Point coordinates error in importing 3D mesh generated from gmsh into fipy

Question

Help with gmsh file import to fipy, I have readed all the questions regarding gmsh and fipy on this forum, but unfortunately I didn't find a similar error. I am importing a 3D mesh generated by gmsh 3.0.6 (as recommanded) into FiPy (3.3). I am currently using python 3.7, and my operation system is Windows 10, 64-bit. My slope1.geo file is:

Point(1) = {0, 0, 0, 1.0};
Point(2) = {1, 0, 0, 1.0};
Point(3) = {0.3, 0.7, 0, 1.0};
Point(4) = {0, 0.7, 0, 1.0};
Line(1) = {1, 2};
Line(2) = {2, 3};
Line(3) = {3, 4};
Line(4) = {4, 1};
Line Loop(1) = {3, 4, 1, 2};
Plane Surface(1) = {1};
Extrude {0, 0, 0.8} {Surface{1}; Layers{8}; Recombine;}

I used the Gmsh command gmsh.exe D:\\gmsh\\slope1.geo -3 -nopopup -format msh3 -o D:\\gmsh\\slope1.msh to generate the slope1.msh file, and then I wrote:

import fipy as fp 
import numpy as np 
import os
mesh = fp.Gmsh3D(os.path.splitext("D:\\gmsh\\slope1")[0] + '.msh', communicator=fipy.serialComm)
np.savetxt("E:\\transfer_data\\gp.txt", mesh.vertexCoords.T,fmt='%f, %f, %f', newline='\n')
np.savetxt("E:\\transfer_data\\ele.txt", mesh._cellVertexIDs.T,fmt='%d, %d, %d,%d, %d, %d, %d, %d', newline='\n')

Produces this warnings:

C:\Users\yang\python\python.exe "E:/python projects/data_file/1.py"
C:\Users\yang\python\lib\site-packages\fipy\meshes\gmshMesh.py:781: SyntaxWarning: Partition count 8 does not agree with number of remaining tags 0.
  facesData) = self._parseElementFile()
C:\Users\yang\python\lib\site-packages\fipy\meshes\mesh.py:201: RuntimeWarning: invalid value encountered in true_divide
  norm = norm / numerix.sqrtDot(norm, norm)
C:\Users\yang\python\lib\site-packages\fipy\meshes\mesh.py:205: RuntimeWarning: invalid value encountered in less
  orientation = 1 - 2 * (numerix.dot(faceNormals, self.cellDistanceVectors) < 0)
C:\Users\yang\python\lib\site-packages\fipy\meshes\mesh.py:219: RuntimeWarning: invalid value encountered in less
  orientation = 1 - 2 * (numerix.dot(self.faceNormals, faceCellToCellNormals) < 0)
C:\Users\yang\python\lib\site-packages\fipy\meshes\mesh.py:256: RuntimeWarning: invalid value encountered in true_divide
  faceTangents1 = tmp / numerix.sqrtDot(tmp, tmp)
C:\Users\yang\python\lib\site-packages\fipy\meshes\mesh.py:363: RuntimeWarning: invalid value encountered in true_divide
  return self._scaledFaceAreas / self._cellDistances

Finally I checked the slope1.msh gp.txt and ele.txt found many point coordinates in gp.txt are 0,0,0 while slope1.msh ele.txt is well, I think this is a importing error, but I can't figure it out. Any pointer is appreciated. Many thanks in advance!

Answer 1

FiPy only understands Gmsh MSH format version 2.

Either

gmsh.exe D:\gmsh\slope1.geo -3 -nopopup -format msh2 -o D:\gmsh\slope1.msh

or

mesh = fp.Gmsh3D("D:\\gmsh\\slope1.geo")