TetrahedralityParamXYZ.cpp

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 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the following paper when you publish your work:
 *
 * [1] Drisko et al., J. Open Source Softw. 9, 7004 (2024).
 *
 * Good starting points for code and simulation methodology are:
 *
 * [2] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
 * [3] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
 * [4] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
 * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 * [7] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
 * [9] Drisko & Gezelter, J. Chem. Theory Comput. 20, 4986-4997 (2024).
 */
 
#include "applications/staticProps/TetrahedralityParamXYZ.hpp"
 
#include <algorithm>
#include <fstream>
#include <vector>
 
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/Constants.hpp"
#include "utils/simError.h"
 
using namespace std;
namespace OpenMD {
  TetrahedralityParamXYZ::TetrahedralityParamXYZ(
      SimInfo* info, const std::string& filename, const std::string& sele1,
      const std::string& sele2, RealType rCut, RealType voxelSize,
      RealType gaussWidth) :
      StaticAnalyser(info, filename, 1),
      selectionScript1_(sele1), selectionScript2_(sele2), seleMan1_(info),
      seleMan2_(info), evaluator1_(info), evaluator2_(info), rCut_(rCut),
      voxelSize_(voxelSize), gaussWidth_(gaussWidth) {
    evaluator1_.loadScriptString(sele1);
    if (!evaluator1_.isDynamic()) {
      seleMan1_.setSelectionSet(evaluator1_.evaluate());
    }
    evaluator2_.loadScriptString(sele2);
    if (!evaluator2_.isDynamic()) {
      seleMan2_.setSelectionSet(evaluator2_.evaluate());
    }
 
    Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
 
    nBins_(0) = int(hmat(0, 0) / voxelSize);
    nBins_(1) = int(hmat(1, 1) / voxelSize);
    nBins_(2) = int(hmat(2, 2) / voxelSize);
 
    hist_.resize(nBins_(0));
    count_.resize(nBins_(0));
    for (int i = 0; i < nBins_(0); ++i) {
      hist_[i].resize(nBins_(1));
      count_[i].resize(nBins_(1));
      for (int j = 0; j < nBins_(1); ++j) {
        hist_[i][j].resize(nBins_(2));
        count_[i][j].resize(nBins_(2));
        std::fill(hist_[i][j].begin(), hist_[i][j].end(), 0.0);
        std::fill(count_[i][j].begin(), count_[i][j].end(), 0.0);
      }
    }
 
    setOutputName(getPrefix(filename) + ".Qxyz");
  }
 
  void TetrahedralityParamXYZ::process() {
    StuntDouble* sd;
    StuntDouble* sd2;
    StuntDouble* sdi;
    StuntDouble* sdj;
    int myIndex;
    Vector3d vec;
    Vector3d ri, rj, rk, rik, rkj;
    RealType r;
    RealType cospsi;
    RealType Qk;
    std::vector<std::pair<RealType, StuntDouble*>> myNeighbors;
    // std::vector<std::pair<Vector3d, RealType> > qvals;
    // std::vector<std::pair<Vector3d, RealType> >::iterator qiter;
    int isd1;
    int isd2;
    bool usePeriodicBoundaryConditions_ =
        info_->getSimParams()->getUsePeriodicBoundaryConditions();
 
    int kMax   = int(5.0 * gaussWidth_ / voxelSize_);
    int kSqLim = kMax * kMax;
    cerr << "gw = " << gaussWidth_ << " vS = " << voxelSize_
         << " kMax = " << kMax << " kSqLim = " << kSqLim << "\n";
 
    DumpReader reader(info_, dumpFilename_);
    int nFrames = reader.getNFrames();
 
    for (int istep = 0; istep < nFrames; istep += step_) {
      reader.readFrame(istep);
 
      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
      Mat3x3d hmat     = currentSnapshot_->getHmat();
      Vector3d halfBox = Vector3d(hmat(0, 0), hmat(1, 1), hmat(2, 2)) / 2.0;
 
      if (evaluator1_.isDynamic()) {
        seleMan1_.setSelectionSet(evaluator1_.evaluate());
      }
 
      if (evaluator2_.isDynamic()) {
        seleMan2_.setSelectionSet(evaluator2_.evaluate());
      }
 
      // qvals.clear();
 
      // outer loop is over the selected StuntDoubles:
      for (sd = seleMan1_.beginSelected(isd1); sd != NULL;
           sd = seleMan1_.nextSelected(isd1)) {
        myIndex = sd->getGlobalIndex();
 
        Qk = 1.0;
        myNeighbors.clear();
 
        for (sd2 = seleMan2_.beginSelected(isd2); sd2 != NULL;
             sd2 = seleMan2_.nextSelected(isd2)) {
          if (sd2->getGlobalIndex() != myIndex) {
            vec = sd->getPos() - sd2->getPos();
 
            if (usePeriodicBoundaryConditions_)
              currentSnapshot_->wrapVector(vec);
 
            r = vec.length();
 
            // Check to see if neighbor is in bond cutoff
 
            if (r < rCut_) { myNeighbors.push_back(std::make_pair(r, sd2)); }
          }
        }
 
        // Sort the vector using predicate and std::sort
        std::sort(myNeighbors.begin(), myNeighbors.end());
 
        // Use only the 4 closest neighbors to do the rest of the work:
 
        int nbors = myNeighbors.size() > 4 ? 4 : myNeighbors.size();
        int nang  = int(0.5 * (nbors * (nbors - 1)));
 
        rk = sd->getPos();
 
        for (int i = 0; i < nbors - 1; i++) {
          sdi = myNeighbors[i].second;
          ri  = sdi->getPos();
          rik = rk - ri;
          if (usePeriodicBoundaryConditions_) currentSnapshot_->wrapVector(rik);
 
          rik.normalize();
 
          for (int j = i + 1; j < nbors; j++) {
            sdj = myNeighbors[j].second;
            rj  = sdj->getPos();
            rkj = rk - rj;
            if (usePeriodicBoundaryConditions_)
              currentSnapshot_->wrapVector(rkj);
            rkj.normalize();
 
            cospsi = dot(rik, rkj);
 
            // Calculates scaled Qk for each molecule using calculated
            // angles from 4 or fewer nearest neighbors.
            Qk -= (pow(cospsi + 1.0 / 3.0, 2) * 2.25 / nang);
          }
        }
 
        if (nang > 0) {
          if (usePeriodicBoundaryConditions_) currentSnapshot_->wrapVector(rk);
          // qvals.push_back(std::make_pair(rk, Qk));
 
          Vector3d pos = rk + halfBox;
 
          Vector3i whichVoxel(int(pos[0] / voxelSize_),
                              int(pos[1] / voxelSize_),
                              int(pos[2] / voxelSize_));
 
          for (int l = -kMax; l <= kMax; l++) {
            for (int m = -kMax; m <= kMax; m++) {
              for (int n = -kMax; n <= kMax; n++) {
                int kk = l * l + m * m + n * n;
                if (kk <= kSqLim) {
                  int ll = (whichVoxel[0] + l) % nBins_(0);
                  ll     = ll < 0 ? nBins_(0) + ll : ll;
                  int mm = (whichVoxel[1] + m) % nBins_(1);
                  mm     = mm < 0 ? nBins_(1) + mm : mm;
                  int nn = (whichVoxel[2] + n) % nBins_(2);
                  nn     = nn < 0 ? nBins_(2) + nn : nn;
 
                  Vector3d bPos = Vector3d(ll, mm, nn) * voxelSize_ - halfBox;
                  Vector3d d    = bPos - rk;
                  currentSnapshot_->wrapVector(d);
                  RealType denom =
                      pow(2.0 * sqrt(Constants::PI) * gaussWidth_, 3);
                  RealType exponent = -dot(d, d) / pow(2.0 * gaussWidth_, 2);
                  RealType weight   = exp(exponent) / denom;
                  count_[ll][mm][nn] += weight;
                  hist_[ll][mm][nn] += weight * Qk;
                }
              }
            }
          }
        }
      }
 
      // for (int i = 0; i < nBins_(0); ++i) {
      //   for(int j = 0; j < nBins_(1); ++j) {
      //     for(int k = 0; k < nBins_(2); ++k) {
      //       Vector3d pos = Vector3d(i, j, k) * voxelSize_ - halfBox;
      //       for(qiter = qvals.begin(); qiter != qvals.end(); ++qiter) {
      //         Vector3d d = pos - (*qiter).first;
      //         currentSnapshot_->wrapVector(d);
      //         RealType denom = pow(2.0 * sqrt(Constants::PI) * gaussWidth_,
      //         3); RealType exponent = -dot(d,d) / pow(2.0*gaussWidth_, 2);
      //         RealType weight = exp(exponent) / denom;
      //         count_[i][j][k] += weight;
      //         hist_[i][j][k] += weight * (*qiter).second;
      //       }
      //     }
      //   }
      // }
    }
    // writeQxyz();
    writeVTKGrid();
  }
 
  void TetrahedralityParamXYZ::writeVTKGrid() {
    Mat3x3d hmat = info_->getSnapshotManager()->getCurrentSnapshot()->getHmat();
 
    // normalize by total weight in voxel:
    for (unsigned int i = 0; i < hist_.size(); ++i) {
      for (unsigned int j = 0; j < hist_[i].size(); ++j) {
        for (unsigned int k = 0; k < hist_[i][j].size(); ++k) {
          hist_[i][j][k] = hist_[i][j][k] / count_[i][j][k];
        }
      }
    }
 
    std::ofstream qXYZstream(outputFilename_.c_str());
    if (qXYZstream.is_open()) {
      qXYZstream << "# vtk DataFile Version 2.0\n";
      qXYZstream << "Tetrahedrality Parameter volume rendering\n";
      qXYZstream << "ASCII\n";
      qXYZstream << "DATASET RECTILINEAR_GRID\n";
      qXYZstream << "DIMENSIONS " << hist_.size() << " " << hist_[0].size()
                 << " " << hist_[0][0].size() << "\n";
      qXYZstream << "X_COORDINATES " << hist_.size() << " float\n";
      for (std::size_t i = 0; i < hist_.size(); ++i) {
        qXYZstream << (RealType(i) / nBins_.x()) * hmat(0, 0) << " ";
      }
      qXYZstream << "\n";
      qXYZstream << "Y_COORDINATES " << hist_[0].size() << " float\n";
      for (std::size_t j = 0; j < hist_[0].size(); ++j) {
        qXYZstream << (RealType(j) / nBins_.y()) * hmat(1, 1) << " ";
      }
      qXYZstream << "\n";
      qXYZstream << "Z_COORDINATES " << hist_[0][0].size() << " float\n";
      for (std::size_t k = 0; k < hist_[0][0].size(); ++k) {
        qXYZstream << (RealType(k) / nBins_.z()) * hmat(2, 2) << " ";
      }
      qXYZstream << "\n";
      qXYZstream << "POINT_DATA "
                 << hist_.size() * hist_[0].size() * hist_[0][0].size() << "\n";
      qXYZstream << "SCALARS scalars float\n";
      qXYZstream << "LOOKUP_TABLE default\n";
 
      for (std::size_t k = 0; k < hist_[0][0].size(); ++k) {
        for (std::size_t j = 0; j < hist_[0].size(); ++j) {
          for (std::size_t i = 0; i < hist_.size(); ++i) {
            qXYZstream << hist_[i][j][k] << " ";
 
            // qXYZstream.write(reinterpret_cast<char *>( &hist_[i][j][k] ),
            // sizeof( hist_[i][j][k] ));
          }
        }
      }
      qXYZstream << "\n";
    } else {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "TetrahedralityParamXYZ: unable to open %s\n",
               outputFilename_.c_str());
      painCave.isFatal = 1;
      simError();
    }
    qXYZstream.close();
  }
 
  void TetrahedralityParamXYZ::writeQxyz() {
    Mat3x3d hmat = info_->getSnapshotManager()->getCurrentSnapshot()->getHmat();
 
    // normalize by total weight in voxel:
    for (unsigned int i = 0; i < hist_.size(); ++i) {
      for (unsigned int j = 0; j < hist_[i].size(); ++j) {
        for (unsigned int k = 0; k < hist_[i][j].size(); ++k) {
          hist_[i][j][k] = hist_[i][j][k] / count_[i][j][k];
        }
      }
    }
 
    std::ofstream qXYZstream(outputFilename_.c_str());
    if (qXYZstream.is_open()) {
      qXYZstream << "# AmiraMesh ASCII 1.0\n\n";
      qXYZstream << "# Dimensions in x-, y-, and z-direction\n";
      qXYZstream << "  define Lattice " << hist_.size() << " "
                 << hist_[0].size() << " " << hist_[0][0].size() << "\n";
 
      qXYZstream << "Parameters {\n";
      qXYZstream << "    CoordType \"uniform\",\n";
      qXYZstream << "    # BoundingBox is xmin xmax ymin ymax zmin zmax\n";
      qXYZstream << "    BoundingBox 0.0 " << hmat(0, 0) << " 0.0 "
                 << hmat(1, 1) << " 0.0 " << hmat(2, 2) << "\n";
      qXYZstream << "}\n";
 
      qXYZstream << "Lattice { double ScalarField } = @1\n";
 
      qXYZstream << "@1\n";
 
      for (std::size_t k = 0; k < hist_[0][0].size(); ++k) {
        for (std::size_t j = 0; j < hist_[0].size(); ++j) {
          for (std::size_t i = 0; i < hist_.size(); ++i) {
            qXYZstream << hist_[i][j][k] << " ";
 
            // qXYZstream.write(reinterpret_cast<char *>( &hist_[i][j][k] ),
            // sizeof( hist_[i][j][k] ));
          }
        }
      }
 
    } else {
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "TetrahedralityParamXYZ: unable to open %s\n",
               outputFilename_.c_str());
      painCave.isFatal = 1;
      simError();
    }
    qXYZstream.close();
  }
}  // namespace OpenMD