NPAT.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 "integrators/NPAT.hpp"
 
#include "brains/SimInfo.hpp"
#include "brains/Thermo.hpp"
#include "integrators/IntegratorCreator.hpp"
#include "primitives/Molecule.hpp"
#include "utils/Constants.hpp"
#include "utils/simError.h"
 
namespace OpenMD {
 
  NPAT::NPAT(SimInfo* info) : NPT(info) {
    Globals* simParams = info_->getSimParams();
 
    // Default value of privilegedAxis is "z"
    if (simParams->getPrivilegedAxis() == "x")
      axis_ = 0;
    else if (simParams->getPrivilegedAxis() == "y")
      axis_ = 1;
    else if (simParams->getPrivilegedAxis() == "z")
      axis_ = 2;
  }
 
  void NPAT::evolveEtaA() {
    eta(axis_, axis_) +=
        dt2 * instaVol *
        (press(axis_, axis_) - targetPressure / Constants::pressureConvert) /
        (NkBT * tb2);
    oldEta_ = eta;
  }
 
  void NPAT::evolveEtaB() {
    prevEta_          = eta;
    eta(axis_, axis_) = oldEta_(axis_, axis_) +
                        dt2 * instaVol *
                            (press(axis_, axis_) -
                             targetPressure / Constants::pressureConvert) /
                            (NkBT * tb2);
  }
 
  void NPAT::calcVelScale() {
    for (int i = 0; i < 3; i++) {
      for (int j = 0; j < 3; j++) {
        vScale_(i, j) = eta(i, j);
 
        if (i == j) { vScale_(i, j) += thermostat.first; }
      }
    }
  }
 
  void NPAT::getVelScaleA(Vector3d& sc, const Vector3d& vel) {
    sc = vScale_ * vel;
  }
 
  void NPAT::getVelScaleB(Vector3d& sc, int index) {
    sc = vScale_ * oldVel[index];
  }
 
  void NPAT::getPosScale(const Vector3d& pos, const Vector3d& COM, int index,
                         Vector3d& sc) {
    /**@todo */
    Vector3d rj = (oldPos[index] + pos) / (RealType)2.0 - COM;
    sc          = eta * rj;
  }
 
  void NPAT::scaleSimBox() {
    Mat3x3d scaleMat;
 
    for (int i = 0; i < 3; i++) {
      for (int j = 0; j < 3; j++) {
        scaleMat(i, j) = 0.0;
        if (i == j) { scaleMat(i, j) = 1.0; }
      }
    }
 
    scaleMat(axis_, axis_) = exp(dt * eta(axis_, axis_));
    Mat3x3d hmat           = snap->getHmat();
    hmat                   = hmat * scaleMat;
    snap->setHmat(hmat);
  }
 
  bool NPAT::etaConverged() {
    int i;
    RealType diffEta, sumEta;
 
    sumEta = 0;
    for (i = 0; i < 3; i++) {
      sumEta += pow(prevEta_(i, i) - eta(i, i), 2);
    }
 
    diffEta = sqrt(sumEta / 3.0);
 
    return (diffEta <= etaTolerance);
  }
 
  RealType NPAT::calcConservedQuantity() {
    thermostat = snap->getThermostat();
    loadEta();
 
    // We need NkBT a lot, so just set it here: This is the RAW number
    // of integrableObjects, so no subtraction or addition of constraints or
    // orientational degrees of freedom:
    NkBT = info_->getNGlobalIntegrableObjects() * Constants::kB * targetTemp;
 
    // fkBT is used because the thermostat operates on more degrees of freedom
    // than the barostat (when there are particles with orientational degrees
    // of freedom).
    fkBT = info_->getNdf() * Constants::kB * targetTemp;
 
    RealType conservedQuantity;
    RealType totalEnergy;
    RealType thermostat_kinetic;
    RealType thermostat_potential;
    RealType barostat_kinetic;
    RealType barostat_potential;
    RealType trEta;
 
    totalEnergy = thermo.getTotalEnergy();
 
    thermostat_kinetic = fkBT * tt2 * thermostat.first * thermostat.first /
                         (2.0 * Constants::energyConvert);
 
    thermostat_potential = fkBT * thermostat.second / Constants::energyConvert;
 
    SquareMatrix<RealType, 3> tmp = eta.transpose() * eta;
    trEta                         = tmp.trace();
 
    barostat_kinetic = NkBT * tb2 * trEta / (2.0 * Constants::energyConvert);
 
    barostat_potential =
        (targetPressure * thermo.getVolume() / Constants::pressureConvert) /
        Constants::energyConvert;
 
    conservedQuantity = totalEnergy + thermostat_kinetic +
                        thermostat_potential + barostat_kinetic +
                        barostat_potential;
 
    return conservedQuantity;
  }
 
  void NPAT::loadEta() {
    eta = snap->getBarostat();
 
    // if (!eta.isDiagonal()) {
    //    snprintf( painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
    //             "NPAT error: the diagonal elements of eta matrix are not the
    //             same or etaMat is not a diagonal matrix");
    //    painCave.isFatal = 1;
    //    simError();
    //}
  }
 
  void NPAT::saveEta() { snap->setBarostat(eta); }
 
}  // namespace OpenMD