Dear Bob I think I have sorted out most of the errors on my class. Now I can add all the atoms in Jmol but still one things very weird happen to me :
1) all atoms have the same position! Is something wrong with the way how crystal print the fractional coordinates? 1 T 26 FE 3.568442544039E-01 3.568442544031E-01 3.568442544031E-01 Do you have any suggestions? Thank you, Piero -- 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 ----------------------------------------------------------- ________________________________________ From: Robert Hanson [hans...@stolaf.edu] Sent: Thursday, February 11, 2010 12:57 PM To: jmol-developers@lists.sourceforge.net Subject: Re: [Jmol-developers] Extend Jmol to crystal files On Thu, Feb 11, 2010 at 5:56 AM, P.Canepa <pc...@kent.ac.uk<mailto:pc...@kent.ac.uk>> wrote: Hi Rob, I am sorry for wasting again your time , I have been trying for while if my new part of the Resolver class works ! I added this code which should look though the file and find at a certain point these text lines within brackets. If these are found it should print out at least the message below, which I cannot see so far ! The code is fine. I think it is working properly. If these are found, it should NOT print out the message because it will return TRUE. Are you saying with this code that ANY ONE of these must be present within the first 16 lines? Isn't there one thing that HAS to be there? Please check on the file specifications and see if there is one unique phrase rather than all these checks. I wouldn't know, but you would. Apperently there is some error! Is the variable lines meant as an array of Strings where each element of the array corresponds to precise line in my text file ? Furthermore Thank you ,Piero private static boolean checkCrystal(String[] lines){ for (int i = 0; i < lines.length; i++ ){ if(lines[i].startsWith(" MOLECULAR CALCULATION ")) return true; if(lines[i].startsWith(" POLYMER CALCULATION ")) return true; if(lines[i].startsWith(" SLAB CALCULATION ")) return true; if(lines[i].startsWith(" CRYSTAL CALCULATION ")) return true; if(lines[i].startsWith(" LOCAL ATOMIC FUNCTIONS BASIS SET ")) return true; System.out.println("This is a crystal file"); } return false; } -- 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<mailto:pc...@kent.ac.uk> mobile: +44 (0) 7772-9756456 ----------------------------------------------------------- ________________________________________ From: Robert Hanson [hans...@stolaf.edu<mailto:hans...@stolaf.edu>] Sent: Wednesday, February 10, 2010 6:29 PM To: jmol-developers@lists.sourceforge.net<mailto:jmol-developers@lists.sourceforge.net> Subject: Re: [Jmol-developers] Extend Jmol to crystal files On Wed, Feb 10, 2010 at 7:10 AM, P.Canepa <pc...@kent.ac.uk<mailto:pc...@kent.ac.uk><mailto:pc...@kent.ac.uk<mailto:pc...@kent.ac.uk>>> wrote: Dear Bob, 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) ? All the readers are subclasses of smarter.AtomCollectionReader. At the end of that class code you will see a whole set of public functions you can tap into. In particular there is a global field "line" that is read with readLine(); When you are reading a mix of text and numbers from a line, first consider whether there is guaranteed white space between them. Not all programs do that. If that is the case, then String[] tokens = getTokens(); // from the NEXT line or String[] tokens = getTokens(line); // from the CURRENT line would be my choice. Then I do something like: atom.set(parseFloat(tokens[0]), parseFloat(tokens[1]), parseFloat(tokens[2])); for example. Or, if you know it is column based, you can just use: readLine(); atom.set(parseFloat(line.substring(10,20)), parseFloat.....) Something like that. Don't worry so much about getting this perfect. I'll edit it down to the simplest way to read the file. Just get it reading the file successfully any way you want. Bob 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 [hans...@stolaf.edu<mailto:hans...@stolaf.edu><mailto:hans...@stolaf.edu<mailto:hans...@stolaf.edu>>] Sent: Tuesday, February 09, 2010 2:27 PM To: jmol-developers@lists.sourceforge.net<mailto:jmol-developers@lists.sourceforge.net><mailto:jmol-developers@lists.sourceforge.net<mailto:jmol-developers@lists.sourceforge.net>> 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 <pc...@kent.ac.uk<mailto:pc...@kent.ac.uk><mailto:pc...@kent.ac.uk<mailto:pc...@kent.ac.uk>><mailto:pc...@kent.ac.uk<mailto:pc...@kent.ac.uk><mailto:pc...@kent.ac.uk<mailto:pc...@kent.ac.uk>>>> 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><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 ----------------------------------------------------------- ------------------------------------------------------------------------------ The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com _______________________________________________ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net<mailto:Jmol-developers@lists.sourceforge.net><mailto:Jmol-developers@lists.sourceforge.net<mailto:Jmol-developers@lists.sourceforge.net>><mailto:Jmol-developers@lists.sourceforge.net<mailto:Jmol-developers@lists.sourceforge.net><mailto:Jmol-developers@lists.sourceforge.net<mailto:Jmol-developers@lists.sourceforge.net>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers -- 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 ------------------------------------------------------------------------------ SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev _______________________________________________ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net<mailto:Jmol-developers@lists.sourceforge.net><mailto:Jmol-developers@lists.sourceforge.net<mailto:Jmol-developers@lists.sourceforge.net>> https://lists.sourceforge.net/lists/listinfo/jmol-developers -- 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 ------------------------------------------------------------------------------ SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev _______________________________________________ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net<mailto:Jmol-developers@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/jmol-developers -- 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 ------------------------------------------------------------------------------ SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev _______________________________________________ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
