def calc_cddf(**kwargs):
ion = kwargs.get("ion", "H I 1216")
# load the simulation
forced_ds = yt.load(
"/Users/molly/foggie/halo_008508/nref11n/nref11n_nref10f_refine200kpc_z4to2/RD0020/RD0020"
)
track_name = "/Users/molly/foggie/halo_008508/nref11n/nref11n_nref10f_refine200kpc_z4to2/halo_track"
output_dir = "/Users/molly/Dropbox/foggie-collab/plots_halo_008508/nref11n/comparisons/"
natural_ds = yt.load(
"/Users/molly/foggie/halo_008508/nref11n/natural/RD0020/RD0020")
## output_dir = "/Users/molly/Dropbox/foggie-collab/plots/halo_008508/natural/nref11/spectra/"
os.chdir(output_dir)
track = Table.read(track_name, format='ascii')
track.sort('col1')
zsnap = forced_ds.get_parameter('CosmologyCurrentRedshift')
proper_box_size = get_proper_box_size(forced_ds)
forced_box, forced_c, width = get_refine_box(forced_ds, zsnap, track)
natural_box, natural_c, width = get_refine_box(natural_ds, zsnap, track)
width = width * proper_box_size
# forced_box = forced_ds.box([xmin, ymin, zmin], [xmax, ymax, zmax])
# forced_c = forced_ds.arr(halo_center,'code_length')
# natural_box = natural_ds.box([xmin, ymin, zmin], [xmax, ymax, zmax])
# natural_c = natural_ds.arr(halo_center,'code_length')
# width = (197./forced_ds.hubble_constant)/(1+forced_ds.current_redshift)
print "width = ", width, "kpc"
axis = 'z'
res = [1000, 1000]
trident.add_ion_fields(forced_ds, ions=['O VI'])
trident.add_ion_fields(natural_ds, ions=['O VI'])
# trident.add_ion_fields(forced_ds, ions=['C II'])
# trident.add_ion_fields(natural_ds, ions=['C II'])
## start with HI
ion = 'O_p5_number_density'
dph_forced = yt.ProjectionPlot(forced_ds,axis,('gas',ion), center=forced_c, \
width=(width,"kpc"), data_source=forced_box)
frb = dph_forced.frb['gas', ion]
hi_forced = np.array(np.log10(frb))
dph_natural = yt.ProjectionPlot(natural_ds,axis,('gas',ion), center=natural_c, \
width=(width,"kpc"), data_source=natural_box)
frb = dph_natural.frb['gas', ion]
hi_natural = np.array(np.log10(frb))
# plot
fig, ax = plt.subplots(figsize=(6, 6))
ax.hist(hi_forced.ravel(), cumulative=True, normed=True, bins=500, \
histtype='step', range=[12,19], lw=2, label="forced")
ax.hist(hi_natural.ravel(), cumulative=True, normed=True, bins=500, \
histtype='step', range=[12,19],lw=2, label="natural")
plt.legend()
plt.xlabel('log OVI')
plt.ylabel('cumulative fraction')
plt.savefig('ovi_cddf_compare.png')
def make_frbs(filename,center,fields,ions,fdbk=False):
ds = yt.load(filename)
args = filename.split('/')
trident.add_ion_fields(ds,ions=ions)
if fdbk== True:
print 'in fdbk'
halo_center, halo_velocity = get_halo_center(ds,center)
refine_box = fdbk_refine_box(ds,halo_center)
width = [(160,'kpc'),(80.,'kpc')]
resolution = (320,160)
for field in fields:
fileout = args[-3]+'_'+args[-2]+'_x_'+field+'.cpkl'
obj = ds.proj(field,'x',data_source=refine_box)
frb = obj.to_frb(width,resolution,center=box_center)
cPickle.dump(frb[field],open(fileout,'wb'),protocol=-1)
else:
print 'in else'
halo_center, halo_velocity = get_halo_center(ds,center)
refine_box = sym_refine_box(ds,halo_center)
width = [(40,'kpc'),(100.,'kpc')]
resolution = (80,200)
for field in fields:
fileout = args[-3]+'_'+args[-2]+'_x_'+field+'.cpkl'
obj = ds.proj(field,'x',data_source=refine_box)
frb = obj.to_frb(width,resolution,center=halo_center)
cPickle.dump(frb[field],open(fileout,'wb'),protocol=-1)
return
def multiplot():
field = 'density'
view = 'projection'
field = 'O_p5_number_density'
track = Table.read('complete_track', format='ascii')
track.sort('col1')
outs = [x+55 for x in range(400)]
for n in outs:
fig = plt.figure()
grid = AxesGrid(fig, (0.5,0.5,1.5,1.5),
nrows_ncols = (1, 5),
axes_pad = 0.1,
label_mode = "1",
share_all = True,
cbar_location="right",
cbar_mode="edge",
cbar_size="5%",
cbar_pad="0%")
strset = 'DD00'+str(n)
if (n > 99): strset = 'DD0'+str(n)
fields = [field, field, field, field, field]
snaps = ['nref10_track_2/'+strset+'/'+strset, 'nref10_track_lowfdbk_1/'+strset+'/'+strset,
'nref10_track_lowfdbk_2/'+strset+'/'+strset, 'nref10_track_lowfdbk_3/'+strset+'/'+strset,
'nref10_track_lowfdbk_4/'+strset+'/'+strset]
for i, (field, snap) in enumerate(zip(fields, snaps)):
ds = yt.load(snap)
zsnap = ds.get_parameter('CosmologyCurrentRedshift')
trident.add_ion_fields(ds, ions=['C IV', 'O VI','H I','Si III'])
centerx = np.interp(zsnap, track['col1'], 0.5*(track['col2']+track['col5']) )
centery = np.interp(zsnap, track['col1'], track['col3']+30./143886.)
centerz = np.interp(zsnap, track['col1'], 0.5*(track['col4']+track['col7']) )
center = [centerx, centery, centerz]
box = ds.r[ center[0]-200./143886:center[0]+200./143886, center[1]-250./143886.:center[1]+250./143886., center[2]-40./143886.:center[2]+40./143886.]
# projection
p = yt.ProjectionPlot(ds, 'z', field, center=center, width=((120,'kpc'),(240,'kpc')), data_source=box)
if (field == 'density'):
p.set_unit('density', 'Msun / pc**2')
p.set_zlim('density', 0.01, 1000)
if ('O_p5' in field):
p.set_zlim("O_p5_number_density",1e11,1e15)
if (i < 1): p.annotate_timestamp(corner='upper_left', redshift=True, draw_inset_box=True, text_args={'color':'white', 'size':'small'} )
# This forces the ProjectionPlot to redraw itself on the AxesGrid axes.
plot = p.plots[field]
plot.figure = fig
plot.axes = grid[i].axes
p._setup_plots() # Finally, redraw the plot.
plt.savefig(strset+'_multiplot_'+field+'_projection.png', bbox_inches='tight')
def calcIntVel(directory, runName, runNumber, ions, velocityBin, frameVel):
#load and add ions to the dataset
velocityBin = velocityBin * 1.0e5 #convert to cm/s
frameVel = frameVel * 1.0e5 #convert to cm/s
data = yt.load(directory + runName + '/KH_hdf5_chk_' + runNumber)
data.add_field(('gas', 'metallicity'),
function=_metallicity,
display_name="Metallicity",
units='Zsun')
#add ion fields to the dataset
IntVels = []
for ion in ions:
tri.add_ion_fields(data, ions=[ion['ion']])
#make cylinder
reg = data.disk([0.0, 0.2 * kpc, 0.0], [0, 1, 0], (0.25, 'kpc'),
(1.6, 'kpc'))
#reg = data.all_data()
#meanVel + frameVel will be the final mean velocity
meanVel = reg.quantities.weighted_average_quantity(
"velocity_y", weight_field=ion['fieldname'])
finalmeanVel = meanVel + frameVel
IntVels.append(finalmeanVel)
return IntVels
def generate_projection_data(output, field_list, weight_list, width):
sim = 'romulusC'
rvir = rom.get_romulus_rvir(sim, output)
# z = get_redshift(output)
# width = width / (1. + z)
# plot_data = h5.File('/nobackup/ibutsky/data/YalePaper/white_paper_plot_data', 'a')
plot_data = h5.File(
'/nobackup/ibutsky/data/YalePaper/multipanel_romulusC_%i_plot_data' %
(output), 'a')
ds = yt.load('/nobackup/ibutsky/simulations/romulusC/romulusC.%06d' %
(output))
z = ds.current_redshift
width = width / (1. + z)
trident.add_ion_fields(ds, ions=['H I'])
cen = rom.get_romulus_yt_center(sim, output, ds)
# set up projection plots for fields that are weighted and unweighted
for field, weight in zip(field_list, weight_list):
dset = field[1]
if dset not in plot_data.keys():
proj = yt.ProjectionPlot(ds,
'y',
field,
weight_field=weight,
center=cen)
proj_frb = proj.data_source.to_frb((width, 'Mpc'), 1600)
plot_data.create_dataset(dset, data=np.array(proj_frb[field]))
plot_data.flush()
def generate_sim_column_densities(sim, ion_list, res = 800):
cdens_file = h5.File('../../data/simulated_ion_column_densities_%s.h5'%(sim), 'a')
if sim == 'ad' or sim == 'stream':
ds = yt.load('/Users/irynabutsky/Work/galaxy/g160_torB_%s/DD2600'%(sim))
elif sim == 'P0':
ds = yt.load('/Users/irynabutsky/Work/galaxy/P0/P0.003195')
trident.add_ion_fields(ds, ion_list)
if sim == 'P0':
# center = YTArray([-1.693207e4, -1.201068e4, 5.303337e3], 'kpc')
center = [-0.42323229, -0.30021773, 0.13256167]
else:
v, center = ds.h.find_max(("gas", "density"))
print(center)
field_list = ipd.generate_ion_field_list(ion_list, 'number_density', model = 'P0')
width = yt.YTQuantity(1000, 'kpc')
px, py = np.mgrid[-width/2:width/2:res*1j, -width/2:width/2:res*1j]
radius = (px**2.0 + py**2.0)**0.5
if "radius" not in cdens_file.keys():
cdens_file.create_dataset("radius", data = radius.ravel())
# note: something weird going on in x-axis with P0
for axis in ['y', 'z']:
frb = ipd.make_projection(ds, axis, field_list, center, width)
for i, ion in enumerate(ion_list):
dset = "%s_%s" % (ion.replace(" ", ""), axis)
if dset not in cdens_file.keys():
cdens_file.create_dataset(dset, data=frb[field_list[i]].ravel())
cdens_file.flush()
def generate_sim_column_densities(sim, ion_list, res=800):
#cdens_file = h5.File('../../data/simulated_ion_column_densities_%s.h5'%(sim), 'w')
cdens_file = h5.File('test.h5', 'w')
ds, center, bv = spg.load_simulation_properties(sim)
print(center)
center = ds.arr(center, 'kpc')
trident.add_ion_fields(ds, ion_list)
field_list = ipd.generate_ion_field_list(ion_list,
'number_density',
model='P0')
width = yt.YTQuantity(110, 'kpc')
px, py = np.mgrid[-width / 2:width / 2:res * 1j,
-width / 2:width / 2:res * 1j]
radius = (px**2.0 + py**2.0)**0.5
if "radius" not in cdens_file.keys():
cdens_file.create_dataset("radius", data=radius.ravel())
# note: something weird going on in x-axis with P0
for axis in ['x', 'y', 'z']:
frb = ipd.make_projection(ds, axis, field_list, center, width)
for i, ion in enumerate(ion_list):
dset = "%s_%s" % (ion.replace(" ", ""), axis)
if dset not in cdens_file.keys():
cdens_file.create_dataset(dset,
data=frb[field_list[i]].ravel())
cdens_file.flush()
def create_coldens_frbs():
dx = np.unique(rb['dx'])[1]
#dx = ds.arr(0.1829591205,'kpc').in_units('code_length')
dxs_list = [0.5,1,5,10]
dxs_list = [ds.quan(q,'kpc').in_units('code_lenght') for q in dxs_list]
res_list = np.append(dx,dxs_list)
res_list = ds.arr(res_list,'code_length')
trident.add_ion_fields(ds, ions=['Si II', 'Si III', 'Si IV',
'C II', 'C III', 'C IV', 'O VI', 'Mg II'])
lines = ['H_p0_number_density','Si_p1_number_density','Si_p2_number_density',
'Si_p3_number_density','C_p1_number_density','C_p2_number_density',
'C_p3_number_density','O_p5_number_density','Mg_p1_number_density']
for line in lines:
field = line
print line
for index in 'xyz':
print index
for res in res_list:
reskpc = round(res.in_units('kpc'),2)
print res,' kpc'
num_cells = np.ceil(rb_width/res)
if res == res_list[0]:
fileout = 'frb'+index+'_'+args[-3]+'_'+args[-2]+'_'+field+'_forcedres.cpkl'
else:
fileout = 'frb'+index+'_'+args[-3]+'_'+args[-2]+'_'+field+'_'+str(reskpc)+'kpc.cpkl'
obj = ds.proj(('gas',field),index,data_source=rb)
frb = obj.to_frb((rb_width,'code_length'),(num_cells,num_cells),center=rb_center)
cPickle.dump(frb[('gas',field)],open(fileout,'wb'),protocol=-1)
return
def generate_spectrum_plot_data(index_start, index_end, output):
ds = yt.load('/nobackupp2/ibutsky/simulations/romulusC/romulusC.%06d'%(output))
ion_list = ['H I', 'C II', 'C III', 'C IV', 'Si II', 'Si III', 'Si IV', 'O VI']
trident.add_ion_fields(ds, ions=ion_list)
ds.add_field(("gas", "particle_H_nuclei_density"), function = ytf._H_nuc, \
particle_type = True, force_override = True, units = "cm**(-3)")
y_start = ds.domain_left_edge[2]
y_end = ds.domain_right_edge[2]
center = rom.get_romulusC_center(output)
center_x = center[0]
center_y = center[1]
center_z = center[2]
print(center_x, center_y, center_z)
ray_id, x_list, z_list = np.loadtxt('/nobackupp2/ibutsky/data/YalePaper/spectra/coordinate_list.dat',\
skiprows = 1, unpack=True)
for i in range(index_start, index_end):
h5file = h5.File('/nobackup/ibutsky/data/YalePaper/romulusC.%06d_sightline_%i_plot_data.h5'%(output, i), 'w')
# note: the plus is important. x_list, z_list counted from center
x = ((x_list[i] + center_x) / ds.length_unit).d
z = ((z_list[i] + center_z) / ds.length_unit).d
print(x_list[i], z_list[i], ds.length_unit)
ycen = (center_y / ds.length_unit).d
# y from -2.5 mpc of center to 2.5 mpc from center
ylen = (2500. / ds.length_unit).d
ray_start = [x, ycen-ylen , z]
ray_end = [x, ycen+ylen, z]
ad = ds.r[ray_start:ray_end]
ray = trident.make_simple_ray(ds,
start_position = ray_start,
end_position = ray_end,
lines=ion_list)
ad_ray = ray.all_data()
field_list = ['y', 'temperature', 'density', 'metallicity', 'dl']
source_list = [ad, ad, ad, ad, ad_ray]
unit_list = ['kpc', 'K', 'g/cm**3', 'Zsun', 'cm']
yt_ion_list = ipd.generate_ion_field_list(ion_list, 'number_density', full_name = False)
yt_ion_list[0] = 'H_number_density'
field_list = np.append(field_list, yt_ion_list)
for j in range(len(yt_ion_list)):
unit_list.append('cm**-3')
source_list.append(ad_ray)
for field,source,unit in zip(field_list, source_list, unit_list):
if field not in h5file.keys():
h5file.create_dataset(field, data = source[('gas', field)].in_units(unit))
h5file.flush()
h5file.create_dataset('y_lr', data = ad_ray['y'].in_units('kpc'))
h5file.flush()
print("saved sightline data %i\n"%(i))
def load_simulation_properties(model,
output=3195,
ion_list=[
'H I', 'O VI', 'Si II', 'Si III', 'Si IV',
'Mg II', 'N V', 'C IV'
]):
# note AHF finds this value for P0: 78.13 -239.42 -65.99
if model == 'P0':
ds = yt.load(
'/Users/irynabutsky/simulations/patient0/pioneer50h243.1536gst1bwK1BH.%06d'
% output)
gcenter = YTArray([-16933.77317667, -12009.28144633, 5305.25448309],
'kpc') # generated with shrink sphere
bulk_velocity = YTArray([73.05701672, -239.32976334, -68.07892736],
'km/s')
ds.add_field(('gas', 'pressure'),
function=_Pressure,
sampling_type='particle',
units=ds.unit_system["pressure"])
elif model == 'P0_agncr':
print('adding cosmic ray')
ds = yt.load(
'/Users/irynabutsky/simulations/patient0_agncr/pioneer.%06d' %
output)
gcenter = YTArray([-16933.48544591, -12006.24067239, 5307.33807425],
'kpc') # generated with shrink sphere
bulk_velocity = YTArray([74.98331176, -240.71723683, -67.77556155],
'km/s')
ds.add_field(('gas', 'cr_pressure'),
function=_CRPressure,
sampling_type='particle',
units=ds.unit_system["pressure"])
ds.add_field(('gas', 'pressure'),
function=_Pressure,
sampling_type='particle',
units=ds.unit_system["pressure"])
ds.add_field(('gas', 'cr_eta'),
display_name=('$P_{\\rm c} / P_{\\rm g}$'),
function=_CRBeta,
sampling_type='particle',
units='')
ds.add_field(('gas', 'O_mass'),
function=_omass,
sampling_type='particle',
units=ds.unit_system['mass'])
ds.add_field(('gas', 'Fe_mass'),
function=_femass,
sampling_type='particle',
units=ds.unit_system['mass'])
trident.add_ion_fields(ds, ions=ion_list)
return ds, gcenter, bulk_velocity
def load_romulusC(output, ions=[]):
ds = yt.load('/nobackup/ibutsky/simulations/romulusC/romulusC.%06d' %
output)
ad = ds.all_data()
cen = YTArray(rom.get_romulus_center('romulusC', output), 'kpc')
bv = rom.get_romulusC_bulk_velocity(output)
ad.set_field_parameter('center', cen)
ad.set_field_parameter('bulk_velocity', bv)
add_thermal_fields(ds)
if len(ions) > 0:
trident.add_ion_fields(ds, ions=ions)
return ds
def generate_column_data(output, ion_list, res=800, axis='y'):
sim = 'romulusC'
field_list = ion_help.generate_ion_field_list(ion_list, 'number_density')
ds = yt.load('/nobackupp2/ibutsky/simulations/%s/%s.%06d' %
(sim, sim, output))
trident.add_ion_fields(ds, ions=ion_list)
cdens_file = h5.File(
'/nobackupp2/ibutsky/data/%s/%s.%06d_column_data.h5' %
(sim, sim, output), 'a')
rom_center = rom_help.get_romulus_center(sim, output)
id_list, center_x_list, center_z_list, width_list = \
np.loadtxt('data/temp_coordinate_list.dat'%(sim, output, axis), skiprows=3, unpack = True)
for region_id, center_x, center_z, width in zip(id_list, center_x_list,
center_z_list, width_list):
cdens_file = h5.File(
'/nobackupp2/ibutsky/data/%s/%s.%06d_column_data_region_%i.h5' %
(sim, sim, output, region_id), 'a')
width = yt.YTQuantity(width, 'kpc')
px, py = np.mgrid[-width / 2:width / 2:res * 1j,
-width / 2:width / 2:res * 1j]
radius = (px**2.0 + py**2.0)**0.5
if "px" not in cdens_file.keys():
cdens_file.create_dataset("px", data=px.ravel())
if "py" not in cdens_file.keys():
cdens_file.create_dataset("py", data=py.ravel())
if "radius" not in cdens_file.keys():
cdens_file.create_dataset("radius", data=radius.ravel())
center = [
rom_center[0] + center_x, rom_center[1], rom_center[2] + center_z
]
center = (center / ds.length_unit).d
frb = ion_help.make_projection(ds,
axis,
field_list,
center,
width,
res=res)
for i, ion in enumerate(ion_list):
dset = "%s_%s" % (ion.replace(" ", ""), axis)
if dset not in cdens_file.keys():
cdens_file.create_dataset(dset,
data=frb[field_list[i]].ravel())
cdens_file.flush()
def generate_column_data(sim, ion_list, width=400, res=800):
field_list = ion_help.generate_ion_field_list(ion_list, 'number_density')
ds, center = rom.load_charlotte_sim(sim)
trident.add_ion_fields(ds, ions=ion_list)
fn = '/nobackupp2/ibutsky/data/charlotte/%s_column_data.h5' % (sim)
cdens_file = h5.File(fn)
axis_list = ['x', 'y', 'z']
width = yt.YTQuantity(width, 'kpc')
px, py = np.mgrid[-width / 2:width / 2:res * 1j,
-width / 2:width / 2:res * 1j]
radius = (px**2.0 + py**2.0)**0.5
if "px" not in cdens_file.keys():
cdens_file.create_dataset("px", data=px.ravel())
if "py" not in cdens_file.keys():
cdens_file.create_dataset("py", data=py.ravel())
if "radius" not in cdens_file.keys():
cdens_file.create_dataset("radius", data=radius.ravel())
for axis in axis_list:
#frb = ion_help.make_projection(ds, axis, field_list, center, width, res = res)
for i, ion in enumerate(ion_list):
dset = "%s_%s" % (ion.replace(" ", ""), axis)
if dset not in cdens_file.keys():
print(dset)
sys.stdout.flush()
#frb = ion_help.make_projection(ds, axis, field_list[i], center, width, res = res)
p = yt.ProjectionPlot(ds,
axis,
field_list[i],
width=width,
weight_field=None,
center=center)
p.set_zlim(field_list[i], 1e13, 1e15)
p.save()
frb = p.data_source.to_frb(width, res)
print(frb)
print(frb.keys())
print(frb[field_list[i]])
cdens_file.create_dataset(dset,
data=frb[field_list[i]].d.ravel())
cdens_file.flush()
def get_spec(ds, halo_center, rho_ray):
proper_box_size = get_proper_box_size(ds)
line_list = ['H', 'O', 'C', 'N', 'Si']
# big rectangle box
ray_start = [
halo_center[0] - 250. / proper_box_size,
halo_center[1] + 71. / proper_box_size,
halo_center[2] - 71. / proper_box_size
]
ray_end = [
halo_center[0] + 250. / proper_box_size,
halo_center[1] + 71. / proper_box_size,
halo_center[2] - 71. / proper_box_size
]
ray = trident.make_simple_ray(ds,
start_position=ray_start,
end_position=ray_end,
data_filename="ray.h5",
lines=line_list,
ftype='gas')
sg = trident.SpectrumGenerator(lambda_min=1020,
lambda_max=1045,
dlambda=0.002)
trident.add_ion_fields(ds, ions=['C IV', 'O VI', 'H I', 'Si III'])
sg.make_spectrum(ray, lines=line_list)
sg.plot_spectrum('spec_final.png')
sg.save_spectrum('spec_final.txt')
# this makes for convenient field extraction from the ray
ad = ray.all_data()
dl = ad["dl"] # line element length
out_dict = {
'nhi': np.sum(ad['H_number_density'] * dl),
'no6': np.sum(ad['O_p5_number_density'] * dl),
'nsi3': np.sum(ad['Si_p2_number_density'] * dl)
}
print np.sum(ad['H_number_density'] * dl)
print np.sum(ad['O_p5_number_density'] * dl)
print np.sum(ad['Si_p2_number_density'] * dl)
return ray, out_dict
def makeProjections(directory, runName, f_list, savefolder, ion, fieldname):
for i in f_list:
data = yt.load(directory+runName+'/KH_hdf5_chk_'+i)
data.add_field(('gas', 'metallicity'), function=_metallicity, display_name="Metallicity", units='Zsun')
#add an ion field to the dataset
tri.add_ion_fields(data, ions=[ion])
#add new fields for projection plots
#data.add_field(('gas', 'vel_squared'), function=_vel_squared, display_name = 'vel squared', units = 'cm**2/s**2')
#data.add_field(('gas', 'b_param'), function=_b_param, display_name = 'b parameter', units = 'cm/s')
#plot the the column density
plot1 = yt.ProjectionPlot(data, 'z', fieldname, origin = 'native')
plot1.set_zlim(fieldname, 1e8, 1e18)
plot1.set_cmap(fieldname,"gist_rainbow")
plot1.save(savefolder)
#plot the average y-velocity
#plot2 = yt.ProjectionPlot(data, 'y', 'velocity_y', origin = 'native', weight_field = fieldname)
#plot2.set_log('velocity_y', False)
#plot2.set_zlim(fieldname, 1e-16, 5e-6)
#plot2.set_cmap(fieldname,"gist_rainbow")
#plot2.save(savefolder)
#reg = data.all_data()
#vel_Proj = reg.mean('velocity_y', 'y', weight = fieldname)
#vel2_proj = reg.mean('vel_squared', 'y', weight = fieldname)
#bparam = np.sqrt(vel2_proj['vel_squared']- vel_Proj['velocity_y']**2)
#plt.scatter(vel_Proj['z'], vel_Proj['x'], c=bparam, marker = 'o')
#plt.contour(vel_Proj['z'], vel_Proj['x'], bparam)
#plt.colorbar()
#fig = plt.gcf()
#fig.savefig('test.png')
#plot3 = yt.ProjectionPlot(vel_Proj, 'y', 'test', origin = 'native')
#plot3.set_log('b_param', False)
#plot3.set_zlim(fieldname, 1e-16, 5e-6)
#plot3.set_cmap(fieldname,"gist_rainbow")
#plot3.save(savefolder)
print('Saved plots as '+savefolder+'KH_......')
print("Finished with run "+runName)
def addTriDens(data, atom, ion):
#add the atom
tri.add_ion_fields(data, ions=[atom], ftype='gas')
def _newDens(field, data):
fracList = atomFracs_tri[atom]
ionNum = ionList[ion]
fieldname = fracList[ionNum][:-7] + 'number_density'
return data[fieldname]
data.add_field(('gas', 'dens' + atom + ion + '_tri'),
function=_newDens,
display_name=atom + ' ' + ion + ' Number Density',
units="1/cm**3",
sampling_type='cell')
#trident already adds the number density! so you're all good here
return data
def addTriFrac(data, atom, ion):
#add the atom
tri.add_ion_fields(data, ions=[atom], ftype='gas')
def _newFrac(field, data):
fracList = atomFracs_tri[atom]
botsum = np.sum([data[f] for f in fracList], axis=0)
ionNum = ionList[ion]
top = data[fracList[ionNum]]
frac = top / data.apply_units(botsum, "g/cm**3")
return frac
data.add_field(('gas', 'frac' + atom + ion + '_tri'),
function=_newFrac,
display_name=atom + ' ' + ion + ' Mass Fraction (Tri)',
units="",
sampling_type='cell')
return data
def _get_coldens_helper(dsparamsvectorions):
try:
ds = dsparamsvectorions[0]
scanparams = dsparamsvectorions[1]
vector = dsparamsvectorions[2]
ions = dsparamsvectorions[3]
print(str(current_process()))
ident = str(current_process()).split(",")[0]
if ident[-2:] == "ss":
ident = ""
else:
ident = ident.split("-")[1]
start = vector[5:8]
end = vector[8:11]
ray = trident.make_simple_ray(ds,
start_position=start,
end_position=end,
data_filename="ray"+ident+".h5",
fields = [('gas',"metallicity")],
ftype='gas')
trident.add_ion_fields(ray,ions)
field_data = ray.all_data()
for i in range(len(ions)):
ion = ions[i]
cdens = np.sum(field_data[("gas",ion_to_field_name(ion))] * field_data['dl'])
#outcdens = np.sum((field_data['radial_velocity']>0)*field_data[ion_to_field_name(ion)]*field_data['dl'])
#incdens = np.sum((field_data['radial_velocity']<0)*field_data[ion_to_field_name(ion)]*field_data['dl'])
vector[11+i] = cdens
#vector[12+3*i+1] = outcdens
#vector[12+3*i+2] = incdens
Z = np.average(field_data[('gas',"metallicity")],weights=field_data['dl'])
vector[-1] = Z
if _platform == 'darwin':
foldername = "/Users/claytonstrawn/Desktop/astroresearch/code/ready_for_pleiades/quasarlines"
else:
foldername = "/u/cstrawn/quasarlines/galaxy_catalogs/"
except Exception:
logging.exception("failed")
try:
os.remove(foldername+"/"+"ray"+ident+".h5")
except:
pass
print("vector = "+str(vector))
return vector
def makeColDist(directory, runName, f_list, savefolder, ion, fieldname):
for i in f_list:
data = yt.load(directory + runName + '/KH_hdf5_chk_' + i)
data.add_field(('gas', 'metallicity'),
function=_metallicity,
display_name="Metallicity",
units='Zsun')
#add an ion field to the dataset
tri.add_ion_fields(data, ions=[ion])
#projection of the number density
p = data.proj(fieldname, 1)
#make fixed resolution buffer (same as when a figure is made)
#to have an array with every value in each pixel
frb = yt.FixedResolutionBuffer(
p, (-2.464e21, 2.464e21, -2.464e21, 2.464e21), (800, 800))
#flatten the frb to a 1d array
flattened_coldens = frb[fieldname].flatten()
if min(flattened_coldens) == 0:
mincol = 8
else:
mincol = np.log10(min(flattened_coldens))
maxcol = np.log10(max(flattened_coldens))
#make histogram!
plt.hist(flattened_coldens,
bins=np.logspace(mincol - 1, maxcol + 1, 50),
fill=False,
color='blue',
log=True)
plt.xscale('log')
#plt.yscale('log')
plt.ylabel('Number of pixels')
plt.xlabel(ion + ' Column Density per pixel')
plt.ylim(1, 1e6)
fig = plt.gcf()
fig.savefig(savefolder + '/' + runName + '_' + i + '_' + fieldname +
'.png')
plt.close()
ion_list = ['O VI']
field = ('gas', 'O_p5_number_density')
weight_field = None
# load in simulation data and add ion fields
ray_id_list, x_list, z_list = np.loadtxt('data/temp_coordinate_list.dat',
skiprows=1,
unpack=True)
plot_data = h5.File(
'/nobackup/ibutsky/data/YalePaper/multipanel_romulusC_%i_sightline_plot_data_fixed2'
% (output), 'w')
center = rom.get_romulus_center('romulusC', output)
ds = yt.load('/nobackup/ibutsky/simulations/romulusC/romulusC.%06d' % (output))
trident.add_ion_fields(ds, ions=ion_list)
# set up projection plots for fields that are weighted and unweighted
# note: ray_x, ray_z ordering should be consistent with data/coordinate_list.dat
for ray_id, ray_x, ray_z in zip(ray_id_list, x_list, z_list):
dset = 'ray_%i_%s' % (ray_id, field[1])
if dset not in plot_data.keys():
plot_center = [center[0] + ray_x, center[1], center[2] + ray_z]
print(center, plot_center)
sys.stdout.flush()
plot_center = (plot_center / ds.length_unit).d
proj = yt.ProjectionPlot(ds,
'y',
field,
weight_field=weight_field,
log("Starting projections for %s" % fn)
if AMIGA:
ds = GizmoDataset(fn)
elif Rockstar:
ds = yt.load(fn)
# These vectors are precalculated to be the correct viewing angle for an edge on view
E1 = ds.arr([0.40607303, 0., -0.91384063], 'code_length')
L = ds.arr([0.83915456, 0.3959494, 0.37288562], 'code_length') # edge-on disk view at z ~ 0.2
#vec1 = [L, -E1]
#vec2 = [E1, L]
vec1 = []
vec2 = []
dir = ['face/', 'edge/']
else:
ds = yt.load(fn)
trident.add_ion_fields(ds, ions=ions, ftype='gas')
#ions.append('O_nuclei_density')
#ion_fields.append('O_nuclei_density')
#full_ion_fields.append(('gas', 'O_nuclei_density'))
#ions.append('density')
#ion_fields.append('density')
#full_ion_fields.append(('gas', 'density'))
#ions.append('metal_density')
#ion_fields.append('metal_density')
#full_ion_fields.append(('gas', 'metal_density'))
# Figure out centroid and r_vir info
if AMIGA:
log("Reading amiga center for halo in %s" % fn)
c = read_amiga_center(amiga_data, fn, ds)
def calcRankTau(directory, runName, runNumber, ions, velocityBin, frameVel):
#load and add ions to the dataset
velocityBin = velocityBin * 1.0e5 #convert to cm/s
frameVel = frameVel * 1.0e5 #convert to cm/s
data = yt.load(directory + runName + '/KH_hdf5_chk_' + runNumber)
data.add_field(('gas', 'metallicity'),
function=_metallicity,
display_name="Metallicity",
units='Zsun')
absorbFracs = []
#add ion fields to the dataset
for ion in ions:
tri.add_ion_fields(data, ions=[ion['ion']])
#define the function for b(x) for this particular ion
### function definition in a for loop... Ew... ###
def _soundSpeed(field, data):
topFrac = 2.0 * kb * data['temperature']
botFrac = ion['massNum'] * mp
b = np.sqrt(topFrac / botFrac)
return b
#add b_soundSpeed to the dataset
data.add_field(('gas', 'b_soundSpeed'),
function=_soundSpeed,
display_name="B Sound Speed",
units='cm/s',
force_override=True)
#define the function for dTau for this particular ion/velocity
### function definition in a for loop... Ew... ###
def _dTau(field, data):
term1 = data[ion['fieldname']] / data['b_soundSpeed']
#assumes velocity is now cm/s
#must add the frame velocity to the y velocity!
expTerm = (((data['velocity_y'] + frameVel *
(centimeter / second)) - velocityBin *
(centimeter / second)) / data['b_soundSpeed'])**2.0
dtau = term1 * np.exp(-1.0 * expTerm)
return dtau
#add dTau to the dataset
data.add_field(('gas', 'tau'),
function=_dTau,
display_name="dTau",
units='s/cm**4',
force_override=True)
#make cylinder, project through the y axis
#reg = data.disk([0.0, 0.2*kpc, 0.0], [0,1,0], (0.25, 'kpc'), (1.6, 'kpc'))
#select entire region
reg = data.all_data()
plot = yt.ProjectionPlot(data, 'y', 'density')
plot.set_zlim('density', 1e-5, 5e-5)
plot.save()
#projection of the number density
p = data.proj('tau', 1)
#make fixed resolution buffer (same as when a figure is made)
#to have an array with every value in each pixel
frb = yt.FixedResolutionBuffer(
p, (-2.464e21, 2.464e21, -2.464e21, 2.464e21), (800, 800))
#flatten the frb to a 1d array
flattened_tau = frb['tau'].flatten()
tau_coef = c_speed * ion['sigma'] / np.sqrt(np.pi)
projectedTau = tau_coef * flattened_tau
#rank sort the projected taus and then make plot
sorted_tau = np.sort(projectedTau, kind='quicksort')
totalpixel = len(sorted_tau)
pixelNum = np.arange(0.0, totalpixel, 1.0)
pixelFrac = pixelNum / totalpixel
print(pixelFrac)
writeFile = open(
'../rankTau' + ion['ionfolder'] + 'rankTau' + runName + '_v' +
str(int(round(velocityBin / 1e5, 0))) + '.txt', 'w')
for i in range(len(pixelFrac)):
writeString = str(sorted_tau[i].value) + '\n'
writeFile.write(writeString)
writeFile.close()
#clip = 620800 #0.97
#plt.plot(pixelFrac[clip:], sorted_tau[clip:])
#fig = plt.gcf()
#fig.savefig('rankTau/test_rankTau'+runName+'_v'+str(int(round(velocityBin/1e5, 0)))+'_'+ion['ion']+'.png')
#fig.clear()
return absorbFracs
import yt
import trident
import sys
yt.enable_parallelism()
workdir = '/media/azton/bigbook/projects/nextGenIGM'
simname = sys.argv[1]
final = int(sys.argv[2])
d = final
rs = '%s/%s/rockstar_halos/halos_RD%04d.0.bin'%(workdir, simname, final)
rs = yt.load(rs)
ad = rs.all_data()
ds = yt.load('%s%s/RD%04d/RedshiftOutput%04d'%(workdir, simname,d,d))
#print(ds.field_list)
trident.add_ion_fields(ds, ['C', "O", "O IV", "O VI", "C IV"], ftype='gas')
for field in ds.derived_field_list:
print (field)
pos = ad['particle_position'][ad['particle_mass'] \
== ad['particle_mass'].max()][0].to('unitary')
r = 4.0*ad['virial_radius'][ad['particle_mass'] \
== ad['particle_mass'].max()][0].to('unitary')
sp = ds.sphere(pos, r)
fields = ['H_p1_density','O_p4_density','C_p0_density', 'H_density']
labels = ['HI', "OIV", "C", "H"]
## make a ray that intersects this most massive halo ##
ray = trident.make_simple_ray(ds, start_position=[pos[0], pos[1],0], end_position=[pos[0], pos[1], 1],\
lines='H')
width = 15. #kpc
zsnap = dsr.current_redshift
refine_box, refine_box_center, refine_width = get_refine_box(dsr, zsnap, track)
mH = 1.6737236e-24 * u.g
total_forced_HI_mass = sum(mH * refine_box['H_p0_number_density'] *
refine_box['cell_volume'].in_units('cm**3'))
print(
'HI mass: ',
total_forced_HI_mass.to('Msun'),
)
print('log HI mass: ', np.log10(total_forced_HI_mass.to('Msun').value))
import trident
trident.add_ion_fields(dsr, ions=['C IV', 'O VI', 'Si II', 'Si IV'])
total_forced_SiII_mass = sum(mH * refine_box['Si_p1_number_density'] *
refine_box['cell_volume'].in_units('cm**3'))
total_forced_SiII_mass = total_forced_SiII_mass * 28.0855
print(
'SiII forced: ',
total_forced_SiII_mass.to('Msun'),
)
total_forced_OVI_mass = sum(mH * refine_box['O_p5_number_density'] *
refine_box['cell_volume'].in_units('cm**3'))
total_forced_OVI_mass = total_forced_OVI_mass * 15.999
print('OVI forced: ', total_forced_OVI_mass.to('Msun'))
total_forced_SiIV_mass = sum(mH * refine_box['Si_p3_number_density'] *
comm = MPI.COMM_WORLD
t_start = time.time()
# number of pixels per dimension (for Aitoff projection)
pixels_per_dim = 512
remove_first_N_kpc = 1.0
# Load dataset
fn = "/mnt/scratch/dsilvia/simulations/reu_sims/MW_1638kpcBox_800pcCGM_200pcDisk_lowres/DD1500/DD1500"
ds = yt.load(fn)
# Add H I & O VI ion fields using Trident
trident.add_ion_fields(ds, ions=['O VI', 'H I'], ftype="gas")
# Specify position where the ray starts (position in the volume)
c = ds.arr([0.5, 0.5, 0.5], 'unitary')
c = c.in_units('kpc')
# location in the disk where we're setting our observations
X = YTArray([8., 0., 0.], 'kpc')
ray_start = c - X
# Length of Ray
R = 200.0
# do you want projections of the spheres? True/False
MakeProjections = True
return data.apply_units(v, "Zsun")
for i in [6, 9, 12, 13, 14, 18, 21, 24, 27, 35]:
if i >= 1000:
data = yt.load('KH_hdf5_chk_' + str(i))
elif i >= 100:
data = yt.load('KH_hdf5_chk_0' + str(i))
elif i >= 10:
data = yt.load('KH_hdf5_chk_00' + str(i))
else:
data = yt.load('KH_hdf5_chk_000' + str(i))
data.add_field(('gas', 'metallicity'),
function=_metallicity,
display_name="Metallicity",
units='Zsun')
#try adding an ion field to the dataset
tri.add_ion_fields(data, ions=['Ne VIII'])
folder = 'NeVIII'
#plot the newly added field's number density
plot = yt.SlicePlot(data, 'z', 'Ne_p7_number_density', origin='native')
plot.set_zlim('Ne_p7_number_density', 1e-16, 5e-6)
plot.set_cmap("Ne_p7_number_density", "gist_rainbow")
plot.save(folder)
print('Saved plot as ' + folder + 'KH_......')
#plot = yt.SlicePlot(data, 'z', 'velocity_y', origin='native')
#plot.save()
def calcRankTau(directory, runName, runNumber, ions, velocityBin, frameVel):
#load and add ions to the dataset
frameVel = frameVel*1.0e5*(centimeter/second) #convert to cm/s
data = yt.load(directory+runName+'/KH_hdf5_chk_'+runNumber)
data.add_field(('gas', 'metallicity'), function=_metallicity, display_name="Metallicity", units='Zsun')
bList = []
vList = []
TList = []
#add ion fields to the dataset
for ion in ions:
tri.add_ion_fields(data, ions=[ion['ion']])
#select entire region
reg = data.all_data()
#projection of the number density (= fieldname)
p = data.proj(ion['fieldname'], 1)
#make fixed resolution buffer (same as when a figure is made)
#to have an array with every value in each pixel
frb = yt.FixedResolutionBuffer(p, (-2.464e21, 2.464e21, -2.464e21, 2.464e21), (800, 800))
#flatten the frb to a 1d array
flattened_num = frb[ion['fieldname']].flatten()
projectedNum = flattened_num
#rank sort the projected taus and then make plot
sorted_num = np.sort(projectedNum, kind='quicksort')
#find the average velocity for the ion
average_vely = reg.quantities.weighted_average_quantity('vely', ion['fieldname'])+frameVel
average_temp = reg.quantities.weighted_average_quantity('temperature', ion['fieldname'])
#write the ranked column densities to a file
writeFile = open('../rankNum'+ion['ionfolder']+'rankNum'+runName+'_v'+str(velocityBin)+'.txt', 'w')
for i in range(len(sorted_num)):
writeString = str(sorted_num[i].value)+'\n'
writeFile.write(writeString)
writeFile.close()
#add b^2 thermal as a field
def _btherm(field, data):
topFrac = 2.0*kb*data['temperature']
botFrac = ion['massNum']*mp
b = topFrac/botFrac
return b
data.add_field(('gas', 'b_therm'), function=_btherm, display_name="B thermal squared", units = 'cm**2/s**2', force_override=True)
#project b thermal
btherm = data.proj('b_therm', 1, weight_field=ion['fieldname'])
frb_therm = yt.FixedResolutionBuffer(btherm, (-2.464e21, 2.464e21, -2.464e21, 2.464e21), (800, 800))
flattened_btherm = frb_therm['b_therm'].flatten()
#add b^2 doppler as a field
def _bdop(field, data):
b = (data['vely'] - average_vely)**2
return b #multiply by number density to weight the b value
data.add_field(('gas', 'b_doppler'), function=_bdop, display_name="B doppler squared", units = 'cm**2/s**2', force_override=True)
#project b doppler
bdop = data.proj('b_doppler', 1, weight_field=ion['fieldname'])
frb_dop = yt.FixedResolutionBuffer(bdop, (-2.464e21, 2.464e21, -2.464e21, 2.464e21), (800, 800))
flattened_bdop = frb_dop['b_doppler'].flatten()
good_btherm = flattened_btherm[~np.isnan(flattened_btherm)]
good_bdop = flattened_bdop[~np.isnan(flattened_bdop)]
#add the two b's and sqrt
b_tot_Sq = good_btherm+good_bdop
b_tot = np.sqrt(b_tot_Sq)
#compute the average of the summation of b projections
b_avg = np.average(b_tot)
bList.append(b_avg)
vList.append(average_vely)
TList.append(average_temp)
print(b_avg)
print(average_vely)
return bList, vList, TList
datafile = sys.argv[1]
start_position = sys.argv[2]
end_position = sys.argv[3]
savename = sys.argv[4]
line_list = ['C','N','O']
ds = yt.load(datafile) # Loading the dataset
if start_position == 'left_edge':
start_position = ds.domain_left_edge
if end_position == 'right_edge':
end_position = ds.domain_right_edge
trident.add_ion_fields(ds,ions=line_list)
actual_ray = trident.make_simple_ray(ds,start_position = np.array([0.,0.,0.]),end_position = np.array([128.,128.,128.]),data_filename="mray.h5",lines=line_list,ftype='gas')
#lr = trident.LightRay(ds)
#lr.make_light_ray(ds,start_position = start_position,end_position = end_position,data_filename="mray.h5",fields=['temperature','density'])
sg = trident.SpectrumGenerator('COS')
#sg = trident.SpectrumGenerator(lambda_min='auto', lambda_max='auto',dlambda=0.01)
sg.make_spectrum(actual_ray, lines=line_list)
sg.save_spectrum(savename + '.txt')
sg.plot_spectrum(savename + '.png')
yt.add_particle_filter("youngstars",
function=_youngstars,
filtered_type='all',
requires=["age"])
yt.add_particle_filter("darkmatter",
function=_darkmatter,
filtered_type='all',
requires=["particle_type"])
ds.add_particle_filter('stars')
ds.add_particle_filter('darkmatter')
ds.add_particle_filter('youngstars')
print('adding trident fields...')
trident.add_ion_fields(ds,
ions=[
'O VI', 'O VII', 'Mg II', 'Si II', 'C II',
'C III', 'C IV', 'Si III', 'Si IV', 'Ne VIII'
])
#Parallel(n_jobs = -1, backend = 'threading')(delayed(measure_mass)(simname = simname, DD = DD, sat_n = sat_n, ds = ds) for sat_n in np.arange(5))
species_dict = {
'dark_matter': ("darkmatter", "particle_mass"),
'gas_tot': ("gas", "cell_mass"),
'gas_metals': ("gas", "metal_mass"),
'stars_mass': ("stars", "particle_mass"),
'stars_youngmass': ("youngstars", "particle_mass"),
'gas_H': ("gas", 'H_mass'),
'gas_H0': ("gas", 'H_p0_mass'),
'gas_H1': ("gas", 'H_p1_mass'),
'gas_CII': ("gas", 'C_p1_mass'),
'gas_CIII': ("gas", 'C_p2_mass'),
def generate_halo_column_data(sim,
output,
ion_list,
res=800,
start_index=0,
end_index=1000):
field_list = ion_help.generate_ion_field_list(ion_list, 'number_density')
ds = yt.load('/nobackupp2/ibutsky/simulations/%s/%s.%06d' %
(sim, sim, output))
trident.add_ion_fields(ds, ions=ion_list)
halo_props = h5.File(
'/nobackupp2/ibutsky/data/%s_halo_data_%i' % (sim, output), 'r')
halo_ids = halo_props['halo_id'][:]
mstars = halo_props['mstar'][:]
centers = halo_props['center'][:]
contamination = halo_props['contamination'][:]
mask = (mstars >= 1e9) & (halo_ids > 0) & (contamination < 0.05)
if start_index > end_index:
counter = -1
else:
counter = 1
for i in np.arange(start_index, end_index, counter):
halo_id = halo_ids[mask][i]
mstar = mstars[mask][i]
halo_center = centers[mask][i]
center = (halo_center / ds.length_unit).d
print(i, halo_id, mstar)
sys.stdout.flush()
cdens_file = h5.File(
'/nobackupp2/ibutsky/data/%s/column_%i_halo%i_600' %
(sim, output, halo_id), 'a')
width = yt.YTQuantity(600, 'kpc')
px, py = np.mgrid[-width / 2:width / 2:res * 1j,
-width / 2:width / 2:res * 1j]
radius = (px**2.0 + py**2.0)**0.5
if "radius" not in cdens_file.keys():
cdens_file.create_dataset("radius", data=radius.ravel())
for j, ion in enumerate(ion_list):
for axis in ['x', 'y', 'z']:
dset = "%s_%s" % (ion, axis)
if dset not in cdens_file.keys():
frb = ion_help.make_projection(ds,
axis,
field_list,
center,
width,
res=res)
if dset not in cdens_file.keys():
cdens_file.create_dataset(
dset, data=frb[field_list[j]].ravel())
cdens_file.flush()
cdens_file.close()