def step(self, mcs):
# #### Write bionetwork state variable names of external oscillators to output file
bionetAPI.writeBionetworkStateToFile(mcs, "ExternalOscillatorA",
"SimpleExample",
self.oscillatorAFileName, "a")
bionetAPI.writeBionetworkStateToFile(mcs, "ExternalOscillatorB",
"SimpleExample",
self.oscillatorBFileName, "a")
# ######### Update integrator(s) for all bionetworks ###########
bionetAPI.timestepBionetworks()
# ######## Modify k1 and k2 as a function of time (MCS) ##########
k1 = self.k1_init * (1 + math.sin(2 * math.pi * mcs / self.mcsPeriod))
k2 = self.k2_init * (1 - math.sin(2 * math.pi * mcs / self.mcsPeriod))
bionetAPI.setBionetworkValue("SE_k1", 0.2 * k1, "ExternalOscillatorA")
bionetAPI.setBionetworkValue("SE_k2", 0.2 * k2, "ExternalOscillatorA")
k1 = self.k1_init * (1 - math.sin(2 * math.pi * mcs / self.mcsPeriod))
k2 = self.k2_init * (1 + math.sin(2 * math.pi * mcs / self.mcsPeriod))
bionetAPI.setBionetworkValue("SE_k1", 0.2 * k1, "ExternalOscillatorB")
bionetAPI.setBionetworkValue("SE_k2", 0.2 * k2, "ExternalOscillatorB")
# ####### Set "Blue-Blue" and "Green-Green" adhesion energies #########
BB_offset = bionetAPI.getBionetworkValue("SE_S1",
"ExternalOscillatorA")
GG_offset = bionetAPI.getBionetworkValue("SE_S1",
"ExternalOscillatorB")
self.modifyContactEnergies(BB_offset, GG_offset, self.steadyState)
# ############## Write adhesion data to an output file ################
self.writeContactEnergies(mcs, self.contactEnergyOutputFile, "a")
def step(self, mcs):
# #### Write bionetwork state variable names of external oscillators to output file
bionetAPI.writeBionetworkStateToFile( mcs, "ExternalOscillatorA", "SimpleExample", self.oscillatorAFileName, "a" )
bionetAPI.writeBionetworkStateToFile( mcs, "ExternalOscillatorB", "SimpleExample", self.oscillatorBFileName, "a" )
# ######### Update integrator(s) for all bionetworks ###########
bionetAPI.timestepBionetworks()
# ######## Modify k1 and k2 as a function of time (MCS) ##########
k1 = self.k1_init * ( 1 + math.sin( 2*math.pi*mcs/self.mcsPeriod ) )
k2 = self.k2_init * ( 1 - math.sin( 2*math.pi*mcs/self.mcsPeriod ) )
bionetAPI.setBionetworkValue( "SE_k1", 0.2*k1, "ExternalOscillatorA" )
bionetAPI.setBionetworkValue( "SE_k2", 0.2*k2, "ExternalOscillatorA" )
k1 = self.k1_init * ( 1 - math.sin( 2*math.pi*mcs/self.mcsPeriod ) )
k2 = self.k2_init * ( 1 + math.sin( 2*math.pi*mcs/self.mcsPeriod ) )
bionetAPI.setBionetworkValue( "SE_k1", 0.2*k1, "ExternalOscillatorB" )
bionetAPI.setBionetworkValue( "SE_k2", 0.2*k2, "ExternalOscillatorB" )
# ####### Set "Blue-Blue" and "Green-Green" adhesion energies #########
BB_offset = bionetAPI.getBionetworkValue( "SE_S1", "ExternalOscillatorA" )
GG_offset = bionetAPI.getBionetworkValue( "SE_S1", "ExternalOscillatorB" )
self.modifyContactEnergies( BB_offset, GG_offset, self.steadyState )
# ############## Write adhesion data to an output file ################
self.writeContactEnergies( mcs, self.contactEnergyOutputFile, "a" )
def step(self, mcs):
# ######### Update all bionetwork integrator(s) ###########
bionetAPI.timestepBionetworks()
print "\n"; print bionetAPI.getBionetworkValue( "dii", "CellTypeB" )
print "\n"; print bionetAPI.getBionetworkValue( "di", "CellTypeB" )
print "\n"; print bionetAPI.getBionetworkValue( "DN_di", "CellTypeB" )
print "\n"; print bionetAPI.getBionetworkValue( "DeltaNotchModel_di", "CellTypeB" )
bionetAPI.setBionetworkValue( "SE_k1", 0.1, "CellTypeD" )
bionetAPI.setBionetworkValue( "SE_k2", 0.3, "CellTypeD" )
cellType = "CellTypeD"; propertyName = "SE_S1"
S1 = bionetAPI.getBionetworkValue( propertyName, cellType )
print "Value of %s in %s: %s" % ( propertyName, cellType, S1 )
if( mcs >= 20 ):
if( mcs == 40 ):
if self.cellTypeMap[bionetAPI.getCC3DCellByID(1).type] == "CellTypeB":
bionetAPI.setBionetworkValue( "TemplateLibrary", "CellTypeA", 1 )
elif self.cellTypeMap[bionetAPI.getCC3DCellByID(1).type] == "CellTypeA":
bionetAPI.setBionetworkValue( "TemplateLibrary", "CellTypeB", "CellTypeA" )
if( mcs < 120 ):
cell1_di = bionetAPI.getBionetworkValue( "di", 1 )
if( cell1_di > 0.0 ): newPropertyValue = 4.0 / cell1_di
else: newPropertyValue = 10.0
for cell in self.cellList:
if self.cellTypeMap[cell.type] == "CellTypeB":
cell.targetVolume = newPropertyValue
def start(self):
# #################### Create SBML models ######################
## Load a Bionetwork SBML model named "SimpleExample"
sbmlModelPath = "Simulation/SimpleExample.sbml"
bionetAPI.loadSBMLModel( "SimpleExample", sbmlModelPath, "SE", 0.5 )
# ################ Add SBML models to Bionetwork Template Libraries ##################
## Add SBML model to non-cell bionetwork template libaries called "ExternalOscillatorA" and "ExternalOscillatorB"
bionetAPI.addSBMLModelToTemplateLibrary( "SimpleExample", "ExternalOscillatorA" )
bionetAPI.addSBMLModelToTemplateLibrary( "SimpleExample", "ExternalOscillatorB" )
# ####### Set initial conditions for Bionetwork properties #########
## Set initial conditions for "ExternalOscillatorA" and "ExternalOscillatorB" bionetwork template libraries
self.k1_init = 0.1; self.k2_init = 0.1; self.mcsPeriod = 500
bionetAPI.setBionetworkInitialCondition( "ExternalOscillatorA", "SE_k1", self.k1_init )
bionetAPI.setBionetworkInitialCondition( "ExternalOscillatorA", "SE_k2", self.k2_init )
bionetAPI.setBionetworkInitialCondition( "ExternalOscillatorA", "SE_X0", 10.0 )
bionetAPI.setBionetworkInitialCondition( "ExternalOscillatorB", "SE_k1", self.k1_init )
bionetAPI.setBionetworkInitialCondition( "ExternalOscillatorB", "SE_k2", self.k2_init )
bionetAPI.setBionetworkInitialCondition( "ExternalOscillatorB", "SE_X0", 10.0 )
# ######## Create Bionetworks (integrators) and initialize their states ##########
bionetAPI.initializeBionetworks()
# ######## Perform initialization tasks and calculations ##########
k1 = bionetAPI.getBionetworkValue( "SE_k1", "ExternalOscillatorA" )
k2 = bionetAPI.getBionetworkValue( "SE_k2", "ExternalOscillatorA" )
X0 = bionetAPI.getBionetworkValue( "SE_X0", "ExternalOscillatorA" )
print "k1=",k1," k2=",k2," X0=",X0
self.steadyState = k1 * X0 / k2
# #### Write bionetwork state variable names of external oscillators to output file
self.oscillatorAFileName = "Demos/BionetSolverExamples/OscillatingContactEnergies/oscillatorStateA.txt"
bionetAPI.writeBionetworkStateVarNamesToFile( "ExternalOscillatorA", "SimpleExample", self.oscillatorAFileName, "w" )
self.oscillatorBFileName = "Demos/BionetSolverExamples/OscillatingContactEnergies/oscillatorStateB.txt"
bionetAPI.writeBionetworkStateVarNamesToFile( "ExternalOscillatorB", "SimpleExample", self.oscillatorBFileName, "w" )
# ############## Write adhesion data to an output file ################
self.contactEnergyOutputFile = "Demos/BionetSolverExamples/OscillatingContactEnergies/contactEnergies.txt"
self.writeContactEnergies( 0, self.contactEnergyOutputFile, "w" )
def step(self, mcs):
# #### Write bionetwork state variable names of external oscillators to output file
bionetAPI.writeBionetworkStateToFile(mcs, "ExternalOscillatorA",
"SimpleExample",
self.oscillatorAFileName, "a")
bionetAPI.writeBionetworkStateToFile(mcs, "ExternalOscillatorB",
"SimpleExample",
self.oscillatorBFileName, "a")
# ######### Update integrator(s) for all bionetworks ###########
bionetAPI.timestepBionetworks()
# ######## Modify k1 and k2 as a function of time (MCS) ##########
k1 = self.k1_init * (1 + math.sin(2 * math.pi * mcs / self.mcsPeriod))
k2 = self.k2_init * (1 - math.sin(2 * math.pi * mcs / self.mcsPeriod))
bionetAPI.setBionetworkValue("SE_k1", 0.2 * k1, "ExternalOscillatorA")
bionetAPI.setBionetworkValue("SE_k2", 0.2 * k2, "ExternalOscillatorA")
k1 = self.k1_init * (1 - math.sin(2 * math.pi * mcs / self.mcsPeriod))
k2 = self.k2_init * (1 + math.sin(2 * math.pi * mcs / self.mcsPeriod))
bionetAPI.setBionetworkValue("SE_k1", 0.2 * k1, "ExternalOscillatorB")
bionetAPI.setBionetworkValue("SE_k2", 0.2 * k2, "ExternalOscillatorB")
# ####### Set "Blue-Blue" and "Green-Green" adhesion energies #########
BB_offset = bionetAPI.getBionetworkValue("SE_S1",
"ExternalOscillatorA")
GG_offset = bionetAPI.getBionetworkValue("SE_S1",
"ExternalOscillatorB")
self.modifyContactEnergies(BB_offset, GG_offset, self.steadyState)
# ############## Write adhesion data to an output file ################
self.writeContactEnergies(mcs, self.contactEnergyOutputFile, "a")
if not (mcs % 10):
for cell in self.cellList:
pixelList = self.getCellPixelList(cell)
for pixelTrackerData in pixelList:
self.cellField.set(pixelTrackerData.pixel, None)
break
if mcs > 200:
for cell in self.cellList:
cell.targetVolume = 0.0
cell.lambdaVolume = 200.0
cell.targetSurface = 0.0
cell.lambdaSurface = 200.0
def step(self, mcs):
# ######### Update bionetwork integrator(s) for all cells ###########
bionetAPI.timestepBionetworks()
# ######## Implement cell growth by increasing target volume ##########
for cell in self.cellList:
if cell.id > self.initialNumberOfCells:
## All new cells are assigned a target volume of 0 to force cell death
cell.targetVolume = 0.
cell.lambdaVolume = 2.
cell.targetSurface = 0.
cell.lambdaSurface = 2.
else:
dictionaryAttrib = CompuCell.getPyAttrib(cell)
cell.targetVolume = cell.volume + 0.15 * dictionaryAttrib[
"InitialVolume"]
# ###### Retrieve delta values and set cell type according to delta concentration ########
for cell in self.cellList:
currentDeltaValue = bionetAPI.getBionetworkValue("DN_di", cell.id)
if (currentDeltaValue > 0.5):
if (self.cellTypeMap[cell.type] == "LowDelta"):
print "ID of cell to undergo type change %s" % cell.id
print "Type of cell to undergo type change %s" % bionetAPI.getBionetworkValue(
"TemplateLibrary", cell.id)
bionetAPI.setBionetworkValue("TemplateLibrary",
"HighDelta", cell.id)
else:
if (self.cellTypeMap[cell.type] == "HighDelta"):
bionetAPI.setBionetworkValue("TemplateLibrary", "LowDelta",
cell.id)
# ####### Set all cell dbari values as a function of neighbor delta values #########
for cell in self.cellList:
weightedSumOfNeighborDeltaValues = 0.0
neighborContactAreas = bionetAPI.getNeighborContactAreas(cell.id)
neighborDeltaValues = bionetAPI.getNeighborProperty(
"DN_di", cell.id)
for neighborID in neighborContactAreas.keys():
weightedSumOfNeighborDeltaValues += (
neighborContactAreas[neighborID] *
neighborDeltaValues[neighborID])
bionetAPI.setBionetworkValue(
"DN_dbari", weightedSumOfNeighborDeltaValues / cell.surface,
cell.id)
def step(self, mcs):
# ######### Update all bionetwork integrator(s) ###########
bionetAPI.timestepBionetworks()
bionetAPI.printBionetworkState(1)
# ######## Implement cell growth by increasing target volume ##########
for cell in self.cellList:
dictionaryAttrib = CompuCell.getPyAttrib( cell )
cell.targetVolume = cell.volume + 0.1*dictionaryAttrib["InitialVolume"]
# ###### Retrieve delta values and set cell bionetwork template libraries according to delta concentration ########
for cell in self.cellList:
currentDelta = bionetAPI.getBionetworkValue( "DN_di", cell.id )
if( currentDelta > 0.5 ):
if self.cellTypeMap[cell.type] == "LowDelta":
bionetAPI.setBionetworkValue( "TemplateLibrary", "HighDelta", cell.id )
else:
if self.cellTypeMap[cell.type] == "HighDelta":
bionetAPI.setBionetworkValue( "TemplateLibrary", "LowDelta", cell.id )
# ####### Set all cell dbari values as a function of neighbor delta values #########
for cell in self.cellList:
weightedSumOfNeighborDeltaValues = 0.0
neighborContactAreas = bionetAPI.getNeighborContactAreas( cell.id )
neighborDeltaValues = bionetAPI.getNeighborProperty( "DN_di", cell.id )
for neighborID in neighborContactAreas.keys():
weightedSumOfNeighborDeltaValues += (neighborContactAreas[neighborID] * neighborDeltaValues[neighborID])
bionetAPI.setBionetworkValue( "DN_dbari", weightedSumOfNeighborDeltaValues/cell.surface, cell.id )
def step(self, mcs):
# #### Write bionetwork state variable names of external oscillators to output file
bionetAPI.writeBionetworkStateToFile( mcs, "ExternalOscillatorA", "SimpleExample", self.oscillatorAFileName, "a" )
bionetAPI.writeBionetworkStateToFile( mcs, "ExternalOscillatorB", "SimpleExample", self.oscillatorBFileName, "a" )
# ######### Update integrator(s) for all bionetworks ###########
bionetAPI.timestepBionetworks()
# ######## Modify k1 and k2 as a function of time (MCS) ##########
k1 = self.k1_init * ( 1 + math.sin( 2*math.pi*mcs/self.mcsPeriod ) )
k2 = self.k2_init * ( 1 - math.sin( 2*math.pi*mcs/self.mcsPeriod ) )
bionetAPI.setBionetworkValue( "SE_k1", 0.2*k1, "ExternalOscillatorA" )
bionetAPI.setBionetworkValue( "SE_k2", 0.2*k2, "ExternalOscillatorA" )
k1 = self.k1_init * ( 1 - math.sin( 2*math.pi*mcs/self.mcsPeriod ) )
k2 = self.k2_init * ( 1 + math.sin( 2*math.pi*mcs/self.mcsPeriod ) )
bionetAPI.setBionetworkValue( "SE_k1", 0.2*k1, "ExternalOscillatorB" )
bionetAPI.setBionetworkValue( "SE_k2", 0.2*k2, "ExternalOscillatorB" )
# ####### Set "Blue-Blue" and "Green-Green" adhesion energies #########
BB_offset = bionetAPI.getBionetworkValue( "SE_S1", "ExternalOscillatorA" )
GG_offset = bionetAPI.getBionetworkValue( "SE_S1", "ExternalOscillatorB" )
self.modifyContactEnergies( BB_offset, GG_offset, self.steadyState )
# ############## Write adhesion data to an output file ################
self.writeContactEnergies( mcs, self.contactEnergyOutputFile, "a" )
if not (mcs %10):
for cell in self.cellList:
pixelList=self.getCellPixelList(cell)
for pixelTrackerData in pixelList:
self.cellField.set(pixelTrackerData.pixel,None)
break
if mcs >200:
for cell in self.cellList:
cell.targetVolume=0.0
cell.lambdaVolume=200.0
cell.targetSurface=0.0
cell.lambdaSurface=200.0
def step(self, mcs):
# ######### Update all bionetwork integrator(s) ###########
bionetAPI.timestepBionetworks()
print "\n"
print bionetAPI.getBionetworkValue("dii", "CellTypeB")
print "\n"
print bionetAPI.getBionetworkValue("di", "CellTypeB")
print "\n"
print bionetAPI.getBionetworkValue("DN_di", "CellTypeB")
print "\n"
print bionetAPI.getBionetworkValue("DeltaNotchModel_di", "CellTypeB")
bionetAPI.setBionetworkValue("SE_k1", 0.1, "CellTypeD")
bionetAPI.setBionetworkValue("SE_k2", 0.3, "CellTypeD")
cellType = "CellTypeD"
propertyName = "SE_S1"
S1 = bionetAPI.getBionetworkValue(propertyName, cellType)
print "Value of %s in %s: %s" % (propertyName, cellType, S1)
if (mcs >= 20):
if (mcs == 40):
if self.cellTypeMap[bionetAPI.getCC3DCellByID(
1).type] == "CellTypeB":
bionetAPI.setBionetworkValue("TemplateLibrary",
"CellTypeA", 1)
elif self.cellTypeMap[bionetAPI.getCC3DCellByID(
1).type] == "CellTypeA":
bionetAPI.setBionetworkValue("TemplateLibrary",
"CellTypeB", "CellTypeA")
if (mcs < 120):
cell1_di = bionetAPI.getBionetworkValue("di", 1)
if (cell1_di > 0.0): newPropertyValue = 4.0 / cell1_di
else: newPropertyValue = 10.0
for cell in self.cellList:
if self.cellTypeMap[cell.type] == "CellTypeB":
cell.targetVolume = newPropertyValue
def step(self, mcs):
# ######### Update bionetwork integrator(s) for all cells ###########
bionetAPI.timestepBionetworks()
# ######## Implement cell growth by increasing target volume ##########
for cell in self.cellList:
if cell.id > self.initialNumberOfCells:
## All new cells are assigned a target volume of 0 to force cell death
cell.targetVolume = 0.
cell.lambdaVolume = 2.
cell.targetSurface = 0.
cell.lambdaSurface = 2.
else:
dictionaryAttrib = CompuCell.getPyAttrib( cell )
cell.targetVolume = cell.volume + 0.15*dictionaryAttrib["InitialVolume"]
# ###### Retrieve delta values and set cell type according to delta concentration ########
for cell in self.cellList:
currentDeltaValue = bionetAPI.getBionetworkValue( "DN_di", cell.id )
if( currentDeltaValue > 0.5 ):
if( self.cellTypeMap[cell.type] == "LowDelta" ):
print "ID of cell to undergo type change %s" % cell.id
print "Type of cell to undergo type change %s" % bionetAPI.getBionetworkValue( "TemplateLibrary", cell.id )
bionetAPI.setBionetworkValue( "TemplateLibrary", "HighDelta", cell.id )
else:
if( self.cellTypeMap[cell.type] == "HighDelta" ):
bionetAPI.setBionetworkValue( "TemplateLibrary", "LowDelta", cell.id )
# ####### Set all cell dbari values as a function of neighbor delta values #########
for cell in self.cellList:
weightedSumOfNeighborDeltaValues = 0.0
neighborContactAreas = bionetAPI.getNeighborContactAreas( cell.id )
neighborDeltaValues = bionetAPI.getNeighborProperty( "DN_di", cell.id )
for neighborID in neighborContactAreas.keys():
weightedSumOfNeighborDeltaValues += (neighborContactAreas[neighborID] * neighborDeltaValues[neighborID])
bionetAPI.setBionetworkValue( "DN_dbari", weightedSumOfNeighborDeltaValues/cell.surface, cell.id )
def step(self, mcs):
# ######### Update all bionetwork integrator(s) ###########
bionetAPI.timestepBionetworks()
bionetAPI.printBionetworkState(1)
# ######## Implement cell growth by increasing target volume ##########
for cell in self.cellList:
dictionaryAttrib = CompuCell.getPyAttrib(cell)
cell.targetVolume = cell.volume + 0.1 * dictionaryAttrib[
"InitialVolume"]
# ###### Retrieve delta values and set cell bionetwork template libraries according to delta concentration ########
for cell in self.cellList:
currentDelta = bionetAPI.getBionetworkValue("DN_di", cell.id)
if (currentDelta > 0.5):
if self.cellTypeMap[cell.type] == "LowDelta":
bionetAPI.setBionetworkValue("TemplateLibrary",
"HighDelta", cell.id)
else:
if self.cellTypeMap[cell.type] == "HighDelta":
bionetAPI.setBionetworkValue("TemplateLibrary", "LowDelta",
cell.id)
# ####### Set all cell dbari values as a function of neighbor delta values #########
for cell in self.cellList:
weightedSumOfNeighborDeltaValues = 0.0
neighborContactAreas = bionetAPI.getNeighborContactAreas(cell.id)
neighborDeltaValues = bionetAPI.getNeighborProperty(
"DN_di", cell.id)
for neighborID in neighborContactAreas.keys():
weightedSumOfNeighborDeltaValues += (
neighborContactAreas[neighborID] *
neighborDeltaValues[neighborID])
bionetAPI.setBionetworkValue(
"DN_dbari", weightedSumOfNeighborDeltaValues / cell.surface,
cell.id)
def start(self):
# #################### Create SBML models ######################
## Load a Bionetwork SBML model named "SimpleExample"
sbmlModelPath = "Simulation/SimpleExample.sbml"
bionetAPI.loadSBMLModel("SimpleExample", sbmlModelPath, "SE", 0.5)
# ################ Add SBML models to Bionetwork Template Libraries ##################
## Add SBML model to non-cell bionetwork template libaries called "ExternalOscillatorA" and "ExternalOscillatorB"
bionetAPI.addSBMLModelToTemplateLibrary("SimpleExample",
"ExternalOscillatorA")
bionetAPI.addSBMLModelToTemplateLibrary("SimpleExample",
"ExternalOscillatorB")
# ####### Set initial conditions for Bionetwork properties #########
## Set initial conditions for "ExternalOscillatorA" and "ExternalOscillatorB" bionetwork template libraries
self.k1_init = 0.1
self.k2_init = 0.1
self.mcsPeriod = 500
bionetAPI.setBionetworkInitialCondition("ExternalOscillatorA", "SE_k1",
self.k1_init)
bionetAPI.setBionetworkInitialCondition("ExternalOscillatorA", "SE_k2",
self.k2_init)
bionetAPI.setBionetworkInitialCondition("ExternalOscillatorA", "SE_X0",
10.0)
bionetAPI.setBionetworkInitialCondition("ExternalOscillatorB", "SE_k1",
self.k1_init)
bionetAPI.setBionetworkInitialCondition("ExternalOscillatorB", "SE_k2",
self.k2_init)
bionetAPI.setBionetworkInitialCondition("ExternalOscillatorB", "SE_X0",
10.0)
# ######## Create Bionetworks (integrators) and initialize their states ##########
bionetAPI.initializeBionetworks()
# ######## Perform initialization tasks and calculations ##########
k1 = bionetAPI.getBionetworkValue("SE_k1", "ExternalOscillatorA")
k2 = bionetAPI.getBionetworkValue("SE_k2", "ExternalOscillatorA")
X0 = bionetAPI.getBionetworkValue("SE_X0", "ExternalOscillatorA")
print "k1=", k1, " k2=", k2, " X0=", X0
self.steadyState = k1 * X0 / k2
# #### Write bionetwork state variable names of external oscillators to output file
self.oscillatorAFileName = "Demos/BionetSolverExamples/OscillatingContactEnergies/oscillatorStateA.txt"
bionetAPI.writeBionetworkStateVarNamesToFile("ExternalOscillatorA",
"SimpleExample",
self.oscillatorAFileName,
"w")
self.oscillatorBFileName = "Demos/BionetSolverExamples/OscillatingContactEnergies/oscillatorStateB.txt"
bionetAPI.writeBionetworkStateVarNamesToFile("ExternalOscillatorB",
"SimpleExample",
self.oscillatorBFileName,
"w")
# ############## Write adhesion data to an output file ################
self.contactEnergyOutputFile = "Demos/BionetSolverExamples/OscillatingContactEnergies/contactEnergies.txt"
self.writeContactEnergies(0, self.contactEnergyOutputFile, "w")