Attachment 'cellsort2D_negative_J.py'
Download 1 def configureSimulation(sim):
2 import CompuCellSetup
3 from XMLUtils import ElementCC3D
4
5 cc3d=ElementCC3D("CompuCell3D")
6 potts=cc3d.ElementCC3D("Potts")
7 potts.ElementCC3D("Dimensions",{"x":100,"y":100,"z":1})
8 potts.ElementCC3D("Steps",{},1000000)
9 potts.ElementCC3D("Anneal",{},10)
10 potts.ElementCC3D("Temperature",{},10)
11 potts.ElementCC3D("Flip2DimRatio",{},1)
12 potts.ElementCC3D("NeighborOrder",{},2)
13
14 cellType=cc3d.ElementCC3D("Plugin",{"Name":"CellType"})
15 cellType.ElementCC3D("CellType", {"TypeName":"Medium", "TypeId":"0"})
16 cellType.ElementCC3D("CellType", {"TypeName":"Condensing", "TypeId":"1"})
17 cellType.ElementCC3D("CellType", {"TypeName":"NonCondensing", "TypeId":"2"})
18
19 volume=cc3d.ElementCC3D("Plugin",{"Name":"Volume"})
20 volume.ElementCC3D("TargetVolume",{},25)
21 volume.ElementCC3D("LambdaVolume",{},5.0)
22
23 volume=cc3d.ElementCC3D("Plugin",{"Name":"Surface"})
24 volume.ElementCC3D("TargetSurface",{},25)
25 volume.ElementCC3D("LambdaSurface",{},5.0)
26
27 centerOfMass=cc3d.ElementCC3D("Plugin",{"Name":"CenterOfMass"})
28
29 contact=cc3d.ElementCC3D("Plugin",{"Name":"Contact"})
30 contact.ElementCC3D("Energy", {"Type1":"Medium", "Type2":"Medium"},0)
31 contact.ElementCC3D("Energy", {"Type1":"NonCondensing", "Type2":"NonCondensing"},-3)
32 contact.ElementCC3D("Energy", {"Type1":"Condensing", "Type2":"Condensing"},-10)
33 contact.ElementCC3D("Energy",{"Type1":"NonCondensing", "Type2":"Condensing"},-2)
34 contact.ElementCC3D("Energy", {"Type1":"NonCondensing", "Type2":"Medium"},1)
35 contact.ElementCC3D("Energy", {"Type1":"Condensing", "Type2":"Medium"},1)
36 contact.ElementCC3D("NeighborOrder", {}, 2)
37
38 chemotaxis=cc3d.ElementCC3D("Plugin",{"Name":"Chemotaxis"})
39 chemicalField=chemotaxis.ElementCC3D("ChemicalField", {"Source":"FlexibleDiffusionSolverFE", "Name":"FGF"})
40 chemicalField.ElementCC3D("ChemotaxisByType", {"Type":"Condensing" ,"Lambda":3})
41
42 flexDiffSolver=cc3d.ElementCC3D("Steppable",{"Type":"FlexibleDiffusionSolverFE"})
43 diffusionField=flexDiffSolver.ElementCC3D("DiffusionField")
44 diffusionData=diffusionField.ElementCC3D("DiffusionData")
45 diffusionData.ElementCC3D("FieldName",{},"FGF")
46 diffusionData.ElementCC3D("DiffusionConstant",{},0.2)
47 diffusionData.ElementCC3D("DecayConstant",{},0.01)
48 secretionData=diffusionField.ElementCC3D("SecretionData")
49 secretionData.ElementCC3D("Secretion",{"Type":"Condensing"},0.0)
50
51
52 uniform = cc3d.ElementCC3D("Steppable",{"Type":"UniformInitializer"})
53 region = uniform.ElementCC3D("Region")
54 region.ElementCC3D("BoxMin",{"x":0, "y":0, "z":0})
55 region.ElementCC3D("BoxMax",{"x":100, "y":100, "z":1})
56 region.ElementCC3D("Types",{}, "NonCondensing,Condensing")
57 region.ElementCC3D("Width", {}, 5)
58
59
60 CompuCellSetup.setSimulationXMLDescription(cc3d)
61
62 import sys
63 from os import environ
64 import string
65 sys.path.append(environ["PYTHON_MODULE_PATH"])
66
67 import CompuCellSetup
68
69 sim,simthread = CompuCellSetup.getCoreSimulationObjects()
70
71 #Create extra player fields here or add attributes
72 pyAttributeAdder,listAdder=CompuCellSetup.attachListToCells(sim)
73
74 configureSimulation(sim)
75
76 CompuCellSetup.initializeSimulationObjects(sim,simthread)
77
78
79 from PySteppables import SteppableRegistry
80 steppableRegistry=SteppableRegistry()
81 from CellDiffusionCalculatorSteppable import *
82 CellDiffusionCalculator=CellDiffusionCalculatorSteppable(_simulator=sim,_frequency=50)
83 steppableRegistry.registerSteppable(CellDiffusionCalculator)
84
85 CompuCellSetup.mainLoop(sim,simthread,steppableRegistry)
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