From 0a46f15d734da4789bb35c3825ae115b4b12d809 Mon Sep 17 00:00:00 2001
From: Carlo Camilloni <carlo.camilloni@gmail.com>
Date: Wed, 11 Jun 2014 11:09:08 +0200
Subject: [PATCH] PLUMEDMAIN: new faster parser for plumed setup
This is the parsing I showed you in belfast
---
src/core/PlumedMain.cpp | 584 +++++++++++++++++++++++-----------------
src/core/PlumedMain.h | 4 +
2 files changed, 339 insertions(+), 249 deletions(-)
diff --git a/src/core/PlumedMain.cpp b/src/core/PlumedMain.cpp
index c12a36e4e..5319d29fd 100644
--- a/src/core/PlumedMain.cpp
+++ b/src/core/PlumedMain.cpp
@@ -46,6 +46,8 @@
using namespace std;
+enum { SETBOX, SETPOSITIONS, SETMASSES, SETCHARGES, SETPOSITIONSX, SETPOSITIONSY, SETPOSITIONSZ, SETVIRIAL, SETENERGY, SETFORCES, SETFORCESX, SETFORCESY, SETFORCESZ, CALC, PREPAREDEPENDENCIES, SHAREDATA, PREPARECALC, PERFORMCALC, SETSTEP, SETSTEPLONG, SETATOMSNLOCAL, SETATOMSGATINDEX, SETATOMSCONTIGUOUS, CREATEFULLLIST, GETFULLLIST, CLEARFULLLIST, READ, CLEAR, GETAPIVERSION, INIT, SETREALPRECISION, SETMDLENGTHUNITS, SETMDENERGYUNITS, SETMDTIMEUNITS, SETNATURALUNITS, SETNOVIRIAL, SETPLUMEDDAT, SETMPICOMM, SETMPIFCOMM, SETMPIMULTISIMCOMM, SETNATOMS, SETTIMESTEP, SETMDENGINE, SETLOG, SETLOGFILE, SETSTOPFLAG, GETEXCHANGESFLAG, SETEXCHANGESSEED, SETNUMBEROFREPLICAS, GETEXCHANGESLIST, RUNFINALJOBS, ISENERGYNEEDED, GETBIAS };
+
namespace PLMD{
PlumedMain::PlumedMain():
@@ -75,6 +77,59 @@ PlumedMain::PlumedMain():
log.setLinePrefix("PLUMED: ");
stopwatch.start();
stopwatch.pause();
+ word_map["setBox"]=SETBOX;
+ word_map["setPositions"]=SETPOSITIONS;
+ word_map["setMasses"]=SETMASSES;
+ word_map["setCharges"]=SETCHARGES;
+ word_map["setPositionsX"]=SETPOSITIONSX;
+ word_map["setPositionsY"]=SETPOSITIONSY;
+ word_map["setPositionsZ"]=SETPOSITIONSZ;
+ word_map["setVirial"]=SETVIRIAL;
+ word_map["setEnergy"]=SETENERGY;
+ word_map["setForces"]=SETFORCES;
+ word_map["setForcesX"]=SETFORCESX;
+ word_map["setForcesY"]=SETFORCESY;
+ word_map["setForcesZ"]=SETFORCESZ;
+ word_map["calc"]=CALC;
+ word_map["prepareDependencies"]=PREPAREDEPENDENCIES;
+ word_map["shareData"]=SHAREDATA;
+ word_map["prepareCalc"]=PREPARECALC;
+ word_map["performCalc"]=PERFORMCALC;
+ word_map["setStep"]=SETSTEP;
+ word_map["setStepLong"]=SETSTEPLONG;
+ word_map["setAtomsNlocal"]=SETATOMSNLOCAL;
+ word_map["setAtomsGatindex"]=SETATOMSGATINDEX;
+ word_map["setAtomsContiguous"]=SETATOMSCONTIGUOUS;
+ word_map["createFullList"]=CREATEFULLLIST;
+ word_map["getFullList"]=GETFULLLIST;
+ word_map["clearFullList"]=CLEARFULLLIST;
+ word_map["read"]=READ;
+ word_map["clear"]=CLEAR;
+ word_map["getApiVersion"]=GETAPIVERSION;
+ word_map["init"]=INIT;
+ word_map["setRealPrecision"]=SETREALPRECISION;
+ word_map["setMDLengthUnits"]=SETMDLENGTHUNITS;
+ word_map["setMDEnergyUnits"]=SETMDENERGYUNITS;
+ word_map["setMDTimeUnits"]=SETMDTIMEUNITS;
+ word_map["setNaturalUnits"]=SETNATURALUNITS;
+ word_map["setNoVirial"]=SETNOVIRIAL;
+ word_map["setPlumedDat"]=SETPLUMEDDAT;
+ word_map["setMPIComm"]=SETMPICOMM;
+ word_map["setMPIFComm"]=SETMPIFCOMM;
+ word_map["setMPImultiSimComm"]=SETMPIMULTISIMCOMM;
+ word_map["setNatoms"]=SETNATOMS;
+ word_map["setTimestep"]=SETTIMESTEP;
+ word_map["setMDEngine"]=SETMDENGINE;
+ word_map["setLog"]=SETLOG;
+ word_map["setLogFile"]=SETLOGFILE;
+ word_map["setStopFlag"]=SETSTOPFLAG;
+ word_map["getExchangesFlag"]=GETEXCHANGESFLAG;
+ word_map["setExchangesSeed"]=SETEXCHANGESSEED;
+ word_map["setNumberOfReplicas"]=SETNUMBEROFREPLICAS;
+ word_map["getExchangesList"]=GETEXCHANGESLIST;
+ word_map["runFinalJobs"]=RUNFINALJOBS;
+ word_map["isEnergyNeeded"]=ISENERGYNEEDED;
+ word_map["getBias"]=GETBIAS;
}
PlumedMain::~PlumedMain(){
@@ -105,245 +160,290 @@ void PlumedMain::cmd(const std::string & word,void*val){
stopwatch.start();
- if(false){
-// for efficiency, words frequently used are checked first
-
-// words used at every MD steps:
- } else if(word=="setBox") {
- CHECK_INIT(initialized,word);
- CHECK_NULL(val,word);
- atoms.setBox(val);
- } else if(word=="setPositions") {
- CHECK_INIT(initialized,word);
- atoms.setPositions(val);
- } else if(word=="setMasses") {
- CHECK_INIT(initialized,word);
- atoms.setMasses(val);
- } else if(word=="setCharges") {
- CHECK_INIT(initialized,word);
- atoms.setCharges(val);
- } else if(word=="setPositionsX") {
- CHECK_INIT(initialized,word);
- atoms.setPositions(val,0);
- } else if(word=="setPositionsY") {
- CHECK_INIT(initialized,word);
- atoms.setPositions(val,1);
- } else if(word=="setPositionsZ") {
- CHECK_INIT(initialized,word);
- atoms.setPositions(val,2);
- } else if(word=="setVirial") {
- CHECK_INIT(initialized,word);
- CHECK_NULL(val,word);
- atoms.setVirial(val);
- } else if(word=="setEnergy") {
- CHECK_INIT(initialized,word);
- CHECK_NULL(val,word);
- atoms.setEnergy(val);
- } else if(word=="setForces") {
- CHECK_INIT(initialized,word);
- atoms.setForces(val);
- } else if(word=="setForcesX") {
- CHECK_INIT(initialized,word);
- atoms.setForces(val,0);
- } else if(word=="setForcesY") {
- CHECK_INIT(initialized,word);
- atoms.setForces(val,1);
- } else if(word=="setForcesZ") {
- CHECK_INIT(initialized,word);
- atoms.setForces(val,2);
- } else if(word=="calc") {
- CHECK_INIT(initialized,word);
- calc();
- } else if(word=="prepareDependencies") {
- CHECK_INIT(initialized,word);
- prepareDependencies();
- } else if(word=="shareData") {
- CHECK_INIT(initialized,word);
- shareData();
- } else if(word=="prepareCalc") {
- CHECK_INIT(initialized,word);
- prepareCalc();
- } else if(word=="performCalc") {
- CHECK_INIT(initialized,word);
- performCalc();
- } else if(word=="setStep") {
- CHECK_INIT(initialized,word);
- CHECK_NULL(val,word);
- step=(*static_cast<int*>(val));
- atoms.startStep();
- } else if(word=="setStepLong") {
- CHECK_INIT(initialized,word);
- CHECK_NULL(val,word);
- step=(*static_cast<long int*>(val));
- atoms.startStep();
-// words used less frequently:
- } else if(word=="setAtomsNlocal"){
- CHECK_INIT(initialized,word);
- CHECK_NULL(val,word);
- atoms.setAtomsNlocal(*static_cast<int*>(val));
- } else if(word=="setAtomsGatindex"){
- CHECK_INIT(initialized,word);
- atoms.setAtomsGatindex(static_cast<int*>(val));
- } else if(word=="setAtomsContiguous"){
- CHECK_INIT(initialized,word);
- CHECK_NULL(val,word);
- atoms.setAtomsContiguous(*static_cast<int*>(val));
- } else if(word=="createFullList"){
- CHECK_INIT(initialized,word);
- CHECK_NULL(val,word);
- atoms.createFullList(static_cast<int*>(val));
- } else if(word=="getFullList"){
- CHECK_INIT(initialized,word);
- CHECK_NULL(val,word);
- atoms.getFullList(static_cast<int**>(val));
- } else if(word=="clearFullList"){
- CHECK_INIT(initialized,word);
- atoms.clearFullList();
- } else if(word=="read"){
- CHECK_INIT(initialized,word);
- if(val)readInputFile(static_cast<char*>(val));
- else readInputFile("plumed.dat");
- } else if(word=="clear"){
- CHECK_INIT(initialized,word);
- actionSet.clearDelete();
- } else if(word=="getApiVersion"){
- CHECK_NULL(val,word);
- *(static_cast<int*>(val))=1;
-// commands which can be used only before initialization:
- } else if(word=="init"){
- CHECK_NOTINIT(initialized,word);
- init();
- } else if(word=="setRealPrecision"){
- CHECK_NOTINIT(initialized,word);
- CHECK_NULL(val,word);
- atoms.setRealPrecision(*static_cast<int*>(val));
- } else if(word=="setMDLengthUnits"){
- CHECK_NOTINIT(initialized,word);
- CHECK_NULL(val,word);
- double d;
- atoms.MD2double(val,d);
- atoms.setMDLengthUnits(d);
- } else if(word=="setMDEnergyUnits"){
- CHECK_NOTINIT(initialized,word);
- CHECK_NULL(val,word);
- double d;
- atoms.MD2double(val,d);
- atoms.setMDEnergyUnits(d);
- } else if(word=="setMDTimeUnits"){
- CHECK_NOTINIT(initialized,word);
- CHECK_NULL(val,word);
- double d;
- atoms.MD2double(val,d);
- atoms.setMDTimeUnits(d);
- } else if(word=="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);
- } else if(word=="setNoVirial"){
- CHECK_NOTINIT(initialized,word);
- novirial=true;
- } else if(word=="setPlumedDat"){
- CHECK_NOTINIT(initialized,word);
- CHECK_NULL(val,word);
- plumedDat=static_cast<char*>(val);
- } else if(word=="setMPIComm"){
- CHECK_NOTINIT(initialized,word);
- comm.Set_comm(val);
- atoms.setDomainDecomposition(comm);
- } else if(word=="setMPIFComm"){
- CHECK_NOTINIT(initialized,word);
- comm.Set_fcomm(val);
- atoms.setDomainDecomposition(comm);
- } else if(word=="setMPImultiSimComm"){
- CHECK_NOTINIT(initialized,word);
- multi_sim_comm.Set_comm(val);
- } else if(word=="setNatoms"){
- CHECK_NOTINIT(initialized,word);
- CHECK_NULL(val,word);
- atoms.setNatoms(*static_cast<int*>(val));
- } else if(word=="setTimestep"){
- CHECK_NOTINIT(initialized,word);
- CHECK_NULL(val,word);
- atoms.setTimeStep(val);
- } else if(word=="setMDEngine"){
- CHECK_NOTINIT(initialized,word);
- CHECK_NULL(val,word);
- MDEngine=static_cast<char*>(val);
- } else if(word=="setLog"){
- CHECK_NOTINIT(initialized,word);
- log.link(static_cast<FILE*>(val));
- } else if(word=="setLogFile"){
- CHECK_NOTINIT(initialized,word);
- CHECK_NULL(val,word);
- log.open(static_cast<char*>(val));
-// other commands that should be used after initialization:
- } else if(word=="setStopFlag"){
- CHECK_INIT(initialized,word);
- CHECK_NULL(val,word);
- stopFlag=static_cast<int*>(val);
- } else if(word=="getExchangesFlag"){
- CHECK_INIT(initialized,word);
- CHECK_NULL(val,word);
- exchangePatterns.getFlag((*static_cast<int*>(val)));
- } else if(word=="setExchangesSeed"){
- CHECK_INIT(initialized,word);
- CHECK_NULL(val,word);
- exchangePatterns.setSeed((*static_cast<int*>(val)));
- } else if(word=="setNumberOfReplicas"){
- CHECK_INIT(initialized,word);
- CHECK_NULL(val,word);
- exchangePatterns.setNofR((*static_cast<int*>(val)));
- } else if(word=="getExchangesList"){
- CHECK_INIT(initialized,word);
- CHECK_NULL(val,word);
- exchangePatterns.getList((static_cast<int*>(val)));
- } else if(word=="runFinalJobs"){
- CHECK_INIT(initialized,word);
- runJobsAtEndOfCalculation();
- } else if(word=="isEnergyNeeded"){
- CHECK_INIT(initialized,word);
- CHECK_NULL(val,word);
- if(atoms.isEnergyNeeded()) *(static_cast<int*>(val))=1;
- else *(static_cast<int*>(val))=0;
- } else if(word=="getBias"){
- CHECK_INIT(initialized,word);
- CHECK_NULL(val,word);
- double x=getBias()/(atoms.getMDUnits().getEnergy()/atoms.getUnits().getEnergy());
- atoms.double2MD(x,val);
- } else {
-// multi word commands
-
- std::vector<std::string> words=Tools::getWords(word);
- int nw=words.size();
-
- if(false){
- } else if(nw==2 && words[0]=="checkAction"){
- int check=0;
- if(actionRegister().check(words[1])) check=1;
- *(static_cast<int*>(val))=check;
- } else if(nw>1 && words[0]=="GREX"){
- if(!grex) grex=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);
- } else if(nw>1 && words[0]=="CLTool"){
- CHECK_NOTINIT(initialized,word);
- if(!cltool) cltool=new CLToolMain;
- std::string kk=words[1];
- for(unsigned i=2;i<words.size();i++) kk+=" "+words[i];
- cltool->cmd(kk.c_str(),val);
- } else{
- plumed_merror("cannot interpret cmd(\"" + word + "\"). check plumed developers manual to see the available commands.");
- };
+ std::vector<std::string> words=Tools::getWords(word);
+ unsigned nw=words.size();
+ if(nw==1) {
+ switch(word_map[word]) {
+ double d;
+ case SETBOX:
+ CHECK_INIT(initialized,word);
+ CHECK_NULL(val,word);
+ atoms.setBox(val);
+ break;
+ case SETPOSITIONS:
+ CHECK_INIT(initialized,word);
+ atoms.setPositions(val);
+ break;
+ case SETMASSES:
+ CHECK_INIT(initialized,word);
+ atoms.setMasses(val);
+ break;
+ case SETCHARGES:
+ CHECK_INIT(initialized,word);
+ atoms.setCharges(val);
+ break;
+ case SETPOSITIONSX:
+ CHECK_INIT(initialized,word);
+ atoms.setPositions(val,0);
+ break;
+ case SETPOSITIONSY:
+ CHECK_INIT(initialized,word);
+ atoms.setPositions(val,1);
+ break;
+ case SETPOSITIONSZ:
+ CHECK_INIT(initialized,word);
+ atoms.setPositions(val,2);
+ break;
+ case SETVIRIAL:
+ CHECK_INIT(initialized,word);
+ CHECK_NULL(val,word);
+ atoms.setVirial(val);
+ break;
+ case SETENERGY:
+ CHECK_INIT(initialized,word);
+ CHECK_NULL(val,word);
+ atoms.setEnergy(val);
+ break;
+ case SETFORCES:
+ CHECK_INIT(initialized,word);
+ atoms.setForces(val);
+ break;
+ case SETFORCESX:
+ CHECK_INIT(initialized,word);
+ atoms.setForces(val,0);
+ break;
+ case SETFORCESY:
+ CHECK_INIT(initialized,word);
+ atoms.setForces(val,1);
+ break;
+ case SETFORCESZ:
+ CHECK_INIT(initialized,word);
+ atoms.setForces(val,2);
+ break;
+ case CALC:
+ CHECK_INIT(initialized,word);
+ calc();
+ break;
+ case PREPAREDEPENDENCIES:
+ CHECK_INIT(initialized,word);
+ prepareDependencies();
+ break;
+ case SHAREDATA:
+ CHECK_INIT(initialized,word);
+ shareData();
+ break;
+ case PREPARECALC:
+ CHECK_INIT(initialized,word);
+ prepareCalc();
+ break;
+ case PERFORMCALC:
+ CHECK_INIT(initialized,word);
+ performCalc();
+ break;
+ case SETSTEP:
+ CHECK_INIT(initialized,word);
+ CHECK_NULL(val,word);
+ step=(*static_cast<int*>(val));
+ atoms.startStep();
+ break;
+ case SETSTEPLONG:
+ CHECK_INIT(initialized,word);
+ CHECK_NULL(val,word);
+ step=(*static_cast<long int*>(val));
+ atoms.startStep();
+ break;
+ // words used less frequently:
+ case SETATOMSNLOCAL:
+ CHECK_INIT(initialized,word);
+ CHECK_NULL(val,word);
+ atoms.setAtomsNlocal(*static_cast<int*>(val));
+ break;
+ case SETATOMSGATINDEX:
+ CHECK_INIT(initialized,word);
+ atoms.setAtomsGatindex(static_cast<int*>(val));
+ break;
+ case SETATOMSCONTIGUOUS:
+ CHECK_INIT(initialized,word);
+ CHECK_NULL(val,word);
+ atoms.setAtomsContiguous(*static_cast<int*>(val));
+ break;
+ case CREATEFULLLIST:
+ CHECK_INIT(initialized,word);
+ CHECK_NULL(val,word);
+ atoms.createFullList(static_cast<int*>(val));
+ break;
+ case GETFULLLIST:
+ CHECK_INIT(initialized,word);
+ CHECK_NULL(val,word);
+ atoms.getFullList(static_cast<int**>(val));
+ break;
+ case CLEARFULLLIST:
+ CHECK_INIT(initialized,word);
+ atoms.clearFullList();
+ break;
+ case READ:
+ CHECK_INIT(initialized,word);
+ if(val)readInputFile(static_cast<char*>(val));
+ else readInputFile("plumed.dat");
+ break;
+ case CLEAR:
+ CHECK_INIT(initialized,word);
+ actionSet.clearDelete();
+ break;
+ case GETAPIVERSION:
+ CHECK_NULL(val,word);
+ *(static_cast<int*>(val))=1;
+ break;
+ // commands which can be used only before initialization:
+ case INIT:
+ CHECK_NOTINIT(initialized,word);
+ init();
+ break;
+ case SETREALPRECISION:
+ CHECK_NOTINIT(initialized,word);
+ CHECK_NULL(val,word);
+ atoms.setRealPrecision(*static_cast<int*>(val));
+ break;
+ case SETMDLENGTHUNITS:
+ CHECK_NOTINIT(initialized,word);
+ CHECK_NULL(val,word);
+ atoms.MD2double(val,d);
+ atoms.setMDLengthUnits(d);
+ break;
+ case SETMDENERGYUNITS:
+ CHECK_NOTINIT(initialized,word);
+ CHECK_NULL(val,word);
+ atoms.MD2double(val,d);
+ atoms.setMDEnergyUnits(d);
+ break;
+ case SETMDTIMEUNITS:
+ CHECK_NOTINIT(initialized,word);
+ CHECK_NULL(val,word);
+ atoms.MD2double(val,d);
+ atoms.setMDTimeUnits(d);
+ break;
+ case 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:
+ CHECK_NOTINIT(initialized,word);
+ novirial=true;
+ break;
+ case SETPLUMEDDAT:
+ CHECK_NOTINIT(initialized,word);
+ CHECK_NULL(val,word);
+ plumedDat=static_cast<char*>(val);
+ break;
+ case SETMPICOMM:
+ CHECK_NOTINIT(initialized,word);
+ comm.Set_comm(val);
+ atoms.setDomainDecomposition(comm);
+ break;
+ case SETMPIFCOMM:
+ CHECK_NOTINIT(initialized,word);
+ comm.Set_fcomm(val);
+ atoms.setDomainDecomposition(comm);
+ break;
+ case SETMPIMULTISIMCOMM:
+ CHECK_NOTINIT(initialized,word);
+ multi_sim_comm.Set_comm(val);
+ break;
+ case SETNATOMS:
+ CHECK_NOTINIT(initialized,word);
+ CHECK_NULL(val,word);
+ atoms.setNatoms(*static_cast<int*>(val));
+ break;
+ case SETTIMESTEP:
+ CHECK_NOTINIT(initialized,word);
+ CHECK_NULL(val,word);
+ atoms.setTimeStep(val);
+ break;
+ case SETMDENGINE:
+ CHECK_NOTINIT(initialized,word);
+ CHECK_NULL(val,word);
+ MDEngine=static_cast<char*>(val);
+ break;
+ case SETLOG:
+ CHECK_NOTINIT(initialized,word);
+ log.link(static_cast<FILE*>(val));
+ break;
+ case 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:
+ CHECK_INIT(initialized,word);
+ CHECK_NULL(val,word);
+ stopFlag=static_cast<int*>(val);
+ break;
+ case GETEXCHANGESFLAG:
+ CHECK_INIT(initialized,word);
+ CHECK_NULL(val,word);
+ exchangePatterns.getFlag((*static_cast<int*>(val)));
+ break;
+ case SETEXCHANGESSEED:
+ CHECK_INIT(initialized,word);
+ CHECK_NULL(val,word);
+ exchangePatterns.setSeed((*static_cast<int*>(val)));
+ break;
+ case SETNUMBEROFREPLICAS:
+ CHECK_INIT(initialized,word);
+ CHECK_NULL(val,word);
+ exchangePatterns.setNofR((*static_cast<int*>(val)));
+ break;
+ case GETEXCHANGESLIST:
+ CHECK_INIT(initialized,word);
+ CHECK_NULL(val,word);
+ exchangePatterns.getList((static_cast<int*>(val)));
+ break;
+ case RUNFINALJOBS:
+ CHECK_INIT(initialized,word);
+ runJobsAtEndOfCalculation();
+ break;
+ case 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:
+ CHECK_INIT(initialized,word);
+ CHECK_NULL(val,word);
+ d=getBias()/(atoms.getMDUnits().getEnergy()/atoms.getUnits().getEnergy());
+ atoms.double2MD(d,val);
+ break;
+ default:
+ plumed_merror("cannot interpret cmd(\"" + word + "\"). check plumed developers manual to see the available commands.");
+ break;
+ }
+ } else if(nw==2 && words[0]=="checkAction"){
+ int check=0;
+ if(actionRegister().check(words[1])) check=1;
+ *(static_cast<int*>(val))=check;
+ } else if(nw>1 && words[0]=="GREX"){
+ if(!grex) grex=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);
+ } else if(nw>1 && words[0]=="CLTool"){
+ CHECK_NOTINIT(initialized,word);
+ if(!cltool) cltool=new CLToolMain;
+ std::string kk=words[1];
+ for(unsigned i=2;i<words.size();i++) kk+=" "+words[i];
+ cltool->cmd(kk.c_str(),val);
+ } else{
+ plumed_merror("cannot interpret cmd(\"" + word + "\"). check plumed developers manual to see the available commands.");
};
-
stopwatch.pause();
}
-/////
////////////////////////////////////////////////////////////////////////
void PlumedMain::init(){
@@ -415,8 +515,6 @@ void PlumedMain::readInputWords(const std::vector<std::string> & words){
pilots=actionSet.select<ActionPilot*>();
}
-
-
////////////////////////////////////////////////////////////////////////
void PlumedMain::exit(int c){
@@ -427,10 +525,6 @@ Log& PlumedMain::getLog(){
return log;
}
-
-
-
-
void PlumedMain::calc(){
prepareCalc();
performCalc();
@@ -441,7 +535,6 @@ void PlumedMain::prepareCalc(){
shareData();
}
-
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////
// here we have the main steps in "calc()"
// they can be called individually, but the standard thing is to
@@ -455,7 +548,6 @@ void PlumedMain::prepareDependencies(){
// before doing that, the prepare() method is called to see if there is some
// new/changed dependency (up to now, only useful for dependences on virtual atoms,
// which can be dynamically changed).
-//
// First switch off all actions
for(ActionSet::iterator p=actionSet.begin();p!=actionSet.end();++p){
@@ -480,7 +572,6 @@ void PlumedMain::prepareDependencies(){
}
stopwatch.stop("1 Prepare dependencies");
-
}
void PlumedMain::shareData(){
@@ -504,7 +595,6 @@ void PlumedMain::waitData(){
stopwatch.stop("3 Waiting for data");
}
-
void PlumedMain::justCalculate(){
if(!active)return;
stopwatch.start("4 Calculating (forward loop)");
@@ -679,8 +769,4 @@ void PlumedMain::runJobsAtEndOfCalculation(){
}
-
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-
-
-
diff --git a/src/core/PlumedMain.h b/src/core/PlumedMain.h
index 3ecb3a9d6..ccf3e0aff 100644
--- a/src/core/PlumedMain.h
+++ b/src/core/PlumedMain.h
@@ -27,6 +27,7 @@
#include <string>
#include <vector>
#include <set>
+#include <map>
// !!!!!!!!!!!!!!!!!!!!!! DANGER !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!11
@@ -145,6 +146,9 @@ public:
/// Add a citation, returning a string containing the reference number, something like "[10]"
std::string cite(const std::string&);
+/// word list command
+ std::map<std::string, int> word_map;
+
public:
PlumedMain();
// this is to access to WithCmd versions of cmd (allowing overloading of a virtual method)
--
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