/**
* 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();
}
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);
}
/** 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);
}
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()));
}