Gvc2Zax

gvc2zax vertical coordinate conversion tool

NOTE/TODO: gvc2zax is not (yet) part of the getm-utils repository. It should be added ASAP. Bjarne.

gvc2zax converts data from GETM netcdf output in general vertical coordinates into data on an equidistant z-grid.

TODO: Need edit - present version is simple copy from previous location at http://getm.eu/

It is assumed that the input netCDF file has GETM output style:

• using COARDS convention
• bathymetry is called "bathymetry"
• layer height is called "h" and is a 4D field h(time,level,y,x)

Usage

 gvc2zax [ -x xstart,xsteps -y ystart,ysteps -t timestart,timesteps ]
   -z [max_z(N),delta_z(N),num_z(N):max_z(N-1),delta_z(N-1),num_z(N-1):...] or [z(N):z(N-1):...] -Z [inverse of -z] [-p  -i  -s  -b -e -f]  -v var1,var2,..
  [ -gmt  {xy,xz,yz,bo} ] input-ncfile [ output-ncfile ]

 Options
 -help   prints help-string
 -x      sets start index and steps for x-range
 -y      sets start index and steps for y-range
 -t      sets start index and steps for time-range
 -z      sets z-grid. This grid needs its maximum_depth in m,
 its z-layer height in m and the number of z-layers.
-gmt    sets the slicetype to create 2d-GMT-gridfiles
              possible slicetypes are:
  bo: bottom value
  xy: xy-slice at a certain depth
  xz: xz-slice at a certain y-value
  yz: yz-slice at a certain x-value
gvc2zax creates a gridfile for every timestep and every fixed 3rd dimension. 
      These files are named: Variable_TimeIndex_3rdDimIndex.grd
      Additional to these files, gvc2zax creates a bath.xy file 
      with xy-data to create a bottom-polygon in GMT.
 -v      gives the list of 4D-variables to interpolate
 -i      The  first  index  of  z-values  is at the surface (default is at max_depth
 -p      Waterdepth is given with positive values (default is negative values)
 -s      Fill surface value from surface to       max_height=max_depth+n_zax*delta_z
 -b      Fill bottom value from max_depth to bottom
 -e      Z-grid is elevation above sea-floor instead of below surface
 -f      Forces GETM flexible ouput detection if e.g 'level' variable does not exist

Examples

 1. You want to convert variable temp and  salt  from  file  sylt.20lay-
   ers.nc  onto a 40 layer z-grid with maximum depth of 50m with a z-layer
   every 1.2m for the  whole  timerange  and  y-range,  but  only  for  x-
   index=20. The outputfile should be sylt.z.nc

    gvc2zax -x 20,1 -z 50.0,1.2,40 -v temp,salt sylt.20layers.nc sylt.z.nc

2. You want to create a xz slice of variable uu and vv out of result.nc for
    timeindex 20-25 and y-index 86 in a depth of 12m-15m in 10 vertical steps:
    gvc2zax -t 20,6 -y 86,1 -z 15.0,0.3,10 -v uu,vv -gmt xz result.nc
    creates uu_20_86.grd, uu_21_86.grd ... uu_25_86.grd  and  vv_20_86.grd,
    vv_21_86.grd ... vv_25_86.grd and bath_86.xy

Author: Richard Hofmeister

Compilation:

In order to compile the program, you need to set two environment variables:
NETCDFLIBDIR - path to netcdf lib directory
NETCDFINC - path to netcdf include directory
See [BuildInstructions].

Both variables are needed to compile GETM itself, so
it may not be necessary to re-set the two variables
in your system.
You can build the program by:

sh/bash style shell:

cd src
export NETCDFLIBDIR=/path/to/netcdf/lib
export NETCDFINC=/path/to/netcdf/include
make

csh/tcsh style shell:

cd src
set NETCDFLIBDIR /path/to/netcdf/lib
set NETCDFINC /path/to/netcdf/include
make

This should generate a bin/ directory and put the executable for gvc2zax in it. It is called "gvc2zax"

The following targets are allowed:

• all: Same as no target.
• clean: Remove some temporary files
• realclean: Remove some more temporary files.
• distclean: Remove all build files.

A usage string is implemented within the binary.
Run the program with option '-help', e,g, as

./bin/gvc2zax -help

For more help on usage see the manpage, located under this directory's man folder. To be able to use man gvc2zax, you have to add the path to man-directory to your system's MANPATH.

Additional environment variables:

BINDIR: Install gvc2zax binary in this directory