ForceDecomposition.cpp

/*
 * Copyright (c) 2004-present, The University of Notre Dame. All rights
 * reserved.
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright notice,
 *    this list of conditions and the following disclaimer.
 *
 * 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.
 *
 * 3. Neither the name of the copyright holder nor the names of its
 *    contributors may be used to endorse or promote products derived from
 *    this software without specific prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
 * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
 * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
 * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 * POSSIBILITY OF SUCH DAMAGE.
 *
 * 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, 234107 (2008).
 * [4] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [5] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 * [6] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
 * [7] Lamichhane, Newman & Gezelter, J. Chem. Phys. 141, 134110 (2014).
 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
 */
 
#include "parallel/ForceDecomposition.hpp"
 
#ifdef IS_MPI
#include <mpi.h>
#endif
 
#include "math/Vector3.hpp"
 
using namespace std;
namespace OpenMD {
 
  ForceDecomposition::ForceDecomposition(SimInfo* info,
                                         InteractionManager* iMan) :
      info_(info),
      interactionMan_(iMan), needVelocities_(false) {
    sman_                     = info_->getSnapshotManager();
    atomStorageLayout_        = sman_->getAtomStorageLayout();
    rigidBodyStorageLayout_   = sman_->getRigidBodyStorageLayout();
    cutoffGroupStorageLayout_ = sman_->getCutoffGroupStorageLayout();
    ff_                       = info_->getForceField();
 
    usePeriodicBoundaryConditions_ =
        info->getSimParams()->getUsePeriodicBoundaryConditions();
 
    Globals* simParams_ = info_->getSimParams();
    if (simParams_->havePrintHeatFlux()) {
      if (simParams_->getPrintHeatFlux()) { needVelocities_ = true; }
    }
 
    if (simParams_->haveSkinThickness()) {
      skinThickness_ = simParams_->getSkinThickness();
    } else {
      skinThickness_ = 1.0;
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "ForceDecomposition: No value was set for the skinThickness.\n"
               "\tOpenMD will use a default value of %f Angstroms\n"
               "\tfor this simulation\n",
               skinThickness_);
      painCave.severity = OPENMD_INFO;
      painCave.isFatal  = 0;
      simError();
    }
 
    // cellOffsets are the partial space for the cell lists used in
    // constructing the neighbor lists
    cellOffsets_.clear();
    cellOffsets_.push_back(Vector3i(0, 0, 0));
    cellOffsets_.push_back(Vector3i(1, 0, 0));
    cellOffsets_.push_back(Vector3i(1, 1, 0));
    cellOffsets_.push_back(Vector3i(0, 1, 0));
    cellOffsets_.push_back(Vector3i(-1, 1, 0));
    cellOffsets_.push_back(Vector3i(0, 0, 1));
    cellOffsets_.push_back(Vector3i(1, 0, 1));
    cellOffsets_.push_back(Vector3i(1, 1, 1));
    cellOffsets_.push_back(Vector3i(0, 1, 1));
    cellOffsets_.push_back(Vector3i(-1, 1, 1));
    cellOffsets_.push_back(Vector3i(-1, 0, 1));
    cellOffsets_.push_back(Vector3i(-1, -1, 1));
    cellOffsets_.push_back(Vector3i(0, -1, 1));
    cellOffsets_.push_back(Vector3i(1, -1, 1));
  }
 
  void ForceDecomposition::setCutoffRadius(RealType rcut) {
    rCut_    = rcut;
    rList_   = rCut_ + skinThickness_;
    rListSq_ = rList_ * rList_;
  }
 
  void ForceDecomposition::fillPreForceData(SelfData& sdat, int atom) {
    sdat.atid    = idents[atom];
    sdat.selfPot = selfPot;
    sdat.selePot = selectedSelfPot;
 
    if (atomStorageLayout_ & DataStorage::dslDensity) {
      sdat.rho = snap_->atomData.density[atom];
    }
 
    if (atomStorageLayout_ & DataStorage::dslParticlePot) {
      sdat.particlePot = snap_->atomData.particlePot[atom];
    }
  }
 
  void ForceDecomposition::fillSelfData(SelfData& sdat, int atom) {
    sdat.atid    = idents[atom];
    sdat.selfPot = selfPot;
    sdat.selePot = selectedSelfPot;
 
    if (atomStorageLayout_ & DataStorage::dslSkippedCharge) {
      sdat.skippedCharge = snap_->atomData.skippedCharge[atom];
    }
 
    if (atomStorageLayout_ & DataStorage::dslParticlePot) {
      sdat.particlePot = snap_->atomData.particlePot[atom];
    }
 
    if (atomStorageLayout_ & DataStorage::dslFlucQPosition) {
      sdat.flucQ = snap_->atomData.flucQPos[atom];
    }
 
    if (atomStorageLayout_ & DataStorage::dslFlucQForce) {
      sdat.flucQfrc = snap_->atomData.flucQFrc[atom];
    }
  }
 
  void ForceDecomposition::unpackPreForceData(SelfData& sdat, int atom) {
    selfPot         = sdat.selfPot;
    selectedSelfPot = sdat.selePot;
 
    if (atomStorageLayout_ & DataStorage::dslFunctional) {
      snap_->atomData.functional[atom] += sdat.frho;
    }
 
    if (atomStorageLayout_ & DataStorage::dslFunctionalDerivative) {
      snap_->atomData.functionalDerivative[atom] += sdat.dfrhodrho;
    }
 
    if (sdat.doParticlePot &&
        (atomStorageLayout_ & DataStorage::dslParticlePot)) {
      snap_->atomData.particlePot[atom] = sdat.particlePot;
    }
  }
 
  void ForceDecomposition::unpackSelfData(SelfData& sdat, int atom) {
    selfPot         = sdat.selfPot;
    selectedSelfPot = sdat.selePot;
 
    if (atomStorageLayout_ & DataStorage::dslFlucQForce) {
      snap_->atomData.flucQFrc[atom] = sdat.flucQfrc;
    }
  }
 
  bool ForceDecomposition::checkNeighborList(vector<Vector3d> savedPositions) {
    RealType st2        = pow(skinThickness_ / 2.0, 2);
    std::size_t nGroups = snap_->cgData.position.size();
    if (needVelocities_)
      snap_->cgData.setStorageLayout(DataStorage::dslPosition |
                                     DataStorage::dslVelocity);
 
    // if we have changed the group identities or haven't set up the
    // saved positions we automatically will need a neighbor list update:
 
    if (savedPositions.size() != nGroups) return true;
 
    RealType dispmax = 0.0;
    Vector3d disp;
 
    for (std::size_t i = 0; i < nGroups; i++) {
      disp    = snap_->cgData.position[i] - savedPositions[i];
      dispmax = max(dispmax, disp.lengthSquare());
    }
 
#ifdef IS_MPI
    MPI_Allreduce(MPI_IN_PLACE, &dispmax, 1, MPI_REALTYPE, MPI_MAX,
                  MPI_COMM_WORLD);
#endif
 
    return (dispmax > st2) ? true : false;
  }
 
  void ForceDecomposition::addToHeatFlux(Vector3d hf) {
    Vector3d chf = snap_->getConductiveHeatFlux();
    chf += hf;
    snap_->setConductiveHeatFlux(chf);
  }
  void ForceDecomposition::setHeatFlux(Vector3d hf) {
    snap_->setConductiveHeatFlux(hf);
  }
}  // namespace OpenMD