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[WIP] ABINIT DFPT SHG #1
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015987f
clean up test_lobster_task_document
janosh 29a5731
Document the option to run LOBSTER with one jobscript only (#811)
JaGeo 3b550be
Add magnetic orderings workflow (#432)
mattmcdermott df7c769
`from_...` class methods now return `typing_extensions.Self` (#840)
janosh d22e247
Update LobsterPy version (#841)
JaGeo 313f809
CI add `repository_dispatch` event for `pymatgen_ci_trigger` (#835)
janosh c77e21f
Bump phonopy from 2.22.1 to 2.23.1 (#846)
dependabot[bot] 7f55cd3
Bump lobsterpy from 0.4.0 to 0.4.4 (#848)
dependabot[bot] aee4be8
Bump furo from 2024.1.29 to 2024.5.6 (#847)
dependabot[bot] 832fdbe
Fix `TrajectoryObserver.to_ase_trajectory` return type (#852)
janosh dd582ff
Fix title hierarchies in VASP documentation (#853)
JaGeo e84f1fa
fix typos
janosh c369c86
Make Fermi Energy Optional for FHI-aims (#793)
tpurcell90 2fefc6f
Bump python-ulid from 2.5.0 to 2.6.0 (#858)
dependabot[bot] 2d24f81
Bump typing-extensions from 4.11.0 to 4.12.0 (#859)
dependabot[bot] f826b29
Bump sphinx-design from 0.5.0 to 0.6.0 (#857)
dependabot[bot] 3079e55
Bump monty from 2024.3.31 to 2024.5.24 (#860)
dependabot[bot] a5e502f
Handling failures in elastic flow (#861)
gpetretto 91e133f
Bump typing-extensions from 4.12.0 to 4.12.1 (#864)
dependabot[bot] 3336910
Bump pymatgen from 2024.5.1 to 2024.5.31 (#867)
dependabot[bot] 58e6c92
Bump ipython from 8.23.0 to 8.25.0 (#869)
dependabot[bot] 25817f4
Bump pydantic from 2.7.1 to 2.7.2 (#868)
dependabot[bot] 760e537
Bump dscribe from 2.1.0 to 2.1.1 (#865)
dependabot[bot] 8016942
transpose matrix (#872)
JaGeo cda583b
Add test for supercell matrix creation in phonon workflow (#873)
JaGeo 5043fe6
Bump typing-extensions from 4.12.1 to 4.12.2 (#877)
dependabot[bot] 179d836
Bump ijson from 3.2.3 to 3.3.0 (#876)
dependabot[bot] 4e86c93
Bump pydantic-settings from 2.2.1 to 2.3.1 (#875)
dependabot[bot] b8ee8a6
Bump matgl from 1.1.1 to 1.1.2 (#882)
dependabot[bot] 905c470
Bump chgnet from 0.3.5 to 0.3.8 (#881)
dependabot[bot] fe52d5a
Bump pydantic from 2.7.2 to 2.7.3 (#884)
dependabot[bot] 50ae3c0
Bump phonopy from 2.23.1 to 2.24.2 (#879)
dependabot[bot] 40bfecd
`ruff` fixes (#894)
janosh 0042441
Bump pydantic from 2.7.3 to 2.7.4 (#886)
dependabot[bot] 40f6f80
Bump pymatgen from 2024.5.31 to 2024.6.10 (#887)
dependabot[bot] 4679806
Bump pydantic-settings from 2.3.1 to 2.3.3 (#888)
dependabot[bot] 1ffc588
Bump python-ulid from 2.6.0 to 2.7.0 (#897)
dependabot[bot] 3875bac
Bump phonopy from 2.24.2 to 2.24.3 (#898)
dependabot[bot] 94ef40f
remove restart_from for mrgddb job
VicTrqt 258b9d9
remove critical events for mrgddb
VicTrqt 19e1c5f
simplify mrgddb resolve_dep_exts and merge MrgddbSetGenerator into Mr…
VicTrqt 5297c3b
turn shg classmethod into subclass
VicTrqt 01a0ac9
check consistency DDK, DDE, DTE, Mrgddb
VicTrqt 861f6d2
add check for output None
VicTrqt 40014fc
use default(field) for DdkMaker and co. in run_ddk_rf
VicTrqt 8c9b64c
create generic run_rf
VicTrqt e7e350b
put core of DdkMaker,... into new ResponseMaker
VicTrqt 9f2a69f
new AbiBroadInputGenerator as common super class of all other Abinit …
VicTrqt b39fc29
add testing possibility
VicTrqt 4fd27c3
debug
VicTrqt 37581a0
start AnaddbMaker
VicTrqt a8e6c0e
finish functional AnaddbMaker
VicTrqt d8740de
linting
VicTrqt d8b1f60
pull trunk main
VicTrqt 0a03331
linting
VicTrqt bfda61a
linting
VicTrqt 35b8635
Bump ipython from 8.25.0 to 8.26.0 (#905)
dependabot[bot] 4c43063
Bump custodian from 2024.4.18 to 2024.6.24 (#908)
dependabot[bot] 8f4c463
Bump phonopy from 2.24.3 to 2.25.0 (#906)
dependabot[bot] 06e4a71
Bump pydantic-settings from 2.3.3 to 2.3.4 (#907)
dependabot[bot] 55c5dd6
linting
VicTrqt 63ec92c
Bump lobsterpy from 0.4.4 to 0.4.5 (#913)
dependabot[bot] d834c3e
Bump phonopy from 2.25.0 to 2.26.2 (#914)
dependabot[bot] def6a4e
Bump pydantic from 2.7.4 to 2.8.2 (#915)
dependabot[bot] d30890f
Add possibility to use your own M3GNet potential (#911)
QuantumChemist 738ea89
Bump sphinx from 7.2.6 to 7.4.0 (#919)
dependabot[bot] 5397132
Bump phonopy from 2.26.2 to 2.26.5 (#921)
dependabot[bot] 0817ede
Equation of State workflow for FHI-aims (#889)
ansobolev 8c96fb3
fix test ddk and dde to handle prev_outputs as gz
VicTrqt fd54870
tests dte and mrgddb + modif flatten prev_outputs mrgddb
VicTrqt 8c49db9
add tests anaddb
VicTrqt 0291106
Fix JobStoreDocument attribute access (#710)
mjwen 7d3e43b
Fix docs
593f962
Fix docs
5984ba9
Update sphinx version
7fa53f5
Docs: add Document Models / emmet tutorial (#917)
rkingsbury 99104ac
Writing tutorial for high level overview of atomate2 concepts. (#757)
QuantumChemist aaa1f7b
Add elastic workflow for FHI-aims (#871)
tpurcell90 42cae12
Tutorial for blob storage with test (#776)
jmmshn 8a9b2fc
Update precommit
58f8b9a
Merge branch 'main' of github.com:materialsproject/atomate2
1118986
Added NEP MLIP relax, static, and MD makers (#893)
naik-aakash 47d5acc
fix CP2K TaskDocument (#900)
lory-w e945136
add additional fields as kwargs to PhononBSDOSDoc (#910)
naik-aakash 7b719e5
Defect: Allow bulk SC calculation to be skipped. (#742)
jmmshn a9e5ede
[WIP] Documentation update (#850)
AntObi 06f0140
Bump sphinx from 7.4.6 to 7.4.7 (#926)
dependabot[bot] fd12860
Bump furo from 2024.5.6 to 2024.7.18 (#931)
dependabot[bot] 42d697b
Bump phonopy from 2.26.5 to 2.26.6 (#930)
dependabot[bot] 3865936
Bump nbmake from 1.5.3 to 1.5.4 (#929)
dependabot[bot] e210b58
Bump pymatgen-analysis-defects from 2024.5.11 to 2024.7.19 (#925)
dependabot[bot] 96f8674
store DDB + add LDA PSP
VicTrqt 5a11071
store _POT files
VicTrqt 92b43e9
save _POT is optional
VicTrqt 1d2e8fd
stored files as generic object + fix encode/decode bytes data
VicTrqt b1a93bc
Merge branch 'main' of github.com:materialsproject/atomate2 into abin…
VicTrqt 22025bf
linting
VicTrqt 018b211
linting
VicTrqt ad68670
add TODO
VicTrqt 1149895
change output of Flow to allow gzip/del files
VicTrqt c5b45b7
Add `SevenNetRelaxMaker` + `SevenNetStaticMaker` to force field jobs …
janosh 270408f
Lobster schema updates (#924)
naik-aakash 0277c8f
add del_gzip job + ScfConvergenceWarning for Ddk for unconverged case
VicTrqt fad9396
Transition to pymatgen VASP input sets (#854)
esoteric-ephemera 8726768
fix del_gzip
VicTrqt 631341e
linting
VicTrqt 42038ce
review Guido PR
VicTrqt 9c84108
Add workflow to compute Gruneisen parameters (#752)
naik-aakash ded305a
address some comments of Guido
VicTrqt f1c7abf
address gpetretto's review
VicTrqt 9ab1b23
add dir of del_gzip_files to zip
VicTrqt 69a3b26
fix del_gzip_files
VicTrqt f2f315d
fix dfpt flow ddk append_name
VicTrqt 6d06014
fix dfpt flow ddk append_name
VicTrqt a7db2ee
linting
VicTrqt 8d57884
ruff fixes (#946)
janosh f5ab8cc
Add back `symprec` kwarg to MP and MatPES set generators (#947)
janosh bad9902
Added documentation about JSONStore usage within Installation (#945)
abhardwaj73 03b62fa
stop_jobflow for ResponseMaker
VicTrqt b48723c
Bump myst-parser from 3.0.1 to 4.0.0 (#950)
dependabot[bot] e9710d2
Bump pyyaml from 6.0.1 to 6.0.2 (#952)
dependabot[bot] cc44049
Bump furo from 2024.7.18 to 2024.8.6 (#951)
dependabot[bot] 3dce3a5
Bump phonopy from 2.26.6 to 2.26.7 (#949)
dependabot[bot] d11b666
Bump pytest from 8.0.2 to 8.3.2 (#937)
dependabot[bot] 409679b
Bump numpydoc from 1.7.0 to 1.8.0 (#948)
dependabot[bot] 28ba426
Remove README note about atomate2 mostly being for VASP (#957)
Andrew-S-Rosen 7c74022
Fix MPID assignment in electrode workflow (#956)
esoteric-ephemera 87ee21a
Update release.yml
utf ef40fa9
Update changelog
54a9645
Merge branch 'main' of github.com:materialsproject/atomate2
1ebc9a7
bump ruff + auto-fixes
janosh 49d1c1d
Anharmonicity Quantification workflow (#901)
4kevinbeck5 2087caf
Bump phonopy from 2.26.7 to 2.27.0 (#964)
dependabot[bot] b343ad2
Bump mp-api from 0.41.2 to 0.42.1 (#963)
dependabot[bot] e51bde7
fix files_to_store, strip_hostname, mrgddb_report
VicTrqt f14586c
Bump ipython from 8.26.0 to 8.27.0 (#966)
dependabot[bot] fdd2c9e
Bump pydantic from 2.8.2 to 2.9.0 (#972)
dependabot[bot] f1894c1
Workflow for Quasi-harmonic approximation (forcefields and VASP) (#903)
JaGeo d64b2f3
Bump pytest from 8.3.2 to 8.3.3 (#978)
dependabot[bot] b56e3d7
Bump pydantic-settings from 2.3.4 to 2.5.2 (#981)
dependabot[bot] a54768a
Bump pydantic from 2.9.0 to 2.9.1 (#977)
dependabot[bot] 1ddf2dd
Bump mp-api from 0.42.1 to 0.42.2 (#983)
dependabot[bot] b837d5d
Bump sevenn from 0.9.3 to 0.9.3.post1 (#982)
dependabot[bot] 00590dd
linting
VicTrqt 103038d
fix stop_jobflow_on_failure
VicTrqt 1fb11a8
fix del_gzip_files bc strip_hostname
VicTrqt 9599178
fix
VicTrqt a8808b1
fix name ddk job in dfpt flow
VicTrqt 8fe6935
Bump pydantic from 2.9.1 to 2.9.2 (#991)
dependabot[bot] 4403858
Remove emmet `==` pin in `pyproject.toml` and update version in `stri…
Andrew-S-Rosen 3d6a3a3
Atomate2 OpenMM integration & broader classical MD framework (#782)
orionarcher 5131932
Frequency Flattening Optimizer (#863)
rohithsrinivaas 7377fca
Input set tutorial (#780)
JonathanSchmidt1 2513903
Including VASP surface adsorption flow (#691)
itsduowang fdb4894
Generalize forcefields for generic ASE calculator support (#940)
esoteric-ephemera 79aaf15
Update changelog
96b2b82
Bump min supported Python to 3.10 (#992)
janosh 9600cef
Excise openff dependency from openmm testing (#993)
orionarcher a24649e
Fix `prev_dir` behavior in input set generator of `MPGGAStaticMaker` …
Andrew-S-Rosen ec1b598
Split tests (#985)
esoteric-ephemera ed853c8
pull trunk main + fix linting
VicTrqt 3c0be95
Update changelog
6a49091
fix run_mrgddb and run_anaddb + AbinitPseudoDoc
VicTrqt e9df035
use iterflow to clean flow
VicTrqt 3055638
fix cleaning function
VicTrqt fb9a6e8
Allow energy minimization maker to report energies (#1004)
orionarcher 2469f1a
history_dirs in AbinitTaskDoc + fix clean_flow
VicTrqt ce55074
allow parallelization for anaddb
VicTrqt 846d3aa
remove some comments
VicTrqt 3a90dce
remove some comments
VicTrqt 4a704f1
merge review PR
VicTrqt 52f1a1f
fix check 1DEN files ext
VicTrqt ae91bf1
Merge branch 'abinit_workflows_dfpt_shg_new_review-PR' into abinit_wo…
VicTrqt 4b71309
Bump lobsterpy from 0.4.5 to 0.4.9 (#1001)
dependabot[bot] 4944aed
Implementation to adjust get_supercell_size to also generate orthorho…
QuantumChemist 480f75e
Aims magnetic ordering (#922)
tpurcell90 7ac2662
add test flows dfpt shg
VicTrqt f4ce054
Merge branch 'abinit_workflows_dfpt_shg_new_review-PR' into abinit_wo…
VicTrqt b110095
add test flow shg
VicTrqt 05d1884
Merge branch 'abinit_workflows_dfpt_shg_new_review-PR' into abinit_wo…
VicTrqt 00a5405
fix ruff PLC0206 Extracting value from dict without calling .items() …
janosh 0c04d1b
Bump chgnet from 0.3.8 to 0.4.0 (#990)
dependabot[bot] 6b53ebd
Bump ipython from 8.27.0 to 8.28.0 (#1010)
dependabot[bot] 078e3b1
fix comments
VicTrqt bc95b4a
Merge branch 'main' of github.com:materialsproject/atomate2 into abin…
VicTrqt 8a12e54
remove unconventional tests
VicTrqt 68f7e07
Bump python-ulid from 2.7.0 to 3.0.0 (#1015)
dependabot[bot] a0b4bda
Ferroelectric Workflow 2 (#1012)
fraricci ab4182f
Bump sphinx from 7.4.7 to 8.1.3 (#1016)
dependabot[bot] cff86cf
Bump custodian from 2024.6.24 to 2024.10.16 (#1020)
dependabot[bot] b285d30
Bump pytest-split from 0.9.0 to 0.10.0 (#1019)
dependabot[bot] d90a074
Bump torch from 2.4.1 to 2.5.0 (#1018)
dependabot[bot] ae97d6b
Bump pydantic-settings from 2.5.2 to 2.6.0 (#1021)
dependabot[bot] 8b19726
Bump ipython from 8.28.0 to 8.29.0 (#1025)
dependabot[bot] 527c4c7
Bump calorine from 2.2.1 to 3.0 (#1026)
dependabot[bot] b69ae55
Bump sevenn from 0.9.3.post1 to 0.10.0 (#1028)
dependabot[bot] 42bc7b8
Update MACE to 0.3.6 (#1032)
orionarcher 9c4447c
Allow custom mace model by specifying "model" in calculator kwargs" (…
orionarcher 6266093
feat: add dedicated fireworks optional dependency (Fix #1033). (#1035)
hongyi-zhao 6d3c351
MPMorph Flows (#938)
BryantLi-BLI faada35
Bump torch from 2.5.0 to 2.5.1 (#1039)
dependabot[bot] f11ac37
Bump pytest-cov from 5.0.0 to 6.0.0 (#1041)
dependabot[bot] fed13c7
Bump pydantic-settings from 2.6.0 to 2.6.1 (#1042)
dependabot[bot] 121936b
Make testing utils importable (#1037)
jmmshn 2d9a1e8
Bump sevenn from 0.10.0 to 0.10.1 (#1050)
dependabot[bot] 237dcdc
Update versioningit requirement from ~=1.0 to >=1,<4 (#1051)
dependabot[bot] c57f9c1
Feat: GW workflow with VASP (#808)
yanghan234 cda2a81
Bump monty from 2024.7.30 to 2024.10.21 (#1027)
dependabot[bot] 071d1c8
Update changelog
0fb73a9
Add trajectory reporter to openmm workflow (#1053)
orionarcher d743a69
CP2K tweaks (#1056)
janosh 7761de4
Bump pymatgen-analysis-defects from 2024.7.19 to 2024.10.22 (#1024)
dependabot[bot] 67efb7f
Minor docs cleanup (#1047)
esoteric-ephemera 7add7ca
`PhononMaker` add options to `calculate_pdos` and save force constant…
chouyoudou 5f0bc75
Allow `MatPesStaticFlowMaker(static2=None)` (#997)
janosh 3d55b2b
bug fix for linear strain passing in qha (#1061)
JaGeo 3f61317
Fix `generate_phonon_displacements` magmom removal side effect (#1064)
janosh df1ae35
Bump emmet-core from 0.84.3rc3 to 0.84.3rc4 (#1065)
dependabot[bot] eaed474
Bump jobflow from 0.1.18 to 0.1.19 (#1067)
dependabot[bot] 4244da9
add openmm description to docs (#1069)
JaGeo 4b84d78
fix minor code formatting issues + typos (#1070)
janosh 11fc0ea
Merge branch 'main' of github.com:materialsproject/atomate2 into abin…
VicTrqt bd336d5
tmp abipy github requirement
VicTrqt 38073cd
linting
VicTrqt f532d27
linting
VicTrqt 4bbda09
fix test generate_dte_perts abipy manager
VicTrqt 9832136
install abinit in env pytest
VicTrqt 6349766
Docs update, forcefield elastic convenience maker, forcefield enum hy…
esoteric-ephemera 7b4a66a
add skip to dfpt test
VicTrqt 4bcf127
Fix bump phonopy (#1006)
naik-aakash bbc4933
Bump mp-api from 0.42.2 to 0.43.0 (#1075)
dependabot[bot] 55a87f0
Bump pytest from 8.3.3 to 8.3.4 (#1077)
dependabot[bot] 44a1125
Bump ipython from 8.29.0 to 8.30.0 (#1076)
dependabot[bot] b79b1c1
Bump sevenn from 0.10.1 to 0.10.2 (#1080)
dependabot[bot] 149f05c
Bump emmet-core from 0.84.3rc4 to 0.84.3rc6 (#1081)
dependabot[bot] 073eac1
update calorine version (#1083)
naik-aakash 906ca38
Bump sevenn from 0.10.2 to 0.10.3 (#1084)
dependabot[bot] 44de991
Bump emmet-core from 0.84.3rc6 to 0.84.4 (#1085)
dependabot[bot] 76d55ea
Bump pydantic-settings from 2.6.1 to 2.7.0 (#1090)
dependabot[bot] 5cccaa2
Bump emmet-core from 0.84.4 to 0.84.5 (#1089)
dependabot[bot] 93ef6d2
Bump ipython from 8.30.0 to 8.31.0 (#1093)
dependabot[bot] 95ea060
Bump nbmake from 1.5.4 to 1.5.5 (#1094)
dependabot[bot] 90e6153
Merge branch 'main' of github.com:materialsproject/atomate2 into abin…
VicTrqt 96ff9e9
add possibility of scissor shift for SHG
VicTrqt 388713d
Merge branch 'abinit_workflows_dfpt_shg_new_review-PR' into abinit_wo…
VicTrqt c526b04
trigger GitHub actions
VicTrqt 3fc9f2e
debug CI fail
VicTrqt 012d1cd
trigger GitHub actions
VicTrqt 784709d
Fix tests comparison values with tolerance
VicTrqt 65b657b
Fix structure check in failing tests
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address some comments of Guido
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Is this used anywhere explicitly?
If not and should be added manually, could it be good to have a powerup that appends it to the Flow as a final job?
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you mean the function itself? no, I thought that the user could use this function at the end any job/flow he is running if he wants it. A powerup is a good idea to simplify its usage, I'll work on it.
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I wrote a simple powerup that returns a new Flow with this function at the end, basically what I was using when launching my own flows, is it sufficient? it won't work on Maker though...
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actually this only works for run_locally... the delete job is not added to the launchpad when I try it...
EDIT: it is being added to the Launchpad if I add metadata to the whole flow after having added this delete job... I don't understand why...
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I am not sure what you mean about this point. It should not work on Maker instances, right? You will only even need to pass the Flow that you get from the after calling the Maker.make() method.
This seems really weird. Since you are making a copy in the powerup, are you sure you are taking the
flow
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Yes precisely. So it is different from the other powerups and I was wondering if that was okay.
Yes I am, but I will reproduce it.