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Revision 3520 - Directory Listing - [select for diffs]
Modified Mon Sep 7 16:31:51 2009 UTC (16 years, 1 month ago) by cli2
Diff to previous 3466 , to selected 2002 
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 3466 - Directory Listing - [select for diffs]
Modified Tue Oct 21 18:23:31 2008 UTC (17 years ago) by gezelter
Diff to previous 3463 , to selected 2002 
many changes to keep track of particle potentials for both bonded and non-bonded interactions
Revision 3463 - Directory Listing - [select for diffs]
Modified Thu Oct 16 18:25:36 2008 UTC (17 years ago) by chuckv
Diff to previous 3462 , to selected 2002 
Returned old LD forces to SMIPDForceManager.
Revision 3462 - Directory Listing - [select for diffs]
Modified Thu Oct 16 18:17:41 2008 UTC (17 years ago) by skuang
Diff to previous 3460 , to selected 2002 
A few simple mods to remove gcc compile warnings
Revision 3460 - Directory Listing - [select for diffs]
Modified Mon Oct 13 21:35:22 2008 UTC (17 years ago) by cli2
Diff to previous 3446 , to selected 2002 
Fixes for Inversions for use with Amber
Revision 3446 - Directory Listing - [select for diffs]
Modified Wed Sep 10 19:51:45 2008 UTC (17 years, 1 month ago) by cli2
Diff to previous 3437 , to selected 2002 
Inversion fixes and amber mostly working
Revision 3437 - Directory Listing - [select for diffs]
Modified Wed Jul 30 18:11:19 2008 UTC (17 years, 3 months ago) by gezelter
Diff to previous 3432 , to selected 2002 
Many fixes
Revision 3432 - Directory Listing - [select for diffs]
Modified Mon Jul 14 12:35:58 2008 UTC (17 years, 3 months ago) by gezelter
Diff to previous 3430 , to selected 2002 
Changes for implementing Amber force field:  Added Inversions and
worked on BaseAtomTypes so that they'd function with the fortran side.
Revision 3430 - Directory Listing - [select for diffs]
Modified Fri Jul 4 20:54:29 2008 UTC (17 years, 4 months ago) by cli2
Diff to previous 3397 , to selected 2002 
Changes required for Inversions and Base Atom types.  This will
break OOPSE badly for a few days or so...
Revision 3397 - Directory Listing - [select for diffs]
Modified Tue May 27 16:39:06 2008 UTC (17 years, 5 months ago) by chuckv
Diff to previous 3320 , to selected 2002 
Checking in changes for Hefland moment calculations
Revision 3320 - Directory Listing - [select for diffs]
Modified Wed Jan 23 16:38:22 2008 UTC (17 years, 9 months ago) by gezelter
Diff to previous 3319 , to selected 2002 
A few formatting changes to prettify the code
Revision 3319 - Directory Listing - [select for diffs]
Modified Wed Jan 23 03:45:33 2008 UTC (17 years, 9 months ago) by gezelter
Diff to previous 3126 , to selected 2002 
Removed older version of openbabel from our code.  We now have a
configure check to see if openbabel is installed and then we link to
the stuff we need.  Conversion to OOPSE's md format is handled by only
one application (atom2md), so most of the work went on there.
ElementsTable still needs some work to function in parallel.
Revision 3126 - Directory Listing - [select for diffs]
Modified Fri Apr 6 21:53:43 2007 UTC (18 years, 7 months ago) by gezelter
Diff to previous 3110 , to selected 2002 
Massive update to do virials (both atomic and cutoff-group) correctly.
The rigid body constraint contributions had been missing and this was
masked by the use of cutoff groups...
Revision 3110 - Directory Listing - [select for diffs]
Modified Wed Jan 3 20:47:00 2007 UTC (18 years, 10 months ago) by chuckv
Diff to previous 2982 , to selected 2002 
Changes to add thetacorr to dynamic props and fixes to radial rcorr.
Revision 2982 - Directory Listing - [select for diffs]
Modified Wed Aug 30 18:42:29 2006 UTC (19 years, 2 months ago) by tim
Diff to previous 2759 , to selected 2002 
Massive changes preparing for release of OOPSE-4: The main difference
is that the new MD file format (.md, .dump, .eor) now contains meta-data
information along with the configuration information.
Revision 2759 - Directory Listing - [select for diffs]
Modified Wed May 17 21:51:42 2006 UTC (19 years, 5 months ago) by tim
Diff to previous 2733 , to selected 2002 
Adding single precision capabilities to c++ side
Revision 2733 - Directory Listing - [select for diffs]
Modified Tue Apr 25 02:09:01 2006 UTC (19 years, 6 months ago) by gezelter
Diff to previous 2625 , to selected 2002 
Adding spherical boundary conditions to LD integrator
Revision 2625 - Directory Listing - [select for diffs]
Modified Wed Mar 15 17:35:12 2006 UTC (19 years, 7 months ago) by tim
Diff to previous 2582 , to selected 2002 
using setFrc in RigidBody::calcForcesAndTorques will discard if there are force and torque applied in rigid body itself. use addFrc instead.
Revision 2582 - Directory Listing - [select for diffs]
Modified Thu Feb 2 16:49:16 2006 UTC (19 years, 9 months ago) by gezelter
Diff to previous 2469 , to selected 2002 
fixed a bug in rigid bodies that contain directional atoms
Revision 2469 - Directory Listing - [select for diffs]
Modified Fri Dec 2 15:38:03 2005 UTC (19 years, 11 months ago) by tim
Diff to previous 2448 , to selected 2002 
End of the Link --> List
Return of the Oject-Oriented
replace yacc/lex parser with antlr parser
Revision 2448 - Directory Listing - [select for diffs]
Modified Wed Nov 16 23:10:02 2005 UTC (19 years, 11 months ago) by tim
Diff to previous 2394 , to selected 2002 
OptionSectionParser get compiled
Revision 2394 - Directory Listing - [select for diffs]
Modified Sun Oct 23 21:08:08 2005 UTC (20 years ago) by chrisfen
Diff to previous 2391 , to selected 2002 
streamlined reaction field for dipoles (now a good bit faster) and added reaction field for charges - still need to do charge-dipole RF
Revision 2391 - Directory Listing - [select for diffs]
Modified Thu Oct 20 20:27:34 2005 UTC (20 years ago) by tim
Diff to previous 2362 , to selected 2002 
Fix the other branch of force calculation in Torision.cpp
Revision 2362 - Directory Listing - [select for diffs]
Modified Wed Oct 12 21:00:59 2005 UTC (20 years ago) by gezelter
Diff to previous 2348 , to selected 2002 
Don't remember what we did
Revision 2348 - Directory Listing - [select for diffs]
Modified Wed Oct 5 21:12:41 2005 UTC (20 years, 1 month ago) by tim
Diff to previous 2347 , to selected 2002 
There is still something wrong with inertia tensor projection
Revision 2347 - Directory Listing - [select for diffs]
Modified Wed Oct 5 19:35:28 2005 UTC (20 years, 1 month ago) by tim
Diff to previous 2345 , to selected 2002 
erase output of inertia tensor. There is still something wrong with current implementation.
Revision 2345 - Directory Listing - [select for diffs]
Modified Wed Oct 5 19:12:02 2005 UTC (20 years, 1 month ago) by tim
Diff to previous 2341 , to selected 2002 
fix a bug in creating cutoffGroup. When cutoffGroup is turned off, there is a mismatch between group and center of mass array
Revision 2341 - Directory Listing - [select for diffs]
Modified Mon Oct 3 15:54:23 2005 UTC (20 years, 1 month ago) by tim
Diff to previous 2340 , to selected 2002 
fix a bug in projecting the inertia tensor of
directional atom in rigibody into rigidbody's body frame (previous commit is wrong)
Revision 2340 - Directory Listing - [select for diffs]
Modified Mon Oct 3 14:31:31 2005 UTC (20 years, 1 month ago) by tim
Diff to previous 2335 , to selected 2002 
fix a bug in projecting the inertia tensor of directional atom in rigibody into rigidbody's body frame
Revision 2335 - Directory Listing - [select for diffs]
Modified Wed Sep 28 16:32:44 2005 UTC (20 years, 1 month ago) by gezelter
Diff to previous 2272 , to selected 2002 
Rotation matrix multiplication order error
Revision 2272 - Directory Listing - [select for diffs]
Modified Wed Aug 10 19:17:39 2005 UTC (20 years, 2 months ago) by gezelter
Diff to previous 2204 , to selected 2002 
putting spaceballs back where they belong
Revision 2204 - Directory Listing - [select for diffs]
Modified Fri Apr 15 22:04:00 2005 UTC (20 years, 6 months ago) by gezelter
Diff to previous 2191 , to selected 2002 
xemacs has been drafted to perform our indentation services
Revision 2191 - Directory Listing - [select for diffs]
Modified Wed Apr 13 22:43:43 2005 UTC (20 years, 6 months ago) by tim
Diff to previous 2187 , to selected 2002 
fix some warning messages
Revision 2187 - Directory Listing - [select for diffs]
Modified Wed Apr 13 18:41:17 2005 UTC (20 years, 6 months ago) by tim
Diff to previous 2114 , to selected 2002 
more memory leak are fixed
Revision 2114 - Directory Listing - [select for diffs]
Modified Thu Mar 10 23:56:42 2005 UTC (20 years, 7 months ago) by tim
Diff to previous 2082 , to selected 2002 
adding exclude pairs for rigidbody and cutoff group
Revision 2082 - Directory Listing - [select for diffs]
Modified Mon Mar 7 22:39:33 2005 UTC (20 years, 8 months ago) by tim
Diff to previous 2058 , to selected 2002 
Fixing a bug in BitSet.cpp
Revision 2058 - Directory Listing - [select for diffs]
Modified Tue Feb 22 18:56:25 2005 UTC (20 years, 8 months ago) by tim
Diff to previous 2056 , to selected 2002 
reactionfield get fixed
Revision 2056 - Directory Listing - [select for diffs]
Modified Mon Feb 21 15:28:56 2005 UTC (20 years, 8 months ago) by tim
Diff to previous 2018 , to selected 2002 
Fix for compilation on the Sun
Revision 2018 - Directory Listing - [select for diffs]
Modified Mon Feb 14 17:57:01 2005 UTC (20 years, 8 months ago) by tim
Diff to previous 2002 
begin bug fix
Revision 2002 - Directory Listing - [selected]
Modified Sun Feb 13 06:57:48 2005 UTC (20 years, 8 months ago) by tim
Diff to previous 1989 
adding dynamicProps
Revision 1989 - Directory Listing - [select for diffs]
Modified Mon Feb 7 22:39:19 2005 UTC (20 years, 8 months ago) by tim
Diff to previous 1973 , to selected 2002 
add getRigidBodyAt  function into Molecule class
Revision 1973 - Directory Listing - [select for diffs]
Modified Fri Feb 4 22:41:23 2005 UTC (20 years, 9 months ago) by tim
Diff to previous 1968 , to selected 2002 
adding missing implementation
Revision 1968 - Directory Listing - [select for diffs]
Modified Fri Feb 4 04:57:04 2005 UTC (20 years, 9 months ago) by tim
Diff to previous 1959 , to selected 2002 
adding wildcard class; NameFinder is finished
Revision 1959 - Directory Listing - [select for diffs]
Modified Wed Jan 26 15:15:09 2005 UTC (20 years, 9 months ago) by tim
Diff to previous 1957 , to selected 2002 
(1)Cast wrong atom to DirectionalAtom in GhostTorsion
(2)get the wrong column of electroframe
Revision 1957 - Directory Listing - [select for diffs]
Modified Tue Jan 25 17:45:23 2005 UTC (20 years, 9 months ago) by tim
Diff to previous 1951 , to selected 2002 
(1) complete section parser's error message
(2) add GhostTorsion
(3) accumulate inertial tensor from the directional atoms before calculate rigidbody's inertial tensor
Revision 1951 - Directory Listing - [select for diffs]
Modified Fri Jan 14 21:13:24 2005 UTC (20 years, 9 months ago) by gezelter
Diff to previous 1943 , to selected 2002 
moved Package variable into subdirectory makefiles to speed up
the building process
Revision 1943 - Directory Listing - [select for diffs]
Modified Fri Jan 14 01:56:04 2005 UTC (20 years, 9 months ago) by tim
Diff to previous 1937 , to selected 2002 
fix a bug in global index
Revision 1937 - Directory Listing - [select for diffs]
Modified Thu Jan 13 19:40:37 2005 UTC (20 years, 9 months ago) by tim
Diff to previous 1930 , to selected 2002 
port to SGI platform
Revision 1930 - Directory Listing - [select for diffs]
Modified Wed Jan 12 22:41:40 2005 UTC (20 years, 9 months ago) by gezelter
Diff to previous 1709 , to selected 2002 
merging new_design branch into OOPSE-2.0
Revision 1709 - Directory Listing - [select for diffs]
Modified Thu Nov 4 16:22:03 2004 UTC (21 years ago) by gezelter
Diff to previous 1698 , to selected 2002 
isLinear and linearAxis are virtual in StuntDouble,
but are implemented by DirectionalAtom and RigidBody
In StuntDouble, they should return false and "-1" but
there should be logic to figure them out in the other
two classes
Revision 1698 - Directory Listing - [select for diffs]
Modified Tue Nov 2 15:28:25 2004 UTC (21 years ago) by chrisfen
Diff to previous 1625 , to selected 2002 
Shapes looks like it's working
Revision 1625 - Directory Listing - [select for diffs]
Modified Thu Oct 21 16:22:01 2004 UTC (21 years ago) by tim
Diff to previous 1559 , to selected 2002 
replace old GebericData with  new GenericData
Revision 1559 - Directory Listing - [select for diffs]
Modified Mon Oct 11 22:15:56 2004 UTC (21 years ago) by tim
Diff to previous 1513 , to selected 2002 
change #include "mpi.h" to #include <mpi.h> in AbstractClasses.hpp
Revision 1513 - Directory Listing - [select for diffs]
Modified Wed Sep 29 21:55:03 2004 UTC (21 years, 1 month ago) by tim
Diff to previous 1503 , to selected 2002 
define DEV_ROOT as relative path
Revision 1503 - Directory Listing - [select for diffs]
Modified Wed Sep 29 14:59:25 2004 UTC (21 years, 1 month ago) by tim
Diff to previous 1492 , to selected 2002 
change Makefile to relative path
Revision 1492 - Directory Listing - [select for diffs]
Modified Fri Sep 24 16:27:58 2004 UTC (21 years, 1 month ago) by tim
Diff to previous 1490 , to selected 2002 
change the #include in source files
Revision 1490 - Directory Listing - [select for diffs]
Added Fri Sep 24 04:16:43 2004 UTC (21 years, 1 month ago) by gezelter
Diff to selected 2002 
Import of OOPSE v. 2.0

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