EB CHOMBO

This page describes additions to VisIt for visualizing Embedded Boundary(EB) CHOMBO data.

Overview

The following features have been added to VisIt to support EB CHOMBO.

  1. An EB CHOMBO database reader that supersedes the existing CHOMBO database reader.
  2. An glyphing operator that can glyph edges and nodes of the graph
  3. A channel generating operator that generates geometry for cut cells, filter covered cells, and generates shoreline
  4. A flood fill operator that takes data from a low resolution multilevel simulation dataset and injects it into a high resolution single level dataset.
  5. A selection operator that highlights a single cell.

These additions are described in depth in the following sections.

EB Chombo Database Reader

The new EB CHOMBO database reader supersedes the existing CHOMBO database reader and is EB aware. EB datasets contain the standard rectilinear mutilevel AMR hierarchy and an additional graph that describes the geometry of cut cells. CHOMBO simulation will need to write the data in the new format to take advantage of the new database reader.

In terms of VisIt's internal organization a database can provide a number of meshes, and variables associated with particular meshes. The mechanism used internally to identify the mesh that a given variable comes from is through a heuristic encoded in the variable name. The rectilinear mesh and it's data are accessed via the Mesh identifier while the graph and it's associated data are accessed via the Eb Graph identifier. The EB CHOMBO database can be used to access either of these as needed at the time a plot is created. This is demonstrated in figures 1 and 2.

The addition of the EB Graph mesh adds some complexity to selecting variables. In the old CHOMBO format variables could be defined on cell, face, or node centers, and VisIt assumed cell centering simplifying the UI. In the new EB CHOMBO format data defined on regular and covered cells can be cell, face or node centered. Additionally, the data from irregular cells can be node or cell centered on the EB Graph. Keep in mind that the terms cell centered and node centered are given with respect to a particular mesh. For example, a cell center variable in the rectilinear data is node centered on the EB Graph data while a cell centered variable in the EB Graph data is face centered in the rectilinear data.

In the new EB CHOMBO file format there are a number of mandatory variables defined. These will always be present and may be useful to visualize when debugging an EB CHOMBO code.

  1. Eb Graph/Node/volume fraction
  2. Eb Graph/Node/boundary area
  3. Eb Graph/Node/boundary normal
  4. Eb Graph/Node/VoF id
  5. Eb Graph/Node/VoF number
  6. Eb Graph/Cell/face area fraction
  7. Eb Graph/Cell/face dir
  8. Eb Graph/Cell/low VoF id
  9. Mesh/Cell/Mask

The new EB CHOMBO database reader currently supports the option of locating nodes in the EB Graph mesh either at the VoF centroid or the boundary centroid. This option is selected just prior to opening the file. To access the database attributes: 1) from the File Open dialog set the Open as type to EB CHOMBO and click on the Set default options button. The attributes dialog is shown in figure 3.

Three important plots that can be made after loading an EB CHOMBO file are Mesh, Pseudocolor, and Label plots. The Mesh plot allows one to visualize the edges of the Eb Graph. The Pseudocolor plot allows one to color graph edges by any of the variables. The Label plot allows one to print variable values on graph nodes or edges. An example of combining these three plots to render the EB graph colored by the face area fraction of the irregular cells, and label the graph edges with the value of face area fraction is shown in figure 4. These three plots provide basic, but essential, functionality which can optionally be augmented by further applying the new operators described below.

EB Graph Nodes Operator

The EB Graph Nodes operator is provided to glyph EB Graph nodes and edges. The generated node glyphs are by default scaled proportionally to the volume fraction of the corresponding VoF. The operator is added only after first adding a plot. The generated edge glyphs are scaled proportionally to the face area fraction of the corresponding face aperture. The operator has a number of options including an outline mode and the option to scale either or both node and edge glyphs by a constant factor. The latter option is useful for seeing graph nodes with zero volume fraction.

EB Channel Operator

Instructions

This will produce:

1) Shoreline
  a) Delete default plot that draws when a file is opened.

  b) i) Add->mesh->ebgraph
   ii)Operator->geometry->ebchannel
   iii)Expand arrow;Double-click ebchannel->shoreline->apply->dismiss
   iv)Draw 

2) Rectilinear mesh:

  c)  i) Add->mesh->mesh
   ii) draw

3) Edges connecting vof centroids passing through face centroids

  d) i)Add->pseudo-color->graph->(node/cell)->variable
  (node refers to vof centroid;cell refers to face centroid)
   ii) draw

4) Vofs Labelled by fraction-0 or other variable
  e) i) Add->label->ebgraph-node->variable
       (ebgraph appears twice; the second one has further menu)
   ii)Double-click on label and consider removing the 200 limit    
   iii) draw

EB Flood Fill Operator

Pathological Cases

Pathological case