gmsh_mesh_transform.py

#!/usr/bin/env python3

from optparse import OptionParser
import sys
import shutil
import math


#####################################################################
# Script starts here.
optparser=OptionParser(usage='usage: %prog region transformation mesh',
                       add_help_option=True,
                       description="""Applies a coordinate transformation to a region of a given mesh.""")

optparser.set_usage(
                  "Usage:\n"+
								  "  %prog (<constants>) (<region>) <transformation> <mesh>\n"+
                  "<constants>       is a list of constant associations separated by commas, for use in region and transformation (optional, although when specified, <region> is required - use 'True' for whole domain (i.e. the default behaviour)).\n"+
                  "<region>          is a python expression which evaluates to true over the region to be transformed (optional, default is True - i.e. the whole domain).\n"+
                  "<transformation>  is a python expression giving the coordinate transformation.\n"+
                  "<mesh>            is the name of the gmsh mesh file.\n"+
                  "Note: Creates a backup of the original mesh file with a '.bak' extension\n"
                  "\n"+
                  "Examples\n"
                  "- To rescale the z-dimension by a factor of 1000.\n"
                  "  %prog '(x,y,1000*z)' mesh.msh\n"
                  "- To project all points that lie within a circle of centre (xcentre,ycentre) in z by a distance zprojection.\n"
                  "  %prog 'xcentre=50, ycentre=50, radius=20, zprojection=50' '(x-xcentre)**2 + (y-ycentre)**2 < radius**2' '(x, y, z+zprojection)' mesh.msh\n"
                  "- To project all points that lie within a circle of centre (xcentre,ycentre) in z in the shape of a cone, by a distance zprojection at the centre.\n"
                  "  %prog 'xcentre=50, ycentre=50, radius=20, zprojection=50' '(x-xcentre)**2 + (y-ycentre)**2 < radius**2' '(x, y, z + zprojection * (1 - sqrt((x-xcentre)**2 + (y-ycentre)**2) / radius ) )' mesh.msh\n"
                  "- To add an ice shelf to a meshed box for x in [0,shelflength] and z in [0,shelfslopeheight + minoceandepth].  Note this applies to both 2d and 3d domains and the ocean domain can extend further.\n"
                  "  %prog 'shelflength = 550, shelfslopeheight = 800, minoceandepth = 100' 'x < shelflength' '(x, y, (z/(shelfslopeheight + minoceandepth)) * ((x/shelflength) * shelfslopeheight + minoceandepth))' mesh.msh\n"
         )

(options, argv) = optparser.parse_args()

# make all definitions of the math module available in
# the transformation expression.
globals=math.__dict__

if len(argv) == 4:
    constants      = argv[0]
    region         = argv[1]
    transformation = argv[2]
    mesh_name      = argv[3]
    constants = constants.replace(' ','')
    constanttextarray = constants.split(',')
    for constanttext in constanttextarray:
      constant = constanttext.split('=')
      globals[constant[0]] = float(constant[1])

elif len(argv) == 3:
    region         = argv[0]
    transformation = argv[1]
    mesh_name      = argv[2]
elif len(argv) == 2:
    transformation = argv[0]
    mesh_name      = argv[1]
else:
    optparser.print_help()
    sys.exit(1)


f=open(mesh_name,'r')
newf=open(mesh_name+'.tmp','w')

flag = 0
for line in f:
  line=line.lstrip().rstrip()
  if flag == 0:
    if line.startswith('$Nodes'):
      flag = 1
  elif flag == 1:
    nodes = line
    flag = 2
  elif flag == 2:
    if line.startswith('$EndNodes'):
      flag = 3
    else:
      cols = line.split(' ')
      index = int(cols[0])
      globals['x'] = float(cols[1])
      globals['y'] = float(cols[2])
      globals['z'] = float(cols[3])
      if eval(region, globals):
        xyz = eval(transformation, globals)
        line = repr(index)+' '+repr(xyz[0])+' '+repr(xyz[1])+' '+repr(xyz[2])
  newf.write(line + '\n')

newf.close()
f.close()

shutil.move(mesh_name, mesh_name+'.bak')
shutil.move(mesh_name+'.tmp', mesh_name)