From 9ab6f051800fd486453ee1aed126940a17978c8b Mon Sep 17 00:00:00 2001
From: Gareth Tribello <gareth.tribello@gmail.com>
Date: Tue, 7 Jul 2015 16:19:57 +0100
Subject: [PATCH] Fixed bug that breaks travis-ci
I also fixed made the data collecting class is aware if we are calculating
a distance. If it knows that we are trying to calculate a distnace
it returns something with which it can calculate a distance and not
the position stored by COLLECT_FRAMES. I am not sure this is necessary
and if it will be ever used but I guess it is better to be safe than
sorry
---
src/analysis/AnalysisBase.h | 6 +++---
src/analysis/AnalysisWithDataCollection.cpp | 6 +++---
src/analysis/AnalysisWithDataCollection.h | 2 +-
src/analysis/EuclideanDissimilarityMatrix.cpp | 2 +-
src/analysis/LandmarkSelectionBase.h | 6 +++---
src/analysis/OutputColvarFile.cpp | 4 ++--
src/analysis/OutputPDBFile.cpp | 4 ++--
src/analysis/ReadDissimilarityMatrix.cpp | 6 +++---
src/dimred/DimensionalityReductionBase.cpp | 4 ++--
src/dimred/DimensionalityReductionBase.h | 2 +-
src/dimred/ProjectNonLandmarkPoints.cpp | 6 +++---
src/reference/ReferenceConfiguration.cpp | 2 +-
12 files changed, 25 insertions(+), 25 deletions(-)
diff --git a/src/analysis/AnalysisBase.h b/src/analysis/AnalysisBase.h
index 9208463ae..3b3b35f9e 100644
--- a/src/analysis/AnalysisBase.h
+++ b/src/analysis/AnalysisBase.h
@@ -84,7 +84,7 @@ public:
/// Get the ith data point
virtual void getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const ;
/// Get a reference configuration (in dimensionality reduction this returns the projection)
- virtual ReferenceConfiguration* getReferenceConfiguration( const unsigned& idata );
+ virtual ReferenceConfiguration* getReferenceConfiguration( const unsigned& idata, const bool& calcdist );
/// This actually performs the analysis
virtual void performAnalysis()=0;
/// These overwrite things from inherited classes (this is a bit of a fudge)
@@ -164,8 +164,8 @@ void AnalysisBase::getDataPoint( const unsigned& idata, std::vector<double>& poi
}
inline
-ReferenceConfiguration* AnalysisBase::getReferenceConfiguration( const unsigned& idata ){
- return mydata->getReferenceConfiguration( idata );
+ReferenceConfiguration* AnalysisBase::getReferenceConfiguration( const unsigned& idata, const bool& calcdist ){
+ return mydata->getReferenceConfiguration( idata, calcdist );
}
}
diff --git a/src/analysis/AnalysisWithDataCollection.cpp b/src/analysis/AnalysisWithDataCollection.cpp
index 361f88ccf..d3e2baa60 100644
--- a/src/analysis/AnalysisWithDataCollection.cpp
+++ b/src/analysis/AnalysisWithDataCollection.cpp
@@ -289,13 +289,13 @@ void AnalysisWithDataCollection::getDataPoint( const unsigned& idat, std::vector
}
}
-ReferenceConfiguration* AnalysisWithDataCollection::getReferenceConfiguration( const unsigned& idat ){
+ReferenceConfiguration* AnalysisWithDataCollection::getReferenceConfiguration( const unsigned& idat, const bool& calcdist ){
if( !mydata ){
plumed_dbg_assert( idat<data.size() );
- if( myframes ) return myframes->getReferenceConfiguration( idat );
+ if( !calcdist && myframes ) return myframes->getReferenceConfiguration( idat, false );
return data[idat];
}
- return AnalysisBase::getReferenceConfiguration( idat );
+ return AnalysisBase::getReferenceConfiguration( idat, calcdist );
}
void AnalysisWithDataCollection::update(){
diff --git a/src/analysis/AnalysisWithDataCollection.h b/src/analysis/AnalysisWithDataCollection.h
index 8697ea147..6bde3447f 100644
--- a/src/analysis/AnalysisWithDataCollection.h
+++ b/src/analysis/AnalysisWithDataCollection.h
@@ -99,7 +99,7 @@ public:
/// Get the ith data point
virtual void getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const ;
/// Get a reference configuration (in dimensionality reduction this returns the projection)
- virtual ReferenceConfiguration* getReferenceConfiguration( const unsigned& idat );
+ virtual ReferenceConfiguration* getReferenceConfiguration( const unsigned& idat, const bool& calcdist );
/// This ensures that the energy is stored if we are reweighting
void prepare();
/// This stores the data and calls the analysis to be performed
diff --git a/src/analysis/EuclideanDissimilarityMatrix.cpp b/src/analysis/EuclideanDissimilarityMatrix.cpp
index 5594bb347..60a5903e5 100644
--- a/src/analysis/EuclideanDissimilarityMatrix.cpp
+++ b/src/analysis/EuclideanDissimilarityMatrix.cpp
@@ -74,7 +74,7 @@ double EuclideanDissimilarityMatrix::getDissimilarity( const unsigned& iframe, c
if( dissimilarities(iframe,jframe)>0. ){ return dissimilarities(iframe,jframe); }
if( iframe!=jframe ){
ReferenceConfiguration* myref1; ReferenceConfiguration* myref2;
- if( mydata ){ myref1=AnalysisBase::getReferenceConfiguration(iframe); myref2=AnalysisBase::getReferenceConfiguration(jframe); }
+ if( mydata ){ myref1=AnalysisBase::getReferenceConfiguration(iframe,true); myref2=AnalysisBase::getReferenceConfiguration(jframe,true); }
else { myref1 = data[iframe]; myref2 = data[jframe]; }
if( myref1->getNumberOfProperties()>0 ){
dissimilarities(iframe,jframe) = dissimilarities(jframe,iframe) = property_distance( myref1, myref2, true );
diff --git a/src/analysis/LandmarkSelectionBase.h b/src/analysis/LandmarkSelectionBase.h
index 61da3a215..801c39ee1 100644
--- a/src/analysis/LandmarkSelectionBase.h
+++ b/src/analysis/LandmarkSelectionBase.h
@@ -53,7 +53,7 @@ public:
/// Get the ith data point
void getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const ;
/// Get a reference configuration
- ReferenceConfiguration* getReferenceConfiguration( const unsigned& idat );
+ ReferenceConfiguration* getReferenceConfiguration( const unsigned& idat, const bool& calcdist );
/// Select landmark configurations
void performAnalysis();
virtual void selectLandmarks()=0;
@@ -84,8 +84,8 @@ void LandmarkSelectionBase::getDataPoint( const unsigned& idata, std::vector<dou
}
inline
-ReferenceConfiguration* LandmarkSelectionBase::getReferenceConfiguration( const unsigned& idat ){
- return AnalysisBase::getReferenceConfiguration( landmark_indices[idat] );
+ReferenceConfiguration* LandmarkSelectionBase::getReferenceConfiguration( const unsigned& idat, const bool& calcdist ){
+ return AnalysisBase::getReferenceConfiguration( landmark_indices[idat], calcdist );
}
inline
diff --git a/src/analysis/OutputColvarFile.cpp b/src/analysis/OutputColvarFile.cpp
index fe56fc3d0..c29577981 100644
--- a/src/analysis/OutputColvarFile.cpp
+++ b/src/analysis/OutputColvarFile.cpp
@@ -88,12 +88,12 @@ void OutputColvarFile::performAnalysis(){
gfile.fmtField(fmt+" ");
gfile.open( filename.c_str() );
- ReferenceConfiguration* myp = getReferenceConfiguration(0);
+ ReferenceConfiguration* myp = getReferenceConfiguration(0,false);
if( myp->getNumberOfProperties()==0 ) plumed_assert( !dynamic_cast<ReferenceAtoms*>( myp ) );
// Print embedding coordinates
for(unsigned i=0;i<getNumberOfDataPoints();++i){
- ReferenceConfiguration* mypoint=getReferenceConfiguration(i);
+ ReferenceConfiguration* mypoint=getReferenceConfiguration(i,false);
for(unsigned j=0;j<mypoint->getNumberOfProperties();++j){
gfile.printField( mypoint->getPropertyName(j), mypoint->getPropertyValue(j) );
}
diff --git a/src/analysis/OutputPDBFile.cpp b/src/analysis/OutputPDBFile.cpp
index 5cdc83e52..0783b0fc2 100644
--- a/src/analysis/OutputPDBFile.cpp
+++ b/src/analysis/OutputPDBFile.cpp
@@ -81,8 +81,8 @@ void OutputPDBFile::performAnalysis(){
for(unsigned j=0;j<getNumberOfDataPoints();++j){
afile.printf("DESCRIPTION: analysis data from calculation done at time %f \n",getLabel().c_str(),getTime() );
afile.printf(descr.c_str(),getWeight(j) );
- if( plumed.getAtoms().usingNaturalUnits() ) getReferenceConfiguration(j)->print( 1.0, afile, fmt );
- else getReferenceConfiguration(j)->print( plumed.getAtoms().getUnits().getLength()/0.1, afile, fmt );
+ if( plumed.getAtoms().usingNaturalUnits() ) getReferenceConfiguration(j,false)->print( 1.0, afile, fmt );
+ else getReferenceConfiguration(j,false)->print( plumed.getAtoms().getUnits().getLength()/0.1, afile, fmt );
}
afile.close();
}
diff --git a/src/analysis/ReadDissimilarityMatrix.cpp b/src/analysis/ReadDissimilarityMatrix.cpp
index b590488ed..3f78848c3 100644
--- a/src/analysis/ReadDissimilarityMatrix.cpp
+++ b/src/analysis/ReadDissimilarityMatrix.cpp
@@ -49,7 +49,7 @@ public:
ReadDissimilarityMatrix( const ActionOptions& ao );
unsigned getNumberOfDataPoints() const ;
/// This gives an error as if we read in the matrix we dont have the coordinates
- ReferenceConfiguration* getReferenceConfiguration( const unsigned& idata );
+ ReferenceConfiguration* getReferenceConfiguration( const unsigned& idata, const bool& calcdist );
/// This gives an error as if we read in the matrix we dont have the coordinates
void getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const ;
/// Tell everyone we have dissimilarities
@@ -142,8 +142,8 @@ double ReadDissimilarityMatrix::getDissimilarity( const unsigned& iframe, const
return dissimilarities( iframe, jframe );
}
-ReferenceConfiguration* ReadDissimilarityMatrix::getReferenceConfiguration( const unsigned& idata ){
- if( mydata ) return AnalysisBase::getReferenceConfiguration( idata );
+ReferenceConfiguration* ReadDissimilarityMatrix::getReferenceConfiguration( const unsigned& idata, const bool& calcdist ){
+ if( mydata ) return AnalysisBase::getReferenceConfiguration( idata, calcdist );
plumed_merror("cannot get reference configurations from read in dissimilarity matrix");
return NULL;
}
diff --git a/src/dimred/DimensionalityReductionBase.cpp b/src/dimred/DimensionalityReductionBase.cpp
index aee9e3424..0861b2d27 100644
--- a/src/dimred/DimensionalityReductionBase.cpp
+++ b/src/dimred/DimensionalityReductionBase.cpp
@@ -52,8 +52,8 @@ dimredbase(NULL)
log.printf(" projecting in %d dimensional space \n",nlow);
}
-ReferenceConfiguration* DimensionalityReductionBase::getReferenceConfiguration( const unsigned& idat ){
- ReferenceConfiguration* myref = mydata->getReferenceConfiguration( idat ); std::string num; myref->clearAllProperties();
+ReferenceConfiguration* DimensionalityReductionBase::getReferenceConfiguration( const unsigned& idat, const bool& calcdist ){
+ ReferenceConfiguration* myref = mydata->getReferenceConfiguration( idat, calcdist ); std::string num; myref->clearAllProperties();
for(unsigned i=0;i<nlow;++i){ Tools::convert(i+1,num); myref->attachProperty( getLabel() + "." + num, projections(idat,i) ); }
return myref;
}
diff --git a/src/dimred/DimensionalityReductionBase.h b/src/dimred/DimensionalityReductionBase.h
index 49fee7c3d..1046c3053 100644
--- a/src/dimred/DimensionalityReductionBase.h
+++ b/src/dimred/DimensionalityReductionBase.h
@@ -47,7 +47,7 @@ public:
/// Get the ith data point (this returns the projection)
void getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const ;
/// Get a reference configuration (this returns the projection)
- ReferenceConfiguration* getReferenceConfiguration( const unsigned& idata );
+ ReferenceConfiguration* getReferenceConfiguration( const unsigned& idata, const bool& calcdist );
/// Actually perform the analysis
void performAnalysis();
/// Calculate the projections of points
diff --git a/src/dimred/ProjectNonLandmarkPoints.cpp b/src/dimred/ProjectNonLandmarkPoints.cpp
index 7838a8880..c0bcc3959 100644
--- a/src/dimred/ProjectNonLandmarkPoints.cpp
+++ b/src/dimred/ProjectNonLandmarkPoints.cpp
@@ -56,7 +56,7 @@ public:
/// Get the ith data point (this returns the projection)
void getDataPoint( const unsigned& idat, std::vector<double>& point );
/// Get a reference configuration (this returns the projection)
- ReferenceConfiguration* getReferenceConfiguration( const unsigned& idat );
+ ReferenceConfiguration* getReferenceConfiguration( const unsigned& idat, const bool& calcdist );
/// This does nothing -- projections are calculated when getDataPoint and getReferenceConfiguration are called
void performAnalysis(){}
/// This just calls calculate stress in the underlying projection object
@@ -104,9 +104,9 @@ void ProjectNonLandmarkPoints::generateProjection( const unsigned& idat, std::ve
myminimiser.minimise( cgtol, point, &ProjectNonLandmarkPoints::calculateStress );
}
-ReferenceConfiguration* ProjectNonLandmarkPoints::getReferenceConfiguration( const unsigned& idat ){
+ReferenceConfiguration* ProjectNonLandmarkPoints::getReferenceConfiguration( const unsigned& idat, const bool& calcdist ){
std::vector<double> pp(nlow); generateProjection( idat, pp ); std::string num;
- ReferenceConfiguration* myref = mydata->getReferenceConfiguration( idat ); myref->clearAllProperties();
+ ReferenceConfiguration* myref = mydata->getReferenceConfiguration( idat, calcdist ); myref->clearAllProperties();
for(unsigned i=0;i<nlow;++i){ Tools::convert(i+1,num); myref->attachProperty( getLabel() + "." + num, pp[i] ); }
return myref;
}
diff --git a/src/reference/ReferenceConfiguration.cpp b/src/reference/ReferenceConfiguration.cpp
index 5b91c3d0f..288aafe15 100644
--- a/src/reference/ReferenceConfiguration.cpp
+++ b/src/reference/ReferenceConfiguration.cpp
@@ -149,7 +149,7 @@ void ReferenceConfiguration::attachProperty( const std::string& name, const doub
}
double property_distance( ReferenceConfiguration* ref1, ReferenceConfiguration* ref2, const bool& squared ){
- plumed_dbg_assert( ref1->property_values.size()>0 && ref2->propert_values.size()==ref1->property_values.size() );
+ plumed_dbg_assert( ref1->property_values.size()>0 && ref2->property_values.size()==ref1->property_values.size() );
unsigned nprop=ref1->property_values.size(); double dist=0;
for(unsigned i=0;i<nprop;++i){ double tmp=ref1->property_values[i]-ref2->property_values[i]; dist+=tmp*tmp; }
if(squared) return dist;
--
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