MultipoleAtomTypesSectionParser.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/MultipoleAtomTypesSectionParser.hpp"
 
#include "brains/ForceField.hpp"
#include "utils/Constants.hpp"
#include "utils/simError.h"
 
namespace OpenMD {
 
  MultipoleAtomTypesSectionParser::MultipoleAtomTypesSectionParser(
      ForceFieldOptions&) {
    setSectionName("MultipoleAtomTypes");
  }
 
  void MultipoleAtomTypesSectionParser::parseLine(ForceField& ff,
                                                  const std::string& line,
                                                  int lineNo) {
    StringTokenizer tokenizer(line);
    int nTokens = tokenizer.countTokens();
 
    // name multipole_type theta phi psi
    // "name" must match the name in the AtomTypes section
    //
    // avaliable multipole types are:
    // d  (dipole)
    // q  (quadrupole)
    // dq (dipole plus quadrupole)
    //
    // Directionality for dipoles and quadrupoles is given by three
    // euler angles (phi, theta, psi), because the body-fixed
    // reference frame for directional atoms is determined by the
    // *mass* distribution and not by the charge distribution.
    //
    // Dipoles are given in units of Debye
    // Quadrupoles are given in units of esu centibarn
    //
    // Examples:
    //
    // name d phi theta psi dipole_moment
    // name q phi theta psi Qxx Qyy Qzz
    // name dq phi theta psi dipole_moment Qxx Qyy Qzz
 
    if (nTokens < 5) {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "MultipoleAtomTypesSectionParser Error: Not enough tokens at "
               "line %d\n",
               lineNo);
      painCave.isFatal = 1;
      simError();
    } else {
      std::string atomTypeName  = tokenizer.nextToken();
      std::string multipoleType = tokenizer.nextToken();
      RealType phi   = tokenizer.nextTokenAsDouble() * Constants::PI / 180.0;
      RealType theta = tokenizer.nextTokenAsDouble() * Constants::PI / 180.0;
      RealType psi   = tokenizer.nextTokenAsDouble() * Constants::PI / 180.0;
 
      AtomType* atomType = ff.getAtomType(atomTypeName);
      if (atomType == NULL) {
        snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
                 "MultipoleAtomTypesSectionParser Error: Can not find matched "
                 "AtomType[%s] "
                 "at line %d\n",
                 atomTypeName.c_str(), lineNo);
        painCave.isFatal = 1;
        simError();
      }
 
      MultipoleAdapter ma = MultipoleAdapter(atomType);
 
      RotMat3x3d eFrame(0.0);
 
      eFrame.setupRotMat(phi, theta, psi);
 
      RealType dipoleMoment(0);
      Vector3d dipole(V3Zero);
      Vector3d quadrupoleMoments(V3Zero);
      Mat3x3d quadrupole(0.0);
 
      bool isDipole(false);
      bool isQuadrupole(false);
 
      if (multipoleType == "d") {
        parseDipole(tokenizer, dipoleMoment, lineNo);
        isDipole = true;
      } else if (multipoleType == "s") {
        snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
                 "MultipoleAtomTypesSectionParser Error: \n"
                 "\tsplit dipoles (type s) have been deprecated (line: %d)\n",
                 lineNo);
        painCave.isFatal = 1;
        simError();
      } else if (multipoleType == "q") {
        parseQuadrupole(tokenizer, quadrupoleMoments, lineNo);
        isQuadrupole = true;
      } else if (multipoleType == "dq") {
        parseDipole(tokenizer, dipoleMoment, lineNo);
        isDipole = true;
        parseQuadrupole(tokenizer, quadrupoleMoments, lineNo);
        isQuadrupole = true;
      } else if (multipoleType == "sq") {
        snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
                 "MultipoleAtomTypesSectionParser Error: \n"
                 "\tsplit dipole quadrupoles (type sq) have been deprecated "
                 "(line: %d)\n",
                 lineNo);
        painCave.isFatal = 1;
        simError();
      } else {
        snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
                 "MultipoleAtomTypesSectionParser Error: unrecognized multiple "
                 "type at line "
                 "%d\n",
                 lineNo);
        painCave.isFatal = 1;
        simError();
      }
      if (isDipole) dipole = dipoleMoment * eFrame.transpose() * V3Z;
      if (isQuadrupole) {
        quadrupole(0, 0) = quadrupoleMoments(0);
        quadrupole(1, 1) = quadrupoleMoments(1);
        quadrupole(2, 2) = quadrupoleMoments(2);
        quadrupole       = eFrame.transpose() * quadrupole * eFrame;
      }
 
      ma.makeMultipole(dipole, quadrupole, isDipole, isQuadrupole);
    }
  }
 
  void MultipoleAtomTypesSectionParser::parseDipole(StringTokenizer& tokenizer,
                                                    RealType& dipoleMoment,
                                                    int lineNo) {
    if (tokenizer.hasMoreTokens()) {
      dipoleMoment = tokenizer.nextTokenAsDouble();
    } else {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "MultipoleAtomTypesSectionParser Error: Not enough tokens at "
               "line %d\n",
               lineNo);
      painCave.isFatal = 1;
      simError();
    }
  }
 
  void MultipoleAtomTypesSectionParser::parseQuadrupole(
      StringTokenizer& tokenizer, Vector3d& quadrupoleMoments, int lineNo) {
    int nTokens = tokenizer.countTokens();
    if (nTokens >= 3) {
      quadrupoleMoments[0] = tokenizer.nextTokenAsDouble();
      quadrupoleMoments[1] = tokenizer.nextTokenAsDouble();
      quadrupoleMoments[2] = tokenizer.nextTokenAsDouble();
 
      // RealType trace =  quadrupoleMoments.sum();
      //
      // if (fabs(trace) > OpenMD::epsilon) {
      //   snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
      //   "MultipoleAtomTypesSectionParser Error: the trace of quadrupole
      //   moments is not zero at line %d\n",   lineNo); painCave.isFatal = 1;
      //   simError();
      // }
 
    } else {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "MultipoleAtomTypesSectionParser Error: Not enough tokens at "
               "line %d\n",
               lineNo);
      painCave.isFatal = 1;
      simError();
    }
  }
}  // namespace OpenMD