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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 "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/doForces_interface.h" |
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#include "UseTheForce/DarkSide/electrostatic_interface.h" |
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#include "UseTheForce/notifyCutoffs_interface.h" |
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#include "utils/MemoryUtils.hpp" |
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#include "utils/simError.h" |
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namespace oopse { |
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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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SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, |
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ForceField* ff, Globals* simParams) : |
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stamps_(stamps), 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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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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for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) { |
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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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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->getCutoffGroup(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->getRigidBody(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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//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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nGlobalMols_ = molStampIds_.size(); |
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nGlobalMols_ = molStampIds_.size(); |
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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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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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delete i->second; |
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} |
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molecules_.clear(); |
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MemoryUtils::deletePointers(moleculeStamps_); |
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delete stamps_; |
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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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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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removeExcludePairs(mol); |
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molecules_.erase(mol->getGlobalIndex()); |
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removeExcludePairs(mol); |
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molecules_.erase(mol->getGlobalIndex()); |
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delete mol; |
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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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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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}//end for (integrableObject) |
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}//end for (integrableObject) |
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}// end for (mol) |
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// n_constraints is local, so subtract them on each processor |
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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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void SimInfo::calcNdfRaw() { |
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void SimInfo::calcNdfRaw() { |
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int ndfRaw_local; |
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MoleculeIterator i; |
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ndfRaw_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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ndfRaw_local += 3; |
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ndfRaw_local += 3; |
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if (integrableObject->isDirectional()) { |
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if (integrableObject->isLinear()) { |
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ndfRaw_local += 2; |
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} else { |
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ndfRaw_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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ndfRaw_local += 2; |
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} else { |
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ndfRaw_local += 3; |
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} |
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} |
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< |
} |
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} |
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} |
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#ifdef IS_MPI |
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#else |
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ndfRaw_ = ndfRaw_local; |
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#endif |
316 |
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} |
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} |
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< |
void SimInfo::calcNdfTrans() { |
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> |
void SimInfo::calcNdfTrans() { |
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int ndfTrans_local; |
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ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_; |
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ndfTrans_ = ndfTrans_ - 3 - nZconstraint_; |
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< |
} |
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} |
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void SimInfo::addExcludePairs(Molecule* mol) { |
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> |
void SimInfo::addExcludePairs(Molecule* mol) { |
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std::vector<Bond*>::iterator bondIter; |
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std::vector<Bend*>::iterator bendIter; |
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std::vector<Torsion*>::iterator torsionIter; |
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int d; |
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for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { |
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a = bond->getAtomA()->getGlobalIndex(); |
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b = bond->getAtomB()->getGlobalIndex(); |
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< |
exclude_.addPair(a, b); |
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a = bond->getAtomA()->getGlobalIndex(); |
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> |
b = bond->getAtomB()->getGlobalIndex(); |
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> |
exclude_.addPair(a, b); |
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} |
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for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) { |
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a = bend->getAtomA()->getGlobalIndex(); |
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b = bend->getAtomB()->getGlobalIndex(); |
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c = bend->getAtomC()->getGlobalIndex(); |
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> |
a = bend->getAtomA()->getGlobalIndex(); |
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> |
b = bend->getAtomB()->getGlobalIndex(); |
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> |
c = bend->getAtomC()->getGlobalIndex(); |
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< |
exclude_.addPair(a, b); |
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< |
exclude_.addPair(a, c); |
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< |
exclude_.addPair(b, c); |
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> |
exclude_.addPair(a, b); |
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> |
exclude_.addPair(a, c); |
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> |
exclude_.addPair(b, c); |
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} |
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for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
363 |
< |
a = torsion->getAtomA()->getGlobalIndex(); |
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< |
b = torsion->getAtomB()->getGlobalIndex(); |
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< |
c = torsion->getAtomC()->getGlobalIndex(); |
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< |
d = torsion->getAtomD()->getGlobalIndex(); |
363 |
> |
a = torsion->getAtomA()->getGlobalIndex(); |
364 |
> |
b = torsion->getAtomB()->getGlobalIndex(); |
365 |
> |
c = torsion->getAtomC()->getGlobalIndex(); |
366 |
> |
d = torsion->getAtomD()->getGlobalIndex(); |
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|
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< |
exclude_.addPair(a, b); |
369 |
< |
exclude_.addPair(a, c); |
370 |
< |
exclude_.addPair(a, d); |
371 |
< |
exclude_.addPair(b, c); |
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< |
exclude_.addPair(b, d); |
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< |
exclude_.addPair(c, d); |
368 |
> |
exclude_.addPair(a, b); |
369 |
> |
exclude_.addPair(a, c); |
370 |
> |
exclude_.addPair(a, d); |
371 |
> |
exclude_.addPair(b, c); |
372 |
> |
exclude_.addPair(b, d); |
373 |
> |
exclude_.addPair(c, d); |
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} |
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< |
|
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< |
} |
376 |
> |
Molecule::RigidBodyIterator rbIter; |
377 |
> |
RigidBody* rb; |
378 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
379 |
> |
std::vector<Atom*> atoms = rb->getAtoms(); |
380 |
> |
for (int i = 0; i < atoms.size() -1 ; ++i) { |
381 |
> |
for (int j = i + 1; j < atoms.size(); ++j) { |
382 |
> |
a = atoms[i]->getGlobalIndex(); |
383 |
> |
b = atoms[j]->getGlobalIndex(); |
384 |
> |
exclude_.addPair(a, b); |
385 |
> |
} |
386 |
> |
} |
387 |
> |
} |
388 |
|
|
389 |
< |
void SimInfo::removeExcludePairs(Molecule* mol) { |
389 |
> |
} |
390 |
> |
|
391 |
> |
void SimInfo::removeExcludePairs(Molecule* mol) { |
392 |
|
std::vector<Bond*>::iterator bondIter; |
393 |
|
std::vector<Bend*>::iterator bendIter; |
394 |
|
std::vector<Torsion*>::iterator torsionIter; |
401 |
|
int d; |
402 |
|
|
403 |
|
for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { |
404 |
< |
a = bond->getAtomA()->getGlobalIndex(); |
405 |
< |
b = bond->getAtomB()->getGlobalIndex(); |
406 |
< |
exclude_.removePair(a, b); |
404 |
> |
a = bond->getAtomA()->getGlobalIndex(); |
405 |
> |
b = bond->getAtomB()->getGlobalIndex(); |
406 |
> |
exclude_.removePair(a, b); |
407 |
|
} |
408 |
|
|
409 |
|
for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) { |
410 |
< |
a = bend->getAtomA()->getGlobalIndex(); |
411 |
< |
b = bend->getAtomB()->getGlobalIndex(); |
412 |
< |
c = bend->getAtomC()->getGlobalIndex(); |
410 |
> |
a = bend->getAtomA()->getGlobalIndex(); |
411 |
> |
b = bend->getAtomB()->getGlobalIndex(); |
412 |
> |
c = bend->getAtomC()->getGlobalIndex(); |
413 |
|
|
414 |
< |
exclude_.removePair(a, b); |
415 |
< |
exclude_.removePair(a, c); |
416 |
< |
exclude_.removePair(b, c); |
414 |
> |
exclude_.removePair(a, b); |
415 |
> |
exclude_.removePair(a, c); |
416 |
> |
exclude_.removePair(b, c); |
417 |
|
} |
418 |
|
|
419 |
|
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
420 |
< |
a = torsion->getAtomA()->getGlobalIndex(); |
421 |
< |
b = torsion->getAtomB()->getGlobalIndex(); |
422 |
< |
c = torsion->getAtomC()->getGlobalIndex(); |
423 |
< |
d = torsion->getAtomD()->getGlobalIndex(); |
420 |
> |
a = torsion->getAtomA()->getGlobalIndex(); |
421 |
> |
b = torsion->getAtomB()->getGlobalIndex(); |
422 |
> |
c = torsion->getAtomC()->getGlobalIndex(); |
423 |
> |
d = torsion->getAtomD()->getGlobalIndex(); |
424 |
|
|
425 |
< |
exclude_.removePair(a, b); |
426 |
< |
exclude_.removePair(a, c); |
427 |
< |
exclude_.removePair(a, d); |
428 |
< |
exclude_.removePair(b, c); |
429 |
< |
exclude_.removePair(b, d); |
430 |
< |
exclude_.removePair(c, d); |
425 |
> |
exclude_.removePair(a, b); |
426 |
> |
exclude_.removePair(a, c); |
427 |
> |
exclude_.removePair(a, d); |
428 |
> |
exclude_.removePair(b, c); |
429 |
> |
exclude_.removePair(b, d); |
430 |
> |
exclude_.removePair(c, d); |
431 |
|
} |
432 |
|
|
433 |
< |
} |
433 |
> |
Molecule::RigidBodyIterator rbIter; |
434 |
> |
RigidBody* rb; |
435 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
436 |
> |
std::vector<Atom*> atoms = rb->getAtoms(); |
437 |
> |
for (int i = 0; i < atoms.size() -1 ; ++i) { |
438 |
> |
for (int j = i + 1; j < atoms.size(); ++j) { |
439 |
> |
a = atoms[i]->getGlobalIndex(); |
440 |
> |
b = atoms[j]->getGlobalIndex(); |
441 |
> |
exclude_.removePair(a, b); |
442 |
> |
} |
443 |
> |
} |
444 |
> |
} |
445 |
|
|
446 |
+ |
} |
447 |
|
|
448 |
< |
void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) { |
448 |
> |
|
449 |
> |
void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) { |
450 |
|
int curStampId; |
451 |
|
|
452 |
|
//index from 0 |
454 |
|
|
455 |
|
moleculeStamps_.push_back(molStamp); |
456 |
|
molStampIds_.insert(molStampIds_.end(), nmol, curStampId); |
457 |
< |
} |
457 |
> |
} |
458 |
|
|
459 |
< |
void SimInfo::update() { |
459 |
> |
void SimInfo::update() { |
460 |
|
|
461 |
|
setupSimType(); |
462 |
|
|
469 |
|
//setup fortran force field |
470 |
|
/** @deprecate */ |
471 |
|
int isError = 0; |
472 |
< |
initFortranFF( &fInfo_.SIM_uses_RF , &isError ); |
472 |
> |
|
473 |
> |
setupElectrostaticSummationMethod( isError ); |
474 |
> |
|
475 |
|
if(isError){ |
476 |
< |
sprintf( painCave.errMsg, |
477 |
< |
"ForceField error: There was an error initializing the forceField in fortran.\n" ); |
478 |
< |
painCave.isFatal = 1; |
479 |
< |
simError(); |
476 |
> |
sprintf( painCave.errMsg, |
477 |
> |
"ForceField error: There was an error initializing the forceField in fortran.\n" ); |
478 |
> |
painCave.isFatal = 1; |
479 |
> |
simError(); |
480 |
|
} |
481 |
|
|
482 |
|
|
487 |
|
calcNdfTrans(); |
488 |
|
|
489 |
|
fortranInitialized_ = true; |
490 |
< |
} |
490 |
> |
} |
491 |
|
|
492 |
< |
std::set<AtomType*> SimInfo::getUniqueAtomTypes() { |
492 |
> |
std::set<AtomType*> SimInfo::getUniqueAtomTypes() { |
493 |
|
SimInfo::MoleculeIterator mi; |
494 |
|
Molecule* mol; |
495 |
|
Molecule::AtomIterator ai; |
498 |
|
|
499 |
|
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
500 |
|
|
501 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
502 |
< |
atomTypes.insert(atom->getAtomType()); |
503 |
< |
} |
501 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
502 |
> |
atomTypes.insert(atom->getAtomType()); |
503 |
> |
} |
504 |
|
|
505 |
|
} |
506 |
|
|
507 |
|
return atomTypes; |
508 |
< |
} |
508 |
> |
} |
509 |
|
|
510 |
< |
void SimInfo::setupSimType() { |
510 |
> |
void SimInfo::setupSimType() { |
511 |
|
std::set<AtomType*>::iterator i; |
512 |
|
std::set<AtomType*> atomTypes; |
513 |
|
atomTypes = getUniqueAtomTypes(); |
520 |
|
int useDipole = 0; |
521 |
|
int useGayBerne = 0; |
522 |
|
int useSticky = 0; |
523 |
+ |
int useStickyPower = 0; |
524 |
|
int useShape = 0; |
525 |
|
int useFLARB = 0; //it is not in AtomType yet |
526 |
|
int useDirectionalAtom = 0; |
527 |
|
int useElectrostatics = 0; |
528 |
|
//usePBC and useRF are from simParams |
529 |
< |
int usePBC = simParams_->getPBC(); |
530 |
< |
int useRF = simParams_->getUseRF(); |
529 |
> |
int usePBC = simParams_->getUsePeriodicBoundaryConditions(); |
530 |
> |
int useRF; |
531 |
> |
std::string myMethod; |
532 |
|
|
533 |
+ |
// set the useRF logical |
534 |
+ |
useRF = 0; |
535 |
+ |
if (simParams_->haveElectrostaticSummationMethod()) { |
536 |
+ |
myMethod = simParams_->getElectrostaticSummationMethod(); |
537 |
+ |
if (myMethod == "REACTION_FIELD") |
538 |
+ |
useRF = 1; |
539 |
+ |
} |
540 |
+ |
|
541 |
|
//loop over all of the atom types |
542 |
|
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
543 |
< |
useLennardJones |= (*i)->isLennardJones(); |
544 |
< |
useElectrostatic |= (*i)->isElectrostatic(); |
545 |
< |
useEAM |= (*i)->isEAM(); |
546 |
< |
useCharge |= (*i)->isCharge(); |
547 |
< |
useDirectional |= (*i)->isDirectional(); |
548 |
< |
useDipole |= (*i)->isDipole(); |
549 |
< |
useGayBerne |= (*i)->isGayBerne(); |
550 |
< |
useSticky |= (*i)->isSticky(); |
551 |
< |
useShape |= (*i)->isShape(); |
543 |
> |
useLennardJones |= (*i)->isLennardJones(); |
544 |
> |
useElectrostatic |= (*i)->isElectrostatic(); |
545 |
> |
useEAM |= (*i)->isEAM(); |
546 |
> |
useCharge |= (*i)->isCharge(); |
547 |
> |
useDirectional |= (*i)->isDirectional(); |
548 |
> |
useDipole |= (*i)->isDipole(); |
549 |
> |
useGayBerne |= (*i)->isGayBerne(); |
550 |
> |
useSticky |= (*i)->isSticky(); |
551 |
> |
useStickyPower |= (*i)->isStickyPower(); |
552 |
> |
useShape |= (*i)->isShape(); |
553 |
|
} |
554 |
|
|
555 |
< |
if (useSticky || useDipole || useGayBerne || useShape) { |
556 |
< |
useDirectionalAtom = 1; |
555 |
> |
if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) { |
556 |
> |
useDirectionalAtom = 1; |
557 |
|
} |
558 |
|
|
559 |
|
if (useCharge || useDipole) { |
560 |
< |
useElectrostatics = 1; |
560 |
> |
useElectrostatics = 1; |
561 |
|
} |
562 |
|
|
563 |
|
#ifdef IS_MPI |
584 |
|
temp = useSticky; |
585 |
|
MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
586 |
|
|
587 |
+ |
temp = useStickyPower; |
588 |
+ |
MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
589 |
+ |
|
590 |
|
temp = useGayBerne; |
591 |
|
MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
592 |
|
|
601 |
|
|
602 |
|
temp = useRF; |
603 |
|
MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
604 |
< |
|
604 |
> |
|
605 |
|
#endif |
606 |
|
|
607 |
|
fInfo_.SIM_uses_PBC = usePBC; |
611 |
|
fInfo_.SIM_uses_Charges = useCharge; |
612 |
|
fInfo_.SIM_uses_Dipoles = useDipole; |
613 |
|
fInfo_.SIM_uses_Sticky = useSticky; |
614 |
+ |
fInfo_.SIM_uses_StickyPower = useStickyPower; |
615 |
|
fInfo_.SIM_uses_GayBerne = useGayBerne; |
616 |
|
fInfo_.SIM_uses_EAM = useEAM; |
617 |
|
fInfo_.SIM_uses_Shapes = useShape; |
618 |
|
fInfo_.SIM_uses_FLARB = useFLARB; |
619 |
|
fInfo_.SIM_uses_RF = useRF; |
620 |
|
|
621 |
< |
if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { |
621 |
> |
if( fInfo_.SIM_uses_Dipoles && myMethod == "REACTION_FIELD") { |
622 |
|
|
623 |
< |
if (simParams_->haveDielectric()) { |
624 |
< |
fInfo_.dielect = simParams_->getDielectric(); |
625 |
< |
} else { |
626 |
< |
sprintf(painCave.errMsg, |
627 |
< |
"SimSetup Error: No Dielectric constant was set.\n" |
628 |
< |
"\tYou are trying to use Reaction Field without" |
629 |
< |
"\tsetting a dielectric constant!\n"); |
630 |
< |
painCave.isFatal = 1; |
631 |
< |
simError(); |
632 |
< |
} |
623 |
> |
if (simParams_->haveDielectric()) { |
624 |
> |
fInfo_.dielect = simParams_->getDielectric(); |
625 |
> |
} else { |
626 |
> |
sprintf(painCave.errMsg, |
627 |
> |
"SimSetup Error: No Dielectric constant was set.\n" |
628 |
> |
"\tYou are trying to use Reaction Field without" |
629 |
> |
"\tsetting a dielectric constant!\n"); |
630 |
> |
painCave.isFatal = 1; |
631 |
> |
simError(); |
632 |
> |
} |
633 |
|
|
634 |
|
} else { |
635 |
< |
fInfo_.dielect = 0.0; |
635 |
> |
fInfo_.dielect = 0.0; |
636 |
|
} |
637 |
|
|
638 |
< |
} |
638 |
> |
} |
639 |
|
|
640 |
< |
void SimInfo::setupFortranSim() { |
640 |
> |
void SimInfo::setupFortranSim() { |
641 |
|
int isError; |
642 |
|
int nExclude; |
643 |
|
std::vector<int> fortranGlobalGroupMembership; |
647 |
|
|
648 |
|
//globalGroupMembership_ is filled by SimCreator |
649 |
|
for (int i = 0; i < nGlobalAtoms_; i++) { |
650 |
< |
fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1); |
650 |
> |
fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1); |
651 |
|
} |
652 |
|
|
653 |
|
//calculate mass ratio of cutoff group |
664 |
|
mfact.reserve(getNCutoffGroups()); |
665 |
|
|
666 |
|
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
667 |
< |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
667 |
> |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
668 |
|
|
669 |
< |
totalMass = cg->getMass(); |
670 |
< |
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
671 |
< |
mfact.push_back(atom->getMass()/totalMass); |
672 |
< |
} |
669 |
> |
totalMass = cg->getMass(); |
670 |
> |
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
671 |
> |
// Check for massless groups - set mfact to 1 if true |
672 |
> |
if (totalMass != 0) |
673 |
> |
mfact.push_back(atom->getMass()/totalMass); |
674 |
> |
else |
675 |
> |
mfact.push_back( 1.0 ); |
676 |
> |
} |
677 |
|
|
678 |
< |
} |
678 |
> |
} |
679 |
|
} |
680 |
|
|
681 |
|
//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!) |
685 |
|
identArray.reserve(getNAtoms()); |
686 |
|
|
687 |
|
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
688 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
689 |
< |
identArray.push_back(atom->getIdent()); |
690 |
< |
} |
688 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
689 |
> |
identArray.push_back(atom->getIdent()); |
690 |
> |
} |
691 |
|
} |
692 |
|
|
693 |
|
//fill molMembershipArray |
694 |
|
//molMembershipArray is filled by SimCreator |
695 |
|
std::vector<int> molMembershipArray(nGlobalAtoms_); |
696 |
|
for (int i = 0; i < nGlobalAtoms_; i++) { |
697 |
< |
molMembershipArray[i] = globalMolMembership_[i] + 1; |
697 |
> |
molMembershipArray[i] = globalMolMembership_[i] + 1; |
698 |
|
} |
699 |
|
|
700 |
|
//setup fortran simulation |
652 |
– |
//gloalExcludes and molMembershipArray should go away (They are never used) |
653 |
– |
//why the hell fortran need to know molecule? |
654 |
– |
//OOPSE = Object-Obfuscated Parallel Simulation Engine |
701 |
|
int nGlobalExcludes = 0; |
702 |
|
int* globalExcludes = NULL; |
703 |
|
int* excludeList = exclude_.getExcludeList(); |
704 |
|
setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList , |
705 |
< |
&nGlobalExcludes, globalExcludes, &molMembershipArray[0], |
706 |
< |
&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError); |
705 |
> |
&nGlobalExcludes, globalExcludes, &molMembershipArray[0], |
706 |
> |
&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError); |
707 |
|
|
708 |
|
if( isError ){ |
709 |
|
|
710 |
< |
sprintf( painCave.errMsg, |
711 |
< |
"There was an error setting the simulation information in fortran.\n" ); |
712 |
< |
painCave.isFatal = 1; |
713 |
< |
painCave.severity = OOPSE_ERROR; |
714 |
< |
simError(); |
710 |
> |
sprintf( painCave.errMsg, |
711 |
> |
"There was an error setting the simulation information in fortran.\n" ); |
712 |
> |
painCave.isFatal = 1; |
713 |
> |
painCave.severity = OOPSE_ERROR; |
714 |
> |
simError(); |
715 |
|
} |
716 |
|
|
717 |
|
#ifdef IS_MPI |
718 |
|
sprintf( checkPointMsg, |
719 |
< |
"succesfully sent the simulation information to fortran.\n"); |
719 |
> |
"succesfully sent the simulation information to fortran.\n"); |
720 |
|
MPIcheckPoint(); |
721 |
|
#endif // is_mpi |
722 |
< |
} |
722 |
> |
} |
723 |
|
|
724 |
|
|
725 |
|
#ifdef IS_MPI |
726 |
< |
void SimInfo::setupFortranParallel() { |
726 |
> |
void SimInfo::setupFortranParallel() { |
727 |
|
|
728 |
|
//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex |
729 |
|
std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0); |
739 |
|
|
740 |
|
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
741 |
|
|
742 |
< |
//local index(index in DataStorge) of atom is important |
743 |
< |
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
744 |
< |
localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1; |
745 |
< |
} |
742 |
> |
//local index(index in DataStorge) of atom is important |
743 |
> |
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
744 |
> |
localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1; |
745 |
> |
} |
746 |
|
|
747 |
< |
//local index of cutoff group is trivial, it only depends on the order of travesing |
748 |
< |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
749 |
< |
localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1); |
750 |
< |
} |
747 |
> |
//local index of cutoff group is trivial, it only depends on the order of travesing |
748 |
> |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
749 |
> |
localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1); |
750 |
> |
} |
751 |
|
|
752 |
|
} |
753 |
|
|
767 |
|
&localToGlobalCutoffGroupIndex[0], &isError); |
768 |
|
|
769 |
|
if (isError) { |
770 |
< |
sprintf(painCave.errMsg, |
771 |
< |
"mpiRefresh errror: fortran didn't like something we gave it.\n"); |
772 |
< |
painCave.isFatal = 1; |
773 |
< |
simError(); |
770 |
> |
sprintf(painCave.errMsg, |
771 |
> |
"mpiRefresh errror: fortran didn't like something we gave it.\n"); |
772 |
> |
painCave.isFatal = 1; |
773 |
> |
simError(); |
774 |
|
} |
775 |
|
|
776 |
|
sprintf(checkPointMsg, " mpiRefresh successful.\n"); |
777 |
|
MPIcheckPoint(); |
778 |
|
|
779 |
|
|
780 |
< |
} |
780 |
> |
} |
781 |
|
|
782 |
|
#endif |
783 |
|
|
784 |
< |
double SimInfo::calcMaxCutoffRadius() { |
784 |
> |
double SimInfo::calcMaxCutoffRadius() { |
785 |
|
|
786 |
|
|
787 |
|
std::set<AtomType*> atomTypes; |
793 |
|
|
794 |
|
//query the max cutoff radius among these atom types |
795 |
|
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
796 |
< |
cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i)); |
796 |
> |
cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i)); |
797 |
|
} |
798 |
|
|
799 |
|
double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end())); |
802 |
|
#endif |
803 |
|
|
804 |
|
return maxCutoffRadius; |
805 |
< |
} |
805 |
> |
} |
806 |
|
|
807 |
< |
void SimInfo::getCutoff(double& rcut, double& rsw) { |
807 |
> |
void SimInfo::getCutoff(double& rcut, double& rsw) { |
808 |
|
|
809 |
|
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
810 |
|
|
811 |
< |
if (!simParams_->haveRcut()){ |
812 |
< |
sprintf(painCave.errMsg, |
811 |
> |
if (!simParams_->haveCutoffRadius()){ |
812 |
> |
sprintf(painCave.errMsg, |
813 |
|
"SimCreator Warning: No value was set for the cutoffRadius.\n" |
814 |
|
"\tOOPSE will use a default value of 15.0 angstroms" |
815 |
|
"\tfor the cutoffRadius.\n"); |
816 |
< |
painCave.isFatal = 0; |
817 |
< |
simError(); |
818 |
< |
rcut = 15.0; |
819 |
< |
} else{ |
820 |
< |
rcut = simParams_->getRcut(); |
821 |
< |
} |
816 |
> |
painCave.isFatal = 0; |
817 |
> |
simError(); |
818 |
> |
rcut = 15.0; |
819 |
> |
} else{ |
820 |
> |
rcut = simParams_->getCutoffRadius(); |
821 |
> |
} |
822 |
|
|
823 |
< |
if (!simParams_->haveRsw()){ |
824 |
< |
sprintf(painCave.errMsg, |
823 |
> |
if (!simParams_->haveSwitchingRadius()){ |
824 |
> |
sprintf(painCave.errMsg, |
825 |
|
"SimCreator Warning: No value was set for switchingRadius.\n" |
826 |
|
"\tOOPSE will use a default value of\n" |
827 |
|
"\t0.95 * cutoffRadius for the switchingRadius\n"); |
828 |
< |
painCave.isFatal = 0; |
829 |
< |
simError(); |
830 |
< |
rsw = 0.95 * rcut; |
831 |
< |
} else{ |
832 |
< |
rsw = simParams_->getRsw(); |
833 |
< |
} |
828 |
> |
painCave.isFatal = 0; |
829 |
> |
simError(); |
830 |
> |
rsw = 0.95 * rcut; |
831 |
> |
} else{ |
832 |
> |
rsw = simParams_->getSwitchingRadius(); |
833 |
> |
} |
834 |
|
|
835 |
|
} else { |
836 |
< |
// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
837 |
< |
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
836 |
> |
// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
837 |
> |
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
838 |
|
|
839 |
< |
if (simParams_->haveRcut()) { |
840 |
< |
rcut = simParams_->getRcut(); |
841 |
< |
} else { |
842 |
< |
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
843 |
< |
rcut = calcMaxCutoffRadius(); |
844 |
< |
} |
839 |
> |
if (simParams_->haveCutoffRadius()) { |
840 |
> |
rcut = simParams_->getCutoffRadius(); |
841 |
> |
} else { |
842 |
> |
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
843 |
> |
rcut = calcMaxCutoffRadius(); |
844 |
> |
} |
845 |
|
|
846 |
< |
if (simParams_->haveRsw()) { |
847 |
< |
rsw = simParams_->getRsw(); |
848 |
< |
} else { |
849 |
< |
rsw = rcut; |
850 |
< |
} |
846 |
> |
if (simParams_->haveSwitchingRadius()) { |
847 |
> |
rsw = simParams_->getSwitchingRadius(); |
848 |
> |
} else { |
849 |
> |
rsw = rcut; |
850 |
> |
} |
851 |
|
|
852 |
|
} |
853 |
< |
} |
853 |
> |
} |
854 |
|
|
855 |
< |
void SimInfo::setupCutoff() { |
855 |
> |
void SimInfo::setupCutoff() { |
856 |
|
getCutoff(rcut_, rsw_); |
857 |
|
double rnblist = rcut_ + 1; // skin of neighbor list |
858 |
|
|
859 |
|
//Pass these cutoff radius etc. to fortran. This function should be called once and only once |
860 |
< |
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist); |
861 |
< |
} |
860 |
> |
|
861 |
> |
int cp = TRADITIONAL_CUTOFF_POLICY; |
862 |
> |
if (simParams_->haveCutoffPolicy()) { |
863 |
> |
std::string myPolicy = simParams_->getCutoffPolicy(); |
864 |
> |
toUpper(myPolicy); |
865 |
> |
if (myPolicy == "MIX") { |
866 |
> |
cp = MIX_CUTOFF_POLICY; |
867 |
> |
} else { |
868 |
> |
if (myPolicy == "MAX") { |
869 |
> |
cp = MAX_CUTOFF_POLICY; |
870 |
> |
} else { |
871 |
> |
if (myPolicy == "TRADITIONAL") { |
872 |
> |
cp = TRADITIONAL_CUTOFF_POLICY; |
873 |
> |
} else { |
874 |
> |
// throw error |
875 |
> |
sprintf( painCave.errMsg, |
876 |
> |
"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() ); |
877 |
> |
painCave.isFatal = 1; |
878 |
> |
simError(); |
879 |
> |
} |
880 |
> |
} |
881 |
> |
} |
882 |
> |
} |
883 |
|
|
884 |
< |
void SimInfo::addProperty(GenericData* genData) { |
884 |
> |
|
885 |
> |
if (simParams_->haveSkinThickness()) { |
886 |
> |
double skinThickness = simParams_->getSkinThickness(); |
887 |
> |
} |
888 |
> |
|
889 |
> |
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp); |
890 |
> |
// also send cutoff notification to electrostatics |
891 |
> |
setElectrostaticCutoffRadius(&rcut_); |
892 |
> |
} |
893 |
> |
|
894 |
> |
void SimInfo::setupElectrostaticSummationMethod( int isError ) { |
895 |
> |
|
896 |
> |
int errorOut; |
897 |
> |
int esm = NONE; |
898 |
> |
double alphaVal; |
899 |
> |
double dielectric; |
900 |
> |
|
901 |
> |
errorOut = isError; |
902 |
> |
alphaVal = simParams_->getDampingAlpha(); |
903 |
> |
dielectric = simParams_->getDielectric(); |
904 |
> |
|
905 |
> |
if (simParams_->haveElectrostaticSummationMethod()) { |
906 |
> |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
907 |
> |
toUpper(myMethod); |
908 |
> |
if (myMethod == "NONE") { |
909 |
> |
esm = NONE; |
910 |
> |
} else { |
911 |
> |
if (myMethod == "UNDAMPED_WOLF") { |
912 |
> |
esm = UNDAMPED_WOLF; |
913 |
> |
} else { |
914 |
> |
if (myMethod == "DAMPED_WOLF") { |
915 |
> |
esm = DAMPED_WOLF; |
916 |
> |
if (!simParams_->haveDampingAlpha()) { |
917 |
> |
//throw error |
918 |
> |
sprintf( painCave.errMsg, |
919 |
> |
"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used for the Damped Wolf Method.", alphaVal); |
920 |
> |
painCave.isFatal = 0; |
921 |
> |
simError(); |
922 |
> |
} |
923 |
> |
} else { |
924 |
> |
if (myMethod == "REACTION_FIELD") { |
925 |
> |
esm = REACTION_FIELD; |
926 |
> |
} else { |
927 |
> |
// throw error |
928 |
> |
sprintf( painCave.errMsg, |
929 |
> |
"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"undamped_wolf\", \"damped_wolf\", or \"reaction_field\".", myMethod.c_str() ); |
930 |
> |
painCave.isFatal = 1; |
931 |
> |
simError(); |
932 |
> |
} |
933 |
> |
} |
934 |
> |
} |
935 |
> |
} |
936 |
> |
} |
937 |
> |
// let's pass some summation method variables to fortran |
938 |
> |
setElectrostaticSummationMethod( &esm ); |
939 |
> |
setDampedWolfAlpha( &alphaVal ); |
940 |
> |
setReactionFieldDielectric( &dielectric ); |
941 |
> |
initFortranFF( &esm, &errorOut ); |
942 |
> |
} |
943 |
> |
|
944 |
> |
void SimInfo::addProperty(GenericData* genData) { |
945 |
|
properties_.addProperty(genData); |
946 |
< |
} |
946 |
> |
} |
947 |
|
|
948 |
< |
void SimInfo::removeProperty(const std::string& propName) { |
948 |
> |
void SimInfo::removeProperty(const std::string& propName) { |
949 |
|
properties_.removeProperty(propName); |
950 |
< |
} |
950 |
> |
} |
951 |
|
|
952 |
< |
void SimInfo::clearProperties() { |
952 |
> |
void SimInfo::clearProperties() { |
953 |
|
properties_.clearProperties(); |
954 |
< |
} |
954 |
> |
} |
955 |
|
|
956 |
< |
std::vector<std::string> SimInfo::getPropertyNames() { |
956 |
> |
std::vector<std::string> SimInfo::getPropertyNames() { |
957 |
|
return properties_.getPropertyNames(); |
958 |
< |
} |
958 |
> |
} |
959 |
|
|
960 |
< |
std::vector<GenericData*> SimInfo::getProperties() { |
961 |
< |
return properties_.getProperties(); |
962 |
< |
} |
960 |
> |
std::vector<GenericData*> SimInfo::getProperties() { |
961 |
> |
return properties_.getProperties(); |
962 |
> |
} |
963 |
|
|
964 |
< |
GenericData* SimInfo::getPropertyByName(const std::string& propName) { |
964 |
> |
GenericData* SimInfo::getPropertyByName(const std::string& propName) { |
965 |
|
return properties_.getPropertyByName(propName); |
966 |
< |
} |
966 |
> |
} |
967 |
|
|
968 |
< |
void SimInfo::setSnapshotManager(SnapshotManager* sman) { |
969 |
< |
//if (sman_ == sman_) { |
970 |
< |
// return; |
971 |
< |
//} |
972 |
< |
|
846 |
< |
//delete sman_; |
968 |
> |
void SimInfo::setSnapshotManager(SnapshotManager* sman) { |
969 |
> |
if (sman_ == sman) { |
970 |
> |
return; |
971 |
> |
} |
972 |
> |
delete sman_; |
973 |
|
sman_ = sman; |
974 |
|
|
975 |
|
Molecule* mol; |
981 |
|
|
982 |
|
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
983 |
|
|
984 |
< |
for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) { |
985 |
< |
atom->setSnapshotManager(sman_); |
986 |
< |
} |
984 |
> |
for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) { |
985 |
> |
atom->setSnapshotManager(sman_); |
986 |
> |
} |
987 |
|
|
988 |
< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
989 |
< |
rb->setSnapshotManager(sman_); |
990 |
< |
} |
988 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
989 |
> |
rb->setSnapshotManager(sman_); |
990 |
> |
} |
991 |
|
} |
992 |
|
|
993 |
< |
} |
993 |
> |
} |
994 |
|
|
995 |
< |
Vector3d SimInfo::getComVel(){ |
995 |
> |
Vector3d SimInfo::getComVel(){ |
996 |
|
SimInfo::MoleculeIterator i; |
997 |
|
Molecule* mol; |
998 |
|
|
1001 |
|
|
1002 |
|
|
1003 |
|
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1004 |
< |
double mass = mol->getMass(); |
1005 |
< |
totalMass += mass; |
1006 |
< |
comVel += mass * mol->getComVel(); |
1004 |
> |
double mass = mol->getMass(); |
1005 |
> |
totalMass += mass; |
1006 |
> |
comVel += mass * mol->getComVel(); |
1007 |
|
} |
1008 |
|
|
1009 |
|
#ifdef IS_MPI |
1016 |
|
comVel /= totalMass; |
1017 |
|
|
1018 |
|
return comVel; |
1019 |
< |
} |
1019 |
> |
} |
1020 |
|
|
1021 |
< |
Vector3d SimInfo::getCom(){ |
1021 |
> |
Vector3d SimInfo::getCom(){ |
1022 |
|
SimInfo::MoleculeIterator i; |
1023 |
|
Molecule* mol; |
1024 |
|
|
1026 |
|
double totalMass = 0.0; |
1027 |
|
|
1028 |
|
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1029 |
< |
double mass = mol->getMass(); |
1030 |
< |
totalMass += mass; |
1031 |
< |
com += mass * mol->getCom(); |
1029 |
> |
double mass = mol->getMass(); |
1030 |
> |
totalMass += mass; |
1031 |
> |
com += mass * mol->getCom(); |
1032 |
|
} |
1033 |
|
|
1034 |
|
#ifdef IS_MPI |
1042 |
|
|
1043 |
|
return com; |
1044 |
|
|
1045 |
< |
} |
1045 |
> |
} |
1046 |
|
|
1047 |
< |
std::ostream& operator <<(std::ostream& o, SimInfo& info) { |
1047 |
> |
std::ostream& operator <<(std::ostream& o, SimInfo& info) { |
1048 |
|
|
1049 |
|
return o; |
1050 |
< |
} |
1050 |
> |
} |
1051 |
> |
|
1052 |
> |
|
1053 |
> |
/* |
1054 |
> |
Returns center of mass and center of mass velocity in one function call. |
1055 |
> |
*/ |
1056 |
> |
|
1057 |
> |
void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){ |
1058 |
> |
SimInfo::MoleculeIterator i; |
1059 |
> |
Molecule* mol; |
1060 |
> |
|
1061 |
> |
|
1062 |
> |
double totalMass = 0.0; |
1063 |
> |
|
1064 |
|
|
1065 |
+ |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1066 |
+ |
double mass = mol->getMass(); |
1067 |
+ |
totalMass += mass; |
1068 |
+ |
com += mass * mol->getCom(); |
1069 |
+ |
comVel += mass * mol->getComVel(); |
1070 |
+ |
} |
1071 |
+ |
|
1072 |
+ |
#ifdef IS_MPI |
1073 |
+ |
double tmpMass = totalMass; |
1074 |
+ |
Vector3d tmpCom(com); |
1075 |
+ |
Vector3d tmpComVel(comVel); |
1076 |
+ |
MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1077 |
+ |
MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1078 |
+ |
MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1079 |
+ |
#endif |
1080 |
+ |
|
1081 |
+ |
com /= totalMass; |
1082 |
+ |
comVel /= totalMass; |
1083 |
+ |
} |
1084 |
+ |
|
1085 |
+ |
/* |
1086 |
+ |
Return intertia tensor for entire system and angular momentum Vector. |
1087 |
+ |
|
1088 |
+ |
|
1089 |
+ |
[ Ixx -Ixy -Ixz ] |
1090 |
+ |
J =| -Iyx Iyy -Iyz | |
1091 |
+ |
[ -Izx -Iyz Izz ] |
1092 |
+ |
*/ |
1093 |
+ |
|
1094 |
+ |
void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){ |
1095 |
+ |
|
1096 |
+ |
|
1097 |
+ |
double xx = 0.0; |
1098 |
+ |
double yy = 0.0; |
1099 |
+ |
double zz = 0.0; |
1100 |
+ |
double xy = 0.0; |
1101 |
+ |
double xz = 0.0; |
1102 |
+ |
double yz = 0.0; |
1103 |
+ |
Vector3d com(0.0); |
1104 |
+ |
Vector3d comVel(0.0); |
1105 |
+ |
|
1106 |
+ |
getComAll(com, comVel); |
1107 |
+ |
|
1108 |
+ |
SimInfo::MoleculeIterator i; |
1109 |
+ |
Molecule* mol; |
1110 |
+ |
|
1111 |
+ |
Vector3d thisq(0.0); |
1112 |
+ |
Vector3d thisv(0.0); |
1113 |
+ |
|
1114 |
+ |
double thisMass = 0.0; |
1115 |
+ |
|
1116 |
+ |
|
1117 |
+ |
|
1118 |
+ |
|
1119 |
+ |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1120 |
+ |
|
1121 |
+ |
thisq = mol->getCom()-com; |
1122 |
+ |
thisv = mol->getComVel()-comVel; |
1123 |
+ |
thisMass = mol->getMass(); |
1124 |
+ |
// Compute moment of intertia coefficients. |
1125 |
+ |
xx += thisq[0]*thisq[0]*thisMass; |
1126 |
+ |
yy += thisq[1]*thisq[1]*thisMass; |
1127 |
+ |
zz += thisq[2]*thisq[2]*thisMass; |
1128 |
+ |
|
1129 |
+ |
// compute products of intertia |
1130 |
+ |
xy += thisq[0]*thisq[1]*thisMass; |
1131 |
+ |
xz += thisq[0]*thisq[2]*thisMass; |
1132 |
+ |
yz += thisq[1]*thisq[2]*thisMass; |
1133 |
+ |
|
1134 |
+ |
angularMomentum += cross( thisq, thisv ) * thisMass; |
1135 |
+ |
|
1136 |
+ |
} |
1137 |
+ |
|
1138 |
+ |
|
1139 |
+ |
inertiaTensor(0,0) = yy + zz; |
1140 |
+ |
inertiaTensor(0,1) = -xy; |
1141 |
+ |
inertiaTensor(0,2) = -xz; |
1142 |
+ |
inertiaTensor(1,0) = -xy; |
1143 |
+ |
inertiaTensor(1,1) = xx + zz; |
1144 |
+ |
inertiaTensor(1,2) = -yz; |
1145 |
+ |
inertiaTensor(2,0) = -xz; |
1146 |
+ |
inertiaTensor(2,1) = -yz; |
1147 |
+ |
inertiaTensor(2,2) = xx + yy; |
1148 |
+ |
|
1149 |
+ |
#ifdef IS_MPI |
1150 |
+ |
Mat3x3d tmpI(inertiaTensor); |
1151 |
+ |
Vector3d tmpAngMom; |
1152 |
+ |
MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1153 |
+ |
MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1154 |
+ |
#endif |
1155 |
+ |
|
1156 |
+ |
return; |
1157 |
+ |
} |
1158 |
+ |
|
1159 |
+ |
//Returns the angular momentum of the system |
1160 |
+ |
Vector3d SimInfo::getAngularMomentum(){ |
1161 |
+ |
|
1162 |
+ |
Vector3d com(0.0); |
1163 |
+ |
Vector3d comVel(0.0); |
1164 |
+ |
Vector3d angularMomentum(0.0); |
1165 |
+ |
|
1166 |
+ |
getComAll(com,comVel); |
1167 |
+ |
|
1168 |
+ |
SimInfo::MoleculeIterator i; |
1169 |
+ |
Molecule* mol; |
1170 |
+ |
|
1171 |
+ |
Vector3d thisr(0.0); |
1172 |
+ |
Vector3d thisp(0.0); |
1173 |
+ |
|
1174 |
+ |
double thisMass; |
1175 |
+ |
|
1176 |
+ |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1177 |
+ |
thisMass = mol->getMass(); |
1178 |
+ |
thisr = mol->getCom()-com; |
1179 |
+ |
thisp = (mol->getComVel()-comVel)*thisMass; |
1180 |
+ |
|
1181 |
+ |
angularMomentum += cross( thisr, thisp ); |
1182 |
+ |
|
1183 |
+ |
} |
1184 |
+ |
|
1185 |
+ |
#ifdef IS_MPI |
1186 |
+ |
Vector3d tmpAngMom; |
1187 |
+ |
MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1188 |
+ |
#endif |
1189 |
+ |
|
1190 |
+ |
return angularMomentum; |
1191 |
+ |
} |
1192 |
+ |
|
1193 |
+ |
|
1194 |
|
}//end namespace oopse |
1195 |
|
|