Colvar: try to to fix travis

Matrix: removed warnings

src/core/Colvar.cpp

@@ -68,29 +68,28 @@ void Colvar::apply(){
 
   if(!isEnergy){
     for(int i=rank;i<getNumberOfComponents();i+=stride){
-      if(getPntrToComponent(i)->applyForce( forces )){
-       for(unsigned j=0;j<nat;++j){
+      if(getPntrToComponent(i)->applyForce(forces)){
+        for(unsigned j=0;j<nat;++j){
           f[j][0]+=forces[3*j+0];
           f[j][1]+=forces[3*j+1];
           f[j][2]+=forces[3*j+2];
-       }
-       v(0,0)+=forces[3*nat+0];
-       v(0,1)+=forces[3*nat+1];
-       v(0,2)+=forces[3*nat+2];
-       v(1,0)+=forces[3*nat+3];
-       v(1,1)+=forces[3*nat+4];
-       v(1,2)+=forces[3*nat+5];
-       v(2,0)+=forces[3*nat+6];
-       v(2,1)+=forces[3*nat+7];
-       v(2,2)+=forces[3*nat+8];
-     }
-   }
-   comm.Sum(&f[0][0],3*nat);
-   comm.Sum(&v[0][0],9);
-   
+        }
+        v(0,0)+=forces[3*nat+0];
+        v(0,1)+=forces[3*nat+1];
+        v(0,2)+=forces[3*nat+2];
+        v(1,0)+=forces[3*nat+3];
+        v(1,1)+=forces[3*nat+4];
+        v(1,2)+=forces[3*nat+5];
+        v(2,0)+=forces[3*nat+6];
+        v(2,1)+=forces[3*nat+7];
+        v(2,2)+=forces[3*nat+8];
+      }
+    }
+    comm.Sum(&f[0][0],3*f.size());
+    comm.Sum(&v[0][0],9);
   } else if( isEnergy ){
-     forces.resize(1);
-     if( getPntrToComponent(0)->applyForce( forces ) ) modifyForceOnEnergy()+=forces[0];
+    forces.resize(1);
+    if(getPntrToComponent(0)->applyForce(forces)) modifyForceOnEnergy()+=forces[0];
   }
 }
 

src/tools/Matrix.h

@@ -241,8 +241,8 @@ template <typename T> int diagMat( const Matrix<T>& A, std::vector<double>& eige
    // of each of them is positive
    // We can do it because the phase is arbitrary, and helps making
    // the result reproducible
-   for(unsigned i=0;i<n;++i) {
-     unsigned j;
+   for(int i=0;i<n;++i) {
+     int j;
      for(j=0;j<n;j++) if(eigenvecs(i,j)*eigenvecs(i,j)>1e-14) break;
      if(j<n) if(eigenvecs(i,j)<0.0) for(unsigned j=0;j<n;j++) eigenvecs(i,j)*=-1;
    }
@@ -277,16 +277,16 @@ template <typename T> int pseudoInvert( const Matrix<T>& A, Matrix<double>& pseu
   if(info!=0) return info; 
 
   // Compute the tolerance on the singular values ( machine epsilon * number of singular values * maximum singular value )
-  double tol; tol=S[0]; for(unsigned i=1;i<nsv;++i){ if( S[i]>tol ){ tol=S[i]; } } tol*=nsv*epsilon;
+  double tol; tol=S[0]; for(int i=1;i<nsv;++i){ if( S[i]>tol ){ tol=S[i]; } } tol*=nsv*epsilon;
 
   // Get the inverses of the singlular values
   Matrix<double> Si( ncols, nrows ); Si=0.0;
-  for(unsigned i=0;i<nsv;++i){ if( S[i]>tol ){ Si(i,i)=1./S[i]; }else{ Si(i,i)=0.0; } }
+  for(int i=0;i<nsv;++i){ if( S[i]>tol ){ Si(i,i)=1./S[i]; }else{ Si(i,i)=0.0; } }
 
   // Now extract matrices for pseudoinverse
   Matrix<double> V( ncols, ncols ), UT( nrows, nrows ), tmp( ncols, nrows ); 
-  k=0; for(unsigned i=0;i<nrows;++i){ for(unsigned j=0;j<nrows;++j){ UT(i,j)=U[k++]; } }
-  k=0; for(unsigned i=0;i<ncols;++i){ for(unsigned j=0;j<ncols;++j){ V(i,j)=VT[k++]; } }
+  k=0; for(int i=0;i<nrows;++i){ for(int j=0;j<nrows;++j){ UT(i,j)=U[k++]; } }
+  k=0; for(int i=0;i<ncols;++i){ for(int j=0;j<ncols;++j){ V(i,j)=VT[k++]; } }
 
   // And do matrix algebra to construct the pseudoinverse
   if( pseudoinverse.rw!=ncols || pseudoinverse.cl!=nrows ) pseudoinverse.resize( ncols, nrows );