Last update:
$Id$
----------------------------------------------------------------------
Right now, there are only three options for the stand-alone driver which can be
used to test two different mixing methods. The first test is to output Bryan-
Lewis mixing on two columns (a high latitude column and a tropical column),
and output the diffusivity coefficients at each level. This can be run using
pointers (allocate memory in the driver, have CVMix data structures point to
it) or using pure memory copies (allocate memory in the driver AND CVMix).
The third driver sets up a single column using the shear mixing formula found in
the Large, et al. KPP paper. For this test, each level is a different local
gradient Richardson number rather than a different depth to show how viscosity
varies with different choices of Ri.
DIRECTORY STRUCTURE
-------------------
bin/ -- Default location for the cvmix executable.
lib/ -- Default location for libcvmix.a, the library that can be linked in
to an ocean model.
include/ -- Default location for the .o and .mod files that need to be included
with libcvmix.a.
doc/ -- Contains documentation. At this point, it only has a PDF of the latest
protex in-code notes and a script to generate said PDF.
manual/ -- This may be moved into doc/ at some point, it is the scientific
description of the CVMix package.
bld/ -- Contains auxiliary files needed by the build system. CompileFlags.mak
has default compile flags for 5 different compilers -- gfortran,
pgf90, ifort, xlf90, and nagfor, as well as ftn (the Cray wrapper for
pgf90). At this time, no other compilers are supported on Cray systems.
cvmix_setup is a python script that saves information about what
compiler to use and where netCDF is installed in .CVMix_env.
bld/obj -- Where .o and .mod files for the stand-alone drivers are stored.
src/ -- Contains the source code, organized as follows. The top directory
contains modules needed by the stand-alone driver (output, for example)
as well as the driver routine itself. Also contains the Makefile used
to build the cvmix executable.
src/drivers -- Subroutines called by the driver (one per tests).
src/shared -- Where all the modules that are needed to use CVMix with an
outside model are stored. (Use as an svn:external!) Also
contains the Makefile used to build the libcvmix.a library.
reg_tests/ -- I envision this becoming a way to do regression tests as we
develop the code, but for now it just contains two functional
tests. One outputs the diffusivity coefficients when using
Bryan-Lewis mixing on two columns (with each column having its
own B-L parameterization) and the other outputs the viscosity
coefficients when using the shear mixing scheme in the KPP
paper. (At this time the tests for double diffusion and tidal
mixing return all 0s because those modules are not complete.)
Note that all scripts have a "-h" (or "--help") flag to print
usage options and a "-nc" (or "--netcdf") flag to turn on netCDF
output.
BL Pointer test
---------------
reg_tests/Bryan-Lewis]$ ./BL_test.sh
BL Mem copy test
----------------
reg_tests/Bryan-Lewis]$ ./BL_test.sh -mc
Shear mixing test
-----------------
reg_Tests/shear-KPP]$ ./Large_test.sh
Both directories also contain a basic NCL script to produce a
plot.
Bryan-Lewis/plot_diff_coeffs.ncl -- makes a plot with depth on
the y-axis and diffusivity (for both columns) on the x-axis.
shear-KPP/plot_visc_coeffs.ncl -- makes a plot with local gradient
Richardson number on the x-axis and normalized viscosity
coefficient on the y-axis.
INSTALLATION NOTES
------------------
The src directory contains a Makefile and a simple 'make' should be sufficient
to build the standalone driver. The first time you build, the 'cvmix_setup'
utility will run and prompt you for compiler and netcdf information - it will
only run once, and the info is saved in bld/.CVMix_env.
To build with netcdf, run 'make netcdf'.
The default executable is $CVMix/bin/cvmix, but it can be overwritten with
'make EXE=[executable]'.