Update gap_fitting_tutorial.ipynb

Using non-zero regularisation values.

Author: albapa

doc_src/gap_fitting_tutorial.ipynb

@@ -415,7 +415,7 @@
     "- `do_copy_at_file=F sparse_separate_file=T` just needed, don't want to copy the training data and using separate files for the xml makes it faster\n",
     "- `gp_file=GAP.xml` filename of the potential parameters, I have always used this name, because I had separate directories for the different trainings potentials\n",
     "- `at_file=train.xyz` training file\n",
-    "- `default_sigma={0.008 0.04 0 0}` sigma values to be used for energies, forces, stresses, hessians in order; this represents the accuracy of the data and the relative weight of them in the fit (more accurate --> more significant in the fit)\n",
+    "- `default_sigma={0.008 0.04 0.01 0.01}` sigma values to be used for energies, forces, stresses, hessians in order; this represents the accuracy of the data and the relative weight of them in the fit (more accurate --> more significant in the fit)\n",
     "- `gap={...}` the potential to be fit, separated by ':'\n",
     "\n",
     "**distance_2b**\n",
@@ -466,7 +466,7 @@
       "local_property0 = 0.0\n",
       "e0_offset = 0.0\n",
       "e0_method = isolated\n",
-      "default_sigma = \"0.008 0.04 0 0\"\n",
+      "default_sigma = \"0.008 0.04 0.01 0.01\"\n",
       "sparse_jitter = 1.0e-10\n",
       "hessian_delta = 1.0e-2\n",
       "core_param_file = quip_params.xml\n",
@@ -579,7 +579,7 @@
     }
    ],
    "source": [
-    "! gap_fit energy_parameter_name=energy force_parameter_name=forces do_copy_at_file=F sparse_separate_file=T gp_file=GAP.xml at_file=train.xyz default_sigma={0.008 0.04 0 0} gap={distance_2b cutoff=4.0 covariance_type=ard_se delta=0.5 theta_uniform=1.0 sparse_method=uniform add_species=T n_sparse=10}\n"
+    "! gap_fit energy_parameter_name=energy force_parameter_name=forces do_copy_at_file=F sparse_separate_file=T gp_file=GAP.xml at_file=train.xyz default_sigma={0.008 0.04 0.01 0.01} gap={distance_2b cutoff=4.0 covariance_type=ard_se delta=0.5 theta_uniform=1.0 sparse_method=uniform add_species=T n_sparse=10}\n"
    ]
   },
   {
@@ -801,7 +801,7 @@
       "local_property0 = 0.0\n",
       "e0_offset = 0.0\n",
       "e0_method = isolated\n",
-      "default_sigma = \"0.008 0.04 0 0\"\n",
+      "default_sigma = \"0.008 0.04 0.01 0.01\"\n",
       "sparse_jitter = 1.0e-10\n",
       "hessian_delta = 1.0e-2\n",
       "core_param_file = quip_params.xml\n",
@@ -975,7 +975,7 @@
     }
    ],
    "source": [
-    "! gap_fit energy_parameter_name=energy force_parameter_name=forces do_copy_at_file=F sparse_separate_file=T gp_file=GAP_3b.xml at_file=train.xyz default_sigma={0.008 0.04 0 0} gap={distance_2b cutoff=4.0 covariance_type=ard_se delta=0.5 theta_uniform=1.0 sparse_method=uniform add_species=T n_sparse=10 : angle_3b cutoff=3.5 covariance_type=ard_se delta=0.5 theta_fac=0.5 add_species=T n_sparse=30 sparse_method=uniform}\n"
+    "! gap_fit energy_parameter_name=energy force_parameter_name=forces do_copy_at_file=F sparse_separate_file=T gp_file=GAP_3b.xml at_file=train.xyz default_sigma={0.008 0.04 0.01 0.01} gap={distance_2b cutoff=4.0 covariance_type=ard_se delta=0.5 theta_uniform=1.0 sparse_method=uniform add_species=T n_sparse=10 : angle_3b cutoff=3.5 covariance_type=ard_se delta=0.5 theta_fac=0.5 add_species=T n_sparse=30 sparse_method=uniform}\n"
    ]
   },
   {