Revision
1254 -
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Modified
Wed Jun 9 16:16:33 2004 UTC
(20 years, 2 months ago)
by
tim
Diff to
previous 1253
1. adding some useful math classes(Mat3x3d, Vector3d, Quaternion, Euler3)
these classes use anonymous union and struct to support
double[3], double[3][3] and double[4]
2. adding roll constraint algorithm
Revision
1253 -
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Modified
Tue Jun 8 16:49:46 2004 UTC
(20 years, 2 months ago)
by
gezelter
Diff to
previous 1252
Fixed a bug in NPTf (vScale was declared in the cpp file in addition
to the declaration in Integrator.hpp file)
Revision
1180 -
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Modified
Thu May 20 20:24:07 2004 UTC
(20 years, 3 months ago)
by
chrisfen
Diff to
previous 1178
Several additions... Restraints.cpp and .hpp were included for restraining particles in thermodynamic integration. By including these, changes were made in Integrator, SimInfo, ForceFeilds, SimSetup, StatWriter, and possibly some other files. Two bass keywords were also added for performing thermodynamic integration: a lambda value one and a k power one.
Revision
1167 -
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Modified
Wed May 12 16:38:45 2004 UTC
(20 years, 3 months ago)
by
tim
Diff to
previous 1166
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
1153 -
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Modified
Tue May 11 04:21:52 2004 UTC
(20 years, 3 months ago)
by
gezelter
Diff to
previous 1152
BASS changes for adding CutoffGroups to molecules. Also restructured
the plethora of cutoff radii into one cutoffRadius and one
switchingRadius. Also removed the useMolecularCutoffs keyword
Revision
1104 -
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Modified
Tue Apr 13 16:26:03 2004 UTC
(20 years, 4 months ago)
by
gezelter
Diff to
previous 1103
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
1023 -
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Modified
Wed Feb 4 22:26:00 2004 UTC
(20 years, 6 months ago)
by
tim
Diff to
previous 1015
Fix a bunch of bugs :-)
Single version of conjugate gradient with golden search linesearch pass a couple of
functions test. Brent's algorithm is still broken
Revision
999 -
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Modified
Fri Jan 30 15:01:09 2004 UTC
(20 years, 6 months ago)
by
chrisfen
Diff to
previous 998
Substantial changes. OOPSE now has a working WATER.cpp forcefield and parser.
This involved changes to WATER.cpp and ForceFields amoung other files. One important
note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. This will be removed on
the next commit...
Revision
986 -
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Modified
Mon Jan 26 22:01:23 2004 UTC
(20 years, 6 months ago)
by
gezelter
Diff to
previous 985
Changes to BASS reader to use Euler angles for orientation instead of
unit vectors required changes in MoLocator
Revision
983 -
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Modified
Mon Jan 26 21:45:03 2004 UTC
(20 years, 6 months ago)
by
gezelter
Diff to
previous 982
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
982 -
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Modified
Mon Jan 26 21:26:40 2004 UTC
(20 years, 6 months ago)
by
gezelter
Diff to
previous 981
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
958 -
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Modified
Mon Jan 19 16:09:52 2004 UTC
(20 years, 7 months ago)
by
gezelter
Diff to
previous 957
BASS changes to add RigidBodies required a change in
how the MoleculeStamps are used by divideLabor in mpiSimulation.cpp
Revision
929 -
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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 -
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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
893 -
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Modified
Mon Dec 29 19:56:39 2003 UTC
(20 years, 7 months ago)
by
chuckv
Diff to
previous 892
Added third-party directory for code not written by us. Also added Mersenne Twister random number generator code. This will eventually replace sprng as the random number generator used by OOPSE.
Revision
882 -
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Modified
Wed Dec 17 20:13:33 2003 UTC
(20 years, 8 months ago)
by
chuckv
Diff to
previous 879
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
876 -
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Modified
Wed Dec 10 16:52:46 2003 UTC
(20 years, 8 months ago)
by
mmeineke
Diff to
previous 875
edited the makefile to add randomBilayer to the build. Also move the random bilayer builder from
bilayerSys to randomBilayer
Revision
875 -
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Modified
Tue Nov 25 15:44:32 2003 UTC
(20 years, 9 months ago)
by
mmeineke
Diff to
previous 874
backed up the old DUFF.frc to backup.DUFF.frc alte4red masses and epsilons of TB2 and TB3 in DUFF.frc
Revision
874 -
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Modified
Fri Nov 21 20:10:02 2003 UTC
(20 years, 9 months ago)
by
mmeineke
Diff to
previous 873
added a more verbose error message in SimInfo. Added a more informative error message in InitializeFromFile
Revision
859 -
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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 -
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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 -
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Modified
Thu Nov 6 22:01:37 2003 UTC
(20 years, 9 months ago)
by
mmeineke
Diff to
previous 854
added the following parameters to BASS:
* useInitialExtendedSystemState
* orthoBoxTolerance
* useIntiTime => useInitialTime
Revision
853 -
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Modified
Thu Nov 6 19:11:38 2003 UTC
(20 years, 9 months ago)
by
mmeineke
Diff to
previous 851
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 -
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Modified
Wed Oct 29 20:41:39 2003 UTC
(20 years, 9 months ago)
by
mmeineke
Diff to
previous 842
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 -
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Modified
Tue Oct 28 22:25:46 2003 UTC
(20 years, 9 months ago)
by
mmeineke
Diff to
previous 835
did a complete overhaul of how c calls fortran. All function pointers and fortran calls are rigidly typecast now.
Revision
829 -
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Modified
Tue Oct 28 16:03:37 2003 UTC
(20 years, 9 months ago)
by
gezelter
Diff to
previous 828
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
828 -
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Modified
Tue Oct 28 16:03:06 2003 UTC
(20 years, 9 months ago)
by
gezelter
Diff to
previous 827
replace c++ header stuff with more portable c header stuff
Also, mod file fixes and portability changes
Revision
825 -
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Modified
Mon Oct 27 22:08:36 2003 UTC
(20 years, 9 months ago)
by
mmeineke
Diff to
previous 823
added routines for the sysbuilder to work with simSetup
remved the QuickBass routines, and had all parsing go through SimSetup.
LatticeBilayer is in complete working order now.
Revision
821 -
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Modified
Fri Oct 24 22:17:45 2003 UTC
(20 years, 10 months ago)
by
mmeineke
Diff to
previous 817
put QuickBass, MoLocator, and latticeBuilder into a Builder Library
overhauled latticeBilayer into its own program. Removed sysBuild from the Makefile
Revision
815 -
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Modified
Thu Oct 23 19:57:37 2003 UTC
(20 years, 10 months ago)
by
mmeineke
Diff to
previous 814
added eam ForceField files to the init
fixed an eam mpi parmeter setup bug
added the init file to the makefile
Revision
812 -
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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 -
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Modified
Tue Oct 21 19:33:19 2003 UTC
(20 years, 10 months ago)
by
mmeineke
Diff to
previous 810
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
810 -
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Modified
Fri Oct 17 21:19:07 2003 UTC
(20 years, 10 months ago)
by
mmeineke
Diff to
previous 809
added the staticProps directory to the build list
for both configure and configure.in
fixed a number of bugs in the staticProps code. gofr is now working.
Revision
804 -
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Modified
Thu Oct 16 19:16:24 2003 UTC
(20 years, 10 months ago)
by
mmeineke
Diff to
previous 803
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
798 -
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Modified
Fri Oct 3 22:02:52 2003 UTC
(20 years, 10 months ago)
by
mmeineke
Diff to
previous 797
changed the formating ogf the error statements in simError
added a function to get the maxCutoff
near completion of the staticProps code. still needs the pair loop, and the loop to allocate and read each frame.
Revision
767 -
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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 -
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Modified
Thu Sep 4 21:48:35 2003 UTC
(20 years, 11 months ago)
by
mmeineke
Diff to
previous 745
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
(20 years, 11 months 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 -
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Modified
Wed Aug 27 16:16:01 2003 UTC
(20 years, 11 months 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
724 -
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Modified
Tue Aug 26 20:13:17 2003 UTC
(20 years, 11 months ago)
by
mmeineke
Diff to
previous 723
added define statemewnt to Statwriter and Dumpwriter to handle files larger than 2 gb.
commented out some print statements in Zconstraint
hard coding some system init into bilayer.sys
Revision
723 -
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Modified
Tue Aug 26 20:12:51 2003 UTC
(20 years, 11 months 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
722 -
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Modified
Tue Aug 26 20:02:29 2003 UTC
(20 years, 11 months ago)
by
tim
Diff to
previous 721
Use make_sprng_seed() to generate seed and check the seed which is specified by user at least contains 9 digits
Revision
721 -
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Modified
Tue Aug 26 18:32:03 2003 UTC
(21 years ago)
by
mmeineke
Diff to
previous 720
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 -
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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 -
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Modified
Wed Aug 20 19:42:31 2003 UTC
(21 years ago)
by
mmeineke
Diff to
previous 706
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
Diff to
previous 689
fixed a really annoying bug in Directional Atom, where mu was getting written to pseudorandom memory location.
Revision
678 -
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Modified
Mon Aug 11 22:12:31 2003 UTC
(21 years ago)
by
chuckv
Diff to
previous 677
Arranged sysbuilder into a subdirectory. Fixed some of sysbuilder to work with new
atom allocation in libmdtools.
Revision
672 -
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Modified
Fri Aug 8 18:32:59 2003 UTC
(21 years ago)
by
mmeineke
Diff to
previous 671
moved frameCount's functionality into DumpReader. also split props into staticProps and dynamicProps. (currently only have staticProps)
Revision
626 -
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Modified
Wed Jul 16 21:30:56 2003 UTC
(21 years, 1 month ago)
by
mmeineke
Diff to
previous 624
Changed how cutoffs were handled from C. Now notifyCutoffs in Fortran notifies those who need the information of any changes to cutoffs.
Revision
624 -
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Modified
Wed Jul 16 17:35:18 2003 UTC
(21 years, 1 month ago)
by
gezelter
Diff to
previous 623
Made quickLate aware of Hmat. quickLate is now somewhat more
intelligent about periodic boundaries and wrapping.
Revision
619 -
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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 -
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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
543 -
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Modified
Fri May 30 21:32:33 2003 UTC
(21 years, 2 months ago)
by
mmeineke
Diff to
previous 542
currently modifiying Symplectic to become the basic integrator.
bilayerSys.cpp altered for building tb3.
Revision
530 -
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Modified
Fri May 9 19:51:30 2003 UTC
(21 years, 3 months ago)
by
mmeineke
Diff to
previous 529
fixed up the TraPPE_Ex force field. there were some duplicate entries
added a two chain lipid to the lipid.mdl in sample
Revision
528 -
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Modified
Fri May 9 16:56:27 2003 UTC
(21 years, 3 months ago)
by
mmeineke
Diff to
previous 527
added the utils subdirectory to the configure script
added the CH branching group to the TraPPE_Ex fource field
Revision
501 -
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Modified
Tue Apr 15 21:20:35 2003 UTC
(21 years, 4 months ago)
by
mmeineke
Diff to
previous 500
finished bilayerSys.cpp
sysBuild still need to write the bass file.
MoLocator.cpp is currently empty
Revision
440 -
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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 -
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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 -
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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 -
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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 -
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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 -
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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.