Piero,
Please send a few sample files.
Notes below.
Bob
On Sat, Feb 13, 2010 at 6:20 AM, P.Canepa <[email protected]> wrote:
> 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 box as
> well! Should I call another function somewhere which print them?
>
This only comes up automatically if there is a unit cell and the coordinates
are fractional. If not, you have to issue
unitcell on
> Further CRYSTAL uses to remove the periodicy in SLAB or POLYMER. the
> former keep periodic just 2 dimensions while the latter just 1, which in
> nutshell 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 type of sytem, should I work out a way to tackle
> it ?
>
>
I think the best way to think about periodicity is to simply load different
sets of unit cells:
load xxxx.xtal {3 3 1}
for instance.
> Crystal can also calculate vibrational frequency in Gamma as Gaussian03/09!
> Do you have some hint as to let Jmol plot them?
>
>
There are readers that show vibrations. Each vibration is created as a
separate model. See, for example, XyzReader.java
> 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: [email protected]
> mobile: +44 (0) 7772-9756456
> -----------------------------------------------------------
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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