def dump_to_vtk(filename, output_filename_trunk=None, step0=0, steps=None,
fields=None, linearization=None):
"""Dump a multi-time-step results file into a sequence of VTK files."""
def _save_step(suffix, out, mesh):
if linearization is not None:
output('linearizing...')
out = _linearize(out, fields, linearization)
output('...done')
for key, val in out.iteritems():
lmesh = val.get('mesh', mesh)
lmesh.write(output_filename_trunk + '_' + key + suffix,
io='auto', out={key : val})
if hasattr(val, 'levels'):
output('max. refinement per group:', val.levels)
else:
mesh.write(output_filename_trunk + suffix, io='auto', out=out)
output('dumping to VTK...')
io = MeshIO.any_from_filename(filename)
mesh = Mesh.from_file(filename, io=io)
if output_filename_trunk is None:
output_filename_trunk = get_trunk(filename)
try:
ts = TimeStepper(*io.read_time_stepper())
times, nts, dts = extract_times(filename)
except ValueError:
output('no time stepping info found, assuming single step')
out = io.read_data(0)
if out is not None:
_save_step('.vtk', out, mesh)
ret = None
else:
ts.times = times
ts.n_step = times.shape[0]
if steps is None:
iterator = ts.iter_from(step0)
else:
iterator = [(step, ts.times[step]) for step in steps]
for step, time in iterator:
output(ts.format % (step, ts.n_step - 1))
out = io.read_data(step)
if out is None: break
_save_step('.' + ts.suffix % step + '.vtk', out, mesh)
ret = ts.suffix
output('...done')
return ret
def dump_to_vtk( filename, options, steps = None ):
output( 'dumping to VTK...' )
mesh = Mesh.from_file( filename )
io = HDF5MeshIO( filename )
ts = TimeStepper( *io.read_time_stepper() )
if options.output_filename_trunk:
ofn_trunk = options.output_filename_trunk
else:
ofn_trunk = get_trunk( filename )
if steps is None:
iterator = ts.iter_from( options.step0 )
else:
iterator = [(step, ts.times[step]) for step in steps]
for step, time in iterator:
output( ts.format % (step, ts.n_step - 1) )
out = io.read_data( step )
if out is None: break
mesh.write( ofn_trunk + ts.suffix % step + '.vtk',
io = 'auto', out = out )
output( '...done' )
return ts.suffix
def main():
parser = OptionParser(usage=usage, version="%prog 42")
parser.add_option("-s", "--scale", type=int, metavar='scale',
action="store", dest="scale",
default=2, help=help['scale'])
parser.add_option("-r", "--repeat", type='str', metavar='nx,ny[,nz]',
action="callback", dest="repeat",
callback=parse_repeat, default=None, help=help['repeat'])
parser.add_option("-e", "--eps", type=float, metavar='eps',
action="store", dest="eps",
default=1e-8, help=help['eps'])
(options, args) = parser.parse_args()
if (len( args ) == 2):
filename_in = args[0]
filename_out = args[1]
else:
parser.print_help()
return
output = Output('genPerMesh:')
output('scale:', options.scale)
output('repeat:', options.repeat)
output('eps:', options.eps)
mesh_in = Mesh.from_file(filename_in)
mesh_out = gen_tiled_mesh(mesh_in, options.repeat, 1./options.scale,
options.eps)
mesh_out.write(filename_out, io='auto')
output('done.')
def test_mesh_smoothing(self):
from sfepy.mesh.mesh_tools import smooth_mesh
from sfepy.fem.mesh import Mesh
from sfepy import data_dir
mesh = Mesh.from_file(data_dir + '/meshes/3d/cylinder.vtk')
vol0 = get_volume(mesh.conns[0], mesh.coors)
mesh.coors = smooth_mesh(mesh, n_iter=10)
vol1 = get_volume(mesh.conns[0], mesh.coors)
filename = op.join(self.options.out_dir, 'smoothed_cylinder.vtk')
mesh.write(filename)
frac = vol1 / vol0
if (frac < 0.967) and (frac > 0.966):
self.report('mesh smoothed')
return True
else:
self.report('mesh smoothed, volume mismatch!')
return False
def test_mesh_smoothing(self):
from sfepy.mesh.mesh_tools import smooth_mesh
from sfepy.fem.mesh import Mesh
from sfepy import data_dir
mesh = Mesh.from_file(data_dir + '/meshes/3d/cylinder.vtk')
vol0 = get_volume(mesh.conns[0], mesh.coors)
mesh.coors = smooth_mesh(mesh, n_iter=10)
vol1 = get_volume(mesh.conns[0], mesh.coors)
filename = op.join(self.options.out_dir, 'smoothed_cylinder.vtk')
mesh.write(filename)
frac = vol1 / vol0
if (frac < 0.967) and (frac > 0.966):
self.report('mesh smoothed')
return True
else:
self.report('mesh smoothed, volume mismatch!')
return False
def dump_to_vtk(filename, output_filename_trunk=None, step0=0, steps=None):
"""Dump a multi-time-step results file into a sequence of VTK files."""
output('dumping to VTK...')
io = MeshIO.any_from_filename(filename)
mesh = Mesh.from_file(filename, io=io)
if output_filename_trunk is None:
output_filename_trunk = get_trunk(filename)
try:
ts = TimeStepper(*io.read_time_stepper())
except:
output('no time stepping info found, assuming single step')
out = io.read_data(0)
if out is not None:
mesh.write(output_filename_trunk + '.vtk', io='auto', out=out)
ret = None
else:
if steps is None:
iterator = ts.iter_from(step0)
else:
iterator = [(step, ts.times[step]) for step in steps]
for step, time in iterator:
output(ts.format % (step, ts.n_step - 1))
out = io.read_data(step)
if out is None: break
mesh.write('.'.join((output_filename_trunk,
ts.suffix % step, 'vtk')),
io='auto', out=out)
ret = ts.suffix
output('...done')
return ret
def main():
parser = OptionParser(usage=usage, version="%prog 42")
parser.add_option(
"-s", "--scale", type=int, metavar="scale", action="store", dest="scale", default=2, help=help["scale"]
)
parser.add_option(
"-r",
"--repeat",
type="str",
metavar="nx,ny[,nz]",
action="callback",
dest="repeat",
callback=parse_repeat,
default=None,
help=help["repeat"],
)
parser.add_option(
"-e", "--eps", type=float, metavar="eps", action="store", dest="eps", default=1e-8, help=help["eps"]
)
parser.add_option("-n", "--no-mvd", action="store_true", dest="nomvd", default=False, help=help["nomvd"])
(options, args) = parser.parse_args()
if len(args) == 2:
filename_in = args[0]
filename_out = args[1]
else:
parser.print_help()
return
output = Output("genPerMesh:")
output("scale:", options.scale)
output("repeat:", options.repeat)
output("eps:", options.eps)
mesh_in = Mesh.from_file(filename_in)
mesh_out = compose_periodic_mesh(mesh_in, options.scale, options.repeat, options.eps, check_mvd=not options.nomvd)
mesh_out.write(filename_out, io="auto")
output("done.")
def extract_time_history( filename, options ):
output( 'extracting selected data...' )
el = options.extract_list
output( 'extraction list:', el )
##
# Parse extractions.
pes = OneTypeList( Struct )
for chunk in el.split( ',' ):
aux = chunk.strip().split()
pes.append( Struct( var = aux[0],
mode = aux[1],
indx = map( int, aux[2:] ),
igs = None ) )
##
# Verify array limits, set igs for element data, shift indx.
mesh = Mesh.from_file( filename )
n_el, n_els, offs = mesh.n_el, mesh.n_els, mesh.el_offsets
for pe in pes:
if pe.mode == 'n':
for ii in pe.indx:
if (ii < 0) or (ii >= mesh.n_nod):
raise IndexError, 'node index 0 <= %d < %d'\
% (ii, mesh.n_nod)
if pe.mode == 'e':
pe.igs = []
for ii, ie in enumerate( pe.indx[:] ):
if (ie < 0) or (ie >= n_el):
raise IndexError, 'element index 0 <= %d < %d'\
% (ie, n_el)
ig = (ie < n_els).argmax()
pe.igs.append( ig )
pe.indx[ii] = ie - offs[ig]
## print pes
##
# Extract data.
# Assumes only one element group (ignores igs)!
io = HDF5MeshIO( filename )
ths = {}
for pe in pes:
mode, nname = io.read_data_header( pe.var )
print mode, nname
if ((pe.mode == 'n' and mode == 'vertex') or
(pe.mode == 'e' and mode == 'cell')):
th = io.read_time_history( nname, pe.indx )
elif pe.mode == 'e' and mode == 'vertex':
conn = mesh.conns[0]
th = {}
for iel in pe.indx:
ips = conn[iel]
th[iel] = io.read_time_history( nname, ips )
else:
raise RuntimeError, 'cannot extract cell data %s in nodes' % pe.var
ths[pe.var] = th
return ths
def gen_mesh_from_goem(geo, a=None, quadratic=False, verbose=True,
refine=False, polyfilename='./meshgen.poly',
out='mesh', **kwargs):
"""
Runs mesh generator - tetgen for 3D or triangle for 2D meshes.
Parameters
----------
geo : geometry
geometry description
a : int, optional
a maximum area/volume constraint
quadratic : bool, optional
set True for quadratic elements
verbose : bool, optional
detailed information
refine : bool, optional
refines mesh
Returns
-------
mesh : Mesh instance
triangular or tetrahedral mesh
"""
import os.path as op
import pexpect
# write geometry to poly file
geo.to_poly_file(polyfilename)
if not refine:
params = "-Apq"
else:
params = "-Arq"
if verbose:
params = params + " -Q"
if a != None and not refine:
params = params + " -a%f" % (a)
if refine:
params = params + " -a"
if quadratic:
params = params + " -o2"
params = params + " %s" % (polyfilename)
meshgen_call = {2: 'triangle', 3: 'tetgen'}
cmd = "%s %s" % (meshgen_call[geo.dim], params)
if verbose: print "Generating mesh using", cmd
if geo.dim == 2:
p=pexpect.run(cmd, timeout=None)
bname, ext = op.splitext(polyfilename)
mesh = Mesh.from_file(bname + '.1.node')
mesh.write(bname + '.' + out)
if geo.dim == 3:
p=pexpect.spawn(cmd, timeout=None)
if not refine:
p.expect("Opening %s." % (polyfilename))
else:
p.expect("Opening %s.node.\r\n" % (polyfilename))
p.expect("Opening %s.ele.\r\n" % (polyfilename))
p.expect("Opening %s.face.\r\n" % (polyfilename))
p.expect("Opening %s.vol." % (polyfilename))
assert p.before == ""
p.expect(pexpect.EOF)
if p.before != "\r\n":
print p.before
raise "Error when running mesh generator (see above for output): %s" % cmd
def extract_time_history(filename, extract, verbose=True):
"""Extract time history of a variable from a multi-time-step results file.
Parameters
----------
filename : str
The name of file to extract from.
extract : str
The description of what to extract in a string of comma-separated
description items. A description item consists of: name of the variable
to extract, mode ('e' for elements, 'n' for nodes), ids of the nodes or
elements (given by the mode). Example: 'u n 10 15, p e 0' means
variable 'u' in nodes 10, 15 and variable 'p' in element 0.
verbose : bool
Verbosity control.
Returns
-------
ths : dict
The time histories in a dict with variable names as keys. If a
nodal variable is requested in elements, its value is a dict of histories
in the element nodes.
ts : TimeStepper instance
The time stepping information.
"""
output('extracting selected data...', verbose=verbose)
output('selection:', extract, verbose=verbose)
##
# Parse extractions.
pes = OneTypeList(Struct)
for chunk in extract.split(','):
aux = chunk.strip().split()
pes.append(Struct(var = aux[0],
mode = aux[1],
indx = map(int, aux[2:]),
igs = None))
##
# Verify array limits, set igs for element data, shift indx.
mesh = Mesh.from_file(filename)
n_el, n_els, offs = mesh.n_el, mesh.n_els, mesh.el_offsets
for pe in pes:
if pe.mode == 'n':
for ii in pe.indx:
if (ii < 0) or (ii >= mesh.n_nod):
raise ValueError('node index 0 <= %d < %d!'
% (ii, mesh.n_nod))
if pe.mode == 'e':
pe.igs = []
for ii, ie in enumerate(pe.indx[:]):
if (ie < 0) or (ie >= n_el):
raise ValueError('element index 0 <= %d < %d!'
% (ie, n_el))
ig = (ie < n_els).argmax()
pe.igs.append(ig)
pe.indx[ii] = ie - offs[ig]
## print pes
##
# Extract data.
# Assumes only one element group (ignores igs)!
io = MeshIO.any_from_filename(filename)
ths = {}
for pe in pes:
mode, nname = io.read_data_header(pe.var)
output(mode, nname, verbose=verbose)
if ((pe.mode == 'n' and mode == 'vertex') or
(pe.mode == 'e' and mode == 'cell')):
th = io.read_time_history(nname, pe.indx)
elif pe.mode == 'e' and mode == 'vertex':
conn = mesh.conns[0]
th = {}
for iel in pe.indx:
ips = conn[iel]
th[iel] = io.read_time_history(nname, ips)
else:
raise ValueError('cannot extract cell data %s in nodes!' % pe.var)
ths[pe.var] = th
output('...done', verbose=verbose)
ts = TimeStepper(*io.read_time_stepper())
return ths, ts
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
def main():
parser = OptionParser(usage=usage, version='%prog ' + sfepy.__version__)
parser.add_option('-c',
'--conf',
metavar='"key : value, ..."',
action='store',
dest='conf',
type='string',
default=None,
help=help['conf'])
parser.add_option('-O',
'--options',
metavar='"key : value, ..."',
action='store',
dest='app_options',
type='string',
default=None,
help=help['options'])
parser.add_option('-o',
'',
metavar='filename',
action='store',
dest='output_filename_trunk',
default=None,
help=help['filename'])
parser.add_option('--create-mesh',
action='store_true',
dest='create_mesh',
default=False,
help=help['create_mesh'])
parser.add_option('--2d',
action='store_true',
dest='dim2',
default=False,
help=help['dim'])
parser.add_option('-m',
'--mesh',
metavar='filename',
action='store',
dest='mesh',
default=None,
help=help['mesh'])
parser.add_option('--mesh-dir',
metavar='dirname',
action='store',
dest='mesh_dir',
default='tmp',
help=help['mesh_dir'])
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'])
options, args = parser.parse_args()
if options.create_mesh and options.mesh:
output('--create-mesh and --mesh options are mutually exclusive!')
return
if len(args) == 1:
filename_in = args[0]
auto_mesh_name = False
elif len(args) == 0:
auto_mesh_name = True
mesh_filename = os.path.join(options.mesh_dir, 'mesh.vtk')
ensure_path(mesh_filename)
if options.oscillator:
filename_in = fix_path("examples/quantum/oscillator.py")
elif options.well:
filename_in = fix_path("examples/quantum/well.py")
elif options.hydrogen:
filename_in = fix_path("examples/quantum/hydrogen.py")
elif options.boron:
filename_in = fix_path("examples/quantum/boron.py")
elif options.create_mesh:
output('generating mesh...')
try:
os.makedirs("tmp")
except OSError, e:
if e.errno != 17: # [Errno 17] File exists
raise
if options.dim2:
output("dimension: 2")
gp = fix_path('meshes/quantum/square.geo')
os.system("cp %s tmp/mesh.geo" % gp)
os.system("gmsh -2 tmp/mesh.geo -format mesh")
mtv = fix_path('script/convert_mesh.py')
os.system("%s tmp/mesh.mesh %s" % (mtv, mesh_filename))
else:
output("dimension: 3")
import sfepy.mesh as geom
from sfepy.fem.mesh import Mesh
try:
from site_cfg import tetgen_path
except ImportError:
tetgen_path = '/usr/bin/tetgen'
gp = fix_path('meshes/quantum/box.geo')
os.system("gmsh -0 %s -o tmp/x.geo" % gp)
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(mesh_filename, io="auto")
output("...mesh written to %s" % mesh_filename)
return
else:
parser.print_help()
return
def dump_to_vtk(filename,
output_filename_trunk=None,
step0=0,
steps=None,
fields=None,
linearization=None):
"""Dump a multi-time-step results file into a sequence of VTK files."""
def _save_step(suffix, out, mesh):
if linearization is not None:
output('linearizing...')
out = _linearize(out, fields, linearization)
output('...done')
for key, val in out.iteritems():
lmesh = val.get('mesh', mesh)
lmesh.write(output_filename_trunk + '_' + key + suffix,
io='auto',
out={key: val})
if hasattr(val, 'levels'):
output('max. refinement per group:', val.levels)
else:
mesh.write(output_filename_trunk + suffix, io='auto', out=out)
output('dumping to VTK...')
io = MeshIO.any_from_filename(filename)
mesh = Mesh.from_file(filename, io=io)
if output_filename_trunk is None:
output_filename_trunk = get_trunk(filename)
try:
ts = TimeStepper(*io.read_time_stepper())
all_steps, times, nts, dts = extract_times(filename)
except ValueError:
output('no time stepping info found, assuming single step')
out = io.read_data(0)
if out is not None:
_save_step('.vtk', out, mesh)
ret = None
else:
ts.times = times
ts.n_step = times.shape[0]
if steps is None:
ii0 = nm.searchsorted(all_steps, step0)
iterator = ((all_steps[ii], times[ii])
for ii in xrange(ii0, len(times)))
else:
iterator = [(step, ts.times[step]) for step in steps]
max_step = all_steps.max()
for step, time in iterator:
output(ts.format % (step, max_step))
out = io.read_data(step)
if out is None: break
_save_step('.' + ts.suffix % step + '.vtk', out, mesh)
ret = ts.suffix
output('...done')
return ret
def extract_time_history(filename, extract, verbose=True):
"""Extract time history of a variable from a multi-time-step results file.
Parameters
----------
filename : str
The name of file to extract from.
extract : str
The description of what to extract in a string of comma-separated
description items. A description item consists of: name of the variable
to extract, mode ('e' for elements, 'n' for nodes), ids of the nodes or
elements (given by the mode). Example: 'u n 10 15, p e 0' means
variable 'u' in nodes 10, 15 and variable 'p' in element 0.
verbose : bool
Verbosity control.
Returns
-------
ths : dict
The time histories in a dict with variable names as keys. If a
nodal variable is requested in elements, its value is a dict of histories
in the element nodes.
ts : TimeStepper instance
The time stepping information.
"""
output('extracting selected data...', verbose=verbose)
output('selection:', extract, verbose=verbose)
##
# Parse extractions.
pes = OneTypeList(Struct)
for chunk in extract.split(','):
aux = chunk.strip().split()
pes.append(
Struct(var=aux[0], mode=aux[1], indx=map(int, aux[2:]), igs=None))
##
# Verify array limits, set igs for element data, shift indx.
mesh = Mesh.from_file(filename)
n_el, n_els, offs = mesh.n_el, mesh.n_els, mesh.el_offsets
for pe in pes:
if pe.mode == 'n':
for ii in pe.indx:
if (ii < 0) or (ii >= mesh.n_nod):
raise ValueError('node index 0 <= %d < %d!' %
(ii, mesh.n_nod))
if pe.mode == 'e':
pe.igs = []
for ii, ie in enumerate(pe.indx[:]):
if (ie < 0) or (ie >= n_el):
raise ValueError('element index 0 <= %d < %d!' %
(ie, n_el))
ig = (ie < n_els).argmax()
pe.igs.append(ig)
pe.indx[ii] = ie - offs[ig]
## print pes
##
# Extract data.
# Assumes only one element group (ignores igs)!
io = MeshIO.any_from_filename(filename)
ths = {}
for pe in pes:
mode, nname = io.read_data_header(pe.var)
output(mode, nname, verbose=verbose)
if ((pe.mode == 'n' and mode == 'vertex')
or (pe.mode == 'e' and mode == 'cell')):
th = io.read_time_history(nname, pe.indx)
elif pe.mode == 'e' and mode == 'vertex':
conn = mesh.conns[0]
th = {}
for iel in pe.indx:
ips = conn[iel]
th[iel] = io.read_time_history(nname, ips)
else:
raise ValueError('cannot extract cell data %s in nodes!' % pe.var)
ths[pe.var] = th
output('...done', verbose=verbose)
ts = TimeStepper(*io.read_time_stepper())
return ths, ts
def main():
parser = OptionParser( usage = usage, version = "%prog 42" )
parser.add_option( "-s", "--scale", type = int, metavar = 'scale',
action = "store", dest = "scale",
default = 2, help = help['scale'] )
parser.add_option( "-e", "--eps", type = float, metavar = 'eps',
action = "store", dest = "eps",
default = 1e-8, help = help['eps'] )
parser.add_option( "-t", "--test",
action = "store_true", dest = "test",
default = False, help = help['test'] )
parser.add_option( "-n", "--no-mvd",
action = "store_true", dest = "nomvd",
default = False, help = help['nomvd'] )
(options, args) = parser.parse_args()
if options.test:
test()
return
if (len( args ) == 2):
filename_in = args[0]
filename_out = args[1]
else:
parser.print_help()
return
print 'scale:', options.scale
print 'eps:', options.eps
mesh_in = Mesh.from_file( filename_in )
bbox = mesh_in.get_bounding_box()
print 'bbox:\n', bbox
mscale = bbox[1] - bbox[0]
centre0 = 0.5 * (bbox[1] + bbox[0])
print 'centre:\n', centre0
scale = nm.array( options.scale, dtype = nm.float64 )
# Normalize original coordinates.
coor0 = (mesh_in.nod0[:,:-1] - centre0) / (mscale)
dim = mesh_in.dim
coor0, mesh_in.conns = fix_double_nodes( coor0, mesh_in.conns, options.eps )
if not options.nomvd:
mes0 = get_min_edge_size( coor0, mesh_in.conns )
mvd0 = get_min_vertex_distance( coor0, mes0 )
if mes0 > (mvd0 + options.eps):
print ' original min. "edge" length: %.5e' % mes0
print 'original approx. min. vertex distance: %.5e' % mvd0
print '-> still double nodes in input mesh!'
print 'try increasing eps...'
raise ValueError
for indx in cycle( [options.scale] * dim ):
aindx = nm.array( indx, dtype = nm.float64 )
centre = 0.5 * (2.0 * aindx - scale + 1.0)
print indx, centre
if aindx.sum() == 0:
coor = coor0 + centre
conns = mesh_in.conns
else:
coor1 = coor0 + centre
conns1 = mesh_in.conns
cmap = find_map( coor, coor1, eps = options.eps )
if not cmap.size:
print 'non-periodic mesh!'
# raise ValueError
else:
print cmap.size / 2
coor, conns = merge_mesh( coor, conns, coor1, conns1, cmap,
eps = options.eps )
if not options.nomvd:
mes = get_min_edge_size( coor, conns )
mvd = get_min_vertex_distance( coor, mes0 )
print ' original min. "edge" length: %.5e' % mes0
print ' final min. "edge" length: %.5e' % mes
print 'original approx. min. vertex distance: %.5e' % mvd0
print ' final approx. min. vertex distance: %.5e' % mvd
if mvd < 0.99999 * mvd0:
if mvd0 < (mes0 - options.eps):
print '-> probably non-periodic input mesh!'
print ' ... adjacent sides were not connected!'
print ' try increasing eps...'
else:
print '-> input mesh might be periodic'
print ' try increasing eps...'
else:
print '-> input mesh looks periodic'
else:
print 'non-periodic input mesh detection skipped!'
print 'renormalizing...'
coor = (coor * mscale) / scale
print 'saving...'
mesh_out = make_mesh( coor, conns, mesh_in )
mesh_out.write( filename_out, io = 'auto' )
print 'done.'
def main():
parser = OptionParser(usage=usage, version='%prog ' + sfepy.__version__)
parser.add_option('-c', '--conf', metavar='"key : value, ..."',
action='store', dest='conf', type='string',
default=None, help= help['conf'])
parser.add_option('-O', '--options', metavar='"key : value, ..."',
action='store', dest='app_options', type='string',
default=None, help=help['options'])
parser.add_option('-o', '', metavar='filename',
action='store', dest='output_filename_trunk',
default=None, help=help['filename'])
parser.add_option('--create-mesh',
action='store_true', dest='create_mesh',
default=False, help=help['create_mesh'])
parser.add_option('--2d',
action='store_true', dest='dim2',
default=False, help=help['dim'])
parser.add_option('-m', '--mesh', metavar='filename',
action='store', dest='mesh',
default=None, help=help['mesh'])
parser.add_option('--mesh-dir', metavar='dirname',
action='store', dest='mesh_dir',
default='tmp', help=help['mesh_dir'])
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'])
options, args = parser.parse_args()
if options.create_mesh and options.mesh:
output('--create-mesh and --mesh options are mutually exclusive!')
return
if len(args) == 1:
filename_in = args[0];
auto_mesh_name = False
elif len(args) == 0:
auto_mesh_name = True
mesh_filename = os.path.join(options.mesh_dir, 'mesh.vtk')
ensure_path(mesh_filename)
if options.oscillator:
filename_in = fix_path("examples/quantum/oscillator.py")
elif options.well:
filename_in = fix_path("examples/quantum/well.py")
elif options.hydrogen:
filename_in = fix_path("examples/quantum/hydrogen.py")
elif options.boron:
filename_in = fix_path("examples/quantum/boron.py")
elif options.create_mesh:
output('generating mesh...')
try:
os.makedirs("tmp")
except OSError, e:
if e.errno != 17: # [Errno 17] File exists
raise
if options.dim2:
output("dimension: 2")
gp = fix_path('meshes/quantum/square.geo')
os.system("cp %s tmp/mesh.geo" % gp)
os.system("gmsh -2 tmp/mesh.geo -format mesh")
mtv = fix_path('script/mesh_to_vtk.py')
os.system("%s tmp/mesh.mesh %s" % (mtv, mesh_filename))
else:
output("dimension: 3")
import sfepy.geom as geom
from sfepy.fem.mesh import Mesh
try:
from site_cfg import tetgen_path
except ImportError:
tetgen_path = '/usr/bin/tetgen'
gp = fix_path('meshes/quantum/box.geo')
os.system("gmsh -0 %s -o tmp/x.geo" % gp)
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(mesh_filename, io="auto")
output("...mesh written to %s" % mesh_filename)
return
else:
parser.print_help()
return
def gen_mesh_from_goem(geo,
a=None,
quadratic=False,
verbose=True,
refine=False,
polyfilename='./meshgen.poly',
out='mesh',
**kwargs):
"""
Runs mesh generator - tetgen for 3D or triangle for 2D meshes.
Parameters
----------
geo : geometry
geometry description
a : int, optional
a maximum area/volume constraint
quadratic : bool, optional
set True for quadratic elements
verbose : bool, optional
detailed information
refine : bool, optional
refines mesh
Returns
-------
mesh : Mesh instance
triangular or tetrahedral mesh
"""
import os.path as op
import pexpect
# write geometry to poly file
geo.to_poly_file(polyfilename)
if not refine:
params = "-Apq"
else:
params = "-Arq"
if verbose:
params = params + " -Q"
if a != None and not refine:
params = params + " -a%f" % (a)
if refine:
params = params + " -a"
if quadratic:
params = params + " -o2"
params = params + " %s" % (polyfilename)
meshgen_call = {2: 'triangle', 3: 'tetgen'}
cmd = "%s %s" % (meshgen_call[geo.dim], params)
if verbose: print "Generating mesh using", cmd
if geo.dim == 2:
p = pexpect.run(cmd, timeout=None)
bname, ext = op.splitext(polyfilename)
mesh = Mesh.from_file(bname + '.1.node')
mesh.write(bname + '.' + out)
if geo.dim == 3:
p = pexpect.spawn(cmd, timeout=None)
if not refine:
p.expect("Opening %s." % (polyfilename))
else:
p.expect("Opening %s.node.\r\n" % (polyfilename))
p.expect("Opening %s.ele.\r\n" % (polyfilename))
p.expect("Opening %s.face.\r\n" % (polyfilename))
p.expect("Opening %s.vol." % (polyfilename))
assert p.before == ""
p.expect(pexpect.EOF)
if p.before != "\r\n":
print p.before
raise "Error when running mesh generator (see above for output): %s" % cmd
def solve_eigen_problem1( conf, options ):
pb = ProblemDefinition.from_conf( conf )
dim = pb.domain.mesh.dim
pb.time_update()
dummy = pb.create_state_vector()
output( 'assembling lhs...' )
tt = time.clock()
mtx_a = eval_term_op( dummy, conf.equations['lhs'], pb,
dw_mode = 'matrix', tangent_matrix = pb.mtx_a )
output( '...done in %.2f s' % (time.clock() - tt) )
output( 'assembling rhs...' )
tt = time.clock()
mtx_b = eval_term_op( dummy, conf.equations['rhs'], pb,
dw_mode = 'matrix', tangent_matrix = pb.mtx_a.copy() )
output( '...done in %.2f s' % (time.clock() - tt) )
#mtxA.save( 'tmp/a.txt', format='%d %d %.12f\n' )
#mtxB.save( 'tmp/b.txt', format='%d %d %.12f\n' )
try:
n_eigs = conf.options.n_eigs
except AttributeError:
n_eigs = mtx_a.shape[0]
if n_eigs is None:
n_eigs = mtx_a.shape[0]
## mtx_a.save( 'a.txt', format='%d %d %.12f\n' )
## mtx_b.save( 'b.txt', format='%d %d %.12f\n' )
print 'computing resonance frequencies...'
eig = Solver.any_from_conf( pb.get_solver_conf( conf.options.eigen_solver ) )
eigs, mtx_s_phi = eig( mtx_a, mtx_b, conf.options.n_eigs )
from sfepy.fem.mesh import Mesh
bounding_box = Mesh.from_file("tmp/mesh.vtk").get_bounding_box()
# this assumes a box (3D), or a square (2D):
a = bounding_box[1][0] - bounding_box[0][0]
E_exact = None
if options.hydrogen or options.boron:
if options.hydrogen:
Z = 1
elif options.boron:
Z = 5
if options.dim == 2:
E_exact = [-float(Z)**2/2/(n-0.5)**2/4 for n in [1]+[2]*3+[3]*5 +\
[4]*8 + [5]*15]
elif options.dim == 3:
E_exact = [-float(Z)**2/2/n**2 for n in [1]+[2]*2**2+[3]*3**2 ]
if options.well:
if options.dim == 2:
E_exact = [pi**2/(2*a**2)*x for x in [2, 5, 5, 8, 10, 10, 13, 13,
17, 17, 18, 20, 20 ] ]
elif options.dim == 3:
E_exact = [pi**2/(2*a**2)*x for x in [3, 6, 6, 6, 9, 9, 9, 11, 11,
11, 12, 14, 14, 14, 14, 14, 14, 17, 17, 17] ]
if options.oscillator:
if options.dim == 2:
E_exact = [1] + [2]*2 + [3]*3 + [4]*4 + [5]*5 + [6]*6
elif options.dim == 3:
E_exact = [float(1)/2+x for x in [1]+[2]*3+[3]*6+[4]*10 ]
if E_exact is not None:
print "a=%f" % a
print "Energies:"
print "n exact FEM error"
for i, e in enumerate(eigs):
from numpy import NaN
if i < len(E_exact):
exact = E_exact[i]
err = 100*abs((exact - e)/exact)
else:
exact = NaN
err = NaN
print "%d: %.8f %.8f %5.2f%%" % (i, exact, e, err)
else:
print eigs
## import sfepy.base.plotutils as plu
## plu.spy( mtx_b, eps = 1e-12 )
## plu.pylab.show()
## pause()
n_eigs = eigs.shape[0]
mtx_phi = nm.empty( (pb.variables.di.ptr[-1], mtx_s_phi.shape[1]),
dtype = nm.float64 )
for ii in xrange( n_eigs ):
mtx_phi[:,ii] = pb.variables.make_full_vec( mtx_s_phi[:,ii] )
save = get_default_attr( conf.options, 'save_eig_vectors', None )
out = {}
for ii in xrange( n_eigs ):
if save is not None:
if (ii > save[0]) and (ii < (n_eigs - save[1])): continue
aux = pb.state_to_output( mtx_phi[:,ii] )
key = aux.keys()[0]
out[key+'%03d' % ii] = aux[key]
ofn_trunk = options.output_filename_trunk
pb.domain.mesh.write( ofn_trunk + '.vtk', io = 'auto', out = out )
fd = open( ofn_trunk + '_eigs.txt', 'w' )
eigs.tofile( fd, ' ' )
fd.close()
return Struct( pb = pb, eigs = eigs, mtx_phi = mtx_phi )
