Transitioning from mesh.xml to mesh.xdmf, from dolfin-convert to meshio

mesh
93

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
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1 5 "back_line"
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2 10 "bottom"
2 11 "top"
3 12 "domain"
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400 4 2 12 1 116 41 83 66
401 4 2 12 1 133 64 36 100
402 4 2 12 1 130 117 108 84
403 4 2 12 1 91 120 113 125
404 4 2 12 1 106 73 123 116
405 4 2 12 1 122 133 36 100
406 4 2 12 1 79 104 115 82
407 4 2 12 1 138 78 116 83
408 4 2 12 1 121 92 81 124
409 4 2 12 1 9 93 126 54
410 4 2 12 1 94 58 18 127
411 4 2 12 1 85 95 30 34
412 4 2 12 1 86 98 131 13
413 4 2 12 1 86 99 14 132
414 4 2 12 1 37 126 68 40
415 4 2 12 1 43 127 46 72
416 4 2 12 1 60 117 84 35
417 4 2 12 1 20 102 80 113
418 4 2 12 1 103 81 114 17
419 4 2 12 1 107 115 89 82
420 4 2 12 1 91 120 76 87
421 4 2 12 1 126 37 68 93
422 4 2 12 1 43 127 72 94
423 4 2 12 1 36 122 100 89
424 4 2 12 1 94 28 103 18
425 4 2 12 1 93 102 19 9
426 4 2 12 1 98 131 13 51
427 4 2 12 1 99 50 14 132
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429 4 2 12 1 102 93 135 9
430 4 2 12 1 23 98 86 13
431 4 2 12 1 24 86 99 14
432 4 2 12 1 74 79 107 82
433 4 2 12 1 117 108 84 95
434 4 2 12 1 135 78 113 111
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436 4 2 12 1 88 77 92 121
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438 4 2 12 1 117 74 89 84
439 4 2 12 1 137 115 44 47
440 4 2 12 1 38 105 41 83
441 4 2 12 1 75 109 129 108
442 4 2 12 1 79 103 136 127
443 4 2 12 1 93 135 78 102
444 4 2 12 1 134 29 62 33
445 4 2 12 1 107 115 122 89
446 4 2 12 1 129 75 95 96
447 4 2 12 1 90 29 134 33
448 4 2 12 1 115 104 44 82
449 4 2 12 1 41 138 116 83
450 4 2 12 1 30 95 128 61
451 4 2 12 1 23 98 13 51
452 4 2 12 1 50 24 99 14
453 4 2 12 1 103 59 17 136
454 4 2 12 1 53 102 10 135
455 4 2 12 1 117 92 74 84
456 4 2 12 1 80 102 78 113
457 4 2 12 1 81 79 103 114
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459 4 2 12 1 76 131 120 109
460 4 2 12 1 74 107 89 82
461 4 2 12 1 130 92 117 84
462 4 2 12 1 70 115 82 45
463 4 2 12 1 42 116 83 66
464 4 2 12 1 103 94 18 127
465 4 2 12 1 93 135 9 126
466 4 2 12 1 37 105 126 40
467 4 2 12 1 127 137 43 46
468 4 2 12 1 104 127 43 94
469 4 2 12 1 93 37 105 126
470 4 2 12 1 79 94 103 127
471 4 2 12 1 135 93 78 126
472 4 2 12 1 120 125 76 109
473 4 2 12 1 30 95 61 34
474 4 2 12 1 129 75 108 95
475 4 2 12 1 105 126 40 138
476 4 2 12 1 127 104 43 137
477 4 2 12 1 128 129 108 95
478 4 2 12 1 20 53 102 10
479 4 2 12 1 27 103 59 17
480 4 2 12 1 92 77 110 121
481 4 2 12 1 64 32 133 36
482 4 2 12 1 120 91 76 125
483 4 2 12 1 32 122 133 36
484 4 2 12 1 136 79 127 112
485 4 2 12 1 78 135 126 111
486 4 2 12 1 92 97 130 110
487 4 2 12 1 115 70 48 45
488 4 2 12 1 39 42 83 66
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490 4 2 12 1 78 93 105 126
491 4 2 12 1 124 92 110 121
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493 4 2 12 1 119 86 14 132
494 4 2 12 1 127 104 137 112
495 4 2 12 1 105 78 126 138
496 4 2 12 1 76 119 131 109
497 4 2 12 1 77 119 110 132
498 4 2 12 1 79 104 127 112
499 4 2 12 1 126 78 111 138
500 4 2 12 1 92 77 97 110
501 4 2 12 1 92 130 124 110
502 4 2 12 1 105 67 41 138
503 4 2 12 1 104 44 71 137
504 4 2 12 1 105 67 38 41
505 4 2 12 1 44 71 137 47
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509 4 2 12 1 6 62 33 101
510 4 2 12 1 12 56 120 11
511 4 2 12 1 68 2 93 37
512 4 2 12 1 25 50 24 99
513 4 2 12 1 67 37 105 38
514 4 2 12 1 2 93 19 54
515 4 2 12 1 22 98 23 51
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517 4 2 12 1 41 116 42 66
518 4 2 12 1 59 17 136 18
519 4 2 12 1 56 21 22 87
520 4 2 12 1 48 7 133 69
521 4 2 12 1 25 88 26 52
522 4 2 12 1 4 28 94 58
523 4 2 12 1 104 44 43 71
524 4 2 12 1 64 32 7 133
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526 4 2 12 1 30 29 118 63
527 4 2 12 1 57 114 17 16
528 4 2 12 1 9 126 1 54
529 4 2 12 1 23 86 24 49
530 4 2 12 1 43 4 94 72
531 4 2 12 1 28 27 103 59
532 4 2 12 1 70 47 115 48
533 4 2 12 1 71 46 137 47
534 4 2 12 1 58 3 18 127
535 4 2 12 1 72 46 3 127
536 4 2 12 1 21 20 80 55
537 4 2 12 1 16 52 121 15
538 4 2 12 1 50 14 132 15
539 4 2 12 1 67 40 41 138
540 4 2 12 1 131 12 13 51
541 4 2 12 1 65 5 134 42
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543 4 2 12 1 34 35 95 61
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545 4 2 12 1 100 69 8 45
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549 4 2 12 1 36 60 84 35
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551 4 2 12 1 39 65 6 101
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554 4 2 12 1 85 118 29 63
555 4 2 12 1 85 90 29 123
556 4 2 12 1 33 85 29 63
557 4 2 12 1 33 29 85 90
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559 4 2 12 1 36 84 117 89
560 4 2 12 1 117 84 36 60
561 4 2 12 1 97 84 108 75
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563 4 2 12 1 108 110 97 75
564 4 2 12 1 97 110 108 130
565 4 2 12 1 61 95 31 35
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567 4 2 12 1 117 31 95 35
568 4 2 12 1 117 95 31 128
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570 4 2 12 1 117 36 32 60
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572 4 2 12 1 100 133 7 69
573 4 2 12 1 100 8 7 64
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577 4 2 12 1 101 6 5 65
578 4 2 12 1 5 6 101 62
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611 4 2 12 1 1 2 93 68
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618 4 2 12 1 127 94 3 72
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620 4 2 12 1 13 86 14 119
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622 4 2 12 1 125 85 96 129
623 4 2 12 1 96 85 125 91
624 4 2 12 1 96 125 109 76
625 4 2 12 1 109 125 96 129
626 4 2 12 1 109 75 96 76
627 4 2 12 1 96 75 109 129
628 4 2 12 1 91 113 106 125
629 4 2 12 1 106 113 91 73
630 4 2 12 1 106 85 91 125
631 4 2 12 1 91 85 106 73
$EndElements

could you please help me with this issue?

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