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

Updated west_tools

Former-commit-id: a811a943f0764b89169097741a6b3e8962792762

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

df08e576c61aa1453342db9193f6cda1a4714ffa authored over 11 years ago by Matt Zwier <[email protected]>

Updated copyright information

7f070b8c82339da427c7432b34a8404c34e25404 authored over 11 years ago by Matt Zwier <[email protected]>

Updated copyright information

022265eba84b05de6ec645b92ce54545b236b595 authored over 11 years ago by Matt Zwier <[email protected]>

Updated copyright information

Former-commit-id: 91887656bee0b3264e4eed44a284ce8cfb35cc14

266905f673ad34521e1c2a8257e965fa105bc393 authored over 11 years ago by Matt Zwier <[email protected]>

Modified README, removed AUTHORS

Former-commit-id: bb0ea17ab00c4d6edfaaebaa27d7433e28149387

fb383efc075bec98f73bf40a2ef3850147b68383 authored over 11 years ago by Matt Zwier <[email protected]>

Merging

Former-commit-id: d3d1517dffb8712036bc319e10d2d28c101a1b64

94f5f1d4476e4bd302589dbf38dc5b457845137a authored over 11 years ago by Matt Zwier <[email protected]>

Updated subrepos

Former-commit-id: 3a72509b73c3cb3568c5668a48761884a00d131a

79d735e55b83a4f9ba55d6d86dfe84600b2d39aa authored over 11 years ago by Matt Zwier <[email protected]>

Adding progress bar license info

4581d660dfe791aae803552a4fabae1a4158ecdc authored over 11 years ago by Matt Zwier <[email protected]>

Merging and updating subrepos

Former-commit-id: 05aa5dd32e7a3028f1ead1a4039d85d9abf811a9

a2fd72804a710b041b9225b10b3005f33f75be64 authored over 11 years ago by Matt Zwier <[email protected]>

Updates to use progress bar

5af1e7d4a1cf3b904322478b76e588caa2b897cc authored over 11 years ago by Matt Zwier <[email protected]>

Merging

d610ca3ff89a9dffa6454b8269a7f722f4583b52 authored over 11 years ago by Matt Zwier <[email protected]>

Merging

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.

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.

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...

c031aecc1f7f08bf677bdfe1cba61d28ffe17d1a authored over 11 years ago by Matt Zwier <[email protected]>

Added ``blessings`` subrepo to support progress bars

Former-commit-id: 5c64ffdfd27e1be564c48cbfe0e8b6bfa34b89cf

d6089bc6b168edcf99aaf3af5b9aa8af121f7568 authored over 11 years ago by Matt Zwier <[email protected]>

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

ce8cfbb95eb5e2bf0e188a5e36c7ccc3f5b83ae2 authored over 11 years ago by Matt Zwier <[email protected]>

Updating west_tools

Former-commit-id: 4b3a4223c6633160ff4d96ea27baada54ccfac22

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.

458be588572f70ec6f979bd3292d81b0d2d6c5bb authored over 11 years ago by Matt Zwier <[email protected]>

fixed a small bug with the zeromq server-client communication

0d9742765901ed8cafe3e446e890f4f7a380d204 authored over 11 years ago by Nick Rego <[email protected]>

Merging

d71b32cbf264f81fb8b88fd69975db5ecd8032c8 authored over 11 years ago by Matt Zwier <[email protected]>

Updated west_tools

Former-commit-id: c34d0c34a29c808a6ef8a02129cfb50319520b4f

393d1cbda46fb4a8eecad2666dfe3510a5ba8c4c authored over 11 years ago by Matt Zwier <[email protected]>

Revert an untested change to sink handling.

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

b8120d49809e51861c92552369b89118b1e94845 authored over 11 years ago by Nick Rego <[email protected]>

Merging

Former-commit-id: 3f0cba7277cc62c161af4974296d76427006e850

acb116016f94a6b45fbf006b788f5bda076894bd authored over 11 years ago by Matt Zwier <[email protected]>

Updated west_tools subrepo to latest

d4f1adcb5cd0a89f85c125ffee5017d56b3fc9c1 authored over 11 years ago by Matt Zwier <[email protected]>

Merging

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...

0c29fea9b5f1f65e86e197224998bb1061d8ac0c authored over 11 years ago by Matt Zwier <[email protected]>

Correction to NAMD NaCl tutorial init.sh

Former-commit-id: d82d1537e2ad76c6ef7f1fb857a51c40ef7a4021

c98512aa3c069dbef8c0d0b502edf05a15e38292 authored over 11 years ago by ktd3 <devnull@localhost>

NAMD NaCl tutorial example directory

Former-commit-id: 7cf521fe23d9b1a86edafd933a411d95873c4f4a

6d6e4eeb52f995890062e2303a3921de92e1cca5 authored over 11 years ago by ktd3 <devnull@localhost>

Na/Cl tutorial example directory

2e6d35791035e02f7d5345e60261fe211799106c authored over 11 years ago by Daniel Hatfield <[email protected]>

W_trace works with h5io

b67181da1bbdba7af0078f619ba9ee1f3f826339 authored over 11 years ago by Nick Rego <[email protected]>

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

72e7b14be85ba61d59242ae313c5bfd8fe6051d3 authored almost 12 years ago by Matt Zwier <[email protected]>

Merging again

cd8ec54be11b2c073e03bb236da49b02f8a7cbd2 authored almost 12 years ago by Matt Zwier <[email protected]>

Merging

cedcdac6e75d1cabf93da263330ba3f63313a9df authored almost 12 years ago by Matt Zwier <[email protected]>

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

d0530ef59d30ae65599319c3d8f2bcf4a40f6cdd authored almost 12 years ago by Matt Zwier <[email protected]>

Merging dbeb689ac093 and 49a9d08474ec

9417101cd4676e9dae27b053f2073ec9f1efd3d2 authored almost 12 years ago by Matt Zwier <[email protected]>

Merging f750d6047ae1 and 78d66a3e3f6e

fcb2ad53f33f604167f0d2f92bd9af74031556a1 authored almost 12 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.

0430a40f78b270c2edd827a3685298853614f374 authored almost 12 years ago by Matt Zwier <[email protected]>

Working parallel rate CI estimation for the matrix case.

0dbc282b466499e392927b9b1f683c29d9207c0f authored almost 12 years ago by Matt Zwier <[email protected]>

Working parallel rate averaging for the tracing method.

380d6cbb71bb6cd3e854c552414bb51c9fa2caed authored almost 12 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.

7497655c3233e41dea52837f3968e8d21578a143 authored almost 12 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

b3428ef392ab9e3d260afc67ad2d815137432986 authored almost 12 years ago by Matt Zwier <[email protected]>

Change starting wallclock for methane tutorial

da46370dd6ce4f781b9595b8cd5fe53aadb09db1 authored almost 12 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

4d0ba1b91a932ba005f6b777b9649c4abf1c4d6d authored almost 12 years ago by Nick Rego <[email protected]>

some more unit tests for w_kinetics

9665a5fbf26e8e0f6c3f013d1fa9053569640479 authored almost 12 years ago by Nick Rego <[email protected]>

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

9317fdc82ee51ab621bef5cafc20030d932ef451 authored almost 12 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

959070311e67faeb921240d523e0f8f6713d276e authored almost 12 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)

d5a442bbb18c892cc73107240417973bdb5f3726 authored almost 12 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...

facc567fb67c20177d3de02782d04003f3729f9d authored almost 12 years ago by Matt Zwier <[email protected]>

Generalized handling of subcommands, synthetic datasets. Improved help.

af2b53812316ac530caeb4450f434273afd41b14 authored almost 12 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)

d1d2a51f625e4c592166eb02be4686c960e038cb authored almost 12 years ago by Nick Rego <[email protected]>

after merge

8a3e91bd8e877025b2c72f4bdd113b38c8b211e6 authored almost 12 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

74e054846120ae4538a3d05a7f118d1546f8c1a8 authored almost 12 years ago by Nick Rego <[email protected]>

Updated to latest subrepo versions

7a12262e85d68649eaee75f4b3869799b6c0a941 authored almost 12 years ago by Matt Zwier <[email protected]>

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

f7aa31f888fda4ea4c0f31295f10ba2701cf6396 authored almost 12 years ago by Matt Zwier <[email protected]>

Fixed indexing bug in _assign.pyx

a4fb4462f6d9302737fe02a98437e3ca110433df authored almost 12 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).

f017193ecd6446799dd3d33ffab189e8b8f98ff5 authored almost 12 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.

b411b39c6d109710ad843a5439f02d31b2642003 authored almost 12 years ago by Matt Zwier <[email protected]>

Merging 3568b062d973 and dfc890b9f5c3

7359efb8910913cf03c065f1dfb72a3228c087d5 authored almost 12 years ago by Matt Zwier <[email protected]>

w_assign parallelization and some unit tests

a96316d917e1e5f9e87f8449f9de8624732d3136 authored almost 12 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

1a79e8b372fb65015682d7a3b0bfde7cecb73832 authored almost 12 years ago by Nick Rego <[email protected]>

Added bin link for w_pdist, generalized probability distribution function.

7464e5f05633ebdc2ff5fbcae751e7df57b46ae1 authored almost 12 years ago by Matt Zwier <[email protected]>

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

west_tools and wwmgr.

e5d9237a640add47fddfb15f50e6e9ee42e74ec7 authored almost 12 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.

d2761328d1966bc75ddf9a466e75d6bd32c196f8 authored almost 12 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...

83bf109718b3cad1d9266de127aede0311857ace authored almost 12 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.

04d1da06c7a1ceaa37b98f3ad619500c6d6ce19d authored almost 12 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

863979315a8781644f6fb0ca4a6b9c17b38df4a9 authored almost 12 years ago by Nick Rego <[email protected]>

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

89ef75065f25d246a59c0c221498e19312252f21 authored almost 12 years ago by Nick Rego <[email protected]>

created unit test script for west_tools

5124821a97d9b546e107002360684c12a863115c authored almost 12 years ago by Nick Rego <[email protected]>

Copyied w_pcpdist.py to start w_pdist.py

edccbd45ad7d5b3d21f4e5208f3f24372853e595 authored almost 12 years ago by Matt Zwier <[email protected]>

Updated west_tools

7213eee0e5df4c25f7d8e17aa524da83d16d01a0 authored almost 12 years ago by Matt Zwier <[email protected]>

Merging 76a57ac6fb2a

df45ee47b65b1b7668f8154beb375bd05926b9cd authored almost 12 years ago by Matt Zwier <[email protected]>

Merging 064f09d534f9 (including west_tools)

12b0a68cb836af3a52d6d93e2dbf99b80862fc53 authored almost 12 years ago by Matt Zwier <[email protected]>

Merging c326331f3b0d

8c7207981ff4251c58e7dacda3274a99aef2e6f4 authored almost 12 years ago by Matt Zwier <[email protected]>

Updated west_tools

f85ca1f0057ebf3c1e4d9c8511f286575c3c945d authored almost 12 years ago by Matt Zwier <[email protected]>

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

dae878a8de6b643c0f9d7b86f6e5852ad5bd8a95 authored almost 12 years ago by Matt Zwier <[email protected]>

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

d0764091c67a901fdeea4f38ec2ee2bde89e0fb5 authored almost 12 years ago by Matt Zwier <[email protected]>

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

5735f02cac54051f0b90252b4d905b407d5ef382 authored almost 12 years ago by Nick Rego <[email protected]>

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

3a5b81e0eb617064165992d9c9822c17e7dacc76 authored almost 12 years ago by Matt Zwier <[email protected]>

merge before push

64821cc0bc6072d8a4a03fc6b6ee86de90e82cc1 authored almost 12 years ago by Nick Rego <[email protected]>

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

d8f0d723e48b73fb849c736b63ed8c4c6c386503 authored almost 12 years ago by Nick Rego <[email protected]>

Using more stable eigenvalue routine for kinetics analysis.

1fdad69ab80158d165ef2c0ac95ee74667dfba05 authored almost 12 years ago by Matt Zwier <[email protected]>

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

cdc298d3584e6be078db40228b9cb1f05b6e029c authored almost 12 years ago by Matt Zwier <[email protected]>

Merging 045437a0753d

6f158e0755fcb0dfa158173570eb2700fccfa7dc authored almost 12 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....

1e04bacdc60f667f13b2ba6223b2e485bde81106 authored almost 12 years ago by Matt Zwier <[email protected]>

Merging in 753c07d3bfc7

8f3bf8ac607c84757d91c753b118f5a67e3bec85 authored almost 12 years ago by Matt Zwier <[email protected]>

New kinetics analysis working for equilibrium simulations

1ff4c067c12df2ebc60ea21ae918a99aed2db64a authored almost 12 years ago by Matt Zwier <[email protected]>

edited wording of zmq command line args

2a33949dd301c2ffa8960d4d809d310642fff6fb authored almost 12 years ago by Nick Rego <[email protected]>

Working kinetic averaging without error bars

9eee6ec4521f769dc70725925e91648153b53205 authored almost 12 years ago by Matt Zwier <[email protected]>

One-pass matrix and tracing kinetics analysis largely complete

5885612e78d1319436dabb0d6b5311893858d2ca authored almost 12 years ago by Matt Zwier <[email protected]>

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

a7ea976165ed8453086a87e13b1a168ef0d49711 authored almost 12 years ago by Matt Zwier <[email protected]>

Added plot title option to plothist.py

63563d899e0ea9cbffd6d6ef0f5248948a5d2c8d authored almost 12 years ago by Matt Zwier <[email protected]>

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

81861554bfec76f3900e449caa3f7cf88798cb6e authored almost 12 years ago by Nick Rego <[email protected]>

Updated to latest wwmgr (again)

10400b7dc671267da65936817b3cfc483857e33f authored almost 12 years ago by Matt Zwier <[email protected]>

Fixed broken MPI environment integration.

ee3c15a1a4c476edcac95af5d69dac335ca3c5ee authored almost 12 years ago by Matt Zwier <[email protected]>

Updated to latest wwmgr

e05fa4ee782ec85ef2876b911774ca130defec96 authored almost 12 years ago by Matt Zwier <[email protected]>

Merging a2300b91475a (MPI work manager)

1bdf985b667fc0e304f4c9fae630297807888db2 authored almost 12 years ago by Matt Zwier <[email protected]>

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

944618a9e53a5dae87d902689dd4f937c3e99577 authored almost 12 years ago by Matt Zwier <[email protected]>