new rattle algorithm is working

Revision 1167 - (view) (annotate) - [select for diffs]
Modified Wed May 12 16:38:45 2004 UTC (20 years, 1 month ago) by tim
File length: 3556 byte(s)
Diff to previous 1157 , to selected 658

get rid of rc and massratio from simState, creat cutoff group forevery atom
which does not belong to
cutoff group defined at mdl file

adding cutoffGroup into OOPSE

Revision 1140 - (view) (annotate) - [select for diffs]
Modified Wed Apr 28 22:34:02 2004 UTC (20 years, 2 months ago) by tim
File length: 3059 byte(s)
Diff to previous 1108 , to selected 658

fix a bug in Molecule.cpp which initialize massRatio before creat the array.
fix two bugs in ZconsVisitor

Change DumpWriter and InitFromFile

Revision 1104 - (view) (annotate) - [select for diffs]
Modified Tue Apr 13 16:26:03 2004 UTC (20 years, 2 months ago) by gezelter
File length: 2955 byte(s)
Diff to previous 1097 , to selected 658

Now molecules can keep track of their own IntegrableObjects (and
RigidBodies).  Also a bug-fix so that SimInfo can keep track of
RigidBodies (which was done incorrectly before).

Changes for RigidBody dynamics (Somewhat extensive)

Revision 658 - (view) (annotate) - [selected]
Modified Thu Jul 31 15:35:07 2003 UTC (20 years, 11 months ago) by tim
File length: 2823 byte(s)
Diff to previous 490

 Added Z constraint.

Bug fix in progress for NPT

Revision 489 - (view) (annotate) - [select for diffs]
Modified Thu Apr 10 20:08:56 2003 UTC (21 years, 2 months ago) by mmeineke
File length: 2838 byte(s)
Diff to previous 483 , to selected 658

 added a globalIndex counter to Molecule

fixes for NPT and NVT

Revision 475 - (view) (annotate) - [select for diffs]
Modified Tue Apr 8 12:44:18 2003 UTC (21 years, 2 months ago) by gezelter
File length: 2569 byte(s)
Diff to previous 468 , to selected 658

Changes to integrate the NVT and NPT ensembles

Many fixes to add extended system

Revision 452 - (view) (annotate) - [select for diffs]
Modified Thu Apr 3 22:19:21 2003 UTC (21 years, 3 months ago) by mmeineke
File length: 2529 byte(s)
Diff to previous 449 , to selected 658

added some little fixes here and there.

a few fixes to simError.h
also some fixes to Molecule.hpp

Revision 446 - (view) (annotate) - [select for diffs]
Modified Thu Apr 3 20:19:50 2003 UTC (21 years, 3 months ago) by gezelter
File length: 2602 byte(s)
Diff to previous 438 , to selected 658

Starting work on NPT

Fixes in MPI force calc and in Trappe_Ex parsing.

Revision 435 - (view) (annotate) - [select for diffs]
Modified Fri Mar 28 19:33:37 2003 UTC (21 years, 3 months ago) by mmeineke
File length: 2368 byte(s)
Diff to previous 425 , to selected 658

fixed a bug where the Excludes were not being created properly

 fixed the makefile

Revision 424 - (view) (annotate) - [select for diffs]
Modified Thu Mar 27 20:36:16 2003 UTC (21 years, 3 months ago) by mmeineke
File length: 2284 byte(s)
Diff to previous 423 , to selected 658

fixing some compile time bugs

I have implemeted Molecules everywhere I could remember to.
will now attempt to compile.

Revision 422 - (view) (annotate) - [select for diffs]
Modified Thu Mar 27 19:21:42 2003 UTC (21 years, 3 months ago) by mmeineke
File length: 1656 byte(s)
Diff to previous 416 , to selected 658

finished updating SimSetup to initialize and use the new MPI division of labour, and Molecule class

bug fixes   many bug fixes

Revision 412 - (view) (annotate) - [select for diffs]
Modified Wed Mar 26 21:50:33 2003 UTC (21 years, 3 months ago) by mmeineke
File length: 1790 byte(s)
Diff to previous 407 , to selected 658

still working on the SimSetup routine. also fixed some things in Exclude.hpp

I'm overhauling the molecule class to contain it's own bonds, bends, and torsions.

may god have mercy on my soul.

Revision 378 - (view) (annotate) - [select for diffs]
Modified Fri Mar 21 17:42:12 2003 UTC (21 years, 3 months ago) by mmeineke
File length: 655 byte(s)
Copied from: branches/mmeineke/OOPSE/libmdtools/Molecule.hpp revision 377
Diff to previous 377 , to selected 658

This commit was generated by cvs2svn to compensate for changes in r377,
which included commits to RCS files with non-trunk default branches.

New OOPSE Tree