File opening tools moved to PlumedMain

I moved the tools to open a file with a specific prefix to PlumedMain.
This allows easily to use them also to open the input file, which in
turn means that we will be able to do bias-exchange and Hamiltonian
replica exchange

src/Action.cpp

@@ -31,20 +31,14 @@ Action::Action(const ActionOptions&ao):
 }
 
 FILE* Action::fopen(const char *path, const char *mode){
-  std::string mmode(mode);
-  std::string ppath(path);
-  std::string suffix(plumed.getSuffix());
-  std::string ppathsuf=ppath+suffix;
-  FILE*fp=std::fopen(const_cast<char*>(ppathsuf.c_str()),const_cast<char*>(mmode.c_str()));
-  if(!fp) std::fopen(const_cast<char*>(ppath.c_str()),const_cast<char*>(mmode.c_str()));
-  assert(fp);
+  FILE* fp=plumed.fopen(path,mode);
   files.insert(fp);
   return fp;
 }
 
 int Action::fclose(FILE*fp){
   files.erase(fp);
-  return std::fclose(fp);
+  return plumed.fclose(fp);
 }
 
 void Action::fflush(){

src/PlumedMain.cpp

@@ -300,6 +300,7 @@ void PlumedMain::init(){
   log.printf("Precision of reals: %d\n",atoms.getRealPrecision());
   log.printf("Running over %d %s\n",comm.Get_size(),(comm.Get_size()>1?"nodes":"node"));
   log.printf("Number of atoms: %d\n",atoms.getNatoms());
+  log.printf("File suffix: %s\n",getSuffix().c_str());
   if(plumedDat.length()>0){
     readInputFile(plumedDat);
     plumedDat="";
@@ -500,6 +501,23 @@ void PlumedMain::load(std::vector<std::string> & words){
 double PlumedMain::getBias() const{
   return bias;
 }
+
+FILE* PlumedMain::fopen(const char *path, const char *mode){
+  std::string mmode(mode);
+  std::string ppath(path);
+  std::string suffix(getSuffix());
+  std::string ppathsuf=ppath+suffix;
+  FILE*fp=std::fopen(const_cast<char*>(ppathsuf.c_str()),const_cast<char*>(mmode.c_str()));
+  if(!fp) fp=std::fopen(const_cast<char*>(ppath.c_str()),const_cast<char*>(mmode.c_str()));
+  assert(fp);
+  return fp;
+}
+
+int PlumedMain::fclose(FILE*fp){
+  return std::fclose(fp);
+}
+
+
 //////////////////////////////////////////////////////////////////////////////////////////////////////////////////
 
 

src/PlumedMain.h

@@ -5,6 +5,7 @@
 #include "ActionSet.h"
 #include "Atoms.h"
 #include "PlumedCommunicator.h"
+#include <cstdio>
 #include <string>
 #include <vector>
 
@@ -136,6 +137,8 @@ public:
   void setSuffix(const std::string&);
 /// get the value of the bias
   double getBias()const;
+  FILE* fopen(const char *path, const char *mode);
+  int fclose(FILE*fp);
 };
 
 /////