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

V3.2.0.C.5 (fine scale)

Grid Team Member: Lucia Short
Grid Version: Version 03.2.0.C.5: multiple polygons
#6, 8, 9, 19, 21, 25, 27, 29, 31, 34, 35, 36, 37, 39, 45, 47, 50, 56
Data Source: LiDAR data Area C from Chandana Gangodagamage
Delivered To: Scott Painter
Date Completed: November 6, 2013
   
V3.2.0.C.5 Mesh (6 layers) : 7,651,908 Nodes and 15,057,664 Cells
V3.2.0.C.4 Mesh (6 layers) : 698,148 Nodes and 1,358,208 Cells
V3.2.0.C.3 Mesh (6 layers): 159,588 Nodes and 301,824 Cells
V3.2.0.C.2 Mesh (6 layers): 330,660 Nodes and 637,184 Cells
V3.2.0.C.1 Mesh (6 layers): 229,284 Nodes and 435,968 Cells

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

LaGriT Finite Element Mesh

Full Stacked Mesh with Ice Wedge
Cut to show internal materials

LaGriT Finite Element Mesh


Mesh and Ice Wedge
with moss and organic layers removed

LaGriT Finite Element Mesh


Ice Wedge

LaGriT Finite Element Mesh

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 :

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
LaGriT Finite Element Mesh

LaGriT Finite Element Mesh

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
LaGriT Finite Element 
Mesh LaGriT Finite Element 
Element Mesh


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


Gallery of All Project Images

Method Description Overview (from V01)

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

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