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root/group/trunk/OOPSE/libmdtools/Integrator.hpp
Revision 1249 - (view) (annotate) - [select for diffs]
Modified Fri Jun 4 20:29:36 2004 UTC (20 years, 10 months ago) by tim
File length: 13264 byte(s)
Diff to previous 1248 
*** empty log message ***
Revision 1248 - (view) (annotate) - [select for diffs]
Modified Fri Jun 4 19:30:05 2004 UTC (20 years, 10 months ago) by tim
File length: 13266 byte(s)
Diff to previous 1234 
constraint algorithm for minimization is working
Revision 1234 - (view) (annotate) - [select for diffs]
Modified Fri Jun 4 03:15:31 2004 UTC (20 years, 11 months ago) by tim
File length: 13264 byte(s)
Diff to previous 1198 
new rattle algorithm is working
Revision 1198 - (view) (annotate) - [select for diffs]
Modified Thu May 27 00:48:12 2004 UTC (20 years, 11 months ago) by tim
File length: 13201 byte(s)
Diff to previous 1187 
in the progress of fixing MPI version of cutoff group
Revision 1187 - (view) (annotate) - [select for diffs]
Modified Sat May 22 18:16:18 2004 UTC (20 years, 11 months ago) by chrisfen
File length: 14382 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 (20 years, 11 months ago) by chrisfen
File length: 14406 byte(s)
Diff to previous 1161 
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 1161 - (view) (annotate) - [select for diffs]
Modified Tue May 11 21:44:05 2004 UTC (20 years, 11 months ago) by tim
File length: 14356 byte(s)
Diff to previous 1141 
adding instantiation of Integrator<BaseIntegrator> in order to make OOPSE compiled by icc8
Revision 1141 - (view) (annotate) - [select for diffs]
Modified Wed Apr 28 23:09:32 2004 UTC (21 years ago) by tim
File length: 14290 byte(s)
Diff to previous 1108 
keep the previous position of cantilever in SMD
Revision 1108 - (view) (annotate) - [select for diffs]
Modified Wed Apr 14 15:37:41 2004 UTC (21 years ago) by tim
File length: 14260 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: 13275 byte(s)
Diff to previous 1093 
Changes for RigidBody dynamics (Somewhat extensive)
Revision 1093 - (view) (annotate) - [select for diffs]
Modified Wed Mar 17 14:22:59 2004 UTC (21 years, 1 month ago) by tim
File length: 13214 byte(s)
Diff to previous 1091 
incorporate SMD into ZConstraint,it does not sound a good choice, next commit will seperate SMD and ZConstraint
Revision 1091 - (view) (annotate) - [select for diffs]
Modified Tue Mar 16 19:22:56 2004 UTC (21 years, 1 month ago) by tim
File length: 13075 byte(s)
Diff to previous 1064 
ZConstraint now can support sequential moving. Refactorying is needed to support SMD in ZConstraint
Revision 1064 - (view) (annotate) - [select for diffs]
Modified Tue Feb 24 15:44:45 2004 UTC (21 years, 2 months ago) by tim
File length: 13363 byte(s)
Diff to previous 1057 
Using inherit instead of compose to implement Minimizer
both versions are working
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: 13358 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: 13293 byte(s)
Diff to previous 1031 
Single version of energy minimization for argon is working, need to add constraint
Revision 1031 - (view) (annotate) - [select for diffs]
Modified Fri Feb 6 18:58:06 2004 UTC (21 years, 2 months ago) by tim
File length: 13299 byte(s)
Diff to previous 1010 
Add some lines into global.cpp to make it work with energy minimization
Revision 1010 - (view) (annotate) - [select for diffs]
Modified Tue Feb 3 20:43:08 2004 UTC (21 years, 2 months ago) by tim
File length: 13189 byte(s)
Diff to previous 987 
to avoid cyclic depency, refactory constraint class
Revision 987 - (view) (annotate) - [select for diffs]
Modified Tue Jan 27 19:15:20 2004 UTC (21 years, 3 months ago) by tim
File length: 13195 byte(s)
Diff to previous 969 
revision of constraint for Nonlinear Optimization Model
Revision 969 - (view) (annotate) - [select for diffs]
Modified Tue Jan 20 20:32:57 2004 UTC (21 years, 3 months ago) by tim
File length: 13176 byte(s)
Diff to previous 857 
Energy Minimizer
Revision 857 - (view) (annotate) - [select for diffs]
Modified Fri Nov 7 17:09:48 2003 UTC (21 years, 5 months ago) by mmeineke
File length: 12715 byte(s)
Diff to previous 843 
moved the velocity scale matrix calculation outside of the atom loop in the NPT family of integrators.
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: 12496 byte(s)
Diff to previous 837 
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 837 - (view) (annotate) - [select for diffs]
Modified Wed Oct 29 00:19:10 2003 UTC (21 years, 6 months ago) by tim
File length: 12386 byte(s)
Diff to previous 812 
add chi and eta to the comment line of dump file.
Revision 812 - (view) (annotate) - [select for diffs]
Modified Wed Oct 22 21:17:32 2003 UTC (21 years, 6 months ago) by mmeineke
File length: 12235 byte(s)
Diff to previous 790 
added a new NPT integrator, NPTxyz. It scales the x, y, and z direction sepeartely. no box skew allowed.
Revision 790 - (view) (annotate) - [select for diffs]
Modified Mon Sep 29 21:16:11 2003 UTC (21 years, 7 months ago) by mmeineke
File length: 13987 byte(s)
Diff to previous 788 
fixed a lot of warnings and errors found with SUN's SUNWspro.s1s7
Revision 788 - (view) (annotate) - [select for diffs]
Modified Thu Sep 25 21:17:16 2003 UTC (21 years, 7 months ago) by mmeineke
File length: 13975 byte(s)
Diff to previous 782 
fixed some additional remarks from icc -w3 (extra verbose output)
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: 13976 byte(s)
Diff to previous 780 
Removed NPTfm from Integrator.hpp.

Some small syntax cleaning in NPTfm and SimSetup
Revision 780 - (view) (annotate) - [select for diffs]
Modified Mon Sep 22 21:23:25 2003 UTC (21 years, 7 months ago) by mmeineke
File length: 16946 byte(s)
Diff to previous 778 
Converted NPTf to work with the NPT base class.

Removed NPTfm and NPTim from cvs
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: 19462 byte(s)
Diff to previous 767 
added NPT base class. NPTi is up to date. NPTf is not.
Revision 767 - (view) (annotate) - [select for diffs]
Modified Tue Sep 16 20:02:11 2003 UTC (21 years, 7 months ago) by tim
File length: 18246 byte(s)
Diff to previous 763 
fixed ecr grow in SimInfo

fixed conserved quantity in NPT (Still some small bug)

NPTi appears very stable.
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: 18215 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: 15752 byte(s)
Diff to previous 747 
updated the ChangeLog

added two new NPT integrators, they still need work.
Revision 747 - (view) (annotate) - [select for diffs]
Modified Fri Sep 5 21:28:52 2003 UTC (21 years, 7 months ago) by gezelter
File length: 13353 byte(s)
Diff to previous 746 
Changes to autoconf / configure method of configuring OOPSE
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: 13351 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 738 - (view) (annotate) - [select for diffs]
Modified Tue Sep 2 14:30:12 2003 UTC (21 years, 8 months ago) by tim
File length: 13061 byte(s)
Diff to previous 718 
fix a bug at MPI version of PolicyByMass
Revision 718 - (view) (annotate) - [select for diffs]
Modified Mon Aug 25 21:51:30 2003 UTC (21 years, 8 months ago) by gezelter
File length: 13054 byte(s)
Diff to previous 701 
*** empty log message ***
Revision 701 - (view) (annotate) - [select for diffs]
Modified Wed Aug 20 14:34:04 2003 UTC (21 years, 8 months ago) by tim
File length: 11955 byte(s)
Diff to previous 699 
reformmating ZConstraint and fixe bug of error msg printing
Revision 699 - (view) (annotate) - [select for diffs]
Modified Fri Aug 15 19:24:13 2003 UTC (21 years, 8 months ago) by tim
File length: 11076 byte(s)
Diff to previous 696 
Tested MPI version of Z-Constraint Method
Revision 696 - (view) (annotate) - [select for diffs]
Modified Thu Aug 14 16:16:39 2003 UTC (21 years, 8 months ago) by tim
File length: 9313 byte(s)
Diff to previous 693 
Stable ZConstraint with average force substraction strategy
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: 9274 byte(s)
Diff to previous 682 
harmonic potential & z-contraint method
Revision 682 - (view) (annotate) - [select for diffs]
Modified Tue Aug 12 17:51:33 2003 UTC (21 years, 8 months ago) by tim
File length: 9227 byte(s)
Diff to previous 677 
added harmonical potential to z-constraint 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: 9169 byte(s)
Diff to previous 658 
added method of moving zconstraint molecules to specified positions
Revision 658 - (view) (annotate) - [select for diffs]
Modified Thu Jul 31 15:35:07 2003 UTC (21 years, 9 months ago) by tim
File length: 8660 byte(s)
Diff to previous 645 
 Added Z constraint.
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: 7255 byte(s)
Diff to previous 605 
*** empty log message ***
Revision 605 - (view) (annotate) - [select for diffs]
Modified Tue Jul 15 03:27:24 2003 UTC (21 years, 9 months ago) by gezelter
File length: 7149 byte(s)
Diff to previous 604 
Bugfix in NPTim, fixes for NPTfm
Revision 604 - (view) (annotate) - [select for diffs]
Modified Tue Jul 15 03:08:00 2003 UTC (21 years, 9 months ago) by gezelter
File length: 7105 byte(s)
Diff to previous 600 
Checking in changes for NPTim
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: 7038 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: 7112 byte(s)
Diff to previous 596 
found a bug. Unit vectors were not being updated
Revision 596 - (view) (annotate) - [select for diffs]
Modified Mon Jul 14 15:04:55 2003 UTC (21 years, 9 months ago) by gezelter
File length: 7115 byte(s)
Diff to previous 594 
Working on NPTim
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: 4933 byte(s)
Diff to previous 588 
working on som integrator bugs
Revision 588 - (view) (annotate) - [select for diffs]
Modified Thu Jul 10 17:10:56 2003 UTC (21 years, 9 months ago) by gezelter
File length: 4650 byte(s)
Diff to previous 586 
Bunch of 1-d array -> 2-d array stuff
Revision 586 - (view) (annotate) - [select for diffs]
Modified Wed Jul 9 22:14:06 2003 UTC (21 years, 9 months ago) by mmeineke
File length: 4647 byte(s)
Diff to previous 576 
Bug fixing NPTi and NPTf. there is some error in the caclulation of HmatInverse.
Revision 576 - (view) (annotate) - [select for diffs]
Modified Tue Jul 8 21:10:16 2003 UTC (21 years, 9 months ago) by gezelter
File length: 4573 byte(s)
Diff to previous 574 
*** empty log message ***
Revision 574 - (view) (annotate) - [select for diffs]
Modified Tue Jul 8 20:56:10 2003 UTC (21 years, 9 months ago) by gezelter
File length: 3625 byte(s)
Diff to previous 565 
NPTi
Revision 565 - (view) (annotate) - [select for diffs]
Modified Tue Jun 24 22:51:57 2003 UTC (21 years, 10 months ago) by gezelter
File length: 3607 byte(s)
Diff to previous 562 
Fixes to NVT.  Check them!
Revision 562 - (view) (annotate) - [select for diffs]
Modified Fri Jun 20 20:50:17 2003 UTC (21 years, 10 months ago) by gezelter
File length: 3819 byte(s)
Diff to previous 561 
NPT fix
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: 3833 byte(s)
Diff to previous 560 
Most of the integrator and NVT seem to be working now.
Revision 560 - (view) (annotate) - [select for diffs]
Modified Fri Jun 20 16:49:33 2003 UTC (21 years, 10 months ago) by gezelter
File length: 3845 byte(s)
Diff to previous 559 
NVT additions
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: 2200 byte(s)
Diff to previous 555 
slowly converting to new integrator and forcefield names.
Revision 555 - (view) (annotate) - [select for diffs]
Modified Tue Jun 17 21:56:15 2003 UTC (21 years, 10 months ago) by mmeineke
File length: 2155 byte(s)
Diff to previous 548 
Added Teng's parmeters fro the ghost Bend in TraPPE_Ex

some work on the integrator. ( incomplete)
Revision 548 - (view) (annotate) - [select for diffs]
Modified Wed Jun 4 21:06:45 2003 UTC (21 years, 11 months ago) by mmeineke
File length: 1975 byte(s)
Diff to previous 542 
added constrainA and constrainB to the Symplectic integrator
Revision 542 - (view) (annotate) - [select for diffs]
Modified Fri May 30 21:31:48 2003 UTC (21 years, 11 months ago) by mmeineke
File length: 1714 byte(s)
Diff to previous 541 
currently modifiying Symplectic to become the basic integrator.
Revision 541 - (view) (annotate) - [select for diffs]
Modified Fri May 30 20:19:44 2003 UTC (21 years, 11 months ago) by mmeineke
File length: 1666 byte(s)
Diff to previous 540 
added some member variables for position, velocity, etc.
Revision 540 - (view) (annotate) - [select for diffs]
Modified Fri May 30 19:07:45 2003 UTC (21 years, 11 months ago) by mmeineke
File length: 1544 byte(s)
Diff to previous 466 
changed how NVT is now derived from Integrator
Revision 466 - (view) (annotate) - [select for diffs]
Modified Mon Apr 7 14:30:36 2003 UTC (22 years ago) by gezelter
File length: 2106 byte(s)
Diff to previous 423 
Added ExtendedSystem infrastructure for NPT and NVT calculations
Revision 423 - (view) (annotate) - [select for diffs]
Modified Thu Mar 27 20:12:15 2003 UTC (22 years, 1 month ago) by mmeineke
File length: 1951 byte(s)
Diff to previous 378 
I have implemeted Molecules everywhere I could remember to.
will now attempt to compile.
Revision 378 - (view) (annotate) - [select for diffs]
Modified Fri Mar 21 17:42:12 2003 UTC (22 years, 1 month ago) by mmeineke
File length: 1993 byte(s)
Copied from: branches/mmeineke/OOPSE/libmdtools/Integrator.hpp revision 377
Diff to previous 377 
This commit was generated by cvs2svn to compensate for changes in r377,
which included commits to RCS files with non-trunk default branches.
Revision 377 - (view) (annotate) - [select for diffs]
Added Fri Mar 21 17:42:12 2003 UTC (22 years, 1 month ago) by mmeineke
Original Path: branches/mmeineke/OOPSE/libmdtools/Integrator.hpp
File length: 1993 byte(s) 
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