OSDN Git Service
toshinagata1964 [Tue, 20 Nov 2012 11:44:38 +0000 (11:44 +0000)]
Some wrong behavior of PME calculation is fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@340
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toshinagata1964 [Mon, 19 Nov 2012 11:03:17 +0000 (11:03 +0000)]
An error in PME energy calculation is corrected. MDArean#ewald_order is implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@339
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toshinagata1964 [Mon, 19 Nov 2012 03:04:31 +0000 (03:04 +0000)]
Error message in Molecule#atoms[] was not working. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@338
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toshinagata1964 [Mon, 19 Nov 2012 02:02:12 +0000 (02:02 +0000)]
MDArena#use_ewald, ewald_beta, ewald_grid, ewald_freq are implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@337
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toshinagata1964 [Wed, 14 Nov 2012 11:45:43 +0000 (11:45 +0000)]
(Retry committing) Particle mesh Ewald (still in progress)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@336
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toshinagata1964 [Wed, 14 Nov 2012 11:44:22 +0000 (11:44 +0000)]
(Re-retry committing) expand_by_symmetry was not working correctly when no symmetry operations are defined (and expansion with only translation is specified). Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@335
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toshinagata1964 [Wed, 14 Nov 2012 11:34:10 +0000 (11:34 +0000)]
Particle mesh Ewald (still in progress)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@334
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toshinagata1964 [Wed, 14 Nov 2012 11:33:44 +0000 (11:33 +0000)]
(Retry committing) expand_by_symmetry was not working correctly when no symmetry operations are defined (and expansion with only translation is specified). Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@333
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toshinagata1964 [Wed, 14 Nov 2012 11:28:54 +0000 (11:28 +0000)]
expand_by_symmetry was not working correctly when no symmetry operations are defined (and expansion with only translation is specified). Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@332
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toshinagata1964 [Mon, 12 Nov 2012 11:22:09 +0000 (11:22 +0000)]
Change in Antechamber/Resp dialog: molecular charge can be always assigned, and 'optimize' checkbox is no longer visible in the Resp dialog
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@331
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toshinagata1964 [Mon, 12 Nov 2012 11:21:23 +0000 (11:21 +0000)]
In calling a subprocess, a wait of 10 msec is inserted between termination check (may be or not useful for more stable handling of subprocesses...?
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@330
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toshinagata1964 [Sun, 11 Nov 2012 05:00:00 +0000 (05:00 +0000)]
Particle Mesh Ewald is being implemented (still not working yet)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@329
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toshinagata1964 [Fri, 2 Nov 2012 11:24:29 +0000 (11:24 +0000)]
Suppress output of pi-anchors when generating GAMESS or Gaussian input files.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@328
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toshinagata1964 [Fri, 2 Nov 2012 11:23:53 +0000 (11:23 +0000)]
Utility methods Enumerable#sum and Enumerable#average are implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@327
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toshinagata1964 [Thu, 1 Nov 2012 02:32:39 +0000 (02:32 +0000)]
When new bonds are created, angles of type X-##-## (## is pi-anchor) should not be automatically added.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@326
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toshinagata1964 [Thu, 1 Nov 2012 02:31:43 +0000 (02:31 +0000)]
Parameter lookup was not working correctly when neither local or global search is specified and 'missing' is turned on. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@325
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toshinagata1964 [Thu, 1 Nov 2012 02:30:31 +0000 (02:30 +0000)]
'==' operator is defined for Parameter, ParameterRef, AtomRef, ParEnumerable, MolEnumerable, and Molecule classes.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@324
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toshinagata1964 [Wed, 31 Oct 2012 15:45:23 +0000 (15:45 +0000)]
Create Pi Anchor menu command is implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@323
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toshinagata1964 [Wed, 31 Oct 2012 11:20:21 +0000 (11:20 +0000)]
Parameter#lookup (and related methods) can now look up parameters from the atom indices, even when the parameter is described in atom types.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@322
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toshinagata1964 [Wed, 31 Oct 2012 09:12:36 +0000 (09:12 +0000)]
History functionality is available in the Ruby console. Handling of fonts in Windows version is improved.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@321
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toshinagata1964 [Wed, 31 Oct 2012 02:34:21 +0000 (02:34 +0000)]
Parameter methods angle, angles, bond, bonds, etc. can now be used as singleton methods (i.e. Parameter.element(1) is now allowed)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@320
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toshinagata1964 [Wed, 31 Oct 2012 02:33:21 +0000 (02:33 +0000)]
Flashing of the table while pressing the shift key (and other modifier keys) is reduced.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@319
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toshinagata1964 [Wed, 31 Oct 2012 00:53:34 +0000 (00:53 +0000)]
Symmetry expanded atoms now can be selected by mouse drag.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@318
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toshinagata1964 [Tue, 30 Oct 2012 15:56:32 +0000 (15:56 +0000)]
Expanding by symmetry (and loading cif file) was not working correctly. Hopefully fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@317
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toshinagata1964 [Tue, 30 Oct 2012 09:59:41 +0000 (09:59 +0000)]
Attribute table was not updated correctly after revert. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@316
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toshinagata1964 [Tue, 30 Oct 2012 00:37:39 +0000 (00:37 +0000)]
Revert command is implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@315
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toshinagata1964 [Tue, 30 Oct 2012 00:12:01 +0000 (00:12 +0000)]
Atom renumbering was not working for pi anchor table. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@314
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toshinagata1964 [Tue, 30 Oct 2012 00:11:43 +0000 (00:11 +0000)]
Two subsequent dragging of different atoms were causing undo failure. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@313
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toshinagata1964 [Mon, 29 Oct 2012 23:43:20 +0000 (23:43 +0000)]
Remove previous pi-anchor codes.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@312
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toshinagata1964 [Mon, 29 Oct 2012 14:57:47 +0000 (14:57 +0000)]
Pi anchor implementation is done.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@311
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toshinagata1964 [Mon, 29 Oct 2012 11:37:08 +0000 (11:37 +0000)]
New implementation of pi anchor atoms is close to complete (not well tested yet)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@310
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toshinagata1964 [Sun, 28 Oct 2012 15:54:19 +0000 (15:54 +0000)]
New create_pi_anchor method is implemented (but not working well yet)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@309
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toshinagata1964 [Sun, 28 Oct 2012 09:26:28 +0000 (09:26 +0000)]
The load/save codes are rewritten, so that the error/warning messages are shown in the console.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@308
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toshinagata1964 [Fri, 26 Oct 2012 11:34:08 +0000 (11:34 +0000)]
Another implementation of pi-anchor is being tried (on the way; doesn't even compile now)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@307
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toshinagata1964 [Thu, 25 Oct 2012 15:59:26 +0000 (15:59 +0000)]
Pi atom positions are now cached within the piatom structure.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@306
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toshinagata1964 [Thu, 25 Oct 2012 10:17:08 +0000 (10:17 +0000)]
Merging/unmerging molecules are extensively revised. Hopefully undo works more consistently than before.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@305
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toshinagata1964 [Wed, 24 Oct 2012 16:31:12 +0000 (16:31 +0000)]
Connection check is rewritten to include the pi anchor bonds (may be incomplete yet)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@304
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toshinagata1964 [Wed, 24 Oct 2012 11:03:35 +0000 (11:03 +0000)]
Pi anchor force calculation is being implemented (not working yet at all)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@303
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toshinagata1964 [Tue, 23 Oct 2012 11:22:48 +0000 (11:22 +0000)]
The third argument to Molecule#get_coord_from_frame() is now obsolete, but causes warning instead of ArgumentError
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@302
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toshinagata1964 [Tue, 23 Oct 2012 08:50:52 +0000 (08:50 +0000)]
Handling of buildInfo.txt and revisionInfo.txt are reworked
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@301
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toshinagata1964 [Tue, 23 Oct 2012 02:54:33 +0000 (02:54 +0000)]
Handling of version numbers in update_version.rb was incomplete. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@300
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toshinagata1964 [Tue, 23 Oct 2012 01:40:51 +0000 (01:40 +0000)]
Molecule#get_coord_from_frame now always tries to copy the cell information.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@299
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toshinagata1964 [Mon, 22 Oct 2012 11:43:48 +0000 (11:43 +0000)]
Kernel#exit is now untouched in the command line version. The command line version now displays version message on startup.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@298
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toshinagata1964 [Fri, 19 Oct 2012 11:46:00 +0000 (11:46 +0000)]
Molecule#cell_flexibility, set_cell_flexibility are obsolete, and the unit cell is always flexible (i.e. different frames can have different cells). Molecule#cell_periodicity and set_cell_periodicity are implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@297
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toshinagata1964 [Sat, 13 Oct 2012 14:36:15 +0000 (14:36 +0000)]
version 0.6.4
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@295
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toshinagata1964 [Sat, 13 Oct 2012 11:36:40 +0000 (11:36 +0000)]
Document is updated, and an appendix describing the filter_kit is written.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@294
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toshinagata1964 [Fri, 12 Oct 2012 11:22:42 +0000 (11:22 +0000)]
Experimental 'filter' mode is removed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@293
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toshinagata1964 [Fri, 12 Oct 2012 06:06:26 +0000 (06:06 +0000)]
Ruby: Dialog#filter_kit is implemented. This looks better than the experimental 'filter' mode.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@292
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toshinagata1964 [Thu, 11 Oct 2012 15:45:00 +0000 (15:45 +0000)]
Filter mode (development continued)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@291
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toshinagata1964 [Thu, 11 Oct 2012 11:52:16 +0000 (11:52 +0000)]
'Filter' mode is implemented (experimentally)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@290
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toshinagata1964 [Wed, 10 Oct 2012 05:41:56 +0000 (05:41 +0000)]
Crash when loading a new molecule failed. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@289
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toshinagata1964 [Wed, 3 Oct 2012 09:37:27 +0000 (09:37 +0000)]
ORTEP export did not generate the same orientation as in the screen. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@288
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toshinagata1964 [Sun, 2 Sep 2012 22:53:38 +0000 (22:53 +0000)]
MM of pi-metal bonds are being implemented (only the parameter search is complete)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@287
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toshinagata1964 [Sat, 1 Sep 2012 15:04:16 +0000 (15:04 +0000)]
Ruby: Molecule#bond_par, angle_par, dihedral_par, improper_par, vdw_par are made obsolete, and instead MDArena#bond_par, angle_par, dihedral_par, improper_par, vdw_par are implemented. These methods returns the 'cached' parameters in the MDArena. The ParameterRef record for these parameters have a negative index, which represents the parameter belongs to the MDArena instead of the molecule.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@286
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toshinagata1964 [Sat, 1 Sep 2012 13:07:13 +0000 (13:07 +0000)]
Opening bond/angle/dihedral/improper table now triggers search of MD parameters (but not rebuilding angle/dihedral/improper tables from bond information)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@285
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toshinagata1964 [Sat, 1 Sep 2012 09:19:45 +0000 (09:19 +0000)]
Handling of view-related attributes of Molecule is improved (specifically, methods like Molecule#show_periodic_image= now work). Best-fit plane dialog is not working in Windows; fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@284
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toshinagata1964 [Sat, 1 Sep 2012 01:38:10 +0000 (01:38 +0000)]
Ruby documents for pi-anchors are written.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@283
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toshinagata1964 [Thu, 30 Aug 2012 15:16:25 +0000 (15:16 +0000)]
Pi-metal bonds are being implemented (molecular mechanics part is not handled yet)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@282
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toshinagata1964 [Wed, 22 Aug 2012 13:47:49 +0000 (13:47 +0000)]
Experimental feature: dummy atoms to represent pi-metal bonds
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@281
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toshinagata1964 [Mon, 20 Aug 2012 04:45:56 +0000 (04:45 +0000)]
Some fields in md_arena were not properly copied when a molecule is duplicated. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@280
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toshinagata1964 [Mon, 20 Aug 2012 04:45:30 +0000 (04:45 +0000)]
'Show Graphite' command was using wrong C-C bond length. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@279
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toshinagata1964 [Sun, 12 Aug 2012 13:19:12 +0000 (13:19 +0000)]
Some unused fields of Molecule were removed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@278
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toshinagata1964 [Sun, 12 Aug 2012 13:18:31 +0000 (13:18 +0000)]
LAMatrix singular value decomposition was implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@277
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toshinagata1964 [Sun, 12 Aug 2012 13:17:51 +0000 (13:17 +0000)]
Ruby: create_graphic was not working correctly when :ellipsoid is given with a single radius.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@276
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toshinagata1964 [Sat, 4 Aug 2012 02:37:10 +0000 (02:37 +0000)]
Loading multiple-frame mbsf sometimes fails to load the cell parameter for the last frame. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@275
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toshinagata1964 [Fri, 3 Aug 2012 15:48:25 +0000 (15:48 +0000)]
Some cleanup of the internal structure; unused fields are removed and AtomConnect struct is introduced
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@274
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toshinagata1964 [Thu, 2 Aug 2012 07:46:07 +0000 (07:46 +0000)]
Property table can now list the unit cell parameters.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@273
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toshinagata1964 [Thu, 2 Aug 2012 04:38:32 +0000 (04:38 +0000)]
Documents for Dialog#show, Dialog#hide are written. (These were somehow missing)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@272
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toshinagata1964 [Thu, 26 Jul 2012 07:19:27 +0000 (07:19 +0000)]
Cell minimization was not working correctly when no symmetry operations are defined. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@271
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toshinagata1964 [Wed, 25 Jul 2012 14:42:54 +0000 (14:42 +0000)]
MDArena#prepare was not working correctly when unit cell is added/created after initialization of MDArena. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@270
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toshinagata1964 [Wed, 25 Jul 2012 01:07:01 +0000 (01:07 +0000)]
Handling of selection from Ruby script was partially broken. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@269
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toshinagata1964 [Tue, 24 Jul 2012 17:22:38 +0000 (17:22 +0000)]
Best fit plane dialog was behaving strangely Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@268
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toshinagata1964 [Tue, 24 Jul 2012 17:21:47 +0000 (17:21 +0000)]
Handling of Molecule object was not consistent. Hopefully fixed...
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@267
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toshinagata1964 [Tue, 24 Jul 2012 11:11:17 +0000 (11:11 +0000)]
Export ORTEP (improved) and best-fit plane calculations are implemented in Scripts/crystal.rb.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@266
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toshinagata1964 [Tue, 24 Jul 2012 10:24:11 +0000 (10:24 +0000)]
The revision number is displayed in the about dialog (and is used for labeling clipboard contents)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@265
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toshinagata1964 [Tue, 24 Jul 2012 09:17:35 +0000 (09:17 +0000)]
Copy/paste of molecules was broken when it had atoms with more than ATOMS_CONNECTS_LIMIT bonds. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@264
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toshinagata1964 [Fri, 20 Jul 2012 14:16:16 +0000 (14:16 +0000)]
Documents for some missing Ruby methods are written.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@263
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toshinagata1964 [Fri, 6 Jul 2012 07:46:33 +0000 (07:46 +0000)]
Cell minimization is improved (hopefully...)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@262
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toshinagata1964 [Thu, 5 Jul 2012 15:25:49 +0000 (15:25 +0000)]
Remove printf() for debugging cell minimization
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@261
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toshinagata1964 [Thu, 5 Jul 2012 14:22:43 +0000 (14:22 +0000)]
Implemented minimization of cell parameters. Looks like working...
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@260
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toshinagata1964 [Thu, 5 Jul 2012 11:19:05 +0000 (11:19 +0000)]
Experimental: trying to implement minimizaion of cell parameters (not sure whether it is possible at all)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@259
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toshinagata1964 [Thu, 5 Jul 2012 00:13:56 +0000 (00:13 +0000)]
Handling of flexible cells were still inconsistent.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@258
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toshinagata1964 [Wed, 4 Jul 2012 15:35:16 +0000 (15:35 +0000)]
Molecule#cell_flexibility and set_cell_flexibility are implemented, and enable/disable_cell_flexibility are removed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@257
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toshinagata1964 [Wed, 4 Jul 2012 13:41:08 +0000 (13:41 +0000)]
Figures for the Ruby tutorial are added to the repository.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@256
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toshinagata1964 [Wed, 4 Jul 2012 11:02:08 +0000 (11:02 +0000)]
Handling of periodic box during MD is being reworked.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@255
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toshinagata1964 [Wed, 4 Jul 2012 05:56:14 +0000 (05:56 +0000)]
Ruby: Molecule#box= was not working as expected. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@254
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toshinagata1964 [Wed, 4 Jul 2012 04:57:18 +0000 (04:57 +0000)]
Memory leak bugs are examined and removed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@253
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toshinagata1964 [Wed, 4 Jul 2012 01:26:35 +0000 (01:26 +0000)]
amend_by_symmetry in MD was still broken. Hopefully fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@252
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toshinagata1964 [Tue, 3 Jul 2012 16:14:08 +0000 (16:14 +0000)]
Tutorial for the Ruby interpreter was (finally) written.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@251
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toshinagata1964 [Tue, 3 Jul 2012 10:43:31 +0000 (10:43 +0000)]
amend_by_symmetry during MD run was causing crash. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@250
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toshinagata1964 [Mon, 2 Jul 2012 07:13:31 +0000 (07:13 +0000)]
Graphite potential calculation is further modified (hope this is complete now!)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@249
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toshinagata1964 [Sat, 30 Jun 2012 08:11:50 +0000 (08:11 +0000)]
When no molecule is open, Ruby scripts are evaluated in the context of 'main' (the toplevel object)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@248
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toshinagata1964 [Fri, 29 Jun 2012 13:43:29 +0000 (13:43 +0000)]
Improving graphite potential calculation (hopefully complete).
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@247
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toshinagata1964 [Fri, 29 Jun 2012 11:28:48 +0000 (11:28 +0000)]
Graphite potential calculation is improved.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@246
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toshinagata1964 [Fri, 29 Jun 2012 08:50:25 +0000 (08:50 +0000)]
The graphite potential calculation is being reworked.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@245
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toshinagata1964 [Fri, 29 Jun 2012 04:28:10 +0000 (04:28 +0000)]
The current working directory is set to the document home on startup.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@244
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toshinagata1964 [Fri, 29 Jun 2012 01:19:09 +0000 (01:19 +0000)]
The anisotropic parameters for the symmetry expanded atoms are now correctly handled.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@243
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toshinagata1964 [Fri, 29 Jun 2012 01:18:40 +0000 (01:18 +0000)]
Pressure control and surface potential are removed from the GUI; they are not well tested and should be used with great care.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@242
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toshinagata1964 [Thu, 28 Jun 2012 10:49:34 +0000 (10:49 +0000)]
The load commands can now include error messages in Ruby exception.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@241
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toshinagata1964 [Thu, 28 Jun 2012 06:38:13 +0000 (06:38 +0000)]
MD minimize was not working properly (especially for the second run with the same molecule). Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@240
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