simpleBuilder.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 <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include <fstream>
#include <iostream>
#include <map>
#include <string>
 
#include "brains/Register.hpp"
#include "brains/SimCreator.hpp"
#include "brains/SimInfo.hpp"
#include "io/DumpWriter.hpp"
#include "lattice/Lattice.hpp"
#include "lattice/LatticeFactory.hpp"
#include "math/SquareMatrix3.hpp"
#include "math/Vector3.hpp"
#include "simpleBuilderCmd.hpp"
#include "utils/MoLocator.hpp"
#include "utils/StringUtils.hpp"
 
using namespace std;
using namespace OpenMD;
 
void createMdFile(const std::string& oldMdFileName,
                  const std::string& newMdFileName, int nMol);
 
int main(int argc, char* argv[]) {
  registerLattice();
 
  gengetopt_args_info args_info;
  std::string latticeType;
  std::string inputFileName;
  std::string outputFileName;
  Lattice* simpleLat;
  RealType latticeConstant;
  std::vector<RealType> lc;
  const RealType rhoConvertConst = 1.66053886;
  RealType density;
  int nx, ny, nz;
  Mat3x3d hmat;
  MoLocator* locator;
  std::vector<Vector3d> latticePos;
  std::vector<Vector3d> latticeOrt;
  int nMolPerCell;
  DumpWriter* writer;
 
  // parse command line arguments
  if (cmdline_parser(argc, argv, &args_info) != 0) exit(1);
 
  density = args_info.density_arg;
 
  // get lattice type
  latticeType = "FCC";
  if (args_info.lattice_given) { latticeType = args_info.lattice_arg; }
 
  simpleLat = LatticeFactory::getInstance().createLattice(latticeType);
 
  if (simpleLat == NULL) {
    snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
             "Lattice Factory can not create %s lattice\n",
             latticeType.c_str());
    painCave.isFatal = 1;
    simError();
  }
  nMolPerCell = simpleLat->getNumSitesPerCell();
 
  // get the number of unit cells in each direction:
 
  nx = args_info.nx_arg;
 
  if (nx <= 0) {
    snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
             "The number of unit cells in the x direction "
             "must be greater than 0.");
    painCave.isFatal = 1;
    simError();
  }
 
  ny = args_info.ny_arg;
 
  if (ny <= 0) {
    snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
             "The number of unit cells in the y direction "
             "must be greater than 0.");
    painCave.isFatal = 1;
    simError();
  }
 
  nz = args_info.nz_arg;
 
  if (nz <= 0) {
    snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
             "The number of unit cells in the z direction "
             "must be greater than 0.");
    painCave.isFatal = 1;
    simError();
  }
 
  int nSites = nMolPerCell * nx * ny * nz;
 
  // get input file name
  if (args_info.inputs_num)
    inputFileName = args_info.inputs[0];
  else {
    snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
             "No input .omd file name was specified "
             "on the command line");
    painCave.isFatal = 1;
    simError();
  }
 
  // parse md file and set up the system
 
  SimCreator oldCreator;
  SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
 
  // Calculate lattice constant (in Angstroms)
 
  RealType avgMass = MoLocator::getMolMass(oldInfo->getMoleculeStamp(0),
                                           oldInfo->getForceField());
 
  latticeConstant = pow(rhoConvertConst * nMolPerCell * avgMass / density,
                        (RealType)(1.0 / 3.0));
 
  // Set the lattice constant
 
  lc.push_back(latticeConstant);
  simpleLat->setLatticeConstant(lc);
 
  // Calculate the lattice sites and fill the lattice vector.
 
  // Get the standard orientations of the cell sites
 
  latticeOrt = simpleLat->getLatticePointsOrt();
 
  vector<Vector3d> sites;
  vector<Vector3d> orientations;
 
  for (int i = 0; i < nx; i++) {
    for (int j = 0; j < ny; j++) {
      for (int k = 0; k < nz; k++) {
        // Get the position of the cell sites
 
        simpleLat->getLatticePointsPos(latticePos, i, j, k);
 
        for (int l = 0; l < nMolPerCell; l++) {
          sites.push_back(latticePos[l]);
          orientations.push_back(latticeOrt[l]);
        }
      }
    }
  }
 
  outputFileName = args_info.output_arg;
 
  // create a new .omd file on the fly which corrects the number of molecules
 
  createMdFile(inputFileName, outputFileName, nSites);
 
  delete oldInfo;
 
  // We need to read in the new SimInfo object, then Parse the
  // md file and set up the system
 
  SimCreator newCreator;
  SimInfo* newInfo = newCreator.createSim(outputFileName, false);
 
  // fill Hmat
 
  hmat(0, 0) = nx * latticeConstant;
  hmat(0, 1) = 0.0;
  hmat(0, 2) = 0.0;
 
  hmat(1, 0) = 0.0;
  hmat(1, 1) = ny * latticeConstant;
  hmat(1, 2) = 0.0;
 
  hmat(2, 0) = 0.0;
  hmat(2, 1) = 0.0;
  hmat(2, 2) = nz * latticeConstant;
 
  // Set Hmat
 
  newInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
 
  // place the molecules
 
  Molecule* mol;
  locator =
      new MoLocator(newInfo->getMoleculeStamp(0), newInfo->getForceField());
  for (int n = 0; n < nSites; n++) {
    mol = newInfo->getMoleculeByGlobalIndex(n);
    locator->placeMol(sites[n], orientations[n], mol);
  }
 
  // Create DumpWriter and write out the coordinates
 
  writer = new DumpWriter(newInfo, outputFileName);
 
  if (writer == NULL) {
    snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
             "error in creating DumpWriter");
    painCave.isFatal = 1;
    simError();
  }
 
  writer->writeDump();
 
  // deleting the writer will put the closing at the end of the dump file.
 
  delete writer;
 
  snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
           "A new OpenMD file called \"%s\" has been generated.\n",
           outputFileName.c_str());
  painCave.isFatal  = 0;
  painCave.severity = OPENMD_INFO;
  simError();
  return 0;
}
 
void createMdFile(const std::string& oldMdFileName,
                  const std::string& newMdFileName, int nMol) {
  ifstream oldMdFile;
  ofstream newMdFile;
  const int MAXLEN = 65535;
  char buffer[MAXLEN];
 
  // create new .omd file based on old .omd file
  oldMdFile.open(oldMdFileName.c_str());
  newMdFile.open(newMdFileName.c_str());
 
  oldMdFile.getline(buffer, MAXLEN);
 
  while (!oldMdFile.eof()) {
    // correct molecule number
    if (strstr(buffer, "nMol") != NULL) {
      snprintf(buffer, MAXLEN, "\t\tnMol = %d;", nMol);
      newMdFile << buffer << std::endl;
    } else
      newMdFile << buffer << std::endl;
 
    oldMdFile.getline(buffer, MAXLEN);
  }
 
  oldMdFile.close();
  newMdFile.close();
}