FiPyexamples.chemotaxis package¶
Submodules¶
examples.chemotaxis.input module¶
Input file for chemotaxis modeling.
Here are some test cases for the model.
>>> from __future__ import division
>>> from builtins import input
>>> from builtins import range
>>> from examples.chemotaxis.parameters import parameters
>>> from fipy import CellVariable, Grid1D, TransientTerm, DiffusionTerm, ImplicitSourceTerm, Viewer, numerix
>>> params = parameters['case 2']
>>> nx = 50
>>> dx = 1.
>>> L = nx * dx
>>> mesh = Grid1D(nx=nx, dx=dx)
>>> shift = 1.
>>> KMVar = CellVariable(mesh=mesh, value=params['KM'] * shift, hasOld=1)
>>> KCVar = CellVariable(mesh=mesh, value=params['KC'] * shift, hasOld=1)
>>> TMVar = CellVariable(mesh=mesh, value=params['TM'] * shift, hasOld=1)
>>> TCVar = CellVariable(mesh=mesh, value=params['TC'] * shift, hasOld=1)
>>> P3Var = CellVariable(mesh=mesh, value=params['P3'] * shift, hasOld=1)
>>> P2Var = CellVariable(mesh=mesh, value=params['P2'] * shift, hasOld=1)
>>> RVar = CellVariable(mesh=mesh, value=params['R'], hasOld=1)
>>> PN = P3Var + P2Var
>>> KMscCoeff = params['chiK'] * (RVar + 1) * (1 - KCVar - KMVar.cellVolumeAverage)
>>> KMspCoeff = params['lambdaK'] / (1 + PN / params['kappaK'])
>>> KMEq = TransientTerm() - KMscCoeff + ImplicitSourceTerm(KMspCoeff)
>>> TMscCoeff = params['chiT'] * (1 - TCVar - TMVar.cellVolumeAverage)
>>> TMspCoeff = params['lambdaT'] * (KMVar + params['zetaT'])
>>> TMEq = TransientTerm() - TMscCoeff + ImplicitSourceTerm(TMspCoeff)
>>> TCscCoeff = params['lambdaT'] * (TMVar * KMVar).cellVolumeAverage
>>> TCspCoeff = params['lambdaTstar']
>>> TCEq = TransientTerm() - TCscCoeff + ImplicitSourceTerm(TCspCoeff)
>>> PIP2PITP = PN / (PN / params['kappam'] + PN.cellVolumeAverage / params['kappac'] + 1) + params['zetaPITP']
>>> P3spCoeff = params['lambda3'] * (TMVar + params['zeta3T'])
>>> P3scCoeff = params['chi3'] * KMVar * (PIP2PITP / (1 + KMVar / params['kappa3']) + params['zeta3PITP']) + params['zeta3']
>>> P3Eq = TransientTerm() - DiffusionTerm(params['diffusionCoeff']) - P3scCoeff + ImplicitSourceTerm(P3spCoeff)
>>> P2scCoeff = scCoeff = params['chi2'] + params['lambda3'] * params['zeta3T'] * P3Var
>>> P2spCoeff = params['lambda2'] * (TMVar + params['zeta2T'])
>>> P2Eq = TransientTerm() - DiffusionTerm(params['diffusionCoeff']) - P2scCoeff + ImplicitSourceTerm(P2spCoeff)
>>> KCscCoeff = params['alphaKstar'] * params['lambdaK'] * (KMVar / (1 + PN / params['kappaK'])).cellVolumeAverage
>>> KCspCoeff = params['lambdaKstar'] / (params['kappaKstar'] + KCVar)
>>> KCEq = TransientTerm() - KCscCoeff + ImplicitSourceTerm(KCspCoeff)
>>> eqs = ((KMVar, KMEq), (TMVar, TMEq), (TCVar, TCEq), (P3Var, P3Eq), (P2Var, P2Eq), (KCVar, KCEq))
>>> if __name__ == '__main__':
... steps = 100
... else:
... steps = 28
>>> for i in range(steps):
... for var, eqn in eqs:
... var.updateOld()
... for var, eqn in eqs:
... eqn.solve(var, dt=1.)
>>> accuracy = 1e-2
>>> print(KMVar.allclose(params['KM'], atol=accuracy))
1
>>> print(TMVar.allclose(params['TM'], atol=accuracy))
1
>>> print(TCVar.allclose(params['TC'], atol=accuracy))
1
>>> print(P2Var.allclose(params['P2'], atol=accuracy))
1
>>> print(P3Var.allclose(params['P3'], atol=accuracy))
1
>>> print(KCVar.allclose(params['KC'], atol=accuracy))
1
>>> PNView = PN / PN.cellVolumeAverage
>>> PNView.name = 'PN'
>>> KMView = KMVar / KMVar.cellVolumeAverage
>>> KMView.name = 'KM'
>>> TMView = TMVar / TMVar.cellVolumeAverage
>>> TMView.naem = 'TM'
>>> RVar[:] = params['S'] + (1 + params['S']) * params['G'] * numerix.cos((2 * numerix.pi * mesh.cellCenters[0]) / L)
>>> if __name__ == '__main__':
... KMViewer = Viewer((PNView, KMView, TMView), title = 'Gradient Stimulus: Profile')
...
... for i in range(100):
... for var, eqn in eqs:
... var.updateOld()
... for var, eqn in eqs:
... eqn.solve(var, dt=0.1)
...
... KMViewer.plot()
...
... input("finished")
examples.chemotaxis.input2D module¶
Input file for chemotaxis modeling.
Here are some test cases for the model.
>>> from __future__ import division
>>> from builtins import input
>>> from builtins import range
>>> from examples.chemotaxis.parameters import parameters
>>> from fipy import CellVariable, Grid2D, TransientTerm, DiffusionTerm, ImplicitSourceTerm, Viewer, numerix
>>> params = parameters['case 2']
>>> nx = 50
>>> ny = 50
>>> dx = 1.
>>> L = nx * dx
>>> mesh = Grid2D(nx=nx, ny=ny, dx=dx, dy=1.)
>>> shift = 1.
>>> KMVar = CellVariable(mesh=mesh, value=params['KM'] * shift, hasOld=1)
>>> KCVar = CellVariable(mesh=mesh, value=params['KC'] * shift, hasOld=1)
>>> TMVar = CellVariable(mesh=mesh, value=params['TM'] * shift, hasOld=1)
>>> TCVar = CellVariable(mesh=mesh, value=params['TC'] * shift, hasOld=1)
>>> P3Var = CellVariable(mesh=mesh, value=params['P3'] * shift, hasOld=1)
>>> P2Var = CellVariable(mesh=mesh, value=params['P2'] * shift, hasOld=1)
>>> RVar = CellVariable(mesh=mesh, value=params['R'], hasOld=1)
>>> PN = P3Var + P2Var
>>> KMscCoeff = params['chiK'] * (RVar + 1) * (1 - KCVar - KMVar.cellVolumeAverage)
>>> KMspCoeff = params['lambdaK'] / (1 + PN / params['kappaK'])
>>> KMEq = TransientTerm() - KMscCoeff + ImplicitSourceTerm(KMspCoeff)
>>> TMscCoeff = params['chiT'] * (1 - TCVar - TMVar.cellVolumeAverage)
>>> TMspCoeff = params['lambdaT'] * (KMVar + params['zetaT'])
>>> TMEq = TransientTerm() - TMscCoeff + ImplicitSourceTerm(TMspCoeff)
>>> TCscCoeff = params['lambdaT'] * (TMVar * KMVar).cellVolumeAverage
>>> TCspCoeff = params['lambdaTstar']
>>> TCEq = TransientTerm() - TCscCoeff + ImplicitSourceTerm(TCspCoeff)
>>> PIP2PITP = PN / (PN / params['kappam'] + PN.cellVolumeAverage / params['kappac'] + 1) + params['zetaPITP']
>>> P3spCoeff = params['lambda3'] * (TMVar + params['zeta3T'])
>>> P3scCoeff = params['chi3'] * KMVar * (PIP2PITP / (1 + KMVar / params['kappa3']) + params['zeta3PITP']) + params['zeta3']
>>> P3Eq = TransientTerm() - DiffusionTerm(params['diffusionCoeff']) - P3scCoeff + ImplicitSourceTerm(P3spCoeff)
>>> P2scCoeff = scCoeff = params['chi2'] + params['lambda3'] * params['zeta3T'] * P3Var
>>> P2spCoeff = params['lambda2'] * (TMVar + params['zeta2T'])
>>> P2Eq = TransientTerm() - DiffusionTerm(params['diffusionCoeff']) - P2scCoeff + ImplicitSourceTerm(P2spCoeff)
>>> KCscCoeff = params['alphaKstar'] * params['lambdaK'] * (KMVar / (1 + PN / params['kappaK'])).cellVolumeAverage
>>> KCspCoeff = params['lambdaKstar'] / (params['kappaKstar'] + KCVar)
>>> KCEq = TransientTerm() - KCscCoeff + ImplicitSourceTerm(KCspCoeff)
>>> eqs = ((KMVar, KMEq), (TMVar, TMEq), (TCVar, TCEq), (P3Var, P3Eq), (P2Var, P2Eq), (KCVar, KCEq))
>>> if __name__ == '__main__':
... steps = 100
... else:
... steps = 10
>>> for i in range(steps):
... for var, eqn in eqs:
... var.updateOld()
... for var, eqn in eqs:
... eqn.solve(var, dt=1.)
>>> accuracy = 1e-2
>>> print(KMVar.allclose(params['KM'], atol=accuracy))
1
>>> print(TMVar.allclose(params['TM'], atol=accuracy))
1
>>> print(TCVar.allclose(params['TC'], atol=accuracy))
1
>>> print(P2Var.allclose(params['P2'], atol=accuracy))
1
>>> print(P3Var.allclose(params['P3'], atol=accuracy))
1
>>> print(KCVar.allclose(params['KC'], atol=accuracy))
1
>>> PNView = PN / PN.cellVolumeAverage
>>> PNView.name = 'PN'
>>> KMView = KMVar / KMVar.cellVolumeAverage
>>> KMView.name = 'KM'
>>> TMView = TMVar / TMVar.cellVolumeAverage
>>> TMView.naem = 'TM'
>>> x, y = mesh.cellCenters
>>> RVar[:] = L / numerix.sqrt((x - L / 2)**2 + (y - 2 * L)**2)
>>> if __name__ == '__main__':
... PNViewer = Viewer(PNView, datamax=2., datamin=0., title='')
... KMViewer = Viewer(KMView, datamax=2., datamin=0., title='')
... TMViewer = Viewer(TMView, datamax=2., datamin=0., title='')
...
... for i in range(100):
... for var, eqn in eqs:
... var.updateOld()
... for var, eqn in eqs:
... eqn.solve(var, dt=1.)
...
... PNViewer.plot()
... KMViewer.plot()
... TMViewer.plot()
...
... input("finished")
examples.chemotaxis.parameters module¶
Input file for parameters
examples.chemotaxis.test module¶
Last updated on Jun 27, 2023.
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