working on XYZ reader

Qt/PRISM-GUI.pro.user

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE QtCreatorProject>
-<!-- Written by QtCreator 4.2.1, 2017-05-05T08:28:19. -->
+<!-- Written by QtCreator 4.2.1, 2017-05-05T22:00:55. -->
 <qtcreator>
  <data>
   <variable>EnvironmentId</variable>

SI100.XYZ

@@ -0,0 +1,11 @@
+one unit cell of 100 silicon
+      5.43    5.43    5.43
+  14  0.0000  0.0000  0.0000  1.0  0.076
+  14  2.7150  2.7150  0.0000  1.0  0.076
+  14  1.3575  4.0725  1.3575  1.0  0.076
+  14  4.0725  1.3575  1.3575  1.0  0.076
+  14  2.7150  0.0000  2.7150  1.0  0.076
+  14  0.0000  2.7150  2.7150  1.0  0.076
+  14  1.3575  1.3575  4.0725  1.0  0.076
+  14  4.0725  4.0725  4.0725  1.0  0.076
+  -1

SRT.XYZ

@@ -0,0 +1,10 @@
+one unit cell of strontium titanate
+      3.9051     3.9051       3.9051
+38         0          0            0       1.0    0.08
+ 8   1.95255    1.95255            0       1.0    0.08
+22   1.95255    1.95255      1.95255       1.0    0.08
+ 8   1.95255          0      1.95255       1.0    0.08
+ 8         0    1.95255      1.95255       1.0    0.08
+-1
+
+

include/atom.h

@@ -56,5 +56,80 @@ namespace PRISM{
 			return atoms;
 	};
 
+	inline std::vector<atom> readAtoms_XYZ(const std::string& filename){
+		std::vector<atom> atoms;
+		std::ifstream f(filename);
+		if (!f)throw std::runtime_error("Unable to open file.\n");
+		std::string line;
+		std::string token;
+		size_t line_num = 0;
+		size_t atom_count = 0;
+		if (!std::getline(f,line)) throw std::runtime_error("Error reading comment line.\n");
+		if (!std::getline(f,line)) throw std::runtime_error("Error reading unit cell params.\n");
+        double a,b,c; // unit cell params
+		{
+			std::stringstream ss(line);
+			if (!(ss >> a))
+				throw std::domain_error(
+						"Bad input data for unit cell dimension a.\n");
+			if (!(ss >> b))
+				throw std::domain_error(
+						"Bad input data for unit cell dimension a.\n");
+			if (!(ss >> c))
+				throw std::domain_error(
+						"Bad input data for unit cell dimension a.\n");
+		}
+        std::cout << "Unit cell a, b, c = " << a << ", " << b << ", " << c << std::endl;
+			while (std::getline(f, line)) {
+                line = line.substr(line.find_first_not_of(" "));
+
+                if (line=="-1"){
+                    break;
+                } else {
+                    std::cout << "line = " << line << std::endl;
+                }
+                {
+                    std::string test("-1\n");
+                    if (test == "-1")std::cout<<"yes\n";
+                    std::cout << test << std::endl;
+                    std::cout << line << std::endl;
+                    std::cout << test.size() << std::endl;
+                    std::cout << line.size() << std::endl;
+                }
+                ++atom_count;
+                ++line_num;
+                std::cout << "atom_count = " << atom_count << " line = " << line <<  std::endl;
+            }
+//				double tx, ty, tz;
+//				size_t tspecies;
+//				std::stringstream ss(line);
+//				if (!(ss >> tx))
+//					throw std::domain_error(
+//							"Bad input data for X. The txt file should continue 4 comma separated values per line (x,y,z,species).\n");
+//				if (ss.peek() == ',')ss.ignore();
+//				if (!(ss >> ty))
+//					throw std::domain_error(
+//							"Bad input data for Y. The txt file should continue 4 comma separated values per line (x,y,z,species).\n");
+//				if (ss.peek() == ',')ss.ignore();
+//				if (!(ss >> tz))
+//					throw std::domain_error(
+//							"Bad input data for Z. The txt file should continue 4 comma separated values per line (x,y,z,species).\n");
+//				if (ss.peek() == ',')ss.ignore();
+//				if (!(ss >> tspecies))
+//					throw std::domain_error(
+//							"Bad input data for atomic species. The txt file should continue 4 comma separated values per line (x,y,z,species).\n");
+//				if (ss.peek() == ',')ss.ignore();
+//				atoms.emplace_back(atom{tx, ty, tz, tspecies});
+//			}
+//			if (atom_count == 0) {
+//				std::domain_error("Bad input data. No atoms were found in this file.\n");
+//			} else {
+//				std::cout << "extracted " << atom_count << " atoms from " << line_num << " lines in " << filename
+//						  << std::endl;
+//			}
+
+		return atoms;
+	};
+
 }
 #endif //PRISM_ATOM_H

include/params.h

@@ -134,7 +134,8 @@ namespace PRISM{
 		    pixelSize[0] /= (T)imageSize[0];
 		    pixelSize[1] /= (T)imageSize[1];
 		    try {
-			    atoms = readAtoms(meta.filename_atoms);
+//			    atoms = readAtoms(meta.filename_atoms);
+				atoms = readAtoms_XYZ(meta.filename_atoms);
 		    }
 		    catch (const std::runtime_error &e) {
 			    std::cout << "PRISM: Error opening " << meta.filename_atoms << std::endl;