Ecosyste.ms: OpenCollective

An open API service for software projects hosted on Open Collective.

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

Updated overview pdf in master branch

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github.com/westpa/westpa - 91466a7f9f373cd77b629e005f3aa25e979baac7 authored over 7 years ago by ASinanSaglam <[email protected]>
Merge pull request #55 from ASinanSaglam/master

Installation instructions update

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github.com/westpa/westpa - 58e1790cc6976dc8d54d5779065a7bbd347d0da3 authored over 7 years ago by Lillian Chong <[email protected]>
Small formatting fix for installation instructions

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github.com/westpa/westpa - d7384e7f3507260a7a6f7fbef688469e61c4bc74 authored over 7 years ago by ASinanSaglam <[email protected]>
Updated readme and documentation landing page installation instructions

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github.com/westpa/westpa - ac4fff186b17fdde9e1695fda015b8f3de34ef81 authored over 7 years ago by ASinanSaglam <[email protected]>
Some changes to make the reweighting estimator return bin populations.

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github.com/westpa/westpa - c1f9626c836fa46df53f81726401d7c74a3ece85 authored over 7 years ago by Adam Pratt <[email protected]>
Ticked up to 1.0B. Seems more or less complete.

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github.com/westpa/westpa - e956a9003a23a58a7f826701da080707b90d5e7e authored over 7 years ago by Adam Pratt <[email protected]>
Extra arguments are now sorted before hashing, ensuring that the order isn't important.

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github.com/westpa/westpa - 6217c083de05e91092c2638abf3c539eba444bac authored over 7 years ago by Adam Pratt <[email protected]>
More adjustments.

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github.com/westpa/westpa - f2342cd740b44685fbece4fcbaea061a5be63c96 authored over 7 years ago by Adam Pratt <[email protected]>
Fixes to the rerun logic; the hash for the assignment file is now part of the hash for the reweight/direct files, so that they can automatically determine if the assignment file is different.

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github.com/westpa/westpa - 5030474fe938ae1ac4d56eab259e5c5ed2ba8f7d authored over 7 years ago by Adam Pratt <[email protected]>
Fixed hashing function, I think.

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github.com/westpa/westpa - a8ba8053a43d9b1fe4d724c6e91214bbfb7ff01f authored over 7 years ago by Adam Pratt <[email protected]>
Merge pull request #53 from ASinanSaglam/master

Quickstart guide, Chignolin tutorial and a few more changes

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github.com/westpa/westpa - 8db36ba15b9cf050c8bc450d14d293c65d939467 authored over 7 years ago by Lillian Chong <[email protected]>
Fixed chinolin png files

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github.com/westpa/westpa - 47d48ce50b70641022f77052edf8d4fe2ec7ac95 authored over 7 years ago by ASinanSaglam <[email protected]>
Fixed header markup

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github.com/westpa/westpa - a293261c8a41663204cffc09732963629b1e574c authored over 7 years ago by ASinanSaglam <[email protected]>
Removed bits of latex markup

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github.com/westpa/westpa - 1294e05fe91d291b4fb6627ac54549643e899fe3 authored over 7 years ago by ASinanSaglam <[email protected]>
Added Chignolin tutorial, quickstart guide and updated the documentation building a bit

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github.com/westpa/westpa - fae17defe37dedcea67539c8c271ccbfd2f6dc8e authored over 7 years ago by ASinanSaglam <[email protected]>
Added westtools to autodoc API

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github.com/westpa/westpa - a410e7d9dbd0524b150e7f229ccde7aac66e6c13 authored over 7 years ago by ASinanSaglam <[email protected]>
Merge pull request #51 from ASinanSaglam/master

Minor subheader mismatch fix and an auto generated API test

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github.com/westpa/westpa - 0e0aafa82a46d242a44d9a773564fbce03470cf6 authored over 7 years ago by Lillian Chong <[email protected]>
Changed what's loaded in API test

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github.com/westpa/westpa - 898e7154bca04c240f1a78e567f931ac0a59d4f1 authored over 7 years ago by ASinanSaglam <[email protected]>
Trying to add __all__ to modules

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github.com/westpa/westpa - 6792438101e8f08909f1d995e9535202eafc486d authored over 7 years ago by ASinanSaglam <[email protected]>
Testing autodoc options

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github.com/westpa/westpa - 01c6df518477ec72c4718c3bff9811077c2f86f9 authored over 7 years ago by ASinanSaglam <[email protected]>
Separated modules, fixed some imports

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github.com/westpa/westpa - b0b798e60173a6d9c5dcdbd8a7ea5ec67d831a01 authored over 7 years ago by ASinanSaglam <[email protected]>
Added undoc members temporarily

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github.com/westpa/westpa - 587f076ebd28c27e9464a9d8a20efa9cc1075db2 authored over 7 years ago by ASinanSaglam <[email protected]>
Further API page testing

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github.com/westpa/westpa - cc24f4e3796439c12169a0dc890d6950b6b68dd6 authored over 7 years ago by ASinanSaglam <[email protected]>
Changed some sphinx defaults for autodoc

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github.com/westpa/westpa - 788a3dfe1eb3ce64cbbadf6bce8a092ed26f1d0f authored over 7 years ago by ASinanSaglam <[email protected]>
Added westpa to api test

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github.com/westpa/westpa - 857c3fb2cedf0389c45d432d2697624a10f7c378 authored over 7 years ago by ASinanSaglam <[email protected]>
Added westpa.rc to API test

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github.com/westpa/westpa - 3272976170608254f673ad24af3ee6f2194203cb authored over 7 years ago by ASinanSaglam <[email protected]>
Testing autodoc members option

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github.com/westpa/westpa - 0f10a4504b456344765de605d9a94339a7ade369 authored over 7 years ago by ASinanSaglam <[email protected]>
Further testing of the auto-api generation

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github.com/westpa/westpa - e068264985d0845309243a64c63009ea6358e81c authored over 7 years ago by ASinanSaglam <[email protected]>
Added some binning API to the test file

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github.com/westpa/westpa - 2539fc4f8be22813e0ee2b845b008c3610a7c7a1 authored over 7 years ago by ASinanSaglam <[email protected]>
Testing auto-api generation

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github.com/westpa/westpa - 2cbff2d8bb128010844ed8faf43014104359aec8 authored over 7 years ago by ASinanSaglam <[email protected]>
Fixed a subheader mismatch

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github.com/westpa/westpa - 4a502ca1c39b5967ba67960fa59f3e77dbe69d7e authored over 7 years ago by ASinanSaglam <[email protected]>
Merge pull request #49 from ASinanSaglam/master

Minor FAQ/tutorial changes, master pull request

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github.com/westpa/westpa - 28c21adad69ea03e4d07866cd010eee6775ba3d5 authored over 7 years ago by Lillian Chong <[email protected]>
Minor fix to FAQ question

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github.com/westpa/westpa - a6d44a1350e5d470e098be7b02e1f1417b50ca4c authored over 7 years ago by ASinanSaglam <[email protected]>
Added a new question to FAQ

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github.com/westpa/westpa - 98e49c704eda38851e8e6e93e9c6236027dd9888 authored over 7 years ago by ASinanSaglam <[email protected]>
Added tags to video tutorials, fixed a tutorial title

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github.com/westpa/westpa - 1b6fbcb693f7cbf29e4c9f1fc246f53ffb581f77 authored over 7 years ago by ASinanSaglam <[email protected]>
Merge pull request #47 from ASinanSaglam/master

Checklist/FAQ changes, master pull request

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github.com/westpa/westpa - aa2d3c1a399e48a5e9751d8288f70f8da3b794e1 authored over 7 years ago by Lillian Chong <[email protected]>
Minor checklist change

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github.com/westpa/westpa - b0d4a4ae06ffb496746a3346dd7d0ce4836751f8 authored over 7 years ago by ASinanSaglam <[email protected]>
Made some basic content changes

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github.com/westpa/westpa - a510ce16e271391ee3ff0bbe96ccf300d9559fdc authored over 7 years ago by ASinanSaglam <[email protected]>
Trying ways to add to sidebar automatically

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github.com/westpa/westpa - bed18c8595573975ec10e51e9d858810c105ca3e authored over 7 years ago by ASinanSaglam <[email protected]>
Cross-ref test

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github.com/westpa/westpa - bdbbd749d76f13ab227674c511b05775ac03fa51 authored over 7 years ago by ASinanSaglam <[email protected]>
Testing separate readme file

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github.com/westpa/westpa - a452d0f4aabd58f398f75323e0135c5965a1e239 authored over 7 years ago by ASinanSaglam <[email protected]>
Fixed links

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github.com/westpa/westpa - 7a0b76d98ea58be5f725d8e59d704b8b3a925446 authored over 7 years ago by ASinanSaglam <[email protected]>
Added faq/checklist links instead

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github.com/westpa/westpa - 3dc89756912ba221bb2ed8a2d6829c5ee4aebbca authored over 7 years ago by ASinanSaglam <[email protected]>
Trying other ways to link to FAQ and checklist

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github.com/westpa/westpa - ae948a2d82a3c2af16ef4eda496f35df4cedd0fa authored over 7 years ago by ASinanSaglam <[email protected]>
Added faq, changed position for checklist

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github.com/westpa/westpa - 012562a3c20c2dc4d86d9c928ecf4870320f5215 authored over 7 years ago by ASinanSaglam <[email protected]>
Hopefully fixed the hashing logic, printed output.

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github.com/westpa/westpa - e030143e9158bedd473b1eed96655fef15456460 authored over 7 years ago by Adam Pratt <[email protected]>
Overrode more operators for the WIPIDataset.

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github.com/westpa/westpa - 953d91268c6b3fe304859f55859a4225134e8b43 authored over 7 years ago by Adam Pratt <[email protected]>
Made names make more sense.

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github.com/westpa/westpa - c8930565f6109def4848bf0051fe4d960cb67125 authored over 7 years ago by Adam Pratt <[email protected]>
Fixed a sloppy edit.

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github.com/westpa/westpa - 98bebb9720dac96bbbe12b6ba4f6f58f666851c5 authored over 7 years ago by Adam Pratt <[email protected]>
Overrode math operators for gussied up numpy datasets.

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github.com/westpa/westpa - 1412db48d2def6d9ad9b1247ba05446e5eb2eba5 authored over 7 years ago by Adam Pratt <[email protected]>
Added debug mode, more fixes for hashing, can ignore hashes now (-ih/--ignore-hash)

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github.com/westpa/westpa - 9e0bd5fed82e13390f0007f2c6e07ffcbeac74a2 authored over 7 years ago by Adam Pratt <[email protected]>
Updated trace function to significantly increase speed.

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github.com/westpa/westpa - 8de767f5f2e31829c6024892b67f5992dd1e4233 authored over 7 years ago by Adam Pratt <[email protected]>
Plotting somewhat fixed.

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github.com/westpa/westpa - 7f2b993908af48094ce82e2e1864bc0aaab3fb1b authored over 7 years ago by Adam Pratt <[email protected]>
From last night.

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github.com/westpa/westpa - 61d5564074a861fbf72760827162ee358d8859ba authored over 7 years ago by Adam Pratt <[email protected]>
Can plot output from trace (not very pretty) in terminal. Needs more work.

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github.com/westpa/westpa - 8bdb50127a212523a3d8ece529012d79a7eaff0e authored over 7 years ago by Adam Pratt <[email protected]>
Moved a LOT of other functionality into westtools/wipi.py

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github.com/westpa/westpa - eeb2b5da314a2c7eb00c47e344b10bb3ea2545fe authored over 7 years ago by Adam Pratt <[email protected]>
Finished moving scheme functionality to own class; WIPI class now just has a few convenient properties for pulling the correct scheme information.

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github.com/westpa/westpa - b5f97131a0227f7e5452386354435e5fac2b3b19 authored over 7 years ago by Adam Pratt <[email protected]>
Moved some functionality, added in some headers.

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github.com/westpa/westpa - 0b6ef828903278bcf7ad6c47c07f1bf048e99443 authored over 7 years ago by Adam Pratt <[email protected]>
Slight cleanup; hiding more dictionaries.

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github.com/westpa/westpa - b799731b853b67564369a944387872dffca41be9 authored over 7 years ago by Adam Pratt <[email protected]>
Fixed plotting issues and hid more dictionaries.

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github.com/westpa/westpa - d5d972f26fe73758ff775e89cddec0e771996bf1 authored over 7 years ago by Adam Pratt <[email protected]>
Future now behaves like current/past; fixed more pointer issues.

Former-commit-id: a6186f3586fb74db1bc33bd9bea4663f29905c6d

github.com/westpa/westpa - 3546f90040d9563509180d51c32455b210073654 authored over 7 years ago by Adam Pratt <[email protected]>
Fixed pointers with custom datasets, and partial plotting support.

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github.com/westpa/westpa - cd81187b5ba90d86c875c159fc3f1b6a80cef439 authored over 7 years ago by Adam Pratt <[email protected]>
From last night.

Former-commit-id: d7984b2ba1a4c7c0d285b2937bee6a25ddec19c8

github.com/westpa/westpa - 3003c3031a5c5a9a20c43310eb675c8350c59a85 authored over 7 years ago by Adam Pratt <[email protected]>
More fun with attributes

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github.com/westpa/westpa - 7f1dac06d6b29f832bfe20965f9841fbafd5f88f authored over 7 years ago by Adam Pratt <[email protected]>
fixed dir issue; things now accessible as attributes and dictionary keys for direct/reweight in current/past properties.

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github.com/westpa/westpa - b0467dbe9fe183738e62947b009e2d3aede184e1 authored over 7 years ago by Adam Pratt <[email protected]>
Building in more consistent accessing routines.

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github.com/westpa/westpa - 0fbb64fee9ebf061d1cc5ff7c23d89590406101d authored over 7 years ago by Adam Pratt <[email protected]>
Fixed hashing, modifications to how kinetics are called (to update to new scheme).

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github.com/westpa/westpa - 5b3fb10d8f860a1c6fa74065b594091c7c7bfa24 authored over 7 years ago by Adam Pratt <[email protected]>
Added in hashing check for files to see if the state/bin/command line definitions have been changed to trigger an automatic reanalysis.

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github.com/westpa/westpa - cead7cb048c4d3976845ab93be85c5c98c9d6314 authored over 7 years ago by Adam Pratt <[email protected]>
Sorting functionality for subsampling...

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github.com/westpa/westpa - 13fa83171fcc388a4f6ee005f012376dcaf3aec5 authored over 7 years ago by Adam Pratt <[email protected]>
Merge branch 'wipython' of https://github.com/westpa/westpa into wipython

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github.com/westpa/westpa - 95f9da8479208a9d2fb628b27ace045acae1ce38 authored over 7 years ago by Adam Pratt <[email protected]>
Merge pull request #45 from westpa/master

Rebase w_ipa off master.

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github.com/westpa/westpa - 29bfdfdc01ac4e3e91234243ccd9a63b5af59f5a authored over 7 years ago by Adam J. Pratt <[email protected]>
Updated assignmention section in w_ipa to support 'extra' flags (for subsampling).

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github.com/westpa/westpa - 6335998e94eb0e080e66bd6b71ee9933e0d778a4 authored over 7 years ago by Adam Pratt <[email protected]>
Merge pull request #35 from westpa/west_tools_KineticsRewrite

West tools kinetics rewrite merged.

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github.com/westpa/westpa - f01e0410545d3295438911057cede8d59dbb5c1f authored over 7 years ago by Adam J. Pratt <[email protected]>
Updated/added copyright date/information to modified files.

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github.com/westpa/westpa - e0a43268b373ae2176fdab1da4053ea965df500b authored over 7 years ago by Adam Pratt <[email protected]>
Added link to overview from documentation

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github.com/westpa/westpa - 0abdff1927f7a8cb26996700a2d2ffe20f47ea94 authored over 7 years ago by ASinanSaglam <[email protected]>
Merge pull request #42 from ASinanSaglam/master

New overview page

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github.com/westpa/westpa - 8d2c6bde56b751bf69e8c68d9c36cdc97e05ac84 authored over 7 years ago by Lillian Chong <[email protected]>
Re-cythoned _assign.pyx

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github.com/westpa/westpa - c984c7f7671deab4728c5d1495789dea8b184c94 authored over 7 years ago by Adam Pratt <[email protected]>
Merge branch 'west_tools_KineticsRewrite' into wipython

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github.com/westpa/westpa - f5dd03b8e2bc71f0cd8d2244f9c85d625617d2b4 authored over 7 years ago by Adam Pratt <[email protected]>
Fixed merge.

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github.com/westpa/westpa - 3fa984550833a17bdb126eabfe2fdc3b2b6f80dc authored over 7 years ago by Adam Pratt <[email protected]>
Updated help text on w_direct.

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github.com/westpa/westpa - 27539dedde17cd44d753b06a91484fe9fa2772ed authored over 7 years ago by Adam Pratt <[email protected]>
Made correlation/bootstrap optional on w_fluxanl.

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github.com/westpa/westpa - 71690124c306ccf36456cdb0a48aa31a6d0353da authored over 7 years ago by Adam Pratt <[email protected]>
Removed errant print statement.

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github.com/westpa/westpa - c8dea15b64b1633a07d1af7878567e5879dce816 authored over 7 years ago by Adam Pratt <[email protected]>
Updated ploterr to plot color/ensemble probabilities, and to support both w_direct and w_reweight.

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github.com/westpa/westpa - b3ced5f6933253d8a49df1ffc58bc1b437f20a57 authored over 7 years ago by Adam Pratt <[email protected]>
Finished removing old rate estimator from Cython and replaced it with current; changed references in w_direct and westpa/__init__ accordingly.

Former-commit-id: 70842ea63b0266a68f64575829e0ff0b6be05caf

github.com/westpa/westpa - 1016f29be710dc683caa053a8dca8c4015e4daec authored over 7 years ago by Adam Pratt <[email protected]>
Added in stubs to w_postanalysis_{reweight/matrix} to ease transition from old toolkit model to new one.

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github.com/westpa/westpa - 6860f2d82446f87ebdad8a94536f8a4d9e85c4b0 authored over 7 years ago by Adam Pratt <[email protected]>
Changed the order of subcommands.

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github.com/westpa/westpa - 9f6a4dc45343cc706e6cca16dd7028960c2f1bae authored over 7 years ago by Adam Pratt <[email protected]>
Changed subcommand values and seriously altered docstring text for w_reweight.

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github.com/westpa/westpa - f4ed1b1604555ac8ce9c782aae706d7f30c6768c authored over 7 years ago by Adam Pratt <[email protected]>
Removed indentation from pi.

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github.com/westpa/westpa - 73c63728d975374175e8fc0e284c250f5af00f40 authored over 7 years ago by Adam Pratt <[email protected]>
More updates on docstrings and help.

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github.com/westpa/westpa - 64926b24956d52cdaf960a117ea4a7f9c29bc867 authored over 7 years ago by Adam Pratt <[email protected]>
Moved lib/west_tools/westpa/kintool.py to lib/west_tools/westtools/kinetics_tool.py

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github.com/westpa/westpa - 82713ffa1d925175eb90e50b48c8cc9f860064d4 authored over 7 years ago by Adam Pratt <[email protected]>
Fixed more imports and headers.

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github.com/westpa/westpa - f8c7fa8ac869d01dcf8602e8d560979f6c931ca8 authored over 7 years ago by Adam Pratt <[email protected]>
Fixed a lot of docstrings in w_direct, and fixed the progress indicator (finally).

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github.com/westpa/westpa - 847ff9056372212f18ec2e4b100c9fa812b4fa72 authored over 7 years ago by Adam Pratt <[email protected]>
Renamed WESTKinAvg to WESTKineticsBase, cleaned up imports for old w_kinetics.

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github.com/westpa/westpa - e5e36433968b7be9d9de8909fd832f49fcd616f6 authored over 7 years ago by Adam Pratt <[email protected]>
Moved arguments to their respective classes; matrix and kinetics no longer have bootstrapping option flags.

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github.com/westpa/westpa - 87c9e2d5a5a954be5cbf4c1c931378a423341ebe authored over 7 years ago by Adam Pratt <[email protected]>
Fixed argument parsing in reweight code.

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github.com/westpa/westpa - ad7f5f6080603ffab163262eac662a529a84660a authored over 7 years ago by Adam Pratt <[email protected]>
Bootstrap for evolution datasets is now optional, but on by default.

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github.com/westpa/westpa - 83c60ad5f89444bc66377c7917761fc22f8335e8 authored over 7 years ago by Adam Pratt <[email protected]>
Ran notebook to add output.

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github.com/westpa/westpa - cb8d20157df0322092c403bea7177609feb28ab9 authored over 7 years ago by Adam Pratt <[email protected]>
Documented west.cfg for ODLD, and added example of jupyter notebook usage with w_jupyter.

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github.com/westpa/westpa - daf6844caf632d409c05cc974fa28c7ced6623ee authored over 7 years ago by Adam Pratt <[email protected]>
Merge pull request #37 from westpa/amber_nacl_fix

Fixed Amber Example

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github.com/westpa/westpa - 8103272edef11b37705a1b73a3e680a14f32020d authored over 7 years ago by Adam J. Pratt <[email protected]>
Merge pull request #40 from ajd98/master

Amber Na+/Cl- tutorial now specifies WE parameters via YAML rather than system.py

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github.com/westpa/westpa - 44ec765648052588c57a1bd9bf6722abfb78b0a6 authored over 7 years ago by Adam J. Pratt <[email protected]>