HISTOGRAM: small changes to have nice free energy

src/analysis/Histogram.cpp

@@ -165,7 +165,6 @@ fenergy(false)
 
   parseFlag("FREQUENCY",frequency);
   parseFlag("FREE-ENERGY",fenergy);
-  if(fenergy) frequency=true;
   if(getTemp()<=0&&fenergy) plumed_merror("Set the temperature (TEMP) if you want a free energy.");
   checkRead();
 
@@ -222,7 +221,10 @@ void Histogram::performAnalysis(){
 
   // Normalize the histogram
   if(!frequency) gg->scaleAllValuesAndDerivatives( 1.0 / getNormalization() );
-  if(fenergy) gg->logAllValuesAndDerivatives( -getTemp() * plumed.getAtoms().getKBoltzmann() );
+  if(fenergy) {
+    gg->logAllValuesAndDerivatives( -getTemp() * plumed.getAtoms().getKBoltzmann() );
+    gg->setMinToZero();
+  }
 
   // Write the grid to a file
   OFile gridfile; gridfile.link(*this); gridfile.setBackupString("analysis");

src/tools/Grid.cpp

@@ -517,6 +517,12 @@ void Grid::logAllValuesAndDerivatives( const double& scalef ){
   }
 }
 
+void Grid::setMinToZero(){
+  double min=grid_[0];
+  for(unsigned i=1;i<grid_.size();++i) if(grid_[i]<min) min=grid_[i];
+  for(unsigned i=0;i<grid_.size();++i) grid_[i] -= min; 
+}
+
 void Grid::applyFunctionAllValuesAndDerivatives( double (*func)(double val), double (*funcder)(double valder) ){
   if(usederiv_){
      for(unsigned i=0;i<grid_.size();++i){

src/tools/Grid.h

@@ -175,6 +175,8 @@ public:
  virtual void scaleAllValuesAndDerivatives( const double& scalef );
 /// Takes the scalef times the logarithm of all grid values and derivatives 
  virtual void logAllValuesAndDerivatives( const double& scalef );
+/// Set the minimum value of the grid to zero and translates accordingly
+ virtual void setMinToZero();
 /// apply function: takes  pointer to  function that accepts a double and apply 
  virtual void applyFunctionAllValuesAndDerivatives( double (*func)(double val), double (*funcder)(double valder) );
 /// add a kernel function to the grid