# Potts and Lattice¶

## Potts Section¶

The first section of the .xml file defines the global parameters of the lattice and the simulation.

<Potts>
<Dimensions x="101" y="101" z="1"/>
<Anneal>0</Anneal>
<Steps>1000</Steps>
<FluctuationAmplitude>5</FluctuationAmplitude>
<Flip2DimRatio>1</Flip2DimRatio>
<Boundary_y>Periodic</Boundary_y>
<Boundary_x>Periodic</Boundary_x>
<NeighborOrder>2</NeighborOrder>
<DebugOutputFrequency>20</DebugOutputFrequency>
<RandomSeed>167473</RandomSeed>
<EnergyFunctionCalculator Type="Statistics">
<OutputFileName Frequency="10">statData.txt</OutputFileName>
<OutputCoreFileNameSpinFlips Frequency="1" GatherResults="" OutputAccepted="" OutputRejected="" OutputTotal=""/>
</EnergyFunctionCalculator>
</Potts>


This section appears at the beginning of the configuration file. Line <Dimensions x="101" y="101" z="1"/> declares the dimensions of the lattice to be101 x 101 x 1, i.e., the lattice is two-dimensional and extends in the xy plane. The basis of the lattice is 0 in each direction, so the 101 lattice sites in the x and y directions have indices ranging from 0 to 100. <Steps>1000</Steps> tells CompuCell how long the simulation lasts in MCS. After executing this number of steps, CompuCell can run simulation at zero temperature for an additional period. In our case it will run for <Anneal>10</Anneal> extra steps. FluctuationAmplitude parameter determines intrinsic fluctuation or motility of cell membrane.

Note

FluctuationAmplitude is a Temperature parameter in classical GGH model formulation. We have decided to use FluctuationAmplitude term instead of temperature because using word Temperature to describe intrinsic motility of cell membrane was quite confusing.

In the above example, fluctuation amplitude applies to all cells in the simulation. To define fluctuation amplitude separately for each cell type we use the following syntax:

<FluctuationAmplitude>
<FluctuationAmplitudeParameters CellType="Condensing" FluctuationAmplitude="10"/>
<FluctuationAmplitudeParameters CellType="NonCondensing" FluctuationAmplitude="5"/>
</FluctuationAmplitude>


When CompuCell3D encounters expanded definition of FluctuationAmplitude it will use it in place of a global definition –

<FluctuationAmplitude>5</FluctuationAmplitude>


To complete the picture CompuCell3D allows users to set fluctuation amplitude individually for each cell. Using Python scripting we write:

for cell in self.cellList:
if cell.type==1:
cell.fluctAmpl=20


When determining which value of fluctuation amplitude to use, CompuCell first checks if fluctAmpl is non-negative. If this is the case it will use this value as fluctuation amplitude. Otherwise it will check if users defined fluctuation amplitude for cell types using expanded CC3DML definition and if so it will use those values as fluctuation amplitudes. Lastly, it will resort to globally defined fluctuation amplitude (Temperature). Thus, it is perfectly fine to use FluctuationAmplitude CC3DML tags and set fluctAmpl for certain cells. In such a case CompuCell3D will use fluctAmpl for cells for which users defined it and for all other cells it will use values defined in the CC3DML.

In GGH model, the fluctuation amplitude is determined taking into account fluctuation amplitude of “source” (expanding) cell and “destination” (being overwritten) cell. Currently CompuCell3D supports 3 type functions used to calculate resultant fluctuation amplitude (those functions take as argument fluctuation amplitude of “source” and “destination” cells and return fluctuation amplitude that is used in calculation of pixel-copy acceptance). The 3 functions are Min, Max, and ArithmeticAverage and we can set them using the following option of the Potts section:

<Potts>
<FluctuationAmplitudeFunctionName>Min</FluctuationAmplitudeFunctionName>
…
</Potts>


By default we use Min function. Notice, that if you use global fluctuation amplitude definition Temperature it does not really matter which function you use. The differences arise when “source” and “destination” cells have different fluctuation amplitudes.

The above concepts are best illustrated by the following example:

<Potts>
<Dimensions x="100" y="100" z="1"/>
<Steps>10000</Steps>
<FluctuationAmplitude>5</FluctuationAmplitude>
<FluctuationAmplitudeFunctionName>ArithmeticAverage</FluctuationAmplitudeFunctionName>
<NeighborOrder>2</NeighborOrder>
</Potts>


Where in the CC3DML section we define global fluctuation amplitude and we also use ArithmeticAverage function to determine resultant fluctuation amplitude for the pixel copy.

In python script we will periodically set higher fluctuation amplitude for lattice quadrants so that when running the simulation we can see that cells belonging to different lattice quadrants have different membrane fluctuations:

class FluctuationAmplitude(SteppableBasePy):
def __init__(self, _simulator, _frequency=1):
SteppableBasePy.__init__(self, _simulator, _frequency)

self.quarters = [[0, 0, 50, 50], [0, 50, 50, 100], [50, 50, 100, 100], [50, 0, 100, 50]]

self.steppableCallCounter = 0

def step(self, mcs):

quarterIndex = self.steppableCallCounter % 4
quarter = self.quarters[quarterIndex]

for cell in self.cellList:

if cell.xCOM >= quarter[0] and cell.yCOM >= quarter[1] and cell.xCOM < quarter[2] and cell.yCOM < quarter[3]:
cell.fluctAmpl = 50
else:
# this means CompuCell3D will use globally defined FluctuationAmplitude
cell.fluctAmpl = -1

self.steppableCallCounter += 1


Assigning negative fluctuationAmplitude, cell.fluctAmpl = -1 is interpreted by CompuCell3D as a hint to use fluctuation amplitude defined in the CC3DML.

Let us revisit our original example of the Potts section CC3DML:

<Potts>
<Dimensions x="101" y="101" z="1"/>
<Anneal>0</Anneal>
<Steps>1000</Steps>
<FluctuationAmplitude>5</FluctuationAmplitude>
<Flip2DimRatio>1</Flip2DimRatio>
<Boundary_y>Periodic</Boundary_y>
<Boundary_x>Periodic</Boundary_x>
<NeighborOrder>2</NeighborOrder>
<DebugOutputFrequency>20</DebugOutputFrequency>
<RandomSeed>167473</RandomSeed>
<EnergyFunctionCalculator Type="Statistics">
<OutputFileName Frequency="10">statData.txt</OutputFileName>
<OutputCoreFileNameSpinFlips Frequency="1" GatherResults="" OutputAccepted="" OutputRejected="" OutputTotal=""/>
</EnergyFunctionCalculator>
</Potts>


Based on discussion about the difference between pixel-flip attempts and MCS (see “Introduction to CompuCell3D”) we can specify how many pixel copies should be attempted in every MCS. We specify this number indirectly by specifying the Flip2DimRatio by using

<Flip2DimRatio>1</Flip2DimRatio>


which tells CompuCell that it should make 1 times number of lattice sites attempts per MCS – in our case one MCS is 101x101x1 pixel-copy attempts. To set 2.5 x 101 x 101 x 1 pixel-copy attempts per MCS you would write:

<Flip2DimRatio>2.5</Flip2DimRatio>


The line beingning with <NeighborOrder>2</NeighborOrder> specifies the neighbor order. The higher neighbor order the longer the Euclidian distance from a given pixel. In previous The pixel neighbors are ranked according to their distance from a reference pixel (i.e. the one you are measuring a distance from). thus we have 1st 2nd, 3rd and so on nearest neighbors for every pixel in the lattice. Using 1st nearest neighbor interactions may cause artifacts due to lattice anisotropy. The longer the interaction range (i.e. 2nd, 3rd or higher NeighborOrder), the more isotropic the simulation and the slower it runs. In addition, if the interaction range is comparable to the cell size, you may generate unexpected effects, since non-adjacent cells will contact each other.

On hex lattice those problems seem to be less severe and there 1st or 2nd nearest neighbor usually are sufficient.

The Potts section also contains tags called <Boundary_y> and <Boundary_x>. These tags impose boundary conditions on the lattice. In this case the x and y axes are periodic.

For example:

<Boundary_x>Periodic</Boundary_x>


will cause that the pixels with coordinates x=0 , y=1, z=1 will neighbor the pixel with coordinates x=100, y=1, z=1. If you do not specify boundary conditions CompuCell will assume them to be of type no-flux, i.e. lattice will not be extended. The conditions are independent in each direction, so you can specify any combination of boundary conditions you like.

DebugOutputFrequency is used to tell CompuCell3D how often it should output text information about the status of the simulation. This tag is optional.

RandomSeed is used to initialize random number generator. If you do not do this all simulations will use same sequence of random numbers. Something you may want to avoid in the real simulations but is very useful while debugging your models.

EnergyFunctionCalculator is another option of Potts object that allows users to output statistical data from the simulation for further analysis.

Note

CC3D has the option to run in the parallel mode but output from energy calculator will only work when running in a single CPU mode.

The OutputFileName tag is used to specify the name of the file to which CompuCell3D will write average changes in energies returned by each plugins with corresponding standard deviations for those MCS whose values are divisible by the Frequency argument. Here it will write these data every 10 MCS.

A second line with OutputCoreFileNameSpinFlips tag is used to tell CompuCell3D to output energy change for every plugin, every pixel-copy for MCS’ divisible by the frequency. Option GatherResults=”” will ensure that there is only one file written for accepted (OutputAccepted), rejected (OutputRejected)and accepted and rejected (OutputTotal) pixel copies. If you will not specify GatherResults CompuCell3D will output separate files for different MCS’s and depending on the Frequency you may end up with many files in your directory.

One option of the Potts section that we have not used here is the ability to customize acceptance function for Metropolis algorithm:

<Offset>-0.1</Offset>
<KBoltzman>1.2</KBoltzman>


This ensures that pixel copies attempts that increase the energy of the system are accepted with probability

\begin{eqnarray} P = e^{(-\Delta E - \delta)/kT} \end{eqnarray}

where $$δ$$ and $$k$$ are specified by Offset and KBoltzman tags respectively. By default $$δ=0$$ and $$k=1$$.

As an alternative to exponential acceptance function you may use a simplified version which is essentially 1 order expansion of the exponential:

\begin{eqnarray} P = 1 - \frac{E-\delta}{kT} \end{eqnarray}

To be able to use this function all you need to do is to add the following line in the Pots section:

<AcceptanceFunctionName>FirstOrderExpansion</AcceptanceFunctionName>


## Lattice Type¶

Early versions of CompuCell3D allowed users to use only square lattice. Most recent versions allow the simulation to be run on hexagonal lattice as well.

Full description of hexagonal lattice including detailed derivations can be found in “Introduction to Hexagonal Lattices” available from http://www.compucell3d.org/BinDoc/cc3d_binaries/Manuals/HexagonalLattice.pdf

To enable hexagonal lattice you need to put

<LatticeType>Hexagonal</LatticeType>


in the Potts section of the CC3DML configuration file.

There are few things to be aware of when using hexagonal lattice. In 2D your pixels are hexagons but in 3D the voxels are rhombic dodecahedrons. It is particularly important to realize that surface or perimeter of the pixel (depending whether in 2D or 3D) is different than in the case of square pixel. The way CompuCell3D hex lattice implementation was done was that the volume of the pixel was constrained to be 1 regardless of the lattice type. There is also one to one correspondence between pixels of the square lattice and pixels of the hex lattice. Consequently, we can come up with transformation equations which give positions of hex pixels as a function of square lattice pixel position:

\begin{cases} & \left [ x_{hex}, y_{hex}, z_{hex} \right ] = \left [ \left ( x_{cart}+\frac{1}{2} \right ) L, \frac{\sqrt[]{3}}{2}y_{cart}L,\frac{\sqrt[]{6}}{3}z_{cart}L \right ] \text{for } y \mod 2=0 \text{ and } z \mod 3 = 0 \\ & \left [ x_{hex}, y_{hex}, z_{hex} \right ] = \left [ x_{cart} L, \frac{\sqrt[]{3}}{2}y_{cart}L,\frac{\sqrt[]{6}}{3}z_{cart}L \right ] \text{for } y \mod 2=1 \text{ and } z \mod 3 = 0 \\ & \left [ x_{hex}, y_{hex}, z_{hex} \right ] = \left [ x_{cart} L, \left ( \frac{\sqrt[]{3}}{2}y_{cart} +\frac{\sqrt[]{3}}{6} \right)L,\frac{\sqrt[]{6}}{3}z_{cart}L \right ] \text{for } y \mod 2=0 \text{ and } z \mod 3 = 1 \\ & \left [ x_{hex}, y_{hex}, z_{hex} \right ] = \left [ \left ( x_{cart}+\frac{1}{2} \right ) L, \left ( \frac{\sqrt[]{3}}{2}y_{cart} +\frac{\sqrt[]{3}}{6} \right)L,\frac{\sqrt[]{6}}{3}z_{cart}L \right ] \text{for } y \mod 2=1 \text{ and } z \mod 3 = 1 \\ & \left [ x_{hex}, y_{hex}, z_{hex} \right ] = \left [ x_{cart}L, \left ( \frac{\sqrt[]{3}}{2}y_{cart} -\frac{\sqrt[]{3}}{6} \right)L,\frac{\sqrt[]{6}}{3}z_{cart}L \right ] \text{for } y \mod 2=0 \text{ and } z \mod 3 = 2 \\ & \left [ x_{hex}, y_{hex}, z_{hex} \right ] = \left [ \left ( x_{cart}+\frac{1}{2} \right ) L, \left ( \frac{\sqrt[]{3}}{2}y_{cart} -\frac{\sqrt[]{3}}{6} \right)L,\frac{\sqrt[]{6}}{3}z_{cart}L \right ] \text{for } y \mod 2=1 \text{ and } z \mod 3 = 2 \\ \end{cases}

Based on the above facts one can work out how unit length and unit surface transform to the hex lattice. The conversion factors are given below:

\begin{eqnarray} S_{hex-unit}=\sqrt[]{\frac{2}{3\sqrt[]{3}}}\approx 0.6204 \end{eqnarray}

For the 2D case, assuming that each pixel has unit volume, we get:

\begin{eqnarray} L_{hex-unit}=\sqrt[]{\frac{2}{\sqrt[]{3}}}\approx 1.075 \end{eqnarray}

where $$S_{hex-unit}$$ denotes length of the hexagon and $$L_{hex-unit}$$ denotes a distance between centers of the hexagons. Notice that unit surface in 2D is simply a length of the hexagon side and surface area of the hexagon with side a is:

\begin{eqnarray} S = 6\frac{{\sqrt[]{3}}}{4}a^2 \end{eqnarray}

In 3D we can derive the corresponding unit quantities starting with the formulae for volume and surface of rhombic dodecahedron (12 hedra)

\begin{align*} &V = \frac{16}{9}{\sqrt[]{3}}a^3 \\ &S = 8{\sqrt[]{2}}a^2 \end{align*}

where a denotes length of dodecahedron edge.

Constraining the volume to be 1 we get:

\begin{eqnarray} a = \sqrt[3]{\frac{9V}{16\sqrt[]{3}}} \end{eqnarray}

and thus unit surface is given by:

\begin{eqnarray} S_{unit-hex} = \frac{S}{12} = \frac{8\sqrt[]{2}}{12}\sqrt[3]{\frac{9V}{16\sqrt[]{3}}}\approx 0.445 \end{eqnarray}

and unit length by:

\begin{eqnarray} L_{unit-hex} = 2\frac{\sqrt[]{2}}{\sqrt[]{3}}a = 2\frac{\sqrt[]{2}}{\sqrt[]{3}} \sqrt[3]{\frac{9V}{16\sqrt[]{3}}}\approx 1.122 \end{eqnarray}