topo_two_dim.cpp

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Code

#include <topo_two_dim.hpp>
 
// -----------------------------------------------------------------------------------------------------
// MONOLAYER ALGORITHMS
// -----------------------------------------------------------------------------------------------------
 
int ring::polygonRingAnalysis(
    std::string path, std::vector<std::vector<int>> rings,
    std::vector<std::vector<int>> nList,
    molSys::PointCloud<molSys::Point<double>, double> *yCloud, int maxDepth,
    double sheetArea, int firstFrame) {
  //
  std::vector<std::vector<int>>
      ringsOneType;           // Vector of vectors of rings of a single size
  int nRings;                 // Number of rings of the current type
  std::vector<int> nRingList; // Vector of the values of the number of prisms
                              // for a particular frame
  std::vector<double> coverageAreaXY; // Coverage area percent on the XY plane
                                      // for a particular n and frame
  std::vector<double> coverageAreaXZ; // Coverage area percent on the XZ plane
                                      // for a particular n and frame
  std::vector<double> coverageAreaYZ; // Coverage area percent on the YZ plane
                                      // for a particular n and frame
  std::vector<double> singleAreas; // Coverage area on the XY, XZ and YZ planes
                                   // for a single ring
  std::vector<int>
      atomTypes; // contains int values for each prism type considered
  // -------------------------------------------------------------------------------
  // Init
  nRingList.resize(
      maxDepth -
      2); // Has a value for every value of ringSize from 3, upto maxDepth
  coverageAreaXY.resize(maxDepth - 2);
  coverageAreaXZ.resize(maxDepth - 2);
  coverageAreaYZ.resize(maxDepth - 2);
  // The atomTypes vector is the same size as the pointCloud atoms
  atomTypes.resize(yCloud->nop, 1); // The dummy or unclassified value is 1
  // -------------------------------------------------------------------------------
  // Run this loop for rings of sizes upto maxDepth
  // The smallest possible ring is of size 3
  for (int ringSize = 3; ringSize <= maxDepth; ringSize++) {
    // Clear ringsOneType
    ring::clearRingList(ringsOneType);
    // Get rings of the current ring size
    ringsOneType = ring::getSingleRingSize(rings, ringSize);
    //
    // Continue if there are zero rings of ringSize
    if (ringsOneType.size() == 0) {
      nRingList[ringSize - 3] = 0; // Update the number of prisms
      // Update the coverage area%
      coverageAreaXY[ringSize - 3] = 0.0;
      coverageAreaXZ[ringSize - 3] = 0.0;
      coverageAreaYZ[ringSize - 3] = 0.0;
      continue;
    } // skip if there are no rings
    //
    // -------------
    // Number of rings with n nodes
    nRings = ringsOneType.size();
    // -------------
    // Now that you have rings of a certain size:
    nRingList[ringSize - 3] = nRings; // Update the number of n-membered rings
    // Update the coverage area% for the n-membered ring phase.
    singleAreas = topoparam::calcCoverageArea(yCloud, ringsOneType, sheetArea);
    // XY plane
    coverageAreaXY[ringSize - 3] = singleAreas[0];
    // XZ plane
    coverageAreaXZ[ringSize - 3] = singleAreas[1];
    // YZ plane
    coverageAreaYZ[ringSize - 3] = singleAreas[2];
    // -------------
  } // end of loop through every possible ringSize
 
  // Get the atom types for all the ring types
  ring::assignPolygonType(rings, &atomTypes, nRingList);
 
  // Write out the ring information
  sout::writeRingNum(path, yCloud->currentFrame, nRingList, coverageAreaXY,
                     coverageAreaXZ, coverageAreaYZ, maxDepth, firstFrame);
  // Write out the lammps data file for the particular frame
  sout::writeLAMMPSdataAllRings(yCloud, nList, atomTypes, maxDepth, path);
 
  return 0;
}
int ring::polygonRingAnalysis( {…}