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Update VASP input sets for atomate2 compatibility #3835

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merged 22 commits into from
May 23, 2024
Merged

Update VASP input sets for atomate2 compatibility #3835

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63728ff
updates for consistency with atomate2 updates
esoteric-ephemera May 13, 2024
a1295b9
Merge remote-tracking branch 'upstream/master'
esoteric-ephemera May 13, 2024
d97ce17
lint
esoteric-ephemera May 13, 2024
04eb1ad
further patch for atomate2 support, make sure tests are respected or …
esoteric-ephemera May 16, 2024
ed0e8ec
linting
esoteric-ephemera May 16, 2024
a31f08b
Merge branch 'materialsproject:master' into master
esoteric-ephemera May 16, 2024
6646b98
merge DictSet into VaspInputSet, deprecate DictSet as an alias of Vas…
janosh May 17, 2024
c50db64
test_dict_set_alias subclass and deprecation message
janosh May 17, 2024
cf8cedc
Change deprecation warning to be on init of DictSet
esoteric-ephemera May 17, 2024
51b25f5
remove deprecated decorator, only works for functions, error msg less…
esoteric-ephemera May 17, 2024
590831f
Merge branch 'materialsproject:master' into master
esoteric-ephemera May 17, 2024
e873ac3
move remaining VaspInputGenerator features to PMG
esoteric-ephemera May 17, 2024
d035806
pre-commit auto-fixes
pre-commit-ci[bot] May 17, 2024
d599611
added tests
esoteric-ephemera May 17, 2024
e1e1a70
add incar, kpoints, poscar, potcar attr to io.vasp.inputs.VaspInput +…
esoteric-ephemera May 17, 2024
ddf74e1
linted
esoteric-ephemera May 17, 2024
c335ce7
Bump rexml from 3.2.5 to 3.2.8 in /docs (#3836)
dependabot[bot] May 17, 2024
9740bba
Bump nokogiri from 1.16.2 to 1.16.5 in /docs (#3828)
dependabot[bot] May 17, 2024
24ad8e9
shift features of VaspInputSet.write_input to VaspInput.write_input
esoteric-ephemera May 20, 2024
c9117f2
pre-commit /linting
esoteric-ephemera May 20, 2024
45c51ec
move file transfer from write_input method of VaspInputSet to VaspInput
esoteric-ephemera May 20, 2024
576db8e
add missing `output_dir` kwarg to vaspinputset.write_input
esoteric-ephemera May 20, 2024
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20 changes: 14 additions & 6 deletions tests/io/vasp/test_sets.py
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Original file line number Diff line number Diff line change
Expand Up @@ -128,15 +128,15 @@ def test_sets_changed(self):
assert hashes[input_set] == known_hashes[input_set], f"{input_set=}\n{msg}"


class TestDictSet(PymatgenTest):
class TestVaspInputSet(PymatgenTest):
@classmethod
def setUpClass(cls):
filepath = f"{VASP_IN_DIR}/POSCAR"
cls.structure = Structure.from_file(filepath)

def test_as_dict(self):
# https://github.com/materialsproject/pymatgen/pull/3031
dict_set = DictSet(self.structure, config_dict={"INCAR": {}}, user_potcar_functional="PBE_54")
dict_set = VaspInputSet(self.structure, config_dict={"INCAR": {}}, user_potcar_functional="PBE_54")
assert {*dict_set.as_dict()} >= {
"@class",
"@module",
Expand Down Expand Up @@ -1580,7 +1580,7 @@ def test_potcar(self):
assert input_set.potcar.functional == "PBE_52"

with pytest.raises(
ValueError, match=r"Invalid self.user_potcar_functional='PBE', must be one of \('PBE_52', 'PBE_54'\)"
ValueError, match=r"Invalid user_potcar_functional='PBE', must be one of \('PBE_52', 'PBE_54'\)"
):
MVLScanRelaxSet(self.struct, user_potcar_functional="PBE")

Expand All @@ -1597,7 +1597,7 @@ def test_potcar(self):
#
# # https://github.com/materialsproject/pymatgen/pull/3022
# # same test also in MITMPRelaxSetTest above (for redundancy,
# # should apply to all classes inheriting from DictSet)
# # should apply to all classes inheriting from VaspInputSet)
# for user_potcar_settings in [{"Fe": "Fe_pv"}, {"W": "W_pv"}, None]:
# for species in [("W", "W"), ("Fe", "W"), ("Fe", "Fe")]:
# struct = Structure(lattice=Lattice.cubic(3), species=species, coords=[[0, 0, 0], [0.5, 0.5, 0.5]])
Expand Down Expand Up @@ -1710,7 +1710,7 @@ def test_potcar(self):
assert input_set.potcar.functional == "PBE_54"

with pytest.raises(
ValueError, match=r"Invalid self.user_potcar_functional='PBE', must be one of \('PBE_52', 'PBE_54'\)"
ValueError, match=r"Invalid user_potcar_functional='PBE', must be one of \('PBE_52', 'PBE_54'\)"
):
MPScanRelaxSet(self.struct, user_potcar_functional="PBE")

Expand Down Expand Up @@ -1880,7 +1880,7 @@ def test_potcar(self):
assert test_potcar_set_1.potcar.functional == "PBE_52"

with pytest.raises(
ValueError, match=r"Invalid self.user_potcar_functional='PBE', must be one of \('PBE_52', 'PBE_54'\)"
ValueError, match=r"Invalid user_potcar_functional='PBE', must be one of \('PBE_52', 'PBE_54'\)"
):
self.set(self.struct, user_potcar_functional="PBE")

Expand Down Expand Up @@ -2094,3 +2094,11 @@ def test_as_from_dict(self):

def test_vasp_input_set_alias():
assert VaspInputSet is VaspInputGenerator


def test_dict_set_alias():
assert isinstance(DictSet(), VaspInputSet)
with pytest.warns(
FutureWarning, match="DictSet is deprecated, and will be removed on 2025-12-31\n; use VaspInputSet"
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@DanielYang59 looks like your recent changes to @deprecated in monty put the new line in front of the semicolon. looks weird to start a line with a semicolon

- 2025-12-31\n;
+ 2025-12-31;\n

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@DanielYang59 DanielYang59 May 17, 2024 •
edited
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Thanks for catching this and apologize for this overlook.

https://github.com/materialsvirtuallab/monty/blob/7568d6abcfc8dec14ba3022523656d5f9217835e/monty/dev.py#L94-L109

It looks like the semicolon was original there, and the deprecation message we inserted was too long so a line break was inserted. It would be a bit tricky to properly format this without breaking, I would think about this later

        msg = f"{old.__name__} is deprecated"


        if deadline is not None:
            msg += f", and will be removed on {_deadline:%Y-%m-%d}\n"


        if replacement is not None:
            if isinstance(replacement, property):
                r = replacement.fget
            elif isinstance(replacement, (classmethod, staticmethod)):
                r = replacement.__func__
            else:
                r = replacement
            msg += f"; use {r.__name__} in {r.__module__} instead."


        if message:
            msg += "\n" + message

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One other change in monty to make if you can add it to the same PR for the message change: this decorator is just for functions. Would be great if there's a way to decorate classes too

):
DictSet()