/
periodic_table_utils.py
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/
periodic_table_utils.py
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"""
Density Function Theory Periodic Table Utilities.
"""
from typing import Union
import numpy as np
import torch
ZType = Union[int, float, torch.Tensor]
periodic_table_atomz = {
"H": 1,
"He": 2,
"Li": 3,
"Be": 4,
"B": 5,
"C": 6,
"N": 7,
"O": 8,
"F": 9,
"Ne": 10,
"Na": 11,
"Mg": 12,
"Al": 13,
"Si": 14,
"P": 15,
"S": 16,
"Cl": 17,
"Ar": 18,
"K": 19,
"Ca": 20,
"Sc": 21,
"Ti": 22,
"V": 23,
"Cr": 24,
"Mn": 25,
"Fe": 26,
"Co": 27,
"Ni": 28,
"Cu": 29,
"Zn": 30,
"Ga": 31,
"Ge": 32,
"As": 33,
"Se": 34,
"Br": 35,
"Kr": 36,
"Rb": 37,
"Sr": 38,
"Y": 39,
"Zr": 40,
"Nb": 41,
"Mo": 42,
"Tc": 43,
"Ru": 44,
"Rh": 45,
"Pd": 46,
"Ag": 47,
"Cd": 48,
"In": 49,
"Sn": 50,
"Sb": 51,
"Te": 52,
"I": 53,
"Xe": 54
}
# isotope-averaged atom masses in a.m.u.
# from https://www.angelo.edu/faculty/kboudrea/periodic/structure_mass.htm
atom_masses = {
1: 1.00797,
2: 4.00260,
3: 6.941,
4: 9.01218,
5: 10.81,
6: 12.011,
7: 14.0067,
8: 15.9994,
9: 18.998403,
10: 20.179,
11: 22.98977,
12: 24.305,
13: 26.98154,
14: 28.0855,
15: 30.97376,
16: 32.06,
17: 35.453,
18: 39.948,
19: 39.0983,
20: 40.08,
21: 44.9559,
22: 47.90,
23: 50.9415,
24: 51.996,
25: 54.9380,
26: 55.847,
27: 58.9332,
28: 58.70,
29: 63.546,
30: 65.38,
31: 69.72,
32: 72.59,
33: 74.9216,
34: 78.96,
35: 79.904,
36: 83.80,
37: 85.4678,
38: 87.62,
39: 88.9059,
40: 91.22,
41: 92.9064,
42: 95.94,
43: 98.0,
44: 101.07,
45: 102.9055,
46: 106.4,
47: 107.868,
48: 112.41,
49: 114.82,
50: 118.69,
51: 121.75,
53: 126.9045,
52: 127.60,
54: 131.30
}
# JCP 41, 3199 (1964); DOI:10.1063/1.1725697
# taken from PySCF:
# https://github.com/pyscf/pyscf/blob/45582e915e91890722fcae2bc30fb04867d5c95f/pyscf/data/radii.py#L23
# I don't know why H has 0.35 while in the reference it is 0.
# They are in angstrom, so we need to convert it to Bohr
atom_bragg_radii = list(
np.array([
2.00, 0.35, 1.40, 1.45, 1.05, 0.85, 0.70, 0.65, 0.60, 0.50, 1.50, 1.80,
1.50, 1.25, 1.10, 1.00, 1.00, 1.00, 1.80, 2.20, 1.80, 1.60, 1.40, 1.35,
1.40, 1.40, 1.40, 1.35, 1.35, 1.35, 1.35, 1.30, 1.25, 1.15, 1.15, 1.15,
1.90, 2.35, 2.00, 1.80, 1.55, 1.45, 1.45, 1.35, 1.30, 1.35, 1.40, 1.60,
1.55, 1.55, 1.45, 1.45, 1.40, 1.40, 2.10, 2.60, 2.15, 1.95, 1.85, 1.85,
1.85, 1.85, 1.85, 1.85, 1.80, 1.75, 1.75, 1.75, 1.75, 1.75, 1.75, 1.75,
1.55, 1.45, 1.35, 1.35, 1.30, 1.35, 1.35, 1.35, 1.50, 1.90, 1.80, 1.60,
1.90, 1.45, 2.10, 1.80, 2.15, 1.95, 1.80, 1.80, 1.75, 1.75, 1.75, 1.75,
1.75, 1.75, 1.75, 1.75, 1.75, 1.75, 1.75, 1.75, 1.75, 1.75, 1.75, 1.75,
1.75, 1.75, 1.75, 1.75, 1.75, 1.75, 1.75, 1.75, 1.75, 1.75, 1.75, 1.75,
1.75, 1.75, 1.75, 1.75, 1.75, 1.75, 1.75, 1.75, 1.75, 1.75, 1.75
]) / 0.52917721092)
atom_expected_radii = [
1.0, 1.0, 0.927272, 3.873661, 2.849396, 2.204757, 1.714495, 1.409631,
1.232198, 1.084786, 0.965273, 4.208762, 3.252938, 3.433889, 2.752216,
2.322712, 2.060717, 1.842024, 1.662954, 5.243652, 4.218469, 3.959716,
3.778855, 3.626288, 3.675012, 3.381917, 3.258487, 3.153572, 3.059109,
3.330979, 2.897648, 3.424103, 2.866859, 2.512233, 2.299617, 2.111601,
1.951590, 5.631401, 4.632850, 4.299870, 4.091705, 3.985219, 3.841740,
3.684647, 3.735235, 3.702057, 1.533028, 3.655961, 3.237216, 3.777242,
3.248093, 2.901067, 2.691328, 2.501704, 2.337950
]
def get_atomz(element: Union[str, ZType]) -> ZType:
"""Returns the atomic number for the given element
Examples
--------
>>> from deepchem.utils import get_atomz
>>> element_symbol = "Al" # Aluminium
>>> get_atomz(element_symbol)
13
>>> get_atomz(17)
17
Parameters
----------
element: Union[str, ZType]
String symbol of Element or Atomic Number.
Ex: H, He, C
Returns
-------
atom_n: ZType
Atomic Number of the given Element.
References
----------
Kasim, Muhammad F., and Sam M. Vinko. "Learning the exchange-correlation
functional from nature with fully differentiable density functional
theory." Physical Review Letters 127.12 (2021): 126403.
https://github.com/diffqc/dqc/blob/master/dqc/utils/periodictable.py
"""
if isinstance(element, str):
try:
atom_z = periodic_table_atomz[element]
except KeyError:
raise KeyError("Element Does Not Exists or Not Documented: %s" %
element)
return atom_z
elif isinstance(element, torch.Tensor): # Just return itself.
try:
assert element.numel() == 1
except:
raise AssertionError("Only 1 element Tensor Allowed.")
return element
else: # float or int | Just return itself.
return element
def get_atom_mass(atom_z: int) -> float:
"""Returns the Atomic mass in Atomic Mass Unit.
Examples
--------
>>> from deepchem.utils import get_atom_mass
>>> atom_number = 13
>>> get_atom_mass(atom_number)
49184.33860618758
Parameters
----------
atom_z: int
Atomic Number of the Element.
Returns
-------
atomic_mass: float
Atomic Mass of the Element.
References
----------
Kasim, Muhammad F., and Sam M. Vinko. "Learning the exchange-correlation
functional from nature with fully differentiable density functional
theory." Physical Review Letters 127.12 (2021): 126403.
https://github.com/diffqc/dqc/blob/master/dqc/utils/periodictable.py
"""
try:
atomic_mass = atom_masses[atom_z]
except KeyError:
raise KeyError("Element Does Not Exists or Not Documented: %d" % atom_z)
return atomic_mass * 1822.888486209
def get_period(atom_z: int) -> int:
"""get the period of the given atom z
Examples
--------
>>> from deepchem.utils import get_period
>>> atom_number = 13
>>> get_period(atom_number)
3
Parameters
----------
atom_z: int
Atomic Number of the Element.
Returns
-------
period: int
Period of the Element.
References
----------
Kasim, Muhammad F., and Sam M. Vinko. "Learning the exchange-correlation
functional from nature with fully differentiable density functional
theory." Physical Review Letters 127.12 (2021): 126403.
https://github.com/diffqc/dqc/blob/master/dqc/utils/periodictable.py
"""
period: int = 0
if atom_z <= 2:
period = 1
elif atom_z <= 10:
period = 2
elif atom_z <= 18:
period = 3
elif atom_z <= 36:
period = 4
elif atom_z <= 54:
period = 5
elif atom_z <= 86:
period = 6
elif atom_z <= 118:
period = 7
else:
raise RuntimeError("Unimplemented atomz: %d" % atom_z)
return period