snek5000.operators

Operators

Information regarding mesh, mathematical operators, and domain decomposition.

Functions

next_power(value[, base])

Compute the perfect power of base greater than or equal to value.

Classes

Operators([sim, params])

Container for parameters and writing box and

snek5000.operators.next_power(value, base=2)

Compute the perfect power of base greater than or equal to value.

Parameters

• value (int or float) –

• base (int) –

Return int

class snek5000.operators.Operators(sim=None, params=None)

Container for parameters and writing box and

SIZE files.

Note

Some values are not available as parameters and instead automatically computed for generating the SIZE file.

SIZE	properties	Comment
lelg	max_n_seq	Max. number of elements globally
lelt	max_n_loc	Max. number of elements per processor (should be not smaller than lelg/lpmin, i.e.
lelx	max_nx	Automatically computed. Max. number of elements along x direction for the global tensor product solver / dimensions.
lely	max_ny	Same as above for y direction.
lelz	max_nz	Same as above for z direction.
lorder	max_order_time	Max. temporal order Automatically computed based params.nek.general.time_stepper
lbelt	order_mhd	Automatically computed as lelt if "MHD" in params.nek.problem_type.equation.
lpelt	order_linear	Automatically computed as lelt if "linear" in params.nek.problem_type.equation.
lcvelt	order_cvode	Automatically computed as lelt if params.nek.cvode._enabled is True
lx1m	order_mesh_solver	p-order for mesh solver. Automatically computed based params.nek.general.stress_formulation and whether Arbitrary Lagrangian-Eulerian (ALE) methods are used or not.

Note

We deliberately try not to use the variable names used in Nek5000, as those are ambiguously named.

Documentation for params.oper

Parameters for mesh description:

• nx, ny, nz: int

  Number of elements in each directions

• origin_x, origin_y, origin_z: float

  Starting coordinate of the mesh (default: 0.0)

• ratio_x, ratio_y, ratio_z: float

  Mesh stretching ratio (default: 1.0)

• Lx, Ly, Lz: float

  Length of the domain

Parameters for boundary conditions:

• boundary: list[str]

  Velocity boundary conditions

• boundary_scalars: list[str]

  Temperature and passive scalar boundary conditions

The following table matches counterpart of mandatory SIZE variables.

SIZE	params.oper	Comment
ldim	dim	Domain dimensions (2 or 3)
lpmin	nproc_min	Min MPI ranks
lpmax	nproc_max	Max MPI ranks
ldimt	scalars	Number of auxilary fields (minimum 1).

Documentation for params.oper.max

The following table matches counterpart of optional SIZE variables. These refer to upper bound number of something. The parameters are considered “optional” and would be ignored with the default values.

SIZE	params.oper.max	Comment
mxprev	dim_proj	Max. dimension of projection space
lgmres	dim_krylov	Max. dimension of Krylov space for GMRES
lhis	hist	Max. number of history (i.e. monitoring) points.
maxobj	obj	Max. number of objects?
lpert	perturb	Max. number of perturbations
toteq	scalars_cons	Max. conserved scalars
ldimt_proj	scalars_proj	Max. scalars for residual projection
nsessmax	sessions	Max. sessions to NEKNEK

Documentation for params.oper.elem

The following table relate to element configuration for certain operations. The parameters are considered “optional” (except for lx1 / order and lxd / coef_dealiasing which are mandatory) and would be ignored with the default values.

SIZE	params.oper.elem	Comment
lxd	coef_dealiasing	p-order 1 for over-integration. Automatically computed from float coef_dealiasing. See order_dealiasing
lx1	order	p-order (avoid uneven and values <6).
lxo	order_out	Max. p-order on output (should be >= order. See order_out)
lx2	staggered	p-order for pressure. Automatically computed. See order_pressure

1

Polynomial order which means the number of GLL / GL points per element.

Documentation for params.oper.misc

Other miscellaneous parameters:

SIZE	params.oper.misc	Comment
lfdm	fast_diag	Equals to True for global tensor product solver (that uses fast diagonalization method). False otherwise.

property max_n_seq

Equivalent to lelg.

property max_n_loc

Equivalent to lelt. The next integer greater than or equals max_n_seq / params.oper.nproc_min.

property max_nx

Equivalent to lelx.

property max_ny

Equivalent to lely.

property max_nz

Equivalent to lelz.

property max_order_time

Equivalent to lorder.

property nb_fields

Used in .box file.

property order

Equivalent to lx1. Controls the polynomial order of the velocity field.

Note

True polynomial order of the element is given by \(\mathbb{P}_N\) = lx1 - 1 = order - 1

property order_out

Equivalent to lxo.

property order_dealiasing

Equivalent to lxd.

property order_pressure

Equivalent to lx2. Controls the order for the pressure field.

Note

The property order_pressure is determined by the value of params.oper.elem.staggered.

• If staggered == “auto”:

  • If “lin” in problemtype_equation \(\implies \mathbb{P}_{N-2}\)

  • Else \(\implies \mathbb{P}_N\)

• If staggered is True \(\implies \mathbb{P}_{N-2}\)

• If staggered is False \(\implies \mathbb{P}_N\)

property order_mesh_solver

Equivalent to lx1m.

Todo

Must include a condition to check if ALE methods are used or not.

property order_mhd

Equivalent to lbelt.

property order_linear

Equivalent to lpelt.

property order_cvode

Equivalent to lcvelt.

memory_required()

According to Nek5000 FAQ the following estimate is made

lx1*ly1*lz1*lelt * 3000byte + lelg * 12byte + MPI + optional libraries
(e.g. CVODE)

Returns

memory_required – in bytes

Return type

int

produce_str_describing_oper()

Produce a string describing the mesh volume and number of elements.

produce_long_str_describing_oper(oper_method='Base')

Produce a multi-line string describing the mesh volume and number of elements.

info_box(comments='')

Gather information for writing a box file.

Return type

dict

write_box(template, fp=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, comments='', **template_vars)

Write the .box file which is input for the genbox meshing tool.

Parameters

• template (jinja2.environment.Template) – Template instance loaded from something like box.j2

• fp (io.TextIOWrapper) – File handler to write to

• comments (str) – Comments on top of the box file

• template_vars (dict) – Keyword arguments passed while rendering the Jinja templates

write_size(template, fp=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, comments='', **template_vars)

Write the SIZE file which is required for compilation.

Parameters

• template (jinja2.environment.Template) – Template instance loaded from something like SIZE.j2

• fp (io.TextIOWrapper) – File handler to write to

• comments (str) – Comments on top of the SIZE file

• template_vars (dict) – Keyword arguments passed while rendering the Jinja templates