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F-Area Two-Dimensional Flow with Reactive Transport
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This is an representative case for the F-Area 2D simulations.  The
model is based on the last family of meshes proposed by Sergio, and
which include the Gordon Aquifer and Gordon Confining Unit.  However,
since these are not included in the TOUGH2 prototyping runs they are
both assigned a very small intrinsic permeabiliy - essentially
removing them from the simulation.

The input files for the different cases that are located in the 
subdirectories are named

2d_f-area*.xml                  - XML problem description

and
ascem-2012-farea.bgd            - geochemistry input (basis, database)

for the cases with geochemistry.

The input files use 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/2012-04-24/

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, in an example subdirectory execute

ln -s /project/projectdirs/m1012/meshes/phase2/f-area/2012-04-24/refine_l0/mesh2_bc01tobc09.exo mesh2_bc01tobc09-l0.exo
ln -s /project/projectdirs/m1012/meshes/phase2/f-area/2012-04-24/refine_l1/mesh2_bc01tobc09.exo mesh2_bc01tobc09-l1.exo
ln -s /project/projectdirs/m1012/meshes/phase2/f-area/2012-04-24/refine_l2/mesh2_bc01tobc09.exo mesh2_bc01tobc09-l2.exo

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

ln -s mesh2_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.xml

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





