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measure_momentum.py
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measure_momentum.py
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import numpy as np
from numpy import *
import os, sys, argparse
import glob
import astropy
from astropy.io import fits
import astropy
from astropy.cosmology import Planck15 as cosmo
from joblib import Parallel, delayed
import scipy
from scipy.interpolate import UnivariateSpline
#This file will be used to store the profile of the momentum
def parse():
'''
Parse command line arguments
'''
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description='''\
Generate the cameras to use in Sunrise and make projection plots
of the data for some of these cameras. Then export the data within
the fov to a FITS file in a format that Sunrise understands.
''')
parser.add_argument('snap_files', nargs='?', default=None, help='Snapshot files to be analyzed.')
#parser.add_argument('-s', '--snap_base', default='10MpcBox_csf512_',
# help='Base of the snapshots file names.')
#parser.add_argument('-d', '--distance', default=100000, type=float,
# help='Distance between cameras and the center of the galaxy (in [kpc]).')
#parser.add_argument('--no_export',action='store_true',
# help='Do not export data to fits for Sunrise.')
args = vars(parser.parse_args())
return args
class momentum_obj():
def __init__(self, simname, aname, snapfile, fits_name):
self.ds = yt.load(snapfile)
self.simname = simname
self.aname = aname
self.snapfile = snapfile
self.fits_name = fits_name
def load(self):
dd = self.ds.all_data()
print 'Loading star velocities...'
try:
self.stars_vx = dd['stars', 'particle_velocity_x'].in_units('km/s')
assert self.stars_vx.shape > 5
except AttributeError,AssertionError:
print "No star particles found, skipping: ", self.ds._file_amr
return 0
self.stars_id = dd['stars', 'particle_index']
self.stars_metallicity1 = dd['stars', 'particle_metallicity1']
self.stars_metallicity2 = dd['stars', 'particle_metallicity2']
self.stars_vy = dd['stars', 'particle_velocity_y'].in_units('km/s')
self.stars_vz = dd['stars', 'particle_velocity_z'].in_units('km/s')
print 'Loading star positions...'
self.stars_x = dd['stars', 'particle_position_x'].in_units('kpc')
self.stars_y = dd['stars', 'particle_position_y'].in_units('kpc')
self.stars_z = dd['stars', 'particle_position_z'].in_units('kpc')
print 'Loading star mass...'
self.star_mass = dd['stars', 'particle_mass'].in_units('Msun')
print 'Loading star age...'
self.star_creation_time = dd['stars', 'particle_creation_time'].in_units('yr')
self.star_age = self.ds.arr(cosmo.age(self.ds.current_redshift).value, 'Gyr').in_units('yr') - self.star_creation_time
print 'Loading gas velocity...'
self.gas_vx = dd['gas', 'velocity_x'].in_units('km/s')
self.gas_vy = dd['gas', 'velocity_y'].in_units('km/s')
self.gas_vz = dd['gas', 'velocity_z'].in_units('km/s')
print 'Loading gas cell position...'
self.gas_x = dd['index', 'x'].in_units('kpc')
self.gas_y = dd['index', 'y'].in_units('kpc')
self.gas_z = dd['index', 'z'].in_units('kpc')
print 'Loading gas temperature...'
self.gas_temp = dd['gas', 'temperature']
print 'Loading gas cell mass...'
self.gas_mass = dd['gas', 'cell_mass']
print 'Finished loading...'
return 1
def recenter(self, nir_cat, nir_disc_cat):
print 'Recentering...'
self.id_cen_star = nir_cat[1].astype('int')
self.cold_cen = nir_disc_cat[1:4].astype('float')
self.cen_star_offset = nir_cat[2:5].astype('float')
self.cen_star_voffset = nir_cat[5:8].astype('float')
self.L_disk_s = nir_cat[8:11].astype('float')
self.L_disk = nir_disc_cat[7:10].astype('float')
#Determine offset
self.cen_x = self.stars_x[self.id_cen_star-1] - self.ds.arr(self.cen_star_offset[0], 'kpc')
self.cen_y = self.stars_y[self.id_cen_star-1] - self.ds.arr(self.cen_star_offset[1], 'kpc')
self.cen_z = self.stars_z[self.id_cen_star-1] - self.ds.arr(self.cen_star_offset[2], 'kpc')
self.cen_vx = self.stars_vx[self.id_cen_star-1] - self.ds.arr(self.cen_star_voffset[0], 'km/s')
self.cen_vy = self.stars_vy[self.id_cen_star-1] - self.ds.arr(self.cen_star_voffset[1], 'km/s')
self.cen_vz = self.stars_vz[self.id_cen_star-1] - self.ds.arr(self.cen_star_voffset[2], 'km/s')
#Recenter positions and velocities for stars
self.stars_x_cen = self.stars_x - self.cen_x
self.stars_y_cen = self.stars_y - self.cen_y
self.stars_z_cen = self.stars_z - self.cen_z
self.stars_pos_cen = array([self.stars_x_cen, self.stars_y_cen, self.stars_z_cen])
self.stars_pos_mag = sqrt(self.stars_x_cen**2. + self.stars_y_cen**2. + self.stars_z_cen**2.)
self.stars_vx_cen = self.stars_vx - self.cen_vx
self.stars_vy_cen = self.stars_vy - self.cen_vy
self.stars_vz_cen = self.stars_vz - self.cen_vz
self.stars_vel_cen = array([self.stars_vx_cen, self.stars_vy_cen, self.stars_vz_cen])
self.stars_vel_mag = sqrt(self.stars_vx_cen**2. + self.stars_vy_cen**2. + self.stars_vz_cen**2.)
#Recenter positions and velocities for gas
self.gas_x_cen = self.gas_x - self.cen_x
self.gas_y_cen = self.gas_y - self.cen_y
self.gas_z_cen = self.gas_z - self.cen_z
self.gas_pos_cen = array([self.gas_x_cen, self.gas_y_cen, self.gas_z_cen])
self.gas_pos_mag = sqrt(self.gas_x_cen**2. + self.gas_y_cen**2. + self.gas_z_cen**2.)
self.gas_vx_cen = self.gas_vx - self.cen_vx
self.gas_vy_cen = self.gas_vy - self.cen_vy
self.gas_vz_cen = self.gas_vz - self.cen_vz
self.gas_vel_cen = array([self.gas_vx_cen, self.gas_vy_cen, self.gas_vz_cen])
self.gas_vel_mag = sqrt(self.gas_vx_cen**2. + self.gas_vy_cen**2. + self.gas_vz_cen**2.)
def calc_momentum(self):
print 'Calculating momentum...'
#Calculate momentum for stars
self.stars_jx_cen = self.stars_vz_cen * self.stars_y_cen - self.stars_z_cen * self.stars_vy_cen
self.stars_jy_cen = self.stars_vx_cen * self.stars_z_cen - self.stars_x_cen * self.stars_vz_cen
self.stars_jz_cen = self.stars_vy_cen * self.stars_x_cen - self.stars_y_cen * self.stars_vx_cen
self.stars_j_cen = array([self.stars_jx_cen, self.stars_jy_cen, self.stars_jz_cen])
self.stars_j_mag = sqrt(self.stars_jx_cen**2. + self.stars_jy_cen**2. + self.stars_jz_cen**2.)
#Calculate momentum for gas
self.gas_jx_cen = self.gas_vz_cen * self.gas_y_cen - self.gas_z_cen * self.gas_vy_cen
self.gas_jy_cen = self.gas_vx_cen * self.gas_z_cen - self.gas_x_cen * self.gas_vz_cen
self.gas_jz_cen = self.gas_vy_cen * self.gas_x_cen - self.gas_y_cen * self.gas_vx_cen
self.gas_j_cen = array([self.gas_jx_cen, self.gas_jy_cen, self.gas_jz_cen])
self.gas_j_mag = sqrt(self.gas_jx_cen**2. + self.gas_jy_cen**2. + self.gas_jz_cen**2.)
def measure_potential(self, r_min = 0.1, r_step1 = 0.3, r_cen1 = 3, r_step2 = 2, r_cen2 = 15, r_step3 = 5, r_max = 110.):
print 'Measuring the potential...'
center = self.ds.arr([self.cen_x, self.cen_y, self.cen_z], 'kpc')
rad_steps = concatenate((arange(r_min, r_cen1, r_step1),
arange(r_cen1, r_cen2, r_step2),
arange(r_cen2, r_max, r_step3)))
self.mass_profile = zeros((2,len(rad_steps)))
for i in arange(0,len(rad_steps)):
print i, rad_steps[i], len(rad_steps)
gc_sphere = self.ds.sphere(center, self.ds.arr(rad_steps[i],'kpc'))
baryon_mass, particle_mass = gc_sphere.quantities.total_quantity(["cell_mass", "particle_mass"])
self.mass_profile[0,i] = rad_steps[i]
self.mass_profile[1,i] = baryon_mass + particle_mass
self.spl = UnivariateSpline(self.mass_profile[0,:], self.mass_profile[1,:])
def measure_circularity(self):
print 'Calculating circularity...'
G = astropy.constants.G.to('kpc^3/Msun*s^2') # in kpc^3/Msun*s^2
internal_mass_gas = self.ds.arr(self.spl(self.gas_pos_mag),'g').in_units('Msun')
self.vcirc_gas = self.ds.arr(sqrt(G*internal_mass_gas/(self.gas_pos_mag)),'kpc/s').in_units('km/s')
self.jcirc_gas = self.vcirc_gas * self.gas_pos_mag
internal_mass_stars = self.ds.arr(self.spl(self.stars_pos_mag),'g').in_units('Msun')
self.vcirc_stars = self.ds.arr(sqrt(G*internal_mass_stars/(self.stars_pos_mag)),'kpc/s').in_units('km/s')
self.jcirc_stars = self.vcirc_stars * self.stars_pos_mag
self.L_mag = sqrt(self.L_disk[0]**2.+self.L_disk[1]**2.+self.L_disk[2]**2.)
costheta_gas = np.dot(self.L_disk, self.gas_j_cen)/(self.gas_j_mag*self.L_mag)
self.jz_gas = costheta_gas*self.gas_j_mag
costheta_stars = np.dot(self.L_disk, self.stars_j_cen)/(self.stars_j_mag*self.L_mag)
self.jz_stars = costheta_stars*self.stars_j_mag
self.epsilon_gas = self.jz_gas/self.jcirc_gas
self.epsilon_stars = self.jz_stars/self.jcirc_stars
costheta_gas = np.dot(self.L_disk, self.gas_pos_cen)/(self.gas_pos_mag*self.L_mag)
self.zz_gas = self.ds.arr(costheta_gas * self.gas_pos_mag, 'kpc')
self.rr_gas = sqrt(self.gas_pos_mag**2. - self.zz_gas**2.)
costheta_stars = np.dot(self.L_disk, self.stars_pos_cen)/(self.stars_pos_mag*self.L_mag)
self.zz_stars = self.ds.arr(costheta_stars * self.stars_pos_mag, 'kpc')
self.rr_stars = sqrt(self.stars_pos_mag**2. - self.zz_stars**2.)
def gas_momentum_heatmap(self):
print 'Measuring gas momentum profiles...'
cold_gas_zz = where((abs(self.rr_gas) < 30) & (self.gas_temp < 1.e4))
eps_min = -2.5
eps_max = 2.5
min_z = -10
max_z = 10
min_r = 0
max_r = 30
min_rad = 0
max_rad = 100.
bins_n = 200
cold_gas_zz = where((abs(self.rr_gas) < max_r) & (self.gas_temp < 1.e4))
weights = self.gas_mass[cold_gas_zz]
self.cg_zz_heatmap, self.cg_zz_xedges, self.cg_zz_yedges = np.histogram2d(self.epsilon_gas[cold_gas_zz], self.zz_gas[cold_gas_zz],
bins=[linspace(eps_min,eps_max,bins_n), linspace(min_z,max_z,bins_n)],
weights = weights)
cold_gas_rr = where((abs(self.zz_gas) < (max_z-min_z)/2.) & (self.gas_temp < 1.e4))
weights = self.gas_mass[cold_gas_rr]
print min_r, max_r
self.cg_rr_heatmap, self.cg_rr_xedges, self.cg_rr_yedges = np.histogram2d(self.epsilon_gas[cold_gas_rr], self.rr_gas[cold_gas_rr],
bins=[linspace(eps_min,eps_max,bins_n), linspace(min_r,max_r,bins_n)],
weights = weights)
print self.cg_rr_xedges.min()
cold_gas = where(self.gas_temp < 1.e4)
weights = self.gas_mass[cold_gas]
self.cg_rad_heatmap, self.cg_rad_xedges, self.cg_rad_yedges = np.histogram2d(self.epsilon_gas[cold_gas], self.gas_pos_mag[cold_gas],
bins=[linspace(eps_min,eps_max,bins_n), linspace(min_rad,max_rad,bins_n)],
weights = weights)
def write_fits(self, nir_mstar_cat):
print '\tGenerating fits for %s...'%self.aname
master_hdulist = []
prihdr = fits.Header()
prihdr['COMMENT'] = "Storing the momentum measurements in this FITS file."
prihdr['simname'] = self.simname
prihdr['scale'] = self.aname.strip('a')
prihdr['snapfile'] = self.snapfile
prihdu = fits.PrimaryHDU(header=prihdr)
master_hdulist.append(prihdu)
colhdr = fits.Header()
master_hdulist.append(fits.ImageHDU(data = nir_mstar_cat , header = colhdr, name = 'nir_mstar_cat'))
master_hdulist.append(fits.ImageHDU(data = self.L_disk , header = colhdr, name = 'nir_net_momentum'))
master_hdulist.append(fits.ImageHDU(data = self.L_disk_s , header = colhdr, name = 'nir_net_momentum_s'))
master_hdulist.append(fits.ImageHDU(data = self.stars_id , header = colhdr, name = 'stars_id'))
master_hdulist.append(fits.ImageHDU(data = np.stack((self.stars_metallicity1 , self.stars_metallicity2)) , header = colhdr, name = 'stars_metallicity'))
master_hdulist.append(fits.ImageHDU(data = np.stack((self.stars_x_cen , self.stars_y_cen , self.stars_z_cen)) , header = colhdr, name = 'stars_xyz_position'))
master_hdulist.append(fits.ImageHDU(data = np.stack((self.stars_vx_cen , self.stars_vy_cen , self.stars_vz_cen)) , header = colhdr, name = 'stars_xyz_velocity'))
master_hdulist.append(fits.ImageHDU(data = np.stack((self.rr_stars, self.zz_stars)) , header = colhdr, name = 'stars_cylindrical_position'))
master_hdulist.append(fits.ImageHDU(data = np.stack((self.stars_jx_cen, self.stars_jy_cen, self.stars_jz_cen)) , header = colhdr, name = 'stars_xyz_momentum'))
master_hdulist.append(fits.ImageHDU(data = self.epsilon_stars , header = colhdr, name = 'stars_epsilon'))
master_hdulist.append(fits.ImageHDU(data = self.mass_profile , header = colhdr, name = 'mass_profile'))
master_hdulist.append(fits.ImageHDU(data = self.star_mass , header = colhdr, name = 'star_mass'))
master_hdulist.append(fits.ImageHDU(data = self.star_creation_time , header = colhdr, name = 'star_creation_time'))
master_hdulist.append(fits.ImageHDU(data = self.star_age , header = colhdr, name = 'star_age'))
master_hdulist.append(fits.ImageHDU(data = np.stack((self.cg_zz_xedges , self.cg_zz_yedges)) , header = colhdr, name = 'gas_zz_epsilon_edges'))
master_hdulist.append(fits.ImageHDU(data = self.cg_zz_heatmap , header = colhdr, name = 'gas_zz_epsilon'))
master_hdulist.append(fits.ImageHDU(data = np.stack((self.cg_rr_xedges , self.cg_rr_yedges)) , header = colhdr, name = 'gas_rr_epsilon_edges'))
master_hdulist.append(fits.ImageHDU(data = self.cg_rr_heatmap , header = colhdr, name = 'gas_rr_epsilon'))
master_hdulist.append(fits.ImageHDU(data = np.stack((self.cg_rad_xedges , self.cg_rad_yedges)) , header = colhdr, name = 'gas_rad_epsilon_edges'))
master_hdulist.append(fits.ImageHDU(data = self.cg_rad_heatmap , header = colhdr, name = 'gas_rad_epsilon'))
#master_hdulist.append(fits.ImageHDU(data = np.stack((self.gas_x_cen , self.gas_y_cen , self.gas_z_cen)) , header = colhdr, name = 'gas_xyz_position'))
#master_hdulist.append(fits.ImageHDU(data = np.stack((self.rr_gas, self.zz_gas)) , header = colhdr, name = 'gas_cylindrical_position'))
#master_hdulist.append(fits.ImageHDU(data = np.stack((self.gas_jx_cen, self.gas_jy_cen, self.gas_jz_cen)) , header = colhdr, name = 'gas_momentum'))
#master_hdulist.append(fits.ImageHDU(data = self.epsilon_gas , header = colhdr, name = 'gas_epsilon'))
#master_hdulist.append(fits.ImageHDU(data = self.gas_temp , header = colhdr, name = 'gas_temperature'))
#master_hdulist.append(fits.ImageHDU(data = self.gas_mass , header = colhdr, name = 'gas_mass'))
print '\tSaving to ' + self.fits_name
thdulist = fits.HDUList(master_hdulist)
thdulist.writeto(self.fits_name, clobber = True)
return master_hdulist
def measure_momentum(snapfile, out_sim_dir, nir_cat, nir_disc_cat, nir_mstar_cat):
print 'Measuring momentum for '+ snapfile
aname = (os.path.basename(snapfile)).split('_')[-1].rstrip('.d')
simname = snapfile.split('_')[0]
fits_name = out_sim_dir+'/'+simname+'_'+aname+'_momentum.fits'
in_nir = where(nir_cat[:,0] == aname)[0]
if len(in_nir) == 0:
print "Not found in Nir's catalog, returning"
return
nir_cat = nir_cat[in_nir[0]]
nir_disc_cat = nir_disc_cat[in_nir[0]]
nir_mstar_cat = nir_mstar_cat[in_nir[0]]
mom = momentum_obj(simname, aname, snapfile, fits_name)
check = mom.load()
if check == 0: return
mom.recenter(nir_cat, nir_disc_cat)
mom.calc_momentum()
mom.measure_potential()
mom.measure_circularity()
mom.gas_momentum_heatmap()
mom.write_fits(nir_mstar_cat)
return mom
if __name__ == "__main__":
args = parse()
import yt
if args['snap_files'] is not None: snaps = [args['snap_files']]
else: snaps = np.asarray(glob.glob("*.d"))
print "Generating Sunrise Input for: ", snaps
abssnap = os.path.abspath(snaps[0])
assert os.path.lexists(abssnap)
dirname = os.path.dirname(abssnap)
simname = os.path.basename(dirname) #assumes directory name for simulation name
nir_cat_name = simname[0:-2]+'_v2_'+simname[-2:]
nir_cat = np.loadtxt('/nobackupp2/rcsimons/catalogs/nir_catalogs/GEN3/'+nir_cat_name+'/galaxy_catalogue/Nir_simplified_disc_cat.txt', skiprows = 1, dtype='str')
nir_disc_cat = np.loadtxt('/nobackupp2/rcsimons/catalogs/nir_catalogs/GEN3/'+nir_cat_name+'/galaxy_catalogue/Nir_disc_cat.txt', skiprows = 1, dtype='str')
nir_mstar_cat = np.loadtxt('/nobackupp2/rcsimons/catalogs/nir_catalogs/GEN3/'+nir_cat_name+'/galaxy_catalogue/Mstar.txt')
print "Simulation name: ", simname
out_sim_dir = os.path.join('/nobackupp2/rcsimons/momentum_measurements/', simname)
print os.path.lexists(out_sim_dir)
if not os.path.lexists(out_sim_dir):
print 'Creating momentum directory for %s'%out_sim_dir
os.mkdir(out_sim_dir)
new_snapfiles = []
for sn in snaps:
aname = sn.split('_')[-1].rstrip('.d')
snap_dir = os.path.join(simname+'_'+aname+'_sunrise')
newf = os.path.join(snap_dir,sn)
new_snapfiles.append(newf)
new_snapfiles = np.asarray(new_snapfiles)
#Make Parallel, send 3 at a time to the node (reduce memory overhead)
Parallel(n_jobs = 2, backend = 'threading')(delayed(measure_momentum)(new_snapfiles[i], out_sim_dir, nir_cat, nir_disc_cat, nir_mstar_cat) for i in arange(len(new_snapfiles)))
#for i in arange(len(new_snapfiles)):
# mom = measure_momentum(new_snapfiles[i], out_sim_dir, nir_cat, nir_disc_cat, nir_mstar_cat)