Define PBE64Base.yaml for new VASP PBE_64 POTCARs (#3470)

* add pymatgen/io/vasp/PBE64Base.yaml

* update MatPESStaticSet PARENT to PBE64Base

* update MatPES known_hash and add PBE64Base hash in test_sets.py

* fix TestMatPESStaticSet to expect PBE_64 as default POTCARs

* use monty zpath in generate_fake_potcar_libraries

* fix TestWavecar.test_standard ValueError

Invalid rtag=-9223372036854775808, must be one of {45200, 45210, 53300, 53310}

/home/runner/work/pymatgen/pymatgen/pymatgen/io/vasp/outputs.py:4252

dev_scripts/potcar_scrambler.py

@@ -5,6 +5,7 @@
 import warnings
 
 import numpy as np
+from monty.os.path import zpath
 from monty.serialization import zopen
 
 from pymatgen.core import SETTINGS
@@ -51,7 +52,7 @@ def _rand_float_from_str_with_prec(self, input_str: str, bloat: float = 1.5):
     def _read_fortran_str_and_scramble(self, input_str: str, bloat: float = 1.5):
         input_str = input_str.strip()
 
-        if input_str.lower() in ["t", "f"] or input_str.lower() in ["true", "false"]:
+        if input_str.lower() in ("t", "f", "true", "false"):
             return bool(np.random.randint(2))
 
         if input_str.upper() == input_str.lower() and input_str[0].isnumeric():
@@ -128,10 +129,8 @@ def generate_fake_potcar_libraries():
         for psp_name in psp_variants:
             rebase_dir = f"{output_dir}/{func_dir}/{psp_name}/"
             paths_to_try = [
-                f"{func_dir}/POTCAR.{psp_name}",
-                f"{func_dir}/POTCAR.{psp_name}.gz",
-                f"{func_dir}/{psp_name}/POTCAR",
-                f"{func_dir}/{psp_name}/POTCAR.gz",
+                zpath(f"{func_dir}/POTCAR.{psp_name}"),
+                zpath(f"{func_dir}/{psp_name}/POTCAR"),
             ]
             if not any(map(os.path.isfile, paths_to_try)):
                 warnings.warn(f"Could not find {psp_name} in {paths_to_try}")

pymatgen/apps/borg/hive.py

@@ -195,8 +195,7 @@ class SimpleVaspToComputedEntryDrone(VaspToComputedEntryDrone):
     def __init__(self, inc_structure=False):
         """
         Args:
-            inc_structure (bool): Set to True if you want
-                ComputedStructureEntries to be returned instead of
+            inc_structure (bool): Set to True if you want ComputedStructureEntries to be returned instead of
                 ComputedEntries. Structure will be parsed from the CONTCAR.
         """
         self._inc_structure = inc_structure

pymatgen/io/vasp/MatPESStaticSet.yaml

@@ -1,7 +1,7 @@
 # Default VASP settings for static calculations in the MatPES Project
 # using the Regularized-Restored Strongly Constrained and Appropriately
 # Normed functional (default PBE, PBE+U or R2SCAN or R2SCAN+U).
-PARENT: PBE54Base
+PARENT: PBE64Base
 INCAR:
   ALGO: Normal # Normal for PBE, ALL for R2SCAN, included to have some reasonable default
   EDIFF: 1.e-05

pymatgen/io/vasp/PBE64Base.yaml

@@ -0,0 +1,101 @@
+# POTCARs for PBE_64
+PARENT: VASPIncarBase
+POTCAR_FUNCTIONAL: PBE_64
+POTCAR:
+  Ac: Ac
+  Ag: Ag
+  Al: Al
+  Am: Am
+  Ar: Ar
+  As: As
+  At: At
+  Au: Au
+  B: B
+  Ba: Ba_sv
+  Be: Be_sv
+  Bi: Bi
+  Br: Br
+  C: C
+  Ca: Ca_sv
+  Cd: Cd
+  Ce: Ce
+  Cf: Cf
+  Cl: Cl
+  Cm: Cm
+  Co: Co
+  Cr: Cr_pv
+  Cs: Cs_sv
+  Cu: Cu_pv
+  Dy: Dy_3
+  Er: Er_3
+  Eu: Eu
+  F: F
+  Fe: Fe_pv
+  Fr: Fr_sv
+  Ga: Ga_d
+  Gd: Gd
+  Ge: Ge_d
+  H: H
+  He: He
+  Hf: Hf_pv
+  Hg: Hg
+  Ho: Ho_3
+  I: I
+  In: In_d
+  Ir: Ir
+  K: K_sv
+  Kr: Kr
+  La: La
+  Li: Li_sv
+  Lu: Lu_3
+  Mg: Mg_pv
+  Mn: Mn_pv
+  Mo: Mo_pv
+  N: N
+  Na: Na_pv
+  Nb: Nb_pv
+  Nd: Nd_3
+  Ne: Ne
+  Ni: Ni_pv
+  Np: Np
+  O: O
+  Os: Os_pv
+  P: P
+  Pa: Pa
+  Pb: Pb_d
+  Pd: Pd
+  Pm: Pm_3
+  Po: Po_d
+  Pr: Pr_3
+  Pt: Pt
+  Pu: Pu
+  Ra: Ra_sv
+  Rb: Rb_sv
+  Re: Re_pv
+  Rh: Rh_pv
+  Rn: Rn
+  Ru: Ru_pv
+  S: S
+  Sb: Sb
+  Sc: Sc_sv
+  Se: Se
+  Si: Si
+  Sm: Sm_3
+  Sn: Sn_d
+  Sr: Sr_sv
+  Ta: Ta_pv
+  Tb: Tb_3
+  Tc: Tc_pv
+  Te: Te
+  Th: Th
+  Ti: Ti_pv
+  Tl: Tl_d
+  Tm: Tm_3
+  U: U
+  V: V_pv
+  W: W_sv
+  Xe: Xe
+  Y: Y_sv
+  Yb: Yb_3
+  Zn: Zn
+  Zr: Zr_sv

pymatgen/io/vasp/outputs.py

@@ -596,7 +596,7 @@ def hubbards(self) -> dict[str, float]:
         if len(js) != len(us):
             js = [0] * len(us)
         if len(us) == len(symbols):
-            return {symbols[i]: us[i] - js[i] for i in range(len(symbols))}
+            return {symbols[idx]: us[idx] - js[idx] for idx in range(len(symbols))}
         if sum(us) == 0 and sum(js) == 0:
             return {}
         raise VaspParseError("Length of U value parameters and atomic symbols are mismatched")

pymatgen/io/vasp/sets.py

@@ -1270,9 +1270,12 @@ def __init__(
             self._config_dict["INCAR"].pop("GGA", None)
         if xc_functional.upper().endswith("+U"):
             self._config_dict["INCAR"]["LDAU"] = True
-        user_potcar_functional = kwargs.get("user_potcar_functional", "PBE_54")
-        if user_potcar_functional.upper() != "PBE_54":
-            warnings.warn(f"{user_potcar_functional=} is inconsistent with the recommended PBE_54.", UserWarning)
+        default_potcars = self.CONFIG["PARENT"].replace("PBE", "PBE_").replace("BASE", "")  # PBE64BASE -> PBE_64
+        user_potcar_functional = kwargs.get("user_potcar_functional", default_potcars)
+        if user_potcar_functional.upper() != default_potcars:
+            warnings.warn(
+                f"{user_potcar_functional=} is inconsistent with the recommended {default_potcars}.", UserWarning
+            )
 
         self.kwargs = kwargs
         self.xc_functional = xc_functional

tests/io/vasp/test_sets.py

@@ -111,7 +111,7 @@ def test_sets_changed(self):
                 hashes[name] = hashlib.sha1(text).hexdigest()
 
         known_hashes = {
-            "MatPESStaticSet.yaml": "8789f974913c935f21ff2fbffc0502714ca39470",
+            "MatPESStaticSet.yaml": "8edecff2bbd1932c53159f56a8e6340e900aaa2f",
             "MITRelaxSet.yaml": "1a0970f8cad9417ec810f7ab349dc854eaa67010",
             "MPAbsorptionSet.yaml": "5931e1cb3cf8ba809b3d4f4a5960d728c682adf1",
             "MPHSERelaxSet.yaml": "0d0d96a620461071cfd416ec9d5d6a8d2dfd0855",
@@ -120,12 +120,13 @@ def test_sets_changed(self):
             "MVLGWSet.yaml": "104ae93c3b3be19a13b0ee46ebdd0f40ceb96597",
             "MVLRelax52Set.yaml": "4cfc6b1bd0548e45da3bde4a9c65b3249da13ecd",
             "PBE54Base.yaml": "ec317781a7f344beb54c17a228db790c0eb49282",
+            "PBE64Base.yaml": "a0d6cd02c6ff8e24b0005e30c56a33b155c2280b",
             "VASPIncarBase.yaml": "19762515f8deefb970f2968fca48a0d67f7964d4",
             "vdW_parameters.yaml": "04bb09bb563d159565bcceac6a11e8bdf0152b79",
         }
 
         for input_set in hashes:
-            assert hashes[input_set] == known_hashes[input_set], f"{input_set} got {hashes[input_set]}\n\n{msg}"
+            assert hashes[input_set] == known_hashes[input_set], f"{input_set=}\n{msg}"
 
 
 class TestDictSet(PymatgenTest):
@@ -774,12 +775,12 @@ def test_default(self):
         assert incar["PREC"] == "Accurate"
         assert incar["SIGMA"] == 0.05
         assert incar["LMAXMIX"] == 6
-        # test POTCAR files are default PBE_54 PSPs and functional
+        # test POTCAR files are default PBE_64 PSPs and functional
         assert input_set.potcar_symbols == ["Fe_pv", "P", "O"]
-        assert input_set.potcar.functional == "PBE_54"
+        assert input_set.potcar.functional == "PBE_64"
         assert input_set.kpoints is None
 
-        assert str(input_set.potcar[0]) == str(PotcarSingle.from_symbol_and_functional("Fe_pv", "PBE_54"))
+        assert str(input_set.potcar[0]) == str(PotcarSingle.from_symbol_and_functional("Fe_pv", "PBE_64"))
 
     def test_with_prev_incar(self):
         default_prev = MatPESStaticSet(structure=self.struct, prev_incar=self.prev_incar)
@@ -811,9 +812,9 @@ def test_with_prev_incar(self):
         assert incar["NSW"] == 0
         assert incar["PREC"] == "Accurate"
         assert incar["SIGMA"] == 0.05
-        # test POTCAR files are default PBE_54 PSPs and functional
+        # test POTCAR files are default PBE_64 PSPs and functional
         assert default_prev.potcar_symbols == ["Fe_pv", "P", "O"]
-        assert default_prev.potcar.functional == "PBE_54"
+        assert default_prev.potcar.functional == "PBE_64"
         assert default_prev.kpoints is None
 
     def test_r2scan(self):
@@ -823,9 +824,9 @@ def test_r2scan(self):
         assert incar_scan.get("GGA") is None
         assert incar_scan["ALGO"] == "All"
         assert incar_scan.get("LDAU") is None
-        # test POTCAR files are default PBE_54 PSPs and functional
+        # test POTCAR files are default PBE_64 PSPs and functional
         assert scan.potcar_symbols == ["Fe_pv", "P", "O"]
-        assert scan.potcar.functional == "PBE_54"
+        assert scan.potcar.functional == "PBE_64"
         assert scan.kpoints is None
 
     def test_default_u(self):
@@ -834,10 +835,10 @@ def test_default_u(self):
         assert incar_u["LDAU"] is True
         assert incar_u["GGA"] == "Pe"
         assert incar_u["ALGO"] == "Normal"
-        # test POTCAR files are default PBE_54 PSPs and functional
+        # test POTCAR files are default PBE_64 PSPs and functional
         assert incar_u["LDAUU"] == [5.3, 0, 0]
         assert default_u.potcar_symbols == ["Fe_pv", "P", "O"]
-        assert default_u.potcar.functional == "PBE_54"
+        assert default_u.potcar.functional == "PBE_64"
         assert default_u.kpoints is None
 
     def test_functionals(self):
@@ -847,7 +848,7 @@ def test_functionals(self):
         ):
             MatPESStaticSet(self.struct, xc_functional=xc_functional)
 
-        with pytest.warns(UserWarning, match="inconsistent with the recommended PBE_54"):
+        with pytest.warns(UserWarning, match="inconsistent with the recommended PBE_64"):
             diff_potcar = MatPESStaticSet(self.struct, user_potcar_functional="PBE")
             assert str(diff_potcar.potcar[0]) == str(PotcarSingle.from_symbol_and_functional("Fe_pv", "PBE"))