--- trunk/src/brains/ForceManager.cpp 2007/04/06 21:53:43 1126 +++ trunk/src/brains/ForceManager.cpp 2011/08/12 14:37:25 1610 @@ -6,19 +6,10 @@ * redistribute this software in source and binary code form, provided * that the following conditions are met: * - * 1. Acknowledgement of the program authors must be made in any - * publication of scientific results based in part on use of the - * program. An acceptable form of acknowledgement is citation of - * the article in which the program was described (Matthew - * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher - * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented - * Parallel Simulation Engine for Molecular Dynamics," - * J. Comput. Chem. 26, pp. 252-271 (2005)) - * - * 2. Redistributions of source code must retain the above copyright + * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * - * 3. Redistributions in binary form must reproduce the above copyright + * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the * distribution. @@ -37,6 +28,15 @@ * arising out of the use of or inability to use software, even if the * University of Notre Dame has been advised of the possibility of * such damages. + * + * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your + * research, please cite the appropriate papers when you publish your + * work. Good starting points are: + * + * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). + * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). + * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). + * [4] Vardeman & Gezelter, in progress (2009). */ /** @@ -50,14 +50,16 @@ #include "brains/ForceManager.hpp" #include "primitives/Molecule.hpp" #include "UseTheForce/doForces_interface.h" -#define __C +#define __OPENMD_C #include "UseTheForce/DarkSide/fInteractionMap.h" #include "utils/simError.h" +#include "primitives/Bond.hpp" #include "primitives/Bend.hpp" -#include "primitives/Bend.hpp" -namespace oopse { +#include "primitives/Torsion.hpp" +#include "primitives/Inversion.hpp" +namespace OpenMD { - void ForceManager::calcForces(bool needPotential, bool needStress) { + void ForceManager::calcForces() { if (!info_->isFortranInitialized()) { info_->update(); @@ -67,9 +69,9 @@ namespace oopse { calcShortRangeInteraction(); - calcLongRangeInteraction(needPotential, needStress); + calcLongRangeInteraction(); - postCalculation(needStress); + postCalculation(); } @@ -83,18 +85,19 @@ namespace oopse { // forces are zeroed here, before any are accumulated. // NOTE: do not rezero the forces in Fortran. - + for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { atom->zeroForcesAndTorques(); } - + //change the positions of atoms which belong to the rigidbodies for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { rb->zeroForcesAndTorques(); } + } // Zero out the stress tensor @@ -108,14 +111,17 @@ namespace oopse { Bond* bond; Bend* bend; Torsion* torsion; + Inversion* inversion; SimInfo::MoleculeIterator mi; Molecule::RigidBodyIterator rbIter; Molecule::BondIterator bondIter;; Molecule::BendIterator bendIter; Molecule::TorsionIterator torsionIter; + Molecule::InversionIterator inversionIter; RealType bondPotential = 0.0; RealType bendPotential = 0.0; RealType torsionPotential = 0.0; + RealType inversionPotential = 0.0; //calculate short range interactions for (mol = info_->beginMolecule(mi); mol != NULL; @@ -139,6 +145,7 @@ namespace oopse { RealType angle; bend->calcForce(angle); RealType currBendPot = bend->getPotential(); + bendPotential += bend->getPotential(); std::map::iterator i = bendDataSets.find(bend); if (i == bendDataSets.end()) { @@ -175,6 +182,30 @@ namespace oopse { i->second.prev.potential = i->second.curr.potential; i->second.curr.angle = angle; i->second.curr.potential = currTorsionPot; + i->second.deltaV = fabs(i->second.curr.potential - + i->second.prev.potential); + } + } + + for (inversion = mol->beginInversion(inversionIter); + inversion != NULL; + inversion = mol->nextInversion(inversionIter)) { + RealType angle; + inversion->calcForce(angle); + RealType currInversionPot = inversion->getPotential(); + inversionPotential += inversion->getPotential(); + std::map::iterator i = inversionDataSets.find(inversion); + if (i == inversionDataSets.end()) { + InversionDataSet dataSet; + dataSet.prev.angle = dataSet.curr.angle = angle; + dataSet.prev.potential = dataSet.curr.potential = currInversionPot; + dataSet.deltaV = 0.0; + inversionDataSets.insert(std::map::value_type(inversion, dataSet)); + }else { + i->second.prev.angle = i->second.curr.angle; + i->second.prev.potential = i->second.curr.potential; + i->second.curr.angle = angle; + i->second.curr.potential = currInversionPot; i->second.deltaV = fabs(i->second.curr.potential - i->second.prev.potential); } @@ -182,17 +213,17 @@ namespace oopse { } RealType shortRangePotential = bondPotential + bendPotential + - torsionPotential; + torsionPotential + inversionPotential; Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential; curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential; curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential; curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential; + curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential; } - void ForceManager::calcLongRangeInteraction(bool needPotential, - bool needStress) { + void ForceManager::calcLongRangeInteraction() { Snapshot* curSnapshot; DataStorage* config; RealType* frc; @@ -201,6 +232,7 @@ namespace oopse { RealType* A; RealType* electroFrame; RealType* rc; + RealType* particlePot; //get current snapshot from SimInfo curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); @@ -212,6 +244,7 @@ namespace oopse { trq = config->getArrayPointer(DataStorage::dslTorque); A = config->getArrayPointer(DataStorage::dslAmat); electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame); + particlePot = config->getArrayPointer(DataStorage::dslParticlePot); //calculate the center of mass of cutoff group SimInfo::MoleculeIterator mi; @@ -243,26 +276,23 @@ namespace oopse { RealType longRangePotential[LR_POT_TYPES]; RealType lrPot = 0.0; Vector3d totalDipole; - short int passedCalcPot = needPotential; - short int passedCalcStress = needStress; int isError = 0; for (int i=0; igetCalcBoxDipole()){ getAccumulatedBoxDipole(totalDipole.getArrayPointer()); @@ -289,7 +319,7 @@ namespace oopse { } - void ForceManager::postCalculation(bool needStress) { + void ForceManager::postCalculation() { SimInfo::MoleculeIterator mi; Molecule* mol; Molecule::RigidBodyIterator rbIter; @@ -302,23 +332,17 @@ namespace oopse { mol = info_->nextMolecule(mi)) { for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { - if (needStress) { - Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial(); - tau += rbTau; - } else{ - rb->calcForcesAndTorques(); - } + Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial(); + tau += rbTau; } } - - if (needStress) { + #ifdef IS_MPI - Mat3x3d tmpTau(tau); - MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(), - 9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); + Mat3x3d tmpTau(tau); + MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(), + 9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); #endif - curSnapshot->statData.setTau(tau); - } + curSnapshot->statData.setTau(tau); } -} //end namespace oopse +} //end namespace OpenMD