Added class to manage bibliography

src/BiasMetaD.cpp

@@ -251,6 +251,12 @@ grid_(false)
   }else{
    hillsfile_=fopen(hillsfname.c_str(),"w");
   } 
+
+  log<<"  Bibliography "<<plumed.cite("Laio and Parrinello, PNAS 99, 12562 (2002)");
+  if(welltemp_) log<<plumed.cite(
+    "Barducci, Bussi, and Parrinello, Phys. Rev. Lett. 100, 020603 (2008)");
+  log<<"\n";
+
 }
 
 void BiasMetaD::readGaussians(FILE* file)

src/Citations.cpp

+#include "Citations.h"
+#include "PlumedException.h"
+#include "Tools.h"
+#include <iostream>
+
+using namespace std;
+using namespace PLMD;
+
+std::string Citations::cite(const std::string & item){
+  unsigned i;
+  for(i=0;i<items.size();++i) if(items[i]==item) break;
+  if(i==items.size()) items.push_back(item);
+  plumed_assert(i<items.size());
+  string ret;
+  Tools::convert(i,ret);
+  ret="["+ret+"]";
+  return ret;
+}
+
+std::ostream & PLMD::operator<<(std::ostream &log,const Citations&cit){
+  for(unsigned i=0;i<cit.items.size();++i)
+    log<<"  ["<<i<<"] "<<cit.items[i]<<"\n";
+  return log;
+}
+
+

src/Citations.h

+#ifndef __PLUMED_Citations_h
+#define __PLUMED_Citations_h
+
+#include <vector>
+#include <string>
+#include <iosfwd>
+
+namespace PLMD{
+
+/**
+Class taking care of bibliography.
+*/
+
+class Citations{
+  std::vector<std::string> items;
+public:
+/// Add a citation.
+/// It returns a string containing the reference number, something like "[10]"
+  std::string cite(const std::string &);
+/// Dumps the bibliography.
+/// It writes on the ostream the list of all the bibliographic itemrs
+/// prefixed with their reference number
+  friend std::ostream &operator<<(std::ostream &,const Citations&);
+};
+
+std::ostream & operator<<(std::ostream &,const Citations&);
+
+}
+
+#endif

src/PlumedMain.cpp

@@ -20,6 +20,7 @@
 #include "PlumedCommunicator.h"
 #include "CLToolMain.h"
 #include "Stopwatch.h"
+#include "Citations.h"
 
 using namespace PLMD;
 using namespace std;
@@ -32,6 +33,7 @@ PlumedMain::PlumedMain():
   grex(NULL),
   initialized(false),
   log(*new Log(comm)),
+  citations(*new Citations),
   step(0),
   active(false),
   atoms(*new Atoms(*this)),
@@ -48,6 +50,7 @@ PlumedMain::~PlumedMain(){
   stopwatch.stop();
   if(initialized) log<<stopwatch;
   delete &actionSet;
+  delete &citations;
   delete &atoms;
   delete &log;
   if(grex)  delete grex;
@@ -302,6 +305,10 @@ void PlumedMain::init(){
   }
   atoms.updateUnits();
   log.printf("Timestep: %f\n",atoms.getTimeStep());
+  log<<"Relevant bibliography:\n";
+  log<<citations;
+  log<<"Please read and cite where appropriate!\n";
+  log<<"Finished setupt\n";
 }
 
 void PlumedMain::readInputFile(std::string str){
@@ -537,6 +544,10 @@ int PlumedMain::fclose(FILE*fp){
   return std::fclose(fp);
 }
 
+std::string PlumedMain::cite(const std::string&item){
+  return citations.cite(item);
+}
+
 
 //////////////////////////////////////////////////////////////////////////////////////////////////////////////////
 

src/PlumedMain.h

@@ -35,6 +35,7 @@ class ActionSet;
 class DLLoader;
 class PlumedCommunicator;
 class Stopwatch;
+class Citations;
 
 /// Main plumed object.
 /// In MD engines this object is not manipulated directly but it is wrapped in
@@ -61,7 +62,8 @@ private:
   std::string MDEngine;
 /// Log stream
   Log& log;
-
+/// Citations holder
+  Citations& citations;
 
 /// Present step number.
   int step;
@@ -94,6 +96,9 @@ public:
 /// Flag to switch off virial calculation (for debug)
   bool novirial;
 
+/// Add a citation, returning a string containing the reference number, something like "[10]"
+  std::string cite(const std::string&);
+
 public:
   PlumedMain();
 // this is to access to WithCmd versions of cmd (allowing overloading of a virtual method)