def main():
parser = argparse.ArgumentParser(description="Test xdmf")
parser.add_argument("--show", "--plot", action="store_true")
parser.add_argument('file', nargs="?", default=None)
args = vutil.common_argparse(parser)
# f3d = readers.load_file(_viscid_root + '/../../sample/sample.3df.xdmf')
# b3d = f3d['b']
# bx, by, bz = b3d.component_fields() # pylint: disable=W0612
if args.file is None:
args.file = "/Users/kmaynard/dev/work/cen4000/cen4000.3d.xdmf"
f3d = readers.load_file(args.file)
bx = f3d["bx"]
by = f3d["by"]
bz = f3d["bz"]
B = field.scalar_fields_to_vector([bx, by, bz], name="B_cc",
_force_layout=field.LAYOUT_INTERLACED)
t0 = time()
lines_single, topo = trace_cython(B, nr_procs=1)
t1 = time()
topo_single = vol.wrap_field(topo, name="CyTopo1")
print("single proc:", t1 - t0, "s")
nr_procs_list = np.array([1, 2, 3])
# nr_procs_list = np.array([1, 2, 3, 4, 5, 6, 7, 8])
times = np.empty_like(nr_procs_list, dtype="float")
print("always parallel overhead now...")
for i, nr_procs in enumerate(nr_procs_list):
t0 = time()
lines, topo = trace_cython(B, nr_procs=nr_procs, force_subprocess=True)
t1 = time()
fld = vol.wrap_field(topo, name="CyTopo")
same_topo = (fld.data == topo_single.data).all()
same_lines = True
for j, line in enumerate(lines):
same_lines = same_lines and (line == lines_single[j]).all()
print("nr_procs:", nr_procs, "time:", t1 - t0, "s",
"same topo:", same_topo, "same lines:", same_lines)
times[i] = t1 - t0
plt.plot(nr_procs_list, times, 'k^')
plt.plot(nr_procs_list, times[0] / nr_procs_list, 'b--')
plt.xscale("log")
plt.yscale("log")
plt.show()
if False:
cmap = plt.get_cmap('spectral')
levels = [4, 5, 6, 7, 8, 13, 14, 16, 17]
norm = BoundaryNorm(levels, cmap.N)
mpl.plot(topo_flds[-1], "y=0", cmap=cmap, norm=norm, show=False)
#mpl.plot_streamlines2d(lines[::5], "y", topology=topo[::5], show=False)
#mpl.plot_streamlines(lines, topology=topo, show=False)
mpl.mplshow()
def main():
xl, xh, nx = -1.0, 1.0, 41
yl, yh, ny = -1.5, 1.5, 41
zl, zh, nz = -2.0, 2.0, 41
x = np.linspace(xl, xh, nx)
y = np.linspace(yl, yh, ny)
z = np.linspace(zl, zh, nz)
crds = coordinate.wrap_crds("nonuniform_cartesian",
[('z', z), ('y', y), ('x', x)])
bx = field.empty(crds, name="$B_x$", center="Node")
by = field.empty(crds, name="$B_y$", center="Node")
bz = field.empty(crds, name="$B_z$", center="Node")
fld = field.empty(crds, name="B", nr_comps=3, center="Node",
layout="interlaced")
X, Y, Z = crds.get_crds(shaped=True)
x01, y01, z01 = 0.5, 0.5, 0.5
x02, y02, z02 = 0.5, 0.5, 0.5
x03, y03, z03 = 0.5, 0.5, 0.5
bx[:] = 0.0 + 1.0 * (X - x01) + 1.0 * (Y - y01) + 1.0 * (Z - z01) + \
1.0 * (X - x01) * (Y - y01) + 1.0 * (Y - y01) * (Z - z01) + \
1.0 * (X - x01) * (Y - y01) * (Z - z01)
by[:] = 0.0 + 1.0 * (X - x02) - 1.0 * (Y - y02) + 1.0 * (Z - z02) + \
1.0 * (X - x02) * (Y - y02) + 1.0 * (Y - y02) * (Z - z02) - \
1.0 * (X - x02) * (Y - y02) * (Z - z02)
bz[:] = 0.0 + 1.0 * (X - x03) + 1.0 * (Y - y03) - 1.0 * (Z - z03) + \
1.0 * (X - x03) * (Y - y03) + 1.0 * (Y - y03) * (Z - z03) + \
1.0 * (X - x03) * (Y - y03) * (Z - z03)
fld[..., 0] = bx
fld[..., 1] = by
fld[..., 2] = bz
fig = mlab.figure(size=(1150, 850),
bgcolor=(1.0, 1.0, 1.0),
fgcolor=(0.0, 0.0, 0.0))
f1_src = mvi.add_field(bx)
f2_src = mvi.add_field(by)
f3_src = mvi.add_field(bz)
mlab.pipeline.iso_surface(f1_src, contours=[0.0],
opacity=1.0, color=(1.0, 0.0, 0.0))
mlab.pipeline.iso_surface(f2_src, contours=[0.0],
opacity=1.0, color=(0.0, 1.0, 0.0))
mlab.pipeline.iso_surface(f3_src, contours=[0.0],
opacity=1.0, color=(0.0, 0.0, 1.0))
mlab.axes()
mlab.show()
nullpt = cycalc.interp_trilin(fld, [(0.5, 0.5, 0.5)])
print("f(0.5, 0.5, 0.5):", nullpt)
ax1 = plt.subplot2grid((4, 3), (0, 0))
all_roots = []
positive_roots = []
ix = iy = iz = 0
for di, d in enumerate([0, -1]):
#### XY face
a1 = bx[iz + d, iy, ix]
b1 = bx[iz + d, iy, ix - 1] - a1
c1 = bx[iz + d, iy - 1, ix] - a1
d1 = bx[iz + d, iy - 1, ix - 1] - c1 - b1 - a1
a2 = by[iz + d, iy, ix]
b2 = by[iz + d, iy, ix - 1] - a2
c2 = by[iz + d, iy - 1, ix] - a2
d2 = by[iz + d, iy - 1, ix - 1] - c2 - b2 - a2
a3 = bz[iz + d, iy, ix]
b3 = bz[iz + d, iy, ix - 1] - a3
c3 = bz[iz + d, iy - 1, ix] - a3
d3 = bz[iz + d, iy - 1, ix - 1] - c3 - b3 - a3
roots1, roots2 = find_roots_face(a1, b1, c1, d1, a2, b2, c2, d2)
# for rt1, rt2 in zip(roots1, roots2):
# print("=")
# print("fx", a1 + b1 * rt1 + c1 * rt2 + d1 * rt1 * rt2)
# print("fy", a2 + b2 * rt1 + c2 * rt2 + d2 * rt1 * rt2)
# print("=")
# find f3 at the root points
f3 = np.empty_like(roots1)
markers = [None] * len(f3)
for i, rt1, rt2 in zip(count(), roots1, roots2):
f3[i] = a3 + b3 * rt1 + c3 * rt2 + d3 * rt1 * rt2
all_roots.append((rt1, rt2, d)) # switch order here
if f3[i] >= 0.0:
markers[i] = 'k^'
positive_roots.append((rt1, rt2, d)) # switch order here
else:
markers[i] = 'w^'
# rescale the roots to the original domain
roots1 = (xh - xl) * roots1 + xl
roots2 = (yh - yl) * roots2 + yl
xp = np.linspace(0.0, 1.0, nx)
# plt.subplot(121)
plt.subplot2grid((4, 3), (0 + 2 * di, 0), sharex=ax1, sharey=ax1)
mpl.plot(fld['x'], "z={0}i".format(d),
plot_opts="x={0}_{1},y={2}_{3},lin_-10_10".format(xl, xh, yl, yh))
y1 = - (a1 + b1 * xp) / (c1 + d1 * xp)
plt.plot(x, (yh - yl) * y1 + yl, 'k')
for i, xrt, yrt in zip(count(), roots1, roots2):
plt.plot(xrt, yrt, markers[i])
# plt.subplot(122)
plt.subplot2grid((4, 3), (1 + 2 * di, 0), sharex=ax1, sharey=ax1)
mpl.plot(fld['y'], "z={0}i".format(d),
plot_opts="x={0}_{1},y={2}_{3},lin_-10_10".format(xl, xh, yl, yh))
y2 = - (a2 + b2 * xp) / (c2 + d2 * xp)
plt.plot(x, (yh - yl) * y2 + yl, 'k')
for xrt, yrt in zip(roots1, roots2):
plt.plot(xrt, yrt, markers[i])
#### YZ face
a1 = bx[iz, iy, ix + d]
b1 = bx[iz, iy - 1, ix + d] - a1
c1 = bx[iz - 1, iy, ix + d] - a1
d1 = bx[iz - 1, iy - 1, ix + d] - c1 - b1 - a1
a2 = by[iz, iy, ix + d]
b2 = by[iz, iy - 1, ix + d] - a2
c2 = by[iz - 1, iy, ix + d] - a2
d2 = by[iz - 1, iy - 1, ix + d] - c2 - b2 - a2
a3 = bz[iz, iy, ix + d]
b3 = bz[iz, iy - 1, ix + d] - a3
c3 = bz[iz - 1, iy, ix + d] - a3
d3 = bz[iz - 1, iy - 1, ix + d] - c3 - b3 - a3
roots1, roots2 = find_roots_face(a1, b1, c1, d1, a2, b2, c2, d2)
# for rt1, rt2 in zip(roots1, roots2):
# print("=")
# print("fx", a1 + b1 * rt1 + c1 * rt2 + d1 * rt1 * rt2)
# print("fy", a2 + b2 * rt1 + c2 * rt2 + d2 * rt1 * rt2)
# print("=")
# find f3 at the root points
f3 = np.empty_like(roots1)
markers = [None] * len(f3)
for i, rt1, rt2 in zip(count(), roots1, roots2):
f3[i] = a3 + b3 * rt1 + c3 * rt2 + d3 * rt1 * rt2
all_roots.append((d, rt1, rt2)) # switch order here
if f3[i] >= 0.0:
markers[i] = 'k^'
positive_roots.append((d, rt1, rt2)) # switch order here
else:
markers[i] = 'w^'
# rescale the roots to the original domain
roots1 = (yh - yl) * roots1 + yl
roots2 = (zh - zl) * roots2 + zl
yp = np.linspace(0.0, 1.0, ny)
# plt.subplot(121)
plt.subplot2grid((4, 3), (0 + 2 * di, 1), sharex=ax1, sharey=ax1)
mpl.plot(fld['x'], "x={0}i".format(d),
plot_opts="x={0}_{1},y={2}_{3},lin_-10_10".format(yl, yh, zl, zh))
z1 = - (a1 + b1 * yp) / (c1 + d1 * yp)
plt.plot(y, (zh - zl) * z1 + zl, 'k')
for i, yrt, zrt in zip(count(), roots1, roots2):
plt.plot(yrt, zrt, markers[i])
# plt.subplot(122)
plt.subplot2grid((4, 3), (1 + 2 * di, 1), sharex=ax1, sharey=ax1)
mpl.plot(fld['y'], "x={0}i".format(d),
plot_opts="x={0}_{1},y={2}_{3},lin_-10_10".format(yl, yh, zl, zh))
z1 = - (a2 + b2 * yp) / (c2 + d2 * yp)
plt.plot(y, (zh - zl) * z1 + zl, 'k')
for i, yrt, zrt in zip(count(), roots1, roots2):
plt.plot(yrt, zrt, markers[i])
#### ZX face
a1 = bx[iz, iy + d, ix]
b1 = bx[iz - 1, iy + d, ix] - a1
c1 = bx[iz, iy + d, ix - 1] - a1
d1 = bx[iz - 1, iy + d, ix - 1] - c1 - b1 - a1
a2 = by[iz, iy + d, ix]
b2 = by[iz - 1, iy + d, ix] - a2
c2 = by[iz, iy + d, ix - 1] - a2
d2 = by[iz - 1, iy + d, ix - 1] - c2 - b2 - a2
a3 = bz[iz, iy + d, ix]
b3 = bz[iz - 1, iy + d, ix] - a3
c3 = bz[iz, iy + d, ix - 1] - a3
d3 = bz[iz - 1, iy + d, ix - 1] - c3 - b3 - a3
roots1, roots2 = find_roots_face(a1, b1, c1, d1, a2, b2, c2, d2)
# for rt1, rt2 in zip(roots1, roots2):
# print("=")
# print("fx", a1 + b1 * rt1 + c1 * rt2 + d1 * rt1 * rt2)
# print("fy", a2 + b2 * rt1 + c2 * rt2 + d2 * rt1 * rt2)
# print("=")
# find f3 at the root points
f3 = np.empty_like(roots1)
markers = [None] * len(f3)
for i, rt1, rt2 in zip(count(), roots1, roots2):
f3[i] = a3 + b3 * rt1 + c3 * rt2 + d3 * rt1 * rt2
all_roots.append((rt2, d, rt1)) # switch order here
if f3[i] >= 0.0:
markers[i] = 'k^'
positive_roots.append((rt2, d, rt1)) # switch order here
else:
markers[i] = 'w^'
# rescale the roots to the original domain
roots1 = (zh - zl) * roots1 + zl
roots2 = (xh - xl) * roots2 + xl
zp = np.linspace(0.0, 1.0, nz)
# plt.subplot(121)
plt.subplot2grid((4, 3), (0 + 2 * di, 2), sharex=ax1, sharey=ax1)
mpl.plot(fld['x'], "y={0}i".format(d),
plot_opts="x={0}_{1},y={2}_{3},lin_-10_10".format(xl, xh, zl, zh))
x1 = - (a1 + b1 * zp) / (c1 + d1 * zp)
plt.plot(z, (xh - xl) * x1 + xl, 'k')
for i, zrt, xrt in zip(count(), roots1, roots2):
plt.plot(xrt, zrt, markers[i])
# plt.subplot(121)
plt.subplot2grid((4, 3), (1 + 2 * di, 2), sharex=ax1, sharey=ax1)
mpl.plot(fld['y'], "y={0}i".format(d),
plot_opts="x={0}_{1},y={2}_{3},lin_-10_10".format(xl, xh, zl, zh))
x1 = - (a2 + b2 * zp) / (c2 + d2 * zp)
plt.plot(z, (xh - xl) * x1 + xl, 'k')
for i, zrt, xrt in zip(count(), roots1, roots2):
plt.plot(xrt, zrt, markers[i])
print("all:", len(all_roots), "positive:", len(positive_roots))
if len(all_roots) % 2 == 1:
print("something is fishy, there are an odd number of root points "
"on the surface of your cube, there is probably a degenerate "
"line or surface of nulls")
print("Null Point?", (len(positive_roots) % 2 == 1))
plt.show()
def main():
parser = argparse.ArgumentParser(description="Streamline a PSC file")
parser.add_argument("-t", default="2000",
help="which time to plot (finds closest)")
parser.add_argument('infile', nargs=1, help='input file')
args = vutil.common_argparse(parser)
# f = readers.load_file("pfd.020000.xdmf")
# ... or ...
# using this way of loading files, one probably wants just to give
# pfd.xdmf to the command line
f = readers.load_file(args.infile[0])
f.activate_time(args.t)
jz = f["jz"]
# recreate hx as a field of 0 to keep streamlines from moving in
# that direction
hx = field.zeros_like(jz, name="hx")
h1 = field.scalar_fields_to_vector([hx, f["hy"], f["hz"]], name="H",
_force_layout="Interlaced",
forget_source=True)
e = field.scalar_fields_to_vector([f["ex"], f["ey"], f["ez"]], name="E",
_force_layout="Interlaced",
forget_source=True)
# plot magnetic fields, just a sanity check
# ax1 = plt.subplot(211)
# mpl.plot(f["hy"], flip_plot=True)
# ax2 = plt.subplot(212, sharex=ax1, sharey=ax1)
# mpl.plot(f["hz"], flip_plot=True)
# mpl.mplshow()
# make a line of 30 seeds straight along the z axis (x, y, z ordered)
seeds1 = seed.Line((0.0, 0.0, 2.0), (1022.0, 0.0, 0.0), 60)
# set outer boundary limits for streamlines
ds = 0.005 # spatial step along the stream line curve
obound0 = np.array([1, -128, -1000], dtype=h1.dtype)
obound1 = np.array([1023, 128, 1000], dtype=h1.dtype)
# calc the streamlines
lines1, topo1 = streamline.streamlines(h1, seeds1, ds0=ds, maxit=200000,
obound0=obound0, obound1=obound1,
ibound=0.0)
# run with -v to see this
logger.info("Topology flags: {0}".format(topo1))
# rotate plot puts the z axis along the horizontal
flip_plot = True
mpl.plot(jz, flip_plot=flip_plot, plot_opts="lin_-.05_.05")
# mpl.plot_streamlines2d(lines1, "x", flip_plot=flip_plot, color='k')
plt.xlim([0, 1024])
plt.ylim([-128, 128])
plt.show()
# interpolate e onto each point of the first field line of lines1
e1 = cycalc.interp_trilin(e, seed.Point(lines1[0]))
print(e1.shape, lines1[0].shape)
plt.clf()
plt.plot(np.linspace(0, ds * e1.shape[0], e1.shape[0]), e1[:, 0])
plt.xlabel("length along field line")
plt.ylabel("Ex")
plt.show()
return 0
