mstk.forcefield.DrudePolarTerm

class mstk.forcefield.DrudePolarTerm(type: str, alpha, thole, k=209200.0, mass=0.4, merge_alpha_H=0.0)

Polarization term described by Drude induced dipole.

Currently, only the isotropic Drude polarization is implemented. The energy function for polarization is

>>> E = k * d^2

The charge assigned to the Drude particle is

>>> q = - sqrt(4 * pi * eps_0 * (2k) * alpha)

If this atom is bonded with hydrogen atoms, the argument merge_alpha_H determines the polarizability of neighbour H atoms. The alpha of these H atoms will be merged into the this atom. Therefore, DrudePolarTerm for H atom types should not be provided explicitly. Otherwise, there will be double count. The H atoms are identified by check the symbol attribute. An atom is considered to be hydrogen if symbol equals ‘H’.

Parameters:

• type (str) –

• alpha (float) –

• thole (float) –

• k (float) –

• mass (float) –

• merge_alpha_H (float) –

type

Type:

str

alpha

Type:

float

thole

Type:

float

k

Type:

float

mass

Type:

float

merge_alpha_H

Type:

float

Methods

__init__(type, alpha, thole[, k, mass, ...])
evaluate_energy(val)	Evaluate the energy for a force field term like HarmonicBondTerm, PeriodicDihedralTerm, etc...
get_alias()	Return a short alias for the name of this class
get_charge([alpha])	Get the charge offset between parent atom and Drude particle.
to_zff()	Pack the attributes of a term into a string so that can be saved into a line in ZFF file.
to_zff_header()	Header string to explain a line in ZFF format

Attributes

name	The name of this force field term.

to_zff()

Pack the attributes of a term into a string so that can be saved into a line in ZFF file.

Every class to be packed should have a class property _term_attrs. This dict records which attributes should be saved into ZFF file, and it is also used as the arguments for initializing a FFTerm. It also tells the data type of these attributes.

Returns:

line

Return type:

string

get_charge(alpha=None)

Get the charge offset between parent atom and Drude particle.

The charge assigned on the Drude particle is the negative of this charge offset.

Parameters:

alpha (float) – The polarizability of parent atom in unit of nm^3.

Returns:

charge – The charge offset from Drude particle to parent atom.

Return type:

float