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Forcefield molecular dynamics and forcefield refactor #722

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Apr 3, 2024
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7637392
FF MD fully implemented
esoteric-ephemera Feb 15, 2024
659ad4a
change MD defaults to be NVT + Langevin dynamics
esoteric-ephemera Feb 15, 2024
ade233e
add md defaults that are as consistent with vasp implementation as po…
esoteric-ephemera Feb 16, 2024
e27b3fa
Merge branch 'materialsproject:main' into mlff_md
esoteric-ephemera Feb 16, 2024
db51e23
correct typing of langevin friction coeff
esoteric-ephemera Feb 16, 2024
1dcad1d
Add option to ForceFieldTaskDocument to store trajectory information …
esoteric-ephemera Feb 16, 2024
47a6180
Merge branch 'materialsproject:main' into mlff_md
esoteric-ephemera Feb 16, 2024
35fa20d
Add tests, remove dependence on pickle for trajectory i/o
esoteric-ephemera Feb 16, 2024
0d8fdef
fix tests, update matgl dependence
esoteric-ephemera Feb 17, 2024
013d113
rename MD forcefield class vars to be consistent with VASP MDSetGener…
esoteric-ephemera Feb 20, 2024
56c81c0
Merge branch 'materialsproject:main' into mlff_md
esoteric-ephemera Feb 22, 2024
1ec5910
Add option to explicitly specify thermostat as ASE MolecularDynamics …
esoteric-ephemera Feb 22, 2024
1e4fcb7
refactoring and add T/P schedule
chiang-yuan Feb 23, 2024
317412c
implement T/P schedule and attach callback func
chiang-yuan Feb 24, 2024
76ffa66
np.nan
chiang-yuan Feb 24, 2024
8253a35
np.nan
chiang-yuan Feb 24, 2024
96ae784
Merge branch 'mlff_md' of github.com:esoteric-ephemera/atomate2 into …
chiang-yuan Feb 24, 2024
298250d
small fixes
chiang-yuan Feb 27, 2024
0045b2b
pass ASE dynamics object instead of class, update docstring
chiang-yuan Feb 27, 2024
b870c04
add temp ramp test and make sure upper tria matrix cell
chiang-yuan Feb 28, 2024
71728a3
add stresses to trajeoctroy observer, add pressure schedule test
chiang-yuan Feb 28, 2024
45ddaa1
avoid `stresses` key not in taskdoc bug
chiang-yuan Feb 29, 2024
74bf6a0
Refactory TrajectoryObserver, add option to save trajectory as either…
esoteric-ephemera Mar 1, 2024
8f7fe84
Merge branch 'materialsproject:main' into mlff_md
esoteric-ephemera Mar 1, 2024
9ff7dae
Change decomposition to upper triangular cell only when Nose-Hoover r…
esoteric-ephemera Mar 1, 2024
9ea1ef9
Fix failing tests
esoteric-ephemera Mar 1, 2024
8727300
Change MD default TaskDoc ionic step to only store mandatory info
esoteric-ephemera Mar 1, 2024
56edc31
update pymatgen requirement because of CifParser deprecation
esoteric-ephemera Mar 1, 2024
b52a888
Merge branch 'materialsproject:main' into mlff_md
esoteric-ephemera Mar 4, 2024
5bbe9d7
Significant refactor to all forcefield jobs. Use commmon ASE calc str…
esoteric-ephemera Mar 6, 2024
656c5d6
Merge branch 'main' into mlff_md
esoteric-ephemera Mar 6, 2024
21dd709
Fix forcefield utils test and lint
esoteric-ephemera Mar 6, 2024
9ba7d29
Add revert_dtype env for running forcefield relax and md jobs / undo …
esoteric-ephemera Mar 6, 2024
0e8cce1
Merge branch 'main' into mlff_md
esoteric-ephemera Mar 7, 2024
8a2451e
refactor nequip jobs, add md default for nequip
esoteric-ephemera Mar 8, 2024
38ad2d6
Add GAP and Nequip MD tests, fix arg / kwarg passing in MD
esoteric-ephemera Mar 8, 2024
ac4916b
remove calculator_args / ase_calculator args, revert phonon job change
esoteric-ephemera Mar 8, 2024
21af2ae
Merge branch 'materialsproject:main' into mlff_md
esoteric-ephemera Mar 8, 2024
c19b39b
remove todo about adding magmoms to forcefield traj observer as that'…
esoteric-ephemera Mar 8, 2024
d95397d
Remove comments, add option to seed rng for MB velocities, turn on id…
esoteric-ephemera Mar 13, 2024
770aa3a
Merge branch 'materialsproject:main' into mlff_md
esoteric-ephemera Mar 13, 2024
3fa7b27
Merge branch 'materialsproject:main' into mlff_md
esoteric-ephemera Mar 25, 2024
8ecc1d1
Ensure CHGNet and M3GNet relax / static makers convert stress to eV/A…
esoteric-ephemera Mar 25, 2024
7b8f584
fix M3GNet test related to outdated cached model
esoteric-ephemera Mar 25, 2024
e4f407d
Merge branch 'materialsproject:main' into mlff_md
esoteric-ephemera Mar 28, 2024
d3aa25d
Fix dependencies, amend forcefield static option parsing
esoteric-ephemera Mar 29, 2024
ecf9356
linting
esoteric-ephemera Mar 29, 2024
733f60e
try to fix ci tests caused by torch / dgl incompatibility
esoteric-ephemera Mar 29, 2024
a0ead20
try to fix ci tests caused by torch / dgl incompatibility
esoteric-ephemera Mar 29, 2024
a4ea304
Merge branch 'materialsproject:main' into mlff_md
esoteric-ephemera Apr 1, 2024
d3c5ad6
Change: default time_step, units for time_step, initialization of tem…
esoteric-ephemera Apr 1, 2024
626b73b
linting / pre-commit
esoteric-ephemera Apr 1, 2024
9cee412
revert default time_step units to fs
esoteric-ephemera Apr 1, 2024
da809df
add missing forcefields to version check in forcefield task document
esoteric-ephemera Apr 1, 2024
2fd3b6b
allow complex schur decomposition
chiang-yuan Apr 1, 2024
a65a207
Merge pull request #1 from chiang-yuan/mlff-md
chiang-yuan Apr 1, 2024
3e7ced3
more snake case
janosh Apr 1, 2024
a4c6bd5
Decrease number of steps in tests for speed. Fix (?) temperature / pr…
esoteric-ephemera Apr 1, 2024
edbb2e7
linting
esoteric-ephemera Apr 1, 2024
400bbc3
fix T/P schedule
chiang-yuan Apr 2, 2024
5fd59dd
Merge pull request #2 from chiang-yuan/mlff_md
chiang-yuan Apr 2, 2024
0a06373
linting
esoteric-ephemera Apr 2, 2024
4a88d7b
replace dunder __getattribute__ --> getattr in forcefield test_md
esoteric-ephemera Apr 2, 2024
78ad999
Merge branch 'materialsproject:main' into mlff_md
esoteric-ephemera Apr 3, 2024
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2 changes: 1 addition & 1 deletion pyproject.toml
Original file line number Diff line number Diff line change
Expand Up @@ -52,7 +52,7 @@ forcefields = [
"ase>=3.22.1",
"chgnet>=0.2.2",
"mace-torch>=0.3.3",
"matgl>=0.9.0",
"matgl>=1.0.0",
"quippy-ase>=0.9.14",
]
docs = [
Expand Down
2 changes: 1 addition & 1 deletion src/atomate2/common/jobs/utils.py
Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@ def structure_to_conventional(
structure: Structure, symprec: float = SETTINGS.SYMPREC
) -> Structure:
"""
Job hat creates a standard conventional structure.
Job that creates a standard conventional structure.

Parameters
----------
Expand Down
1 change: 1 addition & 0 deletions src/atomate2/forcefields/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -10,4 +10,5 @@ class MLFF(Enum): # TODO inherit from StrEnum when 3.11+
GAP = "GAP"
M3GNet = "M3GNet"
CHGNet = "CHGNet"
Forcefield = "Forcefield" # default placeholder option
Nequip = "Nequip"
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