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https://github.com/NGSolve/netgen.git
synced 2025-05-18 08:10:50 +05:00
improved and fixed gmsh import
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Manu
parent
cb9816c244
commit
1bd16797cd
@ -81,7 +81,7 @@ NGX_INLINE DLL_HEADER Ng_Element Ngx_Mesh :: GetElement<1> (size_t nr) const
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if (mesh->GetDimension() == 3)
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ret.mat = mesh->GetCD2NamePtr(el.edgenr-1);
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else
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ret.mat = nullptr;
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ret.mat = mesh->GetMaterialPtr(el.si);
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}
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ret.points.num = el.GetNP();
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@ -213,6 +213,13 @@ DLL_HEADER void ExportNetgenMeshing(py::module &m)
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(*instance)[i] = py::extract<PointIndex>(vertices[i])();
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instance->SetIndex(index);
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}
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else if (py::len(vertices) == 5)
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{
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new (instance) Element(PYRAMID);
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for (int i=0; i < 5; i++)
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(*instance)[i] = py::extract<PointIndex>(vertices[i])();
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instance->SetIndex(index);
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}
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else if (py::len(vertices) == 6)
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{
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new (instance) Element(PRISM);
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@ -1,73 +1,283 @@
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from netgen.meshing import *
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import re
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import shutil
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import os
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def ReadGmsh (filename):
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f = open(filename, 'r')
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mesh = Mesh(dim=3)
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def import_gmsh(filename, extension, dim):
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""" filename: name of the filename
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extension: geo or msh
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dim: dimension of the mesh
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"""
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if extension == "geo":
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filename_tmp = check_geofile(filename)
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if dim == 1:
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os.system("gmsh -1 -saveall -format msh -o ./" + filename + ".msh ./" + filename_tmp + ".geo")
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elif dim == 2:
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os.system("gmsh -2 -saveall -format msh -o ./" + filename + ".msh ./" + filename_tmp + ".geo")
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elif dim == 3:
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os.system("gmsh -3 -saveall -format msh -o ./" + filename + ".msh ./" + filename_tmp + ".geo")
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pointmap = { }
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facedescriptormap = { }
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return ReadGmsh(filename)
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def check_geofile(filename):
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mod = False
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with open(filename + ".geo", 'r') as f:
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with open(filename + "_tmp.geo", 'w') as fw:
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line = "start"
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while line:
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line = f.readline()
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if line[0:8] == "Physical":
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print('WARNING: Physical groups detected - Physical names are not taken into account.')
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print('The physical group is discarded.')
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fw.write("//" + line)
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mod = True
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else:
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fw.write(line)
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if mod:
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filename_tmp = filename + "_tmp"
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else:
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filename_tmp = filename
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os.remove(filename + "_tmp.geo")
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return filename_tmp
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def complete_geofile(filename):
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line_entity = []
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surf_entity = []
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vol_entity = []
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line_phys_gr = []
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surf_phys_gr = []
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vol_phys_gr = []
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num_lines = sum(1 for line in open(filename + ".geo", 'r')) + 1
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with open(filename + ".geo", 'r') as f:
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for i in range(num_lines):
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line = f.readline()
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if not line:
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line = [" "]
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if line[0:2] == '//':
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pass
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elif line[0:5] == 'Line(':
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line_entity += {line.split()[0][5:-1]}
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elif line[0:14] == 'Plane Surface(':
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surf_entity += {line.split()[1][8:-1]}
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elif line[0:7] == 'Volume(':
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vol_entity += {line.split()[0][7:-1]}
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elif line[0:13] == "Physical Line":
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start = line.index('{')
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end = line.index('}')
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number = re.sub(r"\s", "", line[start + 1:end]).split(sep=",")
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line_phys_gr += number
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elif line[0:16] == "Physical Surface":
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start = line.index('{')
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end = line.index('}')
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number = re.sub(r"\s", "", line[start + 1:end]).split(sep=",")
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surf_phys_gr += number
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elif line[0:15] == "Physical Volume":
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start = line.index('{')
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end = line.index('}')
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number = re.sub(r"\s", "", line[start + 1:end]).split(sep=",")
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vol_phys_gr += number
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line_diff = list(set(line_entity) - set(line_phys_gr))
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surf_diff = list(set(surf_entity) - set(surf_phys_gr))
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vol_diff = list(set(vol_entity) - set(vol_phys_gr))
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filename_geo = filename
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if line_diff or surf_diff or vol_diff:
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shutil.copy2(filename + '.geo', filename + '_tmp.geo')
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filename_geo = filename + "_tmp"
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if line_diff:
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fid = open(filename + ".geo", 'a')
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fid.write('//+\n// Added by NGSolve\n')
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fid.write('Physical Line("Remaining_line") = {' + re.sub(r'[\']', '', str(line_diff))[1:-1] + '}; \n')
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fid.close()
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if surf_diff:
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fid = open(filename + ".geo", 'a')
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fid.write('//+\n// Added by NGSolve\n')
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fid.write('Physical Surface("Remaining_surf") = {' + re.sub(r'[\']', '', str(surf_diff))[1:-1] + '}; \n')
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fid.close()
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if vol_diff:
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fid = open(filename + ".geo", 'a')
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fid.write('//+\n// Added by NGSolve\n')
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fid.write('Physical Volume("Remaining_vol") = {' + re.sub(r'[\']', '', str(vol_diff))[1:-1] + '}; \n')
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fid.close()
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return filename_geo
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def ReadGmsh(filename):
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meshdim = 1
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with open(filename + ".msh", 'r') as f:
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while f.readline().split()[0] != "$Elements":
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pass
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nelem = int(f.readline())
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for i in range(nelem):
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line = f.readline()
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eltype = int(line.split()[1])
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if eltype > 1 and eltype != 15:
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meshdim = 2
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if eltype > 3 and eltype != 15:
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meshdim = 3
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break
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f = open(filename + ".msh", 'r')
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mesh = Mesh(dim=meshdim)
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pointmap = {}
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facedescriptormap = {}
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namemap = {}
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materialmap = {}
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bbcmap = {}
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while True:
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line = f.readline()
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if line == "": break
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if line == "":
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break
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if line.split()[0]=="$Nodes":
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if line.split()[0] == "$PhysicalNames":
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print('WARNING: Physical groups detected - Be sure to define them for every geometrical entity.')
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numnames = int(f.readline())
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for i in range(numnames):
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f.readline
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line = f.readline()
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namemap[int(line.split()[1])] = line.split()[2][1:-1]
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if line.split()[0] == "$Nodes":
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num = int(f.readline().split()[0])
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print ("reading",num,"nodes")
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for i in range(num):
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line = f.readline()
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nodenum,x,y,z = line.split()[0:4]
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pnum = mesh.Add (MeshPoint(Pnt(float(x),float(y),float(z))))
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nodenum, x, y, z = line.split()[0:4]
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pnum = mesh.Add(MeshPoint(Pnt(float(x), float(y), float(z))))
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pointmap[int(nodenum)] = pnum
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if line.split()[0]=="$Elements":
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if line.split()[0] == "$Elements":
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num = int(f.readline().split()[0])
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print ("reading",num,"elements")
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for i in range(num):
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line = f.readline().split()
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elmnum = int(line[0])
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elmtype = int(line[1])
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numtags = int(line[2])
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tag1 = int(line[3])
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# the first tag is the physical group nr, the second tag is the group nr of the dim
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tags = [int(line[3 + k]) for k in range(numtags)]
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if elmtype == 2: # 3-node trig
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if elmtype == 1: # 2-node line
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num_nodes = 2
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elif elmtype == 2: # 3-node trig
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num_nodes = 3
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elif elmtype == 3: # 4-node quad
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elif elmtype == 3: # 4-node quad
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num_nodes = 4
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elif elmtype == 4: # 4-node tet
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elif elmtype == 4: # 4-node tet
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num_nodes = 4
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elif elmtype == 5: # 8-node hex
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num_nodes = 8
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elif elmtype == 6: # 6-node prism
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num_nodes = 6
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elif elmtype == 7: # 5-node pyramid
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num_nodes = 5
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elif elmtype == 15: # 1-node point
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num_nodes = 1
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else:
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print ("element type", elmtype, "not implemented")
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raise Exception("element type", elmtype, "not implemented")
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nodenums = line[3+numtags:3+numtags+num_nodes]
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nodenums2 = [ pointmap[int(nn)] for nn in nodenums ]
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nodenums = line[3 + numtags:3 + numtags + num_nodes]
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nodenums2 = [pointmap[int(nn)] for nn in nodenums]
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if elmtype == 1:
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if meshdim == 3:
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if tags[1] in bbcmap:
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index = bbcmap[tags[1]]
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else:
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index = len(bbcmap)
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if len(namemap):
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mesh.SetCD2Name(index + 1, namemap[tags[0]])
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else:
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mesh.SetCD2Name(index+1, "line" + str(tags[1]))
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bbcmap[tags[1]] = index
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if elmtype in [2,3]: # 2d elements
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# generate facedescriptor for boundary conditon number,
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# first tag is used as bc-number
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# element index maps into facedescriptor array
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if tag1 in facedescriptormap.keys():
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fdindex = facedescriptormap[tag1]
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elif meshdim == 2:
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if tags[1] in facedescriptormap.keys():
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index = facedescriptormap[tags[1]]
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else:
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index = len(facedescriptormap) + 1
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fd = FaceDescriptor(bc=index)
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if len(namemap):
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fd.bcname = namemap[tags[0]]
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else:
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fd.bcname = 'line' + str(tags[1])
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mesh.SetBCName(index - 1, fd.bcname)
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mesh.Add(fd)
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facedescriptormap[tags[1]] = index
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else:
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fd = FaceDescriptor(bc=tag1)
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fdindex = mesh.Add(fd)
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facedescriptormap[tag1] = fdindex
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if tags[1] in materialmap:
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index = materialmap[tags[1]]
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else:
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index = len(materialmap) + 1
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if len(namemap):
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mesh.SetMaterial(index, namemap[tags[0]])
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else:
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mesh.SetMaterial(index, "line" + str(tags[1]))
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materialmap[tags[1]] = index
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mesh.Add (Element2D(fdindex, nodenums2))
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mesh.Add(Element1D(index=index, vertices=nodenums2))
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if elmtype == 4: # 4-node tet
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nodenums2 = [ pointmap[int(nn)] for nn in nodenums ]
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mesh.Add (Element3D(tag1, [nodenums2[0],nodenums2[1],nodenums2[3],nodenums2[2]]))
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print (nodenums2)
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# print (mesh)
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# print (pointmap)
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if elmtype in [2, 3]: # 2d elements
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if meshdim == 3:
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if tags[1] in facedescriptormap.keys():
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index = facedescriptormap[tags[1]]
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else:
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index = len(facedescriptormap) + 1
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fd = FaceDescriptor(bc=index)
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if len(namemap):
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fd.bcname = namemap[tags[0]]
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else:
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fd.bcname = "surf" + str(tags[1])
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mesh.SetBCName(index - 1, fd.bcname)
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mesh.Add(fd)
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facedescriptormap[tags[1]] = index
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else:
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if tags[1] in materialmap:
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index = materialmap[tags[1]]
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else:
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index = len(materialmap) + 1
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if len(namemap):
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mesh.SetMaterial(index, namemap[tags[0]])
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else:
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mesh.SetMaterial(index, "surf" + str(tags[1]))
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materialmap[tags[1]] = index
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mesh.Add(Element2D(index, nodenums2))
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if elmtype in [4, 5, 6, 7]: # volume elements
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if tags[1] in materialmap:
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index = materialmap[tags[1]]
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else:
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index = len(materialmap) + 1
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if len(namemap):
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mesh.SetMaterial(index, namemap[tags[0]])
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else:
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mesh.SetMaterial(index, "vol" + str(tags[1]))
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materialmap[tags[1]] = index
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nodenums2 = [pointmap[int(nn)] for nn in nodenums]
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if elmtype == 4:
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mesh.Add(Element3D(index, [nodenums2[0], nodenums2[1], nodenums2[3], nodenums2[2]]))
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elif elmtype in [5, 6, 7]:
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mesh.Add(Element3D(index, nodenums2))
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return mesh
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# ReadGMSH ("test.gmsh")
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