NPTxyz.cpp

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 * 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/NPTxyz.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"
 
// Basic non-isotropic thermostating and barostating via the Melchionna
// modification of the Hoover algorithm:
//
//    Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
//       Molec. Phys., 78, 533.
//
//           and
//
//    Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
 
namespace OpenMD {
 
  RealType NPTxyz::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 NPTxyz::scaleSimBox() {
    int i, j;
    Mat3x3d scaleMat;
    RealType scaleFactor;
    RealType bigScale, smallScale;
    Mat3x3d hm;
    Mat3x3d hmnew;
 
    // Scale the box after all the positions have been moved:
 
    // Use a taylor expansion for eta products:  Hmat = Hmat . exp(dt * etaMat)
    //  Hmat = Hmat . ( Ident + dt * etaMat  + dt^2 * etaMat*etaMat / 2)
 
    bigScale   = 1.0;
    smallScale = 1.0;
 
    for (i = 0; i < 3; i++) {
      for (j = 0; j < 3; j++) {
        scaleMat(i, j) = 0.0;
        if (i == j) { scaleMat(i, j) = 1.0; }
      }
    }
 
    for (i = 0; i < 3; i++) {
      // calculate the scaleFactors
 
      scaleFactor = exp(dt * eta(i, i));
 
      scaleMat(i, i) = scaleFactor;
 
      if (scaleMat(i, i) > bigScale) { bigScale = scaleMat(i, i); }
 
      if (scaleMat(i, i) < smallScale) { smallScale = scaleMat(i, i); }
    }
 
    if ((bigScale > 1.1) || (smallScale < 0.9)) {
      snprintf(
          painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
          "NPTxyz error: Attempting a Box scaling of more than 10 percent.\n"
          " Check your tauBarostat, as it is probably too small!\n\n"
          " scaleMat = [%lf\t%lf\t%lf]\n"
          "            [%lf\t%lf\t%lf]\n"
          "            [%lf\t%lf\t%lf]\n",
          scaleMat(0, 0), scaleMat(0, 1), scaleMat(0, 2), scaleMat(1, 0),
          scaleMat(1, 1), scaleMat(1, 2), scaleMat(2, 0), scaleMat(2, 1),
          scaleMat(2, 2));
      painCave.isFatal = 1;
      simError();
    } else {
      Mat3x3d hmat = snap->getHmat();
      hmat         = hmat * scaleMat;
      snap->setHmat(hmat);
    }
  }
 
  void NPTxyz::loadEta() { eta = snap->getBarostat(); }
 
}  // namespace OpenMD