Patches item #2841139, was opened at 2009-08-20 16:41 Message generated for change (Comment added) made by j-meyer You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379135&aid=2841139&group_id=23629
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Category: File IO Group: None Status: Open Priority: 5 Private: No Submitted By: Joerg Meyer (j-meyer) Assigned to: Nobody/Anonymous (nobody) Summary: file reader for CASTEP and AIMS input files Initial Comment: I have added two readers for input files, which make use of the periodic boundary conditions (PBC) infrastructure of Jmol - CASTEP: http://www.castep.org (.cell files - only PBC) - FHI-aims: http://www.fhi-berlin.mpg.de/aims/ (geometry.in files - both cluster models and PBCs) Using the signed applet, the readers can be tried here http://w3.rz-berlin.mpg.de/~meyer/jmol-demo-20090819/ ---------------------------------------------------------------------- Comment By: Joerg Meyer (j-meyer) Date: 2009-08-25 19:07 Message: Just noticed that revision 11359 compiles nicely with sun-jdk-1.6.0_15-b03 (64bit) including changes below, but crashes even without changes below (!) when trying to run java -jar Jmol.jar: uncaught exception: java.lang.ExceptionInInitializerError java.lang.ExceptionInInitializerError at org.jmol.viewer.StateManager.<clinit>(StateManager.java:487) at org.jmol.viewer.Viewer.<init>(Viewer.java:248) at org.jmol.viewer.Viewer.allocateViewer(Viewer.java:310) at org.jmol.api.JmolViewer.allocateViewer(JmolViewer.java:90) at org.openscience.jmol.app.jmolpanel.JmolPanel.<init>(JmolPanel.java:150) at org.openscience.jmol.app.Jmol.<init>(Jmol.java:36) at org.openscience.jmol.app.jmolpanel.JmolPanel.getJmol(JmolPanel.java:358) at org.openscience.jmol.app.jmolpanel.JmolPanel.startJmol(JmolPanel.java:293) at org.openscience.jmol.app.Jmol.main(Jmol.java:41) Caused by: java.lang.StringIndexOutOfBoundsException: String index out of range: 23 at java.lang.String.substring(String.java:1934) at org.jmol.viewer.JmolConstants.<clinit>(JmolConstants.java:80) ... 9 more Exception in thread "main" java.lang.NullPointerException at org.openscience.jmol.app.jmolpanel.JmolPanel.startJmol(JmolPanel.java:304) at org.openscience.jmol.app.Jmol.main(Jmol.java:41) Hence changes are untested! ---------------------------------------------------------------------- Comment By: Joerg Meyer (j-meyer) Date: 2009-08-25 19:00 Message: 1.) Based on the files you checked into 11.8, I added some comments at the top as requested and did some further changes as detailed in the following. Resulting files CastepReader.20090825.java AimsReader.20090825.java are attached. 2.) Strange - for some reason it seemed to work in 11.6. Looking at your change (which makes perfect sense to avoid the warning) I wonder why it actually does... 3.) I see your point. There are no official specs (yet) for FHI-aims geometry.in files. The code is written in Fortran, and hence you can easily exchange the tabs for spaces without the Fortran IO system (in list mode) bothering. In fact I just convinced myself that both "atom" and "lattice_vector" keywords must be lower case to be accepted by aims. To eliminate the collision with PBD, could you please change the checkAims method in Resolver.java accordingly, to e.g. // FHI-aims only accepts keywords which are lower case - // hence no conflict with PDB reader (which require upper case "ATOM") if ( tokens[0].startsWith("atom") ) return true; if ( tokens[0].startsWith("lattice_vector") ) return true; ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-08-25 16:05 Message: The proposed AIMS reader breaks PDB format. We can't allow "atom" to be a marker, because "ATOM" is a marker for PDB files. So, if you want to read these files, you must force the filetype using load "aims::xxxx.in" I can't find specs for that file type. Why are there tabs in the line? Can we specify that "atom" must be lower case? (PDB must be upper case ATOM) ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-08-24 18:11 Message: %BLOCK POSITIONS_ABS ang was causing a warning -- I've changed that. Please check out the 11.8.RC6 code that I have just checked in and work from that if you can now. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-08-24 17:36 Message: OK, I'm onto this. Please provide some comment text with http references, for example: /** * Gaussian cube file format * * http://www.cup.uni-muenchen.de/oc/zipse/lv18099/orb_MOLDEN.html * this is good because it is source code * http://ftp.ccl.net/cca/software/SOURCES/C/scarecrow/gcube2plt.c * * http://www.nersc.gov/nusers/resources/software/apps/chemistry/gaussian/g98/00000430.htm * * distances are in Bohrs because we are reading Gaussian cube OUTPUT files * not Gaussian cube INPUT files. * * Miguel 2005 07 17 * a negative atom count means * that it is molecular orbital (MO) data * with MO data, the extra line contains the number * of orbitals and the orbital number * * these orbitals are interspersed -- all orbital values are * given together for each coordinate point. * * also used for JVXL and JVXL+ file format * */ ---------------------------------------------------------------------- Comment By: Joerg Meyer (j-meyer) Date: 2009-08-24 13:59 Message: Sorry - haven't thought about the fact that patch components against empty files cannot be conveniently extracted when trying to modify your current development version - I just wanted to have the functionality added to a stable release (which will be available from the AIMS web page quite soon). ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-08-23 07:51 Message: Please send the .java files; I have to patch these into 11.8, not 11.6. Thanks. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379135&aid=2841139&group_id=23629 ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
