carputils.mesh.block.Block Class Reference

Generate a block mesh with the mesher command line utility. More...

Public Member Functions
def	__init__ (self, centre=(0., 0., 0.), size=(1., 1., 1.), resolution=0.1, etype='tetra', periodic=0, periodic_tag=1234, pertb=0.0)
def	resolution (self)
	Return the currently set mesh resolution. More...
def	set_bath (self, thickness, both_sides=True)
	Add a bath region of the specified thickness. More...
def	set_fibres (self, fibre_endo=None, fibre_epi=None, sheet_endo=None, sheet_epi=None)
	Set the angles for generated fibres in the generated geometry. More...
def	corner_at_origin (self)
	Put the corner of the tissue block at the origin. More...
def	tissue_limits (self)
	Return the lower and upper limits of the block, excluding the bath. More...
def	bath_limits (self)
	Return the lower and upper limits of the block, including the bath. More...
def	shape (self, bath=True)
	Determine the number of points in each dimension. More...
def	add_region (self, region)
	Add a region definition. More...
def	mesher_opts (self, meshname)
	Generate a list of command line arguments for mesher. More...

Detailed Description

Generate a block mesh with the mesher command line utility.

This class describes a tissue block with optional additional bath region. For example, to define a 2x2x2mm block centred on the origin with 1mm bath on the positive z side:

>>> geom = Block(size=(2,2,2))
>>> geom.set_bath(thickness=(0,0,1), both_sides=False)

Regions may also be specified using the :class:BoxRegion, :class:SphereRegion and :class:CylinderRegion objects:

>>> reg = BoxRegion((-1,-1,-1), (1,1,0), tag=10)
>>> geom.add_region(reg)

Generate a list of command line options to pass to mesher to generate the described mesh with the :meth:mesher_opts method:

>>> opts = geom.mesher_opts('meshname') # meshname.pts, meshname.elem, etc.

.. note::

While the mesher executable takes arguments in centimetres and
micrometres, this class expects *all* physical sizes to be specified in
millimetres. Arguments are converted to the correct units when
generating the mesher command line.

Parameters

centre	array-like, optional Coordinate of centre of Block, defaults to (0,0,0)
size	array-like, optional Size of Block, defaults to (1,1,1)
resolution	float, optional Resolution at which to tesselate block into mesh, defaults to 0.1
etype	str, optional Element type to generate, either 'tetra' or 'hexa' in 3D, or 'quad' or 'tri' in 2D, defaults to 'tetra' in 3D and 'quad' in 2D
periodic	int, optional If set, the edges along a given direction are connected by linear elements to implement periodic boundary conditions. The range of values spans 0 (none), 1 (X), 2 (Y) and 3 (XY)
periodic_tag	int, optional Tag value assigned to the connecting linear elements. As default the value 1234 is used.

Constructor & Destructor Documentation

__init__()

def carputils.mesh.block.Block.__init__	(		self,
			centre = (0., 0., 0.),
			size = (1., 1., 1.),
			resolution = 0.1,
			etype = 'tetra',
			periodic = 0,
			periodic_tag = 1234,
			pertb = 0.0
	)

Member Function Documentation

add_region()

def carputils.mesh.block.Block.add_region	(		self,
			region
	)

Add a region definition.

Parameters

region

BoxRegion or SphereRegion or CylinderRegion The region description.

bath_limits()

def carputils.mesh.block.Block.bath_limits

(

self

)

Return the lower and upper limits of the block, including the bath.

Returns

lower array The coordinate of the lower left corner of the block

upper array The coordinate of the upper right corner of the block

corner_at_origin()

def carputils.mesh.block.Block.corner_at_origin

(

self

)

Put the corner of the tissue block at the origin.

mesher_opts()

def carputils.mesh.block.Block.mesher_opts	(		self,
			meshname
	)

Generate a list of command line arguments for mesher.

Parameters

meshname

str The base name of the mesh to be generated.

Returns

list The mesher argument list.

resolution()

def carputils.mesh.block.Block.resolution

(

self

)

Return the currently set mesh resolution.

Returns

float The mesh resolution.

set_bath()

def carputils.mesh.block.Block.set_bath	(		self,
			thickness,
			both_sides = True
	)

Add a bath region of the specified thickness.

Note that this method does not use the mesher convention of positive bath size meaning bath on one side and negative bath size meaning bath on both sides. Instead always use positive thickness values and the optional both_sides parameter to control this behaviour.

Parameters

thickness	array-like The thickness of bath to add, one value per coordinate axis
both_side	bool or array-like of bools, optional If True, generate bath on both sides of the object, if False only on one side. Pass an array of bools to control this behaviour for individual directions.

set_fibres()

def carputils.mesh.block.Block.set_fibres	(		self,
			fibre_endo = None,
			fibre_epi = None,
			sheet_endo = None,
			sheet_epi = None
	)

Set the angles for generated fibres in the generated geometry.

Parameters

fibre_endo	float, optional Set the principal fibre direction on the endocardium
fibre_epi	float, optional Set the principal fibre direction on the epicardium
sheet_endo	float, optional Set the sheet direction on the endocardium
sheet_epi	float, optional Set the shhet direction on the epicardium

shape()

def carputils.mesh.block.Block.shape	(		self,
			bath = True
	)

Determine the number of points in each dimension.

tissue_limits()

def carputils.mesh.block.Block.tissue_limits

(

self

)

Return the lower and upper limits of the block, excluding the bath.

Returns

lower array The coordinate of the lower left corner of the tissue block

upper array The coordinate of the upper right corner of the tissue block

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The documentation for this class was generated from the following file:

• carputils/mesh/block.py