fix conc/set command

Syntax:

fix ID conc/set N file Nsp sp1 sp2 ... 

• ID is documented in fix command
• conc/random = style name of this fix command
• N = apply fix every this many timesteps
• file = filename in which time-course data is specified
• Nsp = # of species to set concentration of
• sp1,sp2,etc = IDs of species

Examples:

fix mine conc/set 100 data.time 2 CheA CheAa 

Description:

Set the concentration level of certain species at specified time increments in a non-spatial simulation. This is an effective way of coupling ChemCell to another model or simulation that pre-computed concentration vs time profiles of certain species.

Here is how the fix operates. Every N timesteps, the concentration or count of particles of each species in the specified list is reset to a new value which is listed in the time-course data file, which has the following format. Lines beginning with a "#" character are ignored. Other lines must begin with a time value (in seconds), followed by Nsp values. The time stamp for successive lines in the file should be monotonically increasing. For stochastic simulations (Gillespie), the value for each species is a particle count. For continuum simulations (ODE), the value for each species is a concentration in molarity.

On a timestep when the fix is applied, the file line with a time stamp just smaller (or equal) to the current time is used to set the species concentrations.

Restrictions:

This fix can only be used with non-spatial simulations.

Related commands:

count, fix conc/random

Default: none