diff --git a/src/core/PlumedMain.cpp b/src/core/PlumedMain.cpp
index c32b5939f5ee4c8d8aa96f7bc915bef91bad9e6d..774bf08692ea94d654d9bb9f5e41fa7969ce9bee 100644
--- a/src/core/PlumedMain.cpp
+++ b/src/core/PlumedMain.cpp
@@ -102,367 +102,379 @@ PlumedMain::~PlumedMain() {
void PlumedMain::cmd(const std::string & word,void*val) {
- stopwatch.start();
-
- std::vector<std::string> words=Tools::getWords(word);
- unsigned nw=words.size();
- if(nw==0) {
- // do nothing
- } else {
- int iword=-1;
- double d;
- const auto it=plumedMainWordMap().find(words[0]);
- if(it!=plumedMainWordMap().end()) iword=it->second;
- switch(iword) {
- case cmd_setBox:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- atoms.setBox(val);
- break;
- case cmd_setPositions:
- CHECK_INIT(initialized,word);
- atoms.setPositions(val);
- break;
- case cmd_setMasses:
- CHECK_INIT(initialized,word);
- atoms.setMasses(val);
- break;
- case cmd_setCharges:
- CHECK_INIT(initialized,word);
- atoms.setCharges(val);
- break;
- case cmd_setPositionsX:
- CHECK_INIT(initialized,word);
- atoms.setPositions(val,0);
- break;
- case cmd_setPositionsY:
- CHECK_INIT(initialized,word);
- atoms.setPositions(val,1);
- break;
- case cmd_setPositionsZ:
- CHECK_INIT(initialized,word);
- atoms.setPositions(val,2);
- break;
- case cmd_setVirial:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- atoms.setVirial(val);
- break;
- case cmd_setEnergy:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- atoms.setEnergy(val);
- break;
- case cmd_setForces:
- CHECK_INIT(initialized,word);
- atoms.setForces(val);
- break;
- case cmd_setForcesX:
- CHECK_INIT(initialized,word);
- atoms.setForces(val,0);
- break;
- case cmd_setForcesY:
- CHECK_INIT(initialized,word);
- atoms.setForces(val,1);
- break;
- case cmd_setForcesZ:
- CHECK_INIT(initialized,word);
- atoms.setForces(val,2);
- break;
- case cmd_calc:
- CHECK_INIT(initialized,word);
- calc();
- break;
- case cmd_prepareDependencies:
- CHECK_INIT(initialized,word);
- prepareDependencies();
- break;
- case cmd_shareData:
- CHECK_INIT(initialized,word);
- shareData();
- break;
- case cmd_prepareCalc:
- CHECK_INIT(initialized,word);
- prepareCalc();
- break;
- case cmd_performCalc:
- CHECK_INIT(initialized,word);
- performCalc();
- break;
- case cmd_performCalcNoUpdate:
- CHECK_INIT(initialized,word);
- performCalcNoUpdate();
- break;
- case cmd_update:
- CHECK_INIT(initialized,word);
- update();
- break;
- case cmd_setStep:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- step=(*static_cast<int*>(val));
- atoms.startStep();
- break;
- case cmd_setStepLong:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- step=(*static_cast<long int*>(val));
- atoms.startStep();
- break;
- // words used less frequently:
- case cmd_setAtomsNlocal:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- atoms.setAtomsNlocal(*static_cast<int*>(val));
- break;
- case cmd_setAtomsGatindex:
- CHECK_INIT(initialized,word);
- atoms.setAtomsGatindex(static_cast<int*>(val),false);
- break;
- case cmd_setAtomsFGatindex:
- CHECK_INIT(initialized,word);
- atoms.setAtomsGatindex(static_cast<int*>(val),true);
- break;
- case cmd_setAtomsContiguous:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- atoms.setAtomsContiguous(*static_cast<int*>(val));
- break;
- case cmd_createFullList:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- atoms.createFullList(static_cast<int*>(val));
- break;
- case cmd_getFullList:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- atoms.getFullList(static_cast<int**>(val));
- break;
- case cmd_clearFullList:
- CHECK_INIT(initialized,word);
- atoms.clearFullList();
- break;
- /* ADDED WITH API==6 */
- case cmd_getDataRank:
- CHECK_INIT(initialized,words[0]); plumed_assert(nw==2 || nw==3);
- if( nw==2 ) DataFetchingObject::get_rank( actionSet, words[1], "", static_cast<long*>(val) );
- else DataFetchingObject::get_rank( actionSet, words[1], words[2], static_cast<long*>(val) );
- break;
- /* ADDED WITH API==6 */
- case cmd_getDataShape:
- CHECK_INIT(initialized,words[0]); plumed_assert(nw==2 || nw==3);
- if( nw==2 ) DataFetchingObject::get_shape( actionSet, words[1], "", static_cast<long*>(val) );
- else DataFetchingObject::get_shape( actionSet, words[1], words[2], static_cast<long*>(val) );
- break;
- /* ADDED WITH API==6 */
- case cmd_setMemoryForData:
- CHECK_INIT(initialized,words[0]); plumed_assert(nw==2 || nw==3);
- if( nw==2 ) mydatafetcher->setData( words[1], "", val );
- else mydatafetcher->setData( words[1], words[2], val );
- break;
- case cmd_read:
- CHECK_INIT(initialized,word);
- if(val)readInputFile(static_cast<char*>(val));
- else readInputFile("plumed.dat");
- break;
- case cmd_readInputLine:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- readInputLine(static_cast<char*>(val));
- break;
- case cmd_clear:
- CHECK_INIT(initialized,word);
- actionSet.clearDelete();
- break;
- case cmd_getApiVersion:
- CHECK_NOTNULL(val,word);
- *(static_cast<int*>(val))=6;
- break;
- // commands which can be used only before initialization:
- case cmd_init:
- CHECK_NOTINIT(initialized,word);
- init();
- break;
- case cmd_setRealPrecision:
- CHECK_NOTINIT(initialized,word);
- CHECK_NOTNULL(val,word);
- atoms.setRealPrecision(*static_cast<int*>(val));
- mydatafetcher=DataFetchingObject::create(*static_cast<int*>(val),*this);
- break;
- case cmd_setMDLengthUnits:
- CHECK_NOTINIT(initialized,word);
- CHECK_NOTNULL(val,word);
- atoms.MD2double(val,d);
- atoms.setMDLengthUnits(d);
- break;
- case cmd_setMDChargeUnits:
- CHECK_NOTINIT(initialized,word);
- CHECK_NOTNULL(val,word);
- atoms.MD2double(val,d);
- atoms.setMDChargeUnits(d);
- break;
- case cmd_setMDMassUnits:
- CHECK_NOTINIT(initialized,word);
- CHECK_NOTNULL(val,word);
- atoms.MD2double(val,d);
- atoms.setMDMassUnits(d);
- break;
- case cmd_setMDEnergyUnits:
- CHECK_NOTINIT(initialized,word);
- CHECK_NOTNULL(val,word);
- atoms.MD2double(val,d);
- atoms.setMDEnergyUnits(d);
- break;
- case cmd_setMDTimeUnits:
- CHECK_NOTINIT(initialized,word);
- CHECK_NOTNULL(val,word);
- atoms.MD2double(val,d);
- atoms.setMDTimeUnits(d);
- break;
- case cmd_setNaturalUnits:
- // set the boltzman constant for MD in natural units (kb=1)
- // only needed in LJ codes if the MD is passing temperatures to plumed (so, not yet...)
- // use as cmd("setNaturalUnits")
- CHECK_NOTINIT(initialized,word);
- atoms.setMDNaturalUnits(true);
- break;
- case cmd_setNoVirial:
- CHECK_NOTINIT(initialized,word);
- novirial=true;
- break;
- case cmd_setPlumedDat:
- CHECK_NOTINIT(initialized,word);
- CHECK_NOTNULL(val,word);
- plumedDat=static_cast<char*>(val);
- break;
- case cmd_setMPIComm:
- CHECK_NOTINIT(initialized,word);
- comm.Set_comm(val);
- atoms.setDomainDecomposition(comm);
- break;
- case cmd_setMPIFComm:
- CHECK_NOTINIT(initialized,word);
- comm.Set_fcomm(val);
- atoms.setDomainDecomposition(comm);
- break;
- case cmd_setMPImultiSimComm:
- CHECK_NOTINIT(initialized,word);
- multi_sim_comm.Set_comm(val);
- break;
- case cmd_setNatoms:
- CHECK_NOTINIT(initialized,word);
- CHECK_NOTNULL(val,word);
- atoms.setNatoms(*static_cast<int*>(val));
- break;
- case cmd_setTimestep:
- CHECK_NOTINIT(initialized,word);
- CHECK_NOTNULL(val,word);
- atoms.setTimeStep(val);
- break;
- /* ADDED WITH API==2 */
- case cmd_setKbT:
- CHECK_NOTINIT(initialized,word);
- CHECK_NOTNULL(val,word);
- atoms.setKbT(val);
- break;
- /* ADDED WITH API==3 */
- case cmd_setRestart:
- CHECK_NOTINIT(initialized,word);
- 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);
- MDEngine=static_cast<char*>(val);
- break;
- case cmd_setLog:
- CHECK_NOTINIT(initialized,word);
- log.link(static_cast<FILE*>(val));
- break;
- case cmd_setLogFile:
- CHECK_NOTINIT(initialized,word);
- CHECK_NOTNULL(val,word);
- log.open(static_cast<char*>(val));
- break;
- // other commands that should be used after initialization:
- case cmd_setStopFlag:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- stopFlag=static_cast<int*>(val);
- break;
- case cmd_getExchangesFlag:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- exchangePatterns.getFlag((*static_cast<int*>(val)));
- break;
- case cmd_setExchangesSeed:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- exchangePatterns.setSeed((*static_cast<int*>(val)));
- break;
- case cmd_setNumberOfReplicas:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- exchangePatterns.setNofR((*static_cast<int*>(val)));
- break;
- case cmd_getExchangesList:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- exchangePatterns.getList((static_cast<int*>(val)));
- break;
- case cmd_runFinalJobs:
- CHECK_INIT(initialized,word);
- runJobsAtEndOfCalculation();
- break;
- case cmd_isEnergyNeeded:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- if(atoms.isEnergyNeeded()) *(static_cast<int*>(val))=1;
- else *(static_cast<int*>(val))=0;
- break;
- case cmd_getBias:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- atoms.double2MD(getBias()/(atoms.getMDUnits().getEnergy()/atoms.getUnits().getEnergy()),val);
- break;
- case cmd_checkAction:
- CHECK_NOTNULL(val,word);
- plumed_assert(nw==2);
- *(static_cast<int*>(val))=(actionRegister().check(words[1]) ? 1:0);
- break;
- case cmd_GREX:
- if(!grex) grex.reset(new GREX(*this));
- plumed_massert(grex,"error allocating grex");
- {
- std::string kk=words[1];
- for(unsigned i=2; i<words.size(); i++) kk+=" "+words[i];
- grex->cmd(kk.c_str(),val);
- }
- break;
- case cmd_CLTool:
- CHECK_NOTINIT(initialized,word);
- if(!cltool) cltool.reset(new CLToolMain);
- {
- std::string kk=words[1];
- for(unsigned i=2; i<words.size(); i++) kk+=" "+words[i];
- cltool->cmd(kk.c_str(),val);
+ try {
+
+ stopwatch.start();
+
+ std::vector<std::string> words=Tools::getWords(word);
+ unsigned nw=words.size();
+ if(nw==0) {
+ // do nothing
+ } else {
+ int iword=-1;
+ double d;
+ const auto it=plumedMainWordMap().find(words[0]);
+ if(it!=plumedMainWordMap().end()) iword=it->second;
+ switch(iword) {
+ case cmd_setBox:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ atoms.setBox(val);
+ break;
+ case cmd_setPositions:
+ CHECK_INIT(initialized,word);
+ atoms.setPositions(val);
+ break;
+ case cmd_setMasses:
+ CHECK_INIT(initialized,word);
+ atoms.setMasses(val);
+ break;
+ case cmd_setCharges:
+ CHECK_INIT(initialized,word);
+ atoms.setCharges(val);
+ break;
+ case cmd_setPositionsX:
+ CHECK_INIT(initialized,word);
+ atoms.setPositions(val,0);
+ break;
+ case cmd_setPositionsY:
+ CHECK_INIT(initialized,word);
+ atoms.setPositions(val,1);
+ break;
+ case cmd_setPositionsZ:
+ CHECK_INIT(initialized,word);
+ atoms.setPositions(val,2);
+ break;
+ case cmd_setVirial:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ atoms.setVirial(val);
+ break;
+ case cmd_setEnergy:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ atoms.setEnergy(val);
+ break;
+ case cmd_setForces:
+ CHECK_INIT(initialized,word);
+ atoms.setForces(val);
+ break;
+ case cmd_setForcesX:
+ CHECK_INIT(initialized,word);
+ atoms.setForces(val,0);
+ break;
+ case cmd_setForcesY:
+ CHECK_INIT(initialized,word);
+ atoms.setForces(val,1);
+ break;
+ case cmd_setForcesZ:
+ CHECK_INIT(initialized,word);
+ atoms.setForces(val,2);
+ break;
+ case cmd_calc:
+ CHECK_INIT(initialized,word);
+ calc();
+ break;
+ case cmd_prepareDependencies:
+ CHECK_INIT(initialized,word);
+ prepareDependencies();
+ break;
+ case cmd_shareData:
+ CHECK_INIT(initialized,word);
+ shareData();
+ break;
+ case cmd_prepareCalc:
+ CHECK_INIT(initialized,word);
+ prepareCalc();
+ break;
+ case cmd_performCalc:
+ CHECK_INIT(initialized,word);
+ performCalc();
+ break;
+ case cmd_performCalcNoUpdate:
+ CHECK_INIT(initialized,word);
+ performCalcNoUpdate();
+ break;
+ case cmd_update:
+ CHECK_INIT(initialized,word);
+ update();
+ break;
+ case cmd_setStep:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ step=(*static_cast<int*>(val));
+ atoms.startStep();
+ break;
+ case cmd_setStepLong:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ step=(*static_cast<long int*>(val));
+ atoms.startStep();
+ break;
+ // words used less frequently:
+ case cmd_setAtomsNlocal:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ atoms.setAtomsNlocal(*static_cast<int*>(val));
+ break;
+ case cmd_setAtomsGatindex:
+ CHECK_INIT(initialized,word);
+ atoms.setAtomsGatindex(static_cast<int*>(val),false);
+ break;
+ case cmd_setAtomsFGatindex:
+ CHECK_INIT(initialized,word);
+ atoms.setAtomsGatindex(static_cast<int*>(val),true);
+ break;
+ case cmd_setAtomsContiguous:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ atoms.setAtomsContiguous(*static_cast<int*>(val));
+ break;
+ case cmd_createFullList:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ atoms.createFullList(static_cast<int*>(val));
+ break;
+ case cmd_getFullList:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ atoms.getFullList(static_cast<int**>(val));
+ break;
+ case cmd_clearFullList:
+ CHECK_INIT(initialized,word);
+ atoms.clearFullList();
+ break;
+ /* ADDED WITH API==6 */
+ case cmd_getDataRank:
+ CHECK_INIT(initialized,words[0]); plumed_assert(nw==2 || nw==3);
+ if( nw==2 ) DataFetchingObject::get_rank( actionSet, words[1], "", static_cast<long*>(val) );
+ else DataFetchingObject::get_rank( actionSet, words[1], words[2], static_cast<long*>(val) );
+ break;
+ /* ADDED WITH API==6 */
+ case cmd_getDataShape:
+ CHECK_INIT(initialized,words[0]); plumed_assert(nw==2 || nw==3);
+ if( nw==2 ) DataFetchingObject::get_shape( actionSet, words[1], "", static_cast<long*>(val) );
+ else DataFetchingObject::get_shape( actionSet, words[1], words[2], static_cast<long*>(val) );
+ break;
+ /* ADDED WITH API==6 */
+ case cmd_setMemoryForData:
+ CHECK_INIT(initialized,words[0]); plumed_assert(nw==2 || nw==3);
+ if( nw==2 ) mydatafetcher->setData( words[1], "", val );
+ else mydatafetcher->setData( words[1], words[2], val );
+ break;
+ case cmd_read:
+ CHECK_INIT(initialized,word);
+ if(val)readInputFile(static_cast<char*>(val));
+ else readInputFile("plumed.dat");
+ break;
+ case cmd_readInputLine:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ readInputLine(static_cast<char*>(val));
+ break;
+ case cmd_clear:
+ CHECK_INIT(initialized,word);
+ actionSet.clearDelete();
+ break;
+ case cmd_getApiVersion:
+ CHECK_NOTNULL(val,word);
+ *(static_cast<int*>(val))=6;
+ break;
+ // commands which can be used only before initialization:
+ case cmd_init:
+ CHECK_NOTINIT(initialized,word);
+ init();
+ break;
+ case cmd_setRealPrecision:
+ CHECK_NOTINIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ atoms.setRealPrecision(*static_cast<int*>(val));
+ mydatafetcher=DataFetchingObject::create(*static_cast<int*>(val),*this);
+ break;
+ case cmd_setMDLengthUnits:
+ CHECK_NOTINIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ atoms.MD2double(val,d);
+ atoms.setMDLengthUnits(d);
+ break;
+ case cmd_setMDChargeUnits:
+ CHECK_NOTINIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ atoms.MD2double(val,d);
+ atoms.setMDChargeUnits(d);
+ break;
+ case cmd_setMDMassUnits:
+ CHECK_NOTINIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ atoms.MD2double(val,d);
+ atoms.setMDMassUnits(d);
+ break;
+ case cmd_setMDEnergyUnits:
+ CHECK_NOTINIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ atoms.MD2double(val,d);
+ atoms.setMDEnergyUnits(d);
+ break;
+ case cmd_setMDTimeUnits:
+ CHECK_NOTINIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ atoms.MD2double(val,d);
+ atoms.setMDTimeUnits(d);
+ break;
+ case cmd_setNaturalUnits:
+ // set the boltzman constant for MD in natural units (kb=1)
+ // only needed in LJ codes if the MD is passing temperatures to plumed (so, not yet...)
+ // use as cmd("setNaturalUnits")
+ CHECK_NOTINIT(initialized,word);
+ atoms.setMDNaturalUnits(true);
+ break;
+ case cmd_setNoVirial:
+ CHECK_NOTINIT(initialized,word);
+ novirial=true;
+ break;
+ case cmd_setPlumedDat:
+ CHECK_NOTINIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ plumedDat=static_cast<char*>(val);
+ break;
+ case cmd_setMPIComm:
+ CHECK_NOTINIT(initialized,word);
+ comm.Set_comm(val);
+ atoms.setDomainDecomposition(comm);
+ break;
+ case cmd_setMPIFComm:
+ CHECK_NOTINIT(initialized,word);
+ comm.Set_fcomm(val);
+ atoms.setDomainDecomposition(comm);
+ break;
+ case cmd_setMPImultiSimComm:
+ CHECK_NOTINIT(initialized,word);
+ multi_sim_comm.Set_comm(val);
+ break;
+ case cmd_setNatoms:
+ CHECK_NOTINIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ atoms.setNatoms(*static_cast<int*>(val));
+ break;
+ case cmd_setTimestep:
+ CHECK_NOTINIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ atoms.setTimeStep(val);
+ break;
+ /* ADDED WITH API==2 */
+ case cmd_setKbT:
+ CHECK_NOTINIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ atoms.setKbT(val);
+ break;
+ /* ADDED WITH API==3 */
+ case cmd_setRestart:
+ CHECK_NOTINIT(initialized,word);
+ 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);
+ MDEngine=static_cast<char*>(val);
+ break;
+ case cmd_setLog:
+ CHECK_NOTINIT(initialized,word);
+ log.link(static_cast<FILE*>(val));
+ break;
+ case cmd_setLogFile:
+ CHECK_NOTINIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ log.open(static_cast<char*>(val));
+ break;
+ // other commands that should be used after initialization:
+ case cmd_setStopFlag:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ stopFlag=static_cast<int*>(val);
+ break;
+ case cmd_getExchangesFlag:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ exchangePatterns.getFlag((*static_cast<int*>(val)));
+ break;
+ case cmd_setExchangesSeed:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ exchangePatterns.setSeed((*static_cast<int*>(val)));
+ break;
+ case cmd_setNumberOfReplicas:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ exchangePatterns.setNofR((*static_cast<int*>(val)));
+ break;
+ case cmd_getExchangesList:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ exchangePatterns.getList((static_cast<int*>(val)));
+ break;
+ case cmd_runFinalJobs:
+ CHECK_INIT(initialized,word);
+ runJobsAtEndOfCalculation();
+ break;
+ case cmd_isEnergyNeeded:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ if(atoms.isEnergyNeeded()) *(static_cast<int*>(val))=1;
+ else *(static_cast<int*>(val))=0;
+ break;
+ case cmd_getBias:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ atoms.double2MD(getBias()/(atoms.getMDUnits().getEnergy()/atoms.getUnits().getEnergy()),val);
+ break;
+ case cmd_checkAction:
+ CHECK_NOTNULL(val,word);
+ plumed_assert(nw==2);
+ *(static_cast<int*>(val))=(actionRegister().check(words[1]) ? 1:0);
+ break;
+ case cmd_GREX:
+ if(!grex) grex.reset(new GREX(*this));
+ plumed_massert(grex,"error allocating grex");
+ {
+ std::string kk=words[1];
+ for(unsigned i=2; i<words.size(); i++) kk+=" "+words[i];
+ grex->cmd(kk.c_str(),val);
+ }
+ break;
+ case cmd_CLTool:
+ CHECK_NOTINIT(initialized,word);
+ if(!cltool) cltool.reset(new CLToolMain);
+ {
+ std::string kk=words[1];
+ for(unsigned i=2; i<words.size(); i++) kk+=" "+words[i];
+ cltool->cmd(kk.c_str(),val);
+ }
+ break;
+ default:
+ plumed_merror("cannot interpret cmd(\"" + word + "\"). check plumed developers manual to see the available commands.");
+ break;
}
- break;
- default:
- plumed_merror("cannot interpret cmd(\"" + word + "\"). check plumed developers manual to see the available commands.");
- break;
}
+ stopwatch.pause();
+
+ } catch (Exception &e) {
+ if(log.isOpen()) {
+ log<<"\n\n################################################################################\n\n";
+ log<<e.what();
+ log<<"\n\n################################################################################\n\n";
+ log.flush();
+ }
+ throw;
}
- stopwatch.pause();
}
////////////////////////////////////////////////////////////////////////