Added optimisation for matrix times vector to avoid allocating large arrays.

Author: Gareth Aneurin Tribello

src/adjmat/AdjacencyMatrixBase.cpp

@@ -309,10 +309,10 @@ void AdjacencyMatrixBase::performTask( const std::string& controller, const unsi
     unsigned base = 3*getNumberOfAtoms(); for(unsigned j=0; j<9; ++j) myvals.updateIndex( w_ind, base+j );
     // And the indices for the derivatives of the row of the matrix
     if( chainContinuesAfterThisAction() ) {
-        unsigned nmat = getConstPntrToComponent(0)->getPositionInMatrixStash(), nmat_ind = myvals.getNumberOfMatrixRowDerivatives( nmat );
-        std::vector<unsigned>& matrix_indices( myvals.getMatrixRowDerivativeIndices( nmat ) );
-        matrix_indices[nmat_ind+0]=3*index2+0; matrix_indices[nmat_ind+1]=3*index2+1; matrix_indices[nmat_ind+2]=3*index2+2;
-        myvals.setNumberOfMatrixRowDerivatives( nmat, nmat_ind+3 );
+      unsigned nmat = getConstPntrToComponent(0)->getPositionInMatrixStash(), nmat_ind = myvals.getNumberOfMatrixRowDerivatives( nmat );
+      std::vector<unsigned>& matrix_indices( myvals.getMatrixRowDerivativeIndices( nmat ) );
+      matrix_indices[nmat_ind+0]=3*index2+0; matrix_indices[nmat_ind+1]=3*index2+1; matrix_indices[nmat_ind+2]=3*index2+2;
+      myvals.setNumberOfMatrixRowDerivatives( nmat, nmat_ind+3 );
     }
   }
 
@@ -355,12 +355,12 @@ void AdjacencyMatrixBase::performTask( const std::string& controller, const unsi
       myvals.addDerivative( z_index, base+2, -atom[0] ); myvals.addDerivative( z_index, base+5, -atom[1] ); myvals.addDerivative( z_index, base+8, -atom[2] );
       for(unsigned k=0; k<9; ++k) { myvals.updateIndex( x_index, base+k ); myvals.updateIndex( y_index, base+k ); myvals.updateIndex( z_index, base+k ); }
       if( chainContinuesAfterThisAction() ) {
-          for(unsigned k=1; k<4; ++k) {
-            unsigned nmat = getConstPntrToComponent(k)->getPositionInMatrixStash(), nmat_ind = myvals.getNumberOfMatrixRowDerivatives( nmat );
-            std::vector<unsigned>& matrix_indices( myvals.getMatrixRowDerivativeIndices( nmat ) );
-            matrix_indices[nmat_ind+0]=3*index2+0; matrix_indices[nmat_ind+1]=3*index2+1; matrix_indices[nmat_ind+2]=3*index2+2;
-            myvals.setNumberOfMatrixRowDerivatives( nmat, nmat_ind+3 );
-          }
+        for(unsigned k=1; k<4; ++k) {
+          unsigned nmat = getConstPntrToComponent(k)->getPositionInMatrixStash(), nmat_ind = myvals.getNumberOfMatrixRowDerivatives( nmat );
+          std::vector<unsigned>& matrix_indices( myvals.getMatrixRowDerivativeIndices( nmat ) );
+          matrix_indices[nmat_ind+0]=3*index2+0; matrix_indices[nmat_ind+1]=3*index2+1; matrix_indices[nmat_ind+2]=3*index2+2;
+          myvals.setNumberOfMatrixRowDerivatives( nmat, nmat_ind+3 );
+        }
       }
     }
   }

src/core/ActionWithVector.h

@@ -136,7 +136,7 @@ class ActionWithVector:
 /// This is overridden in ActionWithMatrix
   virtual void getAllActionLabelsInMatrixChain( std::vector<std::string>& matchain ) const {}
 /// Get the number of derivatives in the stream
-  void getNumberOfStreamedDerivatives( unsigned& nderivatives, Value* stopat );
+  virtual void getNumberOfStreamedDerivatives( unsigned& nderivatives, Value* stopat );
 /// Get every the label of every value that is calculated in this chain
   void getAllActionLabelsInChain( std::vector<std::string>& mylabels ) const ;
 /// We override clearInputForces here to ensure that forces are deleted from all values
@@ -186,7 +186,7 @@ bool ActionWithVector::actionInChain() const {
   return (action_to_do_before!=NULL);
 }
 
-inline 
+inline
 bool ActionWithVector::chainContinuesAfterThisAction() const {
   return (action_to_do_after!=NULL);
 }

src/matrixtools/MatrixTimesVector.cpp

@@ -44,7 +44,8 @@ class MatrixTimesVector : public ActionWithMatrix {
   explicit MatrixTimesVector(const ActionOptions&);
   std::string getOutputComponentDescription( const std::string& cname, const Keywords& keys ) const override ;
   unsigned getNumberOfColumns() const override { plumed_error(); }
-  unsigned getNumberOfDerivatives();
+  void getNumberOfStreamedDerivatives( unsigned& nderivatives, Value* stopat ) override ;
+  unsigned getNumberOfDerivatives() override ;
   void prepare() override ;
   void performTask( const unsigned& task_index, MultiValue& myvals ) const override ;
   bool isInSubChain( unsigned& nder ) override { nder = arg_deriv_starts[0]; return true; }
@@ -162,6 +163,16 @@ void MatrixTimesVector::prepare() {
   std::vector<unsigned> shape(1); shape[0] = getPntrToArgument(0)->getShape()[0]; myval->setShape(shape);
 }
 
+void MatrixTimesVector::getNumberOfStreamedDerivatives( unsigned& nderivatives, Value* stopat ) {
+  if( actionInChain() ) { ActionWithVector::getNumberOfStreamedDerivatives( nderivatives, stopat ); return; }
+
+  nderivatives = 0;
+  for(unsigned i=0; i<getNumberOfArguments(); ++i) {
+    arg_deriv_starts[i] = nderivatives;
+    nderivatives += getPntrToArgument(i)->getNumberOfStoredValues();
+  }
+}
+
 void MatrixTimesVector::performTask( const unsigned& task_index, MultiValue& myvals ) const {
   if( actionInChain() ) { ActionWithMatrix::performTask( task_index, myvals ); return; }