Domain

class sknano.core.crystallography.Domain[source] [edit on github][source]

Bases: sknano.core.strings.TabulateMixin, sknano.core.meta.BaseClass

Container class for molecular dynamics simulation box metadata.

Attributes

fmtstr Format string.
lengths tuple of side lengths
lx Alias for Domain.bounding_box.lx.
ly Alias for Domain.bounding_box.ly.
lz Alias for Domain.bounding_box.lz.
tilt_factors Domain tilt factors xy, xz, yz.
xhi Alias for Domain.bounding_box.xmax
xhi_bound Triclinic bounding box maximum extent in the x-dimension
xlo Alias for Domain.bounding_box.xmin
xlo_bound Triclinic bounding box minimum extent in the x-dimension
yhi Alias for Domain.bounding_box.ymax
yhi_bound Triclinic bounding box maximum extent in the y-dimension
ylo Alias for Domain.bounding_box.ymin
ylo_bound Triclinic bounding box minimum extent in the y-dimension
zhi Alias for Domain.bounding_box.zmax
zhi_bound Triclinic bounding box maximum extent in the z-dimension
zlo Alias for Domain.bounding_box.zmin
zlo_bound Triclinic bounding box minimum extent in the z-dimension

Methods

todict() Return dict of constructor parameters.
update([from_lattice, from_region, ...]) Update simulation domain attributes from lattice.

Attributes Summary

lengths tuple of side lengths
lx Alias for Domain.bounding_box.lx.
ly Alias for Domain.bounding_box.ly.
lz Alias for Domain.bounding_box.lz.
tilt_factors Domain tilt factors xy, xz, yz.
xhi Alias for Domain.bounding_box.xmax
xhi_bound Triclinic bounding box maximum extent in the x-dimension
xlo Alias for Domain.bounding_box.xmin
xlo_bound Triclinic bounding box minimum extent in the x-dimension
yhi Alias for Domain.bounding_box.ymax
yhi_bound Triclinic bounding box maximum extent in the y-dimension
ylo Alias for Domain.bounding_box.ymin
ylo_bound Triclinic bounding box minimum extent in the y-dimension
zhi Alias for Domain.bounding_box.zmax
zhi_bound Triclinic bounding box maximum extent in the z-dimension
zlo Alias for Domain.bounding_box.zmin
zlo_bound Triclinic bounding box minimum extent in the z-dimension

Methods Summary

todict() Return dict of constructor parameters.
update([from_lattice, from_region, ...]) Update simulation domain attributes from lattice.

Attributes Documentation

lengths

tuple of side lengths

lx

Alias for Domain.bounding_box.lx.

ly

Alias for Domain.bounding_box.ly.

lz

Alias for Domain.bounding_box.lz.

tilt_factors

Domain tilt factors xy, xz, yz.

xhi

Alias for Domain.bounding_box.xmax

xhi_bound

Triclinic bounding box maximum extent in the x-dimension

xlo

Alias for Domain.bounding_box.xmin

xlo_bound

Triclinic bounding box minimum extent in the x-dimension

yhi

Alias for Domain.bounding_box.ymax

yhi_bound

Triclinic bounding box maximum extent in the y-dimension

ylo

Alias for Domain.bounding_box.ymin

ylo_bound

Triclinic bounding box minimum extent in the y-dimension

zhi

Alias for Domain.bounding_box.zmax

zhi_bound

Triclinic bounding box maximum extent in the z-dimension

zlo

Alias for Domain.bounding_box.zmin

zlo_bound

Triclinic bounding box minimum extent in the z-dimension

Methods Documentation

todict()[source] [edit on github][source]

Return dict of constructor parameters.

update(from_lattice=None, from_region=None, from_array=None, allow_triclinic_box=False, pad_box=False, pad_tol=0.01, xpad=10.0, ypad=10.0, zpad=10.0, verbose=False, **kwargs)[source] [edit on github][source]

Update simulation domain attributes from lattice.