diff --git a/src/GenericDumpDerivatives.cpp b/src/GenericDumpDerivatives.cpp
index f516739b9076d3e35346e6e9ffe301be4f51c49c..1aa3f46e0167e86b46aa778f0d854b4b9ed13cf4 100644
--- a/src/GenericDumpDerivatives.cpp
+++ b/src/GenericDumpDerivatives.cpp
@@ -102,11 +102,6 @@ fmt("%15.10f")
for(unsigned i=1;i<nargs;i++){
if( npar!=getPntrToArgument(i)->getNumberOfDerivatives() ) error("the number of derivatives must be the same in all values being dumped");
}
- of.addField("time");
- of.addField("parameter");
- for(unsigned i=0;i<nargs;i++){
- of.addField(getPntrToArgument(i)->getName());
- };
checkRead();
}
diff --git a/src/GenericDumpForces.cpp b/src/GenericDumpForces.cpp
index 8be1c03ffa3124d2ac73d5aa01448e44e5606930..a4810c10b139383cae3f7d1da3fa203a46e4fcd7 100644
--- a/src/GenericDumpForces.cpp
+++ b/src/GenericDumpForces.cpp
@@ -91,10 +91,6 @@ ActionWithArguments(ao)
of.link(*this);
log.printf(" on file %s\n",file.c_str());
if( getNumberOfArguments()==0 ) error("no arguments have been specified");
- of.addField("time");
- for(unsigned i=0;i<getNumberOfArguments();i++){
- of.addField(getPntrToArgument(i)->getName());
- };
checkRead();
}
diff --git a/src/GenericDumpProjections.cpp b/src/GenericDumpProjections.cpp
index 8d0eb7b52bf1d436829b4105cb08a25baea53a14..5c5457f77f56a33668331381184a906352561513 100644
--- a/src/GenericDumpProjections.cpp
+++ b/src/GenericDumpProjections.cpp
@@ -79,12 +79,6 @@ fmt("%15.10f")
of.open(file.c_str(),"wa");
log.printf(" on file %s\n",file.c_str());
log.printf(" with format %s\n",fmt.c_str());
- of.addField("time");
- for(unsigned i=0;i<getNumberOfArguments();i++){
- for(unsigned j=0;j<getNumberOfArguments();j++){
- of.addField(getPntrToArgument(i)->getName()+"-"+getPntrToArgument(j)->getName());
- }
- };
checkRead();
}
diff --git a/src/GenericPrint.cpp b/src/GenericPrint.cpp
index c2d7bff02b7d1241c279f79977e29d18c18ee8be..009c1d8a365f3c63304f0d8eb749850cb8f7df06 100644
--- a/src/GenericPrint.cpp
+++ b/src/GenericPrint.cpp
@@ -59,7 +59,6 @@ public ActionWithArguments
PlumedOFile ofile;
string fmt;
// small internal utility
- void updateFields();
/////////////////////////////////////////
// these are crazy things just for debug:
// they allow to change regularly the
@@ -108,7 +107,6 @@ rotate(0)
log.printf(" on plumed log file\n");
ofile.link(log);
}
- updateFields();
parse("FMT",fmt);
fmt=" "+fmt;
log.printf(" with format %s\n",fmt.c_str());
@@ -123,7 +121,6 @@ rotate(0)
vector<Value*> a(1,rotateArguments[0]);
requestArguments(vector<Value*>(1,rotateArguments[0]));
rotateLast=0;
- updateFields();
}
/////////////////////////////////////////
checkRead();
@@ -141,7 +138,6 @@ void GenericPrint::prepare(){
rotateLast++;
rotateLast%=rotateArguments.size();
requestArguments(vector<Value*>(1,rotateArguments[rotateLast]));
- updateFields();
}
}
/////////////////////////////////////////
@@ -160,14 +156,6 @@ void GenericPrint::update(){
GenericPrint::~GenericPrint(){
}
-void GenericPrint::updateFields(){
- ofile.clearFields();
- ofile.addField("time");
- for(unsigned i=0;i<getNumberOfArguments();i++){
- ofile.addField(getPntrToArgument(i)->getName());
- }
-}
-
}
diff --git a/src/PlumedFile.cpp b/src/PlumedFile.cpp
index 4da1d7dd192f286d5585978b9949306e3b97e1d7..6cccbb783cf7c8e05a225f61bdc52218bb9c7f58 100644
--- a/src/PlumedFile.cpp
+++ b/src/PlumedFile.cpp
@@ -28,6 +28,8 @@
#include <cstdarg>
#include <cstring>
+#include <iostream>
+
using namespace PLMD;
void PlumedFileBase::test(){
@@ -37,9 +39,7 @@ void PlumedFileBase::test(){
pof.setLinePrefix("plumed: ");
pof.printf("%s\n","test2");
pof.setLinePrefix("");
- pof.addField("x1");
pof.addConstantField("x2").printField("x2",67.0);
- pof.addField("x3");
pof.printField("x1",10.0).printField("x3",20.12345678901234567890).printField();
pof.printField("x1",10.0).printField("x3",-1e70*20.12345678901234567890).printField();
pof.printField("x3",10.0).printField("x2",777.0).printField("x1",-1e70*20.12345678901234567890).printField();
@@ -82,8 +82,10 @@ size_t PlumedIFile::llread(char*ptr,size_t s){
if(feof(fp)) leof=1;
}
if(comm) comm->Bcast(&r,1,0);
- if(comm) comm->Bcast(ptr,r,0);
- if(comm) comm->Bcast(&leof,r,0);
+// I explicitly cast sizes to int, as BCast is getting an int as second argument
+ if(comm) comm->Bcast(ptr,int(r),0);
+// I explicitly cast sizes to int, as BCast is getting an int as second argument
+ if(comm) comm->Bcast(&leof,int(r),0);
if(leof) eof=true;
return r;
}
@@ -165,7 +167,11 @@ PlumedOFile::PlumedOFile():
{
fmtField();
buffer=new char[buflen];
+// these are set to zero to avoid valgrind errors
+ for(unsigned i=0;i<buflen;++i) buffer[i]=0;
buffer_string=new char [1000];
+// these are set to zero to avoid valgrind errors
+ for(unsigned i=0;i<1000;++i) buffer_string[i]=0;
}
PlumedOFile::~PlumedOFile(){
@@ -185,7 +191,7 @@ PlumedOFile& PlumedOFile::setLinePrefix(const std::string&l){
}
int PlumedOFile::printf(const char*fmt,...){
- int pointer=strlen(buffer);
+ size_t pointer=strlen(buffer);
va_list arg;
va_start(arg, fmt);
int r=std::vsnprintf(&buffer[pointer],buflen-pointer,fmt,arg);
@@ -206,27 +212,18 @@ int PlumedOFile::printf(const char*fmt,...){
return r;
}
-PlumedOFile& PlumedOFile::addField(const std::string&name){
- Field f;
- f.name=name;
- fields.push_back(f);
- fieldChanged=true;
- return *this;
-}
-
PlumedOFile& PlumedOFile::addConstantField(const std::string&name){
Field f;
f.name=name;
- f.constant=true;
- fields.push_back(f);
- fieldChanged=true;
+ const_fields.push_back(f);
return *this;
}
PlumedOFile& PlumedOFile::clearFields(){
fields.clear();
- fieldChanged=true;
+ const_fields.clear();
+ previous_fields.clear();
return *this;
}
@@ -240,13 +237,6 @@ PlumedOFile& PlumedOFile::fmtField(){
return *this;
}
-unsigned PlumedOFile::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;
-}
-
PlumedOFile& PlumedOFile::printField(const std::string&name,double v){
sprintf(buffer_string,fieldFmt.c_str(),v);
printField(name,buffer_string);
@@ -260,36 +250,45 @@ PlumedOFile& PlumedOFile::printField(const std::string&name,int v){
}
PlumedOFile& PlumedOFile::printField(const std::string&name,const std::string & v){
- unsigned i=findField(name);
- if(fields[i].constant) fieldChanged=true;
- fields[i].value=v;
- fields[i].set=true;
+ unsigned i;
+ for(i=0;i<const_fields.size();i++) if(const_fields[i].name==name) break;
+ if(i>=const_fields.size()){
+ Field field;
+ field.name=name;
+ field.value=v;
+ fields.push_back(field);
+ } else {
+ if(const_fields[i].value!=v) fieldChanged=true;
+ const_fields[i].value=v;
+ }
return *this;
}
PlumedOFile& PlumedOFile::printField(){
- if(fieldChanged){
- printf("#! FIELDS");
- for(unsigned i=0;i<fields.size();i++){
- if(!fields[i].constant)
- printf(" %s",fields[i].name.c_str());
+ bool reprint=false;
+ if(fieldChanged || fields.size()!=previous_fields.size()){
+ reprint=true;
+ } else for(unsigned i=0;i<fields.size();i++){
+ if( previous_fields[i].name!=fields[i].name ||
+ (fields[i].constant && fields[i].value!=previous_fields[i].value) ){
+ reprint=true;
+ break;
}
+ }
+ if(reprint){
+ printf("#! FIELDS");
+ for(unsigned i=0;i<fields.size();i++) printf(" %s",fields[i].name.c_str());
printf("\n");
- for(unsigned i=0;i<fields.size();i++)
- if(fields[i].constant){
- printf("#! SET %s %s",fields[i].name.c_str(),fields[i].value.c_str());
+ for(unsigned i=0;i<const_fields.size();i++){
+ printf("#! SET %s %s",const_fields[i].name.c_str(),const_fields[i].value.c_str());
printf("\n");
}
}
- fieldChanged=false;
- for(unsigned i=0;i<fields.size();i++){
- plumed_assert(fields[i].set);
- if(!fields[i].constant){
- printf("%s",fields[i].value.c_str());
- fields[i].set=false;
- }
- }
+ for(unsigned i=0;i<fields.size();i++) printf("%s",fields[i].value.c_str());
printf("\n");
+ previous_fields=fields;
+ fields.clear();
+ fieldChanged=false;
return *this;
}
diff --git a/src/PlumedFile.h b/src/PlumedFile.h
index 6bc9ff44cb9bf35820fad9673456fb159a68fdcd..37976af70828f148bd0725983eda87d4caaba2d7 100644
--- a/src/PlumedFile.h
+++ b/src/PlumedFile.h
@@ -163,9 +163,6 @@ public virtual PlumedFileBase{
/// Class identifying a single field for fielded output
class Field:
public FieldBase{
- public:
- bool set;
- Field(): set(false) {}
};
/// Low-level write
size_t llwrite(const char*,size_t);
@@ -175,8 +172,12 @@ public virtual PlumedFileBase{
bool fieldChanged;
/// Format for fields writing
std::string fieldFmt;
-/// All the defined fields
+/// All the previously defined variable fields
+ std::vector<Field> previous_fields;
+/// All the defined variable fields
std::vector<Field> fields;
+/// All the defined constant fields
+ std::vector<Field> const_fields;
/// Prefix for line (e.g. "PLUMED: ")
std::string linePrefix;
/// Temporary ostringstream for << output
@@ -199,15 +200,6 @@ public:
/// Typically "PLUMED: ". Notice that lines with a prefix cannot
/// be parsed using fields in a PlumedIFile.
PlumedOFile& setLinePrefix(const std::string&);
-/// Add a field.
-/// Fields are written as one per column, and a commented header
-/// with the list of fields is written whenever the list of fields
-/// changes.
- PlumedOFile& addField(const std::string&);
-/// Add a constant field.
-/// Constant fields are typically written on separate lines
-/// in the output
- PlumedOFile& addConstantField(const std::string&);
/// Set the format for writing double precision fields
PlumedOFile& fmtField(const std::string&);
/// Reset the format for writing double precision fields to its default
@@ -218,6 +210,8 @@ public:
PlumedOFile& printField(const std::string&,int);
/// Set the value of a string field
PlumedOFile& printField(const std::string&,const std::string&);
+///
+ PlumedOFile& addConstantField(const std::string&);
/** Close a line.
Typically used as
\verbatim
diff --git a/src/PlumedMain.cpp b/src/PlumedMain.cpp
index 30384fbfaefab368d9f840d6c605ead0b57bdb60..2619090b831157069fd666dce41feb034a6e2ee6 100644
--- a/src/PlumedMain.cpp
+++ b/src/PlumedMain.cpp
@@ -355,6 +355,7 @@ void PlumedMain::readInputFile(std::string str){
plumed_assert(initialized);
log.printf("FILE: %s\n",str.c_str());
PlumedIFile ifile;
+ ifile.link(*this);
ifile.open(str,"r");
std::vector<std::string> words;
exchangepatterns.setFlag(exchangepatterns.NONE);