Merge pull request #14 from openworm/test_parameters_pg

Working omv tests

.github/workflows/ci-make.yml

@@ -30,24 +30,41 @@ jobs:
       run: brew install nlohmann-json
       if: matrix.runs-on == 'macos-latest'
 
+    - name: Run C++ tests 
+      run: |
+          make tests
+          ./tests
+
     - name: Test makefile
       run: make
 
     - name: Test directly running main program
       run: |
-        ./main -p 4
+        ./main -p 6  # Note: small population of 6 for quick runtime
         ls -alth
 
     - name: Test Python command line script
       run: |
         pip install numpy matplotlib
-        python run_main.py -R 1234 -p 6 --doEvol --folderName exampleRun2
+        python run_main.py -R 1233 -p 6 --doEvol --folderName exampleRun2  # Note: small population of 6 for quick runtime
 
-    - name: Test using OMV
+    - name: Test using OMV 1
       run: |
         pip install OSBModelValidation
         omv all -V 
         git diff exampleRun/phenotype.dat 
+
+    - name: Test using OMV 2
+      run: |
+        # Running OMV multiple times to test whether run results are nondeterministic
+        omv all -V 
+        git diff exampleRun/phenotype.dat 
+
+    - name: Test using OMV 3
+      run: |
+        # Running OMV multiple times to test whether run results are nondeterministic
+        omv all -V 
+        git diff exampleRun/phenotype.dat 
       
     - name: list generated files
       run: |

.gitignore

@@ -13,4 +13,4 @@
 /nv2.dat
 /phenotype2.dat
 /w_verb.dat
-/exampleRun/
+/tests

.test.example.omt

@@ -15,4 +15,4 @@ experiments:
         spike detection: 
           method: threshold
           threshold: 2
-        tolerance: 0.4944500504540868
+        tolerance: 0

Makefile

@@ -18,5 +18,9 @@ Muscles.o: Muscles.cpp Muscles.h VectorMatrix.h random.h
 	g++ -c -O3 -flto Muscles.cpp
 main.o: main.cpp Worm.h WormBody.h StretchReceptor.h Muscles.h TSearch.h
 	g++ -c -O3 -flto main.cpp
+tests.o: tests.cpp
+	g++ -c -O3 -flto tests.cpp
+tests: tests.o
+	g++ -pthread -o tests tests.o 
 clean:
-	rm -f *.o main
+	rm -f *.o main tests

Worm.cpp

@@ -15,6 +15,14 @@ int nn(int neuronNumber, int unitNumber)
 // The constructor
 Worm::Worm(TVector<double> &v,double output)
 {
+
+  // PG: Setting these to zero as they were not initialised before use!
+  // Note: the usage of these needs to be further investigated!
+  AVA_act = 0;
+  AVA_inact = 0;
+  AVB_act = 0;
+  AVB_inact = 0;
+
   // Muscles
   m.SetMuscleParams(N_muscles, T_muscle);
 

Worm2D.cpp

@@ -563,12 +563,12 @@ Params<double> getBodyParams(WormBody& b)
 Params<double> par;
 
 par.names = {"Medium", "L_worm", "R_min", "C_agar_par_total", 
-"C_agar_perp_total", "C_water_par_total", "C_water_perp_total", "kappa_L_fact", "kappa_D_fact", 
-"kappa_M0_fact", "beta_L_fact", "beta_D_fact", "beta_M0_fact", "delta_M"};
+"C_agar_perp_total", "C_water_par_total", "C_water_perp_total", "kappa_L", "kappa_D", 
+"kappa_M0", "beta_L", "beta_D", "beta_M0", "delta_M"};
 
 par.vals = {Medium, L_worm, R_min, C_agar_par_total, C_agar_perp_total, 
-C_water_par_total, C_water_perp_total, kappa_L_fact, kappa_D_fact, kappa_M0_fact, beta_L_fact, 
-beta_D_fact, beta_M0_fact, delta_M};
+C_water_par_total, C_water_perp_total, kappa_L, kappa_D, kappa_M0, beta_L, 
+beta_D, beta_M0, delta_M};
 
 par.messages_inds.resize(par.vals.size());
 

WormBody.h

@@ -40,19 +40,15 @@ const double C_agar_par_total   = 3.2e-3;                      // Total tangenti
 const double C_agar_perp_total  = 128e-3;                      // Total rod normal drag coefficient in agar in kg/s
 const double C_water_par_total  = 3.3e-6;                      // Total rod tangential drag coefficient for water in kg/s
 const double C_water_perp_total = 5.2e-6;                      // Total rod normal drag coefficient for water in kg/s
-const double kappa_L_fact       =  (10.0e-3/24);
-const double kappa_L            = kappa_L_fact*N_segments;
-const double kappa_D_fact       = 350;                          // Lateral spring constant in kg/s
-const double kappa_D            = kappa_D_fact*kappa_L;         // Diagonal spring constant in kg/s
-const double kappa_M0_fact      = 20;
-const double kappa_M0           = kappa_M0_fact*kappa_L;        // Baseline active muscle spring constant in kg/s
-const double beta_L_fact        = 0.25;
-const double beta_L             = beta_L_fact*kappa_L;          // Lateral passive damping constant in s
-const double beta_D_fact        = 0.01;
-const double beta_D             = beta_D_fact*kappa_D;           // Diagonal passive damping constant in s
-const double beta_M0_fact       = 100;
-const double beta_M0            = beta_M0_fact*beta_L;           // Baseline active damping constant in s
-const double delta_M            = 0.65;                          // Rest muscle length scaling constant
+
+const double kappa_L            = (10.0e-3*N_segments)/24;     // Lateral spring constant in kg/s
+const double kappa_D            = 350*kappa_L;                 // Diagonal spring constant in kg/s
+const double kappa_M0           = 20*kappa_L;                  // Baseline active muscle spring constant in kg/s
+const double beta_L             = 0.025*kappa_L;               // Lateral passive damping constant in s
+const double beta_D             = 0.01*kappa_D;                // Diagonal passive damping constant in s
+const double beta_M0            = 100*beta_L;                  // Baseline active damping constant in s
+const double delta_M            = 0.65;                        // Rest muscle length scaling constant 
+
 
 
 // Derived constants