Merge pull request #36 from RuhiRG/fixup

ENH: simplifying the function readXYZ

src/bulkTUM.cpp

@@ -378,8 +378,8 @@ Eigen::MatrixXd tum3::buildRefHC(std::string fileName) {
  //
  Eigen::MatrixXd refPnts(12, 3); // Reference point set (Eigen matrix)
  // Get the reference HC point set
- molSys::PointCloud<molSys::Point<double>, double>
- setCloud; // PointCloud for holding the reference point values
+ // molSys::PointCloud<molSys::Point<double>, double>
+ // setCloud; // PointCloud for holding the reference point values
  // Variables for rings
  std::vector<std::vector<int>> nList; // Neighbour list
  std::vector<std::vector<int>> rings; // Rings
@@ -392,7 +392,7 @@ Eigen::MatrixXd tum3::buildRefHC(std::string fileName) {
  //
  // read in the XYZ file into the pointCloud setCloud
  //
- sinp::readXYZ(fileName, &setCloud);
+ auto setCloud = sinp::readXYZ(fileName);
  // box lengths
  for (int i = 0; i < 3; i++) {
  setCloud.box[i] = 50;
@@ -452,7 +452,7 @@ Eigen::MatrixXd tum3::buildRefDDC(std::string fileName) {
  //
  // read in the XYZ file into the pointCloud setCloud
  //
- sinp::readXYZ(fileName, &setCloud);
+ setCloud = sinp::readXYZ(fileName);
 
  // box lengths
  for (int i = 0; i < 3; i++) {

src/include/internal/seams_input.hpp

@@ -80,8 +80,7 @@ molSys::PointCloud<molSys::Point<double>, double> readLammpsTrjreduced(
  std::array<double, 3> coordHigh = std::array<double, 3>{0, 0, 0});
 
 //! Function for reading in atom coordinates from an XYZ file
-int readXYZ(std::string filename,
- molSys::PointCloud<molSys::Point<double>, double> *yCloud);
+molSys::PointCloud<molSys::Point<double>, double> readXYZ(std::string filename);
 
 //! Reads bonds into a vector of vectors from a file with a specific format
 std::vector<std::vector<int>> readBonds(std::string filename);

src/pntCorrespondence.cpp

@@ -575,7 +575,7 @@ Eigen::MatrixXd pntToPnt::getPointSetCage(ring::strucType type) {
  // Read in the XYZ file
  std::string fileName = "templates/hc.xyz";
  //
- sinp::readXYZ(fileName, &setCloud);
+ sinp::readXYZ(fileName);
  int n = setCloud.nop; // Number of points in the reference point set
  Eigen::MatrixXd pointSet(n, 3); // Output point set for a regular polygon
 

src/seams_input.cpp

@@ -70,10 +70,11 @@ std::vector<std::vector<int>> sinp::readBonds(std::string filename) {
 /**
  * @details Function for reading in an XYZ file
  */
-int sinp::readXYZ(std::string filename,
- molSys::PointCloud<molSys::Point<double>, double> *yCloud) {
+molSys::PointCloud<molSys::Point<double>, double> sinp::readXYZ(std::string filename) {
  std::unique_ptr<std::ifstream> xyzFile;
  xyzFile = std::make_unique<std::ifstream>(filename);
+ molSys::PointCloud<molSys::Point<double>, double>
+ yCloud;
  std::string line; // Current line being read in
  std::vector<std::string> tokens; // Vector containing word tokens
  std::vector<double> numbers; // Vector containing type double numbers
@@ -87,13 +88,13 @@ int sinp::readXYZ(std::string filename,
  std::cout
  << "Fatal Error: The file does not exist or you gave the wrong path.\n";
  // Throw exception?
- return 1;
+  throw std::runtime_error("Wrong filepath");
  }
 
  // --------
  // Before filling up the PointCloud, if the vectors are filled
  // empty them
- *yCloud = molSys::clearPointCloud(yCloud);
+ //*yCloud = molSys::clearPointCloud(yCloud);
  // --------
 
  // Format of an XYZ file:
@@ -102,6 +103,7 @@ int sinp::readXYZ(std::string filename,
  // O 43.603500 16.926201 15.215700
  // O 39.912601 14.775100 19.379200
  if (xyzFile->is_open()) {
+
  // ----------------------------------------------------------
  // At this point we know that the XYZ file is open
 
@@ -111,11 +113,11 @@ int sinp::readXYZ(std::string filename,
  // Skip the comment line
  std::getline((*xyzFile), line);
  // Reserve memory for atom coordinates using nop read in
- yCloud->pts.reserve(nop);
- yCloud->nop = nop;
-
+ yCloud.pts.reserve(nop);
+ yCloud.nop = nop;
  // Run this until EOF or you reach the next timestep
  while (std::getline((*xyzFile), line)) {
+
  // Read in lines and tokenize them into std::string words and <double>
  // numbers
  tokens = gen::tokenizer(line);
@@ -134,8 +136,8 @@ int sinp::readXYZ(std::string filename,
  iPoint.y = std::stod(tokens[2]);
  iPoint.z = std::stod(tokens[3]);
 
- yCloud->pts.push_back(iPoint);
- yCloud->idIndexMap[iPoint.atomID] = yCloud->pts.size() - 1;
+ yCloud.pts.push_back(iPoint);
+ yCloud.idIndexMap[iPoint.atomID] = yCloud.pts.size() - 1;
  iatom++; // Increase index
 
  // First point
@@ -168,29 +170,28 @@ int sinp::readXYZ(std::string filename,
  zHi = iPoint.z;
  } // zHi
  } // update
-
  } // end of while, looping through lines till EOF
  // ----------------------------------------------------------
  } // End of if file open statement
 
  xyzFile->close();
 
- if (yCloud->pts.size() == 1) {
+ if (yCloud.pts.size() == 1) {
  xHi = xLo + 10;
  yHi = yLo + 10;
  zHi = zLo + 10;
  } // for a single point in the system (never happens)
 
  // Fill up the box lengths
- yCloud->box.push_back(xHi - xLo);
- yCloud->box.push_back(yHi - yLo);
- yCloud->box.push_back(zHi - zLo);
+ yCloud.box.push_back(xHi - xLo);
+ yCloud.box.push_back(yHi - yLo);
+ yCloud.box.push_back(zHi - zLo);
 
- if (yCloud->pts.size() != yCloud->nop) {
+ if (yCloud.pts.size() != yCloud.nop) {
  std::cout << "Atoms didn't get filled in properly.\n";
  }
 
- return 0;
+ return yCloud;
 }
 
 // External Libraries