Sim

sim performs the instructions specified in a config file, and it should generate 3 output files:

File	Type	Content
`properties.cmo`	text	the properties of all objects
`objects.cmo`	binary	positions of the objects at different time points
`messages.cmo`	text	informations such as the execution time

The trajectory file properties.cmo is by default a binary file, but it can be written in to a text-based format (see command write).

By default the config file is config.cym in the current working directory, but another file can be specified on the command line, if its name ends with a .cym extension, for example:

sim spindle.cym

For more instructions on how to use sim, check Running simulations.

Play

play generates a graphical representation of the system, and it is sometimes named cytosim. While sim can run on any computer, play requires OpenGL capabilities, and some of its functionality (eg. GIF support) depends on external libraries.

The Display parameters that control the graphical output can be embedded in the config file. The properties of most object have a display parameter that play will read. These parameters are ignored by sim, but they are copied verbatim to properties.cmo, where they are read by play. The display parameters can also be included in a separate file with extension ".cms", as in play 3d.cms.

play can be used to:

Purpose	Command
Display the simulation in the current folder	`play`
Perform a live simulation	`play live`
Generate images offscreen	`play image`

Display Mode

Use play to display a simulation calculated by sim. By default, play reads properties.cmo and objects.cmo, in the current directory.

A different trajectory file can be specified:

play final.cmo

Live Mode

Use play live to start a simulation and display it online:

play live

play live spindle.cym

This should open a window. This simulation is calculated on the fly, and nothing is saved.

Offscreen Mode

Play can generate images without opening a window, as for example:

Command	Result
`play image frame=10`	An image representing frame 10
`play image frame=10,20,30`	Three images representing the specified frames
`play image frame=10 image_format=png`	a PNG image representing frame 10
`play image magnification=3 frame=10`	an image for frame 10 at 3x magnified resolution
`play movie`	an image for each frame in the trajectory file

Cytosim is always able to generate PPM images, that can be open with ImageJ. Cytosim may be able to generate images in the GIF or PNG formats, if the required libraries were included during compilation.

Keyboard controls

Play is controlled by the keyboard and a pull-down menu. Here are the most useful controls:

Key	Action
`h`	show online help (press again to hide)
`p` `s`	play, stop
`<` `>`	previous, next frame
`+` `=`	zoom in, zoom out
arrow-keys	move around
`R`	write display parameters to terminal
`CTRL-Q`	quit (mac osx)

A list of keyboard commands is given by 'play keys'.

Accessory Programs

Cytosim has a number of other tools:

Program	Typical usage
`report`	generate analysis data from trajectory files
`frametool`	extract frames from trajectory files

See how they are used on Running simulations.

Clickable Icons

On MacOS or Linux, it is possible to use a script to start cytosim with a double-click. See for example bash/play_live.command and bash/play0000.command.