def setup_analytical_cluster(simulation, i=0):
""" Set up an analytical cluster given sampled parameters of the halo.
In Toycluster we have two haloes: halo[0] and halo[1].
Toycluster runtime output is piped to runToycluster.log.
This output is then parsed by `Toycluster2RuntimeOutputParser' class
and saved in the `NumericalCluster' instance `simulation' class
variable `toyclusterlog'.
toyclusterlog has a 2D dict halosetup, where
halosetup[0][...] gives the specific halo properties of halo0
"""
# Caution: parms[0] is number density! Caution: use unitsless numbers!
rho0 = simulation.toyclusterlog.halosetup[i]['rho0gas_cgs']
ne0 = convert.rho_to_ne(rho0.value_in(units.g / units.cm**3),
simulation.toyclusterlog.systemat['z'])
rc = simulation.toyclusterlog.halosetup[i]['rc']
R200 = simulation.toyclusterlog.halosetup[i]['R200']
Mass_in_DM = simulation.toyclusterlog.halosetup[i]['Mass_in_DM']
a = simulation.toyclusterlog.halosetup[i]['a_hernquist']
# print "rho0 :", rho0
# print "ne0 :", ne0
# print "rc :", rc
# print "R200 :", R200
# print "Mass_in_DM :", Mass_in_DM
# print "a :", a
parms = (ne0, rc.value_in(units.kpc), R200.value_in(units.kpc))
dm_parms = (Mass_in_DM, a)
return AnalyticalCluster(parms,
dm_parms,
z=simulation.toyclusterlog.systemat['z'])
def compton_y(r, Rmax, rho_gas, M_tot):
""" SZ 1980 adopted by Donnert (2014; eq. 16)
CAUTION: constants used in this function are in cgs. Make sure that the
rho_gas, M_tot and r are all in cgs units!!
@param Rmax : maximum value in integration, float, [cm]
@param rho_gas: callable gas density profile, function pointer
@param M_tot : callable total mass profile, function pointer
@return : compton-y parameter """
print "Does not work yet"
return
m_e = const.m_e.to(u.g).value
kB = const.k_B.to(u.erg / u.K).value
sT = const.sigma_T.cgs.value
c = const.c.cgs.value
fac = sT * kB * 4 * numpy.pi / m_e / p2(c)
y = scipy.integrate.quad(
lambda t: fac * p2(t) * convert.rho_to_ne(rho_gas(t)) *
hydrostatic_temperature(t, Rmax, rho_gas, M_tot), 0, Rmax)
return y[0]
def total_gravitating_mass(c,
cNFW=None,
bf=0.17,
RCUT_R200_RATIO=None,
verbose=False,
debug=False):
""" Find total gravitating mass under assumption of fixed baryon fraction
at the virial radius (seventeen percent) r200.
The problem is implicit and solved by root-finding (bisection).
@param c : ObservedCluster
@param cNFW: Concentration parameter. If given, cNFW is a free parameter
instead of using the Duffy+ 2008 relation for c(M200, z)
@param bf : Baryon fraction. Default 17% within R200.
@param RCUT_R200_RATIO
: rcut = RCUT_R200_RATIO * r200 to cut-off betamodel and NFW
@return : Dictionary of best-fit halo properties. """
# Set bestfit betamodel parameters
ne0, rho0, beta, rc = c.ne0, c.rho0, c.beta, c.rc
rc *= convert.kpc2cm
# Find r200 such that rho200 / rho_crit == 200 (True by definition)
lower = 10 * convert.kpc2cm
upper = 4000 * convert.kpc2cm
# bisection method
epsilon = 0.001
while upper / lower > 1 + epsilon:
# bisection
r200 = (lower + upper) / 2.
# bf = 0.17 # Critical assumption: bf == 0.17 at r200 (Planelles+ 2013)
if RCUT_R200_RATIO is None:
rcut = None
else:
rcut = r200 * RCUT_R200_RATIO
Mgas200 = profiles.gas_mass_betamodel(r200, rho0, beta, rc, rcut)
Mdm200 = Mgas200 * (1 / bf - 1)
M200 = Mgas200 + Mdm200
if not cNFW: cNFW = profiles.cNFW(M200)
rs = r200 / cNFW
rho0_dm = Mdm200 / profiles.dm_mass_nfw(r200, 1, rs)
""" Now rho_average(r200)/rhocrit should equal 200.
If not? Try different r200"""
rho200_over_rhocrit = (
M200 / (4. / 3 * numpy.pi * p3(r200))) / c.cc.rho_crit()
if debug:
print "Lower = {0:3.1f}".format(lower *
convert.cm2kpc)
print "r200 = {0:3.1f}".format(r200 *
convert.cm2kpc)
print "Upper = {0:3.1f}".format(upper *
convert.cm2kpc)
print "Ratio = {0:.1f}".format(
rho200_over_rhocrit / 200)
print
# bisection
if rho200_over_rhocrit < 200:
upper = r200
if rho200_over_rhocrit > 200:
lower = r200
# r200, thus M200 found
halo = dict()
halo["r200"] = r200 * convert.cm2kpc
halo["rcut"] = rcut * convert.cm2kpc if rcut is not None else None
halo["rho200_over_rhocrit"] = rho200_over_rhocrit
halo["bf200"] = Mgas200 / (Mdm200 + Mgas200)
halo["rho0"] = rho0
halo["ne0"] = convert.rho_to_ne(rho0)
halo["rc"] = rc * convert.cm2kpc
halo["beta"] = beta
halo["Mgas200"] = Mgas200 * convert.g2msun
halo["Mdm200"] = Mdm200 * convert.g2msun
halo["M200"] = M200 * convert.g2msun
halo["cNFW"] = cNFW
halo["rs"] = rs * convert.cm2kpc
halo["rho0_dm"] = rho0_dm
halo["ne0_dm"] = convert.rho_to_ne(rho0_dm)
return halo
def make_all_plots(run, snap, i, replot=False):
print "Generating plots for:", snap
fname = snap.split('/')[-1]
snapnr = fname.split('_')[-1]
if run.IC_only:
snapnr += "00-ICOnly"
mass_filename = run.outdir + "{0}-mass-{1}.png".format(
run.timestamp, snapnr)
density_filename = run.outdir + "{0}-density-{1}.png".format(
run.timestamp, snapnr)
temperature_filename = run.outdir + "{0}-temperature-{1}.png".format(
run.timestamp, snapnr)
if (os.path.isfile(mass_filename) and os.path.exists(mass_filename)
and os.path.isfile(density_filename) \
and os.path.exists(density_filename)) \
and not replot:
print "Plots exist. Skipping", snap
return
numerical = NumericalCluster(
icdir=run.icdir,
snapdir=run.snapdir,
logfile="runToycluster.log",
icfile="IC_single_0" if run.IC_only else "snapshot_" + snapnr,
verbose=False)
""" TODO: can use cluster.py setup_analytical_cluster
to obtain AnalyticalCluster from NumericalCluster"""
# Caution: parms[0] is number density! Caution: use unitsless numbers!
ne0 = convert.rho_to_ne(numerical.rho0gas.value_in(units.g / units.cm**3),
numerical.z)
parms = (ne0, numerical.rc.value_in(units.kpc),
numerical.R200.value_in(units.kpc), float(numerical.beta))
# TODO: not use this, but if doing so then use halo0_sampling...
dm_parms = (numerical.Mass_in_DM, numerical.a)
analytical = AnalyticalCluster(parms,
dm_parms,
z=numerical.z,
free_beta=True)
# 295 for WC6, 50 for Cubic Spline kernel
numerical.get_gas_mass_via_density(DESNNGB=50 if arguments.IC_only else 50)
numerical.get_dm_mass_via_number_density(log_binning=True)
numerical.set_dm_density()
plot_individual_cluster_density(numerical, analytical, run.observed)
# pyplot.title("Time = {0:1.2f} Gyr".format(i*run.TimeBetSnapshot), y=1.03)
if arguments.save:
pyplot.savefig(density_filename)
pyplot.close()
pyplot.show()
# plot_individual_cluster_mass(numerical, analytical)
# pyplot.title("Time = {0:1.2f} Gyr".format(i*run.TimeBetSnapshot), y=1.03)
# if arguments.save:
# pyplot.savefig(mass_filename)
# pyplot.close()
# plot_individual_cluster_temperature(numerical, analytical)
# pyplot.title("Time = {0:1.2f} Gyr".format(i*run.TimeBetSnapshot), y=1.03)
# if arguments.save:
# pyplot.savefig(temperature_filename)
# pyplot.close()
# else:
# pyplot.show()
# break
print "Done with snapshot: ", snap
def gas_number_density(self, r=None):
return (convert.rho_to_ne(
self.gas_density(r).value_in(units.g / units.cm**3), self.z) |
(1 / units.cm**3))