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

Included comment

Former-commit-id: 73288bcd38131a3b569c6780762b949f5ca8efff

49d1dafded5504d0efceb0623d27c4da1ae3ecd5 authored over 7 years ago

Include topology file, so user does not have to generate their own

Former-commit-id: 6a45987cf14e81610327c5186696d6b68ff88934

8ad6eb72df732b220eed022505755613bbe47b05 authored over 7 years ago

Include files so user does not have to run equilibration, if they choose not to.

Former-commit-id: 3b83ebf9372878c3883d172ed0f28d32e0e32003

6af49e8434775438825de2d4e497fc4c99fd90ae authored over 7 years ago

Added files for producing the force field. The force field is automatically generated based on force field files in the user's gromacs installation, in order to avoid possible copyright issues with distributing files based on gromacs

Former-commit-id: 7e35d831637c3cd702f0edf3a8649ad9a97e389e

932b2026b55eb3ec1d6fd3ee36ad1208990ebbc1 authored over 7 years ago

Symlink the forcefield, return all 51 timepoints of the progress coordinate, output only the ions in the pdb files, and clean up more useless files

Former-commit-id: 3a26563077b4bcdfd4d98fa8eef5e5422b90a921

64de01640497a43f361cba186e584dddac913fd6 authored over 7 years ago

Corrected paths in gmx distance call, and return the right part of the output

Former-commit-id: 95d98540545a57facdf9389d177da04f093c9826

4e778389b74243646ec2d0664ae4497b3a6d3e4b authored over 7 years ago

Specify correct path for basis states, and update bin boundaries

Former-commit-id: 3a079f54d79aad5743999e3a81a4a5866c6a8f78

469070aef3a64fdf9191d8c7cbb7d32426df0c57 authored over 7 years ago

Fixed erroneous comment

Former-commit-id: 242d4746d3b664343d031ba1d74d317ce97d0726

a4433302b4d6538e2ed53a7b892c4d7666d5c2e7 authored over 7 years ago

Symlink files from ./prep directory when initializing simulation

Former-commit-id: a7750a567ee7e3de9743394c50e647e5f269aed2

d9e418c0d5fb16248629087d7a8ca3137656523b authored over 7 years ago

Use 1 group for the thermostat

Former-commit-id: c254006fc9c1eca006d9f6db9287153f67409623

f66e6a495b4d31c01e371bc9a4dce2dfd7b2c64f authored over 7 years ago

Use bstates from unbound directory

Former-commit-id: 07d77b7c0549135561a6eb320119631291c12c87

9bd992c8f3868fd4419e8eab0569123235965b97 authored over 7 years ago

Updated analysis bin boundaries

Former-commit-id: bac07a6432047aaccaa44ccba8e3dfa26e535a2a

7dff3f10a123fc505b9e24a81512b9d55989c4bf authored over 7 years ago

Since Python is right-exclusive, w.trace(seg_id) previously traced segment seg_id from iteration (w.iteration-1), rather than w.iteration. Account for right-exclusivity.

Former-commit-id: b3f0639af42b07c9f5fff47af7ed37603f5a200a

a3f82cabf31d5f5788f4e20abe6473a57cfd1564 authored over 7 years ago

Redefined target state

Former-commit-id: 64dddf2e6d69e6b60fc6b04947c82c4275d87634

c8f6191ad03742ab692908cd7d4b523e83e220c5 authored over 7 years ago

Added comments for consistency with nacl_gmx tutorial

Former-commit-id: 007f20bfdbf8dd6d5442e19555f8b3dee3f4c94b

2852c49f57e259edacaed41130a67ed3b3f21bf3 authored over 7 years ago

Consistency with amber nacl tutorial; added docstring

Former-commit-id: 46f5280902b19cd26ea0cc313f50aec0737c2089

6d47f36b855bc3035c1c09b1c2b9159110c626b1 authored over 7 years ago

Updates for consistency with amber nacl tutorial. Added comments to runseg.sh

Former-commit-id: 27aaef33b4bd797639281802906431fdd140cd8a

bec8a7abfb2ae8e54a4e586f3b07890078d8cf3b authored over 7 years ago

consistency with amber nacl tutorial

Former-commit-id: 0d4f580b1f5232404b759b87de31bd2a9346f157

4a67eeb015e1f3983c1f37c14ebedd1a4bffac54 authored over 7 years ago

Consistency with gmx tutorial

Former-commit-id: b965650cc582c8bf69f148f0937aa3d9786e5be4

8dd5cae30332c238a3dee7d1158db31c3840e4a9 authored over 7 years ago

Updated init.sh to be consistent with gmx tutorial

Former-commit-id: 72170902b83b901b3d18de885d68e53b1e543ddd

caf59dbefd8cfb97000b0c01a531c97d05eebe3e authored over 7 years ago

Updated env.sh to be consistent with Gromacs tutorial

Former-commit-id: 86c00dd3812d9e804913b455ba4c5f53cb905535

a9537e33c4fe3522931e2780a99287e862a8adb0 authored over 7 years ago

Added files and scripts for preparing system

Former-commit-id: f914997e6d25514dd98a67906ae64012768a694c

25ba0e16bc35a186432b4f4ca98365a9cd8559ae authored over 7 years ago

Added files for calculating position of bound state

Former-commit-id: c2bc9bbf08c4ab7c166991ea77707f9827e2d82a

722953edcd3e503e6292d8812a612884ac7740f0 authored over 7 years ago

Copy over nacl.parm7 from ./prep when initializing the simulation

Former-commit-id: 758c6daad922735936ed1f1f65f165306aae738a

485fa5641a581d95d8402569e91a07c65888f462 authored over 7 years ago

Updated docstring

Former-commit-id: 6a20e07148be25d8d7ba3022e8ef5387404f137d

94d77535ad2de140b20c8c9dcdc9ac26962859f7 authored over 7 years ago

Increased max wallclock time

Former-commit-id: 3c2f3044f40672cfa3aeedd95f99d0eed22988ab

e86c882ff20a950d79b93a7ec7fbb472c58aec2c authored over 7 years ago

bin boundary update

Former-commit-id: 2d7f36e43f7ca2814d603114e70224a8f3a3bac6

b92b72ee4687282fc88da46a64860e46dc9f9549 authored over 7 years ago

Delete topology symlink at end of iteration

Former-commit-id: 919a1359a7b8e6cc84fc56356c02e9786153d512

a3482bb18f150c762f925943a1b4115ddefa0d78 authored over 7 years ago

Use new md.in

Former-commit-id: 2b53979cc959ea2946c4245c3d37ef5e4a089c08

9e1dc0b006530a14e47efbeff4c41f2acb28207c authored over 7 years ago

Update state definitions

Former-commit-id: 29c1ab7a7b8934e8d2bb748704e81f1e5620ab55

2bf6e80bccceb7d659363688cb54ef6e833c6826 authored over 7 years ago

Use more steps of equilibration. The distance between ions was still changing slightly when only 1000 steps were used.

Former-commit-id: 6026631b05330fd61e81f05ca25a3cc3a441f54b

aeff8b231c370ab046ee7f8b6e29fcd0123f3475 authored over 7 years ago

Increase initial separation of ions. Decrease restraint potentials during equilibration

Former-commit-id: 89c5a3824f036bf698f4820235b3870651ce9b8f

950e9dde0be22012f0b868fc2931ed084f8d32c5 authored over 7 years ago

Updated west.cfg to be consistent with minimum separation of ions after minimization, and to use rounder numbers for the boundaries

Former-commit-id: c306b9f4604e730d5a8fdb64f2a46e7ef5b6b77a

6e376161e99a7a12fb999be35c5d3fb1de28f0ed authored over 7 years ago

Use separation of ions after minimization as definition for the bound state

Former-commit-id: a05da9a6a4cd5ddf1111d70eefdef4fad928776e

f48d86252ecb2845cc37155e4c77ecbbda0ecf32 authored over 7 years ago

Remove restraints from final run. Add analysis scripts for finding bound state definition.

Former-commit-id: 584629afc92aa8841e83e7c87770c943a22cd216

05880f1be77dbc8c2e8fdcd9f1281fa71249c728 authored over 7 years ago

Added run.sh to prep and bound_state_definition directories. Also, use pmemd by default instead of pmemd.cuda

Former-commit-id: 0a504d98e963a5a614289b2246aa747295796213

17fb8406d21dc9964d0e865137f3621ab736b05e authored over 7 years ago

Scripts and input files for new tutorial section on finding definition of bound state before steady-state simulation

Former-commit-id: d3177feef703e004b08bbc7d6505ee437a0eded1

a9e92d3ce129dfa27cdc30a354b3d7f143563f29 authored over 7 years ago

Use Monte Carlo barostat

Former-commit-id: 322f7e8e9f1f464900e56fdc69d687f259813b47

3fca78d82c826a0ff7e30630b687f23f5c250df7 authored over 7 years ago

Image the trajectory so Na+ is at the origin

Former-commit-id: 9bb94643a113b949d940bda6e22f94a00e7783f2

9bb962175c2936cf7a20fc027d989fa916969138 authored over 7 years ago

Use LINCS instead of SHAKE

Former-commit-id: b1b63122e9604f0c79eab8b6557a035bea98c2a1

088a0e9ab95ba54f4d7d7674b8dfaf74129918ae authored over 7 years ago

Merge pull request #65 from agrossfield/master

add support for csh and derived shells

Former-commit-id: 3caf661e0b2e277f506cd3d501836d30a907f7a4

00e3f9d235307c7231184d968369b6be2d74697b authored over 7 years ago

Remove topology and coordinate files to prepare for explicit solvent simulation. Update mdp file for use with explicit solvent simulation (need to check this later).

Former-commit-id: 2df4ca889706bef0daa88b24f49299a7c0ee6d3e

cf97f670d844a626ad91068f3f3b0d3de9eaccfe authored over 7 years ago

add support for csh and derived shells

Former-commit-id: 47a236d5786c452398a2429fd9ec9ca29cff63ca

c55be970e9af5a93f74703a78e9c8a5172e50258 authored over 7 years ago

Always use the velocities from the end of the equilibration

Former-commit-id: 763bbc888f74499f1e4df26326f4f318eb882fe8

5d919656621c86db98b25e8a24f4d8827791ee15 authored over 7 years ago

Add lines for w_ipython configuration (probably need to edit later)

Former-commit-id: 196e37526e4055ec6d44750f836acc1230c28e6b

809d2b5fcba20d238f41cd182fdb4d1465d79aa6 authored over 7 years ago

Add python class for writing out xyz files of trajectory coordinates

Former-commit-id: cecdece306ef516acf87bde03bbd04cb7f0c761b

42297354f575e2c82346cf033202c5dfad5ddd99 authored over 7 years ago

Update annotations

Former-commit-id: e5b654d6dfd8c3db0252f6c1ee8d6ce5b3579ce6

449837bae0202300b67cfdce0f6ae6658f96e9f9 authored over 7 years ago

Add files for preparing explicit solvent simulation. Scripts and amber input files are provided. Also, a complete topology file and final restart file are provided, for users who wish to skip the equilibration

Former-commit-id: cd2a800bfb58181a03eb16ee00684e4199b21664

aaca518f9ca0669a3a1aea57d37a349dbec3454e authored over 7 years ago

basis state is now taken from ./prep, where we prepare and equilibrate explicit solvent simulation

Former-commit-id: f3873e10448c5be37aacec27852a8f4634790e44

c519fa256c24d4b5db2285f6b1365afa6a70d4b6 authored over 7 years ago

Thoroughly comment script; Replace switch (case) statements with if...then statements so less-experienced bash users can read code more easily; Update commands for explicit solvent; Stop piping log to aux

data

Former-commit-id: 91f2059498762c57a71cb39ad181c264df611729

6ebdcbfddaab94933bbf8c6fb8f3b85d407bb6e0 authored over 7 years ago

Add lines for copying initial coordinates from /prep

Former-commit-id: 01a62dd94a89e87c088624cedeacbf5d6f730610

48738f230c9adf24a3abbd46d9330e3232a700da authored over 7 years ago

Update for explicit solvent

Former-commit-id: 34763abb55798c223d922e5907cd822a7e9bca87

bb351ef678eb2ff13297f2accc2e1494be050852 authored over 7 years ago

For explicit solvent simulation, it is not so simple to generate random displacements; we would need to re-equilibrate. Instead, just symlink the basis state to the istate data reference

Former-commit-id: aa3bca624b5b5d48a6565ecec02210ed0cabf6be

86820f67677b76731e06abb7d7ee0f75ae9a1019 authored over 7 years ago

Increase pcoord length to be consistent with Zwier 2011, decrease bin target counts (experimental, need to test), remove log loader

Former-commit-id: 4ee7296098cffd266fb69cebaeb7e98137f3a4f7

832870c6908861954c8004444301fd8705be5c3d authored over 7 years ago

Rename basis state to be more explicit

Former-commit-id: 98c76f1b86e6472ecc97b816578cf90dfe41b5b1

a77e6d757deaf9ce2459d69a0715be8af3d4dcff authored over 7 years ago

To be consistent with Zwier 2011, use more timepoints per iteration. Also remove log loader, as it was prone to breaking with new amber releases

Former-commit-id: 60994f166ad5ccd76d683d664822c59dda08e909

22bd214f1af94cdb2fc249b35c625265a601ff76 authored over 7 years ago

Use periodic boundaries+explicit solvent with SHAKE

Former-commit-id: 2fcfa110b7f1bebd67a4c3e89c1a72aa866ccb73

e15e37187414f7c45eec37674c35c949c64d9bbd authored over 7 years ago

Removing commands for loading gmx logs into westpa

Former-commit-id: 5af32d31d2a90b273e10c0a7a6db2f55511bc8f3

308e20628c833d2ed25051c157e966e9629cd802 authored over 7 years ago

updated comments

Former-commit-id: 3f8b089ebdef428d281498abfb65517978729fe8

5e038f944f9987df464228bdcc2fe89856d68832 authored over 7 years ago

Removed log loader to simply tutorial and improve compatible across gmx versions

Former-commit-id: 7c2fcf7b1706c73a9dc83d2b6ceb84fa3ea5e986

c7629cc13bdc68b310da2211828148177263ecea authored over 7 years ago

No longer recycle at unbound state

Former-commit-id: d9b88f7fad52e9edac82959ac95fedd2329a522e

b1e3710d43bcc4ce026adde5451858204822aad5 authored over 7 years ago

Merge pull request #64 from westpa/tutorials_processes_work_manager

Na+/Cl- Tutorials now use "processes" work manager by default.

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7bd88333562320f17f620cb74d4f12b82982ce56 authored over 7 years ago

Tutorials now use processes work manager by default.

Former-commit-id: 23653112b7925c9668b4a12026b85b401cba5302

bd86b357e182974cf4b702519370d1076a27cc2d authored over 7 years ago

Revert "Add Makefile for conda build."

This reverts commit a7779a076f9098645750e90a5dcf462a25018504 [formerly 58d8e16bb974345d01b52bf64...

f709355e3b3dd39e296a2ee5f01afeeba47a1cc7 authored over 7 years ago

Revert "Update .westpa_gen.py to use PREFIX"

This reverts commit 577c358be852246774eca41c32cf03d3674b40eb [formerly 90908a7539c3fe73da4d61db8...

57ba87926c99ad947460508d58adb24df9730774 authored over 7 years ago

Revert "Fixed Makefile"

This reverts commit 733739fb8f04030e48dc327d31fc3349ac91c687 [formerly 5b1f8dc26cb702f07c096cd50...

8bfeedb989e53fbadf7c27d1b58e7f8fbaebb365 authored over 7 years ago

Revert "Fixed Makefile"

This reverts commit c81447c00c4ff4d5e59dd91b24154732d6498489 [formerly e815a3122f2615041a8652ab3...

311f8fa35ff4c10d130a898620ba52a462a65bd7 authored over 7 years ago

Fixed Makefile

Former-commit-id: e815a3122f2615041a8652ab323257ef534aa0c5

c81447c00c4ff4d5e59dd91b24154732d6498489 authored over 7 years ago

Fixed Makefile

Former-commit-id: 5b1f8dc26cb702f07c096cd50e3fb2c4358af775

733739fb8f04030e48dc327d31fc3349ac91c687 authored over 7 years ago

Update .westpa_gen.py to use PREFIX

Former-commit-id: 90908a7539c3fe73da4d61db82260c71f9acc5b5

577c358be852246774eca41c32cf03d3674b40eb authored over 7 years ago

Add Makefile for conda build.

Former-commit-id: 58d8e16bb974345d01b52bf64b442ed2dc1436ac

a7779a076f9098645750e90a5dcf462a25018504 authored over 7 years ago

Merge pull request #62 from westpa/anaconda2-4.4.0

Compatibility with latest version of Anaconda (2-4.4.0)

Former-commit-id: 71516f32006e32e22c8e2...

a87bc82f72da3a3f9b2c1590c5547b8742f1300b authored over 7 years ago

Made specification of the west_data_file_driver consistent with hierarchical scheme for other options.

Former-commit-id: 72d102242a1caa4b9fe0a2f4f3d6992848bc365a

f8ec0556e83d20a3d5521a615770bef69e9b9ad8 authored over 7 years ago

Numpy no longer supports conversion of a one-element scalar array to an index. Instead, we now manually convert the one-element array to a scalar.

Former-commit-id: 56a570ef70a0548b02e5a4b35808f973b94ecff9

18dc1270f48812d806ebff81ae848bb510bf53a4 authored over 7 years ago

h5py 2.7.0 no longer supports keyword arguments to make_fapl if driver=None. Removed the keyword argument NPY_ARRAY_FORCECAST

Former-commit-id: 0c9c155058affadbdacf2d8ed2d4a5737b5461f6

618e7fd6a14a2ac24c41b7ea37a834e8b3396081 authored over 7 years ago

Updated Sphinx landing page

Former-commit-id: 344bf035e0c8a3bc37b2fd2bed6da3c383b945d9

97d6e31290a43c8fed39e7eb03464caf091f303c authored over 7 years ago

Add executable odld example.

Former-commit-id: 3fb38cd4673f1d163f269489fa594fff692425ea

95b08c2cc3cc3172679a9471427e6fbf631e5ef8 authored over 7 years ago

Commented out images stuff in makefile since we don't need it without tutorials

Former-commit-id: 9ded6dea7222247f8513ef61978c274146422201

3ab3398f329d7c524bb3d33ccd9ff98de7bd9fc3 authored over 7 years ago

Removed individual tutorial links

Former-commit-id: b552e30d01ab16ea844ebf3b09021055004968b0

55e3ae4a1853c77bcc3a106e3ef10810d88a6059 authored over 7 years ago

Fixed tutorials links to point to GitHub wiki

Former-commit-id: 351cc3356958193719176e1f8e36ae5d30590da2

99eafc35fda556de43d261d07e8bab4ee7fa9fa3 authored over 7 years ago

Merge pull request #60 from westpa/nacl_gmx_2016_update

Na+/Cl- Gromacs 2016 update

Former-commit-id: 3b26e2a0417ddb17e4988b86259e422b41b813f9

b14e44b536cb6e4892c8a1ce9cf25aad96f0f3ba authored over 7 years ago

Updated w_ipa handling of --first-iter so that w.current accesses the proper data when first-iter is not 1.

Former-commit-id: 1750f989f6b0e80f3363961b76bd7b83778f768e

d8bf2eae993c93c7ad5995f8aa0dc0983f12fb25 authored over 7 years ago

Added nacl gmx tutorial for gmx 2016. Also uses w_ipa and yaml formatting.

Former-commit-id: acb99d55ec56cf643da414471e9dc293b0dcdee7

164862f32061faecdb62ed55266e6946490fcdad authored over 7 years ago

Merge pull request #44 from westpa/wipython

New Tool w_ipa merged into main branch. Everything is functional, and new examples will be adde...

bd934e990f51f797b679948eb3040719a163e8b8 authored over 7 years ago

Except this time, I ACTUALLY updated the script to check to see whether WEST_PYTHON has been set before overriding it.

Former-commit-id: 20150ac2da865f83e164bbe8f735233964f628b2

f2b639ccba14803290833f4fef0bdf4bfd7369ed authored over 7 years ago

Updated env.sh to check if WEST_PYTHON has already been set.

Former-commit-id: 4ee633e91cd475b62956432ebea8474b1053eb95

1676023a8717487fb07062495d9aac1fadc41722 authored over 7 years ago

Updated example...

Former-commit-id: 6ee8f835770f3ceac249534353a0db2768dd17fc

df2ede85b3f7ce79c98d28027db77c58413f6aeb authored over 7 years ago

Threw in a try/except for making sure it works with w_jupyter, and updated analysis.ipynb to work with the API.

Former-commit-id: d8402a3f28b4a26be9060595f0c054df01ecfdba

1f2a409e54ee8bf37c166693a33752c7cfd53945 authored over 7 years ago

Updated plotting interfaces.

Former-commit-id: fd2f4ed05ef040b0b316be7b3c9e9b989b84fcff

26ad5a402b7d22ce0452af02c755064efe849757 authored over 7 years ago

Made target_flux_evolution accessible as attribute.

Former-commit-id: da094abcd9dc2880577214ab2a75aa73725fe757

9cf379634afb82f7e60bbb2ec7dd1fbafda275ae authored over 7 years ago

Reverted changes to w_pdist

Former-commit-id: 96b25a335f7ec8e3977001fa2502bf34e2aeb68c

b2511a451c2b7c34a549ec746115c4d794336f2f authored over 7 years ago

Modified total fluxes a bit.

Former-commit-id: 60b42da215a71d35816719fc6255748f7c7ae394

8972cb2013f801b55f4b10452c02e2516ca2de36 authored over 7 years ago

Slightly changed successful trajectories.

Former-commit-id: 4583e5f942804982672ae7514dee45ca77a5c45b

3da7e271ee0669aa62c4b8004fb413d33cc5c95a authored over 7 years ago

added in global.

Former-commit-id: 88cac8e3b817133d4afe8a79ece4a364d0fbee55

93404d730e0106b4b9317924ad80155ead26106d authored over 7 years ago

Exposed total fluxes for direct trace only.

Former-commit-id: 0ddaea34c509a76d0a22fb4f492e2c7fb404037f

d1f508c0a29124606fee9045fb3302c123e5e3ef authored over 7 years ago

Merge branch 'wipython' of https://github.com/westpa/westpa into wipython

Updating for consistency with Adam's changes.

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75d0ce5532f992858de6316d07472d7d7f62e0cd authored over 7 years ago

Added in successful trajectories.

Former-commit-id: 14375ee2184c5ae9096e7774399299731e9327e1

6e91d3fa566b82ad8bbc9e2d404370da165c9063 authored over 7 years ago

Changed 'name' to 'key', so that WIPIDataset.__init__ receives the correct kwargs

Former-commit-id: 97cb6d42dee293b2a3963efce1d3796a2232e85e

2ee66411719079a1ad838deaa5808d0a304e5966 authored over 7 years ago

Fixed download link

Former-commit-id: ce8c153bd9ca05ab316610dccdd80b477a4d1b6b

eb238688346e163d5135598fe8c54da9459d21ae authored over 7 years ago

Merge pull request #57 from ASinanSaglam/master

Installation link fix

Former-commit-id: 79a0b5efeb8d4140327ca11998374411a30e967c

5f3bc0c22a0c6bb1c5a0909f4179899135cea8ff authored over 7 years ago