Revision
929 -
Directory Listing
-
[select for diffs]
Modified
Tue Jan 13 15:46:49 2004 UTC
(20 years, 7 months ago)
by
tim
Diff to
previous 927
Merge the code of writeFinal and writeDump;
Adding sortingIndex into DumpWriter;
Fix a bug of writing last frame twice in integrator
Revision
920 -
Directory Listing
-
[select for diffs]
Modified
Sat Jan 10 09:46:47 2004 UTC
(20 years, 7 months ago)
by
tim
Diff to
previous 919
tagub is not a bug. Just roll it back
fix a bug of copying string to a pointer
Still have Seg fault, it looks like a random MPI seg fault in totalview
Revision
882 -
Directory Listing
-
[select for diffs]
Modified
Wed Dec 17 20:13:33 2003 UTC
(20 years, 8 months ago)
by
chuckv
Diff to
previous 878
Fixed bug in parallel EAM. rho_row and rho_col were scattered into the same array. Unfortunately, MPI zeros the array between scatters so half of the sum was being lost. Fixed by added a temp array for column scatter, then sum loop over nlocal.
Revision
874 -
Directory Listing
-
[select for diffs]
Modified
Fri Nov 21 20:10:02 2003 UTC
(20 years, 9 months ago)
by
mmeineke
Diff to
previous 872
added a more verbose error message in SimInfo. Added a more informative error message in InitializeFromFile
Revision
859 -
Directory Listing
-
[select for diffs]
Modified
Mon Nov 10 21:50:36 2003 UTC
(20 years, 9 months ago)
by
mmeineke
Diff to
previous 858
reordered the rcut/ecr/boxSize initialization
removed the rcut/ecr shrink and grow algorithm. the simulation will now exit when it runs into rcut or ecr.
Revision
857 -
Directory Listing
-
[select for diffs]
Modified
Fri Nov 7 17:09:48 2003 UTC
(20 years, 9 months ago)
by
mmeineke
Diff to
previous 855
moved the velocity scale matrix calculation outside of the atom loop in the NPT family of integrators.
Revision
855 -
Directory Listing
-
[select for diffs]
Modified
Thu Nov 6 22:01:37 2003 UTC
(20 years, 9 months ago)
by
mmeineke
Diff to
previous 853
added the following parameters to BASS:
* useInitialExtendedSystemState
* orthoBoxTolerance
* useIntiTime => useInitialTime
Revision
853 -
Directory Listing
-
[select for diffs]
Modified
Thu Nov 6 19:11:38 2003 UTC
(20 years, 9 months ago)
by
mmeineke
Diff to
previous 847
did a merge by hand from the new-templateless branch to the main trunk.
bug Fixes include:
* fixed the switching function from ortho to non-ortho box.
!!!!! THis was responsible for all of the sudden deaths we saw.
* some formating in the string when we write out the extended system state.
* added NPT.cpp to the makefile.in
Revision
843 -
Directory Listing
-
[select for diffs]
Modified
Wed Oct 29 20:41:39 2003 UTC
(20 years, 9 months ago)
by
mmeineke
Diff to
previous 841
fixed a stdlib.h include error in bass.l
fixed a little bug in the first time step, regarding the setting of ecr and est in fortran
Revision
836 -
Directory Listing
-
[select for diffs]
Modified
Tue Oct 28 22:25:46 2003 UTC
(20 years, 9 months ago)
by
mmeineke
Diff to
previous 834
did a complete overhaul of how c calls fortran. All function pointers and fortran calls are rigidly typecast now.
Revision
829 -
Directory Listing
-
[select for diffs]
Modified
Tue Oct 28 16:03:37 2003 UTC
(20 years, 9 months ago)
by
gezelter
Diff to
previous 826
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
812 -
Directory Listing
-
[select for diffs]
Modified
Wed Oct 22 21:17:32 2003 UTC
(20 years, 10 months ago)
by
mmeineke
Diff to
previous 811
added a new NPT integrator, NPTxyz. It scales the x, y, and z direction sepeartely. no box skew allowed.
Revision
811 -
Directory Listing
-
[select for diffs]
Modified
Tue Oct 21 19:33:19 2003 UTC
(20 years, 10 months ago)
by
mmeineke
Diff to
previous 804
added useInitTime to the BASS syntax.
* useInitTime = false: sets the origin time to 0.0 regardless of the time stamp in the .init file
* default=> useInitTime = true;
Revision
804 -
Directory Listing
-
[select for diffs]
Modified
Thu Oct 16 19:16:24 2003 UTC
(20 years, 10 months ago)
by
mmeineke
Diff to
previous 802
Changed DumpReader to use linked lists instead of a vector.
Fixed the makefile to build DumpReader.cpp
Removed a comment output in Exclude.cpp
Modified DumpWriter and Integrator to write an eor file every time a frame is written.
This lets the .eor file represent the last written frame of a simulation.
Revision
767 -
Directory Listing
-
[select for diffs]
Modified
Tue Sep 16 20:02:11 2003 UTC
(20 years, 11 months ago)
by
tim
Diff to
previous 763
fixed ecr grow in SimInfo
fixed conserved quantity in NPT (Still some small bug)
NPTi appears very stable.
Revision
746 -
Directory Listing
-
[select for diffs]
Modified
Thu Sep 4 21:48:35 2003 UTC
(20 years, 11 months ago)
by
mmeineke
Diff to
previous 738
added resetTime to the Global namespace.
added ability to reset the integrators in the NVT and NPT family.
Revision
733 -
Directory Listing
-
[select for diffs]
Modified
Wed Aug 27 19:23:29 2003 UTC
(21 years ago)
by
tim
Diff to
previous 730
fix bug of MPI_Allreduce in ZConstraint, the MPITYPE is set to MPI_DOUBLE,
however, the corret type is MPI_INT. Therefore, when we turn on the
optimization flag, it causes a seg fault
Revision
727 -
Directory Listing
-
[select for diffs]
Modified
Wed Aug 27 16:16:01 2003 UTC
(21 years ago)
by
tim
Diff to
previous 726
fix bug in calc_dipole_dipole.F90 and calc_stikcy_pair.F90
molMembershipList use global index instead of local index
Revision
723 -
Directory Listing
-
[select for diffs]
Modified
Tue Aug 26 20:12:51 2003 UTC
(21 years ago)
by
mmeineke
Diff to
previous 722
added define statemewnt to Statwriter and Dumpwriter to handle files larger than 2 gb.
commented out some print statements in Zconstraint
Revision
721 -
Directory Listing
-
[select for diffs]
Modified
Tue Aug 26 18:32:03 2003 UTC
(21 years ago)
by
mmeineke
Diff to
previous 718
changed the Makefiel a litle.
Fixed a bug in MPI_DUFF. The atom block type was not being properly constucted in MPI. (The MPI struct had 6 doubles declared versus the actual 11)
Revision
708 -
Directory Listing
-
[select for diffs]
Modified
Wed Aug 20 22:23:34 2003 UTC
(21 years ago)
by
tim
Diff to
previous 707
user can setup seed in bass file now, if he does not specify any value for
seed, oopse will take the value of seconds of system time as seed
Revision
707 -
Directory Listing
-
[select for diffs]
Modified
Wed Aug 20 19:42:31 2003 UTC
(21 years ago)
by
mmeineke
Diff to
previous 704
updated the Changelog.
added some bug fixes for setting the random number generator seed value.
fixed a bug where ghostbend atom b was not being set. ( recent bug from SimState conversion)
Revision
690 -
Directory Listing
-
[select for diffs]
Modified
Tue Aug 12 21:44:06 2003 UTC
(21 years ago)
by
mmeineke
Diff to
previous 689
fixed a really annoying bug in Directional Atom, where mu was getting written to pseudorandom memory location.
Revision
626 -
Directory Listing
-
[select for diffs]
Modified
Wed Jul 16 21:30:56 2003 UTC
(21 years, 1 month ago)
by
mmeineke
Diff to
previous 623
Changed how cutoffs were handled from C. Now notifyCutoffs in Fortran notifies those who need the information of any changes to cutoffs.
Revision
619 -
Directory Listing
-
[select for diffs]
Modified
Tue Jul 15 22:22:41 2003 UTC
(21 years, 1 month ago)
by
mmeineke
Diff to
previous 618
fixed a long lived bug in do_forces. Rrf was not being used in the neighborlist correctly. rcut was conssistently being set lowere than Rrf causing the dipole cutoff region to be to small. Also led to the removal of the taper region to buffer the dipole cutoff.
Revision
568 -
Directory Listing
-
[select for diffs]
Modified
Mon Jun 30 22:04:01 2003 UTC
(21 years, 1 month ago)
by
mmeineke
Diff to
previous 567
Updated the ChangeLog, and Converted most of the SImInfo to use non-Isotropic
boxes. wrapVector needs to be finished.
Revision
440 -
Directory Listing
-
[select for diffs]
Modified
Tue Apr 1 16:49:17 2003 UTC
(21 years, 4 months ago)
by
mmeineke
Diff to
previous 439
Fixed DumpWriter to be more robust to errors. also added a little namespace to InitFromFile to wrap it's helper functions in MPI
Revision
420 -
Directory Listing
-
[select for diffs]
Modified
Thu Mar 27 17:32:03 2003 UTC
(21 years, 5 months ago)
by
mmeineke
Diff to
previous 419
LJ_FF has been converted to the new Molecule model. TraPPE_Ex is currently being updated.
SimSetups routines are writtten, but not yet called.
Revision
415 -
Directory Listing
-
[select for diffs]
Modified
Wed Mar 26 22:24:49 2003 UTC
(21 years, 5 months ago)
by
gezelter
Diff to
previous 414
Making DumpWriter less dependent on sequence of atoms on the other
processors. Node 0 now fires potatoes at other processors to get them
to send french fries back.
Revision
407 -
Directory Listing
-
[select for diffs]
Modified
Wed Mar 26 20:22:02 2003 UTC
(21 years, 5 months ago)
by
mmeineke
Diff to
previous 406
I'm overhauling the molecule class to contain it's own bonds, bends, and torsions.
may god have mercy on my soul.
Revision
389 -
Directory Listing
-
[select for diffs]
Modified
Mon Mar 24 15:26:05 2003 UTC
(21 years, 5 months ago)
by
mmeineke
Diff to
previous 388
fixed bug where short range interactions were not being calculated.
removed some debug print statements
Revision
378 -
Directory Listing
-
[select for diffs]
Added
Fri Mar 21 17:42:12 2003 UTC
(21 years, 5 months ago)
by
mmeineke
This commit was generated by cvs2svn to compensate for changes in r377,
which included commits to RCS files with non-trunk default branches.