mstk.forcefield.MorseBondTerm

class mstk.forcefield.MorseBondTerm(type1, type2, length, k, depth)

Bond term in Morse function form

The energy function is

>>> U = depth*(1-exp(-alpha*(r-b0)))^2
>>> alpha = (k / depth) ** 0.5

The k corresponds to the force constant k in HarmonicBondTerm.

During the initialization, the two atom types will be sorted by their string.

Parameters:

• type1 (str) –

• type2 (str) –

• length (float) –

• k (float) –

• depth (float) –

type1

Type:

str

type2

Type:

str

length

Type:

float

k

Type:

float

depth

Type:

float

Methods

__init__(type1, type2, length, k, depth)
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
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
to_zfp()	Pack the attributes of a term into a dict so that can be saved into ZFP xml file.

Attributes

name	The name of this force field term.

evaluate_energy(val)

Evaluate the energy for a force field term like HarmonicBondTerm, PeriodicDihedralTerm, etc…

It is mainly for debugging. It is not (and can not be) implemented for all terms.

Parameters:

val (float) – The value of distance, angle, dihedral or improper.

Returns:

energy

Return type:

float