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Gmsh mesh generation engine support #16

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BinWang0213 opened this issue Apr 21, 2020 · 5 comments · Fixed by #30
Closed

Gmsh mesh generation engine support #16

BinWang0213 opened this issue Apr 21, 2020 · 5 comments · Fixed by #30
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@BinWang0213
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BinWang0213 commented Apr 21, 2020

Is your feature request related to a problem? Please describe.
Gmsh mesh generator is support by many open-source simulation code. It will be nice to add a Gmsh meshing interface.

  • Also, meshio library support Gmsh very well. Once we have gmsh file, we can use meshio to convert the mesh into any mesh format, such as

Abaqus, ANSYS msh, AVS-UCD, CGNS, DOLFIN XML, Exodus, FLAC3D, H5M, Kratos/MDPA, Medit, MED/Salome, Nastran (bulk data), Neuroglancer precomputed format, Gmsh (format versions 2.2, 4.0, and 4.1), OBJ, OFF, PERMAS, PLY, STL, Tecplot .dat, TetGen .node/.ele, SVG (2D only, output only), UGRID, VTK, VTU (not raw binary data), WKT (TIN), XDMF.

Describe the solution you'd like
The working code is attached, please feel free to integrate it into the MicroStructPy. It support to mesh any polymesh.region we want.

Noted that Gmsh is intefaced by generating its built-in script file *.geo. We need to use Gmsh to load the geo file and generate mesh.

pmesh = msp.meshing.PolyMesh.from_seeds(seeds, domain)

tri_basename = 'polymesh_gmsh.geo'
tri_filename = os.path.join(directory, tri_basename)

Material_number=0
MaterialIDs=[i for i,p in enumerate(pmesh.phase_numbers) if p==Material_number]

#Current function usage
#geo=pgm.Mesh.mspPolymesh2geo(pmesh,regionIDs=MaterialIDs,max_edge_size=0.3)
#with open(tri_filename, 'w') as f:
#    f.write(geo)

#Expected msp usage
tmesh = msp.meshing.TriMesh.from_polymesh(pmesh, phases, max_edge_length=0.3)
tmesh.write(tri_filename, "geo", seeds, pmesh)
def mspPolymesh2geo(polymesh,regionIDs=[],max_edge_size=-1):
    """Convert MicroStructPy polymesh to gmsh geo script

    Method
    --------
    Chose the regionID you want to output

    Author: Bin Wang(binwang.0213@gmail.com)
    Date: April. 2020
    """
    NumRegions=len(polymesh.regions)
    if(len(regionIDs)==0): regionIDs=[n for n in range(NumRegions)] #All region
    #Collect Pts,facets and volumes for requested material
    facets_out=[]
    regionIDs_out=[]
    for ri,region in enumerate(polymesh.regions):
        for mID in regionIDs:
            if(ri==mID):
                facets_out+=region
                regionIDs_out+=[ri]
    pts_out=list(set([pi for fi in facets_out for pi in polymesh.facets[fi]]))

    string=''
    string += '/* -------Genetrated by PyGeoMesh------- */\n\n'
    string += 'SetFactory("Built-in");\n' #This is not working well for fixing orientation
    string +='\n'

    #* 1. -----------Collect Points------------
    string += '/* --Model_Points-- */\n'
    for pi, pts in enumerate(polymesh.points):#Loop over regions
        if(pi not in pts_out): continue
        string += "p%d = newp; Point(p%d) = {%.20f,%.20f,%.20f};\n" % (pi,pi, pts[0], pts[1], pts[2])
    string +='\n'

    #* 2. -----------Collect Polyhedron Facet Edges------------
    Line_id=0
    string += '/* --Polyhedron Edges/Facets-- */\n'
    for fi,facet in enumerate(polymesh.facets):
        if(fi not in facets_out): continue
        NumPts=len(facet)
        temp ="clp%d = newll; Curve Loop(clp%d) = {" % (fi,fi)
        for pi in range(NumPts):
            id0,id1 = facet[pi],facet[(pi+1)%NumPts] #round end connect pair
            string += "lp%d = newl; Line(lp%d) = {p%d,p%d};\n" % (Line_id, Line_id, id0, id1)
            temp += "lp%d," % (Line_id)
            Line_id = Line_id + 1
        temp=temp[:-1] + "};\n"
        #handle boundary inward normal vector
        temp += "sp%d = news;  Plane Surface(sp%d) = {clp%d};\n" % (fi,fi,fi)
        string += temp + '\n'
    string += '\n'

    #* 3. -----------Collect Polyhedron------------
    string += '/* --Polyhedron Cells-- */\n'
    for ri,region in enumerate(polymesh.regions):
        if(ri not in regionIDs_out): continue
        string+='vlp%d = newsl; Surface Loop(vlp%d)={' %(ri,ri)
        for fi in region:
            facet_neigh=polymesh.facet_neighbors[fi]
            if(facet_neigh[1]==ri):  string+='-sp%d,'%(fi) #Backside of the facet
            else: string+='sp%d,'%(fi)
        string=string[:-1]+'};\n'
        string+='vp%d = newv; Volume(vp%d)={vlp%d};\n' %(ri,ri,ri)
        string +='\n'

    string += '/* --Combine Duplicated Entites, Polyhedron Edges here-- */\n'
    string+='Coherence;\n'
    
    #* 4. ------------Reverse boundary facet orientation-----------
    inward_facet=[]
    regionIDs_wall=list( set(range(len(polymesh.regions))) - set(regionIDs_out) )
    id2tagName={-1:'X-',-2:'X+',-3:'Y-',-4:'Y+',-5:'Z-',-6:'Z+'}
    boundary_facets={'X-':[],'X+':[],'Y-':[],'Y+':[],'Z-':[],'Z+':[],'Wall':[]}
    for fi,facet in enumerate(polymesh.facets):
        if(fi not in facets_out): continue
        facet_neigh=np.array(polymesh.facet_neighbors[fi])
        check1=facet_neigh[0]<0 or facet_neigh[1]<0 #boundary facet X-,X+...
        check2=facet_neigh[0] in regionIDs_wall or facet_neigh[1] in regionIDs_wall #material interface wall
        #print('facet',fi,'neigh',facet_neigh,check1,check2)
        
        if(check1 or check2):#This is a boundary facet
            if(facet_neigh[1] in regionIDs_out):#Normal always point toward facet_neigh[1] cell
                inward_facet+=[fi]
        if(check1):
            boundary_id=facet_neigh[facet_neigh<0][0]
            boundary_name=id2tagName[boundary_id]
            boundary_facets[boundary_name].append(fi)
        if(check2):
            boundary_facets['Wall'].append(fi)
    string +='\n'

    #print(inward_facet,regionIDs_wall)
    string += '/* --Fix boundary surface orientation-- */\n'
    string += 'ReverseMesh Surface{%s};\n' % ','.join('sp'+str(x) for x in inward_facet)
    string +='\n'

    string += '/* --Physical Tags-- */\n'
    print('boundary facets Tag=',boundary_facets)
    for name,facet_list in boundary_facets.items():
        if(len(facet_list)>0):
            string+='Physical Surface("%s") = {%s};\n' %(name,','.join('sp'+str(f) for f in facet_list))
    
    for ri,region_geo in enumerate(polymesh.regions):
        if(ri not in regionIDs_out): continue
        string+='Physical Volume("Material%d") = {vp%d};\n' %(ri,ri)
    string+='\n'

    string += '/* --Mesh Size Setup-- */\n'
    if(max_edge_size==-1):#Auto mesh size
        max_edge_size=np.sum(polymesh.volumes)**(1/3.0)/8.0

    string +='//Mesh.CharacteristicLengthMin = %s;\n' %(max_edge_size)
    string +='Mesh.CharacteristicLengthMax = %s;\n' %(max_edge_size)

    return string
@kip-hart kip-hart self-assigned this May 14, 2020
@kip-hart
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kip-hart commented May 14, 2020

Hi Bin,

I'm planning on inheriting PolyMesh and TriMesh from the meshio.Mesh class in v2.0 of the code. At that point, I'll integrate gmsh support and include pygmsh so the PolyMesh can be saved to a .geo for externally calling gmsh or the TriMesh can be created with pygmsh like TriMesh.from_poly(..., method='gmsh') then written to a .msh file like TriMesh.write(..., format='msh'). That will also allow for the meshes to be written to a variety of formats. I'll update once I get closer to tackling this.

Best,
Kip

@BinWang0213
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BinWang0213 commented May 15, 2020

Hi Kip,

Sounds good. Please be careful the normal orientation issue. All boundary faces should be outward normal.

You can see my effort @ #16 (comment) to adapt this for Gmsh.

Thanks,
Bin

@kip-hart
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kip-hart commented May 15, 2020

Thanks, that's a good point. The exterior faces can be oriented positive outward, while leaving the interior faces arbitrary.

Since the facets are created by the PolyMesh.from_seeds method (https://github.com/kip-hart/MicroStructPy/blob/v1.2.2/src/microstructpy/meshing/polymesh.py#L603), I can make that modification before adding gmsh.

kip-hart added a commit that referenced this issue Jun 25, 2020
…#23)

* stop tracking duplicate aluminum micro file

* facets on the exterior of the polymesh now have outward normals (#16)

* updated changelog

* changed plot limits, trying to get 3D axes equal

* updated trimesh plotting in CLI

* fixed typo in order of lines for empirical PDFs

* added option to maximize the minimum edge length in a polygonal mesh

* simplified seedlist indexing

* optimized seedlist positioning method

uses BFS in aabb tree for overlap detection and samples 100 positions at a time

* fixed the logo script

* fixed 2d axes behavior

* simplified foam example

* updated changelog

* added missing zlim

* updated sphinx version

* indented changelog

* removed unneeded version string functions

* bumped version

* simplified version getting
@kip-hart kip-hart mentioned this issue Oct 4, 2020
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kip-hart added a commit that referenced this issue Oct 4, 2020
@kip-hart
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kip-hart commented Oct 4, 2020

I realize it's been several months, but I've added gmsh to the code MicroStructPy code. It can be specified using Trimesh.from_polymesh(..., mesher='gmsh'). I'm planning on a v1.4.0 release soon and at that point it'll be part of the PyPI release. Thanks for the feature suggestion!

@MayaStr
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MayaStr commented Mar 9, 2022

Hey Kip,

I have been playing around with your package to import a mesh into FENICS using meshio. I was able to create the triangular mesh like you described. Trimesh.from_polymesh(..., mesher='gmsh'). Is there a possibility now to export the mesh with facets, so it can be imported by meshio? What is the workflow? Or use Bin's script?

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3 participants