Potts simulation set and series

A group of simulation series is called a set. A setup file can only contain one set. A simulation series is a group of simulations that only differ in the random seed. Each series includes additional tags that define various parts of the series. A set can include multiple series tags.

<set prefix="[PREFIX]">
    <series name="[NAME]" start="[START]" end="[END]"
            ds="[DS]" margin="[MARGIN]" length="[LENGTH]" width="[WIDTH]" height="[HEIGHT]"
            dt="[DT]" ticks="[TICKS]" interval="[INTERVAL]">
        ...
    </series>
</set>

ATTRIBUTE	DESCRIPTION	TYPE	DEFAULT
prefix	prefix for all series names	string	””
name	name of the simulation series for output files	string
start	starting random seed	integer	0
end	ending random seed	integer	0
ds	spatial conversion factor (um/voxel)	integer, float, fraction	1
margin	initialization boundary margin	integer	0
length	x size of the simulation environment	integer	100
width	y size of the simulation environment	integer	100
height	z size of the simulation environment	integer	1
dt	temporal conversion factor (hrs/tick)	integer, float, fraction	1
ticks	total number of simulation ticks	integer	100
interval	number of ticks between snapshots	integer	50

If height = 1, the simulation uses 2D rules. If height > 1, the simulation uses 3D rules.

Note that the environment grid assumes a one-voxel border in each direction (except in the z direction in a 2D simulation). For 2D simulations, length and width must be at least 3 for valid simulations. For 3D simulations, length, width, and height must be at least 3 for valid simulations.

The initialization margin defines the number of voxels in the x and y directions that are not used when initializing cells.

Example: Set with single series

Specifies a simulation set with one simulation series. Series A is simulated with random seeds 0, 1, 2.

<set prefix="SET_">
    <series name="A" start="0" end="2">
        <!-- Simulation series produces outputs: SET_A_0000, SET_A_0001, SET_A_0002 -->
    </series>
</set>

Example: Set with multiple series

Specifies a simulation set with three simulation series. Series A is simulated with random seeds 0, 1, 2. Series B is simulated with random seed 2. Series C is simulated with random seeds 1 and 2.

<set prefix="SET_">
    <series name="A" start="0" end="2">
        <!-- Simulation series produces outputs: SET_A_0000, SET_A_0001, SET_A_0002 -->
    </series>
    <series name="B" start="2" end="2">
        <!-- Simulation series produces outputs: SET_B_0002 -->
    </series>
    <series name="C" start="1" end="2">
        <!-- Simulation series produces outputs: SET_C_0001, SET_C_0002 -->
    </series>
</set>