diff --git a/src/analysis/Analysis.cpp b/src/analysis/Analysis.cpp
index ff5dfc428c547fb11a8e8fc95f3e9dc44ab7f4ce..c108897c0066de11ffc7e9b0ec5ef48cdcc4ba74 100644
--- a/src/analysis/Analysis.cpp
+++ b/src/analysis/Analysis.cpp
@@ -170,7 +170,7 @@ old_norm(0.0)
}
void Analysis::readDataFromFile( const std::string& filename ){
- double tstep, oldtstep; PlumedIFile ifile;
+ double tstep, oldtstep; IFile ifile;
if( !ifile.FileExist(filename) ) error("failed to find required restart file " + filename );
ifile.open(filename);
diff --git a/src/analysis/Analysis.h b/src/analysis/Analysis.h
index 0f32a0e5f52a0d4da132aac671bbc60e861087c1..9d3711dc823ad30e9c13f1fdf99df34b0fdb392e 100644
--- a/src/analysis/Analysis.h
+++ b/src/analysis/Analysis.h
@@ -79,7 +79,7 @@ private:
/// The value of the old normalization constant
double norm, old_norm;
/// The checkpoint file
- PlumedOFile rfile;
+ OFile rfile;
/// Read in data from a file
void readDataFromFile( const std::string& filename );
/// This retrieves the value of norm from the analysis action.
diff --git a/src/analysis/Histogram.cpp b/src/analysis/Histogram.cpp
index 92596de446ba8c986c2c45c8943ab293cecc5120..52dc930ce2e26e62a32f8835fd5fa08838461332 100644
--- a/src/analysis/Histogram.cpp
+++ b/src/analysis/Histogram.cpp
@@ -156,7 +156,7 @@ void Histogram::performAnalysis(){
}
Grid* gg;
if( oldfname.length()>0 && usingMemory() ){
- PlumedIFile oldf; oldf.link(*this); oldf.open(oldfname);
+ IFile oldf; oldf.link(*this); oldf.open(oldfname);
gg = Grid::create( "probs", getArguments(), oldf, gmin, gmax, gbin, false, false, false );
oldf.close();
} else {
@@ -175,7 +175,7 @@ void Histogram::performAnalysis(){
gg->scaleAllValuesAndDerivatives( 1.0 / getNormalization() );
// Write the grid to a file
- PlumedOFile gridfile; gridfile.link(*this);
+ OFile gridfile; gridfile.link(*this);
gridfile.open( gridfname ); gg->writeToFile( gridfile );
// Close the file
gridfile.close(); delete gg;
diff --git a/src/bias/External.cpp b/src/bias/External.cpp
index 83c6b9945e7bcb1b76ffe81b080a1f0dd9972e1d..9cdf3b1abde4b541a94423f3cea7a5201d8d3eff 100644
--- a/src/bias/External.cpp
+++ b/src/bias/External.cpp
@@ -23,7 +23,7 @@
#include "ActionRegister.h"
#include "tools/Grid.h"
#include "tools/PlumedException.h"
-#include "tools/PlumedFile.h"
+#include "tools/File.h"
using namespace std;
@@ -141,7 +141,7 @@ BiasGrid_(NULL)
addComponent("bias"); componentIsNotPeriodic("bias");
// read grid
- PlumedIFile gridfile; gridfile.open(filename);
+ IFile gridfile; gridfile.open(filename);
std::string funcl=getLabel() + ".bias";
BiasGrid_=Grid::create(funcl,getArguments(),gridfile,sparsegrid,spline,true);
gridfile.close();
diff --git a/src/bias/MetaD.cpp b/src/bias/MetaD.cpp
index fe76cbfc74344dbd53582e14d8403c8e74f75304..2f27842a46457aef87e05bf716f704881c6d82b1 100644
--- a/src/bias/MetaD.cpp
+++ b/src/bias/MetaD.cpp
@@ -30,7 +30,7 @@
#include "tools/Random.h"
#include <string>
#include <cstring>
-#include "tools/PlumedFile.h"
+#include "tools/File.h"
#include "time.h"
#include <iostream>
@@ -120,7 +120,7 @@ private:
};
vector<double> sigma0_;
vector<Gaussian> hills_;
- PlumedOFile hillsOfile_;
+ OFile hillsOfile_;
Grid* BiasGrid_;
bool storeOldGrids_;
std::string gridfilename_;
@@ -138,11 +138,11 @@ private:
string mw_dir_;
int mw_id_;
int mw_rstride_;
- vector<PlumedIFile*> ifiles;
+ vector<IFile*> ifiles;
vector<string> ifilesnames;
- void readGaussians(PlumedIFile*);
- void writeGaussian(const Gaussian&,PlumedOFile&);
+ void readGaussians(IFile*);
+ void writeGaussian(const Gaussian&,OFile&);
void addGaussian(const Gaussian&);
double getHeight(const vector<double>&);
double getBiasAndDerivatives(const vector<double>&,double* der=NULL);
@@ -337,7 +337,7 @@ mw_n_(1), mw_dir_("./"), mw_id_(0), mw_rstride_(1)
} else {
fname = hillsfname;
}
- PlumedIFile *ifile = new PlumedIFile();
+ IFile *ifile = new IFile();
ifile->link(*this);
ifiles.push_back(ifile);
ifilesnames.push_back(fname);
@@ -369,7 +369,7 @@ mw_n_(1), mw_dir_("./"), mw_id_(0), mw_rstride_(1)
}
-void MetaD::readGaussians(PlumedIFile *ifile)
+void MetaD::readGaussians(IFile *ifile)
{
unsigned ncv=getNumberOfArguments();
double dummy;
@@ -442,7 +442,7 @@ void MetaD::readGaussians(PlumedIFile *ifile)
log.printf(" %d Gaussians read\n",nhills);
}
-void MetaD::writeGaussian(const Gaussian& hill, PlumedOFile&file){
+void MetaD::writeGaussian(const Gaussian& hill, OFile&file){
unsigned ncv=getNumberOfArguments();
file.printField("time",getTimeStep()*getStep());
for(unsigned i=0;i<ncv;++i){
@@ -717,7 +717,7 @@ void MetaD::update(){
}
// dump grid on file
if(wgridstride_>0&&getStep()%wgridstride_==0){
- PlumedOFile gridfile; gridfile.link(*this);
+ OFile gridfile; gridfile.link(*this);
if(!storeOldGrids_) remove( gridfilename_.c_str() );
gridfile.open(gridfilename_);
BiasGrid_->writeToFile(gridfile);
diff --git a/src/core/PlumedMain.cpp b/src/core/PlumedMain.cpp
index b0127fec7d3c6f69af6ca24060138c7a87735dc4..592decf6d98815a32d2f5baa3b537d5d28df5173 100644
--- a/src/core/PlumedMain.cpp
+++ b/src/core/PlumedMain.cpp
@@ -370,7 +370,7 @@ void PlumedMain::init(){
void PlumedMain::readInputFile(std::string str){
plumed_assert(initialized);
log.printf("FILE: %s\n",str.c_str());
- PlumedIFile ifile;
+ IFile ifile;
ifile.link(*this);
ifile.open(str);
std::vector<std::string> words;
@@ -611,11 +611,11 @@ void PlumedMain::fflush(){
}
}
-void PlumedMain::insertFile(PlumedFileBase&f){
+void PlumedMain::insertFile(FileBase&f){
files.insert(&f);
}
-void PlumedMain::eraseFile(PlumedFileBase&f){
+void PlumedMain::eraseFile(FileBase&f){
files.erase(&f);
}
diff --git a/src/core/PlumedMain.h b/src/core/PlumedMain.h
index 395bc4993d67d8e464591925eba4a7cf5fd94d8f..a498189880ff5cbea8614e25520076ed0a646274 100644
--- a/src/core/PlumedMain.h
+++ b/src/core/PlumedMain.h
@@ -59,7 +59,7 @@ class Communicator;
class Stopwatch;
class Citations;
class ExchangePatterns;
-class PlumedFileBase;
+class FileBase;
/**
Main plumed object.
@@ -124,8 +124,8 @@ private:
/// Flag for restart
bool restart;
- std::set<PlumedFileBase*> files;
- typedef std::set<PlumedFileBase*>::iterator files_iterator;
+ std::set<FileBase*> files;
+ typedef std::set<FileBase*>::iterator files_iterator;
/// Stuff to make plumed stop the MD code cleanly
int* stopFlag;
@@ -238,9 +238,9 @@ public:
/// Closes a file opened with PlumedMain::fopen()
int fclose(FILE*fp);
/// Insert a file
- void insertFile(PlumedFileBase&);
+ void insertFile(FileBase&);
/// Erase a file
- void eraseFile(PlumedFileBase&);
+ void eraseFile(FileBase&);
/// Flush all files
void fflush();
/// Check if restarting
diff --git a/src/generic/DumpAtoms.cpp b/src/generic/DumpAtoms.cpp
index 4f8de058190d7cbb2f82cdba6a82ddfbc2c3745f..11eab78f41c939a599315a5c0f0dfc367286a00c 100644
--- a/src/generic/DumpAtoms.cpp
+++ b/src/generic/DumpAtoms.cpp
@@ -23,7 +23,7 @@
#include "core/ActionPilot.h"
#include "core/ActionRegister.h"
#include "tools/Pbc.h"
-#include "tools/PlumedFile.h"
+#include "tools/File.h"
#include "core/PlumedMain.h"
#include "core/Atoms.h"
#include "tools/Units.h"
@@ -63,7 +63,7 @@ class DumpAtoms:
public ActionAtomistic,
public ActionPilot
{
- PlumedOFile of;
+ OFile of;
double lenunit;
public:
DumpAtoms(const ActionOptions&);
diff --git a/src/generic/DumpDerivatives.cpp b/src/generic/DumpDerivatives.cpp
index 04da026b3ec679a5f284184a17050182c919f1c0..7eb9942f81e25455f30e252f7fbbd26d419d654b 100644
--- a/src/generic/DumpDerivatives.cpp
+++ b/src/generic/DumpDerivatives.cpp
@@ -22,7 +22,7 @@
#include "core/ActionPilot.h"
#include "core/ActionWithArguments.h"
#include "core/ActionRegister.h"
-#include "tools/PlumedFile.h"
+#include "tools/File.h"
using namespace std;
@@ -58,7 +58,7 @@ public ActionWithArguments
{
string file;
string fmt;
- PlumedOFile of;
+ OFile of;
public:
void calculate(){};
DumpDerivatives(const ActionOptions&);
diff --git a/src/generic/DumpForces.cpp b/src/generic/DumpForces.cpp
index 7cfda754316e3fd8115548d4a3eebb100383fe65..c010e6650f9efe85e5c73a745315b0d7641693a6 100644
--- a/src/generic/DumpForces.cpp
+++ b/src/generic/DumpForces.cpp
@@ -22,7 +22,7 @@
#include "core/ActionPilot.h"
#include "core/ActionWithArguments.h"
#include "core/ActionRegister.h"
-#include "tools/PlumedFile.h"
+#include "tools/File.h"
using namespace std;
@@ -58,7 +58,7 @@ public ActionPilot,
public ActionWithArguments
{
string file;
- PlumedOFile of;
+ OFile of;
public:
void calculate(){};
DumpForces(const ActionOptions&);
diff --git a/src/generic/DumpProjections.cpp b/src/generic/DumpProjections.cpp
index e50d027c361fec75aaba2331e7a5725d6799ddbc..f8a089c23129d86a2c38fc315bf174a392db4218 100644
--- a/src/generic/DumpProjections.cpp
+++ b/src/generic/DumpProjections.cpp
@@ -22,7 +22,7 @@
#include "core/ActionPilot.h"
#include "core/ActionWithArguments.h"
#include "core/ActionRegister.h"
-#include "tools/PlumedFile.h"
+#include "tools/File.h"
using namespace std;
@@ -42,7 +42,7 @@ public ActionWithArguments
{
string file;
string fmt;
- PlumedOFile of;
+ OFile of;
public:
void calculate(){};
DumpProjections(const ActionOptions&);
diff --git a/src/generic/Print.cpp b/src/generic/Print.cpp
index 5101b67b744b63ae41a492cc54cba3f176c30ef3..3d3e137b6c40f0532968d5807abd59f49c19ed89 100644
--- a/src/generic/Print.cpp
+++ b/src/generic/Print.cpp
@@ -56,7 +56,7 @@ public ActionPilot,
public ActionWithArguments
{
string file;
- PlumedOFile ofile;
+ OFile ofile;
string fmt;
// small internal utility
/////////////////////////////////////////
diff --git a/src/generic/Read.cpp b/src/generic/Read.cpp
index 20a770f13f3ce6b24c3ab0cc5e378aeb8d94079a..bfaca652a18b8b9606a11bfc25a2466625fa7f8a 100644
--- a/src/generic/Read.cpp
+++ b/src/generic/Read.cpp
@@ -46,7 +46,7 @@ private:
bool cloned_file;
unsigned nlinesPerStep;
std::string filename;
- PlumedIFile* ifile;
+ IFile* ifile;
std::vector<Value*> readvals;
public:
static void registerKeywords( Keywords& keys );
@@ -57,7 +57,7 @@ public:
void calculate();
void update();
std::string getFilename() const;
- PlumedIFile* getFile();
+ IFile* getFile();
};
PLUMED_REGISTER_ACTION(Read,"READ")
@@ -91,7 +91,7 @@ nlinesPerStep(1)
}
}
if( !cloned_file ){
- ifile=new PlumedIFile();
+ ifile=new IFile();
if( !ifile->FileExist(filename) ) error("could not find file named " + filename);
ifile->link(*this);
ifile->open(filename);
@@ -144,7 +144,7 @@ std::string Read::getFilename() const {
return filename;
}
-PlumedIFile* Read::getFile(){
+IFile* Read::getFile(){
return ifile;
}
diff --git a/src/tools/PlumedFile.cpp b/src/tools/File.cpp
similarity index 82%
rename from src/tools/PlumedFile.cpp
rename to src/tools/File.cpp
index e612151ff0ba3281d434d51630ba5c96d889a4a6..0fc8a52e21304855f298d350c44a31f7932ad4d0 100644
--- a/src/tools/PlumedFile.cpp
+++ b/src/tools/File.cpp
@@ -19,7 +19,7 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#include "PlumedFile.h"
+#include "File.h"
#include "PlumedException.h"
#include "core/Action.h"
#include "core/PlumedMain.h"
@@ -34,8 +34,8 @@
using namespace PLMD;
-void PlumedFileBase::test(){
- PLMD::PlumedOFile pof;
+void FileBase::test(){
+ PLMD::OFile pof;
pof.open("ciao");
pof.printf("%s\n","test1");
pof.setLinePrefix("plumed: ");
@@ -48,7 +48,7 @@ void PlumedFileBase::test(){
pof.printField("x3",67.0).printField("x1",18.0).printField();
pof.close();
- PLMD::PlumedIFile pif;
+ PLMD::IFile pif;
std::string s;
pif.open("ciao");
pif.getline(s); std::printf("%s\n",s.c_str());
@@ -61,18 +61,18 @@ void PlumedFileBase::test(){
pif.close();
}
-size_t PlumedOFile::llwrite(const char*ptr,size_t s){
+size_t OFile::llwrite(const char*ptr,size_t s){
size_t r;
if(linked) return linked->llwrite(ptr,s);
if(! (comm && comm->Get_rank()>0)){
- if(!fp) plumed_merror("writing on uninitilized PlumedFile");
+ if(!fp) plumed_merror("writing on uninitilized File");
r=fwrite(ptr,1,s,fp);
}
if(comm) comm->Bcast(&r,1,0);
return r;
}
-size_t PlumedIFile::llread(char*ptr,size_t s){
+size_t IFile::llread(char*ptr,size_t s){
plumed_assert(fp);
size_t r;
r=fread(ptr,1,s,fp);
@@ -81,13 +81,13 @@ size_t PlumedIFile::llread(char*ptr,size_t s){
return r;
}
-PlumedFileBase& PlumedFileBase::link(FILE*fp){
+FileBase& FileBase::link(FILE*fp){
this->fp=fp;
cloned=true;
return *this;
}
-PlumedFileBase& PlumedFileBase::flush(){
+FileBase& FileBase::flush(){
fflush(fp);
if(heavyFlush){
fclose(fp);
@@ -96,27 +96,27 @@ PlumedFileBase& PlumedFileBase::flush(){
return *this;
}
-PlumedFileBase& PlumedFileBase::link(Communicator&comm){
+FileBase& FileBase::link(Communicator&comm){
plumed_massert(!fp,"cannot link an already open file");
this->comm=&comm;
return *this;
}
-PlumedFileBase& PlumedFileBase::link(PlumedMain&plumed){
+FileBase& FileBase::link(PlumedMain&plumed){
plumed_massert(!fp,"cannot link an already open file");
this->plumed=&plumed;
link(plumed.comm);
return *this;
}
-PlumedFileBase& PlumedFileBase::link(Action&action){
+FileBase& FileBase::link(Action&action){
plumed_massert(!fp,"cannot link an already open file");
this->action=&action;
link(action.plumed);
return *this;
}
-PlumedFileBase& PlumedFileBase::open(const std::string& path,const std::string& mode){
+FileBase& FileBase::open(const std::string& path,const std::string& mode){
plumed_assert(!cloned);
eof=false;
err=false;
@@ -135,7 +135,7 @@ PlumedFileBase& PlumedFileBase::open(const std::string& path,const std::string&
}
-bool PlumedFileBase::FileExist(const std::string& path){
+bool FileBase::FileExist(const std::string& path){
FILE *ff=NULL;
bool do_exist=false;
if(plumed){
@@ -150,13 +150,13 @@ bool PlumedFileBase::FileExist(const std::string& path){
return do_exist;
}
-bool PlumedFileBase::isOpen(){
+bool FileBase::isOpen(){
bool isopen=false;
if(fp) isopen=true;
return isopen;
}
-void PlumedFileBase::close(){
+void FileBase::close(){
plumed_assert(!cloned);
eof=false;
err=false;
@@ -164,7 +164,7 @@ void PlumedFileBase::close(){
fp=NULL;
}
-PlumedFileBase::PlumedFileBase():
+FileBase::FileBase():
fp(NULL),
comm(NULL),
plumed(NULL),
@@ -176,18 +176,18 @@ PlumedFileBase::PlumedFileBase():
{
}
-PlumedFileBase::~PlumedFileBase()
+FileBase::~FileBase()
{
if(plumed) plumed->eraseFile(*this);
if(!cloned && fp) fclose(fp);
}
-PlumedFileBase::operator bool()const{
+FileBase::operator bool()const{
return !eof;
}
-PlumedOFile::PlumedOFile():
+OFile::OFile():
linked(NULL),
fieldChanged(false)
{
@@ -201,23 +201,23 @@ PlumedOFile::PlumedOFile():
for(unsigned i=0;i<1000;++i) buffer_string[i]=0;
}
-PlumedOFile::~PlumedOFile(){
+OFile::~OFile(){
delete [] buffer_string;
delete [] buffer;
}
-PlumedOFile& PlumedOFile::link(PlumedOFile&l){
+OFile& OFile::link(OFile&l){
fp=NULL;
linked=&l;
return *this;
}
-PlumedOFile& PlumedOFile::setLinePrefix(const std::string&l){
+OFile& OFile::setLinePrefix(const std::string&l){
linePrefix=l;
return *this;
}
-int PlumedOFile::printf(const char*fmt,...){
+int OFile::printf(const char*fmt,...){
size_t pointer=strlen(buffer);
va_list arg;
va_start(arg, fmt);
@@ -253,7 +253,7 @@ int PlumedOFile::printf(const char*fmt,...){
return r;
}
-PlumedOFile& PlumedOFile::addConstantField(const std::string&name){
+OFile& OFile::addConstantField(const std::string&name){
Field f;
f.name=name;
const_fields.push_back(f);
@@ -261,36 +261,36 @@ PlumedOFile& PlumedOFile::addConstantField(const std::string&name){
}
-PlumedOFile& PlumedOFile::clearFields(){
+OFile& OFile::clearFields(){
fields.clear();
const_fields.clear();
previous_fields.clear();
return *this;
}
-PlumedOFile& PlumedOFile::fmtField(const std::string&fmt){
+OFile& OFile::fmtField(const std::string&fmt){
this->fieldFmt=fmt;
return *this;
}
-PlumedOFile& PlumedOFile::fmtField(){
+OFile& OFile::fmtField(){
this->fieldFmt="%23.16lg";
return *this;
}
-PlumedOFile& PlumedOFile::printField(const std::string&name,double v){
+OFile& OFile::printField(const std::string&name,double v){
sprintf(buffer_string,fieldFmt.c_str(),v);
printField(name,buffer_string);
return *this;
}
-PlumedOFile& PlumedOFile::printField(const std::string&name,int v){
+OFile& OFile::printField(const std::string&name,int v){
sprintf(buffer_string," %d",v);
printField(name,buffer_string);
return *this;
}
-PlumedOFile& PlumedOFile::printField(const std::string&name,const std::string & v){
+OFile& OFile::printField(const std::string&name,const std::string & v){
unsigned i;
for(i=0;i<const_fields.size();i++) if(const_fields[i].name==name) break;
if(i>=const_fields.size()){
@@ -305,7 +305,7 @@ PlumedOFile& PlumedOFile::printField(const std::string&name,const std::string &
return *this;
}
-PlumedOFile& PlumedOFile::setupPrintValue( Value *val ){
+OFile& OFile::setupPrintValue( Value *val ){
if( val->isPeriodic() ){
addConstantField("min_" + val->getName() );
addConstantField("max_" + val->getName() );
@@ -313,7 +313,7 @@ PlumedOFile& PlumedOFile::setupPrintValue( Value *val ){
return *this;
}
-PlumedOFile& PlumedOFile::printField( Value* val, const double& v ){
+OFile& OFile::printField( Value* val, const double& v ){
printField( val->getName(), v );
if( val->isPeriodic() ){
std::string min, max; val->getDomain( min, max );
@@ -323,7 +323,7 @@ PlumedOFile& PlumedOFile::printField( Value* val, const double& v ){
return *this;
}
-PlumedOFile& PlumedOFile::printField(){
+OFile& OFile::printField(){
bool reprint=false;
if(fieldChanged || fields.size()!=previous_fields.size()){
reprint=true;
@@ -351,7 +351,7 @@ PlumedOFile& PlumedOFile::printField(){
return *this;
}
-PlumedOFile& PlumedOFile::open(const std::string&path){
+OFile& OFile::open(const std::string&path){
plumed_assert(!cloned);
eof=false;
err=false;
@@ -392,7 +392,7 @@ PlumedOFile& PlumedOFile::open(const std::string&path){
}
-PlumedIFile& PlumedIFile::advanceField(){
+IFile& IFile::advanceField(){
plumed_assert(!inMiddleOfField);
std::string line;
bool done=false;
@@ -436,12 +436,12 @@ PlumedIFile& PlumedIFile::advanceField(){
return *this;
}
-PlumedIFile& PlumedIFile::open(const std::string&name){
- PlumedFileBase::open(name,"r");
+IFile& IFile::open(const std::string&name){
+ FileBase::open(name,"r");
return *this;
}
-PlumedIFile& PlumedIFile::scanFieldList(std::vector<std::string>&s){
+IFile& IFile::scanFieldList(std::vector<std::string>&s){
if(!inMiddleOfField) advanceField();
if(!*this) return *this;
s.clear();
@@ -450,7 +450,7 @@ PlumedIFile& PlumedIFile::scanFieldList(std::vector<std::string>&s){
return *this;
}
-bool PlumedIFile::FieldExist(const std::string& s){
+bool IFile::FieldExist(const std::string& s){
std::vector<std::string> slist;
scanFieldList(slist);
int mycount = (int) std::count(slist.begin(), slist.end(), s);
@@ -458,7 +458,7 @@ bool PlumedIFile::FieldExist(const std::string& s){
else return false;
}
-PlumedIFile& PlumedIFile::scanField(const std::string&name,std::string&str){
+IFile& IFile::scanField(const std::string&name,std::string&str){
if(!inMiddleOfField) advanceField();
if(!*this) return *this;
unsigned i=findField(name);
@@ -467,21 +467,21 @@ PlumedIFile& PlumedIFile::scanField(const std::string&name,std::string&str){
return *this;
}
-PlumedIFile& PlumedIFile::scanField(const std::string&name,double &x){
+IFile& IFile::scanField(const std::string&name,double &x){
std::string str;
scanField(name,str);
if(*this) Tools::convert(str,x);
return *this;
}
-PlumedIFile& PlumedIFile::scanField(const std::string&name,int &x){
+IFile& IFile::scanField(const std::string&name,int &x){
std::string str;
scanField(name,str);
if(*this) Tools::convert(str,x);
return *this;
}
-PlumedIFile& PlumedIFile::scanField(Value* val){
+IFile& IFile::scanField(Value* val){
double ff; scanField( val->getName(), ff );
val->set( ff );
if( FieldExist("min_" + val->getName() ) ){
@@ -495,7 +495,7 @@ PlumedIFile& PlumedIFile::scanField(Value* val){
return *this;
}
-PlumedIFile& PlumedIFile::scanField(){
+IFile& IFile::scanField(){
if(!ignoreFields){
for(unsigned i=0;i<fields.size();i++){
plumed_assert(fields[i].read);
@@ -505,17 +505,17 @@ PlumedIFile& PlumedIFile::scanField(){
return *this;
}
-PlumedIFile::PlumedIFile():
+IFile::IFile():
inMiddleOfField(false),
ignoreFields(false)
{
}
-PlumedIFile::~PlumedIFile(){
+IFile::~IFile(){
plumed_assert(!inMiddleOfField);
}
-PlumedIFile& PlumedIFile::getline(std::string &str){
+IFile& IFile::getline(std::string &str){
char tmp;
str="";
fpos_t pos;
@@ -531,20 +531,20 @@ PlumedIFile& PlumedIFile::getline(std::string &str){
return *this;
}
-unsigned PlumedIFile::findField(const std::string&name)const{
+unsigned IFile::findField(const std::string&name)const{
unsigned i;
for(i=0;i<fields.size();i++) if(fields[i].name==name) break;
if(i>=fields.size()) plumed_merror(name);
return i;
}
-void PlumedIFile::reset(bool reset){
+void IFile::reset(bool reset){
eof = reset;
err = reset;
if(!reset) clearerr(fp);
return;
}
-void PlumedIFile::allowIgnoredFields(){
+void IFile::allowIgnoredFields(){
ignoreFields=true;
}
diff --git a/src/tools/PlumedFile.h b/src/tools/File.h
similarity index 75%
rename from src/tools/PlumedFile.h
rename to src/tools/File.h
index 169ae9875adff17d286f51cb73fde5e35fd3e01a..99888dcebefb4e0ac775c70c0ad05812010095ad 100644
--- a/src/tools/PlumedFile.h
+++ b/src/tools/File.h
@@ -19,8 +19,8 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_tools_PlumedFile_h
-#define __PLUMED_tools_PlumedFile_h
+#ifndef __PLUMED_tools_File_h
+#define __PLUMED_tools_File_h
#include <cstdio>
#include <vector>
@@ -37,17 +37,17 @@ class Value;
/**
Base class for dealing with files.
-This class just provides things which are common among PlumedOFile and PlumedIFile
+This class just provides things which are common among OFile and IFile
*/
-class PlumedFileBase{
+class FileBase{
/// Copy constructor is disabled (private and unimplemented)
- PlumedFileBase(const PlumedFileBase&);
+ FileBase(const FileBase&);
/// Assignment operator is disabled (private and unimplemented)
- PlumedFileBase& operator=(const PlumedFileBase&);
+ FileBase& operator=(const FileBase&);
protected:
/// Internal tool.
-/// Base for PlumedIFile::Field and PlumedOFile::Field
+/// Base for IFile::Field and OFile::Field
class FieldBase{
// everything is public to simplify usage
public:
@@ -69,8 +69,8 @@ protected:
/// If true, file will not be closed in destructor
bool cloned;
/// Private constructor.
-/// In this manner one cannot instantiate a PlumedFileBase object
- PlumedFileBase();
+/// In this manner one cannot instantiate a FileBase object
+ FileBase();
/// Set to true when end of file is encountered
bool eof;
/// Set to true when error is encountered
@@ -81,22 +81,22 @@ protected:
bool heavyFlush;
public:
/// Link to an already open filed
- PlumedFileBase& link(FILE*);
+ FileBase& link(FILE*);
/// Link to a PlumedMain object
/// Automatically links also the corresponding Communicator.
- PlumedFileBase& link(PlumedMain&);
+ FileBase& link(PlumedMain&);
/// Link to a Communicator object
- PlumedFileBase& link(Communicator&);
+ FileBase& link(Communicator&);
/// Link to an Action object.
/// Automatically links also the corresponding PlumedMain and Communicator.
- PlumedFileBase& link(Action&);
+ FileBase& link(Action&);
/// Flushes the file to disk
- PlumedFileBase& flush();
+ FileBase& flush();
/// Closes the file
/// Should be used only for explicitely opened files.
void close();
/// Virtual destructor (allows inheritance)
- virtual ~PlumedFileBase();
+ virtual ~FileBase();
/// Runs a small testcase
static void test();
/// Check for error/eof.
@@ -104,7 +104,7 @@ public:
/// Set heavyFlush flag
void setHeavyFlush(){ heavyFlush=true;};
/// Opens the file (without auto-backup)
- PlumedFileBase& open(const std::string&name,const std::string& mode);
+ FileBase& open(const std::string&name,const std::string& mode);
/// Check if the file exists
bool FileExist(const std::string& path);
/// Check if a file is open
@@ -116,14 +116,14 @@ public:
Class for output files
This class provides features similar to those in the standard C "FILE*" type,
-but only for sequential output. See PlumedIFile for sequential input.
+but only for sequential output. See IFile for sequential input.
See the example here for a possible use:
\verbatim
-#include "PlumedFile.h"
+#include "File.h"
int main(){
- PLMD::PlumedOFile pof;
+ PLMD::OFile pof;
pof.open("ciao","w");
pof.printf("%s\n","test1");
pof.setLinePrefix("plumed: ");
@@ -157,16 +157,16 @@ Notes
- "x2" is declared as "constant", which means that it is written using the "SET"
keyword. Thus, everytime it is modified, all the headers are repeated in the output file.
- printField() without arguments is used as a "newline".
-- most methods return a reference to the PlumedOFile itself, to allow chaining many calls on the same line
+- most methods return a reference to the OFile itself, to allow chaining many calls on the same line
(this is similar to << operator in std::ostream)
*/
-class PlumedOFile:
-public virtual PlumedFileBase{
+class OFile:
+public virtual FileBase{
/// Pointer to a linked OFile.
-/// see link(PlumedOFile&)
- PlumedOFile* linked;
+/// see link(OFile&)
+ OFile* linked;
/// Internal buffer for printf
char* buffer_string;
/// Internal buffer (generic use)
@@ -199,58 +199,58 @@ public virtual PlumedFileBase{
unsigned findField(const std::string&name)const;
public:
/// Constructor
- PlumedOFile();
+ OFile();
/// Destructor
- ~PlumedOFile();
+ ~OFile();
/// Allows overloading of link
- using PlumedFileBase::link;
+ using FileBase::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&);
+ using FileBase::open;
+/// Allows linking this OFile to another one.
+/// In this way, everything written to this OFile will be immediately
+/// written on the linked OFile. Notice that a OFile should
+/// be either opened explicitly, linked to a FILE or linked to a OFile
+ OFile& link(OFile&);
/// Opens the file using automatic append/backup
- PlumedOFile& open(const std::string&name);
+ OFile& 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.
- PlumedOFile& setLinePrefix(const std::string&);
+/// be parsed using fields in a IFile.
+ OFile& setLinePrefix(const std::string&);
/// Set the format for writing double precision fields
- PlumedOFile& fmtField(const std::string&);
+ OFile& fmtField(const std::string&);
/// Reset the format for writing double precision fields to its default
- PlumedOFile& fmtField();
+ OFile& fmtField();
/// Set the value of a double precision field
- PlumedOFile& printField(const std::string&,double);
+ OFile& printField(const std::string&,double);
/// Set the value of a int field
- PlumedOFile& printField(const std::string&,int);
+ OFile& printField(const std::string&,int);
/// Set the value of a string field
- PlumedOFile& printField(const std::string&,const std::string&);
+ OFile& printField(const std::string&,const std::string&);
///
- PlumedOFile& addConstantField(const std::string&);
+ OFile& addConstantField(const std::string&);
/// Used to setup printing of values
- PlumedOFile& setupPrintValue( Value *val );
+ OFile& setupPrintValue( Value *val );
/// Print a value
- PlumedOFile& printField( Value* val, const double& v );
+ OFile& printField( Value* val, const double& v );
/** Close a line.
Typically used as
\verbatim
of.printField("a",a).printField("b",b).printField();
\endverbatim
*/
- PlumedOFile& printField();
+ OFile& printField();
/**
Resets the list of fields.
As it is only possible to add new constant fields (addConstantField()),
this method can be used to clean the field list.
*/
- PlumedOFile& clearFields();
+ OFile& clearFields();
/// Formatted output with explicit format - a la printf
int printf(const char*fmt,...);
/// Formatted output with << operator
template <class T>
- friend PlumedOFile& operator<<(PlumedOFile&,const T &);
+ friend OFile& operator<<(OFile&,const T &);
};
@@ -259,12 +259,12 @@ this method can be used to clean the field list.
Class for input files
This class provides features similar to those in the standard C "FILE*" type,
-but only for sequential input. See PlumedOFile for sequential output.
+but only for sequential input. See OFile for sequential output.
*/
-class PlumedIFile:
+class IFile:
/// Class identifying a single field for fielded output
-public virtual PlumedFileBase{
+public virtual FileBase{
class Field:
public FieldBase{
public:
@@ -281,24 +281,24 @@ public virtual PlumedFileBase{
/// Set to true if you want to allow fields to be ignored in the read in file
bool ignoreFields;
/// Advance to next field (= read one line)
- PlumedIFile& advanceField();
+ IFile& advanceField();
/// Find field index by name
unsigned findField(const std::string&name)const;
public:
/// Constructor
- PlumedIFile();
+ IFile();
/// Destructor
- ~PlumedIFile();
+ ~IFile();
/// Opens the file
- PlumedIFile& open(const std::string&name);
+ IFile& open(const std::string&name);
/// Gets the list of all fields
- PlumedIFile& scanFieldList(std::vector<std::string>&);
+ IFile& scanFieldList(std::vector<std::string>&);
/// Read a double field
- PlumedIFile& scanField(const std::string&,double&);
+ IFile& scanField(const std::string&,double&);
/// Read a int field
- PlumedIFile& scanField(const std::string&,int&);
+ IFile& scanField(const std::string&,int&);
/// Read a string field
- PlumedIFile& scanField(const std::string&,std::string&);
+ IFile& scanField(const std::string&,std::string&);
/**
Ends a field-formatted line.
@@ -307,22 +307,22 @@ Typically used as
if.scanField("a",a).scanField("b",b).scanField();
\endverbatim
*/
- PlumedIFile& scanField();
+ IFile& scanField();
/// Get a full line as a string
- PlumedIFile& getline(std::string&);
+ IFile& getline(std::string&);
/// Reset end of file
void reset(bool);
/// Check if a field exist
bool FieldExist(const std::string& s);
/// Read in a value
- PlumedIFile& scanField(Value* val);
+ IFile& scanField(Value* val);
/// Allow some of the fields in the input to be ignored
void allowIgnoredFields();
};
/// Write using << syntax
template <class T>
-PlumedOFile& operator<<(PlumedOFile&of,const T &t){
+OFile& operator<<(OFile&of,const T &t){
of.oss<<t;
of.printf("%s",of.oss.str().c_str());
of.oss.str("");
diff --git a/src/tools/Grid.cpp b/src/tools/Grid.cpp
index 6561e20d39fad6a8f140962a5c9c317657f3492f..88820bf478618527208b50b2cc8ddb3fa088d395 100644
--- a/src/tools/Grid.cpp
+++ b/src/tools/Grid.cpp
@@ -28,7 +28,7 @@
#include "Grid.h"
#include "Tools.h"
#include "core/Value.h"
-#include "PlumedFile.h"
+#include "File.h"
#include "PlumedException.h"
#include "KernelFunctions.h"
@@ -430,7 +430,7 @@ void Grid::scaleAllValuesAndDerivatives( const double& scalef ){
}
}
-void Grid::writeHeader(PlumedOFile& ofile){
+void Grid::writeHeader(OFile& ofile){
for(unsigned i=0;i<dimension_;++i){
ofile.addConstantField("min_" + argnames[i]);
ofile.addConstantField("max_" + argnames[i]);
@@ -439,7 +439,7 @@ void Grid::writeHeader(PlumedOFile& ofile){
}
}
-void Grid::writeToFile(PlumedOFile& ofile){
+void Grid::writeToFile(OFile& ofile){
vector<double> xx(dimension_);
vector<double> der(dimension_);
double f;
@@ -463,7 +463,7 @@ void Grid::writeToFile(PlumedOFile& ofile){
}
}
-Grid* Grid::create(const std::string& funcl, std::vector<Value*> args, PlumedIFile& ifile,
+Grid* Grid::create(const std::string& funcl, std::vector<Value*> args, IFile& ifile,
const vector<std::string> & gmin,const vector<std::string> & gmax,
const vector<unsigned> & nbin,bool dosparse, bool dospline, bool doder){
Grid* grid=Grid::create(funcl,args,ifile,dosparse,dospline,doder);
@@ -481,7 +481,7 @@ Grid* Grid::create(const std::string& funcl, std::vector<Value*> args, PlumedIFi
return grid;
}
-Grid* Grid::create(const std::string& funcl, std::vector<Value*> args, PlumedIFile& ifile, bool dosparse, bool dospline, bool doder)
+Grid* Grid::create(const std::string& funcl, std::vector<Value*> args, IFile& ifile, bool dosparse, bool dospline, bool doder)
{
Grid* grid=NULL;
unsigned nvar=args.size(); bool hasder=false; std::string pstring;
@@ -597,7 +597,7 @@ void SparseGrid::addValueAndDerivatives
for(unsigned int i=0;i<dimension_;++i) der_[index][i]+=der[i];
}
-void SparseGrid::writeToFile(PlumedOFile& ofile){
+void SparseGrid::writeToFile(OFile& ofile){
vector<double> xx(dimension_);
vector<double> der(dimension_);
double f;
diff --git a/src/tools/Grid.h b/src/tools/Grid.h
index d3999f17a0dbb85ee17f31f935f7c35035f35505..5e639159741f36872b65ca6c013699e91a7a1462 100644
--- a/src/tools/Grid.h
+++ b/src/tools/Grid.h
@@ -29,8 +29,8 @@
namespace PLMD{
class Value;
-class PlumedIFile;
-class PlumedOFile;
+class IFile;
+class OFile;
class KernelFunctions;
/// \ingroup TOOLBOX
@@ -94,12 +94,12 @@ public:
std::vector<unsigned> getNeighbors(const std::vector<double> & x,const std::vector<unsigned> & neigh) const;
/// write header for grid file
- void writeHeader(PlumedOFile& file);
+ void writeHeader(OFile& file);
/// read grid from file
- static Grid* create(const std::string&,std::vector<Value*>,PlumedIFile&,bool,bool,bool);
+ static Grid* create(const std::string&,std::vector<Value*>,IFile&,bool,bool,bool);
/// read grid from file and check boundaries are what is expected from input
- static Grid* create(const std::string&, std::vector<Value*>, PlumedIFile&,
+ static Grid* create(const std::string&, std::vector<Value*>, IFile&,
const std::vector<std::string>&,const std::vector<std::string>&,
const std::vector<unsigned>&,bool,bool,bool);
/// get grid size
@@ -132,7 +132,7 @@ public:
void addKernel( const KernelFunctions& kernel );
/// dump grid on file
- virtual void writeToFile(PlumedOFile&);
+ virtual void writeToFile(OFile&);
virtual ~Grid(){};
};
@@ -181,7 +181,7 @@ class SparseGrid : public Grid
void addValueAndDerivatives(unsigned index, double value, std::vector<double>& der);
/// dump grid on file
- void writeToFile(PlumedOFile&);
+ void writeToFile(OFile&);
virtual ~SparseGrid(){};
};
diff --git a/src/tools/KernelFunctions.cpp b/src/tools/KernelFunctions.cpp
index 3cc37830c9f90060f7249ad87d178d7ba0debe3c..a2c8211e1db94067c0110bc90336a670e1bb8f41 100644
--- a/src/tools/KernelFunctions.cpp
+++ b/src/tools/KernelFunctions.cpp
@@ -212,7 +212,7 @@ double KernelFunctions::evaluate( const std::vector<Value*>& pos, std::vector<do
return kval;
}
-KernelFunctions* KernelFunctions::read( PlumedIFile* ifile, const std::vector<std::string>& valnames ){
+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;
if( sss=="true" ){
diff --git a/src/tools/KernelFunctions.h b/src/tools/KernelFunctions.h
index 3a7b7e72840e45ad7d4c199ff0db486d50b48aaf..36e5080431b43b2d4aa5bba36f109c22ac495749 100644
--- a/src/tools/KernelFunctions.h
+++ b/src/tools/KernelFunctions.h
@@ -59,7 +59,7 @@ public:
/// Evaluate the kernel function
double evaluate( const std::vector<Value*>& pos, std::vector<double>& derivatives, bool usederiv=true ) const;
/// Read a kernel function from a file
- static KernelFunctions* read( PlumedIFile* ifile, const std::vector<std::string>& valnames );
+ static KernelFunctions* read( IFile* ifile, const std::vector<std::string>& valnames );
};
inline
diff --git a/src/tools/Log.h b/src/tools/Log.h
index aa1df3fb44c23f49a5d1b1048d2c0def38e5db99..b75ca716885983a741e88b7da6e58b1aeaf898e9 100644
--- a/src/tools/Log.h
+++ b/src/tools/Log.h
@@ -26,7 +26,7 @@
#include <string>
#include <sstream>
-#include "PlumedFile.h"
+#include "File.h"
namespace PLMD{
@@ -39,7 +39,7 @@ class Communicator;
/// lines with the "PLUMED:" prefix, useful to grep out plumed
/// log from output
class Log :
- public PlumedOFile
+ public OFile
{
};
diff --git a/src/tools/Tools.cpp b/src/tools/Tools.cpp
index 0a5c20b221a491e4f00ed5c092c20d3496d81d07..438226eb9ee0d5a85922d9a361dac9b7018e137b 100644
--- a/src/tools/Tools.cpp
+++ b/src/tools/Tools.cpp
@@ -23,7 +23,7 @@
#include "Tools.h"
#include "AtomNumber.h"
#include "PlumedException.h"
-#include "PlumedFile.h"
+#include "File.h"
#include <cstring>
#include <dirent.h>
@@ -134,7 +134,7 @@ vector<string> Tools::getWords(const string & line,const char* separators,int *
return words;
}
-bool Tools::getParsedLine(PlumedIFile& ifile,vector<string> & words){
+bool Tools::getParsedLine(IFile& ifile,vector<string> & words){
string line("");
words.clear();
bool stat;
diff --git a/src/tools/Tools.h b/src/tools/Tools.h
index b8a9c2c9430d879bea7b4fa88a4adea33499334c..9db36d0132c67bcea281ae0b41f4bb910965509f 100644
--- a/src/tools/Tools.h
+++ b/src/tools/Tools.h
@@ -33,7 +33,7 @@
namespace PLMD{
-class PlumedIFile;
+class IFile;
/// \ingroup TOOLBOX
/// Very small non-zero number
@@ -62,7 +62,7 @@ public:
/// Get a parsed line from the file pointer ifile
/// This function already takes care of joining continued lines and splitting the
/// resulting line into an array of words
- static bool getParsedLine(PlumedIFile&ifile,std::vector<std::string> & line);
+ static bool getParsedLine(IFile&ifile,std::vector<std::string> & line);
/// Convert a string to a double, reading it
static bool convert(const std::string & str,double & t);
/// Convert a string to a int, reading it