Grid Project:   Barrow Ice Wedge Polygon 40 V3 (fine scale)

Purpose of Project

These meshes were developed in support of the Arctic Next Generation Ecosystem Experiment (NGEE-Arctic) Project and LANL Laboratory Directed project LDRD20120068DR. These two projects share a need for high quality computational meshes for use in fine-scale modeling of thermal hydrology in ice-wedge polygon landscapes.

Version 3 is a modification of the Version 2 mesh which adds a third mineral layer between upper and lower organic layers. This mesh design will be used for the version 01 with multiple polygons. This mesh is 3D based on single polygon #40 generated using LiDAR data set (area C). This mesh follows the criteria listed in the Mesh Input Parameters below. The mesh has 1 moss layer, 2 organic layers, and 3 mineral layers with a flat bottom. The Ice Wedge starts at the top of the mineral layers and is aprox 2.8 meters long. The convention of layer order numbering is from top to bottom. Two Exodus II mesh files are written, one multi-material with ice, and one single material.

This version has a correction to file interpolate_icewedge.lgi and now ensures that ice material does not replace any elements in layers 1-4. The layers above ice have a constant thickness throughout the mesh. The bottom layers (mineral 5 and 6) have variable thickness where ice material replaces mineral material.

Summary of email from Joel Rowland referring to the core data the ORNL sent:

There not that many cores and almost all terminate at about 30 cm or less. Observing the ones that have a sequence of an upper organic layer (includes "moss" or live vegation), a mineral layer, then a deeper organic layer.

Based 6 cores the average thickness of the layers were: 11 cm, 11 cm, and 7.5 (biased by one core with a thick lower organic layer). Using relative thicknesses, set the upper organic and the upper mineral to be equal thicknesses and set the lower organic at half to 3/4 the thicknesses of these layers.

Based on the limited descriptions I don't think the properties of the lower organic layer is identical to the upper Organic layer but it is distinctly different from the intervening Mineral layer.

  -----------------
  1 moss           .02 (2 x .01)
  2 upper organic  .18 (9 x .02)  changed from .20 (10 x .02)
  3 upper mineral  .18 (9 x .02)  changed from .20 (10 x .02)
  4 lower organic  .12 (6 x .02)  changed from .08 ( 4 x .02)
  5 lower mineral  .5 (20 x .025)
  6 deep mineral   ~4.8 (50 x .09)
  7 ice            ~2.8 
  -----------------

Full Stacked Mesh with Ice Wedge 6 material layers plus ice material	Full Stacked Mesh with Ice Wedge Cut to show internal materials
Mesh and Ice Wedge with moss and organic layers removed	Ice Wedge

Mesh Input Parameters V3

General Description

Same as V02 using Polygon #40 and following layer definitions with added organic layer :

• Layer 1 (top) is the live organic layer and should be 2 cm thick with 2 cells.
• Add a third organic layer such that all combined are still 48 cm thick with 24 cells (2cm each).
• Top organic and mineral layer are the same. Thickness is 18 cm with 9 cells.
• Lowest organic layer is about 3/4 the thickness of upper 2 layers. Set thickness to 12 cm with 6 cells.
• The bottom Materials 5 and 6 are both mineral soils with higher resolution at the top of the mineral soil.
• The domain bottom should be flat at Z = -1.

Material Ice Wedge

We want the top of the ice wedge to be at 50 cm depth (corresponds to the top of the inorganic layer).

Top of wedge starts at top of mineral layer (replaces cells only in materials 5 and 6)

Top wedge width (distance from polygon) is aprox 1.2

Depth from top of ice to tip is aprox 2.8

Outside Boundaries (Exodus side sets)

The side sets defined are top, bottom, and sides (corresponding to the 4 sectors within 45 degrees of each direction).

Output Mesh Description

Output is a stacked prism mesh written as two Exodus files; a single material mesh and a multi-material Mesh with 7 materials (6 layers plus the Ice Wedge). Files are written in formats; Exodus II (.exo), AVS (.inp), and GMV (.gmv)
Final Mesh files: 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

Mesh Element Type:             prism
Mesh Software Used: LaGriT, ExodusII

Total nodes:       311273       
Total elements:    602112     
Total Volume:      0.2273467E+04      

from file write_exo.out.txt:
Mesh Extents (Meters):
        MIN              MAX             DIFFERENCE    
 x    4.634709930E+01  7.183999634E+01 2.549289703E+01     
 y    1.062200012E+02  1.326065216E+02 2.638652039E+01     
 z   -1.000000000E+00  4.992260933E+00 5.992260933E+00     

from file write_exo.out.txt:
SUMMARY VOLUME/AREA METERS of ELEMENT COLORS (BLOCKS) 
Color    Num. Elements   Volume          Fractional Volume                    
    1       12544      0.7936425E+01     0.003490890                        
    2       56448      0.7142782E+02     0.031418013                        
    3       56448      0.7142801E+02     0.031418096                        
    4       37632      0.4761855E+02     0.020945342                        
    5       95524      0.1464469E+03     0.064415680                        
    6      293616      0.1745817E+04     0.767909504                        
    7/30   49900       0.1827924E+03     0.080402475        

from file stack_full_poly.out.txt:
SUMMARY ELEVATIONS at LAYER TOPS (METERS)
        MIN          MAX       DIFF MAX below (thickness)   
    1 4.504300117  4.992260933   .02
    2 4.484300117  4.972260933   .18
    3 4.304300117  4.792260933   .18
    4 4.124300117  4.612260933   .12
    5 4.004300117  4.492260933   .50
    6 3.504300117  3.992260933  4.99 
      (Bottom is flat at -1.0)

Mesh Layer Definitions (meters)

ID Layer Name Layer Thick Layer Vertical Cells Layer Volume Min Top Elevation Max Top Elevation 1 moss(top) 0.02 2 x .01 7.936425 4.50 4.99 2 upper organic 0.18 9 x .02 79.36425 4.48 4.97 3 upper mineral 0.18 9 x .02 71.42801 4.30 4.79 4 lower organic 0.12 6 x .02 47.61855 4.12 4.61 5 lower mineral 0.50 20 x .025 146.4469 4.00 4.49 6 deep mineral 2.2 - 4.8 50 x .09 1745.817 3.50 3.99 7/30 ice 0.00 - 2.3 variable 182.7924 4.49 4.00

Boundary Side Sets
Top and Bottom: neon-pink top (num_side_ss2) has 6272 faces neon-green bottom (num_side_ss1) has 6272 faces	Sides: red east right (num_side_ss3) has 6144 faces yellow north back (num_side_ss4) has 3072 faces green west left (num_side_ss5) has 1536 faces blue south front (num_side_ss6) has 3072 faces

Project Archive Location

Full Set of files:

/scratch/sft2/lucia/grid_gen/arctic/arctic_fine_v3_0 

tar file sent (*tgz):

Created from clean subdirectory with mesh files:
drwxr-xr-x  3 lucia sftus     12288 Jun  7 14:20 mesh_v3/

LaGriT faceset files with elem number and face (*.faceset):
-rw-r--r--  1 lucia sftus     81639 Jun  7 14:07 fs_1_bot.faceset
-rw-r--r--  1 lucia sftus     69095 Jun  7 14:07 fs_2_top.faceset
-rw-r--r--  1 lucia sftus     86119 Jun  7 14:07 fs_3_rig.faceset
-rw-r--r--  1 lucia sftus     43111 Jun  7 14:07 fs_4_bac.faceset
-rw-r--r--  1 lucia sftus     21607 Jun  7 14:07 fs_5_lef.faceset
-rw-r--r--  1 lucia sftus     43111 Jun  7 14:07 fs_6_fro.faceset

Mesh and faceset files for 6 Materials (mesh_fsets.*):
-rw-r--r--  1 lucia sftus  26953576 Jun  7 14:07 mesh_fsets.exo
-rw-r--r--  1 lucia sftus  46374600 Jun  7 14:08 mesh_fsets.gmv
-rw-r--r--  1 lucia sftus  89405021 Jun  7 14:08 mesh_fsets.inp

Mesh and faceset files for 1 Material (mesh_fsets_1mat.*):
-rw-r--r--  1 lucia sftus  26951604 Jun  7 14:07 mesh_fsets_1mat.exo
-rw-r--r--  1 lucia sftus  42678672 Jun  7 14:07 mesh_fsets_1mat.gmv
-rw-r--r--  1 lucia sftus  89093748 Jun  7 14:07 mesh_fsets_1mat.inp

LaGriT output files contain information reported during the run (*.out):
-rw-r--r-- 1 lucia sftus  20338 Jun  7 14:07 interpolate_icewedge.out
-rw-r--r-- 1 lucia sftus 110772 Jun  7 14:07 make_poly.out
-rw-r--r-- 1 lucia sftus 266584 Jun  7 14:08 stack_full_poly.out
-rw-r--r-- 1 lucia sftus  78740 Jun  7 14:08 write_exo.out

Mesh images:
drwxr-xr-x  2 lucia sftus      4096 Jun  7 14:19 images

Input Data files:

 /scratch/sft2/lucia/grid_gen/arctic/arctic_fine_v3_0/input/

 -rw-r--r--  2 lucia sftus 30928912 Apr 18 13:59 lidar_site3.inp
 -rw-r--r--  1 lucia sftus      123 Apr 18 13:59 poly10001.avs
 -rw-r--r--  1 lucia sftus      178 Apr 18 13:59 poly10002.avs 
						...
 -rw-r--r--  1 lucia sftus      155 Apr 18 13:59 poly10071.avs
 -rw-r--r--  1 lucia sftus      190 Apr 18 13:59 poly10072.avs

Main Work Directory for Polygon Meshing Method:

 /scratch/sft2/lucia/grid_gen/arctic/arctic_fine_v3_0/

Links to Images and Project Details

Input and Output Files Running LaGriT to create the Mesh

These are LaGriT input (.lgi) and output (outx3dgen) files used in creating this mesh. The output files provide good information about the data and mesh, including min and max values of mesh attributes.
The complete set of scripts and input files are in /scratch/sft2/lucia/grid_gen/arctic/arctic_fine_v3_0. The output files for various mesh versions are in /scratch/sft2/lucia/grid_gen/arctic/.

Step 1: Create Ice Object from Polygon (make_poly.lgi)     Input       Output

Step 2: Create and stack layers into full mesh (stack_full_poly.lgi)     Input       Output

Step 3: Interpolate Ice Material on to Full Stacked Mesh (interpolate_icewedge.lgi)     Input       Output

Step 4: Create facesets and write final Exodus files (write_exo.lgi)     Input       Output

 

Grid Team Contacts