pymech.core

This module contains the classes for the data structures used by pymech.neksuite and pymech.simsonsuite. The Contents of core.py are reported at the bottom of this page.

HexaData

The main data class is pymech.core.HexaData which is a structure for general and element by element information on data stored on hexahedral element(s). The general information is constituted by:

ndim	integer	number of spatial dimensions of the data
nel	integer	number of elements included in pymech.core.HexaData
ncurv	integer	number of curved sides (used only by Nek5000)
var	string	variables included in pymech.core.HexaData (e.g. ‘XUPT’)
lr1	ndim-array of integers	number of datapoints per element
time	float	simulation time of the file
istep	integer	simulation time step of the file
wdsz	integer	word size, i.e. double or single precision file
endian	string	endianness of the file (little/big)
lims	DataLims	extrema of all quantities stored

The element by element data is stored in:

elem

nel-array of Elem

array containing element data

Elem

This class contains the data for one hexahedral element organised as follows:

pos	array of floats	x,y,z coordinates of each grid point
curv	array of floats	radius of curvature of the element edges (Nek5000)
ccurv	array of strings	defines the type of curvature
vel	array of floats	u,v,w velocity at each grid point
pres	array of floats	pressure at each grid point
temp	array of floats	temperature at each grid point
scal	array of floats	passive scalars at each grid point
bcs	array of floats	list of boundary condition parameters (Nek5000)

DataLims

This class contains the extrema of all quantities stored in the mesh.

pos	array of floats	max and min of x,y,z coordinates
vel	array of floats	max and min of u,v,w velocity
pres	array of floats	max and min of pressure
temp	array of floats	max and min of temperature
scal	array of floats	max and min of passive scalars

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Contents of core.py

Core data structures for pymech

class pymech.core.DataLims(elements)

A class containing the extrema of all quantities stored in the mesh

- pos

Type:

x,y,z min,max

- vel

Type:

u,v,w min,max

- pres

Type:

p min,max

- temp

Type:

T min,max

- scal

Type:

s_i min,max

class pymech.core.Elem(var, lr1, nbc, dtype='float64')

A class containing one hexahedral element of Nek5000/SIMSON flow field.

Parameters:

• var (iterable) – Iterable of integers of size 5, indicating how many variables are to be initialized

• lr1 (iterable) – Iterable of integers of size 3, defining the shape of an element as (lx, ly, lz)

• nbc (int) – Number of boundary conditions

• dtype (str) – Floating point data type. Typical values are ‘f4’ or ‘float32’ for single precision, ‘f8’ or ‘float64’ for double precision

face_center(i)

Return the coordinates (x, y, z) of the center of the face number i

smallest_edge()

returns the length of the smallest edge, neglecting curvature

class pymech.core.HexaData(ndim, nel, lr1, var, nbc=0, dtype='float64')

A class containing data related to a hexahedral mesh

check_bcs_present()

Returns True if and only if all faces of all elements have boundary conditions applied.

Note that this function returning False does not mean the mesh is invalid: it is not mandatory to define internal boundary conditions for Nek5000.

check_connectivity(tol=0.001)

Check element connectivity, specifically for matching boundary conditions and geometry. Errors are reported as logging messages.

Parameters:

tol (float) – relative tolerance (compared to the smallest edge of adjacent elements) for detecting whether faces are at the same location

get_points()

Returns an array containing the coordinates of all the points in the mesh as a (nel, lx1*ly1*lz1, 3) array

merge(other, tol=0.01, ignore_empty=True, ignore_all_bcs=False)

Merges another pymech.core.HexaData into the current one and connects it

Parameters:

• other (pymech.core.HexaData) – mesh to merge into self

• tol (float) – maximum distance, relative to the smallest edge of neighbouring elements, at which faces are considered touching

• ignore_empty (bool) – if True, the faces with an empty boundary condition (‘’) will be treated as internal faces and will not be merged. This is useful if internal boundary conditions are not defined and will make the operation much faster, but requires boundary conditions to be defined on the faces to be merged.

• ignore_all_bcs (bool) – if True, the boundary conditions will not be changed. This is likely to result in invalid boundary conditions at the interface between the merged meshes. This option is intended for fast merging in a situation in which the boundary conditions are either irrelevant or will be defined or corrected later.

offset_connectivity(offset: int, iel_min=0)

Adds a value to the index of the elements connected via internal or periodic boundary conditions to elements of the mesh. This is used to keep the connectivity valid when deleting or inserting elements in the mesh.

Parameters:

• offset (int) – The value by which to offset the indices

• iel_min (int) – The first element (in zero-based indexing) to offset

update_ncurv()

Updates the metadata ncurv integer to match the actual number of curved faces present in the mesh