1. Unstructured Mesh Conventions for CF
Tom Gross NOAA Rich Signell USGS
Tom Gross & I have put together a presentation on Unstructured Mesh Conventions for CF
We drew straws, so I’m giving the talk. Tom & I are both coastal ocean modelers and we consider ourselves pretty geeky, but the first Java program I ever saw was written by my dad, so draw your own conclusions about programming prowess.
ADCIRC EC95 Grid, Luettich, UNC

2. Unstructured Mesh is Flexibile
Uniform Rectilinear Grid
Unstructured Mesh
Curvilinear Orthogonal Grid

3. UTG Flexibility

4. Explosive Growth in Unstructured Mesh Coastal Modeling
Yesterday (10 years ago)
2D Tides
2D Storm surge
Did not conserve mass locally
Today
Very high resolution 2D surge/inundation modeling
3D finite volume and discontinuous Galerkin methods conserve mass locally
New Coastal Models: FVCOM, ELCIRC, DHI Mike-3DFV, ADCIRC-DG, MOHID

5. ADCIRC
J. Westerink – Notre Dame
R. Luettich - UNC

7. General NOAA Oil Modeling Environment (GNOMETM)
Columbia River Estuary Spill (3 hrs after release)
C.J. Beegle-Krause, NOAA

8. FVCOM using LLNL’s “VisIt” Free software based on VTK w/Java,C++,Python interfaces
Chen & Cowles, UMASSD

9. Mesh Topology node = 6 nele = 5 nface = 3 lon(node) lat(node)1
node = 6
nele = 5
nface = 3
lon(node)
lat(node)
int ele(nele,nface) 3
[1 3 6]
[1 6 4] 4
[6 5 4]
[6 3 2] 6
[6 2 5] 5 2

10. Unstructured Mesh Properties
Horizontal coordinates are described by a 1D array of nodes: lon(node), lat(node)
Elements (e.g. triangles) are bounded by NFACE nodes (nface=3 for triangles)
Topology (Connectivity) is described by an incidence list: int ele(nele,nface)
Vertical coordinate described as in structured grid models. Sigma and other stretched grids are common.

12. QUODDY (3D-FEM) CDL

13. Simple Matlab Access nc=netcdf(‘fem.nc’); lon=nc{‘lon’}(:);
lat=nc{‘lat’}(:);
ele=nc{‘ele’}(:);
salt=nc{‘salt’}(1,1,:);
trisurf(ele,lon,lat,salt)
[t,b,jday,u]=CFtime(nc,’time’)
title([‘Salt ‘,datestr(jday(1))])

14. Post CF-discussion CDL

15. FVCOM 2D Grid Visualization Grid 1 (nodes) Surface elevation
(element centers)
Vertically-Averaged Velocity

16. FVCOM 2D Grid Visualization Grid 1 (nodes) Surface elevation
(element centers)
Vertically-Averaged Velocity

17. FVCOM (3D FVM) CDL

18. Staggering & Supermesh?
General Mesh
Nodes
Surface elevation
Element Centers
Velocity
Edge Centers
Flux (U●Salt), Geographic (levee, weir, B.C.)

19. Visualization Grid 2 FVCOM 3D Grid Visualization Grid 3 (nodes/levels)
Turbulence quantities
(nodes/layers)
Scalars (salinity, temperature, etc.)
(prism centers)
3-D Velocity

20. Consequences
Hyperslabs are only possible along time and depth dimensions
Extraction of lat/lon range of data requires determining points in polygon, and generation of subset topology
Interpolation, analysis and visualization routines are all different than for structured grid data

21. Issues Relationship to GridSpec
Relationship to Unidata Common Data Model
Meshes with multiple element types (e.g. triangles and quads)
High-order FEM methods
Edge, boundary and element properties

22. Existing Unstructured Mesh APIs
VTK: Kitware, “Light” data XML, “Heavy” binary
XDMF: ARL, “Light” data XML, “Heavy” HDF5
XMDF: ERDC, HDF5
CGNS: AIAA, HDF5
EXODUS II: Sandia, NetCDF
Of interest for the Data models that are used

23. TIN in ArcGIS

24. Unstructured Adaptive Grid Imperial College Ocean Model (ICOM)
Matthew Piggott (Imperial College, UK)
The ICOM folks are currently using VTK format, but are switching to CGNS format

26. Generic Visualization Tools via Standards: IDV
from Hawaii
from Woods Hole

27. FVCOM using LLNL’s “VisIt” Free software based on VTK w/Java,C++,Python interfaces
Chen & Cowles, UMASSD

28. Simple Matlab Access nc=netcdf(‘fem.nc’); lon=nc{‘lon’}(:);
lat=nc{‘lat’}(:);
ele=nc{‘ele’}(:);
salt=nc{‘salt’}(1,1,:);
trisurf(ele,lon,lat,salt)
[t,b,jday,u]=CFtime(nc,’time’)
title([‘Salt ‘,datestr(jday(1))])

29. Existing APIs: Sandia’s Exodus II
236 Pages!

30. Unstructured Grid Standards Workshop Oct. 16-18, Boulder Colorado
NOAA and Unidata sponsored workshop
NOAA Oil spill responders wish to unify operational model output so that automated particle tracking methods may be created to aid immediate response in emergency situations.
Goals:
Create an initial draft of CF metadata standards for describing irregular grids.
Create the community process to further the goal of unified output techniques for operational coastal ocean modeling.
Support the adoption of CF standards by the ocean modeling community

31. Unstructured Mesh Priorities
CF Conventions (define and adopt)
CF APIs (C in addition to Java)
CF Reference Applications (e.g. IDV, CDAT, VisIt module)
Remark that tools to work with the multiplicity of models is paramount -- cataloging and simulation metadata can come later

32. XMDF Element Types (3D)
Do we actually need to specify such elements in CF? Perhaps not, if all we are concerned with is extruded 2D descriptions and staggered grids.

33. XMDF (used by SMS)
Norm Jones, BYU
Cary Butler, ERDC

34. XMDF element types (1D)

35. XMDF Element Types (2D)

36. ERDC’s XMDF
104 pages