atomdb.periodic module
- atomdb.periodic.setup_element()
Generate the
Elementclass and helper functions.
- atomdb.periodic.read_csv(file)
Read a CSV file into a list of lists.
- atomdb.periodic.get_data()
Extract the contents of
data/elements_data.csv.
- atomdb.periodic.get_info()
Extract the contents of
data/data_info.csv.
- atomdb.periodic.indent_lines(input_string, indent)
Indent each line of a string by a given number of spaces.
- atomdb.periodic.make_property(data, prop, prop2col)
Construct a property method for the Element class.
- class atomdb.periodic.Element(elem)
Bases:
objectElement properties.
- atnum
Atomic number of the element.
- Type
int
- symbol
Symbol of the element.
- Type
str
- name
Name of the element.
- Type
str
- group
Group of the element.
- Type
int
- period
Period of the element.
- Type
int
- mult
Multiplicity of the element.
- Type
int
- cov_radius
Covalent radius of the element.
- Type
Dict[float]
- vdw_radius
van der Waals radius of the element.
- Type
Dict[float]
- at_radius
atomic radius of the element.
- Type
Dict[float]
- eneg
Electronegativity of the element.
- Type
Dict[float]
- pold
Isolated atom dipole polarizability of the element.
- Type
Dict[float]
- c6
Isolated atom C6 dispersion coefficients of the element.
- Type
Dict[float]
- mass
Atomic mass of the element.
- Type
Dict[float]
Initialize an
Elementinstance.- Parameters
elem ((str | int)) – Symbol, name, or number of an element.
- property at_radius
atomic radius of the element.
- Returns
at_radius
- Return type
Dict[float]
Notes
- This property is a dictionary with the following keys:
- “wc”
- Source
Waber and D. T. Cromer, J. Chem. Phys. 42, 4116 (1965)
- Units
angstrom
- Notes
For each element, the largest radius of the outer orbitals is taken.
- “cr”
- Source
Clementi, D. L. Raimondi, W. P. Reinhardt, J. Chem. Phys. 47, 1300 (1967)
- Units
angstrom
- property atnum
Atomic number of the element.
- Returns
atnum
- Return type
int
- property c6
Isolated atom C6 dispersion coefficients of the element.
- Returns
c6
- Return type
Dict[float]
Notes
- This property is a dictionary with the following keys:
- “chu”
- Source
Chu & A. Dalgarno, J. Chem. Phys., 121(9), 4083–4088 (2004)
- Units
au
- Notes
Theoretical value for hydrogen from this paper: K. T. Tang, J. M. Norbeck and P. R. Certain, J. Chem. Phys. 64, 3063 (1976) http://dx.doi.org/10.1063/1.432569
- property cov_radius
Covalent radius of the element.
- Returns
cov_radius
- Return type
Dict[float]
Notes
- This property is a dictionary with the following keys:
- “cordero”
- Source
B. Cordero, V. Gomez, A. E. Platero-Prats, M. Reves, J. Echeverria,E. Cremades, F. Barragan, and S. Alvarez, Dalton Trans. pp. 2832–2838 (2008)
- Units
angstrom
- Notes
For carbon the number is a weighted average over the data for different hybridizations. For Mn, Fe, and Co, the number is a weighted average over the data for different spins (high spin and low spin)
- “bragg”
- Source
Bragg, Phil. Mag. 40, 169 (1920)
- Units
angstrom
- “slater”
- Source
Slater, J. Chem. Phys. 41, 3199 (1964)
- Units
angstrom
- property eneg
Electronegativity of the element.
- Returns
eneg
- Return type
Dict[float]
Notes
- This property is a dictionary with the following keys:
- “pauling”
- Source
Allred, J. Inorg. Nuc. Chem. 17, 215 (1961)
- Units
float
- property group
Group of the element.
- Returns
group
- Return type
int
- property mass
Atomic mass of the element.
- Returns
mass
- Return type
Dict[float]
Notes
- This property is a dictionary with the following keys:
- “stb”
- Source
Thomas Prohaska et. al. Pure Appl. Chem. 2022, 94
- Units
amu
- Notes
For Tc, Pm, Po - Ac, Np, Pu, Am-Og the mass of the most abundant isotope or with longer half-life taken from https://physics.nist.gov/cgi-bin/Compositions/stand_alone.pl
- “nist”
- Units
amu
- Notes
Mass of the most common isotope
- property mult
Multiplicity of the element.
- Returns
mult
- Return type
int
- property name
Name of the element.
- Returns
name
- Return type
str
- property period
Period of the element.
- Returns
period
- Return type
int
- property pold
Isolated atom dipole polarizability of the element.
- Returns
pold
- Return type
Dict[float]
Notes
- This property is a dictionary with the following keys:
- “crc”
- Source
CRC Handbook of Chemistry and Physics (CRC, Boca Raton, FL, 2003).
- Units
angstrom**3
- Notes
If multiple values were present in the CRC book, the value used in Erin’s postg code is taken
- “chu”
- Source
Chu & A. Dalgarno, J. Chem. Phys., 121(9), 4083–4088 (2004)
- Units
au
- Notes
Theoretical value for hydrogen from this paper: A.D. Buckingham, K.L. Clarke, Chem. Phys. Lett. 57(3), 321–325 (1978) http://dx.doi.org/10.1016/0009-2614(78)85517-1
- property symbol
Symbol of the element.
- Returns
symbol
- Return type
str
- property vdw_radius
van der Waals radius of the element.
- Returns
vdw_radius
- Return type
Dict[float]
Notes
- This property is a dictionary with the following keys:
- “bondi”
- Source
Bondi, J. Phys. Chem. 68, 441 (1964)
- Units
angstrom
- “truhlar”
- Source
Mantina A. C. Chamberlin R. Valero C. J. Cramer D. G. Truhlar J. Phys. Chem. A 113 5806 (2009)
- Units
angstrom
- “rt”
- Source
Rowland and R. Taylor, J. Phys. Chem. 100, 7384 (1996)
- Units
angstrom
- “batsanov”
- Source
Batsanov Inorganic Materials 37 871 (2001)
- Units
angstrom
- “dreiding”
- Source
Stephen L. Mayo, Barry D. Olafson, and William A. Goddard III J. Phys. Chem. 94 8897 (1990)
- Units
2angstrom
- Notes
R_0 parameter, unit 2angstrom is used so that numbers are divided by 2 upon reading
- “uff”
- Source
Rappi, C. J. Casewit, K. S. Colwell, W. A. Goddard III, and W. M. Skid J. Am. Chem. Soc. 114 10024 (1992)
- Units
2angstrom
- Notes
x_I parameter, unit 2angstrom is used so that numbers are divided by 2 upon reading
- “mm3”
- Source
Allinger, X. Zhou, and J. Bergsma, Journal of Molecular Structure: THEOCHEM 312, 69 (1994)
- Units
angstrom
- atomdb.periodic.element_number(elem)
Return the element number from a string or int.
- Parameters
elem ((str | int)) – Symbol, name, or number of an element.
- Returns
atnum – Atomic number.
- Return type
int
- atomdb.periodic.element_symbol(elem)
Return the element symbol from a string or int.
- Parameters
elem ((str | int)) – Symbol, name, or number of an element.
- Returns
symbol – Element symbol.
- Return type
str
- atomdb.periodic.element_name(elem)
Return the element name from a string or int.
- Parameters
elem ((str | int)) – Symbol, name, or number of an element.
- Returns
name – Element name.
- Return type
str