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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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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#include <cmath> |
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#include "restraints/ThermoIntegrationForceManager.hpp" |
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#include "integrators/Integrator.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/simError.h" |
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#include "utils/OOPSEConstant.hpp" |
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#include "utils/StringUtils.hpp" |
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namespace oopse { |
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#ifdef IS_MPI |
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#include <mpi.h> |
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#endif |
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|
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namespace OpenMD { |
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ThermoIntegrationForceManager::ThermoIntegrationForceManager(SimInfo* info): |
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ForceManager(info){ |
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RestraintForceManager(info){ |
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currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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simParam = info_->getSimParams(); |
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if (simParam->haveThermIntLambda()){ |
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tIntLambda_ = simParam->getThermIntLambda(); |
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if (simParam->haveThermodynamicIntegrationLambda()){ |
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tIntLambda_ = simParam->getThermodynamicIntegrationLambda(); |
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} |
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else{ |
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tIntLambda_ = 1.0; |
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sprintf(painCave.errMsg, |
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"ThermoIntegration error: the transformation parameter (lambda) was\n" |
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"\tnot specified. OOPSE will use a default value of %f. To set\n" |
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"\tlambda, use the thermodynamicIntegrationLambda variable.\n", |
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"ThermoIntegration error: the transformation parameter\n" |
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"\t(lambda) was not specified. OpenMD will use a default\n" |
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"\tvalue of %f. To set lambda, use the \n" |
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"\tthermodynamicIntegrationLambda variable.\n", |
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tIntLambda_); |
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painCave.isFatal = 0; |
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simError(); |
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} |
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if (simParam->haveThermIntK()){ |
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tIntK_ = simParam->getThermIntK(); |
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if (simParam->haveThermodynamicIntegrationK()){ |
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tIntK_ = simParam->getThermodynamicIntegrationK(); |
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} |
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else{ |
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tIntK_ = 1.0; |
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sprintf(painCave.errMsg, |
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"ThermoIntegration Warning: the tranformation parameter exponent\n" |
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"\t(k) was not specified. OOPSE will use a default value of %f.\n" |
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"\tTo set k, use the thermodynamicIntegrationK variable.\n", |
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"ThermoIntegration Warning: the tranformation parameter\n" |
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"\texponent (k) was not specified. OpenMD will use a default\n" |
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"\tvalue of %f. To set k, use the thermodynamicIntegrationK\n" |
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"\tvariable.\n", |
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tIntK_); |
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painCave.isFatal = 0; |
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simError(); |
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} |
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if (simParam->getUseSolidThermInt()) { |
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// build a restraint object |
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restraint_ = new Restraints(info_, tIntLambda_, tIntK_); |
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} |
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// build the scaling factor used to modulate the forces and torques |
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factor_ = pow(tIntLambda_, tIntK_); |
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} |
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ThermoIntegrationForceManager::~ThermoIntegrationForceManager(){ |
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} |
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void ThermoIntegrationForceManager::calcForces(bool needPotential, |
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bool needStress){ |
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void ThermoIntegrationForceManager::calcForces(){ |
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Snapshot* curSnapshot; |
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SimInfo::MoleculeIterator mi; |
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Molecule* mol; |
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Molecule::IntegrableObjectIterator ii; |
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StuntDouble* integrableObject; |
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StuntDouble* sd; |
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Vector3d frc; |
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Vector3d trq; |
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Mat3x3d tempTau; |
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curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
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// perform the standard calcForces first |
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ForceManager::calcForces(needPotential, needStress); |
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ForceManager::calcForces(); |
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// now scale forces and torques of all the integrableObjects |
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curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
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// now scale forces and torques of all the sds |
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for (mol = info_->beginMolecule(mi); mol != NULL; |
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mol = info_->nextMolecule(mi)) { |
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for (integrableObject = mol->beginIntegrableObject(ii); |
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integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(ii)) { |
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frc = integrableObject->getFrc(); |
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|
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for (sd = mol->beginIntegrableObject(ii); sd != NULL; |
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sd = mol->nextIntegrableObject(ii)) { |
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frc = sd->getFrc(); |
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frc *= factor_; |
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integrableObject->setFrc(frc); |
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sd->setFrc(frc); |
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if (integrableObject->isDirectional()){ |
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trq = integrableObject->getTrq(); |
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if (sd->isDirectional()){ |
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trq = sd->getTrq(); |
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trq *= factor_; |
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integrableObject->setTrq(trq); |
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sd->setTrq(trq); |
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} |
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} |
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// set vraw to be the unmodulated potential |
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lrPot_ = curSnapshot->statData[Stats::POTENTIAL_ENERGY]; |
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curSnapshot->statData[Stats::VRAW] = lrPot_; |
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// modulate the potential and update the snapshot |
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lrPot_ *= factor_; |
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curSnapshot->statData[Stats::POTENTIAL_ENERGY] = lrPot_; |
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} |
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// do crystal restraint forces for thermodynamic integration |
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if (simParam->getUseSolidThermInt()) { |
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lrPot_ += restraint_->Calc_Restraint_Forces(); |
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curSnapshot->statData[Stats::POTENTIAL_ENERGY] = lrPot_; |
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vHarm_ = restraint_->getVharm(); |
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curSnapshot->statData[Stats::VHARM] = vHarm_; |
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} |
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// set rawPotential to be the unmodulated potential |
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lrPot_ = curSnapshot->getLongRangePotential(); |
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curSnapshot->setRawPotential(lrPot_); |
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} |
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// modulate the potential and update the snapshot |
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lrPot_ *= factor_; |
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curSnapshot->setLongRangePotential(lrPot_); |
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|
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// scale the pressure tensor |
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tempTau = curSnapshot->getStressTensor(); |
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tempTau *= factor_; |
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curSnapshot->setStressTensor(tempTau); |
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|
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// now, on to the applied restraining potentials (if needed): |
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RealType restPot_local = 0.0; |
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RealType vHarm_local = 0.0; |
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|
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if (simParam->getUseRestraints()) { |
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// do restraints from RestraintForceManager: |
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restPot_local = doRestraints(1.0 - factor_); |
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vHarm_local = getUnscaledPotential(); |
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} |
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|
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#ifdef IS_MPI |
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RealType restPot; |
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MPI::COMM_WORLD.Allreduce(&restPot_local, &restPot, 1, |
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MPI::REALTYPE, MPI::SUM); |
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MPI::COMM_WORLD.Allreduce(&vHarm_local, &vHarm_, 1, |
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MPI::REALTYPE, MPI::SUM); |
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lrPot_ += restPot; |
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#else |
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lrPot_ += restPot_local; |
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vHarm_ = vHarm_local; |
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#endif |
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|
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// give the final values to stats |
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curSnapshot->setLongRangePotential(lrPot_); |
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curSnapshot->setRestraintPotential(vHarm_); |
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} |
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} |
