aDiffP = aDiffP + sp.coo_matrix(
(0. * TKL[extF], (extFacesCells[0], extFacesCells[0])), shape=(nVol, nVol))
e = np.ones((1, nVol))
EaDiffP = sp.csc_matrix(
np.concatenate((np.concatenate(
(d * aDiffP.T.todense(),
(mesK * e).T), axis=1), np.array([np.append((mesK * e).T, 0.)])),
axis=0))
# -----------------------------------Dirichlet Boundary condition------------------------------------------
# aDiffP = aDiffP + sp.coo_matrix(-TKL[extF], (extFacesCells[0], extFacesCells[0]), shape=(nVol, nVol))
test = CellVariable(mesh=mesh, value=0.)
phi = CellVariable(name="$\phi(t,x,y)$", mesh=mesh, value=0.0, hasOld=1)
sF = sigmaF.SigmaF2D(params.sF, xt, yt, Rs=0.05)
F = sF
extendedF = np.append(mesK * F, 0.)
phi_new = la.spsolve(d * EaDiffP, extendedF)
phi.setValue(phi_new[0:nVol])
phi.updateOld()
# ------------------------------------------ THE IMMUNE CELLS ------------------------------
# ----------------------------------------- The diffusion matrix -----------------------------------------
aDiffE = np.zeros((nVol, nVol))
aDiffE = sp.csc_matrix(aDiffE)
aDiffE = aDiffE + sp.coo_matrix(
# -----------------------------------Neumann Boundary condition------------------------------------------
aDiffP = aDiffP + sp.coo_matrix(
(0. * TKL[extF], (extFacesCells[0], extFacesCells[0])), shape=(nVol, nVol))
e = np.ones((1, nVol))
EaDiffP = sp.csc_matrix(
np.concatenate((np.concatenate(
(d * aDiffP.T.todense(),
(mesK * e).T), axis=1), np.array([np.append((mesK * e).T, 0.)])),
axis=0))
# -----------------------------------Dirichlet Boundary condition------------------------------------------
test = CellVariable(mesh=mesh, value=0.)
phi = CellVariable(name="$\phi(t,x,y)$", mesh=mesh, value=0.0, hasOld=1)
# sF = sigmaF.SigmaF2D(params.sF, xt, yt, Rs=0.05)
sF = sigmaF.SigmaF2D(1. / x_s, xt, yt, Rs=0.05 / (x_s**2))
F = sF
extendedF = np.append(mesK * U * F, 0.)
phi_new = la.spsolve(EaDiffP, extendedF)
phi.setValue(phi_new[0:nVol])
phi.updateOld()
# ------------------------------------------ The Chemoattractant ------------------------------
aDiffE = np.zeros((nVol, nVol))
aDiffE = sp.csc_matrix(aDiffE)
aDiffE = aDiffE + sp.coo_matrix(
(-TKL[intF], (intFacesCells[0], intFacesCells[0])), shape=(nVol, nVol))
aDiffE = aDiffE + sp.coo_matrix(
(TKL[intF], (intFacesCells[0], intFacesCells[1])), shape=(nVol, nVol))
aDiffE = aDiffE + sp.coo_matrix(
