ElVis Developmentsfor Simulation and

Analysis Programs

Tarun PondicherrySummer 2006 Science Ed High School Intern

Eliot Feibush, Mentor8/16/2006

MSE – Motional Stark Effect

Local Magnetic Field Measurements by Motional Stark Splitting – JET

Determine direction of magnetic field lines inside plasma

MSE diagnostic measures current profiles in plasma

Source: JET Website - jet.efda.org

MSE Simulation

Simulate MSE diagnostic for ITER design Source code from JET

Required GHOST graphics package – impractical to distribute

Modified by Tina Ludescher to output results to netCDF file instead of using GHOST Separated Simulation from Visualization

Display graphs of netCDF variables in ElVis

ElVis Developmentsfor Simulation and

Analysis Programs

Tarun PondicherrySummer 2006 Science Ed High School Intern

Eliot Feibush, Mentor8/16/2006

OverviewBackground

My Topics:1. MSE (Motional Stark Effect)2. Monitoring Simulations3. Interactive Techniques

Demo

Background ElVis – Java based

Visualization Software which graphs outputs of scientific experiments and simulations

Accepts input from a variety of sources including Data Files, Sockets, Simulations, etc.

Graphs 1D and 2D data in several forms (Animated, Surface, Contour, etc.)

Reads variables from netCDF Files; User composes graphs

NetCDF File Format

File format and interface for scientific data storage Machine Independent and accessible through URL Consist of a collection of dimensions, variables and

attributes Variable

Single Value Array of one or more Dimensions

Variables and Dimensions can have attributes specifying units, alternate names or other information

Unidata provides NetCDF API’s in C, Java and Fortran

NetCDF File Elements Global Attributes … Dimensions

Attributes …

… Coordinate Variables [dim name]

Attributes …

… Variables (definition) [dim0 x dim1 x …]

Attributes …

… Variables (data) …

convention = elvis elvis_template = mytemplate.xml time = 50

long_name = time_of_capture unit = seconds

x_coordinate = 200 time [time]

sine [x_coordinate X time] amplitude = 1

time = {0,2,6,17,…} sine = {-1, -0.5, 0, 0.5,…}

{-1, -0.75, -0.5, -0.25,…} …

1. ElVis Enhancements for netCDF Data

MotivationMSE display requirementsGeneralize monitoring of Fusion Simulations

& Analysis programs

My GoalsImprove netCDF Panel in ElVis Insert in first cell of GraphWindow (previously separate frame,

confusing when many files open) List all variables (previously listed only 1D and 2D) Read files with large number of variables (TRANSP)

Add New Capabilities to ElVis Select 2D subset of 3D+ variable Transpose 2D variable Save/Load GW presentation templates Progress pop-up Monitor output files from long-running programs

Data Selection Allows variables with more than 2 dimensions to

be plotted in ElVis Users specify a 2D “slice” by selecting the index

for the fixed dimensions

Result is ordinary 2D data Can be presented as Animated, Surface,

Contour or Multiplot 2D slices can be plotted with normal 2D

variables, other 2D slices or a combination of both – multiple 2D variables

Data Selection and Display

2D Presentation Styles

Allow ElVis to convert between all types of 2D plots (Animated, f(x,i), Contour, Surface)

Original 2D data stored in memory

When presentation changes, data is read from memory to create the desired plot

Added multi-plot – requested by MSE physicists

Logarithmic Surface Plots

Applied logarithmic scaling functions to Surface plots

(Log functions developed by Steve Krenzel)

All axes (X, Y, Z) can be independently scaled as linear or logarithmic

Transpose Data Transposes data within the 2D array prior to plotting Once transposed, data remains that way for any

presentation option Animated swaps X Axis and Index Contour swaps X and Y Surface swaps X and Z Multiplot swaps X Axis and Index

Data Interpolation

Allows Variables of Different Lengths to be plotted against each other

Adds or removes x values to match number f(x) values

Values added created by linear interpolation Values removed by periodic sampling Works for both 1D and 2D data Performed automatically when dataset sizes

vary

Data Interpolation Example

x 0 1 2 3 4 5 6 7 8 9 10

f(x) 10 8 6 4 2 0

x 0 2 4 6 8 10

f(x) 10 8 6 4 2 0

x 0 2 4 6 8 10

f(x) 5 10 15 20 25 30 35 45 50 55 60

x 0 1 2 3 4 5 6 7 8 9 10

f(x) 5 10 15 20 25 30 35 45 50 55 60

Graph Window Templates

Suggested by Steve Scott for MSE Allow ElVis to show NetCDF Files with a

user specified view

Enables author of the data to format graphs (without programming!) for collaborators to view over the Internet

Graph Window Templates

Stored in XML under the user home directory ElVis automatically finds templates in 3 ways:

.cdft file with the same name as the NetCDF File in the same directory

elvis_template attribute specified in NetCDF File default template stored in settings.props in user home

Users can choose a different template from the drop down in the template panel

ElVis stores the most recently used template as the default

2. NetCDF File Monitoring

Allows Elvis to monitor simulations which periodically update a NetCDF File

Polls the file on the server, checks for dimension length change; user specifies rate

Starts and stops automatically if “running” attribute set to true or false in the NetCDF File

When the file is updated, ElVis loads new file and replots with the current template

File Monitoring – Solution

Generalized way to monitor simulations Overcomes the need for custom

programming for monitoring Can be combined with templates to

compose the graphs without programming

Fusion Simulation Projects

3. Interactive Techniques Resize graphs when frame is resized - warm-up exercise

Legend display options Interactive PositioningGraph width

Dataset editorEdit set namesColor, style, thicknessPoints, Lines

Access Greek Letters in Unicode Font

Save/Load to ElVis convention netCDF file

Unicode Font Character Chooser Unicode –16 bit font overcomes limit

of ASCII’s 8 bits Enables storing 1000s of characters

organized by function, e.g. Greek Letters, Math Symbols

Java uses Unicode Fonts

Developed Character Chooser Displays selected section in a grid Displays recently selected

characters at the bottom User clicks on letter to add it to label

Summary – How I spent my summer vacation

ElVis enhancements for MSE display requirements

Generalized solution for monitoring simulations

Interactive techniques

Acknowledgements

Eliot Feibush Jill Foley for MSE background info James Morgan, Andrew Post-Zwicker and

the PPPL Science Education Department Princeton Plasma Physics Lab

Demo

ElVis http://w3.pppl.gov/elvis/