Hello, I am stuck at how to assign different physical groups to different colors shown in image attached below, basically I am trying to given them different material properties in fenics to the physical tags afterwards but I am also confused on how to do that since I don’t know the geometrical locations of these different radii seeds, and I want to export only mesh part in .msh file and use it in fenics which is also attached below. Therefore my humble request to the community is to kindly guide me through this. Thank You [Screenshot 2023-05-30 232658] [Screenshot 2023-05-30 232716]

What are the xyz coordinates in the Dat file? Do They correspond to vertex values or cell midpoints? As you have not given a minimal reproducible example, say a Dat file for a 2x2 unit square mesh, I cannot help you any further.

I have modified code to - msh = meshio.read("/mnt/d/Research Projects/FEM for microstructures/modified_2cmp1.msh") def create_mesh(mesh, cell_type, prune_z=False): cells = mesh.get_cells_type(cell_type) points = mesh.points[:,:2] if prune_z else mesh.points out_mesh = meshio.Mesh(points=points, cells={cell_type: cells}) return out_mesh line_mesh = create_mesh(msh, "line", prune_z=True) meshio.write("mf.xdmf", line_mesh) triangle_mesh = create_mesh(msh, "triangle", prune_z=True) meshio.write("mesh.xdmf", triangle_mesh) mesh = Mesh() with XDMFFile("mesh.xdmf") as infile: infile.read(mesh) mvc = MeshValueCollection("size_t", mesh, 1) with XDMFFile("mf.xdmf") as infile: infile.read(mvc, "name_to_read") but now the following error comes: --------------------------------------------------------------------------- ValueError Traceback (most recent call last) /tmp/ipykernel_142/2838469791.py in 14 15 line_mesh = create_mesh(msh, "line", prune_z=True) ---> 16 meshio.write("mf.xdmf", line_mesh) 17 18 triangle_mesh = create_mesh(msh, "triangle", prune_z=True) ~/.local/lib/python3.10/site-packages/meshio/_helpers.py in write(filename, mesh, file_format, **kwargs) 186 187 # Write --> 188 return writer(filename, mesh, **kwargs) ~/.local/lib/python3.10/site-packages/meshio/xdmf/main.py in write(*args, **kwargs) 544 545 def write(*args, **kwargs): --> 546 XdmfWriter(*args, **kwargs) 547 548 ~/.local/lib/python3.10/site-packages/meshio/xdmf/main.py in __init__(self, filename, mesh, data_format, compression, compression_opts) 352 if data_format == "HDF": 353 self.h5_filename = self.filename.with_suffix(".h5") --> 354 self.h5_file = h5py.File(self.h5_filename, "w") 355 356 xdmf_file = ET.Element("Xdmf", Version="3.0") ~/.local/lib/python3.10/site-packages/h5py/_hl/files.py in __init__(self, name, mode, driver, libver, userblock_size, swmr, rdcc_nslots, rdcc_nbytes, rdcc_w0, track_order, fs_strategy, fs_persist, fs_threshold, fs_page_size, page_buf_size, min_meta_keep, min_raw_keep, locking, alignment_threshold, alignment_interval, meta_block_size, **kwds) 556 557 with phil: --> 558 fapl = make_fapl(driver, libver, rdcc_nslots, rdcc_nbytes, rdcc_w0, 559 locking, page_buf_size, min_meta_keep, min_raw_keep, 560 alignment_threshold=alignment_threshold, ~/.local/lib/python3.10/site-packages/h5py/_hl/files.py in make_fapl(driver, libver, rdcc_nslots, rdcc_nbytes, rdcc_w0, locking, page_buf_size, min_meta_keep, min_raw_keep, alignment_threshold, alignment_interval, meta_block_size, **kwds) 129 # we default to earliest 130 low, high = h5f.LIBVER_EARLIEST, h5f.LIBVER_LATEST --> 131 plist.set_libver_bounds(low, high) 132 plist.set_alignment(alignment_threshold, alignment_interval) 133 h5py/_objects.pyx in h5py._objects.with_phil.wrapper() h5py/_objects.pyx in h5py._objects.with_phil.wrapper() h5py/h5p.pyx in h5py.h5p.PropFAID.set_libver_bounds() ValueError: High bound is not valid (high bound is not valid)

Just remove [image] violetus: line_mesh = create_mesh(msh, "line", prune_z=True) meshio.write("mf.xdmf", line_mesh) As it is not needed when you dont have boundary tags.

I removed the boundary tag part - msh = meshio.read("/mnt/d/Research Projects/FEM for microstructures/modified_2cmp1.msh") def create_mesh(mesh, cell_type, prune_z=False): cells = mesh.get_cells_type(cell_type) points = mesh.points[:,:2] if prune_z else mesh.points out_mesh = meshio.Mesh(points=points, cells={cell_type: cells}) return out_mesh triangle_mesh = create_mesh(msh, "triangle", prune_z=True) meshio.write("mesh.xdmf", triangle_mesh) mesh = Mesh() with XDMFFile("mesh.xdmf") as infile: infile.read(mesh) mvc = MeshValueCollection("size_t", mesh, 1) Now error comes from the triangle one - --------------------------------------------------------------------------- ValueError Traceback (most recent call last) /tmp/ipykernel_142/3638126479.py in 14 15 triangle_mesh = create_mesh(msh, "triangle", prune_z=True) ---> 16 meshio.write("mesh.xdmf", triangle_mesh) 17 18 mesh = Mesh() ~/.local/lib/python3.10/site-packages/meshio/_helpers.py in write(filename, mesh, file_format, **kwargs) 186 187 # Write --> 188 return writer(filename, mesh, **kwargs) ~/.local/lib/python3.10/site-packages/meshio/xdmf/main.py in write(*args, **kwargs) 544 545 def write(*args, **kwargs): --> 546 XdmfWriter(*args, **kwargs) 547 548 ~/.local/lib/python3.10/site-packages/meshio/xdmf/main.py in __init__(self, filename, mesh, data_format, compression, compression_opts) 352 if data_format == "HDF": 353 self.h5_filename = self.filename.with_suffix(".h5") --> 354 self.h5_file = h5py.File(self.h5_filename, "w") 355 356 xdmf_file = ET.Element("Xdmf", Version="3.0") ~/.local/lib/python3.10/site-packages/h5py/_hl/files.py in __init__(self, name, mode, driver, libver, userblock_size, swmr, rdcc_nslots, rdcc_nbytes, rdcc_w0, track_order, fs_strategy, fs_persist, fs_threshold, fs_page_size, page_buf_size, min_meta_keep, min_raw_keep, locking, alignment_threshold, alignment_interval, meta_block_size, **kwds) 556 557 with phil: --> 558 fapl = make_fapl(driver, libver, rdcc_nslots, rdcc_nbytes, rdcc_w0, 559 locking, page_buf_size, min_meta_keep, min_raw_keep, 560 alignment_threshold=alignment_threshold, ~/.local/lib/python3.10/site-packages/h5py/_hl/files.py in make_fapl(driver, libver, rdcc_nslots, rdcc_nbytes, rdcc_w0, locking, page_buf_size, min_meta_keep, min_raw_keep, alignment_threshold, alignment_interval, meta_block_size, **kwds) 129 # we default to earliest 130 low, high = h5f.LIBVER_EARLIEST, h5f.LIBVER_LATEST --> 131 plist.set_libver_bounds(low, high) 132 plist.set_alignment(alignment_threshold, alignment_interval) 133 h5py/_objects.pyx in h5py._objects.with_phil.wrapper() h5py/_objects.pyx in h5py._objects.with_phil.wrapper() h5py/h5p.pyx in h5py.h5p.PropFAID.set_libver_bounds() ValueError: High bound is not valid (high bound is not valid)

How did you install h5py? See [so2liu] Keras model.load_weights() error: ValueError: Invalid high library version bound (invalid high library version bound) python, docker, keras, theano answered by so2liu on 10:16PM - 21 Sep 19 UTC

I am getting the below message from terminal [Screenshot 2023-05-31 230150]

You need to uninstall your current installation of h5py first

I uninstalled and reinstalled h5py using pip install --no-binary=h5py h5py but now this error comes : --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) /tmp/ipykernel_457/3234862839.py in 14 15 triangle_mesh = create_mesh(msh, "triangle", prune_z=True) ---> 16 meshio.write("mesh.xdmf", triangle_mesh) 17 18 mesh = Mesh() ~/.local/lib/python3.10/site-packages/meshio/_helpers.py in write(filename, mesh, file_format, **kwargs) 186 187 # Write --> 188 return writer(filename, mesh, **kwargs) ~/.local/lib/python3.10/site-packages/meshio/xdmf/main.py in write(*args, **kwargs) 544 545 def write(*args, **kwargs): --> 546 XdmfWriter(*args, **kwargs) 547 548 ~/.local/lib/python3.10/site-packages/meshio/xdmf/main.py in __init__(self, filename, mesh, data_format, compression, compression_opts) 352 if data_format == "HDF": 353 self.h5_filename = self.filename.with_suffix(".h5") --> 354 self.h5_file = h5py.File(self.h5_filename, "w") 355 356 xdmf_file = ET.Element("Xdmf", Version="3.0") AttributeError: module 'h5py' has no attribute 'File'

@dokken is the version of h5py causing this error ? [Screenshot 2023-05-31 233508]

Thanks @dokken for the reference, the error was solved when i used sudo apt-get install python3-h5py after uninstalling h5py. Can you please tell me how can I write my .dat file information into this XDMF file. Thank You

See: [image] How to define a subdomain using material data (from data file)? General First of all, does your mesh consist of triangles or quadrilaterals? Secondly, is your mesh uniform and structured (i.e. is it a RectangleMesh with 100 x 100 cells?) I would suggest something like: from dolfin import * import numpy as np mesh = UnitSquareMesh(100, 100) V = FunctionSpace(mesh, "DG", 0) u = Function(V) dx = 1/100 values = np.arange(100*100) local_values = np.zeros_like(u.vector().get_local()) for cell in cells(mesh): midpoint = cell.midpoint().array() i = int(midpoi… Which writes the data to a function, Which you can write to xdmf

Assigning different physical groups to different color in gmsh and mark them as different material in fenics

General

dokken May 31, 2023, 7:42pm 25

See:

Which writes the data to a function, Which you can write to xdmf

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Assigning different physical groups to different color in gmsh and mark them as different material in fenics

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