Merge pull request #118 from Campbell-Muscle-Lab/twitch_loads

Twitch loads

Author: kenatcampbellmusclelab

.gitignore

@@ -511,15 +511,16 @@ Gemfile.lock
 # Demo files
 **/demo_files/**/sim_data/**/*.*
 **/demo_files/**/generated/**/*.*
+**/demo_files/**/working/**/*.*
 **/demo_files/**/generated_char/**/*.*
 **/demo_files/**/analysis/**/*.*
 **/demo_files/**/protocols/**/*.*
 **/demo_files/**/fitting/**/progress/**/*.*
-**/demo_files/**/fitting/**/working/**/*.*
 **/demo_files/**/sim_output/**/*.*
 **/demo_files/**/threads/**/*.*
 **/demo_files/**/mle/**/progress/**/*.*
 **/demo_files/**/target_data/**/sim_input/**/*.*
+**/demo_files/**/electrical_stimulation/**/sim_data_*/**/*.*
 !**/demo_files/**/target_data/**/sim_output/**/*.xlsx
 
 

bin/FiberCpp.exe

@@ -29,26 +29,26 @@
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration">
     <ConfigurationType>Application</ConfigurationType>
     <UseDebugLibraries>true</UseDebugLibraries>
-    <PlatformToolset>v143</PlatformToolset>
+    <PlatformToolset>v145</PlatformToolset>
     <CharacterSet>Unicode</CharacterSet>
   </PropertyGroup>
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration">
     <ConfigurationType>Application</ConfigurationType>
     <UseDebugLibraries>false</UseDebugLibraries>
-    <PlatformToolset>v143</PlatformToolset>
+    <PlatformToolset>v145</PlatformToolset>
     <WholeProgramOptimization>true</WholeProgramOptimization>
     <CharacterSet>Unicode</CharacterSet>
   </PropertyGroup>
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'" Label="Configuration">
     <ConfigurationType>Application</ConfigurationType>
     <UseDebugLibraries>true</UseDebugLibraries>
-    <PlatformToolset>v143</PlatformToolset>
+    <PlatformToolset>v145</PlatformToolset>
     <CharacterSet>Unicode</CharacterSet>
   </PropertyGroup>
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="Configuration">
     <ConfigurationType>Application</ConfigurationType>
     <UseDebugLibraries>false</UseDebugLibraries>
-    <PlatformToolset>v143</PlatformToolset>
+    <PlatformToolset>v145</PlatformToolset>
     <WholeProgramOptimization>true</WholeProgramOptimization>
     <CharacterSet>Unicode</CharacterSet>
   </PropertyGroup>

bin/FiberCpp.pdb

@@ -521,6 +521,11 @@ void FiberSim_model::set_FiberSim_model_parameters_from_JSON_file_string(char JS
         }
     }
 
+    if (JSON_functions::check_JSON_member_exists(mybpc_parameters, "c_binds_only_to_active"))
+        c_binds_only_to_active = mybpc_parameters["c_binds_only_to_active"].GetInt();
+    else
+        c_binds_only_to_active = 1;
+
     // If there is an array of isotypes, save it to the appropriate short vector
     if (JSON_functions::is_JSON_member(mybpc_parameters, "c_isotype_ints"))
     {

code/FiberCpp/FiberSim.vcxproj

@@ -226,6 +226,9 @@ class FiberSim_model
 
     int c_no_of_pc_states;              /**< max number of MyBPC states */
 
+    int c_binds_only_to_active;         /**< 1 means mybpc can only bind to active sites (default)
+                                             0 means can bind to any unbound site on actin */
+
     gsl_vector* c_isotype_props;	    /**< gsl_vector holding the C-protein isotypes proportions */
 
     gsl_vector_short* c_isotype_ints;   /**< gsl_vector_short holding C-protein isotype */

code/FiberCpp/FiberSim_model.cpp

@@ -82,6 +82,8 @@ FiberSim_options::FiberSim_options(char JSON_options_file_string[])
     afterload_factor_s = GSL_POSINF;        /**< default value for afterload factor s */
     afterload_factor_multiplier = 1.0;      /**< default value for afterload multiplier */
 
+    afterload_min_init_time_s = 0;          /**< min time in s to initiate afterload */
+
     start_status_time_step = 0;             /**< default value */
     stop_status_time_step = 0;              /**< default value */
     skip_status_time_step = 0;              /**< default value */
@@ -372,6 +374,11 @@ void FiberSim_options::set_FiberSim_options_from_JSON_file_string(char JSON_file
         {
             afterload_factor_multiplier = afterload["factor_multiplier"].GetDouble();
         }
+
+        if (JSON_functions::check_JSON_member_exists(afterload, "min_init_time_s"))
+        {
+            afterload_min_init_time_s = afterload["min_init_time_s"].GetDouble();
+        }
     }
 
     // Now check for logging

code/FiberCpp/FiberSim_model.h

@@ -152,6 +152,9 @@ class FiberSim_options
     double afterload_factor_multiplier; /** double defining the factor to increase the
                                                 afterload */
 
+    double afterload_min_init_time_s;   /**< min time in s at which to initiate the
+                                                afterload control */
+
     // Functions
 
     /**

code/FiberCpp/FiberSim_options.cpp

@@ -3187,9 +3187,12 @@ int half_sarcomere::return_c_transition(double time_step, int m_counter, int pc_
                         continue;       // binding site is already occupied
                     }
 
-                    if (gsl_vector_short_get(p_af[a_f]->bs_state, bs_ind) == 1)
+                    if (p_fs_model->c_binds_only_to_active)
                     {
-                        continue;       // binding site is off
+                        if (gsl_vector_short_get(p_af[a_f]->bs_state, bs_ind) == 1)
+                        {
+                            continue;       // binding site is off
+                        }
                     }
 
                     // Transition is possible

code/FiberCpp/FiberSim_options.h

@@ -518,6 +518,8 @@ size_t muscle::afterload_time_step(int protocol_index)
 
 	double afterload;							// the afterload to work against
 
+	double afterload_min_init_time_s;			// min time in s to initate the afterload
+
 	// Code
 
 	// Extract the time-step and pCa
@@ -531,6 +533,8 @@ size_t muscle::afterload_time_step(int protocol_index)
 		afterload = afterload * p_fs_options->afterload_factor_multiplier;
 	}
 
+	afterload_min_init_time_s = p_fs_options->afterload_min_init_time_s;
+
 	// Check what kind of muscle we have
 	if ((p_fs_model[0]->no_of_half_sarcomeres == 1) && (p_sc == NULL))
 	{
@@ -578,7 +582,9 @@ size_t muscle::afterload_time_step(int protocol_index)
 			m_length = m_length + adjustment;
 			lattice_iterations = p_hs[0]->update_lattice(time_step_s, adjustment);
 
-			if ((afterload_mode == 0) && (p_hs[0]->hs_force >= afterload))
+			if ((afterload_mode == 0) &&
+				(m_force >= afterload) &&
+				(m_time_s >= afterload_min_init_time_s))
 			{
 				// Switch to isotonic mode
 				afterload_mode = 1;
@@ -641,7 +647,9 @@ size_t muscle::afterload_time_step(int protocol_index)
 			// Length control
 			lattice_iterations = length_control_myofibril_with_series_compliance(protocol_index);
 
-			if ((afterload_mode == 0) && (m_force >= afterload))
+			if ((afterload_mode == 0) &&
+				(m_force >= afterload) &&
+				(m_time_s >= afterload_min_init_time_s))
 			{
 				afterload_mode = 1;
 			}