def __init__(self, massratio=1. / 3):
# Set up directories to store data in
self.timestamp = datetime.today().strftime('%Y%m%dT%H%M')
if not os.path.exists('out/{0}'.format(self.timestamp)):
os.mkdir('out/{0}'.format(self.timestamp))
if not os.path.exists('out/{0}/plots'.format(self.timestamp)):
os.mkdir('out/{0}/plots'.format(self.timestamp))
if not os.path.exists('out/{0}/data'.format(self.timestamp)):
os.mkdir('out/{0}/data'.format(self.timestamp))
# Set up sub clusters
self.subClusterA = SubCluster(name="Sub Cluster A")
self.subClusterB = SubCluster(name="Sub Cluster B",
Mtot=massratio * (1e15 | units.MSun),
Rvir=(200 | units.kpc))
self.converter = self.subClusterA.converter
self.timesteps = VectorQuantity.arange(0 | units.Myr, 1 | units.Gyr,
50 | units.Myr)
# Set up world and gravity/hydro solvers
self.place_clusters_in_world()
# Write simulation parameters to text file
filename = "out/{0}/data/merger.dat".format(self.timestamp)
print "Dumping ClusterMerger instance to", filename, "\n"
pickle.dump(self, open(filename, 'wb'))
# Set up simulation codes
self.setup_codes()
print "Created subclusters.\n", str(self)
def __init__(self,
parms,
dm_parms=None,
radius=None,
z=0,
free_beta=False):
""" parms = ne0, rc, [rcut], [ne0_fac, rc_fac]
dm_parms = M_DM, a """
# TODO: implement without need for dm_parms
if radius is None:
self.radius = VectorQuantity.arange(units.kpc(1), units.kpc(1e5),
units.parsec(100))
else:
if type(radius) == numpy.ndarray:
self.radius = radius | units.kpc
else:
self.radius = radius
self.z = z
self.ne0 = parms[0]
self.rho0 = convert.ne_to_rho(self.ne0, self.z) | units.g / units.cm**3
self.ne0 = self.ne0 | units.cm**-3
self.rc = parms[1] | units.kpc
self.model = 0
self.rcut = None
self.ne0_cc = None
self.rho0_cc = None
self.rc_cc = None
self.free_beta = free_beta
if len(parms) == 3 and not free_beta:
self.model = 1
self.rcut = parms[2] | units.kpc
if len(parms) == 3 and free_beta:
self.model = 3
self.beta = parms[2]
if len(parms) == 4 and free_beta:
self.model = 4
self.rcut = parms[2] | units.kpc
self.beta = parms[3]
if len(parms) == 5:
self.model = 2
ne0_fac = parms[3]
rc_fac = parms[4]
self.ne0_cc = ne0 * ne0_fac
self.rho0_cc = self.ne0_cc * globals.mu * (globals.m_p | units.g)
self.rc_cc = rc / rc_fac
modelnames = {
0: r"$\beta=2/3$",
1: r"cut-off $\beta=2/3$",
2: r"cut-off double $\beta (2/3)$",
3: r"free $\beta$",
4: r"cut-off free $\beta$"
}
self.modelname = modelnames[self.model]
if dm_parms:
self.M_dm = dm_parms[0]
self.a = dm_parms[1]
def get_mass_via_number_density(cluster):
# progressbar
import sys
pbwidth = 42
# TODO: find different method to calculate M(<r)
print "Counting particles for which radii < r to obtain M(<r)"
radii = VectorQuantity.arange(units.kpc(1), units.kpc(10000),
units.parsec(1000))
M_gas_below_r = numpy.zeros(len(radii))
M_dm_below_r = numpy.zeros(len(radii))
N = len(radii)
for i, r in enumerate(radii):
M_gas_below_r[i] = ((numpy.where(cluster.gas.r < r)[0]).size)
M_dm_below_r[i] = ((numpy.where(cluster.dm.r < r)[0]).size)
if i % 1000 == 0:
# update the bar
progress = float(i + 1000) / N
block = int(round(pbwidth * progress))
text = "\rProgress: [{0}] {1:.1f}%".format(
"#" * block + "-" * (pbwidth - block), progress * 100)
sys.stdout.write(text)
sys.stdout.flush()
sys.stdout.write("\n")
print "Done counting particles :-)... TODO: improve this method?!"
M_gas_below_r *= cluster.M_gas / cluster.raw_data.Ngas
M_dm_below_r *= cluster.M_dm / cluster.raw_data.Ndm
amuse_plot.scatter(radii, M_gas_below_r, c="g", label="Gas")
amuse_plot.scatter(radii, M_dm_below_r, c="b", label="DM")
def integrate_and_store():
sun, planets = Solarsystem.new_solarsystem()
#timerange = units.day(numpy.arange(20, 120 * 365.25, 12))
timerange = Vq.arange(20 | units.day, 120 | units.yr, 10 | units.day)
pdb.set_trace()
instance = MercuryWayWard()
instance.initialize_code()
instance.central_particle.add_particles(sun)
instance.orbiters.add_particles(planets)
instance.commit_particles()
channels = instance.orbiters.new_channel_to(planets)
err = instance.evolve_model(10 | units.day)
pdb.set_trace()
channels.copy()
planets.savepoint(10 | units.day)
pdb.set_trace()
for time in timerange:
err = instance.evolve_model(time)
channels.copy()
planets.savepoint(time)
instance.stop()
pdb.set_trace()
def animate(self):
# Set up figure, axes, and PathCollection instances
fig = pyplot.figure(figsize=(20, 12))
gs = gridspec.GridSpec(2, 2, height_ratios=[1, 4])
self.ax_text = pyplot.subplot(gs[0, :])
self.ax_text.axis('off')
self.time_text = self.ax_text.text(0.02,
1.0,
'',
transform=self.ax_text.transAxes,
fontsize=42)
self.energy_text = self.ax_text.text(0.02,
-0.2,
'',
transform=self.ax_text.transAxes,
fontsize=42)
lim = max(
abs((self.dmA.center_of_mass() -
self.dmB.center_of_mass()).value_in(units.Mpc)))
self.ax_dm = pyplot.subplot(gs[1, 0],
xlim=(-4 * lim, 4 * lim),
ylim=(-4 * lim, 4 * lim))
self.ax_dm.set_xlabel(r'$x$')
self.ax_dm.set_ylabel(r'$y$')
self.subAdm_scat, = self.ax_dm.plot([], [], 'ro', ms=6, label="A")
self.subBdm_scat, = self.ax_dm.plot([], [], 'go', ms=6, label="B")
pyplot.legend()
self.ax_gas = pyplot.subplot(gs[1, 1],
aspect='equal',
sharex=self.ax_dm,
sharey=self.ax_dm,
xlim=(-4 * lim, 4 * lim),
ylim=(-4 * lim, 4 * lim))
self.ax_gas.set_xlabel(r'$x$')
self.ax_gas.set_ylabel(r'$y$')
self.ax_gas.set_axis_bgcolor('#101010')
self.subAgas_scat = self.ax_gas.scatter([], [],
alpha=0.1,
edgecolors="none")
self.subBgas_scat = self.ax_gas.scatter([], [],
alpha=0.1,
edgecolors="none")
# 20 fps at 5 Myr interval --> 1 second in animation is 100 Myr
self.timesteps = VectorQuantity.arange(0.0 | units.Myr,
100 | units.Myr, 5 | units.Myr)
# pyplot.show()
self.anim = animation.FuncAnimation(fig,
self.update,
frames=self.timesteps,
blit=True,
init_func=self.clear)
def planetplot():
sun, planets = new_solar_system_for_mercury()
initial = 12.2138 | units.Gyr
final = 12.3300 | units.Gyr
step = 10000.0 | units.yr
timerange = VectorQuantity.arange(initial, final, step)
gd = MercuryWayWard()
gd.initialize_code()
# gd.stopping_conditions.timeout_detection.disable()
gd.central_particle.add_particles(sun)
gd.orbiters.add_particles(planets)
gd.commit_particles()
se = SSE()
# se.initialize_code()
se.commit_parameters()
se.particles.add_particles(sun)
se.commit_particles()
channelp = gd.orbiters.new_channel_to(planets)
channels = se.particles.new_channel_to(sun)
for time in timerange:
err = gd.evolve_model(time-initial)
channelp.copy()
# planets.savepoint(time)
err = se.evolve_model(time)
channels.copy()
gd.central_particle.mass = sun.mass
print(
sun[0].mass.value_in(units.MSun),
time.value_in(units.Myr),
planets[4].x.value_in(units.AU),
planets[4].y.value_in(units.AU),
planets[4].z.value_in(units.AU)
)
gd.stop()
se.stop()
for planet in planets:
t, x = planet.get_timeline_of_attribute_as_vector("x")
t, y = planet.get_timeline_of_attribute_as_vector("y")
plot(x, y, '.')
native_plot.gca().set_aspect('equal')
native_plot.show()
def run_simulation():
merger = ClusterMerger()
timesteps = VectorQuantity.arange(0 | units.Myr, 1 | units.Gyr,
50 | units.Myr)
tot = len(timesteps)
end_time = timesteps[-1]
print "Starting Simulation :-)"
print "Generating plots on the fly :-)"
gasA_vel_list = []
dmA_vel_list = []
gasB_vel_list = []
dmB_vel_list = []
time_list = []
for i, time in enumerate(timesteps):
print_progressbar(i, tot, end_time)
merger.code.evolve_model(time)
merger.dm_gas_sph_subplot(i)
gasA_vel_list.append(merger.gasA.center_of_mass_velocity())
dmA_vel_list.append(merger.dmA.center_of_mass_velocity())
gasB_vel_list.append(merger.gasB.center_of_mass_velocity())
dmB_vel_list.append(merger.dmB.center_of_mass_velocity())
time_list.append(time)
write_set_to_file(
merger.code.particles,
'{0}/data/cluster_{1}.amuse'.format(merger.timestamp, i), "amuse")
print "Plotting velocity as functio of time"
fig = pyplot.figure(figsize=(12, 10), dpi=50)
plot(time_list, gasA_vel, label="gasA", c='r', ls='solid')
plot(time_list, dmA_vel, label="dmA", c='r', ls='dashed')
plot(time_list, gasB_vel, label="gasB", c='g', ls='solid')
plot(time_list, dmB_vel, label="dmB", c='g', ls='dashed')
xlabel("Time")
ylabel("Velocity")
pyplot.legend()
pyplot.show()
print "Generating gif :-)"
merger.create_gif()
print "Stopping the code. End of pipeline :-)"
merger.code.stop()
def planetplot():
sun, planets = new_solar_system_for_mercury()
initial = 12.2138 | units.Gyr
final = 12.3300 | units.Gyr
step = 10000.0 | units.yr
timerange = VectorQuantity.arange(initial, final, step)
gd = MercuryWayWard()
gd.initialize_code()
# gd.stopping_conditions.timeout_detection.disable()
gd.central_particle.add_particles(sun)
gd.orbiters.add_particles(planets)
gd.commit_particles()
se = SSE()
# se.initialize_code()
se.commit_parameters()
se.particles.add_particles(sun)
se.commit_particles()
channelp = gd.orbiters.new_channel_to(planets)
channels = se.particles.new_channel_to(sun)
for time in timerange:
err = gd.evolve_model(time - initial)
channelp.copy()
# planets.savepoint(time)
err = se.evolve_model(time)
channels.copy()
gd.central_particle.mass = sun.mass
print(
(sun[0].mass.value_in(units.MSun), time.value_in(units.Myr),
planets[4].x.value_in(units.AU), planets[4].y.value_in(units.AU),
planets[4].z.value_in(units.AU)))
gd.stop()
se.stop()
for planet in planets:
t, x = planet.get_timeline_of_attribute_as_vector("x")
t, y = planet.get_timeline_of_attribute_as_vector("y")
plot(x, y, '.')
native_plot.gca().set_aspect('equal')
native_plot.show()
def plot_individual_cluster_mass(cluster):
pyplot.figure(figsize=(24, 18))
# TODO: use different method :-)...
get_mass_via_number_density(cluster)
# get_mass_via_number_density_parallel(cluster)
# get_mass_via_density(cluster)
pyplot.gca().set_xscale("log")
pyplot.gca().set_yscale("log")
# M_gas = (cluster.gas.mass.value_in(units.MSun))
# M_dm = (cluster.dm.mass.value_in(units.MSun))
# amuse_plot.scatter(cluster.gas.r, units.MSun(M_gas), c="g", label="Gas")
# amuse_plot.scatter(cluster.dm.r, units.MSun(M_dm), c="b", label="DM")
# Analytical solutions. Sample radii and plug into analytical expression.
r = VectorQuantity.arange(units.kpc(1), units.kpc(10000),
units.parsec(100))
# Plot analytical Hernquist model for the DM mass M(<r)
amuse_plot.plot(r,
cluster.dm_cummulative_mass(r),
ls="solid",
c="k",
label="DM")
# Plot analytical beta model (Donnert 2014) for the gas mass M(<r)
amuse_plot.plot(r,
cluster.gas_cummulative_mass_beta(r),
ls="dotted",
c="k",
label=r"$\beta$-model")
# Plot analytical double beta model (Donnert et al. 2016, in prep) gas M(<r)
amuse_plot.plot(r,
cluster.gas_cummulative_mass_double_beta(r),
ls="dashed",
c="k",
label=r"double $\beta$-model")
pyplot.xlabel(r"$r$ [kpc]")
pyplot.ylabel(r"$M (<r)$ [MSun]")
pyplot.gca().set_xscale("log")
pyplot.gca().set_yscale("log")
pyplot.legend(loc=4)
def __init__(self):
self.merger = ClusterMerger()
timesteps = VectorQuantity.arange(0 | units.Myr, 1 | units.Gyr, 50 | units.Myr)
tot = len(timesteps)
end_time = timesteps[-1]
print "Starting Simulation :-)"
print "Generating plots on the fly :-)"
gasA_vel_list = [] | (units.km/units.s)
dmA_vel_list = [] | (units.km/units.s)
gasB_vel_list = [] | (units.km/units.s)
dmB_vel_list = [] | (units.km/units.s)
time_list = [] | units.Gyr
for i, time in enumerate(timesteps):
print_progressbar(i, tot)
self.merger.code.evolve_model(time)
self.merger.dm_gas_sph_subplot(i)
gasA_vel_list.append(self.merger.gasA.center_of_mass_velocity())
dmA_vel_list.append(self.merger.dmA.center_of_mass_velocity())
gasB_vel_list.append(self.merger.gasB.center_of_mass_velocity())
dmB_vel_list.append(self.merger.dmB.center_of_mass_velocity())
time_list.append(time)
write_set_to_file(self.merger.code.particles,
'out/{0}/data/cluster_{1}.amuse'.format(self.merger.timestamp, i),
"amuse")
print "Plotting velocity as function of time"
fig = pyplot.figure(figsize=(12, 10), dpi=50)
plot(time_list.number, gasA_vel_list.number, label="gasA", c='r', ls='solid')
plot(time_list.number, dmA_vel_list.number, label="dmA", c='r', ls='dashed')
plot(time_list.number, gasB_vel_list.number, label="gasB", c='g', ls='solid')
plot(time_list.number, dmB_vel_list.number, label="dmB", c='g', ls='dashed')
xlabel("Time")
ylabel("Velocity")
pyplot.legend()
pyplot.show()
print "Generating gif :-)"
self.merger.create_gif()
print "Stopping the code. End of pipeline :-)"
self.merger.code.stop()
earth.radius = 6371.0 | units.km
earth.position = [0.0, 1.0, 0.0] | units.AU
earth.velocity = [2.0*numpy.pi, -0.0001, 0.0] | units.AU / units.yr
instance = Hermite(convert_nbody)
instance.initialize_code()
instance.particles.add_particles(particles)
instance.commit_particles()
channelp = instance.particles.new_channel_to(particles)
start = 0 |units.yr
end = 150 | units.yr
step = 10|units.day
timerange = VectorQuantity.arange(start, end, step)
masses = []|units.MSun
for i, time in enumerate(timerange):
instance.evolve_model(time)
channelp.copy()
particles.savepoint(time)
if (i % 220 == 0):
instance.particles[0].mass = simulate_massloss(time)
masses.append(instance.particles[0].mass)
instance.stop()
particle = particles[1]
earth = particles[1]
earth.mass = 5.9736e24 | units.kg
earth.radius = 6371.0 | units.km
earth.position = [0.0, 1.0, 0.0] | units.AU
earth.velocity = [2.0*numpy.pi, -0.0001, 0.0] | units.AU / units.yr
instance = Hermite(convert_nbody)
instance.particles.add_particles(particles)
channelp = instance.particles.new_channel_to(particles)
start = 0 |units.yr
end = 150 | units.yr
step = 10|units.day
timerange = VectorQuantity.arange(start, end, step)
masses = []|units.MSun
for i, time in enumerate(timerange):
instance.evolve_model(time)
channelp.copy()
particles.savepoint(time)
if (i % 220 == 0):
instance.particles[0].mass = simulate_massloss(time)
masses.append(instance.particles[0].mass)
instance.stop()
particle = particles[1]
def donnert_2014_figure1(analytical_P500=False):
# Well, I will just eyeball the value of rho_0 in Figure 1 in Donnert (2014) and adopt this value, I suppose...
# disturbed = InitialCluster(rho_0=(9e-27 | units.g/units.cm**3),
# plot=False, do_print=False,
# disturbed_cluster=True, cool_core_cluster=False)
# coolcore = InitialCluster(rho_0=(3e-25 | units.g/units.cm**3),
# plot=False, do_print=False,
# disturbed_cluster=False, cool_core_cluster=True)
# rickersarazin = InitialCluster(plot=False, do_print=False, disturbed_cluster=False, cool_core_cluster=False)
r = VectorQuantity.arange(units.kpc(1), units.kpc(10000),
units.parsec(100))
#fig, ((ax1, ax2), (ax3, ax4)) = pyplot.subplots(2, 2, figsize=(20, 20), dpi=500)
fig, ((ax1, ax2), (ax3, ax4)) = pyplot.subplots(2, 2)
# Plot the density situation
pyplot.sca(ax1)
amuse_plot.hist(r, bins=int(numpy.sqrt(len(r))), label="Hanky")
# amuse_plot.loglog(coolcore.r, coolcore.rho_gas.as_quantity_in(units.g / units.cm**3),
# c='k', ls='dotted', label="Gas, cool core")
# amuse_plot.loglog(disturbed.r, disturbed.rho_gas.as_quantity_in(units.g / units.cm**3),
# c='k', ls='dashed', label="Gas, disturbed")
# amuse_plot.loglog(disturbed.r, disturbed.rho_dm.as_quantity_in(units.g / units.cm**3),
# c='k', ls='solid', label="Dark Matter")
amuse_plot.ylabel(r'$\rho$')
amuse_plot.xlabel(r'$r$')
pyplot.legend(loc=3, frameon=False, fontsize=12)
ax1.set_ylim(ymin=1e-28, ymax=1e-23)
# pyplot.axvline(x=disturbed.r_200.value_in(units.kpc), lw=2, c='k')
# pyplot.text(disturbed.r_200.value_in(units.kpc), 7e-24, r'$r_{200}$', fontsize=12)
# pyplot.axvline(x=disturbed.r_500.value_in(units.kpc), lw=2, c='k')
# pyplot.text(disturbed.r_500.value_in(units.kpc), 7e-24, r'$r_{500}$', fontsize=12)
# # a_hernq
# intersect = disturbed.dm_density(disturbed.a)
# ymin, ymax = ax1.get_ylim()
# ymin = (numpy.log(intersect.value_in(units.g/units.cm**3)/ymin)) / (numpy.log(ymax/ymin))
# pyplot.axvline(x=disturbed.a.value_in(units.kpc), ymin=ymin, ymax=1, lw=2, c='k')
# pyplot.text(disturbed.a.value_in(units.kpc), 5e-24, r'$a_{\rm Hernq}$', fontsize=12)
# # r_core,dist
# intersect = disturbed.gas_density(disturbed.r_c)
# ymin, ymax = ax1.get_ylim()
# ymin = (numpy.log(intersect.value_in(units.g/units.cm**3)/ymin)) / (numpy.log(ymax/ymin))
# pyplot.axvline(x=disturbed.r_c.value_in(units.kpc), ymin=ymin, ymax=1, lw=2, ls='--', c='k')
# pyplot.text(disturbed.r_c.value_in(units.kpc), 5e-24, r'$r_{\rm core,dist}$', fontsize=12)
# # r_core,cc
# intersect = coolcore.gas_density(coolcore.r_c)
# ymin, ymax = ax1.get_ylim()
# ymin = (numpy.log(intersect.value_in(units.g/units.cm**3)/ymin)) / (numpy.log(ymax/ymin))
# pyplot.axvline(x=coolcore.r_c.value_in(units.kpc), ymin=ymin, ymax=1, lw=2, ls=':', c='k')
# pyplot.text(coolcore.r_c.value_in(units.kpc), 5e-24, r'$r_{\rm core,cc}$', fontsize=12)
# Plot the mass situation
pyplot.sca(ax2)
amuse_plot.hist(r, bins=int(numpy.sqrt(len(r))), label="Hanky")
# amuse_plot.loglog(coolcore.r, coolcore.M_gas_below_r.as_quantity_in(units.MSun),
# c='k', ls='dotted', label="Gas, cool core")
# amuse_plot.loglog(disturbed.r, disturbed.M_gas_below_r.as_quantity_in(units.MSun),
# c='k', ls='dashed', label="Gas, disturbed")
# amuse_plot.loglog(disturbed.r, disturbed.M_dm_below_r.as_quantity_in(units.MSun),
# c='k', ls='solid', label="Dark Matter")
amuse_plot.ylabel(r'$M(<r)$')
amuse_plot.xlabel(r'$r$')
pyplot.legend(loc=8, frameon=False, fontsize=12)
ax2.set_ylim(ymin=1e10, ymax=5e15)
# pyplot.axvline(x=disturbed.r_200.value_in(units.kpc), lw=2, c='k')
# pyplot.text(disturbed.r_200.value_in(units.kpc), 3e15, r'$r_{200}$', fontsize=12)
# pyplot.axvline(x=disturbed.r_500.value_in(units.kpc), lw=2, c='k')
# pyplot.text(disturbed.r_500.value_in(units.kpc), 3e15, r'$r_{500}$', fontsize=12)
# # a_hernq
# intersect = disturbed.dm_cummulative_mass(disturbed.a)
# ymin, ymax = ax2.get_ylim()
# ymin = (numpy.log(intersect.value_in(units.MSun)/ymin)) / (numpy.log(ymax/ymin))
# pyplot.axvline(x=disturbed.a.value_in(units.kpc), ymin=ymin, ymax=1, lw=2, c='k')
# pyplot.text(disturbed.a.value_in(units.kpc), 2e15, r'$a_{\rm Hernq}$', fontsize=12)
# # r_core,dist
# intersect = disturbed.dm_cummulative_mass(disturbed.r_c)
# ymin, ymax = ax2.get_ylim()
# ymin = (numpy.log(intersect.value_in(units.MSun)/ymin)) / (numpy.log(ymax/ymin))
# pyplot.axvline(x=disturbed.r_c.value_in(units.kpc), ymin=ymin, ymax=1, lw=2, ls='--', c='k')
# pyplot.text(disturbed.r_c.value_in(units.kpc), 2e15, r'$r_{\rm core,dist}$', fontsize=12)
# # r_core,cc
# intersect = coolcore.dm_cummulative_mass(coolcore.r_c)
# ymin, ymax = ax2.get_ylim()
# ymin = (numpy.log(intersect.value_in(units.MSun)/ymin)) / (numpy.log(ymax/ymin))
# pyplot.axvline(x=coolcore.r_c.value_in(units.kpc), ymin=ymin, ymax=1, lw=2, ls=':', c='k')
# pyplot.text(coolcore.r_c.value_in(units.kpc), 2e15, r'$r_{\rm core,cc}$', fontsize=12)
# Plot the temperature situation
pyplot.sca(ax3)
amuse_plot.hist(r, bins=int(numpy.sqrt(len(r))), label="Hanky")
# amuse_plot.loglog(disturbed.r, disturbed.T_r.as_quantity_in(units.K),
# c='k', ls='solid', label="disturbed")
# amuse_plot.loglog(disturbed.r, disturbed.T_r_dm.as_quantity_in(units.K),
# c='k', ls='dashdot', label="from DM, disturbed")
# amuse_plot.loglog(disturbed.r, disturbed.T_r_gas.as_quantity_in(units.K),
# c='k', ls='dashed', label="from Gas, disturbed")
# amuse_plot.loglog(coolcore.r, coolcore.T_r.as_quantity_in(units.K),
# c='k', ls='dotted', label="cool core")
amuse_plot.ylabel(r'$T$')
amuse_plot.xlabel(r'$r$')
pyplot.legend(loc=10, frameon=False, fontsize=12)
ax3.set_ylim(ymin=6e6, ymax=3e8)
# pyplot.axvline(x=disturbed.r_200.value_in(units.kpc), lw=2, c='k')
# pyplot.text(disturbed.r_200.value_in(units.kpc), 2.6e8, r'$r_{200}$', fontsize=12)
# pyplot.axvline(x=disturbed.r_500.value_in(units.kpc), lw=2, c='k')
# pyplot.text(disturbed.r_500.value_in(units.kpc), 2.6e8, r'$r_{500}$', fontsize=12)
# pyplot.axvline(x=disturbed.a.value_in(units.kpc), lw=2, c='k')
# pyplot.text(disturbed.a.value_in(units.kpc), 2.4e8, r'$a_{\rm Hernq}$', fontsize=12)
# # r_core,dist
# intersect = disturbed.temperature(disturbed.r_c)
# ymin, ymax = ax3.get_ylim()
# ymin = (numpy.log(intersect.value_in(units.K)/ymin)) / (numpy.log(ymax/ymin))
# pyplot.axvline(x=disturbed.r_c.value_in(units.kpc), ymin=ymin, ymax=1, lw=2, ls='--', c='k')
# pyplot.text(disturbed.r_c.value_in(units.kpc), 2.4e8, r'$r_{\rm core,dist}$', fontsize=12)
# # r_core,cc
# intersect = coolcore.temperature(coolcore.r_c)
# ymin, ymax = ax3.get_ylim()
# ymin = (numpy.log(intersect.value_in(units.K)/ymin)) / (numpy.log(ymax/ymin))
# pyplot.axvline(x=coolcore.r_c.value_in(units.kpc), ymin=ymin, ymax=1, lw=2, ls=':', c='k')
# pyplot.text(coolcore.r_c.value_in(units.kpc), 2.4e8, r'$r_{\rm core,cc}$', fontsize=12)
# TODO: pressure situation
pyplot.sca(ax4)
amuse_plot.hist(r, bins=int(numpy.sqrt(len(r))), label="Hanky")
colours = [(255. / 255, 127. / 255, 0. / 255),
(152. / 255, 78. / 255, 163. / 255),
(77. / 255, 175. / 255, 74. / 255),
(52. / 255, 126. / 255, 184. / 255),
(228. / 255, 26. / 255, 28. / 255)]
# print "Warning, the pressure plots make little sense because for each M_DM is the same but M_200 differs"
# for i, M_200 in enumerate(VectorQuantity([3e15, 1.5e15, 1e15, 0.5e15, 0.1e15], units.MSun)):
# disturbed = InitialCluster(rho_0=(9e-27 | units.g/units.cm**3), M_200=M_200,
# plot=False, do_print=False,
# disturbed_cluster=True, cool_core_cluster=False)
# coolcore = InitialCluster(rho_0=(3e-25 | units.g/units.cm**3), M_200=M_200,
# plot=False, do_print=False,
# disturbed_cluster=False, cool_core_cluster=True)
# if analytical_P500:
# amuse_plot.loglog(disturbed.r/disturbed.r_500, (disturbed.P_gas/disturbed.find_p500_analytically()),
# c=colours[i], ls='solid', label=r'{0} $M_\odot$'.format(disturbed.M_200.value_in(units.MSun)))
# amuse_plot.loglog(coolcore.r/coolcore.r_500, (coolcore.P_gas/coolcore.find_p500_analytically()),
# c=colours[i], ls='dashed')
# else:
# amuse_plot.loglog(disturbed.r/disturbed.r_500, (disturbed.P_gas/disturbed.P_500),
# c=colours[i], ls='solid', label=r'{0} $M_\odot$'.format(disturbed.M_200.value_in(units.MSun)))
# amuse_plot.loglog(coolcore.r/coolcore.r_500, (coolcore.P_gas/coolcore.P_500),
# c=colours[i], ls='dashed')
amuse_plot.ylabel(r'$P(r)/P_{500}$')
amuse_plot.xlabel(r'$r/r_{500}$')
legend = pyplot.legend(loc=3, frameon=False, fontsize=16)
# Set the color situation
# for colour, text in zip(colours, legend.get_texts()):
# text.set_color(colour)
ax4.set_ylim(ymin=1e-2, ymax=1e3)
ax4.set_xticks((0.01, 0.10, 1.00))
ax4.set_xticklabels(("0.01", "0.10", "1.00"))
ax4.set_xlim(xmin=0.01, xmax=2.0)
ax4.minorticks_on()
ax4.tick_params('both', length=10, width=2, which='major')
ax4.tick_params('both', length=5, width=1, which='minor')
ax4.text(0.015, 4, "disturbed", color="grey", fontsize=15)
ax4.text(0.02, 110, "cool cores", color="grey", fontsize=15)
ax4.text(0.2, 50, "Arnaud et al. 2010", color="black", fontsize=15)
# Set the xticks situation
for ax in [ax1, ax2, ax3]:
ax.set_xscale("log")
ax.set_yscale("log")
ax.set_xticks((10, 100, 1000))
ax.set_xticklabels(("10", "100", "1000"))
ax.set_xlim(xmin=10, xmax=5000)
ax.minorticks_on()
ax.tick_params('both', length=10, width=2, which='major')
ax.tick_params('both', length=5, width=1, which='minor')
# pyplot.savefig("../img/Donnert2014_Figure1_by_TLRH.pdf", format="pdf", dpi=1000)
pyplot.show()
def plot_individual_cluster_density(cluster):
""" Plot the particles' density radial profile and compare to model """
pyplot.figure(figsize=(24, 18))
# AMUSE datamodel particles. Gas has RHO and RHOm; dm rho from model.
amuse_plot.scatter(cluster.gas.r,
cluster.gas.rho,
c="g",
edgecolor="face",
s=1,
label=r"Generated IC: gas $\rho$")
# amuse_plot.scatter(cluster.gas.r,
# cluster.gas.rhom,
# c="r", edgecolor="face", s=1, label=r"Generated IC: gas $\rho_{\rm model}$")
amuse_plot.scatter(cluster.dm.r,
cluster.dm.rho,
c="b",
edgecolor="none",
label=r"Generated IC: DM $\rho$")
# Analytical solutions. Sample radii and plug into analytical expression.
r = VectorQuantity.arange(units.kpc(1), units.kpc(10000),
units.parsec(100))
# Plot analytical beta model (Donnert 2014) for the gas density
amuse_plot.plot(r,
cluster.gas_density_double_beta(r),
c="k",
ls="dashed",
label=r"Analytical, $\beta$-model:"
"\n"
r"$\rho_0$ = {0} g/cm$^3$; $rc = ${1} kpc".format(
cluster.rho0gas.number, cluster.rc.number))
# Plot analytical double beta model (Donnert et al. 2016, in prep) for gas
amuse_plot.plot(
r,
cluster.gas_density_beta(r),
c="k",
ls="dotted",
label=r"Analytical, double $\beta$-model:"
"\n"
r"$\rho_0$ = {0} g/cm$^3$; $rc =$ {1} kpc; $r_{{\rm cut}}$ = {2} kpc".
format(cluster.rho0gas.number, cluster.rc.number, cluster.rcut.number))
# Plot analytical Hernquist model for the DM density
amuse_plot.plot(r,
cluster.dm_density(r),
c="k",
ls="solid",
label=r"Analytical, Hernquist-model"
"\n"
r"$M_{{\rm dm}}= ${0:.2e} MSun; $a = $ {1} kpc".format(
cluster.M_dm.number, cluster.a.number))
pyplot.legend(loc=3)
amuse_plot.xlabel(r"$r$")
amuse_plot.ylabel(r"$\rho$")
pyplot.gca().set_xlim(xmin=10, xmax=1e4)
pyplot.gca().set_ylim(ymin=1e-30, ymax=9e-24)
pyplot.gca().set_xscale("log")
pyplot.gca().set_yscale("log")
pyplot.axvline(x=cluster.R200.value_in(units.kpc), lw=1, c="grey")
pyplot.text(cluster.R200.value_in(units.kpc), 5e-24,
r"$r_{{cut}} =$ {0}".format(cluster.rcut))
pyplot.axvline(x=cluster.rc.value_in(units.kpc), lw=1, c="grey")
pyplot.text(cluster.rc.value_in(units.kpc), 5e-24,
r"$rc =$ {0}".format(cluster.rc))
pyplot.axvline(x=cluster.a.value_in(units.kpc), lw=1, c="grey")
pyplot.text(cluster.a.value_in(units.kpc), 1e-24,
r"$a =$ {0}".format(cluster.a))
