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/* |
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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#include <algorithm> |
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#include <set> |
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#include <map> |
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#include "brains/SimInfo.hpp" |
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#include "math/Vector3.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "UseTheForce/fCutoffPolicy.h" |
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#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h" |
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#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h" |
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#include "UseTheForce/DarkSide/fSwitchingFunctionType.h" |
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#include "UseTheForce/doForces_interface.h" |
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#include "UseTheForce/notifyCutoffs_interface.h" |
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#include "UseTheForce/DarkSide/electrostatic_interface.h" |
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#include "UseTheForce/DarkSide/switcheroo_interface.h" |
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#include "utils/MemoryUtils.hpp" |
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#include "utils/simError.h" |
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#include "selection/SelectionManager.hpp" |
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#endif |
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namespace oopse { |
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std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) { |
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std::map<int, std::set<int> >::iterator i = container.find(index); |
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std::set<int> result; |
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if (i != container.end()) { |
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result = i->second; |
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} |
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|
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SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, |
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ForceField* ff, Globals* simParams) : |
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forceField_(ff), simParams_(simParams), |
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ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0), |
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nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0), |
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nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), |
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nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0), |
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nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0), |
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sman_(NULL), fortranInitialized_(false), selectMan_(NULL) { |
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return result; |
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} |
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|
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SimInfo::SimInfo(ForceField* ff, Globals* simParams) : |
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forceField_(ff), simParams_(simParams), |
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ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0), |
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nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0), |
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nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), |
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nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0), |
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nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0), |
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sman_(NULL), fortranInitialized_(false) { |
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std::vector<std::pair<MoleculeStamp*, int> >::iterator i; |
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MoleculeStamp* molStamp; |
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int nMolWithSameStamp; |
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int nCutoffAtoms = 0; // number of atoms belong to cutoff groups |
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int nGroups = 0; //total cutoff groups defined in meta-data file |
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CutoffGroupStamp* cgStamp; |
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RigidBodyStamp* rbStamp; |
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int nRigidAtoms = 0; |
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|
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for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) { |
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molStamp = i->first; |
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nMolWithSameStamp = i->second; |
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MoleculeStamp* molStamp; |
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int nMolWithSameStamp; |
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int nCutoffAtoms = 0; // number of atoms belong to cutoff groups |
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int nGroups = 0; //total cutoff groups defined in meta-data file |
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CutoffGroupStamp* cgStamp; |
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RigidBodyStamp* rbStamp; |
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int nRigidAtoms = 0; |
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std::vector<Component*> components = simParams->getComponents(); |
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|
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for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) { |
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molStamp = (*i)->getMoleculeStamp(); |
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nMolWithSameStamp = (*i)->getNMol(); |
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addMoleculeStamp(molStamp, nMolWithSameStamp); |
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//calculate atoms in molecules |
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nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp; |
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|
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//calculate atoms in cutoff groups |
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int nAtomsInGroups = 0; |
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int nCutoffGroupsInStamp = molStamp->getNCutoffGroups(); |
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for (int j=0; j < nCutoffGroupsInStamp; j++) { |
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cgStamp = molStamp->getCutoffGroup(j); |
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nAtomsInGroups += cgStamp->getNMembers(); |
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cgStamp = molStamp->getCutoffGroupStamp(j); |
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nAtomsInGroups += cgStamp->getNMembers(); |
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} |
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nGroups += nCutoffGroupsInStamp * nMolWithSameStamp; |
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nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp; |
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//calculate atoms in rigid bodies |
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int nRigidBodiesInStamp = molStamp->getNRigidBodies(); |
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for (int j=0; j < nRigidBodiesInStamp; j++) { |
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rbStamp = molStamp->getRigidBody(j); |
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nAtomsInRigidBodies += rbStamp->getNMembers(); |
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rbStamp = molStamp->getRigidBodyStamp(j); |
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nAtomsInRigidBodies += rbStamp->getNMembers(); |
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} |
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nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp; |
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nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp; |
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} |
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} |
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//every free atom (atom does not belong to cutoff groups) is a cutoff group |
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//therefore the total number of cutoff groups in the system is equal to |
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//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data |
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//file plus the number of cutoff groups defined in meta-data file |
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nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; |
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//every free atom (atom does not belong to cutoff groups) is a cutoff |
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//group therefore the total number of cutoff groups in the system is |
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//equal to the total number of atoms minus number of atoms belong to |
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//cutoff group defined in meta-data file plus the number of cutoff |
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//groups defined in meta-data file |
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nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; |
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|
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//every free atom (atom does not belong to rigid bodies) is an integrable object |
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//therefore the total number of integrable objects in the system is equal to |
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//the total number of atoms minus number of atoms belong to rigid body defined in meta-data |
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//file plus the number of rigid bodies defined in meta-data file |
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nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_; |
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//every free atom (atom does not belong to rigid bodies) is an |
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//integrable object therefore the total number of integrable objects |
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//in the system is equal to the total number of atoms minus number of |
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//atoms belong to rigid body defined in meta-data file plus the number |
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//of rigid bodies defined in meta-data file |
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nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms |
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+ nGlobalRigidBodies_; |
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|
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nGlobalMols_ = molStampIds_.size(); |
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nGlobalMols_ = molStampIds_.size(); |
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|
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#ifdef IS_MPI |
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molToProcMap_.resize(nGlobalMols_); |
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molToProcMap_.resize(nGlobalMols_); |
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#endif |
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selectMan_ = new SelectionManager(this); |
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selectMan_->selectAll(); |
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} |
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} |
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SimInfo::~SimInfo() { |
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//MemoryUtils::deleteVectorOfPointer(molecules_); |
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|
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MemoryUtils::deleteVectorOfPointer(moleculeStamps_); |
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SimInfo::~SimInfo() { |
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std::map<int, Molecule*>::iterator i; |
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for (i = molecules_.begin(); i != molecules_.end(); ++i) { |
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delete i->second; |
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} |
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molecules_.clear(); |
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|
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delete sman_; |
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delete simParams_; |
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delete forceField_; |
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delete selectMan_; |
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} |
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} |
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int SimInfo::getNGlobalConstraints() { |
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int SimInfo::getNGlobalConstraints() { |
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int nGlobalConstraints; |
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#ifdef IS_MPI |
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MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM, |
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nGlobalConstraints = nConstraints_; |
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#endif |
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return nGlobalConstraints; |
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} |
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} |
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bool SimInfo::addMolecule(Molecule* mol) { |
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bool SimInfo::addMolecule(Molecule* mol) { |
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MoleculeIterator i; |
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i = molecules_.find(mol->getGlobalIndex()); |
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if (i == molecules_.end() ) { |
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molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol)); |
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molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol)); |
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nAtoms_ += mol->getNAtoms(); |
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nBonds_ += mol->getNBonds(); |
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nBends_ += mol->getNBends(); |
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nTorsions_ += mol->getNTorsions(); |
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nRigidBodies_ += mol->getNRigidBodies(); |
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nIntegrableObjects_ += mol->getNIntegrableObjects(); |
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nCutoffGroups_ += mol->getNCutoffGroups(); |
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nConstraints_ += mol->getNConstraintPairs(); |
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nAtoms_ += mol->getNAtoms(); |
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nBonds_ += mol->getNBonds(); |
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nBends_ += mol->getNBends(); |
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nTorsions_ += mol->getNTorsions(); |
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nRigidBodies_ += mol->getNRigidBodies(); |
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nIntegrableObjects_ += mol->getNIntegrableObjects(); |
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nCutoffGroups_ += mol->getNCutoffGroups(); |
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nConstraints_ += mol->getNConstraintPairs(); |
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addExcludePairs(mol); |
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addExcludePairs(mol); |
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return true; |
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return true; |
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} else { |
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return false; |
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return false; |
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} |
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} |
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} |
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bool SimInfo::removeMolecule(Molecule* mol) { |
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bool SimInfo::removeMolecule(Molecule* mol) { |
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MoleculeIterator i; |
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i = molecules_.find(mol->getGlobalIndex()); |
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if (i != molecules_.end() ) { |
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assert(mol == i->second); |
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assert(mol == i->second); |
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nAtoms_ -= mol->getNAtoms(); |
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nBonds_ -= mol->getNBonds(); |
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nBends_ -= mol->getNBends(); |
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nTorsions_ -= mol->getNTorsions(); |
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nRigidBodies_ -= mol->getNRigidBodies(); |
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nIntegrableObjects_ -= mol->getNIntegrableObjects(); |
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nCutoffGroups_ -= mol->getNCutoffGroups(); |
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nConstraints_ -= mol->getNConstraintPairs(); |
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|
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removeExcludePairs(mol); |
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molecules_.erase(mol->getGlobalIndex()); |
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|
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delete mol; |
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nAtoms_ -= mol->getNAtoms(); |
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nBonds_ -= mol->getNBonds(); |
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nBends_ -= mol->getNBends(); |
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nTorsions_ -= mol->getNTorsions(); |
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nRigidBodies_ -= mol->getNRigidBodies(); |
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nIntegrableObjects_ -= mol->getNIntegrableObjects(); |
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nCutoffGroups_ -= mol->getNCutoffGroups(); |
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nConstraints_ -= mol->getNConstraintPairs(); |
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|
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removeExcludePairs(mol); |
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molecules_.erase(mol->getGlobalIndex()); |
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delete mol; |
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return true; |
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return true; |
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} else { |
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return false; |
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return false; |
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} |
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} |
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} |
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Molecule* SimInfo::beginMolecule(MoleculeIterator& i) { |
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Molecule* SimInfo::beginMolecule(MoleculeIterator& i) { |
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i = molecules_.begin(); |
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return i == molecules_.end() ? NULL : i->second; |
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} |
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} |
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Molecule* SimInfo::nextMolecule(MoleculeIterator& i) { |
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Molecule* SimInfo::nextMolecule(MoleculeIterator& i) { |
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++i; |
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return i == molecules_.end() ? NULL : i->second; |
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} |
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} |
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void SimInfo::calcNdf() { |
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void SimInfo::calcNdf() { |
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int ndf_local; |
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MoleculeIterator i; |
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std::vector<StuntDouble*>::iterator j; |
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ndf_local = 0; |
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for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
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for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(j)) { |
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for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(j)) { |
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|
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ndf_local += 3; |
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ndf_local += 3; |
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if (integrableObject->isDirectional()) { |
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if (integrableObject->isLinear()) { |
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ndf_local += 2; |
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} else { |
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ndf_local += 3; |
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} |
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} |
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if (integrableObject->isDirectional()) { |
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if (integrableObject->isLinear()) { |
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ndf_local += 2; |
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} else { |
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ndf_local += 3; |
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} |
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} |
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|
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}//end for (integrableObject) |
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}// end for (mol) |
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} |
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} |
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|
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// n_constraints is local, so subtract them on each processor |
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ndf_local -= nConstraints_; |
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// entire system: |
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ndf_ = ndf_ - 3 - nZconstraint_; |
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|
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} |
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} |
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|
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void SimInfo::calcNdfRaw() { |
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> |
void SimInfo::calcNdfRaw() { |
292 |
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int ndfRaw_local; |
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|
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MoleculeIterator i; |
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ndfRaw_local = 0; |
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|
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for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
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< |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
304 |
< |
integrableObject = mol->nextIntegrableObject(j)) { |
303 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
304 |
> |
integrableObject = mol->nextIntegrableObject(j)) { |
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|
306 |
< |
ndfRaw_local += 3; |
306 |
> |
ndfRaw_local += 3; |
307 |
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|
308 |
< |
if (integrableObject->isDirectional()) { |
309 |
< |
if (integrableObject->isLinear()) { |
310 |
< |
ndfRaw_local += 2; |
311 |
< |
} else { |
312 |
< |
ndfRaw_local += 3; |
313 |
< |
} |
314 |
< |
} |
308 |
> |
if (integrableObject->isDirectional()) { |
309 |
> |
if (integrableObject->isLinear()) { |
310 |
> |
ndfRaw_local += 2; |
311 |
> |
} else { |
312 |
> |
ndfRaw_local += 3; |
313 |
> |
} |
314 |
> |
} |
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|
316 |
< |
} |
316 |
> |
} |
317 |
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} |
318 |
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|
319 |
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#ifdef IS_MPI |
321 |
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#else |
322 |
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ndfRaw_ = ndfRaw_local; |
323 |
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#endif |
324 |
< |
} |
324 |
> |
} |
325 |
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|
326 |
< |
void SimInfo::calcNdfTrans() { |
326 |
> |
void SimInfo::calcNdfTrans() { |
327 |
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int ndfTrans_local; |
328 |
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|
329 |
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ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_; |
337 |
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|
338 |
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ndfTrans_ = ndfTrans_ - 3 - nZconstraint_; |
339 |
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|
340 |
< |
} |
340 |
> |
} |
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|
342 |
< |
void SimInfo::addExcludePairs(Molecule* mol) { |
342 |
> |
void SimInfo::addExcludePairs(Molecule* mol) { |
343 |
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std::vector<Bond*>::iterator bondIter; |
344 |
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std::vector<Bend*>::iterator bendIter; |
345 |
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std::vector<Torsion*>::iterator torsionIter; |
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int b; |
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int c; |
352 |
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int d; |
353 |
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|
354 |
+ |
std::map<int, std::set<int> > atomGroups; |
355 |
+ |
|
356 |
+ |
Molecule::RigidBodyIterator rbIter; |
357 |
+ |
RigidBody* rb; |
358 |
+ |
Molecule::IntegrableObjectIterator ii; |
359 |
+ |
StuntDouble* integrableObject; |
360 |
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|
361 |
+ |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
362 |
+ |
integrableObject = mol->nextIntegrableObject(ii)) { |
363 |
+ |
|
364 |
+ |
if (integrableObject->isRigidBody()) { |
365 |
+ |
rb = static_cast<RigidBody*>(integrableObject); |
366 |
+ |
std::vector<Atom*> atoms = rb->getAtoms(); |
367 |
+ |
std::set<int> rigidAtoms; |
368 |
+ |
for (int i = 0; i < atoms.size(); ++i) { |
369 |
+ |
rigidAtoms.insert(atoms[i]->getGlobalIndex()); |
370 |
+ |
} |
371 |
+ |
for (int i = 0; i < atoms.size(); ++i) { |
372 |
+ |
atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms)); |
373 |
+ |
} |
374 |
+ |
} else { |
375 |
+ |
std::set<int> oneAtomSet; |
376 |
+ |
oneAtomSet.insert(integrableObject->getGlobalIndex()); |
377 |
+ |
atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet)); |
378 |
+ |
} |
379 |
+ |
} |
380 |
+ |
|
381 |
+ |
|
382 |
+ |
|
383 |
|
for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { |
384 |
< |
a = bond->getAtomA()->getGlobalIndex(); |
385 |
< |
b = bond->getAtomB()->getGlobalIndex(); |
386 |
< |
exclude_.addPair(a, b); |
384 |
> |
a = bond->getAtomA()->getGlobalIndex(); |
385 |
> |
b = bond->getAtomB()->getGlobalIndex(); |
386 |
> |
exclude_.addPair(a, b); |
387 |
|
} |
388 |
|
|
389 |
|
for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) { |
390 |
< |
a = bend->getAtomA()->getGlobalIndex(); |
391 |
< |
b = bend->getAtomB()->getGlobalIndex(); |
392 |
< |
c = bend->getAtomC()->getGlobalIndex(); |
390 |
> |
a = bend->getAtomA()->getGlobalIndex(); |
391 |
> |
b = bend->getAtomB()->getGlobalIndex(); |
392 |
> |
c = bend->getAtomC()->getGlobalIndex(); |
393 |
> |
std::set<int> rigidSetA = getRigidSet(a, atomGroups); |
394 |
> |
std::set<int> rigidSetB = getRigidSet(b, atomGroups); |
395 |
> |
std::set<int> rigidSetC = getRigidSet(c, atomGroups); |
396 |
|
|
397 |
< |
exclude_.addPair(a, b); |
398 |
< |
exclude_.addPair(a, c); |
399 |
< |
exclude_.addPair(b, c); |
397 |
> |
exclude_.addPairs(rigidSetA, rigidSetB); |
398 |
> |
exclude_.addPairs(rigidSetA, rigidSetC); |
399 |
> |
exclude_.addPairs(rigidSetB, rigidSetC); |
400 |
> |
|
401 |
> |
//exclude_.addPair(a, b); |
402 |
> |
//exclude_.addPair(a, c); |
403 |
> |
//exclude_.addPair(b, c); |
404 |
|
} |
405 |
|
|
406 |
|
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
407 |
< |
a = torsion->getAtomA()->getGlobalIndex(); |
408 |
< |
b = torsion->getAtomB()->getGlobalIndex(); |
409 |
< |
c = torsion->getAtomC()->getGlobalIndex(); |
410 |
< |
d = torsion->getAtomD()->getGlobalIndex(); |
407 |
> |
a = torsion->getAtomA()->getGlobalIndex(); |
408 |
> |
b = torsion->getAtomB()->getGlobalIndex(); |
409 |
> |
c = torsion->getAtomC()->getGlobalIndex(); |
410 |
> |
d = torsion->getAtomD()->getGlobalIndex(); |
411 |
> |
std::set<int> rigidSetA = getRigidSet(a, atomGroups); |
412 |
> |
std::set<int> rigidSetB = getRigidSet(b, atomGroups); |
413 |
> |
std::set<int> rigidSetC = getRigidSet(c, atomGroups); |
414 |
> |
std::set<int> rigidSetD = getRigidSet(d, atomGroups); |
415 |
|
|
416 |
< |
exclude_.addPair(a, b); |
417 |
< |
exclude_.addPair(a, c); |
418 |
< |
exclude_.addPair(a, d); |
419 |
< |
exclude_.addPair(b, c); |
420 |
< |
exclude_.addPair(b, d); |
421 |
< |
exclude_.addPair(c, d); |
416 |
> |
exclude_.addPairs(rigidSetA, rigidSetB); |
417 |
> |
exclude_.addPairs(rigidSetA, rigidSetC); |
418 |
> |
exclude_.addPairs(rigidSetA, rigidSetD); |
419 |
> |
exclude_.addPairs(rigidSetB, rigidSetC); |
420 |
> |
exclude_.addPairs(rigidSetB, rigidSetD); |
421 |
> |
exclude_.addPairs(rigidSetC, rigidSetD); |
422 |
> |
|
423 |
> |
/* |
424 |
> |
exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end()); |
425 |
> |
exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end()); |
426 |
> |
exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end()); |
427 |
> |
exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end()); |
428 |
> |
exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end()); |
429 |
> |
exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end()); |
430 |
> |
|
431 |
> |
|
432 |
> |
exclude_.addPair(a, b); |
433 |
> |
exclude_.addPair(a, c); |
434 |
> |
exclude_.addPair(a, d); |
435 |
> |
exclude_.addPair(b, c); |
436 |
> |
exclude_.addPair(b, d); |
437 |
> |
exclude_.addPair(c, d); |
438 |
> |
*/ |
439 |
|
} |
440 |
|
|
441 |
< |
|
442 |
< |
} |
441 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
442 |
> |
std::vector<Atom*> atoms = rb->getAtoms(); |
443 |
> |
for (int i = 0; i < atoms.size() -1 ; ++i) { |
444 |
> |
for (int j = i + 1; j < atoms.size(); ++j) { |
445 |
> |
a = atoms[i]->getGlobalIndex(); |
446 |
> |
b = atoms[j]->getGlobalIndex(); |
447 |
> |
exclude_.addPair(a, b); |
448 |
> |
} |
449 |
> |
} |
450 |
> |
} |
451 |
|
|
452 |
< |
void SimInfo::removeExcludePairs(Molecule* mol) { |
452 |
> |
} |
453 |
> |
|
454 |
> |
void SimInfo::removeExcludePairs(Molecule* mol) { |
455 |
|
std::vector<Bond*>::iterator bondIter; |
456 |
|
std::vector<Bend*>::iterator bendIter; |
457 |
|
std::vector<Torsion*>::iterator torsionIter; |
462 |
|
int b; |
463 |
|
int c; |
464 |
|
int d; |
465 |
+ |
|
466 |
+ |
std::map<int, std::set<int> > atomGroups; |
467 |
+ |
|
468 |
+ |
Molecule::RigidBodyIterator rbIter; |
469 |
+ |
RigidBody* rb; |
470 |
+ |
Molecule::IntegrableObjectIterator ii; |
471 |
+ |
StuntDouble* integrableObject; |
472 |
|
|
473 |
+ |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
474 |
+ |
integrableObject = mol->nextIntegrableObject(ii)) { |
475 |
+ |
|
476 |
+ |
if (integrableObject->isRigidBody()) { |
477 |
+ |
rb = static_cast<RigidBody*>(integrableObject); |
478 |
+ |
std::vector<Atom*> atoms = rb->getAtoms(); |
479 |
+ |
std::set<int> rigidAtoms; |
480 |
+ |
for (int i = 0; i < atoms.size(); ++i) { |
481 |
+ |
rigidAtoms.insert(atoms[i]->getGlobalIndex()); |
482 |
+ |
} |
483 |
+ |
for (int i = 0; i < atoms.size(); ++i) { |
484 |
+ |
atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms)); |
485 |
+ |
} |
486 |
+ |
} else { |
487 |
+ |
std::set<int> oneAtomSet; |
488 |
+ |
oneAtomSet.insert(integrableObject->getGlobalIndex()); |
489 |
+ |
atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet)); |
490 |
+ |
} |
491 |
+ |
} |
492 |
+ |
|
493 |
+ |
|
494 |
|
for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { |
495 |
< |
a = bond->getAtomA()->getGlobalIndex(); |
496 |
< |
b = bond->getAtomB()->getGlobalIndex(); |
497 |
< |
exclude_.removePair(a, b); |
495 |
> |
a = bond->getAtomA()->getGlobalIndex(); |
496 |
> |
b = bond->getAtomB()->getGlobalIndex(); |
497 |
> |
exclude_.removePair(a, b); |
498 |
|
} |
499 |
|
|
500 |
|
for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) { |
501 |
< |
a = bend->getAtomA()->getGlobalIndex(); |
502 |
< |
b = bend->getAtomB()->getGlobalIndex(); |
503 |
< |
c = bend->getAtomC()->getGlobalIndex(); |
501 |
> |
a = bend->getAtomA()->getGlobalIndex(); |
502 |
> |
b = bend->getAtomB()->getGlobalIndex(); |
503 |
> |
c = bend->getAtomC()->getGlobalIndex(); |
504 |
|
|
505 |
< |
exclude_.removePair(a, b); |
506 |
< |
exclude_.removePair(a, c); |
507 |
< |
exclude_.removePair(b, c); |
505 |
> |
std::set<int> rigidSetA = getRigidSet(a, atomGroups); |
506 |
> |
std::set<int> rigidSetB = getRigidSet(b, atomGroups); |
507 |
> |
std::set<int> rigidSetC = getRigidSet(c, atomGroups); |
508 |
> |
|
509 |
> |
exclude_.removePairs(rigidSetA, rigidSetB); |
510 |
> |
exclude_.removePairs(rigidSetA, rigidSetC); |
511 |
> |
exclude_.removePairs(rigidSetB, rigidSetC); |
512 |
> |
|
513 |
> |
//exclude_.removePair(a, b); |
514 |
> |
//exclude_.removePair(a, c); |
515 |
> |
//exclude_.removePair(b, c); |
516 |
|
} |
517 |
|
|
518 |
|
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
519 |
< |
a = torsion->getAtomA()->getGlobalIndex(); |
520 |
< |
b = torsion->getAtomB()->getGlobalIndex(); |
521 |
< |
c = torsion->getAtomC()->getGlobalIndex(); |
522 |
< |
d = torsion->getAtomD()->getGlobalIndex(); |
519 |
> |
a = torsion->getAtomA()->getGlobalIndex(); |
520 |
> |
b = torsion->getAtomB()->getGlobalIndex(); |
521 |
> |
c = torsion->getAtomC()->getGlobalIndex(); |
522 |
> |
d = torsion->getAtomD()->getGlobalIndex(); |
523 |
|
|
524 |
< |
exclude_.removePair(a, b); |
525 |
< |
exclude_.removePair(a, c); |
526 |
< |
exclude_.removePair(a, d); |
527 |
< |
exclude_.removePair(b, c); |
528 |
< |
exclude_.removePair(b, d); |
529 |
< |
exclude_.removePair(c, d); |
524 |
> |
std::set<int> rigidSetA = getRigidSet(a, atomGroups); |
525 |
> |
std::set<int> rigidSetB = getRigidSet(b, atomGroups); |
526 |
> |
std::set<int> rigidSetC = getRigidSet(c, atomGroups); |
527 |
> |
std::set<int> rigidSetD = getRigidSet(d, atomGroups); |
528 |
> |
|
529 |
> |
exclude_.removePairs(rigidSetA, rigidSetB); |
530 |
> |
exclude_.removePairs(rigidSetA, rigidSetC); |
531 |
> |
exclude_.removePairs(rigidSetA, rigidSetD); |
532 |
> |
exclude_.removePairs(rigidSetB, rigidSetC); |
533 |
> |
exclude_.removePairs(rigidSetB, rigidSetD); |
534 |
> |
exclude_.removePairs(rigidSetC, rigidSetD); |
535 |
> |
|
536 |
> |
/* |
537 |
> |
exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end()); |
538 |
> |
exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end()); |
539 |
> |
exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end()); |
540 |
> |
exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end()); |
541 |
> |
exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end()); |
542 |
> |
exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end()); |
543 |
> |
|
544 |
> |
|
545 |
> |
exclude_.removePair(a, b); |
546 |
> |
exclude_.removePair(a, c); |
547 |
> |
exclude_.removePair(a, d); |
548 |
> |
exclude_.removePair(b, c); |
549 |
> |
exclude_.removePair(b, d); |
550 |
> |
exclude_.removePair(c, d); |
551 |
> |
*/ |
552 |
|
} |
553 |
|
|
554 |
< |
} |
554 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
555 |
> |
std::vector<Atom*> atoms = rb->getAtoms(); |
556 |
> |
for (int i = 0; i < atoms.size() -1 ; ++i) { |
557 |
> |
for (int j = i + 1; j < atoms.size(); ++j) { |
558 |
> |
a = atoms[i]->getGlobalIndex(); |
559 |
> |
b = atoms[j]->getGlobalIndex(); |
560 |
> |
exclude_.removePair(a, b); |
561 |
> |
} |
562 |
> |
} |
563 |
> |
} |
564 |
|
|
565 |
+ |
} |
566 |
|
|
567 |
< |
void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) { |
567 |
> |
|
568 |
> |
void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) { |
569 |
|
int curStampId; |
570 |
|
|
571 |
|
//index from 0 |
573 |
|
|
574 |
|
moleculeStamps_.push_back(molStamp); |
575 |
|
molStampIds_.insert(molStampIds_.end(), nmol, curStampId); |
576 |
< |
} |
576 |
> |
} |
577 |
|
|
578 |
< |
void SimInfo::update() { |
578 |
> |
void SimInfo::update() { |
579 |
|
|
580 |
|
setupSimType(); |
581 |
|
|
588 |
|
//setup fortran force field |
589 |
|
/** @deprecate */ |
590 |
|
int isError = 0; |
591 |
< |
initFortranFF( &fInfo_.SIM_uses_RF , &isError ); |
591 |
> |
|
592 |
> |
setupElectrostaticSummationMethod( isError ); |
593 |
> |
setupSwitchingFunction(); |
594 |
> |
|
595 |
|
if(isError){ |
596 |
< |
sprintf( painCave.errMsg, |
597 |
< |
"ForceField error: There was an error initializing the forceField in fortran.\n" ); |
598 |
< |
painCave.isFatal = 1; |
599 |
< |
simError(); |
596 |
> |
sprintf( painCave.errMsg, |
597 |
> |
"ForceField error: There was an error initializing the forceField in fortran.\n" ); |
598 |
> |
painCave.isFatal = 1; |
599 |
> |
simError(); |
600 |
|
} |
601 |
|
|
602 |
|
|
607 |
|
calcNdfTrans(); |
608 |
|
|
609 |
|
fortranInitialized_ = true; |
610 |
< |
} |
610 |
> |
} |
611 |
|
|
612 |
< |
std::set<AtomType*> SimInfo::getUniqueAtomTypes() { |
612 |
> |
std::set<AtomType*> SimInfo::getUniqueAtomTypes() { |
613 |
|
SimInfo::MoleculeIterator mi; |
614 |
|
Molecule* mol; |
615 |
|
Molecule::AtomIterator ai; |
618 |
|
|
619 |
|
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
620 |
|
|
621 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
622 |
< |
atomTypes.insert(atom->getAtomType()); |
623 |
< |
} |
621 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
622 |
> |
atomTypes.insert(atom->getAtomType()); |
623 |
> |
} |
624 |
|
|
625 |
|
} |
626 |
|
|
627 |
|
return atomTypes; |
628 |
< |
} |
628 |
> |
} |
629 |
|
|
630 |
< |
void SimInfo::setupSimType() { |
630 |
> |
void SimInfo::setupSimType() { |
631 |
|
std::set<AtomType*>::iterator i; |
632 |
|
std::set<AtomType*> atomTypes; |
633 |
|
atomTypes = getUniqueAtomTypes(); |
635 |
|
int useLennardJones = 0; |
636 |
|
int useElectrostatic = 0; |
637 |
|
int useEAM = 0; |
638 |
+ |
int useSC = 0; |
639 |
|
int useCharge = 0; |
640 |
|
int useDirectional = 0; |
641 |
|
int useDipole = 0; |
642 |
|
int useGayBerne = 0; |
643 |
|
int useSticky = 0; |
644 |
+ |
int useStickyPower = 0; |
645 |
|
int useShape = 0; |
646 |
|
int useFLARB = 0; //it is not in AtomType yet |
647 |
|
int useDirectionalAtom = 0; |
648 |
|
int useElectrostatics = 0; |
649 |
|
//usePBC and useRF are from simParams |
650 |
< |
int usePBC = simParams_->getPBC(); |
651 |
< |
int useRF = simParams_->getUseRF(); |
650 |
> |
int usePBC = simParams_->getUsePeriodicBoundaryConditions(); |
651 |
> |
int useRF; |
652 |
> |
int useSF; |
653 |
> |
std::string myMethod; |
654 |
|
|
655 |
+ |
// set the useRF logical |
656 |
+ |
useRF = 0; |
657 |
+ |
useSF = 0; |
658 |
+ |
|
659 |
+ |
|
660 |
+ |
if (simParams_->haveElectrostaticSummationMethod()) { |
661 |
+ |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
662 |
+ |
toUpper(myMethod); |
663 |
+ |
if (myMethod == "REACTION_FIELD") { |
664 |
+ |
useRF=1; |
665 |
+ |
} else { |
666 |
+ |
if (myMethod == "SHIFTED_FORCE") { |
667 |
+ |
useSF = 1; |
668 |
+ |
} |
669 |
+ |
} |
670 |
+ |
} |
671 |
+ |
|
672 |
|
//loop over all of the atom types |
673 |
|
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
674 |
< |
useLennardJones |= (*i)->isLennardJones(); |
675 |
< |
useElectrostatic |= (*i)->isElectrostatic(); |
676 |
< |
useEAM |= (*i)->isEAM(); |
677 |
< |
useCharge |= (*i)->isCharge(); |
678 |
< |
useDirectional |= (*i)->isDirectional(); |
679 |
< |
useDipole |= (*i)->isDipole(); |
680 |
< |
useGayBerne |= (*i)->isGayBerne(); |
681 |
< |
useSticky |= (*i)->isSticky(); |
682 |
< |
useShape |= (*i)->isShape(); |
674 |
> |
useLennardJones |= (*i)->isLennardJones(); |
675 |
> |
useElectrostatic |= (*i)->isElectrostatic(); |
676 |
> |
useEAM |= (*i)->isEAM(); |
677 |
> |
useSC |= (*i)->isSC(); |
678 |
> |
useCharge |= (*i)->isCharge(); |
679 |
> |
useDirectional |= (*i)->isDirectional(); |
680 |
> |
useDipole |= (*i)->isDipole(); |
681 |
> |
useGayBerne |= (*i)->isGayBerne(); |
682 |
> |
useSticky |= (*i)->isSticky(); |
683 |
> |
useStickyPower |= (*i)->isStickyPower(); |
684 |
> |
useShape |= (*i)->isShape(); |
685 |
|
} |
686 |
|
|
687 |
< |
if (useSticky || useDipole || useGayBerne || useShape) { |
688 |
< |
useDirectionalAtom = 1; |
687 |
> |
if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) { |
688 |
> |
useDirectionalAtom = 1; |
689 |
|
} |
690 |
|
|
691 |
|
if (useCharge || useDipole) { |
692 |
< |
useElectrostatics = 1; |
692 |
> |
useElectrostatics = 1; |
693 |
|
} |
694 |
|
|
695 |
|
#ifdef IS_MPI |
716 |
|
temp = useSticky; |
717 |
|
MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
718 |
|
|
719 |
+ |
temp = useStickyPower; |
720 |
+ |
MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
721 |
+ |
|
722 |
|
temp = useGayBerne; |
723 |
|
MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
724 |
|
|
725 |
|
temp = useEAM; |
726 |
|
MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
727 |
|
|
728 |
+ |
temp = useSC; |
729 |
+ |
MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
730 |
+ |
|
731 |
|
temp = useShape; |
732 |
|
MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
733 |
|
|
736 |
|
|
737 |
|
temp = useRF; |
738 |
|
MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
739 |
< |
|
739 |
> |
|
740 |
> |
temp = useSF; |
741 |
> |
MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
742 |
> |
|
743 |
|
#endif |
744 |
|
|
745 |
|
fInfo_.SIM_uses_PBC = usePBC; |
749 |
|
fInfo_.SIM_uses_Charges = useCharge; |
750 |
|
fInfo_.SIM_uses_Dipoles = useDipole; |
751 |
|
fInfo_.SIM_uses_Sticky = useSticky; |
752 |
+ |
fInfo_.SIM_uses_StickyPower = useStickyPower; |
753 |
|
fInfo_.SIM_uses_GayBerne = useGayBerne; |
754 |
|
fInfo_.SIM_uses_EAM = useEAM; |
755 |
+ |
fInfo_.SIM_uses_SC = useSC; |
756 |
|
fInfo_.SIM_uses_Shapes = useShape; |
757 |
|
fInfo_.SIM_uses_FLARB = useFLARB; |
758 |
|
fInfo_.SIM_uses_RF = useRF; |
759 |
+ |
fInfo_.SIM_uses_SF = useSF; |
760 |
|
|
761 |
< |
if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { |
762 |
< |
|
763 |
< |
if (simParams_->haveDielectric()) { |
764 |
< |
fInfo_.dielect = simParams_->getDielectric(); |
765 |
< |
} else { |
766 |
< |
sprintf(painCave.errMsg, |
767 |
< |
"SimSetup Error: No Dielectric constant was set.\n" |
768 |
< |
"\tYou are trying to use Reaction Field without" |
769 |
< |
"\tsetting a dielectric constant!\n"); |
770 |
< |
painCave.isFatal = 1; |
771 |
< |
simError(); |
772 |
< |
} |
584 |
< |
|
585 |
< |
} else { |
586 |
< |
fInfo_.dielect = 0.0; |
761 |
> |
if( myMethod == "REACTION_FIELD") { |
762 |
> |
|
763 |
> |
if (simParams_->haveDielectric()) { |
764 |
> |
fInfo_.dielect = simParams_->getDielectric(); |
765 |
> |
} else { |
766 |
> |
sprintf(painCave.errMsg, |
767 |
> |
"SimSetup Error: No Dielectric constant was set.\n" |
768 |
> |
"\tYou are trying to use Reaction Field without" |
769 |
> |
"\tsetting a dielectric constant!\n"); |
770 |
> |
painCave.isFatal = 1; |
771 |
> |
simError(); |
772 |
> |
} |
773 |
|
} |
774 |
|
|
775 |
< |
} |
775 |
> |
} |
776 |
|
|
777 |
< |
void SimInfo::setupFortranSim() { |
777 |
> |
void SimInfo::setupFortranSim() { |
778 |
|
int isError; |
779 |
|
int nExclude; |
780 |
|
std::vector<int> fortranGlobalGroupMembership; |
784 |
|
|
785 |
|
//globalGroupMembership_ is filled by SimCreator |
786 |
|
for (int i = 0; i < nGlobalAtoms_; i++) { |
787 |
< |
fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1); |
787 |
> |
fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1); |
788 |
|
} |
789 |
|
|
790 |
|
//calculate mass ratio of cutoff group |
801 |
|
mfact.reserve(getNCutoffGroups()); |
802 |
|
|
803 |
|
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
804 |
< |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
804 |
> |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
805 |
|
|
806 |
< |
totalMass = cg->getMass(); |
807 |
< |
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
808 |
< |
mfact.push_back(atom->getMass()/totalMass); |
809 |
< |
} |
806 |
> |
totalMass = cg->getMass(); |
807 |
> |
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
808 |
> |
// Check for massless groups - set mfact to 1 if true |
809 |
> |
if (totalMass != 0) |
810 |
> |
mfact.push_back(atom->getMass()/totalMass); |
811 |
> |
else |
812 |
> |
mfact.push_back( 1.0 ); |
813 |
> |
} |
814 |
|
|
815 |
< |
} |
815 |
> |
} |
816 |
|
} |
817 |
|
|
818 |
|
//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!) |
822 |
|
identArray.reserve(getNAtoms()); |
823 |
|
|
824 |
|
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
825 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
826 |
< |
identArray.push_back(atom->getIdent()); |
827 |
< |
} |
825 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
826 |
> |
identArray.push_back(atom->getIdent()); |
827 |
> |
} |
828 |
|
} |
829 |
|
|
830 |
|
//fill molMembershipArray |
831 |
|
//molMembershipArray is filled by SimCreator |
832 |
|
std::vector<int> molMembershipArray(nGlobalAtoms_); |
833 |
|
for (int i = 0; i < nGlobalAtoms_; i++) { |
834 |
< |
molMembershipArray[i] = globalMolMembership_[i] + 1; |
834 |
> |
molMembershipArray[i] = globalMolMembership_[i] + 1; |
835 |
|
} |
836 |
|
|
837 |
|
//setup fortran simulation |
648 |
– |
//gloalExcludes and molMembershipArray should go away (They are never used) |
649 |
– |
//why the hell fortran need to know molecule? |
650 |
– |
//OOPSE = Object-Obfuscated Parallel Simulation Engine |
838 |
|
int nGlobalExcludes = 0; |
839 |
|
int* globalExcludes = NULL; |
840 |
|
int* excludeList = exclude_.getExcludeList(); |
841 |
|
setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList , |
842 |
< |
&nGlobalExcludes, globalExcludes, &molMembershipArray[0], |
843 |
< |
&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError); |
842 |
> |
&nGlobalExcludes, globalExcludes, &molMembershipArray[0], |
843 |
> |
&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError); |
844 |
|
|
845 |
|
if( isError ){ |
846 |
|
|
847 |
< |
sprintf( painCave.errMsg, |
848 |
< |
"There was an error setting the simulation information in fortran.\n" ); |
849 |
< |
painCave.isFatal = 1; |
850 |
< |
painCave.severity = OOPSE_ERROR; |
851 |
< |
simError(); |
847 |
> |
sprintf( painCave.errMsg, |
848 |
> |
"There was an error setting the simulation information in fortran.\n" ); |
849 |
> |
painCave.isFatal = 1; |
850 |
> |
painCave.severity = OOPSE_ERROR; |
851 |
> |
simError(); |
852 |
|
} |
853 |
|
|
854 |
|
#ifdef IS_MPI |
855 |
|
sprintf( checkPointMsg, |
856 |
< |
"succesfully sent the simulation information to fortran.\n"); |
856 |
> |
"succesfully sent the simulation information to fortran.\n"); |
857 |
|
MPIcheckPoint(); |
858 |
|
#endif // is_mpi |
859 |
< |
} |
859 |
> |
} |
860 |
|
|
861 |
|
|
862 |
|
#ifdef IS_MPI |
863 |
< |
void SimInfo::setupFortranParallel() { |
863 |
> |
void SimInfo::setupFortranParallel() { |
864 |
|
|
865 |
|
//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex |
866 |
|
std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0); |
876 |
|
|
877 |
|
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
878 |
|
|
879 |
< |
//local index(index in DataStorge) of atom is important |
880 |
< |
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
881 |
< |
localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1; |
882 |
< |
} |
879 |
> |
//local index(index in DataStorge) of atom is important |
880 |
> |
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
881 |
> |
localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1; |
882 |
> |
} |
883 |
|
|
884 |
< |
//local index of cutoff group is trivial, it only depends on the order of travesing |
885 |
< |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
886 |
< |
localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1); |
887 |
< |
} |
884 |
> |
//local index of cutoff group is trivial, it only depends on the order of travesing |
885 |
> |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
886 |
> |
localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1); |
887 |
> |
} |
888 |
|
|
889 |
|
} |
890 |
|
|
904 |
|
&localToGlobalCutoffGroupIndex[0], &isError); |
905 |
|
|
906 |
|
if (isError) { |
907 |
< |
sprintf(painCave.errMsg, |
908 |
< |
"mpiRefresh errror: fortran didn't like something we gave it.\n"); |
909 |
< |
painCave.isFatal = 1; |
910 |
< |
simError(); |
907 |
> |
sprintf(painCave.errMsg, |
908 |
> |
"mpiRefresh errror: fortran didn't like something we gave it.\n"); |
909 |
> |
painCave.isFatal = 1; |
910 |
> |
simError(); |
911 |
|
} |
912 |
|
|
913 |
|
sprintf(checkPointMsg, " mpiRefresh successful.\n"); |
914 |
|
MPIcheckPoint(); |
915 |
|
|
916 |
|
|
917 |
< |
} |
917 |
> |
} |
918 |
|
|
919 |
|
#endif |
920 |
|
|
921 |
< |
double SimInfo::calcMaxCutoffRadius() { |
735 |
< |
|
736 |
< |
|
737 |
< |
std::set<AtomType*> atomTypes; |
738 |
< |
std::set<AtomType*>::iterator i; |
739 |
< |
std::vector<double> cutoffRadius; |
740 |
< |
|
741 |
< |
//get the unique atom types |
742 |
< |
atomTypes = getUniqueAtomTypes(); |
743 |
< |
|
744 |
< |
//query the max cutoff radius among these atom types |
745 |
< |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
746 |
< |
cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i)); |
747 |
< |
} |
748 |
< |
|
749 |
< |
double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end())); |
750 |
< |
#ifdef IS_MPI |
751 |
< |
//pick the max cutoff radius among the processors |
752 |
< |
#endif |
753 |
< |
|
754 |
< |
return maxCutoffRadius; |
755 |
< |
} |
756 |
< |
|
757 |
< |
void SimInfo::getCutoff(double& rcut, double& rsw) { |
921 |
> |
void SimInfo::setupCutoff() { |
922 |
|
|
923 |
< |
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
923 |
> |
// Check the cutoff policy |
924 |
> |
int cp = TRADITIONAL_CUTOFF_POLICY; |
925 |
> |
if (simParams_->haveCutoffPolicy()) { |
926 |
> |
std::string myPolicy = simParams_->getCutoffPolicy(); |
927 |
> |
toUpper(myPolicy); |
928 |
> |
if (myPolicy == "MIX") { |
929 |
> |
cp = MIX_CUTOFF_POLICY; |
930 |
> |
} else { |
931 |
> |
if (myPolicy == "MAX") { |
932 |
> |
cp = MAX_CUTOFF_POLICY; |
933 |
> |
} else { |
934 |
> |
if (myPolicy == "TRADITIONAL") { |
935 |
> |
cp = TRADITIONAL_CUTOFF_POLICY; |
936 |
> |
} else { |
937 |
> |
// throw error |
938 |
> |
sprintf( painCave.errMsg, |
939 |
> |
"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() ); |
940 |
> |
painCave.isFatal = 1; |
941 |
> |
simError(); |
942 |
> |
} |
943 |
> |
} |
944 |
> |
} |
945 |
> |
} |
946 |
> |
notifyFortranCutoffPolicy(&cp); |
947 |
> |
|
948 |
> |
// Check the Skin Thickness for neighborlists |
949 |
> |
double skin; |
950 |
> |
if (simParams_->haveSkinThickness()) { |
951 |
> |
skin = simParams_->getSkinThickness(); |
952 |
> |
notifyFortranSkinThickness(&skin); |
953 |
> |
} |
954 |
|
|
955 |
< |
if (!simParams_->haveRcut()){ |
956 |
< |
sprintf(painCave.errMsg, |
955 |
> |
// Check if the cutoff was set explicitly: |
956 |
> |
if (simParams_->haveCutoffRadius()) { |
957 |
> |
rcut_ = simParams_->getCutoffRadius(); |
958 |
> |
if (simParams_->haveSwitchingRadius()) { |
959 |
> |
rsw_ = simParams_->getSwitchingRadius(); |
960 |
> |
} else { |
961 |
> |
rsw_ = rcut_; |
962 |
> |
} |
963 |
> |
notifyFortranCutoffs(&rcut_, &rsw_); |
964 |
> |
|
965 |
> |
} else { |
966 |
> |
|
967 |
> |
// For electrostatic atoms, we'll assume a large safe value: |
968 |
> |
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
969 |
> |
sprintf(painCave.errMsg, |
970 |
|
"SimCreator Warning: No value was set for the cutoffRadius.\n" |
971 |
|
"\tOOPSE will use a default value of 15.0 angstroms" |
972 |
|
"\tfor the cutoffRadius.\n"); |
973 |
< |
painCave.isFatal = 0; |
974 |
< |
simError(); |
975 |
< |
rcut = 15.0; |
976 |
< |
} else{ |
977 |
< |
rcut = simParams_->getRcut(); |
973 |
> |
painCave.isFatal = 0; |
974 |
> |
simError(); |
975 |
> |
rcut_ = 15.0; |
976 |
> |
|
977 |
> |
if (simParams_->haveElectrostaticSummationMethod()) { |
978 |
> |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
979 |
> |
toUpper(myMethod); |
980 |
> |
if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") { |
981 |
> |
if (simParams_->haveSwitchingRadius()){ |
982 |
> |
sprintf(painCave.errMsg, |
983 |
> |
"SimInfo Warning: A value was set for the switchingRadius\n" |
984 |
> |
"\teven though the electrostaticSummationMethod was\n" |
985 |
> |
"\tset to %s\n", myMethod.c_str()); |
986 |
> |
painCave.isFatal = 1; |
987 |
> |
simError(); |
988 |
> |
} |
989 |
> |
} |
990 |
|
} |
991 |
< |
|
992 |
< |
if (!simParams_->haveRsw()){ |
993 |
< |
sprintf(painCave.errMsg, |
994 |
< |
"SimCreator Warning: No value was set for switchingRadius.\n" |
995 |
< |
"\tOOPSE will use a default value of\n" |
996 |
< |
"\t0.95 * cutoffRadius for the switchingRadius\n"); |
997 |
< |
painCave.isFatal = 0; |
998 |
< |
simError(); |
999 |
< |
rsw = 0.95 * rcut; |
1000 |
< |
} else{ |
1001 |
< |
rsw = simParams_->getRsw(); |
991 |
> |
|
992 |
> |
if (simParams_->haveSwitchingRadius()){ |
993 |
> |
rsw_ = simParams_->getSwitchingRadius(); |
994 |
> |
} else { |
995 |
> |
sprintf(painCave.errMsg, |
996 |
> |
"SimCreator Warning: No value was set for switchingRadius.\n" |
997 |
> |
"\tOOPSE will use a default value of\n" |
998 |
> |
"\t0.85 * cutoffRadius for the switchingRadius\n"); |
999 |
> |
painCave.isFatal = 0; |
1000 |
> |
simError(); |
1001 |
> |
rsw_ = 0.85 * rcut_; |
1002 |
|
} |
1003 |
< |
|
1004 |
< |
} else { |
1005 |
< |
// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
1006 |
< |
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
1003 |
> |
notifyFortranCutoffs(&rcut_, &rsw_); |
1004 |
> |
} else { |
1005 |
> |
// We didn't set rcut explicitly, and we don't have electrostatic atoms, so |
1006 |
> |
// We'll punt and let fortran figure out the cutoffs later. |
1007 |
|
|
1008 |
< |
if (simParams_->haveRcut()) { |
790 |
< |
rcut = simParams_->getRcut(); |
791 |
< |
} else { |
792 |
< |
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
793 |
< |
rcut = calcMaxCutoffRadius(); |
794 |
< |
} |
1008 |
> |
notifyFortranYouAreOnYourOwn(); |
1009 |
|
|
1010 |
< |
if (simParams_->haveRsw()) { |
797 |
< |
rsw = simParams_->getRsw(); |
798 |
< |
} else { |
799 |
< |
rsw = rcut; |
800 |
< |
} |
801 |
< |
|
1010 |
> |
} |
1011 |
|
} |
1012 |
< |
} |
1012 |
> |
} |
1013 |
|
|
1014 |
< |
void SimInfo::setupCutoff() { |
1015 |
< |
getCutoff(rcut_, rsw_); |
1016 |
< |
double rnblist = rcut_ + 1; // skin of neighbor list |
1014 |
> |
void SimInfo::setupElectrostaticSummationMethod( int isError ) { |
1015 |
> |
|
1016 |
> |
int errorOut; |
1017 |
> |
int esm = NONE; |
1018 |
> |
int sm = UNDAMPED; |
1019 |
> |
double alphaVal; |
1020 |
> |
double dielectric; |
1021 |
|
|
1022 |
< |
//Pass these cutoff radius etc. to fortran. This function should be called once and only once |
1023 |
< |
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist); |
1024 |
< |
} |
1022 |
> |
errorOut = isError; |
1023 |
> |
alphaVal = simParams_->getDampingAlpha(); |
1024 |
> |
dielectric = simParams_->getDielectric(); |
1025 |
|
|
1026 |
< |
void SimInfo::addProperty(GenericData* genData) { |
1027 |
< |
properties_.addProperty(genData); |
1028 |
< |
} |
1029 |
< |
|
1030 |
< |
void SimInfo::removeProperty(const std::string& propName) { |
1031 |
< |
properties_.removeProperty(propName); |
1032 |
< |
} |
1033 |
< |
|
1034 |
< |
void SimInfo::clearProperties() { |
1035 |
< |
properties_.clearProperties(); |
1036 |
< |
} |
1037 |
< |
|
1038 |
< |
std::vector<std::string> SimInfo::getPropertyNames() { |
1039 |
< |
return properties_.getPropertyNames(); |
1040 |
< |
} |
1041 |
< |
|
1042 |
< |
std::vector<GenericData*> SimInfo::getProperties() { |
1043 |
< |
return properties_.getProperties(); |
1044 |
< |
} |
1045 |
< |
|
1046 |
< |
GenericData* SimInfo::getPropertyByName(const std::string& propName) { |
1047 |
< |
return properties_.getPropertyByName(propName); |
1048 |
< |
} |
1026 |
> |
if (simParams_->haveElectrostaticSummationMethod()) { |
1027 |
> |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
1028 |
> |
toUpper(myMethod); |
1029 |
> |
if (myMethod == "NONE") { |
1030 |
> |
esm = NONE; |
1031 |
> |
} else { |
1032 |
> |
if (myMethod == "SWITCHING_FUNCTION") { |
1033 |
> |
esm = SWITCHING_FUNCTION; |
1034 |
> |
} else { |
1035 |
> |
if (myMethod == "SHIFTED_POTENTIAL") { |
1036 |
> |
esm = SHIFTED_POTENTIAL; |
1037 |
> |
} else { |
1038 |
> |
if (myMethod == "SHIFTED_FORCE") { |
1039 |
> |
esm = SHIFTED_FORCE; |
1040 |
> |
} else { |
1041 |
> |
if (myMethod == "REACTION_FIELD") { |
1042 |
> |
esm = REACTION_FIELD; |
1043 |
> |
} else { |
1044 |
> |
// throw error |
1045 |
> |
sprintf( painCave.errMsg, |
1046 |
> |
"SimInfo error: Unknown electrostaticSummationMethod.\n" |
1047 |
> |
"\t(Input file specified %s .)\n" |
1048 |
> |
"\telectrostaticSummationMethod must be one of: \"none\",\n" |
1049 |
> |
"\t\"shifted_potential\", \"shifted_force\", or \n" |
1050 |
> |
"\t\"reaction_field\".\n", myMethod.c_str() ); |
1051 |
> |
painCave.isFatal = 1; |
1052 |
> |
simError(); |
1053 |
> |
} |
1054 |
> |
} |
1055 |
> |
} |
1056 |
> |
} |
1057 |
> |
} |
1058 |
> |
} |
1059 |
> |
|
1060 |
> |
if (simParams_->haveElectrostaticScreeningMethod()) { |
1061 |
> |
std::string myScreen = simParams_->getElectrostaticScreeningMethod(); |
1062 |
> |
toUpper(myScreen); |
1063 |
> |
if (myScreen == "UNDAMPED") { |
1064 |
> |
sm = UNDAMPED; |
1065 |
> |
} else { |
1066 |
> |
if (myScreen == "DAMPED") { |
1067 |
> |
sm = DAMPED; |
1068 |
> |
if (!simParams_->haveDampingAlpha()) { |
1069 |
> |
//throw error |
1070 |
> |
sprintf( painCave.errMsg, |
1071 |
> |
"SimInfo warning: dampingAlpha was not specified in the input file.\n" |
1072 |
> |
"\tA default value of %f (1/ang) will be used.\n", alphaVal); |
1073 |
> |
painCave.isFatal = 0; |
1074 |
> |
simError(); |
1075 |
> |
} |
1076 |
> |
} else { |
1077 |
> |
// throw error |
1078 |
> |
sprintf( painCave.errMsg, |
1079 |
> |
"SimInfo error: Unknown electrostaticScreeningMethod.\n" |
1080 |
> |
"\t(Input file specified %s .)\n" |
1081 |
> |
"\telectrostaticScreeningMethod must be one of: \"undamped\"\n" |
1082 |
> |
"or \"damped\".\n", myScreen.c_str() ); |
1083 |
> |
painCave.isFatal = 1; |
1084 |
> |
simError(); |
1085 |
> |
} |
1086 |
> |
} |
1087 |
> |
} |
1088 |
> |
|
1089 |
> |
// let's pass some summation method variables to fortran |
1090 |
> |
setElectrostaticSumMethod( &esm ); |
1091 |
> |
setFortranElectrostaticMethod( &esm ); |
1092 |
> |
setScreeningMethod( &sm ); |
1093 |
> |
setDampingAlpha( &alphaVal ); |
1094 |
> |
setReactionFieldDielectric( &dielectric ); |
1095 |
> |
initFortranFF( &errorOut ); |
1096 |
> |
} |
1097 |
|
|
1098 |
< |
void SimInfo::setSnapshotManager(SnapshotManager* sman) { |
1098 |
> |
void SimInfo::setupSwitchingFunction() { |
1099 |
> |
int ft = CUBIC; |
1100 |
> |
|
1101 |
> |
if (simParams_->haveSwitchingFunctionType()) { |
1102 |
> |
std::string funcType = simParams_->getSwitchingFunctionType(); |
1103 |
> |
toUpper(funcType); |
1104 |
> |
if (funcType == "CUBIC") { |
1105 |
> |
ft = CUBIC; |
1106 |
> |
} else { |
1107 |
> |
if (funcType == "FIFTH_ORDER_POLYNOMIAL") { |
1108 |
> |
ft = FIFTH_ORDER_POLY; |
1109 |
> |
} else { |
1110 |
> |
// throw error |
1111 |
> |
sprintf( painCave.errMsg, |
1112 |
> |
"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() ); |
1113 |
> |
painCave.isFatal = 1; |
1114 |
> |
simError(); |
1115 |
> |
} |
1116 |
> |
} |
1117 |
> |
} |
1118 |
> |
|
1119 |
> |
// send switching function notification to switcheroo |
1120 |
> |
setFunctionType(&ft); |
1121 |
> |
|
1122 |
> |
} |
1123 |
> |
|
1124 |
> |
void SimInfo::addProperty(GenericData* genData) { |
1125 |
> |
properties_.addProperty(genData); |
1126 |
> |
} |
1127 |
> |
|
1128 |
> |
void SimInfo::removeProperty(const std::string& propName) { |
1129 |
> |
properties_.removeProperty(propName); |
1130 |
> |
} |
1131 |
> |
|
1132 |
> |
void SimInfo::clearProperties() { |
1133 |
> |
properties_.clearProperties(); |
1134 |
> |
} |
1135 |
> |
|
1136 |
> |
std::vector<std::string> SimInfo::getPropertyNames() { |
1137 |
> |
return properties_.getPropertyNames(); |
1138 |
> |
} |
1139 |
> |
|
1140 |
> |
std::vector<GenericData*> SimInfo::getProperties() { |
1141 |
> |
return properties_.getProperties(); |
1142 |
> |
} |
1143 |
> |
|
1144 |
> |
GenericData* SimInfo::getPropertyByName(const std::string& propName) { |
1145 |
> |
return properties_.getPropertyByName(propName); |
1146 |
> |
} |
1147 |
> |
|
1148 |
> |
void SimInfo::setSnapshotManager(SnapshotManager* sman) { |
1149 |
> |
if (sman_ == sman) { |
1150 |
> |
return; |
1151 |
> |
} |
1152 |
> |
delete sman_; |
1153 |
|
sman_ = sman; |
1154 |
|
|
1155 |
|
Molecule* mol; |
1161 |
|
|
1162 |
|
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
1163 |
|
|
1164 |
< |
for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) { |
1165 |
< |
atom->setSnapshotManager(sman_); |
1166 |
< |
} |
1164 |
> |
for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) { |
1165 |
> |
atom->setSnapshotManager(sman_); |
1166 |
> |
} |
1167 |
|
|
1168 |
< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
1169 |
< |
rb->setSnapshotManager(sman_); |
1170 |
< |
} |
1168 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
1169 |
> |
rb->setSnapshotManager(sman_); |
1170 |
> |
} |
1171 |
|
} |
1172 |
|
|
1173 |
< |
} |
1173 |
> |
} |
1174 |
|
|
1175 |
< |
Vector3d SimInfo::getComVel(){ |
1175 |
> |
Vector3d SimInfo::getComVel(){ |
1176 |
|
SimInfo::MoleculeIterator i; |
1177 |
|
Molecule* mol; |
1178 |
|
|
1181 |
|
|
1182 |
|
|
1183 |
|
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1184 |
< |
double mass = mol->getMass(); |
1185 |
< |
totalMass += mass; |
1186 |
< |
comVel += mass * mol->getComVel(); |
1184 |
> |
double mass = mol->getMass(); |
1185 |
> |
totalMass += mass; |
1186 |
> |
comVel += mass * mol->getComVel(); |
1187 |
|
} |
1188 |
|
|
1189 |
|
#ifdef IS_MPI |
1196 |
|
comVel /= totalMass; |
1197 |
|
|
1198 |
|
return comVel; |
1199 |
< |
} |
1199 |
> |
} |
1200 |
|
|
1201 |
< |
Vector3d SimInfo::getCom(){ |
1201 |
> |
Vector3d SimInfo::getCom(){ |
1202 |
|
SimInfo::MoleculeIterator i; |
1203 |
|
Molecule* mol; |
1204 |
|
|
1206 |
|
double totalMass = 0.0; |
1207 |
|
|
1208 |
|
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1209 |
< |
double mass = mol->getMass(); |
1210 |
< |
totalMass += mass; |
1211 |
< |
com += mass * mol->getCom(); |
1209 |
> |
double mass = mol->getMass(); |
1210 |
> |
totalMass += mass; |
1211 |
> |
com += mass * mol->getCom(); |
1212 |
|
} |
1213 |
|
|
1214 |
|
#ifdef IS_MPI |
1222 |
|
|
1223 |
|
return com; |
1224 |
|
|
1225 |
< |
} |
1225 |
> |
} |
1226 |
|
|
1227 |
< |
std::ostream& operator <<(std::ostream& o, SimInfo& info) { |
1227 |
> |
std::ostream& operator <<(std::ostream& o, SimInfo& info) { |
1228 |
|
|
1229 |
|
return o; |
1230 |
< |
} |
1230 |
> |
} |
1231 |
> |
|
1232 |
> |
|
1233 |
> |
/* |
1234 |
> |
Returns center of mass and center of mass velocity in one function call. |
1235 |
> |
*/ |
1236 |
> |
|
1237 |
> |
void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){ |
1238 |
> |
SimInfo::MoleculeIterator i; |
1239 |
> |
Molecule* mol; |
1240 |
> |
|
1241 |
> |
|
1242 |
> |
double totalMass = 0.0; |
1243 |
> |
|
1244 |
|
|
1245 |
+ |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1246 |
+ |
double mass = mol->getMass(); |
1247 |
+ |
totalMass += mass; |
1248 |
+ |
com += mass * mol->getCom(); |
1249 |
+ |
comVel += mass * mol->getComVel(); |
1250 |
+ |
} |
1251 |
+ |
|
1252 |
+ |
#ifdef IS_MPI |
1253 |
+ |
double tmpMass = totalMass; |
1254 |
+ |
Vector3d tmpCom(com); |
1255 |
+ |
Vector3d tmpComVel(comVel); |
1256 |
+ |
MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1257 |
+ |
MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1258 |
+ |
MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1259 |
+ |
#endif |
1260 |
+ |
|
1261 |
+ |
com /= totalMass; |
1262 |
+ |
comVel /= totalMass; |
1263 |
+ |
} |
1264 |
+ |
|
1265 |
+ |
/* |
1266 |
+ |
Return intertia tensor for entire system and angular momentum Vector. |
1267 |
+ |
|
1268 |
+ |
|
1269 |
+ |
[ Ixx -Ixy -Ixz ] |
1270 |
+ |
J =| -Iyx Iyy -Iyz | |
1271 |
+ |
[ -Izx -Iyz Izz ] |
1272 |
+ |
*/ |
1273 |
+ |
|
1274 |
+ |
void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){ |
1275 |
+ |
|
1276 |
+ |
|
1277 |
+ |
double xx = 0.0; |
1278 |
+ |
double yy = 0.0; |
1279 |
+ |
double zz = 0.0; |
1280 |
+ |
double xy = 0.0; |
1281 |
+ |
double xz = 0.0; |
1282 |
+ |
double yz = 0.0; |
1283 |
+ |
Vector3d com(0.0); |
1284 |
+ |
Vector3d comVel(0.0); |
1285 |
+ |
|
1286 |
+ |
getComAll(com, comVel); |
1287 |
+ |
|
1288 |
+ |
SimInfo::MoleculeIterator i; |
1289 |
+ |
Molecule* mol; |
1290 |
+ |
|
1291 |
+ |
Vector3d thisq(0.0); |
1292 |
+ |
Vector3d thisv(0.0); |
1293 |
+ |
|
1294 |
+ |
double thisMass = 0.0; |
1295 |
+ |
|
1296 |
+ |
|
1297 |
+ |
|
1298 |
+ |
|
1299 |
+ |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1300 |
+ |
|
1301 |
+ |
thisq = mol->getCom()-com; |
1302 |
+ |
thisv = mol->getComVel()-comVel; |
1303 |
+ |
thisMass = mol->getMass(); |
1304 |
+ |
// Compute moment of intertia coefficients. |
1305 |
+ |
xx += thisq[0]*thisq[0]*thisMass; |
1306 |
+ |
yy += thisq[1]*thisq[1]*thisMass; |
1307 |
+ |
zz += thisq[2]*thisq[2]*thisMass; |
1308 |
+ |
|
1309 |
+ |
// compute products of intertia |
1310 |
+ |
xy += thisq[0]*thisq[1]*thisMass; |
1311 |
+ |
xz += thisq[0]*thisq[2]*thisMass; |
1312 |
+ |
yz += thisq[1]*thisq[2]*thisMass; |
1313 |
+ |
|
1314 |
+ |
angularMomentum += cross( thisq, thisv ) * thisMass; |
1315 |
+ |
|
1316 |
+ |
} |
1317 |
+ |
|
1318 |
+ |
|
1319 |
+ |
inertiaTensor(0,0) = yy + zz; |
1320 |
+ |
inertiaTensor(0,1) = -xy; |
1321 |
+ |
inertiaTensor(0,2) = -xz; |
1322 |
+ |
inertiaTensor(1,0) = -xy; |
1323 |
+ |
inertiaTensor(1,1) = xx + zz; |
1324 |
+ |
inertiaTensor(1,2) = -yz; |
1325 |
+ |
inertiaTensor(2,0) = -xz; |
1326 |
+ |
inertiaTensor(2,1) = -yz; |
1327 |
+ |
inertiaTensor(2,2) = xx + yy; |
1328 |
+ |
|
1329 |
+ |
#ifdef IS_MPI |
1330 |
+ |
Mat3x3d tmpI(inertiaTensor); |
1331 |
+ |
Vector3d tmpAngMom; |
1332 |
+ |
MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1333 |
+ |
MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1334 |
+ |
#endif |
1335 |
+ |
|
1336 |
+ |
return; |
1337 |
+ |
} |
1338 |
+ |
|
1339 |
+ |
//Returns the angular momentum of the system |
1340 |
+ |
Vector3d SimInfo::getAngularMomentum(){ |
1341 |
+ |
|
1342 |
+ |
Vector3d com(0.0); |
1343 |
+ |
Vector3d comVel(0.0); |
1344 |
+ |
Vector3d angularMomentum(0.0); |
1345 |
+ |
|
1346 |
+ |
getComAll(com,comVel); |
1347 |
+ |
|
1348 |
+ |
SimInfo::MoleculeIterator i; |
1349 |
+ |
Molecule* mol; |
1350 |
+ |
|
1351 |
+ |
Vector3d thisr(0.0); |
1352 |
+ |
Vector3d thisp(0.0); |
1353 |
+ |
|
1354 |
+ |
double thisMass; |
1355 |
+ |
|
1356 |
+ |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1357 |
+ |
thisMass = mol->getMass(); |
1358 |
+ |
thisr = mol->getCom()-com; |
1359 |
+ |
thisp = (mol->getComVel()-comVel)*thisMass; |
1360 |
+ |
|
1361 |
+ |
angularMomentum += cross( thisr, thisp ); |
1362 |
+ |
|
1363 |
+ |
} |
1364 |
+ |
|
1365 |
+ |
#ifdef IS_MPI |
1366 |
+ |
Vector3d tmpAngMom; |
1367 |
+ |
MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1368 |
+ |
#endif |
1369 |
+ |
|
1370 |
+ |
return angularMomentum; |
1371 |
+ |
} |
1372 |
+ |
|
1373 |
+ |
|
1374 |
|
}//end namespace oopse |
1375 |
|
|