UFFAtomTypesSectionParser.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/UFFAtomTypesSectionParser.hpp"
 
#include "brains/ForceField.hpp"
#include "types/UFFAdapter.hpp"
#include "utils/simError.h"
 
namespace OpenMD {
 
  UFFAtomTypesSectionParser::UFFAtomTypesSectionParser(
      ForceFieldOptions& options) :
      options_(options) {
    setSectionName("UFFAtomTypes");
  }
 
  void UFFAtomTypesSectionParser::parseLine(ForceField& ff,
                                            const std::string& line,
                                            int lineNo) {
    StringTokenizer tokenizer(line);
    int nTokens = tokenizer.countTokens();
 
    // in UFFAtomTypesSectionParser, a line at least contains 12 tokens:
    // Atom r1 theta0 x1 D1 zeta Z1 Vi Uj Xi Hard Radius
 
    if (nTokens < 12) {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "UFFAtomTypesSectionParser 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) {
        UFFAdapter uffa = UFFAdapter(atomType);
 
        RealType r1     = tokenizer.nextTokenAsDouble();
        RealType theta0 = tokenizer.nextTokenAsDouble();
        RealType x1     = tokenizer.nextTokenAsDouble();
        RealType D1     = tokenizer.nextTokenAsDouble();
        RealType zeta   = tokenizer.nextTokenAsDouble();
        RealType Z1     = tokenizer.nextTokenAsDouble();
        RealType Vi     = tokenizer.nextTokenAsDouble();
        RealType Uj     = tokenizer.nextTokenAsDouble();
        RealType Xi     = tokenizer.nextTokenAsDouble();
        RealType Hard   = tokenizer.nextTokenAsDouble();
        RealType Radius = tokenizer.nextTokenAsDouble();
 
        r1 *= options_.getDistanceUnitScaling();
        theta0 *= options_.getAngleUnitScaling();
        x1 *= options_.getDistanceUnitScaling();
        D1 *= options_.getEnergyUnitScaling();
        Z1 *= options_.getChargeUnitScaling();
        Vi *= options_.getEnergyUnitScaling();
        Uj *= options_.getEnergyUnitScaling();
 
        uffa.makeUFF(r1, theta0, x1, D1, zeta, Z1, Vi, Uj, Xi, Hard, Radius);
 
      } else {
        snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
                 "UFFAtomTypesSectionParser Error: Atom Type [%s]"
                 " has not been created yet\n",
                 atomTypeName.c_str());
        painCave.isFatal = 1;
        simError();
      }
    }
  }
 
  void UFFAtomTypesSectionParser::validateSection(ForceField&) {
    // ForceField::AtomTypeContainer* atomTypes = ff.getAtomTypes();
    // ForceField::AtomTypeContainer::MapTypeIterator i;
    // AtomType* at;
 
    // std::vector<AtomType*> uffTypes;
 
    // for (at = atomTypes->beginType(i); at != NULL; at =
    // atomTypes->nextType(i))
    // {
 
    //   UFFAdapter uffa = UFFAdapter(at);
    //   if (uffa.isUFF())
    //     uffTypes.push_back(at);
    // }
 
    // for (std::size_t i = 0; i < uffTypes.size(); ++i) {
    //   RealType ri = uffTypes[i]->getR1();
    //   RealType chiI = uffTypes[i]->getXi();
    //   RealType Ra = uffTypes[i]->getX1();
    //   RealType ka = uffTypes[i]->getD1();
 
    //   for (std::size_t j = 0; j < uffTypes.size(); ++j) {
    //     RealType rj = uffTypes[j]->getR1();
    //     RealType chiJ = uffTypes[j]->getXi();
    //     RealType Rb = uffTypes[j]->getX1();
    //     RealType kb = uffTypes[j]->getD1();
 
    //     // Precompute the equilibrium bond distance
    //     // From equation 3
    //     rbo = -0.1332*(ri+rj)*log(bondorder);
    //     // From equation 4
    //     ren = ri*rj*(pow((sqrt(chiI) - sqrt(chiJ)),2.0)) / (chiI*ri +
    //     chiJ*rj);
    //     // From equation 2
    //     // NOTE: See http://towhee.sourceforge.net/forcefields/uff.html
    //     // There is a typo in the published paper
    //     rij = ri + rj + rbo - ren;
 
    //     kab = sqrt(ka * kb);
 
    //     // ka now represents the xij in equation 20 -- the expected vdw
    //     distance kaSquared = (Ra * Rb); ka = sqrt(kaSquared);
  }
}  // namespace OpenMD