Пример #1
0
 /**
  * A DL_Poly CONFIG file generated from a gulp output file. 0 3 18.009484000000000
  * 0.000000000000000 0.000000000000000 0.000000000000000 18.530232000000002 0.000000000000000
  * 0.000000000000000 0.000000000000000 6.570309000000000 Sic 1 0.000000000 0.000000000 0.000000000
  * Sic 2 18.009484000 9.265116000 3.285154500 Sic 3 9.004742000 18.530232000 3.285154500
  */
 private void process(List<String> lines) {
   iline = 0;
   cml.setTitle(lines.get(iline++));
   processLine1();
   processCell();
   processMolecule();
 }
Пример #2
0
 private void processCell() {
   CMLLatticeVector[] vv = new CMLLatticeVector[3];
   for (int i = 0; i < 3; i++) {
     String s = lines.get(iline++);
     double[] xyz = new double[3];
     xyz[0] = new Double(s.substring(0, 20).trim());
     xyz[1] = new Double(s.substring(20, 40).trim());
     xyz[2] = new Double(s.substring(40, 60).trim());
     vv[i] = new CMLLatticeVector(xyz);
   }
   CMLLattice lattice = new CMLLattice(vv);
   crystal = new CMLCrystal(lattice);
   crystal.appendChild(lattice);
   cml.appendChild(crystal);
 }
Пример #3
0
 /** Sic 1 0.000000000 0.000000000 0.000000000 Sic 2 18.009484000 9.265116000 3.285154500 */
 private void processMolecule() {
   molecule = new CMLMolecule();
   while (iline < lines.size()) {
     String line1 = lines.get(iline++);
     if (line1 == null || line1.trim() == "") {
       break;
     }
     String atomS = line1.substring(5, 13).trim();
     // elements seem to be symbol+label
     // try for 2-letter elements
     String elemS = atomS.substring(0, 2);
     String labelS = atomS.substring(2);
     ChemicalElement elem = ChemicalElement.getChemicalElement(elemS);
     if (elem == null) {
       elemS = atomS.substring(0, 1);
       labelS = atomS.substring(1);
       elem = ChemicalElement.getChemicalElement(elemS);
     }
     if (elem == null) {
       throw new RuntimeException("Cannot parse line as element " + line1);
     }
     int ser = Integer.parseInt((line1 + "       ").substring(13, 20).trim());
     String line2 = lines.get(iline++);
     double[] xyz = new double[3];
     xyz[0] = new Double(line2.substring(0, 20).trim());
     xyz[1] = new Double(line2.substring(20, 40).trim());
     xyz[2] = new Double(line2.substring(40, 60).trim());
     CMLAtom atom = new CMLAtom("a" + ser, elem);
     CMLAtomType atomType = new CMLAtomType();
     atomType.setName(labelS);
     atom.appendChild(atomType);
     atom.setXYZ3(new Point3(xyz));
     molecule.addAtom(atom);
   }
   cml.appendChild(molecule);
 }
Пример #4
0
 private void processLine1() {
   String line = lines.get(iline++);
   cml.appendChild(createIntProperty("dlpoly:var1", line.substring(0, 10).trim()));
   cml.appendChild(createIntProperty("dlpoly:var1", line.substring(10, 20).trim()));
 }