--- trunk/OOPSE/libmdtools/SimSetup.cpp 2003/07/22 16:41:08 644 +++ trunk/OOPSE/libmdtools/SimSetup.cpp 2003/07/31 19:59:34 660 @@ -1,6 +1,8 @@ +#include #include #include #include +#include #include "SimSetup.hpp" #include "parse_me.h" @@ -14,22 +16,34 @@ // some defines for ensemble and Forcefield cases -#define NVE_ENS 0 -#define NVT_ENS 1 -#define NPTi_ENS 2 -#define NPTf_ENS 3 -#define NPTim_ENS 4 -#define NPTfm_ENS 5 - +#define NVE_ENS 0 +#define NVT_ENS 1 +#define NPTi_ENS 2 +#define NPTf_ENS 3 +#define NPTim_ENS 4 +#define NPTfm_ENS 5 +#define NVEZCONS_ENS 6 +#define NVTZCONS_ENS 7 +#define NPTiZCONS_ENS 8 +#define NPTfZCONS_ENS 9 +#define NPTimZCONS_ENS 10 +#define NPTfmZCONS_ENS 11 #define FF_DUFF 0 #define FF_LJ 1 +#define FF_EAM 2 +using namespace std; SimSetup::SimSetup(){ + + isInfoArray = 0; + nInfo = 1; + stamps = new MakeStamps(); globals = new Globals(); + #ifdef IS_MPI strcpy( checkPointMsg, "SimSetup creation successful" ); MPIcheckPoint(); @@ -41,6 +55,13 @@ SimSetup::~SimSetup(){ delete globals; } +void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) { + info = the_info; + nInfo = theNinfo; + isInfoArray = 1; + } + + void SimSetup::parseFile( char* fileName ){ #ifdef IS_MPI @@ -586,6 +607,7 @@ void SimSetup::gatherInfo( void ){ if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; + else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; else{ sprintf( painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n", @@ -605,6 +627,15 @@ void SimSetup::gatherInfo( void ){ else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; + + else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS; + else if( !strcasecmp( ensemble, "NVTZCONS")) ensembleCase = NVTZCONS_ENS; + else if( !strcasecmp( ensemble, "NPTiZCONS") || !strcasecmp( ensemble, "NPT")) + ensembleCase = NPTiZCONS_ENS; + else if( !strcasecmp( ensemble, "NPTfCONS")) ensembleCase = NPTfZCONS_ENS; + else if( !strcasecmp( ensemble, "NPTimZCONS")) ensembleCase = NPTimZCONS_ENS; + else if( !strcasecmp( ensemble, "NPTfmCONS")) ensembleCase = NPTfmZCONS_ENS; + else{ sprintf( painCave.errMsg, "SimSetup Warning. Unrecognized Ensemble -> %s, " @@ -1030,6 +1061,10 @@ void SimSetup::createFF( void ){ case FF_LJ: the_ff = new LJFF(); + break; + + case FF_EAM: + the_ff = new EAM_FF(); break; default: @@ -1281,20 +1316,28 @@ void SimSetup::makeIntegrator( void ){ void SimSetup::makeIntegrator( void ){ - NVT* myNVT = NULL; - NPTi* myNPTi = NULL; - NPTf* myNPTf = NULL; - NPTim* myNPTim = NULL; - NPTfm* myNPTfm = NULL; - + NVT* myNVT = NULL; + NPTi* myNPTi = NULL; + NPTf* myNPTf = NULL; + NPTim* myNPTim = NULL; + NPTfm* myNPTfm = NULL; + ZConstraint >* myNVEZCons = NULL; + ZConstraint >* myNVTZCons = NULL; + ZConstraint >* myNPTiZCons = NULL; + ZConstraint >* myNPTfZCons = NULL; + ZConstraint >* myNPTimZCons = NULL; + ZConstraint >* myNPTfmZCons = NULL; + + cerr << "setting integrator" <( info, the_ff ); break; case NVT_ENS: - myNVT = new NVT( info, the_ff ); + myNVT = new NVT( info, the_ff ); myNVT->setTargetTemp(globals->getTargetTemp()); if (globals->haveTauThermostat()) @@ -1310,7 +1353,7 @@ void SimSetup::makeIntegrator( void ){ break; case NPTi_ENS: - myNPTi = new NPTi( info, the_ff ); + myNPTi = new NPTi( info, the_ff ); myNPTi->setTargetTemp( globals->getTargetTemp() ); if (globals->haveTargetPressure()) @@ -1345,7 +1388,7 @@ void SimSetup::makeIntegrator( void ){ break; case NPTf_ENS: - myNPTf = new NPTf( info, the_ff ); + myNPTf = new NPTf( info, the_ff ); myNPTf->setTargetTemp( globals->getTargetTemp()); if (globals->haveTargetPressure()) @@ -1380,7 +1423,7 @@ void SimSetup::makeIntegrator( void ){ break; case NPTim_ENS: - myNPTim = new NPTim( info, the_ff ); + myNPTim = new NPTim( info, the_ff ); myNPTim->setTargetTemp( globals->getTargetTemp()); if (globals->haveTargetPressure()) @@ -1415,7 +1458,7 @@ void SimSetup::makeIntegrator( void ){ break; case NPTfm_ENS: - myNPTfm = new NPTfm( info, the_ff ); + myNPTfm = new NPTfm( info, the_ff ); myNPTfm->setTargetTemp( globals->getTargetTemp()); if (globals->haveTargetPressure()) @@ -1440,15 +1483,204 @@ void SimSetup::makeIntegrator( void ){ if( globals->haveTauBarostat() ) myNPTfm->setTauBarostat( globals->getTauBarostat() ); + else{ + sprintf( painCave.errMsg, + "SimSetup error: If you use an NPT\n" + " ensemble, you must set tauBarostat.\n"); + painCave.isFatal = 1; + simError(); + } + break; + + case NVEZCONS_ENS: + + + //setup index of z-constraint molecules, z-constraint sampel time + //and z-constraint force output name. These parameter should be known + //before constructing the z-constraint integrator + setupZConstraint(); + + myNVEZCons = new ZConstraint >( info, the_ff ); + + break; + + + case NVTZCONS_ENS: + + setupZConstraint(); + + myNVTZCons = new ZConstraint >( info, the_ff ); + myNVTZCons->setTargetTemp(globals->getTargetTemp()); + + if (globals->haveTauThermostat()) + myNVTZCons->setTauThermostat(globals->getTauThermostat()); + + else { + sprintf( painCave.errMsg, + "SimSetup error: If you use the NVT\n" + " ensemble, you must set tauThermostat.\n"); + painCave.isFatal = 1; + simError(); + } + break; + + case NPTiZCONS_ENS: + + setupZConstraint(); + + myNPTiZCons = new ZConstraint >( info, the_ff ); + myNPTiZCons->setTargetTemp( globals->getTargetTemp() ); + + if (globals->haveTargetPressure()) + myNPTiZCons->setTargetPressure(globals->getTargetPressure()); + else { + sprintf( painCave.errMsg, + "SimSetup error: If you use a constant pressure\n" + " ensemble, you must set targetPressure in the BASS file.\n"); + painCave.isFatal = 1; + simError(); + } + + if( globals->haveTauThermostat() ) + myNPTiZCons->setTauThermostat( globals->getTauThermostat() ); + else{ + sprintf( painCave.errMsg, + "SimSetup error: If you use an NPT\n" + " ensemble, you must set tauThermostat.\n"); + painCave.isFatal = 1; + simError(); + } + + if( globals->haveTauBarostat() ) + myNPTiZCons->setTauBarostat( globals->getTauBarostat() ); + else{ + sprintf( painCave.errMsg, + "SimSetup error: If you use an NPT\n" + " ensemble, you must set tauBarostat.\n"); + painCave.isFatal = 1; + simError(); + } + + break; + + case NPTfZCONS_ENS: + + setupZConstraint(); + + myNPTfZCons = new ZConstraint >( info, the_ff ); + myNPTfZCons->setTargetTemp( globals->getTargetTemp()); + + if (globals->haveTargetPressure()) + myNPTfZCons->setTargetPressure(globals->getTargetPressure()); + else { + sprintf( painCave.errMsg, + "SimSetup error: If you use a constant pressure\n" + " ensemble, you must set targetPressure in the BASS file.\n"); + painCave.isFatal = 1; + simError(); + } + + if( globals->haveTauThermostat() ) + myNPTfZCons->setTauThermostat( globals->getTauThermostat() ); else{ sprintf( painCave.errMsg, "SimSetup error: If you use an NPT\n" + " ensemble, you must set tauThermostat.\n"); + painCave.isFatal = 1; + simError(); + } + + if( globals->haveTauBarostat() ) + myNPTfZCons->setTauBarostat( globals->getTauBarostat() ); + else{ + sprintf( painCave.errMsg, + "SimSetup error: If you use an NPT\n" " ensemble, you must set tauBarostat.\n"); painCave.isFatal = 1; simError(); + } + + break; + + case NPTimZCONS_ENS: + + setupZConstraint(); + + myNPTimZCons = new ZConstraint >( info, the_ff ); + myNPTimZCons->setTargetTemp( globals->getTargetTemp()); + + if (globals->haveTargetPressure()) + myNPTimZCons->setTargetPressure(globals->getTargetPressure()); + else { + sprintf( painCave.errMsg, + "SimSetup error: If you use a constant pressure\n" + " ensemble, you must set targetPressure in the BASS file.\n"); + painCave.isFatal = 1; + simError(); } + + if( globals->haveTauThermostat() ) + myNPTimZCons->setTauThermostat( globals->getTauThermostat() ); + else{ + sprintf( painCave.errMsg, + "SimSetup error: If you use an NPT\n" + " ensemble, you must set tauThermostat.\n"); + painCave.isFatal = 1; + simError(); + } + + if( globals->haveTauBarostat() ) + myNPTimZCons->setTauBarostat( globals->getTauBarostat() ); + else{ + sprintf( painCave.errMsg, + "SimSetup error: If you use an NPT\n" + " ensemble, you must set tauBarostat.\n"); + painCave.isFatal = 1; + simError(); + } + break; + + case NPTfmZCONS_ENS: + + setupZConstraint(); + + myNPTfmZCons = new ZConstraint >( info, the_ff ); + myNPTfmZCons->setTargetTemp( globals->getTargetTemp()); + if (globals->haveTargetPressure()) + myNPTfmZCons->setTargetPressure(globals->getTargetPressure()); + else { + sprintf( painCave.errMsg, + "SimSetup error: If you use a constant pressure\n" + " ensemble, you must set targetPressure in the BASS file.\n"); + painCave.isFatal = 1; + simError(); + } + + if( globals->haveTauThermostat() ) + myNPTfmZCons->setTauThermostat( globals->getTauThermostat() ); + else{ + sprintf( painCave.errMsg, + "SimSetup error: If you use an NPT\n" + " ensemble, you must set tauThermostat.\n"); + painCave.isFatal = 1; + simError(); + } + + if( globals->haveTauBarostat() ) + myNPTfmZCons->setTauBarostat( globals->getTauBarostat() ); + else{ + sprintf( painCave.errMsg, + "SimSetup error: If you use an NPT\n" + " ensemble, you must set tauBarostat.\n"); + painCave.isFatal = 1; + simError(); + } + break; + + + default: sprintf( painCave.errMsg, "SimSetup Error. Unrecognized ensemble in case statement.\n"); @@ -1484,3 +1716,59 @@ void SimSetup::initFortran( void ){ #endif // is_mpi } + +void SimSetup::setupZConstraint() +{ + if(globals->haveZConsTime()){ + + //add sample time of z-constraint into SimInfo's property list + DoubleData* zconsTimeProp = new DoubleData(); + zconsTimeProp->setID("zconstime"); + zconsTimeProp->setData(globals->getZConsTime()); + info->addProperty(zconsTimeProp); + } + else{ + sprintf( painCave.errMsg, + "ZConstraint error: If you use an ZConstraint\n" + " , you must set sample time.\n"); + painCave.isFatal = 1; + simError(); + } + + if(globals->haveIndexOfAllZConsMols()){ + + //add index of z-constraint molecules into SimInfo's property list + vector tempIndex = globals->getIndexOfAllZConsMols(); + + //sort the index + sort(tempIndex.begin(), tempIndex.end()); + + IndexData* zconsIndex = new IndexData(); + zconsIndex->setID("zconsindex"); + zconsIndex->setIndexData(tempIndex); + info->addProperty(zconsIndex); + } + else{ + sprintf( painCave.errMsg, + "SimSetup error: If you use an ZConstraint\n" + " , you must set index of z-constraint molecules.\n"); + painCave.isFatal = 1; + simError(); + + } + + //Determine the name of ouput file and add it into SimInfo's property list + //Be careful, do not use inFileName, since it is a pointer which + //point to a string at master node, and slave nodes do not contain that string + + string zconsOutput(info->finalName); + + zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; + + StringData* zconsFilename = new StringData(); + zconsFilename->setID("zconsfilename"); + zconsFilename->setData(zconsOutput); + + info->addProperty(zconsFilename); + +}