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

Simplified ZeroMQ work manager appears to work.

3fe7c651f318955e7b7df96c48852d3d7f40aad4 authored over 13 years ago by Matt Zwier <[email protected]>

Working commit of revamped zmq work manager.

232bb591fe5d3c138ac0902a1039aae78fd63831 authored over 13 years ago by Matt Zwier <[email protected]>

Working commit

99cd8c6faf38c84c3d7a979619ba03ac1e415044 authored over 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.

da4c0dc330367dd1e1ceb6dbb98d19fc760c056f authored over 13 years ago by Matt Zwier <[email protected]>

Analysis framework working commit

64979328469828c2c6216a56ff7e4a3492e80ad2 authored over 13 years ago by Matt Zwier <[email protected]>

Removed deprecated w_avgbinprobs

68071b59bee2984ccaf6ec6b0fa17240da5a7e07 authored over 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).

a0d5a8650b252cbd7ec28e6d6ea79424049f214a authored over 13 years ago by Matt Zwier <[email protected]>

w_binprobs complete, but error bars seem too small (completely wrong, actually)

d71a9c19296c7a00056c746f846e07813dd0c751 authored over 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.

b320c82c15163daf082b52d2fc4a629e8b28a1ae authored over 13 years ago by Matt Zwier <[email protected]>

Yet another working commit.

17240e3206cede1fe61665c9efb8ccc75704c29b authored over 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.

8d4330bd046bd5e9efabf7bd8f7ece2f8cc5d11d authored over 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.

6bf639cfd98f2ff0ca142977932a94480cec92ef authored over 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.

88afa13a76e65d32acb062795273cb4e9ff0fbf0 authored over 13 years ago by Matt Zwier <[email protected]>

Functional (though insufficiently tested) w_ttimes

ff0ce56e20488857b359a15b4ee0eb4b8bf565b8 authored over 13 years ago by Matt Zwier <[email protected]>

Fixed bug in w_pcpdist which pooled data from multiple progress coordinate dimensions.

90ebe74a9451d1281dcda5be484c2fe06ee0d082 authored over 13 years ago by Matt Zwier <[email protected]>

added symlink for w_ttimes in bin/

0ea1ae1165c4cd41e2b2e96fc1974b6986116ce3 authored over 13 years ago by Matt Zwier <[email protected]>

Created w_ttimes anew from w_ttimes_bf

71c9df7860b013874a41ef401bb89a2e6ae3fecd authored over 13 years ago by Matt Zwier <[email protected]>

Deleted old w_ttimes

1d74188fe2856beb2842fe7c67711a72ad43a6ff authored over 13 years ago by Matt Zwier <[email protected]>

Tweaks to w_fluxanl

f8cee08c24ef3b225af9567ec7489c6a09f9fc01 authored over 13 years ago by Matt Zwier <[email protected]>

Cleaned up w_ttimes_bf, rewrote w_fluxanl to support multiple targets.

8b5c2ff7b19ce018c7df62380a243aedff2e0d03 authored over 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.

7a77bf74a2dd4e975537fbf46e2875ed0d8f6a74 authored over 13 years ago by Matt Zwier <[email protected]>

Working w_ttimes_bf with slow MCBS error analysis

ca54ef8fe1ad4ccd7fb249f41dcc5b2e7ba08325 authored over 13 years ago by Matt Zwier <[email protected]>

Began reworking w_ttimes...again.

edcebe85521ee4cdd96620e27f53a10c6ccf8f34 authored over 13 years ago by Matt Zwier <[email protected]>

Removed '_cmd' from each script in lib/cmds

b68fe73f861e2d8fd77e72ffeb5d80779e841e06 authored over 13 years ago by Matt Zwier <[email protected]>

Merged in global changes from WEED development.

3efb686fb1f229d7cc37fd7b38abb12aaa2cdaa5 authored over 13 years ago by Matt Zwier <[email protected]>

Changed 2-page PDF output of w_pcpdist to single-page PDF output.

8603222d11c7ce4d4774571a3be05e6edb0efe9f authored over 13 years ago by Matt Zwier <[email protected]>

fixed missing w_pcpdist symlink

68e0c3e6394ab74bbd054f94816f1a2d45e33ea5 authored over 13 years ago by Matt Zwier <[email protected]>

Working commit

5f5755f245ebee22a843a181264b815061167848 authored over 13 years ago by Matt Zwier <[email protected]>

Added w_pcpdist command to generate probability distributions for progress coordinates from all available WEMD data.

a77ed153181f725a6d18dcc6cff70780b73556c5 authored over 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).

63d42841ff18e50ea6a542789b0c3a54d0bf13ac authored over 13 years ago by Matt Zwier <[email protected]>

Updated CHANGELOG.

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.

c8acd5978ee6572b33861f7e6b161a913574c9e4 authored over 13 years ago by Matt Zwier <[email protected]>

Fixed regression in w_steady_state.

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.

be027ef88f60d4b0287fc89ec715dba4ffe05c46 authored over 13 years ago by Matt Zwier <[email protected]>

Added preliminary support (with Brandon and David) for coordinate storage in HDF5.

91831eb5353eb1d0842ffc2bd9c8170d95aa33bf authored over 13 years ago by Matt Zwier <[email protected]>

Fixed errant \r in w_avgbinprobs

77a8e2856188c2bbffb84d48dc2f9630364b68cd authored over 13 years ago by Matt Zwier <[email protected]>

Removed wemd_cmd.py (replaced with w_init and w_run), updated CHANGELOG.

2d1c2a847216eac67ca30149999dc79568dbd091 authored over 13 years ago by Matt Zwier <[email protected]>

Merge with 97f37ed6871347f94812cddd6ea8ddf731608dd4

4ca76bbb303d970a851589f6baeb5455ce85b661 authored over 13 years ago by Matt Zwier <[email protected]>

Merge with 658fc40d8ec9a0042e2ace6cd973dad2ffc31116

735009d0db858637151ab0b75ad166a7c7c7d823 authored over 13 years ago by Matt Zwier <[email protected]>

Tweaks and bugfixes

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).

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.

7845d140e99ccf09fbf073ee4c7efbe3ae3707ec authored over 13 years ago by Matt Zwier <[email protected]>

Working commit

4dc90d8b328fbd43fc5c201728f1d35d0954f3b5 authored over 13 years ago by Matt Zwier <[email protected]>

Edited w_avgbinprobs script so the -e flag works

77ddd39a1e27fad4e9eecf8eefda88770177700e authored over 13 years ago by daw88 <[email protected]>

zmq: node device works

f28ed78a5d5bf254db3555c2669c09a258a68b30 authored over 13 years ago by Matt Zwier <[email protected]>

zmq: it's alive!

2a4badcb5d95d46ae019d074af17a745f9a20297 authored over 13 years ago by Matt Zwier <[email protected]>

Initial implementation of VoronoiRegionSet

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

2991d0c3117131ac094ba5955b2b34811a2b6d92 authored over 13 years ago by Joshua Adelman <[email protected]>

Independent client/server processes work (in any startup order!)

30f2de1d1e83242ca0037a019263cd7f8e478148 authored over 13 years ago by Matt Zwier <[email protected]>

ZMQ: ODLD test succeeds

d29ccf6c25210a6b50e2155bfba649f6546edf68 authored over 13 years ago by Matt Zwier <[email protected]>

ZMQ client and server widgets can round-trip work

b93e53cb73d767d4d8db5a8cc7f9d691d7d7fa2d authored over 13 years ago by Matt Zwier <[email protected]>

ZeroMQ work in progress

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.

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.

db4f3fc895a447f4b26b61dabc6762713c586b38 authored over 13 years ago by Matt Zwier <[email protected]>

Forgot w_trace symlink

99b8bf2b1c0b1ae01d851610f7cd978ee790283e authored over 13 years ago by Matt Zwier <[email protected]>

Added (very first pass at) w_trace command to trace trajectories.

492dbac47f3327daa6cc32906bbb9d8ae2f2f370 authored over 13 years ago by Matt Zwier <[email protected]>

Updated the steady state code.

f34dcf5d7293b79cf0d88a14566cb90bda2cee55 authored over 13 years ago by Joseph Kaus <[email protected]>

Added support for analyzing all living trajectories in w_ttimes

ebd5c0bd9c5285e47adf10a7e528f90d7d14f9c6 authored over 13 years ago by Matt Zwier <[email protected]>

Working commit

b11dca08ef4ca9c335be3a9c1d1b3c1d7314b5a5 authored over 13 years ago by Matt Zwier <[email protected]>

Cleaned up a spurious log.debug() in the WE loop.

a29a79d245e2b1cd6a7ab70255d43509f0c89496 authored over 13 years ago by Matt Zwier <[email protected]>

Added support for (easier) non-recycling simulations.

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.

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.

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()

5d1d0af7c14af466147e88c8b872ef1ef3ed565c authored over 13 years ago by Matt Zwier <[email protected]>

Moved the "--profile" switch out of wemd.rc and into bin/wemd

f35e1de6f0c682addfbea5feec6c51fc978828d7 authored over 13 years ago by Matt Zwier <[email protected]>

Show developer warnings by default using PYTHONWARNINGS env. var.

10b44f360aa8a11ae6b6697ca90024873d14d77e authored over 13 years ago by Matt Zwier <[email protected]>

Increased flexibility and speed in pcoord handling, began constructing test suite.

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.

696b8b591724c5ad1b0be264de393d728fd001d1 authored over 13 years ago by Matt Zwier <[email protected]>

Added w_succ and w_segstats scripts

ef265e6265eced4f0f2c4128d0af92a8de236ded authored over 13 years ago by Matt Zwier <[email protected]>

Minor bugfixes to w_avgbinprobs, updated w_binprobs to use wemdtools.bins framework.

690ccad5288991a34c585391cb2ac8a7a8b42210 authored over 13 years ago by Matt Zwier <[email protected]>

Modified w_avgbinprobs to calculate bin occupancies from segments

7e015cfa021c93fc06a8de3863a1cc432d635b6e authored over 13 years ago by Matt Zwier <[email protected]>

Fixed bug in CPU time collection for executable backend.

50c647158c7c972206a8d49fe417aebcb43a7606 authored over 13 years ago by mczwier <devnull@localhost>

Catch-up commit

6583a1869c6acbd36130528fe978305976419d17 authored almost 14 years ago by Matt Zwier <[email protected]>

Updated trajectory tree walker, added w_sqlite2hdf5 conversion tool.

6cc166716546620ebdfa89578380e60ec61e08a1 authored almost 14 years ago by Matt Zwier <[email protected]>

Greatly increased transition time analysis throughput by copious numpy vectorization.

671a57b51529acd7d60afd2568a5cb28820cecac authored almost 14 years ago by Matt Zwier <[email protected]>

Renamed wemd.types to wemd.segment, tripled bin assignment throughput for RectilinearRegionSets

a1e29e56f3d1de969e144c9c286502445fb99f91 authored almost 14 years ago by Matt Zwier <[email protected]>

Merge with 6eeb657702f0800d756bd09755a2736cbd2296d3

810ee060408895eaa06e96db8a581efb369cd6d3 authored almost 14 years ago by joekaus <devnull@localhost>

Modified steady state code

Added truncate command

811b96ec9bc73292981db26e32b7a58b6fcca35d authored almost 14 years ago by joekaus <devnull@localhost>

Added w_avgbinprobs tool

3b502595ca5e1d9eafa8f15693bb1d18f8f661a9 authored almost 14 years ago by Matt Zwier <[email protected]>

Near-final but only modestly optimized brute force transition time analysis done.

f7f1ab9ffc3b58db0562583c49123db6698e213c authored almost 14 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.

dabd11e054f8e34aee52a0c6a7138f29b534e516 authored almost 14 years ago by Matt Zwier <[email protected]>

Completed removal of Particle class.

71ce5131fc6ecad777866955ed47ffd7d2e7e787 authored almost 14 years ago by Matt Zwier <[email protected]>

Fixed bugs in parent tracking, simplified WE driver, added w_sanity error checker.

43a07a70582614af1eb7e4766516e56384c21a1d authored almost 14 years ago by Matt Zwier <[email protected]>

Added w_dumpsegs to look at segments as stored in the data manager.

1007e3830486d6e7b7a1f3e9f15856f9dafd1aa0 authored almost 14 years ago by Matt Zwier <[email protected]>

Fixed wrong probability normalization in w_ntop.

0f5b77b1ca44326de105906fa90c3bb361b8975e authored almost 14 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).

0743523b2177db4cdb0ffb0d4dfc3d95dd193f44 authored almost 14 years ago by Matt Zwier <[email protected]>

Merge with c6e36e6ad67cd76413c56163c4f05740b28aba04

0c9c2e51cb6a52a41715a4ae3dffd2fe4faaa843 authored almost 14 years ago by joekaus <devnull@localhost>

Steady state wip

da6718408ab1e0f4026aeb92634ec956465481b2 authored almost 14 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.

688f0d11d6de5a66384b83881eda89837b3e5c00 authored almost 14 years ago by Matt Zwier <[email protected]>

Added w_fluxanl tool to get rate constant and its error from WE probability flux measurements.

82260772fa00747863ff66da0dfabf24a9939145 authored almost 14 years ago by Matt Zwier <[email protected]>

Merge with 73cbad2936b6b031030d9c1b7d8e58d0248825e3

90f6c1d07493db701b36f414f4462a080c124114 authored almost 14 years ago by joekaus <devnull@localhost>

Work in progress of steady state code

689d1e680c9ae6403154e4beb88290c8a4c8d8a8 authored almost 14 years ago by joekaus <devnull@localhost>

Cleanup and clarification.

716c40f514f8d7a32d0f4b637455c489d8ec68f9 authored almost 14 years ago by Matt Zwier <[email protected]>

Simplified and clarified processes work manager.

5b62f102b32a742cca7ce5df9250c96c79cf51ae authored almost 14 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.

ff96f63f94b2c1de28fa1ff7d88abfd6fb97d798 authored almost 14 years ago by Matt Zwier <[email protected]>

Added CHANGELOG, modified tcp/ip driver to support argparse command-line parsing.

da39867a30c01aeaa0ed2ff7a01fe65a58aef48d authored almost 14 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.

5e109ce7ea3d1aef2a2be49efee6b80cacf9388c authored almost 14 years ago by Matt Zwier <[email protected]>

Added bin probability extraction script w_binprobs

781abdc962161b19b6b2bb937c2ac0a3bf869bc1 authored almost 14 years ago by Matt Zwier <[email protected]>

Fixed broken --profile option, removed antiquated MPI driver

791bc4b05cdf595dbe7b666458b5718b7fba4076 authored almost 14 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.

66a1ff1b679547c09dfe776ca963dc4c99501f63 authored almost 14 years ago by Matt Zwier <[email protected]>