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 Cartesian boxes

CartBoxRefinement allows refining boxes (aligned with the principal axes).

Example:

tagging.labels = static
tagging.static.type = CartBoxRefinement
tagging.static.static_refinement_def = static_box.txt

tagging.CartBoxRefinement.static_refinement_def

type: String, required

The text file that contains a list of bounding boxes used to perform refinement at various levels.

Refinement using field error criteria

Example:

tagging.f1.type = FieldRefinement
tagging.f1.field_name = density
tagging.f1.grad_error = 0.1. 0.1 0.1
tagging.f1.box_lo = 10.0 10.0 10.0
tagging.f1.box_hi = 20.0 20.0 20.0

tagging.FieldRefinement.field_name

type: String, required

The name of the field used to tag cells

tagging.FieldRefinement.field_error

type: Vector<Real>, optional

List of field error values at each level. The user must specify a value for each level desired.

tagging.FieldRefinement.grad_error

type: Vector<Real>, optional

List of gradient error values at each level. The user must specify a value for each level desired.

tagging.FieldRefinement.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.FieldRefinement.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.

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, and 2. cylinder – refines the region inside a cylindrical block.

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

This example defines two different refinement definitions acting on level 0 and 1 respectively. The refinement at level 0 (g1) contains two box regions, whereas the refinement at level 1 (g2) only contains one cylinder definition.

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 Q-Criterion

Example:

tagging.qc1.type = QCriterionRefinement
tagging.qc1.nondim = false
tagging.qc1.values = 10.0 20.0 20.0

tagging.QCriterionRefinement.nondim

type: Boolean, optional, default = true

Boolean determining if the dimensional or non-dimensional form of Q-criterion should be used. Dimensional version may require modifying values depending on physical scales. For the non-dimensional form positive thresholds indicate regions where the rotational strength is larger than the shear rate strength. A threshold of unity indicates that the rotational strength is equal to the background shear strength.

tagging.QCriterionRefinement.values

type: Vector<Real>, optional

List of Q-criterion values at each level. If the absolute value of Q-criterion exceeds this value the cell is tagged for refinement. The user must specify a value for each level desired.

Static refinement

This section is for controlling the static mesh refinement of the grid. This is done a bit differently than the tagging criteria above in that an external file species the refinement regions.

tagging.static_refinement

type: Boolean, optional, default = false

Static refinement with Cartesian-aligned bounding boxes.

tagging.static_refinement_def

type: String

Static refinement with Cartesian-aligned bounding boxes input file name.