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WIP: add script to generate lobster basis information #4262

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WIP: add script to generate lobster basis information #4262

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2cac764
add script to generate lobster basis information
JaGeo Jan 24, 2025
108e6cd
pre-commit auto-fixes
pre-commit-ci[bot] Jan 24, 2025
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103 changes: 103 additions & 0 deletions dev_scripts/all_basis_functions_pbeVaspFit2015_lobster.txt
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1 H 1s
2 He 1s
3 Li 1s 2s 2p
4 Be 1s 2s 2p
5 B 1s 2s 2p
6 C 1s 2s 2p
7 N 1s 2s 2p
8 O 1s 2s 2p
9 F 1s 2s 2p
10 Ne 1s 2s 2p
11 Na 1s 2s 2p 3s 3p
12 Mg 1s 2s 2p 3s 3p
13 Al 1s 2s 2p 3s 3p
14 Si 1s 2s 2p 3s 3p
15 P 1s 2s 2p 3s 3p
16 S 1s 2s 2p 3s 3p
17 Cl 1s 2s 2p 3s 3p
18 Ar 1s 2s 2p 3s 3p
19 K 1s 2s 2p 3s 3p 4s 4p
20 Ca 1s 2s 2p 3s 3p 4s 4p
21 Sc 1s 2s 2p 3s 3p 3d 4s 4p
22 Ti 1s 2s 2p 3s 3p 3d 4s 4p
23 V 1s 2s 2p 3s 3p 3d 4s 4p
24 Cr 1s 2s 2p 3s 3p 3d 4s 4p
25 Mn 1s 2s 2p 3s 3p 3d 4s 4p
26 Fe 1s 2s 2p 3s 3p 3d 4s 4p
27 Co 1s 2s 2p 3s 3p 3d 4s 4p
28 Ni 1s 2s 2p 3s 3p 3d 4s 4p
29 Cu 1s 2s 2p 3s 3p 3d 4s 4p
30 Zn 1s 2s 2p 3s 3p 3d 4s 4p
31 Ga 1s 2s 2p 3s 3p 3d 4s 4p
32 Ge 1s 2s 2p 3s 3p 3d 4s 4p
33 As 1s 2s 2p 3s 3p 3d 4s 4p
34 Se 1s 2s 2p 3s 3p 3d 4s 4p
35 Br 1s 2s 2p 3s 3p 3d 4s 4p
36 Kr 1s 2s 2p 3s 3p 3d 4s 4p
37 Rb 1s 2s 2p 3s 3p 3d 4s 4p 5s 5p
38 Sr 1s 2s 2p 3s 3p 3d 4s 4p 5s 5p
39 Y 1s 2s 2p 3s 3p 3d 4s 4p 4d 5s 5p
40 Zr 1s 2s 2p 3s 3p 3d 4s 4p 4d 5s 5p
41 Nb 1s 2s 2p 3s 3p 3d 4s 4p 4d 5s 5p
42 Mo 1s 2s 2p 3s 3p 3d 4s 4p 4d 5s 5p
43 Tc 1s 2s 2p 3s 3p 3d 4s 4p 4d 5s 5p
44 Ru 1s 2s 2p 3s 3p 3d 4s 4p 4d 5s 5p
45 Rh 1s 2s 2p 3s 3p 3d 4s 4p 4d 5s 5p
46 Pd 1s 2s 2p 3s 3p 3d 4s 4p 4d 5s 5p
47 Ag 1s 2s 2p 3s 3p 3d 4s 4p 4d 5s 5p
48 Cd 1s 2s 2p 3s 3p 3d 4s 4p 4d 5s 5p
49 In 1s 2s 2p 3s 3p 3d 4s 4p 4d 5s 5p
50 Sn 1s 2s 2p 3s 3p 3d 4s 4p 4d 5s 5p
51 Sb 1s 2s 2p 3s 3p 3d 4s 4p 4d 5s 5p
52 Te 1s 2s 2p 3s 3p 3d 4s 4p 4d 5s 5p
53 I 1s 2s 2p 3s 3p 3d 4s 4p 4d 5s 5p
54 Xe 1s 2s 2p 3s 3p 3d 4s 4p 4d 5s 5p
55 Cs 1s 2s 2p 3s 3p 3d 4s 4p 4d 5s 5p 6s 6p
56 Ba 1s 2s 2p 3s 3p 3d 4s 4p 4d 5s 5p 6s 6p
57 La 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p
58 Ce 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p
59 Pr 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p
60 Nd 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p
61 Pm 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p
62 Sm 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p
63 Eu 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p
64 Gd 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p
65 Tb 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p
66 Dy 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p
67 Ho 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p
68 Er 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p
69 Tm 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p
70 Yb 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p
71 Lu 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p
72 Hf 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p
73 Ta 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p
74 W 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p
75 Re 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s
76 Os 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p
77 Ir 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p
78 Pt 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p
79 Au 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p
80 Hg 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p
81 Tl 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p
82 Pb 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p
83 Bi 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p
84 Po 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p
85 At 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p
86 Rn 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p
87 Fr 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p 7s 7p
88 Ra 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p 7s 7p
89 Ac 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 5f 6s 6p 6d 7s 7p
90 Th 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 5f 6s 6p 6d 7s 7p
91 Pa 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 5f 6s 6p 6d 7s 7p
92 U 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 5f 6s 6p 6d 7s 7p
93 Np 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 5f 6s 6p 6d 7s 7p
94 Pu 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 5f 6s 6p 6d 7s 7p
95 Am 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 5f 6s 6p 6d 7s 7p
96 Cm 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 5f 6s 6p 6d 7s 7p
97 Bk 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 5f 6s 6p 6d 7s
98 Cf 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 5f 6s 6p 7s
99 Es 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 5f 6s 6p 7s
100 Fm 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 5f 6s 6p 7s
101 Md 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 5f 6s 6p 7s
102 No 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 5f 6s 6p 7s
103 Lr 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 5f 6s 6p 6d 7s
125 changes: 125 additions & 0 deletions dev_scripts/get_lobster_basis_from_potcars.py
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"""Script to generate potential basis functions for the LOBSTER input files."""

from __future__ import annotations

import os
from pathlib import Path

import yaml
from monty.io import zopen

from pymatgen.core import SETTINGS
from pymatgen.io.vasp.inputs import Potcar


def get_valence(
filename: str = "POTCAR", available_basis_functions: list[str] | None = None, occupation_cutoff: float = 0.01
) -> str:
"""
Extracts the valence configuration from a POTCAR file.

Args:
filename (str): Path to the POTCAR file.
available_basis_functions (list[str] | None): List of available basis functions.
occupation_cutoff (float): Cutoff below which the orbital is considered to be empty.

Returns:
str: A string of basis functions.
"""
nextline = False
ready = False
counter = 0
orbitals: list[list[int]] = []
occupations: list[float] = []
linenumber = 0

with zopen(filename, "rt") as f:
for line in f:
if linenumber == 1:
valence = float(line.split()[0])
if not ready:
if not nextline:
if "Atomic configuration" in line:
nextline = True
else:
number_atomic_orbitals = int(line.split()[0])
ready = True
elif counter <= number_atomic_orbitals:
if counter != 0:
orbitals.append([int(line.split()[0]), int(line.split()[1])])
occupations.append(float(line.split()[4]))
counter += 1
else:
break
linenumber += 1

# Reverse the lists for processing
rev_orb = list(reversed(orbitals))

rev_occ = list(reversed(occupations))
basis: list[list[int]] = []

valence_checker = valence
for orbital in range(len(rev_orb)):
if not abs(valence_checker - 0.0) < 0.01 and abs(rev_occ[orbital] - 0.0) >= occupation_cutoff:
valence_checker -= rev_occ[orbital]
basis.append(rev_orb[orbital])

basis.reverse()

# Convert orbital numbers to strings
basis_result: list[str] = []
for orbital in basis:
match orbital[1]:
case 0:
basis_result.append(f"{orbital[0]}s")
case 1:
basis_result.append(f"{orbital[0]}p")
case 2:
basis_result.append(f"{orbital[0]}d")
case 3:
basis_result.append(f"{orbital[0]}f")

if available_basis_functions is not None:
basis_string = " ".join(e for e in sorted(set(basis_result)) if e in available_basis_functions)
else:
basis_string = " ".join(sorted(set(basis_result)))

return basis_string


# Set occupation cutoff
occupation_cutoff = 0.2 # if set to 0, also empty basis functions will be included

# Path to the POTCAR directory
source_potcar = Path(SETTINGS["PMG_VASP_PSP_DIR"]) / "POT_GGA_PAW_PBE_54"

# Get all POTCAR subfolders, excluding GW potcars
potcar_names: list[str] = list(os.listdir(source_potcar))

# Read in all available basis functions
available_basis_functions: dict[str, list[str]] = {}
with zopen("all_basis_functions_pbeVaspFit2015_lobster.txt") as f:
data = f.read().split("\n")

for datum in data:
datum_raw = datum.split(" ")
if len(datum_raw) > 2:
available_basis_functions[datum_raw[1]] = datum_raw[2:]

basis_dict: dict[str, dict[str, str]] = {"BASIS": {}}
for potcar in potcar_names:
potential_type = potcar.split(".")[1]
element = potential_type.split("_")[0]

if element in available_basis_functions:
potcar_object = Potcar.from_file(source_potcar / potcar)
basis_dict["BASIS"][potcar_object.spec[0]["symbol"]] = get_valence(
filename=source_potcar / potcar,
available_basis_functions=available_basis_functions[element],
occupation_cutoff=occupation_cutoff,
)

# Save the basis dictionary to a YAML file
with open("BASIS_PBE_54.yaml", "w") as outfile:
yaml.dump(basis_dict, outfile, default_flow_style=False)
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