AtomTypesSectionParser.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 "io/AtomTypesSectionParser.hpp"
 
#include "brains/ForceField.hpp"
#include "types/AtomType.hpp"
#include "utils/simError.h"
 
namespace OpenMD {
 
  AtomTypesSectionParser::AtomTypesSectionParser() {
    setSectionName("AtomTypes");
  }
 
  void AtomTypesSectionParser::parseLine(ForceField& ff,
                                         const std::string& line, int lineNo) {
    StringTokenizer tokenizer(line);
    int nTokens = tokenizer.countTokens();
 
    // in AtomTypeSection, a line at least contains 2 tokens
    // atomTypeName and mass
    if (nTokens < 2) {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "AtomTypesSectionParser Error: Not enough tokens at line %d\n",
               lineNo);
      painCave.isFatal = 1;
      simError();
 
    } else {
      std::string atomTypeName     = tokenizer.nextToken();
      std::string baseAtomTypeName = tokenizer.nextToken();
 
      AtomType* baseAtomType =
          dynamic_cast<AtomType*>(ff.getAtomType(baseAtomTypeName));
 
      if (baseAtomType == NULL) {
        snprintf(
            painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
            "AtomTypesSectionParser Error: Could not find matching base atom "
            "type to "
            "%s at line %d\n",
            baseAtomTypeName.c_str(), lineNo);
        painCave.isFatal = 1;
        simError();
      }
 
      AtomType* atomType = ff.getAtomType(atomTypeName);
 
      if (atomType == NULL) {
        atomType = new AtomType();
        atomType->useBase(baseAtomType);
        int ident = ff.getNAtomType();
        atomType->setIdent(ident);
        atomType->setName(atomTypeName);
        ff.addAtomType(atomTypeName, atomType);
      } else {
        std::cerr << "duplicate atom type: " << atomTypeName << " on line "
                  << lineNo << "\n";
      }
 
      if (tokenizer.hasMoreTokens()) {
        RealType mass = tokenizer.nextTokenAsDouble();
        atomType->setMass(mass);
      }
    }
  }
 
}  // namespace OpenMD