checkpointing: preliminary feature, a checkpoinitng flag is read

that is used to flush all the actions
[ makedoc ]

CHANGES/Unreleased.txt

@@ -58,6 +58,7 @@ Changes from version 2.2 which are relevant for users:
     the patch is still backward compatible with older PLUMED version, but the charges will only be passed
     when using PLUMED 2.3 or later.
   - Patches for GROMACS 4.6 and 5.1 incorporate Hamiltonian replica exchange, see \ref hrex
+  - Gromacs 5.1 flushes the plumed output files upon checkpointing 
 - New features for existing actions:
   - The SPECIES and SPECIESA keyword in MultiColvars can now take a multicolvar as input.  This allows one
     to calculate quantities such as the Q4 parameters for those atoms that have a coordination number greater
@@ -75,7 +76,7 @@ Changes from version 2.2 which are relevant for users:
   - PLUMED now generate a VIM syntax file, see \ref VimSyntax
 
 For developers:
-- Added new strings for plumed cmd: setMDMassUnits, setMDChargeUnits, readInputLine, performCalcNoUpdate, and update.
+- Added new strings for plumed cmd: setMDMassUnits, setMDChargeUnits, readInputLine, performCalcNoUpdate, update and doCheckPoint.
 
 
 */

src/core/PlumedMain.cpp

@@ -80,6 +80,7 @@ PlumedMain::PlumedMain():
   exchangePatterns(*new(ExchangePatterns)),
   exchangeStep(false),
   restart(false),
+  doCheckPoint(false),
   stopFlag(NULL),
   stopNow(false),
   novirial(false),
@@ -368,6 +369,14 @@ void PlumedMain::cmd(const std::string & word,void*val){
         CHECK_NOTNULL(val,word);
         if(*static_cast<int*>(val)!=0) restart=true;
         break;
+      /* ADDED WITH API==4 */
+      case cmd_doCheckPoint:
+        CHECK_INIT(initialized,word);
+        CHECK_NOTNULL(val,word);
+        doCheckPoint = false;
+        if(*static_cast<int*>(val)!=0) doCheckPoint = true;
+        break;
+      /* STOP API */
       case cmd_setMDEngine:
         CHECK_NOTINIT(initialized,word);
         CHECK_NOTNULL(val,word);
@@ -505,9 +514,6 @@ void PlumedMain::readInputFile(std::string str){
   log.printf("END FILE: %s\n",str.c_str());
   log.flush();
 
-  //comm.Barrier();	
-  //if(comm.Get_rank()==0) multi_sim_comm.Barrier();	
-
   pilots=actionSet.select<ActionPilot*>();
 }
 
@@ -736,7 +742,8 @@ void PlumedMain::update(){
 
 // flush by default every 10000 steps
 // hopefully will not affect performance
-  if(step%10000==0){
+// also if receive checkpointing signal
+  if(step%10000==0||doCheckPoint){
     fflush();
     log.flush();
     for(ActionSet::const_iterator p=actionSet.begin();p!=actionSet.end();++p) (*p)->fflush();

src/core/PlumedMain.h

@@ -133,6 +133,9 @@ private:
 /// Flag for restart
   bool restart;
 
+/// Flag for checkpointig
+  bool doCheckPoint;
+
   std::set<FileBase*> files;
   typedef std::set<FileBase*>::iterator files_iterator;