"using neumann ( Effective Transpiration = " + str(eff_trans) +
" m^3 s^-1)", "top potential", x[0])
if dirichlet or (x[0] < top_pot):
Q, b = xylem_flux.linear_system(seg, nodes, radius, kr, kz, rho, g,
soil_p2)
dirichlet = True
Q, b = xylem_flux.bc_dirichlet(Q, b, np.array([0]),
np.array([top_pot]))
x = LA.spsolve(Q, b) # direct
eff_trans = xylem_flux.axial_flux0(x, seg, nodes, kz, rho, g)
dirichlet = eff_trans < pot_trans
print("using dirichlet ( Effective Transpiration = " + str(eff_trans) +
" m^3 s^-1)")
radial_flux = xylem_flux.radial_flux(
x, seg, nodes, radius, kr, soil_p2) # used to calculate the sink term
# print("Minimal xylem potential", min(x), " Maximal xylem potential ", max(x))
#
# 4. Sink term
#
t4 = timer.time()
# print("4 . Apply sink")
sink = np.zeros(inf.n)
for i in range(0, len(seg)):
z1 = nodes[seg[i, 0], 2]
z2 = nodes[seg[i, 1], 2]
z = 0.5 * (z1 + z2)
if z > -1:
ind = math.floor(-z / soil[-1].lowerDepth * inf.n)
sink[ind] += radial_flux[i] * dt
kz = np.vstack((shoot1, kz))
# Call back function for soil potential
soil = lambda x, y, z : soil_psi
# Calculate fluxes within the root system
Q, b = xylem_flux.linear_system(seg, nodes, radius, kr, kz, rho, g, soil)
# plt.spy(Q)
# plt.show()
Q, b = xylem_flux.bc_neumann(Q, b, np.array([0]), np.array([pot_trans]))
start = timeit.default_timer()
x = LA.spsolve(Q, b, use_umfpack = True) # direct
stop = timeit.default_timer()
print ("linear system solved in", stop - start, " s")
# Save results into vtp
segP = nodes2seg(nodes, seg, x) # save vtp
axial_flux = xylem_flux.axial_flux(x, seg, nodes, kz, rho, g)
radial_flux = xylem_flux.radial_flux(x, seg, nodes, radius, kr, soil)
net_flux = axial_flux + radial_flux
rs_ana.addUserData(a2v(segP[sseg.shape[0]:]), "pressure")
rs_ana.addUserData(a2v(axial_flux[sseg.shape[0]:]), "axial_flux")
rs_ana.addUserData(a2v(radial_flux[sseg.shape[0]:]), "radial_flux")
rs_ana.addUserData(a2v(net_flux[sseg.shape[0]:]), "net_flux")
rs_ana.write("results/example_5a.vtp")
print("done.")