diff --git a/CHANGES/Unreleased.txt b/CHANGES/Unreleased.txt
index e6d50af6e2a5198632b473ee1f8c61209f33d29a..0c4c1f8dc29014ba47f819df72594e7af8d2e203 100644
--- a/CHANGES/Unreleased.txt
+++ b/CHANGES/Unreleased.txt
@@ -42,6 +42,8 @@ Changes from version 2.0 which are relevant for users:
- \ref HISTOGRAM: GRID_SPACING (alternative to GRID_BIN to set grid spacing),
FREQUENCY and FREE-ENERGY flags in addition to standard probability density,
additional option for KERNEL=NONE to accumulate standard histograms.
+ - \ref sum_hills: added options --spacing (alternative to --bin to set grid spacing)
+ and --setmintozero to translate the minimum of the output files to zero.
- New features in MD patches (require repatch):
- Gromacs 4.6.5 support \ref COMMITTOR analysis.
- Gromacs 4.6.5 can be now be used to perform energy minimization.
diff --git a/src/cltools/SumHills.cpp b/src/cltools/SumHills.cpp
index 43c1a0ee4410de5631d0fdd438ccc3c6fddf0146..fdc932f8c42715ab86b47bd1a0fb61ff865921fd 100644
--- a/src/cltools/SumHills.cpp
+++ b/src/cltools/SumHills.cpp
@@ -206,6 +206,7 @@ void CLToolSumHills::registerKeywords( Keywords& keys ){
keys.add("optional","--min","the lower bounds for the grid");
keys.add("optional","--max","the upper bounds for the grid");
keys.add("optional","--bin","the number of bins for the grid");
+ keys.add("optional","--spacing","grid spacing, alternative to the number of bins");
keys.add("optional","--idw","specify the variables to be integrated (default is all)");
keys.add("optional","--outfile","specify the outputfile for sumhills");
keys.add("optional","--outhisto","specify the outputfile for the histogram");
@@ -213,6 +214,7 @@ void CLToolSumHills::registerKeywords( Keywords& keys ){
keys.add("optional","--sigma"," a vector that specify the sigma for binning (only needed when doing histogram ");
keys.addFlag("--negbias",false," print the negative bias instead of the free energy (only needed with welltempered runs and flexible hills) ");
keys.addFlag("--nohistory",false," to be used with --stride: it splits the bias/histogram in pieces without previous history ");
+ keys.addFlag("--mintozero",false," it translate all the minimum value in bias/histogram to zero (usefull to compare results) ");
keys.add("optional","--fmt","specify the output format");
}
@@ -301,6 +303,12 @@ int CLToolSumHills::main(FILE* in,FILE*out,Communicator& pc){
if(gbin.size()!=cvs.size() && gbin.size()!=0) plumed_merror("not enough values for --bin");
grid_has_bin=true;
}
+ vector<std::string> gspacing(cvs.size());
+ bool grid_has_spacing; grid_has_spacing=false;
+ if(parseVector("--spacing",gspacing)){
+ if(gspacing.size()!=cvs.size() && gspacing.size()!=0) plumed_merror("not enough values for --spacing");
+ grid_has_spacing=true;
+ }
// allowed: no grids only bin
// not allowed: partial grid definition
plumed_massert( gmin.size()==gmax.size() && (gmin.size()==0 || gmin.size()==cvs.size() ) ,"you should specify --min and --max together with same number of components");
@@ -453,10 +461,10 @@ int CLToolSumHills::main(FILE* in,FILE*out,Communicator& pc){
if(grid_has_bin){
addme="GRID_BIN="; for(unsigned i=0;i<(ncv-1);i++)addme+=gbin[i]+","; addme+=gbin[ncv-1];
actioninput.push_back(addme);
-// }else{
-// //automatic bin: 50 per dimension;
-// addme="GRID_BIN="; for(unsigned i=0;i<(ncv-1);i++)addme+="50,"; addme+="50";
-// actioninput.push_back(addme);
+ }
+ if(grid_has_spacing){
+ addme="GRID_SPACING="; for(unsigned i=0;i<(ncv-1);i++)addme+=gspacing[i]+","; addme+=gspacing[ncv-1];
+ actioninput.push_back(addme);
}
std::string stride; stride="";
if(parse("--stride",stride)){
@@ -467,6 +475,11 @@ int CLToolSumHills::main(FILE* in,FILE*out,Communicator& pc){
actioninput.push_back("NOHISTORY");
}
}
+ bool mintozero;
+ parseFlag("--mintozero",mintozero);
+ if(mintozero){
+ actioninput.push_back("MINTOZERO");
+ }
if(idw.size()!=0){
addme="PROJ=";
for(unsigned i=0;i<idw.size()-1;i++){addme+=idw[i]+",";}
diff --git a/src/function/FuncSumHills.cpp b/src/function/FuncSumHills.cpp
index e57eab05bee2509d58192466db843cc0feaaf224..724bdffb4cddbff5fd7a38699129fa184155e3ef 100644
--- a/src/function/FuncSumHills.cpp
+++ b/src/function/FuncSumHills.cpp
@@ -146,7 +146,7 @@ bool FilesHandler::scanOneHill(BiasRepresentation *br, IFile *ifile ){
double dummy;
if(ifile->scanField("time",dummy)){
//(*log)<<" scanning one hill: "<<dummy<<" \n";
- ifile->scanField("biasf",dummy);
+ if(ifile->FieldExist("biasf")) ifile->scanField("biasf",dummy);
if(ifile->FieldExist("clock")) ifile->scanField("clock",dummy);
// keep this intermediate function in case you need to parse more data in the future
br->pushKernel(ifile);
@@ -179,6 +179,7 @@ class FuncSumHills :
bool iscltool,integratehills,integratehisto,parallelread;
bool negativebias;
bool nohistory;
+ bool minTOzero;
double beta;
string outhills,outhisto,fmt;
BiasRepresentation *biasrep;
@@ -204,6 +205,7 @@ void FuncSumHills::registerKeywords(Keywords& keys){
keys.add("optional","GRID_MIN","the lower bounds for the grid");
keys.add("optional","GRID_MAX","the upper bounds for the grid");
keys.add("optional","GRID_BIN","the number of bins for the grid");
+ keys.add("optional","GRID_SPACING","the approximate grid spacing (to be used as an alternative or together with GRID_BIN)");
keys.add("optional","OUTHILLS"," output file for hills ");
keys.add("optional","OUTHISTO"," output file for histogram ");
keys.add("optional","INITSTRIDE"," stride if you want an initial dump ");
@@ -212,6 +214,7 @@ void FuncSumHills::registerKeywords(Keywords& keys){
keys.addFlag("PARALLELREAD",false,"read parallel HILLS file");
keys.addFlag("NEGBIAS",false,"dump negative bias ( -bias ) instead of the free energy: needed in welltempered with flexible hills ");
keys.addFlag("NOHISTORY",false,"to be used with INITSTRIDE: it splits the bias/histogram in pieces without previous history ");
+ keys.addFlag("MINTOZERO",false,"translate the resulting bias/histogram to have the minimum to zero ");
keys.add("optional","FMT","the format that should be used to output real numbers");
}
@@ -225,6 +228,7 @@ integratehisto(false),
parallelread(false),
negativebias(false),
nohistory(false),
+minTOzero(false),
beta(-1.),
fmt("%14.9f")
{
@@ -243,10 +247,27 @@ fmt("%14.9f")
if(gmax.size()!=getNumberOfArguments() && gmax.size()!=0) error("not enough values for GRID_MAX");
plumed_massert(gmax.size()==getNumberOfArguments() || gmax.size()==0,"need GRID_MAX argument for this") ;
vector<unsigned> gbin;
+ vector<double> gspacing;
parseVector("GRID_BIN",gbin);
- plumed_massert(gbin.size()==getNumberOfArguments() || gbin.size()==0,"need GRID_BIN argument for this");
+ plumed_massert(gbin.size()==getNumberOfArguments() || gbin.size()==0,"need GRID_BIN argument for this") ;
if(gbin.size()!=getNumberOfArguments() && gbin.size()!=0) error("not enough values for GRID_BIN");
- //plumed_assert(getNumberOfArguments()==gbin.size());
+ parseVector("GRID_SPACING",gspacing);
+ plumed_massert(gspacing.size()==getNumberOfArguments() || gspacing.size()==0,"need GRID_SPACING argument for this") ;
+ if(gspacing.size()!=getNumberOfArguments() && gspacing.size()!=0) error("not enough values for GRID_SPACING");
+ if(gspacing.size()!=0 && gbin.size()==0){
+ log<<" The number of bins will be estimated from GRID_SPACING\n";
+ } else if(gspacing.size()!=0 && gbin.size()!=0){
+ log<<" You specified both GRID_BIN and GRID_SPACING\n";
+ log<<" The more conservative (highest) number of bins will be used for each variable\n";
+ }
+ if(gspacing.size()!=0) for(unsigned i=0;i<getNumberOfArguments();i++){
+ if(gbin.size()==0) gbin.assign(getNumberOfArguments(),1);
+ double a,b;
+ Tools::convert(gmin[i],a);
+ Tools::convert(gmax[i],b);
+ unsigned n=((b-a)/gspacing[i])+1;
+ if(gbin[i]<n) gbin[i]=n;
+ }
// hills file:
parseVector("HILLSFILES",hillsFiles);
@@ -351,7 +372,8 @@ fmt("%14.9f")
parseFlag("NOHISTORY",nohistory);
if(nohistory)log<<" nohistory: each stride block has no memory of the previous block\n";
}
-
+ parseFlag("MINTOZERO",minTOzero);
+ if(minTOzero)log<<" mintozero: bias/histogram will be translated to have the minimum value equal to zero\n";
//what might it be this?
// here start
// want something right now?? do it and return
@@ -477,7 +499,8 @@ fmt("%14.9f")
if(initstride>0){ myout=outhills+ostr.str()+".dat" ;}else{myout=outhills;}
log<<" Writing full grid on file "<<myout<<" \n";
gridfile.open(myout);
-
+
+ if(minTOzero) biasGrid.setMinToZero();
biasGrid.setOutputFmt(fmt);
biasGrid.writeToFile(gridfile);
gridfile.close();
@@ -496,7 +519,8 @@ fmt("%14.9f")
if(initstride>0){ myout=outhisto+ostr.str()+".dat" ;}else{myout=outhisto;}
log<<" Writing full grid on file "<<myout<<" \n";
gridfile.open(myout);
-
+
+ if(minTOzero) histoGrid.setMinToZero();
histoGrid.setOutputFmt(fmt);
histoGrid.writeToFile(gridfile);
gridfile.close();