NgammaT.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 following paper when you publish your work:
 *
 * [1] Drisko et al., J. Open Source Softw. 9, 7004 (2024).
 *
 * Good starting points for code and simulation methodology are:
 *
 * [2] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
 * [3] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
 * [4] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
 * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 * [7] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
 * [9] Drisko & Gezelter, J. Chem. Theory Comput. 20, 4986-4997 (2024).
 */
 
#include "integrators/NgammaT.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 {
  NgammaT::NgammaT(SimInfo* info) : NPT(info) {
    Globals* simParams = info_->getSimParams();
    if (!simParams->haveSurfaceTension()) {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "If you use the NgammaT integrator, you must "
               "set a surface tension.\n");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal  = 1;
      simError();
    } else {
      surfaceTension_ = simParams->getSurfaceTension() *
                        Constants::surfaceTensionConvert *
                        Constants::energyConvert;
 
      // 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;
 
      // Compute complementary axes to the privileged axis
      axis1_ = (axis_ + 1) % 3;
      axis2_ = (axis_ + 2) % 3;
    }
  }
  void NgammaT::evolveEtaA() {
    Mat3x3d hmat = snap->getHmat();
    RealType hz  = hmat(axis_, axis_);
    RealType Axy = hmat(axis1_, axis1_) * hmat(axis2_, axis2_);
    RealType sx  = -hz * (press(axis1_, axis1_) -
                         targetPressure / Constants::pressureConvert);
    RealType sy  = -hz * (press(axis2_, axis2_) -
                         targetPressure / Constants::pressureConvert);
    eta(axis1_, axis1_) -= dt2 * Axy * (sx - surfaceTension_) / (NkBT * tb2);
    eta(axis2_, axis2_) -= dt2 * Axy * (sy - surfaceTension_) / (NkBT * tb2);
    eta(axis_, axis_) = 0.0;
    oldEta_           = eta;
  }
 
  void NgammaT::evolveEtaB() {
    Mat3x3d hmat      = snap->getHmat();
    RealType hz       = hmat(axis_, axis_);
    RealType Axy      = hmat(axis1_, axis1_) * hmat(axis2_, axis2_);
    prevEta_          = eta;
    RealType sx       = -hz * (press(axis1_, axis1_) -
                         targetPressure / Constants::pressureConvert);
    RealType sy       = -hz * (press(axis2_, axis2_) -
                         targetPressure / Constants::pressureConvert);
    eta(axis_, axis_) = oldEta_(axis_, axis_) -
                        dt2 * Axy * (sx - surfaceTension_) / (NkBT * tb2);
    eta(axis2_, axis2_) = oldEta_(axis2_, axis2_) -
                          dt2 * Axy * (sy - surfaceTension_) / (NkBT * tb2);
    eta(axis_, axis_) = 0.0;
  }
 
  void NgammaT::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 NgammaT::getVelScaleA(Vector3d& sc, const Vector3d& vel) {
    sc = vScale_ * vel;
  }
 
  void NgammaT::getVelScaleB(Vector3d& sc, int index) {
    sc = vScale_ * oldVel[index];
  }
 
  void NgammaT::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 NgammaT::scaleSimBox() {
    Mat3x3d scaleMat;
 
    scaleMat(axis1_, axis1_) = exp(dt * eta(axis1_, axis1_));
    scaleMat(axis2_, axis2_) = exp(dt * eta(axis2_, axis2_));
    scaleMat(axis_, axis_)   = exp(dt * eta(axis_, axis_));
    Mat3x3d hmat             = snap->getHmat();
    hmat                     = hmat * scaleMat;
    snap->setHmat(hmat);
  }
 
  bool NgammaT::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 NgammaT::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 totalEnergy = thermo.getTotalEnergy();
 
    RealType thermostat_kinetic = fkBT * tt2 * thermostat.first *
                                  thermostat.first /
                                  (2.0 * Constants::energyConvert);
 
    RealType thermostat_potential =
        fkBT * thermostat.second / Constants::energyConvert;
 
    SquareMatrix<RealType, 3> tmp = eta.transpose() * eta;
    RealType trEta                = tmp.trace();
 
    RealType barostat_kinetic =
        NkBT * tb2 * trEta / (2.0 * Constants::energyConvert);
 
    RealType barostat_potential =
        (targetPressure * thermo.getVolume() / Constants::pressureConvert) /
        Constants::energyConvert;
 
    Mat3x3d hmat  = snap->getHmat();
    RealType area = hmat(axis1_, axis1_) * hmat(axis2_, axis2_);
 
    RealType conservedQuantity =
        totalEnergy + thermostat_kinetic + thermostat_potential +
        barostat_kinetic + barostat_potential -
        surfaceTension_ * area / Constants::energyConvert;
 
    return conservedQuantity;
  }
 
  void NgammaT::loadEta() {
    eta = snap->getBarostat();
 
    // if (!eta.isDiagonal()) {
    //    snprintf( painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
    //             "NgammaT error: the diagonal elements of eta matrix are not
    //             the same or etaMat is not a diagonal matrix");
    //    painCave.isFatal = 1;
    //    simError();
    //}
  }
 
  void NgammaT::saveEta() { snap->setBarostat(eta); }
 
}  // namespace OpenMD