Bueno-Orovio parameters (#130)

* Expose tau_fi and tau_si from BO in the XML interface * Tests
SimVascular · Oct 31, 2023 · d18a1fe · d18a1fe
1 parent eec4bd7
commit d18a1fe
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Showing 12 changed files with 27 additions and 26 deletions.
diff --git a/Code/Source/svFSI/CepModBo.h b/Code/Source/svFSI/CepModBo.h
@@ -36,7 +36,7 @@
 #include "Vector.h"
 #include <array>
 
-using BoModelParam = std::array<double,3>;
+using BoModelParam = Vector<double>;
 
 /// @brief This module defines data structures for Bueno-Orovio cellular
 /// activation model for cardiac electrophysiology.

diff --git a/Code/Source/svFSI/Parameters.cpp b/Code/Source/svFSI/Parameters.cpp
@@ -1234,6 +1234,9 @@ DomainParameters::DomainParameters()
  set_parameter("G_Ks", 0.392, !required, G_Ks);
  set_parameter("G_to", 0.294, !required, G_to);
 
+ set_parameter("tau_fi", 0.110, !required, tau_fi);
+ set_parameter("tau_si", 1.88750, !required, tau_si);
+
  set_parameter("ODE_solver", "euler", !required, ode_solver);
 
  set_parameter("Penalty_parameter", 0.0, !required, penalty_parameter);

diff --git a/Code/Source/svFSI/Parameters.h b/Code/Source/svFSI/Parameters.h
@@ -1009,6 +1009,9 @@ class DomainParameters : public ParameterLists
  Parameter<double> G_Ks;
  Parameter<double> G_to;
 
+ Parameter<double> tau_fi;
+ Parameter<double> tau_si;
+
  Parameter<std::string> ode_solver;
  Parameter<double> penalty_parameter;
  Parameter<double> poisson_ratio;

diff --git a/Code/Source/svFSI/distribute.cpp b/Code/Source/svFSI/distribute.cpp
@@ -1043,6 +1043,9 @@ void dist_eq(ComMod& com_mod, const CmMod& cm_mod, const cmType& cm, const std::
  cm.bcast(cm_mod, &cep_mod.ttp.G_Kr);
  cm.bcast(cm_mod, cep_mod.ttp.G_Ks);
  cm.bcast(cm_mod, cep_mod.ttp.G_to);
+
+ cm.bcast(cm_mod, cep_mod.bo.tau_si);
+ cm.bcast(cm_mod, cep_mod.bo.tau_fi);
  } 
 
  if ((dmn.phys == EquationType::phys_struct) || (dmn.phys == EquationType::phys_ustruct)) {

diff --git a/Code/Source/svFSI/read_files.cpp b/Code/Source/svFSI/read_files.cpp
@@ -867,6 +867,10 @@ void read_cep_domain(Simulation* simulation, EquationParameters* eq_params, Doma
  if (domain_params->G_to.defined()) { cep_mod.ttp.G_to[lDmn.cep.imyo - 1] = domain_params->G_to.value(); }
  if (domain_params->G_CaL.defined()) { cep_mod.ttp.G_CaL = domain_params->G_CaL.value(); }
 
+ // Set Bo parameters.
+ //
+ if (domain_params->tau_si.defined()) { cep_mod.bo.tau_si[lDmn.cep.imyo - 1] = domain_params->tau_si.value(); }
+ if (domain_params->tau_fi.defined()) { cep_mod.bo.tau_fi[lDmn.cep.imyo - 1] = domain_params->tau_fi.value(); }
 
  // Set stimulus parameters. 
  //

diff --git a/tests/cases/niederer_benchmark_ECGs_quadrature/result_BICG_CN_epicardium_BO_001.vtu b/tests/cases/niederer_benchmark_ECGs_quadrature/result_BICG_CN_epicardium_BO_001.vtu
diff --git a/tests/cases/niederer_benchmark_ECGs_quadrature/result_BICG_CN_myocardium_BO_001.vtu b/tests/cases/niederer_benchmark_ECGs_quadrature/result_BICG_CN_myocardium_BO_001.vtu
diff --git a/tests/cases/niederer_benchmark_ECGs_quadrature/result_CG_RK4_endocardium_BO_001.vtu b/tests/cases/niederer_benchmark_ECGs_quadrature/result_CG_RK4_endocardium_BO_001.vtu
diff --git a/tests/cases/niederer_benchmark_ECGs_quadrature/result_CG_RK4_myocardium_BO_001.vtu b/tests/cases/niederer_benchmark_ECGs_quadrature/result_CG_RK4_myocardium_BO_001.vtu
diff --git a/...uadrature/svFSI_BICG_CN_myocardium_BO.xml → ...uadrature/svFSI_BICG_CN_epicardium_BO.xml b/...uadrature/svFSI_BICG_CN_myocardium_BO.xml → ...uadrature/svFSI_BICG_CN_epicardium_BO.xml
@@ -73,33 +73,21 @@
  <Domain id="1" >
  <Electrophysiology_model> BO </Electrophysiology_model>
 
- <G_Na> 14.838 </G_Na>
- <G_CaL> 3.98E-5 </G_CaL>
- <G_Kr> 0.153 </G_Kr>
- <G_Ks> 0.392 </G_Ks> 
- <G_to> 0.294 </G_to>
-
  <Isotropic_conductivity> 0.012571 </Isotropic_conductivity>
  <Anisotropic_conductivity> 0.082715 </Anisotropic_conductivity>
 
- <Myocardial_zone> myocardium </Myocardial_zone>
+ <Myocardial_zone> epicardium </Myocardial_zone>
 
  <ODE_solver> CN </ODE_solver>
  </Domain>
 
  <Domain id="2" >
  <Electrophysiology_model> BO </Electrophysiology_model>
 
- <G_Na> 14.838 </G_Na>
- <G_CaL> 3.98E-5 </G_CaL>
- <G_Kr> 0.153 </G_Kr>
- <G_Ks> 0.392 </G_Ks> 
- <G_to> 0.294 </G_to>
-
  <Isotropic_conductivity> 0.012571 </Isotropic_conductivity>
  <Anisotropic_conductivity> 0.082715 </Anisotropic_conductivity>
 
- <Myocardial_zone> myocardium </Myocardial_zone>
+ <Myocardial_zone> epicardium </Myocardial_zone>
 
  <Stimulus type="Istim" >
  <Amplitude> -35.714 </Amplitude>
@@ -108,7 +96,7 @@
  <Cycle_length> 10000.0 </Cycle_length>
  </Stimulus>
 
- <ODE_solver> CN </ODE_solver> 
+ <ODE_solver> FE </ODE_solver> 
  </Domain>
 
  <Output type="Spatial" >

diff --git a/...uadrature/svFSI_CG_RK4_endocardium_BO.xml → ...quadrature/svFSI_CG_RK4_myocardium_BO.xml b/...uadrature/svFSI_CG_RK4_endocardium_BO.xml → ...quadrature/svFSI_CG_RK4_myocardium_BO.xml
@@ -76,7 +76,7 @@
  <Isotropic_conductivity> 0.012571 </Isotropic_conductivity>
  <Anisotropic_conductivity> 0.082715 </Anisotropic_conductivity>
 
- <Myocardial_zone> endocardium </Myocardial_zone>
+ <Myocardial_zone> myocardium </Myocardial_zone>
 
  <ODE_solver> RK4 </ODE_solver>
  </Domain>
@@ -87,7 +87,7 @@
  <Isotropic_conductivity> 0.012571 </Isotropic_conductivity>
  <Anisotropic_conductivity> 0.082715 </Anisotropic_conductivity>
 
- <Myocardial_zone> endocardium </Myocardial_zone>
+ <Myocardial_zone> myocardium </Myocardial_zone>
 
  <Stimulus type="Istim" >
  <Amplitude> -35.714 </Amplitude>

diff --git a/tests/test_integration.py b/tests/test_integration.py
@@ -131,8 +131,8 @@ def test_purkinje(n_proc):
  name_ref = "result_" + str(t_max).zfill(3) + ".vtu"
  run_with_reference(folder, name_inp, name_ref, field, t_max, n_proc)
 
-@pytest.mark.parametrize("confs_ecgs", [["BICG_CN_myocardium_BO" , -0.0781125, 0.0781125, 0.00885273],
- ["CG_RK4_endocardium_BO" , -0.0780188, 0.0780188, 0.00884210],
+@pytest.mark.parametrize("confs_ecgs", [["BICG_CN_epicardium_BO" , -0.0786707, 0.0786707, 0.00891599],
+ ["CG_RK4_myocardium_BO"  , -0.0781115, 0.0781115, 0.00885261],
  ["GMRES_FE_epicardium_TTP", -0.0786707, 0.0786707, 0.00891599],
  ["GMRES_FE_pfib_AP" , 0.0786707, -0.0786707, -0.00891599]])
 @pytest.mark.parametrize("n_proc", procs)