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/* |
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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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* 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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* 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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* 3. Redistributions in binary form must reproduce the above copyright |
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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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* 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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/** |
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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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namespace oopse { |
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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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> |
void ForceManager::calcForces() { |
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|
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if (!info_->isFortranInitialized()) { |
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info_->update(); |
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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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> |
|
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calcShortRangeInteraction(); |
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|
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calcLongRangeInteraction(needPotential, needStress); |
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calcLongRangeInteraction(); |
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|
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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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} |
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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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|
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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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for (mol = info_->beginMolecule(mi); mol != NULL; 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; rb = mol->nextRigidBody(rbIter)) { |
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rb->zeroForcesAndTorques(); |
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} |
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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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} |
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|
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void ForceManager::calcShortRangeInteraction() { |
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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; mol = info_->nextMolecule(mi)) { |
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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; rb = mol->nextRigidBody(rbIter)) { |
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rb->updateAtoms(); |
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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; bond = mol->nextBond(bondIter)) { |
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< |
bond->calcForce(); |
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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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> |
} |
| 141 |
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|
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< |
for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) { |
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bend->calcForce(); |
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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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> |
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; torsion = mol->nextTorsion(torsionIter)) { |
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< |
torsion->calcForce(); |
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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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+ |
} |
| 189 |
|
|
| 190 |
< |
} |
| 191 |
< |
|
| 192 |
< |
double shortRangePotential = 0.0; |
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< |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 194 |
< |
shortRangePotential += mol->getPotential(); |
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> |
for (inversion = mol->beginInversion(inversionIter); |
| 191 |
> |
inversion != NULL; |
| 192 |
> |
inversion = mol->nextInversion(inversionIter)) { |
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> |
RealType angle; |
| 194 |
> |
inversion->calcForce(angle); |
| 195 |
> |
RealType currInversionPot = inversion->getPotential(); |
| 196 |
> |
inversionPotential += inversion->getPotential(); |
| 197 |
> |
std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion); |
| 198 |
> |
if (i == inversionDataSets.end()) { |
| 199 |
> |
InversionDataSet dataSet; |
| 200 |
> |
dataSet.prev.angle = dataSet.curr.angle = angle; |
| 201 |
> |
dataSet.prev.potential = dataSet.curr.potential = currInversionPot; |
| 202 |
> |
dataSet.deltaV = 0.0; |
| 203 |
> |
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; |
| 206 |
> |
i->second.prev.potential = i->second.curr.potential; |
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> |
i->second.curr.angle = angle; |
| 208 |
> |
i->second.curr.potential = currInversionPot; |
| 209 |
> |
i->second.deltaV = fabs(i->second.curr.potential - |
| 210 |
> |
i->second.prev.potential); |
| 211 |
> |
} |
| 212 |
> |
} |
| 213 |
|
} |
| 214 |
|
|
| 215 |
+ |
RealType shortRangePotential = bondPotential + bendPotential + |
| 216 |
+ |
torsionPotential + inversionPotential; |
| 217 |
|
Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 218 |
|
curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential; |
| 219 |
< |
} |
| 219 |
> |
curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential; |
| 220 |
> |
curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential; |
| 221 |
> |
curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential; |
| 222 |
> |
curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential; |
| 223 |
|
|
| 224 |
< |
void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) { |
| 224 |
> |
} |
| 225 |
> |
|
| 226 |
> |
void ForceManager::calcLongRangeInteraction() { |
| 227 |
|
Snapshot* curSnapshot; |
| 228 |
|
DataStorage* config; |
| 229 |
< |
double* frc; |
| 230 |
< |
double* pos; |
| 231 |
< |
double* trq; |
| 232 |
< |
double* A; |
| 233 |
< |
double* electroFrame; |
| 234 |
< |
double* rc; |
| 235 |
< |
|
| 229 |
> |
RealType* frc; |
| 230 |
> |
RealType* pos; |
| 231 |
> |
RealType* vel; |
| 232 |
> |
RealType* trq; |
| 233 |
> |
RealType* A; |
| 234 |
> |
RealType* electroFrame; |
| 235 |
> |
RealType* rc; |
| 236 |
> |
RealType* vc; |
| 237 |
> |
RealType* particlePot; |
| 238 |
> |
|
| 239 |
|
//get current snapshot from SimInfo |
| 240 |
|
curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 241 |
|
|
| 243 |
|
config = &(curSnapshot->atomData); |
| 244 |
|
frc = config->getArrayPointer(DataStorage::dslForce); |
| 245 |
|
pos = config->getArrayPointer(DataStorage::dslPosition); |
| 246 |
+ |
vel = config->getArrayPointer(DataStorage::dslVelocity); |
| 247 |
|
trq = config->getArrayPointer(DataStorage::dslTorque); |
| 248 |
|
A = config->getArrayPointer(DataStorage::dslAmat); |
| 249 |
|
electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame); |
| 250 |
+ |
particlePot = config->getArrayPointer(DataStorage::dslParticlePot); |
| 251 |
|
|
| 252 |
|
//calculate the center of mass of cutoff group |
| 253 |
|
SimInfo::MoleculeIterator mi; |
| 255 |
|
Molecule::CutoffGroupIterator ci; |
| 256 |
|
CutoffGroup* cg; |
| 257 |
|
Vector3d com; |
| 258 |
+ |
Vector3d comv; |
| 259 |
|
std::vector<Vector3d> rcGroup; |
| 260 |
< |
|
| 260 |
> |
std::vector<Vector3d> vcGroup; |
| 261 |
> |
|
| 262 |
|
if(info_->getNCutoffGroups() > 0){ |
| 263 |
|
|
| 264 |
< |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 265 |
< |
for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
| 266 |
< |
cg->getCOM(com); |
| 267 |
< |
rcGroup.push_back(com); |
| 264 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 265 |
> |
mol = info_->nextMolecule(mi)) { |
| 266 |
> |
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 267 |
> |
cg = mol->nextCutoffGroup(ci)) { |
| 268 |
> |
cg->getCOM(com); |
| 269 |
> |
cg->getCOMV(comv); |
| 270 |
> |
rcGroup.push_back(com); |
| 271 |
> |
vcGroup.push_back(comv); |
| 272 |
|
} |
| 273 |
< |
}// end for (mol) |
| 274 |
< |
|
| 275 |
< |
rc = rcGroup[0].getArrayPointer(); |
| 273 |
> |
}// end for (mol) |
| 274 |
> |
|
| 275 |
> |
rc = rcGroup[0].getArrayPointer(); |
| 276 |
> |
vc = vcGroup[0].getArrayPointer(); |
| 277 |
|
} else { |
| 278 |
< |
// center of mass of the group is the same as position of the atom if cutoff group does not exist |
| 279 |
< |
rc = pos; |
| 278 |
> |
// center of mass of the group is the same as position of the atom |
| 279 |
> |
// if cutoff group does not exist |
| 280 |
> |
rc = pos; |
| 281 |
> |
vc = vel; |
| 282 |
|
} |
| 283 |
< |
|
| 283 |
> |
|
| 284 |
|
//initialize data before passing to fortran |
| 285 |
< |
double longRangePotential = 0.0; |
| 286 |
< |
Mat3x3d tau; |
| 287 |
< |
short int passedCalcPot = needPotential; |
| 288 |
< |
short int passedCalcStress = needStress; |
| 285 |
> |
RealType longRangePotential[LR_POT_TYPES]; |
| 286 |
> |
RealType lrPot = 0.0; |
| 287 |
> |
Vector3d totalDipole; |
| 288 |
> |
Jv_ = 0.0; |
| 289 |
> |
|
| 290 |
> |
|
| 291 |
> |
|
| 292 |
|
int isError = 0; |
| 293 |
|
|
| 294 |
< |
doForceLoop( pos, |
| 295 |
< |
rc, |
| 296 |
< |
A, |
| 192 |
< |
electroFrame, |
| 193 |
< |
frc, |
| 194 |
< |
trq, |
| 195 |
< |
tau.getArrayPointer(), |
| 196 |
< |
&longRangePotential, |
| 197 |
< |
&passedCalcPot, |
| 198 |
< |
&passedCalcStress, |
| 199 |
< |
&isError ); |
| 294 |
> |
for (int i=0; i<LR_POT_TYPES;i++){ |
| 295 |
> |
longRangePotential[i]=0.0; //Initialize array |
| 296 |
> |
} |
| 297 |
|
|
| 298 |
+ |
doForceLoop(pos, |
| 299 |
+ |
vel, |
| 300 |
+ |
rc, |
| 301 |
+ |
vc, |
| 302 |
+ |
A, |
| 303 |
+ |
electroFrame, |
| 304 |
+ |
frc, |
| 305 |
+ |
trq, |
| 306 |
+ |
tau.getArrayPointer(), |
| 307 |
+ |
Jv_.getArrayPointer(), |
| 308 |
+ |
longRangePotential, |
| 309 |
+ |
particlePot, |
| 310 |
+ |
&isError ); |
| 311 |
+ |
|
| 312 |
|
if( isError ){ |
| 313 |
< |
sprintf( painCave.errMsg, |
| 314 |
< |
"Error returned from the fortran force calculation.\n" ); |
| 315 |
< |
painCave.isFatal = 1; |
| 316 |
< |
simError(); |
| 313 |
> |
sprintf( painCave.errMsg, |
| 314 |
> |
"Error returned from the fortran force calculation.\n" ); |
| 315 |
> |
painCave.isFatal = 1; |
| 316 |
> |
simError(); |
| 317 |
|
} |
| 318 |
+ |
for (int i=0; i<LR_POT_TYPES;i++){ |
| 319 |
+ |
lrPot += longRangePotential[i]; //Quick hack |
| 320 |
+ |
} |
| 321 |
|
|
| 322 |
< |
//store the tau and long range potential |
| 323 |
< |
curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = longRangePotential; |
| 324 |
< |
curSnapshot->statData.setTau(tau); |
| 211 |
< |
} |
| 322 |
> |
// grab the simulation box dipole moment if specified |
| 323 |
> |
if (info_->getCalcBoxDipole()){ |
| 324 |
> |
getAccumulatedBoxDipole(totalDipole.getArrayPointer()); |
| 325 |
|
|
| 326 |
+ |
curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0); |
| 327 |
+ |
curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1); |
| 328 |
+ |
curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2); |
| 329 |
+ |
} |
| 330 |
|
|
| 331 |
< |
void ForceManager::postCalculation() { |
| 331 |
> |
//store the tau and long range potential |
| 332 |
> |
curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot; |
| 333 |
> |
curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT]; |
| 334 |
> |
curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT]; |
| 335 |
> |
} |
| 336 |
> |
|
| 337 |
> |
|
| 338 |
> |
void ForceManager::postCalculation() { |
| 339 |
|
SimInfo::MoleculeIterator mi; |
| 340 |
|
Molecule* mol; |
| 341 |
|
Molecule::RigidBodyIterator rbIter; |
| 342 |
|
RigidBody* rb; |
| 343 |
< |
|
| 343 |
> |
Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 344 |
> |
|
| 345 |
|
// collect the atomic forces onto rigid bodies |
| 346 |
< |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 347 |
< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 348 |
< |
rb->calcForcesAndTorques(); |
| 349 |
< |
} |
| 346 |
> |
|
| 347 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 348 |
> |
mol = info_->nextMolecule(mi)) { |
| 349 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 350 |
> |
rb = mol->nextRigidBody(rbIter)) { |
| 351 |
> |
Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial(); |
| 352 |
> |
tau += rbTau; |
| 353 |
> |
} |
| 354 |
|
} |
| 355 |
|
|
| 356 |
< |
} |
| 356 |
> |
#ifdef IS_MPI |
| 357 |
> |
Mat3x3d tmpTau(tau); |
| 358 |
> |
MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(), |
| 359 |
> |
9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 360 |
> |
#endif |
| 361 |
> |
curSnapshot->statData.setTau(tau); |
| 362 |
> |
curSnapshot->statData.setJv(Jv_); |
| 363 |
> |
} |
| 364 |
|
|
| 365 |
< |
} //end namespace oopse |
| 365 |
> |
} //end namespace OpenMD |
