How to Output Energy Changes

EnergyFunctionCalculator: allows you to output statistical data from the simulation for further analysis.

You can define this in XML like so:

<Potts>
    <Dimensions x="256" y="256" z="1"/>
    <Steps>100000</Steps>
    <Temperature>5</Temperature>
    <NeighborOrder>2</NeighborOrder>
    <EnergyFunctionCalculator Type="Statistics">
        <OutputFileName Frequency="10">statData.txt</OutputFileName>
        <OutputCoreFileNameSpinFlips Frequency="1" GatherResults="" OutputAccepted="" OutputRejected="" OutputTotal=""/>
    </EnergyFunctionCalculator>
</Potts>

Note

CC3D has the option to run in parallel mode, but output from the energy calculator will only work when running in 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 plugin along with the corresponding standard deviations. Frequency controls how often to record this data. In the above example, we would write data every 10 MCS.

Furthermore, the OutputCoreFileNameSpinFlips tag is used to tell CompuCell3D to output the energy change for every plugin’s pixel-copy operations.

Finally, GatherResults=”” will ensure that there is only one file written for accepted (OutputAccepted), rejected (OutputRejected), and both accepted and rejected (OutputTotal) pixel copies. If you do 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.