Create the `available_basis_functions` used by lobster. #171

hongyi-zhao · 2024-06-27T15:15:08Z

hongyi-zhao
Jun 27, 2024

I try to create the available_basis_functions used by lobster as follows:

from mendeleev import element

def get_available_orbitals(elem):
    # Obtain the electron configuration of an element.
    ec = elem.ec.conf

    # Parse the electron configuration to obtain the orbitals.
    orbitals = []
    for orbital in ec:
        orbitals.append(f"{orbital[0]}{orbital[1]}")

    return sorted(orbitals)

with open("available_basis_functions.txt", "w") as f:
    for atomic_number in range(1, 104):
        elem = element(atomic_number)
        orbitals = get_available_orbitals(elem)
        f.write(f"{atomic_number} {elem.symbol} {' '.join(orbitals)}\n")

print("File 'available_basis_functions.txt' has been created.")

In [19]: from mendeleev import element
    ...: 
    ...: def get_available_orbitals(elem):
    ...:     # Obtain the electron configuration of an element.
    ...:     ec = elem.ec.conf
    ...: 
    ...:     # Parse the electron configuration to obtain the orbitals.
    ...:     orbitals = []
    ...:     for orbital in ec:
    ...:         orbitals.append(f"{orbital[0]}{orbital[1]}")
    ...: 
    ...:     return sorted(orbitals)
    ...: 
    ...: with open("available_basis_functions.txt", "w") as f:
    ...:     for atomic_number in range(1, 104):
    ...:         elem = element(atomic_number)
    ...:         orbitals = get_available_orbitals(elem)
    ...:         f.write(f"{atomic_number} {elem.symbol} {' '.join(orbitals)}\n")
    ...: 
    ...: print("File 'available_basis_functions.txt' has been created.")
File 'available_basis_functions.txt' has been created.

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

But the above result is very different from the target file format, as shown below:

werner@x13dai-t:~/Public/repo/github.com/JaGeo/Script_to_get_available_basis_functions$ cat MaxBasis/availabe_basis_functions 
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

I wonder whether I can generate the exact same target file by using this package. Any tips/comments will be appreciated.

All the files mentioned above are attached.

availabe_basis_functions.zip

Regards,
Zhao

lmmentel · 2024-06-27T16:53:17Z

lmmentel
Jun 27, 2024
Maintainer

Hey, I'm not quite certain what is the outcome you want to achieve here, do you have some more details?

0 replies

hongyi-zhao · 2024-06-28T00:43:27Z

hongyi-zhao
Jun 28, 2024
Author

I hope to get the same output as the following:

werner@x13dai-t:~/Public/repo/github.com/JaGeo/Script_to_get_available_basis_functions$ cat MaxBasis/availabe_basis_functions 
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

0 replies

lmmentel · 2024-07-10T16:17:30Z

lmmentel
Jul 10, 2024
Maintainer

It is hard to guess what are those entries in the file whose output you are trying to reproduce. It does not seem these are electronic configurations since entry for Li is 3 Li 1s 2s 2p but there is no 2p electrons for Li, same goes for Na, your files says 11 Na 1s 2s 2p 3s 3p but Na has no 3p electrons.

Regardless I noticed the other difference is ordering of orbitals, where your files follows principal quantum number first whereas mendeleev prints aufbau ordering by default. Here is how you can reorder orbitals to match the output you are showing:

from mendeleev import element
from mendeleev.econf import ORBITALS
 
 for atomic_number in range(1, 104):
    elem = element(atomic_number)
    conf = sorted(elem.ec.conf, key=lambda x: (x[0], ORBITALS.index(x[1])))
    conf_str = " ".join(f"{n}{o}" for n,o in conf) 
    print(f"{elem.atomic_number} {elem.symbol} {conf_str}")

which produces the following

1 H 1s
2 He 1s
3 Li 1s 2s
4 Be 1s 2s
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
12 Mg 1s 2s 2p 3s
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
20 Ca 1s 2s 2p 3s 3p 4s
21 Sc 1s 2s 2p 3s 3p 3d 4s
22 Ti 1s 2s 2p 3s 3p 3d 4s
23 V 1s 2s 2p 3s 3p 3d 4s
24 Cr 1s 2s 2p 3s 3p 3d 4s
25 Mn 1s 2s 2p 3s 3p 3d 4s
26 Fe 1s 2s 2p 3s 3p 3d 4s
27 Co 1s 2s 2p 3s 3p 3d 4s
28 Ni 1s 2s 2p 3s 3p 3d 4s
29 Cu 1s 2s 2p 3s 3p 3d 4s
30 Zn 1s 2s 2p 3s 3p 3d 4s
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
38 Sr 1s 2s 2p 3s 3p 3d 4s 4p 5s
39 Y 1s 2s 2p 3s 3p 3d 4s 4p 4d 5s
40 Zr 1s 2s 2p 3s 3p 3d 4s 4p 4d 5s
41 Nb 1s 2s 2p 3s 3p 3d 4s 4p 4d 5s
42 Mo 1s 2s 2p 3s 3p 3d 4s 4p 4d 5s
43 Tc 1s 2s 2p 3s 3p 3d 4s 4p 4d 5s
44 Ru 1s 2s 2p 3s 3p 3d 4s 4p 4d 5s
45 Rh 1s 2s 2p 3s 3p 3d 4s 4p 4d 5s
46 Pd 1s 2s 2p 3s 3p 3d 4s 4p 4d
47 Ag 1s 2s 2p 3s 3p 3d 4s 4p 4d 5s
48 Cd 1s 2s 2p 3s 3p 3d 4s 4p 4d 5s
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
56 Ba 1s 2s 2p 3s 3p 3d 4s 4p 4d 5s 5p 6s
57 La 1s 2s 2p 3s 3p 3d 4s 4p 4d 5s 5p 5d 6s
58 Ce 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s
59 Pr 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 6s
60 Nd 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 6s
61 Pm 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 6s
62 Sm 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 6s
63 Eu 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 6s
64 Gd 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s
65 Tb 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 6s
66 Dy 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 6s
67 Ho 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 6s
68 Er 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 6s
69 Tm 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 6s
70 Yb 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 6s
71 Lu 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s
72 Hf 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s
73 Ta 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s
74 W 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s
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
77 Ir 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s
78 Pt 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s
79 Au 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s
80 Hg 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s
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
88 Ra 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p 7s
89 Ac 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p 6d 7s
90 Th 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 6s 6p 6d 7s
91 Pa 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 5f 6s 6p 6d 7s
92 U 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 5f 6s 6p 6d 7s
93 Np 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 5f 6s 6p 6d 7s
94 Pu 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 5f 6s 6p 7s
95 Am 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 5f 6s 6p 7s
96 Cm 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 5f 6s 6p 6d 7s
97 Bk 1s 2s 2p 3s 3p 3d 4s 4p 4d 4f 5s 5p 5d 5f 6s 6p 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

Hope that helps.

0 replies

hongyi-zhao · 2024-07-11T05:52:43Z

hongyi-zhao
Jul 11, 2024
Author

It is hard to guess what are those entries in the file whose output you are trying to reproduce. It does not seem these are electronic configurations since entry for Li is 3 Li 1s 2s 2p but there is no 2p electrons for Li, same goes for Na, your files says 11 Na 1s 2s 2p 3s 3p but Na has no 3p electrons.

According to the description here, the availabe_basis_functionsorbital file, which is created by lobster developers, including all potentially available unoccupied orbitals.

which produces the following

I tried the code snippet above, but the results still differ a little from the availabe_basis_functionsorbital file as compared in meld:

0 replies

lmmentel · 2024-07-11T20:58:18Z

lmmentel
Jul 11, 2024
Maintainer

It's not sufficiently specified what the required format should be for the file you're trying to produce. Feel free to modify the snippet to fit your needs if that's an option.

This is not really an issue with mendeleev so I'm going to close it. You are welcome to move it to github discussions.

0 replies

hongyi-zhao · 2024-07-12T00:07:06Z

hongyi-zhao
Jul 12, 2024
Author

How to move it to github discussions?

0 replies

lmmentel · 2024-07-13T22:25:30Z

lmmentel
Jul 13, 2024
Maintainer

Here are the github discussions for mendeleev :)

0 replies

hongyi-zhao · 2024-07-13T23:58:13Z

hongyi-zhao
Jul 13, 2024
Author

What I mean is that it seems like the repository owner can convert an issue into a discussion, instead of creating it from scratch.

0 replies

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Create the `available_basis_functions` used by lobster. #171

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Create the available_basis_functions used by lobster. #171

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Create the `available_basis_functions` used by lobster. #171

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