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Herck/2023paper #214

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2035fe1
Use Tor-Land model when loading state
IlsevanHerck Apr 2, 2023
8bf8fd9
Add drug files for Omecamtiv Mecarbil
IlsevanHerck Apr 3, 2023
1bbfb5a
Add drug files for Omecamtiv Mecarbil for ORd-Land
IlsevanHerck Apr 3, 2023
075f2b7
use lambda instead of lmbda in postprocess
IlsevanHerck Apr 14, 2023
bc4f559
Hardcode the default stimulus domain for travelling wave starting fro…
IlsevanHerck Apr 14, 2023
3c7f531
Fix mistake Tor-Land cellmodel in calculation of I for GK1
IlsevanHerck Apr 14, 2023
0d4470b
Fix return in stimulus domain function
IlsevanHerck Apr 14, 2023
8650c6b
Merge pull request #178 from ComputationalPhysiology/finsberg/PETScDM…
finsberg May 10, 2023
a343785
Add interpolation trick for Tord model and explicit coupled model
finsberg May 10, 2023
257544a
Merge pull request #179 from ComputationalPhysiology/finsberg/PETScDM…
finsberg May 10, 2023
0955a51
Change name lmbda to lambda in postprocess and calculate inv_lambda
IlsevanHerck May 10, 2023
7cc5eb9
Merge pull request #175 from ComputationalPhysiology/finsberg/subresults
finsberg May 5, 2023
c5ac1d3
Export results of comparing peak values for steady state
IlsevanHerck May 11, 2023
76fd678
Merge pull request #181 from ComputationalPhysiology/petsc-memory-issue
finsberg May 16, 2023
a938400
Merge pull request #183 from ComputationalPhysiology/fix-disease-stat…
finsberg May 22, 2023
8ba4405
Use optional instead of | in postprocess
IlsevanHerck Jun 6, 2023
1a343a0
Add workflow for running test suite in paralell
finsberg Jun 22, 2023
deba29f
Add pytest-mpi to dev dependencies
finsberg Jun 22, 2023
2e39bd0
Add a lot of debug log messages
finsberg Jun 23, 2023
be56c04
Add default argument to remove file function
finsberg Jun 23, 2023
c2bbeea
Add timeout to github workflow
finsberg Jun 23, 2023
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Hardcode the default stimulus domain for travelling wave starting fro…
…m x<1
IlsevanHerck committed Apr 14, 2023
commit bc4f559efa2c96448084e9cc0a164a7a4f9eec7c
8 changes: 6 additions & 2 deletions src/simcardems/geometry.py
Original file line number Diff line number Diff line change
@@ -159,9 +159,13 @@ def default_parameters() -> Dict[str, Any]:
def default_stimulus_domain(mesh: dolfin.Mesh) -> StimulusDomain:
# Default is to stimulate the entire tissue
marker = 1
#domain = dolfin.MeshFunction("size_t", mesh, mesh.topology().dim())
#domain.set_all(marker)
subdomain = dolfin.CompiledSubDomain("x[0] < 1.0")
domain = dolfin.MeshFunction("size_t", mesh, mesh.topology().dim())
domain.set_all(marker)
return StimulusDomain(domain=domain, marker=marker)
domain.set_all(0)
subdomain.mark(domain, marker)
return StimulusDomain(domain=domain, marker=marker)

@staticmethod
def default_schema() -> Dict[str, H5Path]: