From 00f78531ffad1b49d46395e2b49ff03360e9387c Mon Sep 17 00:00:00 2001
From: Javiera Jilberto Vallejos <jilberto@umich.edu>
Date: Wed, 11 Feb 2026 10:51:19 -0800
Subject: [PATCH 1/5] adding domain specific conductances

---
 Code/Source/solver/CepMod.h       | 12 ++++++
 Code/Source/solver/cep_ion.cpp    | 62 +++++++++++++++----------------
 Code/Source/solver/distribute.cpp | 17 +++++----
 Code/Source/solver/read_files.cpp | 18 ++++-----
 4 files changed, 61 insertions(+), 48 deletions(-)

diff --git a/Code/Source/solver/CepMod.h b/Code/Source/solver/CepMod.h
index 55e112bb7..783d1dd1b 100644
--- a/Code/Source/solver/CepMod.h
+++ b/Code/Source/solver/CepMod.h
@@ -165,6 +165,18 @@ class cepModelType
 
     /// @brief  Time integration options
     odeType odes;
+
+    /// @brief Domain-specific interface for Aliev-Panfilov cellular activation model
+    CepModAp ap;
+
+    /// @brief Domain-specific interface for Bueno-Orovio cellular activation model
+    CepModBo bo;
+
+    /// @brief Domain-specific interface for Fitzhugh-Nagumo cellular activation model
+    CepModFn fn;
+
+    /// @brief Domain-specific interface for Tusscher-Panfilov cellular activation model
+    CepModTtp ttp;
 };
 
 /// @brief Cardiac electromechanics model type
diff --git a/Code/Source/solver/cep_ion.cpp b/Code/Source/solver/cep_ion.cpp
index 2f805e66a..f340f0c28 100644
--- a/Code/Source/solver/cep_ion.cpp
+++ b/Code/Source/solver/cep_ion.cpp
@@ -119,19 +119,19 @@ void cep_init_l(CepMod& cep_mod, cepModelType& cep, int nX, int nG, Vector<doubl
   switch (cep.cepType) {
 
     case ElectrophysiologyModelType::AP:
-      cep_mod.ap.init(nX, X);
+      cep.ap.init(nX, X);
     break;
 
     case ElectrophysiologyModelType::BO:
-      cep_mod.bo.init(nX, X);
+      cep.bo.init(nX, X);
     break;
 
     case ElectrophysiologyModelType::FN:
-      cep_mod.fn.init(nX, X);
+      cep.fn.init(nX, X);
     break;
 
     case ElectrophysiologyModelType::TTP:
-      cep_mod.ttp.init(cep.imyo, nX, nG, X, Xg);
+      cep.ttp.init(cep.imyo, nX, nG, X, Xg);
     break;
   }
 }
@@ -383,12 +383,12 @@ void cep_integ_l(CepMod& cep_mod, cepModelType& cep, int nX, int nG, Vector<doub
             } else {
               Istim = 0.0;
             }
-            cep_mod.ap.integ_fe(nX, X, t, cep.dt, Istim, Ksac);
+            cep.ap.integ_fe(nX, X, t, cep.dt, Istim, Ksac);
   
             // Electromechanics excitation-activation
             if (cem.aStress) {
               double epsX;
-              cep_mod.ap.actv_strs(X(0), cep.dt, yl, epsX);
+              cep.ap.actv_strs(X(0), cep.dt, yl, epsX);
             }
           }
         } break; 
@@ -402,12 +402,12 @@ void cep_integ_l(CepMod& cep_mod, cepModelType& cep, int nX, int nG, Vector<doub
             } else {
               Istim = 0.0;
             }
-            cep_mod.ap.integ_rk(nX, X, t, cep.dt, Istim, Ksac);
+            cep.ap.integ_rk(nX, X, t, cep.dt, Istim, Ksac);
 
             //  Electromechanics excitation-activation
             if (cem.aStress) {
               double epsX;
-              cep_mod.ap.actv_strs(X(0), cep.dt, yl, epsX);
+              cep.ap.actv_strs(X(0), cep.dt, yl, epsX);
             }
           }
         } break; 
@@ -422,12 +422,12 @@ void cep_integ_l(CepMod& cep_mod, cepModelType& cep, int nX, int nG, Vector<doub
               Istim = 0.0;
             }
 
-            cep_mod.ap.integ_cn2(nX, X, t, cep.dt, Istim, Ksac, IPAR, RPAR);
+            cep.ap.integ_cn2(nX, X, t, cep.dt, Istim, Ksac, IPAR, RPAR);
 
             // Electromechanics excitation-activation
             if (cem.aStress) {
               double epsX;
-              cep_mod.ap.actv_strs(X(0), cep.dt, yl, epsX);
+              cep.ap.actv_strs(X(0), cep.dt, yl, epsX);
             }
           }
         } break; 
@@ -453,14 +453,14 @@ void cep_integ_l(CepMod& cep_mod, cepModelType& cep, int nX, int nG, Vector<doub
               Istim = 0.0;
             }
 
-            cep_mod.bo.integ_fe(cep.imyo, nX, X, t, cep.dt, Istim, Ksac, RPAR);
+            cep.bo.integ_fe(cep.imyo, nX, X, t, cep.dt, Istim, Ksac, RPAR);
 
             // Electromechanics excitation-activation
             if (cem.aStress) {
               double epsX;
-              cep_mod.bo.actv_strs(X(0), cep.dt, yl, epsX);
+              cep.bo.actv_strs(X(0), cep.dt, yl, epsX);
             } else if (cem.aStrain) {
-              cep_mod.bo.actv_strn(X(3), I4f, cep.dt, yl);
+              cep.bo.actv_strn(X(3), I4f, cep.dt, yl);
             }
           }
         } break;
@@ -475,14 +475,14 @@ void cep_integ_l(CepMod& cep_mod, cepModelType& cep, int nX, int nG, Vector<doub
               Istim = 0.0;
             }
 
-            cep_mod.bo.integ_rk(cep.imyo, nX, X, t, cep.dt, Istim, Ksac, RPAR);
+            cep.bo.integ_rk(cep.imyo, nX, X, t, cep.dt, Istim, Ksac, RPAR);
 
             // Electromechanics excitation-activation
             if (cem.aStress) {
               double epsX;
-              cep_mod.bo.actv_strs(X(0), cep.dt, yl, epsX);
+              cep.bo.actv_strs(X(0), cep.dt, yl, epsX);
             } else if (cem.aStrain) {
-              cep_mod.bo.actv_strn(X(3), I4f, cep.dt, yl);
+              cep.bo.actv_strn(X(3), I4f, cep.dt, yl);
             }
           }
         } break;
@@ -497,14 +497,14 @@ void cep_integ_l(CepMod& cep_mod, cepModelType& cep, int nX, int nG, Vector<doub
               Istim = 0.0;
             }
 
-            cep_mod.bo.integ_cn2(cep.imyo, nX, X, t, cep.dt, Istim, Ksac, IPAR, RPAR);
+            cep.bo.integ_cn2(cep.imyo, nX, X, t, cep.dt, Istim, Ksac, IPAR, RPAR);
 
             // Electromechanics excitation-activation
             if (cem.aStress) {
               double epsX;
-              cep_mod.bo.actv_strs(X(0), cep.dt, yl, epsX);
+              cep.bo.actv_strs(X(0), cep.dt, yl, epsX);
             } else if (cem.aStrain) {
-              cep_mod.bo.actv_strn(X(3), I4f, cep.dt, yl);
+              cep.bo.actv_strn(X(3), I4f, cep.dt, yl);
             }
           }
         } break;
@@ -530,7 +530,7 @@ void cep_integ_l(CepMod& cep_mod, cepModelType& cep, int nX, int nG, Vector<doub
             } else {
               Istim = 0.0;
             }
-            cep_mod.fn.integ_fe(nX, X, t, cep.dt, Istim);
+            cep.fn.integ_fe(nX, X, t, cep.dt, Istim);
           }
         } break;
 
@@ -543,7 +543,7 @@ void cep_integ_l(CepMod& cep_mod, cepModelType& cep, int nX, int nG, Vector<doub
             } else {
               Istim = 0.0;
             }
-            cep_mod.fn.integ_rk(nX, X, t, cep.dt, Istim);
+            cep.fn.integ_rk(nX, X, t, cep.dt, Istim);
           }
         } break;
 
@@ -556,7 +556,7 @@ void cep_integ_l(CepMod& cep_mod, cepModelType& cep, int nX, int nG, Vector<doub
             } else {
               Istim = 0.0;
             }
-            cep_mod.fn.integ_cn2(nX, X, t, cep.dt, Istim, IPAR, RPAR);
+            cep.fn.integ_cn2(nX, X, t, cep.dt, Istim, IPAR, RPAR);
            }
         } break;
       }
@@ -580,14 +580,14 @@ void cep_integ_l(CepMod& cep_mod, cepModelType& cep, int nX, int nG, Vector<doub
             } else {
               Istim = 0.0;
             }
-            cep_mod.ttp.integ_fe(cep.imyo, nX, nG, X, Xg, t, cep.dt, Istim, Ksac, RPAR);
+            cep.ttp.integ_fe(cep.imyo, nX, nG, X, Xg, t, cep.dt, Istim, Ksac, RPAR);
 
             // Electromechanics excitation-activation
             if (cem.aStress) {
               double epsX;
-              cep_mod.ttp.actv_strs(X(3), cep.dt, yl, epsX);
+              cep.ttp.actv_strs(X(3), cep.dt, yl, epsX);
             } else if (cem.aStrain) {
-              cep_mod.ttp.actv_strn(X(3), I4f, cep.dt, yl);
+              cep.ttp.actv_strn(X(3), I4f, cep.dt, yl);
             }
           }
         } break;
@@ -602,14 +602,14 @@ void cep_integ_l(CepMod& cep_mod, cepModelType& cep, int nX, int nG, Vector<doub
               Istim = 0.0;
             }
 
-            cep_mod.ttp.integ_rk(cep.imyo, nX, nG, X, Xg, t, cep.dt, Istim, Ksac, RPAR);
+            cep.ttp.integ_rk(cep.imyo, nX, nG, X, Xg, t, cep.dt, Istim, Ksac, RPAR);
 
             // Electromechanics excitation-activation
             if (cem.aStress) {
               double epsX;
-              cep_mod.ttp.actv_strs(X(3), cep.dt, yl, epsX);
+              cep.ttp.actv_strs(X(3), cep.dt, yl, epsX);
             } else if (cem.aStrain) {
-              cep_mod.ttp.actv_strn(X(3), I4f, cep.dt, yl);
+              cep.ttp.actv_strn(X(3), I4f, cep.dt, yl);
             }
           }
         } break;
@@ -624,14 +624,14 @@ void cep_integ_l(CepMod& cep_mod, cepModelType& cep, int nX, int nG, Vector<doub
               Istim = 0.0;
             }
 
-            cep_mod.ttp.integ_cn2(cep.imyo, nX, nG, X, Xg, t, cep.dt, Istim, Ksac, IPAR, RPAR);
+            cep.ttp.integ_cn2(cep.imyo, nX, nG, X, Xg, t, cep.dt, Istim, Ksac, IPAR, RPAR);
 
             // Electromechanics excitation-activation
             if (cem.aStress) {
               double epsX;
-              cep_mod.ttp.actv_strs(X(3), cep.dt, yl, epsX);
+              cep.ttp.actv_strs(X(3), cep.dt, yl, epsX);
             } else if (cem.aStrain) {
-              cep_mod.ttp.actv_strn(X(3), I4f, cep.dt, yl);
+              cep.ttp.actv_strn(X(3), I4f, cep.dt, yl);
             }
           }
         } break;
diff --git a/Code/Source/solver/distribute.cpp b/Code/Source/solver/distribute.cpp
index 932d301ea..ec1fdd730 100644
--- a/Code/Source/solver/distribute.cpp
+++ b/Code/Source/solver/distribute.cpp
@@ -1557,14 +1557,15 @@ void dist_eq(ComMod& com_mod, const CmMod& cm_mod, const cmType& cm, const std::
         cm.bcast(cm_mod, &cep.odes.relTol);
       }
 
-      cm.bcast(cm_mod, &cep_mod.ttp.G_Na);
-      cm.bcast(cm_mod, &cep_mod.ttp.G_CaL);
-      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);
+      // Broadcast domain-specific model parameters
+      cm.bcast(cm_mod, &cep.ttp.G_Na);
+      cm.bcast(cm_mod, &cep.ttp.G_CaL);
+      cm.bcast(cm_mod, &cep.ttp.G_Kr);
+      cm.bcast(cm_mod, cep.ttp.G_Ks);
+      cm.bcast(cm_mod, cep.ttp.G_to);
+
+      cm.bcast(cm_mod, cep.bo.tau_si);
+      cm.bcast(cm_mod, cep.bo.tau_fi);
     } 
 
     if ((dmn.phys == EquationType::phys_struct) || (dmn.phys == EquationType::phys_ustruct)) {
diff --git a/Code/Source/solver/read_files.cpp b/Code/Source/solver/read_files.cpp
index 9a644e3db..5af261224 100644
--- a/Code/Source/solver/read_files.cpp
+++ b/Code/Source/solver/read_files.cpp
@@ -999,18 +999,18 @@ void read_cep_domain(Simulation* simulation, EquationParameters* eq_params, Doma
     }
   }
 
-  // Set Ttp parameters.
+  // Set Ttp parameters (domain-specific).
   //
-  if (domain_params->G_Na.defined())  { cep_mod.ttp.G_Na = domain_params->G_Na.value(); }
-  if (domain_params->G_Kr.defined())  { cep_mod.ttp.G_Kr = domain_params->G_Kr.value(); }
-  if (domain_params->G_Ks.defined())  { cep_mod.ttp.G_Ks[lDmn.cep.imyo - 1] = domain_params->G_Ks.value(); }
-  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(); }
+  if (domain_params->G_Na.defined())  { lDmn.cep.ttp.G_Na = domain_params->G_Na.value(); }
+  if (domain_params->G_Kr.defined())  { lDmn.cep.ttp.G_Kr = domain_params->G_Kr.value(); }
+  if (domain_params->G_Ks.defined())  { lDmn.cep.ttp.G_Ks[lDmn.cep.imyo - 1] = domain_params->G_Ks.value(); }
+  if (domain_params->G_to.defined())  { lDmn.cep.ttp.G_to[lDmn.cep.imyo - 1] = domain_params->G_to.value(); }
+  if (domain_params->G_CaL.defined()) { lDmn.cep.ttp.G_CaL = domain_params->G_CaL.value(); }
 
-  // Set Bo parameters.
+  // Set Bo parameters (domain-specific).
   //
-  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(); }
+  if (domain_params->tau_si.defined())  { lDmn.cep.bo.tau_si[lDmn.cep.imyo - 1] = domain_params->tau_si.value(); }
+  if (domain_params->tau_fi.defined())  { lDmn.cep.bo.tau_fi[lDmn.cep.imyo - 1] = domain_params->tau_fi.value(); }
 
   // Set stimulus parameters. 
   //

From f46eedc46a1f2380881eea9e89b371cebbd4f518 Mon Sep 17 00:00:00 2001
From: Javiera Jilberto Vallejos <jilberto@umich.edu>
Date: Wed, 11 Feb 2026 11:44:58 -0800
Subject: [PATCH 2/5] adding test for domain

---
 tests/cases/cep/slab_domains/README.md        |   11 +
 tests/cases/cep/slab_domains/domains.png      |    3 +
 tests/cases/cep/slab_domains/mesh/VOLUME.vtu  |    3 +
 tests/cases/cep/slab_domains/mesh/domain.txt  | 3360 +++++++++++++++++
 .../cep/slab_domains/mesh/surface_x0.vtp      |    3 +
 .../cep/slab_domains/mesh/surface_x20.vtp     |    3 +
 tests/cases/cep/slab_domains/result_020.vtu   |    3 +
 tests/cases/cep/slab_domains/solver.xml       |  106 +
 8 files changed, 3492 insertions(+)
 create mode 100755 tests/cases/cep/slab_domains/README.md
 create mode 100644 tests/cases/cep/slab_domains/domains.png
 create mode 100644 tests/cases/cep/slab_domains/mesh/VOLUME.vtu
 create mode 100644 tests/cases/cep/slab_domains/mesh/domain.txt
 create mode 100644 tests/cases/cep/slab_domains/mesh/surface_x0.vtp
 create mode 100644 tests/cases/cep/slab_domains/mesh/surface_x20.vtp
 create mode 100644 tests/cases/cep/slab_domains/result_020.vtu
 create mode 100644 tests/cases/cep/slab_domains/solver.xml

diff --git a/tests/cases/cep/slab_domains/README.md b/tests/cases/cep/slab_domains/README.md
new file mode 100755
index 000000000..1295b64f0
--- /dev/null
+++ b/tests/cases/cep/slab_domains/README.md
@@ -0,0 +1,11 @@
+
+# **Problem Description**
+ 
+Simulate the propagation of a planar wave in a slab with different domain conductances using the ten-Tusscher-Panfilov cell activation model.
+
+![Slab domains visualization](domains.png)
+
+## References
+K. H. W. J. ten Tusscher, D. Noble, P. J. Noble, and A. V. Panfilov. A model for human ventricular tissue. American Journal of Physiology-Heart and Circulatory Physiology,
+286(4):H1573–H1589, apr 2004.
+
diff --git a/tests/cases/cep/slab_domains/domains.png b/tests/cases/cep/slab_domains/domains.png
new file mode 100644
index 000000000..5d34e8463
--- /dev/null
+++ b/tests/cases/cep/slab_domains/domains.png
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:c6d518a844a4fbba6b7b558ae40ae8ebcbbea160dc226c6fd3fc0164a25c01f5
+size 40034
diff --git a/tests/cases/cep/slab_domains/mesh/VOLUME.vtu b/tests/cases/cep/slab_domains/mesh/VOLUME.vtu
new file mode 100644
index 000000000..1af37fdce
--- /dev/null
+++ b/tests/cases/cep/slab_domains/mesh/VOLUME.vtu
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:69bb6a21296fa79919d0a19669a33a28ae28efdb1bd38124f854815d5d406e8f
+size 89215
diff --git a/tests/cases/cep/slab_domains/mesh/domain.txt b/tests/cases/cep/slab_domains/mesh/domain.txt
new file mode 100644
index 000000000..ff6768cac
--- /dev/null
+++ b/tests/cases/cep/slab_domains/mesh/domain.txt
@@ -0,0 +1,3360 @@
+3
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diff --git a/tests/cases/cep/slab_domains/mesh/surface_x0.vtp b/tests/cases/cep/slab_domains/mesh/surface_x0.vtp
new file mode 100644
index 000000000..eaebcc0eb
--- /dev/null
+++ b/tests/cases/cep/slab_domains/mesh/surface_x0.vtp
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:3c0889ad4a8a4659996309b5bba825c1ac5c3f03d2faca2e84e48f1e035ca240
+size 5219
diff --git a/tests/cases/cep/slab_domains/mesh/surface_x20.vtp b/tests/cases/cep/slab_domains/mesh/surface_x20.vtp
new file mode 100644
index 000000000..07ad82435
--- /dev/null
+++ b/tests/cases/cep/slab_domains/mesh/surface_x20.vtp
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:8248936f54f9537dcad8e2344beb804485d0f5cbfb960f0a8b025310e1af99ae
+size 5128
diff --git a/tests/cases/cep/slab_domains/result_020.vtu b/tests/cases/cep/slab_domains/result_020.vtu
new file mode 100644
index 000000000..861423d34
--- /dev/null
+++ b/tests/cases/cep/slab_domains/result_020.vtu
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:ebe1c77349ecc5143c5b62e0cb6cfb62d8730a5f2ac0e3516d3c56790f27d4a1
+size 75127
diff --git a/tests/cases/cep/slab_domains/solver.xml b/tests/cases/cep/slab_domains/solver.xml
new file mode 100644
index 000000000..50fcfbd6f
--- /dev/null
+++ b/tests/cases/cep/slab_domains/solver.xml
@@ -0,0 +1,106 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+<svMultiPhysicsFile version="0.1">
+
+  <GeneralSimulationParameters>
+    <Continue_previous_simulation> false </Continue_previous_simulation>
+    <Number_of_spatial_dimensions> 3 </Number_of_spatial_dimensions> 
+    <Number_of_time_steps> 20 </Number_of_time_steps> 
+    <Time_step_size> 0.1 </Time_step_size> 
+    <Spectral_radius_of_infinite_time_step> 0.50 </Spectral_radius_of_infinite_time_step> 
+    <Searched_file_name_to_trigger_stop> STOP_SIM </Searched_file_name_to_trigger_stop> 
+
+    <Save_results_to_VTK_format> true </Save_results_to_VTK_format> 
+    <Name_prefix_of_saved_VTK_files> result </Name_prefix_of_saved_VTK_files> 
+    <Increment_in_saving_VTK_files> 1 </Increment_in_saving_VTK_files> 
+    <Start_saving_after_time_step> 0 </Start_saving_after_time_step> 
+
+    <Increment_in_saving_restart_files> 1000 </Increment_in_saving_restart_files> 
+    <Convert_BIN_to_VTK_format> 0 </Convert_BIN_to_VTK_format> 
+
+    <Verbose> 1 </Verbose> 
+    <Warning> 1 </Warning> 
+    <Debug> 0 </Debug>
+  </GeneralSimulationParameters>
+
+  <Add_mesh name="block"> 
+    <Mesh_file_path> ./mesh/VOLUME.vtu </Mesh_file_path>
+
+    <Add_face name="x0">
+      <Face_file_path> ./mesh/surface_x0.vtp </Face_file_path>
+    </Add_face>
+
+    <Add_face name="x1">
+      <Face_file_path> ./mesh/surface_x20.vtp </Face_file_path>
+    </Add_face>
+
+    <Domain_file_path> ./mesh/domain.txt </Domain_file_path>
+
+    <Mesh_scale_factor> 1.0 </Mesh_scale_factor>
+  </Add_mesh>
+
+  <Add_equation type="CEP">
+
+    <Coupled> true </Coupled>
+    <Min_iterations> 1 </Min_iterations>  
+    <Max_iterations> 20 </Max_iterations> 
+    <Tolerance> 1e-10 </Tolerance> 
+
+    <Domain id="1">
+      <Electrophysiology_model> TTP </Electrophysiology_model>
+      <G_Na> 29.68 </G_Na> 
+      <G_CaL> 7.96e-5 </G_CaL>
+      <G_Kr> 0.31 </G_Kr>
+      <Myocardial_zone> epi </Myocardial_zone>
+      <Isotropic_conductivity> 0.033192 </Isotropic_conductivity>
+      <ODE_solver> RK </ODE_solver>
+    </Domain>
+
+    <Domain id="2">
+      <Electrophysiology_model> TTP </Electrophysiology_model>
+      <G_Na> 7.42  </G_Na> 
+      <G_CaL> 1.99e-5 </G_CaL>
+      <G_Kr> 0.08 </G_Kr>
+      <Myocardial_zone> epi </Myocardial_zone>
+      <Isotropic_conductivity> 0.033192 </Isotropic_conductivity>
+      <ODE_solver> RK </ODE_solver>
+    </Domain>
+
+    <Domain id="3">
+      <Electrophysiology_model> TTP </Electrophysiology_model>
+
+      <G_Na> 29.68 </G_Na> 
+      <G_CaL> 7.96e-5 </G_CaL>
+      <G_Kr> 0.31 </G_Kr>
+
+      <Myocardial_zone> epi </Myocardial_zone>
+
+      <Isotropic_conductivity> 0.033192 </Isotropic_conductivity>
+
+      <Stimulus type="Istim">
+        <Amplitude> -35.714 </Amplitude>
+        <Start_time> 0.0 </Start_time>
+        <Duration> 2.0 </Duration>
+        <Cycle_length> 10000.0 </Cycle_length>
+      </Stimulus>
+
+      <ODE_solver> RK4 </ODE_solver>      
+    </Domain>
+
+    <Output type="Spatial">
+      <Action_potential> true </Action_potential>
+    </Output>
+
+    <LS type="GMRES">
+      <Linear_algebra type="fsils">
+        <Preconditioner> fsils </Preconditioner>
+      </Linear_algebra>
+      <Max_iterations> 500 </Max_iterations>
+      <Tolerance> 1e-10 </Tolerance>
+      <Krylov_space_dimension> 50 </Krylov_space_dimension>
+    </LS>
+
+  </Add_equation>
+
+</svMultiPhysicsFile>
+
+

From 15c866d94cfe8f99e9732a864c401614a9f7e09d Mon Sep 17 00:00:00 2001
From: Javiera Jilberto Vallejos <jilberto@umich.edu>
Date: Wed, 11 Feb 2026 19:01:36 -0800
Subject: [PATCH 3/5] adding test to test_cep.py

---
 tests/test_cep.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/tests/test_cep.py b/tests/test_cep.py
index 6195019b8..9ad915dd0 100644
--- a/tests/test_cep.py
+++ b/tests/test_cep.py
@@ -36,6 +36,12 @@ def test_cylinder_purkinje_1d3d(n_proc):
     test_folder = "cylinder_purkinje_1d3d"
     run_with_reference(base_folder, test_folder, fields, n_proc)
 
+
+def test_slab_domains(n_proc):
+    test_folder = "slab_domains"
+    run_with_reference(base_folder, test_folder, fields, n_proc, t_max=20)
+
+
 @pytest.mark.parametrize(
     "confs_ecgs",
     [

From 06a3f3354bb6aa4eca104f5463c56ef8498c3b15 Mon Sep 17 00:00:00 2001
From: Javiera Jilberto Vallejos <jilberto@umich.edu>
Date: Thu, 12 Feb 2026 15:33:28 -0800
Subject: [PATCH 4/5] removing unused function parameter; clarifying comments;
 fixing bug in cep_ion.cpp

---
 Code/Source/solver/CepMod.h       | 8 ++++----
 Code/Source/solver/cep_ion.cpp    | 6 +++---
 Code/Source/solver/cep_ion.h      | 2 +-
 Code/Source/solver/read_files.cpp | 4 ++--
 4 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/Code/Source/solver/CepMod.h b/Code/Source/solver/CepMod.h
index 783d1dd1b..b9edf28f8 100644
--- a/Code/Source/solver/CepMod.h
+++ b/Code/Source/solver/CepMod.h
@@ -166,16 +166,16 @@ class cepModelType
     /// @brief  Time integration options
     odeType odes;
 
-    /// @brief Domain-specific interface for Aliev-Panfilov cellular activation model
+    /// @brief Interface for Aliev-Panfilov cellular activation model
     CepModAp ap;
 
-    /// @brief Domain-specific interface for Bueno-Orovio cellular activation model
+    /// @brief Interface for Bueno-Orovio cellular activation model
     CepModBo bo;
 
-    /// @brief Domain-specific interface for Fitzhugh-Nagumo cellular activation model
+    /// @brief Interface for Fitzhugh-Nagumo cellular activation model
     CepModFn fn;
 
-    /// @brief Domain-specific interface for Tusscher-Panfilov cellular activation model
+    /// @brief Interface for Tusscher-Panfilov cellular activation model
     CepModTtp ttp;
 };
 
diff --git a/Code/Source/solver/cep_ion.cpp b/Code/Source/solver/cep_ion.cpp
index f340f0c28..53aa4cadb 100644
--- a/Code/Source/solver/cep_ion.cpp
+++ b/Code/Source/solver/cep_ion.cpp
@@ -62,7 +62,7 @@ void cep_init(Simulation* simulation)
           Vector<double> Xl(nX); 
           Vector<double> Xgl(nG);
 
-          cep_init_l(cep_mod, eq.dmn[iDmn].cep, nX, nG, Xl, Xgl);
+          cep_init_l(eq.dmn[iDmn].cep, nX, nG, Xl, Xgl);
 
           sA(a) = sA(a) + 1.0;
 
@@ -97,7 +97,7 @@ void cep_init(Simulation* simulation)
         Vector<double> Xl(nX); 
         Vector<double> Xgl(nG);
 
-        cep_init_l(cep_mod, eq.dmn[1].cep, nX, nG, Xl, Xgl);
+        cep_init_l(eq.dmn[0].cep, nX, nG, Xl, Xgl);
 
         for (int i = 0; i < nX; i++) {
           cep_mod.Xion(i,a) = Xl(i);
@@ -114,7 +114,7 @@ void cep_init(Simulation* simulation)
 // cep_init_l
 //------------
 //
-void cep_init_l(CepMod& cep_mod, cepModelType& cep, int nX, int nG, Vector<double>& X, Vector<double>& Xg)
+void cep_init_l(cepModelType& cep, int nX, int nG, Vector<double>& X, Vector<double>& Xg)
 {
   switch (cep.cepType) {
 
diff --git a/Code/Source/solver/cep_ion.h b/Code/Source/solver/cep_ion.h
index d5831da89..0eeb3c0ac 100644
--- a/Code/Source/solver/cep_ion.h
+++ b/Code/Source/solver/cep_ion.h
@@ -17,7 +17,7 @@ namespace cep_ion {
 
 void cep_init(Simulation* simulation);
 
-void cep_init_l(CepMod& cep_mod, cepModelType& cep, int nX, int nG, Vector<double>& X, Vector<double>& Xg);
+void cep_init_l(cepModelType& cep, int nX, int nG, Vector<double>& X, Vector<double>& Xg);
 
 void cep_integ(Simulation* simulation, const int iEq, const int iDof, const Array<double>& Dg);
 
diff --git a/Code/Source/solver/read_files.cpp b/Code/Source/solver/read_files.cpp
index 84d03d7e6..6d9ac8a8d 100644
--- a/Code/Source/solver/read_files.cpp
+++ b/Code/Source/solver/read_files.cpp
@@ -999,7 +999,7 @@ void read_cep_domain(Simulation* simulation, EquationParameters* eq_params, Doma
     }
   }
 
-  // Set Ttp parameters (domain-specific).
+  // Set Ttp parameters.
   //
   if (domain_params->G_Na.defined())  { lDmn.cep.ttp.G_Na = domain_params->G_Na.value(); }
   if (domain_params->G_Kr.defined())  { lDmn.cep.ttp.G_Kr = domain_params->G_Kr.value(); }
@@ -1007,7 +1007,7 @@ void read_cep_domain(Simulation* simulation, EquationParameters* eq_params, Doma
   if (domain_params->G_to.defined())  { lDmn.cep.ttp.G_to[lDmn.cep.imyo - 1] = domain_params->G_to.value(); }
   if (domain_params->G_CaL.defined()) { lDmn.cep.ttp.G_CaL = domain_params->G_CaL.value(); }
 
-  // Set Bo parameters (domain-specific).
+  // Set Bo parameters.
   //
   if (domain_params->tau_si.defined())  { lDmn.cep.bo.tau_si[lDmn.cep.imyo - 1] = domain_params->tau_si.value(); }
   if (domain_params->tau_fi.defined())  { lDmn.cep.bo.tau_fi[lDmn.cep.imyo - 1] = domain_params->tau_fi.value(); }

From bb4887b8b822a149f45366eaa329bf07e5002d87 Mon Sep 17 00:00:00 2001
From: Javiera Jilberto Vallejos <jilberto@umich.edu>
Date: Wed, 18 Feb 2026 21:37:01 -0800
Subject: [PATCH 5/5] no domains in equations fixed; updated parameter
 assignment

---
 Code/Source/solver/cep_ion.cpp    |  6 +++---
 Code/Source/solver/read_files.cpp | 29 +++++++++++++++++++----------
 2 files changed, 22 insertions(+), 13 deletions(-)

diff --git a/Code/Source/solver/cep_ion.cpp b/Code/Source/solver/cep_ion.cpp
index 53aa4cadb..2cf78b836 100644
--- a/Code/Source/solver/cep_ion.cpp
+++ b/Code/Source/solver/cep_ion.cpp
@@ -52,7 +52,7 @@ void cep_init(Simulation* simulation)
         for (int iDmn = 0; iDmn < eq.nDmn; iDmn++) {
           auto cPhys = eq.dmn[iDmn].phys;
           int dID = eq.dmn[iDmn].Id;
-          if ((cPhys != EquationType::phys_CEP) || !utils::btest(com_mod.dmnId(a),dID)) {
+          if ((cPhys != EquationType::phys_CEP) || (dID >= 0 && !utils::btest(com_mod.dmnId(a),dID))) {
             continue;
           }
           int nX = eq.dmn[iDmn].cep.nX;
@@ -220,9 +220,9 @@ void cep_integ(Simulation* simulation, const int iEq, const int iDof, const Arra
         auto cPhys = dmn.phys;
         int dID = dmn.Id;
 
-        if (cPhys != Equation_CEP || !utils::btest(com_mod.dmnId(Ac),dID)) {
+        if (cPhys != Equation_CEP || (dID >= 0 && !utils::btest(com_mod.dmnId(Ac),dID))) {
           continue;
-	}
+	      }
 
         int nX = dmn.cep.nX;
         int nG = dmn.cep.nG;
diff --git a/Code/Source/solver/read_files.cpp b/Code/Source/solver/read_files.cpp
index 6d9ac8a8d..846f03d6b 100644
--- a/Code/Source/solver/read_files.cpp
+++ b/Code/Source/solver/read_files.cpp
@@ -1000,17 +1000,26 @@ void read_cep_domain(Simulation* simulation, EquationParameters* eq_params, Doma
   }
 
   // Set Ttp parameters.
-  //
-  if (domain_params->G_Na.defined())  { lDmn.cep.ttp.G_Na = domain_params->G_Na.value(); }
-  if (domain_params->G_Kr.defined())  { lDmn.cep.ttp.G_Kr = domain_params->G_Kr.value(); }
-  if (domain_params->G_Ks.defined())  { lDmn.cep.ttp.G_Ks[lDmn.cep.imyo - 1] = domain_params->G_Ks.value(); }
-  if (domain_params->G_to.defined())  { lDmn.cep.ttp.G_to[lDmn.cep.imyo - 1] = domain_params->G_to.value(); }
-  if (domain_params->G_CaL.defined()) { lDmn.cep.ttp.G_CaL = domain_params->G_CaL.value(); }
+  // Scalar params
+  std::map<Parameter<double>*,double*> simple_ttp_params{
+    {&domain_params->G_Na, &lDmn.cep.ttp.G_Na},
+    {&domain_params->G_Kr, &lDmn.cep.ttp.G_Kr},
+    {&domain_params->G_CaL, &lDmn.cep.ttp.G_CaL}
+  };
 
-  // Set Bo parameters.
-  //
-  if (domain_params->tau_si.defined())  { lDmn.cep.bo.tau_si[lDmn.cep.imyo - 1] = domain_params->tau_si.value(); }
-  if (domain_params->tau_fi.defined())  { lDmn.cep.bo.tau_fi[lDmn.cep.imyo - 1] = domain_params->tau_fi.value(); }
+  for (auto& [param, value] : simple_ttp_params) {
+    if (param->defined()) {
+      *value = param->value();
+    }
+  }
+
+  // Array params
+  if (domain_params->G_Ks.defined()) {
+    lDmn.cep.ttp.G_Ks[lDmn.cep.imyo - 1] = domain_params->G_Ks.value();
+  }
+  if (domain_params->G_to.defined()) {
+    lDmn.cep.ttp.G_to[lDmn.cep.imyo - 1] = domain_params->G_to.value();
+  }
 
   // Set stimulus parameters. 
   //