[ViewVC] Log of: group/trunk/OOPSE/libmdtools/SimSetup.cpp

Revision 787 - (view) (annotate) - [select for diffs]
Modified Thu Sep 25 19:27:15 2003 UTC (20 years, 9 months ago) by mmeineke
File length: 42121 byte(s)
Diff to previous 782

cleaned things with gcc -Wall and g++ -Wall

Revision 782 - (view) (annotate) - [select for diffs]
Modified Tue Sep 23 20:34:31 2003 UTC (20 years, 9 months ago) by mmeineke
File length: 42171 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 (20 years, 9 months ago) by mmeineke
File length: 41983 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 (20 years, 9 months ago) by mmeineke
File length: 45061 byte(s)
Diff to previous 746

added NPT base class. NPTi is up to date. NPTf is not.

Revision 746 - (view) (annotate) - [select for diffs]
Modified Thu Sep 4 21:48:35 2003 UTC (20 years, 9 months ago) by mmeineke
File length: 45042 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 (20 years, 9 months ago) by tim
File length: 44880 byte(s)
Diff to previous 736

fix a bug at MPI version of PolicyByMass

Revision 736 - (view) (annotate) - [select for diffs]
Modified Thu Aug 28 21:09:47 2003 UTC (20 years, 10 months ago) by tim
File length: 44882 byte(s)
Diff to previous 733

Added: check uniqueness of molIndex

Revision 733 - (view) (annotate) - [select for diffs]
Modified Wed Aug 27 19:23:29 2003 UTC (20 years, 10 months ago) by tim
File length: 44691 byte(s)
Diff to previous 722

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 722 - (view) (annotate) - [select for diffs]
Modified Tue Aug 26 20:02:29 2003 UTC (20 years, 10 months ago) by tim
File length: 44689 byte(s)
Diff to previous 708

Use make_sprng_seed() to generate seed and check the seed which is specified by user at least contains 9 digits

Revision 708 - (view) (annotate) - [select for diffs]
Modified Wed Aug 20 22:23:34 2003 UTC (20 years, 10 months ago) by tim
File length: 42901 byte(s)
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 - (view) (annotate) - [select for diffs]
Modified Wed Aug 20 19:42:31 2003 UTC (20 years, 10 months ago) by mmeineke
File length: 42238 byte(s)
Diff to previous 701

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 701 - (view) (annotate) - [select for diffs]
Modified Wed Aug 20 14:34:04 2003 UTC (20 years, 10 months ago) by tim
File length: 42241 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 (20 years, 10 months ago) by tim
File length: 41040 byte(s)
Diff to previous 693

Tested MPI version of Z-Constraint Method

Revision 693 - (view) (annotate) - [select for diffs]
Modified Wed Aug 13 19:21:53 2003 UTC (20 years, 10 months ago) by tim
File length: 40394 byte(s)
Diff to previous 690

harmonic potential & z-contraint method

Revision 690 - (view) (annotate) - [select for diffs]
Modified Tue Aug 12 21:44:06 2003 UTC (20 years, 10 months ago) by mmeineke
File length: 40301 byte(s)
Diff to previous 689

fixed a really annoying bug in Directional Atom, where mu was getting written to pseudorandom memory location.

Revision 689 - (view) (annotate) - [select for diffs]
Modified Tue Aug 12 19:56:49 2003 UTC (20 years, 10 months ago) by tim
File length: 40516 byte(s)
Diff to previous 682

debugging globals

Revision 682 - (view) (annotate) - [select for diffs]
Modified Tue Aug 12 17:51:33 2003 UTC (20 years, 10 months ago) by tim
File length: 40284 byte(s)
Diff to previous 676

added harmonical potential to z-constraint method

Revision 676 - (view) (annotate) - [select for diffs]
Modified Mon Aug 11 19:40:06 2003 UTC (20 years, 10 months ago) by tim
File length: 39445 byte(s)
Diff to previous 670

*** empty log message ***

Revision 670 - (view) (annotate) - [select for diffs]
Modified Thu Aug 7 21:47:18 2003 UTC (20 years, 10 months ago) by mmeineke
File length: 45076 byte(s)
Diff to previous 661

switched SimInfo to use a system configuration from SimState rather than arrays from Atom

Revision 661 - (view) (annotate) - [select for diffs]
Modified Fri Aug 1 16:18:13 2003 UTC (20 years, 10 months ago) by tim
File length: 44488 byte(s)
Diff to previous 660

stable version of Z-Constraint

Revision 660 - (view) (annotate) - [select for diffs]
Modified Thu Jul 31 19:59:34 2003 UTC (20 years, 11 months ago) by tim
File length: 44525 byte(s)
Diff to previous 658

add index range checking into ZConstraint

Revision 658 - (view) (annotate) - [select for diffs]
Modified Thu Jul 31 15:35:07 2003 UTC (20 years, 11 months ago) by tim
File length: 38158 byte(s)
Diff to previous 656

 Added Z constraint.

Revision 656 - (view) (annotate) - [select for diffs]
Modified Tue Jul 29 16:32:37 2003 UTC (20 years, 11 months ago) by mmeineke
File length: 35946 byte(s)
Diff to previous 653

working on the props code

Revision 653 - (view) (annotate) - [select for diffs]
Modified Fri Jul 25 20:00:17 2003 UTC (20 years, 11 months ago) by chuckv
File length: 35772 byte(s)
Diff to previous 645

Added eam to simSetup and added changecutoffeam.

Revision 645 - (view) (annotate) - [select for diffs]
Modified Tue Jul 22 19:54:52 2003 UTC (20 years, 11 months ago) by tim
File length: 35638 byte(s)
Diff to previous 644

*** empty log message ***

Revision 644 - (view) (annotate) - [select for diffs]
Modified Tue Jul 22 16:41:08 2003 UTC (20 years, 11 months ago) by mmeineke
File length: 35462 byte(s)
Diff to previous 626

Fixed a current time initialization bug in InitFromFile.

Revision 626 - (view) (annotate) - [select for diffs]
Modified Wed Jul 16 21:30:56 2003 UTC (20 years, 11 months ago) by mmeineke
File length: 35462 byte(s)
Diff to previous 621

Changed how cutoffs were handled from C. Now notifyCutoffs in Fortran notifies those who need the information of any changes to cutoffs.

Revision 621 - (view) (annotate) - [select for diffs]
Modified Wed Jul 16 02:11:02 2003 UTC (20 years, 11 months ago) by gezelter
File length: 35617 byte(s)
Diff to previous 616

more fixes for box changes

Revision 616 - (view) (annotate) - [select for diffs]
Modified Tue Jul 15 18:52:16 2003 UTC (20 years, 11 months ago) by mmeineke
File length: 35585 byte(s)
Diff to previous 614

cleaned up simSetup

Revision 614 - (view) (annotate) - [select for diffs]
Modified Tue Jul 15 17:57:04 2003 UTC (20 years, 11 months ago) by mmeineke
File length: 35613 byte(s)
Diff to previous 605

fixed some bugs, Changed entry_plug to info where appropriate

Revision 605 - (view) (annotate) - [select for diffs]
Modified Tue Jul 15 03:27:24 2003 UTC (20 years, 11 months ago) by gezelter
File length: 37502 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 (20 years, 11 months ago) by gezelter
File length: 36357 byte(s)
Diff to previous 586

Checking in changes for NPTim

Revision 586 - (view) (annotate) - [select for diffs]
Modified Wed Jul 9 22:14:06 2003 UTC (20 years, 11 months ago) by mmeineke
File length: 35019 byte(s)
Diff to previous 582

Bug fixing NPTi and NPTf. there is some error in the caclulation of HmatInverse.

Revision 582 - (view) (annotate) - [select for diffs]
Modified Wed Jul 9 15:33:46 2003 UTC (20 years, 11 months ago) by mmeineke
File length: 32900 byte(s)
Diff to previous 580

adding in dan's NPT stuff

Revision 580 - (view) (annotate) - [select for diffs]
Modified Wed Jul 9 13:56:36 2003 UTC (20 years, 11 months ago) by gezelter
File length: 32896 byte(s)
Diff to previous 572

Fixes and merging NPTf

Revision 572 - (view) (annotate) - [select for diffs]
Modified Wed Jul 2 21:26:55 2003 UTC (20 years, 11 months ago) by mmeineke
File length: 32766 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 ago) by mmeineke
File length: 32648 byte(s)
Diff to previous 561

Changed over the bonds to Harmonic bonds in the DUFF frc file

fixed constraints.

Revision 561 - (view) (annotate) - [select for diffs]
Modified Fri Jun 20 20:29:36 2003 UTC (21 years ago) by mmeineke
File length: 32642 byte(s)
Diff to previous 558

Most of the integrator and NVT seem to be working now.

Revision 558 - (view) (annotate) - [select for diffs]
Modified Thu Jun 19 19:21:23 2003 UTC (21 years ago) by mmeineke
File length: 31983 byte(s)
Diff to previous 557

finished the basics of the integrator and SimSetup.cpp

Revision 557 - (view) (annotate) - [select for diffs]
Modified Thu Jun 19 19:11:53 2003 UTC (21 years ago) by mmeineke
File length: 31945 byte(s)
Diff to previous 555

 doing some work on SimSetup to clean it up / get it to work with the new Integrator.

Revision 555 - (view) (annotate) - [select for diffs]
Modified Tue Jun 17 21:56:15 2003 UTC (21 years ago) by mmeineke
File length: 31242 byte(s)
Diff to previous 504

Added Teng's parmeters fro the ghost Bend in TraPPE_Ex

some work on the integrator. ( incomplete)

Revision 504 - (view) (annotate) - [select for diffs]
Modified Thu Apr 17 21:54:18 2003 UTC (21 years, 2 months ago) by mmeineke
File length: 31304 byte(s)
Diff to previous 491

fixed up sysBuild to where it should now build our systems

Revision 491 - (view) (annotate) - [select for diffs]
Modified Fri Apr 11 18:46:37 2003 UTC (21 years, 2 months ago) by mmeineke
File length: 31408 byte(s)
Diff to previous 490

fixed a memory bug in Fortran, where molMembershipArray was declared nLocal instead of nGlobal.

Revision 490 - (view) (annotate) - [select for diffs]
Modified Fri Apr 11 15:16:59 2003 UTC (21 years, 2 months ago) by gezelter
File length: 31580 byte(s)
Diff to previous 489

Bug fix in progress for NPT

Revision 489 - (view) (annotate) - [select for diffs]
Modified Thu Apr 10 20:08:56 2003 UTC (21 years, 2 months ago) by mmeineke
File length: 31137 byte(s)
Diff to previous 487

 added a globalIndex counter to Molecule

Revision 487 - (view) (annotate) - [select for diffs]
Modified Thu Apr 10 16:27:21 2003 UTC (21 years, 2 months ago) by mmeineke
File length: 31028 byte(s)
Diff to previous 483

fixed a n mpi init bug in SimSetup. caused a miscalculation of nLocal.

Revision 483 - (view) (annotate) - [select for diffs]
Modified Wed Apr 9 04:06:43 2003 UTC (21 years, 2 months ago) by gezelter
File length: 31023 byte(s)
Diff to previous 481

fixes for NPT and NVT

Revision 481 - (view) (annotate) - [select for diffs]
Modified Tue Apr 8 21:35:49 2003 UTC (21 years, 2 months ago) by gezelter
File length: 31056 byte(s)
Diff to previous 474

Fixes for NPT / NVT

Revision 474 - (view) (annotate) - [select for diffs]
Modified Mon Apr 7 21:42:19 2003 UTC (21 years, 2 months ago) by gezelter
File length: 29435 byte(s)
Diff to previous 469

Fixes for NPT and NVT

Revision 469 - (view) (annotate) - [select for diffs]
Modified Mon Apr 7 20:06:31 2003 UTC (21 years, 2 months ago) by mmeineke
File length: 29248 byte(s)
Diff to previous 466

bug fixes

Revision 466 - (view) (annotate) - [select for diffs]
Modified Mon Apr 7 14:30:36 2003 UTC (21 years, 2 months ago) by gezelter
File length: 29095 byte(s)
Diff to previous 443

Added ExtendedSystem infrastructure for NPT and NVT calculations

Revision 443 - (view) (annotate) - [select for diffs]
Modified Wed Apr 2 22:19:03 2003 UTC (21 years, 2 months ago) by mmeineke
File length: 28017 byte(s)
Diff to previous 438

dipoles mostly work, but there is a memory leak somewhere.

Revision 438 - (view) (annotate) - [select for diffs]
Modified Mon Mar 31 21:50:59 2003 UTC (21 years, 3 months ago) by chuckv
File length: 28076 byte(s)
Diff to previous 435

Fixes in MPI force calc and in Trappe_Ex parsing.

Revision 435 - (view) (annotate) - [select for diffs]
Modified Fri Mar 28 19:33:37 2003 UTC (21 years, 3 months ago) by mmeineke
File length: 27960 byte(s)
Diff to previous 434

fixed a bug where the Excludes were not being created properly

Revision 434 - (view) (annotate) - [select for diffs]
Modified Fri Mar 28 19:30:59 2003 UTC (21 years, 3 months ago) by chuckv
File length: 27959 byte(s)
Diff to previous 432

mpi fixes and debugging mpi read write from file.

Revision 432 - (view) (annotate) - [select for diffs]
Modified Thu Mar 27 23:33:40 2003 UTC (21 years, 3 months ago) by chuckv
File length: 27837 byte(s)
Diff to previous 431

MPI buggy, fixed mpiRefresh issue.

Revision 431 - (view) (annotate) - [select for diffs]
Modified Thu Mar 27 22:16:27 2003 UTC (21 years, 3 months ago) by mmeineke
File length: 27796 byte(s)
Diff to previous 429

fixed a bug where excludes were not being initialized

Revision 429 - (view) (annotate) - [select for diffs]
Modified Thu Mar 27 21:52:21 2003 UTC (21 years, 3 months ago) by mmeineke
File length: 27653 byte(s)
Diff to previous 427

Fixed a single processor segfault bug.

Revision 427 - (view) (annotate) - [select for diffs]
Modified Thu Mar 27 20:48:37 2003 UTC (21 years, 3 months ago) by mmeineke
File length: 27616 byte(s)
Diff to previous 424

fixed a few more bugs.

Revision 424 - (view) (annotate) - [select for diffs]
Modified Thu Mar 27 20:36:16 2003 UTC (21 years, 3 months ago) by mmeineke
File length: 27444 byte(s)
Diff to previous 422

fixing some compile time bugs

Revision 422 - (view) (annotate) - [select for diffs]
Modified Thu Mar 27 19:21:42 2003 UTC (21 years, 3 months ago) by mmeineke
File length: 27745 byte(s)
Diff to previous 420

finished updating SimSetup to initialize and use the new MPI division of labour, and Molecule class

Revision 420 - (view) (annotate) - [select for diffs]
Modified Thu Mar 27 17:32:03 2003 UTC (21 years, 3 months ago) by mmeineke
File length: 27388 byte(s)
Diff to previous 414

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 414 - (view) (annotate) - [select for diffs]
Modified Wed Mar 26 22:02:36 2003 UTC (21 years, 3 months ago) by mmeineke
File length: 35191 byte(s)
Diff to previous 412

the skeleton for making the molecules is in place. ForceField needs to be updated next.

Revision 412 - (view) (annotate) - [select for diffs]
Modified Wed Mar 26 21:50:33 2003 UTC (21 years, 3 months ago) by mmeineke
File length: 34732 byte(s)
Diff to previous 407

still working on the SimSetup routine. also fixed some things in Exclude.hpp

Revision 407 - (view) (annotate) - [select for diffs]
Modified Wed Mar 26 20:22:02 2003 UTC (21 years, 3 months ago) by mmeineke
File length: 31453 byte(s)
Diff to previous 394

I'm overhauling the molecule class to contain it's own bonds, bends, and torsions.

may god have mercy on my soul.

Revision 394 - (view) (annotate) - [select for diffs]
Modified Mon Mar 24 21:55:34 2003 UTC (21 years, 3 months ago) by gezelter
File length: 28848 byte(s)
Diff to previous 378

electrostatic changes for dipole / RF separation

Revision 378 - (view) (annotate) - [select for diffs]
Modified Fri Mar 21 17:42:12 2003 UTC (21 years, 3 months ago) by mmeineke
File length: 26871 byte(s)
Copied from: branches/mmeineke/OOPSE/libmdtools/SimSetup.cpp 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 (21 years, 3 months ago) by mmeineke
Original Path: branches/mmeineke/OOPSE/libmdtools/SimSetup.cpp
File length: 26871 byte(s)

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