Westpa 2.0 restruct #15
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* remove references to 1/kT in plothist * fix axes.images deprecation
* WESTPA 2 citations * badges for README * tutorial buttons * Update README.rst buttons to two rows
* initial attempt to add directional MAB binning * removed unnecessary bin number protection in the MAB code * Made direction an optional parameter for the MAB scheme (default is bidirectional) * removed print statements and formatting changes * added back in the print statements for min/max and directions Co-authored-by: She Zhang <[email protected]> Co-authored-by: She Zhang <[email protected]> Co-authored-by: Anthony Bogetti <[email protected]>
* Changed group_function to subgroup_function * Added binless mapper for general use with clusters * changed name of Kim's grouping to subgroups in driver test * fixed binless resampling, now works flawlessly in n dimensions * no printing cluster centers if not splitting * adjusted groups when walkers is less than requested num of groups * added option to cluster in 2D * fix _rc.py by removing old lines * added auto-detect of BinlessMapper and edited DocStrings * code cleanup for we_driver and sim_manager * run remove_node in recursive mode for h5io Co-authored-by: Anthony Bogetti <[email protected]> Co-authored-by: Jeremy Leung <[email protected]> Co-authored-by: Jeremy Leung <[email protected]>
#245) * setting aux_data to None if the dataset does not exist in west.h5 (as opposed to triggering an error in h5py) * minor change * allowing WEED to use a different bin mapper than the one used by the simulation Co-authored-by: She Zhang <[email protected]>
…(Attempt #2) (#221) * added options for weight thresholds in west.cfg * fixed formatting * rerun CI * allow while loop in adjust_count to run multiple times * lint * clean up * soft-limit the while loops in adjust_counts instead * add warning for min_weight < 1e-100 * moved 1e-100 weight warning to sim_manager instead * check length instead of bin object in adjust_count * additional checks to threshold bounds * fixed log messages * swap check order for threshold bounds Co-authored-by: Anthony Bogetti <[email protected]> Co-authored-by: Jeremy Leung <[email protected]> Co-authored-by: Jeremy Leung <[email protected]>
* fix * Added version history for version 8 * initial commit for the HDF5 trajectory loader * allowing iteration 0 * minor fix * fixed an issue when loading the pcoords from west.h5 with overlapping frames * minor bug fix for printing the traceback properly * fixed documentation for HDF5MDTrajectory * minor fix * fixes according to comments * extracting the last frame from the parent trajectory for the init point * moving import to the file header * explicitly handles the initial states in HDF5MDTrajectory * copy/pasted README to ReadtheDocs * fixed an error when atom_indices is passed to WESTIterationFile.read * Fixed a bug in default pcoord assignment in WESTTrajectory * custom dataset loader from config fix * setting aux_data to None if the dataset does not exist in west.h5 (as opposed to triggering an error in h5py) * minor change * allowed initial states to be stored when using the HDF5 framework * added a note to the H5MDTrajectory reader * use recursive mode in remove_node in h5io * seglog bug fix Co-authored-by: She Zhang <[email protected]> Co-authored-by: Jeff Thompson <[email protected]> Co-authored-by: Jeremy Leung <[email protected]>
* mab fix to add back in isfinal * fix mab_manager so it doesn't run assign MAB twice after a restart on a subset of segs * final fix to walkers out of bound error
* move we_driver thresholds checks to separate method * modify binless to take group_arguments from YAML * update w_run to report error message * add group_arguments option to binless * lint for binless.py * spacing fix for error message in w_run * fix binless_manager so it doesn't run assign twice after a restart on a subset of segs * print w_run.py Exception message more elegantly * better detaction for group_arguments * renaming remaining references to 'groups' as subgroups * move number of subgroups output to debug
#248) * added a MAB option to skip splitting in a specified pcoord dimension * Improved error messages for incorrect direction/skip list shapes * Logging used the westpa.rc logger * logging name now reflects the MAB binning script. Co-authored-by: Anthony Bogetti <[email protected]>
* port of w_pdist custom weights Co-authored-by: ASinanSaglam <[email protected]> * fix w_pdist test * fix w_trace test memory leak while I'm at it Co-authored-by: ASinanSaglam <[email protected]>
* added logging details to binless manager and driver * update to west file version 9 and fix Istate probability error during recycling * move logger for binless.py to itself Co-authored-by: Anthony Bogetti <[email protected]>
Co-authored-by: Anthony Bogetti <[email protected]>
* change it so processes will run with 'fork' on macs * Added commentary on multiprocessing start methods * lint for processes.py Co-authored-by: JD Russo <[email protected]>
* initial try to fix bin reporting * fixed init bin reporting and mab bin reporting * moved bin pop reporting to finalize iteration * moved bin reporting to finalize_iteration, commented code throughout * fix cases when 'direction' or 'skip' are not specified * moved MAB kwargs logic to __init__ so it only runs at the start of w_run/w_init and not at every iteration * fixed an issue with bin reporting and added helpful log statements * no longer need double-checks * moved reporting back to prepare iteration, various clean-ups * changed the weight threshold back to 10*39 * added splitting back in for recycled walkers Co-authored-by: Anthony Bogetti <[email protected]> Co-authored-by: Jeremy Leung <[email protected]>
* added mab_log option * mab.py lint * refine mab_log to output only at end of iteration * lint fixes for mab.py
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