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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/notifyCutoffs_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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#ifdef IS_MPI |
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#include "UseTheForce/mpiComponentPlan.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) { |
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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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//calculate atoms in rigid bodies |
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int nAtomsInRigidBodies = 0; |
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int nRigidBodiesInStamp = molStamp->getNCutoffGroups(); |
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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 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 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 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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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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} |
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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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delete stamps_; |
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delete sman_; |
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delete simParams_; |
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delete forceField_; |
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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 |
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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)) { |
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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(); |
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> |
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(); |
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< |
exclude_.addPair(a, b); |
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exclude_.addPair(a, c); |
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exclude_.addPair(a, d); |
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< |
exclude_.addPair(b, c); |
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< |
exclude_.addPair(b, d); |
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< |
exclude_.addPair(c, d); |
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> |
exclude_.addPair(a, b); |
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> |
exclude_.addPair(a, c); |
365 |
> |
exclude_.addPair(a, d); |
366 |
> |
exclude_.addPair(b, c); |
367 |
> |
exclude_.addPair(b, d); |
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> |
exclude_.addPair(c, d); |
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} |
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< |
|
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} |
371 |
> |
Molecule::RigidBodyIterator rbIter; |
372 |
> |
RigidBody* rb; |
373 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
374 |
> |
std::vector<Atom*> atoms = rb->getAtoms(); |
375 |
> |
for (int i = 0; i < atoms.size() -1 ; ++i) { |
376 |
> |
for (int j = i + 1; j < atoms.size(); ++j) { |
377 |
> |
a = atoms[i]->getGlobalIndex(); |
378 |
> |
b = atoms[j]->getGlobalIndex(); |
379 |
> |
exclude_.addPair(a, b); |
380 |
> |
} |
381 |
> |
} |
382 |
> |
} |
383 |
|
|
384 |
< |
void SimInfo::removeExcludePairs(Molecule* mol) { |
384 |
> |
} |
385 |
> |
|
386 |
> |
void SimInfo::removeExcludePairs(Molecule* mol) { |
387 |
|
std::vector<Bond*>::iterator bondIter; |
388 |
|
std::vector<Bend*>::iterator bendIter; |
389 |
|
std::vector<Torsion*>::iterator torsionIter; |
396 |
|
int d; |
397 |
|
|
398 |
|
for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { |
399 |
< |
a = bond->getAtomA()->getGlobalIndex(); |
400 |
< |
b = bond->getAtomB()->getGlobalIndex(); |
401 |
< |
exclude_.removePair(a, b); |
399 |
> |
a = bond->getAtomA()->getGlobalIndex(); |
400 |
> |
b = bond->getAtomB()->getGlobalIndex(); |
401 |
> |
exclude_.removePair(a, b); |
402 |
|
} |
403 |
|
|
404 |
|
for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) { |
405 |
< |
a = bend->getAtomA()->getGlobalIndex(); |
406 |
< |
b = bend->getAtomB()->getGlobalIndex(); |
407 |
< |
c = bend->getAtomC()->getGlobalIndex(); |
405 |
> |
a = bend->getAtomA()->getGlobalIndex(); |
406 |
> |
b = bend->getAtomB()->getGlobalIndex(); |
407 |
> |
c = bend->getAtomC()->getGlobalIndex(); |
408 |
|
|
409 |
< |
exclude_.removePair(a, b); |
410 |
< |
exclude_.removePair(a, c); |
411 |
< |
exclude_.removePair(b, c); |
409 |
> |
exclude_.removePair(a, b); |
410 |
> |
exclude_.removePair(a, c); |
411 |
> |
exclude_.removePair(b, c); |
412 |
|
} |
413 |
|
|
414 |
|
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
415 |
< |
a = torsion->getAtomA()->getGlobalIndex(); |
416 |
< |
b = torsion->getAtomB()->getGlobalIndex(); |
417 |
< |
c = torsion->getAtomC()->getGlobalIndex(); |
418 |
< |
d = torsion->getAtomD()->getGlobalIndex(); |
415 |
> |
a = torsion->getAtomA()->getGlobalIndex(); |
416 |
> |
b = torsion->getAtomB()->getGlobalIndex(); |
417 |
> |
c = torsion->getAtomC()->getGlobalIndex(); |
418 |
> |
d = torsion->getAtomD()->getGlobalIndex(); |
419 |
|
|
420 |
< |
exclude_.removePair(a, b); |
421 |
< |
exclude_.removePair(a, c); |
422 |
< |
exclude_.removePair(a, d); |
423 |
< |
exclude_.removePair(b, c); |
424 |
< |
exclude_.removePair(b, d); |
425 |
< |
exclude_.removePair(c, d); |
420 |
> |
exclude_.removePair(a, b); |
421 |
> |
exclude_.removePair(a, c); |
422 |
> |
exclude_.removePair(a, d); |
423 |
> |
exclude_.removePair(b, c); |
424 |
> |
exclude_.removePair(b, d); |
425 |
> |
exclude_.removePair(c, d); |
426 |
|
} |
427 |
|
|
428 |
< |
} |
428 |
> |
Molecule::RigidBodyIterator rbIter; |
429 |
> |
RigidBody* rb; |
430 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
431 |
> |
std::vector<Atom*> atoms = rb->getAtoms(); |
432 |
> |
for (int i = 0; i < atoms.size() -1 ; ++i) { |
433 |
> |
for (int j = i + 1; j < atoms.size(); ++j) { |
434 |
> |
a = atoms[i]->getGlobalIndex(); |
435 |
> |
b = atoms[j]->getGlobalIndex(); |
436 |
> |
exclude_.removePair(a, b); |
437 |
> |
} |
438 |
> |
} |
439 |
> |
} |
440 |
|
|
441 |
+ |
} |
442 |
|
|
443 |
< |
void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) { |
443 |
> |
|
444 |
> |
void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) { |
445 |
|
int curStampId; |
446 |
|
|
447 |
|
//index from 0 |
449 |
|
|
450 |
|
moleculeStamps_.push_back(molStamp); |
451 |
|
molStampIds_.insert(molStampIds_.end(), nmol, curStampId); |
452 |
< |
} |
452 |
> |
} |
453 |
|
|
454 |
< |
void SimInfo::update() { |
454 |
> |
void SimInfo::update() { |
455 |
|
|
456 |
|
setupSimType(); |
457 |
|
|
464 |
|
//setup fortran force field |
465 |
|
/** @deprecate */ |
466 |
|
int isError = 0; |
467 |
< |
initFortranFF( &fInfo_.SIM_uses_RF , &isError ); |
467 |
> |
|
468 |
> |
setupElectrostaticSummationMethod( isError ); |
469 |
> |
|
470 |
|
if(isError){ |
471 |
< |
sprintf( painCave.errMsg, |
472 |
< |
"ForceField error: There was an error initializing the forceField in fortran.\n" ); |
473 |
< |
painCave.isFatal = 1; |
474 |
< |
simError(); |
471 |
> |
sprintf( painCave.errMsg, |
472 |
> |
"ForceField error: There was an error initializing the forceField in fortran.\n" ); |
473 |
> |
painCave.isFatal = 1; |
474 |
> |
simError(); |
475 |
|
} |
476 |
|
|
477 |
|
|
482 |
|
calcNdfTrans(); |
483 |
|
|
484 |
|
fortranInitialized_ = true; |
485 |
< |
} |
485 |
> |
} |
486 |
|
|
487 |
< |
std::set<AtomType*> SimInfo::getUniqueAtomTypes() { |
487 |
> |
std::set<AtomType*> SimInfo::getUniqueAtomTypes() { |
488 |
|
SimInfo::MoleculeIterator mi; |
489 |
|
Molecule* mol; |
490 |
|
Molecule::AtomIterator ai; |
493 |
|
|
494 |
|
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
495 |
|
|
496 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
497 |
< |
atomTypes.insert(atom->getAtomType()); |
498 |
< |
} |
496 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
497 |
> |
atomTypes.insert(atom->getAtomType()); |
498 |
> |
} |
499 |
|
|
500 |
|
} |
501 |
|
|
502 |
|
return atomTypes; |
503 |
< |
} |
503 |
> |
} |
504 |
|
|
505 |
< |
void SimInfo::setupSimType() { |
505 |
> |
void SimInfo::setupSimType() { |
506 |
|
std::set<AtomType*>::iterator i; |
507 |
|
std::set<AtomType*> atomTypes; |
508 |
|
atomTypes = getUniqueAtomTypes(); |
515 |
|
int useDipole = 0; |
516 |
|
int useGayBerne = 0; |
517 |
|
int useSticky = 0; |
518 |
+ |
int useStickyPower = 0; |
519 |
|
int useShape = 0; |
520 |
|
int useFLARB = 0; //it is not in AtomType yet |
521 |
|
int useDirectionalAtom = 0; |
522 |
|
int useElectrostatics = 0; |
523 |
|
//usePBC and useRF are from simParams |
524 |
|
int usePBC = simParams_->getPBC(); |
492 |
– |
int useRF = simParams_->getUseRF(); |
525 |
|
|
526 |
|
//loop over all of the atom types |
527 |
|
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
528 |
< |
useLennardJones |= (*i)->isLennardJones(); |
529 |
< |
useElectrostatic |= (*i)->isElectrostatic(); |
530 |
< |
useEAM |= (*i)->isEAM(); |
531 |
< |
useCharge |= (*i)->isCharge(); |
532 |
< |
useDirectional |= (*i)->isDirectional(); |
533 |
< |
useDipole |= (*i)->isDipole(); |
534 |
< |
useGayBerne |= (*i)->isGayBerne(); |
535 |
< |
useSticky |= (*i)->isSticky(); |
536 |
< |
useShape |= (*i)->isShape(); |
528 |
> |
useLennardJones |= (*i)->isLennardJones(); |
529 |
> |
useElectrostatic |= (*i)->isElectrostatic(); |
530 |
> |
useEAM |= (*i)->isEAM(); |
531 |
> |
useCharge |= (*i)->isCharge(); |
532 |
> |
useDirectional |= (*i)->isDirectional(); |
533 |
> |
useDipole |= (*i)->isDipole(); |
534 |
> |
useGayBerne |= (*i)->isGayBerne(); |
535 |
> |
useSticky |= (*i)->isSticky(); |
536 |
> |
useStickyPower |= (*i)->isStickyPower(); |
537 |
> |
useShape |= (*i)->isShape(); |
538 |
|
} |
539 |
|
|
540 |
< |
if (useSticky || useDipole || useGayBerne || useShape) { |
541 |
< |
useDirectionalAtom = 1; |
540 |
> |
if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) { |
541 |
> |
useDirectionalAtom = 1; |
542 |
|
} |
543 |
|
|
544 |
|
if (useCharge || useDipole) { |
545 |
< |
useElectrostatics = 1; |
545 |
> |
useElectrostatics = 1; |
546 |
|
} |
547 |
|
|
548 |
|
#ifdef IS_MPI |
569 |
|
temp = useSticky; |
570 |
|
MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
571 |
|
|
572 |
+ |
temp = useStickyPower; |
573 |
+ |
MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
574 |
+ |
|
575 |
|
temp = useGayBerne; |
576 |
|
MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
577 |
|
|
584 |
|
temp = useFLARB; |
585 |
|
MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
586 |
|
|
551 |
– |
temp = useRF; |
552 |
– |
MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
553 |
– |
|
587 |
|
#endif |
588 |
|
|
589 |
|
fInfo_.SIM_uses_PBC = usePBC; |
593 |
|
fInfo_.SIM_uses_Charges = useCharge; |
594 |
|
fInfo_.SIM_uses_Dipoles = useDipole; |
595 |
|
fInfo_.SIM_uses_Sticky = useSticky; |
596 |
+ |
fInfo_.SIM_uses_StickyPower = useStickyPower; |
597 |
|
fInfo_.SIM_uses_GayBerne = useGayBerne; |
598 |
|
fInfo_.SIM_uses_EAM = useEAM; |
599 |
|
fInfo_.SIM_uses_Shapes = useShape; |
600 |
|
fInfo_.SIM_uses_FLARB = useFLARB; |
567 |
– |
fInfo_.SIM_uses_RF = useRF; |
601 |
|
|
602 |
|
if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { |
603 |
|
|
604 |
< |
if (simParams_->haveDielectric()) { |
605 |
< |
fInfo_.dielect = simParams_->getDielectric(); |
606 |
< |
} else { |
607 |
< |
sprintf(painCave.errMsg, |
608 |
< |
"SimSetup Error: No Dielectric constant was set.\n" |
609 |
< |
"\tYou are trying to use Reaction Field without" |
610 |
< |
"\tsetting a dielectric constant!\n"); |
611 |
< |
painCave.isFatal = 1; |
612 |
< |
simError(); |
613 |
< |
} |
604 |
> |
if (simParams_->haveDielectric()) { |
605 |
> |
fInfo_.dielect = simParams_->getDielectric(); |
606 |
> |
} else { |
607 |
> |
sprintf(painCave.errMsg, |
608 |
> |
"SimSetup Error: No Dielectric constant was set.\n" |
609 |
> |
"\tYou are trying to use Reaction Field without" |
610 |
> |
"\tsetting a dielectric constant!\n"); |
611 |
> |
painCave.isFatal = 1; |
612 |
> |
simError(); |
613 |
> |
} |
614 |
|
|
615 |
|
} else { |
616 |
< |
fInfo_.dielect = 0.0; |
616 |
> |
fInfo_.dielect = 0.0; |
617 |
|
} |
618 |
|
|
619 |
< |
} |
619 |
> |
} |
620 |
|
|
621 |
< |
void SimInfo::setupFortranSim() { |
621 |
> |
void SimInfo::setupFortranSim() { |
622 |
|
int isError; |
623 |
|
int nExclude; |
624 |
|
std::vector<int> fortranGlobalGroupMembership; |
628 |
|
|
629 |
|
//globalGroupMembership_ is filled by SimCreator |
630 |
|
for (int i = 0; i < nGlobalAtoms_; i++) { |
631 |
< |
fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1); |
631 |
> |
fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1); |
632 |
|
} |
633 |
|
|
634 |
|
//calculate mass ratio of cutoff group |
645 |
|
mfact.reserve(getNCutoffGroups()); |
646 |
|
|
647 |
|
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
648 |
< |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
648 |
> |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
649 |
|
|
650 |
< |
totalMass = cg->getMass(); |
651 |
< |
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
652 |
< |
mfact.push_back(atom->getMass()/totalMass); |
653 |
< |
} |
650 |
> |
totalMass = cg->getMass(); |
651 |
> |
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
652 |
> |
mfact.push_back(atom->getMass()/totalMass); |
653 |
> |
} |
654 |
|
|
655 |
< |
} |
655 |
> |
} |
656 |
|
} |
657 |
|
|
658 |
|
//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!) |
662 |
|
identArray.reserve(getNAtoms()); |
663 |
|
|
664 |
|
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
665 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
666 |
< |
identArray.push_back(atom->getIdent()); |
667 |
< |
} |
665 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
666 |
> |
identArray.push_back(atom->getIdent()); |
667 |
> |
} |
668 |
|
} |
669 |
|
|
670 |
|
//fill molMembershipArray |
671 |
|
//molMembershipArray is filled by SimCreator |
672 |
|
std::vector<int> molMembershipArray(nGlobalAtoms_); |
673 |
|
for (int i = 0; i < nGlobalAtoms_; i++) { |
674 |
< |
molMembershipArray[i] = globalMolMembership_[i] + 1; |
674 |
> |
molMembershipArray[i] = globalMolMembership_[i] + 1; |
675 |
|
} |
676 |
|
|
677 |
|
//setup fortran simulation |
645 |
– |
//gloalExcludes and molMembershipArray should go away (They are never used) |
646 |
– |
//why the hell fortran need to know molecule? |
647 |
– |
//OOPSE = Object-Obfuscated Parallel Simulation Engine |
678 |
|
int nGlobalExcludes = 0; |
679 |
|
int* globalExcludes = NULL; |
680 |
|
int* excludeList = exclude_.getExcludeList(); |
681 |
|
setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList , |
682 |
< |
&nGlobalExcludes, globalExcludes, &molMembershipArray[0], |
683 |
< |
&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError); |
682 |
> |
&nGlobalExcludes, globalExcludes, &molMembershipArray[0], |
683 |
> |
&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError); |
684 |
|
|
685 |
|
if( isError ){ |
686 |
|
|
687 |
< |
sprintf( painCave.errMsg, |
688 |
< |
"There was an error setting the simulation information in fortran.\n" ); |
689 |
< |
painCave.isFatal = 1; |
690 |
< |
painCave.severity = OOPSE_ERROR; |
691 |
< |
simError(); |
687 |
> |
sprintf( painCave.errMsg, |
688 |
> |
"There was an error setting the simulation information in fortran.\n" ); |
689 |
> |
painCave.isFatal = 1; |
690 |
> |
painCave.severity = OOPSE_ERROR; |
691 |
> |
simError(); |
692 |
|
} |
693 |
|
|
694 |
|
#ifdef IS_MPI |
695 |
|
sprintf( checkPointMsg, |
696 |
< |
"succesfully sent the simulation information to fortran.\n"); |
696 |
> |
"succesfully sent the simulation information to fortran.\n"); |
697 |
|
MPIcheckPoint(); |
698 |
|
#endif // is_mpi |
699 |
< |
} |
699 |
> |
} |
700 |
|
|
701 |
|
|
702 |
|
#ifdef IS_MPI |
703 |
< |
void SimInfo::setupFortranParallel() { |
703 |
> |
void SimInfo::setupFortranParallel() { |
704 |
|
|
705 |
|
//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex |
706 |
|
std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0); |
716 |
|
|
717 |
|
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
718 |
|
|
719 |
< |
//local index(index in DataStorge) of atom is important |
720 |
< |
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
721 |
< |
localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1; |
722 |
< |
} |
719 |
> |
//local index(index in DataStorge) of atom is important |
720 |
> |
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
721 |
> |
localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1; |
722 |
> |
} |
723 |
|
|
724 |
< |
//local index of cutoff group is trivial, it only depends on the order of travesing |
725 |
< |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
726 |
< |
localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1); |
727 |
< |
} |
724 |
> |
//local index of cutoff group is trivial, it only depends on the order of travesing |
725 |
> |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
726 |
> |
localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1); |
727 |
> |
} |
728 |
|
|
729 |
|
} |
730 |
|
|
744 |
|
&localToGlobalCutoffGroupIndex[0], &isError); |
745 |
|
|
746 |
|
if (isError) { |
747 |
< |
sprintf(painCave.errMsg, |
748 |
< |
"mpiRefresh errror: fortran didn't like something we gave it.\n"); |
749 |
< |
painCave.isFatal = 1; |
750 |
< |
simError(); |
747 |
> |
sprintf(painCave.errMsg, |
748 |
> |
"mpiRefresh errror: fortran didn't like something we gave it.\n"); |
749 |
> |
painCave.isFatal = 1; |
750 |
> |
simError(); |
751 |
|
} |
752 |
|
|
753 |
|
sprintf(checkPointMsg, " mpiRefresh successful.\n"); |
754 |
|
MPIcheckPoint(); |
755 |
|
|
756 |
|
|
757 |
< |
} |
757 |
> |
} |
758 |
|
|
759 |
|
#endif |
760 |
|
|
761 |
< |
double SimInfo::calcMaxCutoffRadius() { |
761 |
> |
double SimInfo::calcMaxCutoffRadius() { |
762 |
|
|
763 |
|
|
764 |
|
std::set<AtomType*> atomTypes; |
770 |
|
|
771 |
|
//query the max cutoff radius among these atom types |
772 |
|
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
773 |
< |
cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i)); |
773 |
> |
cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i)); |
774 |
|
} |
775 |
|
|
776 |
|
double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end())); |
779 |
|
#endif |
780 |
|
|
781 |
|
return maxCutoffRadius; |
782 |
< |
} |
782 |
> |
} |
783 |
|
|
784 |
< |
void SimInfo::setupCutoff() { |
755 |
< |
double rcut_; //cutoff radius |
756 |
< |
double rsw_; //switching radius |
784 |
> |
void SimInfo::getCutoff(double& rcut, double& rsw) { |
785 |
|
|
786 |
|
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
787 |
|
|
788 |
< |
if (!simParams_->haveRcut()){ |
789 |
< |
sprintf(painCave.errMsg, |
788 |
> |
if (!simParams_->haveRcut()){ |
789 |
> |
sprintf(painCave.errMsg, |
790 |
|
"SimCreator Warning: No value was set for the cutoffRadius.\n" |
791 |
|
"\tOOPSE will use a default value of 15.0 angstroms" |
792 |
|
"\tfor the cutoffRadius.\n"); |
793 |
< |
painCave.isFatal = 0; |
794 |
< |
simError(); |
795 |
< |
rcut_ = 15.0; |
796 |
< |
} else{ |
797 |
< |
rcut_ = simParams_->getRcut(); |
798 |
< |
} |
793 |
> |
painCave.isFatal = 0; |
794 |
> |
simError(); |
795 |
> |
rcut = 15.0; |
796 |
> |
} else{ |
797 |
> |
rcut = simParams_->getRcut(); |
798 |
> |
} |
799 |
|
|
800 |
< |
if (!simParams_->haveRsw()){ |
801 |
< |
sprintf(painCave.errMsg, |
800 |
> |
if (!simParams_->haveRsw()){ |
801 |
> |
sprintf(painCave.errMsg, |
802 |
|
"SimCreator Warning: No value was set for switchingRadius.\n" |
803 |
|
"\tOOPSE will use a default value of\n" |
804 |
|
"\t0.95 * cutoffRadius for the switchingRadius\n"); |
805 |
< |
painCave.isFatal = 0; |
806 |
< |
simError(); |
807 |
< |
rsw_ = 0.95 * rcut_; |
808 |
< |
} else{ |
809 |
< |
rsw_ = simParams_->getRsw(); |
810 |
< |
} |
805 |
> |
painCave.isFatal = 0; |
806 |
> |
simError(); |
807 |
> |
rsw = 0.95 * rcut; |
808 |
> |
} else{ |
809 |
> |
rsw = simParams_->getRsw(); |
810 |
> |
} |
811 |
|
|
812 |
|
} else { |
813 |
< |
// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
814 |
< |
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
813 |
> |
// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
814 |
> |
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
815 |
|
|
816 |
< |
if (simParams_->haveRcut()) { |
817 |
< |
rcut_ = simParams_->getRcut(); |
818 |
< |
} else { |
819 |
< |
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
820 |
< |
rcut_ = calcMaxCutoffRadius(); |
821 |
< |
} |
816 |
> |
if (simParams_->haveRcut()) { |
817 |
> |
rcut = simParams_->getRcut(); |
818 |
> |
} else { |
819 |
> |
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
820 |
> |
rcut = calcMaxCutoffRadius(); |
821 |
> |
} |
822 |
|
|
823 |
< |
if (simParams_->haveRsw()) { |
824 |
< |
rsw_ = simParams_->getRsw(); |
825 |
< |
} else { |
826 |
< |
rsw_ = rcut_; |
827 |
< |
} |
823 |
> |
if (simParams_->haveRsw()) { |
824 |
> |
rsw = simParams_->getRsw(); |
825 |
> |
} else { |
826 |
> |
rsw = rcut; |
827 |
> |
} |
828 |
|
|
829 |
|
} |
830 |
< |
|
830 |
> |
} |
831 |
> |
|
832 |
> |
void SimInfo::setupCutoff() { |
833 |
> |
getCutoff(rcut_, rsw_); |
834 |
|
double rnblist = rcut_ + 1; // skin of neighbor list |
835 |
|
|
836 |
|
//Pass these cutoff radius etc. to fortran. This function should be called once and only once |
837 |
< |
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist); |
838 |
< |
} |
837 |
> |
|
838 |
> |
int cp = TRADITIONAL_CUTOFF_POLICY; |
839 |
> |
if (simParams_->haveCutoffPolicy()) { |
840 |
> |
std::string myPolicy = simParams_->getCutoffPolicy(); |
841 |
> |
if (myPolicy == "MIX") { |
842 |
> |
cp = MIX_CUTOFF_POLICY; |
843 |
> |
} else { |
844 |
> |
if (myPolicy == "MAX") { |
845 |
> |
cp = MAX_CUTOFF_POLICY; |
846 |
> |
} else { |
847 |
> |
if (myPolicy == "TRADITIONAL") { |
848 |
> |
cp = TRADITIONAL_CUTOFF_POLICY; |
849 |
> |
} else { |
850 |
> |
// throw error |
851 |
> |
sprintf( painCave.errMsg, |
852 |
> |
"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() ); |
853 |
> |
painCave.isFatal = 1; |
854 |
> |
simError(); |
855 |
> |
} |
856 |
> |
} |
857 |
> |
} |
858 |
> |
} |
859 |
> |
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp); |
860 |
> |
} |
861 |
|
|
862 |
< |
void SimInfo::addProperty(GenericData* genData) { |
862 |
> |
void SimInfo::setupElectrostaticSummationMethod( int isError ) { |
863 |
> |
|
864 |
> |
int errorOut; |
865 |
> |
int esm = NONE; |
866 |
> |
double alphaVal; |
867 |
> |
|
868 |
> |
errorOut = isError; |
869 |
> |
|
870 |
> |
if (simParams_->haveElectrostaticSummationMethod()) { |
871 |
> |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
872 |
> |
if (myMethod == "NONE") { |
873 |
> |
esm = NONE; |
874 |
> |
} else { |
875 |
> |
if (myMethod == "UNDAMPED_WOLF") { |
876 |
> |
esm = UNDAMPED_WOLF; |
877 |
> |
} else { |
878 |
> |
if (myMethod == "DAMPED_WOLF") { |
879 |
> |
esm = DAMPED_WOLF; |
880 |
> |
if (!simParams_->haveDampingAlpha()) { |
881 |
> |
//throw error |
882 |
> |
sprintf( painCave.errMsg, |
883 |
> |
"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.", simParams_->getDampingAlpha()); |
884 |
> |
painCave.isFatal = 0; |
885 |
> |
simError(); |
886 |
> |
} |
887 |
> |
alphaVal = simParams_->getDampingAlpha(); |
888 |
> |
} else { |
889 |
> |
if (myMethod == "REACTION_FIELD") { |
890 |
> |
esm = REACTION_FIELD; |
891 |
> |
} else { |
892 |
> |
// throw error |
893 |
> |
sprintf( painCave.errMsg, |
894 |
> |
"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() ); |
895 |
> |
painCave.isFatal = 1; |
896 |
> |
simError(); |
897 |
> |
} |
898 |
> |
} |
899 |
> |
} |
900 |
> |
} |
901 |
> |
} |
902 |
> |
initFortranFF( &fInfo_.SIM_uses_RF, &esm, &alphaVal, &errorOut ); |
903 |
> |
} |
904 |
> |
|
905 |
> |
void SimInfo::addProperty(GenericData* genData) { |
906 |
|
properties_.addProperty(genData); |
907 |
< |
} |
907 |
> |
} |
908 |
|
|
909 |
< |
void SimInfo::removeProperty(const std::string& propName) { |
909 |
> |
void SimInfo::removeProperty(const std::string& propName) { |
910 |
|
properties_.removeProperty(propName); |
911 |
< |
} |
911 |
> |
} |
912 |
|
|
913 |
< |
void SimInfo::clearProperties() { |
913 |
> |
void SimInfo::clearProperties() { |
914 |
|
properties_.clearProperties(); |
915 |
< |
} |
915 |
> |
} |
916 |
|
|
917 |
< |
std::vector<std::string> SimInfo::getPropertyNames() { |
917 |
> |
std::vector<std::string> SimInfo::getPropertyNames() { |
918 |
|
return properties_.getPropertyNames(); |
919 |
< |
} |
919 |
> |
} |
920 |
|
|
921 |
< |
std::vector<GenericData*> SimInfo::getProperties() { |
921 |
> |
std::vector<GenericData*> SimInfo::getProperties() { |
922 |
|
return properties_.getProperties(); |
923 |
< |
} |
924 |
< |
|
925 |
< |
GenericData* SimInfo::getPropertyByName(const std::string& propName) { |
923 |
> |
} |
924 |
> |
|
925 |
> |
GenericData* SimInfo::getPropertyByName(const std::string& propName) { |
926 |
|
return properties_.getPropertyByName(propName); |
927 |
< |
} |
927 |
> |
} |
928 |
|
|
929 |
< |
void SimInfo::setSnapshotManager(SnapshotManager* sman) { |
929 |
> |
void SimInfo::setSnapshotManager(SnapshotManager* sman) { |
930 |
> |
if (sman_ == sman) { |
931 |
> |
return; |
932 |
> |
} |
933 |
> |
delete sman_; |
934 |
|
sman_ = sman; |
935 |
|
|
936 |
|
Molecule* mol; |
942 |
|
|
943 |
|
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
944 |
|
|
945 |
< |
for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) { |
946 |
< |
atom->setSnapshotManager(sman_); |
947 |
< |
} |
945 |
> |
for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) { |
946 |
> |
atom->setSnapshotManager(sman_); |
947 |
> |
} |
948 |
|
|
949 |
< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
950 |
< |
rb->setSnapshotManager(sman_); |
951 |
< |
} |
949 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
950 |
> |
rb->setSnapshotManager(sman_); |
951 |
> |
} |
952 |
|
} |
953 |
|
|
954 |
< |
} |
954 |
> |
} |
955 |
|
|
956 |
< |
Vector3d SimInfo::getComVel(){ |
956 |
> |
Vector3d SimInfo::getComVel(){ |
957 |
|
SimInfo::MoleculeIterator i; |
958 |
|
Molecule* mol; |
959 |
|
|
962 |
|
|
963 |
|
|
964 |
|
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
965 |
< |
double mass = mol->getMass(); |
966 |
< |
totalMass += mass; |
967 |
< |
comVel += mass * mol->getComVel(); |
965 |
> |
double mass = mol->getMass(); |
966 |
> |
totalMass += mass; |
967 |
> |
comVel += mass * mol->getComVel(); |
968 |
|
} |
969 |
|
|
970 |
|
#ifdef IS_MPI |
977 |
|
comVel /= totalMass; |
978 |
|
|
979 |
|
return comVel; |
980 |
< |
} |
980 |
> |
} |
981 |
|
|
982 |
< |
Vector3d SimInfo::getCom(){ |
982 |
> |
Vector3d SimInfo::getCom(){ |
983 |
|
SimInfo::MoleculeIterator i; |
984 |
|
Molecule* mol; |
985 |
|
|
987 |
|
double totalMass = 0.0; |
988 |
|
|
989 |
|
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
990 |
< |
double mass = mol->getMass(); |
991 |
< |
totalMass += mass; |
992 |
< |
com += mass * mol->getCom(); |
990 |
> |
double mass = mol->getMass(); |
991 |
> |
totalMass += mass; |
992 |
> |
com += mass * mol->getCom(); |
993 |
|
} |
994 |
|
|
995 |
|
#ifdef IS_MPI |
1003 |
|
|
1004 |
|
return com; |
1005 |
|
|
1006 |
< |
} |
1006 |
> |
} |
1007 |
|
|
1008 |
< |
std::ostream& operator <<(std::ostream& o, SimInfo& info) { |
1008 |
> |
std::ostream& operator <<(std::ostream& o, SimInfo& info) { |
1009 |
|
|
1010 |
|
return o; |
1011 |
< |
} |
1011 |
> |
} |
1012 |
> |
|
1013 |
> |
|
1014 |
> |
/* |
1015 |
> |
Returns center of mass and center of mass velocity in one function call. |
1016 |
> |
*/ |
1017 |
> |
|
1018 |
> |
void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){ |
1019 |
> |
SimInfo::MoleculeIterator i; |
1020 |
> |
Molecule* mol; |
1021 |
> |
|
1022 |
> |
|
1023 |
> |
double totalMass = 0.0; |
1024 |
> |
|
1025 |
|
|
1026 |
+ |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1027 |
+ |
double mass = mol->getMass(); |
1028 |
+ |
totalMass += mass; |
1029 |
+ |
com += mass * mol->getCom(); |
1030 |
+ |
comVel += mass * mol->getComVel(); |
1031 |
+ |
} |
1032 |
+ |
|
1033 |
+ |
#ifdef IS_MPI |
1034 |
+ |
double tmpMass = totalMass; |
1035 |
+ |
Vector3d tmpCom(com); |
1036 |
+ |
Vector3d tmpComVel(comVel); |
1037 |
+ |
MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1038 |
+ |
MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1039 |
+ |
MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1040 |
+ |
#endif |
1041 |
+ |
|
1042 |
+ |
com /= totalMass; |
1043 |
+ |
comVel /= totalMass; |
1044 |
+ |
} |
1045 |
+ |
|
1046 |
+ |
/* |
1047 |
+ |
Return intertia tensor for entire system and angular momentum Vector. |
1048 |
+ |
|
1049 |
+ |
|
1050 |
+ |
[ Ixx -Ixy -Ixz ] |
1051 |
+ |
J =| -Iyx Iyy -Iyz | |
1052 |
+ |
[ -Izx -Iyz Izz ] |
1053 |
+ |
*/ |
1054 |
+ |
|
1055 |
+ |
void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){ |
1056 |
+ |
|
1057 |
+ |
|
1058 |
+ |
double xx = 0.0; |
1059 |
+ |
double yy = 0.0; |
1060 |
+ |
double zz = 0.0; |
1061 |
+ |
double xy = 0.0; |
1062 |
+ |
double xz = 0.0; |
1063 |
+ |
double yz = 0.0; |
1064 |
+ |
Vector3d com(0.0); |
1065 |
+ |
Vector3d comVel(0.0); |
1066 |
+ |
|
1067 |
+ |
getComAll(com, comVel); |
1068 |
+ |
|
1069 |
+ |
SimInfo::MoleculeIterator i; |
1070 |
+ |
Molecule* mol; |
1071 |
+ |
|
1072 |
+ |
Vector3d thisq(0.0); |
1073 |
+ |
Vector3d thisv(0.0); |
1074 |
+ |
|
1075 |
+ |
double thisMass = 0.0; |
1076 |
+ |
|
1077 |
+ |
|
1078 |
+ |
|
1079 |
+ |
|
1080 |
+ |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1081 |
+ |
|
1082 |
+ |
thisq = mol->getCom()-com; |
1083 |
+ |
thisv = mol->getComVel()-comVel; |
1084 |
+ |
thisMass = mol->getMass(); |
1085 |
+ |
// Compute moment of intertia coefficients. |
1086 |
+ |
xx += thisq[0]*thisq[0]*thisMass; |
1087 |
+ |
yy += thisq[1]*thisq[1]*thisMass; |
1088 |
+ |
zz += thisq[2]*thisq[2]*thisMass; |
1089 |
+ |
|
1090 |
+ |
// compute products of intertia |
1091 |
+ |
xy += thisq[0]*thisq[1]*thisMass; |
1092 |
+ |
xz += thisq[0]*thisq[2]*thisMass; |
1093 |
+ |
yz += thisq[1]*thisq[2]*thisMass; |
1094 |
+ |
|
1095 |
+ |
angularMomentum += cross( thisq, thisv ) * thisMass; |
1096 |
+ |
|
1097 |
+ |
} |
1098 |
+ |
|
1099 |
+ |
|
1100 |
+ |
inertiaTensor(0,0) = yy + zz; |
1101 |
+ |
inertiaTensor(0,1) = -xy; |
1102 |
+ |
inertiaTensor(0,2) = -xz; |
1103 |
+ |
inertiaTensor(1,0) = -xy; |
1104 |
+ |
inertiaTensor(1,1) = xx + zz; |
1105 |
+ |
inertiaTensor(1,2) = -yz; |
1106 |
+ |
inertiaTensor(2,0) = -xz; |
1107 |
+ |
inertiaTensor(2,1) = -yz; |
1108 |
+ |
inertiaTensor(2,2) = xx + yy; |
1109 |
+ |
|
1110 |
+ |
#ifdef IS_MPI |
1111 |
+ |
Mat3x3d tmpI(inertiaTensor); |
1112 |
+ |
Vector3d tmpAngMom; |
1113 |
+ |
MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1114 |
+ |
MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1115 |
+ |
#endif |
1116 |
+ |
|
1117 |
+ |
return; |
1118 |
+ |
} |
1119 |
+ |
|
1120 |
+ |
//Returns the angular momentum of the system |
1121 |
+ |
Vector3d SimInfo::getAngularMomentum(){ |
1122 |
+ |
|
1123 |
+ |
Vector3d com(0.0); |
1124 |
+ |
Vector3d comVel(0.0); |
1125 |
+ |
Vector3d angularMomentum(0.0); |
1126 |
+ |
|
1127 |
+ |
getComAll(com,comVel); |
1128 |
+ |
|
1129 |
+ |
SimInfo::MoleculeIterator i; |
1130 |
+ |
Molecule* mol; |
1131 |
+ |
|
1132 |
+ |
Vector3d thisr(0.0); |
1133 |
+ |
Vector3d thisp(0.0); |
1134 |
+ |
|
1135 |
+ |
double thisMass; |
1136 |
+ |
|
1137 |
+ |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1138 |
+ |
thisMass = mol->getMass(); |
1139 |
+ |
thisr = mol->getCom()-com; |
1140 |
+ |
thisp = (mol->getComVel()-comVel)*thisMass; |
1141 |
+ |
|
1142 |
+ |
angularMomentum += cross( thisr, thisp ); |
1143 |
+ |
|
1144 |
+ |
} |
1145 |
+ |
|
1146 |
+ |
#ifdef IS_MPI |
1147 |
+ |
Vector3d tmpAngMom; |
1148 |
+ |
MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1149 |
+ |
#endif |
1150 |
+ |
|
1151 |
+ |
return angularMomentum; |
1152 |
+ |
} |
1153 |
+ |
|
1154 |
+ |
|
1155 |
|
}//end namespace oopse |
1156 |
|
|