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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, 234107 (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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|
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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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#include "parallel/ForceDecomposition.hpp" |
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#include "math/Vector3.hpp" |
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|
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using namespace std; |
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namespace OpenMD { |
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|
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ForceDecomposition::ForceDecomposition(SimInfo* info, InteractionManager* iMan) : info_(info), interactionMan_(iMan), needVelocities_(false) { |
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|
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sman_ = info_->getSnapshotManager(); |
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storageLayout_ = sman_->getStorageLayout(); |
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ff_ = info_->getForceField(); |
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userChoseCutoff_ = false; |
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|
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usePeriodicBoundaryConditions_ = info->getSimParams()->getUsePeriodicBoundaryConditions(); |
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|
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Globals* simParams_ = info_->getSimParams(); |
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if (simParams_->havePrintHeatFlux()) { |
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if (simParams_->getPrintHeatFlux()) { |
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needVelocities_ = true; |
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} |
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} |
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|
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if (simParams_->haveSkinThickness()) { |
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skinThickness_ = simParams_->getSkinThickness(); |
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} else { |
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skinThickness_ = 1.0; |
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sprintf(painCave.errMsg, |
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"ForceDecomposition: No value was set for the skinThickness.\n" |
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"\tOpenMD will use a default value of %f Angstroms\n" |
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"\tfor this simulation\n", skinThickness_); |
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painCave.severity = OPENMD_INFO; |
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painCave.isFatal = 0; |
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simError(); |
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} |
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|
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// cellOffsets are the partial space for the cell lists used in |
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// constructing the neighbor lists |
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cellOffsets_.clear(); |
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cellOffsets_.push_back( Vector3i(0, 0, 0) ); |
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cellOffsets_.push_back( Vector3i(1, 0, 0) ); |
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cellOffsets_.push_back( Vector3i(1, 1, 0) ); |
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cellOffsets_.push_back( Vector3i(0, 1, 0) ); |
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cellOffsets_.push_back( Vector3i(-1,1, 0) ); |
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cellOffsets_.push_back( Vector3i(0, 0, 1) ); |
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cellOffsets_.push_back( Vector3i(1, 0, 1) ); |
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cellOffsets_.push_back( Vector3i(1, 1, 1) ); |
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cellOffsets_.push_back( Vector3i(0, 1, 1) ); |
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cellOffsets_.push_back( Vector3i(-1,1, 1) ); |
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cellOffsets_.push_back( Vector3i(-1,0, 1) ); |
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cellOffsets_.push_back( Vector3i(-1,-1,1) ); |
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cellOffsets_.push_back( Vector3i(0, -1,1) ); |
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cellOffsets_.push_back( Vector3i(1, -1,1) ); |
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} |
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|
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void ForceDecomposition::fillSelfData(SelfData &sdat, int atom1) { |
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|
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//sdat.atype = atypesLocal[atom1]; |
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sdat.atid = idents[atom1]; |
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|
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sdat.pot = &embeddingPot; |
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sdat.excludedPot = &excludedSelfPot; |
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|
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if (storageLayout_ & DataStorage::dslDipole) { |
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sdat.dipole = &(snap_->atomData.dipole[atom1]); |
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} |
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|
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if (storageLayout_ & DataStorage::dslQuadrupole) { |
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sdat.quadrupole = &(snap_->atomData.quadrupole[atom1]); |
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} |
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|
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if (storageLayout_ & DataStorage::dslTorque) { |
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sdat.t = &(snap_->atomData.torque[atom1]); |
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} |
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|
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if (storageLayout_ & DataStorage::dslDensity) { |
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sdat.rho = &(snap_->atomData.density[atom1]); |
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} |
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|
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if (storageLayout_ & DataStorage::dslFunctional) { |
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sdat.frho = &(snap_->atomData.functional[atom1]); |
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} |
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|
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if (storageLayout_ & DataStorage::dslFunctionalDerivative) { |
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sdat.dfrhodrho = &(snap_->atomData.functionalDerivative[atom1]); |
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} |
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|
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if (storageLayout_ & DataStorage::dslSkippedCharge) { |
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sdat.skippedCharge = &(snap_->atomData.skippedCharge[atom1]); |
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} |
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|
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if (storageLayout_ & DataStorage::dslParticlePot) { |
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sdat.particlePot = &(snap_->atomData.particlePot[atom1]); |
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} |
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|
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if (storageLayout_ & DataStorage::dslFlucQPosition) { |
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sdat.flucQ = &(snap_->atomData.flucQPos[atom1]); |
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} |
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|
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if (storageLayout_ & DataStorage::dslFlucQForce) { |
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sdat.flucQfrc = &(snap_->atomData.flucQFrc[atom1]); |
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} |
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} |
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|
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bool ForceDecomposition::checkNeighborList() { |
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|
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int nGroups = snap_->cgData.position.size(); |
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if (needVelocities_) |
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snap_->cgData.setStorageLayout(DataStorage::dslPosition | DataStorage::dslVelocity); |
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|
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// if we have changed the group identities or haven't set up the |
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// saved positions we automatically will need a neighbor list update: |
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|
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if ( saved_CG_positions_.size() != nGroups ) return true; |
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|
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RealType dispmax = 0.0; |
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Vector3d disp; |
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|
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for (int i = 0; i < nGroups; i++) { |
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disp = snap_->cgData.position[i] - saved_CG_positions_[i]; |
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for (int j = 0; j < 3; j++) |
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dispmax = max( abs(disp[j]), dispmax); |
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} |
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|
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#ifdef IS_MPI |
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MPI::COMM_WORLD.Allreduce(&dispmax, &dispmax, 1, MPI::REALTYPE, MPI::MAX); |
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#endif |
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|
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// a conservative test of list skin crossings |
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dispmax = 2.0 * sqrt (3.0 * dispmax * dispmax); |
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|
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|
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if (dispmax > skinThickness_) |
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return (dispmax > skinThickness_); |
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|
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return false; |
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} |
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|
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void ForceDecomposition::addToHeatFlux(Vector3d hf) { |
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Vector3d chf = snap_->getConductiveHeatFlux(); |
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chf += hf; |
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snap_->setConductiveHeatFlux(chf); |
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} |
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void ForceDecomposition::setHeatFlux(Vector3d hf) { |
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snap_->setConductiveHeatFlux(hf); |
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} |
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|
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} |
