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WESTPA

Highly scalable software for running extended-timescale simulations with any dynamics engine
Collective - Host: opensource - https://opencollective.com/westpa - Website: https://westpa.github.io/westpa/ - Code: https://github.com/westpa/westpa

Updated docstrings and comments and wwmgr subrepo

github.com/westpa/westpa - 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.

github.com/westpa/westpa - 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.

github.com/westpa/westpa - 5aeba2e07ec897be2d37f6b718cbee7aebc73c15 authored about 12 years ago by Matt Zwier <[email protected]>
Updated to new WE driver interface (with internal used initial state tracking)

github.com/westpa/westpa - 551e3103af14b404e7e2e94028ad44bd19c3e46f authored about 12 years ago by Matt Zwier <[email protected]>
Merged with upstream

github.com/westpa/westpa - 397dad5c593c77f1c83159e3528b05a047af6d23 authored about 12 years ago by Matt Zwier <[email protected]>
Updated to latest west_tools

github.com/westpa/westpa - c191cd667e405add17d931147bf9a5b661f8bc3f authored about 12 years ago by Matt Zwier <[email protected]>
Removed "-march=native" from setup.py

github.com/westpa/westpa - 0cb38ea8778b6a3c4b5e65d7a19a62d8765bc8f9 authored about 12 years ago by Matt Zwier <[email protected]>
Fixed bug in initial state generation futures tracking.

github.com/westpa/westpa - 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.

github.com/westpa/westpa - 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.

github.com/westpa/westpa - ee23b3deab65665e58cc1a766840448e8b57d580 authored about 12 years ago by Matt Zwier <[email protected]>
Fixed small typo introduced in last commit

github.com/westpa/westpa - 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

github.com/westpa/westpa - cd2038d714eda69f94105ab5a9a6abddba299c49 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

github.com/westpa/westpa - 72ac82344fe8a4898fc4136e31b0cf986117c75b authored about 12 years ago by joshua.adelman <[email protected]>
Updated change log and added link for w_fork.

github.com/westpa/westpa - 2e19e5b32d7e01ba07eba3f47340bbdf127a1e8d authored about 12 years ago by Matt Zwier <[email protected]>
Merge with 23f003a25f8d0304c37af75970ab63a1dae20e16

github.com/westpa/westpa - 530cc8f29e9267ce978db0b9600f2e6c4f31fc3f authored about 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...

github.com/westpa/westpa - 9712672e685dcfb6611c6ce44276589785444dd9 authored about 12 years ago by Matt Zwier <[email protected]>
Added new w_bins tool, to display or manipulate bins.

github.com/westpa/westpa - 17f53b05494b7f0b3b98c3c0330710790e831f97 authored about 12 years ago by Matt Zwier <[email protected]>
Added steady state reweighting plugin (wess) that handles target states

github.com/westpa/westpa - f26567a7a6096f93b0174d31b389a3bc6eb0e1be authored about 12 years ago by joshua.adelman <[email protected]>
Added w_fork tool for creating a new simulation from an old one.

github.com/westpa/westpa - 041e80e9aa548c8b4941f47df1ffc18b842f6e25 authored about 12 years ago by Matt Zwier <[email protected]>
Merge with 51fa1eac31579f1a1db77916b3ee859076b58459

github.com/westpa/westpa - 0ee5131078fa7d3fd7372b53a8bd74879ce2ede3 authored about 12 years ago by Matt Zwier <[email protected]>
Merge with 51fa1eac31579f1a1db77916b3ee859076b58459

github.com/westpa/westpa - 9ebc8238759bc175f6b1a63f0e745fbcd459ed6b authored about 12 years ago by Matt Zwier <[email protected]>
Renamed westtools to oldtools.

github.com/westpa/westpa - 2b264bbcb35eb4417d1aabb0e5965219af7220f3 authored about 12 years ago by Matt Zwier <[email protected]>
Renamed westtools to oldtools.

github.com/westpa/westpa - 31c0cb4a07ef63fd5ed7172f415696c2cc481013 authored about 12 years ago by Matt Zwier <[email protected]>
Renamed wt2 to westtools

github.com/westpa/westpa - 887f18e7bd14d80c98d961da80a6c01524f6688f authored about 12 years ago by Matt Zwier <[email protected]>
Fixed several bugs with RecursiveBinMapper.

github.com/westpa/westpa - 39ce876f5aa326919e08db205d135b34fabc65b4 authored about 12 years ago by Matt Zwier <[email protected]>
Fixed several bugs with RecursiveBinMapper.

github.com/westpa/westpa - baf328b6c00e1c058d28ba48da86c6f8b7325fc2 authored about 12 years ago by Matt Zwier <[email protected]>
Added subrepository for west_tools and updated bin/west to reflect

github.com/westpa/westpa - 8de843c556ef3a46031c8a0f38bbc393f51236a1 authored about 12 years ago by Matt Zwier <[email protected]>
Renamed WEMD->WEST

github.com/westpa/westpa - eaac70a8fdd1217740ee231e066b961c47471220 authored about 12 years ago by Matt Zwier <[email protected]>
Updated to wwmgr revision 30909438b5dc.

github.com/westpa/westpa - 59a8e441bf832d786ebd30f9dcecb0f5973fffb9 authored about 12 years ago by Matt Zwier <[email protected]>
Added WM_PROCESS_ID to processes and zmq work managers (resolves issue #5).

github.com/westpa/westpa - 29edb74eac49daca54bef7e7f8467353c2233724 authored about 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 ...

github.com/westpa/westpa - f723d1bc0ad33e4afd64f05179e2eed125dc06bc authored about 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 ...

github.com/westpa/westpa - 4ee45bd6f19c77df75a667b6af76bbbf26f564c6 authored about 12 years ago by Matt Zwier <[email protected]>
Added subrepository for wwmgr in lib/, modified bin/west to reflect its

location.

github.com/westpa/westpa - ad49d5052cb38b96be575c89cebe29f4ce6fdce2 authored about 12 years ago by Matt Zwier <[email protected]>
Really fixed symlinks

github.com/westpa/westpa - 5ebff77214667dcc328a2e27afc5bc7a337add33 authored about 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.

github.com/westpa/westpa - 65ed7d170dad783fc2d3be9fb1be38da23fd9aab authored about 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.

github.com/westpa/westpa - 5703e5aa79a78146154be06865ce32122af58f9c authored about 12 years ago by Matt Zwier <[email protected]>
Renamed all WEMD/wemd references WEST/west, respectively.

github.com/westpa/westpa - 5a9e738e102f93e2352b2c427f083188eedba986 authored about 12 years ago by Matt Zwier <[email protected]>
Merge with 7420a1c72a22a235a7c26af0d5cfc66864cd0f49

github.com/westpa/westpa - 5c3e9e1e1e3402351384c76eacf4988278a3f885 authored about 12 years ago by Matt Zwier <[email protected]>
Added list of valid work managers to command line help.

github.com/westpa/westpa - 786815b88b710edfa0d305db369a82154e60cee9 authored about 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.

github.com/westpa/westpa - 924d29fc71431efe4833ed2f633d1fda32e52367 authored about 12 years ago by Matt Zwier <[email protected]>
Updated to handle the command line argument functionality of wwmgr revision 5c81b23fb28.

github.com/westpa/westpa - 877bb14c37529a59d23dc31324ca9977eca265d0 authored about 12 years ago by Matt Zwier <[email protected]>
Reworked environment variable handling, added support for command-line argument parsing.

github.com/westpa/westpa - 8e694cb531efaa637fe52f7039f755639a2cdebd authored about 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).

github.com/westpa/westpa - 610269d9e90d29d4c9ee90f5996e787597b05ce5 authored about 12 years ago by Matt Zwier <[email protected]>
Fixed bug (outdated data.h5file -> data.wemd_data_file) in methane example wemd.cfg

github.com/westpa/westpa - ffda227494b2649ed4eaca9416b89afe350dc35d authored about 12 years ago by Matt Zwier <[email protected]>
Minor performance updates

github.com/westpa/westpa - 6547c1983e3f85289d6014ad1e2f68b5e71895ea authored about 12 years ago by Matt Zwier <[email protected]>
Updated wemd.version, added config file entries for split/merge thresholds.

github.com/westpa/westpa - d494b8d9efd3463d6f2575663852f5af9e822514 authored about 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.

github.com/westpa/westpa - 2c780d28afefceb7ff16499a5070f5da7a01a1a5 authored about 12 years ago by Matt Zwier <[email protected]>
A little cleanup.

github.com/westpa/westpa - 19c131e2a4f7ae9e4a3115c6be855f910f3b5444 authored about 12 years ago by Matt Zwier <[email protected]>
Updates for WEMD integration: client-mode startup for ZMQWorkManager

github.com/westpa/westpa - c8bcdcaec61fcc27f166055559d8f956fe6a04d6 authored about 12 years ago by Matt Zwier <[email protected]>
Updates to use wwmgr work manager.

github.com/westpa/westpa - 79236f2b3799bbc6bf3a22672205e6e7110116e9 authored about 12 years ago by Matt Zwier <[email protected]>
Nearly complete framework, with only client script remaining.

github.com/westpa/westpa - 57967c2e1c62c8fa2f01d320cf4bbb4b468af762 authored about 12 years ago by Matt Zwier <[email protected]>
Merge with 904dc1b0874240f6aebf7e6cfaa665acde050794

github.com/westpa/westpa - 230f384a858558b460822676d67300f0d5956895 authored about 12 years ago by Matt Zwier <[email protected]>
Beginnings of updated startup/environment for work managers

github.com/westpa/westpa - 116f0ff956167cfc788cdeaa2818efd92ae6eaa5 authored about 12 years ago by Matt Zwier <[email protected]>
ZMQ almost done; restructured tests to factor out common tests.

github.com/westpa/westpa - 0c396de83f6c2564dc1e26a02972cc1384491ea4 authored about 12 years ago by Matt Zwier <[email protected]>
Randomized ports for testing to elminate mysterious TCP collisions.

github.com/westpa/westpa - 6972010ceb44b3188afb9fa1dc8decabb11e3753 authored about 12 years ago by Matt Zwier <[email protected]>
Autokill of hung workers, with error reporting, works.

github.com/westpa/westpa - f61e9ad3dec435402639e249a436667d59d33e77 authored about 12 years ago by Matt Zwier <[email protected]>
Made client task forwarder capable of exiting; eliminated ops.py leftover from initial WEMD import.

github.com/westpa/westpa - 328a775cea3c5dec10ab8ce0699c960471a6195e authored about 12 years ago by Matt Zwier <[email protected]>
ZMQ: Components appear to work independently.

github.com/westpa/westpa - 75a43956ec3cadc9462513ae2246dc7278556325 authored about 12 years ago by Matt Zwier <[email protected]>
Fixed several issues with weed plugin including backporting incorrect averaging fix from main repo

github.com/westpa/westpa - 379863d1005dffbc8e559a12b55f2b5aba372d16 authored about 12 years ago by joshua.adelman <[email protected]>
ZMQ work in progress: client starts up/shuts down cleanly (now to make it work)

github.com/westpa/westpa - 7c6a16ae8810626688940578b1e18994ab31c77e authored about 12 years ago by Matt Zwier <[email protected]>
Continued work on zeromq work manager; working client process.

github.com/westpa/westpa - d6ebe1c7849b67695b48ebb1a2acdab5b750ba11 authored about 12 years ago by Matt Zwier <[email protected]>
Small bug fixes for weed driver

github.com/westpa/westpa - 001952e259f94706f2952423851dfe92263e8d00 authored about 12 years ago by joshua.adelman <[email protected]>
Fixed argument parsing bug in w_pcpdist preventing use of --vrange/--lvrange

github.com/westpa/westpa - 734bd61ec0d822c9eb774399da42d966db6b934e authored about 12 years ago by Matt Zwier <[email protected]>
Merge with f05b5128bc27116449ac1a2e198294889765a8a3

github.com/westpa/westpa - b86dad6f83695dacfd2e9571202cf40c7049346e authored about 12 years ago by Matt Zwier <[email protected]>
A few optimizations to the data manager for use with new wemdtools.

github.com/westpa/westpa - 730481c4b4f473b4f0b107644ba2313071f018bd authored about 12 years ago by Matt Zwier <[email protected]>
Merge with e46a29119d21cbd4020b5369331aa5ce59787964

github.com/westpa/westpa - b89305df8a81c821018125eed21584e95b4f76a0 authored about 12 years ago by joshua.adelman <[email protected]>
Initial port of string method plugin to wemd_feat

github.com/westpa/westpa - 2066f8ba2d4b4aaed3da141b65540fecae68a59f authored about 12 years ago by joshua.adelman <[email protected]>
Fixed two bugs: (1) prepare_new_segments missing as valid callback (2) Incorrect initialization of states

github.com/westpa/westpa - 0bf5637b65dc8e7e223f75774afbcd1cd1511d4b authored about 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

github.com/westpa/westpa - de08adb935efdc96d407bf709d523d6d3df7ac21 authored about 12 years ago by joshua.adelman <[email protected]>
Added cfg option we.adjust_counts to toggle strict adherence to target_counts

github.com/westpa/westpa - df0fa40927adda7e20d3753b42953b95dead0623 authored about 12 years ago by joshua.adelman <[email protected]>
Write iteration timings into log file

github.com/westpa/westpa - e6d86da209c7b2a74ac8854bc5b70b3958079e82 authored about 12 years ago by joshua.adelman <[email protected]>
Fixed naming convention of wemd data file keywork in w_init

github.com/westpa/westpa - e5c34ab503336be8bf6825b8213c2144b61ae5fa authored about 12 years ago by joshua.adelman <[email protected]>
Fixed bug in which simulations without target states (non-recycling) were not handled properly

github.com/westpa/westpa - ea511f4ac18d79be4c523c225b9e9d218d03c3e7 authored about 12 years ago by Joshua Adelman <[email protected]>
Fixed bug in finding istate with w_trace

github.com/westpa/westpa - c73491983fff7888e0bca178169838732e46e0f9 authored over 12 years ago by David Wang <[email protected]>
Added flux analysis script and plotting example.

github.com/westpa/westpa - 2806da423521bb1f292ece76da0212d557e18513 authored over 12 years ago by Matt Zwier <[email protected]>
Created documentation for mclib.

github.com/westpa/westpa - 4b5d9cac30fcd0551228ed25fde0d92aee73f08b authored over 12 years ago by Matt Zwier <[email protected]>
Updated tree walker, added Monte Carlo bootstrapping package

github.com/westpa/westpa - 2cfbb31d6c1c556d28e3ad91e8b5ec5b6b09e3b8 authored over 12 years ago by Matt Zwier <[email protected]>
Completed tree walker and example ex_fpp script.

github.com/westpa/westpa - 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.

github.com/westpa/westpa - 193df3961e264fe1820be46b84863a88bd102b7b authored over 12 years ago by Matt Zwier <[email protected]>
Working but slow

github.com/westpa/westpa - 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.

github.com/westpa/westpa - 1d213aad2682e9773ad20140a602ec9e62968fae authored over 12 years ago by Matt Zwier <[email protected]>
Working commit of cython-based trajectory tree system

github.com/westpa/westpa - a6213b1c4315435541be18b5bbba71daab621bc8 authored over 12 years ago by Matt Zwier <[email protected]>
Working w_pdist

github.com/westpa/westpa - 3e721dc5378954ec4dfeb696254044b3a226c9e2 authored over 12 years ago by Matt Zwier <[email protected]>
Working w_pdist

github.com/westpa/westpa - 29af03a0ee5ea57db94924975f07eda5c9811c39 authored over 12 years ago by Matt Zwier <[email protected]>
First pass at w_pdist

github.com/westpa/westpa - 8c48bdc246e45f14c3c88fcb7e438abce8878c45 authored over 12 years ago by Matt Zwier <[email protected]>
Pulled "WE-like dataset" support out of w_trace into data_reader.py

github.com/westpa/westpa - 2bbcb1ae86fdf0460c4f9c535c8fd6a589414b5b authored over 12 years ago by Matt Zwier <[email protected]>
Added w_select.

github.com/westpa/westpa - 5895ffc6b8fbe9830faaffaf64dbcf99f906a46b authored over 12 years ago by Matt Zwier <[email protected]>
Working commit

github.com/westpa/westpa - 03caed87982a7089e541c40ef0940f0d0519a703 authored over 12 years ago by mczwier <devnull@localhost>
working commit

github.com/westpa/westpa - be232dab77d69304fa264820ed9e4f23dc8819fd authored over 12 years ago by Matt Zwier <[email protected]>
Working commit.

github.com/westpa/westpa - f7f12f355dbbf9d0551866432a5c32c60fa29c14 authored over 12 years ago by Matt Zwier <[email protected]>
zmq work in progress

github.com/westpa/westpa - 7459c20373ed2647c383a1cb9d0c5ec4270b1981 authored over 12 years ago by Matt Zwier <[email protected]>
More zmq work manager work and associated tests.

github.com/westpa/westpa - 1566a17ccecc73903cd594e29564a0ae328cab81 authored over 12 years ago by Matt Zwier <[email protected]>
Initial commit of test cases and partial ZMQ implementation.

github.com/westpa/westpa - 28075ea82815f6f2bd2e8bccf2d96be72f66700f authored over 12 years ago by Matt Zwier <[email protected]>
Initial import of work_managers package from wemd_feat.

github.com/westpa/westpa - 53944a97923d138cf91814d617bb1ecb542f0429 authored over 12 years ago by Matt Zwier <[email protected]>
Backwards compatibility tweaks for data manager.

github.com/westpa/westpa - d2411bdbcbabd43d5ca4f26ead6f8420ada0d901 authored over 12 years ago by Matt Zwier <[email protected]>
Working trajectory tree construction and iteration.

github.com/westpa/westpa - 054521464bd503a896c9afe0e44b2b6e0551d097 authored over 12 years ago by Matt Zwier <[email protected]>
Partially-working trajectory tree facility.

github.com/westpa/westpa - 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.

github.com/westpa/westpa - f4fa0d80d9321cefb056fd7fee81831ceb09dcee authored over 12 years ago by Matt Zwier <[email protected]>
Fixed bug in w_trace

github.com/westpa/westpa - 03b72958e77083753a42f01d586a86256dbebc97 authored over 12 years ago by daw88 <devnull@localhost>
Fixed bug in w_succ.py

github.com/westpa/westpa - 311738e03293243f20a875b95c38a5b686d1df93 authored over 12 years ago by daw88 <devnull@localhost>