<commit_before>This is the Transport Matrix Method (TMM) code repository. It includes both 
the core TMM time-stepping driver code (under driver/), as well as various 
biogeochemical models (under models/) adapted to the TMM framework. The driver 
code and interface to models are written using the PETSc framework 
(http://www.mcs.anl.gov/petsc/) but you don't need this code to use the TMM. 
Simply skip to step (3) below. Otherwise keep reading and if you have any 
questions feel free to email: <NAME> <<EMAIL>>

If you use the TMM, please cite Khatiwala et al. (2005; https://doi.org/10.1016/j.ocemod.2004.04.002) 
and Khatiwala (2007; https://doi.org/10.1029/2007GB002923). Furthermore, if you use this code 
please also cite Khatiwala (2018; https://doi.org/10.5281/zenodo.1246300). Thank you!

For a quick overview of the TMM and the PETSc driver also have a look at this excellent 
presentation by <NAME>: https://ftp.geomar.de/users/ikriest/TMM/MOPS-TMM-2016-June.pdf

Quick-start instructions:

1) Install PETSc (http://www.mcs.anl.gov/petsc/) and set the PETSC_DIR and PETSC_ARCH 
environment variables. The TMM driver code is compatible with PETSc version 3.13 
(this is the latest version as of June 12, 2020). For the older version of the TMM 
code compatible with PETSc 3.6.x, you can checkout branch petsc3.6.

2) Download Matlab scripts and add to your Matlab path:
http://kelvin.earth.ox.ac.uk/spk/Research/TMM/tmm_matlab_code.tar.gz

3) Download transport matrices and related data for the ocean model of your 
choice: http://kelvin.earth.ox.ac.uk/spk/Research/TMM/TransportMatrixConfigs/<commit_msg>Changes to be committed:   modified:   README.txt<commit_after>This is the Transport Matrix Method (TMM) code repository. It includes both 
the core TMM time-stepping driver code (under driver/), as well as various 
biogeochemical models (under models/) adapted to the TMM framework. The driver 
code and interface to models are written using the PETSc framework 
(http://www.mcs.anl.gov/petsc/) but you don't need this code to use the TMM. 
Simply skip to step (3) below. Otherwise keep reading and if you have any 
questions feel free to email: <NAME> <<EMAIL>>

IMPORTANT: Please do NOT post the TMM code or any data files downloaded from this or related 
websites on your own github or other website. You do NOT have permission to do so.

If you use the TMM, please cite Khatiwala et al. (2005; https://doi.org/10.1016/j.ocemod.2004.04.002) 
and Khatiwala (2007; https://doi.org/10.1029/2007GB002923). Furthermore, if you use this code 
please also cite Khatiwala (2018; https://doi.org/10.5281/zenodo.1246300). If you use any of 
my transport matrices please cite the relevant paper (see 
http://kelvin.earth.ox.ac.uk/spk/Research/TMM/TransportMatrixConfigs/). Thank you!

For a quick overview of the TMM and the PETSc driver also have a look at this excellent 
presentation by <NAME>: https://ftp.geomar.de/users/ikriest/TMM/MOPS-TMM-2016-June.pdf

Quick-start instructions:

1) Install PETSc (http://www.mcs.anl.gov/petsc/) and set the PETSC_DIR and PETSC_ARCH 
environment variables. The TMM driver code is compatible with PETSc version 3.16.x 
(as of Jan 20, 2022). For the older version of the TMM code compatible with PETSc 3.6.x, 
you can checkout branch petsc3.6.

2) Download Matlab scripts and add to your Matlab path:
http://kelvin.earth.ox.ac.uk/spk/Research/TMM/tmm_matlab_code.tar.gz

3) Download transport matrices and related data for the ocean model of your 
choice: http://kelvin.earth.ox.ac.uk/spk/Research/TMM/TransportMatrixConfigs/
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