removed getFullStateSize from mechanism

+xolotl/version.m

@@ -1,2 +1,2 @@
 function version()
-disp('v20.12.11');
+disp('v20.12.12');

c++/compartment.hpp

@@ -453,7 +453,7 @@ void compartment::addMechanism(mechanism *mech_) {
     n_mech++;
 
     // also store the mechanism's full state size
-    mechanism_sizes.push_back(mech_->getFullStateSize());
+    mechanism_sizes.push_back(mech_->fullStateSize);
 }
 
 /*
@@ -640,7 +640,7 @@ what their data dimension is, and adding up all those numbers.
 int compartment::getFullMechanismSize(void) {
     int full_size = 0;
     for (int i=0; i<n_mech; i++) {
-        full_size += mech[i]->getFullStateSize();
+        full_size += mech[i]->fullStateSize;
     }
     return full_size;
 }

c++/mechanism.hpp

@@ -52,6 +52,8 @@ class mechanism {
 
     int verbosity = -1;
 
+    int fullStateSize = 0;
+
     mechanism()
     {
         // null pointers to all
@@ -66,7 +68,6 @@ class mechanism {
     virtual void integrate(void);
     virtual void integrateMS(int, double, double);
 
-    virtual int getFullStateSize(void);
     virtual int getFullState(double*, int);
     virtual double getState(int);
     virtual string getClass(void) = 0;
@@ -172,14 +173,6 @@ double mechanism::getState(int i) {
 }
 
 
-/* This virtual method does nothing, but should return the full state
-size of your mechanism
-*/
-
-int mechanism::getFullStateSize() {
-    return 0;
-}
-
 
 /* This virtual method does nothing, but can return as many dynamic
 variables as you want 

c++/mechanisms/ChannelProbe.hpp

@@ -21,11 +21,11 @@ class ChannelProbe: public mechanism {
     // specify parameters + initial conditions for
     ChannelProbe(double dummy_) {
         dummy = dummy_;
+        fullStateSize = 2;
     }
 
     void connectConductance(conductance *);
 
-    int getFullStateSize(void);
     int getFullState(double * cont_state, int idx);
     string getClass(void);
 
@@ -40,9 +40,6 @@ string ChannelProbe::getClass() {
 
 
 
-int ChannelProbe::getFullStateSize(){return 2; }
-
-
 int ChannelProbe::getFullState(double *cont_state, int idx) {
     // read out m and h
     cont_state[idx] = channel->m;

c++/mechanisms/gorur-shandilya/CalciumSensor.hpp

@@ -25,12 +25,12 @@ class CalciumSensor: public mechanism {
 
     // specify parameters + initial conditions for
     // mechanism that controls a conductance
-    CalciumSensor(double tau_, double Ca_average_)
-    {
+    CalciumSensor(double tau_, double Ca_average_) {
         tau = tau_;
         controlling_class = "unset";
         Ca_average = Ca_average_;
 
+        fullStateSize = 1;
     }
 
 
@@ -40,7 +40,6 @@ class CalciumSensor: public mechanism {
     void connectCompartment(compartment*);
 
 
-    int getFullStateSize(void);
     int getFullState(double * cont_state, int idx);
     string getClass(void);
 
@@ -51,10 +50,6 @@ string CalciumSensor::getClass() {
 }
 
 
-int CalciumSensor::getFullStateSize() {
-    return 1;
-}
-
 
 int CalciumSensor::getFullState(double *cont_state, int idx) {
     // return internal variable

c++/mechanisms/liu/DCSensor.hpp

@@ -43,8 +43,9 @@ class DCSensor: public mechanism {
         X = X_;
         m = m_;
 
+        fullStateSize = 1;
 
-        // these defaults make it a "F" type sensor
+        // these defaults make it a "DC" type sensor
         if (isnan(ZM)) {ZM = 3;}
         if (isnan(tau_m)) {tau_m = 500; } // ms
         if (isnan(G)) {G = 1;}
@@ -62,8 +63,6 @@ class DCSensor: public mechanism {
 
     double boltzmann(double);
 
-
-    int getFullStateSize(void);
     int getFullState(double * cont_state, int idx);
     double getState(int);
     string getClass(void);
@@ -78,8 +77,6 @@ string DCSensor::getClass() {
 double DCSensor::getState(int idx){return X;}
 
 
-int DCSensor::getFullStateSize(){return 1; }
-
 
 int DCSensor::getFullState(double *cont_state, int idx) {
     cont_state[idx] = X;

c++/mechanisms/liu/FastSensor.hpp

@@ -48,6 +48,8 @@ class FastSensor: public mechanism {
         X = X_;
 
 
+        fullStateSize = 1;
+
         // these defaults make it a "F" type sensor
         if (isnan(ZM)) {ZM = 14.2;}
         if (isnan(ZH)) {ZH = 9.8;}
@@ -84,8 +86,6 @@ string FastSensor::getClass() {
 double FastSensor::getState(int idx){return X;}
 
 
-int FastSensor::getFullStateSize(){return 1; }
-
 
 int FastSensor::getFullState(double *cont_state, int idx) {
     cont_state[idx] = X;

c++/mechanisms/liu/LiuController.hpp

@@ -47,7 +47,7 @@ class LiuController: public mechanism {
         // defaults
         if (isnan(tau)) {tau = 5000; } // ms
 
-
+        fullStateSize = 1;
 
     }
 
@@ -61,7 +61,6 @@ class LiuController: public mechanism {
     double boltzmann(double);
 
 
-    int getFullStateSize(void);
     int getFullState(double * cont_state, int idx);
     string getClass(void);
 
@@ -121,8 +120,6 @@ string LiuController::getClass() {
 
 
 
-int LiuController::getFullStateSize(){return 1; }
-
 
 int LiuController::getFullState(double *cont_state, int idx) {
     cont_state[idx] = channel->gbar;

c++/mechanisms/liu/SlowSensor.hpp

@@ -46,6 +46,8 @@ class SlowSensor: public mechanism {
         G = G_;
         X = X_;
 
+        fullStateSize = 1;
+
         // these defaults make it a "S" type sensor
         if (isnan(ZM)) {ZM = 7.2;}
         if (isnan(ZH)) {ZH = 2.8;}
@@ -67,7 +69,6 @@ class SlowSensor: public mechanism {
     double boltzmann(double);
 
 
-    int getFullStateSize(void);
     int getFullState(double * cont_state, int idx);
     double getState(int);
     string getClass(void);
@@ -82,9 +83,6 @@ string SlowSensor::getClass() {
 double SlowSensor::getState(int idx){return X;}
 
 
-int SlowSensor::getFullStateSize(){return 1; }
-
-
 int SlowSensor::getFullState(double *cont_state, int idx) {
     cont_state[idx] = X;
     idx++;

c++/mechanisms/oleary/IntegralController.hpp

@@ -42,6 +42,8 @@ class IntegralController: public mechanism {
         m = m_;
 
 
+        fullStateSize = 2;
+
         // if (tau_m<=0) {mexErrMsgTxt("[IntegralController] tau_m must be > 0. Perhaps you meant to set it to Inf?\n");}
         if (tau_g<=0) {mexErrMsgTxt("[IntegralController] tau_g must be > 0. Perhaps you meant to set it to Inf?\n");}
     }
@@ -55,7 +57,6 @@ class IntegralController: public mechanism {
     void connectConductance(conductance*);
     void connectSynapse(synapse*);
 
-    int getFullStateSize(void);
     int getFullState(double * cont_state, int idx);
     double getState(int);
     string getClass(void);
@@ -116,8 +117,6 @@ double IntegralController::getState(int idx) {
 }
 
 
-int IntegralController::getFullStateSize(){return 2; }
-
 
 int IntegralController::getFullState(double *cont_state, int idx) {
     // give it the current mRNA level

c++/mechanisms/soto-trevino/ProportionalController.hpp

@@ -45,18 +45,17 @@ class ProportionalController: public mechanism {
         m = m_;
         tau_m = tau_m_;
         if (isnan(tau_m)) {tau_m = 10e3;};
+
+        fullStateSize = 1;
     }
 
 
     void integrate(void);
 
-    void checkSolvers(int);
-
     void connect(conductance *);
     void connect(synapse*);
     void connect(compartment*);
 
-    int getFullStateSize(void);
     int getFullState(double * cont_state, int idx);
     double getState(int);
     string getClass(void);
@@ -76,8 +75,6 @@ double ProportionalController::getState(int idx) {
 }
 
 
-int ProportionalController::getFullStateSize(){return 1; }
-
 
 int ProportionalController::getFullState(double *cont_state, int idx) {
 
@@ -115,9 +112,6 @@ void ProportionalController::connect(conductance * channel_) {
 
 }
 
-void ProportionalController::connect(compartment* comp_) {
-    mexErrMsgTxt("[ProportionalController] This mechanism cannot connect to a compartment object");
-}
 
 void ProportionalController::connect(synapse* syn_) {
 
@@ -211,14 +205,6 @@ void ProportionalController::integrate(void) {
 
 
 
-void ProportionalController::checkSolvers(int k) {
-    if (k == 0){
-        return;
-    } else {
-        mexErrMsgTxt("[ProportionalController] unsupported solver order\n");
-    }
-}
-
 
 
 

c++/mexTemplate.cpp

@@ -209,7 +209,7 @@ void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
         int idx = 0;
         for(int j = 0; j < n_comp; j++) {
             for (int k = 0; k < xolotl_network.comp[j]->n_mech; k++) {
-                int mech_size = (xolotl_network.comp[j]->getMechanismPointer(k))->getFullStateSize();
+                int mech_size = (xolotl_network.comp[j]->getMechanismPointer(k))->fullStateSize;
                 mech_sizes_out[idx] = mech_size;
                 idx++;
             }

docs/how-to/make-own-models.md

@@ -109,8 +109,6 @@ public:
 
         // defaults
         if (isnan(gbar)) { gbar = 0; }
-
-
         if (isnan (E)) { E = 30; }
 
         // specify exponents of m and h
@@ -190,16 +188,12 @@ public:
     double B = 1;
 
     // constructor
-    NewMech(double A_, B_)
-    {
+    NewMech(double A_, B_) {
         A = A_;
         B = B_;
         controlling_class = "unset";
     }
 
-    // declare methods
-    void checkSolvers(int);
-
     void integrate(void);
     void integrateMS(int, double, double);
 
@@ -214,19 +208,12 @@ public:
 
     // these methods allow reading out of the mechanism
     // state
-    int getFullStateSize(void);
     int getFullState(double * mech_state, int idx);
     double getState(int);
 
 };
 
 
-double NewMech::getState(int idx){return std::numeric_limits<double>::quiet_NaN();}
-
-// specify the dimensions of your mechanism
-// this size must match the getState method
-int NewMech::getFullStateSize(){return 0; }
-
 // this does nothing since our state size is 0
 // otherwise we should increment idx, and
 // fill in values in the mech_state array
@@ -236,19 +223,12 @@ int NewMech::getFullState(double *mech_state, int idx) {
 
 // connection methods
 // we allow the mechanism to connect to a compartment
+// all other connection attempts will lead to a runtime error
 void NewMech::connect(compartment* comp_) {
     comp = comp_;
     comp->addMechanism(this);
 }
 
-// disallow other connections
-void NewMech::connect(conductance* cond_) {
-    mexErrMsgTxt("[NewMech] This mechanism cannot connect to a conductance object");
-}
-
-void NewMech::connect(synapse* syn_) {
-    mexErrMsgTxt("[NewMech] This mechanism cannot connect to a synapse object");
-}
 
 
 // specify how we integrate it with the default
@@ -263,24 +243,6 @@ double NewMech::NewMechCustomMethod(double X_) {
     // insert your code here
 }
 
-// Runge-Kutta 4 integrator
-// you don't have to code this...see checkSolvers
-void NewMech::integrateMS(int k, double V, double Ca_) {
-    if (k == 4){return;}
-   // insert RK4 code here
-}
-
-// throw an error to disallow solver_orders
-// 0 must always work, though
-void NewMech::checkSolvers(int k) {
-    if (k == 0){
-        return;
-    } else if (k == 4){
-        return;
-    } else {
-        mexErrMsgTxt("[CalciumMech] unsupported solver order\n");
-    }
-}
 
 #endif