ENH: simplifying the function readXYZ

src/bulkTUM.cpp

@@ -202,19 +202,19 @@ int tum3::topoUnitMatchingBulk(
   dumpAtomTypes.resize(atomTypes.size());
   // Change from enum to int
   for (int i = 0; i < atomTypes.size(); i++) {
-    if (atomTypes[i] == cage::hc) {
+    if (atomTypes[i] == cage::iceType::hc) {
       dumpAtomTypes[i] = 1;
     } // HC
-    else if (atomTypes[i] == cage::ddc) {
+    else if (atomTypes[i] == cage::iceType::ddc) {
       dumpAtomTypes[i] = 2;
     } // DDC
-    else if (atomTypes[i] == cage::mixed) {
+    else if (atomTypes[i] == cage::iceType::mixed) {
       dumpAtomTypes[i] = 3;
     } // mixed rings
-    else if (atomTypes[i] == cage::pnc) {
+    else if (atomTypes[i] == cage::iceType::pnc) {
       dumpAtomTypes[i] = 4;
     } // pnc
-    else if (atomTypes[i] == cage::mixed2) {
+    else if (atomTypes[i] == cage::iceType::mixed2) {
       dumpAtomTypes[i] = 5;
     } // shared by pnc and ddc/hc
     else {
@@ -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++) {
@@ -504,7 +504,7 @@ int tum3::updateRMSDatom(std::vector<std::vector<int>> rings,
       iatom = rings[iring][j]; // Current atom index
 
       // Skip for PNC atoms
-      if (atomTypes[iatom] == cage::pnc || atomTypes[iatom] == cage::mixed2) {
+      if (atomTypes[iatom] == cage::iceType::pnc || atomTypes[iatom] == cage::iceType::mixed2) {
         continue;
       } // Do not update if the atom is a PNC
       //
@@ -730,7 +730,7 @@ int tum3::clusterCages(
     // If only one cage is in the cluster
     if (linkedList[i] == i) {
       // Add to the number of single DDCs
-      if (cageList[i].type == cage::DoubleDiaC) {
+      if (cageList[i].type == cage::cageType::DoubleDiaC) {
         singleDDCs++;
       } // add to the single DDCs
       else {

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;
+    return yCloud;
   }
 
   // --------
   // 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
 
@@ -111,16 +113,18 @@ 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);
       numbers = gen::tokenizerDouble(line);
 
+    std::cout
+        << "I am here at." << nop << "\n";
       // Skip whitespace
       if (tokens.size() == 0) {
         continue;
@@ -134,8 +138,8 @@ 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 +172,28 @@ 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