Test Mesh: Test 1

Grid Team Member:	Lucia Short
Test Mesh:	Test 1: column with flat top
Data Source:	3 points
Delivered To:	Scott Painter
Date Completed:	October 31, 2013
T1 Mesh:	291 Nodes and 96 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.

Test 1 uses the following layers:

  -----------------
  1 moss           .02 (2 x .01)
  2 upper organic  .18 (9 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   ~4.8 (50 x .09)
  -----------------

Full Stacked Mesh
6 material layers with bottom at -1

Full Stacked Mesh
Closeup to show upper materials

Test Mesh Input Parameters

General Description

Following layer definitions :

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.

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:       291       
Total elements:     96     
Total Volume:      0.2100000E+01      

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  6.999999881E-01 6.999999881E-01
 z -1.000000000E+00  5.000000000E+00 6.000000000E+00     

from file write_exo.out.txt:
SUMMARY VOLUME/AREA METERS of ELEMENT COLORS (BLOCKS) 
Color    Num. Elements   Volume          Fractional Volume                    
    1           2       0.6999993E-02     0.003333330
    2           9       0.6299994E-01     0.029999971
    3           9       0.6300011E-01     0.030000051
    4           6       0.4199996E-01     0.019999981
    5          20       0.1750000E+00     0.083333333
    6          50       0.1750000E+01     0.833333333        

from file stack_full_poly.out.txt:
SUMMARY ELEVATIONS at LAYER TOPS (METERS)
        MIN          MAX       DIFF MAX below (thickness)   
    1 5.000000000  5.000000000   .02
    2 4.980000000  4.980000000   .18
    3 4.800000000  4.800000000   .18
    4 4.620000000  4.620000000   .12
    5 4.500000000  4.500000000   .50
    6 4.000000000  4.000000000  4.99 
      (Bottom is flat at -1.0)

Mesh Layer Definitions (meters)

ID	Layer Name	Layer Thick	Layer Vertical Cells	Layer Volume
1	moss(top)	0.02	2 x .01	0.6999993E-02
2	upper organic	0.18	9 x .02	0.6299994E-01
3	upper mineral	0.18	9 x .02	0.6300011E-01
4	lower organic	0.12	6 x .02	0.4199996E-01
5	lower mineral	0.50	20 x .025	0.1750000E+00
6	deep mineral	2.2 - 4.8	50 x .09	0.1750000E+01

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_1 

LaGriT faceset files with elem number and face (*.faceset):
-rw-r--r-- 1 lucia sftus  112 Oct 31 13:20 fs_1_bot.faceset
-rw-r--r-- 1 lucia sftus  110 Oct 31 13:20 fs_2_top.faceset
-rw-r--r-- 1 lucia sftus 1063 Oct 31 13:20 fs_3_rig.faceset
-rw-r--r-- 1 lucia sftus 1063 Oct 31 13:20 fs_4_bac.faceset
-rw-r--r-- 1 lucia sftus 1063 Oct 31 13:20 fs_6_fro.faceset

Mesh and faceset files for 6 Materials (mesh_fsets.*):
-rw-r--r-- 1 lucia sftus 16396 Oct 31 13:20 mesh_fsets.exo
-rw-r--r-- 1 lucia sftus 31708 Oct 31 13:20 mesh_fsets.gmv
-rw-r--r-- 1 lucia sftus 36210 Oct 31 13:20 mesh_fsets.inp

Mesh and faceset files for 1 Material (mesh_fsets_1mat.*):
-rw-r--r-- 1 lucia sftus 14752 Oct 31 13:20 mesh_fsets_1mat.exo
-rw-r--r-- 1 lucia sftus 31188 Oct 31 13:20 mesh_fsets_1mat.gmv
-rw-r--r-- 1 lucia sftus 35919 Oct 31 13:20 mesh_fsets_1mat.inp

LaGriT output files contain information reported during the run (*.out.txt):
-rw-r--r-- 1 lucia sftus   4963 Oct 31 13:20 get_boundary_pts.out.txt
-rw-r--r-- 1 lucia sftus   4313 Oct 31 13:20 get_poly_surf.out.txt
-rw-r--r-- 1 lucia sftus   7243 Oct 31 13:20 interpolate.out.txt
-rw-r--r-- 1 lucia sftus   7573 Oct 31 13:20 merge_polys.out.txt
-rw-r--r-- 1 lucia sftus   5546 Oct 31 13:20 process_lidar.out.txt
-rw-r--r-- 1 lucia sftus   3748 Oct 31 13:20 set_zeroz.out.txt
-rw-r--r-- 1 lucia sftus 264154 Oct 31 13:20 stack_full_poly.out.txt
-rw-r--r-- 1 lucia sftus  75893 Oct 31 13:20 write_exo.out.txt

Mesh images:
drwxr-xr-x  2 lucia sftus   4096 Mar 18 12:34 images

Input Data files:

 /scratch/sft2/lucia/grid_gen/arctic/column_1/input/

-rw-r--r-- 1 lucia sftus    54 Oct 31 13:17 lidar_site3.inp
-rw-r--r-- 1 lucia sftus    58 Oct 31 13:17 poly10001.avs

Main Work Directory for Polygon Meshing Method:

 /scratch/sft2/lucia/grid_gen/arctic/

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/column_1. 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

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