From 8e59fbec0063231c0571a5627255ac4244312903 Mon Sep 17 00:00:00 2001
From: Gareth Tribello <gt@eider.asg>
Date: Fri, 26 Jul 2013 09:24:56 +0100
Subject: [PATCH] Better backup of old files in analysis routines
In analysis runs results from previous analysis are saved as
analysis.0.<filename>, analysis.1.<filename> etc. If the calculation
is NOT restarted and there are files with these names hanging about they are
renamed bck.0.analysis.0.<filename> bck.0.analysis.1.<filename> etc.
---
src/analysis/Analysis.cpp | 9 +++++
src/analysis/Analysis.h | 4 +++
src/analysis/Histogram.cpp | 3 +-
src/tools/OFile.cpp | 67 ++++++++++++++++++++++++--------------
src/tools/OFile.h | 8 +++++
5 files changed, 66 insertions(+), 25 deletions(-)
diff --git a/src/analysis/Analysis.cpp b/src/analysis/Analysis.cpp
index e4ab30dc8..dd8ff1722 100644
--- a/src/analysis/Analysis.cpp
+++ b/src/analysis/Analysis.cpp
@@ -192,6 +192,15 @@ void Analysis::readDataFromFile( const std::string& filename ){
if(old_norm>0) firstAnalysisDone=true;
}
+void Analysis::parseOutputFile( const std::string& key, std::string& filename ){
+ parse(key,filename);
+ if( !plumed.getRestart() ){
+ OFile ofile; ofile.link(*this);
+ ofile.setBackupString("analysis");
+ ofile.backupAllFiles(filename);
+ }
+}
+
void Analysis::prepare(){
if(needeng) plumed.getAtoms().setCollectEnergy(true);
}
diff --git a/src/analysis/Analysis.h b/src/analysis/Analysis.h
index 6358c1adb..3e2f50066 100644
--- a/src/analysis/Analysis.h
+++ b/src/analysis/Analysis.h
@@ -88,6 +88,10 @@ private:
/// you probably need getNormalization()
double retrieveNorm() const ;
protected:
+/// This is used to read in output file names for analysis methods. When
+/// this method is used and the calculation is not restarted old analysis
+/// files are backed up.
+ void parseOutputFile( const std::string& key, std::string& filename );
/// Return the number of arguments (this overwrites the one in ActionWithArguments)
unsigned getNumberOfArguments() const;
/// Return the number of data points
diff --git a/src/analysis/Histogram.cpp b/src/analysis/Histogram.cpp
index aaa6cfd62..2e8d39111 100644
--- a/src/analysis/Histogram.cpp
+++ b/src/analysis/Histogram.cpp
@@ -124,7 +124,8 @@ gbin(getNumberOfArguments())
parseVector("GRID_MIN",gmin);
parseVector("GRID_MAX",gmax);
parseVector("GRID_BIN",gbin);
- parse("GRID_WFILE",gridfname);
+ parseOutputFile("GRID_WFILE",gridfname);
+
// Read stuff for window functions
parseVector("BANDWIDTH",bw);
// Read the type of kernel we are using
diff --git a/src/tools/OFile.cpp b/src/tools/OFile.cpp
index caca9a9a7..7820ee202 100644
--- a/src/tools/OFile.cpp
+++ b/src/tools/OFile.cpp
@@ -215,6 +215,48 @@ void OFile::setBackupString( const std::string& str ){
backstring=str;
}
+void OFile::backupAllFiles( const std::string& str ){
+ plumed_assert( backstring!="bck" && plumed && !plumed->getRestart() );
+ size_t found=str.find_last_of("/\\");
+ std::string filename = str + plumed->getSuffix();
+ std::string directory=filename.substr(0,found+1);
+ std::string file=filename.substr(found+1);
+ if( FileExist(filename) ) backupFile("bck", filename);
+ for(int i=0;;i++){
+ std::string num; Tools::convert(i,num);
+ std::string filestr = directory + backstring + "." + num + "." + file;
+ if( !FileExist(filestr) ) break;
+ backupFile( "bck", filestr);
+ }
+}
+
+void OFile::backupFile( const std::string& bstring, const std::string& fname ){
+ int maxbackup=100;
+ if(std::getenv("PLUMED_MAXBACKUP")) Tools::convert(std::getenv("PLUMED_MAXBACKUP"),maxbackup);
+ if(maxbackup>0 && (!comm || comm->Get_rank()==0)){
+ FILE* ff=std::fopen(const_cast<char*>(fname.c_str()),"r");
+ FILE* fff=NULL;
+ if(ff){
+ std::string backup;
+ size_t found=fname.find_last_of("/\\");
+ std::string directory=fname.substr(0,found+1);
+ std::string file=fname.substr(found+1);
+ for(int i=0;;i++){
+ std::string num;
+ Tools::convert(i,num);
+ if(i>maxbackup) plumed_merror("cannot backup file "+file+" maximum number of backup is "+num+"\n");
+ backup=directory+bstring +"."+num+"."+file;
+ fff=std::fopen(backup.c_str(),"r");
+ if(!fff) break;
+ }
+ int check=rename(fname.c_str(),backup.c_str());
+ plumed_massert(check==0,"renaming "+fname+" into "+backup+" failed for some reason");
+ }
+ if(ff) std::fclose(ff);
+ if(fff) std::fclose(fff);
+ }
+}
+
OFile& OFile::open(const std::string&path){
plumed_assert(!cloned);
eof=false;
@@ -227,30 +269,7 @@ OFile& OFile::open(const std::string&path){
if(plumed && plumed->getRestart()){
fp=std::fopen(const_cast<char*>(this->path.c_str()),"a");
} else {
- int maxbackup=100;
- if(std::getenv("PLUMED_MAXBACKUP")) Tools::convert(std::getenv("PLUMED_MAXBACKUP"),maxbackup);
- if(maxbackup>0 && (!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;
- size_t found=this->path.find_last_of("/\\");
- std::string directory=this->path.substr(0,found+1);
- std::string file=this->path.substr(found+1);
- for(int i=0;;i++){
- std::string num;
- Tools::convert(i,num);
- if(i>maxbackup) plumed_merror("cannot backup file "+file+" maximum number of backup is "+num+"\n");
- backup=directory+backstring +"."+num+"."+file;
- fff=std::fopen(backup.c_str(),"r");
- if(!fff) break;
- }
- int check=rename(this->path.c_str(),backup.c_str());
- plumed_massert(check==0,"renaming "+this->path+" into "+backup+" failed for some reason");
- }
- if(ff) std::fclose(ff);
- if(fff) std::fclose(fff);
- }
+ backupFile( backstring, this->path );
if(comm)comm->Barrier();
fp=std::fopen(const_cast<char*>(this->path.c_str()),"w");
}
diff --git a/src/tools/OFile.h b/src/tools/OFile.h
index cb96116f1..74732c167 100644
--- a/src/tools/OFile.h
+++ b/src/tools/OFile.h
@@ -134,6 +134,14 @@ public:
OFile& link(OFile&);
/// Set the string name to be used for automatic backup
void setBackupString( const std::string& );
+/// Backup a file by giving it a different name
+ void backupFile( const std::string& bstring, const std::string& fname );
+/// This backs up all the files that would have been created with the
+/// name str. It is used in analysis when you are not restarting. Analysis
+/// output files at different times, which are names analysis.0.<filename>,
+/// analysis.1.<filename> and <filename>, are backed up to bck.0.analysis.0.<filename>,
+/// bck.0.analysis.1.<filename> and bck.0.<filename>
+ void backupAllFiles( const std::string& str );
/// Opens the file using automatic append/backup
OFile& open(const std::string&name);
/// Set the prefix for output.
--
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