Grid Project:  
Barrow Ice Wedge Watershed Region
"lobster extended"

V3.2.0.C.5 (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.5 runs the Version 3.C.1.1 "lobster+" extending the deep mineral layer (layer 6) to -45 deep. This mesh is 3D based on multiple polygons ##6, 8, 9, 19, 21, 25, 27, 29, 31, 34, 35, 36, 37, 39, 45, 47, 50, 56 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

This version doesn't have any changes besides using the number of polygons "lobster+".

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.C.2.1

General Description

Same as V03 using Polygons ## 6, 8, 9, 19, 21, 25, 27, 29, 31, 34, 35, 36, 37, 39, 45, 47, 50, 56. The only change was in the mesh_adjoin.py file in set_poly_surf_file. I added loop to break up the number of polygons to separate them with "&" in order to fix the "long line" error in lagrit. 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 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:         5622993       
Total elements:     11034624 
Total Volume:  0.3873006E+05      

from file write_exo.out.txt:
Mesh Extents (Meters):
              MIN               MAX       DIFFERENCE 
 x   7.933999634E+01  1.909821930E+02 1.116421967E+02
 y   4.647000122E+01  1.706046448E+02 1.241346436E+02
 z  -1.000000000E+00  4.908469200E+00 5.908469200E+00   

from file write_exo.out.txt:
SUMMARY VOLUME/AREA METERS of ELEMENT COLORS (BLOCKS) 
Color    Num. Elements   Volume          Fractional Volume                    
    1      229888          0.1391476E+03     0.003592755
    2     1034496          0.1252329E+04     0.032334795
    3     1034496          0.1252332E+04     0.032334881
    4      689664          0.8348857E+03     0.021556530
    5     1686367          0.2512783E+04     0.064879402
    6     5323696          0.2932920E+05     0.757272174
   30     1036017          0.3409386E+04     0.088029463

from file stack_full_poly.out.txt:
SUMMARY ELEVATIONS at LAYER TOPS (METERS)
        MIN          MAX       DIFF MAX below (thickness)   
    1 4.262400150  4.908469200   .02
    2 4.242400150  4.888469200   .18
    
    3 4.062400150  4.708469200   .18
    4 3.882400150  4.528469200   .12
    5 3.762400150  4.408469200   .50
    6 3.262400150  3.908469200  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 114944 faces neon-green bottom (num_side_ss1) has 114944 faces	Sides: red east right (num_side_ss3) has 26112 faces yellow north back (num_side_ss4) has 30720 faces green west left (num_side_ss5) has 18432 faces blue south front (num_side_ss6) has 19968 faces

Project Archive Location

Full Set of files:

/scratch/sft2/lucia/grid_gen/arctic/arctic_fine_v3_C_1_1/

tar files created (not sent) (*tgz):
-rw-r--r--   1 lucia  sft    2653739829 Feb 26 17:02 mesh_v3_c_1_1.tgz

Created from clean subdirectories with mesh files:
drwxr-xr-x   3 lucia  staff        4096 Feb 26 16:37 images
drwxr-xr-x   3 lucia  sft         20480 Feb 26 16:50 v3_c_1_1

LaGriT faceset files with elem number and face (*.faceset):
-rw-r--r--  1 lucia  sft  1609319 Feb 26 16:44 fs_1_bot.faceset
-rw-r--r--  1 lucia  sft  1379431 Feb 26 16:44 fs_2_top.faceset
-rw-r--r--  1 lucia  sft   391783 Feb 26 16:44 fs_3_rig.faceset
-rw-r--r--  1 lucia  sft   460903 Feb 26 16:44 fs_4_bac.faceset
-rw-r--r--  1 lucia  sft   276583 Feb 26 16:44 fs_5_lef.faceset
-rw-r--r--  1 lucia  sft   299623 Feb 26 16:44 fs_6_fro.faceset

Mesh and faceset files for 6 Materials (mesh_fsets.*):
-rw-r--r--  1 lucia  sft   490665256 Feb 26 16:45 mesh_fsets.exo
-rw-r--r--  1 lucia  sft   840594560 Feb 26 16:45 mesh_fsets.gmv
-rw-r--r--  1 lucia  sft  1756152536 Feb 26 16:46 mesh_fsets.inp

Mesh and faceset files for 1 Material (mesh_fsets_1mat.*):
-rw-r--r--  1 lucia  sft   490663284 Feb 26 16:46 mesh_fsets_1mat.exo
-rw-r--r--  1 lucia  sft   770030032 Feb 26 16:46 mesh_fsets_1mat.gmv
-rw-r--r--  1 lucia  sft  1750529543 Feb 26 16:47 mesh_fsets_1mat.inp

LaGriT output files contain information reported during the run (*.out.txt):
-rw-r--r--  1 lucia  sftus    7992 Sep 26 16:05 get_poly_surf.out.txt
-rw-r--r--  1 lucia  sftus   22768 Sep 26 16:22 interpolate_icewedge.out.txt
-rw-r--r--  1 lucia  sftus  105831 Sep 26 16:05 make_poly10006.out.txt
-rw-r--r--  1 lucia  sftus  108585 Sep 26 16:05 make_poly10008.out.txt
                          . . . 
-rw-r--r--  1 lucia  sftus  113607 Sep 26 16:11 make_poly10050.out.txt
-rw-r--r--  1 lucia  sftus  106305 Sep 26 16:11 make_poly10056.out.txt
-rw-r--r--  1 lucia  sftus   51520 Sep 26 16:11 merge_ice.out.txt
-rw-r--r--  1 lucia  sftus  269338 Sep 26 16:16 stack_full_poly.out.txt
-rw-r--r--  1 lucia  sftus   78740 Sep 26 16:41 write_exo.out.txt

Mesh images:
/scratch/sft2/lucia/grid_gen/arctic/arctic_fine_v3_C_1_1/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/arctic_fine_v3_C_1_1

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_C_1_1. 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 #6:  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