Dear Bob,
I modified successfully the org.jmol.adapter.smarter.Resolver.java, this way
Jmol should be able to recognize CRYSTAL output.
Then I started thinking as how to create the reader for crystal. So far I just
went trough the other files like Wien2kReader.java and CastepReader.java.
Since crystal outputs end up more or less as below
FINAL OPTIMIZED GEOMETRY - DIMENSIONALITY OF THE SYSTEM 3
(NON PERIODIC DIRECTION: LATTICE PARAMETER FORMALLY SET TO 500)
*******************************************************************************
LATTICE PARAMETERS (ANGSTROMS AND DEGREES) - BOHR = 0.5291772083 ANGSTROM
PRIMITIVE CELL - CENTRING CODE 5/0 VOLUME= 31.338272 - DENSITY11.020 g/cm^3
A B C ALPHA BETA GAMMA
3.53885972 3.53885972 3.53885972 60.000000 60.000000 60.000000
*******************************************************************************
ATOMS IN THE ASYMMETRIC UNIT 1 - ATOMS IN THE UNIT CELL: 1
ATOM X/A Y/B Z/C
*******************************************************************************
1 T 282 PB 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
TRANSFORMATION MATRIX PRIMITIVE-CRYSTALLOGRAPHIC CELL
-1.0000 1.0000 1.0000 1.0000 -1.0000 1.0000 1.0000 1.0000 -1.0000
*******************************************************************************
CRYSTALLOGRAPHIC CELL (VOLUME= 125.35308769)
A B C ALPHA BETA GAMMA
5.00470341 5.00470341 5.00470341 90.000000 90.000000 90.000000
COORDINATES IN THE CRYSTALLOGRAPHIC CELL
ATOM X/A Y/B Z/C
*******************************************************************************
1 T 282 PB 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
T = ATOM BELONGING TO THE ASYMMETRIC UNIT
INFORMATION **** fort.34 **** GEOMETRY OUTPUT FILE
DIRECT LATTICE VECTORS CARTESIAN COMPONENTS (ANGSTROM)
X Y Z
0.000000000000E+00 0.250235170500E+01 0.250235170500E+01
0.250235170500E+01 0.000000000000E+00 0.250235170500E+01
0.250235170500E+01 0.250235170500E+01 0.000000000000E+00
I thought I could let Jmol read the following strings:
1) FINAL OPTIMIZED GEOMETRY which determines the final geometry
2) LATTICE PARAMETERS which opens the lattice parameter section
3) ATOMS IN THE ASYMMETRIC UNIT that starts the atomic coordinates section
As you seethe numbers of lattice parameters and atomic coordinates are found
two lines below.
In addition the values of the lattice parameters and x y z per each atoms are
on the same line, how can I tackle this problem reading line by line (as you
did in Wien2kReader.java) ? Can you help me?
Furthermore does jmol need the direct lattice vector to define the cell?
Thank you
--
Pieremanuele Canepa
Room 104
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom
-----------------------------------------------------------
________________________________________
From: Robert Hanson [[email protected]]
Sent: Tuesday, February 09, 2010 2:27 PM
To: [email protected]
Subject: Re: [Jmol-developers] Extend Jmol to crystal files
That would be great. Please:
1) Check out the Jmol code using SVN/Eclipse.
2) Create your reader. Please add this to org.jmol.adapter.readers.xtal (unless
it is XML, then use ....xml). Take a look at
org.jmol.adapter.smarter.AtomSetCollectionReader.java to get a sense of what is
going to happen in the reader.
I can help if you get stuck. This mostly involves:
(a) adding a bit of code to org.jmol.adapter.smarter.Resolver.java
(b) copying one of the other readers as a template as CrystalReader.java
(c) modifying the template as needed
3) Create a working patch and send it to us. This should be just two files --
Resolver.java and CrystalReader.java
4) I will check over your code, make sure it doesn't conflict with other
readers, make sure it properly accounts for various options, and probably edit
it a bit to be consistent with our styling. Then I will add it to Jmol 11.9.x
Bob
On Tue, Feb 9, 2010 at 5:19 AM, P.Canepa
<[email protected]<mailto:[email protected]>> wrote:
I am physic PhD student and I am willing to contribute to the development of
Jmol.
Reading trough Jmol web-page I realized that it is already capable to save
file for other famous period code such as: CASTEP, WIEN2k, VASP, etc... I would
like to extend it to CRYSTAL09, the periodic code developed at the University
of Turin, Italy (http:\\www.crystal.unito.it<http://www.crystal.unito.it>). I
have a bit of experience with java (especially java swing) and I use daily
CRYSTAL . Can you give me some hint as to start developing class to deal with
crystal files?
Many Thanks, Piero
--
Pieremanuele Canepa
Room 104
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom
-----------------------------------------------------------
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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,
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-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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