-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathJuly20_CR_mask5_mass.py
214 lines (168 loc) · 8.92 KB
/
July20_CR_mask5_mass.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import numpy as np
#import illustris_python as il
import h5py
#import illustris_python.snapshot as snapp
import os
import sys
import sphviewer
import pdb
from matplotlib.pyplot import cm
from mpl_toolkits.axes_grid1 import make_axes_locatable
from sphviewer.tools import QuickView
from glob import glob
import trident
import yt
import trident
from numpy import *
from yt import *
yt.enable_parallelism()
from mpl_toolkits.axes_grid1 import AxesGrid
#import glob
from yt import YTQuantity
from matplotlib.pyplot import *
from matplotlib.pyplot import cm
unit_base = {'UnitLength_in_cm' : 3.08568e+21,
'UnitMass_in_g' : 1.989e+43,
'UnitVelocity_in_cm_per_s' : 100000}
"""
Here we present some explanations.
Camera:
The Camera class is a container that stores the camera parameters. The camera is an object that lives in the space and has spherical coordinates (r,theta,phi), centred around the location (x,y,z). Angles *theta* and *phi* are given in degrees, and enable to rotate the camera along the x-axis and y-axis, respectively. The *roll* angle induces rotations along the line-of-sight, i.e., the z-axis.
"""
### Interesting toturial: http://alejandrobll.github.io/py-sphviewer/content/tutorial_projections.html
### Here we study the density profile of the gas particles. We consider two different cases. 1) When we take into account all of the gas particles and monitor their density profile. 2) When we consider the star forming gas and see how do they look like!!!
#data.keys()
#data["PartType0"].keys()
"""
<KeysViewHDF5 ['CoolingRate', 'Coordinates', 'Density', 'DivBcleaningFunctionGradPhi', 'DivBcleaningFunctionPhi', 'DivergenceOfMagneticField', 'ElectronAbundance', 'HeatingRate', 'HydroHeatingRate', 'IMFFormationProperties', 'InternalEnergy', 'MagneticField', 'Masses', 'MetalCoolingRate', 'Metallicity', 'NetHeatingRateQ', 'NeutralHydrogenAbundance', 'ParticleChildIDsNumber', 'ParticleIDGenerationNumber', 'ParticleIDs', 'SmoothingLength', 'StarFormationRate', 'Velocities']>
"""
# you could put a for loop here that replaces 'm12_mcvt_default_64 ' with whaterver directories are in /hernquist_lab/AGN_Feedback_Fire then goes to the 'output' folder in each
print("Checkpoint 0")
Directory_path = '/n/holylfs05/LABS/hernquist_lab/AGN_Feedback_Fire/m12_mcvt_m2_t7_3000_tor3_CR10_t4/output/'
diir = glob(Directory_path + '*.hdf5')
List_diir = np.atleast_1d(diir)
snap_order = []
List_diir_image = []
List_diir = np.atleast_1d(diir)
snap_order = []
for ii in range(len(List_diir)):
AA = List_diir[ii]
snap_ii = int(AA[AA.find('snapshot_')+len('snapshot_'):AA.find('.hdf5')])
snap_order = np.append(snap_order, [snap_ii])
List_diir_image = np.append(List_diir_image, List_diir[ii])
# add txt conversion line later!
print("Checkpoint 0B")
# this puts the snapshots in the correct numerical order when they are runa nd saved
int_snap = snap_order.astype(int)
sorted = np.sort(int_snap)
List_diir = List_diir_image[np.argsort(int_snap)]
print("Checkpoint 0C")
oo = 0
for fname in List_diir:
data = h5py.File(fname,"r")
BH_Center = data["PartType5"]["Coordinates"][:]
print(BH_Center)
BH_Center = data["PartType5"]["Coordinates"][:]
Gas_location = data["PartType0"]["Coordinates"][:] - BH_Center
Gas_mass = 1e10*data["PartType0"]["Masses"][:]
Gas_Softening = data["PartType0"]["SmoothingLength"][:]
print("Checkpoint 1")
# this is where I started adding additional parameters
ds = yt.load(fname, unit_base=unit_base)
#ds.derived_field_list # This displays all the different parameters that I can customize
ions_names=['H I','Mg II','C IV','N V','O VI', 'O VII', 'O VIII', 'Ne VIII'] ## Exploration!
# I think that if we include the number (I, II, III etc) then it only analyzes that singlular ion, but if you include just the atom name (H, C, O, etc.) then it will inlcude all ions from that element
trident.add_ion_fields(ds, ions=ions_names, ftype="PartType0") #PartType0 is for GIZMO and GADGET
mass = Gas_mass
Oxygen5_mass = ds.all_data()[('gas', 'O_p5_mass')].in_units('Msun') # should give Msun/kpc^2
Oxygen6_mass = ds.all_data()[('gas', 'O_p6_mass')].in_units('Msun')
Oxygen7_mass = ds.all_data()[('gas', 'O_p7_mass')].in_units('Msun')
# Magnesium goes here
print("Checkpoint 2")
NN = 100 # this defines the x, y, and z axis ranges for the plots
hh = Gas_Softening #what does gas softening mean?
Particles = sphviewer.Particles(Gas_location, mass, hh) # CHANGE PARAMETER HERE!
Scene = sphviewer.Scene(Particles)
fig = plt.figure(1,figsize=(15,5))
fig.suptitle(r"Cosmic Ray Jet : Snapshot #" + str(sorted[oo]+1) + " with Mass & Mask 5", fontsize=17, x=0.5, y=1.5) #set a figure title on top
plt.subplots_adjust(top =1.8, bottom=0.2, hspace=0.3, wspace=0.3)
ax1 = fig.add_subplot(131)
ax2 = fig.add_subplot(132)
ax3 = fig.add_subplot(133)
extendd = [-NN,NN,-NN,NN]
# Begin Masking
z = Gas_location[:,2]
mask_z = np.abs(z)<5 # 5 is the parameter that we can modify
Particles1 = sphviewer.Particles(Gas_location[mask_z], mass[mask_z], hh[mask_z]) # CHANGE PARAMETER HERE!
Scene1 = sphviewer.Scene(Particles1)
Scene1.update_camera(r='infinity', t=0, p = 0, roll = 0, x = 0, y = 0, z = 0, vmin= 6.3, vmax= 7.4, extent=extendd)
Render1 = sphviewer.Render(Scene1)
Render1.set_logscale()
img1 = Render1.get_image()
extent1 = Render1.get_extent()
divider = make_axes_locatable(ax1)
#ax1.imshow(img1, extent=extent1, origin='lower', cmap=plt.cm.jet, vmax= 3.0, rasterized=True)
image1 = ax1.imshow(img1, extent=extent1, origin='lower', cmap=plt.cm.jet, rasterized=True, vmin=0, vmax=8)
cax = divider.new_vertical(size="7%", pad=0.7, pack_start=True)
fig.add_axes(cax)
cb = fig.colorbar(image1, cax=cax, orientation="horizontal")
cb.ax.tick_params(labelsize=15)
ax1.set_xlabel('$X$(kpc)', size=12)
ax1.set_ylabel('$Y$(kpc)', size=12)
x = Gas_location[:,0]
mask_x=np.abs(x)<5 # 5 is the parameter that we can modify
Particles2 = sphviewer.Particles(Gas_location[mask_x], mass[mask_x], hh[mask_x]) # CHANGE PARAMETER HERE!
Scene2 = sphviewer.Scene(Particles2)
Scene2.update_camera(r='infinity', t=-90, p = -90, roll = 0, x = 0, y = 0, z = 0, vmin= 6.3, vmax= 7.4, extent= extendd)
Render2 = sphviewer.Render(Scene2)
Render2.set_logscale()
img2 = Render2.get_image()
extent2 = Render2.get_extent()
#divider = make_axes_locatable(ax2)
#ax2.imshow(img2, extent=extent2, origin='lower',cmap=plt.cm.jet, vmax= 3.0, rasterized=True)
image2 = ax2.imshow(img2, extent=extent2, origin='lower',cmap=plt.cm.jet, rasterized=True, vmin=0, vmax=8)
divider = make_axes_locatable(ax2)
cax = divider.new_vertical(size="7%", pad=0.7, pack_start=True)
fig.add_axes(cax)
cb = fig.colorbar(image2, cax=cax, orientation="horizontal")
#cb.set_label(label='Temperature ($^{\circ}$C)', size='large', weight='bold')
cb.ax.tick_params(labelsize=15)
ax2.set_xlabel('$Y$(kpc)', size=12)
ax2.set_ylabel('$Z$(kpc)', size=12)
y = Gas_location[:,1]
mask_y=np.abs(y)<5 #5 is the parameter that we can modify
Particles3 = sphviewer.Particles(Gas_location[mask_y], mass[mask_y], hh[mask_y]) # CHANGE PARAMETER HERE!
Scene3 = sphviewer.Scene(Particles3) # MODIFIED!
Scene3.update_camera(r='infinity', t=90, p = 0, roll = -90, x = 0, y = 0, z = 0, vmin= 6.3, vmax= 7.4, extent= extendd)
Render3 = sphviewer.Render(Scene3)
Render3.set_logscale()
img3 = Render3.get_image()
extent3 = Render3.get_extent()
divider = make_axes_locatable(ax3)
#ax3.imshow(img3, extent=extent3, origin='lower', cmap=plt.cm.jet, vmax= 3.0, rasterized=True)
image3 = ax3.imshow(img3, extent=extent2, origin='lower',cmap=plt.cm.jet, rasterized=True, vmin=0, vmax=8)
cax = divider.new_vertical(size="7%", pad=0.7, pack_start=True)
fig.add_axes(cax)
cb = fig.colorbar(image3, cax=cax, orientation="horizontal")
#cb.set_label(label='Temperature ($^{\circ}$C)', size='large', weight='bold')
cb.ax.tick_params(labelsize=15)
ax3.set_xlabel('$Z$(kpc)', size=12)
ax3.set_ylabel('$X$(kpc)', size=12)
Default_dir = '/n/home13/nqutob/AGN_Feedback/ion_snapshots/' + 'CR_mask5_mass'
#Default_dir_pdf = '/n/home13/nqutob/AGN_Feedback/ion_snapshots/' + 'm12_mcvt_default_64_mask5_pdf'
try:
os.mkdir(Default_dir)
except:
pass
#try:
# os.mkdir(Default_dir_pdf)
#except:
# pass
plt.savefig(Default_dir + '/Fire' + str(sorted[oo]).zfill(3) + '_CR_mask5_mass' + '.png', dpi = 600, transparent = True, bbox_inches='tight')
#plt.savefig(Default_dir_pdf + '/Fire' + str(sorted[oo]).zfill(3) + '_m12_mcvt_default_64_mask5_O6' + '.pdf', dpi = 600, transparent = True, bbox_inches='tight')
plt.close()
oo += 1
#pdb.set_trace()