def refine(self):
"refines the mesh"
grad = self.grad
g = grad[0]**2 + grad[1]**2 + grad[2]**2
g = convert_grad2constrain(g)
savevol("%s/t.1.vol"%self.tmp,g)
geom.runtetgen("/home/ondra/femgeom/tetgen/tetgen","%s/t.1"%self.tmp,
a=0.01,quadratic=True,refine=True)
m=geom.read_tetgen("%s/t.2"%self.tmp)
m.printinfo()
m.writemsh("%s/t12-2.msh"%self.tmp)
def meshit(self):
"meshes the geometry in tetgen, "
geom.write_tetgen(self.g,"%s/t.poly"%self.tmp)
geom.runtetgen("/home/ondra/femgeom/tetgen/tetgen","%s/t.poly"%self.tmp,
a=0.1,quadratic=True)
m=geom.read_tetgen("%s/t.1"%self.tmp)
m.printinfo()
m.writemsh("%s/t12.msh"%self.tmp)
m.writexda("%s/in.xda"%self.tmp)
m.writeBC("%s/t12.boundaries"%self.tmp)
self.regions=m.regions
self.nele=len(m.elements)
def meshit(self):
"meshes the geometry in tetgen, "
geom.write_tetgen(self.g, "%s/t.poly" % self.tmp)
geom.runtetgen("/home/ondra/femgeom/tetgen/tetgen",
"%s/t.poly" % self.tmp,
a=0.1,
quadratic=True)
m = geom.read_tetgen("%s/t.1" % self.tmp)
m.printinfo()
m.writemsh("%s/t12.msh" % self.tmp)
m.writexda("%s/in.xda" % self.tmp)
m.writeBC("%s/t12.boundaries" % self.tmp)
self.regions = m.regions
self.nele = len(m.elements)
def mesh():
meshgeometry="../meshes/t.geo"
pexpect.run("gmsh -0 %s -o tmp/x.geo"%(meshgeometry))
g=geom.read_gmsh("../tmp/x.geo")
g.printinfo()
geom.write_tetgen(g,"../tmp/t.poly")
geom.runtetgen("/home/ondra/femgeom/tetgen/tetgen","../tmp/t.poly",
a=0.001,Q=0.8)
m=geom.read_tetgen("../tmp/t.1")
m.printinfo()
m.writemsh("../tmp/t12.msh")
m.writexda("../tmp/in.xda")
m.writeregions("../tmp/t12.regions")
m.writeBC("../tmp/t12.boundaries")
def refine(self):
"refines the mesh"
grad = self.grad
g = grad[0]**2 + grad[1]**2 + grad[2]**2
g = convert_grad2constrain(g)
savevol("%s/t.1.vol" % self.tmp, g)
geom.runtetgen("/home/ondra/femgeom/tetgen/tetgen",
"%s/t.1" % self.tmp,
a=0.01,
quadratic=True,
refine=True)
m = geom.read_tetgen("%s/t.2" % self.tmp)
m.printinfo()
m.writemsh("%s/t12-2.msh" % self.tmp)
def mesh():
meshgeometry = "../meshes/t.geo"
pexpect.run("gmsh -0 %s -o tmp/x.geo" % (meshgeometry))
g = geom.read_gmsh("../tmp/x.geo")
g.printinfo()
geom.write_tetgen(g, "../tmp/t.poly")
geom.runtetgen("/home/ondra/femgeom/tetgen/tetgen",
"../tmp/t.poly",
a=0.001,
Q=0.8)
m = geom.read_tetgen("../tmp/t.1")
m.printinfo()
m.writemsh("../tmp/t12.msh")
m.writexda("../tmp/in.xda")
m.writeregions("../tmp/t12.regions")
m.writeBC("../tmp/t12.boundaries")
def mesh():
if len( sys.argv ) == 3:
geom_filename = sys.argv[1]
vtk_filename = sys.argv[2]
if len( sys.argv ) == 2:
geom_filename = sys.argv[1]
vtk_filename = "tmp/t.1.vtk"
else:
geom_filename = "database/box.geo"
vtk_filename = "tmp/t.1.vtk"
os.system( "gmsh -0 %s -o tmp/x.geo" % geom_filename )
g=geom.read_gmsh("tmp/x.geo")
g.printinfo()
geom.write_tetgen(g,"tmp/t.poly")
geom.runtetgen("tmp/t.poly",a=0.03,Q=1.0,quadratic=False,
tetgenpath = tetgen_path)
m = Mesh.from_file("tmp/t.1.node")
m.write( vtk_filename, io = "auto" )
def mesh(tipr=0.5, mesha=0.01, meshQ=0.8, verbose=False):
s = "".join(open("afm-templ.geo").readlines())
meshgeometry = "../tmp/t.geo"
open(meshgeometry, "w").write(s % (tipr))
pexpect.run("gmsh -0 %s -o ../tmp/x.geo" % (meshgeometry))
g = geom.read_gmsh("../tmp/x.geo")
if verbose: g.printinfo()
geom.write_tetgen(g, "../tmp/t.poly")
geom.runtetgen("/home/ondra/femgeom/tetgen/tetgen",
"../tmp/t.poly",
a=mesha,
Q=meshQ,
quadratic=True,
verbose=verbose)
m = geom.read_tetgen("../tmp/t.1", verbose)
if verbose: m.printinfo()
m.writemsh("../tmp/t12.msh", verbose)
m.writexda("../tmp/in.xda", verbose)
m.writeBC("../tmp/t12.boundaries", verbose)
regions = m.regions
nele = len(m.elements)
return regions, nele
#! /usr/bin/env python
#problem: probably with surface holes, it doesn't work correctly. Also with
# arcs - they approximated by lines.
import sys
sys.path.append("../..")
import pexpect
import geom
pexpect.run("gmsh -0 t.geo -o /tmp/x.geo")
g = geom.read_gmsh("/tmp/x.geo")
g.printinfo()
geom.write_tetgen(g, "/tmp/t.poly")
print "Generating mesh using tetgen..."
geom.runtetgen("/home/ondra/fzu/mesh/tetgen", "/tmp/t.poly")
print "Reading mesh from tetgen..."
m = geom.read_tetgen("/tmp/t.1")
m.writemsh("/tmp/t12.msh")
print "Mesh written to /tmp/t12.msh"
m.writexda("/tmp/in.xda")
print "Mesh written to /tmp/in.xda"
m.writeregions("/tmp/t12.regions")
print "Regions written to /tmp/t12.regions"
m.writeBC("/tmp/t12.boundaries")
print "Boundaries written to /tmp/t12.boundaries"
#! /usr/bin/env python
import sys
sys.path.append("../..")
import pexpect
import geom
pexpect.run("gmsh -0 t.geo -o /tmp/x.geo")
g=geom.read_gmsh("/tmp/x.geo")
g.printinfo()
geom.write_tetgen(g,"/tmp/t.poly")
print "Generating mesh using tetgen..."
geom.runtetgen("/home/ondra/fzu/mesh/tetgen","/tmp/t.poly")
print "Reading mesh from tetgen..."
m=geom.read_tetgen("/tmp/t.1")
m.writemsh("/tmp/t12.msh")
print "Mesh written to /tmp/t12.msh"
m.writexda("/tmp/in.xda")
print "Mesh written to /tmp/in.xda"
m.writeregions("/tmp/t12.regions")
print "Regions written to /tmp/t12.regions"
m.writeBC("/tmp/t12.boundaries")
print "Boundaries written to /tmp/t12.boundaries"
def main():
version = open( op.join( init_sfepy.install_dir,
'VERSION' ) ).readlines()[0][:-1]
parser = OptionParser( usage = usage, version = "%prog " + version )
parser.add_option( "--mesh",
action = "store_true", dest = "mesh",
default = False, help = help['mesh'] )
parser.add_option( "--2d",
action = "store_true", dest = "dim2",
default = False, help = help['dim'] )
parser.add_option( "-o", "", metavar = 'filename',
action = "store", dest = "output_filename_trunk",
default = "mesh", help = help['filename'] )
parser.add_option( "--oscillator",
action = "store_true", dest = "oscillator",
default = False, help = help['oscillator'] )
parser.add_option( "--well",
action = "store_true", dest = "well",
default = False, help = help['well'] )
parser.add_option( "--hydrogen",
action = "store_true", dest = "hydrogen",
default = False, help = help['hydrogen'] )
parser.add_option( "--boron",
action = "store_true", dest = "boron",
default = False, help = help['boron'] )
parser.add_option( "--dft",
action = "store_true", dest = "dft",
default = False, help = help['dft'] )
parser.add_option( "-p", "--plot",
action = "store_true", dest = "plot",
default = False, help = help['plot'] )
options, args = parser.parse_args()
if len( args ) == 1:
filename_in = args[0];
elif len( args ) == 0:
if options.oscillator:
dim = MeshIO.any_from_filename("tmp/mesh.vtk").read_dimension()
if dim == 2:
filename_in = "input/quantum/oscillator2d.py"
else:
assert_( dim == 3 )
filename_in = "input/quantum/oscillator3d.py"
options.dim = dim
print "Dimension:", dim
elif options.well:
dim = MeshIO.any_from_filename("tmp/mesh.vtk").read_dimension()
if dim == 2:
filename_in = "input/quantum/well2d.py"
else:
assert_( dim == 3 )
filename_in = "input/quantum/well3d.py"
options.dim = dim
print "Dimension:", dim
elif options.hydrogen:
dim = MeshIO.any_from_filename("tmp/mesh.vtk").read_dimension()
if dim == 2:
filename_in = "input/quantum/hydrogen2d.py"
else:
assert_( dim == 3 )
filename_in = "input/quantum/hydrogen3d.py"
options.dim = dim
print "Dimension:", dim
elif options.boron:
dim = MeshIO.any_from_filename("tmp/mesh.vtk").read_dimension()
if dim == 2:
filename_in = "input/quantum/boron2d.py"
else:
assert_( dim == 3 )
filename_in = "input/quantum/boron3d.py"
options.dim = dim
print "Dimension:", dim
elif options.mesh:
try:
os.makedirs("tmp")
except OSError, e:
if e.errno != 17: # [Errno 17] File exists
raise
if options.dim2:
print "Dimension: 2"
os.system("cp database/quantum/square.geo tmp/mesh.geo")
os.system("gmsh -2 tmp/mesh.geo -format mesh")
os.system("script/mesh_to_vtk.py tmp/mesh.mesh tmp/mesh.vtk")
else:
print "Dimension: 3"
import geom
from sfepy.fem.mesh import Mesh
try:
from site_cfg import tetgen_path
except ImportError:
tetgen_path = '/usr/bin/tetgen'
os.system("gmsh -0 database/box.geo -o tmp/x.geo")
g = geom.read_gmsh("tmp/x.geo")
g.printinfo()
geom.write_tetgen(g, "tmp/t.poly")
geom.runtetgen("tmp/t.poly", a=0.03, Q=1.0, quadratic=False,
tetgenpath=tetgen_path)
m = Mesh.from_file("tmp/t.1.node")
m.write("tmp/mesh.vtk", io="auto")
print "Mesh written to tmp/mesh.vtk"
return
elif options.dft:
dim = MeshIO.any_from_filename("tmp/mesh.vtk").read_dimension()
if dim == 2:
filename_in = "input/quantum/dft2d.py"
else:
assert_( dim == 3 )
filename_in = "input/quantum/dft3d.py"
print "Dimension:", dim
options.dim = dim
else:
parser.print_help()
return