CompuCell3d manual and Tutorial Version 2
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- IX.2.10. ExternalPotential plugin
- IX.2.11. CellOrientation Plugin
CAUTION: when you use chemotaxis plugin you have to make sure that fields that you refer to and module that contains this fields are declared in the xml file. Otherwise you will most likely cause either program crash (which is not as bad as it sounds) or unpredicted behavior (much worse scenario, although unlikely as we made sure that in the case of undefined symbols, CompuCell3D exits)
IX.2.10. ExternalPotential pluginChemotaxis plugin is used to cause directional cell movement. Another way to achieve directional movement is to use ExternalPotential plugin. This plugin is responsible for imposing a directed pressure (or rather force) on cells. It is used mainly in fluid flow studies with periodic boundary conditions along these coordinates along which force acts. If NoFlux boundary conditions are set instead , the cells will be squeezed. This is the example usage of this plugin: Lambda is a vector quantity and determines components of force along three axes. In this case we apply force along x. We can also apply external potential to specific cell types:
Where in ExternalPotentialParameters we specity which cell type is subject to external potential (Lambda is specified using x,y,z attributes). We can also apply external potential to individual cells. In that case, in the XML section we only need to specify: and in the Python file we change lambdaVecX, lambdaVecY, lambdaVecZ, which are properties of cell. For example in Python we could write: cell.lambdaVecX=-10 Calculations done by ExternalPotential Plugin are by default based on direction of pixel copy (similarly as in chemotaxis plugin). One can however force CC3D to do calculations based on movement of center of mass of cell. To use algorithm based on center of mass movement we use the following XML syntax: …
IX.2.11. CellOrientation PluginSimilarly as ExternalPotential plugin this plugin gives preference to those pixel copies whose direction aligns with polarization vector (which is a property of each cell):  ,
where (i) denotes cell at site i,  is polarization vector for cell at site i and  pixel copy vector. Because two cell participate in the pixel copy process the net energy change is simply a sum of above expressions: one for growing cell and one for shrinking cell. To set lambda we have two options: use global setting in the XML:
Or set individually for each cell and manage values of from Python. In this case we use the following XML syntax: If we manage values in Python we would use the following syntax to acces and modify values of lambda: self.cellOrientationPlugin.getLambdaCellOrientation(cell) self.cellOrientationPlugin.setLambdaCellOrientation(cell,0.5) Directory: BinDoc -> cc3d binaries -> Manuals Manuals -> 111Equation Chapter 1 Section 1 CompuCell3d reference Manual Version 4 Download 6.67 Mb. Share with your friends:
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