DirectionalAtomTypesSectionParser.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/DirectionalAtomTypesSectionParser.hpp"
 
#include "brains/ForceField.hpp"
#include "types/DirectionalAdapter.hpp"
#include "utils/simError.h"
 
namespace OpenMD {
 
  DirectionalAtomTypesSectionParser::DirectionalAtomTypesSectionParser(
      ForceFieldOptions&) {
    setSectionName("DirectionalAtomTypes");
  }
 
  void DirectionalAtomTypesSectionParser::parseLine(ForceField& ff,
                                                    const std::string& line,
                                                    int lineNo) {
    StringTokenizer tokenizer(line);
    int nTokens = tokenizer.countTokens();
 
    // in DirectionalAtomTypeSection, a line contains 4 tokens
 
    if (nTokens < 4) {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "DirectionalAtomTypesSectionParser 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) {
        snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
                 "DirectionalAtomTypesSectionParser:: AtomType %s was not\n"
                 "\tdeclared in the BaseAtomTypes or AtomTypes before being\n"
                 "\tdeclared as a DirectionalAtomType!\n",
                 atomTypeName.c_str());
        painCave.isFatal = 1;
        simError();
      }
 
      DirectionalAdapter da = DirectionalAdapter(atomType);
      Mat3x3d I;
 
      I(0, 0) = tokenizer.nextTokenAsDouble();
      I(1, 1) = tokenizer.nextTokenAsDouble();
      I(2, 2) = tokenizer.nextTokenAsDouble();
 
      da.makeDirectional(I);
    }
  }
}  // namespace OpenMD