Getting numbers out of Cytosim using report

You can extract formatted data from Cytosim in two different ways:

• by using the report command in the configuration file.
• by running the report executable on the trajectory file.

Both methods produce nearly identical formatted text output with selected data, such as the coordinates of the filaments, their state or length, etc.

The report command

The command report can be called from the config file. The report will be generated by sim in the course of the simulation, but will be ignored by play. The output can be sent to specific files of your choice, for example forces.txt and positions.txt:

repeat 100
{
	run 100 system
	{
        nb_frames = 100
	}
	report fiber:force forces.txt
	report solid:position positions.txt
}

A star sends the reports to the terminal:

report single:force *
report fiber:force *

The report executable

If the simulation is already completed, you can use a separate executable called report to analyse the results. In this case report will read cytosim’s output files, and is limited to the frames that have been saved.

It is important to use a report made with the same settings as sim, in particular the dimensionality DIM defined in dim.h should be the same. To compile report:

make report

Invoke the report executable from the command line:

report fiber:force

This will analyse all the frames in the trajectory file, and send the output to the terminal. Example output:

% frame   10
% time    25
% identity      posX      posY    forceX    forceY   tension
% fiber f1:0001
         1    -4.142    -2.815     1.366    0.9282    -1.061
         1    -3.796   -0.8463         0         0   -0.8617
         1    -3.061     1.006         0         0   -0.7094
         1   -0.8413     2.949         0         0   -0.6838
         1     1.108     3.346         0         0   -0.8099
         1     3.093     3.136         0         0    -1.004
         1     4.069      2.92     -1.36    -0.976         0

It is possible to redirect the output to a file in UNIX:

report fiber:points > fiber_points.txt

You can also restrict reporting to a particular frame:

report fiber:points frame=10 > fiber_points.txt

or to some selected frames:

report fiber:points frame=10,20,30 > fiber_points.txt

For more info, please check:

report help

The framewise report executable

The executable reportF is similar to report, excepts that it sends the report of each frame into a different file. Hence,

reportF fiber:points

will create multiple files:

report0000.txt
report0001.txt
report0002.txt
report0003.txt
...

What can be reported?

There are many options to report and the list below may not be accurate. Please, try them out to see what information you can obtain. It is relatively easy to extend the report functions, declared in src/sim/simul.h and defined in src/sim/simul_report.cc to output something specific for a project.