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root/group/trunk/OOPSE/libmdtools/Integrator.cpp
Revision 1150 - (view) (annotate) - [select for diffs]
Modified Fri May 7 21:35:05 2004 UTC (20 years, 11 months ago) by gezelter
File length: 18117 byte(s)
Diff to previous 1144 
Many changes to get group-based cutoffs to work
Revision 1144 - (view) (annotate) - [select for diffs]
Modified Sat May 1 18:52:38 2004 UTC (21 years ago) by tim
File length: 18210 byte(s)
Diff to previous 1127 
C++ pass groupList to fortran
Revision 1127 - (view) (annotate) - [select for diffs]
Modified Tue Apr 20 16:56:40 2004 UTC (21 years ago) by tim
File length: 18117 byte(s)
Diff to previous 1125 
fixed getCOMVel  and velocitize at thermo
Revision 1125 - (view) (annotate) - [select for diffs]
Modified Mon Apr 19 22:13:01 2004 UTC (21 years ago) by gezelter
File length: 17985 byte(s)
Diff to previous 1118 
Fixed a charge bug
Revision 1118 - (view) (annotate) - [select for diffs]
Modified Mon Apr 19 03:52:27 2004 UTC (21 years ago) by tim
File length: 17935 byte(s)
Diff to previous 1113 
new implement of quickLate using visitor and composite pattern
Revision 1113 - (view) (annotate) - [select for diffs]
Modified Thu Apr 15 16:18:26 2004 UTC (21 years ago) by tim
File length: 17590 byte(s)
Diff to previous 1108 
fix whole bunch of bugs :-)
Revision 1108 - (view) (annotate) - [select for diffs]
Modified Wed Apr 14 15:37:41 2004 UTC (21 years ago) by tim
File length: 17630 byte(s)
Diff to previous 1097 
Change DumpWriter and InitFromFile
Revision 1097 - (view) (annotate) - [select for diffs]
Modified Mon Apr 12 20:32:20 2004 UTC (21 years ago) by gezelter
File length: 17610 byte(s)
Diff to previous 1057 
Changes for RigidBody dynamics (Somewhat extensive)
Revision 1057 - (view) (annotate) - [select for diffs]
Modified Tue Feb 17 19:23:44 2004 UTC (21 years, 2 months ago) by tim
File length: 17369 byte(s)
Diff to previous 1035 
adding function shakeF in order to remove the constraint force along bond direction
Revision 1035 - (view) (annotate) - [select for diffs]
Modified Fri Feb 6 21:37:59 2004 UTC (21 years, 2 months ago) by tim
File length: 17368 byte(s)
Diff to previous 999 
Single version of energy minimization for argon is working, need to add constraint
Revision 999 - (view) (annotate) - [select for diffs]
Modified Fri Jan 30 15:01:09 2004 UTC (21 years, 3 months ago) by chrisfen
File length: 17325 byte(s)
Diff to previous 929 
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 929 - (view) (annotate) - [select for diffs]
Modified Tue Jan 13 15:46:49 2004 UTC (21 years, 3 months ago) by tim
File length: 17326 byte(s)
Diff to previous 892 
 Merge the code of writeFinal and writeDump;
 Adding sortingIndex into DumpWriter;
 Fix a bug of writing last frame twice in integrator
Revision 892 - (view) (annotate) - [select for diffs]
Modified Mon Dec 22 21:27:04 2003 UTC (21 years, 4 months ago) by chuckv
File length: 17393 byte(s)
Diff to previous 843 
Fixes to profile code.
Revision 843 - (view) (annotate) - [select for diffs]
Modified Wed Oct 29 20:41:39 2003 UTC (21 years, 6 months ago) by mmeineke
File length: 16796 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 - (view) (annotate) - [select for diffs]
Modified Wed Oct 29 17:55:28 2003 UTC (21 years, 6 months ago) by mmeineke
File length: 16945 byte(s)
Diff to previous 837 
som efixes to the way rcut is setup, as well as additional debugging comments.
Revision 837 - (view) (annotate) - [select for diffs]
Modified Wed Oct 29 00:19:10 2003 UTC (21 years, 6 months ago) by tim
File length: 16795 byte(s)
Diff to previous 829 
add chi and eta to the comment line of dump file.
Revision 829 - (view) (annotate) - [select for diffs]
Modified Tue Oct 28 16:03:37 2003 UTC (21 years, 6 months ago) by gezelter
File length: 16556 byte(s)
Diff to previous 804 
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 804 - (view) (annotate) - [select for diffs]
Modified Thu Oct 16 19:16:24 2003 UTC (21 years, 6 months ago) by mmeineke
File length: 16554 byte(s)
Diff to previous 787 
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 787 - (view) (annotate) - [select for diffs]
Modified Thu Sep 25 19:27:15 2003 UTC (21 years, 7 months ago) by mmeineke
File length: 16528 byte(s)
Diff to previous 784 
cleaned things with gcc -Wall and g++ -Wall
Revision 784 - (view) (annotate) - [select for diffs]
Modified Wed Sep 24 19:34:39 2003 UTC (21 years, 7 months ago) by mmeineke
File length: 16659 byte(s)
Diff to previous 782 
moved readyCheck in the integrator so that it is called before the first Statistics are written.
Revision 782 - (view) (annotate) - [select for diffs]
Modified Tue Sep 23 20:34:31 2003 UTC (21 years, 7 months ago) by mmeineke
File length: 16657 byte(s)
Diff to previous 781 
Removed NPTfm from Integrator.hpp.

Some small syntax cleaning in NPTfm and SimSetup
Revision 781 - (view) (annotate) - [select for diffs]
Modified Mon Sep 22 23:07:57 2003 UTC (21 years, 7 months ago) by tim
File length: 16686 byte(s)
Diff to previous 778 
fix bug in calculating maxCutoff
Revision 778 - (view) (annotate) - [select for diffs]
Modified Fri Sep 19 20:00:27 2003 UTC (21 years, 7 months ago) by mmeineke
File length: 16584 byte(s)
Diff to previous 768 
added NPT base class. NPTi is up to date. NPTf is not.
Revision 768 - (view) (annotate) - [select for diffs]
Modified Wed Sep 17 14:22:15 2003 UTC (21 years, 7 months ago) by mmeineke
File length: 16481 byte(s)
Diff to previous 763 
fixed NPTi to now work with constraints.
Revision 763 - (view) (annotate) - [select for diffs]
Modified Mon Sep 15 16:52:02 2003 UTC (21 years, 7 months ago) by tim
File length: 16475 byte(s)
Diff to previous 755 
add conserved quantity to statWriter
fix bug of vector wrapping at NPTi
Revision 755 - (view) (annotate) - [select for diffs]
Modified Tue Sep 9 20:35:25 2003 UTC (21 years, 7 months ago) by mmeineke
File length: 16372 byte(s)
Diff to previous 746 
updated the ChangeLog

added two new NPT integrators, they still need work.
Revision 746 - (view) (annotate) - [select for diffs]
Modified Thu Sep 4 21:48:35 2003 UTC (21 years, 7 months ago) by mmeineke
File length: 16373 byte(s)
Diff to previous 733 
added resetTime to the Global namespace.

added ability to reset the integrators in the NVT and NPT family.
Revision 733 - (view) (annotate) - [select for diffs]
Modified Wed Aug 27 19:23:29 2003 UTC (21 years, 8 months ago) by tim
File length: 16232 byte(s)
Diff to previous 726 
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 726 - (view) (annotate) - [select for diffs]
Modified Tue Aug 26 20:37:30 2003 UTC (21 years, 8 months ago) by tim
File length: 16256 byte(s)
Diff to previous 725 
set default force substraction policy to PolicyByMass
Revision 725 - (view) (annotate) - [select for diffs]
Modified Tue Aug 26 20:29:26 2003 UTC (21 years, 8 months ago) by tim
File length: 16269 byte(s)
Diff to previous 711 
*** empty log message ***
Revision 711 - (view) (annotate) - [select for diffs]
Modified Fri Aug 22 20:04:39 2003 UTC (21 years, 8 months ago) by mmeineke
File length: 15738 byte(s)
Diff to previous 693 
small bug fix on frequency of output dumps.
Revision 693 - (view) (annotate) - [select for diffs]
Modified Wed Aug 13 19:21:53 2003 UTC (21 years, 8 months ago) by tim
File length: 15685 byte(s)
Diff to previous 677 
harmonic potential & z-contraint method
Revision 677 - (view) (annotate) - [select for diffs]
Modified Mon Aug 11 19:41:36 2003 UTC (21 years, 8 months ago) by tim
File length: 15660 byte(s)
Diff to previous 645 
added method of moving zconstraint molecules to specified positions
Revision 645 - (view) (annotate) - [select for diffs]
Modified Tue Jul 22 19:54:52 2003 UTC (21 years, 9 months ago) by tim
File length: 15473 byte(s)
Diff to previous 643 
*** empty log message ***
Revision 643 - (view) (annotate) - [select for diffs]
Modified Mon Jul 21 21:27:40 2003 UTC (21 years, 9 months ago) by mmeineke
File length: 15208 byte(s)
Diff to previous 641 
some initial changes to Dumpwriter and friends to accomadate random file access
Revision 641 - (view) (annotate) - [select for diffs]
Modified Mon Jul 21 16:23:10 2003 UTC (21 years, 9 months ago) by mmeineke
File length: 15235 byte(s)
Diff to previous 637 
fixed Initializefrom file to start the simulation from the time specified in the init file.
Revision 637 - (view) (annotate) - [select for diffs]
Modified Thu Jul 17 21:50:01 2003 UTC (21 years, 9 months ago) by gezelter
File length: 15197 byte(s)
Diff to previous 614 
Started work on a DumpReader
Revision 614 - (view) (annotate) - [select for diffs]
Modified Tue Jul 15 17:57:04 2003 UTC (21 years, 9 months ago) by mmeineke
File length: 15168 byte(s)
Diff to previous 601 
fixed some bugs, Changed entry_plug to info where appropriate
Revision 601 - (view) (annotate) - [select for diffs]
Modified Mon Jul 14 23:06:09 2003 UTC (21 years, 9 months ago) by gezelter
File length: 15009 byte(s)
Diff to previous 600 
Removed some debugging write statements
Revision 600 - (view) (annotate) - [select for diffs]
Modified Mon Jul 14 22:38:13 2003 UTC (21 years, 9 months ago) by gezelter
File length: 15099 byte(s)
Diff to previous 597 
Fixes for get and set routines in Atom and DirectionalAtom
Revision 597 - (view) (annotate) - [select for diffs]
Modified Mon Jul 14 21:28:54 2003 UTC (21 years, 9 months ago) by mmeineke
File length: 15329 byte(s)
Diff to previous 594 
found a bug. Unit vectors were not being updated
Revision 594 - (view) (annotate) - [select for diffs]
Modified Fri Jul 11 22:34:48 2003 UTC (21 years, 9 months ago) by mmeineke
File length: 15654 byte(s)
Diff to previous 572 
working on som integrator bugs
Revision 572 - (view) (annotate) - [select for diffs]
Modified Wed Jul 2 21:26:55 2003 UTC (21 years, 10 months ago) by mmeineke
File length: 14634 byte(s)
Diff to previous 567 
fixed the bugs introduced by switching the periodic box to a matrix
Revision 567 - (view) (annotate) - [select for diffs]
Modified Wed Jun 25 21:12:14 2003 UTC (21 years, 10 months ago) by mmeineke
File length: 15366 byte(s)
Diff to previous 563 
Changed over the bonds to Harmonic bonds in the DUFF frc file

fixed constraints.
Revision 563 - (view) (annotate) - [select for diffs]
Modified Mon Jun 23 21:24:03 2003 UTC (21 years, 10 months ago) by mmeineke
File length: 15623 byte(s)
Diff to previous 561 
Doing some work to debug the constraint code.
Revision 561 - (view) (annotate) - [select for diffs]
Modified Fri Jun 20 20:29:36 2003 UTC (21 years, 10 months ago) by mmeineke
File length: 15512 byte(s)
Diff to previous 559 
Most of the integrator and NVT seem to be working now.
Revision 559 - (view) (annotate) - [select for diffs]
Modified Thu Jun 19 22:02:44 2003 UTC (21 years, 10 months ago) by mmeineke
File length: 15958 byte(s)
Diff to previous 558 
slowly converting to new integrator and forcefield names.
Revision 558 - (view) (annotate) - [select for diffs]
Added Thu Jun 19 19:21:23 2003 UTC (21 years, 10 months ago) by mmeineke
File length: 15703 byte(s) 
finished the basics of the integrator and SimSetup.cpp

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