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):
# Set up figure
fig = plot.figure(figsize = (7, 6), dpi = dpi)
ax = fig.add_subplot(111)
# Data
if merge > 0:
num_merged_cores = merge
energy = util.read_merged_data(frame, num_merged_cores, num_rad, num_theta)
elif mpi:
field = "dens"
energy = Fields("./", 'gas', frame).get_field(field).reshape(num_rad, num_theta)
else:
energy = fromfile("gasenergy%d.dat" % frame).reshape(num_rad, num_theta)
averagedEnergy = np.average(energy, axis = 1)
normalized_energy = averagedEnergy
### Plot ###
x = rad
y = normalized_energy
result = plot.plot(x, y, linewidth = linewidth, zorder = 99)
if args.zero:
energy_zero = fromfile("gasenergy0.dat").reshape(num_rad, num_theta)
averagedEnergy_zero = np.average(energy_zero, axis = 1)
normalized_energy_zero = averagedEnergy_zero
x = rad
y_zero = normalized_energy_zero
result = plot.plot(x, y_zero, linewidth = linewidth, zorder = 0)
if args.compare is not None:
directory = args.compare
density_compare = (fromfile("%s/gasdens%d.dat" % (directory, frame)).reshape(num_rad, num_theta))
averagedDensity_compare = np.average(density_compare, axis = 1)
normalized_density_compare = averagedDensity_compare / surface_density_zero
### Plot ###
x = rad
y_compare = normalized_density_compare
result = plot.plot(x, y_compare, linewidth = linewidth, alpha = 0.6, zorder = 99, label = "compare")
plot.legend()
# Axes
if args.max_y is None:
x_min_i = np.searchsorted(x, x_min)
x_max_i = np.searchsorted(x, x_max)
max_y = 1.1 * max(y[x_min_i : x_max_i])
else:
max_y = args.max_y
plot.xlim(x_min, x_max)
#plot.ylim(0, max_y)
# Annotate Axes
orbit = (dt / (2 * np.pi)) * frame
if orbit >= taper_time:
current_mass = planet_mass
else:
current_mass = np.power(np.sin((np.pi / 2) * (1.0 * orbit / taper_time)), 2) * planet_mass
current_mass += accreted_mass[frame]
#title = readTitle()
unit = "r_\mathrm{p}"
plot.xlabel(r"Radius [$%s$]" % unit, fontsize = fontsize)
plot.ylabel(r"$\Sigma / \Sigma_0$", fontsize = fontsize)
#if title is None:
# plot.title("Dust Density Map\n(t = %.1f)" % (orbit), fontsize = fontsize + 1)
#else:
# plot.title("Dust Density Map\n%s\n(t = %.1f)" % (title, orbit), fontsize = fontsize + 1)
x_range = x_max - x_min; x_mid = x_min + x_range / 2.0
y_text = 1.14
#title1 = r"$T_\mathrm{growth} = %d$ $\mathrm{orbits}$" % (taper_time)
title1 = r"$\Sigma_0 = %.3e$ $M_c = %.2f\ M_J$ $A = %.2f$" % (surface_density_zero, planet_mass, accretion)
title2 = r"$t = %d$ $\mathrm{orbits}}$ [$m_\mathrm{p}(t)\ =\ %.2f$ $M_\mathrm{Jup}$]" % (orbit, current_mass)
plot.title("%s" % (title2), y = 1.015, fontsize = fontsize + 1)
plot.text(x_mid, y_text * plot.ylim()[-1], title1, horizontalalignment = 'center', bbox = dict(facecolor = 'none', edgecolor = 'black', linewidth = 1.5, pad = 7.0), fontsize = fontsize + 2)
# Text
text_mass = r"$M_\mathrm{p} = %d$ $M_\mathrm{Jup}$" % (int(planet_mass))
text_visc = r"$\alpha_\mathrm{disk} = 3 \times 10^{%d}$" % (int(np.log(viscosity) / np.log(10)) + 2)
#plot.text(-0.9 * box_size, 2, text_mass, fontsize = fontsize, color = 'black', horizontalalignment = 'left', bbox=dict(facecolor = 'white', edgecolor = 'black', pad = 10.0))
#plot.text(0.9 * box_size, 2, text_visc, fontsize = fontsize, color = 'black', horizontalalignment = 'right', bbox=dict(facecolor = 'white', edgecolor = 'black', pad = 10.0))
#plot.text(-0.84 * x_range / 2.0 + x_mid, y_text * plot.ylim()[-1], text_mass, fontsize = fontsize, color = 'black', horizontalalignment = 'right')
#plot.text(0.84 * x_range / 2.0 + x_mid, y_text * plot.ylim()[-1], text_visc, fontsize = fontsize, color = 'black', horizontalalignment = 'left')
# Save, Show, and Close
if version is None:
save_fn = "%s/averagedEnergy_%04d.png" % (save_directory, frame)
else:
save_fn = "%s/v%04d_averagedEnergy_%04d.png" % (save_directory, version, frame)
plot.savefig(save_fn, bbox_inches = 'tight', dpi = dpi)
if show:
plot.show()
plot.close(fig) # Close Figure (to avoid too many figures)
def add_to_plot(i, grain):
# Identify Subplot
number = i + 1
ax = plot.subplot(3, 1, number)
# Data
if merge > 0:
num_merged_cores = merge
gas_density = util.read_merged_data(frame, num_merged_cores,
num_rad, num_theta)
if i > 0:
density = util.read_merged_data(frame,
num_merged_cores,
num_rad,
num_theta,
fluid='dust%d' % i)
elif mpi:
field = "dens"
gas_density = Fields("./", 'gas', frame).get_field(field).reshape(
num_rad, num_theta)
if i > 0:
density = Fields("./", 'dust%d' % i,
frame).get_field(field).reshape(
num_rad, num_theta)
else:
gas_density = fromfile("gasdens%d.dat" % frame).reshape(
num_rad, num_theta)
if i > 0:
density = fromfile("dust%ddens%d.dat" % (i, frame)).reshape(
num_rad, num_theta)
normalized_gas_density = gas_density / surface_density_zero
if i > 0:
normalized_density = density / dust_surface_density_zero
if center:
if i > 0:
normalized_density, shift_c = shift_density(
normalized_density,
fargo_par,
reference_density=normalized_gas_density)
normalized_gas_density, shift_c = shift_density(
normalized_gas_density,
fargo_par,
reference_density=normalized_gas_density)
### Plot ###
x = theta * (180.0 / np.pi)
y = rad
if i == 0:
cmap = 'viridis'
result = ax.pcolormesh(x, y, normalized_gas_density, cmap=cmap)
cbar = fig.colorbar(result)
result.set_clim(0, cmaxGas)
else:
cmap = args.cmap
result = ax.pcolormesh(x, y, normalized_density, cmap=cmap)
cbar = fig.colorbar(result)
result.set_clim(0, cmax[i - 1])
if number == 1:
cbar.set_label(r"$\Sigma$ / $\Sigma_\mathrm{0,}$ $_\mathrm{gas}$",
fontsize=fontsize,
rotation=270,
labelpad=25)
elif number == 3:
cbar.set_label(r"$\Sigma$ / $\Sigma_\mathrm{0,}$ $_\mathrm{dust}$",
fontsize=fontsize,
rotation=270,
labelpad=25)
if use_contours and i > 0:
levels = np.linspace(low_contour, high_contour, num_levels)
colors = generate_colors(num_levels)
plot.contour(x,
y,
normalized_gas_density,
levels=levels,
origin='upper',
linewidths=1,
colors=colors)
# Axes
plot.xlim(0, 360)
plot.ylim(y_min, y_max)
angles = np.linspace(0, 360, 7)
plot.xticks(angles)
ax.spines['bottom'].set_color('w')
ax.spines['top'].set_color('w')
ax.spines['left'].set_color('w')
ax.spines['right'].set_color('w')
ax.tick_params(colors='white', labelcolor='black', width=1, length=6)
# Annotate Axes
orbit = (dt / (2 * np.pi)) * frame
if orbit >= taper_time:
current_mass = planet_mass
else:
current_mass = np.power(
np.sin(
(np.pi / 2) * (1.0 * orbit / taper_time)), 2) * planet_mass
current_mass += accreted_mass[frame]
if number == 3:
plot.xlabel(r"$\phi$ $\mathrm{(degrees)}$", fontsize=fontsize)
if number == 1 or number == 3:
plot.ylabel(r"Radius [$r_\mathrm{p}$]", fontsize=fontsize)
if number == 1:
plot.title(
r"$t = %d$ $\mathrm{orbits}}$ [$m_\mathrm{p}(t)\ =\ %.2f$ $M_\mathrm{J}$]"
% (orbit, current_mass),
bbox=dict(facecolor='w', edgecolor='k', pad=10.0),
y=1.08,
fontsize=fontsize + 1)
# Label
left_x = plot.xlim()[0]
right_x = plot.xlim()[-1]
range_x = right_x - left_x
margin_x = 0.05 * range_x
bottom_y = plot.ylim()[0]
top_y = plot.ylim()[-1]
range_y = top_y - bottom_y
margin_y = 0.15 * range_y
if number == 1:
# Gas
title = r"$\mathrm{Gas\ Density}$"
#plot.text(left_x + margin_x, top_y - margin_y, title, fontsize = fontsize, color = 'black', horizontalalignment = 'left', bbox=dict(facecolor = 'white', edgecolor = 'black', pad = 10.0))
else:
# Dust
this_size = util.get_size(grain)
size_label = util.get_size_label(this_size)
stokes_number = util.get_stokes_number(this_size)
title = r"%s$\mathrm{-size}$" % size_label
stokes = r"$\mathrm{St}_\mathrm{0}$ $=$ $%.03f$" % stokes_number
#plot.text(left_x + margin_x, top_y - margin_y, title, fontsize = fontsize, color = 'white', horizontalalignment = 'left', bbox=dict(facecolor = 'black', edgecolor = 'white', pad = 10.0))
#plot.text(right_x - margin_x, top_y - margin_y, stokes, fontsize = fontsize, color = 'white', horizontalalignment = 'right', bbox=dict(facecolor = 'black', edgecolor = 'white', pad = 10.0))
# Text
line_y = top_y + 0.31 * range_y
linebreak = 0.16 * range_y
left_start_x = left_x - 3.0 * margin_x
right_end_x = right_x + 4.0 * margin_x
if number == 1:
line1 = r'$M_p = %d$ $M_J$' % planet_mass
line2 = r'$\nu = 10^{%d}$' % round(
np.log(viscosity) / np.log(10), 0)
plot.text(left_start_x,
line_y + linebreak,
line1,
horizontalalignment='left',
fontsize=fontsize + 1)
plot.text(left_start_x,
line_y,
line2,
horizontalalignment='left',
fontsize=fontsize + 1)
line3 = r'$T_\mathrm{growth} = %d$ $\rm{orbits}$' % taper_time
line4 = r"$N_\mathrm{r} \times \ N_\mathrm{\phi} = %d \times \ %d$" % (
num_rad, num_theta)
plot.text(right_end_x,
line_y + linebreak,
line3,
horizontalalignment='right',
fontsize=fontsize + 1)
plot.text(right_end_x,
line_y,
line4,
horizontalalignment='right',
fontsize=fontsize + 1)
def get_excess_mass(args_here):
# Unwrap Args
i, frame = args_here
# Get Data
if mpi:
field = "dens"
density = Fields("./", 'gas', frame).get_field(field).reshape(
num_rad, num_theta) / surface_density_zero
#background_density = Fields("./", 'gas', frame - 1).get_field(field).reshape(num_rad, num_theta) / surface_density_zero
else:
density = fromfile("dust%ddens%d.dat" % (dust_number, frame)).reshape(
num_rad, num_theta) / dust_surface_density_zero
#background_density = fromfile("dust1dens%d.dat" % (frame - 1)).reshape(num_rad, num_theta) / dust_surface_density_zero
if args.compare:
fargo_directory = args.compare
density_compare = (fromfile(
"%s/dust%ddens%d.dat" %
(fargo_directory, dust_number, frame)).reshape(
num_rad, num_theta)) / dust_surface_density_zero
#background_density_compare = (fromfile("%s/dust1dens%d.dat" % (fargo_directory, frame - 1)).reshape(num_rad, num_theta)) / dust_surface_density_zero
def helper(density):
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=0)
variance = np.std(vortex_excess)
average = np.average(vortex_excess)
# 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)
#return excess_mass, vortex_excess
return variance / average, vortex_excess
excess_mass, vortex_excess = helper(density)
if args.compare:
excess_mass_compare, vortex_excess_compare = helper(density_compare)
# Get Peak
peak_diff_density = np.max(vortex_excess)
if args.compare:
peak_diff_density_compare = np.max(vortex_excess_compare)
# Print Update
print "%d: %.4f, %.4f" % (frame, excess_mass, peak_diff_density)
if args.compare:
print "%d: %.4f, %.4f" % (frame, excess_mass_compare,
peak_diff_density_compare)
# Store Data
mass_over_time[i] = excess_mass
peak_over_time[i] = peak_diff_density
if args.compare:
mass_over_time_compare[i] = excess_mass_compare
peak_over_time_compare[i] = peak_diff_density_compare
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
gas_density = util.read_merged_data(frame, num_merged_cores, num_rad,
num_theta)
velocity = util.read_merged_data(frame,
num_merged_cores,
num_rad,
num_theta,
field="vx")
elif mpi:
gas_density = Fields("./", 'gas', frame).get_field("dens").reshape(
num_rad, num_theta)
velocity = Fields("./", 'gas',
frame).get_field("vx").reshape(num_rad, num_theta)
else:
gas_density = fromfile("gasdens%d.dat" % frame).reshape(
num_rad, num_theta)
velocity = fromfile("gasvx%d.dat" % frame).reshape(num_rad, num_theta)
normalized_gas_density = gas_density / surface_density_zero
if center:
velocity, shift_c = shift_data(
velocity, fargo_par, reference_density=normalized_gas_density)
normalized_gas_density, shift_c = shift_data(
normalized_gas_density,
fargo_par,
reference_density=normalized_gas_density)
# Take Residual
keplerian_velocity = rad * (np.power(
rad, -1.5) - 1) # in rotating frame, v_k = r * (r^-1.5 - r_p^-1.5)
sub_keplerian_velocity = keplerian_velocity - 0.5 * np.power(
scale_height, 2)
velocity -= keplerian_velocity[:, None]
### Plot ###
x = rad
y = theta * (180.0 / np.pi)
result = ax.pcolormesh(x, y, np.transpose(velocity), cmap=cmap)
fig.colorbar(result)
result.set_clim(clim[0], clim[1])
if ref:
for i, value in enumerate(np.arange(x[0], x[-1], 0.1)):
plot.plot([value, value], [0, 360], c='k', linewidth=1)
for i, value in enumerate(np.arange(y[0], y[-1], 10)):
plot.plot([x[0], x[-1]], [value, value], c='k', linewidth=1)
if use_contours:
levels = np.linspace(low_contour, high_contour, num_levels)
colors = generate_colors(num_levels)
plot.contour(x,
y,
np.transpose(normalized_gas_density),
levels=levels,
origin='upper',
linewidths=1,
colors=colors)
# Axes
plot.xlim(x_min, x_max)
plot.ylim(0, 360)
angles = np.linspace(0, 360, 7)
plot.yticks(angles)
# Annotate Axes
orbit = (dt / (2 * np.pi)) * frame
if orbit >= taper_time:
current_mass = planet_mass
else:
current_mass = np.power(
np.sin((np.pi / 2) * (1.0 * orbit / taper_time)), 2) * planet_mass
current_mass += accreted_mass[frame]
#title = readTitle()
unit = "r_\mathrm{p}"
plot.xlabel(r"Radius [$%s$]" % unit, fontsize=fontsize)
plot.ylabel(r"$\phi$", fontsize=fontsize)
title2 = r"$t = %d$ $\mathrm{orbits}}$ [$m_\mathrm{p}(t)\ =\ %.2f$ $M_\mathrm{Jup}$]" % (
orbit, current_mass)
plot.title("%s" % (title2), y=1.015, fontsize=fontsize + 1)
# Save, Show, and Close
if version is None:
save_fn = "%s/azimuthalVelocityMap_%04d.png" % (save_directory, frame)
else:
save_fn = "%s/v%04d_azimuthalVelocityMap_%04d.png" % (save_directory,
version, frame)
plot.savefig(save_fn, bbox_inches='tight', dpi=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
gas_density = util.read_merged_data(frame, num_merged_cores, num_rad,
num_theta)
velocity = util.read_merged_data(frame,
num_merged_cores,
num_rad,
num_theta,
field="vx",
fluid="dust%d" % dust_number)
elif mpi:
gas_density = Fields("./", 'gas', frame).get_field("dens").reshape(
num_rad, num_theta)
velocity = Fields("./", 'dust%d' % dust_number,
frame).get_field("vx").reshape(num_rad, num_theta)
else:
gas_density = fromfile("gasdens%d.dat" % frame).reshape(
num_rad, num_theta)
velocity = fromfile("dust%dvx%d.dat" % (dust_number, frame)).reshape(
num_rad, num_theta)
normalized_gas_density = gas_density / surface_density_zero
## Subtract Keplerian Velocity ##
keplerian_velocity = rad * (np.power(rad, -1.5) - 1)
velocity -= keplerian_velocity[:, np.newaxis]
### Plot ###
x = rad
y = theta * (180.0 / np.pi)
result = ax.pcolormesh(x, y, np.transpose(velocity), cmap=cmap)
fig.colorbar(result)
result.set_clim(clim[0], clim[1])
if use_contours:
levels = np.linspace(low_contour, high_contour, num_levels)
colors = generate_colors(num_levels)
plot.contour(x,
y,
np.transpose(normalized_density),
levels=levels,
origin='upper',
linewidths=1,
colors=colors)
# Axes
plot.xlim(x_min, x_max)
plot.ylim(0, 360)
angles = np.linspace(0, 360, 7)
plot.yticks(angles)
# Annotate Axes
orbit = (dt / (2 * np.pi)) * frame
if orbit >= taper_time:
current_mass = planet_mass
else:
current_mass = np.power(
np.sin((np.pi / 2) * (1.0 * orbit / taper_time)), 2) * planet_mass
#title = readTitle()
unit = "r_\mathrm{p}"
plot.xlabel(r"Radius [$%s$]" % unit, fontsize=fontsize)
plot.ylabel(r"$\phi$", fontsize=fontsize)
title2 = r"$t = %d$ $\mathrm{orbits}}$ [$m_\mathrm{p}(t)\ =\ %.2f$ $M_\mathrm{Jup}$]" % (
orbit, current_mass)
plot.title("%s" % (title2), y=1.015, fontsize=fontsize + 1)
# Save, Show, and Close
if version is None:
save_fn = "%s/azimuthalVelocityMap_%04d.png" % (save_directory, frame)
else:
save_fn = "%s/v%04d_azimuthalVelocityMap_%04d.png" % (save_directory,
version, frame)
plot.savefig(save_fn, bbox_inches='tight', dpi=dpi)
if show:
plot.show()
plot.close(fig) # Close Figure (to avoid too many figures)
def old_make_plot(frame, show=False):
# Set up figure
fig = plot.figure(figsize=(7, 6), dpi=dpi)
ax = fig.add_subplot(111)
# Data
density = (fromfile("gasdens%d.dat" % frame).reshape(num_rad, num_theta))
if center:
if taper_time < 10.1:
shift_c = az.get_azimuthal_peak(density, fargo_par)
else:
threshold = util.get_threshold(size)
shift_c = az.get_azimuthal_center(density,
fargo_par,
threshold=threshold *
surface_density_zero)
density = np.roll(density, shift_c)
normalized_density = density / dust_surface_density_zero
### Plot ###
x = rad
y = theta * (180.0 / np.pi)
result = ax.pcolormesh(x, y, np.transpose(normalized_density), cmap=cmap)
fig.colorbar(result)
result.set_clim(clim[0], clim[1])
if use_contours:
gas_density = Fields("./", 'gas', frame).get_field(field).reshape(
num_rad, num_theta) / surface_density_zero
levels = np.linspace(low_contour, high_contour, num_levels)
colors = generate_colors(num_levels)
plot.contour(x,
y,
np.transpose(gas_density),
levels=levels,
origin='upper',
linewidths=1,
colors=colors)
# Axes
plot.xlim(x_min, x_max)
plot.ylim(0, 360)
angles = np.linspace(0, 360, 7)
plot.yticks(angles)
# Annotate Axes
time = fargo_par["Ninterm"] * fargo_par["DT"]
orbit = (time / (2 * np.pi)) * frame
if orbit >= taper_time:
current_mass = planet_mass
else:
current_mass = np.power(
np.sin((np.pi / 2) * (1.0 * orbit / taper_time)), 2) * planet_mass
#title = readTitle()
unit = "r_\mathrm{p}"
plot.xlabel(r"Radius [$%s$]" % unit, fontsize=fontsize)
plot.ylabel(r"$\phi$", fontsize=fontsize)
#if title is None:
# plot.title("Dust Density Map\n(t = %.1f)" % (orbit), fontsize = fontsize + 1)
#else:
# plot.title("Dust Density Map\n%s\n(t = %.1f)" % (title, orbit), fontsize = fontsize + 1)
x_range = x_max - x_min
x_mid = x_min + x_range / 2.0
y_text = 1.14
title1 = r"$T_\mathrm{growth} = %d$ $\mathrm{orbits}$" % (taper_time)
title2 = r"$t = %d$ $\mathrm{orbits}}$ [$m_\mathrm{p}(t)\ =\ %.2f$ $M_\mathrm{Jup}$]" % (
orbit, current_mass)
plot.title("%s" % (title2), y=1.015, fontsize=fontsize + 1)
plot.text(x_mid,
y_text * plot.ylim()[-1],
title1,
horizontalalignment='center',
bbox=dict(facecolor='none',
edgecolor='black',
linewidth=1.5,
pad=7.0),
fontsize=fontsize + 2)
# Text
text_mass = r"$M_\mathrm{p} = %d$ $M_\mathrm{Jup}$" % (int(planet_mass))
text_visc = r"$\alpha_\mathrm{disk} = 3 \times 10^{%d}$" % (
int(np.log(viscosity) / np.log(10)) + 2)
#plot.text(-0.9 * box_size, 2, text_mass, fontsize = fontsize, color = 'black', horizontalalignment = 'left', bbox=dict(facecolor = 'white', edgecolor = 'black', pad = 10.0))
#plot.text(0.9 * box_size, 2, text_visc, fontsize = fontsize, color = 'black', horizontalalignment = 'right', bbox=dict(facecolor = 'white', edgecolor = 'black', pad = 10.0))
plot.text(-0.84 * x_range / 2.0 + x_mid,
y_text * plot.ylim()[-1],
text_mass,
fontsize=fontsize,
color='black',
horizontalalignment='right')
plot.text(0.84 * x_range / 2.0 + x_mid,
y_text * plot.ylim()[-1],
text_visc,
fontsize=fontsize,
color='black',
horizontalalignment='left')
# Save, Show, and Close
if version is None:
save_fn = "%s/dustDensityMap_%04d.png" % (save_directory, frame)
else:
save_fn = "%s/v%04d_dustDensityMap_%04d.png" % (save_directory,
version, frame)
plot.savefig(save_fn, bbox_inches='tight', dpi=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
gas_density = util.read_merged_data(frame, num_merged_cores, num_rad,
num_theta)
density = util.read_merged_data(frame,
num_merged_cores,
num_rad,
num_theta,
fluid='dust%d' % dust_number)
elif mpi:
field = "dens"
gas_density = Fields("./", 'gas', frame).get_field(field).reshape(
num_rad, num_theta)
density = Fields("./", 'dust%d' % dust_number,
frame).get_field(field).reshape(num_rad, num_theta)
else:
gas_density = fromfile("gasdens%d.dat" % frame).reshape(
num_rad, num_theta)
density = fromfile("dust%ddens%d.dat" % (dust_number, frame)).reshape(
num_rad, num_theta)
normalized_gas_density = gas_density / surface_density_zero
normalized_density = density / dust_surface_density_zero
if center:
normalized_density, shift_c = shift_density(
normalized_density,
fargo_par,
reference_density=normalized_gas_density)
normalized_gas_density, shift_c = shift_density(
normalized_gas_density,
fargo_par,
reference_density=normalized_gas_density)
### Plot ###
x = rad
y = theta * (180.0 / np.pi)
result = ax.pcolormesh(x, y, np.transpose(normalized_density), cmap=cmap)
fig.colorbar(result)
result.set_clim(clim[0], clim[1])
if use_contours:
levels = np.linspace(low_contour, high_contour, num_levels)
colors = generate_colors(num_levels)
plot.contour(x,
y,
np.transpose(normalized_gas_density),
levels=levels,
origin='upper',
linewidths=1,
colors=colors)
# Axes
plot.xlim(x_min, x_max)
plot.ylim(0, 360)
angles = np.linspace(0, 360, 7)
plot.yticks(angles)
# Annotate Axes
orbit = (dt / (2 * np.pi)) * frame
if orbit >= taper_time:
current_mass = planet_mass
else:
current_mass = np.power(
np.sin((np.pi / 2) * (1.0 * orbit / taper_time)), 2) * planet_mass
current_mass += accreted_mass[frame]
x_range = x_max - x_min
x_mid = x_min + x_range / 2.0
y_text = 1.14
#title = readTitle()
title1 = r"$\Sigma_0 = %.3e$ $M_c = %.2f\ M_J$ $A = %.2f$" % (
surface_density_zero, planet_mass, accretion)
title2 = r"$t = %d$ $\mathrm{orbits}}$ [$m_\mathrm{p}(t)\ =\ %.2f$ $M_\mathrm{Jup}$]" % (
orbit, current_mass)
plot.title("%s" % (title2), y=1.015, fontsize=fontsize + 1)
plot.text(x_mid,
y_text * plot.ylim()[-1],
title1,
horizontalalignment='center',
bbox=dict(facecolor='none',
edgecolor='black',
linewidth=1.5,
pad=7.0),
fontsize=fontsize + 2)
unit = "r_\mathrm{p}"
plot.xlabel(r"Radius [$%s$]" % unit, fontsize=fontsize)
plot.ylabel(r"$\phi$", fontsize=fontsize)
# Save, Show, and Close
if version is None:
save_fn = "%s/dustDensityMap_%04d.png" % (save_directory, frame)
else:
save_fn = "%s/v%04d_dustDensityMap_%04d.png" % (save_directory,
version, frame)
plot.savefig(save_fn, bbox_inches='tight', dpi=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
if center:
normalized_density, shift_c = shift_density(
normalized_density,
fargo_par,
reference_density=normalized_density)
### Plot ###
x = rad
y = theta * (180.0 / np.pi)
result = ax.pcolormesh(x, y, np.transpose(normalized_density), cmap=cmap)
cbar = fig.colorbar(result)
result.set_clim(clim[0], clim[1])
if use_contours:
levels = np.linspace(low_contour, high_contour, num_levels)
colors = generate_colors(num_levels)
plot.contour(x,
y,
np.transpose(normalized_density),
levels=levels,
origin='upper',
linewidths=1,
colors=colors)
if quiver:
# Velocity
radial_velocity = np.array(
fromfile("gasvy%d.dat" % frame).reshape(num_rad,
num_theta)) # Radial
azimuthal_velocity = np.array(
fromfile("gasvx%d.dat" % frame).reshape(num_rad,
num_theta)) # Azimuthal
keplerian_velocity = rad * (np.power(rad, -1.5) - 1)
azimuthal_velocity -= keplerian_velocity[:, None]
if center:
radial_velocity = np.roll(radial_velocity, shift_c, axis=-1)
azimuthal_velocity = np.roll(azimuthal_velocity, shift_c, axis=-1)
# Sub-sample the grid
start_i = np.searchsorted(rad, start_quiver)
end_i = np.searchsorted(rad, end_quiver)
x_q = x[start_i:end_i]
y_q = y[:]
u = np.transpose(radial_velocity)[:, start_i:end_i]
v = np.transpose(azimuthal_velocity)[:, start_i:end_i]
plot.quiver(x_q[::rate_x],
y_q[::rate_y],
u[::rate_y, ::rate_x],
v[::rate_y, ::rate_x],
scale=scale)
# Axes
plot.xlim(x_min, x_max)
plot.ylim(0, 360)
angles = np.linspace(0, 360, 7)
plot.yticks(angles)
# Annotate Axes
orbit = (dt / (2 * np.pi)) * frame
if orbit >= taper_time:
current_mass = planet_mass
else:
current_mass = np.power(
np.sin((np.pi / 2) * (1.0 * orbit / taper_time)), 2) * planet_mass
current_mass += accreted_mass[frame]
#title = readTitle()
unit = "r_\mathrm{p}"
plot.xlabel(r"Radius [$%s$]" % unit, fontsize=fontsize)
plot.ylabel(r"$\phi$ [degrees]", fontsize=fontsize)
x_range = x_max - x_min
x_mid = x_min + x_range / 2.0
y_text = 1.14
alpha_coefficent = "3"
if scale_height == 0.08:
alpha_coefficent = "1.5"
elif scale_height == 0.04:
alpha_coefficent = "6"
title1 = r"$h/r = %.2f$ $\alpha \approx %s \times 10^{%d}$ $A = %.2f$" % (
scale_height, alpha_coefficent,
int(np.log(viscosity) / np.log(10)) + 2, accretion)
#title1 = r"$\Sigma_0 = %.3e$ $M_c = %.2f\ M_J$ $A = %.2f$" % (surface_density_zero, planet_mass, accretion)
title2 = r"$t = %d$ $\mathrm{orbits}}$ [$m_\mathrm{p}(t)\ =\ %.2f$ $M_\mathrm{Jup}$]" % (
orbit, current_mass)
plot.title("%s" % (title2), y=1.015, fontsize=fontsize + 1)
plot.text(x_mid,
y_text * plot.ylim()[-1],
title1,
horizontalalignment='center',
bbox=dict(facecolor='none',
edgecolor='black',
linewidth=1.5,
pad=7.0),
fontsize=fontsize + 2)
cbar.set_label(r"Gas Surface Density $\Sigma$ $/$ $\Sigma_0$",
fontsize=fontsize,
rotation=270,
labelpad=25)
# Save, Show, and Close
if version is None:
save_fn = "%s/densityMap_%04d.png" % (save_directory, frame)
else:
save_fn = "%s/v%04d_densityMap_%04d.png" % (save_directory, version,
frame)
plot.savefig(save_fn, bbox_inches='tight', dpi=dpi)
if show:
plot.show()
plot.close(fig) # Close Figure (to avoid too many figures)
from pylab import *
import sys
sys.path.insert(0, '../../utils/python')
from reader import Fields
from advanced import Parameters
n = 1
outputdir = "../../outputs/fargo_dusty"
fluids = ["gas", "dust1", "dust2", "dust3"]
field = "dens"
fig = figure(figsize=(20, 5))
p = Parameters(outputdir)
for i, fluid in enumerate(fluids):
data = Fields("../../outputs/fargo_dusty", fluid,
n).get_field(field).reshape(p.ny, p.nx)
ax = fig.add_subplot(1, len(fluids), i + 1)
ax.imshow(log10(data), origin='lower', aspect='auto')
show()
def make_plot(frame, show=False):
# Set up figure
fig = plot.figure(figsize=(7, 6), dpi=dpi)
ax = fig.add_subplot(111)
# Data
field = "dens"
density = Fields("./", 'gas',
frame).get_field(field).reshape(num_rad, num_theta)
normalized_density = density / surface_density_zero
field = "dens"
density = Fields("./", 'dust%d' % dust_number,
frame).get_field(field).reshape(num_rad, num_theta)
normalized_density = density / dust_surface_density_zero
field = "vx" # radial
radial_velocity = Fields("./", 'dust%d' % dust_number,
frame).get_field(field).reshape(
num_rad, num_theta)
field = "vy" # azimuthal
azimuthal_velocity = Fields("./", 'dust%d' % dust_number,
frame).get_field(field).reshape(
num_rad, num_theta)
if center:
if taper_time < 10.1:
shift_c = az.get_azimuthal_peak(dust_density, fargo_par)
else:
threshold = util.get_threshold(size) * 1.5
shift_c = az.get_azimuthal_center(dust_density,
fargo_par,
threshold=threshold *
surface_density_zero)
radial_velocity = np.roll(radial_velocity, shift_c)
azimuthal_velocity = np.roll(azimuthal_velocity, shift_c)
# Calculate CFL Timestep
keplerian_velocity = rad * (np.power(
rad, -1.5) - 1) # in rotating frame, v_k = r * (r^-1.5 - r_p^-1.5)
azimuthal_velocity -= keplerian_velocity[:, None]
delta_r = rad[1] - rad[0]
r_delta_theta = (rad * (theta[1] - theta[0]))[:, None]
cfl = np.abs(radial_velocity) / (delta_r) + np.abs(azimuthal_velocity) / (
r_delta_theta)
cfl_max = 0.4
delta_t = cfl_max / cfl
critical_location = np.unravel_index(np.argmin(delta_t), np.shape(delta_t))
critical_location = (rad[critical_location[0]], theta[critical_location[1]]
) # convert to rad and theta
# Print Overall Min
print np.min(delta_t), critical_location
# Print min at each radius
minima = np.min(delta_t, axis=0)
for i, (rad_i, min_i) in enumerate(zip(rad, minima)):
if i % 4 == 0:
print rad_i, min_i
### Plot ###
x = rad
y = theta * (180.0 / np.pi)
result = ax.pcolormesh(x, y, np.transpose(azimuthal_velocity), cmap=cmap)
fig.colorbar(result)
#result.set_clim(clim[0], clim[1])
if use_contours:
levels = np.linspace(low_contour, high_contour, num_levels)
colors = generate_colors(num_levels)
plot.contour(x,
y,
np.transpose(gas_density / gas_surface_density_zero),
levels=levels,
origin='upper',
linewidths=1,
colors=colors)
# Axes
plot.xlim(x_min, x_max)
plot.ylim(0, 360)
angles = np.linspace(0, 360, 7)
plot.yticks(angles)
# Annotate Axes
time = fargo_par["Ninterm"] * fargo_par["DT"]
orbit = (time / (2 * np.pi)) * frame
if orbit >= taper_time:
current_mass = planet_mass
else:
current_mass = np.power(
np.sin((np.pi / 2) * (1.0 * orbit / taper_time)), 2) * planet_mass
#title = readTitle()
unit = "r_\mathrm{p}"
plot.xlabel(r"Radius [$%s$]" % unit, fontsize=fontsize)
plot.ylabel(r"$\phi$", fontsize=fontsize)
#if title is None:
# plot.title("Dust Density Map\n(t = %.1f)" % (orbit), fontsize = fontsize + 1)
#else:
# plot.title("Dust Density Map\n%s\n(t = %.1f)" % (title, orbit), fontsize = fontsize + 1)
x_range = x_max - x_min
x_mid = x_min + x_range / 2.0
y_text = 1.14
title1 = r"$T_\mathrm{growth} = %d$ $\mathrm{orbits}$" % (taper_time)
title2 = r"$t = %d$ $\mathrm{orbits}}$ [$m_\mathrm{p}(t)\ =\ %.2f$ $M_\mathrm{Jup}$]" % (
orbit, current_mass)
plot.title("%s" % (title2), y=1.015, fontsize=fontsize + 1)
plot.text(x_mid,
y_text * plot.ylim()[-1],
title1,
horizontalalignment='center',
bbox=dict(facecolor='none',
edgecolor='black',
linewidth=1.5,
pad=7.0),
fontsize=fontsize + 2)
# Text
text_mass = r"$M_\mathrm{p} = %d$ $M_\mathrm{Jup}$" % (int(planet_mass))
text_visc = r"$\alpha_\mathrm{disk} = 3 \times 10^{%d}$" % (
int(np.log(viscosity) / np.log(10)) + 2)
#plot.text(-0.9 * box_size, 2, text_mass, fontsize = fontsize, color = 'black', horizontalalignment = 'left', bbox=dict(facecolor = 'white', edgecolor = 'black', pad = 10.0))
#plot.text(0.9 * box_size, 2, text_visc, fontsize = fontsize, color = 'black', horizontalalignment = 'right', bbox=dict(facecolor = 'white', edgecolor = 'black', pad = 10.0))
plot.text(-0.84 * x_range / 2.0 + x_mid,
y_text * plot.ylim()[-1],
text_mass,
fontsize=fontsize,
color='black',
horizontalalignment='right')
plot.text(0.84 * x_range / 2.0 + x_mid,
y_text * plot.ylim()[-1],
text_visc,
fontsize=fontsize,
color='black',
horizontalalignment='left')
# Save, Show, and Close
if version is None:
save_fn = "%s/cflTimestep_%04d.png" % (save_directory, frame)
else:
save_fn = "%s/v%04d_cflTimestep_%04d.png" % (save_directory, version,
frame)
plot.savefig(save_fn, bbox_inches='tight', dpi=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
velocity = util.read_merged_data(frame,
num_merged_cores,
num_rad,
num_theta,
field="vx")
elif mpi:
velocity = Fields("./", 'gas',
frame).get_field("vx").reshape(num_rad, num_theta)
else:
velocity = fromfile("gasvx%d.dat" % frame).reshape(num_rad, num_theta)
# Average
averaged_velocity = np.average(velocity, axis=1)
# Shift out of rotating frame
rotating_frame = rad # in rotating frame, v_k = r * (r^-1.5 - r_p^-1.5)
averaged_velocity += rotating_frame
averaged_orbital_frequency = averaged_velocity / rad
# Reference Lines
keplerian_velocity = np.power(rad, -1.5)
y_ref1 = 1.0 * keplerian_velocity
y_ref2 = y_ref1 - 0.5 * np.power(scale_height, 2)
if args.normalize:
averaged_orbital_frequency /= keplerian_velocity
y_ref2 /= keplerian_velocity
y_ref1 /= keplerian_velocity
### Plot ###
x = rad
y = averaged_orbital_frequency
result = plot.plot(x, y, linewidth=linewidth, zorder=99)
plot.plot(x, y_ref1, c='k', linewidth=linewidth - 1)
plot.plot(x, y_ref2, c='midnightblue', linewidth=linewidth - 1)
if args.normalize:
resonance_curve = 0.5 * y_ref1 / keplerian_velocity
plot.plot(x, resonance_curve)
look_for_resonance = resonance_curve / y
r_start_i = np.searchsorted(rad, 1.4)
r_end_i = np.searchsorted(rad, 1.8)
resonance_i = np.searchsorted(look_for_resonance[r_start_i:r_end_i],
1.0)
resonance_r = rad[r_start_i + resonance_i]
plot.text(1.05 * x_min, 1.02, r"$r = %.3f$" % resonance_r)
else:
plot.plot([x[0], x[-1]], [0.5, 0.5], linewidth=linewidth - 1)
# Axes
if args.max_y is None:
x_min_i = np.searchsorted(x, x_min)
x_max_i = np.searchsorted(x, x_max)
max_y = 1.1 * max(y[x_min_i:x_max_i])
else:
max_y = args.max_y
plot.xlim(x_min, x_max)
plot.ylim(min_y, max_y)
# Annotate Axes
orbit = (dt / (2 * np.pi)) * frame
if orbit >= taper_time:
current_mass = planet_mass
else:
current_mass = np.power(
np.sin((np.pi / 2) * (1.0 * orbit / taper_time)), 2) * planet_mass
current_mass += accreted_mass[frame]
#title = readTitle()
unit = "r_\mathrm{p}"
plot.xlabel(r"Radius [$%s$]" % unit, fontsize=fontsize)
plot.ylabel(r"$\Omega$ $/$ $\Omega_\mathrm{K}$", fontsize=fontsize)
title2 = r"$t = %d$ $\mathrm{orbits}}$ [$m_\mathrm{p}(t)\ =\ %.2f$ $M_\mathrm{Jup}$]" % (
orbit, current_mass)
plot.title("%s" % (title2), y=1.015, fontsize=fontsize + 1)
# Save, Show, and Close
if version is None:
save_fn = "%s/averagedOrbitalFrequency_%04d.png" % (save_directory,
frame)
else:
save_fn = "%s/v%04d_averagedOrbitalFrequency_%04d.png" % (
save_directory, version, frame)
plot.savefig(save_fn, bbox_inches='tight', dpi=dpi)
if show:
plot.show()
plot.close(fig) # Close Figure (to avoid too many figures)
def add_to_plot(i):
# Identify Subplot
frame = frames[i]; number = i + 1
ax = plot.subplot(1, 4, number)
# Data
if mpi:
density = Fields("./", 'gas', frame).get_field("dens").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)
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, :, :]
dz = z_angles[1] - z_angles[0]
surface_density = np.sum(density[:, :, :], axis = 0) * dz
normalized_midplane_density = midplane_density / surface_density_zero # / np.sqrt(2.0 * np.pi) / scale_height_function[:, None]
normalized_density = surface_density / surface_density_zero # / np.sqrt(2.0 * np.pi) / scale_height_function[:, None]
vorticity = utilVorticity.velocity_curl(midplane_vrad, midplane_vtheta, rad, theta, rossby = rossby, residual = residual)
### Plot ###
x = rad
y = theta * (180.0 / np.pi)
result = ax.pcolormesh(x, y, np.transpose(vorticity), cmap = cmap)
result.set_clim(clim[0], clim[1])
# Contours
if use_contours:
levels = np.linspace(low_contour, high_contour, num_levels)
colors = generate_colors(num_levels)
plot.contour(x, y, np.transpose(normalized_density), levels = levels, origin = 'upper', linewidths = 1, colors = colors)
# Axes
plot.xlim(x_min, x_max)
plot.ylim(0, 360)
angles = np.linspace(0, 360, 7)
plot.yticks(angles)
# Annotate Axes
orbit = (dt / (2 * np.pi)) * frame
if orbit >= taper_time:
current_mass = planet_mass
else:
current_mass = np.power(np.sin((np.pi / 2) * (1.0 * orbit / taper_time)), 2) * planet_mass
current_mass += accreted_mass[frame]
unit = "r_\mathrm{p}"
plot.xlabel(r"Radius [$%s$]" % unit, fontsize = fontsize)
if number == 1:
plot.ylabel(r"$\phi$ [degrees]", fontsize = fontsize)
x_range = x_max - x_min; x_mid = x_min + x_range / 2.0
y_text = 1.14
title = r"$t = %d$ [$m_\mathrm{p}=%.2f$ $M_\mathrm{J}$]" % (orbit, current_mass)
plot.title("%s" % (title), y = 1.035, fontsize = fontsize + 1)
# Add Colorbar (Source: http://stackoverflow.com/questions/23270445/adding-a-colorbar-to-two-subplots-with-equal-aspect-ratios)
divider = make_axes_locatable(ax)
cax = divider.append_axes("right", size = "6%", pad = 0.2)
#cax = fig.add_axes([0.9, 0.1, 0.03, 0.8])
cbar = fig.colorbar(result, cax = cax)
# Label colorbar
if rossby:
cbar_name = r"$\mathrm{Rossby}$ $\mathrm{number}$"
else:
cbar_name = r"$\mathrm{Vorticity}$"
cbar.set_label(cbar_name, fontsize = fontsize, rotation = 270, labelpad = 25)
if number != len(frames):
fig.delaxes(cax) # to balance out frames that don't have colorbar with the one that does
def get_excess_mass(args):
# Unwrap Args
i, frame = args
# Get Data
if mpi:
field = "dens"
density = Fields("./", 'gas', frame).get_field(field).reshape(
num_rad, num_theta) / surface_density_zero
background_density = Fields(
"./", 'gas', frame - 1).get_field(field).reshape(
num_rad, num_theta) / surface_density_zero
else:
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
#fargo_directory = "taper750_fargo_comparison"
#density_compare = (fromfile("../%s/gasdens%d.dat" % (fargo_directory, frame)).reshape(num_rad, num_theta)) / surface_density_zero
#background_density_compare = (fromfile("../%s/gasdens%d.dat" % (fargo_directory, frame - 1)).reshape(num_rad, num_theta)) / surface_density_zero
def helper(density, background_density):
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)
return excess_mass, vortex_excess
excess_mass, vortex_excess = helper(density, background_density)
#excess_mass_compare, vortex_excess_compare = helper(density_compare, background_density_compare)
# Get Peak
peak_diff_density = np.max(vortex_excess)
#peak_diff_density_compare = np.max(vortex_excess_compare)
# Print Update
print "%d: %.4f, %.4f" % (frame, excess_mass, peak_diff_density)
#print "%d: %.4f, %.4f" % (frame, excess_mass_compare, peak_diff_density_compare)
# Store Data
mass_over_time[i] = excess_mass
peak_over_time[i] = peak_diff_density
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
if center:
normalized_density, shift_c = shift_density(
normalized_density,
fargo_par,
reference_density=normalized_density)
# Convert to cartesian
xs, ys, _, _, normalized_density_cart = sq.polar_to_cartesian(
normalized_density, rad, theta)
### Plot ###
result = ax.pcolormesh(xs,
ys,
np.transpose(normalized_density_cart),
cmap=cmap)
cbar = fig.colorbar(result)
result.set_clim(clim[0], clim[1])
cbar.set_label(r"Normalized Surface Density",
fontsize=fontsize + 2,
rotation=270,
labelpad=20)
if use_contours:
levels = np.linspace(low_contour, high_contour, num_levels)
colors = generate_colors(num_levels)
plot.contour(x,
y,
np.transpose(normalized_density_cart),
levels=levels,
origin='upper',
linewidths=1,
colors=colors)
# Get rid of interior
circle = plot.Circle((0, 0), min(rad), color="black")
fig.gca().add_artist(circle)
# Add planet orbit
planet_orbit = plot.Circle((0, 0),
1,
color="white",
fill=False,
alpha=0.8,
linestyle="dashed",
zorder=50)
fig.gca().add_artist(planet_orbit)
# Label star and planet
time = fargo_par["Ninterm"] * fargo_par["DT"]
orbit = (time / (2 * np.pi)) * frame
if orbit >= taper_time:
current_mass = planet_mass
else:
current_mass = np.power(
np.sin((np.pi / 2) * (1.0 * orbit / taper_time)), 2) * planet_mass
#current_mass += accreted_mass[frame]
if center:
# Locate Planet
if shift_c < -len(theta):
shift_c += len(theta)
planet_theta = theta[shift_c]
planet_theta -= (
np.pi / 2.0
) # Note: the conversion from polar to cartesian rotates everything forward by 90 degrees
planet_theta = planet_theta % (2 * np.pi) # Keep 0 < theta < 2 * np.pi
planet_x = np.cos(planet_theta)
planet_y = np.sin(planet_theta)
else:
planet_x = 0
planet_y = 1
planet_size = (current_mass / planet_mass)
plot.scatter(0, 0, c="white", s=300, marker="*", zorder=100) # star
plot.scatter(planet_x,
planet_y,
c="white",
s=int(70 * planet_size),
marker="D") # planet
# Axes
plot.xlim(-box, box)
plot.ylim(-box, box)
plot.axes().set_aspect('equal')
# Annotate Axes
# Annotate Axes
unit = "r_\mathrm{p}"
plot.xlabel(r"$x$ [$%s$]" % unit, fontsize=fontsize)
plot.ylabel(r"$y$ [$%s$]" % unit, fontsize=fontsize)
title1 = r"$T_\mathrm{growth} = %d$ $\mathrm{orbits}$" % (taper_time)
title2 = r"$t = %d$ $\mathrm{orbits}}$ [$m_\mathrm{p}(t)\ =\ %.2f$ $M_\mathrm{Jup}$]" % (
orbit, current_mass)
plot.title("%s" % (title2), y=1.015, fontsize=fontsize + 1)
plot.text(0.0,
3.24,
title1,
horizontalalignment='center',
bbox=dict(facecolor='none',
edgecolor='black',
linewidth=1.5,
pad=7.0),
fontsize=fontsize + 2)
# Text
text_mass = r"$M_\mathrm{p} = %d$ $M_\mathrm{Jup}$" % (int(planet_mass))
text_visc = r"$\alpha_\mathrm{disk} = 3 \times 10^{%d}$" % (
int(np.log(viscosity) / np.log(10)) + 2)
#plot.text(-0.9 * box_size, 2, text_mass, fontsize = fontsize, color = 'black', horizontalalignment = 'left', bbox=dict(facecolor = 'white', edgecolor = 'black', pad = 10.0))
#plot.text(0.9 * box_size, 2, text_visc, fontsize = fontsize, color = 'black', horizontalalignment = 'right', bbox=dict(facecolor = 'white', edgecolor = 'black', pad = 10.0))
plot.text(-1.7,
3.24,
text_mass,
fontsize=fontsize,
color='black',
horizontalalignment='right')
plot.text(1.7,
3.24,
text_visc,
fontsize=fontsize,
color='black',
horizontalalignment='left')
# Save, Show, and Close
if version is None:
save_fn = "%s/squareDensityMap_%04d.png" % (save_directory, frame)
else:
save_fn = "%s/v%04d_squareDensityMap_%04d.png" % (save_directory,
version, frame)
plot.savefig(save_fn, bbox_inches='tight', dpi=dpi)
if show:
plot.show()
plot.close(fig) # Close Figure (to avoid too many figures)
