Ran astyle

plumed · Sep 8, 2024 · 14c8511 · 14c8511 · PlumedBot · Sep 8, 2024
1 parent 85bd330
commit 14c8511
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Showing 10 changed files with 175 additions and 175 deletions.
diff --git a/src/cltools/ShowGraph.cpp b/src/cltools/ShowGraph.cpp
@@ -194,7 +194,7 @@ int ShowGraph::main(FILE* in, FILE*out,Communicator& pc) {
         ActionWithVector* avv=dynamic_cast<ActionWithVector*>(a);
         ActionWithArguments* aaa=dynamic_cast<ActionWithArguments*>(a);
         if( avv ) {
-            for(const auto & v : aaa->getArguments() ) v->addForce();
+          for(const auto & v : aaa->getArguments() ) v->addForce();
         } else a->apply();
         bool hasforce=false;
         for(int i=0; i<av->getNumberOfComponents(); ++i) {

diff --git a/src/core/ActionWithVector.cpp b/src/core/ActionWithVector.cpp
@@ -86,7 +86,7 @@ ActionWithVector::ActionWithVector(const ActionOptions&ao):
           if( av->getPntrToArgument(i)!=mask[j] ) error("the masks in subsequent actions do not match");
           j++;
         }
-      } 
+      }
       if( getNumberOfArguments()>0 && getPntrToArgument(0)->hasDerivatives() ) error("input for mask should be vector or matrix");
       else if( mask[0]->getRank()==2 ) {
         if( mask.size()>1 ) error("MASK should only have one argument");
@@ -438,38 +438,38 @@ void ActionWithVector::prepare() {
 int ActionWithVector::checkTaskIsActive( const unsigned& itask ) const {
   unsigned nargs = getNumberOfArguments();
   if( nargs==0 ) {
-     return 1;
+    return 1;
   } else if( nmask>0 ) {
-     for(unsigned j=nargs-nmask; j<nargs; ++j) {
-         Value* myarg = getPntrToArgument(j);
-         if( myarg->getRank()==1 && !myarg->hasDerivatives() ) {
-             if( fabs(myarg->get(itask))>0 ) return 1;
-         } else if( myarg->getRank()==2 && !myarg->hasDerivatives() ) {
-             unsigned ncol = myarg->getRowLength(itask);
-             unsigned base = itask*myarg->getNumberOfColumns();
-             for(unsigned k=0; k<ncol; ++k) {
-                 if( fabs(myarg->get(base+k,false))>0 ) return 1;
-             }
-         } else plumed_merror("only matrices and vectors should be used as masks"); 
-     }
+    for(unsigned j=nargs-nmask; j<nargs; ++j) {
+      Value* myarg = getPntrToArgument(j);
+      if( myarg->getRank()==1 && !myarg->hasDerivatives() ) {
+        if( fabs(myarg->get(itask))>0 ) return 1;
+      } else if( myarg->getRank()==2 && !myarg->hasDerivatives() ) {
+        unsigned ncol = myarg->getRowLength(itask);
+        unsigned base = itask*myarg->getNumberOfColumns();
+        for(unsigned k=0; k<ncol; ++k) {
+          if( fabs(myarg->get(base+k,false))>0 ) return 1;
+        }
+      } else plumed_merror("only matrices and vectors should be used as masks");
+    }
   } else {
-     for(unsigned i=0; i<nargs; ++i) {
-       if( getName()=="OUTER_PRODUCT" && i>0 ) return -1;
-
-       Value* myarg = getPntrToArgument(i);
-       if( myarg->getRank()==0 ) continue;
-       else if( myarg->getRank()==1 && !myarg->hasDerivatives() ) {
-         if( fabs(myarg->get(itask))>0 ) return 1;
-       } else if( myarg->getRank()==2 && !myarg->hasDerivatives() ) {
-           unsigned ncol = myarg->getRowLength(itask);
-           unsigned base = itask*myarg->getNumberOfColumns();
-           for(unsigned k=0; k<ncol; ++k) {
-               if( fabs(myarg->get(base+k,false))>0 ) return 1;
-           }
-       } else if( myarg->getRank()>0 ) {
-           return 1; 
-       } else plumed_merror("should not be in action " + getName() );
-     }
+    for(unsigned i=0; i<nargs; ++i) {
+      if( getName()=="OUTER_PRODUCT" && i>0 ) return -1;
+
+      Value* myarg = getPntrToArgument(i);
+      if( myarg->getRank()==0 ) continue;
+      else if( myarg->getRank()==1 && !myarg->hasDerivatives() ) {
+        if( fabs(myarg->get(itask))>0 ) return 1;
+      } else if( myarg->getRank()==2 && !myarg->hasDerivatives() ) {
+        unsigned ncol = myarg->getRowLength(itask);
+        unsigned base = itask*myarg->getNumberOfColumns();
+        for(unsigned k=0; k<ncol; ++k) {
+          if( fabs(myarg->get(base+k,false))>0 ) return 1;
+        }
+      } else if( myarg->getRank()>0 ) {
+        return 1;
+      } else plumed_merror("should not be in action " + getName() );
+    }
   }
   return -1;
 }
@@ -798,10 +798,10 @@ bool ActionWithVector::checkForForces() {
   // Get the number of tasks
   std::vector<unsigned> force_tasks;
   if( getenvChainForbidden()==Option::yes ) {
-      std::vector<unsigned> & partialTaskList( getListOfActiveTasks( this ) );
-      for(unsigned i=0; i<partialTaskList.size(); ++i) force_tasks.push_back( partialTaskList[i] );
+    std::vector<unsigned> & partialTaskList( getListOfActiveTasks( this ) );
+    for(unsigned i=0; i<partialTaskList.size(); ++i) force_tasks.push_back( partialTaskList[i] );
   } else {
-      getForceTasks( force_tasks ); Tools::removeDuplicates(force_tasks); 
+    getForceTasks( force_tasks ); Tools::removeDuplicates(force_tasks);
   }
   unsigned nf_tasks=force_tasks.size();
   if( nf_tasks==0 ) return false;

diff --git a/src/crystdistrib/QuaternionBondProductMatrix.cpp b/src/crystdistrib/QuaternionBondProductMatrix.cpp
@@ -370,28 +370,28 @@ void QuaternionBondProductMatrix::runEndOfRowJobs( const unsigned& ival, const s
     for(unsigned k=0; k<4; ++k) { matrix_indices[nmat_ind] = arg_deriv_starts[k] + ival; nmat_ind++; }
 
     if( actionInChain() ) {
-        // Loop over row of matrix
-        for(unsigned n=4; n<8; ++n) {
-          bool found=false;
-          for(unsigned k=4; k<n; ++k) {
-            if( arg_deriv_starts[k]==arg_deriv_starts[n] ) { found=true; break; }
-          }
-          if( found ) continue;
-          unsigned istrn = getPntrToArgument(n)->getPositionInMatrixStash();
-          std::vector<unsigned>& imat_indices( myvals.getMatrixRowDerivativeIndices( istrn ) );
-          for(unsigned k=0; k<myvals.getNumberOfMatrixRowDerivatives( istrn ); ++k) matrix_indices[nmat_ind + k] = arg_deriv_starts[n] + imat_indices[k];
-          nmat_ind += myvals.getNumberOfMatrixRowDerivatives( getPntrToArgument(4)->getPositionInMatrixStash() );
+      // Loop over row of matrix
+      for(unsigned n=4; n<8; ++n) {
+        bool found=false;
+        for(unsigned k=4; k<n; ++k) {
+          if( arg_deriv_starts[k]==arg_deriv_starts[n] ) { found=true; break; }
         }
+        if( found ) continue;
+        unsigned istrn = getPntrToArgument(n)->getPositionInMatrixStash();
+        std::vector<unsigned>& imat_indices( myvals.getMatrixRowDerivativeIndices( istrn ) );
+        for(unsigned k=0; k<myvals.getNumberOfMatrixRowDerivatives( istrn ); ++k) matrix_indices[nmat_ind + k] = arg_deriv_starts[n] + imat_indices[k];
+        nmat_ind += myvals.getNumberOfMatrixRowDerivatives( getPntrToArgument(4)->getPositionInMatrixStash() );
+      }
     } else {
-       unsigned base=0; for(unsigned k=0; k<4; ++k) base += getPntrToArgument(k)->getNumberOfStoredValues();
-       for(unsigned n=4; n<8; ++n) {
-          unsigned coltot = ival*getPntrToArgument(n)->getNumberOfColumns();
-          for(unsigned k=1; k<indices.size(); ++k) {
-              unsigned ind2=indices[k]; if( ind2>=getPntrToArgument(0)->getShape()[0] ) ind2 = ind2 - getPntrToArgument(0)->getShape()[0];
-              matrix_indices[nmat_ind] = base + coltot + ind2; nmat_ind++; 
-          }
-          base += getPntrToArgument(n)->getNumberOfStoredValues();
-       } 
+      unsigned base=0; for(unsigned k=0; k<4; ++k) base += getPntrToArgument(k)->getNumberOfStoredValues();
+      for(unsigned n=4; n<8; ++n) {
+        unsigned coltot = ival*getPntrToArgument(n)->getNumberOfColumns();
+        for(unsigned k=1; k<indices.size(); ++k) {
+          unsigned ind2=indices[k]; if( ind2>=getPntrToArgument(0)->getShape()[0] ) ind2 = ind2 - getPntrToArgument(0)->getShape()[0];
+          matrix_indices[nmat_ind] = base + coltot + ind2; nmat_ind++;
+        }
+        base += getPntrToArgument(n)->getNumberOfStoredValues();
+      }
     }
     myvals.setNumberOfMatrixRowDerivatives( nmat, nmat_ind );
   }

diff --git a/src/function/Combine.cpp b/src/function/Combine.cpp
@@ -123,7 +123,7 @@ void Combine::registerKeywords(Keywords& keys) {
 }
 
 void Combine::read( ActionWithArguments* action ) {
-  unsigned nargs = action->getNumberOfArguments(); ActionWithVector* av=dynamic_cast<ActionWithVector*>(action); 
+  unsigned nargs = action->getNumberOfArguments(); ActionWithVector* av=dynamic_cast<ActionWithVector*>(action);
   if(av && av->getNumberOfMasks()>0) nargs = nargs - av->getNumberOfMasks();
   coefficients.resize( nargs ); parameters.resize( nargs ); powers.resize( nargs );
   parseVector(action,"COEFFICIENTS",coefficients);

diff --git a/src/function/FunctionOfMatrix.h b/src/function/FunctionOfMatrix.h
@@ -232,7 +232,7 @@ template <class T>
 void FunctionOfMatrix<T>::setupForTask( const unsigned& task_index, std::vector<unsigned>& indices, MultiValue& myvals ) const {
   unsigned basemat;
   for(unsigned i=0; i<getNumberOfArguments(); ++i) {
-      if( getPntrToArgument(i)->getRank()==2 ) { basemat=i; break; }
+    if( getPntrToArgument(i)->getRank()==2 ) { basemat=i; break; }
   }
   unsigned start_n = getPntrToArgument(basemat)->getShape()[0], size_v = getPntrToArgument(basemat)->getShape()[1];
   if( getNumberOfMasks()>0 ) {
@@ -241,16 +241,16 @@ void FunctionOfMatrix<T>::setupForTask( const unsigned& task_index, std::vector<
     if( indices.size()!=size_v+1 ) indices.resize( size_v+1 );
     for(unsigned i=0; i<size_v; ++i) indices[i+1] = start_n + getPntrToArgument(maskarg)->getRowIndex(task_index, i);
     myvals.setSplitIndex( size_v + 1 ); return;
-  } 
+  }
   unsigned maskarg=0; size_v = size_v+1;
   for(unsigned i=0; i<getNumberOfArguments(); ++i) {
-      if( getPntrToArgument(i)->getRank()!=2 ) continue ;
-      unsigned ss = getPntrToArgument(i)->getRowLength(task_index);
-      if( ss<size_v ) { maskarg=i; size_v = ss; }
+    if( getPntrToArgument(i)->getRank()!=2 ) continue ;
+    unsigned ss = getPntrToArgument(i)->getRowLength(task_index);
+    if( ss<size_v ) { maskarg=i; size_v = ss; }
   }
   if( indices.size()!=size_v+1 ) indices.resize( size_v+1 );
   for(unsigned i=0; i<size_v; ++i) indices[i+1] = start_n + getPntrToArgument(maskarg)->getRowIndex(task_index, i);
-  myvals.setSplitIndex( size_v + 1 ); 
+  myvals.setSplitIndex( size_v + 1 );
 }
 
 template <class T>
@@ -343,7 +343,7 @@ void FunctionOfMatrix<T>::performTask( const std::string& controller, const unsi
       if( getPntrToArgument(j)->getRank()==2 ) {
         for(int i=0; i<getNumberOfComponents(); ++i) {
           unsigned ostrn=getConstPntrToComponent(i)->getPositionInStream();
-          unsigned myind = base + getPntrToArgument(j)->getIndexInStore( index1*getPntrToArgument(j)->getShape()[1] + ind2 );  
+          unsigned myind = base + getPntrToArgument(j)->getIndexInStore( index1*getPntrToArgument(j)->getShape()[1] + ind2 );
           myvals.addDerivative( ostrn, myind, derivatives(i,j) );
           myvals.updateIndex( ostrn, myind );
         }
@@ -419,13 +419,13 @@ void FunctionOfMatrix<T>::runEndOfRowJobs( const unsigned& ind, const std::vecto
       if( mat_indices.size()<nderivatives ) mat_indices.resize( nderivatives ); unsigned matderbase = 0;
       for(unsigned i=argstart; i<getNumberOfArguments(); ++i) {
         if( getPntrToArgument(i)->getRank()==0 ) {
-            mat_indices[ntot_mat] = matderbase; ntot_mat++;
+          mat_indices[ntot_mat] = matderbase; ntot_mat++;
         } else {
-            unsigned ss = getPntrToArgument(i)->getRowLength(ind); unsigned tbase = matderbase + getPntrToArgument(i)->getNumberOfColumns()*myvals.getTaskIndex();
-            for(unsigned k=0; k<ss; ++k) mat_indices[ntot_mat + k] = tbase + k;
-            ntot_mat += ss; 
+          unsigned ss = getPntrToArgument(i)->getRowLength(ind); unsigned tbase = matderbase + getPntrToArgument(i)->getNumberOfColumns()*myvals.getTaskIndex();
+          for(unsigned k=0; k<ss; ++k) mat_indices[ntot_mat + k] = tbase + k;
+          ntot_mat += ss;
         }
-        matderbase += getPntrToArgument(i)->getNumberOfStoredValues(); 
+        matderbase += getPntrToArgument(i)->getNumberOfStoredValues();
       }
       myvals.setNumberOfMatrixRowDerivatives( nmat, ntot_mat );
     }

diff --git a/src/gridtools/KDE.cpp b/src/gridtools/KDE.cpp
@@ -372,11 +372,11 @@ int KDE::checkTaskIsActive( const unsigned& itask ) const {
     if( hasheight && getPntrToArgument(gridobject.getDimension())->getRank()>0
         && fabs(getPntrToArgument(gridobject.getDimension())->get(itask))<epsilon ) return -1;
     return 1;
-  }     
+  }
   for(unsigned i=0; i<num_neigh; ++i) {
-    if( itask==neighbors[i] ) return 1; 
-  }         
-  return -1; 
+    if( itask==neighbors[i] ) return 1;
+  }
+  return -1;
 }
 
 int KDE::checkTaskStatus( const unsigned& taskno, int& flag ) const {