StickyAtomTypesSectionParser.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/StickyAtomTypesSectionParser.hpp"
 
#include "brains/ForceField.hpp"
#include "types/StickyAdapter.hpp"
#include "utils/simError.h"
using namespace std;
namespace OpenMD {
 
  StickyAtomTypesSectionParser::StickyAtomTypesSectionParser(
      ForceFieldOptions& options) :
      options_(options) {
    setSectionName("StickyAtomTypes");
  }
 
  void StickyAtomTypesSectionParser::parseLine(ForceField& ff,
                                               const string& line, int lineNo) {
    StringTokenizer tokenizer(line);
    int nTokens  = tokenizer.countTokens();
    RealType dus = options_.getDistanceUnitScaling();
    RealType eus = options_.getEnergyUnitScaling();
 
    // in AtomTypeSection, a line at least contains 8 tokens
    // atomTypeName and 7 different sticky parameters
    if (nTokens < 8) {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "StickyAtomTypesSectionParser Error: Not enough "
               "tokens at line %d\n",
               lineNo);
      painCave.isFatal = 1;
      simError();
    } else {
      string atomTypeName = tokenizer.nextToken();
      AtomType* atomType  = ff.getAtomType(atomTypeName);
 
      if (atomType != NULL) {
        StickyAdapter sa = StickyAdapter(atomType);
 
        RealType w0  = tokenizer.nextTokenAsDouble();
        RealType v0  = eus * tokenizer.nextTokenAsDouble();
        RealType v0p = eus * tokenizer.nextTokenAsDouble();
        RealType rl  = dus * tokenizer.nextTokenAsDouble();
        RealType ru  = dus * tokenizer.nextTokenAsDouble();
        RealType rlp = dus * tokenizer.nextTokenAsDouble();
        RealType rup = dus * tokenizer.nextTokenAsDouble();
        bool isPower = false;
 
        sa.makeSticky(w0, v0, v0p, rl, ru, rlp, rup, isPower);
 
      } else {
        snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
                 "StickyAtomTypesSectionParser Error: "
                 "Can not find matching AtomType %s\n",
                 atomTypeName.c_str());
        painCave.isFatal = 1;
        simError();
      }
    }
  }
}  // namespace OpenMD