From 94d33a9d2406273e94554936c208a98c25172fed Mon Sep 17 00:00:00 2001
From: Gareth Aneurin Tribello <garethtribello@gareths-mbp.mp.qub.ac.uk>
Date: Thu, 18 Jul 2024 10:32:35 +0100
Subject: [PATCH] Added some optimisations in AdjacencyMatrixBase

---
 src/adjmat/AdjacencyMatrixBase.cpp | 24 ++++++++++++++----------
 src/core/ActionWithVector.h        |  6 ++++++
 2 files changed, 20 insertions(+), 10 deletions(-)

diff --git a/src/adjmat/AdjacencyMatrixBase.cpp b/src/adjmat/AdjacencyMatrixBase.cpp
index 98eb5ed620..8b569829da 100644
--- a/src/adjmat/AdjacencyMatrixBase.cpp
+++ b/src/adjmat/AdjacencyMatrixBase.cpp
@@ -308,10 +308,12 @@ void AdjacencyMatrixBase::performTask( const std::string& controller, const unsi
     // Update dynamic list indices for virial
     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
-    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 );
+    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 );
+    }
   }
 
   // Calculate the components if we need them
@@ -352,18 +354,20 @@ void AdjacencyMatrixBase::performTask( const std::string& controller, const unsi
       myvals.addDerivative( z_index, base+1, 0 ); myvals.addDerivative( z_index, base+4, 0 ); myvals.addDerivative( z_index, base+7, 0 );
       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 ); }
-      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 );
+      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 );
+          }
       }
     }
   }
 }
 
 void AdjacencyMatrixBase::runEndOfRowJobs( const unsigned& ind, const std::vector<unsigned> & indices, MultiValue& myvals ) const {
-  if( doNotCalculateDerivatives() ) return;
+  if( doNotCalculateDerivatives() || !chainContinuesAfterThisAction() ) return;
 
   for(int k=0; k<getNumberOfComponents(); ++k) {
     unsigned nmat = getConstPntrToComponent(k)->getPositionInMatrixStash(), nmat_ind = myvals.getNumberOfMatrixRowDerivatives( nmat );
diff --git a/src/core/ActionWithVector.h b/src/core/ActionWithVector.h
index 6327715da5..c8daa8980b 100644
--- a/src/core/ActionWithVector.h
+++ b/src/core/ActionWithVector.h
@@ -125,6 +125,7 @@ class ActionWithVector:
   bool doNotCalculateDerivatives() const override ;
 /// Are we running this command in a chain
   bool actionInChain() const ;
+  bool chainContinuesAfterThisAction() const ;
 /// This is overwritten within ActionWithMatrix and is used to build the chain of just matrix actions
   virtual void finishChainBuild( ActionWithVector* act );
 /// Check if there are any stored values in arguments
@@ -185,6 +186,11 @@ bool ActionWithVector::actionInChain() const {
   return (action_to_do_before!=NULL);
 }
 
+inline 
+bool ActionWithVector::chainContinuesAfterThisAction() const {
+  return (action_to_do_after!=NULL);
+}
+
 inline
 bool ActionWithVector::runInSerial() const {
   return serial;