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FAQ
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#------------------------------------------------------------------------
#
# Copyright (C) 1985-2018 Georg Umgiesser
#
# This file is part of SHYFEM.
#
#------------------------------------------------------------------------
General questions:
How do I construct a grid to be used with SHYFEM?
This is very general question. Basically you will need information on the
coast line and bathymetry information. You will then have to elaborate
these data. A good point to start is the document GridGeneration.txt
in femdoc.
Basically you will have to fit your coastline to your desired resolution,
then you will have to manually adjust the line with "grid", and then you
have to create a mesh with "mesh". After this you will have to interpolate
the bathymetric data to the mesh.
What is dos and unix file format?
One more problem I saw was that the format of the grd file is dos. This
should normally not be of a problem, but sometimes it is. You can convert
from dos to unix with d2u, and vice-versa with u2d.
Questions about "grid":
What is the format of the GRD file?
Please have a look at the document grd_format.txt in femdoc.
How can I work with grid?
which are too close to be processed. You should have a look on these.
You can find them easily. Just fire up "grid" and then choose show node.
Then insert a node number from the keyboard and hit Enter.
The program shows you the node.
Questions about "mesh":
mesh: CircumCicle error
Thanks for the reply. I have adjusted the nodal distance on the perimeter
input grd file form 10 to 20 meters and mesh run without errors. There
was nothing wrong specific with the nodes mentioned in the previous error
message. It could have been any node because the distance between the
boundary nodes was 10 meters everywhere. It must have been the relative
large contrast between the interior nodal distance and the one on the
perimeter of the lake in question.
How do I get a nice transition of the mesh close to the boundary line?
Still the mesh I got (see picture) is not showing a gradual change in
nodal distance from edge to centre, so the question remains how to use
the -g command in mesh to get the nice transition like in the example,
you have sent, of the coast of israel.
How to include internal islands?
Do you have an manual available of mesh ? Because I also want to included
internal islands and I have not got a clue how to do that.
Internal islands: just put them as closed lines inside the outer coast
line. The only thing is, you have to look out that the lines have the
right type:
1 external coast line
2 internal islands
4 internal lines where elements do not cross (are not closed, so no islands)
I asked earlier a question about the SHYFEM model and it's been running
fine after your instructions. Now I'm just waiting to get the actual
data. I still have one problem to solve relating to the surface heat
flux. I have not found, what are the exact parameters "qflux" needs as
input values. I thought I could find it easily from the code, but it
still crashes due unrealistic values on test runs.
you can find what is read from the file in subqfxf.f at around line
320. There are also some comments. The only thing you have to look out
is if you use relative humidity or wet bulb temperature. The program
is set up in order to use humidity. Otherwise you have to change bhumid
to .false.
If you continue to have problems, just send me the offending file and
I will have a look at it.
Is there any windows version of SHYFEM Software?
There is no native windos version of SHYFEM. However, with the help
of cygwin you can install an environment that is close to a Linux
environment, and under which you will be able to run SHYFEM. Please go
toe the web site http://www.cygwin.com/ and copy the program setup.exe
to your computer. Than run this program which will install the cygwin
environment on your computer.
I have installed cygwin in my computer. When I try to run the command
"make fem". It shows me "-bash: make: command not found". What is the
solution to this problem?
cygwin only provides basic functionality to run Linux programs. With
the basic install it does not provide all programs that are needed
to run SHYFEM. Therefore, some more programs have to be installed
additionally. With cygwin it is easy. Just run the same program you used
to install cygwin one more time. At a certain point you will get to the
page where you can install/uninstall/upgrade programs. Here you spcify
the programs that you need.
To find out what programs you will need, please go to femcheck and run
the script check_setup.sh. This will tell you what are programs are
installed and what programs you still might to have to instal.
How do I have to adjust the Rules.make file?
The Rules.make file contains basic settings for the model. Here you
have to specify the dimension of the arrays for your application and
the compiler you want to use. Other options are relative to parallel
execution, the matrix solver, the turbulence closure scheme and the
ecological module to use (if any).
The only thing you really have to change in the Rules.make file are the
choice of a compiler and the dimensions relative to the application you
want to use. Please look through the parameters and adjust the dimensions
to your application. Dimensions may be bigger than actually needed.
What concerns the compiler, if you have the Intel compiler installed,
then this is normally a good option. Otherwise you can use the Gnu
compilers (gfortran, or the older version g77).
Why do I get a "segmentation fault" when I run "grid"?
There are basically two reasons for this behavior. The first is that
you are running "grid" in a non-X11 environment. Typically this happens
in a cygwin environment if you have not started the X11 environment
("startx"). The second reason can be the fact that you have coonected with
"ssh" to another computer and forgot to use the "-X" flag. Therefore,
if you want to run "grid" from a remote computer, please log into the
computer with "ssh -X".