Fixing the polynomial function

Campbell-Muscle-Lab · Nov 2, 2021 · 92c4bcc · 92c4bcc
1 parent b4da46b
commit 92c4bcc
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Showing 9 changed files with 26 additions and 20 deletions.
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_version.h b/code/FiberCpp/FiberSim_version.h
@@ -9,4 +9,4 @@
 using namespace std::filesystem;
 
 // Variables
-static inline std::string const code_version = "2.0.0";
+static inline std::string const code_version = "2.0.1";
diff --git a/code/FiberCpp/half_sarcomere.cpp b/code/FiberCpp/half_sarcomere.cpp
@@ -854,13 +854,6 @@ void half_sarcomere::initialise_filament_y_z_coordinates(int m_n)
         exit(1);
     }
 
-    // Check for valid m_n
-    if (m_n != 9)
-    {
-        printf("m_n is not == 3. Intialize filament_y_z_coordinates has not been checked\n");
-        //exit(1);
-    }
-
     // Variables
     int n_rows = (int)round(sqrt(m_n));         /**< no_of_rows of myosins, y_direction */
     int n_cols = n_rows;                        /**< no of cols of myosins, z direction */

diff --git a/code/FiberCpp/transition.cpp b/code/FiberCpp/transition.cpp
@@ -40,7 +40,7 @@ transition::transition(const rapidjson::Value& tr, m_state* set_p_parent_m_state
 	const rapidjson::Value& rp = tr["rate_parameters"];
 
 	rate_parameters = gsl_vector_alloc(MAX_NO_OF_RATE_PARAMETERS);
-	gsl_vector_set_zero(rate_parameters);
+	gsl_vector_set_all(rate_parameters, GSL_NAN);
 
 	for (int i = 0; i < (int)rp.Size(); i++)
 	{
@@ -210,7 +210,7 @@ double transition::calculate_rate(double x, double x_ext, double node_force, int
 	{
 		double x_center = gsl_vector_get(rate_parameters, 3); // optional parameter defining the zero of the polynomial
 
-		if (isnan(x_center)) { // optional parameter is not specified, use the state extension instead
+		if (gsl_isnan(x_center)) { // optional parameter is not specified, use the state extension instead
 			x_center = x_ext;
 		}	
 
@@ -223,9 +223,9 @@ double transition::calculate_rate(double x, double x_ext, double node_force, int
 	// Poly_asymmetric
 	if (!strcmp(rate_type, "poly_asym"))
 	{
-		double x_center = gsl_vector_get(rate_parameters, 3); // optional parameter defining the zero of the polynomial
+		double x_center = gsl_vector_get(rate_parameters, 5); // optional parameter defining the zero of the polynomial
 
-		if (isnan(x_center)) { // optional parameter is not specified, use the state extension instead
+		if (gsl_isnan(x_center)) { // optional parameter is not specified, use the state extension instead
 			x_center = x_ext;
 		}
 
@@ -236,7 +236,7 @@ double transition::calculate_rate(double x, double x_ext, double node_force, int
 		else
 			rate = gsl_vector_get(rate_parameters, 0) +
 			(gsl_vector_get(rate_parameters, 2) *
-				gsl_pow_int(x - x_center, (int)gsl_vector_get(rate_parameters, 3)));
+				gsl_pow_int(x - x_center, (int)gsl_vector_get(rate_parameters, 4)));
 	}
 
 	// Curtail at max rate

diff --git a/demo_files/getting_started/isometric_activation/sim_input/model.json b/demo_files/getting_started/isometric_activation/sim_input/model.json
@@ -113,7 +113,8 @@
               "rate_parameters": [
                 75,
                 1,
-                2
+                2,
+                0
               ]
             }
           ]

diff --git a/docs/pages/installation/installation.md b/docs/pages/installation/installation.md
@@ -11,7 +11,7 @@ This page discusses how to install FiberSim and the necessary support software.
 
 FiberSim is available for free download under the GPL3 license. The latest release in hosted on Zenodo and can be downloaded [here](https://doi.org/10.5281/zenodo.4929389). 
 
-1. Download the .zip file hosted on <https://doi.org/10.5281/zenodo.4929389>. Make sure you download version 2.0.0.
+1. Download the .zip file hosted on <https://doi.org/10.5281/zenodo.4929389>. Make sure you download version 2.0.1.
 2. Extract the data. We recommend to use a simple path to extract them, such as `C:\Users\<user-name>\Documents`.
 3. Rename the extracted folder to `FiberSim` (instead of `Campbell-Muscle-Lab-FiberSim-xxxxxx`).
 4. Make sure the `FiberSim` folder look like this:

diff --git a/docs/pages/structures/kinetics/kinetics.md b/docs/pages/structures/kinetics/kinetics.md
@@ -129,9 +129,22 @@ Super-relaxed heads can only exist as dimers. Thus, if a head transitions from a
     + b, depends on c
     + c, integer
 	+ d, nm (optional)
-  + rate = a + b * (x - d)<sup>c
+  + rate = a + b * (x - d)<sup>c</sup>
 
 Note: if d is not specified, the code sets d = the state extension (5.0 in the myosin scheme example shown above)
+
++ `poly_asym`
+  + rate_parameters
+    + a, s<sup>-1</sup> 
+    + b, depends on d
+    + c, depends on d
+	+ d, integer
+	+ e, integer
+	+ f, nm (optional)
+  + rate = a + b * (x - f)<sup>d</sup> if x > f
+  + rate = a + c * (x - f)<sup>e</sup> if x < f
+
+Note: if f is not specified, the code sets f = the state extension (5.0 in the myosin scheme example shown above)
 
 
 
diff --git a/docs/pages/structures/model/model.md b/docs/pages/structures/model/model.md
@@ -18,8 +18,8 @@ Inevitably, even a simple model file is quite long. Here is an example from [iso
 
 ````
 {  
-	"FiberSim": {
-	"version":  "2.0.0"
+"FiberSim": {
+"version":  "2.0.0"
   },
     "muscle": {
         "no_of_half_sarcomeres": 1,
@@ -132,8 +132,7 @@ Inevitably, even a simple model file is quite long. Here is an example from [iso
               "rate_parameters": [
                 75,
                 1,
-                2,
-				0
+                2
               ]
             }
           ]