Renaming of XML to TTP_initial_conditions

Author: kko27

Code/Source/solver/Parameters.cpp

@@ -1665,7 +1665,7 @@ void DomainParameters::print_parameters()
 
   stimulus.print_parameters();
 
-  initial_conditions.print_parameters();
+  ttp_initial_conditions.print_parameters();
 
   fluid_viscosity.print_parameters();
 
@@ -1713,7 +1713,7 @@ void DomainParameters::set_values(tinyxml2::XMLElement* domain_elem, bool from_e
       stimulus.set_values(item);
 
     } else if (name == InitialConditionsParameters::xml_element_name_) {
-      initial_conditions.set_values(item);
+      ttp_initial_conditions.set_values(item);
 
     } else if (name == FluidViscosityParameters::xml_element_name_ || name == SolidViscosityParameters::xml_element_name_) {
       auto eq_type = consts::equation_name_to_type.at(equation.value());
@@ -3145,10 +3145,10 @@ void LinearSolverParameters::set_values(tinyxml2::XMLElement* xml_elem)
 //            InitialConditionsParameters               //
 //////////////////////////////////////////////////////////
 
-// Process parameters for the 'Initial_conditions' XML element.
+// Process parameters for the 'TTP_initial_conditions' XML element.
 
 /// @brief Define the XML element name for initial conditions parameters.
-const std::string InitialConditionsParameters::xml_element_name_ = "Initial_conditions";
+const std::string InitialConditionsParameters::xml_element_name_ = "TTP_initial_conditions";
 
 InitialConditionsParameters::InitialConditionsParameters()
 {
@@ -3196,8 +3196,8 @@ void InitialConditionsParameters::set_values(tinyxml2::XMLElement* xml_elem)
 //            InitialStatesParameters                   //
 //////////////////////////////////////////////////////////
 
-/// @brief Define the XML element name for initial states parameters.
-const std::string InitialStatesParameters::xml_element_name_ = "Initial_States";
+/// @brief Define the XML element name for initial states parameters (Initial_states).
+const std::string InitialStatesParameters::xml_element_name_ = "Initial_states";
 
 InitialStatesParameters::InitialStatesParameters()
 {

Code/Source/solver/Parameters.h

@@ -1181,7 +1181,7 @@ class FiberReinforcementStressParameters : public ParameterLists
 };
 
 /// @brief The GatingVariablesParameters class stores parameters for the
-/// 'Gating_variables' XML element under Initial_conditions.
+/// 'Gating_variables' XML element under TTP_initial_conditions.
 class GatingVariablesParameters : public ParameterLists
 {
   public:
@@ -1217,7 +1217,7 @@ class GatingVariablesParameters : public ParameterLists
 };
 
 /// @brief The InitialStatesParameters class stores parameters for the
-/// 'Initial_States' XML element under Initial_conditions.
+/// 'Initial_states' XML element under TTP_initial_conditions.
 class InitialStatesParameters : public ParameterLists
 {
   public:
@@ -1241,7 +1241,7 @@ class InitialStatesParameters : public ParameterLists
 };
 
 /// @brief The InitialConditionsParameters class stores parameters for the
-/// 'Initial_conditions' XML element under Domain.
+/// 'TTP_initial_conditions' XML element under Domain.
 class InitialConditionsParameters : public ParameterLists
 {
   public:
@@ -1288,7 +1288,7 @@ class DomainParameters : public ParameterLists
     StimulusParameters stimulus;
     FluidViscosityParameters fluid_viscosity;
     SolidViscosityParameters solid_viscosity;
-    InitialConditionsParameters initial_conditions;
+    InitialConditionsParameters ttp_initial_conditions;
 
     // Attributes.
     Parameter<std::string> id;

Code/Source/solver/read_files.cpp

@@ -1039,11 +1039,11 @@ void read_cep_domain(Simulation* simulation, EquationParameters* eq_params, Doma
     }
   }
 
-  if (domain_params->initial_conditions.defined()) {
+  if (domain_params->ttp_initial_conditions.defined()) {
 
-    auto& initial_conditions_params = domain_params->initial_conditions;
-    if (initial_conditions_params.initial_states.defined()) {
-      auto& initial_states_params = initial_conditions_params.initial_states;
+    auto& ttp_initial_conditions_params = domain_params->ttp_initial_conditions;
+    if (ttp_initial_conditions_params.initial_states.defined()) {
+      auto& initial_states_params = ttp_initial_conditions_params.initial_states;
       bool any_set = false;
       if (initial_states_params.V.defined()) { lDmn.cep.ttp_initial_state.V = initial_states_params.V.value(); any_set = true; }
       if (initial_states_params.K_i.defined()) { lDmn.cep.ttp_initial_state.K_i = initial_states_params.K_i.value(); any_set = true; }
@@ -1055,8 +1055,8 @@ void read_cep_domain(Simulation* simulation, EquationParameters* eq_params, Doma
       lDmn.cep.ttp_user_initial_state = any_set;
     }
 
-    if (initial_conditions_params.gating_variables.defined()) {
-      auto& gating_variables_params = initial_conditions_params.gating_variables;
+    if (ttp_initial_conditions_params.gating_variables.defined()) {
+      auto& gating_variables_params = ttp_initial_conditions_params.gating_variables;
       bool any_set = false;
       // Rectifier current gating variables
       if (gating_variables_params.x_r1_rectifier.defined()) { lDmn.cep.ttp_initial_state.x_r1 = gating_variables_params.x_r1_rectifier.value(); any_set = true; }

TTP_Initial_Conditions_Flow_Control.md

@@ -54,21 +54,21 @@ auto root_element = doc.FirstChildElement(FSI_FILE.c_str());
 - **Location**: `Code/Source/solver/Parameters.cpp:1673`
 - **Action**:
   - Iterates through child elements of `<Domain>`
-  - When encountering `<Initial_conditions>` element:
+  - When encountering `<TTP_initial_conditions>` element:
     - Creates/calls `InitialConditionsParameters::set_values()`
 
 ### Step 1.5: Initial States Parsing
 - **Function**: `InitialConditionsParameters::set_values(tinyxml2::XMLElement* xml_elem)`
 - **Location**: `Code/Source/solver/Parameters.cpp:2986`
 - **Action**:
-  - Checks for `<Initial_States>` child element
+  - Checks for `<Initial_states>` child element
   - If found, calls `InitialStatesParameters::set_values()`
 
 ### Step 1.6: Individual State Variable Parsing
 - **Function**: `InitialStatesParameters::set_values(tinyxml2::XMLElement* xml_elem)`
 - **Location**: `Code/Source/solver/Parameters.cpp:3043`
 - **Action**:
-  - Iterates through child elements of `<Initial_States>`
+  - Iterates through child elements of `<Initial_states>`
   - For each element (e.g., `<V>`, `<K_i>`, `<Na_i>`, etc.):
     - Extracts text value using `item->GetText()`
     - Calls `set_parameter_value(name, value)` to store the value
@@ -97,7 +97,7 @@ auto root_element = doc.FirstChildElement(FSI_FILE.c_str());
 - **Function**: `read_cep_domain(CepMod* cep_mod, Simulation* simulation, DomainParameters* domain_params, cepModelType& lDmn)`
 - **Location**: `Code/Source/solver/read_files.cpp:1058`
 - **Action**:
-  - Checks if `domain_params->initial_conditions.defined()` is true
+  - Checks if `domain_params->ttp_initial_conditions.defined()` is true
   - If initial conditions are defined in XML, proceeds to extract and store values
 
 ### Step 2.2: Initial States Storage
@@ -378,16 +378,16 @@ XML File (solver.xml)
     <Electrophysiology_model> TTP </Electrophysiology_model>
     <Myocardial_zone> epi </Myocardial_zone>
 
-    <Initial_conditions>
-        <Initial_States>
+    <TTP_initial_conditions>
+        <Initial_states>
             <V>18.167</V>
             <K_i>136.897</K_i>
             <Na_i>8.6105</Na_i>
             <Ca_i>1.2592E-4</Ca_i>
             <Ca_ss>3.6181E-4</Ca_ss>
             <Ca_sr>3.6399</Ca_sr>
             <R_bar>0.9078</R_bar>
-        </Initial_States>
+        </Initial_states>
 
         <Gating_variables>
             <x_r1_rectifier>6.368E-3</x_r1_rectifier>
@@ -403,7 +403,7 @@ XML File (solver.xml)
             <s_out>0.9941</s_out>
             <r_out>4.2757E-5</r_out>
         </Gating_variables>
-    </Initial_conditions>
+    </TTP_initial_conditions>
 </Domain>
 ```
 

tests/cases/cep/spiral_TTP_2d/README.md

@@ -10,14 +10,14 @@ Initial conditions for the Ten-tusscher-Panfilov (TTP) EP model to be specified
 
 ## Overview
 
-The user-defined initial conditions override system allows users to specify custom initial states and gating variables directly in the XML configuration file. When `Initial_conditions` is specified in the XML, it automatically overrides the default initial conditions that would normally be set based on the myocardial zone (epicardium, endocardium, or midmyocardium).
+The user-defined initial conditions override system allows users to specify custom initial states and gating variables directly in the XML configuration file. When `TTP_initial_conditions` is specified in the XML, it automatically overrides the default initial conditions that would normally be set based on the myocardial zone (epicardium, endocardium, or midmyocardium).
 
 ## How It Works
 
-1. **XML Specification**: Users specify `Initial_conditions` in the domain configuration
+1. **XML Specification**: Users specify `TTP_initial_conditions` in the domain configuration
 2. **Flag Activation**: The system automatically sets a flag indicating user-defined initial conditions are being used
 3. **Override Logic**: During initialization, the system uses the user-defined values instead of defaults
-4. **Fallback**: If no `Initial_conditions` are specified, the system uses default initialization based on myocardial zone
+4. **Fallback**: If no `TTP_initial_conditions` are specified, the system uses default initialization based on myocardial zone
 
 ## XML Configuration
 
@@ -28,16 +28,16 @@ The user-defined initial conditions override system allows users to specify cust
     <Electrophysiology_model> TTP </Electrophysiology_model>
     <Myocardial_zone> epicardium </Myocardial_zone>
     <!-- User-defined initial conditions - these override the default epicardium values -->
-    <Initial_conditions>
-        <Initial_States>
+    <TTP_initial_conditions>
+        <Initial_states>
             <V>-82.0</V>
             <K_i>135.0</K_i>
             <Na_i>9.5</Na_i>
             <Ca_i>0.00015</Ca_i>
             <Ca_ss>0.00015</Ca_ss>
             <Ca_sr>0.18</Ca_sr>
             <R_bar>0.0</R_bar>
-        </Initial_States>
+        </Initial_states>
         <Gating_variables>
             <Rectifier_current>
                 <x_r1>0.008</x_r1>
@@ -60,7 +60,7 @@ The user-defined initial conditions override system allows users to specify cust
                 <r>0.001</r>
             </Transient_outward_current>
         </Gating_variables>
-    </Initial_conditions>
+    </TTP_initial_conditions>
 </Domain>
 ```
 
@@ -71,20 +71,20 @@ The user-defined initial conditions override system allows users to specify cust
     <Electrophysiology_model> TTP </Electrophysiology_model>
     <Myocardial_zone> epicardium </Myocardial_zone>
     <!-- Partial override - only specified values override defaults -->
-    <Initial_conditions>
-        <Initial_States>
+    <TTP_initial_conditions>
+        <Initial_states>
             <V>-82.0</V>
             <K_i>135.0</K_i>
             <!-- Other values (Na_i, Ca_i, Ca_ss, Ca_sr, R_bar) use epicardium defaults -->
-        </Initial_States>
+        </Initial_states>
         <Gating_variables>
             <Rectifier_current>
                 <x_r1>0.008</x_r1>
                 <!-- x_r2 and x_s use epicardium defaults -->
             </Rectifier_current>
             <!-- Other gating variable groups use epicardium defaults -->
         </Gating_variables>
-    </Initial_conditions>
+    </TTP_initial_conditions>
 </Domain>
 ```
 
@@ -94,7 +94,7 @@ The user-defined initial conditions override system allows users to specify cust
 <Domain id="1">
     <Electrophysiology_model> TTP </Electrophysiology_model>
     <Myocardial_zone> epicardium </Myocardial_zone>
-    <!-- No Initial_conditions specified - uses epicardium defaults -->
+    <!-- No TTP_initial_conditions specified - uses epicardium defaults -->
 </Domain>
 ```
 
@@ -137,7 +137,7 @@ The user-defined initial conditions override system allows users to specify cust
 
 1. **Added Flag**: `user_initial_conditions_defined` flag in `CepModTtp` class
 2. **Modified Initialization**: `init()` method checks the flag and uses user values when set
-3. **XML Integration**: `read_cep_domain()` sets the flag when `Initial_conditions` is specified
+3. **XML Integration**: `read_cep_domain()` sets the flag when `TTP_initial_conditions` is specified
 
 ### Logic Flow
 
@@ -150,7 +150,7 @@ The user-defined initial conditions override system allows users to specify cust
 
 ```cpp
 // In read_files.cpp
-if (domain_params->initial_conditions.defined()) {
+if (domain_params->ttp_initial_conditions.defined()) {
     // Read and set user-defined values
     cep_mod.ttp.set_user_initial_conditions_flag(true);
 }

tests/cases/cep/spiral_TTP_2d/solver.xml

@@ -62,16 +62,16 @@
       <Isotropic_conductivity> 0.1171 </Isotropic_conductivity>
 
       <Myocardial_zone> epi </Myocardial_zone>
-        <Initial_conditions>
-            <Initial_States>
+        <TTP_initial_conditions>
+            <Initial_states>
                 <V>18.167</V>
                 <K_i>136.897</K_i>
                 <Na_i>8.6105</Na_i>
                 <Ca_i>1.2592E-4</Ca_i>
                 <Ca_ss>3.6181E-4</Ca_ss>
                 <Ca_sr>3.6399</Ca_sr>
                 <R_bar>0.9078</R_bar>
-            </Initial_States>
+            </Initial_states>
 
             <Gating_variables>
                 <x_r1_rectifier>6.368E-3</x_r1_rectifier>
@@ -87,7 +87,7 @@
                 <s_out>0.9941</s_out>
                 <r_out>4.2757E-5</r_out>
             </Gating_variables>
-        </Initial_conditions>
+        </TTP_initial_conditions>
       <ODE_solver> RK </ODE_solver>
    </Domain>
 
@@ -113,16 +113,16 @@
       <Isotropic_conductivity> 0.1171 </Isotropic_conductivity>
 
       <Myocardial_zone> epi </Myocardial_zone>
-        <Initial_conditions>
-            <Initial_States>
+        <TTP_initial_conditions>
+            <Initial_states>
                 <V>-44.756</V>
                 <K_i>136.88</K_i>
                 <Na_i>8.5907</Na_i>
                 <Ca_i>3.0084E-4</Ca_i>
                 <Ca_ss>2.5462E-3</Ca_ss>
                 <Ca_sr>3.5292</Ca_sr>
                 <R_bar>0.7235</R_bar>
-            </Initial_States>
+            </Initial_states>
 
             <Gating_variables>
                 <x_r1_rectifier>0.9739</x_r1_rectifier>
@@ -138,7 +138,7 @@
                 <s_out>0.4095</s_out>
                 <r_out>7.857E-4</r_out>
             </Gating_variables>
-        </Initial_conditions>
+        </TTP_initial_conditions>
       <ODE_solver> RK </ODE_solver>
    </Domain>
 
@@ -152,16 +152,16 @@
       <Isotropic_conductivity> 0.1171 </Isotropic_conductivity>
 
       <Myocardial_zone> epi </Myocardial_zone>
-        <Initial_conditions>
-            <Initial_States>
+        <TTP_initial_conditions>
+            <Initial_states>
                 <V>-11.612</V>
                 <K_i>136.88</K_i>
                 <Na_i>8.5916</Na_i>
                 <Ca_i>3.486E-4</Ca_i>
                 <Ca_ss>1.312E-2</Ca_ss>
                 <Ca_sr>3.4619</Ca_sr>
                 <R_bar>0.6875</R_bar>
-            </Initial_States>
+            </Initial_states>
 
             <Gating_variables>
                 <x_r1_rectifier>9.882E-1</x_r1_rectifier>
@@ -177,7 +177,7 @@
                 <s_out>7.9355E-2</s_out>
                 <r_out>1.0429E-2</r_out>
             </Gating_variables>
-        </Initial_conditions>
+        </TTP_initial_conditions>
       <ODE_solver> RK </ODE_solver>
    </Domain>
 

tests/cases/cep/spiral_TTP_xmlsep/domain-1_EPmodel.xml

@@ -2,7 +2,7 @@
 <svMultiPhysicsFile version="0.1">
 
 <Electrophysiology_model> TTP </Electrophysiology_model>
-<G_Na> 10 </G_Na>
+<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>
@@ -11,16 +11,16 @@
 
 <Myocardial_zone> epi </Myocardial_zone>
 
-<Initial_conditions>
-    <Initial_States>
+<TTP_initial_conditions>
+    <Initial_states>
         <V>18.167</V>
         <K_i>136.897</K_i>
         <Na_i>8.6105</Na_i>
         <Ca_i>1.2592E-4</Ca_i>
         <Ca_ss>3.6181E-4</Ca_ss>
         <Ca_sr>3.6399</Ca_sr>
         <R_bar>0.9078</R_bar>
-    </Initial_States>
+    </Initial_states>
 
     <Gating_variables>
         <x_r1_rectifier>6.368E-3</x_r1_rectifier>
@@ -36,7 +36,7 @@
         <s_out>0.9941</s_out>
         <r_out>4.2757E-5</r_out>
     </Gating_variables>
-</Initial_conditions>
+</TTP_initial_conditions>
 
 <ODE_solver> RK </ODE_solver>