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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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#include "UseTheForce/doForces_interface.h" |
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#define __OPENMD_C |
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#include "UseTheForce/DarkSide/fInteractionMap.h" |
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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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namespace OpenMD { |
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|
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void ForceManager::calcForces(bool needPotential, bool needStress) { |
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|
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if (!info_->isFortranInitialized()) { |
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info_->update(); |
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} |
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|
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preCalculation(); |
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|
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calcShortRangeInteraction(); |
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|
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calcLongRangeInteraction(needPotential, needStress); |
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|
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postCalculation(needStress); |
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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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|
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// forces are zeroed here, before any are accumulated. |
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// NOTE: do not rezero the forces in Fortran. |
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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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} |
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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::calcShortRangeInteraction() { |
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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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bendPotential += bend->getPotential(); |
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std::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(std::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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std::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(std::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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std::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(std::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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|
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void ForceManager::calcLongRangeInteraction(bool needPotential, |
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bool needStress) { |
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Snapshot* curSnapshot; |
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DataStorage* config; |
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RealType* frc; |
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RealType* pos; |
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RealType* trq; |
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RealType* A; |
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RealType* electroFrame; |
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RealType* rc; |
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RealType* particlePot; |
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|
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//get current snapshot from SimInfo |
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curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
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|
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//get array pointers |
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config = &(curSnapshot->atomData); |
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frc = config->getArrayPointer(DataStorage::dslForce); |
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pos = config->getArrayPointer(DataStorage::dslPosition); |
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trq = config->getArrayPointer(DataStorage::dslTorque); |
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A = config->getArrayPointer(DataStorage::dslAmat); |
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electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame); |
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particlePot = config->getArrayPointer(DataStorage::dslParticlePot); |
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|
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//calculate the center of mass of cutoff group |
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SimInfo::MoleculeIterator mi; |
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Molecule* mol; |
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Molecule::CutoffGroupIterator ci; |
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CutoffGroup* cg; |
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Vector3d com; |
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std::vector<Vector3d> rcGroup; |
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|
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if(info_->getNCutoffGroups() > 0){ |
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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(cg = mol->beginCutoffGroup(ci); cg != NULL; |
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cg = mol->nextCutoffGroup(ci)) { |
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cg->getCOM(com); |
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rcGroup.push_back(com); |
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} |
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}// end for (mol) |
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|
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rc = rcGroup[0].getArrayPointer(); |
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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[LR_POT_TYPES]; |
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RealType lrPot = 0.0; |
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Vector3d totalDipole; |
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short int passedCalcPot = needPotential; |
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short int passedCalcStress = needStress; |
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int isError = 0; |
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|
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for (int i=0; i<LR_POT_TYPES;i++){ |
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longRangePotential[i]=0.0; //Initialize array |
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} |
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|
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doForceLoop(pos, |
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rc, |
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A, |
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electroFrame, |
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frc, |
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trq, |
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tau.getArrayPointer(), |
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longRangePotential, |
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particlePot, |
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&passedCalcPot, |
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&passedCalcStress, |
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&isError ); |
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|
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if( isError ){ |
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sprintf( painCave.errMsg, |
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"Error returned from the fortran force calculation.\n" ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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for (int i=0; i<LR_POT_TYPES;i++){ |
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lrPot += longRangePotential[i]; //Quick hack |
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} |
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|
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// grab the simulation box dipole moment if specified |
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if (info_->getCalcBoxDipole()){ |
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getAccumulatedBoxDipole(totalDipole.getArrayPointer()); |
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|
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curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0); |
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curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1); |
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curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2); |
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} |
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|
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//store the tau and long range potential |
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curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot; |
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curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT]; |
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curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT]; |
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} |
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|
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|
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void ForceManager::postCalculation(bool needStress) { |
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SimInfo::MoleculeIterator mi; |
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Molecule* mol; |
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Molecule::RigidBodyIterator rbIter; |
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RigidBody* rb; |
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Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
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|
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// collect the atomic forces onto rigid bodies |
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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 (rb = mol->beginRigidBody(rbIter); rb != NULL; |
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rb = mol->nextRigidBody(rbIter)) { |
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if (needStress) { |
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Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial(); |
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tau += rbTau; |
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} else{ |
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rb->calcForcesAndTorques(); |
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} |
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} |
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} |
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|
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if (needStress) { |
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#ifdef IS_MPI |
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Mat3x3d tmpTau(tau); |
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MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(), |
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9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
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#endif |
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curSnapshot->statData.setTau(tau); |
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} |
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} |
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|
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} //end namespace OpenMD |
