def hypersphere(filename):
s = zeros((25,25,25,25))
x, y, z, q = mgrid[-1:1:25j,-1:1:25j,-1:1:25j,-1:1:25j]
dist = sqrt(x**2 + y**2 + z**2 + q**2)
s[dist < dist] = 1.
hdf5.write_S(filename, s)
def geom_to_h5(domain_shape, feature_count, nd_radius, out_filename=None, prefix=None):
# Calculate the aspect of the domain (usually 1,1[,1])
aspect = tuple(array(domain_shape)/domain_shape[0])
# Generate the random points
print "Packing. . .",
t = time.time()
points = random_pack_nd_points(aspect, nd_radius, feature_count)
print time.time() - t, "seconds . . ."
# Generate the actual solid array
print "Creating array. . .",
t = time.time()
solid_array = nd_points_to_domain(points, nd_radius, domain_shape)
print time.time() - t, "seconds . . ."
# Generate the automatic name
if out_filename==None:
print "Creating file name hash. . .",
t = time.time()
out_filename = os.path.join(prefix, name_file(solid_array, int( (1. / nd_radius) + 0.5), feature_count))
print time.time() - t, "seconds . . ."
# Write the solid array to the h5 file
print "Writing to h5. . .",
t = time.time()
hdf5.write_S(out_filename, solid_array)
# Write the geometry
hdf5.write_geometry(out_filename, points, nd_radius * ones(feature_count))
print time.time() - t, "seconds . . ."
def make_dilute_meshstudy(start=10, stop=60, steps=11):
for x in linspace(start,stop,steps):
print "writing", x
domain = zeros((x,x,x))
domain[0,0,0] = 1
mesh_str = "%ix%ix%i.h5" % (x,x,x)
filename = os.path.join("dilute-refine", mesh_str)
hdf5.write_S(filename, domain)
def make_2d_cyl_validation_set(folder_to_save, lower=0.01, upper = 0.49, steps=100, shape = (200,200)):
radii = linspace(lower, upper, steps)
for num, radius in enumerate(radii):
filename = os.path.join(folder_to_save, str(num) + ".h5")
print num, filename
domain = nd_points_to_domain(array([[0.5,0.5]]), radius, shape)
print "Writing for fraction:", domain.mean()
hdf5.write_S(filename, domain)
hdf5.write_geometry(filename, fcc[3], radius * ones(4))
def make_3d_bcc_series(folder_to_save, number, resolution):
radaii = linspace(0, 0.25 * sqrt(3), number+1)[0:]
for num, radius in enumerate(radaii):
print num
domain = nd_points_to_domain(bcc[3], radius, resolution)
filename = os.path.join(folder_to_save, str(num) + ".h5")
print "Writing for fraction:", domain.mean()
hdf5.write_S(filename, domain)
hdf5.write_geometry(filename, fcc[3], radius * ones(4))
def make_3d_fcc_mesh_refine_study(smallest=10, largest=100, steps=10):
mesh_sizes = linspace(smallest, largest, steps)
radius = sqrt(2) / 4.
for mesh_size in mesh_sizes:
# Make the solid
resolution = (mesh_size, mesh_size, mesh_size)
domain = nd_points_to_domain(fcc[3], radius, resolution)
mesh_str = "%ix%ix%i" % resolution
print "Writing for fraction: %f (%s)" % (domain.mean(), mesh_str)
filename = os.path.join("fcc-meshrefine", mesh_str + ".h5")
hdf5.write_S(filename, domain)
hdf5.write_geometry(filename, fcc[3], radius * ones(4))
def seimran_geom_to_h5(domain_shape, feature_count, nd_radius, out_filename):
# Calculate the aspect of the domain (usually 1,1[,1])
aspect = tuple(array(domain_shape)/domain_shape[0])
# Generate the random points
points = semirandom_pack_nd_points(aspect, nd_radius, feature_count)
# Generate the actual solid array
solid_array = nd_points_to_domain(points, nd_radius, domain_shape)
# Write the solid array to the h5 file
hdf5.write_S(out_filename, solid_array)
# Write the geometry
hdf5.write_geometry(out_filename, points, nd_radius * ones(feature_count))
def make_2_circle_series():
nd_radius = 0.1
aspect=(1.,1.)
ndim = 2
domain_shape = (150,150)
center_point = array([[0.5,0.5]])
for nx, dx in enumerate(linspace(0,0.5,100)):
for ny, dy in enumerate(linspace(0,0.5,100)):
new_point = center_point.copy()
new_point[0,0] += dx
new_point[0,1] += dy
# Non periodic vector
dist_vector = center_point - new_point
# If a distance in a given vector direction is greater than half the domain width
# Then the real distance is the domain length minus the apperent distance
for dim in range(ndim):
to_subtract = abs(dist_vector[:,dim]) > (aspect[dim]/2.)
dist_vector[to_subtract,dim] = aspect[dim] - abs(dist_vector[to_subtract,dim])
# Find Vector Magnitude
dist_vector = dist_vector ** 2
dist = sqrt(dist_vector.sum(axis=1))
too_close = dist < (2 * nd_radius)
if too_close:
continue
points = r_[center_point, new_point]
out_filename = "explore_two/x-%03i_y-%03i.h5" % (nx, ny)
print out_filename
# Generate the actual solid array
solid_array = nd_points_to_domain(points, nd_radius, domain_shape)
# Write the solid array to the h5 file
hdf5.write_S(out_filename, solid_array)
# Write the geometry
hdf5.write_geometry(out_filename, points, nd_radius * ones(2))
def make_halfpipe_meshrefine(smallest=10, largest=100, steps=10):
mesh_sizes = linspace(smallest, largest, steps)
print mesh_sizes
# Match exactly zick's concentration
for mesh_size in mesh_sizes:
# Make the solid
resolution = (mesh_size, mesh_size, mesh_size)
x, y, z = mgrid[-1:1:1j*resolution[0],
-1:1:1j*resolution[0],
-1:1:1j*resolution[0]]
domain = 1.0 * ((x**2 + y**2) > 0.5**2)
mesh_str = "%ix%ix%i" % resolution
print "Writing for fraction: %f (%s)" % (domain.mean(), mesh_str)
filename = os.path.join("halfpipe", mesh_str + ".h5")
hdf5.write_S(filename, domain)
def make_3d_bcc_mesh_refine_study(smallest=10, largest=80, steps=8):
mesh_sizes = linspace(smallest, largest, steps)
print mesh_sizes
# Match exactly zick's concentration
conc = 0.6
radius = (conc * (3./(8 * pi)))**(1./3)
for mesh_size in mesh_sizes:
# Make the solid
resolution = (mesh_size, mesh_size, mesh_size)
domain = nd_points_to_domain(bcc[3], radius, resolution)
mesh_str = "%ix%ix%i" % resolution
print "Writing for fraction: %f (%s)" % (domain.mean(), mesh_str)
filename = os.path.join("bcc-final-0.6-final-refine", mesh_str + ".h5")
hdf5.write_S(filename, domain)
hdf5.write_geometry(filename, bcc[3], radius * ones(2))
def points_to_sim(filename, points, ndradius, extent):
point_count = points.shape[0]
domain = nd_points_to_domain(points, ndradius, extent)
print "Domain Fraction:", domain.mean()
hdf5.write_S(filename, domain)
hdf5.write_geometry(filename, points, ndradius * ones(point_count))
# open the h5 and get the dimensionality
h5 = hdf5.openFile(f)
ndim = len(h5.root.geometry.S.shape)
h5.close()
else:
# Default to trying an image . . .
print f, "is not and HDF5 file . . . trying image?"
S = 1. * ( misc.imread(f, flatten=True) < (255/2.) )
# Appropriate image transformation to make x/y convention meaningful
S = S[::-1].T
ndim = 2
# Make a h5 file for the results
hdf5.write_S(save_path, S)
# Get the domain dimensionality
print "Dimension:", ndim
# Populate the pressure drops based on user input
# Done here and not earlier b/c we need to know the dimensionality
dPs = []
# Have dp/dx
if options.x and ndim == 2:
dPs.append((1,0))
elif options.x and ndim == 3:
dPs.append((1,0,0))
# have dp/dy
if options.y and ndim == 2: