--- trunk/OOPSE/libmdtools/SimSetup.cpp 2004/04/15 16:18:26 1113 +++ trunk/OOPSE/libmdtools/SimSetup.cpp 2004/05/27 00:48:12 1198 @@ -183,6 +183,10 @@ void SimSetup::makeMolecules(void){ BendStamp* currentBend; TorsionStamp* currentTorsion; RigidBodyStamp* currentRigidBody; + CutoffGroupStamp* currentCutoffGroup; + CutoffGroup* myCutoffGroup; + int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file + set cutoffAtomSet; //atoms belong to cutoffgroup defined at mdl file bond_pair* theBonds; bend_set* theBends; @@ -216,21 +220,23 @@ void SimSetup::makeMolecules(void){ molInfo.nBends = comp_stamps[stampID]->getNBends(); molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies(); + + nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups(); 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; @@ -464,11 +470,11 @@ void SimSetup::makeMolecules(void){ // used for the exclude list: #ifdef IS_MPI - exI = info[k].atoms[tempI]->getGlobalIndex() + 1; - exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; + exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1; + exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1; #else - exI = tempI + 1; - exJ = tempJ + 1; + exI = molInfo.myAtoms[tempI]->getIndex() + 1; + exJ = molInfo.myAtoms[tempJ]->getIndex() + 1; #endif info[k].excludes->addPair(exI, exJ); @@ -481,6 +487,49 @@ void SimSetup::makeMolecules(void){ } + //create cutoff group for molecule + + cutoffAtomSet.clear(); + molInfo.myCutoffGroups.clear(); + + for (j = 0; j < nCutoffGroups; j++){ + + currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j); + nMembers = currentCutoffGroup->getNMembers(); + + myCutoffGroup = new CutoffGroup(); + + for (int cg = 0; cg < nMembers; cg++) { + + // molI is atom numbering inside this molecule + molI = currentCutoffGroup->getMember(cg); + + // tempI is atom numbering on local processor + tempI = molI + atomOffset; + + myCutoffGroup->addAtom(info[k].atoms[tempI]); + + cutoffAtomSet.insert(tempI); + } + + molInfo.myCutoffGroups.push_back(myCutoffGroup); + }//end for (j = 0; j < molInfo.nCutoffGroups; j++) + + //creat a cutoff group for every atom in current molecule which does not belong to cutoffgroup defined at mdl file + + for(j = 0; j < molInfo.nAtoms; j++){ + + if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){ + myCutoffGroup = new CutoffGroup(); + myCutoffGroup->addAtom(molInfo.myAtoms[j]); + molInfo.myCutoffGroups.push_back(myCutoffGroup); + } + + } + + + + // After this is all set up, scan through the atoms to // see if they can be added to the integrableObjects: @@ -535,19 +584,7 @@ void SimSetup::makeMolecules(void){ sprintf(checkPointMsg, "all molecules initialized succesfully"); MPIcheckPoint(); #endif // is_mpi - - // clean up the forcefield - - if (!globals->haveLJrcut()){ - - the_ff->calcRcut(); - - } else { - - the_ff->setRcut( globals->getLJrcut() ); - } - the_ff->cleanMe(); } void SimSetup::initFromBass(void){ @@ -834,7 +871,7 @@ void SimSetup::gatherInfo(void){ } //check whether sample time, status time, thermal time and reset time are divisble by dt - if (!isDivisible(globals->getSampleTime(), globals->getDt())){ + if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){ sprintf(painCave.errMsg, "Sample time is not divisible by dt.\n" "\tThis will result in samples that are not uniformly\n" @@ -844,7 +881,7 @@ void SimSetup::gatherInfo(void){ simError(); } - if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){ + if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){ sprintf(painCave.errMsg, "Status time is not divisible by dt.\n" "\tThis will result in status reports that are not uniformly\n" @@ -880,12 +917,10 @@ void SimSetup::gatherInfo(void){ if (globals->haveSampleTime()){ info[i].sampleTime = globals->getSampleTime(); info[i].statusTime = info[i].sampleTime; - info[i].thermalTime = info[i].sampleTime; } else{ info[i].sampleTime = globals->getRunTime(); info[i].statusTime = info[i].sampleTime; - info[i].thermalTime = info[i].sampleTime; } if (globals->haveStatusTime()){ @@ -894,6 +929,8 @@ void SimSetup::gatherInfo(void){ if (globals->haveThermalTime()){ info[i].thermalTime = globals->getThermalTime(); + } else { + info[i].thermalTime = globals->getRunTime(); } info[i].resetIntegrator = 0; @@ -911,7 +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 @@ -987,39 +1054,61 @@ void SimSetup::finalInfoCheck(void){ MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); #endif //is_mpi - double theEcr, theEst; + double theRcut, theRsw; - if (globals->getUseRF()){ - info[i].useReactionField = 1; + if (globals->haveRcut()) { + theRcut = globals->getRcut(); - if (!globals->haveECR()){ - sprintf(painCave.errMsg, - "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n" + if (globals->haveRsw()) + theRsw = globals->getRsw(); + else + theRsw = theRcut; + + info[i].setDefaultRcut(theRcut, theRsw); + + } else { + + the_ff->calcRcut(); + theRcut = info[i].getRcut(); + + if (globals->haveRsw()) + theRsw = globals->getRsw(); + else + theRsw = theRcut; + + info[i].setDefaultRcut(theRcut, theRsw); + } + + if (globals->getUseRF()){ + info[i].useReactionField = 1; + + if (!globals->haveRcut()){ + sprintf(painCave.errMsg, + "SimSetup Warning: No value was set for the cutoffRadius.\n" "\tOOPSE will use a default value of 15.0 angstroms" - "\tfor the electrostaticCutoffRadius.\n"); + "\tfor the cutoffRadius.\n"); painCave.isFatal = 0; simError(); - theEcr = 15.0; + theRcut = 15.0; } else{ - theEcr = globals->getECR(); + theRcut = globals->getRcut(); } - if (!globals->haveEST()){ + if (!globals->haveRsw()){ sprintf(painCave.errMsg, - "SimSetup Warning: No value was set for electrostaticSkinThickness.\n" + "SimSetup Warning: No value was set for switchingRadius.\n" "\tOOPSE will use a default value of\n" - "\t0.05 * electrostaticCutoffRadius\n" - "\tfor the electrostaticSkinThickness\n"); + "\t0.95 * cutoffRadius for the switchingRadius\n"); painCave.isFatal = 0; simError(); - theEst = 0.05 * theEcr; + theRsw = 0.95 * theRcut; } else{ - theEst = globals->getEST(); + theRsw = globals->getRsw(); } - info[i].setDefaultEcr(theEcr, theEst); + info[i].setDefaultRcut(theRcut, theRsw); if (!globals->haveDielectric()){ sprintf(painCave.errMsg, @@ -1033,34 +1122,35 @@ void SimSetup::finalInfoCheck(void){ } else{ if (usesDipoles || usesCharges){ - if (!globals->haveECR()){ + + if (!globals->haveRcut()){ sprintf(painCave.errMsg, - "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n" + "SimSetup Warning: No value was set for the cutoffRadius.\n" "\tOOPSE will use a default value of 15.0 angstroms" - "\tfor the electrostaticCutoffRadius.\n"); - painCave.isFatal = 0; - simError(); - theEcr = 15.0; - } + "\tfor the cutoffRadius.\n"); + painCave.isFatal = 0; + simError(); + theRcut = 15.0; + } else{ - theEcr = globals->getECR(); + theRcut = globals->getRcut(); } - - if (!globals->haveEST()){ + + if (!globals->haveRsw()){ sprintf(painCave.errMsg, - "SimSetup Warning: No value was set for electrostaticSkinThickness.\n" + "SimSetup Warning: No value was set for switchingRadius.\n" "\tOOPSE will use a default value of\n" - "\t0.05 * electrostaticCutoffRadius\n" - "\tfor the electrostaticSkinThickness\n"); + "\t0.95 * cutoffRadius for the switchingRadius\n"); painCave.isFatal = 0; simError(); - theEst = 0.05 * theEcr; + theRsw = 0.95 * theRcut; } else{ - theEst = globals->getEST(); + theRsw = globals->getRsw(); } + + info[i].setDefaultRcut(theRcut, theRsw); - info[i].setDefaultEcr(theEcr, theEst); } } } @@ -1068,6 +1158,9 @@ void SimSetup::finalInfoCheck(void){ strcpy(checkPointMsg, "post processing checks out"); MPIcheckPoint(); #endif // is_mpi + + // clean up the forcefield + the_ff->cleanMe(); } void SimSetup::initSystemCoords(void){ @@ -1198,6 +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 } @@ -1282,7 +1397,10 @@ void SimSetup::compList(void){ LinkedMolStamp* headStamp = new LinkedMolStamp(); LinkedMolStamp* currentStamp = NULL; comp_stamps = new MoleculeStamp * [n_components]; + bool haveCutoffGroups; + haveCutoffGroups = false; + // make an array of molecule stamps that match the components used. // also extract the used stamps out into a separate linked list @@ -1317,7 +1435,13 @@ void SimSetup::compList(void){ headStamp->add(currentStamp); comp_stamps[i] = headStamp->match(id); } + + if(comp_stamps[i]->getNCutoffGroups() > 0) + haveCutoffGroups = true; } + + for (i = 0; i < nInfo; i++) + info[i].haveCutoffGroups = haveCutoffGroups; #ifdef IS_MPI strcpy(checkPointMsg, "Component stamps successfully extracted\n"); @@ -1365,14 +1489,13 @@ void SimSetup::mpiMolDivide(void){ int localMol, allMol; int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; int local_rigid; - vector globalAtomIndex; vector globalMolIndex; mpiSim = new mpiSimulation(info); mpiSim->divideLabor(); globalAtomIndex = mpiSim->getGlobalAtomIndex(); - globalMolIndex = mpiSim->getGlobalMolIndex(); + //globalMolIndex = mpiSim->getGlobalMolIndex(); // set up the local variables @@ -1408,7 +1531,7 @@ void SimSetup::mpiMolDivide(void){ } local_SRI = local_bonds + local_bends + local_torsions; - info[0].n_atoms = mpiSim->getMyNlocal(); + info[0].n_atoms = mpiSim->getLocalNatoms(); if (local_atoms != info[0].n_atoms){ @@ -1493,7 +1616,7 @@ void SimSetup::makeSysArrays(void){ info[l].atoms = the_atoms; info[l].molecules = the_molecules; info[l].nGlobalExcludes = 0; - + the_ff->setSimInfo(info); } }