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Add VASP setting for the dftd4 vdW functional and extend PBE_64 support. #3967

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merged 7 commits into from
Aug 24, 2024
Merged

Add VASP setting for the dftd4 vdW functional and extend PBE_64 support. #3967

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4c2be2c
Add VASP setting for the dftd4 vdW functional and extend PBE_64 support
hongyi-zhao Aug 2, 2024
ea4d3d5
Merge https://github.com/materialsproject/pymatgen into add-pbe64-dft…
hongyi-zhao Aug 2, 2024
df14616
Update the warning message of LobsterSet to include PBE_52 POTCARs as…
hongyi-zhao Aug 2, 2024
0a3359b
fix the conflict of using the sha256 for yaml configuration files.
hongyi-zhao Aug 9, 2024
24edfc0
Merge branch 'master' into add-pbe64-dftd4-support
hongyi-zhao Aug 22, 2024
e99ac3c
Merge branch 'master' into add-pbe64-dftd4-support
janosh Aug 23, 2024
c45e583
update vdW_parameters.yaml expected hash
janosh Aug 24, 2024
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27 changes: 17 additions & 10 deletions src/pymatgen/io/vasp/sets.py
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Original file line number Diff line number Diff line change
Expand Up @@ -145,7 +145,7 @@ class VaspInputSet(InputGenerator, abc.ABC):
atomic species are grouped together.
user_potcar_functional (str): Functional to use. Default (None) is to use the
functional in the config dictionary. Valid values: "PBE", "PBE_52",
"PBE_54", "LDA", "LDA_52", "LDA_54", "PW91", "LDA_US", "PW91_US".
"PBE_54", "PBE_64", "LDA", "LDA_52", "LDA_54", "PW91", "LDA_US", "PW91_US".
force_gamma (bool): Force gamma centered kpoint generation. Default (False) is
to use the Automatic Density kpoint scheme, which will use the Gamma
centered generation scheme for hexagonal cells, and Monkhorst-Pack otherwise.
Expand Down Expand Up @@ -1281,7 +1281,7 @@ class MPScanRelaxSet(VaspInputSet):

2. Meta-GGA calculations require POTCAR files that include
information on the kinetic energy density of the core-electrons,
i.e. "PBE_52" or "PBE_54". Make sure the POTCARs include the
i.e. "PBE_52", "PBE_54" or "PBE_64". Make sure the POTCARs include the
following lines (see VASP wiki for more details):

$ grep kinetic POTCAR
Expand Down Expand Up @@ -1322,7 +1322,7 @@ class MPScanRelaxSet(VaspInputSet):
user_potcar_functional: UserPotcarFunctional = "PBE_54"
auto_ismear: bool = True
CONFIG = _load_yaml_config("MPSCANRelaxSet")
_valid_potcars: Sequence[str] | None = ("PBE_52", "PBE_54")
_valid_potcars: Sequence[str] | None = ("PBE_52", "PBE_54", "PBE_64")

def __post_init__(self) -> None:
super().__post_init__()
Expand Down Expand Up @@ -2295,13 +2295,13 @@ class MVLRelax52Set(VaspInputSet):

Args:
structure (Structure): input structure.
user_potcar_functional (str): choose from "PBE_52" and "PBE_54".
user_potcar_functional (str): choose from "PBE_52", "PBE_54" and "PBE_64".
**kwargs: Other kwargs supported by VaspInputSet.
"""

user_potcar_functional: UserPotcarFunctional = "PBE_52"
CONFIG = _load_yaml_config("MVLRelax52Set")
_valid_potcars: Sequence[str] | None = ("PBE_52", "PBE_54")
_valid_potcars: Sequence[str] | None = ("PBE_52", "PBE_54", "PBE_64")


class MITNEBSet(VaspInputSet):
Expand Down Expand Up @@ -2635,7 +2635,7 @@ class MVLScanRelaxSet(VaspInputSet):

2. Meta-GGA calculations require POTCAR files that include
information on the kinetic energy density of the core-electrons,
i.e. "PBE_52" or "PBE_54". Make sure the POTCAR including the
i.e. "PBE_52", "PBE_54" or "PBE_64". Make sure the POTCAR including the
following lines (see VASP wiki for more details):

$ grep kinetic POTCAR
Expand All @@ -2652,13 +2652,13 @@ class MVLScanRelaxSet(VaspInputSet):
"""

user_potcar_functional: UserPotcarFunctional = "PBE_52"
_valid_potcars: Sequence[str] | None = ("PBE_52", "PBE_54")
_valid_potcars: Sequence[str] | None = ("PBE_52", "PBE_54", "PBE_64")
CONFIG = MPRelaxSet.CONFIG

def __post_init__(self) -> None:
super().__post_init__()
if self.user_potcar_functional not in {"PBE_52", "PBE_54"}:
raise ValueError("SCAN calculations require PBE_52 or PBE_54!")
if self.user_potcar_functional not in {"PBE_52", "PBE_54", "PBE_64"}:
raise ValueError("SCAN calculations require PBE_52, PBE_54, or PBE_64!")

@property
def incar_updates(self) -> dict[str, Any]:
Expand Down Expand Up @@ -2708,12 +2708,19 @@ class LobsterSet(VaspInputSet):
user_potcar_functional: UserPotcarFunctional = "PBE_54"

CONFIG = MPRelaxSet.CONFIG
_valid_potcars: Sequence[str] | None = ("PBE_52", "PBE_54")
_valid_potcars: Sequence[str] | None = ("PBE_52", "PBE_54", "PBE_64")

def __post_init__(self) -> None:
super().__post_init__()
warnings.warn("Make sure that all parameters are okay! This is a brand new implementation.")

if self.user_potcar_functional in ["PBE_52", "PBE_64"]:
warnings.warn(
f"Using {self.user_potcar_functional} POTCARs with basis functions generated for PBE_54 POTCARs. "
"Basis functions for elements with obsoleted, updated or newly added POTCARs in "
f"{self.user_potcar_functional} will not be available and may cause errors or inaccuracies.",
BadInputSetWarning,
)
if self.isym not in {-1, 0}:
raise ValueError("Lobster cannot digest WAVEFUNCTIONS with symmetry. isym must be -1 or 0")
if self.ismear not in {-5, 0}:
Expand Down
2 changes: 2 additions & 0 deletions src/pymatgen/io/vasp/vdW_parameters.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,8 @@ dftd3:
IVDW: 11
dftd3-bj:
IVDW: 12
dftd4:
IVDW: 13
ts:
IVDW: 2
ts-hirshfeld:
Expand Down
10 changes: 5 additions & 5 deletions tests/io/vasp/test_sets.py
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Original file line number Diff line number Diff line change
Expand Up @@ -119,7 +119,7 @@ def test_sets_changed(self):
"PBE64Base.yaml": "3434c918c17706feae397d0852f2224e771db94d7e4c988039e8658e66d87494",
"MPRelaxSet.yaml": "c9b0a519588fb3709509a9f9964632692584905e2961a0fe2e5f657561913083",
"MITRelaxSet.yaml": "0b4bec619fa860dac648584853c3b3d5407e4148a85d0e95024fbd1dc315669d",
"vdW_parameters.yaml": "977c226a1b44831382e772a464aecb7f6297c98d7efc9190f8c18e0b73be2666",
"vdW_parameters.yaml": "7d2599a855533865335a313c043b6f89e03fc2633c88b6bc721723d94cc862bd",
"MatPESStaticSet.yaml": "4ec60ad4bbbb9a756f1b3fea8ca4eab8fc767d8f6a67332e7af3908c910fd7c5",
"MPAbsorptionSet.yaml": "e49cd0ab87864f1c244e9b5ceb4703243116ec1fbb8958a374ddff07f7a5625c",
"PBE54Base.yaml": "cdffe123eca8b19354554b60a7f8de9b8776caac9e1da2bd2a0516b7bfac8634",
Expand Down Expand Up @@ -1676,7 +1676,7 @@ def test_potcar(self):
assert input_set.potcar.functional == "PBE_52"

with pytest.raises(
ValueError, match=r"Invalid user_potcar_functional='PBE', must be one of \('PBE_52', 'PBE_54'\)"
ValueError, match=r"Invalid user_potcar_functional='PBE', must be one of \('PBE_52', 'PBE_54', 'PBE_64'\)"
):
MVLScanRelaxSet(self.struct, user_potcar_functional="PBE")

Expand All @@ -1687,7 +1687,7 @@ def test_potcar(self):
# assert test_potcar_set_1.potcar.functional == "PBE_54"
#
# with pytest.raises(
# ValueError, match=r"Invalid user_potcar_functional='PBE', must be one of \('PBE_52', 'PBE_54'\)"
# ValueError, match=r"Invalid user_potcar_functional='PBE', must be one of \('PBE_52', 'PBE_54', 'PBE_64'\)"
# ):
# self.set(self.struct, user_potcar_functional="PBE")
#
Expand Down Expand Up @@ -1806,7 +1806,7 @@ def test_potcar(self):
assert input_set.potcar.functional == "PBE_54"

with pytest.raises(
ValueError, match=r"Invalid user_potcar_functional='PBE', must be one of \('PBE_52', 'PBE_54'\)"
ValueError, match=r"Invalid user_potcar_functional='PBE', must be one of \('PBE_52', 'PBE_54', 'PBE_64'\)"
):
MPScanRelaxSet(self.struct, user_potcar_functional="PBE")

Expand Down Expand Up @@ -1976,7 +1976,7 @@ def test_potcar(self):
assert test_potcar_set_1.potcar.functional == "PBE_52"

with pytest.raises(
ValueError, match=r"Invalid user_potcar_functional='PBE', must be one of \('PBE_52', 'PBE_54'\)"
ValueError, match=r"Invalid user_potcar_functional='PBE', must be one of \('PBE_52', 'PBE_54', 'PBE_64'\)"
):
self.set(self.struct, user_potcar_functional="PBE")

Expand Down