--- branches/development/src/brains/SimInfo.cpp 2011/04/29 17:25:12 1553 +++ branches/development/src/brains/SimInfo.cpp 2011/09/13 22:05:04 1627 @@ -60,6 +60,9 @@ #include "io/ForceFieldOptions.hpp" #include "UseTheForce/ForceField.hpp" #include "nonbonded/SwitchingFunction.hpp" +#ifdef IS_MPI +#include +#endif using namespace std; namespace OpenMD { @@ -71,7 +74,7 @@ namespace OpenMD { nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nInversions_(0), nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0), - nConstraints_(0), sman_(NULL), fortranInitialized_(false), + nConstraints_(0), sman_(NULL), topologyDone_(false), calcBoxDipole_(false), useAtomicVirial_(true) { MoleculeStamp* molStamp; @@ -125,13 +128,8 @@ namespace OpenMD { //equal to the total number of atoms minus number of atoms belong to //cutoff group defined in meta-data file plus the number of cutoff //groups defined in meta-data file - std::cerr << "nGA = " << nGlobalAtoms_ << "\n"; - std::cerr << "nCA = " << nCutoffAtoms << "\n"; - std::cerr << "nG = " << nGroups << "\n"; nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; - - std::cerr << "nGCG = " << nGlobalCutoffGroups_ << "\n"; //every free atom (atom does not belong to rigid bodies) is an //integrable object therefore the total number of integrable objects @@ -273,6 +271,25 @@ namespace OpenMD { fdf_ = fdf_local; #endif return fdf_; + } + + unsigned int SimInfo::getNLocalCutoffGroups(){ + int nLocalCutoffAtoms = 0; + Molecule* mol; + MoleculeIterator mi; + CutoffGroup* cg; + Molecule::CutoffGroupIterator ci; + + for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { + + for (cg = mol->beginCutoffGroup(ci); cg != NULL; + cg = mol->nextCutoffGroup(ci)) { + nLocalCutoffAtoms += cg->getNumAtom(); + + } + } + + return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_; } void SimInfo::calcNdfRaw() { @@ -680,17 +697,18 @@ namespace OpenMD { Atom* atom; set atomTypes; - for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { - for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { + for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { + for(atom = mol->beginAtom(ai); atom != NULL; + atom = mol->nextAtom(ai)) { atomTypes.insert(atom->getAtomType()); } } - + #ifdef IS_MPI // loop over the found atom types on this processor, and add their // numerical idents to a vector: - + vector foundTypes; set::iterator i; for (i = atomTypes.begin(); i != atomTypes.end(); ++i) @@ -699,41 +717,50 @@ namespace OpenMD { // count_local holds the number of found types on this processor int count_local = foundTypes.size(); - // count holds the total number of found types on all processors - // (some will be redundant with the ones found locally): - int count; - MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM); - - // create a vector to hold the globally found types, and resize it: - vector ftGlobal; - ftGlobal.resize(count); - vector counts; - int nproc = MPI::COMM_WORLD.Get_size(); - counts.resize(nproc); - vector disps; - disps.resize(nproc); - // now spray out the foundTypes to all the other processors: + // we need arrays to hold the counts and displacement vectors for + // all processors + vector counts(nproc, 0); + vector disps(nproc, 0); + + // fill the counts array + MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0], + 1, MPI::INT); + + // use the processor counts to compute the displacement array + disps[0] = 0; + int totalCount = counts[0]; + for (int iproc = 1; iproc < nproc; iproc++) { + disps[iproc] = disps[iproc-1] + counts[iproc-1]; + totalCount += counts[iproc]; + } + + // we need a (possibly redundant) set of all found types: + vector ftGlobal(totalCount); + // now spray out the foundTypes to all the other processors: MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT, - &ftGlobal[0], &counts[0], &disps[0], MPI::INT); + &ftGlobal[0], &counts[0], &disps[0], + MPI::INT); + vector::iterator j; + // foundIdents is a stl set, so inserting an already found ident // will have no effect. set foundIdents; - vector::iterator j; + for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j) foundIdents.insert((*j)); // now iterate over the foundIdents and get the actual atom types // that correspond to these: set::iterator it; - for (it = foundIdents.begin(); it != foundIdents.end(); ++it) + for (it = foundIdents.begin(); it != foundIdents.end(); ++it) atomTypes.insert( forceField_->getAtomType((*it)) ); #endif - + return atomTypes; } @@ -745,7 +772,7 @@ namespace OpenMD { if ( simParams_->getAccumulateBoxDipole() ) { calcBoxDipole_ = true; } - + set::iterator i; set atomTypes; atomTypes = getSimulatedAtomTypes(); @@ -758,18 +785,28 @@ namespace OpenMD { usesMetallic |= (*i)->isMetal(); usesDirectional |= (*i)->isDirectional(); } - + #ifdef IS_MPI int temp; temp = usesDirectional; MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); - + temp = usesMetallic; MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); - + temp = usesElectrostatic; MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); +#else + + usesDirectionalAtoms_ = usesDirectional; + usesMetallicAtoms_ = usesMetallic; + usesElectrostaticAtoms_ = usesElectrostatic; + #endif + + requiresPrepair_ = usesMetallicAtoms_ ? true : false; + requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false; + requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false; } @@ -812,20 +849,10 @@ namespace OpenMD { } - void SimInfo::setupFortran() { - int isError; + void SimInfo::prepareTopology() { int nExclude, nOneTwo, nOneThree, nOneFour; - vector fortranGlobalGroupMembership; - - isError = 0; - - //globalGroupMembership_ is filled by SimCreator - for (int i = 0; i < nGlobalAtoms_; i++) { - fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1); - } //calculate mass ratio of cutoff group - vector mfact; SimInfo::MoleculeIterator mi; Molecule* mol; Molecule::CutoffGroupIterator ci; @@ -834,19 +861,28 @@ namespace OpenMD { Atom* atom; RealType totalMass; - //to avoid memory reallocation, reserve enough space for mfact - mfact.reserve(getNCutoffGroups()); + /** + * The mass factor is the relative mass of an atom to the total + * mass of the cutoff group it belongs to. By default, all atoms + * are their own cutoff groups, and therefore have mass factors of + * 1. We need some special handling for massless atoms, which + * will be treated as carrying the entire mass of the cutoff + * group. + */ + massFactors_.clear(); + massFactors_.resize(getNAtoms(), 1.0); for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { - for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { + for (cg = mol->beginCutoffGroup(ci); cg != NULL; + cg = mol->nextCutoffGroup(ci)) { totalMass = cg->getMass(); for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { // Check for massless groups - set mfact to 1 if true - if (totalMass != 0) - mfact.push_back(atom->getMass()/totalMass); + if (totalMass != 0) + massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass; else - mfact.push_back( 1.0 ); + massFactors_[atom->getLocalIndex()] = 1.0; } } } @@ -860,15 +896,8 @@ namespace OpenMD { identArray_.push_back(atom->getIdent()); } } - - //fill molMembershipArray - //molMembershipArray is filled by SimCreator - vector molMembershipArray(nGlobalAtoms_); - for (int i = 0; i < nGlobalAtoms_; i++) { - molMembershipArray[i] = globalMolMembership_[i] + 1; - } - //setup fortran simulation + //scan topology nExclude = excludedInteractions_.getSize(); nOneTwo = oneTwoInteractions_.getSize(); @@ -880,72 +909,7 @@ namespace OpenMD { int* oneThreeList = oneThreeInteractions_.getPairList(); int* oneFourList = oneFourInteractions_.getPairList(); - //setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray_[0], - // &nExclude, excludeList, - // &nOneTwo, oneTwoList, - // &nOneThree, oneThreeList, - // &nOneFour, oneFourList, - // &molMembershipArray[0], &mfact[0], &nCutoffGroups_, - // &fortranGlobalGroupMembership[0], &isError); - - // if( isError ){ - // - // sprintf( painCave.errMsg, - // "There was an error setting the simulation information in fortran.\n" ); - // painCave.isFatal = 1; - // painCave.severity = OPENMD_ERROR; - // simError(); - //} - - - // sprintf( checkPointMsg, - // "succesfully sent the simulation information to fortran.\n"); - - // errorCheckPoint(); - - // Setup number of neighbors in neighbor list if present - //if (simParams_->haveNeighborListNeighbors()) { - // int nlistNeighbors = simParams_->getNeighborListNeighbors(); - // setNeighbors(&nlistNeighbors); - //} - -#ifdef IS_MPI - // mpiSimData parallelData; - - //fill up mpiSimData struct - // parallelData.nMolGlobal = getNGlobalMolecules(); - // parallelData.nMolLocal = getNMolecules(); - // parallelData.nAtomsGlobal = getNGlobalAtoms(); - // parallelData.nAtomsLocal = getNAtoms(); - // parallelData.nGroupsGlobal = getNGlobalCutoffGroups(); - // parallelData.nGroupsLocal = getNCutoffGroups(); - // parallelData.myNode = worldRank; - // MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors)); - - //pass mpiSimData struct and index arrays to fortran - //setFsimParallel(¶llelData, &(parallelData.nAtomsLocal), - // &localToGlobalAtomIndex[0], &(parallelData.nGroupsLocal), - // &localToGlobalCutoffGroupIndex[0], &isError); - - // if (isError) { - // sprintf(painCave.errMsg, - // "mpiRefresh errror: fortran didn't like something we gave it.\n"); - // painCave.isFatal = 1; - // simError(); - // } - - // sprintf(checkPointMsg, " mpiRefresh successful.\n"); - // errorCheckPoint(); -#endif - - // initFortranFF(&isError); - // if (isError) { - // sprintf(painCave.errMsg, - // "initFortranFF errror: fortran didn't like something we gave it.\n"); - // painCave.isFatal = 1; - // simError(); - // } - // fortranInitialized_ = true; + topologyDone_ = true; } void SimInfo::addProperty(GenericData* genData) {