diff --git a/src/analysis/Histogram.cpp b/src/analysis/Histogram.cpp
index 48e749bc03cda52d9f115853d3c230bede0c1cbc..16b909bfe670f8803fb568ba8e18e9a0cf26b71a 100644
--- a/src/analysis/Histogram.cpp
+++ b/src/analysis/Histogram.cpp
@@ -166,7 +166,7 @@ void Histogram::performAnalysis(){
double weight; std::vector<double> point( getNumberOfArguments() );
for(unsigned i=0;i<getNumberOfDataPoints();++i){
getDataPoint( i, point, weight );
- KernelFunctions kernel( point, bw, kerneltype, weight, true);
+ KernelFunctions kernel( point, bw, kerneltype, false, weight, true);
gg->addKernel( kernel );
}
diff --git a/src/cltools/SumHills.cpp b/src/cltools/SumHills.cpp
index 6e03a55303678dc9bf8f7019046626867b7af982..99f7da2646b4e2c2013a633c54a2a0d88de95c40 100644
--- a/src/cltools/SumHills.cpp
+++ b/src/cltools/SumHills.cpp
@@ -153,6 +153,36 @@ plumed sum_hills --hills PATHTOMYHILLSFILE --fmt %8.3f
where here we chose a float with length of 8 and 3 digits
+The output can be named in a arbitrary way :
+
+\verbatim
+plumed sum_hills --hills PATHTOMYHILLSFILE --outfile myfes.dat
+\endverbatim
+
+will produce a file myfes.dat which contains the free energy.
+
+If you use stride, this keyword is the suffix
+
+\verbatim
+plumed sum_hills --hills PATHTOMYHILLSFILE --outfile myfes_ --stride 100
+\endverbatim
+
+will produce myfes_0.dat, myfes_1.dat, myfes_2.dat etc.
+
+The same is true for the output coming from histogram corrections
+\verbatim
+plumed sum_hills --histo HILLS --kt 2.5 --sigma 0.01 --outhisto mycorrection.dat
+\endverbatim
+
+is producing a file mycorrection.dat
+while, when using stride, this is the suffix
+
+\verbatim
+plumed sum_hills --histo HILLS --kt 2.5 --sigma 0.01 --outhisto mycorrection_ --stride 100
+\endverbatim
+
+that gives mycorrection_0.dat, mycorrection_1.dat, mycorrection_3.dat etc..
+
*/
//+ENDPLUMEDOC
@@ -377,15 +407,22 @@ int CLToolSumHills::main(FILE* in,FILE*out,Communicator& pc){
plumed_massert(parse("--kt",kt),"if you make a dimensionality reduction (--idw) or a histogram (--histo) then you need to define --kt ");
}
- /*
-
- different implementation through function
-
- */
-
std::string addme;
+
actioninput.push_back("FUNCSUMHILLS");
actioninput.push_back("ISCLTOOL");
+
+ // set names
+ std::string outfile;
+ if(parse("--outfile",outfile)){
+ actioninput.push_back("btim="+outfile);
+ }
+ std::string outhisto;
+ if(parse("--outhisto",outhisto)){
+ actioninput.push_back("OUTHISTO="+outhisto);
+ }
+
+
addme="ARG=";
for(unsigned i=0;i<(ncv-1);i++){
if(cvs[i].size()==1){
diff --git a/src/tools/BiasRepresentation.cpp b/src/tools/BiasRepresentation.cpp
index 7d27322341354015926db7cce0b878603587fdde..bdbb47afab7010e4e49d50211b6bfcba36231a3e 100644
--- a/src/tools/BiasRepresentation.cpp
+++ b/src/tools/BiasRepresentation.cpp
@@ -113,7 +113,7 @@ KernelFunctions* BiasRepresentation::readFromPoint(IFile *ifile){
ifile->scanField(names[i],cc[i]);
}
double h=1.0;
- return new KernelFunctions(cc,histosigma,"gaussian",h,false);
+ return new KernelFunctions(cc,histosigma,"gaussian",false,h,false);
}
void BiasRepresentation::pushKernel( IFile *ifile ){
KernelFunctions *kk;
diff --git a/src/tools/KernelFunctions.cpp b/src/tools/KernelFunctions.cpp
index d1fd90c95aca0e62e35c7cd8ca63dc4bf401d76c..197ddc31c1888172a78bf7cefb73e1cdb9f0a692 100644
--- a/src/tools/KernelFunctions.cpp
+++ b/src/tools/KernelFunctions.cpp
@@ -85,14 +85,12 @@ the kernels we can use in this method.
*/
//+ENDPLUMEDOC
-KernelFunctions::KernelFunctions( const std::vector<double>& at, const std::vector<double>& sig, const std::string& type, const double& w, const bool& norm ):
+KernelFunctions::KernelFunctions( const std::vector<double>& at, const std::vector<double>& sig, const std::string& type, const bool multivariate, const double& w, const bool norm ):
center(at),
width(sig)
{
- unsigned ncv=center.size();
- if( width.size()==ncv ) diagonal=true;
- else if( width.size()==(ncv*(ncv+1))/2 ) diagonal=false;
- else plumed_merror("specified sigma is neither diagonal or full covariance matrix");
+ if (multivariate==true)diagonal=false;
+ if (multivariate==false)diagonal=true;
// Setup the kernel type
if(type=="GAUSSIAN" || type=="gaussian"){
@@ -105,10 +103,10 @@ width(sig)
if( norm ){
double det;
+ unsigned ncv=ndim();
if(diagonal){
det=1; for(unsigned i=0;i<width.size();++i) det*=width[i];
} else {
- unsigned ncv=ndim();
Matrix<double> mymatrix( getMatrix() ), myinv( ncv, ncv );
Invert(mymatrix,myinv); double logd;
logdet( myinv, logd );
@@ -233,13 +231,16 @@ double KernelFunctions::evaluate( const std::vector<Value*>& pos, std::vector<do
KernelFunctions* KernelFunctions::read( IFile* ifile, const std::vector<std::string>& valnames ){
std::string sss; ifile->scanField("multivariate",sss);
std::vector<double> cc( valnames.size() ), sig;
+ bool multivariate;
if( sss=="false" ){
+ multivariate=false;
sig.resize( valnames.size() );
for(unsigned i=0;i<valnames.size();++i){
ifile->scanField(valnames[i],cc[i]);
ifile->scanField("sigma_"+valnames[i],sig[i]);
}
} else if( sss=="true" ){
+ multivariate=true;
unsigned ncv=valnames.size();
sig.resize( (ncv*(ncv+1))/2 );
Matrix<double> upper(ncv,ncv), lower(ncv,ncv);
@@ -257,7 +258,7 @@ KernelFunctions* KernelFunctions::read( IFile* ifile, const std::vector<std::str
plumed_merror("multivariate flag should equal true or false");
}
double h; ifile->scanField("height",h);
- return new KernelFunctions( cc, sig, "gaussian", h, false );
+ return new KernelFunctions( cc, sig, "gaussian", multivariate ,h, false);
}
}
diff --git a/src/tools/KernelFunctions.h b/src/tools/KernelFunctions.h
index 78fc5bba5d3889d3a96e62dc121f0d1a8d6dea00..de80735a9decfbd8dfdac2094b2cd1c96e2b4321 100644
--- a/src/tools/KernelFunctions.h
+++ b/src/tools/KernelFunctions.h
@@ -47,7 +47,7 @@ private:
/// Get the cutoff for a kernel
double getCutoff( const double& width ) const ;
public:
- KernelFunctions( const std::vector<double>& at, const std::vector<double>& sig, const std::string& type, const double& w, const bool& norm );
+ KernelFunctions( const std::vector<double>& at, const std::vector<double>& sig, const std::string& type, const bool multivariate ,const double& w, const bool norm );
/// Get the dimensionality of the kernel
unsigned ndim() const;
/// Get the position of the center