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F-Area Two-Dimensional Flow with Reactive Transport
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This is a representative case for the F-Area 2D simulations.  The
model is based on meshes created by Rao Garimella from Sergio last
family of meshes, but with the Gordon Aquifer and Gordon Confining
Units removed.  This better aligns our geologic model with the one
that was used in the TOUGH2 prototyping runs.

The input files are named:

2d_f-area_flow_full_chem_no_gordon.xml  - XML problem description
ascem-2012-farea.bgd                    - geochemistry input (basis, database)

The input file uses a generic name for the mesh

f_area_mesh_2D.exo

and so you need to provide the desired F-Area mesh in Exodus format
with this name.  The meshes are available on Hopper, in the ascem
project directory:

/project/projectdirs/m1012/meshes/phase2/f-area/2012-07-31

There is a README in this directory explaining the different resolutions
and different files.  But I find it easiest to create links to each
resolution, and then link the one that I want to the generic name that
is in the input file.  For example, 

ln -s /project/projectdirs/m1012/meshes/phase2/f-area/2012-07-31/refine_l0_nogordon/mesh3_bc01tobc09.exo  mesh3_bc01tobc09-l0.exo
ln -s /project/projectdirs/m1012/meshes/phase2/f-area/2012-07-31/refine_l1_nogordon/mesh3_bc01tobc09.exo  mesh3_bc01tobc09-l1.exo
ln -s /project/projectdirs/m1012/meshes/phase2/f-area/2012-07-31/refine_l2_nogordon/mesh3_bc01tobc09.exo  mesh3_bc01tobc09-l2.exo

and then link the one that you want.  For example, assume you want the
coarsest one:

ln -s mesh3_bc01tobc09-l0.exo f_area_mesh_2D.exo

Now you have all the input you need, and you can run this test case.  We
are typically using 24 cores as a reasonable tradeoff between the needs
of the flow solve, and the geochemistry

aprun -n 24 ${SOME_PATH_TO_AMANZI}/bin/amanzi --xml_file=2d_f-area_flow_full_chem_no_gordon.xml

You may want to redirect output, and/or put this in a batch script.





