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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/fCutoffPolicy.h" |
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#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h" |
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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(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, |
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ForceField* ff, Globals* simParams) : |
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stamps_(stamps), forceField_(ff), simParams_(simParams), |
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ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0), |
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nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0), |
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nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), |
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nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0), |
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nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0), |
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sman_(NULL), fortranInitialized_(false) { |
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|
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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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} |
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|
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SimInfo::~SimInfo() { |
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std::map<int, Molecule*>::iterator i; |
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for (i = molecules_.begin(); i != molecules_.end(); ++i) { |
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delete i->second; |
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} |
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molecules_.clear(); |
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|
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delete stamps_; |
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delete sman_; |
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delete simParams_; |
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delete forceField_; |
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} |
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|
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int SimInfo::getNGlobalConstraints() { |
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int 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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Molecule::RigidBodyIterator rbIter; |
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RigidBody* rb; |
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for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
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std::vector<Atom*> atoms = rb->getAtoms(); |
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for (int i = 0; i < atoms.size() -1 ; ++i) { |
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for (int j = i + 1; j < atoms.size(); ++j) { |
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a = atoms[i]->getGlobalIndex(); |
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b = atoms[j]->getGlobalIndex(); |
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exclude_.addPair(a, b); |
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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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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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|
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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(); |
408 |
|
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exclude_.removePair(a, b); |
410 |
exclude_.removePair(a, c); |
411 |
exclude_.removePair(b, c); |
412 |
} |
413 |
|
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for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
415 |
a = torsion->getAtomA()->getGlobalIndex(); |
416 |
b = torsion->getAtomB()->getGlobalIndex(); |
417 |
c = torsion->getAtomC()->getGlobalIndex(); |
418 |
d = torsion->getAtomD()->getGlobalIndex(); |
419 |
|
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exclude_.removePair(a, b); |
421 |
exclude_.removePair(a, c); |
422 |
exclude_.removePair(a, d); |
423 |
exclude_.removePair(b, c); |
424 |
exclude_.removePair(b, d); |
425 |
exclude_.removePair(c, d); |
426 |
} |
427 |
|
428 |
Molecule::RigidBodyIterator rbIter; |
429 |
RigidBody* rb; |
430 |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
431 |
std::vector<Atom*> atoms = rb->getAtoms(); |
432 |
for (int i = 0; i < atoms.size() -1 ; ++i) { |
433 |
for (int j = i + 1; j < atoms.size(); ++j) { |
434 |
a = atoms[i]->getGlobalIndex(); |
435 |
b = atoms[j]->getGlobalIndex(); |
436 |
exclude_.removePair(a, b); |
437 |
} |
438 |
} |
439 |
} |
440 |
|
441 |
} |
442 |
|
443 |
|
444 |
void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) { |
445 |
int curStampId; |
446 |
|
447 |
//index from 0 |
448 |
curStampId = moleculeStamps_.size(); |
449 |
|
450 |
moleculeStamps_.push_back(molStamp); |
451 |
molStampIds_.insert(molStampIds_.end(), nmol, curStampId); |
452 |
} |
453 |
|
454 |
void SimInfo::update() { |
455 |
|
456 |
setupSimType(); |
457 |
|
458 |
#ifdef IS_MPI |
459 |
setupFortranParallel(); |
460 |
#endif |
461 |
|
462 |
setupFortranSim(); |
463 |
|
464 |
//setup fortran force field |
465 |
/** @deprecate */ |
466 |
int isError = 0; |
467 |
|
468 |
setupElectrostaticSummationMethod( isError ); |
469 |
|
470 |
if(isError){ |
471 |
sprintf( painCave.errMsg, |
472 |
"ForceField error: There was an error initializing the forceField in fortran.\n" ); |
473 |
painCave.isFatal = 1; |
474 |
simError(); |
475 |
} |
476 |
|
477 |
|
478 |
setupCutoff(); |
479 |
|
480 |
calcNdf(); |
481 |
calcNdfRaw(); |
482 |
calcNdfTrans(); |
483 |
|
484 |
fortranInitialized_ = true; |
485 |
} |
486 |
|
487 |
std::set<AtomType*> SimInfo::getUniqueAtomTypes() { |
488 |
SimInfo::MoleculeIterator mi; |
489 |
Molecule* mol; |
490 |
Molecule::AtomIterator ai; |
491 |
Atom* atom; |
492 |
std::set<AtomType*> atomTypes; |
493 |
|
494 |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
495 |
|
496 |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
497 |
atomTypes.insert(atom->getAtomType()); |
498 |
} |
499 |
|
500 |
} |
501 |
|
502 |
return atomTypes; |
503 |
} |
504 |
|
505 |
void SimInfo::setupSimType() { |
506 |
std::set<AtomType*>::iterator i; |
507 |
std::set<AtomType*> atomTypes; |
508 |
atomTypes = getUniqueAtomTypes(); |
509 |
|
510 |
int useLennardJones = 0; |
511 |
int useElectrostatic = 0; |
512 |
int useEAM = 0; |
513 |
int useCharge = 0; |
514 |
int useDirectional = 0; |
515 |
int useDipole = 0; |
516 |
int useGayBerne = 0; |
517 |
int useSticky = 0; |
518 |
int useStickyPower = 0; |
519 |
int useShape = 0; |
520 |
int useFLARB = 0; //it is not in AtomType yet |
521 |
int useDirectionalAtom = 0; |
522 |
int useElectrostatics = 0; |
523 |
//usePBC and useRF are from simParams |
524 |
int usePBC = simParams_->getPBC(); |
525 |
|
526 |
//loop over all of the atom types |
527 |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
528 |
useLennardJones |= (*i)->isLennardJones(); |
529 |
useElectrostatic |= (*i)->isElectrostatic(); |
530 |
useEAM |= (*i)->isEAM(); |
531 |
useCharge |= (*i)->isCharge(); |
532 |
useDirectional |= (*i)->isDirectional(); |
533 |
useDipole |= (*i)->isDipole(); |
534 |
useGayBerne |= (*i)->isGayBerne(); |
535 |
useSticky |= (*i)->isSticky(); |
536 |
useStickyPower |= (*i)->isStickyPower(); |
537 |
useShape |= (*i)->isShape(); |
538 |
} |
539 |
|
540 |
if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) { |
541 |
useDirectionalAtom = 1; |
542 |
} |
543 |
|
544 |
if (useCharge || useDipole) { |
545 |
useElectrostatics = 1; |
546 |
} |
547 |
|
548 |
#ifdef IS_MPI |
549 |
int temp; |
550 |
|
551 |
temp = usePBC; |
552 |
MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
553 |
|
554 |
temp = useDirectionalAtom; |
555 |
MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
556 |
|
557 |
temp = useLennardJones; |
558 |
MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
559 |
|
560 |
temp = useElectrostatics; |
561 |
MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
562 |
|
563 |
temp = useCharge; |
564 |
MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
565 |
|
566 |
temp = useDipole; |
567 |
MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
568 |
|
569 |
temp = useSticky; |
570 |
MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
571 |
|
572 |
temp = useStickyPower; |
573 |
MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
574 |
|
575 |
temp = useGayBerne; |
576 |
MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
577 |
|
578 |
temp = useEAM; |
579 |
MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
580 |
|
581 |
temp = useShape; |
582 |
MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
583 |
|
584 |
temp = useFLARB; |
585 |
MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
586 |
|
587 |
#endif |
588 |
|
589 |
fInfo_.SIM_uses_PBC = usePBC; |
590 |
fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom; |
591 |
fInfo_.SIM_uses_LennardJones = useLennardJones; |
592 |
fInfo_.SIM_uses_Electrostatics = useElectrostatics; |
593 |
fInfo_.SIM_uses_Charges = useCharge; |
594 |
fInfo_.SIM_uses_Dipoles = useDipole; |
595 |
fInfo_.SIM_uses_Sticky = useSticky; |
596 |
fInfo_.SIM_uses_StickyPower = useStickyPower; |
597 |
fInfo_.SIM_uses_GayBerne = useGayBerne; |
598 |
fInfo_.SIM_uses_EAM = useEAM; |
599 |
fInfo_.SIM_uses_Shapes = useShape; |
600 |
fInfo_.SIM_uses_FLARB = useFLARB; |
601 |
|
602 |
if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { |
603 |
|
604 |
if (simParams_->haveDielectric()) { |
605 |
fInfo_.dielect = simParams_->getDielectric(); |
606 |
} else { |
607 |
sprintf(painCave.errMsg, |
608 |
"SimSetup Error: No Dielectric constant was set.\n" |
609 |
"\tYou are trying to use Reaction Field without" |
610 |
"\tsetting a dielectric constant!\n"); |
611 |
painCave.isFatal = 1; |
612 |
simError(); |
613 |
} |
614 |
|
615 |
} else { |
616 |
fInfo_.dielect = 0.0; |
617 |
} |
618 |
|
619 |
} |
620 |
|
621 |
void SimInfo::setupFortranSim() { |
622 |
int isError; |
623 |
int nExclude; |
624 |
std::vector<int> fortranGlobalGroupMembership; |
625 |
|
626 |
nExclude = exclude_.getSize(); |
627 |
isError = 0; |
628 |
|
629 |
//globalGroupMembership_ is filled by SimCreator |
630 |
for (int i = 0; i < nGlobalAtoms_; i++) { |
631 |
fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1); |
632 |
} |
633 |
|
634 |
//calculate mass ratio of cutoff group |
635 |
std::vector<double> mfact; |
636 |
SimInfo::MoleculeIterator mi; |
637 |
Molecule* mol; |
638 |
Molecule::CutoffGroupIterator ci; |
639 |
CutoffGroup* cg; |
640 |
Molecule::AtomIterator ai; |
641 |
Atom* atom; |
642 |
double totalMass; |
643 |
|
644 |
//to avoid memory reallocation, reserve enough space for mfact |
645 |
mfact.reserve(getNCutoffGroups()); |
646 |
|
647 |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
648 |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
649 |
|
650 |
totalMass = cg->getMass(); |
651 |
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
652 |
mfact.push_back(atom->getMass()/totalMass); |
653 |
} |
654 |
|
655 |
} |
656 |
} |
657 |
|
658 |
//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!) |
659 |
std::vector<int> identArray; |
660 |
|
661 |
//to avoid memory reallocation, reserve enough space identArray |
662 |
identArray.reserve(getNAtoms()); |
663 |
|
664 |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
665 |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
666 |
identArray.push_back(atom->getIdent()); |
667 |
} |
668 |
} |
669 |
|
670 |
//fill molMembershipArray |
671 |
//molMembershipArray is filled by SimCreator |
672 |
std::vector<int> molMembershipArray(nGlobalAtoms_); |
673 |
for (int i = 0; i < nGlobalAtoms_; i++) { |
674 |
molMembershipArray[i] = globalMolMembership_[i] + 1; |
675 |
} |
676 |
|
677 |
//setup fortran simulation |
678 |
int nGlobalExcludes = 0; |
679 |
int* globalExcludes = NULL; |
680 |
int* excludeList = exclude_.getExcludeList(); |
681 |
setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList , |
682 |
&nGlobalExcludes, globalExcludes, &molMembershipArray[0], |
683 |
&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError); |
684 |
|
685 |
if( isError ){ |
686 |
|
687 |
sprintf( painCave.errMsg, |
688 |
"There was an error setting the simulation information in fortran.\n" ); |
689 |
painCave.isFatal = 1; |
690 |
painCave.severity = OOPSE_ERROR; |
691 |
simError(); |
692 |
} |
693 |
|
694 |
#ifdef IS_MPI |
695 |
sprintf( checkPointMsg, |
696 |
"succesfully sent the simulation information to fortran.\n"); |
697 |
MPIcheckPoint(); |
698 |
#endif // is_mpi |
699 |
} |
700 |
|
701 |
|
702 |
#ifdef IS_MPI |
703 |
void SimInfo::setupFortranParallel() { |
704 |
|
705 |
//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex |
706 |
std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0); |
707 |
std::vector<int> localToGlobalCutoffGroupIndex; |
708 |
SimInfo::MoleculeIterator mi; |
709 |
Molecule::AtomIterator ai; |
710 |
Molecule::CutoffGroupIterator ci; |
711 |
Molecule* mol; |
712 |
Atom* atom; |
713 |
CutoffGroup* cg; |
714 |
mpiSimData parallelData; |
715 |
int isError; |
716 |
|
717 |
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
718 |
|
719 |
//local index(index in DataStorge) of atom is important |
720 |
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
721 |
localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1; |
722 |
} |
723 |
|
724 |
//local index of cutoff group is trivial, it only depends on the order of travesing |
725 |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
726 |
localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1); |
727 |
} |
728 |
|
729 |
} |
730 |
|
731 |
//fill up mpiSimData struct |
732 |
parallelData.nMolGlobal = getNGlobalMolecules(); |
733 |
parallelData.nMolLocal = getNMolecules(); |
734 |
parallelData.nAtomsGlobal = getNGlobalAtoms(); |
735 |
parallelData.nAtomsLocal = getNAtoms(); |
736 |
parallelData.nGroupsGlobal = getNGlobalCutoffGroups(); |
737 |
parallelData.nGroupsLocal = getNCutoffGroups(); |
738 |
parallelData.myNode = worldRank; |
739 |
MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors)); |
740 |
|
741 |
//pass mpiSimData struct and index arrays to fortran |
742 |
setFsimParallel(¶llelData, &(parallelData.nAtomsLocal), |
743 |
&localToGlobalAtomIndex[0], &(parallelData.nGroupsLocal), |
744 |
&localToGlobalCutoffGroupIndex[0], &isError); |
745 |
|
746 |
if (isError) { |
747 |
sprintf(painCave.errMsg, |
748 |
"mpiRefresh errror: fortran didn't like something we gave it.\n"); |
749 |
painCave.isFatal = 1; |
750 |
simError(); |
751 |
} |
752 |
|
753 |
sprintf(checkPointMsg, " mpiRefresh successful.\n"); |
754 |
MPIcheckPoint(); |
755 |
|
756 |
|
757 |
} |
758 |
|
759 |
#endif |
760 |
|
761 |
double SimInfo::calcMaxCutoffRadius() { |
762 |
|
763 |
|
764 |
std::set<AtomType*> atomTypes; |
765 |
std::set<AtomType*>::iterator i; |
766 |
std::vector<double> cutoffRadius; |
767 |
|
768 |
//get the unique atom types |
769 |
atomTypes = getUniqueAtomTypes(); |
770 |
|
771 |
//query the max cutoff radius among these atom types |
772 |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
773 |
cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i)); |
774 |
} |
775 |
|
776 |
double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end())); |
777 |
#ifdef IS_MPI |
778 |
//pick the max cutoff radius among the processors |
779 |
#endif |
780 |
|
781 |
return maxCutoffRadius; |
782 |
} |
783 |
|
784 |
void SimInfo::getCutoff(double& rcut, double& rsw) { |
785 |
|
786 |
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
787 |
|
788 |
if (!simParams_->haveRcut()){ |
789 |
sprintf(painCave.errMsg, |
790 |
"SimCreator Warning: No value was set for the cutoffRadius.\n" |
791 |
"\tOOPSE will use a default value of 15.0 angstroms" |
792 |
"\tfor the cutoffRadius.\n"); |
793 |
painCave.isFatal = 0; |
794 |
simError(); |
795 |
rcut = 15.0; |
796 |
} else{ |
797 |
rcut = simParams_->getRcut(); |
798 |
} |
799 |
|
800 |
if (!simParams_->haveRsw()){ |
801 |
sprintf(painCave.errMsg, |
802 |
"SimCreator Warning: No value was set for switchingRadius.\n" |
803 |
"\tOOPSE will use a default value of\n" |
804 |
"\t0.95 * cutoffRadius for the switchingRadius\n"); |
805 |
painCave.isFatal = 0; |
806 |
simError(); |
807 |
rsw = 0.95 * rcut; |
808 |
} else{ |
809 |
rsw = simParams_->getRsw(); |
810 |
} |
811 |
|
812 |
} else { |
813 |
// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
814 |
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
815 |
|
816 |
if (simParams_->haveRcut()) { |
817 |
rcut = simParams_->getRcut(); |
818 |
} else { |
819 |
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
820 |
rcut = calcMaxCutoffRadius(); |
821 |
} |
822 |
|
823 |
if (simParams_->haveRsw()) { |
824 |
rsw = simParams_->getRsw(); |
825 |
} else { |
826 |
rsw = rcut; |
827 |
} |
828 |
|
829 |
} |
830 |
} |
831 |
|
832 |
void SimInfo::setupCutoff() { |
833 |
getCutoff(rcut_, rsw_); |
834 |
double rnblist = rcut_ + 1; // skin of neighbor list |
835 |
|
836 |
//Pass these cutoff radius etc. to fortran. This function should be called once and only once |
837 |
|
838 |
int cp = TRADITIONAL_CUTOFF_POLICY; |
839 |
if (simParams_->haveCutoffPolicy()) { |
840 |
std::string myPolicy = simParams_->getCutoffPolicy(); |
841 |
if (myPolicy == "MIX") { |
842 |
cp = MIX_CUTOFF_POLICY; |
843 |
} else { |
844 |
if (myPolicy == "MAX") { |
845 |
cp = MAX_CUTOFF_POLICY; |
846 |
} else { |
847 |
if (myPolicy == "TRADITIONAL") { |
848 |
cp = TRADITIONAL_CUTOFF_POLICY; |
849 |
} else { |
850 |
// throw error |
851 |
sprintf( painCave.errMsg, |
852 |
"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() ); |
853 |
painCave.isFatal = 1; |
854 |
simError(); |
855 |
} |
856 |
} |
857 |
} |
858 |
} |
859 |
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp); |
860 |
} |
861 |
|
862 |
void SimInfo::setupElectrostaticSummationMethod( int isError ) { |
863 |
|
864 |
int errorOut; |
865 |
int esm = NONE; |
866 |
double alphaVal; |
867 |
|
868 |
errorOut = isError; |
869 |
|
870 |
if (simParams_->haveElectrostaticSummationMethod()) { |
871 |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
872 |
if (myMethod == "NONE") { |
873 |
esm = NONE; |
874 |
} else { |
875 |
if (myMethod == "UNDAMPED_WOLF") { |
876 |
esm = UNDAMPED_WOLF; |
877 |
} else { |
878 |
if (myMethod == "DAMPED_WOLF") { |
879 |
esm = DAMPED_WOLF; |
880 |
if (!simParams_->haveDampingAlpha()) { |
881 |
//throw error |
882 |
sprintf( painCave.errMsg, |
883 |
"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used for the Damped Wolf Method.", simParams_->getDampingAlpha()); |
884 |
painCave.isFatal = 0; |
885 |
simError(); |
886 |
} |
887 |
alphaVal = simParams_->getDampingAlpha(); |
888 |
} else { |
889 |
if (myMethod == "REACTION_FIELD") { |
890 |
esm = REACTION_FIELD; |
891 |
} else { |
892 |
// throw error |
893 |
sprintf( painCave.errMsg, |
894 |
"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"undamped_wolf\", \"damped_wolf\", or \"reaction_field\".", myMethod.c_str() ); |
895 |
painCave.isFatal = 1; |
896 |
simError(); |
897 |
} |
898 |
} |
899 |
} |
900 |
} |
901 |
} |
902 |
initFortranFF( &esm, &alphaVal, &errorOut ); |
903 |
} |
904 |
|
905 |
void SimInfo::addProperty(GenericData* genData) { |
906 |
properties_.addProperty(genData); |
907 |
} |
908 |
|
909 |
void SimInfo::removeProperty(const std::string& propName) { |
910 |
properties_.removeProperty(propName); |
911 |
} |
912 |
|
913 |
void SimInfo::clearProperties() { |
914 |
properties_.clearProperties(); |
915 |
} |
916 |
|
917 |
std::vector<std::string> SimInfo::getPropertyNames() { |
918 |
return properties_.getPropertyNames(); |
919 |
} |
920 |
|
921 |
std::vector<GenericData*> SimInfo::getProperties() { |
922 |
return properties_.getProperties(); |
923 |
} |
924 |
|
925 |
GenericData* SimInfo::getPropertyByName(const std::string& propName) { |
926 |
return properties_.getPropertyByName(propName); |
927 |
} |
928 |
|
929 |
void SimInfo::setSnapshotManager(SnapshotManager* sman) { |
930 |
if (sman_ == sman) { |
931 |
return; |
932 |
} |
933 |
delete sman_; |
934 |
sman_ = sman; |
935 |
|
936 |
Molecule* mol; |
937 |
RigidBody* rb; |
938 |
Atom* atom; |
939 |
SimInfo::MoleculeIterator mi; |
940 |
Molecule::RigidBodyIterator rbIter; |
941 |
Molecule::AtomIterator atomIter;; |
942 |
|
943 |
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
944 |
|
945 |
for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) { |
946 |
atom->setSnapshotManager(sman_); |
947 |
} |
948 |
|
949 |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
950 |
rb->setSnapshotManager(sman_); |
951 |
} |
952 |
} |
953 |
|
954 |
} |
955 |
|
956 |
Vector3d SimInfo::getComVel(){ |
957 |
SimInfo::MoleculeIterator i; |
958 |
Molecule* mol; |
959 |
|
960 |
Vector3d comVel(0.0); |
961 |
double totalMass = 0.0; |
962 |
|
963 |
|
964 |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
965 |
double mass = mol->getMass(); |
966 |
totalMass += mass; |
967 |
comVel += mass * mol->getComVel(); |
968 |
} |
969 |
|
970 |
#ifdef IS_MPI |
971 |
double tmpMass = totalMass; |
972 |
Vector3d tmpComVel(comVel); |
973 |
MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
974 |
MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
975 |
#endif |
976 |
|
977 |
comVel /= totalMass; |
978 |
|
979 |
return comVel; |
980 |
} |
981 |
|
982 |
Vector3d SimInfo::getCom(){ |
983 |
SimInfo::MoleculeIterator i; |
984 |
Molecule* mol; |
985 |
|
986 |
Vector3d com(0.0); |
987 |
double totalMass = 0.0; |
988 |
|
989 |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
990 |
double mass = mol->getMass(); |
991 |
totalMass += mass; |
992 |
com += mass * mol->getCom(); |
993 |
} |
994 |
|
995 |
#ifdef IS_MPI |
996 |
double tmpMass = totalMass; |
997 |
Vector3d tmpCom(com); |
998 |
MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
999 |
MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1000 |
#endif |
1001 |
|
1002 |
com /= totalMass; |
1003 |
|
1004 |
return com; |
1005 |
|
1006 |
} |
1007 |
|
1008 |
std::ostream& operator <<(std::ostream& o, SimInfo& info) { |
1009 |
|
1010 |
return o; |
1011 |
} |
1012 |
|
1013 |
|
1014 |
/* |
1015 |
Returns center of mass and center of mass velocity in one function call. |
1016 |
*/ |
1017 |
|
1018 |
void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){ |
1019 |
SimInfo::MoleculeIterator i; |
1020 |
Molecule* mol; |
1021 |
|
1022 |
|
1023 |
double totalMass = 0.0; |
1024 |
|
1025 |
|
1026 |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1027 |
double mass = mol->getMass(); |
1028 |
totalMass += mass; |
1029 |
com += mass * mol->getCom(); |
1030 |
comVel += mass * mol->getComVel(); |
1031 |
} |
1032 |
|
1033 |
#ifdef IS_MPI |
1034 |
double tmpMass = totalMass; |
1035 |
Vector3d tmpCom(com); |
1036 |
Vector3d tmpComVel(comVel); |
1037 |
MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1038 |
MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1039 |
MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1040 |
#endif |
1041 |
|
1042 |
com /= totalMass; |
1043 |
comVel /= totalMass; |
1044 |
} |
1045 |
|
1046 |
/* |
1047 |
Return intertia tensor for entire system and angular momentum Vector. |
1048 |
|
1049 |
|
1050 |
[ Ixx -Ixy -Ixz ] |
1051 |
J =| -Iyx Iyy -Iyz | |
1052 |
[ -Izx -Iyz Izz ] |
1053 |
*/ |
1054 |
|
1055 |
void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){ |
1056 |
|
1057 |
|
1058 |
double xx = 0.0; |
1059 |
double yy = 0.0; |
1060 |
double zz = 0.0; |
1061 |
double xy = 0.0; |
1062 |
double xz = 0.0; |
1063 |
double yz = 0.0; |
1064 |
Vector3d com(0.0); |
1065 |
Vector3d comVel(0.0); |
1066 |
|
1067 |
getComAll(com, comVel); |
1068 |
|
1069 |
SimInfo::MoleculeIterator i; |
1070 |
Molecule* mol; |
1071 |
|
1072 |
Vector3d thisq(0.0); |
1073 |
Vector3d thisv(0.0); |
1074 |
|
1075 |
double thisMass = 0.0; |
1076 |
|
1077 |
|
1078 |
|
1079 |
|
1080 |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1081 |
|
1082 |
thisq = mol->getCom()-com; |
1083 |
thisv = mol->getComVel()-comVel; |
1084 |
thisMass = mol->getMass(); |
1085 |
// Compute moment of intertia coefficients. |
1086 |
xx += thisq[0]*thisq[0]*thisMass; |
1087 |
yy += thisq[1]*thisq[1]*thisMass; |
1088 |
zz += thisq[2]*thisq[2]*thisMass; |
1089 |
|
1090 |
// compute products of intertia |
1091 |
xy += thisq[0]*thisq[1]*thisMass; |
1092 |
xz += thisq[0]*thisq[2]*thisMass; |
1093 |
yz += thisq[1]*thisq[2]*thisMass; |
1094 |
|
1095 |
angularMomentum += cross( thisq, thisv ) * thisMass; |
1096 |
|
1097 |
} |
1098 |
|
1099 |
|
1100 |
inertiaTensor(0,0) = yy + zz; |
1101 |
inertiaTensor(0,1) = -xy; |
1102 |
inertiaTensor(0,2) = -xz; |
1103 |
inertiaTensor(1,0) = -xy; |
1104 |
inertiaTensor(1,1) = xx + zz; |
1105 |
inertiaTensor(1,2) = -yz; |
1106 |
inertiaTensor(2,0) = -xz; |
1107 |
inertiaTensor(2,1) = -yz; |
1108 |
inertiaTensor(2,2) = xx + yy; |
1109 |
|
1110 |
#ifdef IS_MPI |
1111 |
Mat3x3d tmpI(inertiaTensor); |
1112 |
Vector3d tmpAngMom; |
1113 |
MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1114 |
MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1115 |
#endif |
1116 |
|
1117 |
return; |
1118 |
} |
1119 |
|
1120 |
//Returns the angular momentum of the system |
1121 |
Vector3d SimInfo::getAngularMomentum(){ |
1122 |
|
1123 |
Vector3d com(0.0); |
1124 |
Vector3d comVel(0.0); |
1125 |
Vector3d angularMomentum(0.0); |
1126 |
|
1127 |
getComAll(com,comVel); |
1128 |
|
1129 |
SimInfo::MoleculeIterator i; |
1130 |
Molecule* mol; |
1131 |
|
1132 |
Vector3d thisr(0.0); |
1133 |
Vector3d thisp(0.0); |
1134 |
|
1135 |
double thisMass; |
1136 |
|
1137 |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1138 |
thisMass = mol->getMass(); |
1139 |
thisr = mol->getCom()-com; |
1140 |
thisp = (mol->getComVel()-comVel)*thisMass; |
1141 |
|
1142 |
angularMomentum += cross( thisr, thisp ); |
1143 |
|
1144 |
} |
1145 |
|
1146 |
#ifdef IS_MPI |
1147 |
Vector3d tmpAngMom; |
1148 |
MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1149 |
#endif |
1150 |
|
1151 |
return angularMomentum; |
1152 |
} |
1153 |
|
1154 |
|
1155 |
}//end namespace oopse |
1156 |
|