magres.atoms¶

magres.atoms is a collection of user-friendly data structures for representing groups of atoms and their NMR parameters. The NMR parameter structures can calculate a variety of properties from the underlying tensors, according to a variety of conventions.

class magres.atoms.MagresAtoms(atoms=None, lattice=None)¶

A collection of atoms, including lattice parameters, and (if available) lists of NMR parameters.

classmethod load_magres(f)¶

A class method to easily load a magres.format.MagresFile and return the corresponding MagresAtoms.

>>> MagresAtoms.load_magres("path/to/magres/file.magres")

or

>>> MagresAtoms.load_magres(open("path/to/magres/file.magres"))

class magres.atoms.MagresAtomsView(atoms=None, lattice=None)¶

A container for a collection of atoms with an optional lattice.

add(atoms)¶: Add an extra atom or list of atoms.

get_label(label, index=None)¶

Get a single atom of a particular label and index.

>>> atoms.get_label("C1", 2)

get_species(species, index=None)¶

Get a single atom of a particular species and index.

>>> atoms.get_species('C', 2)

label(label)¶

Return a MagresAtomsView containing only atoms of the specified label.

>>> atoms.label("C1")

species(species)¶

Return a MagresAtomsView containing only atoms of the specified species.

>>> atoms.species('C')

within(pos, max_dr)¶

Return all atoms within max_dr Angstroms of pos, including all images.

>>> atoms.within(p, 5.0)

class magres.atoms.MagresAtom(magres_atom)¶

Q¶: The quadrupole moment of this atom’s species and isotope.

dist(r)¶: Calculate distance from this atom to another position or atom.

gamma¶: The gyromagnetic ratio constant of this atom’s species and isotope.

index¶: This atom’s label index.

isotope¶: The isotope of this atom. Assumed to be most common NMR-active nucleus unless specified otherwise.

label¶: This atom’s label.

position¶: This atom’s position in cartesian coordinates. Units are Angstroms.

species¶: This atom’s species.

class magres.atoms.MagresAtomMs(atom, magres_ms, reference=None)¶

Representation of the magnetic shielding of a particular atom.

aniso¶

The shielding anisotropy. Defined by

$\Delta \sigma = \sigma_{ZZ} - (\sigma_{XX} + \sigma_{YY})/2$

asym¶

The asymmetric part of sigma.

$\sigma_{asym} = (\sigma - \sigma^T)/2$

eta¶

The shielding asymmetry. Defined by

$\eta = (\sigma_{YY} - \sigma_{XX}) / \zeta$

evals¶

The eigenvalues of sigma, ordered according to the Haeberlen convention:

$|\sigma_{ZZ} - \sigma_{iso}| \geq |\sigma_{XX} - \sigma_{iso}| \geq |\sigma_{YY} - \sigma_{iso}|$

where

sigma_XX = evals[0] sigma_YY = evals[1] sigma_ZZ = evals[2]

evals_mehring¶

The eigenvalues of sigma ordered according to the Mehring notation:

$\sigma_{11} \leq \sigma_{22} \leq \sigma_{33}$

evalsvecs¶

The eigenvalues and eigenvectors of the symmetric part of sigma, ordered according to the Haeberlen convention:

$|\sigma_{ZZ} - \sigma_{iso}| \geq |\sigma_{XX} - \sigma_{iso}| \geq |\sigma_{YY} - \sigma_{iso}|$

where

sigma_XX = evals[0] sigma_YY = evals[1] sigma_ZZ = evals[2]

evalsvecs_mehring¶

The eigenvalues and eigenvectors of the symmetric part of sigma ordered according to the Mehring notation:

$\sigma_{11} \leq \sigma_{22} \leq \sigma_{33}$

evecs¶

The eigenvectors of sigma, ordered according to the Haeberlen convention:

$|\sigma_{ZZ} - \sigma_{iso}| \geq |\sigma_{XX} - \sigma_{iso}| \geq |\sigma_{YY} - \sigma_{iso}|$

where

sigma_XX = evals[0] sigma_YY = evals[1] sigma_ZZ = evals[2]

evecs_mehring¶

The eigenvectors of sigma ordered according to the Mehring notation:

$\sigma_{11} \leq \sigma_{22} \leq \sigma_{33}$

iso¶

The isotropic part of sigma. Defined by

$\sigma_{iso} = (\sigma_{XX} + \sigma_{YY} + \sigma_{ZZ})/3$

sigma¶: The sigma tensor, i.e. the magnetic shielding.

skew¶

The skew of sigma. Defined by

$\kappa = 3(\sigma_{iso} - \sigma_{22}) / \Omega$

span¶

The span of sigma. Defined by

$\Omega = \sigma_{33} - \sigma_{11}$

sym¶

The symmetric part of sigma.

$\sigma_{sym} = (\sigma + \sigma^T)/2$

zeta¶

The shielding anisotropy (alternative). Defined by

$\zeta = \sigma_{ZZ} - \sigma_{iso}$

class magres.atoms.MagresAtomEfg(atom, magres_efg)¶

Representation of the electric field gradient on a particular atom.

Cq¶

The Cq of the V tensor.

$C_q = eV_{ZZ} Q / h$

Where Q is the quadrupole moment of this particular species, e is the electron charge and h is Planck’s constant.

V¶: The EFG V tensor in atomic units.

evals¶

The eigenvalues of V, ordered according to the Haeberlen convention:

$|V_{ZZ}| \geq |V_{XX}| \geq |V_{YY}|$

where

$V_{XX}$ = evals[0]

$V_{YY}$ = evals[1]

$V_{ZZ}$ = evals[2]

evalsvecs¶

The eigenvalues and eigenvectors of V, ordered according to the Haeberlen convention:

$|V_{ZZ}| \geq |V_{XX}| \geq |V_{YY}|$

where

$V_{XX}$ = evals[0]

$V_{YY}$ = evals[1]

$V_{ZZ}$ = evals[2]

evecs¶

The eigenvectors of V, ordered according to the Haeberlen convention:

$|V_{ZZ}| \geq |V_{XX}| \geq |V_{YY}|$

where

$V_{XX}$ = evals[0]

$V_{YY}$ = evals[1]

$V_{ZZ}$ = evals[2]

class magres.atoms.MagresAtomIsc(atom1, atom2, magres_isc)¶

Representation of the indirect spin coupling between two atoms.

J¶: The spin-spin coupling J tensor.

J_aniso¶: The J anisotropy.

J_asym¶: The asymmetric component of the indirect spin-spin coupling tensor J.

J_eta¶: The K principal component asymmetry.

J_iso¶: The isotropic component of the indirect spin-spin coupling J tensor.

J_sym¶: The symmetric component of the indirect spin-spin coupling tensor J.

K¶: The reduced indirect spin-spin coupling K tensor.

K_aniso¶: The K anisotropy.

K_asym¶: The asymmetric component of the reduced indirect spin-spin coupling tensor K.

K_eta¶: The K principal component asymmetry.

K_iso¶: The isotropic component of the reduced indirect spin-spin coupling tensor.

K_sym¶: The symmetric component of the reduced indirect spin-spin coupling tensor K.

dist¶: The distance between the two atoms involved.

symbol¶: A textual symbol representing this coupling.

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