thermalizer.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 <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include <fstream>
#include <iostream>
#include <map>
#include <memory>
#include <string>
 
#include "brains/ForceManager.hpp"
#include "brains/Register.hpp"
#include "brains/SimCreator.hpp"
#include "brains/SimInfo.hpp"
#include "brains/Thermo.hpp"
#include "brains/Velocitizer.hpp"
#include "io/DumpReader.hpp"
#include "io/DumpWriter.hpp"
#include "thermalizerCmd.hpp"
#include "utils/StringUtils.hpp"
 
using namespace OpenMD;
 
int main(int argc, char* argv[]) {
  gengetopt_args_info args_info;
  std::string inputFileName;
  std::string outputFileName;
 
  // parse command line arguments
  if (cmdline_parser(argc, argv, &args_info) != 0) {
    cmdline_parser_print_help();
    exit(1);
  }
 
  // get input file name
  if (args_info.input_given) {
    inputFileName = args_info.input_arg;
  } else {
    if (args_info.inputs_num) {
      inputFileName = args_info.inputs[0];
    } else {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "No input file name was specified on the command line");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal  = 1;
      simError();
    }
  }
 
  // get output file name
  outputFileName = args_info.output_arg;
 
  if (!outputFileName.compare(inputFileName)) {
    snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
             "Input and Output File names should be different!");
    painCave.severity = OPENMD_ERROR;
    painCave.isFatal  = 1;
    simError();
  }
 
  // Parse the input file, set up the system, and read the last frame:
  SimCreator creator;
  SimInfo* info = creator.createSim(inputFileName, true);
  // communicate velocity information onto the atoms:
  info->update();
 
  // Important utility classes for computing system properties:
  Thermo thermo(info);
 
  std::unique_ptr<Velocitizer> veloSet {std::make_unique<Velocitizer>(info)};
 
  ForceManager* forceMan = new ForceManager(info);
 
  // Just in case we were passed a system that is on the move:
  veloSet->removeComDrift();
  forceMan->calcForces();
 
  RealType instPE = thermo.getPotential();
  RealType instKE = thermo.getKinetic();
 
  // Now that we have the information from the current frame, advance
  // the snapshot to make a modified frame:
  info->getSnapshotManager()->advance();
 
  // Create DumpWriter to hold the modified frame:
  DumpWriter* writer = new DumpWriter(info, outputFileName);
  if (writer == NULL) {
    snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
             "error in creating DumpWriter");
    painCave.severity = OPENMD_ERROR;
    painCave.isFatal  = 1;
    simError();
  }
 
  // If resampling temperature, we call the randomizer method:
  if (args_info.temperature_given) {
    RealType temperature = args_info.temperature_arg;
 
    if (temperature < 0.0) {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "Temperatures must be positive numbers.");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal  = 1;
      simError();
    }
 
    veloSet->randomize(temperature);
  }
 
  // If resampling charge temperature, we call the randomizeChargeVelocity
  // method
  if (args_info.chargetemperature_given) {
    RealType charge_temperature = args_info.chargetemperature_arg;
 
    if (charge_temperature < 0.0) {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "Temperatures must be positive numbers.");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal  = 1;
      simError();
    }
 
    veloSet->randomizeChargeVelocity(charge_temperature);
  }
 
  // If scaling total energy, scale only the kinetic:
  if (args_info.energy_given) {
    RealType energy  = args_info.energy_arg;
    RealType epsilon = 1e-6;
    RealType lambda  = 0.0;
 
    if (energy < instPE) {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "Energy must be larger than current potential energy.");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal  = 1;
      simError();
    } else {
      if (instKE >= epsilon) {
        lambda = sqrt((energy - instPE) / instKE);
        veloSet->scale(lambda);
      }
      // If the current kinetic energy is close to zero, we will
      // sample velocities from a 10K distribution and then
      // subsequently scale from 10K to the desired energy.
      else {
        veloSet->randomize(10.0);
        instKE = thermo.getKinetic();
        lambda = sqrt((energy - instPE) / instKE);
        veloSet->scale(lambda);
      }
    }
  }
 
  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;
}