import py_rootbox as rb
# from pyevtk.hl import gridToVTK
import numpy as np
import matplotlib.pyplot as plt
from matplotlib import ticker
import matplotlib.colors as colors
def v2a(vd): # rb.std_vector_double_ to numpy array
l = np.zeros(len(vd))
for i in range(0, len(vd)):
l[i] = vd[i]
return l
rootsystem = rb.RootSystem()
name = "Anagallis_straight_simple"
#
# Open plant and root parameter from a file
#
rootsystem.openFile(name)
for i in range(0, 10):
p = rootsystem.getRootTypeParameter(i + 1)
p.gf = 2 # linear growth function
#
# Initialize
#
rootsystem.initialize()
import py_rootbox as rb
from rb_tools import *
import sys
import numpy as np
import matplotlib.pyplot as plt
import csv
rs = rb.RootSystem()
#name = "Triticum_aestivum_a_Bingham_2011" # is this the same as your wheat, Shehan?
name = "Zea_mays_1_Leitner_2010"
rs.openFile(name)
# Pore Geometry
x_ = (-10, -5, 1, 15) # not 0, otherwise we start in crack
y_ = (0, 0, 0, 0)
x_ = (-10, -5)
y_ = (0, 0)
crack = rb.SDF_PlantBox(1.0, 100, 160) # cm
cracks_ = rb.std_vector_SDF_()
py_cracks = []
for i in range(0, len(y_)):
v = rb.Vector3d(x_[i], y_[i], 0)
py_cracks.append(rb.SDF_RotateTranslate(crack, v))
cracks_.append(py_cracks[-1])
cracks = rb.SDF_Union(cracks_)
rs.setPoreGeometry(cracks)
# Increased elongation within the pores
maxS = 20 # twice the elongation rate within the pore
def simulate(name, simtime):
rs = rb.RootSystem()
rs.openFile(name, "params/")
rs.initialize()
rs.simulate(simtime, True)
return rs
