Amanzi - Walkabout Workflow Test slab_v01 coarse

May 1 2017. Workflow using particleDriver to convert Amanzi files for input into Walkabout for particle tracking. This test mesh is based on Source Hex Mesh /scratch/ymp/gable/grid_gen/ufd/particle_tracking/mesh_w_barriers/ver_01_slab/hex_np26.gmv

Based on demonstration problem in:
Pathline tracing on fully unstructured control-volume grids
SL Painter, CW Gable, S Kelkar
Computational Geosciences, 1-10 17 2012

Known Issues for this Workflow

1) Material (block) information is not written and the resulting mesh has a default single material id of 1.

2) This workflow requires that LaGriT connect the cell center points and boundary nodes into a tet mesh. The connect algorithm works in general for a reasonable number of nodes (under 2 Mil) and a convex shape. The LaGriT output must be inspected to check that the tet mesh successful and make sure the expected number of points are connected.

3) By converting Amanzi mesh points to tets there can be mesh errors introduced. Check the LaGriT output for mesh quality metrics and for Negative Coupling Coeficients.

4) The particleDriver output file walk00058.h5.avs is expected to have 4 property values for the mesh points. The AVS header indicates 4, but there are only 3 fields in the file.

5)The creation of boundary outside zones assumes the mesh has flat sides in 6 directions. This may not work for meshes of irregular shape or with sloping outside surfaces.

6) The Walkabout User Manual V1.0 and does not yet have descriptions for the Amanzi workflow and files.

Workflow Steps for Test slab_v01

Download Files used and described in this workflow: walkabout-amanzi_v01.tar.gz (2.3M)

1) Create ExodusII Hex Mesh for Amanzi Model

Mesh Directory: /scratch/nts/tam/ascem/walkabout/test_slab_v01/EXO_output

Dimensions 25 x 25 x 3 cells with size 4x4x1
Facesets: 1=bottom 2=top 3=right 4=back 5=left 6=front
Block Materials: 1=Background 2=Left Barrier 3=Right Barrier

Title: LAGRIT TO EXODUS                                                         
number of nodes:                2704                                            
number of elements:             1875                                            
number of element blocks:          3                                            
number of side sets:               6       

NAME        MIN               MAX           DIFFERENCE          
 xic     0.000000000E+00  1.000000000E+02   1.000000000E+02 
 yic     0.000000000E+00  1.000000000E+02   1.000000000E+02 
 zic     0.000000000E+00  3.000000000E+00   3.000000000E+00  

Color      Num. Elements   Volume          Fractional Volume                    
    1        1650          0.2640000E+05     0.880000000                        
    2         135          0.2160000E+04     0.072000000                        
    3          90          0.1440000E+04     0.048000000                        
Total cells: 1875          Total Volume:     0.3000000E+05             

Mesh Description: README.txt  
LaGriT Mesh Output: mesh.out.txt  

Exodus Hex Mesh for Amanzi
LaGriT Finite Element Mesh
Exodus Hex Mesh Nodes for Amanzi
LaGriT Finite Element Mesh
Exodus Boundary facesets for Amanzi
LaGriT Finite Element Mesh

2) Run Amanzi Model and Write Files

Directory: /scratch/nts/zhiming/RM_SM/walkabout_workflow
Amanzi INPUT files: 
   mesh_fsets.exo, wf.xml

Amanzi OUTPUT files:
   plot_mesh.h5 = data for plotting elements (not used)
   walk00058.h5 = Binary file with mesh data from Amanzi

   These points are the mesh cell centers plus outside edge points
   DATASET "x" "y" "z"

   For each mesh point, these are the node properties
   DATASET "pore velocity x" "pore velocity y" "pore velocity z" "porosity" "pressure" "saturation"

3) Run particleDriver and Write Walkabout Files

Directory: /scratch/nts/tam/ascem/walkabout/test_slab_v01/walkabout_workflow

Compile h5output.cpp using makefile for program particleDriver
RUN particleDriver

INPUT: walk00058.h5 from Amanzi (last time step in h5 format)
       (to view binary file: h5dump walk00058.h5 > walk00058.h5.ascii.txt)

PREPROCESS STEP These data are extracted from walk00058.h5 and are written in ASCII format.
walk00058.h5.avs - AVS file with point properties from .h5 file. Required for Walkabout Note this file is incorrect, the header indicates 4 properties, but there are only 3. The Liquid Density is probably the one missing. Liquid Pressure (MPa), (MPa) Saturation, (no dim) Porosity, (no dim) Liquid Density (kg/m**3), (kg/m**3) walk00058.h5.ama - cell velocity file. Required for Walkabout. walk00058.h5.inp - AVS file with point x,y,z from .h5 file. Required for LaGriT walk00058.h5.lgi - command file to connect tets and write files. Required for LaGriT. walk00058.h5.files - specifies input/output files. Required for Walkabout. walk00058.h5.rock - density, Kd, porosity properties. Optional. walk00058.h5.ply - view file showing domain points colored by Velocity control.dat - specifies parameters. Required for Walkabout.
Exodus Hex Mesh with Amanzi output points
LaGriT Finite Element Mesh
Amanzi cell center points with Pressure
LaGriT Finite Element Mesh
Amanzi mesh boundary points with Pressure
LaGriT Finite Element Mesh
MESHING STEP Run LaGriT with walk00058.h5.lgi (from preprocess step) Connect delaunay (will add elements across non-convex shapes) Set point material = 1 Set element material = 1 INPUT: walk00058.h5.inp (cell center and edge nodes from walk00058.h5)
walk00058.h5.fehmn - FEHM geometry file for the tet mesh. Required for Walkabout. walk00058.h5.stor - FEHM tet connectivity and interface areas. Required for Walkabout. walk00058.h5.graph - Mesh element adjacency list. Required for Walkabout. - FEHM boundary zones for mesh points. Optional. walk00058.h5_outside_vor.area - FEHM Voronoi areas for boundary points. Optional. - FEHM material zones for mesh points. Optional. walk00058.h5.tet.inp - AVS file for viewing the tet mesh. walk00058.h5.gmv - binary GMV file for viewing the tet mesh. logx3dgen, outx3dgen - LaGriT log and screen output files.
LaGriT Connect Points to Tet Mesh
LaGriT Finite Element Mesh
LaGriT Tet Mesh with Amanzi Points
LaGriT Finite Element Mesh
Tet Volumes cutaway at Boundary
LaGriT Finite Element Mesh
POSTPROCESS STEP (optional and not selected for this example)
.obj - Wavefront OBJ file for viewing tetrahedral mesh. .csv - text file for viewing cell center point positions and velocities. .vtk - Binary VTK file for viewing particle path lines from Walkabout.

4) Run Walkabout

(Zhiming will run and evaluate results)

Contact tamiller at