Ecosyste.ms: OpenCollective

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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

Fixed broken link in README

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github.com/westpa/westpa - 9f95fc14da1034909542dfd68bde2da3b1641c75 authored over 7 years ago by ASinanSaglam <[email protected]>
Removed all links to chong.chem.pitt.edu domain

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github.com/westpa/westpa - 648a780b9f0440bc8d2cde615e12b5b4b9c2d58a authored over 7 years ago by ASinanSaglam <[email protected]>
Added hyperlink to new wishlist form

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github.com/westpa/westpa - 48ff4fe1071918ea48d2383c8017692e8d51fe68 authored over 7 years ago by ASinanSaglam <[email protected]>
Fixed scaling for trans matrix, error in mclib

All values output from the estimator for w_reweight are now properly
scaled by the subtau value,...

github.com/westpa/westpa - 250a83182dcfe8b141e18b27b40e70497c2ebbf0 authored almost 8 years ago by Adam Pratt <[email protected]>
Cleanup on w_reweight.

Removed extra code leftover from w_postanalysis_matrix and
w_postanalysis_reweight, as well as c...

github.com/westpa/westpa - 9d7702fb7619bf06466bc742aa4fea603cad2371 authored almost 8 years ago by Adam Pratt <[email protected]>
Fixed start at iter 1 bug w/ w_reweight.

The function accumulate_statistics did not work properly when starting
at any iteration than the...

github.com/westpa/westpa - cf0ea42358b3e52b542e170ceaa519503f2eb975 authored almost 8 years ago by Adam Pratt <[email protected]>
Most of the functionality now exists within the one tool, and it seems to be working (more or less). A lot of cleanup and organization remains, however.

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github.com/westpa/westpa - 848adaeffa9b1a67227fbf8c43df4c209ef7486f authored almost 8 years ago by Adam Pratt <[email protected]>
Fixed NaN problem.

Before, the presence of NaNs could wreak havoc on the correlation
analysis.
Now, we should be go...

github.com/westpa/westpa - 16d20b368839247c0572ca3adc09407705268d3b authored almost 8 years ago by Adam Pratt <[email protected]>
The pre-calculated dataset is done by mclib.

This should make things easier, as there's no longer a need to
pre-generate data within the actu...

github.com/westpa/westpa - 4d0e4078df08147d7228eb9e8091e4fcfa360b8f authored almost 8 years ago by Adam Pratt <[email protected]>
McLib now pre-generates the dataset.

You no longer have to pre-calculate your observable for determining
the correlation length, grea...

github.com/westpa/westpa - 534c72fa3e78af500328449fb93f9052f0d73bd9 authored almost 8 years ago by Adam Pratt <[email protected]>
Reweight mostly working.

Major changes: no longer any using non-Cython code for the estimator.
ISSUE: is the pre-calculat...

github.com/westpa/westpa - 547bbf4c687d7cd351aba4cc1b889e3a6db6da1e authored almost 8 years ago by Adam Pratt <[email protected]>
Fixed apparent merge issue.

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github.com/westpa/westpa - 96614c2dbb12e8433aba519ce8a42df99db7582c authored almost 8 years ago by Adam Pratt <[email protected]>
Switched to using python to generate westpa.sh after suggestion by @synapticarbors; properly exporting WEST_PYTHON in setup.sh. Sourcing the script should just work.

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github.com/westpa/westpa - 27ac6019318b0a46dc6f6ffde1d2df49a4752efe authored almost 8 years ago by Adam Pratt <[email protected]>
Modified setup.sh to find a specific python2.7, such that the value of the python WESTPA was installed with is hardcoded into the resulting script.

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github.com/westpa/westpa - ab94c841785bfc4247dbf35a1f000e6801914026 authored almost 8 years ago by Adam Pratt <[email protected]>
Modified readme, a bit.

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github.com/westpa/westpa - 9f6817d1b61a954c67823d078016cfabc3f33e07 authored almost 8 years ago by Adam Pratt <[email protected]>
Initial commit (a move from a different repo); a script that is created upon setup to make setting WESTPA variables on a machine easier.

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github.com/westpa/westpa - fb07fe77c78699eb0ee305380e94fdb74652e052 authored almost 8 years ago by Adam Pratt <[email protected]>
Lots of architectural changes, designed to clean up the workflow. Also, bootstrapping on the reweighted flux appears to work, thus far, meaning the changes are good. Lots more changes to make.

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github.com/westpa/westpa - c3fd27f9de807d1b6e4cb3e4ac58f6988473c3d0 authored almost 8 years ago by Adam Pratt <[email protected]>
Minor cleanup to w_reweight. It doesn't work yet, but it runs, the shims are there, and this prep was necessary to begin writing again.

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github.com/westpa/westpa - 1c6377fdab0bb4b5c5b075dadf5d671cea710381 authored almost 8 years ago by Adam Pratt <[email protected]>
Checking whether history works properly...

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github.com/westpa/westpa - cff633819e011337f425c7275154d35e885a0d39 authored almost 8 years ago by Adam Pratt <[email protected]>
Added in shortcuts to w_direct and w_reweight

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github.com/westpa/westpa - a9dac4274f71a859d455b88d007a1e93a9dcb62f authored almost 8 years ago by Adam Pratt <[email protected]>
Merge remote-tracking branch 'old_west_tools/KineticsRewrite' into west_tools_KineticsRewrite

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github.com/westpa/westpa - 44e402204268d5f850d18afbe65ddb729183595d authored almost 8 years ago by Matthew Zwier <[email protected]>
Merge remote-tracking branch 'old_west_tools/DEVELOPMENT' into west_tools_DEVELOPMENT

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github.com/westpa/westpa - 37308fcc0e454e1baa5d1c90f99f94dd8e3e9d7e authored almost 8 years ago by Matthew Zwier <[email protected]>
Moved west_tools stuff to lib/west_tools; updated setup.sh

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github.com/westpa/westpa - 3893c76a0bf7471adde4af740eb02e6119e941f8 authored almost 8 years ago by Matthew Zwier <[email protected]>
Merge remote-tracking branch 'old_west_tools/master'

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github.com/westpa/westpa - 4bbafa25729448d5b50213b4685722e39ee1f9b9 authored almost 8 years ago by Matthew Zwier <[email protected]>
Tinkering with old Mercurial records to avoid merge conflicts with west_tools

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github.com/westpa/westpa - 98ce46b3eaced41412e79e329f9930505ad35cc2 authored almost 8 years ago by Matthew Zwier <[email protected]>
Removed wwmgr fetch from setup.sh

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github.com/westpa/westpa - ae9755ea4a4bb9a026bef63c33c9b040087706ac authored almost 8 years ago by Matthew Zwier <[email protected]>
Moved wwmgr files to lib/wwmgr

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github.com/westpa/westpa - 33664ea51a1288334238dbd103d2ed90e0c71519 authored almost 8 years ago by Matthew Zwier <[email protected]>
Merge remote-tracking branch 'old_wwmgr/master'

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github.com/westpa/westpa - 715c8f9f6b9d7805f68238ebdf1eb9068cf1763d authored almost 8 years ago by Matthew Zwier <[email protected]>
Started moving things around to rewrite/wire the postanalysis toolkit in the same way that the direct trace code has been modified.

github.com/westpa/westpa - a6798d5bc6d84e0cfd33484428aeb1f8c43e400c authored almost 8 years ago by Adam Pratt <[email protected]>
More shims in place. Moved a lot of the functionality into a seperate tool class which tries to ease development of tools that interface with the mclib. The new reweighting code will be based heavily on this, as well.

github.com/westpa/westpa - a80686c32309bb77a673b05dcf3d462802521f38 authored almost 8 years ago by Adam Pratt <[email protected]>
Moved proper text from old w_kinetics to w_kinetics, instead of accidentally using the help from w_kinavg.

github.com/westpa/westpa - 9c3ef30dfa416dfdd1fefb8b53cf0df3e38b02e4 authored almost 8 years ago by Adam Pratt <[email protected]>
Finished altering w_kinetics as a shim for w_direct, as well.

github.com/westpa/westpa - ddfdeba6e26579a234a6908e7e7929ae0d197d64 authored almost 8 years ago by Adam Pratt <[email protected]>
Added in shim for w_kinavg. Should work more or less the same with 'trace', although I'd like to not necessarily need that behavior. We'll see how it sorts itself.

github.com/westpa/westpa - 3ef6e829bacedeefd807118ac0ae55b97e2f2235 authored almost 8 years ago by Adam Pratt <[email protected]>
Moved bulk of actual subcommand calculations into unique functions; go, when called on a subcommand, now merely calls the appropriate command. This allows for a subcommand to inherit from another subcommand, allowing us to override the go function to make unique calls. This allows for convenient batching of subcommands, such as when we simply want to run everything and call it a day.

github.com/westpa/westpa - a887290596c7632867369e4555616d076979772b authored almost 8 years ago by Adam Pratt <[email protected]>
Cleaning up some of the changes made in mclib. We want to send in two sets of data for each estimator: datasets which can and MUST be decimated for the subsampling procedure, and kwargs which may or may not include datasets (but definitely include estimator parameters), but ones which should NOT be decimated. Trying to formalize this.

github.com/westpa/westpa - d43ff8e0e4abb801d236b5f4e039f8b1a3a95bb9 authored almost 8 years ago by Adam Pratt <[email protected]>
Lots of changes. More streamlined and modular; more code moved into parent classes to allow tools to be written in an easier fashion. 'replace_dataset' functionality added into WESTPAH5 files. Generalized eval blocks for simple datasets and moved into mclib.

github.com/westpa/westpa - ed2a548134d76056441ebc3cb6afe8ea4c0c5fb1 authored almost 8 years ago by Adam Pratt <[email protected]>
Better framework established.

github.com/westpa/westpa - 203198827846b27068eb6e9434515097a918002f authored almost 8 years ago by Adam Pratt <[email protected]>
Moving calculations around and rewriting w_kinavg, w_kinetics, and w_stateprobs into w_direct. Standardizing the eval_block submission.

github.com/westpa/westpa - 5f9a0d69366d18108d52ea5b9b1ec2819f16a677 authored almost 8 years ago by Adam Pratt <[email protected]>
Initial work to get w_ipython to work within Jupyter notebook.

github.com/westpa/westpa - a99e6648fdaca70f69d67155053dbdccd91bf43a authored almost 8 years ago by Adam Pratt <[email protected]>
Fixed, a bit. And also added in color probs to the reweighting code.

github.com/westpa/westpa - 4e6531e98818bdbdb852348a44ed7f75d6cf96c8 authored almost 8 years ago by ajpratt <[email protected]>
Initial modification to support bootstrapping over color populations.

github.com/westpa/westpa - f27c280893c1deb88fa8ee8556a30398ced95385 authored almost 8 years ago by Adam Pratt <[email protected]>
Updated _rc.py to work with new error module; updated w_ipython to work with aux coordinates.

github.com/westpa/westpa - 32b9c614050736f943ea219f88e1f12e62c5afd9 authored about 8 years ago by Adam Pratt <[email protected]>
Added in support for new executable shell propagator. Will handle more explicit error checking.

github.com/westpa/westpa - 826ebca44f57d9e4f9d1c0dced70e36151a6f05d authored about 8 years ago by Adam Pratt <[email protected]>
Updated setup.sh to pull in updated work manager

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github.com/westpa/westpa - ddecc5058b6a308bc0bd804a78dc77f08191a490 authored about 8 years ago by Matthew Zwier <[email protected]>
Merge pull request #16 from westpa/split_merge

Done und done.

github.com/westpa/westpa - 1cb32ac2187ce2a9546553c46ee5ce12a5007df7 authored about 8 years ago by Adam J. Pratt <[email protected]>
Merge pull request #3 from mczwier/zmq-rewrite

Zmq rewrite tested in production for over a year. Merging now.

github.com/westpa/westpa - eac79a7d90f481548f829ae7053efefa05092711 authored about 8 years ago by Matthew Zwier <[email protected]>
Updated heartbeats to something more reasonable for loaded networks

github.com/westpa/westpa - c129fd6b62fe33391d40ea5ee56ee7e889876827 authored about 8 years ago by Matthew Zwier <[email protected]>
updated authors file

github.com/westpa/westpa - cd3d26a254b0000f573537d54f3733100da6b350 authored about 8 years ago by Matthew Zwier <[email protected]>
Deleted ancient mercurial remnants

github.com/westpa/westpa - e70062535d07009f0ffefdb12a8ba23f8d419fb0 authored about 8 years ago by Matthew Zwier <[email protected]>
Deleted deprecated w_zmqrouter.py

github.com/westpa/westpa - 4b0a8bfe68b695dd826b95334fe76aef42426550 authored about 8 years ago by Matthew Zwier <[email protected]>
Issue w/ kinavg getting 0 corrlen fixed.

github.com/westpa/westpa - 66c219222ae8e6e2e4eb085c8937595565ec34c4 authored about 8 years ago by ajpratt <[email protected]>
Merge pull request #15 from westpa/duration_time_fix

Fixed array bounds error that occasionally resulted in negative durat…

github.com/westpa/westpa - c2497ecd439b3d3770ed7d6155e4457d601cc61d authored about 8 years ago by Adam J. Pratt <[email protected]>
Fixed array bounds error that occasionally resulted in negative duration times with transitions out of unknown states; thanks also to Adam.

github.com/westpa/westpa - 7eb4bf78013ab2a70794c9ef6d82de28a35e7f35 authored about 8 years ago by Alex DeGrave <[email protected]>
Updated setup.sh

Made sure we're pulling in the correct, most up to date west_tools.

Former-commit-id: 87e6d7799...

github.com/westpa/westpa - cb4ca48d70c4ff2980a9cc8ebb5d21793cec946b authored about 8 years ago by Adam J. Pratt <[email protected]>
Merge branch 'DEVELOPMENT' of github.com:westpa/west_tools into DEVELOPMENT

github.com/westpa/westpa - c5fc7b95908ebf4fab55ab31f7b0222784c51706 authored over 8 years ago by ajpratt <[email protected]>
Fixed bin output in w.trace in w_ipython

github.com/westpa/westpa - 534598bbf687084f948c717f3597b5c006f69fe2 authored over 8 years ago by ajpratt <[email protected]>
Fixed bin output in w.trace()

github.com/westpa/westpa - 5b13645fc74e19fc34bf0704c76669686e151cb0 authored over 8 years ago by Adam Pratt <[email protected]>
Reverted changes made to w_kinavg.

From the earlier edit ("trying new stuff" or whatever).
In addition, fixed reweighting code to en...

github.com/westpa/westpa - 0103ede452637b8681fa808154ce08517ae0ff97 authored over 8 years ago by ajpratt <[email protected]>
Sped up plotting, significantly.

github.com/westpa/westpa - 5d5dec55cd6c00c366f69e1d38eb9adb218a4757 authored over 8 years ago by ajpratt <[email protected]>
Added in expected value to kinetics plot.

github.com/westpa/westpa - 2c1a1b4d729fe8f169879c11e3f3926afa1b81f9 authored over 8 years ago by ajpratt <[email protected]>
Added in basic text plotting interface. Fun!

github.com/westpa/westpa - 9fc7df2889d0e1bd292e05be8057093780069cbe authored over 8 years ago by ajpratt <[email protected]>
More useful error message.

github.com/westpa/westpa - 2139c67e8f6a94b9c49ac93c84c571bde7ff4083 authored over 8 years ago by ajpratt <[email protected]>
Added in rudimentary plotting interface.

github.com/westpa/westpa - 087447c924a86b17ac4c42e566aeb809683b6176 authored over 8 years ago by ajpratt <[email protected]>
More fixes.

github.com/westpa/westpa - a8e5a7f8d58da7d8e38b6522b7b33cad45c9c8d3 authored over 8 years ago by Adam Pratt <[email protected]>
Testing some potential fixes to w_kinavg.

github.com/westpa/westpa - 3e66db8bde084d58aac760538cb87ff4f96acd2e authored over 8 years ago by ajpratt <[email protected]>
Fixed analysis mode && reanalyze mode.

github.com/westpa/westpa - 999182e3edbb224d106d3ced6b35a3560bd11577 authored over 8 years ago by ajpratt <[email protected]>
Removed accidental mutually exclusive options.

github.com/westpa/westpa - 8c2a876b021fde4c02f4344a9ee4066e41b66ba4 authored over 8 years ago by ajpratt <[email protected]>
Added in schematic style analysis to each tool.

Simply run --config-from-file --scheme-name SCHEME
as options on any of the tools, and it will cr...

github.com/westpa/westpa - 9e2e95f4cc30c0c31f74c790aa118c4d2aa1016a authored over 8 years ago by ajpratt <[email protected]>
w_assign can now automatically run an analysis 'scheme'.

github.com/westpa/westpa - 0b1483fe862823c89faef568230b9997e63e00f4 authored over 8 years ago by ajpratt <[email protected]>
Removed other unnecessary files, as well.

github.com/westpa/westpa - 2f071ab85152c0c74f1e0b23a6ecfd5841bf5175 authored over 8 years ago by ajpratt <[email protected]>
Removed unnecessary README.md

github.com/westpa/westpa - 445877e5078f442cb19ee24f07123ca604ca786b authored over 8 years ago by ajpratt <[email protected]>
Merge remote-tracking branch 'w_ipython/master' into DEVELOPMENT

Adding in w_ipython tool.

github.com/westpa/westpa - 35420495e62422437ec2fa83374bbb0f9a6daa93 authored over 8 years ago by ajpratt <[email protected]>
Removing multitool parts that won't be brought in.

github.com/westpa/westpa - ce06ca3f203880e7dbf2a69da82b15259882011f authored over 8 years ago by ajpratt <[email protected]>
Tiny cleanup.

github.com/westpa/westpa - d9564e3069543ed78674020db06fb1160ee3ccec authored over 8 years ago by ajpratt <[email protected]>
Added in ability to reanalyse, if desired.

github.com/westpa/westpa - 25142b62dbc10302c613bb7e621a349e38eda230 authored over 8 years ago by ajpratt <[email protected]>
Cleaned up and enabled analysis only mode.

github.com/westpa/westpa - 94043edcc6ecdb8d4a9fb67326f266b7f725797c authored over 8 years ago by ajpratt <[email protected]>
Updated tool to work with actual iPython session

No more is a modified west required. IPython is now embedded into the
tool itself.

github.com/westpa/westpa - b2620bf262854daf0cfd801e7604b8556213e196 authored over 8 years ago by ajpratt <[email protected]>
Merge branch 'master' of https://github.com/ajoshpratt/w_ipython

github.com/westpa/westpa - 70387301bc0d28eab1f63119046c8d9714ceae45 authored over 8 years ago by ajpratt <[email protected]>
Sorted issue with kinrw and kinavg.

Removed warnings from ipython session.
With more than analysis scheme enabled, the bootstrap code...

github.com/westpa/westpa - 46993fbd54728011f4d1de8fc759799d5045b376 authored over 8 years ago by ajpratt <[email protected]>
Fixed w_stateprobs

Now works with the mclib, as well.

github.com/westpa/westpa - 0445d6b12834ba5e0e7b359da2c074fcbb1e33f3 authored over 8 years ago by ajpratt <[email protected]>
w_fluxanl fixed.

Works with the mclib, now.

github.com/westpa/westpa - 6536ed8bfb8691001ed08ccfd4bdee8d3e3c9775 authored over 8 years ago by ajpratt <[email protected]>
Moved some code back into place.

github.com/westpa/westpa - ba87f1d2880902c1366d8a4abb93e8c07ac1e8ac authored over 8 years ago by ajpratt <[email protected]>
Modified fluxanl and stateprobs to work.

Should now be compatible with updated mclib.

github.com/westpa/westpa - bd271f281b5aa3caeb8616ec969f0028fd044908 authored over 8 years ago by ajpratt <[email protected]>
Cleaned up more code, now does conditional fluxes.

Not sure if we should leave it like this, as it doubles the calculation
time.
But there it is.

github.com/westpa/westpa - 4e63e49fe67ed6358934255cdf467d587ae5136b authored over 8 years ago by ajpratt <[email protected]>
Modified the cython to return the fluxes, if requested.

github.com/westpa/westpa - a4c5e6cde333dd9efd4ac12b015ec9f934fed4c1 authored over 8 years ago by ajpratt <[email protected]>
Cleaning up codepaths.

github.com/westpa/westpa - ed2ebc287ace3130065a6cb4f021dc24c63fc386 authored over 8 years ago by ajpratt <[email protected]>
Restored averaging functionality into w_kinavg.

In addition, ensured average display could be disabled.

github.com/westpa/westpa - 99a4c0a026aaca5bbdebb953c67e90338bb77375 authored over 8 years ago by ajpratt <[email protected]>
Removed 'matrix' method, and in the previous edit, added in subsampling

functionality.

github.com/westpa/westpa - bf9dae463a1fdff110ce9a283b36069cbea86d00 authored over 8 years ago by ajpratt <[email protected]>
Added in functionality to adjust the correlation.

github.com/westpa/westpa - 6284c1c307a22dc0e5df0c8018f2572f5f72dea8 authored over 8 years ago by ajpratt <[email protected]>
Create README.md

github.com/westpa/westpa - 20ca1bbeb4467d3afb86dc5481fc0803356d7964 authored over 8 years ago by Adam J. Pratt <[email protected]>
Staging final changes in from yesterday.

github.com/westpa/westpa - 5546406552a9e0d61f0c5f407c1baf9abd8bbe41 authored over 8 years ago by ajpratt <[email protected]>

github.com/westpa/westpa - 7a1772d48c60887b3b4653ef56ab1bfb6e11dc56 authored over 8 years ago by Adam J. Pratt <[email protected]>

github.com/westpa/westpa - 57cb132ab01b6bcacb3b63db350c95606f8a12f4 authored over 8 years ago by Adam J. Pratt <[email protected]>

github.com/westpa/westpa - 1c341720bef96483f3126ee20b5efaadbd3015e0 authored over 8 years ago by Adam J. Pratt <[email protected]>

github.com/westpa/westpa - 26b07a472f893ced7afe99ae14a279d637288bb4 authored over 8 years ago by Adam J. Pratt <[email protected]>

github.com/westpa/westpa - bc9f3b6dd9aeff01a3397bd507e57752597529a0 authored over 8 years ago by Adam J. Pratt <[email protected]>

github.com/westpa/westpa - 0fada17c570fb325bd8ab007c721d380757ecd0d authored over 8 years ago by Adam J. Pratt <[email protected]>

github.com/westpa/westpa - 9c32cb930829a1b9d7ae5d605bce1819848e2b88 authored over 8 years ago by Adam J. Pratt <[email protected]>

github.com/westpa/westpa - 409d5c36efc751c48c42b9e94ff6ddb23001bf3d authored over 8 years ago by Adam J. Pratt <[email protected]>

github.com/westpa/westpa - ce273ddf0b08d09fb84704a60d9d1ec0d1a2d466 authored over 8 years ago by Adam J. Pratt <[email protected]>