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Accumulated changes from dev since Jan. 25. #114

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merged 163 commits into from
Mar 22, 2023
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c6776e1
updated license
Jan 25, 2023
1db9216
added basic docs
Jan 25, 2023
f9f6f19
added installation instructions to docs
Jan 25, 2023
e8c68ad
fixed spelling mistake in training
Jan 25, 2023
a2110fc
module docs outline
Jan 25, 2023
5b988c2
new layout experiment
Jan 25, 2023
bf93b90
added some sphinx extensions
Jan 25, 2023
b5b83de
Merge branch 'dev' into docs
Jan 26, 2023
da1bdde
added sphionx autodoc typehints
Jan 26, 2023
88898c7
added tutorial drafts
Jan 31, 2023
4e2e2d9
removed roadmap, added badges, added references to README.md
Jan 31, 2023
1096278
added usage authors and contributing sections to README.md
Jan 31, 2023
4181b2f
cleanup
Tetracarbonylnickel Feb 6, 2023
477a0ef
displacement and neighbor functions now can be initialized
Tetracarbonylnickel Feb 8, 2023
30fe768
Added frac coordinates to atoms list processing
Tetracarbonylnickel Feb 8, 2023
d76a5db
added frac_coord bool to config
Tetracarbonylnickel Feb 8, 2023
c282717
added frac_coords to dataset_neighborlist
Tetracarbonylnickel Feb 8, 2023
0519f12
changed cell to box
Tetracarbonylnickel Feb 10, 2023
4094021
linting
Tetracarbonylnickel Feb 10, 2023
6f700e6
fix
Tetracarbonylnickel Feb 13, 2023
3f48d84
linthing
Tetracarbonylnickel Feb 13, 2023
0f93173
updated poetry lock and toml
Feb 13, 2023
e492cb7
fixed typo
Feb 13, 2023
4ad0a17
bug fix
Feb 13, 2023
e2db33d
not ready
Feb 14, 2023
14a3843
renaming variables
Feb 14, 2023
f07212a
linthing
Feb 14, 2023
22d7fcc
implemented Flax version of NTKLinear
Feb 20, 2023
9ffc0b7
Separated atomistic readout class form main model
Feb 20, 2023
fbaf87c
implemented per element shift scale flax version
Feb 20, 2023
27e5f0c
implemented flax versions of the baiss and radial functions
Feb 20, 2023
b3648ed
implemented Flax version of GM descriptor
Feb 20, 2023
4ede5a3
implemented atomistic Flax model
Feb 20, 2023
f07a0e4
added unit tests for flax versions of the layers
Feb 20, 2023
5d1ac66
fixed bug in atomic masking unit test
Feb 20, 2023
bfdbf3a
dtype64
Tetracarbonylnickel Feb 20, 2023
d208b4e
added fp64_sum, EnergyModel, EnergyForceModel and ModelBuilder classes
Feb 20, 2023
2cbc9cc
added ModelBuilder Class
Feb 20, 2023
f9d92a8
added Energy and EnergyForceModel unit tests
Feb 20, 2023
ab384cf
linting
Feb 20, 2023
f54260e
linting 2
Feb 20, 2023
4297a97
removed comment from model unit test
Feb 20, 2023
142af52
fixed neighborlist bug
Tetracarbonylnickel Feb 20, 2023
535f45b
added scale shift args to readout in model builder
Feb 20, 2023
3ef3aac
disabled pretty printing in cli
Feb 21, 2023
92733b6
stronger enforement of TF GPU restriction
Feb 21, 2023
cfb3d79
added temporary use_flax config option
Feb 21, 2023
1951747
added dr type cast to radial fn
Feb 21, 2023
6d839d7
removed same shape requirement from scaling
Feb 21, 2023
dfe1fe4
added type casts to GM layer
Feb 21, 2023
3728e94
fixed modelbuilder
Feb 21, 2023
bec3ddf
added model builder to run
Feb 21, 2023
0483cf2
fixed model and opt unit tests
Feb 21, 2023
6a2395e
added use_flax option to get_opt
Feb 21, 2023
a9da45b
fixed haiku LR schedules
Feb 21, 2023
ff17ebf
Merge remote-tracking branch 'origin/flax_model' into variable_cell_size
Tetracarbonylnickel Feb 21, 2023
c821295
opt test fix
Tetracarbonylnickel Feb 21, 2023
2c25f0d
temporary chenge to GPU settings
Feb 21, 2023
34b7ced
added small value to dr to avoid div by 0
Feb 21, 2023
43aa900
poetry update
Feb 21, 2023
a9b11bc
Merge remote-tracking branch 'origin/flax_model' into variable_cell_size
Tetracarbonylnickel Feb 22, 2023
d37facf
linting
Tetracarbonylnickel Feb 22, 2023
2a81142
different cell sizes for the flax model
Tetracarbonylnickel Feb 22, 2023
a76d305
small fix
Feb 22, 2023
2ff7981
added flax model to ase calc
Feb 22, 2023
945c2fa
added default args to scale shift params in model builder
Feb 22, 2023
2a8ac66
added Flax Model to NVT jaxmd
Feb 22, 2023
b5d1ae0
Merge remote-tracking branch 'origin/flax_model' into variable_cell_size
Feb 23, 2023
46ac71e
added type conversion to radial_fn
Feb 27, 2023
c01fe0d
added type casts to descriptor
Feb 27, 2023
9c6f445
Merge branch 'flax_model' into flax_cell_size
Feb 28, 2023
1bbf074
turned lr config from PositiveFloat to NonNegative Float to allow par…
Feb 28, 2023
70893d9
get_opt now freezes parameters with lr=0
Feb 28, 2023
a9be10d
linting
Feb 28, 2023
b465919
added transfer learning option to run
Feb 28, 2023
250a6bb
added parameter transfer in transfer_learning module
Feb 28, 2023
0d1a226
added unit test for parameter transfer
Feb 28, 2023
1bc9aa0
linting of opt test
Feb 28, 2023
de42454
unit test linting
Feb 28, 2023
61eb489
get_opt linting
Feb 28, 2023
035e7d8
added docstrings to CheckpointConfig parameters
Feb 28, 2023
78fa87b
descriptor now always computes distances in fp64
Mar 1, 2023
8346a14
disabled cell list in jaxmd NVT
Mar 1, 2023
5a65878
fixes comments of PR #90
Mar 1, 2023
92d7618
removed unnecessary comments from init
Mar 2, 2023
e9a5c6c
set Flax model as default
Mar 2, 2023
988b0ab
refactored model builder into separate module
Mar 2, 2023
65be9cb
included flax model in the model evaluation.
Mar 2, 2023
00a6d9b
Merge branch 'transfer_learning' of https://github.com/GM-NN/gmnn-jax…
Mar 2, 2023
f7e7129
linting
Mar 2, 2023
d918b57
bug fix
Mar 2, 2023
558ed2a
Merge pull request #90 from GM-NN/transfer_learning
Tetracarbonylnickel Mar 2, 2023
a28e13c
Merge remote-tracking branch 'origin/dev' into name_change
Mar 2, 2023
7c03f73
linting
Mar 2, 2023
25bf8f4
name change
Mar 2, 2023
6df5e63
Organisation name change
Mar 2, 2023
4c487e4
name change
Mar 2, 2023
469829f
bug fix
Mar 2, 2023
51b92ed
test bug fix
Mar 2, 2023
0897fa1
git action debug
Mar 2, 2023
f7fbf47
git action debug
Mar 2, 2023
6d2c1c8
was not tracked
Tetracarbonylnickel Mar 2, 2023
6a290e6
model name change
Tetracarbonylnickel Mar 2, 2023
7465efd
PR #98 comments
Tetracarbonylnickel Mar 2, 2023
3566a6d
lining
Tetracarbonylnickel Mar 2, 2023
d525896
Merge pull request #98 from GM-NN/name_change
Tetracarbonylnickel Mar 2, 2023
0390f85
removed debug print statement
Mar 5, 2023
128c95e
added logging to parameter transfer
Mar 5, 2023
eb95de5
added logging to checkpoint loading
Mar 5, 2023
ed78b3c
fixed typo in eval logging
Mar 5, 2023
7b598b6
set all train configs to forbid extra fields, fixed docstring typo, u…
Mar 5, 2023
5789502
removed old GMNN-JAX logo
Mar 5, 2023
4998eb5
added validator for whether both/neither data_path, train_data_path a…
Mar 5, 2023
b224068
improved error message for data path validator by switching to ValueE…
Mar 5, 2023
cd3888e
linting
Mar 6, 2023
c256983
linting
Mar 6, 2023
c2cf8e2
changing dependencies of the organisation name
Tetracarbonylnickel Mar 6, 2023
06b16b5
Merge pull request #101 from apax-hub/validation
Tetracarbonylnickel Mar 6, 2023
30d7e92
Merge pull request #100 from apax-hub/logging_additions
Tetracarbonylnickel Mar 6, 2023
743f857
Merge pull request #102 from apax-hub/rename_org
M-R-Schaefer Mar 6, 2023
7bf0602
updated README
Mar 6, 2023
73d0aab
Merge pull request #103 from apax-hub/readme_update
Tetracarbonylnickel Mar 6, 2023
29f60e7
moved computation of current temperature into jitted function
Mar 6, 2023
dc7741d
nvt trajectory now contains energy
Mar 6, 2023
7fdd23a
moved JaxMD trajectory writing to utility class
Mar 7, 2023
96acb97
fix traj handler mathod name bug
Mar 7, 2023
87e9a49
added option tonot have embedding params and to limit the number of c…
Mar 7, 2023
4a3ec7f
uncommented emb and n_contr for hk compatibility
Mar 7, 2023
ca42f72
fixed wrong default for contractions
Mar 7, 2023
f1a21a8
fix again
Mar 7, 2023
d9ddb9a
removed haiku model
Mar 7, 2023
58f9eb3
Merge pull request #105 from apax-hub/md_loop
M-R-Schaefer Mar 8, 2023
dc7ff60
Merge pull request #106 from apax-hub/g_params
M-R-Schaefer Mar 8, 2023
90aee18
fixed comment on the shape of the species coeffs
Mar 8, 2023
46312b2
Merge branch 'dev' of https://github.com/GM-NN/gmnn-jax into dev
Mar 8, 2023
b077678
bumped np version, updated email, added keywords
Mar 15, 2023
aacd687
bug fix issue #108
Mar 22, 2023
cd11f26
linting
Mar 22, 2023
4fac657
temporarily bug fix #111 memory allocation
Mar 22, 2023
cb1bc06
clean up
Mar 22, 2023
10491ae
tensorboard bugt fix #104
Mar 22, 2023
faa8778
linting
Mar 22, 2023
958fdd6
comment
Mar 22, 2023
443be1b
Merge pull request #112 from apax-hub/neighborlist_bug
M-R-Schaefer Mar 22, 2023
d7b4c2a
updated visualise command to use flax
Mar 22, 2023
2f92792
removed `Flax` from layer names
Mar 22, 2023
d7a97d0
atomistic model now accepts both idxs and NLs
Mar 22, 2023
c2f2d3f
linting remove hk option
Mar 22, 2023
7e6ca32
rm hk from eval
Mar 22, 2023
f06bba7
rm hk from run
Mar 22, 2023
cd3c0da
removed superfluous visualize function
Mar 22, 2023
9256563
added box to create minimal input
Mar 22, 2023
ad0838e
updated integration test configs
Mar 22, 2023
87d36b2
moved all tests over to flax
Mar 22, 2023
b4c6f5f
bump up python version
Mar 22, 2023
d1a6ba4
Merge branch 'dev' into rm_hk
Mar 22, 2023
099666b
poetry update
Mar 22, 2023
4d2b492
added back slicing with elipses in descriptor
Mar 22, 2023
771f61c
turned positions back intop jnp array in tun md test
Mar 22, 2023
0624962
Merge pull request #113 from apax-hub/rm_hk
M-R-Schaefer Mar 22, 2023
f35ba27
Merge branch 'dev' into update_np
Mar 22, 2023
d299282
Merge pull request #110 from apax-hub/update_np
M-R-Schaefer Mar 22, 2023
7dd478c
Merge branch 'main' into dev
Mar 22, 2023
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temporarily bug fix #111 memory allocation
Tretracarbonylnickel committed Mar 22, 2023

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commit 4fac6575fbcc16bf83885fa45bda54eccb14404d
2 changes: 2 additions & 0 deletions apax/__init__.py
Original file line number Diff line number Diff line change
@@ -1,10 +1,12 @@
import os
import warnings

import tensorflow as tf
from jax.config import config as jax_config

tf.config.set_visible_devices([], "GPU")

os.environ["XLA_PYTHON_CLIENT_PREALLOCATE"] = "false"
warnings.filterwarnings(action="ignore", category=FutureWarning, module=r"jax.*scatter")
jax_config.update("jax_enable_x64", True)
# jax_config.update("jax_debug_nans", True)