Added method to compute virial automatically for variables without PBC

src/Colvar.cpp

@@ -87,3 +87,13 @@ void Colvar::apply(){
      if( getPntrToComponent(0)->applyForce( forces ) ) modifyForceOnEnergy()+=forces[0];
   }
 }
+
+void Colvar::setBoxDerivativesNoPbc(Value* v){
+  Tensor virial;
+  unsigned nat=getNumberOfAtoms();
+  for(unsigned i=0;i<nat;i++) virial-=Tensor(getPosition(i),
+    Vector(v->getDerivative(3*i+0),
+           v->getDerivative(3*i+1),
+           v->getDerivative(3*i+2)));
+  setBoxDerivatives(v,virial);
+}

src/Colvar.h

@@ -58,6 +58,12 @@ protected:
   const Tensor & getBoxDerivatives()const;
   const double & getForce()const;
   void apply();
+/// Set box derivatives automatically.
+/// It should be called after the setAtomsDerivatives has been used for all
+/// single atoms.
+/// \warning It only works for collective variable NOT using PBCs!
+  void           setBoxDerivativesNoPbc();
+  void           setBoxDerivativesNoPbc(Value*);
 public:
   bool checkIsEnergy(){return isEnergy;};
   Colvar(const ActionOptions&);
@@ -97,6 +103,12 @@ void Colvar::setBoxDerivatives(const Tensor&d){
   setBoxDerivatives(getPntrToValue(),d);
 }
 
+inline
+void Colvar::setBoxDerivativesNoPbc(){
+  setBoxDerivativesNoPbc(getPntrToValue());
+}
+
+
 }
 
 #endif

src/ColvarDipole.cpp

@@ -86,7 +86,6 @@ PLUMED_COLVAR_INIT(ao)
 void ColvarDipole::calculate()
 {
  double dipole=0.;
- Tensor virial;
  vector<Vector> deriv(getNumberOfAtoms());
  Vector dipje;
  vector<double> charges(getNumberOfAtoms());
@@ -111,13 +110,12 @@ void ColvarDipole::calculate()
  for(unsigned int i=0;i<ga_lista.size();i++) {
    double dfunc=charges[i]/dipole;
    deriv[i] = deriv[i] + (dfunc)*dipje;
-   virial=virial-Tensor(getPosition(i),deriv[i]);
  }
 
 // for(unsigned i=0;i<getPositions().size();++i) setAtomsDerivatives(i,deriv[i]);
  for(unsigned i=0;i<getNumberOfAtoms();++i) setAtomsDerivatives(i,deriv[i]);
  setValue           (dipole);
- setBoxDerivatives  (virial);
+ setBoxDerivativesNoPbc();
 }
 
 }

src/ColvarGyration.cpp

@@ -144,7 +144,6 @@ use_masses(true)
 void ColvarGyration::calculate(){
 
   std::vector<Vector> derivatives( getNumberOfAtoms() );
-  Tensor virial; virial.zero();
   double totmass = 0.; 
   double d=0., rgyr=0.;
   Vector pos0, com, diff;
@@ -212,7 +211,6 @@ void ColvarGyration::calculate(){
       for(unsigned i=0;i<getNumberOfAtoms();i++){
         derivatives[i] /= rgyr*totmass;
         setAtomsDerivatives(i,derivatives[i]);
-        virial=virial+(-1.0*Tensor(getPosition(i),derivatives[i]));
       }
       break;
     }
@@ -222,7 +220,6 @@ void ColvarGyration::calculate(){
       for(unsigned i=0;i<getNumberOfAtoms();i++) {
         derivatives[i] *= 4.;  
         setAtomsDerivatives(i,derivatives[i]);
-        virial=virial+(-1.0*Tensor(getPosition(i),derivatives[i]));
       }
       break;
     }
@@ -345,13 +342,12 @@ void ColvarGyration::calculate(){
             derivatives[i][j]=(prefactor[0]*transf[j][0]*tX[0]+prefactor[1]*transf[j][1]*tX[1]+prefactor[2]*transf[j][2]*tX[2]);
         }
         setAtomsDerivatives(i,derivatives[i]);
-        virial=virial+(-1.0*Tensor(getPosition(i),derivatives[i]));
       }
       break;
     }
   }
   setValue(rgyr);
-  setBoxDerivatives(virial);
+  setBoxDerivativesNoPbc();
 }
 
 }

src/ColvarPathMSDBase.cpp

@@ -153,15 +153,13 @@ void ColvarPathMSDBase::calculate(){
        for(unsigned i=0;i< derivs_s.size();i++){ derivs_s[i]+=tmp*(*it).distder[i] ;} 
        if(j==0){for(unsigned i=0;i< derivs_z.size();i++){ derivs_z[i]+=(*it).distder[i]*expval/partition;}} 
     }
-    Tensor virial,virialz;
     for(unsigned i=0;i< derivs_s.size();i++){
           setAtomsDerivatives (val_s_path[j],i,derivs_s[i]); 
-          virial=virial+(-1.0*Tensor(getPosition(i),derivs_s[i]));
-          if(j==0){setAtomsDerivatives (val_z_path,i,derivs_z[i]);virialz=virialz+(-1.0*Tensor(getPosition(i),derivs_z[i]));} 
+          if(j==0){setAtomsDerivatives (val_z_path,i,derivs_z[i]);} 
     }
-    setBoxDerivatives(val_s_path[j],virial);
-    if(j==0)setBoxDerivatives(val_z_path,virialz);
   }
+  for(unsigned i=0;i<val_s_path.size();++i) setBoxDerivativesNoPbc(val_s_path[i]);
+  setBoxDerivativesNoPbc(val_z_path);
   //
   //  here set next round neighbors
   //

src/ColvarRMSD.cpp

@@ -158,8 +158,7 @@ void ColvarRMSD::calculate(){
   setValue(r);
   for(unsigned i=0;i<derivs.size();i++) setAtomsDerivatives(i,derivs[i]);
   Tensor virial;
-  for(unsigned i=0;i<derivs.size();i++) virial=virial+(-1.0*Tensor(getPosition(i),derivs[i]));
-  setBoxDerivatives(virial);
+  setBoxDerivativesNoPbc();
 }
 
 }