This demo explains how to use Measure to restrict facet integration.
Hi,
sorry, I probably did not explain it well.
I wrote two functions to convert a .msh file to XDMF file using the code example provided by @dokken .
Now my first function generates from a .msh file three separated XDMF files for the mesh, the subdomains and the boundary subdomains.
At a later time I can load the files using the second functions that returns a dictionary containing the mesh, the marker functions (for volume and boundary subdomains) and the corresponding measures.
How I can generalize this code to include also internal boundary subdomains.
Should I also generate a separate xdmf file for internal boundaries?
How can I mark in gmsh an internal boundary subdomain? The command Physical surface doesn’t seem to distinguish external surfaces from internal ones.
Best.
Iacopo
Here is my code
import meshio
import dolfin as dol
def convert_to_XDMF(filename):
'''reads a .msh file and writes mesh, subdomains, and boundary subdomains
to XDMF files'''
#check if input file i in msh
if filename.split(sep = '.')[-1] != 'msh':
raise TypeError('.msh file required')
msh = meshio.read(filename)
#write mesh xdmf file
meshio.write(''.join(filename.split(sep ='.')[:-1]) + '_mesh.xdmf',
meshio.Mesh(points = msh.points,
cells = {'tetra': msh.cells['tetra']}))
#write boundary subdomains xdmf file
meshio.write(''.join(filename.split(sep ='.')[:-1]) + '_boundary_subdomains.xdmf',
meshio.Mesh(points = msh.points,
cells = {'triangle': msh.cells['triangle']},
cell_data = {'triangle': {'name_to_read' : msh.cell_data['triangle']['gmsh:physical']}}))
#write subdomains xdmf file
meshio.write(''.join(filename.split(sep ='.')[:-1]) + '_subdomains.xdmf',
meshio.Mesh(points = msh.points,
cells = {'tetra' : msh.cells['tetra']},
cell_data = {'tetra' : {'name_to_read' : msh.cell_data['tetra']['gmsh:physical']}}))
def load_XDMF_files(filename):
#create mesh from msh file
mesh = dol.Mesh()
with dol.XDMFFile(filename) as infile:
infile.read(mesh)
#create subdomain cell function
mvc = dol.MeshValueCollection('size_t', mesh, 3)
with dol.XDMFFile(''.join(filename.split(sep ='_')[:-1]) + '_subdomains.xdmf') as infile:
infile.read(mvc, 'name_to_read')
subdomain_marker = dol.cpp.mesh.MeshFunctionSizet(mesh, mvc)
#create boundary subdomain facet function
mvc = dol.MeshValueCollection('size_t', mesh, 2)
with dol.XDMFFile(''.join(filename.split(sep ='_')[:-1]) + '_boundary_subdomains.xdmf') as infile:
infile.read(mvc, 'name_to_read')
boundary_marker = dol.cpp.mesh.MeshFunctionSizet(mesh, mvc)
del(mvc)
#define measures
dx = dol.Measure('dx', domain = mesh, subdomain_data = subdomain_marker)
ds = dol.Measure('ds', domain = mesh, subdomain_data = boundary_marker)
#return dictionary
return {'mesh' : mesh,
'volume_measure' : dx,
'boundary_measure' : ds,
'subdomain_marker' : subdomain_marker,
'boundary_marker' : boundary_marker}
1 Like
You can just proceed analogously as for exterior boundaries, even write everything into the same xdmf file.
For gmsh you just mark the corresponding internal boundaries as physical line or surface (depending on your dimension).
When you create your Measures with
ds = dol.Measure('ds', domain = mesh, subdomain_data = boundary_marker)
dS = dol.Measure('dS', domain=mesh, subdomain_data = boundary_marker)
everything is taken care of (as the Measures are for external and internal surfaces)
Ok, dS ignores informations on facets that are on the boundary, while ds ignores internal boundaries.
I just need to use different indicators (I cannot have an internal boundary with integration measure dS(1) and an external boundary with integration measure ds(1) ) but is probably never a good idea to use the same number for two different things.
Thanks for the super-fast reply.
I
Hi,
I not familiar with using xml or xdmf files but I used Gmsh to create a simple mesh in order to refine it later. As you explained using gmsh -3 plate.geo to generate plate.msh. and with the same code you have provided for conversion into xdmf .
Unfortuentaly I was not able to figure out how to avoid this error message:
File "Dye3D.py", line 70, in <module>
meshio.write("mesh.xdmf", meshio.Mesh(points=msh.points, cells={"tetra": msh.cells["tetra"]}))
AttributeError: module 'meshio' has no attribute 'Mesh'
here is the plate.geo file from Gmsh:
//+
Physical Line("left_line") = {4};
//+
SetFactory("OpenCASCADE");
Box(1) = {e, e, 0, 50, 100, 2};
//+
Physical Line("left_line") += {4};
//+
Physical Line("right_line") = {8};
//+
Physical Line("front_line") = {11};
//+
Physical Line("back_line") = {9};
//+
Physical Surface("left") = {1};
//+
Physical Surface("right") = {2};
//+
Physical Surface("front") = {4};
//+
Physical Surface("back") = {3};
//+
Physical Surface("bottom") = {5};
//+
Physical Surface("top") = {6};
//+
Physical Volume("domain") = {1};
//+
Field[1] = Box;
//+
Field[1].VIn = 0.7;
//+
Field[1].VOut = 5;
//+
Field[1].XMax = 50;
//+
Field[1].XMin = 45;
//+
Field[1].YMax = 100;
//+
Field[1].ZMax = 2;
//+
Background Field = 1;
Can you please advise any solution to this error and if I am using the correct way for the file generation.
Thank you!
Which version of meshio are you using?
I have no issues with the following code with meshio 4.0.8:
import meshio
msh = meshio.read("mesh.msh")
meshio.write("mesh.xdmf",
meshio.Mesh(points = msh.points,
cells = {'tetra': msh.cells_dict['tetra']}))
thanks for reply
It is meshio-2.3.10
I have checked for the version 4.0.8. but could not install it!
Have you tried pip3 install meshio --upgrade
I tried this with meshio-4.0.8:
import meshio
msh = meshio.read("Monopole2.msh")
for cell in msh.cells:
if cell.type == "tetra":
tet_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]
tet_mesh = meshio.Mesh(points=msh.points, cells={"tetra": tet_cells})
meshio.write("mesh.xdmf", tet_mesh)and it dies with the following error message:
Traceback (most recent call last):
File "Monopole2.py", line 10, in <module>
meshio.write("mesh.xdmf", tet_mesh)
File "/home/bill/.local/lib/python3.6/site-packages/meshio/_helpers.py", line 119, in write
file_format = _filetype_from_path(path)
File "/home/bill/.local/lib/python3.6/site-packages/meshio/_helpers.py", line 33, in _filetype_from_path
raise ReadError("Could not deduce file format from extension '{}'.".format(ext))
meshio._exceptions.ReadError: Could not deduce file format from extension '.xdmf'.How can I make this work?
My full 3D GMSH mesh file found here. It is a bit big to post as code for E-Z copy paste.
PS- Just tried this code posted by @dokken earlier. It gives the same error.
import meshio
msh = meshio.read("Monopole2.msh")
meshio.write("mesh.xdmf",
meshio.Mesh(points = msh.points,
cells = {'tetra': msh.cells_dict['tetra']}))
You have to install h5py. pip3 install h5py.
2 Likes
@dokken That fixed it! Thanks!
Thanks, it is updated now.
I have read this thread and tried to use the generated files but it did not work.
I want to use the physical_groups names for Dirichlet and Neumann boundary conditions (this may include boundaries on edge lines).
The problem that I want to solve will include a Mixed finite element. Here is a simple version with heat diffusion as it was possible to generate the xdmf files:
Edit: best what I was able to achieve is to use from mf.xdmf file.
I could not create the cf.xdmf file in order to use it in the volume measure.
Now the minimal code is
import meshio
msh = meshio.read("plate.msh")
for cell in msh.cells:
if cell.type == "triangle":
triangle_cells = cell.data
elif cell.type == "tetra":
tetra_cells = cell.data
for key in msh.cell_data_dict["gmsh:physical"].keys():
if key == "triangle":
triangle_data = msh.cell_data_dict["gmsh:physical"][key]
elif key == "tetra":
tetra_data = msh.cell_data_dict["gmsh:physical"][key]
tetra_mesh = meshio.Mesh(points=msh.points, cells={"tetra": tetra_cells})
triangle_mesh =meshio.Mesh(points=msh.points,
cells=[("triangle", triangle_cells)],
cell_data={"name_to_read":[triangle_data]})
meshio.write("plate.xdmf", tetra_mesh)
meshio.write("mf.xdmf", triangle_mesh)
from dolfin import *
import numpy
import time
import matplotlib.pyplot as plt
set_log_level(LogLevel.ERROR)
mesh = Mesh()
with XDMFFile("plate.xdmf") as infile:
infile.read(mesh)
mvc = MeshValueCollection("size_t", mesh, 2)
with XDMFFile("mf.xdmf") as infile:
infile.read(mvc, "name_to_read")
mf = cpp.mesh.MeshFunctionSizet(mesh, mvc)
'''mvc = MeshValueCollection("size_t", mesh, 3)
with XDMFFile("cf.xdmf") as infile:
infile.read(mvc, "name_to_read")
cf = cpp.mesh.MeshFunctionSizet(mesh, mvc)'''
ds_top = Measure("ds", domain=mesh, subdomain_data=mf, subdomain_id=11)
ds_right = Measure("ds", domain=mesh, subdomain_data=mf, subdomain_id=7)
dx_volume = Measure("dx", domain=mesh, subdomain_data=mf, subdomain_id=12) # cf, need to create cf.xdmf
print('assemble(1*ds_top)',assemble(1*ds_top))
print('assemble(1*ds_right)',assemble(1*ds_right))
Tref = 298 #300. # in K
Tamb = Tref
Ts = Constant(1273.) # Solid temp
Tl = Constant(1514.) # Liquid temp
Tm = Constant(1514.) # Melting temperature (K)
rho = 7737.0e-12 # in tonne/mm3
kappa = 28. # mJ/(smmK)
Cp = 600.0e6 # mJ/(tonK)
h = 35.0e-3 # mJ/(smm^2K)
t = 0.0
tMax = 50 #
Dt = 1 # time step
WIDTH, LENGTH, thickness = 50., 100., 2. # width, length and thickness (mm)
xMin, xMax = 0.0, WIDTH
yMin, yMax = 0.0, LENGTH
zMin, zMax = 0.0, thickness
##mesh = BoxMesh(Point(xMin,yMin,zMin), Point(xMax,yMax,zMax),20, 60, 3)
# Define space function
Space = FunctionSpace(mesh,'P',1)
#cells = MeshFunction('size_t',mesh, 3, 0)
#facets = MeshFunction('size_t',mesh, 2, 0)
#dA = Measure('ds', domain=mesh, subdomain_data=facets, metadata={'quadrature_degree':2})
#dV = Measure('dx', domain=mesh, subdomain_data=cells, metadata={'quadrature_degree':2})
#boundaries
#bc1 = DirichletBC(Space,Constant(1000.),right)
bc = []#[bc1]
# define functions
dT = TrialFunction(Space)
delT = TestFunction(Space)
T = Function(Space)
T0 = Function(Space)
T_init = Expression(('Tini'),Tini=Tref, degree=1) #degree=2
T = interpolate(T_init,Space)
T0.assign(T)
cutoff_Tc = 113.2 ##
Sour_surface = Expression( "t <= tc ? eta *Q_app/(pi*a*a)*exp(- (pow((x[0]-x0),2)+ pow((x[1]-y0-v*t),2))/(2.*a*a) ): 0",
t=t, tc=cutoff_Tc, eta=0.57, a=4 , Q_app =Constant(580e3),v=1.59, x0=0,y0=LENGTH*0.05, degree=2)
qHat = h*(T-Tref) # heat losses
F = rho*Cp*(T-T0)/Dt*delT*dx_volume +kappa*dot(grad(T),grad(delT))*dx_volume\
-1.0*Sour_surface*delT*ds_top +qHat*delT*(ds_top+ds_right) #1.0*Sour_surface*delT*dA(6)
J = derivative(F, T, dT)
file_results = XDMFFile("Results.xdmf")
file_results.parameters["flush_output"] = True
file_results.parameters["functions_share_mesh"] = True
it= 0 #
while t < tMax:
it +=1
print('iteration_No:',it)
Sour_surface.t= t
solve(F==0, T, bc, J=J,
solver_parameters={'newton_solver':{'linear_solver': 'mumps', 'relative_tolerance':1e-5}}, \
form_compiler_parameters={'cpp_optimize':True, 'representation': 'uflacs'})
T0.assign(T)
file_results.write(T, t)
t+= Dt
and the msh file with smaller dimensions:
$MeshFormat
2.2 0 8
$EndMeshFormat
$PhysicalNames
11
1 1 "left_line"
1 3 "right_line"
1 4 "front_line"
1 5 "back_line"
2 6 "left"
2 7 "right"
2 8 "front"
2 9 "back"
2 10 "bottom"
2 11 "top"
3 12 "domain"
$EndPhysicalNames
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$EndElements
could you please help me with this issue?
1 Like
With all this code, I’m not really sure what you are asking for. Especially since you do not supply any error message. However, with the following modifications to the meshio and loading to dolfin code everything seems to run smoothly. (note that i’ve renamed the input mesh to meshi.read)
import meshio
msh = meshio.read("mesh.msh")
for key in msh.cell_data_dict["gmsh:physical"].keys():
if key == "triangle":
triangle_data = msh.cell_data_dict["gmsh:physical"][key]
elif key == "tetra":
tetra_data = msh.cell_data_dict["gmsh:physical"][key]
for cell in msh.cells:
if cell.type == "tetra":
tetra_cells = cell.data
elif cell.type == "triangle":
triangle_cells = cell.data
tetra_mesh = meshio.Mesh(points=msh.points, cells={"tetra": tetra_cells},
cell_data={"name_to_read":[tetra_data]})
triangle_mesh =meshio.Mesh(points=msh.points,
cells=[("triangle", triangle_cells)],
cell_data={"name_to_read":[triangle_data]})
meshio.write("plate.xdmf", tetra_mesh)
meshio.write("mf.xdmf", triangle_mesh)
from dolfin import *
set_log_level(LogLevel.ERROR)
mesh = Mesh()
with XDMFFile("plate.xdmf") as infile:
infile.read(mesh)
mvc = MeshValueCollection("size_t", mesh, 2)
with XDMFFile("mf.xdmf") as infile:
infile.read(mvc, "name_to_read")
mf = cpp.mesh.MeshFunctionSizet(mesh, mvc)
mvc2 = MeshValueCollection("size_t", mesh, 3)
with XDMFFile("plate.xdmf") as infile:
infile.read(mvc2, "name_to_read")
cf = cpp.mesh.MeshFunctionSizet(mesh, mvc2)
ds_top = Measure("ds", domain=mesh, subdomain_data=mf, subdomain_id=11)
ds_right = Measure("ds", domain=mesh, subdomain_data=mf, subdomain_id=7)
dx_volume = Measure("dx", domain=mesh, subdomain_data=cf, subdomain_id=12)
As you see here, you can save the cell function data along with the mesh, in a similar fashion to how it was saved for the facets
5 Likes
Thank you for the support and sorry that forgot to post the error message which was related to the defining cf even I tried the same way
mvc2 = MeshValueCollection("size_t", mesh, 3)
with XDMFFile("plate.xdmf") as infile:
infile.read(mvc2, "name_to_read")
cf = cpp.mesh.MeshFunctionSizet(mesh, mvc2)
Does it now work or not?
Yes it does work. Thanks
@dokken I had a quick question regarding the usage of meshio to write meshes for subdomains that can be loaded into dolfin. As of now I have 2 numpy arrays each containing the cells for a subdomain. Something like:
import meshio, os
meshFolder = os.getcwd()
msh = meshio.read("abaqusMesh.inp")
# msh.points -- all the nodes
# msh.cells[0] -- cells corresponding to one of the subdomain
# msh.cells[1] -- cells corresponding to the other
entireMesh = meshio.Mesh(msh.points, np.vstack((msh.cells[0], msh.cells[1])))
particlesMesh = meshio.Mesh(msh.points, msh.cells[1])
# subdomainMesh = meshio.Mesh(msh.points, ...) # what could be done here?
meshio.write(os.path.join(meshFolder, "entireMesh.xdmf"), entireMesh)
meshio.write(os.path.join(meshFolder, "particles.xdmf"), particlesMesh) # -- only the second subdomain
# and consequently this...
# meshio.write(os.path.join(meshFolder, "subdomains.xdmf"), subdomainMesh)
I want to be able to assemble forms on subdomains like
from dolfin import *
msh = Mesh()
with XDMFFile("entireMesh.xdmf") as sdf:
sdf.read(msh)
subdomains = MeshFunction("size_t", msh, "subdomains.xdmf")
dx = Measure('dx')(subdomain_data=subdomains)
Could you guide me on this or point to appropriate resources?
So, first of all, you only need the entire mesh.
For the entire mesh, you should be able to save the mesh with the corresponding subdomains as shown in the post above and define the appropriate measures: Transitioning from mesh.xml to mesh.xdmf, from dolfin-convert to meshio
I did see the above comment. I think that is based off of a premise that the mesh is read from a Gmsh.-generated one. For instance,
import meshio
msh = meshio.read("filename.inp")
for cell in msh.cells:
if cell.type == "tetra":
tetra_cells = cell.data
wouldn’t work in my case (as I have two CellBlocks each with type “tetra” and pointing to a separate subdomain). Also msh.cell_data_dict is an empty dictionary in my case. That is why in order to write the entire mesh I have to do
completeMesh = meshio.Mesh(msh.points, cells = {"tetra":np.vstack((msh.cells[0].data, msh.cells[1].data)) })
meshio.write("entireMesh.xdmf", completeMesh)
But then you do not save any subdomain information, so how should you Get any data to Measure. The code above is easily generalized to multiple cell blocks, by stacking inside the for loop.