Section: tagging

This section manages the various mesh refinement criteria that can be used to activate either static or adaptive mesh refinement during simulations. The parameters are read from the prefix tagging and can contain different types of tagging logic. Note that this section is only active if amr.max_level is greater than zero. Regridding interval is controlled by time.regrid_interval .

Example:

tagging.labels = s1 f1 g1
tagging.s1.type = CartBoxRefinement
tagging.s1.static_refinement_def = static_box.txt

tagging.f1.type = FieldRefinement
tagging.f1.field_name = density
tagging.f1.grad_error = 0.1. 0.1 0.1

tagging.g1.type = GeometryRefinement
tagging.g1.shapes = c1 b1

tagging.g1.c1.type = cylinder
tagging.g1.c1.start = 500.0 500.0 250.0
tagging.g1.c1.end = 500.0 500.0 750.0
tagging.g1.c1.outer_radius = 300.0
tagging.g1.c1.inner_radius = 275.0

tagging.g1.b1.type = box
tagging.g1.b1.origin = 300.0 150.0 250.0
tagging.g1.b1.xaxis =  450.0 600.0 0.0
tagging.g1.b1.yaxis =  -150.0 100.0 0.0
tagging.g1.b1.zaxis = 0.0 0.0 500.0

Each section must contain the keyword type that is one of the refinement types:

`CartBoxRefinement`	Nested refinement using Cartesian boxes
`FieldRefinement`	Refinement based on error metric for field or its gradient
`OversetRefinement`	Refinement around fringe/field interface
`GeometryRefinement`	Refinement using geometric shapes
`QCriterionRefinement`	Refinement using Q-Criterion
`VorticityMagRefinement`	Refinement using vorticity

tagging.labels

type: List of one or more names

Labels indicate a list of prefixes for different types of refinement criteria active during the simulation.

The parameters for the subsections are determined by the type of refinement being performed.

Refinement using geometry

This section controls refinement using pre-defined geometric shapes. Currently, two options are supported: 1. box – refines the region inside a hexahedral block, 2. cylinder – refines the region inside a cylindrical block, and 3. udf – refines along an analytical function depending on time and spatial coordinate.

tagging.GeometryRefinement.shapes

type: List of strings, required

Names of the input subsections that define specific geometries for refinement.

tagging.GeoemtryRefinement.level

type: Integer, optional, default: -1

If level is provided and is greater than or equal to 0, then the refinement based on geometries defined for this section is only performed at that level.

tagging.GeometryRefinement.min_level

type: Integer, optional, default: 0

If level is not specified, then this option specifies the minimum level where this refinement is active.

tagging.GeometryRefinement.max_level

type: Integer, optional, default: mesh.maxLevel()

If level is not specified, then this option specifies the maximum level where this refinement is active.

Note that the specification of level overrides, min_level and max_level specifications. This can be used to control the different levels where refinement regions are active.

Example:

tagging.g1.type = GeometryRefinement
tagging.g1.shapes = b1 b2
tagging.g1.level = 0
tagging.g1.b1.type = box
tagging.g1.b1.origin = 300.0 150.0 250.0
tagging.g1.b1.xaxis =  450.0 600.0 0.0
tagging.g1.b1.yaxis =  -150.0 100.0 0.0
tagging.g1.b1.zaxis = 0.0 0.0 500.0
tagging.g1.b2.type = box
tagging.g1.b2.origin = 600.0 350.0 250.0
tagging.g1.b2.xaxis =  50.0 30.0 0.0
tagging.g1.b2.yaxis =  -50.0 60.0 0.0
tagging.g1.b2.zaxis = 0.0 0.0 500.0

tagging.g2.type = GeometryRefinement
tagging.g2.shapes = c1
tagging.g2.level = 1
tagging.g2.c1.type = cylinder
tagging.g2.c1.start = 500.0 500.0 250.0
tagging.g2.c1.end = 500.0 500.0 750.0
tagging.g2.c1.outer_radius = 300.0
tagging.g2.c1.inner_radius = 275.0

tagging.g3.type = GeometryRefinement
tagging.g3.shapes = udf0
tagging.g3.level = 0
tagging.g3.udf0.type = udf
tagging.g3.udf0.udf = "if(x > 500, 1.0, 0.0)"
tagging.g3.udf0.box_lo = 0.0 0.0 0.0
tagging.g3.udf0.box_hi = 1000.0 1000.0 500.0

This example defines three different refinement definitions acting on levels 0, 1 and 0 respectively. The first refinement at level 0 (g1) contains two box regions, whereas the refinement at level 1 (g2) only contains one cylinder definition. The second refinement at level 0 (g3) uses a user defined function (UDF) to specify a geometrical refinement region.

Refinement using hexahedral block definitions

To perform box refinement, the user specifies the origin of the box and three vectors: xaxis, yaxis, zaxis that defines the directions and the extents of the hexahedral block. Denoting \(\mathbf{O}\) as origin vector and \(\mathbf{x}\), \(\mathbf{y}\) and \(\mathbf{z}\) as the three vectors given by the user, the position vectors of the eight corners of the hexahedral box are given by

\[\begin{split}\mathbf{x}_0 &= \mathbf{O} && \mathbf{x}_4 &= \mathbf{O} + \mathbf{z} \\ \mathbf{x}_1 &= \mathbf{O} + \mathbf{x} && \mathbf{x}_5 &= \mathbf{O} + \mathbf{z} + \mathbf{x} \\ \mathbf{x}_2 &= \mathbf{O} + \mathbf{x} + \mathbf{y} \qquad && \mathbf{x}_6 &= \mathbf{O} + \mathbf{z} + \mathbf{x} + \mathbf{y} \\ \mathbf{x}_3 &= \mathbf{O} + \mathbf{y} && \mathbf{x}_7 &= \mathbf{O} + \mathbf{z} + \mathbf{y} \\\end{split}\]

Refinement using cylindrical block definitions

The axis and the extents along the axis are defined by two position vectors start and end. The radial extent is specified by outer_radius. An optional inner_radius can be specified to restrict tagging to an annulus between the inner and outer radii.

Refinement using a user specified function

The UDF uses AMReX’s Parser class to parse a string in the input file, udf key in the input file. For more information on the AMReX Parser and supported functions, consult the AMReX Parser documentation. The UDF can be (almost) arbitrarily complex, leveraging standard functions, boolean operators, local variables, etc. The following assumptions are imposed on the UDF: 1. it must evaluate to 0 (tagging off) or 1 (tagging on) (the return value of the UDF is cast to a boolean and that is used to set the tags), 2. the allowed variables are t, x, y, and z.

tagging.GeometryRefinement.UDFRefiner.udf

type: String, required

String specifying the user defined function.

tagging.GeometryRefinement.UDFRefiner.box_lo

type: Vector<Real>, optional

List of the low corner values for a bounding box where the tagging will be active. By default the bounding box will span the entire domain.

tagging.GeometryRefinement.UDFRefiner.box_hi

type: Vector<Real>, optional

List of the high corner values for a bounding box where the tagging will be active. By default the bounding box will span the entire domain.

Section: tagging

Refinement using Cartesian boxes

Refinement using field error criteria

Refinement using geometry

Refinement using Q-Criterion

Static refinement