create_aligned_mesh.py

#!/usr/bin/env python3

from optparse import OptionParser
import re
import sys
import os.path
import fluidity.diagnostics.meshes as meshes
import fluidity.diagnostics.elements as eles
import fluidity.diagnostics.gmshtools as gmshtools

face_number=1

def write_side_boundary(mesh, face_start, start, stride1, stride2, N1, N2, boundarymarker):
  # adds the faces of one side of the box to the .face file
  face_number=face_start
  for i2 in range(N2-1):
    for i1 in range(N1-1):
      node1 = start+i1*stride1+i2*stride2+1
      node2 = node1+stride1
      node3 = node2+stride2
      mesh.AddSurfaceElement(eles.Element(nodes=[node1-1, node2-1, node3-1], ids=[boundarymarker]))
      node4=node1+stride2
      mesh.AddSurfaceElement(eles.Element(nodes=[node1-1, node4-1, node3-1], ids=[boundarymarker]))

#####################################################################
# Script starts here.
optparser=OptionParser(
                       add_help_option=True,
                       description="""Creates mesh that lines up in all directions, so that you can make it into a singly, doubly or triply periodic mesh.""")

optparser.set_usage(
                  "usage: %prog meshname Lx Ly Lz Nx Ny Nz [Ox Oy Oz]\n\n"+
                  "Lx,Ly,Lz are dimensions of the box.\n"+
                  "Nx,Ny,Nz are the number of layers in each direction."+
                  "Ox,Oy,Oz is the origin (defaults to 0,0,0)."                  
		     )

(options, argv) = optparser.parse_args()

if len(argv)<7:
    optparser.print_help()
    sys.exit(1)

meshname=argv[0]
# dimensions of the box
Lx=float(argv[1])
Ly=float(argv[2])
Lz=float(argv[3])
# number of nodes in each direction
Nx=int(argv[4])+1
Ny=int(argv[5])+1
Nz=int(argv[6])+1
# origin
if len(argv)>7:
  Ox=float(argv[7])
  Oy=float(argv[8])
  Oz=float(argv[9])
else:
  Ox=0.0
  Oy=0.0
  Oz=0.0

nodes=Nx*Ny*Nz
dx=Lx/(Nx-1)
dy=Ly/(Ny-1)
dz=Lz/(Nz-1)

# We're building a 3D mesh
mesh = meshes.Mesh(3)


###
### Add node coordinates
for i in range(nodes):
  zlayer=int(i/(Nx*Ny))
  j=i-zlayer*(Nx*Ny)
  ylayer=int(j/Nx)
  xlayer=int(j-ylayer*Nx)
  x=Ox+xlayer*dx
  y=Oy+ylayer*dy
  z=Oz+zlayer*dz
  column=j+1
  mesh.AddNodeCoord([x, y, z])
  
###
### Create and add facets / surface elements
faces=4*((Nx-1)*(Ny-1)+(Ny-1)*(Nz-1)+(Nx-1)*(Nz-1))
# bottom side
face_number=1
write_side_boundary(mesh, face_number, 0, 1, Nx, Nx, Ny, 1)
face_number=face_number+2*(Nx-1)*(Ny-1)
# top side
write_side_boundary(mesh, face_number, Nx*Ny*(Nz-1), 1, Nx, Nx, Ny, 2)
face_number=face_number+2*(Nx-1)*(Ny-1)
# front 
write_side_boundary(mesh, face_number, 0, 1, Nx*Ny, Nx, Nz, 3)
face_number=face_number+2*(Nx-1)*(Nz-1)
# back
write_side_boundary(mesh, face_number, Nx*(Ny-1), 1, Nx*Ny, Nx, Nz, 4)
face_number=face_number+2*(Nx-1)*(Nz-1)
# left side
write_side_boundary(mesh, face_number, 0, Nx, Nx*Ny, Ny, Nz, 5)
face_number=face_number+2*(Ny-1)*(Nz-1)
# right side
write_side_boundary(mesh, face_number, Nx-1, Nx, Nx*Ny, Ny, Nz, 6)

###
### Create and add volume elements
elements=6*(Nx-1)*(Ny-1)*(Nz-1)
region_id=0 # this doesn't change at the moment
ele_number=1
for ix in range(Nx-1):
  for iy in range(Ny-1):
    for iz in range(Nz-1):
      # the first node in the cube
      start=ix+iy*Nx+iz*(Nx*Ny)
      # work out the 8 nodes in the cube
      node1=start
      node2=start+1
      node3=start+Nx
      node4=node3+1
      node5=start+Nx*Ny
      node6=node5+1
      node8=node5+Nx
      node7=node8+1
      # trust us, the following is right:
      mesh.AddVolumeElement(eles.Element(nodes=[node1, node4, node3, node7], ids=[region_id]))
      mesh.AddVolumeElement(eles.Element(nodes=[node1, node7, node8, node5], ids=[region_id]))
      mesh.AddVolumeElement(eles.Element(nodes=[node8, node3, node7, node1], ids=[region_id]))
      mesh.AddVolumeElement(eles.Element(nodes=[node1, node2, node4, node7], ids=[region_id]))
      mesh.AddVolumeElement(eles.Element(nodes=[node1, node7, node5, node6], ids=[region_id]))
      mesh.AddVolumeElement(eles.Element(nodes=[node1, node2, node7, node6], ids=[region_id]))

# Now write the constructed mesh to file
gmshtools.WriteMsh(mesh, "%s.msh" % (meshname))