Stable 0.2.4 - Flare active learning & 2+3 body kernel

This is the stable version of flare, which is compatible with the flare_pp v0.1.3

Below are the auto-generated release notes

What's Changed

• Add punchout-related files, methods, and functions by @stevetorr in #1
• Mapped gp by @jonpvandermause in #2
• Mapped gp by @jonpvandermause in #3
• remove untested modules by @jonpvandermause in #4
• Docs by @jonpvandermause in #5
• Gitignore by @jonpvandermause in #6
• add additional information about pushing a forked repo by @jonpvandermause in #7
• add direct push guidelines by @jonpvandermause in #8
• Close #9 by @jonpvandermause in #11
• update mff in development branch by @jonpvandermause in #12
• Code standards by @jonpvandermause in #33
• Added Z_to_element function, tested, tightened up unit tests by @stevetorr in #32
• GP from AIMD + Serialization by @stevetorr in #27
• Edit lammps calculator by @jonpvandermause in #25
• Shorten/fix gp aimd test by @stevetorr in #44
• fix import in mff test by @jonpvandermause in #46
• new output class and add configuration output in ".xyz" format by @nw13slx in #42
• Now skips tests with QE if PWSCF_COMMAND is not found by @stevetorr in #48
• changed mff name #29 & tested update_L_alpha #23 by @YuuuXie in #50
• automatically write lmp file when mgp constructed #28 by @YuuuXie in #51
• CI with coverage by @anjohan in #60
• Merging master onto Serialization branch by @stevetorr in #65
• GP from AIMD Bugfix by @stevetorr in #68
• Bug/jon/gp update by @jonpvandermause in #71
• Added flexibility to user to frequency of output writing by @stevetorr in #69
• OTF will always flush buffer when writing Output by @stevetorr in #74
• create dft_interface module to interface with multiple DFT software. by @nw13slx in #61
• Serialization and representation GP + Small fixes by @stevetorr in #64
• Added to / from PMG methods, with pymatgen as an optional import by @stevetorr in #67
• Add setup.py for easy installation by @anjohan in #80
• change coverage report to only flare dir by @anjohan in #79
• Register on pypi, more badges by @anjohan in #81
• Feature/jon/npool by @jonpvandermause in #76
• Ase interface by @YuuuXie in #77
• Feature/lixin/gp from aimd by @nw13slx in #88
• Added draft of vasp_util.py for VASP trajectories and OTF by @kylebystrom in #82
• Quick fix to suppress pymatgen warnings by @kylebystrom in #93
• Bugfix/lixin/multiprocessing by @nw13slx in #90
• Fix: NP training labels now set for from_dict GPs by @stevetorr in #96
• Feature/steven/gpfa checkpoints by @stevetorr in #99
• WIP: GP now takes opt_params argument by @stevetorr in #92
• STD Species refactor + 100% coverage by @stevetorr in #104
• Yu/parallelize - close #83 & changed MGP by @YuuuXie in #105
• GP_FROM_AIMD change by @nw13slx in #103
• GPFA now has train by error option by @stevetorr in #106
• GPFA Output now prints gp forces, stds, dft forces by @stevetorr in #111
• Allow passing of kwargs to vasprun object by @stevetorr in #114
• WIP: vasp util compatibility with OTF by @stevetorr in #117
• WIP: Docstrings and typehints by @stevetorr in #118
• Ase interface - add stress & tested OTF parser by @YuuuXie in #107
• GP algebra docstring by @nw13slx in #120
• Ase interface by @YuuuXie in #121
• Added & unit tested store_dft_output by @stevetorr in #123
• Move store_dft_output logic to run_dft method by @stevetorr in #125
• Fix n_cpu in gpfa docstrings and logic by @stevetorr in #126
• Bugfix: OTF ignores structure species, when using pre-trained GP by @stevetorr in #130
• WIP: Merge development since merge onto branch by @stevetorr in #138
• WIP: merge multihyperparameters into energy_mgp by @nw13slx in #140
• Ase interface - close #133 by @YuuuXie in #136
• merge features/lixin/share_memory to yu/energy_mgp by @nw13slx in #141
• Merge/mc simple+development by @nw13slx in #146
• give the option to print hyperparameters to console by @jonpvandermause in #149
• Add custom force module and otf helper functions; remove xyz logs by @jonpvandermause in #152
• WIP: enable multiple hyperparameter groups and improve mp performance by @nw13slx in #139
• remove extraneous print statements by @jonpvandermause in #156
• Add space between floats in the output file by @jonpvandermause in #157
• fix manybody kernel etype issue by @nw13slx in #166
• [WIP] Development branch with many body feature and energy mapping by @nw13slx in #162
• Training on energy labels by @jonpvandermause in #128
• Added GPFA parser function to gp_from_aimd by @stevetorr in #173
• Jon/feature/auto sweep by @jonpvandermause in #174
• Enable multiple cutoff for two-, three- and manybody kernel by @nw13slx in #170
• fix predict by @jonpvandermause in #177
• Fixes minor typo in doc-string for gp by @dmclark17 in #179
• Predict.py now has 100% coverage by @stevetorr in #182
• Add, test method to remove force data from a gp by @stevetorr in #183
• Attempt to solve unit tests failing due to pytest by @stevetorr in #186
• Better user interface and consistency check through out env/gp/kernel modules by @nw13slx in #184
• Steven/feature/gp write choice by @stevetorr in #188
• [WIP]Add backwards compatibility for pickled envs by @stevetorr in #189
• fix optimization flag in ParameterHelper class by @nw13slx in #191
• Steven/bugfix/mgp predict by @stevetorr in #192
• Stress kernels and other kernel related changes by @jonpvandermause in #187
• Feature/lixin/gpfa improvement by @nw13slx in #195
• Clarify how to adjust GP hyp masks and cutoffs by @stevetorr in #200
• Steven/bugfix/cherrypicked bugfix by @stevetorr in #203
• Quality of life method: Structure valid method by @stevetorr in #204
• MGP - var upper bound & ASE Atoms by @YuuuXie in #198
• Merge development into master by @jonpvandermause in #199
• GPFA now has 'training plan' feature by @stevetorr in #207
• Fix MGP issues & Add LAMMPS pair styles by @YuuuXie in #215
• Bugfix: OTF parser, ASE md step, OTF checkpoint by @YuuuXie in #214
• Merge Development to master by @YuuuXie in #218
• Apply black formatting to flare and tests directories by @jonpvandermause in #226
• Env now has force attribute by @stevetorr in #229
• nose-hoover thermostat by @simonbatzner in #227
• Enable on-the-fly training in the NPT ensemble by @jonpvandermause in #225
• Integrate RBCMs onto development branch by @stevetorr in #238
• Add 2+MB Kernel by @stevetorr in #241
• Rewrite Active & Passive Learning for GPFA by @stevetorr in #230
• compile lammps+mgp during travis build by @jonpvandermause in #256
• remove assignment of wrapped positions to structure by @jonpvandermause in #255
• Add option for force_only & Add set_atoms by @YuuuXie in #254
• add min steps option by @jonpvandermause in #252
• Bugfix/yu/uncertainty print by @YuuuXie in #259
• Feature/simon/nosehoover update by @simonbatzner in #260
• Fix ASE calculator returning stale forces (#261) by @smheidrich in #262
• Development by @YuuuXie in #265
• Development - minor fixes to gp.py by @YuuuXie in #266
• Add optional calculator input to ase otf constructor by @jonpvandermause in #271
• Give the option in otf to add all atoms above a specified threshold by @jonpvandermause in #272
• Add stress argument to struc, serialization by @stevetorr in #276
• Revert "Add stress argument to struc, serialization" by @stevetorr in #277
• reset thermostat when rescaling temperature by @jonpvandermause in #275
• Steven/update/stress struc by @stevetorr in #278
• Development by @jonpvandermause in #279
• GPFA now can include energies by @stevetorr in #282
• Fix stress order in ASE calculator & update reference by @YuuuXie in #283
• bug fix by @aaronchen0316 in #287
• Development by @jonpvandermause in #293
• Jon/sgp checkpoint by @jonpvandermause in #294
• Bugfix: opt_algorithm for #298, and write_model for #299 by @YuuuXie in #300
• Add io feature to OTF by @YuuuXie in #302

New Contributors

• @jonpvandermause made their first contribution in #2
• @nw13slx made their first contribution in #42
• @anjohan made their first contribution in #60
• @kylebystrom made their first contribution in #82
• @simonbatzner made their first contribution in #227
• @smheidrich made their first contribution in #262
• @aaronchen0316 made their first contribution in #287

Full Changelog: https://github.com/mir-group/flare/commits/0.2.4