atomdb package#
AtomDB, a database of atomic and ionic properties.
- class atomdb.Element(elem)#
Bases:
objectElement properties.
Attributes#
- atnumint
Atomic number of the element.
- symbolstr
Symbol of the element.
- namestr
Name of the element.
- property at_radius#
atomic radius of the element.
Returns#
at_radius : 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#
- property c6#
Isolated atom C6 dispersion coefficients of the element.
Returns#
c6 : 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 : 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 : 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 mass#
Atomic mass of the element.
Returns#
mass : 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 pold#
Isolated atom dipole polarizability of the element.
Returns#
pold : 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 vdw_radius#
van der Waals radius of the element.
Returns#
vdw_radius : 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
- class atomdb.Promolecule#
Bases:
objectPromolecule class.
A promolecule is an approximation of a molecule constructed from a linear combination of atomic and/or ionic species. Properties of this promolecule can be computed from those of the atomic and/or ionic species, depending on whether the property is an extensive one or an intensive one.
For an extensive property, the formula is a linear combination:
\[\text{prop.}_{\text{mol;extensive}} = \sum_{A=1}^{N_{\text{atoms}}} c_A \text{prop.}_A\]For an intensive property, the formula is a mean:
\[\text{prop.}_{\text{mol;intensive}} = {\left\langle \left\{ \text{prop.}_A \right\}_{A=1}^{N_{\text{atoms}}} \right\rangle}_p\]where the parameter
pdefines the type of mean used (1 = linear, 2 = geometric, etc.).Attributes#
- atoms: list of Species
Species instances out of which the promolecule is composed.
- coords: np.ndarray((N, 3), dtype=float)
Coordinates of each species component of the promolecule.
- coeffs: np.ndarray((N,), dtype=float)
Coefficients of each species component of the promolecule.
- density(points, spin='t', log=False)#
Compute the electron density of the promolecule at the desired points.
Parameters#
- points: np.ndarray((N, 3), dtype=float)
Points at which to compute the density.
- spin: (‘t’ | ‘a’ | ‘b’ | ‘m’), default=’t’
Type of density to compute; either total, alpha-spin, beta-spin, or magnetization density.
- log: bool, default=False
Whether to compute the log of the density instead of the density. May be slightly more accurate.
Returns#
- density: np.ndarray((N,), dtype=float)
Density evaluated at N points.
- eta(p=1)#
Compute the chemical hardness of the promolecule.
Parameters#
- p: int, default=1 (linear mean)
Type of mean used in the computation.
Returns#
- eta: float
Chemical hardness of the promolecule.
- gradient(points, spin='t', log=False)#
Compute the electron density gradient of the promolecule at the desired points.
Promolecular gradient:
\[\nabla \rho_{\text{mol}}^{(0)} (\mathbf{R}) = \sum_{A=1}^{N_{\text{atoms}}}\ c_A \nabla \rho_A^{(0)}(\mathbf{R})\]where
\(N_{\text{atoms}}\) is the number of atoms in the molecule,
\(c_A\) are the coefficients of the species,
\(R\) are points in 3D cartesian coordinates,
\(\nabla \rho_A^{(0)}(\mathbf{R})\) is the gradient of the species.
Parameters#
- points: np.ndarray((N, 3), dtype=float)
Points at which to compute the electron density gradient.
- spin: (‘t’ | ‘a’ | ‘b’ | ‘m’), default=’t’
Type of density to compute; either total, alpha-spin, beta-spin, or magnetization density.
- log: bool, default=False
Whether to compute the log of the density instead of the density. May be slightly more accurate.
Returns#
- gradient: np.ndarray((N, 3), dtype=float)
Electron density gradient of the promolecule evaluated at N points.
- hessian(points, spin='t', log=False)#
Compute the promolecule’s electron density Hessian at the desired points.
Parameters#
- points: np.ndarray((N, 3), dtype=float)
Points at which to compute the electron density Hessian.
- spin: (‘t’ | ‘a’ | ‘b’ | ‘m’), default=’t’
Type of density to compute; either total, alpha-spin, beta-spin, or magnetization density.
- log: bool, default=False
Whether to compute the log of the density instead of the density. May be slightly more accurate.
Returns#
- hess: np.ndarray((N, 3, 3), dtype=float)
Electron density Hessian of the promolecule evaluated at N points.
- ip(p=1)#
Compute the ionization potential of the promolecule.
Parameters#
- p: int, default=1 (linear mean)
Type of mean used in the computation.
Returns#
- ip: float
Ionization potential of the promolecule.
- ked(points, spin='t', log=False)#
Compute the kinetic energy density of the promolecule at the desired points.
- points: np.ndarray((N, 3), dtype=float)
Points at which to compute the kinetic energy density.
- spin: (‘t’ | ‘a’ | ‘b’ | ‘m’), default=’t’
Type of density to compute; either total, alpha-spin, beta-spin, or magnetization density.
- log: bool, default=False
Whether to compute the log of the density instead of the density. May be slightly more accurate.
Returns#
- ked: np.ndarray((N,), dtype=float)
Kinetic energy density evaluated at N points.
- laplacian(points, spin='t', log=False)#
Compute the promolecule’s electron density Laplacian at the desired points.
Parameters#
- points: np.ndarray((N, 3), dtype=float)
Points at which to compute the electron density Laplacian.
- spin: (‘t’ | ‘a’ | ‘b’ | ‘m’), default=’t’
Type of density to compute; either total, alpha-spin, beta-spin, or magnetization density.
- log: bool, default=False
Whether to compute the log of the density instead of the density. May be slightly more accurate.
Returns#
- laplacian: np.ndarray((N,), dtype=float)
Electron density Laplacian of the promolecule evaluated at N points.
- mu(p=1)#
Compute the chemical potential of the promolecule.
Parameters#
- p: int, default=1 (linear mean)
Type of mean used in the computation.
Returns#
- mu: float
Chemical potential of the promolecule.
- mult(p=1)#
Compute the multiplicity of the promolecule.
Parameters#
- p: int, default=1 (linear mean)
Type of mean used in the computation.
Returns#
- mult: float
Multiplicity of the promolecule.
- class atomdb.Species(dataset, fields, spinpol=1)#
Bases:
objectProperties of atomic and ionic species.
- property at_radius#
Atomic radius.
Returns#
- at_radiusdict, float
The return dictionary contains atomic radii types wc and cr. For references corresponding to each type check theochem/AtomDB
- property atmass#
Atomic mass in atomic units.
Returns#
- atmassdict
Two options are available: the isotopically averaged mass ‘stb’, and the mass of the most common isotope ‘nist’. For references corresponding to each type check theochem/AtomDB
- property charge#
Charge
\[Q = Z - N\]Where Q is the charge, Z the atomic number and N the total number of electrons stored in SpeciesData object.
Returns#
charge : int
- property cov_radius#
Covalent radius (derived from crystallographic data).
Returns#
- cov_radiusdict, float
The return dictionary contains crystallographic covalent radii types cordero, bragg and slater. For references corresponding to each type check theochem/AtomDB
- d_dens_func(spin='t', index=None, log=False)#
Return a cubic spline of the first derivative of the electronic density.
The derivarive of the density as a function of the distance to the atomic center (a set of points along a 1-D grid) is modeled by a cubic spline. The property can be computed for the alpha, beta, alpha + beta, and alpha - beta components of the electron density.
Parameters#
- spinstr, optional
Type of occupied spin orbitals which can be either “a” (for alpha), “b” (for beta), “ab” (for alpha + beta), and, “m” (for alpha - beta), by default ‘ab’
- indexsequence of int, optional
Sequence of integers representing the spin orbitals which are indexed from 1 to the number basis functions. If
None, all orbitals of the given spin(s) are included- logbool, optional
Whether the logarithm of the density property is used for interpolation
Returns#
- Callable[[np.ndarray(N,), int] -> np.ndarray(N,)]
a callable function evaluating the derivative of the density given a set of radial points (1-D array).
- dd_dens_func(spin='t', index=None, log=False)#
Return a cubic spline of the electronic density Laplacian.
Parameters#
- spinstr, default=”t”
Type of occupied spin orbitals. Can be either “t” (for alpha + beta), “a” (for alpha), “b” (for beta), or “m” (for alpha - beta).
- indexsequence of int, optional
Sequence of integers representing the spin orbitals. These are indexed from 0 to the number of basis functions. By default, all orbitals of the given spin(s) are included.
- logbool, default=False
Whether the logarithm of the density is used for interpolation.
Returns#
- DensitySpline
A DensitySpline instance for the density and its derivatives. Given a set of radial points, it can evaluate densities and derivatives up to order 2.
- dens_func(spin='t', index=None, log=False)#
Return a cubic spline of the electronic density.
Parameters#
- spinstr, default=”t”
Type of occupied spin orbitals. Can be either “t” (for alpha + beta), “a” (for alpha), “b” (for beta), or “m” (for alpha - beta).
- indexsequence of int, optional
Sequence of integers representing the spin orbitals. These are indexed from 0 to the number of basis functions. By default, all orbitals of the given spin(s) are included.
- logbool, default=False
Whether the logarithm of the density is used for interpolation.
Returns#
- DensitySpline
A DensitySpline instance for the density and its derivatives. Given a set of radial points, it can evaluate densities and derivatives up to order 2.
- property dispersion_c6#
Isolated atom C6 dispersion coefficients.
Returns#
- dispersion_c6dict, float
The return dictionary contains isolated atom C6 dispersion coefficients types chu. For references corresponding to each type check theochem/AtomDB
- get_docstring()#
Docstring of the species’ dataset.
- ked_func(spin='t', index=None, log=False)#
Return a cubic spline of the kinetic energy density.
Parameters#
- spinstr, default=”t”
Type of occupied spin orbitals. Can be either “t” (for alpha + beta), “a” (for alpha), “b” (for beta), or “m” (for alpha - beta).
- indexsequence of int, optional
Sequence of integers representing the spin orbitals. These are indexed from 0 to the number of basis functions. By default, all orbitals of the given spin(s) are included.
- logbool, default=False
Whether the logarithm of the density is used for interpolation.
Returns#
- DensitySpline
A DensitySpline instance for the density and its derivatives. Given a set of radial points, it can evaluate densities and derivatives up to order 2.
- property mult#
Multiplicity
\[M = \left|N_S\right| + 1\]Where \(\left|N_S\right|\) is the spin number.
Returns#
mult : int
- property nspin#
Spin number
\[N_S = N_α - N_β\]- Where \(N_S\) is the spin number and \(N_α\) and \(N_β\) number of alpha and
beta electrons.
Returns#
nspin : int
- property polarizability#
Isolated atom dipole polarizability.
Returns#
- polarizabilitydict, float
The return dictionary contains isolated atom dipole polarizability types crc and chu. For references corresponding to each type check theochem/AtomDB
- to_dict()#
Return the dictionary representation of the Species instance.
- to_json()#
Return the JSON string representation of the Species instance.
- property vdw_radius#
Van der Waals radii.
Returns#
- vdw_radiusdict, float
The return dictionary contains van der wals radii types bondi, truhlar, rt, batsanov, dreiding, uff and mm3. For references corresponding to each type check theochem/AtomDB
- atomdb.compile(elem, charge, mult, nexc=0, dataset='slater', datapath='/home/runner/.local/lib/python3.10/site-packages/atomdb/datasets')#
Compile an atomic or ionic species into the AtomDB database.
Parameters#
- elemstr
Element symbol.
- chargeint
Charge.
- multint
Multiplicity.
- nexcint, optional
Excitation level, by default 0.
- datasetstr, optional
Dataset name, by default DEFAULT_DATASET.
- datapathstr, optional
Path to the local AtomDB cache, by default DEFAULT_DATAPATH variable value.
- atomdb.dump(*species, datapath='/home/runner/.local/lib/python3.10/site-packages/atomdb/datasets')#
Dump the Species instance(s) to a MessagePack file in the database.
Parameters#
- species: Iterable
Iterables of objects of class Species
- datapathstr, optional
Path to the local AtomDB cache, by default DEFAULT_DATAPATH variable value.
- atomdb.element_name(elem)#
Return the element name from a string or int.
Parameters#
- elem: (str | int)
Symbol, name, or number of an element.
Returns#
- namestr
Element name.
- atomdb.element_number(elem)#
Return the element number from a string or int.
Parameters#
- elem: (str | int)
Symbol, name, or number of an element.
Returns#
- atnumint
Atomic number.
- atomdb.element_symbol(elem)#
Return the element symbol from a string or int.
Parameters#
- elem: (str | int)
Symbol, name, or number of an element.
Returns#
- symbolstr
Element symbol.
- atomdb.load(elem, charge, mult, nexc=0, dataset='slater', datapath='/home/runner/.local/lib/python3.10/site-packages/atomdb/datasets', remotepath='https://raw.githubusercontent.com/theochem/AtomDBdata/main/')#
Load one or many atomic or ionic species from the AtomDB database.
Parameters#
- elemstr
Element symbol.
- chargeint
Charge.
- multint
Multiplicity.
- nexcint, optional
Excitation level, by default 0.
- datasetstr, optional
Dataset name, by default DEFAULT_DATASET.
- datapathstr, optional
Path to the local AtomDB cache, by default DEFAULT_DATAPATH variable value.
- remotepathstr, optional
Remote URL for AtomDB datasets, by default DEFAULT_REMOTE variable value
Returns#
Object of class Species
- atomdb.raw_datafile(suffix, elem, charge, mult, nexc=0, dataset='slater', datapath='/home/runner/.local/lib/python3.10/site-packages/atomdb/datasets', remotepath='https://raw.githubusercontent.com/theochem/AtomDBdata/main/')#
Returns the local path to the raw data file of a species
This function retrieves the raw data file of a species from the AtomDB cache if present. If the file is not found, it is downloaded from the remote URL.
Parameters#
- suffixstr
File extension of the raw data file.
- elemstr
Element symbol.
- chargeint
Charge.
- multint
Multiplicity.
- nexcint, optional
Excitation level, by default 0.
- datasetstr, optional
Dataset name, by default DEFAULT_DATASET.
- datapathstr, optional
Path to the local AtomDB cache, by default DEFAULT_DATAPATH variable value.
- remotepathstr, optional
Remote URL for AtomDB datasets, by default DEFAULT_REMOTE variable value.
Returns#
- str
Path to the raw data file.
Subpackages#
Submodules#
atomdb.periodic module#
- class atomdb.periodic.Element(elem)#
Bases:
objectElement properties.
Attributes#
- atnumint
Atomic number of the element.
- symbolstr
Symbol of the element.
- namestr
Name of the element.
- property at_radius#
atomic radius of the element.
Returns#
at_radius : 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#
- property c6#
Isolated atom C6 dispersion coefficients of the element.
Returns#
c6 : 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 : 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 : 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 mass#
Atomic mass of the element.
Returns#
mass : 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 pold#
Isolated atom dipole polarizability of the element.
Returns#
pold : 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 vdw_radius#
van der Waals radius of the element.
Returns#
vdw_radius : 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_name(elem)#
Return the element name from a string or int.
Parameters#
- elem: (str | int)
Symbol, name, or number of an element.
Returns#
- namestr
Element name.
atomdb.promolecule module#
AtomDB promolecule submodule.
- class atomdb.promolecule.Promolecule#
Bases:
objectPromolecule class.
A promolecule is an approximation of a molecule constructed from a linear combination of atomic and/or ionic species. Properties of this promolecule can be computed from those of the atomic and/or ionic species, depending on whether the property is an extensive one or an intensive one.
For an extensive property, the formula is a linear combination:
\[\text{prop.}_{\text{mol;extensive}} = \sum_{A=1}^{N_{\text{atoms}}} c_A \text{prop.}_A\]For an intensive property, the formula is a mean:
\[\text{prop.}_{\text{mol;intensive}} = {\left\langle \left\{ \text{prop.}_A \right\}_{A=1}^{N_{\text{atoms}}} \right\rangle}_p\]where the parameter
pdefines the type of mean used (1 = linear, 2 = geometric, etc.).Attributes#
- atoms: list of Species
Species instances out of which the promolecule is composed.
- coords: np.ndarray((N, 3), dtype=float)
Coordinates of each species component of the promolecule.
- coeffs: np.ndarray((N,), dtype=float)
Coefficients of each species component of the promolecule.
- density(points, spin='t', log=False)#
Compute the electron density of the promolecule at the desired points.
Parameters#
- points: np.ndarray((N, 3), dtype=float)
Points at which to compute the density.
- spin: (‘t’ | ‘a’ | ‘b’ | ‘m’), default=’t’
Type of density to compute; either total, alpha-spin, beta-spin, or magnetization density.
- log: bool, default=False
Whether to compute the log of the density instead of the density. May be slightly more accurate.
Returns#
- density: np.ndarray((N,), dtype=float)
Density evaluated at N points.
- eta(p=1)#
Compute the chemical hardness of the promolecule.
Parameters#
- p: int, default=1 (linear mean)
Type of mean used in the computation.
Returns#
- eta: float
Chemical hardness of the promolecule.
- gradient(points, spin='t', log=False)#
Compute the electron density gradient of the promolecule at the desired points.
Promolecular gradient:
\[\nabla \rho_{\text{mol}}^{(0)} (\mathbf{R}) = \sum_{A=1}^{N_{\text{atoms}}}\ c_A \nabla \rho_A^{(0)}(\mathbf{R})\]where
\(N_{\text{atoms}}\) is the number of atoms in the molecule,
\(c_A\) are the coefficients of the species,
\(R\) are points in 3D cartesian coordinates,
\(\nabla \rho_A^{(0)}(\mathbf{R})\) is the gradient of the species.
Parameters#
- points: np.ndarray((N, 3), dtype=float)
Points at which to compute the electron density gradient.
- spin: (‘t’ | ‘a’ | ‘b’ | ‘m’), default=’t’
Type of density to compute; either total, alpha-spin, beta-spin, or magnetization density.
- log: bool, default=False
Whether to compute the log of the density instead of the density. May be slightly more accurate.
Returns#
- gradient: np.ndarray((N, 3), dtype=float)
Electron density gradient of the promolecule evaluated at N points.
- hessian(points, spin='t', log=False)#
Compute the promolecule’s electron density Hessian at the desired points.
Parameters#
- points: np.ndarray((N, 3), dtype=float)
Points at which to compute the electron density Hessian.
- spin: (‘t’ | ‘a’ | ‘b’ | ‘m’), default=’t’
Type of density to compute; either total, alpha-spin, beta-spin, or magnetization density.
- log: bool, default=False
Whether to compute the log of the density instead of the density. May be slightly more accurate.
Returns#
- hess: np.ndarray((N, 3, 3), dtype=float)
Electron density Hessian of the promolecule evaluated at N points.
- ip(p=1)#
Compute the ionization potential of the promolecule.
Parameters#
- p: int, default=1 (linear mean)
Type of mean used in the computation.
Returns#
- ip: float
Ionization potential of the promolecule.
- ked(points, spin='t', log=False)#
Compute the kinetic energy density of the promolecule at the desired points.
- points: np.ndarray((N, 3), dtype=float)
Points at which to compute the kinetic energy density.
- spin: (‘t’ | ‘a’ | ‘b’ | ‘m’), default=’t’
Type of density to compute; either total, alpha-spin, beta-spin, or magnetization density.
- log: bool, default=False
Whether to compute the log of the density instead of the density. May be slightly more accurate.
Returns#
- ked: np.ndarray((N,), dtype=float)
Kinetic energy density evaluated at N points.
- laplacian(points, spin='t', log=False)#
Compute the promolecule’s electron density Laplacian at the desired points.
Parameters#
- points: np.ndarray((N, 3), dtype=float)
Points at which to compute the electron density Laplacian.
- spin: (‘t’ | ‘a’ | ‘b’ | ‘m’), default=’t’
Type of density to compute; either total, alpha-spin, beta-spin, or magnetization density.
- log: bool, default=False
Whether to compute the log of the density instead of the density. May be slightly more accurate.
Returns#
- laplacian: np.ndarray((N,), dtype=float)
Electron density Laplacian of the promolecule evaluated at N points.
- mu(p=1)#
Compute the chemical potential of the promolecule.
Parameters#
- p: int, default=1 (linear mean)
Type of mean used in the computation.
Returns#
- mu: float
Chemical potential of the promolecule.
- mult(p=1)#
Compute the multiplicity of the promolecule.
Parameters#
- p: int, default=1 (linear mean)
Type of mean used in the computation.
Returns#
- mult: float
Multiplicity of the promolecule.
- atomdb.promolecule.make_promolecule(atnums, coords, charges=None, mults=None, units=None, dataset='slater', datapath='/home/runner/.local/lib/python3.10/site-packages/atomdb/datasets', remotepath='https://raw.githubusercontent.com/theochem/AtomDBdata/main/')#
Construct a Promolecule instance from a set of atoms and their coordinates, charges, and multiplicities.
Parameters#
- atnums: list of (str|int)
List of element number for each atom.
- coords: list of np.ndarray((3,), dtype=float)
List of coordinates for each atom.
- charges: list of (int | float), default=[0, …, 0]
List of charges.
- mults: list of (int), default=[1, …, 1]
List of multiplicities for each atom.
- units: (‘bohr’ | ‘angstrom’)
Units of
coordsvalues. Default is Bohr.- dataset: str, default=DEFAULT_DATASET
Data set from which to load atomic species.
- datapath: str, default=DEFAULT_DATAPATH
System path where the desired data set is located.
- remotepath: str, default=DEFAULT_REMOTE
Remote path where the desired data set is located.
Returns#
- promol: Promolecule
Promolecule instance.
atomdb.species module#
AtomDB, a database of atomic and ionic properties.
- class atomdb.species.Species(dataset, fields, spinpol=1)#
Bases:
objectProperties of atomic and ionic species.
- property at_radius#
Atomic radius.
Returns#
- at_radiusdict, float
The return dictionary contains atomic radii types wc and cr. For references corresponding to each type check theochem/AtomDB
- property atmass#
Atomic mass in atomic units.
Returns#
- atmassdict
Two options are available: the isotopically averaged mass ‘stb’, and the mass of the most common isotope ‘nist’. For references corresponding to each type check theochem/AtomDB
- property charge#
Charge
\[Q = Z - N\]Where Q is the charge, Z the atomic number and N the total number of electrons stored in SpeciesData object.
Returns#
charge : int
- property cov_radius#
Covalent radius (derived from crystallographic data).
Returns#
- cov_radiusdict, float
The return dictionary contains crystallographic covalent radii types cordero, bragg and slater. For references corresponding to each type check theochem/AtomDB
- d_dens_func(spin='t', index=None, log=False)#
Return a cubic spline of the first derivative of the electronic density.
The derivarive of the density as a function of the distance to the atomic center (a set of points along a 1-D grid) is modeled by a cubic spline. The property can be computed for the alpha, beta, alpha + beta, and alpha - beta components of the electron density.
Parameters#
- spinstr, optional
Type of occupied spin orbitals which can be either “a” (for alpha), “b” (for beta), “ab” (for alpha + beta), and, “m” (for alpha - beta), by default ‘ab’
- indexsequence of int, optional
Sequence of integers representing the spin orbitals which are indexed from 1 to the number basis functions. If
None, all orbitals of the given spin(s) are included- logbool, optional
Whether the logarithm of the density property is used for interpolation
Returns#
- Callable[[np.ndarray(N,), int] -> np.ndarray(N,)]
a callable function evaluating the derivative of the density given a set of radial points (1-D array).
- dd_dens_func(spin='t', index=None, log=False)#
Return a cubic spline of the electronic density Laplacian.
Parameters#
- spinstr, default=”t”
Type of occupied spin orbitals. Can be either “t” (for alpha + beta), “a” (for alpha), “b” (for beta), or “m” (for alpha - beta).
- indexsequence of int, optional
Sequence of integers representing the spin orbitals. These are indexed from 0 to the number of basis functions. By default, all orbitals of the given spin(s) are included.
- logbool, default=False
Whether the logarithm of the density is used for interpolation.
Returns#
- DensitySpline
A DensitySpline instance for the density and its derivatives. Given a set of radial points, it can evaluate densities and derivatives up to order 2.
- dens_func(spin='t', index=None, log=False)#
Return a cubic spline of the electronic density.
Parameters#
- spinstr, default=”t”
Type of occupied spin orbitals. Can be either “t” (for alpha + beta), “a” (for alpha), “b” (for beta), or “m” (for alpha - beta).
- indexsequence of int, optional
Sequence of integers representing the spin orbitals. These are indexed from 0 to the number of basis functions. By default, all orbitals of the given spin(s) are included.
- logbool, default=False
Whether the logarithm of the density is used for interpolation.
Returns#
- DensitySpline
A DensitySpline instance for the density and its derivatives. Given a set of radial points, it can evaluate densities and derivatives up to order 2.
- property dispersion_c6#
Isolated atom C6 dispersion coefficients.
Returns#
- dispersion_c6dict, float
The return dictionary contains isolated atom C6 dispersion coefficients types chu. For references corresponding to each type check theochem/AtomDB
- get_docstring()#
Docstring of the species’ dataset.
- ked_func(spin='t', index=None, log=False)#
Return a cubic spline of the kinetic energy density.
Parameters#
- spinstr, default=”t”
Type of occupied spin orbitals. Can be either “t” (for alpha + beta), “a” (for alpha), “b” (for beta), or “m” (for alpha - beta).
- indexsequence of int, optional
Sequence of integers representing the spin orbitals. These are indexed from 0 to the number of basis functions. By default, all orbitals of the given spin(s) are included.
- logbool, default=False
Whether the logarithm of the density is used for interpolation.
Returns#
- DensitySpline
A DensitySpline instance for the density and its derivatives. Given a set of radial points, it can evaluate densities and derivatives up to order 2.
- property mult#
Multiplicity
\[M = \left|N_S\right| + 1\]Where \(\left|N_S\right|\) is the spin number.
Returns#
mult : int
- property nspin#
Spin number
\[N_S = N_α - N_β\]- Where \(N_S\) is the spin number and \(N_α\) and \(N_β\) number of alpha and
beta electrons.
Returns#
nspin : int
- property polarizability#
Isolated atom dipole polarizability.
Returns#
- polarizabilitydict, float
The return dictionary contains isolated atom dipole polarizability types crc and chu. For references corresponding to each type check theochem/AtomDB
- to_dict()#
Return the dictionary representation of the Species instance.
- to_json()#
Return the JSON string representation of the Species instance.
- property vdw_radius#
Van der Waals radii.
Returns#
- vdw_radiusdict, float
The return dictionary contains van der wals radii types bondi, truhlar, rt, batsanov, dreiding, uff and mm3. For references corresponding to each type check theochem/AtomDB
- atomdb.species.compile(elem, charge, mult, nexc=0, dataset='slater', datapath='/home/runner/.local/lib/python3.10/site-packages/atomdb/datasets')#
Compile an atomic or ionic species into the AtomDB database.
Parameters#
- elemstr
Element symbol.
- chargeint
Charge.
- multint
Multiplicity.
- nexcint, optional
Excitation level, by default 0.
- datasetstr, optional
Dataset name, by default DEFAULT_DATASET.
- datapathstr, optional
Path to the local AtomDB cache, by default DEFAULT_DATAPATH variable value.
- atomdb.species.dump(*species, datapath='/home/runner/.local/lib/python3.10/site-packages/atomdb/datasets')#
Dump the Species instance(s) to a MessagePack file in the database.
Parameters#
- species: Iterable
Iterables of objects of class Species
- datapathstr, optional
Path to the local AtomDB cache, by default DEFAULT_DATAPATH variable value.
- atomdb.species.load(elem, charge, mult, nexc=0, dataset='slater', datapath='/home/runner/.local/lib/python3.10/site-packages/atomdb/datasets', remotepath='https://raw.githubusercontent.com/theochem/AtomDBdata/main/')#
Load one or many atomic or ionic species from the AtomDB database.
Parameters#
- elemstr
Element symbol.
- chargeint
Charge.
- multint
Multiplicity.
- nexcint, optional
Excitation level, by default 0.
- datasetstr, optional
Dataset name, by default DEFAULT_DATASET.
- datapathstr, optional
Path to the local AtomDB cache, by default DEFAULT_DATAPATH variable value.
- remotepathstr, optional
Remote URL for AtomDB datasets, by default DEFAULT_REMOTE variable value
Returns#
Object of class Species
- atomdb.species.raw_datafile(suffix, elem, charge, mult, nexc=0, dataset='slater', datapath='/home/runner/.local/lib/python3.10/site-packages/atomdb/datasets', remotepath='https://raw.githubusercontent.com/theochem/AtomDBdata/main/')#
Returns the local path to the raw data file of a species
This function retrieves the raw data file of a species from the AtomDB cache if present. If the file is not found, it is downloaded from the remote URL.
Parameters#
- suffixstr
File extension of the raw data file.
- elemstr
Element symbol.
- chargeint
Charge.
- multint
Multiplicity.
- nexcint, optional
Excitation level, by default 0.
- datasetstr, optional
Dataset name, by default DEFAULT_DATASET.
- datapathstr, optional
Path to the local AtomDB cache, by default DEFAULT_DATAPATH variable value.
- remotepathstr, optional
Remote URL for AtomDB datasets, by default DEFAULT_REMOTE variable value.
Returns#
- str
Path to the raw data file.
atomdb.utils module#
Constants and utility functions.
- atomdb.utils.DEFAULT_DATAPATH = '/home/runner/.local/lib/python3.10/site-packages/atomdb/datasets'#
The path for AtomDB local cache.
- atomdb.utils.DEFAULT_DATASET = 'slater'#
Default dataset to query.
- atomdb.utils.DEFAULT_REMOTE = 'https://raw.githubusercontent.com/theochem/AtomDBdata/main/'#
Default remote URL for AtomDB datasets.
- atomdb.utils.MODULE_DATAPATH = '/home/runner/.local/lib/python3.10/site-packages/atomdb/data'#
The path for AtomDB data files.
- atomdb.utils.MULTIPLICITIES = {(1, -2): 2, (1, -1): 1, (1, 0): 2, (2, -2): 1, (2, -1): 2, (2, 0): 1, (2, 1): 2, (3, -2): 2, (3, -1): 1, (3, 0): 2, (3, 1): 1, (3, 2): 2, (4, -2): 3, (4, -1): 2, (4, 0): 1, (4, 1): 2, (4, 2): 1, (4, 3): 2, (5, -2): 4, (5, -1): 3, (5, 0): 2, (5, 1): 1, (5, 2): 2, (5, 3): 1, (5, 4): 2, (6, -2): 3, (6, -1): 4, (6, 0): 3, (6, 1): 2, (6, 2): 1, (6, 3): 2, (6, 4): 1, (6, 5): 2, (7, -2): 2, (7, -1): 3, (7, 0): 4, (7, 1): 3, (7, 2): 2, (7, 3): 1, (7, 4): 2, (7, 5): 1, (7, 6): 2, (8, -2): 1, (8, -1): 2, (8, 0): 3, (8, 1): 4, (8, 2): 3, (8, 3): 2, (8, 4): 1, (8, 5): 2, (8, 6): 1, (8, 7): 2, (9, -2): 2, (9, -1): 1, (9, 0): 2, (9, 1): 3, (9, 2): 4, (9, 3): 3, (9, 4): 2, (9, 5): 1, (9, 6): 2, (9, 7): 1, (9, 8): 2, (10, -2): 1, (10, -1): 2, (10, 0): 1, (10, 1): 2, (10, 2): 3, (10, 3): 4, (10, 4): 3, (10, 5): 2, (10, 6): 1, (10, 7): 2, (10, 8): 1, (10, 9): 2, (11, -2): 2, (11, -1): 1, (11, 0): 2, (11, 1): 1, (11, 2): 2, (11, 3): 3, (11, 4): 4, (11, 5): 3, (11, 6): 2, (11, 7): 1, (11, 8): 2, (11, 9): 1, (11, 10): 2, (12, -2): 3, (12, -1): 2, (12, 0): 1, (12, 1): 2, (12, 2): 1, (12, 3): 2, (12, 4): 3, (12, 5): 4, (12, 6): 3, (12, 7): 2, (12, 8): 1, (12, 9): 2, (12, 10): 1, (12, 11): 2, (13, -2): 4, (13, -1): 3, (13, 0): 2, (13, 1): 1, (13, 2): 2, (13, 3): 1, (13, 4): 2, (13, 5): 3, (13, 6): 4, (13, 7): 3, (13, 8): 2, (13, 9): 1, (13, 10): 2, (13, 11): 1, (13, 12): 2, (14, -2): 3, (14, -1): 4, (14, 0): 3, (14, 1): 2, (14, 2): 1, (14, 3): 2, (14, 4): 1, (14, 5): 2, (14, 6): 3, (14, 7): 4, (14, 8): 3, (14, 9): 2, (14, 10): 1, (14, 11): 2, (14, 12): 1, (14, 13): 2, (15, -2): 2, (15, -1): 3, (15, 0): 4, (15, 1): 3, (15, 2): 2, (15, 3): 1, (15, 4): 2, (15, 5): 1, (15, 6): 2, (15, 7): 3, (15, 8): 4, (15, 9): 3, (15, 10): 2, (15, 11): 1, (15, 12): 2, (15, 13): 1, (15, 14): 2, (16, -2): 1, (16, -1): 2, (16, 0): 3, (16, 1): 4, (16, 2): 3, (16, 3): 2, (16, 4): 1, (16, 5): 2, (16, 6): 1, (16, 7): 2, (16, 8): 3, (16, 9): 4, (16, 10): 3, (16, 11): 2, (16, 12): 1, (16, 13): 2, (16, 14): 1, (16, 15): 2, (17, -2): 2, (17, -1): 1, (17, 0): 2, (17, 1): 3, (17, 2): 4, (17, 3): 3, (17, 4): 2, (17, 5): 1, (17, 6): 2, (17, 7): 1, (17, 8): 2, (17, 9): 3, (17, 10): 4, (17, 11): 3, (17, 12): 2, (17, 13): 1, (17, 14): 2, (17, 15): 1, (17, 16): 2, (18, -2): 1, (18, -1): 2, (18, 0): 1, (18, 1): 2, (18, 2): 3, (18, 3): 4, (18, 4): 3, (18, 5): 2, (18, 6): 1, (18, 7): 2, (18, 8): 1, (18, 9): 2, (18, 10): 3, (18, 11): 4, (18, 12): 3, (18, 13): 2, (18, 14): 1, (18, 15): 2, (18, 16): 1, (18, 17): 2, (19, -2): 2, (19, -1): 1, (19, 0): 2, (19, 1): 1, (19, 2): 2, (19, 3): 3, (19, 4): 4, (19, 5): 3, (19, 6): 2, (19, 7): 1, (19, 8): 2, (19, 9): 1, (19, 10): 2, (19, 11): 3, (19, 12): 4, (19, 13): 3, (19, 14): 2, (19, 15): 1, (19, 16): 2, (19, 17): 1, (19, 18): 2, (20, -2): 3, (20, -1): 2, (20, 0): 1, (20, 1): 2, (20, 2): 1, (20, 3): 2, (20, 4): 3, (20, 5): 4, (20, 6): 3, (20, 7): 2, (20, 8): 1, (20, 9): 2, (20, 10): 1, (20, 11): 2, (20, 12): 3, (20, 13): 4, (20, 14): 3, (20, 15): 2, (20, 16): 1, (20, 17): 2, (20, 18): 1, (20, 19): 2, (21, -2): 4, (21, -1): 3, (21, 0): 2, (21, 1): 3, (21, 2): 2, (21, 3): 1, (21, 4): 2, (21, 5): 3, (21, 6): 4, (21, 7): 3, (21, 8): 2, (21, 9): 1, (21, 10): 2, (21, 11): 1, (21, 12): 2, (21, 13): 3, (21, 14): 4, (21, 15): 3, (21, 16): 2, (21, 17): 1, (21, 18): 2, (21, 19): 1, (21, 20): 2, (22, -2): 7, (22, -1): 4, (22, 0): 3, (22, 1): 4, (22, 2): 3, (22, 3): 2, (22, 4): 1, (22, 5): 2, (22, 6): 3, (22, 7): 4, (22, 8): 3, (22, 9): 2, (22, 10): 1, (22, 11): 2, (22, 12): 1, (22, 13): 2, (22, 14): 3, (22, 15): 4, (22, 16): 3, (22, 17): 2, (22, 18): 1, (22, 19): 2, (22, 20): 1, (22, 21): 2, (23, -2): 6, (23, -1): 7, (23, 0): 4, (23, 1): 5, (23, 2): 4, (23, 3): 3, (23, 4): 2, (23, 5): 1, (23, 6): 2, (23, 7): 3, (23, 8): 4, (23, 9): 3, (23, 10): 2, (23, 11): 1, (23, 12): 2, (23, 13): 1, (23, 14): 2, (23, 15): 3, (23, 16): 4, (23, 17): 3, (23, 18): 2, (23, 19): 1, (23, 20): 2, (23, 21): 1, (23, 22): 2, (24, -2): 5, (24, -1): 6, (24, 0): 7, (24, 1): 6, (24, 2): 5, (24, 3): 4, (24, 4): 3, (24, 5): 2, (24, 6): 1, (24, 7): 2, (24, 8): 3, (24, 9): 4, (24, 10): 3, (24, 11): 2, (24, 12): 1, (24, 13): 2, (24, 14): 1, (24, 15): 2, (24, 16): 3, (24, 17): 4, (24, 18): 3, (24, 19): 2, (24, 20): 1, (24, 21): 2, (24, 22): 1, (24, 23): 2, (25, -2): 4, (25, -1): 5, (25, 0): 6, (25, 1): 7, (25, 2): 6, (25, 3): 5, (25, 4): 4, (25, 5): 3, (25, 6): 2, (25, 7): 1, (25, 8): 2, (25, 9): 3, (25, 10): 4, (25, 11): 3, (25, 12): 2, (25, 13): 1, (25, 14): 2, (25, 15): 1, (25, 16): 2, (25, 17): 3, (25, 18): 4, (25, 19): 3, (25, 20): 2, (25, 21): 1, (25, 22): 2, (25, 23): 1, (25, 24): 2, (26, -2): 3, (26, -1): 4, (26, 0): 5, (26, 1): 6, (26, 2): 5, (26, 3): 6, (26, 4): 5, (26, 5): 4, (26, 6): 3, (26, 7): 2, (26, 8): 1, (26, 9): 2, (26, 10): 3, (26, 11): 4, (26, 12): 3, (26, 13): 2, (26, 14): 1, (26, 15): 2, (26, 16): 1, (26, 17): 2, (26, 18): 3, (26, 19): 4, (26, 20): 3, (26, 21): 2, (26, 22): 1, (26, 23): 2, (26, 24): 1, (26, 25): 2, 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(94, 78): 3, (94, 79): 2, (94, 80): 3, (94, 81): 2, (94, 82): 1, (94, 83): 2, (94, 84): 1, (94, 85): 2, (94, 86): 3, (94, 88): 3, (94, 89): 2, (94, 90): 1, (94, 91): 2, (94, 92): 1, (94, 93): 2, (95, -2): 6, (95, -1): 9, (95, 0): 8, (95, 1): 9, (95, 2): 8, (95, 3): 7, (95, 4): 6, (95, 5): 5, (95, 6): 4, (95, 13): 3, (95, 14): 2, (95, 15): 1, (95, 16): 2, (95, 17): 1, (95, 18): 2, (95, 19): 3, (95, 20): 4, (95, 21): 5, (95, 22): 6, (95, 23): 5, (95, 24): 4, (95, 25): 3, (95, 26): 2, (95, 27): 1, (95, 28): 2, (95, 29): 3, (95, 30): 2, (95, 31): 3, (95, 32): 2, (95, 33): 1, (95, 34): 2, (95, 35): 1, (95, 36): 2, (95, 38): 4, (95, 39): 5, (95, 40): 6, (95, 41): 7, (95, 42): 8, (95, 43): 7, (95, 44): 6, (95, 45): 5, (95, 46): 4, (95, 47): 3, (95, 48): 2, (95, 49): 1, (95, 50): 2, (95, 51): 3, (95, 52): 4, (95, 53): 5, (95, 55): 5, (95, 56): 4, (95, 57): 3, (95, 58): 2, (95, 59): 1, (95, 60): 2, (95, 61): 3, (95, 63): 3, (95, 64): 2, (95, 65): 1, (95, 66): 2, (95, 67): 1, (95, 68): 2, (95, 69): 3, (95, 70): 4, (95, 73): 5, (95, 74): 4, (95, 75): 3, (95, 76): 2, (95, 77): 1, (95, 78): 2, (95, 79): 3, (95, 80): 2, (95, 81): 3, (95, 82): 2, (95, 83): 1, (95, 84): 2, (95, 85): 1, (95, 86): 2, (95, 87): 3, (95, 89): 3, (95, 90): 2, (95, 91): 1, (95, 92): 2, (95, 93): 1, (95, 94): 2, (96, -2): 5, (96, -1): 6, (96, 0): 9, (96, 1): 8, (96, 2): 7, (96, 3): 8, (96, 4): 7, (96, 5): 6, (96, 6): 5, (96, 15): 2, (96, 16): 1, (96, 17): 2, (96, 18): 1, (96, 19): 2, (96, 20): 3, (96, 21): 4, (96, 22): 5, (96, 23): 6, (96, 24): 5, (96, 25): 4, (96, 26): 3, (96, 27): 2, (96, 28): 1, (96, 29): 2, (96, 30): 3, (96, 31): 2, (96, 32): 3, (96, 33): 2, (96, 34): 1, (96, 35): 2, (96, 36): 1, (96, 37): 2, (96, 39): 4, (96, 40): 5, (96, 41): 6, (96, 42): 7, (96, 43): 8, (96, 44): 7, (96, 45): 6, (96, 46): 5, (96, 47): 4, (96, 48): 3, (96, 49): 2, (96, 50): 1, (96, 51): 2, (96, 52): 3, (96, 53): 4, (96, 54): 5, (96, 56): 5, (96, 57): 4, (96, 58): 3, (96, 59): 2, (96, 60): 1, (96, 61): 2, (96, 62): 3, (96, 64): 3, (96, 65): 2, (96, 66): 1, (96, 67): 2, (96, 68): 1, (96, 69): 2, (96, 70): 3, (96, 71): 4, (96, 74): 5, (96, 75): 4, (96, 76): 3, (96, 77): 2, (96, 78): 1, (96, 79): 2, (96, 80): 3, (96, 81): 2, (96, 82): 3, (96, 83): 2, (96, 84): 1, (96, 85): 2, (96, 86): 1, (96, 87): 2, (96, 88): 3, (96, 90): 3, (96, 91): 2, (96, 92): 1, (96, 93): 2, (96, 94): 1, (96, 95): 2, (97, -2): 4, (97, -1): 5, (97, 0): 6, (97, 1): 7, (97, 2): 6, (97, 3): 7, (97, 4): 8, (97, 5): 7, (97, 6): 6, (97, 7): 5, (97, 16): 2, (97, 17): 1, (97, 18): 2, (97, 19): 1, (97, 20): 2, (97, 21): 3, (97, 22): 4, (97, 23): 5, (97, 24): 6, (97, 25): 5, (97, 26): 4, (97, 27): 3, (97, 28): 2, (97, 29): 1, (97, 30): 2, (97, 31): 3, (97, 32): 2, (97, 33): 3, (97, 34): 2, (97, 35): 1, (97, 36): 2, (97, 37): 1, (97, 38): 2, (97, 40): 4, (97, 41): 5, (97, 42): 6, (97, 43): 7, (97, 44): 8, (97, 45): 7, (97, 46): 6, (97, 47): 5, (97, 48): 4, (97, 49): 3, (97, 50): 2, (97, 51): 1, (97, 52): 2, (97, 53): 3, (97, 54): 4, (97, 55): 5, (97, 57): 5, (97, 58): 4, (97, 59): 3, (97, 60): 2, (97, 61): 1, (97, 62): 2, (97, 63): 3, (97, 65): 3, (97, 66): 2, (97, 67): 1, (97, 68): 2, (97, 69): 1, (97, 70): 2, (97, 71): 3, (97, 72): 4, (97, 75): 5, (97, 76): 4, (97, 77): 3, (97, 78): 2, (97, 79): 1, (97, 80): 2, (97, 81): 3, (97, 82): 2, (97, 83): 3, (97, 84): 2, (97, 85): 1, (97, 86): 2, (97, 87): 1, (97, 88): 2, (97, 89): 3, (97, 91): 3, (97, 92): 2, (97, 93): 1, (97, 94): 2, (97, 95): 1, (97, 96): 2, (98, -1): 4, (98, 0): 5, (98, 1): 6, (98, 2): 5, (98, 3): 6, (98, 4): 7, (98, 5): 8, (98, 6): 7, (98, 7): 6, (98, 8): 5, (98, 17): 2, (98, 18): 1, (98, 19): 2, (98, 20): 1, (98, 21): 2, (98, 22): 3, (98, 23): 4, (98, 24): 5, (98, 25): 6, (98, 26): 5, (98, 27): 4, (98, 28): 3, (98, 29): 2, (98, 30): 1, (98, 31): 2, (98, 32): 3, (98, 33): 2, (98, 34): 3, (98, 35): 2, (98, 36): 1, (98, 37): 2, (98, 38): 1, (98, 39): 2, (98, 41): 4, (98, 42): 5, (98, 43): 6, (98, 44): 7, (98, 45): 8, (98, 46): 7, (98, 47): 6, (98, 48): 5, (98, 49): 4, (98, 50): 3, (98, 51): 2, (98, 52): 1, (98, 53): 2, (98, 54): 3, (98, 55): 4, (98, 56): 5, (98, 58): 5, (98, 59): 4, (98, 60): 3, (98, 61): 2, (98, 62): 1, (98, 63): 2, (98, 64): 3, (98, 66): 3, (98, 67): 2, (98, 68): 1, (98, 69): 2, (98, 70): 1, (98, 71): 2, (98, 72): 3, (98, 73): 4, (98, 76): 5, (98, 77): 4, (98, 78): 3, (98, 79): 2, (98, 80): 1, (98, 81): 2, (98, 82): 3, (98, 83): 2, (98, 84): 3, (98, 85): 2, (98, 86): 1, (98, 87): 2, (98, 88): 1, (98, 89): 2, (98, 90): 3, (98, 92): 3, (98, 93): 2, (98, 94): 1, (98, 95): 2, (98, 96): 1, (98, 97): 2, (99, 0): 4, (99, 1): 5, (99, 2): 4, (99, 3): 5, (99, 4): 6, (99, 5): 7, (99, 6): 8, (99, 7): 7, (99, 8): 6, (99, 9): 5, (99, 18): 2, (99, 19): 1, (99, 20): 2, (99, 21): 1, (99, 22): 2, (99, 23): 3, (99, 24): 4, (99, 25): 5, (99, 26): 6, (99, 27): 5, (99, 28): 4, (99, 29): 3, (99, 30): 2, (99, 31): 1, (99, 32): 2, (99, 33): 3, (99, 34): 2, (99, 35): 3, (99, 36): 2, (99, 37): 1, (99, 38): 2, (99, 39): 1, (99, 40): 2, (99, 42): 4, (99, 43): 5, (99, 44): 6, (99, 45): 7, (99, 46): 8, (99, 47): 7, (99, 48): 6, (99, 49): 5, (99, 50): 4, (99, 51): 3, (99, 52): 2, (99, 53): 1, (99, 54): 2, (99, 55): 3, (99, 56): 4, (99, 57): 5, (99, 59): 5, (99, 60): 4, (99, 61): 3, (99, 62): 2, (99, 63): 1, (99, 64): 2, (99, 65): 3, (99, 67): 3, (99, 68): 2, (99, 69): 1, (99, 70): 2, (99, 71): 1, (99, 72): 2, (99, 73): 3, (99, 74): 4, (99, 77): 5, (99, 78): 4, (99, 79): 3, (99, 80): 2, (99, 81): 1, (99, 82): 2, (99, 83): 3, (99, 84): 2, (99, 85): 3, (99, 86): 2, (99, 87): 1, (99, 88): 2, (99, 89): 1, (99, 90): 2, (99, 91): 3, (99, 93): 3, (99, 94): 2, (99, 95): 1, (99, 96): 2, (99, 97): 1, (99, 98): 2, (100, 0): 3, (100, 1): 4, (100, 2): 3, (100, 3): 4, (100, 4): 5, (100, 5): 6, (100, 6): 7, (100, 7): 8, (100, 8): 7, (100, 9): 6, (100, 10): 5, (100, 19): 2, (100, 20): 1, (100, 21): 2, (100, 22): 1, (100, 23): 2, (100, 24): 3, (100, 25): 4, (100, 26): 5, (100, 27): 6, (100, 28): 5, (100, 29): 4, (100, 30): 3, (100, 31): 2, (100, 32): 1, (100, 33): 2, (100, 34): 3, (100, 35): 2, (100, 36): 3, (100, 37): 2, (100, 38): 1, (100, 39): 2, (100, 40): 1, (100, 41): 2, (100, 43): 4, (100, 44): 5, (100, 45): 6, (100, 46): 7, (100, 47): 8, (100, 48): 7, (100, 49): 6, (100, 50): 5, (100, 51): 4, (100, 52): 3, (100, 53): 2, (100, 54): 1, (100, 55): 2, (100, 56): 3, (100, 57): 4, (100, 58): 5, (100, 60): 5, (100, 61): 4, (100, 62): 3, (100, 63): 2, (100, 64): 1, (100, 65): 2, (100, 66): 3, (100, 68): 3, (100, 69): 2, (100, 70): 1, (100, 71): 2, (100, 72): 1, (100, 73): 2, (100, 74): 3, (100, 75): 4, (100, 78): 5, (100, 79): 4, (100, 80): 3, (100, 81): 2, (100, 82): 1, (100, 83): 2, (100, 84): 3, (100, 85): 2, (100, 86): 3, (100, 87): 2, (100, 88): 1, (100, 89): 2, (100, 90): 1, (100, 91): 2, (100, 92): 3, (100, 94): 3, (100, 95): 2, (100, 96): 1, (100, 97): 2, (100, 98): 1, (100, 99): 2}#
Dictionary of species’ ground state multiplicities.
Has items
(atnum, charge): Tuple[int, int].
- atomdb.utils.generate_mult_csv(max_atnum=100)#
Write a table of multiplicities to a CSV file.
Values retrieved from
database_beta_1.3.0.h5are organized into a table, with rows corresponding to atomic numbers and columns to charges.The maximum atomic number (
max_atnum) must not exceed 100, which is the database’s limit.The charge range spans from
-2tomax_atnum - 1.Missing entries have multiplicities set to zero.
Parameters#
- max_atnumint, default=100
Highest atomic number of the elements to be added to the table.
Raises#
- ValueError
If the maximum allowed atomic number is greater than 100.
atomdb.version module#
AtomDB version information.
- atomdb.version.version = '0.0.1'#
AtomDB version string.