From 0a9bb6600d608f40dec8736f043dd8a69abc1497 Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Thu, 20 Sep 2012 18:25:31 +0200
Subject: [PATCH] Implementation of RESTART
Using a RESTART keyword in the input, files are automatically
appended. When not used, files are backed up (a la gromacs).
Notice that this works only when using open("file"). The rationale
is that if you say open("file","a") or open("file","w") then you
know what you are doing. I also removed the extra mode specifier
for PlumedIFile (it was redundant: always "r").
If the behavior is not clear enough we can change it...
---
src/BiasMetaD.cpp | 11 ++++-------
src/GenericPrint.cpp | 2 +-
src/PlumedFile.cpp | 45 +++++++++++++++++++++++++++++++++++++++++---
src/PlumedFile.h | 10 ++++++++--
src/PlumedMain.cpp | 9 +++++++--
src/PlumedMain.h | 10 ++++++++++
6 files changed, 72 insertions(+), 15 deletions(-)
diff --git a/src/BiasMetaD.cpp b/src/BiasMetaD.cpp
index adec967c9..03e4b116c 100644
--- a/src/BiasMetaD.cpp
+++ b/src/BiasMetaD.cpp
@@ -127,7 +127,6 @@ private:
int stride_;
int wgridstride_;
bool welltemp_;
- bool restart_;
bool grid_;
int adaptive_;
FlexibleBin *flexbin;
@@ -166,7 +165,6 @@ void BiasMetaD::registerKeywords(Keywords& keys){
keys.add("compulsory","HEIGHT","the heights of the Gaussian hills");
keys.add("compulsory","PACE","the frequency for hill addition");
keys.add("compulsory","FILE","HILLS","a file in which the list of added hills is stored");
- keys.addFlag("RESTART",false,"restart the calculation from a previous metadynamics calculation.");
keys.add("optional","BIASFACTOR","use well tempered metadynamics and use this biasfactor. Please note you must also specify temp");
keys.add("optional","TEMP","the system temperature - this is only needed if you are doing well-tempered metadynamics");
keys.add("optional","GRID_MIN","the lower bounds for the grid");
@@ -203,7 +201,7 @@ PLUMED_BIAS_INIT(ao),
BiasGrid_(NULL), gridfile_(NULL), wgridstride_(0), grid_(false),
// Metadynamics basic parameters
height0_(0.0), biasf_(1.0), temp_(0.0),
-stride_(0), welltemp_(false), restart_(false),
+stride_(0), welltemp_(false),
// Other stuff
dp_(NULL), adaptive_(FlexibleBin::none),
// Multiple walkers initialization
@@ -243,7 +241,6 @@ mw_n_(-1), mw_dir_("./"), mw_id_(0), mw_rstride_(1)
plumed_assert(stride_>0);
string hillsfname="HILLS";
parse("FILE",hillsfname);
- parseFlag("RESTART",restart_);
parse("BIASFACTOR",biasf_);
plumed_assert(biasf_>=1.0);
parse("TEMP",temp_);
@@ -346,19 +343,19 @@ mw_n_(-1), mw_dir_("./"), mw_id_(0), mw_rstride_(1)
ifilesnames.push_back(fname);
PlumedIFile *ifile = new PlumedIFile();
ifile->link(*this);
- ifile->open(fname,"r");
+ ifile->open(fname);
ifiles.push_back(ifile);
}
}else{
ifilesnames.push_back(hillsfname);
PlumedIFile *ifile = new PlumedIFile();
ifile->link(*this);
- ifile->open(hillsfname,"r");
+ ifile->open(hillsfname);
ifiles.push_back(ifile);
}
// restarting from HILLS file
- if(restart_){
+ if(plumed.getRestart()){
for(unsigned i=0;i<ifilesnames.size();++i){
log.printf(" Restarting from %s:",ifilesnames[i].c_str());
readGaussians(ifiles[i]);
diff --git a/src/GenericPrint.cpp b/src/GenericPrint.cpp
index 009c1d8a3..9fe64214d 100644
--- a/src/GenericPrint.cpp
+++ b/src/GenericPrint.cpp
@@ -101,7 +101,7 @@ rotate(0)
ofile.link(*this);
parse("FILE",file);
if(file.length()>0){
- ofile.open(file.c_str(),"wa");
+ ofile.open(file.c_str());
log.printf(" on file %s\n",file.c_str());
} else {
log.printf(" on plumed log file\n");
diff --git a/src/PlumedFile.cpp b/src/PlumedFile.cpp
index d547767ae..b8935b91c 100644
--- a/src/PlumedFile.cpp
+++ b/src/PlumedFile.cpp
@@ -34,7 +34,7 @@ using namespace PLMD;
void PlumedFileBase::test(){
PLMD::PlumedOFile pof;
- pof.open("ciao","w");
+ pof.open("ciao");
pof.printf("%s\n","test1");
pof.setLinePrefix("plumed: ");
pof.printf("%s\n","test2");
@@ -48,7 +48,7 @@ void PlumedFileBase::test(){
PLMD::PlumedIFile pif;
std::string s;
- pif.open("ciao","r");
+ pif.open("ciao");
pif.getline(s); std::printf("%s\n",s.c_str());
pif.getline(s); std::printf("%s\n",s.c_str());
@@ -87,7 +87,6 @@ PlumedFileBase& PlumedFileBase::link(FILE*fp){
PlumedFileBase& PlumedFileBase::flush(){
fflush(fp);
-std::cerr<<"FLUSHING "<<path<<"\n";
if(heavyFlush){
fclose(fp);
fp=std::fopen(const_cast<char*>(path.c_str()),"a");
@@ -292,6 +291,41 @@ PlumedOFile& PlumedOFile::printField(){
return *this;
}
+PlumedOFile& PlumedOFile::open(const std::string&path){
+ plumed_assert(!cloned);
+ eof=false;
+ err=false;
+ fp=NULL;
+ this->path=path;
+ if(plumed && plumed->getRestart()){
+ fp=std::fopen(const_cast<char*>(this->path.c_str()),"a");
+ } else {
+ if(!comm || comm->Get_rank()==0){
+ FILE* ff=std::fopen(const_cast<char*>(this->path.c_str()),"r");
+ FILE* fff=NULL;
+ if(ff){
+ std::string backup;
+ for(int i=0;;i++){
+ std::string num;
+ Tools::convert(i,num);
+ backup="bck."+num+"."+path;
+ fff=std::fopen(backup.c_str(),"r");
+ if(!fff) break;
+ }
+ int check=rename(path.c_str(),backup.c_str());
+ plumed_massert(check==0,"renaming "+path+" into "+backup+" failed for some reason");
+ }
+ if(ff) std::fclose(ff);
+ if(fff) std::fclose(fff);
+ }
+ comm->Barrier();
+ fp=std::fopen(const_cast<char*>(this->path.c_str()),"w");
+ }
+ if(plumed) plumed->insertFile(*this);
+ return *this;
+}
+
+
PlumedIFile& PlumedIFile::advanceField(){
plumed_assert(!inMiddleOfField);
std::string line;
@@ -354,6 +388,11 @@ PlumedIFile& PlumedIFile::advanceField(){
return *this;
}
+PlumedIFile& PlumedIFile::open(const std::string&name){
+ PlumedFileBase::open(name,"r");
+ return *this;
+}
+
PlumedIFile& PlumedIFile::scanFieldList(std::vector<std::string>&s){
if(!inMiddleOfField) advanceField();
if(!*this) return *this;
diff --git a/src/PlumedFile.h b/src/PlumedFile.h
index 71e9a349c..5fec82886 100644
--- a/src/PlumedFile.h
+++ b/src/PlumedFile.h
@@ -89,8 +89,6 @@ public:
PlumedFileBase& link(Action&);
/// Flushes the file to disk
PlumedFileBase& flush();
-/// Opens the file
- PlumedFileBase& open(const std::string&name,const std::string& mode);
/// Closes the file
/// Should be used only for explicitely opened files.
void close();
@@ -102,6 +100,8 @@ public:
operator bool () const;
/// Set heavyFlush flag
void setHeavyFlush(){ heavyFlush=true;};
+/// Opens the file (without auto-backup)
+ PlumedFileBase& open(const std::string&name,const std::string& mode);
};
/**
@@ -195,11 +195,15 @@ public:
~PlumedOFile();
/// Allows overloading of link
using PlumedFileBase::link;
+/// Allows overloading of open
+ using PlumedFileBase::open;
/// Allows linking this PlumedOFile to another one.
/// In this way, everything written to this PlumedOFile will be immediately
/// written on the linked PlumedOFile. Notice that a PlumedOFile should
/// be either opened explicitly, linked to a FILE or linked to a PlumedOFile
PlumedOFile& link(PlumedOFile&);
+/// Opens the file using automatic append/backup
+ PlumedOFile& open(const std::string&name);
/// Set the prefix for output.
/// Typically "PLUMED: ". Notice that lines with a prefix cannot
/// be parsed using fields in a PlumedIFile.
@@ -270,6 +274,8 @@ public:
PlumedIFile();
/// Destructor
~PlumedIFile();
+/// Opens the file
+ PlumedIFile& open(const std::string&name);
/// Gets the list of all fields
PlumedIFile& scanFieldList(std::vector<std::string>&);
/// Read a double field
diff --git a/src/PlumedMain.cpp b/src/PlumedMain.cpp
index eec2949cd..4a1c34018 100644
--- a/src/PlumedMain.cpp
+++ b/src/PlumedMain.cpp
@@ -60,7 +60,8 @@ PlumedMain::PlumedMain():
atoms(*new Atoms(*this)),
actionSet(*new ActionSet(*this)),
bias(0.0),
- novirial(false)
+ novirial(false),
+ restart(false)
{
log.link(comm);
log.setLinePrefix("PLUMED: ");
@@ -356,7 +357,7 @@ void PlumedMain::readInputFile(std::string str){
log.printf("FILE: %s\n",str.c_str());
PlumedIFile ifile;
ifile.link(*this);
- ifile.open(str,"r");
+ ifile.open(str);
std::vector<std::string> words;
exchangepatterns.setFlag(exchangepatterns.NONE);
while(Tools::getParsedLine(ifile,words)){
@@ -372,6 +373,10 @@ void PlumedMain::readInputFile(std::string str){
// I convert the seed to -seed because I think it is more general to use a positive seed in input
if(words.size()>2&&words[1]=="SEED") {int seed; Tools::convert(words[2],seed); exchangepatterns.setSeed(-seed); }
}
+ else if(words[0]=="RESTART"){
+ restart=true;
+ log<<"Restarting simulation: files will be appended\n";
+ }
else if(words[0]=="INCLUDE"){
plumed_assert(words.size()==2);
readInputFile(words[1]);
diff --git a/src/PlumedMain.h b/src/PlumedMain.h
index a795b85e3..73dacb067 100644
--- a/src/PlumedMain.h
+++ b/src/PlumedMain.h
@@ -122,6 +122,9 @@ private:
/// Class of possible exchange patterns, used for BIASEXCHANGE but also for future parallel tempering
ExchangePatterns exchangepatterns;
+/// Flag for restart
+ bool restart;
+
std::set<PlumedFileBase*> files;
typedef std::set<PlumedFileBase*>::iterator files_iterator;
@@ -231,6 +234,8 @@ public:
void eraseFile(PlumedFileBase&);
/// Flush all files
void fflush();
+/// Check if restarting
+ bool getRestart()const;
};
/////
@@ -256,6 +261,11 @@ void PlumedMain::setSuffix(const std::string&s){
suffix=s;
}
+inline
+bool PlumedMain::getRestart()const{
+ return restart;
+}
+
}
#endif
--
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