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/* |
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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#include "brains/SimInfo.hpp" |
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#include "math/Vector3.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "UseTheForce/fCutoffPolicy.h" |
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#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h" |
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#include "UseTheForce/DarkSide/fScreeningMethod.h" |
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#include "UseTheForce/doForces_interface.h" |
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#include "UseTheForce/DarkSide/electrostatic_interface.h" |
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#include "UseTheForce/notifyCutoffs_interface.h" |
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#include "utils/MemoryUtils.hpp" |
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#include "utils/simError.h" |
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#include "selection/SelectionManager.hpp" |
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#ifdef IS_MPI |
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#include "UseTheForce/mpiComponentPlan.h" |
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namespace oopse { |
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SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, |
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ForceField* ff, Globals* simParams) : |
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forceField_(ff), simParams_(simParams), |
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ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0), |
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nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0), |
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nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), |
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nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0), |
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nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0), |
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sman_(NULL), fortranInitialized_(false) { |
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SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, |
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ForceField* ff, Globals* simParams) : |
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stamps_(stamps), forceField_(ff), simParams_(simParams), |
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ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0), |
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nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0), |
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nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), |
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nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0), |
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nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0), |
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sman_(NULL), fortranInitialized_(false) { |
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std::vector<std::pair<MoleculeStamp*, int> >::iterator i; |
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MoleculeStamp* molStamp; |
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int nMolWithSameStamp; |
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int nCutoffAtoms = 0; // number of atoms belong to cutoff groups |
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int nGroups = 0; //total cutoff groups defined in meta-data file |
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CutoffGroupStamp* cgStamp; |
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RigidBodyStamp* rbStamp; |
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int nRigidAtoms = 0; |
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std::vector<std::pair<MoleculeStamp*, int> >::iterator i; |
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MoleculeStamp* molStamp; |
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int nMolWithSameStamp; |
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int nCutoffAtoms = 0; // number of atoms belong to cutoff groups |
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int nGroups = 0; //total cutoff groups defined in meta-data file |
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CutoffGroupStamp* cgStamp; |
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RigidBodyStamp* rbStamp; |
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int nRigidAtoms = 0; |
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for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) { |
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for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) { |
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molStamp = i->first; |
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nMolWithSameStamp = i->second; |
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int nCutoffGroupsInStamp = molStamp->getNCutoffGroups(); |
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for (int j=0; j < nCutoffGroupsInStamp; j++) { |
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cgStamp = molStamp->getCutoffGroup(j); |
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nAtomsInGroups += cgStamp->getNMembers(); |
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cgStamp = molStamp->getCutoffGroup(j); |
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nAtomsInGroups += cgStamp->getNMembers(); |
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} |
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nGroups += nCutoffGroupsInStamp * nMolWithSameStamp; |
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nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp; |
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//calculate atoms in rigid bodies |
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int nAtomsInRigidBodies = 0; |
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int nRigidBodiesInStamp = molStamp->getNCutoffGroups(); |
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int nRigidBodiesInStamp = molStamp->getNRigidBodies(); |
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for (int j=0; j < nRigidBodiesInStamp; j++) { |
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rbStamp = molStamp->getRigidBody(j); |
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nAtomsInRigidBodies += rbStamp->getNMembers(); |
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rbStamp = molStamp->getRigidBody(j); |
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nAtomsInRigidBodies += rbStamp->getNMembers(); |
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} |
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nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp; |
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nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp; |
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} |
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} |
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//every free atom (atom does not belong to cutoff groups) is a cutoff group |
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//therefore the total number of cutoff groups in the system is equal to |
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//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data |
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//file plus the number of cutoff groups defined in meta-data file |
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nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; |
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//every free atom (atom does not belong to cutoff groups) is a cutoff |
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//group therefore the total number of cutoff groups in the system is |
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//equal to the total number of atoms minus number of atoms belong to |
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//cutoff group defined in meta-data file plus the number of cutoff |
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//groups defined in meta-data file |
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nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; |
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//every free atom (atom does not belong to rigid bodies) is an integrable object |
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//therefore the total number of integrable objects in the system is equal to |
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//the total number of atoms minus number of atoms belong to rigid body defined in meta-data |
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//file plus the number of rigid bodies defined in meta-data file |
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nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_; |
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//every free atom (atom does not belong to rigid bodies) is an |
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//integrable object therefore the total number of integrable objects |
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//in the system is equal to the total number of atoms minus number of |
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//atoms belong to rigid body defined in meta-data file plus the number |
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//of rigid bodies defined in meta-data file |
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nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms |
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+ nGlobalRigidBodies_; |
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|
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nGlobalMols_ = molStampIds_.size(); |
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nGlobalMols_ = molStampIds_.size(); |
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#ifdef IS_MPI |
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molToProcMap_.resize(nGlobalMols_); |
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molToProcMap_.resize(nGlobalMols_); |
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#endif |
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} |
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SimInfo::~SimInfo() { |
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//MemoryUtils::deleteVectorOfPointer(molecules_); |
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} |
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MemoryUtils::deleteVectorOfPointer(moleculeStamps_); |
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SimInfo::~SimInfo() { |
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std::map<int, Molecule*>::iterator i; |
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for (i = molecules_.begin(); i != molecules_.end(); ++i) { |
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delete i->second; |
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} |
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molecules_.clear(); |
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delete stamps_; |
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delete sman_; |
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delete simParams_; |
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delete forceField_; |
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} |
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} |
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int SimInfo::getNGlobalConstraints() { |
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int SimInfo::getNGlobalConstraints() { |
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int nGlobalConstraints; |
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#ifdef IS_MPI |
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MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM, |
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nGlobalConstraints = nConstraints_; |
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#endif |
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return nGlobalConstraints; |
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} |
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} |
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bool SimInfo::addMolecule(Molecule* mol) { |
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bool SimInfo::addMolecule(Molecule* mol) { |
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MoleculeIterator i; |
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i = molecules_.find(mol->getGlobalIndex()); |
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if (i == molecules_.end() ) { |
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molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol)); |
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molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol)); |
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nAtoms_ += mol->getNAtoms(); |
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nBonds_ += mol->getNBonds(); |
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nBends_ += mol->getNBends(); |
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nTorsions_ += mol->getNTorsions(); |
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nRigidBodies_ += mol->getNRigidBodies(); |
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nIntegrableObjects_ += mol->getNIntegrableObjects(); |
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nCutoffGroups_ += mol->getNCutoffGroups(); |
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nConstraints_ += mol->getNConstraintPairs(); |
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nAtoms_ += mol->getNAtoms(); |
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nBonds_ += mol->getNBonds(); |
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nBends_ += mol->getNBends(); |
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nTorsions_ += mol->getNTorsions(); |
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nRigidBodies_ += mol->getNRigidBodies(); |
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nIntegrableObjects_ += mol->getNIntegrableObjects(); |
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nCutoffGroups_ += mol->getNCutoffGroups(); |
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nConstraints_ += mol->getNConstraintPairs(); |
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addExcludePairs(mol); |
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addExcludePairs(mol); |
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return true; |
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return true; |
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} else { |
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return false; |
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return false; |
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} |
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} |
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} |
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bool SimInfo::removeMolecule(Molecule* mol) { |
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bool SimInfo::removeMolecule(Molecule* mol) { |
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MoleculeIterator i; |
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i = molecules_.find(mol->getGlobalIndex()); |
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if (i != molecules_.end() ) { |
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assert(mol == i->second); |
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assert(mol == i->second); |
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nAtoms_ -= mol->getNAtoms(); |
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nBonds_ -= mol->getNBonds(); |
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nBends_ -= mol->getNBends(); |
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nTorsions_ -= mol->getNTorsions(); |
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nRigidBodies_ -= mol->getNRigidBodies(); |
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nIntegrableObjects_ -= mol->getNIntegrableObjects(); |
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nCutoffGroups_ -= mol->getNCutoffGroups(); |
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nConstraints_ -= mol->getNConstraintPairs(); |
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nAtoms_ -= mol->getNAtoms(); |
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nBonds_ -= mol->getNBonds(); |
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nBends_ -= mol->getNBends(); |
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nTorsions_ -= mol->getNTorsions(); |
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nRigidBodies_ -= mol->getNRigidBodies(); |
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nIntegrableObjects_ -= mol->getNIntegrableObjects(); |
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nCutoffGroups_ -= mol->getNCutoffGroups(); |
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nConstraints_ -= mol->getNConstraintPairs(); |
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removeExcludePairs(mol); |
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molecules_.erase(mol->getGlobalIndex()); |
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removeExcludePairs(mol); |
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molecules_.erase(mol->getGlobalIndex()); |
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delete mol; |
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delete mol; |
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return true; |
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return true; |
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} else { |
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return false; |
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return false; |
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} |
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} |
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} |
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Molecule* SimInfo::beginMolecule(MoleculeIterator& i) { |
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Molecule* SimInfo::beginMolecule(MoleculeIterator& i) { |
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i = molecules_.begin(); |
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return i == molecules_.end() ? NULL : i->second; |
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} |
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} |
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Molecule* SimInfo::nextMolecule(MoleculeIterator& i) { |
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Molecule* SimInfo::nextMolecule(MoleculeIterator& i) { |
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++i; |
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return i == molecules_.end() ? NULL : i->second; |
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} |
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} |
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void SimInfo::calcNdf() { |
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void SimInfo::calcNdf() { |
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int ndf_local; |
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MoleculeIterator i; |
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std::vector<StuntDouble*>::iterator j; |
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ndf_local = 0; |
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for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
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for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(j)) { |
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for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(j)) { |
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ndf_local += 3; |
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ndf_local += 3; |
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if (integrableObject->isDirectional()) { |
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if (integrableObject->isLinear()) { |
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ndf_local += 2; |
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} else { |
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ndf_local += 3; |
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} |
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} |
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if (integrableObject->isDirectional()) { |
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if (integrableObject->isLinear()) { |
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ndf_local += 2; |
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} else { |
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ndf_local += 3; |
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} |
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} |
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}//end for (integrableObject) |
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}//end for (integrableObject) |
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}// end for (mol) |
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// n_constraints is local, so subtract them on each processor |
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// entire system: |
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ndf_ = ndf_ - 3 - nZconstraint_; |
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} |
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} |
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void SimInfo::calcNdfRaw() { |
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void SimInfo::calcNdfRaw() { |
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int ndfRaw_local; |
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MoleculeIterator i; |
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ndfRaw_local = 0; |
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for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
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for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(j)) { |
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for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
297 |
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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()) { |
302 |
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if (integrableObject->isLinear()) { |
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ndfRaw_local += 2; |
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} else { |
305 |
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ndfRaw_local += 3; |
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} |
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} |
301 |
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if (integrableObject->isDirectional()) { |
302 |
> |
if (integrableObject->isLinear()) { |
303 |
> |
ndfRaw_local += 2; |
304 |
> |
} else { |
305 |
> |
ndfRaw_local += 3; |
306 |
> |
} |
307 |
> |
} |
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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 |
317 |
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} |
317 |
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} |
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< |
void SimInfo::calcNdfTrans() { |
319 |
> |
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)) { |
364 |
< |
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(); |
365 |
> |
b = torsion->getAtomB()->getGlobalIndex(); |
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> |
c = torsion->getAtomC()->getGlobalIndex(); |
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> |
d = torsion->getAtomD()->getGlobalIndex(); |
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|
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< |
exclude_.addPair(a, b); |
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< |
exclude_.addPair(a, c); |
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< |
exclude_.addPair(a, d); |
372 |
< |
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); |
372 |
> |
exclude_.addPair(b, c); |
373 |
> |
exclude_.addPair(b, d); |
374 |
> |
exclude_.addPair(c, d); |
375 |
|
} |
376 |
|
|
377 |
< |
|
378 |
< |
} |
377 |
> |
Molecule::RigidBodyIterator rbIter; |
378 |
> |
RigidBody* rb; |
379 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
380 |
> |
std::vector<Atom*> atoms = rb->getAtoms(); |
381 |
> |
for (int i = 0; i < atoms.size() -1 ; ++i) { |
382 |
> |
for (int j = i + 1; j < atoms.size(); ++j) { |
383 |
> |
a = atoms[i]->getGlobalIndex(); |
384 |
> |
b = atoms[j]->getGlobalIndex(); |
385 |
> |
exclude_.addPair(a, b); |
386 |
> |
} |
387 |
> |
} |
388 |
> |
} |
389 |
|
|
390 |
< |
void SimInfo::removeExcludePairs(Molecule* mol) { |
390 |
> |
} |
391 |
> |
|
392 |
> |
void SimInfo::removeExcludePairs(Molecule* mol) { |
393 |
|
std::vector<Bond*>::iterator bondIter; |
394 |
|
std::vector<Bend*>::iterator bendIter; |
395 |
|
std::vector<Torsion*>::iterator torsionIter; |
402 |
|
int d; |
403 |
|
|
404 |
|
for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { |
405 |
< |
a = bond->getAtomA()->getGlobalIndex(); |
406 |
< |
b = bond->getAtomB()->getGlobalIndex(); |
407 |
< |
exclude_.removePair(a, b); |
405 |
> |
a = bond->getAtomA()->getGlobalIndex(); |
406 |
> |
b = bond->getAtomB()->getGlobalIndex(); |
407 |
> |
exclude_.removePair(a, b); |
408 |
|
} |
409 |
|
|
410 |
|
for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) { |
411 |
< |
a = bend->getAtomA()->getGlobalIndex(); |
412 |
< |
b = bend->getAtomB()->getGlobalIndex(); |
413 |
< |
c = bend->getAtomC()->getGlobalIndex(); |
411 |
> |
a = bend->getAtomA()->getGlobalIndex(); |
412 |
> |
b = bend->getAtomB()->getGlobalIndex(); |
413 |
> |
c = bend->getAtomC()->getGlobalIndex(); |
414 |
|
|
415 |
< |
exclude_.removePair(a, b); |
416 |
< |
exclude_.removePair(a, c); |
417 |
< |
exclude_.removePair(b, c); |
415 |
> |
exclude_.removePair(a, b); |
416 |
> |
exclude_.removePair(a, c); |
417 |
> |
exclude_.removePair(b, c); |
418 |
|
} |
419 |
|
|
420 |
|
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
421 |
< |
a = torsion->getAtomA()->getGlobalIndex(); |
422 |
< |
b = torsion->getAtomB()->getGlobalIndex(); |
423 |
< |
c = torsion->getAtomC()->getGlobalIndex(); |
424 |
< |
d = torsion->getAtomD()->getGlobalIndex(); |
421 |
> |
a = torsion->getAtomA()->getGlobalIndex(); |
422 |
> |
b = torsion->getAtomB()->getGlobalIndex(); |
423 |
> |
c = torsion->getAtomC()->getGlobalIndex(); |
424 |
> |
d = torsion->getAtomD()->getGlobalIndex(); |
425 |
|
|
426 |
< |
exclude_.removePair(a, b); |
427 |
< |
exclude_.removePair(a, c); |
428 |
< |
exclude_.removePair(a, d); |
429 |
< |
exclude_.removePair(b, c); |
430 |
< |
exclude_.removePair(b, d); |
431 |
< |
exclude_.removePair(c, d); |
426 |
> |
exclude_.removePair(a, b); |
427 |
> |
exclude_.removePair(a, c); |
428 |
> |
exclude_.removePair(a, d); |
429 |
> |
exclude_.removePair(b, c); |
430 |
> |
exclude_.removePair(b, d); |
431 |
> |
exclude_.removePair(c, d); |
432 |
|
} |
433 |
|
|
434 |
< |
} |
434 |
> |
Molecule::RigidBodyIterator rbIter; |
435 |
> |
RigidBody* rb; |
436 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
437 |
> |
std::vector<Atom*> atoms = rb->getAtoms(); |
438 |
> |
for (int i = 0; i < atoms.size() -1 ; ++i) { |
439 |
> |
for (int j = i + 1; j < atoms.size(); ++j) { |
440 |
> |
a = atoms[i]->getGlobalIndex(); |
441 |
> |
b = atoms[j]->getGlobalIndex(); |
442 |
> |
exclude_.removePair(a, b); |
443 |
> |
} |
444 |
> |
} |
445 |
> |
} |
446 |
|
|
447 |
+ |
} |
448 |
|
|
449 |
< |
void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) { |
449 |
> |
|
450 |
> |
void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) { |
451 |
|
int curStampId; |
452 |
|
|
453 |
|
//index from 0 |
455 |
|
|
456 |
|
moleculeStamps_.push_back(molStamp); |
457 |
|
molStampIds_.insert(molStampIds_.end(), nmol, curStampId); |
458 |
< |
} |
458 |
> |
} |
459 |
|
|
460 |
< |
void SimInfo::update() { |
460 |
> |
void SimInfo::update() { |
461 |
|
|
462 |
|
setupSimType(); |
463 |
|
|
470 |
|
//setup fortran force field |
471 |
|
/** @deprecate */ |
472 |
|
int isError = 0; |
473 |
< |
initFortranFF( &fInfo_.SIM_uses_RF , &isError ); |
473 |
> |
|
474 |
> |
setupElectrostaticSummationMethod( isError ); |
475 |
> |
|
476 |
|
if(isError){ |
477 |
< |
sprintf( painCave.errMsg, |
478 |
< |
"ForceField error: There was an error initializing the forceField in fortran.\n" ); |
479 |
< |
painCave.isFatal = 1; |
480 |
< |
simError(); |
477 |
> |
sprintf( painCave.errMsg, |
478 |
> |
"ForceField error: There was an error initializing the forceField in fortran.\n" ); |
479 |
> |
painCave.isFatal = 1; |
480 |
> |
simError(); |
481 |
|
} |
482 |
|
|
483 |
|
|
488 |
|
calcNdfTrans(); |
489 |
|
|
490 |
|
fortranInitialized_ = true; |
491 |
< |
} |
491 |
> |
} |
492 |
|
|
493 |
< |
std::set<AtomType*> SimInfo::getUniqueAtomTypes() { |
493 |
> |
std::set<AtomType*> SimInfo::getUniqueAtomTypes() { |
494 |
|
SimInfo::MoleculeIterator mi; |
495 |
|
Molecule* mol; |
496 |
|
Molecule::AtomIterator ai; |
499 |
|
|
500 |
|
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
501 |
|
|
502 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
503 |
< |
atomTypes.insert(atom->getAtomType()); |
504 |
< |
} |
502 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
503 |
> |
atomTypes.insert(atom->getAtomType()); |
504 |
> |
} |
505 |
|
|
506 |
|
} |
507 |
|
|
508 |
|
return atomTypes; |
509 |
< |
} |
509 |
> |
} |
510 |
|
|
511 |
< |
void SimInfo::setupSimType() { |
511 |
> |
void SimInfo::setupSimType() { |
512 |
|
std::set<AtomType*>::iterator i; |
513 |
|
std::set<AtomType*> atomTypes; |
514 |
|
atomTypes = getUniqueAtomTypes(); |
521 |
|
int useDipole = 0; |
522 |
|
int useGayBerne = 0; |
523 |
|
int useSticky = 0; |
524 |
+ |
int useStickyPower = 0; |
525 |
|
int useShape = 0; |
526 |
|
int useFLARB = 0; //it is not in AtomType yet |
527 |
|
int useDirectionalAtom = 0; |
528 |
|
int useElectrostatics = 0; |
529 |
|
//usePBC and useRF are from simParams |
530 |
< |
int usePBC = simParams_->getPBC(); |
531 |
< |
int useRF = simParams_->getUseRF(); |
530 |
> |
int usePBC = simParams_->getUsePeriodicBoundaryConditions(); |
531 |
> |
int useRF; |
532 |
> |
int useDW; |
533 |
> |
std::string myMethod; |
534 |
|
|
535 |
+ |
// set the useRF logical |
536 |
+ |
useRF = 0; |
537 |
+ |
useDW = 0; |
538 |
+ |
|
539 |
+ |
|
540 |
+ |
if (simParams_->haveElectrostaticSummationMethod()) { |
541 |
+ |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
542 |
+ |
toUpper(myMethod); |
543 |
+ |
if (myMethod == "REACTION_FIELD") { |
544 |
+ |
useRF=1; |
545 |
+ |
} else { |
546 |
+ |
if (myMethod == "SHIFTED_POTENTIAL") { |
547 |
+ |
useDW = 1; |
548 |
+ |
} |
549 |
+ |
} |
550 |
+ |
} |
551 |
+ |
|
552 |
|
//loop over all of the atom types |
553 |
|
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
554 |
< |
useLennardJones |= (*i)->isLennardJones(); |
555 |
< |
useElectrostatic |= (*i)->isElectrostatic(); |
556 |
< |
useEAM |= (*i)->isEAM(); |
557 |
< |
useCharge |= (*i)->isCharge(); |
558 |
< |
useDirectional |= (*i)->isDirectional(); |
559 |
< |
useDipole |= (*i)->isDipole(); |
560 |
< |
useGayBerne |= (*i)->isGayBerne(); |
561 |
< |
useSticky |= (*i)->isSticky(); |
562 |
< |
useShape |= (*i)->isShape(); |
554 |
> |
useLennardJones |= (*i)->isLennardJones(); |
555 |
> |
useElectrostatic |= (*i)->isElectrostatic(); |
556 |
> |
useEAM |= (*i)->isEAM(); |
557 |
> |
useCharge |= (*i)->isCharge(); |
558 |
> |
useDirectional |= (*i)->isDirectional(); |
559 |
> |
useDipole |= (*i)->isDipole(); |
560 |
> |
useGayBerne |= (*i)->isGayBerne(); |
561 |
> |
useSticky |= (*i)->isSticky(); |
562 |
> |
useStickyPower |= (*i)->isStickyPower(); |
563 |
> |
useShape |= (*i)->isShape(); |
564 |
|
} |
565 |
|
|
566 |
< |
if (useSticky || useDipole || useGayBerne || useShape) { |
567 |
< |
useDirectionalAtom = 1; |
566 |
> |
if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) { |
567 |
> |
useDirectionalAtom = 1; |
568 |
|
} |
569 |
|
|
570 |
|
if (useCharge || useDipole) { |
571 |
< |
useElectrostatics = 1; |
571 |
> |
useElectrostatics = 1; |
572 |
|
} |
573 |
|
|
574 |
|
#ifdef IS_MPI |
595 |
|
temp = useSticky; |
596 |
|
MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
597 |
|
|
598 |
+ |
temp = useStickyPower; |
599 |
+ |
MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
600 |
+ |
|
601 |
|
temp = useGayBerne; |
602 |
|
MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
603 |
|
|
612 |
|
|
613 |
|
temp = useRF; |
614 |
|
MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
615 |
< |
|
615 |
> |
|
616 |
> |
temp = useDW; |
617 |
> |
MPI_Allreduce(&temp, &useDW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
618 |
> |
|
619 |
|
#endif |
620 |
|
|
621 |
|
fInfo_.SIM_uses_PBC = usePBC; |
625 |
|
fInfo_.SIM_uses_Charges = useCharge; |
626 |
|
fInfo_.SIM_uses_Dipoles = useDipole; |
627 |
|
fInfo_.SIM_uses_Sticky = useSticky; |
628 |
+ |
fInfo_.SIM_uses_StickyPower = useStickyPower; |
629 |
|
fInfo_.SIM_uses_GayBerne = useGayBerne; |
630 |
|
fInfo_.SIM_uses_EAM = useEAM; |
631 |
|
fInfo_.SIM_uses_Shapes = useShape; |
632 |
|
fInfo_.SIM_uses_FLARB = useFLARB; |
633 |
|
fInfo_.SIM_uses_RF = useRF; |
634 |
+ |
fInfo_.SIM_uses_DampedWolf = useDW; |
635 |
|
|
636 |
< |
if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { |
637 |
< |
|
638 |
< |
if (simParams_->haveDielectric()) { |
639 |
< |
fInfo_.dielect = simParams_->getDielectric(); |
640 |
< |
} else { |
641 |
< |
sprintf(painCave.errMsg, |
642 |
< |
"SimSetup Error: No Dielectric constant was set.\n" |
643 |
< |
"\tYou are trying to use Reaction Field without" |
644 |
< |
"\tsetting a dielectric constant!\n"); |
645 |
< |
painCave.isFatal = 1; |
646 |
< |
simError(); |
647 |
< |
} |
581 |
< |
|
582 |
< |
} else { |
583 |
< |
fInfo_.dielect = 0.0; |
636 |
> |
if( myMethod == "REACTION_FIELD") { |
637 |
> |
|
638 |
> |
if (simParams_->haveDielectric()) { |
639 |
> |
fInfo_.dielect = simParams_->getDielectric(); |
640 |
> |
} else { |
641 |
> |
sprintf(painCave.errMsg, |
642 |
> |
"SimSetup Error: No Dielectric constant was set.\n" |
643 |
> |
"\tYou are trying to use Reaction Field without" |
644 |
> |
"\tsetting a dielectric constant!\n"); |
645 |
> |
painCave.isFatal = 1; |
646 |
> |
simError(); |
647 |
> |
} |
648 |
|
} |
649 |
|
|
650 |
< |
} |
650 |
> |
} |
651 |
|
|
652 |
< |
void SimInfo::setupFortranSim() { |
652 |
> |
void SimInfo::setupFortranSim() { |
653 |
|
int isError; |
654 |
|
int nExclude; |
655 |
|
std::vector<int> fortranGlobalGroupMembership; |
659 |
|
|
660 |
|
//globalGroupMembership_ is filled by SimCreator |
661 |
|
for (int i = 0; i < nGlobalAtoms_; i++) { |
662 |
< |
fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1); |
662 |
> |
fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1); |
663 |
|
} |
664 |
|
|
665 |
|
//calculate mass ratio of cutoff group |
676 |
|
mfact.reserve(getNCutoffGroups()); |
677 |
|
|
678 |
|
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
679 |
< |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
679 |
> |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
680 |
|
|
681 |
< |
totalMass = cg->getMass(); |
682 |
< |
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
683 |
< |
mfact.push_back(atom->getMass()/totalMass); |
684 |
< |
} |
681 |
> |
totalMass = cg->getMass(); |
682 |
> |
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
683 |
> |
// Check for massless groups - set mfact to 1 if true |
684 |
> |
if (totalMass != 0) |
685 |
> |
mfact.push_back(atom->getMass()/totalMass); |
686 |
> |
else |
687 |
> |
mfact.push_back( 1.0 ); |
688 |
> |
} |
689 |
|
|
690 |
< |
} |
690 |
> |
} |
691 |
|
} |
692 |
|
|
693 |
|
//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!) |
697 |
|
identArray.reserve(getNAtoms()); |
698 |
|
|
699 |
|
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
700 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
701 |
< |
identArray.push_back(atom->getIdent()); |
702 |
< |
} |
700 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
701 |
> |
identArray.push_back(atom->getIdent()); |
702 |
> |
} |
703 |
|
} |
704 |
|
|
705 |
|
//fill molMembershipArray |
706 |
|
//molMembershipArray is filled by SimCreator |
707 |
|
std::vector<int> molMembershipArray(nGlobalAtoms_); |
708 |
|
for (int i = 0; i < nGlobalAtoms_; i++) { |
709 |
< |
molMembershipArray[i] = globalMolMembership_[i] + 1; |
709 |
> |
molMembershipArray[i] = globalMolMembership_[i] + 1; |
710 |
|
} |
711 |
|
|
712 |
|
//setup fortran simulation |
645 |
– |
//gloalExcludes and molMembershipArray should go away (They are never used) |
646 |
– |
//why the hell fortran need to know molecule? |
647 |
– |
//OOPSE = Object-Obfuscated Parallel Simulation Engine |
713 |
|
int nGlobalExcludes = 0; |
714 |
|
int* globalExcludes = NULL; |
715 |
|
int* excludeList = exclude_.getExcludeList(); |
716 |
|
setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList , |
717 |
< |
&nGlobalExcludes, globalExcludes, &molMembershipArray[0], |
718 |
< |
&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError); |
717 |
> |
&nGlobalExcludes, globalExcludes, &molMembershipArray[0], |
718 |
> |
&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError); |
719 |
|
|
720 |
|
if( isError ){ |
721 |
|
|
722 |
< |
sprintf( painCave.errMsg, |
723 |
< |
"There was an error setting the simulation information in fortran.\n" ); |
724 |
< |
painCave.isFatal = 1; |
725 |
< |
painCave.severity = OOPSE_ERROR; |
726 |
< |
simError(); |
722 |
> |
sprintf( painCave.errMsg, |
723 |
> |
"There was an error setting the simulation information in fortran.\n" ); |
724 |
> |
painCave.isFatal = 1; |
725 |
> |
painCave.severity = OOPSE_ERROR; |
726 |
> |
simError(); |
727 |
|
} |
728 |
|
|
729 |
|
#ifdef IS_MPI |
730 |
|
sprintf( checkPointMsg, |
731 |
< |
"succesfully sent the simulation information to fortran.\n"); |
731 |
> |
"succesfully sent the simulation information to fortran.\n"); |
732 |
|
MPIcheckPoint(); |
733 |
|
#endif // is_mpi |
734 |
< |
} |
734 |
> |
} |
735 |
|
|
736 |
|
|
737 |
|
#ifdef IS_MPI |
738 |
< |
void SimInfo::setupFortranParallel() { |
738 |
> |
void SimInfo::setupFortranParallel() { |
739 |
|
|
740 |
|
//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex |
741 |
|
std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0); |
751 |
|
|
752 |
|
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
753 |
|
|
754 |
< |
//local index(index in DataStorge) of atom is important |
755 |
< |
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
756 |
< |
localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1; |
757 |
< |
} |
754 |
> |
//local index(index in DataStorge) of atom is important |
755 |
> |
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
756 |
> |
localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1; |
757 |
> |
} |
758 |
|
|
759 |
< |
//local index of cutoff group is trivial, it only depends on the order of travesing |
760 |
< |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
761 |
< |
localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1); |
762 |
< |
} |
759 |
> |
//local index of cutoff group is trivial, it only depends on the order of travesing |
760 |
> |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
761 |
> |
localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1); |
762 |
> |
} |
763 |
|
|
764 |
|
} |
765 |
|
|
779 |
|
&localToGlobalCutoffGroupIndex[0], &isError); |
780 |
|
|
781 |
|
if (isError) { |
782 |
< |
sprintf(painCave.errMsg, |
783 |
< |
"mpiRefresh errror: fortran didn't like something we gave it.\n"); |
784 |
< |
painCave.isFatal = 1; |
785 |
< |
simError(); |
782 |
> |
sprintf(painCave.errMsg, |
783 |
> |
"mpiRefresh errror: fortran didn't like something we gave it.\n"); |
784 |
> |
painCave.isFatal = 1; |
785 |
> |
simError(); |
786 |
|
} |
787 |
|
|
788 |
|
sprintf(checkPointMsg, " mpiRefresh successful.\n"); |
789 |
|
MPIcheckPoint(); |
790 |
|
|
791 |
|
|
792 |
< |
} |
792 |
> |
} |
793 |
|
|
794 |
|
#endif |
795 |
|
|
796 |
< |
double SimInfo::calcMaxCutoffRadius() { |
796 |
> |
double SimInfo::calcMaxCutoffRadius() { |
797 |
|
|
798 |
|
|
799 |
|
std::set<AtomType*> atomTypes; |
805 |
|
|
806 |
|
//query the max cutoff radius among these atom types |
807 |
|
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
808 |
< |
cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i)); |
808 |
> |
cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i)); |
809 |
|
} |
810 |
|
|
811 |
|
double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end())); |
814 |
|
#endif |
815 |
|
|
816 |
|
return maxCutoffRadius; |
817 |
< |
} |
817 |
> |
} |
818 |
|
|
819 |
< |
void SimInfo::setupCutoff() { |
755 |
< |
double rcut_; //cutoff radius |
756 |
< |
double rsw_; //switching radius |
819 |
> |
void SimInfo::getCutoff(double& rcut, double& rsw) { |
820 |
|
|
821 |
|
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
822 |
|
|
823 |
< |
if (!simParams_->haveRcut()){ |
824 |
< |
sprintf(painCave.errMsg, |
823 |
> |
if (!simParams_->haveCutoffRadius()){ |
824 |
> |
sprintf(painCave.errMsg, |
825 |
|
"SimCreator Warning: No value was set for the cutoffRadius.\n" |
826 |
|
"\tOOPSE will use a default value of 15.0 angstroms" |
827 |
|
"\tfor the cutoffRadius.\n"); |
828 |
< |
painCave.isFatal = 0; |
829 |
< |
simError(); |
830 |
< |
rcut_ = 15.0; |
831 |
< |
} else{ |
832 |
< |
rcut_ = simParams_->getRcut(); |
833 |
< |
} |
828 |
> |
painCave.isFatal = 0; |
829 |
> |
simError(); |
830 |
> |
rcut = 15.0; |
831 |
> |
} else{ |
832 |
> |
rcut = simParams_->getCutoffRadius(); |
833 |
> |
} |
834 |
|
|
835 |
< |
if (!simParams_->haveRsw()){ |
836 |
< |
sprintf(painCave.errMsg, |
835 |
> |
if (!simParams_->haveSwitchingRadius()){ |
836 |
> |
sprintf(painCave.errMsg, |
837 |
|
"SimCreator Warning: No value was set for switchingRadius.\n" |
838 |
|
"\tOOPSE will use a default value of\n" |
839 |
< |
"\t0.95 * cutoffRadius for the switchingRadius\n"); |
840 |
< |
painCave.isFatal = 0; |
841 |
< |
simError(); |
842 |
< |
rsw_ = 0.95 * rcut_; |
843 |
< |
} else{ |
844 |
< |
rsw_ = simParams_->getRsw(); |
845 |
< |
} |
839 |
> |
"\t0.85 * cutoffRadius for the switchingRadius\n"); |
840 |
> |
painCave.isFatal = 0; |
841 |
> |
simError(); |
842 |
> |
rsw = 0.85 * rcut; |
843 |
> |
} else{ |
844 |
> |
rsw = simParams_->getSwitchingRadius(); |
845 |
> |
} |
846 |
|
|
847 |
|
} else { |
848 |
< |
// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
849 |
< |
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
848 |
> |
// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
849 |
> |
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
850 |
|
|
851 |
< |
if (simParams_->haveRcut()) { |
852 |
< |
rcut_ = simParams_->getRcut(); |
853 |
< |
} else { |
854 |
< |
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
855 |
< |
rcut_ = calcMaxCutoffRadius(); |
856 |
< |
} |
851 |
> |
if (simParams_->haveCutoffRadius()) { |
852 |
> |
rcut = simParams_->getCutoffRadius(); |
853 |
> |
} else { |
854 |
> |
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
855 |
> |
rcut = calcMaxCutoffRadius(); |
856 |
> |
} |
857 |
|
|
858 |
< |
if (simParams_->haveRsw()) { |
859 |
< |
rsw_ = simParams_->getRsw(); |
860 |
< |
} else { |
861 |
< |
rsw_ = rcut_; |
862 |
< |
} |
858 |
> |
if (simParams_->haveSwitchingRadius()) { |
859 |
> |
rsw = simParams_->getSwitchingRadius(); |
860 |
> |
} else { |
861 |
> |
rsw = rcut; |
862 |
> |
} |
863 |
|
|
864 |
|
} |
865 |
< |
|
865 |
> |
} |
866 |
> |
|
867 |
> |
void SimInfo::setupCutoff() { |
868 |
> |
getCutoff(rcut_, rsw_); |
869 |
|
double rnblist = rcut_ + 1; // skin of neighbor list |
870 |
|
|
871 |
|
//Pass these cutoff radius etc. to fortran. This function should be called once and only once |
872 |
< |
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist); |
873 |
< |
} |
872 |
> |
|
873 |
> |
int cp = TRADITIONAL_CUTOFF_POLICY; |
874 |
> |
if (simParams_->haveCutoffPolicy()) { |
875 |
> |
std::string myPolicy = simParams_->getCutoffPolicy(); |
876 |
> |
toUpper(myPolicy); |
877 |
> |
if (myPolicy == "MIX") { |
878 |
> |
cp = MIX_CUTOFF_POLICY; |
879 |
> |
} else { |
880 |
> |
if (myPolicy == "MAX") { |
881 |
> |
cp = MAX_CUTOFF_POLICY; |
882 |
> |
} else { |
883 |
> |
if (myPolicy == "TRADITIONAL") { |
884 |
> |
cp = TRADITIONAL_CUTOFF_POLICY; |
885 |
> |
} else { |
886 |
> |
// throw error |
887 |
> |
sprintf( painCave.errMsg, |
888 |
> |
"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() ); |
889 |
> |
painCave.isFatal = 1; |
890 |
> |
simError(); |
891 |
> |
} |
892 |
> |
} |
893 |
> |
} |
894 |
> |
} |
895 |
|
|
809 |
– |
void SimInfo::addProperty(GenericData* genData) { |
810 |
– |
properties_.addProperty(genData); |
811 |
– |
} |
896 |
|
|
897 |
< |
void SimInfo::removeProperty(const std::string& propName) { |
898 |
< |
properties_.removeProperty(propName); |
899 |
< |
} |
897 |
> |
if (simParams_->haveSkinThickness()) { |
898 |
> |
double skinThickness = simParams_->getSkinThickness(); |
899 |
> |
} |
900 |
|
|
901 |
< |
void SimInfo::clearProperties() { |
902 |
< |
properties_.clearProperties(); |
903 |
< |
} |
901 |
> |
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp); |
902 |
> |
// also send cutoff notification to electrostatics |
903 |
> |
setElectrostaticCutoffRadius(&rcut_, &rsw_); |
904 |
> |
} |
905 |
|
|
906 |
< |
std::vector<std::string> SimInfo::getPropertyNames() { |
907 |
< |
return properties_.getPropertyNames(); |
908 |
< |
} |
909 |
< |
|
910 |
< |
std::vector<GenericData*> SimInfo::getProperties() { |
911 |
< |
return properties_.getProperties(); |
912 |
< |
} |
906 |
> |
void SimInfo::setupElectrostaticSummationMethod( int isError ) { |
907 |
> |
|
908 |
> |
int errorOut; |
909 |
> |
int esm = NONE; |
910 |
> |
int sm = UNDAMPED; |
911 |
> |
double alphaVal; |
912 |
> |
double dielectric; |
913 |
|
|
914 |
< |
GenericData* SimInfo::getPropertyByName(const std::string& propName) { |
915 |
< |
return properties_.getPropertyByName(propName); |
916 |
< |
} |
914 |
> |
errorOut = isError; |
915 |
> |
alphaVal = simParams_->getDampingAlpha(); |
916 |
> |
dielectric = simParams_->getDielectric(); |
917 |
|
|
918 |
< |
void SimInfo::setSnapshotManager(SnapshotManager* sman) { |
918 |
> |
if (simParams_->haveElectrostaticSummationMethod()) { |
919 |
> |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
920 |
> |
toUpper(myMethod); |
921 |
> |
if (myMethod == "NONE") { |
922 |
> |
esm = NONE; |
923 |
> |
} else { |
924 |
> |
if (myMethod == "SWITCHING_FUNCTION") { |
925 |
> |
esm = SWITCHING_FUNCTION; |
926 |
> |
} else { |
927 |
> |
if (myMethod == "SHIFTED_POTENTIAL") { |
928 |
> |
esm = SHIFTED_POTENTIAL; |
929 |
> |
} else { |
930 |
> |
if (myMethod == "SHIFTED_FORCE") { |
931 |
> |
esm = SHIFTED_FORCE; |
932 |
> |
} else { |
933 |
> |
if (myMethod == "REACTION_FIELD") { |
934 |
> |
esm = REACTION_FIELD; |
935 |
> |
} else { |
936 |
> |
// throw error |
937 |
> |
sprintf( painCave.errMsg, |
938 |
> |
"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"shifted_potential\", \"shifted_force\", or \"reaction_field\".", myMethod.c_str() ); |
939 |
> |
painCave.isFatal = 1; |
940 |
> |
simError(); |
941 |
> |
} |
942 |
> |
} |
943 |
> |
} |
944 |
> |
} |
945 |
> |
} |
946 |
> |
} |
947 |
> |
|
948 |
> |
if (simParams_->haveScreeningMethod()) { |
949 |
> |
std::string myScreen = simParams_->getScreeningMethod(); |
950 |
> |
toUpper(myScreen); |
951 |
> |
if (myScreen == "UNDAMPED") { |
952 |
> |
sm = UNDAMPED; |
953 |
> |
} else { |
954 |
> |
if (myScreen == "DAMPED") { |
955 |
> |
sm = DAMPED; |
956 |
> |
if (!simParams_->haveDampingAlpha()) { |
957 |
> |
//throw error |
958 |
> |
sprintf( painCave.errMsg, |
959 |
> |
"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal); |
960 |
> |
painCave.isFatal = 0; |
961 |
> |
simError(); |
962 |
> |
} else { |
963 |
> |
// throw error |
964 |
> |
sprintf( painCave.errMsg, |
965 |
> |
"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() ); |
966 |
> |
painCave.isFatal = 1; |
967 |
> |
simError(); |
968 |
> |
} |
969 |
> |
} |
970 |
> |
} |
971 |
> |
} |
972 |
> |
// let's pass some summation method variables to fortran |
973 |
> |
setElectrostaticSummationMethod( &esm ); |
974 |
> |
setScreeningMethod( &sm ); |
975 |
> |
setDampingAlpha( &alphaVal ); |
976 |
> |
setReactionFieldDielectric( &dielectric ); |
977 |
> |
initFortranFF( &esm, &errorOut ); |
978 |
> |
} |
979 |
> |
|
980 |
> |
void SimInfo::addProperty(GenericData* genData) { |
981 |
> |
properties_.addProperty(genData); |
982 |
> |
} |
983 |
> |
|
984 |
> |
void SimInfo::removeProperty(const std::string& propName) { |
985 |
> |
properties_.removeProperty(propName); |
986 |
> |
} |
987 |
> |
|
988 |
> |
void SimInfo::clearProperties() { |
989 |
> |
properties_.clearProperties(); |
990 |
> |
} |
991 |
> |
|
992 |
> |
std::vector<std::string> SimInfo::getPropertyNames() { |
993 |
> |
return properties_.getPropertyNames(); |
994 |
> |
} |
995 |
> |
|
996 |
> |
std::vector<GenericData*> SimInfo::getProperties() { |
997 |
> |
return properties_.getProperties(); |
998 |
> |
} |
999 |
> |
|
1000 |
> |
GenericData* SimInfo::getPropertyByName(const std::string& propName) { |
1001 |
> |
return properties_.getPropertyByName(propName); |
1002 |
> |
} |
1003 |
> |
|
1004 |
> |
void SimInfo::setSnapshotManager(SnapshotManager* sman) { |
1005 |
> |
if (sman_ == sman) { |
1006 |
> |
return; |
1007 |
> |
} |
1008 |
> |
delete sman_; |
1009 |
|
sman_ = sman; |
1010 |
|
|
1011 |
|
Molecule* mol; |
1017 |
|
|
1018 |
|
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
1019 |
|
|
1020 |
< |
for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) { |
1021 |
< |
atom->setSnapshotManager(sman_); |
1022 |
< |
} |
1020 |
> |
for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) { |
1021 |
> |
atom->setSnapshotManager(sman_); |
1022 |
> |
} |
1023 |
|
|
1024 |
< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
1025 |
< |
rb->setSnapshotManager(sman_); |
1026 |
< |
} |
1024 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
1025 |
> |
rb->setSnapshotManager(sman_); |
1026 |
> |
} |
1027 |
|
} |
1028 |
|
|
1029 |
< |
} |
1029 |
> |
} |
1030 |
|
|
1031 |
< |
Vector3d SimInfo::getComVel(){ |
1031 |
> |
Vector3d SimInfo::getComVel(){ |
1032 |
|
SimInfo::MoleculeIterator i; |
1033 |
|
Molecule* mol; |
1034 |
|
|
1037 |
|
|
1038 |
|
|
1039 |
|
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1040 |
< |
double mass = mol->getMass(); |
1041 |
< |
totalMass += mass; |
1042 |
< |
comVel += mass * mol->getComVel(); |
1040 |
> |
double mass = mol->getMass(); |
1041 |
> |
totalMass += mass; |
1042 |
> |
comVel += mass * mol->getComVel(); |
1043 |
|
} |
1044 |
|
|
1045 |
|
#ifdef IS_MPI |
1052 |
|
comVel /= totalMass; |
1053 |
|
|
1054 |
|
return comVel; |
1055 |
< |
} |
1055 |
> |
} |
1056 |
|
|
1057 |
< |
Vector3d SimInfo::getCom(){ |
1057 |
> |
Vector3d SimInfo::getCom(){ |
1058 |
|
SimInfo::MoleculeIterator i; |
1059 |
|
Molecule* mol; |
1060 |
|
|
1062 |
|
double totalMass = 0.0; |
1063 |
|
|
1064 |
|
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1065 |
< |
double mass = mol->getMass(); |
1066 |
< |
totalMass += mass; |
1067 |
< |
com += mass * mol->getCom(); |
1065 |
> |
double mass = mol->getMass(); |
1066 |
> |
totalMass += mass; |
1067 |
> |
com += mass * mol->getCom(); |
1068 |
|
} |
1069 |
|
|
1070 |
|
#ifdef IS_MPI |
1078 |
|
|
1079 |
|
return com; |
1080 |
|
|
1081 |
< |
} |
1081 |
> |
} |
1082 |
|
|
1083 |
< |
std::ostream& operator <<(std::ostream& o, SimInfo& info) { |
1083 |
> |
std::ostream& operator <<(std::ostream& o, SimInfo& info) { |
1084 |
|
|
1085 |
|
return o; |
1086 |
< |
} |
1086 |
> |
} |
1087 |
> |
|
1088 |
> |
|
1089 |
> |
/* |
1090 |
> |
Returns center of mass and center of mass velocity in one function call. |
1091 |
> |
*/ |
1092 |
> |
|
1093 |
> |
void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){ |
1094 |
> |
SimInfo::MoleculeIterator i; |
1095 |
> |
Molecule* mol; |
1096 |
> |
|
1097 |
> |
|
1098 |
> |
double totalMass = 0.0; |
1099 |
> |
|
1100 |
|
|
1101 |
+ |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1102 |
+ |
double mass = mol->getMass(); |
1103 |
+ |
totalMass += mass; |
1104 |
+ |
com += mass * mol->getCom(); |
1105 |
+ |
comVel += mass * mol->getComVel(); |
1106 |
+ |
} |
1107 |
+ |
|
1108 |
+ |
#ifdef IS_MPI |
1109 |
+ |
double tmpMass = totalMass; |
1110 |
+ |
Vector3d tmpCom(com); |
1111 |
+ |
Vector3d tmpComVel(comVel); |
1112 |
+ |
MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1113 |
+ |
MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1114 |
+ |
MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1115 |
+ |
#endif |
1116 |
+ |
|
1117 |
+ |
com /= totalMass; |
1118 |
+ |
comVel /= totalMass; |
1119 |
+ |
} |
1120 |
+ |
|
1121 |
+ |
/* |
1122 |
+ |
Return intertia tensor for entire system and angular momentum Vector. |
1123 |
+ |
|
1124 |
+ |
|
1125 |
+ |
[ Ixx -Ixy -Ixz ] |
1126 |
+ |
J =| -Iyx Iyy -Iyz | |
1127 |
+ |
[ -Izx -Iyz Izz ] |
1128 |
+ |
*/ |
1129 |
+ |
|
1130 |
+ |
void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){ |
1131 |
+ |
|
1132 |
+ |
|
1133 |
+ |
double xx = 0.0; |
1134 |
+ |
double yy = 0.0; |
1135 |
+ |
double zz = 0.0; |
1136 |
+ |
double xy = 0.0; |
1137 |
+ |
double xz = 0.0; |
1138 |
+ |
double yz = 0.0; |
1139 |
+ |
Vector3d com(0.0); |
1140 |
+ |
Vector3d comVel(0.0); |
1141 |
+ |
|
1142 |
+ |
getComAll(com, comVel); |
1143 |
+ |
|
1144 |
+ |
SimInfo::MoleculeIterator i; |
1145 |
+ |
Molecule* mol; |
1146 |
+ |
|
1147 |
+ |
Vector3d thisq(0.0); |
1148 |
+ |
Vector3d thisv(0.0); |
1149 |
+ |
|
1150 |
+ |
double thisMass = 0.0; |
1151 |
+ |
|
1152 |
+ |
|
1153 |
+ |
|
1154 |
+ |
|
1155 |
+ |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1156 |
+ |
|
1157 |
+ |
thisq = mol->getCom()-com; |
1158 |
+ |
thisv = mol->getComVel()-comVel; |
1159 |
+ |
thisMass = mol->getMass(); |
1160 |
+ |
// Compute moment of intertia coefficients. |
1161 |
+ |
xx += thisq[0]*thisq[0]*thisMass; |
1162 |
+ |
yy += thisq[1]*thisq[1]*thisMass; |
1163 |
+ |
zz += thisq[2]*thisq[2]*thisMass; |
1164 |
+ |
|
1165 |
+ |
// compute products of intertia |
1166 |
+ |
xy += thisq[0]*thisq[1]*thisMass; |
1167 |
+ |
xz += thisq[0]*thisq[2]*thisMass; |
1168 |
+ |
yz += thisq[1]*thisq[2]*thisMass; |
1169 |
+ |
|
1170 |
+ |
angularMomentum += cross( thisq, thisv ) * thisMass; |
1171 |
+ |
|
1172 |
+ |
} |
1173 |
+ |
|
1174 |
+ |
|
1175 |
+ |
inertiaTensor(0,0) = yy + zz; |
1176 |
+ |
inertiaTensor(0,1) = -xy; |
1177 |
+ |
inertiaTensor(0,2) = -xz; |
1178 |
+ |
inertiaTensor(1,0) = -xy; |
1179 |
+ |
inertiaTensor(1,1) = xx + zz; |
1180 |
+ |
inertiaTensor(1,2) = -yz; |
1181 |
+ |
inertiaTensor(2,0) = -xz; |
1182 |
+ |
inertiaTensor(2,1) = -yz; |
1183 |
+ |
inertiaTensor(2,2) = xx + yy; |
1184 |
+ |
|
1185 |
+ |
#ifdef IS_MPI |
1186 |
+ |
Mat3x3d tmpI(inertiaTensor); |
1187 |
+ |
Vector3d tmpAngMom; |
1188 |
+ |
MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1189 |
+ |
MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1190 |
+ |
#endif |
1191 |
+ |
|
1192 |
+ |
return; |
1193 |
+ |
} |
1194 |
+ |
|
1195 |
+ |
//Returns the angular momentum of the system |
1196 |
+ |
Vector3d SimInfo::getAngularMomentum(){ |
1197 |
+ |
|
1198 |
+ |
Vector3d com(0.0); |
1199 |
+ |
Vector3d comVel(0.0); |
1200 |
+ |
Vector3d angularMomentum(0.0); |
1201 |
+ |
|
1202 |
+ |
getComAll(com,comVel); |
1203 |
+ |
|
1204 |
+ |
SimInfo::MoleculeIterator i; |
1205 |
+ |
Molecule* mol; |
1206 |
+ |
|
1207 |
+ |
Vector3d thisr(0.0); |
1208 |
+ |
Vector3d thisp(0.0); |
1209 |
+ |
|
1210 |
+ |
double thisMass; |
1211 |
+ |
|
1212 |
+ |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1213 |
+ |
thisMass = mol->getMass(); |
1214 |
+ |
thisr = mol->getCom()-com; |
1215 |
+ |
thisp = (mol->getComVel()-comVel)*thisMass; |
1216 |
+ |
|
1217 |
+ |
angularMomentum += cross( thisr, thisp ); |
1218 |
+ |
|
1219 |
+ |
} |
1220 |
+ |
|
1221 |
+ |
#ifdef IS_MPI |
1222 |
+ |
Vector3d tmpAngMom; |
1223 |
+ |
MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1224 |
+ |
#endif |
1225 |
+ |
|
1226 |
+ |
return angularMomentum; |
1227 |
+ |
} |
1228 |
+ |
|
1229 |
+ |
|
1230 |
|
}//end namespace oopse |
1231 |
|
|