--- trunk/OOPSE/libmdtools/SimSetup.cpp 2004/05/12 16:38:45 1167 +++ trunk/OOPSE/libmdtools/SimSetup.cpp 2004/05/27 19:26:42 1204 @@ -226,17 +226,17 @@ void SimSetup::makeMolecules(void){ molInfo.myAtoms = &(info[k].atoms[atomOffset]); if (molInfo.nBonds > 0) - molInfo.myBonds = new (Bond *) [molInfo.nBonds]; + molInfo.myBonds = new Bond*[molInfo.nBonds]; else molInfo.myBonds = NULL; if (molInfo.nBends > 0) - molInfo.myBends = new (Bend *) [molInfo.nBends]; + molInfo.myBends = new Bend*[molInfo.nBends]; else molInfo.myBends = NULL; if (molInfo.nTorsions > 0) - molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions]; + molInfo.myTorsions = new Torsion *[molInfo.nTorsions]; else molInfo.myTorsions = NULL; @@ -948,7 +948,37 @@ void SimSetup::gatherInfo(void){ info[i].useInitXSstate = globals->getUseInitXSstate(); info[i].orthoTolerance = globals->getOrthoBoxTolerance(); - + + // check for thermodynamic integration + if (globals->getUseThermInt()) { + if (globals->haveThermIntLambda() && globals->haveThermIntK()) { + info[i].useThermInt = globals->getUseThermInt(); + info[i].thermIntLambda = globals->getThermIntLambda(); + info[i].thermIntK = globals->getThermIntK(); + + Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK); + info[i].restraint = myRestraint; + } + else { + sprintf(painCave.errMsg, + "SimSetup Error:\n" + "\tKeyword useThermInt was set to 'true' but\n" + "\tthermodynamicIntegrationLambda (and/or\n" + "\tthermodynamicIntegrationK) was not specified.\n" + "\tPlease provide a lambda value and k value in your .bass file.\n"); + painCave.isFatal = 1; + simError(); + } + } + else if(globals->haveThermIntLambda() || globals->haveThermIntK()){ + sprintf(painCave.errMsg, + "SimSetup Warning: If you want to use Thermodynamic\n" + "\tIntegration, set useThermInt to 'true' in your .bass file.\n" + "\tThe useThermInt keyword is 'false' by default, so your\n" + "\tlambda and/or k values are being ignored.\n"); + painCave.isFatal = 0; + simError(); + } } //setup seed for random number generator @@ -1261,6 +1291,28 @@ void SimSetup::makeOutNames(void){ } } + strcpy(info[k].rawPotName, inFileName); + nameLength = strlen(info[k].rawPotName); + endTest = &(info[k].rawPotName[nameLength - 5]); + if (!strcmp(endTest, ".bass")){ + strcpy(endTest, ".raw"); + } + else if (!strcmp(endTest, ".BASS")){ + strcpy(endTest, ".raw"); + } + else{ + endTest = &(info[k].rawPotName[nameLength - 4]); + if (!strcmp(endTest, ".bss")){ + strcpy(endTest, ".raw"); + } + else if (!strcmp(endTest, ".mdl")){ + strcpy(endTest, ".raw"); + } + else{ + strcat(info[k].rawPotName, ".raw"); + } + } + #ifdef IS_MPI } @@ -1398,21 +1450,33 @@ void SimSetup::calcSysValues(void){ } void SimSetup::calcSysValues(void){ - int i; + int i, j; + int ncutgroups, atomsingroups, ngroupsinstamp; int* molMembershipArray; + CutoffGroupStamp* cg; tot_atoms = 0; tot_bonds = 0; tot_bends = 0; tot_torsions = 0; tot_rigid = 0; + tot_groups = 0; for (i = 0; i < n_components; i++){ tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies(); + + ncutgroups = comp_stamps[i]->getNCutoffGroups(); + atomsingroups = 0; + for (j=0; j < ncutgroups; j++) { + cg = comp_stamps[i]->getCutoffGroup(j); + atomsingroups += cg->getNMembers(); + } + ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups; + tot_groups += components_nmol[i] * ngroupsinstamp; } tot_SRI = tot_bonds + tot_bends + tot_torsions; @@ -1425,7 +1489,7 @@ void SimSetup::calcSysValues(void){ info[i].n_torsions = tot_torsions; info[i].n_SRI = tot_SRI; info[i].n_mol = tot_nmol; - + info[i].ngroup = tot_groups; info[i].molMembershipArray = molMembershipArray; } } @@ -1436,8 +1500,10 @@ void SimSetup::mpiMolDivide(void){ int i, j, k; int localMol, allMol; int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; - int local_rigid; + int local_rigid, local_groups; vector globalMolIndex; + int ncutgroups, atomsingroups, ngroupsinstamp; + CutoffGroupStamp* cg; mpiSim = new mpiSimulation(info); @@ -1457,6 +1523,7 @@ void SimSetup::mpiMolDivide(void){ local_bends = 0; local_torsions = 0; local_rigid = 0; + local_groups = 0; globalAtomCounter = 0; for (i = 0; i < n_components; i++){ @@ -1467,6 +1534,17 @@ void SimSetup::mpiMolDivide(void){ local_bends += comp_stamps[i]->getNBends(); local_torsions += comp_stamps[i]->getNTorsions(); local_rigid += comp_stamps[i]->getNRigidBodies(); + + ncutgroups = comp_stamps[i]->getNCutoffGroups(); + atomsingroups = 0; + for (k=0; k < ncutgroups; k++) { + cg = comp_stamps[i]->getCutoffGroup(k); + atomsingroups += cg->getNMembers(); + } + ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + + ncutgroups; + local_groups += ngroupsinstamp; + localMol++; } for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ @@ -1479,9 +1557,8 @@ void SimSetup::mpiMolDivide(void){ } local_SRI = local_bonds + local_bends + local_torsions; - info[0].n_atoms = mpiSim->getMyNlocal(); + info[0].n_atoms = mpiSim->getNAtomsLocal(); - if (local_atoms != info[0].n_atoms){ sprintf(painCave.errMsg, "SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n" @@ -1491,6 +1568,16 @@ void SimSetup::mpiMolDivide(void){ simError(); } + info[0].ngroup = mpiSim->getNGroupsLocal(); + if (local_groups != info[0].ngroup){ + sprintf(painCave.errMsg, + "SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n" + "\tlocalGroups (%d) are not equal.\n", + info[0].ngroup, local_groups); + painCave.isFatal = 1; + simError(); + } + info[0].n_bonds = local_bonds; info[0].n_bends = local_bends; info[0].n_torsions = local_torsions; @@ -1527,7 +1614,7 @@ void SimSetup::makeSysArrays(void){ molIndex = 0; - for (i = 0; i < mpiSim->getTotNmol(); i++){ + for (i = 0; i < mpiSim->getNMolGlobal(); i++){ if (mol2proc[i] == worldRank){ the_molecules[molIndex].setStampID(molCompType[i]); the_molecules[molIndex].setMyIndex(molIndex);