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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. 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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* 2. 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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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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|
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/** |
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* @file ForceManager.cpp |
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* @author tlin |
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* @date 11/09/2004 |
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* @time 10:39am |
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* @version 1.0 |
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*/ |
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|
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#include "brains/ForceManager.hpp" |
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#include "primitives/Molecule.hpp" |
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#define __OPENMD_C |
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#include "utils/simError.h" |
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#include "primitives/Bond.hpp" |
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#include "primitives/Bend.hpp" |
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#include "primitives/Torsion.hpp" |
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#include "primitives/Inversion.hpp" |
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#include "nonbonded/NonBondedInteraction.hpp" |
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#include "parallel/ForceMatrixDecomposition.hpp" |
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|
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using namespace std; |
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namespace OpenMD { |
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|
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ForceManager::ForceManager(SimInfo * info) : info_(info) { |
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|
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#ifdef IS_MPI |
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fDecomp_ = new ForceMatrixDecomposition(info_); |
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#else |
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// fDecomp_ = new ForceSerialDecomposition(info); |
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#endif |
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} |
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|
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void ForceManager::calcForces() { |
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|
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if (!info_->isTopologyDone()) { |
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info_->update(); |
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interactionMan_->setSimInfo(info_); |
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interactionMan_->initialize(); |
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swfun_ = interactionMan_->getSwitchingFunction(); |
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fDecomp_->distributeInitialData(); |
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info_->prepareTopology(); |
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} |
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|
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preCalculation(); |
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shortRangeInteractions(); |
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longRangeInteractions(); |
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postCalculation(); |
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|
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} |
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|
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void ForceManager::preCalculation() { |
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SimInfo::MoleculeIterator mi; |
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Molecule* mol; |
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Molecule::AtomIterator ai; |
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Atom* atom; |
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Molecule::RigidBodyIterator rbIter; |
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RigidBody* rb; |
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Molecule::CutoffGroupIterator ci; |
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CutoffGroup* cg; |
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|
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// forces are zeroed here, before any are accumulated. |
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|
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for (mol = info_->beginMolecule(mi); mol != NULL; |
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mol = info_->nextMolecule(mi)) { |
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for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
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atom->zeroForcesAndTorques(); |
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} |
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|
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//change the positions of atoms which belong to the rigidbodies |
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for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
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rb = mol->nextRigidBody(rbIter)) { |
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rb->zeroForcesAndTorques(); |
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} |
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|
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if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){ |
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for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
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cg = mol->nextCutoffGroup(ci)) { |
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//calculate the center of mass of cutoff group |
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cg->updateCOM(); |
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} |
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} |
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} |
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|
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// Zero out the stress tensor |
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tau *= 0.0; |
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|
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} |
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|
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void ForceManager::shortRangeInteractions() { |
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Molecule* mol; |
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RigidBody* rb; |
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Bond* bond; |
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Bend* bend; |
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Torsion* torsion; |
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Inversion* inversion; |
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SimInfo::MoleculeIterator mi; |
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Molecule::RigidBodyIterator rbIter; |
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Molecule::BondIterator bondIter;; |
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Molecule::BendIterator bendIter; |
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Molecule::TorsionIterator torsionIter; |
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Molecule::InversionIterator inversionIter; |
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RealType bondPotential = 0.0; |
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RealType bendPotential = 0.0; |
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RealType torsionPotential = 0.0; |
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RealType inversionPotential = 0.0; |
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|
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//calculate short range interactions |
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for (mol = info_->beginMolecule(mi); mol != NULL; |
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mol = info_->nextMolecule(mi)) { |
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|
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//change the positions of atoms which belong to the rigidbodies |
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for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
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rb = mol->nextRigidBody(rbIter)) { |
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rb->updateAtoms(); |
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} |
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|
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for (bond = mol->beginBond(bondIter); bond != NULL; |
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bond = mol->nextBond(bondIter)) { |
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bond->calcForce(); |
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bondPotential += bond->getPotential(); |
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} |
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|
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for (bend = mol->beginBend(bendIter); bend != NULL; |
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bend = mol->nextBend(bendIter)) { |
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|
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RealType angle; |
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bend->calcForce(angle); |
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RealType currBendPot = bend->getPotential(); |
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|
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bendPotential += bend->getPotential(); |
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map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend); |
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if (i == bendDataSets.end()) { |
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BendDataSet dataSet; |
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dataSet.prev.angle = dataSet.curr.angle = angle; |
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dataSet.prev.potential = dataSet.curr.potential = currBendPot; |
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dataSet.deltaV = 0.0; |
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bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet)); |
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}else { |
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i->second.prev.angle = i->second.curr.angle; |
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i->second.prev.potential = i->second.curr.potential; |
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i->second.curr.angle = angle; |
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i->second.curr.potential = currBendPot; |
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i->second.deltaV = fabs(i->second.curr.potential - |
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i->second.prev.potential); |
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} |
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} |
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|
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for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; |
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torsion = mol->nextTorsion(torsionIter)) { |
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RealType angle; |
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torsion->calcForce(angle); |
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RealType currTorsionPot = torsion->getPotential(); |
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torsionPotential += torsion->getPotential(); |
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map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion); |
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if (i == torsionDataSets.end()) { |
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TorsionDataSet dataSet; |
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dataSet.prev.angle = dataSet.curr.angle = angle; |
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dataSet.prev.potential = dataSet.curr.potential = currTorsionPot; |
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dataSet.deltaV = 0.0; |
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torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet)); |
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}else { |
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i->second.prev.angle = i->second.curr.angle; |
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i->second.prev.potential = i->second.curr.potential; |
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i->second.curr.angle = angle; |
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i->second.curr.potential = currTorsionPot; |
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i->second.deltaV = fabs(i->second.curr.potential - |
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i->second.prev.potential); |
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} |
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} |
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|
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for (inversion = mol->beginInversion(inversionIter); |
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inversion != NULL; |
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inversion = mol->nextInversion(inversionIter)) { |
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RealType angle; |
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inversion->calcForce(angle); |
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RealType currInversionPot = inversion->getPotential(); |
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inversionPotential += inversion->getPotential(); |
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map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion); |
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if (i == inversionDataSets.end()) { |
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InversionDataSet dataSet; |
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dataSet.prev.angle = dataSet.curr.angle = angle; |
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dataSet.prev.potential = dataSet.curr.potential = currInversionPot; |
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dataSet.deltaV = 0.0; |
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inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet)); |
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}else { |
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i->second.prev.angle = i->second.curr.angle; |
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i->second.prev.potential = i->second.curr.potential; |
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i->second.curr.angle = angle; |
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i->second.curr.potential = currInversionPot; |
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i->second.deltaV = fabs(i->second.curr.potential - |
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i->second.prev.potential); |
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} |
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} |
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} |
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|
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RealType shortRangePotential = bondPotential + bendPotential + |
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torsionPotential + inversionPotential; |
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Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
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curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential; |
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curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential; |
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curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential; |
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curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential; |
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curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential; |
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} |
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|
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void ForceManager::longRangeInteractions() { |
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|
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// some of this initial stuff will go away: |
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Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
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DataStorage* config = &(curSnapshot->atomData); |
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DataStorage* cgConfig = &(curSnapshot->cgData); |
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RealType* frc = config->getArrayPointer(DataStorage::dslForce); |
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RealType* pos = config->getArrayPointer(DataStorage::dslPosition); |
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RealType* trq = config->getArrayPointer(DataStorage::dslTorque); |
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RealType* A = config->getArrayPointer(DataStorage::dslAmat); |
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RealType* electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame); |
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RealType* particlePot = config->getArrayPointer(DataStorage::dslParticlePot); |
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RealType* rc; |
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|
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if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){ |
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rc = cgConfig->getArrayPointer(DataStorage::dslPosition); |
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} else { |
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// center of mass of the group is the same as position of the atom |
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// if cutoff group does not exist |
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rc = pos; |
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} |
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|
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//initialize data before passing to fortran |
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RealType longRangePotential[N_INTERACTION_FAMILIES]; |
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RealType lrPot = 0.0; |
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int isError = 0; |
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|
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// dangerous to iterate over enums, but we'll live on the edge: |
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for (int i = NO_FAMILY; i != N_INTERACTION_FAMILIES; ++i){ |
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longRangePotential[i]=0.0; //Initialize array |
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} |
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|
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// new stuff starts here: |
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|
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fDecomp_->distributeData(); |
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|
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int cg1, cg2, atom1, atom2; |
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Vector3d d_grp, dag; |
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RealType rgrpsq, rgrp; |
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RealType vij; |
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Vector3d fij, fg; |
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pair<int, int> gtypes; |
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RealType rCutSq; |
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bool in_switching_region; |
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RealType sw, dswdr, swderiv; |
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vector<int> atomListColumn, atomListRow, atomListLocal; |
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InteractionData idat; |
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SelfData sdat; |
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RealType mf; |
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|
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int loopStart, loopEnd; |
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|
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loopEnd = PAIR_LOOP; |
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if (info_->requiresPrepair() ) { |
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loopStart = PREPAIR_LOOP; |
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} else { |
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loopStart = PAIR_LOOP; |
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} |
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|
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for (int iLoop = loopStart; iLoop < loopEnd; iLoop++) { |
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|
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if (iLoop == loopStart) { |
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bool update_nlist = fDecomp_->checkNeighborList(); |
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if (update_nlist) |
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neighborList = fDecomp_->buildNeighborList(); |
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} |
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|
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for (vector<pair<int, int> >::iterator it = neighborList.begin(); |
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it != neighborList.end(); ++it) { |
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|
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cg1 = (*it).first; |
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cg2 = (*it).second; |
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|
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gtypes = fDecomp_->getGroupTypes(cg1, cg2); |
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d_grp = fDecomp_->getIntergroupVector(cg1, cg2); |
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curSnapshot->wrapVector(d_grp); |
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rgrpsq = d_grp.lengthSquare(); |
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rCutSq = groupCutoffMap[gtypes].first; |
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|
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if (rgrpsq < rCutSq) { |
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*(idat.rcut) = groupCutoffMap[gtypes].second; |
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if (iLoop == PAIR_LOOP) { |
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vij *= 0.0; |
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fij = V3Zero; |
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} |
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|
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in_switching_region = swfun_->getSwitch(rgrpsq, *(idat.sw), dswdr, |
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rgrp); |
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atomListRow = fDecomp_->getAtomsInGroupRow(cg1); |
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atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2); |
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|
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for (vector<int>::iterator ia = atomListRow.begin(); |
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ia != atomListRow.end(); ++ia) { |
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atom1 = (*ia); |
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|
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for (vector<int>::iterator jb = atomListColumn.begin(); |
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jb != atomListColumn.end(); ++jb) { |
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atom2 = (*jb); |
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|
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if (!fDecomp_->skipAtomPair(atom1, atom2)) { |
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|
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idat = fDecomp_->fillInteractionData(atom1, atom2); |
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|
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if (atomListRow.size() == 1 && atomListColumn.size() == 1) { |
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*(idat.d) = d_grp; |
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*(idat.r2) = rgrpsq; |
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} else { |
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*(idat.d) = fDecomp_->getInteratomicVector(atom1, atom2); |
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curSnapshot->wrapVector( *(idat.d) ); |
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*(idat.r2) = idat.d->lengthSquare(); |
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} |
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|
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*(idat.rij) = sqrt( *(idat.r2) ); |
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|
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if (iLoop == PREPAIR_LOOP) { |
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interactionMan_->doPrePair(idat); |
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} else { |
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interactionMan_->doPair(idat); |
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vij += *(idat.vpair); |
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fij += *(idat.f1); |
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tau -= outProduct( *(idat.d), *(idat.f1)); |
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} |
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} |
| 369 |
} |
| 370 |
} |
| 371 |
|
| 372 |
if (iLoop == PAIR_LOOP) { |
| 373 |
if (in_switching_region) { |
| 374 |
swderiv = vij * dswdr / rgrp; |
| 375 |
fg = swderiv * d_grp; |
| 376 |
|
| 377 |
fij += fg; |
| 378 |
|
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if (atomListRow.size() == 1 && atomListColumn.size() == 1) { |
| 380 |
tau -= outProduct( *(idat.d), fg); |
| 381 |
} |
| 382 |
|
| 383 |
for (vector<int>::iterator ia = atomListRow.begin(); |
| 384 |
ia != atomListRow.end(); ++ia) { |
| 385 |
atom1 = (*ia); |
| 386 |
mf = fDecomp_->getMassFactorRow(atom1); |
| 387 |
// fg is the force on atom ia due to cutoff group's |
| 388 |
// presence in switching region |
| 389 |
fg = swderiv * d_grp * mf; |
| 390 |
fDecomp_->addForceToAtomRow(atom1, fg); |
| 391 |
|
| 392 |
if (atomListRow.size() > 1) { |
| 393 |
if (info_->usesAtomicVirial()) { |
| 394 |
// find the distance between the atom |
| 395 |
// and the center of the cutoff group: |
| 396 |
dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1); |
| 397 |
tau -= outProduct(dag, fg); |
| 398 |
} |
| 399 |
} |
| 400 |
} |
| 401 |
for (vector<int>::iterator jb = atomListColumn.begin(); |
| 402 |
jb != atomListColumn.end(); ++jb) { |
| 403 |
atom2 = (*jb); |
| 404 |
mf = fDecomp_->getMassFactorColumn(atom2); |
| 405 |
// fg is the force on atom jb due to cutoff group's |
| 406 |
// presence in switching region |
| 407 |
fg = -swderiv * d_grp * mf; |
| 408 |
fDecomp_->addForceToAtomColumn(atom2, fg); |
| 409 |
|
| 410 |
if (atomListColumn.size() > 1) { |
| 411 |
if (info_->usesAtomicVirial()) { |
| 412 |
// find the distance between the atom |
| 413 |
// and the center of the cutoff group: |
| 414 |
dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2); |
| 415 |
tau -= outProduct(dag, fg); |
| 416 |
} |
| 417 |
} |
| 418 |
} |
| 419 |
} |
| 420 |
//if (!SIM_uses_AtomicVirial) { |
| 421 |
// tau -= outProduct(d_grp, fij); |
| 422 |
//} |
| 423 |
} |
| 424 |
} |
| 425 |
} |
| 426 |
|
| 427 |
if (iLoop == PREPAIR_LOOP) { |
| 428 |
if (info_->requiresPrepair()) { |
| 429 |
fDecomp_->collectIntermediateData(); |
| 430 |
|
| 431 |
for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 432 |
sdat = fDecomp_->fillSelfData(atom1); |
| 433 |
interactionMan_->doPreForce(sdat); |
| 434 |
} |
| 435 |
|
| 436 |
fDecomp_->distributeIntermediateData(); |
| 437 |
} |
| 438 |
} |
| 439 |
|
| 440 |
} |
| 441 |
|
| 442 |
fDecomp_->collectData(); |
| 443 |
|
| 444 |
if ( info_->requiresSkipCorrection() ) { |
| 445 |
|
| 446 |
for (int atom1 = 0; atom1 < fDecomp_->getNAtomsInRow(); atom1++) { |
| 447 |
|
| 448 |
vector<int> skipList = fDecomp_->getSkipsForRowAtom( atom1 ); |
| 449 |
|
| 450 |
for (vector<int>::iterator jb = skipList.begin(); |
| 451 |
jb != skipList.end(); ++jb) { |
| 452 |
|
| 453 |
atom2 = (*jb); |
| 454 |
idat = fDecomp_->fillSkipData(atom1, atom2); |
| 455 |
interactionMan_->doSkipCorrection(idat); |
| 456 |
|
| 457 |
} |
| 458 |
} |
| 459 |
} |
| 460 |
|
| 461 |
if (info_->requiresSelfCorrection()) { |
| 462 |
|
| 463 |
for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 464 |
sdat = fDecomp_->fillSelfData(atom1); |
| 465 |
interactionMan_->doSelfCorrection(sdat); |
| 466 |
} |
| 467 |
|
| 468 |
} |
| 469 |
|
| 470 |
// dangerous to iterate over enums, but we'll live on the edge: |
| 471 |
for (int i = NO_FAMILY; i != N_INTERACTION_FAMILIES; ++i){ |
| 472 |
lrPot += longRangePotential[i]; //Quick hack |
| 473 |
} |
| 474 |
|
| 475 |
//store the tau and long range potential |
| 476 |
curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot; |
| 477 |
curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY]; |
| 478 |
curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY]; |
| 479 |
} |
| 480 |
|
| 481 |
|
| 482 |
void ForceManager::postCalculation() { |
| 483 |
SimInfo::MoleculeIterator mi; |
| 484 |
Molecule* mol; |
| 485 |
Molecule::RigidBodyIterator rbIter; |
| 486 |
RigidBody* rb; |
| 487 |
Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 488 |
|
| 489 |
// collect the atomic forces onto rigid bodies |
| 490 |
|
| 491 |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 492 |
mol = info_->nextMolecule(mi)) { |
| 493 |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 494 |
rb = mol->nextRigidBody(rbIter)) { |
| 495 |
Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial(); |
| 496 |
tau += rbTau; |
| 497 |
} |
| 498 |
} |
| 499 |
|
| 500 |
#ifdef IS_MPI |
| 501 |
Mat3x3d tmpTau(tau); |
| 502 |
MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(), |
| 503 |
9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 504 |
#endif |
| 505 |
curSnapshot->statData.setTau(tau); |
| 506 |
} |
| 507 |
|
| 508 |
} //end namespace OpenMD |
