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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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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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|
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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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|
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#include <algorithm> |
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#include <set> |
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|
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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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#include "selection/SelectionManager.hpp" |
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|
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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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|
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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), selectMan_(NULL) { |
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|
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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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|
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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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|
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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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|
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nGroups += nCutoffGroupsInStamp * nMolWithSameStamp; |
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nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp; |
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|
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//calculate atoms in rigid bodies |
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int nAtomsInRigidBodies = 0; |
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int nRigidBodiesInStamp = molStamp->getNRigidBodies(); |
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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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|
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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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|
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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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|
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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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selectMan_ = new SelectionManager(this); |
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selectMan_->selectAll(); |
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} |
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|
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SimInfo::~SimInfo() { |
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//MemoryUtils::deleteVectorOfPointer(molecules_); |
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|
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MemoryUtils::deleteVectorOfPointer(moleculeStamps_); |
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|
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delete sman_; |
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delete simParams_; |
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delete forceField_; |
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delete selectMan_; |
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} |
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|
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int SimInfo::getNGlobalConstraints() { |
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int 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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MPI_COMM_WORLD); |
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#else |
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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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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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|
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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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|
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addExcludePairs(mol); |
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|
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return true; |
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} else { |
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return false; |
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} |
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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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|
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if (i != molecules_.end() ) { |
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|
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assert(mol == i->second); |
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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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|
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removeExcludePairs(mol); |
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molecules_.erase(mol->getGlobalIndex()); |
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|
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delete mol; |
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|
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return true; |
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} else { |
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return false; |
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} |
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|
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|
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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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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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++i; |
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return i == molecules_.end() ? NULL : i->second; |
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} |
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|
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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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|
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ndf_local = 0; |
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|
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for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
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for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(j)) { |
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|
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ndf_local += 3; |
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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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|
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}//end for (integrableObject) |
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}// end for (mol) |
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|
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// n_constraints is local, so subtract them on each processor |
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ndf_local -= nConstraints_; |
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|
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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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|
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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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} |
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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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|
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// Raw degrees of freedom that we have to set |
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ndfRaw_local = 0; |
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|
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for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
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for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(j)) { |
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|
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ndfRaw_local += 3; |
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|
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if (integrableObject->isDirectional()) { |
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if (integrableObject->isLinear()) { |
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ndfRaw_local += 2; |
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} else { |
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ndfRaw_local += 3; |
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} |
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} |
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|
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} |
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} |
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|
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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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|
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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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|
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|
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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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|
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ndfTrans_ = ndfTrans_ - 3 - nZconstraint_; |
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|
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} |
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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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|
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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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|
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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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|
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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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|
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exclude_.addPair(a, b); |
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exclude_.addPair(a, c); |
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exclude_.addPair(a, d); |
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exclude_.addPair(b, c); |
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exclude_.addPair(b, d); |
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exclude_.addPair(c, d); |
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} |
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|
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|
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} |
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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; |
377 |
Bend* bend; |
378 |
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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|
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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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|
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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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|
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exclude_.removePair(a, b); |
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exclude_.removePair(a, c); |
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exclude_.removePair(b, c); |
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} |
399 |
|
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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(); |
405 |
|
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exclude_.removePair(a, b); |
407 |
exclude_.removePair(a, c); |
408 |
exclude_.removePair(a, d); |
409 |
exclude_.removePair(b, c); |
410 |
exclude_.removePair(b, d); |
411 |
exclude_.removePair(c, d); |
412 |
} |
413 |
|
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} |
415 |
|
416 |
|
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void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) { |
418 |
int curStampId; |
419 |
|
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//index from 0 |
421 |
curStampId = moleculeStamps_.size(); |
422 |
|
423 |
moleculeStamps_.push_back(molStamp); |
424 |
molStampIds_.insert(molStampIds_.end(), nmol, curStampId); |
425 |
} |
426 |
|
427 |
void SimInfo::update() { |
428 |
|
429 |
setupSimType(); |
430 |
|
431 |
#ifdef IS_MPI |
432 |
setupFortranParallel(); |
433 |
#endif |
434 |
|
435 |
setupFortranSim(); |
436 |
|
437 |
//setup fortran force field |
438 |
/** @deprecate */ |
439 |
int isError = 0; |
440 |
initFortranFF( &fInfo_.SIM_uses_RF , &isError ); |
441 |
if(isError){ |
442 |
sprintf( painCave.errMsg, |
443 |
"ForceField error: There was an error initializing the forceField in fortran.\n" ); |
444 |
painCave.isFatal = 1; |
445 |
simError(); |
446 |
} |
447 |
|
448 |
|
449 |
setupCutoff(); |
450 |
|
451 |
calcNdf(); |
452 |
calcNdfRaw(); |
453 |
calcNdfTrans(); |
454 |
|
455 |
fortranInitialized_ = true; |
456 |
} |
457 |
|
458 |
std::set<AtomType*> SimInfo::getUniqueAtomTypes() { |
459 |
SimInfo::MoleculeIterator mi; |
460 |
Molecule* mol; |
461 |
Molecule::AtomIterator ai; |
462 |
Atom* atom; |
463 |
std::set<AtomType*> atomTypes; |
464 |
|
465 |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
466 |
|
467 |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
468 |
atomTypes.insert(atom->getAtomType()); |
469 |
} |
470 |
|
471 |
} |
472 |
|
473 |
return atomTypes; |
474 |
} |
475 |
|
476 |
void SimInfo::setupSimType() { |
477 |
std::set<AtomType*>::iterator i; |
478 |
std::set<AtomType*> atomTypes; |
479 |
atomTypes = getUniqueAtomTypes(); |
480 |
|
481 |
int useLennardJones = 0; |
482 |
int useElectrostatic = 0; |
483 |
int useEAM = 0; |
484 |
int useCharge = 0; |
485 |
int useDirectional = 0; |
486 |
int useDipole = 0; |
487 |
int useGayBerne = 0; |
488 |
int useSticky = 0; |
489 |
int useShape = 0; |
490 |
int useFLARB = 0; //it is not in AtomType yet |
491 |
int useDirectionalAtom = 0; |
492 |
int useElectrostatics = 0; |
493 |
//usePBC and useRF are from simParams |
494 |
int usePBC = simParams_->getPBC(); |
495 |
int useRF = simParams_->getUseRF(); |
496 |
|
497 |
//loop over all of the atom types |
498 |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
499 |
useLennardJones |= (*i)->isLennardJones(); |
500 |
useElectrostatic |= (*i)->isElectrostatic(); |
501 |
useEAM |= (*i)->isEAM(); |
502 |
useCharge |= (*i)->isCharge(); |
503 |
useDirectional |= (*i)->isDirectional(); |
504 |
useDipole |= (*i)->isDipole(); |
505 |
useGayBerne |= (*i)->isGayBerne(); |
506 |
useSticky |= (*i)->isSticky(); |
507 |
useShape |= (*i)->isShape(); |
508 |
} |
509 |
|
510 |
if (useSticky || useDipole || useGayBerne || useShape) { |
511 |
useDirectionalAtom = 1; |
512 |
} |
513 |
|
514 |
if (useCharge || useDipole) { |
515 |
useElectrostatics = 1; |
516 |
} |
517 |
|
518 |
#ifdef IS_MPI |
519 |
int temp; |
520 |
|
521 |
temp = usePBC; |
522 |
MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
523 |
|
524 |
temp = useDirectionalAtom; |
525 |
MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
526 |
|
527 |
temp = useLennardJones; |
528 |
MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
529 |
|
530 |
temp = useElectrostatics; |
531 |
MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
532 |
|
533 |
temp = useCharge; |
534 |
MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
535 |
|
536 |
temp = useDipole; |
537 |
MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
538 |
|
539 |
temp = useSticky; |
540 |
MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
541 |
|
542 |
temp = useGayBerne; |
543 |
MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
544 |
|
545 |
temp = useEAM; |
546 |
MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
547 |
|
548 |
temp = useShape; |
549 |
MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
550 |
|
551 |
temp = useFLARB; |
552 |
MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
553 |
|
554 |
temp = useRF; |
555 |
MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
556 |
|
557 |
#endif |
558 |
|
559 |
fInfo_.SIM_uses_PBC = usePBC; |
560 |
fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom; |
561 |
fInfo_.SIM_uses_LennardJones = useLennardJones; |
562 |
fInfo_.SIM_uses_Electrostatics = useElectrostatics; |
563 |
fInfo_.SIM_uses_Charges = useCharge; |
564 |
fInfo_.SIM_uses_Dipoles = useDipole; |
565 |
fInfo_.SIM_uses_Sticky = useSticky; |
566 |
fInfo_.SIM_uses_GayBerne = useGayBerne; |
567 |
fInfo_.SIM_uses_EAM = useEAM; |
568 |
fInfo_.SIM_uses_Shapes = useShape; |
569 |
fInfo_.SIM_uses_FLARB = useFLARB; |
570 |
fInfo_.SIM_uses_RF = useRF; |
571 |
|
572 |
if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { |
573 |
|
574 |
if (simParams_->haveDielectric()) { |
575 |
fInfo_.dielect = simParams_->getDielectric(); |
576 |
} else { |
577 |
sprintf(painCave.errMsg, |
578 |
"SimSetup Error: No Dielectric constant was set.\n" |
579 |
"\tYou are trying to use Reaction Field without" |
580 |
"\tsetting a dielectric constant!\n"); |
581 |
painCave.isFatal = 1; |
582 |
simError(); |
583 |
} |
584 |
|
585 |
} else { |
586 |
fInfo_.dielect = 0.0; |
587 |
} |
588 |
|
589 |
} |
590 |
|
591 |
void SimInfo::setupFortranSim() { |
592 |
int isError; |
593 |
int nExclude; |
594 |
std::vector<int> fortranGlobalGroupMembership; |
595 |
|
596 |
nExclude = exclude_.getSize(); |
597 |
isError = 0; |
598 |
|
599 |
//globalGroupMembership_ is filled by SimCreator |
600 |
for (int i = 0; i < nGlobalAtoms_; i++) { |
601 |
fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1); |
602 |
} |
603 |
|
604 |
//calculate mass ratio of cutoff group |
605 |
std::vector<double> mfact; |
606 |
SimInfo::MoleculeIterator mi; |
607 |
Molecule* mol; |
608 |
Molecule::CutoffGroupIterator ci; |
609 |
CutoffGroup* cg; |
610 |
Molecule::AtomIterator ai; |
611 |
Atom* atom; |
612 |
double totalMass; |
613 |
|
614 |
//to avoid memory reallocation, reserve enough space for mfact |
615 |
mfact.reserve(getNCutoffGroups()); |
616 |
|
617 |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
618 |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
619 |
|
620 |
totalMass = cg->getMass(); |
621 |
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
622 |
mfact.push_back(atom->getMass()/totalMass); |
623 |
} |
624 |
|
625 |
} |
626 |
} |
627 |
|
628 |
//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!) |
629 |
std::vector<int> identArray; |
630 |
|
631 |
//to avoid memory reallocation, reserve enough space identArray |
632 |
identArray.reserve(getNAtoms()); |
633 |
|
634 |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
635 |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
636 |
identArray.push_back(atom->getIdent()); |
637 |
} |
638 |
} |
639 |
|
640 |
//fill molMembershipArray |
641 |
//molMembershipArray is filled by SimCreator |
642 |
std::vector<int> molMembershipArray(nGlobalAtoms_); |
643 |
for (int i = 0; i < nGlobalAtoms_; i++) { |
644 |
molMembershipArray[i] = globalMolMembership_[i] + 1; |
645 |
} |
646 |
|
647 |
//setup fortran simulation |
648 |
//gloalExcludes and molMembershipArray should go away (They are never used) |
649 |
//why the hell fortran need to know molecule? |
650 |
//OOPSE = Object-Obfuscated Parallel Simulation Engine |
651 |
int nGlobalExcludes = 0; |
652 |
int* globalExcludes = NULL; |
653 |
int* excludeList = exclude_.getExcludeList(); |
654 |
setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList , |
655 |
&nGlobalExcludes, globalExcludes, &molMembershipArray[0], |
656 |
&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError); |
657 |
|
658 |
if( isError ){ |
659 |
|
660 |
sprintf( painCave.errMsg, |
661 |
"There was an error setting the simulation information in fortran.\n" ); |
662 |
painCave.isFatal = 1; |
663 |
painCave.severity = OOPSE_ERROR; |
664 |
simError(); |
665 |
} |
666 |
|
667 |
#ifdef IS_MPI |
668 |
sprintf( checkPointMsg, |
669 |
"succesfully sent the simulation information to fortran.\n"); |
670 |
MPIcheckPoint(); |
671 |
#endif // is_mpi |
672 |
} |
673 |
|
674 |
|
675 |
#ifdef IS_MPI |
676 |
void SimInfo::setupFortranParallel() { |
677 |
|
678 |
//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex |
679 |
std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0); |
680 |
std::vector<int> localToGlobalCutoffGroupIndex; |
681 |
SimInfo::MoleculeIterator mi; |
682 |
Molecule::AtomIterator ai; |
683 |
Molecule::CutoffGroupIterator ci; |
684 |
Molecule* mol; |
685 |
Atom* atom; |
686 |
CutoffGroup* cg; |
687 |
mpiSimData parallelData; |
688 |
int isError; |
689 |
|
690 |
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
691 |
|
692 |
//local index(index in DataStorge) of atom is important |
693 |
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
694 |
localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1; |
695 |
} |
696 |
|
697 |
//local index of cutoff group is trivial, it only depends on the order of travesing |
698 |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
699 |
localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1); |
700 |
} |
701 |
|
702 |
} |
703 |
|
704 |
//fill up mpiSimData struct |
705 |
parallelData.nMolGlobal = getNGlobalMolecules(); |
706 |
parallelData.nMolLocal = getNMolecules(); |
707 |
parallelData.nAtomsGlobal = getNGlobalAtoms(); |
708 |
parallelData.nAtomsLocal = getNAtoms(); |
709 |
parallelData.nGroupsGlobal = getNGlobalCutoffGroups(); |
710 |
parallelData.nGroupsLocal = getNCutoffGroups(); |
711 |
parallelData.myNode = worldRank; |
712 |
MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors)); |
713 |
|
714 |
//pass mpiSimData struct and index arrays to fortran |
715 |
setFsimParallel(¶llelData, &(parallelData.nAtomsLocal), |
716 |
&localToGlobalAtomIndex[0], &(parallelData.nGroupsLocal), |
717 |
&localToGlobalCutoffGroupIndex[0], &isError); |
718 |
|
719 |
if (isError) { |
720 |
sprintf(painCave.errMsg, |
721 |
"mpiRefresh errror: fortran didn't like something we gave it.\n"); |
722 |
painCave.isFatal = 1; |
723 |
simError(); |
724 |
} |
725 |
|
726 |
sprintf(checkPointMsg, " mpiRefresh successful.\n"); |
727 |
MPIcheckPoint(); |
728 |
|
729 |
|
730 |
} |
731 |
|
732 |
#endif |
733 |
|
734 |
double SimInfo::calcMaxCutoffRadius() { |
735 |
|
736 |
|
737 |
std::set<AtomType*> atomTypes; |
738 |
std::set<AtomType*>::iterator i; |
739 |
std::vector<double> cutoffRadius; |
740 |
|
741 |
//get the unique atom types |
742 |
atomTypes = getUniqueAtomTypes(); |
743 |
|
744 |
//query the max cutoff radius among these atom types |
745 |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
746 |
cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i)); |
747 |
} |
748 |
|
749 |
double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end())); |
750 |
#ifdef IS_MPI |
751 |
//pick the max cutoff radius among the processors |
752 |
#endif |
753 |
|
754 |
return maxCutoffRadius; |
755 |
} |
756 |
|
757 |
void SimInfo::getCutoff(double& rcut, double& rsw) { |
758 |
|
759 |
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
760 |
|
761 |
if (!simParams_->haveRcut()){ |
762 |
sprintf(painCave.errMsg, |
763 |
"SimCreator Warning: No value was set for the cutoffRadius.\n" |
764 |
"\tOOPSE will use a default value of 15.0 angstroms" |
765 |
"\tfor the cutoffRadius.\n"); |
766 |
painCave.isFatal = 0; |
767 |
simError(); |
768 |
rcut_ = 15.0; |
769 |
} else{ |
770 |
rcut_ = simParams_->getRcut(); |
771 |
} |
772 |
|
773 |
if (!simParams_->haveRsw()){ |
774 |
sprintf(painCave.errMsg, |
775 |
"SimCreator Warning: No value was set for switchingRadius.\n" |
776 |
"\tOOPSE will use a default value of\n" |
777 |
"\t0.95 * cutoffRadius for the switchingRadius\n"); |
778 |
painCave.isFatal = 0; |
779 |
simError(); |
780 |
rsw_ = 0.95 * rcut_; |
781 |
} else{ |
782 |
rsw_ = simParams_->getRsw(); |
783 |
} |
784 |
|
785 |
} else { |
786 |
// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
787 |
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
788 |
|
789 |
if (simParams_->haveRcut()) { |
790 |
rcut_ = simParams_->getRcut(); |
791 |
} else { |
792 |
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
793 |
rcut_ = calcMaxCutoffRadius(); |
794 |
} |
795 |
|
796 |
if (simParams_->haveRsw()) { |
797 |
rsw_ = simParams_->getRsw(); |
798 |
} else { |
799 |
rsw_ = rcut_; |
800 |
} |
801 |
|
802 |
} |
803 |
} |
804 |
|
805 |
void SimInfo::setupCutoff() { |
806 |
getCutoff(rcut_, rsw_); |
807 |
double rnblist = rcut_ + 1; // skin of neighbor list |
808 |
|
809 |
//Pass these cutoff radius etc. to fortran. This function should be called once and only once |
810 |
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist); |
811 |
} |
812 |
|
813 |
void SimInfo::addProperty(GenericData* genData) { |
814 |
properties_.addProperty(genData); |
815 |
} |
816 |
|
817 |
void SimInfo::removeProperty(const std::string& propName) { |
818 |
properties_.removeProperty(propName); |
819 |
} |
820 |
|
821 |
void SimInfo::clearProperties() { |
822 |
properties_.clearProperties(); |
823 |
} |
824 |
|
825 |
std::vector<std::string> SimInfo::getPropertyNames() { |
826 |
return properties_.getPropertyNames(); |
827 |
} |
828 |
|
829 |
std::vector<GenericData*> SimInfo::getProperties() { |
830 |
return properties_.getProperties(); |
831 |
} |
832 |
|
833 |
GenericData* SimInfo::getPropertyByName(const std::string& propName) { |
834 |
return properties_.getPropertyByName(propName); |
835 |
} |
836 |
|
837 |
void SimInfo::setSnapshotManager(SnapshotManager* sman) { |
838 |
sman_ = sman; |
839 |
|
840 |
Molecule* mol; |
841 |
RigidBody* rb; |
842 |
Atom* atom; |
843 |
SimInfo::MoleculeIterator mi; |
844 |
Molecule::RigidBodyIterator rbIter; |
845 |
Molecule::AtomIterator atomIter;; |
846 |
|
847 |
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
848 |
|
849 |
for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) { |
850 |
atom->setSnapshotManager(sman_); |
851 |
} |
852 |
|
853 |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
854 |
rb->setSnapshotManager(sman_); |
855 |
} |
856 |
} |
857 |
|
858 |
} |
859 |
|
860 |
Vector3d SimInfo::getComVel(){ |
861 |
SimInfo::MoleculeIterator i; |
862 |
Molecule* mol; |
863 |
|
864 |
Vector3d comVel(0.0); |
865 |
double totalMass = 0.0; |
866 |
|
867 |
|
868 |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
869 |
double mass = mol->getMass(); |
870 |
totalMass += mass; |
871 |
comVel += mass * mol->getComVel(); |
872 |
} |
873 |
|
874 |
#ifdef IS_MPI |
875 |
double tmpMass = totalMass; |
876 |
Vector3d tmpComVel(comVel); |
877 |
MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
878 |
MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
879 |
#endif |
880 |
|
881 |
comVel /= totalMass; |
882 |
|
883 |
return comVel; |
884 |
} |
885 |
|
886 |
Vector3d SimInfo::getCom(){ |
887 |
SimInfo::MoleculeIterator i; |
888 |
Molecule* mol; |
889 |
|
890 |
Vector3d com(0.0); |
891 |
double totalMass = 0.0; |
892 |
|
893 |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
894 |
double mass = mol->getMass(); |
895 |
totalMass += mass; |
896 |
com += mass * mol->getCom(); |
897 |
} |
898 |
|
899 |
#ifdef IS_MPI |
900 |
double tmpMass = totalMass; |
901 |
Vector3d tmpCom(com); |
902 |
MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
903 |
MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
904 |
#endif |
905 |
|
906 |
com /= totalMass; |
907 |
|
908 |
return com; |
909 |
|
910 |
} |
911 |
|
912 |
std::ostream& operator <<(std::ostream& o, SimInfo& info) { |
913 |
|
914 |
return o; |
915 |
} |
916 |
|
917 |
}//end namespace oopse |
918 |
|