From 8c0513ba8ece11602a9d540845c71db02f0b0fc1 Mon Sep 17 00:00:00 2001
From: sandipde <1sandipde@gmail.com>
Date: Thu, 18 Aug 2016 14:20:04 +0200
Subject: [PATCH] Added lowmem option to Euclidean dissimilarity stuff to lower
memory requirements
---
src/analysis/EuclideanDissimilarityMatrix.cpp | 14 +++++++++++---
1 file changed, 11 insertions(+), 3 deletions(-)
diff --git a/src/analysis/EuclideanDissimilarityMatrix.cpp b/src/analysis/EuclideanDissimilarityMatrix.cpp
index 60a5903e5..4ce620338 100644
--- a/src/analysis/EuclideanDissimilarityMatrix.cpp
+++ b/src/analysis/EuclideanDissimilarityMatrix.cpp
@@ -37,6 +37,7 @@ namespace analysis {
class EuclideanDissimilarityMatrix : public AnalysisWithDataCollection {
private:
+ bool lowmem;
Matrix<double> dissimilarities;
public:
static void registerKeywords( Keywords& keys );
@@ -56,22 +57,29 @@ PLUMED_REGISTER_ACTION(EuclideanDissimilarityMatrix,"EUCLIDEAN_DISSIMILARITIES")
void EuclideanDissimilarityMatrix::registerKeywords( Keywords& keys ){
AnalysisWithDataCollection::registerKeywords( keys );
keys.reset_style("METRIC","atoms-1"); keys.use("FRAMES");
+ keys.addFlag("LOWMEM",false,"lower the memory requirements of the calculation");
}
EuclideanDissimilarityMatrix::EuclideanDissimilarityMatrix( const ActionOptions& ao ):
Action(ao),
AnalysisWithDataCollection(ao)
{
+ parseFlag("LOWMEM",lowmem);
+ if( lowmem ) log.printf(" lowering memory requirements \n");
}
void EuclideanDissimilarityMatrix::performAnalysis(){
// Resize dissimilarities matrix and set all elements to zero
- dissimilarities.resize( getNumberOfDataPoints(), getNumberOfDataPoints() ); dissimilarities=0;
+ if( !lowmem ){
+ dissimilarities.resize( getNumberOfDataPoints(), getNumberOfDataPoints() ); dissimilarities=0;
+ }
}
double EuclideanDissimilarityMatrix::getDissimilarity( const unsigned& iframe, const unsigned& jframe ){
- plumed_dbg_assert( iframe<dissimilarities.nrows() && jframe<dissimilarities.ncols() );
- if( dissimilarities(iframe,jframe)>0. ){ return dissimilarities(iframe,jframe); }
+ plumed_dbg_assert( iframe<getNumberOfDataPoints() && jframe<getNumberOfDataPoints() );
+ if( !lowmem ){
+ if( dissimilarities(iframe,jframe)>0. ){ return dissimilarities(iframe,jframe); }
+ }
if( iframe!=jframe ){
ReferenceConfiguration* myref1; ReferenceConfiguration* myref2;
if( mydata ){ myref1=AnalysisBase::getReferenceConfiguration(iframe,true); myref2=AnalysisBase::getReferenceConfiguration(jframe,true); }
--
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