Listed below are the additional data to run the SWAT-MRMT-R model apart from those for the native SWAT model:

1. Reaction input file for single hyporheic zone in vertical and lateral direction is located in PFLOTRAN_INPUT/SingleHZ/.

2. Reaction input file for 10 sub-storage zones in vertical and lateral direction is located in PFLOTRAN_INPUT/MultipleHZ/.

3. Reaction database is located in reaction_database/.

4. The native NEXSS output is located in NEXSS_OUTPUT/.

5. NEXSS mapped to the simulated watershed is located in NEXSStoSWAT/SingleHZ/ for mean residence time and single hyporheic zone, and NEXSStoSWAT/MulitpleHZ/ for distributed residence time in 10 sub-storage zones. The source code and input files for the mapping are in NEXSStoSWAT/mapping/.

The following notes are for running the SWAT-MRMT-R model on PNNL's constance supercomputer.

Notes for source codes:

1. SWAT originated from revision 664
2. PFLOTRAN originated from hash bc0bb2d
3. petsc hash 1a9d3c3 is needed to compile PFLOTRAN and SWAT

To generate an executable:

1. Install petsc git clone https://gitlab.com/petsc/petsc petsc cd petsc git checkout 1a9d3c3

   module purge module load precision/i4 module load intel module load openmpi module load mkl module load gcc/4.8.2 module load cmake

   export PETSC_DIR=pwd export PETSC_ARCH=contance_intel15_O

   ./config/configure.py
   --with-fc=mpif90
   --with-cxx=mpicxx
   --with-clanguage=c
   --with-blas-lapack-dir=/share/apps/intel/2015u1/mkl
   --with-shared-libraries=1
   --download-hdf5=yes
   --download-parmetis=yes
   --download-metis=yes
   --with-debugging=0

   make PETSC_DIR=$PETSC_DIR PETSC_ARCH=$PETSC_ARCH all

2. Download swatmrmtr

3. Compile PFLOTRAN to create library libpflotranchem.a cd swatmrmtr/pflotran/src/pflotran make pflotran_rxn

4. Compile SWAT-MRMT-R cd swatmrmtr/SWAT-MRMT-R make swatmrmtr.e

To run the model: swatmrmtr.e

Apart from the input files for the native swat model, four more files are required to run swatmrmtr.e:

1. Input file for the reaction parameters. Default file name: pflotran.in.
2. Input file for user defined database.
3. Input file for hyporheic exchange flow rates and residence times. Default file name: nxs2swat.txt.
4. Initial chemical composition in the hyporheic zones. Default file name: hz_init_conc.dat

The definition of parameters related to multirate mass transfer and hyporheic biological reactions can be found in function CyberRead in pflotran/src/pflotran/reaction_sandbox_pnnl_cyber_mrmt.F90. Note: reactions in reaction_sandbox_pnnl_cyber_mrmt.F90 only assume two-step reactions for denitrification and an aerobic respiration reaction. Otherwise, the code has to be modified following steps documented in https://www.pflotran.org/documentation/theory_guide/reaction_sandbox.html

Disclaimer SWAT-MRMT-R is an open-source software distributed under the terms of the GNU Lesser General Public License as published by the Free Software Foundation either version 2.1 of the License, or any later version.