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4. Example problems

The ChemCell distribution includes an examples sub-directory with several sample problems. Each problem is in a sub-directory of its own. Each problem has an input script (in.*) and produces a log file (log.*). If may also produce a dump file (dump.*) when it runs. Some use one or more data files (data.*) of geometry or particle info as additional input. These were created via the Pizza.py pre-processing tool using the *.py scripts in the same directory.

Plots can be made from the log files using the "clog" and plotting tools in Pizza.py. Images and movies can be made from the dump and data files using the "cdata", "dump", and various visualization tools in Pizza.py. Examples are shown on the ChemCell WWW Site.

These are the sample problems in the examples sub-directories:

abc simple A + B -> C reaction
kinase 3-stage kinase cascade
lotka Lotka-Volterra predator-prey system
ecoli E Coli chemotaxis signaling pathway model

Here is how you might run and visualize one of the sample problems:

cd kinase
cp ../../src/ccell_linux .         # copy ChemCell executable to this dir
ccell_linux < in.kinase            # run the problem 

Running the simulation produces the files dump.kinase and log.ccell. Assuming you have Pizza.py installed, you could visualize the dump file as follows:

pizza -f dview.py dump.kinase