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

Resurrected wemd.rc, moved and renamed wemd.py and provided a shell wrapper.

* This in preparation for creation of analysis scripts.
* bin/wemd.py moved to lib/cmds/wemd_...

15e1e3095ed89680964af9b49cb4a9984f120d92 authored almost 14 years ago by Matt Zwier <[email protected]>

Fixed incorrect cpu time in executable propagator (didn't count child processes...oops)

a72d6b68e5d3c98b5e08351382d0270c2c3dcd8e authored almost 14 years ago by Matt Zwier <[email protected]>

Merge with 53f5cf893ed568de2d7702971ab9eaf7bc56e569

5b116f28b76e0d248b299496d59a25aa422a377a authored almost 14 years ago by joekaus <devnull@localhost>

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3e270ba1a97aa836e21ed31216befaf613aba9dd authored almost 14 years ago by joekaus <devnull@localhost>

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a9108224110c38fd17f6fd552e8577496712d442 authored almost 14 years ago by joekaus <devnull@localhost>

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bb84297388722edec073e954125b7615a85d82f7 authored almost 14 years ago by joekaus <devnull@localhost>

Small fix so tcpip code will cleanly shutdown

60f1f6e844f65a0e9491bd2bf1dbc33665074e56 authored almost 14 years ago by joekaus <devnull@localhost>

Merge with faeb5dda173998fc73dc18d9ced9af67d02f5525

56d616d3f834fde8707a2f8e63ae89d270dce593 authored almost 14 years ago by Matt Zwier <[email protected]>

Bugs galore in pcoords.py

dfd2fed61872c6f3b12f28a20d2ac7ac6fd62fa8 authored almost 14 years ago by Matt Zwier <[email protected]>

Fixed bugs in multidimensional pcoord handling (Joe's fixes, my commit)

465a669fdfd1448b56b8ace5256baacc8558987a authored almost 14 years ago by Matt Zwier <[email protected]>

Removed reference to no-longer-existing exit codes from the former wemd.rc

326221d6666baa635bb8cd195ccefa173c17e2d6 authored almost 14 years ago by Matt Zwier <[email protected]>

Merge with Joe's work

66bb4dfbd3b2894bcb02f58a0e9f51053c7d7cbe authored almost 14 years ago by Matt Zwier <[email protected]>

Numerous bugfixes for new code

fe3447e49769697e91c5a2df43c56e5281eb431c authored almost 14 years ago by Matt Zwier <[email protected]>

Processes work manager now works

Tcp/ip is now faster

4613ac61ad82ff3657054d609aa31ffd24453c34 authored almost 14 years ago by joekaus <devnull@localhost>

Updated Tcp/ip work manager to work with new code

8405cc9660e2c929ae79d8f1f8c2291ca00ec6f0 authored almost 14 years ago by joekaus <devnull@localhost>

Restructuring largely done; ready for collaborative development.

c9e682e5731ac09ce06cbed07a64880cc0e4d63a authored almost 14 years ago by Matt Zwier <[email protected]>

Executable backend done, but untested

5be7f904932acea3961edd7bbb5d97c2e9aef4d9 authored almost 14 years ago by Matt Zwier <[email protected]>

Working bin population and recycling tracking

a30a79d3b332cdbdd12c3307aaad4c5fa325f96a authored almost 14 years ago by Matt Zwier <[email protected]>

--profile option added, slow HDF5 update_segments() partially ameliorated

75c8e3681a2d3f63b49d52ab59eef7ca2d2b6dcb authored almost 14 years ago by Matt Zwier <[email protected]>

Working commit of rework. Entire propagation/WE loop runs for ODLD test system.

4de248dc3c1945f3dd77a4a76f5525b90ec9af77 authored almost 14 years ago by Matt Zwier <[email protected]>

Working sim init up to commit of initial segments

7b71d449d34dedd3841e6310c0837a190d86d769 authored almost 14 years ago by Matt Zwier <[email protected]>

Merge with 0a7f98c6b69d9ae5f001b08ab15347632896eba9

46a38f3ca8da06f495f13a02d0270e32ed7a41ae authored almost 14 years ago by Matt Zwier <[email protected]>

Working commit

793dd0ff77d86202a5f6c142fb9ee5348d5b966d authored almost 14 years ago by Matt Zwier <[email protected]>

Fixed bug in tcp code

Added Steady State Resampling Code

2dd6fb8ee0766022a110ed3c09bd37d09ec0e1dd authored almost 14 years ago by joekaus <devnull@localhost>

Modified analysis code to work with the new hdf5 data manager

cefbe0a3c003e8e963490fd7a105a3e72fd7f7bd authored almost 14 years ago by joekaus <devnull@localhost>

Working commit prior to another pcoord rework

1e5ef14d0b04d048956f1972d42061d1aa7e68ce authored almost 14 years ago by Matt Zwier <[email protected]>

Working commit of restructuring/cleanup

103c07773177ed748dbe2bba370a58b7b6de93b0 authored about 14 years ago by Matt Zwier <[email protected]>

Merge with cb514be31c97ee4e8b3a2b2f765f28ad4912ccd0

2dd143d54c03ec4b24068e7ff32a811ddccc2a20 authored about 14 years ago by Matt Zwier <[email protected]>

Rebin, truncate restored

Initialization with multiple structures added

e87bb3f2696ba7f4c85acaac6fcd9fbd90eefb8c authored about 14 years ago by joekaus <devnull@localhost>

Working commit of cleanup and restructuring

4767a582b8d354784e5ce7261e6a150a06713c78 authored about 14 years ago by Matt Zwier <[email protected]>

Fixed segment caching so it doesn't cause memory explosion

10fef3f8577f1503b4bca1bfcc61098875b076f5 authored about 14 years ago by joekaus <devnull@localhost>

Small Modification to TCP ping thread

cc1f4145b4684c8bb2080bf4ff2a4e431de1af58 authored about 14 years ago by joekaus <devnull@localhost>

Modified TCPIP server

469bfe506fe95e90482acaa31b90009ea18eb032 authored about 14 years ago by joekaus <devnull@localhost>

Added Debug/Added missing sim_manager

701db2728330d757dd095b3f8eefa47128a64ccb authored about 14 years ago by joekaus <devnull@localhost>

HDF5 datamanager (replacing sqlite)

Separation of Work and Sim Managers

785c143e4398de71c2272d9260708b9b2db56f71 authored about 14 years ago by joekaus <devnull@localhost>

Added tcp/ip server for internode communication (as an alternative to mpi)

Load backend driver from a py file

6398bd8961ad21c4321ef9f890896ea97a6215fd authored over 14 years ago by joekaus <devnull@localhost>

Two pass split/merge to reduce the range of probability in a bin while maintaining a constant number of particles

max_wallclock setting in run.cfg will cleanly exit if the next iteration would go over the wallcl...

daf963e4f9d9306df489321daffb40df105d688c authored over 14 years ago by joekaus <devnull@localhost>

Added 'reinit' to wemdctl to initialize a new simulation from the last iteration of an old simulation

Fixed minor bug in we_driver that caused the number of particles to not be fixed when a recycling...

8b3fbf0aa40feb4a50a259bd1684fa10df1fc923 authored over 14 years ago by joekaus <devnull@localhost>

Merge with bc4f3556146eb35bd5c5a2738b8d6133dfc322cf

c83286a079b5c7d012feda547209616053c0c432 authored over 14 years ago by joekaus <devnull@localhost>

Added Proportional Recycling

Small change to Test Backend

a5438232a37ff72f043583d4f2f933e0afc15b3c authored over 14 years ago by joekaus <devnull@localhost>

Added hackish updater script

638ec7f0268f4c38e1572a8d4ea58904d90b6cf1 authored over 14 years ago by Matt Zwier <[email protected]>

Merge with b6babefae1f39fab0b3ce1d724435d86b348f038

393ab6f03769de08b6438f2c52ab24101c2f40bb authored over 14 years ago by joekaus <devnull@localhost>

Working update

1205fcdc7dffdd6326c16889b06ccacd5a3de4e0 authored over 14 years ago by joekaus <devnull@localhost>

Added rudimentary reweighting in anticipation of enhanced steady-state sampling

* Requires a pickled numpy array of the same shape as the bin space containing the new weights.
...

10b65cef88aea65cd07a62a66741f7ca7958ca07 authored over 14 years ago by Matt Zwier <[email protected]>

Refined core WE binning and added refined Langevin dynamics test driver (backend=odld)

* ODLD driver based on Joe's code, optimized for speed
* ODLD driver tested for 1-D, 1-D with p...

b9c3a84c6251994b586e4776f181c3c6503ff87e authored over 14 years ago by Matt Zwier <[email protected]>

Step 1 of massive core cleanup

* Cleaner separation of simulation and runtime configuration
* Eliminated useless Bin/BinArray ...

cb601c7211244f03c57c6f7998a1c7bccdd663fb authored over 14 years ago by Matt Zwier <[email protected]>

Static backend parameter setup moved to sim.cfg

8ac68665fb5313748e574388c0dccfa151f52079 authored over 14 years ago by Matt Zwier <[email protected]>

Added orphaned test.py, fixed spacing problem

1682388c485916272bdec60687b90819e9cbf41b authored over 14 years ago by Matt Zwier <[email protected]>

Merged Joe's changes for simple Langevin test driver and updated sink code

54a383350ec01b3a6fef392371d375eb4c2da245 authored over 14 years ago by Matt Zwier <[email protected]>

Added TestBackend Driver

Added Rectilinear Recyling -- must update sim.cfg
Fixed minor bug with splitting recycled particles

f012148d6c44515e6ba012d5dbca8c21912a922d authored over 14 years ago by Joseph Kaus <[email protected]>

Moved tools from wemd to wemdtools (and eliminated redundant genpc.py)

66ef6ca767e088b4b4d78f9e881a5ca4a95eb722 authored over 14 years ago by Matt Zwier <[email protected]>

current_taudep.py moved to a new \"wemdtools\" repo

bb8b9fd506a03d81c409a8094037e0dff4aba59c authored over 14 years ago by Matt Zwier <[email protected]>

Added block-averaging/MC bootstrap probability current analysis tool

372897b4e72033627520fc102b698810043763cf authored over 14 years ago by Matt Zwier <[email protected]>

Cleaned up data manager for independent analysis use, fixed broken MPI with

blocksize 1.

441f96bcaa0063e8ad752607e0dcf08e3798c45a authored over 14 years ago by Matt Zwier <[email protected]>

Refactored table names (for cleanliness) in SQLAlchemy metadata

51976e513c88e7a0d2a4ebf5f0142c14e4d1f717 authored over 14 years ago by Matt Zwier <[email protected]>

Cleaned up wemd.environment; now wemd.rc. DB connection fixes.

* Improved separation of the command-line tool classes and RC file parsing
* create_engine now ...

9d596b9370fa19cb61f856ad3d417087d1c7a9e5 authored over 14 years ago by Matt Zwier <[email protected]>

Merge Josh's and Matt's changes

2224f0ef3bdac8f82b0e762edc86e7768ce8075d authored over 14 years ago by Matt Zwier <[email protected]>

Added multi-segment processing to sim drivers, updated pyopenmm driver

3cc58d6275d0f67c54d4b0159612cace34f783bc authored over 14 years ago by joshua.adelman <devnull@localhost>

Console operates without readline, truncate works properly

6f14d0539d2d86f11c1aabeeb6f566c2bfd8bb44 authored over 14 years ago by Matt Zwier <[email protected]>

More MPI fixes.

ecd081b9967bf722f7c022456223bae6e932f6bd authored over 14 years ago by Matt Zwier <[email protected]>

Added some options to transanl.py, continued fixing MPI bugs and \"features\".

* transanl.py now supports options to override input and output settings in analysis.conf, sui...

556e10d252454c9e37fc7d970ed8c3b012aaba03 authored over 14 years ago by Matt Zwier <[email protected]>

Fixed lost exception in wemdrun.py

e1013478fe0d672b349de590407a940ce68ee4ba authored over 14 years ago by Matt Zwier <[email protected]>

Merged fixed-particles-per-bin with current bitbucket tip

711aa102a0f1d7e97b60461048af9133ce0d4199 authored over 14 years ago by joekaus <[email protected]>

Implemented one-pass fixed-particles-per-bin driver

2c08a37a173a1a3fc757755048b549ee9a7927ab authored over 14 years ago by joekaus <[email protected]>

How about MPI refinements that actually work

00a160b1c1fb11637f89a07e697d5d3f40d341c9 authored over 14 years ago by Matt Zwier <[email protected]>

More MPI refinements

30eafb37bd13709c0c58a5c88edb8055f6a866bb authored over 14 years ago by Matt Zwier <[email protected]>

MPI cleanup

6ad596067d266726dace31b3997fde4204716c4f authored over 14 years ago by Matt Zwier <[email protected]>

Updated pyopenmm driver

* Dynamic import of a driver module
* Fixed race condition

ac6baba1ee03c153c61fc627c646fc2ea058a1a3 authored almost 15 years ago by joshua.adelman <devnull@localhost>

Fixed bug in rebin, changed txt2hdf5.py to support type selection

2775432bb9e74b039faa019eca48ad45e08f2b90 authored almost 15 years ago by Matt Zwier <[email protected]>

Added 'rebin' and 'truncate' options to wemdctl.py

* rebin allows on-line replacement of the WE driver
* truncate allows truncation of a WE simula...

618bac0a2070acdd1f9eca9af2b6cac4b3642200 authored almost 15 years ago by Matt Zwier <[email protected]>

Added output filename option to \"wemdanl.py transanl\"

442c6943ca616af87f95596a64e67be1260ddf88 authored almost 15 years ago by Matt Zwier <[email protected]>

Removed spurious \"-t\" option from wemdanl.py transanl

91b2f9707f9a4f900dc6a6a1f6d646d6857d3ca3 authored almost 15 years ago by Matt Zwier <[email protected]>

Finalized tree-walking transition analysis.

5765921313e7f4b538dcc892d6a29e0c91d27ae3 authored almost 15 years ago by Matt Zwier <[email protected]>

Working transition analysis for brute-force (once again)

* Now with reasonable speed!

eb51ded11ac40092aa58d7b144e3ff11ff5188bd authored almost 15 years ago by Matt Zwier <[email protected]>

Continued working on new transition analysis; almost right

f28c255a724f7a9384efd25cac55826bd29ebe19 authored almost 15 years ago by Matt Zwier <[email protected]>

New transition analysis in progress

a68a6f678e3b3df67e366854dc46a58ac1199180 authored almost 15 years ago by Matt Zwier <[email protected]>

Fixing botched commit; also, completed generalized trajectory walker

f0e803fb803e4aaac56b60c298f829b1460eca33 authored almost 15 years ago by Matt Zwier <[email protected]>

Fixed bug in endpoint_type assignment for merged particles

(the continuing trajectory segment was marked as merged)
Added working examples of recursive an...

6ccf9ee37cfe0926855ccc9aa812606eac1e6161 authored almost 15 years ago by Matt Zwier <[email protected]>

Decoupled backend driver from analysis routines

0fb6d6b808a6a858a582498b3a4d379e505acd25 authored almost 15 years ago by Matt Zwier <[email protected]>

Completed integration of pyopenmm/fixed_bins_we, general cleanup

b0538911ee598f31b60d483f53886f3d144abd73 authored almost 15 years ago by Matt Zwier <[email protected]>

Added pyopenmm driver

241d8b99dc1fb76042ecc4e8a24f45f3a14b8734 authored almost 15 years ago by Matt Zwier <[email protected]>

Merged fixed bins branch

a07ee005cfe80d09bafd323f061721680bff1737 authored almost 15 years ago by Matt Zwier <[email protected]>

Cleaned up transition analysis a bit, added a pared-down trans. analysis

* Pared analysis matches more complex analysis

1db84653ee0857987964d26f7c87984076a95a48 authored almost 15 years ago by Matt Zwier <[email protected]>

patch to include fixed number of particles and openmm driver to wemd

88799d31d3b4d35a397178148be3b9a64fab0f81 authored almost 15 years ago by joshua.adelman <devnull@localhost>

Fixed transanl.py so that only the first two columns (time, weight) are

considered when writing files.

c904f0952029e54c782d230b2e47daebe3981f6f authored almost 15 years ago by Matt Zwier <[email protected]>

Fixed stupid session.merge() bug

986da228172d1f0858c484416d9316cccbbd3aa0 authored almost 15 years ago by Matt Zwier <[email protected]>

Finished with analysis rewrite

e405fe748eeb2bf14bef4184fbf5437db1cad606 authored almost 15 years ago by Matt Zwier <[email protected]>

Added better trajectory retrieval/handling

fa7410cfa4033cf3da2ae0a40e21d47b72274db5 authored almost 15 years ago by Matt Zwier <[email protected]>

Cleaned up brute-force code a little, added trajectory listing/tracing.

b21415a32e7b5a51591ef46222dc598d095ae245 authored almost 15 years ago by Matt Zwier <[email protected]>

Cleaned up a things a little, added brute force transition analysis

3740dea4655918aea7b9cf047fb4b14d37ffaa68 authored almost 15 years ago by Matt Zwier <[email protected]>

A few fixes to the brute-force analysis code (soon to be removed).

9f06381ec35df0a066cf68d0e2a64875cbf95511 authored almost 15 years ago by Matt Zwier <[email protected]>

Added a little documentation

9200af46605b0c5b231615ec6a1ce1f53b61fa6b authored almost 15 years ago by Matt Zwier <[email protected]>

Yet another head merge

297a7c248ad031736e1f7541de602f057c8c6d14 authored almost 15 years ago by Matt Zwier <[email protected]>

Quick bugfix

f642fb7c0b15f32c5c3c7d0fd700d3d077d4095d authored almost 15 years ago by Matt Zwier <[email protected]>

Rudimentary source-sink in place

When particles fall off the end of the world, they are designated as having
no parent, which ...

5a99215394601bb689ff6bea80121a65598dbffa authored almost 15 years ago by Matt Zwier <[email protected]>

merged pesky head

8ec450be962ea97d94371025237415e0593a4026 authored almost 15 years ago by Matt Zwier <[email protected]>

Adding run.cfg

2b32a071c39988bdd9d93f9cb646c7b24a0ff5a4 authored almost 15 years ago by Matt Zwier <[email protected]>

Working low-efficiency trajectory map

e6b004d719ec43a42994c3b5960c8061a82fbce1 authored almost 15 years ago by Matt Zwier <[email protected]>

Another step toward a good trajectory analysis

0dd31ccf5d08d1e064c0ce5a0d901b51db50f576 authored almost 15 years ago by Matt Zwier <[email protected]>

Beginnings of unified trajectory extraction within the data layer

f6d629d89acdb8fe398402ea519f3dbbf3f1dece authored almost 15 years ago by Matt Zwier <[email protected]>