Running PFLOTRAN linked to FMDM

STEP 1:

It is recommended that you clone a fresh PFLOTRAN repository, for example, calling it ~/software/pflotran-fmdm. Build PFLOTRAN-FMDM using the following commands (the upper level directories are an example only):

> cd ~/software/pflotran-fmdm/src/pflotran
> make clean
> make libpflotran.a fmdm=1

STEP 2:

Clone the Fuel Matrix Degradation Model (FMDM) repository:

> cd ~/software
> hg clone https://bitbucket.org/pflotran_snl/fmdm

STEP 3:

Move into the FMDM respository directory v2.3 and compile pflotran_fmdm using the same PETSC_DIR and PETSC_ARCH evironmental settings as the PFLOTRAN-FMDM repository which contains the libpflotran.a file (e.g. see STEP 1 above).

> cd ~/software/fmdm/v2.3
> make pflotran_fmdm PFLOTRANFMDM_DIR=~/software/pflotran-fmdm

STEP 4:

Use the pflotran_fmdm executable to run simulations where the FMDM is linked, not the executable in your PFLOTRAN-FMDM repository. For example,

> mpirun -np 1 ~/software/fmdm/v2.3/pflotran_fmdm -input_prefix my_fmdm_simulation