Region#
A geometric or discrete subdomain of the full domain.
Regions are geometrical constructs used to define subsets of the computational domain in order to specify the problem to be solved, and the output desired. Regions may represents zero-, one-, two- or three-dimensional subsets of physical space. For a three-dimensional problem, the simulation domain will be a three-dimensional region bounded by a set of two-dimensional regions. If the simulation domain is N-dimensional, the boundary conditions must be specified over a set of regions are (N-1)-dimensional.
Warning
Surface files contain labeled triangulated face sets. The user is responsible for ensuring that the intersections with other surfaces in the problem, including the boundaries, are exact (i.e. that surface intersections are watertight where applicable), and that the surfaces are contained within the computational domain. If nodes in the surface fall outside the domain, the elements they define are ignored.
Examples of surface files are given in the Exodus II file format here.
Warning
Region names must NOT be repeated.
Example:
<ParameterList> <!-- parent list -->
<ParameterList name="regions">
<ParameterList name="TOP SECTION">
<ParameterList name="region: box">
<Parameter name="low coordinate" type="Array(double)" value="{2, 3, 5}"/>
<Parameter name="high coordinate" type="Array(double)" value="{4, 5, 8}"/>
</ParameterList>
</ParameterList>
<ParameterList name="MIDDLE SECTION">
<ParameterList name="region: box">
<Parameter name="low coordinate" type="Array(double)" value="{2, 3, 3}"/>
<Parameter name="high coordinate" type="Array(double)" value="{4, 5, 5}"/>
</ParameterList>
</ParameterList>
<ParameterList name="BOTTOM SECTION">
<ParameterList name="region: box">
<Parameter name="low coordinate" type="Array(double)" value="{2, 3, 0}"/>
<Parameter name="high coordinate" type="Array(double)" value="{4, 5, 3}"/>
</ParameterList>
</ParameterList>
<ParameterList name="INFLOW SURFACE">
<ParameterList name="region: labeled set">
<Parameter name="label" type="string" value="sideset_2"/>
<Parameter name="file" type="string" value="F_area_mesh.exo"/>
<Parameter name="format" type="string" value="Exodus II"/>
<Parameter name="entity" type="string" value="face"/>
</ParameterList>
</ParameterList>
<ParameterList name="OUTFLOW PLANE">
<ParameterList name="region: plane">
<Parameter name="point" type="Array(double)" value="{0.5, 0.5, 0.5}"/>
<Parameter name="normal" type="Array(double)" value="{0, 0, 1}"/>
</ParameterList>
</ParameterList>
<ParameterList name="BLOODY SAND">
<ParameterList name="region: color function">
<Parameter name="file" type="string" value="F_area_col.txt"/>
<Parameter name="value" type="int" value="25"/>
</ParameterList>
</ParameterList>
<ParameterList name="FLUX PLANE">
<ParameterList name="region: polygon">
<Parameter name="number of points" type="int" value="5"/>
<Parameter name="points" type="Array(double)" value="{-0.5, -0.5, -0.5,
0.5, -0.5, -0.5,
0.8, 0.0, 0.0,
0.5, 0.5, 0.5,
-0.5, 0.5, 0.5}"/>
</ParameterList>
</ParameterList>
</ParameterList>
</ParameterList>
In this example, TOP SECTION, MIDDLE SECTION and BOTTOM SECTION are three box-shaped volumetric regions. INFLOW SURFACE is a surface region defined in an Exodus II-formatted labeled set file and OUTFLOW PLANE is a planar region. BLOODY SAND is a volumetric region defined by the value 25 in color function file.
All#
A region consisting of all entities on a mesh.
No parameters required.
[region-all-spec]
“empty”
[bool]True This is simply here to avoid issues with empty lists.
Example:
<ParameterList name="domain"> <!-- parent list -->
<ParameterList name="region: all">
</ParameterList>
</ParameterList>
Box#
RegionBox: a rectangular region in space, defined by two corners
List region: box defines a region bounded by coordinate-aligned planes. Boxes are allowed to be of zero thickness in only one direction in which case they are equivalent to planes.
region-box-spec
“low coordinate”
[Array(double)]Location of the boundary point with the lowest coordinates.“high coordinate”
[Array(double)]Location of the boundary points with the highest coordinates.
Example:
<ParameterList name="WELL"> <!-- parent list -->
<ParameterList name="region: box">
<Parameter name="low coordinate" type="Array(double)" value="{-5.0,-5.0, -5.0}"/>
<Parameter name="high coordinate" type="Array(double)" value="{5.0, 5.0, 5.0}"/>
</ParameterList>
</ParameterList>
Plane#
RegionPlane: A planar (infinite) region in space, defined by a point and a normal.
List region: plane defines a plane using a point lying on the plane and normal to the plane.
region-plane-spec
“normal”
[Array(double)]Normal to the plane.“point”
[Array(double)]Point in space.
Example:
<ParameterList name="TOP_SECTION"> <!-- parent list -->
<ParameterList name="region: plane">
<Parameter name="point" type="Array(double)" value="{2, 3, 5}"/>
<Parameter name="normal" type="Array(double)" value="{1, 1, 0}"/>
<ParameterList name="expert parameters">
<Parameter name="tolerance" type="double" value="1.0e-05"/>
</ParameterList>
</ParameterList>
</ParameterList>
Labeled Set#
RegionLabeledSet: A region defined by a set of mesh entities in a mesh file
The list region: labeled set defines a named set of mesh entities existing in an input mesh file. This is the same file that contains the computational mesh. The name of the entity set is given by label. For example, a mesh file in the Exodus II format can be processed to tag cells, faces and/or nodes with specific labels, using a variety of external tools. Regions based on such sets are assigned a user-defined label for Amanzi, which may or may not correspond to the original label in the exodus file. Note that the file used to express this labeled set may be in any Amanzi-supported mesh format (the mesh format is specified in the parameters for this option). The entity parameter may be necessary to specify a unique set. For example, an Exodus file requires cell, face or node as well as a label (which is an integer). The resulting region will have the dimensionality associated with the entities in the indicated set.
region-labeled-set-spec
“label”
[string]Set per label defined in the mesh file.“file”
[string]File name.“format”
[string]Currently, we only support mesh files in the “Exodus II” format.“entity”
[string]Type of the mesh object (cell, face, etc).
Example:
<ParameterList name="AQUIFER">
<ParameterList name="region: labeled set">
<Parameter name="entity" type="string" value="cell"/>
<Parameter name="file" type="string" value="porflow4_4.exo"/>
<Parameter name="format" type="string" value="Exodus II"/>
<Parameter name="label" type="string" value="1"/>
</ParameterList>
</ParameterList>
Function Color#
RegionFunctionColor: A region defined by the value of an indicator function in a file.
The list region: color function defines a region based a specified integer color, value, in a structured color function file, file. The format of the color function file is given below in the “Tabulated function file format” section. As shown in the file, the color values may be specified at the nodes or cells of the color function grid. A computational cell is assigned the ‘color’ of the data grid cell containing its cell centroid (cell-based colors) or the data grid nearest its cell-centroid (node-based colors). Computational cells sets are then built from all cells with the specified color Value.
In order to avoid, gaps and overlaps in specifying materials, it is strongly recommended that regions be defined using a single color function file.
region-color-function-spec
“file”
[string]File name containing color function.“value”
[int]Color that defines the set in the tabulated function file.
Example:
<ParameterList name="SOIL_TOP">
<ParameterList name="region: color function">
<Parameter name="file" type="string" value="geology_resamp_2D.tf3"/>
<Parameter name="value" type="int" value="1"/>
</ParameterList>
</ParameterList>
Point#
RegionPoint: a point in space.
List region: point defines a point in space. This region consists of cells containing this point.
region-point-spec
“coordinate”
[Array(double)]Location of point in space.
Example:
<ParameterList name="DOWN_WIND150"> <!-- parent list defining the name -->
<ParameterList name="region: point">
<Parameter name="coordinate" type="Array(double)" value="{-150.0, 0.0, 0.0}"/>
</ParameterList>
</ParameterList>
Logical#
RegionLogical: A region defined by a logical operation on one or two other regions
The list region: logical defines logical operations on regions allow for more advanced region definitions. At this time the logical region allows for logical operations on a list of regions. union and intersection are self-evident. In the case of subtraction, subtraction is performed from the first region in the list. The complement is a special case in that it is the only case that operates on single region, and returns the complement to it within the domain ENTIRE_DOMAIN. Currently, multi-region booleans are not supported in the same expression.
region-logical-spec
“operation”
[string]defines operation on the list of regions. One of: “union”, “intersect”, “subtract”, “complement”“regions”
[Array(string)]specifies the list of involved regions.
Example:
<ParameterList name="LOWER_LAYERs">
<ParameterList name="region: logical">
<Parameter name="operation" type="string" value="union"/>
<Parameter name="regions" type="Array(string)" value="{Middle1, Middle2, Bottom}"/>
</ParameterList>
</ParameterList>
Polygon#
RegionPolygon: A closed polygonal segment of a plane.
The list region: polygon defines a polygonal region on which mesh faces and nodes can be queried. NOTE that one cannot ask for cells in a polygonal surface region. In 2D, the polygonal region is a line and is specified by 2 points. In 3D, the polygonal region is specified by an arbitrary number of points. In both cases the point coordinates are given as a linear array. The polygon can be non-convex.
This provides a set of faces with a normal for computing flux.
The polygonal surface region can be queried for a normal. In 2D, the normal is defined as [Vy,-Vx] where [Vx,Vy] is the vector from point 1 to point 2. In 3D, the normal of the polygon is defined by the order in which points are specified.
[region-polygon-spec]
“number of points”
[int]Number of polygon points.“points”
[Array(double)]Point coordinates in a linear array.
Example:
<ParameterList name="XY_PENTAGON">
<ParameterList name="region: polygon">
<Parameter name="number of points" type="int" value="5"/>
<Parameter name="points" type="Array(double)" value="{-0.5, -0.5, -0.5,
0.5, -0.5, -0.5,
0.8, 0.0, 0.0,
0.5, 0.5, 0.5,
-0.5, 0.5, 0.5}"/>
<ParameterList name="expert parameters">
<Parameter name="tolerance" type="double" value="1.0e-3"/>
</ParameterList>
</ParameterList>
</ParameterList>
Enumerated#
RegionEnumerated: A region enumerated as a list of IDs.
List region: enumerated set defines a set of mesh entities via the list of input global ids. Note that global ids are not defined correctly when parallel mesh is created on a fly.
region-enumerated-spec
“entity”
[string]Type of the mesh object. One of: “cell”, “face”, “edge”, “node”“entity gids”
[Array(int)]List of the global IDs of the entities.
Example:
<ParameterList name="WELL"> <!-- parent list -->
<ParameterList name="region: enumerated set">
<Parameter name="entity" type="string" value="face"/>
<Parameter name="entity gids" type="Array(int)" value="{1, 12, 23, 34}"/>
</ParameterList>
</ParameterList>
Boundary#
RegionBoundary: A region consisting of all entities on the domain boundary
List region: boundary defines a set of all boundary faces. Using this definition, faces located on the domain boundary are extracted.
region-boundary-spec
“entity”
[string]Type of the mesh object. Unclear whether this is used or can be other things than “face”?
Example:
<ParameterList name="DOMAIN_BOUNDARY"> <!-- parent list names the region -->
<ParameterList name="region: boundary">
<Parameter name="entity" type="string" value="face"/>
</ParameterList>
</ParameterList>
Box Volume Fractions#
RegionBoxVolumeFractions: A rectangular region in space, defined by two corner points and normals to sides.
List region: box volume fraction defines a region bounded by a box not aligned with coordinate axes. Boxes are allowed to be of zero thickness in only one direction in which case they are equivalent to rectangles on a plane or segments on a line.
region-box-volume-fractions-spec
“corner coordinate”
[Array(double)]Location of one box corner.“opposite corner coordinate”
[Array(double)]Location of the opposite box corner.“normals”
[Array(double)]Normals to sides in a linear array. Default is columns of the identity matrix. The normals may be scaled arbitrarily but must be orthogonal to one another and form the right coordinate frame.
Example:
<ParameterList name="BASIN"> <!-- parent list -->
<ParameterList name="region: box volume fractions">
<Parameter name="corner coordinate" type="Array(double)" value="{-1.0,-1.0, 1.0}"/>
<Parameter name="opposite corner coordinate" type="Array(double)" value="{1.0, 1.0, 1.0}"/>
<Parameter name="normals" type="Array(double)" value="{1.0, 0.0, 0.0
0.0, 2.0, 0.0,
0.0, 0.0, 3.0}"/>
</ParameterList>
</ParameterList>
This example defines a degenerate box, a square on a surface z=1.
Line Segment#
RegionLineSegment: A line segment, defined by two points in space.
List region: line segment desribes a region defined by a line segment. This region is a set of cells which intersect with a line segment. The line segment is allowed to intersect with one or more cells. Zero length line segments are allowed. The line segment is defined by its ends points.
region-line-segment-spec
“end coordinate”
[Array(double)]Location of one end of a line segment.“opposite end coordinate”
[Array(double)]Location of the opposite end of a line segment.
Example:
<ParameterList name="WELL"> <!-- parent list -->
<ParameterList name="region: line segment">
<Parameter name="end coordinate" type="Array(double)" value="{497542.44, 5393755.77, 0.0}"/>
<Parameter name="opposite end coordinate" type="Array(double)" value="{497542.44, 5393755.77, 100.0}"/>
</ParameterList>
</ParameterList>