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[WIP] ABINIT DFPT SHG #1

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015987f
clean up test_lobster_task_document
janosh May 11, 2024
29a5731
Document the option to run LOBSTER with one jobscript only (#811)
JaGeo May 11, 2024
3b550be
Add magnetic orderings workflow (#432)
mattmcdermott May 11, 2024
df7c769
`from_...` class methods now return `typing_extensions.Self` (#840)
janosh May 11, 2024
d22e247
Update LobsterPy version (#841)
JaGeo May 11, 2024
313f809
CI add `repository_dispatch` event for `pymatgen_ci_trigger` (#835)
janosh May 11, 2024
c77e21f
Bump phonopy from 2.22.1 to 2.23.1 (#846)
dependabot[bot] May 13, 2024
7f55cd3
Bump lobsterpy from 0.4.0 to 0.4.4 (#848)
dependabot[bot] May 13, 2024
aee4be8
Bump furo from 2024.1.29 to 2024.5.6 (#847)
dependabot[bot] May 13, 2024
832fdbe
Fix `TrajectoryObserver.to_ase_trajectory` return type (#852)
janosh May 14, 2024
dd582ff
Fix title hierarchies in VASP documentation (#853)
JaGeo May 15, 2024
e84f1fa
fix typos
janosh May 15, 2024
c369c86
Make Fermi Energy Optional for FHI-aims (#793)
tpurcell90 May 16, 2024
2fefc6f
Bump python-ulid from 2.5.0 to 2.6.0 (#858)
dependabot[bot] May 27, 2024
2d24f81
Bump typing-extensions from 4.11.0 to 4.12.0 (#859)
dependabot[bot] May 27, 2024
f826b29
Bump sphinx-design from 0.5.0 to 0.6.0 (#857)
dependabot[bot] May 27, 2024
3079e55
Bump monty from 2024.3.31 to 2024.5.24 (#860)
dependabot[bot] May 27, 2024
a5e502f
Handling failures in elastic flow (#861)
gpetretto May 29, 2024
91e133f
Bump typing-extensions from 4.12.0 to 4.12.1 (#864)
dependabot[bot] Jun 3, 2024
3336910
Bump pymatgen from 2024.5.1 to 2024.5.31 (#867)
dependabot[bot] Jun 3, 2024
58e6c92
Bump ipython from 8.23.0 to 8.25.0 (#869)
dependabot[bot] Jun 3, 2024
25817f4
Bump pydantic from 2.7.1 to 2.7.2 (#868)
dependabot[bot] Jun 3, 2024
760e537
Bump dscribe from 2.1.0 to 2.1.1 (#865)
dependabot[bot] Jun 3, 2024
8016942
transpose matrix (#872)
JaGeo Jun 4, 2024
cda583b
Add test for supercell matrix creation in phonon workflow (#873)
JaGeo Jun 5, 2024
5043fe6
Bump typing-extensions from 4.12.1 to 4.12.2 (#877)
dependabot[bot] Jun 10, 2024
179d836
Bump ijson from 3.2.3 to 3.3.0 (#876)
dependabot[bot] Jun 10, 2024
4e86c93
Bump pydantic-settings from 2.2.1 to 2.3.1 (#875)
dependabot[bot] Jun 10, 2024
b8ee8a6
Bump matgl from 1.1.1 to 1.1.2 (#882)
dependabot[bot] Jun 10, 2024
905c470
Bump chgnet from 0.3.5 to 0.3.8 (#881)
dependabot[bot] Jun 10, 2024
fe52d5a
Bump pydantic from 2.7.2 to 2.7.3 (#884)
dependabot[bot] Jun 10, 2024
50ae3c0
Bump phonopy from 2.23.1 to 2.24.2 (#879)
dependabot[bot] Jun 10, 2024
40bfecd
`ruff` fixes (#894)
janosh Jun 22, 2024
0042441
Bump pydantic from 2.7.3 to 2.7.4 (#886)
dependabot[bot] Jun 22, 2024
40f6f80
Bump pymatgen from 2024.5.31 to 2024.6.10 (#887)
dependabot[bot] Jun 22, 2024
4679806
Bump pydantic-settings from 2.3.1 to 2.3.3 (#888)
dependabot[bot] Jun 22, 2024
1ffc588
Bump python-ulid from 2.6.0 to 2.7.0 (#897)
dependabot[bot] Jun 24, 2024
3875bac
Bump phonopy from 2.24.2 to 2.24.3 (#898)
dependabot[bot] Jun 24, 2024
94ef40f
remove restart_from for mrgddb job
VicTrqt Jun 24, 2024
258b9d9
remove critical events for mrgddb
VicTrqt Jun 24, 2024
19e1c5f
simplify mrgddb resolve_dep_exts and merge MrgddbSetGenerator into Mr…
VicTrqt Jun 24, 2024
5297c3b
turn shg classmethod into subclass
VicTrqt Jun 24, 2024
01a0ac9
check consistency DDK, DDE, DTE, Mrgddb
VicTrqt Jun 24, 2024
861f6d2
add check for output None
VicTrqt Jun 25, 2024
40014fc
use default(field) for DdkMaker and co. in run_ddk_rf
VicTrqt Jun 25, 2024
8c9b64c
create generic run_rf
VicTrqt Jun 26, 2024
e7e350b
put core of DdkMaker,... into new ResponseMaker
VicTrqt Jun 26, 2024
9f2a69f
new AbiBroadInputGenerator as common super class of all other Abinit …
VicTrqt Jun 26, 2024
b39fc29
add testing possibility
VicTrqt Jun 26, 2024
4fd27c3
debug
VicTrqt Jun 26, 2024
37581a0
start AnaddbMaker
VicTrqt Jun 27, 2024
a8e6c0e
finish functional AnaddbMaker
VicTrqt Jun 28, 2024
d8740de
linting
VicTrqt Jun 28, 2024
d8b1f60
pull trunk main
VicTrqt Jun 28, 2024
0a03331
linting
VicTrqt Jun 28, 2024
bfda61a
linting
VicTrqt Jun 28, 2024
35b8635
Bump ipython from 8.25.0 to 8.26.0 (#905)
dependabot[bot] Jul 1, 2024
4c43063
Bump custodian from 2024.4.18 to 2024.6.24 (#908)
dependabot[bot] Jul 1, 2024
8f4c463
Bump phonopy from 2.24.3 to 2.25.0 (#906)
dependabot[bot] Jul 1, 2024
06e4a71
Bump pydantic-settings from 2.3.3 to 2.3.4 (#907)
dependabot[bot] Jul 1, 2024
55c5dd6
linting
VicTrqt Jul 1, 2024
63ec92c
Bump lobsterpy from 0.4.4 to 0.4.5 (#913)
dependabot[bot] Jul 8, 2024
d834c3e
Bump phonopy from 2.25.0 to 2.26.2 (#914)
dependabot[bot] Jul 8, 2024
def6a4e
Bump pydantic from 2.7.4 to 2.8.2 (#915)
dependabot[bot] Jul 8, 2024
d30890f
Add possibility to use your own M3GNet potential (#911)
QuantumChemist Jul 10, 2024
738ea89
Bump sphinx from 7.2.6 to 7.4.0 (#919)
dependabot[bot] Jul 15, 2024
5397132
Bump phonopy from 2.26.2 to 2.26.5 (#921)
dependabot[bot] Jul 15, 2024
0817ede
Equation of State workflow for FHI-aims (#889)
ansobolev Jul 16, 2024
8c96fb3
fix test ddk and dde to handle prev_outputs as gz
VicTrqt Jul 16, 2024
fd54870
tests dte and mrgddb + modif flatten prev_outputs mrgddb
VicTrqt Jul 17, 2024
8c49db9
add tests anaddb
VicTrqt Jul 17, 2024
0291106
Fix JobStoreDocument attribute access (#710)
mjwen Jul 18, 2024
7d3e43b
Fix docs
Jul 18, 2024
593f962
Fix docs
Jul 18, 2024
5984ba9
Update sphinx version
Jul 18, 2024
7fa53f5
Docs: add Document Models / emmet tutorial (#917)
rkingsbury Jul 18, 2024
99104ac
Writing tutorial for high level overview of atomate2 concepts. (#757)
QuantumChemist Jul 18, 2024
aaa1f7b
Add elastic workflow for FHI-aims (#871)
tpurcell90 Jul 18, 2024
42cae12
Tutorial for blob storage with test (#776)
jmmshn Jul 18, 2024
8a9b2fc
Update precommit
Jul 18, 2024
58f8b9a
Merge branch 'main' of github.com:materialsproject/atomate2
Jul 18, 2024
1118986
Added NEP MLIP relax, static, and MD makers (#893)
naik-aakash Jul 18, 2024
47d5acc
fix CP2K TaskDocument (#900)
lory-w Jul 18, 2024
e945136
add additional fields as kwargs to PhononBSDOSDoc (#910)
naik-aakash Jul 18, 2024
7b719e5
Defect: Allow bulk SC calculation to be skipped. (#742)
jmmshn Jul 18, 2024
a9e5ede
[WIP] Documentation update (#850)
AntObi Jul 18, 2024
06f0140
Bump sphinx from 7.4.6 to 7.4.7 (#926)
dependabot[bot] Jul 22, 2024
fd12860
Bump furo from 2024.5.6 to 2024.7.18 (#931)
dependabot[bot] Jul 22, 2024
42d697b
Bump phonopy from 2.26.5 to 2.26.6 (#930)
dependabot[bot] Jul 22, 2024
3865936
Bump nbmake from 1.5.3 to 1.5.4 (#929)
dependabot[bot] Jul 22, 2024
e210b58
Bump pymatgen-analysis-defects from 2024.5.11 to 2024.7.19 (#925)
dependabot[bot] Jul 22, 2024
96f8674
store DDB + add LDA PSP
VicTrqt Jul 22, 2024
5a11071
store _POT files
VicTrqt Jul 22, 2024
92b43e9
save _POT is optional
VicTrqt Jul 22, 2024
1d2e8fd
stored files as generic object + fix encode/decode bytes data
VicTrqt Jul 23, 2024
b1a93bc
Merge branch 'main' of github.com:materialsproject/atomate2 into abin…
VicTrqt Jul 23, 2024
22025bf
linting
VicTrqt Jul 23, 2024
018b211
linting
VicTrqt Jul 23, 2024
ad68670
add TODO
VicTrqt Jul 24, 2024
1149895
change output of Flow to allow gzip/del files
VicTrqt Jul 29, 2024
c5b45b7
Add `SevenNetRelaxMaker` + `SevenNetStaticMaker` to force field jobs …
janosh Jul 29, 2024
270408f
Lobster schema updates (#924)
naik-aakash Jul 30, 2024
0277c8f
add del_gzip job + ScfConvergenceWarning for Ddk for unconverged case
VicTrqt Jul 30, 2024
fad9396
Transition to pymatgen VASP input sets (#854)
esoteric-ephemera Jul 30, 2024
8726768
fix del_gzip
VicTrqt Jul 30, 2024
631341e
linting
VicTrqt Jul 30, 2024
42038ce
review Guido PR
VicTrqt Jul 31, 2024
9c84108
Add workflow to compute Gruneisen parameters (#752)
naik-aakash Jul 31, 2024
ded305a
address some comments of Guido
VicTrqt Jul 31, 2024
f1c7abf
address gpetretto's review
VicTrqt Jul 31, 2024
9ab1b23
add dir of del_gzip_files to zip
VicTrqt Jul 31, 2024
69a3b26
fix del_gzip_files
VicTrqt Aug 2, 2024
f2f315d
fix dfpt flow ddk append_name
VicTrqt Aug 2, 2024
6d06014
fix dfpt flow ddk append_name
VicTrqt Aug 2, 2024
a7db2ee
linting
VicTrqt Aug 2, 2024
8d57884
ruff fixes (#946)
janosh Aug 7, 2024
f5ab8cc
Add back `symprec` kwarg to MP and MatPES set generators (#947)
janosh Aug 7, 2024
bad9902
Added documentation about JSONStore usage within Installation (#945)
abhardwaj73 Aug 7, 2024
03b62fa
stop_jobflow for ResponseMaker
VicTrqt Aug 8, 2024
b48723c
Bump myst-parser from 3.0.1 to 4.0.0 (#950)
dependabot[bot] Aug 12, 2024
e9710d2
Bump pyyaml from 6.0.1 to 6.0.2 (#952)
dependabot[bot] Aug 12, 2024
cc44049
Bump furo from 2024.7.18 to 2024.8.6 (#951)
dependabot[bot] Aug 12, 2024
3dce3a5
Bump phonopy from 2.26.6 to 2.26.7 (#949)
dependabot[bot] Aug 12, 2024
d11b666
Bump pytest from 8.0.2 to 8.3.2 (#937)
dependabot[bot] Aug 12, 2024
409679b
Bump numpydoc from 1.7.0 to 1.8.0 (#948)
dependabot[bot] Aug 12, 2024
28ba426
Remove README note about atomate2 mostly being for VASP (#957)
Andrew-S-Rosen Aug 17, 2024
7c74022
Fix MPID assignment in electrode workflow (#956)
esoteric-ephemera Aug 20, 2024
87ee21a
Update release.yml
utf Aug 20, 2024
ef40fa9
Update changelog
Aug 20, 2024
54a9645
Merge branch 'main' of github.com:materialsproject/atomate2
Aug 20, 2024
1ebc9a7
bump ruff + auto-fixes
janosh Aug 20, 2024
49d1c1d
Anharmonicity Quantification workflow (#901)
4kevinbeck5 Aug 24, 2024
2087caf
Bump phonopy from 2.26.7 to 2.27.0 (#964)
dependabot[bot] Aug 26, 2024
b343ad2
Bump mp-api from 0.41.2 to 0.42.1 (#963)
dependabot[bot] Aug 26, 2024
e51bde7
fix files_to_store, strip_hostname, mrgddb_report
VicTrqt Aug 26, 2024
f14586c
Bump ipython from 8.26.0 to 8.27.0 (#966)
dependabot[bot] Sep 2, 2024
fdd2c9e
Bump pydantic from 2.8.2 to 2.9.0 (#972)
dependabot[bot] Sep 9, 2024
f1894c1
Workflow for Quasi-harmonic approximation (forcefields and VASP) (#903)
JaGeo Sep 9, 2024
d64b2f3
Bump pytest from 8.3.2 to 8.3.3 (#978)
dependabot[bot] Sep 16, 2024
b56e3d7
Bump pydantic-settings from 2.3.4 to 2.5.2 (#981)
dependabot[bot] Sep 16, 2024
a54768a
Bump pydantic from 2.9.0 to 2.9.1 (#977)
dependabot[bot] Sep 16, 2024
1ddf2dd
Bump mp-api from 0.42.1 to 0.42.2 (#983)
dependabot[bot] Sep 16, 2024
b837d5d
Bump sevenn from 0.9.3 to 0.9.3.post1 (#982)
dependabot[bot] Sep 16, 2024
00590dd
linting
VicTrqt Sep 17, 2024
103038d
fix stop_jobflow_on_failure
VicTrqt Sep 17, 2024
1fb11a8
fix del_gzip_files bc strip_hostname
VicTrqt Sep 18, 2024
9599178
fix
VicTrqt Sep 20, 2024
a8808b1
fix name ddk job in dfpt flow
VicTrqt Sep 23, 2024
8fe6935
Bump pydantic from 2.9.1 to 2.9.2 (#991)
dependabot[bot] Sep 23, 2024
4403858
Remove emmet `==` pin in `pyproject.toml` and update version in `stri…
Andrew-S-Rosen Sep 23, 2024
3d6a3a3
Atomate2 OpenMM integration & broader classical MD framework (#782)
orionarcher Sep 23, 2024
5131932
Frequency Flattening Optimizer (#863)
rohithsrinivaas Sep 24, 2024
7377fca
Input set tutorial (#780)
JonathanSchmidt1 Sep 24, 2024
2513903
Including VASP surface adsorption flow (#691)
itsduowang Sep 24, 2024
fdb4894
Generalize forcefields for generic ASE calculator support (#940)
esoteric-ephemera Sep 25, 2024
79aaf15
Update changelog
Sep 26, 2024
96b2b82
Bump min supported Python to 3.10 (#992)
janosh Sep 26, 2024
9600cef
Excise openff dependency from openmm testing (#993)
orionarcher Sep 27, 2024
a24649e
Fix `prev_dir` behavior in input set generator of `MPGGAStaticMaker` …
Andrew-S-Rosen Sep 29, 2024
ec1b598
Split tests (#985)
esoteric-ephemera Sep 29, 2024
ed853c8
pull trunk main + fix linting
VicTrqt Sep 30, 2024
3c0be95
Update changelog
Sep 30, 2024
6a49091
fix run_mrgddb and run_anaddb + AbinitPseudoDoc
VicTrqt Oct 1, 2024
e9df035
use iterflow to clean flow
VicTrqt Oct 1, 2024
3055638
fix cleaning function
VicTrqt Oct 1, 2024
fb9a6e8
Allow energy minimization maker to report energies (#1004)
orionarcher Oct 1, 2024
2469f1a
history_dirs in AbinitTaskDoc + fix clean_flow
VicTrqt Oct 2, 2024
ce55074
allow parallelization for anaddb
VicTrqt Oct 2, 2024
846d3aa
remove some comments
VicTrqt Oct 2, 2024
3a90dce
remove some comments
VicTrqt Oct 2, 2024
4a704f1
merge review PR
VicTrqt Oct 2, 2024
52f1a1f
fix check 1DEN files ext
VicTrqt Oct 3, 2024
ae91bf1
Merge branch 'abinit_workflows_dfpt_shg_new_review-PR' into abinit_wo…
VicTrqt Oct 3, 2024
4b71309
Bump lobsterpy from 0.4.5 to 0.4.9 (#1001)
dependabot[bot] Oct 3, 2024
4944aed
Implementation to adjust get_supercell_size to also generate orthorho…
QuantumChemist Oct 3, 2024
480f75e
Aims magnetic ordering (#922)
tpurcell90 Oct 3, 2024
7ac2662
add test flows dfpt shg
VicTrqt Oct 4, 2024
f4ce054
Merge branch 'abinit_workflows_dfpt_shg_new_review-PR' into abinit_wo…
VicTrqt Oct 4, 2024
b110095
add test flow shg
VicTrqt Oct 4, 2024
05d1884
Merge branch 'abinit_workflows_dfpt_shg_new_review-PR' into abinit_wo…
VicTrqt Oct 4, 2024
00a5405
fix ruff PLC0206 Extracting value from dict without calling .items() …
janosh Oct 6, 2024
0c04d1b
Bump chgnet from 0.3.8 to 0.4.0 (#990)
dependabot[bot] Oct 6, 2024
6b53ebd
Bump ipython from 8.27.0 to 8.28.0 (#1010)
dependabot[bot] Oct 7, 2024
078e3b1
fix comments
VicTrqt Oct 10, 2024
bc95b4a
Merge branch 'main' of github.com:materialsproject/atomate2 into abin…
VicTrqt Oct 10, 2024
8a12e54
remove unconventional tests
VicTrqt Oct 10, 2024
68f7e07
Bump python-ulid from 2.7.0 to 3.0.0 (#1015)
dependabot[bot] Oct 14, 2024
a0b4bda
Ferroelectric Workflow 2 (#1012)
fraricci Oct 15, 2024
ab4182f
Bump sphinx from 7.4.7 to 8.1.3 (#1016)
dependabot[bot] Oct 16, 2024
cff86cf
Bump custodian from 2024.6.24 to 2024.10.16 (#1020)
dependabot[bot] Oct 21, 2024
b285d30
Bump pytest-split from 0.9.0 to 0.10.0 (#1019)
dependabot[bot] Oct 21, 2024
d90a074
Bump torch from 2.4.1 to 2.5.0 (#1018)
dependabot[bot] Oct 21, 2024
ae97d6b
Bump pydantic-settings from 2.5.2 to 2.6.0 (#1021)
dependabot[bot] Oct 21, 2024
8b19726
Bump ipython from 8.28.0 to 8.29.0 (#1025)
dependabot[bot] Oct 28, 2024
527c4c7
Bump calorine from 2.2.1 to 3.0 (#1026)
dependabot[bot] Oct 28, 2024
b69ae55
Bump sevenn from 0.9.3.post1 to 0.10.0 (#1028)
dependabot[bot] Oct 28, 2024
42bc7b8
Update MACE to 0.3.6 (#1032)
orionarcher Oct 30, 2024
9c4447c
Allow custom mace model by specifying "model" in calculator kwargs" (…
orionarcher Oct 31, 2024
6266093
feat: add dedicated fireworks optional dependency (Fix #1033). (#1035)
hongyi-zhao Nov 1, 2024
6d3c351
MPMorph Flows (#938)
BryantLi-BLI Nov 1, 2024
faada35
Bump torch from 2.5.0 to 2.5.1 (#1039)
dependabot[bot] Nov 4, 2024
f11ac37
Bump pytest-cov from 5.0.0 to 6.0.0 (#1041)
dependabot[bot] Nov 4, 2024
fed13c7
Bump pydantic-settings from 2.6.0 to 2.6.1 (#1042)
dependabot[bot] Nov 4, 2024
121936b
Make testing utils importable (#1037)
jmmshn Nov 6, 2024
2d9a1e8
Bump sevenn from 0.10.0 to 0.10.1 (#1050)
dependabot[bot] Nov 11, 2024
237dcdc
Update versioningit requirement from ~=1.0 to >=1,<4 (#1051)
dependabot[bot] Nov 11, 2024
c57f9c1
Feat: GW workflow with VASP (#808)
yanghan234 Nov 12, 2024
cda2a81
Bump monty from 2024.7.30 to 2024.10.21 (#1027)
dependabot[bot] Nov 12, 2024
071d1c8
Update changelog
Nov 12, 2024
0fb73a9
Add trajectory reporter to openmm workflow (#1053)
orionarcher Nov 13, 2024
d743a69
CP2K tweaks (#1056)
janosh Nov 14, 2024
7761de4
Bump pymatgen-analysis-defects from 2024.7.19 to 2024.10.22 (#1024)
dependabot[bot] Nov 14, 2024
67efb7f
Minor docs cleanup (#1047)
esoteric-ephemera Nov 14, 2024
7add7ca
`PhononMaker` add options to `calculate_pdos` and save force constant…
chouyoudou Nov 14, 2024
5f0bc75
Allow `MatPesStaticFlowMaker(static2=None)` (#997)
janosh Nov 14, 2024
3d55b2b
bug fix for linear strain passing in qha (#1061)
JaGeo Nov 22, 2024
3f61317
Fix `generate_phonon_displacements` magmom removal side effect (#1064)
janosh Nov 22, 2024
df1ae35
Bump emmet-core from 0.84.3rc3 to 0.84.3rc4 (#1065)
dependabot[bot] Nov 25, 2024
eaed474
Bump jobflow from 0.1.18 to 0.1.19 (#1067)
dependabot[bot] Nov 25, 2024
4244da9
add openmm description to docs (#1069)
JaGeo Nov 25, 2024
4b84d78
fix minor code formatting issues + typos (#1070)
janosh Nov 25, 2024
11fc0ea
Merge branch 'main' of github.com:materialsproject/atomate2 into abin…
VicTrqt Nov 26, 2024
bd336d5
tmp abipy github requirement
VicTrqt Nov 26, 2024
38073cd
linting
VicTrqt Nov 26, 2024
f532d27
linting
VicTrqt Nov 26, 2024
4bbda09
fix test generate_dte_perts abipy manager
VicTrqt Nov 26, 2024
9832136
install abinit in env pytest
VicTrqt Nov 26, 2024
6349766
Docs update, forcefield elastic convenience maker, forcefield enum hy…
esoteric-ephemera Nov 26, 2024
7b4a66a
add skip to dfpt test
VicTrqt Nov 26, 2024
4bcf127
Fix bump phonopy (#1006)
naik-aakash Nov 30, 2024
bbc4933
Bump mp-api from 0.42.2 to 0.43.0 (#1075)
dependabot[bot] Dec 2, 2024
55a87f0
Bump pytest from 8.3.3 to 8.3.4 (#1077)
dependabot[bot] Dec 2, 2024
44a1125
Bump ipython from 8.29.0 to 8.30.0 (#1076)
dependabot[bot] Dec 2, 2024
b79b1c1
Bump sevenn from 0.10.1 to 0.10.2 (#1080)
dependabot[bot] Dec 9, 2024
149f05c
Bump emmet-core from 0.84.3rc4 to 0.84.3rc6 (#1081)
dependabot[bot] Dec 9, 2024
073eac1
update calorine version (#1083)
naik-aakash Dec 9, 2024
906ca38
Bump sevenn from 0.10.2 to 0.10.3 (#1084)
dependabot[bot] Dec 16, 2024
44de991
Bump emmet-core from 0.84.3rc6 to 0.84.4 (#1085)
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Merge branch 'main' of github.com:materialsproject/atomate2 into abin…
VicTrqt Jan 7, 2025
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from_... class methods now return typing_extensions.Self (materia…
…lsproject#840)

* more clean up of schemas/test_lobster.py

* from_... class methods return typing_extensions.Self

* fix NameError: name 'Self' is not defined in schema files

* missed one NameError: name 'Self' is not defined

* start doc strings on 1st line
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janosh authored May 11, 2024
commit df7c76992db2bd2c6659dd301d786e5d5a4073b5
6 changes: 2 additions & 4 deletions src/atomate2/abinit/flows/core.py
Original file line number Diff line number Diff line change
@@ -50,8 +50,7 @@ def make(
structure: Structure,
restart_from: str | Path | None = None,
) -> Flow:
"""
Create a band structure flow.
"""Create a band structure flow.

Parameters
----------
@@ -109,8 +108,7 @@ def make(
structure: Structure | None = None,
restart_from: str | Path | None = None,
) -> Flow:
"""
Create a relaxation flow.
"""Create a relaxation flow.

Parameters
----------
3 changes: 1 addition & 2 deletions src/atomate2/abinit/jobs/base.py
Original file line number Diff line number Diff line change
@@ -144,8 +144,7 @@ def make(
restart_from: str | Path | list[str] | None = None,
history: JobHistory | None = None,
) -> jobflow.Job:
"""
Return an ABINIT jobflow.Job.
"""Get an ABINIT jobflow.Job.

Parameters
----------
3 changes: 1 addition & 2 deletions src/atomate2/abinit/jobs/core.py
Original file line number Diff line number Diff line change
@@ -123,8 +123,7 @@ def make(
history: JobHistory | None = None,
mode: str = "uniform",
) -> Job:
"""
Run a non-scf ABINIT job.
"""Run a non-scf ABINIT job.

Parameters
----------
37 changes: 16 additions & 21 deletions src/atomate2/abinit/schemas/calculation.py
Original file line number Diff line number Diff line change
@@ -6,10 +6,7 @@
import os
from datetime import datetime
from pathlib import Path
from typing import TYPE_CHECKING, Optional, Union

if TYPE_CHECKING:
pass
from typing import Optional, Union

from abipy.electrons.gsr import GsrFile
from abipy.flowtk import events
@@ -18,6 +15,7 @@
from jobflow.utils import ValueEnum
from pydantic import BaseModel, Field
from pymatgen.core import Structure
from typing_extensions import Self

from atomate2.abinit.utils.common import LOG_FILE_NAME, MPIABORTFILE, get_event_report

@@ -110,9 +108,8 @@ class CalculationOutput(BaseModel):
def from_abinit_gsr(
cls,
output: GsrFile, # Must use auto_load kwarg when passed
) -> CalculationOutput:
"""
Create an Abinit output document from Abinit outputs.
) -> Self:
"""Create an Abinit output document from Abinit outputs.

Parameters
----------
@@ -211,9 +208,8 @@ def from_abinit_files(
abinit_gsr_file: Path | str = "out_GSR.nc",
abinit_log_file: Path | str = LOG_FILE_NAME,
abinit_abort_file: Path | str = MPIABORTFILE,
) -> tuple[Calculation, dict[AbinitObject, dict]]:
"""
Create an Abinit calculation document from a directory and file paths.
) -> tuple[Self, dict[AbinitObject, dict]]:
"""Create an Abinit calculation document from a directory and file paths.

Parameters
----------
@@ -263,15 +259,14 @@ def from_abinit_files(
msg = f"{cls} exception while parsing event_report:\n{exc}"
logger.critical(msg)

return (
cls(
dir_name=str(dir_name),
task_name=task_name,
abinit_version=abinit_gsr.abinit_version,
has_abinit_completed=has_abinit_completed,
completed_at=completed_at,
output=output_doc,
event_report=report,
),
None, # abinit_objects,
instance = cls(
dir_name=str(dir_name),
task_name=task_name,
abinit_version=abinit_gsr.abinit_version,
has_abinit_completed=has_abinit_completed,
completed_at=completed_at,
output=output_doc,
event_report=report,
)

return instance, None # abinit_objects,
12 changes: 6 additions & 6 deletions src/atomate2/abinit/schemas/task.py
Original file line number Diff line number Diff line change
@@ -5,22 +5,22 @@
import logging
from collections.abc import Sequence
from pathlib import Path
from typing import Any, Optional, TypeVar, Union
from typing import Any, Optional, Union

from abipy.abio.inputs import AbinitInput
from abipy.flowtk import events
from emmet.core.math import Matrix3D, Vector3D
from emmet.core.structure import StructureMetadata
from pydantic import BaseModel, Field
from pymatgen.core import Structure
from typing_extensions import Self

from atomate2.abinit.files import load_abinit_input
from atomate2.abinit.schemas.calculation import AbinitObject, Calculation, TaskState
from atomate2.abinit.utils.common import LOG_FILE_NAME, MPIABORTFILE
from atomate2.utils.datetime import datetime_str
from atomate2.utils.path import get_uri, strip_hostname

_T = TypeVar("_T", bound="AbinitTaskDoc")
logger = logging.getLogger(__name__)


@@ -42,7 +42,7 @@ class InputDoc(BaseModel):
)

@classmethod
def from_abinit_calc_doc(cls, calc_doc: Calculation) -> InputDoc:
def from_abinit_calc_doc(cls, calc_doc: Calculation) -> Self:
"""Create a summary from an abinit CalculationDocument.

Parameters
@@ -111,7 +111,7 @@ class OutputDoc(BaseModel):
)

@classmethod
def from_abinit_calc_doc(cls, calc_doc: Calculation) -> OutputDoc:
def from_abinit_calc_doc(cls, calc_doc: Calculation) -> Self:
"""Create a summary from an abinit CalculationDocument.

Parameters
@@ -237,11 +237,11 @@ class AbinitTaskDoc(StructureMetadata):

@classmethod
def from_directory(
cls: type[_T],
cls,
dir_name: Path | str,
additional_fields: dict[str, Any] = None,
**abinit_calculation_kwargs,
) -> AbinitTaskDoc:
) -> Self:
"""Create a task document from a directory containing Abinit files.

Parameters
3 changes: 1 addition & 2 deletions src/atomate2/abinit/sets/base.py
Original file line number Diff line number Diff line change
@@ -541,8 +541,7 @@ def get_abinit_input(
kpoints_settings: dict | KSampling | None = None,
input_index: int | None = None,
) -> AbinitInput:
"""
Generate the AbinitInput for the input set.
"""Generate the AbinitInput for the input set.

Uses the defined factory function and additional parameters from user
and subclasses.
6 changes: 2 additions & 4 deletions src/atomate2/abinit/sets/core.py
Original file line number Diff line number Diff line change
@@ -45,8 +45,7 @@ def get_abinit_input(
kpoints_settings: dict | KSampling | None = None,
input_index: int | None = None,
) -> AbinitInput:
"""
Generate the AbinitInput for the input set.
"""Generate the AbinitInput for the input set.

Removes some standard variables related to relaxation.
"""
@@ -207,8 +206,7 @@ def get_abinit_input(
kpoints_settings: dict | KSampling | None = None,
input_index: int | None = None,
) -> AbinitInput:
"""
Generate the AbinitInput for the input set.
"""Generate the AbinitInput for the input set.

Sets tolmxf and determines the index of the MultiDataset.
"""
23 changes: 12 additions & 11 deletions src/atomate2/abinit/utils/common.py
Original file line number Diff line number Diff line change
@@ -6,24 +6,25 @@
import os
from typing import TYPE_CHECKING

from abipy.abio.outputs import AbinitOutputFile
from abipy.dfpt.ddb import DdbFile
from abipy.electrons.gsr import GsrFile
from abipy.flowtk import events
from abipy.flowtk.utils import Directory, File
from monty.json import MSONable
from monty.serialization import MontyDecoder

if TYPE_CHECKING:
from pathlib import Path

from abipy.abio.inputs import AbinitInput
from abipy.core.structure import Structure
from abipy.flowtk.events import EventReport
from jobflow import Flow, Job
from typing_extensions import Self

from atomate2.abinit.utils.history import JobHistory

from abipy.abio.outputs import AbinitOutputFile
from abipy.dfpt.ddb import DdbFile
from abipy.electrons.gsr import GsrFile
from abipy.flowtk import events
from abipy.flowtk.utils import Directory, File
from monty.json import MSONable
from monty.serialization import MontyDecoder

TMPDIR_NAME = "tmpdata"
OUTDIR_NAME = "outdata"
INDIR_NAME = "indata"
@@ -163,7 +164,7 @@ def as_dict(self) -> dict:
return self.to_dict()

@classmethod
def from_dict(cls, d: dict) -> AbinitRuntimeError:
def from_dict(cls, d: dict) -> Self:
"""Create instance of the error from its dictionary representation."""
dec = MontyDecoder()
warnings = (
@@ -245,7 +246,7 @@ def to_dict(self) -> dict:
return d

@classmethod
def from_dict(cls, d: dict) -> UnconvergedError:
def from_dict(cls, d: dict) -> Self:
"""Create instance of the error from its dictionary representation."""
dec = MontyDecoder()
warnings = (
@@ -319,7 +320,7 @@ def as_dict(self) -> dict:
}

@classmethod
def from_dict(cls, d: dict) -> RestartInfo:
def from_dict(cls, d: dict) -> Self:
"""Create instance of the error from its dictionary representation."""
return cls(
previous_dir=d["previous_dir"],
9 changes: 5 additions & 4 deletions src/atomate2/abinit/utils/history.py
Original file line number Diff line number Diff line change
@@ -10,15 +10,16 @@

from monty.json import MontyDecoder, MSONable, jsanitize

from atomate2.abinit.utils.common import OUTDIR_NAME

if TYPE_CHECKING:
from pathlib import Path

from abipy.abio.inputs import AbinitInput
from abipy.flowtk.events import AbinitEvent
from abipy.flowtk.utils import Directory
from jobflow import Flow, Job

from atomate2.abinit.utils.common import OUTDIR_NAME
from typing_extensions import Self

logger = logging.getLogger(__name__)

@@ -46,7 +47,7 @@ def as_dict(self) -> dict:
}

@classmethod
def from_dict(cls, d: dict) -> JobHistory:
def from_dict(cls, d: dict) -> Self:
"""Create instance of the history from its dictionary representation."""
dec = MontyDecoder()
return cls([dec.process_decoded(i) for i in d["items"]])
@@ -232,7 +233,7 @@ def as_dict(self) -> dict:
return d

@classmethod
def from_dict(cls, d: dict) -> JobEvent:
def from_dict(cls, d: dict) -> Self:
"""Create instance of the job event from its dictionary representation."""
dec = MontyDecoder()
details = dec.process_decoded(d["details"]) if "details" in d else None
3 changes: 2 additions & 1 deletion src/atomate2/aims/flows/core.py
Original file line number Diff line number Diff line change
@@ -14,6 +14,7 @@

if TYPE_CHECKING:
from pymatgen.core import Molecule, Structure
from typing_extensions import Self

from atomate2.aims.jobs.base import BaseAimsMaker

@@ -68,7 +69,7 @@ def from_parameters(
cls,
parameters: dict[str, Any],
species_defaults: list[str] | tuple[str, str] = ("light", "tight"),
) -> DoubleRelaxMaker:
) -> Self:
"""Create the maker from an ASE parameter set.

Creates a DoubleRelaxFlow for the same parameters with two different
3 changes: 1 addition & 2 deletions src/atomate2/aims/jobs/base.py
Original file line number Diff line number Diff line change
@@ -88,8 +88,7 @@ def make(
structure: Structure | Molecule,
prev_dir: str | Path | None = None,
) -> Response:
"""
Run an FHI-aims calculation.
"""Run an FHI-aims calculation.

Parameters
----------
34 changes: 15 additions & 19 deletions src/atomate2/aims/schemas/calculation.py
Original file line number Diff line number Diff line change
@@ -17,6 +17,7 @@
from pymatgen.electronic_structure.dos import Dos
from pymatgen.io.aims.outputs import AimsOutput
from pymatgen.io.common import VolumetricData
from typing_extensions import Self

if TYPE_CHECKING:
from emmet.core.math import Matrix3D, Vector3D
@@ -133,9 +134,8 @@ def from_aims_output(
cls,
output: AimsOutput, # Must use auto_load kwarg when passed
# store_trajectory: bool = False,
) -> CalculationOutput:
"""
Create an FHI-aims output document from FHI-aims outputs.
) -> Self:
"""Create an FHI-aims output document from FHI-aims outputs.

Parameters
----------
@@ -240,9 +240,8 @@ def from_aims_files(
store_trajectory: bool = False,
# store_scf: bool = False,
store_volumetric_data: Optional[Sequence[str]] = STORE_VOLUMETRIC_DATA,
) -> tuple[Calculation, dict[AimsObject, dict]]:
"""
Create an FHI-aims calculation document from a directory and file paths.
) -> tuple[Self, dict[AimsObject, dict]]:
"""Create an FHI-aims calculation document from a directory and file paths.

Parameters
----------
@@ -319,21 +318,18 @@ def from_aims_files(
traj = _parse_trajectory(aims_output=aims_output)
aims_objects[AimsObject.TRAJECTORY] = traj # type: ignore # noqa: PGH003

return (
cls(
dir_name=str(dir_name),
task_name=task_name,
aims_version=aims_output.aims_version,
has_aims_completed=has_aims_completed,
completed_at=completed_at,
output=output_doc,
output_file_paths={
k.name.lower(): v for k, v in output_file_paths.items()
},
),
aims_objects,
instance = cls(
dir_name=str(dir_name),
task_name=task_name,
aims_version=aims_output.aims_version,
has_aims_completed=has_aims_completed,
completed_at=completed_at,
output=output_doc,
output_file_paths={k.name.lower(): v for k, v in output_file_paths.items()},
)

return instance, aims_objects


def _get_output_file_paths(volumetric_files: list[str]) -> dict[AimsObject, str]:
"""Get the output file paths for FHI-aims output files.
Loading