Grid Project:  Arctic Intermediate Scale

Grid Team Member: Terry Miller
Version: Intermediate scale
Data Source: LiDAR and polygon data from Chandana and Arctic program
Delivered To: Scott Painter, Rao Garimella, Ethan Coon
Date: December 2013 to present

Version History

Version Scope Finished Nodes Cells
Proto Full 2 Lobster Prism with convex polygons pending

Proto Full Lobster Prism with Phedra numbers Sep 22 2015 59,532 113,184
Proto 2Poly Proto Prism of 2 Polys, 3 materials Sep 20 2015 270 396
V03.2 Lobster Quad to 4 Tri Tall Jan 10 2014 59,532 113,184
V03.1 Lobster Quad to 4 Tri Jan 10 2014 43,747 82,944
V02.2 Lobster Quads Tall Jan 10 2014 34,188 37,859
V02.1 Lobster Quads Fixed Jan 10 2014 25,123 27,744
V01 Lobster Quads Proto Jan 7 2014 25,414 28,608

Project Overview

This project is for Arctic Intermediate Scale Modeling. These meshes are developed based on work for fine-scale modeling of thermal hydrology in ice-wedge polygon landscapes. The conceptual design for these models are the same as the fine-scale models and are based on observations and data collected for the Arctic project.

The top surfaces of these models are polygonal tundra shapes and elevations derived from LIDAR data sets.
Each polygon is processed with offsets calculated to represent the half-trough, rim, and center. Each poly ring is converted to quad cells with thickness equal to the defined offsets. The center is filled with cell edges at rim and connecting to a center point. Polygon cells are merged to create a top surface layer. The surface elevations are interpolated from the Lidar data on to each cell vertice point.
The subsurface layers are derived from the top surface to selected depths. These surfaces are stacked and filled with cell volumes with thickness defined by the stacked layers. The layer thickness for each material are based on descriptions and observations of core data. The material layers represented are
      moss (part of the active layer)
      upper and lower organic
      upper, lower, and deep mineral

The methods and data used for these intermediate-scale meshes were developed during design and meshing for the Arctic Fine-scale work. See fine-scale project pages at

Polyhedral Meshing

These start with the Arctic polygon meshes used for modeling, but explore stategies to represent the meshes as column cells with unique polyhedral id's. Rao Garimella using a prototype code to coalesce elements of a particular type (material ID, same polyhedral ID, etc) to create Intermediate scale polygonal meshes for modeling.

Images of Polyhedral Mesh Prototypes

Prototype Lobster Prism with convex Polygons, no rings

The concave polygons ## 8, 45, and 56 got divided each into 2 polygons such that polygon #8 became ## 8 and 74, #45 => ## 45 and 75, #56 => #56 and 76.

Subset Lobster with 4 convex polygons: ## 8, 74, 6, 9

Local: /scratch/sft2/lucia/grid_gen/arctic/lobster/subset01 

  Download Archive lobster_convex_proto01.tar.gz    ( 0.18 M )  

Prototype Lobster Prism with Polyhedral Id's

Prototype Prism with 2 Polygons

Proto Mesh types that did not work:

Proto hex with 2 polygons, quad elements converted so shared center have duplicate nodes
This enables the quad and hex elements to have a unique node index rather than repeating.
Local: /scratch/sft/tam/grid_gen/arctic/intermediate_scale/proto_polyhedral/quad2_to_hex/output_files

Proto Hex 1 with Single Node at degen center.
The hex indices have repeated numbers rather than unique numbers from duplicate nodes.
Local: /scratch/sft/tam/grid_gen/arctic/intermediate_scale/proto_polyhedral/quad1_to_hex/output_files

Lobster Mesh and Output Files

Files are available on local servers or you can download the compressed ".tar.gz" archive. See mesh details and locations below.

Mesh Overview and Images

View Gallery of All Mesh Images

Local: /scratch/sft/tam/grid_gen/arctic/intermediate_scale/mesh_hex_lobster/images

Polygon Overview and Images

View Gallery of All Polygon Images
Local: /scratch/sft/tam/grid_gen/arctic/intermediate_scale/polys_intermediate/images

V2 Mesh (Lobster Quads Stacked into Hex) : 259 nodes and 289 quad cells per layer
V2 Hex
This mesh starts with polygons converted to quad cells the same thickness as the polygon offsets. The center polygon is made up of degenerate quad cells which converge at a center point. This strategy has the fewest number of cells and nodes. Two sets of mesh files are written (multi-material and single) in formats: AVS, GMV, and Exodus II.

V2.1 Hex Mesh:
Download Archive V02.1_stack_quad.tar.gz    ( 6.2 MB )

V2.2 Tall Hex Mesh:
Download Archive V02.2_stack_quad_tall.tar.gz    ( 7.6 MB )

V3 Mesh (Lobster Triangles Stacked into Prism) : 451 nodes and 864 triangle cells per layer
V3 Prism
This mesh starts with polygons converted to quad cells the same thickness as the polygon offsets. Each quad cell is converted to 4 triangles with added center point. The degenerate quad cells making up the center piece are converted to triangles sharing a vertice at the center point. Two sets of mesh files are written (multi-material and single) in formats: AVS, GMV, and Exodus II.

V3.1 Prism Mesh:
Download Archive V03.1_stack_tri.tar.gz    ( 14 MB )

V3.2 Tall Hex Mesh:
Download Archive V03.2_stack_tri_tall.tar.gz    ( 17 MB )

The following definitions apply to all the meshes:

Polygons from Site C called extended lobster (adds 56):
1  2  3  4   5   6   7   8   9   10  11  12  13  14  15  16  17  18
6, 8, 9, 19, 21, 25, 27, 29, 31, 34, 35, 36, 37, 39, 45, 47, 50, 56

Materials for all grids:
1 Moss (top)
2 Upper Organic
3 Upper Mineral
4 Lower Organic
5 Lower Mineral
6 Deep Mineral

Boundary Side Sets (Facesets) for all grids:
Top     (num_side_ss2)
Bottom  (num_side_ss1)
Side east right   (num_side_ss3)
Side north back   (num_side_ss4)
Side west left    (num_side_ss5)
Side south front  (num_side_ss6)

Mesh Vertical Layers for all:
1       top at Lidar elevations
1       .02 Thick       2  cells x .01
2       .18 Thick       9  cells x .02
3       .18 Thick       9  cells x .02
4       .12 Thick       6  cells x .02
5       .50 Thick       20 cells x .025

Bottom layers for short:
6       variable thickness with 50 cells near .09
6       bottom at -1.

Bottom layers for tall:
6       5.  Thick       50 cells x  .1
6       4.  Thick       10 cells x  .4
6       10. Thick       10 cells x 1.0
6       variable thickness with 15 cells near 1.9
6       bottom at -45.

Exodus Facesets:
1 Bottom  (num_side_ss1) 
2 Top     (num_side_ss2) 
3 Side east right   (num_side_ss3) 
4 Side north back   (num_side_ss4) 
5 Side west left    (num_side_ss5) 
6 Side south front  (num_side_ss6) 

Mesh information can be found in mesh directory in README.txt, RUNS, *.out
Mesh Files are written in formats; Exodus II (.exo), AVS (.inp), and GMV (.gmv)
Final Top surface for deriving layers: poly_top_surf.inp poly_top_surf.gmv
Final Mesh with multi-materials: mesh_fsets.exo, mesh_fsets.gmv, mesh_fsets.inp
Final Mesh with single material: mesh_fsets_1mat.exo, mesh_fsets_1mat.gmv, mesh_fsets_1mat.inp

Input Data

Area C Polygons and Elevations

The input data is organized into a set of files that contain data extracted from lidar data. The data set is canonized by Chandana Gangodagamage and organized into a set of input files. These input files include ground surface elevations, polygon shape coordinates, and widths for rims and troughs. Thank you to Craig Tweedie, University of Texas, El Paso, for providing the Lidar data for use in these projects.

Area C

NGEE extensive site-C Lidar Elevations with Polygon Id's
ASCII AVS file with elevation for each x,y location:

2D polys
Lobster Polygons as Quad Cells with Polygon Id's
ASCII AVS file with half-trough and rim widths for each polygon:


Input Data Processing Prepare elevation data and polygon offset data:
/scratch/sft/tam/grid_gen/arctic/intermediate_scale/ input_poly_data/README.txt

Polygon Processing Create offsets and connect into poly surface:
/scratch/sft/tam/grid_gen/arctic/intermediate_scale/ polys_intermediate/RUNS

Mesh Generation Stack poly surface into layered volumes:
/scratch/sft/tam/grid_gen/arctic/intermediate_scale/ mesh_hex_lobster/Methods.txt

Grid Team Contacts

Carl Gable <gable -at- lanl -dot- gov> 505-665-3533
Terry Miller <tamiller -at- lanl -dot- gov> 505-667-8009
Lucia Short <lucia -at- lanl -dot- gov> 505-665-7957