Cell Specific Plugin Energy
27 days ago by
I saw the post below for deltaH and am wondering its it's possible to extract a specific plugin energy for a specific cell. For example, if neighbor order is set to 2 and we have cell 1 surrounded by other cells, is it possible to extract the total contact energy cell 1 shares with its environment? Ideally, I would like to do this in python if possible.
Also forgot to include, as long as the lattice is relatively larger than the cpu, will these extracted plugin energies be "accurate" if I run CC3D in parallel? By accurate I mean the energy is effectively not modified twice in the same MCS by 2 or more cpus. My sim conditions are: 10-16 cpus on a 100x100x100 lattice with default flip to dim ratio, which I believe is 1).
Sorry for the long paragraph and thanks!
27 days ago by
What are you trying to do? If you want to modify the adhesion properties of a cell based on its adhesion partners I think you could do that more efficiently by just using the contact surface area to modify the adhesion constant or to modify the expression level of the adhesion molecules.
Regarding the use of multiple CPUs, I think the only time the energies would be inaccurate would be if you were tracking them on a per spin flip attempt basis. Normally you would access the energy at the end of an MCS so all the cpu's will have completed their work for that step.
23 days ago by
The demos that output detailed "energy statistics" (see Demo/SimulationSettings/SimulationStatistics) do require that you run on a single CPU. In fact before you start runing CC3D on multiple CPU's it is best to make sure your simulation works fine on 1 CPU.
So in summary, if you really need that detailed level of output you would need to compile CC3D from source and modify e.g. contact plugin to output this information. It is not difficult to do but exposing such capability to Python has not been done.
Hope it helps
23 days ago by
will output detailed data for change in energy at ever pixel copy attempt. It does not however output which cell it a given pixel belongs to. This is however something we could add to the code
when you add the following code to the Potts section
CC3D will output 3 files (they will be stored in the directory from which you execute CC3D Player - most likely <CC3D installation dir>/player5 - thi sia a bit of an inconvenience - we will fix it though)
<EnergyFunctionCalculator Type="Statistics"> <OutputFileName Frequency="10">cellsort_2D_statistics_spin_flip_statData.txt</OutputFileName> <OutputCoreFileNameSpinFlips Frequency="1" GatherResults="" OutputAccepted="" OutputRejected="" OutputTotal="">statDataSingleFlip</OutputCoreFileNameSpinFlips> </EnergyFunctionCalculator>
Those files have information about what happened at ever pixel copy.
we could add more information there to make it more usefu.l What type of information would you like to have included in addition to the one that we output currently?
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