Description
This article is from the Electrochemistry FAQ, by Zoltan Nagy nagy@anl.gov with numerous contributions by
others.
7.2) Software package: Chemical reaction network toolbox (CRNT), Version 1.02
The Chemical Reaction Network Toolbox, Version 1.02 is now avail-
able via anonymous FTP at the site: ftp.che.rochester.edu in the directory
pub/feinberg.
There is no charge for the program. (It was developed as a suite of tools
in connection with research sponsored in part by the United States National
Science Foundation and the Petroleum Research Fund.)
The Chemical Reaction Network Toolbox (CRNT) is a program for IBM-
compatible personal computers. It does many, many things. People who use the
program tell me that it's VERY easy to use and that they like it a lot.
CRNT should be of interest to chemists, chemical engineers and mathemati-
cians at all levels of expertise (ranging from undergraduates to those
engaged in very advanced research). I know that CRNT will provide chemical
engineering students with lots of help with their kinetics homework!
The program consists of two parts, ChemLab and Network Analyst, that
"talk to each other". ChemLab is the part of CRNT that will probably be of
interest to most users, so I'll describe that first.
ChemLab is essentially a simulation environment. In response to a
user-specified network of chemical reactions (and a user-specified
assignment of rate constants), ChemLab will generate the appropriate
(isothermal mass action) system of ordinary differential equations governing
the species concentrations. (These differential equations will generally be
nonlinear and can be very complex.) In response to user-specified initial
conditions, ChemLab will solve the differential equations and display the
results in a variety of numerical and graphical formats. In particular,
ChemLab will plot species concentrations vs. time and will draw two- and
three-dimensional composition trajectories. ChemLab will also draw several
trajectories simultaneously so that you can see two- and three-dimensional
phase portraits.
Network Analyst, on the other hand, is somewhat more advanced. It
implements certain results in chemical reaction network theory. Chemical
reaction network theory deals with the relationship between reaction net-
work structure and qualitative properties of the corresponding differential
equations. For example, in response to a user-specified reaction network,
Network Analyst will try to determine if there can be rate constants such
that the resulting differential equations admit composition oscillations,
an unstable steady state, multiple steady states, a degenerate steady state
(i.e., one with a zero eigenvalue), and so on. When the Network Analyst
determines that the answer is NO, it will tell you so. On the other hand,
if Network Analyst determines, for example, that a reaction network has the
capacity for multiple steady states, it will exhibit a sample set of
rate constants along with a pair of steady states consistent with them.
(The rate constants and the steady states can be exported to ChemLab for
further study.) It should be mentioned in particular that Network Analyst
provides powerful tools for mechanism discrimination in heterogeneous
catalysis
CRNT comes with an on-screen tutorial and a help system that get
you up and running pretty quickly. (Or so I'm told.) The tutorial was
written primarily with chemical engineers and chemists in mind, but there's
an appendix for mathematicians who want to understand how the differential
equations come about. Again, ChemLab is probably the part of CRNT that will
be of interest to most users, so it's probably best to concentrate on that
first.
There are two files you'll want to retrieve via FTP: The first,
CRNTPACK.TXT, is a text file that explains how to use the main file,
CRNTPACK.EXE. (CRNTPACK.EXE is a compressed, self-extracting file that
"unpacks" all the files that CRNT need to run properly.) Before retrieving
CRNTPACK.TXT via FTP, the FTP mode should be ASCII (usually the default).
Just before retrieving CRNTPACK.EXE, you should change the FTP mode to
BINARY. This is done simply by entering BINARY at the FTP prompt.
Once the unpacking is finished, enter CRNT at the DOS prompt, and
you'll be up and running. On your first time out, you should select "Hello,
New User!" from the main menu. Have fun.
WHAT'S NEW IN VERSION 1.02
Apart from some minor bug fixes, there are three things that are new
in Version 1.02:
a. As of Version 1.02, the Chemical Reaction Network Toolbox is a protected
mode program. This means that it can use all of your computer's memory, not
just conventional memory. The program should run (as a DOS program) under
Windows reasonably well. That's been my experience with Windows 3.11, but I
don't yet know what will happen under Windows 95. You should know that
protected mode DOS programs (which is what CRNT is now) tend to run a little
slower than real mode programs. Moreover, they are more prone to bugs.
Please let me know if you find any and how they are provoked.
b. Users of previous versions have asked that results of ChemLab experiments
be exportable to text files. The idea is to have a plain output that can
then be imported to spreadsheet programs such as Excel, Lotus 123 or Quattro
Pro. You'll now find a new line in the Run Experiment menu labeled Write
Output to Text File. As before, the F1 key will provide help.
c. The old limitation of 32,767 integration steps is gone. You can now
choose 100,000 steps (actually 99,999). If anyone feels there's a need for
more, let me know.
*******************************************************************************
This freeware is courtesy of Martin Feinberg, Department of Chemical
Engineering, University of Rochester, Rochester, NY 14627.
With problems/questions contact:
CRNT@CHE.ROCHESTER.EDU
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