# r.plot_conductivities()
# shoot_segs = rs.getShootSegments()
# print("Shoot segments", [str(s) for s in shoot_segs])
# print("Shoot type", rs.subTypes[0])
""" numerical solution of transpiration -1 cm3/day"""
krs_, l_, jc_ = [], [], []
for t in np.linspace(10, simtime, simtime - 10 + 1):
# l_.append(rs.getSummed("length")) # does not work, since rs is precomputed
ana = pb.SegmentAnalyser(rs)
ana.filter("creationTime", -1, t + 1.e-4)
l_.append(
ana.getSummed("length")
) # does not work, all rs is precomputedana.getParameter("length")
suf = r.get_suf(t)
krs, jc = r.get_krs(t) # in xylem flux.h
krs_.append(krs)
jc_.append(jc)
if t > 10 and t % 10 == 0: # for the suf plot
suf_[-1].append(suf)
time = np.linspace(10, simtime, simtime - 10 + 1)
ax1.plot(time, krs_, cols[ii], label=labels[ii], alpha=0.7)
ax2.plot(time, jc_, cols[ii], label=labels[ii])
# """ Krs plot """
ax3.set_xlabel("simulation time")
ax1.set_ylabel("root system conductance $krs$ $[cm^2 d^{-1}]$")
ax2.set_ylabel("Transpiration at eswp -500 cm $[cm^3/day]$")
ax1.legend()
v_[j] = np.sum(v)
v1_[j] = np.sum(v[t == 1])
v2_[j] = np.sum(v[t == 2])
v3_[j] = np.sum(v[t == 3])
v4_[j] = np.sum(v[t == 4])
segment_[j] = np.sum(segment)
""" set up xylem parameters """
r = XylemFluxPython(rs)
r.setKrTables(
[kr0[:, 1], kr1[:, 1], kr2[:, 1], kr3[:, 1], kr4[:, 1], kr5[:, 1]],
[kr0[:, 0], kr1[:, 0], kr2[:, 0], kr3[:, 0], kr4[:, 0], kr5[:, 0]])
r.setKxTables(
[kz0[:, 1], kz1[:, 1], kz2[:, 1], kz3[:, 1], kz4[:, 1], kz5[:, 1]],
[kz0[:, 0], kz1[:, 0], kz2[:, 0], kz3[:, 0], kz4[:, 0], kz5[:, 0]])
suf = r.get_suf(j)
print("Sum of SUF", np.sum(suf), "from", np.min(suf), "to", np.max(suf),
"summed positive", np.sum(suf[suf >= 0]))
krs, jc = r.get_krs(j)
print("Krs: ", krs)
print("time: ", j)
krs_.append(krs)
if j > 10 and j % 30 == 0:
suf_.append(suf)
jc_.append(jc)
print("Total number of segments: ", segment_[-1])
""" Krs and length plot """
simtime = 20 # [day] for task b
""" root system """
rs = pb.MappedRootSystem()
path = "../../../CPlantBox//modelparameter/rootsystem/"
name = "Glycine_max"
rs.setSeed(1)
rs.readParameters(path + name + ".xml")
rs.getRootSystemParameter().seedPos.z = -0.1
rs.initialize()
rs.simulate(simtime, False)
print()
print("Shoot segments: ", [str(s) for s in rs.getShootSegments()])
print()
""" set up xylem parameters """
r = XylemFluxPython(rs)
r.setKr([kr]) # or use setKrTables, see XylemFlux.h
r.setKx([kz])
r.test()
""" numerical solution of transpiration -1 cm3/day"""
suf = r.get_suf(0.)
print("Sum of SUF", np.sum(suf), "from", np.min(suf), "to", np.max(suf),
"summed positive", np.sum(suf[suf >= 0]))
krs = r.get_krs(0.)
print("Krs: ", krs)
""" Additional vtk plot """
ana = pb.SegmentAnalyser(r.rs)
ana.addData("SUF", suf) # cut off for vizualisation
vp.plot_roots(ana, "SUF", "Soil uptake fraction (cm3 day)") # "fluxes"