--- branches/development/src/brains/SimInfo.cpp 2010/12/29 19:59:21 1532 +++ branches/development/src/brains/SimInfo.cpp 2013/05/15 15:09:35 1874 @@ -35,8 +35,9 @@ * * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). - * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). - * [4] Vardeman & Gezelter, in progress (2009). + * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). + * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). */ /** @@ -54,20 +55,15 @@ #include "math/Vector3.hpp" #include "primitives/Molecule.hpp" #include "primitives/StuntDouble.hpp" -#include "UseTheForce/doForces_interface.h" -#include "UseTheForce/DarkSide/neighborLists_interface.h" #include "utils/MemoryUtils.hpp" #include "utils/simError.h" #include "selection/SelectionManager.hpp" #include "io/ForceFieldOptions.hpp" -#include "UseTheForce/ForceField.hpp" +#include "brains/ForceField.hpp" #include "nonbonded/SwitchingFunction.hpp" - - #ifdef IS_MPI -#include "UseTheForce/mpiComponentPlan.h" -#include "UseTheForce/DarkSide/simParallel_interface.h" -#endif +#include +#endif using namespace std; namespace OpenMD { @@ -76,10 +72,10 @@ namespace OpenMD { forceField_(ff), simParams_(simParams), ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0), nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0), - nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), + nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), nGlobalFluctuatingCharges_(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), nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false), calcBoxDipole_(false), useAtomicVirial_(true) { MoleculeStamp* molStamp; @@ -92,7 +88,8 @@ namespace OpenMD { vector components = simParams->getComponents(); - for (vector::iterator i = components.begin(); i !=components.end(); ++i) { + for (vector::iterator i = components.begin(); + i !=components.end(); ++i) { molStamp = (*i)->getMoleculeStamp(); nMolWithSameStamp = (*i)->getNMol(); @@ -133,6 +130,7 @@ 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 + nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; //every free atom (atom does not belong to rigid bodies) is an @@ -228,38 +226,54 @@ namespace OpenMD { void SimInfo::calcNdf() { - int ndf_local; + int ndf_local, nfq_local; MoleculeIterator i; vector::iterator j; + vector::iterator k; + Molecule* mol; - StuntDouble* integrableObject; + StuntDouble* sd; + Atom* atom; ndf_local = 0; + nfq_local = 0; for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { - for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; - integrableObject = mol->nextIntegrableObject(j)) { + for (sd = mol->beginIntegrableObject(j); sd != NULL; + sd = mol->nextIntegrableObject(j)) { + ndf_local += 3; - if (integrableObject->isDirectional()) { - if (integrableObject->isLinear()) { + if (sd->isDirectional()) { + if (sd->isLinear()) { ndf_local += 2; } else { ndf_local += 3; } } - } + + for (atom = mol->beginFluctuatingCharge(k); atom != NULL; + atom = mol->nextFluctuatingCharge(k)) { + if (atom->isFluctuatingCharge()) { + nfq_local++; + } + } } + ndfLocal_ = ndf_local; + // n_constraints is local, so subtract them on each processor ndf_local -= nConstraints_; #ifdef IS_MPI - MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); + MPI::COMM_WORLD.Allreduce(&ndf_local, &ndf_, 1, MPI::INT,MPI::SUM); + MPI::COMM_WORLD.Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1, + MPI::INT, MPI::SUM); #else ndf_ = ndf_local; + nGlobalFluctuatingCharges_ = nfq_local; #endif // nZconstraints_ is global, as are the 3 COM translations for the @@ -270,32 +284,52 @@ namespace OpenMD { int SimInfo::getFdf() { #ifdef IS_MPI - MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); + MPI::COMM_WORLD.Allreduce(&fdf_local, &fdf_, 1, MPI::INT, MPI::SUM); #else 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() { int ndfRaw_local; MoleculeIterator i; vector::iterator j; Molecule* mol; - StuntDouble* integrableObject; + StuntDouble* sd; // Raw degrees of freedom that we have to set ndfRaw_local = 0; for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { - for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; - integrableObject = mol->nextIntegrableObject(j)) { + for (sd = mol->beginIntegrableObject(j); sd != NULL; + sd = mol->nextIntegrableObject(j)) { + ndfRaw_local += 3; - if (integrableObject->isDirectional()) { - if (integrableObject->isLinear()) { + if (sd->isDirectional()) { + if (sd->isLinear()) { ndfRaw_local += 2; } else { ndfRaw_local += 3; @@ -306,7 +340,7 @@ namespace OpenMD { } #ifdef IS_MPI - MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); + MPI::COMM_WORLD.Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI::INT, MPI::SUM); #else ndfRaw_ = ndfRaw_local; #endif @@ -319,7 +353,8 @@ namespace OpenMD { #ifdef IS_MPI - MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); + MPI::COMM_WORLD.Allreduce(&ndfTrans_local, &ndfTrans_, 1, + MPI::INT, MPI::SUM); #else ndfTrans_ = ndfTrans_local; #endif @@ -355,14 +390,13 @@ namespace OpenMD { Molecule::RigidBodyIterator rbIter; RigidBody* rb; Molecule::IntegrableObjectIterator ii; - StuntDouble* integrableObject; - - for (integrableObject = mol->beginIntegrableObject(ii); - integrableObject != NULL; - integrableObject = mol->nextIntegrableObject(ii)) { + StuntDouble* sd; + + for (sd = mol->beginIntegrableObject(ii); sd != NULL; + sd = mol->nextIntegrableObject(ii)) { - if (integrableObject->isRigidBody()) { - rb = static_cast(integrableObject); + if (sd->isRigidBody()) { + rb = static_cast(sd); vector atoms = rb->getAtoms(); set rigidAtoms; for (int i = 0; i < static_cast(atoms.size()); ++i) { @@ -373,8 +407,8 @@ namespace OpenMD { } } else { set oneAtomSet; - oneAtomSet.insert(integrableObject->getGlobalIndex()); - atomGroups.insert(map >::value_type(integrableObject->getGlobalIndex(), oneAtomSet)); + oneAtomSet.insert(sd->getGlobalIndex()); + atomGroups.insert(map >::value_type(sd->getGlobalIndex(), oneAtomSet)); } } @@ -508,14 +542,13 @@ namespace OpenMD { Molecule::RigidBodyIterator rbIter; RigidBody* rb; Molecule::IntegrableObjectIterator ii; - StuntDouble* integrableObject; + StuntDouble* sd; - for (integrableObject = mol->beginIntegrableObject(ii); - integrableObject != NULL; - integrableObject = mol->nextIntegrableObject(ii)) { + for (sd = mol->beginIntegrableObject(ii); sd != NULL; + sd = mol->nextIntegrableObject(ii)) { - if (integrableObject->isRigidBody()) { - rb = static_cast(integrableObject); + if (sd->isRigidBody()) { + rb = static_cast(sd); vector atoms = rb->getAtoms(); set rigidAtoms; for (int i = 0; i < static_cast(atoms.size()); ++i) { @@ -526,8 +559,8 @@ namespace OpenMD { } } else { set oneAtomSet; - oneAtomSet.insert(integrableObject->getGlobalIndex()); - atomGroups.insert(map >::value_type(integrableObject->getGlobalIndex(), oneAtomSet)); + oneAtomSet.insert(sd->getGlobalIndex()); + atomGroups.insert(map >::value_type(sd->getGlobalIndex(), oneAtomSet)); } } @@ -657,29 +690,24 @@ namespace OpenMD { /** * update * - * Performs the global checks and variable settings after the objects have been - * created. + * Performs the global checks and variable settings after the + * objects have been created. * */ - void SimInfo::update() { - + void SimInfo::update() { setupSimVariables(); - setupCutoffs(); - setupSwitching(); - setupElectrostatics(); - setupNeighborlists(); - -#ifdef IS_MPI - setupFortranParallel(); -#endif - setupFortranSim(); - fortranInitialized_ = true; - calcNdf(); calcNdfRaw(); calcNdfTrans(); } + /** + * getSimulatedAtomTypes + * + * Returns an STL set of AtomType* that are actually present in this + * simulation. Must query all processors to assemble this information. + * + */ set SimInfo::getSimulatedAtomTypes() { SimInfo::MoleculeIterator mi; Molecule* mol; @@ -687,236 +715,188 @@ 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()); } } - return atomTypes; - } + +#ifdef IS_MPI - /** - * setupCutoffs - * - * Sets the values of cutoffRadius and cutoffMethod - * - * cutoffRadius : realType - * If the cutoffRadius was explicitly set, use that value. - * If the cutoffRadius was not explicitly set: - * Are there electrostatic atoms? Use 12.0 Angstroms. - * No electrostatic atoms? Poll the atom types present in the - * simulation for suggested cutoff values (e.g. 2.5 * sigma). - * Use the maximum suggested value that was found. - * - * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL) - * If cutoffMethod was explicitly set, use that choice. - * If cutoffMethod was not explicitly set, use SHIFTED_FORCE - */ - void SimInfo::setupCutoffs() { + // loop over the found atom types on this processor, and add their + // numerical idents to a vector: - if (simParams_->haveCutoffRadius()) { - cutoffRadius_ = simParams_->getCutoffRadius(); - } else { - if (usesElectrostaticAtoms_) { - sprintf(painCave.errMsg, - "SimInfo: No value was set for the cutoffRadius.\n" - "\tOpenMD will use a default value of 12.0 angstroms" - "\tfor the cutoffRadius.\n"); - painCave.isFatal = 0; - painCave.severity = OPENMD_INFO; - simError(); - cutoffRadius_ = 12.0; - } else { - RealType thisCut; - set::iterator i; - set atomTypes; - atomTypes = getSimulatedAtomTypes(); - for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { - thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i)); - cutoffRadius_ = max(thisCut, cutoffRadius_); - } - sprintf(painCave.errMsg, - "SimInfo: No value was set for the cutoffRadius.\n" - "\tOpenMD will use %lf angstroms.\n", - cutoffRadius_); - painCave.isFatal = 0; - painCave.severity = OPENMD_INFO; - simError(); - } - } + vector foundTypes; + set::iterator i; + for (i = atomTypes.begin(); i != atomTypes.end(); ++i) + foundTypes.push_back( (*i)->getIdent() ); - InteractionManager::Instance()->setCutoffRadius(cutoffRadius_); + // count_local holds the number of found types on this processor + int count_local = foundTypes.size(); - map stringToCutoffMethod; - stringToCutoffMethod["HARD"] = HARD; - stringToCutoffMethod["SWITCHING_FUNCTION"] = SWITCHING_FUNCTION; - stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL; - stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE; + int nproc = MPI::COMM_WORLD.Get_size(); + + // 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); - if (simParams_->haveCutoffMethod()) { - string cutMeth = toUpperCopy(simParams_->getCutoffMethod()); - map::iterator i; - i = stringToCutoffMethod.find(cutMeth); - if (i == stringToCutoffMethod.end()) { - sprintf(painCave.errMsg, - "SimInfo: Could not find chosen cutoffMethod %s\n" - "\tShould be one of: " - "HARD, SWITCHING_FUNCTION, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n", - cutMeth.c_str()); - painCave.isFatal = 1; - painCave.severity = OPENMD_ERROR; - simError(); - } else { - cutoffMethod_ = i->second; - } - } else { - sprintf(painCave.errMsg, - "SimInfo: No value was set for the cutoffMethod.\n" - "\tOpenMD will use SHIFTED_FORCE.\n"); - painCave.isFatal = 0; - painCave.severity = OPENMD_INFO; - simError(); - cutoffMethod_ = SHIFTED_FORCE; + // 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]; } - InteractionManager::Instance()->setCutoffMethod(cutoffMethod_); - } - - /** - * setupSwitching - * - * Sets the values of switchingRadius and - * If the switchingRadius was explicitly set, use that value (but check it) - * If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_ - */ - void SimInfo::setupSwitching() { + // we need a (possibly redundant) set of all found types: + vector ftGlobal(totalCount); - if (simParams_->haveSwitchingRadius()) { - switchingRadius_ = simParams_->getSwitchingRadius(); - if (switchingRadius_ > cutoffRadius_) { - sprintf(painCave.errMsg, - "SimInfo: switchingRadius (%f) is larger than cutoffRadius(%f)\n", - switchingRadius_, cutoffRadius_); - painCave.isFatal = 1; - painCave.severity = OPENMD_ERROR; - simError(); - } - } else { - switchingRadius_ = 0.85 * cutoffRadius_; - sprintf(painCave.errMsg, - "SimInfo: No value was set for the switchingRadius.\n" - "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n" - "\tswitchingRadius = %f. for this simulation\n", switchingRadius_); - painCave.isFatal = 0; - painCave.severity = OPENMD_WARNING; - simError(); - } - - InteractionManager::Instance()->setSwitchingRadius(switchingRadius_); + // 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); - SwitchingFunctionType ft; + vector::iterator j; + + // foundIdents is a stl set, so inserting an already found ident + // will have no effect. + set foundIdents; + + for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j) + foundIdents.insert((*j)); - if (simParams_->haveSwitchingFunctionType()) { - string funcType = simParams_->getSwitchingFunctionType(); - toUpper(funcType); - if (funcType == "CUBIC") { - ft = cubic; - } else { - if (funcType == "FIFTH_ORDER_POLYNOMIAL") { - ft = fifth_order_poly; - } else { - // throw error - sprintf( painCave.errMsg, - "SimInfo : Unknown switchingFunctionType. (Input file specified %s .)\n" - "\tswitchingFunctionType must be one of: " - "\"cubic\" or \"fifth_order_polynomial\".", - funcType.c_str() ); - painCave.isFatal = 1; - painCave.severity = OPENMD_ERROR; - simError(); - } - } - } + // 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) + atomTypes.insert( forceField_->getAtomType((*it)) ); + +#endif - InteractionManager::Instance()->setSwitchingFunctionType(ft); + return atomTypes; } - /** - * setupSkinThickness - * - * If the skinThickness was explicitly set, use that value (but check it) - * If the skinThickness was not explicitly set: use 1.0 angstroms - */ - void SimInfo::setupSkinThickness() { - if (simParams_->haveSkinThickness()) { - skinThickness_ = simParams_->getSkinThickness(); - } else { - skinThickness_ = 1.0; - sprintf(painCave.errMsg, - "SimInfo Warning: No value was set for the skinThickness.\n" - "\tOpenMD will use a default value of %f Angstroms\n" - "\tfor this simulation\n", skinThickness_); - painCave.isFatal = 0; - simError(); - } + + int getGlobalCountOfType(AtomType* atype) { + /* + set atypes = getSimulatedAtomTypes(); + map counts_; + + for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { + for(atom = mol->beginAtom(ai); atom != NULL; + atom = mol->nextAtom(ai)) { + atom->getAtomType(); + } + } + */ + return 0; } - void SimInfo::setupSimType() { + void SimInfo::setupSimVariables() { + useAtomicVirial_ = simParams_->getUseAtomicVirial(); + // we only call setAccumulateBoxDipole if the accumulateBoxDipole + // parameter is true + calcBoxDipole_ = false; + if ( simParams_->haveAccumulateBoxDipole() ) + if ( simParams_->getAccumulateBoxDipole() ) { + calcBoxDipole_ = true; + } + set::iterator i; set atomTypes; - atomTypes = getSimulatedAtomTypes(); - - useAtomicVirial_ = simParams_->getUseAtomicVirial(); - - int usesElectrostatic = 0; - int usesMetallic = 0; - int usesDirectional = 0; + atomTypes = getSimulatedAtomTypes(); + bool usesElectrostatic = false; + bool usesMetallic = false; + bool usesDirectional = false; + bool usesFluctuatingCharges = false; //loop over all of the atom types for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { usesElectrostatic |= (*i)->isElectrostatic(); usesMetallic |= (*i)->isMetal(); usesDirectional |= (*i)->isDirectional(); + usesFluctuatingCharges |= (*i)->isFluctuatingCharge(); } -#ifdef IS_MPI - int temp; +#ifdef IS_MPI + bool temp; temp = usesDirectional; - MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); - + MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL, + MPI::LOR); + temp = usesMetallic; - MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); - + MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL, + MPI::LOR); + temp = usesElectrostatic; - MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); + MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL, + MPI::LOR); + + temp = usesFluctuatingCharges; + MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL, + MPI::LOR); +#else + + usesDirectionalAtoms_ = usesDirectional; + usesMetallicAtoms_ = usesMetallic; + usesElectrostaticAtoms_ = usesElectrostatic; + usesFluctuatingCharges_ = usesFluctuatingCharges; + #endif - fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_; - fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_; - fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_; - fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_; - fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_; - fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_; + + requiresPrepair_ = usesMetallicAtoms_ ? true : false; + requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false; + requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false; } - void SimInfo::setupFortranSim() { - int isError; - int nExclude, nOneTwo, nOneThree, nOneFour; - vector fortranGlobalGroupMembership; + + vector SimInfo::getGlobalAtomIndices() { + SimInfo::MoleculeIterator mi; + Molecule* mol; + Molecule::AtomIterator ai; + Atom* atom; + + vector GlobalAtomIndices(getNAtoms(), 0); - notifyFortranSkinThickness(&skinThickness_); + for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { + + for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { + GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex(); + } + } + return GlobalAtomIndices; + } - int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0; - int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0; - notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf); - isError = 0; + vector SimInfo::getGlobalGroupIndices() { + SimInfo::MoleculeIterator mi; + Molecule* mol; + Molecule::CutoffGroupIterator ci; + CutoffGroup* cg; - //globalGroupMembership_ is filled by SimCreator - for (int i = 0; i < nGlobalAtoms_; i++) { - fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1); + vector GlobalGroupIndices; + + for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { + + //local index of cutoff group is trivial, it only depends on the + //order of travesing + for (cg = mol->beginCutoffGroup(ci); cg != NULL; + cg = mol->nextCutoffGroup(ci)) { + GlobalGroupIndices.push_back(cg->getGlobalIndex()); + } } + return GlobalGroupIndices; + } + + void SimInfo::prepareTopology() { + //calculate mass ratio of cutoff group - vector mfact; SimInfo::MoleculeIterator mi; Molecule* mol; Molecule::CutoffGroupIterator ci; @@ -925,158 +905,45 @@ 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; } } } - //fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!) - vector identArray; + // Build the identArray_ - //to avoid memory reallocation, reserve enough space identArray - identArray.reserve(getNAtoms()); - + identArray_.clear(); + identArray_.reserve(getNAtoms()); for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { - identArray.push_back(atom->getIdent()); + 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 - - nExclude = excludedInteractions_.getSize(); - nOneTwo = oneTwoInteractions_.getSize(); - nOneThree = oneThreeInteractions_.getSize(); - nOneFour = oneFourInteractions_.getSize(); - - int* excludeList = excludedInteractions_.getPairList(); - int* oneTwoList = oneTwoInteractions_.getPairList(); - 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); - } - - + topologyDone_ = true; } - - void SimInfo::setupFortranParallel() { -#ifdef IS_MPI - //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex - vector localToGlobalAtomIndex(getNAtoms(), 0); - vector localToGlobalCutoffGroupIndex; - SimInfo::MoleculeIterator mi; - Molecule::AtomIterator ai; - Molecule::CutoffGroupIterator ci; - Molecule* mol; - Atom* atom; - CutoffGroup* cg; - mpiSimData parallelData; - int isError; - - for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { - - //local index(index in DataStorge) of atom is important - for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { - localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1; - } - - //local index of cutoff group is trivial, it only depends on the order of travesing - for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { - localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1); - } - - } - - //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 - } - - - void SimInfo::setupSwitchingFunction() { - - } - - void SimInfo::setupAccumulateBoxDipole() { - - // we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true - if ( simParams_->haveAccumulateBoxDipole() ) - if ( simParams_->getAccumulateBoxDipole() ) { - calcBoxDipole_ = true; - } - - } - void SimInfo::addProperty(GenericData* genData) { properties_.addProperty(genData); } @@ -1111,282 +978,60 @@ namespace OpenMD { Molecule* mol; RigidBody* rb; Atom* atom; + CutoffGroup* cg; SimInfo::MoleculeIterator mi; Molecule::RigidBodyIterator rbIter; - Molecule::AtomIterator atomIter;; + Molecule::AtomIterator atomIter; + Molecule::CutoffGroupIterator cgIter; for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { - for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) { + for (atom = mol->beginAtom(atomIter); atom != NULL; + atom = mol->nextAtom(atomIter)) { atom->setSnapshotManager(sman_); } - for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { + for (rb = mol->beginRigidBody(rbIter); rb != NULL; + rb = mol->nextRigidBody(rbIter)) { rb->setSnapshotManager(sman_); } + + for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; + cg = mol->nextCutoffGroup(cgIter)) { + cg->setSnapshotManager(sman_); + } } } - - Vector3d SimInfo::getComVel(){ - SimInfo::MoleculeIterator i; - Molecule* mol; - - Vector3d comVel(0.0); - RealType totalMass = 0.0; - - - for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { - RealType mass = mol->getMass(); - totalMass += mass; - comVel += mass * mol->getComVel(); - } - -#ifdef IS_MPI - RealType tmpMass = totalMass; - Vector3d tmpComVel(comVel); - MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); - MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); -#endif - - comVel /= totalMass; - - return comVel; - } - - Vector3d SimInfo::getCom(){ - SimInfo::MoleculeIterator i; - Molecule* mol; - - Vector3d com(0.0); - RealType totalMass = 0.0; - - for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { - RealType mass = mol->getMass(); - totalMass += mass; - com += mass * mol->getCom(); - } -#ifdef IS_MPI - RealType tmpMass = totalMass; - Vector3d tmpCom(com); - MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); - MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); -#endif - com /= totalMass; - - return com; - - } - ostream& operator <<(ostream& o, SimInfo& info) { return o; } - - /* - Returns center of mass and center of mass velocity in one function call. - */ - - void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){ - SimInfo::MoleculeIterator i; - Molecule* mol; - - - RealType totalMass = 0.0; - - - for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { - RealType mass = mol->getMass(); - totalMass += mass; - com += mass * mol->getCom(); - comVel += mass * mol->getComVel(); - } - -#ifdef IS_MPI - RealType tmpMass = totalMass; - Vector3d tmpCom(com); - Vector3d tmpComVel(comVel); - MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); - MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); - MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); -#endif - - com /= totalMass; - comVel /= totalMass; - } - - /* - Return intertia tensor for entire system and angular momentum Vector. - - - [ Ixx -Ixy -Ixz ] - J =| -Iyx Iyy -Iyz | - [ -Izx -Iyz Izz ] - */ - - void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){ - - - RealType xx = 0.0; - RealType yy = 0.0; - RealType zz = 0.0; - RealType xy = 0.0; - RealType xz = 0.0; - RealType yz = 0.0; - Vector3d com(0.0); - Vector3d comVel(0.0); - - getComAll(com, comVel); - - SimInfo::MoleculeIterator i; - Molecule* mol; - - Vector3d thisq(0.0); - Vector3d thisv(0.0); - - RealType thisMass = 0.0; - - - - - for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { - - thisq = mol->getCom()-com; - thisv = mol->getComVel()-comVel; - thisMass = mol->getMass(); - // Compute moment of intertia coefficients. - xx += thisq[0]*thisq[0]*thisMass; - yy += thisq[1]*thisq[1]*thisMass; - zz += thisq[2]*thisq[2]*thisMass; - - // compute products of intertia - xy += thisq[0]*thisq[1]*thisMass; - xz += thisq[0]*thisq[2]*thisMass; - yz += thisq[1]*thisq[2]*thisMass; - - angularMomentum += cross( thisq, thisv ) * thisMass; - - } - - - inertiaTensor(0,0) = yy + zz; - inertiaTensor(0,1) = -xy; - inertiaTensor(0,2) = -xz; - inertiaTensor(1,0) = -xy; - inertiaTensor(1,1) = xx + zz; - inertiaTensor(1,2) = -yz; - inertiaTensor(2,0) = -xz; - inertiaTensor(2,1) = -yz; - inertiaTensor(2,2) = xx + yy; - -#ifdef IS_MPI - Mat3x3d tmpI(inertiaTensor); - Vector3d tmpAngMom; - MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); - MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); -#endif - - return; - } - - //Returns the angular momentum of the system - Vector3d SimInfo::getAngularMomentum(){ - - Vector3d com(0.0); - Vector3d comVel(0.0); - Vector3d angularMomentum(0.0); - - getComAll(com,comVel); - - SimInfo::MoleculeIterator i; - Molecule* mol; - - Vector3d thisr(0.0); - Vector3d thisp(0.0); - - RealType thisMass; - - for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { - thisMass = mol->getMass(); - thisr = mol->getCom()-com; - thisp = (mol->getComVel()-comVel)*thisMass; - - angularMomentum += cross( thisr, thisp ); - - } - -#ifdef IS_MPI - Vector3d tmpAngMom; - MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD); -#endif - - return angularMomentum; - } - + StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) { - return IOIndexToIntegrableObject.at(index); + if (index >= int(IOIndexToIntegrableObject.size())) { + sprintf(painCave.errMsg, + "SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n" + "\tindex exceeds number of known objects!\n"); + painCave.isFatal = 1; + simError(); + return NULL; + } else + return IOIndexToIntegrableObject.at(index); } void SimInfo::setIOIndexToIntegrableObject(const vector& v) { IOIndexToIntegrableObject= v; } - /* Returns the Volume of the simulation based on a ellipsoid with semi-axes - based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3 - where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to - V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536. - */ - void SimInfo::getGyrationalVolume(RealType &volume){ - Mat3x3d intTensor; - RealType det; - Vector3d dummyAngMom; - RealType sysconstants; - RealType geomCnst; - - geomCnst = 3.0/2.0; - /* Get the inertial tensor and angular momentum for free*/ - getInertiaTensor(intTensor,dummyAngMom); - - det = intTensor.determinant(); - sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_; - volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det); - return; - } - - void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){ - Mat3x3d intTensor; - Vector3d dummyAngMom; - RealType sysconstants; - RealType geomCnst; - - geomCnst = 3.0/2.0; - /* Get the inertial tensor and angular momentum for free*/ - getInertiaTensor(intTensor,dummyAngMom); - - detI = intTensor.determinant(); - sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_; - volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI); - return; - } -/* - void SimInfo::setStuntDoubleFromGlobalIndex(vector v) { - assert( v.size() == nAtoms_ + nRigidBodies_); - sdByGlobalIndex_ = v; - } - - StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) { - //assert(index < nAtoms_ + nRigidBodies_); - return sdByGlobalIndex_.at(index); - } -*/ int SimInfo::getNGlobalConstraints() { int nGlobalConstraints; #ifdef IS_MPI - MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM, - MPI_COMM_WORLD); + MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1, + MPI::INT, MPI::SUM); #else nGlobalConstraints = nConstraints_; #endif