OSDN Git Service
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
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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
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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
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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
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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
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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
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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.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@127
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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
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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
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toshinagata1964 [Wed, 28 Sep 2011 11:47:14 +0000 (11:47 +0000)]
Implementation of alchemical perturbation seems to be working.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@124
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toshinagata1964 [Tue, 27 Sep 2011 23:05:08 +0000 (23:05 +0000)]
Experimental implementation of alchemical perturbation (not tested yet)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@123
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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
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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
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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
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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)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@119
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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
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toshinagata1964 [Thu, 15 Sep 2011 10:29:51 +0000 (10:29 +0000)]
Remove \'build xxxxxxxx\' string from the version description.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@117
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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
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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.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@115
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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
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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
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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
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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
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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
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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
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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.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@108
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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
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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
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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
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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
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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
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@102
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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
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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
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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
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toshinagata1964 [Fri, 5 Aug 2011 11:38:11 +0000 (11:38 +0000)]
memo update
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@98
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toshinagata1964 [Wed, 3 Aug 2011 10:13:34 +0000 (10:13 +0000)]
memo update
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@96
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toshinagata1964 [Wed, 3 Aug 2011 10:12:54 +0000 (10:12 +0000)]
Loading GAMESS dat file now can be interrupted by ESC.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@95
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toshinagata1964 [Wed, 3 Aug 2011 10:12:02 +0000 (10:12 +0000)]
Occasionally, termination of the subprocess (like antechamber) was not detected properly, and the subprocess was left as a zombie. Improved, but may not be completely fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@94
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toshinagata1964 [Wed, 3 Aug 2011 10:10:16 +0000 (10:10 +0000)]
Disable close box of RubyDialogFrame.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@93
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toshinagata1964 [Wed, 3 Aug 2011 10:09:48 +0000 (10:09 +0000)]
On importing frcmod, atom type with a single character (like "c") was not recognized properly. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@92
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toshinagata1964 [Wed, 3 Aug 2011 10:02:52 +0000 (10:02 +0000)]
Mac: config.h/Makefiles for AmberTools is modified so that gfortran library is statically linked
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@91
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toshinagata1964 [Wed, 3 Aug 2011 10:01:03 +0000 (10:01 +0000)]
ruby-1.8.7-p160.tar.gz is added (required for building)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@90
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toshinagata1964 [Tue, 2 Aug 2011 11:24:36 +0000 (11:24 +0000)]
MO import from GAMESS log/dat files seems to be working. Crash on running antechamber/parmchk on PPC Mac is (hopefully) fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@89
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toshinagata1964 [Mon, 1 Aug 2011 12:04:34 +0000 (12:04 +0000)]
MO import from GAMESS output is being implemented (not complete yet)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@88
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toshinagata1964 [Sat, 30 Jul 2011 10:28:12 +0000 (10:28 +0000)]
Memo update.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@86
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toshinagata1964 [Sat, 30 Jul 2011 10:01:29 +0000 (10:01 +0000)]
Add missing document figures.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@85
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toshinagata1964 [Sat, 30 Jul 2011 09:14:53 +0000 (09:14 +0000)]
Parameter cut was not working correctly when the selection was non-contiguous; fixed. Mac: property table did not get focus under certain conditions; fixed. Document: the English version had the page titles in Japanese; fixed. Navigation prev/next has been added on top of each page.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@84
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toshinagata1964 [Sat, 30 Jul 2011 06:40:37 +0000 (06:40 +0000)]
Step 5 of the tutorial is complete.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@83
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toshinagata1964 [Fri, 29 Jul 2011 11:51:16 +0000 (11:51 +0000)]
Import AMBER Frcmod menu command is implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@82
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toshinagata1964 [Thu, 28 Jul 2011 16:28:40 +0000 (16:28 +0000)]
The property table section of the tutorial is being written. Trying to fix the problem (on Mac) that the table does not get focus after MyGLCanvas get one, but still unsuccessful.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@81
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toshinagata1964 [Thu, 28 Jul 2011 11:42:06 +0000 (11:42 +0000)]
CIF import is implemented (maybe still incomplete)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@80
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toshinagata1964 [Tue, 26 Jul 2011 15:54:43 +0000 (15:54 +0000)]
Create New Parameter menu command is implemented. MoleculePrepareMDArena() is implmeneted in Molecule.c. Crash in RubyDialogFrame.cpp (sizeOfString) was fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@79
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toshinagata1964 [Thu, 21 Jul 2011 16:45:41 +0000 (16:45 +0000)]
Create New Atom menu command is being implemented (not tested at all yet)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@78
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toshinagata1964 [Thu, 21 Jul 2011 11:44:31 +0000 (11:44 +0000)]
Document is being updated (the property table section)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@77
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toshinagata1964 [Thu, 21 Jul 2011 08:44:49 +0000 (08:44 +0000)]
Importing frcmod is improved. Import AMBER Lib (in MM/MD->Tools menu) is implemented. Ruby: Molecule#resize_to_fit is implemented. Molecule.open now accepts empty arguments for creating a new untitled document. Kernel.message_box was causing exception when :ok is given; fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@76
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toshinagata1964 [Wed, 20 Jul 2011 10:00:50 +0000 (10:00 +0000)]
Importing mdcrd with periodic box now works correctly.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@75
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toshinagata1964 [Wed, 20 Jul 2011 09:29:07 +0000 (09:29 +0000)]
AMBER prmtop/inpcrd export is improved for periodic systems.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@74
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toshinagata1964 [Thu, 7 Jul 2011 17:58:01 +0000 (17:58 +0000)]
Copy/paste now handle parameters properly (hopefully...). The Ruby method 'duplicate' also now copies parameters.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@73
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toshinagata1964 [Thu, 7 Jul 2011 04:13:35 +0000 (04:13 +0000)]
.gets now appends a newline after the input string. AmberTools: antechamber sometimes created strange intermediate file; fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@72
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toshinagata1964 [Wed, 6 Jul 2011 23:13:28 +0000 (23:13 +0000)]
Ruby: stdin.{gets, readline} are implemented (other stdin methods will cause exception).
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@71
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toshinagata1964 [Wed, 6 Jul 2011 06:25:01 +0000 (06:25 +0000)]
Importing Amber mdcrd files is implemented.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@70
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toshinagata1964 [Tue, 5 Jul 2011 17:46:20 +0000 (17:46 +0000)]
Molecule#{bond,angle,dihedral,improper,vdw}_par were wrongly implemented. Fixed. 'Create SANDER input' is implemented (still not tested much).
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@69
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toshinagata1964 [Sun, 3 Jul 2011 15:53:23 +0000 (15:53 +0000)]
Ruby: AtomRef#exclusion method was incorrectly calling Molecule#md_arena. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@68
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toshinagata1964 [Sun, 3 Jul 2011 14:46:35 +0000 (14:46 +0000)]
Ruby: Molecule#bond_par, angle_par, dihedral_par, improper_par, vdw_par are implemented. Molecule#each_atom now accepts an IntGroup argument to limit iteration in some atom group. Initialition of the MDArena is now explicitly two-stage (specified by the is_initialized flag 0 -> 1 -> 2). molecule.rb: the solvate procedure now set the segment name 'SOLV' for the added solvent atoms.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@67
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toshinagata1964 [Sat, 2 Jul 2011 15:24:26 +0000 (15:24 +0000)]
Gaff and parm99 parameters: the equilibrium bond lengths have now three significant digits after the decimal point. Ruby: AtomRef#exclusion method is implemented. MM/MD: minimization sometimes caused crash. Hopefully fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@66
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toshinagata1964 [Tue, 26 Apr 2011 14:06:19 +0000 (14:06 +0000)]
Memo update.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@65
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toshinagata1964 [Tue, 26 Apr 2011 04:40:11 +0000 (04:40 +0000)]
Importing GaussianW fch(k) files were not working because of the different end-of-line characters. Fixed. The extension '.fch' is now recognized as a Gaussian formatted checkpoint files.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@63
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toshinagata1964 [Wed, 2 Mar 2011 10:25:09 +0000 (10:25 +0000)]
Pasting MD parameters to a molecule with no parameters was not working. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@62
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toshinagata1964 [Thu, 3 Jun 2010 13:47:32 +0000 (13:47 +0000)]
Crash in MM minimization when no unit cell is defined (enbug in r59); fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@61
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toshinagata1964 [Wed, 2 Jun 2010 15:45:11 +0000 (15:45 +0000)]
Xcode project: GCC4.0 is explicitly designated (necessary for building for Mac OS 10.4 on Snow Leopard)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@60
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toshinagata1964 [Mon, 31 May 2010 11:41:11 +0000 (11:41 +0000)]
The nearest-neighbor lookup of nonbonding force calculation was problematic; fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@59
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toshinagata1964 [Tue, 18 May 2010 14:36:00 +0000 (14:36 +0000)]
The view settings for mbsf files now can be restored correctly (hopefully). A comment in the mbsf format file was fixed (the description 'charge' was erroneously omitted).
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@58
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toshinagata1964 [Mon, 17 May 2010 15:09:10 +0000 (15:09 +0000)]
wxSources/docview.cpp is added to the project. Trackball.c is added to the Molby_command target (xcode only, still experimental)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@57
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toshinagata1964 [Sun, 16 May 2010 03:09:36 +0000 (03:09 +0000)]
The native format (mbsf) now preserves the display conditions, such as scale, orientation, and show/hide unit cell, periodic images, etc.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@56
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toshinagata1964 [Fri, 14 May 2010 16:03:12 +0000 (16:03 +0000)]
Inconsistency between the Xcode project settings and Makefile_amber11 was resolved. Exception from 'Show periodic image' dialog box was fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@55
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toshinagata1964 [Wed, 12 May 2010 16:29:02 +0000 (16:29 +0000)]
Calculation of vdw/elect forces was wrong when the periodic cell is small; fixed. No new frame is generated when md_frame.run/minimize is called from Ruby script.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@54
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toshinagata1964 [Tue, 11 May 2010 22:50:35 +0000 (22:50 +0000)]
Flags for 'show graphite' and 'show periodic images' are implemented. In MM/MD engine, the handling of Verlet list seems to be incomplete, but this is still being worked on.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@53
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toshinagata1964 [Sat, 8 May 2010 07:29:22 +0000 (07:29 +0000)]
Handling of MD dialog is improved. MM/MD calculation bug (introduced in rev 50) is fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@52
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toshinagata1964 [Sat, 8 May 2010 04:09:23 +0000 (04:09 +0000)]
The Ruby command wrap_unit_cell was not working correctly.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@51
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toshinagata1964 [Fri, 7 May 2010 16:20:03 +0000 (16:20 +0000)]
The MM/MD re-initialization after modification of coordinates was incomplete.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@50
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toshinagata1964 [Thu, 6 May 2010 15:29:52 +0000 (15:29 +0000)]
Version 0.5.4
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@48
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toshinagata1964 [Thu, 6 May 2010 15:15:39 +0000 (15:15 +0000)]
Introduce MolbyResourcePath global constant, which points to the directory containing 'Scripts' and 'amber11' resources. Ruby command Kernel.call_subprocess is implemented. ParameterRef.par_type= wrongly parsed the atom type string; fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@47
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toshinagata1964 [Thu, 6 May 2010 15:14:32 +0000 (15:14 +0000)]
Windows: the radio buttons with no explicit radio group showed stranged behavior; fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@46
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toshinagata1964 [Thu, 6 May 2010 15:13:59 +0000 (15:13 +0000)]
Some parameter editing caused segmentation fault; fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@45
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toshinagata1964 [Thu, 6 May 2010 15:13:26 +0000 (15:13 +0000)]
Undo of creating atoms caused segmentation fault; fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@44
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toshinagata1964 [Thu, 6 May 2010 15:12:58 +0000 (15:12 +0000)]
Improved handling of DOSish file paths. The functions strdup() and wcsdup() are implemented here so that the malloc libaries for debugging can be used.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@43
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toshinagata1964 [Thu, 6 May 2010 15:12:18 +0000 (15:12 +0000)]
Importing GAMESS dat file was broken; fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@42
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toshinagata1964 [Thu, 6 May 2010 15:11:39 +0000 (15:11 +0000)]
Added instruction for building and copying resp.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@41
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toshinagata1964 [Thu, 6 May 2010 15:11:06 +0000 (15:11 +0000)]
Removal of double-call of wxDocument::Close() (revision 31) was undone, because it caused occasional crashes.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@40
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toshinagata1964 [Thu, 6 May 2010 15:10:27 +0000 (15:10 +0000)]
Undo is kept enabled during 'molload' and related calls. The 'do not keep logs' option for antechamber was not working; fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@39
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toshinagata1964 [Thu, 6 May 2010 15:09:22 +0000 (15:09 +0000)]
Add hydrogen was broken; fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@38
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toshinagata1964 [Thu, 6 May 2010 15:09:03 +0000 (15:09 +0000)]
Ambertools dialog is improved.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@37
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toshinagata1964 [Thu, 6 May 2010 15:08:45 +0000 (15:08 +0000)]
generation of internal coordinates (NZVAR=#{3n-5}) is supported in the 'Create GAMESS input' dialog.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@36
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toshinagata1964 [Thu, 6 May 2010 15:07:54 +0000 (15:07 +0000)]
The amber11 binaries are now built in the project directory, instead of the 'build' subdirectory. Windows: event.cpp (from wxMSW) is included in the project with a slight modification.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@35
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toshinagata1964 [Thu, 6 May 2010 15:06:52 +0000 (15:06 +0000)]
Windows: interrupting the subprocess (antechamber etc.) caused grandchildren processes to survive as zombies; fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@34
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toshinagata1964 [Sun, 25 Apr 2010 08:07:57 +0000 (08:07 +0000)]
Mac: the text field in the list control remained on the screen even after the window is inactivated; fixed. Win: the text field in the list control often led to crash; (hopefully) fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@32
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toshinagata1964 [Sat, 24 Apr 2010 15:31:32 +0000 (15:31 +0000)]
Work around the wxWidgets bug where wxDocument::Close() is called twice. Fix the problem in the Mac version in which the hidden top-level window gets sometimes visible in the Window menu.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@31
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toshinagata1964 [Fri, 23 Apr 2010 15:46:48 +0000 (15:46 +0000)]
Improved handling of copy/cut/paste in the parameter table (but still very unsatisfactory)
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@30
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toshinagata1964 [Thu, 22 Apr 2010 14:50:27 +0000 (14:50 +0000)]
Experimental command-line tool for Mac platform.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@29
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toshinagata1964 [Thu, 22 Apr 2010 13:15:11 +0000 (13:15 +0000)]
The MM/MD engine was not aware of modification of coordinates via Ruby scripts. Fixed.
git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@28
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