From eeb1da233a09dfb80d72ccf55e9848793ebad110 Mon Sep 17 00:00:00 2001
From: Gareth Tribello <gareth.tribello@gmail.com>
Date: Thu, 4 May 2017 12:01:27 +0100
Subject: [PATCH] Some optimization improvements in histograms
---
src/analysis/Histogram.cpp | 17 ++++++++++++++---
src/gridtools/GridVessel.cpp | 8 ++++++--
src/gridtools/GridVessel.h | 1 +
src/gridtools/HistogramOnGrid.cpp | 4 ++--
4 files changed, 23 insertions(+), 7 deletions(-)
diff --git a/src/analysis/Histogram.cpp b/src/analysis/Histogram.cpp
index 16abb4a6d..58e981598 100644
--- a/src/analysis/Histogram.cpp
+++ b/src/analysis/Histogram.cpp
@@ -311,6 +311,8 @@ void Histogram::turnOnDerivatives() {
if( !mbase ) error("do not know how to get histogram derivatives for actions of type " + myvessels[i]->getName() );
tmp_atoms = mbase->getAbsoluteIndexes();
for(unsigned j=0; j<tmp_atoms.size(); ++j) all_atoms.push_back( tmp_atoms[j] );
+ // Make a tempory multi value so we can avoid vector resizing
+ stashes[i]->resizeTemporyMultiValues( 1 );
}
ActionAtomistic::requestAtoms( all_atoms );
finalForces.resize( 3*all_atoms.size() + 9 );
@@ -386,7 +388,10 @@ void Histogram::compute( const unsigned& current, MultiValue& myvals ) const {
for(unsigned i=2; i<myvessels[0]->getNumberOfQuantities(); ++i) myvals.setValue( i-1, cvals[i] );
myvals.setValue( 0, cvals[0] ); myvals.setValue( myvessels[0]->getNumberOfQuantities() - 1, ww );
if( in_apply ) {
- MultiValue tmpval( myvessels[0]->getNumberOfQuantities(), myvessels[0]->getNumberOfDerivatives() );
+ MultiValue& tmpval = stashes[0]->getTemporyMultiValue(0);
+ if( tmpval.getNumberOfValues()!=myvessels[0]->getNumberOfQuantities() ||
+ tmpval.getNumberOfDerivatives()!=myvessels[0]->getNumberOfDerivatives() )
+ tmpval.resize( myvessels[0]->getNumberOfQuantities(), myvessels[0]->getNumberOfDerivatives() );
stashes[0]->retrieveDerivatives( stashes[0]->getTrueIndex(current), true, tmpval );
for(unsigned j=0; j<tmpval.getNumberActive(); ++j) {
unsigned jder=tmpval.getActiveIndex(j); myvals.addDerivative( 0, jder, tmpval.getDerivative(0, jder) );
@@ -406,7 +411,10 @@ void Histogram::compute( const unsigned& current, MultiValue& myvals ) const {
stashes[j]->retrieveSequentialValue( current, false, cvals ); totweight *= cvals[0];
}
// And this bit the derivatives
- MultiValue tmpval( myvessels[0]->getNumberOfQuantities(), myvessels[0]->getNumberOfDerivatives() );
+ MultiValue& tmpval = stashes[0]->getTemporyMultiValue(0);
+ if( tmpval.getNumberOfValues()!=myvessels[0]->getNumberOfQuantities() ||
+ tmpval.getNumberOfDerivatives()!=myvessels[0]->getNumberOfDerivatives() )
+ tmpval.resize( myvessels[0]->getNumberOfQuantities(), myvessels[0]->getNumberOfDerivatives() );
stashes[0]->retrieveDerivatives( stashes[0]->getTrueIndex(current), false, tmpval );
for(unsigned j=0; j<tmpval.getNumberActive(); ++j) {
unsigned jder=tmpval.getActiveIndex(j);
@@ -421,7 +429,10 @@ void Histogram::compute( const unsigned& current, MultiValue& myvals ) const {
tnorm *= cvals[0]; myvals.setValue( 1+i, cvals[1] );
// Get the derivatives as well if we are in apply
if( in_apply ) {
- MultiValue tmpval( myvessels[i]->getNumberOfQuantities(), myvessels[i]->getNumberOfDerivatives() );
+ MultiValue& tmpval = stashes[0]->getTemporyMultiValue(0);
+ if( tmpval.getNumberOfValues()!=myvessels[0]->getNumberOfQuantities() ||
+ tmpval.getNumberOfDerivatives()!=myvessels[0]->getNumberOfDerivatives() )
+ tmpval.resize( myvessels[0]->getNumberOfQuantities(), myvessels[0]->getNumberOfDerivatives() );
stashes[i]->retrieveDerivatives( stashes[i]->getTrueIndex(current), false, tmpval );
for(unsigned j=0; j<tmpval.getNumberActive(); ++j) {
unsigned jder=tmpval.getActiveIndex(j);
diff --git a/src/gridtools/GridVessel.cpp b/src/gridtools/GridVessel.cpp
index 5282667a4..3b89af0f2 100644
--- a/src/gridtools/GridVessel.cpp
+++ b/src/gridtools/GridVessel.cpp
@@ -191,9 +191,13 @@ void GridVessel::getIndices( const unsigned& index, std::vector<unsigned>& indic
}
void GridVessel::getGridPointCoordinates( const unsigned& ipoint, std::vector<double>& x ) const {
- plumed_dbg_assert( bounds_set && x.size()==dimension && ipoint<npoints );
+ std::vector<unsigned> tindices( dimension ); getGridPointCoordinates( ipoint, tindices, x );
+}
+
+void GridVessel::getGridPointCoordinates( const unsigned& ipoint, std::vector<unsigned>& tindices, std::vector<double>& x ) const {
+ plumed_dbg_assert( bounds_set && x.size()==dimension && tindices.size()==dimension && ipoint<npoints );
if( gtype==flat ) {
- std::vector<unsigned> tindices( dimension ); getIndices( ipoint, tindices );
+ getIndices( ipoint, tindices );
for(unsigned i=0; i<dimension; ++i) x[i] = min[i] + dx[i]*tindices[i];
} else if( gtype==fibonacci ) {
x[1] = ((ipoint*fib_offset) - 1) + (fib_offset/2);
diff --git a/src/gridtools/GridVessel.h b/src/gridtools/GridVessel.h
index 4cb3c7bee..120b9bba4 100644
--- a/src/gridtools/GridVessel.h
+++ b/src/gridtools/GridVessel.h
@@ -117,6 +117,7 @@ public:
unsigned getNumberOfPoints() const;
/// Get the coordinates for a point in the grid
void getGridPointCoordinates( const unsigned&, std::vector<double>& ) const ;
+ void getGridPointCoordinates( const unsigned&, std::vector<unsigned>&, std::vector<double>& ) const ;
/// Get the dimensionality of the function
unsigned getDimension() const ;
/// Get the number of components in the vector stored on each grid point
diff --git a/src/gridtools/HistogramOnGrid.cpp b/src/gridtools/HistogramOnGrid.cpp
index 43fe891c2..1ddae05a4 100644
--- a/src/gridtools/HistogramOnGrid.cpp
+++ b/src/gridtools/HistogramOnGrid.cpp
@@ -121,11 +121,11 @@ void HistogramOnGrid::calculate( const unsigned& current, MultiValue& myvals, st
std::vector<double> intforce( 2*dimension, 0.0 );
std::vector<Value*> vv( getVectorOfValues() );
- double newval; std::vector<double> xx( dimension );
+ double newval; std::vector<unsigned> tindices( dimension ); std::vector<double> xx( dimension );
for(unsigned i=0; i<num_neigh; ++i) {
unsigned ineigh=neighbors[i];
if( inactive( ineigh ) ) continue ;
- getGridPointCoordinates( ineigh, xx );
+ getGridPointCoordinates( ineigh, tindices, xx );
if( kernel ) {
for(unsigned j=0; j<dimension; ++j) vv[j]->set(xx[j]);
newval = kernel->evaluate( vv, der, true );
--
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