Revision
983 -
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Modified
Mon Jan 26 21:45:03 2004 UTC
(20 years, 7 months ago)
by
gezelter
File length: 45921 byte(s)
Diff to
previous 965
Changed default orientation in BASS to use Euler angles in the
following order: phi, theta, psi
Removed the ability to set orientation using a unit vector
Revision
962 -
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Modified
Mon Jan 19 18:36:21 2004 UTC
(20 years, 7 months ago)
by
tim
File length: 43514 byte(s)
Diff to
previous 859
Adding warning if sample time, status time, thermal time and reset time are not divisible by dt
Revision
859 -
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Modified
Mon Nov 10 21:50:36 2003 UTC
(20 years, 9 months ago)
by
mmeineke
File length: 42069 byte(s)
Diff to
previous 855
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
855 -
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Modified
Thu Nov 6 22:01:37 2003 UTC
(20 years, 9 months ago)
by
mmeineke
File length: 42813 byte(s)
Diff to
previous 845
added the following parameters to BASS:
* useInitialExtendedSystemState
* orthoBoxTolerance
* useIntiTime => useInitialTime
Revision
843 -
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Modified
Wed Oct 29 20:41:39 2003 UTC
(20 years, 10 months ago)
by
mmeineke
File length: 42595 byte(s)
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
841 -
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Modified
Wed Oct 29 17:55:28 2003 UTC
(20 years, 10 months ago)
by
mmeineke
File length: 42593 byte(s)
Diff to
previous 829
som efixes to the way rcut is setup, as well as additional debugging comments.
Revision
829 -
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Modified
Tue Oct 28 16:03:37 2003 UTC
(20 years, 10 months ago)
by
gezelter
File length: 43867 byte(s)
Diff to
previous 823
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
823 -
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Modified
Mon Oct 27 22:07:48 2003 UTC
(20 years, 10 months ago)
by
mmeineke
File length: 43865 byte(s)
Diff to
previous 814
added routines for the sysbuilder to work with simSetup
Revision
814 -
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Modified
Thu Oct 23 19:57:25 2003 UTC
(20 years, 10 months ago)
by
mmeineke
File length: 43815 byte(s)
Diff to
previous 812
added eam ForceField files to the init
fixed an eam mpi parmeter setup bug
Revision
812 -
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Modified
Wed Oct 22 21:17:32 2003 UTC
(20 years, 10 months ago)
by
mmeineke
File length: 43816 byte(s)
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 -
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Modified
Tue Oct 21 19:33:19 2003 UTC
(20 years, 10 months ago)
by
mmeineke
File length: 42194 byte(s)
Diff to
previous 787
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
782 -
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Modified
Tue Sep 23 20:34:31 2003 UTC
(20 years, 11 months ago)
by
mmeineke
File length: 42171 byte(s)
Diff to
previous 780
Removed NPTfm from Integrator.hpp.
Some small syntax cleaning in NPTfm and SimSetup
Revision
780 -
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Modified
Mon Sep 22 21:23:25 2003 UTC
(20 years, 11 months ago)
by
mmeineke
File length: 41983 byte(s)
Diff to
previous 778
Converted NPTf to work with the NPT base class.
Removed NPTfm and NPTim from cvs
Revision
778 -
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Modified
Fri Sep 19 20:00:27 2003 UTC
(20 years, 11 months ago)
by
mmeineke
File length: 45061 byte(s)
Diff to
previous 746
added NPT base class. NPTi is up to date. NPTf is not.
Revision
746 -
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Modified
Thu Sep 4 21:48:35 2003 UTC
(20 years, 11 months ago)
by
mmeineke
File length: 45042 byte(s)
Diff to
previous 738
added resetTime to the Global namespace.
added ability to reset the integrators in the NVT and NPT family.
Revision
733 -
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Modified
Wed Aug 27 19:23:29 2003 UTC
(21 years ago)
by
tim
File length: 44691 byte(s)
Diff to
previous 722
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
722 -
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Modified
Tue Aug 26 20:02:29 2003 UTC
(21 years ago)
by
tim
File length: 44689 byte(s)
Diff to
previous 708
Use make_sprng_seed() to generate seed and check the seed which is specified by user at least contains 9 digits
Revision
708 -
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Modified
Wed Aug 20 22:23:34 2003 UTC
(21 years ago)
by
tim
File length: 42901 byte(s)
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 -
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Modified
Wed Aug 20 19:42:31 2003 UTC
(21 years ago)
by
mmeineke
File length: 42238 byte(s)
Diff to
previous 701
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 -
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Modified
Tue Aug 12 21:44:06 2003 UTC
(21 years ago)
by
mmeineke
File length: 40301 byte(s)
Diff to
previous 689
fixed a really annoying bug in Directional Atom, where mu was getting written to pseudorandom memory location.
Revision
670 -
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Modified
Thu Aug 7 21:47:18 2003 UTC
(21 years ago)
by
mmeineke
File length: 45076 byte(s)
Diff to
previous 661
switched SimInfo to use a system configuration from SimState rather than arrays from Atom
Revision
644 -
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Modified
Tue Jul 22 16:41:08 2003 UTC
(21 years, 1 month ago)
by
mmeineke
File length: 35462 byte(s)
Diff to
previous 626
Fixed a current time initialization bug in InitFromFile.
Revision
626 -
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Modified
Wed Jul 16 21:30:56 2003 UTC
(21 years, 1 month ago)
by
mmeineke
File length: 35462 byte(s)
Diff to
previous 621
Changed how cutoffs were handled from C. Now notifyCutoffs in Fortran notifies those who need the information of any changes to cutoffs.
Revision
614 -
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Modified
Tue Jul 15 17:57:04 2003 UTC
(21 years, 1 month ago)
by
mmeineke
File length: 35613 byte(s)
Diff to
previous 605
fixed some bugs, Changed entry_plug to info where appropriate
Revision
586 -
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Modified
Wed Jul 9 22:14:06 2003 UTC
(21 years, 1 month ago)
by
mmeineke
File length: 35019 byte(s)
Diff to
previous 582
Bug fixing NPTi and NPTf. there is some error in the caclulation of HmatInverse.
Revision
572 -
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Modified
Wed Jul 2 21:26:55 2003 UTC
(21 years, 2 months ago)
by
mmeineke
File length: 32766 byte(s)
Diff to
previous 567
fixed the bugs introduced by switching the periodic box to a matrix
Revision
567 -
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Modified
Wed Jun 25 21:12:14 2003 UTC
(21 years, 2 months ago)
by
mmeineke
File length: 32648 byte(s)
Diff to
previous 561
Changed over the bonds to Harmonic bonds in the DUFF frc file
fixed constraints.
Revision
561 -
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Modified
Fri Jun 20 20:29:36 2003 UTC
(21 years, 2 months ago)
by
mmeineke
File length: 32642 byte(s)
Diff to
previous 558
Most of the integrator and NVT seem to be working now.
Revision
558 -
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Modified
Thu Jun 19 19:21:23 2003 UTC
(21 years, 2 months ago)
by
mmeineke
File length: 31983 byte(s)
Diff to
previous 557
finished the basics of the integrator and SimSetup.cpp
Revision
557 -
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Modified
Thu Jun 19 19:11:53 2003 UTC
(21 years, 2 months ago)
by
mmeineke
File length: 31945 byte(s)
Diff to
previous 555
doing some work on SimSetup to clean it up / get it to work with the new Integrator.
Revision
555 -
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Modified
Tue Jun 17 21:56:15 2003 UTC
(21 years, 2 months ago)
by
mmeineke
File length: 31242 byte(s)
Diff to
previous 504
Added Teng's parmeters fro the ghost Bend in TraPPE_Ex
some work on the integrator. ( incomplete)
Revision
504 -
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Modified
Thu Apr 17 21:54:18 2003 UTC
(21 years, 4 months ago)
by
mmeineke
File length: 31304 byte(s)
Diff to
previous 491
fixed up sysBuild to where it should now build our systems
Revision
491 -
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Modified
Fri Apr 11 18:46:37 2003 UTC
(21 years, 4 months ago)
by
mmeineke
File length: 31408 byte(s)
Diff to
previous 490
fixed a memory bug in Fortran, where molMembershipArray was declared nLocal instead of nGlobal.
Revision
487 -
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Modified
Thu Apr 10 16:27:21 2003 UTC
(21 years, 4 months ago)
by
mmeineke
File length: 31028 byte(s)
Diff to
previous 483
fixed a n mpi init bug in SimSetup. caused a miscalculation of nLocal.
Revision
466 -
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Modified
Mon Apr 7 14:30:36 2003 UTC
(21 years, 4 months ago)
by
gezelter
File length: 29095 byte(s)
Diff to
previous 443
Added ExtendedSystem infrastructure for NPT and NVT calculations
Revision
443 -
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Modified
Wed Apr 2 22:19:03 2003 UTC
(21 years, 5 months ago)
by
mmeineke
File length: 28017 byte(s)
Diff to
previous 438
dipoles mostly work, but there is a memory leak somewhere.
Revision
435 -
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Modified
Fri Mar 28 19:33:37 2003 UTC
(21 years, 5 months ago)
by
mmeineke
File length: 27960 byte(s)
Diff to
previous 434
fixed a bug where the Excludes were not being created properly
Revision
431 -
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Modified
Thu Mar 27 22:16:27 2003 UTC
(21 years, 5 months ago)
by
mmeineke
File length: 27796 byte(s)
Diff to
previous 429
fixed a bug where excludes were not being initialized
Revision
422 -
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Modified
Thu Mar 27 19:21:42 2003 UTC
(21 years, 5 months ago)
by
mmeineke
File length: 27745 byte(s)
Diff to
previous 420
finished updating SimSetup to initialize and use the new MPI division of labour, and Molecule class
Revision
420 -
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Modified
Thu Mar 27 17:32:03 2003 UTC
(21 years, 5 months ago)
by
mmeineke
File length: 27388 byte(s)
Diff to
previous 414
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
414 -
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Modified
Wed Mar 26 22:02:36 2003 UTC
(21 years, 5 months ago)
by
mmeineke
File length: 35191 byte(s)
Diff to
previous 412
the skeleton for making the molecules is in place. ForceField needs to be updated next.
Revision
412 -
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Modified
Wed Mar 26 21:50:33 2003 UTC
(21 years, 5 months ago)
by
mmeineke
File length: 34732 byte(s)
Diff to
previous 407
still working on the SimSetup routine. also fixed some things in Exclude.hpp
Revision
407 -
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Modified
Wed Mar 26 20:22:02 2003 UTC
(21 years, 5 months ago)
by
mmeineke
File length: 31453 byte(s)
Diff to
previous 394
I'm overhauling the molecule class to contain it's own bonds, bends, and torsions.
may god have mercy on my soul.
Revision
394 -
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Modified
Mon Mar 24 21:55:34 2003 UTC
(21 years, 5 months ago)
by
gezelter
File length: 28848 byte(s)
Diff to
previous 378
electrostatic changes for dipole / RF separation