git.osdn.net Git - molby/Molby.git/log

toshinagata1964 [Tue, 8 May 2012 05:27:51 +0000 (05:27 +0000)]

Windows version does not display last build date in the about dialog. Fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@201 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Tue, 8 May 2012 04:37:53 +0000 (04:37 +0000)]

MyAppCallback_lookupScriptMenu() is added to cmdtool_stubs.c, to allow compilation of the command line tool.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@200 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Tue, 8 May 2012 04:30:35 +0000 (04:30 +0000)]

Parameters now can be specified by using both explicit indices and atom types, like '7-ca-8'.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@199 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Tue, 8 May 2012 02:05:36 +0000 (02:05 +0000)]

Parameter editing is under overhaul.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@198 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Mon, 7 May 2012 16:36:02 +0000 (16:36 +0000)]

Handling of parameters are being improved, but still not complete

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@197 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Mon, 7 May 2012 11:48:21 +0000 (11:48 +0000)]

Handling of parameters is being reworked (still going on)

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@196 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Mon, 7 May 2012 09:10:17 +0000 (09:10 +0000)]

Restructure MolAction.c

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@195 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Mon, 7 May 2012 02:55:55 +0000 (02:55 +0000)]

Atom range specification for the vdw cutoff parameter is now made obsolete

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@194 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 3 May 2012 10:23:34 +0000 (10:23 +0000)]

LAMatrix.html was added to the repository.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@193 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 3 May 2012 10:22:50 +0000 (10:22 +0000)]

Vector3D[] and Transform[] are modified to accept an LAMatrix argument. The document is written for LAMatrix.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@192 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 3 May 2012 10:22:06 +0000 (10:22 +0000)]

Load Script Menu caused crash when no window is open. Fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@191 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 3 May 2012 04:04:39 +0000 (04:04 +0000)]

Ruby: Kernel.lookup_menu is implemented.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@190 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 3 May 2012 03:19:34 +0000 (03:19 +0000)]

LAMatrix.multiply was not working correctly when on-the-fly size conversion was required. Fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@189 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Wed, 2 May 2012 10:00:56 +0000 (10:00 +0000)]

Execute Script command was broken. Fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@188 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 29 Mar 2012 11:18:56 +0000 (11:18 +0000)]

CIF import may fail when _geom_bond_site_symmetry_1 field is missing. Fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@187 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 1 Mar 2012 13:50:30 +0000 (13:50 +0000)]

Figures for the document are added

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@186 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Sun, 26 Feb 2012 07:54:03 +0000 (07:54 +0000)]

Document was written for the collaboration with other quantum chemistry softwares.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@185 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Sun, 26 Feb 2012 07:50:23 +0000 (07:50 +0000)]

.log and .out are both accepted as the extension of the Gaussian and GAMESS log files.

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toshinagata1964 [Sat, 11 Feb 2012 15:03:36 +0000 (15:03 +0000)]

update_version.rb is improved.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@183 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Sat, 11 Feb 2012 14:34:15 +0000 (14:34 +0000)]

version 0.6.2

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@181 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Wed, 1 Feb 2012 15:57:45 +0000 (15:57 +0000)]

Document is updated to include new graphic objects in the model view.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@180 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Tue, 31 Jan 2012 10:04:29 +0000 (10:04 +0000)]

Ruby: Molecule#make_front, set_name, get_view_rotation, get_view_scale, get_view_translation, set_view_rotation, set_view_scale, set_view_translation, set_graphic_color, hide_graphic, show_graphic are implemented.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@179 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Mon, 30 Jan 2012 16:39:24 +0000 (16:39 +0000)]

Drawing custom graphics on the model view is being implemented.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@178 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Mon, 30 Jan 2012 10:59:30 +0000 (10:59 +0000)]

Ruby Dialog: modeless dialog is now implemented; interval timer is implemented. Ruby: $KCODE is set on startup, and coding:{shift-jis, utf-8} is recognized as the source code encoding (for executing script from file). Molecule#all returns IntGroup[0] when the molecule is empty (it should return IntGroup[]), which causes crash on Molecule#delete.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@177 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Tue, 17 Jan 2012 09:17:08 +0000 (09:17 +0000)]

Dialog#layout: the :align and :vertical_align options can now be specified as item attributes

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@176 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Tue, 17 Jan 2012 08:06:49 +0000 (08:06 +0000)]

The separator line in the Ruby Dialog was not working correctly.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@175 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Tue, 17 Jan 2012 06:42:55 +0000 (06:42 +0000)]

Vector3D and Transform objects are converted to LAMatrix object with dimensions 3 or 4 depending upon the context.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@174 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Mon, 16 Jan 2012 10:45:21 +0000 (10:45 +0000)]

LAMatrix#new errornously allows matrix with dimension 0. Fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@173 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Mon, 16 Jan 2012 10:43:56 +0000 (10:43 +0000)]

AtomRef#molecule is implemented.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@172 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Mon, 16 Jan 2012 10:13:37 +0000 (10:13 +0000)]

Empty Console Window command is implemented.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@171 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Fri, 13 Jan 2012 11:07:55 +0000 (11:07 +0000)]

LAMatrix.multiply was not working correctly when the first argument is a scalar. Fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@170 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 22 Dec 2011 11:32:49 +0000 (11:32 +0000)]

General matrix calculation (LAMatrix class in Ruby) is implemented. Seems to be working.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@169 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Wed, 21 Dec 2011 00:40:23 +0000 (00:40 +0000)]

Some of the document figures are updated.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@168 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Wed, 21 Dec 2011 00:02:41 +0000 (00:02 +0000)]

General matrix calculation is being implemented (still on the way)

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@167 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Tue, 20 Dec 2011 23:53:21 +0000 (23:53 +0000)]

Figures in the MD section of the document are added.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@166 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Tue, 20 Dec 2011 10:48:33 +0000 (10:48 +0000)]

In the document, navigation between the English/Japanese versions is possible in most pages.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@165 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Tue, 20 Dec 2011 09:00:53 +0000 (09:00 +0000)]

Document for MD calculation is written.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@164 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Mon, 19 Dec 2011 10:24:13 +0000 (10:24 +0000)]

The "log file" field is set to blank unless explicitly set by the user.

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toshinagata1964 [Mon, 19 Dec 2011 10:23:10 +0000 (10:23 +0000)]

Document for MD calculation is being written.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@162 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Wed, 7 Dec 2011 11:07:33 +0000 (11:07 +0000)]

The structure Mat33 and Transform are now column-first arrangement (no change on Ruby interface and mbsf file format)

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@161 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Wed, 30 Nov 2011 11:10:35 +0000 (11:10 +0000)]

Rms of crystallographic parameters (from the CIF file) are now kept in the molecule. Copying/saving of such parameters are not yet supported.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@160 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Wed, 30 Nov 2011 04:59:56 +0000 (04:59 +0000)]

Memo update for 0.6.1; also updated molby.iss for building Windows executable.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@159 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Sat, 26 Nov 2011 16:18:03 +0000 (16:18 +0000)]

Version 0.6.1

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@158 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Sat, 26 Nov 2011 16:15:44 +0000 (16:15 +0000)]

Document on ring fusion capability is written.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@157 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Sat, 26 Nov 2011 16:15:00 +0000 (16:15 +0000)]

Selection after ring fusion by 'double-click and type-in' now includes all atoms in the newly formed ring.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@156 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Sat, 26 Nov 2011 11:11:31 +0000 (11:11 +0000)]

Behavior of paste is improved when two dangling bonds are present in the fragment and the target molecule (i.e. ring fusion does work)

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@155 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Sat, 26 Nov 2011 07:25:35 +0000 (07:25 +0000)]

Some typical cyclic structures as well as solvent boxes are now accessible from 'Open Predefined' menu.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@154 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Fri, 25 Nov 2011 09:31:13 +0000 (09:31 +0000)]

Ruby: Molecule object is now unique to each open molecule, i.e. the same Molecule object is returned when requested for the same molecule.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@153 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Wed, 23 Nov 2011 16:08:17 +0000 (16:08 +0000)]

Ring fusion (e.g. expanding benzene to naphthalene) is implemented; still experimental, but seems to be working.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@152 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Tue, 22 Nov 2011 11:59:39 +0000 (11:59 +0000)]

__FILE__ is now set to the script file during execute_script.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@151 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Mon, 31 Oct 2011 06:22:35 +0000 (06:22 +0000)]

Some cleanup to suppress warnings

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@150 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Mon, 31 Oct 2011 06:10:41 +0000 (06:10 +0000)]

CIF import is improved, so that bonds including the calculated hydrogen atoms are created by guess.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@149 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Mon, 31 Oct 2011 05:26:04 +0000 (05:26 +0000)]

Ruby: Molecule#find_close_atoms is implemented.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@148 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Fri, 21 Oct 2011 00:45:13 +0000 (00:45 +0000)]

Enable undo for importing pdb and dcd.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@147 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Wed, 19 Oct 2011 07:56:10 +0000 (07:56 +0000)]

Import/export of dcd format is implemented.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@146 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Wed, 19 Oct 2011 07:55:18 +0000 (07:55 +0000)]

Creating AMBER input now allows to select between AMBER8 (also for NAMD) and AMBER11 formats.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@145 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Sat, 15 Oct 2011 15:07:41 +0000 (15:07 +0000)]

Version 0.6

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@143 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Sat, 15 Oct 2011 14:00:33 +0000 (14:00 +0000)]

On Windows, Molby::{Mbsf,Resource,Script}Path return slash-separated strings instead of backslash-separated strings.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@142 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 13 Oct 2011 11:57:37 +0000 (11:57 +0000)]

The solvate command does not correctly remove conflicting solvent molecules. Fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@141 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 13 Oct 2011 11:56:48 +0000 (11:56 +0000)]

Ruby: find_conflicts now exclude atom pairs separated by 0-3 bonds.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@140 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 13 Oct 2011 00:27:00 +0000 (00:27 +0000)]

export_prmtop can now be used from script

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@139 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Wed, 12 Oct 2011 16:13:25 +0000 (16:13 +0000)]

Merging molecule was resulting in strange order of merged parameters. Fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@138 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Wed, 12 Oct 2011 16:12:42 +0000 (16:12 +0000)]

Occasional crash on merging molecules is fixed. (Duplicating parameters was causing problems.)

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@137 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Wed, 12 Oct 2011 10:38:37 +0000 (10:38 +0000)]

Some solvent box are included in Scripts/mbsf folder. MolbyResourcePath is now called Molby::ResourcePath (old name is still usable for backward compatibility). Molby::ScriptPath, Molby::MbsfPath are also implemented.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@136 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Wed, 12 Oct 2011 10:14:07 +0000 (10:14 +0000)]

rotate_with_axis now can accept atom indices or names as the first three arguments.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@135 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Wed, 12 Oct 2011 10:13:08 +0000 (10:13 +0000)]

Setting external forces during MM/MD is implemented.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@134 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Tue, 11 Oct 2011 16:45:16 +0000 (16:45 +0000)]

Special parameters with atom indices were not working. Fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@133 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Tue, 11 Oct 2011 15:09:27 +0000 (15:09 +0000)]

Inserting/removing frames now work more consistently. The minimum number of frames is 1 instead of 0.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@132 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Wed, 5 Oct 2011 15:45:32 +0000 (15:45 +0000)]

Atoms to be excluded from MM/MD calculations are now specified by mm_exclude instead of occupancy.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@131 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Wed, 5 Oct 2011 14:44:26 +0000 (14:44 +0000)]

MM/MD calculation crashed when periodic cell is removed after calculation with non-nil cell. Fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@130 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Fri, 30 Sep 2011 16:02:19 +0000 (16:02 +0000)]

Makefile: "make depend" now creates a dependency file in the building directory.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@129 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Fri, 30 Sep 2011 09:33:21 +0000 (09:33 +0000)]

On windows, Molecule#path, Molecule#dir does not work correctly when the path includes double-byte characters. Fixed. (MyMBConv.h added)

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@128 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Fri, 30 Sep 2011 09:32:27 +0000 (09:32 +0000)]

On windows, Molecule#path, Molecule#dir does not work correctly when the path includes double-byte characters. Fixed.

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toshinagata1964 [Fri, 30 Sep 2011 02:45:53 +0000 (02:45 +0000)]

After MD run, coordinates are copied back to the molecule even when MD stopped abnormally. MDArena#init_velocities and MDArena#scale_velocities are implemented.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@126 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Fri, 30 Sep 2011 02:44:17 +0000 (02:44 +0000)]

During alchemical perturbation, graphite energy/forces were calculated incorrectly; fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@125 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Wed, 28 Sep 2011 11:47:14 +0000 (11:47 +0000)]

Implementation of alchemical perturbation seems to be working.

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toshinagata1964 [Tue, 27 Sep 2011 23:05:08 +0000 (23:05 +0000)]

Experimental implementation of alchemical perturbation (not tested yet)

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toshinagata1964 [Mon, 26 Sep 2011 15:50:15 +0000 (15:50 +0000)]

Improve crd/mdcrd import.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@122 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Mon, 26 Sep 2011 10:14:36 +0000 (10:14 +0000)]

The \'r_eq14\' parameter was not editable in the property table. Fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@121 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Mon, 26 Sep 2011 10:13:45 +0000 (10:13 +0000)]

Crash occurs when a Ruby exception is raised while editing property table. Fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@120 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Tue, 20 Sep 2011 11:49:19 +0000 (11:49 +0000)]

Mac: use pthread instead of SIGALRM for interval timer (experimental)

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toshinagata1964 [Sun, 18 Sep 2011 13:41:46 +0000 (13:41 +0000)]

Ruby: Molecule#dup now duplicates the unit cell, symmetry operations, and MD settings.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@118 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 15 Sep 2011 10:29:51 +0000 (10:29 +0000)]

Remove \'build xxxxxxxx\' string from the version description.

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toshinagata1964 [Wed, 14 Sep 2011 16:21:31 +0000 (16:21 +0000)]

AtomRef.exclusion causes bus error when the MDArena is not yet built. Fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@116 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Tue, 13 Sep 2011 16:17:53 +0000 (16:17 +0000)]

After loading the molecule, occupancy factors are checked, and if all atoms have zero occupancy then all are set to 1.0.

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toshinagata1964 [Wed, 7 Sep 2011 16:00:28 +0000 (16:00 +0000)]

Remove some startup code when building a command line tool

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@114 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Wed, 7 Sep 2011 15:59:51 +0000 (15:59 +0000)]

Exclude atoms with occupancy = 0 from MM/MD-graphite calculations

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@113 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Tue, 6 Sep 2011 15:06:15 +0000 (15:06 +0000)]

Ruby command get_coord_from_frame(index, group=nil, cflag=nil) is implemented.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@112 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Tue, 6 Sep 2011 10:24:16 +0000 (10:24 +0000)]

Exclude atoms with occupancy = 0 from MM/MD calculations

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@111 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Tue, 6 Sep 2011 09:22:36 +0000 (09:22 +0000)]

Exclude atoms with occupancy = 0 from MM/MD calculations

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@110 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Mon, 5 Sep 2011 10:06:12 +0000 (10:06 +0000)]

The (experimental) command line version does not compile; empty MainView_resizeToFit() is added to cmdtool_stubs.c.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@109 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Thu, 1 Sep 2011 11:51:05 +0000 (11:51 +0000)]

The MO info table is renamed to MO energy, and the alpha and beta orbitals of same indices are shown in the same row.

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toshinagata1964 [Wed, 31 Aug 2011 08:32:48 +0000 (08:32 +0000)]

MO import from GAMESS log file was broken

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@107 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Wed, 31 Aug 2011 08:06:50 +0000 (08:06 +0000)]

Fchk import: zero is accepted as the number of alpha/beta electrons

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@106 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Tue, 23 Aug 2011 09:59:21 +0000 (09:59 +0000)]

Memo update for version 0.5.6.2

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@104 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Tue, 23 Aug 2011 09:49:47 +0000 (09:49 +0000)]

Fchk import was broken (enbug in 0.5.6.1); fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@103 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Fri, 19 Aug 2011 11:43:22 +0000 (11:43 +0000)]

Final compile date/time is shown in the 'About' window

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toshinagata1964 [Fri, 19 Aug 2011 11:42:45 +0000 (11:42 +0000)]

Importing mdcrd was still broken. Fixed (hopefully)

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@101 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Fri, 5 Aug 2011 11:40:07 +0000 (11:40 +0000)]

Fix mdcrd import to allow coordinates using full 8 digits (like -123.456 or 1234.567)

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@100 a2be9bc6-48de-4e38-9406-05402d4bc13c

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toshinagata1964 [Fri, 5 Aug 2011 11:38:52 +0000 (11:38 +0000)]

Occasional crash during minimization is fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@99 a2be9bc6-48de-4e38-9406-05402d4bc13c