Materials Project GGA and meta-GGA workflows #504

janosh · 2023-09-01T14:18:20Z

This PR branches off from #362. It implements the future Materials Project PBE and r2SCAN relaxations as 3-step workflows consisting of a double-relaxation followed by a higher-quality static job (all as in #362 so far) but builds these 3 steps out of MP(Meta)GGADoubleRelaxMakers that are exported for standalone use, as well as called inside MP(Meta)GGADoubleRelaxStatic (the main workflows intended for public use).

The difference to #362 is intended to address #362 (comment) and more closely align the MP workflow API with the existing DoubleRelaxMaker in atomate2.vasp.flows.core.

Closes #352. Closes #363. Closes #364.

This has been a team effort with @esoteric-ephemera and @Andrew-S-Rosen. 🙏

…not needed

…project

…s/phonons.py

wrong key user_incar_settings -> INCAR and raises ruamel/yaml/comments.py:881: in update self._ok.add(*kw.keys()) E TypeError: set.add() takes exactly one argument (3 given)

for consistency with MPPreRelaxMaker

…elaxMaker was passed to __init__, needs to be passed to make()

…ests just test_MP2023RelaxMaker_default_values() for now

fix bandgap doc str in the wrong place

rename test_mp_(meta_)gga_relax to test_mp_(meta_)gga_double_relax_static

pytest tests/vasp/jobs/test_mp.py now passes

codecov · 2023-09-27T22:03:54Z

Codecov Report

Merging #504 (1a6882c) into main (59f47ee) will increase coverage by 0.56%.
Report is 39 commits behind head on main.
The diff coverage is 84.69%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #504      +/-   ##
==========================================
+ Coverage   75.09%   75.66%   +0.56%     
==========================================
  Files          74       77       +3     
  Lines        6570     6727     +157     
  Branches      952      986      +34     
==========================================
+ Hits         4934     5090     +156     
- Misses       1330     1331       +1     
  Partials      306      306

Files	Coverage Δ
src/atomate2/common/flows/defect.py	`81.33% <100.00%> (ø)`
src/atomate2/settings.py	`100.00% <100.00%> (+4.25%)`	⬆️
src/atomate2/vasp/flows/defect.py	`77.46% <100.00%> (ø)`
src/atomate2/vasp/jobs/base.py	`96.55% <100.00%> (ø)`
src/atomate2/vasp/jobs/defect.py	`100.00% <ø> (ø)`
src/atomate2/common/jobs/defect.py	`85.71% <0.00%> (ø)`
src/atomate2/vasp/run.py	`40.98% <0.00%> (ø)`
src/atomate2/vasp/sets/core.py	`81.59% <0.00%> (ø)`
src/atomate2/vasp/flows/core.py	`89.51% <83.33%> (-1.09%)`	⬇️
src/atomate2/vasp/jobs/mp.py	`92.85% <92.85%> (ø)`
... and 3 more

... and 6 files with indirect coverage changes

janosh · 2023-09-27T22:04:46Z

Wow, 1st time ever this PR has had green CI! 🎉 Only took a few months. 😅

janosh · 2023-09-27T22:07:04Z

src/atomate2/vasp/sets/base.py

-            vasprun=vasprun,
-            outcar=outcar,
-        )
+        prev_incar = prev_incar if self.inherit_incar else {}


@utf To get the tests passing, we needed to disable INCAR inheritance. This PR (2177b0f) adds a new keyword inherit_incar: bool = None to VaspInputGenerator which disables INCAR inheritance by default.

Why do you need to disable inheritance for the tests to pass? Surely the test data can be changed?

janosh · 2023-09-27T22:08:11Z

src/atomate2/settings.py

+    VASP_INHERIT_INCAR: bool = Field(
+        False,
+        description="Whether to inherit INCAR settings from previous calculation. "
+        "This might be useful to port Custodian fixes to child jobs but can also be "
+        "dangerous e.g. when switching from GGA to meta-GGA or relax to static jobs.",
+    )


As advocated for by @Andrew-S-Rosen during the atomate2 maintainer meeting, INCAR inheritance can also be controlled by the global VASP_INHERIT_INCAR flag.

This has changed the default behaviour for all input sets. Please can you change this to True and we can assess this as a separate issue. This discussion should probably happen on the pymatgen issues since the default pymatgen behaviour is to inherit incar settings and we will be merging the atomate2 inputs with those in pymatgen soon.

Good point. VASP_INHERIT_INCAR now defaults to True.

also revert to Yb_2 and W_pv

utf · 2023-09-29T08:07:11Z

src/atomate2/vasp/sets/base.py

@@ -305,6 +311,7 @@ class VaspInputGenerator(InputGenerator):
    symprec: float = SETTINGS.SYMPREC
    vdw: str = None
    config_dict: dict = field(default_factory=lambda: _BASE_VASP_SET)
+    inherit_incar: bool = None


Please add docstring for this option.

utf · 2023-10-02T16:14:33Z

This looks good to me!

Andrew-S-Rosen and others added 30 commits June 2, 2023 12:53

Initial attempt at MP workflows

0d30189

First attempt

892c911

Remove MAGMOM.yaml

2dab928

drop added **kwargs from RelaxSetGenerator.get_incar_updates() since …

230e504

…not needed

black .

56b0fa2

Merge remote-tracking branch 'origin/materialsproject' into materials…

aceeb11

…project

Remove unused function

a7a3b8f

Fix __all__

7e47522

Remove sets/mp.py

c08f549

Fix ISMEAR and SIGMA

18c0d20

Fix imports

0003b28

More robust KSPACING

01f2000

Fix linting

9323435

Fix linting

1fcff17

fix ruff

6692dfe

mv tests/vasp/flows/test_phonon{,s}.py to match module names vasp/job…

5927eed

…s/phonons.py

fix self.input_set_generator.config_dict["user_incar_settings"].update()

493b4c6

wrong key user_incar_settings -> INCAR and raises ruamel/yaml/comments.py:881: in update self._ok.add(*kw.keys()) E TypeError: set.add() takes exactly one argument (3 given)

rename prerelax_maker to pre_relax_maker

cea4d28

for consistency with MPPreRelaxMaker

fix MPRelaxR2SCANGenerator arg type

4eb86b5

fix passing bandgap estimate for kspacing from MPPreRelaxMaker to MPR…

c7bcb82

…elaxMaker was passed to __init__, needs to be passed to make()

add module tests/vasp/flows/test_mp.py for soon-to-come MP workflow t…

c98cf7c

…ests just test_MP2023RelaxMaker_default_values() for now

add BaseVaspMaker.make() return type and doc str

cbab233

add bandgap_tol: float = 1e-4 to MPRelaxMaker.make()

9374e93

fix bandgap doc str in the wrong place

Copy CHGCAR etc.

d9bfa2c

Update class name

e033dc0

Fix tests

a9355b6

Address Ryan's comments

d470fd7

Add missing type hints

01b8571

Fix docstring

8b25884

Fix docstring

c49668e

janosh added 11 commits September 27, 2023 09:54

rename relax_job to relax_flow (since it's a double relax)

0b0bdc8

fix MPGGAStaticMaker.name casing

2783dfa

add test_mp_gga_relax_maker

57df7ed

add test_mp_gga_double_relax

075075d

rename test_mp_(meta_)gga_relax to test_mp_(meta_)gga_double_relax_static

rm tests/test_data/**/FW.json.gz

33b0f68

rename MP(Meta)GGADoubleRelaxStatic to MPMetaGGADoubleRelaxStaticMaker

ecd2052

add Atomate2Settings.VASP_INHERIT_INCAR

b0e06be

add VaspInputGenerator keyword inherit_incar: bool = None

2177b0f

fix MPGGAStaticMaker using wrong set generator

7ad43d6

fix missing incar updates in MP set generators

0943466

fix MP jobs tests

a1132e2

pytest tests/vasp/jobs/test_mp.py now passes

janosh commented Sep 27, 2023

View reviewed changes

janosh mentioned this pull request Sep 28, 2023

Add MatPES GGA and r2SCAN static makers #532

Merged

revert BaseMPGGASet.yaml to POTCAR_FUNCTIONAL: PBE (from PBE_54)

36c2529

also revert to Yb_2 and W_pv

utf reviewed Sep 29, 2023

View reviewed changes

janosh added 3 commits September 29, 2023 08:49

change VASP_INHERIT_INCAR default to True

a3f2d87

add inherit_incar to VaspInputGenerator doc str

a3c6fb3

set inherit_incar = False on all MP sets

1a6882c

utf merged commit 468fb57 into main Oct 2, 2023

janosh mentioned this pull request Oct 2, 2023

[WIP] MP-compatible r2SCAN workflow (and a few general INCAR improvements) #362

Merged

janosh deleted the mp-wf branch October 2, 2023 16:38

This was referenced Oct 3, 2023

Fix wrong INCAR values in MP workflows #550

Merged

Are bandgap_tol or bandgap_override used anywhere in the MP workflows? #552

Closed

This was referenced Oct 17, 2023

_parse_additional_json ignore FW.json(.gz) materialsproject/emmet#864

Merged

parse_additional_json() ignore FW.json.gz in output directories #574

Merged

esoteric-ephemera mentioned this pull request Sep 28, 2024

BUG: INCAR parameter inheritance with prev_dir has changed for MPGGAStaticMaker #995

Closed

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Materials Project GGA and meta-GGA workflows #504

Materials Project GGA and meta-GGA workflows #504

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Materials Project GGA and meta-GGA workflows #504

Materials Project GGA and meta-GGA workflows #504

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