Dear Bob
So far with the code I worked out I can correctly see my atom within Jmol. What
I miss are cell parameters on the top -left corner and the cell as well! Should
I call another function somewhere which print them?
Further CRYSTAL use treat SLAB and POLYMER as 2 dimensional and one dimensional
system which means having the Z (for slab) and Y and Z (for polymer) expresses
as Cartesian coordinates since the periodicity is reduced! Does Jmol has
already implemented this kind of situation should I work out a way to tackle
it ?
Crystal can also calculate vibrational frequency in Gamma as Gaussian03/09! Do
you have some int as to let Jmol read them?
Thanks a lot and have a Good Weekend, Piero
public class CrystalReader extends AtomSetCollectionReader{
float a;
float b;
float c;
float alpha;
float beta ;
float gamma;
public void readAtomSetCollection(BufferedReader reader) {
atomSetCollection = new AtomSetCollection("Crystal0X_output", this);
try{
this.reader = reader;
atomSetCollection.setCollectionName(readLine());
readSystem();
}catch (Exception e) {
setError(e);
}
}
private void readSystem() throws Exception{
do{
readLine();
if(line.startsWith("MOLECULE")){
setFractionalCoordinates(false);
readAtomCoords();
break;
}
if (line.startsWith("CRYSTAL")|| line.startsWith("SLAB")||
line.startsWith("POLYMER") || line.startsWith("EXTERNAL") ){
setFractionalCoordinates(true);
readCellParams();
readAtomCoords();
break;
}
}while(line != null);
}
private void readCellParams() throws Exception{
do{
readLine();
if(line.startsWith(" PRIMITIVE CELL")){
readLine();
readLine();
a = parseFloat(line.substring(2,17)) ;
b = parseFloat(line.substring(18,33)) ;
c = parseFloat(line.substring(34,42)) ;
alpha = parseFloat(line.substring(43,60)) ;
beta = parseFloat(line.substring(61,71)) ;
gamma = parseFloat(line.substring(72,80)) ;
//this method works fine so far
setFractionalCoordinates(true);
setUnitCell(a, b, c, alpha, beta, gamma);
break;
}
}while (line != null);
}
private void readAtomCoords() throws Exception{
setFractionalCoordinates(true);
do{
readLine();
if(line.startsWith(" ATOMS IN THE ASYMMETRIC")){
int numberAtoms = parseInt(line.substring(61,65));
readLine();
readLine();
int j=0;
for(int i=0; i<numberAtoms ; i++){
readLine();
addNewatom();
String atomName = line.substring(8,11);
String sym =atomName.substring(0,2).trim();
int atomicnumber = parseInt(sym);
Atom atom = atomSetCollection.getAtom(i);
sym =getElementSymbol(atomicnumber);
atom.elementSymbol=sym ;
atom.atomName= atomName + "_" + (j++);
}
break;
}
}while (line != null);
}
private void addNewatom(){
float x = parseFloat(line.substring(15,35));
float y = parseFloat(line.substring(36,55));
float z = parseFloat(line.substring(56,75));
Atom atom=atomSetCollection.addNewAtom();
setAtomCoord(atom, x, y,z);
}
}
--
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom
e-mail: pc...@kent.ac.uk
mobile: +44 (0) 7772-9756456
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