def fubar_halo(obj):
"""Halo-by-halo group finding procedure.
Romeel Davé March 2020
FUBAR stands for Friends-of-friends Unbinding after Rockstar; the
name is no longer valid, but it stuck. Here we perform an FOF
operation for each grouping and create the master caesar lists.
For halos we consider dark matter + gas + stars. For galaxies
however, we only consider high density gas and stars (dust and
blackholes if included).
For clouds we consider all gas particles.
Parameters
----------
obj : :class:`main.CAESAR`
Main caesar object.
group_type : str
Can be either 'halo', 'galaxy' or 'cloud'; determines what objects
we find with FOF.
"""
#pdb.set_trace()
from caesar.fof6d import fof6d
from caesar.group import get_group_properties
from caesar.fubar import get_mean_interparticle_separation
# set up number of processors
obj.nproc = 1 # defaults to single core
if 'nproc' in obj._kwargs:
obj.nproc = int(obj._kwargs['nproc'])
if obj.nproc != 1:
import joblib
if obj.nproc < 0:
obj.nproc += joblib.cpu_count() + 1
if obj.nproc == 0:
obj.nproc = joblib.cpu_count()
mylog.info('member_search() running on %d cores' % obj.nproc)
obj.load_haloid = False
if 'haloid' in obj._kwargs and 'snap' in obj._kwargs['haloid']:
obj.load_haloid = True
# Process halos
halos = fof6d(obj, 'halo') #instantiate a fof6d object
halos.MIS = get_mean_interparticle_separation(
obj).d # also computes omega_baryon and related quantities
halos.load_haloid()
halos.obj.data_manager._member_search_init(
select=halos.haloid
) # load particle info, but only those selected to be in a halo
if not halos.plist_init(
): # not enough halo particles found, nothing to do!
return
halos.load_lists() # create halos, load particle indexes for halos
if len(halos.obj.halo_list) == 0: # no valid halos found
mylog.warning('No valid halos found! Aborting member search')
return
get_group_properties(halos, halos.obj.halo_list) # compute halo properties
# Find galaxies, or load galaxy membership info
if not obj.simulation.baryons_present: # if no baryons, we're done
return
fof6d_flag = True
if 'fof6d' in obj._kwargs and not obj._kwargs[
'fof6d']: # fof6d for galaxies/clouds not requested
mylog.warning(
'fof6d not requested, and no other galaxy finder available! Aborting member search'
)
return
if 'fof6d_file' in obj._kwargs and obj._kwargs['fof6d_file'] is not None:
fof6d_flag = halos.load_fof6dfile() # load galaxy ID's from fof6d_file
if fof6d_flag:
halos.run_fof6d('galaxy') # run fof6d on halos to find galaxies
halos.save_fof6dfile() # save fof6d info
#snapname = ('%s/%s'%(obj.simulation.fullpath,obj.simulation.basename))
#nparts,gas_index,star_index,bh_index = run_fof_6d(snapname,16,0.02,1.0,nproc)
# Process galaxies
galaxies = fof6d(obj, 'galaxy') #instantiate a fof6d object
galaxies.plist_init(
parent=halos) # get particle list for computing galaxy properties
if galaxies.nparttot == 0: # plist_init didn't find any particles in a galaxy
mylog.warning('Not enough eligible galaxy particles found!')
return
galaxies.load_lists(
parent=halos
) # create galaxy_list, load particle index lists for galaxies
get_group_properties(galaxies,
galaxies.obj.galaxy_list) # compute galaxy properties
if ('fsps_bands' in obj._kwargs) and obj._kwargs['fsps_bands'] is not None:
from caesar.pyloser.pyloser import photometry
galphot = photometry(obj, galaxies.obj.galaxy_list)
galphot.run_pyloser()
# Find and process clouds
if ('fofclouds' in obj._kwargs) and obj._kwargs['fofclouds']:
galaxies.run_fof6d('cloud') # run fof6d to find cloudid's
galaxies.load_lists('cloud') # load particle index lists for galaxies
clouds = fof6d(obj, 'cloud') #instantiate a fof6d object
clouds.plist_init(
parent=galaxies) # initialize comptutation of cloud properties
if clouds.nparttot == 0:
return # plist_init didn't find enough particles to group
galaxies.load_lists('cloud')
get_group_properties(clouds,
clouds.obj.cloud_list) # compute cloud properties
# reset particle lists to have original snapshot ID's; must do this after all group processing is finished
reset_global_particle_IDs(obj)
# load global lists
load_global_lists(obj)
return
import caesar
from caesar.pyloser import pyloser
from caesar.cyloser import compute_AV
# _dir = '/cosma7/data/dp104/dc-dave2/sim/m100n1024/s50j7k/'
_dir = '/orange/narayanan/desika.narayanan/gizmo_runs/simba/m100n1024/'
cs = caesar.load(_dir + 'Groups/m100n1024_078.hdf5')
_dat = json.load(open('m100/galaxy_selection.json', 'r'))
halos = [cs.halos[n['hidx']] for k, n in _dat['078'].items()]
# subset_dir='/blue/narayanan/c.lovell/simba/m100n1024/out/snap_078/'
# ds = yt.load(subset_dir+'subset_00000.h5')
ds = yt.load(_dir + 'snap_m100n1024_078.hdf5')
phot = pyloser.photometry(cs, [halos[0]], ds=ds)
phot.ssp_table_file = \
'/home/c.lovell/codes/caesar/FSPS_Chab_EL.hdf5'
# '/cosma7/data/dp004/dc-love2/codes/caesar/FSPS_Chab_EL.hdf5'
phot.init_pyloser()
def transform_coods(theta, phi, tol=20, test=False):
alpha = np.arcsin(-1 * np.round(np.sin(theta), tol) *
np.round(np.sin(phi), tol))
beta = np.round(
np.arcsin((np.round(np.cos(phi), tol) * np.round(np.sin(theta), tol)) /
np.round(np.cos(alpha), tol)), tol)
sim.simulation.effective_resolution**
3) # galaxy mass resolution limit: 32 gas particle masses
sfr = np.asarray([i.sfr for i in myobjs])
ssfr = np.log10(
1.e9 * sfr / ms +
10**(-2.5 +
0.3 * sim.simulation.redshift)) # with a floor to prevent NaN's
# now do photometry in post-processing
#from caesar.pyloser.pyloser import photometry
#ds = sim.yt_dataset
myobjs = sim.galaxies
from caesar.pyloser.pyloser import photometry
galphot = photometry(sim,
myobjs,
ds=ds,
band_names='sdss',
ext_law='composite',
nproc=16)
#galphot.run_pyloser(ssp_model='BPASS')
spect_dust, spec_nodust = galphot.run_pyloser()
print('Default (should be same):', galphot.groups[0].absmag['sdss_r'])
galphot = photometry(sim,
myobjs,
ds=ds,
band_names='sdss',
ssp_model='BPASS',
ssp_table_file='/home/rad/caesar/BPASS_Chab100.hdf5',
ext_law='composite',
nproc=16)
spect_dust, spec_nodust = galphot.run_pyloser()
fig, ((ax1, ax2, ax3), (ax4, ax5, ax6)) = plt.subplots(2, 3, figsize=(10, 5))
axes = [ax1, ax2, ax3, ax4, ax5, ax6]
cmap = cmaps.night()
roll, extent = 0, 30
## ---------- ##
for s, s_file in enumerate(subset_files):
# if True:
# s = 0
# s_file = subset_files[0]
ds = yt.load(subset_dir + s_file)
halo = halos[s]
galaxy = galaxies[s]
phot = pyloser.photometry(cs, halo)
phot.ssp_table_file = '/home/c.lovell/codes/caesar/FSPS_Chab_EL.hdf5'
init_kerntab(phot)
hcood = galaxy.pos.value
with h5py.File(subset_dir + s_file, 'r') as f:
_fact = 1 / cs.simulation.hubble_constant
gpos = f['PartType0']['Coordinates'][:] * _fact
spos = f['PartType4']['Coordinates'][:] * _fact
gm = f['PartType0']['Masses'][:] * 1e10
gZ = f['PartType0']['Dust_Masses'][:] * 1e10
gZ /= gm
ghsm = f['PartType0']['SmoothingLength'][:]
_pos = galaxy.pos.to('kpccm').value
_mask = (cdist(spos, [_pos]) < 30).flatten()