exatomic.adf.tape21 module

ADF TAPE21 ASCII converted output

this module provides the primary (user facing) parser for an ASCII converted TAPE21 file from ADF

exception exatomic.adf.tape21.MissingSection

Bases: Exception

class exatomic.adf.tape21.Tape21Meta(name, bases, clsdict)

Bases: TypedMeta

atom

alias of Atom

frequency

alias of Frequency

gradient

alias of Gradient

j_coupling

alias of JCoupling

nmr_shielding

alias of NMRShielding

class exatomic.adf.tape21.Tape21(path_stream_or_string, as_interned=False, nprint=30, name=None, description=None, meta=None, encoding=None, ignore=False)

Bases: Editor

Parser for ADF Tape21 that have been converted to an ASCII file with their dmpkf utility.

All properties are parsed based on the input order.

Note

This is not yet tested for ADF versions newer than 2017.

static rmass_mwc(data, symbol)

Calculate the reduced masses from the mass-weighted normal modes. With the equation,

\[\mu_i = \left(\sum_k^{3N} \left(\frac{l_{MWCk,i}} {\sqrt{m_k}}\right)^2\right)^{-1}\]

Note

This assumes that the normal modes have already been placed in the ['dx', 'dy', 'dz'] columns.

Parameters:

• data (pandas.DataFrame) – Data frame the has the mass-weighted normal modes.

• symbol (list) – List-like object that has the atomic symbols.

Returns:

r_mass (numpy.ndarray) –

Array containing the calculated reduced

masses.

static rmass_cart(data, symbol)

Calculate the reduced masses from the normalized non-mass-weighted cartesian normal modes. With the equation,

\[\mu_i = \left(\sum_k^{3N} l_{CARTk,i}^2\right)^{-1}\]

Note

This assumes that the normal modes have already been placed in the ['dx', 'dy', 'dz'] columns.

Parameters:

• data (pandas.DataFrame) – Data frame the has the non-mass-weighted cartesian normal modes.

• symbol (list) – List-like object that has the atomic symbols.

Returns:

r_mass (numpy.ndarray) –

Array containing the calculated reduced

masses.

parse_frequency(cart=True)

ADF frequency parser.

Note

This will toss a warning if it cannot find the mass-weighted normal modes which must be used to generate the displaced structures for vibrational averaging. Also, it will be unable to calculate the reduced masses as it will have normalized cartesian coordinates where it expects normalized mass-weighted cartesian normal modes.

Parameters:

cart (bool, optional) – Parse the normalized cartesian coordinates or the mass-weighted normal modes. Defaults to True.

parse_atom(input_order=False)

Parse the atom table.

Parameters:

input_order (bool, optional) – Parse the atom table in the input order format. Defaults to False.

parse_gradient(input_order=False)

Parse the gradients in the input order.

parse_nmr_shielding()

Parse the NMR shielding tensors in the input order.

parse_j_coupling()

Parse the J Coupling in the Cartesian representation.

property atom

property frequency

property gradient

property j_coupling

property nmr_shielding