verification/atm_gray/README.md

4287557481 Jean*0001 Gray atmosphere physics example on Cubed-Sphere grid
                0002 ============================================================
                0003
                0004 Use gray atmospheric physics (O'Gorman and Schneider, JCl, 2008)
                0005 from package `atm_phys` inside  MITgcm dynamical core, in a global
                0006 cubed-sphere grid set-up (6 faces 32x32, 26 levels, non uniform deltaP).
                0007
                0008 ### Overview:
                0009 This experiment contains 2 aqua-planet like set-ups (with corresponding `input[.*]/` dir)
                0010 that can be run with the same executable (built from `build/` dir using customized
                0011 code from `code/`); binary input files have been generated using matlab script
                0012 `gendata.m` from the `input` dir.
                0013 Both test experiments start from a spin-up state using pickup files written after 1 year.
                0014
                0015 The **primary** test, using input files from `input/` dir,
                0016 has an interactive SST with a 10m mixed layer depth and a prescribed,
                0017 time-invariant Q-flux. It also includes a weak damping of stratospheric winds.
                0018
                0019 The **secondary** test, using files from `input.ape/` dir, is the same as the primary
                0020 test but without stratospheric wind damping, and uses prescribed idealized SST from
                0021 Neale and Hoskins, 2001, Aqua-Planet Experiment (APE) project.
                0022
                0023 ### Instructions:
                0024 Configure and compile the code:
                0025
                0026 ```
                0027   cd build
                0028   ../../../tools/genmake2 -mods ../code [-of my_platform_optionFile]
                0029   make depend
                0030   make
                0031   cd ..
                0032 ```
                0033
                0034 To run primary test:
                0035
                0036 ```
                0037   cd run
                0038   ln -s ../input/* .
                0039   ./prepare_run
                0040   ../build/mitgcmuv > output.txt
                0041 ```
                0042
                0043 There is comparison output in the directory:
                0044
                0045   `results/output.txt`
                0046
                0047 To run secondary "ape" test:
                0048
                0049 ```
                0050   cd run
                0051   rm *
                0052   ln -s ../input.ape/* .
                0053   ln -s ../input/* .
                0054   ./prepare_run
                0055   ../build/mitgcmuv > output.txt
                0056 ```
                0057 There is comparison output in the directory:
                0058
                0059   `results/output.ape.txt`
                0060
                0061 ### Notes:
                0062 There are special compiler options inside `build/genmake_local` to allow to compile
                0063 some of the files from `pkg/atm_phy` ; this requires to provide explicitly an optfile
                0064 to the `genmake2` command.