Eliot Feibush Plasma Princeton Physics Laboratory PICSciE Princeton Institute for Computational Science and Engineering Getting to Know Your Data Geometric range Numerical domain min max Histogram ID: 144142
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Slide1
Scientific Visualization with VisIt
Eliot Feibush
Plasma Princeton Physics Laboratory
PICSciE
Princeton Institute for Computational Science and EngineeringSlide2
Getting to Know Your Data
Geometric rangeNumerical domain (min, max) Histogram
Outliers Features Local / Global (steps)PresentationSlide3
Scientific
Visualization
Simulations generate dataAcquire data from experiments Biology
Chemistry Physics Engineering
Explore
Communicate
Based on computer graphics
points
lines
polygons, surface mesh
3D transformations
hidden surface removal
shading
lightingSlide4
Implementation
Visualization – VisIt GUI
VTK – Visualization ToolKit
Graphics Primitives
PixelsSlide5
VisIt Plot Types
PointsLinesVectorsContour lines & isosurfaces
Polygons, meshVolumeMoleculeSlide6
Designing a Visualization
I want a visualization of my climate model
.
Map your data to a plot type.
2-D/3-D Compute grid: scalar or vector
per point, per cell
Selection + Operators
Scientist
Vis GuySlide7
VisIt Can Read Data Files
Silo
Chombo
GTCM3DH5NimrodSAMRAI
S3DEnzo
ITAPS
XDMF
Exodus
FLASH
EnSight
VTK
NetCDF
CGNS
NASTRAN
TecPlot
Protein Databank (PDB)
Plot3D
GIS (ESRI Shapefile, DEM, many more)
Image formats
Database reader plug-ins can be developed for new formats
Variable types
Scalar
Vector
Tensor
Arrays
LabelMaterialSpeciesX,Y pairs
7
VTK is Internal FormatSlide8
https://wci.llnl.gov/codes/visit
- downloads just search for: visit visualization
Getting Data Into VisIt - document ( & your project )
Silo VTK - text or binaryVTK File Formats Slide9
Exercise 1
Open File ... Desktop
Visit Data Files scalar30000.Point3DAdd Pseudocolor Plot
density Attributes Point size
Visit Data FilesSlide10
Exercise 2
Open File poloidalplane.vtkAdd Mesh
mesh AttributesOpen File
flowV30000.vtkAdd VectorToroidal_Flow
Visit Data FilesSlide11
Exercise 3
Open File FLOW_equilibrium.xmdv
Add PseudocolorpsiAdd Pseudocolorb_vector_z
OperatorsTransformsTransformSlide12
Exercise 4
Open File interplines.vtkAdd Pseudocolor temperature
Add Label temperatureSlide13
Exercise 5
Open File strpts3d.vtkAdd Pseudocolordensity
VTK:STRUCTURED_POINTS3x2x2 = 12 points
SCALARS density doubleSlide14
Exercise 6
Open File cellblock.vtkAdd PseudocolorairVf
OperatorsSlicingSlice ToolsPlane
OperatorsSlicingThreeSlice ToolsPointSlide15
Three-Slice Operator on Adaptive MeshSlide16
Clip operator
The Clip operator clips 2D or 3D plots against planes or a sphere to remove sections of the plots
Use this operator when you want to see a cross section of a 3D plot, while still leaving the plot in 3D
Original plots
Plots clipped with 2 planes
Plots clipped with a sphere
16Slide17
Threshold operator
Removes cells whose value is not in the specified range
Use this operator when you only want to look at cells that have values within an interesting range
17Slide18
Molecular Dynamics Example
Draw points as spheres
Data Binning Operator shows particle densitySlide19
Exercise 7
Open File crotamine.pdf( GUESS Extension ! )Add Molecule
element attributesSlide20
Exercise 8
Open File base.vtkOpen File fluxtube.vtkControls
AnnotationOptionsRendering ...Slide21
Animation
Time step
Variable indexGeometry changeView Operators (slice, clip, etc.)
VisIt – Simple vtk time step to mpeg or Complex scripting to jpeg files QuickTime mov file
Python interpreter -
import myscript
[ edit, retry ]
reload(myscript)
Slide22
Movie Maker Program
Java – portable to Linux, Mac, Windows
Based on Sun’s javax.media package.
Reads all images in directory – JPEG, PNGImageMagick: mogrify -resize 100% *.jpeg
Creates QuickTime movie file - .MOV
Eliot’s pppl.gov website
w3.pppl.gov/~efeibushSlide23
Parallel Rendering Set Up
on della – runs engine_par as batch job .cshrc or .bashrc: module load openmpi/intel-11.1/1.4.3/64
on your desktop computer - ~/.visit/hosts/host_della.xml config file for client-server operationSlide24
Summary of Today’s Features
Plots + Attributes
Mesh Pseudocolor Points, Lines, Vectors, Polygons, Mesh – Color Tables
Contour Molecule VolumeData files
Point3D, xmdv VTK
Transform operators
Scale, Rotate, Translate
Selection operators
Clip
Box
Threshold
Slicing operators
Slice, ThreeSlice
Isosurface
Viewing
Lighting, Shadow, Depth-Cue
Annotation
Animation
Simple Time Slider movie
Python scripting
Parallel Rendering
JPEGs to QuickTime movieSlide25
Resources
www.princeton.edu/~efeibush Visualization with VisIt mini-course
https://wci.llnl.gov/codes/visit - downloads web search: visit visualization
https://trac.princeton.edu/vislab parallel rendering config file: host_della.xml visitusers.org
search ...Slide26
Contact
Eliot Feibush efeibush@pppl.gov 243-2695
www.princeton.edu/~efeibushSlide27Slide28
Supported mesh types
1D Curves
2D/3D meshes
RectilinearCurvilinearUnstructuredPoints
AMRMolecular
AMR
Unstructured
Rectilinear
Curve
Curvilinear
Points
Molecular