added evolution class

Author: adampdp

Worm2D/Evolution.h

@@ -1,52 +1,16 @@
 #include "TSearch.h"
 #include "VectorMatrix.h"
-//#include "Worm2D.h"
+#include "../argUtils.h"
 
 class Evolution
 {
     public:
+    Evolution():supArgs1_ptr(nullptr){}
     virtual void GenPhenMapping(TVector<double> &gen, TVector<double> &phen) = 0;
     virtual double EvaluationFunction(TVector<double> &v, RandomState &rs) = 0;
 
-};
-
-class EvolutionRS18:public Evolution
-{
-    public:
-    void GenPhenMapping(TVector<double> &gen, TVector<double> &phen);
-    double EvaluationFunction(TVector<double> &v, RandomState &rs);
-
-    private:
-
-    double Duration = 50.0;           // Seconds
-    double Transient = 10.0;          // 
-    double StepSize = 0.01;
-    int N_curvs = 23;                 // Number of cuvature points
-
-// Used for Dumping: Frame rate for recording datais set to 50 frames per second
-    double fps = 25.0;
-    int skip = (int) (1/(StepSize*fps));
+    
+    protected:
+    SuppliedArgs* supArgs1_ptr;
 
-// Genotype -> Phenotype Mapping (Ventral cord)
-    double	  BiasRange			         	= 15.0;
-    double    SCRange                 = 15.0;
-    double    CSRange                 = 15.0;
-    double    TauMin                  = 0.5; //
-    double    TauMax                  = 2.0;
-
-    double    ESRange                 = 2.0;
-
-    double    SRmax                   = 200.0;
-    double    NMJmax                  = 1.0;
-
-// (Head)
-    double    HCSRange                = 15.0;
-
-// Fitness
-    double    AvgSpeed = 0.00022;              // Average speed of the worm in meters per seconds
-    double    BBCfit = AvgSpeed*Duration;
-
-// Size of genotype (VC)
-    int VectSize = 30;
-
-};
+};

Worm2D/EvolutionRS18.cpp

@@ -1,4 +1,4 @@
-#include "Evolution.h"
+#include "EvolutionRS18.h"
 #include <math.h>
 #include "WormRS18.h"
 
@@ -81,6 +81,8 @@ double EvolutionRS18::EvaluationFunction(TVector<double> &v, RandomState &rs)
 {
     double fitness;
     ofstream fitfile;
+  
+
     if (supArgs1.speedoutput)
     {
 
@@ -116,17 +118,19 @@ if (supArgs1.output){
 
 if (supArgs1.output){
     w.DumpParams(paramsfile);
-    writeParsToJson(w);
+    //writeParsToJson(w);
 }
 
 
     w.InitializeState(rs);
 
+
+
     // Transient
     for (double t = 0.0; t <= Transient; t += StepSize)
     {
         w.Step(StepSize, 1);
-        if (supArgs1.output)
+       
 
 if (supArgs1.output)
     {

Worm2D/EvolutionRS18.h

@@ -0,0 +1,51 @@
+#include "TSearch.h"
+#include "VectorMatrix.h"
+#include "Evolution.h"
+
+class EvolutionRS18:public Evolution
+{
+    public:
+    EvolutionRS18(){
+
+    supArgs1_ptr = new SuppliedArgs2018();
+
+    }
+    void GenPhenMapping(TVector<double> &gen, TVector<double> &phen);
+    double EvaluationFunction(TVector<double> &v, RandomState &rs);
+
+    SuppliedArgs2018& supArgs1 = static_cast<SuppliedArgs2018&>(*supArgs1_ptr);
+    
+    private:
+
+    double Duration = 50.0;           // Seconds
+    double Transient = 10.0;          // 
+    double StepSize = 0.01;
+    int N_curvs = 23;                 // Number of cuvature points
+
+// Used for Dumping: Frame rate for recording datais set to 50 frames per second
+    double fps = 25.0;
+    int skip = (int) (1/(StepSize*fps));
+
+// Genotype -> Phenotype Mapping (Ventral cord)
+    double	  BiasRange			         	= 15.0;
+    double    SCRange                 = 15.0;
+    double    CSRange                 = 15.0;
+    double    TauMin                  = 0.5; //
+    double    TauMax                  = 2.0;
+
+    double    ESRange                 = 2.0;
+
+    double    SRmax                   = 200.0;
+    double    NMJmax                  = 1.0;
+
+// (Head)
+    double    HCSRange                = 15.0;
+
+// Fitness
+    double    AvgSpeed = 0.00022;              // Average speed of the worm in meters per seconds
+    double    BBCfit = AvgSpeed*Duration;
+
+// Size of genotype (VC)
+    int VectSize = 30;
+
+};

Worm2D/Makefile

@@ -9,9 +9,9 @@ TSearch.o: TSearch.cpp TSearch.h
 argUtils.o: ../argUtils.cpp ../argUtils.h
 	g++ -c -O3 -flto ../argUtils.cpp
 Worm2D.o: Worm2D.cpp Worm2D.h
-	g++ -c -O3 -flto Worm2D.cpp
+	g++ -c -O3 -std=c++11 -flto Worm2D.cpp
 WormRS18.o: WormRS18.cpp WormRS18.h
-	g++ -c -O3 -flto WormRS18.cpp
+	g++ -c -O3 -std=c++11 -flto WormRS18.cpp
 WormBody.o: WormBody.cpp WormBody.h
 	g++ -c -O3 -flto WormBody.cpp
 NervousSystem.o: NervousSystem.cpp NervousSystem.h VectorMatrix.h random.h

Worm2D/Worm2D.cpp

@@ -1,5 +1,5 @@
 #include "Worm2D.h"
-
+#include <iomanip>
 
 WormIzq::WormIzq(wormIzqParams par1_):par1(par1_),n_ptr(new NervousSystem)
 {
@@ -14,7 +14,6 @@ WormIzq::WormIzq(wormIzqParams par1_):par1(par1_),n_ptr(new NervousSystem)
 void WormIzq::setUp()
 {
     m.SetMuscleParams(par1.N_muscles, par1.T_muscle);
-
 }
 
 int WormIzq::nn(int neuronNumber, int unitNumber)
@@ -126,6 +125,18 @@ void WormIzq::DumpBodyState(ofstream &ofs, int skips)
     }
 }
 
+void WormIzq::writeJsonFile()
+{
+
+    json j;
+    addParsToJson(j);
+    //ofstream json_out(supArgs1.rename_file("worm_data.json"));
+    ofstream json_out("worm_data.json");
+    json_out << std::setw(4) << j << std::endl;
+    json_out.close();
+
+}
+
 void WormIzq::addParsToJson(json & j)
 {  
      // addwormIzqParams

Worm2D/Worm2D.h

@@ -3,11 +3,11 @@
 #include "Muscles.h"
 #include "WormBody.h"
 #include "NervousSystem.h"
-#include <nlohmann/json.hpp>
+//#include <nlohmann/json.hpp>
 #include "jsonUtils.h"
 
 
-using json = nlohmann::json;
+//using json = nlohmann::json;
 
 #define PI 3.14159265
 
@@ -48,7 +48,7 @@ class WormIzq: public Worm2D
     virtual void InitializeState(RandomState &rs) = 0;
     virtual void Step(double StepSize, double output) = 0;
     void addParsToJson(json & j);
-    
+    void writeJsonFile();
 
     double CoMx();
     double CoMy();

Worm2D/WormRS18.cpp

@@ -12,7 +12,8 @@
 #define HEADSR
 #define VNCSR
 
-//extern SuppliedArgs2018 supArgs1;
+extern SuppliedArgs2018 supArgs1;
+
 
 RS18Macros Worm18::setMacros()
 {
@@ -30,7 +31,7 @@ return {headsr,vncsr};
 // The constructor
 Worm18::Worm18(TVector<double> &v,double output):WormIzq({6,24,0.1,6}),rS18Macros(setMacros())
 {
-    
+    supArgs1.writeMessage();
     // Nervous system // Ventral cord
     n_ptr->SetCircuitSize(par1.N_units*par1.N_neuronsperunit, 4, 4);
 
@@ -309,7 +310,7 @@ void Worm18::addExtraParsToJson(json & j)
     string nsHead = "Head Nervous system";
     appendAllNSJson(j[nsHead], h);
     vector<string> cell_names = {"SMDD", "RMDD", "SMDV", "RMDV"};
-    appendCellNamesToJson(j[nsHead], cell_names, par1.N_units);
+    appendCellNamesToJson(j[nsHead], cell_names, 1);
     Params<double> par = sr.getStretchReceptorParams();
     appendToJson<double>(j["Stretch receptor"], par);
 }