LennardJonesAtomTypesSectionParser.cpp

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 * 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/LennardJonesAtomTypesSectionParser.hpp"
 
#include "brains/ForceField.hpp"
#include "io/ForceFieldOptions.hpp"
#include "types/LennardJonesAdapter.hpp"
#include "utils/simError.h"
 
namespace OpenMD {
 
  LennardJonesAtomTypesSectionParser::LennardJonesAtomTypesSectionParser(
      ForceFieldOptions& options) :
      options_(options) {
    setSectionName("LennardJonesAtomTypes");
  }
 
  void LennardJonesAtomTypesSectionParser::parseLine(ForceField& ff,
                                                     const std::string& line,
                                                     int lineNo) {
    StringTokenizer tokenizer(line);
    int nTokens = tokenizer.countTokens();
 
    // in LennardJonesAtomTypesSectionParser, a line at least contains 3 tokens
    // atomTypeName, epsilon and sigma
    if (nTokens < 3) {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "LennardJonesAtomTypesSectionParser Error: Not enough tokens at "
               "line %d\n",
               lineNo);
      painCave.isFatal = 1;
      simError();
    } else {
      std::string atomTypeName = tokenizer.nextToken();
      AtomType* atomType       = ff.getAtomType(atomTypeName);
 
      if (atomType != NULL) {
        RealType epsilon = tokenizer.nextTokenAsDouble();
        RealType sigma   = tokenizer.nextTokenAsDouble();
        bool isSoft      = false;
 
        epsilon *= options_.getEnergyUnitScaling();
        sigma *= options_.getDistanceUnitScaling();
 
        if (tokenizer.hasMoreTokens()) {
          std::string pot_type = tokenizer.nextToken();
          if (pot_type == "soft") { isSoft = true; }
        }
 
        LennardJonesAdapter lj = LennardJonesAdapter(atomType);
        lj.makeLennardJones(sigma, epsilon, isSoft);
 
      } else {
        snprintf(
            painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
            "LennardJonesAtomTypesSectionParser Error: Atom Type [%s] is not "
            "created yet\n",
            atomTypeName.c_str());
        painCave.isFatal = 1;
        simError();
      }
    }
  }
 
}  // namespace OpenMD