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.hglog
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changeset: 533:ce80c484d94b
tag: tip
user: ajamesonpratt
date: Tue Jul 29 16:33:27 2014 -0400
files: .hgsubstate
description:
Added ability to overlay contour plot to plothist
changeset: 532:6db17e6ea578
user: Nick Rego <nbr2@pitt.edu>
date: Mon Oct 07 21:25:58 2013 -0400
files: src/west/data_manager.py
description:
refixed indent error in data_manager update_segments
changeset: 531:6054703e2fc3
user: Matt Zwier <mczwier@gmail.com>
date: Wed Oct 02 15:31:37 2013 -0500
files: .hgsubstate
description:
Bumped west_tools
changeset: 530:b68495cdf76f
parent: 529:050fb32b0599
parent: 528:c78b8e05774c
user: Matt Zwier <mczwier@gmail.com>
date: Fri Sep 27 17:34:16 2013 -0500
files: src/west/data_manager.py
description:
Merge
changeset: 529:050fb32b0599
parent: 527:d9febd38972f
user: Matt Zwier <mczwier@gmail.com>
date: Fri Sep 27 17:32:11 2013 -0500
files: .hgsub .hgsubstate
description:
Removed h5py subrepository as 2.2 contains required changes.
A custom h5py in lib/h5py will still be picked up and built if present.
changeset: 528:c78b8e05774c
parent: 524:c98e7a00e0e2
user: Matt Zwier <mczwier@gmail.com>
date: Fri Sep 27 17:21:01 2013 -0500
files: src/west/data_manager.py src/west/sim_manager.py src/westext/wess/wess_driver.py
description:
Updates to allow periodic flushing of HDF5 file instead of with every segment; might help speed things up on slow network FSs when segments return quickly.
changeset: 527:d9febd38972f
user: Asinan
date: Wed Sep 25 13:20:16 2013 -0400
files: lib/examples/methane_gmx/west.cfg
description:
Fixed methane example not pointing to the right object for reweighting.
changeset: 526:e0b0680a9397
user: Nick Rego <nbr2@pitt.edu>
date: Tue Sep 24 12:11:00 2013 -0400
files: .hgignore .hgsubstate bin/w_eddist lib/examples/odld/init.sh lib/examples/odld/odld_system.py lib/examples/odld/west.cfg src/west/data_manager.py
description:
added preliminary event duration distribution tool (used like w_pdist)
changeset: 525:c5632bc44b61
user: joshua.adelman <joshua.adelman@gmail.com>
date: Tue Sep 10 12:53:54 2013 -0400
files: .hgsubstate
description:
Bumped west_tools
changeset: 524:c98e7a00e0e2
user: Matt Zwier <mczwier@gmail.com>
date: Fri Aug 30 12:01:09 2013 -0500
files: src/west/data_manager.py
description:
Fixed indentation error in data_manager.py
changeset: 523:076824ed0c8c
user: ajamesonpratt
date: Wed Jul 31 15:53:48 2013 -0400
files: .hgsubstate src/west/data_manager.py
description:
Adjusted kinetics scripts (w_kinetics.py and _kinetics.pyx) to dump seg_id in kinetics.h5
changeset: 522:c53fd097ceed
user: Matt Zwier <mczwier@gmail.com>
date: Thu Jul 18 21:06:22 2013 -0400
files: .hgsubstate
description:
west_tools bump to get updated correct multi-state tracing kinetics code
changeset: 521:eb21bb8438e3
user: Matt Zwier <mczwier@gmail.com>
date: Sat Jul 06 13:32:17 2013 -0400
files: .hgsubstate bin/w_ntop
description:
Added w_ntop link, bumped west_tools
changeset: 520:df5343b5dea9
user: Matt Zwier <mczwier@gmail.com>
date: Wed Jun 26 07:54:29 2013 -0400
files: .hgsubstate
description:
bump
changeset: 519:7f7e65d5bcca
parent: 518:03441bc289be
parent: 517:ba7d0f0a769d
user: Matt Zwier <mczwier@gmail.com>
date: Wed Jun 26 07:53:34 2013 -0400
description:
Merged ba7d0f0a769d and 03441bc289be
changeset: 518:03441bc289be
parent: 514:71a33eb43a5c
user: Matt Zwier <mczwier@gmail.com>
date: Wed Jun 26 07:52:36 2013 -0400
files: .hgsubstate
description:
Bumped west_tools
changeset: 517:ba7d0f0a769d
user: Matt Zwier <mczwier@gmail.com>
date: Wed Jun 12 12:31:29 2013 -0400
files: .hgsubstate
description:
Bumped west_tools
changeset: 516:5c48b1dcfa0f
user: Matt Zwier <mczwier@gmail.com>
date: Wed Jun 12 12:30:05 2013 -0400
files: .hgsubstate
description:
Fixed incorrect use of list vs dict in RecursiveBinMapper. Added unit test for
regression testing. Fixes #37.
changeset: 515:0cc9ccf4a367
user: joshua.adelman <joshua.adelman@gmail.com>
date: Fri Jun 07 21:07:32 2013 -0400
files: bin/west
description:
Modified the west script to make setting WEST_ROOT os agnostic
changeset: 514:71a33eb43a5c
user: Matt Zwier <mczwier@gmail.com>
date: Wed Jun 05 16:06:06 2013 -0400
files: .hgsubstate
description:
west_tools bump
changeset: 513:17a3a97dfad3
user: joshua.adelman <joshua.adelman@gmail.com>
date: Thu May 23 17:02:14 2013 -0400
files: .hgsubstate
description:
Update to west_tools subrepo addressing issue #34 and issue #35
changeset: 512:bc44b6cf8242
user: Adam P <ajp105@pitt.edu>
date: Thu May 23 14:07:52 2013 -0400
files: lib/cmds/w_states.py
description:
Update of w_states.py to correctly run
changeset: 511:a6a83fd145da
user: joshua.adelman <joshua.adelman@gmail.com>
date: Wed May 22 10:59:13 2013 -0400
files: .hgsubstate src/westext/weed/BinCluster.py src/westext/weed/ProbAdjustEquil.py src/westext/weed/UncertMath.py src/westext/weed/weed_driver.py
description:
Updated copyright information
changeset: 510:c0a102b20557
user: Adam P <ajp105@pitt.edu>
date: Mon May 20 15:39:01 2013 -0400
files: .hgsubstate
description:
Fix for the instant 2d plot method of plothist
changeset: 509:1ea932aeb138
parent: 508:6605f003e78d
parent: 507:9bc0bfe38a5f
user: Matt Zwier <mczwier@gmail.com>
date: Mon May 20 11:49:54 2013 -0400
description:
Merging
changeset: 508:6605f003e78d
parent: 506:ba835b52c13a
user: Matt Zwier <mczwier@gmail.com>
date: Mon May 20 11:49:20 2013 -0400
files: .hgsubstate
description:
Bumped west_tools
changeset: 507:9bc0bfe38a5f
user: ktd3
date: Thu May 16 11:37:33 2013 -0400
files: lib/examples/nacl_namd/init.sh
description:
correction to nacl_namd tutorial
changeset: 506:ba835b52c13a
user: Matt Zwier <mczwier@gmail.com>
date: Fri May 10 22:46:27 2013 -0400
files: .hgsubstate bin/w_crawl
description:
Added link for w_crawl, bumped west_tools
changeset: 505:ccbd996ce72d
user: Matt Zwier <mczwier@gmail.com>
date: Mon May 06 14:13:48 2013 -0400
files: .hgsubstate
description:
west_tools bump
changeset: 504:b0daf9d01bd2
user: joshua.adelman <joshua.adelman@gmail.com>
date: Fri May 03 14:47:39 2013 -0400
files: lib/examples/nacl_openmm/bstates/nacl.inpcrd lib/examples/nacl_openmm/build_system.py lib/examples/nacl_openmm/env.sh lib/examples/nacl_openmm/init.sh lib/examples/nacl_openmm/nacl.inpcrd lib/examples/nacl_openmm/nacl.prmtop lib/examples/nacl_openmm/openmm_propagator.py lib/examples/nacl_openmm/restart_plugin.py lib/examples/nacl_openmm/run.sh lib/examples/nacl_openmm/system.py lib/examples/nacl_openmm/west.cfg
description:
Added OpenMM NaCl example
changeset: 503:863dca28be75
user: Matt Zwier <mczwier@gmail.com>
date: Wed May 01 10:22:13 2013 -0400
files: .hgsubstate lib/examples/odld/odld_system.py lib/examples/odld/west.cfg
description:
Tweaks
changeset: 502:faf8f947ab86
user: Matt Zwier <mczwier@gmail.com>
date: Mon Apr 29 13:59:39 2013 -0400
files: .hgsubstate bin/w_stateprobs
description:
Added link for w_stateprobs, updated west_tools
changeset: 501:0da30dd04cfa
user: Matt Zwier <mczwier@gmail.com>
date: Wed Apr 24 17:10:11 2013 -0400
files: .hgsubstate
description:
Added link for w_stateprobs
changeset: 500:b0edc3bea57f
user: Matt Zwier <mczwier@gmail.com>
date: Wed Apr 24 11:23:26 2013 -0400
files: .hgsubstate bin/ploterr
description:
Added link for ploterr
changeset: 499:004499522a89
parent: 498:ad825806d402
parent: 494:3c81a3200cf0
user: Matt Zwier <mczwier@gmail.com>
date: Tue Apr 23 17:00:31 2013 -0400
description:
Merging
changeset: 498:ad825806d402
user: Matt Zwier <mczwier@gmail.com>
date: Tue Apr 23 17:00:02 2013 -0400
files: .hgsubstate
description:
Subrepo update
changeset: 497:09343f17a96d
parent: 496:3e7628f85ced
parent: 495:debc1178bdff
user: Matt Zwier <mczwier@gmail.com>
date: Tue Apr 23 14:17:30 2013 -0400
files: bin/w_binprobs bin/w_pcpdist lib/cmds/w_binprobs.py lib/cmds/w_edpdist.py lib/cmds/w_fluxanl.py lib/cmds/w_trace.py lib/cmds/w_ttimes.py
description:
Merging
changeset: 496:3e7628f85ced
parent: 492:2b2bab8914dc
user: Matt Zwier <mczwier@gmail.com>
date: Tue Apr 23 14:06:17 2013 -0400
files: .hgsubstate
description:
And again
changeset: 495:debc1178bdff
parent: 486:066ad21a9ed5
user: Matt Zwier <mczwier@gmail.com>
date: Sat Apr 20 21:46:54 2013 -0400
files: .hgsubstate bin/w_binprobs bin/w_pcpdist lib/cmds/w_binprobs.py lib/cmds/w_edpdist.py lib/cmds/w_fluxanl.py lib/cmds/w_trace.py lib/cmds/w_ttimes.py
description:
Merging and updating subrepos
changeset: 494:3c81a3200cf0
user: Matt Zwier <mczwier@gmail.com>
date: Tue Apr 23 16:57:52 2013 -0400
files: .hgsubstate
description:
Subrepo update
changeset: 493:c64642a9cebf
user: Matt Zwier <mczwier@gmail.com>
date: Tue Apr 23 14:59:15 2013 -0400
files: .hgsubstate
description:
Updated west_tools (seen enough of these lately?)
changeset: 492:2b2bab8914dc
user: Matt Zwier <mczwier@gmail.com>
date: Tue Apr 23 13:33:43 2013 -0400
files: .hgsubstate
description:
Updated west_tools
changeset: 491:71ba76ae8625
user: Matt Zwier <mczwier@gmail.com>
date: Tue Apr 23 11:54:05 2013 -0400
files: .hgsubstate bin/west lib/cmds/w_binprobs.py lib/cmds/w_edpdist.py lib/cmds/w_fluxanl.py lib/cmds/w_fork.py lib/cmds/w_init.py lib/cmds/w_run.py lib/cmds/w_states.py lib/cmds/w_succ.py lib/cmds/w_trace.py lib/cmds/w_truncate.py src/oldtools/aframe/__init__.py src/oldtools/aframe/atool.py src/oldtools/aframe/binning.py src/oldtools/aframe/data_reader.py src/oldtools/aframe/iter_range.py src/oldtools/aframe/kinetics.py src/oldtools/aframe/mcbs.py src/oldtools/aframe/output.py src/oldtools/aframe/plotting.py src/oldtools/aframe/trajwalker.py src/oldtools/aframe/transitions.py src/oldtools/cmds/w_ttimes.py src/oldtools/files.py src/oldtools/miscfn.py src/oldtools/stats/accumulator.py src/oldtools/stats/edfs.py src/oldtools/stats/mcbs.py src/west/data_manager.py src/west/propagators/__init__.py src/west/propagators/executable.py src/west/segment.py src/west/sim_manager.py src/west/states.py src/west/systems.py src/west/tests/test_we_driver.py src/west/we_driver.py src/west/wm_ops.py src/westext/weed/weed_driver.py src/westext/wess/wess_driver.py
description:
Updated copyright information
changeset: 490:aedd14a6aac5
user: Matt Zwier <mczwier@gmail.com>
date: Tue Apr 23 11:46:12 2013 -0400
files: AUTHORS README src/westext/weed/weed_driver.py
description:
Modified README, removed AUTHORS
changeset: 489:c4d24efe0809
parent: 488:3993825c1d7f
parent: 487:405753ef766c
user: Matt Zwier <mczwier@gmail.com>
date: Sat Apr 20 22:16:05 2013 -0400
files: CHANGELOG bin/west doc/config_entries.rst
description:
Merging
changeset: 488:3993825c1d7f
parent: 486:066ad21a9ed5
user: Matt Zwier <mczwier@gmail.com>
date: Sat Apr 20 22:12:44 2013 -0400
files: .hgsubstate
description:
Updated subrepos
changeset: 487:405753ef766c
parent: 483:33945e69cf00
user: Matt Zwier <mczwier@gmail.com>
date: Sat Apr 20 21:43:25 2013 -0400
files: .hgsubstate AUTHORS CHANGELOG COPYING README bin/west doc/config_entries.rst lib/cmds/w_binprobs.py lib/cmds/w_edpdist.py lib/cmds/w_fluxanl.py lib/cmds/w_fork.py lib/cmds/w_init.py lib/cmds/w_run.py lib/cmds/w_states.py lib/cmds/w_succ.py lib/cmds/w_trace.py lib/cmds/w_truncate.py src/oldtools/aframe/__init__.py src/oldtools/aframe/atool.py src/oldtools/aframe/binning.py src/oldtools/aframe/data_reader.py src/oldtools/aframe/iter_range.py src/oldtools/aframe/kinetics.py src/oldtools/aframe/mcbs.py src/oldtools/aframe/output.py src/oldtools/aframe/plotting.py src/oldtools/aframe/trajwalker.py src/oldtools/aframe/transitions.py src/oldtools/cmds/w_ttimes.py src/oldtools/files.py src/oldtools/miscfn.py src/oldtools/stats/accumulator.py src/oldtools/stats/edfs.py src/oldtools/stats/mcbs.py src/west/__init__.py src/west/data_manager.py src/west/propagators/__init__.py src/west/propagators/executable.py src/west/segment.py src/west/sim_manager.py src/west/states.py src/west/systems.py src/west/tests/test_sim_manager.py src/west/tests/test_we_driver.py src/west/we_driver.py src/west/wm_ops.py src/westext/stringmethod/__init__.py src/westext/stringmethod/fourier_fitting.py src/westext/stringmethod/string_driver.py src/westext/stringmethod/string_method.py src/westext/weed/BinCluster.py src/westext/weed/ProbAdjustEquil.py src/westext/weed/UncertMath.py src/westext/weed/weed_driver.py src/westext/wess/ProbAdjust.py src/westext/wess/wess_driver.py
description:
Added copyright and license info. General cleanup.
Source files are (c) individual contributors; package is (c) MCZ and LTC.
changeset: 486:066ad21a9ed5
user: Matt Zwier <mczwier@gmail.com>
date: Wed Apr 17 13:03:29 2013 -0400
files: .hgsub .hgsubstate bin/west
description:
Added ``blessings`` subrepo to support progress bars
changeset: 485:5637fa246943
user: Matt Zwier <mczwier@gmail.com>
date: Tue Apr 16 19:32:49 2013 -0400
files: .hgsubstate
description:
Updating west_tools
changeset: 484:e2a77d7e8c86
user: Matt Zwier <mczwier@gmail.com>
date: Tue Apr 16 07:39:14 2013 -0400
files: .hgsubstate
description:
Updated west_tools
changeset: 483:33945e69cf00
parent: 482:89fb2ff6f22f
parent: 481:7c4f3583cb2e
user: Matt Zwier <mczwier@gmail.com>
date: Mon Apr 15 14:51:28 2013 -0400
description:
Merging
changeset: 482:89fb2ff6f22f
parent: 478:603d84ff9fe9
user: Matt Zwier <mczwier@gmail.com>
date: Mon Apr 15 14:51:08 2013 -0400
files: .hgsubstate
description:
Updated west_tools subrepo to latest
changeset: 481:7c4f3583cb2e
user: ktd3
date: Sun Apr 14 20:41:00 2013 -0400
files: lib/examples/nacl_namd/init.sh
description:
Correction to NAMD NaCl tutorial init.sh
changeset: 480:b05785f88f4c
user: ktd3
date: Sun Apr 14 17:55:10 2013 -0400
files: lib/examples/nacl_namd/bstates/bstates.txt lib/examples/nacl_namd/bstates/nacl.pdb lib/examples/nacl_namd/env.sh lib/examples/nacl_namd/init.sh lib/examples/nacl_namd/namd_config/md-continue.conf lib/examples/nacl_namd/namd_config/md-genvel.conf lib/examples/nacl_namd/namd_config/nacl.pdb lib/examples/nacl_namd/namd_config/nacl.psf lib/examples/nacl_namd/namd_config/par_all27_prot_na.prm lib/examples/nacl_namd/namd_config/preparation.sh lib/examples/nacl_namd/namd_config/sys_build.tcl lib/examples/nacl_namd/namd_config/toppar_water_ions.str lib/examples/nacl_namd/run.sh lib/examples/nacl_namd/system.py lib/examples/nacl_namd/west.cfg lib/examples/nacl_namd/westpa_scripts/cat_trajectory.py lib/examples/nacl_namd/westpa_scripts/gen_istate.sh lib/examples/nacl_namd/westpa_scripts/get_pcoord.sh lib/examples/nacl_namd/westpa_scripts/runseg.sh
description:
NAMD NaCl tutorial example directory
changeset: 479:0f77f132e2f6
user: Daniel Hatfield <djh71@pitt.edu>
date: Fri Apr 12 15:48:48 2013 -0400
files: lib/examples/nacl_amb/bstates/nacl.inpcrd lib/examples/nacl_amb/change_distance.py lib/examples/nacl_amb/env.sh lib/examples/nacl_amb/gen_istate.sh lib/examples/nacl_amb/get_pcoord.sh lib/examples/nacl_amb/init.sh lib/examples/nacl_amb/md-continue.in lib/examples/nacl_amb/md-genvel.in lib/examples/nacl_amb/nacl.prmtop lib/examples/nacl_amb/node.sh lib/examples/nacl_amb/post_iter.sh lib/examples/nacl_amb/ptraj.continue lib/examples/nacl_amb/run.sh lib/examples/nacl_amb/runseg.sh lib/examples/nacl_amb/system.py lib/examples/nacl_amb/west.cfg
description:
Na/Cl tutorial example directory
changeset: 478:603d84ff9fe9
parent: 477:f3801d4f75f1
parent: 475:0924536a1ed3
user: Matt Zwier <mczwier@gmail.com>
date: Tue Apr 09 22:43:00 2013 -0400
files: lib/examples/methane_gmx/init.sh
description:
Merging again
changeset: 477:f3801d4f75f1
parent: 476:16bdb1533283
parent: 473:715e7e1644f9
user: Matt Zwier <mczwier@gmail.com>
date: Tue Apr 09 22:42:01 2013 -0400
description:
Merging
changeset: 476:16bdb1533283
parent: 472:3afe1b17a43f
user: Matt Zwier <mczwier@gmail.com>
date: Tue Apr 09 22:37:50 2013 -0400
files: .hgsubstate lib/examples/methane_gmx/init.sh lib/examples/methane_gmx/methane.tpr lib/examples/methane_gmx/run.sh lib/examples/methane_gmx/runwe_sge.sh
description:
Updated examples to use new wwmgr command-line arguments, updated subrepos.
changeset: 475:0924536a1ed3
user: Matt Zwier <mczwier@gmail.com>
date: Fri Apr 05 07:06:07 2013 -0400
files: lib/examples/methane_gmx/init.sh
description:
Modified methane example ``init.sh`` to regenerate TPR file to avoid
occasional insensible failure to read methane.tpr.
changeset: 474:bde55b81ca7c
user: Daniel Hatfield <djhatfield77@gmail.com>
date: Wed Apr 03 11:38:09 2013 -0400
files: lib/examples/methane_gmx/west.cfg
description:
Change starting wallclock for methane tutorial
changeset: 473:715e7e1644f9
user: Nick Rego <nbr2@pitt.edu>
date: Tue Apr 02 18:18:07 2013 -0400
files: .hgsubstate src/west/states.py
description:
fixed bug with w_trace - actually a bug involved in west.states, specifically with representing a BasisState object as a numpy array
changeset: 472:3afe1b17a43f
user: Matt Zwier <mczwier@gmail.com>
date: Tue Mar 26 12:06:44 2013 -0400
files: .hgsubstate
description:
Updated to latest subrepo versions
changeset: 471:10ae2447817d
user: Matt Zwier <mczwier@gmail.com>
date: Mon Mar 25 15:03:49 2013 -0400
files: bin/w_pdist
description:
Added bin link for w_pdist, generalized probability distribution function.
changeset: 470:963dae56dc39
user: Matt Zwier <mczwier@gmail.com>
date: Mon Mar 25 15:02:54 2013 -0400
files: .hgsubstate src/west/data_manager.py
description:
Changed data manager we_h5file to be an instance of h5io.WESTPAH5File, updated
west_tools and wwmgr.
changeset: 469:8eb61f0e8518
user: Matt Zwier <mczwier@gmail.com>
date: Thu Mar 14 16:23:29 2013 -0400
files: .hgsubstate
description:
Updated west_tools
changeset: 468:9b8c8f49eede
parent: 467:33ec593b38c3
parent: 465:064f09d534f9
user: Matt Zwier <mczwier@gmail.com>
date: Thu Mar 14 16:22:15 2013 -0400
files: .hgsubstate
description:
Merging 064f09d534f9 (including west_tools)
changeset: 467:33ec593b38c3
user: Matt Zwier <mczwier@gmail.com>
date: Thu Mar 14 16:20:30 2013 -0400
files: .hgsubstate
description:
Updated west_tools
changeset: 466:60645c4b13e1
parent: 464:681cfa78e543
user: Matt Zwier <mczwier@gmail.com>
date: Thu Mar 14 16:16:32 2013 -0400
files: src/west/tests/__init__.py
description:
Fixed test suite so that it doesn't depend on testbinning (moved to tools)
changeset: 465:064f09d534f9
user: Matt Zwier <mczwier@gmail.com>
date: Tue Mar 12 21:08:30 2013 -0400
files: .hgsubstate lib/examples/odld/west.cfg
description:
Updated west_tools and removed "executable" section from ODLD example west.cfg
changeset: 464:681cfa78e543
user: Matt Zwier <mczwier@gmail.com>
date: Wed Mar 06 11:41:36 2013 -0500
files: .hgignore
description:
Added more .hgignore entries for methane/methane example (tip from Dan Hatfield)
changeset: 463:7f00e98bf5e5
parent: 462:c63202ab8c19
parent: 461:045437a0753d
user: Matt Zwier <mczwier@gmail.com>
date: Tue Mar 05 17:19:25 2013 -0500
files: .hgsubstate
description:
Merging 045437a0753d
changeset: 462:c63202ab8c19
parent: 455:91e1c3900bc3
user: Matt Zwier <mczwier@gmail.com>
date: Tue Mar 05 17:18:16 2013 -0500
files: .hgsubstate bin/w_assign bin/w_edpdist bin/w_kinavg bin/w_kinetics bin/w_pdist bin/w_ttimes
description:
Updated west_tools to latest, added/removed links in bin/.
Removed w_edpdist and w_ttimes because they are being replaced with
w_assign/w_kinetics/w_kinavg. Removed w_pdist because it wasn't as useful as I
had originally hoped (and was polluting data_reader.py).
changeset: 461:045437a0753d
user: Matt Zwier <mczwier@gmail.com>
date: Fri Mar 01 13:24:41 2013 -0500
files: .hgsubstate
description:
Updated to latest wwmgr (again)
changeset: 460:65f2b684cc3b
user: Matt Zwier <mczwier@gmail.com>
date: Fri Mar 01 13:11:03 2013 -0500
files: .hgsubstate
description:
Updated to latest wwmgr
changeset: 459:60a7c0df0229
user: Matt Zwier <mczwier@gmail.com>
date: Fri Mar 01 13:10:10 2013 -0500
files: lib/examples/odld/env.sh
description:
Removed another local env reference from ODLD example env.sh.
changeset: 458:fa084aae4831
user: Matt Zwier <mczwier@gmail.com>
date: Fri Mar 01 12:33:18 2013 -0500
files: lib/examples/methane_gmx/md-continue.mdp lib/examples/methane_gmx/md-genvel.mdp
description:
imported patch mdpfix
changeset: 457:96e3dfedcf90
user: joshua.adelman <joshua.adelman@gmail.com>
date: Thu Feb 28 14:28:00 2013 -0500
files: .hgsubstate lib/examples/odld/west.cfg
description:
Update west_tools subrepo
changeset: 456:50a794548431
user: joshua.adelman <joshua.adelman@gmail.com>
date: Thu Feb 28 13:36:42 2013 -0500
files: .hgsubstate
description:
Update west_tools subrepo
changeset: 455:91e1c3900bc3
user: Matt Zwier <mczwier@gmail.com>
date: Wed Feb 27 16:32:11 2013 -0500
files: .hgignore
description:
Updated .hgignore to ignore more files generated by examples
changeset: 454:a3d1840647d6
user: Matt Zwier <mczwier@gmail.com>
date: Wed Feb 27 16:23:54 2013 -0500
files: .hgsubstate lib/examples/methane_gmx/system.py lib/examples/odld/odld_system.py setup.sh src/oldtools/aframe/binning.py src/setup.py src/west/__init__.py src/west/binning/__init__.py src/west/binning/_assign.pyx src/west/binning/assign.py src/west/binning/bins.py src/west/kinetics/__init__.py src/west/kinetics/_kinetics.pyx src/west/kinetics/rate_averaging.py src/west/systems.py src/west/tests/test_sim_manager.py src/west/tests/test_we_driver.py src/west/tests/testbinning.py src/westext/stringmethod/string_driver.py src/westext/weed/weed_driver.py src/westext/wess/wess_driver.py
description:
Moved binning and kinetics extensions to west_tools
changeset: 453:d661794c1dd0
user: Matt Zwier <mczwier@gmail.com>
date: Wed Feb 27 15:32:46 2013 -0500
files: .hgsubstate lib/cmds/w_binprobs.py lib/cmds/w_edpdist.py lib/cmds/w_fluxanl.py lib/cmds/w_fork.py lib/cmds/w_init.py lib/cmds/w_run.py lib/cmds/w_states.py lib/cmds/w_succ.py lib/cmds/w_trace.py lib/cmds/w_truncate.py lib/examples/odld/env.sh src/oldtools/aframe/binning.py src/oldtools/aframe/data_reader.py src/oldtools/aframe/iter_range.py src/oldtools/aframe/kinetics.py src/oldtools/aframe/mcbs.py src/oldtools/aframe/transitions.py src/oldtools/cmds/w_ttimes.py src/west/data_manager.py src/west/kinetics/rate_averaging.py src/west/tests/test_sim_manager.py src/west/we_driver.py src/westext/stringmethod/string_driver.py src/westext/weed/weed_driver.py src/westext/wess/wess_driver.py
description:
Changed all west.rc references to westpa.rc
changeset: 452:d764dd73d633
parent: 451:ec42976967a7
parent: 450:b90ad753864f
user: Matt Zwier <mczwier@gmail.com>
date: Wed Feb 27 15:15:10 2013 -0500
description:
Merging b90ad753864f and 2a88258c58db
changeset: 451:ec42976967a7
parent: 449:2a88258c58db
user: Matt Zwier <mczwier@gmail.com>
date: Wed Feb 27 15:14:41 2013 -0500
files: .hgsubstate
description:
Possibly spurious subrepo update
changeset: 450:b90ad753864f
parent: 443:ce46dca24ba3
user: Matt Zwier <mczwier@gmail.com>
date: Wed Feb 27 15:04:08 2013 -0500
files: bin/west src/west/binning/assign.py
description:
Allowed bin/west to pass arguments to scripts invoked by filename, added
"unknown bin" flag to assign.py, optimized application of numpy.require in
assign.py for a ~2x speed gain in binning.
changeset: 449:2a88258c58db
user: Matt Zwier <mczwier@gmail.com>
date: Wed Feb 27 13:49:44 2013 -0500
files: .hgsub
description:
Updated west_tools subrepo upstream location
changeset: 448:9b0c324173ea
parent: 447:908e2f9b2629
parent: 445:b90397d3082c
user: Matt Zwier <mczwier@gmail.com>
date: Wed Feb 27 12:46:39 2013 -0500
description:
Merging b90397d3082c and 908e2f9b2629
changeset: 447:908e2f9b2629
user: Matt Zwier <mczwier@gmail.com>
date: Wed Feb 27 12:40:52 2013 -0500
files: .hgsubstate lib/examples/methane_gmx/env.sh lib/examples/methane_gmx/node.sh lib/examples/methane_gmx/runwe_sge.sh
description:
Removed local cluster dependence in methane_gmx example, updated wwmgr
changeset: 446:6370208d78a4
parent: 444:a12df03eae88
user: Matt Zwier <mczwier@gmail.com>
date: Wed Feb 27 11:56:22 2013 -0500
files: lib/cmds/w_pcpdist.py
description:
Removed old (and generally unreachable) lib/cmds/w_pcpdist.py
changeset: 445:b90397d3082c
user: joshua.adelman <joshua.adelman@gmail.com>
date: Wed Feb 27 10:20:18 2013 -0500
files: src/westext/stringmethod/string_driver.py
description:
Updated string method plugin to accept positional and keyword args assoc. with the dfunc method
changeset: 444:a12df03eae88
user: Matt Zwier <mczwier@gmail.com>
date: Fri Feb 15 12:20:09 2013 -0500
files: src/west/kinetics/rate_averaging.py
description:
Fixed UnboundLocal error in rate averager.
changeset: 443:ce46dca24ba3
user: Matt Zwier <mczwier@gmail.com>
date: Thu Feb 14 11:43:18 2013 -0500
files: .hgtags
description:
Added tag legacy-branch-close for changeset 3fbccfd4e1fe
changeset: 442:91324dfe8e43
parent: 440:348923da9b11
user: Matt Zwier <mczwier@gmail.com>
date: Thu Feb 14 11:43:07 2013 -0500
files: .hgtags
description:
Added tag legacy-branch-open for changeset aa49cd7d8777
changeset: 441:3fbccfd4e1fe
tag: legacy-branch-close
parent: 314:66abeb5533e2
user: Matt Zwier <mczwier@gmail.com>
date: Thu Feb 14 11:38:05 2013 -0500
description:
Closing legacy branch
changeset: 440:348923da9b11
parent: 439:b363007b8086
parent: 436:66531a16a51c
user: Matt Zwier <mczwier@gmail.com>
date: Tue Feb 12 14:05:50 2013 -0500
description:
Merged changesets b363007b8086 and 66531a16a51c
changeset: 439:b363007b8086
user: Matt Zwier <mczwier@gmail.com>
date: Tue Feb 12 14:04:30 2013 -0500
files: .hgsubstate
description:
Updated to latest wwmgr
changeset: 438:7fb4acbff2ff
user: Matt Zwier <mczwier@gmail.com>
date: Wed Feb 06 10:35:53 2013 -0500
files: .hgsubstate
description:
Updated to latest h5py upstream
changeset: 437:25711fb3b8a5
parent: 435:14f3b2f5ecf7
user: Matt Zwier <mczwier@gmail.com>
date: Wed Feb 06 10:35:05 2013 -0500
files: .hgsub
description:
Updated h5py subrepository path to h5py upstream
changeset: 436:66531a16a51c
user: joshua.adelman <joshua.adelman@gmail.com>
date: Mon Feb 11 11:04:27 2013 -0500
files: .hgsubstate src/west/kinetics/rate_averaging.py src/westext/weed/weed_driver.py src/westext/wess/wess_driver.py
description:
Parallelized rate averaging calculation and updated wwmgr to newest version
changeset: 435:14f3b2f5ecf7
user: Matt Zwier <mczwier@gmail.com>
date: Fri Jan 18 15:11:21 2013 -0500
files: .hgsubstate src/west/sim_manager.py
description:
Updated to newest version of wwmgr.
changeset: 434:ffcae080775d
parent: 433:a36863351c8a
parent: 430:11e9e6de2cad
user: Matt Zwier <mczwier@gmail.com>
date: Thu Jan 17 16:22:55 2013 -0500
description:
Merge with 11e9e6de2cad8b5b491095a9f2ffa77bc6ad2a12
changeset: 433:a36863351c8a
user: Matt Zwier <mczwier@gmail.com>
date: Thu Jan 17 16:17:14 2013 -0500
files: src/west/data_manager.py
description:
Updated data manager to use appropriate scaleoffset syntax for git version of
h5py.
changeset: 432:84da0a2f8b1f
user: Matt Zwier <mczwier@gmail.com>
date: Thu Jan 17 13:24:39 2013 -0500
files: .hgsub .hgsubstate
description:
Updated h5py subrepo to use git (as upstream does)
changeset: 431:52baa208eb91
parent: 428:8878da0be0c8
user: Matt Zwier <mczwier@gmail.com>
date: Thu Jan 17 13:15:21 2013 -0500
files: setup.sh
description:
Tweaked setup.sh to delete .so files from all directories, including h5py's.
changeset: 430:11e9e6de2cad
user: Ali Sinan Saglam <asinansaglam@gmail.com>
date: Wed Jan 02 17:39:51 2013 -0500
files: src/west/states.py
description:
Fixed method for target states to work for both files and for --tstates
argument.
changeset: 429:35530f2d97a7
user: Ali Sinan Saglam <asinansaglam@gmail.com>
date: Wed Jan 02 17:16:24 2013 -0500
files: src/west/states.py
description:
Fixed small bug in states.py when parsing target states from file.
changeset: 428:8878da0be0c8
user: Matt Zwier <mczwier@gmail.com>
date: Tue Dec 11 11:12:51 2012 -0500
files: lib/cmds/w_init.py setup.sh
description:
Minor updates to w_init and setup.sh
changeset: 427:ee472cacb223
user: Matt Zwier <mczwier@gmail.com>
date: Mon Dec 10 13:28:30 2012 -0500
files: src/west/tests/test_we_driver.py src/west/we_driver.py
description:
(WE) Fix bug in initial state tracking where initial state walkers first split and then merged could trigger a KeyError. Resolves WESTPA issue #8.
changeset: 426:d3d518804eb4
user: Matt Zwier <mczwier@gmail.com>
date: Mon Dec 03 14:04:25 2012 -0500
files: .hgsub .hgsubstate bin/west setup.sh
description:
Added patched h5py subrepo, modified setup.sh to build and bin/west to use
included h5py.
changeset: 425:4f7025a8503f
parent: 424:542ca18cf47f
parent: 423:765122d4dbb2
user: Matt Zwier <mczwier@gmail.com>
date: Fri Nov 30 21:03:49 2012 -0500
description:
Merge with 765122d4dbb269ef656293771fad2414b3b7e379
changeset: 424:542ca18cf47f
parent: 421:595f1b26ac83
user: Matt Zwier <mczwier@gmail.com>
date: Fri Nov 30 21:01:55 2012 -0500
files: src/west/data_manager.py
description:
Fixed bug in data manager wherein pcoord dataset was always compressed if sufficiently large and not expressly prohibited in west.cfg.
changeset: 423:765122d4dbb2
user: joshua.adelman <joshua.adelman@gmail.com>
date: Mon Nov 26 13:27:52 2012 -0500
files: src/westext/weed/weed_driver.py
description:
Updated weed plugin for new yaml-based config files
changeset: 422:a2edb8f0662c
user: joshua.adelman <joshua.adelman@gmail.com>
date: Mon Nov 26 12:49:15 2012 -0500
files: src/west/tests/test_sim_manager.py src/westext/stringmethod/string_driver.py
description:
Updated string method plugin for new yaml-based config files; Updated sim_manager tests
changeset: 421:595f1b26ac83
user: Matt Zwier <mczwier@gmail.com>
date: Sat Nov 24 12:53:26 2012 -0500
files: src/west/data_manager.py
description:
Do not fail if a build of h5py without scaleoffset is used.
changeset: 420:e0051cc61839
user: Matt Zwier <mczwier@gmail.com>
date: Sat Nov 24 12:11:32 2012 -0500
files: .hgsubstate
description:
Updated to latest WWMGR revision.
changeset: 419:c58b644c8cc4
user: Matt Zwier <mczwier@gmail.com>
date: Sat Nov 24 12:11:15 2012 -0500
files: lib/examples/odld/run.sh
description:
Minor change to ODLD run script.
changeset: 418:07ba61922e62
user: Matt Zwier <mczwier@gmail.com>
date: Thu Nov 22 13:57:07 2012 -0500
files: .hgsubstate lib/examples/methane_gmx/run.sh lib/examples/methane_gmx/runseg.sh lib/examples/methane_gmx/system.py lib/examples/methane_gmx/west.cfg src/west/data_manager.py src/west/propagators/executable.py src/west/sim_manager.py src/west/wm_ops.py src/westext/wess/wess_driver.py
description:
Completed YAML-based config file with support for per-dataset HDF5 storage
options.
changeset: 417:311b67e9833f
user: Matt Zwier <mczwier@gmail.com>
date: Fri Nov 16 17:52:45 2012 -0500
files: .hgsubstate lib/cmds/w_init.py lib/cmds/w_run.py lib/examples/methane_gmx/west.cfg lib/examples/odld/odld_system.py lib/examples/odld/west.cfg src/oldtools/aframe/data_reader.py src/west/__init__.py src/west/_rc.py src/west/data_manager.py src/west/propagators/__init__.py src/west/propagators/executable.py src/west/sim_manager.py src/west/systems.py src/west/util/__init__.py src/west/util/config_dict.py src/west/util/extloader.py src/west/util/miscfn.py src/west/util/rtracker.py src/west/we_driver.py src/westext/stringmethod/string_driver.py
description:
Working commit of transition to YAML-based config files and some source
reorganization.
changeset: 416:7e92c0b6031d
user: Matt Zwier <mczwier@gmail.com>
date: Mon Nov 12 16:20:20 2012 -0500
files: src/west/sim_manager.py
description:
Fixed bug in sim manager resulting in per-iteration CPU times being recorded as zero (the individual segment values were not affected).