github.com/westpa/westpa commits | Ecosyste.ms: OpenCollective

Updated docstrings and comments and wwmgr subrepo

285d2390f574aa0d6fe207572eefd84ca99f0a17 authored about 12 years ago by Matt Zwier <[email protected]>

Fixed seriously stupid bug in server ping code that led to constant pings and

pegged CPU on both server and client. Added better debugging messages.

6baa6bbafea57ba516c110dcda848a47ca48bdea authored about 12 years ago by Matt Zwier <[email protected]>

Updated WE driver to handle all initial state tracking internally.

Added setup.sh to save developers a few commands after clones.

5aeba2e07ec897be2d37f6b718cbee7aebc73c15 authored about 12 years ago by Matt Zwier <[email protected]>

Updated to new WE driver interface (with internal used initial state tracking)

551e3103af14b404e7e2e94028ad44bd19c3e46f authored about 12 years ago by Matt Zwier <[email protected]>

Merged with upstream

397dad5c593c77f1c83159e3528b05a047af6d23 authored about 12 years ago by Matt Zwier <[email protected]>

Updated to latest west_tools

c191cd667e405add17d931147bf9a5b661f8bc3f authored about 12 years ago by Matt Zwier <[email protected]>

Removed "-march=native" from setup.py

0cb38ea8778b6a3c4b5e65d7a19a62d8765bc8f9 authored about 12 years ago by Matt Zwier <[email protected]>

Fixed bug in initial state generation futures tracking.

664519ee192214faa146f59c53a949175f4c5f89 authored about 12 years ago by Matt Zwier <[email protected]>

Fixed bug in RecursiveBinMapper that arises when every bin in the base mapper is recursively processed.

a06b769957212fc9f7d84ca5a61be4c347e1f312 authored about 12 years ago by Matt Zwier <[email protected]>

Fixed bug in RecursiveBinMapper that arises when every bin in the base mapper is recursively processed.

ee23b3deab65665e58cc1a766840448e8b57d580 authored about 12 years ago by Matt Zwier <[email protected]>

Fixed small typo introduced in last commit

b693c4de1b8b1785faf72fde9cf73ab28c18e6dc authored about 12 years ago by joshua.adelman <[email protected]>

Update string method plugin to work with new binning aparatus; Fixed bug in VoronoiBinMapper; Fixed get_bin_mapper

cd2038d714eda69f94105ab5a9a6abddba299c49 authored over 12 years ago by joshua.adelman <[email protected]>

Update string method plugin to work with new binning aparatus; Fixed bug in VoronoiBinMapper; Fixed get_bin_mapper

72ac82344fe8a4898fc4136e31b0cf986117c75b authored over 12 years ago by joshua.adelman <[email protected]>

Updated change log and added link for w_fork.

2e19e5b32d7e01ba07eba3f47340bbdf127a1e8d authored over 12 years ago by Matt Zwier <[email protected]>

Merge with 23f003a25f8d0304c37af75970ab63a1dae20e16

530cc8f29e9267ce978db0b9600f2e6c4f31fc3f authored over 12 years ago by Matt Zwier <[email protected]>

Modifications to support updated west_tools. bin/wemd now prefers scripts

found in lib/west_tools to those in lib/cmds; bin/wemd lib/cmds/SCRIPTNAME.py
can still be used f...

9712672e685dcfb6611c6ce44276589785444dd9 authored over 12 years ago by Matt Zwier <[email protected]>

Added new w_bins tool, to display or manipulate bins.

17f53b05494b7f0b3b98c3c0330710790e831f97 authored over 12 years ago by Matt Zwier <[email protected]>

Added steady state reweighting plugin (wess) that handles target states

f26567a7a6096f93b0174d31b389a3bc6eb0e1be authored over 12 years ago by joshua.adelman <[email protected]>

Added w_fork tool for creating a new simulation from an old one.

041e80e9aa548c8b4941f47df1ffc18b842f6e25 authored over 12 years ago by Matt Zwier <[email protected]>

Merge with 51fa1eac31579f1a1db77916b3ee859076b58459

0ee5131078fa7d3fd7372b53a8bd74879ce2ede3 authored over 12 years ago by Matt Zwier <[email protected]>

Merge with 51fa1eac31579f1a1db77916b3ee859076b58459

9ebc8238759bc175f6b1a63f0e745fbcd459ed6b authored over 12 years ago by Matt Zwier <[email protected]>

Renamed westtools to oldtools.

2b264bbcb35eb4417d1aabb0e5965219af7220f3 authored over 12 years ago by Matt Zwier <[email protected]>

Renamed westtools to oldtools.

31c0cb4a07ef63fd5ed7172f415696c2cc481013 authored over 12 years ago by Matt Zwier <[email protected]>

Renamed wt2 to westtools

887f18e7bd14d80c98d961da80a6c01524f6688f authored over 12 years ago by Matt Zwier <[email protected]>

Fixed several bugs with RecursiveBinMapper.

39ce876f5aa326919e08db205d135b34fabc65b4 authored over 12 years ago by Matt Zwier <[email protected]>

Fixed several bugs with RecursiveBinMapper.

baf328b6c00e1c058d28ba48da86c6f8b7325fc2 authored over 12 years ago by Matt Zwier <[email protected]>

Added subrepository for west_tools and updated bin/west to reflect

8de843c556ef3a46031c8a0f38bbc393f51236a1 authored over 12 years ago by Matt Zwier <[email protected]>

Renamed WEMD->WEST

eaac70a8fdd1217740ee231e066b961c47471220 authored over 12 years ago by Matt Zwier <[email protected]>

Updated to wwmgr revision 30909438b5dc.

59a8e441bf832d786ebd30f9dcecb0f5973fffb9 authored over 12 years ago by Matt Zwier <[email protected]>

Added WM_PROCESS_ID to processes and zmq work managers (resolves issue #5).

29edb74eac49daca54bef7e7f8467353c2233724 authored over 12 years ago by Matt Zwier <[email protected]>

Rewrote binning system, refactored sim manager and WE driver for greater

orthogonality, added support for pickling bin topologies, refactored rate
matrix calculation for ...

f723d1bc0ad33e4afd64f05179e2eed125dc06bc authored over 12 years ago by Matt Zwier <[email protected]>

Rewrote binning system, refactored sim manager and WE driver for greater

orthogonality, added support for pickling bin topologies, refactored rate
matrix calculation for ...

4ee45bd6f19c77df75a667b6af76bbbf26f564c6 authored over 12 years ago by Matt Zwier <[email protected]>

Added subrepository for wwmgr in lib/, modified bin/west to reflect its

location.

ad49d5052cb38b96be575c89cebe29f4ce6fdce2 authored over 12 years ago by Matt Zwier <[email protected]>

Really fixed symlinks

5ebff77214667dcc328a2e27afc5bc7a337add33 authored over 12 years ago by Matt Zwier <[email protected]>

Added instance variable WorkManager.running and tests in startup/shutdown for whether the work manager is running. Added envirionment support for ZMQ hangcheck timeout.

65ed7d170dad783fc2d3be9fb1be38da23fd9aab authored over 12 years ago by Matt Zwier <[email protected]>

Prevented sim manager from creating duplicate work manager (resulted in hangs on shutdown for some work managers), updated logging formatting, removed outdated symlinks and broken analysis tools.

5703e5aa79a78146154be06865ce32122af58f9c authored over 12 years ago by Matt Zwier <[email protected]>

Renamed all WEMD/wemd references WEST/west, respectively.

5a9e738e102f93e2352b2c427f083188eedba986 authored over 12 years ago by Matt Zwier <[email protected]>

Merge with 7420a1c72a22a235a7c26af0d5cfc66864cd0f49

5c3e9e1e1e3402351384c76eacf4988278a3f885 authored over 12 years ago by Matt Zwier <[email protected]>

Added list of valid work managers to command line help.

786815b88b710edfa0d305db369a82154e60cee9 authored over 12 years ago by Matt Zwier <[email protected]>

Updated methane_gmx example to reflect new work manager parameters, and added proper SGE $PE_HOSTFILE support to its batch script.

924d29fc71431efe4833ed2f633d1fda32e52367 authored over 12 years ago by Matt Zwier <[email protected]>

Updated to handle the command line argument functionality of wwmgr revision 5c81b23fb28.

877bb14c37529a59d23dc31324ca9977eca265d0 authored over 12 years ago by Matt Zwier <[email protected]>

Reworked environment variable handling, added support for command-line argument parsing.

8e694cb531efaa637fe52f7039f755639a2cdebd authored over 12 years ago by Matt Zwier <[email protected]>

Fixed a few bugs with the methane example (missing ch4.itp, bad syntax in

runwe_sge.sh).

610269d9e90d29d4c9ee90f5996e787597b05ce5 authored over 12 years ago by Matt Zwier <[email protected]>

Fixed bug (outdated data.h5file -> data.wemd_data_file) in methane example wemd.cfg

ffda227494b2649ed4eaca9416b89afe350dc35d authored over 12 years ago by Matt Zwier <[email protected]>

Minor performance updates

6547c1983e3f85289d6014ad1e2f68b5e71895ea authored over 12 years ago by Matt Zwier <[email protected]>

Updated wemd.version, added config file entries for split/merge thresholds.

d494b8d9efd3463d6f2575663852f5af9e822514 authored over 12 years ago by Matt Zwier <[email protected]>

Added a simple overdamped Langevin dynamics test driver, fixed a few minor bugs related to basis/initial state management and analysis tools.

2c780d28afefceb7ff16499a5070f5da7a01a1a5 authored over 12 years ago by Matt Zwier <[email protected]>

A little cleanup.

19c131e2a4f7ae9e4a3115c6be855f910f3b5444 authored over 12 years ago by Matt Zwier <[email protected]>

Updates for WEMD integration: client-mode startup for ZMQWorkManager

c8bcdcaec61fcc27f166055559d8f956fe6a04d6 authored over 12 years ago by Matt Zwier <[email protected]>

Updates to use wwmgr work manager.

79236f2b3799bbc6bf3a22672205e6e7110116e9 authored over 12 years ago by Matt Zwier <[email protected]>

Nearly complete framework, with only client script remaining.

57967c2e1c62c8fa2f01d320cf4bbb4b468af762 authored over 12 years ago by Matt Zwier <[email protected]>

Merge with 904dc1b0874240f6aebf7e6cfaa665acde050794

230f384a858558b460822676d67300f0d5956895 authored over 12 years ago by Matt Zwier <[email protected]>

Beginnings of updated startup/environment for work managers

116f0ff956167cfc788cdeaa2818efd92ae6eaa5 authored over 12 years ago by Matt Zwier <[email protected]>

ZMQ almost done; restructured tests to factor out common tests.

0c396de83f6c2564dc1e26a02972cc1384491ea4 authored over 12 years ago by Matt Zwier <[email protected]>

Randomized ports for testing to elminate mysterious TCP collisions.

6972010ceb44b3188afb9fa1dc8decabb11e3753 authored over 12 years ago by Matt Zwier <[email protected]>

Autokill of hung workers, with error reporting, works.

f61e9ad3dec435402639e249a436667d59d33e77 authored over 12 years ago by Matt Zwier <[email protected]>

Made client task forwarder capable of exiting; eliminated ops.py leftover from initial WEMD import.

328a775cea3c5dec10ab8ce0699c960471a6195e authored over 12 years ago by Matt Zwier <[email protected]>

ZMQ: Components appear to work independently.

75a43956ec3cadc9462513ae2246dc7278556325 authored over 12 years ago by Matt Zwier <[email protected]>

Fixed several issues with weed plugin including backporting incorrect averaging fix from main repo

379863d1005dffbc8e559a12b55f2b5aba372d16 authored over 12 years ago by joshua.adelman <[email protected]>

ZMQ work in progress: client starts up/shuts down cleanly (now to make it work)

7c6a16ae8810626688940578b1e18994ab31c77e authored over 12 years ago by Matt Zwier <[email protected]>

Continued work on zeromq work manager; working client process.

d6ebe1c7849b67695b48ebb1a2acdab5b750ba11 authored over 12 years ago by Matt Zwier <[email protected]>

Small bug fixes for weed driver

001952e259f94706f2952423851dfe92263e8d00 authored over 12 years ago by joshua.adelman <[email protected]>

Fixed argument parsing bug in w_pcpdist preventing use of --vrange/--lvrange

734bd61ec0d822c9eb774399da42d966db6b934e authored over 12 years ago by Matt Zwier <[email protected]>

Merge with f05b5128bc27116449ac1a2e198294889765a8a3

b86dad6f83695dacfd2e9571202cf40c7049346e authored over 12 years ago by Matt Zwier <[email protected]>

A few optimizations to the data manager for use with new wemdtools.

730481c4b4f473b4f0b107644ba2313071f018bd authored over 12 years ago by Matt Zwier <[email protected]>

Merge with e46a29119d21cbd4020b5369331aa5ce59787964

b89305df8a81c821018125eed21584e95b4f76a0 authored over 12 years ago by joshua.adelman <[email protected]>

Initial port of string method plugin to wemd_feat

2066f8ba2d4b4aaed3da141b65540fecae68a59f authored over 12 years ago by joshua.adelman <[email protected]>

Fixed two bugs: (1) prepare_new_segments missing as valid callback (2) Incorrect initialization of states

0bf5637b65dc8e7e223f75774afbcd1cd1511d4b authored over 12 years ago by joshua.adelman <[email protected]>

Added ability to specify the number of segments to pass to propagator as a block in the cfg file

de08adb935efdc96d407bf709d523d6d3df7ac21 authored over 12 years ago by joshua.adelman <[email protected]>

Added cfg option we.adjust_counts to toggle strict adherence to target_counts

df0fa40927adda7e20d3753b42953b95dead0623 authored over 12 years ago by joshua.adelman <[email protected]>

Write iteration timings into log file

e6d86da209c7b2a74ac8854bc5b70b3958079e82 authored over 12 years ago by joshua.adelman <[email protected]>

Fixed naming convention of wemd data file keywork in w_init

e5c34ab503336be8bf6825b8213c2144b61ae5fa authored over 12 years ago by joshua.adelman <[email protected]>

Fixed bug in which simulations without target states (non-recycling) were not handled properly

ea511f4ac18d79be4c523c225b9e9d218d03c3e7 authored over 12 years ago by Joshua Adelman <[email protected]>

Fixed bug in finding istate with w_trace

c73491983fff7888e0bca178169838732e46e0f9 authored over 12 years ago by David Wang <[email protected]>

Added flux analysis script and plotting example.

2806da423521bb1f292ece76da0212d557e18513 authored over 12 years ago by Matt Zwier <[email protected]>

Created documentation for mclib.

4b5d9cac30fcd0551228ed25fde0d92aee73f08b authored over 12 years ago by Matt Zwier <[email protected]>

Updated tree walker, added Monte Carlo bootstrapping package

2cfbb31d6c1c556d28e3ad91e8b5ec5b6b09e3b8 authored over 12 years ago by Matt Zwier <[email protected]>

Completed tree walker and example ex_fpp script.

74d1d376c92805b685f5231ee0f84be14645b9d5 authored over 12 years ago by Matt Zwier <[email protected]>

Tracer correct and as fast as it gets without cutting more numpy out of the loops.

193df3961e264fe1820be46b84863a88bd102b7b authored over 12 years ago by Matt Zwier <[email protected]>

Working but slow

5067280b9c974486f84fb45c207691f516ffdf60 authored over 12 years ago by Matt Zwier <[email protected]>

Visit algorithm works, but construction of table from HDF5 does not appear to work yet.

1d213aad2682e9773ad20140a602ec9e62968fae authored over 12 years ago by Matt Zwier <[email protected]>

Working commit of cython-based trajectory tree system

a6213b1c4315435541be18b5bbba71daab621bc8 authored over 12 years ago by Matt Zwier <[email protected]>

Working w_pdist

3e721dc5378954ec4dfeb696254044b3a226c9e2 authored over 12 years ago by Matt Zwier <[email protected]>

Working w_pdist

29af03a0ee5ea57db94924975f07eda5c9811c39 authored over 12 years ago by Matt Zwier <[email protected]>

First pass at w_pdist

8c48bdc246e45f14c3c88fcb7e438abce8878c45 authored over 12 years ago by Matt Zwier <[email protected]>

Pulled "WE-like dataset" support out of w_trace into data_reader.py

2bbcb1ae86fdf0460c4f9c535c8fd6a589414b5b authored over 12 years ago by Matt Zwier <[email protected]>

Added w_select.

5895ffc6b8fbe9830faaffaf64dbcf99f906a46b authored over 12 years ago by Matt Zwier <[email protected]>

Working commit

03caed87982a7089e541c40ef0940f0d0519a703 authored over 12 years ago by mczwier <devnull@localhost>

working commit

be232dab77d69304fa264820ed9e4f23dc8819fd authored over 12 years ago by Matt Zwier <[email protected]>

Working commit.

f7f12f355dbbf9d0551866432a5c32c60fa29c14 authored over 12 years ago by Matt Zwier <[email protected]>

zmq work in progress

7459c20373ed2647c383a1cb9d0c5ec4270b1981 authored over 12 years ago by Matt Zwier <[email protected]>

More zmq work manager work and associated tests.

1566a17ccecc73903cd594e29564a0ae328cab81 authored over 12 years ago by Matt Zwier <[email protected]>

Initial commit of test cases and partial ZMQ implementation.

28075ea82815f6f2bd2e8bccf2d96be72f66700f authored over 12 years ago by Matt Zwier <[email protected]>

Initial import of work_managers package from wemd_feat.

53944a97923d138cf91814d617bb1ecb542f0429 authored over 12 years ago by Matt Zwier <[email protected]>

Backwards compatibility tweaks for data manager.

d2411bdbcbabd43d5ca4f26ead6f8420ada0d901 authored over 12 years ago by Matt Zwier <[email protected]>

Working trajectory tree construction and iteration.

054521464bd503a896c9afe0e44b2b6e0551d097 authored over 12 years ago by Matt Zwier <[email protected]>

Partially-working trajectory tree facility.

cacd236ff988d5f3cae632a256119e39fd96a700 authored over 12 years ago by Matt Zwier <[email protected]>

Disabled specialized SIGINT shutdown handling for zeromq work manager because it leaves zombie processes on SGE and PBS.

f4fa0d80d9321cefb056fd7fee81831ceb09dcee authored almost 13 years ago by Matt Zwier <[email protected]>

Fixed bug in w_trace

03b72958e77083753a42f01d586a86256dbebc97 authored almost 13 years ago by daw88 <devnull@localhost>

Fixed bug in w_succ.py

311738e03293243f20a875b95c38a5b686d1df93 authored almost 13 years ago by daw88 <devnull@localhost>