mstk.forcefield.MieTerm¶

class mstk.forcefield.MieTerm(type1, type2, epsilon, sigma, repulsion, attraction)¶

vdW term with generalized LJ function form.

The energy function is

>>> U = C * epsilon * ((sigma/r)^n - (sigma/r)^m)
>>> C = n/(n-m) * (n/m)^(m/(n-m))
>>> r_min = (n/m)^(1/(n-m)) * sigma

This term is mainly used for Coarse-Grained force field.

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

Parameters:

type1¶

type2¶

epsilon¶

sigma¶

repulsion¶

attraction¶

Methods

`__init__`(type1, type2, epsilon, sigma, ...)
`evaluate_energy`(r)	Evaluate the energy for a force field term like HarmonicBondTerm, PeriodicDihedralTerm, etc...
`factor_energy`()	Get the energy pre-factor of the Mie function.
`factor_r_min`()	Get the converting factor from sigma to the distance of energy minimum.
`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

`is_sdk`	SDK CGFF use LJ-9-6 and LJ-12-4
`name`	The name of this force field term.

evaluate_energy(r)¶

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

factor_energy()¶

Get the energy pre-factor of the Mie function.

>>> C = n/(n-m) * (n/m)^(m/(n-m))

factor_r_min()¶

Get the converting factor from sigma to the distance of energy minimum.

>>> f = (n/m)^(1/(n-m))

property is_sdk¶

SDK CGFF use LJ-9-6 and LJ-12-4

mstk