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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

Imported MPI work manager courtesy of Kim Wong ([email protected])

github.com/westpa/westpa - 9055c2a92650a124148135ee4e6c88f5f6c75596 authored over 11 years ago by Matt Zwier <[email protected]>
imported patch mdpfix

github.com/westpa/westpa - d648c077a5264d435b0aa20d3330d7e27911d415 authored over 11 years ago by Matt Zwier <[email protected]>
Merged upstream (d15db6db5f57)

github.com/westpa/westpa - 7eabe0f3da23a02a15ab5079926b102763604dc4 authored over 11 years ago by Matt Zwier <[email protected]>
Kinetics assignment prototype complete. westpa.assign now uses the buffer

interface instead of the numpy interface where possible.

github.com/westpa/westpa - 3dc843aecac228109d09ba2f1335c0411b059f61 authored over 11 years ago by Matt Zwier <[email protected]>
Update west_tools subrepo

github.com/westpa/westpa - 37f17aa35605877bb01b1ba0ba937cc623193011 authored over 11 years ago by joshua.adelman <[email protected]>
Fixed bug in rate_averaging for recycling simulations. Resolves issue #21

github.com/westpa/westpa - 5f7cd114e7afec627b444e4c495764f3f3da6071 authored over 11 years ago by joshua.adelman <[email protected]>
Update west_tools subrepo

github.com/westpa/westpa - 58ea1c479d6b18f5a42ad272f4a03a6335fc9f61 authored over 11 years ago by joshua.adelman <[email protected]>
Updated setup.py to compile extensions from source if cython is not available and started tracking .c files in repo. Resolves WESTPA issue #18

github.com/westpa/westpa - bacd0e6c7a40a114948c15fbf37d15327051d474 authored over 11 years ago by joshua.adelman <[email protected]>
Updated working kinetics analysis code to relocated binning extension

github.com/westpa/westpa - d3a61015948fb9dec4e5044f5b5bd798eb5c2dc9 authored over 11 years ago by Matt Zwier <[email protected]>
Merging in dcf0bdd3f498 (transplant of binning/assign extensions)

github.com/westpa/westpa - f1f6c054fd97b662f18a0ca14d70587fc71e5271 authored over 11 years ago by Matt Zwier <[email protected]>
Updated .hgignore to ignore more files generated by examples

github.com/westpa/westpa - 91e97b833ff27dec009a3e9d60eedf0ec60b1728 authored over 11 years ago by Matt Zwier <[email protected]>
Moved binning and kinetics extensions to west_tools

github.com/westpa/westpa - 806570b6be06c241002358581941612493274597 authored over 11 years ago by Matt Zwier <[email protected]>
Moved binning and kinetics extensions to west_tools

github.com/westpa/westpa - 8fbc883df04a7e9805d1ed76e04c2d0f23e3d9b5 authored over 11 years ago by Matt Zwier <[email protected]>
Merging dcf0bdd3f498 (transplant of west.binning/west.assign history)

github.com/westpa/westpa - 945286414d5881f529918897f92cc5d52f4b5ed4 authored over 11 years ago by Matt Zwier <[email protected]>
Relocated files prior to import into west_tools

github.com/westpa/westpa - e6b3714ca062ce4c3e943b1d18cb35bba85bc808 authored over 11 years ago by Matt Zwier <[email protected]>
Merged in f4c809a9d9c4

github.com/westpa/westpa - 48617e7ccc9a22f648e4d2e950a259b32bcf2967 authored over 11 years ago by Matt Zwier <[email protected]>
Updated assignment code and prototype flux accumulator.

github.com/westpa/westpa - a0cd65177bd762393f18d428b8265f707b5475e3 authored over 11 years ago by Matt Zwier <[email protected]>
Fixed occasional crash due to dtype oddity.

github.com/westpa/westpa - 449422ca4d27b25ec5fb6b5845b3f86a05a350e8 authored over 11 years ago by Matt Zwier <[email protected]>
Changed all west.rc references to westpa.rc

github.com/westpa/westpa - d59d1150b436a6fbfa90b4caa11103c8bde7e5a7 authored over 11 years ago by Matt Zwier <[email protected]>
Changed all west.rc references to westpa.rc

github.com/westpa/westpa - 9fc5f1a42b477799d292bc77381dd7df8dff1ca0 authored over 11 years ago by Matt Zwier <[email protected]>
Changed all west.rc references to westpa.rc

github.com/westpa/westpa - 6c8e2db48a8ef6c08bcc27be45063dfa9701307e authored over 11 years ago by Matt Zwier <[email protected]>
Merging b90ad753864f and 2a88258c58db

github.com/westpa/westpa - 3d5106c0d253dc7719faf237e01b64a14d60f760 authored over 11 years ago by Matt Zwier <[email protected]>
Merging b90ad753864f and 2a88258c58db

github.com/westpa/westpa - 1c3fc92f53cebfbf3a304e36fd8c66f6d84b48e5 authored over 11 years ago by Matt Zwier <[email protected]>
Possibly spurious subrepo update

github.com/westpa/westpa - 28d6eab78b22c9d04862586480d1aa21bc1fcdf2 authored over 11 years ago by Matt Zwier <[email protected]>
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 sp...

github.com/westpa/westpa - aab185cd20386c8ae6f4c67dd01d0c53263903ba authored over 11 years ago by Matt Zwier <[email protected]>
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 sp...

github.com/westpa/westpa - e655877b3b23b7f8dcc8893cd1bb50ef759189e6 authored over 11 years ago by Matt Zwier <[email protected]>
Updated west_tools subrepo upstream location

github.com/westpa/westpa - 899ed3948c2833173f60652806dc4b6718c913fd authored over 11 years ago by Matt Zwier <[email protected]>
Merging b90397d3082c and 908e2f9b2629

github.com/westpa/westpa - 7d4ed98c0753e9a5d61df40b8dd3a2ac2ed899ba authored over 11 years ago by Matt Zwier <[email protected]>
Removed local cluster dependence in methane_gmx example, updated wwmgr

github.com/westpa/westpa - b7cb299cc42a5a7d72d1f47f27011b06aa654f43 authored over 11 years ago by Matt Zwier <[email protected]>
Removed old (and generally unreachable) lib/cmds/w_pcpdist.py

github.com/westpa/westpa - 6386d6deb8dd683a5a698d5d564437f9ed117207 authored over 11 years ago by Matt Zwier <[email protected]>
Updated string method plugin to accept positional and keyword args assoc. with the dfunc method

github.com/westpa/westpa - 0ed99bcd0360773920e206683fa4774b24974571 authored over 11 years ago by joshua.adelman <[email protected]>
Added ZMQ Router class for use with ZMQ work manager. Added relevant unit tests for router. Split up zeromq unit tests to test core functionality and environment initialization separately.

github.com/westpa/westpa - 3b10e136be8c1d07b50a02185902abbdab281296 authored over 11 years ago by Nick Rego <[email protected]>
DMZ algorithm refinements

github.com/westpa/westpa - 1bac1e1ee9ed1b5ac6a988bf010277f5b6a54fdd authored over 11 years ago by Matt Zwier <[email protected]>
First pass at DMZ algorithm

github.com/westpa/westpa - d0afa13582258983a994aa6406d47c1b6472ae9d authored over 11 years ago by Matt Zwier <[email protected]>
w_kinetics gets an overall flux and event durations, but reverse rates could be trouble

github.com/westpa/westpa - db6d8109ba926a6a51ef79032af1f59b664f2e56 authored over 11 years ago by Matt Zwier <[email protected]>
Skeleton of required bits of w_kinetics

github.com/westpa/westpa - 4e6ab3073a4e36b21516b832eeeb31054112c8d8 authored over 11 years ago by Matt Zwier <[email protected]>
Created w_assign for generalized assignments. Axed crazy generalized dataset

access in data_reader.py. Moved some things about.

github.com/westpa/westpa - 22a0e5d7442496c279515d7c0c8f438b19c16c1e authored over 11 years ago by Matt Zwier <[email protected]>
Working commit for kinetics analysis

github.com/westpa/westpa - fb3ff7c4839308e94cf2713c56dd1a7f30132df7 authored over 11 years ago by Matt Zwier <[email protected]>
Fixed UnboundLocal error in rate averager.

github.com/westpa/westpa - 563bf18b58e4c581032da2c76bcf22f7cd985658 authored over 11 years ago by Matt Zwier <[email protected]>
Fixed UnboundLocal error in rate averager.

github.com/westpa/westpa - 90aa18f0413fb38d5a6da82f107bc502f5af52d9 authored over 11 years ago by Matt Zwier <[email protected]>
Added tag legacy-branch-close for changeset 3fbccfd4e1fe

github.com/westpa/westpa - 374c787584d0185b3836e22b6086838b52fe4b62 authored over 11 years ago by Matt Zwier <[email protected]>
Added tag legacy-branch-open for changeset aa49cd7d8777

github.com/westpa/westpa - 871646e1f941699642c382a966fe58bdfa2a0ec2 authored over 11 years ago by Matt Zwier <[email protected]>
Merged changesets b363007b8086 and 66531a16a51c

github.com/westpa/westpa - 09b293be678abfdfcee4c4c6cd26e3956ae559c1 authored over 11 years ago by Matt Zwier <[email protected]>
Updated to latest wwmgr

github.com/westpa/westpa - 001e3eb4a684e499e8338ec3ea5e957765ec4253 authored over 11 years ago by Matt Zwier <[email protected]>
Merged changesets 8dd6f0369366 and 576e40485177

github.com/westpa/westpa - 56869e4294389444d1c44cb5a17a0e17a207cd50 authored over 11 years ago by Matt Zwier <[email protected]>
Properly removed tasks from "pending" list when results received. Resolves wwmgr issue #10.

github.com/westpa/westpa - 58f8ac2a93ba8f766a328434760c3c30a193b1a7 authored over 11 years ago by Matt Zwier <[email protected]>
Parallelized rate averaging calculation and updated wwmgr to newest version

github.com/westpa/westpa - f28d47cad9706825da145f426a65cf139e7286c2 authored over 11 years ago by joshua.adelman <[email protected]>
Parallelized rate averaging calculation and updated wwmgr to newest version

github.com/westpa/westpa - 455e77e875032db3bf80cd497a51f76f07c01fa7 authored over 11 years ago by joshua.adelman <[email protected]>
Added submit_as_completed() method to core and add() method to FutureWatcher

github.com/westpa/westpa - c30eb173971e0cef14c1b4377a6c6d109d1a97b9 authored over 11 years ago by joshua.adelman <[email protected]>
Updated to latest h5py upstream

github.com/westpa/westpa - 1da265ccf595f71e6092b322346b0138b4cab8cb authored over 11 years ago by Matt Zwier <[email protected]>
Updated h5py subrepository path to h5py upstream

github.com/westpa/westpa - 249d7b208d678144a5344147da364154ffced669 authored over 11 years ago by Matt Zwier <[email protected]>
Updated to newest version of wwmgr.

github.com/westpa/westpa - 9c3c30e3c79d145a4dcb1a80dc35fb5b02a8352b authored almost 12 years ago by Matt Zwier <[email protected]>
Split ZMQ work manager into multiple files, added command-line/environment options for all tunables. NB that constructor argument lists have changed for ZMQClient, ZMQServer, and ZMQWorkManager

github.com/westpa/westpa - 580c76ab7836ef66e755bc5777293f8ed75febe5 authored almost 12 years ago by Matt Zwier <[email protected]>
Merge with 11e9e6de2cad8b5b491095a9f2ffa77bc6ad2a12

github.com/westpa/westpa - 6bb50e343f521f1b9efd436d4407cf23a76e88d3 authored almost 12 years ago by Matt Zwier <[email protected]>
Updated data manager to use appropriate scaleoffset syntax for git version of

h5py.

github.com/westpa/westpa - 448a8793d2f3bcf8d8c7c0b8fcaf3f5cb8906d50 authored almost 12 years ago by Matt Zwier <[email protected]>
Updated h5py subrepo to use git (as upstream does)

github.com/westpa/westpa - 5830385856600c4c06d148aebebca89293cfefb3 authored almost 12 years ago by Matt Zwier <[email protected]>
Tweaked setup.sh to delete .so files from all directories, including h5py's.

github.com/westpa/westpa - 39fe4116469a52288bd77e41983aeff064ae45a7 authored almost 12 years ago by Matt Zwier <[email protected]>
Changed submit() interface to (eventually) support keyword options separate from those passed along to the task function to execute. Rewrote ZMQ wire protocol to use REQ/REP instead of PUSH/PULL for tasks and results, to provide an opportunity for keepalive pulses so that long-idle connections do not result in lost messages and hangs when those connections are forcefully terminated (presumably by a switch).

github.com/westpa/westpa - 682009925d213b1319101f68924d92813139b49d authored almost 12 years ago by Matt Zwier <[email protected]>
Added a function to close cached inproc sockets to prevent ZMQ aborts during unit tests.

github.com/westpa/westpa - 1b446726f7777944a2dc9a15c019964c78d0fe66 authored almost 12 years ago by Matt Zwier <[email protected]>
Fixed method for target states to work for both files and for --tstates

argument.

github.com/westpa/westpa - 7a917a24d1d74b80f3f86438253bd019e1dfbe13 authored almost 12 years ago by Ali Sinan Saglam <[email protected]>
Fixed small bug in states.py when parsing target states from file.

github.com/westpa/westpa - ff155fb0ed9abb9b00620cb8f4269fba84406d34 authored almost 12 years ago by Ali Sinan Saglam <[email protected]>
Minor updates to w_init and setup.sh

github.com/westpa/westpa - 8581556f8cce35effbc1688efbf1ef7be5d4e840 authored almost 12 years ago by Matt Zwier <[email protected]>
(WE) Fix bug in initial state tracking where initial state walkers first split and then merged could trigger a KeyError. Resolves WESTPA issue #8.

github.com/westpa/westpa - f365b5870e4e0a916a9db86879c996e3ed981c9d authored almost 12 years ago by Matt Zwier <[email protected]>
Cleaned up some import trouble.

github.com/westpa/westpa - 928b3b515add9cd4c9566091353661f192bccdc0 authored almost 12 years ago by Matt Zwier <[email protected]>
Added patched h5py subrepo, modified setup.sh to build and bin/west to use

included h5py.

github.com/westpa/westpa - 8a56a931e35a8614ec28aa1ac70b8125f2882621 authored almost 12 years ago by Matt Zwier <[email protected]>
Merge with 765122d4dbb269ef656293771fad2414b3b7e379

github.com/westpa/westpa - 6f0cb38c4a91cdcf0e0e81d6a026b15f36763b24 authored almost 12 years ago by Matt Zwier <[email protected]>
Fixed bug in data manager wherein pcoord dataset was always compressed if sufficiently large and not expressly prohibited in west.cfg.

github.com/westpa/westpa - 0f975f8f70bf0bc7e80231d8c809a954d87b3b8f authored almost 12 years ago by Matt Zwier <[email protected]>
Updated weed plugin for new yaml-based config files

github.com/westpa/westpa - 6b0ce7001315ec91d364215610d48295336f7ded authored almost 12 years ago by joshua.adelman <[email protected]>
Updated string method plugin for new yaml-based config files; Updated sim_manager tests

github.com/westpa/westpa - 066db452f73dcfa3fd34a202b122a324a9789139 authored almost 12 years ago by joshua.adelman <[email protected]>
Do not fail if a build of h5py without scaleoffset is used.

github.com/westpa/westpa - 22742647e5ca833554b666798700fcdee21f847e authored almost 12 years ago by Matt Zwier <[email protected]>
Updated to latest WWMGR revision.

github.com/westpa/westpa - 6228d6aa45f213ade82c044991b484cade7d4233 authored almost 12 years ago by Matt Zwier <[email protected]>
Minor change to ODLD run script.

github.com/westpa/westpa - 35385acab8fe00905f5514304fec4962b306c338 authored almost 12 years ago by Matt Zwier <[email protected]>
Added command-line option and environment variable for ZMQ server timeout. Removed remarkably useless zmq_comm_mode (which should have been client-specific anyway).

github.com/westpa/westpa - 7502a31cd0fb1c4cb097a6559cb3f984b6cdfc0f authored almost 12 years ago by Matt Zwier <[email protected]>
Completed YAML-based config file with support for per-dataset HDF5 storage

options.

github.com/westpa/westpa - 3a4d7ad3ca0fcdb1b0af693c41613278cad77881 authored almost 12 years ago by Matt Zwier <[email protected]>
Completed YAML-based config file with support for per-dataset HDF5 storage

options.

github.com/westpa/westpa - b7dc3ccfee9d1ac01b896338572ab72add357d5e authored almost 12 years ago by Matt Zwier <[email protected]>
Working commit of transition to YAML-based config files and some source

reorganization.

github.com/westpa/westpa - 1891d119252624200ab1013c8c8f6f5ad27d4161 authored almost 12 years ago by Matt Zwier <[email protected]>
Working commit of transition to YAML-based config files and some source

reorganization.

github.com/westpa/westpa - b6b7175fa52d0b98386401db8b023c77ddbb3414 authored almost 12 years ago by Matt Zwier <[email protected]>
Fixed bug in sim manager resulting in per-iteration CPU times being recorded as zero (the individual segment values were not affected).

github.com/westpa/westpa - a3fc50375357d1f329ff42dbcec01b1590003bc8 authored almost 12 years ago by Matt Zwier <[email protected]>
Greatly increased HDF5 write speed by modifying data manager to use low-level HDF5 routines in update_segments().

github.com/westpa/westpa - b9b3bce1aa802a75597dfda02a29f976889d7fe1 authored almost 12 years ago by Matt Zwier <[email protected]>
ZMQ: Fixed "too many open files" error triggered by submitting many tasks using submit() instead of submit_many(), by keeping an open control socket for each thread using _signal_thread.

ZMQ: Made server task dispatch thread dispatch one task per submit()-generated task announcement ...

github.com/westpa/westpa - 2f653e34dad6485e197ae5df885306e7d8a8a00e authored almost 12 years ago by Matt Zwier <[email protected]>
Added link for plothist

github.com/westpa/westpa - 53b8345f2c2f5b6f3f909976bbbba5c17575754b authored almost 12 years ago by Matt Zwier <[email protected]>
Updated comments and docstrings in plothist.py

github.com/westpa/westpa - b47d40fd9a790a4f12e8d63f9b81e4199d9dd169 authored almost 12 years ago by Matt Zwier <[email protected]>
Fixed bug in pre/post iter template formatting, made "do_reweighting" a valid switch for the WEED plugin (though no effort is made to make sure that only one of "do_reweighting" and "do_equilibrium_reweighting" is used; if one is true, then reweighting is done).

github.com/westpa/westpa - 01e6c287909b6cdb092bc8e0562e18e661c7be26 authored almost 12 years ago by Matt Zwier <[email protected]>
Added a new configuration file option "system.save_transition_matrices" (defaulting to False) for whether to save per-iteration transition count and flux matrices (perhaps necessary for some third-party analysis tools, but expensive in space and not currently used by any in-package analysis tools).

github.com/westpa/westpa - cd2e2d41e7808ca3bd9e2f029a4175e5add2dcc5 authored almost 12 years ago by Matt Zwier <[email protected]>
plothist.py has working evolution blocked by iteration

github.com/westpa/westpa - d9276f4ed966099b4d6df69b4a2a162c94ba82e8 authored almost 12 years ago by Matt Zwier <[email protected]>
Added initial plotting tool for histogram output (plothist.py), which works

except for blocking evolution by iteration (not implemented yet).

github.com/westpa/westpa - 8148461254f24b36ae235a46ac2660d6f9c91778 authored almost 12 years ago by Matt Zwier <[email protected]>
Added preliminary unit tests for sim_manager and expanded we_driver tests

github.com/westpa/westpa - 81436b8f2ac1da8fc6acb7382acbded6a9a194cf authored almost 12 years ago by joshua.adelman <[email protected]>
Updated west_tools subrepo, removed warning about WEST_SIM_ROOT being set to current dir.

github.com/westpa/westpa - 588fa2e2a4b617dee8ffbfd7d23a9afec42f1cd5 authored almost 12 years ago by Matt Zwier <[email protected]>
Resurrected w_dumpsegs.

github.com/westpa/westpa - ae9c272f50413ee1010eea301a3065d5d70b74a1 authored almost 12 years ago by Matt Zwier <[email protected]>
Fixed small bug in InitialState pcoord initialization

github.com/westpa/westpa - 35d631f7ed120df0d3ede3329fe46d8904c3e754 authored almost 12 years ago by joshua.adelman <[email protected]>
Added updated w_pcpdist, optimized for speed. Rewrote fasthist to work on

N-dimensional histograms of any core numpy non-complex numeric type.

github.com/westpa/westpa - 0f8d46cce21e3f0539b67c0cb960190e669094c7 authored almost 12 years ago by Matt Zwier <[email protected]>
Added .hgignore from westpa

github.com/westpa/westpa - a903e511ac8948fec921fae06c9ab5c4ba4e28b6 authored almost 12 years ago by Matt Zwier <[email protected]>
Merge with 3c45db2555cf

github.com/westpa/westpa - dff79bd8168d1c7ab6471ab3502989fde0c950e3 authored almost 12 years ago by Matt Zwier <[email protected]>
Fixed bug in WESS driver related to reworking of WE driver.

Worked around memory leak in h5py related to enums.

github.com/westpa/westpa - 258ea7da5408ed76525753d225c9fd73f1741321 authored almost 12 years ago by Matt Zwier <[email protected]>
Fixed coordinate reading in the propagator script and system.py in methane

example.

github.com/westpa/westpa - bf630e883ce3b799de45515cc1bb367e65a0787c authored almost 12 years ago by Ali Sinan Saglam <[email protected]>
Updated to latest west_tools

github.com/westpa/westpa - a628be462706be8ec94612547c3fd815e325c7a4 authored almost 12 years ago by Matt Zwier <[email protected]>
Fixed serious bug in recycling tracking which would mis-label final state IDs.

github.com/westpa/westpa - 6768c9c8a4d27b4d573b8b4cbddd7357b3b20d3d authored almost 12 years ago by Matt Zwier <[email protected]>
Updated w_fluxanl to new HDF5 format

github.com/westpa/westpa - fabfc2db623542aff48da22447c6eeac44e9c324 authored almost 12 years ago by Matt Zwier <[email protected]>
Added reflecting boundary for ODLD test system, on by default and deactivated by setting self.reflect_at=None in the propagator.

github.com/westpa/westpa - 86bde639d70dd93ca336736d002355cdfea97a65 authored almost 12 years ago by Matt Zwier <[email protected]>
Fixed broken "enabled" flag for auxiliary data sets in executable propagator.

github.com/westpa/westpa - 710bdbe4247ca70134292c29ee3b6e0277549d4c authored almost 12 years ago by Matt Zwier <[email protected]>