When running the case code, dolfin cannot export the vtkplotter package

sohar · October 24, 2023, 4:39pm

I found an example of aI found an example of a monopole array antenna, but importing vtkplotter.dolfin got an error when I ran the code
vtkplotter 导入错误
I think it is the version problem, but i do not how to solve it.
my dolfin version is 2019.2.0.dev0

dokken · October 24, 2023, 4:58pm

Please add the code in plaintext with 3x` encapsulation, and Also the full trace of your error messagw

sohar · October 25, 2023, 2:38am

import meshio
from dolfin import *
import numpy as np
import cmath as cm
import matplotlib.pyplot as plt
import os, sys, traceback
a = 2.25
b = 0.5;
d = 0.3;
s = 0.5;
l = 10.0;
w = 3.0;
pi = 3.1415926536
tol = 1.0e-12
eta = 377.0
Dk = 1.0
qoffset = 0.0
poffset = 1.75

class PEC(SubDomain):
def inside(self, x, on_boundary):
return on_boundary

class InputBC(SubDomain):
def inside(self, x, on_boundary):
return on_boundary and near(x[2], -1, tol)

class OutputBC(SubDomain):
def inside(self, x, on_boundary):
rb = sqrt(x[0] * x[0] + (x[1] + 1.25)* (x[1] + 1.25) + x[2] * x[2])
return on_boundary and near(rb, 10.0, 5.0e-2)

class PMC(SubDomain):
def inside(self, x, on_boundary):
return on_boundary and (near(x[0], 0.0, tol) or near(x[1], -1.25, tol))

mesh = Mesh()
with XDMFFile(“mesh.xdmf”) as infile:
infile.read(mesh)
mvc = MeshValueCollection(“size_t”, mesh, 3)

info(mesh)
#plot(mesh)
#plt.show()

Mark boundaries

sub_domains = MeshFunction(“size_t”, mesh, mesh.topology().dim() - 1)
sub_domains.set_all(4)
pec = PEC()
pec.mark(sub_domains, 0)
in_port = InputBC()
in_port.mark(sub_domains, 1)
out_port = OutputBC()
out_port.mark(sub_domains, 2)
pmc = PMC()
pmc.mark(sub_domains, 3)
File(“BoxSubDomains.pvd”).write(sub_domains)

dk = 0.025
#for m in range(40):
for m in range(1):

K = 0.500 + m * dk

K = 0.5
k0 = Constant(K)
beta = K
b0 = Constant(beta)
Kr = Dk

Set up function spaces

For low order problem

cell = tetrahedron
ele_type = FiniteElement(‘N1curl’, cell, 2) # H(curl) element for EM
V2 = FunctionSpace(mesh, MixedElement([ele_type, ele_type]))
V = FunctionSpace(mesh, ele_type)
u_r, u_i = TrialFunctions(V2)
v_r, v_i = TestFunctions(V2)

#surface integral definitions from boundaries
ds = Measure(‘ds’, domain = mesh, subdomain_data = sub_domains)

with source and sink terms

u0 = Constant((0.0, 0.0, 0.0)) #PEC definition
h_src = Expression((‘-(x[1] - poffset) / (2.0 * pi * (pow((x[0]-qoffset), 2.0) + pow(x[1] - poffset,2.0)))’, ‘(x[0]-qoffset) / (2.0 * pi *(pow((x[0]-qoffset),2.0) + pow(x[1] - poffset,2.0)))’, 0.0), degree = 2, poffset = poffset, qoffset = qoffset)
e_src = Expression((‘(x[0] - qoffset) / (2.0 * pi * (pow((x[0]-qoffset), 2.0) + pow(x[1] - poffset,2.0)))’, ‘(x[1]-poffset) / (2.0 * pi *(pow((x[0]-qoffset),2.0) + pow(x[1] - poffset,2.0)))’, 0.0), degree = 2, poffset = poffset, qoffset = qoffset)
Rrad = Expression((‘sqrt(x[0] * x[0] + (x[1] + 1.25) * (x[1] + 1.25) + x[2] * x[2])’), degree = 2)
#Boundary condition dictionary
boundary_conditions = {0: {‘PEC’ : u0},
1: {‘InputBC’: (h_src, Dk)},
2: {‘OutputBC’: Rrad},
3: {‘PMC’: 0.0}}

n = FacetNormal(mesh)

#Build PEC boundary conditions for real and imaginary parts
bcs =
for i in boundary_conditions:
if ‘PEC’ in boundary_conditions[i]:
bc = DirichletBC(V2.sub(0), boundary_conditions[i][‘PEC’], sub_domains, i)
bcs.append(bc)
bc = DirichletBC(V2.sub(1), boundary_conditions[i][‘PEC’], sub_domains, i)
bcs.append(bc)

Build input BC source term and loading term

integral_source =
integrals_load =
for i in boundary_conditions:
if ‘InputBC’ in boundary_conditions[i]:
r, s = boundary_conditions[i][‘InputBC’]
bb1 = 2.0 * k0 * eta * inner(v_i, cross(n, r)) * ds(i) #Factor of two from field equivalence principle
integral_source.append(bb1)
bb2 = inner(cross(n, v_i), cross(n, u_r)) * b0 * ds(i)
integrals_load.append(bb2)
bb2 = inner(-cross(n, v_r), cross(n, u_i)) * b0 * ds(i)
integrals_load.append(bb2)

for i in boundary_conditions:
if ‘OutputBC’ in boundary_conditions[i]:
r = boundary_conditions[i][‘OutputBC’]
bb2 = (inner(cross(n, v_i), cross(n, u_r)) * k0 + 0.5 * inner(cross(n, v_i), cross(n, u_i)) / r)* ds(i)
integrals_load.append(bb2)
bb2 = (inner(-cross(n, v_r), cross(n, u_i)) * k0 + 0.5 * inner(cross(n, v_r), cross(n, u_r)) / r)* ds(i)
integrals_load.append(bb2)

for PMC, do nothing. Natural BC.

af = (inner(curl(v_r), curl(u_r)) + inner(curl(v_i), curl(u_i)) - Kr * k0 * k0 * (inner(v_r, u_r) + inner(v_i, u_i))) * dx + sum(integrals_load)
L = sum(integral_source)

u1 = Function(V2)
vdim = u1.vector().size()
print("Vdim = ", vdim)

solve(af == L, u1, bcs, solver_parameters = {‘linear_solver’ : ‘mumps’})

u1_r, u1_i = u1.split(True)

fp = File(“EField_r.pvd”)
fp << u1_r
fp = File(“EField_i.pvd”)
fp << u1_i
fp = File(‘SIWWaveFile.pvd’)

ut = u1_r.copy(deepcopy=True)
for i in range(50):
ut.vector().zero()
ut.vector().axpy(-sin(pi * i / 25.0), u1_i.vector())
ut.vector().axpy(cos(pi * i / 25.0), u1_r.vector())
fp << (ut, i)

H = interpolate(h_src, V) # Get input field
P = assemble((-dot(u1_r,cross(curl(u1_i),n))+dot(u1_i,cross(curl(u1_r),n))) * ds(2))
P_refl = assemble((-dot(u1_i,cross(curl(u1_r), n)) + dot(u1_r, cross(curl(u1_i), n))) * ds(1))
P_inc = assemble((dot(H, H) * 0.5 * eta * b0 / k0) * ds(1))
print("k0 = ", K)
print("Beta = ", beta)
print(“Integrated power on rad boundary:”, P/(2.0 * K * eta))
print(“Incident power at port 1:”, P_inc)
print(“Integrated reflected power on port 1:”, P_inc - P_refl / (2.0 * K * eta))
eps_c = 1.0
lc = 1.0
E = interpolate(e_src, V) # Incident E field
ccr = assemble(-dot(u1_r - E * (eta / sqrt(eps_c)), E * (eta / sqrt(eps_c))) * ds(1))
cci = assemble(dot(u1_i, E) * ds(1)) * eta / sqrt(eps_c)
cc = assemble(dot(E, E) * ds(1)) * eta * eta / eps_c
Zo = 50.0
rho = complex(ccr / cc, cci / cc)
print(“Input port reflection coefficient: {0:<f}+j{1:<f}”.format(rho.real, rho.imag))
Zin = Zo * (1.0 + rho) / (1.0 - rho)
print(“Input port impedance: {0:<f} + j{1:<f}”.format(Zin.real, Zin.imag))
Zl = Zo * (Zin - (1j) * Zo * tan(K * sqrt(eps_c) * lc)) / (Zo - (1j) * Zin * tan(K * sqrt(eps_c) * lc))
print(“Antenna feedpoint impedance: {0:<f} + j{1:<f}”.format(Zl.real, Zl.imag))

Generate radiation pattern!

print(“Generate radiation pattern.”)
metadata = {“quadrature_degree”: 6, “quadrature_scheme”: “default”}
dsm = ds(metadata=metadata)
NumTheta = 25
NumPhi = 100
TwoPi = 6.2831853071
PiOverTwo = 1.5707963268
fp = open(“MonoPattern1.txt”, “w”)
print(“#Elevation Azimuth Pvert Phoriz”, file = fp)

Reflection transformations

PMC

JCx = Constant(((-1.0, 0.0, 0.0), (0.0, 1.0, 0.0), (0.0, 0.0, 1.0))) # PMC Reflection thru x = 0 plane
#JCy = Constant(((-1.0, 0.0, 0.0), (0.0, 1.0, 0.0), (0.0, 0.0, -1.0))) # PEC Reflection thru y = -5 plane
JCy = Constant(((1.0, 0.0, 0.0), (0.0, -1.0, 0.0), (0.0, 0.0, 1.0))) # PMC Reflection thru y = -5 plane
MCx = Constant(((1.0, 0.0, 0.0), (0.0, -1.0, 0.0), (0.0, 0.0, -1.0)))
#MCy = Constant(((1.0, 0.0, 0.0), (0.0, -1.0, 0.0), (0.0, 0.0, 1.0)))
MCy = Constant(((-1.0, 0.0, 0.0), (0.0, 1.0, 0.0), (0.0, 0.0, -1.0)))

PEC ground plane

JCz = Constant(((-1.0, 0.0, 0.0), (0.0, -1.0, 0.0), (0.0, 0.0, 1.0))) #PEC reflection thru z = 0 plane
MCz = Constant(((1.0, 0.0, 0.0), (0.0, 1.0, 0.0), (0.0, 0.0, -1.0)))

Surface currents on external boundary

M_r = -cross(n, u1_r)
M_i = -cross(n, u1_i)
J_r = -cross(n, curl(u1_i)) / (k0 * eta)
J_i = cross(n, curl(u1_r)) / (k0 * eta)

for m in range(NumTheta+1):
theta = m * PiOverTwo / NumTheta
print(" ", file = fp) # for Gnuplot
for nn in range(NumPhi+1):
L_r = #List objects for integrals
L_i =
N_r =
N_i =

Do NFF transformation

    phi = nn * TwoPi / NumPhi
    rr = Expression(('sin(theta)*cos(phi)', 'sin(theta)*sin(phi)', 'cos(theta)'), degree = 3, phi = phi, theta = theta)
    rtheta = Expression(('cos(theta)*cos(phi)', 'cos(theta)*sin(phi)', '-sin(theta)'), degree = 3, phi = phi, theta = theta)
    rphi = Expression(('-sin(phi)', 'cos(phi)', '0.0'), degree = 3, phi = phi)

Sum up all the image sources taking into account the proper symmetries

First octant

    rp1 = Expression(('x[0]', 'x[1]+1.25', 'x[2]'), degree = 1)
    sr = J_r * cos(k0 * dot(rr, rp1)) - J_i * sin(k0 * dot(rr, rp1))
    si = J_i * cos(k0 * dot(rr, rp1)) + J_r * sin(k0 * dot(rr, rp1))
    N_r.append(sr)
    N_i.append(si)
    qr = M_r * cos(k0 * dot(rr, rp1)) - M_i * sin(k0 * dot(rr, rp1))
    qi = M_i * cos(k0 * dot(rr, rp1)) + M_r * sin(k0 * dot(rr, rp1))
    L_r.append(qr)
    L_i.append(qi)

Second octant x < 0, y > 0, z > 0

    rp2 = Expression(('-x[0]', 'x[1]+1.25', 'x[2]'), degree = 1)
    sr = JCx * (J_r * cos(k0 * dot(rr, rp2)) - J_i * sin(k0 * dot(rr, rp2)))
    si = JCx * (J_i * cos(k0 * dot(rr, rp2)) + J_r * sin(k0 * dot(rr, rp2)))
    N_r.append(sr)
    N_i.append(si)
    qr = MCx * (M_r * cos(k0 * dot(rr, rp2)) - M_i * sin(k0 * dot(rr, rp2)))
    qi = MCx * (M_i * cos(k0 * dot(rr, rp2)) + M_r * sin(k0 * dot(rr, rp2)))
    L_r.append(qr)
    L_i.append(qi)

third octant x < 0, y < 0, z > 0

    rp3 = Expression(('-x[0]', '-x[1]-1.25', 'x[2]'), degree = 1)
    sr = JCy * JCx * (J_r * cos(k0 * dot(rr, rp3)) - J_i * sin(k0 * dot(rr, rp3)))
    si = JCy * JCx * (J_i * cos(k0 * dot(rr, rp3)) + J_r * sin(k0 * dot(rr, rp3)))
    N_r.append(sr)
    N_i.append(si)
    qr = MCy * MCx * (M_r * cos(k0 * dot(rr, rp3)) - M_i * sin(k0 * dot(rr, rp3)))
    qi = MCy * MCx * (M_i * cos(k0 * dot(rr, rp3)) + M_r * sin(k0 * dot(rr, rp3)))
    L_r.append(qr)
    L_i.append(qi)

fourth octant x > 0, y < 0, z > 0

    rp4 = Expression(('x[0]', '-x[1]-1.25', 'x[2]'), degree = 1)
    sr = JCy * (J_r * cos(k0 * dot(rr, rp4)) - J_i * sin(k0 * dot(rr, rp4)))
    si = JCy * (J_i * cos(k0 * dot(rr, rp4)) + J_r * sin(k0 * dot(rr, rp4)))
    N_r.append(sr)
    N_i.append(si)
    qr = MCy * (M_r * cos(k0 * dot(rr, rp4)) - M_i * sin(k0 * dot(rr, rp4)))
    qi = MCy * (M_i * cos(k0 * dot(rr, rp4)) + M_r * sin(k0 * dot(rr, rp4)))
    L_r.append(qr)
    L_i.append(qi)

Fifth octant x > 0, y > 0, z < 0

    rp5 = Expression(('x[0]', 'x[1]+1.25', '-x[2]'), degree = 1)
    sr = JCz * (J_r * cos(k0 * dot(rr, rp5)) - J_i * sin(k0 * dot(rr, rp5)))
    si = JCz * (J_i * cos(k0 * dot(rr, rp5)) + J_r * sin(k0 * dot(rr, rp5)))
    N_r.append(sr)
    N_i.append(si)
    qr = MCz * (M_r * cos(k0 * dot(rr, rp5)) - M_i * sin(k0 * dot(rr, rp5)))
    qi = MCz * (M_i * cos(k0 * dot(rr, rp5)) + M_r * sin(k0 * dot(rr, rp5)))
    L_r.append(qr)
    L_i.append(qi)

Sixth octant x < 0, y > 0, z < 0

    rp6 = Expression(('-x[0]', 'x[1]+1.25', '-x[2]'), degree = 1)
    sr = JCx * JCz * (J_r * cos(k0 * dot(rr, rp6)) - J_i * sin(k0 * dot(rr, rp6)))
    si = JCx * JCz * (J_i * cos(k0 * dot(rr, rp6)) + J_r * sin(k0 * dot(rr, rp6)))
    N_r.append(sr)
    N_i.append(si)
    qr = MCx * MCz * (M_r * cos(k0 * dot(rr, rp6)) - M_i * sin(k0 * dot(rr, rp6)))
    qi = MCx * MCz * (M_i * cos(k0 * dot(rr, rp6)) + M_r * sin(k0 * dot(rr, rp6)))
    L_r.append(qr)
    L_i.append(qi)

seventh octant x < 0, y < 0, z < 0

    rp7 = Expression(('-x[0]', '-x[1]-1.25', '-x[2]'), degree = 1)
    sr = JCy * JCx * JCz * (J_r * cos(k0 * dot(rr, rp7)) - J_i * sin(k0 * dot(rr, rp7)))
    si = JCy * JCx * JCz * (J_i * cos(k0 * dot(rr, rp7)) + J_r * sin(k0 * dot(rr, rp7)))
    N_r.append(sr)
    N_i.append(si)
    qr = MCy * MCx * MCz * (M_r * cos(k0 * dot(rr, rp7)) - M_i * sin(k0 * dot(rr, rp7)))
    qi = MCy * MCx * MCz * (M_i * cos(k0 * dot(rr, rp7)) + M_r * sin(k0 * dot(rr, rp7)))
    L_r.append(qr)
    L_i.append(qi)

Eighth octant x > 0, y < 0, z < 0

    rp8 = Expression(('x[0]', '-x[1]-1.25', '-x[2]'), degree = 1)
    sr = JCy * JCz * (J_r * cos(k0 * dot(rr, rp8)) - J_i * sin(k0 * dot(rr, rp8)))
    si = JCy * JCz * (J_i * cos(k0 * dot(rr, rp8)) + J_r * sin(k0 * dot(rr, rp8)))
    N_r.append(sr)
    N_i.append(si)
    qr = MCy * MCz * (M_r * cos(k0 * dot(rr, rp8)) - M_i * sin(k0 * dot(rr, rp8)))
    qi = MCy * MCz * (M_i * cos(k0 * dot(rr, rp8)) + M_r * sin(k0 * dot(rr, rp8)))
    L_r.append(qr)
    L_i.append(qi)

Compute E_ff

    Et_i = -K * assemble((dot(sum(L_r), rphi) + eta * dot(sum(N_r), rtheta)) * dsm(2))
    Et_r = K * assemble((dot(sum(L_i), rphi) + eta * dot(sum(N_i), rtheta)) * dsm(2))
    Ep_i = K * assemble((dot(sum(L_r), rtheta) - eta * dot(sum(N_r), rphi)) * dsm(2))
    Ep_r = -K * assemble((dot(sum(L_i), rtheta) - eta * dot(sum(N_i), rphi)) * dsm(2))

Compute magnitudes

    Gvert = (Et_r * Et_r + Et_i * Et_i) / (2.0 * TwoPi * eta * (P * 8.0 / (2.0 * K * eta)))
    Ghoriz = (Ep_r * Ep_r + Ep_i * Ep_i) / (2.0 * TwoPi * eta * (P * 8.0 / (2.0 * K * eta)))

    print(" {0:f} {1:f} {2:f} {3:f}".format(theta, phi, Gvert, Ghoriz))
    print(" {0:f} {1:f} {2:f} {3:f}".format(theta, phi, Gvert, Ghoriz), file = fp)

fp.close()
sys.exit(0)
the error messagw
Traceback (most recent call last):
File “/mnt/hgfs/PMSM-X-main/DualMonopole（单极子阵列天线）/DualMonopoleRevPhase.py”, line 39, in
infile.read(mesh)
RuntimeError:

*** -------------------------------------------------------------------------
*** DOLFIN encountered an error. If you are not able to resolve this issue
*** using the information listed below, you can ask for help at

*** fenics-support@googlegroups.com

*** Remember to include the error message listed below and, if possible,
*** include a minimal running example to reproduce the error.

*** -------------------------------------------------------------------------
*** Error: Unable to open XDMF file.
*** Reason: XDMF file “mesh.xdmf” does not exist.
*** Where: This error was encountered inside XDMFFile.cpp.
*** Process: 0

*** DOLFIN version: 2019.2.0.dev0
*** Git changeset: ubuntu
*** -------------------------------------------------------------------------

Process finished with exit code 1

dokken · October 25, 2023, 2:44am

Well, your error message relates to

Ie you mesh file does not exist.
This has nothing to do with vtkplotter.

Please reduce the code to a minimal reproducible example and use 3x` encapsulation, ie

```python
# add code here
```

sohar · October 25, 2023, 3:04am

This is strange, I put the grid file under the same folder, but it was not detected
mesh

dokken · October 25, 2023, 4:38am

That is an .msh file, not .xdmf file. You Need to convert your mesh

sohar · October 25, 2023, 8:40am

There is already code in the code to convert the.msh file, and it is this code that has the problem

import meshio
msh = meshio.read("DualMonopole.msh")
for cell in msh.cells:
    if  cell.type == "tetra":
        tetra_cells = cell.data

for key in msh.cell_data_dict["gmsh:physical"].keys():
    if key == "tetra":
        tetra_data = msh.cell_data_dict["gmsh:physical"][key]

tetra_mesh = meshio.Mesh(points=msh.points, cells={"tetra": tetra_cells},
                           cell_data={"VolumeRegions":[tetra_data]})

meshio.write("mesh.xdmf", tetra_mesh)



from dolfin import *
from vtkplotter.dolfin import datadir, plot


mesh = Mesh()
with XDMFFile("mesh.xdmf") as infile:
    infile.read(mesh)
mvc = MeshValueCollection("size_t", mesh, 3)
with XDMFFile("mesh.xdmf") as infile:
    infile.read(mvc, "VolumeRegions")
cf = cpp.mesh.MeshFunctionSizet(mesh, mvc)

info(mesh)

# Volume domains
File("VolSubDomains.pvd").write(cf)
File("Mesh.pvd").write(mesh)

plot(mesh)

dokken · October 25, 2023, 8:41am

Well, that is not the code you gave above. What error do you get with this code:

sohar:

import meshio
msh = meshio.read("DualMonopole.msh")
for cell in msh.cells:
    if  cell.type == "tetra":
        tetra_cells = cell.data

for key in msh.cell_data_dict["gmsh:physical"].keys():
    if key == "tetra":
        tetra_data = msh.cell_data_dict["gmsh:physical"][key]

tetra_mesh = meshio.Mesh(points=msh.points, cells={"tetra": tetra_cells},
                           cell_data={"VolumeRegions":[tetra_data]})

meshio.write("mesh.xdmf", tetra_mesh)



from dolfin import *
from vtkplotter.dolfin import datadir, plot


mesh = Mesh()
with XDMFFile("mesh.xdmf") as infile:
    infile.read(mesh)
mvc = MeshValueCollection("size_t", mesh, 3)
with XDMFFile("mesh.xdmf") as infile:
    infile.read(mvc, "VolumeRegions")
cf = cpp.mesh.MeshFunctionSizet(mesh, mvc)

info(mesh)

# Volume domains
File("VolSubDomains.pvd").write(cf)
File("Mesh.pvd").write(mesh)

plot(mesh)

sohar · October 25, 2023, 8:44am

this is the error
Traceback (most recent call last):
File “/mnt/hgfs/PMSM-X-main/DualMonopole（单极子阵列天线）/DualMonopoleConv.py”, line 15, in
meshio.write(“mesh.xdmf”, tetra_mesh)
File “/home/sohar/.local/lib/python3.10/site-packages/meshio/_helpers.py”, line 188, in write
return writer(filename, mesh, **kwargs)
File “/home/sohar/.local/lib/python3.10/site-packages/meshio/xdmf/main.py”, line 546, in write
XdmfWriter(*args, **kwargs)
File “/home/sohar/.local/lib/python3.10/site-packages/meshio/xdmf/main.py”, line 338, in init
import h5py
ModuleNotFoundError: No module named ‘h5py’

dokken · October 25, 2023, 10:50am

The error is very clear, you have not installed h5py, which can be installed with python3 -m pip install --no-binary=h5py h5py.

sohar · October 25, 2023, 11:32am

I have now downloaded h5py, run the code and it says h5py have no attribute ‘File’.Is this a version problem?

Traceback (most recent call last):
  File "/mnt/hgfs/PMSM-X-main/DualMonopole（单极子阵列天线）/DualMonopoleConv.py", line 15, in <module>
    meshio.write("mesh.xdmf", tetra_mesh)
  File "/home/sohar/.local/lib/python3.10/site-packages/meshio/_helpers.py", line 188, in write
    return writer(filename, mesh, **kwargs)
  File "/home/sohar/.local/lib/python3.10/site-packages/meshio/xdmf/main.py", line 546, in write
    XdmfWriter(*args, **kwargs)
  File "/home/sohar/.local/lib/python3.10/site-packages/meshio/xdmf/main.py", line 354, in __init__
    self.h5_file = h5py.File(self.h5_filename, "w")
AttributeError: module 'h5py' has no attribute 'File'

Process finished with exit code 1

dokken · October 25, 2023, 2:05pm

Then your h5py installation is not successful.

sohar · October 26, 2023, 2:49am

I’ve fixed the h5py issue and now it’s back to my original question, I can’t install the vtkplotter。
I installed the module with the command

pip install vtkplotter

or

pip3 install vtkplotter

The error are the same
ERROR: Could not find a version that satisfies the requirement vtkplotter (from versions: none)
ERROR: No matching distribution found for vtkplotter
when I use this command

sudo apt-get python3-vtkplotter

the error is

There is no package available for python3-vtkplotter, but it is referenced by other packages.

This could mean that the missing package may have been discarded,

Or it can only be found in other publishing sources

However, the following packages will replace it:

python3-vedo.

then i install vedo ,but the erorr still exist

dokken · October 26, 2023, 6:04am

As far as I can recall vtkplotter was renamed vedo, thus you have to change the import statement to import vedo if you have installed GitHub - marcomusy/vedo: A python module for scientific analysis of 3D data based on VTK and Numpy
Maybe @marcomusy can comment?

sohar · October 26, 2023, 7:03am

This is a lower version of the code, now that vtkplotter has been recall vedo, I think the datadir in the import vtkplotter has also changed, but I don’t know what the datdir has been changed to.

import meshio
msh = meshio.read("DualMonopole.msh")
for cell in msh.cells:
    if  cell.type == "tetra":
        tetra_cells = cell.data

for key in msh.cell_data_dict["gmsh:physical"].keys():
    if key == "tetra":
        tetra_data = msh.cell_data_dict["gmsh:physical"][key]

tetra_mesh = meshio.Mesh(points=msh.points, cells={"tetra": tetra_cells},
                           cell_data={"VolumeRegions":[tetra_data]})

meshio.write("mesh.xdmf", tetra_mesh)



from dolfin import *
from vedo.dolfin import datadir, plot


mesh = Mesh()
with XDMFFile("mesh.xdmf") as infile:
    infile.read(mesh)
mvc = MeshValueCollection("size_t", mesh, 3)
with XDMFFile("mesh.xdmf") as infile:
    infile.read(mvc, "VolumeRegions")
cf = cpp.mesh.MeshFunctionSizet(mesh, mvc)

info(mesh)

# Volume domains
File("VolSubDomains.pvd").write(cf)
File("Mesh.pvd").write(mesh)

plot(mesh)

this is the erorr

Traceback (most recent call last):
  File "/home/sohar/桌面/DualMonopole（单极子阵列天线）/DualMonopoleConv.py", line 20, in <module>
    from vedo.dolfin import datadir, plot
  File "/usr/lib/python3/dist-packages/vedo/__init__.py", line 47, in <module>
    settings._init()
  File "/usr/lib/python3/dist-packages/vedo/settings.py", line 600, in _init
    np.warnings.filterwarnings('ignore', category=np.VisibleDeprecationWarning)
  File "/home/sohar/.local/lib/python3.10/site-packages/numpy/__init__.py", line 328, in __getattr__
    raise AttributeError("module {!r} has no attribute "
AttributeError: module 'numpy' has no attribute 'warnings'. Did you mean: 'hanning'?

Process finished with exit code 1

marcomusy · October 26, 2023, 11:46pm

This is very confusing… you seem to have a very old installation of vedo try:

pip uninstall vedo
pip install vedo -U

sohar · October 27, 2023, 3:26am

I reinstalled vedo2023.4.6 but as I said before cannot import name 'datadir

Traceback (most recent call last):
  File "/mnt/hgfs/PMSM-X-main/DualMonopole（单极子阵列天线）/DualMonopoleConv.py", line 20, in <module>
    from vedo.dolfin import datadir, plot
ImportError: cannot import name 'datadir' from 'vedo.dolfin' (/home/sohar/.local/lib/python3.10/site-packages/vedo/dolfin.py)

marcomusy · October 27, 2023, 2:18pm

There is no datadir in vedo2023.4.6, it does not exist, this means that there is something else going wrong in your environment, unrelated to vedo or dolfin…

sohar · November 1, 2023, 3:26am

Sorry for not replying to you immediately. I delet datadir, .msh file was successfully convert to .xdmf file, but the operation results can not converge. I find that dolfinx and dolfin2019.2 are downloaded on my virtual machine. Since the code writer used dolfin2019.2, I successfully run the code in the dolfin2019.2 environment and get the result.