Test Mesh: Test 5

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.

Thest 5 is the same as Test 4 with the layer 1 (moss) removed. Test 5 uses the following layers:

  -----------------
  1 moss           .02 (2 x .01) (removed)
  2 upper organic  .12 (6 x .02)
  3 upper mineral  .18 (9 x .02)
  4 lower organic  .12 (6 x .02)
  5 lower mineral  .5 (20 x .025)
  6 deep mineral   ~49.00 (variable)
  -----------------

Full Stacked Mesh 5 material layers with bottom at -45

Full Stacked Mesh with Ice Wedge Cut to show internal materials

Test Mesh Input Parameters

General Description

Following layer definitions :

• Layer 1 (top) is removed.
• Add a third organic layer such that it is 12 cm thick with with 6 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 = -45.

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:       381       
Total elements:    126     
Total Volume:      0.2400000E+02      

from file write_exo.out.txt:
Mesh Extents (Meters):
        MIN              MAX             DIFFERENCE    
 x   0.000000000E+00  1.000000000E+00 1.000000000E+00
 y   0.000000000E+00  1.000000000E+00 1.000000000E+00 
 z  -4.500000000E+01  4.980000019E+00 4.998000002E+01     

from file write_exo.out.txt:
SUMMARY VOLUME/AREA METERS of ELEMENT COLORS (BLOCKS) 
Color    Num. Elements   Volume          Fractional Volume                    
    2           6          0.5999994E-01     0.002400958  
    3           9          0.9000015E-01     0.003601447  
    4           6          0.5999994E-01     0.002400958  
    5          20          0.2500000E+00     0.010004002  
    6          85          0.2453000E+02     0.981592636      

from file stack_full_poly.out.txt:
SUMMARY ELEVATIONS at LAYER TOPS (METERS)
        MIN          MAX       DIFF MAX below (thickness)   
    2  4.980000000  4.980000000   .12
    3  4.860000000  4.860000000   .18
    4  4.680000000  4.680000000   .12
    5  4.560000000  4.560000000   .50
    6  4.060000000  4.060000000 49.06 
      (Bottom is flat at -45.0)

Mesh Layer Definitions (meters)
ID Layer Name Layer Thick Layer Vertical Cells Layer Volume 2 upper organic 0.18 9 x .02 0.5999994E-01 3 upper mineral 0.18 9 x .02 0.9000015E-01 4 lower organic 0.12 6 x .02 0.5999994E-01 5 lower mineral 0.50 20 x .025 0.2500000E+00 6 deep mineral 49.00 50 x 0.1 10 x 0.4 10 x 1 15 x 2  0.2453000E+02

Boundary Side Sets
Top and Bottom: neon-pink top (num_side_ss2) has 1 faces neon-green bottom (num_side_ss1) has 1 faces

Project Archive Location

Full Set of files:

/scratch/sft2/lucia/grid_gen/arctic/column_5 

LaGriT faceset files with elem number and face (*.faceset):
-rw-r--r-- 1 lucia sftus  112 Mar 17 13:40 fs_1_bot.faceset
-rw-r--r-- 1 lucia sftus  111 Mar 17 13:40 fs_2_top.faceset
-rw-r--r-- 1 lucia sftus 1363 Mar 17 13:40 fs_5_lef.faceset
-rw-r--r-- 1 lucia sftus 1363 Mar 17 13:40 fs_6_fro.faceset

Mesh and faceset files for 6 Materials (mesh_fsets.*):
-rw-r--r-- 1 lucia sftus 18748 Mar 17 13:40 mesh_fsets.exo
-rw-r--r-- 1 lucia sftus 41220 Mar 17 13:40 mesh_fsets.gmv
-rw-r--r-- 1 lucia sftus 47877 Mar 17 13:40 mesh_fsets.inp

Mesh and faceset files for 1 Material (mesh_fsets_1mat.*):
-rw-r--r-- 1 lucia sftus 17432 Mar 17 13:40 mesh_fsets_1mat.exo
-rw-r--r-- 1 lucia sftus 40788 Mar 17 13:40 mesh_fsets_1mat.gmv
-rw-r--r-- 1 lucia sftus 47496 Mar 17 13:40 mesh_fsets_1mat.inp

LaGriT output files contain information reported during the run (*.out.txt):
-rw-r--r-- 1 lucia sftus   4963 Mar 17 13:40 get_boundary_pts.out.txt
-rw-r--r-- 1 lucia sftus   4313 Mar 17 13:40 get_poly_surf.out.txt
-rw-r--r-- 1 lucia sftus   7243 Mar 17 13:40 interpolate.out.txt
-rw-r--r-- 1 lucia sftus   7573 Mar 17 13:40 merge_polys.out.txt
-rw-r--r-- 1 lucia sftus   5546 Mar 17 13:40 process_lidar.out.txt
-rw-r--r-- 1 lucia sftus   3748 Mar 17 13:40 set_zeroz.out.txt
-rw-r--r-- 1 lucia sftus 344072 Mar 17 13:40 stack_full_poly.out.txt
-rw-r--r-- 1 lucia sftus  74672 Mar 17 13:40 write_exo.out.txt

Mesh images:
/scratch/sft2/lucia/grid_gen/arctic/column_5/images

Input Data files:

 /scratch/sft2/lucia/grid_gen/arctic/column_5/input/

-rw-r--r-- 1 lucia sftus    54 Feb 10 15:31 lidar_site3.inp
-rw-r--r-- 1 lucia sftus    58 Feb 10 15:31 poly10001.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/column_5. The output files for various mesh versions are in /scratch/sft2/lucia/grid_gen/arctic/.

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

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

 

Grid Team Contacts