From 3319395aca70c30762931ad792eecee479ac8712 Mon Sep 17 00:00:00 2001
From: Carlo Camilloni <carlo.camilloni@gmail.com>
Date: Tue, 21 Jun 2016 19:48:16 +0200
Subject: [PATCH] checkpointing: preliminary feature, a checkpoinitng flag is
read that is used to flush all the actions [ makedoc ]
---
CHANGES/Unreleased.txt | 3 ++-
src/core/PlumedMain.cpp | 15 +++++++++++----
src/core/PlumedMain.h | 3 +++
3 files changed, 16 insertions(+), 5 deletions(-)
diff --git a/CHANGES/Unreleased.txt b/CHANGES/Unreleased.txt
index 0fc300440..43f5e1cda 100644
--- a/CHANGES/Unreleased.txt
+++ b/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.
*/
diff --git a/src/core/PlumedMain.cpp b/src/core/PlumedMain.cpp
index 0fe1d5dbf..4a3f52b1d 100644
--- a/src/core/PlumedMain.cpp
+++ b/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();
diff --git a/src/core/PlumedMain.h b/src/core/PlumedMain.h
index c6ca0910c..829b7ba47 100644
--- a/src/core/PlumedMain.h
+++ b/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;
--
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