============================================
This is the README file for the SHYFEM model
============================================

    Copyright (c) 1992-2012 by Georg Umgiesser

    Comments and additions should be sent to the author:

      Georg Umgiesser                                  
      Oceanography, ISMAR-CNR
      Arsenale Tesa 104, Castello 2737/F
      30122 Venezia
      Italy

      Tel.   : ++39-041-2407943
      Fax    : ++39-041-2407940
      E-Mail : georg.umgiesser@ismar.cnr.it


    This file is part of SHYFEM.

    SHYFEM is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    SHYFEM is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with SHYFEM.  If not, see <http://www.gnu.org/licenses/>.


Directory structure
===================

fem3d		FEM model and utility routines
femadj		Routines for the adjustment of the grid after the
		automatic mesh generation. The program to run
		is adjele
femanim		Routines to generate animations from postscript files
fembin		Binaries used by the model
femcheck	Routines to set up and check the installation
femdoc		Documentation, manual, etc.
femersem	Routines for BFM (ERSEM) ecological model
femgotm		Routines for GOTM turbulence clousre model
femlib		Library routines (filled during compilation)
femplot		Plotting routines for post processing. The routine
		to run is plotsim, but this routine is more
		conveniently run through the command plots
femregres	Routines to do regression testing. Developers only.
femspline	Programs to smooth and reduce lines. These programs
		are used to change the resolution of the boundary
		line before running the automatic mesh generator.
		Please use the routine gridr.
grid		Visualization routine for GRD files
hcbs		Outdated files for plotting to monitor
mesh		Automatic mesh generator
post		Library for plotting to Postscript files.



Compiling the model
===================

You can compile everything from this directory (fem) by running the
command "make fem". Other commands are:

make fem	compiles everything
make clean	deletes objetc and executable files in all subdirectories
make cleanall	as clean, but cleans also libraries
make doc	makes documentation in femdoc (manual)
make all	compiles (fem) and makes documents (doc)



Utility routines
================

fembin:

diffs		compares files within two directories
tkdiff		compares two files using graphical user interface
gp		plots time series using gnuplot
gps		converts between image formats
splitcol	splits columns into single files

femrun		runs the model in batch mode
basinf		information on basin - calls fem3d/basinf
vpgrd		pre-processing routine for basin - calls fem3d/vp
splitext	splits ext files into time series - calls fem3d/splitext
splitflx	splits flx files into time series - calls fem3d/splitflx
plots		post-processing (plotting) routine - calls femplot/plotsim
makebline.pl	creates boundary line from grd file

fem3d:

basinf		information on the basin
*inf		information on simulation files (ext,flx,out,ous,nos,vol)

ht		the FEM model
vp		pre-processing routine for basin - creates bas file

laplap		does laplacian interpolation from single points
nos*		manipolate NOS files
splitext	splits ext files into time series
splitflx	splits flx files into time series