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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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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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#include <algorithm> |
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#include <set> |
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#include "brains/SimInfo.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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|
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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* globals) : |
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forceField_(ff), globals_(globals), nAtoms_(0), nBonds_(0), |
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nBends_(0), nTorsions_(0), nRigidBodies_(0), nIntegrableObjects_(0), |
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nCutoffGroups_(0), nConstraints_(0), nZconstraint_(0), sman_(NULL), |
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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; // number of atoms belong to cutoff groups |
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int nGroups; //total cutoff groups defined in meta-data file |
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CutoffGroupStamp* cgStamp; |
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int nAtomsInGroups; |
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int nCutoffGroupsInStamp; |
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RigidBodyStamp* rbStamp; |
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int nAtomsInRigidBodies; |
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int nRigidBodiesInStamp; |
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int nRigidAtoms; |
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int nRigidBodies; |
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nGlobalAtoms_ = 0; |
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nGroups = 0; |
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nCutoffAtoms = 0; |
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nRigidBodies = 0; |
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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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//calculate atoms in cutoff groups |
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nAtomsInGroups = 0; |
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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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} |
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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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nAtomsInRigidBodies = 0; |
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nRigidBodiesInStamp = molStamp->getNCutoffGroups(); |
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for (int j=0; j < nRigidBodiesInStamp; j++) { |
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rbStamp = molStamp->getRigidBody(j); |
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nRigidBodiesInStamp += rbStamp->getNMembers(); |
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} |
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nRigidBodies += 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 a rigid body |
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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 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 + nRigidBodies; |
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//initialize globalGroupMembership_, every element of this array will be 0 |
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globalGroupMembership_.insert(globalGroupMembership_.end(), nGlobalAtoms_, 0); |
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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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MemoryUtils::deleteVectorOfPointer(moleculeStamps_); |
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delete sman_; |
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delete globals_; |
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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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i = molecules_.find(mol->getGlobalIndex()); |
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if (i != molecules_.end() ) { |
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molecules_.insert(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->getNConstraints(); |
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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->getNConstraints(); |
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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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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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// 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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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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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(); |
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b = bend->getAtomB()->getGlobalIndex(); |
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|
c = bend->getAtomC()->getGlobalIndex(); |
366 |
|
|
|
367 |
|
|
exclude_.removePair(a, b); |
368 |
|
|
exclude_.removePair(a, c); |
369 |
|
|
exclude_.removePair(b, c); |
370 |
|
|
} |
371 |
|
|
|
372 |
tim |
1804 |
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
373 |
tim |
1719 |
a = torsion->getAtomA()->getGlobalIndex(); |
374 |
|
|
b = torsion->getAtomB()->getGlobalIndex(); |
375 |
|
|
c = torsion->getAtomC()->getGlobalIndex(); |
376 |
|
|
d = torsion->getAtomD()->getGlobalIndex(); |
377 |
|
|
|
378 |
|
|
exclude_.removePair(a, b); |
379 |
|
|
exclude_.removePair(a, c); |
380 |
|
|
exclude_.removePair(a, d); |
381 |
|
|
exclude_.removePair(b, c); |
382 |
|
|
exclude_.removePair(b, d); |
383 |
|
|
exclude_.removePair(c, d); |
384 |
|
|
} |
385 |
|
|
|
386 |
|
|
} |
387 |
|
|
|
388 |
|
|
|
389 |
tim |
1725 |
void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) { |
390 |
|
|
int curStampId; |
391 |
|
|
|
392 |
|
|
//index from 0 |
393 |
|
|
curStampId = molStampIds_.size(); |
394 |
|
|
|
395 |
|
|
moleculeStamps_.push_back(molStamp); |
396 |
tim |
1804 |
molStampIds_.insert(molStampIds_.end(), nmol, curStampId); |
397 |
tim |
1725 |
} |
398 |
|
|
|
399 |
tim |
1727 |
void SimInfo::update() { |
400 |
|
|
|
401 |
tim |
1738 |
setupSimType(); |
402 |
|
|
|
403 |
tim |
1733 |
#ifdef IS_MPI |
404 |
|
|
setupFortranParallel(); |
405 |
|
|
#endif |
406 |
tim |
1727 |
|
407 |
tim |
1733 |
setupFortranSim(); |
408 |
|
|
|
409 |
tim |
1807 |
//setup fortran force field |
410 |
|
|
/** @deprecate */ |
411 |
|
|
int isError = 0; |
412 |
|
|
initFortranFF( &fInfo_.SIM_uses_RF , &isError ); |
413 |
|
|
if(isError){ |
414 |
|
|
sprintf( painCave.errMsg, |
415 |
|
|
"ForceField error: There was an error initializing the forceField in fortran.\n" ); |
416 |
|
|
painCave.isFatal = 1; |
417 |
|
|
simError(); |
418 |
|
|
} |
419 |
|
|
|
420 |
|
|
|
421 |
tim |
1738 |
setupCutoff(); |
422 |
|
|
|
423 |
tim |
1733 |
calcNdf(); |
424 |
|
|
calcNdfRaw(); |
425 |
|
|
calcNdfTrans(); |
426 |
tim |
1738 |
|
427 |
|
|
fortranInitialized_ = true; |
428 |
tim |
1733 |
} |
429 |
|
|
|
430 |
|
|
std::set<AtomType*> SimInfo::getUniqueAtomTypes() { |
431 |
tim |
1804 |
SimInfo::MoleculeIterator mi; |
432 |
tim |
1733 |
Molecule* mol; |
433 |
tim |
1804 |
Molecule::AtomIterator ai; |
434 |
tim |
1733 |
Atom* atom; |
435 |
|
|
std::set<AtomType*> atomTypes; |
436 |
|
|
|
437 |
|
|
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
438 |
|
|
|
439 |
|
|
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
440 |
|
|
atomTypes.insert(atom->getAtomType()); |
441 |
|
|
} |
442 |
|
|
|
443 |
|
|
} |
444 |
|
|
|
445 |
|
|
return atomTypes; |
446 |
|
|
} |
447 |
|
|
|
448 |
|
|
void SimInfo::setupSimType() { |
449 |
|
|
std::set<AtomType*>::iterator i; |
450 |
|
|
std::set<AtomType*> atomTypes; |
451 |
|
|
atomTypes = getUniqueAtomTypes(); |
452 |
tim |
1727 |
|
453 |
tim |
1733 |
int useLennardJones = 0; |
454 |
|
|
int useElectrostatic = 0; |
455 |
|
|
int useEAM = 0; |
456 |
|
|
int useCharge = 0; |
457 |
|
|
int useDirectional = 0; |
458 |
|
|
int useDipole = 0; |
459 |
|
|
int useGayBerne = 0; |
460 |
|
|
int useSticky = 0; |
461 |
|
|
int useShape = 0; |
462 |
|
|
int useFLARB = 0; //it is not in AtomType yet |
463 |
|
|
int useDirectionalAtom = 0; |
464 |
|
|
int useElectrostatics = 0; |
465 |
|
|
//usePBC and useRF are from globals |
466 |
|
|
bool usePBC = globals_->getPBC(); |
467 |
|
|
bool useRF = globals_->getUseRF(); |
468 |
|
|
|
469 |
|
|
//loop over all of the atom types |
470 |
|
|
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
471 |
tim |
1804 |
useLennardJones |= (*i)->isLennardJones(); |
472 |
|
|
useElectrostatic |= (*i)->isElectrostatic(); |
473 |
|
|
useEAM |= (*i)->isEAM(); |
474 |
|
|
useCharge |= (*i)->isCharge(); |
475 |
|
|
useDirectional |= (*i)->isDirectional(); |
476 |
|
|
useDipole |= (*i)->isDipole(); |
477 |
|
|
useGayBerne |= (*i)->isGayBerne(); |
478 |
|
|
useSticky |= (*i)->isSticky(); |
479 |
|
|
useShape |= (*i)->isShape(); |
480 |
tim |
1733 |
} |
481 |
|
|
|
482 |
|
|
if (useSticky || useDipole || useGayBerne || useShape) { |
483 |
|
|
useDirectionalAtom = 1; |
484 |
|
|
} |
485 |
|
|
|
486 |
|
|
if (useCharge || useDipole) { |
487 |
|
|
useElectrostatics = 1; |
488 |
|
|
} |
489 |
|
|
|
490 |
|
|
#ifdef IS_MPI |
491 |
|
|
int temp; |
492 |
|
|
|
493 |
|
|
temp = usePBC; |
494 |
|
|
MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
495 |
|
|
|
496 |
|
|
temp = useDirectionalAtom; |
497 |
|
|
MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
498 |
|
|
|
499 |
|
|
temp = useLennardJones; |
500 |
|
|
MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
501 |
|
|
|
502 |
|
|
temp = useElectrostatics; |
503 |
|
|
MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
504 |
|
|
|
505 |
|
|
temp = useCharge; |
506 |
|
|
MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
507 |
|
|
|
508 |
|
|
temp = useDipole; |
509 |
|
|
MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
510 |
|
|
|
511 |
|
|
temp = useSticky; |
512 |
|
|
MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
513 |
|
|
|
514 |
|
|
temp = useGayBerne; |
515 |
|
|
MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
516 |
|
|
|
517 |
|
|
temp = useEAM; |
518 |
|
|
MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
519 |
|
|
|
520 |
|
|
temp = useShape; |
521 |
|
|
MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
522 |
|
|
|
523 |
|
|
temp = useFLARB; |
524 |
|
|
MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
525 |
|
|
|
526 |
|
|
temp = useRF; |
527 |
|
|
MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
528 |
|
|
|
529 |
|
|
#endif |
530 |
|
|
|
531 |
|
|
fInfo_.SIM_uses_PBC = usePBC; |
532 |
|
|
fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom; |
533 |
|
|
fInfo_.SIM_uses_LennardJones = useLennardJones; |
534 |
|
|
fInfo_.SIM_uses_Electrostatics = useElectrostatics; |
535 |
|
|
fInfo_.SIM_uses_Charges = useCharge; |
536 |
|
|
fInfo_.SIM_uses_Dipoles = useDipole; |
537 |
|
|
fInfo_.SIM_uses_Sticky = useSticky; |
538 |
|
|
fInfo_.SIM_uses_GayBerne = useGayBerne; |
539 |
|
|
fInfo_.SIM_uses_EAM = useEAM; |
540 |
|
|
fInfo_.SIM_uses_Shapes = useShape; |
541 |
|
|
fInfo_.SIM_uses_FLARB = useFLARB; |
542 |
|
|
fInfo_.SIM_uses_RF = useRF; |
543 |
|
|
|
544 |
|
|
if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { |
545 |
tim |
1804 |
|
546 |
|
|
if (globals_->haveDielectric()) { |
547 |
|
|
fInfo_.dielect = globals_->getDielectric(); |
548 |
|
|
} else { |
549 |
|
|
sprintf(painCave.errMsg, |
550 |
|
|
"SimSetup Error: No Dielectric constant was set.\n" |
551 |
|
|
"\tYou are trying to use Reaction Field without" |
552 |
|
|
"\tsetting a dielectric constant!\n"); |
553 |
|
|
painCave.isFatal = 1; |
554 |
|
|
simError(); |
555 |
|
|
} |
556 |
|
|
|
557 |
tim |
1733 |
} else { |
558 |
|
|
fInfo_.dielect = 0.0; |
559 |
|
|
} |
560 |
|
|
|
561 |
|
|
} |
562 |
|
|
|
563 |
|
|
void SimInfo::setupFortranSim() { |
564 |
|
|
int isError; |
565 |
|
|
int nExclude; |
566 |
|
|
std::vector<int> fortranGlobalGroupMembership; |
567 |
|
|
|
568 |
|
|
nExclude = exclude_.getSize(); |
569 |
|
|
isError = 0; |
570 |
|
|
|
571 |
|
|
//globalGroupMembership_ is filled by SimCreator |
572 |
|
|
for (int i = 0; i < nGlobalAtoms_; i++) { |
573 |
|
|
fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1); |
574 |
|
|
} |
575 |
|
|
|
576 |
|
|
//calculate mass ratio of cutoff group |
577 |
|
|
std::vector<double> mfact; |
578 |
tim |
1804 |
SimInfo::MoleculeIterator mi; |
579 |
tim |
1733 |
Molecule* mol; |
580 |
tim |
1804 |
Molecule::CutoffGroupIterator ci; |
581 |
tim |
1733 |
CutoffGroup* cg; |
582 |
tim |
1804 |
Molecule::AtomIterator ai; |
583 |
tim |
1733 |
Atom* atom; |
584 |
|
|
double totalMass; |
585 |
|
|
|
586 |
|
|
//to avoid memory reallocation, reserve enough space for mfact |
587 |
|
|
mfact.reserve(getNCutoffGroups()); |
588 |
|
|
|
589 |
|
|
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
590 |
|
|
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
591 |
|
|
|
592 |
|
|
totalMass = cg->getMass(); |
593 |
|
|
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
594 |
|
|
mfact.push_back(atom->getMass()/totalMass); |
595 |
|
|
} |
596 |
|
|
|
597 |
|
|
} |
598 |
|
|
} |
599 |
|
|
|
600 |
|
|
//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!) |
601 |
|
|
std::vector<int> identArray; |
602 |
|
|
|
603 |
|
|
//to avoid memory reallocation, reserve enough space identArray |
604 |
|
|
identArray.reserve(getNAtoms()); |
605 |
|
|
|
606 |
|
|
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
607 |
|
|
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
608 |
|
|
identArray.push_back(atom->getIdent()); |
609 |
|
|
} |
610 |
|
|
} |
611 |
|
|
|
612 |
tim |
1735 |
//fill molMembershipArray |
613 |
|
|
//molMembershipArray is filled by SimCreator |
614 |
|
|
std::vector<int> molMembershipArray(nGlobalAtoms_); |
615 |
|
|
for (int i = 0; i < nGlobalAtoms_; i++) { |
616 |
|
|
molMembershipArray.push_back(globalMolMembership_[i] + 1); |
617 |
|
|
} |
618 |
|
|
|
619 |
tim |
1733 |
//setup fortran simulation |
620 |
|
|
//gloalExcludes and molMembershipArray should go away (They are never used) |
621 |
|
|
//why the hell fortran need to know molecule? |
622 |
|
|
//OOPSE = Object-Obfuscated Parallel Simulation Engine |
623 |
tim |
1804 |
int nGlobalExcludes = 0; |
624 |
|
|
int* globalExcludes = NULL; |
625 |
|
|
int* excludeList = exclude_.getExcludeList(); |
626 |
|
|
setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList , |
627 |
|
|
&nGlobalExcludes, globalExcludes, &molMembershipArray[0], |
628 |
tim |
1733 |
&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError); |
629 |
|
|
|
630 |
|
|
if( isError ){ |
631 |
|
|
|
632 |
|
|
sprintf( painCave.errMsg, |
633 |
|
|
"There was an error setting the simulation information in fortran.\n" ); |
634 |
|
|
painCave.isFatal = 1; |
635 |
|
|
painCave.severity = OOPSE_ERROR; |
636 |
|
|
simError(); |
637 |
|
|
} |
638 |
|
|
|
639 |
|
|
#ifdef IS_MPI |
640 |
|
|
sprintf( checkPointMsg, |
641 |
|
|
"succesfully sent the simulation information to fortran.\n"); |
642 |
|
|
MPIcheckPoint(); |
643 |
|
|
#endif // is_mpi |
644 |
|
|
} |
645 |
|
|
|
646 |
|
|
|
647 |
|
|
#ifdef IS_MPI |
648 |
|
|
void SimInfo::setupFortranParallel() { |
649 |
|
|
|
650 |
tim |
1727 |
//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex |
651 |
|
|
std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0); |
652 |
|
|
std::vector<int> localToGlobalCutoffGroupIndex; |
653 |
tim |
1804 |
SimInfo::MoleculeIterator mi; |
654 |
|
|
Molecule::AtomIterator ai; |
655 |
|
|
Molecule::CutoffGroupIterator ci; |
656 |
tim |
1727 |
Molecule* mol; |
657 |
|
|
Atom* atom; |
658 |
|
|
CutoffGroup* cg; |
659 |
|
|
mpiSimData parallelData; |
660 |
|
|
int isError; |
661 |
|
|
|
662 |
|
|
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
663 |
|
|
|
664 |
|
|
//local index(index in DataStorge) of atom is important |
665 |
|
|
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
666 |
|
|
localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1; |
667 |
|
|
} |
668 |
|
|
|
669 |
|
|
//local index of cutoff group is trivial, it only depends on the order of travesing |
670 |
|
|
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
671 |
|
|
localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1); |
672 |
|
|
} |
673 |
|
|
|
674 |
|
|
} |
675 |
|
|
|
676 |
tim |
1733 |
//fill up mpiSimData struct |
677 |
|
|
parallelData.nMolGlobal = getNGlobalMolecules(); |
678 |
|
|
parallelData.nMolLocal = getNMolecules(); |
679 |
|
|
parallelData.nAtomsGlobal = getNGlobalAtoms(); |
680 |
|
|
parallelData.nAtomsLocal = getNAtoms(); |
681 |
|
|
parallelData.nGroupsGlobal = getNGlobalCutoffGroups(); |
682 |
|
|
parallelData.nGroupsLocal = getNCutoffGroups(); |
683 |
tim |
1727 |
parallelData.myNode = worldRank; |
684 |
|
|
MPI_Comm_size(MPI_COMM_WORLD, &(parallelData->nProcessors)); |
685 |
tim |
1733 |
|
686 |
|
|
//pass mpiSimData struct and index arrays to fortran |
687 |
|
|
setFsimParallel(parallelData, &(parallelData->nAtomsLocal), |
688 |
tim |
1727 |
&localToGlobalAtomIndex[0], &(parallelData->nGroupsLocal), |
689 |
|
|
&localToGlobalCutoffGroupIndex[0], &isError); |
690 |
|
|
|
691 |
|
|
if (isError) { |
692 |
|
|
sprintf(painCave.errMsg, |
693 |
|
|
"mpiRefresh errror: fortran didn't like something we gave it.\n"); |
694 |
|
|
painCave.isFatal = 1; |
695 |
|
|
simError(); |
696 |
|
|
} |
697 |
|
|
|
698 |
|
|
sprintf(checkPointMsg, " mpiRefresh successful.\n"); |
699 |
|
|
MPIcheckPoint(); |
700 |
|
|
|
701 |
|
|
|
702 |
|
|
} |
703 |
|
|
|
704 |
tim |
1733 |
#endif |
705 |
|
|
|
706 |
tim |
1735 |
double SimInfo::calcMaxCutoffRadius() { |
707 |
|
|
|
708 |
|
|
|
709 |
tim |
1804 |
std::set<AtomType*> atomTypes; |
710 |
|
|
std::set<AtomType*>::iterator i; |
711 |
tim |
1735 |
std::vector<double> cutoffRadius; |
712 |
|
|
|
713 |
|
|
//get the unique atom types |
714 |
|
|
atomTypes = getUniqueAtomTypes(); |
715 |
|
|
|
716 |
|
|
//query the max cutoff radius among these atom types |
717 |
|
|
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
718 |
|
|
cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i)); |
719 |
|
|
} |
720 |
|
|
|
721 |
tim |
1804 |
double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end())); |
722 |
tim |
1735 |
#ifdef IS_MPI |
723 |
|
|
//pick the max cutoff radius among the processors |
724 |
|
|
#endif |
725 |
|
|
|
726 |
|
|
return maxCutoffRadius; |
727 |
|
|
} |
728 |
|
|
|
729 |
tim |
1738 |
void SimInfo::setupCutoff() { |
730 |
|
|
double rcut_; //cutoff radius |
731 |
|
|
double rsw_; //switching radius |
732 |
|
|
|
733 |
|
|
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
734 |
|
|
|
735 |
|
|
if (!globals_->haveRcut()){ |
736 |
|
|
sprintf(painCave.errMsg, |
737 |
|
|
"SimCreator Warning: No value was set for the cutoffRadius.\n" |
738 |
|
|
"\tOOPSE will use a default value of 15.0 angstroms" |
739 |
|
|
"\tfor the cutoffRadius.\n"); |
740 |
|
|
painCave.isFatal = 0; |
741 |
|
|
simError(); |
742 |
|
|
rcut_ = 15.0; |
743 |
|
|
} else{ |
744 |
|
|
rcut_ = globals_->getRcut(); |
745 |
|
|
} |
746 |
|
|
|
747 |
|
|
if (!globals_->haveRsw()){ |
748 |
|
|
sprintf(painCave.errMsg, |
749 |
|
|
"SimCreator Warning: No value was set for switchingRadius.\n" |
750 |
|
|
"\tOOPSE will use a default value of\n" |
751 |
|
|
"\t0.95 * cutoffRadius for the switchingRadius\n"); |
752 |
|
|
painCave.isFatal = 0; |
753 |
|
|
simError(); |
754 |
|
|
rsw_ = 0.95 * rcut_; |
755 |
|
|
} else{ |
756 |
|
|
rsw_ = globals_->getRsw(); |
757 |
|
|
} |
758 |
|
|
|
759 |
|
|
} else { |
760 |
|
|
// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
761 |
|
|
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
762 |
|
|
|
763 |
|
|
if (globals_->haveRcut()) { |
764 |
|
|
rcut_ = globals_->getRcut(); |
765 |
|
|
} else { |
766 |
|
|
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
767 |
|
|
rcut_ = calcMaxCutoffRadius(); |
768 |
|
|
} |
769 |
|
|
|
770 |
|
|
if (globals_->haveRsw()) { |
771 |
tim |
1804 |
rsw_ = globals_->getRsw(); |
772 |
tim |
1738 |
} else { |
773 |
|
|
rsw_ = rcut_; |
774 |
|
|
} |
775 |
|
|
|
776 |
|
|
} |
777 |
|
|
|
778 |
|
|
double rnblist = rcut_ + 1; // skin of neighbor list |
779 |
|
|
|
780 |
|
|
//Pass these cutoff radius etc. to fortran. This function should be called once and only once |
781 |
|
|
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist); |
782 |
|
|
} |
783 |
|
|
|
784 |
tim |
1733 |
void SimInfo::addProperty(GenericData* genData) { |
785 |
|
|
properties_.addProperty(genData); |
786 |
|
|
} |
787 |
|
|
|
788 |
|
|
void SimInfo::removeProperty(const std::string& propName) { |
789 |
|
|
properties_.removeProperty(propName); |
790 |
|
|
} |
791 |
|
|
|
792 |
|
|
void SimInfo::clearProperties() { |
793 |
|
|
properties_.clearProperties(); |
794 |
|
|
} |
795 |
|
|
|
796 |
|
|
std::vector<std::string> SimInfo::getPropertyNames() { |
797 |
|
|
return properties_.getPropertyNames(); |
798 |
|
|
} |
799 |
|
|
|
800 |
|
|
std::vector<GenericData*> SimInfo::getProperties() { |
801 |
|
|
return properties_.getProperties(); |
802 |
|
|
} |
803 |
|
|
|
804 |
|
|
GenericData* SimInfo::getPropertyByName(const std::string& propName) { |
805 |
|
|
return properties_.getPropertyByName(propName); |
806 |
|
|
} |
807 |
|
|
|
808 |
tim |
1807 |
void SimInfo::setSnapshotManager(SnapshotManager* sman) { |
809 |
|
|
sman_ = sman; |
810 |
tim |
1733 |
|
811 |
tim |
1807 |
Molecule* mol; |
812 |
|
|
RigidBody* rb; |
813 |
|
|
Atom* atom; |
814 |
|
|
SimInfo::MoleculeIterator mi; |
815 |
|
|
Molecule::RigidBodyIterator rbIter; |
816 |
|
|
Molecule::AtomIterator atomIter;; |
817 |
|
|
|
818 |
|
|
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
819 |
|
|
|
820 |
|
|
for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) { |
821 |
|
|
atom->setSnapshotManager(sman_); |
822 |
|
|
} |
823 |
|
|
|
824 |
|
|
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
825 |
|
|
rb->setSnapshotManager(sman_); |
826 |
|
|
} |
827 |
|
|
} |
828 |
|
|
|
829 |
|
|
} |
830 |
|
|
|
831 |
tim |
1725 |
std::ostream& operator <<(ostream& o, SimInfo& info) { |
832 |
|
|
|
833 |
|
|
return o; |
834 |
|
|
} |
835 |
|
|
|
836 |
tim |
1710 |
}//end namespace oopse |