fix command

Syntax:

fix ID style args 

• ID = user-assigned name for the fix
• style = style name of fix (see possible styles below)
• args = arguments used by a particular style

Examples:

fix 1 conc 100 data.file 2 CheA CheAa 2 CheAa CheA 

Description:

Set a fix that will be applied during a simulation. In ChemCell, a "fix" is any operation that is applied to the system during timestepping. Examples include adjusting reaction rates, applying boundary conditions, or computing diagnostics. There is currently only a small number of fixes defined in ChemCell, but others can be added - see this section of the documentation for a discussion.

The ID of a fix can contain alphanumeric characters and underscores.

Each fix style has its own documentation page which describes its arguments and what it does. For example, see the fix conc/set page for information on style conc/set.

Fixes perform their operations at different stages of the timestep. If 2 or more fixes both operate at the same stage of the timestep, they are invoked in the order they were specified in the input script.

Specifying a new fix with the same ID as an existing fix effectively replaces the old fix (and its parameters) with the new fix. This can only be done if the new fix has the same style as the existing fix.

Fixes can be deleted with the unfix command. Note that this is the only way to turn off a fix; simply specifying a new fix with a similar style will not turn off the first one.

Here is an alphabetic list of fix styles currently defined in ChemCell:

• fix conc/random - set the concentration of one or more species
• fix conc/set - set the concentration of one or more species
• fix dna/toggle - model DNA toggling on/off to modulate mRNA production
• fix rate/saturate - adjust the rate of one or more reactions

Restrictions: none

Related commands:

unfix

Default: none