Meg simula/create mms config example

src/design-prototype/model_A_2D.yml

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+# Authors: Marie E. Rognes, Marius Causemann and Halvor Herlyng
+# Date: March 18 2024
+
+# EMIx benchmark collection Model "A": Unified KNP-EMI problem specification
+
+# Time interval
+T : [0.0, 0.3] # [s]
+
+# Problem constants (given in SI units here)
+physical_constants:
+  T : 300                    # temperature [K]
+  F : 9.64853321233100184E+4 # Faraday constant [C/mol]
+  R : 8.314                  # Gas constant [J/(K*mol)]
+
+# Define data functions that map from mesh cell index to region label
+# and from facet index to interface label.
+# FIXME
+cell_tag_file : "meshes/region_tags.xdmf"
+facet_tag_file : "meshes/interface_tags.xdmf"
+
+# Define which tags that belong to the intracellular domain (ICS) and
+# which tags that belong to the extracellular space (ECS)
+ics_tags : [1]
+ecs_tags : [0]
+
+# Membrane capacitance
+C_m : 0.02 # [F]
+
+# Define which ion species that are involved, their valence, effective
+# diffusivities, initial concentration, and volume source functions if any
+ion_species:
+  Na : 
+    valence : 1
+    diffusivity : 1.33E-9 # m^2/s
+    initial :     
+      ics : 12.0  # mM
+      ecs : 100.0 # mM
+    source : 0.0
+
+  K :
+    valence : 1
+    diffusivity : 1.96E-9 # m^2/s
+    initial :
+      ics : 125 # mM
+      ecs : 4   # mM
+    source : 0.0
+
+  Cl :
+    valence : -1
+    diffusivity : 2.03E-9 # m^2/s
+    initial : 
+      ics : 137 # mM
+      ecs : 104 # mM
+    source : 0.0
+
+boundary_conditions: []
+
+# FIXME: More work needed here. 
+ionic_membrane_models:
+  1 : 
+    model: "HH" # Hodgkin-Huxley
+    stimuli: 
+      Na : "40.*exp(-(t mod 10)/0.002)" 
+    initial_potential: -67.74E-3 # V
+
+
+
+

src/design-prototype/notes/Makefile

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+FILE=main
+
+default:
+	pdflatex $(FILE).tex
+
+final:
+	pdflatex $(FILE).tex
+	bibtex $(FILE)
+	pdflatex $(FILE).tex
+	pdflatex $(FILE).tex
+
+diff:
+	latexdiff old.tex paper.tex > diff.tex
+	pdflatex diff.tex
+	bibtex diff
+	pdflatex diff.tex
+	pdflatex diff.tex
+
+clean:
+	rm *~ *.aux *.out *.toc *.blg *.bbl *.log *.tdo *.dvi