def sum_vorticity(args):
i, frame = args
# Get Data
density = (fromfile("gasdens%d.dat" % frame).reshape(num_rad, num_theta)) / surface_density_zero
vrad = np.array(fromfile("gasvrad%d.dat" % frame).reshape(num_rad, num_theta))
vtheta = np.array(fromfile("gasvtheta%d.dat" % frame).reshape(num_rad, num_theta))
# Get Background Data
vtheta_keplerian = np.array(fromfile("gasvtheta0.dat").reshape(num_rad, num_theta))
# Subtract off Keplerian velocity (and rotate back into non-rotating frame???)
vtheta -= (vtheta_keplerian)
vorticity = util.velocity_curl(vrad, vtheta, rad, theta, frame = 0)
#vorticity = np.abs(vorticity) # should be all negative
# Add up vorticity
dr = rad[1] - rad[0] # assumes arithmetic grid
d_phi = theta[1] - theta[0]
radial_vorticity = np.average(vorticity, axis = 1)
total_vorticity = np.sum((dr * d_phi) * rad[:-1, None] * radial_vorticity)
# Print Update
print "%d: %.4f" % (frame, total_vorticity)
# Store Data
vorticity_over_time[i] = total_vorticity
def get_data(frame_i, frame, modes = default_modes):
""" frame_i is ith frame, frame is frame number """
# Load Data Files
normalized_density = (fromfile("gasdens%d.dat" % frame).reshape(num_rad, num_theta)) / surface_density
averagedDensity = np.average(normalized_density, axis = 1)
vrad = (fromfile("gasvrad%d.dat" % frame).reshape(num_rad, num_theta))
vtheta = (fromfile("gasvtheta%d.dat" % frame).reshape(num_rad, num_theta))
vorticity = util.velocity_curl(vrad, vtheta, rad, theta, frame = ref_frame)
vortensity = vorticity / normalized_density[1:, 1:]
# Find Peak in Radial Profile (in Outer Disk)
peak_rad, peak_density = find_peak(averagedDensity)
min_rad, min_density = find_min(averagedDensity, peak_rad)
# Gather Azimuthal Profiles
num_profiles = 5
spread = 1.0 * scale_height # half-width
azimuthal_radii = np.linspace(peak_rad - spread, peak_rad + spread, num_profiles)
azimuthal_indices = [np.searchsorted(rad, this_radius) for this_radius in azimuthal_radii]
azimuthal_profiles = np.array([np.fft.fft(vortensity[azimuthal_index, :]) for azimuthal_index in azimuthal_indices])
# Normalize by m = 0 mode (integral of density), Take Absolute Value
azimuthal_profiles = np.array([np.abs(azimuthal_profile / azimuthal_profile[0]) for azimuthal_profile in azimuthal_profiles])
for m, mode in enumerate(modes):
modes_over_time[m, frame_i] = np.max(azimuthal_profiles[:, mode])
print "%d: %.4f, %.4f, %.4f, %.4f, %.4f" % (frame, np.max(azimuthal_profiles[:, 1]), np.max(azimuthal_profiles[:, 2]), np.max(azimuthal_profiles[:, 3]), np.max(azimuthal_profiles[:, 4]), np.max(azimuthal_profiles[:, 5]))
def find_extrema(args):
# Unwrap Args
i, frame = args
# Data
density = (fromfile("gasdens%d.dat" % frame).reshape(num_rad, num_theta)) / surface_density
averagedDensity = np.average(density, axis = 1)
vrad = (fromfile("gasvrad%d.dat" % frame).reshape(num_rad, num_theta))
vtheta = (fromfile("gasvtheta%d.dat" % frame).reshape(num_rad, num_theta))
vorticity = util.velocity_curl(vrad, vtheta, rad, theta, frame = ref_frame)
vortensity = vorticity / density[1:, 1:]
# Find Peak in Radial Profile (in Outer Disk)
peak_rad, peak_rad_index, peak_density = find_radial_peak(averagedDensity)
# Find Peaks in Azimuthal Profiles (and center around that peak)
density_peak_theta, density_theta_index, max_density = find_azimuthal_extrema(density[peak_rad_index], maximum = True) # Max
vortensity_peak_theta, vortensity_peak_theta_index, min_vortensity = find_azimuthal_extrema(vortensity[peak_rad_index], maximum = False) # Min
print "%d, %.2f, %.3f" % (frame, max_density, min_vortensity)
#return max_density, min_vortensity
maximum_densities[i] = max_density
minimum_vortensities[i] = min_vortensity
def get_data(frame):
# Find Peak in Radial Profile (in Outer Disk)
density = (fromfile("gasdens%d.dat" % frame).reshape(
num_rad, num_theta)) / surface_density
dust_density = (fromfile("gasddens%d.dat" % frame).reshape(
num_rad, num_theta)) / surface_density
averagedDensity = np.average(density, axis=1)
peak_rad, peak_density = find_peak(averagedDensity)
min_rad, min_density = find_min(averagedDensity, peak_rad)
# Gather Azimuthal Profiles
num_profiles = 5
spread = 2.0 * scale_height # half-width
azimuthal_radii = np.linspace(peak_rad - spread, peak_rad + spread,
num_profiles)
azimuthal_indices = [
np.searchsorted(rad, this_radius) for this_radius in azimuthal_radii
]
azimuthal_profiles = [
density[azimuthal_index, :] for azimuthal_index in azimuthal_indices
]
dust_azimuthal_profiles = [
dust_density[azimuthal_index, :]
for azimuthal_index in azimuthal_indices
]
return azimuthal_radii, azimuthal_profiles, dust_azimuthal_profiles
def get_data(frame):
# Load Data Files
normalized_density = (fromfile("gasdens%d.dat" % frame).reshape(
num_rad, num_theta)) / surface_density
averagedDensity = np.average(normalized_density, axis=1)
vrad = (fromfile("gasvrad%d.dat" % frame).reshape(num_rad, num_theta))
vtheta = (fromfile("gasvtheta%d.dat" % frame).reshape(num_rad, num_theta))
vorticity = util.velocity_curl(vrad, vtheta, rad, theta, frame=ref_frame)
vortensity = vorticity / normalized_density[1:, 1:]
# Find Peak in Radial Profile (in Outer Disk)
peak_rad, peak_density = find_peak(averagedDensity)
min_rad, min_density = find_min(averagedDensity, peak_rad)
# Gather Azimuthal Profiles
num_profiles = 5
spread = 2.0 * scale_height # half-width
azimuthal_radii = np.linspace(peak_rad - spread, peak_rad + spread,
num_profiles)
azimuthal_indices = [
np.searchsorted(rad, this_radius) for this_radius in azimuthal_radii
]
azimuthal_profiles = [
vortensity[azimuthal_index, :] for azimuthal_index in azimuthal_indices
]
return azimuthal_radii, azimuthal_profiles
def get_data(frame):
# Load Data Files
normalized_density = (fromfile("gasdens%d.dat" % frame).reshape(num_rad, num_theta)) / surface_density
averagedDensity = np.average(normalized_density, axis = 1)
vrad = (fromfile("gasvrad%d.dat" % frame).reshape(num_rad, num_theta))
vtheta = (fromfile("gasvtheta%d.dat" % frame).reshape(num_rad, num_theta))
vorticity = util.velocity_curl(vrad, vtheta, rad, theta, frame = ref_frame)
vortensity = vorticity / normalized_density[1:, 1:]
# Find Peak in Radial Profile (in Outer Disk)
peak_rad, peak_density = find_peak(averagedDensity)
min_rad, min_density = find_min(averagedDensity, peak_rad)
# Gather Azimuthal Profiles
num_profiles = 5
spread = 2.0 * scale_height # half-width
azimuthal_radii = np.linspace(peak_rad - spread, peak_rad + spread, num_profiles)
azimuthal_indices = [np.searchsorted(rad, this_radius) for this_radius in azimuthal_radii]
azimuthal_profiles = [vortensity[azimuthal_index, :] for azimuthal_index in azimuthal_indices]
return azimuthal_radii, azimuthal_profiles
def get_min(args_here):
# Unwrap Args
i, frame, directory = args_here
# Get Data
density = fromfile("../%s/gasdens%d.dat" % (directory, frame)).reshape(
num_rad, num_theta)
averagedDensity = np.average(density, axis=1)
normalized_density = averagedDensity / surface_density_zero
vrad = (fromfile("../%s/gasvy%d.dat" % (directory, frame)).reshape(
num_rad, num_theta)) # add a read_vrad to util.py!
vtheta = (fromfile("../%s/gasvx%d.dat" % (directory, frame)).reshape(
num_rad, num_theta)) # add a read_vrad to util.py!
vorticity = utilVorticity.velocity_curl(vrad,
vtheta,
rad,
theta,
rossby=rossby,
residual=residual)
averaged_vorticity = np.average(vorticity, axis=1)
# Get Minima
min_density = find_rossby_density(normalized_density, averaged_vorticity)
# Print Update
print "%d: %.3f, %.3f" % (frame, min_density, 1.0 / min_density)
# Store Data
gap_depth_over_time[i] = 1.0 / min_density
def get_velocity(args_here):
# Unwrap Args
i, frame = args_here
# Data
if mpi:
density = Fields("./", 'gas', frame).get_field("dens").reshape(num_z, num_rad, num_theta)
vz = Fields("./", 'gas', frame).get_field("vz").reshape(num_z, num_rad, num_theta)
vrad = Fields("./", 'gas', frame).get_field("vy").reshape(num_z, num_rad, num_theta)
vtheta = Fields("./", 'gas', frame).get_field("vx").reshape(num_z, num_rad, num_theta)
else:
density = fromfile("gasdens%d.dat" % frame).reshape(num_z, num_rad, num_theta)
vz = (fromfile("gasvz%d.dat" % frame).reshape(num_z, num_rad, num_theta)) # add a read_vrad to util.py!
vrad = (fromfile("gasvy%d.dat" % frame).reshape(num_z, num_rad, num_theta)) # add a read_vrad to util.py!
vtheta = (fromfile("gasvx%d.dat" % frame).reshape(num_z, num_rad, num_theta)) # add a read_vrad to util.py!
midplane_density = density[num_z / 2 + args.sliver, :, :]
midplane_vrad = vrad[num_z / 2 + args.sliver, :, :]
midplane_vtheta = vtheta[num_z / 2 + args.sliver, :, :]
midplane_vz = vz[num_z / 2 + args.sliver, :, :]
dz = z_angles[1] - z_angles[0]
surface_density = np.sum(density[:, :, :], axis = 0) * dz
averagedDensity = np.average(surface_density, axis = -1)
average_midplane_vz = np.average(np.abs(midplane_vz), axis = -1)
composite_vz[i, :] = average_midplane_vz
peak, _ = az.get_radial_peak(averagedDensity, fargo_par)
composite_peak[i] = peak
def choose_axis(i, axis):
# Orbit Number
time = float(fargo_par["Ninterm"]) * float(fargo_par["DT"])
orbit = int(round(time / (2 * np.pi), 0)) * i
# Axis
if axis == "zoom":
x = (rad - 1) / scale_height
prefix = "zoom_"
plot.xlim(0, 40) # to match the ApJL paper
plot.ylim(0, 1.2)
xlabel = r"($r - r_p$) $/$ $h$"
else:
x = rad
prefix = ""
plot.xlim(float(fargo_par["Rmin"]) - 0.05, float(fargo_par["Rmax"]) + 0.05)
plot.ylim(0, 5.0)
xlabel = "Radius"
# Data
density = (fromfile("gasdens%d.dat" % i).reshape(num_rad, num_theta))
log_density = np.log(fromfile("gasdens%d.dat" % i).reshape(num_rad, num_theta))
averagedDensity = np.average(density, axis = 1) / surface_density
### Plot ###
plot.plot(x, averagedDensity, linewidth = linewidth, label = "%d" % frame)
# Annotate
this_title = readTitle()
plot.xlabel(xlabel, fontsize = fontsize)
plot.ylabel("Azimuthally Averaged Density", fontsize = fontsize)
plot.title("%s" % this_title, fontsize = fontsize + 1)
def get_rossby_number(args_here):
# Unwrap Args
i, frame, directory = args_here
if frame == 8800:
frame = 8801 # Remove problem frame
# Get Data
density = fromfile("../%s/gasdens%d.dat" % (directory, frame)).reshape(
num_rad, num_theta) / surface_density_zero
averagedDensity = np.average(density, axis=-1)
peak_rad, peak_density = az.get_radial_peak(averagedDensity, fargo_par)
vrad = (fromfile("../%s/gasvy%d.dat" % (directory, frame)).reshape(
num_rad, num_theta)) # add a read_vrad to util.py!
vtheta = (fromfile("../%s/gasvx%d.dat" % (directory, frame)).reshape(
num_rad, num_theta)) # add a read_vrad to util.py!
vorticity = utilVorticity.velocity_curl(vrad,
vtheta,
rad,
theta,
rossby=True,
residual=True)
#vorticity, shift_c = shift_data(vorticity, fargo_par, reference_density = density)
# Find minimum
start_rad = min([peak_rad - 0.05, 1.5])
start_rad_i = np.searchsorted(rad, start_rad) # Is this necessary?
end_rad_i = np.searchsorted(rad, 2.5)
azimuthal_profile = vorticity[start_rad_i:end_rad_i]
rossby_number_over_time[i] = np.percentile(azimuthal_profile, 0.25)
print i, frame, rossby_number_over_time[i]
def sum_vorticity(args):
i, frame = args
# Get Data
density = (fromfile("gasdens%d.dat" % frame).reshape(
num_rad, num_theta)) / surface_density_zero
vrad = np.array(
fromfile("gasvrad%d.dat" % frame).reshape(num_rad, num_theta))
vtheta = np.array(
fromfile("gasvtheta%d.dat" % frame).reshape(num_rad, num_theta))
# Get Background Data
vtheta_keplerian = np.array(
fromfile("gasvtheta0.dat").reshape(num_rad, num_theta))
# Subtract off Keplerian velocity (and rotate back into non-rotating frame???)
vtheta -= (vtheta_keplerian)
vorticity = util.velocity_curl(vrad, vtheta, rad, theta, frame=0)
#vorticity = np.abs(vorticity) # should be all negative
# Add up vorticity
dr = rad[1] - rad[0] # assumes arithmetic grid
d_phi = theta[1] - theta[0]
radial_vorticity = np.average(vorticity, axis=1)
total_vorticity = np.sum((dr * d_phi) * rad[:-1, None] * radial_vorticity)
# Print Update
print "%d: %.4f" % (frame, total_vorticity)
# Store Data
vorticity_over_time[i] = total_vorticity
def get_data(frame, size_a, size_b):
# Find Peak in Radial Profile (in Outer Disk)
density_a = (fromfile("../%s-size/gasdens%d.dat" %
(size_a, frame)).reshape(
num_rad, num_theta)) / surface_density
density_b = (fromfile("../%s-size/gasdens%d.dat" %
(size_b, frame)).reshape(
num_rad, num_theta)) / surface_density
averagedDensity_a = np.average(density_a, axis=1)
peak_rad, peak_density = find_peak(averagedDensity_a)
min_rad, min_density = find_min(averagedDensity_a, peak_rad)
# Gather Azimuthal Profiles
num_profiles = 5
spread = 2.0 * scale_height # half-width
azimuthal_radii = np.linspace(peak_rad - spread, peak_rad + spread,
num_profiles)
azimuthal_indices = [
np.searchsorted(rad, this_radius) for this_radius in azimuthal_radii
]
azimuthal_profiles_a = [
density_a[azimuthal_index, :] for azimuthal_index in azimuthal_indices
]
azimuthal_profiles_b = [
density_b[azimuthal_index, :] for azimuthal_index in azimuthal_indices
]
return azimuthal_radii, azimuthal_profiles_a, azimuthal_profiles_b
def find_vortensity_min(frame):
""" returns radius with maximum azimuthally averaged density """
i = frame
# Find density max (Search for vortensity minimum only near the density max)
density_max = find_density_max(frame)
start = density_max - (0.2 * (scale_height / 0.06))
stop = density_max + (0.1 * (scale_height / 0.06))
# Data
truncated_rad = truncate(rad, start = start, stop = stop)
density = (fromfile("gasdens%d.dat" % i).reshape(num_rad, num_theta))
normalized_density = density / surface_density_zero
vrad = (fromfile("gasvrad%d.dat" % i).reshape(num_rad, num_theta))
vtheta = (fromfile("gasvtheta%d.dat" % i).reshape(num_rad, num_theta))
vorticity = curl(vrad, vtheta, rad, theta)
vortensity = vorticity / normalized_density[1:, 1:]
avg_vortensity = truncate(np.average(vortensity, axis = 1), start = start, stop = stop)
kernel_size = 1
smoothed_avg_vortensity = smooth(avg_vortensity, kernel_size)
# Retrieve radius with min value
arg_min = np.argmin(smoothed_avg_vortensity)
radius_min = truncated_rad[arg_min]
return radius_min
def get_contrasts(args_here):
# Unwrap Args
i, frame = args_here
# Get Data
density = fromfile("gasdens%d.dat" % frame).reshape(
num_rad, num_theta) / surface_density_zero
averagedDensity = np.average(density, axis=-1)
peak_rad, peak_density = az.get_radial_peak(averagedDensity, fargo_par)
vrad = (fromfile("gasvy%d.dat" % frame).reshape(num_rad, num_theta)
) # add a read_vrad to util.py!
vtheta = (fromfile("gasvx%d.dat" % frame).reshape(num_rad, num_theta)
) # add a read_vrad to util.py!
vorticity = utilVorticity.velocity_curl(vrad,
vtheta,
rad,
theta,
rossby=True,
residual=True)
#vorticity, shift_c = shift_data(vorticity, fargo_par, reference_density = density)
# Find minimum
start_rad_i = np.searchsorted(rad, peak_rad - 0.1) # Is this necessary?
end_rad_i = np.searchsorted(rad, peak_rad + 1.0)
azimuthal_profile = vorticity[start_rad_i:end_rad_i]
rossby_number_over_time[i] = np.min(azimuthal_profile)
rossby_number_over_time_98[i] = np.percentile(azimuthal_profile, 0.2)
rossby_number_over_time_95[i] = np.percentile(azimuthal_profile, 0.5)
print i, frame, rossby_number_over_time[i], rossby_number_over_time_98[
i], rossby_number_over_time_95[i]
def read_rgb(fname): fid = open(fname, 'rb') res = fromfile(fid, 'd', 2) x = int(res[0]) y = int(res[1]) img = fromfile(fid, 'd', x*y*3).reshape(x, y, 3).swapaxes(0, 1) fid.close() return img
def get_vortensity_variation(frame, vortex_location, figure = False):
"""
return variation in vortensity (defined to be min / avg at a particular radius)
"""
i = frame
# Data
density = (fromfile("gasdens%d.dat" % i).reshape(num_rad, num_theta))
normalized_density = density / surface_density_zero
vrad = (fromfile("gasvrad%d.dat" % i).reshape(num_rad, num_theta))
vtheta = (fromfile("gasvtheta%d.dat" % i).reshape(num_rad, num_theta))
vorticity = curl(vrad, vtheta, rad, theta)
vortensity = vorticity / normalized_density[1:, 1:]
# Azimuthal Profile (Average over width of vortex)
arg_vortex = np.searchsorted(rad, vortex_location)
half_width = int(16 * (num_rad / 512.0))
kernel_size = num_theta / 200
vortensity_at_vortex = smooth(np.average(vortensity[(arg_vortex - half_width):(arg_vortex + half_width), :],
weights = weights(half_width), axis = 0), kernel_size)
# Replace values above maximum with maximum
max_value = 0.3
vortensity_at_vortex[vortensity_at_vortex > max_value] = max_value
# Plot
if figure:
fig = plot.figure()
# Axis
angles = np.linspace(0, 2 * np.pi, 7)
degree_angles = ["%d" % d_a for d_a in np.linspace(0, 360, 7)]
plot.xlim(0, 2 * np.pi)
plot.xticks(angles, degree_angles)
# Plot
plot.plot(theta[1:], vortensity_at_vortex, linewidth = linewidth)
# Annotate
plot.xlabel("Theta", fontsize = fontsize)
plot.ylabel("Vortensity", fontsize = fontsize)
# Save and Close
directory = "azimuthalVortensity"
plot.savefig("%s/azimuthalVortensity_%04d.png" % (directory, i), bbox_inches = 'tight', dpi = my_dpi)
#plot.show()
plot.close(fig) # Close Figure (to avoid too many figures)
# Variation
min_vortensity = np.min(vortensity_at_vortex)
avg_vortensity = np.average(vortensity_at_vortex)
#print min_vortensity
variation = (1 + avg_vortensity - min_vortensity) / (2 * avg_vortensity)
return variation
def choose_axis(i, axis):
# Orbit Number
time = float(fargo_par["Ninterm"]) * float(fargo_par["DT"])
orbit = int(round(time / (2 * np.pi), 0)) * i
# Set up figure
fig = plot.figure(figsize=(700 / my_dpi, 600 / my_dpi), dpi=my_dpi)
ax = fig.add_subplot(111)
# Axis
angles = np.linspace(0, 2 * np.pi, 7)
degree_angles = ["%d" % d_a for d_a in np.linspace(0, 360, 7)]
plot.ylim(0, 2 * np.pi)
plot.yticks(angles, degree_angles)
if axis == "zoom":
x = (rad - 1) / scale_height
prefix = "zoom_"
plot.xlim(0, 40) # to match the ApJL paper
xlabel = r"($r - r_p$) $/$ $h$"
else:
x = rad
prefix = ""
plot.xlim(float(fargo_par["Rmin"]), float(fargo_par["Rmax"]))
xlabel = "Radius"
# Data
density = (fromfile("gasdens%d.dat" % i).reshape(num_rad, num_theta))
normalized_density = density / surface_density_zero
vrad = (fromfile("gasvrad%d.dat" % i).reshape(num_rad, num_theta))
vtheta = (fromfile("gasvtheta%d.dat" % i).reshape(num_rad, num_theta))
vortensity = util.velocity_curl(
vrad, vtheta, rad, theta, frame=ref_frame) / normalized_density[1:,
1:]
### Plot ###
result = ax.pcolormesh(x, theta, np.transpose(vortensity), cmap=cmap)
fig.colorbar(result)
result.set_clim(clim[0], clim[1])
# Annotate
plot.xlabel(xlabel, fontsize=fontsize)
plot.ylabel(r"$\phi$", fontsize=fontsize)
plot.title("Vortensity Map at Orbit %d" % orbit, fontsize=fontsize + 1)
# Save and Close
plot.savefig("%s/%svortensityMap_%03d.png" %
(save_directory, prefix, i),
bbox_inches='tight',
dpi=my_dpi)
if show:
plot.show()
plot.close(fig) # Close Figure (to avoid too many figures)
def choose_axis(i, axis):
# Orbit Number
time = float(fargo_par["Ninterm"]) * float(fargo_par["DT"])
orbit = int(round(time / (2 * np.pi), 0)) * i
# Set up figure
fig = plot.figure(figsize = (700 / my_dpi, 600 / my_dpi), dpi = my_dpi)
ax = fig.add_subplot(111)
# Axis
angles = np.linspace(0, 2 * np.pi, 7)
degree_angles = ["%d" % d_a for d_a in np.linspace(0, 360, 7)]
plot.ylim(0, 2 * np.pi)
plot.yticks(angles, degree_angles)
if axis == "zoom":
x = (rad - 1) / scale_height
prefix = "zoom_"
plot.xlim(0, 40) # to match the ApJL paper
xlabel = r"($r - r_p$) $/$ $h$"
else:
x = rad
prefix = ""
plot.xlim(float(fargo_par["Rmin"]), float(fargo_par["Rmax"]))
xlabel = "Radius"
# Data
vrad = np.array(fromfile("gasvrad%d.dat" % i).reshape(num_rad, num_theta))
vtheta = np.array(fromfile("gasvtheta%d.dat" % i).reshape(num_rad, num_theta))
vtheta_keplerian = np.array(fromfile("gasvtheta0.dat").reshape(num_rad, num_theta))
# Subtract off Keplerian velocity (and rotate back into non-rotating frame???)
vtheta -= (vtheta_keplerian)
vorticity = util.velocity_curl(vrad, vtheta, rad, theta, frame = 0)
# Divide out Angular Frequency (for Rossby Number)
vorticity = vorticity / (np.array([r**(-1.5) for r in rad[:-1]]))[:, None]
### Plot ###
result = ax.pcolormesh(x, theta, np.transpose(vorticity), cmap = cmap)
fig.colorbar(result)
result.set_clim(clim[0], clim[1])
# Annotate
plot.xlabel(xlabel, fontsize = fontsize)
plot.ylabel(r"$\phi$", fontsize = fontsize)
plot.title("Vorticity (v - vK) Map at Orbit %d" % orbit, fontsize = fontsize + 1)
# Save and Close
plot.savefig("%s/%sexcessVorticityMap_%03d.png" % (save_directory, prefix, i), bbox_inches = 'tight', dpi = my_dpi)
if show:
plot.show()
plot.close(fig) # Close Figure (to avoid too many figures)
def make_plot(frame):
# Orbit Number
time = float(fargo_par["Ninterm"]) * float(fargo_par["DT"])
orbit = int(round(time / (2 * np.pi), 0)) * frame
# Set up figure
fig = plot.figure(figsize=(700 / my_dpi, 600 / my_dpi), dpi=my_dpi)
# Data
fargo_fn = "fargo2D1D"
if os.path.exists(fargo_fn):
# fargo2D1D
rad = np.loadtxt("used_rad1D.dat")[:-1]
vrad = fromfile("gasvrad1D%d.dat" % frame)
avg_pseudo_viscosity = (2.0 / 3) * (np.multiply(rad, vrad)
) # should be equal to viscosity
else:
# fargo
rad = np.loadtxt("used_rad.dat")[:-1]
vrad = (fromfile("gasvrad%d.dat" % frame).reshape(num_rad, num_theta))
pseudo_viscosity = (2.0 / 3) * (np.multiply(rad[:, None], vrad)
) # should be equal to viscosity
avg_pseudo_viscosity = np.average(pseudo_viscosity,
axis=1) # radial pseudo-viscosity
# Curves
plot.plot(rad,
avg_pseudo_viscosity,
color="blue",
label="+",
linewidth=linewidth) # positive
plot.plot(rad,
-avg_pseudo_viscosity,
color="red",
label="-",
linewidth=linewidth) # negative
plot.plot([rad[0], rad[-1]], [viscosity, viscosity],
color="black",
linewidth=linewidth - 1)
# Limits
plot.xlim(rad[0], rad[-1])
plot.yscale('log')
# Annotate
plot.xlabel("Radius", fontsize=fontsize)
plot.ylabel("Pseudo Viscosity", fontsize=fontsize)
plot.title("Orbit %d" % orbit, fontsize=fontsize + 1)
plot.legend(loc="upper right")
# Save + Close
plot.savefig("%s/viscosity_diagnosis_%04d.png" % (directory, frame),
bbox_inches='tight',
dpi=my_dpi)
plot.show()
plot.close(fig) # Close Figure (to avoid too many figures)
def choose_axis(i, axis):
# Orbit Number
time = float(fargo_par["Ninterm"]) * float(fargo_par["DT"])
orbit = int(round(time / (2 * np.pi), 0)) * i
# Set up figure
fig = plot.figure(figsize = (700 / my_dpi, 600 / my_dpi), dpi = my_dpi)
ax = fig.add_subplot(111)
# Axis
angles = np.linspace(0, 2 * np.pi, 7)
degree_angles = ["%d" % d_a for d_a in np.linspace(0, 360, 7)]
plot.ylim(0, 2 * np.pi)
plot.yticks(angles, degree_angles)
if axis == "zoom":
x = (rad - 1) / scale_height
prefix = "zoom_"
plot.xlim(0, 40) # to match the ApJL paper
xlabel = r"($r - r_p$) $/$ $h$"
else:
x = rad
prefix = ""
plot.xlim(float(fargo_par["Rmin"]), float(fargo_par["Rmax"]))
xlabel = "Radius"
# Data
density = (fromfile("gasdens%d.dat" % i).reshape(num_rad, num_theta))
normalized_density = density / surface_density_zero
vrad = (fromfile("gasvrad%d.dat" % i).reshape(num_rad, num_theta))
vtheta = (fromfile("gasvtheta%d.dat" % i).reshape(num_rad, num_theta))
vortensity = util.velocity_curl(vrad, vtheta, rad, theta, frame = ref_frame) / normalized_density[1:, 1:]
avg_vortensity = np.average(vortensity, axis = 1)
excess_vortensity = avg_vortensity[:, None] - vortensity #### Vortex is Positive ####
### Plot ###
result = ax.pcolormesh(x, theta, np.transpose(excess_vortensity), cmap = cmap)
fig.colorbar(result)
result.set_clim(clim[0], clim[1])
# Annotate
plot.xlabel(xlabel, fontsize = fontsize)
plot.ylabel(r"$\phi$", fontsize = fontsize)
plot.title("Excess Vortensity Map at Orbit %d" % orbit, fontsize = fontsize + 1)
# Save and Close
plot.savefig("%s/%sexcessVortensityMap_%03d.png" % (save_directory, prefix, i), bbox_inches = 'tight', dpi = my_dpi)
if show:
plot.show()
plot.close(fig) # Close Figure (to avoid too many figures)
def choose_axis(i, axis):
# Orbit Number
time = float(fargo_par["Ninterm"]) * float(fargo_par["DT"])
orbit = int(round(time / (2 * np.pi), 0)) * i
# Set up figure
fig = plot.figure(figsize=(700 / my_dpi, 600 / my_dpi), dpi=my_dpi)
# Axis
plot.ylim(0, 1.3)
if axis == "zoom":
x = (rad - 1) / scale_height
prefix = "zoom_"
plot.xlim(0, 40) # to match the ApJL paper
#plot.ylim(0, 1.3)
xlabel = r"($r - r_p$) $/$ $h$"
else:
x = rad
prefix = ""
plot.xlim(float(fargo_par["Rmin"]), float(fargo_par["Rmax"]))
xlabel = "Radius"
# Data
density = (fromfile("gasdens%d.dat" % i).reshape(num_rad, num_theta))
normalized_density = density / surface_density_zero
vrad = (fromfile("gasvrad%d.dat" % i).reshape(num_rad, num_theta))
vtheta = (fromfile("gasvtheta%d.dat" % i).reshape(num_rad, num_theta))
vorticity = util.velocity_curl(vrad,
vtheta,
rad,
theta,
average=True,
frame=ref_frame)
vortensity = vorticity / normalized_density[1:, 1:]
averaged_w = np.average(vortensity, axis=1)
### Plot ###
plot.plot(x[1:], averaged_w, linewidth=linewidth)
# Annotate
this_title = readTitle()
plot.xlabel(xlabel, fontsize=fontsize)
plot.ylabel("Azimuthally Averaged Vortensity", fontsize=fontsize)
plot.title("Orbit %d: %s" % (orbit, this_title), fontsize=fontsize + 1)
# Save and Close
plot.savefig("%s/%saveragedVortensity_%03d.png" %
(save_directory, prefix, i),
bbox_inches='tight',
dpi=my_dpi)
if show:
plot.show()
plot.close(fig) # Close Figure (to avoid too many figures)
def convert_to_cylindrical(frame):
# Converts Vector Field from Spherical to Cylindrical Coordinates
radial_velocity = (fromfile("vx1.%04d.dbl" % frame).reshape(num_theta, num_z, num_rad))
theta_velocity = (fromfile("vx2.%04d.dbl" % frame).reshape(num_theta, num_z, num_rad))
phi_velocity = (fromfile("vx3.%04d.dbl" % frame).reshape(num_theta, num_z, num_rad))
# Velocity Fields
velocity_field = np.zeros((3, num_theta, num_z, num_rad))
velocity_field[0] = radial_velocity
velocity_field[1] = theta_velocity
velocity_field[2] = phi_velocity
# Angle Grids
theta_field = np.zeros((num_theta, num_z, num_rad))
theta_field[:, :, :] = zs[np.newaxis, :, np.newaxis]
phi_field = np.zeros((num_theta, num_z, num_rad))
phi_field[:, 0, 0] = theta
phi_field[:, :, :] = phi_field[:, 0, 0]
# cos, sin of angles (3-D grid)
cos_theta = np.cos(theta_field)
sin_theta = np.sin(theta_field)
cos_phi = np.cos(phi_field)
sin_phi = np.sin(phi_field)
# combinations of angles (3-D grid)
cos_theta_cos_phi = cos_theta * cos_phi
cos_theta_sin_phi = cos_theta * sin_phi
sin_theta_cos_phi = sin_theta * cos_phi
sin_theta_sin_phi = sin_theta * sin_phi
# Transform to Cartesian
first_transformation_matrix = np.zeros((3, 3, num_theta, num_z, num_rad))
f = first_transformation_matrix
f[0, 0] = sin_theta_cos_phi; f[0, 1] = cos_theta_cos_phi; f[0, 2] = -sin_phi
f[1, 0] = sin_theta_sin_phi; f[1, 1] = cos_theta_sin_phi; f[1, 2] = cos_phi
f[2, 0] = cos_theta; f[2, 1] = -sin_theta; f[2, 2] = 0
# Transform to Cylindrical
second_transformation_matrix = np.zeros((3, 3, num_theta, num_z, num_rad))
s = second_transformation_matrix
s[0, 0] = cos_phi; s[0, 1] = sin_phi; s[0, 2] = 0
s[1, 0] = -sin_phi; s[1, 1] = cos_phi; s[1, 2] = 0
s[2, 0] = 0; s[2, 1] = 0; s[2, 2] = 1
# Apply Transformations
cartesian_velocity_field = np.einsum('ij...,j...->i...', first_transformation_matrix, velocity_field)
cylindrical_field = np.einsum('ij...,j...->i...', second_transformation_matrix, cartesian_velocity_field)
cylindrical_radial_velocity = cylindrical_field[0]
return cylindrical_radial_velocity
def get_data(frame):
# Load Data Files
normalized_density = (fromfile("gasdens%d.dat" % frame).reshape(
num_rad, num_theta)) / surface_density
averagedDensity = np.average(normalized_density, axis=1)
vrad = (fromfile("gasvrad%d.dat" % frame).reshape(num_rad, num_theta))
vtheta = (fromfile("gasvtheta%d.dat" % frame).reshape(num_rad, num_theta))
vorticity = util.velocity_curl(vrad, vtheta, rad, theta, frame=ref_frame)
vortensity = vorticity / normalized_density[1:, 1:]
# Find Peak in Radial Profile (in Outer Disk)
peak_rad, peak_density = find_peak(averagedDensity)
min_rad, min_density = find_min(averagedDensity, peak_rad)
# Gather Azimuthal Profiles
num_profiles = 5
spread = 1.0 * scale_height # half-width
azimuthal_radii = np.linspace(peak_rad - spread, peak_rad + spread,
num_profiles)
azimuthal_indices = [
np.searchsorted(rad, this_radius) for this_radius in azimuthal_radii
]
azimuthal_profiles = [
np.fft.fft(vortensity[azimuthal_index, :])
for azimuthal_index in azimuthal_indices
]
# Normalize by m = 0 mode (integral of vortensity), Take Absolute Value
azimuthal_profiles = [
np.abs(azimuthal_profile / azimuthal_profile[0])
for azimuthal_profile in azimuthal_profiles
]
### Gather Averaged Profiles ###
start_half = azimuthal_indices[1]
end_half = azimuthal_indices[-2]
avg_half_profile = np.average(vortensity[start_half:end_half, :], axis=0)
avg_half = np.fft.fft(avg_half_profile)
start_full = azimuthal_indices[0]
end_full = azimuthal_indices[-1]
avg_full_profile = np.average(vortensity[start_full:end_full, :], axis=0)
avg_full = np.fft.fft(avg_full_profile)
# Normalize
avg_half = np.abs(avg_half / avg_half[0])
avg_full = np.abs(avg_full / avg_full[0])
return azimuthal_radii, azimuthal_profiles, avg_half, avg_full
def sum_vorticity(args):
i, frame = args
# Get Data
density = (fromfile("gasdens%d.dat" % frame).reshape(num_rad, num_theta)) / surface_density_zero
vrad = np.array(fromfile("gasvrad%d.dat" % frame).reshape(num_rad, num_theta))
vtheta = np.array(fromfile("gasvtheta%d.dat" % frame).reshape(num_rad, num_theta))
# Get Background Data
vtheta_keplerian = np.array(fromfile("gasvtheta0.dat").reshape(num_rad, num_theta))
# Subtract off Keplerian velocity (and rotate back into non-rotating frame???)
vtheta -= (vtheta_keplerian)
vorticity = util.velocity_curl(vrad, vtheta, rad, theta, frame = 0)
# Mask Non-Vortex Regions
min_vorticity = -0.65
vorticity[density[:-1, :-1] < 0.45] = 0 # if density is too low, it's not in the vortex
vorticity[vorticity > 0] = 0 # if vorticity is positive, it's not in the vortex
vorticity[vorticity < min_vorticity] = min_vorticity # if vorticity is too low, it's not in the vortex
vorticity = np.abs(vorticity) # everything that remains should be negative. switch to positive.
# Extract Near Vortex
averagedDensity = np.average(density, axis = 1)
peak_rad, peak_density = find_peak(averagedDensity)
vortex_start = np.max([1.0, peak_rad - 5.0 * scale_height])
vortex_end = peak_rad + 5.0 * scale_height
vortex_start_i = np.searchsorted(rad, vortex_start)
vortex_end_i = np.searchsorted(rad, vortex_end)
vortex_rad = rad[vortex_start_i : vortex_end_i]
vortex_vorticity_grid = vorticity[vortex_start_i : vortex_end_i]
vortex_vorticity = np.average(vortex_vorticity_grid, axis = 1)
# Add up vorticity
dr = rad[1] - rad[0] # assumes arithmetic grid
d_phi = theta[1] - theta[0]
total_vorticity = np.sum((dr * d_phi) * vortex_rad[:, None] * vortex_vorticity)
##### Instead: take max vorticity (90th percentile???) #####
# Print Update
print "%d: %.4f" % (frame, total_vorticity)
# Store Data
vorticity_over_time[i] = total_vorticity
def get_data(frame_i, frame, modes=default_modes):
""" frame_i is ith frame, frame is frame number """
# Load Data Files
normalized_density = (fromfile("gasdens%d.dat" % frame).reshape(
num_rad, num_theta)) / surface_density
averagedDensity = np.average(normalized_density, axis=1)
vrad = np.array(
fromfile("gasvrad%d.dat" % frame).reshape(num_rad, num_theta))
vtheta = np.array(
fromfile("gasvtheta%d.dat" % frame).reshape(
num_rad, num_theta)) - vtheta_keplerian
vorticity = util.velocity_curl(vrad, vtheta, rad, theta, frame=ref_frame)
combo = normalized_density[:-1, :-1] * vorticity
# Find Peak in Radial Profile (in Outer Disk)
peak_rad, peak_density = find_peak(averagedDensity)
min_rad, min_density = find_min(averagedDensity, peak_rad)
# Gather Azimuthal Profiles
num_profiles = 5
spread = 1.0 * scale_height # half-width
azimuthal_radii = np.linspace(peak_rad - spread, peak_rad + spread,
num_profiles)
azimuthal_indices = [
np.searchsorted(rad, this_radius) for this_radius in azimuthal_radii
]
azimuthal_profiles = np.array([
np.fft.fft(combo[azimuthal_index, :])
for azimuthal_index in azimuthal_indices
])
# Normalize by m = 0 mode (integral of density), Take Absolute Value
azimuthal_profiles = np.array([
np.abs(azimuthal_profile / azimuthal_profile[0])
for azimuthal_profile in azimuthal_profiles
])
for m, mode in enumerate(modes):
modes_over_time[m, frame_i] = np.max(azimuthal_profiles[:, mode])
single_mode_strength[frame_i] = modes_over_time[0, frame_i] / np.max(
modes_over_time[1:, frame_i]) # m = 1 / Max of Higher Number Modes
print "%d: %.4f, %.4f, %.4f, %.4f, %.4f - [%.4f]" % (
frame, np.max(azimuthal_profiles[:, 1]),
np.max(azimuthal_profiles[:, 2]), np.max(azimuthal_profiles[:, 3]),
np.max(azimuthal_profiles[:, 4]), np.max(
azimuthal_profiles[:, 5]), single_mode_strength[frame_i])
def polish(density,
frame,
shift_i,
size,
cavity_cutoff=0.92,
scale_density=1,
scale_sizes=1):
""" Step 1: get rid of inner cavity, scale dust densities to different grain size, and only keep dust with negative vorticity """
# Cavity
if cavity_cutoff is not None:
cavity_cutoff_i = np.searchsorted(rad, cavity_cutoff)
density[:cavity_cutoff_i] = 0.0
outer_cutoff = 2.75
outer_cutoff_i = np.searchsorted(rad, outer_cutoff)
density[outer_cutoff_i:] = 0.0
# Scale
density *= scale_density
size *= scale_sizes
if negative_vorticity_only > 0:
tmp_density = density[1:, 1:]
# Get rid of dust where there is positive vorticity
vrad = (fromfile("gasvy%d.dat" % frame).reshape(num_rad, num_theta)
) # add a read_vrad to util.py!
vtheta = (fromfile("gasvx%d.dat" % frame).reshape(num_rad, num_theta)
) # add a read_vrad to util.py!
vorticity = utilVorticity.velocity_curl(vrad,
vtheta,
rad,
theta,
rossby=True,
residual=True)
# Remember to shift the vorticity!
vorticity = np.roll(vorticity, shift_i, axis=1)
tmp_density[vorticity > 0] = 0.0
density[1:, 1:] = tmp_density
# Get rid of dust where density is below a threshold
gas_density = fromfile("gasdens%d.dat" % frame).reshape(
num_rad, num_theta) / surface_density_zero
gas_density = np.roll(gas_density, shift_i, axis=1)
threshold = negative_vorticity_only
density[gas_density < threshold] = 0.0
return density, size
def gather_vortex_over_time():
""" add up vortex mass over time """
for frame in times:
density = (fromfile("gasdens%d.dat" % frame).reshape(num_rad, num_theta))
normalized_density = density / surface_density_zero
vrad = (fromfile("gasvrad%d.dat" % frame).reshape(num_rad, num_theta))
vtheta = (fromfile("gasvtheta%d.dat" % frame).reshape(num_rad, num_theta))
vorticity = curl(vrad, vtheta, rad, theta)
vortensity = vorticity / normalized_density[1:, 1:]
vortex_mass_i, _ = vortex_mass(rad, theta, density, vortensity)
vortex_masses.append(vortex_mass_i)
def map_one_vortex(frame):
""" get 2-D grid showing vortex """
density = (fromfile("gasdens%d.dat" % frame).reshape(num_rad, num_theta))
normalized_density = density / surface_density_zero
vrad = (fromfile("gasvrad%d.dat" % frame).reshape(num_rad, num_theta))
vtheta = (fromfile("gasvtheta%d.dat" % frame).reshape(num_rad, num_theta))
vorticity = curl(vrad, vtheta, rad, theta)
vortensity = vorticity / normalized_density[1:, 1:]
this_vortex_mass, vortex_map = vortex_mass(rad, theta, density, vortensity)
print "Vortex Mass at Frame %d: %.8f" % (frame, this_vortex_mass)
return vortex_map
def map_one_vortex(frame):
""" get 2-D grid showing vortex """
density = (fromfile("gasdens%d.dat" % frame).reshape(num_rad, num_theta))
normalized_density = density / surface_density_zero
vrad = (fromfile("gasvrad%d.dat" % frame).reshape(num_rad, num_theta))
vtheta = (fromfile("gasvtheta%d.dat" % frame).reshape(num_rad, num_theta))
vorticity = curl(vrad, vtheta, rad, theta)
vortensity = vorticity / normalized_density[1:, 1:]
this_vortex_mass, vortex_map = vortex_mass(rad, theta, density, vortensity)
print "Vortex Mass at Frame %d: %.8f" % (frame, this_vortex_mass)
return vortex_map
def choose_axis(i, axis):
# Orbit Number
time = float(fargo_par["Ninterm"]) * float(fargo_par["DT"])
orbit = int(round(time / (2 * np.pi), 0)) * i
# Set up figure
fig = plot.figure(figsize = (700 / my_dpi, 600 / my_dpi), dpi = my_dpi)
ax = fig.add_subplot(111)
# Axis
angles = np.linspace(0, 2 * np.pi, 7)
degree_angles = ["%d" % d_a for d_a in np.linspace(0, 360, 7)]
plot.ylim(0, 2 * np.pi)
plot.yticks(angles, degree_angles)
if axis == "zoom":
x = (rad - 1) / scale_height
prefix = "zoom_"
plot.xlim(0, 40) # to match the ApJL paper
xlabel = r"($r - r_p$) $/$ $h$"
else:
x = rad
prefix = ""
plot.xlim(float(fargo_par["Rmin"]), float(fargo_par["Rmax"]))
xlabel = "Radius"
# Data
blank_density = (fromfile("gasdens%d.dat" % blank_frame).reshape(num_rad, num_theta))
density = (fromfile("gasdens%d.dat" % i).reshape(num_rad, num_theta))
normalized_density = (density - blank_density) / surface_density_zero # Diff
### Plot ###
result = ax.pcolormesh(x, theta, np.transpose(normalized_density), cmap = cmap)
fig.colorbar(result)
result.set_clim(clim[0], clim[1])
# Annotate
this_title = readTitle()
plot.xlabel(xlabel, fontsize = fontsize)
plot.ylabel(r"$\phi$", fontsize = fontsize)
plot.title("Gas Difference Density Map at Orbit %d (- Orbit %d)\n%s" % (orbit, blank_frame, this_title), fontsize = fontsize + 1)
# Save and Close
plot.savefig("%s/%sdiff_densityMap_%04d-%04d.png" % (save_directory, prefix, blank_frame, i), bbox_inches = 'tight', dpi = my_dpi)
if show:
plot.show()
plot.close(fig) # Close Figure (to avoid too many figures)
def make_plot(frame, show=False):
# Orbit Number
time = float(fargo_par["Ninterm"]) * float(fargo_par["DT"])
orbit = int(round(time / (2 * np.pi), 0)) * frame
# Set up figure
fig = plot.figure()
ax = fig.add_subplot(111)
# Axis
angles = np.linspace(0, 2 * np.pi, 7)
degree_angles = ["%d" % d_a for d_a in np.linspace(0, 360, 7)]
plot.ylim(0, 2 * np.pi)
plot.yticks(angles, degree_angles)
plot.xlim(float(fargo_par["Rmin"]), 1.0)
# Data
x = rad
density = (fromfile("gasdens%d.dat" % frame).reshape(num_rad, num_theta))
normalized_density = density / surface_density_zero
vrad = (fromfile("gasvrad%d.dat" % frame).reshape(num_rad, num_theta))
vtheta = (fromfile("gasvtheta%d.dat" % frame).reshape(num_rad, num_theta))
vorticity = curl(vrad, vtheta, rad, theta) / normalized_density[1:, 1:]
### Plot ###
result = ax.pcolormesh(x, theta, np.transpose(vorticity), cmap=cmap)
fig.colorbar(result)
result.set_clim(clim[0], clim[1])
# Annotate
this_title = readTitle()
plot.xlabel("Radius", fontsize=fontsize)
plot.ylabel(r"$\phi$", fontsize=fontsize)
plot.title("Vortensity Map at Orbit %d: %s" % (orbit, this_title),
fontsize=fontsize + 1)
# Save and Close
plot.savefig("%s/vorticityMap_%03d.png" % (save_directory, frame),
bbox_inches='tight',
dpi=my_dpi)
if show:
plot.show()
plot.close(fig) # Close Figure (to avoid too many figures)
def get_data(frame_i, frame, modes = default_modes):
""" frame_i is ith frame, frame is frame number """
# Find Peak in Radial Profile (in Outer Disk)
density = (fromfile("gasdens%d.dat" % frame).reshape(num_rad, num_theta)) / surface_density
averagedDensity = np.average(density, axis = 1)
density = subtract_wave(density) # First, subtract wave!
peak_rad, peak_density = find_peak(averagedDensity)
min_rad, min_density = find_min(averagedDensity, peak_rad)
# Gather Azimuthal Profiles
num_profiles = 7
spread = 1.0 * scale_height # half-width
azimuthal_radii = np.linspace(peak_rad - spread, peak_rad + spread, num_profiles)
azimuthal_indices = [np.searchsorted(rad, this_radius) for this_radius in azimuthal_radii]
azimuthal_profiles = np.array([np.fft.fft(density[azimuthal_index, :]) for azimuthal_index in azimuthal_indices])
# Normalize by m = 0 mode (integral of density), Take Absolute Value
azimuthal_profiles = np.array([np.abs(azimuthal_profile / azimuthal_profile[0]) for azimuthal_profile in azimuthal_profiles])
for m, mode in enumerate(modes):
modes_over_time[m, frame_i] = np.max(azimuthal_profiles[:, mode]) #np.sqrt(np.sum(np.power(azimuthal_profiles[:, mode], 2)))
single_mode_strength[frame_i] = modes_over_time[0, frame_i] / np.max(modes_over_time[1:, frame_i]) # m = 1 / Max of Higher Number Modes
single_mode_concentration[frame_i] = np.std(azimuthal_profiles[:, 1]) / modes_over_time[0, frame_i]
print "%d: %.4f, %.4f, %.4f, %.4f, %.4f - [%.4f, %.4f]" % (frame, np.max(azimuthal_profiles[:, 1]), np.max(azimuthal_profiles[:, 2]), np.max(azimuthal_profiles[:, 3]), np.max(azimuthal_profiles[:, 4]), np.max(azimuthal_profiles[:, 5]), single_mode_strength[frame_i], single_mode_concentration[frame_i])
def choose_axis(i, axis):
# Orbit Number
time = float(fargo_par["Ninterm"]) * float(fargo_par["DT"])
orbit = int(round(time / (2 * np.pi), 0)) * i
# Axis
if axis == "zoom":
x = (rad - 1) / scale_height
prefix = "zoom_"
plot.xlim(0, 40) # to match the ApJL paper
#plot.ylim(0, 1.2)
xlabel = r"($r - r_p$) $/$ $h$"
else:
x = rad
prefix = ""
plot.xlim(float(fargo_par["Rmin"]) - 0.05, float(fargo_par["Rmax"]) + 0.05)
#plot.ylim(0, 5.0)
xlabel = "Radius"
# Data
vrad = (fromfile("gasvrad%d.dat" % i).reshape(num_rad, num_theta))
averaged_vrad = np.average(vrad, axis = 1)
### Plot ###
plot.plot(x, averaged_vrad, linewidth = linewidth, label = "%d" % frame)
# Annotate
this_title = readTitle()
plot.xlabel(xlabel, fontsize = fontsize)
plot.ylabel(r"Azimuthally Averaged $V_{rad}$", fontsize = fontsize)
plot.title("%s" % this_title, fontsize = fontsize + 1)
def get_data(frame_i, frame, modes = default_modes):
""" frame_i is ith frame, frame is frame number """
# Find Peak in Radial Profile (in Outer Disk)
density = (fromfile("gasdens%d.dat" % frame).reshape(num_rad, num_theta)) / surface_density
averagedDensity = np.average(density, axis = 1)
peak_rad, peak_density = find_peak(averagedDensity)
min_rad, min_density = find_min(averagedDensity, peak_rad)
# Gather Azimuthal Profiles
num_profiles = 7
spread = 1.0 * scale_height # half-width
azimuthal_radii = np.linspace(peak_rad - spread, peak_rad + spread, num_profiles)
azimuthal_indices = [np.searchsorted(rad, this_radius) for this_radius in azimuthal_radii]
azimuthal_profiles = np.array([np.fft.fft(density[azimuthal_index, :]) for azimuthal_index in azimuthal_indices])
# Normalize by m = 0 mode (integral of density), Take Absolute Value
azimuthal_profiles = np.array([np.abs(azimuthal_profile / azimuthal_profile[0]) for azimuthal_profile in azimuthal_profiles])
for m, mode in enumerate(modes):
modes_over_time[m, frame_i] = np.max(azimuthal_profiles[:, mode]) #np.sqrt(np.sum(np.power(azimuthal_profiles[:, mode], 2)))
single_mode_strength[frame_i] = modes_over_time[0, frame_i] / np.max(modes_over_time[1:, frame_i]) # m = 1 / Max of Higher Number Modes
single_mode_concentration[frame_i] = np.std(azimuthal_profiles[:, 1]) / modes_over_time[0, frame_i]
print "%d: %.4f, %.4f, %.4f, %.4f, %.4f - [%.4f, %.4f]" % (frame, np.max(azimuthal_profiles[:, 1]), np.max(azimuthal_profiles[:, 2]), np.max(azimuthal_profiles[:, 3]), np.max(azimuthal_profiles[:, 4]), np.max(azimuthal_profiles[:, 5]), single_mode_strength[frame_i], single_mode_concentration[frame_i])
def get_data(frame):
# Find Peak in Radial Profile (in Outer Disk)
density = (fromfile("gasdens%d.dat" % frame).reshape(num_rad, num_theta)) / surface_density
averagedDensity = np.average(density, axis = 1)
peak_rad, peak_index, peak_density = find_peak(averagedDensity)
min_rad, min_density = find_min(averagedDensity, peak_rad)
peak_theta, peak_theta_index, peak_azimuthal_density = find_azimuthal_peak(density[peak_index])
if len(sys.argv) > 2:
# Supply central theta as an argument
peak_theta = float(sys.argv[2])
# Gather Azimuthal Profiles
pressure = density * (scale_height)**2 * np.power(rad, -1)[:, None]
num_profiles = 5
spread = 30.0 # half-width
radial_theta = np.linspace(peak_theta - spread, peak_theta + spread, num_profiles)
radial_theta[radial_theta < 0] += 360.0
radial_theta[radial_theta > 360] -= 360.0
radial_indices = [np.searchsorted(theta, this_theta * (np.pi / 180.0)) for this_theta in radial_theta]
radial_profiles = [pressure[:, radial_index] for radial_index in radial_indices]
return radial_theta, radial_profiles
def read_nse(fin):
"""Read single electrode spike record.
Inputs:
fin - file handle
only_timestamps - if true, only load the timestamps, ignoring the waveform and feature data
Output: Dictionary with fields
'header' - header info
'packets' - pylab data structure with the spike data
Notes:
0. What is spike acquizition entity number? Ask neuralynx
1. Removing LOAD_ATTR overhead by defining time_stamp_append = [time_stamp[n].append for n in xrange(100)] and using
time_stamp_append[dwCellNumber](qwTimeStamp) in the loop does not seem to improve performance.
It reduces readability so I did not use it.
2. Disabling garbage collection did not help
3. In general, dictionary lookups slow things down
4. using numpy arrays, with preallocation is slower than the dumb, straightforward python list appending
"""
hdr = read_header(fin)
nse_packet = pylab.dtype([
('timestamp', 'Q'),
('saen', 'I'),
('cellno', 'I'),
('Features', '8I'),
('waveform', '32h')
])
data = pylab.fromfile(fin, dtype=nse_packet, count=-1)
return {'header': hdr, 'packets': data}
def gather_vortex_over_time():
""" add up vortex mass over time """
for frame in times:
density = (fromfile("gasdens%d.dat" % frame).reshape(
num_rad, num_theta))
normalized_density = density / surface_density_zero
vrad = (fromfile("gasvrad%d.dat" % frame).reshape(num_rad, num_theta))
vtheta = (fromfile("gasvtheta%d.dat" % frame).reshape(
num_rad, num_theta))
vorticity = curl(vrad, vtheta, rad, theta)
vortensity = vorticity / normalized_density[1:, 1:]
vortex_mass_i, _ = vortex_mass(rad, theta, density, vortensity)
vortex_masses.append(vortex_mass_i)
def get_data(frame):
# Find Peak in Radial Profile (in Outer Disk)
density = (fromfile("gasdens%d.dat" % frame).reshape(num_rad, num_theta)) / surface_density
averagedDensity = np.average(density, axis = 1)
peak_rad, peak_density = find_peak(averagedDensity)
min_rad, min_density = find_min(averagedDensity, peak_rad)
### Gather Azimuthal Profiles ###
num_profiles = 5
spread = 1.0 * scale_height # half-width
azimuthal_radii = np.linspace(peak_rad - spread, peak_rad + spread, num_profiles)
azimuthal_indices = [np.searchsorted(rad, this_radius) for this_radius in azimuthal_radii]
azimuthal_profiles = np.array([np.fft.fft(density[azimuthal_index, :]) for azimuthal_index in azimuthal_indices])
# Normalize by m = 0 mode (integral of density), Take Absolute Value
azimuthal_profiles = [np.abs(azimuthal_profile / azimuthal_profile[0]) for azimuthal_profile in azimuthal_profiles]
### Gather Averaged Profiles ###
start_half = azimuthal_indices[1]
end_half = azimuthal_indices[-2]
avg_half_profile = np.average(density[start_half : end_half, :], axis = 0)
avg_half = np.fft.fft(avg_half_profile)
start_full = azimuthal_indices[0]
end_full = azimuthal_indices[-1]
avg_full_profile = np.average(density[start_full : end_full, :], axis = 0)
avg_full = np.fft.fft(avg_full_profile)
# Normalize
avg_half = np.abs(avg_half / avg_half[0])
avg_full = np.abs(avg_full / avg_full[0])
return azimuthal_radii, azimuthal_profiles, avg_half, avg_full
def retrieve_density(frame, size):
""" Step 0: Retrieve density """
fn_i = "../%s-size/gasddens%d.dat" % (size, frame)
density = fromfile(fn_i).reshape(num_rad, num_theta)
return density
def read_nse(fin):
"""Read single electrode spike record.
Inputs:
fin - file handle
only_timestamps - if true, only load the timestamps, ignoring the waveform and feature data
Output: Dictionary with fields
'header' - header info
'packets' - pylab data structure with the spike data
Notes:
0. What is spike acquizition entity number? Ask neuralynx
1. Removing LOAD_ATTR overhead by defining time_stamp_append = [time_stamp[n].append for n in xrange(100)] and using
time_stamp_append[dwCellNumber](qwTimeStamp) in the loop does not seem to improve performance.
It reduces readability so I did not use it.
2. Disabling garbage collection did not help
3. In general, dictionary lookups slow things down
4. using numpy arrays, with preallocation is slower than the dumb, straightforward python list appending
"""
hdr = read_header(fin)
nse_packet = pylab.dtype([('timestamp', 'Q'), ('saen', 'I'),
('cellno', 'I'), ('Features', '8I'),
('waveform', '32h')])
data = pylab.fromfile(fin, dtype=nse_packet, count=-1)
return {'header': hdr, 'packets': data}
def read_data(frame, fn, fargo_par, id_number = None, version = None, directory = "."):
""" read data"""
######## Get Parameters #########
num_rad = fargo_par["Nrad"]
num_theta = fargo_par["Nsec"]
########### Method ##############
# Dictionary
basenames = {}
basenames['gas'] = "gasdens%d.dat"; basenames['dust'] = "gasddens%d.dat"; basenames['input_density'] = "id%04d_gasddens%d.p";
basenames['intensity'] = "id%04d_intensity%04d.dat"; basenames['polar_intensity'] = "id%04d_intensityMap%04d.p"; basenames['cartesian_intensity'] = "id%04d_intensityCartGrid%04d.p"
# Specific Data
basename = basenames[fn]
if "id" in basename:
basename = basename % (id_number, frame)
else:
basename = basename % frame
# Add Version
if version is not None:
basename = "v%04d_%s" % (version, basename)
# Load properly based on extension
ext = basename[basename.find("."):]
if fn == 'intensity':
data = (np.loadtxt("%s/%s" % (directory, basename))[:, -1]).reshape(num_rad, num_theta)
elif ext == ".dat":
data = (fromfile("%s/%s" % (directory, basename)).reshape(num_rad, num_theta))
elif ext == ".p":
data = pickle.load(open("%s/%s" % (directory, basename), "rb"))
return data
def get_contrasts(args_here):
# Unwrap Args
i, frame, directory = args_here
if frame == 8800:
frame = 8801 # Remove problem frame
# Get Data
density = fromfile("../%s/gasdens%d.dat" % (directory, frame)).reshape(
num_rad, num_theta) / surface_density_zero
density, shift_c = shift_density(density,
fargo_par,
reference_density=density)
azimuthal_profile = az.get_mean_azimuthal_profile(density,
fargo_par,
sliver_width=1.5,
end=1.85)
if "low_mass" in directory:
azimuthal_profile /= (0.3) # low-mass case
maxima_over_time[i] = np.percentile(azimuthal_profile, 90)
minima_over_time[i] = np.percentile(azimuthal_profile, 5)
contrasts_over_time[i] = maxima_over_time[i] / minima_over_time[i]
differences_over_time[i] = maxima_over_time[i] - minima_over_time[i]
print i, frame, differences_over_time[i], maxima_over_time[
i], minima_over_time[i], contrasts_over_time[i]
def make_plot(frame, show = False):
# Orbit Number
time = float(fargo_par["Ninterm"]) * float(fargo_par["DT"])
orbit = int(round(time / (2 * np.pi), 0)) * frame
# Set up figure
fig = plot.figure()
ax = fig.add_subplot(111, polar = True)
# Axis
rmax = 1.0 # to match ApJL paper
plot.xticks([], []) # Angles
plot.yticks([rmax], ["%.1f" % rmax]) # Max Radius
plot.ylim(0, rmax)
# Data
density = (fromfile("gasdens%d.dat" % frame).reshape(num_rad, num_theta))
normalized_density = density / surface_density_zero
### Plot ###
result = ax.pcolormesh(theta, rad, normalized_density, cmap = cmap)
fig.colorbar(result)
result.set_clim(clim[0], clim[1])
# Annotate
this_title = readTitle()
plot.title("Gas Density Map at Orbit %d: %s" % (orbit, this_title), fontsize = fontsize + 1)
# Save and Close
plot.savefig("%s/innerDensityMap_%04d.png" % (save_directory, frame), bbox_inches = 'tight', dpi = my_dpi)
if show:
plot.show()
plot.close(fig) # Close Figure (to avoid too many figures)
def get_quartiles(args):
# Unwrap Args
i, frame = args
# Get Dust Data
density = (fromfile("gasddens%d.dat" % frame).reshape(
num_rad, num_theta)) / surface_density_zero
background_density = (fromfile("gasddens0.dat").reshape(
num_rad, num_theta)) / surface_density_zero
# Get Vortex Vicinity Indices
averagedDensity = np.average(density, axis=1)
peak_rad, peak_density = find_peak(averagedDensity)
vortex_start = np.max([1.05, peak_rad - 5.0 * scale_height])
vortex_end = peak_rad + 5.0 * scale_height
vortex_start_i = np.searchsorted(rad, vortex_start)
vortex_end_i = np.searchsorted(rad, vortex_end)
# Extract Near Vortex
vortex_rad = rad[vortex_start_i:vortex_end_i]
vortex_density = density[vortex_start_i:vortex_end_i]
vortex_background_density = background_density[vortex_start_i:vortex_end_i]
# Look for 2x initial density (mask everything else)
not_overdense = np.array(vortex_density < 2.0 * vortex_background_density)
masked_density = (np.ma.array(
vortex_density,
mask=not_overdense)).compressed() # return non-masked data only
# Get Data (if not all masked)
if not np.all(not_overdense):
m50 = np.percentile(masked_density,
50) # Note: mask has no effect on np.percentile
m75 = np.percentile(masked_density, 75)
m90 = np.percentile(masked_density, 90)
m99 = np.percentile(masked_density, 99)
# Store Data
track50[i] = m50
track75[i] = m75
track90[i] = m90
track99[i] = m99
# Print Update
print "%d: %.4f, %.4f, %.4f, %.4f" % (frame, m50, m75, m90, m99)
def choose_axis(i, axis):
# Orbit Number
time = float(fargo_par["Ninterm"]) * float(fargo_par["DT"])
orbit = int(round(time / (2 * np.pi), 0)) * i
# Set up figure
fig = plot.figure(figsize = (700 / my_dpi, 600 / my_dpi), dpi = my_dpi)
# Axis
plot.ylim(0, 1.3)
if axis == "zoom":
x = (rad - 1) / scale_height
prefix = "zoom_"
plot.xlim(0, 40) # to match the ApJL paper
#plot.ylim(0, 1.3)
xlabel = r"($r - r_p$) $/$ $h$"
else:
x = rad
prefix = ""
plot.xlim(float(fargo_par["Rmin"]), float(fargo_par["Rmax"]))
xlabel = "Radius"
# Data
density = (fromfile("gasdens%d.dat" % i).reshape(num_rad, num_theta))
normalized_density = density / surface_density_zero
vrad = (fromfile("gasvrad%d.dat" % i).reshape(num_rad, num_theta))
vtheta = (fromfile("gasvtheta%d.dat" % i).reshape(num_rad, num_theta))
vorticity = util.velocity_curl(vrad, vtheta, rad, theta, average = True, frame = ref_frame)
vortensity = vorticity / normalized_density[1:, 1:]
averaged_w = np.average(vortensity, axis = 1)
### Plot ###
plot.plot(x[1:], averaged_w, linewidth = linewidth)
# Annotate
this_title = readTitle()
plot.xlabel(xlabel, fontsize = fontsize)
plot.ylabel("Azimuthally Averaged Vortensity", fontsize = fontsize)
plot.title("Orbit %d: %s" % (orbit, this_title), fontsize = fontsize + 1)
# Save and Close
plot.savefig("%s/%saveragedVortensity_%03d.png" % (save_directory, prefix, i), bbox_inches = 'tight', dpi = my_dpi)
if show:
plot.show()
plot.close(fig) # Close Figure (to avoid too many figures)
def make_plot(frame, show = False):
# Set up figure
#fig = plot.figure(figsize = (7, 6), dpi = dpi)
#ax = fig.add_subplot(111)
# Data
if merge > 0:
num_merged_cores = merge
density = util.read_merged_data(frame, num_merged_cores, num_rad, num_theta)
elif mpi:
field = "dens"
density = Fields("./", 'gas', frame).get_field(field).reshape(num_rad, num_theta)
else:
density = fromfile("gasdens%d.dat" % frame).reshape(num_rad, num_theta)
normalized_density = density / surface_density_zero
start = np.searchsorted(rad, 0.9)
end = np.searchsorted(rad, 1.1)
density_sliver = density[start:end]
planet_x = 1
planet_y = 0
planet_r = np.sqrt(planet_x**2 + planet_y**2)
dt = all_times[1] # 0.00410595556163
accreted_mass = 0.0
count1 = 0; count2 = 0
for i, r_i in enumerate(rad[start:end]):
for j, az_i in enumerate(theta):
xc = r_i * np.cos(az_i)
yc = r_i * np.sin(az_i)
dx = planet_x - xc
dy = planet_y - yc
distance = np.sqrt(dx**2 + dy**2)
r_roche = (planet_mass * 1e-3 / 3.0)**(1.0 / 3.0) * planet_r
cell_mass = density[start+i, j] * (np.pi / num_theta) * (rad[start+i+1]**2 - r_i**2)
dm = 0.0
if distance < 0.75 * r_roche:
dm = (1.0 / 3.0 * dt) * cell_mass
cell_mass *= (1.0 - 1.0 / 3.0 * dt)
count1 += 1
accreted_mass += dm
if distance < 0.45 * r_roche:
dm = (2.0 / 3.0 * dt) * cell_mass
count2 += 1
accreted_mass += dm
print count1, count2
print accreted_mass, accreted[0]
def make_plot(frame, show = False):
# Orbit Number
time = float(fargo_par["Ninterm"]) * float(fargo_par["DT"])
orbit = int(round(time / (2 * np.pi), 0)) * frame
# Set up figure
fig = plot.figure()
ax = fig.add_subplot(111)
# Axis
angles = np.linspace(0, 2 * np.pi, 7)
degree_angles = ["%d" % d_a for d_a in np.linspace(0, 360, 7)]
plot.ylim(0, 2 * np.pi)
plot.yticks(angles, degree_angles)
plot.xlim(float(fargo_par["Rmin"]), 1.0)
# Data
x = rad
density = (fromfile("gasdens%d.dat" % frame).reshape(num_rad, num_theta))
normalized_density = density / surface_density_zero
vrad = (fromfile("gasvrad%d.dat" % frame).reshape(num_rad, num_theta))
vtheta = (fromfile("gasvtheta%d.dat" % frame).reshape(num_rad, num_theta))
vorticity = curl(vrad, vtheta, rad, theta) / normalized_density[1:, 1:]
### Plot ###
result = ax.pcolormesh(x, theta, np.transpose(vorticity), cmap = cmap)
fig.colorbar(result)
result.set_clim(clim[0], clim[1])
# Annotate
this_title = readTitle()
plot.xlabel("Radius", fontsize = fontsize)
plot.ylabel(r"$\phi$", fontsize = fontsize)
plot.title("Vortensity Map at Orbit %d: %s" % (orbit, this_title), fontsize = fontsize + 1)
# Save and Close
plot.savefig("%s/vorticityMap_%03d.png" % (save_directory, frame), bbox_inches = 'tight', dpi = my_dpi)
if show:
plot.show()
plot.close(fig) # Close Figure (to avoid too many figures)
def choose_axis(i, axis):
# Orbit Number
time = float(fargo_par["Ninterm"]) * float(fargo_par["DT"])
orbit = int(round(time / (2 * np.pi), 0)) * i
# Set up figure
fig = plot.figure(figsize = (700 / my_dpi, 600 / my_dpi), dpi = my_dpi)
ax = fig.add_subplot(111, polar = True)
# Axis
if axis == "zoom":
prefix = "zoom_"
rmax = 2.4 # to match ApJL paper
else:
prefix = ""
rmax = float(fargo_par["Rmax"])
plot.xticks([], []) # Angles
plot.yticks([rmax], ["%.1f" % rmax]) # Max Radius
plot.ylim(0, rmax)
# Data
density = (fromfile("gasdens%d.dat" % i).reshape(num_rad, num_theta))
normalized_density = density / surface_density_zero
vrad = (fromfile("gasvrad%d.dat" % i).reshape(num_rad, num_theta))
vtheta = (fromfile("gasvtheta%d.dat" % i).reshape(num_rad, num_theta))
vorticity = util.velocity_curl(vrad, vtheta, rad, theta) / normalized_density[1:, 1:]
### Plot ###
result = ax.pcolormesh(theta, rad, vorticity, cmap = cmap)
fig.colorbar(result)
result.set_clim(clim[0], clim[1])
# Annotate
this_title = readTitle()
plot.title("Vortensity Map at Orbit %d\n%s" % (orbit, this_title), fontsize = fontsize + 1)
# Save and Close
plot.savefig("%s/%svortensityMap_%03d.png" % (save_directory, prefix, i), bbox_inches = 'tight', dpi = my_dpi)
if show:
plot.show()
plot.close(fig) # Close Figure (to avoid too many figures)
def make_plot(frame):
# Orbit Number
time = float(fargo_par["Ninterm"]) * float(fargo_par["DT"])
orbit = int(round(time / (2 * np.pi), 0)) * frame
# Set up figure
fig = plot.figure(figsize = (700 / my_dpi, 600 / my_dpi), dpi = my_dpi)
# Data
fargo_fn = "fargo2D1D"
if os.path.exists(fargo_fn):
# fargo2D1D
rad = np.loadtxt("used_rad1D.dat")[:-1]
vrad = fromfile("gasvrad1D%d.dat" % frame)
avg_pseudo_viscosity = (2.0 / 3) * (np.multiply(rad, vrad)) # should be equal to viscosity
else:
# fargo
rad = np.loadtxt("used_rad.dat")[:-1]
vrad = (fromfile("gasvrad%d.dat" % frame).reshape(num_rad, num_theta))
pseudo_viscosity = (2.0 / 3) * (np.multiply(rad[:, None], vrad)) # should be equal to viscosity
avg_pseudo_viscosity = np.average(pseudo_viscosity, axis = 1) # radial pseudo-viscosity
# Curves
plot.plot(rad, avg_pseudo_viscosity, color = "blue", label = "+", linewidth = linewidth) # positive
plot.plot(rad, -avg_pseudo_viscosity, color = "red", label = "-", linewidth = linewidth) # negative
plot.plot([rad[0], rad[-1]], [viscosity, viscosity], color = "black", linewidth = linewidth - 1)
# Limits
plot.xlim(rad[0], rad[-1])
plot.yscale('log')
# Annotate
plot.xlabel("Radius", fontsize = fontsize)
plot.ylabel("Pseudo Viscosity", fontsize = fontsize)
plot.title("Orbit %d" % orbit, fontsize = fontsize + 1)
plot.legend(loc = "upper right")
# Save + Close
plot.savefig("%s/viscosity_diagnosis_%04d.png" % (directory, frame), bbox_inches = 'tight', dpi = my_dpi)
plot.show()
plot.close(fig) # Close Figure (to avoid too many figures)
def measure_asymmetry(frame):
# Find Peak in Radial Profile (in Outer Disk)
density = (fromfile("gasdens%d.dat" % frame).reshape(num_rad, num_theta)) / surface_density
averagedDensity = np.average(density, axis = 1)
peak_rad, peak_rad_index, peak_density = find_radial_peak(averagedDensity)
# Take Weighted Average of Azimuthal Profiles
num_profiles = 7
weights = gaussian(num_profiles, scale = num_profiles / 2.0)
spread = 1.5 * scale_height # half-width
azimuthal_radii = np.linspace(peak_rad - spread, peak_rad + spread, num_profiles)
azimuthal_indices = [np.searchsorted(rad, this_radius) for this_radius in azimuthal_radii]
azimuthal_profiles = np.array([density[azimuthal_index, :] for azimuthal_index in azimuthal_indices])
weighted_azimuthal_profile = np.average(azimuthal_profiles, weights = weights, axis = 0)
# Find Peak in Azimuthal Profile (and center around that peak)
peak_theta, peak_theta_index = find_azimuthal_peak(weighted_azimuthal_profile)
initial_center = np.searchsorted(theta, np.pi)
centered_profiles = np.roll(azimuthal_profiles, initial_center - peak_theta_index, axis = 1)
centered_profile = np.roll(weighted_azimuthal_profile, initial_center - peak_theta_index)
# Choose Threshold
#pass
# Find Bounds Marked by Threshold
high_bound_index = np.argmax(centered_profile[initial_center : ] < threshold)
low_bound_index = np.argmax((centered_profile[::-1])[len(centered_profile) - initial_center : ] < threshold)
# Convert Back to Thetas and Indices
high_theta_index = (initial_center) + high_bound_index
low_theta_index = (len(centered_profile) - initial_center) - low_bound_index
high_theta = theta[high_theta_index]
low_theta = theta[low_theta_index]
azimuthal_extent = (180.0 / np.pi) * (high_theta - low_theta)
print "%d: %.1f, %d, %d" % (frame, azimuthal_extent, low_theta_index, high_theta_index)
if azimuthal_extent > 5:
# Find Quartiles (25%, 50%, 75%)
lower_quartile = np.percentile(centered_profiles[:, low_theta_index : high_theta_index], 25)
avg_density = np.percentile(centered_profiles[:, low_theta_index : high_theta_index], 50)
upper_quartile = np.percentile(centered_profiles[:, low_theta_index : high_theta_index], 75)
return azimuthal_extent, avg_density, lower_quartile, upper_quartile
else:
# No Vortex Yet (or any features really)
return azimuthal_extent, threshold, threshold, threshold
def get_excess_mass(args):
# Unwrap Args
i, frame = args
# Get Data
density = (fromfile("gasdens%d.dat" % frame).reshape(num_rad, num_theta)) / surface_density_zero
background_density = (fromfile("gasdens%d.dat" % (frame - 1)).reshape(num_rad, num_theta)) / surface_density_zero
diff_density = density - background_density
diff_density[diff_density < 0] = 0 # only include excess
# Extract Near Vortex
averagedDensity = np.average(density, axis = 1)
peak_rad, peak_density = find_peak(averagedDensity)
vortex_start = np.max([1.0, peak_rad - 5.0 * scale_height])
vortex_end = peak_rad + 5.0 * scale_height
vortex_start_i = np.searchsorted(rad, vortex_start)
vortex_end_i = np.searchsorted(rad, vortex_end)
vortex_rad = rad[vortex_start_i : vortex_end_i]
vortex_diff_density = diff_density[vortex_start_i : vortex_end_i]
vortex_excess = np.average(vortex_diff_density, axis = 1)
# Add up mass
dr = rad[1] - rad[0] # assumes arithmetic grid
d_phi = theta[1] - theta[0]
excess_mass = np.sum((dr * d_phi) * vortex_rad[:, None] * vortex_diff_density)
# Get Peak
peak_diff_density = np.max(vortex_excess)
# Print Update
print "%d: %.4f, %.4f" % (frame, excess_mass, peak_diff_density)
# Store Data
mass_over_time[i] = excess_mass
peak_over_time[i] = peak_diff_density
def make_plot():
# Set up figure
fig = plot.figure(figsize = (700 / my_dpi, 600 / my_dpi), dpi = my_dpi)
### Data ###
xs = range(mass_taper)
# Measure 1: Diff Mass Accretion
data = np.loadtxt(planet_fn)
masses = (data[:, 5]) # Planet Mass from 0 to Mass Taper
tapering_accretion = np.diff(masses[:mass_taper + 1])
# Measure 2: Viscosity
viscous_accretion = 3.0 * np.pi * surface_density * viscosity
# Measure 3: Radial Velocity
near_planet = 1.0
radius_near_planet = np.searchsorted(rad, near_planet)
rate = 10
xs_vrad = range(0, mass_taper, rate)
radial_velocity_at_planet = np.zeros(len(xs_vrad))
for i, frame in enumerate(xs_vrad):
vrad = (fromfile("gasvrad%d.dat" % frame).reshape(num_rad, num_theta))
radial_velocity_at_planet[i] = np.average(vrad[radius_near_planet, :])
radius = 1.0
radial_accretion = 2.0 * np.pi * radius * surface_density * radial_velocity_at_planet
# Curves
plot.plot(xs, tapering_accretion, color = "blue", label = "taper", linewidth = linewidth)
plot.plot([xs[0], xs[-1]], [viscous_accretion, viscous_accretion], color = "black", label = "viscous", linewidth = linewidth)
plot.plot(xs_vrad, radial_velocity_at_planet, color = "red", label = "v_rad (+)", linewidth = linewidth) # Positive
plot.plot(xs_vrad, -radial_velocity_at_planet, color = "orange", label = "v_rad (-)", linewidth = linewidth) # Negative
# Limits
plot.xlim(xs[0], xs[-1])
plot.yscale('log')
# Annotate
this_title = readTitle()
plot.xlabel("Number of Orbits", fontsize = fontsize)
plot.ylabel("Accretion Rate", fontsize = fontsize)
plot.title("Accretion for %s" % (this_title), fontsize = fontsize + 1)
plot.legend(loc = "upper right", bbox_to_anchor = (1.36, 1.0)) # outside of plot
# Save + Close
plot.savefig("accretion_diagnosis.png", bbox_inches = 'tight', dpi = my_dpi)
plot.show()
plot.close(fig) # Close Figure (to avoid too many figures)
def choose_axis(i, axis):
# Orbit Number
time = float(fargo_par["Ninterm"]) * float(fargo_par["DT"])
orbit = int(round(time / (2 * np.pi), 0)) * i
# Set up figure
fig = plot.figure(figsize = (700 / my_dpi, 600 / my_dpi), dpi = my_dpi)
ax = fig.add_subplot(111)
# Axis
angles = np.linspace(0, 2 * np.pi, 7)
degree_angles = ["%d" % d_a for d_a in np.linspace(0, 360, 7)]
plot.ylim(0, 2 * np.pi)
plot.yticks(angles, degree_angles)
if axis == "zoom":
x = (rad - 1) / scale_height
prefix = "zoom_"
plot.xlim(0, 40) # to match the ApJL paper
xlabel = r"($r - r_p$) $/$ $h$"
else:
x = rad
prefix = ""
plot.xlim(float(fargo_par["Rmin"]), float(fargo_par["Rmax"]))
xlabel = "Radius"
# Data
density = (fromfile("gasdens%d.dat" % i).reshape(num_rad, num_theta))
normalized_density = density / surface_density_zero
torque_map = util.torque(rad, theta, normalized_density, )
abs_torque = np.abs(torque_map)
log_torque = np.log(abs_torque) / np.log(10) # log torque in base 10
### Plot ###
result = ax.pcolormesh(x, theta, np.transpose(abs_torque), cmap = cmap)
fig.colorbar(result)
result.set_clim(clim[0], clim[1])
# Annotate
plot.xlabel(xlabel, fontsize = fontsize)
plot.ylabel(r"$\phi$", fontsize = fontsize)
plot.title("Torque Map at Orbit %d" % orbit, fontsize = fontsize + 1)
# Save and Close
plot.savefig("%s/%storqueMap_%03d.png" % (save_directory, prefix, i), bbox_inches = 'tight', dpi = my_dpi)
if show:
plot.show()
plot.close(fig) # Close Figure (to avoid too many figures)
def choose_axis(i, axis):
# Orbit Number
time = float(fargo_par["Ninterm"]) * float(fargo_par["DT"])
orbit = int(round(time / (2 * np.pi), 0)) * i
# Axis
if axis == "zoom":
x = (rad - 1) / scale_height
prefix = "zoom_"
plot.xlim(0, 40) # to match the ApJL paper
#plot.ylim(0, 1.2)
xlabel = r"($r - r_p$) $/$ $h$"
else:
x = rad
prefix = ""
plot.xlim(float(fargo_par["Rmin"]) - 0.05, float(fargo_par["Rmax"]) + 0.05)
#plot.ylim(0, 5.0)
xlabel = "Radius"
# Data
density = (fromfile("gasdens%d.dat" % i).reshape(num_rad, num_theta))
normalized_density = density / surface_density_zero
vrad = (fromfile("gasvrad%d.dat" % i).reshape(num_rad, num_theta))
vtheta = (fromfile("gasvtheta%d.dat" % i).reshape(num_rad, num_theta))
vorticity = util.velocity_curl(vrad, vtheta, rad, theta, average = True, frame = ref_frame)
vortensity = vorticity / normalized_density[1:, 1:]
averaged_w = np.average(vortensity, axis = 1)
### Plot ###
plot.plot(x, averaged_w, linewidth = linewidth, label = "%d" % frame)
# Annotate
this_title = readTitle()
plot.xlabel(xlabel, fontsize = fontsize)
plot.ylabel(r"Azimuthally Averaged Vortensity", fontsize = fontsize)
plot.title("%s" % this_title, fontsize = fontsize + 1)
def choose_axis(i, axis):
# Orbit Number
time = float(fargo_par["Ninterm"]) * float(fargo_par["DT"])
orbit = int(round(time / (2 * np.pi), 0)) * i
# Set up figure
fig = plot.figure(figsize = (700 / my_dpi, 600 / my_dpi), dpi = my_dpi)
ax = fig.add_subplot(111, polar = True)
# Axis
angles = np.linspace(0, 2 * np.pi, 7)
degree_angles = ["%d" % d_a for d_a in np.linspace(0, 360, 7)]
plot.ylim(0, 2 * np.pi)
plot.yticks(angles, degree_angles)
# Axis
if axis == "zoom":
prefix = "zoom_"
rmax = 2.4 # to match ApJL paper
else:
prefix = ""
rmax = float(fargo_par["Rmax"])
plot.xticks([], []) # Angles
plot.yticks([rmax], ["%.1f" % rmax]) # Max Radius
plot.ylim(0, rmax)
# Data
density = (fromfile("gasdens%d.dat" % i).reshape(num_rad, num_theta))
normalized_density = density / surface_density_zero
torque_map = util.torque(rad, theta, normalized_density, planet_mass = planet_mass)
abs_torque = np.abs(torque_map)
log_torque = np.log(abs_torque) / np.log(10) # log torque in base 10
### Plot ###
result = ax.pcolormesh(theta, rad, log_torque, cmap = cmap)
fig.colorbar(result)
result.set_clim(clim[0], clim[1])
# Annotate
plot.title("Torque Map at Orbit %d" % orbit, fontsize = fontsize + 1)
# Save and Close
plot.savefig("%s/%storqueMap_%03d.png" % (save_directory, prefix, i), bbox_inches = 'tight', dpi = my_dpi)
if show:
plot.show()
plot.close(fig) # Close Figure (to avoid too many figures)
def read_nev(fin, parse_event_string=False):
"""Read an event file.
Input:
fin - file handle
parse_event_string - If set to true then parse the eventstrings nicely. This takes extra time. Default is False
Ouput:
Dictionary with fields
'header' - the file header
'packets' - the events. This is a new pylab dtype with fields corresponding to the event packets.
'nstx'
'npkt_id'
'npkt_data_size'
'timestamp' - timestamp (us)
'eventid'
'nttl' - value of the TTL port
'ncrc'
'ndummy1'
'ndummy2'
'dnExtra'
'eventstring' - The alphanumeric string NeuraLynx attaches to this event
'eventstring' - Only is parse_event_string is set to True. This is a nicely formatted eventstring
"""
hdr = read_header(fin)
nev_packet = pylab.dtype([
('nstx', 'h'),
('npkt_id', 'h'),
('npkt_data_size', 'h'),
('timestamp', 'Q'),
('eventid', 'h'),
('nttl', 'H'),
('ncrc', 'h'),
('ndummy1', 'h'),
('ndummy2', 'h'),
('dnExtra', '8i'),
('eventstring', '128c')
])
data = pylab.fromfile(fin, dtype=nev_packet, count=-1)
logger.debug('{:d} events'.format(data['timestamp'].size))
if parse_event_string:
logging.info('Packaging the event strings. This makes things slower.')
# Makes things slow. Often this field is not needed
evstring = [None]*data['timestamp'].size
for n in xrange(data['timestamp'].size):
str = ''.join(data['eventstring'][n])
evstring[n] = str.replace('\00','').strip()
return {'header': hdr, 'packets': data, 'eventstring': evstring}
else:
return {'header': hdr, 'packets': data}