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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

Simplified ZeroMQ work manager appears to work.

github.com/westpa/westpa - 3fe7c651f318955e7b7df96c48852d3d7f40aad4 authored about 13 years ago by Matt Zwier <[email protected]>
Working commit of revamped zmq work manager.

github.com/westpa/westpa - 232bb591fe5d3c138ac0902a1039aae78fd63831 authored about 13 years ago by Matt Zwier <[email protected]>
Working commit

github.com/westpa/westpa - 99cd8c6faf38c84c3d7a979619ba03ac1e415044 authored about 13 years ago by Matt Zwier <[email protected]>
Added --tcponly option to ZMQ work manager to avoid use of Unix sockets (since they don't work properly on Kraken). Added --strace option to bin/wemd to run scripts under strace.

github.com/westpa/westpa - da4c0dc330367dd1e1ceb6dbb98d19fc760c056f authored about 13 years ago by Matt Zwier <[email protected]>
Analysis framework working commit

github.com/westpa/westpa - 64979328469828c2c6216a56ff7e4a3492e80ad2 authored about 13 years ago by Matt Zwier <[email protected]>
Removed deprecated w_avgbinprobs

github.com/westpa/westpa - 68071b59bee2984ccaf6ec6b0fa17240da5a7e07 authored about 13 years ago by Matt Zwier <[email protected]>
Corrected improper use of MCBS in w_binprobs; w_binprobs now correctly reports average bin population and the confidence interval of the bin population (not the confidence interval of the mean bin population).

github.com/westpa/westpa - a0d5a8650b252cbd7ec28e6d6ea79424049f214a authored about 13 years ago by Matt Zwier <[email protected]>
w_binprobs complete, but error bars seem too small (completely wrong, actually)

github.com/westpa/westpa - d71a9c19296c7a00056c746f846e07813dd0c751 authored about 13 years ago by Matt Zwier <[email protected]>
Analysis framework working commit. Added support for using the line_profiler module with the "--lprofile" switch to any script called by bin/wemd.

github.com/westpa/westpa - b320c82c15163daf082b52d2fc4a629e8b28a1ae authored about 13 years ago by Matt Zwier <[email protected]>
Yet another working commit.

github.com/westpa/westpa - 17240e3206cede1fe61665c9efb8ccc75704c29b authored about 13 years ago by Matt Zwier <[email protected]>
Working commit. Merged CachingDataReader with DataReaderMixin. General methods for checking and storing bin information and recalculating automatically seem to work.

github.com/westpa/westpa - 8d4330bd046bd5e9efabf7bd8f7ece2f8cc5d11d authored about 13 years ago by Matt Zwier <[email protected]>
Working commit of analysis revamp. Fixed spurious newline printed at every tool invocation. Added preliminary bin topology identification using a hash of bin centers.

github.com/westpa/westpa - 6bf639cfd98f2ff0ca142977932a94480cec92ef authored about 13 years ago by Matt Zwier <[email protected]>
Preliminary conversion to new rc system, removal of sim_manager as de facto global object. w_init and w_run seem to work; analysis tools not updated.

github.com/westpa/westpa - 88afa13a76e65d32acb062795273cb4e9ff0fbf0 authored about 13 years ago by Matt Zwier <[email protected]>
Functional (though insufficiently tested) w_ttimes

github.com/westpa/westpa - ff0ce56e20488857b359a15b4ee0eb4b8bf565b8 authored about 13 years ago by Matt Zwier <[email protected]>
Fixed bug in w_pcpdist which pooled data from multiple progress coordinate dimensions.

github.com/westpa/westpa - 90ebe74a9451d1281dcda5be484c2fe06ee0d082 authored about 13 years ago by Matt Zwier <[email protected]>
added symlink for w_ttimes in bin/

github.com/westpa/westpa - 0ea1ae1165c4cd41e2b2e96fc1974b6986116ce3 authored about 13 years ago by Matt Zwier <[email protected]>
Created w_ttimes anew from w_ttimes_bf

github.com/westpa/westpa - 71c9df7860b013874a41ef401bb89a2e6ae3fecd authored about 13 years ago by Matt Zwier <[email protected]>
Deleted old w_ttimes

github.com/westpa/westpa - 1d74188fe2856beb2842fe7c67711a72ad43a6ff authored about 13 years ago by Matt Zwier <[email protected]>
Tweaks to w_fluxanl

github.com/westpa/westpa - f8cee08c24ef3b225af9567ec7489c6a09f9fc01 authored about 13 years ago by Matt Zwier <[email protected]>
Cleaned up w_ttimes_bf, rewrote w_fluxanl to support multiple targets.

github.com/westpa/westpa - 8b5c2ff7b19ce018c7df62380a243aedff2e0d03 authored about 13 years ago by Matt Zwier <[email protected]>
w_ttimes_bf: More correct approach to processing short transitions (i.e. between adjacent bins), compression in analysis.h5, mondo optimizations in the MCBS processing.

github.com/westpa/westpa - 7a77bf74a2dd4e975537fbf46e2875ed0d8f6a74 authored about 13 years ago by Matt Zwier <[email protected]>
Working w_ttimes_bf with slow MCBS error analysis

github.com/westpa/westpa - ca54ef8fe1ad4ccd7fb249f41dcc5b2e7ba08325 authored about 13 years ago by Matt Zwier <[email protected]>
Began reworking w_ttimes...again.

github.com/westpa/westpa - edcebe85521ee4cdd96620e27f53a10c6ccf8f34 authored about 13 years ago by Matt Zwier <[email protected]>
Removed '_cmd' from each script in lib/cmds

github.com/westpa/westpa - b68fe73f861e2d8fd77e72ffeb5d80779e841e06 authored about 13 years ago by Matt Zwier <[email protected]>
Merged in global changes from WEED development.

github.com/westpa/westpa - 3efb686fb1f229d7cc37fd7b38abb12aaa2cdaa5 authored about 13 years ago by Matt Zwier <[email protected]>
Changed 2-page PDF output of w_pcpdist to single-page PDF output.

github.com/westpa/westpa - 8603222d11c7ce4d4774571a3be05e6edb0efe9f authored about 13 years ago by Matt Zwier <[email protected]>
fixed missing w_pcpdist symlink

github.com/westpa/westpa - 68e0c3e6394ab74bbd054f94816f1a2d45e33ea5 authored about 13 years ago by Matt Zwier <[email protected]>
Working commit

github.com/westpa/westpa - 5f5755f245ebee22a843a181264b815061167848 authored about 13 years ago by Matt Zwier <[email protected]>
Added w_pcpdist command to generate probability distributions for progress coordinates from all available WEMD data.

github.com/westpa/westpa - a77ed153181f725a6d18dcc6cff70780b73556c5 authored about 13 years ago by Matt Zwier <[email protected]>
Fixed an incorrect conversion in w_ttimes (divided by dt instead of multiplied for EDs and lifetimes).

github.com/westpa/westpa - 63d42841ff18e50ea6a542789b0c3a54d0bf13ac authored over 13 years ago by Matt Zwier <[email protected]>
Updated CHANGELOG.

github.com/westpa/westpa - 1f58dd16e8bc54fc651eaf543fa06f44a1e90ded authored over 13 years ago by Matt Zwier <[email protected]>
Greatly revamped transition time analysis, including correct flux and rate treatment (matches A->B rates from JCTC study). HDF5 storage of intermediate data for w_ttimes.

github.com/westpa/westpa - c8acd5978ee6572b33861f7e6b161a913574c9e4 authored over 13 years ago by Matt Zwier <[email protected]>
Fixed regression in w_steady_state.

github.com/westpa/westpa - e485a7696377ebe8310e52607d13d2fd510caf2c authored over 13 years ago by Matt Zwier <[email protected]>
Fixed a bug in w_steady_state which causes a crash when recycling targets are enabled.

github.com/westpa/westpa - be027ef88f60d4b0287fc89ec715dba4ffe05c46 authored over 13 years ago by Matt Zwier <[email protected]>
Added preliminary support (with Brandon and David) for coordinate storage in HDF5.

github.com/westpa/westpa - 91831eb5353eb1d0842ffc2bd9c8170d95aa33bf authored over 13 years ago by Matt Zwier <[email protected]>
Fixed errant \r in w_avgbinprobs

github.com/westpa/westpa - 77a8e2856188c2bbffb84d48dc2f9630364b68cd authored over 13 years ago by Matt Zwier <[email protected]>
Removed wemd_cmd.py (replaced with w_init and w_run), updated CHANGELOG.

github.com/westpa/westpa - 2d1c2a847216eac67ca30149999dc79568dbd091 authored over 13 years ago by Matt Zwier <[email protected]>
Merge with 97f37ed6871347f94812cddd6ea8ddf731608dd4

github.com/westpa/westpa - 4ca76bbb303d970a851589f6baeb5455ce85b661 authored over 13 years ago by Matt Zwier <[email protected]>
Merge with 658fc40d8ec9a0042e2ace6cd973dad2ffc31116

github.com/westpa/westpa - 735009d0db858637151ab0b75ad166a7c7c7d823 authored over 13 years ago by Matt Zwier <[email protected]>
Tweaks and bugfixes

github.com/westpa/westpa - 9429149eb6b4b430a42d15aeb4f397921ad89d8a authored over 13 years ago by Matt Zwier <[email protected]>
Tweaks and cleanups to transition/rate analysis. Rate analysis now considers transitions of the form A -> X1 -> X2 -> ... -> A (full-circle sojourns).

github.com/westpa/westpa - a1e8fbd3f3616622771e3e16a88b7dcadd6a087c authored over 13 years ago by Matt Zwier <[email protected]>
Added preliminary rate analysis to w_ttimes, removed brute-force analysis option from w_ttimes.

github.com/westpa/westpa - 7845d140e99ccf09fbf073ee4c7efbe3ae3707ec authored over 13 years ago by Matt Zwier <[email protected]>
Working commit

github.com/westpa/westpa - 4dc90d8b328fbd43fc5c201728f1d35d0954f3b5 authored over 13 years ago by Matt Zwier <[email protected]>
Edited w_avgbinprobs script so the -e flag works

github.com/westpa/westpa - 77ddd39a1e27fad4e9eecf8eefda88770177700e authored over 13 years ago by daw88 <[email protected]>
zmq: node device works

github.com/westpa/westpa - f28ed78a5d5bf254db3555c2669c09a258a68b30 authored over 13 years ago by Matt Zwier <[email protected]>
zmq: it's alive!

github.com/westpa/westpa - 2a4badcb5d95d46ae019d074af17a745f9a20297 authored over 13 years ago by Matt Zwier <[email protected]>
Initial implementation of VoronoiRegionSet

github.com/westpa/westpa - 640f36bcd4d656920529cb8ba7187afb5df8b5f4 authored over 13 years ago by Joshua Adelman <[email protected]>
Modified w_steady_state to address issue #3 in main repo and add functionality

github.com/westpa/westpa - 2991d0c3117131ac094ba5955b2b34811a2b6d92 authored over 13 years ago by Joshua Adelman <[email protected]>
Independent client/server processes work (in any startup order!)

github.com/westpa/westpa - 30f2de1d1e83242ca0037a019263cd7f8e478148 authored over 13 years ago by Matt Zwier <[email protected]>
ZMQ: ODLD test succeeds

github.com/westpa/westpa - d29ccf6c25210a6b50e2155bfba649f6546edf68 authored over 13 years ago by Matt Zwier <[email protected]>
ZMQ client and server widgets can round-trip work

github.com/westpa/westpa - b93e53cb73d767d4d8db5a8cc7f9d691d7d7fa2d authored over 13 years ago by Matt Zwier <[email protected]>
ZeroMQ work in progress

github.com/westpa/westpa - 5bad3698a40d49647402592508f23224715db8b5 authored over 13 years ago by Matt Zwier <[email protected]>
Moved caching data retrieval functions out of trajtree.py and into a new wemdtools.data_manager module; misc. other updates.

github.com/westpa/westpa - c8bcb803ed922630981faab208ec5da8c2e65895 authored over 13 years ago by Matt Zwier <[email protected]>
Added new environment variables for executable backend providing 16, 32, 64, and 128-bit random integers and [0,1) random reals.

github.com/westpa/westpa - db4f3fc895a447f4b26b61dabc6762713c586b38 authored over 13 years ago by Matt Zwier <[email protected]>
Forgot w_trace symlink

github.com/westpa/westpa - 99b8bf2b1c0b1ae01d851610f7cd978ee790283e authored over 13 years ago by Matt Zwier <[email protected]>
Added (very first pass at) w_trace command to trace trajectories.

github.com/westpa/westpa - 492dbac47f3327daa6cc32906bbb9d8ae2f2f370 authored over 13 years ago by Matt Zwier <[email protected]>
Updated the steady state code.

github.com/westpa/westpa - f34dcf5d7293b79cf0d88a14566cb90bda2cee55 authored over 13 years ago by Joseph Kaus <[email protected]>
Added support for analyzing all living trajectories in w_ttimes

github.com/westpa/westpa - ebd5c0bd9c5285e47adf10a7e528f90d7d14f9c6 authored over 13 years ago by Matt Zwier <[email protected]>
Working commit

github.com/westpa/westpa - b11dca08ef4ca9c335be3a9c1d1b3c1d7314b5a5 authored over 13 years ago by Matt Zwier <[email protected]>
Cleaned up a spurious log.debug() in the WE loop.

github.com/westpa/westpa - a29a79d245e2b1cd6a7ab70255d43509f0c89496 authored over 13 years ago by Matt Zwier <[email protected]>
Added support for (easier) non-recycling simulations.

github.com/westpa/westpa - e5667be05c11d9f8eee969bd11e2501a1f8ce1ad authored over 13 years ago by Matt Zwier <[email protected]>
Fixed broken HDF5-sans-system w_ttimes argument parsing, clarified a few comments and docstrings.

github.com/westpa/westpa - 560b97e7bb6df2304391d7181b635d3d9f15c4f5 authored over 13 years ago by Matt Zwier <[email protected]>
Abstracted "bin to index in get_all_bins()" functionality out of w_ttimes, w_binprobs, and w_avgbinprobs. Updated w_ttimes for new wemd.pcoords and wemdtools.bins functions. Added optimizations for binning in non-nested topologies to recover most of the binning performance formerly seen in w_ttimes but only valid for non-nested bins.

github.com/westpa/westpa - 15b696fe58953e428b92188dc8430872b50e578a authored over 13 years ago by Matt Zwier <[email protected]>
pcoord refactoring broke main WE loop; generator expressions now prohibited in calls to map_to_bins()

github.com/westpa/westpa - 5d1d0af7c14af466147e88c8b872ef1ef3ed565c authored over 13 years ago by Matt Zwier <[email protected]>
Moved the "--profile" switch out of wemd.rc and into bin/wemd

github.com/westpa/westpa - f35e1de6f0c682addfbea5feec6c51fc978828d7 authored over 13 years ago by Matt Zwier <[email protected]>
Show developer warnings by default using PYTHONWARNINGS env. var.

github.com/westpa/westpa - 10b44f360aa8a11ae6b6697ca90024873d14d77e authored over 13 years ago by Matt Zwier <[email protected]>
Increased flexibility and speed in pcoord handling, began constructing test suite.

github.com/westpa/westpa - c013b750d0e31fb79b90dabd1e640c24c32e752a authored over 13 years ago by Matt Zwier <[email protected]>
Added symlinks for w_segstats and w_succ, which somehow slipped through the

last commit.

github.com/westpa/westpa - 696b8b591724c5ad1b0be264de393d728fd001d1 authored over 13 years ago by Matt Zwier <[email protected]>
Added w_succ and w_segstats scripts

github.com/westpa/westpa - ef265e6265eced4f0f2c4128d0af92a8de236ded authored over 13 years ago by Matt Zwier <[email protected]>
Minor bugfixes to w_avgbinprobs, updated w_binprobs to use wemdtools.bins framework.

github.com/westpa/westpa - 690ccad5288991a34c585391cb2ac8a7a8b42210 authored over 13 years ago by Matt Zwier <[email protected]>
Modified w_avgbinprobs to calculate bin occupancies from segments

github.com/westpa/westpa - 7e015cfa021c93fc06a8de3863a1cc432d635b6e authored over 13 years ago by Matt Zwier <[email protected]>
Fixed bug in CPU time collection for executable backend.

github.com/westpa/westpa - 50c647158c7c972206a8d49fe417aebcb43a7606 authored over 13 years ago by mczwier <devnull@localhost>
Catch-up commit

github.com/westpa/westpa - 6583a1869c6acbd36130528fe978305976419d17 authored over 13 years ago by Matt Zwier <[email protected]>
Updated trajectory tree walker, added w_sqlite2hdf5 conversion tool.

github.com/westpa/westpa - 6cc166716546620ebdfa89578380e60ec61e08a1 authored over 13 years ago by Matt Zwier <[email protected]>
Greatly increased transition time analysis throughput by copious numpy vectorization.

github.com/westpa/westpa - 671a57b51529acd7d60afd2568a5cb28820cecac authored over 13 years ago by Matt Zwier <[email protected]>
Renamed wemd.types to wemd.segment, tripled bin assignment throughput for RectilinearRegionSets

github.com/westpa/westpa - a1e29e56f3d1de969e144c9c286502445fb99f91 authored over 13 years ago by Matt Zwier <[email protected]>
Merge with 6eeb657702f0800d756bd09755a2736cbd2296d3

github.com/westpa/westpa - 810ee060408895eaa06e96db8a581efb369cd6d3 authored over 13 years ago by joekaus <devnull@localhost>
Modified steady state code

Added truncate command

github.com/westpa/westpa - 811b96ec9bc73292981db26e32b7a58b6fcca35d authored over 13 years ago by joekaus <devnull@localhost>
Added w_avgbinprobs tool

github.com/westpa/westpa - 3b502595ca5e1d9eafa8f15693bb1d18f8f661a9 authored over 13 years ago by Matt Zwier <[email protected]>
Near-final but only modestly optimized brute force transition time analysis done.

github.com/westpa/westpa - f7f1ab9ffc3b58db0562583c49123db6698e213c authored over 13 years ago by Matt Zwier <[email protected]>
Prototype (pre-alpha, incomplete) transition time analysis tool added. Gets EDs and FPTs correct for the methane/methane brute force test data.

github.com/westpa/westpa - dabd11e054f8e34aee52a0c6a7138f29b534e516 authored over 13 years ago by Matt Zwier <[email protected]>
Completed removal of Particle class.

github.com/westpa/westpa - 71ce5131fc6ecad777866955ed47ffd7d2e7e787 authored over 13 years ago by Matt Zwier <[email protected]>
Fixed bugs in parent tracking, simplified WE driver, added w_sanity error checker.

github.com/westpa/westpa - 43a07a70582614af1eb7e4766516e56384c21a1d authored over 13 years ago by Matt Zwier <[email protected]>
Added w_dumpsegs to look at segments as stored in the data manager.

github.com/westpa/westpa - 1007e3830486d6e7b7a1f3e9f15856f9dafd1aa0 authored over 13 years ago by Matt Zwier <[email protected]>
Fixed wrong probability normalization in w_ntop.

github.com/westpa/westpa - 0f5b77b1ca44326de105906fa90c3bb361b8975e authored over 13 years ago by Matt Zwier <[email protected]>
Added p_parent_id to w_ntop output. Also added close_backing()/open_backing() wrapper to propagate_segments() to attempt to ameliorate crashes due to non-threaded HDF5 (which is unsupported, but seems to be a particularly insidious problem to prevent).

github.com/westpa/westpa - 0743523b2177db4cdb0ffb0d4dfc3d95dd193f44 authored over 13 years ago by Matt Zwier <[email protected]>
Merge with c6e36e6ad67cd76413c56163c4f05740b28aba04

github.com/westpa/westpa - 0c9c2e51cb6a52a41715a4ae3dffd2fe4faaa843 authored over 13 years ago by joekaus <devnull@localhost>
Steady state wip

github.com/westpa/westpa - da6718408ab1e0f4026aeb92634ec956465481b2 authored over 13 years ago by joekaus <devnull@localhost>
Fixed serious bug in data manager which set the initial points of all segments to zero for restarted simulations only.

github.com/westpa/westpa - 688f0d11d6de5a66384b83881eda89837b3e5c00 authored over 13 years ago by Matt Zwier <[email protected]>
Added w_fluxanl tool to get rate constant and its error from WE probability flux measurements.

github.com/westpa/westpa - 82260772fa00747863ff66da0dfabf24a9939145 authored over 13 years ago by Matt Zwier <[email protected]>
Merge with 73cbad2936b6b031030d9c1b7d8e58d0248825e3

github.com/westpa/westpa - 90f6c1d07493db701b36f414f4462a080c124114 authored over 13 years ago by joekaus <devnull@localhost>
Work in progress of steady state code

github.com/westpa/westpa - 689d1e680c9ae6403154e4beb88290c8a4c8d8a8 authored over 13 years ago by joekaus <devnull@localhost>
Cleanup and clarification.

github.com/westpa/westpa - 716c40f514f8d7a32d0f4b637455c489d8ec68f9 authored over 13 years ago by Matt Zwier <[email protected]>
Simplified and clarified processes work manager.

github.com/westpa/westpa - 5b62f102b32a742cca7ce5df9250c96c79cf51ae authored over 13 years ago by Matt Zwier <[email protected]>
Added support for separate initial/recycle probabilities and the ability to read initial state data from a text file, added w_ntop tool to extract the top N highest-weight replicas per bin.

github.com/westpa/westpa - ff96f63f94b2c1de28fa1ff7d88abfd6fb97d798 authored over 13 years ago by Matt Zwier <[email protected]>
Added CHANGELOG, modified tcp/ip driver to support argparse command-line parsing.

github.com/westpa/westpa - da39867a30c01aeaa0ed2ff7a01fe65a58aef48d authored over 13 years ago by Matt Zwier <[email protected]>
Minor improvements to w_binprobs and fix for crash wherein timedelta won't accept a numpy.float* as an argument for seconds.

github.com/westpa/westpa - 5e109ce7ea3d1aef2a2be49efee6b80cacf9388c authored over 13 years ago by Matt Zwier <[email protected]>
Added bin probability extraction script w_binprobs

github.com/westpa/westpa - 781abdc962161b19b6b2bb937c2ac0a3bf869bc1 authored over 13 years ago by Matt Zwier <[email protected]>
Fixed broken --profile option, removed antiquated MPI driver

github.com/westpa/westpa - 791bc4b05cdf595dbe7b666458b5718b7fba4076 authored over 13 years ago by Matt Zwier <[email protected]>
Added manual update of segment list in sim_manager.run() to account for case where workers return different segment objects than are dispatched to them.

github.com/westpa/westpa - 66a1ff1b679547c09dfe776ca963dc4c99501f63 authored over 13 years ago by Matt Zwier <[email protected]>