--- trunk/OOPSE/libmdtools/SimSetup.cpp 2003/09/04 21:48:35 746 +++ trunk/OOPSE/libmdtools/SimSetup.cpp 2003/10/21 19:33:19 811 @@ -22,8 +22,6 @@ #define NVT_ENS 1 #define NPTi_ENS 2 #define NPTf_ENS 3 -#define NPTim_ENS 4 -#define NPTfm_ENS 5 #define FF_DUFF 0 #define FF_LJ 1 @@ -92,7 +90,6 @@ void SimSetup::createSim(void){ #endif // is_mpi void SimSetup::createSim(void){ - int i, j, k, globalAtomIndex; // gather all of the information from the Bass file @@ -110,6 +107,9 @@ void SimSetup::createSim(void){ if (!isInfoArray){ initSystemCoords(); + + if( !(globals->getUseInitTime()) ) + info[0].currentTime = 0.0; } // make the output filenames @@ -131,7 +131,7 @@ void SimSetup::makeMolecules(void){ void SimSetup::makeMolecules(void){ - int k, l; + int k; int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; molInit molInfo; DirectionalAtom* dAtom; @@ -553,7 +553,7 @@ void SimSetup::gatherInfo(void){ void SimSetup::gatherInfo(void){ - int i, j, k; + int i; ensembleCase = -1; ffCase = -1; @@ -603,12 +603,6 @@ 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{ sprintf(painCave.errMsg, @@ -922,7 +916,6 @@ void SimSetup::initSystemCoords(void){ if (worldRank == 0){ #endif //is_mpi inName = globals->getInitialConfig(); - double* tempDouble = new double[1000000]; fileInit = new InitializeFromFile(inName); #ifdef IS_MPI } @@ -940,7 +933,7 @@ void SimSetup::initSystemCoords(void){ sprintf(painCave.errMsg, "Cannot intialize a parallel simulation without an initial configuration file.\n"); - painCave.isFatal; + painCave.isFatal = 1;; simError(); #else @@ -1166,7 +1159,7 @@ void SimSetup::calcSysValues(void){ } void SimSetup::calcSysValues(void){ - int i, j, k; + int i; int* molMembershipArray; @@ -1265,7 +1258,11 @@ void SimSetup::makeSysArrays(void){ void SimSetup::makeSysArrays(void){ - int i, j, k, l; + +#ifndef IS_MPI + int k, j; +#endif // is_mpi + int i, l; Atom** the_atoms; Molecule* the_molecules; @@ -1348,21 +1345,23 @@ void SimSetup::makeIntegrator(void){ void SimSetup::makeIntegrator(void){ int k; + NVE* myNVE = NULL; NVT* myNVT = NULL; - NPTi* myNPTi = NULL; - NPTf* myNPTf = NULL; - NPTim* myNPTim = NULL; - NPTfm* myNPTfm = NULL; + NPTi >* myNPTi = NULL; + NPTf >* myNPTf = NULL; for (k = 0; k < nInfo; k++){ switch (ensembleCase){ case NVE_ENS: if (globals->haveZconstraints()){ setupZConstraint(info[k]); - new ZConstraint >(&(info[k]), the_ff); + myNVE = new ZConstraint >(&(info[k]), the_ff); } - else - new NVE(&(info[k]), the_ff); + else{ + myNVE = new NVE(&(info[k]), the_ff); + } + + info->the_integrator = myNVE; break; case NVT_ENS: @@ -1384,15 +1383,17 @@ void SimSetup::makeIntegrator(void){ painCave.isFatal = 1; simError(); } + + info->the_integrator = myNVT; break; case NPTi_ENS: if (globals->haveZconstraints()){ setupZConstraint(info[k]); - myNPTi = new ZConstraint >(&(info[k]), the_ff); + myNPTi = new ZConstraint > >(&(info[k]), the_ff); } else - myNPTi = new NPTi(&(info[k]), the_ff); + myNPTi = new NPTi >(&(info[k]), the_ff); myNPTi->setTargetTemp(globals->getTargetTemp()); @@ -1425,15 +1426,17 @@ void SimSetup::makeIntegrator(void){ painCave.isFatal = 1; simError(); } + + info->the_integrator = myNPTi; break; case NPTf_ENS: if (globals->haveZconstraints()){ setupZConstraint(info[k]); - myNPTf = new ZConstraint >(&(info[k]), the_ff); + myNPTf = new ZConstraint > >(&(info[k]), the_ff); } else - myNPTf = new NPTf(&(info[k]), the_ff); + myNPTf = new NPTf >(&(info[k]), the_ff); myNPTf->setTargetTemp(globals->getTargetTemp()); @@ -1466,90 +1469,10 @@ void SimSetup::makeIntegrator(void){ painCave.isFatal = 1; simError(); } - break; - case NPTim_ENS: - if (globals->haveZconstraints()){ - setupZConstraint(info[k]); - myNPTim = new ZConstraint >(&(info[k]), the_ff); - } - else - myNPTim = new NPTim(&(info[k]), the_ff); - - myNPTim->setTargetTemp(globals->getTargetTemp()); - - if (globals->haveTargetPressure()) - myNPTim->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()) - myNPTim->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()) - myNPTim->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(); - } + info->the_integrator = myNPTf; break; - case NPTfm_ENS: - if (globals->haveZconstraints()){ - setupZConstraint(info[k]); - myNPTfm = new ZConstraint >(&(info[k]), the_ff); - } - else - myNPTfm = new NPTfm(&(info[k]), the_ff); - - myNPTfm->setTargetTemp(globals->getTargetTemp()); - - if (globals->haveTargetPressure()) - myNPTfm->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()) - myNPTfm->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()) - 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; - default: sprintf(painCave.errMsg, "SimSetup Error. Unrecognized ensemble in case statement.\n");