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root/group/trunk/OOPSE/libmdtools/Integrator.cpp
Revision 1284 - (view) (annotate) - [select for diffs]
Modified Mon Jun 21 18:52:21 2004 UTC (21 years, 4 months ago) by tim
File length: 19066 byte(s)
Diff to previous 1268 
roll in progress
Revision 1268 - (view) (annotate) - [select for diffs]
Modified Fri Jun 11 17:16:21 2004 UTC (21 years, 4 months ago) by tim
File length: 19058 byte(s)
Diff to previous 1234 
roll in progress
Revision 1234 - (view) (annotate) - [select for diffs]
Modified Fri Jun 4 03:15:31 2004 UTC (21 years, 5 months ago) by tim
File length: 18956 byte(s)
Diff to previous 1221 
new rattle algorithm is working
Revision 1221 - (view) (annotate) - [select for diffs]
Modified Wed Jun 2 14:56:18 2004 UTC (21 years, 5 months ago) by chrisfen
File length: 18536 byte(s)
Diff to previous 1212 
Formatting Changes, removed writeRaw
Revision 1212 - (view) (annotate) - [select for diffs]
Modified Tue Jun 1 17:15:43 2004 UTC (21 years, 5 months ago) by chrisfen
File length: 18634 byte(s)
Diff to previous 1207 
Implemented a separate solid and liquid thermodynamic integration routines
Revision 1207 - (view) (annotate) - [select for diffs]
Modified Thu May 27 20:06:38 2004 UTC (21 years, 5 months ago) by chrisfen
File length: 18536 byte(s)
Diff to previous 1187 
Fixed a bug in Integrator.cpp where it called writeRaw() when useThermInt = false...
Revision 1187 - (view) (annotate) - [select for diffs]
Modified Sat May 22 18:16:18 2004 UTC (21 years, 5 months ago) by chrisfen
File length: 18512 byte(s)
Diff to previous 1180 
Fixed Thermodynamic integration code.
Revision 1180 - (view) (annotate) - [select for diffs]
Modified Thu May 20 20:24:07 2004 UTC (21 years, 5 months ago) by chrisfen
File length: 18519 byte(s)
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 1178 - (view) (annotate) - [select for diffs]
Modified Thu May 13 21:08:05 2004 UTC (21 years, 5 months ago) by gezelter
File length: 18195 byte(s)
Diff to previous 1150 
fixes for skip list
Revision 1150 - (view) (annotate) - [select for diffs]
Modified Fri May 7 21:35:05 2004 UTC (21 years, 5 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, 6 months 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, 6 months 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, 6 months 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, 6 months 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, 6 months 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, 6 months 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, 6 months 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, 8 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, 8 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, 9 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, 9 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, 10 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 (22 years 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 (22 years 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 (22 years 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 (22 years 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 (22 years 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 (22 years, 1 month 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 (22 years, 1 month 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 (22 years, 1 month 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 (22 years, 1 month 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 (22 years, 1 month 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 (22 years, 1 month 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 (22 years, 1 month 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 (22 years, 1 month 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 (22 years, 2 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 (22 years, 2 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 (22 years, 2 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 (22 years, 2 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 (22 years, 2 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 (22 years, 2 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 (22 years, 2 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 (22 years, 3 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 (22 years, 3 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 (22 years, 3 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 (22 years, 3 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 (22 years, 3 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 (22 years, 3 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 (22 years, 3 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 (22 years, 3 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 (22 years, 3 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 (22 years, 4 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 (22 years, 4 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 (22 years, 4 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 (22 years, 4 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 (22 years, 4 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 (22 years, 4 months ago) by mmeineke
File length: 15703 byte(s) 
finished the basics of the integrator and SimSetup.cpp

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