readme

This simple simulation of a pulse traveling down a parallel-plate guide makes a handy test code for

README file for ToyBoxFDTDbezhig 1.0
 Copyright (C) 1998, 1999 Laurie E. Miller, Paul Hayes, Matthew O'Keefe

With this README file you should also have received

gpl.txt			A copy of the GNU General Public License

ToyBoxFDTDbezhig.c	A listing of the ToyBoxFDTDbezhig source code

Makefile		         The makefile for compiling ToyBoxFDTDbezhig

chengGbry2.cmap	A useful colormap for viewing the results of 
			ToyBoxFDTDbezhig in animabob or viz.

/////////////////////////////////////////////////////////////////////////////
Regarding ToyBoxFDTDbezhig, version 1.0:
 Copyright (C) 1998, 1999 Laurie E. Miller, Paul Hayes, Matthew O'Keefe 

 This program 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 2
     of the License, or any later version, with the following conditions
     attached in addition to any and all conditions of the GNU
     General Public License:
     When reporting or displaying any results or animations created
     using this code or modification of this code, make the appropriate
     citation referencing ToyBoxFDTDbezhig by name and including the 
     version number.  

 This program 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 this program; if not, or if you cannot read your copy,
     write to the Free Software Foundation, Inc.
     59 Temple Place, Suite 330, Boston, MA  
     02111-1307  USA

/////////////////////////////////////////////////////////////////////////////

ToyBoxFDTDbezhig 1.0 as delivered uses 1.2 Mbytes of main memory to run and 
generates 200 files of 25 kbytes each for about 5 Mbytes total output.
If this will choke your machine, you should alter the global constants at the
beginning of the code as a preventative measure. However, this is a very tiny
mesh for 3D FDTD, so if it's going to choke your machine, you'll be needing 
to find another if you're going to FDTD much.  

/////////////////////////////////////////////////////////////////////////////

What to do with the source now that you've got it:
(The suggested commands in these notes are Unix commands.  If you're using
 a different operating system, you'll want to use your system's equivalent
 commands.)

If you're reading this, I assume you've

1. downloaded the tar file: ToyBoxFDTDbezhig-1.0.tar.gz or 
  ToyBoxFDTDbezhig-1.0.tar

2. if you chose ToyBoxFDTDbezhig-1.0.tar.gz, un-gzipped it with a command 
  like: 

	gunzip ToyBoxFDTDbezhig-1.0.tar.gz

     for more info on gzip compression/uncompression see the web page at
	http://cemtach.org/software/software.html

3. untarred the tar file with a command like: 

	tar xvf ToyBoxFDTDbezhig-1.0.tar

4. changed to the new directory just created: cd ToyBoxFDTDbezhig

Unless of course you're reading this on the web page, in which case you should
go and do steps 1-4, and then

5. compile the file -- type the command: make

6. run that baby: you can either
	a. just type the name of the executable: 

		ToyBoxFDTDbezhig

	   in which case the progress notes during the course of the 
	   simulation will appear on the screen, or

	b. use a command like: 

		ToyBoxFDTDbezhig >&! runlog &

	   in which case all the progress notes will be written to a file
	   named runlog which you can view a screenful at a time using the
	   command: more runlog

/////////////////////////////////////////////////////////////////////////////

OK, now you've got a whole bunch of files named somethingorother.bob in your 
directory.  Each of these files is a string of data bytes.  You probably want 
to look at them somehow.  If you have a volume visualization tool you know 
and like, you should use that one, though you may need to alter the output 
portion of the ToyBoxFDTDbezhig source code to suit your tool.


Here's another way:

On the CEM TACH software page, 

	http://cemtach.org/software/software.html

you will see a link to BoB/AnimaBoB.  It's free.  Download yourself a copy 
if you haven't already got one and get it running. 

Next check those progress notes from your run; you'll see a command like:

	bob -cmap chengGbry2.cmap -s 133x21x9 *.bob

at the beginning and at the end of the notes.  This activates bob with the
colormap included in the tar file and feeds it the appropriate dimensions
of the simulation mesh.  If you change the dimensions of the waveguide,
the progress notes will show the new correct bob command for the different-
sized mesh.  This is one good reason to keep your progress notes in a runlog
file.  Once bob has fired up and loaded, make sure the x, y, and z dimensions
are set to maximum, and then just hit "start" to see the files play.


Or, here's another way:

On the CEM TACH software page, 

	http://cemtach.org/software/software.html

you will see a link to Viz.  It's also free.  Download yourself a copy and get
it running.  

Next check those progress notes from your run; you'll see a command like:

	viz ToyBoxFDTDbezhig.viz

at the beginning and at the end of the notes.  This activates viz with the
colormap included in the tar file and feeds it the appropriate dimensions
of the simulation mesh.  If you change the dimensions of the waveguide, the 
ToyBoxFDTDbezhig.viz file will update accordingly when you run the new 
simulation.

-----

You also now have files named bezhigCenter.dat and bezhigStimulus.dat sitting
in your directory.  bezhigCenter.dat has recorded two numbers per timestep, 
the current simulated time and the electric field intensity in the z direction
for a point near the center of the mesh. bezhigStimulus.dat has recorded the 
current simulated time and the value of the stimulus for each timestep.  You
can view them using commands like:

	more bezhigCenter.dat
	more bezhigStimulus.dat

but that's really boring 'cause you just get a long double column of numbers
down your screen.  Any 2D graphing or plotting tool should be able to open it
and plot it for you.  The two I've used are grace/xmgr and excel.  Grace 
and xmgr are free, excel is extremely un-free.  Grace is a newer version 
of xmgr available free under the GNU GPL.

To view them in grace/xmgr: On the CEM TACH software page, 

	http://cemtach.org/software/software.html

you will see a link to grace.  Once again, it's free.  Download yourself a 
copy and get it running.  To start it up, type

	xmgrace bezhigCenter.dat bezhigStimulus.dat

or, if you're using xmgr,

	xmgr bezhigCenter.dat bezhigStimulus.dat

and grace/xmgr will plot and display both data sets on the same plot.  

Here are some useful features in xmgr (they work exactly the same in grace).
To zoom in, I use the graph->world scaling controls.  There are also buttons 
along side the main window for x-axis and y-axis zooming.  The data->status
controls are handy for adding and deleting data series on one plot; if you
hit the deact button and click on a series, it disappears from the display,
but can be reinstated by hitting react and clicking on the area for that 
series in the data window.

To view them in excel, assuming you have excel on some handy machine, fire 
up excel and use the File->Open command and type in the file name of one of
the files.  Depending on the version you have, excel will probably ask you 
various questions about the file; you want to tell it that the file is 
space-delimited.  Excel should then load the file as two columns of data.
The Plot Wizard function should then walk you through plotting the data.
One peculiarity of Excel is that it will plot the field intensities and 
times as two separate functions, instead of field intensity as a function 
of time.  There's a way to make it plot one as a function of the other,
but how to do it varies from version to version.  So before invoking the 
Plot Wizard, I highlight just the second column of data, and then the Plot
Wizard just plots the intensity values and ignores the time data.

In my highly subjective opinion, grace/xmgr is easier to use, but I've found
excel handy for making plots that insert neatly into a powerpoint set of
slides.  

/////////////////////////////////////////////////////////////////////////////

Playing with your ToyBoxFDTDbezhig:

You can vary the simulation quite a bit and see different things just by
changing the #define statements at the beginning.  With these you can choose
either the pulse stimulus or a continuous plane wave as input, and you can
choose whether you want the sides of the guide to be PMC (parallel-plate 
waveguide), or PEC (rectangular waveguide).  You can also alter the length,
simulated width, and height of the waveguide, the frequency of the 
stimulus, the number of timesteps it runs, and how often it writes data to an 
output file.  I set this last control, (PLOT_MODULO) to a fairly high number, 
which means it doesn't output very often.  This is to keep the amount of
data choking your system low, but it also makes for a jerky animation.  You
may want to set it to a smaller number to smooth things out a bit so the
results look nice when you view the data files with your volume visualization
tool of choice.  

With regards to autoscaling/no autoscaling, read the comments in the code
thoroughly before playing with those options.  Otherwise you may not like 
what you get.  

You can of course alter the code in other ways to make different simulations.
That's what it's there for.  Further suggestions on playing with it will 
start to appear on the ToyBoxFDTD page at

	http://cemtach.org/software/ToyBoxFDTD/ToyBoxFDTD.html

when I get past final exams... and when my hand fatigue gets better.

/////////////////////////////////////////////////////////////////////////////

About the Makefile and make commands:

If you type: 

	make cleandata 

in your ToyBoxFDTDbezhig directory, it will remove all the data files (all 
files ending in .bob, the .viz file, the bezhigCenter.dat and 
bezhigStimulus.dat files, and the runlog file, if you made one).  If you 
want to keep your runlog file to keep track of simulations you've done or 
keep any other file, rename it something else first:

	mv runlog whatever


If you type:

	make clean

in your ToyBoxFDTDbezhig directory, it will remove all the object and 
executable files, file copies ending in ~, and core files from any core dumps 
you've managed to generate. 


If you view the Makefile, you'll see a bunch of lines starting with CFLAGS.
All of them are commented out (by a # at the beginning of the line) except 
the last.  Only one of these should ever be uncommented at once.  The last, 

	CFLAGS = -Xcpluscomm -g

is what you want to use if you're going to run a debugger on the executable.
The others (different level of compiler optimization) are there for your 
convenience.  If you don't know what they are, you should talk to a 
friendly neighborhood compiler guru before you try messing with them.

/////////////////////////////////////////////////////////////////////////////

 Contacting the perpetrators:

 Laurie E. Miller, Paul Hayes, Matthew O'Keefe
 Department of Electrical and Computer Engineering
      200 Union Street S. E.
      Minneapolis, MN 55455

 [e-mail]
 [e-mail]
 
 http://cemtach.org
 http://cemtach.org/software/ToyBoxFDTD/ToyBoxFDTD.html

/////////////////////////////////////////////////////////////////////////////