def test():
x1 = nm.fix( nm.random.rand( 5, 3 ) * 5 ) / 10
x2 = nm.fix( nm.random.rand( 10, 3 ) * 5 ) / 10
cmap = find_map( x1, x2 )
conn1 = nm.array( [[range( 5 )], [range( 5 )]] ).squeeze()
conn2 = nm.array( [[range( 10 )], [range( 10 )]] ).squeeze()
conn2.shape = (4, 5)
print x1
print conn1
print x2
print conn2
print cmap
xx, conns = merge_mesh( x1, [conn1], x2, [conn2], cmap )
print xx
print conns
def compose_periodic_mesh(mesh_in, scale, repeat, eps, check_mvd=False):
"""
Create a new mesh from a periodic mesh by scaling it and repeating
along each axis,
Parameters
----------
mesh_in : Mesh instance
The input periodic mesh.
scale : float
The scale parameter.
repeat : array
The number of repetitions of `mesh_in` along each axis.
eps : float
Tolerance for finding matching mesh vertices.
check_mvd : bool
If True, verify periodicity by checking approximate minimum
vertex distance and minimum edge length.
Returns
-------
mesh_out : Mesh instance
The composed periodic mesh.
"""
dim = mesh_in.dim
bbox = mesh_in.get_bounding_box()
mscale = bbox[1] - bbox[0]
output('bbox:\n', bbox)
centre0 = 0.5 * (bbox[1] + bbox[0])
output('centre:\n', centre0)
scale = float(scale)
if repeat is None:
repeat = [scale] * dim
repeat = nm.asarray(repeat)
# Normalize original coordinates.
coor0 = (mesh_in.coors - centre0) / (mscale)
aux = fix_double_nodes(coor0, mesh_in.ngroups, mesh_in.conns, eps)
coor0, ngroups0, mesh_in.conns = aux
if check_mvd:
mes0 = get_min_edge_size(coor0, mesh_in.conns)
mvd0 = get_min_vertex_distance(coor0, mes0)
if mes0 > (mvd0 + eps):
output(' original min. "edge" length: %.5e' % mes0)
output('original approx. min. vertex distance: %.5e' % mvd0)
output('-> still double nodes in input mesh!')
output('try increasing eps')
raise ValueError('cannot fix double nodes!')
output('composing periodic mesh...')
for indx in cycle(repeat):
aindx = nm.array(indx, dtype=nm.float64)
centre = 0.5 * (2.0 * aindx - repeat + 1.0)
output(indx, centre)
if aindx.sum() == 0:
coor = coor0 + centre
ngroups = ngroups0
conns = mesh_in.conns
else:
coor1 = coor0 + centre
ngroups1 = ngroups0
conns1 = mesh_in.conns
cmap = find_map(coor, coor1, eps=eps)
if not cmap.size:
raise ValueError('non-periodic mesh!')
else:
output(cmap.size / 2)
coor, ngroups, conns = merge_mesh(coor, ngroups, conns,
coor1, ngroups1, conns1,
cmap, eps=eps)
if check_mvd:
mes = get_min_edge_size( coor, conns )
mvd = get_min_vertex_distance( coor, mes0 )
output(' original min. "edge" length: %.5e' % mes0)
output(' final min. "edge" length: %.5e' % mes)
output('original approx. min. vertex distance: %.5e' % mvd0)
output(' final approx. min. vertex distance: %.5e' % mvd)
if mvd < 0.99999 * mvd0:
if mvd0 < (mes0 - eps):
output('-> probably non-periodic input mesh!')
output(' - adjacent sides were not connected!')
output(' try increasing eps')
else:
output('-> input mesh might be periodic')
output(' try increasing eps')
else:
output('-> input mesh looks periodic')
else:
output('non-periodic input mesh detection skipped!')
# Renormalize.
coor = (coor * mscale) / scale
mesh_out = make_mesh(coor, ngroups, conns, mesh_in)
output('...done')
return mesh_out
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.'