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Commit 7000d664 authored by Loic Hausammann's avatar Loic Hausammann
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GEAR: small improvement to the example

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1 merge request!1052Gear cosmological simulations
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examples/GEAR/ZoomIn/add_fields.py
+ 23
− 0
View file @ 7000d664
...@@ -3,6 +3,7 @@ ...@@ -3,6 +3,7 @@
import numpy as np import numpy as np
import yt.utilities.physical_constants as constants import yt.utilities.physical_constants as constants
from yt.mods import YTArray from yt.mods import YTArray
from yt import derived_field
def addMassDeposit(f): def addMassDeposit(f):
...@@ -65,3 +66,25 @@ def addTemperature(f): ...@@ -65,3 +66,25 @@ def addTemperature(f):
return YTArray(convert_T_over_mu_to_T(T_over_mu), 'K') # now T return YTArray(convert_T_over_mu_to_T(T_over_mu), 'K') # now T
f.add_field(("PartType0", "Temperature"), function=_Temperature_3, f.add_field(("PartType0", "Temperature"), function=_Temperature_3,
particle_type=True, force_override=True, units="K") particle_type=True, force_override=True, units="K")
def addMetals(f):
def _metallicity(field, data):
if len(data["PartType0", "Metals"].shape) == 1:
return data["PartType0", "Metals"]
else:
# in_units("") turned out to be crucial!;
# otherwise code_metallicity will be used
return data["PartType0", "Metals"][:, -1].in_units("")
# We are creating ("Gas", "Metallicity") here, different from
# ("Gas", "metallicity") which is auto-generated by yt
# but doesn't work properly
f.add_field(("PartType0", "Metallicity"), function=_metallicity,
display_name="Metal mass fraction", particle_type=True,
take_log=True, units="")
def _density_squared(field, data):
return data[("PartType0", "density")]**2
f.add_field(("PartType0", "density_squared"), function=_density_squared,
particle_type=True, units="g**2/cm**6")
examples/GEAR/ZoomIn/cleanupSwift.py
+ 5
− 10
View file @ 7000d664
...@@ -11,7 +11,7 @@ out = sys.argv[-1] ...@@ -11,7 +11,7 @@ out = sys.argv[-1]
copyfile(filename, out) copyfile(filename, out)
f = File(out) f = File(out, "a")
# read cosmological parameters # read cosmological parameters
a = f["Cosmology"].attrs["Scale-factor"][0] a = f["Cosmology"].attrs["Scale-factor"][0]
...@@ -23,12 +23,6 @@ f["Header"].attrs["BoxSize"] = f["Header"].attrs["BoxSize"][0] * h ...@@ -23,12 +23,6 @@ f["Header"].attrs["BoxSize"] = f["Header"].attrs["BoxSize"][0] * h
# avoid the snapshot to be taken for SWIFT # avoid the snapshot to be taken for SWIFT
del f["Header"].attrs["Code"] del f["Header"].attrs["Code"]
# Delete problematic fields
for i in range(NPartType):
name = "PartType{}/ElementAbundances".format(i)
if name in f:
del f[name]
# Update the fields (name + cosmo) # Update the fields (name + cosmo)
for i in range(NPartType): for i in range(NPartType):
name = "PartType%i" % i name = "PartType%i" % i
...@@ -43,11 +37,12 @@ for i in range(NPartType): ...@@ -43,11 +37,12 @@ for i in range(NPartType):
fields = [ fields = [
("Coordinates", "Coordinates", h), ("Coordinates", "Coordinates", h),
("Masses", "Masses", h), ("Masses", "Masses", h),
("Velocities", "Velocities", a**0.5), ("Velocities", "Velocities", 1. / a**0.5),
("Density", "Densities", 1. / h**2), ("Density", "Densities", 1. / h**2),
("Entropies", "Entropies", 1.), ("Entropies", "Entropies", 1.),
("InternalEnergy", "InternalEnergies", 1. / a**2), ("InternalEnergy", "InternalEnergies", 1. / a**2),
("SmoothingLength", "SmoothingLengths", h) ("SmoothingLength", "SmoothingLengths", h),
("Metals", "SmoothedElementAbundances", 1.)
] ]
# create links # create links
...@@ -67,7 +62,7 @@ cosmo = f["Cosmology"].attrs ...@@ -67,7 +62,7 @@ cosmo = f["Cosmology"].attrs
head = f["Header"].attrs head = f["Header"].attrs
head["Redshift"] = float(cosmo["Redshift"]) head["Redshift"] = float(cosmo["Redshift"])
head["OmegaLambda"] = cosmo["Omega_lambda"] head["OmegaLambda"] = cosmo["Omega_lambda"]
head["Omega0"] = cosmo["Omega_b"] head["Omega0"] = cosmo["Omega_m"]
head["HubbleParam"] = cosmo["h"][0] head["HubbleParam"] = cosmo["h"][0]
head["Time"] = float(a) head["Time"] = float(a)
......
examples/GEAR/ZoomIn/make_image.py
+ 123
− 25
View file @ 7000d664
#!/usr/bin/env python3 #!/usr/bin/env python3
import yt import yt
from yt.units import Msun, kpc, s, km
import unyt
import sys import sys
import matplotlib
import projection_plot import projection_plot
import velocity_plot import velocity_plot
import phase_plot import phase_plot
import halo_distribution import halo_distribution
import metal_plot
import add_fields import add_fields
import star_plot
import profile_plot
import matplotlib.pyplot as plt import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1 import AxesGrid from mpl_toolkits.axes_grid1 import AxesGrid
from matplotlib.offsetbox import AnchoredText
matplotlib.use('Agg')
# Parameters # Parameters
...@@ -23,14 +21,29 @@ swift = "swift/snapshot_%04i.hdf5" % snap ...@@ -23,14 +21,29 @@ swift = "swift/snapshot_%04i.hdf5" % snap
gear = "gear/snapshot_%04i.hdf5" % snap gear = "gear/snapshot_%04i.hdf5" % snap
do_dmo = False
do_hydro = False
do_stars = True
do_feedback = True
do_plot = { do_plot = {
"projection_density": False, # DMO
"projection_temperature": False, "projection_mass": do_dmo,
"projection_mass": False, "velocity": do_dmo,
"halo_distribution": False, "halo_distribution": False, # very slow
"phase_1d": False, "profile": do_dmo,
"phase_2d": False, # hydro
"velocity": True "projection_density": True, #do_hydro,
"projection_temperature": do_hydro,
"phase_1d_density": do_hydro,
"phase_1d_temperature": do_hydro,
"phase_2d": do_hydro,
"metals": do_hydro,
# stars
"SFR": do_stars,
"projection_mass_stars": do_stars,
# feedback
"abundances": do_feedback,
"projection_metals": do_feedback,
} }
# Generate the figures # Generate the figures
...@@ -39,7 +52,9 @@ figsize = (100, 100) ...@@ -39,7 +52,9 @@ figsize = (100, 100)
figures = { figures = {
"projection_density": plt.figure(figsize=figsize), "projection_density": plt.figure(figsize=figsize),
"projection_temperature": plt.figure(figsize=figsize), "projection_temperature": plt.figure(figsize=figsize),
"projection_metals": plt.figure(figsize=figsize),
"projection_mass": plt.figure(figsize=figsize), "projection_mass": plt.figure(figsize=figsize),
"projection_mass_stars": plt.figure(figsize=figsize),
"phase_2d": plt.figure(figsize=figsize) "phase_2d": plt.figure(figsize=figsize)
} }
...@@ -63,18 +78,31 @@ axes = { ...@@ -63,18 +78,31 @@ axes = {
figures["projection_mass"], fig_size, subgrid, figures["projection_mass"], fig_size, subgrid,
add_all=True, share_all=True, cbar_mode="single", add_all=True, share_all=True, cbar_mode="single",
cbar_size="2%", cbar_pad=0.02), cbar_size="2%", cbar_pad=0.02),
"projection_mass_stars": AxesGrid(
figures["projection_mass_stars"], fig_size, subgrid,
add_all=True, share_all=True, cbar_mode="single",
cbar_size="2%", cbar_pad=0.02),
"phase_2d": AxesGrid( "phase_2d": AxesGrid(
figures["phase_2d"], fig_size, subgrid, axes_pad=0.05, figures["phase_2d"], fig_size, subgrid, axes_pad=0.05,
add_all=True, share_all=True, cbar_mode="single", add_all=True, share_all=True, cbar_mode="single",
cbar_size="2%", cbar_pad=0.05, aspect=False) cbar_size="2%", cbar_pad=0.05, aspect=False),
"projection_metals": AxesGrid(
figures["projection_metals"], fig_size, subgrid,
add_all=True, share_all=True, cbar_mode="single",
cbar_size="2%", cbar_pad=0.02),
} }
# Data # Data
data = { data = {
"phase_1d": ([], []), "phase_1d_density": ([], []),
"phase_1d_temperature": ([], []),
"halo_distribution": ([], []), "halo_distribution": ([], []),
"velocity": ([], []), "velocity": ([], []),
"metals": ([], []),
"SFR": ([], []),
"profile": ([], []),
"abundances": ([], []),
} }
names = [] names = []
...@@ -88,13 +116,25 @@ def savePlot(): ...@@ -88,13 +116,25 @@ def savePlot():
projection_plot.savePlot(figures["projection_temperature"], projection_plot.savePlot(figures["projection_temperature"],
"temperature") "temperature")
if do_plot["projection_metals"]:
projection_plot.savePlot(figures["projection_metals"],
"metals")
if do_plot["projection_mass"]: if do_plot["projection_mass"]:
projection_plot.savePlot(figures["projection_mass"], projection_plot.savePlot(figures["projection_mass"],
"mass") "mass")
if do_plot["phase_1d"]: if do_plot["projection_mass_stars"]:
data["phase_1d"][1].extend(names) projection_plot.savePlot(figures["projection_mass_stars"],
phase_plot.save1DPlot(data["phase_1d"]) "mass_stars")
if do_plot["phase_1d_density"]:
data["phase_1d_density"][1].extend(names)
phase_plot.save1DPlotDensity(data["phase_1d_density"])
if do_plot["phase_1d_temperature"]:
data["phase_1d_temperature"][1].extend(names)
phase_plot.save1DPlotTemperature(data["phase_1d_temperature"])
if do_plot["phase_2d"]: if do_plot["phase_2d"]:
phase_plot.save2DPlot(figures["phase_2d"]) phase_plot.save2DPlot(figures["phase_2d"])
...@@ -108,13 +148,38 @@ def savePlot(): ...@@ -108,13 +148,38 @@ def savePlot():
data["velocity"][1].extend(names) data["velocity"][1].extend(names)
velocity_plot.save1DPlot(data["velocity"]) velocity_plot.save1DPlot(data["velocity"])
if do_plot["metals"]:
data["metals"][1].extend(names)
metal_plot.save1DPlot(data["metals"])
if do_plot["SFR"]:
data["SFR"][1].extend(names)
star_plot.saveSFRPlot(data["SFR"])
if do_plot["profile"]:
data["profile"][1].extend(names)
profile_plot.savePlot(data["profile"])
def doPlot(filename, i, name): if do_plot["abundances"]:
data["abundances"][1].extend(names)
star_plot.saveAbundancesPlot(data["abundances"])
def doPlot(filename, i, name, center):
names.append(name) names.append(name)
f = yt.load(filename) f = yt.load(filename)
if center is None:
center = f.find_max("Density")[1]
f.center = center
if (do_plot["projection_temperature"] or do_plot["phase_2d"]): if (do_plot["projection_temperature"] or do_plot["phase_2d"]):
add_fields.addTemperature(f) add_fields.addTemperature(f)
add_fields.addMassDeposit(f)
if (do_plot["projection_metals"] or do_plot["metals"]):
add_fields.addMetals(f)
global scale_factor global scale_factor
if scale_factor is None: if scale_factor is None:
...@@ -135,17 +200,31 @@ def doPlot(filename, i, name): ...@@ -135,17 +200,31 @@ def doPlot(filename, i, name):
f, name, i, figures["projection_temperature"], f, name, i, figures["projection_temperature"],
axes["projection_temperature"]) axes["projection_temperature"])
if do_plot["projection_metals"]:
projection_plot.doMetalsPlot(
f, name, i, figures["projection_metals"],
axes["projection_metals"])
# Do mass projection plot # Do mass projection plot
if do_plot["projection_mass"]: if do_plot["projection_mass"]:
add_fields.addMassDeposit(f)
projection_plot.doMassPlot( projection_plot.doMassPlot(
f, name, i, figures["projection_mass"], f, name, i, figures["projection_mass"],
axes["projection_mass"]) axes["projection_mass"], "all")
# Do stellar mass projection plot
if do_plot["projection_mass_stars"]:
projection_plot.doMassPlot(
f, name, i, figures["projection_mass_stars"],
axes["projection_mass_stars"], "stars")
# 1D Phase plot # 1D Phase plot
if do_plot["phase_1d"]: if do_plot["phase_1d_density"]:
p = phase_plot.do1DPlot(f, name, i) p = phase_plot.do1DPlotDensity(f, name, i)
data["phase_1d"][0].append(p) data["phase_1d_density"][0].append(p)
if do_plot["phase_1d_temperature"]:
p = phase_plot.do1DPlotTemperature(f, name, i)
data["phase_1d_temperature"][0].append(p)
# 2D Phase plot # 2D Phase plot
if do_plot["phase_2d"]: if do_plot["phase_2d"]:
...@@ -162,7 +241,26 @@ def doPlot(filename, i, name): ...@@ -162,7 +241,26 @@ def doPlot(filename, i, name):
p = velocity_plot.do1DPlot(f, name, i) p = velocity_plot.do1DPlot(f, name, i)
data["velocity"][0].append(p) data["velocity"][0].append(p)
# metal plot
if do_plot["metals"]:
p = metal_plot.do1DPlot(f, name, i)
data["metals"][0].append(p)
if do_plot["SFR"]:
p = star_plot.doSFRPlot(f, name, i)
data["SFR"][0].append(p)
if do_plot["profile"]:
p = profile_plot.doPlot(f, name, i)
data["profile"][0].append(p)
if do_plot["abundances"]:
p = star_plot.doAbundancesPlot(f, name, i)
data["abundances"][0].append(p)
return center
doPlot(swift, 0, "SWIFT") center = doPlot(gear, 1, "GEAR", center=None)
doPlot(gear, 1, "GEAR") doPlot(swift, 0, "SWIFT", center=center)
savePlot() savePlot()
examples/GEAR/ZoomIn/phase_plot.py
+ 63
− 11
View file @ 7000d664
...@@ -4,10 +4,12 @@ import yt ...@@ -4,10 +4,12 @@ import yt
from yt.units import Msun, amu, cm, K, kpc from yt.units import Msun, amu, cm, K, kpc
from matplotlib.offsetbox import AnchoredText from matplotlib.offsetbox import AnchoredText
import matplotlib.pyplot as plt import matplotlib.pyplot as plt
import matplotlib.lines as ln
import numpy as np
width = 5 * kpc width = 10 * kpc
limits_temperature = (1e1 * K, 1e7 * K) limits_temperature = (1e1 * K, 1e5 * K)
limits_density = (1e-10 * amu / cm**3, 1e3 * amu / cm**3) limits_density = (1e-7 * amu / cm**3, 1e7 * amu / cm**3)
limits_mass = (1e3 * Msun, 1e7 * Msun) limits_mass = (1e3 * Msun, 1e7 * Msun)
...@@ -16,27 +18,54 @@ def save2DPlot(fig): ...@@ -16,27 +18,54 @@ def save2DPlot(fig):
pad_inches=0.03, dpi=300) pad_inches=0.03, dpi=300)
def save1DPlot(profiles): def save1DPlotDensity(profiles):
plt.figure(figsize=(8, 8)) plt.figure(figsize=(8, 8))
plt.tight_layout(pad=0.4, w_pad=0.5, h_pad=0.5) plt.tight_layout(pad=0.4, w_pad=0.5, h_pad=0.5)
markers = ["s", "o"] markers = ["s", "o"]
for i, p in enumerate(profiles[0]): for i, p in enumerate(profiles[0]):
rho = p.x.in_units("g/cm**3").d rho = p.x.in_units("g/cm**3").d
mass = p["Masses"].in_units("Msun").d mass = p["Masses"].in_units("Msun").d
mass[mass == 0] = np.nan
plt.plot(rho, mass, linestyle="-", marker=markers[i], plt.plot(rho, mass, linestyle="-", marker=markers[i],
markeredgecolor='none', linewidth=1.2, alpha=0.8) markeredgecolor='none', linewidth=1.2, alpha=0.8)
plt.semilogx() plt.semilogx()
plt.semilogy() plt.semilogy()
plt.xlabel("$\mathrm{Density\ (g/cm^3)}$", fontsize='large') plt.xlabel("$\mathrm{Density\ (g/cm^3)}$", fontsize='large')
plt.ylabel(r"$\mathrm{Mass,}\/\mathrm{d}M\mathrm{/dlog}\/\mathrm{\rho}\/\mathrm{(M_{\odot})}$", fontsize='large') plt.ylabel(r"$\mathrm{Mass}\/\mathrm{(M_{\odot})}$", fontsize='large')
plt.legend(profiles[1], loc=4, frameon=True, ncol=2, fancybox=True) plt.legend(profiles[1], loc=4, frameon=True, ncol=2, fancybox=True)
leg = plt.gca().get_legend() leg = plt.gca().get_legend()
ltext = leg.get_texts() ltext = leg.get_texts()
plt.setp(ltext, fontsize='small') plt.setp(ltext, fontsize='small')
plt.grid(True) plt.grid(True)
plt.savefig("phase_1d.png", bbox_inches='tight', pad_inches=0.03, dpi=300) plt.savefig("phase_1d_density.png", bbox_inches='tight',
pad_inches=0.03, dpi=300)
def save1DPlotTemperature(profiles):
plt.figure(figsize=(8, 8))
plt.tight_layout(pad=0.4, w_pad=0.5, h_pad=0.5)
markers = ["s", "o"]
for i, p in enumerate(profiles[0]):
rho = p.x.in_units("K").d
mass = p["Masses"].in_units("Msun").d
mass[mass == 0] = np.nan
plt.plot(rho, mass, linestyle="-", marker=markers[i],
markeredgecolor='none', linewidth=1.2, alpha=0.8)
plt.semilogx()
plt.semilogy()
plt.xlabel("$\mathrm{Temperature\ K}$", fontsize='large')
plt.ylabel(r"$\mathrm{Mass}\/\mathrm{(M_{\odot})}$", fontsize='large')
plt.legend(profiles[1], loc=4, frameon=True, ncol=2, fancybox=True)
leg = plt.gca().get_legend()
ltext = leg.get_texts()
plt.setp(ltext, fontsize='small')
plt.grid(True)
plt.savefig("phase_1d_temperature.png", bbox_inches='tight',
pad_inches=0.03, dpi=300)
def do2DPlot(f, name, i, fig, axes): def do2DPlot(f, name, i, fig, axes):
...@@ -77,12 +106,35 @@ def do2DPlot(f, name, i, fig, axes): ...@@ -77,12 +106,35 @@ def do2DPlot(f, name, i, fig, axes):
at = AnchoredText(name, loc=2, prop=dict(size=6), frameon=True) at = AnchoredText(name, loc=2, prop=dict(size=6), frameon=True)
plot.axes.add_artist(at) plot.axes.add_artist(at)
# Make a grid
x_ticks = plot.axes.get_xticks()
y_ticks = plot.axes.get_yticks()
for x in x_ticks:
N = len(y_ticks)
line = ln.Line2D([x]*N, y_ticks, linestyle=":", linewidth=0.6,
color="k", alpha=0.7)
plot.axes.add_line(line)
for y in y_ticks:
N = len(x_ticks)
line = ln.Line2D(x_ticks, [y]*N, linestyle=":", linewidth=0.6,
color="k", alpha=0.7)
plot.axes.add_line(line)
def do1DPlotDensity(f, name, i):
sp = f.sphere(f.center, width)
# Because ParticleProfilePlot doesn't exist, I will do the following trick.
p = yt.create_profile(sp, ("PartType0", "density"),
("PartType0", "Masses"), weight_field=None,
n_bins=40, accumulation=False)
return p
def do1DPlot(f, name, i): def do1DPlotTemperature(f, name, i):
sp = f.sphere("max", width) sp = f.sphere(f.center, width)
# Because ParticleProfilePlot doesn't exist, I will do the following trick. # Because ParticleProfilePlot doesn't exist, I will do the following trick.
p = yt.create_profile(sp, ("PartType0", "density"), ("PartType0", "Masses"), p = yt.create_profile(sp, ("PartType0", "Temperature"),
weight_field=None, n_bins=50, ("PartType0", "Masses"), weight_field=None,
accumulation=False) n_bins=40, accumulation=False)
return p return p
examples/GEAR/ZoomIn/profile_plot.py 0 → 100644
+ 43
− 0
View file @ 7000d664
#!/usr/bin/env python3
import yt
from yt.units import Msun, kpc
import matplotlib.pyplot as plt
width = 20 * kpc
limits_mass = (1e3 * Msun, 1e7 * Msun)
def savePlot(profiles):
plt.figure(figsize=(8, 8))
plt.tight_layout(pad=0.4, w_pad=0.5, h_pad=0.5)
markers = ["s", "o"]
for i, p in enumerate(profiles[0]):
r = p.x.in_units("pc").d
mass = p["Masses"].in_units("Msun").d
plt.plot(r, mass, linestyle="-", marker=markers[i],
markeredgecolor='none', linewidth=1.2, alpha=0.8)
plt.semilogx()
plt.semilogy()
plt.xlabel(r"$\mathrm{Radius}\/\mathrm{(pc)}$", fontsize='large')
plt.ylabel("$\mathrm{Integrated}\ \mathrm{mass}\ (Msun)}$",
fontsize='large')
plt.legend(profiles[1], loc=4, frameon=True, ncol=2, fancybox=True)
leg = plt.gca().get_legend()
ltext = leg.get_texts()
plt.setp(ltext, fontsize='small')
plt.grid(True)
plt.savefig("integrated_mass.png", bbox_inches='tight',
pad_inches=0.03, dpi=300)
def doPlot(f, name, i):
sp = f.sphere(f.center, width)
# Because ParticleProfilePlot doesn't exist, I will do the following trick.
p = yt.create_profile(sp, "particle_radius", "Masses",
weight_field=None, n_bins=50,
accumulation=True)
return p
examples/GEAR/ZoomIn/projection_plot.py
+ 123
− 32
View file @ 7000d664
...@@ -3,17 +3,17 @@ ...@@ -3,17 +3,17 @@
import yt import yt
from yt.units import kpc, g, cm, K from yt.units import kpc, g, cm, K
from matplotlib.offsetbox import AnchoredText from matplotlib.offsetbox import AnchoredText
import numpy as np
cmap_density = "algae" cmap_density = "algae"
cmap_temperature = "magma" cmap_temperature = "magma"
cmap_mass = "inferno" cmap_mass = "inferno"
center = (1441.9954833984375000, cmap_metals = "coolwarm"
1666.1169433593750000, small_width = 400 * kpc
1891.6248779296875000) large_width = 400 * kpc
small_width = 250 * kpc limits_density = (1e-10 * g / cm**2, 1e2 * g / cm**2)
large_width = 3000 * kpc
limits_density = (1e-10 * g / cm**2, 1e-2 * g / cm**2)
limits_temperature = (10 * K, 1e5 * K) limits_temperature = (10 * K, 1e5 * K)
limits_metals = None
limits_mass = None limits_mass = None
...@@ -58,10 +58,11 @@ def doDensityPlot(f, name, i, fig, axes): ...@@ -58,10 +58,11 @@ def doDensityPlot(f, name, i, fig, axes):
""" """
direction = "x" direction = "x"
field = ("PartType0", "density") field = ("PartType0", "density")
a = f.scale_factor
# compute the projection # compute the projection
p = yt.ProjectionPlot(f, direction, field, center=center, p = yt.ProjectionPlot(f, direction, field, center=f.center,
width=small_width, buff_size=(800, 800)) width=small_width * a, buff_size=(800, 800))
# Compute the limits # Compute the limits
p.set_unit("density", "g / cm**2") p.set_unit("density", "g / cm**2")
...@@ -130,11 +131,12 @@ def doTemperaturePlot(f, name, i, fig, axes): ...@@ -130,11 +131,12 @@ def doTemperaturePlot(f, name, i, fig, axes):
""" """
direction = "x" direction = "x"
field = ("PartType0", "Temperature") field = ("PartType0", "Temperature")
a = f.scale_factor
# compute the projection # compute the projection
p = yt.ProjectionPlot(f, direction, field, center=center, p = yt.ProjectionPlot(f, direction, field, center=f.center,
weight_field="density", weight_field="density",
width=small_width, buff_size=(800, 800)) width=small_width * a, buff_size=(800, 800))
# Compute the limits # Compute the limits
p.set_unit("Temperature", "K") p.set_unit("Temperature", "K")
...@@ -179,7 +181,7 @@ def doTemperaturePlot(f, name, i, fig, axes): ...@@ -179,7 +181,7 @@ def doTemperaturePlot(f, name, i, fig, axes):
plot.axes.add_artist(at) plot.axes.add_artist(at)
def doMassPlot(f, name, i, fig, axes): def doMassPlot(f, name, i, fig, axes, parttype):
""" """
Generate a mass projection (including dark matter) plot. Generate a mass projection (including dark matter) plot.
...@@ -200,36 +202,116 @@ def doMassPlot(f, name, i, fig, axes): ...@@ -200,36 +202,116 @@ def doMassPlot(f, name, i, fig, axes):
axes: list axes: list
The list of axes to use for the plot The list of axes to use for the plot
parttype: str
The name of the particle type to use
""" """
direction = "y" width = large_width
field = ("all", "Masses") if parttype == "stars":
width = small_width
if name == "GEAR":
parttype = "PartType1"
else:
parttype = "PartType4"
direction = "x"
field = (parttype, "Masses")
a = f.scale_factor
# compute the projection # compute the projection
p = yt.ParticleProjectionPlot(f, direction, field, center=center, p = yt.ParticleProjectionPlot(f, direction, field, center=f.center,
width=large_width) width=width * a)
# # Compute the limits # # Compute the limits
# p.set_unit("masses", "Msun * kpc") p.set_unit("Masses", "Msun")
# data = p.to_fits_data()["masses"].data data = p.to_fits_data()["Masses"].data
# global limits_mass global limits_mass
# if limits_mass is None: if limits_mass is None:
# dmin = data.min() dmin = np.nanmin(data)
# if data.min() == 0: if np.nanmin(data) == 0:
# dmin = 1e-6 * data.max() dmin = 1e-6 * np.nanmax(data)
# else: else:
# dmin *= 0.5 dmin *= 0.5
# dmax = data.max() * 2 dmax = np.nanmax(data) * 2
# limits_mass = (dmin, dmax) limits_mass = (dmin, dmax)
# else: else:
# if limits_mass[0] > data.min(): if limits_mass[0] > np.nanmin(data):
# print("WARNING: data below min", data.min()) print("WARNING: data below min", np.nanmin(data))
# if limits_mass[1] < data.max(): if limits_mass[1] < np.nanmax(data):
# print("WARNING: data above max", data.max()) print("WARNING: data above max", np.nanmax(data))
# Adjust the plot # Adjust the plot
p.set_cmap(field=field, cmap=cmap_mass) p.set_cmap(field=field, cmap=cmap_mass)
# p.set_log(field, True) # p.set_log(field, True)
# p.set_zlim(field, limits_mass[0], limits_mass[1]) p.set_zlim(field, limits_mass[0], limits_mass[1])
# Draw it into the correct figure
plot = p.plots[field]
plot.figure = fig
plot.axes = axes[i].axes
# Add code name
at = AnchoredText(name, loc=2, prop=dict(size=6), frameon=True)
plot.axes.add_artist(at)
# plot color bar
if i != 0:
plot.cax = axes.cbar_axes[0]
p.hide_axes()
p._setup_plots()
# Add code name
at = AnchoredText(name, loc=2, prop=dict(size=6), frameon=True)
plot.axes.add_artist(at)
def doMetalsPlot(f, name, i, fig, axes):
"""
Generate a metal projection plot.
Parameters
----------
f: yt dataset
The data set to use in the projection
name: str
The name to print on the plot
i: int
The index of the plot
fig: matplotlib figure
The figure to use
axes: list
The list of axes to use for the plot
"""
direction = "x"
field = ("PartType0", "Metallicity")
a = f.scale_factor
# compute the projection
p = yt.ProjectionPlot(f, direction, field, center=f.center,
width=small_width * a, buff_size=(800, 800),
weight_field=("PartType0", "Density"))
# Compute the limits
# p.set_unit("metallicity", "g / cm**2")
data = p.to_fits_data()["Metallicity"].data
global limits_metals
if limits_metals is None:
limits_metals = (data.min(), data.max())
if limits_metals[0] > data.min():
print("WARNING: data below min", data.min())
if limits_metals[1] < data.max():
print("WARNING: data above max", data.max())
# Adjust the plot
p.set_cmap(field=field, cmap=cmap_metals)
p.set_log(field, True)
#p.set_zlim(field, limits_metals[0], limits_metals[1])
# Draw it into the correct figure # Draw it into the correct figure
plot = p.plots[field] plot = p.plots[field]
...@@ -247,6 +329,15 @@ def doMassPlot(f, name, i, fig, axes): ...@@ -247,6 +329,15 @@ def doMassPlot(f, name, i, fig, axes):
p.hide_axes() p.hide_axes()
p._setup_plots() p._setup_plots()
if i == 0:
z = 1. / f.scale_factor - 1.
text = "Redshift = %.2g" % z
prop = {
"color": "w"
}
at = AnchoredText(text, loc=3, prop=prop, frameon=False)
plot.axes.add_artist(at)
# Add code name # Add code name
at = AnchoredText(name, loc=2, prop=dict(size=6), frameon=True) at = AnchoredText(name, loc=2, prop=dict(size=6), frameon=True)
plot.axes.add_artist(at) plot.axes.add_artist(at)
examples/GEAR/ZoomIn/star_plot.py 0 → 100644
+ 127
− 0
View file @ 7000d664
#!/usr/bin/env python3
import matplotlib.pyplot as plt
import numpy as np
from yt.units import kpc
from yt.utilities.cosmology import Cosmology
from multiprocessing import Pool
from functools import partial
from h5py import File
width = 10 * kpc
fe_sol_abund = 1.76603e-3
mg_sol_abund = 9.24316e-4
def saveSFRPlot(profiles):
plt.figure(figsize=(8, 8))
plt.tight_layout(pad=0.4, w_pad=0.5, h_pad=0.5)
markers = ["s", "o"]
sfr_fig = plt.figure()
mstar_fig = plt.figure()
for i, p in enumerate(profiles[0]):
masses = p[0]
form_time = p[1]
time_range = [0, 14] # Gyr
n_bins = 1000
hist, bins = np.histogram(form_time, bins=n_bins, range=time_range)
inds = np.digitize(form_time, bins=bins)
time = (bins[:-1] + bins[1:])/2
sfr = np.array([masses[inds == j+1].sum()/(bins[j+1]-bins[j])
for j in range(len(time))])
sfr[sfr == 0] = np.nan
sfr /= 1e9 # convert M / Gyr -> M / yr
plt.figure(sfr_fig.number)
plt.plot(time, sfr, linestyle="-", marker=markers[i],
markeredgecolor="none", linewidth=1.2, alpha=0.8)
mstars = np.array([masses[inds == j+1].sum()
for j in range(len(time))])
mstars = np.cumsum(mstars)
plt.figure(mstar_fig.number)
plt.plot(time, mstars, linestyle="-",
markeredgecolor="none", linewidth=1.2, alpha=0.8)
plt.figure(sfr_fig.number)
plt.xlabel('Time [Gyr]')
plt.ylabel('SFR [M$_\odot$ yr$^{-1}$]')
plt.legend(profiles[1])
plt.savefig("sfr.png")
plt.figure(mstar_fig.number)
plt.xlabel('Time [Gyr]')
plt.ylabel('Stellar mass [M$_\odot$]')
plt.legend(profiles[1])
plt.savefig("mstars.png")
def doSFRPlot(f, name, i):
sp = f.sphere(f.center, width)
if name == "GEAR":
masses = sp["PartType1", "particle_mass"].in_units("Msun")
a = sp["PartType1", "StarFormationTime"]
else:
masses = sp["PartType4", "particle_mass"].in_units("Msun")
a = sp["PartType4", "BirthScaleFactors"]
cosmo = Cosmology(hubble_constant=f.hubble_constant,
omega_matter=f.omega_matter,
omega_lambda=f.omega_lambda)
z = np.array(1. / a - 1.)
with Pool() as p:
formation_time = p.map(
partial(cosmo.lookback_time, z_f=1e6), z)
formation_time = f.arr(list(formation_time), "s").in_units("Gyr")
return masses, formation_time
def saveAbundancesPlot(profiles):
plt.figure(figsize=(8, 8))
plt.tight_layout(pad=0.4, w_pad=0.5, h_pad=0.5)
markers = ["s", "o"]
for i, p in enumerate(profiles[0]):
mg = np.log10(p[0] / mg_sol_abund)
fe = np.log10(p[1] / fe_sol_abund)
plt.plot(fe, mg - fe, linestyle="", marker=markers[i],
markeredgecolor="none", alpha=0.8)
plt.xlim([-4, 0.5])
plt.ylim([-1, 1.5])
plt.xlabel('[Fe / H]')
plt.ylabel('[Mg / Fe]')
plt.legend(profiles[1])
plt.savefig("abundances.png")
def doAbundancesPlot(f, name, i):
sp = f.sphere(f.center, width)
if name == "GEAR":
metals = sp["PartType1", "StarMetals"]
h = File(f.filename_template, "r")
names = h["Header"].attrs["ChimieLabels"]
names = names.split(b",")
# remove garbage
names = names[:-2]
# bytes to unicode
names = [name.decode() for name in names]
h.close()
else:
metals = sp["PartType4", "ElementAbundances"]
h = File(f.filename_template, "r")
sub = h["SubgridScheme"].attrs
names = []
for i in range(metals.shape[1]):
name = sub["Element %i" % i].decode()
names.append(name)
mg = names.index("Mg")
fe = names.index("Fe")
return metals[:, mg], metals[:, fe]
examples/GEAR/ZoomIn/velocity_plot.py
+ 17
− 3
View file @ 7000d664
...@@ -5,6 +5,7 @@ from yt.units import kpc ...@@ -5,6 +5,7 @@ from yt.units import kpc
import matplotlib.pyplot as plt import matplotlib.pyplot as plt
width = 1500 * kpc width = 1500 * kpc
DMO = True
def save1DPlot(profiles): def save1DPlot(profiles):
...@@ -20,7 +21,12 @@ def save1DPlot(profiles): ...@@ -20,7 +21,12 @@ def save1DPlot(profiles):
plt.semilogy() plt.semilogy()
plt.xlabel("$\mathrm{Velocity\ (km/s)}$", fontsize='large') plt.xlabel("$\mathrm{Velocity\ (km/s)}$", fontsize='large')
plt.ylabel(r"$\mathrm{Mass,}\/\mathrm{d}M\mathrm{/dlog}\/\mathrm{\rho}\/\mathrm{(M_{\odot})}$", fontsize='large') if DMO:
plt.ylabel(r"$\mathrm{Mass}\/\mathrm{all}\/\mathrm{(M_{\odot})}$",
fontsize='large')
else:
plt.ylabel(r"$\mathrm{Mass}\/\mathrm{Gas}\/\mathrm{(M_{\odot})}$",
fontsize='large')
plt.legend(profiles[1], loc=4, frameon=True, ncol=2, fancybox=True) plt.legend(profiles[1], loc=4, frameon=True, ncol=2, fancybox=True)
leg = plt.gca().get_legend() leg = plt.gca().get_legend()
ltext = leg.get_texts() ltext = leg.get_texts()
...@@ -31,10 +37,18 @@ def save1DPlot(profiles): ...@@ -31,10 +37,18 @@ def save1DPlot(profiles):
def do1DPlot(f, name, i): def do1DPlot(f, name, i):
sp = f.sphere("max", width) global DMO
part_type = "all"
if f.particle_type_counts["PartType0"] != 0:
DMO = False
part_type = "PartType0"
a = f.scale_factor
sp = f.sphere("c", width * a)
# Because ParticleProfilePlot doesn't exist, I will do the following trick. # Because ParticleProfilePlot doesn't exist, I will do the following trick.
p = yt.create_profile(sp, ("PartType0", "velocity_magnitude"), ("PartType0", "Masses"), p = yt.create_profile(sp, (part_type, "particle_velocity_magnitude"),
(part_type, "Masses"),
weight_field=None, n_bins=50, weight_field=None, n_bins=50,
accumulation=False) accumulation=False)
......
tools/task_plots/iplot_tasks.py
+ 1
− 1
View file @ 7000d664
...@@ -40,7 +40,7 @@ matplotlib.use('TkAgg') ...@@ -40,7 +40,7 @@ matplotlib.use('TkAgg')
import numpy as np import numpy as np
import matplotlib.backends.backend_tkagg as tkagg import matplotlib.backends.backend_tkagg as tkagg
from matplotlib.figure import Figure from matplotlib.figure import Figure
import Tkinter as tk import tkinter as tk
import matplotlib.collections as collections import matplotlib.collections as collections
import matplotlib.ticker as plticker import matplotlib.ticker as plticker
import pylab as pl import pylab as pl
......
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