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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 transition analysis. Front-end still incomplete.

Backend overcounts transitions along common paths.

github.com/westpa/westpa - 65c98a062f8b01621175118ad682daf9209c71d9 authored almost 15 years ago by Matt Zwier <[email protected]>
A bit of code to backcheck the HDF5 storage

github.com/westpa/westpa - 3863221937276fe08063f208ab4f8e6152f73702 authored almost 15 years ago by Matt Zwier <[email protected]>
Updated analysis, cleaned up data manager, restored bin tracking

github.com/westpa/westpa - 56f836d010d7b03ff2263b998832b84119d32d9d authored almost 15 years ago by Matt Zwier <[email protected]>
New working wemdanl.py code

github.com/westpa/westpa - 6a3be87d3ca2842232844f1c9a142404157af21d authored almost 15 years ago by Matt Zwier <[email protected]>
Working commit of updated analysis system

github.com/westpa/westpa - 10f4c87873a89b0e63224c2a96131aa4639f8ac1 authored almost 15 years ago by Matt Zwier <[email protected]>
Added tag v0.3 for changeset 73415cb5e641

github.com/westpa/westpa - 1a5434f947b9dcbaad44887c904246f747ce4671 authored almost 15 years ago by Matt Zwier <[email protected]>
Reverted to SQL data management with a data manager abstraction layer.

Seems to work!

github.com/westpa/westpa - 4f74f31ca3b0cf793f756db2a9dff79a56c761e6 authored almost 15 years ago by mzwier <devnull@localhost>
HDF5 sucks. Final commit before branching and rolling back to SQLite

* Though somewhat tunable, overhead for indices ~3x data size
* Recreated linked lists in HDF5 ...

github.com/westpa/westpa - fb4a890384c3aafc8848c7898739f844b4aa84a7 authored almost 15 years ago by Matt Zwier <[email protected]>
HDF5 apparently working

github.com/westpa/westpa - 316a13105ac95b20cde414f19ecc634d61e91250 authored almost 15 years ago by Matt Zwier <[email protected]>
Done with most of the HDF5 storage?

github.com/westpa/westpa - 26e4ef0b73bb1cdec4421878cddb3ba4d795d779 authored almost 15 years ago by Matt Zwier <[email protected]>
renamed i_iter to n_iter, a few bugfixes

github.com/westpa/westpa - fb312b16fa69c254dd3d66d78612836ad367145f authored almost 15 years ago by Matt Zwier <[email protected]>
Closing in on a saner HDF5 data backend

github.com/westpa/westpa - da8d701cda6f609f7daf3ff740f969439c938cdb authored almost 15 years ago by Matt Zwier <[email protected]>
Very primitive and inefficient HDF5 backing

About to be redone in a more sane way

github.com/westpa/westpa - 7c97196f7537b84428dfbd8ebaee359aaed8b369 authored almost 15 years ago by mzwier <devnull@localhost>
Tagging last rev before gutting for HDF5 rewrite

github.com/westpa/westpa - 114510465ce9d873788476256ea6ecc00b3827f6 authored about 15 years ago by Matt Zwier <[email protected]>
Added run.cfg

github.com/westpa/westpa - 21a73e4f4f0e62d2ef71e9a8cbcc2b52a8807b75 authored about 15 years ago by Matt Zwier <[email protected]>
Working HDF5-based analysis

github.com/westpa/westpa - a4771d6c72c929661da3c519b05aa68fa656d7a1 authored about 15 years ago by Matt Zwier <[email protected]>
On the way to analysis

github.com/westpa/westpa - 2c6c31b1ecf1219341b2e3a6d2ea5f66dc56620e authored about 15 years ago by Matt Zwier <[email protected]>
Added mkdist.py

github.com/westpa/westpa - 7cf7df5456d2d318c7654eca8df8a60c951a82ce authored about 15 years ago by Matt Zwier <[email protected]>
Long time since a general commit

github.com/westpa/westpa - 3bca5a0c19f6ec7ecc2d34cc421d7411d92e44cb authored about 15 years ago by Matt Zwier <[email protected]>
Modularized and cleaned up ttimes.py

github.com/westpa/westpa - 7bb850670f78cf56f873f75b8df6e9a26446e8c6 authored about 15 years ago by Matt Zwier <[email protected]>
Updated ttimes.py for efficiency and sanity

github.com/westpa/westpa - 820f3d864508e0b42dbb9c9c94e663acd25e34cc authored about 15 years ago by Matt Zwier <[email protected]>
Added support for pre-/post- iteration/segment hooks

github.com/westpa/westpa - 4a5b76889215f94e36f2cdb34d54015e2c890b65 authored about 15 years ago by Matt Zwier <[email protected]>
Cleaned up executable interface in preparation for pre-/post-processing hooks

github.com/westpa/westpa - feac66017c230b374d9e711da00a495c634a31cb authored about 15 years ago by Matt Zwier <[email protected]>
Cleanup of deprecated code

github.com/westpa/westpa - c47e821b0728587f9176ca32c93656354aa3a053 authored about 15 years ago by Matt Zwier <[email protected]>
Nice, clean MPI interface done

github.com/westpa/westpa - fa2d9f37c6b814968f26c2db07f4294279211a36 authored about 15 years ago by Matt Zwier <[email protected]>
Heisenbug resolved.

* Something about the Waitall() or inconsistent use of status objects was
causing incorre...

github.com/westpa/westpa - 01d218cbddab1d505bb7824bc6246cea7cdcc54b authored about 15 years ago by Matt Zwier <[email protected]>
MPI almost working

* MPI scatter/gather works correctly
* Currently working on a way to avoid calling MPI_Abort() ...

github.com/westpa/westpa - a6b66455c42831e98c9a45a1226c61b84fdbe7b0 authored about 15 years ago by Matt Zwier <[email protected]>
Refactoring for better MPI; serial execution seems to work

github.com/westpa/westpa - ba77cdbe2cf1f00fa6efdabafc859cf23873bca7 authored about 15 years ago by Matt Zwier <[email protected]>
More DB improvements, saner separation of tasks among WESimDriver and friends

github.com/westpa/westpa - b27cc311a8fc464f7c409f7ca21ecdbd0a0a0e35 authored about 15 years ago by Matt Zwier <[email protected]>
More sane time storage and calculation

github.com/westpa/westpa - 2f6ac9f7c15a24f70d20db9e1461a3ed6f7b28d8 authored about 15 years ago by Matt Zwier <[email protected]>
Core of a sane complete system

github.com/westpa/westpa - 030766363a542d7c3a27d7766e566eff2f7f2c33 authored about 15 years ago by Matt Zwier <[email protected]>
DB layer finally sane?

github.com/westpa/westpa - 1bfc2e94127dcebebb29e73f24b3d21da2bfa5ea authored about 15 years ago by Matt Zwier <[email protected]>
Continuing DB fun

github.com/westpa/westpa - 0f4f5d8250fe32d62c295e304a6b569da954f957 authored about 15 years ago by Matt Zwier <[email protected]>
Nice to have the simulation driver included in the repo

github.com/westpa/westpa - d44caf055017a7c72f41ae1d2fbf42fbc63754f5 authored about 15 years ago by Matt Zwier <[email protected]>
DB layer continuing to come together; segment lineage seems to work

github.com/westpa/westpa - 5c5d14234700d0359eb974d2415b1da2763c8cf0 authored about 15 years ago by Matt Zwier <[email protected]>
A little restructuring

github.com/westpa/westpa - cb16a0780d410592f9ee84fb4a8d2d7b213481db authored over 15 years ago by Matt Zwier <[email protected]>
Initial SQLAlchemy support complete

github.com/westpa/westpa - 22b200828694f312600370426ea584228391773c authored over 15 years ago by Matt Zwier <[email protected]>
Yet another name change

github.com/westpa/westpa - 0d348222c941505619fdde53badc384905123249 authored over 15 years ago by mzwier <devnull@localhost>
Final working commit before major restructuring

github.com/westpa/westpa - 5538601576d1f3dbefefc4c21bfce1be67f65457 authored over 15 years ago by Matt Zwier <[email protected]>
Eliminated sleep(0) which may have been hanging simulations with contested

locks.

github.com/westpa/westpa - a325c99ed073121ff22414cfa8ecc4eb3f968c24 authored over 15 years ago by Matt Zwier <[email protected]>
Added random-wait fallback to "unable to open"/"database locked"

error handling. Probably time to consider MySQL

github.com/westpa/westpa - 2153399febe51928041fa15d390cc8e775dd06ef authored over 15 years ago by Matt Zwier <[email protected]>
Added "database is locked" case to retry system

github.com/westpa/westpa - 855fe19593b4d563ee907b2a4a73059434edce12 authored over 15 years ago by Matt Zwier <[email protected]>
Fixed broken pysqlite2 import

github.com/westpa/westpa - ce9216da0660db4280cf38f76d07791bd58301d8 authored over 15 years ago by Matt Zwier <[email protected]>
Fixed buggy "scrub"

github.com/westpa/westpa - 0e7d0a65d7c2fcea5c5c94d5d94e1bc1f5d21af6 authored over 15 years ago by Matt Zwier <[email protected]>
Better status output

github.com/westpa/westpa - c6c9874e003522776321c5d179d4132be0bdc752 authored over 15 years ago by Matt Zwier <[email protected]>
Added connection/cursor proxies for retry when "cannot open database file"

occurs

github.com/westpa/westpa - 27bd129160560a227bd254a0e7ebaecb0fa2a3db authored over 15 years ago by Matt Zwier <[email protected]>
Added sample scripts

github.com/westpa/westpa - 32a770ca1665eaf5dd8d013f86c7cd16d89100fa authored over 15 years ago by Matt Zwier <[email protected]>
Initial commit of cleaned-up code

github.com/westpa/westpa - 5155730c4fa7e91447a27d6e9e729d2be14cadf5 authored over 15 years ago by Matt Zwier <[email protected]>