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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

Included comment

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github.com/westpa/westpa - 49d1dafded5504d0efceb0623d27c4da1ae3ecd5 authored about 7 years ago by Alex DeGrave <[email protected]>
Include topology file, so user does not have to generate their own

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github.com/westpa/westpa - 8ad6eb72df732b220eed022505755613bbe47b05 authored about 7 years ago by Alex DeGrave <[email protected]>
Include files so user does not have to run equilibration, if they choose not to.

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github.com/westpa/westpa - 6af49e8434775438825de2d4e497fc4c99fd90ae authored about 7 years ago by Alex DeGrave <[email protected]>
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

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github.com/westpa/westpa - 932b2026b55eb3ec1d6fd3ee36ad1208990ebbc1 authored about 7 years ago by Alex DeGrave <[email protected]>
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

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github.com/westpa/westpa - 64de01640497a43f361cba186e584dddac913fd6 authored about 7 years ago by Alex DeGrave <[email protected]>
Corrected paths in gmx distance call, and return the right part of the output

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github.com/westpa/westpa - 4e778389b74243646ec2d0664ae4497b3a6d3e4b authored about 7 years ago by Alex DeGrave <[email protected]>
Specify correct path for basis states, and update bin boundaries

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github.com/westpa/westpa - 469070aef3a64fdf9191d8c7cbb7d32426df0c57 authored about 7 years ago by Alex DeGrave <[email protected]>
Fixed erroneous comment

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github.com/westpa/westpa - a4433302b4d6538e2ed53a7b892c4d7666d5c2e7 authored about 7 years ago by Alex DeGrave <[email protected]>
Symlink files from ./prep directory when initializing simulation

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github.com/westpa/westpa - d9e418c0d5fb16248629087d7a8ca3137656523b authored about 7 years ago by Alex DeGrave <[email protected]>
Use 1 group for the thermostat

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github.com/westpa/westpa - f66e6a495b4d31c01e371bc9a4dce2dfd7b2c64f authored about 7 years ago by Alex DeGrave <[email protected]>
Use bstates from unbound directory

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github.com/westpa/westpa - 9bd992c8f3868fd4419e8eab0569123235965b97 authored about 7 years ago by Alex DeGrave <[email protected]>
Updated analysis bin boundaries

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github.com/westpa/westpa - 7dff3f10a123fc505b9e24a81512b9d55989c4bf authored about 7 years ago by Alex DeGrave <[email protected]>
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.

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github.com/westpa/westpa - a3f82cabf31d5f5788f4e20abe6473a57cfd1564 authored about 7 years ago by Alex DeGrave <[email protected]>
Redefined target state

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github.com/westpa/westpa - c8f6191ad03742ab692908cd7d4b523e83e220c5 authored about 7 years ago by Alex DeGrave <[email protected]>
Added comments for consistency with nacl_gmx tutorial

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github.com/westpa/westpa - 2852c49f57e259edacaed41130a67ed3b3f21bf3 authored about 7 years ago by Alex DeGrave <[email protected]>
Consistency with amber nacl tutorial; added docstring

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github.com/westpa/westpa - 6d47f36b855bc3035c1c09b1c2b9159110c626b1 authored about 7 years ago by Alex DeGrave <[email protected]>
Updates for consistency with amber nacl tutorial. Added comments to runseg.sh

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github.com/westpa/westpa - bec8a7abfb2ae8e54a4e586f3b07890078d8cf3b authored about 7 years ago by Alex DeGrave <[email protected]>
consistency with amber nacl tutorial

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github.com/westpa/westpa - 4a67eeb015e1f3983c1f37c14ebedd1a4bffac54 authored about 7 years ago by Alex DeGrave <[email protected]>
Consistency with gmx tutorial

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github.com/westpa/westpa - 8dd5cae30332c238a3dee7d1158db31c3840e4a9 authored about 7 years ago by Alex DeGrave <[email protected]>
Updated init.sh to be consistent with gmx tutorial

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github.com/westpa/westpa - caf59dbefd8cfb97000b0c01a531c97d05eebe3e authored about 7 years ago by Alex DeGrave <[email protected]>
Updated env.sh to be consistent with Gromacs tutorial

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github.com/westpa/westpa - a9537e33c4fe3522931e2780a99287e862a8adb0 authored about 7 years ago by Alex DeGrave <[email protected]>
Added files and scripts for preparing system

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github.com/westpa/westpa - 25ba0e16bc35a186432b4f4ca98365a9cd8559ae authored about 7 years ago by Alex DeGrave <[email protected]>
Added files for calculating position of bound state

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github.com/westpa/westpa - 722953edcd3e503e6292d8812a612884ac7740f0 authored about 7 years ago by Alex DeGrave <[email protected]>
Copy over nacl.parm7 from ./prep when initializing the simulation

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github.com/westpa/westpa - 485fa5641a581d95d8402569e91a07c65888f462 authored about 7 years ago by Alex DeGrave <[email protected]>
Updated docstring

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github.com/westpa/westpa - 94d77535ad2de140b20c8c9dcdc9ac26962859f7 authored about 7 years ago by Alex DeGrave <[email protected]>
Increased max wallclock time

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github.com/westpa/westpa - e86c882ff20a950d79b93a7ec7fbb472c58aec2c authored about 7 years ago by Alex DeGrave <[email protected]>
bin boundary update

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github.com/westpa/westpa - b92b72ee4687282fc88da46a64860e46dc9f9549 authored about 7 years ago by Alex DeGrave <[email protected]>
Delete topology symlink at end of iteration

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github.com/westpa/westpa - a3482bb18f150c762f925943a1b4115ddefa0d78 authored about 7 years ago by Alex DeGrave <[email protected]>
Use new md.in

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github.com/westpa/westpa - 9e1dc0b006530a14e47efbeff4c41f2acb28207c authored about 7 years ago by Alex DeGrave <[email protected]>
Update state definitions

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github.com/westpa/westpa - 2bf6e80bccceb7d659363688cb54ef6e833c6826 authored about 7 years ago by Alex DeGrave <[email protected]>
Use more steps of equilibration. The distance between ions was still changing slightly when only 1000 steps were used.

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github.com/westpa/westpa - aeff8b231c370ab046ee7f8b6e29fcd0123f3475 authored about 7 years ago by Alex DeGrave <[email protected]>
Increase initial separation of ions. Decrease restraint potentials during equilibration

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github.com/westpa/westpa - 950e9dde0be22012f0b868fc2931ed084f8d32c5 authored about 7 years ago by Alex DeGrave <[email protected]>
Updated west.cfg to be consistent with minimum separation of ions after minimization, and to use rounder numbers for the boundaries

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github.com/westpa/westpa - 6e376161e99a7a12fb999be35c5d3fb1de28f0ed authored about 7 years ago by Alex DeGrave <[email protected]>
Use separation of ions after minimization as definition for the bound state

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github.com/westpa/westpa - f48d86252ecb2845cc37155e4c77ecbbda0ecf32 authored about 7 years ago by Alex DeGrave <[email protected]>
Remove restraints from final run. Add analysis scripts for finding bound state definition.

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github.com/westpa/westpa - 05880f1be77dbc8c2e8fdcd9f1281fa71249c728 authored about 7 years ago by Alex DeGrave <[email protected]>
Added run.sh to prep and bound_state_definition directories. Also, use pmemd by default instead of pmemd.cuda

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github.com/westpa/westpa - 17fb8406d21dc9964d0e865137f3621ab736b05e authored about 7 years ago by Alex DeGrave <[email protected]>
Scripts and input files for new tutorial section on finding definition of bound state before steady-state simulation

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github.com/westpa/westpa - a9e92d3ce129dfa27cdc30a354b3d7f143563f29 authored about 7 years ago by Alex DeGrave <[email protected]>
Use Monte Carlo barostat

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github.com/westpa/westpa - 3fca78d82c826a0ff7e30630b687f23f5c250df7 authored about 7 years ago by Alex DeGrave <[email protected]>
Image the trajectory so Na+ is at the origin

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github.com/westpa/westpa - 9bb962175c2936cf7a20fc027d989fa916969138 authored about 7 years ago by Alex DeGrave <[email protected]>
Use LINCS instead of SHAKE

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github.com/westpa/westpa - 088a0e9ab95ba54f4d7d7674b8dfaf74129918ae authored about 7 years ago by Alex DeGrave <[email protected]>
Merge pull request #65 from agrossfield/master

add support for csh and derived shells

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github.com/westpa/westpa - 00e3f9d235307c7231184d968369b6be2d74697b authored about 7 years ago by Matthew Zwier <[email protected]>
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).

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github.com/westpa/westpa - cf97f670d844a626ad91068f3f3b0d3de9eaccfe authored about 7 years ago by Alex DeGrave <[email protected]>
add support for csh and derived shells

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github.com/westpa/westpa - c55be970e9af5a93f74703a78e9c8a5172e50258 authored about 7 years ago by Alan Grossfield <[email protected]>
Always use the velocities from the end of the equilibration

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github.com/westpa/westpa - 5d919656621c86db98b25e8a24f4d8827791ee15 authored about 7 years ago by Alex DeGrave <[email protected]>
Add lines for w_ipython configuration (probably need to edit later)

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github.com/westpa/westpa - 809d2b5fcba20d238f41cd182fdb4d1465d79aa6 authored about 7 years ago by Alex DeGrave <[email protected]>
Add python class for writing out xyz files of trajectory coordinates

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github.com/westpa/westpa - 42297354f575e2c82346cf033202c5dfad5ddd99 authored about 7 years ago by Alex DeGrave <[email protected]>
Update annotations

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github.com/westpa/westpa - 449837bae0202300b67cfdce0f6ae6658f96e9f9 authored about 7 years ago by Alex DeGrave <[email protected]>
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

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github.com/westpa/westpa - aaca518f9ca0669a3a1aea57d37a349dbec3454e authored about 7 years ago by Alex DeGrave <[email protected]>
basis state is now taken from ./prep, where we prepare and equilibrate explicit solvent simulation

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github.com/westpa/westpa - c519fa256c24d4b5db2285f6b1365afa6a70d4b6 authored about 7 years ago by Alex DeGrave <[email protected]>
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

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github.com/westpa/westpa - 6ebdcbfddaab94933bbf8c6fb8f3b85d407bb6e0 authored about 7 years ago by Alex DeGrave <[email protected]>
Add lines for copying initial coordinates from /prep

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github.com/westpa/westpa - 48738f230c9adf24a3abbd46d9330e3232a700da authored about 7 years ago by Alex DeGrave <[email protected]>
Update for explicit solvent

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github.com/westpa/westpa - bb351ef678eb2ff13297f2accc2e1494be050852 authored about 7 years ago by Alex DeGrave <[email protected]>
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

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github.com/westpa/westpa - 86820f67677b76731e06abb7d7ee0f75ae9a1019 authored about 7 years ago by Alex DeGrave <[email protected]>
Increase pcoord length to be consistent with Zwier 2011, decrease bin target counts (experimental, need to test), remove log loader

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github.com/westpa/westpa - 832870c6908861954c8004444301fd8705be5c3d authored about 7 years ago by Alex DeGrave <[email protected]>
Rename basis state to be more explicit

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github.com/westpa/westpa - a77e6d757deaf9ce2459d69a0715be8af3d4dcff authored about 7 years ago by Alex DeGrave <[email protected]>
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

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github.com/westpa/westpa - 22bd214f1af94cdb2fc249b35c625265a601ff76 authored about 7 years ago by Alex DeGrave <[email protected]>
Use periodic boundaries+explicit solvent with SHAKE

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github.com/westpa/westpa - e15e37187414f7c45eec37674c35c949c64d9bbd authored about 7 years ago by Alex DeGrave <[email protected]>
Removing commands for loading gmx logs into westpa

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github.com/westpa/westpa - 308e20628c833d2ed25051c157e966e9629cd802 authored about 7 years ago by Alex DeGrave <[email protected]>
updated comments

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github.com/westpa/westpa - 5e038f944f9987df464228bdcc2fe89856d68832 authored about 7 years ago by Alex DeGrave <[email protected]>
Removed log loader to simply tutorial and improve compatible across gmx versions

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github.com/westpa/westpa - c7629cc13bdc68b310da2211828148177263ecea authored about 7 years ago by Alex DeGrave <[email protected]>
No longer recycle at unbound state

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github.com/westpa/westpa - b1e3710d43bcc4ce026adde5451858204822aad5 authored about 7 years ago by Alex DeGrave <[email protected]>
Merge pull request #64 from westpa/tutorials_processes_work_manager

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

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github.com/westpa/westpa - 7bd88333562320f17f620cb74d4f12b82982ce56 authored about 7 years ago by Matthew Zwier <[email protected]>
Tutorials now use processes work manager by default.

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github.com/westpa/westpa - bd86b357e182974cf4b702519370d1076a27cc2d authored about 7 years ago by Alex DeGrave <[email protected]>
Revert "Add Makefile for conda build."

This reverts commit a7779a076f9098645750e90a5dcf462a25018504 [formerly 58d8e16bb974345d01b52bf64...

github.com/westpa/westpa - f709355e3b3dd39e296a2ee5f01afeeba47a1cc7 authored over 7 years ago by kimwong <[email protected]>
Revert "Update .westpa_gen.py to use PREFIX"

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

github.com/westpa/westpa - 57ba87926c99ad947460508d58adb24df9730774 authored over 7 years ago by kimwong <[email protected]>
Revert "Fixed Makefile"

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

github.com/westpa/westpa - 8bfeedb989e53fbadf7c27d1b58e7f8fbaebb365 authored over 7 years ago by kimwong <[email protected]>
Revert "Fixed Makefile"

This reverts commit c81447c00c4ff4d5e59dd91b24154732d6498489 [formerly e815a3122f2615041a8652ab3...

github.com/westpa/westpa - 311f8fa35ff4c10d130a898620ba52a462a65bd7 authored over 7 years ago by kimwong <[email protected]>
Fixed Makefile

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github.com/westpa/westpa - c81447c00c4ff4d5e59dd91b24154732d6498489 authored over 7 years ago by kimwong <[email protected]>
Fixed Makefile

Former-commit-id: 5b1f8dc26cb702f07c096cd50e3fb2c4358af775

github.com/westpa/westpa - 733739fb8f04030e48dc327d31fc3349ac91c687 authored over 7 years ago by kimwong <[email protected]>
Update .westpa_gen.py to use PREFIX

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github.com/westpa/westpa - 577c358be852246774eca41c32cf03d3674b40eb authored over 7 years ago by kimwong <[email protected]>
Add Makefile for conda build.

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github.com/westpa/westpa - a7779a076f9098645750e90a5dcf462a25018504 authored over 7 years ago by kimwong <[email protected]>
Merge pull request #62 from westpa/anaconda2-4.4.0

Compatibility with latest version of Anaconda (2-4.4.0)

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github.com/westpa/westpa - a87bc82f72da3a3f9b2c1590c5547b8742f1300b authored over 7 years ago by Matthew Zwier <[email protected]>
Made specification of the west_data_file_driver consistent with hierarchical scheme for other options.

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github.com/westpa/westpa - f8ec0556e83d20a3d5521a615770bef69e9b9ad8 authored over 7 years ago by Alex DeGrave <[email protected]>
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.

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github.com/westpa/westpa - 18dc1270f48812d806ebff81ae848bb510bf53a4 authored over 7 years ago by Alex DeGrave <[email protected]>
h5py 2.7.0 no longer supports keyword arguments to make_fapl if driver=None. Removed the keyword argument NPY_ARRAY_FORCECAST

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github.com/westpa/westpa - 618e7fd6a14a2ac24c41b7ea37a834e8b3396081 authored over 7 years ago by Alex DeGrave <[email protected]>
Updated Sphinx landing page

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github.com/westpa/westpa - 97d6e31290a43c8fed39e7eb03464caf091f303c authored over 7 years ago by ASinanSaglam <[email protected]>
Add executable odld example.

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github.com/westpa/westpa - 95b08c2cc3cc3172679a9471427e6fbf631e5ef8 authored over 7 years ago by kimwong <[email protected]>
Commented out images stuff in makefile since we don't need it without tutorials

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github.com/westpa/westpa - 3ab3398f329d7c524bb3d33ccd9ff98de7bd9fc3 authored over 7 years ago by ASinanSaglam <[email protected]>
Removed individual tutorial links

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github.com/westpa/westpa - 55e3ae4a1853c77bcc3a106e3ef10810d88a6059 authored over 7 years ago by ASinanSaglam <[email protected]>
Fixed tutorials links to point to GitHub wiki

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github.com/westpa/westpa - 99eafc35fda556de43d261d07e8bab4ee7fa9fa3 authored over 7 years ago by ASinanSaglam <[email protected]>
Merge pull request #60 from westpa/nacl_gmx_2016_update

Na+/Cl- Gromacs 2016 update

Former-commit-id: 3b26e2a0417ddb17e4988b86259e422b41b813f9

github.com/westpa/westpa - b14e44b536cb6e4892c8a1ce9cf25aad96f0f3ba authored over 7 years ago by Lillian Chong <[email protected]>
Updated w_ipa handling of --first-iter so that w.current accesses the proper data when first-iter is not 1.

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github.com/westpa/westpa - d8bf2eae993c93c7ad5995f8aa0dc0983f12fb25 authored over 7 years ago by Alex DeGrave <[email protected]>
Added nacl gmx tutorial for gmx 2016. Also uses w_ipa and yaml formatting.

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github.com/westpa/westpa - 164862f32061faecdb62ed55266e6946490fcdad authored over 7 years ago by Alex DeGrave <[email protected]>
Merge pull request #44 from westpa/wipython

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

github.com/westpa/westpa - bd934e990f51f797b679948eb3040719a163e8b8 authored over 7 years ago by Adam J. Pratt <[email protected]>
Except this time, I ACTUALLY updated the script to check to see whether WEST_PYTHON has been set before overriding it.

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github.com/westpa/westpa - f2b639ccba14803290833f4fef0bdf4bfd7369ed authored over 7 years ago by Adam Pratt <[email protected]>
Updated env.sh to check if WEST_PYTHON has already been set.

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github.com/westpa/westpa - 1676023a8717487fb07062495d9aac1fadc41722 authored over 7 years ago by Adam Pratt <[email protected]>
Updated example...

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github.com/westpa/westpa - df2ede85b3f7ce79c98d28027db77c58413f6aeb authored over 7 years ago by Adam Pratt <[email protected]>
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

github.com/westpa/westpa - 1f2a409e54ee8bf37c166693a33752c7cfd53945 authored over 7 years ago by Adam Pratt <[email protected]>
Updated plotting interfaces.

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github.com/westpa/westpa - 26ad5a402b7d22ce0452af02c755064efe849757 authored over 7 years ago by Adam Pratt <[email protected]>
Made target_flux_evolution accessible as attribute.

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github.com/westpa/westpa - 9cf379634afb82f7e60bbb2ec7dd1fbafda275ae authored over 7 years ago by Alex DeGrave <[email protected]>
Reverted changes to w_pdist

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github.com/westpa/westpa - b2511a451c2b7c34a549ec746115c4d794336f2f authored over 7 years ago by Adam Pratt <[email protected]>
Modified total fluxes a bit.

Former-commit-id: 60b42da215a71d35816719fc6255748f7c7ae394

github.com/westpa/westpa - 8972cb2013f801b55f4b10452c02e2516ca2de36 authored over 7 years ago by Adam Pratt <[email protected]>
Slightly changed successful trajectories.

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github.com/westpa/westpa - 3da7e271ee0669aa62c4b8004fb413d33cc5c95a authored over 7 years ago by Adam Pratt <[email protected]>
added in global.

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github.com/westpa/westpa - 93404d730e0106b4b9317924ad80155ead26106d authored over 7 years ago by Adam Pratt <[email protected]>
Exposed total fluxes for direct trace only.

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github.com/westpa/westpa - d1f508c0a29124606fee9045fb3302c123e5e3ef authored over 7 years ago by Adam Pratt <[email protected]>
Merge branch 'wipython' of https://github.com/westpa/westpa into wipython

Updating for consistency with Adam's changes.

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github.com/westpa/westpa - 75d0ce5532f992858de6316d07472d7d7f62e0cd authored over 7 years ago by Alex DeGrave <[email protected]>
Added in successful trajectories.

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github.com/westpa/westpa - 6e91d3fa566b82ad8bbc9e2d404370da165c9063 authored over 7 years ago by Adam Pratt <[email protected]>
Changed 'name' to 'key', so that WIPIDataset.__init__ receives the correct kwargs

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github.com/westpa/westpa - 2ee66411719079a1ad838deaa5808d0a304e5966 authored over 7 years ago by Alex DeGrave <[email protected]>
Fixed download link

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github.com/westpa/westpa - eb238688346e163d5135598fe8c54da9459d21ae authored over 7 years ago by ASinanSaglam <[email protected]>
Merge pull request #57 from ASinanSaglam/master

Installation link fix

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github.com/westpa/westpa - 5f3bc0c22a0c6bb1c5a0909f4179899135cea8ff authored over 7 years ago by Lillian Chong <[email protected]>