SCDOrderParameter.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 "applications/staticProps/SCDOrderParameter.hpp"
 
#include <string>
#include <tuple>
#include <vector>
 
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/simError.h"
 
namespace OpenMD {
 
  SCDElem::SCDElem(SimInfo* info, const std::string& sele1,
                   const std::string& sele2, const std::string& sele3) :
      sele1_(sele1),
      sele2_(sele2), sele3_(sele3) {
    usePeriodicBoundaryConditions_ =
        info->getSimParams()->getUsePeriodicBoundaryConditions();
 
    SelectionManager seleMan1_(info);
    SelectionManager seleMan2_(info);
    SelectionManager seleMan3_(info);
    SelectionEvaluator evaluator1_(info);
    SelectionEvaluator evaluator2_(info);
    SelectionEvaluator evaluator3_(info);
 
    evaluator1_.loadScriptString(sele1_);
    evaluator2_.loadScriptString(sele2_);
    evaluator3_.loadScriptString(sele3_);
 
    if (!evaluator1_.isDynamic()) {
      seleMan1_.setSelectionSet(evaluator1_.evaluate());
    } else {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "dynamic selection is not allowed\n");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal  = 1;
      simError();
    }
 
    if (!evaluator2_.isDynamic()) {
      seleMan2_.setSelectionSet(evaluator2_.evaluate());
    } else {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "dynamic selection is not allowed\n");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal  = 1;
      simError();
    }
 
    if (!evaluator3_.isDynamic()) {
      seleMan3_.setSelectionSet(evaluator3_.evaluate());
    } else {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "dynamic selection is not allowed\n");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal  = 1;
      simError();
    }
 
    int nselected1 = seleMan1_.getSelectionCount();
    int nselected2 = seleMan2_.getSelectionCount();
    int nselected3 = seleMan3_.getSelectionCount();
 
    if (nselected1 != nselected2 || nselected1 != nselected3) {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "The number of selected Stuntdoubles must be the same\n");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal  = 1;
      simError();
    }
 
    int i;
    int j;
    int k;
    StuntDouble* sd1;
    StuntDouble* sd2;
    StuntDouble* sd3;
    for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan2_.beginSelected(j),
        sd3 = seleMan3_.beginSelected(k);
         sd1 != NULL && sd2 != NULL && sd3 != NULL;
         sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j),
        sd3 = seleMan3_.nextSelected(k)) {
      tuples_.push_back(std::make_tuple(sd1, sd2, sd3));
    }
  }
 
  RealType SCDElem::calcSCD(Snapshot* snapshot) {
    Vector3d normal(0.0, 0.0, 1.0);
    RealType scd = 0.0;
 
    for (auto& [first, second, third] : tuples_) {
      // Egberts B. and Berendsen H.J.C, J.Chem.Phys. 89(6), 3718-3732, 1988
      Vector3d zAxis = third->getPos() - first->getPos();
      if (usePeriodicBoundaryConditions_) snapshot->wrapVector(zAxis);
      Vector3d v12 = second->getPos() - first->getPos();
      if (usePeriodicBoundaryConditions_) snapshot->wrapVector(v12);
      Vector3d xAxis = cross(v12, zAxis);
      Vector3d yAxis = cross(zAxis, xAxis);
 
      xAxis.normalize();
      yAxis.normalize();
      zAxis.normalize();
      RealType cosThetaX = dot(xAxis, normal);
      RealType sxx       = 0.5 * (3 * cosThetaX * cosThetaX - 1.0);
      RealType cosThetaY = dot(yAxis, normal);
      RealType syy       = 0.5 * (3 * cosThetaY * cosThetaY - 1.0);
      scd += 2.0 / 3.0 * sxx + 1.0 / 3.0 * syy;
    }
 
    scd /= tuples_.size();
 
    return scd;
  }
 
  SCDOrderParameter::SCDOrderParameter(SimInfo* info,
                                       const std::string& filename,
                                       const std::string& sele1,
                                       const std::string& sele2,
                                       const std::string& sele3) :
      StaticAnalyser(info, filename, 1) {
    setOutputName(getPrefix(filename) + ".scd");
 
    scdElems_.push_back(SCDElem(info, sele1, sele2, sele3));
    scdParam_.resize(scdElems_.size());
    std::fill(scdParam_.begin(), scdParam_.end(), 0.0);
  }
 
  SCDOrderParameter::SCDOrderParameter(SimInfo* info,
                                       const std::string& filename,
                                       const std::string& molname,
                                       int beginIndex, int endIndex) :
      StaticAnalyser(info, filename, 1) {
    setOutputName(getPrefix(filename) + ".scd");
 
    assert(beginIndex >= 0 && endIndex >= 0 && beginIndex <= endIndex - 2);
    for (int i = beginIndex; i <= endIndex - 2; ++i) {
      std::string selectionTemplate = "select " + molname + ".";
      std::string sele1             = selectionTemplate + OpenMD_itoa(i);
      std::string sele2             = selectionTemplate + OpenMD_itoa(i + 1);
      std::string sele3             = selectionTemplate + OpenMD_itoa(i + 2);
 
      scdElems_.push_back(SCDElem(info, sele1, sele2, sele3));
    }
 
    scdParam_.resize(scdElems_.size());
    std::fill(scdParam_.begin(), scdParam_.end(), 0.0);
  }
 
  void SCDOrderParameter::process() {
    DumpReader reader(info_, dumpFilename_);
    int nFrames = reader.getNFrames();
 
    for (int i = 0; i < nFrames; i += step_) {
      reader.readFrame(i);
      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
 
      for (std::size_t j = 0; j < scdElems_.size(); ++j) {
        scdParam_[j] += scdElems_[j].calcSCD(currentSnapshot_);
      }
    }
 
    int nProcessed = nFrames / step_;
    for (std::size_t j = 0; j < scdElems_.size(); ++j) {
      scdParam_[j] /= nProcessed;
    }
 
    writeSCD();
  }
 
  void SCDOrderParameter::writeSCD() {
    std::ofstream os(getOutputFileName().c_str());
    os << "#scd parameter\n";
    for (std::size_t i = 0; i < scdElems_.size(); ++i) {
      os << "#[column " << i + 1 << "]\t"
         << "sele1: \"" << scdElems_[i].getSelection1() << "\",\t"
         << "sele2: \"" << scdElems_[i].getSelection2() << "\",\t"
         << "sele3: \"" << scdElems_[i].getSelection3() << "\"\n";
    }
 
    for (std::size_t i = 0; i < scdElems_.size(); ++i) {
      os << scdParam_[i] << "\t";
    }
    os << std::endl;
  }
 
}  // namespace OpenMD