added rush-larsen treatment to rush-larsen-c output

Author: MauriceHendrix

.github/workflows/pytest.yml

@@ -5,7 +5,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.5, 3.6, 3.7, 3.8, 3.9]
+        python-version: [3.6, 3.7, 3.8, 3.9]
     steps:
     - name: Checkout repository and submodules
       uses: actions/checkout@v1

RELEASE.md

@@ -1,3 +1,6 @@
+# Release 0.9.4
+- Corrected Rush-Larsen output for `--rush-larsen-c`
+
 # Release 0.9.3
 - Performance upgrade for `--rush-larsen` using caching on linearity checking.
 

chaste_codegen/data/tests/chaste_reference_models/RL_C/aslanidi_Purkinje_model_2009.c

@@ -22,12 +22,17 @@
 // State variables
 //------------------------------------------------------------------------------
 
-double Y[_NB_OF_STATE_VARIABLES_];
+extern double Y[_NB_OF_STATE_VARIABLES_];
 double dY[_NB_OF_STATE_VARIABLES_];
+double Ynew[_NB_OF_STATE_VARIABLES_];
+
 {%- for state_var in state_vars %}
 // {{loop.index0}}: {{state_var.var}} (units: {{state_var.units}}, initial value: {{state_var.initial_value}}, component: {{components[loop.index0]}})
 {%- endfor %}
 
+double Vmem;
+double time;
+
 char YNames[_NB_OF_STATE_VARIABLES_][{{stat_var_name_max_length +1}}];
 char YUnits[_NB_OF_STATE_VARIABLES_][{{unit_name_max_length +1}}];
 char YComponents[_NB_OF_STATE_VARIABLES_][{{component_name_max_length +1 }}];
@@ -61,12 +66,17 @@ void init()
 {%for state_var in state_vars %}
     Y[{{loop.index0}}] = {{state_var.initial_value}}; // {{state_var.var}} ({{state_var.units}}) (in {{components[loop.index0]}})
 {%- endfor %}
+    Y[{{state_vars | length}}]; // ({{free_variable.var_name}}} (milliseconds)
+
 {%for state_var in state_vars %}
     strcpy(YNames[{{loop.index0}}], "{{state_var.var}}");
 {%- endfor %}
+    strcpy(YNames[{{state_vars | length}}], "{{free_variable.var_name}}");
+
 {%for state_var in state_vars %}
     strcpy(YUnits[{{loop.index0}}], "{{state_var.units}}");
 {%- endfor %}
+    strcpy(YUnits[{{state_vars | length}}], "milliseconds");
 
     //------------------------------------------------------------------------------
     // Constants
@@ -79,7 +89,10 @@ void init()
 {% endif %}{%- endfor %}
 }
 
-void compute(double {{free_variable.var_name}})
+    //---------------------------------------------------------------------------
+    // Computation
+    //---------------------------------------------------------------------------
+void compute()
 {
    // time: {{free_variable.var_name}} (millisecond)
 {% for deriv in y_derivative_equations %}
@@ -96,6 +109,46 @@ void compute(double {{free_variable.var_name}})
 {%- endfor %}
 }
 
+    //------------------------------------------------------------------------------
+    // Integration & Output
+    //------------------------------------------------------------------------------
+    // Rush-Larsen method
+
+
+// get tau/inf or alpha/beta
+void computeTauInf()
+  {% for deriv in derivative_alpha_beta %}{% if deriv.type!='non_linear'%}double alphaOrTau_{{loop.index0}} = {{deriv.r_alpha_or_tau}};
+  double betaOrInf_{{loop.index0}} = {{deriv.r_beta_or_inf}};
+  {% endif %}{%- endfor %}
+  // gating variables: Exponential integration
+  {% for deriv in derivative_alpha_beta %}{%- if deriv.type=='inftau'%}
+  Ynew[{{loop.index0}}] = betaOrInf_{{loop.index0}} + (Y[{{loop.index0}}] - betaOrInf_{{loop.index0}})*exp(-dt/alphaOrTau_{{loop.index0}});
+  {%- elif deriv.type!='non_linear'%}
+  double tau_inv_{{loop.index0}} = alphaOrTau_{{loop.index0}} + betaOrInf_{{loop.index0}};
+  double y_inf_{{loop.index0}} = alphaOrTau_{{loop.index0}} / tau_inv_{{loop.index0}};
+  Ynew[{{loop.index0}}] = y_inf_{{loop.index0}} + (Y[{{loop.index0}}] - y_inf_{{loop.index0}})*exp(-dt*tau_inv_{{loop.index0}});
+  {%- endif %}
+  {%- endfor %}
+}
+
+// Remainder: Forward Euler
+void computeRemainderForaredEuler(){
+{% for deriv in derivative_alpha_beta %}
+  {%- if deriv.type=='non_linear'%}
+  Ynew[{{loop.index0}}] = Y[{{loop.index0}}] + dt * {{deriv.deriv}};{%- endif %}{%- endfor %}
+  Ynew[{{state_vars | length}}] = Y[{{state_vars | length}}] + dt;
+}
+
+compute();
+computeTauInf();
+computeRemainderForaredEuler();
+
+
+Vmem = Ynew[0];
+time = Ynew[{{state_vars | length}}];
+
+
+
 //==============================================================================
 // End of file
 //==============================================================================

chaste_codegen/data/tests/chaste_reference_models/RL_C/aslanidi_Purkinje_model_2009.h

@@ -17,14 +17,18 @@
 // State variables
 //------------------------------------------------------------------------------
 
-#define _NB_OF_STATE_VARIABLES_ {{state_vars | length}}
+#define _NB_OF_STATE_VARIABLES_ {{state_vars | length +1}}
 
 extern double Y[_NB_OF_STATE_VARIABLES_];
-extern double dY[_NB_OF_STATE_VARIABLES_];
+extern double Y[_NB_OF_STATE_VARIABLES_];
+extern double double dY[_NB_OF_STATE_VARIABLES_];
 {%- for state_var in state_vars %}
 // {{loop.index0}}: {{state_var.var}} ({{state_var.units}}) (in {{components[loop.index0]}}) (Initial value: {{state_var.initial_value}})
 {%- endfor %}
 
+extern double Vmem;
+extern double time;
+
 extern char YNames[_NB_OF_STATE_VARIABLES_][{{stat_var_name_max_length +1}}];
 extern char YUnits[_NB_OF_STATE_VARIABLES_][{{unit_name_max_length +1}}];
 extern char YComponents[_NB_OF_STATE_VARIABLES_][{{component_name_max_length +1 }}];
@@ -51,7 +55,9 @@ extern double {{param["comment_name"]}}; // {{param["units"]}} (in {{param["comp
 //------------------------------------------------------------------------------
 
 extern void init();
-extern void compute(double {{free_variable.var_name}});
+extern void compute();
+extern void computeTauInf();
+extern void computeRemainderForaredEuler();
 
 //------------------------------------------------------------------------------
 

chaste_codegen/templates/labview.c

@@ -1 +1 @@
-0.9.3
+0.9.4