[ViewVC] Log of: group/trunk/OOPSE/libmdtools/Molecule.cpp

Revision 1167 - (view) (annotate) - [select for diffs]
Modified Wed May 12 16:38:45 2004 UTC (20 years, 2 months ago) by tim
File length: 4830 byte(s)
Diff to previous 1158

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

Revision 1158 - (view) (annotate) - [selected]
Modified Tue May 11 21:14:26 2004 UTC (20 years, 2 months ago) by tim
File length: 5409 byte(s)
Diff to previous 1157

fix two bugs in siminfo which cause infinite loop; fix anoter one in CutoffGroup which causes seg fault

Revision 1157 - (view) (annotate) - [select for diffs]
Modified Tue May 11 20:33:41 2004 UTC (20 years, 2 months ago) by tim
File length: 5410 byte(s)
Diff to previous 1140 , to selected 1158

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: 4754 byte(s)
Diff to previous 1136 , to selected 1158

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

Revision 1136 - (view) (annotate) - [select for diffs]
Modified Tue Apr 27 16:26:44 2004 UTC (20 years, 2 months ago) by tim
File length: 4686 byte(s)
Diff to previous 1113 , to selected 1158

add center of mass of the molecule and massRation into atom class

Revision 1113 - (view) (annotate) - [select for diffs]
Modified Thu Apr 15 16:18:26 2004 UTC (20 years, 2 months ago) by tim
File length: 4260 byte(s)
Diff to previous 1109 , to selected 1158

fix whole bunch of bugs :-)

Revision 1109 - (view) (annotate) - [select for diffs]
Modified Wed Apr 14 16:32:15 2004 UTC (20 years, 2 months ago) by gezelter
File length: 4043 byte(s)
Diff to previous 1104 , to selected 1158

fixed for get_potential

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: 3959 byte(s)
Diff to previous 1097 , to selected 1158

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).

Revision 1097 - (view) (annotate) - [select for diffs]
Modified Mon Apr 12 20:32:20 2004 UTC (20 years, 2 months ago) by gezelter
File length: 4162 byte(s)
Diff to previous 829 , to selected 1158

Changes for RigidBody dynamics (Somewhat extensive)

Revision 829 - (view) (annotate) - [select for diffs]
Modified Tue Oct 28 16:03:37 2003 UTC (20 years, 8 months ago) by gezelter
File length: 3522 byte(s)
Diff to previous 658 , to selected 1158

replace c++ header stuff with more portable c header stuff
Also, mod file fixes and portability changes
Some fortran changes will need to be reversed.

Revision 658 - (view) (annotate) - [select for diffs]
Modified Thu Jul 31 15:35:07 2003 UTC (20 years, 11 months ago) by tim
File length: 3521 byte(s)
Diff to previous 610 , to selected 1158

 Added Z constraint.

Revision 610 - (view) (annotate) - [select for diffs]
Modified Tue Jul 15 15:50:55 2003 UTC (20 years, 11 months ago) by gezelter
File length: 3269 byte(s)
Diff to previous 607 , to selected 1158

more archaic code fixes

Revision 607 - (view) (annotate) - [select for diffs]
Modified Tue Jul 15 14:28:54 2003 UTC (20 years, 11 months ago) by gezelter
File length: 3347 byte(s)
Diff to previous 490 , to selected 1158

removing get_vx

Revision 490 - (view) (annotate) - [select for diffs]
Modified Fri Apr 11 15:16:59 2003 UTC (21 years, 3 months ago) by gezelter
File length: 3402 byte(s)
Diff to previous 489 , to selected 1158

Bug fix in progress for NPT

Revision 489 - (view) (annotate) - [select for diffs]
Modified Thu Apr 10 20:08:56 2003 UTC (21 years, 3 months ago) by mmeineke
File length: 3625 byte(s)
Diff to previous 483 , to selected 1158

 added a globalIndex counter to Molecule

Revision 483 - (view) (annotate) - [select for diffs]
Modified Wed Apr 9 04:06:43 2003 UTC (21 years, 3 months ago) by gezelter
File length: 3627 byte(s)
Diff to previous 475 , to selected 1158

fixes for NPT and NVT

Revision 475 - (view) (annotate) - [select for diffs]
Modified Tue Apr 8 12:44:18 2003 UTC (21 years, 3 months ago) by gezelter
File length: 3408 byte(s)
Diff to previous 468 , to selected 1158

Changes to integrate the NVT and NPT ensembles

Revision 468 - (view) (annotate) - [select for diffs]
Modified Mon Apr 7 16:56:38 2003 UTC (21 years, 3 months ago) by gezelter
File length: 3397 byte(s)
Diff to previous 450 , to selected 1158

Many fixes to add extended system

Revision 450 - (view) (annotate) - [select for diffs]
Modified Thu Apr 3 21:12:51 2003 UTC (21 years, 3 months ago) by mmeineke
File length: 2887 byte(s)
Diff to previous 449 , to selected 1158

just little things like deleteing unused variables and such.

Revision 449 - (view) (annotate) - [select for diffs]
Modified Thu Apr 3 20:57:56 2003 UTC (21 years, 3 months ago) by mmeineke
File length: 2901 byte(s)
Diff to previous 446 , to selected 1158

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: 2887 byte(s)
Diff to previous 438 , to selected 1158

Starting work on NPT

Revision 438 - (view) (annotate) - [select for diffs]
Modified Mon Mar 31 21:50:59 2003 UTC (21 years, 3 months ago) by chuckv
File length: 2083 byte(s)
Diff to previous 435 , to selected 1158

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: 2061 byte(s)
Diff to previous 428 , to selected 1158

fixed a bug where the Excludes were not being created properly

Revision 428 - (view) (annotate) - [select for diffs]
Modified Thu Mar 27 21:07:14 2003 UTC (21 years, 3 months ago) by mmeineke
File length: 1831 byte(s)
Diff to previous 427 , to selected 1158

fixed the compile time bugs, Source builds and links

Revision 427 - (view) (annotate) - [select for diffs]
Modified Thu Mar 27 20:48:37 2003 UTC (21 years, 3 months ago) by mmeineke
File length: 1830 byte(s)
Diff to previous 426 , to selected 1158

fixed a few more bugs.

Revision 426 - (view) (annotate) - [select for diffs]
Added Thu Mar 27 20:40:01 2003 UTC (21 years, 3 months ago) by mmeineke
File length: 1829 byte(s)
Diff to selected 1158

added the Molecule.cpp file

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