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 820
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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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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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
775 -
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Modified
Fri Sep 19 19:16:36 2003 UTC
(20 years, 11 months ago)
by
chrisfen
Diff to
previous 774
Added the integrator.tex file with figure. This is the same as the ssdePaper, so it needs to be adjusted for the OOPSE paper. Also updated the oopse.bib file.
Revision
767 -
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Tue Sep 16 20:02:11 2003 UTC
(20 years, 11 months ago)
by
tim
Diff to
previous 766
fixed ecr grow in SimInfo
fixed conserved quantity in NPT (Still some small bug)
NPTi appears very stable.
Revision
746 -
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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
742 -
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Wed Sep 3 15:13:36 2003 UTC
(20 years, 11 months ago)
by
mmeineke
Diff to
previous 741
added zConstraint types to the AtomTypes file.
added two rendering scripts to to aid in rendering. Note:renderRange does not work.
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 732
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
729 -
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Modified
Wed Aug 27 16:18:05 2003 UTC
(20 years, 11 months ago)
by
mmeineke
Diff to
previous 727
This commit was generated by cvs2svn to compensate for changes in r728,
which included commits to RCS files with non-trunk default branches.
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
(21 years 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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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 -
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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
714 -
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Modified
Sun Aug 24 02:36:10 2003 UTC
(21 years ago)
by
mmeineke
Diff to
previous 713
overhauled the makefile to build oopse.tex from the infiles rather than mess with includes.
Also renamed header and footer to preamble and bibEnd respectively.
make current has been replaced with currMake to tke a look at a single tex section.
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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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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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
664 -
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Mon Aug 4 21:52:29 2003 UTC
(21 years ago)
by
mmeineke
Diff to
previous 663
added a current.tex to allow for looking at your current work, just change the include to the current tex file
also seperated all header info into header.tex so that oopse.tex and current.tex will behave the same.
Revision
663 -
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Fri Aug 1 20:22:36 2003 UTC
(21 years ago)
by
mmeineke
Diff to
previous 661
This commit was generated by cvs2svn to compensate for changes in r662,
which included commits to RCS files with non-trunk default branches.
Revision
649 -
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Thu Jul 24 15:50:41 2003 UTC
(21 years, 1 month ago)
by
mmeineke
Diff to
previous 648
added a '-' to the formating of the pov output file.
also removed pov2anim from the project. It will be replaced with shell scripts
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 625
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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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
545 -
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Wed Jun 4 16:07:35 2003 UTC
(21 years, 2 months ago)
by
mmeineke
Diff to
previous 543
This commit was generated by cvs2svn to compensate for changes in r544,
which included commits to RCS files with non-trunk default branches.
Revision
543 -
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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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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
517 -
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Mon May 5 21:29:11 2003 UTC
(21 years, 3 months ago)
by
mmeineke
Diff to
previous 515
This commit was generated by cvs2svn to compensate for changes in r516,
which included commits to RCS files with non-trunk default branches.
Revision
515 -
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Thu May 1 17:36:33 2003 UTC
(21 years, 3 months ago)
by
mmeineke
Diff to
previous 514
updated xyz2pov to put out better pov scripts. I'm begining to think pov2anim isn't as useful.
not sure if I should up date it, or just leave the rendering steps to shell scripts.
Revision
509 -
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Tue Apr 29 17:45:47 2003 UTC
(21 years, 3 months ago)
by
mmeineke
Diff to
previous 508
Rearranged the source tree to be easier to distribute.
Added autoconf and automatic dependency generation
Revision
501 -
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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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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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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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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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Modified
Fri Mar 21 17:42:12 2003 UTC
(21 years, 5 months ago)
by
mmeineke
Diff to
previous 376
This commit was generated by cvs2svn to compensate for changes in r377,
which included commits to RCS files with non-trunk default branches.
Revision
376 -
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Modified
Fri Mar 21 15:24:37 2003 UTC
(21 years, 5 months ago)
by
chuckv
Diff to
previous 375
Bug fixes in TraPPE.
calc_LJ_FF.F90: Removed print lines.
TraPPE_ExFF.cpp: Fixed so idents are being set.
Revision
371 -
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Thu Mar 20 17:26:37 2003 UTC
(21 years, 5 months ago)
by
chuckv
Diff to
previous 370
Fixed bugs in atype_module.F90
atype_module.F90:new_atype: status was reused for force field checks, created
new variable FFcheckStatus to be result of FF checks.
Revision
368 -
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Thu Mar 20 00:02:39 2003 UTC
(21 years, 5 months ago)
by
chuckv
Diff to
previous 367
Fixed bugs. Single version now runs w/o segfault. Still a conservation of energy bug.
do_Forces.F90: Fixed pot not being passed to do_pair.
neighborLists.F90: Fixed bugs in checkNeighborLists
atype_module.F90: Fixed bug with allocating atypes on each new_atype call.Now checks to see if atypes is null, then calles initialize(16).
vector_class.F90: Fixed some bugs with how MatchList was being allocated.
Revision
348 -
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Fri Mar 14 21:33:10 2003 UTC
(21 years, 5 months ago)
by
mmeineke
Diff to
previous 347
mostly compiles. interface twixt c and fortran is broken. (c needs to be brought up to date with fortran.)
Revision
289 -
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Thu Feb 27 18:47:45 2003 UTC
(21 years, 5 months ago)
by
mmeineke
Diff to
previous 288
added randomSPRNG.hpp to the package (oops, should have beenthere to begin with.)
added ssdFF++.cpp to the makefile
Revision
287 -
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Thu Feb 27 18:39:55 2003 UTC
(21 years, 5 months ago)
by
mmeineke
Diff to
previous 286
fixed some changes to the Globals in libBASS
Added some files to the Makefile and added ssdFF++.cpp to the C++ side of things
Revision
285 -
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Wed Feb 26 18:45:57 2003 UTC
(21 years, 5 months ago)
by
mmeineke
Diff to
previous 284
OOPSE has been braought up to date with the mdtools devfelopment tree. mdtools should no longer be used. All development should take place in the OOPSE tree.
Revision
253 -
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Thu Jan 30 15:20:21 2003 UTC
(21 years, 6 months ago)
by
chuckv
Diff to
previous 252
Added a generic util code directory and moved Linux_ifc_machdep to it.
MPI changes to compile MPI modules.
Revision
227 -
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Thu Jan 9 16:45:32 2003 UTC
(21 years, 7 months ago)
by
mmeineke
Diff to
previous 225
This commit was generated by cvs2svn to compensate for changes in r226,
which included commits to RCS files with non-trunk default branches.
Revision
221 -
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Thu Jan 2 20:14:08 2003 UTC
(21 years, 7 months ago)
by
chuckv
Diff to
previous 220
Thermo now can use SPRNG or rand48 (if not MPI).
Finished up work on randomSPRNG. Still need to fix
access to MPISimulation.
Revision
218 -
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Sun Dec 29 19:11:05 2002 UTC
(21 years, 7 months ago)
by
chuckv
Diff to
previous 217
Changed thermo getKinetic and getPotential for MPI.
Added header for SPRNG random number generator class.
Revision
203 -
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Tue Dec 10 22:09:44 2002 UTC
(21 years, 8 months ago)
by
chuckv
Diff to
previous 202
Added mpiComponentPlan.h a dual fortran c header file defining mpi
simulation parameters for both c and fortran.
Revision
197 -
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Fri Dec 6 21:20:39 2002 UTC
(21 years, 8 months ago)
by
mmeineke
Diff to
previous 196
added the extraction routines so that the moleculeStamps corresponding to the actual components used in the simulation
are now persistent throughout, and accessable through the SimInfo object.
Revision
196 -
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Thu Dec 5 21:37:51 2002 UTC
(21 years, 8 months ago)
by
chuckv
Diff to
previous 195
Working on the clean removal of key Molecule stamps from the Hash table.
stamps will be moved into a persitient linked list.
Revision
183 -
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Thu Nov 21 20:33:02 2002 UTC
(21 years, 9 months ago)
by
mmeineke
Diff to
previous 182
The simulation can run successfully on parrallel computers!! Now all that is need is the parrallel io routines, and parrallel forces
Revision
180 -
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Tue Nov 19 19:57:06 2002 UTC
(21 years, 9 months ago)
by
mmeineke
Diff to
previous 178
This commit was generated by cvs2svn to compensate for changes in r179,
which included commits to RCS files with non-trunk default branches.
Revision
177 -
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Mon Nov 18 21:23:58 2002 UTC
(21 years, 9 months ago)
by
mmeineke
Diff to
previous 176
overhauled the makefiles to be more elegant with regard to builds.
ie. now the name of the library will change when you select single or mpi
build in the Makefile.inc compilers and flags will also be updated
Revision
146 -
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Fri Oct 18 16:15:05 2002 UTC
(21 years, 10 months ago)
by
mmeineke
Diff to
previous 145
finished adding in the extra structures needed to pass info through mpi. Still need to add the implementation.
Revision
144 -
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Thu Oct 17 21:59:12 2002 UTC
(21 years, 10 months ago)
by
mmeineke
Diff to
previous 143
Changing internal storage of positions, torqes, forces, velocities, etc.
not sure here, still working
Revision
118 -
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Wed Sep 25 22:51:14 2002 UTC
(21 years, 11 months ago)
by
chuckv
Diff to
previous 117
begin the pain that is MPI.
abandon all hope ye who check out this branch..
P.S. we've added consistent BASS error checking
Revision
114 -
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Mon Sep 23 15:13:10 2002 UTC
(21 years, 11 months ago)
by
mmeineke
Diff to
previous 113
starting work on the molecule class
starting to add in the molecule class
adding in the molecule class
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107 -
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Wed Sep 11 03:51:11 2002 UTC
(21 years, 11 months ago)
by
mmeineke
Diff to
previous 106
finished the revisions of the first draft
now only lacks a complete results section, and a future Directions section
Revision
94 -
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Wed Aug 21 17:39:00 2002 UTC
(22 years ago)
by
mmeineke
Diff to
previous 92
This commit was generated by cvs2svn to compensate for changes in r93, which
included commits to RCS files with non-trunk default branches.
Revision
87 -
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Fri Aug 16 22:08:24 2002 UTC
(22 years ago)
by
mmeineke
Diff to
previous 86
VS: ----------------------------------------------------------------------
added more figures, and fixed the slides. GFave a practice talk 6-16-02 with this.
Revision
79 -
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Thu Aug 15 21:58:43 2002 UTC
(22 years ago)
by
mmeineke
Diff to
previous 78
I think I have most of it the way I like it, just need to change the correlation functions, and the final pictures
Revision
62 -
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Tue Aug 6 22:06:13 2002 UTC
(22 years ago)
by
mmeineke
Diff to
previous 61
added a crapload of crap that may or may norbe neccassary. Time will tell. Also, got footnote references working.
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61 -
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Thu Aug 1 21:12:33 2002 UTC
(22 years ago)
by
mmeineke
Diff to
previous 59
This commit was generated by cvs2svn to compensate for changes in r60, which
included commits to RCS files with non-trunk default branches.
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59 -
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Tue Jul 30 18:57:05 2002 UTC
(22 years ago)
by
mmeineke
Diff to
previous 57
This commit was generated by cvs2svn to compensate for changes in r58, which
included commits to RCS files with non-trunk default branches.
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57 -
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Tue Jul 30 18:47:17 2002 UTC
(22 years ago)
by
mmeineke
Diff to
previous 55
This commit was generated by cvs2svn to compensate for changes in r56, which
included commits to RCS files with non-trunk default branches.
Revision
54 -
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Tue Jul 30 17:25:26 2002 UTC
(22 years ago)
by
mmeineke
Diff to
previous 53
added all of the pictures. And gave a practice talk based on this version. Now begins the process of cleanup and additions
of citations.
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53 -
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Sun Jul 28 18:22:07 2002 UTC
(22 years ago)
by
mmeineke
Diff to
previous 52
getting there. Most everything but the motivation slide has been filled out. Lacks only pictures and Diagrams.
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50 -
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Fri Jul 26 20:51:52 2002 UTC
(22 years, 1 month ago)
by
mmeineke
Diff to
previous 48
This commit was generated by cvs2svn to compensate for changes in r49, which
included commits to RCS files with non-trunk default branches.
Revision
48 -
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Wed Jul 24 16:51:43 2002 UTC
(22 years, 1 month ago)
by
mmeineke
Diff to
previous 46
This commit was generated by cvs2svn to compensate for changes in r47, which
included commits to RCS files with non-trunk default branches.
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44 -
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Fri Jul 19 19:06:32 2002 UTC
(22 years, 1 month ago)
by
mmeineke
Diff to
previous 43
finished working on the command line options, and started working on the GofR
added the GofR header, and moved the strructure definitions to the madProps.h
Revision
39 -
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Modified
Fri Jul 19 01:37:38 2002 UTC
(22 years, 1 month ago)
by
mmeineke
Diff to
previous 37
This commit was generated by cvs2svn to compensate for changes in r38, which
included commits to RCS files with non-trunk default branches.
Revision
36 -
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Modified
Fri Jul 19 00:48:45 2002 UTC
(22 years, 1 month ago)
by
mmeineke
Diff to
previous 35
moved the actual routine into a seperate source from the main. This allows the routine to
be used in other applications.
Revision
35 -
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Modified
Fri Jul 19 00:01:59 2002 UTC
(22 years, 1 month ago)
by
mmeineke
Diff to
previous 33
This commit was generated by cvs2svn to compensate for changes in r34, which
included commits to RCS files with non-trunk default branches.
Revision
30 -
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Modified
Tue Jul 16 21:10:49 2002 UTC
(22 years, 1 month ago)
by
mmeineke
Diff to
previous 29
added the getA( double the_A[3][3] ) routine to the Directional Atom Class, to facilitate easier RotMat aquisition
Revision
25 -
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Modified
Tue Jul 9 21:46:32 2002 UTC
(22 years, 1 month ago)
by
mmeineke
Diff to
previous 24
fixed a precision error in the calculation of the temperature.
Also fixed the order that dump file are written.
Revision
23 -
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Modified
Tue Jul 9 19:00:04 2002 UTC
(22 years, 1 month ago)
by
mmeineke
Diff to
previous 21
This commit was generated by cvs2svn to compensate for changes in r22, which
included commits to RCS files with non-trunk default branches.
Revision
21 -
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Modified
Tue Jul 9 18:55:29 2002 UTC
(22 years, 1 month ago)
by
mmeineke
Diff to
previous 19
This commit was generated by cvs2svn to compensate for changes in r20, which
included commits to RCS files with non-trunk default branches.
Revision
19 -
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Modified
Tue Jul 9 18:46:04 2002 UTC
(22 years, 1 month ago)
by
mmeineke
Diff to
previous 17
This commit was generated by cvs2svn to compensate for changes in r18, which
included commits to RCS files with non-trunk default branches.
Revision
17 -
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Modified
Tue Jul 9 18:45:04 2002 UTC
(22 years, 1 month ago)
by
mmeineke
Diff to
previous 15
This commit was generated by cvs2svn to compensate for changes in r16, which
included commits to RCS files with non-trunk default branches.
Revision
15 -
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Modified
Tue Jul 9 18:44:39 2002 UTC
(22 years, 1 month ago)
by
mmeineke
Diff to
previous 13
This commit was generated by cvs2svn to compensate for changes in r14, which
included commits to RCS files with non-trunk default branches.
Revision
13 -
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Modified
Tue Jul 9 18:43:18 2002 UTC
(22 years, 1 month ago)
by
mmeineke
Diff to
previous 11
This commit was generated by cvs2svn to compensate for changes in r12, which
included commits to RCS files with non-trunk default branches.
Revision
11 -
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Modified
Tue Jul 9 18:40:59 2002 UTC
(22 years, 1 month ago)
by
mmeineke
Diff to
previous 9
This commit was generated by cvs2svn to compensate for changes in r10, which
included commits to RCS files with non-trunk default branches.
Revision
1 -
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Added
Mon Jun 10 17:09:30 2002 UTC
(22 years, 2 months ago)
by
(unknown author)
Standard project directories initialized by cvs2svn.