Scientific Visualization with VisIt - PowerPoint Presentation

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

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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 VectorToroidal_Flow

Visit Data FilesSlide11

Exercise 3

Open File FLOW_equilibrium.xmdv

Add PseudocolorpsiAdd Pseudocolorb_vector_z

OperatorsTransformsTransformSlide12

Exercise 4

Open File interplines.vtkAdd Pseudocolor temperature

Add Label temperatureSlide13

Exercise 5

Open File strpts3d.vtkAdd Pseudocolordensity

VTK:STRUCTURED_POINTS3x2x2 = 12 points

SCALARS density doubleSlide14

Exercise 6

Open File cellblock.vtkAdd PseudocolorairVf

OperatorsSlicingSlice ToolsPlane

OperatorsSlicingThreeSlice ToolsPointSlide15

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

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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

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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

AnnotationOptionsRendering ...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/~efeibushSlide27
Slide28

Supported mesh types

1D Curves

2D/3D meshes

RectilinearCurvilinearUnstructuredPoints

AMRMolecular

AMR

Unstructured

Rectilinear

Curve

Curvilinear

Points

Molecular