Numeric metropolis energy

.travis.yml

@@ -16,4 +16,4 @@ script:
   - make install
   - cd test
   - cp $HOME/ProtoMol/bin/ProtoMol .
-  - python test.py --serial --parallel --errorfailure
+  - go run test.go --verbose --parallel --errorfailure

protomol/integrator/hessian/BlockHessian.cpp

@@ -1273,8 +1273,8 @@ void BlockHessian::evaluateNumericalResidues(const Vector3DBlock *myPositions,
     unsigned int block_start = 0;
 
     const unsigned int size = myPositions->size();
-    
-    const Real epsilon = 1e-12;
+
+    const Real epsilon = 1e-6;
 
     const Real inv_epsilon = 1.0 / epsilon;
 

protomol/integrator/hessian/BlockHessianDiagonalize.cpp

@@ -231,7 +231,7 @@ namespace ProtoMol {
     Vector3DBlock tempForce = *(intg->getForces());
 
     //define epsilon
-    Real epsilon = 1e-9;
+    Real epsilon = 1e-6;
 
     //loop over each eigenvector purtubation
     for(int eg=0; eg<residues_total_eigs; eg++ ){

protomol/integrator/hessian/Hessian.cpp

@@ -351,7 +351,6 @@ void Hessian::findForces(ForceGroup *overloadedForces) {
             }
           }
         } else if (equalStartNocase("LennardJones Coulomb", ListForces[i]->getId())) {
-            std::cout << "LJ Test" << std::endl;
             myLennardJones = true; myCoulomb = true;
             vector<Parameter> Fparam;
             //lSwitch = cSwitch = 1;