Added faster version of matrix vector multiply that is used when not employing the chain

Author: Gareth Aneurin Tribello

src/core/ActionWithMatrix.h

@@ -75,7 +75,7 @@ class ActionWithMatrix : public ActionWithVector {
 //// This does some setup before we run over the row of the matrix
   virtual void setupForTask( const unsigned& task_index, std::vector<unsigned>& indices, MultiValue& myvals ) const = 0;
 /// Run over one row of the matrix
-  void performTask( const unsigned& task_index, MultiValue& myvals ) const override ;
+  virtual void performTask( const unsigned& task_index, MultiValue& myvals ) const ;
 /// Gather a row of the matrix
   void gatherStoredValue( const unsigned& valindex, const unsigned& code, const MultiValue& myvals, const unsigned& bufstart, std::vector<double>& buffer ) const override;
 /// Gather all the data from the threads

src/matrixtools/MatrixTimesVector.cpp

@@ -46,6 +46,7 @@ class MatrixTimesVector : public ActionWithMatrix {
   unsigned getNumberOfColumns() const override { plumed_error(); }
   unsigned getNumberOfDerivatives();
   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; }
   void setupForTask( const unsigned& task_index, std::vector<unsigned>& indices, MultiValue& myvals ) const ;
   void performTask( const std::string& controller, const unsigned& index1, const unsigned& index2, MultiValue& myvals ) const override;
@@ -161,6 +162,74 @@ void MatrixTimesVector::prepare() {
   std::vector<unsigned> shape(1); shape[0] = getPntrToArgument(0)->getShape()[0]; myval->setShape(shape);
 }
 
+void MatrixTimesVector::performTask( const unsigned& task_index, MultiValue& myvals ) const {
+  if( actionInChain() ) { ActionWithMatrix::performTask( task_index, myvals ); return; }
+
+  if( sumrows ) {
+    unsigned n=getNumberOfArguments()-1; Value* myvec = getPntrToArgument(n);
+    for(unsigned i=0; i<n; ++i) {
+      Value* mymat = getPntrToArgument(i);
+      unsigned ncol = mymat->getNumberOfColumns();
+      unsigned nmat = mymat->getRowLength(task_index);
+      double val=0; for(unsigned j=0; j<nmat; ++j) val += mymat->get( task_index*ncol + j, false );
+      unsigned ostrn = getConstPntrToComponent(i)->getPositionInStream();
+      myvals.setValue( ostrn, val );
+
+      // And the derivatives
+      if( doNotCalculateDerivatives() ) continue;
+
+      unsigned dloc = arg_deriv_starts[i] + task_index*ncol;
+      for(unsigned j=0; j<nmat; ++j) {
+        myvals.addDerivative( ostrn, dloc + j, 1.0 ); myvals.updateIndex( ostrn, dloc + j );
+      }
+    }
+  } else if( getPntrToArgument(1)->getRank()==1 ) {
+    Value* mymat = getPntrToArgument(0);
+    unsigned ncol = mymat->getNumberOfColumns();
+    unsigned nmat = mymat->getRowLength(task_index);
+    unsigned dloc = arg_deriv_starts[0] + task_index*ncol;
+    for(unsigned i=0; i<getNumberOfArguments()-1; ++i) {
+      Value* myvec = getPntrToArgument(i+1);
+      double val=0; for(unsigned j=0; j<nmat; ++j) val += mymat->get( task_index*ncol + j, false )*myvec->get( mymat->getRowIndex( task_index, j ) );
+      unsigned ostrn = getConstPntrToComponent(i)->getPositionInStream();
+      myvals.setValue( ostrn, val );
+
+      // And the derivatives
+      if( doNotCalculateDerivatives() ) continue;
+
+      for(unsigned j=0; j<nmat; ++j) {
+        unsigned kind = mymat->getRowIndex( task_index, j );
+        double vecval = myvec->get( kind );
+        double matval = mymat->get( task_index*ncol + j, false );
+        myvals.addDerivative( ostrn, dloc + j, vecval ); myvals.updateIndex( ostrn, dloc + j );
+        myvals.addDerivative( ostrn, arg_deriv_starts[i+1] + kind, matval ); myvals.updateIndex( ostrn, arg_deriv_starts[i+1] + kind );
+      }
+    }
+  } else {
+    unsigned n=getNumberOfArguments()-1; Value* myvec = getPntrToArgument(n);
+    for(unsigned i=0; i<n; ++i) {
+      Value* mymat = getPntrToArgument(i);
+      unsigned ncol = mymat->getNumberOfColumns();
+      unsigned nmat = mymat->getRowLength(task_index);
+      double val=0; for(unsigned j=0; j<nmat; ++j) val += mymat->get( task_index*ncol + j, false )*myvec->get( mymat->getRowIndex( task_index, j ) );
+      unsigned ostrn = getConstPntrToComponent(i)->getPositionInStream();
+      myvals.setValue( ostrn, val );
+
+      // And the derivatives
+      if( doNotCalculateDerivatives() ) continue;
+
+      unsigned dloc = arg_deriv_starts[i] + task_index*ncol;
+      for(unsigned j=0; j<nmat; ++j) {
+        unsigned kind = mymat->getRowIndex( task_index, j );
+        double vecval = myvec->get( kind );
+        double matval = mymat->get( task_index*ncol + j, false );
+        myvals.addDerivative( ostrn, dloc + j, vecval ); myvals.updateIndex( ostrn, dloc + j );
+        myvals.addDerivative( ostrn, arg_deriv_starts[n] + kind, matval ); myvals.updateIndex( ostrn, arg_deriv_starts[n] + kind );
+      }
+    }
+  }
+}
+
 void MatrixTimesVector::setupForTask( const unsigned& task_index, std::vector<unsigned>& indices, MultiValue& myvals ) const {
   unsigned start_n = getPntrToArgument(0)->getShape()[0], size_v = getPntrToArgument(0)->getRowLength(task_index);
   if( indices.size()!=size_v+1 ) indices.resize( size_v + 1 );