def configure_simulation():
from cc3d.core.XMLUtils import ElementCC3D
dim = 300
cc3d = ElementCC3D("CompuCell3D")
metadata = cc3d.ElementCC3D("Metadata")
metadata.ElementCC3D("NumberOfProcessors", {}, 4)
potts = cc3d.ElementCC3D("Potts")
potts.ElementCC3D("Dimensions", {"x": dim, "y": dim, "z": dim})
potts.ElementCC3D("Steps", {}, 100)
potts.ElementCC3D("Temperature", {}, 0)
potts.ElementCC3D("Flip2DimRatio", {}, 0.0)
cellType = cc3d.ElementCC3D("Plugin", {"Name": "CellType"})
cellType.ElementCC3D("CellType", {"TypeName": "Medium", "TypeId": "0"})
flexDiffSolver = cc3d.ElementCC3D("Steppable",
{"Type": "DiffusionSolverFE"})
diffusionField = flexDiffSolver.ElementCC3D("DiffusionField")
diffusionData = diffusionField.ElementCC3D("DiffusionData")
diffusionData.ElementCC3D("FieldName", {}, "FGF")
diffusionData.ElementCC3D("DiffusionConstant", {}, 0.10)
diffusionData.ElementCC3D("DecayConstant", {}, 0.0)
diffusionData.ElementCC3D("ConcentrationFileName", {},
"Simulation/diffusion_3D.pulse.txt")
CompuCellSetup.setSimulationXMLDescription(cc3d)
def step(self, mcs):
print("This function is called every 10 MCS")
for cell in self.cellList:
print("CELL ID=", cell.id, " CELL TYPE=", cell.type, " volume=",
cell.volume)
if not (mcs % 20):
counter = 0
for cell in self.cellListByType(self.CONDENSING):
print("BY TYPE CELL ID=", cell.id, " CELL TYPE=", cell.type,
" volume=", cell.volume)
counter += 1
for cell in self.cellListByType(self.NONCONDENSING):
print("BY TYPE CELL ID=", cell.id, " CELL TYPE=", cell.type,
" volume=", cell.volume)
counter += 1
for cell in self.cellListByType(self.CONDENSING,
self.NONCONDENSING):
print("MULTI TYPE LIST - CELL ID=", cell.id, " CELL TYPE=",
cell.type, " volume=", cell.volume)
print("number of cells in typeInventory=",
len(self.cellListByType))
print("number of cells in the entire cell inventory=",
len(self.cellListByType))
if mcs > 500:
CompuCellSetup.stopSimulation()
def mainLoop(*args, **kwds):
"""
:param args:
:param kwds:
:return:
"""
CompuCellSetup.run()
def prepareSimulation(self):
(self.sim,
self.simthread) = CompuCellSetup.get_core_simulation_objects()
CompuCellSetup.initialize_simulation_objects(self.sim, self.simthread)
CompuCellSetup.extra_init_simulation_objects(self.sim, self.simthread)
self.simulationInitialized = True
self.callingWidget.sim = self.sim
def configure_simulation():
from cc3d.core.XMLUtils import ElementCC3D
cc3d = ElementCC3D("CompuCell3D")
potts = cc3d.ElementCC3D("Potts")
potts.ElementCC3D("Dimensions", {"x": 100, "y": 100, "z": 1})
potts.ElementCC3D("Steps", {}, 1000)
potts.ElementCC3D("Anneal", {}, 10)
potts.ElementCC3D("Temperature", {}, 10)
potts.ElementCC3D("Flip2DimRatio", {}, 1)
potts.ElementCC3D("NeighborOrder", {}, 2)
cellType = cc3d.ElementCC3D("Plugin", {"Name": "CellType"})
cellType.ElementCC3D("CellType", {"TypeName": "Medium", "TypeId": "0"})
cellType.ElementCC3D("CellType", {"TypeName": "Condensing", "TypeId": "1"})
cellType.ElementCC3D("CellType", {
"TypeName": "NonCondensing",
"TypeId": "2"
})
volume = cc3d.ElementCC3D("Plugin", {"Name": "Volume"})
volume.ElementCC3D("TargetVolume", {}, 25)
volume.ElementCC3D("LambdaVolume", {}, 2.0)
contact = cc3d.ElementCC3D("Plugin", {"Name": "Contact"})
contact.ElementCC3D("Energy", {"Type1": "Medium", "Type2": "Medium"}, 0)
contact.ElementCC3D("Energy", {
"Type1": "NonCondensing",
"Type2": "NonCondensing"
}, 16)
contact.ElementCC3D("Energy", {
"Type1": "Condensing",
"Type2": "Condensing"
}, 2)
contact.ElementCC3D("Energy", {
"Type1": "NonCondensing",
"Type2": "Condensing"
}, 11)
contact.ElementCC3D("Energy", {
"Type1": "NonCondensing",
"Type2": "Medium"
}, 16)
contact.ElementCC3D("Energy", {
"Type1": "Condensing",
"Type2": "Medium"
}, 16)
contact.ElementCC3D("NeighborOrder", {}, 2)
blobInitializer = cc3d.ElementCC3D("Steppable",
{"Type": "BlobInitializer"})
blobInitializer.ElementCC3D("Gap", {}, 0)
blobInitializer.ElementCC3D("Width", {}, 5)
blobInitializer.ElementCC3D("CellSortInit", {}, "yes")
blobInitializer.ElementCC3D("Radius", {}, 40)
CompuCellSetup.setSimulationXMLDescription(cc3d)
def configure_simulation():
from cc3d.core.XMLUtils import ElementCC3D
cc3d = ElementCC3D("CompuCell3D")
potts = cc3d.ElementCC3D("Potts")
potts.ElementCC3D("Dimensions", {"x": 100, "y": 100, "z": 1})
potts.ElementCC3D("Steps", {}, 10000)
potts.ElementCC3D("Temperature", {}, 5)
potts.ElementCC3D("NeighborOrder", {}, 2)
potts.ElementCC3D("Boundary_x", {}, "Periodic")
cell_type = cc3d.ElementCC3D("Plugin", {"Name": "CellType"})
cell_type.ElementCC3D("CellType", {"TypeName": "Medium", "TypeId": "0"})
cell_type.ElementCC3D("CellType", {"TypeName": "Body1", "TypeId": "1"})
cell_type.ElementCC3D("CellType", {"TypeName": "Body2", "TypeId": "2"})
cell_type.ElementCC3D("CellType", {"TypeName": "Body3", "TypeId": "3"})
volume = cc3d.ElementCC3D("Plugin", {"Name": "Volume"})
volume.ElementCC3D("TargetVolume", {}, 25)
volume.ElementCC3D("LambdaVolume", {}, 4.0)
contact = cc3d.ElementCC3D("Plugin", {"Name": "Contact"})
contact.ElementCC3D("Energy", {"Type1": "Medium", "Type2": "Medium"}, 0)
contact.ElementCC3D("Energy", {"Type1": "Body1", "Type2": "Body1"}, 16)
contact.ElementCC3D("Energy", {"Type1": "Body1", "Type2": "Medium"}, 4)
contact.ElementCC3D("Energy", {"Type1": "Body2", "Type2": "Body2"}, 16)
contact.ElementCC3D("Energy", {"Type1": "Body2", "Type2": "Medium"}, 4)
contact.ElementCC3D("Energy", {"Type1": "Body3", "Type2": "Body3"}, 16)
contact.ElementCC3D("Energy", {"Type1": "Body3", "Type2": "Medium"}, 4)
contact.ElementCC3D("Energy", {"Type1": "Body1", "Type2": "Body2"}, 16)
contact.ElementCC3D("Energy", {"Type1": "Body1", "Type2": "Body3"}, 16)
contact.ElementCC3D("Energy", {"Type1": "Body2", "Type2": "Body3"}, 16)
contact.ElementCC3D("neighborOrder", {}, 2)
center_of_mass = cc3d.ElementCC3D("Plugin", {"Name": "CenterOfMass"})
elasticity_tracker = cc3d.ElementCC3D("Plugin", {"Name": "ElasticityTracker"})
elasticity_tracker.ElementCC3D("IncludeType", {}, "Body1")
elasticity_tracker.ElementCC3D("IncludeType", {}, "Body2")
elasticity_tracker.ElementCC3D("IncludeType", {}, "Body3")
elasticity_energy = cc3d.ElementCC3D("Plugin", {"Name": "ElasticityEnergy"})
elasticity_energy.ElementCC3D("Local", {})
# elasticity_energy.ElementCC3D("LambdaElasticity",{},200.0)
# elasticity_energy.ElementCC3D("TargetLengthElasticity",{},6)
external_potential = cc3d.ElementCC3D("Plugin", {"Name": "ExternalPotential"})
external_potential.ElementCC3D("Lambda", {"x": -10, "y": 0, "z": 0})
pif_initializer = cc3d.ElementCC3D("Steppable", {"Type": "PIFInitializer"})
pif_initializer.ElementCC3D("PIFName", {}, "Simulation/elasticitytest.piff")
CompuCellSetup.setSimulationXMLDescription(cc3d)
def extract_lattice_description_info(self, file_name: str) -> None:
"""
Reads the xml that summarizes serialized simulation files
:param file_name:{str} xml metadata file name
:return: None
"""
# lattice data simulation file
lds_file = os.path.abspath(file_name)
lds_reader = LatticeDataSummaryReader(lds_file=lds_file)
self.ldsDir = lds_reader.lds_dir
self.fieldDim = lds_reader.field_dim
self.ldsCoreFileName = lds_reader.lds_core_file_name
self.frequency = lds_reader.frequency
self.numberOfSteps = lds_reader.number_of_steps
self.latticeType = lds_reader.lattice_type
self.typeIdTypeNameDict = lds_reader.type_id_type_name_dict
self.typeIdTypeNameCppMap = lds_reader.type_id_type_name_cpp_map
self.ldsFileList = lds_reader.lds_file_list
self.fieldsUsed = lds_reader.fields_used
for field_name, custom_vis_script in lds_reader.custom_vis_scripts.items():
self.customVis = CompuCellSetup.createCustomVisPy(field_name)
self.customVis.registerVisCallbackFunction(CompuCellSetup.vtkScriptCallback)
self.customVis.addActor(field_name, "vtkActor")
# we'll piggyback off the actorsDict
self.customVis.addActor("customVTKScript", custom_vis_script)
def core_init(self, reinitialize_cell_types=True):
super().core_init(reinitialize_cell_types)
# Share self
if self.unique_key is None:
raise AttributeError("Steppable key not set")
elif self.unique_key in self.shared_steppable_vars.keys():
# Handling the occurence where core_init is called multiple times on consecutive runs for some steppables
return
else:
print("Registering nCoVSteppableBase:", self.unique_key)
self.shared_steppable_vars[self.unique_key] = self
self._register_base()
# Register ODEManagerSteppable if necessary
from cc3d import CompuCellSetup
steppable_registry = CompuCellSetup.persistent_globals.steppable_registry
if ODEManagerSteppable.__name__ not in steppable_registry.steppableDict.keys(
):
CompuCellSetup.register_steppable(ODEManagerSteppable(frequency=1))
def configure_simulation():
from cc3d.core.XMLUtils import ElementCC3D
cc3d = ElementCC3D("CompuCell3D")
potts = cc3d.ElementCC3D("Potts")
potts.ElementCC3D("Dimensions", {"x": 42, "y": 42, "z": 1})
potts.ElementCC3D("Steps", {}, 10000)
potts.ElementCC3D("Anneal", {}, 10)
potts.ElementCC3D("Temperature", {}, 10)
potts.ElementCC3D("NeighborOrder", {}, 2)
potts.ElementCC3D("Boundary_x", {}, "Periodic")
potts.ElementCC3D("Boundary_y", {}, "Periodic")
cellType = cc3d.ElementCC3D("Plugin", {"Name": "CellType"})
cellType.ElementCC3D("CellType", {"TypeName": "Medium", "TypeId": "0"})
cellType.ElementCC3D("CellType", {"TypeName": "TypeA", "TypeId": "1"})
contact = cc3d.ElementCC3D("Plugin", {"Name": "Contact"})
contact.ElementCC3D("Energy", {"Type1": "Medium", "Type2": "Medium"}, 0)
contact.ElementCC3D("Energy", {"Type1": "Medium", "Type2": "TypeA"}, 5)
contact.ElementCC3D("Energy", {"Type1": "TypeA", "Type2": "TypeA"}, 5)
contact.ElementCC3D("NeighborOrder", {}, 4)
vp = cc3d.ElementCC3D("Plugin", {"Name": "Volume"})
vp.ElementCC3D("TargetVolume", {}, 49)
vp.ElementCC3D("LambdaVolume", {}, 5)
ntp = cc3d.ElementCC3D("Plugin", {"Name": "NeighborTracker"})
uipd = cc3d.ElementCC3D("Steppable", {"Type": "UniformInitializer"})
region = uipd.ElementCC3D("Region")
region.ElementCC3D("BoxMin", {"x": 0, "y": 0, "z": 0})
region.ElementCC3D("BoxMax", {"x": 42, "y": 42, "z": 1})
region.ElementCC3D("Types", {}, "TypeA")
region.ElementCC3D("Width", {}, 7)
CompuCellSetup.setSimulationXMLDescription(cc3d)
Jessica Crawshaw, James M. Osborne, Ellen M. Quardokus, Richard K. Plemper, James A. Glazier, "A modular framework for multiscale, multicellular, spatiotemporal modeling of acute primary viral infection and immune response in epithelial tissues and its application to drug therapy timing and effectiveness", PLoS Comput Biol 16(12): e1008451. https://doi.org/10.1371/journal.pcbi.1008451 """ import os from ViralInfectionVTMModelInputs import __file__ as f sys.path.append(os.path.dirname(os.path.dirname(f))) os.environ["ViralInfectionVTM"] = os.path.dirname(os.path.dirname(f)) from cc3d import CompuCellSetup from Models.SegoAponte2020.ViralInfectionVTMSteppables import ViralReplicationSteppable CompuCellSetup.register_steppable(steppable=ViralReplicationSteppable(frequency=1)) from Models.SegoAponte2020.ViralInfectionVTMSteppables import ViralInternalizationSteppable CompuCellSetup.register_steppable(steppable=ViralInternalizationSteppable(frequency=1)) from Models.RandomSusceptibility.SusceptibilitySteppables import RandomSusceptibilitySteppable steppable = RandomSusceptibilitySteppable(frequency=1) steppable.track_susc = True CompuCellSetup.register_steppable(steppable=steppable) from Models.SegoAponte2020.ViralInfectionVTMSteppables import CellsInitializerSteppable CompuCellSetup.register_steppable(steppable=CellsInitializerSteppable(frequency=1)) from Models.SegoAponte2020.ViralInfectionVTMSteppables import ViralSecretionSteppable
############################################################################################################### # To cite this model please use the following: # # Josua Aponte-Serrano, T.J. Sego, Juliano F. Gianlupi, James A. Glazier, # "Model of Viral Tissue Infection" # https://github.com/covid-tissue-models/covid-tissue-response-models/tree/master/CC3D/Models/BiocIU/SARSCoV2MultiscaleVTM ############################################################################################################### from cc3d import CompuCellSetup from CoronavirusSteppables import CellsInitializerSteppable CompuCellSetup.register_steppable(steppable=CellsInitializerSteppable(frequency=1)) from CoronavirusSteppables import Viral_ReplicationSteppable CompuCellSetup.register_steppable(steppable=Viral_ReplicationSteppable(frequency=1)) from CoronavirusSteppables import Viral_SecretionSteppable CompuCellSetup.register_steppable(steppable=Viral_SecretionSteppable(frequency=1)) from CoronavirusSteppables import ImmuneCellKillingSteppable CompuCellSetup.register_steppable(steppable=ImmuneCellKillingSteppable(frequency=1)) from CoronavirusSteppables import ChemotaxisSteppable CompuCellSetup.register_steppable(steppable=ChemotaxisSteppable(frequency=1)) from CoronavirusSteppables import RecoverySteppable CompuCellSetup.register_steppable(steppable=RecoverySteppable(frequency=1)) from CoronavirusSteppables import ImmuneCellSeedingSteppable CompuCellSetup.register_steppable(steppable=ImmuneCellSeedingSteppable(frequency=1))
from cc3d import CompuCellSetup
from .MomentOfInertiaSteppables import MomentOfInertiaPrinter
CompuCellSetup.register_steppable(steppable=MomentOfInertiaPrinter(
frequency=10))
CompuCellSetup.run()
from cc3d import CompuCellSetup from cellsort_2D_hexSteppables import cellsort_2D_hexSteppable CompuCellSetup.register_steppable(steppable=cellsort_2D_hexSteppable(frequency=1)) CompuCellSetup.run()
from cc3d import CompuCellSetup
from diffusion_steady_state_ext_potential_3DSteppables import diffusion_steady_state_ext_potential_3DSteppable
CompuCellSetup.register_steppable(
steppable=diffusion_steady_state_ext_potential_3DSteppable(frequency=1))
CompuCellSetup.run()
from cc3d import CompuCellSetup
from SBMLSolverAntimony2Steppables import SBMLSolverSteppable
from SBMLSolverAntimony2Steppables import IdFieldVisualizationSteppable
from SBMLSolverAntimony2Steppables import SecretionSteppable
CompuCellSetup.register_steppable(steppable=SBMLSolverSteppable(frequency=1))
CompuCellSetup.register_steppable(steppable=IdFieldVisualizationSteppable(
frequency=1))
CompuCellSetup.register_steppable(steppable=SecretionSteppable(frequency=1))
CompuCellSetup.run()
from cc3d import CompuCellSetup
from cellsort_2D_box_watcherSteppables import cellsort_2D_box_watcherSteppable
CompuCellSetup.register_steppable(steppable=cellsort_2D_box_watcherSteppable(
frequency=1))
CompuCellSetup.run()
from cc3d import CompuCellSetup
from .ContactLocalProductExampleModules import ContactLocalProductSteppable
from .ContactLocalProductExampleModules import ContactSpecVisualizationSteppable
clp_steppable = ContactLocalProductSteppable(frequency=10)
clp_steppable.set_type_contact_energy_table({0: 0.0, 1: 20, 2: 30})
# alternative call when we select random number for adhesion molecules form the specified interval e.g. [20,30]
# clp_steppable.set_type_contact_energy_table({0:0.0 , 1:[20,30], 2:[30,50]})
CompuCellSetup.register_steppable(steppable=clp_steppable)
CompuCellSetup.register_steppable(steppable=ContactSpecVisualizationSteppable(
frequency=50))
CompuCellSetup.run()
from cc3d import CompuCellSetup from .cellsort_2D_steppables_info_printer import InfoPrinterSteppable CompuCellSetup.register_steppable(steppable=InfoPrinterSteppable(frequency=1)) CompuCellSetup.run()
from cc3d import CompuCellSetup from .scientificPlotsMultipleAxesSteppables import ExtraPlotSteppable CompuCellSetup.register_steppable(steppable=ExtraPlotSteppable(frequency=1)) CompuCellSetup.run()
from cc3d import CompuCellSetup from .amoeba_2DSteppables import amoeba_2DSteppable CompuCellSetup.register_steppable(steppable=amoeba_2DSteppable(frequency=1)) CompuCellSetup.run()
from cc3d import CompuCellSetup
from .SteppableCommunicationSteppables import CommunicationSteppable
from .SteppableCommunicationSteppables import ExtraSteppable
CompuCellSetup.register_steppable(steppable=CommunicationSteppable(
frequency=1))
CompuCellSetup.register_steppable(steppable=ExtraSteppable(frequency=1))
CompuCellSetup.run()
from cc3d import CompuCellSetup from randomBlobInitializerSteppables import randomBlobInitializerSteppable CompuCellSetup.register_steppable(steppable=randomBlobInitializerSteppable(frequency=1)) CompuCellSetup.run()
from cc3d import CompuCellSetup
from .elongationFlexSteppables import ElongationFlexSteppable
CompuCellSetup.register_steppable(steppable=ElongationFlexSteppable(
frequency=50))
CompuCellSetup.run()
import cc3d.CompuCellSetup as CompuCellSetup
from .SBMLSolverOscilatorDemoSteppables import SBMLSolverOscilatorDemoSteppable
CompuCellSetup.register_steppable(steppable=SBMLSolverOscilatorDemoSteppable(
frequency=1))
CompuCellSetup.run()
# import sys
# from os import environ
# from os import getcwd
# import string
#
# sys.path.append(environ["PYTHON_MODULE_PATH"])
#
# import CompuCellSetup
#
# sim,simthread = CompuCellSetup.getCoreSimulationObjects()
#
# CompuCellSetup.initializeSimulationObjects(sim,simthread)
# #Add Python steppables here
# steppableRegistry=CompuCellSetup.getSteppableRegistry()
#
# from SBMLSolverOscilatorDemoSteppables import SBMLSolverOscilatorDemoSteppable
# steppableInstance=SBMLSolverOscilatorDemoSteppable(sim,_frequency=1)
# steppableRegistry.registerSteppable(steppableInstance)
#
# CompuCellSetup.mainLoop(sim,simthread,steppableRegistry)
#
#
cellType.ElementCC3D("CellType", {"TypeName": "TypeA", "TypeId": "1"})
contact = cc3d.ElementCC3D("Plugin", {"Name": "Contact"})
contact.ElementCC3D("Energy", {"Type1": "Medium", "Type2": "Medium"}, 0)
contact.ElementCC3D("Energy", {"Type1": "Medium", "Type2": "TypeA"}, 5)
contact.ElementCC3D("Energy", {"Type1": "TypeA", "Type2": "TypeA"}, 5)
contact.ElementCC3D("NeighborOrder", {}, 4)
vp = cc3d.ElementCC3D("Plugin", {"Name": "Volume"})
vp.ElementCC3D("TargetVolume", {}, 49)
vp.ElementCC3D("LambdaVolume", {}, 5)
ntp = cc3d.ElementCC3D("Plugin", {"Name": "NeighborTracker"})
uipd = cc3d.ElementCC3D("Steppable", {"Type": "UniformInitializer"})
region = uipd.ElementCC3D("Region")
region.ElementCC3D("BoxMin", {"x": 0, "y": 0, "z": 0})
region.ElementCC3D("BoxMax", {"x": 42, "y": 42, "z": 1})
region.ElementCC3D("Types", {}, "TypeA")
region.ElementCC3D("Width", {}, 7)
CompuCellSetup.setSimulationXMLDescription(cc3d)
CompuCellSetup.register_steppable(steppable=DeltaNotchClass(frequency=1))
CompuCellSetup.register_steppable(steppable=ExtraFields(frequency=1))
configure_simulation()
CompuCellSetup.run()
from cc3d import CompuCellSetup
def configure_simulation():
from cc3d.core.XMLUtils import ElementCC3D
cc3d = ElementCC3D("CompuCell3D")
potts = cc3d.ElementCC3D("Potts")
potts.ElementCC3D("Dimensions", {"x": 55, "y": 55, "z": 1})
potts.ElementCC3D("Steps", {}, 1000)
potts.ElementCC3D("Temperature", {}, 0)
potts.ElementCC3D("Flip2DimRatio", {}, 0.0)
cellType = cc3d.ElementCC3D("Plugin", {"Name": "CellType"})
cellType.ElementCC3D("CellType", {"TypeName": "Medium", "TypeId": "0"})
flexDiffSolver = cc3d.ElementCC3D("Steppable", {"Type": "DiffusionSolverFE"})
diffusionField = flexDiffSolver.ElementCC3D("DiffusionField")
diffusionData = diffusionField.ElementCC3D("DiffusionData")
diffusionData.ElementCC3D("FieldName", {}, "FGF")
diffusionData.ElementCC3D("DiffusionConstant", {}, 0.10)
diffusionData.ElementCC3D("DecayConstant", {}, 0.0)
diffusionData.ElementCC3D("ConcentrationFileName", {}, "Simulation/diffusion_2D.pulse.txt")
CompuCellSetup.setSimulationXMLDescription(cc3d)
configure_simulation()
CompuCellSetup.run()
from cc3d import CompuCellSetup
from diffusion_3D_ADESteppables import diffusion_3D_ADESteppable
CompuCellSetup.register_steppable(steppable=diffusion_3D_ADESteppable(
frequency=1))
CompuCellSetup.run()
from cc3d import CompuCellSetup
from DiffusionSolverFE_OpenCL_3DSteppables import DiffusionSolverFE_OpenCL_3DSteppable
CompuCellSetup.register_steppable(
steppable=DiffusionSolverFE_OpenCL_3DSteppable(frequency=1))
CompuCellSetup.run()
from cc3d import CompuCellSetup
from cellsort_3D_open_mpSteppables import cellsort_3D_open_mpSteppable
CompuCellSetup.register_steppable(steppable=cellsort_3D_open_mpSteppable(
frequency=1))
CompuCellSetup.run()
contact.ElementCC3D("neighborOrder", {}, 2)
center_of_mass = cc3d.ElementCC3D("Plugin", {"Name": "CenterOfMass"})
elasticity_tracker = cc3d.ElementCC3D("Plugin", {"Name": "ElasticityTracker"})
elasticity_tracker.ElementCC3D("IncludeType", {}, "Body1")
elasticity_tracker.ElementCC3D("IncludeType", {}, "Body2")
elasticity_tracker.ElementCC3D("IncludeType", {}, "Body3")
elasticity_energy = cc3d.ElementCC3D("Plugin", {"Name": "ElasticityEnergy"})
elasticity_energy.ElementCC3D("Local", {})
# elasticity_energy.ElementCC3D("LambdaElasticity",{},200.0)
# elasticity_energy.ElementCC3D("TargetLengthElasticity",{},6)
external_potential = cc3d.ElementCC3D("Plugin", {"Name": "ExternalPotential"})
external_potential.ElementCC3D("Lambda", {"x": -10, "y": 0, "z": 0})
pif_initializer = cc3d.ElementCC3D("Steppable", {"Type": "PIFInitializer"})
pif_initializer.ElementCC3D("PIFName", {}, "Simulation/elasticitytest.piff")
CompuCellSetup.setSimulationXMLDescription(cc3d)
configure_simulation()
CompuCellSetup.register_steppable(steppable=ElasticityLocalSteppable(frequency=50))
CompuCellSetup.run()
