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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 "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), 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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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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selectMan_ = new SelectionManager(nGlobalAtoms_ + nGlobalRigidBodies_); |
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selectMan_->selectAll(); |
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} |
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} |
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SimInfo::~SimInfo() { |
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//MemoryUtils::deleteVectorOfPointer(molecules_); |
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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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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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addExcludePairs(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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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); |
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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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} |
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|
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} |
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Molecule::RigidBodyIterator rbIter; |
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> |
RigidBody* rb; |
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> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
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std::vector<Atom*> atoms = rb->getAtoms(); |
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> |
for (int i = 0; i < atoms.size() -1 ; ++i) { |
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for (int j = i + 1; j < atoms.size(); ++j) { |
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a = atoms[i]->getGlobalIndex(); |
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> |
b = atoms[j]->getGlobalIndex(); |
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exclude_.addPair(a, b); |
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} |
379 |
> |
} |
380 |
> |
} |
381 |
|
|
382 |
< |
void SimInfo::removeExcludePairs(Molecule* mol) { |
382 |
> |
} |
383 |
> |
|
384 |
> |
void SimInfo::removeExcludePairs(Molecule* mol) { |
385 |
|
std::vector<Bond*>::iterator bondIter; |
386 |
|
std::vector<Bend*>::iterator bendIter; |
387 |
|
std::vector<Torsion*>::iterator torsionIter; |
394 |
|
int d; |
395 |
|
|
396 |
|
for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { |
397 |
< |
a = bond->getAtomA()->getGlobalIndex(); |
398 |
< |
b = bond->getAtomB()->getGlobalIndex(); |
399 |
< |
exclude_.removePair(a, b); |
397 |
> |
a = bond->getAtomA()->getGlobalIndex(); |
398 |
> |
b = bond->getAtomB()->getGlobalIndex(); |
399 |
> |
exclude_.removePair(a, b); |
400 |
|
} |
401 |
|
|
402 |
|
for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) { |
403 |
< |
a = bend->getAtomA()->getGlobalIndex(); |
404 |
< |
b = bend->getAtomB()->getGlobalIndex(); |
405 |
< |
c = bend->getAtomC()->getGlobalIndex(); |
403 |
> |
a = bend->getAtomA()->getGlobalIndex(); |
404 |
> |
b = bend->getAtomB()->getGlobalIndex(); |
405 |
> |
c = bend->getAtomC()->getGlobalIndex(); |
406 |
|
|
407 |
< |
exclude_.removePair(a, b); |
408 |
< |
exclude_.removePair(a, c); |
409 |
< |
exclude_.removePair(b, c); |
407 |
> |
exclude_.removePair(a, b); |
408 |
> |
exclude_.removePair(a, c); |
409 |
> |
exclude_.removePair(b, c); |
410 |
|
} |
411 |
|
|
412 |
|
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
413 |
< |
a = torsion->getAtomA()->getGlobalIndex(); |
414 |
< |
b = torsion->getAtomB()->getGlobalIndex(); |
415 |
< |
c = torsion->getAtomC()->getGlobalIndex(); |
416 |
< |
d = torsion->getAtomD()->getGlobalIndex(); |
413 |
> |
a = torsion->getAtomA()->getGlobalIndex(); |
414 |
> |
b = torsion->getAtomB()->getGlobalIndex(); |
415 |
> |
c = torsion->getAtomC()->getGlobalIndex(); |
416 |
> |
d = torsion->getAtomD()->getGlobalIndex(); |
417 |
|
|
418 |
< |
exclude_.removePair(a, b); |
419 |
< |
exclude_.removePair(a, c); |
420 |
< |
exclude_.removePair(a, d); |
421 |
< |
exclude_.removePair(b, c); |
422 |
< |
exclude_.removePair(b, d); |
423 |
< |
exclude_.removePair(c, d); |
418 |
> |
exclude_.removePair(a, b); |
419 |
> |
exclude_.removePair(a, c); |
420 |
> |
exclude_.removePair(a, d); |
421 |
> |
exclude_.removePair(b, c); |
422 |
> |
exclude_.removePair(b, d); |
423 |
> |
exclude_.removePair(c, d); |
424 |
|
} |
425 |
|
|
426 |
< |
} |
426 |
> |
Molecule::RigidBodyIterator rbIter; |
427 |
> |
RigidBody* rb; |
428 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
429 |
> |
std::vector<Atom*> atoms = rb->getAtoms(); |
430 |
> |
for (int i = 0; i < atoms.size() -1 ; ++i) { |
431 |
> |
for (int j = i + 1; j < atoms.size(); ++j) { |
432 |
> |
a = atoms[i]->getGlobalIndex(); |
433 |
> |
b = atoms[j]->getGlobalIndex(); |
434 |
> |
exclude_.removePair(a, b); |
435 |
> |
} |
436 |
> |
} |
437 |
> |
} |
438 |
|
|
439 |
+ |
} |
440 |
|
|
441 |
< |
void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) { |
441 |
> |
|
442 |
> |
void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) { |
443 |
|
int curStampId; |
444 |
|
|
445 |
|
//index from 0 |
447 |
|
|
448 |
|
moleculeStamps_.push_back(molStamp); |
449 |
|
molStampIds_.insert(molStampIds_.end(), nmol, curStampId); |
450 |
< |
} |
450 |
> |
} |
451 |
|
|
452 |
< |
void SimInfo::update() { |
452 |
> |
void SimInfo::update() { |
453 |
|
|
454 |
|
setupSimType(); |
455 |
|
|
464 |
|
int isError = 0; |
465 |
|
initFortranFF( &fInfo_.SIM_uses_RF , &isError ); |
466 |
|
if(isError){ |
467 |
< |
sprintf( painCave.errMsg, |
468 |
< |
"ForceField error: There was an error initializing the forceField in fortran.\n" ); |
469 |
< |
painCave.isFatal = 1; |
470 |
< |
simError(); |
467 |
> |
sprintf( painCave.errMsg, |
468 |
> |
"ForceField error: There was an error initializing the forceField in fortran.\n" ); |
469 |
> |
painCave.isFatal = 1; |
470 |
> |
simError(); |
471 |
|
} |
472 |
|
|
473 |
|
|
478 |
|
calcNdfTrans(); |
479 |
|
|
480 |
|
fortranInitialized_ = true; |
481 |
< |
} |
481 |
> |
} |
482 |
|
|
483 |
< |
std::set<AtomType*> SimInfo::getUniqueAtomTypes() { |
483 |
> |
std::set<AtomType*> SimInfo::getUniqueAtomTypes() { |
484 |
|
SimInfo::MoleculeIterator mi; |
485 |
|
Molecule* mol; |
486 |
|
Molecule::AtomIterator ai; |
489 |
|
|
490 |
|
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
491 |
|
|
492 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
493 |
< |
atomTypes.insert(atom->getAtomType()); |
494 |
< |
} |
492 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
493 |
> |
atomTypes.insert(atom->getAtomType()); |
494 |
> |
} |
495 |
|
|
496 |
|
} |
497 |
|
|
498 |
|
return atomTypes; |
499 |
< |
} |
499 |
> |
} |
500 |
|
|
501 |
< |
void SimInfo::setupSimType() { |
501 |
> |
void SimInfo::setupSimType() { |
502 |
|
std::set<AtomType*>::iterator i; |
503 |
|
std::set<AtomType*> atomTypes; |
504 |
|
atomTypes = getUniqueAtomTypes(); |
521 |
|
|
522 |
|
//loop over all of the atom types |
523 |
|
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
524 |
< |
useLennardJones |= (*i)->isLennardJones(); |
525 |
< |
useElectrostatic |= (*i)->isElectrostatic(); |
526 |
< |
useEAM |= (*i)->isEAM(); |
527 |
< |
useCharge |= (*i)->isCharge(); |
528 |
< |
useDirectional |= (*i)->isDirectional(); |
529 |
< |
useDipole |= (*i)->isDipole(); |
530 |
< |
useGayBerne |= (*i)->isGayBerne(); |
531 |
< |
useSticky |= (*i)->isSticky(); |
532 |
< |
useShape |= (*i)->isShape(); |
524 |
> |
useLennardJones |= (*i)->isLennardJones(); |
525 |
> |
useElectrostatic |= (*i)->isElectrostatic(); |
526 |
> |
useEAM |= (*i)->isEAM(); |
527 |
> |
useCharge |= (*i)->isCharge(); |
528 |
> |
useDirectional |= (*i)->isDirectional(); |
529 |
> |
useDipole |= (*i)->isDipole(); |
530 |
> |
useGayBerne |= (*i)->isGayBerne(); |
531 |
> |
useSticky |= (*i)->isSticky(); |
532 |
> |
useShape |= (*i)->isShape(); |
533 |
|
} |
534 |
|
|
535 |
|
if (useSticky || useDipole || useGayBerne || useShape) { |
536 |
< |
useDirectionalAtom = 1; |
536 |
> |
useDirectionalAtom = 1; |
537 |
|
} |
538 |
|
|
539 |
|
if (useCharge || useDipole) { |
540 |
< |
useElectrostatics = 1; |
540 |
> |
useElectrostatics = 1; |
541 |
|
} |
542 |
|
|
543 |
|
#ifdef IS_MPI |
596 |
|
|
597 |
|
if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { |
598 |
|
|
599 |
< |
if (simParams_->haveDielectric()) { |
600 |
< |
fInfo_.dielect = simParams_->getDielectric(); |
601 |
< |
} else { |
602 |
< |
sprintf(painCave.errMsg, |
603 |
< |
"SimSetup Error: No Dielectric constant was set.\n" |
604 |
< |
"\tYou are trying to use Reaction Field without" |
605 |
< |
"\tsetting a dielectric constant!\n"); |
606 |
< |
painCave.isFatal = 1; |
607 |
< |
simError(); |
608 |
< |
} |
599 |
> |
if (simParams_->haveDielectric()) { |
600 |
> |
fInfo_.dielect = simParams_->getDielectric(); |
601 |
> |
} else { |
602 |
> |
sprintf(painCave.errMsg, |
603 |
> |
"SimSetup Error: No Dielectric constant was set.\n" |
604 |
> |
"\tYou are trying to use Reaction Field without" |
605 |
> |
"\tsetting a dielectric constant!\n"); |
606 |
> |
painCave.isFatal = 1; |
607 |
> |
simError(); |
608 |
> |
} |
609 |
|
|
610 |
|
} else { |
611 |
< |
fInfo_.dielect = 0.0; |
611 |
> |
fInfo_.dielect = 0.0; |
612 |
|
} |
613 |
|
|
614 |
< |
} |
614 |
> |
} |
615 |
|
|
616 |
< |
void SimInfo::setupFortranSim() { |
616 |
> |
void SimInfo::setupFortranSim() { |
617 |
|
int isError; |
618 |
|
int nExclude; |
619 |
|
std::vector<int> fortranGlobalGroupMembership; |
623 |
|
|
624 |
|
//globalGroupMembership_ is filled by SimCreator |
625 |
|
for (int i = 0; i < nGlobalAtoms_; i++) { |
626 |
< |
fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1); |
626 |
> |
fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1); |
627 |
|
} |
628 |
|
|
629 |
|
//calculate mass ratio of cutoff group |
640 |
|
mfact.reserve(getNCutoffGroups()); |
641 |
|
|
642 |
|
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
643 |
< |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
643 |
> |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
644 |
|
|
645 |
< |
totalMass = cg->getMass(); |
646 |
< |
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
647 |
< |
mfact.push_back(atom->getMass()/totalMass); |
648 |
< |
} |
645 |
> |
totalMass = cg->getMass(); |
646 |
> |
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
647 |
> |
mfact.push_back(atom->getMass()/totalMass); |
648 |
> |
} |
649 |
|
|
650 |
< |
} |
650 |
> |
} |
651 |
|
} |
652 |
|
|
653 |
|
//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!) |
657 |
|
identArray.reserve(getNAtoms()); |
658 |
|
|
659 |
|
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
660 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
661 |
< |
identArray.push_back(atom->getIdent()); |
662 |
< |
} |
660 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
661 |
> |
identArray.push_back(atom->getIdent()); |
662 |
> |
} |
663 |
|
} |
664 |
|
|
665 |
|
//fill molMembershipArray |
666 |
|
//molMembershipArray is filled by SimCreator |
667 |
|
std::vector<int> molMembershipArray(nGlobalAtoms_); |
668 |
|
for (int i = 0; i < nGlobalAtoms_; i++) { |
669 |
< |
molMembershipArray[i] = globalMolMembership_[i] + 1; |
669 |
> |
molMembershipArray[i] = globalMolMembership_[i] + 1; |
670 |
|
} |
671 |
|
|
672 |
|
//setup fortran simulation |
647 |
– |
//gloalExcludes and molMembershipArray should go away (They are never used) |
648 |
– |
//why the hell fortran need to know molecule? |
649 |
– |
//OOPSE = Object-Obfuscated Parallel Simulation Engine |
673 |
|
int nGlobalExcludes = 0; |
674 |
|
int* globalExcludes = NULL; |
675 |
|
int* excludeList = exclude_.getExcludeList(); |
676 |
|
setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList , |
677 |
< |
&nGlobalExcludes, globalExcludes, &molMembershipArray[0], |
678 |
< |
&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError); |
677 |
> |
&nGlobalExcludes, globalExcludes, &molMembershipArray[0], |
678 |
> |
&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError); |
679 |
|
|
680 |
|
if( isError ){ |
681 |
|
|
682 |
< |
sprintf( painCave.errMsg, |
683 |
< |
"There was an error setting the simulation information in fortran.\n" ); |
684 |
< |
painCave.isFatal = 1; |
685 |
< |
painCave.severity = OOPSE_ERROR; |
686 |
< |
simError(); |
682 |
> |
sprintf( painCave.errMsg, |
683 |
> |
"There was an error setting the simulation information in fortran.\n" ); |
684 |
> |
painCave.isFatal = 1; |
685 |
> |
painCave.severity = OOPSE_ERROR; |
686 |
> |
simError(); |
687 |
|
} |
688 |
|
|
689 |
|
#ifdef IS_MPI |
690 |
|
sprintf( checkPointMsg, |
691 |
< |
"succesfully sent the simulation information to fortran.\n"); |
691 |
> |
"succesfully sent the simulation information to fortran.\n"); |
692 |
|
MPIcheckPoint(); |
693 |
|
#endif // is_mpi |
694 |
< |
} |
694 |
> |
} |
695 |
|
|
696 |
|
|
697 |
|
#ifdef IS_MPI |
698 |
< |
void SimInfo::setupFortranParallel() { |
698 |
> |
void SimInfo::setupFortranParallel() { |
699 |
|
|
700 |
|
//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex |
701 |
|
std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0); |
711 |
|
|
712 |
|
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
713 |
|
|
714 |
< |
//local index(index in DataStorge) of atom is important |
715 |
< |
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
716 |
< |
localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1; |
717 |
< |
} |
714 |
> |
//local index(index in DataStorge) of atom is important |
715 |
> |
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
716 |
> |
localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1; |
717 |
> |
} |
718 |
|
|
719 |
< |
//local index of cutoff group is trivial, it only depends on the order of travesing |
720 |
< |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
721 |
< |
localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1); |
722 |
< |
} |
719 |
> |
//local index of cutoff group is trivial, it only depends on the order of travesing |
720 |
> |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
721 |
> |
localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1); |
722 |
> |
} |
723 |
|
|
724 |
|
} |
725 |
|
|
739 |
|
&localToGlobalCutoffGroupIndex[0], &isError); |
740 |
|
|
741 |
|
if (isError) { |
742 |
< |
sprintf(painCave.errMsg, |
743 |
< |
"mpiRefresh errror: fortran didn't like something we gave it.\n"); |
744 |
< |
painCave.isFatal = 1; |
745 |
< |
simError(); |
742 |
> |
sprintf(painCave.errMsg, |
743 |
> |
"mpiRefresh errror: fortran didn't like something we gave it.\n"); |
744 |
> |
painCave.isFatal = 1; |
745 |
> |
simError(); |
746 |
|
} |
747 |
|
|
748 |
|
sprintf(checkPointMsg, " mpiRefresh successful.\n"); |
749 |
|
MPIcheckPoint(); |
750 |
|
|
751 |
|
|
752 |
< |
} |
752 |
> |
} |
753 |
|
|
754 |
|
#endif |
755 |
|
|
756 |
< |
double SimInfo::calcMaxCutoffRadius() { |
756 |
> |
double SimInfo::calcMaxCutoffRadius() { |
757 |
|
|
758 |
|
|
759 |
|
std::set<AtomType*> atomTypes; |
765 |
|
|
766 |
|
//query the max cutoff radius among these atom types |
767 |
|
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
768 |
< |
cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i)); |
768 |
> |
cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i)); |
769 |
|
} |
770 |
|
|
771 |
|
double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end())); |
774 |
|
#endif |
775 |
|
|
776 |
|
return maxCutoffRadius; |
777 |
< |
} |
777 |
> |
} |
778 |
|
|
779 |
< |
void SimInfo::setupCutoff() { |
757 |
< |
double rcut_; //cutoff radius |
758 |
< |
double rsw_; //switching radius |
779 |
> |
void SimInfo::getCutoff(double& rcut, double& rsw) { |
780 |
|
|
781 |
|
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
782 |
|
|
783 |
< |
if (!simParams_->haveRcut()){ |
784 |
< |
sprintf(painCave.errMsg, |
783 |
> |
if (!simParams_->haveRcut()){ |
784 |
> |
sprintf(painCave.errMsg, |
785 |
|
"SimCreator Warning: No value was set for the cutoffRadius.\n" |
786 |
|
"\tOOPSE will use a default value of 15.0 angstroms" |
787 |
|
"\tfor the cutoffRadius.\n"); |
788 |
< |
painCave.isFatal = 0; |
789 |
< |
simError(); |
790 |
< |
rcut_ = 15.0; |
791 |
< |
} else{ |
792 |
< |
rcut_ = simParams_->getRcut(); |
793 |
< |
} |
788 |
> |
painCave.isFatal = 0; |
789 |
> |
simError(); |
790 |
> |
rcut = 15.0; |
791 |
> |
} else{ |
792 |
> |
rcut = simParams_->getRcut(); |
793 |
> |
} |
794 |
|
|
795 |
< |
if (!simParams_->haveRsw()){ |
796 |
< |
sprintf(painCave.errMsg, |
795 |
> |
if (!simParams_->haveRsw()){ |
796 |
> |
sprintf(painCave.errMsg, |
797 |
|
"SimCreator Warning: No value was set for switchingRadius.\n" |
798 |
|
"\tOOPSE will use a default value of\n" |
799 |
|
"\t0.95 * cutoffRadius for the switchingRadius\n"); |
800 |
< |
painCave.isFatal = 0; |
801 |
< |
simError(); |
802 |
< |
rsw_ = 0.95 * rcut_; |
803 |
< |
} else{ |
804 |
< |
rsw_ = simParams_->getRsw(); |
805 |
< |
} |
800 |
> |
painCave.isFatal = 0; |
801 |
> |
simError(); |
802 |
> |
rsw = 0.95 * rcut; |
803 |
> |
} else{ |
804 |
> |
rsw = simParams_->getRsw(); |
805 |
> |
} |
806 |
|
|
807 |
|
} else { |
808 |
< |
// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
809 |
< |
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
808 |
> |
// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
809 |
> |
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
810 |
|
|
811 |
< |
if (simParams_->haveRcut()) { |
812 |
< |
rcut_ = simParams_->getRcut(); |
813 |
< |
} else { |
814 |
< |
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
815 |
< |
rcut_ = calcMaxCutoffRadius(); |
816 |
< |
} |
811 |
> |
if (simParams_->haveRcut()) { |
812 |
> |
rcut = simParams_->getRcut(); |
813 |
> |
} else { |
814 |
> |
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
815 |
> |
rcut = calcMaxCutoffRadius(); |
816 |
> |
} |
817 |
|
|
818 |
< |
if (simParams_->haveRsw()) { |
819 |
< |
rsw_ = simParams_->getRsw(); |
820 |
< |
} else { |
821 |
< |
rsw_ = rcut_; |
822 |
< |
} |
818 |
> |
if (simParams_->haveRsw()) { |
819 |
> |
rsw = simParams_->getRsw(); |
820 |
> |
} else { |
821 |
> |
rsw = rcut; |
822 |
> |
} |
823 |
|
|
824 |
|
} |
825 |
< |
|
825 |
> |
} |
826 |
> |
|
827 |
> |
void SimInfo::setupCutoff() { |
828 |
> |
getCutoff(rcut_, rsw_); |
829 |
|
double rnblist = rcut_ + 1; // skin of neighbor list |
830 |
|
|
831 |
|
//Pass these cutoff radius etc. to fortran. This function should be called once and only once |
832 |
|
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist); |
833 |
< |
} |
833 |
> |
} |
834 |
|
|
835 |
< |
void SimInfo::addProperty(GenericData* genData) { |
835 |
> |
void SimInfo::addProperty(GenericData* genData) { |
836 |
|
properties_.addProperty(genData); |
837 |
< |
} |
837 |
> |
} |
838 |
|
|
839 |
< |
void SimInfo::removeProperty(const std::string& propName) { |
839 |
> |
void SimInfo::removeProperty(const std::string& propName) { |
840 |
|
properties_.removeProperty(propName); |
841 |
< |
} |
841 |
> |
} |
842 |
|
|
843 |
< |
void SimInfo::clearProperties() { |
843 |
> |
void SimInfo::clearProperties() { |
844 |
|
properties_.clearProperties(); |
845 |
< |
} |
845 |
> |
} |
846 |
|
|
847 |
< |
std::vector<std::string> SimInfo::getPropertyNames() { |
847 |
> |
std::vector<std::string> SimInfo::getPropertyNames() { |
848 |
|
return properties_.getPropertyNames(); |
849 |
< |
} |
849 |
> |
} |
850 |
|
|
851 |
< |
std::vector<GenericData*> SimInfo::getProperties() { |
851 |
> |
std::vector<GenericData*> SimInfo::getProperties() { |
852 |
|
return properties_.getProperties(); |
853 |
< |
} |
853 |
> |
} |
854 |
|
|
855 |
< |
GenericData* SimInfo::getPropertyByName(const std::string& propName) { |
855 |
> |
GenericData* SimInfo::getPropertyByName(const std::string& propName) { |
856 |
|
return properties_.getPropertyByName(propName); |
857 |
< |
} |
857 |
> |
} |
858 |
|
|
859 |
< |
void SimInfo::setSnapshotManager(SnapshotManager* sman) { |
859 |
> |
void SimInfo::setSnapshotManager(SnapshotManager* sman) { |
860 |
> |
if (sman_ == sman) { |
861 |
> |
return; |
862 |
> |
} |
863 |
> |
delete sman_; |
864 |
|
sman_ = sman; |
865 |
|
|
866 |
|
Molecule* mol; |
872 |
|
|
873 |
|
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
874 |
|
|
875 |
< |
for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) { |
876 |
< |
atom->setSnapshotManager(sman_); |
877 |
< |
} |
875 |
> |
for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) { |
876 |
> |
atom->setSnapshotManager(sman_); |
877 |
> |
} |
878 |
|
|
879 |
< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
880 |
< |
rb->setSnapshotManager(sman_); |
881 |
< |
} |
879 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
880 |
> |
rb->setSnapshotManager(sman_); |
881 |
> |
} |
882 |
|
} |
883 |
|
|
884 |
< |
} |
884 |
> |
} |
885 |
|
|
886 |
< |
Vector3d SimInfo::getComVel(){ |
886 |
> |
Vector3d SimInfo::getComVel(){ |
887 |
|
SimInfo::MoleculeIterator i; |
888 |
|
Molecule* mol; |
889 |
|
|
892 |
|
|
893 |
|
|
894 |
|
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
895 |
< |
double mass = mol->getMass(); |
896 |
< |
totalMass += mass; |
897 |
< |
comVel += mass * mol->getComVel(); |
895 |
> |
double mass = mol->getMass(); |
896 |
> |
totalMass += mass; |
897 |
> |
comVel += mass * mol->getComVel(); |
898 |
|
} |
899 |
|
|
900 |
|
#ifdef IS_MPI |
907 |
|
comVel /= totalMass; |
908 |
|
|
909 |
|
return comVel; |
910 |
< |
} |
910 |
> |
} |
911 |
|
|
912 |
< |
Vector3d SimInfo::getCom(){ |
912 |
> |
Vector3d SimInfo::getCom(){ |
913 |
|
SimInfo::MoleculeIterator i; |
914 |
|
Molecule* mol; |
915 |
|
|
917 |
|
double totalMass = 0.0; |
918 |
|
|
919 |
|
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
920 |
< |
double mass = mol->getMass(); |
921 |
< |
totalMass += mass; |
922 |
< |
com += mass * mol->getCom(); |
920 |
> |
double mass = mol->getMass(); |
921 |
> |
totalMass += mass; |
922 |
> |
com += mass * mol->getCom(); |
923 |
|
} |
924 |
|
|
925 |
|
#ifdef IS_MPI |
933 |
|
|
934 |
|
return com; |
935 |
|
|
936 |
< |
} |
936 |
> |
} |
937 |
|
|
938 |
< |
std::ostream& operator <<(std::ostream& o, SimInfo& info) { |
938 |
> |
std::ostream& operator <<(std::ostream& o, SimInfo& info) { |
939 |
|
|
940 |
|
return o; |
941 |
< |
} |
941 |
> |
} |
942 |
|
|
943 |
|
}//end namespace oopse |
944 |
|
|