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Read INCAR SYSTEM as is, check_params use proc_val (#4136)
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* remove unnecessary processing

* stupid manual update of GGA recording

* stupid manually add ZAB_VDW tag

* avoid casing SYSTEM value

* fix SYSTEM case and add test

* tweak comment

* use a non capitalized string for test

* fix test string

* revert str compare, startswith is slower

* add test for Incar pop method

* check_params consider lower str exception

* reuse proc_val in check_params, thanks @yantar92
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@DanielYang59
DanielYang59 authored Nov 12, 2024
1 parent d883f98 commit 29b21bf
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Showing 4 changed files with 70 additions and 26 deletions.
47 changes: 36 additions & 11 deletions src/pymatgen/io/vasp/incar_parameters.json
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Original file line number Diff line number Diff line change
Expand Up @@ -191,24 +191,35 @@
"GGA": {
"type": "str",
"values": [
"91",
"PE",
"AM",
"HL",
"CA",
"MK",
"RE",
"VW",
"B3",
"PZ",
"SL",
"CA_C",
"PZ_C",
"VW",
"HL",
"WI",
"LIBXC",
"LI",
"91",
"PE",
"PBE_X",
"PBE_C",
"RE",
"RP",
"B5",
"BF",
"CO",
"PS",
"AM",
"B3",
"B5",
"OR",
"BO",
"MK",
"ML",
"CX",
"BF",
"RP",
"CO",
"RE",
"03",
"05",
"10",
Expand Down Expand Up @@ -970,6 +981,17 @@
"ML_FF_WTSIF": {
"type": "float"
},
"ML_MODE": {
"type": "str",
"values": [
"train",
"select",
"refit",
"refitbayesian",
"run",
"none"
]
},
"NBANDS": {
"type": "int"
},
Expand Down Expand Up @@ -1444,5 +1466,8 @@
},
"MAGDIPOLOUT": {
"type": "bool"
},
"ZAB_VDW": {
"type": "float"
}
}
13 changes: 9 additions & 4 deletions src/pymatgen/io/vasp/inputs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -723,7 +723,7 @@ class Incar(UserDict, MSONable):
- Keys are stored in uppercase to allow case-insensitive access (set, get, del, update, setdefault).
- String values are capitalized by default, except for keys specified
in the `lower_str_keys` of the `proc_val` method.
in the `lower_str_keys/as_is_str_keys` of the `proc_val` method.
"""

def __init__(self, params: dict[str, Any] | None = None) -> None:
Expand Down Expand Up @@ -971,6 +971,8 @@ def proc_val(key: str, val: str) -> list | bool | float | int | str:
"IVDW",
)
lower_str_keys = ("ML_MODE",)
# String keywords to read "as is" (no case transformation, only stripped)
as_is_str_keys = ("SYSTEM",)

def smart_int_or_float(num_str: str) -> float:
"""Determine whether a string represents an integer or a float."""
Expand Down Expand Up @@ -1006,6 +1008,9 @@ def smart_int_or_float(num_str: str) -> float:
if key in lower_str_keys:
return val.strip().lower()

if key in as_is_str_keys:
return val.strip()

except ValueError:
pass

Expand Down Expand Up @@ -1087,9 +1092,9 @@ def check_params(self) -> None:
# Only check value when it's not None,
# meaning there is recording for corresponding value
if allowed_values is not None:
# Note: param_type could be a Union type, e.g. "str | bool"
if "str" in param_type:
allowed_values = [item.capitalize() if isinstance(item, str) else item for item in allowed_values]
allowed_values = [
self.proc_val(tag, item) if isinstance(item, str) else item for item in allowed_values
]

if val not in allowed_values:
warnings.warn(
Expand Down
8 changes: 4 additions & 4 deletions src/pymatgen/io/vasp/outputs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -474,7 +474,7 @@ def _parse(
elif tag == "dielectricfunction":
label = elem.attrib.get("comment", None)
if label is None:
if self.incar.get("ALGO", "Normal").upper() == "BSE":
if self.incar.get("ALGO", "Normal") == "Bse":
label = "freq_dependent"
elif "density" not in self.dielectric_data:
label = "density"
Expand Down Expand Up @@ -634,7 +634,7 @@ def converged_electronic(self) -> bool:
while set(final_elec_steps[idx]) == to_check:
idx += 1
return idx + 1 != self.parameters["NELM"]
if self.incar.get("ALGO", "").upper() == "EXACT" and self.incar.get("NELM") == 1:
if self.incar.get("ALGO", "") == "Exact" and self.incar.get("NELM") == 1:
return True
return len(final_elec_steps) < self.parameters["NELM"]

Expand Down Expand Up @@ -793,10 +793,10 @@ def run_type(self) -> str:
"--",
"None",
}:
incar_tag = self.incar.get("METAGGA", "").strip().upper()
incar_tag = self.incar.get("METAGGA", "").upper()
run_type = METAGGA_TYPES.get(incar_tag, incar_tag)
elif self.parameters.get("GGA"):
incar_tag = self.parameters.get("GGA", "").strip().upper()
incar_tag = self.parameters.get("GGA", "").upper()
run_type = GGA_TYPES.get(incar_tag, incar_tag)
elif self.potcar_symbols[0].split()[0] == "PAW":
run_type = "LDA"
Expand Down
28 changes: 21 additions & 7 deletions tests/io/vasp/test_inputs.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -615,6 +615,14 @@ def test_key_case_insensitive(self):
incar.setdefault("NPAR", 4)
assert incar["npar"] == 4

# Test pop
assert incar.pop(test_tag.lower()) == 520
assert test_tag.upper() not in incar
assert test_tag.lower() not in incar

# Test pop with default value
assert incar.pop("missing_key", 42) == 42

def test_copy(self):
incar2 = self.incar.copy()
assert isinstance(incar2, Incar), f"Expected Incar, got {type(incar2).__name__}"
Expand Down Expand Up @@ -678,9 +686,11 @@ def test_diff(self):
"ISMEAR": {"INCAR1": 0, "INCAR2": -5},
"NPAR": {"INCAR1": 8, "INCAR2": 1},
"SYSTEM": {
"INCAR1": "Id=[0] dblock_code=[97763-icsd] formula=[li mn (p o4)] sg_name=[p n m a]",
"INCAR2": "Id=[91090] dblock_code=[20070929235612linio-59.53134651-vasp] formula=[li3 ni3 o6] "
"sg_name=[r-3m]",
"INCAR1": "id=[0] dblock_code=[97763-ICSD] formula=[Li Mn (P O4)] sg_name=[P n m a]",
"INCAR2": (
"id=[91090] dblock_code=[20070929235612LiNiO-59.53134651-VASP] "
"formula=[Li3 Ni3 O6] sg_name=[R-3m]"
),
},
"ALGO": {"INCAR1": "Damped", "INCAR2": "Fast"},
"LHFCALC": {"INCAR1": True, "INCAR2": None},
Expand Down Expand Up @@ -715,14 +725,15 @@ def test_from_file_and_from_dict(self):
float/int, and might yield values in wrong type.
"""
# Init from dict
incar_dict = {"ENCUT": 500, "GGA": "PS", "NELM": 60.0}
incar_dict = {"ENCUT": 500, "GGA": "PS", "NELM": 60.0, "SYSTEM": "This should NOT BE capitalized"}
incar_from_dict = Incar(incar_dict)

# Init from file (from string)
incar_str = """\
ENCUT = 500
GGA = PS
NELM = 60.0
SYSTEM = This should NOT BE capitalized
"""

with ScratchDir("."):
Expand All @@ -739,6 +750,7 @@ def test_from_file_and_from_dict(self):
assert incar_from_dict == incar_from_file
for key in incar_from_dict:
assert type(incar_from_dict[key]) is type(incar_from_file[key])
assert incar_from_file["SYSTEM"] == "This should NOT BE capitalized"

def test_write(self):
tmp_file = f"{self.tmp_path}/INCAR.testing"
Expand Down Expand Up @@ -774,7 +786,7 @@ def test_get_str(self):
NUPDOWN = 0
PREC = Accurate
SIGMA = 0.05
SYSTEM = Id=[0] dblock_code=[97763-icsd] formula=[li mn (p o4)] sg_name=[p n m a]
SYSTEM = id=[0] dblock_code=[97763-ICSD] formula=[Li Mn (P O4)] sg_name=[P n m a]
TIME = 0.4"""
assert incar_str == expected

Expand Down Expand Up @@ -876,13 +888,15 @@ def test_check_params(self):
"AMIN": 0.01,
"ICHARG": 1,
"MAGMOM": [1, 2, 4, 5],
"ML_MODE": "RUN", # lower case string
"SYSTEM": "Hello world", # as is string
"ENCUT": 500, # make sure float key is casted
"GGA": "PS", # test string case insensitivity
"LREAL": True, # special case: Union type
"NBAND": 250, # typo in tag
"METAGGA": "SCAM", # typo in value
"EDIFF": 5 + 1j, # value should be a float
"ISIF": 9, # value out of range
"EDIFF": 5 + 1j, # value should be float
"ISIF": 9, # value not unknown
"LASPH": 5, # value should be bool
"PHON_TLIST": "is_a_str", # value should be a list
}
Expand Down

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