HODGE-C(1) Version 0.98j HODGE-C(1)
22 March 1993
NAME
hodge - an implementation of Gerhard & Schuster's hodge-podge machine
SYNOPSIS
hodge [ options ]
[-A, --animation-file-name <name>]
[-C, --color-map-file-name <name>]
[-D, --dump-data-file-name <name>]
[-F, --number-of-frames <number>]
[-G, --groth-rate <number>]
[-I, --init-at-hotspot <number>]
[-J, --ill-cells-denominator <number>]
[-K, --infected-cells-denominator <number>]
[-M, --monitor-process <process>]
[-N, --number-of-cell-states <number>]
[-P, --plot-file-name <name>]
[-S, --size-of-grid <size>]
[-T, --time-steps <number>]
[-V, --version]
[-W, --warranty]
[-X, --start-of-film <timestep>]
[-Y, --skip-between-takes <number>]
[-b, --batch]
[-d, --no-dump]
[-f, --number-of-dumps <number>]
[-g, --gnuplot-data-format]
[-h, --help]
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[-i, --idl-data-format]
[-m, --moore-neighbourhood]
[-n, --no-film]
[-o, --on-line-visualization]
[-s, --seed-for-random <seedvalue>]
[-t, --torus]
[-x, --start-of-dump <timestep>]
[-y, --skip-between-dumps <number>]
DESCRIPTION
hodge implements a class of cellular automata (CA), that are also
known as hodge-podge machines. They have caught great attention when
being discussed in A.K. Dewdney's ``Computer Recreations'' column in
Scientific American. hodge, resembles the currently closest to reality
simulation of the Belousov-Zhabotinskii (BZ) reaction, the most
complex anorganic, oscillating reaction; but hasn't been invented for
this special purpose though (refer to the BIBLIOGRAPHY section below).
hodge's input and output streams, and all of it's default parameters
may be changed using various options (see the OPTIONS section below).
By default hodge generates 3 types of data files:
+ a single plot file, containing a per line statistical snapshot of
the CA's internal state
+ one or more dump file(s), each containing a snapshot of all cell
values of the CA, in either Gnuplot (line-oriented) or IDL (block-
oriented) format, and
+ one or more animation data file(s), each containing a snapshot of
all cell values of the CA, written in portable pixmap format, using
as much colors, as specified with the `--number-of-cell-states'
option.
Please, refer to the FORMATS section below.
ANIMATION
hodge's main purpose is to generate the previously mentioned snapshot
files for `making movies'. All you need is, eg. E. I. du Pont de
Nemours & Company's ImageMagick PD software (available via anonymous
ftp from export.lcs.mit.edu, as file `contrib/ImageMagick.tar.Z.')
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using the package's animate(1) command you'll soon see BZ waves move
across the grid. An example for this is given in the hodge/movie
folder of the HODGE-C distribution.
A different approach is to use IDL from Research Systems, Inc.
Boulder, CO, USA. An example for this purpose is given in the
hodge/idl folder of the HODGE-C distribution.
An animation companion to pixmon(1) called playmate(1) is also in the
making, and will be distributed in near future (refer to the
AVAILABILITY section below). Its application is rather simple: all
there is to do is to include a ``tee-log'' in the `--monitor-process'
eg.:
--monitor-process 'tee >pmdata.pix | pixmon ...'
to collect pixmon(1) data, that is later turned into animated pixmaps
by playmate(1).
A final, powerful and low cost solution for animation is to install
the KHOROS visualization package on your system. It comes for free
from the University of New Mexico, and is better than most commercial
products. KHOROS also features an easy to use graphical programming
interface called CANTATA and is very easy to learn for beginners in
scientific visualization. KHOROS features a bunch of converters to
it's internal VIFF(5) format, that is easily generated from hodge's
dump (eg. asc2viff(1)) and animation data files (eg. pbm2viff(1),
rast2viff, raw2viff(1), etc.)
OPTIONS
-A, --animation-file-name filename
Set the animation data file name pattern. (Defaults to hodge-
%0003d.ppm.)
-C, --color-map-file-name filename
Set the color map file name. (Defaults to hodge.map.)
-D, --dump-data-file-name filename
Set the data file name pattern. (Defaults to hodge-%0003d.dmp.)
-F, --number-of-frames number
Set the number of frames, ie. the number of animation data files
to write.
-G, --groth-rate number
The rate the value of an infected cell increases; described as
parameter g in A.K. Dewdney's article (defaults to 25).
-I, --init-at-hotspot number
Initialize every cell of the starting configuration as SANE and
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set value number to the center and its von Neumann neighbourhood
on the lattice.
-J, --ill-cells-denominator number
This parameter is used in the equation A/k1 + B/k2, where A is
the count of all ILL neighbour cells and B is a counter of all
INFECTED neighbour cells; this is parameter k1 (k2) in A.K.
Dewdney's article (defaults to 2).
-K, --infected-cells-denominator number
This parameter is used in the equation A/k1 + B/k2, where A is
the count of all ILL neighbour cells and B is a counter of all
INFECTED neighbour cells; this is parameter k2 (k1) in A.K.
Dewdney's article (defaults to 3).
-M, --monitor-process process
Set a monitor process; hodge opens a pipe to the given process
and writes it's CA's contents to this pipe, enabling the process
to visualize the incoming data. Defining a monitor process,
implies the `--on-line-visualization' option. (See the OPTION
SUMMARY for the process default.)
-N, --number-of-cell-states number
Set the number of states a SANE cell has to go through, being
INFECTED to finally become an ILL cell (defaults to 100).
-P, --plot-file filename
Plot data will go to filename (defaults to hodge.plt).
-S, --size-of-grid size
Set the CA's grid size, ie. the grid's x and y dimensions (x=y).
-T, --time-steps number
Run the simulation for number of timesteps.
-V, --version
Print a version and copyright message.
-W, --warranty
Print a warranty information message.
-X, --start-of-film timestep
Set the time step, when to start writing animation data.
-Y, --skip-between-takes number
Set the amount of timesteps to pass between successive animation
data takes.
-b, --batch
Run hodge in batch mode, ie. don't prompt the user for any input;
and don't produce any user notification output.
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-d, --no-dump
Don't write any dump files.
-f, --number-of-dumps number
Set the number of dump files to write.
-g, --gnuplot-data-format
Set the dump file format to Gnuplot (default).
-h, --help
Print a usage message containing all options.
-i, --idl-data-format
Set the dump file format to IDL.
-m, --moore-neighbourhood
Use a Moore neighbourhood, during computation of the CA's next
state, by default a Von-Neumann neighbourhood is used, ie. to
North, East, South and West, North-East, South-East, South-West
and North-West are added, when using this flag.
-n, --no-film
Don't write any animation data files.
-o, --on-line-visualization
Start the process given with the `--monitor-process' option, and
display the CA's contents on each time step. (Note: you need
either the pixmon(1) facility, or an appropriate double.)
-s, --seed-for-random seed value
Set the random number generator's seed with the integer seed
value.
-t, --torus
Make the 2D space of the CA grid borderless, ie. the 2D grid is
folded to a 3D torus.
-x, --start-of-dump timestep
Set the time step, when to start dumping.
-y, --skip-between-dumps number
Set the amount of timesteps to pass between successive dumps.
OPTION SUMMARY
To give no option at all is the same as to give the following options:
--monitor-process 'pixmon -dx 128 -dy 128 -scale 5 -
cmap hodge.map'
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--animation-file-name hodge-%0003d.ppm
--color-map-file-name hodge.map
--number-of-frames 1
--start-of-film 1
--skip-between-takes 1
--dump-data-file-name hodge-%0003d.dmp
--gnuplot-data-format
--start-of-dump 1
--skip-between-dumps 1
--time-steps 1000
--grid-size 128
--number-of-cell-states 100
--ill-cells-denominator 2
--infected-cells-denominator 3
--groth-rate 25
--plot-file-name hodge.plt
--seed-for-random 12345678
FORMATS
The only INPUT FORMAT hodge acknowledges, is a color map file, using
256 colors with the following RGB format:
# File: demo.map
# Creator: joke
# <- this is a comment line: '#' in the 1st column
<red intensity 0> <green intensity 0> <blue intensity 0>
<red intensity 1> <green intensity 1> <blue intensity 1>
<red intensity 2> <green intensity 2> <blue intensity 2>
...
<red intensity 255> <green intensity 255> <blue intensity 255>
Thus a non-commented color map file consist of 256 lines each one
containing such a color description. Eg. to get a greyscale `color'
map, simply use the same intensities for all colors.
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The OUTPUT FORMATS are as follows:
+ The plot file format is precisely specified as:
<timestep 0> <# sane> <# infected> <# ill> <percentage of infected cells>
<timestep 1> <# sane> <# infected> <# ill> <percentage of infected cells>
<timestep 2> <# sane> <# infected> <# ill> <percentage of infected cells>
...
<timestep n> <# sane> <# infected> <# ill> <percentage of infected cells>
on a per line base, with <timestep 0> running from 1 to n, the
latter being specified by the `--time-steps' option.
+ The dump file format depends on whether the Gnuplot data file
format, or the IDL data file format has been chosen, with the first
being the default, when no user-specification via run-time option
has taken place.
+ The Gnuplot (line-oriented) data file format:
<xcell index 0> <ycell index 0> <xycell value 0,0>
<xcell index 1> <ycell index 0> <xycell value 1,0>
<xcell index 2> <ycell index 0> <xycell value 2,0>
...
<xcell index n> <ycell index 0> <xycell value n,0>
<xcell index 0> <ycell index 1> <xycell value 0,0>
<xcell index 1> <ycell index 1> <xycell value 1,1>
<xcell index 2> <ycell index 1> <xycell value 2,1>
...
<xcell index n> <ycell index 1> <xycell value n,1>
...
<xcell index n> <ycell index n> <xycell value n,n>
+ The IDL (block-oriented) data file format:
<xcell-index 0>
<xcell-index 1>
<xcell-index 2>
...
<ycell-index 0>
<ycell-index 1>
<ycell-index 2>
...
<xycell value 0,0>
<xycell value 1,0>
<xycell value n,0>
...
<xycell value n,n>
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+ The animation file format is the portable pixmap format, as defined
by Jeff Poskanzer for his bitmap conversion collection pbmplus. I
thus direct the reader to the appropriate manual page(s) of that
package, ie. pbmplus(1), and ppm(5).
EXAMPLES
The following are two examples displaying the dumps of a 2x2 grid:
The Gnuplot data file format:
1 1 0
1 2 10
2 1 37
2 2 100
The IDL data file format:
1
2
1
2
1
2
1
2
0
10
37
100
FILES
Unless specified otherwise hodge reads in the first, and writes the
following files at run-time:
hodge.map default color map
hodge.plt plot data file
hodge-xyz.ppm animation data file(s) in ppm format
hodge-xyz.dmp dump data file(s) in either Gnuplot or IDL format
The distribution of HODGE-C contains, besides the usual source and
makefiles, the following files:
INSTALL hints for installation of hodge on your system
configure C shell script to configure hodge for your system
config/*.cf various system's configuration files
contrib/infekt2.c Martin Gerhard's original source
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cmaps/*.map various color maps
khoros/README hints for making movies with KHOROS
khoros/movie C shell script to run hodge
khoros/bz-*.vif demo animation data
magick/README hints for making movies with IMAGEMAGICK
magick/movie C shell script to run hodge
magick/bz-*.gif demo animation data
magick/gif2vif shell script converting GIF to VIFF files
idl/README hints for making movies with IDL
idl/idemo C shell script to run hodge
idl/iload shell script that uncompresses and loads idata.Z
idl/idata.Z demo animation data
typ? demo C shell script to produce type #? (1-4) plot files
typ?.gnu gnuplot(1) command file to produce 2D and 3D plots
BUGS
hodge has even more options than ls.
The pseudo code given in the Scientific American article contains a
subtle bug: Dewdney confused the meaning of A and B, ie. he says ``A
counts the infected neighbours and B the ill ones,'' but it's the
other way round. For the interested, Martin Gerhard's original ATART
ST version of the hodge-podge machine is included in this
distribution.
ALGORITHM
Due to this confusion I give here the correct algorithm core in pseudo
code:
foreach cell do
A := count of ill neighbour cells // range: [0..8]
B := count of infected neighbour cells // range: [0..8]
S := value of all neighbour cells + value of cell // range: [0..8*n]
case state(cell) of
SANE:
begin
newval := A/k1 + B/k2
end
INFECTED:
begin
B := B + 1 // count self (sic!)
newval := S/B + g // ...else B could be zero
end
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ILL:
begin
newval := 0 // 0 means SANE
end
esac
if newval > MAXVALUE // number-of-cell-states option (=n)
value(cell) := 0
else
value(cell) := newval
od
BIBLIOGRAPHY
BZ specific publications:
A.K. Dewdney, Computer Recreations, Scientific American, August, 1988.
Stefan C. Mueller, Theo Plesser and Benno Hess, The Structure of the
Core of the Spiral Wave in the Belousov-Zhabotinskii Reaction,
Science, 230(4726), November, 1985.
Stefan C. Mueller, Theo Plesser and Benno Hess, Three-dimensional
Representation of Chemical Gradients, Biophysical Chemistry, February,
1987.
Cellular automata theory and practice:
D. Farmer, T. Toffoli and S. Wolfram, Cellular Automata, North-
Holland, Amsterdam, 1984.
S. Wolfram, Theory and Applications of Cellular Automata, World
Scientific Publishing, Singapore, 1986.
Christopher G. Langton, Artificial Life, Addison-Wesley, Redwood City,
CA, 1989. (The Proceedings of an Interdisciplinary Workshop on the
Synthesis and Simulation of Living Systems held September, 1987 in Los
Alamos, New Mexico.)
Christopher G. Langton, et al., Artificial Life II, A proceedings
volume in the Santa Fe Institute Studies in the Science of Complexity,
Addison-Wesley, Reading, MA, 1990. (Proceedings of the Workshop on
Artificial Life held February, 1990 in Santa Fe, New Mexico.)
Introductory books:
Paul Davies, Cosmic Blueprint, Heinemann, London, UK, 1988.
John Briggs and F. David Peat, An Illustrated Guide to Chaos Theory
and the Science of Wholeness, Harper & Row, New York, NY 1989.
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SEE ALSO
gnuplot(1), imagemagick(1), khoros(1), pbmplus(1), pixmon(1),
playmate(1), xv(1), ppm(5)
AUTHOR
Copyright (C) 1993 by Joerg Heitkoetter
Systems Analysis Group, University of Dortmund, Germany.
Send bugs, comments, etc., to (joke@ls11.informatik.uni-dortmund.de).
CREDITS
I'd like to thank Joachim Sprave, of the Systems Analysis Group for
lending and extending his pixmon(1) visualization package, to suit my
needs; moreover Uli Hermes and Frank Kursawe for help with IDL. I am
also greatfully indepted to Heike Schuster and Martin Gerhard for
their enthusiasm and friendly explanations, when we met at the
Biomathematics Research Group, at the former Max-Planck-Institute for
Nutrition Physiology, in 1988, which has been renamed to MPI for
Molecular Physiology, in February 1993. More thanks go to Jenna W.
Dea, currently at UCSC, for lots of questions on CAs, and giving me an
opportunity; to once again spend my time on things, I do not have time
for.
AVAILABILITY
This work is protected by the terms of the GNU General Public License.
Please refer to the LICENSE file accompanying the sources of this
software package for a lengthy, boring, but absolute complete
description.
The sources come from MAGPIE -- The European Free Software Factory
Project. For more information on MAGPIE send email to
(joke@ls11.informatik.uni-dortmund.de).
HODGE-C is available via anonymous ftp from the group's server
lumpi.informatik.uni-dortmunde.de (129.217.36.140) as file `hodge-c-
0.98j.tar.Z' in /pub/CA/src.
WARRANTY
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 (at
your option) any later version.
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.
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You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
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