Added "force_dep_gaussian" in transition.cpp

Campbell-Muscle-Lab · Sep 1, 2021 · 65731c5 · 65731c5
1 parent 8bbf1cf
commit 65731c5
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Showing 4 changed files with 37 additions and 1 deletion.
diff --git a/bin/FiberCpp.exe b/bin/FiberCpp.exe
diff --git a/bin/FiberCpp.pdb b/bin/FiberCpp.pdb
diff --git a/code/FiberCpp/FiberSim_options.cpp b/code/FiberCpp/FiberSim_options.cpp
@@ -22,7 +22,7 @@ FiberSim_options::FiberSim_options(char JSON_options_file_string[])
     // Initialise
 
     // Set default values
-    x_pos_rel_tol = 0.001;                  /**< default value of relative tolerance for
+    x_pos_rel_tol = 0.001;                  /**< default value of absolute tolerance for
                                                  calculating x positions */
 
     adjacent_bs = 0;                        /**< default value of adjacent binding sites
@@ -200,6 +200,14 @@ void FiberSim_options::set_FiberSim_options_from_JSON_file_string(char JSON_file
         x_pos_rel_tol = options["x_pos_rel_tol"].GetDouble();
     }
 
+    // In FiberSim versions > 1.2.0, x_pos_tol notation is preferred over x_pos_rel_tol
+
+    if (JSON_functions::is_JSON_member(options, "x_pos_tol"))
+    {
+        JSON_functions::check_JSON_member_number(options, "x_pos_tol");
+        x_pos_rel_tol = options["x_pos_tol"].GetDouble();
+    }
+
     // Check if the dump precision was specified.
     if (JSON_functions::is_JSON_member(options, "dump_precision"))
     {

diff --git a/code/FiberCpp/transition.cpp b/code/FiberCpp/transition.cpp
@@ -163,6 +163,34 @@ double transition::calculate_rate(double x, double node_force, int mybpc_state,
 				(1e18 * 1.38e-23 * 310.0));
 	}
 
+	// Force-dependent Gaussian
+
+	if (!strcmp(rate_type, "force_dependent_gaussian"))
+	{
+
+		FiberSim_model* p_model = p_parent_m_state->p_parent_scheme->p_fs_model;
+		double k_cb = p_model->m_k_cb;
+
+		rate = gsl_vector_get(rate_parameters, 0) *
+			exp(-(0.5 * k_cb * gsl_pow_int(x, 2)) /
+				(1e18 * 1.38e-23 * 310.0)) *
+			(1.0 + gsl_max(node_force, 0.0) * gsl_vector_get(rate_parameters, 1));
+	}
+
+	// Force-dependent Gaussian for MyBPC
+
+	if (!strcmp(rate_type, "force_dependent_gaussian_pc"))
+	{
+
+		FiberSim_model* p_model = p_parent_m_state->p_parent_scheme->p_fs_model;
+		double k_pc = p_model->c_k_stiff;
+
+		rate = gsl_vector_get(rate_parameters, 0) *
+			exp(-(0.5 * k_pc * gsl_pow_int(x, 2)) /
+				(1e18 * 1.38e-23 * 310.0)) *
+			(1.0 + gsl_max(node_force, 0.0) * gsl_vector_get(rate_parameters, 1));
+	}
+
 	// Poly
 	if (!strcmp(rate_type, "poly"))
 	{