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Update DictSet to allow direct initialisation #3031

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Jun 1, 2023
Merged

Update DictSet to allow direct initialisation #3031

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24 changes: 14 additions & 10 deletions pymatgen/io/vasp/sets.py
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Original file line number Diff line number Diff line change
Expand Up @@ -346,15 +346,6 @@ def __init__(
if (valid_potcars := self._valid_potcars) and user_potcar_functional not in valid_potcars:
raise ValueError(f"Invalid {user_potcar_functional=}, must be one of {valid_potcars}")

struct_has_Yb = any(specie.symbol == "Yb" for site in structure for specie in site.species)
uses_Yb_2_psp = self.CONFIG["POTCAR"]["Yb"] == "Yb_2"
if struct_has_Yb and uses_Yb_2_psp:
warnings.warn(
"The structure contains Ytterbium (Yb) and this InputSet uses the Yb_2 PSP.\n"
"Yb_2 is known to often give bad results since Yb has oxidation state 3+ in most compounds.\n"
"See https://github.com/materialsproject/pymatgen/issues/2968 for details.",
BadInputSetWarning,
)
if reduce_structure:
structure = structure.get_reduced_structure(reduce_structure)
if sort_structure:
Expand All @@ -366,6 +357,19 @@ def __init__(
# when using 5.4 POTCARs, default Tungsten POTCAR to W_Sv but still allow user to override
user_potcar_settings = {"W": "W_sv", **(user_potcar_settings or {})}

struct_has_Yb = any(specie.symbol == "Yb" for site in structure for specie in site.species)
potcar_settings = config_dict.get("POTCAR", {})
if user_potcar_settings:
potcar_settings.update(user_potcar_settings)
uses_Yb_2_psp = potcar_settings.get("Yb", None) == "Yb_2"
if struct_has_Yb and uses_Yb_2_psp:
warnings.warn(
"The structure contains Ytterbium (Yb) and this InputSet uses the Yb_2 PSP.\n"
"Yb_2 is known to often give bad results since Yb has oxidation state 3+ in most compounds.\n"
"See https://github.com/materialsproject/pymatgen/issues/2968 for details.",
BadInputSetWarning,
)

self._structure = structure
self._config_dict = deepcopy(config_dict)
self.files_to_transfer = files_to_transfer or {}
Expand Down Expand Up @@ -404,7 +408,7 @@ def __init__(
self.potcar_functional = user_potcar_functional or self._config_dict.get("POTCAR_FUNCTIONAL", "PBE")

# warn if a user is overriding POTCAR_FUNCTIONAL
if self.potcar_functional != self._config_dict.get("POTCAR_FUNCTIONAL"):
if self.potcar_functional != self._config_dict.get("POTCAR_FUNCTIONAL", "PBE"):
warnings.warn(
"Overriding the POTCAR functional is generally not recommended "
" as it significantly affect the results of calculations and "
Expand Down