Grid Project:  
Barrow Ice Wedge
Polygon 45

V3.2.0.C.4 (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 3.2.C.2 runs the Version 3.2.C.1 with polygon #45. This mesh is 3D based on single polygon #6 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.

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. The bottom layer (mineral 6) is exteded to -45 in this version.

Changes in Files

The layer 6 has nonuniform mesh with vertical spasing (resolution) as folloing:
5 m deep with 50 cells,
4 m deep with 10 cells,
10 m deep with 10 cells,
30 m deep with 15 cells,
bottom is at -45.

File stack_full_poly.lgi:

< define / Z_BOTTOM / -45.

. . . 

< # L5 --------------------- tmp_lay5.inp 5,49
< #     mat 6 =  variable ? / 5 thick now
< # L6 --------------------- tmp_lay6.inp 6,9
< #     mat 6 =  4. thick
< # L7 --------------------- tmp_lay7.inp 7,9
< #     mat 6 = 10.thick
< # L8 --------------------- tmp_lay8.inp 8,14
< #     mat 6 = 30.thick
< # BOT--------------------- tmp_lay_bot.inp 9

. . .

< 	  tmp_lay8.inp    6,14 &
< 	  tmp_lay7.inp    6,9  &
<    tmp_lay6.inp    6,9  &

Full Stacked Mesh with Ice Wedge 6 material layers plus ice material

Full Stacked Mesh with Ice Wedge closeup

Mesh Input Parameters V3.2.C.4

General Description

Same as V03.C# for polygon #45. The only change was in the stack_full_poly.lgi file.This version uses the following layer definitions :

• Layer 1 (top) is the live organic layer and should be 2 cm thick with 2 cells.
• Organic layer such that all combined are 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 bottom material 6 has nonuniform mesh with higher resolution at the top.
  
• The domain bottom should be flat at Z = -45.

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:          159588       
Total elements:       301824 
Total Volume:  0.8000887E+04      

from file write_exo.out.txt:
Mesh Extents (Meters):
              MIN               MAX       DIFFERENCE 
 x      1.861005859E+02  2.057198792E+02 1.961929321E+01 
 y      1.298191681E+02  1.469042206E+02 1.708505249E+01 
 z     -4.500000000E+01  4.588950157E+00 4.958895016E+01  

from file write_exo.out.txt:
SUMMARY VOLUME/AREA METERS of ELEMENT COLORS (BLOCKS) 
Color    Num. Elements   Volume          Fractional Volume                    
    1        4608          0.3238193E+01     0.000404729
    2       20736          0.2914373E+02     0.003642563
    3       20736          0.2914381E+02     0.003642572
    4       13824          0.1942916E+02     0.002428375
    5       26721          0.4553578E+02     0.005691341
    6      183762          0.7748124E+04     0.968408048
   30       31437          0.1262730E+03     0.015782372

from file stack_full_poly.out.txt:
SUMMARY ELEVATIONS at LAYER TOPS (METERS)
        MIN          MAX       DIFF MAX below (thickness)   
  1   4.219137192  4.588950157   .02
  2   4.199137192  4.568950157   .18
   
  3   4.019137192  4.388950157   .18
  4   3.839137192  4.208950157   .12
  5   3.719137192  4.088950157   .50
  6 -1.578086281  -1.541104984  19.49 
      (Bottom is flat at -45.0)

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 4.250232 4.50 4.99 2 upper organic 0.18 9 x .02 38.25209 4.48 4.97 3 upper mineral 0.18 9 x .02 38.25219 4.30 4.79 4 lower organic 0.12 6 x .02 25.50139 4.12 4.61 5 lower mineral 0.50 20 x .025 68.73682 4.00 4.49 6 deep mineral 2.2 - 19.49 50 x 0.1 10 x 0.4 10 x 1 15 x 2 10238.34 3.50 3.99 7/30 ice 0.00 - 2.3 variable 133.6607 4.49 4.00

Top and Bottom:
neon-pink  top     (num_side_ss2) has  2304 faces
neon-green bottom  (num_side_ss1) has  2304 faces

Sides:
red     east right   (num_side_ss3) has  4192 faces
yellow  north back   (num_side_ss4) has  4192 faces
green   west left    (num_side_ss5) has  2096 faces
blue    south front  (num_side_ss6) has  4192 faces

Project Archive Location

Full Set of files:

/scratch/sft2/lucia/grid_gen/arctic/arctic_fine_deep_poly45/

tar files created (*tgz):
-rw-r--r--   1 lucia  sft    341173463 Mar  6 16:05 poly45_fine_deep.tgz

Created from clean subdirectories with mesh files:
drwxr-xr-x   2 lucia  sftus       8192 Jan  7 16:52 poly45_fine_deep

LaGriT faceset files with elem number and face (*.faceset):
-rw-r--r--  1 lucia  sft    134887 Nov  6 12:16 fs_1_bot.faceset
-rw-r--r--  1 lucia  sft    114151 Nov  6 12:16 fs_2_top.faceset
-rw-r--r--  1 lucia  sft     58791 Nov  6 12:16 fs_3_rig.faceset
-rw-r--r--  1 lucia  sft    176167 Nov  6 12:16 fs_4_bac.faceset
-rw-r--r--  1 lucia  sft     29447 Nov  6 12:16 fs_5_lef.faceset
-rw-r--r--  1 lucia  sft    117479 Nov  6 12:16 fs_6_fro.faceset
-rw-r--r--  1 lucia  sft       271 Nov  6 12:16 fs_7_Csides.faceset
-rw-r--r--  1 lucia  sft       312 Nov  6 12:16 fs_8_Ctop.faceset

Mesh and faceset files for 6 Materials (mesh_fsets.*):
-rw-r--r--  1 lucia  sft   60607136 Nov  6 12:16 mesh_fsets.exo
-rw-r--r--  1 lucia  sft  101534328 Nov  6 12:17 mesh_fsets.gmv
-rw-r--r--  1 lucia  sft  203262200 Nov  6 12:16 mesh_fsets.inp

Mesh and faceset files for 1 Material (mesh_fsets_1mat.*):
-rw-r--r--  1 lucia  sft   60605164 Nov  6 12:17 mesh_fsets_1mat.exo
-rw-r--r--  1 lucia  sft   95558472 Nov  6 12:17 mesh_fsets_1mat.gmv
-rw-r--r--  1 lucia  sft  202564052 Nov  6 12:17 mesh_fsets_1mat.inp

LaGriT output files contain information reported during the run (*.out.txt):
-rw-r--r--  1 lucia  sft      4963 Nov  6 12:14 get_boundary_pts.out.txt
-rw-r--r--  1 lucia  sft      4799 Nov  6 12:13 get_poly_surf.out.txt
-rw-r--r--  1 lucia  sft     11698 Nov  6 12:12 interpolate.out.txt
-rw-r--r--  1 lucia  sft     22768 Nov  6 12:15 interpolate_icewedge.out.txt
-rw-r--r--  1 lucia  sft    112635 Nov  6 12:14 make_poly10045.out.txt
-rw-r--r--  1 lucia  sft      5781 Nov  6 12:14 merge_ice.out.txt
-rw-r--r--  1 lucia  sft    302436 Nov  6 12:13 merge_polys.out.txt
-rw-r--r--  1 lucia  sft      5546 Nov  6 12:13 process_lidar.out.txt
-rw-r--r--  1 lucia  sft    550714 Nov  6 12:13 refine.out.txt
-rw-r--r--  1 lucia  sft      3748 Nov  6 12:13 set_zeroz.out.txt
-rw-r--r--  1 lucia  sftus   36132 Mar  6 15:26 stack_full_poly.out.txt
-rw-r--r--  1 lucia  sft    105639 Nov  6 12:17 write_exo.out.txt

Mesh images:
/scratch/sft2/lucia/grid_gen/arctic/arctic_fine_deep_poly45/images

Input Data files:

/scratch/sft2/lucia/grid_gen/arctic/arctic_fine_v3_C_1/input

-rw-r--r--  2 lucia  sftus  30928912 Jul  9 11:47 lidar_site3.inp
-rw-r--r--  1 lucia  sftus       123 Jul  9 11:47 poly10001.avs
-rw-r--r--  1 lucia  sftus       178 Jul  9 11:47 poly10002.avs 
						...
-rw-r--r--  1 lucia  sftus       155 Jul  9 11:47 poly10071.avs
-rw-r--r--  1 lucia  sftus       190 Jul  9 11:47 poly10072.avs

Main Work Directory for Polygon Meshing Method:

/scratch/sft2/lucia/grid_gen/arctic/

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_deep_poly06. The output files for various mesh versions are in /home/lucia/sandbox/arctic and /scratch/sft2/lucia/grid_gen/arctic/.

Steps to create the surface mesh for all polygons

To create a surface mesh, we run 2 python scripts. Normally, the Path 1 doesn't need to be re-run, so we just copy output files from this run to the output folder from the folder output_surf_mesh. If any of the Part 1 scripts are changed, then the Part 1 should be re-run, so Path 1 or 2 should be taken.

Path 1: Run script surf_mesh.py.

Path 2: (If you didn't run Part 1, remove all the files from the ouput folder. Then copy files from directory output_surf_mesh into the output folder.) Run script mesh_adjoin.py

Steps to create the 3D mesh for several polygons

The easiest path is to run surf_mesh.py and then mesh_adjoin.py scripts. That creates necessary LaGriT files and runs other scripts.

Step 1: Create Ice Objects from Polygon make_poly.lgi. This script is used to create all polygons separately. The Input is the same for all polygons. The output is different for all the polygons, but it is similar. To get the output for the polygon you are interested in, change the # of the polygon in the link: make_poly<enter_your_number>.out.txt
- Polygon #45:  Output

Step 2: Merge all the ice objects created in Step 1. Input      Output

Step 3: Create and stack layers into full mesh (stack_full_poly.lgi)     Input       Output

Step 4: Interpolate Ice Material on to Full Stacked Mesh (interpolate_icewedge.lgi)     Input       Output

Step 5: Create facesets and write final Exodus files (write_exo.lgi)     Input       Output

 

Grid Team Contacts