From 12dd30350d43947d1306ffb4a0474764dd41a976 Mon Sep 17 00:00:00 2001
From: Gareth Tribello <gareth.tribello@gmail.com>
Date: Mon, 2 May 2016 20:40:04 +0100
Subject: [PATCH] Using new weight actions in analysis
---
.../rt-mds/analysis.0.list_embed.reference | 2 +-
regtest/analysis/rt-mds/list_embed.reference | 2 +-
regtest/analysis/rt-mds/plumed.dat | 5 +-
src/analysis/Analysis.cpp | 182 ++++--------------
src/analysis/Analysis.h | 74 +------
src/bias/ReweightTemperature.cpp | 6 +-
src/vesselbase/ActionWithAveraging.cpp | 5 +-
src/vesselbase/ActionWithAveraging.h | 13 +-
src/vesselbase/ActionWithVessel.h | 2 -
9 files changed, 71 insertions(+), 220 deletions(-)
diff --git a/regtest/analysis/rt-mds/analysis.0.list_embed.reference b/regtest/analysis/rt-mds/analysis.0.list_embed.reference
index a5fdcd999..a0932b381 100644
--- a/regtest/analysis/rt-mds/analysis.0.list_embed.reference
+++ b/regtest/analysis/rt-mds/analysis.0.list_embed.reference
@@ -1,4 +1,4 @@
-#! FIELDS @17.1 @17.2
+#! FIELDS @18.1 @18.2
0.0873 0.0013
0.0535 0.0044
0.0150 0.0044
diff --git a/regtest/analysis/rt-mds/list_embed.reference b/regtest/analysis/rt-mds/list_embed.reference
index 6f40ac6e8..e653af32a 100644
--- a/regtest/analysis/rt-mds/list_embed.reference
+++ b/regtest/analysis/rt-mds/list_embed.reference
@@ -1,4 +1,4 @@
-#! FIELDS @17.1 @17.2
+#! FIELDS @18.1 @18.2
0.0594 0.0053
0.0683 0.0034
0.0705 0.0006
diff --git a/regtest/analysis/rt-mds/plumed.dat b/regtest/analysis/rt-mds/plumed.dat
index 385718a58..7fe2ce0ee 100755
--- a/regtest/analysis/rt-mds/plumed.dat
+++ b/regtest/analysis/rt-mds/plumed.dat
@@ -16,13 +16,16 @@ DISTANCE ATOMS=7,com LABEL=d7
UPPER_WALLS ARG=d7 AT=2.0 KAPPA=100.
COORDINATIONNUMBER SPECIES=1-7 MOMENTS=2-3 SWITCH={RATIONAL R_0=1.5 NN=8} LABEL=c1
+
+ww: REWEIGHT_TEMP REWEIGHT_TEMP=0.1 TEMP=0.2
+
CLASSICAL_MDS ...
ARG=c1.moment-2,c1.moment-3
- REWEIGHT_TEMP=0.1 TEMP=0.2
STRIDE=10
RUN=1000
NLOW_DIM=2
FMT=%8.4f
OUTPUT_FILE=list_embed
EMBEDDING_OFILE=embed
+ LOGWEIGHTS=ww
... CLASSICAL_MDS
diff --git a/src/analysis/Analysis.cpp b/src/analysis/Analysis.cpp
index a05f92f63..8dd4a7866 100644
--- a/src/analysis/Analysis.cpp
+++ b/src/analysis/Analysis.cpp
@@ -57,47 +57,28 @@ P(s',t) = \frac{ \sum_{t'}^t \delta( s(x) - s' ) \exp\left( +\frac{V(x,t')}{k_B
//+ENDPLUMEDOC
void Analysis::registerKeywords( Keywords& keys ){
- Action::registerKeywords( keys );
- ActionPilot::registerKeywords( keys );
- ActionAtomistic::registerKeywords( keys );
- ActionWithArguments::registerKeywords( keys );
+ vesselbase::ActionWithAveraging::registerKeywords( keys );
keys.use("ARG"); keys.reset_style("ARG","optional");
keys.add("atoms","ATOMS","the atoms whose positions we are tracking for the purpose of analysing the data");
keys.add("compulsory","METRIC","EUCLIDEAN","how are we measuring the distances between configurations");
- keys.add("compulsory","STRIDE","1","the frequency with which data should be stored for analysis");
- keys.addFlag("USE_ALL_DATA",false,"use the data from the entire trajectory to perform the analysis");
- keys.add("compulsory","RUN","the frequency with which to run the analysis algorithm. This is not required if you specify USE_ALL_DATA");
+ keys.add("compulsory","RUN","0","the frequency with which to run the analysis algorithm. The default value of zero assumes you want to analyse the whole trajectory");
keys.add("optional","FMT","the format that should be used in analysis output files");
- keys.addFlag("REWEIGHT_BIAS",false,"reweight the data using all the biases acting on the dynamics. For more information see \\ref reweighting.");
- keys.add("optional","TEMP","the system temperature. This is required if you are reweighting or doing free energies.");
- keys.add("optional","REWEIGHT_TEMP","reweight data from a trajectory at one temperature and output the probability "
- "distribution at a second temperature. For more information see \\ref reweighting. "
- "This is not possible during postprocessing.");
keys.addFlag("WRITE_CHECKPOINT",false,"write out a checkpoint so that the analysis can be restarted in a later run");
keys.add("hidden","REUSE_DATA_FROM","eventually this will allow you to analyse the same set of data multiple times");
keys.add("hidden","IGNORE_REWEIGHTING","this allows you to ignore any reweighting factors");
- keys.use("RESTART");
- keys.use("UPDATE_FROM");
- keys.use("UPDATE_UNTIL");
- ActionWithVessel::registerKeywords( keys ); keys.remove("TOL");
+ keys.use("RESTART"); keys.use("UPDATE_FROM"); keys.use("UPDATE_UNTIL"); keys.remove("TOL");
}
Analysis::Analysis(const ActionOptions&ao):
Action(ao),
-ActionPilot(ao),
-ActionAtomistic(ao),
-ActionWithArguments(ao),
-ActionWithVessel(ao),
-single_run(true),
+ActionWithAveraging(ao),
nomemory(true),
write_chq(false),
reusing_data(false),
ignore_reweight(false),
-freq(0),
-needeng(false),
idata(0),
-firstAnalysisDone(false),
-old_norm(0.0),
+//firstAnalysisDone(false),
+//old_norm(0.0),
ofmt("%f"),
current_args(getNumberOfArguments()),
argument_names(getNumberOfArguments())
@@ -132,59 +113,18 @@ argument_names(getNumberOfArguments())
if( ignore_reweight ) log.printf(" reusing data stored by %s but ignoring all reweighting\n",prev_analysis.c_str() );
else log.printf(" reusing data stored by %s\n",prev_analysis.c_str() );
} else {
- if( keywords.exists("REWEIGHT_BIAS") ){
- bool dobias; parseFlag("REWEIGHT_BIAS",dobias);
- if( dobias ){
- std::vector<ActionWithValue*> all=plumed.getActionSet().select<ActionWithValue*>();
- if( all.empty() ) error("your input file is not telling plumed to calculate anything");
- std::vector<Value*> arg( getArguments() );
- log.printf(" reweigting using the following biases ");
- for(unsigned j=0;j<all.size();j++){
- std::string flab; flab=all[j]->getLabel() + ".rbias";
- if( all[j]->exists(flab) ){
- biases.push_back( all[j]->copyOutput(flab) );
- arg.push_back( all[j]->copyOutput(flab) );
- log.printf(" %s",flab.c_str());
- } else {
- std::string flab2; flab2=all[j]->getLabel() + ".bias";
- if( all[j]->exists(flab2) ){
- biases.push_back( all[j]->copyOutput(flab2) );
- arg.push_back( all[j]->copyOutput(flab2) );
- log.printf(" %s",flab2.c_str());
- }
- }
- }
- log.printf("\n");
- if( biases.empty() ) error("you are asking to reweight bias but there does not appear to be a bias acting on your system");
- requestArguments( arg );
- }
- }
-
- rtemp=0;
- if( keywords.exists("REWEIGHT_TEMP") ) parse("REWEIGHT_TEMP",rtemp);
- if( rtemp!=0 ){
- needeng=true;
- log.printf(" reweighting simulation to probabilities at temperature %f\n",rtemp);
- rtemp*=plumed.getAtoms().getKBoltzmann();
+ parse("RUN",freq);
+ if( freq==0 ){
+ log.printf(" analyzing all data in trajectory\n");
+ } else {
+ if( freq%getStride()!=0 ) error("frequncy of running is not a multiple of the stride");
+ log.printf(" running analysis every %u steps\n",freq);
+ ndata=freq/getStride(); data.resize( ndata ); logweights.resize( ndata );
+ for(unsigned i=0;i<ndata;++i){
+ data[i]=metricRegister().create<ReferenceConfiguration>( metricname );
+ data[i]->setNamesAndAtomNumbers( getAbsoluteIndexes(), argument_names );
+ }
}
- simtemp=0.; parse("TEMP",simtemp);
- if(simtemp>0) simtemp*=plumed.getAtoms().getKBoltzmann();
- else simtemp=plumed.getAtoms().getKbT();
-
- if( rtemp>0 || !biases.empty() ){
- if(simtemp==0) error("The MD engine does not pass the temperature to plumed so you have to specify it using TEMP");
- }
-
- if( keywords.exists("USE_ALL_DATA") ){
- parseFlag("USE_ALL_DATA",single_run);
- if( !single_run ){
- unsigned astride; parse("RUN",astride);
- log.printf(" running analysis every %u steps\n",astride);
- setAnalysisStride( false, astride );
- } else {
- log.printf(" analyzing all data in trajectory\n");
- }
- }
parseFlag("WRITE_CHECKPOINT",write_chq);
if( write_chq && single_run ){
write_chq=false;
@@ -208,26 +148,12 @@ argument_names(getNumberOfArguments())
rfile.open( filename.c_str() ); // In overwrite mode automatically because there is no restart
}
if( write_chq ){
- rfile.addConstantField("old_normalization");
+ //rfile.addConstantField("old_normalization");
for(unsigned i=0;i<getNumberOfArguments();++i) rfile.setupPrintValue( getPntrToArgument(i) );
}
}
}
-void Analysis::setAnalysisStride( const bool& use_all, const unsigned& astride ){
- if( freq>0 && astride!=freq ) error("each histogram can only be output with one stride");
- else if( use_all ) return;
-
- freq=astride; single_run=false;
- if( astride%getStride()!= 0 ) error("Frequncy of running is not a multiple of the stride");
- ndata=freq/getStride(); data.resize( ndata );
- for(unsigned i=0;i<ndata;++i){
- data[i]=metricRegister().create<ReferenceConfiguration>( metricname );
- data[i]->setNamesAndAtomNumbers( getAbsoluteIndexes(), argument_names );
- }
- logweights.resize( ndata );
-}
-
void Analysis::readDataFromFile( const std::string& filename ){
FILE* fp=fopen(filename.c_str(),"r");
if(fp!=NULL){
@@ -243,7 +169,7 @@ void Analysis::readDataFromFile( const std::string& filename ){
error("frequency of data storage in " + filename + " is not equal to frequency of data storage plumed.dat file");
}
data[idata]->parse("LOG_WEIGHT",logweights[idata]);
- data[idata]->parse("OLD_NORM",old_norm);
+ //data[idata]->parse("OLD_NORM",old_norm);
data[idata]->checkRead();
idata++; first=false; oldtstep=tstep;
} else{
@@ -252,7 +178,7 @@ void Analysis::readDataFromFile( const std::string& filename ){
}
fclose(fp);
}
- if(old_norm>0) firstAnalysisDone=true;
+ // if(old_norm>0) firstAnalysisDone=true;
}
void Analysis::parseOutputFile( const std::string& key, std::string& filename ){
@@ -266,32 +192,11 @@ void Analysis::parseOutputFile( const std::string& key, std::string& filename ){
}
}
-void Analysis::prepare(){
- if(needeng) plumed.getAtoms().setCollectEnergy(true);
-}
-
-void Analysis::calculate(){
-// do nothing
-}
-
void Analysis::accumulate(){
// Don't store the first step (also don't store if we are getting data from elsewhere)
if( (!single_run && getStep()==0) || reusing_data ) return;
// This is used when we have a full quota of data from the first run
if( !single_run && idata==logweights.size() ) return;
-
- // Retrieve the bias
- double bias=0.0; for(unsigned i=0;i<biases.size();++i) bias+=biases[i]->get();
-
- double ww=0;
- if(needeng){
- double energy=plumed.getAtoms().getEnergy()+bias;
- // Reweighting because of temperature difference
- ww=-( (1.0/rtemp) - (1.0/simtemp) )*(energy+bias);
- }
- // Reweighting because of biases
- if( !biases.empty() ) ww += bias/ simtemp;
-
// Get the arguments ready to transfer to reference configuration
for(unsigned i=0;i<getNumberOfArguments();++i) current_args[i]=getArgument(i);
@@ -300,17 +205,17 @@ void Analysis::accumulate(){
plumed_dbg_assert( data.size()==idata+1 );
data[idata]->setNamesAndAtomNumbers( getAbsoluteIndexes(), argument_names );
data[idata]->setReferenceConfig( getPositions(), current_args, getMetric() );
- logweights.push_back(ww);
+ logweights.push_back(lweight);
} else {
// Get the arguments and store them in a vector of vectors
data[idata]->setReferenceConfig( getPositions(), current_args, getMetric() );
- logweights[idata] = ww;
+ logweights[idata] = lweight;
}
// Write data to checkpoint file
if( write_chq ){
rfile.rewind();
- data[idata]->print( rfile, getTime(), logweights[idata], atoms.getUnits().getLength()/0.1, old_norm );
+ data[idata]->print( rfile, getTime(), logweights[idata], atoms.getUnits().getLength()/0.1, 1.0 ); //old_norm );
rfile.flush();
}
// Increment data counter
@@ -344,7 +249,7 @@ void Analysis::finalizeWeights( const bool& ignore_weights ){
// Check that we have the correct ammount of data
if( !reusing_data && idata!=logweights.size() ) error("something has gone wrong. Am trying to run analysis but I don't have sufficient data");
- norm=0; // Reset normalization constant
+ double norm=0; // Reset normalization constant
if( ignore_weights ){
for(unsigned i=0;i<logweights.size();++i){
data[i]->setWeight(1.0); norm+=1.0;
@@ -365,18 +270,20 @@ void Analysis::finalizeWeights( const bool& ignore_weights ){
}
// Calculate normalized weights (with memory)
} else {
- if( !firstAnalysisDone ) finalizeWeightsNoLogSums( 1.0 );
- else finalizeWeightsNoLogSums( old_norm );
+ plumed_merror("analysis can now only support block averages");
+ // if( !firstAnalysisDone )
+ // finalizeWeightsNoLogSums( 1.0 );
+ // else finalizeWeightsNoLogSums( old_norm );
}
}
-void Analysis::finalizeWeightsNoLogSums( const double& onorm ){
- if( !reusing_data && idata!=logweights.size() ) error("something has gone wrong. Am trying to run analysis but I don't have sufficient data");
- // Calculate normalization constant
- norm=0; for(unsigned i=0;i<logweights.size();++i) norm+=exp( logweights[i] );
- // Calculate weights (with memory)
- for(unsigned i=0;i<logweights.size();++i) data[i]->setWeight( exp( logweights[i] ) / onorm );
-}
+// void Analysis::finalizeWeightsNoLogSums( const double& onorm ){
+// if( !reusing_data && idata!=logweights.size() ) error("something has gone wrong. Am trying to run analysis but I don't have sufficient data");
+// // Calculate normalization constant
+// double norm=0; for(unsigned i=0;i<logweights.size();++i) norm+=exp( logweights[i] );
+// // Calculate weights (with memory)
+// for(unsigned i=0;i<logweights.size();++i) data[i]->setWeight( exp( logweights[i] ) / norm );
+// }
void Analysis::getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const {
plumed_dbg_assert( getNumberOfAtoms()==0 );
@@ -399,27 +306,18 @@ void Analysis::runAnalysis(){
finalizeWeights( ignore_reweight );
} else {
mydatastash->finalizeWeights( ignore_reweight );
- norm=mydatastash->retrieveNorm();
+ // norm=mydatastash->retrieveNorm();
}
// This ensures everything is set up to run the calculation
- if( single_run ) setAnalysisStride( single_run, freq );
+ // if( single_run ) setAnalysisStride( single_run, freq );
// And run the analysis
performAnalysis(); idata=0;
// Update total normalization constant
- old_norm+=norm; firstAnalysisDone=true;
-
-}
-
-double Analysis::getNormalization() const {
- if( nomemory || !firstAnalysisDone ) return norm;
- return ( 1. + norm/old_norm );
-}
+ // old_norm+=norm; firstAnalysisDone=true;
-double Analysis::getTemp() const {
- return simtemp;
}
-void Analysis::update(){
+void Analysis::performOperations( const bool& from_update ){
accumulate();
if( !single_run ){
if( getStep()>0 && getStep()%freq==0 ) runAnalysis();
@@ -434,7 +332,7 @@ bool Analysis::getPeriodicityInformation(const unsigned& i, std::string& dmin, s
}
void Analysis::runFinalJobs() {
- if( !single_run ) return;
+ if( freq>0 ) return;
if( getNumberOfDataPoints()==0 ) error("no data is available for analysis");
runAnalysis();
}
diff --git a/src/analysis/Analysis.h b/src/analysis/Analysis.h
index ac716c064..0a59bb770 100644
--- a/src/analysis/Analysis.h
+++ b/src/analysis/Analysis.h
@@ -22,10 +22,7 @@
#ifndef __PLUMED_analysis_Analysis_h
#define __PLUMED_analysis_Analysis_h
-#include "core/ActionPilot.h"
-#include "core/ActionAtomistic.h"
-#include "core/ActionWithArguments.h"
-#include "vesselbase/ActionWithVessel.h"
+#include "vesselbase/ActionWithAveraging.h"
#define PLUMED_ANALYSIS_INIT(ao) Action(ao),Analysis(ao)
@@ -42,12 +39,7 @@ is information as to how to go about implementing a new analysis method.
*/
-class Analysis :
- public ActionPilot,
- public ActionAtomistic,
- public ActionWithArguments,
- public vesselbase::ActionWithVessel
- {
+class Analysis : public vesselbase::ActionWithAveraging {
private:
/// Are we running only once for the whole trajectory
bool single_run;
@@ -71,16 +63,14 @@ private:
double rtemp;
/// Do we need the energy (are we reweighting at a different temperature)
bool needeng;
-/// The biases we are using in reweighting and the args we store them separately
- std::vector<Value*> biases;
/// The piece of data we are inserting
unsigned idata;
/// The weights of all the data points
std::vector<double> logweights;
/// Have we analyzed the data for the first time
- bool firstAnalysisDone;
+// bool firstAnalysisDone;
/// The value of the old normalization constant
- double norm, old_norm;
+// double norm, old_norm;
/// The format to use in output files
std::string ofmt;
/// Tempory vector to store values of arguments
@@ -91,11 +81,6 @@ private:
OFile rfile;
/// Read in data from a file
void readDataFromFile( const std::string& filename );
-/// This retrieves the value of norm from the analysis action.
-/// It is only used to transfer data from one analysis action to
-/// another. You should never need to use it. If you think you need it
-/// you probably need getNormalization()
- double retrieveNorm() const ;
/// Get the metric if we are using malonobius distance and flexible hill
std::vector<double> getMetric() const ;
protected:
@@ -109,8 +94,6 @@ protected:
std::vector<ReferenceConfiguration*> data;
/// Get the name of the metric we are using to measure distances
std::string getMetricName() const ;
-/// Return the number of arguments (this overwrites the one in ActionWithArguments)
- unsigned getNumberOfArguments() const;
/// Return the number of data points
unsigned getNumberOfDataPoints() const;
/// Return the weight of the ith point
@@ -119,37 +102,22 @@ protected:
void getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const ;
/// Returns true if argument i is periodic together with the domain
bool getPeriodicityInformation(const unsigned& i, std::string& dmin, std::string& dmax);
-/// Return the normalization constant
- double getNormalization() const;
-/// Return the set temperature (N.B. k_B T is what is returned by this function)
- double getTemp () const;
/// Are we analyzing each data block separately (if we are not this also returns the old normalization )
bool usingMemory() const;
-/// Overwrite ActionWithArguments getArguments() so that we don't return
-/// the bias
- std::vector<Value*> getArguments();
/// Return the format to use for numbers in output files
std::string getOutputFormat() const ;
/// Finalize the weights without using the log sums
- void finalizeWeightsNoLogSums( const double& onorm );
+// void finalizeWeightsNoLogSums( const double& onorm );
public:
static void registerKeywords( Keywords& keys );
explicit Analysis(const ActionOptions&);
~Analysis();
- void prepare();
- void calculate();
- void update();
void accumulate();
+ void performOperations( const bool& from_update );
virtual void performAnalysis()=0;
- void apply(){}
void runFinalJobs();
void runAnalysis();
- void lockRequests();
- void unlockRequests();
- void calculateNumericalDerivatives( ActionWithValue* a=NULL ){ plumed_error(); }
bool isPeriodic(){ plumed_error(); return false; }
- unsigned getNumberOfDerivatives(){ return 0; }
- virtual void setAnalysisStride( const bool& use_all, const unsigned& astride );
/// Convert the stored log weights to proper weights
virtual void finalizeWeights( const bool& ignore_weights );
};
@@ -159,18 +127,6 @@ std::string Analysis::getMetricName() const {
return metricname;
}
-inline
-void Analysis::lockRequests(){
- ActionAtomistic::lockRequests();
- ActionWithArguments::lockRequests();
-}
-
-inline
-void Analysis::unlockRequests(){
- ActionAtomistic::unlockRequests();
- ActionWithArguments::unlockRequests();
-}
-
inline
unsigned Analysis::getNumberOfDataPoints() const {
if( !reusing_data ){
@@ -190,24 +146,6 @@ bool Analysis::usingMemory() const {
}
}
-inline
-unsigned Analysis::getNumberOfArguments() const {
- unsigned nargs=ActionWithArguments::getNumberOfArguments();
- return nargs - biases.size();
-}
-
-inline
-double Analysis::retrieveNorm() const {
- return norm;
-}
-
-inline
-std::vector<Value*> Analysis::getArguments(){
- std::vector<Value*> arg_vals( ActionWithArguments::getArguments() );
- for(unsigned i=0;i<biases.size();++i) arg_vals.erase(arg_vals.end()-1);
- return arg_vals;
-}
-
inline
std::string Analysis::getOutputFormat() const {
return ofmt;
diff --git a/src/bias/ReweightTemperature.cpp b/src/bias/ReweightTemperature.cpp
index e503ebfd7..2d25876c7 100644
--- a/src/bias/ReweightTemperature.cpp
+++ b/src/bias/ReweightTemperature.cpp
@@ -44,6 +44,7 @@ private:
public:
static void registerKeywords(Keywords&);
explicit ReweightTemperature(const ActionOptions&ao);
+ void prepare();
double getLogWeight() const ;
};
@@ -59,7 +60,6 @@ ReweightTemperature::ReweightTemperature(const ActionOptions&ao):
Action(ao),
ReweightBase(ao)
{
- plumed.getAtoms().setCollectEnergy(true);
parse("REWEIGHT_TEMP",rtemp);
log.printf(" reweighting simulation to probabilities at temperature %f\n",rtemp);
rtemp*=plumed.getAtoms().getKBoltzmann();
@@ -67,6 +67,10 @@ ReweightBase(ao)
retrieveAllBiases( "bias", biases );
}
+void ReweightTemperature::prepare(){
+ plumed.getAtoms().setCollectEnergy(true);
+}
+
double ReweightTemperature::getLogWeight() const {
// Retrieve the bias
double bias=0.0; for(unsigned i=0;i<biases.size();++i) bias+=biases[i]->get();
diff --git a/src/vesselbase/ActionWithAveraging.cpp b/src/vesselbase/ActionWithAveraging.cpp
index abe50da5c..372bb272c 100644
--- a/src/vesselbase/ActionWithAveraging.cpp
+++ b/src/vesselbase/ActionWithAveraging.cpp
@@ -43,6 +43,7 @@ ActionAtomistic(ao),
ActionWithArguments(ao),
ActionWithValue(ao),
ActionWithVessel(ao),
+lweight(0),cweight(0),
myaverage(NULL),
useRunAllTasks(false),
clearstride(0)
@@ -100,9 +101,9 @@ void ActionWithAveraging::update(){
// Calculate the weight for all reweighting
if ( weights.size()>0 ){
double sum=0; for(unsigned i=0;i<weights.size();++i) sum+=weights[i]->get();
- cweight = exp( sum );
+ lweight=sum; cweight = exp( sum );
} else {
- cweight=1.0;
+ lweight=0; cweight=1.0;
}
// Prepare to do the averaging
prepareForAveraging();
diff --git a/src/vesselbase/ActionWithAveraging.h b/src/vesselbase/ActionWithAveraging.h
index 8a91b2657..295085591 100644
--- a/src/vesselbase/ActionWithAveraging.h
+++ b/src/vesselbase/ActionWithAveraging.h
@@ -62,8 +62,8 @@ private:
/// Are we accumulated the unormalized quantity
bool unormalised;
protected:
-/// The current weight
- double cweight;
+/// The current weight and its logarithm
+ double lweight, cweight;
/// Set the averaging action
void setAveragingAction( AveragingVessel* av_vessel, const bool& usetasks );
public:
@@ -74,6 +74,8 @@ public:
void calculateNumericalDerivatives(PLMD::ActionWithValue*);
virtual unsigned getNumberOfDerivatives(){ return 0; }
unsigned getNumberOfArguments() const ;
+/// Overwrite ActionWithArguments getArguments() so that we don't return the bias
+ std::vector<Value*> getArguments();
void calculate(){}
void apply(){}
void update();
@@ -92,6 +94,13 @@ unsigned ActionWithAveraging::getNumberOfArguments() const {
return ActionWithArguments::getNumberOfArguments() - weights.size();
}
+inline
+std::vector<Value*> ActionWithAveraging::getArguments(){
+ std::vector<Value*> arg_vals( ActionWithArguments::getArguments() );
+ for(unsigned i=0;i<weights.size();++i) arg_vals.erase(arg_vals.end()-1);
+ return arg_vals;
+}
+
}
}
#endif
diff --git a/src/vesselbase/ActionWithVessel.h b/src/vesselbase/ActionWithVessel.h
index 2abc5d441..6225bfe93 100644
--- a/src/vesselbase/ActionWithVessel.h
+++ b/src/vesselbase/ActionWithVessel.h
@@ -188,8 +188,6 @@ public:
Vessel* getVesselWithName( const std::string& mynam );
/// Does the weight have derivatives
bool weightWithDerivatives() const ;
-/// This is used to set the stride for the output of histograms
- virtual void setAnalysisStride( const bool& use_all, const unsigned& astride ){}
/// Return the position in the current task list
unsigned getPositionInCurrentTaskList( const unsigned& myind ) const ;
};
--
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