mstk.forcefield.HarmonicBondTerm

class mstk.forcefield.HarmonicBondTerm(type1, type2, length, k, fixed=False)

Bond term in harmonic function form

The energy function is

>>> U = k * (b-b0)^2

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

Parameters:

  • type1 (str) –

  • type2 (str) –

  • length (float) –

  • k (float) –

  • fixed (bool) –

type1
Type:

str

type2
Type:

str

length
Type:

float

k
Type:

float

fixed
Type:

bool

Methods

__init__(type1, type2, length, k[, fixed])

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

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