[ViewVC] Log of: group/trunk/OOPSE-4/src/applications/utilities

Revision 3556 - Directory Listing - [select for diffs]
Modified Thu Oct 22 19:12:14 2009 UTC (16 years, 1 month ago) by gezelter
Diff to previous 3543

pythonification of affineScale, translate in md2md, removed spurious cutoffGroups
in waterBoxer.   Perhaps we need a python md-file parsing library?

Revision 3543 - Directory Listing - [selected]
Modified Mon Oct 19 14:29:14 2009 UTC (16 years, 1 month ago) by gezelter
Diff to previous 3520

fixes for surface atoms that expose multiple hydrogens, updated python
set syntax

Revision 3520 - Directory Listing - [select for diffs]
Modified Mon Sep 7 16:31:51 2009 UTC (16 years, 2 months ago) by cli2
Diff to previous 3450 , to selected 3543

Added new restraint infrastructure
Added MolecularRestraints
Added ObjectRestraints
Added RestraintStamp
Updated thermodynamic integration to use ObjectRestraints
Added Quaternion mathematics for twist swing decompositions
Significantly updated RestWriter and RestReader to use dump-like files
Added selections for x, y, and z coordinates of atoms
Removed monolithic Restraints class
Fixed a few bugs in gradients of Euler angles in DirectionalAtom and RigidBody
Added some rotational capabilities to prinicpalAxisCalculator

Revision 3450 - Directory Listing - [select for diffs]
Modified Sun Sep 14 01:32:26 2008 UTC (17 years, 2 months ago) by chuckv
Diff to previous 3427 , to selected 3543

Added large quantities of code for convex hull and constant pressure langevin dynamics.

Revision 3427 - Directory Listing - [select for diffs]
Modified Tue Jul 1 18:05:41 2008 UTC (17 years, 4 months ago) by chuckv
Diff to previous 3423 , to selected 3543

Hopefully md-solvator is done.

Revision 3423 - Directory Listing - [select for diffs]
Modified Mon Jun 30 19:46:43 2008 UTC (17 years, 4 months ago) by chuckv
Diff to previous 3421 , to selected 3543

More md-solvator work.

Revision 3421 - Directory Listing - [select for diffs]
Modified Fri Jun 27 15:47:06 2008 UTC (17 years, 5 months ago) by chuckv
Diff to previous 3420 , to selected 3543

Md solvator writes out md files now. Index problem.

Revision 3420 - Directory Listing - [select for diffs]
Modified Thu Jun 26 15:50:22 2008 UTC (17 years, 5 months ago) by chuckv
Diff to previous 3419 , to selected 3543

More progress...

Revision 3419 - Directory Listing - [select for diffs]
Modified Thu Jun 26 14:48:51 2008 UTC (17 years, 5 months ago) by chuckv
Diff to previous 3418 , to selected 3543

More changes to md-solvator. Still don't know if it works.

Revision 3418 - Directory Listing - [select for diffs]
Modified Thu Jun 26 14:23:49 2008 UTC (17 years, 5 months ago) by chuckv
Diff to previous 3417 , to selected 3543

More work on python version of md-solvator. Pretty sure mol loop is busted.

Revision 3417 - Directory Listing - [select for diffs]
Modified Wed Jun 25 18:22:08 2008 UTC (17 years, 5 months ago) by kfletch2
Diff to previous 3393 , to selected 3543

*** empty log message ***

Revision 3393 - Directory Listing - [select for diffs]
Modified Wed May 14 20:49:17 2008 UTC (17 years, 6 months ago) by xsun
Diff to previous 3345 , to selected 3543

Added repeat box options to make larger systems

Revision 3345 - Directory Listing - [select for diffs]
Modified Wed Feb 13 16:44:14 2008 UTC (17 years, 9 months ago) by gezelter
Diff to previous 3323 , to selected 3543

Adding new md2md utility program

Revision 3323 - Directory Listing - [select for diffs]
Modified Wed Jan 23 21:22:18 2008 UTC (17 years, 10 months ago) by xsun
Diff to previous 3276 , to selected 3543

added stat2visco

Revision 3276 - Directory Listing - [select for diffs]
Modified Mon Nov 26 19:23:36 2007 UTC (18 years ago) by cpuglis
Diff to previous 3123 , to selected 3543

*** empty log message ***

Revision 3123 - Directory Listing - [select for diffs]
Modified Tue Mar 6 00:01:51 2007 UTC (18 years, 8 months ago) by chrisfen
Diff to previous 3117 , to selected 3543

forgot a tolerance for simple cubic lattice magic number determination

Revision 3117 - Directory Listing - [select for diffs]
Modified Mon Jan 22 22:27:37 2007 UTC (18 years, 10 months ago) by gezelter
Diff to previous 3114 , to selected 3543

fixed a bug in waterBoxer

Revision 3114 - Directory Listing - [select for diffs]
Modified Thu Jan 11 21:46:14 2007 UTC (18 years, 10 months ago) by gezelter
Diff to previous 3113 , to selected 3543

adding md-solvator

Revision 3113 - Directory Listing - [select for diffs]
Modified Tue Jan 9 03:42:14 2007 UTC (18 years, 10 months ago) by gezelter
Diff to previous 3107 , to selected 3543

Added the ability of waterBoxer to deal with non-cubical boxes.

Revision 3107 - Directory Listing - [select for diffs]
Modified Tue Jan 2 20:42:44 2007 UTC (18 years, 10 months ago) by chuckv
Diff to previous 3106 , to selected 3543

More changes to mdsplit.

Revision 3106 - Directory Listing - [select for diffs]
Modified Tue Jan 2 20:30:18 2007 UTC (18 years, 10 months ago) by chuckv
Diff to previous 3105 , to selected 3543

Breaking more mdsplit stuff....

Revision 3105 - Directory Listing - [select for diffs]
Modified Tue Jan 2 20:12:34 2007 UTC (18 years, 10 months ago) by chuckv
Diff to previous 3049 , to selected 3543

Changed how mdsplit gets file names. Full path is now removed from name.

Revision 3049 - Directory Listing - [select for diffs]
Modified Sun Oct 15 18:02:29 2006 UTC (19 years, 1 month ago) by chuckv
Diff to previous 3048 , to selected 3543

More typos...

Revision 3048 - Directory Listing - [select for diffs]
Modified Sun Oct 15 17:59:37 2006 UTC (19 years, 1 month ago) by chuckv
Diff to previous 3047 , to selected 3543

Typo in mdSplit.

Revision 3047 - Directory Listing - [select for diffs]
Modified Sun Oct 15 17:02:49 2006 UTC (19 years, 1 month ago) by chuckv
Diff to previous 3043 , to selected 3543

Fixed printing of OOPSE version at header and trailer.

Revision 3043 - Directory Listing - [select for diffs]
Modified Wed Oct 11 19:24:37 2006 UTC (19 years, 1 month ago) by chrisfen
Diff to previous 3038 , to selected 3543

now the -n command works

Revision 3038 - Directory Listing - [select for diffs]
Modified Tue Oct 10 14:36:02 2006 UTC (19 years, 1 month ago) by chrisfen
Diff to previous 3037 , to selected 3543

oops with the affineScale

Revision 3037 - Directory Listing - [select for diffs]
Modified Tue Oct 10 14:08:10 2006 UTC (19 years, 1 month ago) by chrisfen
Diff to previous 3034 , to selected 3543

who needs .in files for perl?  using env

Revision 3034 - Directory Listing - [select for diffs]
Modified Fri Oct 6 21:29:14 2006 UTC (19 years, 1 month ago) by chuckv
Diff to previous 3033 , to selected 3543

Added utility to split dump file frames into md files.

Revision 3033 - Directory Listing - [select for diffs]
Modified Tue Oct 3 22:39:53 2006 UTC (19 years, 1 month ago) by chrisfen
Diff to previous 3032 , to selected 3543

forgot to adjust the makefile

Revision 3032 - Directory Listing - [select for diffs]
Modified Tue Oct 3 22:38:50 2006 UTC (19 years, 1 month ago) by chrisfen
Diff to previous 3031 , to selected 3543

added solvator and adjusted waterBoxer

Revision 3031 - Directory Listing - [select for diffs]
Modified Mon Oct 2 23:54:30 2006 UTC (19 years, 1 month ago) by chrisfen
Diff to previous 3030 , to selected 3543

improvements to waterBoxer

Revision 3030 - Directory Listing - [select for diffs]
Modified Mon Oct 2 23:27:40 2006 UTC (19 years, 1 month ago) by chrisfen
Diff to previous 2998 , to selected 3543

fixed a bug in waterBoxer for invalid water names

Revision 2998 - Directory Listing - [select for diffs]
Modified Mon Sep 4 13:37:15 2006 UTC (19 years, 2 months ago) by gezelter
Diff to previous 2997 , to selected 3543

changing configure script to process the new utilities

Revision 2997 - Directory Listing - [select for diffs]
Modified Fri Sep 1 22:58:33 2006 UTC (19 years, 2 months ago) by chrisfen
Diff to previous 2996 , to selected 3543

added some features to waterBoxer

Revision 2996 - Directory Listing - [select for diffs]
Modified Fri Sep 1 21:08:03 2006 UTC (19 years, 2 months ago) by chrisfen
Diff to previous 2995 , to selected 3543

added the waterBoxer script

Revision 2995 - Directory Listing - [select for diffs]
Modified Fri Sep 1 19:22:06 2006 UTC (19 years, 2 months ago) by chrisfen
Diff to previous 2993 , to selected 3543

added comment info

Revision 2993 - Directory Listing - [select for diffs]
Modified Fri Sep 1 18:29:19 2006 UTC (19 years, 2 months ago) by chrisfen
Diff to previous 2984 , to selected 3543

modified affineScale to work with the new OOPSE files

Revision 2984 - Directory Listing - [select for diffs]
Modified Wed Aug 30 21:04:04 2006 UTC (19 years, 2 months ago) by gezelter
Diff to previous 2967 , to selected 3543

Changing utility programs to use the new file format

Revision 2967 - Directory Listing - [select for diffs]
Modified Thu Jul 27 21:02:54 2006 UTC (19 years, 4 months ago) by chrisfen
Diff to previous 2966 , to selected 3543

fixed a pvf bug

Revision 2966 - Directory Listing - [select for diffs]
Modified Thu Jul 27 20:36:54 2006 UTC (19 years, 4 months ago) by tim
Diff to previous 2965 , to selected 3543

fixed dumpConverter problems

Revision 2965 - Directory Listing - [select for diffs]
Modified Thu Jul 27 19:05:16 2006 UTC (19 years, 4 months ago) by gezelter
Diff to previous 2963 , to selected 3543

added dumpConverter

Revision 2963 - Directory Listing - [select for diffs]
Modified Wed Jul 26 21:45:05 2006 UTC (19 years, 4 months ago) by gezelter
Diff to previous 2959 , to selected 3543

fixed a spelling bug

Revision 2959 - Directory Listing - [select for diffs]
Added Wed Jul 26 21:00:07 2006 UTC (19 years, 4 months ago) by gezelter
Diff to selected 3543

Adding a directory for scripts
Adding affineScale script

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