def picd(a): # creats vtu data with cell situation at time step
x_list = [0]
y_list = [0]
z_list = [0]
r_list = [0]
F_x = [0]
F_y = [0]
F_z = [0]
vtk_writer = vtktools.VTK_XML_Serial_Unstructured()
for elem in c_ary:
if c_ary[elem].name == 'maybe':
x_list.append(c_ary[elem].xcor)
y_list.append(c_ary[elem].ycor)
z_list.append(c_ary[elem].zcor)
r_list.append(c_ary[elem].radius)
F_x.append(fx[elem])
F_y.append(fy[elem])
F_z.append(fz[elem])
vtk_writer.snapshot("cell_arrangements_maybe" + str(a) + ".vtu",
x_list,
y_list,
z_list,
radii=r_list,
x_force=F_x,
y_force=F_y,
z_force=F_z)
vtk_writer.writePVD("cell_arrangements_maybe" + str(a) + ".pvd")
def run(self):
"""
Use Verlet integral method to do the simulation, return the trajectory in the form of
traj[time_slice, particle_index, dim]
"""
if self.inter_range is not None:
cells_shape = (self.box // self.inter_range).astype(int)
for k in range(len(cells_shape)):
if cells_shape[k] == 0:
cells_shape[k] = 1
cell_size = self.box / cells_shape
else:
cells_shape = None
cell_size = None
vtk_writer = vtktools.VTK_XML_Serial_Unstructured()
if not self.initialized:
# create random points inthe box
self.traj[0] = np.random.rand(self.par_num, self.dim) * self.box
self.v0 = np.zeros((self.par_num, self.dim), dtype=float)
self.traj[1] = np.mod(self.traj[0] + self.v0, self.box)
next = 2
while next < self.traj.shape[0]:
# calculate force
if self.inter_range is not None:
self.linked_cell = Linked_cell(self.traj[next - 1], self.box,
self.inter_range)
force = self.cal_force(self.traj[next - 1], self.linked_cell,
cells_shape, cell_size)
# verlet step
self.traj[next] = 2 * self.traj[next - 1] - self.traj[
next - 2] + self.dt**2 * force
# periodic boundary
self.traj[next] = np.mod(
self.traj[next],
self.box) #??????????????????? mod could be a problem
#vktools
r_x = self.traj[next][:, 0]
r_y = self.traj[next][:, 1]
r_z = self.traj[next][:, 2]
F_x = force[:, 0]
F_y = force[:, 1]
F_z = force[:, 2]
vtk_writer.snapshot("simu/MD_" + str(self.dt) + ".vtu",
r_x,
r_y,
r_z,
x_force=F_x,
y_force=F_y,
z_force=F_z)
next += 1
# vtk_writer.writePVD("MD.pvd")
return self.traj
def vtk_generator(simType, resultdir, resfile_i, dempath, nx, ny, dxy):
#simname = dm.getsimname_2(resultdir, simType)
vtk_writer = vtktools.VTK_XML_Serial_Unstructured()
simpath = resultdir + resfile_i
#simpath = 'model_geo.txt'
xyz_columndata_all = pd.read_csv(simpath, error_bad_lines=False)
xyz_columndata_all = xyz_columndata_all.values
xyz_columndata = dm.xyz_extract_z_column(
xyz_columndata_all, 0, 1, 4, 5) # extract relevant column (x,y,z,h)
x = xyz_columndata[:, 0]
y = xyz_columndata[:, 1]
z = xyz_columndata[:, 2]
h = xyz_columndata[:, 3]
xyz_columndata_2 = dm.xyz_extract_z_column(
xyz_columndata_all, 8, 9, 11,
12) # extract relevant column (ux,uy,qx,qy)
ux = xyz_columndata_2[:, 0] * 1000 / (dxy * dxy) # m3/s -> l/s
uy = xyz_columndata_2[:, 1] * 1000 / (dxy * dxy) # m3/s -> l/s
qx = xyz_columndata_2[:, 0] # m3/s
qy = xyz_columndata_2[:, 1] # m3/s
conc_sw = xyz_columndata_2[:, 2]
conc_soil = xyz_columndata_2[:, 3]
xyz_columndata_4 = dm.xyz_extract_z_column(
xyz_columndata_all, 15, 0, 0,
0) # extract relevant column (ux,uy,qx,qy)
timeconnect_h = xyz_columndata_4[:, 0]
outputnam = resultdir + "vtk/" + resfile_i[0:len(resfile_i) - 4]
#vtk_writer.snapshot(outputnam + ".vtu", x, y, z, h, ux, uy, qx, qy, conc_sw, conc_soil)
vtk_writer.snapshot(outputnam + ".vtu", x, y, z, h, ux, uy, qy, qx,
conc_sw, conc_soil, timeconnect_h)
#vtk_writer.snapshot(outputnam + ".vtu", x, y, h, ux, uy, qy, qx, conc_soil)
vtk_writer.writePVD(outputnam + ".pvd")
import vtktools
vtk_writer = vtktools.VTK_XML_Serial_Unstructured()
''' Only plot cells '''
x = [-2.0, 0.0, 1.5]
y = [2.0, -2.5, 3.0]
z = [0.0, 0.0, 0.0]
R = [2.0, 2.5, 3.0]
''' Plot cells and forces '''
F_x = [10.0, 10.0, 20.0]
F_y = [15.0, -5.0, 0.0]
F_z = [0.0, 0.0, 0.0]
vtk_writer.snapshot("cell_arrangements.vtu",
x,
y,
z,
radii=R,
x_force=F_x,
y_force=F_y,
z_force=F_z)
vtk_writer.writePVD("cell_arrangements.pvd")
#vtk_writer.snapshot("cell_arrangements.vtu", x, y, z, radii = R)
#vtk_writer.writePVD("cell_arrangements.pvd")