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

Abstracted node-local workers for both master and node; tests pass.

ce25f1236f96d413cfe1a31a318d8773d2f1ab64 authored over 9 years ago by Matthew Zwier <[email protected]>

Merge pull request #8 from ASinanSaglam/yamlBranch

Yaml branch

fdc0378aecb5f1b1986237c3b170e91239867cd1 authored over 9 years ago by Matthew Zwier <[email protected]>

Removed initialization to avoid any ordering issues.

5e7fd3676e75431359afb661416d57a4f6fe20f2 authored over 9 years ago by Ali <boltzmann@Monoid.(none)>

Shifted around some code to avoid two classes

c2117fedfba7a5e45d980a9cc5c67c7c8358bffc authored over 9 years ago by Ali <boltzmann@Monoid.(none)>

Added the first commit of yaml tests

fe71f23c0d802540a6b44838b0b14de4d0a9c76d authored over 9 years ago by Ali <boltzmann@Monoid.(none)>

Failed startup timeouts set up, ZMQNode uses inproc

cbcc0537d38404d705f1947399c94d746591e315 authored over 9 years ago by Matthew Zwier <[email protected]>

Fixed a small bug when printing out the 'only system driver' case.

cacfd32ddfeef9d8293aad55068b648d7b9ce358 authored over 9 years ago by Ali <boltzmann@Monoid.(none)>

Now tells you if the system was only built off of system driver.

c58d33f041abca711ef4b02b54e7bd74c8db0b4d authored over 9 years ago by Ali <boltzmann@Monoid.(none)>

Added more verbose options, logging of each option and printing of update/create status of YAML options.

9d2034aa38ded7554eaef286b6de17e4cca726d5 authored over 9 years ago by Ali <boltzmann@Monoid.(none)>

Corrected normalization factor.

9e8c73f891622ae53e248e989d97c03878ee9763 authored over 9 years ago by ajpratt <[email protected]>

A ZMQNode class that appears to work.

c5f932047d426be9791b8db51f16df9c3c0d2953 authored over 9 years ago by Matthew Zwier <[email protected]>

Deleted outdated master.py (superseded by work manager itself)

08a7c2863c88989e5c1a942cfc2a159da624559d authored over 9 years ago by Matthew Zwier <[email protected]>

Cleaned up shutdown logic

d426ea987667c7186a79251c7d01e70a066a7c14 authored over 9 years ago by Matthew Zwier <[email protected]>

Cleanup of code.

f82e6a568507273e31ca8c47599c879199bb5817 authored over 9 years ago by ajpratt <[email protected]>

Moved the initialization earlier to avoid overwriting YAML settings

d86c80cfc8ddca0734e75bb2392b95c6c7638afb authored over 9 years ago by Ali <boltzmann@Monoid.(none)>

Save flux as 'per tau', even if we calculate at the sub tau level.

0a3a24cf07d0d686fbf13a395a9f1d72a6cc5569 authored over 9 years ago by ajpratt <[email protected]>

Successfully cythoned iterating over the entire progress coordinate.

2af4cc1de3f33b49845546f3bdbbac610006078b authored over 9 years ago by ajpratt <[email protected]>

Fixed more bugs, YAMLSystem correctly initializes now.

95e6fe48df5b24989fc98fe9e5fcd20ca05bd12f authored over 9 years ago by Ali <boltzmann@Monoid.(none)>

Initial commit of adjustments to use full resolution.

4c5e4b1d2cc89a6f9c17cfdc231e8330b8fdcae3 authored over 9 years ago by ajpratt <[email protected]>

Removed some comments.

9ea24133b82c92d012c415365b146c8118b8c237 authored over 9 years ago by Ali <boltzmann@Monoid.(none)>

More bug squashing time.

f1544a2e86f775225dd3a93bac7b7ee154ca92b3 authored over 9 years ago by Ali <boltzmann@Monoid.(none)>

Squashed some bugs after edge case tests (and some embarassing errors).

cec2b570cb1c4bde19e9e5d52b92183fe05d0737 authored over 9 years ago by Ali <boltzmann@Monoid.(none)>

Mostly finished YAML system builder. Rewrote most of the initial code, added some error handling.

a3f5fbbb96b95c6b992875f565c77063dbccd50b authored over 9 years ago by Ali <boltzmann@Monoid.(none)>

More speed/reliability fixes

fd0dae2b858436c68752f5bf7fc6d829a9f92d80 authored over 9 years ago by Matthew Zwier <[email protected]>

Merge pull request #6 from westpa/ed_kinetics

Event Duration Kinetics Pull Request, merged.

6b4bf330df51205c7dc1a1e3d63d0ca5c1854604 authored over 9 years ago by Adam J. Pratt <[email protected]>

ZMQ WM passes all standard test, but performance is poor

7f02da7af116fbde4d4d6c8d109f68f4b6473496 authored over 9 years ago by Matthew Zwier <[email protected]>

Proper startup sequence for manager, worker, executor

638da8dc0559d7544139642e5d3d9bf67d3c2988 authored over 9 years ago by Matthew Zwier <[email protected]>

Worker can round-trip tasks and kill hung processes

7121060676b10d4fb697db90d7d3644f6424cce6 authored over 9 years ago by Matthew Zwier <[email protected]>

Deleted accidentally added file.

f56958df432357cf5f4f9fe3d4c8253b506fd25a authored over 9 years ago by kenjita <[email protected]>

Slight modification to functions.

640c71cc53be25bccbb109443d153babaca74ce9 authored over 9 years ago by kenjita <[email protected]>

Minimal working master/work manager

cf09babc29dbf1e3027faa863b13ac5abf29b458 authored over 9 years ago by Matthew Zwier <[email protected]>

About to merge ZMQMaster and ZMQWorkManager

66cb49b54d7f99a911b77a93ddd76591451126e9 authored over 9 years ago by Matthew Zwier <[email protected]>

Restructured tests

b9c729861f1f8bd5750039f443fe95e9da56d6e4 authored over 9 years ago by Matthew Zwier <[email protected]>

wip

2135ea7920b2c32b76feecc32be3863c8e7f4ecd authored over 9 years ago by Matthew Zwier <[email protected]>

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30c54719ee5d875596a9fa8e1fada215309afd5a authored over 9 years ago by Matthew Zwier <[email protected]>

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54476b005a9634c253c782a47d4c809126c96cbf authored over 9 years ago by Matthew Zwier <[email protected]>

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4a5637d3f9c71af4e5226e610fb286de033b0d94 authored over 9 years ago by Matthew Zwier <[email protected]>

added .gitignore

503ed825e312a17fb02d623132d724cf457a4d4d authored over 9 years ago by Matthew Zwier <[email protected]>

wip

191743a0d2a840ffee3d78e923510901fc13ae3b authored over 9 years ago by Matthew Zwier <[email protected]>

Added in state_labels.

40fb6417343c5d636d80d2966188d57903b181cf authored over 9 years ago by kenjita <[email protected]>

Temp hack to get stuff working on the direct trace.

87cd351685a8d7c84a5e16a39522033c1f574396 authored over 9 years ago by kenjita <[email protected]>

Staging in my edits to w_multi_kin.py.

f9659216fa57a84c867e1b584080b3117a279011 authored over 9 years ago by kenjita <[email protected]>

First commit of w_multi_kin.py

22510ea009105b5a4756152cf8997f241dfe7288 authored over 9 years ago by Lewis Baker <[email protected]>

Added in functions which should generalise the current routine in the tool built by Lewis Baker.

0151c4580e721faba687458185bc1b3630601d3d authored over 9 years ago by kenjita <[email protected]>

Beginning of function to average generic datasets.

611cecd1f71a8fd49d6d57b3c6c26855918e7041 authored over 9 years ago by [email protected] <[email protected]>

Initial commit of multitool, a suite of tools designed for

averaging together multiple weighted ensemble simulations.

9b05cfa2ae042f534a9a7c3fd9f18fe662e176bf authored over 9 years ago by kenjita <[email protected]>

wip

f2b673d88a5e42c1960d7855091a1d260a912bc2 authored over 9 years ago by Matthew Zwier <[email protected]>

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821f5c7fa475b17e0d8496dc010574de11c5e473 authored over 9 years ago by Matthew Zwier <[email protected]>

Modified w_eddist.py to fix binning issue.

Lower boundary would adjust itself by small increments
such that it was unable to run in the case...

13f50df9bdaa09cd7b2f8929ceee476188eb8b69 authored over 9 years ago by Adam J. Pratt <[email protected]>

Finished modifying it such that _kinetics.pyx uses a second counter

to determine the event duration time. Modified the
_fast_transition_copy function such that it c...

6e5f4cc6074946275e0931a3dc1c8e87817e01d3 authored over 9 years ago by Adam J. Pratt <[email protected]>

Added docstrings for _kinetics.pyx

8487d60782e4216cbf9527046c8b60fa2073eb1b authored over 9 years ago by Adam J. Pratt <[email protected]>

Added in logic to w_assign to create assignment dataset

which shows what macrostate you are currently in, ignoring
what state you were last in.

1d48be81a86c7ecc45910c7899f2338205476a55 authored over 9 years ago by Adam J. Pratt <[email protected]>

Initial modifications to add in dataset which tracks macrostate changes.

67064aba9fde84d3d9c2a4080f7de283b1cec8bb authored over 9 years ago by Adam J. Pratt <[email protected]>

wip

3e05637862a351a2f3d3bef21e767e751c677e6f authored over 9 years ago by Matthew Zwier <[email protected]>

wip

1ab12904bbe289f28e79cb38c0b1ae6298918c0d authored over 9 years ago by Matthew Zwier <[email protected]>

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59003a0b700db2469da255c3b03d42ae7c0fd9ed authored over 9 years ago by Matthew Zwier <[email protected]>

Moving old ZMQ WM out of the way.

a69c4f41b9cc9455d3a2985df88a0267fe6b3693 authored over 9 years ago by Matthew Zwier <[email protected]>

Add checks to w_postanalysis_matrix

- Fail if attempt to run with recycling simulation
- Fail if using assignment file generated from...

8dd43887a3104dc3ba20e4defc64a0ace249ea8f authored over 9 years ago by Joshua L. Adelman <[email protected]>

Removed special logical branch in postanalysis reweighting for simulations run with and without color in bin space

d479cd53033e73afad612d572b0698fd3659ee50 authored over 9 years ago by Joshua L. Adelman <[email protected]>

Working commit

89e5f5f195851b6542fc485d608d84b8a35f4645 authored over 9 years ago by Joshua L. Adelman <[email protected]>

Merge pull request #14 from westpa/remove-readlink-jla

Force users to explicitly set WEST_ROOT in examples

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d90773b4bd3ed017025441a355fe43ec790b2e04 authored over 9 years ago by Joshua Adelman <[email protected]>

Cleaned the code a bit, changed a few names around and added bin reading support.

6f03a873c04c9ac00561dcf3cdaf5291b202e3c4 authored over 9 years ago by Ali <boltzmann@Monoid.(none)>

A working prototype! A bit ugly but works.

3fcbbe956d4c3b1c3f347935ed8c0ed9862e1fbf authored over 9 years ago by Ali <boltzmann@Monoid.(none)>

You raise errors not return them.

9a609c7d72a3646c8516d346992f4f5edd6c0fd8 authored over 9 years ago by Ali <boltzmann@Monoid.(none)>

Updated the code to actually make some sense (not really).

fbb4bfcebc2a5de1da589be0f0056ba87410591d authored over 9 years ago by Ali <boltzmann@Monoid.(none)>

First commit for the YAML system builder. The initial bit of code added, need to further think about how to implement.

b36c16e28321104356c380f50988590517b4941e authored over 9 years ago by Ali <boltzmann@Monoid.(none)>

Progress on cleaning up post-analysis reweighting tools

ec224fc19223c7ae95590382793a5997bb88ff74 authored over 9 years ago by Joshua L. Adelman <[email protected]>

Change examples so user explicitly sets WEST_ROOT

Former-commit-id: 0ad979882f018eba02e3971e9e2545a3e8761ce8

0b65ddd5232a090806e2121a39425bc289bb6a2c authored almost 10 years ago by Joshua Adelman <[email protected]>

Merge pull request #13 from westpa/clarify-truncate-jla

Add warning to w_truncate to remove corresponding file-system data

Former-commit-id: 79dcdd8110...

61c5c022b6be057834ad15dfd69302e475969a28 authored almost 10 years ago by Matthew Zwier <[email protected]>

Add warning to w_truncate to remove corresponding file-system data

Former-commit-id: ec374530fcefe80577f4c212baf3446e5839ec7e

9c6d011105864653f7dbd539a0cf0eb484a2d3c4 authored almost 10 years ago by Joshua Adelman <[email protected]>

Merge pull request #11 from KarlTDebiec/master

First steps towards sphinx documentation

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0c91ae380b18449922fd29b1b3db94d843ee58f8 authored almost 10 years ago by Karl T Debiec <[email protected]>

integrated most remaining wiki pages into sphinx

Former-commit-id: f1b31d7cff4001a6f0833acd28c63d2b89fd555f

3c857037ab9c323e9eff51855e2989a8b54a7ed2 authored almost 10 years ago by Karl Debiec <[email protected]>

added html version of documentation

Former-commit-id: 95bab7740754990a4480b288745c144514ba3bd4

f19d9951aa0582d610b6f9d7f7d82c1f32cc9cca authored almost 10 years ago by Karl Debiec <[email protected]>

initialzed sphinx documentation

Former-commit-id: 34381f779e6ef3e6cfb8dd6dee2081f18083e030

78ea14498b185082501e09c1ad40fc22f54ec480 authored almost 10 years ago by Karl Debiec <[email protected]>

Initial commit of post-analysis reweighting tools

d442edb24ee8dd5170db9f6ede82b1c0545f186a authored almost 10 years ago by Joshua L. Adelman <[email protected]>

Update README.rst

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5546502e1eb6e403bd3576ca48a5398aaf78fd3b authored almost 10 years ago by Lillian Chong <[email protected]>

Update README.rst

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95c5ad270c2c04efb1fb681855b217a31d231be7 authored almost 10 years ago by Lillian Chong <[email protected]>

Update README.rst

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3ef55fdd6c43e641c9c918940c1b2a90616b89c0 authored almost 10 years ago by Lillian Chong <[email protected]>

Update README.rst

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ebabcf434d5d0fff30f197c77bfaa520022aa07a authored almost 10 years ago by Lillian Chong <[email protected]>

Update README.rst

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f399f2b9ef88de0e7c30580949b42746bf9accdd authored almost 10 years ago by Lillian Chong <[email protected]>

Update README.rst

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f0f04fa131f9687090472f2731c760214a87fb2c authored almost 10 years ago by Lillian Chong <[email protected]>

Update README.rst

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85d18a27c5a28e47e6b2d5a67b1ac8931e603bfa authored almost 10 years ago by Lillian Chong <[email protected]>

Update README.rst

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65ed824b7468ba47956786ddfc46ed1aa2cad133 authored almost 10 years ago by Lillian Chong <[email protected]>

Update README.rst

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3f3b7aa8a7acec75050efbbe206fb9c16367d733 authored almost 10 years ago by Lillian Chong <[email protected]>

Rename README to README.rst

Former-commit-id: efc475c382d5c3039f9ec172dbdad5865bfba251

a099afe5938dd77321330908ca9abfe06004fa7b authored almost 10 years ago by Lillian Chong <[email protected]>

Update README

Former-commit-id: b6728085dff9deac2fb973bdfb87b8f00d873df7

ad000c3ed849ee373d74c875062dfe6b5ab4120d authored almost 10 years ago by Lillian Chong <[email protected]>

Update README

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36c93b93091579e63f2545948caab8673e61e510 authored almost 10 years ago by Lillian Chong <[email protected]>

Update README

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80c89319ac3db9e1111e64af87b42b829bc0b619 authored almost 10 years ago by Lillian Chong <[email protected]>

Updated README with citation

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644af33e56e361ac3dfadfda9ef5ed850af7157b authored almost 10 years ago by Matthew Zwier <[email protected]>

Merge pull request #10 from KarlTDebiec/master

Updated tutorials: replaced methane_gmx with nacl_gmx; updated nacl_amb and nacl_namd

Former-c...

710ee295ada19206c510edb7178de75d27f528c9 authored almost 10 years ago by Matthew Zwier <[email protected]>

updated nacl_namd tutorial; bound state corrected from second bin to first; progress coordinate, coordinates, and log are now correctly stored for frame 0 of each segment rather than starting at frame 1.

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f55f41bc5ed462488a0eeaaa21931acb49d6cee6 authored almost 10 years ago by Karl Debiec <[email protected]>

updated nacl_amb tutorial; bound state corrected from second bin to first; progress coordinate, coordinates, and log are now correctly stored for frame 0 of each segment rather than starting at frame 1.

Former-commit-id: b88b472e6d45a683a7456e274a542d3c83a5b735

5f897092bc741cbc3f591898c6553ec791358f13 authored almost 10 years ago by Karl Debiec <[email protected]>

updated nacl_gmx tutorial; log loader much cleaner

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d4b0c821128d4a868579e597b09127f17eb987dd authored almost 10 years ago by Karl Debiec <[email protected]>

updated nacl_namd tutorial to be more consistent with new nacl_gmx tutorial

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04a7565a43c6922b52c8863a4b1e1f0bfe3f49e1 authored almost 10 years ago by Karl Debiec <[email protected]>

updated nacl_amb tutorial to be more consistent with new nacl_gmx tutorial

Former-commit-id: 250387c0335ab75cbc8346c767798aa0d7cc14bf

c5a8ea9aae7a03ceea5f02a9d0cfe7d2c83e6908 authored almost 10 years ago by Karl Debiec <[email protected]>

removed methane_gmx tutorial

Former-commit-id: 931f35e14dc7474ffbb76dca55cf20021ea440c8

14e6768cb541be6459e7833e7a307ac1292f259e authored almost 10 years ago by Karl Debiec <[email protected]>

added nacl_gmx tutorial; consistent with nacl_amb and nacl_namd tutorials

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d166afabf92123f3d5bb01140b7fd34bba52daee authored almost 10 years ago by Karl Debiec <[email protected]>

Merge pull request #9 from KarlTDebiec/master

Updates and revisions to nacl_amb and nacl_namd tutorials

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cfce935e371227b1850197fcc1b71b260224f365 authored about 10 years ago by Matthew Zwier <[email protected]>

updates to nacl_namd tutorial

Former-commit-id: 825ad99a5a4ce4a5e18216cea71b632736725ff7

50d0d6581660dd63743c954c4dac259a836f1337 authored about 10 years ago by Karl Debiec <[email protected]>

Major updates and revisions to nacl_amb tutorial

Former-commit-id: a52b4981bd6f288272a4ef708d339eb86df22b7e

16775003bca7d323fa16cb9a75bfca6aa0e8b6ef authored about 10 years ago by Karl Debiec <[email protected]>