BondTypesSectionParser.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/BondTypesSectionParser.hpp"
 
#include "brains/ForceField.hpp"
#include "types/BondTypeParser.hpp"
#include "utils/simError.h"
 
namespace OpenMD {
 
  BondTypesSectionParser::BondTypesSectionParser(ForceFieldOptions& options) :
      options_(options) {
    setSectionName("BondTypes");
  }
 
  void BondTypesSectionParser::parseLine(ForceField& ff,
                                         const std::string& line, int lineNo) {
    StringTokenizer tokenizer(line);
    BondTypeParser btParser;
    BondType* bondType = NULL;
    int nTokens        = tokenizer.countTokens();
 
    if (nTokens < 4) {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "BondTypesSectionParser Error: Not enough tokens at line %d\n",
               lineNo);
      painCave.isFatal = 1;
      simError();
    }
 
    std::string at1       = tokenizer.nextToken();
    std::string at2       = tokenizer.nextToken();
    std::string remainder = tokenizer.getRemainingString();
    RealType kScale       = options_.getBondForceConstantScaling();
 
    try {
      bondType = btParser.parseLine(remainder, kScale);
    } catch (OpenMDException& e) {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "BondTypesSectionParser Error: %s "
               "at line %d\n",
               e.what(), lineNo);
      painCave.isFatal = 1;
      simError();
    }
 
    if (bondType != NULL) { ff.addBondType(at1, at2, bondType); }
  }
}  // namespace OpenMD