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/* |
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* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project |
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* |
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* Contact: oopse@oopse.org |
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* |
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* This program is free software; you can redistribute it and/or |
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* modify it under the terms of the GNU Lesser General Public License |
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* as published by the Free Software Foundation; either version 2.1 |
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* of the License, or (at your option) any later version. |
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* All we ask is that proper credit is given for our work, which includes |
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* - but is not limited to - adding the above copyright notice to the beginning |
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* of your source code files, and to any copyright notice that you may distribute |
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* with programs based on this work. |
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* |
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* This program is distributed in the hope that it will be useful, |
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* but WITHOUT ANY WARRANTY; without even the implied warranty of |
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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* GNU Lesser General Public License for more details. |
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* |
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* You should have received a copy of the GNU Lesser General Public License |
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* along with this program; if not, write to the Free Software |
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. |
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* |
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*/ |
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gezelter |
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|
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tim |
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/** |
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* @file SimInfo.cpp |
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* @author tlin |
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* @date 11/02/2004 |
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* @version 1.0 |
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*/ |
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gezelter |
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|
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#include <algorithm> |
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#include <set> |
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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/doForces_interface.h" |
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#include "UseTheForce/notifyCutoffs_interface.h" |
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#include "utils/MemoryUtils.hpp" |
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#include "utils/simError.h" |
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#ifdef IS_MPI |
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#include "UseTheForce/mpiComponentPlan.h" |
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#include "UseTheForce/DarkSide/simParallel_interface.h" |
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#endif |
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namespace oopse { |
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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) { |
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|
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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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addMoleculeStamp(molStamp, nMolWithSameStamp); |
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|
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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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|
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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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} |
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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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|
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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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} |
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nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp; |
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nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp; |
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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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|
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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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|
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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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#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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delete sman_; |
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delete simParams_; |
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delete forceField_; |
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} |
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bool SimInfo::addMolecule(Molecule* mol) { |
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MoleculeIterator i; |
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|
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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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|
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nAtoms_ += mol->getNAtoms(); |
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nBonds_ += mol->getNBonds(); |
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nBends_ += mol->getNBends(); |
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nTorsions_ += mol->getNTorsions(); |
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nRigidBodies_ += mol->getNRigidBodies(); |
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nIntegrableObjects_ += mol->getNIntegrableObjects(); |
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nCutoffGroups_ += mol->getNCutoffGroups(); |
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nConstraints_ += mol->getNConstraintPairs(); |
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addExcludePairs(mol); |
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return true; |
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} else { |
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return false; |
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} |
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} |
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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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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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gezelter |
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removeExcludePairs(mol); |
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molecules_.erase(mol->getGlobalIndex()); |
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delete mol; |
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return true; |
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} else { |
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return false; |
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} |
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} |
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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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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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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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Molecule* mol; |
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StuntDouble* integrableObject; |
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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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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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}//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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ndf_local -= nConstraints_; |
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#ifdef IS_MPI |
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MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
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#else |
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ndf_ = ndf_local; |
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#endif |
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// nZconstraints_ is global, as are the 3 COM translations for the |
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// entire system: |
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ndf_ = ndf_ - 3 - nZconstraint_; |
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} |
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void SimInfo::calcNdfRaw() { |
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int ndfRaw_local; |
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|
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MoleculeIterator i; |
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std::vector<StuntDouble*>::iterator j; |
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Molecule* mol; |
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StuntDouble* integrableObject; |
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gezelter |
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// Raw degrees of freedom that we have to set |
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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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ndfRaw_local += 3; |
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if (integrableObject->isDirectional()) { |
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if (integrableObject->isLinear()) { |
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ndfRaw_local += 2; |
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} else { |
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ndfRaw_local += 3; |
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} |
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} |
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} |
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} |
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#ifdef IS_MPI |
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MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
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#else |
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ndfRaw_ = ndfRaw_local; |
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#endif |
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} |
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void SimInfo::calcNdfTrans() { |
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int ndfTrans_local; |
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|
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ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_; |
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#ifdef IS_MPI |
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MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
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#else |
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ndfTrans_ = ndfTrans_local; |
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#endif |
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ndfTrans_ = ndfTrans_ - 3 - nZconstraint_; |
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} |
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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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Bond* bond; |
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Bend* bend; |
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Torsion* torsion; |
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int a; |
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int b; |
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int c; |
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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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} |
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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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exclude_.addPair(a, b); |
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exclude_.addPair(a, c); |
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exclude_.addPair(b, c); |
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} |
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for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
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a = torsion->getAtomA()->getGlobalIndex(); |
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b = torsion->getAtomB()->getGlobalIndex(); |
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c = torsion->getAtomC()->getGlobalIndex(); |
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d = torsion->getAtomD()->getGlobalIndex(); |
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exclude_.addPair(a, b); |
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exclude_.addPair(a, c); |
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exclude_.addPair(a, d); |
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exclude_.addPair(b, c); |
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exclude_.addPair(b, d); |
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exclude_.addPair(c, d); |
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} |
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} |
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void SimInfo::removeExcludePairs(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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Bond* bond; |
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Bend* bend; |
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Torsion* torsion; |
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int a; |
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int b; |
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int c; |
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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_.removePair(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(); |
363 |
|
|
b = bend->getAtomB()->getGlobalIndex(); |
364 |
|
|
c = bend->getAtomC()->getGlobalIndex(); |
365 |
|
|
|
366 |
|
|
exclude_.removePair(a, b); |
367 |
|
|
exclude_.removePair(a, c); |
368 |
|
|
exclude_.removePair(b, c); |
369 |
|
|
} |
370 |
|
|
|
371 |
tim |
1804 |
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
372 |
tim |
1719 |
a = torsion->getAtomA()->getGlobalIndex(); |
373 |
|
|
b = torsion->getAtomB()->getGlobalIndex(); |
374 |
|
|
c = torsion->getAtomC()->getGlobalIndex(); |
375 |
|
|
d = torsion->getAtomD()->getGlobalIndex(); |
376 |
|
|
|
377 |
|
|
exclude_.removePair(a, b); |
378 |
|
|
exclude_.removePair(a, c); |
379 |
|
|
exclude_.removePair(a, d); |
380 |
|
|
exclude_.removePair(b, c); |
381 |
|
|
exclude_.removePair(b, d); |
382 |
|
|
exclude_.removePair(c, d); |
383 |
|
|
} |
384 |
|
|
|
385 |
|
|
} |
386 |
|
|
|
387 |
|
|
|
388 |
tim |
1725 |
void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) { |
389 |
|
|
int curStampId; |
390 |
|
|
|
391 |
|
|
//index from 0 |
392 |
tim |
1895 |
curStampId = moleculeStamps_.size(); |
393 |
tim |
1725 |
|
394 |
|
|
moleculeStamps_.push_back(molStamp); |
395 |
tim |
1804 |
molStampIds_.insert(molStampIds_.end(), nmol, curStampId); |
396 |
tim |
1725 |
} |
397 |
|
|
|
398 |
tim |
1727 |
void SimInfo::update() { |
399 |
|
|
|
400 |
tim |
1738 |
setupSimType(); |
401 |
|
|
|
402 |
tim |
1733 |
#ifdef IS_MPI |
403 |
|
|
setupFortranParallel(); |
404 |
|
|
#endif |
405 |
tim |
1727 |
|
406 |
tim |
1733 |
setupFortranSim(); |
407 |
|
|
|
408 |
tim |
1807 |
//setup fortran force field |
409 |
|
|
/** @deprecate */ |
410 |
|
|
int isError = 0; |
411 |
|
|
initFortranFF( &fInfo_.SIM_uses_RF , &isError ); |
412 |
|
|
if(isError){ |
413 |
|
|
sprintf( painCave.errMsg, |
414 |
|
|
"ForceField error: There was an error initializing the forceField in fortran.\n" ); |
415 |
|
|
painCave.isFatal = 1; |
416 |
|
|
simError(); |
417 |
|
|
} |
418 |
|
|
|
419 |
|
|
|
420 |
tim |
1738 |
setupCutoff(); |
421 |
|
|
|
422 |
tim |
1733 |
calcNdf(); |
423 |
|
|
calcNdfRaw(); |
424 |
|
|
calcNdfTrans(); |
425 |
tim |
1738 |
|
426 |
|
|
fortranInitialized_ = true; |
427 |
tim |
1733 |
} |
428 |
|
|
|
429 |
|
|
std::set<AtomType*> SimInfo::getUniqueAtomTypes() { |
430 |
tim |
1804 |
SimInfo::MoleculeIterator mi; |
431 |
tim |
1733 |
Molecule* mol; |
432 |
tim |
1804 |
Molecule::AtomIterator ai; |
433 |
tim |
1733 |
Atom* atom; |
434 |
|
|
std::set<AtomType*> atomTypes; |
435 |
|
|
|
436 |
|
|
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
437 |
|
|
|
438 |
|
|
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
439 |
|
|
atomTypes.insert(atom->getAtomType()); |
440 |
|
|
} |
441 |
|
|
|
442 |
|
|
} |
443 |
|
|
|
444 |
|
|
return atomTypes; |
445 |
|
|
} |
446 |
|
|
|
447 |
|
|
void SimInfo::setupSimType() { |
448 |
|
|
std::set<AtomType*>::iterator i; |
449 |
|
|
std::set<AtomType*> atomTypes; |
450 |
|
|
atomTypes = getUniqueAtomTypes(); |
451 |
tim |
1727 |
|
452 |
tim |
1733 |
int useLennardJones = 0; |
453 |
|
|
int useElectrostatic = 0; |
454 |
|
|
int useEAM = 0; |
455 |
|
|
int useCharge = 0; |
456 |
|
|
int useDirectional = 0; |
457 |
|
|
int useDipole = 0; |
458 |
|
|
int useGayBerne = 0; |
459 |
|
|
int useSticky = 0; |
460 |
|
|
int useShape = 0; |
461 |
|
|
int useFLARB = 0; //it is not in AtomType yet |
462 |
|
|
int useDirectionalAtom = 0; |
463 |
|
|
int useElectrostatics = 0; |
464 |
tim |
1841 |
//usePBC and useRF are from simParams |
465 |
tim |
1886 |
int usePBC = simParams_->getPBC(); |
466 |
|
|
int useRF = simParams_->getUseRF(); |
467 |
tim |
1733 |
|
468 |
|
|
//loop over all of the atom types |
469 |
|
|
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
470 |
tim |
1804 |
useLennardJones |= (*i)->isLennardJones(); |
471 |
|
|
useElectrostatic |= (*i)->isElectrostatic(); |
472 |
|
|
useEAM |= (*i)->isEAM(); |
473 |
|
|
useCharge |= (*i)->isCharge(); |
474 |
|
|
useDirectional |= (*i)->isDirectional(); |
475 |
|
|
useDipole |= (*i)->isDipole(); |
476 |
|
|
useGayBerne |= (*i)->isGayBerne(); |
477 |
|
|
useSticky |= (*i)->isSticky(); |
478 |
|
|
useShape |= (*i)->isShape(); |
479 |
tim |
1733 |
} |
480 |
|
|
|
481 |
|
|
if (useSticky || useDipole || useGayBerne || useShape) { |
482 |
|
|
useDirectionalAtom = 1; |
483 |
|
|
} |
484 |
|
|
|
485 |
|
|
if (useCharge || useDipole) { |
486 |
|
|
useElectrostatics = 1; |
487 |
|
|
} |
488 |
|
|
|
489 |
|
|
#ifdef IS_MPI |
490 |
|
|
int temp; |
491 |
|
|
|
492 |
|
|
temp = usePBC; |
493 |
|
|
MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
494 |
|
|
|
495 |
|
|
temp = useDirectionalAtom; |
496 |
|
|
MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
497 |
|
|
|
498 |
|
|
temp = useLennardJones; |
499 |
|
|
MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
500 |
|
|
|
501 |
|
|
temp = useElectrostatics; |
502 |
|
|
MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
503 |
|
|
|
504 |
|
|
temp = useCharge; |
505 |
|
|
MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
506 |
|
|
|
507 |
|
|
temp = useDipole; |
508 |
|
|
MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
509 |
|
|
|
510 |
|
|
temp = useSticky; |
511 |
|
|
MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
512 |
|
|
|
513 |
|
|
temp = useGayBerne; |
514 |
|
|
MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
515 |
|
|
|
516 |
|
|
temp = useEAM; |
517 |
|
|
MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
518 |
|
|
|
519 |
|
|
temp = useShape; |
520 |
|
|
MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
521 |
|
|
|
522 |
|
|
temp = useFLARB; |
523 |
|
|
MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
524 |
|
|
|
525 |
|
|
temp = useRF; |
526 |
|
|
MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
527 |
|
|
|
528 |
|
|
#endif |
529 |
|
|
|
530 |
|
|
fInfo_.SIM_uses_PBC = usePBC; |
531 |
|
|
fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom; |
532 |
|
|
fInfo_.SIM_uses_LennardJones = useLennardJones; |
533 |
|
|
fInfo_.SIM_uses_Electrostatics = useElectrostatics; |
534 |
|
|
fInfo_.SIM_uses_Charges = useCharge; |
535 |
|
|
fInfo_.SIM_uses_Dipoles = useDipole; |
536 |
|
|
fInfo_.SIM_uses_Sticky = useSticky; |
537 |
|
|
fInfo_.SIM_uses_GayBerne = useGayBerne; |
538 |
|
|
fInfo_.SIM_uses_EAM = useEAM; |
539 |
|
|
fInfo_.SIM_uses_Shapes = useShape; |
540 |
|
|
fInfo_.SIM_uses_FLARB = useFLARB; |
541 |
|
|
fInfo_.SIM_uses_RF = useRF; |
542 |
|
|
|
543 |
|
|
if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { |
544 |
tim |
1804 |
|
545 |
tim |
1841 |
if (simParams_->haveDielectric()) { |
546 |
|
|
fInfo_.dielect = simParams_->getDielectric(); |
547 |
tim |
1804 |
} else { |
548 |
|
|
sprintf(painCave.errMsg, |
549 |
|
|
"SimSetup Error: No Dielectric constant was set.\n" |
550 |
|
|
"\tYou are trying to use Reaction Field without" |
551 |
|
|
"\tsetting a dielectric constant!\n"); |
552 |
|
|
painCave.isFatal = 1; |
553 |
|
|
simError(); |
554 |
|
|
} |
555 |
|
|
|
556 |
tim |
1733 |
} else { |
557 |
|
|
fInfo_.dielect = 0.0; |
558 |
|
|
} |
559 |
|
|
|
560 |
|
|
} |
561 |
|
|
|
562 |
|
|
void SimInfo::setupFortranSim() { |
563 |
|
|
int isError; |
564 |
|
|
int nExclude; |
565 |
|
|
std::vector<int> fortranGlobalGroupMembership; |
566 |
|
|
|
567 |
|
|
nExclude = exclude_.getSize(); |
568 |
|
|
isError = 0; |
569 |
|
|
|
570 |
|
|
//globalGroupMembership_ is filled by SimCreator |
571 |
|
|
for (int i = 0; i < nGlobalAtoms_; i++) { |
572 |
|
|
fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1); |
573 |
|
|
} |
574 |
|
|
|
575 |
|
|
//calculate mass ratio of cutoff group |
576 |
|
|
std::vector<double> mfact; |
577 |
tim |
1804 |
SimInfo::MoleculeIterator mi; |
578 |
tim |
1733 |
Molecule* mol; |
579 |
tim |
1804 |
Molecule::CutoffGroupIterator ci; |
580 |
tim |
1733 |
CutoffGroup* cg; |
581 |
tim |
1804 |
Molecule::AtomIterator ai; |
582 |
tim |
1733 |
Atom* atom; |
583 |
|
|
double totalMass; |
584 |
|
|
|
585 |
|
|
//to avoid memory reallocation, reserve enough space for mfact |
586 |
|
|
mfact.reserve(getNCutoffGroups()); |
587 |
|
|
|
588 |
|
|
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
589 |
|
|
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
590 |
|
|
|
591 |
|
|
totalMass = cg->getMass(); |
592 |
|
|
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
593 |
|
|
mfact.push_back(atom->getMass()/totalMass); |
594 |
|
|
} |
595 |
|
|
|
596 |
|
|
} |
597 |
|
|
} |
598 |
|
|
|
599 |
|
|
//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!) |
600 |
|
|
std::vector<int> identArray; |
601 |
|
|
|
602 |
|
|
//to avoid memory reallocation, reserve enough space identArray |
603 |
|
|
identArray.reserve(getNAtoms()); |
604 |
|
|
|
605 |
|
|
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
606 |
|
|
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
607 |
|
|
identArray.push_back(atom->getIdent()); |
608 |
|
|
} |
609 |
|
|
} |
610 |
|
|
|
611 |
tim |
1735 |
//fill molMembershipArray |
612 |
|
|
//molMembershipArray is filled by SimCreator |
613 |
|
|
std::vector<int> molMembershipArray(nGlobalAtoms_); |
614 |
|
|
for (int i = 0; i < nGlobalAtoms_; i++) { |
615 |
tim |
1854 |
molMembershipArray[i] = globalMolMembership_[i] + 1; |
616 |
tim |
1735 |
} |
617 |
|
|
|
618 |
tim |
1733 |
//setup fortran simulation |
619 |
|
|
//gloalExcludes and molMembershipArray should go away (They are never used) |
620 |
|
|
//why the hell fortran need to know molecule? |
621 |
|
|
//OOPSE = Object-Obfuscated Parallel Simulation Engine |
622 |
tim |
1804 |
int nGlobalExcludes = 0; |
623 |
|
|
int* globalExcludes = NULL; |
624 |
|
|
int* excludeList = exclude_.getExcludeList(); |
625 |
|
|
setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList , |
626 |
|
|
&nGlobalExcludes, globalExcludes, &molMembershipArray[0], |
627 |
tim |
1733 |
&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError); |
628 |
|
|
|
629 |
|
|
if( isError ){ |
630 |
|
|
|
631 |
|
|
sprintf( painCave.errMsg, |
632 |
|
|
"There was an error setting the simulation information in fortran.\n" ); |
633 |
|
|
painCave.isFatal = 1; |
634 |
|
|
painCave.severity = OOPSE_ERROR; |
635 |
|
|
simError(); |
636 |
|
|
} |
637 |
|
|
|
638 |
|
|
#ifdef IS_MPI |
639 |
|
|
sprintf( checkPointMsg, |
640 |
|
|
"succesfully sent the simulation information to fortran.\n"); |
641 |
|
|
MPIcheckPoint(); |
642 |
|
|
#endif // is_mpi |
643 |
|
|
} |
644 |
|
|
|
645 |
|
|
|
646 |
|
|
#ifdef IS_MPI |
647 |
|
|
void SimInfo::setupFortranParallel() { |
648 |
|
|
|
649 |
tim |
1727 |
//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex |
650 |
|
|
std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0); |
651 |
|
|
std::vector<int> localToGlobalCutoffGroupIndex; |
652 |
tim |
1804 |
SimInfo::MoleculeIterator mi; |
653 |
|
|
Molecule::AtomIterator ai; |
654 |
|
|
Molecule::CutoffGroupIterator ci; |
655 |
tim |
1727 |
Molecule* mol; |
656 |
|
|
Atom* atom; |
657 |
|
|
CutoffGroup* cg; |
658 |
|
|
mpiSimData parallelData; |
659 |
|
|
int isError; |
660 |
|
|
|
661 |
|
|
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
662 |
|
|
|
663 |
|
|
//local index(index in DataStorge) of atom is important |
664 |
|
|
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
665 |
|
|
localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1; |
666 |
|
|
} |
667 |
|
|
|
668 |
|
|
//local index of cutoff group is trivial, it only depends on the order of travesing |
669 |
|
|
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
670 |
|
|
localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1); |
671 |
|
|
} |
672 |
|
|
|
673 |
|
|
} |
674 |
|
|
|
675 |
tim |
1733 |
//fill up mpiSimData struct |
676 |
|
|
parallelData.nMolGlobal = getNGlobalMolecules(); |
677 |
|
|
parallelData.nMolLocal = getNMolecules(); |
678 |
|
|
parallelData.nAtomsGlobal = getNGlobalAtoms(); |
679 |
|
|
parallelData.nAtomsLocal = getNAtoms(); |
680 |
|
|
parallelData.nGroupsGlobal = getNGlobalCutoffGroups(); |
681 |
|
|
parallelData.nGroupsLocal = getNCutoffGroups(); |
682 |
tim |
1727 |
parallelData.myNode = worldRank; |
683 |
tim |
1883 |
MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors)); |
684 |
tim |
1733 |
|
685 |
|
|
//pass mpiSimData struct and index arrays to fortran |
686 |
tim |
1883 |
setFsimParallel(¶llelData, &(parallelData.nAtomsLocal), |
687 |
|
|
&localToGlobalAtomIndex[0], &(parallelData.nGroupsLocal), |
688 |
tim |
1727 |
&localToGlobalCutoffGroupIndex[0], &isError); |
689 |
|
|
|
690 |
|
|
if (isError) { |
691 |
|
|
sprintf(painCave.errMsg, |
692 |
|
|
"mpiRefresh errror: fortran didn't like something we gave it.\n"); |
693 |
|
|
painCave.isFatal = 1; |
694 |
|
|
simError(); |
695 |
|
|
} |
696 |
|
|
|
697 |
|
|
sprintf(checkPointMsg, " mpiRefresh successful.\n"); |
698 |
|
|
MPIcheckPoint(); |
699 |
|
|
|
700 |
|
|
|
701 |
|
|
} |
702 |
|
|
|
703 |
tim |
1733 |
#endif |
704 |
|
|
|
705 |
tim |
1735 |
double SimInfo::calcMaxCutoffRadius() { |
706 |
|
|
|
707 |
|
|
|
708 |
tim |
1804 |
std::set<AtomType*> atomTypes; |
709 |
|
|
std::set<AtomType*>::iterator i; |
710 |
tim |
1735 |
std::vector<double> cutoffRadius; |
711 |
|
|
|
712 |
|
|
//get the unique atom types |
713 |
|
|
atomTypes = getUniqueAtomTypes(); |
714 |
|
|
|
715 |
|
|
//query the max cutoff radius among these atom types |
716 |
|
|
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
717 |
|
|
cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i)); |
718 |
|
|
} |
719 |
|
|
|
720 |
tim |
1804 |
double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end())); |
721 |
tim |
1735 |
#ifdef IS_MPI |
722 |
|
|
//pick the max cutoff radius among the processors |
723 |
|
|
#endif |
724 |
|
|
|
725 |
|
|
return maxCutoffRadius; |
726 |
|
|
} |
727 |
|
|
|
728 |
tim |
1738 |
void SimInfo::setupCutoff() { |
729 |
|
|
double rcut_; //cutoff radius |
730 |
|
|
double rsw_; //switching radius |
731 |
|
|
|
732 |
|
|
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
733 |
|
|
|
734 |
tim |
1841 |
if (!simParams_->haveRcut()){ |
735 |
tim |
1738 |
sprintf(painCave.errMsg, |
736 |
|
|
"SimCreator Warning: No value was set for the cutoffRadius.\n" |
737 |
|
|
"\tOOPSE will use a default value of 15.0 angstroms" |
738 |
|
|
"\tfor the cutoffRadius.\n"); |
739 |
|
|
painCave.isFatal = 0; |
740 |
|
|
simError(); |
741 |
|
|
rcut_ = 15.0; |
742 |
|
|
} else{ |
743 |
tim |
1841 |
rcut_ = simParams_->getRcut(); |
744 |
tim |
1738 |
} |
745 |
|
|
|
746 |
tim |
1841 |
if (!simParams_->haveRsw()){ |
747 |
tim |
1738 |
sprintf(painCave.errMsg, |
748 |
|
|
"SimCreator Warning: No value was set for switchingRadius.\n" |
749 |
|
|
"\tOOPSE will use a default value of\n" |
750 |
|
|
"\t0.95 * cutoffRadius for the switchingRadius\n"); |
751 |
|
|
painCave.isFatal = 0; |
752 |
|
|
simError(); |
753 |
|
|
rsw_ = 0.95 * rcut_; |
754 |
|
|
} else{ |
755 |
tim |
1841 |
rsw_ = simParams_->getRsw(); |
756 |
tim |
1738 |
} |
757 |
|
|
|
758 |
|
|
} else { |
759 |
|
|
// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
760 |
|
|
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
761 |
|
|
|
762 |
tim |
1841 |
if (simParams_->haveRcut()) { |
763 |
|
|
rcut_ = simParams_->getRcut(); |
764 |
tim |
1738 |
} else { |
765 |
|
|
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
766 |
|
|
rcut_ = calcMaxCutoffRadius(); |
767 |
|
|
} |
768 |
|
|
|
769 |
tim |
1841 |
if (simParams_->haveRsw()) { |
770 |
|
|
rsw_ = simParams_->getRsw(); |
771 |
tim |
1738 |
} else { |
772 |
|
|
rsw_ = rcut_; |
773 |
|
|
} |
774 |
|
|
|
775 |
|
|
} |
776 |
|
|
|
777 |
|
|
double rnblist = rcut_ + 1; // skin of neighbor list |
778 |
|
|
|
779 |
|
|
//Pass these cutoff radius etc. to fortran. This function should be called once and only once |
780 |
|
|
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist); |
781 |
|
|
} |
782 |
|
|
|
783 |
tim |
1733 |
void SimInfo::addProperty(GenericData* genData) { |
784 |
|
|
properties_.addProperty(genData); |
785 |
|
|
} |
786 |
|
|
|
787 |
|
|
void SimInfo::removeProperty(const std::string& propName) { |
788 |
|
|
properties_.removeProperty(propName); |
789 |
|
|
} |
790 |
|
|
|
791 |
|
|
void SimInfo::clearProperties() { |
792 |
|
|
properties_.clearProperties(); |
793 |
|
|
} |
794 |
|
|
|
795 |
|
|
std::vector<std::string> SimInfo::getPropertyNames() { |
796 |
|
|
return properties_.getPropertyNames(); |
797 |
|
|
} |
798 |
|
|
|
799 |
|
|
std::vector<GenericData*> SimInfo::getProperties() { |
800 |
|
|
return properties_.getProperties(); |
801 |
|
|
} |
802 |
|
|
|
803 |
|
|
GenericData* SimInfo::getPropertyByName(const std::string& propName) { |
804 |
|
|
return properties_.getPropertyByName(propName); |
805 |
|
|
} |
806 |
|
|
|
807 |
tim |
1807 |
void SimInfo::setSnapshotManager(SnapshotManager* sman) { |
808 |
|
|
sman_ = sman; |
809 |
tim |
1733 |
|
810 |
tim |
1807 |
Molecule* mol; |
811 |
|
|
RigidBody* rb; |
812 |
|
|
Atom* atom; |
813 |
|
|
SimInfo::MoleculeIterator mi; |
814 |
|
|
Molecule::RigidBodyIterator rbIter; |
815 |
|
|
Molecule::AtomIterator atomIter;; |
816 |
|
|
|
817 |
|
|
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
818 |
|
|
|
819 |
|
|
for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) { |
820 |
|
|
atom->setSnapshotManager(sman_); |
821 |
|
|
} |
822 |
|
|
|
823 |
|
|
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
824 |
|
|
rb->setSnapshotManager(sman_); |
825 |
|
|
} |
826 |
|
|
} |
827 |
|
|
|
828 |
|
|
} |
829 |
|
|
|
830 |
tim |
1843 |
Vector3d SimInfo::getComVel(){ |
831 |
|
|
SimInfo::MoleculeIterator i; |
832 |
|
|
Molecule* mol; |
833 |
|
|
|
834 |
|
|
Vector3d comVel(0.0); |
835 |
|
|
double totalMass = 0.0; |
836 |
|
|
|
837 |
|
|
|
838 |
|
|
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
839 |
|
|
double mass = mol->getMass(); |
840 |
|
|
totalMass += mass; |
841 |
|
|
comVel += mass * mol->getComVel(); |
842 |
|
|
} |
843 |
|
|
|
844 |
tim |
1887 |
#ifdef IS_MPI |
845 |
|
|
double tmpMass = totalMass; |
846 |
|
|
Vector3d tmpComVel(comVel); |
847 |
|
|
MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
848 |
|
|
MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
849 |
|
|
#endif |
850 |
|
|
|
851 |
tim |
1843 |
comVel /= totalMass; |
852 |
|
|
|
853 |
|
|
return comVel; |
854 |
|
|
} |
855 |
|
|
|
856 |
|
|
Vector3d SimInfo::getCom(){ |
857 |
|
|
SimInfo::MoleculeIterator i; |
858 |
|
|
Molecule* mol; |
859 |
|
|
|
860 |
|
|
Vector3d com(0.0); |
861 |
|
|
double totalMass = 0.0; |
862 |
|
|
|
863 |
|
|
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
864 |
|
|
double mass = mol->getMass(); |
865 |
|
|
totalMass += mass; |
866 |
|
|
com += mass * mol->getCom(); |
867 |
|
|
} |
868 |
|
|
|
869 |
tim |
1887 |
#ifdef IS_MPI |
870 |
|
|
double tmpMass = totalMass; |
871 |
|
|
Vector3d tmpCom(com); |
872 |
|
|
MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
873 |
|
|
MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
874 |
|
|
#endif |
875 |
|
|
|
876 |
tim |
1843 |
com /= totalMass; |
877 |
|
|
|
878 |
|
|
return com; |
879 |
|
|
|
880 |
|
|
} |
881 |
|
|
|
882 |
tim |
1832 |
std::ostream& operator <<(std::ostream& o, SimInfo& info) { |
883 |
tim |
1725 |
|
884 |
|
|
return o; |
885 |
|
|
} |
886 |
|
|
|
887 |
tim |
1710 |
}//end namespace oopse |
888 |
tim |
1842 |
|