diff --git a/src/core/PlumedMain.cpp b/src/core/PlumedMain.cpp
index 1a17ebb60db54a89dad0e47c9bf26031bd574ec3..aba7e2afbd8f5c839f087b4aa08f89ea53d5a488 100644
--- a/src/core/PlumedMain.cpp
+++ b/src/core/PlumedMain.cpp
@@ -127,293 +127,295 @@ void PlumedMain::cmd(const std::string & word,void*val){
if(it!=plumedMainWordMap().end()) iword=it->second;
switch(iword) {
double d;
- case SETBOX: // cmd setBox
+ case cmd_setBox:
CHECK_INIT(initialized,word);
CHECK_NULL(val,word);
atoms.setBox(val);
break;
- case SETPOSITIONS: // cmd setPositions
+ case cmd_setPositions:
CHECK_INIT(initialized,word);
atoms.setPositions(val);
break;
- case SETMASSES: // cmd setMasses
+ case cmd_setMasses:
CHECK_INIT(initialized,word);
atoms.setMasses(val);
break;
- case SETCHARGES: // cmd setCharges
+ case cmd_setCharges:
CHECK_INIT(initialized,word);
atoms.setCharges(val);
break;
- case SETPOSITIONSX: // cmd setPositionsX
+ case cmd_setPositionsX:
CHECK_INIT(initialized,word);
atoms.setPositions(val,0);
break;
- case SETPOSITIONSY: // cmd setPositionsY
+ case cmd_setPositionsY:
CHECK_INIT(initialized,word);
atoms.setPositions(val,1);
break;
- case SETPOSITIONSZ: // cmd setPositionsZ
+ case cmd_setPositionsZ:
CHECK_INIT(initialized,word);
atoms.setPositions(val,2);
break;
- case SETVIRIAL: // cmd setVirial
+ case cmd_setVirial:
CHECK_INIT(initialized,word);
CHECK_NULL(val,word);
atoms.setVirial(val);
break;
- case SETENERGY: // cmd setEnergy
+ case cmd_setEnergy:
CHECK_INIT(initialized,word);
CHECK_NULL(val,word);
atoms.setEnergy(val);
break;
- case SETFORCES: // cmd setForces
+ case cmd_setForces:
CHECK_INIT(initialized,word);
atoms.setForces(val);
break;
- case SETFORCESX: // cmd setForcesX
+ case cmd_setForcesX:
CHECK_INIT(initialized,word);
atoms.setForces(val,0);
break;
- case SETFORCESY: // cmd setForcesY
+ case cmd_setForcesY:
CHECK_INIT(initialized,word);
atoms.setForces(val,1);
break;
- case SETFORCESZ: // cmd setForcesZ
+ case cmd_setForcesZ:
CHECK_INIT(initialized,word);
atoms.setForces(val,2);
break;
- case CALC: // cmd calc
+ case cmd_calc:
CHECK_INIT(initialized,word);
calc();
break;
- case PREPAREDEPENDENCIES: // cmd prepareDependencies
+ case cmd_prepareDependencies:
CHECK_INIT(initialized,word);
prepareDependencies();
break;
- case SHAREDATA: // cmd shareData
+ case cmd_shareData:
CHECK_INIT(initialized,word);
shareData();
break;
- case PREPARECALC: // cmd prepareCalc
+ case cmd_prepareCalc:
CHECK_INIT(initialized,word);
prepareCalc();
break;
- case PERFORMCALC: // cmd performCalc
+ case cmd_performCalc:
CHECK_INIT(initialized,word);
performCalc();
break;
- case PERFORMCALCNOUPDATE: // cmd performCalcNoUpdate
+ case cmd_performCalcNoUpdate:
CHECK_INIT(initialized,word);
performCalcNoUpdate();
break;
- case UPDATE: // cmd update
+ case cmd_update:
CHECK_INIT(initialized,word);
update();
break;
- case SETSTEP: // cmd setStep
+ case cmd_setStep:
CHECK_INIT(initialized,word);
CHECK_NULL(val,word);
step=(*static_cast<int*>(val));
atoms.startStep();
break;
- case SETSTEPLONG: // cmd setStepLong
+ case cmd_setStepLong:
CHECK_INIT(initialized,word);
CHECK_NULL(val,word);
step=(*static_cast<long int*>(val));
atoms.startStep();
break;
// words used less frequently:
- case SETATOMSNLOCAL: // cmd setAtomsNlocal
+ case cmd_setAtomsNlocal:
CHECK_INIT(initialized,word);
CHECK_NULL(val,word);
atoms.setAtomsNlocal(*static_cast<int*>(val));
break;
- case SETATOMSGATINDEX: // cmd setAtomsGatindex
+ case cmd_setAtomsGatindex:
CHECK_INIT(initialized,word);
atoms.setAtomsGatindex(static_cast<int*>(val),false);
break;
- case SETATOMSFGATINDEX: // cmd setAtomsFGatindex
+ case cmd_setAtomsFGatindex:
CHECK_INIT(initialized,word);
atoms.setAtomsGatindex(static_cast<int*>(val),true);
break;
- case SETATOMSCONTIGUOUS: // cmd setAtomsContiguous
+ case cmd_setAtomsContiguous:
CHECK_INIT(initialized,word);
CHECK_NULL(val,word);
atoms.setAtomsContiguous(*static_cast<int*>(val));
break;
- case CREATEFULLLIST: // cmd createFullList
+ case cmd_createFullList:
CHECK_INIT(initialized,word);
CHECK_NULL(val,word);
atoms.createFullList(static_cast<int*>(val));
break;
- case GETFULLLIST: // cmd getFullList
+ case cmd_getFullList:
CHECK_INIT(initialized,word);
CHECK_NULL(val,word);
atoms.getFullList(static_cast<int**>(val));
break;
- case CLEARFULLLIST: // cmd clearFullList
+ case cmd_clearFullList:
CHECK_INIT(initialized,word);
atoms.clearFullList();
break;
- case READ: // cmd read
+ case cmd_read:
CHECK_INIT(initialized,word);
if(val)readInputFile(static_cast<char*>(val));
else readInputFile("plumed.dat");
break;
- case READINPUTLINE: // cmd readInputLine
+ case cmd_readInputLine:
CHECK_INIT(initialized,word);
CHECK_NULL(val,word);
readInputLine(static_cast<char*>(val));
break;
- case CLEAR: // cmd clear
+ case cmd_clear:
CHECK_INIT(initialized,word);
actionSet.clearDelete();
break;
- case GETAPIVERSION: // cmd getApiVersion
+ case cmd_getApiVersion:
CHECK_NULL(val,word);
*(static_cast<int*>(val))=4;
break;
// commands which can be used only before initialization:
- case INIT: // cmd init
+ case cmd_init:
CHECK_NOTINIT(initialized,word);
init();
break;
- case SETREALPRECISION: // cmd setRealPrecision
+ case cmd_setRealPrecision:
CHECK_NOTINIT(initialized,word);
CHECK_NULL(val,word);
atoms.setRealPrecision(*static_cast<int*>(val));
break;
- case SETMDLENGTHUNITS: // cmd setMDLengthUnits
+ case cmd_setMDLengthUnits:
CHECK_NOTINIT(initialized,word);
CHECK_NULL(val,word);
atoms.MD2double(val,d);
atoms.setMDLengthUnits(d);
break;
- case SETMDCHARGEUNITS: // cmd setMDChargeUnits
+ case cmd_setMDChargeUnits:
CHECK_NOTINIT(initialized,word);
CHECK_NULL(val,word);
atoms.MD2double(val,d);
atoms.setMDChargeUnits(d);
break;
- case SETMDMASSUNITS: // cmd setMDMassUnits
+ case cmd_setMDMassUnits:
CHECK_NOTINIT(initialized,word);
CHECK_NULL(val,word);
atoms.MD2double(val,d);
atoms.setMDMassUnits(d);
break;
- case SETMDENERGYUNITS: // cmd setMDEnergyUnits
+ case cmd_setMDEnergyUnits:
CHECK_NOTINIT(initialized,word);
CHECK_NULL(val,word);
atoms.MD2double(val,d);
atoms.setMDEnergyUnits(d);
break;
- case SETMDTIMEUNITS: // cmd setMDTimeUnits
+ case cmd_setMDTimeUnits:
CHECK_NOTINIT(initialized,word);
CHECK_NULL(val,word);
atoms.MD2double(val,d);
atoms.setMDTimeUnits(d);
break;
- case SETNATURALUNITS: // cmd setNaturalUnits
+ 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 SETNOVIRIAL: // cmd setNoVirial
+ case cmd_setNoVirial:
CHECK_NOTINIT(initialized,word);
novirial=true;
break;
- case SETPLUMEDDAT: // cmd setPlumedDat
+ case cmd_setPlumedDat:
CHECK_NOTINIT(initialized,word);
CHECK_NULL(val,word);
plumedDat=static_cast<char*>(val);
break;
- case SETMPICOMM: // cmd setMPIComm
+ case cmd_setMPIComm:
CHECK_NOTINIT(initialized,word);
comm.Set_comm(val);
atoms.setDomainDecomposition(comm);
break;
- case SETMPIFCOMM: // cmd setMPIFComm
+ case cmd_setMPIFComm:
CHECK_NOTINIT(initialized,word);
comm.Set_fcomm(val);
atoms.setDomainDecomposition(comm);
break;
- case SETMPIMULTISIMCOMM: // cmd setMPImultiSimComm
+ case cmd_setMPImultiSimComm:
CHECK_NOTINIT(initialized,word);
multi_sim_comm.Set_comm(val);
break;
- case SETNATOMS: // cmd setNatoms
+ case cmd_setNatoms:
CHECK_NOTINIT(initialized,word);
CHECK_NULL(val,word);
atoms.setNatoms(*static_cast<int*>(val));
break;
- case SETTIMESTEP: // cmd setTimestep
+ case cmd_setTimestep:
CHECK_NOTINIT(initialized,word);
CHECK_NULL(val,word);
atoms.setTimeStep(val);
break;
- case SETKBT: /* ADDED WITH API==2 */ // cmd setKbT
+ /* ADDED WITH API==2 */
+ case cmd_setKbT:
CHECK_NOTINIT(initialized,word);
CHECK_NULL(val,word);
atoms.setKbT(val);
break;
- case SETRESTART: /* ADDED WITH API==3 */ // cmd setRestart
+ /* ADDED WITH API==3 */
+ case cmd_setRestart:
CHECK_NOTINIT(initialized,word);
CHECK_NULL(val,word);
if(*static_cast<int*>(val)!=0) restart=true;
break;
- case SETMDENGINE: // cmd setMDEngine
+ case cmd_setMDEngine:
CHECK_NOTINIT(initialized,word);
CHECK_NULL(val,word);
MDEngine=static_cast<char*>(val);
break;
- case SETLOG: // cmd setLog
+ case cmd_setLog:
CHECK_NOTINIT(initialized,word);
log.link(static_cast<FILE*>(val));
break;
- case SETLOGFILE: // cmd setLogFile
+ case cmd_setLogFile:
CHECK_NOTINIT(initialized,word);
CHECK_NULL(val,word);
log.open(static_cast<char*>(val));
break;
// other commands that should be used after initialization:
- case SETSTOPFLAG: // cmd setStopFlag
+ case cmd_setStopFlag:
CHECK_INIT(initialized,word);
CHECK_NULL(val,word);
stopFlag=static_cast<int*>(val);
break;
- case GETEXCHANGESFLAG: // cmd getExchangesFlag
+ case cmd_getExchangesFlag:
CHECK_INIT(initialized,word);
CHECK_NULL(val,word);
exchangePatterns.getFlag((*static_cast<int*>(val)));
break;
- case SETEXCHANGESSEED: // cmd setExchangesSeed
+ case cmd_setExchangesSeed:
CHECK_INIT(initialized,word);
CHECK_NULL(val,word);
exchangePatterns.setSeed((*static_cast<int*>(val)));
break;
- case SETNUMBEROFREPLICAS: // cmd setNumberOfReplicas
+ case cmd_setNumberOfReplicas:
CHECK_INIT(initialized,word);
CHECK_NULL(val,word);
exchangePatterns.setNofR((*static_cast<int*>(val)));
break;
- case GETEXCHANGESLIST: // cmd getExchangesList
+ case cmd_getExchangesList:
CHECK_INIT(initialized,word);
CHECK_NULL(val,word);
exchangePatterns.getList((static_cast<int*>(val)));
break;
- case RUNFINALJOBS: // cmd runFinalJobs
+ case cmd_runFinalJobs:
CHECK_INIT(initialized,word);
runJobsAtEndOfCalculation();
break;
- case ISENERGYNEEDED: // cmd isEnergyNeeded
+ case cmd_isEnergyNeeded:
CHECK_INIT(initialized,word);
CHECK_NULL(val,word);
if(atoms.isEnergyNeeded()) *(static_cast<int*>(val))=1;
else *(static_cast<int*>(val))=0;
break;
- case GETBIAS: // cmd getBias
+ case cmd_getBias:
CHECK_INIT(initialized,word);
CHECK_NULL(val,word);
d=getBias()/(atoms.getMDUnits().getEnergy()/atoms.getUnits().getEnergy());
diff --git a/src/maketools/makecmd b/src/maketools/makecmd
index 21fe1b43021f0ba166b7b2bc1a3e936b426ce358..e469dffb2dfcd19519df3c712d7923639a451ecf 100755
--- a/src/maketools/makecmd
+++ b/src/maketools/makecmd
@@ -2,12 +2,15 @@
awk -v opt=$1 '
{
- if($1=="case" && $(NF-1)=="cmd"){
- i++;
- string[i]=$NF
- enum[i]=$2
- sub(":","",enum[i]);
- } }END{
+ if($1=="case" && match($2,"^cmd_.*:")){
+ i++;
+ enum[i]=$2;
+ sub(":","",enum[i]);
+ string[i]=$2;
+ sub(":","",string[i]);
+ sub("^cmd_","",string[i]);
+ }
+ }END{
n=i;
if(opt=="enum"){
print "enum {"