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6. Modifying & extending ChemCell

ChemCell is designed in a modular fashion so as to be easy to modify and extend with new functionality. In this section, changes and additions users can make are listed along with some minimal instructions. Realistically, the best way to add a new feature is to find a similar feature in ChemCell and look at the corresponding source and header files to figure out what it does. You will need some knowledge of C++ to be able to understand the hi-level structure of ChemCell and its class organization, but functions (class methods) that do actual computations are written in vanilla C-style code and typically operate on simple C-style data structures (vectors and arrays).

The new features described in this section require you to write a new C++ class. Creating a new class requires 2 files, a source code file (*.cpp) and a header file (*.h). Their contents are briefly discussed below. Enabling ChemCell to invoke the new class is as simple as adding two definition lines to the style.h file, in the same syntax as the existing ChemCell classes are defined in the style.h file.

The power of C++ and its object-orientation is that usually, all the code and variables needed to define the new feature are contained in the 2 files you write, and thus shouldn't make the rest of the code more complex or cause side-effect bugs.

Here is a concrete example. Suppose you write 2 files fix_foo.cpp and fix_foo.h that define a new class FixFoo that implements a boundary condition described in the classic 1997 paper by Foo, et. al. If you wish to invoke that boundary condition in a ChemCell input script with a command like

fix 1 foo 0.1 3.5 

you simply need to put your 2 files in the ChemCell src directory, add 2 lines to the style.h file, and re-make the code.

The first line added to style.h would be


in the #ifdef FixClass section, where "foo" is the style keyword in the pair_style command, and FixFoo is the class name in your C++ files.

The 2nd line added to style.h would be

#include "fix_foo.h" 

in the #ifdef FixInclude section, where fix_foo.h is the name of your new include file.

When you re-make ChemCell, your new boundary condition becomes part of the executable and can be invoked with a fix command like the example above. Arguments like 0.1 and 3.5 can be defined and processed by your new class.

Note that if you are using Makefile.list instead of Makefile to build ChemCell, you will need to explicitly add the names of your new .cpp and .h file to Makefile.list.

Here is a list of the kinds of new features that can be added in this way:

As illustrated by the fix example, these options are referred to in the ChemCell documentation as the "style" of a particular command.

The instructions below for each category will list the header file for the parent class that these styles are sub-classes of. Public variables in that file are ones used and set by the sub-classes which are also used by the parent class. Sometimes they are also used by the rest of ChemCell. Virtual functions in the header file which are set = 0 are ones you must define in your new class to give it the functionality ChemCell expects. Virtual functions that are not set to 0 are functions you can optionally define.

Region geometry options

Classes that define simple geometric regions are sub-classes of the Region class. See the region.h file for a list of methods these classes defines. Regions are used in ChemCell to define surfaces which particles diffuse between or on.

Region_sphere.cpp and region_sphere.h are the simplest example of a Region class. They implement the sphere style of the region command.

Here is a brief description of the class methods required:

bbox bounding box
inside determine whether a point is in the region
hex_intersect check if region surface intersects a hex cell
line_intersect check if line segment intersects region surface
compute_normal unit normal to region at a point
move2d perform a 2d move on region surface
distance compute distance from point to region surface

Fix options

In ChemCell, a "fix" is any operation that is computed during timestepping that alters some property of the system. It could be alteration of a rate or a rate equation, implementation of a boundary condition, or calculation of some diagnostic property. See the fix.h file for a list of methods these classes define.

Here is a brief description of the class methods. All of these methods are optional.

init called before timestepping
initial called at the beginning of each timestep
final called at the end of each timestep
cleanup called after timestepping

Simulator options

Classes that define the style of simulation being performed via the run_style command are sub-classes of the Simulator class. These include ODE solvers, a Gillespie solve, and a spatial solver for spatial simulations. See the simulator.h file for a list of methods these classed define.

Here is a brief description of the class methods required:

init setup a simulation
run the timestepper

New Top-level Commands

It is possible to add a new command to a ChemCell input script as opposed to adding a new style to an existing command (region, fix, simulator). For example the run and write_restart commands are top-level ChemCell commands that are listed in the Command section of style.h. When such a command is encountered in the ChemCell input script, the topmost level of ChemCell (ChemCell.cpp) simply creates a class with the corresponding name, invokes the "command" method of the class, and passes it the arguments from the input script. The command method can perform whatever operations it wishes on the ChemCell data structures.

Thus to add a new command, you simply need to add a *.cpp and *.h file containing a single class:

command operations performed by the new command

Of course, the new class can define other methods and variables that it uses internally.

(Foo) Foo, Morefoo, and Maxfoo, J of Biological Boundary Conditions, 75, 345 (1997).