Compucell3d manual

You can, of course, leave them unimplemented in which case they will have no effect on the simulation. Those 3 functions are imported , via inheritance, from SteppableBasePy. The nice feature of inheritance is that once you import functions from base class you are free to redefine their content in the child class.

We can redefine any combination of these functions. Had we not redefined e. Looping over select cell types. Finding cell in the inventory. Writing data files in the simulation output directory. Steering — changing Python parameters using Graphical User Interface. Applying force to cells. Setting cell membrane fluctuation ona cell-by-cell basis Modifying attributes of CellG object Controling steppable call frequency. Stopping simulation on demand or increasing maximum Monte Carlo Step.

Building a wall it is going to be terrific. Believe me Resizing the lattice Changing number of Worknodes Iterating over cell neighbors Mitosis Dividing Clusters aka compartmental cells Changing cluster id of a cell. For slow diffusion fields we can use standard explicit solvers e.

FlexibleDiffusionSolverFE but once the diffusion constant becomes large the number of extra calls to explicit solvers becomes so large that solving diffusion equation using Forward-Euler based solvers is simply impractical.

In situations where the diffusion constant is so large that the solution of the diffusion equation is not that much different from the asymptotic solution i. The CC3D stead state diffusion solvers are stable and allow solutions for large values of diffusion constants. The example syntax for the steady-state solver is shown below:. The only difference is that while FlexibleDiffusionSolverFE works in in both 2D and 3D users need to specify the dimensionality of the steady state solver.

We use. We can use Python to control secretion in the steady state solvers but it requires a little bit of low level coding. However, this means that if at each MCS secretion changes we have to do three things 1 zero entire field, 2 set secretion rate 3 solve steady state solver. An example below demonstrates how we control secretion of the steady state in Python.

Make sure you inherit from SecretionBasePy when you try to manage secretion in the steady state solver using Python. In other words, for this solver you cannot mix secretion specification in Python and secretion specification in the XML. Notice that all the pixels that do not secrete have to be 0. Fluctuation Compensator is an optional PDE solver add-on introduced in v4. The algorithm does not impose advection by domain deformation, but rather homogeneously applies a correction factor in each subdomain to all field solutions of a solver such that the total amount of each simulated species in each subdomain is unchanged over all spin flips.

Exactly one Fluctuation Compensator can be attached to each supported solver instance. An attached Fluctuation Compensator performs corrections on all fields of the solver to which it is attached.

For example, to attach a Fluctuation Compensator to a simple use-case with DiffusionSolverFE might look like the following. PDE solution field values can be modified outside of the solver routines without invalidating the correction factors of Fluctuation Compensators so long as they are notified that field values have been modified. Call this method after modifying field values and before the next PDE solution step to refresh Fluctuation Compensators according to your changes.

CC3D Reference Manual latest. Tip Starting from version 3. Warning When you want to solve more than one diffusive field using given diffusion you should declare those multiple fiuelds within a single definition of the diffusion solver. Warning We use Forward Euler Method to solve these equations. Note Depending on your computer hardware you may or may not be able to take advantage of GPU capabilities. To fix this you could use two approaches: 1.

Note We can use Python to control secretion in the steady state solvers but it requires a little bit of low level coding. Note Make sure you inherit from SecretionBasePy when you try to manage secretion in the steady state solver using Python. Warning Notice that all the pixels that do not secrete have to be 0. The Fluctuation Compensator algorithm consists of the following three rules. Stopping simulation on demand or increasing maximum Monte Carlo Step. Building a wall it is going to be terrific.

Believe me Resizing the lattice Changing number of Worknodes Iterating over cell neighbors Mitosis Dividing Clusters aka compartmental cells Changing cluster id of a cell. Here we introduced for user convenience a simple tag that does rescaling automatically. On a square lattice all those values have numerical value of 1.

All other quantities have values different than 1. As one can see the only addition that is required to couple diffusion equations has simple syntax:. CC3D Reference Manual latest. Tip Starting from version 3. Warning When you want to solve more than one diffusive field using given diffusion you should declare those multiple fiuelds within a single definition of the diffusion solver.

Warning We use Forward Euler Method to solve these equations. Read the Docs v: latest Versions latest stable 4.