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Update POTCAR summary stats to include 6.4 POTCARs and add dev_script utils for future updates #3370

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merged 17 commits into from
Oct 3, 2023
Merged

Update POTCAR summary stats to include 6.4 POTCARs and add dev_script utils for future updates #3370

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afbbf79
Added option for 64 POTCARs, hidden func to regenerate potcar_summary…
Oct 2, 2023
4a84723
Updated potcar_summary_stats.json.gz to include 64 POTCARs
Oct 2, 2023
f3b62f8
Verify new POTCAR_64 summary_stats work; prep for PR
Oct 2, 2023
5828944
pre-commit auto-fixes
pre-commit-ci[bot] Oct 2, 2023
404bbb9
Merge branch 'master' into master
janosh Oct 3, 2023
a90e2a4
Added (1) support for LDA 64 POTCARs; (2) ability to generate fake PO…
Oct 3, 2023
66cfac8
pre-commit auto-fixes
pre-commit-ci[bot] Oct 3, 2023
cca9d39
cleanup for ruff/lint/etc
Oct 3, 2023
ac2408d
google-style doc str
janosh Oct 3, 2023
ca5d50d
replace print with warnings.warn
janosh Oct 3, 2023
b955eeb
refactor test_gen_potcar_summary_stats using pytest fixtures
janosh Oct 3, 2023
5c54cd0
rename function arg PMG_VASP_PSP_DIR to vasp_psp_dir
janosh Oct 3, 2023
93d3bcd
cleanup fake potcar library to only include a few required examples
Oct 3, 2023
a916a68
replace os.system('rm -rf') with shutil.rmtree() and system(f"mkdir -…
janosh Oct 3, 2023
6ace41b
git mv tests/files/fake_{POTCAR,potcar}_library
janosh Oct 3, 2023
209c0b0
generate_fake_potcar_libraries prefix src_dirs with SETTINGS["PMG_VAS…
janosh Oct 3, 2023
baef777
fix overlooked rename fake_(POTCAR->potcar)_library
janosh Oct 3, 2023
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48 changes: 44 additions & 4 deletions pymatgen/io/vasp/inputs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1607,6 +1607,7 @@ class PotcarSingle:
PBE="POT_GGA_PAW_PBE",
PBE_52="POT_GGA_PAW_PBE_52",
PBE_54="POT_GGA_PAW_PBE_54",
PBE_64="POT_PAW_PBE_64",
LDA="POT_LDA_PAW",
LDA_52="POT_LDA_PAW_52",
LDA_54="POT_LDA_PAW_54",
Expand Down Expand Up @@ -2150,7 +2151,7 @@ def is_valid(self) -> bool:
tol is then used to match statistical values within a tolerance
"""
functional_lexch = {
"PE": ["PBE", "PBE_52", "PBE_54"],
"PE": ["PBE", "PBE_52", "PBE_54", "PBE_64"],
"CA": ["LDA", "LDA_52", "LDA_54", "LDA_US", "Perdew_Zunger81"],
"91": ["PW91", "PW91_US"],
}
Expand Down Expand Up @@ -2231,7 +2232,9 @@ def data_stats(data_list: Sequence) -> dict:
"MAX": arr.max(),
}

summary_stats = { # for this PotcarSingle instance
# NB: to add future summary stats in a way that's consistent with PMG,
# it's easiest to save the summary stats as an attr of PotcarSingle
self._summary_stats = { # for this PotcarSingle instance
"keywords": {
"header": [kwd.lower() for kwd in self.keywords],
"data": psp_keys,
Expand All @@ -2245,12 +2248,12 @@ def data_stats(data_list: Sequence) -> dict:
data_match_tol = 1e-6
for ref_psp in possible_potcar_matches:
key_match = all(
set(ref_psp["keywords"][key]) == set(summary_stats["keywords"][key]) # type: ignore
set(ref_psp["keywords"][key]) == set(self._summary_stats["keywords"][key]) # type: ignore
for key in ["header", "data"]
)

data_diff = [
abs(ref_psp["stats"][key][stat] - summary_stats["stats"][key][stat]) # type: ignore
abs(ref_psp["stats"][key][stat] - self._summary_stats["stats"][key][stat]) # type: ignore
for stat in ["MEAN", "ABSMEAN", "VAR", "MIN", "MAX"]
for key in ["header", "data"]
]
Expand Down Expand Up @@ -2280,6 +2283,43 @@ def __repr__(self) -> str:
return f"{cls_name}({symbol=}, {functional=}, {TITEL=}, {VRHFIN=}, {n_valence_elec=:.0f})"


def _gen_potcar_summary_stats():
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This is fine here, but noting there is also a top-level dev_scripts folder (largely undocumented). On balance it's probably better here for discoverability for anyone curious how this file was generated.

Minor comments: the bare return is unnecessary, and monty.serialization.dumpfn can be used directly with dumpfn(new_summary_stats, "filename.json.gz") which is a convenience function we use a lot.

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Thanks! Much better way of doing this. For placement, you and @janosh probably have a better sense of where this belongs. _gen_potcar_summary_stats is a "destructive" function, in that it overwrites the file that's distributed with PMG. dev_scripts might then be a better place for it

"""
This function solely intended to be used for PMG development to regenerate the
potcar_summary_stats.json.gz file used to validate POTCARs
"""
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Perfect! This is great to have. Even though it's marked as private, we should add a test for this.

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Added a Test_gen_potcar_summary_stats to tests/io/vasp/test_inputs.py. Requires generating a library of fake POTCARs, which are in tests/fake_POTCAR_library. Code to generate this library from a real library of POTCARs is in dev_scripts/potcar_scrambler.py

from monty.shutil import compress_file

func_dir_exist = {}
PMG_VASP_PSP_DIR = SETTINGS.get("PMG_VASP_PSP_DIR")
for func in PotcarSingle.functional_dir:
cpsp_dir = f"{PMG_VASP_PSP_DIR}/{PotcarSingle.functional_dir[func]}"
if os.path.isdir(cpsp_dir):
func_dir_exist[func] = PotcarSingle.functional_dir[func]
else:
print(f"WARNING: missing {PotcarSingle.functional_dir[func]} POTCAR directory")

new_summary_stats = {func: {} for func in func_dir_exist}
for func in func_dir_exist:
potcar_list = glob(f"{PMG_VASP_PSP_DIR}/{func_dir_exist[func]}/POTCAR*") + glob(
f"{PMG_VASP_PSP_DIR}/{func_dir_exist[func]}/*/POTCAR"
)
for potcar in potcar_list:
psp = PotcarSingle.from_file(potcar)
new_summary_stats[func][psp.TITEL.replace(" ", "")] = {
"LEXCH": psp.LEXCH,
"VRHFIN": psp.VRHFIN.replace(" ", ""),
**psp._summary_stats,
}

with open(f"{module_dir}/potcar_summary_stats.json", "w+") as _fl:
json.dump(new_summary_stats, _fl)

compress_file(f"{module_dir}/potcar_summary_stats.json")

return


class Potcar(list, MSONable):
"""
Object for reading and writing POTCAR files for calculations. Consists of a
Expand Down
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