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github.com/westpa/westpa

WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis
https://github.com/westpa/westpa

Updated README for wca dimer example

Former-commit-id: 843400289520f3052bb0f7eaff20ef114c7cb2d6

1b5ce0a56306208373261408aa06698f39e7c573 authored about 10 years ago by Joshua Adelman <[email protected]>
Merge pull request #8 from westpa/wca-dimer-jla

wca-dimer example system

Former-commit-id: 5d8ce55cd5463121e48eecb6875bf74544e8411c

1bf416f21b86c588f8e2e0fde1ad0a02612a7f62 authored about 10 years ago by Matthew Zwier <[email protected]>
Updated wca-dimer example to allow the use of the OpenMM CPU platform

Former-commit-id: aac14e9b39b6c874097c81f7bfd17a86df850f31

4c1fcda61274c1607eef835b9493fbedf6e6cf9f authored about 10 years ago by Joshua Adelman <[email protected]>
Added wca-dimer example system

Former-commit-id: 569528b9842f721e1727c5f80af7b51e7d1df805

f75d77f26cc8bed8645247e38ea2255ee120cf26 authored about 10 years ago by Joshua Adelman <[email protected]>
Merge pull request #1 from westpa/setup-jla

Modify setup.sh to allow updating of subcomponents

Former-commit-id: 2acb000e4b9b512a1cc98d988b...

9ab97c358b1a40ae5c73de7910dc66e0816d5df3 authored over 10 years ago by Matthew Zwier <[email protected]>
Modified setup.sh so that running will update lib repos

Former-commit-id: 54aa8847d8ea3eecb6c59e4d5e85b15fd4254190

ee5634e98aee454f6a86d3952fc9f67fa20e1566 authored over 10 years ago by Joshua L. Adelman <[email protected]>
Added a basic .gitignore

Former-commit-id: 57d4b3edc0ca944988da3fd605a2a0f90ce70e1a

fe55c952c23310883a6fd8a2d651085f5606b3e3 authored over 10 years ago by Matthew Zwier <[email protected]>
Updated setup.sh to auto-clone former hg subrepos

Former-commit-id: d83905dcced9724da2e2c811d1fa89081557cb05

8aa1c080c836de059805e8b10e86ac13b1c4d083 authored over 10 years ago by Matthew Zwier <[email protected]>
Added output of 'hg log' to aid in correlating old subrepo versions with .hgsubstate

06199824dbadd5e6ea184ac1f849339dff05e652 authored over 10 years ago by Matthew Zwier <[email protected]>
Added output of 'hg log' to aid in correlating old subrepo versions with .hgsubstate

15ac2534bb94c7386938192bd6d70dbf8401bf24 authored over 10 years ago by Matthew Zwier <[email protected]>
Added output of 'hg log' to aid in correlating old subrepo versions with .hgsubstate

Former-commit-id: 14bfa2982cf34d6c406fd614def23fe737cb2bec

5e8acc5087b46118cc577ef5df61cadbd15d9969 authored over 10 years ago by Matthew Zwier <[email protected]>
Added ability to overlay contour plot to plothist

6cb7abbaa00678ea98bf389105d366d47d399c73 authored over 10 years ago by ajamesonpratt <devnull@localhost>
Added ability to overlay contour plot to plothist

Former-commit-id: 62309354f489ee84e9cb6175cf4761694b1e1363

0652d54ecc77e8aada2506a24787cbd403e03376 authored over 10 years ago by ajamesonpratt <devnull@localhost>
refixed indent error in data_manager update_segments

Former-commit-id: e8876c9754dd3e5fff28a115bcba425f139ada7d

40e673bfe730dcf458c12934df4cd855239a28d6 authored over 11 years ago by Nick Rego <[email protected]>
Minor change to w_zmqrouter.py logging config

60ab484c4f3a73a401a270cb988ddcdb104ef03a authored over 11 years ago by Nick Rego <[email protected]>
Bumped west_tools

Former-commit-id: f225bbb6cd0fcce2c5a123d221e82960d442289c

e753542379d6d14f260752c08a1eee402a881c3a authored over 11 years ago by Matt Zwier <[email protected]>
Fixed bug #44: w_assign produces error when using RecursiveMapper

fc13f10f10c9ff640d39e99c86851f232092bc2a authored over 11 years ago by joshua.adelman <[email protected]>
Merge

Former-commit-id: 62356019f069d61c34323d54d0a577e984598ea5

04fa41c840cbe96f9f604f8f640003ab2b91d2b6 authored over 11 years ago by Matt Zwier <[email protected]>
Removed h5py subrepository as 2.2 contains required changes.

A custom h5py in lib/h5py will still be picked up and built if present.

Former-commit-id: 60910...

9199d84cbcd671ef309fa8c83ace23fb5a2bd9e7 authored over 11 years ago by Matt Zwier <[email protected]>
Updates to allow periodic flushing of HDF5 file instead of with every segment; might help speed things up on slow network FSs when segments return quickly.

Former-commit-id: 4dc7e7d57a9c82dda0ee486a89c658cd169da4ad

3da3db1b652f1bd7c8eb5d3ee6be6bf96308c90e authored over 11 years ago by Matt Zwier <[email protected]>
Fixed methane example not pointing to the right object for reweighting.

Former-commit-id: d3916c0713f1d2201aa5481000e36ce9f3fdb5d5

b0e991268780a22fe29991e9cd4df72d762f08f1 authored over 11 years ago by Asinan <devnull@localhost>
another push

c63fd59df0eeaf7d9e0fd60066cb666550a3946f authored over 11 years ago by Nick Rego <[email protected]>
change to dsspec class in eddist

af73be0692fe4a066a7b083734b094d7fdb9a62e authored over 11 years ago by Nick Rego <[email protected]>
progress indicator for w_eddist

fef6f0e60c3b431eb2404323b0aad4bbe4b6a18c authored over 11 years ago by Nick Rego <[email protected]>
added preliminary event duration distribution tool (used like w_pdist)

3ae27de218001190520218d80664842f4bcb8f86 authored over 11 years ago by Nick Rego <[email protected]>
added preliminary event duration distribution tool (used like w_pdist)

Former-commit-id: d81cf3a51d0dd15a8b2f0a4630a56d2480d79ac5

593224fda880d3f93a1fc792a819968a2294c9a6 authored over 11 years ago by Nick Rego <[email protected]>
Bumped west_tools

Former-commit-id: eb96bf6b730331a515e75e31ae464e4601422fc5

925ca94ce935090fbe20c92e31a5578b50cd4f35 authored over 11 years ago by joshua.adelman <[email protected]>
Fixed bug in w_kinavg in which the conditional flux evolution results were not being recorded to the .h5 file correctly

354c69bb9c6a1cf774d673cf3c47d5c183748a22 authored over 11 years ago by joshua.adelman <[email protected]>
Added ability to define a fractional window in cumulative evolution mode for w_kinavg

de1dcce86650d772f78bfd9a0f9de1bfb1c3bbf7 authored over 11 years ago by joshua.adelman <[email protected]>
Fixed indentation error in data_manager.py

Former-commit-id: 8e35cff40eb1dd6aeeffd5990552367c8fc3bb77

74a4bdb9d67ade4b4788dde24b7dc6e5c3c65bbc authored over 11 years ago by Matt Zwier <[email protected]>
Adjusted kinetics scripts (w_kinetics.py and _kinetics.pyx) to dump seg_id in kinetics.h5

Former-commit-id: 0c72b733c348eee1f4413cf145330d8db962d2da

69c32ab8cc6a6be8c5e9418360d0600acf172b76 authored over 11 years ago by ajamesonpratt <devnull@localhost>
Adjusted kinetics scripts (w_kinetics.py and _kinetics.pyx) to dump seg_id in kinetics.h5

98004697700a51f2491a88323d4958a8f8421115 authored over 11 years ago by ajamesonpratt <devnull@localhost>
west_tools bump to get updated correct multi-state tracing kinetics code

Former-commit-id: e264636b7a95f68c182856b299506acc4cad1cf5

2bb9d68ebd1521c57c7f0c3d15ea557dd848292e authored over 11 years ago by Matt Zwier <[email protected]>
Added pairwise factoring for multistate rate calculations.

f1280d99b2282698c5d6717088007dd36b5a89c6 authored over 11 years ago by Matt Zwier <[email protected]>
Added w_ntop link, bumped west_tools

Former-commit-id: e9f97666b7560a8209ea064720dc856166783c16

275f999980176653f819cd4a49b1cabe48a01b61 authored over 11 years ago by Matt Zwier <[email protected]>
Added w_ntop to select segments from bins.

Modified w_select to include weights for convenience.
Modified w_kinetics to support post-hoc ana...

b52e2b4be084d25713e847c7bf98f24811a80506 authored over 11 years ago by Matt Zwier <[email protected]>
bump

Former-commit-id: 589579f7c54b6e97a9b6363e1e128f20c7691229

47e1ef39065e71875358c5fc3fc02fbc9c9c0df4 authored over 11 years ago by Matt Zwier <[email protected]>
Merging cc3d6394acdd and 0a6c07c2e68c

32b58ae30de9ff5b3d3958505b63475a468294af authored over 11 years ago by Matt Zwier <[email protected]>
Merged ba7d0f0a769d and 03441bc289be

Former-commit-id: 825e7229a02ac5a46db5f53ed13dbecc89e3f13a

795f13820519367c2591d85ab47270071c4d677b authored over 11 years ago by Matt Zwier <[email protected]>
Bumped west_tools

Former-commit-id: c065eeb8456003aa59bc474ae8c4a40adaafe2cf

2fffc8d61967443a9083115ff262a95227ef0793 authored over 11 years ago by Matt Zwier <[email protected]>
Added support for simply skipping points that are out of range in fasthist

(and thus w_pdist), handy for conditional probability distribution plots.
Fixed Heisenbug in mult...

cd464ced20695d91ccac03c28f6bd06bb3119def authored over 11 years ago by Matt Zwier <[email protected]>
Changed algorithm for calculating accumulating statistics in _kinetics.pyx to improve numerical stability

a513a7f231ee00a2bf1970f1e7dc5478e79eebee authored over 11 years ago by joshua.adelman <[email protected]>
Removed outdated arg processing in w_crawl

02cfe6ea4b8a8c12e9ec713f30178a8fcbe54217 authored over 11 years ago by Matt Zwier <[email protected]>
Fixed performance regression in RecursiveBinMapper, added warning that w_kinetics matrix is experimental.

08fb9ef7d52d281011140e5f7c70554b8351639f authored over 11 years ago by Matt Zwier <[email protected]>
Merging ccef54debee0 and 86d7659599a8

db0f6ba2ae28df9334ff2e02719b4a0ab7879dfb authored over 11 years ago by Matt Zwier <[email protected]>
Changed all parallel tools to use submit_as_completed() instead of submit() to control RAM use. Activate by using --max-queue-length.

2d8e60ece83c4dacc73972268973c819d4376511 authored over 11 years ago by Matt Zwier <[email protected]>
Eliminated largely dead treewalker, eliminated west_tools package.

af6f2f562e5f6cccf0a1c5e9091be4038fe6d3c3 authored over 11 years ago by Matt Zwier <[email protected]>
Bumped west_tools

Former-commit-id: e9bc470b2ba8a35967ee388226f49fbd4ff35975

a75605feafcb5fd183a064a9c8622d709065c8b1 authored over 11 years ago by Matt Zwier <[email protected]>
Merging b95d61a6458d and 79f9259d02d0

58f6baf1eb2bb98c0228e35242ce53359a63f0ad authored over 11 years ago by Matt Zwier <[email protected]>
Fixed incorrect use of list vs dict in RecursiveBinMapper. Added unit test for

regression testing. Fixes #37.

0ff12c709043a97e5c86cccf25314a0b24f76dd9 authored over 11 years ago by Matt Zwier <[email protected]>
Fixed incorrect use of list vs dict in RecursiveBinMapper. Added unit test for

regression testing. Fixes #37.

Former-commit-id: dc9b7f69497d7dd4f9b7ca3aaf7edc0d798c8089

ca3b3c7cd87f155a463fc05536e974cf5b1c45ef authored over 11 years ago by Matt Zwier <[email protected]>
Modified the west script to make setting WEST_ROOT os agnostic

Former-commit-id: 3264caebb86446da6daa32cf47a295d589fbf55d

df2f9b856f623b9b7ffe979e45fee0d01b118896 authored over 11 years ago by joshua.adelman <[email protected]>
Merging 9a31a6449b63 and 79f9259d02d0

1197a461fd6a2529c4d780d5dd6ae64012c0d228 authored over 11 years ago by Matt Zwier <[email protected]>
Fixed minor plothist bug - plotting in instant mode no longer always plots the last iteration

1bce86172c6dc1334588887a8842a75a2c28c356 authored over 11 years ago by Nick Rego <[email protected]>
Minor modification to w_assign to support ZMQ work manager in dedicated

server mode.

0f8ea7877713896174759a04712b0e1996d0057e authored over 11 years ago by Matt Zwier <[email protected]>
west_tools bump

Former-commit-id: 394cdb0a8c390a9c9607069b863ae1c72c8785f1

66217bad4fbdb3596b0cded75ecd912577ab4f9b authored over 11 years ago by Matt Zwier <[email protected]>
Merging adff73e44247 and 6df9a9dca29c

8f8739bbf7276de17970018464a39b3aca65177b authored over 11 years ago by Matt Zwier <[email protected]>
Added option to suppress steady state population extrapolations in w_kinavg.

Modifications to support kinetics analysis on ancient (WEMD) HDF5 files.

29e6f124eacccacf987fdbbba1f236ac30f55c05 authored over 11 years ago by Matt Zwier <[email protected]>
merge

ac8ef3ef47b52b146b0a4b948a823c9d40333601 authored over 11 years ago by Nick Rego <[email protected]>
Fixed h5io bug in SingleSegDSSPEC's get_iter_data() method

96190b2f57eed0f1316da81bd97803e8634c9a1f authored over 11 years ago by Nick Rego <[email protected]>
Fixed bug in parsing dataset options in w_trace

ee537c950b33e6a6c42fc8215ce289cb56f98644 authored over 11 years ago by joshua.adelman <[email protected]>
Update to west_tools subrepo addressing issue #34 and issue #35

Former-commit-id: 0b33e9cae2f3b2bfce920bb85f2e18e0ac1731ad

448e7dd0c9bbf817c00098167306e6ae2e5a51b3 authored over 11 years ago by joshua.adelman <[email protected]>
Bug fix addressing issue #34 and issue #35; Uses new online statistics algorithm

to calculate mean and variance of flux and rate matrices, reducing the memory footprint of the ca...

211659fbd84861fa1d89369218efab51788fbae7 authored over 11 years ago by joshua.adelman <[email protected]>
Update of w_states.py to correctly run

Former-commit-id: 51798d6ddb8b4658de462312499b008c0327515d

e3e7ddf2cac068f7e296050737a770f8be76770a authored over 11 years ago by Adam P <[email protected]>
Updated copyright information

Former-commit-id: 241e66d9f8c16d09180f7ddb878234771316bf3f

ec4d3099ef58bb6060bade178c88cd79997af71a authored over 11 years ago by joshua.adelman <[email protected]>
Updated copyright information

56f737517e103dcb88a877e3521b43870ce6d258 authored over 11 years ago by joshua.adelman <[email protected]>
Fix for the instant 2d plot method of plothist

Former-commit-id: 1a3c52110cc29ca98ed90c96c6b94eedeb5b9c27

81669a486060136bfe9ee19d4ea9ce092d6d68e3 authored over 11 years ago by Adam P <[email protected]>
Fix for the instant 2d plotting mechanism of plothist

657a5d6341e7b32adb5f3ec88af738eb16ee3b6e authored over 11 years ago by Adam P <[email protected]>
Merging

Former-commit-id: a182ddfe853c69830499431f449c5babe99fc129

dea0084f40cde9b0e0c7b2d8c312706819f8449c authored over 11 years ago by Matt Zwier <[email protected]>
Bumped west_tools

Former-commit-id: 4201050412e931be7ca666ce2d0c23275c663c91

c1834d420a96b323f3ae057d8ecdffcba8c32729 authored over 11 years ago by Matt Zwier <[email protected]>
Added plot postprocess hook to plothist.py

9ace0d9311715bb1fea40aeed8fa50edf6d64862 authored over 11 years ago by Matt Zwier <[email protected]>
correction to nacl_namd tutorial

Former-commit-id: f512799faa4dd7e213aff2a4b1acc5460e5c8ca9

4a30ea5030caafa2eeb01c1884e7fe7fa3a1021d authored over 11 years ago by ktd3 <devnull@localhost>
Added try...finally wrapping for w_crawl that calls finalize(), modified

progress.py so that the cursor is only hidden in fancy mode.

90285a843ac406c5461481af8044b167102ef34b authored over 11 years ago by Matt Zwier <[email protected]>
Added link for w_crawl, bumped west_tools

Former-commit-id: eba291e047d81c85deb18ad713092f24ebf3affc

95cc8f02896feba208b823c9c6d2f445f56f67c4 authored over 11 years ago by Matt Zwier <[email protected]>
Added w_crawl, a simple general task coordinator for WESTPA data.

907160c0ad28e7084d51508af773bb17ee1e1f9f authored over 11 years ago by Matt Zwier <[email protected]>
Retooled w_select

d951dc20ec9205c85bdc17b3c7c579e2c415c62b authored over 11 years ago by Matt Zwier <[email protected]>
Modified trace routines to return number of transitions and w_kinetics to store.

b2041984284bd5cfe8816ece69248f825ccfc09c authored over 11 years ago by Matt Zwier <[email protected]>
west_tools bump

Former-commit-id: f3a3d0a5006a74a0cd4ba6394033cea254c033b0

fbb4f19ee9f8424e085f704253b4ce9ac9f413d4 authored over 11 years ago by Matt Zwier <[email protected]>
Corrected normalization for non-uniform bin widths in fasthist. Fixed UnboundLocal error in h5io.py.

db1d442f38b6b0d7691cd51d0a1b7d74e09f97b7 authored over 11 years ago by Matt Zwier <[email protected]>
Added OpenMM NaCl example

Former-commit-id: d0c841ad844a12e725c8fb552a2b2532fbb889c5

cccb14fc94ca1fec9cd9c40f863c389eab116ceb authored over 11 years ago by joshua.adelman <[email protected]>
Tweaks

8ee1370ac46819487f6abd272118900b576da728 authored over 11 years ago by Matt Zwier <[email protected]>
Tweaks

Former-commit-id: c8d42c277e3e0621e72b95770e32aa70f150cd60

b453654c30dab7532f4a3361306df0016b3e6a6c authored over 11 years ago by Matt Zwier <[email protected]>
Tweaks

6006439312222a0fe854390166a5551d2d2e8533 authored over 11 years ago by Matt Zwier <[email protected]>
Added link for w_stateprobs, updated west_tools

Former-commit-id: bd679f3f5475efdc6af4a3ededef80109406a1ca

0f4cfdb7adcfac578294a6317f4fe1a06be30c61 authored over 11 years ago by Matt Zwier <[email protected]>
Added support to w_assign to get bins from a YAML file.

Added support to w_kinetics and w_kinavg to report state-to-state fluxes as
well as rates.

513e7c5f984b8f21ed94127c4c97c079ddbd64b2 authored over 11 years ago by Matt Zwier <[email protected]>
Forced update of Cython files to fix mysterious inconsistency in _kinetics.c

e5577e5a64e48d3b498adbe82993258afc4eff86 authored over 11 years ago by Matt Zwier <[email protected]>
Added link for w_stateprobs

Former-commit-id: 5cbfed613cad817d417c86ebc19278f81751fdfa

e6718c6a30346a92aec4cc5f9061adf3c104750b authored over 11 years ago by Matt Zwier <[email protected]>
Added ``w_stateprobs`` tool (and corresponding plot mode to ``ploterr``) to

calculate block-bootstrapped macrostate populations (replaces ``w_binprobs``).

7c0c045fe9b202a09ca527f1beb6ae8d39d3d356 authored over 11 years ago by Matt Zwier <[email protected]>
Added link for ploterr

Former-commit-id: 56033643bc2567bc5090e88017b80e437cdb31d1

9c73c8ed3f8275cb0a2a2b0bb11103d899dc2d80 authored over 11 years ago by Matt Zwier <[email protected]>
Added new "ploterr" script to plot output of w_kinavg --evolution-mode.

0940a16107f9c4fdb12dc5205a7e442ffd189b3a authored over 11 years ago by Matt Zwier <[email protected]>
Merging

Former-commit-id: 19bd83d58f9547069bf7d25bec2f5b4f631507d6

ef459039f399d52ef6e5958961ed1f63209bd460 authored over 11 years ago by Matt Zwier <[email protected]>
Subrepo update

Former-commit-id: b22b7a13302f94d99371e2917e49a0f71c06af58

01ed93520be3109dace11255771ce082f15a7200 authored over 11 years ago by Matt Zwier <[email protected]>
Merging

fadf30bb0fb00da3cd65ee446910103a9333d1db authored over 11 years ago by Matt Zwier <[email protected]>
Subrepo update

Former-commit-id: f1d6b1ad32b0336607b6ef19351cc342f022f7bc

b9d9c74ef4932e7457d9095e9bc7246aa3490136 authored over 11 years ago by Matt Zwier <[email protected]>
Removed dangling UsesMCBS import

0dc3e223ce1c2728ffb71732e1749a9ef8dd22a2 authored over 11 years ago by Matt Zwier <[email protected]>
Updated west_tools (seen enough of these lately?)

Former-commit-id: 067bf9e7c9871378c9f3f8874fb990ee1e0eea73

4480de39ad35c8b276366167b3041724b920c936 authored over 11 years ago by Matt Zwier <[email protected]>
Reverted changes to _assign.pyx, changed to numpy buffer protocol

978704e1017cedd29490b7e2f0942e51eea09ce9 authored over 11 years ago by Matt Zwier <[email protected]>
Merging

Former-commit-id: 41c71f2741354328f40f18b656c852e1db78e4e9

ac01bc1e17d37988e18749591fab606e402f5e62 authored over 11 years ago by Matt Zwier <[email protected]>
And again

Former-commit-id: b325e1abba83e80fcd4057bec5be0cdda8a29c29

48304b8612f6a2b15b75aee76502ac2509f06bad authored over 11 years ago by Matt Zwier <[email protected]>
Merging

d6bab5abe7dc3dc4d9fcb60a4da2e51d52cb9e5e authored over 11 years ago by Matt Zwier <[email protected]>