def make_vector_fld():
x, y, z = make_grid()
f0 = viscid.empty((x, y, z), dtype=DTYPE, nr_comps=3, center='node')
viscid.fill_dipole(f0)
# seeds = viscid.Sphere(r=10.0, nphi=64, ntheta=32)
seeds = viscid.Sphere(r=10.0, nphi=32, ntheta=48)
return f0, seeds
def make_vector_fld():
x, y, z = make_grid()
f0 = viscid.empty((x, y, z), dtype=DTYPE, nr_comps=3, center='node')
viscid.fill_dipole(f0)
# seeds = viscid.Sphere(r=10.0, nphi=64, ntheta=32)
seeds = viscid.Sphere(r=10.0, nphi=32, ntheta=48)
return f0, seeds
def _main():
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument("--show", "--plot", action="store_true")
parser.add_argument("--interact", "-i", action="store_true")
args = vutil.common_argparse(parser)
f3d = viscid.load_file(os.path.join(sample_dir, 'sample_xdmf.3d.[0].xdmf'))
f_iono = viscid.load_file(os.path.join(sample_dir, "sample_xdmf.iof.[0].xdmf"))
b = f3d["b"]
v = f3d["v"]
pp = f3d["pp"]
e = f3d["e_cc"]
vlab.figure(size=(1280, 800), offscreen=not args.show)
##########################################################
# make b a dipole inside 3.1Re and set e = 0 inside 4.0Re
cotr = viscid.Cotr(time='1990-03-21T14:48', dip_tilt=0.0) # pylint: disable=not-callable
moment = cotr.get_dipole_moment(crd_system=b)
isphere_mask = viscid.make_spherical_mask(b, rmax=3.1)
viscid.fill_dipole(b, m=moment, mask=isphere_mask)
e_mask = viscid.make_spherical_mask(b, rmax=4.0)
viscid.set_in_region(e, 0.0, alpha=0.0, mask=e_mask, out=e)
######################################
# plot a scalar cut plane of pressure
pp_src = vlab.field2source(pp, center='node')
scp = vlab.scalar_cut_plane(pp_src, plane_orientation='z_axes', opacity=0.5,
transparent=True, view_controls=False,
cmap="inferno", logscale=True)
scp.implicit_plane.normal = [0, 0, -1]
scp.implicit_plane.origin = [0, 0, 0]
scp.enable_contours = True
scp.contour.filled_contours = True
scp.contour.number_of_contours = 64
cbar = vlab.colorbar(scp, title=pp.name, orientation='vertical')
cbar.scalar_bar_representation.position = (0.01, 0.13)
cbar.scalar_bar_representation.position2 = (0.08, 0.76)
######################################
# plot a vector cut plane of the flow
vcp = vlab.vector_cut_plane(v, scalars=pp_src, plane_orientation='z_axes',
view_controls=False, mode='arrow',
cmap='Greens_r')
vcp.implicit_plane.normal = [0, 0, -1]
vcp.implicit_plane.origin = [0, 0, 0]
##############################
# plot very faint isosurfaces
vx_src = vlab.field2source(v['x'], center='node')
iso = vlab.iso_surface(vx_src, contours=[0.0], opacity=0.008, cmap='Pastel1')
##############################################################
# calculate B field lines && topology in Viscid and plot them
seedsA = viscid.SphericalPatch([0, 0, 0], [2, 0, 1], 30, 15, r=5.0,
nalpha=5, nbeta=5)
seedsB = viscid.SphericalPatch([0, 0, 0], [1.9, 0, -20], 30, 15, r=5.0,
nalpha=1, nbeta=5)
seeds = np.concatenate([seedsA, seedsB], axis=1)
b_lines, topo = viscid.calc_streamlines(b, seeds, ibound=3.5,
obound0=[-25, -20, -20],
obound1=[15, 20, 20], wrap=True)
vlab.plot_lines(b_lines, scalars=viscid.topology2color(topo))
######################################################################
# plot a random circle at geosynchronus orbit with scalars colored
# by the Matplotlib viridis color map, just because we can; this is
# a useful toy for debugging
circle = viscid.Circle(p0=[0, 0, 0], r=6.618, n=128, endpoint=True)
scalar = np.sin(circle.as_local_coordinates().get_crd('phi'))
surf = vlab.plot_line(circle.get_points(), scalars=scalar, clim=0.8,
cmap="Spectral_r")
######################################################################
# Use Mayavi (VTK) to calculate field lines using an interactive seed
# These field lines are colored by E parallel
epar = viscid.project(e, b)
epar.name = "Epar"
bsl2 = vlab.streamline(b, epar, seedtype='plane', seed_resolution=4,
integration_direction='both', clim=(-0.05, 0.05))
# now tweak the VTK streamlines
bsl2.stream_tracer.maximum_propagation = 20.
bsl2.seed.widget.origin = [-11, -5.0, -2.0]
bsl2.seed.widget.point1 = [-11, 5.0, -2.0]
bsl2.seed.widget.point2 = [-11.0, -5.0, 2.0]
bsl2.streamline_type = 'tube'
bsl2.tube_filter.radius = 0.03
bsl2.stop() # this stop/start was a hack to get something to update
bsl2.start()
bsl2.seed.widget.enabled = False
cbar = vlab.colorbar(bsl2, title=epar.name, label_fmt='%.3f',
orientation='horizontal')
cbar.scalar_bar_representation.position = (0.15, 0.01)
cbar.scalar_bar_representation.position2 = (0.72, 0.10)
###############################################################
# Make a contour at the open-closed boundary in the ionosphere
seeds_iono = viscid.Sphere(r=1.063, pole=-moment, ntheta=256, nphi=256,
thetalim=(0, 180), philim=(0, 360), crd_system=b)
_, topo_iono = viscid.calc_streamlines(b, seeds_iono, ibound=1.0,
nr_procs='all',
output=viscid.OUTPUT_TOPOLOGY)
topo_iono = np.log2(topo_iono)
m = vlab.mesh_from_seeds(seeds_iono, scalars=topo_iono, opacity=1.0,
clim=(0, 3), color=(0.992, 0.445, 0.0))
m.enable_contours = True
m.actor.property.line_width = 4.0
m.contour.number_of_contours = 4
####################################################################
# Plot the ionosphere, note that the sample data has the ionosphere
# at a different time, so the open-closed boundary found above
# will not be consistant with the field aligned currents
fac_tot = 1e9 * f_iono['fac_tot']
m = vlab.plot_ionosphere(fac_tot, bounding_lat=30.0, vmin=-300, vmax=300,
opacity=0.75, rotate=cotr, crd_system=b)
m.actor.property.backface_culling = True
########################################################################
# Add some markers for earth, i.e., real earth, and dayside / nightside
# representation
vlab.plot_blue_marble(r=1.0, lines=False, ntheta=64, nphi=128,
rotate=cotr, crd_system=b)
# now shade the night side with a transparent black hemisphere
vlab.plot_earth_3d(radius=1.01, night_only=True, opacity=0.5, crd_system=b)
####################
# Finishing Touches
# vlab.axes(pp_src, nb_labels=5)
oa = vlab.orientation_axes()
oa.marker.set_viewport(0.75, 0.75, 1.0, 1.0)
# note that resize won't work if the current figure has the
# off_screen_rendering flag set
# vlab.resize([1200, 800])
vlab.view(azimuth=45, elevation=70, distance=35.0, focalpoint=[-2, 0, 0])
##############
# Save Figure
# print("saving png")
# vlab.savefig('mayavi_msphere_sample.png')
# print("saving x3d")
# # x3d files can be turned into COLLADA files with meshlab, and
# # COLLADA (.dae) files can be opened in OS X's preview
# #
# # IMPORTANT: for some reason, using bounding_lat in vlab.plot_ionosphere
# # causes a segfault when saving x3d files
# #
# vlab.savefig('mayavi_msphere_sample.x3d')
# print("done")
vlab.savefig(next_plot_fname(__file__))
###########################
# Interact Programatically
if args.interact:
vlab.interact()
#######################
# Interact Graphically
if args.show:
vlab.show()
try:
vlab.mlab.close()
except AttributeError:
pass
return 0
def main():
mhd_type = "C3"
make_plots = 1
mhd_type = mhd_type.upper()
if mhd_type.startswith("C"):
if mhd_type in ("C",):
f = viscid.load_file("$WORK/tmedium/*.3d.[-1].xdmf")
elif mhd_type in ("C2", "C3"):
f = viscid.load_file("$WORK/tmedium2/*.3d.[-1].xdmf")
else:
raise ValueError()
catol = 1e-8
rtol = 2e-6
elif mhd_type in ("F", "FORTRAN"):
f = viscid.load_file("$WORK/tmedium3/*.3df.[-1]")
catol = 1e-8
rtol = 7e-2
else:
raise ValueError()
b = f['b_cc']
b1 = f['b_fc']
e_cc = f['e_cc']
e_ec = f['e_ec']
# divb = f['divB']
# viscid.interact()
if True:
bD = viscid.empty_like(b)
bD.data = np.array(b.data)
b1D = viscid.empty_like(b1)
b1D.data = np.array(b1.data)
mask5 = viscid.make_spherical_mask(bD, rmax=3.5)
mask1_5 = viscid.make_spherical_mask(bD, rmax=1.5)
viscid.fill_dipole(bD, mask=mask5)
viscid.set_in_region(bD, bD, 0.0, 0.0, mask=mask1_5, out=bD)
# compare_vectors(_b, bD, make_plots=True)
mask5 = viscid.make_spherical_mask(b1D, rmax=3.5)
mask1_5 = viscid.make_spherical_mask(b1D, rmax=1.5)
viscid.fill_dipole(b1D, mask=mask5)
viscid.set_in_region(b1D, b1D, 0.0, 0.0, mask=mask1_5, out=b1D)
compare_vectors(bD["x=1:-1, y=1:-1, z=1:-1"], b1D.as_cell_centered(),
make_plots=True)
# plt.clf()
# dkwargs = dict(symmetric=True, earth=True, clim=(-1e2, 1e2))
# ax1 = plt.subplot(311)
# vlt.plot(viscid.div(b1)['y=0j'], **dkwargs)
# plt.subplot(312, sharex=ax1, sharey=ax1)
# vlt.plot(viscid.div(b)['y=0j'], **dkwargs)
# plt.subplot(313, sharex=ax1, sharey=ax1)
# vlt.plot(viscid.div(b1D)['y=0j'], **dkwargs)
# vlt.show()
bD = b1D = mask5 = mask1_5 = None
# straight up interpolate b1 to cc crds and compare with b
if True:
b1_cc = viscid.interp_trilin(b1, b).as_flat()
viscid.set_in_region(b, b, alpha=0.0, beta=0.0, out=b,
mask=viscid.make_spherical_mask(b, rmax=5.0))
viscid.set_in_region(b1_cc, b1_cc, alpha=0.0, beta=0.0, out=b1_cc,
mask=viscid.make_spherical_mask(b1_cc, rmax=5.0))
compare_vectors(b, b1_cc, make_plots=True)
# make div?
if True:
# make seeds for 1.5x supersampling b1
n = 128
seeds = viscid.Volume((5.1, -0.02, -5.0), (12.0, 0.02, 5.0), (n, 3, n))
# do interpolation onto new seeds
b2 = viscid.interp_trilin(b1, seeds)
div_b = viscid.div(b)
div_b1 = viscid.div(b1)
div_b2 = viscid.div(b2)
viscid.set_in_region(div_b, div_b, alpha=0.0, beta=0.0, out=div_b,
mask=viscid.make_spherical_mask(div_b, rmax=5.0))
viscid.set_in_region(div_b1, div_b1, alpha=0.0, beta=0.0, out=div_b1,
mask=viscid.make_spherical_mask(div_b1, rmax=5.0))
viscid.set_in_region(div_b2, div_b2, alpha=0.0, beta=0.0, out=div_b2,
mask=viscid.make_spherical_mask(div_b2, rmax=5.0))
viscid.set_in_region(divb, divb, alpha=0.0, beta=0.0, out=divb,
mask=viscid.make_spherical_mask(divb, rmax=5.0))
plt.clf()
ax1 = vlt.subplot(311)
vlt.plot(div_b['y=0j'], symmetric=True, earth=True)
vlt.subplot(312, sharex=ax1, sharey=ax1)
# vlt.plot(div_b1['y=0j'], symmetric=True, earth=True)
vlt.plot(div_b2['y=0j'], symmetric=True, earth=True)
vlt.subplot(313, sharex=ax1, sharey=ax1)
vlt.plot(divb['y=0j'], symmetric=True, earth=True)
vlt.show()
return 0
def main():
mhd_type = "C3"
make_plots = 1
mhd_type = mhd_type.upper()
if mhd_type.startswith("C"):
if mhd_type in ("C", ):
f = viscid.load_file("$WORK/tmedium/*.3d.[-1].xdmf")
elif mhd_type in ("C2", "C3"):
f = viscid.load_file("$WORK/tmedium2/*.3d.[-1].xdmf")
else:
raise ValueError()
catol = 1e-8
rtol = 2e-6
elif mhd_type in ("F", "FORTRAN"):
f = viscid.load_file("$WORK/tmedium3/*.3df.[-1]")
catol = 1e-8
rtol = 7e-2
else:
raise ValueError()
b = f['b_cc']
b1 = f['b_fc']
e_cc = f['e_cc']
e_ec = f['e_ec']
# divb = f['divB']
# viscid.interact()
if True:
bD = viscid.empty_like(b)
bD.data = np.array(b.data)
b1D = viscid.empty_like(b1)
b1D.data = np.array(b1.data)
mask5 = viscid.make_spherical_mask(bD, rmax=3.5)
mask1_5 = viscid.make_spherical_mask(bD, rmax=1.5)
viscid.fill_dipole(bD, mask=mask5)
viscid.set_in_region(bD, bD, 0.0, 0.0, mask=mask1_5, out=bD)
# compare_vectors(_b, bD, make_plots=True)
mask5 = viscid.make_spherical_mask(b1D, rmax=3.5)
mask1_5 = viscid.make_spherical_mask(b1D, rmax=1.5)
viscid.fill_dipole(b1D, mask=mask5)
viscid.set_in_region(b1D, b1D, 0.0, 0.0, mask=mask1_5, out=b1D)
compare_vectors(bD["x=1:-1, y=1:-1, z=1:-1"],
b1D.as_cell_centered(),
make_plots=True)
# plt.clf()
# dkwargs = dict(symmetric=True, earth=True, clim=(-1e2, 1e2))
# ax1 = plt.subplot(311)
# vlt.plot(viscid.div(b1)['y=0j'], **dkwargs)
# plt.subplot(312, sharex=ax1, sharey=ax1)
# vlt.plot(viscid.div(b)['y=0j'], **dkwargs)
# plt.subplot(313, sharex=ax1, sharey=ax1)
# vlt.plot(viscid.div(b1D)['y=0j'], **dkwargs)
# vlt.show()
bD = b1D = mask5 = mask1_5 = None
# straight up interpolate b1 to cc crds and compare with b
if True:
b1_cc = viscid.interp_trilin(b1, b).as_flat()
viscid.set_in_region(b,
b,
alpha=0.0,
beta=0.0,
out=b,
mask=viscid.make_spherical_mask(b, rmax=5.0))
viscid.set_in_region(b1_cc,
b1_cc,
alpha=0.0,
beta=0.0,
out=b1_cc,
mask=viscid.make_spherical_mask(b1_cc, rmax=5.0))
compare_vectors(b, b1_cc, make_plots=True)
# make div?
if True:
# make seeds for 1.5x supersampling b1
n = 128
seeds = viscid.Volume((5.1, -0.02, -5.0), (12.0, 0.02, 5.0), (n, 3, n))
# do interpolation onto new seeds
b2 = viscid.interp_trilin(b1, seeds)
div_b = viscid.div(b)
div_b1 = viscid.div(b1)
div_b2 = viscid.div(b2)
viscid.set_in_region(div_b,
div_b,
alpha=0.0,
beta=0.0,
out=div_b,
mask=viscid.make_spherical_mask(div_b, rmax=5.0))
viscid.set_in_region(div_b1,
div_b1,
alpha=0.0,
beta=0.0,
out=div_b1,
mask=viscid.make_spherical_mask(div_b1, rmax=5.0))
viscid.set_in_region(div_b2,
div_b2,
alpha=0.0,
beta=0.0,
out=div_b2,
mask=viscid.make_spherical_mask(div_b2, rmax=5.0))
viscid.set_in_region(divb,
divb,
alpha=0.0,
beta=0.0,
out=divb,
mask=viscid.make_spherical_mask(divb, rmax=5.0))
plt.clf()
ax1 = vlt.subplot(311)
vlt.plot(div_b['y=0j'], symmetric=True, earth=True)
vlt.subplot(312, sharex=ax1, sharey=ax1)
# vlt.plot(div_b1['y=0j'], symmetric=True, earth=True)
vlt.plot(div_b2['y=0j'], symmetric=True, earth=True)
vlt.subplot(313, sharex=ax1, sharey=ax1)
vlt.plot(divb['y=0j'], symmetric=True, earth=True)
vlt.show()
return 0
def main():
mhd_type = "C"
make_plots = 1
mhd_type = mhd_type.upper()
if mhd_type.startswith("C"):
if mhd_type in ("C",):
f = viscid.load_file("$WORK/tmedium/*.3d.[-1].xdmf")
elif mhd_type in ("C2", "C3"):
f = viscid.load_file("$WORK/tmedium2/*.3d.[-1].xdmf")
else:
raise ValueError()
catol = 1e-8
rtol = 2e-6
elif mhd_type in ("F", "FORTRAN"):
f = viscid.load_file("$WORK/tmedium3/*.3df.[-1]")
catol = 1e-8
rtol = 7e-2
else:
raise ValueError()
do_fill_dipole = True
gslc = "x=-21.2j:12j, y=-11j:11j, z=-11j:11j"
b = f['b_cc'][gslc]
b1 = f['b_fc'][gslc]
e_cc = f['e_cc'][gslc]
e_ec = f['e_ec'][gslc]
if do_fill_dipole:
mask = viscid.make_spherical_mask(b, rmax=3.5)
viscid.fill_dipole(b, mask=mask)
mask = viscid.make_spherical_mask(b1, rmax=3.5)
viscid.fill_dipole(b1, mask=mask)
mask = None
# seeds = viscid.SphericalCap(r=1.02, ntheta=64, nphi=32, angle0=17, angle=20,
# philim=(100, 260), roll=-180.0)
# seeds = viscid.SphericalCap(r=1.02, ntheta=64, nphi=32, angle0=17, angle=20,
# philim=(0, 10), roll=0.0)
seedsN = viscid.Sphere(r=1.02, ntheta=16, nphi=16, thetalim=(15, 25),
philim=(0, 300), crd_system=b)
seedsS = viscid.Sphere(r=1.02, ntheta=16, nphi=16, thetalim=(155, 165),
philim=(0, 300), crd_system=b)
bl_kwargs = dict(ibound=0.9, obound0=(-20, -10, -10), obound1=(11, 10, 10))
# blines_cc, topo_cc = viscid.streamlines(b, seeds, **bl_kwargs)
blinesN_fc, topoN_fc = viscid.streamlines(b1, seedsN, **bl_kwargs)
_, topoS_fc = viscid.streamlines(b1, seedsS, output=viscid.OUTPUT_TOPOLOGY,
**bl_kwargs)
if True:
from viscid.plot import vlab
mesh = vlab.mesh_from_seeds(seedsN, scalars=topoN_fc)
mesh.actor.property.backface_culling = True
# vlab.plot_lines(blines_cc, scalars="#000000", tube_radius=0.03)
vlab.plot_lines(blinesN_fc, scalars=viscid.topology2color(topoN_fc),
opacity=0.7)
vlab.plot_blue_marble(r=1.0)
vlab.plot_earth_3d(radius=1.01, crd_system=b, night_only=True,
opacity=0.5)
vlab.show()
if True:
vlt.subplot(121, projection='polar')
vlt.plot(topoN_fc)
vlt.subplot(122, projection='polar')
vlt.plot(topoS_fc)
vlt.show()
return 0
def main():
mhd_type = "C"
make_plots = 1
test_fc = 1
test_ec = 1
test_div = 1
test_interp = 1
test_streamline = 1
mhd_type = mhd_type.upper()
if mhd_type.startswith("C"):
if mhd_type in ("C",):
f = viscid.load_file("$WORK/tmedium/*.3d.[-1].xdmf")
elif mhd_type in ("C2", "C3"):
f = viscid.load_file("$WORK/tmedium2/*.3d.[-1].xdmf")
else:
raise ValueError()
catol = 1e-8
rtol = 5e-6
elif mhd_type in ("F", "FORTRAN"):
f = viscid.load_file("$WORK/tmedium3/*.3df.[-1]")
catol = 1e-8
rtol = 7e-2
else:
raise ValueError()
ISLICE = slice(None)
# ISLICE = 'y=0j:0.15j'
# #################
# # test out fc2cc
if test_fc:
b = f['b'][ISLICE]
b1 = f['b1'][ISLICE]
compare_vectors(b, b1, viscid.fc2cc, catol=catol, rtol=rtol,
make_plots=make_plots)
#################
# test out ec2cc
if test_ec:
e_cc = f['e_cc'][ISLICE]
e_ec = f['e_ec'][ISLICE]
if mhd_type not in ("F", "FORTRAN"):
compare_vectors(e_cc, e_ec, viscid.ec2cc, catol=catol, rtol=rtol,
make_plots=make_plots)
#################
# test out divfc
# Note: Relative error on Div B is meaningless b/c the coordinates
# are not the same up to order (dx/4) I think. You can see this
# since (fcdiv - divb_trimmed) is both noisy and stripy
if test_div:
bnd = 0
if mhd_type not in ("F", "FORTRAN"):
b1 = f['b1'][ISLICE]
divb = f['divB'][ISLICE]
if bnd:
trimmed = divb
else:
trimmed = divb['x=1:-1, y=1:-1, z=1:-1']
b1mag = viscid.magnitude(viscid.fc2cc(b1, bnd=bnd))
divb1 = viscid.div_fc(b1, bnd=bnd)
viscid.set_in_region(trimmed, trimmed, alpha=0.0, beta=0.0, out=trimmed,
mask=viscid.make_spherical_mask(trimmed, rmax=5.0))
viscid.set_in_region(divb1, divb1, alpha=0.0, beta=0.0, out=divb1,
mask=viscid.make_spherical_mask(divb1, rmax=5.0))
reldiff = (divb1 - trimmed) / b1mag
reldiff = reldiff["x=1:-1, y=1:-1, z=1:-1"]
reldiff.name = divb1.name + " - " + trimmed.name
reldiff.pretty_name = divb1.pretty_name + " - " + trimmed.pretty_name
abs_max_rel_diff = np.nanmax(np.abs(reldiff))
max_crd_diff = [0.0] * 3
for i, d in enumerate('xyz'):
max_crd_diff[i] = np.max(trimmed.get_crd(d) - divb1.get_crd(d))
print("divB max absolute relative diff: {0:.3e} "
"(crds: X: {1[0]:.3e}, Y: {1[1]:.3e}, Z: {1[2]:.3e})"
"".format(abs_max_rel_diff, max_crd_diff))
# plot differences?
if make_plots:
ax1 = plt.subplot(311)
vlt.plot(divb['y=0j'], symmetric=True, earth=True)
plt.subplot(312, sharex=ax1, sharey=ax1)
vlt.plot(divb1['y=0j'], symmetric=True, earth=True)
plt.subplot(313, sharex=ax1, sharey=ax1)
vlt.plot(reldiff['y=0j'], symmetric=True, earth=True)
vlt.show()
# Since the coordinates will be different by order dx^2 (i think),
# there is no way to compare the divB from simulation with the
# one we get here. However, they should be the same up to a few %, and
# down to noise level with stripes of enhanced noise. These stripes
# are the errors in the coordinate values (since the output only
# gives us weird nc = averaged cc locations)
#
# if abs_max_rel_diff > rtol or np.any(np.abs(max_crd_diff) > catol):
# raise RuntimeError("Tolerance exceeded on divB calculation")
if test_streamline:
b_cc = f['b_cc']['x=-40j:12j, y=-15j:15j, z=-15j:15j']
b_fc = f['b_fc']['x=-40j:12j, y=-15j:15j, z=-15j:15j']
cotr = viscid.cotr.Cotr()
r_mask = 3.0
# set b_cc to dipole inside some sphere
isphere_mask = viscid.make_spherical_mask(b_cc, rmax=r_mask)
moment = cotr.get_dipole_moment(crd_system=b_cc)
viscid.fill_dipole(b_cc, m=moment, mask=isphere_mask)
# set b_fc to dipole inside some sphere
isphere_mask = viscid.make_spherical_mask(b_fc, rmax=r_mask)
moment = cotr.get_dipole_moment(crd_system=b_fc)
viscid.fill_dipole(b_fc, m=moment, mask=isphere_mask)
seeds = viscid.Volume([-10, 0, -5], [10, 0, 5], (16, 1, 3))
sl_kwargs = dict(ibound=1.0, method=viscid.EULER1A)
lines_cc, topo_cc = viscid.calc_streamlines(b_cc, seeds, **sl_kwargs)
lines_fc, topo_fc = viscid.calc_streamlines(b_fc, seeds, **sl_kwargs)
if make_plots:
plt.figure(figsize=(10, 6))
ax0 = plt.subplot(211)
topo_cc_colors = viscid.topology2color(topo_cc)
vlt.plot(f['pp']['y=0j'], logscale=True, earth=True, cmap='plasma')
vlt.plot2d_lines(lines_cc, topo_cc_colors, symdir='y')
ax0 = plt.subplot(212, sharex=ax0, sharey=ax0)
topo_fc_colors = viscid.topology2color(topo_fc)
vlt.plot(f['pp']['y=0j'], logscale=True, earth=True, cmap='plasma')
vlt.plot2d_lines(lines_fc, topo_fc_colors, symdir='y')
plt.xlim(-20, 10)
plt.ylim(-10, 10)
vlt.auto_adjust_subplots()
vlt.show()
if test_interp:
# test interpolation with E . B / B
b_cc = f['b_cc']
b_fc = f['b_fc']
e_cc = f['e_cc']
e_ec = f['e_ec']
cotr = viscid.cotr.Cotr()
r_mask = 3.0
# set b_cc to dipole inside some sphere
isphere_mask = viscid.make_spherical_mask(b_cc, rmax=r_mask)
moment = cotr.get_dipole_moment(crd_system=b_cc)
viscid.fill_dipole(b_cc, m=moment, mask=isphere_mask)
# set b_fc to dipole inside some sphere
isphere_mask = viscid.make_spherical_mask(b_fc, rmax=r_mask)
moment = cotr.get_dipole_moment(crd_system=b_fc)
viscid.fill_dipole(b_fc, m=moment, mask=isphere_mask)
# zero out e_cc inside some sphere
viscid.set_in_region(e_cc, e_cc, alpha=0.0, beta=0.0, out=e_cc,
mask=viscid.make_spherical_mask(e_cc, rmax=r_mask))
# zero out e_ec inside some sphere
viscid.set_in_region(e_ec, e_ec, alpha=0.0, beta=0.0, out=e_ec,
mask=viscid.make_spherical_mask(e_ec, rmax=r_mask))
tmp = viscid.empty([np.linspace(-10, 10, 64), np.linspace(-10, 10, 64),
np.linspace(-10, 10, 64)], center="Cell")
b_cc_interp = viscid.interp_linear(b_cc, tmp)
b_fc_interp = viscid.interp_linear(b_fc, tmp)
e_cc_interp = viscid.interp_linear(e_cc, tmp)
e_ec_interp = viscid.interp_linear(e_ec, tmp)
epar_cc = viscid.dot(e_cc_interp, b_cc_interp) / viscid.magnitude(b_cc_interp)
epar_ecfc = viscid.dot(e_ec_interp, b_fc_interp) / viscid.magnitude(b_fc_interp)
if make_plots:
# plt.figure()
# ax0 = plt.subplot(121)
# vlt.plot(b_cc['x']['y=0j'], clim=(-40, 40))
# plt.subplot(122, sharex=ax0, sharey=ax0)
# vlt.plot(b_fc['x']['y=0j'], clim=(-40, 40))
# vlt.show()
plt.figure(figsize=(14, 5))
ax0 = plt.subplot(131)
vlt.plot(epar_cc['y=0j'], symmetric=True, cbarlabel="Epar CC")
plt.subplot(132, sharex=ax0, sharey=ax0)
vlt.plot(epar_ecfc['y=0j'], symmetric=True, cbarlabel="Epar ECFC")
plt.subplot(133, sharex=ax0, sharey=ax0)
vlt.plot(((epar_cc - epar_ecfc) / epar_cc)['y=0j'], clim=(-10, 10),
cbarlabel="Rel Diff")
vlt.auto_adjust_subplots()
vlt.show()
return 0
def main():
mhd_type = "C"
make_plots = 1
test_fc = 1
test_ec = 1
test_div = 1
test_interp = 1
test_streamline = 1
mhd_type = mhd_type.upper()
if mhd_type.startswith("C"):
if mhd_type in ("C", ):
f = viscid.load_file("$WORK/tmedium/*.3d.[-1].xdmf")
elif mhd_type in ("C2", "C3"):
f = viscid.load_file("$WORK/tmedium2/*.3d.[-1].xdmf")
else:
raise ValueError()
catol = 1e-8
rtol = 5e-6
elif mhd_type in ("F", "FORTRAN"):
f = viscid.load_file("$WORK/tmedium3/*.3df.[-1]")
catol = 1e-8
rtol = 7e-2
else:
raise ValueError()
ISLICE = slice(None)
# ISLICE = 'y=0f:0.15f'
# #################
# # test out fc2cc
if test_fc:
b = f['b'][ISLICE]
b1 = f['b1'][ISLICE]
compare_vectors(b,
b1,
viscid.fc2cc,
catol=catol,
rtol=rtol,
make_plots=make_plots)
#################
# test out ec2cc
if test_ec:
e_cc = f['e_cc'][ISLICE]
e_ec = f['e_ec'][ISLICE]
if mhd_type not in ("F", "FORTRAN"):
compare_vectors(e_cc,
e_ec,
viscid.ec2cc,
catol=catol,
rtol=rtol,
make_plots=make_plots)
#################
# test out divfc
# Note: Relative error on Div B is meaningless b/c the coordinates
# are not the same up to order (dx/4) I think. You can see this
# since (fcdiv - divb_trimmed) is both noisy and stripy
if test_div:
bnd = 0
if mhd_type not in ("F", "FORTRAN"):
b1 = f['b1'][ISLICE]
divb = f['divB'][ISLICE]
if bnd:
trimmed = divb
else:
trimmed = divb['x=1:-1, y=1:-1, z=1:-1']
b1mag = viscid.magnitude(viscid.fc2cc(b1, bnd=bnd))
divb1 = viscid.div_fc(b1, bnd=bnd)
viscid.set_in_region(trimmed,
trimmed,
alpha=0.0,
beta=0.0,
out=trimmed,
mask=viscid.make_spherical_mask(trimmed,
rmax=5.0))
viscid.set_in_region(divb1,
divb1,
alpha=0.0,
beta=0.0,
out=divb1,
mask=viscid.make_spherical_mask(divb1,
rmax=5.0))
reldiff = (divb1 - trimmed) / b1mag
reldiff = reldiff["x=1:-1, y=1:-1, z=1:-1"]
reldiff.name = divb1.name + " - " + trimmed.name
reldiff.pretty_name = divb1.pretty_name + " - " + trimmed.pretty_name
abs_max_rel_diff = np.nanmax(np.abs(reldiff))
max_crd_diff = [0.0] * 3
for i, d in enumerate('xyz'):
max_crd_diff[i] = np.max(trimmed.get_crd(d) - divb1.get_crd(d))
print("divB max absolute relative diff: {0:.3e} "
"(crds: X: {1[0]:.3e}, Y: {1[1]:.3e}, Z: {1[2]:.3e})"
"".format(abs_max_rel_diff, max_crd_diff))
# plot differences?
if make_plots:
ax1 = plt.subplot(311)
vlt.plot(divb['y=0f'], symmetric=True, earth=True)
plt.subplot(312, sharex=ax1, sharey=ax1)
vlt.plot(divb1['y=0f'], symmetric=True, earth=True)
plt.subplot(313, sharex=ax1, sharey=ax1)
vlt.plot(reldiff['y=0f'], symmetric=True, earth=True)
vlt.show()
# Since the coordinates will be different by order dx^2 (i think),
# there is no way to compare the divB from simulation with the
# one we get here. However, they should be the same up to a few %, and
# down to noise level with stripes of enhanced noise. These stripes
# are the errors in the coordinate values (since the output only
# gives us weird nc = averaged cc locations)
#
# if abs_max_rel_diff > rtol or np.any(np.abs(max_crd_diff) > catol):
# raise RuntimeError("Tolerance exceeded on divB calculation")
if test_streamline:
b_cc = f['b_cc']['x=-40f:12f, y=-15f:15f, z=-15f:15f']
b_fc = f['b_fc']['x=-40f:12f, y=-15f:15f, z=-15f:15f']
cotr = viscid.cotr.Cotr()
r_mask = 3.0
# set b_cc to dipole inside some sphere
isphere_mask = viscid.make_spherical_mask(b_cc, rmax=r_mask)
moment = cotr.get_dipole_moment(crd_system=b_cc)
viscid.fill_dipole(b_cc, m=moment, mask=isphere_mask)
# set b_fc to dipole inside some sphere
isphere_mask = viscid.make_spherical_mask(b_fc, rmax=r_mask)
moment = cotr.get_dipole_moment(crd_system=b_fc)
viscid.fill_dipole(b_fc, m=moment, mask=isphere_mask)
seeds = viscid.Volume([-10, 0, -5], [10, 0, 5], (16, 1, 3))
sl_kwargs = dict(ibound=1.0, method=viscid.EULER1A)
lines_cc, topo_cc = viscid.calc_streamlines(b_cc, seeds, **sl_kwargs)
lines_fc, topo_fc = viscid.calc_streamlines(b_fc, seeds, **sl_kwargs)
if make_plots:
plt.figure(figsize=(10, 6))
ax0 = plt.subplot(211)
topo_cc_colors = viscid.topology2color(topo_cc)
vlt.plot(f['pp']['y=0f'], logscale=True, earth=True, cmap='plasma')
vlt.plot2d_lines(lines_cc, topo_cc_colors, symdir='y')
ax0 = plt.subplot(212, sharex=ax0, sharey=ax0)
topo_fc_colors = viscid.topology2color(topo_fc)
vlt.plot(f['pp']['y=0f'], logscale=True, earth=True, cmap='plasma')
vlt.plot2d_lines(lines_fc, topo_fc_colors, symdir='y')
plt.xlim(-20, 10)
plt.ylim(-10, 10)
vlt.auto_adjust_subplots()
vlt.show()
if test_interp:
# test interpolation with E . B / B
b_cc = f['b_cc']
b_fc = f['b_fc']
e_cc = f['e_cc']
e_ec = f['e_ec']
cotr = viscid.cotr.Cotr()
r_mask = 3.0
# set b_cc to dipole inside some sphere
isphere_mask = viscid.make_spherical_mask(b_cc, rmax=r_mask)
moment = cotr.get_dipole_moment(crd_system=b_cc)
viscid.fill_dipole(b_cc, m=moment, mask=isphere_mask)
# set b_fc to dipole inside some sphere
isphere_mask = viscid.make_spherical_mask(b_fc, rmax=r_mask)
moment = cotr.get_dipole_moment(crd_system=b_fc)
viscid.fill_dipole(b_fc, m=moment, mask=isphere_mask)
# zero out e_cc inside some sphere
viscid.set_in_region(e_cc,
e_cc,
alpha=0.0,
beta=0.0,
out=e_cc,
mask=viscid.make_spherical_mask(e_cc,
rmax=r_mask))
# zero out e_ec inside some sphere
viscid.set_in_region(e_ec,
e_ec,
alpha=0.0,
beta=0.0,
out=e_ec,
mask=viscid.make_spherical_mask(e_ec,
rmax=r_mask))
tmp = viscid.empty([
np.linspace(-10, 10, 64),
np.linspace(-10, 10, 64),
np.linspace(-10, 10, 64)
],
center="Cell")
b_cc_interp = viscid.interp_linear(b_cc, tmp)
b_fc_interp = viscid.interp_linear(b_fc, tmp)
e_cc_interp = viscid.interp_linear(e_cc, tmp)
e_ec_interp = viscid.interp_linear(e_ec, tmp)
epar_cc = viscid.dot(e_cc_interp,
b_cc_interp) / viscid.magnitude(b_cc_interp)
epar_ecfc = viscid.dot(e_ec_interp,
b_fc_interp) / viscid.magnitude(b_fc_interp)
if make_plots:
# plt.figure()
# ax0 = plt.subplot(121)
# vlt.plot(b_cc['x']['y=0f'], clim=(-40, 40))
# plt.subplot(122, sharex=ax0, sharey=ax0)
# vlt.plot(b_fc['x']['y=0f'], clim=(-40, 40))
# vlt.show()
plt.figure(figsize=(14, 5))
ax0 = plt.subplot(131)
vlt.plot(epar_cc['y=0f'], symmetric=True, cbarlabel="Epar CC")
plt.subplot(132, sharex=ax0, sharey=ax0)
vlt.plot(epar_ecfc['y=0f'], symmetric=True, cbarlabel="Epar ECFC")
plt.subplot(133, sharex=ax0, sharey=ax0)
vlt.plot(((epar_cc - epar_ecfc) / epar_cc)['y=0f'],
clim=(-10, 10),
cbarlabel="Rel Diff")
vlt.auto_adjust_subplots()
vlt.show()
return 0
def _main():
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument("--show", "--plot", action="store_true")
parser.add_argument("--interact", "-i", action="store_true")
args = vutil.common_argparse(parser)
f3d = viscid.load_file(os.path.join(sample_dir, 'sample_xdmf.3d.[0].xdmf'))
f_iono = viscid.load_file(
os.path.join(sample_dir, "sample_xdmf.iof.[0].xdmf"))
b = f3d["b"]
v = f3d["v"]
pp = f3d["pp"]
e = f3d["e_cc"]
vlab.mlab.options.offscreen = not args.show
vlab.figure(size=(1280, 800))
##########################################################
# make b a dipole inside 3.1Re and set e = 0 inside 4.0Re
cotr = viscid.Cotr(time='1990-03-21T14:48', dip_tilt=0.0) # pylint: disable=not-callable
moment = cotr.get_dipole_moment(crd_system=b)
isphere_mask = viscid.make_spherical_mask(b, rmax=3.1)
viscid.fill_dipole(b, m=moment, mask=isphere_mask)
e_mask = viscid.make_spherical_mask(b, rmax=4.0)
viscid.set_in_region(e, 0.0, alpha=0.0, mask=e_mask, out=e)
######################################
# plot a scalar cut plane of pressure
pp_src = vlab.field2source(pp, center='node')
scp = vlab.scalar_cut_plane(pp_src,
plane_orientation='z_axes',
opacity=0.5,
transparent=True,
view_controls=False,
cmap="inferno",
logscale=True)
scp.implicit_plane.normal = [0, 0, -1]
scp.implicit_plane.origin = [0, 0, 0]
scp.enable_contours = True
scp.contour.filled_contours = True
scp.contour.number_of_contours = 64
cbar = vlab.colorbar(scp, title=pp.name, orientation='vertical')
cbar.scalar_bar_representation.position = (0.01, 0.13)
cbar.scalar_bar_representation.position2 = (0.08, 0.76)
######################################
# plot a vector cut plane of the flow
vcp = vlab.vector_cut_plane(v,
scalars=pp_src,
plane_orientation='z_axes',
view_controls=False,
mode='arrow',
cmap='Greens_r')
vcp.implicit_plane.normal = [0, 0, -1]
vcp.implicit_plane.origin = [0, 0, 0]
##############################
# plot very faint isosurfaces
vx_src = vlab.field2source(v['x'], center='node')
iso = vlab.iso_surface(vx_src,
contours=[0.0],
opacity=0.008,
cmap='Pastel1')
##############################################################
# calculate B field lines && topology in Viscid and plot them
seedsA = viscid.SphericalPatch([0, 0, 0], [2, 0, 1],
30,
15,
r=5.0,
nalpha=5,
nbeta=5)
seedsB = viscid.SphericalPatch([0, 0, 0], [1.9, 0, -20],
30,
15,
r=5.0,
nalpha=1,
nbeta=5)
seeds = np.concatenate([seedsA, seedsB], axis=1)
b_lines, topo = viscid.calc_streamlines(b,
seeds,
ibound=3.5,
obound0=[-25, -20, -20],
obound1=[15, 20, 20],
wrap=True)
vlab.plot_lines(b_lines, scalars=viscid.topology2color(topo))
######################################################################
# plot a random circle at geosynchronus orbit with scalars colored
# by the Matplotlib viridis color map, just because we can; this is
# a useful toy for debugging
circle = viscid.Circle(p0=[0, 0, 0], r=6.618, n=128, endpoint=True)
scalar = np.sin(circle.as_local_coordinates().get_crd('phi'))
surf = vlab.plot_line(circle.get_points(),
scalars=scalar,
clim=0.8,
cmap="Spectral_r")
######################################################################
# Use Mayavi (VTK) to calculate field lines using an interactive seed
# These field lines are colored by E parallel
epar = viscid.project(e, b)
epar.name = "Epar"
bsl2 = vlab.streamline(b,
epar,
seedtype='plane',
seed_resolution=4,
integration_direction='both',
clim=(-0.05, 0.05))
# now tweak the VTK streamlines
bsl2.stream_tracer.maximum_propagation = 20.
bsl2.seed.widget.origin = [-11, -5.0, -2.0]
bsl2.seed.widget.point1 = [-11, 5.0, -2.0]
bsl2.seed.widget.point2 = [-11.0, -5.0, 2.0]
bsl2.streamline_type = 'tube'
bsl2.tube_filter.radius = 0.03
bsl2.stop() # this stop/start was a hack to get something to update
bsl2.start()
bsl2.seed.widget.enabled = False
cbar = vlab.colorbar(bsl2,
title=epar.name,
label_fmt='%.3f',
orientation='horizontal')
cbar.scalar_bar_representation.position = (0.15, 0.01)
cbar.scalar_bar_representation.position2 = (0.72, 0.10)
###############################################################
# Make a contour at the open-closed boundary in the ionosphere
seeds_iono = viscid.Sphere(r=1.063,
pole=-moment,
ntheta=256,
nphi=256,
thetalim=(0, 180),
philim=(0, 360),
crd_system=b)
_, topo_iono = viscid.calc_streamlines(b,
seeds_iono,
ibound=1.0,
nr_procs='all',
output=viscid.OUTPUT_TOPOLOGY)
topo_iono = np.log2(topo_iono)
m = vlab.mesh_from_seeds(seeds_iono,
scalars=topo_iono,
opacity=1.0,
clim=(0, 3),
color=(0.992, 0.445, 0.0))
m.enable_contours = True
m.actor.property.line_width = 4.0
m.contour.number_of_contours = 4
####################################################################
# Plot the ionosphere, note that the sample data has the ionosphere
# at a different time, so the open-closed boundary found above
# will not be consistant with the field aligned currents
fac_tot = 1e9 * f_iono['fac_tot']
m = vlab.plot_ionosphere(fac_tot,
bounding_lat=30.0,
vmin=-300,
vmax=300,
opacity=0.75,
rotate=cotr,
crd_system=b)
m.actor.property.backface_culling = True
########################################################################
# Add some markers for earth, i.e., real earth, and dayside / nightside
# representation
vlab.plot_blue_marble(r=1.0,
lines=False,
ntheta=64,
nphi=128,
rotate=cotr,
crd_system=b)
# now shade the night side with a transparent black hemisphere
vlab.plot_earth_3d(radius=1.01, night_only=True, opacity=0.5, crd_system=b)
####################
# Finishing Touches
# vlab.axes(pp_src, nb_labels=5)
oa = vlab.orientation_axes()
oa.marker.set_viewport(0.75, 0.75, 1.0, 1.0)
# note that resize won't work if the current figure has the
# off_screen_rendering flag set
# vlab.resize([1200, 800])
vlab.view(azimuth=45, elevation=70, distance=35.0, focalpoint=[-2, 0, 0])
##############
# Save Figure
# print("saving png")
# vlab.savefig('mayavi_msphere_sample.png')
# print("saving x3d")
# # x3d files can be turned into COLLADA files with meshlab, and
# # COLLADA (.dae) files can be opened in OS X's preview
# #
# # IMPORTANT: for some reason, using bounding_lat in vlab.plot_ionosphere
# # causes a segfault when saving x3d files
# #
# vlab.savefig('mayavi_msphere_sample.x3d')
# print("done")
vlab.savefig(next_plot_fname(__file__))
###########################
# Interact Programatically
if args.interact:
vlab.interact()
#######################
# Interact Graphically
if args.show:
vlab.show()
try:
vlab.mlab.close()
except AttributeError:
pass
return 0
def main():
mhd_type = "C"
make_plots = 1
mhd_type = mhd_type.upper()
if mhd_type.startswith("C"):
if mhd_type in ("C", ):
f = viscid.load_file("$WORK/tmedium/*.3d.[-1].xdmf")
elif mhd_type in ("C2", "C3"):
f = viscid.load_file("$WORK/tmedium2/*.3d.[-1].xdmf")
else:
raise ValueError()
catol = 1e-8
rtol = 2e-6
elif mhd_type in ("F", "FORTRAN"):
f = viscid.load_file("$WORK/tmedium3/*.3df.[-1]")
catol = 1e-8
rtol = 7e-2
else:
raise ValueError()
do_fill_dipole = True
gslc = "x=-21.2j:12j, y=-11j:11j, z=-11j:11j"
b = f['b_cc'][gslc]
b1 = f['b_fc'][gslc]
e_cc = f['e_cc'][gslc]
e_ec = f['e_ec'][gslc]
if do_fill_dipole:
mask = viscid.make_spherical_mask(b, rmax=3.5)
viscid.fill_dipole(b, mask=mask)
mask = viscid.make_spherical_mask(b1, rmax=3.5)
viscid.fill_dipole(b1, mask=mask)
mask = None
# seeds = viscid.SphericalCap(r=1.02, ntheta=64, nphi=32, angle0=17, angle=20,
# philim=(100, 260), roll=-180.0)
# seeds = viscid.SphericalCap(r=1.02, ntheta=64, nphi=32, angle0=17, angle=20,
# philim=(0, 10), roll=0.0)
seedsN = viscid.Sphere(r=1.02,
ntheta=16,
nphi=16,
thetalim=(15, 25),
philim=(0, 300),
crd_system=b)
seedsS = viscid.Sphere(r=1.02,
ntheta=16,
nphi=16,
thetalim=(155, 165),
philim=(0, 300),
crd_system=b)
bl_kwargs = dict(ibound=0.9, obound0=(-20, -10, -10), obound1=(11, 10, 10))
# blines_cc, topo_cc = viscid.streamlines(b, seeds, **bl_kwargs)
blinesN_fc, topoN_fc = viscid.streamlines(b1, seedsN, **bl_kwargs)
_, topoS_fc = viscid.streamlines(b1,
seedsS,
output=viscid.OUTPUT_TOPOLOGY,
**bl_kwargs)
if True:
from viscid.plot import vlab
mesh = vlab.mesh_from_seeds(seedsN, scalars=topoN_fc)
mesh.actor.property.backface_culling = True
# vlab.plot_lines(blines_cc, scalars="#000000", tube_radius=0.03)
vlab.plot_lines(blinesN_fc,
scalars=viscid.topology2color(topoN_fc),
opacity=0.7)
vlab.plot_blue_marble(r=1.0)
vlab.plot_earth_3d(radius=1.01,
crd_system=b,
night_only=True,
opacity=0.5)
vlab.show()
if True:
vlt.subplot(121, projection='polar')
vlt.plot(topoN_fc)
vlt.subplot(122, projection='polar')
vlt.plot(topoS_fc)
vlt.show()
return 0
