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()
import matplotlib.pylab as plt
import sys
import yt
from yt.units.yt_array import YTQuantity
import numpy as np
import yt_functions as ytf
import ion_plot_definitions as ipd
import romulus_analysis_helper as rom_help
#output = int(sys.argv[1])
output = 3035
ds = ytf.load_romulusC(output)
cen = rom_help.get_romulus_yt_center('romulusC', output, ds)
ad = ds.sphere(cen, (3300, 'kpc'))
#sp = ad.cut_region(["(obj[('gas', 'metal_cooling_time')]>0) & (obj[('gas', 'metal_primordial_cooling_time_ratio')] > 0) & (obj[('gas', 'temperature')] >= 1e4) & (obj[('gas', 'temperature')] <= 1e6) & (obj[('gas', 'particle_H_nuclei_density')] > 1e-6) & (obj[('gas', 'particle_H_nuclei_density')] < 1e-2)"])
sp = ad.cut_region(["(obj[('gas', 'temperature')] >= 1e4) & (obj[('gas', 'temperature')] <= 1e6) & (obj[('gas', 'particle_H_nuclei_density')] > 1e-6) & (obj[('gas', 'particle_H_nuclei_density')] < 1e-2)"])
#sp = ad
xfield = ('gas', 'spherical_position_radius')
yfield = ('Gas', 'Mass')
#mass enclosed needs to have all mass, not just CGM mass
pm = yt.ProfilePlot(ad, xfield, yfield, weight_field = None, accumulation = True, n_bins = 128)
pm.set_unit(xfield, 'cm')
pm.set_unit(yfield, 'g')
pm.set_log(xfield, False)
profile = pm.profiles[0]
import yt
import trident
import h5py as h5
import numpy as np
import sys
import romulus_analysis_helper as rom
sim = 'romulusC'
output = 3035
field = ('gas', 'H_p0_number_density')
plot_data = h5.File('/nobackup/ibutsky/data/YalePaper/white_paper_plot_data',
'a')
ds = yt.load('/nobackup/ibutsky/simulations/romulusC/romulusC.%06d' % (output))
cen = rom.get_romulus_yt_center(sim, output, ds)
rvir = rom.get_romulus_rvir(sim, output)
trident.add_ion_fields(ds, ions=['H I', 'O VI'])
p = yt.ProjectionPlot(ds,
'y',
field,
weight_field=None,
center=cen,
width=(5, 'Mpc'))
p.set_cmap(field, 'purple_mm')
p.set_zlim(field, 3e12, 1e17)
p.set_colorbar_label(field, '$\mathrm{H\ I\ Column\ Density\ (cm}^{-2})$')
p.set_font_size(26)
p.save('HI_fg2009.png')
def generate_phase_plot_data(output, xfield, yfield, zfield, icm_cut = None, weight_field = ('Gas', 'Mass'), \
xbins = 128, ybins = 128, fractional = False, xlim = None, ylim = None, xunit = None, \
yunit = None, zunit = None, xlog = None, ylog = None, zlog = None, radius = None):
sim = 'romulusC'
ds = ytf.load_romulusC(output, ions=['H I', 'C IV', 'O VI'])
redshift = ds.current_redshift
if output == 4096:
redshift = 0.01
#xray_fields = yt.add_xray_emissivity_field(ds, 0.5, 7.0, redshift=redshift, \
# cosmology=ds.cosmology, metallicity=("Gas", "metallicity2"), table_type='cloudy')
# ds.add_field(('gas', 'xray_luminosity'), function = _xray_luminosity2, particle_type = True)
# ds.add_field(('gas', 'xray_intensity'), function = _xray_intensity2, units = 'erg/(arcsec**2*cm**3*s)', particle_type = True)
cen = rom.get_romulus_yt_center(sim, output, ds)
rvir = rom.get_romulus_rvir(sim, output)
icm_mask = None
if radius:
sp = ds.sphere(cen, (radius, 'kpc'))
else:
sp = ds.sphere(cen, (3. * rvir, 'kpc'))
bv = sp.quantities.bulk_velocity().in_units('km/s')
print(bv)
if icm_cut == 'xray':
icm_mask = "(obj[('gas', 'xray_intensity')] > 1e-44)"
elif icm_cut == 'uv':
icm_mask = "(obj[('gas', 'particle_H_nuclei_density')] > 1e-6) & (obj[('gas', 'particle_H_nuclei_density')] < 1e-2)"
icm_mask = "& (obj[('gas', 'temperature')] > 1e4) & (obj[('gas', 'temperature')] < 1e6)"
elif icm_cut == 'cold':
icm_mask = "(obj[('gas', 'temperature')] < 1e4)"
elif icm_cut == 'cool':
icm_mask = " (obj[('gas', 'temperature')] >= 1e4) & (obj[('gas', 'temperature')] < 1e5)"
elif icm_cut == 'coolwarm':
icm_mask = "(obj[('gas', 'temperature')] >= 1e4) & (obj[('gas', 'temperature')] <= 1e6)"
elif icm_cut == 'warm':
icm_mask = "(obj[('gas', 'temperature')] >= 1e5) & (obj[('gas', 'temperature')] < 1e6)"
elif icm_cut == 'hot':
icm_mask = "(obj[('gas', 'temperature')] >= 1e6)"
elif icm_cut == 'hot_icm':
icm_mask = "(obj[('gas', 'particle_H_nuclei_density')] < 0.1) & (obj[('gas', 'temperature')] >= 1e6)"
elif icm_cut == 'warm_icm':
icm_mask = "(obj[('gas', 'particle_H_nuclei_density')] < 0.1) & (obj[('gas', 'temperature')] >= 1e5) & (obj[('gas', 'temperature')] < 1e6)"
elif icm_cut == 'cool_icm':
icm_mask = "(obj[('gas', 'particle_H_nuclei_density')] < 0.1) & (obj[('gas', 'temperature')] >= 1e4) & (obj[('gas', 'temperature')] < 1e5)"
elif icm_cut == 'cold_icm':
icm_mask = "(obj[('gas', 'particle_H_nuclei_density')] < 0.1) & (obj[('gas', 'temperature')] <= 1e4)"
elif icm_cut == 'hot_icm2':
icm_mask = "(obj[('gas', 'particle_H_nuclei_density')] < 0.01) & (obj[('gas', 'temperature')] >= 1e6)"
if yfield[1] == 'metallicity':
if icm_mask:
icm_mask += "& (obj[('gas', 'metallicity')] > 0)"
else:
icm_mask = "(obj[('gas', 'metallicity')] > 0)"
if icm_mask == None:
icm = sp
else:
icm = sp.cut_region(icm_mask)
ph = yt.PhasePlot(icm, xfield, yfield, zfield, weight_field = weight_field, \
fractional = fractional, x_bins = xbins, y_bins = ybins)
ytf.setup_phase_axes(ph, [xfield, yfield, zfield],
unit_list=[xunit, yunit, zunit],
log_list=[xlog, ylog, zlog])
if ylim:
ph.set_ylim(ylim[0], ylim[1])
if xlim:
ph.set_xlim(xlim[0], xlim[1])
profile = ph.profile
ph.save()
outfile_name = '/nobackup/ibutsky/data/YalePaper/romulusC.%06d_phase_data_%s_%s_%s'\
%(output, xfield[1], yfield[1], zfield[1])
if weight_field:
outfile_name += '_%s' % (weight_field[1])
if icm_cut:
outfile_name += '_%s' % (icm_cut)
outfile = h5.File(outfile_name + '.h5', 'w')
outfile.create_dataset(xfield[1], data=profile.x)
outfile.create_dataset(yfield[1], data=profile.y)
outfile.create_dataset(zfield[1], data=profile[zfield])
outfile.create_dataset('weight_field', data=str(weight_field))
outfile.flush()
def generate_column_data(sim,
output,
ion_list,
width,
res=800,
cluster_center=True,
ionization_table='hm2012'):
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)
# "regular" column density measured as impact parameter from cluster center
if cluster_center:
fn = '/nobackupp2/ibutsky/data/%s/%s.%06d_column_data.h5' % (sim, sim,
output)
if ionization_table == 'fg2009':
fn = '/nobackupp2/ibutsky/data/%s/%s.%06d_fg2009_column_data.h5' % (
sim, sim, output)
cdens_file = h5.File(fn)
print(list(cdens_file.keys()))
center = rom_help.get_romulus_yt_center(sim, output, ds)
axis_list = ['x', 'y', 'z']
print('using cluster center')
else:
cdens_file = h5.File(
'/nobackupp2/ibutsky/data/%s/%s.%06d_column_data_special_regions.h5'
% (sim, sim, output), 'a')
id_list, center_x, center_y, width_list = \
np.loadtxt('/nobackup/ibutsky/data/YalePaper/%s.%06d_gas_rich_y_coordinate_list.dat', skiprows=2)
axis_list = ['y']
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)
cdens_file.create_dataset(dset,
data=frb[field_list[i]].ravel())
cdens_file.flush()