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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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* such damages. |
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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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* @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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#include "brains/ForceManager.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/simError.h" |
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namespace oopse { |
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void ForceManager::calcForces(bool needPotential, bool needStress) { |
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void ForceManager::calcForces(bool needPotential, bool needStress) { |
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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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preCalculation(); |
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postCalculation(); |
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} |
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} |
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void ForceManager::preCalculation() { |
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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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// 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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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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//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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//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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} |
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} |
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void ForceManager::calcShortRangeInteraction() { |
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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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//calculate short range interactions |
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for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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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; rb = mol->nextRigidBody(rbIter)) { |
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rb->updateAtoms(); |
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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; bond = mol->nextBond(bondIter)) { |
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bond->calcForce(); |
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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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} |
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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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} |
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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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} |
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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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} |
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} |
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double shortRangePotential = 0.0; |
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for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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shortRangePotential += mol->getPotential(); |
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shortRangePotential += mol->getPotential(); |
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} |
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Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
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curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential; |
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} |
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} |
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void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) { |
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void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) { |
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Snapshot* curSnapshot; |
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DataStorage* config; |
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double* frc; |
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if(info_->getNCutoffGroups() > 0){ |
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for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
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cg->getCOM(com); |
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rcGroup.push_back(com); |
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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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}// end for (mol) |
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rc = rcGroup[0].getArrayPointer(); |
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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 if cutoff group does not exist |
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rc = pos; |
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// center of mass of the group is the same as position of the atom if cutoff group does not exist |
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rc = pos; |
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} |
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//initialize data before passing to fortran |
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int isError = 0; |
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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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&passedCalcPot, |
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&passedCalcStress, |
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&isError ); |
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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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&passedCalcPot, |
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&passedCalcStress, |
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&isError ); |
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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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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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//store the tau and long range potential |
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curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = longRangePotential; |
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curSnapshot->statData.setTau(tau); |
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} |
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} |
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void ForceManager::postCalculation() { |
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void ForceManager::postCalculation() { |
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SimInfo::MoleculeIterator mi; |
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Molecule* mol; |
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Molecule::RigidBodyIterator rbIter; |
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// collect the atomic forces onto rigid bodies |
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for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
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rb->calcForcesAndTorques(); |
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} |
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for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
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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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} //end namespace oopse |