Re: [Jmol-developers] Still Crystal development

[P.Canepa <pc...@ke...>]

Hi Bob,

Please find in the attachment  two Crystal outputs, the former is  a MgO slab, the latter a polymer. You will recognize in the slab that a and b are expressed in fractional units whereas c in Cartesians. For the polymer b and c are  in Cartesian and just a in fractional due to its periodicity just along a.

I have sort out the problem I was stuck during last week. Now Jmol can draw beautiful cell and atom retrieved from CRYSTAL06/09 outputs. 

Futhermore there is any class which exploit the symmetry of the crystal in Jmol? It is compatible with the 230 space groups defined into the international tables for crystallographers? Does this read Space Groups express with the Hermann-Mauguin notation? 

Many thanks  

--
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...@ke...
mobile: +44 (0) 7772-9756456
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________________________________________
From: Robert Hanson [ha...@st...]
Sent: Saturday, February 13, 2010 3:39 PM
To: jmo...@li...
Subject: Re: [Jmol-developers] Still Crystal development

Piero,

Please send a few sample files.
Notes below.

Bob

On Sat, Feb 13, 2010 at 6:20 AM, P.Canepa <pc...@ke...<mailto:pc...@ke...>> 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: pc...@ke...<mailto:pc...@ke...>
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