WESTPA commits | Ecosyste.ms: OpenCollective

Updated west_tools

Former-commit-id: a811a943f0764b89169097741a6b3e8962792762

github.com/westpa/westpa - a91a9c9f0818696af1493b3dca3664e6c65336ff authored over 11 years ago by Matt Zwier <[email protected]>

Coerce slices to numpy arrays in apply_down and apply_down_argmin_across in _assign.pyx

github.com/westpa/westpa - df08e576c61aa1453342db9193f6cda1a4714ffa authored over 11 years ago by Matt Zwier <[email protected]>

Updated copyright information

github.com/westpa/westpa - 7f070b8c82339da427c7432b34a8404c34e25404 authored over 11 years ago by Matt Zwier <[email protected]>

Updated copyright information

github.com/westpa/westpa - 022265eba84b05de6ec645b92ce54545b236b595 authored over 11 years ago by Matt Zwier <[email protected]>

Updated copyright information

Former-commit-id: 91887656bee0b3264e4eed44a284ce8cfb35cc14

github.com/westpa/westpa - 266905f673ad34521e1c2a8257e965fa105bc393 authored over 11 years ago by Matt Zwier <[email protected]>

Modified README, removed AUTHORS

Former-commit-id: bb0ea17ab00c4d6edfaaebaa27d7433e28149387

github.com/westpa/westpa - fb383efc075bec98f73bf40a2ef3850147b68383 authored over 11 years ago by Matt Zwier <[email protected]>

Merging

Former-commit-id: d3d1517dffb8712036bc319e10d2d28c101a1b64

github.com/westpa/westpa - 94f5f1d4476e4bd302589dbf38dc5b457845137a authored over 11 years ago by Matt Zwier <[email protected]>

Updated subrepos

Former-commit-id: 3a72509b73c3cb3568c5668a48761884a00d131a

github.com/westpa/westpa - 79d735e55b83a4f9ba55d6d86dfe84600b2d39aa authored over 11 years ago by Matt Zwier <[email protected]>

Adding progress bar license info

github.com/westpa/westpa - 4581d660dfe791aae803552a4fabae1a4158ecdc authored over 11 years ago by Matt Zwier <[email protected]>

Merging and updating subrepos

Former-commit-id: 05aa5dd32e7a3028f1ead1a4039d85d9abf811a9

github.com/westpa/westpa - a2fd72804a710b041b9225b10b3005f33f75be64 authored over 11 years ago by Matt Zwier <[email protected]>

Updates to use progress bar

github.com/westpa/westpa - 5af1e7d4a1cf3b904322478b76e588caa2b897cc authored over 11 years ago by Matt Zwier <[email protected]>

Merging

github.com/westpa/westpa - d610ca3ff89a9dffa6454b8269a7f722f4583b52 authored over 11 years ago by Matt Zwier <[email protected]>

Merging

github.com/westpa/westpa - ea93f6bc116a9d0842c7f7ea67c9d6af14e4af9c authored over 11 years ago by Matt Zwier <[email protected]>

Added copyright and license info. General cleanup.

Source files are (c) individual contributors; package is (c) MCZ and LTC.

github.com/westpa/westpa - 004a792cab0c5292855b4ef9999a11aa6af2b623 authored over 11 years ago by Matt Zwier <[email protected]>

Added copyright and license info. General cleanup.

Source files are (c) individual contributors; package is (c) MCZ and LTC.

github.com/westpa/westpa - 87123d901271755749fae1ec137df7f3d418bfad authored over 11 years ago by Matt Zwier <[email protected]>

Added copyright and license info. General cleanup.

Source files are (c) individual contributors; package is (c) MCZ and LTC.

Former-commit-id: ea5...

github.com/westpa/westpa - c031aecc1f7f08bf677bdfe1cba61d28ffe17d1a authored over 11 years ago by Matt Zwier <[email protected]>

Added ``blessings`` subrepo to support progress bars

Former-commit-id: 5c64ffdfd27e1be564c48cbfe0e8b6bfa34b89cf

github.com/westpa/westpa - d6089bc6b168edcf99aaf3af5b9aa8af121f7568 authored over 11 years ago by Matt Zwier <[email protected]>

Added support for progress bars (requires ``blessings`` library)

github.com/westpa/westpa - ce8cfbb95eb5e2bf0e188a5e36c7ccc3f5b83ae2 authored over 11 years ago by Matt Zwier <[email protected]>

Updating west_tools

Former-commit-id: 4b3a4223c6633160ff4d96ea27baada54ccfac22

github.com/westpa/westpa - 68f0c910c96be5afb877068ebd39f42a258ceef1 authored over 11 years ago by Matt Zwier <[email protected]>

Updated plothist to use subcommand framework, added a check in subcommands

framework for forgetting to set the "subcommand" class variable on subcommand
classes.

github.com/westpa/westpa - 458be588572f70ec6f979bd3292d81b0d2d6c5bb authored over 11 years ago by Matt Zwier <[email protected]>

fixed a small bug with the zeromq server-client communication

github.com/westpa/westpa - 0d9742765901ed8cafe3e446e890f4f7a380d204 authored over 11 years ago by Nick Rego <[email protected]>

Merging

github.com/westpa/westpa - d71b32cbf264f81fb8b88fd69975db5ecd8032c8 authored over 11 years ago by Matt Zwier <[email protected]>

Updated west_tools

Former-commit-id: c34d0c34a29c808a6ef8a02129cfb50319520b4f

github.com/westpa/westpa - 393d1cbda46fb4a8eecad2666dfe3510a5ba8c4c authored over 11 years ago by Matt Zwier <[email protected]>

Revert an untested change to sink handling.

github.com/westpa/westpa - 61b775ba4a3f3d1af78d139ea6dd7ed3af6a61be authored over 11 years ago by Matt Zwier <[email protected]>

Added some unit tests for command line tools - these require a west.h5 output file in the tool_tests directory to work properly

github.com/westpa/westpa - b8120d49809e51861c92552369b89118b1e94845 authored over 11 years ago by Nick Rego <[email protected]>

Merging

Former-commit-id: 3f0cba7277cc62c161af4974296d76427006e850

github.com/westpa/westpa - acb116016f94a6b45fbf006b788f5bda076894bd authored over 11 years ago by Matt Zwier <[email protected]>

Updated west_tools subrepo to latest

github.com/westpa/westpa - d4f1adcb5cd0a89f85c125ffee5017d56b3fc9c1 authored over 11 years ago by Matt Zwier <[email protected]>

Merging

github.com/westpa/westpa - 2750812708fff2b9603bc875f1eb030314be3f79 authored over 11 years ago by Matt Zwier <[email protected]>

Added --no-compression option to w_kinetics to reduce I/O costs for w_kinavg.

Removed multiprocessing debug messages from default logging configs. Made
consistency warnings fo...

github.com/westpa/westpa - 0c29fea9b5f1f65e86e197224998bb1061d8ac0c authored over 11 years ago by Matt Zwier <[email protected]>

Correction to NAMD NaCl tutorial init.sh

Former-commit-id: d82d1537e2ad76c6ef7f1fb857a51c40ef7a4021

github.com/westpa/westpa - c98512aa3c069dbef8c0d0b502edf05a15e38292 authored over 11 years ago by ktd3 <devnull@localhost>

NAMD NaCl tutorial example directory

Former-commit-id: 7cf521fe23d9b1a86edafd933a411d95873c4f4a

github.com/westpa/westpa - 6d6e4eeb52f995890062e2303a3921de92e1cca5 authored over 11 years ago by ktd3 <devnull@localhost>

Na/Cl tutorial example directory

github.com/westpa/westpa - 2e6d35791035e02f7d5345e60261fe211799106c authored over 11 years ago by Daniel Hatfield <[email protected]>

W_trace works with h5io

github.com/westpa/westpa - b67181da1bbdba7af0078f619ba9ee1f3f826339 authored over 11 years ago by Nick Rego <[email protected]>

Fixed bug in kinetics tracing that gave completely wrong results for >2 states

github.com/westpa/westpa - 72e7b14be85ba61d59242ae313c5bfd8fe6051d3 authored over 11 years ago by Matt Zwier <[email protected]>

Merging again

github.com/westpa/westpa - cd8ec54be11b2c073e03bb236da49b02f8a7cbd2 authored over 11 years ago by Matt Zwier <[email protected]>

Merging

github.com/westpa/westpa - cedcdac6e75d1cabf93da263330ba3f63313a9df authored over 11 years ago by Matt Zwier <[email protected]>

Updated examples to use new wwmgr command-line arguments, updated subrepos.

github.com/westpa/westpa - d0530ef59d30ae65599319c3d8f2bcf4a40f6cdd authored over 11 years ago by Matt Zwier <[email protected]>

Merging dbeb689ac093 and 49a9d08474ec

github.com/westpa/westpa - 9417101cd4676e9dae27b053f2073ec9f1efd3d2 authored over 11 years ago by Matt Zwier <[email protected]>

Merging f750d6047ae1 and 78d66a3e3f6e

github.com/westpa/westpa - fcb2ad53f33f604167f0d2f92bd9af74031556a1 authored over 11 years ago by Matt Zwier <[email protected]>

Modified command line arguments to not require the "wm" prefix by default

(since they just seem to get in the way). Updated unit tests to match.

github.com/westpa/westpa - 0430a40f78b270c2edd827a3685298853614f374 authored over 11 years ago by Matt Zwier <[email protected]>

Working parallel rate CI estimation for the matrix case.

github.com/westpa/westpa - 0dbc282b466499e392927b9b1f683c29d9207c0f authored over 11 years ago by Matt Zwier <[email protected]>

Working parallel rate averaging for the tracing method.

github.com/westpa/westpa - 380d6cbb71bb6cd3e854c552414bb51c9fa2caed authored over 11 years ago by Matt Zwier <[email protected]>

Modified methane example ``init.sh`` to regenerate TPR file to avoid

occasional insensible failure to read methane.tpr.

github.com/westpa/westpa - 7497655c3233e41dea52837f3968e8d21578a143 authored over 11 years ago by Matt Zwier <[email protected]>

Migrated w_kinmat and w_kintrace into subcommands under w_kinetics. Improved

subcommand support in westtools.tool_classes

github.com/westpa/westpa - b3428ef392ab9e3d260afc67ad2d815137432986 authored over 11 years ago by Matt Zwier <[email protected]>

Change starting wallclock for methane tutorial

github.com/westpa/westpa - da46370dd6ce4f781b9595b8cd5fe53aadb09db1 authored over 11 years ago by Daniel Hatfield <[email protected]>

fixed bug with w_trace - actually a bug involved in west.states, specifically with representing a BasisState object as a numpy array

github.com/westpa/westpa - 4d0ba1b91a932ba005f6b777b9649c4abf1c4d6d authored over 11 years ago by Nick Rego <[email protected]>

some more unit tests for w_kinetics

github.com/westpa/westpa - 9665a5fbf26e8e0f6c3f013d1fa9053569640479 authored over 11 years ago by Nick Rego <[email protected]>

added some coordination unit tests for the zmq work manager to test n_workers functionality

github.com/westpa/westpa - 9317fdc82ee51ab621bef5cafc20030d932ef451 authored over 11 years ago by Nick Rego <[email protected]>

ZMQWorkManager (as server) can dynamically determine the number of active client nodes and total number of worker processes it's associated with; also added some appropriate unit tests

github.com/westpa/westpa - 959070311e67faeb921240d523e0f8f6713d276e authored over 11 years ago by Nick Rego <[email protected]>

w_assign sets number of workers to 1 if n_workers is 0 (possible for zeromq work manager to have a delay in counting workers on startup)

github.com/westpa/westpa - d5a442bbb18c892cc73107240417973bdb5f3726 authored over 11 years ago by Nick Rego <[email protected]>

Reworked w_assign to work in parallel and with same dsspec mechanism as

w_pdist. Split w_kinetics into w_kintrace (tracing analyses) and w_kinmat
(matrix analyses). w_ki...

github.com/westpa/westpa - facc567fb67c20177d3de02782d04003f3729f9d authored over 11 years ago by Matt Zwier <[email protected]>

Generalized handling of subcommands, synthetic datasets. Improved help.

github.com/westpa/westpa - af2b53812316ac530caeb4450f434273afd41b14 authored over 11 years ago by Matt Zwier <[email protected]>

small change to w_assign unit tests (to account for directly using n_workers attribute of work managers)

github.com/westpa/westpa - d1d2a51f625e4c592166eb02be4686c960e038cb authored over 11 years ago by Nick Rego <[email protected]>

after merge

github.com/westpa/westpa - 8a3e91bd8e877025b2c72f4bdd113b38c8b211e6 authored over 11 years ago by Nick Rego <[email protected]>

zmq work managers now accept a 4th endpoint for server-client listening socket; modified zmq unit tests to account for this

github.com/westpa/westpa - 74e054846120ae4538a3d05a7f118d1546f8c1a8 authored over 11 years ago by Nick Rego <[email protected]>

Updated to latest subrepo versions

github.com/westpa/westpa - 7a12262e85d68649eaee75f4b3869799b6c0a941 authored over 11 years ago by Matt Zwier <[email protected]>

Honor ``discard`` flag (whoops) on ``WMFuture.get_result()``

github.com/westpa/westpa - f7aa31f888fda4ea4c0f31295f10ba2701cf6396 authored over 11 years ago by Matt Zwier <[email protected]>

Fixed indexing bug in _assign.pyx

github.com/westpa/westpa - a4fb4462f6d9302737fe02a98437e3ca110433df authored over 11 years ago by Matt Zwier <[email protected]>

Modified w_assign to use plain n_workers attribute from work manager (now that SerialWorkManager specifies that attribute).

github.com/westpa/westpa - f017193ecd6446799dd3d33ffab189e8b8f98ff5 authored over 11 years ago by Matt Zwier <[email protected]>

Added ``n_workers`` attribute to serial work manager, and created a docstring on WorkManager (in core.py) to note that n_workers is a required attribute.

github.com/westpa/westpa - b411b39c6d109710ad843a5439f02d31b2642003 authored over 11 years ago by Matt Zwier <[email protected]>

Merging 3568b062d973 and dfc890b9f5c3

github.com/westpa/westpa - 7359efb8910913cf03c065f1dfb72a3228c087d5 authored over 11 years ago by Matt Zwier <[email protected]>

w_assign parallelization and some unit tests

github.com/westpa/westpa - a96316d917e1e5f9e87f8449f9de8624732d3136 authored over 11 years ago by Nick Rego <[email protected]>

w_assign should support parallelization (for now - for all work managers but zmq); most unit tests for w_assign set up

github.com/westpa/westpa - 1a79e8b372fb65015682d7a3b0bfde7cecb73832 authored over 11 years ago by Nick Rego <[email protected]>

Added bin link for w_pdist, generalized probability distribution function.

github.com/westpa/westpa - 7464e5f05633ebdc2ff5fbcae751e7df57b46ae1 authored over 11 years ago by Matt Zwier <[email protected]>

Changed data manager we_h5file to be an instance of h5io.WESTPAH5File, updated

west_tools and wwmgr.

github.com/westpa/westpa - e5d9237a640add47fddfb15f50e6e9ee42e74ec7 authored over 11 years ago by Matt Zwier <[email protected]>

Added option ``discard`` (defaulting to False) to WMFuture.get_result, so that

when used, a list of outstanding futures does not automatically turn into a
cache of results.

github.com/westpa/westpa - d2761328d1966bc75ddf9a466e75d6bd32c196f8 authored over 11 years ago by Matt Zwier <[email protected]>

Moved h5io and textio from westtools/ to westpa/ to avoid an import conflict

with data_manager.py. Fixed multiple problems with plothist, particularly for
3-D cases. Made DSS...

github.com/westpa/westpa - 83bf109718b3cad1d9266de127aede0311857ace authored over 11 years ago by Matt Zwier <[email protected]>

Working w_pdist for extracting probability distributions from arbitrary data sets.

Needs to be optimized for memory use.

github.com/westpa/westpa - 04d1da06c7a1ceaa37b98f3ad619500c6d6ce19d authored over 11 years ago by Matt Zwier <[email protected]>

added some test cases for west_tools (w_assign); assign_and_label method in _assign.pyx modified to allow slicing over a subset of the segments

github.com/westpa/westpa - 863979315a8781644f6fb0ca4a6b9c17b38df4a9 authored over 11 years ago by Nick Rego <[email protected]>

w_assign works if you don't specify macrostates (but subsequent analysis may require macrostates)

github.com/westpa/westpa - 89ef75065f25d246a59c0c221498e19312252f21 authored over 11 years ago by Nick Rego <[email protected]>

created unit test script for west_tools

github.com/westpa/westpa - 5124821a97d9b546e107002360684c12a863115c authored over 11 years ago by Nick Rego <[email protected]>

Copyied w_pcpdist.py to start w_pdist.py

github.com/westpa/westpa - edccbd45ad7d5b3d21f4e5208f3f24372853e595 authored over 11 years ago by Matt Zwier <[email protected]>

Updated west_tools

github.com/westpa/westpa - 7213eee0e5df4c25f7d8e17aa524da83d16d01a0 authored over 11 years ago by Matt Zwier <[email protected]>

Merging 76a57ac6fb2a

github.com/westpa/westpa - df45ee47b65b1b7668f8154beb375bd05926b9cd authored over 11 years ago by Matt Zwier <[email protected]>

Merging 064f09d534f9 (including west_tools)

github.com/westpa/westpa - 12b0a68cb836af3a52d6d93e2dbf99b80862fc53 authored over 11 years ago by Matt Zwier <[email protected]>

Merging c326331f3b0d

github.com/westpa/westpa - 8c7207981ff4251c58e7dacda3274a99aef2e6f4 authored over 11 years ago by Matt Zwier <[email protected]>

Updated west_tools

github.com/westpa/westpa - f85ca1f0057ebf3c1e4d9c8511f286575c3c945d authored over 11 years ago by Matt Zwier <[email protected]>

Allowed w_assign to run with 0, 2, or more macrostates. Resolves #30.

github.com/westpa/westpa - dae878a8de6b643c0f9d7b86f6e5852ad5bd8a95 authored over 11 years ago by Matt Zwier <[email protected]>

Fixed test suite so that it doesn't depend on testbinning (moved to tools)

github.com/westpa/westpa - d0764091c67a901fdeea4f38ec2ee2bde89e0fb5 authored over 11 years ago by Matt Zwier <[email protected]>

plothist: can add a plot title when plotting in 'evolution' mode

github.com/westpa/westpa - 5735f02cac54051f0b90252b4d905b407d5ef382 authored over 11 years ago by Nick Rego <[email protected]>

Updated west_tools and removed "executable" section from ODLD example west.cfg

github.com/westpa/westpa - 3a5b81e0eb617064165992d9c9822c17e7dacc76 authored over 11 years ago by Matt Zwier <[email protected]>

merge before push

github.com/westpa/westpa - 64821cc0bc6072d8a4a03fc6b6ee86de90e82cc1 authored over 11 years ago by Nick Rego <[email protected]>

Plothist plot options - title not mutually exclusive with log transformation, etc

github.com/westpa/westpa - d8f0d723e48b73fb849c736b63ed8c4c6c386503 authored over 11 years ago by Nick Rego <[email protected]>

Using more stable eigenvalue routine for kinetics analysis.

github.com/westpa/westpa - 1fdad69ab80158d165ef2c0ac95ee74667dfba05 authored over 11 years ago by Matt Zwier <[email protected]>

Added more .hgignore entries for methane/methane example (tip from Dan Hatfield)

github.com/westpa/westpa - cdc298d3584e6be078db40228b9cb1f05b6e029c authored over 11 years ago by Matt Zwier <[email protected]>

Merging 045437a0753d

github.com/westpa/westpa - 6f158e0755fcb0dfa158173570eb2700fccfa7dc authored over 11 years ago by Matt Zwier <[email protected]>

Updated west_tools to latest, added/removed links in bin/.

Removed w_edpdist and w_ttimes because they are being replaced with
w_assign/w_kinetics/w_kinavg....

github.com/westpa/westpa - 1e04bacdc60f667f13b2ba6223b2e485bde81106 authored over 11 years ago by Matt Zwier <[email protected]>

Merging in 753c07d3bfc7

github.com/westpa/westpa - 8f3bf8ac607c84757d91c753b118f5a67e3bec85 authored over 11 years ago by Matt Zwier <[email protected]>

New kinetics analysis working for equilibrium simulations

github.com/westpa/westpa - 1ff4c067c12df2ebc60ea21ae918a99aed2db64a authored over 11 years ago by Matt Zwier <[email protected]>

edited wording of zmq command line args

github.com/westpa/westpa - 2a33949dd301c2ffa8960d4d809d310642fff6fb authored over 11 years ago by Nick Rego <[email protected]>

Working kinetic averaging without error bars

github.com/westpa/westpa - 9eee6ec4521f769dc70725925e91648153b53205 authored over 11 years ago by Matt Zwier <[email protected]>

One-pass matrix and tracing kinetics analysis largely complete

github.com/westpa/westpa - 5885612e78d1319436dabb0d6b5311893858d2ca authored over 11 years ago by Matt Zwier <[email protected]>

Prototype state-to-state flux tracer in-line with matrix calculations

github.com/westpa/westpa - a7ea976165ed8453086a87e13b1a168ef0d49711 authored over 11 years ago by Matt Zwier <[email protected]>

Added plot title option to plothist.py

github.com/westpa/westpa - 63563d899e0ea9cbffd6d6ef0f5248948a5d2c8d authored over 11 years ago by Matt Zwier <[email protected]>

Bug-fix (#14): w_trace should now work

github.com/westpa/westpa - 81861554bfec76f3900e449caa3f7cf88798cb6e authored over 11 years ago by Nick Rego <[email protected]>

Updated to latest wwmgr (again)

github.com/westpa/westpa - 10400b7dc671267da65936817b3cfc483857e33f authored over 11 years ago by Matt Zwier <[email protected]>

Fixed broken MPI environment integration.

github.com/westpa/westpa - ee3c15a1a4c476edcac95af5d69dac335ca3c5ee authored over 11 years ago by Matt Zwier <[email protected]>

Updated to latest wwmgr

github.com/westpa/westpa - e05fa4ee782ec85ef2876b911774ca130defec96 authored over 11 years ago by Matt Zwier <[email protected]>

Merging a2300b91475a (MPI work manager)

github.com/westpa/westpa - 1bdf985b667fc0e304f4c9fae630297807888db2 authored over 11 years ago by Matt Zwier <[email protected]>

Removed another local env reference from ODLD example env.sh.

github.com/westpa/westpa - 944618a9e53a5dae87d902689dd4f937c3e99577 authored over 11 years ago by Matt Zwier <[email protected]>