rhs/model.external.c b/tests/resources/generator/algebraic_eqn_computed_var_on_rhs/model.external.c index ff8bcd858..c25ea1e13 100644 --- a/tests/resources/generator/algebraic_eqn_computed_var_on_rhs/model.external.c +++ b/tests/resources/generator/algebraic_eqn_computed_var_on_rhs/model.external.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t CONSTANT_COUNT = 0; @@ -80,7 +80,7 @@ void initialiseArrays(double *constants, double *computedConstants, double *alge { } -void computeComputedConstants(double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/algebraic_eqn_computed_var_on_rhs/model.external.h b/tests/resources/generator/algebraic_eqn_computed_var_on_rhs/model.external.h index 26566dac7..ff187a798 100644 --- a/tests/resources/generator/algebraic_eqn_computed_var_on_rhs/model.external.h +++ b/tests/resources/generator/algebraic_eqn_computed_var_on_rhs/model.external.h @@ -33,5 +33,5 @@ void deleteArray(double *array); typedef double (* ExternalVariable)(double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, size_t index); void initialiseArrays(double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); diff --git a/tests/resources/generator/algebraic_eqn_computed_var_on_rhs/model.external.py b/tests/resources/generator/algebraic_eqn_computed_var_on_rhs/model.external.py index 259240b44..6c86343cc 100644 --- a/tests/resources/generator/algebraic_eqn_computed_var_on_rhs/model.external.py +++ b/tests/resources/generator/algebraic_eqn_computed_var_on_rhs/model.external.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" CONSTANT_COUNT = 0 @@ -47,10 +47,10 @@ def initialise_arrays(constants, computed_constants, algebraic_variables): pass -def compute_computed_constants(constants, computed_constants, algebraic): +def compute_computed_constants(constants, computed_constants, algebraic_variables): pass def compute_variables(constants, computed_constants, algebraic_variables, external_variables, external_variable): - externalVariables[0] = external_variable(constants, computed_constants, algebraic_variables, external_variables, 0) - algebraicVariables[0] = externalVariables[0] + external_variables[0] = external_variable(constants, computed_constants, algebraic_variables, external_variables, 0) + algebraic_variables[0] = external_variables[0] diff --git a/tests/resources/generator/algebraic_eqn_computed_var_on_rhs/model.h b/tests/resources/generator/algebraic_eqn_computed_var_on_rhs/model.h index bb6d32ca8..7ff6f4fa5 100644 --- a/tests/resources/generator/algebraic_eqn_computed_var_on_rhs/model.h +++ b/tests/resources/generator/algebraic_eqn_computed_var_on_rhs/model.h @@ -28,5 +28,5 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/algebraic_eqn_computed_var_on_rhs/model.py b/tests/resources/generator/algebraic_eqn_computed_var_on_rhs/model.py index 20dbcfa05..5f291ca13 100644 --- a/tests/resources/generator/algebraic_eqn_computed_var_on_rhs/model.py +++ b/tests/resources/generator/algebraic_eqn_computed_var_on_rhs/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" CONSTANT_COUNT = 0 @@ -39,7 +39,7 @@ def initialise_arrays(constants, computed_constants, algebraic_variables): computed_constants[0] = 1.0 -def compute_computed_constants(constants, computed_constants, algebraic): +def compute_computed_constants(constants, computed_constants, algebraic_variables): computed_constants[1] = computed_constants[0] diff --git a/tests/resources/generator/algebraic_eqn_const_var_on_rhs/model.c b/tests/resources/generator/algebraic_eqn_const_var_on_rhs/model.c index 1c3c778e5..f982c1701 100644 --- a/tests/resources/generator/algebraic_eqn_const_var_on_rhs/model.c +++ b/tests/resources/generator/algebraic_eqn_const_var_on_rhs/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t CONSTANT_COUNT = 1; @@ -66,7 +66,7 @@ void initialiseArrays(double *constants, double *computedConstants, double *alge constants[0] = 1.0; } -void computeComputedConstants(double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables) { computedConstants[0] = constants[0]; } diff --git a/tests/resources/generator/algebraic_eqn_const_var_on_rhs/model.h b/tests/resources/generator/algebraic_eqn_const_var_on_rhs/model.h index bb6d32ca8..7ff6f4fa5 100644 --- a/tests/resources/generator/algebraic_eqn_const_var_on_rhs/model.h +++ b/tests/resources/generator/algebraic_eqn_const_var_on_rhs/model.h @@ -28,5 +28,5 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/algebraic_eqn_const_var_on_rhs/model.py b/tests/resources/generator/algebraic_eqn_const_var_on_rhs/model.py index 893bc667b..efc69cf8d 100644 --- a/tests/resources/generator/algebraic_eqn_const_var_on_rhs/model.py +++ b/tests/resources/generator/algebraic_eqn_const_var_on_rhs/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" CONSTANT_COUNT = 1 @@ -39,7 +39,7 @@ def initialise_arrays(constants, computed_constants, algebraic_variables): constants[0] = 1.0 -def compute_computed_constants(constants, computed_constants, algebraic): +def compute_computed_constants(constants, computed_constants, algebraic_variables): computed_constants[0] = constants[0] diff --git a/tests/resources/generator/algebraic_eqn_constant_on_rhs/model.c b/tests/resources/generator/algebraic_eqn_constant_on_rhs/model.c index 978140be5..1a90501d5 100644 --- a/tests/resources/generator/algebraic_eqn_constant_on_rhs/model.c +++ b/tests/resources/generator/algebraic_eqn_constant_on_rhs/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t CONSTANT_COUNT = 0; @@ -65,7 +65,7 @@ void initialiseArrays(double *constants, double *computedConstants, double *alge computedConstants[0] = 1.0; } -void computeComputedConstants(double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/algebraic_eqn_constant_on_rhs/model.h b/tests/resources/generator/algebraic_eqn_constant_on_rhs/model.h index ec9899059..6d857143b 100644 --- a/tests/resources/generator/algebraic_eqn_constant_on_rhs/model.h +++ b/tests/resources/generator/algebraic_eqn_constant_on_rhs/model.h @@ -28,5 +28,5 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/algebraic_eqn_constant_on_rhs/model.py b/tests/resources/generator/algebraic_eqn_constant_on_rhs/model.py index ce891673e..ae5776298 100644 --- a/tests/resources/generator/algebraic_eqn_constant_on_rhs/model.py +++ b/tests/resources/generator/algebraic_eqn_constant_on_rhs/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" CONSTANT_COUNT = 0 @@ -38,7 +38,7 @@ def initialise_arrays(constants, computed_constants, algebraic_variables): computed_constants[0] = 1.0 -def compute_computed_constants(constants, computed_constants, algebraic): +def compute_computed_constants(constants, computed_constants, algebraic_variables): pass diff --git a/tests/resources/generator/algebraic_eqn_derivative_on_rhs/model.c b/tests/resources/generator/algebraic_eqn_derivative_on_rhs/model.c index d47ff38ea..71b36cea0 100644 --- a/tests/resources/generator/algebraic_eqn_derivative_on_rhs/model.c +++ b/tests/resources/generator/algebraic_eqn_derivative_on_rhs/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 1; @@ -85,7 +85,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * computedConstants[0] = 1.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/algebraic_eqn_derivative_on_rhs/model.h b/tests/resources/generator/algebraic_eqn_derivative_on_rhs/model.h index b04e145af..20692b80a 100644 --- a/tests/resources/generator/algebraic_eqn_derivative_on_rhs/model.h +++ b/tests/resources/generator/algebraic_eqn_derivative_on_rhs/model.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/algebraic_eqn_derivative_on_rhs/model.py b/tests/resources/generator/algebraic_eqn_derivative_on_rhs/model.py index 01035f604..a11054c85 100644 --- a/tests/resources/generator/algebraic_eqn_derivative_on_rhs/model.py +++ b/tests/resources/generator/algebraic_eqn_derivative_on_rhs/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 1 @@ -51,7 +51,7 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va computed_constants[0] = 1.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass @@ -60,4 +60,4 @@ def compute_rates(voi, states, rates, constants, computed_constants, algebraic_v def compute_variables(voi, states, rates, constants, computed_constants, algebraic_variables): - algebraicVariables[0] = rates[0] + algebraic_variables[0] = rates[0] diff --git a/tests/resources/generator/algebraic_eqn_derivative_on_rhs_one_component/model.c b/tests/resources/generator/algebraic_eqn_derivative_on_rhs_one_component/model.c index 10fe320c6..494a06548 100644 --- a/tests/resources/generator/algebraic_eqn_derivative_on_rhs_one_component/model.c +++ b/tests/resources/generator/algebraic_eqn_derivative_on_rhs_one_component/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 1; @@ -85,7 +85,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * computedConstants[0] = 1.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/algebraic_eqn_derivative_on_rhs_one_component/model.h b/tests/resources/generator/algebraic_eqn_derivative_on_rhs_one_component/model.h index 94ce70879..ef2c23c08 100644 --- a/tests/resources/generator/algebraic_eqn_derivative_on_rhs_one_component/model.h +++ b/tests/resources/generator/algebraic_eqn_derivative_on_rhs_one_component/model.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/algebraic_eqn_derivative_on_rhs_one_component/model.py b/tests/resources/generator/algebraic_eqn_derivative_on_rhs_one_component/model.py index 22079d115..fb9d832ef 100644 --- a/tests/resources/generator/algebraic_eqn_derivative_on_rhs_one_component/model.py +++ b/tests/resources/generator/algebraic_eqn_derivative_on_rhs_one_component/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 1 @@ -51,7 +51,7 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va computed_constants[0] = 1.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass @@ -60,4 +60,4 @@ def compute_rates(voi, states, rates, constants, computed_constants, algebraic_v def compute_variables(voi, states, rates, constants, computed_constants, algebraic_variables): - algebraicVariables[0] = rates[0] + algebraic_variables[0] = rates[0] diff --git a/tests/resources/generator/algebraic_eqn_state_var_on_rhs/model.c b/tests/resources/generator/algebraic_eqn_state_var_on_rhs/model.c index 87cc4b108..5db05cb0e 100644 --- a/tests/resources/generator/algebraic_eqn_state_var_on_rhs/model.c +++ b/tests/resources/generator/algebraic_eqn_state_var_on_rhs/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 1; @@ -85,7 +85,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * computedConstants[0] = 1.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/algebraic_eqn_state_var_on_rhs/model.h b/tests/resources/generator/algebraic_eqn_state_var_on_rhs/model.h index 28cbf9e97..dc974d569 100644 --- a/tests/resources/generator/algebraic_eqn_state_var_on_rhs/model.h +++ b/tests/resources/generator/algebraic_eqn_state_var_on_rhs/model.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/algebraic_eqn_state_var_on_rhs/model.py b/tests/resources/generator/algebraic_eqn_state_var_on_rhs/model.py index 24b1386bc..6bae524fc 100644 --- a/tests/resources/generator/algebraic_eqn_state_var_on_rhs/model.py +++ b/tests/resources/generator/algebraic_eqn_state_var_on_rhs/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 1 @@ -51,7 +51,7 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va computed_constants[0] = 1.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass @@ -60,4 +60,4 @@ def compute_rates(voi, states, rates, constants, computed_constants, algebraic_v def compute_variables(voi, states, rates, constants, computed_constants, algebraic_variables): - algebraicVariables[0] = 2.0*states[0] + algebraic_variables[0] = 2.0*states[0] diff --git a/tests/resources/generator/algebraic_eqn_state_var_on_rhs_one_component/model.c b/tests/resources/generator/algebraic_eqn_state_var_on_rhs_one_component/model.c index 51d093497..98bcd5918 100644 --- a/tests/resources/generator/algebraic_eqn_state_var_on_rhs_one_component/model.c +++ b/tests/resources/generator/algebraic_eqn_state_var_on_rhs_one_component/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 1; @@ -85,7 +85,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * computedConstants[0] = 1.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/algebraic_eqn_state_var_on_rhs_one_component/model.h b/tests/resources/generator/algebraic_eqn_state_var_on_rhs_one_component/model.h index 91fd15c3d..e128458c6 100644 --- a/tests/resources/generator/algebraic_eqn_state_var_on_rhs_one_component/model.h +++ b/tests/resources/generator/algebraic_eqn_state_var_on_rhs_one_component/model.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/algebraic_eqn_state_var_on_rhs_one_component/model.py b/tests/resources/generator/algebraic_eqn_state_var_on_rhs_one_component/model.py index 225a95da3..7fe853ea8 100644 --- a/tests/resources/generator/algebraic_eqn_state_var_on_rhs_one_component/model.py +++ b/tests/resources/generator/algebraic_eqn_state_var_on_rhs_one_component/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 1 @@ -51,7 +51,7 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va computed_constants[0] = 1.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass @@ -60,4 +60,4 @@ def compute_rates(voi, states, rates, constants, computed_constants, algebraic_v def compute_variables(voi, states, rates, constants, computed_constants, algebraic_variables): - algebraicVariables[0] = 2.0*states[0] + algebraic_variables[0] = 2.0*states[0] diff --git a/tests/resources/generator/algebraic_eqn_with_one_non_isolated_unknown/model.c b/tests/resources/generator/algebraic_eqn_with_one_non_isolated_unknown/model.c index 5d76e1c8d..fca10d92d 100644 --- a/tests/resources/generator/algebraic_eqn_with_one_non_isolated_unknown/model.c +++ b/tests/resources/generator/algebraic_eqn_with_one_non_isolated_unknown/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t CONSTANT_COUNT = 0; @@ -103,7 +103,7 @@ void initialiseArrays(double *constants, double *computedConstants, double *alge algebraicVariables[0] = 1.0; } -void computeComputedConstants(double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/algebraic_eqn_with_one_non_isolated_unknown/model.external.c b/tests/resources/generator/algebraic_eqn_with_one_non_isolated_unknown/model.external.c index 4d2556fd0..6e836c415 100644 --- a/tests/resources/generator/algebraic_eqn_with_one_non_isolated_unknown/model.external.c +++ b/tests/resources/generator/algebraic_eqn_with_one_non_isolated_unknown/model.external.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t CONSTANT_COUNT = 0; @@ -119,7 +119,7 @@ void initialiseArrays(double *constants, double *computedConstants, double *alge algebraicVariables[0] = 1.0; } -void computeComputedConstants(double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/algebraic_eqn_with_one_non_isolated_unknown/model.external.h b/tests/resources/generator/algebraic_eqn_with_one_non_isolated_unknown/model.external.h index 26566dac7..ff187a798 100644 --- a/tests/resources/generator/algebraic_eqn_with_one_non_isolated_unknown/model.external.h +++ b/tests/resources/generator/algebraic_eqn_with_one_non_isolated_unknown/model.external.h @@ -33,5 +33,5 @@ void deleteArray(double *array); typedef double (* ExternalVariable)(double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, size_t index); void initialiseArrays(double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); diff --git a/tests/resources/generator/algebraic_eqn_with_one_non_isolated_unknown/model.external.py b/tests/resources/generator/algebraic_eqn_with_one_non_isolated_unknown/model.external.py index c07550e8d..20956363a 100644 --- a/tests/resources/generator/algebraic_eqn_with_one_non_isolated_unknown/model.external.py +++ b/tests/resources/generator/algebraic_eqn_with_one_non_isolated_unknown/model.external.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" CONSTANT_COUNT = 0 @@ -54,31 +54,31 @@ def objective_function_0(u, f, data): algebraic_variables = data[2] external_variables = data[3] - algebraicVariables[0] = u[0] + algebraic_variables[0] = u[0] - f[0] = algebraicVariables[0]+computed_constants[0]-(externalVariables[0]+computed_constants[1]) + f[0] = algebraic_variables[0]+computed_constants[0]-(external_variables[0]+computed_constants[1]) def find_root_0(constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[0] + u[0] = algebraic_variables[0] u = nla_solve(objective_function_0, u, 1, [constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[0] = u[0] + algebraic_variables[0] = u[0] def initialise_arrays(constants, computed_constants, algebraic_variables): computed_constants[0] = 3.0 computed_constants[1] = 7.0 - algebraicVariables[0] = 1.0 + algebraic_variables[0] = 1.0 -def compute_computed_constants(constants, computed_constants, algebraic): +def compute_computed_constants(constants, computed_constants, algebraic_variables): pass def compute_variables(constants, computed_constants, algebraic_variables, external_variables, external_variable): - externalVariables[0] = external_variable(constants, computed_constants, algebraic_variables, external_variables, 0) + external_variables[0] = external_variable(constants, computed_constants, algebraic_variables, external_variables, 0) find_root_0(constants, computed_constants, algebraic_variables, external_variables) diff --git a/tests/resources/generator/algebraic_eqn_with_one_non_isolated_unknown/model.h b/tests/resources/generator/algebraic_eqn_with_one_non_isolated_unknown/model.h index bb6d32ca8..7ff6f4fa5 100644 --- a/tests/resources/generator/algebraic_eqn_with_one_non_isolated_unknown/model.h +++ b/tests/resources/generator/algebraic_eqn_with_one_non_isolated_unknown/model.h @@ -28,5 +28,5 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/algebraic_eqn_with_one_non_isolated_unknown/model.py b/tests/resources/generator/algebraic_eqn_with_one_non_isolated_unknown/model.py index eec5b9b28..be69833f2 100644 --- a/tests/resources/generator/algebraic_eqn_with_one_non_isolated_unknown/model.py +++ b/tests/resources/generator/algebraic_eqn_with_one_non_isolated_unknown/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" CONSTANT_COUNT = 0 @@ -45,29 +45,29 @@ def objective_function_0(u, f, data): computed_constants = data[1] algebraic_variables = data[2] - algebraicVariables[0] = u[0] + algebraic_variables[0] = u[0] - f[0] = algebraicVariables[0]+computed_constants[0]-(computed_constants[1]+computed_constants[2]) + f[0] = algebraic_variables[0]+computed_constants[0]-(computed_constants[1]+computed_constants[2]) def find_root_0(constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[0] + u[0] = algebraic_variables[0] u = nla_solve(objective_function_0, u, 1, [constants, computed_constants, algebraic_variables]) - algebraicVariables[0] = u[0] + algebraic_variables[0] = u[0] def initialise_arrays(constants, computed_constants, algebraic_variables): computed_constants[0] = 3.0 computed_constants[1] = 5.0 computed_constants[2] = 7.0 - algebraicVariables[0] = 1.0 + algebraic_variables[0] = 1.0 -def compute_computed_constants(constants, computed_constants, algebraic): +def compute_computed_constants(constants, computed_constants, algebraic_variables): pass diff --git a/tests/resources/generator/algebraic_system_with_three_linked_unknowns/model.c b/tests/resources/generator/algebraic_system_with_three_linked_unknowns/model.c index 2e57251d3..a8a0e2677 100644 --- a/tests/resources/generator/algebraic_system_with_three_linked_unknowns/model.c +++ b/tests/resources/generator/algebraic_system_with_three_linked_unknowns/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t CONSTANT_COUNT = 0; @@ -109,7 +109,7 @@ void initialiseArrays(double *constants, double *computedConstants, double *alge algebraicVariables[2] = 1.0; } -void computeComputedConstants(double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/algebraic_system_with_three_linked_unknowns/model.external.c b/tests/resources/generator/algebraic_system_with_three_linked_unknowns/model.external.c index bd5abe872..b1615f032 100644 --- a/tests/resources/generator/algebraic_system_with_three_linked_unknowns/model.external.c +++ b/tests/resources/generator/algebraic_system_with_three_linked_unknowns/model.external.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t CONSTANT_COUNT = 0; @@ -81,7 +81,7 @@ void initialiseArrays(double *constants, double *computedConstants, double *alge { } -void computeComputedConstants(double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/algebraic_system_with_three_linked_unknowns/model.external.h b/tests/resources/generator/algebraic_system_with_three_linked_unknowns/model.external.h index d52fe2527..8bff6e342 100644 --- a/tests/resources/generator/algebraic_system_with_three_linked_unknowns/model.external.h +++ b/tests/resources/generator/algebraic_system_with_three_linked_unknowns/model.external.h @@ -33,5 +33,5 @@ void deleteArray(double *array); typedef double (* ExternalVariable)(double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, size_t index); void initialiseArrays(double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); diff --git a/tests/resources/generator/algebraic_system_with_three_linked_unknowns/model.external.py b/tests/resources/generator/algebraic_system_with_three_linked_unknowns/model.external.py index 9281341ea..a07760651 100644 --- a/tests/resources/generator/algebraic_system_with_three_linked_unknowns/model.external.py +++ b/tests/resources/generator/algebraic_system_with_three_linked_unknowns/model.external.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" CONSTANT_COUNT = 0 @@ -48,11 +48,11 @@ def initialise_arrays(constants, computed_constants, algebraic_variables): pass -def compute_computed_constants(constants, computed_constants, algebraic): +def compute_computed_constants(constants, computed_constants, algebraic_variables): pass def compute_variables(constants, computed_constants, algebraic_variables, external_variables, external_variable): - externalVariables[0] = external_variable(constants, computed_constants, algebraic_variables, external_variables, 0) - externalVariables[1] = external_variable(constants, computed_constants, algebraic_variables, external_variables, 1) - externalVariables[2] = external_variable(constants, computed_constants, algebraic_variables, external_variables, 2) + external_variables[0] = external_variable(constants, computed_constants, algebraic_variables, external_variables, 0) + external_variables[1] = external_variable(constants, computed_constants, algebraic_variables, external_variables, 1) + external_variables[2] = external_variable(constants, computed_constants, algebraic_variables, external_variables, 2) diff --git a/tests/resources/generator/algebraic_system_with_three_linked_unknowns/model.h b/tests/resources/generator/algebraic_system_with_three_linked_unknowns/model.h index 25248242e..a4be7e733 100644 --- a/tests/resources/generator/algebraic_system_with_three_linked_unknowns/model.h +++ b/tests/resources/generator/algebraic_system_with_three_linked_unknowns/model.h @@ -28,5 +28,5 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/algebraic_system_with_three_linked_unknowns/model.py b/tests/resources/generator/algebraic_system_with_three_linked_unknowns/model.py index d31e68c1d..c1257e663 100644 --- a/tests/resources/generator/algebraic_system_with_three_linked_unknowns/model.py +++ b/tests/resources/generator/algebraic_system_with_three_linked_unknowns/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" CONSTANT_COUNT = 0 @@ -44,36 +44,36 @@ def objective_function_0(u, f, data): computed_constants = data[1] algebraic_variables = data[2] - algebraicVariables[0] = u[0] - algebraicVariables[1] = u[1] - algebraicVariables[2] = u[2] + algebraic_variables[0] = u[0] + algebraic_variables[1] = u[1] + algebraic_variables[2] = u[2] - f[0] = 2.0*algebraicVariables[2]+algebraicVariables[1]-2.0*algebraicVariables[0]-(-1.0) - f[1] = 3.0*algebraicVariables[2]-3.0*algebraicVariables[1]-algebraicVariables[0]-5.0 - f[2] = algebraicVariables[2]-2.0*algebraicVariables[1]+3.0*algebraicVariables[0]-6.0 + f[0] = 2.0*algebraic_variables[2]+algebraic_variables[1]-2.0*algebraic_variables[0]-(-1.0) + f[1] = 3.0*algebraic_variables[2]-3.0*algebraic_variables[1]-algebraic_variables[0]-5.0 + f[2] = algebraic_variables[2]-2.0*algebraic_variables[1]+3.0*algebraic_variables[0]-6.0 def find_root_0(constants, computed_constants, algebraic_variables): u = [nan]*3 - u[0] = algebraicVariables[0] - u[1] = algebraicVariables[1] - u[2] = algebraicVariables[2] + u[0] = algebraic_variables[0] + u[1] = algebraic_variables[1] + u[2] = algebraic_variables[2] u = nla_solve(objective_function_0, u, 3, [constants, computed_constants, algebraic_variables]) - algebraicVariables[0] = u[0] - algebraicVariables[1] = u[1] - algebraicVariables[2] = u[2] + algebraic_variables[0] = u[0] + algebraic_variables[1] = u[1] + algebraic_variables[2] = u[2] def initialise_arrays(constants, computed_constants, algebraic_variables): - algebraicVariables[0] = 1.0 - algebraicVariables[1] = 1.0 - algebraicVariables[2] = 1.0 + algebraic_variables[0] = 1.0 + algebraic_variables[1] = 1.0 + algebraic_variables[2] = 1.0 -def compute_computed_constants(constants, computed_constants, algebraic): +def compute_computed_constants(constants, computed_constants, algebraic_variables): pass diff --git a/tests/resources/generator/algebraic_system_with_various_dependencies/model.not.ordered.c b/tests/resources/generator/algebraic_system_with_various_dependencies/model.not.ordered.c index 381aa4fba..74d20de93 100644 --- a/tests/resources/generator/algebraic_system_with_various_dependencies/model.not.ordered.c +++ b/tests/resources/generator/algebraic_system_with_various_dependencies/model.not.ordered.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t CONSTANT_COUNT = 2; @@ -109,7 +109,7 @@ void initialiseArrays(double *constants, double *computedConstants, double *alge algebraicVariables[1] = 1.0; } -void computeComputedConstants(double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables) { computedConstants[0] = 3.0*constants[1]+constants[0]; } diff --git a/tests/resources/generator/algebraic_system_with_various_dependencies/model.not.ordered.h b/tests/resources/generator/algebraic_system_with_various_dependencies/model.not.ordered.h index 25248242e..a4be7e733 100644 --- a/tests/resources/generator/algebraic_system_with_various_dependencies/model.not.ordered.h +++ b/tests/resources/generator/algebraic_system_with_various_dependencies/model.not.ordered.h @@ -28,5 +28,5 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/algebraic_system_with_various_dependencies/model.not.ordered.py b/tests/resources/generator/algebraic_system_with_various_dependencies/model.not.ordered.py index bd237fa92..dc310d35c 100644 --- a/tests/resources/generator/algebraic_system_with_various_dependencies/model.not.ordered.py +++ b/tests/resources/generator/algebraic_system_with_various_dependencies/model.not.ordered.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" CONSTANT_COUNT = 2 @@ -47,36 +47,36 @@ def objective_function_0(u, f, data): computed_constants = data[1] algebraic_variables = data[2] - algebraicVariables[0] = u[0] - algebraicVariables[1] = u[1] + algebraic_variables[0] = u[0] + algebraic_variables[1] = u[1] - f[0] = 3.0*computed_constants[0]+2.0*algebraicVariables[1]+algebraicVariables[0]-57.0 - f[1] = computed_constants[0]+3.0*algebraicVariables[1]-algebraicVariables[0]-19.0 + f[0] = 3.0*computed_constants[0]+2.0*algebraic_variables[1]+algebraic_variables[0]-57.0 + f[1] = computed_constants[0]+3.0*algebraic_variables[1]-algebraic_variables[0]-19.0 def find_root_0(constants, computed_constants, algebraic_variables): u = [nan]*2 - u[0] = algebraicVariables[0] - u[1] = algebraicVariables[1] + u[0] = algebraic_variables[0] + u[1] = algebraic_variables[1] u = nla_solve(objective_function_0, u, 2, [constants, computed_constants, algebraic_variables]) - algebraicVariables[0] = u[0] - algebraicVariables[1] = u[1] + algebraic_variables[0] = u[0] + algebraic_variables[1] = u[1] def initialise_arrays(constants, computed_constants, algebraic_variables): constants[0] = 5.0 constants[1] = 3.0 - algebraicVariables[0] = 1.0 - algebraicVariables[1] = 1.0 + algebraic_variables[0] = 1.0 + algebraic_variables[1] = 1.0 -def compute_computed_constants(constants, computed_constants, algebraic): +def compute_computed_constants(constants, computed_constants, algebraic_variables): computed_constants[0] = 3.0*constants[1]+constants[0] def compute_variables(constants, computed_constants, algebraic_variables): find_root_0(constants, computed_constants, algebraic_variables) - algebraicVariables[2] = algebraicVariables[1]+algebraicVariables[0] + algebraic_variables[2] = algebraic_variables[1]+algebraic_variables[0] diff --git a/tests/resources/generator/algebraic_system_with_various_dependencies/model.ordered.c b/tests/resources/generator/algebraic_system_with_various_dependencies/model.ordered.c index 7744f0b49..1d151a664 100644 --- a/tests/resources/generator/algebraic_system_with_various_dependencies/model.ordered.c +++ b/tests/resources/generator/algebraic_system_with_various_dependencies/model.ordered.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t CONSTANT_COUNT = 2; @@ -109,7 +109,7 @@ void initialiseArrays(double *constants, double *computedConstants, double *alge algebraicVariables[1] = 1.0; } -void computeComputedConstants(double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables) { computedConstants[0] = 3.0*constants[1]+constants[0]; } diff --git a/tests/resources/generator/algebraic_system_with_various_dependencies/model.ordered.h b/tests/resources/generator/algebraic_system_with_various_dependencies/model.ordered.h index 25248242e..a4be7e733 100644 --- a/tests/resources/generator/algebraic_system_with_various_dependencies/model.ordered.h +++ b/tests/resources/generator/algebraic_system_with_various_dependencies/model.ordered.h @@ -28,5 +28,5 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/algebraic_system_with_various_dependencies/model.ordered.py b/tests/resources/generator/algebraic_system_with_various_dependencies/model.ordered.py index bd237fa92..dc310d35c 100644 --- a/tests/resources/generator/algebraic_system_with_various_dependencies/model.ordered.py +++ b/tests/resources/generator/algebraic_system_with_various_dependencies/model.ordered.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" CONSTANT_COUNT = 2 @@ -47,36 +47,36 @@ def objective_function_0(u, f, data): computed_constants = data[1] algebraic_variables = data[2] - algebraicVariables[0] = u[0] - algebraicVariables[1] = u[1] + algebraic_variables[0] = u[0] + algebraic_variables[1] = u[1] - f[0] = 3.0*computed_constants[0]+2.0*algebraicVariables[1]+algebraicVariables[0]-57.0 - f[1] = computed_constants[0]+3.0*algebraicVariables[1]-algebraicVariables[0]-19.0 + f[0] = 3.0*computed_constants[0]+2.0*algebraic_variables[1]+algebraic_variables[0]-57.0 + f[1] = computed_constants[0]+3.0*algebraic_variables[1]-algebraic_variables[0]-19.0 def find_root_0(constants, computed_constants, algebraic_variables): u = [nan]*2 - u[0] = algebraicVariables[0] - u[1] = algebraicVariables[1] + u[0] = algebraic_variables[0] + u[1] = algebraic_variables[1] u = nla_solve(objective_function_0, u, 2, [constants, computed_constants, algebraic_variables]) - algebraicVariables[0] = u[0] - algebraicVariables[1] = u[1] + algebraic_variables[0] = u[0] + algebraic_variables[1] = u[1] def initialise_arrays(constants, computed_constants, algebraic_variables): constants[0] = 5.0 constants[1] = 3.0 - algebraicVariables[0] = 1.0 - algebraicVariables[1] = 1.0 + algebraic_variables[0] = 1.0 + algebraic_variables[1] = 1.0 -def compute_computed_constants(constants, computed_constants, algebraic): +def compute_computed_constants(constants, computed_constants, algebraic_variables): computed_constants[0] = 3.0*constants[1]+constants[0] def compute_variables(constants, computed_constants, algebraic_variables): find_root_0(constants, computed_constants, algebraic_variables) - algebraicVariables[2] = algebraicVariables[1]+algebraicVariables[0] + algebraic_variables[2] = algebraic_variables[1]+algebraic_variables[0] diff --git a/tests/resources/generator/algebraic_unknown_var_on_rhs/model.c b/tests/resources/generator/algebraic_unknown_var_on_rhs/model.c index 766d46c33..41f290356 100644 --- a/tests/resources/generator/algebraic_unknown_var_on_rhs/model.c +++ b/tests/resources/generator/algebraic_unknown_var_on_rhs/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t CONSTANT_COUNT = 0; @@ -66,7 +66,7 @@ void initialiseArrays(double *constants, double *computedConstants, double *alge computedConstants[0] = 1.0; } -void computeComputedConstants(double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables) { computedConstants[1] = computedConstants[0]; } diff --git a/tests/resources/generator/algebraic_unknown_var_on_rhs/model.h b/tests/resources/generator/algebraic_unknown_var_on_rhs/model.h index ec9899059..6d857143b 100644 --- a/tests/resources/generator/algebraic_unknown_var_on_rhs/model.h +++ b/tests/resources/generator/algebraic_unknown_var_on_rhs/model.h @@ -28,5 +28,5 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/algebraic_unknown_var_on_rhs/model.py b/tests/resources/generator/algebraic_unknown_var_on_rhs/model.py index 71ac8681a..cb8733ad5 100644 --- a/tests/resources/generator/algebraic_unknown_var_on_rhs/model.py +++ b/tests/resources/generator/algebraic_unknown_var_on_rhs/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" CONSTANT_COUNT = 0 @@ -39,7 +39,7 @@ def initialise_arrays(constants, computed_constants, algebraic_variables): computed_constants[0] = 1.0 -def compute_computed_constants(constants, computed_constants, algebraic): +def compute_computed_constants(constants, computed_constants, algebraic_variables): computed_constants[1] = computed_constants[0] diff --git a/tests/resources/generator/cell_geometry_model/model.c b/tests/resources/generator/cell_geometry_model/model.c index cca5884ab..c069e46b6 100644 --- a/tests/resources/generator/cell_geometry_model/model.c +++ b/tests/resources/generator/cell_geometry_model/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t CONSTANT_COUNT = 2; @@ -69,7 +69,7 @@ void initialiseArrays(double *constants, double *computedConstants, double *alge constants[1] = 0.0011; } -void computeComputedConstants(double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables) { computedConstants[0] = 1000.0*3.14*constants[1]*constants[1]*constants[0]; computedConstants[1] = 0.02*computedConstants[0]; diff --git a/tests/resources/generator/cell_geometry_model/model.external.c b/tests/resources/generator/cell_geometry_model/model.external.c index 480f52c68..f56880b98 100644 --- a/tests/resources/generator/cell_geometry_model/model.external.c +++ b/tests/resources/generator/cell_geometry_model/model.external.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t CONSTANT_COUNT = 0; @@ -82,7 +82,7 @@ void initialiseArrays(double *constants, double *computedConstants, double *alge { } -void computeComputedConstants(double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/cell_geometry_model/model.external.h b/tests/resources/generator/cell_geometry_model/model.external.h index 5ca6ded49..564ab959f 100644 --- a/tests/resources/generator/cell_geometry_model/model.external.h +++ b/tests/resources/generator/cell_geometry_model/model.external.h @@ -33,5 +33,5 @@ void deleteArray(double *array); typedef double (* ExternalVariable)(double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, size_t index); void initialiseArrays(double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); diff --git a/tests/resources/generator/cell_geometry_model/model.external.py b/tests/resources/generator/cell_geometry_model/model.external.py index 713e37587..bc32c0d88 100644 --- a/tests/resources/generator/cell_geometry_model/model.external.py +++ b/tests/resources/generator/cell_geometry_model/model.external.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" CONSTANT_COUNT = 0 @@ -49,12 +49,12 @@ def initialise_arrays(constants, computed_constants, algebraic_variables): pass -def compute_computed_constants(constants, computed_constants, algebraic): +def compute_computed_constants(constants, computed_constants, algebraic_variables): pass def compute_variables(constants, computed_constants, algebraic_variables, external_variables, external_variable): - externalVariables[0] = external_variable(constants, computed_constants, algebraic_variables, external_variables, 0) - externalVariables[1] = external_variable(constants, computed_constants, algebraic_variables, external_variables, 1) - algebraicVariables[0] = 1000.0*3.14*externalVariables[1]*externalVariables[1]*externalVariables[0] - algebraicVariables[1] = 0.02*algebraicVariables[0] + external_variables[0] = external_variable(constants, computed_constants, algebraic_variables, external_variables, 0) + external_variables[1] = external_variable(constants, computed_constants, algebraic_variables, external_variables, 1) + algebraic_variables[0] = 1000.0*3.14*external_variables[1]*external_variables[1]*external_variables[0] + algebraic_variables[1] = 0.02*algebraic_variables[0] diff --git a/tests/resources/generator/cell_geometry_model/model.h b/tests/resources/generator/cell_geometry_model/model.h index ac83a1e38..bda4fb20b 100644 --- a/tests/resources/generator/cell_geometry_model/model.h +++ b/tests/resources/generator/cell_geometry_model/model.h @@ -28,5 +28,5 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/cell_geometry_model/model.py b/tests/resources/generator/cell_geometry_model/model.py index 7194e2704..769e5b0b1 100644 --- a/tests/resources/generator/cell_geometry_model/model.py +++ b/tests/resources/generator/cell_geometry_model/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" CONSTANT_COUNT = 2 @@ -42,7 +42,7 @@ def initialise_arrays(constants, computed_constants, algebraic_variables): constants[1] = 0.0011 -def compute_computed_constants(constants, computed_constants, algebraic): +def compute_computed_constants(constants, computed_constants, algebraic_variables): computed_constants[0] = 1000.0*3.14*constants[1]*constants[1]*constants[0] computed_constants[1] = 0.02*computed_constants[0] diff --git a/tests/resources/generator/cellml_mappings_and_encapsulations/model.c b/tests/resources/generator/cellml_mappings_and_encapsulations/model.c index 83aeb3155..936b38e81 100644 --- a/tests/resources/generator/cellml_mappings_and_encapsulations/model.c +++ b/tests/resources/generator/cellml_mappings_and_encapsulations/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 2; @@ -86,7 +86,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * states[1] = 0.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/cellml_mappings_and_encapsulations/model.h b/tests/resources/generator/cellml_mappings_and_encapsulations/model.h index a250c3ea6..4db5b8f4c 100644 --- a/tests/resources/generator/cellml_mappings_and_encapsulations/model.h +++ b/tests/resources/generator/cellml_mappings_and_encapsulations/model.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/cellml_mappings_and_encapsulations/model.py b/tests/resources/generator/cellml_mappings_and_encapsulations/model.py index d9b9a9e4e..d16ba6511 100644 --- a/tests/resources/generator/cellml_mappings_and_encapsulations/model.py +++ b/tests/resources/generator/cellml_mappings_and_encapsulations/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 2 @@ -52,7 +52,7 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va states[1] = 0.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass @@ -62,5 +62,5 @@ def compute_rates(voi, states, rates, constants, computed_constants, algebraic_v def compute_variables(voi, states, rates, constants, computed_constants, algebraic_variables): - algebraicVariables[0] = states[0]+5.0*states[0]/3.0+1.0*exp(states[0]/2.0) - algebraicVariables[1] = 2.0*states[1] + algebraic_variables[0] = states[0]+5.0*states[0]/3.0+1.0*exp(states[0]/2.0) + algebraic_variables[1] = 2.0*states[1] diff --git a/tests/resources/generator/cellml_slc_example/model.py b/tests/resources/generator/cellml_slc_example/model.py index 846e029ad..ec99342b5 100644 --- a/tests/resources/generator/cellml_slc_example/model.py +++ b/tests/resources/generator/cellml_slc_example/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" CONSTANT_COUNT = 9 @@ -55,7 +55,7 @@ def initialise_arrays(constants, computed_constants, algebraic_variables): constants[8] = 1.1 -def compute_computed_constants(constants, computed_constants, algebraic): +def compute_computed_constants(constants, computed_constants, algebraic_variables): computed_constants[0] = constants[8]*(constants[7]*constants[1]-constants[6]*constants[2])/(constants[5]*constants[2]+constants[4]*constants[1]+constants[3]*constants[2]*constants[1]+constants[0]) diff --git a/tests/resources/generator/cellml_state_initialised_using_variable/model.c b/tests/resources/generator/cellml_state_initialised_using_variable/model.c index cce19d524..9735689f0 100644 --- a/tests/resources/generator/cellml_state_initialised_using_variable/model.c +++ b/tests/resources/generator/cellml_state_initialised_using_variable/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 1; @@ -84,7 +84,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * states[0] = constants[0]; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/cellml_state_initialised_using_variable/model.h b/tests/resources/generator/cellml_state_initialised_using_variable/model.h index 2e26a1fd8..64a37ea65 100644 --- a/tests/resources/generator/cellml_state_initialised_using_variable/model.h +++ b/tests/resources/generator/cellml_state_initialised_using_variable/model.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/cellml_state_initialised_using_variable/model.py b/tests/resources/generator/cellml_state_initialised_using_variable/model.py index e2b042ce9..2684941d1 100644 --- a/tests/resources/generator/cellml_state_initialised_using_variable/model.py +++ b/tests/resources/generator/cellml_state_initialised_using_variable/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 1 @@ -50,7 +50,7 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va states[0] = constants[0] -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass diff --git a/tests/resources/generator/cellml_unit_scaling_constant/model.c b/tests/resources/generator/cellml_unit_scaling_constant/model.c index dc22819b2..f50fd85ef 100644 --- a/tests/resources/generator/cellml_unit_scaling_constant/model.c +++ b/tests/resources/generator/cellml_unit_scaling_constant/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t CONSTANT_COUNT = 9; @@ -91,7 +91,7 @@ void initialiseArrays(double *constants, double *computedConstants, double *alge constants[8] = constants[7]; } -void computeComputedConstants(double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables) { computedConstants[0] = constants[1]+constants[0]; computedConstants[1] = 0.001*constants[1]+0.001*constants[0]; diff --git a/tests/resources/generator/cellml_unit_scaling_constant/model.h b/tests/resources/generator/cellml_unit_scaling_constant/model.h index a183ef741..bd0315ab4 100644 --- a/tests/resources/generator/cellml_unit_scaling_constant/model.h +++ b/tests/resources/generator/cellml_unit_scaling_constant/model.h @@ -28,5 +28,5 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/cellml_unit_scaling_constant/model.py b/tests/resources/generator/cellml_unit_scaling_constant/model.py index f85680f55..d2fe82732 100644 --- a/tests/resources/generator/cellml_unit_scaling_constant/model.py +++ b/tests/resources/generator/cellml_unit_scaling_constant/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" CONSTANT_COUNT = 9 @@ -64,7 +64,7 @@ def initialise_arrays(constants, computed_constants, algebraic_variables): constants[8] = constants[7] -def compute_computed_constants(constants, computed_constants, algebraic): +def compute_computed_constants(constants, computed_constants, algebraic_variables): computed_constants[0] = constants[1]+constants[0] computed_constants[1] = 0.001*constants[1]+0.001*constants[0] computed_constants[2] = 1000.0*constants[3]+1000.0*constants[4] diff --git a/tests/resources/generator/cellml_unit_scaling_rate/model.c b/tests/resources/generator/cellml_unit_scaling_rate/model.c index 5c4e633af..24738401c 100644 --- a/tests/resources/generator/cellml_unit_scaling_rate/model.c +++ b/tests/resources/generator/cellml_unit_scaling_rate/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 1; @@ -84,7 +84,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * states[0] = 123.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/cellml_unit_scaling_rate/model.h b/tests/resources/generator/cellml_unit_scaling_rate/model.h index 2e26a1fd8..64a37ea65 100644 --- a/tests/resources/generator/cellml_unit_scaling_rate/model.h +++ b/tests/resources/generator/cellml_unit_scaling_rate/model.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/cellml_unit_scaling_rate/model.py b/tests/resources/generator/cellml_unit_scaling_rate/model.py index 9b7d90ad8..ef329e9d6 100644 --- a/tests/resources/generator/cellml_unit_scaling_rate/model.py +++ b/tests/resources/generator/cellml_unit_scaling_rate/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 1 @@ -50,7 +50,7 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va states[0] = 123.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass @@ -59,5 +59,5 @@ def compute_rates(voi, states, rates, constants, computed_constants, algebraic_v def compute_variables(voi, states, rates, constants, computed_constants, algebraic_variables): - algebraicVariables[0] = 1000.0*rates[0]+1000.0*rates[0] - algebraicVariables[1] = 1000.0*0.001*rates[0]+1000.0*0.001*rates[0] + algebraic_variables[0] = 1000.0*rates[0]+1000.0*rates[0] + algebraic_variables[1] = 1000.0*0.001*rates[0]+1000.0*0.001*rates[0] diff --git a/tests/resources/generator/cellml_unit_scaling_state/model.c b/tests/resources/generator/cellml_unit_scaling_state/model.c index 73d795648..c39a118d2 100644 --- a/tests/resources/generator/cellml_unit_scaling_state/model.c +++ b/tests/resources/generator/cellml_unit_scaling_state/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 1; @@ -84,7 +84,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * states[0] = 123.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/cellml_unit_scaling_state/model.h b/tests/resources/generator/cellml_unit_scaling_state/model.h index 2e26a1fd8..64a37ea65 100644 --- a/tests/resources/generator/cellml_unit_scaling_state/model.h +++ b/tests/resources/generator/cellml_unit_scaling_state/model.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/cellml_unit_scaling_state/model.py b/tests/resources/generator/cellml_unit_scaling_state/model.py index b2454a768..93c71f5ad 100644 --- a/tests/resources/generator/cellml_unit_scaling_state/model.py +++ b/tests/resources/generator/cellml_unit_scaling_state/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 1 @@ -50,7 +50,7 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va states[0] = 123.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass @@ -59,5 +59,5 @@ def compute_rates(voi, states, rates, constants, computed_constants, algebraic_v def compute_variables(voi, states, rates, constants, computed_constants, algebraic_variables): - algebraicVariables[0] = states[0]+states[0] - algebraicVariables[1] = 0.001*states[0]+0.001*states[0] + algebraic_variables[0] = states[0]+states[0] + algebraic_variables[1] = 0.001*states[0]+0.001*states[0] diff --git a/tests/resources/generator/cellml_unit_scaling_state_initialised_using_constant/model.c b/tests/resources/generator/cellml_unit_scaling_state_initialised_using_constant/model.c index a65c53da8..ffcfe8fd3 100644 --- a/tests/resources/generator/cellml_unit_scaling_state_initialised_using_constant/model.c +++ b/tests/resources/generator/cellml_unit_scaling_state_initialised_using_constant/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 2; @@ -84,7 +84,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * states[1] = 0.001*789.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/cellml_unit_scaling_state_initialised_using_constant/model.h b/tests/resources/generator/cellml_unit_scaling_state_initialised_using_constant/model.h index d27f4f5e7..f6c4c923d 100644 --- a/tests/resources/generator/cellml_unit_scaling_state_initialised_using_constant/model.h +++ b/tests/resources/generator/cellml_unit_scaling_state_initialised_using_constant/model.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/cellml_unit_scaling_state_initialised_using_constant/model.py b/tests/resources/generator/cellml_unit_scaling_state_initialised_using_constant/model.py index d77590f17..625baf84e 100644 --- a/tests/resources/generator/cellml_unit_scaling_state_initialised_using_constant/model.py +++ b/tests/resources/generator/cellml_unit_scaling_state_initialised_using_constant/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 2 @@ -50,7 +50,7 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va states[1] = 0.001*789.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass diff --git a/tests/resources/generator/cellml_unit_scaling_state_initialised_using_variable/model.c b/tests/resources/generator/cellml_unit_scaling_state_initialised_using_variable/model.c index a7d21b7c6..d30449340 100644 --- a/tests/resources/generator/cellml_unit_scaling_state_initialised_using_variable/model.c +++ b/tests/resources/generator/cellml_unit_scaling_state_initialised_using_variable/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 2; @@ -88,7 +88,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * states[1] = 0.001*constants[1]; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/cellml_unit_scaling_state_initialised_using_variable/model.h b/tests/resources/generator/cellml_unit_scaling_state_initialised_using_variable/model.h index 91b6f8df3..319468912 100644 --- a/tests/resources/generator/cellml_unit_scaling_state_initialised_using_variable/model.h +++ b/tests/resources/generator/cellml_unit_scaling_state_initialised_using_variable/model.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/cellml_unit_scaling_state_initialised_using_variable/model.py b/tests/resources/generator/cellml_unit_scaling_state_initialised_using_variable/model.py index 61db6240c..d5fda40a2 100644 --- a/tests/resources/generator/cellml_unit_scaling_state_initialised_using_variable/model.py +++ b/tests/resources/generator/cellml_unit_scaling_state_initialised_using_variable/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 2 @@ -54,7 +54,7 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va states[1] = 0.001*constants[1] -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass diff --git a/tests/resources/generator/cellml_unit_scaling_voi_direct/model.c b/tests/resources/generator/cellml_unit_scaling_voi_direct/model.c index 71e07eb6a..8b992ef43 100644 --- a/tests/resources/generator/cellml_unit_scaling_voi_direct/model.c +++ b/tests/resources/generator/cellml_unit_scaling_voi_direct/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 2; @@ -84,7 +84,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * states[1] = 5.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/cellml_unit_scaling_voi_direct/model.h b/tests/resources/generator/cellml_unit_scaling_voi_direct/model.h index 77fc3ba73..3d1b51eab 100644 --- a/tests/resources/generator/cellml_unit_scaling_voi_direct/model.h +++ b/tests/resources/generator/cellml_unit_scaling_voi_direct/model.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/cellml_unit_scaling_voi_direct/model.py b/tests/resources/generator/cellml_unit_scaling_voi_direct/model.py index d76c8c661..78baa3685 100644 --- a/tests/resources/generator/cellml_unit_scaling_voi_direct/model.py +++ b/tests/resources/generator/cellml_unit_scaling_voi_direct/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 2 @@ -50,7 +50,7 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va states[1] = 5.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass diff --git a/tests/resources/generator/cellml_unit_scaling_voi_indirect/model.c b/tests/resources/generator/cellml_unit_scaling_voi_indirect/model.c index f56b39c72..7de9dedd7 100644 --- a/tests/resources/generator/cellml_unit_scaling_voi_indirect/model.c +++ b/tests/resources/generator/cellml_unit_scaling_voi_indirect/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 3; @@ -86,7 +86,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * states[2] = 11.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/cellml_unit_scaling_voi_indirect/model.h b/tests/resources/generator/cellml_unit_scaling_voi_indirect/model.h index 91d20c68c..9c423e67f 100644 --- a/tests/resources/generator/cellml_unit_scaling_voi_indirect/model.h +++ b/tests/resources/generator/cellml_unit_scaling_voi_indirect/model.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/cellml_unit_scaling_voi_indirect/model.py b/tests/resources/generator/cellml_unit_scaling_voi_indirect/model.py index 3e2a7e1c5..b4e80510c 100644 --- a/tests/resources/generator/cellml_unit_scaling_voi_indirect/model.py +++ b/tests/resources/generator/cellml_unit_scaling_voi_indirect/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 3 @@ -52,7 +52,7 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va states[2] = 11.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass diff --git a/tests/resources/generator/dae_cellml_1_1_model/model.c b/tests/resources/generator/dae_cellml_1_1_model/model.c index a5ebbb5eb..f5f697d94 100644 --- a/tests/resources/generator/dae_cellml_1_1_model/model.c +++ b/tests/resources/generator/dae_cellml_1_1_model/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 2; @@ -165,7 +165,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * algebraicVariables[2] = 0.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/dae_cellml_1_1_model/model.h b/tests/resources/generator/dae_cellml_1_1_model/model.h index 3350366ae..ed1fe9acf 100644 --- a/tests/resources/generator/dae_cellml_1_1_model/model.h +++ b/tests/resources/generator/dae_cellml_1_1_model/model.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/dae_cellml_1_1_model/model.py b/tests/resources/generator/dae_cellml_1_1_model/model.py index e84732552..75a73466e 100644 --- a/tests/resources/generator/dae_cellml_1_1_model/model.py +++ b/tests/resources/generator/dae_cellml_1_1_model/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 2 @@ -66,19 +66,19 @@ def objective_function_0(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[0] = u[0] + algebraic_variables[0] = u[0] - f[0] = constants[0]-(algebraicVariables[0]+algebraicVariables[1]) + f[0] = constants[0]-(algebraic_variables[0]+algebraic_variables[1]) def find_root_0(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[0] + u[0] = algebraic_variables[0] u = nla_solve(objective_function_0, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[0] = u[0] + algebraic_variables[0] = u[0] def objective_function_1(u, f, data): @@ -89,19 +89,19 @@ def objective_function_1(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[2] = u[0] + algebraic_variables[2] = u[0] - f[0] = algebraicVariables[4]-(algebraicVariables[3]+algebraicVariables[2]) + f[0] = algebraic_variables[4]-(algebraic_variables[3]+algebraic_variables[2]) def find_root_1(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[2] + u[0] = algebraic_variables[2] u = nla_solve(objective_function_1, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[2] = u[0] + algebraic_variables[2] = u[0] def initialise_arrays(states, rates, constants, computed_constants, algebraic_variables): @@ -112,27 +112,27 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[2] = 20.0 constants[3] = 2.0 constants[4] = 10.0 - algebraicVariables[0] = 0.0 - algebraicVariables[2] = 0.0 + algebraic_variables[0] = 0.0 + algebraic_variables[2] = 0.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass def compute_rates(voi, states, rates, constants, computed_constants, algebraic_variables): - algebraicVariables[1] = states[1]+constants[1] + algebraic_variables[1] = states[1]+constants[1] find_root_0(voi, states, rates, constants, computed_constants, algebraic_variables) - rates[0] = algebraicVariables[0] - algebraicVariables[3] = constants[3]*algebraicVariables[1] - algebraicVariables[4] = states[0]/constants[2] + rates[0] = algebraic_variables[0] + algebraic_variables[3] = constants[3]*algebraic_variables[1] + algebraic_variables[4] = states[0]/constants[2] find_root_1(voi, states, rates, constants, computed_constants, algebraic_variables) - rates[1] = algebraicVariables[2]/constants[4] + rates[1] = algebraic_variables[2]/constants[4] def compute_variables(voi, states, rates, constants, computed_constants, algebraic_variables): - algebraicVariables[1] = states[1]+constants[1] + algebraic_variables[1] = states[1]+constants[1] find_root_0(voi, states, rates, constants, computed_constants, algebraic_variables) - algebraicVariables[3] = constants[3]*algebraicVariables[1] - algebraicVariables[4] = states[0]/constants[2] + algebraic_variables[3] = constants[3]*algebraic_variables[1] + algebraic_variables[4] = states[0]/constants[2] find_root_1(voi, states, rates, constants, computed_constants, algebraic_variables) diff --git a/tests/resources/generator/dependent_eqns/model.c b/tests/resources/generator/dependent_eqns/model.c index 4764fb652..15d2f8d5c 100644 --- a/tests/resources/generator/dependent_eqns/model.c +++ b/tests/resources/generator/dependent_eqns/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 1; @@ -84,7 +84,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * states[0] = 0.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/dependent_eqns/model.h b/tests/resources/generator/dependent_eqns/model.h index 04fbb2071..321668382 100644 --- a/tests/resources/generator/dependent_eqns/model.h +++ b/tests/resources/generator/dependent_eqns/model.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/dependent_eqns/model.py b/tests/resources/generator/dependent_eqns/model.py index 9ffd00bc2..559451b3c 100644 --- a/tests/resources/generator/dependent_eqns/model.py +++ b/tests/resources/generator/dependent_eqns/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 1 @@ -50,7 +50,7 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va states[0] = 0.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass @@ -59,5 +59,5 @@ def compute_rates(voi, states, rates, constants, computed_constants, algebraic_v def compute_variables(voi, states, rates, constants, computed_constants, algebraic_variables): - algebraicVariables[0] = 2.0*voi - algebraicVariables[1] = 3.0*algebraicVariables[0] + algebraic_variables[0] = 2.0*voi + algebraic_variables[1] = 3.0*algebraic_variables[0] diff --git a/tests/resources/generator/fabbri_fantini_wilders_severi_human_san_model_2017/model.c b/tests/resources/generator/fabbri_fantini_wilders_severi_human_san_model_2017/model.c index 2bb7d60ae..74e1f8099 100644 --- a/tests/resources/generator/fabbri_fantini_wilders_severi_human_san_model_2017/model.c +++ b/tests/resources/generator/fabbri_fantini_wilders_severi_human_san_model_2017/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 33; @@ -454,7 +454,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * constants[90] = 1.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { computedConstants[0] = constants[62]*constants[61]/constants[6]; computedConstants[1] = computedConstants[0]*log(constants[4]/constants[3]); diff --git a/tests/resources/generator/fabbri_fantini_wilders_severi_human_san_model_2017/model.h b/tests/resources/generator/fabbri_fantini_wilders_severi_human_san_model_2017/model.h index 3a126e50d..280b766fa 100644 --- a/tests/resources/generator/fabbri_fantini_wilders_severi_human_san_model_2017/model.h +++ b/tests/resources/generator/fabbri_fantini_wilders_severi_human_san_model_2017/model.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/fabbri_fantini_wilders_severi_human_san_model_2017/model.py b/tests/resources/generator/fabbri_fantini_wilders_severi_human_san_model_2017/model.py index 5dcdbd888..0785cf957 100644 --- a/tests/resources/generator/fabbri_fantini_wilders_severi_human_san_model_2017/model.py +++ b/tests/resources/generator/fabbri_fantini_wilders_severi_human_san_model_2017/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 33 @@ -440,7 +440,7 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[90] = 1.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): computed_constants[0] = constants[62]*constants[61]/constants[6] computed_constants[1] = computed_constants[0]*log(constants[4]/constants[3]) computed_constants[4] = 1.2 if gt_func(constants[1], 0.0) else 1.0 @@ -469,235 +469,235 @@ def compute_computed_constants(states, rates, constants, computed_constants, alg def compute_rates(voi, states, rates, constants, computed_constants, algebraic_variables): - algebraicVariables[0] = states[1] - algebraicVariables[47] = constants[64] if and_func(gt_func(voi, constants[66]), lt_func(voi, constants[66]+constants[65])) else constants[67] - algebraicVariables[8] = algebraicVariables[47] if geq_func(constants[63], 1.0) else states[15] - algebraicVariables[5] = 0.0000185*constants[77]*(algebraicVariables[8]-0.0)/(computed_constants[0]*(1.0-exp(-1.0*(algebraicVariables[8]-0.0)/computed_constants[0])))*(algebraicVariables[0]-constants[2]*exp(-1.0*(algebraicVariables[8]-0.0)/computed_constants[0]))*states[23]*states[22]*states[21] - algebraicVariables[1] = computed_constants[0]*log(constants[2]/algebraicVariables[0]) - algebraicVariables[6] = states[16]*computed_constants[14]*(algebraicVariables[8]-algebraicVariables[1])*(1.0-constants[71]) - algebraicVariables[51] = computed_constants[0]*log((constants[2]+0.12*constants[4])/(algebraicVariables[0]+0.12*constants[3])) - algebraicVariables[53] = constants[74]*pow(states[18], 3.0)*(algebraicVariables[8]-algebraicVariables[51]) - algebraicVariables[52] = constants[73]*pow(states[18], 3.0)*states[17]*(algebraicVariables[8]-algebraicVariables[51]) - algebraicVariables[7] = algebraicVariables[52]+algebraicVariables[53] - algebraicVariables[4] = computed_constants[4]*constants[10]*pow(1.0+pow(constants[9]/constants[4], 1.2), -1.0)*pow(1.0+pow(constants[8]/algebraicVariables[0], 1.3), -1.0)*pow(1.0+exp(-(algebraicVariables[8]-algebraicVariables[1]+110.0)/20.0), -1.0) - algebraicVariables[20] = 1.0+states[0]/constants[15]*(1.0+exp(-constants[14]*algebraicVariables[8]/computed_constants[0])+algebraicVariables[0]/constants[19])+algebraicVariables[0]/constants[18]*(1.0+algebraicVariables[0]/constants[17]*(1.0+algebraicVariables[0]/constants[13])) - algebraicVariables[13] = states[0]/constants[15]*exp(-constants[14]*algebraicVariables[8]/computed_constants[0])/algebraicVariables[20] - algebraicVariables[21] = 1.0+constants[5]/constants[22]*(1.0+exp(constants[21]*algebraicVariables[8]/computed_constants[0]))+constants[2]/constants[24]*(1.0+constants[2]/constants[23]*(1.0+constants[2]/constants[20])) - algebraicVariables[14] = constants[5]/constants[22]*exp(constants[21]*algebraicVariables[8]/computed_constants[0])/algebraicVariables[21] - algebraicVariables[17] = exp(constants[16]*algebraicVariables[8]/(2.0*computed_constants[0])) - algebraicVariables[19] = algebraicVariables[0]/constants[18]*algebraicVariables[0]/constants[17]*(1.0+algebraicVariables[0]/constants[13])*exp(constants[16]*algebraicVariables[8]/(2.0*computed_constants[0]))/algebraicVariables[20] - algebraicVariables[18] = constants[2]/constants[24]*constants[2]/constants[23]*(1.0+constants[2]/constants[20])*exp(-constants[16]*algebraicVariables[8]/(2.0*computed_constants[0]))/algebraicVariables[21] - algebraicVariables[9] = algebraicVariables[18]*computed_constants[5]*(algebraicVariables[19]+algebraicVariables[13])+algebraicVariables[19]*algebraicVariables[14]*(computed_constants[5]+algebraicVariables[17]) - algebraicVariables[16] = algebraicVariables[0]/(constants[13]+algebraicVariables[0]) - algebraicVariables[15] = exp(-constants[16]*algebraicVariables[8]/(2.0*computed_constants[0])) - algebraicVariables[10] = algebraicVariables[19]*algebraicVariables[16]*(algebraicVariables[18]+algebraicVariables[14])+algebraicVariables[13]*algebraicVariables[18]*(algebraicVariables[16]+algebraicVariables[15]) - algebraicVariables[11] = algebraicVariables[17]*algebraicVariables[16]*(algebraicVariables[19]+algebraicVariables[13])+algebraicVariables[15]*algebraicVariables[13]*(computed_constants[5]+algebraicVariables[17]) - algebraicVariables[12] = algebraicVariables[15]*computed_constants[5]*(algebraicVariables[18]+algebraicVariables[14])+algebraicVariables[14]*algebraicVariables[17]*(algebraicVariables[16]+algebraicVariables[15]) - algebraicVariables[3] = (1.0-constants[12])*constants[11]*(algebraicVariables[11]*algebraicVariables[14]-algebraicVariables[12]*algebraicVariables[13])/(algebraicVariables[12]+algebraicVariables[11]+algebraicVariables[10]+algebraicVariables[9]) - rates[1] = (1.0-constants[7])*-1.0*(algebraicVariables[7]+algebraicVariables[6]+algebraicVariables[5]+3.0*algebraicVariables[4]+3.0*algebraicVariables[3])/(1.0*(computed_constants[3]+computed_constants[2])*constants[6]) - algebraicVariables[24] = constants[29]-(constants[29]-constants[28])/(1.0+pow(constants[27]/states[2], constants[26])) - algebraicVariables[25] = constants[30]/algebraicVariables[24] - algebraicVariables[26] = constants[31]*algebraicVariables[24] - rates[4] = constants[33]*states[5]-algebraicVariables[26]*states[0]*states[4]-(algebraicVariables[25]*pow(states[0], 2.0)*states[4]-constants[32]*states[3]) - rates[3] = algebraicVariables[25]*pow(states[0], 2.0)*states[4]-constants[32]*states[3]-(algebraicVariables[26]*states[0]*states[3]-constants[33]*states[6]) - rates[6] = algebraicVariables[26]*states[0]*states[3]-constants[33]*states[6]-(constants[32]*states[6]-algebraicVariables[25]*pow(states[0], 2.0)*states[5]) - rates[5] = constants[32]*states[6]-algebraicVariables[25]*pow(states[0], 2.0)*states[5]-(constants[33]*states[5]-algebraicVariables[26]*states[0]*states[4]) - algebraicVariables[31] = constants[40]*states[7]*(1.0-states[9])-constants[39]*states[9] - rates[9] = algebraicVariables[31] - algebraicVariables[32] = constants[42]*states[7]*(1.0-(states[10]+states[11]))-constants[41]*states[10] - rates[10] = algebraicVariables[32] - algebraicVariables[33] = constants[45]*constants[44]*(1.0-(states[10]+states[11]))-constants[43]*states[11] - rates[11] = algebraicVariables[33] - algebraicVariables[34] = constants[47]*states[7]*(1.0-states[12])-constants[46]*states[12] - rates[12] = algebraicVariables[34] - algebraicVariables[35] = constants[47]*states[0]*(1.0-states[13])-constants[46]*states[13] - rates[13] = algebraicVariables[35] - algebraicVariables[36] = constants[49]*states[2]*(1.0-states[14])-constants[48]*states[14] - rates[14] = algebraicVariables[36] - algebraicVariables[29] = computed_constants[7]/(1.0+exp((-states[7]+constants[37])/constants[36])) - algebraicVariables[28] = (states[0]-states[7])/constants[35] - rates[7] = 1.0*(algebraicVariables[28]*computed_constants[2]-algebraicVariables[29]*computed_constants[8])/computed_constants[3]-(constants[52]*algebraicVariables[34]+constants[50]*algebraicVariables[31]+constants[51]*algebraicVariables[32]) - algebraicVariables[22] = constants[25]*states[3]*(states[2]-states[0]) - algebraicVariables[37] = 2.0*constants[84]*algebraicVariables[8]/(computed_constants[0]*(1.0-exp(-1.0*algebraicVariables[8]*2.0/computed_constants[0])))*(states[0]-constants[5]*exp(-2.0*algebraicVariables[8]/computed_constants[0]))*states[25]*states[24] - algebraicVariables[38] = 2.0*constants[77]*(algebraicVariables[8]-0.0)/(computed_constants[0]*(1.0-exp(-1.0*(algebraicVariables[8]-0.0)*2.0/computed_constants[0])))*(states[0]-constants[5]*exp(-2.0*(algebraicVariables[8]-0.0)/computed_constants[0]))*states[23]*states[22]*states[21] - rates[0] = algebraicVariables[22]*computed_constants[9]/computed_constants[2]-((algebraicVariables[38]+algebraicVariables[37]-2.0*algebraicVariables[3])/(2.0*constants[6]*computed_constants[2])+algebraicVariables[28]+constants[52]*algebraicVariables[35]) - algebraicVariables[30] = (states[8]-states[2])/constants[38] - rates[8] = algebraicVariables[29]-algebraicVariables[30]*computed_constants[9]/computed_constants[8] - rates[2] = algebraicVariables[30]-(algebraicVariables[22]+constants[53]*algebraicVariables[36]) - algebraicVariables[39] = constants[76]*states[20]*states[19]*(algebraicVariables[8]-computed_constants[1]) - algebraicVariables[40] = constants[90]*constants[89]*(algebraicVariables[8]-computed_constants[1])*(1.0+exp((algebraicVariables[8]+20.0)/20.0))*states[32] if gt_func(constants[0], 0.0) else 0.0 - algebraicVariables[67] = 0.000365*constants[77]*(algebraicVariables[8]-0.0)/(computed_constants[0]*(1.0-exp(-1.0*(algebraicVariables[8]-0.0)/computed_constants[0])))*(constants[3]-constants[4]*exp(-1.0*(algebraicVariables[8]-0.0)/computed_constants[0]))*states[23]*states[22]*states[21] - algebraicVariables[41] = (algebraicVariables[38]+algebraicVariables[67]+algebraicVariables[5])*(1.0-computed_constants[19])*1.0*computed_constants[18] - algebraicVariables[42] = constants[86]*(algebraicVariables[8]-computed_constants[1])*states[27]*states[26] - algebraicVariables[93] = computed_constants[0]*log((constants[4]+0.12*constants[2])/(constants[3]+0.12*algebraicVariables[0])) - algebraicVariables[43] = computed_constants[22]*(algebraicVariables[8]-algebraicVariables[93])*pow(states[31], 2.0) - algebraicVariables[44] = constants[87]*(algebraicVariables[8]-computed_constants[1])*(0.9*states[30]+0.1*states[29])*states[28] - algebraicVariables[48] = states[16]*computed_constants[15]*(algebraicVariables[8]-computed_constants[1])*(1.0-constants[71]) - algebraicVariables[45] = algebraicVariables[6]+algebraicVariables[48] - algebraicVariables[46] = algebraicVariables[45]+algebraicVariables[44]+algebraicVariables[43]+algebraicVariables[42]+algebraicVariables[4]+algebraicVariables[3]+algebraicVariables[7]+algebraicVariables[41]+algebraicVariables[37]+algebraicVariables[40]+algebraicVariables[39] - rates[15] = -algebraicVariables[46]/constants[60] - algebraicVariables[49] = 1.0/(0.36*(algebraicVariables[8]+148.8-computed_constants[16]-computed_constants[17])/(exp(0.066*(algebraicVariables[8]+148.8-computed_constants[16]-computed_constants[17]))-1.0)+0.1*(algebraicVariables[8]+87.3-computed_constants[16]-computed_constants[17])/(1.0-exp(-0.2*(algebraicVariables[8]+87.3-computed_constants[16]-computed_constants[17]))))-0.054 - algebraicVariables[50] = 0.01329+0.99921/(1.0+exp((algebraicVariables[8]+97.134-computed_constants[16]-computed_constants[17]-constants[72])/8.1752)) if lt_func(algebraicVariables[8], -(80.0-computed_constants[16]-computed_constants[17]-constants[72])) else 0.0002501*exp(-(algebraicVariables[8]-computed_constants[16]-computed_constants[17]-constants[72])/12.861) - rates[16] = (algebraicVariables[50]-states[16])/algebraicVariables[49] - algebraicVariables[57] = 8000.0*exp(-0.056*(algebraicVariables[8]+66.0)) - algebraicVariables[55] = algebraicVariables[8]+41.0 - algebraicVariables[56] = 2000.0 if lt_func(fabs(algebraicVariables[55]), constants[75]) else 200.0*algebraicVariables[55]/(1.0-exp(-0.1*algebraicVariables[55])) - algebraicVariables[58] = 1.0/(algebraicVariables[56]+algebraicVariables[57]) - algebraicVariables[54] = 1.0/(1.0+exp(-(algebraicVariables[8]+42.0504)/8.3106)) - rates[18] = (algebraicVariables[54]-states[18])/algebraicVariables[58] - algebraicVariables[61] = 2000.0/(320.0*exp(-0.1*(algebraicVariables[8]+75.0))+1.0) - algebraicVariables[60] = 20.0*exp(-0.125*(algebraicVariables[8]+75.0)) - algebraicVariables[62] = 1.0/(algebraicVariables[60]+algebraicVariables[61]) - algebraicVariables[59] = 1.0/(1.0+exp((algebraicVariables[8]+69.804)/4.4565)) - rates[17] = (algebraicVariables[59]-states[17])/algebraicVariables[62] - algebraicVariables[63] = 0.009/(1.0+exp((algebraicVariables[8]+5.0)/12.0))+0.0005 - algebraicVariables[64] = 1.0/(1.0+exp((algebraicVariables[8]+6.0)/-8.6)) - rates[20] = (algebraicVariables[64]-states[20])/algebraicVariables[63] - algebraicVariables[65] = 0.59/(1.0+exp((algebraicVariables[8]+60.0)/10.0))+3.05 - algebraicVariables[66] = 1.0/(1.0+exp((algebraicVariables[8]+7.5)/10.0)) - rates[19] = (algebraicVariables[66]-states[19])/algebraicVariables[65] - algebraicVariables[68] = 1.0/(1.0+exp(-(algebraicVariables[8]-constants[79]-computed_constants[20])/(constants[78]*(1.0+computed_constants[21]/100.0)))) - algebraicVariables[73] = -1.80001 if eq_func(algebraicVariables[8], -1.8) else algebraicVariables[8] - algebraicVariables[69] = 0.01143*(algebraicVariables[73]+1.8)/(exp((algebraicVariables[73]+1.8)/2.5)-1.0) - algebraicVariables[72] = -41.80001 if eq_func(algebraicVariables[8], -41.8) else 0.0 if eq_func(algebraicVariables[8], 0.0) else -6.80001 if eq_func(algebraicVariables[8], -6.8) else algebraicVariables[8] - algebraicVariables[70] = -0.02839*(algebraicVariables[72]+41.8)/(exp(-(algebraicVariables[72]+41.8)/2.5)-1.0)-0.0849*(algebraicVariables[72]+6.8)/(exp(-(algebraicVariables[72]+6.8)/4.8)-1.0) - algebraicVariables[71] = 0.001/(algebraicVariables[70]+algebraicVariables[69]) - rates[23] = (algebraicVariables[68]-states[23])/algebraicVariables[71] - algebraicVariables[75] = 0.001*(44.3+230.0*exp(-pow((algebraicVariables[8]+36.0)/10.0, 2.0))) - algebraicVariables[74] = 1.0/(1.0+exp((algebraicVariables[8]+37.4+constants[81])/(5.3+constants[80]))) - rates[22] = (algebraicVariables[74]-states[22])/algebraicVariables[75] - algebraicVariables[76] = constants[82]/(constants[82]+states[0]) - algebraicVariables[77] = 0.001*algebraicVariables[76]/constants[83] - rates[21] = (algebraicVariables[76]-states[21])/algebraicVariables[77] - algebraicVariables[79] = 0.001/(1.068*exp((algebraicVariables[8]+38.3)/30.0)+1.068*exp(-(algebraicVariables[8]+38.3)/30.0)) - algebraicVariables[78] = 1.0/(1.0+exp(-(algebraicVariables[8]+38.3)/5.5)) - rates[25] = (algebraicVariables[78]-states[25])/algebraicVariables[79] - algebraicVariables[81] = 1.0/(16.67*exp(-(algebraicVariables[8]+75.0)/83.3)+16.67*exp((algebraicVariables[8]+75.0)/15.38))+constants[85] - algebraicVariables[80] = 1.0/(1.0+exp((algebraicVariables[8]+58.7)/3.8)) - rates[24] = (algebraicVariables[80]-states[24])/algebraicVariables[81] - algebraicVariables[83] = 0.001*0.6*(65.17/(0.57*exp(-0.08*(algebraicVariables[8]+44.0))+0.065*exp(0.1*(algebraicVariables[8]+45.93)))+10.1) - algebraicVariables[82] = 1.0/(1.0+exp((algebraicVariables[8]+49.0)/13.0)) - rates[27] = (algebraicVariables[82]-states[27])/algebraicVariables[83] - algebraicVariables[85] = 0.001*0.66*1.4*(15.59/(1.037*exp(0.09*(algebraicVariables[8]+30.61))+0.369*exp(-0.12*(algebraicVariables[8]+23.84)))+2.98) - algebraicVariables[84] = 1.0/(1.0+exp(-(algebraicVariables[8]-19.3)/15.0)) - rates[26] = (algebraicVariables[84]-states[26])/algebraicVariables[85] - algebraicVariables[89] = 0.84655354/(4.2*exp(algebraicVariables[8]/17.0)+0.15*exp(-algebraicVariables[8]/21.6)) - algebraicVariables[88] = 1.0/(1.0+exp(-(algebraicVariables[8]+10.0144)/7.6607)) - rates[29] = (algebraicVariables[88]-states[29])/algebraicVariables[89] - algebraicVariables[90] = 1.0/(30.0*exp(algebraicVariables[8]/10.0)+exp(-algebraicVariables[8]/12.0)) - rates[30] = (algebraicVariables[88]-states[30])/algebraicVariables[90] - algebraicVariables[91] = 1.0/(100.0*exp(-algebraicVariables[8]/54.645)+656.0*exp(algebraicVariables[8]/106.157)) - algebraicVariables[92] = 1.0/(1.0+exp((algebraicVariables[8]+28.6)/17.1)) - rates[28] = (algebraicVariables[92]-states[28])/algebraicVariables[91] - algebraicVariables[94] = sqrt(1.0/(1.0+exp(-(algebraicVariables[8]+0.6383-computed_constants[23])/10.7071))) - algebraicVariables[95] = 1.0*exp(-(algebraicVariables[8]-computed_constants[23]-5.0)/25.0) - algebraicVariables[96] = 28.0/(1.0+exp(-(algebraicVariables[8]-40.0-computed_constants[23])/3.0)) - algebraicVariables[97] = 1.0/(algebraicVariables[96]+algebraicVariables[95]) - rates[31] = (algebraicVariables[94]-states[31])/algebraicVariables[97] - algebraicVariables[98] = 10.0*exp(0.0133*(algebraicVariables[8]+40.0)) - algebraicVariables[100] = 1.0/(computed_constants[24]+algebraicVariables[98]) - algebraicVariables[99] = computed_constants[24]/(computed_constants[24]+algebraicVariables[98]) - rates[32] = (algebraicVariables[99]-states[32])/algebraicVariables[100] + algebraic_variables[0] = states[1] + algebraic_variables[47] = constants[64] if and_func(gt_func(voi, constants[66]), lt_func(voi, constants[66]+constants[65])) else constants[67] + algebraic_variables[8] = algebraic_variables[47] if geq_func(constants[63], 1.0) else states[15] + algebraic_variables[5] = 0.0000185*constants[77]*(algebraic_variables[8]-0.0)/(computed_constants[0]*(1.0-exp(-1.0*(algebraic_variables[8]-0.0)/computed_constants[0])))*(algebraic_variables[0]-constants[2]*exp(-1.0*(algebraic_variables[8]-0.0)/computed_constants[0]))*states[23]*states[22]*states[21] + algebraic_variables[1] = computed_constants[0]*log(constants[2]/algebraic_variables[0]) + algebraic_variables[6] = states[16]*computed_constants[14]*(algebraic_variables[8]-algebraic_variables[1])*(1.0-constants[71]) + algebraic_variables[51] = computed_constants[0]*log((constants[2]+0.12*constants[4])/(algebraic_variables[0]+0.12*constants[3])) + algebraic_variables[53] = constants[74]*pow(states[18], 3.0)*(algebraic_variables[8]-algebraic_variables[51]) + algebraic_variables[52] = constants[73]*pow(states[18], 3.0)*states[17]*(algebraic_variables[8]-algebraic_variables[51]) + algebraic_variables[7] = algebraic_variables[52]+algebraic_variables[53] + algebraic_variables[4] = computed_constants[4]*constants[10]*pow(1.0+pow(constants[9]/constants[4], 1.2), -1.0)*pow(1.0+pow(constants[8]/algebraic_variables[0], 1.3), -1.0)*pow(1.0+exp(-(algebraic_variables[8]-algebraic_variables[1]+110.0)/20.0), -1.0) + algebraic_variables[20] = 1.0+states[0]/constants[15]*(1.0+exp(-constants[14]*algebraic_variables[8]/computed_constants[0])+algebraic_variables[0]/constants[19])+algebraic_variables[0]/constants[18]*(1.0+algebraic_variables[0]/constants[17]*(1.0+algebraic_variables[0]/constants[13])) + algebraic_variables[13] = states[0]/constants[15]*exp(-constants[14]*algebraic_variables[8]/computed_constants[0])/algebraic_variables[20] + algebraic_variables[21] = 1.0+constants[5]/constants[22]*(1.0+exp(constants[21]*algebraic_variables[8]/computed_constants[0]))+constants[2]/constants[24]*(1.0+constants[2]/constants[23]*(1.0+constants[2]/constants[20])) + algebraic_variables[14] = constants[5]/constants[22]*exp(constants[21]*algebraic_variables[8]/computed_constants[0])/algebraic_variables[21] + algebraic_variables[17] = exp(constants[16]*algebraic_variables[8]/(2.0*computed_constants[0])) + algebraic_variables[19] = algebraic_variables[0]/constants[18]*algebraic_variables[0]/constants[17]*(1.0+algebraic_variables[0]/constants[13])*exp(constants[16]*algebraic_variables[8]/(2.0*computed_constants[0]))/algebraic_variables[20] + algebraic_variables[18] = constants[2]/constants[24]*constants[2]/constants[23]*(1.0+constants[2]/constants[20])*exp(-constants[16]*algebraic_variables[8]/(2.0*computed_constants[0]))/algebraic_variables[21] + algebraic_variables[9] = algebraic_variables[18]*computed_constants[5]*(algebraic_variables[19]+algebraic_variables[13])+algebraic_variables[19]*algebraic_variables[14]*(computed_constants[5]+algebraic_variables[17]) + algebraic_variables[16] = algebraic_variables[0]/(constants[13]+algebraic_variables[0]) + algebraic_variables[15] = exp(-constants[16]*algebraic_variables[8]/(2.0*computed_constants[0])) + algebraic_variables[10] = algebraic_variables[19]*algebraic_variables[16]*(algebraic_variables[18]+algebraic_variables[14])+algebraic_variables[13]*algebraic_variables[18]*(algebraic_variables[16]+algebraic_variables[15]) + algebraic_variables[11] = algebraic_variables[17]*algebraic_variables[16]*(algebraic_variables[19]+algebraic_variables[13])+algebraic_variables[15]*algebraic_variables[13]*(computed_constants[5]+algebraic_variables[17]) + algebraic_variables[12] = algebraic_variables[15]*computed_constants[5]*(algebraic_variables[18]+algebraic_variables[14])+algebraic_variables[14]*algebraic_variables[17]*(algebraic_variables[16]+algebraic_variables[15]) + algebraic_variables[3] = (1.0-constants[12])*constants[11]*(algebraic_variables[11]*algebraic_variables[14]-algebraic_variables[12]*algebraic_variables[13])/(algebraic_variables[12]+algebraic_variables[11]+algebraic_variables[10]+algebraic_variables[9]) + rates[1] = (1.0-constants[7])*-1.0*(algebraic_variables[7]+algebraic_variables[6]+algebraic_variables[5]+3.0*algebraic_variables[4]+3.0*algebraic_variables[3])/(1.0*(computed_constants[3]+computed_constants[2])*constants[6]) + algebraic_variables[24] = constants[29]-(constants[29]-constants[28])/(1.0+pow(constants[27]/states[2], constants[26])) + algebraic_variables[25] = constants[30]/algebraic_variables[24] + algebraic_variables[26] = constants[31]*algebraic_variables[24] + rates[4] = constants[33]*states[5]-algebraic_variables[26]*states[0]*states[4]-(algebraic_variables[25]*pow(states[0], 2.0)*states[4]-constants[32]*states[3]) + rates[3] = algebraic_variables[25]*pow(states[0], 2.0)*states[4]-constants[32]*states[3]-(algebraic_variables[26]*states[0]*states[3]-constants[33]*states[6]) + rates[6] = algebraic_variables[26]*states[0]*states[3]-constants[33]*states[6]-(constants[32]*states[6]-algebraic_variables[25]*pow(states[0], 2.0)*states[5]) + rates[5] = constants[32]*states[6]-algebraic_variables[25]*pow(states[0], 2.0)*states[5]-(constants[33]*states[5]-algebraic_variables[26]*states[0]*states[4]) + algebraic_variables[31] = constants[40]*states[7]*(1.0-states[9])-constants[39]*states[9] + rates[9] = algebraic_variables[31] + algebraic_variables[32] = constants[42]*states[7]*(1.0-(states[10]+states[11]))-constants[41]*states[10] + rates[10] = algebraic_variables[32] + algebraic_variables[33] = constants[45]*constants[44]*(1.0-(states[10]+states[11]))-constants[43]*states[11] + rates[11] = algebraic_variables[33] + algebraic_variables[34] = constants[47]*states[7]*(1.0-states[12])-constants[46]*states[12] + rates[12] = algebraic_variables[34] + algebraic_variables[35] = constants[47]*states[0]*(1.0-states[13])-constants[46]*states[13] + rates[13] = algebraic_variables[35] + algebraic_variables[36] = constants[49]*states[2]*(1.0-states[14])-constants[48]*states[14] + rates[14] = algebraic_variables[36] + algebraic_variables[29] = computed_constants[7]/(1.0+exp((-states[7]+constants[37])/constants[36])) + algebraic_variables[28] = (states[0]-states[7])/constants[35] + rates[7] = 1.0*(algebraic_variables[28]*computed_constants[2]-algebraic_variables[29]*computed_constants[8])/computed_constants[3]-(constants[52]*algebraic_variables[34]+constants[50]*algebraic_variables[31]+constants[51]*algebraic_variables[32]) + algebraic_variables[22] = constants[25]*states[3]*(states[2]-states[0]) + algebraic_variables[37] = 2.0*constants[84]*algebraic_variables[8]/(computed_constants[0]*(1.0-exp(-1.0*algebraic_variables[8]*2.0/computed_constants[0])))*(states[0]-constants[5]*exp(-2.0*algebraic_variables[8]/computed_constants[0]))*states[25]*states[24] + algebraic_variables[38] = 2.0*constants[77]*(algebraic_variables[8]-0.0)/(computed_constants[0]*(1.0-exp(-1.0*(algebraic_variables[8]-0.0)*2.0/computed_constants[0])))*(states[0]-constants[5]*exp(-2.0*(algebraic_variables[8]-0.0)/computed_constants[0]))*states[23]*states[22]*states[21] + rates[0] = algebraic_variables[22]*computed_constants[9]/computed_constants[2]-((algebraic_variables[38]+algebraic_variables[37]-2.0*algebraic_variables[3])/(2.0*constants[6]*computed_constants[2])+algebraic_variables[28]+constants[52]*algebraic_variables[35]) + algebraic_variables[30] = (states[8]-states[2])/constants[38] + rates[8] = algebraic_variables[29]-algebraic_variables[30]*computed_constants[9]/computed_constants[8] + rates[2] = algebraic_variables[30]-(algebraic_variables[22]+constants[53]*algebraic_variables[36]) + algebraic_variables[39] = constants[76]*states[20]*states[19]*(algebraic_variables[8]-computed_constants[1]) + algebraic_variables[40] = constants[90]*constants[89]*(algebraic_variables[8]-computed_constants[1])*(1.0+exp((algebraic_variables[8]+20.0)/20.0))*states[32] if gt_func(constants[0], 0.0) else 0.0 + algebraic_variables[67] = 0.000365*constants[77]*(algebraic_variables[8]-0.0)/(computed_constants[0]*(1.0-exp(-1.0*(algebraic_variables[8]-0.0)/computed_constants[0])))*(constants[3]-constants[4]*exp(-1.0*(algebraic_variables[8]-0.0)/computed_constants[0]))*states[23]*states[22]*states[21] + algebraic_variables[41] = (algebraic_variables[38]+algebraic_variables[67]+algebraic_variables[5])*(1.0-computed_constants[19])*1.0*computed_constants[18] + algebraic_variables[42] = constants[86]*(algebraic_variables[8]-computed_constants[1])*states[27]*states[26] + algebraic_variables[93] = computed_constants[0]*log((constants[4]+0.12*constants[2])/(constants[3]+0.12*algebraic_variables[0])) + algebraic_variables[43] = computed_constants[22]*(algebraic_variables[8]-algebraic_variables[93])*pow(states[31], 2.0) + algebraic_variables[44] = constants[87]*(algebraic_variables[8]-computed_constants[1])*(0.9*states[30]+0.1*states[29])*states[28] + algebraic_variables[48] = states[16]*computed_constants[15]*(algebraic_variables[8]-computed_constants[1])*(1.0-constants[71]) + algebraic_variables[45] = algebraic_variables[6]+algebraic_variables[48] + algebraic_variables[46] = algebraic_variables[45]+algebraic_variables[44]+algebraic_variables[43]+algebraic_variables[42]+algebraic_variables[4]+algebraic_variables[3]+algebraic_variables[7]+algebraic_variables[41]+algebraic_variables[37]+algebraic_variables[40]+algebraic_variables[39] + rates[15] = -algebraic_variables[46]/constants[60] + algebraic_variables[49] = 1.0/(0.36*(algebraic_variables[8]+148.8-computed_constants[16]-computed_constants[17])/(exp(0.066*(algebraic_variables[8]+148.8-computed_constants[16]-computed_constants[17]))-1.0)+0.1*(algebraic_variables[8]+87.3-computed_constants[16]-computed_constants[17])/(1.0-exp(-0.2*(algebraic_variables[8]+87.3-computed_constants[16]-computed_constants[17]))))-0.054 + algebraic_variables[50] = 0.01329+0.99921/(1.0+exp((algebraic_variables[8]+97.134-computed_constants[16]-computed_constants[17]-constants[72])/8.1752)) if lt_func(algebraic_variables[8], -(80.0-computed_constants[16]-computed_constants[17]-constants[72])) else 0.0002501*exp(-(algebraic_variables[8]-computed_constants[16]-computed_constants[17]-constants[72])/12.861) + rates[16] = (algebraic_variables[50]-states[16])/algebraic_variables[49] + algebraic_variables[57] = 8000.0*exp(-0.056*(algebraic_variables[8]+66.0)) + algebraic_variables[55] = algebraic_variables[8]+41.0 + algebraic_variables[56] = 2000.0 if lt_func(fabs(algebraic_variables[55]), constants[75]) else 200.0*algebraic_variables[55]/(1.0-exp(-0.1*algebraic_variables[55])) + algebraic_variables[58] = 1.0/(algebraic_variables[56]+algebraic_variables[57]) + algebraic_variables[54] = 1.0/(1.0+exp(-(algebraic_variables[8]+42.0504)/8.3106)) + rates[18] = (algebraic_variables[54]-states[18])/algebraic_variables[58] + algebraic_variables[61] = 2000.0/(320.0*exp(-0.1*(algebraic_variables[8]+75.0))+1.0) + algebraic_variables[60] = 20.0*exp(-0.125*(algebraic_variables[8]+75.0)) + algebraic_variables[62] = 1.0/(algebraic_variables[60]+algebraic_variables[61]) + algebraic_variables[59] = 1.0/(1.0+exp((algebraic_variables[8]+69.804)/4.4565)) + rates[17] = (algebraic_variables[59]-states[17])/algebraic_variables[62] + algebraic_variables[63] = 0.009/(1.0+exp((algebraic_variables[8]+5.0)/12.0))+0.0005 + algebraic_variables[64] = 1.0/(1.0+exp((algebraic_variables[8]+6.0)/-8.6)) + rates[20] = (algebraic_variables[64]-states[20])/algebraic_variables[63] + algebraic_variables[65] = 0.59/(1.0+exp((algebraic_variables[8]+60.0)/10.0))+3.05 + algebraic_variables[66] = 1.0/(1.0+exp((algebraic_variables[8]+7.5)/10.0)) + rates[19] = (algebraic_variables[66]-states[19])/algebraic_variables[65] + algebraic_variables[68] = 1.0/(1.0+exp(-(algebraic_variables[8]-constants[79]-computed_constants[20])/(constants[78]*(1.0+computed_constants[21]/100.0)))) + algebraic_variables[73] = -1.80001 if eq_func(algebraic_variables[8], -1.8) else algebraic_variables[8] + algebraic_variables[69] = 0.01143*(algebraic_variables[73]+1.8)/(exp((algebraic_variables[73]+1.8)/2.5)-1.0) + algebraic_variables[72] = -41.80001 if eq_func(algebraic_variables[8], -41.8) else 0.0 if eq_func(algebraic_variables[8], 0.0) else -6.80001 if eq_func(algebraic_variables[8], -6.8) else algebraic_variables[8] + algebraic_variables[70] = -0.02839*(algebraic_variables[72]+41.8)/(exp(-(algebraic_variables[72]+41.8)/2.5)-1.0)-0.0849*(algebraic_variables[72]+6.8)/(exp(-(algebraic_variables[72]+6.8)/4.8)-1.0) + algebraic_variables[71] = 0.001/(algebraic_variables[70]+algebraic_variables[69]) + rates[23] = (algebraic_variables[68]-states[23])/algebraic_variables[71] + algebraic_variables[75] = 0.001*(44.3+230.0*exp(-pow((algebraic_variables[8]+36.0)/10.0, 2.0))) + algebraic_variables[74] = 1.0/(1.0+exp((algebraic_variables[8]+37.4+constants[81])/(5.3+constants[80]))) + rates[22] = (algebraic_variables[74]-states[22])/algebraic_variables[75] + algebraic_variables[76] = constants[82]/(constants[82]+states[0]) + algebraic_variables[77] = 0.001*algebraic_variables[76]/constants[83] + rates[21] = (algebraic_variables[76]-states[21])/algebraic_variables[77] + algebraic_variables[79] = 0.001/(1.068*exp((algebraic_variables[8]+38.3)/30.0)+1.068*exp(-(algebraic_variables[8]+38.3)/30.0)) + algebraic_variables[78] = 1.0/(1.0+exp(-(algebraic_variables[8]+38.3)/5.5)) + rates[25] = (algebraic_variables[78]-states[25])/algebraic_variables[79] + algebraic_variables[81] = 1.0/(16.67*exp(-(algebraic_variables[8]+75.0)/83.3)+16.67*exp((algebraic_variables[8]+75.0)/15.38))+constants[85] + algebraic_variables[80] = 1.0/(1.0+exp((algebraic_variables[8]+58.7)/3.8)) + rates[24] = (algebraic_variables[80]-states[24])/algebraic_variables[81] + algebraic_variables[83] = 0.001*0.6*(65.17/(0.57*exp(-0.08*(algebraic_variables[8]+44.0))+0.065*exp(0.1*(algebraic_variables[8]+45.93)))+10.1) + algebraic_variables[82] = 1.0/(1.0+exp((algebraic_variables[8]+49.0)/13.0)) + rates[27] = (algebraic_variables[82]-states[27])/algebraic_variables[83] + algebraic_variables[85] = 0.001*0.66*1.4*(15.59/(1.037*exp(0.09*(algebraic_variables[8]+30.61))+0.369*exp(-0.12*(algebraic_variables[8]+23.84)))+2.98) + algebraic_variables[84] = 1.0/(1.0+exp(-(algebraic_variables[8]-19.3)/15.0)) + rates[26] = (algebraic_variables[84]-states[26])/algebraic_variables[85] + algebraic_variables[89] = 0.84655354/(4.2*exp(algebraic_variables[8]/17.0)+0.15*exp(-algebraic_variables[8]/21.6)) + algebraic_variables[88] = 1.0/(1.0+exp(-(algebraic_variables[8]+10.0144)/7.6607)) + rates[29] = (algebraic_variables[88]-states[29])/algebraic_variables[89] + algebraic_variables[90] = 1.0/(30.0*exp(algebraic_variables[8]/10.0)+exp(-algebraic_variables[8]/12.0)) + rates[30] = (algebraic_variables[88]-states[30])/algebraic_variables[90] + algebraic_variables[91] = 1.0/(100.0*exp(-algebraic_variables[8]/54.645)+656.0*exp(algebraic_variables[8]/106.157)) + algebraic_variables[92] = 1.0/(1.0+exp((algebraic_variables[8]+28.6)/17.1)) + rates[28] = (algebraic_variables[92]-states[28])/algebraic_variables[91] + algebraic_variables[94] = sqrt(1.0/(1.0+exp(-(algebraic_variables[8]+0.6383-computed_constants[23])/10.7071))) + algebraic_variables[95] = 1.0*exp(-(algebraic_variables[8]-computed_constants[23]-5.0)/25.0) + algebraic_variables[96] = 28.0/(1.0+exp(-(algebraic_variables[8]-40.0-computed_constants[23])/3.0)) + algebraic_variables[97] = 1.0/(algebraic_variables[96]+algebraic_variables[95]) + rates[31] = (algebraic_variables[94]-states[31])/algebraic_variables[97] + algebraic_variables[98] = 10.0*exp(0.0133*(algebraic_variables[8]+40.0)) + algebraic_variables[100] = 1.0/(computed_constants[24]+algebraic_variables[98]) + algebraic_variables[99] = computed_constants[24]/(computed_constants[24]+algebraic_variables[98]) + rates[32] = (algebraic_variables[99]-states[32])/algebraic_variables[100] def compute_variables(voi, states, rates, constants, computed_constants, algebraic_variables): - algebraicVariables[0] = states[1] - algebraicVariables[1] = computed_constants[0]*log(constants[2]/algebraicVariables[0]) - algebraicVariables[2] = 0.5*computed_constants[0]*log(constants[5]/states[0]) - algebraicVariables[8] = algebraicVariables[47] if geq_func(constants[63], 1.0) else states[15] - algebraicVariables[4] = computed_constants[4]*constants[10]*pow(1.0+pow(constants[9]/constants[4], 1.2), -1.0)*pow(1.0+pow(constants[8]/algebraicVariables[0], 1.3), -1.0)*pow(1.0+exp(-(algebraicVariables[8]-algebraicVariables[1]+110.0)/20.0), -1.0) - algebraicVariables[20] = 1.0+states[0]/constants[15]*(1.0+exp(-constants[14]*algebraicVariables[8]/computed_constants[0])+algebraicVariables[0]/constants[19])+algebraicVariables[0]/constants[18]*(1.0+algebraicVariables[0]/constants[17]*(1.0+algebraicVariables[0]/constants[13])) - algebraicVariables[13] = states[0]/constants[15]*exp(-constants[14]*algebraicVariables[8]/computed_constants[0])/algebraicVariables[20] - algebraicVariables[21] = 1.0+constants[5]/constants[22]*(1.0+exp(constants[21]*algebraicVariables[8]/computed_constants[0]))+constants[2]/constants[24]*(1.0+constants[2]/constants[23]*(1.0+constants[2]/constants[20])) - algebraicVariables[14] = constants[5]/constants[22]*exp(constants[21]*algebraicVariables[8]/computed_constants[0])/algebraicVariables[21] - algebraicVariables[17] = exp(constants[16]*algebraicVariables[8]/(2.0*computed_constants[0])) - algebraicVariables[19] = algebraicVariables[0]/constants[18]*algebraicVariables[0]/constants[17]*(1.0+algebraicVariables[0]/constants[13])*exp(constants[16]*algebraicVariables[8]/(2.0*computed_constants[0]))/algebraicVariables[20] - algebraicVariables[18] = constants[2]/constants[24]*constants[2]/constants[23]*(1.0+constants[2]/constants[20])*exp(-constants[16]*algebraicVariables[8]/(2.0*computed_constants[0]))/algebraicVariables[21] - algebraicVariables[9] = algebraicVariables[18]*computed_constants[5]*(algebraicVariables[19]+algebraicVariables[13])+algebraicVariables[19]*algebraicVariables[14]*(computed_constants[5]+algebraicVariables[17]) - algebraicVariables[16] = algebraicVariables[0]/(constants[13]+algebraicVariables[0]) - algebraicVariables[15] = exp(-constants[16]*algebraicVariables[8]/(2.0*computed_constants[0])) - algebraicVariables[10] = algebraicVariables[19]*algebraicVariables[16]*(algebraicVariables[18]+algebraicVariables[14])+algebraicVariables[13]*algebraicVariables[18]*(algebraicVariables[16]+algebraicVariables[15]) - algebraicVariables[11] = algebraicVariables[17]*algebraicVariables[16]*(algebraicVariables[19]+algebraicVariables[13])+algebraicVariables[15]*algebraicVariables[13]*(computed_constants[5]+algebraicVariables[17]) - algebraicVariables[12] = algebraicVariables[15]*computed_constants[5]*(algebraicVariables[18]+algebraicVariables[14])+algebraicVariables[14]*algebraicVariables[17]*(algebraicVariables[16]+algebraicVariables[15]) - algebraicVariables[3] = (1.0-constants[12])*constants[11]*(algebraicVariables[11]*algebraicVariables[14]-algebraicVariables[12]*algebraicVariables[13])/(algebraicVariables[12]+algebraicVariables[11]+algebraicVariables[10]+algebraicVariables[9]) - algebraicVariables[22] = constants[25]*states[3]*(states[2]-states[0]) - algebraicVariables[23] = states[2]-states[0] - algebraicVariables[24] = constants[29]-(constants[29]-constants[28])/(1.0+pow(constants[27]/states[2], constants[26])) - algebraicVariables[25] = constants[30]/algebraicVariables[24] - algebraicVariables[26] = constants[31]*algebraicVariables[24] - algebraicVariables[27] = states[4]+states[3]+states[6]+states[5] - algebraicVariables[28] = (states[0]-states[7])/constants[35] - algebraicVariables[29] = computed_constants[7]/(1.0+exp((-states[7]+constants[37])/constants[36])) - algebraicVariables[30] = (states[8]-states[2])/constants[38] - algebraicVariables[31] = constants[40]*states[7]*(1.0-states[9])-constants[39]*states[9] - algebraicVariables[32] = constants[42]*states[7]*(1.0-(states[10]+states[11]))-constants[41]*states[10] - algebraicVariables[33] = constants[45]*constants[44]*(1.0-(states[10]+states[11]))-constants[43]*states[11] - algebraicVariables[34] = constants[47]*states[7]*(1.0-states[12])-constants[46]*states[12] - algebraicVariables[35] = constants[47]*states[0]*(1.0-states[13])-constants[46]*states[13] - algebraicVariables[36] = constants[49]*states[2]*(1.0-states[14])-constants[48]*states[14] - algebraicVariables[39] = constants[76]*states[20]*states[19]*(algebraicVariables[8]-computed_constants[1]) - algebraicVariables[40] = constants[90]*constants[89]*(algebraicVariables[8]-computed_constants[1])*(1.0+exp((algebraicVariables[8]+20.0)/20.0))*states[32] if gt_func(constants[0], 0.0) else 0.0 - algebraicVariables[37] = 2.0*constants[84]*algebraicVariables[8]/(computed_constants[0]*(1.0-exp(-1.0*algebraicVariables[8]*2.0/computed_constants[0])))*(states[0]-constants[5]*exp(-2.0*algebraicVariables[8]/computed_constants[0]))*states[25]*states[24] - algebraicVariables[5] = 0.0000185*constants[77]*(algebraicVariables[8]-0.0)/(computed_constants[0]*(1.0-exp(-1.0*(algebraicVariables[8]-0.0)/computed_constants[0])))*(algebraicVariables[0]-constants[2]*exp(-1.0*(algebraicVariables[8]-0.0)/computed_constants[0]))*states[23]*states[22]*states[21] - algebraicVariables[67] = 0.000365*constants[77]*(algebraicVariables[8]-0.0)/(computed_constants[0]*(1.0-exp(-1.0*(algebraicVariables[8]-0.0)/computed_constants[0])))*(constants[3]-constants[4]*exp(-1.0*(algebraicVariables[8]-0.0)/computed_constants[0]))*states[23]*states[22]*states[21] - algebraicVariables[38] = 2.0*constants[77]*(algebraicVariables[8]-0.0)/(computed_constants[0]*(1.0-exp(-1.0*(algebraicVariables[8]-0.0)*2.0/computed_constants[0])))*(states[0]-constants[5]*exp(-2.0*(algebraicVariables[8]-0.0)/computed_constants[0]))*states[23]*states[22]*states[21] - algebraicVariables[41] = (algebraicVariables[38]+algebraicVariables[67]+algebraicVariables[5])*(1.0-computed_constants[19])*1.0*computed_constants[18] - algebraicVariables[51] = computed_constants[0]*log((constants[2]+0.12*constants[4])/(algebraicVariables[0]+0.12*constants[3])) - algebraicVariables[53] = constants[74]*pow(states[18], 3.0)*(algebraicVariables[8]-algebraicVariables[51]) - algebraicVariables[52] = constants[73]*pow(states[18], 3.0)*states[17]*(algebraicVariables[8]-algebraicVariables[51]) - algebraicVariables[7] = algebraicVariables[52]+algebraicVariables[53] - algebraicVariables[42] = constants[86]*(algebraicVariables[8]-computed_constants[1])*states[27]*states[26] - algebraicVariables[93] = computed_constants[0]*log((constants[4]+0.12*constants[2])/(constants[3]+0.12*algebraicVariables[0])) - algebraicVariables[43] = computed_constants[22]*(algebraicVariables[8]-algebraicVariables[93])*pow(states[31], 2.0) - algebraicVariables[44] = constants[87]*(algebraicVariables[8]-computed_constants[1])*(0.9*states[30]+0.1*states[29])*states[28] - algebraicVariables[48] = states[16]*computed_constants[15]*(algebraicVariables[8]-computed_constants[1])*(1.0-constants[71]) - algebraicVariables[6] = states[16]*computed_constants[14]*(algebraicVariables[8]-algebraicVariables[1])*(1.0-constants[71]) - algebraicVariables[45] = algebraicVariables[6]+algebraicVariables[48] - algebraicVariables[46] = algebraicVariables[45]+algebraicVariables[44]+algebraicVariables[43]+algebraicVariables[42]+algebraicVariables[4]+algebraicVariables[3]+algebraicVariables[7]+algebraicVariables[41]+algebraicVariables[37]+algebraicVariables[40]+algebraicVariables[39] - algebraicVariables[49] = 1.0/(0.36*(algebraicVariables[8]+148.8-computed_constants[16]-computed_constants[17])/(exp(0.066*(algebraicVariables[8]+148.8-computed_constants[16]-computed_constants[17]))-1.0)+0.1*(algebraicVariables[8]+87.3-computed_constants[16]-computed_constants[17])/(1.0-exp(-0.2*(algebraicVariables[8]+87.3-computed_constants[16]-computed_constants[17]))))-0.054 - algebraicVariables[50] = 0.01329+0.99921/(1.0+exp((algebraicVariables[8]+97.134-computed_constants[16]-computed_constants[17]-constants[72])/8.1752)) if lt_func(algebraicVariables[8], -(80.0-computed_constants[16]-computed_constants[17]-constants[72])) else 0.0002501*exp(-(algebraicVariables[8]-computed_constants[16]-computed_constants[17]-constants[72])/12.861) - algebraicVariables[54] = 1.0/(1.0+exp(-(algebraicVariables[8]+42.0504)/8.3106)) - algebraicVariables[55] = algebraicVariables[8]+41.0 - algebraicVariables[56] = 2000.0 if lt_func(fabs(algebraicVariables[55]), constants[75]) else 200.0*algebraicVariables[55]/(1.0-exp(-0.1*algebraicVariables[55])) - algebraicVariables[57] = 8000.0*exp(-0.056*(algebraicVariables[8]+66.0)) - algebraicVariables[58] = 1.0/(algebraicVariables[56]+algebraicVariables[57]) - algebraicVariables[59] = 1.0/(1.0+exp((algebraicVariables[8]+69.804)/4.4565)) - algebraicVariables[60] = 20.0*exp(-0.125*(algebraicVariables[8]+75.0)) - algebraicVariables[61] = 2000.0/(320.0*exp(-0.1*(algebraicVariables[8]+75.0))+1.0) - algebraicVariables[62] = 1.0/(algebraicVariables[60]+algebraicVariables[61]) - algebraicVariables[64] = 1.0/(1.0+exp((algebraicVariables[8]+6.0)/-8.6)) - algebraicVariables[63] = 0.009/(1.0+exp((algebraicVariables[8]+5.0)/12.0))+0.0005 - algebraicVariables[66] = 1.0/(1.0+exp((algebraicVariables[8]+7.5)/10.0)) - algebraicVariables[65] = 0.59/(1.0+exp((algebraicVariables[8]+60.0)/10.0))+3.05 - algebraicVariables[68] = 1.0/(1.0+exp(-(algebraicVariables[8]-constants[79]-computed_constants[20])/(constants[78]*(1.0+computed_constants[21]/100.0)))) - algebraicVariables[73] = -1.80001 if eq_func(algebraicVariables[8], -1.8) else algebraicVariables[8] - algebraicVariables[69] = 0.01143*(algebraicVariables[73]+1.8)/(exp((algebraicVariables[73]+1.8)/2.5)-1.0) - algebraicVariables[72] = -41.80001 if eq_func(algebraicVariables[8], -41.8) else 0.0 if eq_func(algebraicVariables[8], 0.0) else -6.80001 if eq_func(algebraicVariables[8], -6.8) else algebraicVariables[8] - algebraicVariables[70] = -0.02839*(algebraicVariables[72]+41.8)/(exp(-(algebraicVariables[72]+41.8)/2.5)-1.0)-0.0849*(algebraicVariables[72]+6.8)/(exp(-(algebraicVariables[72]+6.8)/4.8)-1.0) - algebraicVariables[71] = 0.001/(algebraicVariables[70]+algebraicVariables[69]) - algebraicVariables[74] = 1.0/(1.0+exp((algebraicVariables[8]+37.4+constants[81])/(5.3+constants[80]))) - algebraicVariables[75] = 0.001*(44.3+230.0*exp(-pow((algebraicVariables[8]+36.0)/10.0, 2.0))) - algebraicVariables[76] = constants[82]/(constants[82]+states[0]) - algebraicVariables[77] = 0.001*algebraicVariables[76]/constants[83] - algebraicVariables[78] = 1.0/(1.0+exp(-(algebraicVariables[8]+38.3)/5.5)) - algebraicVariables[79] = 0.001/(1.068*exp((algebraicVariables[8]+38.3)/30.0)+1.068*exp(-(algebraicVariables[8]+38.3)/30.0)) - algebraicVariables[80] = 1.0/(1.0+exp((algebraicVariables[8]+58.7)/3.8)) - algebraicVariables[81] = 1.0/(16.67*exp(-(algebraicVariables[8]+75.0)/83.3)+16.67*exp((algebraicVariables[8]+75.0)/15.38))+constants[85] - algebraicVariables[82] = 1.0/(1.0+exp((algebraicVariables[8]+49.0)/13.0)) - algebraicVariables[83] = 0.001*0.6*(65.17/(0.57*exp(-0.08*(algebraicVariables[8]+44.0))+0.065*exp(0.1*(algebraicVariables[8]+45.93)))+10.1) - algebraicVariables[84] = 1.0/(1.0+exp(-(algebraicVariables[8]-19.3)/15.0)) - algebraicVariables[85] = 0.001*0.66*1.4*(15.59/(1.037*exp(0.09*(algebraicVariables[8]+30.61))+0.369*exp(-0.12*(algebraicVariables[8]+23.84)))+2.98) - algebraicVariables[86] = 1.0/(1.0+exp(-(algebraicVariables[8]+23.2)/6.6))/(0.84655354/(37.2*exp(algebraicVariables[8]/11.9)+0.96*exp(-algebraicVariables[8]/18.5))) - algebraicVariables[87] = 4.0*((37.2*exp(algebraicVariables[8]/15.9)+0.96*exp(-algebraicVariables[8]/22.5))/0.84655354-1.0/(1.0+exp(-(algebraicVariables[8]+23.2)/10.6))/(0.84655354/(37.2*exp(algebraicVariables[8]/15.9)+0.96*exp(-algebraicVariables[8]/22.5)))) - algebraicVariables[88] = 1.0/(1.0+exp(-(algebraicVariables[8]+10.0144)/7.6607)) - algebraicVariables[89] = 0.84655354/(4.2*exp(algebraicVariables[8]/17.0)+0.15*exp(-algebraicVariables[8]/21.6)) - algebraicVariables[90] = 1.0/(30.0*exp(algebraicVariables[8]/10.0)+exp(-algebraicVariables[8]/12.0)) - algebraicVariables[91] = 1.0/(100.0*exp(-algebraicVariables[8]/54.645)+656.0*exp(algebraicVariables[8]/106.157)) - algebraicVariables[92] = 1.0/(1.0+exp((algebraicVariables[8]+28.6)/17.1)) - algebraicVariables[94] = sqrt(1.0/(1.0+exp(-(algebraicVariables[8]+0.6383-computed_constants[23])/10.7071))) - algebraicVariables[95] = 1.0*exp(-(algebraicVariables[8]-computed_constants[23]-5.0)/25.0) - algebraicVariables[96] = 28.0/(1.0+exp(-(algebraicVariables[8]-40.0-computed_constants[23])/3.0)) - algebraicVariables[97] = 1.0/(algebraicVariables[96]+algebraicVariables[95]) - algebraicVariables[98] = 10.0*exp(0.0133*(algebraicVariables[8]+40.0)) - algebraicVariables[99] = computed_constants[24]/(computed_constants[24]+algebraicVariables[98]) - algebraicVariables[100] = 1.0/(computed_constants[24]+algebraicVariables[98]) + algebraic_variables[0] = states[1] + algebraic_variables[1] = computed_constants[0]*log(constants[2]/algebraic_variables[0]) + algebraic_variables[2] = 0.5*computed_constants[0]*log(constants[5]/states[0]) + algebraic_variables[8] = algebraic_variables[47] if geq_func(constants[63], 1.0) else states[15] + algebraic_variables[4] = computed_constants[4]*constants[10]*pow(1.0+pow(constants[9]/constants[4], 1.2), -1.0)*pow(1.0+pow(constants[8]/algebraic_variables[0], 1.3), -1.0)*pow(1.0+exp(-(algebraic_variables[8]-algebraic_variables[1]+110.0)/20.0), -1.0) + algebraic_variables[20] = 1.0+states[0]/constants[15]*(1.0+exp(-constants[14]*algebraic_variables[8]/computed_constants[0])+algebraic_variables[0]/constants[19])+algebraic_variables[0]/constants[18]*(1.0+algebraic_variables[0]/constants[17]*(1.0+algebraic_variables[0]/constants[13])) + algebraic_variables[13] = states[0]/constants[15]*exp(-constants[14]*algebraic_variables[8]/computed_constants[0])/algebraic_variables[20] + algebraic_variables[21] = 1.0+constants[5]/constants[22]*(1.0+exp(constants[21]*algebraic_variables[8]/computed_constants[0]))+constants[2]/constants[24]*(1.0+constants[2]/constants[23]*(1.0+constants[2]/constants[20])) + algebraic_variables[14] = constants[5]/constants[22]*exp(constants[21]*algebraic_variables[8]/computed_constants[0])/algebraic_variables[21] + algebraic_variables[17] = exp(constants[16]*algebraic_variables[8]/(2.0*computed_constants[0])) + algebraic_variables[19] = algebraic_variables[0]/constants[18]*algebraic_variables[0]/constants[17]*(1.0+algebraic_variables[0]/constants[13])*exp(constants[16]*algebraic_variables[8]/(2.0*computed_constants[0]))/algebraic_variables[20] + algebraic_variables[18] = constants[2]/constants[24]*constants[2]/constants[23]*(1.0+constants[2]/constants[20])*exp(-constants[16]*algebraic_variables[8]/(2.0*computed_constants[0]))/algebraic_variables[21] + algebraic_variables[9] = algebraic_variables[18]*computed_constants[5]*(algebraic_variables[19]+algebraic_variables[13])+algebraic_variables[19]*algebraic_variables[14]*(computed_constants[5]+algebraic_variables[17]) + algebraic_variables[16] = algebraic_variables[0]/(constants[13]+algebraic_variables[0]) + algebraic_variables[15] = exp(-constants[16]*algebraic_variables[8]/(2.0*computed_constants[0])) + algebraic_variables[10] = algebraic_variables[19]*algebraic_variables[16]*(algebraic_variables[18]+algebraic_variables[14])+algebraic_variables[13]*algebraic_variables[18]*(algebraic_variables[16]+algebraic_variables[15]) + algebraic_variables[11] = algebraic_variables[17]*algebraic_variables[16]*(algebraic_variables[19]+algebraic_variables[13])+algebraic_variables[15]*algebraic_variables[13]*(computed_constants[5]+algebraic_variables[17]) + algebraic_variables[12] = algebraic_variables[15]*computed_constants[5]*(algebraic_variables[18]+algebraic_variables[14])+algebraic_variables[14]*algebraic_variables[17]*(algebraic_variables[16]+algebraic_variables[15]) + algebraic_variables[3] = (1.0-constants[12])*constants[11]*(algebraic_variables[11]*algebraic_variables[14]-algebraic_variables[12]*algebraic_variables[13])/(algebraic_variables[12]+algebraic_variables[11]+algebraic_variables[10]+algebraic_variables[9]) + algebraic_variables[22] = constants[25]*states[3]*(states[2]-states[0]) + algebraic_variables[23] = states[2]-states[0] + algebraic_variables[24] = constants[29]-(constants[29]-constants[28])/(1.0+pow(constants[27]/states[2], constants[26])) + algebraic_variables[25] = constants[30]/algebraic_variables[24] + algebraic_variables[26] = constants[31]*algebraic_variables[24] + algebraic_variables[27] = states[4]+states[3]+states[6]+states[5] + algebraic_variables[28] = (states[0]-states[7])/constants[35] + algebraic_variables[29] = computed_constants[7]/(1.0+exp((-states[7]+constants[37])/constants[36])) + algebraic_variables[30] = (states[8]-states[2])/constants[38] + algebraic_variables[31] = constants[40]*states[7]*(1.0-states[9])-constants[39]*states[9] + algebraic_variables[32] = constants[42]*states[7]*(1.0-(states[10]+states[11]))-constants[41]*states[10] + algebraic_variables[33] = constants[45]*constants[44]*(1.0-(states[10]+states[11]))-constants[43]*states[11] + algebraic_variables[34] = constants[47]*states[7]*(1.0-states[12])-constants[46]*states[12] + algebraic_variables[35] = constants[47]*states[0]*(1.0-states[13])-constants[46]*states[13] + algebraic_variables[36] = constants[49]*states[2]*(1.0-states[14])-constants[48]*states[14] + algebraic_variables[39] = constants[76]*states[20]*states[19]*(algebraic_variables[8]-computed_constants[1]) + algebraic_variables[40] = constants[90]*constants[89]*(algebraic_variables[8]-computed_constants[1])*(1.0+exp((algebraic_variables[8]+20.0)/20.0))*states[32] if gt_func(constants[0], 0.0) else 0.0 + algebraic_variables[37] = 2.0*constants[84]*algebraic_variables[8]/(computed_constants[0]*(1.0-exp(-1.0*algebraic_variables[8]*2.0/computed_constants[0])))*(states[0]-constants[5]*exp(-2.0*algebraic_variables[8]/computed_constants[0]))*states[25]*states[24] + algebraic_variables[5] = 0.0000185*constants[77]*(algebraic_variables[8]-0.0)/(computed_constants[0]*(1.0-exp(-1.0*(algebraic_variables[8]-0.0)/computed_constants[0])))*(algebraic_variables[0]-constants[2]*exp(-1.0*(algebraic_variables[8]-0.0)/computed_constants[0]))*states[23]*states[22]*states[21] + algebraic_variables[67] = 0.000365*constants[77]*(algebraic_variables[8]-0.0)/(computed_constants[0]*(1.0-exp(-1.0*(algebraic_variables[8]-0.0)/computed_constants[0])))*(constants[3]-constants[4]*exp(-1.0*(algebraic_variables[8]-0.0)/computed_constants[0]))*states[23]*states[22]*states[21] + algebraic_variables[38] = 2.0*constants[77]*(algebraic_variables[8]-0.0)/(computed_constants[0]*(1.0-exp(-1.0*(algebraic_variables[8]-0.0)*2.0/computed_constants[0])))*(states[0]-constants[5]*exp(-2.0*(algebraic_variables[8]-0.0)/computed_constants[0]))*states[23]*states[22]*states[21] + algebraic_variables[41] = (algebraic_variables[38]+algebraic_variables[67]+algebraic_variables[5])*(1.0-computed_constants[19])*1.0*computed_constants[18] + algebraic_variables[51] = computed_constants[0]*log((constants[2]+0.12*constants[4])/(algebraic_variables[0]+0.12*constants[3])) + algebraic_variables[53] = constants[74]*pow(states[18], 3.0)*(algebraic_variables[8]-algebraic_variables[51]) + algebraic_variables[52] = constants[73]*pow(states[18], 3.0)*states[17]*(algebraic_variables[8]-algebraic_variables[51]) + algebraic_variables[7] = algebraic_variables[52]+algebraic_variables[53] + algebraic_variables[42] = constants[86]*(algebraic_variables[8]-computed_constants[1])*states[27]*states[26] + algebraic_variables[93] = computed_constants[0]*log((constants[4]+0.12*constants[2])/(constants[3]+0.12*algebraic_variables[0])) + algebraic_variables[43] = computed_constants[22]*(algebraic_variables[8]-algebraic_variables[93])*pow(states[31], 2.0) + algebraic_variables[44] = constants[87]*(algebraic_variables[8]-computed_constants[1])*(0.9*states[30]+0.1*states[29])*states[28] + algebraic_variables[48] = states[16]*computed_constants[15]*(algebraic_variables[8]-computed_constants[1])*(1.0-constants[71]) + algebraic_variables[6] = states[16]*computed_constants[14]*(algebraic_variables[8]-algebraic_variables[1])*(1.0-constants[71]) + algebraic_variables[45] = algebraic_variables[6]+algebraic_variables[48] + algebraic_variables[46] = algebraic_variables[45]+algebraic_variables[44]+algebraic_variables[43]+algebraic_variables[42]+algebraic_variables[4]+algebraic_variables[3]+algebraic_variables[7]+algebraic_variables[41]+algebraic_variables[37]+algebraic_variables[40]+algebraic_variables[39] + algebraic_variables[49] = 1.0/(0.36*(algebraic_variables[8]+148.8-computed_constants[16]-computed_constants[17])/(exp(0.066*(algebraic_variables[8]+148.8-computed_constants[16]-computed_constants[17]))-1.0)+0.1*(algebraic_variables[8]+87.3-computed_constants[16]-computed_constants[17])/(1.0-exp(-0.2*(algebraic_variables[8]+87.3-computed_constants[16]-computed_constants[17]))))-0.054 + algebraic_variables[50] = 0.01329+0.99921/(1.0+exp((algebraic_variables[8]+97.134-computed_constants[16]-computed_constants[17]-constants[72])/8.1752)) if lt_func(algebraic_variables[8], -(80.0-computed_constants[16]-computed_constants[17]-constants[72])) else 0.0002501*exp(-(algebraic_variables[8]-computed_constants[16]-computed_constants[17]-constants[72])/12.861) + algebraic_variables[54] = 1.0/(1.0+exp(-(algebraic_variables[8]+42.0504)/8.3106)) + algebraic_variables[55] = algebraic_variables[8]+41.0 + algebraic_variables[56] = 2000.0 if lt_func(fabs(algebraic_variables[55]), constants[75]) else 200.0*algebraic_variables[55]/(1.0-exp(-0.1*algebraic_variables[55])) + algebraic_variables[57] = 8000.0*exp(-0.056*(algebraic_variables[8]+66.0)) + algebraic_variables[58] = 1.0/(algebraic_variables[56]+algebraic_variables[57]) + algebraic_variables[59] = 1.0/(1.0+exp((algebraic_variables[8]+69.804)/4.4565)) + algebraic_variables[60] = 20.0*exp(-0.125*(algebraic_variables[8]+75.0)) + algebraic_variables[61] = 2000.0/(320.0*exp(-0.1*(algebraic_variables[8]+75.0))+1.0) + algebraic_variables[62] = 1.0/(algebraic_variables[60]+algebraic_variables[61]) + algebraic_variables[64] = 1.0/(1.0+exp((algebraic_variables[8]+6.0)/-8.6)) + algebraic_variables[63] = 0.009/(1.0+exp((algebraic_variables[8]+5.0)/12.0))+0.0005 + algebraic_variables[66] = 1.0/(1.0+exp((algebraic_variables[8]+7.5)/10.0)) + algebraic_variables[65] = 0.59/(1.0+exp((algebraic_variables[8]+60.0)/10.0))+3.05 + algebraic_variables[68] = 1.0/(1.0+exp(-(algebraic_variables[8]-constants[79]-computed_constants[20])/(constants[78]*(1.0+computed_constants[21]/100.0)))) + algebraic_variables[73] = -1.80001 if eq_func(algebraic_variables[8], -1.8) else algebraic_variables[8] + algebraic_variables[69] = 0.01143*(algebraic_variables[73]+1.8)/(exp((algebraic_variables[73]+1.8)/2.5)-1.0) + algebraic_variables[72] = -41.80001 if eq_func(algebraic_variables[8], -41.8) else 0.0 if eq_func(algebraic_variables[8], 0.0) else -6.80001 if eq_func(algebraic_variables[8], -6.8) else algebraic_variables[8] + algebraic_variables[70] = -0.02839*(algebraic_variables[72]+41.8)/(exp(-(algebraic_variables[72]+41.8)/2.5)-1.0)-0.0849*(algebraic_variables[72]+6.8)/(exp(-(algebraic_variables[72]+6.8)/4.8)-1.0) + algebraic_variables[71] = 0.001/(algebraic_variables[70]+algebraic_variables[69]) + algebraic_variables[74] = 1.0/(1.0+exp((algebraic_variables[8]+37.4+constants[81])/(5.3+constants[80]))) + algebraic_variables[75] = 0.001*(44.3+230.0*exp(-pow((algebraic_variables[8]+36.0)/10.0, 2.0))) + algebraic_variables[76] = constants[82]/(constants[82]+states[0]) + algebraic_variables[77] = 0.001*algebraic_variables[76]/constants[83] + algebraic_variables[78] = 1.0/(1.0+exp(-(algebraic_variables[8]+38.3)/5.5)) + algebraic_variables[79] = 0.001/(1.068*exp((algebraic_variables[8]+38.3)/30.0)+1.068*exp(-(algebraic_variables[8]+38.3)/30.0)) + algebraic_variables[80] = 1.0/(1.0+exp((algebraic_variables[8]+58.7)/3.8)) + algebraic_variables[81] = 1.0/(16.67*exp(-(algebraic_variables[8]+75.0)/83.3)+16.67*exp((algebraic_variables[8]+75.0)/15.38))+constants[85] + algebraic_variables[82] = 1.0/(1.0+exp((algebraic_variables[8]+49.0)/13.0)) + algebraic_variables[83] = 0.001*0.6*(65.17/(0.57*exp(-0.08*(algebraic_variables[8]+44.0))+0.065*exp(0.1*(algebraic_variables[8]+45.93)))+10.1) + algebraic_variables[84] = 1.0/(1.0+exp(-(algebraic_variables[8]-19.3)/15.0)) + algebraic_variables[85] = 0.001*0.66*1.4*(15.59/(1.037*exp(0.09*(algebraic_variables[8]+30.61))+0.369*exp(-0.12*(algebraic_variables[8]+23.84)))+2.98) + algebraic_variables[86] = 1.0/(1.0+exp(-(algebraic_variables[8]+23.2)/6.6))/(0.84655354/(37.2*exp(algebraic_variables[8]/11.9)+0.96*exp(-algebraic_variables[8]/18.5))) + algebraic_variables[87] = 4.0*((37.2*exp(algebraic_variables[8]/15.9)+0.96*exp(-algebraic_variables[8]/22.5))/0.84655354-1.0/(1.0+exp(-(algebraic_variables[8]+23.2)/10.6))/(0.84655354/(37.2*exp(algebraic_variables[8]/15.9)+0.96*exp(-algebraic_variables[8]/22.5)))) + algebraic_variables[88] = 1.0/(1.0+exp(-(algebraic_variables[8]+10.0144)/7.6607)) + algebraic_variables[89] = 0.84655354/(4.2*exp(algebraic_variables[8]/17.0)+0.15*exp(-algebraic_variables[8]/21.6)) + algebraic_variables[90] = 1.0/(30.0*exp(algebraic_variables[8]/10.0)+exp(-algebraic_variables[8]/12.0)) + algebraic_variables[91] = 1.0/(100.0*exp(-algebraic_variables[8]/54.645)+656.0*exp(algebraic_variables[8]/106.157)) + algebraic_variables[92] = 1.0/(1.0+exp((algebraic_variables[8]+28.6)/17.1)) + algebraic_variables[94] = sqrt(1.0/(1.0+exp(-(algebraic_variables[8]+0.6383-computed_constants[23])/10.7071))) + algebraic_variables[95] = 1.0*exp(-(algebraic_variables[8]-computed_constants[23]-5.0)/25.0) + algebraic_variables[96] = 28.0/(1.0+exp(-(algebraic_variables[8]-40.0-computed_constants[23])/3.0)) + algebraic_variables[97] = 1.0/(algebraic_variables[96]+algebraic_variables[95]) + algebraic_variables[98] = 10.0*exp(0.0133*(algebraic_variables[8]+40.0)) + algebraic_variables[99] = computed_constants[24]/(computed_constants[24]+algebraic_variables[98]) + algebraic_variables[100] = 1.0/(computed_constants[24]+algebraic_variables[98]) diff --git a/tests/resources/generator/garny_kohl_hunter_boyett_noble_rabbit_san_model_2003/model.c b/tests/resources/generator/garny_kohl_hunter_boyett_noble_rabbit_san_model_2003/model.c index d3dd33e91..649e17eb0 100644 --- a/tests/resources/generator/garny_kohl_hunter_boyett_noble_rabbit_san_model_2003/model.c +++ b/tests/resources/generator/garny_kohl_hunter_boyett_noble_rabbit_san_model_2003/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 15; @@ -405,7 +405,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * constants[109] = 0.006875; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { computedConstants[0] = (constants[1] == 0.0)?1.07*(3.0*constants[0]-0.1)/(3.0*(1.0+0.7745*exp(-(3.0*constants[0]-2.05)/0.295))):(constants[1] == 1.0)?constants[2]*constants[0]/(1.0+0.7745*exp(-(3.0*constants[0]-2.05)/0.295)):1.07*29.0*constants[0]/(30.0*(1.0+0.7745*exp(-(29.0*constants[0]-24.5)/1.95))); computedConstants[1] = constants[3]+computedConstants[0]*(constants[4]-constants[3]); diff --git a/tests/resources/generator/garny_kohl_hunter_boyett_noble_rabbit_san_model_2003/model.h b/tests/resources/generator/garny_kohl_hunter_boyett_noble_rabbit_san_model_2003/model.h index 115dc5443..b6c0adce3 100644 --- a/tests/resources/generator/garny_kohl_hunter_boyett_noble_rabbit_san_model_2003/model.h +++ b/tests/resources/generator/garny_kohl_hunter_boyett_noble_rabbit_san_model_2003/model.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/garny_kohl_hunter_boyett_noble_rabbit_san_model_2003/model.py b/tests/resources/generator/garny_kohl_hunter_boyett_noble_rabbit_san_model_2003/model.py index b7702ec72..ecc05d51b 100644 --- a/tests/resources/generator/garny_kohl_hunter_boyett_noble_rabbit_san_model_2003/model.py +++ b/tests/resources/generator/garny_kohl_hunter_boyett_noble_rabbit_san_model_2003/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 15 @@ -379,7 +379,7 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[109] = 0.006875 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): computed_constants[0] = 1.07*(3.0*constants[0]-0.1)/(3.0*(1.0+0.7745*exp(-(3.0*constants[0]-2.05)/0.295))) if eq_func(constants[1], 0.0) else constants[2]*constants[0]/(1.0+0.7745*exp(-(3.0*constants[0]-2.05)/0.295)) if eq_func(constants[1], 1.0) else 1.07*29.0*constants[0]/(30.0*(1.0+0.7745*exp(-(29.0*constants[0]-24.5)/1.95))) computed_constants[1] = constants[3]+computed_constants[0]*(constants[4]-constants[3]) computed_constants[3] = constants[8]+computed_constants[0]*(constants[9]-constants[8]) if eq_func(constants[1], 0.0) else constants[12]+computed_constants[0]*(constants[13]-constants[12]) if eq_func(constants[1], 1.0) else constants[10]+computed_constants[0]*(constants[11]-constants[10]) @@ -406,125 +406,125 @@ def compute_computed_constants(states, rates, constants, computed_constants, alg def compute_rates(voi, states, rates, constants, computed_constants, algebraic_variables): - algebraicVariables[0] = computed_constants[10]*pow(constants[32]/(constants[46]+constants[32]), 3.0)*pow(constants[44]/(constants[45]+constants[44]), 2.0)*1.6/(1.5+exp(-(states[0]+60.0)/40.0)) - algebraicVariables[1] = computed_constants[9]*(pow(constants[32], 3.0)*constants[33]*exp(0.03743*states[0]*constants[37])-pow(constants[34], 3.0)*constants[35]*exp(0.0374*states[0]*(constants[37]-1.0)))/(1.0+constants[36]*(constants[35]*pow(constants[34], 3.0)+constants[33]*pow(constants[32], 3.0))) if eq_func(constants[1], 0.0) else computed_constants[9]*(pow(constants[32], 3.0)*constants[33]*exp(0.03743*states[0]*constants[37])-pow(constants[34], 3.0)*constants[35]*exp(0.03743*states[0]*(constants[37]-1.0)))/(1.0+constants[36]*(constants[35]*pow(constants[34], 3.0)+constants[33]*pow(constants[32], 3.0))) - algebraicVariables[5] = computed_constants[22]*states[14]*(states[0]-computed_constants[6]) if neq_func(constants[1], 2.0) else computed_constants[22]*states[14]*(states[0]+102.0) - algebraicVariables[6] = computed_constants[21]*states[14]*(states[0]-computed_constants[4]) if neq_func(constants[1], 2.0) else computed_constants[21]*states[14]*(states[0]-77.6) - algebraicVariables[7] = computed_constants[20]*pow(states[13], 2.0)*(states[0]-computed_constants[12]) - algebraicVariables[9] = computed_constants[17]*states[8]*(states[0]-computed_constants[6]) - algebraicVariables[10] = computed_constants[16]*states[9]*states[8]*(states[0]-computed_constants[6]) - algebraicVariables[11] = computed_constants[15]*states[7]*states[6]*(states[0]-constants[73]) - algebraicVariables[12] = computed_constants[14]*(states[5]*states[4]+0.006/(1.0+exp(-(states[0]+14.1)/6.0)))*(states[0]-constants[66]) - algebraicVariables[2] = computed_constants[5]*(states[0]-computed_constants[6]) - algebraicVariables[3] = computed_constants[7]*(states[0]-computed_constants[8]) - algebraicVariables[4] = computed_constants[3]*(states[0]-computed_constants[4]) - algebraicVariables[42] = 0.6*states[12]+0.4*states[11] - algebraicVariables[8] = computed_constants[18]*algebraicVariables[42]*states[10]*(states[0]-computed_constants[6]) - algebraicVariables[17] = 0.0952*exp(-0.063*(states[0]+34.4))/(1.0+1.66*exp(-0.225*(states[0]+63.7)))+0.0869 if eq_func(constants[1], 0.0) else 0.09518*exp(-0.06306*(states[0]+34.4))/(1.0+1.662*exp(-0.2251*(states[0]+63.7)))+0.08693 - algebraicVariables[14] = (1.0-algebraicVariables[17])*states[3]+algebraicVariables[17]*states[2] - algebraicVariables[13] = computed_constants[13]*pow(states[1], 3.0)*algebraicVariables[14]*constants[34]*pow(constants[7], 2.0)/(constants[5]*constants[6])*(exp((states[0]-computed_constants[4])*constants[7]/(constants[5]*constants[6]))-1.0)/(exp(states[0]*constants[7]/(constants[5]*constants[6]))-1.0)*states[0] - rates[0] = -1.0/computed_constants[1]*(algebraicVariables[13]+algebraicVariables[12]+algebraicVariables[11]+algebraicVariables[10]+algebraicVariables[9]+algebraicVariables[8]+algebraicVariables[7]+algebraicVariables[6]+algebraicVariables[5]+algebraicVariables[4]+algebraicVariables[3]+algebraicVariables[2]+algebraicVariables[1]+algebraicVariables[0]+computed_constants[2]) - algebraicVariables[15] = 0.0006247/(0.832*exp(-0.335*(states[0]+56.7))+0.627*exp(0.082*(states[0]+65.01)))+4.0e-5 if eq_func(constants[1], 0.0) else 0.0006247/(0.8322166*exp(-0.33566*(states[0]+56.7062))+0.6274*exp(0.0823*(states[0]+65.0131)))+4.569e-5 - algebraicVariables[16] = pow(1.0/(1.0+exp(-states[0]/5.46)), 1.0/3.0) if eq_func(constants[1], 0.0) else pow(1.0/(1.0+exp(-(states[0]+30.32)/5.46)), 1.0/3.0) - rates[1] = (algebraicVariables[16]-states[1])/algebraicVariables[15] - algebraicVariables[18] = 3.717e-6*exp(-0.2815*(states[0]+17.11))/(1.0+0.003732*exp(-0.3426*(states[0]+37.76)))+0.0005977 - algebraicVariables[19] = 1.0/(1.0+exp((states[0]+66.1)/6.4)) - rates[3] = (algebraicVariables[19]-states[3])/algebraicVariables[18] - algebraicVariables[20] = 3.186e-8*exp(-0.6219*(states[0]+18.8))/(1.0+7.189e-5*exp(-0.6683*(states[0]+34.07)))+0.003556 - algebraicVariables[21] = algebraicVariables[19] - rates[2] = (algebraicVariables[21]-states[2])/algebraicVariables[20] - algebraicVariables[25] = 11.43*(states[0]-5.0)/(exp(0.4*(states[0]-5.0))-1.0) if eq_func(constants[1], 1.0) else 11.42*(states[0]-5.0)/(exp(0.4*(states[0]-5.0))-1.0) - algebraicVariables[24] = -28.38*(states[0]+35.0)/(exp(-(states[0]+35.0)/2.5)-1.0)-84.9*states[0]/(exp(-0.208*states[0])-1.0) if eq_func(constants[1], 0.0) else -28.39*(states[0]+35.0)/(exp(-(states[0]+35.0)/2.5)-1.0)-84.9*states[0]/(exp(-0.208*states[0])-1.0) if eq_func(constants[1], 1.0) else -28.4*(states[0]+35.0)/(exp(-(states[0]+35.0)/2.5)-1.0)-84.9*states[0]/(exp(-0.208*states[0])-1.0) - algebraicVariables[22] = 2.0/(algebraicVariables[24]+algebraicVariables[25]) - algebraicVariables[23] = 1.0/(1.0+exp(-(states[0]+23.1)/6.0)) if eq_func(constants[1], 0.0) else 1.0/(1.0+exp(-(states[0]+22.3+0.8*computed_constants[0])/6.0)) if eq_func(constants[1], 1.0) else 1.0/(1.0+exp(-(states[0]+22.2)/6.0)) - rates[4] = (algebraicVariables[23]-states[4])/algebraicVariables[22] - algebraicVariables[29] = 30.0/(1.0+exp(-(states[0]+28.0)/4.0)) if eq_func(constants[1], 1.0) else 25.0/(1.0+exp(-(states[0]+28.0)/4.0)) - algebraicVariables[28] = 3.75*(states[0]+28.0)/(exp((states[0]+28.0)/4.0)-1.0) if eq_func(constants[1], 1.0) else 3.12*(states[0]+28.0)/(exp((states[0]+28.0)/4.0)-1.0) - algebraicVariables[26] = (1.2-0.2*computed_constants[0])/(algebraicVariables[28]+algebraicVariables[29]) if eq_func(constants[1], 1.0) else 1.0/(algebraicVariables[28]+algebraicVariables[29]) - algebraicVariables[27] = 1.0/(1.0+exp((states[0]+45.0)/5.0)) - rates[5] = (algebraicVariables[27]-states[5])/algebraicVariables[26] - algebraicVariables[33] = 1068.0*exp(-(states[0]+26.3)/30.0) - algebraicVariables[32] = 1068.0*exp((states[0]+26.3)/30.0) - algebraicVariables[30] = 1.0/(algebraicVariables[32]+algebraicVariables[33]) - algebraicVariables[31] = 1.0/(1.0+exp(-(states[0]+37.0)/6.8)) - rates[7] = (algebraicVariables[31]-states[7])/algebraicVariables[30] - algebraicVariables[37] = 15.0*exp((states[0]+71.0)/15.38) if eq_func(constants[1], 1.0) else 15.0*exp((states[0]+71.7)/15.38) - algebraicVariables[36] = 15.3*exp(-(states[0]+71.0+0.7*computed_constants[0])/83.3) if eq_func(constants[1], 1.0) else 15.3*exp(-(states[0]+71.7)/83.3) - algebraicVariables[34] = 1.0/(algebraicVariables[36]+algebraicVariables[37]) - algebraicVariables[35] = 1.0/(1.0+exp((states[0]+71.0)/9.0)) - rates[6] = (algebraicVariables[35]-states[6])/algebraicVariables[34] - algebraicVariables[38] = 0.0101+0.06517/(0.57*exp(-0.08*(states[0]+49.0)))+2.4e-5*exp(0.1*(states[0]+50.93)) if eq_func(constants[1], 0.0) else 0.001/3.0*(30.31+195.5/(0.5686*exp(-0.08161*(states[0]+39.0+10.0*computed_constants[0]))+0.7174*exp((0.2719-0.1719*computed_constants[0])*1.0*(states[0]+40.93+10.0*computed_constants[0])))) if eq_func(constants[1], 1.0) else 0.0101+0.06517/(0.5686*exp(-0.08161*(states[0]+39.0))+0.7174*exp(0.2719*(states[0]+40.93))) - algebraicVariables[39] = 1.0/(1.0+exp((states[0]+59.37)/13.1)) - rates[9] = (algebraicVariables[39]-states[9])/algebraicVariables[38] - algebraicVariables[40] = 0.001*(2.98+15.59/(1.037*exp(0.09*(states[0]+30.61))+0.369*exp(-0.12*(states[0]+23.84)))) if eq_func(constants[1], 0.0) else 0.0025*(1.191+7.838/(1.037*exp(0.09012*(states[0]+30.61))+0.369*exp(-0.119*(states[0]+23.84)))) if eq_func(constants[1], 1.0) else 0.001*(2.98+19.59/(1.037*exp(0.09012*(states[0]+30.61))+0.369*exp(-0.119*(states[0]+23.84)))) - algebraicVariables[41] = 1.0/(1.0+exp(-(states[0]-10.93)/19.7)) - rates[8] = (algebraicVariables[41]-states[8])/algebraicVariables[40] - algebraicVariables[43] = 1.0/(37.2*exp((states[0]-9.0)/15.9)+0.96*exp(-(states[0]-9.0)/22.5)) if neq_func(constants[1], 2.0) else 1.0/(37.2*exp((states[0]-10.0)/15.9)+0.96*exp(-(states[0]-10.0)/22.5)) - algebraicVariables[44] = 1.0/(1.0+exp(-(states[0]+14.2)/10.6)) if neq_func(constants[1], 2.0) else 1.0/(1.0+exp(-(states[0]+13.2)/10.6)) - rates[12] = (algebraicVariables[44]-states[12])/algebraicVariables[43] - algebraicVariables[45] = 1.0/(4.2*exp((states[0]-9.0)/17.0)+0.15*exp(-(states[0]-9.0)/21.6)) if neq_func(constants[1], 2.0) else 1.0/(4.2*exp((states[0]-10.0)/17.0)+0.15*exp(-(states[0]-10.0)/21.6)) - algebraicVariables[46] = algebraicVariables[44] - rates[11] = (algebraicVariables[46]-states[11])/algebraicVariables[45] - algebraicVariables[47] = 1.0/(1.0+exp((states[0]+18.6)/10.1)) - rates[10] = (algebraicVariables[47]-states[10])/computed_constants[19] - algebraicVariables[48] = 1.0*exp(-states[0]/45.0) - algebraicVariables[49] = 14.0/(1.0+exp(-(states[0]-40.0)/9.0)) - rates[13] = algebraicVariables[49]*(1.0-states[13])-algebraicVariables[48]*states[13] - algebraicVariables[50] = 1.0*exp((states[0]+75.13)/21.25) - algebraicVariables[51] = 1.0*exp(-(states[0]+78.91)/26.62) if eq_func(constants[1], 0.0) else 1.0*exp(-(states[0]+78.91)/26.63) - rates[14] = algebraicVariables[51]*(1.0-states[14])-algebraicVariables[50]*states[14] + algebraic_variables[0] = computed_constants[10]*pow(constants[32]/(constants[46]+constants[32]), 3.0)*pow(constants[44]/(constants[45]+constants[44]), 2.0)*1.6/(1.5+exp(-(states[0]+60.0)/40.0)) + algebraic_variables[1] = computed_constants[9]*(pow(constants[32], 3.0)*constants[33]*exp(0.03743*states[0]*constants[37])-pow(constants[34], 3.0)*constants[35]*exp(0.0374*states[0]*(constants[37]-1.0)))/(1.0+constants[36]*(constants[35]*pow(constants[34], 3.0)+constants[33]*pow(constants[32], 3.0))) if eq_func(constants[1], 0.0) else computed_constants[9]*(pow(constants[32], 3.0)*constants[33]*exp(0.03743*states[0]*constants[37])-pow(constants[34], 3.0)*constants[35]*exp(0.03743*states[0]*(constants[37]-1.0)))/(1.0+constants[36]*(constants[35]*pow(constants[34], 3.0)+constants[33]*pow(constants[32], 3.0))) + algebraic_variables[5] = computed_constants[22]*states[14]*(states[0]-computed_constants[6]) if neq_func(constants[1], 2.0) else computed_constants[22]*states[14]*(states[0]+102.0) + algebraic_variables[6] = computed_constants[21]*states[14]*(states[0]-computed_constants[4]) if neq_func(constants[1], 2.0) else computed_constants[21]*states[14]*(states[0]-77.6) + algebraic_variables[7] = computed_constants[20]*pow(states[13], 2.0)*(states[0]-computed_constants[12]) + algebraic_variables[9] = computed_constants[17]*states[8]*(states[0]-computed_constants[6]) + algebraic_variables[10] = computed_constants[16]*states[9]*states[8]*(states[0]-computed_constants[6]) + algebraic_variables[11] = computed_constants[15]*states[7]*states[6]*(states[0]-constants[73]) + algebraic_variables[12] = computed_constants[14]*(states[5]*states[4]+0.006/(1.0+exp(-(states[0]+14.1)/6.0)))*(states[0]-constants[66]) + algebraic_variables[2] = computed_constants[5]*(states[0]-computed_constants[6]) + algebraic_variables[3] = computed_constants[7]*(states[0]-computed_constants[8]) + algebraic_variables[4] = computed_constants[3]*(states[0]-computed_constants[4]) + algebraic_variables[42] = 0.6*states[12]+0.4*states[11] + algebraic_variables[8] = computed_constants[18]*algebraic_variables[42]*states[10]*(states[0]-computed_constants[6]) + algebraic_variables[17] = 0.0952*exp(-0.063*(states[0]+34.4))/(1.0+1.66*exp(-0.225*(states[0]+63.7)))+0.0869 if eq_func(constants[1], 0.0) else 0.09518*exp(-0.06306*(states[0]+34.4))/(1.0+1.662*exp(-0.2251*(states[0]+63.7)))+0.08693 + algebraic_variables[14] = (1.0-algebraic_variables[17])*states[3]+algebraic_variables[17]*states[2] + algebraic_variables[13] = computed_constants[13]*pow(states[1], 3.0)*algebraic_variables[14]*constants[34]*pow(constants[7], 2.0)/(constants[5]*constants[6])*(exp((states[0]-computed_constants[4])*constants[7]/(constants[5]*constants[6]))-1.0)/(exp(states[0]*constants[7]/(constants[5]*constants[6]))-1.0)*states[0] + rates[0] = -1.0/computed_constants[1]*(algebraic_variables[13]+algebraic_variables[12]+algebraic_variables[11]+algebraic_variables[10]+algebraic_variables[9]+algebraic_variables[8]+algebraic_variables[7]+algebraic_variables[6]+algebraic_variables[5]+algebraic_variables[4]+algebraic_variables[3]+algebraic_variables[2]+algebraic_variables[1]+algebraic_variables[0]+computed_constants[2]) + algebraic_variables[15] = 0.0006247/(0.832*exp(-0.335*(states[0]+56.7))+0.627*exp(0.082*(states[0]+65.01)))+4.0e-5 if eq_func(constants[1], 0.0) else 0.0006247/(0.8322166*exp(-0.33566*(states[0]+56.7062))+0.6274*exp(0.0823*(states[0]+65.0131)))+4.569e-5 + algebraic_variables[16] = pow(1.0/(1.0+exp(-states[0]/5.46)), 1.0/3.0) if eq_func(constants[1], 0.0) else pow(1.0/(1.0+exp(-(states[0]+30.32)/5.46)), 1.0/3.0) + rates[1] = (algebraic_variables[16]-states[1])/algebraic_variables[15] + algebraic_variables[18] = 3.717e-6*exp(-0.2815*(states[0]+17.11))/(1.0+0.003732*exp(-0.3426*(states[0]+37.76)))+0.0005977 + algebraic_variables[19] = 1.0/(1.0+exp((states[0]+66.1)/6.4)) + rates[3] = (algebraic_variables[19]-states[3])/algebraic_variables[18] + algebraic_variables[20] = 3.186e-8*exp(-0.6219*(states[0]+18.8))/(1.0+7.189e-5*exp(-0.6683*(states[0]+34.07)))+0.003556 + algebraic_variables[21] = algebraic_variables[19] + rates[2] = (algebraic_variables[21]-states[2])/algebraic_variables[20] + algebraic_variables[25] = 11.43*(states[0]-5.0)/(exp(0.4*(states[0]-5.0))-1.0) if eq_func(constants[1], 1.0) else 11.42*(states[0]-5.0)/(exp(0.4*(states[0]-5.0))-1.0) + algebraic_variables[24] = -28.38*(states[0]+35.0)/(exp(-(states[0]+35.0)/2.5)-1.0)-84.9*states[0]/(exp(-0.208*states[0])-1.0) if eq_func(constants[1], 0.0) else -28.39*(states[0]+35.0)/(exp(-(states[0]+35.0)/2.5)-1.0)-84.9*states[0]/(exp(-0.208*states[0])-1.0) if eq_func(constants[1], 1.0) else -28.4*(states[0]+35.0)/(exp(-(states[0]+35.0)/2.5)-1.0)-84.9*states[0]/(exp(-0.208*states[0])-1.0) + algebraic_variables[22] = 2.0/(algebraic_variables[24]+algebraic_variables[25]) + algebraic_variables[23] = 1.0/(1.0+exp(-(states[0]+23.1)/6.0)) if eq_func(constants[1], 0.0) else 1.0/(1.0+exp(-(states[0]+22.3+0.8*computed_constants[0])/6.0)) if eq_func(constants[1], 1.0) else 1.0/(1.0+exp(-(states[0]+22.2)/6.0)) + rates[4] = (algebraic_variables[23]-states[4])/algebraic_variables[22] + algebraic_variables[29] = 30.0/(1.0+exp(-(states[0]+28.0)/4.0)) if eq_func(constants[1], 1.0) else 25.0/(1.0+exp(-(states[0]+28.0)/4.0)) + algebraic_variables[28] = 3.75*(states[0]+28.0)/(exp((states[0]+28.0)/4.0)-1.0) if eq_func(constants[1], 1.0) else 3.12*(states[0]+28.0)/(exp((states[0]+28.0)/4.0)-1.0) + algebraic_variables[26] = (1.2-0.2*computed_constants[0])/(algebraic_variables[28]+algebraic_variables[29]) if eq_func(constants[1], 1.0) else 1.0/(algebraic_variables[28]+algebraic_variables[29]) + algebraic_variables[27] = 1.0/(1.0+exp((states[0]+45.0)/5.0)) + rates[5] = (algebraic_variables[27]-states[5])/algebraic_variables[26] + algebraic_variables[33] = 1068.0*exp(-(states[0]+26.3)/30.0) + algebraic_variables[32] = 1068.0*exp((states[0]+26.3)/30.0) + algebraic_variables[30] = 1.0/(algebraic_variables[32]+algebraic_variables[33]) + algebraic_variables[31] = 1.0/(1.0+exp(-(states[0]+37.0)/6.8)) + rates[7] = (algebraic_variables[31]-states[7])/algebraic_variables[30] + algebraic_variables[37] = 15.0*exp((states[0]+71.0)/15.38) if eq_func(constants[1], 1.0) else 15.0*exp((states[0]+71.7)/15.38) + algebraic_variables[36] = 15.3*exp(-(states[0]+71.0+0.7*computed_constants[0])/83.3) if eq_func(constants[1], 1.0) else 15.3*exp(-(states[0]+71.7)/83.3) + algebraic_variables[34] = 1.0/(algebraic_variables[36]+algebraic_variables[37]) + algebraic_variables[35] = 1.0/(1.0+exp((states[0]+71.0)/9.0)) + rates[6] = (algebraic_variables[35]-states[6])/algebraic_variables[34] + algebraic_variables[38] = 0.0101+0.06517/(0.57*exp(-0.08*(states[0]+49.0)))+2.4e-5*exp(0.1*(states[0]+50.93)) if eq_func(constants[1], 0.0) else 0.001/3.0*(30.31+195.5/(0.5686*exp(-0.08161*(states[0]+39.0+10.0*computed_constants[0]))+0.7174*exp((0.2719-0.1719*computed_constants[0])*1.0*(states[0]+40.93+10.0*computed_constants[0])))) if eq_func(constants[1], 1.0) else 0.0101+0.06517/(0.5686*exp(-0.08161*(states[0]+39.0))+0.7174*exp(0.2719*(states[0]+40.93))) + algebraic_variables[39] = 1.0/(1.0+exp((states[0]+59.37)/13.1)) + rates[9] = (algebraic_variables[39]-states[9])/algebraic_variables[38] + algebraic_variables[40] = 0.001*(2.98+15.59/(1.037*exp(0.09*(states[0]+30.61))+0.369*exp(-0.12*(states[0]+23.84)))) if eq_func(constants[1], 0.0) else 0.0025*(1.191+7.838/(1.037*exp(0.09012*(states[0]+30.61))+0.369*exp(-0.119*(states[0]+23.84)))) if eq_func(constants[1], 1.0) else 0.001*(2.98+19.59/(1.037*exp(0.09012*(states[0]+30.61))+0.369*exp(-0.119*(states[0]+23.84)))) + algebraic_variables[41] = 1.0/(1.0+exp(-(states[0]-10.93)/19.7)) + rates[8] = (algebraic_variables[41]-states[8])/algebraic_variables[40] + algebraic_variables[43] = 1.0/(37.2*exp((states[0]-9.0)/15.9)+0.96*exp(-(states[0]-9.0)/22.5)) if neq_func(constants[1], 2.0) else 1.0/(37.2*exp((states[0]-10.0)/15.9)+0.96*exp(-(states[0]-10.0)/22.5)) + algebraic_variables[44] = 1.0/(1.0+exp(-(states[0]+14.2)/10.6)) if neq_func(constants[1], 2.0) else 1.0/(1.0+exp(-(states[0]+13.2)/10.6)) + rates[12] = (algebraic_variables[44]-states[12])/algebraic_variables[43] + algebraic_variables[45] = 1.0/(4.2*exp((states[0]-9.0)/17.0)+0.15*exp(-(states[0]-9.0)/21.6)) if neq_func(constants[1], 2.0) else 1.0/(4.2*exp((states[0]-10.0)/17.0)+0.15*exp(-(states[0]-10.0)/21.6)) + algebraic_variables[46] = algebraic_variables[44] + rates[11] = (algebraic_variables[46]-states[11])/algebraic_variables[45] + algebraic_variables[47] = 1.0/(1.0+exp((states[0]+18.6)/10.1)) + rates[10] = (algebraic_variables[47]-states[10])/computed_constants[19] + algebraic_variables[48] = 1.0*exp(-states[0]/45.0) + algebraic_variables[49] = 14.0/(1.0+exp(-(states[0]-40.0)/9.0)) + rates[13] = algebraic_variables[49]*(1.0-states[13])-algebraic_variables[48]*states[13] + algebraic_variables[50] = 1.0*exp((states[0]+75.13)/21.25) + algebraic_variables[51] = 1.0*exp(-(states[0]+78.91)/26.62) if eq_func(constants[1], 0.0) else 1.0*exp(-(states[0]+78.91)/26.63) + rates[14] = algebraic_variables[51]*(1.0-states[14])-algebraic_variables[50]*states[14] def compute_variables(voi, states, rates, constants, computed_constants, algebraic_variables): - algebraicVariables[4] = computed_constants[3]*(states[0]-computed_constants[4]) - algebraicVariables[2] = computed_constants[5]*(states[0]-computed_constants[6]) - algebraicVariables[3] = computed_constants[7]*(states[0]-computed_constants[8]) - algebraicVariables[1] = computed_constants[9]*(pow(constants[32], 3.0)*constants[33]*exp(0.03743*states[0]*constants[37])-pow(constants[34], 3.0)*constants[35]*exp(0.0374*states[0]*(constants[37]-1.0)))/(1.0+constants[36]*(constants[35]*pow(constants[34], 3.0)+constants[33]*pow(constants[32], 3.0))) if eq_func(constants[1], 0.0) else computed_constants[9]*(pow(constants[32], 3.0)*constants[33]*exp(0.03743*states[0]*constants[37])-pow(constants[34], 3.0)*constants[35]*exp(0.03743*states[0]*(constants[37]-1.0)))/(1.0+constants[36]*(constants[35]*pow(constants[34], 3.0)+constants[33]*pow(constants[32], 3.0))) - algebraicVariables[0] = computed_constants[10]*pow(constants[32]/(constants[46]+constants[32]), 3.0)*pow(constants[44]/(constants[45]+constants[44]), 2.0)*1.6/(1.5+exp(-(states[0]+60.0)/40.0)) - algebraicVariables[17] = 0.0952*exp(-0.063*(states[0]+34.4))/(1.0+1.66*exp(-0.225*(states[0]+63.7)))+0.0869 if eq_func(constants[1], 0.0) else 0.09518*exp(-0.06306*(states[0]+34.4))/(1.0+1.662*exp(-0.2251*(states[0]+63.7)))+0.08693 - algebraicVariables[14] = (1.0-algebraicVariables[17])*states[3]+algebraicVariables[17]*states[2] - algebraicVariables[13] = computed_constants[13]*pow(states[1], 3.0)*algebraicVariables[14]*constants[34]*pow(constants[7], 2.0)/(constants[5]*constants[6])*(exp((states[0]-computed_constants[4])*constants[7]/(constants[5]*constants[6]))-1.0)/(exp(states[0]*constants[7]/(constants[5]*constants[6]))-1.0)*states[0] - algebraicVariables[16] = pow(1.0/(1.0+exp(-states[0]/5.46)), 1.0/3.0) if eq_func(constants[1], 0.0) else pow(1.0/(1.0+exp(-(states[0]+30.32)/5.46)), 1.0/3.0) - algebraicVariables[15] = 0.0006247/(0.832*exp(-0.335*(states[0]+56.7))+0.627*exp(0.082*(states[0]+65.01)))+4.0e-5 if eq_func(constants[1], 0.0) else 0.0006247/(0.8322166*exp(-0.33566*(states[0]+56.7062))+0.6274*exp(0.0823*(states[0]+65.0131)))+4.569e-5 - algebraicVariables[19] = 1.0/(1.0+exp((states[0]+66.1)/6.4)) - algebraicVariables[21] = algebraicVariables[19] - algebraicVariables[18] = 3.717e-6*exp(-0.2815*(states[0]+17.11))/(1.0+0.003732*exp(-0.3426*(states[0]+37.76)))+0.0005977 - algebraicVariables[20] = 3.186e-8*exp(-0.6219*(states[0]+18.8))/(1.0+7.189e-5*exp(-0.6683*(states[0]+34.07)))+0.003556 - algebraicVariables[12] = computed_constants[14]*(states[5]*states[4]+0.006/(1.0+exp(-(states[0]+14.1)/6.0)))*(states[0]-constants[66]) - algebraicVariables[24] = -28.38*(states[0]+35.0)/(exp(-(states[0]+35.0)/2.5)-1.0)-84.9*states[0]/(exp(-0.208*states[0])-1.0) if eq_func(constants[1], 0.0) else -28.39*(states[0]+35.0)/(exp(-(states[0]+35.0)/2.5)-1.0)-84.9*states[0]/(exp(-0.208*states[0])-1.0) if eq_func(constants[1], 1.0) else -28.4*(states[0]+35.0)/(exp(-(states[0]+35.0)/2.5)-1.0)-84.9*states[0]/(exp(-0.208*states[0])-1.0) - algebraicVariables[25] = 11.43*(states[0]-5.0)/(exp(0.4*(states[0]-5.0))-1.0) if eq_func(constants[1], 1.0) else 11.42*(states[0]-5.0)/(exp(0.4*(states[0]-5.0))-1.0) - algebraicVariables[22] = 2.0/(algebraicVariables[24]+algebraicVariables[25]) - algebraicVariables[23] = 1.0/(1.0+exp(-(states[0]+23.1)/6.0)) if eq_func(constants[1], 0.0) else 1.0/(1.0+exp(-(states[0]+22.3+0.8*computed_constants[0])/6.0)) if eq_func(constants[1], 1.0) else 1.0/(1.0+exp(-(states[0]+22.2)/6.0)) - algebraicVariables[28] = 3.75*(states[0]+28.0)/(exp((states[0]+28.0)/4.0)-1.0) if eq_func(constants[1], 1.0) else 3.12*(states[0]+28.0)/(exp((states[0]+28.0)/4.0)-1.0) - algebraicVariables[29] = 30.0/(1.0+exp(-(states[0]+28.0)/4.0)) if eq_func(constants[1], 1.0) else 25.0/(1.0+exp(-(states[0]+28.0)/4.0)) - algebraicVariables[26] = (1.2-0.2*computed_constants[0])/(algebraicVariables[28]+algebraicVariables[29]) if eq_func(constants[1], 1.0) else 1.0/(algebraicVariables[28]+algebraicVariables[29]) - algebraicVariables[27] = 1.0/(1.0+exp((states[0]+45.0)/5.0)) - algebraicVariables[11] = computed_constants[15]*states[7]*states[6]*(states[0]-constants[73]) - algebraicVariables[32] = 1068.0*exp((states[0]+26.3)/30.0) - algebraicVariables[33] = 1068.0*exp(-(states[0]+26.3)/30.0) - algebraicVariables[30] = 1.0/(algebraicVariables[32]+algebraicVariables[33]) - algebraicVariables[31] = 1.0/(1.0+exp(-(states[0]+37.0)/6.8)) - algebraicVariables[36] = 15.3*exp(-(states[0]+71.0+0.7*computed_constants[0])/83.3) if eq_func(constants[1], 1.0) else 15.3*exp(-(states[0]+71.7)/83.3) - algebraicVariables[37] = 15.0*exp((states[0]+71.0)/15.38) if eq_func(constants[1], 1.0) else 15.0*exp((states[0]+71.7)/15.38) - algebraicVariables[34] = 1.0/(algebraicVariables[36]+algebraicVariables[37]) - algebraicVariables[35] = 1.0/(1.0+exp((states[0]+71.0)/9.0)) - algebraicVariables[10] = computed_constants[16]*states[9]*states[8]*(states[0]-computed_constants[6]) - algebraicVariables[9] = computed_constants[17]*states[8]*(states[0]-computed_constants[6]) - algebraicVariables[39] = 1.0/(1.0+exp((states[0]+59.37)/13.1)) - algebraicVariables[38] = 0.0101+0.06517/(0.57*exp(-0.08*(states[0]+49.0)))+2.4e-5*exp(0.1*(states[0]+50.93)) if eq_func(constants[1], 0.0) else 0.001/3.0*(30.31+195.5/(0.5686*exp(-0.08161*(states[0]+39.0+10.0*computed_constants[0]))+0.7174*exp((0.2719-0.1719*computed_constants[0])*1.0*(states[0]+40.93+10.0*computed_constants[0])))) if eq_func(constants[1], 1.0) else 0.0101+0.06517/(0.5686*exp(-0.08161*(states[0]+39.0))+0.7174*exp(0.2719*(states[0]+40.93))) - algebraicVariables[41] = 1.0/(1.0+exp(-(states[0]-10.93)/19.7)) - algebraicVariables[40] = 0.001*(2.98+15.59/(1.037*exp(0.09*(states[0]+30.61))+0.369*exp(-0.12*(states[0]+23.84)))) if eq_func(constants[1], 0.0) else 0.0025*(1.191+7.838/(1.037*exp(0.09012*(states[0]+30.61))+0.369*exp(-0.119*(states[0]+23.84)))) if eq_func(constants[1], 1.0) else 0.001*(2.98+19.59/(1.037*exp(0.09012*(states[0]+30.61))+0.369*exp(-0.119*(states[0]+23.84)))) - algebraicVariables[42] = 0.6*states[12]+0.4*states[11] - algebraicVariables[8] = computed_constants[18]*algebraicVariables[42]*states[10]*(states[0]-computed_constants[6]) - algebraicVariables[44] = 1.0/(1.0+exp(-(states[0]+14.2)/10.6)) if neq_func(constants[1], 2.0) else 1.0/(1.0+exp(-(states[0]+13.2)/10.6)) - algebraicVariables[43] = 1.0/(37.2*exp((states[0]-9.0)/15.9)+0.96*exp(-(states[0]-9.0)/22.5)) if neq_func(constants[1], 2.0) else 1.0/(37.2*exp((states[0]-10.0)/15.9)+0.96*exp(-(states[0]-10.0)/22.5)) - algebraicVariables[46] = algebraicVariables[44] - algebraicVariables[45] = 1.0/(4.2*exp((states[0]-9.0)/17.0)+0.15*exp(-(states[0]-9.0)/21.6)) if neq_func(constants[1], 2.0) else 1.0/(4.2*exp((states[0]-10.0)/17.0)+0.15*exp(-(states[0]-10.0)/21.6)) - algebraicVariables[47] = 1.0/(1.0+exp((states[0]+18.6)/10.1)) - algebraicVariables[7] = computed_constants[20]*pow(states[13], 2.0)*(states[0]-computed_constants[12]) - algebraicVariables[49] = 14.0/(1.0+exp(-(states[0]-40.0)/9.0)) - algebraicVariables[48] = 1.0*exp(-states[0]/45.0) - algebraicVariables[6] = computed_constants[21]*states[14]*(states[0]-computed_constants[4]) if neq_func(constants[1], 2.0) else computed_constants[21]*states[14]*(states[0]-77.6) - algebraicVariables[5] = computed_constants[22]*states[14]*(states[0]-computed_constants[6]) if neq_func(constants[1], 2.0) else computed_constants[22]*states[14]*(states[0]+102.0) - algebraicVariables[51] = 1.0*exp(-(states[0]+78.91)/26.62) if eq_func(constants[1], 0.0) else 1.0*exp(-(states[0]+78.91)/26.63) - algebraicVariables[50] = 1.0*exp((states[0]+75.13)/21.25) + algebraic_variables[4] = computed_constants[3]*(states[0]-computed_constants[4]) + algebraic_variables[2] = computed_constants[5]*(states[0]-computed_constants[6]) + algebraic_variables[3] = computed_constants[7]*(states[0]-computed_constants[8]) + algebraic_variables[1] = computed_constants[9]*(pow(constants[32], 3.0)*constants[33]*exp(0.03743*states[0]*constants[37])-pow(constants[34], 3.0)*constants[35]*exp(0.0374*states[0]*(constants[37]-1.0)))/(1.0+constants[36]*(constants[35]*pow(constants[34], 3.0)+constants[33]*pow(constants[32], 3.0))) if eq_func(constants[1], 0.0) else computed_constants[9]*(pow(constants[32], 3.0)*constants[33]*exp(0.03743*states[0]*constants[37])-pow(constants[34], 3.0)*constants[35]*exp(0.03743*states[0]*(constants[37]-1.0)))/(1.0+constants[36]*(constants[35]*pow(constants[34], 3.0)+constants[33]*pow(constants[32], 3.0))) + algebraic_variables[0] = computed_constants[10]*pow(constants[32]/(constants[46]+constants[32]), 3.0)*pow(constants[44]/(constants[45]+constants[44]), 2.0)*1.6/(1.5+exp(-(states[0]+60.0)/40.0)) + algebraic_variables[17] = 0.0952*exp(-0.063*(states[0]+34.4))/(1.0+1.66*exp(-0.225*(states[0]+63.7)))+0.0869 if eq_func(constants[1], 0.0) else 0.09518*exp(-0.06306*(states[0]+34.4))/(1.0+1.662*exp(-0.2251*(states[0]+63.7)))+0.08693 + algebraic_variables[14] = (1.0-algebraic_variables[17])*states[3]+algebraic_variables[17]*states[2] + algebraic_variables[13] = computed_constants[13]*pow(states[1], 3.0)*algebraic_variables[14]*constants[34]*pow(constants[7], 2.0)/(constants[5]*constants[6])*(exp((states[0]-computed_constants[4])*constants[7]/(constants[5]*constants[6]))-1.0)/(exp(states[0]*constants[7]/(constants[5]*constants[6]))-1.0)*states[0] + algebraic_variables[16] = pow(1.0/(1.0+exp(-states[0]/5.46)), 1.0/3.0) if eq_func(constants[1], 0.0) else pow(1.0/(1.0+exp(-(states[0]+30.32)/5.46)), 1.0/3.0) + algebraic_variables[15] = 0.0006247/(0.832*exp(-0.335*(states[0]+56.7))+0.627*exp(0.082*(states[0]+65.01)))+4.0e-5 if eq_func(constants[1], 0.0) else 0.0006247/(0.8322166*exp(-0.33566*(states[0]+56.7062))+0.6274*exp(0.0823*(states[0]+65.0131)))+4.569e-5 + algebraic_variables[19] = 1.0/(1.0+exp((states[0]+66.1)/6.4)) + algebraic_variables[21] = algebraic_variables[19] + algebraic_variables[18] = 3.717e-6*exp(-0.2815*(states[0]+17.11))/(1.0+0.003732*exp(-0.3426*(states[0]+37.76)))+0.0005977 + algebraic_variables[20] = 3.186e-8*exp(-0.6219*(states[0]+18.8))/(1.0+7.189e-5*exp(-0.6683*(states[0]+34.07)))+0.003556 + algebraic_variables[12] = computed_constants[14]*(states[5]*states[4]+0.006/(1.0+exp(-(states[0]+14.1)/6.0)))*(states[0]-constants[66]) + algebraic_variables[24] = -28.38*(states[0]+35.0)/(exp(-(states[0]+35.0)/2.5)-1.0)-84.9*states[0]/(exp(-0.208*states[0])-1.0) if eq_func(constants[1], 0.0) else -28.39*(states[0]+35.0)/(exp(-(states[0]+35.0)/2.5)-1.0)-84.9*states[0]/(exp(-0.208*states[0])-1.0) if eq_func(constants[1], 1.0) else -28.4*(states[0]+35.0)/(exp(-(states[0]+35.0)/2.5)-1.0)-84.9*states[0]/(exp(-0.208*states[0])-1.0) + algebraic_variables[25] = 11.43*(states[0]-5.0)/(exp(0.4*(states[0]-5.0))-1.0) if eq_func(constants[1], 1.0) else 11.42*(states[0]-5.0)/(exp(0.4*(states[0]-5.0))-1.0) + algebraic_variables[22] = 2.0/(algebraic_variables[24]+algebraic_variables[25]) + algebraic_variables[23] = 1.0/(1.0+exp(-(states[0]+23.1)/6.0)) if eq_func(constants[1], 0.0) else 1.0/(1.0+exp(-(states[0]+22.3+0.8*computed_constants[0])/6.0)) if eq_func(constants[1], 1.0) else 1.0/(1.0+exp(-(states[0]+22.2)/6.0)) + algebraic_variables[28] = 3.75*(states[0]+28.0)/(exp((states[0]+28.0)/4.0)-1.0) if eq_func(constants[1], 1.0) else 3.12*(states[0]+28.0)/(exp((states[0]+28.0)/4.0)-1.0) + algebraic_variables[29] = 30.0/(1.0+exp(-(states[0]+28.0)/4.0)) if eq_func(constants[1], 1.0) else 25.0/(1.0+exp(-(states[0]+28.0)/4.0)) + algebraic_variables[26] = (1.2-0.2*computed_constants[0])/(algebraic_variables[28]+algebraic_variables[29]) if eq_func(constants[1], 1.0) else 1.0/(algebraic_variables[28]+algebraic_variables[29]) + algebraic_variables[27] = 1.0/(1.0+exp((states[0]+45.0)/5.0)) + algebraic_variables[11] = computed_constants[15]*states[7]*states[6]*(states[0]-constants[73]) + algebraic_variables[32] = 1068.0*exp((states[0]+26.3)/30.0) + algebraic_variables[33] = 1068.0*exp(-(states[0]+26.3)/30.0) + algebraic_variables[30] = 1.0/(algebraic_variables[32]+algebraic_variables[33]) + algebraic_variables[31] = 1.0/(1.0+exp(-(states[0]+37.0)/6.8)) + algebraic_variables[36] = 15.3*exp(-(states[0]+71.0+0.7*computed_constants[0])/83.3) if eq_func(constants[1], 1.0) else 15.3*exp(-(states[0]+71.7)/83.3) + algebraic_variables[37] = 15.0*exp((states[0]+71.0)/15.38) if eq_func(constants[1], 1.0) else 15.0*exp((states[0]+71.7)/15.38) + algebraic_variables[34] = 1.0/(algebraic_variables[36]+algebraic_variables[37]) + algebraic_variables[35] = 1.0/(1.0+exp((states[0]+71.0)/9.0)) + algebraic_variables[10] = computed_constants[16]*states[9]*states[8]*(states[0]-computed_constants[6]) + algebraic_variables[9] = computed_constants[17]*states[8]*(states[0]-computed_constants[6]) + algebraic_variables[39] = 1.0/(1.0+exp((states[0]+59.37)/13.1)) + algebraic_variables[38] = 0.0101+0.06517/(0.57*exp(-0.08*(states[0]+49.0)))+2.4e-5*exp(0.1*(states[0]+50.93)) if eq_func(constants[1], 0.0) else 0.001/3.0*(30.31+195.5/(0.5686*exp(-0.08161*(states[0]+39.0+10.0*computed_constants[0]))+0.7174*exp((0.2719-0.1719*computed_constants[0])*1.0*(states[0]+40.93+10.0*computed_constants[0])))) if eq_func(constants[1], 1.0) else 0.0101+0.06517/(0.5686*exp(-0.08161*(states[0]+39.0))+0.7174*exp(0.2719*(states[0]+40.93))) + algebraic_variables[41] = 1.0/(1.0+exp(-(states[0]-10.93)/19.7)) + algebraic_variables[40] = 0.001*(2.98+15.59/(1.037*exp(0.09*(states[0]+30.61))+0.369*exp(-0.12*(states[0]+23.84)))) if eq_func(constants[1], 0.0) else 0.0025*(1.191+7.838/(1.037*exp(0.09012*(states[0]+30.61))+0.369*exp(-0.119*(states[0]+23.84)))) if eq_func(constants[1], 1.0) else 0.001*(2.98+19.59/(1.037*exp(0.09012*(states[0]+30.61))+0.369*exp(-0.119*(states[0]+23.84)))) + algebraic_variables[42] = 0.6*states[12]+0.4*states[11] + algebraic_variables[8] = computed_constants[18]*algebraic_variables[42]*states[10]*(states[0]-computed_constants[6]) + algebraic_variables[44] = 1.0/(1.0+exp(-(states[0]+14.2)/10.6)) if neq_func(constants[1], 2.0) else 1.0/(1.0+exp(-(states[0]+13.2)/10.6)) + algebraic_variables[43] = 1.0/(37.2*exp((states[0]-9.0)/15.9)+0.96*exp(-(states[0]-9.0)/22.5)) if neq_func(constants[1], 2.0) else 1.0/(37.2*exp((states[0]-10.0)/15.9)+0.96*exp(-(states[0]-10.0)/22.5)) + algebraic_variables[46] = algebraic_variables[44] + algebraic_variables[45] = 1.0/(4.2*exp((states[0]-9.0)/17.0)+0.15*exp(-(states[0]-9.0)/21.6)) if neq_func(constants[1], 2.0) else 1.0/(4.2*exp((states[0]-10.0)/17.0)+0.15*exp(-(states[0]-10.0)/21.6)) + algebraic_variables[47] = 1.0/(1.0+exp((states[0]+18.6)/10.1)) + algebraic_variables[7] = computed_constants[20]*pow(states[13], 2.0)*(states[0]-computed_constants[12]) + algebraic_variables[49] = 14.0/(1.0+exp(-(states[0]-40.0)/9.0)) + algebraic_variables[48] = 1.0*exp(-states[0]/45.0) + algebraic_variables[6] = computed_constants[21]*states[14]*(states[0]-computed_constants[4]) if neq_func(constants[1], 2.0) else computed_constants[21]*states[14]*(states[0]-77.6) + algebraic_variables[5] = computed_constants[22]*states[14]*(states[0]-computed_constants[6]) if neq_func(constants[1], 2.0) else computed_constants[22]*states[14]*(states[0]+102.0) + algebraic_variables[51] = 1.0*exp(-(states[0]+78.91)/26.62) if eq_func(constants[1], 0.0) else 1.0*exp(-(states[0]+78.91)/26.63) + algebraic_variables[50] = 1.0*exp((states[0]+75.13)/21.25) diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.algebraic.c b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.algebraic.c index df64cf045..8bfcf3cbb 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.algebraic.c +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.algebraic.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 4; @@ -126,7 +126,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * constants[4] = 36.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { computedConstants[0] = constants[1]-10.613; computedConstants[1] = constants[1]-115.0; diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.algebraic.h b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.algebraic.h index ce6057728..79abbba9c 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.algebraic.h +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.algebraic.h @@ -37,6 +37,6 @@ void deleteArray(double *array); typedef double (* ExternalVariable)(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, size_t index); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.algebraic.py b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.algebraic.py index 87c4c38f1..e4d4b2bbf 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.algebraic.py +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.algebraic.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 4 @@ -97,37 +97,37 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[4] = 36.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): computed_constants[0] = constants[1]-10.613 computed_constants[1] = constants[1]-115.0 computed_constants[2] = constants[1]+12.0 def compute_rates(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, external_variable): - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) - algebraicVariables[0] = constants[2]*(states[0]-computed_constants[0]) - algebraicVariables[1] = constants[4]*pow(states[3], 4.0)*(states[0]-computed_constants[2]) - algebraicVariables[2] = constants[3]*pow(states[2], 3.0)*states[1]*(states[0]-computed_constants[1]) - rates[0] = -(-externalVariables[0]+algebraicVariables[2]+algebraicVariables[1]+algebraicVariables[0])/constants[0] - algebraicVariables[4] = 4.0*exp(states[0]/18.0) - algebraicVariables[3] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - rates[2] = algebraicVariables[3]*(1.0-states[2])-algebraicVariables[4]*states[2] - algebraicVariables[6] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) - algebraicVariables[5] = 0.07*exp(states[0]/20.0) - rates[1] = algebraicVariables[5]*(1.0-states[1])-algebraicVariables[6]*states[1] - algebraicVariables[8] = 0.125*exp(states[0]/80.0) - algebraicVariables[7] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) - rates[3] = algebraicVariables[7]*(1.0-states[3])-algebraicVariables[8]*states[3] + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + algebraic_variables[0] = constants[2]*(states[0]-computed_constants[0]) + algebraic_variables[1] = constants[4]*pow(states[3], 4.0)*(states[0]-computed_constants[2]) + algebraic_variables[2] = constants[3]*pow(states[2], 3.0)*states[1]*(states[0]-computed_constants[1]) + rates[0] = -(-external_variables[0]+algebraic_variables[2]+algebraic_variables[1]+algebraic_variables[0])/constants[0] + algebraic_variables[4] = 4.0*exp(states[0]/18.0) + algebraic_variables[3] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + rates[2] = algebraic_variables[3]*(1.0-states[2])-algebraic_variables[4]*states[2] + algebraic_variables[6] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) + algebraic_variables[5] = 0.07*exp(states[0]/20.0) + rates[1] = algebraic_variables[5]*(1.0-states[1])-algebraic_variables[6]*states[1] + algebraic_variables[8] = 0.125*exp(states[0]/80.0) + algebraic_variables[7] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) + rates[3] = algebraic_variables[7]*(1.0-states[3])-algebraic_variables[8]*states[3] def compute_variables(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, external_variable): - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) - algebraicVariables[0] = constants[2]*(states[0]-computed_constants[0]) - algebraicVariables[2] = constants[3]*pow(states[2], 3.0)*states[1]*(states[0]-computed_constants[1]) - algebraicVariables[3] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - algebraicVariables[4] = 4.0*exp(states[0]/18.0) - algebraicVariables[5] = 0.07*exp(states[0]/20.0) - algebraicVariables[6] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) - algebraicVariables[1] = constants[4]*pow(states[3], 4.0)*(states[0]-computed_constants[2]) - algebraicVariables[7] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) - algebraicVariables[8] = 0.125*exp(states[0]/80.0) + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + algebraic_variables[0] = constants[2]*(states[0]-computed_constants[0]) + algebraic_variables[2] = constants[3]*pow(states[2], 3.0)*states[1]*(states[0]-computed_constants[1]) + algebraic_variables[3] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + algebraic_variables[4] = 4.0*exp(states[0]/18.0) + algebraic_variables[5] = 0.07*exp(states[0]/20.0) + algebraic_variables[6] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) + algebraic_variables[1] = constants[4]*pow(states[3], 4.0)*(states[0]-computed_constants[2]) + algebraic_variables[7] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) + algebraic_variables[8] = 0.125*exp(states[0]/80.0) diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.c b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.c index 77bbfadd4..04c6065eb 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.c +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 4; @@ -111,7 +111,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * constants[4] = 36.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { computedConstants[0] = constants[1]-10.613; computedConstants[1] = constants[1]-115.0; diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.computed.constant.c b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.computed.constant.c index dcd6f4146..4144ef0cc 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.computed.constant.c +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.computed.constant.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 4; @@ -126,7 +126,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * constants[4] = 36.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { computedConstants[0] = constants[1]-115.0; computedConstants[1] = constants[1]+12.0; diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.computed.constant.h b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.computed.constant.h index ce6057728..79abbba9c 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.computed.constant.h +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.computed.constant.h @@ -37,6 +37,6 @@ void deleteArray(double *array); typedef double (* ExternalVariable)(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, size_t index); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.computed.constant.py b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.computed.constant.py index 0b2ef3ca9..89a94b490 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.computed.constant.py +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.computed.constant.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 4 @@ -97,37 +97,37 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[4] = 36.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): computed_constants[0] = constants[1]-115.0 computed_constants[1] = constants[1]+12.0 def compute_rates(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, external_variable): - algebraicVariables[0] = -20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0 - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) - algebraicVariables[1] = constants[2]*(states[0]-externalVariables[0]) - algebraicVariables[2] = constants[4]*pow(states[3], 4.0)*(states[0]-computed_constants[1]) - algebraicVariables[3] = constants[3]*pow(states[2], 3.0)*states[1]*(states[0]-computed_constants[0]) - rates[0] = -(-algebraicVariables[0]+algebraicVariables[3]+algebraicVariables[2]+algebraicVariables[1])/constants[0] - algebraicVariables[5] = 4.0*exp(states[0]/18.0) - algebraicVariables[4] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - rates[2] = algebraicVariables[4]*(1.0-states[2])-algebraicVariables[5]*states[2] - algebraicVariables[7] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) - algebraicVariables[6] = 0.07*exp(states[0]/20.0) - rates[1] = algebraicVariables[6]*(1.0-states[1])-algebraicVariables[7]*states[1] - algebraicVariables[9] = 0.125*exp(states[0]/80.0) - algebraicVariables[8] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) - rates[3] = algebraicVariables[8]*(1.0-states[3])-algebraicVariables[9]*states[3] + algebraic_variables[0] = -20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0 + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + algebraic_variables[1] = constants[2]*(states[0]-external_variables[0]) + algebraic_variables[2] = constants[4]*pow(states[3], 4.0)*(states[0]-computed_constants[1]) + algebraic_variables[3] = constants[3]*pow(states[2], 3.0)*states[1]*(states[0]-computed_constants[0]) + rates[0] = -(-algebraic_variables[0]+algebraic_variables[3]+algebraic_variables[2]+algebraic_variables[1])/constants[0] + algebraic_variables[5] = 4.0*exp(states[0]/18.0) + algebraic_variables[4] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + rates[2] = algebraic_variables[4]*(1.0-states[2])-algebraic_variables[5]*states[2] + algebraic_variables[7] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) + algebraic_variables[6] = 0.07*exp(states[0]/20.0) + rates[1] = algebraic_variables[6]*(1.0-states[1])-algebraic_variables[7]*states[1] + algebraic_variables[9] = 0.125*exp(states[0]/80.0) + algebraic_variables[8] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) + rates[3] = algebraic_variables[8]*(1.0-states[3])-algebraic_variables[9]*states[3] def compute_variables(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, external_variable): - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) - algebraicVariables[1] = constants[2]*(states[0]-externalVariables[0]) - algebraicVariables[3] = constants[3]*pow(states[2], 3.0)*states[1]*(states[0]-computed_constants[0]) - algebraicVariables[4] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - algebraicVariables[5] = 4.0*exp(states[0]/18.0) - algebraicVariables[6] = 0.07*exp(states[0]/20.0) - algebraicVariables[7] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) - algebraicVariables[2] = constants[4]*pow(states[3], 4.0)*(states[0]-computed_constants[1]) - algebraicVariables[8] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) - algebraicVariables[9] = 0.125*exp(states[0]/80.0) + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + algebraic_variables[1] = constants[2]*(states[0]-external_variables[0]) + algebraic_variables[3] = constants[3]*pow(states[2], 3.0)*states[1]*(states[0]-computed_constants[0]) + algebraic_variables[4] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + algebraic_variables[5] = 4.0*exp(states[0]/18.0) + algebraic_variables[6] = 0.07*exp(states[0]/20.0) + algebraic_variables[7] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) + algebraic_variables[2] = constants[4]*pow(states[3], 4.0)*(states[0]-computed_constants[1]) + algebraic_variables[8] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) + algebraic_variables[9] = 0.125*exp(states[0]/80.0) diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.constant.c b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.constant.c index cbb2ec3a0..9d9777f39 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.constant.c +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.constant.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 4; @@ -125,7 +125,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * constants[3] = 36.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { computedConstants[0] = constants[0]-10.613; computedConstants[1] = constants[0]-115.0; diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.constant.h b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.constant.h index ce6057728..79abbba9c 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.constant.h +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.constant.h @@ -37,6 +37,6 @@ void deleteArray(double *array); typedef double (* ExternalVariable)(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, size_t index); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.constant.py b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.constant.py index 4d168187c..d0c3c52dc 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.constant.py +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.constant.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 4 @@ -96,38 +96,38 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[3] = 36.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): computed_constants[0] = constants[0]-10.613 computed_constants[1] = constants[0]-115.0 computed_constants[2] = constants[0]+12.0 def compute_rates(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, external_variable): - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) - algebraicVariables[0] = -20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0 - algebraicVariables[1] = constants[1]*(states[0]-computed_constants[0]) - algebraicVariables[2] = constants[3]*pow(states[3], 4.0)*(states[0]-computed_constants[2]) - algebraicVariables[3] = constants[2]*pow(states[2], 3.0)*states[1]*(states[0]-computed_constants[1]) - rates[0] = -(-algebraicVariables[0]+algebraicVariables[3]+algebraicVariables[2]+algebraicVariables[1])/externalVariables[0] - algebraicVariables[5] = 4.0*exp(states[0]/18.0) - algebraicVariables[4] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - rates[2] = algebraicVariables[4]*(1.0-states[2])-algebraicVariables[5]*states[2] - algebraicVariables[7] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) - algebraicVariables[6] = 0.07*exp(states[0]/20.0) - rates[1] = algebraicVariables[6]*(1.0-states[1])-algebraicVariables[7]*states[1] - algebraicVariables[9] = 0.125*exp(states[0]/80.0) - algebraicVariables[8] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) - rates[3] = algebraicVariables[8]*(1.0-states[3])-algebraicVariables[9]*states[3] + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + algebraic_variables[0] = -20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0 + algebraic_variables[1] = constants[1]*(states[0]-computed_constants[0]) + algebraic_variables[2] = constants[3]*pow(states[3], 4.0)*(states[0]-computed_constants[2]) + algebraic_variables[3] = constants[2]*pow(states[2], 3.0)*states[1]*(states[0]-computed_constants[1]) + rates[0] = -(-algebraic_variables[0]+algebraic_variables[3]+algebraic_variables[2]+algebraic_variables[1])/external_variables[0] + algebraic_variables[5] = 4.0*exp(states[0]/18.0) + algebraic_variables[4] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + rates[2] = algebraic_variables[4]*(1.0-states[2])-algebraic_variables[5]*states[2] + algebraic_variables[7] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) + algebraic_variables[6] = 0.07*exp(states[0]/20.0) + rates[1] = algebraic_variables[6]*(1.0-states[1])-algebraic_variables[7]*states[1] + algebraic_variables[9] = 0.125*exp(states[0]/80.0) + algebraic_variables[8] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) + rates[3] = algebraic_variables[8]*(1.0-states[3])-algebraic_variables[9]*states[3] def compute_variables(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, external_variable): - algebraicVariables[1] = constants[1]*(states[0]-computed_constants[0]) - algebraicVariables[3] = constants[2]*pow(states[2], 3.0)*states[1]*(states[0]-computed_constants[1]) - algebraicVariables[4] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - algebraicVariables[5] = 4.0*exp(states[0]/18.0) - algebraicVariables[6] = 0.07*exp(states[0]/20.0) - algebraicVariables[7] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) - algebraicVariables[2] = constants[3]*pow(states[3], 4.0)*(states[0]-computed_constants[2]) - algebraicVariables[8] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) - algebraicVariables[9] = 0.125*exp(states[0]/80.0) - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + algebraic_variables[1] = constants[1]*(states[0]-computed_constants[0]) + algebraic_variables[3] = constants[2]*pow(states[2], 3.0)*states[1]*(states[0]-computed_constants[1]) + algebraic_variables[4] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + algebraic_variables[5] = 4.0*exp(states[0]/18.0) + algebraic_variables[6] = 0.07*exp(states[0]/20.0) + algebraic_variables[7] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) + algebraic_variables[2] = constants[3]*pow(states[3], 4.0)*(states[0]-computed_constants[2]) + algebraic_variables[8] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) + algebraic_variables[9] = 0.125*exp(states[0]/80.0) + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.c b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.c index f00efa362..95d848512 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.c +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 4; @@ -582,7 +582,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * algebraicVariables[12] = 0.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.external.c b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.external.c index 1386eb196..3eef99ca2 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.external.c +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.external.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 3; @@ -530,7 +530,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * algebraicVariables[10] = 0.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.external.h b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.external.h index ce6057728..79abbba9c 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.external.h +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.external.h @@ -37,6 +37,6 @@ void deleteArray(double *array); typedef double (* ExternalVariable)(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, size_t index); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.external.py b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.external.py index 11a049b37..0f463364e 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.external.py +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.external.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 3 @@ -97,19 +97,19 @@ def objective_function_0(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[0] = u[0] + algebraic_variables[0] = u[0] - f[0] = algebraicVariables[0]-(-20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0)-0.0 + f[0] = algebraic_variables[0]-(-20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0)-0.0 def find_root_0(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[0] + u[0] = algebraic_variables[0] u = nla_solve(objective_function_0, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[0] = u[0] + algebraic_variables[0] = u[0] def objective_function_2(u, f, data): @@ -121,19 +121,19 @@ def objective_function_2(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[3] = u[0] + algebraic_variables[3] = u[0] - f[0] = algebraicVariables[3]-(constants[1]-10.613)-0.0 + f[0] = algebraic_variables[3]-(constants[1]-10.613)-0.0 def find_root_2(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[3] + u[0] = algebraic_variables[3] u = nla_solve(objective_function_2, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[3] = u[0] + algebraic_variables[3] = u[0] def objective_function_3(u, f, data): @@ -145,19 +145,19 @@ def objective_function_3(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[1] = u[0] + algebraic_variables[1] = u[0] - f[0] = algebraicVariables[1]-constants[2]*(externalVariables[1]-algebraicVariables[3])-0.0 + f[0] = algebraic_variables[1]-constants[2]*(external_variables[1]-algebraic_variables[3])-0.0 def find_root_3(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[1] + u[0] = algebraic_variables[1] u = nla_solve(objective_function_3, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[1] = u[0] + algebraic_variables[1] = u[0] def objective_function_4(u, f, data): @@ -169,19 +169,19 @@ def objective_function_4(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[4] = u[0] + algebraic_variables[4] = u[0] - f[0] = algebraicVariables[4]-(constants[1]-115.0)-0.0 + f[0] = algebraic_variables[4]-(constants[1]-115.0)-0.0 def find_root_4(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[4] + u[0] = algebraic_variables[4] u = nla_solve(objective_function_4, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[4] = u[0] + algebraic_variables[4] = u[0] def objective_function_6(u, f, data): @@ -193,19 +193,19 @@ def objective_function_6(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[5] = u[0] + algebraic_variables[5] = u[0] - f[0] = algebraicVariables[5]-0.1*(externalVariables[1]+25.0)/(exp((externalVariables[1]+25.0)/10.0)-1.0)-0.0 + f[0] = algebraic_variables[5]-0.1*(external_variables[1]+25.0)/(exp((external_variables[1]+25.0)/10.0)-1.0)-0.0 def find_root_6(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[5] + u[0] = algebraic_variables[5] u = nla_solve(objective_function_6, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[5] = u[0] + algebraic_variables[5] = u[0] def objective_function_7(u, f, data): @@ -217,19 +217,19 @@ def objective_function_7(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[6] = u[0] + algebraic_variables[6] = u[0] - f[0] = algebraicVariables[6]-4.0*exp(externalVariables[1]/18.0)-0.0 + f[0] = algebraic_variables[6]-4.0*exp(external_variables[1]/18.0)-0.0 def find_root_7(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[6] + u[0] = algebraic_variables[6] u = nla_solve(objective_function_7, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[6] = u[0] + algebraic_variables[6] = u[0] def objective_function_8(u, f, data): @@ -243,7 +243,7 @@ def objective_function_8(u, f, data): rates[1] = u[0] - f[0] = rates[1]-(algebraicVariables[5]*(1.0-states[1])-algebraicVariables[6]*states[1])-0.0 + f[0] = rates[1]-(algebraic_variables[5]*(1.0-states[1])-algebraic_variables[6]*states[1])-0.0 def find_root_8(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): @@ -265,19 +265,19 @@ def objective_function_9(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[7] = u[0] + algebraic_variables[7] = u[0] - f[0] = algebraicVariables[7]-0.07*exp(externalVariables[1]/20.0)-0.0 + f[0] = algebraic_variables[7]-0.07*exp(external_variables[1]/20.0)-0.0 def find_root_9(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[7] + u[0] = algebraic_variables[7] u = nla_solve(objective_function_9, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[7] = u[0] + algebraic_variables[7] = u[0] def objective_function_10(u, f, data): @@ -289,19 +289,19 @@ def objective_function_10(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[8] = u[0] + algebraic_variables[8] = u[0] - f[0] = algebraicVariables[8]-1.0/(exp((externalVariables[1]+30.0)/10.0)+1.0)-0.0 + f[0] = algebraic_variables[8]-1.0/(exp((external_variables[1]+30.0)/10.0)+1.0)-0.0 def find_root_10(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[8] + u[0] = algebraic_variables[8] u = nla_solve(objective_function_10, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[8] = u[0] + algebraic_variables[8] = u[0] def objective_function_11(u, f, data): @@ -315,7 +315,7 @@ def objective_function_11(u, f, data): rates[0] = u[0] - f[0] = rates[0]-(algebraicVariables[7]*(1.0-states[0])-algebraicVariables[8]*states[0])-0.0 + f[0] = rates[0]-(algebraic_variables[7]*(1.0-states[0])-algebraic_variables[8]*states[0])-0.0 def find_root_11(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): @@ -337,19 +337,19 @@ def objective_function_12(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[9] = u[0] + algebraic_variables[9] = u[0] - f[0] = algebraicVariables[9]-(constants[1]+12.0)-0.0 + f[0] = algebraic_variables[9]-(constants[1]+12.0)-0.0 def find_root_12(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[9] + u[0] = algebraic_variables[9] u = nla_solve(objective_function_12, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[9] = u[0] + algebraic_variables[9] = u[0] def objective_function_13(u, f, data): @@ -361,19 +361,19 @@ def objective_function_13(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[2] = u[0] + algebraic_variables[2] = u[0] - f[0] = algebraicVariables[2]-constants[4]*pow(states[2], 4.0)*(externalVariables[1]-algebraicVariables[9])-0.0 + f[0] = algebraic_variables[2]-constants[4]*pow(states[2], 4.0)*(external_variables[1]-algebraic_variables[9])-0.0 def find_root_13(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[2] + u[0] = algebraic_variables[2] u = nla_solve(objective_function_13, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[2] = u[0] + algebraic_variables[2] = u[0] def objective_function_15(u, f, data): @@ -385,19 +385,19 @@ def objective_function_15(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[10] = u[0] + algebraic_variables[10] = u[0] - f[0] = algebraicVariables[10]-0.125*exp(externalVariables[1]/80.0)-0.0 + f[0] = algebraic_variables[10]-0.125*exp(external_variables[1]/80.0)-0.0 def find_root_15(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[10] + u[0] = algebraic_variables[10] u = nla_solve(objective_function_15, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[10] = u[0] + algebraic_variables[10] = u[0] def objective_function_16(u, f, data): @@ -411,7 +411,7 @@ def objective_function_16(u, f, data): rates[2] = u[0] - f[0] = rates[2]-(externalVariables[2]*(1.0-states[2])-algebraicVariables[10]*states[2])-0.0 + f[0] = rates[2]-(external_variables[2]*(1.0-states[2])-algebraic_variables[10]*states[2])-0.0 def find_root_16(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): @@ -436,25 +436,25 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[2] = 0.3 constants[3] = 120.0 constants[4] = 36.0 - algebraicVariables[0] = 0.0 - algebraicVariables[1] = 0.0 - algebraicVariables[2] = 0.0 - algebraicVariables[3] = 0.0 - algebraicVariables[4] = 0.0 - algebraicVariables[5] = 0.0 - algebraicVariables[6] = 0.0 - algebraicVariables[7] = 0.0 - algebraicVariables[8] = 0.0 - algebraicVariables[9] = 0.0 - algebraicVariables[10] = 0.0 - - -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): + algebraic_variables[0] = 0.0 + algebraic_variables[1] = 0.0 + algebraic_variables[2] = 0.0 + algebraic_variables[3] = 0.0 + algebraic_variables[4] = 0.0 + algebraic_variables[5] = 0.0 + algebraic_variables[6] = 0.0 + algebraic_variables[7] = 0.0 + algebraic_variables[8] = 0.0 + algebraic_variables[9] = 0.0 + algebraic_variables[10] = 0.0 + + +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass def compute_rates(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, external_variable): - externalVariables[1] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 1) + external_variables[1] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 1) find_root_7(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_6(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_8(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) @@ -462,17 +462,17 @@ def compute_rates(voi, states, rates, constants, computed_constants, algebraic_v find_root_9(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_11(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_15(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) - externalVariables[2] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 2) + external_variables[2] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 2) find_root_16(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) def compute_variables(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, external_variable): find_root_0(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_2(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) - externalVariables[1] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 1) + external_variables[1] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 1) find_root_3(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_4(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_12(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_13(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) - externalVariables[2] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 2) - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + external_variables[2] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 2) + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.control.c b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.control.c index 1d492ef11..0ce81bf43 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.control.c +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.control.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 4; @@ -528,7 +528,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * algebraicVariables[11] = 0.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { computedConstants[0] = constants[1]+12.0; } diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.control.h b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.control.h index 42166250c..fc447c7a3 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.control.h +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.control.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.control.py b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.control.py index cf694f89f..d1c304d0b 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.control.py +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.control.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 4 @@ -88,19 +88,19 @@ def objective_function_0(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[0] = u[0] + algebraic_variables[0] = u[0] - f[0] = algebraicVariables[0]-(-20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0)-0.0 + f[0] = algebraic_variables[0]-(-20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0)-0.0 def find_root_0(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[0] + u[0] = algebraic_variables[0] u = nla_solve(objective_function_0, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[0] = u[0] + algebraic_variables[0] = u[0] def objective_function_1(u, f, data): @@ -113,7 +113,7 @@ def objective_function_1(u, f, data): rates[0] = u[0] - f[0] = rates[0]-(-(-algebraicVariables[0]+algebraicVariables[3]+algebraicVariables[2]+algebraicVariables[1])/constants[0])-0.0 + f[0] = rates[0]-(-(-algebraic_variables[0]+algebraic_variables[3]+algebraic_variables[2]+algebraic_variables[1])/constants[0])-0.0 def find_root_1(voi, states, rates, constants, computed_constants, algebraic_variables): @@ -134,19 +134,19 @@ def objective_function_2(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[4] = u[0] + algebraic_variables[4] = u[0] - f[0] = algebraicVariables[4]-(constants[1]-10.613)-0.0 + f[0] = algebraic_variables[4]-(constants[1]-10.613)-0.0 def find_root_2(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[4] + u[0] = algebraic_variables[4] u = nla_solve(objective_function_2, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[4] = u[0] + algebraic_variables[4] = u[0] def objective_function_3(u, f, data): @@ -157,19 +157,19 @@ def objective_function_3(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[1] = u[0] + algebraic_variables[1] = u[0] - f[0] = algebraicVariables[1]-constants[2]*(states[0]-algebraicVariables[4])-0.0 + f[0] = algebraic_variables[1]-constants[2]*(states[0]-algebraic_variables[4])-0.0 def find_root_3(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[1] + u[0] = algebraic_variables[1] u = nla_solve(objective_function_3, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[1] = u[0] + algebraic_variables[1] = u[0] def objective_function_4(u, f, data): @@ -180,19 +180,19 @@ def objective_function_4(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[5] = u[0] + algebraic_variables[5] = u[0] - f[0] = algebraicVariables[5]-(constants[1]-115.0)-0.0 + f[0] = algebraic_variables[5]-(constants[1]-115.0)-0.0 def find_root_4(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[5] + u[0] = algebraic_variables[5] u = nla_solve(objective_function_4, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[5] = u[0] + algebraic_variables[5] = u[0] def objective_function_5(u, f, data): @@ -203,19 +203,19 @@ def objective_function_5(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[3] = u[0] + algebraic_variables[3] = u[0] - f[0] = algebraicVariables[3]-constants[3]*pow(states[2], 3.0)*states[1]*(states[0]-algebraicVariables[5])-0.0 + f[0] = algebraic_variables[3]-constants[3]*pow(states[2], 3.0)*states[1]*(states[0]-algebraic_variables[5])-0.0 def find_root_5(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[3] + u[0] = algebraic_variables[3] u = nla_solve(objective_function_5, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[3] = u[0] + algebraic_variables[3] = u[0] def objective_function_6(u, f, data): @@ -226,19 +226,19 @@ def objective_function_6(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[7] = u[0] + algebraic_variables[7] = u[0] - f[0] = algebraicVariables[7]-4.0*exp(states[0]/18.0)-0.0 + f[0] = algebraic_variables[7]-4.0*exp(states[0]/18.0)-0.0 def find_root_6(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[7] + u[0] = algebraic_variables[7] u = nla_solve(objective_function_6, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[7] = u[0] + algebraic_variables[7] = u[0] def objective_function_7(u, f, data): @@ -251,7 +251,7 @@ def objective_function_7(u, f, data): rates[2] = u[0] - f[0] = rates[2]-(algebraicVariables[6]*(1.0-states[2])-algebraicVariables[7]*states[2])-0.0 + f[0] = rates[2]-(algebraic_variables[6]*(1.0-states[2])-algebraic_variables[7]*states[2])-0.0 def find_root_7(voi, states, rates, constants, computed_constants, algebraic_variables): @@ -272,19 +272,19 @@ def objective_function_8(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[8] = u[0] + algebraic_variables[8] = u[0] - f[0] = algebraicVariables[8]-0.07*exp(states[0]/20.0)-0.0 + f[0] = algebraic_variables[8]-0.07*exp(states[0]/20.0)-0.0 def find_root_8(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[8] + u[0] = algebraic_variables[8] u = nla_solve(objective_function_8, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[8] = u[0] + algebraic_variables[8] = u[0] def objective_function_9(u, f, data): @@ -295,19 +295,19 @@ def objective_function_9(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[9] = u[0] + algebraic_variables[9] = u[0] - f[0] = algebraicVariables[9]-1.0/(exp((states[0]+30.0)/10.0)+1.0)-0.0 + f[0] = algebraic_variables[9]-1.0/(exp((states[0]+30.0)/10.0)+1.0)-0.0 def find_root_9(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[9] + u[0] = algebraic_variables[9] u = nla_solve(objective_function_9, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[9] = u[0] + algebraic_variables[9] = u[0] def objective_function_10(u, f, data): @@ -320,7 +320,7 @@ def objective_function_10(u, f, data): rates[1] = u[0] - f[0] = rates[1]-(algebraicVariables[8]*(1.0-states[1])-algebraicVariables[9]*states[1])-0.0 + f[0] = rates[1]-(algebraic_variables[8]*(1.0-states[1])-algebraic_variables[9]*states[1])-0.0 def find_root_10(voi, states, rates, constants, computed_constants, algebraic_variables): @@ -341,19 +341,19 @@ def objective_function_11(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[2] = u[0] + algebraic_variables[2] = u[0] - f[0] = algebraicVariables[2]-constants[4]*pow(states[3], 4.0)*(states[0]-computed_constants[0])-0.0 + f[0] = algebraic_variables[2]-constants[4]*pow(states[3], 4.0)*(states[0]-computed_constants[0])-0.0 def find_root_11(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[2] + u[0] = algebraic_variables[2] u = nla_solve(objective_function_11, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[2] = u[0] + algebraic_variables[2] = u[0] def objective_function_12(u, f, data): @@ -364,19 +364,19 @@ def objective_function_12(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[10] = u[0] + algebraic_variables[10] = u[0] - f[0] = algebraicVariables[10]-0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0)-0.0 + f[0] = algebraic_variables[10]-0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0)-0.0 def find_root_12(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[10] + u[0] = algebraic_variables[10] u = nla_solve(objective_function_12, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[10] = u[0] + algebraic_variables[10] = u[0] def objective_function_13(u, f, data): @@ -387,19 +387,19 @@ def objective_function_13(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[11] = u[0] + algebraic_variables[11] = u[0] - f[0] = algebraicVariables[11]-0.125*exp(states[0]/80.0)-0.0 + f[0] = algebraic_variables[11]-0.125*exp(states[0]/80.0)-0.0 def find_root_13(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[11] + u[0] = algebraic_variables[11] u = nla_solve(objective_function_13, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[11] = u[0] + algebraic_variables[11] = u[0] def objective_function_14(u, f, data): @@ -412,7 +412,7 @@ def objective_function_14(u, f, data): rates[3] = u[0] - f[0] = rates[3]-(algebraicVariables[10]*(1.0-states[3])-algebraicVariables[11]*states[3])-0.0 + f[0] = rates[3]-(algebraic_variables[10]*(1.0-states[3])-algebraic_variables[11]*states[3])-0.0 def find_root_14(voi, states, rates, constants, computed_constants, algebraic_variables): @@ -439,20 +439,20 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[2] = 0.3 constants[3] = 120.0 constants[4] = 36.0 - algebraicVariables[0] = 0.0 - algebraicVariables[1] = 0.0 - algebraicVariables[2] = 0.0 - algebraicVariables[3] = 0.0 - algebraicVariables[4] = 0.0 - algebraicVariables[5] = 0.0 - algebraicVariables[7] = 0.0 - algebraicVariables[8] = 0.0 - algebraicVariables[9] = 0.0 - algebraicVariables[10] = 0.0 - algebraicVariables[11] = 0.0 - - -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): + algebraic_variables[0] = 0.0 + algebraic_variables[1] = 0.0 + algebraic_variables[2] = 0.0 + algebraic_variables[3] = 0.0 + algebraic_variables[4] = 0.0 + algebraic_variables[5] = 0.0 + algebraic_variables[7] = 0.0 + algebraic_variables[8] = 0.0 + algebraic_variables[9] = 0.0 + algebraic_variables[10] = 0.0 + algebraic_variables[11] = 0.0 + + +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): computed_constants[0] = constants[1]+12.0 @@ -467,7 +467,7 @@ def compute_rates(voi, states, rates, constants, computed_constants, algebraic_v find_root_9(voi, states, rates, constants, computed_constants, algebraic_variables) find_root_8(voi, states, rates, constants, computed_constants, algebraic_variables) find_root_10(voi, states, rates, constants, computed_constants, algebraic_variables) - algebraicVariables[6] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + algebraic_variables[6] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) find_root_6(voi, states, rates, constants, computed_constants, algebraic_variables) find_root_7(voi, states, rates, constants, computed_constants, algebraic_variables) find_root_4(voi, states, rates, constants, computed_constants, algebraic_variables) @@ -484,7 +484,7 @@ def compute_variables(voi, states, rates, constants, computed_constants, algebra find_root_9(voi, states, rates, constants, computed_constants, algebraic_variables) find_root_8(voi, states, rates, constants, computed_constants, algebraic_variables) find_root_10(voi, states, rates, constants, computed_constants, algebraic_variables) - algebraicVariables[6] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + algebraic_variables[6] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) find_root_6(voi, states, rates, constants, computed_constants, algebraic_variables) find_root_7(voi, states, rates, constants, computed_constants, algebraic_variables) find_root_5(voi, states, rates, constants, computed_constants, algebraic_variables) diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.control.with.externals.c b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.control.with.externals.c index 8d627701c..01621eb5c 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.control.with.externals.c +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.control.with.externals.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 4; @@ -531,7 +531,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * algebraicVariables[10] = 0.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { computedConstants[0] = constants[1]+12.0; } diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.control.with.externals.h b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.control.with.externals.h index ce6057728..79abbba9c 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.control.with.externals.h +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.control.with.externals.h @@ -37,6 +37,6 @@ void deleteArray(double *array); typedef double (* ExternalVariable)(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, size_t index); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.control.with.externals.py b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.control.with.externals.py index 1a6636938..22909c2ee 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.control.with.externals.py +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.control.with.externals.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 4 @@ -97,19 +97,19 @@ def objective_function_0(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[0] = u[0] + algebraic_variables[0] = u[0] - f[0] = algebraicVariables[0]-(-20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0)-0.0 + f[0] = algebraic_variables[0]-(-20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0)-0.0 def find_root_0(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[0] + u[0] = algebraic_variables[0] u = nla_solve(objective_function_0, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[0] = u[0] + algebraic_variables[0] = u[0] def objective_function_1(u, f, data): @@ -123,7 +123,7 @@ def objective_function_1(u, f, data): rates[0] = u[0] - f[0] = rates[0]-(-(-algebraicVariables[0]+externalVariables[0]+algebraicVariables[2]+algebraicVariables[1])/constants[0])-0.0 + f[0] = rates[0]-(-(-algebraic_variables[0]+external_variables[0]+algebraic_variables[2]+algebraic_variables[1])/constants[0])-0.0 def find_root_1(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): @@ -145,19 +145,19 @@ def objective_function_2(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[3] = u[0] + algebraic_variables[3] = u[0] - f[0] = algebraicVariables[3]-(constants[1]-10.613)-0.0 + f[0] = algebraic_variables[3]-(constants[1]-10.613)-0.0 def find_root_2(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[3] + u[0] = algebraic_variables[3] u = nla_solve(objective_function_2, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[3] = u[0] + algebraic_variables[3] = u[0] def objective_function_3(u, f, data): @@ -169,19 +169,19 @@ def objective_function_3(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[1] = u[0] + algebraic_variables[1] = u[0] - f[0] = algebraicVariables[1]-constants[2]*(states[0]-algebraicVariables[3])-0.0 + f[0] = algebraic_variables[1]-constants[2]*(states[0]-algebraic_variables[3])-0.0 def find_root_3(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[1] + u[0] = algebraic_variables[1] u = nla_solve(objective_function_3, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[1] = u[0] + algebraic_variables[1] = u[0] def objective_function_4(u, f, data): @@ -193,19 +193,19 @@ def objective_function_4(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[4] = u[0] + algebraic_variables[4] = u[0] - f[0] = algebraicVariables[4]-(constants[1]-115.0)-0.0 + f[0] = algebraic_variables[4]-(constants[1]-115.0)-0.0 def find_root_4(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[4] + u[0] = algebraic_variables[4] u = nla_solve(objective_function_4, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[4] = u[0] + algebraic_variables[4] = u[0] def objective_function_6(u, f, data): @@ -217,19 +217,19 @@ def objective_function_6(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[6] = u[0] + algebraic_variables[6] = u[0] - f[0] = algebraicVariables[6]-4.0*exp(states[0]/18.0)-0.0 + f[0] = algebraic_variables[6]-4.0*exp(states[0]/18.0)-0.0 def find_root_6(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[6] + u[0] = algebraic_variables[6] u = nla_solve(objective_function_6, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[6] = u[0] + algebraic_variables[6] = u[0] def objective_function_7(u, f, data): @@ -243,7 +243,7 @@ def objective_function_7(u, f, data): rates[2] = u[0] - f[0] = rates[2]-(algebraicVariables[5]*(1.0-states[2])-algebraicVariables[6]*states[2])-0.0 + f[0] = rates[2]-(algebraic_variables[5]*(1.0-states[2])-algebraic_variables[6]*states[2])-0.0 def find_root_7(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): @@ -265,19 +265,19 @@ def objective_function_8(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[7] = u[0] + algebraic_variables[7] = u[0] - f[0] = algebraicVariables[7]-0.07*exp(states[0]/20.0)-0.0 + f[0] = algebraic_variables[7]-0.07*exp(states[0]/20.0)-0.0 def find_root_8(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[7] + u[0] = algebraic_variables[7] u = nla_solve(objective_function_8, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[7] = u[0] + algebraic_variables[7] = u[0] def objective_function_9(u, f, data): @@ -289,19 +289,19 @@ def objective_function_9(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[8] = u[0] + algebraic_variables[8] = u[0] - f[0] = algebraicVariables[8]-1.0/(exp((states[0]+30.0)/10.0)+1.0)-0.0 + f[0] = algebraic_variables[8]-1.0/(exp((states[0]+30.0)/10.0)+1.0)-0.0 def find_root_9(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[8] + u[0] = algebraic_variables[8] u = nla_solve(objective_function_9, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[8] = u[0] + algebraic_variables[8] = u[0] def objective_function_10(u, f, data): @@ -315,7 +315,7 @@ def objective_function_10(u, f, data): rates[1] = u[0] - f[0] = rates[1]-(algebraicVariables[7]*(1.0-states[1])-algebraicVariables[8]*states[1])-0.0 + f[0] = rates[1]-(algebraic_variables[7]*(1.0-states[1])-algebraic_variables[8]*states[1])-0.0 def find_root_10(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): @@ -337,19 +337,19 @@ def objective_function_11(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[2] = u[0] + algebraic_variables[2] = u[0] - f[0] = algebraicVariables[2]-constants[4]*pow(states[3], 4.0)*(states[0]-computed_constants[0])-0.0 + f[0] = algebraic_variables[2]-constants[4]*pow(states[3], 4.0)*(states[0]-computed_constants[0])-0.0 def find_root_11(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[2] + u[0] = algebraic_variables[2] u = nla_solve(objective_function_11, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[2] = u[0] + algebraic_variables[2] = u[0] def objective_function_12(u, f, data): @@ -361,19 +361,19 @@ def objective_function_12(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[9] = u[0] + algebraic_variables[9] = u[0] - f[0] = algebraicVariables[9]-0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0)-0.0 + f[0] = algebraic_variables[9]-0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0)-0.0 def find_root_12(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[9] + u[0] = algebraic_variables[9] u = nla_solve(objective_function_12, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[9] = u[0] + algebraic_variables[9] = u[0] def objective_function_13(u, f, data): @@ -385,19 +385,19 @@ def objective_function_13(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[10] = u[0] + algebraic_variables[10] = u[0] - f[0] = algebraicVariables[10]-0.125*exp(states[0]/80.0)-0.0 + f[0] = algebraic_variables[10]-0.125*exp(states[0]/80.0)-0.0 def find_root_13(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[10] + u[0] = algebraic_variables[10] u = nla_solve(objective_function_13, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[10] = u[0] + algebraic_variables[10] = u[0] def objective_function_14(u, f, data): @@ -411,7 +411,7 @@ def objective_function_14(u, f, data): rates[3] = u[0] - f[0] = rates[3]-(algebraicVariables[9]*(1.0-states[3])-algebraicVariables[10]*states[3])-0.0 + f[0] = rates[3]-(algebraic_variables[9]*(1.0-states[3])-algebraic_variables[10]*states[3])-0.0 def find_root_14(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): @@ -438,19 +438,19 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[2] = 0.3 constants[3] = 120.0 constants[4] = 36.0 - algebraicVariables[0] = 0.0 - algebraicVariables[1] = 0.0 - algebraicVariables[2] = 0.0 - algebraicVariables[3] = 0.0 - algebraicVariables[4] = 0.0 - algebraicVariables[6] = 0.0 - algebraicVariables[7] = 0.0 - algebraicVariables[8] = 0.0 - algebraicVariables[9] = 0.0 - algebraicVariables[10] = 0.0 - - -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): + algebraic_variables[0] = 0.0 + algebraic_variables[1] = 0.0 + algebraic_variables[2] = 0.0 + algebraic_variables[3] = 0.0 + algebraic_variables[4] = 0.0 + algebraic_variables[6] = 0.0 + algebraic_variables[7] = 0.0 + algebraic_variables[8] = 0.0 + algebraic_variables[9] = 0.0 + algebraic_variables[10] = 0.0 + + +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): computed_constants[0] = constants[1]+12.0 @@ -462,8 +462,8 @@ def compute_rates(voi, states, rates, constants, computed_constants, algebraic_v find_root_12(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_14(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_11(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) - algebraicVariables[5] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + algebraic_variables[5] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) find_root_1(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_6(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_7(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) @@ -478,8 +478,8 @@ def compute_variables(voi, states, rates, constants, computed_constants, algebra find_root_12(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_14(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_11(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) - algebraicVariables[5] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + algebraic_variables[5] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) find_root_1(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_4(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_6(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.algebraic.variables.c b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.algebraic.variables.c index 9f29da79c..d96a4ec10 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.algebraic.variables.c +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.algebraic.variables.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 4; @@ -529,7 +529,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * algebraicVariables[10] = 0.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { computedConstants[0] = constants[1]+12.0; } diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.algebraic.variables.h b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.algebraic.variables.h index 42166250c..fc447c7a3 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.algebraic.variables.h +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.algebraic.variables.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.algebraic.variables.py b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.algebraic.variables.py index a0d5e4799..8c2b31277 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.algebraic.variables.py +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.algebraic.variables.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 4 @@ -87,19 +87,19 @@ def objective_function_0(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[0] = u[0] + algebraic_variables[0] = u[0] - f[0] = algebraicVariables[0]-(-20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0)-0.0 + f[0] = algebraic_variables[0]-(-20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0)-0.0 def find_root_0(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[0] + u[0] = algebraic_variables[0] u = nla_solve(objective_function_0, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[0] = u[0] + algebraic_variables[0] = u[0] def objective_function_1(u, f, data): @@ -112,7 +112,7 @@ def objective_function_1(u, f, data): rates[0] = u[0] - f[0] = rates[0]-(-(-algebraicVariables[0]+algebraicVariables[3]+algebraicVariables[2]+algebraicVariables[1])/constants[0])-0.0 + f[0] = rates[0]-(-(-algebraic_variables[0]+algebraic_variables[3]+algebraic_variables[2]+algebraic_variables[1])/constants[0])-0.0 def find_root_1(voi, states, rates, constants, computed_constants, algebraic_variables): @@ -133,19 +133,19 @@ def objective_function_2(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[4] = u[0] + algebraic_variables[4] = u[0] - f[0] = algebraicVariables[4]-(constants[1]-10.613)-0.0 + f[0] = algebraic_variables[4]-(constants[1]-10.613)-0.0 def find_root_2(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[4] + u[0] = algebraic_variables[4] u = nla_solve(objective_function_2, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[4] = u[0] + algebraic_variables[4] = u[0] def objective_function_3(u, f, data): @@ -156,19 +156,19 @@ def objective_function_3(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[1] = u[0] + algebraic_variables[1] = u[0] - f[0] = algebraicVariables[1]-constants[2]*(states[0]-algebraicVariables[4])-0.0 + f[0] = algebraic_variables[1]-constants[2]*(states[0]-algebraic_variables[4])-0.0 def find_root_3(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[1] + u[0] = algebraic_variables[1] u = nla_solve(objective_function_3, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[1] = u[0] + algebraic_variables[1] = u[0] def objective_function_4(u, f, data): @@ -179,19 +179,19 @@ def objective_function_4(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[5] = u[0] + algebraic_variables[5] = u[0] - f[0] = algebraicVariables[5]-(constants[1]-115.0)-0.0 + f[0] = algebraic_variables[5]-(constants[1]-115.0)-0.0 def find_root_4(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[5] + u[0] = algebraic_variables[5] u = nla_solve(objective_function_4, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[5] = u[0] + algebraic_variables[5] = u[0] def objective_function_5(u, f, data): @@ -202,19 +202,19 @@ def objective_function_5(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[3] = u[0] + algebraic_variables[3] = u[0] - f[0] = algebraicVariables[3]-constants[3]*pow(states[2], 3.0)*states[1]*(states[0]-algebraicVariables[5])-0.0 + f[0] = algebraic_variables[3]-constants[3]*pow(states[2], 3.0)*states[1]*(states[0]-algebraic_variables[5])-0.0 def find_root_5(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[3] + u[0] = algebraic_variables[3] u = nla_solve(objective_function_5, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[3] = u[0] + algebraic_variables[3] = u[0] def objective_function_6(u, f, data): @@ -225,19 +225,19 @@ def objective_function_6(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[6] = u[0] + algebraic_variables[6] = u[0] - f[0] = algebraicVariables[6]-4.0*exp(states[0]/18.0)-0.0 + f[0] = algebraic_variables[6]-4.0*exp(states[0]/18.0)-0.0 def find_root_6(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[6] + u[0] = algebraic_variables[6] u = nla_solve(objective_function_6, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[6] = u[0] + algebraic_variables[6] = u[0] def objective_function_7(u, f, data): @@ -252,7 +252,7 @@ def objective_function_7(u, f, data): sodium_channel_m_gate_alpha_m = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - f[0] = rates[2]-(sodium_channel_m_gate_alpha_m*(1.0-states[2])-algebraicVariables[6]*states[2])-0.0 + f[0] = rates[2]-(sodium_channel_m_gate_alpha_m*(1.0-states[2])-algebraic_variables[6]*states[2])-0.0 def find_root_7(voi, states, rates, constants, computed_constants, algebraic_variables): @@ -273,19 +273,19 @@ def objective_function_8(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[7] = u[0] + algebraic_variables[7] = u[0] - f[0] = algebraicVariables[7]-0.07*exp(states[0]/20.0)-0.0 + f[0] = algebraic_variables[7]-0.07*exp(states[0]/20.0)-0.0 def find_root_8(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[7] + u[0] = algebraic_variables[7] u = nla_solve(objective_function_8, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[7] = u[0] + algebraic_variables[7] = u[0] def objective_function_9(u, f, data): @@ -296,19 +296,19 @@ def objective_function_9(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[8] = u[0] + algebraic_variables[8] = u[0] - f[0] = algebraicVariables[8]-1.0/(exp((states[0]+30.0)/10.0)+1.0)-0.0 + f[0] = algebraic_variables[8]-1.0/(exp((states[0]+30.0)/10.0)+1.0)-0.0 def find_root_9(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[8] + u[0] = algebraic_variables[8] u = nla_solve(objective_function_9, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[8] = u[0] + algebraic_variables[8] = u[0] def objective_function_10(u, f, data): @@ -321,7 +321,7 @@ def objective_function_10(u, f, data): rates[1] = u[0] - f[0] = rates[1]-(algebraicVariables[7]*(1.0-states[1])-algebraicVariables[8]*states[1])-0.0 + f[0] = rates[1]-(algebraic_variables[7]*(1.0-states[1])-algebraic_variables[8]*states[1])-0.0 def find_root_10(voi, states, rates, constants, computed_constants, algebraic_variables): @@ -342,19 +342,19 @@ def objective_function_11(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[2] = u[0] + algebraic_variables[2] = u[0] - f[0] = algebraicVariables[2]-constants[4]*pow(states[3], 4.0)*(states[0]-computed_constants[0])-0.0 + f[0] = algebraic_variables[2]-constants[4]*pow(states[3], 4.0)*(states[0]-computed_constants[0])-0.0 def find_root_11(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[2] + u[0] = algebraic_variables[2] u = nla_solve(objective_function_11, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[2] = u[0] + algebraic_variables[2] = u[0] def objective_function_12(u, f, data): @@ -365,19 +365,19 @@ def objective_function_12(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[9] = u[0] + algebraic_variables[9] = u[0] - f[0] = algebraicVariables[9]-0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0)-0.0 + f[0] = algebraic_variables[9]-0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0)-0.0 def find_root_12(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[9] + u[0] = algebraic_variables[9] u = nla_solve(objective_function_12, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[9] = u[0] + algebraic_variables[9] = u[0] def objective_function_13(u, f, data): @@ -388,19 +388,19 @@ def objective_function_13(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[10] = u[0] + algebraic_variables[10] = u[0] - f[0] = algebraicVariables[10]-0.125*exp(states[0]/80.0)-0.0 + f[0] = algebraic_variables[10]-0.125*exp(states[0]/80.0)-0.0 def find_root_13(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[10] + u[0] = algebraic_variables[10] u = nla_solve(objective_function_13, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[10] = u[0] + algebraic_variables[10] = u[0] def objective_function_14(u, f, data): @@ -413,7 +413,7 @@ def objective_function_14(u, f, data): rates[3] = u[0] - f[0] = rates[3]-(algebraicVariables[9]*(1.0-states[3])-algebraicVariables[10]*states[3])-0.0 + f[0] = rates[3]-(algebraic_variables[9]*(1.0-states[3])-algebraic_variables[10]*states[3])-0.0 def find_root_14(voi, states, rates, constants, computed_constants, algebraic_variables): @@ -440,20 +440,20 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[2] = 0.3 constants[3] = 120.0 constants[4] = 36.0 - algebraicVariables[0] = 0.0 - algebraicVariables[1] = 0.0 - algebraicVariables[2] = 0.0 - algebraicVariables[3] = 0.0 - algebraicVariables[4] = 0.0 - algebraicVariables[5] = 0.0 - algebraicVariables[6] = 0.0 - algebraicVariables[7] = 0.0 - algebraicVariables[8] = 0.0 - algebraicVariables[9] = 0.0 - algebraicVariables[10] = 0.0 - - -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): + algebraic_variables[0] = 0.0 + algebraic_variables[1] = 0.0 + algebraic_variables[2] = 0.0 + algebraic_variables[3] = 0.0 + algebraic_variables[4] = 0.0 + algebraic_variables[5] = 0.0 + algebraic_variables[6] = 0.0 + algebraic_variables[7] = 0.0 + algebraic_variables[8] = 0.0 + algebraic_variables[9] = 0.0 + algebraic_variables[10] = 0.0 + + +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): computed_constants[0] = constants[1]+12.0 diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.algebraic.variables.with.externals.c b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.algebraic.variables.with.externals.c index 2378daeb5..c3e26317a 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.algebraic.variables.with.externals.c +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.algebraic.variables.with.externals.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 4; @@ -531,7 +531,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * algebraicVariables[10] = 0.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { computedConstants[0] = constants[1]+12.0; } diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.algebraic.variables.with.externals.h b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.algebraic.variables.with.externals.h index ce6057728..79abbba9c 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.algebraic.variables.with.externals.h +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.algebraic.variables.with.externals.h @@ -37,6 +37,6 @@ void deleteArray(double *array); typedef double (* ExternalVariable)(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, size_t index); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.algebraic.variables.with.externals.py b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.algebraic.variables.with.externals.py index 1a6636938..22909c2ee 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.algebraic.variables.with.externals.py +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.algebraic.variables.with.externals.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 4 @@ -97,19 +97,19 @@ def objective_function_0(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[0] = u[0] + algebraic_variables[0] = u[0] - f[0] = algebraicVariables[0]-(-20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0)-0.0 + f[0] = algebraic_variables[0]-(-20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0)-0.0 def find_root_0(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[0] + u[0] = algebraic_variables[0] u = nla_solve(objective_function_0, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[0] = u[0] + algebraic_variables[0] = u[0] def objective_function_1(u, f, data): @@ -123,7 +123,7 @@ def objective_function_1(u, f, data): rates[0] = u[0] - f[0] = rates[0]-(-(-algebraicVariables[0]+externalVariables[0]+algebraicVariables[2]+algebraicVariables[1])/constants[0])-0.0 + f[0] = rates[0]-(-(-algebraic_variables[0]+external_variables[0]+algebraic_variables[2]+algebraic_variables[1])/constants[0])-0.0 def find_root_1(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): @@ -145,19 +145,19 @@ def objective_function_2(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[3] = u[0] + algebraic_variables[3] = u[0] - f[0] = algebraicVariables[3]-(constants[1]-10.613)-0.0 + f[0] = algebraic_variables[3]-(constants[1]-10.613)-0.0 def find_root_2(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[3] + u[0] = algebraic_variables[3] u = nla_solve(objective_function_2, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[3] = u[0] + algebraic_variables[3] = u[0] def objective_function_3(u, f, data): @@ -169,19 +169,19 @@ def objective_function_3(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[1] = u[0] + algebraic_variables[1] = u[0] - f[0] = algebraicVariables[1]-constants[2]*(states[0]-algebraicVariables[3])-0.0 + f[0] = algebraic_variables[1]-constants[2]*(states[0]-algebraic_variables[3])-0.0 def find_root_3(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[1] + u[0] = algebraic_variables[1] u = nla_solve(objective_function_3, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[1] = u[0] + algebraic_variables[1] = u[0] def objective_function_4(u, f, data): @@ -193,19 +193,19 @@ def objective_function_4(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[4] = u[0] + algebraic_variables[4] = u[0] - f[0] = algebraicVariables[4]-(constants[1]-115.0)-0.0 + f[0] = algebraic_variables[4]-(constants[1]-115.0)-0.0 def find_root_4(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[4] + u[0] = algebraic_variables[4] u = nla_solve(objective_function_4, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[4] = u[0] + algebraic_variables[4] = u[0] def objective_function_6(u, f, data): @@ -217,19 +217,19 @@ def objective_function_6(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[6] = u[0] + algebraic_variables[6] = u[0] - f[0] = algebraicVariables[6]-4.0*exp(states[0]/18.0)-0.0 + f[0] = algebraic_variables[6]-4.0*exp(states[0]/18.0)-0.0 def find_root_6(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[6] + u[0] = algebraic_variables[6] u = nla_solve(objective_function_6, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[6] = u[0] + algebraic_variables[6] = u[0] def objective_function_7(u, f, data): @@ -243,7 +243,7 @@ def objective_function_7(u, f, data): rates[2] = u[0] - f[0] = rates[2]-(algebraicVariables[5]*(1.0-states[2])-algebraicVariables[6]*states[2])-0.0 + f[0] = rates[2]-(algebraic_variables[5]*(1.0-states[2])-algebraic_variables[6]*states[2])-0.0 def find_root_7(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): @@ -265,19 +265,19 @@ def objective_function_8(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[7] = u[0] + algebraic_variables[7] = u[0] - f[0] = algebraicVariables[7]-0.07*exp(states[0]/20.0)-0.0 + f[0] = algebraic_variables[7]-0.07*exp(states[0]/20.0)-0.0 def find_root_8(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[7] + u[0] = algebraic_variables[7] u = nla_solve(objective_function_8, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[7] = u[0] + algebraic_variables[7] = u[0] def objective_function_9(u, f, data): @@ -289,19 +289,19 @@ def objective_function_9(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[8] = u[0] + algebraic_variables[8] = u[0] - f[0] = algebraicVariables[8]-1.0/(exp((states[0]+30.0)/10.0)+1.0)-0.0 + f[0] = algebraic_variables[8]-1.0/(exp((states[0]+30.0)/10.0)+1.0)-0.0 def find_root_9(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[8] + u[0] = algebraic_variables[8] u = nla_solve(objective_function_9, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[8] = u[0] + algebraic_variables[8] = u[0] def objective_function_10(u, f, data): @@ -315,7 +315,7 @@ def objective_function_10(u, f, data): rates[1] = u[0] - f[0] = rates[1]-(algebraicVariables[7]*(1.0-states[1])-algebraicVariables[8]*states[1])-0.0 + f[0] = rates[1]-(algebraic_variables[7]*(1.0-states[1])-algebraic_variables[8]*states[1])-0.0 def find_root_10(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): @@ -337,19 +337,19 @@ def objective_function_11(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[2] = u[0] + algebraic_variables[2] = u[0] - f[0] = algebraicVariables[2]-constants[4]*pow(states[3], 4.0)*(states[0]-computed_constants[0])-0.0 + f[0] = algebraic_variables[2]-constants[4]*pow(states[3], 4.0)*(states[0]-computed_constants[0])-0.0 def find_root_11(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[2] + u[0] = algebraic_variables[2] u = nla_solve(objective_function_11, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[2] = u[0] + algebraic_variables[2] = u[0] def objective_function_12(u, f, data): @@ -361,19 +361,19 @@ def objective_function_12(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[9] = u[0] + algebraic_variables[9] = u[0] - f[0] = algebraicVariables[9]-0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0)-0.0 + f[0] = algebraic_variables[9]-0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0)-0.0 def find_root_12(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[9] + u[0] = algebraic_variables[9] u = nla_solve(objective_function_12, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[9] = u[0] + algebraic_variables[9] = u[0] def objective_function_13(u, f, data): @@ -385,19 +385,19 @@ def objective_function_13(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[10] = u[0] + algebraic_variables[10] = u[0] - f[0] = algebraicVariables[10]-0.125*exp(states[0]/80.0)-0.0 + f[0] = algebraic_variables[10]-0.125*exp(states[0]/80.0)-0.0 def find_root_13(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[10] + u[0] = algebraic_variables[10] u = nla_solve(objective_function_13, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[10] = u[0] + algebraic_variables[10] = u[0] def objective_function_14(u, f, data): @@ -411,7 +411,7 @@ def objective_function_14(u, f, data): rates[3] = u[0] - f[0] = rates[3]-(algebraicVariables[9]*(1.0-states[3])-algebraicVariables[10]*states[3])-0.0 + f[0] = rates[3]-(algebraic_variables[9]*(1.0-states[3])-algebraic_variables[10]*states[3])-0.0 def find_root_14(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): @@ -438,19 +438,19 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[2] = 0.3 constants[3] = 120.0 constants[4] = 36.0 - algebraicVariables[0] = 0.0 - algebraicVariables[1] = 0.0 - algebraicVariables[2] = 0.0 - algebraicVariables[3] = 0.0 - algebraicVariables[4] = 0.0 - algebraicVariables[6] = 0.0 - algebraicVariables[7] = 0.0 - algebraicVariables[8] = 0.0 - algebraicVariables[9] = 0.0 - algebraicVariables[10] = 0.0 - - -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): + algebraic_variables[0] = 0.0 + algebraic_variables[1] = 0.0 + algebraic_variables[2] = 0.0 + algebraic_variables[3] = 0.0 + algebraic_variables[4] = 0.0 + algebraic_variables[6] = 0.0 + algebraic_variables[7] = 0.0 + algebraic_variables[8] = 0.0 + algebraic_variables[9] = 0.0 + algebraic_variables[10] = 0.0 + + +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): computed_constants[0] = constants[1]+12.0 @@ -462,8 +462,8 @@ def compute_rates(voi, states, rates, constants, computed_constants, algebraic_v find_root_12(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_14(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_11(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) - algebraicVariables[5] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + algebraic_variables[5] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) find_root_1(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_6(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_7(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) @@ -478,8 +478,8 @@ def compute_variables(voi, states, rates, constants, computed_constants, algebra find_root_12(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_14(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_11(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) - algebraicVariables[5] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + algebraic_variables[5] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) find_root_1(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_4(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_6(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.computed.constants.c b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.computed.constants.c index 30b1053df..d701421d7 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.computed.constants.c +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.computed.constants.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 4; @@ -529,7 +529,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * algebraicVariables[11] = 0.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.computed.constants.h b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.computed.constants.h index 42166250c..fc447c7a3 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.computed.constants.h +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.computed.constants.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.computed.constants.py b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.computed.constants.py index 8646765e4..f8f020686 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.computed.constants.py +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.computed.constants.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 4 @@ -87,19 +87,19 @@ def objective_function_0(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[0] = u[0] + algebraic_variables[0] = u[0] - f[0] = algebraicVariables[0]-(-20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0)-0.0 + f[0] = algebraic_variables[0]-(-20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0)-0.0 def find_root_0(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[0] + u[0] = algebraic_variables[0] u = nla_solve(objective_function_0, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[0] = u[0] + algebraic_variables[0] = u[0] def objective_function_1(u, f, data): @@ -112,7 +112,7 @@ def objective_function_1(u, f, data): rates[0] = u[0] - f[0] = rates[0]-(-(-algebraicVariables[0]+algebraicVariables[3]+algebraicVariables[2]+algebraicVariables[1])/constants[0])-0.0 + f[0] = rates[0]-(-(-algebraic_variables[0]+algebraic_variables[3]+algebraic_variables[2]+algebraic_variables[1])/constants[0])-0.0 def find_root_1(voi, states, rates, constants, computed_constants, algebraic_variables): @@ -133,19 +133,19 @@ def objective_function_2(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[4] = u[0] + algebraic_variables[4] = u[0] - f[0] = algebraicVariables[4]-(constants[1]-10.613)-0.0 + f[0] = algebraic_variables[4]-(constants[1]-10.613)-0.0 def find_root_2(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[4] + u[0] = algebraic_variables[4] u = nla_solve(objective_function_2, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[4] = u[0] + algebraic_variables[4] = u[0] def objective_function_3(u, f, data): @@ -156,19 +156,19 @@ def objective_function_3(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[1] = u[0] + algebraic_variables[1] = u[0] - f[0] = algebraicVariables[1]-constants[2]*(states[0]-algebraicVariables[4])-0.0 + f[0] = algebraic_variables[1]-constants[2]*(states[0]-algebraic_variables[4])-0.0 def find_root_3(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[1] + u[0] = algebraic_variables[1] u = nla_solve(objective_function_3, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[1] = u[0] + algebraic_variables[1] = u[0] def objective_function_4(u, f, data): @@ -179,19 +179,19 @@ def objective_function_4(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[5] = u[0] + algebraic_variables[5] = u[0] - f[0] = algebraicVariables[5]-(constants[1]-115.0)-0.0 + f[0] = algebraic_variables[5]-(constants[1]-115.0)-0.0 def find_root_4(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[5] + u[0] = algebraic_variables[5] u = nla_solve(objective_function_4, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[5] = u[0] + algebraic_variables[5] = u[0] def objective_function_5(u, f, data): @@ -202,19 +202,19 @@ def objective_function_5(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[3] = u[0] + algebraic_variables[3] = u[0] - f[0] = algebraicVariables[3]-constants[3]*pow(states[2], 3.0)*states[1]*(states[0]-algebraicVariables[5])-0.0 + f[0] = algebraic_variables[3]-constants[3]*pow(states[2], 3.0)*states[1]*(states[0]-algebraic_variables[5])-0.0 def find_root_5(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[3] + u[0] = algebraic_variables[3] u = nla_solve(objective_function_5, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[3] = u[0] + algebraic_variables[3] = u[0] def objective_function_6(u, f, data): @@ -225,19 +225,19 @@ def objective_function_6(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[7] = u[0] + algebraic_variables[7] = u[0] - f[0] = algebraicVariables[7]-4.0*exp(states[0]/18.0)-0.0 + f[0] = algebraic_variables[7]-4.0*exp(states[0]/18.0)-0.0 def find_root_6(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[7] + u[0] = algebraic_variables[7] u = nla_solve(objective_function_6, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[7] = u[0] + algebraic_variables[7] = u[0] def objective_function_7(u, f, data): @@ -250,7 +250,7 @@ def objective_function_7(u, f, data): rates[2] = u[0] - f[0] = rates[2]-(algebraicVariables[6]*(1.0-states[2])-algebraicVariables[7]*states[2])-0.0 + f[0] = rates[2]-(algebraic_variables[6]*(1.0-states[2])-algebraic_variables[7]*states[2])-0.0 def find_root_7(voi, states, rates, constants, computed_constants, algebraic_variables): @@ -271,19 +271,19 @@ def objective_function_8(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[8] = u[0] + algebraic_variables[8] = u[0] - f[0] = algebraicVariables[8]-0.07*exp(states[0]/20.0)-0.0 + f[0] = algebraic_variables[8]-0.07*exp(states[0]/20.0)-0.0 def find_root_8(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[8] + u[0] = algebraic_variables[8] u = nla_solve(objective_function_8, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[8] = u[0] + algebraic_variables[8] = u[0] def objective_function_9(u, f, data): @@ -294,19 +294,19 @@ def objective_function_9(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[9] = u[0] + algebraic_variables[9] = u[0] - f[0] = algebraicVariables[9]-1.0/(exp((states[0]+30.0)/10.0)+1.0)-0.0 + f[0] = algebraic_variables[9]-1.0/(exp((states[0]+30.0)/10.0)+1.0)-0.0 def find_root_9(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[9] + u[0] = algebraic_variables[9] u = nla_solve(objective_function_9, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[9] = u[0] + algebraic_variables[9] = u[0] def objective_function_10(u, f, data): @@ -319,7 +319,7 @@ def objective_function_10(u, f, data): rates[1] = u[0] - f[0] = rates[1]-(algebraicVariables[8]*(1.0-states[1])-algebraicVariables[9]*states[1])-0.0 + f[0] = rates[1]-(algebraic_variables[8]*(1.0-states[1])-algebraic_variables[9]*states[1])-0.0 def find_root_10(voi, states, rates, constants, computed_constants, algebraic_variables): @@ -340,21 +340,21 @@ def objective_function_11(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[2] = u[0] + algebraic_variables[2] = u[0] potassium_channel_E_K = constants[1]+12.0 - f[0] = algebraicVariables[2]-constants[4]*pow(states[3], 4.0)*(states[0]-potassium_channel_E_K)-0.0 + f[0] = algebraic_variables[2]-constants[4]*pow(states[3], 4.0)*(states[0]-potassium_channel_E_K)-0.0 def find_root_11(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[2] + u[0] = algebraic_variables[2] u = nla_solve(objective_function_11, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[2] = u[0] + algebraic_variables[2] = u[0] def objective_function_12(u, f, data): @@ -365,19 +365,19 @@ def objective_function_12(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[10] = u[0] + algebraic_variables[10] = u[0] - f[0] = algebraicVariables[10]-0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0)-0.0 + f[0] = algebraic_variables[10]-0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0)-0.0 def find_root_12(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[10] + u[0] = algebraic_variables[10] u = nla_solve(objective_function_12, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[10] = u[0] + algebraic_variables[10] = u[0] def objective_function_13(u, f, data): @@ -388,19 +388,19 @@ def objective_function_13(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[11] = u[0] + algebraic_variables[11] = u[0] - f[0] = algebraicVariables[11]-0.125*exp(states[0]/80.0)-0.0 + f[0] = algebraic_variables[11]-0.125*exp(states[0]/80.0)-0.0 def find_root_13(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[11] + u[0] = algebraic_variables[11] u = nla_solve(objective_function_13, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[11] = u[0] + algebraic_variables[11] = u[0] def objective_function_14(u, f, data): @@ -413,7 +413,7 @@ def objective_function_14(u, f, data): rates[3] = u[0] - f[0] = rates[3]-(algebraicVariables[10]*(1.0-states[3])-algebraicVariables[11]*states[3])-0.0 + f[0] = rates[3]-(algebraic_variables[10]*(1.0-states[3])-algebraic_variables[11]*states[3])-0.0 def find_root_14(voi, states, rates, constants, computed_constants, algebraic_variables): @@ -440,20 +440,20 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[2] = 0.3 constants[3] = 120.0 constants[4] = 36.0 - algebraicVariables[0] = 0.0 - algebraicVariables[1] = 0.0 - algebraicVariables[2] = 0.0 - algebraicVariables[3] = 0.0 - algebraicVariables[4] = 0.0 - algebraicVariables[5] = 0.0 - algebraicVariables[7] = 0.0 - algebraicVariables[8] = 0.0 - algebraicVariables[9] = 0.0 - algebraicVariables[10] = 0.0 - algebraicVariables[11] = 0.0 - - -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): + algebraic_variables[0] = 0.0 + algebraic_variables[1] = 0.0 + algebraic_variables[2] = 0.0 + algebraic_variables[3] = 0.0 + algebraic_variables[4] = 0.0 + algebraic_variables[5] = 0.0 + algebraic_variables[7] = 0.0 + algebraic_variables[8] = 0.0 + algebraic_variables[9] = 0.0 + algebraic_variables[10] = 0.0 + algebraic_variables[11] = 0.0 + + +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass @@ -468,7 +468,7 @@ def compute_rates(voi, states, rates, constants, computed_constants, algebraic_v find_root_9(voi, states, rates, constants, computed_constants, algebraic_variables) find_root_8(voi, states, rates, constants, computed_constants, algebraic_variables) find_root_10(voi, states, rates, constants, computed_constants, algebraic_variables) - algebraicVariables[6] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + algebraic_variables[6] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) find_root_6(voi, states, rates, constants, computed_constants, algebraic_variables) find_root_7(voi, states, rates, constants, computed_constants, algebraic_variables) find_root_4(voi, states, rates, constants, computed_constants, algebraic_variables) @@ -485,7 +485,7 @@ def compute_variables(voi, states, rates, constants, computed_constants, algebra find_root_9(voi, states, rates, constants, computed_constants, algebraic_variables) find_root_8(voi, states, rates, constants, computed_constants, algebraic_variables) find_root_10(voi, states, rates, constants, computed_constants, algebraic_variables) - algebraicVariables[6] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + algebraic_variables[6] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) find_root_6(voi, states, rates, constants, computed_constants, algebraic_variables) find_root_7(voi, states, rates, constants, computed_constants, algebraic_variables) find_root_5(voi, states, rates, constants, computed_constants, algebraic_variables) diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.computed.constants.with.externals.c b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.computed.constants.with.externals.c index 10a0dfc65..c9a0b6d60 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.computed.constants.with.externals.c +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.computed.constants.with.externals.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 4; @@ -531,7 +531,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * algebraicVariables[10] = 0.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { computedConstants[0] = constants[1]+12.0; } diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.computed.constants.with.externals.h b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.computed.constants.with.externals.h index ce6057728..79abbba9c 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.computed.constants.with.externals.h +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.computed.constants.with.externals.h @@ -37,6 +37,6 @@ void deleteArray(double *array); typedef double (* ExternalVariable)(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, size_t index); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.computed.constants.with.externals.py b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.computed.constants.with.externals.py index 1a6636938..22909c2ee 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.computed.constants.with.externals.py +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.computed.constants.with.externals.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 4 @@ -97,19 +97,19 @@ def objective_function_0(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[0] = u[0] + algebraic_variables[0] = u[0] - f[0] = algebraicVariables[0]-(-20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0)-0.0 + f[0] = algebraic_variables[0]-(-20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0)-0.0 def find_root_0(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[0] + u[0] = algebraic_variables[0] u = nla_solve(objective_function_0, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[0] = u[0] + algebraic_variables[0] = u[0] def objective_function_1(u, f, data): @@ -123,7 +123,7 @@ def objective_function_1(u, f, data): rates[0] = u[0] - f[0] = rates[0]-(-(-algebraicVariables[0]+externalVariables[0]+algebraicVariables[2]+algebraicVariables[1])/constants[0])-0.0 + f[0] = rates[0]-(-(-algebraic_variables[0]+external_variables[0]+algebraic_variables[2]+algebraic_variables[1])/constants[0])-0.0 def find_root_1(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): @@ -145,19 +145,19 @@ def objective_function_2(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[3] = u[0] + algebraic_variables[3] = u[0] - f[0] = algebraicVariables[3]-(constants[1]-10.613)-0.0 + f[0] = algebraic_variables[3]-(constants[1]-10.613)-0.0 def find_root_2(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[3] + u[0] = algebraic_variables[3] u = nla_solve(objective_function_2, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[3] = u[0] + algebraic_variables[3] = u[0] def objective_function_3(u, f, data): @@ -169,19 +169,19 @@ def objective_function_3(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[1] = u[0] + algebraic_variables[1] = u[0] - f[0] = algebraicVariables[1]-constants[2]*(states[0]-algebraicVariables[3])-0.0 + f[0] = algebraic_variables[1]-constants[2]*(states[0]-algebraic_variables[3])-0.0 def find_root_3(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[1] + u[0] = algebraic_variables[1] u = nla_solve(objective_function_3, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[1] = u[0] + algebraic_variables[1] = u[0] def objective_function_4(u, f, data): @@ -193,19 +193,19 @@ def objective_function_4(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[4] = u[0] + algebraic_variables[4] = u[0] - f[0] = algebraicVariables[4]-(constants[1]-115.0)-0.0 + f[0] = algebraic_variables[4]-(constants[1]-115.0)-0.0 def find_root_4(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[4] + u[0] = algebraic_variables[4] u = nla_solve(objective_function_4, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[4] = u[0] + algebraic_variables[4] = u[0] def objective_function_6(u, f, data): @@ -217,19 +217,19 @@ def objective_function_6(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[6] = u[0] + algebraic_variables[6] = u[0] - f[0] = algebraicVariables[6]-4.0*exp(states[0]/18.0)-0.0 + f[0] = algebraic_variables[6]-4.0*exp(states[0]/18.0)-0.0 def find_root_6(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[6] + u[0] = algebraic_variables[6] u = nla_solve(objective_function_6, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[6] = u[0] + algebraic_variables[6] = u[0] def objective_function_7(u, f, data): @@ -243,7 +243,7 @@ def objective_function_7(u, f, data): rates[2] = u[0] - f[0] = rates[2]-(algebraicVariables[5]*(1.0-states[2])-algebraicVariables[6]*states[2])-0.0 + f[0] = rates[2]-(algebraic_variables[5]*(1.0-states[2])-algebraic_variables[6]*states[2])-0.0 def find_root_7(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): @@ -265,19 +265,19 @@ def objective_function_8(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[7] = u[0] + algebraic_variables[7] = u[0] - f[0] = algebraicVariables[7]-0.07*exp(states[0]/20.0)-0.0 + f[0] = algebraic_variables[7]-0.07*exp(states[0]/20.0)-0.0 def find_root_8(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[7] + u[0] = algebraic_variables[7] u = nla_solve(objective_function_8, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[7] = u[0] + algebraic_variables[7] = u[0] def objective_function_9(u, f, data): @@ -289,19 +289,19 @@ def objective_function_9(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[8] = u[0] + algebraic_variables[8] = u[0] - f[0] = algebraicVariables[8]-1.0/(exp((states[0]+30.0)/10.0)+1.0)-0.0 + f[0] = algebraic_variables[8]-1.0/(exp((states[0]+30.0)/10.0)+1.0)-0.0 def find_root_9(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[8] + u[0] = algebraic_variables[8] u = nla_solve(objective_function_9, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[8] = u[0] + algebraic_variables[8] = u[0] def objective_function_10(u, f, data): @@ -315,7 +315,7 @@ def objective_function_10(u, f, data): rates[1] = u[0] - f[0] = rates[1]-(algebraicVariables[7]*(1.0-states[1])-algebraicVariables[8]*states[1])-0.0 + f[0] = rates[1]-(algebraic_variables[7]*(1.0-states[1])-algebraic_variables[8]*states[1])-0.0 def find_root_10(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): @@ -337,19 +337,19 @@ def objective_function_11(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[2] = u[0] + algebraic_variables[2] = u[0] - f[0] = algebraicVariables[2]-constants[4]*pow(states[3], 4.0)*(states[0]-computed_constants[0])-0.0 + f[0] = algebraic_variables[2]-constants[4]*pow(states[3], 4.0)*(states[0]-computed_constants[0])-0.0 def find_root_11(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[2] + u[0] = algebraic_variables[2] u = nla_solve(objective_function_11, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[2] = u[0] + algebraic_variables[2] = u[0] def objective_function_12(u, f, data): @@ -361,19 +361,19 @@ def objective_function_12(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[9] = u[0] + algebraic_variables[9] = u[0] - f[0] = algebraicVariables[9]-0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0)-0.0 + f[0] = algebraic_variables[9]-0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0)-0.0 def find_root_12(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[9] + u[0] = algebraic_variables[9] u = nla_solve(objective_function_12, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[9] = u[0] + algebraic_variables[9] = u[0] def objective_function_13(u, f, data): @@ -385,19 +385,19 @@ def objective_function_13(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[10] = u[0] + algebraic_variables[10] = u[0] - f[0] = algebraicVariables[10]-0.125*exp(states[0]/80.0)-0.0 + f[0] = algebraic_variables[10]-0.125*exp(states[0]/80.0)-0.0 def find_root_13(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[10] + u[0] = algebraic_variables[10] u = nla_solve(objective_function_13, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[10] = u[0] + algebraic_variables[10] = u[0] def objective_function_14(u, f, data): @@ -411,7 +411,7 @@ def objective_function_14(u, f, data): rates[3] = u[0] - f[0] = rates[3]-(algebraicVariables[9]*(1.0-states[3])-algebraicVariables[10]*states[3])-0.0 + f[0] = rates[3]-(algebraic_variables[9]*(1.0-states[3])-algebraic_variables[10]*states[3])-0.0 def find_root_14(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): @@ -438,19 +438,19 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[2] = 0.3 constants[3] = 120.0 constants[4] = 36.0 - algebraicVariables[0] = 0.0 - algebraicVariables[1] = 0.0 - algebraicVariables[2] = 0.0 - algebraicVariables[3] = 0.0 - algebraicVariables[4] = 0.0 - algebraicVariables[6] = 0.0 - algebraicVariables[7] = 0.0 - algebraicVariables[8] = 0.0 - algebraicVariables[9] = 0.0 - algebraicVariables[10] = 0.0 - - -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): + algebraic_variables[0] = 0.0 + algebraic_variables[1] = 0.0 + algebraic_variables[2] = 0.0 + algebraic_variables[3] = 0.0 + algebraic_variables[4] = 0.0 + algebraic_variables[6] = 0.0 + algebraic_variables[7] = 0.0 + algebraic_variables[8] = 0.0 + algebraic_variables[9] = 0.0 + algebraic_variables[10] = 0.0 + + +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): computed_constants[0] = constants[1]+12.0 @@ -462,8 +462,8 @@ def compute_rates(voi, states, rates, constants, computed_constants, algebraic_v find_root_12(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_14(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_11(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) - algebraicVariables[5] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + algebraic_variables[5] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) find_root_1(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_6(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_7(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) @@ -478,8 +478,8 @@ def compute_variables(voi, states, rates, constants, computed_constants, algebra find_root_12(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_14(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_11(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) - algebraicVariables[5] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + algebraic_variables[5] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) find_root_1(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_4(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_6(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.constants.c b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.constants.c index 684ff7842..9738a57b7 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.constants.c +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.constants.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 4; @@ -530,7 +530,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * algebraicVariables[11] = 0.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { double membrane_E_R = 0.0; computedConstants[0] = membrane_E_R+12.0; diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.constants.h b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.constants.h index 42166250c..fc447c7a3 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.constants.h +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.constants.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.constants.py b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.constants.py index a4f28ae36..a60852f2b 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.constants.py +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.constants.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 4 @@ -83,19 +83,19 @@ def objective_function_0(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[0] = u[0] + algebraic_variables[0] = u[0] - f[0] = algebraicVariables[0]-(-20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0)-0.0 + f[0] = algebraic_variables[0]-(-20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0)-0.0 def find_root_0(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[0] + u[0] = algebraic_variables[0] u = nla_solve(objective_function_0, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[0] = u[0] + algebraic_variables[0] = u[0] def objective_function_1(u, f, data): @@ -110,7 +110,7 @@ def objective_function_1(u, f, data): membrane_Cm = 1.0 - f[0] = rates[0]-(-(-algebraicVariables[0]+algebraicVariables[3]+algebraicVariables[2]+algebraicVariables[1])/membrane_Cm)-0.0 + f[0] = rates[0]-(-(-algebraic_variables[0]+algebraic_variables[3]+algebraic_variables[2]+algebraic_variables[1])/membrane_Cm)-0.0 def find_root_1(voi, states, rates, constants, computed_constants, algebraic_variables): @@ -131,21 +131,21 @@ def objective_function_2(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[4] = u[0] + algebraic_variables[4] = u[0] membrane_E_R = 0.0 - f[0] = algebraicVariables[4]-(membrane_E_R-10.613)-0.0 + f[0] = algebraic_variables[4]-(membrane_E_R-10.613)-0.0 def find_root_2(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[4] + u[0] = algebraic_variables[4] u = nla_solve(objective_function_2, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[4] = u[0] + algebraic_variables[4] = u[0] def objective_function_3(u, f, data): @@ -156,21 +156,21 @@ def objective_function_3(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[1] = u[0] + algebraic_variables[1] = u[0] leakage_current_g_L = 0.3 - f[0] = algebraicVariables[1]-leakage_current_g_L*(states[0]-algebraicVariables[4])-0.0 + f[0] = algebraic_variables[1]-leakage_current_g_L*(states[0]-algebraic_variables[4])-0.0 def find_root_3(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[1] + u[0] = algebraic_variables[1] u = nla_solve(objective_function_3, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[1] = u[0] + algebraic_variables[1] = u[0] def objective_function_4(u, f, data): @@ -181,21 +181,21 @@ def objective_function_4(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[5] = u[0] + algebraic_variables[5] = u[0] membrane_E_R = 0.0 - f[0] = algebraicVariables[5]-(membrane_E_R-115.0)-0.0 + f[0] = algebraic_variables[5]-(membrane_E_R-115.0)-0.0 def find_root_4(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[5] + u[0] = algebraic_variables[5] u = nla_solve(objective_function_4, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[5] = u[0] + algebraic_variables[5] = u[0] def objective_function_5(u, f, data): @@ -206,21 +206,21 @@ def objective_function_5(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[3] = u[0] + algebraic_variables[3] = u[0] sodium_channel_g_Na = 120.0 - f[0] = algebraicVariables[3]-sodium_channel_g_Na*pow(states[2], 3.0)*states[1]*(states[0]-algebraicVariables[5])-0.0 + f[0] = algebraic_variables[3]-sodium_channel_g_Na*pow(states[2], 3.0)*states[1]*(states[0]-algebraic_variables[5])-0.0 def find_root_5(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[3] + u[0] = algebraic_variables[3] u = nla_solve(objective_function_5, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[3] = u[0] + algebraic_variables[3] = u[0] def objective_function_6(u, f, data): @@ -231,19 +231,19 @@ def objective_function_6(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[7] = u[0] + algebraic_variables[7] = u[0] - f[0] = algebraicVariables[7]-4.0*exp(states[0]/18.0)-0.0 + f[0] = algebraic_variables[7]-4.0*exp(states[0]/18.0)-0.0 def find_root_6(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[7] + u[0] = algebraic_variables[7] u = nla_solve(objective_function_6, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[7] = u[0] + algebraic_variables[7] = u[0] def objective_function_7(u, f, data): @@ -256,7 +256,7 @@ def objective_function_7(u, f, data): rates[2] = u[0] - f[0] = rates[2]-(algebraicVariables[6]*(1.0-states[2])-algebraicVariables[7]*states[2])-0.0 + f[0] = rates[2]-(algebraic_variables[6]*(1.0-states[2])-algebraic_variables[7]*states[2])-0.0 def find_root_7(voi, states, rates, constants, computed_constants, algebraic_variables): @@ -277,19 +277,19 @@ def objective_function_8(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[8] = u[0] + algebraic_variables[8] = u[0] - f[0] = algebraicVariables[8]-0.07*exp(states[0]/20.0)-0.0 + f[0] = algebraic_variables[8]-0.07*exp(states[0]/20.0)-0.0 def find_root_8(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[8] + u[0] = algebraic_variables[8] u = nla_solve(objective_function_8, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[8] = u[0] + algebraic_variables[8] = u[0] def objective_function_9(u, f, data): @@ -300,19 +300,19 @@ def objective_function_9(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[9] = u[0] + algebraic_variables[9] = u[0] - f[0] = algebraicVariables[9]-1.0/(exp((states[0]+30.0)/10.0)+1.0)-0.0 + f[0] = algebraic_variables[9]-1.0/(exp((states[0]+30.0)/10.0)+1.0)-0.0 def find_root_9(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[9] + u[0] = algebraic_variables[9] u = nla_solve(objective_function_9, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[9] = u[0] + algebraic_variables[9] = u[0] def objective_function_10(u, f, data): @@ -325,7 +325,7 @@ def objective_function_10(u, f, data): rates[1] = u[0] - f[0] = rates[1]-(algebraicVariables[8]*(1.0-states[1])-algebraicVariables[9]*states[1])-0.0 + f[0] = rates[1]-(algebraic_variables[8]*(1.0-states[1])-algebraic_variables[9]*states[1])-0.0 def find_root_10(voi, states, rates, constants, computed_constants, algebraic_variables): @@ -346,21 +346,21 @@ def objective_function_11(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[2] = u[0] + algebraic_variables[2] = u[0] potassium_channel_g_K = 36.0 - f[0] = algebraicVariables[2]-potassium_channel_g_K*pow(states[3], 4.0)*(states[0]-computed_constants[0])-0.0 + f[0] = algebraic_variables[2]-potassium_channel_g_K*pow(states[3], 4.0)*(states[0]-computed_constants[0])-0.0 def find_root_11(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[2] + u[0] = algebraic_variables[2] u = nla_solve(objective_function_11, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[2] = u[0] + algebraic_variables[2] = u[0] def objective_function_12(u, f, data): @@ -371,19 +371,19 @@ def objective_function_12(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[10] = u[0] + algebraic_variables[10] = u[0] - f[0] = algebraicVariables[10]-0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0)-0.0 + f[0] = algebraic_variables[10]-0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0)-0.0 def find_root_12(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[10] + u[0] = algebraic_variables[10] u = nla_solve(objective_function_12, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[10] = u[0] + algebraic_variables[10] = u[0] def objective_function_13(u, f, data): @@ -394,19 +394,19 @@ def objective_function_13(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[11] = u[0] + algebraic_variables[11] = u[0] - f[0] = algebraicVariables[11]-0.125*exp(states[0]/80.0)-0.0 + f[0] = algebraic_variables[11]-0.125*exp(states[0]/80.0)-0.0 def find_root_13(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[11] + u[0] = algebraic_variables[11] u = nla_solve(objective_function_13, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[11] = u[0] + algebraic_variables[11] = u[0] def objective_function_14(u, f, data): @@ -419,7 +419,7 @@ def objective_function_14(u, f, data): rates[3] = u[0] - f[0] = rates[3]-(algebraicVariables[10]*(1.0-states[3])-algebraicVariables[11]*states[3])-0.0 + f[0] = rates[3]-(algebraic_variables[10]*(1.0-states[3])-algebraic_variables[11]*states[3])-0.0 def find_root_14(voi, states, rates, constants, computed_constants, algebraic_variables): @@ -441,20 +441,20 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va rates[1] = 0.0 rates[2] = 0.0 rates[3] = 0.0 - algebraicVariables[0] = 0.0 - algebraicVariables[1] = 0.0 - algebraicVariables[2] = 0.0 - algebraicVariables[3] = 0.0 - algebraicVariables[4] = 0.0 - algebraicVariables[5] = 0.0 - algebraicVariables[7] = 0.0 - algebraicVariables[8] = 0.0 - algebraicVariables[9] = 0.0 - algebraicVariables[10] = 0.0 - algebraicVariables[11] = 0.0 - - -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): + algebraic_variables[0] = 0.0 + algebraic_variables[1] = 0.0 + algebraic_variables[2] = 0.0 + algebraic_variables[3] = 0.0 + algebraic_variables[4] = 0.0 + algebraic_variables[5] = 0.0 + algebraic_variables[7] = 0.0 + algebraic_variables[8] = 0.0 + algebraic_variables[9] = 0.0 + algebraic_variables[10] = 0.0 + algebraic_variables[11] = 0.0 + + +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): membrane_E_R = 0.0 computed_constants[0] = membrane_E_R+12.0 @@ -470,7 +470,7 @@ def compute_rates(voi, states, rates, constants, computed_constants, algebraic_v find_root_9(voi, states, rates, constants, computed_constants, algebraic_variables) find_root_8(voi, states, rates, constants, computed_constants, algebraic_variables) find_root_10(voi, states, rates, constants, computed_constants, algebraic_variables) - algebraicVariables[6] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + algebraic_variables[6] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) find_root_6(voi, states, rates, constants, computed_constants, algebraic_variables) find_root_7(voi, states, rates, constants, computed_constants, algebraic_variables) find_root_4(voi, states, rates, constants, computed_constants, algebraic_variables) @@ -487,7 +487,7 @@ def compute_variables(voi, states, rates, constants, computed_constants, algebra find_root_9(voi, states, rates, constants, computed_constants, algebraic_variables) find_root_8(voi, states, rates, constants, computed_constants, algebraic_variables) find_root_10(voi, states, rates, constants, computed_constants, algebraic_variables) - algebraicVariables[6] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + algebraic_variables[6] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) find_root_6(voi, states, rates, constants, computed_constants, algebraic_variables) find_root_7(voi, states, rates, constants, computed_constants, algebraic_variables) find_root_5(voi, states, rates, constants, computed_constants, algebraic_variables) diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.constants.with.externals.c b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.constants.with.externals.c index 402b069e4..dc9238386 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.constants.with.externals.c +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.constants.with.externals.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 4; @@ -531,7 +531,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * algebraicVariables[10] = 0.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { double membrane_E_R = 0.0; computedConstants[0] = membrane_E_R+12.0; diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.constants.with.externals.h b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.constants.with.externals.h index ce6057728..79abbba9c 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.constants.with.externals.h +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.constants.with.externals.h @@ -37,6 +37,6 @@ void deleteArray(double *array); typedef double (* ExternalVariable)(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, size_t index); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.constants.with.externals.py b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.constants.with.externals.py index 2ba6ac032..6b659adcd 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.constants.with.externals.py +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.constants.with.externals.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 4 @@ -93,19 +93,19 @@ def objective_function_0(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[0] = u[0] + algebraic_variables[0] = u[0] - f[0] = algebraicVariables[0]-(-20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0)-0.0 + f[0] = algebraic_variables[0]-(-20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0)-0.0 def find_root_0(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[0] + u[0] = algebraic_variables[0] u = nla_solve(objective_function_0, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[0] = u[0] + algebraic_variables[0] = u[0] def objective_function_1(u, f, data): @@ -119,7 +119,7 @@ def objective_function_1(u, f, data): rates[0] = u[0] - f[0] = rates[0]-(-(-algebraicVariables[0]+externalVariables[0]+algebraicVariables[2]+algebraicVariables[1])/constants[0])-0.0 + f[0] = rates[0]-(-(-algebraic_variables[0]+external_variables[0]+algebraic_variables[2]+algebraic_variables[1])/constants[0])-0.0 def find_root_1(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): @@ -141,21 +141,21 @@ def objective_function_2(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[3] = u[0] + algebraic_variables[3] = u[0] membrane_E_R = 0.0 - f[0] = algebraicVariables[3]-(membrane_E_R-10.613)-0.0 + f[0] = algebraic_variables[3]-(membrane_E_R-10.613)-0.0 def find_root_2(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[3] + u[0] = algebraic_variables[3] u = nla_solve(objective_function_2, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[3] = u[0] + algebraic_variables[3] = u[0] def objective_function_3(u, f, data): @@ -167,21 +167,21 @@ def objective_function_3(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[1] = u[0] + algebraic_variables[1] = u[0] leakage_current_g_L = 0.3 - f[0] = algebraicVariables[1]-leakage_current_g_L*(states[0]-algebraicVariables[3])-0.0 + f[0] = algebraic_variables[1]-leakage_current_g_L*(states[0]-algebraic_variables[3])-0.0 def find_root_3(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[1] + u[0] = algebraic_variables[1] u = nla_solve(objective_function_3, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[1] = u[0] + algebraic_variables[1] = u[0] def objective_function_4(u, f, data): @@ -193,21 +193,21 @@ def objective_function_4(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[4] = u[0] + algebraic_variables[4] = u[0] membrane_E_R = 0.0 - f[0] = algebraicVariables[4]-(membrane_E_R-115.0)-0.0 + f[0] = algebraic_variables[4]-(membrane_E_R-115.0)-0.0 def find_root_4(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[4] + u[0] = algebraic_variables[4] u = nla_solve(objective_function_4, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[4] = u[0] + algebraic_variables[4] = u[0] def objective_function_6(u, f, data): @@ -219,19 +219,19 @@ def objective_function_6(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[6] = u[0] + algebraic_variables[6] = u[0] - f[0] = algebraicVariables[6]-4.0*exp(states[0]/18.0)-0.0 + f[0] = algebraic_variables[6]-4.0*exp(states[0]/18.0)-0.0 def find_root_6(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[6] + u[0] = algebraic_variables[6] u = nla_solve(objective_function_6, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[6] = u[0] + algebraic_variables[6] = u[0] def objective_function_7(u, f, data): @@ -245,7 +245,7 @@ def objective_function_7(u, f, data): rates[2] = u[0] - f[0] = rates[2]-(algebraicVariables[5]*(1.0-states[2])-algebraicVariables[6]*states[2])-0.0 + f[0] = rates[2]-(algebraic_variables[5]*(1.0-states[2])-algebraic_variables[6]*states[2])-0.0 def find_root_7(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): @@ -267,19 +267,19 @@ def objective_function_8(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[7] = u[0] + algebraic_variables[7] = u[0] - f[0] = algebraicVariables[7]-0.07*exp(states[0]/20.0)-0.0 + f[0] = algebraic_variables[7]-0.07*exp(states[0]/20.0)-0.0 def find_root_8(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[7] + u[0] = algebraic_variables[7] u = nla_solve(objective_function_8, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[7] = u[0] + algebraic_variables[7] = u[0] def objective_function_9(u, f, data): @@ -291,19 +291,19 @@ def objective_function_9(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[8] = u[0] + algebraic_variables[8] = u[0] - f[0] = algebraicVariables[8]-1.0/(exp((states[0]+30.0)/10.0)+1.0)-0.0 + f[0] = algebraic_variables[8]-1.0/(exp((states[0]+30.0)/10.0)+1.0)-0.0 def find_root_9(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[8] + u[0] = algebraic_variables[8] u = nla_solve(objective_function_9, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[8] = u[0] + algebraic_variables[8] = u[0] def objective_function_10(u, f, data): @@ -317,7 +317,7 @@ def objective_function_10(u, f, data): rates[1] = u[0] - f[0] = rates[1]-(algebraicVariables[7]*(1.0-states[1])-algebraicVariables[8]*states[1])-0.0 + f[0] = rates[1]-(algebraic_variables[7]*(1.0-states[1])-algebraic_variables[8]*states[1])-0.0 def find_root_10(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): @@ -339,21 +339,21 @@ def objective_function_11(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[2] = u[0] + algebraic_variables[2] = u[0] potassium_channel_g_K = 36.0 - f[0] = algebraicVariables[2]-potassium_channel_g_K*pow(states[3], 4.0)*(states[0]-computed_constants[0])-0.0 + f[0] = algebraic_variables[2]-potassium_channel_g_K*pow(states[3], 4.0)*(states[0]-computed_constants[0])-0.0 def find_root_11(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[2] + u[0] = algebraic_variables[2] u = nla_solve(objective_function_11, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[2] = u[0] + algebraic_variables[2] = u[0] def objective_function_12(u, f, data): @@ -365,19 +365,19 @@ def objective_function_12(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[9] = u[0] + algebraic_variables[9] = u[0] - f[0] = algebraicVariables[9]-0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0)-0.0 + f[0] = algebraic_variables[9]-0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0)-0.0 def find_root_12(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[9] + u[0] = algebraic_variables[9] u = nla_solve(objective_function_12, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[9] = u[0] + algebraic_variables[9] = u[0] def objective_function_13(u, f, data): @@ -389,19 +389,19 @@ def objective_function_13(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[10] = u[0] + algebraic_variables[10] = u[0] - f[0] = algebraicVariables[10]-0.125*exp(states[0]/80.0)-0.0 + f[0] = algebraic_variables[10]-0.125*exp(states[0]/80.0)-0.0 def find_root_13(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[10] + u[0] = algebraic_variables[10] u = nla_solve(objective_function_13, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[10] = u[0] + algebraic_variables[10] = u[0] def objective_function_14(u, f, data): @@ -415,7 +415,7 @@ def objective_function_14(u, f, data): rates[3] = u[0] - f[0] = rates[3]-(algebraicVariables[9]*(1.0-states[3])-algebraicVariables[10]*states[3])-0.0 + f[0] = rates[3]-(algebraic_variables[9]*(1.0-states[3])-algebraic_variables[10]*states[3])-0.0 def find_root_14(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): @@ -438,19 +438,19 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va rates[2] = 0.0 rates[3] = 0.0 constants[0] = 1.0 - algebraicVariables[0] = 0.0 - algebraicVariables[1] = 0.0 - algebraicVariables[2] = 0.0 - algebraicVariables[3] = 0.0 - algebraicVariables[4] = 0.0 - algebraicVariables[6] = 0.0 - algebraicVariables[7] = 0.0 - algebraicVariables[8] = 0.0 - algebraicVariables[9] = 0.0 - algebraicVariables[10] = 0.0 - - -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): + algebraic_variables[0] = 0.0 + algebraic_variables[1] = 0.0 + algebraic_variables[2] = 0.0 + algebraic_variables[3] = 0.0 + algebraic_variables[4] = 0.0 + algebraic_variables[6] = 0.0 + algebraic_variables[7] = 0.0 + algebraic_variables[8] = 0.0 + algebraic_variables[9] = 0.0 + algebraic_variables[10] = 0.0 + + +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): membrane_E_R = 0.0 computed_constants[0] = membrane_E_R+12.0 @@ -463,8 +463,8 @@ def compute_rates(voi, states, rates, constants, computed_constants, algebraic_v find_root_12(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_14(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_11(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) - algebraicVariables[5] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + algebraic_variables[5] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) find_root_1(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_6(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_7(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) @@ -479,8 +479,8 @@ def compute_variables(voi, states, rates, constants, computed_constants, algebra find_root_12(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_14(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_11(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) - algebraicVariables[5] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + algebraic_variables[5] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) find_root_1(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_4(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_6(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.variables.c b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.variables.c index 7c27928bf..baea5e9a8 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.variables.c +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.variables.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 4; @@ -532,7 +532,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * algebraicVariables[10] = 0.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.variables.h b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.variables.h index 42166250c..fc447c7a3 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.variables.h +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.variables.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.variables.py b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.variables.py index c45b1acbe..ec50fce6b 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.variables.py +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.variables.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 4 @@ -81,19 +81,19 @@ def objective_function_0(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[0] = u[0] + algebraic_variables[0] = u[0] - f[0] = algebraicVariables[0]-(-20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0)-0.0 + f[0] = algebraic_variables[0]-(-20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0)-0.0 def find_root_0(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[0] + u[0] = algebraic_variables[0] u = nla_solve(objective_function_0, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[0] = u[0] + algebraic_variables[0] = u[0] def objective_function_1(u, f, data): @@ -108,7 +108,7 @@ def objective_function_1(u, f, data): membrane_Cm = 1.0 - f[0] = rates[0]-(-(-algebraicVariables[0]+algebraicVariables[3]+algebraicVariables[2]+algebraicVariables[1])/membrane_Cm)-0.0 + f[0] = rates[0]-(-(-algebraic_variables[0]+algebraic_variables[3]+algebraic_variables[2]+algebraic_variables[1])/membrane_Cm)-0.0 def find_root_1(voi, states, rates, constants, computed_constants, algebraic_variables): @@ -129,21 +129,21 @@ def objective_function_2(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[4] = u[0] + algebraic_variables[4] = u[0] membrane_E_R = 0.0 - f[0] = algebraicVariables[4]-(membrane_E_R-10.613)-0.0 + f[0] = algebraic_variables[4]-(membrane_E_R-10.613)-0.0 def find_root_2(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[4] + u[0] = algebraic_variables[4] u = nla_solve(objective_function_2, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[4] = u[0] + algebraic_variables[4] = u[0] def objective_function_3(u, f, data): @@ -154,21 +154,21 @@ def objective_function_3(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[1] = u[0] + algebraic_variables[1] = u[0] leakage_current_g_L = 0.3 - f[0] = algebraicVariables[1]-leakage_current_g_L*(states[0]-algebraicVariables[4])-0.0 + f[0] = algebraic_variables[1]-leakage_current_g_L*(states[0]-algebraic_variables[4])-0.0 def find_root_3(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[1] + u[0] = algebraic_variables[1] u = nla_solve(objective_function_3, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[1] = u[0] + algebraic_variables[1] = u[0] def objective_function_4(u, f, data): @@ -179,21 +179,21 @@ def objective_function_4(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[5] = u[0] + algebraic_variables[5] = u[0] membrane_E_R = 0.0 - f[0] = algebraicVariables[5]-(membrane_E_R-115.0)-0.0 + f[0] = algebraic_variables[5]-(membrane_E_R-115.0)-0.0 def find_root_4(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[5] + u[0] = algebraic_variables[5] u = nla_solve(objective_function_4, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[5] = u[0] + algebraic_variables[5] = u[0] def objective_function_5(u, f, data): @@ -204,21 +204,21 @@ def objective_function_5(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[3] = u[0] + algebraic_variables[3] = u[0] sodium_channel_g_Na = 120.0 - f[0] = algebraicVariables[3]-sodium_channel_g_Na*pow(states[2], 3.0)*states[1]*(states[0]-algebraicVariables[5])-0.0 + f[0] = algebraic_variables[3]-sodium_channel_g_Na*pow(states[2], 3.0)*states[1]*(states[0]-algebraic_variables[5])-0.0 def find_root_5(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[3] + u[0] = algebraic_variables[3] u = nla_solve(objective_function_5, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[3] = u[0] + algebraic_variables[3] = u[0] def objective_function_6(u, f, data): @@ -229,19 +229,19 @@ def objective_function_6(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[6] = u[0] + algebraic_variables[6] = u[0] - f[0] = algebraicVariables[6]-4.0*exp(states[0]/18.0)-0.0 + f[0] = algebraic_variables[6]-4.0*exp(states[0]/18.0)-0.0 def find_root_6(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[6] + u[0] = algebraic_variables[6] u = nla_solve(objective_function_6, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[6] = u[0] + algebraic_variables[6] = u[0] def objective_function_7(u, f, data): @@ -256,7 +256,7 @@ def objective_function_7(u, f, data): sodium_channel_m_gate_alpha_m = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - f[0] = rates[2]-(sodium_channel_m_gate_alpha_m*(1.0-states[2])-algebraicVariables[6]*states[2])-0.0 + f[0] = rates[2]-(sodium_channel_m_gate_alpha_m*(1.0-states[2])-algebraic_variables[6]*states[2])-0.0 def find_root_7(voi, states, rates, constants, computed_constants, algebraic_variables): @@ -277,19 +277,19 @@ def objective_function_8(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[7] = u[0] + algebraic_variables[7] = u[0] - f[0] = algebraicVariables[7]-0.07*exp(states[0]/20.0)-0.0 + f[0] = algebraic_variables[7]-0.07*exp(states[0]/20.0)-0.0 def find_root_8(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[7] + u[0] = algebraic_variables[7] u = nla_solve(objective_function_8, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[7] = u[0] + algebraic_variables[7] = u[0] def objective_function_9(u, f, data): @@ -300,19 +300,19 @@ def objective_function_9(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[8] = u[0] + algebraic_variables[8] = u[0] - f[0] = algebraicVariables[8]-1.0/(exp((states[0]+30.0)/10.0)+1.0)-0.0 + f[0] = algebraic_variables[8]-1.0/(exp((states[0]+30.0)/10.0)+1.0)-0.0 def find_root_9(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[8] + u[0] = algebraic_variables[8] u = nla_solve(objective_function_9, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[8] = u[0] + algebraic_variables[8] = u[0] def objective_function_10(u, f, data): @@ -325,7 +325,7 @@ def objective_function_10(u, f, data): rates[1] = u[0] - f[0] = rates[1]-(algebraicVariables[7]*(1.0-states[1])-algebraicVariables[8]*states[1])-0.0 + f[0] = rates[1]-(algebraic_variables[7]*(1.0-states[1])-algebraic_variables[8]*states[1])-0.0 def find_root_10(voi, states, rates, constants, computed_constants, algebraic_variables): @@ -346,23 +346,23 @@ def objective_function_11(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[2] = u[0] + algebraic_variables[2] = u[0] potassium_channel_g_K = 36.0 membrane_E_R = 0.0 potassium_channel_E_K = membrane_E_R+12.0 - f[0] = algebraicVariables[2]-potassium_channel_g_K*pow(states[3], 4.0)*(states[0]-potassium_channel_E_K)-0.0 + f[0] = algebraic_variables[2]-potassium_channel_g_K*pow(states[3], 4.0)*(states[0]-potassium_channel_E_K)-0.0 def find_root_11(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[2] + u[0] = algebraic_variables[2] u = nla_solve(objective_function_11, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[2] = u[0] + algebraic_variables[2] = u[0] def objective_function_12(u, f, data): @@ -373,19 +373,19 @@ def objective_function_12(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[9] = u[0] + algebraic_variables[9] = u[0] - f[0] = algebraicVariables[9]-0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0)-0.0 + f[0] = algebraic_variables[9]-0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0)-0.0 def find_root_12(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[9] + u[0] = algebraic_variables[9] u = nla_solve(objective_function_12, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[9] = u[0] + algebraic_variables[9] = u[0] def objective_function_13(u, f, data): @@ -396,19 +396,19 @@ def objective_function_13(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[10] = u[0] + algebraic_variables[10] = u[0] - f[0] = algebraicVariables[10]-0.125*exp(states[0]/80.0)-0.0 + f[0] = algebraic_variables[10]-0.125*exp(states[0]/80.0)-0.0 def find_root_13(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[10] + u[0] = algebraic_variables[10] u = nla_solve(objective_function_13, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[10] = u[0] + algebraic_variables[10] = u[0] def objective_function_14(u, f, data): @@ -421,7 +421,7 @@ def objective_function_14(u, f, data): rates[3] = u[0] - f[0] = rates[3]-(algebraicVariables[9]*(1.0-states[3])-algebraicVariables[10]*states[3])-0.0 + f[0] = rates[3]-(algebraic_variables[9]*(1.0-states[3])-algebraic_variables[10]*states[3])-0.0 def find_root_14(voi, states, rates, constants, computed_constants, algebraic_variables): @@ -443,20 +443,20 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va rates[1] = 0.0 rates[2] = 0.0 rates[3] = 0.0 - algebraicVariables[0] = 0.0 - algebraicVariables[1] = 0.0 - algebraicVariables[2] = 0.0 - algebraicVariables[3] = 0.0 - algebraicVariables[4] = 0.0 - algebraicVariables[5] = 0.0 - algebraicVariables[6] = 0.0 - algebraicVariables[7] = 0.0 - algebraicVariables[8] = 0.0 - algebraicVariables[9] = 0.0 - algebraicVariables[10] = 0.0 - - -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): + algebraic_variables[0] = 0.0 + algebraic_variables[1] = 0.0 + algebraic_variables[2] = 0.0 + algebraic_variables[3] = 0.0 + algebraic_variables[4] = 0.0 + algebraic_variables[5] = 0.0 + algebraic_variables[6] = 0.0 + algebraic_variables[7] = 0.0 + algebraic_variables[8] = 0.0 + algebraic_variables[9] = 0.0 + algebraic_variables[10] = 0.0 + + +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.variables.with.externals.c b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.variables.with.externals.c index 01a666804..c1aa4c9f6 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.variables.with.externals.c +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.variables.with.externals.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 4; @@ -531,7 +531,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * algebraicVariables[10] = 0.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { double membrane_E_R = 0.0; computedConstants[0] = membrane_E_R+12.0; diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.variables.with.externals.h b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.variables.with.externals.h index ce6057728..79abbba9c 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.variables.with.externals.h +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.variables.with.externals.h @@ -37,6 +37,6 @@ void deleteArray(double *array); typedef double (* ExternalVariable)(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, size_t index); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.variables.with.externals.py b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.variables.with.externals.py index 2ba6ac032..6b659adcd 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.variables.with.externals.py +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.for.tracking.untracked.variables.with.externals.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 4 @@ -93,19 +93,19 @@ def objective_function_0(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[0] = u[0] + algebraic_variables[0] = u[0] - f[0] = algebraicVariables[0]-(-20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0)-0.0 + f[0] = algebraic_variables[0]-(-20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0)-0.0 def find_root_0(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[0] + u[0] = algebraic_variables[0] u = nla_solve(objective_function_0, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[0] = u[0] + algebraic_variables[0] = u[0] def objective_function_1(u, f, data): @@ -119,7 +119,7 @@ def objective_function_1(u, f, data): rates[0] = u[0] - f[0] = rates[0]-(-(-algebraicVariables[0]+externalVariables[0]+algebraicVariables[2]+algebraicVariables[1])/constants[0])-0.0 + f[0] = rates[0]-(-(-algebraic_variables[0]+external_variables[0]+algebraic_variables[2]+algebraic_variables[1])/constants[0])-0.0 def find_root_1(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): @@ -141,21 +141,21 @@ def objective_function_2(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[3] = u[0] + algebraic_variables[3] = u[0] membrane_E_R = 0.0 - f[0] = algebraicVariables[3]-(membrane_E_R-10.613)-0.0 + f[0] = algebraic_variables[3]-(membrane_E_R-10.613)-0.0 def find_root_2(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[3] + u[0] = algebraic_variables[3] u = nla_solve(objective_function_2, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[3] = u[0] + algebraic_variables[3] = u[0] def objective_function_3(u, f, data): @@ -167,21 +167,21 @@ def objective_function_3(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[1] = u[0] + algebraic_variables[1] = u[0] leakage_current_g_L = 0.3 - f[0] = algebraicVariables[1]-leakage_current_g_L*(states[0]-algebraicVariables[3])-0.0 + f[0] = algebraic_variables[1]-leakage_current_g_L*(states[0]-algebraic_variables[3])-0.0 def find_root_3(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[1] + u[0] = algebraic_variables[1] u = nla_solve(objective_function_3, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[1] = u[0] + algebraic_variables[1] = u[0] def objective_function_4(u, f, data): @@ -193,21 +193,21 @@ def objective_function_4(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[4] = u[0] + algebraic_variables[4] = u[0] membrane_E_R = 0.0 - f[0] = algebraicVariables[4]-(membrane_E_R-115.0)-0.0 + f[0] = algebraic_variables[4]-(membrane_E_R-115.0)-0.0 def find_root_4(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[4] + u[0] = algebraic_variables[4] u = nla_solve(objective_function_4, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[4] = u[0] + algebraic_variables[4] = u[0] def objective_function_6(u, f, data): @@ -219,19 +219,19 @@ def objective_function_6(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[6] = u[0] + algebraic_variables[6] = u[0] - f[0] = algebraicVariables[6]-4.0*exp(states[0]/18.0)-0.0 + f[0] = algebraic_variables[6]-4.0*exp(states[0]/18.0)-0.0 def find_root_6(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[6] + u[0] = algebraic_variables[6] u = nla_solve(objective_function_6, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[6] = u[0] + algebraic_variables[6] = u[0] def objective_function_7(u, f, data): @@ -245,7 +245,7 @@ def objective_function_7(u, f, data): rates[2] = u[0] - f[0] = rates[2]-(algebraicVariables[5]*(1.0-states[2])-algebraicVariables[6]*states[2])-0.0 + f[0] = rates[2]-(algebraic_variables[5]*(1.0-states[2])-algebraic_variables[6]*states[2])-0.0 def find_root_7(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): @@ -267,19 +267,19 @@ def objective_function_8(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[7] = u[0] + algebraic_variables[7] = u[0] - f[0] = algebraicVariables[7]-0.07*exp(states[0]/20.0)-0.0 + f[0] = algebraic_variables[7]-0.07*exp(states[0]/20.0)-0.0 def find_root_8(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[7] + u[0] = algebraic_variables[7] u = nla_solve(objective_function_8, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[7] = u[0] + algebraic_variables[7] = u[0] def objective_function_9(u, f, data): @@ -291,19 +291,19 @@ def objective_function_9(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[8] = u[0] + algebraic_variables[8] = u[0] - f[0] = algebraicVariables[8]-1.0/(exp((states[0]+30.0)/10.0)+1.0)-0.0 + f[0] = algebraic_variables[8]-1.0/(exp((states[0]+30.0)/10.0)+1.0)-0.0 def find_root_9(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[8] + u[0] = algebraic_variables[8] u = nla_solve(objective_function_9, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[8] = u[0] + algebraic_variables[8] = u[0] def objective_function_10(u, f, data): @@ -317,7 +317,7 @@ def objective_function_10(u, f, data): rates[1] = u[0] - f[0] = rates[1]-(algebraicVariables[7]*(1.0-states[1])-algebraicVariables[8]*states[1])-0.0 + f[0] = rates[1]-(algebraic_variables[7]*(1.0-states[1])-algebraic_variables[8]*states[1])-0.0 def find_root_10(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): @@ -339,21 +339,21 @@ def objective_function_11(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[2] = u[0] + algebraic_variables[2] = u[0] potassium_channel_g_K = 36.0 - f[0] = algebraicVariables[2]-potassium_channel_g_K*pow(states[3], 4.0)*(states[0]-computed_constants[0])-0.0 + f[0] = algebraic_variables[2]-potassium_channel_g_K*pow(states[3], 4.0)*(states[0]-computed_constants[0])-0.0 def find_root_11(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[2] + u[0] = algebraic_variables[2] u = nla_solve(objective_function_11, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[2] = u[0] + algebraic_variables[2] = u[0] def objective_function_12(u, f, data): @@ -365,19 +365,19 @@ def objective_function_12(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[9] = u[0] + algebraic_variables[9] = u[0] - f[0] = algebraicVariables[9]-0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0)-0.0 + f[0] = algebraic_variables[9]-0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0)-0.0 def find_root_12(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[9] + u[0] = algebraic_variables[9] u = nla_solve(objective_function_12, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[9] = u[0] + algebraic_variables[9] = u[0] def objective_function_13(u, f, data): @@ -389,19 +389,19 @@ def objective_function_13(u, f, data): algebraic_variables = data[5] external_variables = data[6] - algebraicVariables[10] = u[0] + algebraic_variables[10] = u[0] - f[0] = algebraicVariables[10]-0.125*exp(states[0]/80.0)-0.0 + f[0] = algebraic_variables[10]-0.125*exp(states[0]/80.0)-0.0 def find_root_13(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): u = [nan]*1 - u[0] = algebraicVariables[10] + u[0] = algebraic_variables[10] u = nla_solve(objective_function_13, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables, external_variables]) - algebraicVariables[10] = u[0] + algebraic_variables[10] = u[0] def objective_function_14(u, f, data): @@ -415,7 +415,7 @@ def objective_function_14(u, f, data): rates[3] = u[0] - f[0] = rates[3]-(algebraicVariables[9]*(1.0-states[3])-algebraicVariables[10]*states[3])-0.0 + f[0] = rates[3]-(algebraic_variables[9]*(1.0-states[3])-algebraic_variables[10]*states[3])-0.0 def find_root_14(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables): @@ -438,19 +438,19 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va rates[2] = 0.0 rates[3] = 0.0 constants[0] = 1.0 - algebraicVariables[0] = 0.0 - algebraicVariables[1] = 0.0 - algebraicVariables[2] = 0.0 - algebraicVariables[3] = 0.0 - algebraicVariables[4] = 0.0 - algebraicVariables[6] = 0.0 - algebraicVariables[7] = 0.0 - algebraicVariables[8] = 0.0 - algebraicVariables[9] = 0.0 - algebraicVariables[10] = 0.0 - - -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): + algebraic_variables[0] = 0.0 + algebraic_variables[1] = 0.0 + algebraic_variables[2] = 0.0 + algebraic_variables[3] = 0.0 + algebraic_variables[4] = 0.0 + algebraic_variables[6] = 0.0 + algebraic_variables[7] = 0.0 + algebraic_variables[8] = 0.0 + algebraic_variables[9] = 0.0 + algebraic_variables[10] = 0.0 + + +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): membrane_E_R = 0.0 computed_constants[0] = membrane_E_R+12.0 @@ -463,8 +463,8 @@ def compute_rates(voi, states, rates, constants, computed_constants, algebraic_v find_root_12(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_14(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_11(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) - algebraicVariables[5] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + algebraic_variables[5] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) find_root_1(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_6(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_7(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) @@ -479,8 +479,8 @@ def compute_variables(voi, states, rates, constants, computed_constants, algebra find_root_12(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_14(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_11(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) - algebraicVariables[5] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + algebraic_variables[5] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) find_root_1(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_4(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) find_root_6(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables) diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.h b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.h index 42166250c..fc447c7a3 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.h +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.py b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.py index 19e1d5d42..6ce607435 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.py +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dae.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 4 @@ -88,19 +88,19 @@ def objective_function_0(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[0] = u[0] + algebraic_variables[0] = u[0] - f[0] = algebraicVariables[0]-(-20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0)-0.0 + f[0] = algebraic_variables[0]-(-20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0)-0.0 def find_root_0(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[0] + u[0] = algebraic_variables[0] u = nla_solve(objective_function_0, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[0] = u[0] + algebraic_variables[0] = u[0] def objective_function_1(u, f, data): @@ -113,7 +113,7 @@ def objective_function_1(u, f, data): rates[0] = u[0] - f[0] = rates[0]-(-(-algebraicVariables[0]+algebraicVariables[3]+algebraicVariables[2]+algebraicVariables[1])/constants[0])-0.0 + f[0] = rates[0]-(-(-algebraic_variables[0]+algebraic_variables[3]+algebraic_variables[2]+algebraic_variables[1])/constants[0])-0.0 def find_root_1(voi, states, rates, constants, computed_constants, algebraic_variables): @@ -134,19 +134,19 @@ def objective_function_2(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[4] = u[0] + algebraic_variables[4] = u[0] - f[0] = algebraicVariables[4]-(constants[1]-10.613)-0.0 + f[0] = algebraic_variables[4]-(constants[1]-10.613)-0.0 def find_root_2(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[4] + u[0] = algebraic_variables[4] u = nla_solve(objective_function_2, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[4] = u[0] + algebraic_variables[4] = u[0] def objective_function_3(u, f, data): @@ -157,19 +157,19 @@ def objective_function_3(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[1] = u[0] + algebraic_variables[1] = u[0] - f[0] = algebraicVariables[1]-constants[2]*(states[0]-algebraicVariables[4])-0.0 + f[0] = algebraic_variables[1]-constants[2]*(states[0]-algebraic_variables[4])-0.0 def find_root_3(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[1] + u[0] = algebraic_variables[1] u = nla_solve(objective_function_3, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[1] = u[0] + algebraic_variables[1] = u[0] def objective_function_4(u, f, data): @@ -180,19 +180,19 @@ def objective_function_4(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[5] = u[0] + algebraic_variables[5] = u[0] - f[0] = algebraicVariables[5]-(constants[1]-115.0)-0.0 + f[0] = algebraic_variables[5]-(constants[1]-115.0)-0.0 def find_root_4(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[5] + u[0] = algebraic_variables[5] u = nla_solve(objective_function_4, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[5] = u[0] + algebraic_variables[5] = u[0] def objective_function_5(u, f, data): @@ -203,19 +203,19 @@ def objective_function_5(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[3] = u[0] + algebraic_variables[3] = u[0] - f[0] = algebraicVariables[3]-constants[3]*pow(states[2], 3.0)*states[1]*(states[0]-algebraicVariables[5])-0.0 + f[0] = algebraic_variables[3]-constants[3]*pow(states[2], 3.0)*states[1]*(states[0]-algebraic_variables[5])-0.0 def find_root_5(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[3] + u[0] = algebraic_variables[3] u = nla_solve(objective_function_5, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[3] = u[0] + algebraic_variables[3] = u[0] def objective_function_6(u, f, data): @@ -226,19 +226,19 @@ def objective_function_6(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[6] = u[0] + algebraic_variables[6] = u[0] - f[0] = algebraicVariables[6]-0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0)-0.0 + f[0] = algebraic_variables[6]-0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0)-0.0 def find_root_6(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[6] + u[0] = algebraic_variables[6] u = nla_solve(objective_function_6, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[6] = u[0] + algebraic_variables[6] = u[0] def objective_function_7(u, f, data): @@ -249,19 +249,19 @@ def objective_function_7(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[7] = u[0] + algebraic_variables[7] = u[0] - f[0] = algebraicVariables[7]-4.0*exp(states[0]/18.0)-0.0 + f[0] = algebraic_variables[7]-4.0*exp(states[0]/18.0)-0.0 def find_root_7(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[7] + u[0] = algebraic_variables[7] u = nla_solve(objective_function_7, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[7] = u[0] + algebraic_variables[7] = u[0] def objective_function_8(u, f, data): @@ -274,7 +274,7 @@ def objective_function_8(u, f, data): rates[2] = u[0] - f[0] = rates[2]-(algebraicVariables[6]*(1.0-states[2])-algebraicVariables[7]*states[2])-0.0 + f[0] = rates[2]-(algebraic_variables[6]*(1.0-states[2])-algebraic_variables[7]*states[2])-0.0 def find_root_8(voi, states, rates, constants, computed_constants, algebraic_variables): @@ -295,19 +295,19 @@ def objective_function_9(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[8] = u[0] + algebraic_variables[8] = u[0] - f[0] = algebraicVariables[8]-0.07*exp(states[0]/20.0)-0.0 + f[0] = algebraic_variables[8]-0.07*exp(states[0]/20.0)-0.0 def find_root_9(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[8] + u[0] = algebraic_variables[8] u = nla_solve(objective_function_9, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[8] = u[0] + algebraic_variables[8] = u[0] def objective_function_10(u, f, data): @@ -318,19 +318,19 @@ def objective_function_10(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[9] = u[0] + algebraic_variables[9] = u[0] - f[0] = algebraicVariables[9]-1.0/(exp((states[0]+30.0)/10.0)+1.0)-0.0 + f[0] = algebraic_variables[9]-1.0/(exp((states[0]+30.0)/10.0)+1.0)-0.0 def find_root_10(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[9] + u[0] = algebraic_variables[9] u = nla_solve(objective_function_10, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[9] = u[0] + algebraic_variables[9] = u[0] def objective_function_11(u, f, data): @@ -343,7 +343,7 @@ def objective_function_11(u, f, data): rates[1] = u[0] - f[0] = rates[1]-(algebraicVariables[8]*(1.0-states[1])-algebraicVariables[9]*states[1])-0.0 + f[0] = rates[1]-(algebraic_variables[8]*(1.0-states[1])-algebraic_variables[9]*states[1])-0.0 def find_root_11(voi, states, rates, constants, computed_constants, algebraic_variables): @@ -364,19 +364,19 @@ def objective_function_12(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[10] = u[0] + algebraic_variables[10] = u[0] - f[0] = algebraicVariables[10]-(constants[1]+12.0)-0.0 + f[0] = algebraic_variables[10]-(constants[1]+12.0)-0.0 def find_root_12(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[10] + u[0] = algebraic_variables[10] u = nla_solve(objective_function_12, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[10] = u[0] + algebraic_variables[10] = u[0] def objective_function_13(u, f, data): @@ -387,19 +387,19 @@ def objective_function_13(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[2] = u[0] + algebraic_variables[2] = u[0] - f[0] = algebraicVariables[2]-constants[4]*pow(states[3], 4.0)*(states[0]-algebraicVariables[10])-0.0 + f[0] = algebraic_variables[2]-constants[4]*pow(states[3], 4.0)*(states[0]-algebraic_variables[10])-0.0 def find_root_13(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[2] + u[0] = algebraic_variables[2] u = nla_solve(objective_function_13, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[2] = u[0] + algebraic_variables[2] = u[0] def objective_function_14(u, f, data): @@ -410,19 +410,19 @@ def objective_function_14(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[11] = u[0] + algebraic_variables[11] = u[0] - f[0] = algebraicVariables[11]-0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0)-0.0 + f[0] = algebraic_variables[11]-0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0)-0.0 def find_root_14(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[11] + u[0] = algebraic_variables[11] u = nla_solve(objective_function_14, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[11] = u[0] + algebraic_variables[11] = u[0] def objective_function_15(u, f, data): @@ -433,19 +433,19 @@ def objective_function_15(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[12] = u[0] + algebraic_variables[12] = u[0] - f[0] = algebraicVariables[12]-0.125*exp(states[0]/80.0)-0.0 + f[0] = algebraic_variables[12]-0.125*exp(states[0]/80.0)-0.0 def find_root_15(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[12] + u[0] = algebraic_variables[12] u = nla_solve(objective_function_15, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[12] = u[0] + algebraic_variables[12] = u[0] def objective_function_16(u, f, data): @@ -458,7 +458,7 @@ def objective_function_16(u, f, data): rates[3] = u[0] - f[0] = rates[3]-(algebraicVariables[11]*(1.0-states[3])-algebraicVariables[12]*states[3])-0.0 + f[0] = rates[3]-(algebraic_variables[11]*(1.0-states[3])-algebraic_variables[12]*states[3])-0.0 def find_root_16(voi, states, rates, constants, computed_constants, algebraic_variables): @@ -485,22 +485,22 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[2] = 0.3 constants[3] = 120.0 constants[4] = 36.0 - algebraicVariables[0] = 0.0 - algebraicVariables[1] = 0.0 - algebraicVariables[2] = 0.0 - algebraicVariables[3] = 0.0 - algebraicVariables[4] = 0.0 - algebraicVariables[5] = 0.0 - algebraicVariables[6] = 0.0 - algebraicVariables[7] = 0.0 - algebraicVariables[8] = 0.0 - algebraicVariables[9] = 0.0 - algebraicVariables[10] = 0.0 - algebraicVariables[11] = 0.0 - algebraicVariables[12] = 0.0 - - -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): + algebraic_variables[0] = 0.0 + algebraic_variables[1] = 0.0 + algebraic_variables[2] = 0.0 + algebraic_variables[3] = 0.0 + algebraic_variables[4] = 0.0 + algebraic_variables[5] = 0.0 + algebraic_variables[6] = 0.0 + algebraic_variables[7] = 0.0 + algebraic_variables[8] = 0.0 + algebraic_variables[9] = 0.0 + algebraic_variables[10] = 0.0 + algebraic_variables[11] = 0.0 + algebraic_variables[12] = 0.0 + + +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.algebraic.c b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.algebraic.c index 8e4ccdb9c..e0ad01f7d 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.algebraic.c +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.algebraic.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 4; @@ -126,7 +126,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * constants[4] = 36.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { computedConstants[0] = constants[1]-10.613; computedConstants[1] = constants[1]-115.0; diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.algebraic.h b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.algebraic.h index ce6057728..79abbba9c 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.algebraic.h +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.algebraic.h @@ -37,6 +37,6 @@ void deleteArray(double *array); typedef double (* ExternalVariable)(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, size_t index); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.algebraic.py b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.algebraic.py index e6db35ecf..581d1506f 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.algebraic.py +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.algebraic.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 4 @@ -97,37 +97,37 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[4] = 36.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): computed_constants[0] = constants[1]-10.613 computed_constants[1] = constants[1]-115.0 computed_constants[2] = constants[1]+12.0 def compute_rates(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, external_variable): - externalVariables[1] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 1) - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) - algebraicVariables[0] = constants[2]*(states[0]-computed_constants[0]) - algebraicVariables[1] = constants[4]*pow(states[3], 4.0)*(states[0]-computed_constants[2]) - algebraicVariables[2] = constants[3]*pow(states[2], 3.0)*states[1]*(states[0]-computed_constants[1]) - rates[0] = -(-externalVariables[0]+algebraicVariables[2]+algebraicVariables[1]+algebraicVariables[0])/constants[0] - algebraicVariables[4] = 4.0*exp(states[0]/18.0) - algebraicVariables[3] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - rates[2] = algebraicVariables[3]*(1.0-states[2])-algebraicVariables[4]*states[2] - algebraicVariables[6] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) - algebraicVariables[5] = 0.07*exp(states[0]/20.0) - rates[1] = algebraicVariables[5]*(1.0-states[1])-algebraicVariables[6]*states[1] - algebraicVariables[7] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) - rates[3] = algebraicVariables[7]*(1.0-states[3])-externalVariables[1]*states[3] + external_variables[1] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 1) + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + algebraic_variables[0] = constants[2]*(states[0]-computed_constants[0]) + algebraic_variables[1] = constants[4]*pow(states[3], 4.0)*(states[0]-computed_constants[2]) + algebraic_variables[2] = constants[3]*pow(states[2], 3.0)*states[1]*(states[0]-computed_constants[1]) + rates[0] = -(-external_variables[0]+algebraic_variables[2]+algebraic_variables[1]+algebraic_variables[0])/constants[0] + algebraic_variables[4] = 4.0*exp(states[0]/18.0) + algebraic_variables[3] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + rates[2] = algebraic_variables[3]*(1.0-states[2])-algebraic_variables[4]*states[2] + algebraic_variables[6] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) + algebraic_variables[5] = 0.07*exp(states[0]/20.0) + rates[1] = algebraic_variables[5]*(1.0-states[1])-algebraic_variables[6]*states[1] + algebraic_variables[7] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) + rates[3] = algebraic_variables[7]*(1.0-states[3])-external_variables[1]*states[3] def compute_variables(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, external_variable): - externalVariables[1] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 1) - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) - algebraicVariables[0] = constants[2]*(states[0]-computed_constants[0]) - algebraicVariables[2] = constants[3]*pow(states[2], 3.0)*states[1]*(states[0]-computed_constants[1]) - algebraicVariables[3] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - algebraicVariables[4] = 4.0*exp(states[0]/18.0) - algebraicVariables[5] = 0.07*exp(states[0]/20.0) - algebraicVariables[6] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) - algebraicVariables[1] = constants[4]*pow(states[3], 4.0)*(states[0]-computed_constants[2]) - algebraicVariables[7] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) + external_variables[1] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 1) + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + algebraic_variables[0] = constants[2]*(states[0]-computed_constants[0]) + algebraic_variables[2] = constants[3]*pow(states[2], 3.0)*states[1]*(states[0]-computed_constants[1]) + algebraic_variables[3] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + algebraic_variables[4] = 4.0*exp(states[0]/18.0) + algebraic_variables[5] = 0.07*exp(states[0]/20.0) + algebraic_variables[6] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) + algebraic_variables[1] = constants[4]*pow(states[3], 4.0)*(states[0]-computed_constants[2]) + algebraic_variables[7] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.computed.constant.c b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.computed.constant.c index c3526688c..68dc08f49 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.computed.constant.c +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.computed.constant.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 4; @@ -125,7 +125,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * constants[3] = 36.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.computed.constant.h b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.computed.constant.h index ce6057728..79abbba9c 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.computed.constant.h +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.computed.constant.h @@ -37,6 +37,6 @@ void deleteArray(double *array); typedef double (* ExternalVariable)(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, size_t index); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.computed.constant.py b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.computed.constant.py index 2d6d09a09..2eca7253a 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.computed.constant.py +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.computed.constant.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 4 @@ -96,42 +96,42 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[3] = 36.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass def compute_rates(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, external_variable): - algebraicVariables[0] = -20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0 - externalVariables[1] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 1) - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) - algebraicVariables[4] = externalVariables[0]-10.613 - algebraicVariables[1] = constants[1]*(states[0]-algebraicVariables[4]) - algebraicVariables[2] = constants[3]*pow(states[3], 4.0)*(states[0]-externalVariables[1]) - algebraicVariables[5] = externalVariables[0]-115.0 - algebraicVariables[3] = constants[2]*pow(states[2], 3.0)*states[1]*(states[0]-algebraicVariables[5]) - rates[0] = -(-algebraicVariables[0]+algebraicVariables[3]+algebraicVariables[2]+algebraicVariables[1])/constants[0] - algebraicVariables[7] = 4.0*exp(states[0]/18.0) - algebraicVariables[6] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - rates[2] = algebraicVariables[6]*(1.0-states[2])-algebraicVariables[7]*states[2] - algebraicVariables[9] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) - algebraicVariables[8] = 0.07*exp(states[0]/20.0) - rates[1] = algebraicVariables[8]*(1.0-states[1])-algebraicVariables[9]*states[1] - algebraicVariables[11] = 0.125*exp(states[0]/80.0) - algebraicVariables[10] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) - rates[3] = algebraicVariables[10]*(1.0-states[3])-algebraicVariables[11]*states[3] + algebraic_variables[0] = -20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0 + external_variables[1] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 1) + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + algebraic_variables[4] = external_variables[0]-10.613 + algebraic_variables[1] = constants[1]*(states[0]-algebraic_variables[4]) + algebraic_variables[2] = constants[3]*pow(states[3], 4.0)*(states[0]-external_variables[1]) + algebraic_variables[5] = external_variables[0]-115.0 + algebraic_variables[3] = constants[2]*pow(states[2], 3.0)*states[1]*(states[0]-algebraic_variables[5]) + rates[0] = -(-algebraic_variables[0]+algebraic_variables[3]+algebraic_variables[2]+algebraic_variables[1])/constants[0] + algebraic_variables[7] = 4.0*exp(states[0]/18.0) + algebraic_variables[6] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + rates[2] = algebraic_variables[6]*(1.0-states[2])-algebraic_variables[7]*states[2] + algebraic_variables[9] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) + algebraic_variables[8] = 0.07*exp(states[0]/20.0) + rates[1] = algebraic_variables[8]*(1.0-states[1])-algebraic_variables[9]*states[1] + algebraic_variables[11] = 0.125*exp(states[0]/80.0) + algebraic_variables[10] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) + rates[3] = algebraic_variables[10]*(1.0-states[3])-algebraic_variables[11]*states[3] def compute_variables(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, external_variable): - externalVariables[1] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 1) - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) - algebraicVariables[4] = externalVariables[0]-10.613 - algebraicVariables[1] = constants[1]*(states[0]-algebraicVariables[4]) - algebraicVariables[5] = externalVariables[0]-115.0 - algebraicVariables[3] = constants[2]*pow(states[2], 3.0)*states[1]*(states[0]-algebraicVariables[5]) - algebraicVariables[6] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - algebraicVariables[7] = 4.0*exp(states[0]/18.0) - algebraicVariables[8] = 0.07*exp(states[0]/20.0) - algebraicVariables[9] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) - algebraicVariables[2] = constants[3]*pow(states[3], 4.0)*(states[0]-externalVariables[1]) - algebraicVariables[10] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) - algebraicVariables[11] = 0.125*exp(states[0]/80.0) + external_variables[1] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 1) + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + algebraic_variables[4] = external_variables[0]-10.613 + algebraic_variables[1] = constants[1]*(states[0]-algebraic_variables[4]) + algebraic_variables[5] = external_variables[0]-115.0 + algebraic_variables[3] = constants[2]*pow(states[2], 3.0)*states[1]*(states[0]-algebraic_variables[5]) + algebraic_variables[6] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + algebraic_variables[7] = 4.0*exp(states[0]/18.0) + algebraic_variables[8] = 0.07*exp(states[0]/20.0) + algebraic_variables[9] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) + algebraic_variables[2] = constants[3]*pow(states[3], 4.0)*(states[0]-external_variables[1]) + algebraic_variables[10] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) + algebraic_variables[11] = 0.125*exp(states[0]/80.0) diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.constant.c b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.constant.c index 56cec3ef8..2396c517c 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.constant.c +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.constant.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 4; @@ -124,7 +124,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * constants[2] = 36.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { computedConstants[0] = constants[0]-10.613; computedConstants[1] = constants[0]-115.0; diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.constant.h b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.constant.h index ce6057728..79abbba9c 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.constant.h +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.constant.h @@ -37,6 +37,6 @@ void deleteArray(double *array); typedef double (* ExternalVariable)(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, size_t index); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.constant.py b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.constant.py index 0eecf8dae..e683c9510 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.constant.py +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.constant.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 4 @@ -95,40 +95,40 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[2] = 36.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): computed_constants[0] = constants[0]-10.613 computed_constants[1] = constants[0]-115.0 computed_constants[2] = constants[0]+12.0 def compute_rates(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, external_variable): - externalVariables[1] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 1) - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) - algebraicVariables[0] = -20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0 - algebraicVariables[1] = constants[1]*(states[0]-computed_constants[0]) - algebraicVariables[2] = constants[2]*pow(states[3], 4.0)*(states[0]-computed_constants[2]) - algebraicVariables[3] = externalVariables[1]*pow(states[2], 3.0)*states[1]*(states[0]-computed_constants[1]) - rates[0] = -(-algebraicVariables[0]+algebraicVariables[3]+algebraicVariables[2]+algebraicVariables[1])/externalVariables[0] - algebraicVariables[5] = 4.0*exp(states[0]/18.0) - algebraicVariables[4] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - rates[2] = algebraicVariables[4]*(1.0-states[2])-algebraicVariables[5]*states[2] - algebraicVariables[7] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) - algebraicVariables[6] = 0.07*exp(states[0]/20.0) - rates[1] = algebraicVariables[6]*(1.0-states[1])-algebraicVariables[7]*states[1] - algebraicVariables[9] = 0.125*exp(states[0]/80.0) - algebraicVariables[8] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) - rates[3] = algebraicVariables[8]*(1.0-states[3])-algebraicVariables[9]*states[3] + external_variables[1] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 1) + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + algebraic_variables[0] = -20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0 + algebraic_variables[1] = constants[1]*(states[0]-computed_constants[0]) + algebraic_variables[2] = constants[2]*pow(states[3], 4.0)*(states[0]-computed_constants[2]) + algebraic_variables[3] = external_variables[1]*pow(states[2], 3.0)*states[1]*(states[0]-computed_constants[1]) + rates[0] = -(-algebraic_variables[0]+algebraic_variables[3]+algebraic_variables[2]+algebraic_variables[1])/external_variables[0] + algebraic_variables[5] = 4.0*exp(states[0]/18.0) + algebraic_variables[4] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + rates[2] = algebraic_variables[4]*(1.0-states[2])-algebraic_variables[5]*states[2] + algebraic_variables[7] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) + algebraic_variables[6] = 0.07*exp(states[0]/20.0) + rates[1] = algebraic_variables[6]*(1.0-states[1])-algebraic_variables[7]*states[1] + algebraic_variables[9] = 0.125*exp(states[0]/80.0) + algebraic_variables[8] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) + rates[3] = algebraic_variables[8]*(1.0-states[3])-algebraic_variables[9]*states[3] def compute_variables(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, external_variable): - algebraicVariables[1] = constants[1]*(states[0]-computed_constants[0]) - externalVariables[1] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 1) - algebraicVariables[3] = externalVariables[1]*pow(states[2], 3.0)*states[1]*(states[0]-computed_constants[1]) - algebraicVariables[4] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - algebraicVariables[5] = 4.0*exp(states[0]/18.0) - algebraicVariables[6] = 0.07*exp(states[0]/20.0) - algebraicVariables[7] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) - algebraicVariables[2] = constants[2]*pow(states[3], 4.0)*(states[0]-computed_constants[2]) - algebraicVariables[8] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) - algebraicVariables[9] = 0.125*exp(states[0]/80.0) - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + algebraic_variables[1] = constants[1]*(states[0]-computed_constants[0]) + external_variables[1] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 1) + algebraic_variables[3] = external_variables[1]*pow(states[2], 3.0)*states[1]*(states[0]-computed_constants[1]) + algebraic_variables[4] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + algebraic_variables[5] = 4.0*exp(states[0]/18.0) + algebraic_variables[6] = 0.07*exp(states[0]/20.0) + algebraic_variables[7] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) + algebraic_variables[2] = constants[2]*pow(states[3], 4.0)*(states[0]-computed_constants[2]) + algebraic_variables[8] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) + algebraic_variables[9] = 0.125*exp(states[0]/80.0) + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.state.c b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.state.c index fda55001d..b99860b96 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.state.c +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.state.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 2; @@ -124,7 +124,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * constants[4] = 36.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { computedConstants[0] = constants[1]-10.613; computedConstants[1] = constants[1]-115.0; diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.state.h b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.state.h index ce6057728..79abbba9c 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.state.h +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.state.h @@ -37,6 +37,6 @@ void deleteArray(double *array); typedef double (* ExternalVariable)(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, size_t index); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.state.py b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.state.py index 090628993..d28c2e7c0 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.state.py +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.dependent.state.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 2 @@ -95,28 +95,28 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[4] = 36.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): computed_constants[0] = constants[1]-10.613 computed_constants[1] = constants[1]-115.0 computed_constants[2] = constants[1]+12.0 def compute_rates(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, external_variable): - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) - algebraicVariables[7] = 1.0/(exp((externalVariables[0]+30.0)/10.0)+1.0) - algebraicVariables[6] = 0.07*exp(externalVariables[0]/20.0) - rates[0] = algebraicVariables[6]*(1.0-states[0])-algebraicVariables[7]*states[0] - algebraicVariables[9] = 0.125*exp(externalVariables[0]/80.0) - algebraicVariables[8] = 0.01*(externalVariables[0]+10.0)/(exp((externalVariables[0]+10.0)/10.0)-1.0) - rates[1] = algebraicVariables[8]*(1.0-states[1])-algebraicVariables[9]*states[1] + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + algebraic_variables[7] = 1.0/(exp((external_variables[0]+30.0)/10.0)+1.0) + algebraic_variables[6] = 0.07*exp(external_variables[0]/20.0) + rates[0] = algebraic_variables[6]*(1.0-states[0])-algebraic_variables[7]*states[0] + algebraic_variables[9] = 0.125*exp(external_variables[0]/80.0) + algebraic_variables[8] = 0.01*(external_variables[0]+10.0)/(exp((external_variables[0]+10.0)/10.0)-1.0) + rates[1] = algebraic_variables[8]*(1.0-states[1])-algebraic_variables[9]*states[1] def compute_variables(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, external_variable): - algebraicVariables[0] = -20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0 - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) - algebraicVariables[1] = constants[2]*(externalVariables[0]-computed_constants[0]) - externalVariables[1] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 1) - algebraicVariables[3] = constants[3]*pow(externalVariables[1], 3.0)*states[0]*(externalVariables[0]-computed_constants[1]) - algebraicVariables[4] = 0.1*(externalVariables[0]+25.0)/(exp((externalVariables[0]+25.0)/10.0)-1.0) - algebraicVariables[5] = 4.0*exp(externalVariables[0]/18.0) - algebraicVariables[2] = constants[4]*pow(states[1], 4.0)*(externalVariables[0]-computed_constants[2]) + algebraic_variables[0] = -20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0 + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + algebraic_variables[1] = constants[2]*(external_variables[0]-computed_constants[0]) + external_variables[1] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 1) + algebraic_variables[3] = constants[3]*pow(external_variables[1], 3.0)*states[0]*(external_variables[0]-computed_constants[1]) + algebraic_variables[4] = 0.1*(external_variables[0]+25.0)/(exp((external_variables[0]+25.0)/10.0)-1.0) + algebraic_variables[5] = 4.0*exp(external_variables[0]/18.0) + algebraic_variables[2] = constants[4]*pow(states[1], 4.0)*(external_variables[0]-computed_constants[2]) diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.external.c b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.external.c index 247e8ff16..e77e615b5 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.external.c +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.external.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 3; @@ -125,7 +125,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * constants[4] = 36.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { computedConstants[0] = constants[1]-10.613; computedConstants[1] = constants[1]-115.0; diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.external.h b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.external.h index ce6057728..79abbba9c 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.external.h +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.external.h @@ -37,6 +37,6 @@ void deleteArray(double *array); typedef double (* ExternalVariable)(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, size_t index); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.external.py b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.external.py index c3b13c212..8a0f01cf3 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.external.py +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.external.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 3 @@ -96,29 +96,29 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[4] = 36.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): computed_constants[0] = constants[1]-10.613 computed_constants[1] = constants[1]-115.0 computed_constants[2] = constants[1]+12.0 def compute_rates(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, external_variable): - externalVariables[1] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 1) - algebraicVariables[4] = 4.0*exp(externalVariables[1]/18.0) - algebraicVariables[3] = 0.1*(externalVariables[1]+25.0)/(exp((externalVariables[1]+25.0)/10.0)-1.0) - rates[1] = algebraicVariables[3]*(1.0-states[1])-algebraicVariables[4]*states[1] - algebraicVariables[6] = 1.0/(exp((externalVariables[1]+30.0)/10.0)+1.0) - algebraicVariables[5] = 0.07*exp(externalVariables[1]/20.0) - rates[0] = algebraicVariables[5]*(1.0-states[0])-algebraicVariables[6]*states[0] - algebraicVariables[7] = 0.125*exp(externalVariables[1]/80.0) - externalVariables[2] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 2) - rates[2] = externalVariables[2]*(1.0-states[2])-algebraicVariables[7]*states[2] + external_variables[1] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 1) + algebraic_variables[4] = 4.0*exp(external_variables[1]/18.0) + algebraic_variables[3] = 0.1*(external_variables[1]+25.0)/(exp((external_variables[1]+25.0)/10.0)-1.0) + rates[1] = algebraic_variables[3]*(1.0-states[1])-algebraic_variables[4]*states[1] + algebraic_variables[6] = 1.0/(exp((external_variables[1]+30.0)/10.0)+1.0) + algebraic_variables[5] = 0.07*exp(external_variables[1]/20.0) + rates[0] = algebraic_variables[5]*(1.0-states[0])-algebraic_variables[6]*states[0] + algebraic_variables[7] = 0.125*exp(external_variables[1]/80.0) + external_variables[2] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 2) + rates[2] = external_variables[2]*(1.0-states[2])-algebraic_variables[7]*states[2] def compute_variables(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, external_variable): - algebraicVariables[0] = -20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0 - externalVariables[1] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 1) - algebraicVariables[1] = constants[2]*(externalVariables[1]-computed_constants[0]) - externalVariables[2] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 2) - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) - algebraicVariables[2] = constants[4]*pow(states[2], 4.0)*(externalVariables[1]-computed_constants[2]) + algebraic_variables[0] = -20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0 + external_variables[1] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 1) + algebraic_variables[1] = constants[2]*(external_variables[1]-computed_constants[0]) + external_variables[2] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 2) + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + algebraic_variables[2] = constants[4]*pow(states[2], 4.0)*(external_variables[1]-computed_constants[2]) diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.h b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.h index 42166250c..fc447c7a3 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.h +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.py b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.py index 296d6f267..f0d0ddca2 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.py +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 4 @@ -89,36 +89,36 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[4] = 36.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): computed_constants[0] = constants[1]-10.613 computed_constants[1] = constants[1]-115.0 computed_constants[2] = constants[1]+12.0 def compute_rates(voi, states, rates, constants, computed_constants, algebraic_variables): - algebraicVariables[0] = -20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0 - algebraicVariables[1] = constants[2]*(states[0]-computed_constants[0]) - algebraicVariables[2] = constants[4]*pow(states[3], 4.0)*(states[0]-computed_constants[2]) - algebraicVariables[3] = constants[3]*pow(states[2], 3.0)*states[1]*(states[0]-computed_constants[1]) - rates[0] = -(-algebraicVariables[0]+algebraicVariables[3]+algebraicVariables[2]+algebraicVariables[1])/constants[0] - algebraicVariables[5] = 4.0*exp(states[0]/18.0) - algebraicVariables[4] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - rates[2] = algebraicVariables[4]*(1.0-states[2])-algebraicVariables[5]*states[2] - algebraicVariables[7] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) - algebraicVariables[6] = 0.07*exp(states[0]/20.0) - rates[1] = algebraicVariables[6]*(1.0-states[1])-algebraicVariables[7]*states[1] - algebraicVariables[9] = 0.125*exp(states[0]/80.0) - algebraicVariables[8] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) - rates[3] = algebraicVariables[8]*(1.0-states[3])-algebraicVariables[9]*states[3] + algebraic_variables[0] = -20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0 + algebraic_variables[1] = constants[2]*(states[0]-computed_constants[0]) + algebraic_variables[2] = constants[4]*pow(states[3], 4.0)*(states[0]-computed_constants[2]) + algebraic_variables[3] = constants[3]*pow(states[2], 3.0)*states[1]*(states[0]-computed_constants[1]) + rates[0] = -(-algebraic_variables[0]+algebraic_variables[3]+algebraic_variables[2]+algebraic_variables[1])/constants[0] + algebraic_variables[5] = 4.0*exp(states[0]/18.0) + algebraic_variables[4] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + rates[2] = algebraic_variables[4]*(1.0-states[2])-algebraic_variables[5]*states[2] + algebraic_variables[7] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) + algebraic_variables[6] = 0.07*exp(states[0]/20.0) + rates[1] = algebraic_variables[6]*(1.0-states[1])-algebraic_variables[7]*states[1] + algebraic_variables[9] = 0.125*exp(states[0]/80.0) + algebraic_variables[8] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) + rates[3] = algebraic_variables[8]*(1.0-states[3])-algebraic_variables[9]*states[3] def compute_variables(voi, states, rates, constants, computed_constants, algebraic_variables): - algebraicVariables[1] = constants[2]*(states[0]-computed_constants[0]) - algebraicVariables[3] = constants[3]*pow(states[2], 3.0)*states[1]*(states[0]-computed_constants[1]) - algebraicVariables[4] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - algebraicVariables[5] = 4.0*exp(states[0]/18.0) - algebraicVariables[6] = 0.07*exp(states[0]/20.0) - algebraicVariables[7] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) - algebraicVariables[2] = constants[4]*pow(states[3], 4.0)*(states[0]-computed_constants[2]) - algebraicVariables[8] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) - algebraicVariables[9] = 0.125*exp(states[0]/80.0) + algebraic_variables[1] = constants[2]*(states[0]-computed_constants[0]) + algebraic_variables[3] = constants[3]*pow(states[2], 3.0)*states[1]*(states[0]-computed_constants[1]) + algebraic_variables[4] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + algebraic_variables[5] = 4.0*exp(states[0]/18.0) + algebraic_variables[6] = 0.07*exp(states[0]/20.0) + algebraic_variables[7] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) + algebraic_variables[2] = constants[4]*pow(states[3], 4.0)*(states[0]-computed_constants[2]) + algebraic_variables[8] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) + algebraic_variables[9] = 0.125*exp(states[0]/80.0) diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.state.c b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.state.c index 0a34fbaff..5525b7446 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.state.c +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.state.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 3; @@ -125,7 +125,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * constants[4] = 36.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { computedConstants[0] = constants[1]-10.613; computedConstants[1] = constants[1]-115.0; diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.state.h b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.state.h index ce6057728..79abbba9c 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.state.h +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.state.h @@ -37,6 +37,6 @@ void deleteArray(double *array); typedef double (* ExternalVariable)(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, size_t index); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.state.py b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.state.py index 8a869a934..e23635a08 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.state.py +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.state.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 3 @@ -96,35 +96,35 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[4] = 36.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): computed_constants[0] = constants[1]-10.613 computed_constants[1] = constants[1]-115.0 computed_constants[2] = constants[1]+12.0 def compute_rates(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, external_variable): - algebraicVariables[0] = -20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0 - algebraicVariables[1] = constants[2]*(states[0]-computed_constants[0]) - algebraicVariables[2] = constants[4]*pow(states[2], 4.0)*(states[0]-computed_constants[2]) - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) - algebraicVariables[3] = constants[3]*pow(externalVariables[0], 3.0)*states[1]*(states[0]-computed_constants[1]) - rates[0] = -(-algebraicVariables[0]+algebraicVariables[3]+algebraicVariables[2]+algebraicVariables[1])/constants[0] - algebraicVariables[7] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) - algebraicVariables[6] = 0.07*exp(states[0]/20.0) - rates[1] = algebraicVariables[6]*(1.0-states[1])-algebraicVariables[7]*states[1] - algebraicVariables[9] = 0.125*exp(states[0]/80.0) - algebraicVariables[8] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) - rates[2] = algebraicVariables[8]*(1.0-states[2])-algebraicVariables[9]*states[2] + algebraic_variables[0] = -20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0 + algebraic_variables[1] = constants[2]*(states[0]-computed_constants[0]) + algebraic_variables[2] = constants[4]*pow(states[2], 4.0)*(states[0]-computed_constants[2]) + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + algebraic_variables[3] = constants[3]*pow(external_variables[0], 3.0)*states[1]*(states[0]-computed_constants[1]) + rates[0] = -(-algebraic_variables[0]+algebraic_variables[3]+algebraic_variables[2]+algebraic_variables[1])/constants[0] + algebraic_variables[7] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) + algebraic_variables[6] = 0.07*exp(states[0]/20.0) + rates[1] = algebraic_variables[6]*(1.0-states[1])-algebraic_variables[7]*states[1] + algebraic_variables[9] = 0.125*exp(states[0]/80.0) + algebraic_variables[8] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) + rates[2] = algebraic_variables[8]*(1.0-states[2])-algebraic_variables[9]*states[2] def compute_variables(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, external_variable): - algebraicVariables[1] = constants[2]*(states[0]-computed_constants[0]) - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) - algebraicVariables[3] = constants[3]*pow(externalVariables[0], 3.0)*states[1]*(states[0]-computed_constants[1]) - algebraicVariables[4] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - algebraicVariables[5] = 4.0*exp(states[0]/18.0) - algebraicVariables[6] = 0.07*exp(states[0]/20.0) - algebraicVariables[7] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) - algebraicVariables[2] = constants[4]*pow(states[2], 4.0)*(states[0]-computed_constants[2]) - algebraicVariables[8] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) - algebraicVariables[9] = 0.125*exp(states[0]/80.0) + algebraic_variables[1] = constants[2]*(states[0]-computed_constants[0]) + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + algebraic_variables[3] = constants[3]*pow(external_variables[0], 3.0)*states[1]*(states[0]-computed_constants[1]) + algebraic_variables[4] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + algebraic_variables[5] = 4.0*exp(states[0]/18.0) + algebraic_variables[6] = 0.07*exp(states[0]/20.0) + algebraic_variables[7] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) + algebraic_variables[2] = constants[4]*pow(states[2], 4.0)*(states[0]-computed_constants[2]) + algebraic_variables[8] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) + algebraic_variables[9] = 0.125*exp(states[0]/80.0) diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.algebraic.variables.c b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.algebraic.variables.c index 5916e75f6..86a7cce8a 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.algebraic.variables.c +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.algebraic.variables.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 4; @@ -101,7 +101,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * constants[4] = 36.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { computedConstants[0] = constants[1]-10.613; computedConstants[1] = constants[1]-115.0; diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.algebraic.variables.h b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.algebraic.variables.h index cfc013f3b..c2e162982 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.algebraic.variables.h +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.algebraic.variables.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.algebraic.variables.py b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.algebraic.variables.py index 970d2e57d..a63e0c99b 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.algebraic.variables.py +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.algebraic.variables.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 4 @@ -79,7 +79,7 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[4] = 36.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): computed_constants[0] = constants[1]-10.613 computed_constants[1] = constants[1]-115.0 computed_constants[2] = constants[1]+12.0 diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.algebraic.variables.with.externals.c b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.algebraic.variables.with.externals.c index ecfede2bd..c4eb86832 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.algebraic.variables.with.externals.c +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.algebraic.variables.with.externals.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 4; @@ -118,7 +118,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * constants[4] = 36.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { computedConstants[0] = constants[1]-10.613; computedConstants[1] = constants[1]-115.0; diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.algebraic.variables.with.externals.h b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.algebraic.variables.with.externals.h index ce6057728..79abbba9c 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.algebraic.variables.with.externals.h +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.algebraic.variables.with.externals.h @@ -37,6 +37,6 @@ void deleteArray(double *array); typedef double (* ExternalVariable)(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, size_t index); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.algebraic.variables.with.externals.py b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.algebraic.variables.with.externals.py index cdc3538a4..159732578 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.algebraic.variables.with.externals.py +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.algebraic.variables.with.externals.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 4 @@ -89,7 +89,7 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[4] = 36.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): computed_constants[0] = constants[1]-10.613 computed_constants[1] = constants[1]-115.0 computed_constants[2] = constants[1]+12.0 @@ -99,11 +99,11 @@ def compute_rates(voi, states, rates, constants, computed_constants, algebraic_v membrane_i_Stim = -20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0 leakage_current_i_L = constants[2]*(states[0]-computed_constants[0]) potassium_channel_i_K = constants[4]*pow(states[3], 4.0)*(states[0]-computed_constants[2]) - algebraicVariables[0] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) - rates[0] = -(-membrane_i_Stim+externalVariables[0]+potassium_channel_i_K+leakage_current_i_L)/constants[0] + algebraic_variables[0] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + rates[0] = -(-membrane_i_Stim+external_variables[0]+potassium_channel_i_K+leakage_current_i_L)/constants[0] sodium_channel_m_gate_beta_m = 4.0*exp(states[0]/18.0) - rates[2] = algebraicVariables[0]*(1.0-states[2])-sodium_channel_m_gate_beta_m*states[2] + rates[2] = algebraic_variables[0]*(1.0-states[2])-sodium_channel_m_gate_beta_m*states[2] sodium_channel_h_gate_beta_h = 1.0/(exp((states[0]+30.0)/10.0)+1.0) sodium_channel_h_gate_alpha_h = 0.07*exp(states[0]/20.0) rates[1] = sodium_channel_h_gate_alpha_h*(1.0-states[1])-sodium_channel_h_gate_beta_h*states[1] @@ -113,5 +113,5 @@ def compute_rates(voi, states, rates, constants, computed_constants, algebraic_v def compute_variables(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, external_variable): - algebraicVariables[0] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + algebraic_variables[0] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.computed.constants.c b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.computed.constants.c index 1a0f8548c..44fd3cd02 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.computed.constants.c +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.computed.constants.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 4; @@ -108,7 +108,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * constants[4] = 36.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.computed.constants.h b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.computed.constants.h index 42166250c..fc447c7a3 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.computed.constants.h +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.computed.constants.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.computed.constants.py b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.computed.constants.py index e08938232..73245eb29 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.computed.constants.py +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.computed.constants.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 4 @@ -86,40 +86,40 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[4] = 36.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass def compute_rates(voi, states, rates, constants, computed_constants, algebraic_variables): - algebraicVariables[0] = -20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0 + algebraic_variables[0] = -20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0 leakage_current_E_L = constants[1]-10.613 - algebraicVariables[1] = constants[2]*(states[0]-leakage_current_E_L) + algebraic_variables[1] = constants[2]*(states[0]-leakage_current_E_L) potassium_channel_E_K = constants[1]+12.0 - algebraicVariables[2] = constants[4]*pow(states[3], 4.0)*(states[0]-potassium_channel_E_K) + algebraic_variables[2] = constants[4]*pow(states[3], 4.0)*(states[0]-potassium_channel_E_K) sodium_channel_E_Na = constants[1]-115.0 - algebraicVariables[3] = constants[3]*pow(states[2], 3.0)*states[1]*(states[0]-sodium_channel_E_Na) - rates[0] = -(-algebraicVariables[0]+algebraicVariables[3]+algebraicVariables[2]+algebraicVariables[1])/constants[0] - algebraicVariables[5] = 4.0*exp(states[0]/18.0) - algebraicVariables[4] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - rates[2] = algebraicVariables[4]*(1.0-states[2])-algebraicVariables[5]*states[2] - algebraicVariables[7] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) - algebraicVariables[6] = 0.07*exp(states[0]/20.0) - rates[1] = algebraicVariables[6]*(1.0-states[1])-algebraicVariables[7]*states[1] - algebraicVariables[9] = 0.125*exp(states[0]/80.0) - algebraicVariables[8] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) - rates[3] = algebraicVariables[8]*(1.0-states[3])-algebraicVariables[9]*states[3] + algebraic_variables[3] = constants[3]*pow(states[2], 3.0)*states[1]*(states[0]-sodium_channel_E_Na) + rates[0] = -(-algebraic_variables[0]+algebraic_variables[3]+algebraic_variables[2]+algebraic_variables[1])/constants[0] + algebraic_variables[5] = 4.0*exp(states[0]/18.0) + algebraic_variables[4] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + rates[2] = algebraic_variables[4]*(1.0-states[2])-algebraic_variables[5]*states[2] + algebraic_variables[7] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) + algebraic_variables[6] = 0.07*exp(states[0]/20.0) + rates[1] = algebraic_variables[6]*(1.0-states[1])-algebraic_variables[7]*states[1] + algebraic_variables[9] = 0.125*exp(states[0]/80.0) + algebraic_variables[8] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) + rates[3] = algebraic_variables[8]*(1.0-states[3])-algebraic_variables[9]*states[3] def compute_variables(voi, states, rates, constants, computed_constants, algebraic_variables): leakage_current_E_L = constants[1]-10.613 - algebraicVariables[1] = constants[2]*(states[0]-leakage_current_E_L) + algebraic_variables[1] = constants[2]*(states[0]-leakage_current_E_L) sodium_channel_E_Na = constants[1]-115.0 - algebraicVariables[3] = constants[3]*pow(states[2], 3.0)*states[1]*(states[0]-sodium_channel_E_Na) - algebraicVariables[4] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - algebraicVariables[5] = 4.0*exp(states[0]/18.0) - algebraicVariables[6] = 0.07*exp(states[0]/20.0) - algebraicVariables[7] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) + algebraic_variables[3] = constants[3]*pow(states[2], 3.0)*states[1]*(states[0]-sodium_channel_E_Na) + algebraic_variables[4] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + algebraic_variables[5] = 4.0*exp(states[0]/18.0) + algebraic_variables[6] = 0.07*exp(states[0]/20.0) + algebraic_variables[7] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) potassium_channel_E_K = constants[1]+12.0 - algebraicVariables[2] = constants[4]*pow(states[3], 4.0)*(states[0]-potassium_channel_E_K) - algebraicVariables[8] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) - algebraicVariables[9] = 0.125*exp(states[0]/80.0) + algebraic_variables[2] = constants[4]*pow(states[3], 4.0)*(states[0]-potassium_channel_E_K) + algebraic_variables[8] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) + algebraic_variables[9] = 0.125*exp(states[0]/80.0) diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.computed.constants.with.externals.c b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.computed.constants.with.externals.c index db11b6482..19a840ebf 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.computed.constants.with.externals.c +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.computed.constants.with.externals.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 4; @@ -124,7 +124,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * constants[4] = 36.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { computedConstants[0] = constants[1]+12.0; } diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.computed.constants.with.externals.h b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.computed.constants.with.externals.h index ce6057728..79abbba9c 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.computed.constants.with.externals.h +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.computed.constants.with.externals.h @@ -37,6 +37,6 @@ void deleteArray(double *array); typedef double (* ExternalVariable)(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, size_t index); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.computed.constants.with.externals.py b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.computed.constants.with.externals.py index 8121562c6..1be9e6eaa 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.computed.constants.with.externals.py +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.computed.constants.with.externals.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 4 @@ -95,36 +95,36 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[4] = 36.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): computed_constants[0] = constants[1]+12.0 def compute_rates(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, external_variable): - algebraicVariables[0] = -20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0 + algebraic_variables[0] = -20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0 leakage_current_E_L = constants[1]-10.613 - algebraicVariables[1] = constants[2]*(states[0]-leakage_current_E_L) - algebraicVariables[2] = constants[4]*pow(states[3], 4.0)*(states[0]-computed_constants[0]) - algebraicVariables[3] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) - rates[0] = -(-algebraicVariables[0]+externalVariables[0]+algebraicVariables[2]+algebraicVariables[1])/constants[0] - algebraicVariables[4] = 4.0*exp(states[0]/18.0) - rates[2] = algebraicVariables[3]*(1.0-states[2])-algebraicVariables[4]*states[2] - algebraicVariables[6] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) - algebraicVariables[5] = 0.07*exp(states[0]/20.0) - rates[1] = algebraicVariables[5]*(1.0-states[1])-algebraicVariables[6]*states[1] - algebraicVariables[8] = 0.125*exp(states[0]/80.0) - algebraicVariables[7] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) - rates[3] = algebraicVariables[7]*(1.0-states[3])-algebraicVariables[8]*states[3] + algebraic_variables[1] = constants[2]*(states[0]-leakage_current_E_L) + algebraic_variables[2] = constants[4]*pow(states[3], 4.0)*(states[0]-computed_constants[0]) + algebraic_variables[3] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + rates[0] = -(-algebraic_variables[0]+external_variables[0]+algebraic_variables[2]+algebraic_variables[1])/constants[0] + algebraic_variables[4] = 4.0*exp(states[0]/18.0) + rates[2] = algebraic_variables[3]*(1.0-states[2])-algebraic_variables[4]*states[2] + algebraic_variables[6] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) + algebraic_variables[5] = 0.07*exp(states[0]/20.0) + rates[1] = algebraic_variables[5]*(1.0-states[1])-algebraic_variables[6]*states[1] + algebraic_variables[8] = 0.125*exp(states[0]/80.0) + algebraic_variables[7] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) + rates[3] = algebraic_variables[7]*(1.0-states[3])-algebraic_variables[8]*states[3] def compute_variables(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, external_variable): leakage_current_E_L = constants[1]-10.613 - algebraicVariables[1] = constants[2]*(states[0]-leakage_current_E_L) - algebraicVariables[3] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) - algebraicVariables[4] = 4.0*exp(states[0]/18.0) - algebraicVariables[5] = 0.07*exp(states[0]/20.0) - algebraicVariables[6] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) - algebraicVariables[2] = constants[4]*pow(states[3], 4.0)*(states[0]-computed_constants[0]) - algebraicVariables[7] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) - algebraicVariables[8] = 0.125*exp(states[0]/80.0) + algebraic_variables[1] = constants[2]*(states[0]-leakage_current_E_L) + algebraic_variables[3] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + algebraic_variables[4] = 4.0*exp(states[0]/18.0) + algebraic_variables[5] = 0.07*exp(states[0]/20.0) + algebraic_variables[6] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) + algebraic_variables[2] = constants[4]*pow(states[3], 4.0)*(states[0]-computed_constants[0]) + algebraic_variables[7] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) + algebraic_variables[8] = 0.125*exp(states[0]/80.0) diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.constants.c b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.constants.c index 43c8bf1c4..2ef8438a0 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.constants.c +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.constants.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 4; @@ -101,7 +101,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * states[3] = 0.325; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { double membrane_E_R = 0.0; computedConstants[0] = membrane_E_R-10.613; diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.constants.h b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.constants.h index 42166250c..fc447c7a3 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.constants.h +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.constants.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.constants.py b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.constants.py index 11b5db173..06dd6a12c 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.constants.py +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.constants.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 4 @@ -79,7 +79,7 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va states[3] = 0.325 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): membrane_E_R = 0.0 computed_constants[0] = membrane_E_R-10.613 computed_constants[1] = membrane_E_R-115.0 @@ -88,35 +88,35 @@ def compute_computed_constants(states, rates, constants, computed_constants, alg def compute_rates(voi, states, rates, constants, computed_constants, algebraic_variables): membrane_Cm = 1.0 - algebraicVariables[0] = -20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0 + algebraic_variables[0] = -20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0 leakage_current_g_L = 0.3 - algebraicVariables[1] = leakage_current_g_L*(states[0]-computed_constants[0]) + algebraic_variables[1] = leakage_current_g_L*(states[0]-computed_constants[0]) potassium_channel_g_K = 36.0 - algebraicVariables[2] = potassium_channel_g_K*pow(states[3], 4.0)*(states[0]-computed_constants[2]) + algebraic_variables[2] = potassium_channel_g_K*pow(states[3], 4.0)*(states[0]-computed_constants[2]) sodium_channel_g_Na = 120.0 - algebraicVariables[3] = sodium_channel_g_Na*pow(states[2], 3.0)*states[1]*(states[0]-computed_constants[1]) - rates[0] = -(-algebraicVariables[0]+algebraicVariables[3]+algebraicVariables[2]+algebraicVariables[1])/membrane_Cm - algebraicVariables[5] = 4.0*exp(states[0]/18.0) - algebraicVariables[4] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - rates[2] = algebraicVariables[4]*(1.0-states[2])-algebraicVariables[5]*states[2] - algebraicVariables[7] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) - algebraicVariables[6] = 0.07*exp(states[0]/20.0) - rates[1] = algebraicVariables[6]*(1.0-states[1])-algebraicVariables[7]*states[1] - algebraicVariables[9] = 0.125*exp(states[0]/80.0) - algebraicVariables[8] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) - rates[3] = algebraicVariables[8]*(1.0-states[3])-algebraicVariables[9]*states[3] + algebraic_variables[3] = sodium_channel_g_Na*pow(states[2], 3.0)*states[1]*(states[0]-computed_constants[1]) + rates[0] = -(-algebraic_variables[0]+algebraic_variables[3]+algebraic_variables[2]+algebraic_variables[1])/membrane_Cm + algebraic_variables[5] = 4.0*exp(states[0]/18.0) + algebraic_variables[4] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + rates[2] = algebraic_variables[4]*(1.0-states[2])-algebraic_variables[5]*states[2] + algebraic_variables[7] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) + algebraic_variables[6] = 0.07*exp(states[0]/20.0) + rates[1] = algebraic_variables[6]*(1.0-states[1])-algebraic_variables[7]*states[1] + algebraic_variables[9] = 0.125*exp(states[0]/80.0) + algebraic_variables[8] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) + rates[3] = algebraic_variables[8]*(1.0-states[3])-algebraic_variables[9]*states[3] def compute_variables(voi, states, rates, constants, computed_constants, algebraic_variables): leakage_current_g_L = 0.3 - algebraicVariables[1] = leakage_current_g_L*(states[0]-computed_constants[0]) + algebraic_variables[1] = leakage_current_g_L*(states[0]-computed_constants[0]) sodium_channel_g_Na = 120.0 - algebraicVariables[3] = sodium_channel_g_Na*pow(states[2], 3.0)*states[1]*(states[0]-computed_constants[1]) - algebraicVariables[4] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - algebraicVariables[5] = 4.0*exp(states[0]/18.0) - algebraicVariables[6] = 0.07*exp(states[0]/20.0) - algebraicVariables[7] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) + algebraic_variables[3] = sodium_channel_g_Na*pow(states[2], 3.0)*states[1]*(states[0]-computed_constants[1]) + algebraic_variables[4] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + algebraic_variables[5] = 4.0*exp(states[0]/18.0) + algebraic_variables[6] = 0.07*exp(states[0]/20.0) + algebraic_variables[7] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) potassium_channel_g_K = 36.0 - algebraicVariables[2] = potassium_channel_g_K*pow(states[3], 4.0)*(states[0]-computed_constants[2]) - algebraicVariables[8] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) - algebraicVariables[9] = 0.125*exp(states[0]/80.0) + algebraic_variables[2] = potassium_channel_g_K*pow(states[3], 4.0)*(states[0]-computed_constants[2]) + algebraic_variables[8] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) + algebraic_variables[9] = 0.125*exp(states[0]/80.0) diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.constants.with.externals.c b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.constants.with.externals.c index ea555fbb0..caca8974a 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.constants.with.externals.c +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.constants.with.externals.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 4; @@ -118,7 +118,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * constants[0] = 1.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { double membrane_E_R = 0.0; computedConstants[0] = membrane_E_R-10.613; diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.constants.with.externals.h b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.constants.with.externals.h index ce6057728..79abbba9c 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.constants.with.externals.h +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.constants.with.externals.h @@ -37,6 +37,6 @@ void deleteArray(double *array); typedef double (* ExternalVariable)(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, size_t index); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.constants.with.externals.py b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.constants.with.externals.py index 2ad0d6571..fede24957 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.constants.with.externals.py +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.constants.with.externals.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 4 @@ -89,7 +89,7 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[0] = 1.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): membrane_E_R = 0.0 computed_constants[0] = membrane_E_R-10.613 computed_constants[1] = membrane_E_R-115.0 @@ -97,33 +97,33 @@ def compute_computed_constants(states, rates, constants, computed_constants, alg def compute_rates(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, external_variable): - algebraicVariables[0] = -20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0 + algebraic_variables[0] = -20.0 if and_func(geq_func(voi, 10.0), leq_func(voi, 10.5)) else 0.0 leakage_current_g_L = 0.3 - algebraicVariables[1] = leakage_current_g_L*(states[0]-computed_constants[0]) + algebraic_variables[1] = leakage_current_g_L*(states[0]-computed_constants[0]) potassium_channel_g_K = 36.0 - algebraicVariables[2] = potassium_channel_g_K*pow(states[3], 4.0)*(states[0]-computed_constants[2]) - algebraicVariables[3] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) - rates[0] = -(-algebraicVariables[0]+externalVariables[0]+algebraicVariables[2]+algebraicVariables[1])/constants[0] - algebraicVariables[4] = 4.0*exp(states[0]/18.0) - rates[2] = algebraicVariables[3]*(1.0-states[2])-algebraicVariables[4]*states[2] - algebraicVariables[6] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) - algebraicVariables[5] = 0.07*exp(states[0]/20.0) - rates[1] = algebraicVariables[5]*(1.0-states[1])-algebraicVariables[6]*states[1] - algebraicVariables[8] = 0.125*exp(states[0]/80.0) - algebraicVariables[7] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) - rates[3] = algebraicVariables[7]*(1.0-states[3])-algebraicVariables[8]*states[3] + algebraic_variables[2] = potassium_channel_g_K*pow(states[3], 4.0)*(states[0]-computed_constants[2]) + algebraic_variables[3] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + rates[0] = -(-algebraic_variables[0]+external_variables[0]+algebraic_variables[2]+algebraic_variables[1])/constants[0] + algebraic_variables[4] = 4.0*exp(states[0]/18.0) + rates[2] = algebraic_variables[3]*(1.0-states[2])-algebraic_variables[4]*states[2] + algebraic_variables[6] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) + algebraic_variables[5] = 0.07*exp(states[0]/20.0) + rates[1] = algebraic_variables[5]*(1.0-states[1])-algebraic_variables[6]*states[1] + algebraic_variables[8] = 0.125*exp(states[0]/80.0) + algebraic_variables[7] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) + rates[3] = algebraic_variables[7]*(1.0-states[3])-algebraic_variables[8]*states[3] def compute_variables(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, external_variable): leakage_current_g_L = 0.3 - algebraicVariables[1] = leakage_current_g_L*(states[0]-computed_constants[0]) - algebraicVariables[3] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) - algebraicVariables[4] = 4.0*exp(states[0]/18.0) - algebraicVariables[5] = 0.07*exp(states[0]/20.0) - algebraicVariables[6] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) + algebraic_variables[1] = leakage_current_g_L*(states[0]-computed_constants[0]) + algebraic_variables[3] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + algebraic_variables[4] = 4.0*exp(states[0]/18.0) + algebraic_variables[5] = 0.07*exp(states[0]/20.0) + algebraic_variables[6] = 1.0/(exp((states[0]+30.0)/10.0)+1.0) potassium_channel_g_K = 36.0 - algebraicVariables[2] = potassium_channel_g_K*pow(states[3], 4.0)*(states[0]-computed_constants[2]) - algebraicVariables[7] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) - algebraicVariables[8] = 0.125*exp(states[0]/80.0) + algebraic_variables[2] = potassium_channel_g_K*pow(states[3], 4.0)*(states[0]-computed_constants[2]) + algebraic_variables[7] = 0.01*(states[0]+10.0)/(exp((states[0]+10.0)/10.0)-1.0) + algebraic_variables[8] = 0.125*exp(states[0]/80.0) diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.variables.c b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.variables.c index 14eceb062..d36ac71b9 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.variables.c +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.variables.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 4; @@ -88,7 +88,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * states[3] = 0.325; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.variables.h b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.variables.h index 48c35e85f..defea664d 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.variables.h +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.variables.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.variables.py b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.variables.py index 5d123acf2..f2b8ec14e 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.variables.py +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.variables.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 4 @@ -66,7 +66,7 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va states[3] = 0.325 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.variables.with.externals.c b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.variables.with.externals.c index af325fec9..808fc86fc 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.variables.with.externals.c +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.variables.with.externals.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 4; @@ -108,7 +108,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * constants[0] = 1.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { double membrane_E_R = 0.0; computedConstants[0] = membrane_E_R+12.0; diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.variables.with.externals.h b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.variables.with.externals.h index ce6057728..79abbba9c 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.variables.with.externals.h +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.variables.with.externals.h @@ -37,6 +37,6 @@ void deleteArray(double *array); typedef double (* ExternalVariable)(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, size_t index); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); diff --git a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.variables.with.externals.py b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.variables.with.externals.py index 417ff539b..8507693f2 100644 --- a/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.variables.with.externals.py +++ b/tests/resources/generator/hodgkin_huxley_squid_axon_model_1952/model.untracked.variables.with.externals.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 4 @@ -79,7 +79,7 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[0] = 1.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): membrane_E_R = 0.0 computed_constants[0] = membrane_E_R+12.0 @@ -92,11 +92,11 @@ def compute_rates(voi, states, rates, constants, computed_constants, algebraic_v leakage_current_i_L = leakage_current_g_L*(states[0]-leakage_current_E_L) potassium_channel_g_K = 36.0 potassium_channel_i_K = potassium_channel_g_K*pow(states[3], 4.0)*(states[0]-computed_constants[0]) - algebraicVariables[0] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) - rates[0] = -(-membrane_i_Stim+externalVariables[0]+potassium_channel_i_K+leakage_current_i_L)/constants[0] + algebraic_variables[0] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + rates[0] = -(-membrane_i_Stim+external_variables[0]+potassium_channel_i_K+leakage_current_i_L)/constants[0] sodium_channel_m_gate_beta_m = 4.0*exp(states[0]/18.0) - rates[2] = algebraicVariables[0]*(1.0-states[2])-sodium_channel_m_gate_beta_m*states[2] + rates[2] = algebraic_variables[0]*(1.0-states[2])-sodium_channel_m_gate_beta_m*states[2] sodium_channel_h_gate_beta_h = 1.0/(exp((states[0]+30.0)/10.0)+1.0) sodium_channel_h_gate_alpha_h = 0.07*exp(states[0]/20.0) rates[1] = sodium_channel_h_gate_alpha_h*(1.0-states[1])-sodium_channel_h_gate_beta_h*states[1] @@ -106,5 +106,5 @@ def compute_rates(voi, states, rates, constants, computed_constants, algebraic_v def compute_variables(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, external_variable): - algebraicVariables[0] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) - externalVariables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) + algebraic_variables[0] = 0.1*(states[0]+25.0)/(exp((states[0]+25.0)/10.0)-1.0) + external_variables[0] = external_variable(voi, states, rates, constants, computed_constants, algebraic_variables, external_variables, 0) diff --git a/tests/resources/generator/noble_model_1962/model.c b/tests/resources/generator/noble_model_1962/model.c index 478d6313b..0d945d3c0 100644 --- a/tests/resources/generator/noble_model_1962/model.c +++ b/tests/resources/generator/noble_model_1962/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 4; @@ -110,7 +110,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * constants[4] = 40.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/noble_model_1962/model.h b/tests/resources/generator/noble_model_1962/model.h index ab8a773bd..6a7a9320e 100644 --- a/tests/resources/generator/noble_model_1962/model.h +++ b/tests/resources/generator/noble_model_1962/model.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/noble_model_1962/model.py b/tests/resources/generator/noble_model_1962/model.py index 364e1e0aa..78396758f 100644 --- a/tests/resources/generator/noble_model_1962/model.py +++ b/tests/resources/generator/noble_model_1962/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 4 @@ -76,39 +76,39 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[4] = 40.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass def compute_rates(voi, states, rates, constants, computed_constants, algebraic_variables): - algebraicVariables[0] = constants[2]*(states[0]-constants[1]) - algebraicVariables[3] = pow(states[2], 3.0)*states[1]*constants[3] - algebraicVariables[2] = (algebraicVariables[3]+0.14)*(states[0]-constants[4]) - algebraicVariables[8] = 1.2*pow(states[3], 4.0) - algebraicVariables[9] = 1.2*exp((-states[0]-90.0)/50.0)+0.015*exp((states[0]+90.0)/60.0) - algebraicVariables[1] = (algebraicVariables[9]+algebraicVariables[8])*(states[0]+100.0) - rates[0] = -(algebraicVariables[2]+algebraicVariables[1]+algebraicVariables[0])/constants[0] - algebraicVariables[5] = 0.12*(states[0]+8.0)/(exp((states[0]+8.0)/5.0)-1.0) - algebraicVariables[4] = 0.1*(-states[0]-48.0)/(exp((-states[0]-48.0)/15.0)-1.0) - rates[2] = algebraicVariables[4]*(1.0-states[2])-algebraicVariables[5]*states[2] - algebraicVariables[7] = 1.0/(1.0+exp((-states[0]-42.0)/10.0)) - algebraicVariables[6] = 0.17*exp((-states[0]-90.0)/20.0) - rates[1] = algebraicVariables[6]*(1.0-states[1])-algebraicVariables[7]*states[1] - algebraicVariables[11] = 0.002*exp((-states[0]-90.0)/80.0) - algebraicVariables[10] = 0.0001*(-states[0]-50.0)/(exp((-states[0]-50.0)/10.0)-1.0) - rates[3] = algebraicVariables[10]*(1.0-states[3])-algebraicVariables[11]*states[3] + algebraic_variables[0] = constants[2]*(states[0]-constants[1]) + algebraic_variables[3] = pow(states[2], 3.0)*states[1]*constants[3] + algebraic_variables[2] = (algebraic_variables[3]+0.14)*(states[0]-constants[4]) + algebraic_variables[8] = 1.2*pow(states[3], 4.0) + algebraic_variables[9] = 1.2*exp((-states[0]-90.0)/50.0)+0.015*exp((states[0]+90.0)/60.0) + algebraic_variables[1] = (algebraic_variables[9]+algebraic_variables[8])*(states[0]+100.0) + rates[0] = -(algebraic_variables[2]+algebraic_variables[1]+algebraic_variables[0])/constants[0] + algebraic_variables[5] = 0.12*(states[0]+8.0)/(exp((states[0]+8.0)/5.0)-1.0) + algebraic_variables[4] = 0.1*(-states[0]-48.0)/(exp((-states[0]-48.0)/15.0)-1.0) + rates[2] = algebraic_variables[4]*(1.0-states[2])-algebraic_variables[5]*states[2] + algebraic_variables[7] = 1.0/(1.0+exp((-states[0]-42.0)/10.0)) + algebraic_variables[6] = 0.17*exp((-states[0]-90.0)/20.0) + rates[1] = algebraic_variables[6]*(1.0-states[1])-algebraic_variables[7]*states[1] + algebraic_variables[11] = 0.002*exp((-states[0]-90.0)/80.0) + algebraic_variables[10] = 0.0001*(-states[0]-50.0)/(exp((-states[0]-50.0)/10.0)-1.0) + rates[3] = algebraic_variables[10]*(1.0-states[3])-algebraic_variables[11]*states[3] def compute_variables(voi, states, rates, constants, computed_constants, algebraic_variables): - algebraicVariables[0] = constants[2]*(states[0]-constants[1]) - algebraicVariables[3] = pow(states[2], 3.0)*states[1]*constants[3] - algebraicVariables[2] = (algebraicVariables[3]+0.14)*(states[0]-constants[4]) - algebraicVariables[4] = 0.1*(-states[0]-48.0)/(exp((-states[0]-48.0)/15.0)-1.0) - algebraicVariables[5] = 0.12*(states[0]+8.0)/(exp((states[0]+8.0)/5.0)-1.0) - algebraicVariables[6] = 0.17*exp((-states[0]-90.0)/20.0) - algebraicVariables[7] = 1.0/(1.0+exp((-states[0]-42.0)/10.0)) - algebraicVariables[8] = 1.2*pow(states[3], 4.0) - algebraicVariables[9] = 1.2*exp((-states[0]-90.0)/50.0)+0.015*exp((states[0]+90.0)/60.0) - algebraicVariables[1] = (algebraicVariables[9]+algebraicVariables[8])*(states[0]+100.0) - algebraicVariables[10] = 0.0001*(-states[0]-50.0)/(exp((-states[0]-50.0)/10.0)-1.0) - algebraicVariables[11] = 0.002*exp((-states[0]-90.0)/80.0) + algebraic_variables[0] = constants[2]*(states[0]-constants[1]) + algebraic_variables[3] = pow(states[2], 3.0)*states[1]*constants[3] + algebraic_variables[2] = (algebraic_variables[3]+0.14)*(states[0]-constants[4]) + algebraic_variables[4] = 0.1*(-states[0]-48.0)/(exp((-states[0]-48.0)/15.0)-1.0) + algebraic_variables[5] = 0.12*(states[0]+8.0)/(exp((states[0]+8.0)/5.0)-1.0) + algebraic_variables[6] = 0.17*exp((-states[0]-90.0)/20.0) + algebraic_variables[7] = 1.0/(1.0+exp((-states[0]-42.0)/10.0)) + algebraic_variables[8] = 1.2*pow(states[3], 4.0) + algebraic_variables[9] = 1.2*exp((-states[0]-90.0)/50.0)+0.015*exp((states[0]+90.0)/60.0) + algebraic_variables[1] = (algebraic_variables[9]+algebraic_variables[8])*(states[0]+100.0) + algebraic_variables[10] = 0.0001*(-states[0]-50.0)/(exp((-states[0]-50.0)/10.0)-1.0) + algebraic_variables[11] = 0.002*exp((-states[0]-90.0)/80.0) diff --git a/tests/resources/generator/ode_computed_var_on_rhs/model.c b/tests/resources/generator/ode_computed_var_on_rhs/model.c index fcc7ff203..b5e5fd19a 100644 --- a/tests/resources/generator/ode_computed_var_on_rhs/model.c +++ b/tests/resources/generator/ode_computed_var_on_rhs/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 1; @@ -84,7 +84,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * computedConstants[0] = 1.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/ode_computed_var_on_rhs/model.h b/tests/resources/generator/ode_computed_var_on_rhs/model.h index 77fc3ba73..3d1b51eab 100644 --- a/tests/resources/generator/ode_computed_var_on_rhs/model.h +++ b/tests/resources/generator/ode_computed_var_on_rhs/model.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/ode_computed_var_on_rhs/model.py b/tests/resources/generator/ode_computed_var_on_rhs/model.py index df9a63a65..cc3abbde2 100644 --- a/tests/resources/generator/ode_computed_var_on_rhs/model.py +++ b/tests/resources/generator/ode_computed_var_on_rhs/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 1 @@ -50,7 +50,7 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va computed_constants[0] = 1.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass diff --git a/tests/resources/generator/ode_computed_var_on_rhs_one_component/model.c b/tests/resources/generator/ode_computed_var_on_rhs_one_component/model.c index 1cfd3811e..831659dc2 100644 --- a/tests/resources/generator/ode_computed_var_on_rhs_one_component/model.c +++ b/tests/resources/generator/ode_computed_var_on_rhs_one_component/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 1; @@ -84,7 +84,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * computedConstants[0] = 1.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/ode_computed_var_on_rhs_one_component/model.h b/tests/resources/generator/ode_computed_var_on_rhs_one_component/model.h index 94ce70879..ef2c23c08 100644 --- a/tests/resources/generator/ode_computed_var_on_rhs_one_component/model.h +++ b/tests/resources/generator/ode_computed_var_on_rhs_one_component/model.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/ode_computed_var_on_rhs_one_component/model.py b/tests/resources/generator/ode_computed_var_on_rhs_one_component/model.py index a168ec78d..054d248ac 100644 --- a/tests/resources/generator/ode_computed_var_on_rhs_one_component/model.py +++ b/tests/resources/generator/ode_computed_var_on_rhs_one_component/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 1 @@ -50,7 +50,7 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va computed_constants[0] = 1.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass diff --git a/tests/resources/generator/ode_const_var_on_rhs/model.c b/tests/resources/generator/ode_const_var_on_rhs/model.c index aa63c71a8..922f30cf5 100644 --- a/tests/resources/generator/ode_const_var_on_rhs/model.c +++ b/tests/resources/generator/ode_const_var_on_rhs/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 1; @@ -84,7 +84,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * constants[0] = 1.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/ode_const_var_on_rhs/model.h b/tests/resources/generator/ode_const_var_on_rhs/model.h index 77fc3ba73..3d1b51eab 100644 --- a/tests/resources/generator/ode_const_var_on_rhs/model.h +++ b/tests/resources/generator/ode_const_var_on_rhs/model.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/ode_const_var_on_rhs/model.py b/tests/resources/generator/ode_const_var_on_rhs/model.py index 9b8635746..0901d5c10 100644 --- a/tests/resources/generator/ode_const_var_on_rhs/model.py +++ b/tests/resources/generator/ode_const_var_on_rhs/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 1 @@ -50,7 +50,7 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[0] = 1.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass diff --git a/tests/resources/generator/ode_const_var_on_rhs_one_component/model.c b/tests/resources/generator/ode_const_var_on_rhs_one_component/model.c index 91ff04853..978168e5d 100644 --- a/tests/resources/generator/ode_const_var_on_rhs_one_component/model.c +++ b/tests/resources/generator/ode_const_var_on_rhs_one_component/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 1; @@ -84,7 +84,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * constants[0] = 1.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/ode_const_var_on_rhs_one_component/model.h b/tests/resources/generator/ode_const_var_on_rhs_one_component/model.h index 94ce70879..ef2c23c08 100644 --- a/tests/resources/generator/ode_const_var_on_rhs_one_component/model.h +++ b/tests/resources/generator/ode_const_var_on_rhs_one_component/model.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/ode_const_var_on_rhs_one_component/model.py b/tests/resources/generator/ode_const_var_on_rhs_one_component/model.py index fefb2b70e..a73f20f89 100644 --- a/tests/resources/generator/ode_const_var_on_rhs_one_component/model.py +++ b/tests/resources/generator/ode_const_var_on_rhs_one_component/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 1 @@ -50,7 +50,7 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[0] = 1.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass diff --git a/tests/resources/generator/ode_constant_on_rhs/model.c b/tests/resources/generator/ode_constant_on_rhs/model.c index dbc6d14ed..116e6f767 100644 --- a/tests/resources/generator/ode_constant_on_rhs/model.c +++ b/tests/resources/generator/ode_constant_on_rhs/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 1; @@ -82,7 +82,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * states[0] = 1.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/ode_constant_on_rhs/model.h b/tests/resources/generator/ode_constant_on_rhs/model.h index 77fc3ba73..3d1b51eab 100644 --- a/tests/resources/generator/ode_constant_on_rhs/model.h +++ b/tests/resources/generator/ode_constant_on_rhs/model.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/ode_constant_on_rhs/model.py b/tests/resources/generator/ode_constant_on_rhs/model.py index f44993163..399e90be4 100644 --- a/tests/resources/generator/ode_constant_on_rhs/model.py +++ b/tests/resources/generator/ode_constant_on_rhs/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 1 @@ -48,7 +48,7 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va states[0] = 1.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass diff --git a/tests/resources/generator/ode_constant_on_rhs_one_component/model.c b/tests/resources/generator/ode_constant_on_rhs_one_component/model.c index 501d29487..ae7824130 100644 --- a/tests/resources/generator/ode_constant_on_rhs_one_component/model.c +++ b/tests/resources/generator/ode_constant_on_rhs_one_component/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 1; @@ -82,7 +82,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * states[0] = 1.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/ode_constant_on_rhs_one_component/model.h b/tests/resources/generator/ode_constant_on_rhs_one_component/model.h index 94ce70879..ef2c23c08 100644 --- a/tests/resources/generator/ode_constant_on_rhs_one_component/model.h +++ b/tests/resources/generator/ode_constant_on_rhs_one_component/model.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/ode_constant_on_rhs_one_component/model.py b/tests/resources/generator/ode_constant_on_rhs_one_component/model.py index 7ceec19df..9a5b24a75 100644 --- a/tests/resources/generator/ode_constant_on_rhs_one_component/model.py +++ b/tests/resources/generator/ode_constant_on_rhs_one_component/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 1 @@ -48,7 +48,7 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va states[0] = 1.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass diff --git a/tests/resources/generator/ode_multiple_dependent_odes/model.c b/tests/resources/generator/ode_multiple_dependent_odes/model.c index fccb0c0fd..1779ef016 100644 --- a/tests/resources/generator/ode_multiple_dependent_odes/model.c +++ b/tests/resources/generator/ode_multiple_dependent_odes/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 2; @@ -86,7 +86,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * constants[0] = 1.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/ode_multiple_dependent_odes/model.h b/tests/resources/generator/ode_multiple_dependent_odes/model.h index 990b801ab..dc5fb0e33 100644 --- a/tests/resources/generator/ode_multiple_dependent_odes/model.h +++ b/tests/resources/generator/ode_multiple_dependent_odes/model.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/ode_multiple_dependent_odes/model.py b/tests/resources/generator/ode_multiple_dependent_odes/model.py index 3a6e55180..d0873a51d 100644 --- a/tests/resources/generator/ode_multiple_dependent_odes/model.py +++ b/tests/resources/generator/ode_multiple_dependent_odes/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 2 @@ -52,7 +52,7 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[0] = 1.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass diff --git a/tests/resources/generator/ode_multiple_dependent_odes_one_component/model.c b/tests/resources/generator/ode_multiple_dependent_odes_one_component/model.c index 8bf0e0c15..1f1ebca94 100644 --- a/tests/resources/generator/ode_multiple_dependent_odes_one_component/model.c +++ b/tests/resources/generator/ode_multiple_dependent_odes_one_component/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 2; @@ -86,7 +86,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * constants[0] = 1.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/ode_multiple_dependent_odes_one_component/model.h b/tests/resources/generator/ode_multiple_dependent_odes_one_component/model.h index 1e0a626c6..eaedbc019 100644 --- a/tests/resources/generator/ode_multiple_dependent_odes_one_component/model.h +++ b/tests/resources/generator/ode_multiple_dependent_odes_one_component/model.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/ode_multiple_dependent_odes_one_component/model.py b/tests/resources/generator/ode_multiple_dependent_odes_one_component/model.py index 63bfb2913..36b40edce 100644 --- a/tests/resources/generator/ode_multiple_dependent_odes_one_component/model.py +++ b/tests/resources/generator/ode_multiple_dependent_odes_one_component/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 2 @@ -52,7 +52,7 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[0] = 1.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass diff --git a/tests/resources/generator/ode_multiple_odes_with_same_name/model.c b/tests/resources/generator/ode_multiple_odes_with_same_name/model.c index 6c51205d8..a585346a3 100644 --- a/tests/resources/generator/ode_multiple_odes_with_same_name/model.c +++ b/tests/resources/generator/ode_multiple_odes_with_same_name/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 2; @@ -86,7 +86,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * constants[0] = 1.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/ode_multiple_odes_with_same_name/model.h b/tests/resources/generator/ode_multiple_odes_with_same_name/model.h index b31ed3b01..51e2a0e7f 100644 --- a/tests/resources/generator/ode_multiple_odes_with_same_name/model.h +++ b/tests/resources/generator/ode_multiple_odes_with_same_name/model.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/ode_multiple_odes_with_same_name/model.py b/tests/resources/generator/ode_multiple_odes_with_same_name/model.py index 1eb1dc56e..4110af0c4 100644 --- a/tests/resources/generator/ode_multiple_odes_with_same_name/model.py +++ b/tests/resources/generator/ode_multiple_odes_with_same_name/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 2 @@ -52,7 +52,7 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[0] = 1.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass diff --git a/tests/resources/generator/ode_unknown_var_on_rhs/model.c b/tests/resources/generator/ode_unknown_var_on_rhs/model.c index 0c5cd74ca..1d9e11796 100644 --- a/tests/resources/generator/ode_unknown_var_on_rhs/model.c +++ b/tests/resources/generator/ode_unknown_var_on_rhs/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 2; @@ -84,7 +84,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * states[1] = 1.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/ode_unknown_var_on_rhs/model.h b/tests/resources/generator/ode_unknown_var_on_rhs/model.h index 77fc3ba73..3d1b51eab 100644 --- a/tests/resources/generator/ode_unknown_var_on_rhs/model.h +++ b/tests/resources/generator/ode_unknown_var_on_rhs/model.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/ode_unknown_var_on_rhs/model.py b/tests/resources/generator/ode_unknown_var_on_rhs/model.py index 58b203c3a..b145d050a 100644 --- a/tests/resources/generator/ode_unknown_var_on_rhs/model.py +++ b/tests/resources/generator/ode_unknown_var_on_rhs/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 2 @@ -50,7 +50,7 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va states[1] = 1.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass diff --git a/tests/resources/generator/robertson_model_1966/model.dae.c b/tests/resources/generator/robertson_model_1966/model.dae.c index a9d620fdb..68e7d3da4 100644 --- a/tests/resources/generator/robertson_model_1966/model.dae.c +++ b/tests/resources/generator/robertson_model_1966/model.dae.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 2; @@ -131,7 +131,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * algebraicVariables[0] = 0.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/robertson_model_1966/model.dae.h b/tests/resources/generator/robertson_model_1966/model.dae.h index e0920c811..c5e11dbaf 100644 --- a/tests/resources/generator/robertson_model_1966/model.dae.h +++ b/tests/resources/generator/robertson_model_1966/model.dae.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/robertson_model_1966/model.dae.py b/tests/resources/generator/robertson_model_1966/model.dae.py index 464d0d2c8..1064fce6c 100644 --- a/tests/resources/generator/robertson_model_1966/model.dae.py +++ b/tests/resources/generator/robertson_model_1966/model.dae.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 2 @@ -61,19 +61,19 @@ def objective_function_0(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[0] = u[0] + algebraic_variables[0] = u[0] - f[0] = 1.0-(states[1]+states[0]+algebraicVariables[0]) + f[0] = 1.0-(states[1]+states[0]+algebraic_variables[0]) def find_root_0(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[0] + u[0] = algebraic_variables[0] u = nla_solve(objective_function_0, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[0] = u[0] + algebraic_variables[0] = u[0] def initialise_arrays(states, rates, constants, computed_constants, algebraic_variables): @@ -82,19 +82,19 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[0] = 1.0e4 constants[1] = 0.04 constants[2] = 3.0e7 - algebraicVariables[0] = 0.0 + algebraic_variables[0] = 0.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass def compute_rates(voi, states, rates, constants, computed_constants, algebraic_variables): find_root_0(voi, states, rates, constants, computed_constants, algebraic_variables) - rates[1] = -constants[1]*states[1]+constants[0]*states[0]*algebraicVariables[0] - rates[0] = constants[1]*states[1]-constants[2]*pow(states[0], 2.0)-constants[0]*states[0]*algebraicVariables[0] + rates[1] = -constants[1]*states[1]+constants[0]*states[0]*algebraic_variables[0] + rates[0] = constants[1]*states[1]-constants[2]*pow(states[0], 2.0)-constants[0]*states[0]*algebraic_variables[0] def compute_variables(voi, states, rates, constants, computed_constants, algebraic_variables): find_root_0(voi, states, rates, constants, computed_constants, algebraic_variables) - algebraicVariables[1] = 10000.0*states[0] + algebraic_variables[1] = 10000.0*states[0] diff --git a/tests/resources/generator/robertson_model_1966/model.ode.c b/tests/resources/generator/robertson_model_1966/model.ode.c index d6d2380c0..0b16722fe 100644 --- a/tests/resources/generator/robertson_model_1966/model.ode.c +++ b/tests/resources/generator/robertson_model_1966/model.ode.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 3; @@ -93,7 +93,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * constants[2] = 3.0e7; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/robertson_model_1966/model.ode.h b/tests/resources/generator/robertson_model_1966/model.ode.h index e0920c811..c5e11dbaf 100644 --- a/tests/resources/generator/robertson_model_1966/model.ode.h +++ b/tests/resources/generator/robertson_model_1966/model.ode.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/robertson_model_1966/model.ode.py b/tests/resources/generator/robertson_model_1966/model.ode.py index beabee914..16dd5b103 100644 --- a/tests/resources/generator/robertson_model_1966/model.ode.py +++ b/tests/resources/generator/robertson_model_1966/model.ode.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 3 @@ -59,7 +59,7 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va constants[2] = 3.0e7 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass @@ -70,4 +70,4 @@ def compute_rates(voi, states, rates, constants, computed_constants, algebraic_v def compute_variables(voi, states, rates, constants, computed_constants, algebraic_variables): - algebraicVariables[0] = 10000.0*states[1] + algebraic_variables[0] = 10000.0*states[1] diff --git a/tests/resources/generator/sine_model_imports/model.c b/tests/resources/generator/sine_model_imports/model.c index 5eb541fa9..e56a58f53 100644 --- a/tests/resources/generator/sine_model_imports/model.c +++ b/tests/resources/generator/sine_model_imports/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 1; @@ -99,7 +99,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * computedConstants[4] = 3.0*3.14159265358979/2.0; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/sine_model_imports/model.h b/tests/resources/generator/sine_model_imports/model.h index bdf368648..0f67ed538 100644 --- a/tests/resources/generator/sine_model_imports/model.h +++ b/tests/resources/generator/sine_model_imports/model.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/sine_model_imports/model.py b/tests/resources/generator/sine_model_imports/model.py index 635b0ebad..a50724a6b 100644 --- a/tests/resources/generator/sine_model_imports/model.py +++ b/tests/resources/generator/sine_model_imports/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 1 @@ -69,7 +69,7 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va computed_constants[4] = 3.0*3.14159265358979/2.0 -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): pass @@ -78,6 +78,6 @@ def compute_rates(voi, states, rates, constants, computed_constants, algebraic_v def compute_variables(voi, states, rates, constants, computed_constants, algebraic_variables): - algebraicVariables[0] = sin(voi) - algebraicVariables[2] = voi*computed_constants[0]-0.5 if lt_func(voi, computed_constants[2]) else (3.14159265358979-voi)*computed_constants[0]-0.5 if lt_func(voi, computed_constants[3]) else (voi-3.14159265358979)*computed_constants[0]-0.5 if lt_func(voi, computed_constants[4]) else (computed_constants[1]-voi)*computed_constants[0]-0.5 - algebraicVariables[1] = -algebraicVariables[2]*algebraicVariables[2]+constants[1]+algebraicVariables[2] if lt_func(voi, computed_constants[2]) else -algebraicVariables[2]*algebraicVariables[2]+constants[1]+algebraicVariables[2] if lt_func(voi, computed_constants[3]) else algebraicVariables[2]*algebraicVariables[2]-constants[1]-algebraicVariables[2] if lt_func(voi, computed_constants[4]) else algebraicVariables[2]*algebraicVariables[2]-constants[1]-algebraicVariables[2] + algebraic_variables[0] = sin(voi) + algebraic_variables[2] = voi*computed_constants[0]-0.5 if lt_func(voi, computed_constants[2]) else (3.14159265358979-voi)*computed_constants[0]-0.5 if lt_func(voi, computed_constants[3]) else (voi-3.14159265358979)*computed_constants[0]-0.5 if lt_func(voi, computed_constants[4]) else (computed_constants[1]-voi)*computed_constants[0]-0.5 + algebraic_variables[1] = -algebraic_variables[2]*algebraic_variables[2]+constants[1]+algebraic_variables[2] if lt_func(voi, computed_constants[2]) else -algebraic_variables[2]*algebraic_variables[2]+constants[1]+algebraic_variables[2] if lt_func(voi, computed_constants[3]) else algebraic_variables[2]*algebraic_variables[2]-constants[1]-algebraic_variables[2] if lt_func(voi, computed_constants[4]) else algebraic_variables[2]*algebraic_variables[2]-constants[1]-algebraic_variables[2] diff --git a/tests/resources/generator/unknown_variable_as_external_variable/model.c b/tests/resources/generator/unknown_variable_as_external_variable/model.c index 59259bcc5..f0c3f2672 100644 --- a/tests/resources/generator/unknown_variable_as_external_variable/model.c +++ b/tests/resources/generator/unknown_variable_as_external_variable/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t CONSTANT_COUNT = 8; @@ -96,7 +96,7 @@ void initialiseArrays(double *constants, double *computedConstants, double *alge constants[7] = 1.1; } -void computeComputedConstants(double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables) { } diff --git a/tests/resources/generator/unknown_variable_as_external_variable/model.h b/tests/resources/generator/unknown_variable_as_external_variable/model.h index 75c0733e2..277efa5c4 100644 --- a/tests/resources/generator/unknown_variable_as_external_variable/model.h +++ b/tests/resources/generator/unknown_variable_as_external_variable/model.h @@ -33,5 +33,5 @@ void deleteArray(double *array); typedef double (* ExternalVariable)(double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, size_t index); void initialiseArrays(double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double *constants, double *computedConstants, double *algebraicVariables, double *externalVariables, ExternalVariable externalVariable); diff --git a/tests/resources/generator/unknown_variable_as_external_variable/model.py b/tests/resources/generator/unknown_variable_as_external_variable/model.py index 6e488c804..1205a26e4 100644 --- a/tests/resources/generator/unknown_variable_as_external_variable/model.py +++ b/tests/resources/generator/unknown_variable_as_external_variable/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" CONSTANT_COUNT = 8 @@ -62,10 +62,10 @@ def initialise_arrays(constants, computed_constants, algebraic_variables): constants[7] = 1.1 -def compute_computed_constants(constants, computed_constants, algebraic): +def compute_computed_constants(constants, computed_constants, algebraic_variables): pass def compute_variables(constants, computed_constants, algebraic_variables, external_variables, external_variable): - externalVariables[0] = external_variable(constants, computed_constants, algebraic_variables, external_variables, 0) - algebraicVariables[0] = constants[7]*(constants[6]*constants[1]-constants[5]*constants[2])/(constants[4]*constants[2]+externalVariables[0]*constants[1]+constants[3]*constants[2]*constants[1]+constants[0]) + external_variables[0] = external_variable(constants, computed_constants, algebraic_variables, external_variables, 0) + algebraic_variables[0] = constants[7]*(constants[6]*constants[1]-constants[5]*constants[2])/(constants[4]*constants[2]+external_variables[0]*constants[1]+constants[3]*constants[2]*constants[1]+constants[0]) diff --git a/tests/resources/generator/variable_initialised_using_another_variable/model.c b/tests/resources/generator/variable_initialised_using_another_variable/model.c index 69f212522..4d96c5c9c 100644 --- a/tests/resources/generator/variable_initialised_using_another_variable/model.c +++ b/tests/resources/generator/variable_initialised_using_another_variable/model.c @@ -5,7 +5,7 @@ #include #include -const char VERSION[] = "0.7.0"; +const char VERSION[] = "0.8.0"; const char LIBCELLML_VERSION[] = "0.6.3"; const size_t STATE_COUNT = 22; @@ -748,7 +748,7 @@ void initialiseArrays(double *states, double *rates, double *constants, double * algebraicVariables[20] = algebraicVariables[21]; } -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic) +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables) { computedConstants[0] = 1.23*constants[0]; states[3] = computedConstants[0]; diff --git a/tests/resources/generator/variable_initialised_using_another_variable/model.h b/tests/resources/generator/variable_initialised_using_another_variable/model.h index da5835c72..f293b7be3 100644 --- a/tests/resources/generator/variable_initialised_using_another_variable/model.h +++ b/tests/resources/generator/variable_initialised_using_another_variable/model.h @@ -32,6 +32,6 @@ double * createAlgebraicVariablesArray(); void deleteArray(double *array); void initialiseArrays(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); -void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraic); +void computeComputedConstants(double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeRates(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); void computeVariables(double voi, double *states, double *rates, double *constants, double *computedConstants, double *algebraicVariables); diff --git a/tests/resources/generator/variable_initialised_using_another_variable/model.py b/tests/resources/generator/variable_initialised_using_another_variable/model.py index 3c6dab99a..109e996dc 100644 --- a/tests/resources/generator/variable_initialised_using_another_variable/model.py +++ b/tests/resources/generator/variable_initialised_using_another_variable/model.py @@ -4,7 +4,7 @@ from math import * -__version__ = "0.6.0" +__version__ = "0.8.0" LIBCELLML_VERSION = "0.6.3" STATE_COUNT = 22 @@ -102,19 +102,19 @@ def objective_function_0(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[0] = u[0] + algebraic_variables[0] = u[0] - f[0] = voi-algebraicVariables[0] + f[0] = voi-algebraic_variables[0] def find_root_0(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[0] + u[0] = algebraic_variables[0] u = nla_solve(objective_function_0, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[0] = u[0] + algebraic_variables[0] = u[0] def objective_function_1(u, f, data): @@ -125,19 +125,19 @@ def objective_function_1(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[1] = u[0] + algebraic_variables[1] = u[0] - f[0] = voi-algebraicVariables[1] + f[0] = voi-algebraic_variables[1] def find_root_1(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[1] + u[0] = algebraic_variables[1] u = nla_solve(objective_function_1, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[1] = u[0] + algebraic_variables[1] = u[0] def objective_function_2(u, f, data): @@ -148,19 +148,19 @@ def objective_function_2(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[2] = u[0] + algebraic_variables[2] = u[0] - f[0] = voi-algebraicVariables[2] + f[0] = voi-algebraic_variables[2] def find_root_2(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[2] + u[0] = algebraic_variables[2] u = nla_solve(objective_function_2, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[2] = u[0] + algebraic_variables[2] = u[0] def objective_function_3(u, f, data): @@ -171,19 +171,19 @@ def objective_function_3(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[3] = u[0] + algebraic_variables[3] = u[0] - f[0] = voi-algebraicVariables[3] + f[0] = voi-algebraic_variables[3] def find_root_3(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[3] + u[0] = algebraic_variables[3] u = nla_solve(objective_function_3, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[3] = u[0] + algebraic_variables[3] = u[0] def objective_function_4(u, f, data): @@ -194,19 +194,19 @@ def objective_function_4(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[4] = u[0] + algebraic_variables[4] = u[0] - f[0] = voi-algebraicVariables[4] + f[0] = voi-algebraic_variables[4] def find_root_4(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[4] + u[0] = algebraic_variables[4] u = nla_solve(objective_function_4, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[4] = u[0] + algebraic_variables[4] = u[0] def objective_function_5(u, f, data): @@ -217,19 +217,19 @@ def objective_function_5(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[5] = u[0] + algebraic_variables[5] = u[0] - f[0] = voi-algebraicVariables[5] + f[0] = voi-algebraic_variables[5] def find_root_5(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[5] + u[0] = algebraic_variables[5] u = nla_solve(objective_function_5, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[5] = u[0] + algebraic_variables[5] = u[0] def objective_function_6(u, f, data): @@ -240,19 +240,19 @@ def objective_function_6(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[6] = u[0] + algebraic_variables[6] = u[0] - f[0] = voi-algebraicVariables[6] + f[0] = voi-algebraic_variables[6] def find_root_6(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[6] + u[0] = algebraic_variables[6] u = nla_solve(objective_function_6, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[6] = u[0] + algebraic_variables[6] = u[0] def objective_function_7(u, f, data): @@ -263,19 +263,19 @@ def objective_function_7(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[7] = u[0] + algebraic_variables[7] = u[0] - f[0] = voi-algebraicVariables[7] + f[0] = voi-algebraic_variables[7] def find_root_7(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[7] + u[0] = algebraic_variables[7] u = nla_solve(objective_function_7, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[7] = u[0] + algebraic_variables[7] = u[0] def objective_function_8(u, f, data): @@ -286,19 +286,19 @@ def objective_function_8(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[8] = u[0] + algebraic_variables[8] = u[0] - f[0] = voi-algebraicVariables[8] + f[0] = voi-algebraic_variables[8] def find_root_8(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[8] + u[0] = algebraic_variables[8] u = nla_solve(objective_function_8, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[8] = u[0] + algebraic_variables[8] = u[0] def objective_function_9(u, f, data): @@ -309,19 +309,19 @@ def objective_function_9(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[9] = u[0] + algebraic_variables[9] = u[0] - f[0] = voi-algebraicVariables[9] + f[0] = voi-algebraic_variables[9] def find_root_9(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[9] + u[0] = algebraic_variables[9] u = nla_solve(objective_function_9, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[9] = u[0] + algebraic_variables[9] = u[0] def objective_function_10(u, f, data): @@ -332,19 +332,19 @@ def objective_function_10(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[10] = u[0] + algebraic_variables[10] = u[0] - f[0] = voi-algebraicVariables[10] + f[0] = voi-algebraic_variables[10] def find_root_10(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[10] + u[0] = algebraic_variables[10] u = nla_solve(objective_function_10, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[10] = u[0] + algebraic_variables[10] = u[0] def objective_function_11(u, f, data): @@ -355,19 +355,19 @@ def objective_function_11(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[11] = u[0] + algebraic_variables[11] = u[0] - f[0] = voi-algebraicVariables[11] + f[0] = voi-algebraic_variables[11] def find_root_11(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[11] + u[0] = algebraic_variables[11] u = nla_solve(objective_function_11, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[11] = u[0] + algebraic_variables[11] = u[0] def objective_function_12(u, f, data): @@ -378,19 +378,19 @@ def objective_function_12(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[12] = u[0] + algebraic_variables[12] = u[0] - f[0] = voi-algebraicVariables[12] + f[0] = voi-algebraic_variables[12] def find_root_12(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[12] + u[0] = algebraic_variables[12] u = nla_solve(objective_function_12, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[12] = u[0] + algebraic_variables[12] = u[0] def objective_function_13(u, f, data): @@ -401,19 +401,19 @@ def objective_function_13(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[13] = u[0] + algebraic_variables[13] = u[0] - f[0] = voi-algebraicVariables[13] + f[0] = voi-algebraic_variables[13] def find_root_13(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[13] + u[0] = algebraic_variables[13] u = nla_solve(objective_function_13, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[13] = u[0] + algebraic_variables[13] = u[0] def objective_function_14(u, f, data): @@ -424,19 +424,19 @@ def objective_function_14(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[14] = u[0] + algebraic_variables[14] = u[0] - f[0] = voi-algebraicVariables[14] + f[0] = voi-algebraic_variables[14] def find_root_14(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[14] + u[0] = algebraic_variables[14] u = nla_solve(objective_function_14, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[14] = u[0] + algebraic_variables[14] = u[0] def objective_function_15(u, f, data): @@ -447,19 +447,19 @@ def objective_function_15(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[15] = u[0] + algebraic_variables[15] = u[0] - f[0] = voi-algebraicVariables[15] + f[0] = voi-algebraic_variables[15] def find_root_15(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[15] + u[0] = algebraic_variables[15] u = nla_solve(objective_function_15, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[15] = u[0] + algebraic_variables[15] = u[0] def objective_function_16(u, f, data): @@ -470,19 +470,19 @@ def objective_function_16(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[16] = u[0] + algebraic_variables[16] = u[0] - f[0] = voi-algebraicVariables[16] + f[0] = voi-algebraic_variables[16] def find_root_16(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[16] + u[0] = algebraic_variables[16] u = nla_solve(objective_function_16, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[16] = u[0] + algebraic_variables[16] = u[0] def objective_function_17(u, f, data): @@ -493,19 +493,19 @@ def objective_function_17(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[17] = u[0] + algebraic_variables[17] = u[0] - f[0] = voi-algebraicVariables[17] + f[0] = voi-algebraic_variables[17] def find_root_17(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[17] + u[0] = algebraic_variables[17] u = nla_solve(objective_function_17, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[17] = u[0] + algebraic_variables[17] = u[0] def objective_function_18(u, f, data): @@ -516,19 +516,19 @@ def objective_function_18(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[18] = u[0] + algebraic_variables[18] = u[0] - f[0] = voi-algebraicVariables[18] + f[0] = voi-algebraic_variables[18] def find_root_18(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[18] + u[0] = algebraic_variables[18] u = nla_solve(objective_function_18, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[18] = u[0] + algebraic_variables[18] = u[0] def objective_function_19(u, f, data): @@ -539,19 +539,19 @@ def objective_function_19(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[19] = u[0] + algebraic_variables[19] = u[0] - f[0] = voi-algebraicVariables[19] + f[0] = voi-algebraic_variables[19] def find_root_19(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[19] + u[0] = algebraic_variables[19] u = nla_solve(objective_function_19, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[19] = u[0] + algebraic_variables[19] = u[0] def objective_function_20(u, f, data): @@ -562,19 +562,19 @@ def objective_function_20(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[20] = u[0] + algebraic_variables[20] = u[0] - f[0] = voi-algebraicVariables[20] + f[0] = voi-algebraic_variables[20] def find_root_20(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[20] + u[0] = algebraic_variables[20] u = nla_solve(objective_function_20, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[20] = u[0] + algebraic_variables[20] = u[0] def objective_function_21(u, f, data): @@ -585,19 +585,19 @@ def objective_function_21(u, f, data): computed_constants = data[4] algebraic_variables = data[5] - algebraicVariables[21] = u[0] + algebraic_variables[21] = u[0] - f[0] = voi-algebraicVariables[21] + f[0] = voi-algebraic_variables[21] def find_root_21(voi, states, rates, constants, computed_constants, algebraic_variables): u = [nan]*1 - u[0] = algebraicVariables[21] + u[0] = algebraic_variables[21] u = nla_solve(objective_function_21, u, 1, [voi, states, rates, constants, computed_constants, algebraic_variables]) - algebraicVariables[21] = u[0] + algebraic_variables[21] = u[0] def initialise_arrays(states, rates, constants, computed_constants, algebraic_variables): @@ -607,51 +607,51 @@ def initialise_arrays(states, rates, constants, computed_constants, algebraic_va states[19] = 5.0 states[5] = states[19] states[4] = states[5] - algebraicVariables[16] = 7.0 - states[7] = algebraicVariables[16] + algebraic_variables[16] = 7.0 + states[7] = algebraic_variables[16] states[6] = states[7] states[8] = constants[0] states[10] = states[19] - states[11] = algebraicVariables[16] + states[11] = algebraic_variables[16] constants[1] = 3.0 - algebraicVariables[4] = constants[1] - states[12] = algebraicVariables[4] + algebraic_variables[4] = constants[1] + states[12] = algebraic_variables[4] states[21] = 5.0 - algebraicVariables[6] = states[21] - states[14] = algebraicVariables[6] - algebraicVariables[21] = 7.0 - algebraicVariables[7] = algebraicVariables[21] - states[15] = algebraicVariables[7] + algebraic_variables[6] = states[21] + states[14] = algebraic_variables[6] + algebraic_variables[21] = 7.0 + algebraic_variables[7] = algebraic_variables[21] + states[15] = algebraic_variables[7] states[16] = constants[0] states[18] = states[19] - states[20] = algebraicVariables[16] - algebraicVariables[0] = states[8] - algebraicVariables[2] = states[10] - algebraicVariables[3] = states[11] - algebraicVariables[9] = constants[1] - algebraicVariables[8] = algebraicVariables[9] - algebraicVariables[13] = states[21] - algebraicVariables[12] = algebraicVariables[13] - algebraicVariables[15] = algebraicVariables[21] - algebraicVariables[14] = algebraicVariables[15] - algebraicVariables[17] = constants[1] - algebraicVariables[19] = states[21] - algebraicVariables[20] = algebraicVariables[21] - - -def compute_computed_constants(states, rates, constants, computed_constants, algebraic): + states[20] = algebraic_variables[16] + algebraic_variables[0] = states[8] + algebraic_variables[2] = states[10] + algebraic_variables[3] = states[11] + algebraic_variables[9] = constants[1] + algebraic_variables[8] = algebraic_variables[9] + algebraic_variables[13] = states[21] + algebraic_variables[12] = algebraic_variables[13] + algebraic_variables[15] = algebraic_variables[21] + algebraic_variables[14] = algebraic_variables[15] + algebraic_variables[17] = constants[1] + algebraic_variables[19] = states[21] + algebraic_variables[20] = algebraic_variables[21] + + +def compute_computed_constants(states, rates, constants, computed_constants, algebraic_variables ): computed_constants[0] = 1.23*constants[0] states[3] = computed_constants[0] states[2] = states[3] states[9] = computed_constants[0] computed_constants[1] = 1.23*constants[1] - algebraicVariables[5] = computed_constants[1] - states[13] = algebraicVariables[5] + algebraic_variables[5] = computed_constants[1] + states[13] = algebraic_variables[5] states[17] = computed_constants[0] - algebraicVariables[1] = states[9] - algebraicVariables[11] = computed_constants[1] - algebraicVariables[10] = algebraicVariables[11] - algebraicVariables[18] = computed_constants[1] + algebraic_variables[1] = states[9] + algebraic_variables[11] = computed_constants[1] + algebraic_variables[10] = algebraic_variables[11] + algebraic_variables[18] = computed_constants[1] def compute_rates(voi, states, rates, constants, computed_constants, algebraic_variables):