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/* |
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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#include <algorithm> |
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#include <set> |
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#include <map> |
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#include "brains/SimInfo.hpp" |
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#include "math/Vector3.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "UseTheForce/fCutoffPolicy.h" |
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#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h" |
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#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h" |
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#include "UseTheForce/DarkSide/fSwitchingFunctionType.h" |
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#include "UseTheForce/doForces_interface.h" |
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#include "UseTheForce/notifyCutoffs_interface.h" |
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#include "UseTheForce/DarkSide/electrostatic_interface.h" |
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#include "UseTheForce/DarkSide/switcheroo_interface.h" |
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#include "utils/MemoryUtils.hpp" |
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#include "utils/simError.h" |
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#include "selection/SelectionManager.hpp" |
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#include "io/ForceFieldOptions.hpp" |
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#include "UseTheForce/ForceField.hpp" |
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#ifdef IS_MPI |
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#include "UseTheForce/mpiComponentPlan.h" |
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#endif |
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namespace oopse { |
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std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) { |
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std::map<int, std::set<int> >::iterator i = container.find(index); |
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std::set<int> result; |
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if (i != container.end()) { |
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result = i->second; |
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} |
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|
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SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, |
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ForceField* ff, Globals* simParams) : |
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forceField_(ff), simParams_(simParams), |
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ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0), |
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nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0), |
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nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), |
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nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0), |
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nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0), |
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sman_(NULL), fortranInitialized_(false), selectMan_(NULL) { |
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return result; |
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} |
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|
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SimInfo::SimInfo(ForceField* ff, Globals* simParams) : |
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forceField_(ff), simParams_(simParams), |
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ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0), |
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nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0), |
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nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), |
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nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0), |
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nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0), |
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sman_(NULL), fortranInitialized_(false) { |
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std::vector<std::pair<MoleculeStamp*, int> >::iterator i; |
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MoleculeStamp* molStamp; |
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int nMolWithSameStamp; |
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int nCutoffAtoms = 0; // number of atoms belong to cutoff groups |
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int nGroups = 0; //total cutoff groups defined in meta-data file |
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CutoffGroupStamp* cgStamp; |
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RigidBodyStamp* rbStamp; |
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int nRigidAtoms = 0; |
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|
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for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) { |
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molStamp = i->first; |
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nMolWithSameStamp = i->second; |
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MoleculeStamp* molStamp; |
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int nMolWithSameStamp; |
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int nCutoffAtoms = 0; // number of atoms belong to cutoff groups |
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int nGroups = 0; //total cutoff groups defined in meta-data file |
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CutoffGroupStamp* cgStamp; |
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RigidBodyStamp* rbStamp; |
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int nRigidAtoms = 0; |
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std::vector<Component*> components = simParams->getComponents(); |
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|
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for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) { |
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molStamp = (*i)->getMoleculeStamp(); |
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nMolWithSameStamp = (*i)->getNMol(); |
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addMoleculeStamp(molStamp, nMolWithSameStamp); |
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//calculate atoms in molecules |
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nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp; |
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|
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//calculate atoms in cutoff groups |
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int nAtomsInGroups = 0; |
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int nCutoffGroupsInStamp = molStamp->getNCutoffGroups(); |
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for (int j=0; j < nCutoffGroupsInStamp; j++) { |
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cgStamp = molStamp->getCutoffGroup(j); |
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nAtomsInGroups += cgStamp->getNMembers(); |
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cgStamp = molStamp->getCutoffGroupStamp(j); |
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nAtomsInGroups += cgStamp->getNMembers(); |
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} |
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nGroups += nCutoffGroupsInStamp * nMolWithSameStamp; |
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nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp; |
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//calculate atoms in rigid bodies |
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int nRigidBodiesInStamp = molStamp->getNRigidBodies(); |
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for (int j=0; j < nRigidBodiesInStamp; j++) { |
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rbStamp = molStamp->getRigidBody(j); |
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nAtomsInRigidBodies += rbStamp->getNMembers(); |
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rbStamp = molStamp->getRigidBodyStamp(j); |
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nAtomsInRigidBodies += rbStamp->getNMembers(); |
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} |
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nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp; |
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nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp; |
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} |
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} |
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//every free atom (atom does not belong to cutoff groups) is a cutoff group |
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//therefore the total number of cutoff groups in the system is equal to |
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//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data |
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//file plus the number of cutoff groups defined in meta-data file |
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nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; |
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//every free atom (atom does not belong to cutoff groups) is a cutoff |
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//group therefore the total number of cutoff groups in the system is |
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//equal to the total number of atoms minus number of atoms belong to |
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//cutoff group defined in meta-data file plus the number of cutoff |
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//groups defined in meta-data file |
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nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; |
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|
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//every free atom (atom does not belong to rigid bodies) is an integrable object |
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//therefore the total number of integrable objects in the system is equal to |
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//the total number of atoms minus number of atoms belong to rigid body defined in meta-data |
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//file plus the number of rigid bodies defined in meta-data file |
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nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_; |
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//every free atom (atom does not belong to rigid bodies) is an |
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//integrable object therefore the total number of integrable objects |
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//in the system is equal to the total number of atoms minus number of |
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//atoms belong to rigid body defined in meta-data file plus the number |
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//of rigid bodies defined in meta-data file |
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nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms |
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+ nGlobalRigidBodies_; |
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|
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nGlobalMols_ = molStampIds_.size(); |
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nGlobalMols_ = molStampIds_.size(); |
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|
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#ifdef IS_MPI |
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molToProcMap_.resize(nGlobalMols_); |
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molToProcMap_.resize(nGlobalMols_); |
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#endif |
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selectMan_ = new SelectionManager(this); |
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selectMan_->selectAll(); |
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} |
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} |
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SimInfo::~SimInfo() { |
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//MemoryUtils::deleteVectorOfPointer(molecules_); |
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MemoryUtils::deleteVectorOfPointer(moleculeStamps_); |
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SimInfo::~SimInfo() { |
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std::map<int, Molecule*>::iterator i; |
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for (i = molecules_.begin(); i != molecules_.end(); ++i) { |
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delete i->second; |
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} |
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molecules_.clear(); |
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|
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delete sman_; |
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delete simParams_; |
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delete forceField_; |
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delete selectMan_; |
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} |
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} |
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int SimInfo::getNGlobalConstraints() { |
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int SimInfo::getNGlobalConstraints() { |
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int nGlobalConstraints; |
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#ifdef IS_MPI |
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MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM, |
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nGlobalConstraints = nConstraints_; |
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#endif |
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return nGlobalConstraints; |
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} |
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} |
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bool SimInfo::addMolecule(Molecule* mol) { |
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bool SimInfo::addMolecule(Molecule* mol) { |
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MoleculeIterator i; |
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i = molecules_.find(mol->getGlobalIndex()); |
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if (i == molecules_.end() ) { |
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molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol)); |
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molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol)); |
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nAtoms_ += mol->getNAtoms(); |
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nBonds_ += mol->getNBonds(); |
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nBends_ += mol->getNBends(); |
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nTorsions_ += mol->getNTorsions(); |
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nRigidBodies_ += mol->getNRigidBodies(); |
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nIntegrableObjects_ += mol->getNIntegrableObjects(); |
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nCutoffGroups_ += mol->getNCutoffGroups(); |
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nConstraints_ += mol->getNConstraintPairs(); |
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nAtoms_ += mol->getNAtoms(); |
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nBonds_ += mol->getNBonds(); |
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nBends_ += mol->getNBends(); |
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nTorsions_ += mol->getNTorsions(); |
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nRigidBodies_ += mol->getNRigidBodies(); |
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nIntegrableObjects_ += mol->getNIntegrableObjects(); |
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nCutoffGroups_ += mol->getNCutoffGroups(); |
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nConstraints_ += mol->getNConstraintPairs(); |
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addExcludePairs(mol); |
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addExcludePairs(mol); |
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return true; |
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return true; |
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} else { |
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return false; |
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return false; |
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} |
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} |
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} |
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bool SimInfo::removeMolecule(Molecule* mol) { |
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bool SimInfo::removeMolecule(Molecule* mol) { |
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MoleculeIterator i; |
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i = molecules_.find(mol->getGlobalIndex()); |
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if (i != molecules_.end() ) { |
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assert(mol == i->second); |
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assert(mol == i->second); |
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nAtoms_ -= mol->getNAtoms(); |
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nBonds_ -= mol->getNBonds(); |
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nBends_ -= mol->getNBends(); |
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nTorsions_ -= mol->getNTorsions(); |
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nRigidBodies_ -= mol->getNRigidBodies(); |
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nIntegrableObjects_ -= mol->getNIntegrableObjects(); |
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nCutoffGroups_ -= mol->getNCutoffGroups(); |
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nConstraints_ -= mol->getNConstraintPairs(); |
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|
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removeExcludePairs(mol); |
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molecules_.erase(mol->getGlobalIndex()); |
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|
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delete mol; |
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|
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return true; |
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nAtoms_ -= mol->getNAtoms(); |
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nBonds_ -= mol->getNBonds(); |
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nBends_ -= mol->getNBends(); |
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nTorsions_ -= mol->getNTorsions(); |
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nRigidBodies_ -= mol->getNRigidBodies(); |
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nIntegrableObjects_ -= mol->getNIntegrableObjects(); |
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nCutoffGroups_ -= mol->getNCutoffGroups(); |
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nConstraints_ -= mol->getNConstraintPairs(); |
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|
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removeExcludePairs(mol); |
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molecules_.erase(mol->getGlobalIndex()); |
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delete mol; |
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|
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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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} |
267 |
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if (integrableObject->isDirectional()) { |
268 |
> |
if (integrableObject->isLinear()) { |
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> |
ndf_local += 2; |
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} else { |
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ndf_local += 3; |
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} |
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} |
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|
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}//end for (integrableObject) |
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}// end for (mol) |
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} |
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} |
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|
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// n_constraints is local, so subtract them on each processor |
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ndf_local -= nConstraints_; |
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// entire system: |
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ndf_ = ndf_ - 3 - nZconstraint_; |
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|
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} |
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> |
} |
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|
293 |
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void SimInfo::calcNdfRaw() { |
293 |
> |
void SimInfo::calcNdfRaw() { |
294 |
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int ndfRaw_local; |
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|
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MoleculeIterator i; |
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ndfRaw_local = 0; |
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|
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for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
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< |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
306 |
< |
integrableObject = mol->nextIntegrableObject(j)) { |
305 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
306 |
> |
integrableObject = mol->nextIntegrableObject(j)) { |
307 |
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|
308 |
< |
ndfRaw_local += 3; |
308 |
> |
ndfRaw_local += 3; |
309 |
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|
310 |
< |
if (integrableObject->isDirectional()) { |
311 |
< |
if (integrableObject->isLinear()) { |
312 |
< |
ndfRaw_local += 2; |
313 |
< |
} else { |
314 |
< |
ndfRaw_local += 3; |
315 |
< |
} |
316 |
< |
} |
310 |
> |
if (integrableObject->isDirectional()) { |
311 |
> |
if (integrableObject->isLinear()) { |
312 |
> |
ndfRaw_local += 2; |
313 |
> |
} else { |
314 |
> |
ndfRaw_local += 3; |
315 |
> |
} |
316 |
> |
} |
317 |
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|
318 |
< |
} |
318 |
> |
} |
319 |
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} |
320 |
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|
321 |
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#ifdef IS_MPI |
323 |
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#else |
324 |
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ndfRaw_ = ndfRaw_local; |
325 |
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#endif |
326 |
< |
} |
326 |
> |
} |
327 |
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|
328 |
< |
void SimInfo::calcNdfTrans() { |
328 |
> |
void SimInfo::calcNdfTrans() { |
329 |
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int ndfTrans_local; |
330 |
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|
331 |
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ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_; |
339 |
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|
340 |
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ndfTrans_ = ndfTrans_ - 3 - nZconstraint_; |
341 |
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|
342 |
< |
} |
342 |
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} |
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|
344 |
< |
void SimInfo::addExcludePairs(Molecule* mol) { |
344 |
> |
void SimInfo::addExcludePairs(Molecule* mol) { |
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std::vector<Bond*>::iterator bondIter; |
346 |
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std::vector<Bend*>::iterator bendIter; |
347 |
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std::vector<Torsion*>::iterator torsionIter; |
352 |
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int b; |
353 |
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int c; |
354 |
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int d; |
355 |
+ |
|
356 |
+ |
std::map<int, std::set<int> > atomGroups; |
357 |
+ |
|
358 |
+ |
Molecule::RigidBodyIterator rbIter; |
359 |
+ |
RigidBody* rb; |
360 |
+ |
Molecule::IntegrableObjectIterator ii; |
361 |
+ |
StuntDouble* integrableObject; |
362 |
|
|
363 |
+ |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
364 |
+ |
integrableObject = mol->nextIntegrableObject(ii)) { |
365 |
+ |
|
366 |
+ |
if (integrableObject->isRigidBody()) { |
367 |
+ |
rb = static_cast<RigidBody*>(integrableObject); |
368 |
+ |
std::vector<Atom*> atoms = rb->getAtoms(); |
369 |
+ |
std::set<int> rigidAtoms; |
370 |
+ |
for (int i = 0; i < atoms.size(); ++i) { |
371 |
+ |
rigidAtoms.insert(atoms[i]->getGlobalIndex()); |
372 |
+ |
} |
373 |
+ |
for (int i = 0; i < atoms.size(); ++i) { |
374 |
+ |
atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms)); |
375 |
+ |
} |
376 |
+ |
} else { |
377 |
+ |
std::set<int> oneAtomSet; |
378 |
+ |
oneAtomSet.insert(integrableObject->getGlobalIndex()); |
379 |
+ |
atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet)); |
380 |
+ |
} |
381 |
+ |
} |
382 |
+ |
|
383 |
+ |
|
384 |
+ |
|
385 |
|
for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { |
386 |
< |
a = bond->getAtomA()->getGlobalIndex(); |
387 |
< |
b = bond->getAtomB()->getGlobalIndex(); |
388 |
< |
exclude_.addPair(a, b); |
386 |
> |
a = bond->getAtomA()->getGlobalIndex(); |
387 |
> |
b = bond->getAtomB()->getGlobalIndex(); |
388 |
> |
exclude_.addPair(a, b); |
389 |
|
} |
390 |
|
|
391 |
|
for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) { |
392 |
< |
a = bend->getAtomA()->getGlobalIndex(); |
393 |
< |
b = bend->getAtomB()->getGlobalIndex(); |
394 |
< |
c = bend->getAtomC()->getGlobalIndex(); |
392 |
> |
a = bend->getAtomA()->getGlobalIndex(); |
393 |
> |
b = bend->getAtomB()->getGlobalIndex(); |
394 |
> |
c = bend->getAtomC()->getGlobalIndex(); |
395 |
> |
std::set<int> rigidSetA = getRigidSet(a, atomGroups); |
396 |
> |
std::set<int> rigidSetB = getRigidSet(b, atomGroups); |
397 |
> |
std::set<int> rigidSetC = getRigidSet(c, atomGroups); |
398 |
|
|
399 |
< |
exclude_.addPair(a, b); |
400 |
< |
exclude_.addPair(a, c); |
401 |
< |
exclude_.addPair(b, c); |
399 |
> |
exclude_.addPairs(rigidSetA, rigidSetB); |
400 |
> |
exclude_.addPairs(rigidSetA, rigidSetC); |
401 |
> |
exclude_.addPairs(rigidSetB, rigidSetC); |
402 |
> |
|
403 |
> |
//exclude_.addPair(a, b); |
404 |
> |
//exclude_.addPair(a, c); |
405 |
> |
//exclude_.addPair(b, c); |
406 |
|
} |
407 |
|
|
408 |
|
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
409 |
< |
a = torsion->getAtomA()->getGlobalIndex(); |
410 |
< |
b = torsion->getAtomB()->getGlobalIndex(); |
411 |
< |
c = torsion->getAtomC()->getGlobalIndex(); |
412 |
< |
d = torsion->getAtomD()->getGlobalIndex(); |
409 |
> |
a = torsion->getAtomA()->getGlobalIndex(); |
410 |
> |
b = torsion->getAtomB()->getGlobalIndex(); |
411 |
> |
c = torsion->getAtomC()->getGlobalIndex(); |
412 |
> |
d = torsion->getAtomD()->getGlobalIndex(); |
413 |
> |
std::set<int> rigidSetA = getRigidSet(a, atomGroups); |
414 |
> |
std::set<int> rigidSetB = getRigidSet(b, atomGroups); |
415 |
> |
std::set<int> rigidSetC = getRigidSet(c, atomGroups); |
416 |
> |
std::set<int> rigidSetD = getRigidSet(d, atomGroups); |
417 |
|
|
418 |
< |
exclude_.addPair(a, b); |
419 |
< |
exclude_.addPair(a, c); |
420 |
< |
exclude_.addPair(a, d); |
421 |
< |
exclude_.addPair(b, c); |
422 |
< |
exclude_.addPair(b, d); |
423 |
< |
exclude_.addPair(c, d); |
418 |
> |
exclude_.addPairs(rigidSetA, rigidSetB); |
419 |
> |
exclude_.addPairs(rigidSetA, rigidSetC); |
420 |
> |
exclude_.addPairs(rigidSetA, rigidSetD); |
421 |
> |
exclude_.addPairs(rigidSetB, rigidSetC); |
422 |
> |
exclude_.addPairs(rigidSetB, rigidSetD); |
423 |
> |
exclude_.addPairs(rigidSetC, rigidSetD); |
424 |
> |
|
425 |
> |
/* |
426 |
> |
exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end()); |
427 |
> |
exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end()); |
428 |
> |
exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end()); |
429 |
> |
exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end()); |
430 |
> |
exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end()); |
431 |
> |
exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end()); |
432 |
> |
|
433 |
> |
|
434 |
> |
exclude_.addPair(a, b); |
435 |
> |
exclude_.addPair(a, c); |
436 |
> |
exclude_.addPair(a, d); |
437 |
> |
exclude_.addPair(b, c); |
438 |
> |
exclude_.addPair(b, d); |
439 |
> |
exclude_.addPair(c, d); |
440 |
> |
*/ |
441 |
|
} |
442 |
|
|
443 |
< |
|
444 |
< |
} |
443 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
444 |
> |
std::vector<Atom*> atoms = rb->getAtoms(); |
445 |
> |
for (int i = 0; i < atoms.size() -1 ; ++i) { |
446 |
> |
for (int j = i + 1; j < atoms.size(); ++j) { |
447 |
> |
a = atoms[i]->getGlobalIndex(); |
448 |
> |
b = atoms[j]->getGlobalIndex(); |
449 |
> |
exclude_.addPair(a, b); |
450 |
> |
} |
451 |
> |
} |
452 |
> |
} |
453 |
|
|
454 |
< |
void SimInfo::removeExcludePairs(Molecule* mol) { |
454 |
> |
} |
455 |
> |
|
456 |
> |
void SimInfo::removeExcludePairs(Molecule* mol) { |
457 |
|
std::vector<Bond*>::iterator bondIter; |
458 |
|
std::vector<Bend*>::iterator bendIter; |
459 |
|
std::vector<Torsion*>::iterator torsionIter; |
464 |
|
int b; |
465 |
|
int c; |
466 |
|
int d; |
467 |
+ |
|
468 |
+ |
std::map<int, std::set<int> > atomGroups; |
469 |
+ |
|
470 |
+ |
Molecule::RigidBodyIterator rbIter; |
471 |
+ |
RigidBody* rb; |
472 |
+ |
Molecule::IntegrableObjectIterator ii; |
473 |
+ |
StuntDouble* integrableObject; |
474 |
|
|
475 |
+ |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
476 |
+ |
integrableObject = mol->nextIntegrableObject(ii)) { |
477 |
+ |
|
478 |
+ |
if (integrableObject->isRigidBody()) { |
479 |
+ |
rb = static_cast<RigidBody*>(integrableObject); |
480 |
+ |
std::vector<Atom*> atoms = rb->getAtoms(); |
481 |
+ |
std::set<int> rigidAtoms; |
482 |
+ |
for (int i = 0; i < atoms.size(); ++i) { |
483 |
+ |
rigidAtoms.insert(atoms[i]->getGlobalIndex()); |
484 |
+ |
} |
485 |
+ |
for (int i = 0; i < atoms.size(); ++i) { |
486 |
+ |
atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms)); |
487 |
+ |
} |
488 |
+ |
} else { |
489 |
+ |
std::set<int> oneAtomSet; |
490 |
+ |
oneAtomSet.insert(integrableObject->getGlobalIndex()); |
491 |
+ |
atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet)); |
492 |
+ |
} |
493 |
+ |
} |
494 |
+ |
|
495 |
+ |
|
496 |
|
for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { |
497 |
< |
a = bond->getAtomA()->getGlobalIndex(); |
498 |
< |
b = bond->getAtomB()->getGlobalIndex(); |
499 |
< |
exclude_.removePair(a, b); |
497 |
> |
a = bond->getAtomA()->getGlobalIndex(); |
498 |
> |
b = bond->getAtomB()->getGlobalIndex(); |
499 |
> |
exclude_.removePair(a, b); |
500 |
|
} |
501 |
|
|
502 |
|
for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) { |
503 |
< |
a = bend->getAtomA()->getGlobalIndex(); |
504 |
< |
b = bend->getAtomB()->getGlobalIndex(); |
505 |
< |
c = bend->getAtomC()->getGlobalIndex(); |
503 |
> |
a = bend->getAtomA()->getGlobalIndex(); |
504 |
> |
b = bend->getAtomB()->getGlobalIndex(); |
505 |
> |
c = bend->getAtomC()->getGlobalIndex(); |
506 |
|
|
507 |
< |
exclude_.removePair(a, b); |
508 |
< |
exclude_.removePair(a, c); |
509 |
< |
exclude_.removePair(b, c); |
507 |
> |
std::set<int> rigidSetA = getRigidSet(a, atomGroups); |
508 |
> |
std::set<int> rigidSetB = getRigidSet(b, atomGroups); |
509 |
> |
std::set<int> rigidSetC = getRigidSet(c, atomGroups); |
510 |
> |
|
511 |
> |
exclude_.removePairs(rigidSetA, rigidSetB); |
512 |
> |
exclude_.removePairs(rigidSetA, rigidSetC); |
513 |
> |
exclude_.removePairs(rigidSetB, rigidSetC); |
514 |
> |
|
515 |
> |
//exclude_.removePair(a, b); |
516 |
> |
//exclude_.removePair(a, c); |
517 |
> |
//exclude_.removePair(b, c); |
518 |
|
} |
519 |
|
|
520 |
|
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
521 |
< |
a = torsion->getAtomA()->getGlobalIndex(); |
522 |
< |
b = torsion->getAtomB()->getGlobalIndex(); |
523 |
< |
c = torsion->getAtomC()->getGlobalIndex(); |
524 |
< |
d = torsion->getAtomD()->getGlobalIndex(); |
521 |
> |
a = torsion->getAtomA()->getGlobalIndex(); |
522 |
> |
b = torsion->getAtomB()->getGlobalIndex(); |
523 |
> |
c = torsion->getAtomC()->getGlobalIndex(); |
524 |
> |
d = torsion->getAtomD()->getGlobalIndex(); |
525 |
|
|
526 |
< |
exclude_.removePair(a, b); |
527 |
< |
exclude_.removePair(a, c); |
528 |
< |
exclude_.removePair(a, d); |
529 |
< |
exclude_.removePair(b, c); |
530 |
< |
exclude_.removePair(b, d); |
531 |
< |
exclude_.removePair(c, d); |
526 |
> |
std::set<int> rigidSetA = getRigidSet(a, atomGroups); |
527 |
> |
std::set<int> rigidSetB = getRigidSet(b, atomGroups); |
528 |
> |
std::set<int> rigidSetC = getRigidSet(c, atomGroups); |
529 |
> |
std::set<int> rigidSetD = getRigidSet(d, atomGroups); |
530 |
> |
|
531 |
> |
exclude_.removePairs(rigidSetA, rigidSetB); |
532 |
> |
exclude_.removePairs(rigidSetA, rigidSetC); |
533 |
> |
exclude_.removePairs(rigidSetA, rigidSetD); |
534 |
> |
exclude_.removePairs(rigidSetB, rigidSetC); |
535 |
> |
exclude_.removePairs(rigidSetB, rigidSetD); |
536 |
> |
exclude_.removePairs(rigidSetC, rigidSetD); |
537 |
> |
|
538 |
> |
/* |
539 |
> |
exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end()); |
540 |
> |
exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end()); |
541 |
> |
exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end()); |
542 |
> |
exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end()); |
543 |
> |
exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end()); |
544 |
> |
exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end()); |
545 |
> |
|
546 |
> |
|
547 |
> |
exclude_.removePair(a, b); |
548 |
> |
exclude_.removePair(a, c); |
549 |
> |
exclude_.removePair(a, d); |
550 |
> |
exclude_.removePair(b, c); |
551 |
> |
exclude_.removePair(b, d); |
552 |
> |
exclude_.removePair(c, d); |
553 |
> |
*/ |
554 |
|
} |
555 |
|
|
556 |
< |
} |
556 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
557 |
> |
std::vector<Atom*> atoms = rb->getAtoms(); |
558 |
> |
for (int i = 0; i < atoms.size() -1 ; ++i) { |
559 |
> |
for (int j = i + 1; j < atoms.size(); ++j) { |
560 |
> |
a = atoms[i]->getGlobalIndex(); |
561 |
> |
b = atoms[j]->getGlobalIndex(); |
562 |
> |
exclude_.removePair(a, b); |
563 |
> |
} |
564 |
> |
} |
565 |
> |
} |
566 |
|
|
567 |
+ |
} |
568 |
|
|
569 |
< |
void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) { |
569 |
> |
|
570 |
> |
void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) { |
571 |
|
int curStampId; |
572 |
|
|
573 |
|
//index from 0 |
575 |
|
|
576 |
|
moleculeStamps_.push_back(molStamp); |
577 |
|
molStampIds_.insert(molStampIds_.end(), nmol, curStampId); |
578 |
< |
} |
578 |
> |
} |
579 |
|
|
580 |
< |
void SimInfo::update() { |
580 |
> |
void SimInfo::update() { |
581 |
|
|
582 |
|
setupSimType(); |
583 |
|
|
590 |
|
//setup fortran force field |
591 |
|
/** @deprecate */ |
592 |
|
int isError = 0; |
593 |
< |
initFortranFF( &fInfo_.SIM_uses_RF , &isError ); |
593 |
> |
|
594 |
> |
setupElectrostaticSummationMethod( isError ); |
595 |
> |
setupSwitchingFunction(); |
596 |
> |
|
597 |
|
if(isError){ |
598 |
< |
sprintf( painCave.errMsg, |
599 |
< |
"ForceField error: There was an error initializing the forceField in fortran.\n" ); |
600 |
< |
painCave.isFatal = 1; |
601 |
< |
simError(); |
598 |
> |
sprintf( painCave.errMsg, |
599 |
> |
"ForceField error: There was an error initializing the forceField in fortran.\n" ); |
600 |
> |
painCave.isFatal = 1; |
601 |
> |
simError(); |
602 |
|
} |
603 |
|
|
604 |
|
|
609 |
|
calcNdfTrans(); |
610 |
|
|
611 |
|
fortranInitialized_ = true; |
612 |
< |
} |
612 |
> |
} |
613 |
|
|
614 |
< |
std::set<AtomType*> SimInfo::getUniqueAtomTypes() { |
614 |
> |
std::set<AtomType*> SimInfo::getUniqueAtomTypes() { |
615 |
|
SimInfo::MoleculeIterator mi; |
616 |
|
Molecule* mol; |
617 |
|
Molecule::AtomIterator ai; |
620 |
|
|
621 |
|
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
622 |
|
|
623 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
624 |
< |
atomTypes.insert(atom->getAtomType()); |
625 |
< |
} |
623 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
624 |
> |
atomTypes.insert(atom->getAtomType()); |
625 |
> |
} |
626 |
|
|
627 |
|
} |
628 |
|
|
629 |
|
return atomTypes; |
630 |
< |
} |
630 |
> |
} |
631 |
|
|
632 |
< |
void SimInfo::setupSimType() { |
632 |
> |
void SimInfo::setupSimType() { |
633 |
|
std::set<AtomType*>::iterator i; |
634 |
|
std::set<AtomType*> atomTypes; |
635 |
|
atomTypes = getUniqueAtomTypes(); |
637 |
|
int useLennardJones = 0; |
638 |
|
int useElectrostatic = 0; |
639 |
|
int useEAM = 0; |
640 |
+ |
int useSC = 0; |
641 |
|
int useCharge = 0; |
642 |
|
int useDirectional = 0; |
643 |
|
int useDipole = 0; |
644 |
|
int useGayBerne = 0; |
645 |
|
int useSticky = 0; |
646 |
+ |
int useStickyPower = 0; |
647 |
|
int useShape = 0; |
648 |
|
int useFLARB = 0; //it is not in AtomType yet |
649 |
|
int useDirectionalAtom = 0; |
650 |
|
int useElectrostatics = 0; |
651 |
|
//usePBC and useRF are from simParams |
652 |
< |
int usePBC = simParams_->getPBC(); |
653 |
< |
int useRF = simParams_->getUseRF(); |
652 |
> |
int usePBC = simParams_->getUsePeriodicBoundaryConditions(); |
653 |
> |
int useRF; |
654 |
> |
int useSF; |
655 |
> |
std::string myMethod; |
656 |
|
|
657 |
+ |
// set the useRF logical |
658 |
+ |
useRF = 0; |
659 |
+ |
useSF = 0; |
660 |
+ |
|
661 |
+ |
|
662 |
+ |
if (simParams_->haveElectrostaticSummationMethod()) { |
663 |
+ |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
664 |
+ |
toUpper(myMethod); |
665 |
+ |
if (myMethod == "REACTION_FIELD") { |
666 |
+ |
useRF=1; |
667 |
+ |
} else { |
668 |
+ |
if (myMethod == "SHIFTED_FORCE") { |
669 |
+ |
useSF = 1; |
670 |
+ |
} |
671 |
+ |
} |
672 |
+ |
} |
673 |
+ |
|
674 |
|
//loop over all of the atom types |
675 |
|
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
676 |
< |
useLennardJones |= (*i)->isLennardJones(); |
677 |
< |
useElectrostatic |= (*i)->isElectrostatic(); |
678 |
< |
useEAM |= (*i)->isEAM(); |
679 |
< |
useCharge |= (*i)->isCharge(); |
680 |
< |
useDirectional |= (*i)->isDirectional(); |
681 |
< |
useDipole |= (*i)->isDipole(); |
682 |
< |
useGayBerne |= (*i)->isGayBerne(); |
683 |
< |
useSticky |= (*i)->isSticky(); |
684 |
< |
useShape |= (*i)->isShape(); |
676 |
> |
useLennardJones |= (*i)->isLennardJones(); |
677 |
> |
useElectrostatic |= (*i)->isElectrostatic(); |
678 |
> |
useEAM |= (*i)->isEAM(); |
679 |
> |
useSC |= (*i)->isSC(); |
680 |
> |
useCharge |= (*i)->isCharge(); |
681 |
> |
useDirectional |= (*i)->isDirectional(); |
682 |
> |
useDipole |= (*i)->isDipole(); |
683 |
> |
useGayBerne |= (*i)->isGayBerne(); |
684 |
> |
useSticky |= (*i)->isSticky(); |
685 |
> |
useStickyPower |= (*i)->isStickyPower(); |
686 |
> |
useShape |= (*i)->isShape(); |
687 |
|
} |
688 |
|
|
689 |
< |
if (useSticky || useDipole || useGayBerne || useShape) { |
690 |
< |
useDirectionalAtom = 1; |
689 |
> |
if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) { |
690 |
> |
useDirectionalAtom = 1; |
691 |
|
} |
692 |
|
|
693 |
|
if (useCharge || useDipole) { |
694 |
< |
useElectrostatics = 1; |
694 |
> |
useElectrostatics = 1; |
695 |
|
} |
696 |
|
|
697 |
|
#ifdef IS_MPI |
718 |
|
temp = useSticky; |
719 |
|
MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
720 |
|
|
721 |
+ |
temp = useStickyPower; |
722 |
+ |
MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
723 |
+ |
|
724 |
|
temp = useGayBerne; |
725 |
|
MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
726 |
|
|
727 |
|
temp = useEAM; |
728 |
|
MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
729 |
|
|
730 |
+ |
temp = useSC; |
731 |
+ |
MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
732 |
+ |
|
733 |
|
temp = useShape; |
734 |
|
MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
735 |
|
|
738 |
|
|
739 |
|
temp = useRF; |
740 |
|
MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
741 |
< |
|
741 |
> |
|
742 |
> |
temp = useSF; |
743 |
> |
MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
744 |
> |
|
745 |
|
#endif |
746 |
|
|
747 |
|
fInfo_.SIM_uses_PBC = usePBC; |
751 |
|
fInfo_.SIM_uses_Charges = useCharge; |
752 |
|
fInfo_.SIM_uses_Dipoles = useDipole; |
753 |
|
fInfo_.SIM_uses_Sticky = useSticky; |
754 |
+ |
fInfo_.SIM_uses_StickyPower = useStickyPower; |
755 |
|
fInfo_.SIM_uses_GayBerne = useGayBerne; |
756 |
|
fInfo_.SIM_uses_EAM = useEAM; |
757 |
+ |
fInfo_.SIM_uses_SC = useSC; |
758 |
|
fInfo_.SIM_uses_Shapes = useShape; |
759 |
|
fInfo_.SIM_uses_FLARB = useFLARB; |
760 |
|
fInfo_.SIM_uses_RF = useRF; |
761 |
+ |
fInfo_.SIM_uses_SF = useSF; |
762 |
|
|
763 |
< |
if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { |
764 |
< |
|
765 |
< |
if (simParams_->haveDielectric()) { |
766 |
< |
fInfo_.dielect = simParams_->getDielectric(); |
767 |
< |
} else { |
768 |
< |
sprintf(painCave.errMsg, |
769 |
< |
"SimSetup Error: No Dielectric constant was set.\n" |
770 |
< |
"\tYou are trying to use Reaction Field without" |
771 |
< |
"\tsetting a dielectric constant!\n"); |
772 |
< |
painCave.isFatal = 1; |
773 |
< |
simError(); |
774 |
< |
} |
584 |
< |
|
585 |
< |
} else { |
586 |
< |
fInfo_.dielect = 0.0; |
763 |
> |
if( myMethod == "REACTION_FIELD") { |
764 |
> |
|
765 |
> |
if (simParams_->haveDielectric()) { |
766 |
> |
fInfo_.dielect = simParams_->getDielectric(); |
767 |
> |
} else { |
768 |
> |
sprintf(painCave.errMsg, |
769 |
> |
"SimSetup Error: No Dielectric constant was set.\n" |
770 |
> |
"\tYou are trying to use Reaction Field without" |
771 |
> |
"\tsetting a dielectric constant!\n"); |
772 |
> |
painCave.isFatal = 1; |
773 |
> |
simError(); |
774 |
> |
} |
775 |
|
} |
776 |
|
|
777 |
< |
} |
777 |
> |
} |
778 |
|
|
779 |
< |
void SimInfo::setupFortranSim() { |
779 |
> |
void SimInfo::setupFortranSim() { |
780 |
|
int isError; |
781 |
|
int nExclude; |
782 |
|
std::vector<int> fortranGlobalGroupMembership; |
786 |
|
|
787 |
|
//globalGroupMembership_ is filled by SimCreator |
788 |
|
for (int i = 0; i < nGlobalAtoms_; i++) { |
789 |
< |
fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1); |
789 |
> |
fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1); |
790 |
|
} |
791 |
|
|
792 |
|
//calculate mass ratio of cutoff group |
803 |
|
mfact.reserve(getNCutoffGroups()); |
804 |
|
|
805 |
|
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
806 |
< |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
806 |
> |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
807 |
|
|
808 |
< |
totalMass = cg->getMass(); |
809 |
< |
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
810 |
< |
mfact.push_back(atom->getMass()/totalMass); |
811 |
< |
} |
808 |
> |
totalMass = cg->getMass(); |
809 |
> |
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
810 |
> |
// Check for massless groups - set mfact to 1 if true |
811 |
> |
if (totalMass != 0) |
812 |
> |
mfact.push_back(atom->getMass()/totalMass); |
813 |
> |
else |
814 |
> |
mfact.push_back( 1.0 ); |
815 |
> |
} |
816 |
|
|
817 |
< |
} |
817 |
> |
} |
818 |
|
} |
819 |
|
|
820 |
|
//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!) |
824 |
|
identArray.reserve(getNAtoms()); |
825 |
|
|
826 |
|
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
827 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
828 |
< |
identArray.push_back(atom->getIdent()); |
829 |
< |
} |
827 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
828 |
> |
identArray.push_back(atom->getIdent()); |
829 |
> |
} |
830 |
|
} |
831 |
|
|
832 |
|
//fill molMembershipArray |
833 |
|
//molMembershipArray is filled by SimCreator |
834 |
|
std::vector<int> molMembershipArray(nGlobalAtoms_); |
835 |
|
for (int i = 0; i < nGlobalAtoms_; i++) { |
836 |
< |
molMembershipArray[i] = globalMolMembership_[i] + 1; |
836 |
> |
molMembershipArray[i] = globalMolMembership_[i] + 1; |
837 |
|
} |
838 |
|
|
839 |
|
//setup fortran simulation |
648 |
– |
//gloalExcludes and molMembershipArray should go away (They are never used) |
649 |
– |
//why the hell fortran need to know molecule? |
650 |
– |
//OOPSE = Object-Obfuscated Parallel Simulation Engine |
840 |
|
int nGlobalExcludes = 0; |
841 |
|
int* globalExcludes = NULL; |
842 |
|
int* excludeList = exclude_.getExcludeList(); |
843 |
|
setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList , |
844 |
< |
&nGlobalExcludes, globalExcludes, &molMembershipArray[0], |
845 |
< |
&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError); |
844 |
> |
&nGlobalExcludes, globalExcludes, &molMembershipArray[0], |
845 |
> |
&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError); |
846 |
|
|
847 |
|
if( isError ){ |
848 |
|
|
849 |
< |
sprintf( painCave.errMsg, |
850 |
< |
"There was an error setting the simulation information in fortran.\n" ); |
851 |
< |
painCave.isFatal = 1; |
852 |
< |
painCave.severity = OOPSE_ERROR; |
853 |
< |
simError(); |
849 |
> |
sprintf( painCave.errMsg, |
850 |
> |
"There was an error setting the simulation information in fortran.\n" ); |
851 |
> |
painCave.isFatal = 1; |
852 |
> |
painCave.severity = OOPSE_ERROR; |
853 |
> |
simError(); |
854 |
|
} |
855 |
|
|
856 |
|
#ifdef IS_MPI |
857 |
|
sprintf( checkPointMsg, |
858 |
< |
"succesfully sent the simulation information to fortran.\n"); |
858 |
> |
"succesfully sent the simulation information to fortran.\n"); |
859 |
|
MPIcheckPoint(); |
860 |
|
#endif // is_mpi |
861 |
< |
} |
861 |
> |
} |
862 |
|
|
863 |
|
|
864 |
|
#ifdef IS_MPI |
865 |
< |
void SimInfo::setupFortranParallel() { |
865 |
> |
void SimInfo::setupFortranParallel() { |
866 |
|
|
867 |
|
//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex |
868 |
|
std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0); |
878 |
|
|
879 |
|
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
880 |
|
|
881 |
< |
//local index(index in DataStorge) of atom is important |
882 |
< |
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
883 |
< |
localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1; |
884 |
< |
} |
881 |
> |
//local index(index in DataStorge) of atom is important |
882 |
> |
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
883 |
> |
localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1; |
884 |
> |
} |
885 |
|
|
886 |
< |
//local index of cutoff group is trivial, it only depends on the order of travesing |
887 |
< |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
888 |
< |
localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1); |
889 |
< |
} |
886 |
> |
//local index of cutoff group is trivial, it only depends on the order of travesing |
887 |
> |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
888 |
> |
localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1); |
889 |
> |
} |
890 |
|
|
891 |
|
} |
892 |
|
|
906 |
|
&localToGlobalCutoffGroupIndex[0], &isError); |
907 |
|
|
908 |
|
if (isError) { |
909 |
< |
sprintf(painCave.errMsg, |
910 |
< |
"mpiRefresh errror: fortran didn't like something we gave it.\n"); |
911 |
< |
painCave.isFatal = 1; |
912 |
< |
simError(); |
909 |
> |
sprintf(painCave.errMsg, |
910 |
> |
"mpiRefresh errror: fortran didn't like something we gave it.\n"); |
911 |
> |
painCave.isFatal = 1; |
912 |
> |
simError(); |
913 |
|
} |
914 |
|
|
915 |
|
sprintf(checkPointMsg, " mpiRefresh successful.\n"); |
916 |
|
MPIcheckPoint(); |
917 |
|
|
918 |
|
|
919 |
< |
} |
919 |
> |
} |
920 |
|
|
921 |
|
#endif |
922 |
|
|
923 |
< |
double SimInfo::calcMaxCutoffRadius() { |
923 |
> |
void SimInfo::setupCutoff() { |
924 |
> |
|
925 |
> |
ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions(); |
926 |
|
|
927 |
+ |
// Check the cutoff policy |
928 |
+ |
int cp = TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default |
929 |
|
|
930 |
< |
std::set<AtomType*> atomTypes; |
931 |
< |
std::set<AtomType*>::iterator i; |
932 |
< |
std::vector<double> cutoffRadius; |
933 |
< |
|
934 |
< |
//get the unique atom types |
742 |
< |
atomTypes = getUniqueAtomTypes(); |
743 |
< |
|
744 |
< |
//query the max cutoff radius among these atom types |
745 |
< |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
746 |
< |
cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i)); |
930 |
> |
std::string myPolicy; |
931 |
> |
if (forceFieldOptions_.haveCutoffPolicy()){ |
932 |
> |
myPolicy = forceFieldOptions_.getCutoffPolicy(); |
933 |
> |
}else if (simParams_->haveCutoffPolicy()) { |
934 |
> |
myPolicy = simParams_->getCutoffPolicy(); |
935 |
|
} |
936 |
|
|
937 |
< |
double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end())); |
938 |
< |
#ifdef IS_MPI |
939 |
< |
//pick the max cutoff radius among the processors |
940 |
< |
#endif |
937 |
> |
if (!myPolicy.empty()){ |
938 |
> |
toUpper(myPolicy); |
939 |
> |
if (myPolicy == "MIX") { |
940 |
> |
cp = MIX_CUTOFF_POLICY; |
941 |
> |
} else { |
942 |
> |
if (myPolicy == "MAX") { |
943 |
> |
cp = MAX_CUTOFF_POLICY; |
944 |
> |
} else { |
945 |
> |
if (myPolicy == "TRADITIONAL") { |
946 |
> |
cp = TRADITIONAL_CUTOFF_POLICY; |
947 |
> |
} else { |
948 |
> |
// throw error |
949 |
> |
sprintf( painCave.errMsg, |
950 |
> |
"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() ); |
951 |
> |
painCave.isFatal = 1; |
952 |
> |
simError(); |
953 |
> |
} |
954 |
> |
} |
955 |
> |
} |
956 |
> |
} |
957 |
> |
notifyFortranCutoffPolicy(&cp); |
958 |
|
|
959 |
< |
return maxCutoffRadius; |
960 |
< |
} |
961 |
< |
|
962 |
< |
void SimInfo::getCutoff(double& rcut, double& rsw) { |
963 |
< |
|
964 |
< |
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
959 |
> |
// Check the Skin Thickness for neighborlists |
960 |
> |
double skin; |
961 |
> |
if (simParams_->haveSkinThickness()) { |
962 |
> |
skin = simParams_->getSkinThickness(); |
963 |
> |
notifyFortranSkinThickness(&skin); |
964 |
> |
} |
965 |
|
|
966 |
< |
if (!simParams_->haveRcut()){ |
967 |
< |
sprintf(painCave.errMsg, |
966 |
> |
// Check if the cutoff was set explicitly: |
967 |
> |
if (simParams_->haveCutoffRadius()) { |
968 |
> |
rcut_ = simParams_->getCutoffRadius(); |
969 |
> |
if (simParams_->haveSwitchingRadius()) { |
970 |
> |
rsw_ = simParams_->getSwitchingRadius(); |
971 |
> |
} else { |
972 |
> |
rsw_ = rcut_; |
973 |
> |
} |
974 |
> |
notifyFortranCutoffs(&rcut_, &rsw_); |
975 |
> |
|
976 |
> |
} else { |
977 |
> |
|
978 |
> |
// For electrostatic atoms, we'll assume a large safe value: |
979 |
> |
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
980 |
> |
sprintf(painCave.errMsg, |
981 |
|
"SimCreator Warning: No value was set for the cutoffRadius.\n" |
982 |
|
"\tOOPSE will use a default value of 15.0 angstroms" |
983 |
|
"\tfor the cutoffRadius.\n"); |
984 |
< |
painCave.isFatal = 0; |
985 |
< |
simError(); |
986 |
< |
rcut = 15.0; |
987 |
< |
} else{ |
988 |
< |
rcut = simParams_->getRcut(); |
984 |
> |
painCave.isFatal = 0; |
985 |
> |
simError(); |
986 |
> |
rcut_ = 15.0; |
987 |
> |
|
988 |
> |
if (simParams_->haveElectrostaticSummationMethod()) { |
989 |
> |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
990 |
> |
toUpper(myMethod); |
991 |
> |
if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") { |
992 |
> |
if (simParams_->haveSwitchingRadius()){ |
993 |
> |
sprintf(painCave.errMsg, |
994 |
> |
"SimInfo Warning: A value was set for the switchingRadius\n" |
995 |
> |
"\teven though the electrostaticSummationMethod was\n" |
996 |
> |
"\tset to %s\n", myMethod.c_str()); |
997 |
> |
painCave.isFatal = 1; |
998 |
> |
simError(); |
999 |
> |
} |
1000 |
> |
} |
1001 |
|
} |
1002 |
< |
|
1003 |
< |
if (!simParams_->haveRsw()){ |
1004 |
< |
sprintf(painCave.errMsg, |
1005 |
< |
"SimCreator Warning: No value was set for switchingRadius.\n" |
1006 |
< |
"\tOOPSE will use a default value of\n" |
1007 |
< |
"\t0.95 * cutoffRadius for the switchingRadius\n"); |
1008 |
< |
painCave.isFatal = 0; |
1009 |
< |
simError(); |
1010 |
< |
rsw = 0.95 * rcut; |
1011 |
< |
} else{ |
1012 |
< |
rsw = simParams_->getRsw(); |
1002 |
> |
|
1003 |
> |
if (simParams_->haveSwitchingRadius()){ |
1004 |
> |
rsw_ = simParams_->getSwitchingRadius(); |
1005 |
> |
} else { |
1006 |
> |
sprintf(painCave.errMsg, |
1007 |
> |
"SimCreator Warning: No value was set for switchingRadius.\n" |
1008 |
> |
"\tOOPSE will use a default value of\n" |
1009 |
> |
"\t0.85 * cutoffRadius for the switchingRadius\n"); |
1010 |
> |
painCave.isFatal = 0; |
1011 |
> |
simError(); |
1012 |
> |
rsw_ = 0.85 * rcut_; |
1013 |
|
} |
1014 |
< |
|
1015 |
< |
} else { |
1016 |
< |
// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
1017 |
< |
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
1014 |
> |
notifyFortranCutoffs(&rcut_, &rsw_); |
1015 |
> |
} else { |
1016 |
> |
// We didn't set rcut explicitly, and we don't have electrostatic atoms, so |
1017 |
> |
// We'll punt and let fortran figure out the cutoffs later. |
1018 |
|
|
1019 |
< |
if (simParams_->haveRcut()) { |
790 |
< |
rcut = simParams_->getRcut(); |
791 |
< |
} else { |
792 |
< |
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
793 |
< |
rcut = calcMaxCutoffRadius(); |
794 |
< |
} |
1019 |
> |
notifyFortranYouAreOnYourOwn(); |
1020 |
|
|
1021 |
< |
if (simParams_->haveRsw()) { |
797 |
< |
rsw = simParams_->getRsw(); |
798 |
< |
} else { |
799 |
< |
rsw = rcut; |
800 |
< |
} |
801 |
< |
|
1021 |
> |
} |
1022 |
|
} |
1023 |
< |
} |
1023 |
> |
} |
1024 |
|
|
1025 |
< |
void SimInfo::setupCutoff() { |
1026 |
< |
getCutoff(rcut_, rsw_); |
1027 |
< |
double rnblist = rcut_ + 1; // skin of neighbor list |
1025 |
> |
void SimInfo::setupElectrostaticSummationMethod( int isError ) { |
1026 |
> |
|
1027 |
> |
int errorOut; |
1028 |
> |
int esm = NONE; |
1029 |
> |
int sm = UNDAMPED; |
1030 |
> |
double alphaVal; |
1031 |
> |
double dielectric; |
1032 |
|
|
1033 |
< |
//Pass these cutoff radius etc. to fortran. This function should be called once and only once |
1034 |
< |
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist); |
1035 |
< |
} |
1033 |
> |
errorOut = isError; |
1034 |
> |
alphaVal = simParams_->getDampingAlpha(); |
1035 |
> |
dielectric = simParams_->getDielectric(); |
1036 |
|
|
1037 |
< |
void SimInfo::addProperty(GenericData* genData) { |
1038 |
< |
properties_.addProperty(genData); |
1039 |
< |
} |
1040 |
< |
|
1041 |
< |
void SimInfo::removeProperty(const std::string& propName) { |
1042 |
< |
properties_.removeProperty(propName); |
1043 |
< |
} |
1044 |
< |
|
1045 |
< |
void SimInfo::clearProperties() { |
1046 |
< |
properties_.clearProperties(); |
1047 |
< |
} |
1048 |
< |
|
1049 |
< |
std::vector<std::string> SimInfo::getPropertyNames() { |
1050 |
< |
return properties_.getPropertyNames(); |
1051 |
< |
} |
1052 |
< |
|
1053 |
< |
std::vector<GenericData*> SimInfo::getProperties() { |
1054 |
< |
return properties_.getProperties(); |
1055 |
< |
} |
1056 |
< |
|
1057 |
< |
GenericData* SimInfo::getPropertyByName(const std::string& propName) { |
1058 |
< |
return properties_.getPropertyByName(propName); |
1059 |
< |
} |
1060 |
< |
|
1061 |
< |
void SimInfo::setSnapshotManager(SnapshotManager* sman) { |
1062 |
< |
if (sman_ == sman_) { |
1063 |
< |
return; |
1037 |
> |
if (simParams_->haveElectrostaticSummationMethod()) { |
1038 |
> |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
1039 |
> |
toUpper(myMethod); |
1040 |
> |
if (myMethod == "NONE") { |
1041 |
> |
esm = NONE; |
1042 |
> |
} else { |
1043 |
> |
if (myMethod == "SWITCHING_FUNCTION") { |
1044 |
> |
esm = SWITCHING_FUNCTION; |
1045 |
> |
} else { |
1046 |
> |
if (myMethod == "SHIFTED_POTENTIAL") { |
1047 |
> |
esm = SHIFTED_POTENTIAL; |
1048 |
> |
} else { |
1049 |
> |
if (myMethod == "SHIFTED_FORCE") { |
1050 |
> |
esm = SHIFTED_FORCE; |
1051 |
> |
} else { |
1052 |
> |
if (myMethod == "REACTION_FIELD") { |
1053 |
> |
esm = REACTION_FIELD; |
1054 |
> |
} else { |
1055 |
> |
// throw error |
1056 |
> |
sprintf( painCave.errMsg, |
1057 |
> |
"SimInfo error: Unknown electrostaticSummationMethod.\n" |
1058 |
> |
"\t(Input file specified %s .)\n" |
1059 |
> |
"\telectrostaticSummationMethod must be one of: \"none\",\n" |
1060 |
> |
"\t\"shifted_potential\", \"shifted_force\", or \n" |
1061 |
> |
"\t\"reaction_field\".\n", myMethod.c_str() ); |
1062 |
> |
painCave.isFatal = 1; |
1063 |
> |
simError(); |
1064 |
> |
} |
1065 |
> |
} |
1066 |
> |
} |
1067 |
> |
} |
1068 |
> |
} |
1069 |
|
} |
1070 |
|
|
1071 |
+ |
if (simParams_->haveElectrostaticScreeningMethod()) { |
1072 |
+ |
std::string myScreen = simParams_->getElectrostaticScreeningMethod(); |
1073 |
+ |
toUpper(myScreen); |
1074 |
+ |
if (myScreen == "UNDAMPED") { |
1075 |
+ |
sm = UNDAMPED; |
1076 |
+ |
} else { |
1077 |
+ |
if (myScreen == "DAMPED") { |
1078 |
+ |
sm = DAMPED; |
1079 |
+ |
if (!simParams_->haveDampingAlpha()) { |
1080 |
+ |
//throw error |
1081 |
+ |
sprintf( painCave.errMsg, |
1082 |
+ |
"SimInfo warning: dampingAlpha was not specified in the input file.\n" |
1083 |
+ |
"\tA default value of %f (1/ang) will be used.\n", alphaVal); |
1084 |
+ |
painCave.isFatal = 0; |
1085 |
+ |
simError(); |
1086 |
+ |
} |
1087 |
+ |
} else { |
1088 |
+ |
// throw error |
1089 |
+ |
sprintf( painCave.errMsg, |
1090 |
+ |
"SimInfo error: Unknown electrostaticScreeningMethod.\n" |
1091 |
+ |
"\t(Input file specified %s .)\n" |
1092 |
+ |
"\telectrostaticScreeningMethod must be one of: \"undamped\"\n" |
1093 |
+ |
"or \"damped\".\n", myScreen.c_str() ); |
1094 |
+ |
painCave.isFatal = 1; |
1095 |
+ |
simError(); |
1096 |
+ |
} |
1097 |
+ |
} |
1098 |
+ |
} |
1099 |
+ |
|
1100 |
+ |
// let's pass some summation method variables to fortran |
1101 |
+ |
setElectrostaticSumMethod( &esm ); |
1102 |
+ |
setFortranElectrostaticMethod( &esm ); |
1103 |
+ |
setScreeningMethod( &sm ); |
1104 |
+ |
setDampingAlpha( &alphaVal ); |
1105 |
+ |
setReactionFieldDielectric( &dielectric ); |
1106 |
+ |
initFortranFF( &errorOut ); |
1107 |
+ |
} |
1108 |
+ |
|
1109 |
+ |
void SimInfo::setupSwitchingFunction() { |
1110 |
+ |
int ft = CUBIC; |
1111 |
+ |
|
1112 |
+ |
if (simParams_->haveSwitchingFunctionType()) { |
1113 |
+ |
std::string funcType = simParams_->getSwitchingFunctionType(); |
1114 |
+ |
toUpper(funcType); |
1115 |
+ |
if (funcType == "CUBIC") { |
1116 |
+ |
ft = CUBIC; |
1117 |
+ |
} else { |
1118 |
+ |
if (funcType == "FIFTH_ORDER_POLYNOMIAL") { |
1119 |
+ |
ft = FIFTH_ORDER_POLY; |
1120 |
+ |
} else { |
1121 |
+ |
// throw error |
1122 |
+ |
sprintf( painCave.errMsg, |
1123 |
+ |
"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() ); |
1124 |
+ |
painCave.isFatal = 1; |
1125 |
+ |
simError(); |
1126 |
+ |
} |
1127 |
+ |
} |
1128 |
+ |
} |
1129 |
+ |
|
1130 |
+ |
// send switching function notification to switcheroo |
1131 |
+ |
setFunctionType(&ft); |
1132 |
+ |
|
1133 |
+ |
} |
1134 |
+ |
|
1135 |
+ |
void SimInfo::addProperty(GenericData* genData) { |
1136 |
+ |
properties_.addProperty(genData); |
1137 |
+ |
} |
1138 |
+ |
|
1139 |
+ |
void SimInfo::removeProperty(const std::string& propName) { |
1140 |
+ |
properties_.removeProperty(propName); |
1141 |
+ |
} |
1142 |
+ |
|
1143 |
+ |
void SimInfo::clearProperties() { |
1144 |
+ |
properties_.clearProperties(); |
1145 |
+ |
} |
1146 |
+ |
|
1147 |
+ |
std::vector<std::string> SimInfo::getPropertyNames() { |
1148 |
+ |
return properties_.getPropertyNames(); |
1149 |
+ |
} |
1150 |
+ |
|
1151 |
+ |
std::vector<GenericData*> SimInfo::getProperties() { |
1152 |
+ |
return properties_.getProperties(); |
1153 |
+ |
} |
1154 |
+ |
|
1155 |
+ |
GenericData* SimInfo::getPropertyByName(const std::string& propName) { |
1156 |
+ |
return properties_.getPropertyByName(propName); |
1157 |
+ |
} |
1158 |
+ |
|
1159 |
+ |
void SimInfo::setSnapshotManager(SnapshotManager* sman) { |
1160 |
+ |
if (sman_ == sman) { |
1161 |
+ |
return; |
1162 |
+ |
} |
1163 |
|
delete sman_; |
1164 |
|
sman_ = sman; |
1165 |
|
|
1172 |
|
|
1173 |
|
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
1174 |
|
|
1175 |
< |
for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) { |
1176 |
< |
atom->setSnapshotManager(sman_); |
1177 |
< |
} |
1175 |
> |
for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) { |
1176 |
> |
atom->setSnapshotManager(sman_); |
1177 |
> |
} |
1178 |
|
|
1179 |
< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
1180 |
< |
rb->setSnapshotManager(sman_); |
1181 |
< |
} |
1179 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
1180 |
> |
rb->setSnapshotManager(sman_); |
1181 |
> |
} |
1182 |
|
} |
1183 |
|
|
1184 |
< |
} |
1184 |
> |
} |
1185 |
|
|
1186 |
< |
Vector3d SimInfo::getComVel(){ |
1186 |
> |
Vector3d SimInfo::getComVel(){ |
1187 |
|
SimInfo::MoleculeIterator i; |
1188 |
|
Molecule* mol; |
1189 |
|
|
1192 |
|
|
1193 |
|
|
1194 |
|
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1195 |
< |
double mass = mol->getMass(); |
1196 |
< |
totalMass += mass; |
1197 |
< |
comVel += mass * mol->getComVel(); |
1195 |
> |
double mass = mol->getMass(); |
1196 |
> |
totalMass += mass; |
1197 |
> |
comVel += mass * mol->getComVel(); |
1198 |
|
} |
1199 |
|
|
1200 |
|
#ifdef IS_MPI |
1207 |
|
comVel /= totalMass; |
1208 |
|
|
1209 |
|
return comVel; |
1210 |
< |
} |
1210 |
> |
} |
1211 |
|
|
1212 |
< |
Vector3d SimInfo::getCom(){ |
1212 |
> |
Vector3d SimInfo::getCom(){ |
1213 |
|
SimInfo::MoleculeIterator i; |
1214 |
|
Molecule* mol; |
1215 |
|
|
1217 |
|
double totalMass = 0.0; |
1218 |
|
|
1219 |
|
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1220 |
< |
double mass = mol->getMass(); |
1221 |
< |
totalMass += mass; |
1222 |
< |
com += mass * mol->getCom(); |
1220 |
> |
double mass = mol->getMass(); |
1221 |
> |
totalMass += mass; |
1222 |
> |
com += mass * mol->getCom(); |
1223 |
|
} |
1224 |
|
|
1225 |
|
#ifdef IS_MPI |
1233 |
|
|
1234 |
|
return com; |
1235 |
|
|
1236 |
< |
} |
1236 |
> |
} |
1237 |
|
|
1238 |
< |
std::ostream& operator <<(std::ostream& o, SimInfo& info) { |
1238 |
> |
std::ostream& operator <<(std::ostream& o, SimInfo& info) { |
1239 |
|
|
1240 |
|
return o; |
1241 |
< |
} |
1241 |
> |
} |
1242 |
> |
|
1243 |
> |
|
1244 |
> |
/* |
1245 |
> |
Returns center of mass and center of mass velocity in one function call. |
1246 |
> |
*/ |
1247 |
> |
|
1248 |
> |
void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){ |
1249 |
> |
SimInfo::MoleculeIterator i; |
1250 |
> |
Molecule* mol; |
1251 |
> |
|
1252 |
> |
|
1253 |
> |
double totalMass = 0.0; |
1254 |
> |
|
1255 |
|
|
1256 |
+ |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1257 |
+ |
double mass = mol->getMass(); |
1258 |
+ |
totalMass += mass; |
1259 |
+ |
com += mass * mol->getCom(); |
1260 |
+ |
comVel += mass * mol->getComVel(); |
1261 |
+ |
} |
1262 |
+ |
|
1263 |
+ |
#ifdef IS_MPI |
1264 |
+ |
double tmpMass = totalMass; |
1265 |
+ |
Vector3d tmpCom(com); |
1266 |
+ |
Vector3d tmpComVel(comVel); |
1267 |
+ |
MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1268 |
+ |
MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1269 |
+ |
MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1270 |
+ |
#endif |
1271 |
+ |
|
1272 |
+ |
com /= totalMass; |
1273 |
+ |
comVel /= totalMass; |
1274 |
+ |
} |
1275 |
+ |
|
1276 |
+ |
/* |
1277 |
+ |
Return intertia tensor for entire system and angular momentum Vector. |
1278 |
+ |
|
1279 |
+ |
|
1280 |
+ |
[ Ixx -Ixy -Ixz ] |
1281 |
+ |
J =| -Iyx Iyy -Iyz | |
1282 |
+ |
[ -Izx -Iyz Izz ] |
1283 |
+ |
*/ |
1284 |
+ |
|
1285 |
+ |
void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){ |
1286 |
+ |
|
1287 |
+ |
|
1288 |
+ |
double xx = 0.0; |
1289 |
+ |
double yy = 0.0; |
1290 |
+ |
double zz = 0.0; |
1291 |
+ |
double xy = 0.0; |
1292 |
+ |
double xz = 0.0; |
1293 |
+ |
double yz = 0.0; |
1294 |
+ |
Vector3d com(0.0); |
1295 |
+ |
Vector3d comVel(0.0); |
1296 |
+ |
|
1297 |
+ |
getComAll(com, comVel); |
1298 |
+ |
|
1299 |
+ |
SimInfo::MoleculeIterator i; |
1300 |
+ |
Molecule* mol; |
1301 |
+ |
|
1302 |
+ |
Vector3d thisq(0.0); |
1303 |
+ |
Vector3d thisv(0.0); |
1304 |
+ |
|
1305 |
+ |
double thisMass = 0.0; |
1306 |
+ |
|
1307 |
+ |
|
1308 |
+ |
|
1309 |
+ |
|
1310 |
+ |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1311 |
+ |
|
1312 |
+ |
thisq = mol->getCom()-com; |
1313 |
+ |
thisv = mol->getComVel()-comVel; |
1314 |
+ |
thisMass = mol->getMass(); |
1315 |
+ |
// Compute moment of intertia coefficients. |
1316 |
+ |
xx += thisq[0]*thisq[0]*thisMass; |
1317 |
+ |
yy += thisq[1]*thisq[1]*thisMass; |
1318 |
+ |
zz += thisq[2]*thisq[2]*thisMass; |
1319 |
+ |
|
1320 |
+ |
// compute products of intertia |
1321 |
+ |
xy += thisq[0]*thisq[1]*thisMass; |
1322 |
+ |
xz += thisq[0]*thisq[2]*thisMass; |
1323 |
+ |
yz += thisq[1]*thisq[2]*thisMass; |
1324 |
+ |
|
1325 |
+ |
angularMomentum += cross( thisq, thisv ) * thisMass; |
1326 |
+ |
|
1327 |
+ |
} |
1328 |
+ |
|
1329 |
+ |
|
1330 |
+ |
inertiaTensor(0,0) = yy + zz; |
1331 |
+ |
inertiaTensor(0,1) = -xy; |
1332 |
+ |
inertiaTensor(0,2) = -xz; |
1333 |
+ |
inertiaTensor(1,0) = -xy; |
1334 |
+ |
inertiaTensor(1,1) = xx + zz; |
1335 |
+ |
inertiaTensor(1,2) = -yz; |
1336 |
+ |
inertiaTensor(2,0) = -xz; |
1337 |
+ |
inertiaTensor(2,1) = -yz; |
1338 |
+ |
inertiaTensor(2,2) = xx + yy; |
1339 |
+ |
|
1340 |
+ |
#ifdef IS_MPI |
1341 |
+ |
Mat3x3d tmpI(inertiaTensor); |
1342 |
+ |
Vector3d tmpAngMom; |
1343 |
+ |
MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1344 |
+ |
MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1345 |
+ |
#endif |
1346 |
+ |
|
1347 |
+ |
return; |
1348 |
+ |
} |
1349 |
+ |
|
1350 |
+ |
//Returns the angular momentum of the system |
1351 |
+ |
Vector3d SimInfo::getAngularMomentum(){ |
1352 |
+ |
|
1353 |
+ |
Vector3d com(0.0); |
1354 |
+ |
Vector3d comVel(0.0); |
1355 |
+ |
Vector3d angularMomentum(0.0); |
1356 |
+ |
|
1357 |
+ |
getComAll(com,comVel); |
1358 |
+ |
|
1359 |
+ |
SimInfo::MoleculeIterator i; |
1360 |
+ |
Molecule* mol; |
1361 |
+ |
|
1362 |
+ |
Vector3d thisr(0.0); |
1363 |
+ |
Vector3d thisp(0.0); |
1364 |
+ |
|
1365 |
+ |
double thisMass; |
1366 |
+ |
|
1367 |
+ |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1368 |
+ |
thisMass = mol->getMass(); |
1369 |
+ |
thisr = mol->getCom()-com; |
1370 |
+ |
thisp = (mol->getComVel()-comVel)*thisMass; |
1371 |
+ |
|
1372 |
+ |
angularMomentum += cross( thisr, thisp ); |
1373 |
+ |
|
1374 |
+ |
} |
1375 |
+ |
|
1376 |
+ |
#ifdef IS_MPI |
1377 |
+ |
Vector3d tmpAngMom; |
1378 |
+ |
MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1379 |
+ |
#endif |
1380 |
+ |
|
1381 |
+ |
return angularMomentum; |
1382 |
+ |
} |
1383 |
+ |
|
1384 |
+ |
|
1385 |
|
}//end namespace oopse |
1386 |
|
|