Revision 3319 - (view) (annotate) - [select for diffs]
Modified Wed Jan 23 03:45:33 2008 UTC (16 years, 5 months ago) by gezelter
File length: 17221 byte(s)
Diff to previous 3250

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.

Fixed some bugs in LDForceManager.cpp

Revision 3129 - (view) (annotate) - [select for diffs]
Modified Fri Apr 20 18:15:48 2007 UTC (17 years, 2 months ago) by chrisfen
File length: 15327 byte(s)
Diff to previous 3126

SF Lennard-Jones was added for everyones' enjoyment.  The behavior is tethered to the electrostaticSummationMethod keyword.

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 3118 - (view) (annotate) - [select for diffs]
Modified Fri Feb 2 18:55:21 2007 UTC (17 years, 5 months ago) by chuckv
File length: 15361 byte(s)
Diff to previous 2802

Spherical boundary conditions.

testing GB, removing CM drift in Langevin Dynamics, fixing a memory
leak, adding a visitor

Revision 2787 - (view) (annotate) - [select for diffs]
Modified Mon Jun 5 18:24:45 2006 UTC (18 years, 1 month ago) by gezelter
File length: 15097 byte(s)
Diff to previous 2767

Massive changes for GB code with multiple ellipsoid types (a la
Cleaver's paper).

Also, changes in hydrodynamics code to make HydroProp a somewhat
smarter class (rather than just a struct).

fix a bug in parsing HydroProp file

Revision 2766 - (view) (annotate) - [select for diffs]
Modified Wed May 24 15:24:52 2006 UTC (18 years, 1 month ago) by gezelter
File length: 18039 byte(s)
Diff to previous 2759

Fixed a bug when spherical boundary conditions were off.

Adding single precision capabilities to c++ side

Revision 2752 - (view) (annotate) - [select for diffs]
Modified Tue May 16 02:06:37 2006 UTC (18 years, 1 month ago) by gezelter
File length: 17992 byte(s)
Diff to previous 2733

*** empty log message ***

Adding spherical boundary conditions to LD integrator

Revision 2646 - (view) (annotate) - [select for diffs]
Modified Tue Mar 21 00:26:55 2006 UTC (18 years, 3 months ago) by tim
File length: 11184 byte(s)
Diff to previous 2644

Fix a bug in friction calculation for ellipsoid

Verify the correctness of Ellipsoid's hydrodynamics properties

Revision 2634 - (view) (annotate) - [select for diffs]
Modified Fri Mar 17 23:20:35 2006 UTC (18 years, 3 months ago) by tim
File length: 12251 byte(s)
Diff to previous 2632

refactor Hydrodynamics module.

LagevinDynamics is working?

Revision 2611 - (view) (annotate) - [select for diffs]
Added Mon Mar 13 22:42:40 2006 UTC (18 years, 3 months ago) by tim
File length: 11894 byte(s)

LangevinDynamics in progress