def run_nose(verbose=False,
run_answer_tests=False,
answer_big_data=False,
call_pdb=False):
import nose, os, sys, yt
from yt.funcs import mylog
orig_level = mylog.getEffectiveLevel()
mylog.setLevel(50)
nose_argv = sys.argv
nose_argv += ['--exclude=answer_testing', '--detailed-errors', '--exe']
if call_pdb:
nose_argv += ["--pdb", "--pdb-failures"]
if verbose:
nose_argv.append('-v')
if run_answer_tests:
nose_argv.append('--with-answer-testing')
if answer_big_data:
nose_argv.append('--answer-big-data')
initial_dir = os.getcwd()
yt_file = os.path.abspath(yt.__file__)
yt_dir = os.path.dirname(yt_file)
os.chdir(yt_dir)
try:
nose.run(argv=nose_argv)
finally:
os.chdir(initial_dir)
mylog.setLevel(orig_level)
def ReynoldsDecomp(nfiles, path, basename, fieldname):
time = np.zeros(nfiles) # Initialize time array
for i in range(nfiles):
# Append the correct index to each file
if i > 9 and i <= 99:
file = basename + "00" + str(i)
elif i > 99 and i <= 999:
file = basename + "0" + str(i)
elif i > 999:
file = basename + str(i)
else:
file = basename + "000" + str(i)
# Check if file exist or path is correct
try:
my_abs_path = Path(path + file).resolve()
except FileNotFoundError:
print("{} file does not exist or path is wrong!\n".format(file))
else:
mylog.setLevel(40)
print("Reading file {}".format(file))
ds = yt.load(path + file) # Load the file to the scope
data = ds.r[fieldname]
time[i] = ds.current_time
if i == 0:
averaged_data = np.zeros(len(data)) # Initialize accumulator
averaged_data = averaged_data + data
average = averaged_data / nfiles
fluctuations = data - average
return (average, fluctuations)
def __init__(self, table_type, redshift=0.0, data_dir=None, use_metals=True):
mylog.setLevel(50)
filename = _get_data_file(table_type, data_dir=data_dir)
only_on_root(mylog.info, "Loading emissivity data from %s." % filename)
in_file = h5py.File(filename, "r")
if "info" in in_file.attrs:
only_on_root(mylog.info, parse_h5_attr(in_file, "info"))
if parse_h5_attr(in_file, "version") != data_version[table_type]:
raise ObsoleteDataException(table_type)
else:
only_on_root(mylog.info, "X-ray '%s' emissivity data version: %s." % \
(table_type, parse_h5_attr(in_file, "version")))
self.log_T = in_file["log_T"][:]
self.emissivity_primordial = in_file["emissivity_primordial"][:]
if "log_nH" in in_file:
self.log_nH = in_file["log_nH"][:]
if use_metals:
self.emissivity_metals = in_file["emissivity_metals"][:]
self.ebin = YTArray(in_file["E"], "keV")
in_file.close()
self.dE = np.diff(self.ebin)
self.emid = 0.5*(self.ebin[1:]+self.ebin[:-1]).to("erg")
self.redshift = redshift
def run_nose(verbose=False, run_answer_tests=False, answer_big_data=False,
call_pdb = False):
import nose, os, sys, yt
from yt.funcs import mylog
orig_level = mylog.getEffectiveLevel()
mylog.setLevel(50)
nose_argv = sys.argv
nose_argv += ['--exclude=answer_testing','--detailed-errors', '--exe']
if call_pdb:
nose_argv += ["--pdb", "--pdb-failures"]
if verbose:
nose_argv.append('-v')
if run_answer_tests:
nose_argv.append('--with-answer-testing')
if answer_big_data:
nose_argv.append('--answer-big-data')
initial_dir = os.getcwd()
yt_file = os.path.abspath(yt.__file__)
yt_dir = os.path.dirname(yt_file)
os.chdir(yt_dir)
try:
nose.run(argv=nose_argv)
finally:
os.chdir(initial_dir)
mylog.setLevel(orig_level)
def getFileName(initfile, finalfile, path, basename):
nfiles = finalfile - initfile
files = [None] * nfiles
for i in range(initfile, finalfile):
# Append the correct index to each file
if i > 9 and i <= 99:
file = basename + "00" + str(i)
elif i > 99 and i <= 999:
file = basename + "0" + str(i)
elif i > 999:
file = basename + str(i)
else:
file = basename + "000" + str(i)
# Check if file exist or path is correct
try:
my_abs_path = Path(path + file).resolve()
except FileNotFoundError:
print("{} file does not exist or path is wrong!\n".format(file))
else:
mylog.setLevel(40)
# print("Reading file {}".format(file))
files[i - initfile] = file
return files
#average = pod.FlowAverage(nfiles, path, fieldName, files)
time = np.zeros(nfiles)
b = np.zeros(nfiles)
else:
files = None
time = None
b = None
p_time = np.zeros(local_nfiles)
p_b = np.zeros(local_nfiles)
comm.Barrier() # Children wait for Master node to finish
files = comm.bcast(files, root=0)
for i in range(local_start,
local_end): # complete the file name with the correct index
print("Reading file ", files[i], ' with processor ', Pid)
# Load file
mylog.setLevel(40) # Show no yt INFO in command prompt
ds = yt.load(path + files[i])
center = ds.domain_left_edge
sp = ds.sphere(center, r_max)
rp0 = yt.create_profile(sp,
'radius',
fieldName,
n_bins=p_res,
units={
'radius': 'cm',
"density": "kg/m**3",
"specific_volume": "m**3/kg"
},
logs={
'radius': False,
"density": False,
def read_virial(self,
num,
Rsph_over_Rcl=1.95,
prefix='virial',
savdir=None,
force_override=False):
"""
Function to calculate volume integral of various thermal/magnetic/gravitational
energy terms in virial theorem
Also calculates center of mass, half mass radius of neutral gas etc.
"""
# Print no log messages
from yt.funcs import mylog
mylog.setLevel(50)
ds = self.load_vtk(num, load_method='yt')
da = ds.all_data()
# Set threshold
xCL = 'specific_scalar_CL'
xCL_min = 1e-2 # Cloud gas if xCL > xCL_min
xneu_min = 0.5 # Neutral if xHI + 2xH2 > xneu_min
xH2_min = 0.25
x0 = ds.domain_center
# Volume of a cell in cm**3
dV = ((ds.domain_width / ds.domain_dimensions).prod()).to('pc**3')
# Find indices for cloud and neutral portion of it
idx_neu = (da['xHI'] + 2.0 * da['xH2'] > xneu_min)
idx_ion = (da['xHI'] + 2.0 * da['xH2'] <= xneu_min)
idx_cl = da[xCL] > xCL_min
idx_neu_cl = (da['xHI'] + 2.0 * da['xH2'] > xneu_min) & (da[xCL] >
xCL_min)
idx_ion_cl = (da['xHI'] + 2.0 * da['xH2'] <= xneu_min) & (da[xCL] >
xCL_min)
idx_H2_cl = (2.0 * da['xH2'] > xH2_min) & (da[xCL] > xCL_min)
# Calculate initial magnetic field
if self.par['configure']['gas'] == 'hydro':
mhd = False
else:
mhd = True
if mhd:
muB = self.par['problem']['muB']
else:
muB = np.inf
M0 = self.par['problem']['M_cloud']
R0 = self.par['problem']['R_cloud']
B0mag = 1.3488004135072468e-05 * (M0 * 1e-5) * (20.0 / R0)**2 * (
2.0 / muB) * yu.gauss
thetaB = self.par['problem']['theta_B0'] * np.pi / 180.0
phiB = self.par['problem']['phi_B0'] * np.pi / 180.0
B0 = B0mag * yt.YTArray([
np.sin(thetaB) * np.cos(phiB),
np.sin(thetaB) * np.sin(phiB),
np.cos(thetaB)
])
print('B0', B0)
# Save results to a dictionary
r = dict()
# r['model'] = self.basename
r['Rsph_over_Rcl'] = Rsph_over_Rcl
r['time_code'] = ds.current_time.item()
r['time'] = ds.current_time.to('Myr')
# Mass
r['Mgas_tot'] = (da['density'].sum() * dV).to('Msun')
r['Mgas_neu'] = (da['density'][idx_neu].sum() * dV).to('Msun')
r['Mgas_ion'] = (da['density'][idx_ion].sum() * dV).to('Msun')
r['Mgas_cl'] = (da['density'][idx_cl].sum() * dV).to('Msun')
r['Mgas_neu_cl'] = (da['density'][idx_neu_cl].sum() * dV).to('Msun')
r['Mgas_ion_cl'] = (da['density'][idx_ion_cl].sum() * dV).to('Msun')
r['Mgas_H2_cl'] = (da['density'][idx_H2_cl].sum() * dV).to('Msun')
# Volume
r['V_tot'] = ds.domain_width.prod().to('pc**3')
r['V_neu'] = dV * idx_neu.sum()
r['V_ion'] = dV * idx_ion.sum()
r['V_cl'] = dV * idx_cl.sum()
r['V_neu_cl'] = dV * idx_neu_cl.sum()
r['V_ion_cl'] = dV * idx_ion_cl.sum()
r['V_H2_cl'] = dV * idx_H2_cl.sum()
# Center of mass
r['xCM'] = yt.YTArray([(da[ax]*da['density']).sum()/da['density'].sum() \
for ax in ('x','y','z')]).to('pc')
r['xCM_cl'] = yt.YTArray([(da[ax][idx_cl]*da['density'][idx_cl]).sum()/\
da['density'][idx_cl].sum() \
for ax in ('x','y','z')]).to('pc')
r['xCM_neu_cl'] = yt.YTArray([(da[ax][idx_neu_cl]*da['density'][idx_neu_cl]).sum()/\
da['density'][idx_neu_cl].sum() \
for ax in ('x','y','z')]).to('pc')
r['xCM_ion_cl'] = yt.YTArray([(da[ax][idx_ion_cl]*da['density'][idx_ion_cl]).sum()/\
da['density'][idx_ion_cl].sum() \
for ax in ('x','y','z')]).to('pc')
# Add fields
ds = self.add_fields_virial(ds, mhd, x0=x0, xCM_neu_cl=r['xCM_neu_cl'])
# Calculate radius that encloses xx % of neutral cloud mass
# (distance is measured from xCM_neu_cl)
# and corresponding free-fall time
M_encl_tot = r['Mgas_neu_cl']
dist_neu_cl = da['dist_neu_cl'][idx_neu_cl]
idx_srt = np.argsort(dist_neu_cl)
dist_neu_cl_srt = dist_neu_cl[idx_srt]
M_encl = (da['density'][idx_neu_cl][idx_srt].cumsum() * dV).to('Msun')
percentage = [50, 67, 90, 95]
for p in percentage:
idx = np.where(M_encl / M_encl_tot > p * 1e-2)[0]
r['R{0:d}'.format(p)] = dist_neu_cl_srt[idx[0]]
r['rho{0:d}'.format(p)] = p*1e-2*M_encl_tot/\
(4.0*np.pi*r['R{0:d}'.format(p)]**3/3.0)
r['tff{0:d}'.format(p)] = np.sqrt(3.0*np.pi/\
(32.0*yu.G*r['rho{0:d}'.format(p)])).to('Myr')
r['Ekin_neu_cl'] = (0.5*da['density'][idx_neu_cl]* \
da['velocity_magnitude'][idx_neu_cl]**2*dV).sum().to('erg')
r['Ekin_ion_cl'] = (0.5*da['density'][idx_ion_cl]* \
da['velocity_magnitude'][idx_ion_cl]**2*dV).sum().to('erg')
r['vdisp_neu_cl'] = (np.sqrt(2.0 * r['Ekin_neu_cl'] /
r['Mgas_neu_cl'])).to('km/s')
r['vdisp_ion_cl'] = (np.sqrt(2.0 * r['Ekin_ion_cl'] /
r['Mgas_ion_cl'])).to('km/s')
# Velocity dispersion within spheres of radii R50, R67, R90, R95
for p in percentage:
sph_p = ds.sphere(r['xCM_neu_cl'],
(r['R{0:d}'.format(p)].value.item(), "pc"))
idx_p = (sph_p['xHI'] + 2.0 * sph_p['xH2'] >
xneu_min) & (sph_p[xCL] > xCL_min)
for ax in ('x', 'y', 'z'):
r[f'vmean_{ax}_neu_cl_{p}'] = \
((sph_p['density']*sph_p[f'velocity_{ax}'])[idx_p].sum()/
(sph_p['density'][idx_p]).sum()).to('km/s')
r[f'vrms_{ax}_neu_cl_{p}'] = \
(sph_p['density'][idx_p]*((sph_p[f'velocity_{ax}'])[idx_p] -
r[f'vmean_{ax}_neu_cl_{p}'])**2).sum()/\
(sph_p['density'][idx_p].sum())
r[f'vrms_{ax}_neu_cl_{p}'] = np.sqrt(
r[f'vrms_{ax}_neu_cl_{p}']).to('km/s')
for ax in ('x', 'y', 'z'):
r[f'vmean_{ax}_neu_cl'] = (
(da['density'] * da[f'velocity_{ax}'])[idx_neu_cl].sum() /
(da['density'][idx_neu_cl]).sum()).to('km/s')
r[f'vrms_{ax}_neu_cl'] =\
(da['density'][idx_neu_cl]*((da[f'velocity_{ax}'])[idx_neu_cl] -
r[f'vmean_{ax}_neu_cl'])**2).sum()/\
(da['density'][idx_neu_cl].sum())
r[f'vrms_{ax}_neu_cl'] = np.sqrt(r[f'vrms_{ax}_neu_cl']).to('km/s')
Rcl = self.par['problem']['R_cloud']
sph_ = ds.sphere(x0, (1.99 * Rcl, "pc"))
surf = ds.surface(sph_, "dist", (Rsph_over_Rcl * Rcl, "pc"))
sph = ds.sphere(x0, (Rsph_over_Rcl * Rcl, "pc"))
# These are the coordinates of all triangle vertices in the surface
triangles = surf.triangles
# construct triange normal vectors
w1 = surf.triangles[:, 1] - surf.triangles[:, 0]
w2 = surf.triangles[:, 1] - surf.triangles[:, 2]
# calculate triangle areas
vector_area = np.cross(w1, w2) / 2 * (yu.pc**2).to('cm**2')
scalar_area = np.linalg.norm(vector_area, axis=1)
surf_area = scalar_area.sum()
# idx for neutral cloud within sphere
idx = (sph['xHI'] + 2.0 * sph['xH2'] > xneu_min) & (sph[xCL] > xCL_min)
# Surface integral
if mhd:
rdotTM = np.column_stack([surf['rdotTM_{0:s}'.format(x)] \
for x in 'xyz'])*(yu.erg/yu.cm**2)
rdotPi = np.column_stack([surf['rdotPi_{0:s}'.format(x)] \
for x in 'xyz'])*(yu.erg/yu.cm**2)
rdotPi_thm = np.column_stack([surf['rdotPi_thm_{0:s}'.format(x)] \
for x in 'xyz'])*(yu.erg/yu.cm**2)
rhovrsq = np.column_stack([surf['rhovrsq_{0:s}'.format(x)] \
for x in 'xyz'])*(yu.g/yu.s)
r['Mgas_sph'] = ((sph['cell_volume'] *
sph['density']).sum()).to('Msun')
r['Mgas_neu_cl_sph'] = ((sph['cell_volume'][idx] *
sph['density'][idx]).sum()).to('Msun')
r['I_E'] = ((sph['cell_volume'] * sph['rho_rsq']).sum()).to('g*cm**2')
r['I_E_neu_cl'] = ((sph['cell_volume'][idx] *
sph['rho_rsq'][idx]).sum()).to('g*cm**2')
r['V_neu_cl_sph'] = ((sph['cell_volume'][idx]).sum()).to('pc**3')
# Effective radius # Incorrect
r['R_rms'] = np.sqrt(5.0 / 3.0 * r['I_E'] / r['Mgas_sph']).to('pc')
r['R_rms_neu_cl'] = np.sqrt(5.0 / 3.0 * r['I_E_neu_cl'] /
r['Mgas_neu_cl_sph']).to('pc')
# Flux of momentum of inertia
r['S_surf_sph'] = 0.5 * np.sum(vector_area * rhovrsq)
# Surface integral of Reynolds stress
r['T_surf_sph'] = 0.5 * np.sum(vector_area * rdotPi)
# Surface integral of Reynolds stress (only themal pressure term)
r['T_surf_thm_sph'] = 0.5 * np.sum(vector_area * rdotPi_thm)
# Thermal + kinetic energy (for sphere)
r['T_thm_sph'] = 1.5 * (
(sph['cell_volume'] * sph['pressure']).sum()).to('erg')
r['T_kin_sph'] = 0.5 * ((sph['cell_volume'] * sph['density'] *
sph['velocity_magnitude']**2).sum()).to('erg')
r['T_thm_neu_cl_sph'] = 1.5 * (
(sph['cell_volume'][idx] * sph['pressure'][idx]).sum()).to('erg')
r['T_kin_neu_cl_sph'] = 0.5 * (
(sph['cell_volume'][idx] * sph['density'][idx] *
sph['velocity_magnitude'][idx]**2).sum()).to('erg')
# Thermal + kinetic energy (for entire volume)
r['T_thm'] = 1.5 * (
(da['cell_volume'] * da['pressure']).sum()).to('erg')
r['T_kin'] = 0.5 * ((da['cell_volume'] * da['density'] *
da['velocity_magnitude']**2).sum()).to('erg')
r['T_thm_neu_cl'] = 1.5 * (
(da['cell_volume'][idx_neu_cl] *
da['pressure'][idx_neu_cl]).sum()).to('erg')
r['T_kin_neu_cl'] = 0.5 * (
(da['cell_volume'][idx_neu_cl] * da['density'][idx_neu_cl] *
da['velocity_magnitude'][idx_neu_cl]**2).sum()).to('erg')
# Surface integral of Maxwell stress
if mhd:
r['M_surf_sph'] = np.sum(vector_area * rdotTM)
# Alternative way
# r['M_surf_'] = surf.calculate_flux('rdotTM_x', 'rdotTM_y', 'rdotTM_z', fluxing_field="ones")
# Volume integral of magnetic energy density
r['M_vol_sph'] = (sph['cell_volume'] *
sph['magnetic_energy']).sum().to('erg')
r['M_sph'] = r['M_vol_sph'] + r['M_surf_sph']
# Define average magnetic field on surface
r['B_surf_avg_x'] = (surf['magnetic_field_x'] *
scalar_area).sum() / surf_area
r['B_surf_avg_y'] = (surf['magnetic_field_y'] *
scalar_area).sum() / surf_area
r['B_surf_avg_z'] = (surf['magnetic_field_z'] *
scalar_area).sum() / surf_area
r['B_surf_avg_mag'] = np.sqrt(r['B_surf_avg_x']**2 +
r['B_surf_avg_y']**2 +
r['B_surf_avg_z']**2)
# Alternative method to calculate surface-averaged B-field magnitude
# Bmag^2 = -6*M_surf/R_sph^3
r['B_surf_avg_mag_alt'] = (np.sqrt(
-6.0 * r['M_surf_sph'] /
((r['Rsph_over_Rcl'] * Rcl * yu.pc)**3))).to('gauss')
# Magnetic energy as obtaind by volume integral of B^2 - B_avg^2
# Using B_avg=B0. This is incorrect because B_avg changes with time
r['M_neu_cl0_sph'] = (
((sph['magnetic_field_magnitude'][idx]**2 - B0mag**2) *
sph['cell_volume'][idx]).sum()).to('erg') / (8.0 * np.pi)
# This will be our fiducial choice
r['M_neu_cl_sph'] = (
((sph['magnetic_field_magnitude'][idx]**2 -
r['B_surf_avg_mag']**2) *
sph['cell_volume'][idx]).sum()).to('erg') / (8.0 * np.pi)
# Alternative
r['M_neu_cl_sph_alt'] = (
((sph['magnetic_field_magnitude'][idx]**2 -
r['B_surf_avg_mag_alt']**2) *
sph['cell_volume'][idx]).sum()).to('erg') / (8.0 * np.pi)
r['M_neu_cl0'] = ((
(da['magnetic_field_magnitude'][idx_neu_cl]**2 - B0mag**2) *
da['cell_volume'][idx_neu_cl]).sum()).to('erg') / (8.0 * np.pi)
r['M_neu_cl'] = ((
(da['magnetic_field_magnitude'][idx_neu_cl]**2 -
r['B_surf_avg_mag']**2) *
da['cell_volume'][idx_neu_cl]).sum()).to('erg') / (8.0 * np.pi)
r['M_neu_cl_alt'] = ((
(da['magnetic_field_magnitude'][idx_neu_cl]**2 -
r['B_surf_avg_mag_alt']**2) *
da['cell_volume'][idx_neu_cl]).sum()).to('erg') / (8.0 * np.pi)
else:
r['M_surf_sph'] = 0.0
r['M_vol_sph'] = 0.0
r['M_sph'] = 0.0
r['B_surf_avg_x'] = 0.0
r['B_surf_avg_y'] = 0.0
r['B_surf_avg_z'] = 0.0
r['B_surf_avg_mag'] = 0.0
r['B_surf_avg_mag_alt'] = 0.0
r['M_neu_cl0_sph'] = 0.0
r['M_neu_cl_sph'] = 0.0
r['M_neu_cl_sph_alt'] = 0.0
r['M_neu_cl0'] = 0.0
r['M_neu_cl'] = 0.0
r['M_neu_cl_alt'] = 0.0
# Gravitational term (gravitational energy in the absence of external potential)
r['W_sph'] = (sph['density']*\
(sph['x']*sph['gravitational_potential_gradient_x'] +\
sph['y']*sph['gravitational_potential_gradient_y'] +\
sph['z']*sph['gravitational_potential_gradient_z'])*
sph['cell_volume']).sum().to('erg')
r['W_neu_cl_sph'] = (sph['density'][idx]*\
(sph['x'][idx]*sph['gravitational_potential_gradient_x'][idx] +\
sph['y'][idx]*sph['gravitational_potential_gradient_y'][idx] +\
sph['z'][idx]*sph['gravitational_potential_gradient_z'][idx])*
sph['cell_volume'][idx]).sum().to('erg')
r['W'] = (da['density']*\
(da['x']*da['gravitational_potential_gradient_x'] +\
da['y']*da['gravitational_potential_gradient_y'] +\
da['z']*da['gravitational_potential_gradient_z'])*
da['cell_volume']).sum().to('erg')
r['W_neu_cl'] = (da['density'][idx_neu_cl]*\
(da['x'][idx_neu_cl]*da['gravitational_potential_gradient_x'][idx_neu_cl] +\
da['y'][idx_neu_cl]*da['gravitational_potential_gradient_y'][idx_neu_cl] +\
da['z'][idx_neu_cl]*da['gravitational_potential_gradient_z'][idx_neu_cl])*
da['cell_volume'][idx_neu_cl]).sum().to('erg')
return r
import sys
import yt
from yt.funcs import mylog
mylog.setLevel(50)
import numpy as np
from yt import derived_field
import matplotlib.pyplot as plt
from yt.units import yr, Myr, pc,gram,second
from scipy.interpolate import interp1d
from yt.data_objects.particle_filters import add_particle_filter
from yt.fields.derived_field import \
ValidateGridType, \
ValidateParameter, \
ValidateSpatial, \
NeedsParameter
from astropy.table import Table , Column
def _Disk_H(field, data):
center = data.get_field_parameter('center')
z = data["z"] - center[2]
return np.abs(z)
yt.add_field("Disk_H",
function=_Disk_H,
units="pc",
take_log=False,
validators=[ValidateParameter('center')])
def _radial_velocity(field,data):
if data.has_field_parameter("bulk_velocity"):
bv = data.get_field_parameter("bulk_velocity").in_units("cm/s")
'---Processor---\n')
comm.Barrier()
t_start = MPI.Wtime() # Start run time measurement
for i in range(local_start,
local_end): # complete the file name with the correct index
if i > 9 and i <= 99:
file = fname + "00" + str(i)
elif i > 99 and i <= 999:
file = fname + "0" + str(i)
elif i > 999:
file = fname + str(i)
else:
file = fname + "000" + str(i)
# Load file
mylog.setLevel(40) # Show INFO only in command prompt
ds = yt.load(file)
#ad = ds.all_data()
#fd = ad['gas', fieldName]
print(' ',file,'\t\t', float(ds.current_time)*1000, \
'\t\t', Pid)
rad = 15.0
res = 2048
xmix = np.array([])
ymix = np.array([])
rmix = np.array([])
mylog.setLevel(40) # Hide output log in command line
for j in range(
0, 90): # Loop for changing the angle of the line from 0 to 90 deg
xp = rad * np.cos(
def plot_kin_e():
# set ytlog.setLevel(40) to suppress logging up to a certain level
# set ytlog.setLevel(20) to enable more logging
ytlog.setLevel(40)
# load data as time series of individual data sets
# would yt recognise our data as 2d? Since override_geometry does not seem to work?
ts = yt.load(data_dir + basename + '????.dat')
# initialise arrays
times = []
E_kin = []
Palinstrophy = []
Enstrophy = []
grid_level = 2 # maximal refinement level used
# add field: kinetic energy per cell
# the cell-volume is important as weight, s.t. data with different mesh sizes can be compared
# TODO yt does not recognise our data as 2d
def _kinetic_energy_per_cell(field, data):
return data["kinetic_energy_density"] * data["cell_volume"]
yt.add_field(("gas", "_kinetic_energy_per_cell"),
function=_kinetic_energy_per_cell,
units='g*cm**2/s**2')
# add field: kinetic energy per cell
# the cell-volume is important as weight, s.t. data with different mesh sizes can be compared
# TODO yt does not recognise our data as 2d
# TODO dimensionless?
def _quad_omega(field, data):
return data["omega"]**2
yt.add_field(("amrvac", "_quad_omega"),
function=_quad_omega,
units='dimensionless')
# add field: kinetic energy per cell
# the cell-volume is important as weight, s.t. data with different mesh sizes can be compared
# TODO yt does not recognise our data as 2d
# TODO dimensionless?
def _norm_grad_omega(field, data):
return data["grad_omega_x_"]**2 + data["grad_omega_y_"]**2
yt.add_field(("gas", "_norm_grad_omega"),
function=_norm_grad_omega,
units='dimensionless')
# compute kinetic energy for each time step
for ds in ts:
#print(ds.shape)
dd = ds.all_data()
#print(dd)
#TODO use smoothed_covering_grid() for top down regridding of data
# or find out whether dd.max_level uses interpolation
dd.max_level = grid_level
times.append(ds.current_time.in_units("s"))
E_kin.append(
dd.quantities.total_quantity([("gas", "_kinetic_energy_per_cell")
]))
Enstrophy.append(
0.5 * dd.quantities.total_quantity([("amrvac", "_quad_omega")]))
Palinstrophy.append(
0.5 * dd.quantities.total_quantity([("gas", "_norm_grad_omega")]))
E_kin = np.array(E_kin)
Palinstrophy = np.array(Palinstrophy)
# plot data
fig, axs = plt.subplots(3)
#fig.suptitle('Vertically stacked subplots')
#axs[0].plot(x, y)
#axs[1].plot(x, -y)
axs[0].plot(times, E_kin)
axs[0].set(xlabel='Time (s)', ylabel='Kinetic energy ($g\cdot cm^2/s^2$)')
axs[1].plot(times, Enstrophy)
axs[1].set(xlabel='Time (s)', ylabel='Enstrophy')
axs[2].plot(times, Palinstrophy)
axs[2].set(xlabel='Time (s)', ylabel='Palinstrophy')
fig.show()
fig.savefig(out_dir + 'kinetic_energy_' + basename + '.pdf')
def __init__(self,
outputs,
indices,
fields=None,
suppress_logging=False,
ptype=None):
indices.sort() # Just in case the caller wasn't careful
self.field_data = YTFieldData()
self.data_series = outputs
self.masks = []
self.sorts = []
self.array_indices = []
self.indices = indices
self.num_indices = len(indices)
self.num_steps = len(outputs)
self.times = []
self.suppress_logging = suppress_logging
self.ptype = ptype
if fields is None:
fields = []
fields = list(OrderedDict.fromkeys(fields))
if self.suppress_logging:
old_level = int(ytcfg.get("yt", "loglevel"))
mylog.setLevel(40)
ds_first = self.data_series[0]
dd_first = ds_first.all_data()
fds = {}
for field in (
"particle_index",
"particle_position_x",
"particle_position_y",
"particle_position_z",
):
fds[field] = self._get_full_field_name(field)[0]
my_storage = {}
pbar = get_pbar("Constructing trajectory information",
len(self.data_series))
for i, (sto,
ds) in enumerate(self.data_series.piter(storage=my_storage)):
dd = ds.all_data()
newtags = dd[fds["particle_index"]].d.astype("int64")
mask = np.in1d(newtags, indices, assume_unique=True)
sort = np.argsort(newtags[mask])
array_indices = np.where(
np.in1d(indices, newtags, assume_unique=True))[0]
self.array_indices.append(array_indices)
self.masks.append(mask)
self.sorts.append(sort)
pfields = {}
for field in (f"particle_position_{ax}" for ax in "xyz"):
pfields[field] = dd[fds[field]].ndarray_view()[mask][sort]
sto.result_id = ds.parameter_filename
sto.result = (ds.current_time, array_indices, pfields)
pbar.update(i)
pbar.finish()
if self.suppress_logging:
mylog.setLevel(old_level)
sorted_storage = sorted(my_storage.items())
times = [time for _fn, (time, *_) in sorted_storage]
self.times = self.data_series[0].arr(times, times[0].units)
self.particle_fields = []
output_field = np.empty((self.num_indices, self.num_steps))
output_field.fill(np.nan)
for field in (f"particle_position_{ax}" for ax in "xyz"):
for i, (_fn, (_time, indices,
pfields)) in enumerate(sorted_storage):
try:
# This will fail if particles ids are
# duplicate. This is due to the fact that the rhs
# would then have a different shape as the lhs
output_field[indices, i] = pfields[field]
except ValueError as e:
raise YTIllDefinedParticleData(
"This dataset contains duplicate particle indices!"
) from e
self.field_data[field] = array_like_field(dd_first,
output_field.copy(),
fds[field])
self.particle_fields.append(field)
# Instantiate fields the caller requested
self._get_data(fields)
def __init__(self, outputs, indices, fields=None, suppress_logging=False):
indices.sort() # Just in case the caller wasn't careful
self.field_data = YTFieldData()
self.data_series = outputs
self.masks = []
self.sorts = []
self.array_indices = []
self.indices = indices
self.num_indices = len(indices)
self.num_steps = len(outputs)
self.times = []
self.suppress_logging = suppress_logging
if fields is None: fields = []
fields = list(OrderedDict.fromkeys(fields))
if self.suppress_logging:
old_level = int(ytcfg.get("yt","loglevel"))
mylog.setLevel(40)
fds = {}
ds_first = self.data_series[0]
dd_first = ds_first.all_data()
idx_field = dd_first._determine_fields("particle_index")[0]
for field in ("particle_position_%s" % ax for ax in "xyz"):
fds[field] = dd_first._determine_fields(field)[0]
my_storage = {}
pbar = get_pbar("Constructing trajectory information", len(self.data_series))
for i, (sto, ds) in enumerate(self.data_series.piter(storage=my_storage)):
dd = ds.all_data()
newtags = dd[idx_field].d.astype("int64")
mask = np.in1d(newtags, indices, assume_unique=True)
sort = np.argsort(newtags[mask])
array_indices = np.where(np.in1d(indices, newtags, assume_unique=True))[0]
self.array_indices.append(array_indices)
self.masks.append(mask)
self.sorts.append(sort)
pfields = {}
for field in ("particle_position_%s" % ax for ax in "xyz"):
pfields[field] = dd[fds[field]].ndarray_view()[mask][sort]
sto.result_id = ds.parameter_filename
sto.result = (ds.current_time, array_indices, pfields)
pbar.update(i)
pbar.finish()
if self.suppress_logging:
mylog.setLevel(old_level)
times = []
for fn, (time, indices, pfields) in sorted(my_storage.items()):
times.append(time)
self.times = self.data_series[0].arr([time for time in times], times[0].units)
self.particle_fields = []
output_field = np.empty((self.num_indices, self.num_steps))
output_field.fill(np.nan)
for field in ("particle_position_%s" % ax for ax in "xyz"):
for i, (fn, (time, indices, pfields)) in enumerate(sorted(my_storage.items())):
output_field[indices, i] = pfields[field]
self.field_data[field] = array_like_field(
dd_first, output_field.copy(), fds[field])
self.particle_fields.append(field)
# Instantiate fields the caller requested
self._get_data(fields)
import matplotlib as mpl
mpl.use('Agg')
import yt
from yt import YTArray
import trident
import numpy as np
import numpy.random as npr
import matplotlib.pyplot as plt
import time
from mpi4py import MPI
import os
import shutil
from yt.funcs import mylog
mylog.setLevel(40) # only logs errors and critical problems
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
#script to pull out the list of column densities within the center of the simulations
#centered on the cloud. These are then written to a file to be used to
#calculate the cumulative distribution of the column densities
import yt
import numpy as np
import trident as tri
import h5py
from massFracs import *
import pandas as pd
from yt.units import centimeter, gram, second, Kelvin, erg
from yt.funcs import mylog
mylog.setLevel(50) # This sets the log level to "CRITICAL"
kpc = 3.086e+21 * centimeter
c_speed = 3.0e10 #cm/s
mp = 1.6726e-24 * gram #grams
kb = 1.3806e-16 * erg / Kelvin #egs/K
#add metallicity to dataset, constant Z = 1 Zsun
def _metallicity(field, data):
v = data['ones'] #sets metallicity to 1 Zsun
return data.apply_units(v, "Zsun")
#function to read in spectrum, convert to velocity and return
#wavelength and flux numpy arrays
def convert_to_vel(filename, rest_wave):
-- Bug persist even if we do cut one-by-one. We modified yt clump_handling.py to fix this..
last mod: 23 July 2018
"""
import sys
assert 'yt' in sys.path[1] # instead of using the anaconda version
import yt
import os
from yt.funcs import mylog
# This sets the log level to "ERROR", http://yt-project.org/doc/faq/index.html
mylog.setLevel(0)
import numpy as np
from clump_modules.clump_wrapper import ytclumpfind_H2, get_phyprop_of_leaf
from io_modules.manipulate_fetch_gal_fields import import_fetch_gal, import_fetch_stars, prepare_unigrid, check_hist_h2, check_power
from plot_modules.plot_cloud_prop import setup_plot
setup_plot()
outdir = 'test_brute/'
if not os.path.isdir(outdir):
os.mkdir(outdir)
field_select = "h2density"
#!/usr/bin/env python
import yt
from yt.funcs import mylog
import yaml
import numpy as np
import psutil
# Wavenumber to load?
number = '0'
# Is it partial?
parital = False
numcpus = psutil.cpu_count(logical=False)
mylog.setLevel(40)
# Load configuration data
with open('wafer.yaml') as config_file:
config = yaml.safe_load(config_file)
num = config['grid']['size']
dn = config['grid']['dn']
dt = config['grid']['dt']
x = (dn*num['x']-dn)/2
y = (dn*num['y']-dn)/2
z = (dn*num['z']-dn)/2
# Load potential data
def prepare_unigrid(data,
regionsize_kpc=7.,
verbose=False,
add_unit=False,
debug=False):
import yt
if (not verbose):
from yt.funcs import mylog
mylog.setLevel(40)
if (add_unit):
# see http://yt-project.org/doc/examining/generic_array_data.html
# for reference
from astropy import constants as cc
mp = cc.m_p.cgs.value
# reminder: it should be
# read from the camera
bbox_lim = regionsize_kpc / 2.
bbox = np.array([[-bbox_lim, bbox_lim], [-bbox_lim, bbox_lim],
[-bbox_lim, bbox_lim]])
shape_data = data['density'].shape
# data should be added with proper units here
# (maybe get_units from pymses can be used)
print data.keys()
data = dict(density=(mp * data['density'], "g/cm**3"),
h2density=(data["density"] * data["H2"], "1/cm**3"),
P=(data['P'], "K/cm**3"),
P_nt=(data['P_nt'], "K/cm**3"),
Z=(data['Z'], ""),
velx=(data['velx'], "km/s"),
vely=(data['vely'], "km/s"),
velz=(data['velz'], "km/s"))
ds = yt.load_uniform_grid(data,
shape_data,
length_unit='kpc',
bbox=bbox)
else:
ds = yt.load_uniform_grid(data, data["density"].shape)
field = ("h2density")
def _h2density(field, data):
try:
return data["density"] * data["H2"]
except:
return data[("stream", "density")] * data[("stream", "H2")]
# unit is in 1/cc only if convert_unit is properly called when loading
# in data
ds.add_field(("stream", "h2density"),
function=_h2density,
units="g/cm**3")
dd = ds.all_data()
if debug:
prj = yt.ProjectionPlot(ds,
0,
'h2density',
center='c',
weight_field='density')
prj.set_unit('h2density', '1/cm**3')
prj.save('test_h2density_yt_unit_plot.png')
print 'dump to ', 'test_h2density_yt_unit_plot.png'
prj = yt.ProjectionPlot(ds,
0,
'density',
center='c',
weight_field='density')
#prj.set_unit('density', 'g/cm**3')
prj.set_unit('density', 'Msun/pc**3')
#prj.set_unit('density', 'code_mass/code_length**3')
prj.save('test_density_yt_unit_plot.png')
print 'dump to ', 'test_density_yt_unit_plot.png'
print dd['h2density'].max(), dd['h2density'].min()
print dd['density'].max(), dd['density'].min()
return ds, dd
def read_virial2(self, num, Rsph_over_Rcl=1.95, xCL_min=1.0e-2,
prefix='virial2', savdir=None, force_override=False):
"""
Function to calculate volume integral of various thermal/magnetic/gravitational
energy terms in virial theorem
Also calculates center of mass, half mass radius of neutral gas etc.
"""
# Print no log messages
from yt.funcs import mylog
mylog.setLevel(50)
ds = self.load_vtk(num, load_method='yt')
da = ds.all_data()
# Set threshold
xCL = 'specific_scalar_CL'
xneu_min = 0.5 # Neutral if xHI + 2xH2 > xneu_min
x0 = ds.domain_center
# Volume of a cell in cm**3
dV = ((ds.domain_width/ds.domain_dimensions).prod()).to('pc**3')
# Find indices for cloud and neutral portion of it
idx_neu = (da['xHI'] + 2.0*da['xH2'] > xneu_min)
idx_neu_cl = (da['xHI'] + 2.0*da['xH2'] > xneu_min) & (da[xCL] > xCL_min)
# Calculate initial magnetic field
if self.par['configure']['gas'] == 'hydro':
mhd = False
else:
mhd = True
if mhd:
muB = self.par['problem']['muB']
else:
muB = np.inf
M0 = self.par['problem']['M_cloud']
R0 = self.par['problem']['R_cloud']
B0mag = 1.3488004135072468e-05*(M0/1e5)*(20.0/R0)**2*(2.0/muB)*yu.gauss
thetaB = self.par['problem']['theta_B0']*np.pi/180.0
phiB = self.par['problem']['phi_B0']*np.pi/180.0
B0 = B0mag*yt.YTArray([np.sin(thetaB)*np.cos(phiB),
np.sin(thetaB)*np.sin(phiB),
np.cos(thetaB)])
# Save results to a dictionary
r = dict()
r['xCL_min'] = xCL_min
r['Rsph_over_Rcl'] = Rsph_over_Rcl
r['time_code'] = ds.current_time.item()
r['time'] = ds.current_time.to('Myr')
r['B0'] = B0
# Center of mass
r['xCM'] = yt.YTArray([(da[ax][idx_neu_cl]*da['density'][idx_neu_cl]).sum()/\
da['density'][idx_neu_cl].sum() \
for ax in ('x','y','z')]).to('pc')
# Add fields
ds = self.add_fields_virial2(ds, mhd, x0=x0, xCM_neu_cl=r['xCM'])
Rcl = self.par['problem']['R_cloud']
sph_ = ds.sphere(x0, (1.99*Rcl, "pc"))
surf = ds.surface(sph_, "dist", (Rsph_over_Rcl*Rcl, "pc"))
sph = ds.sphere(x0, (Rsph_over_Rcl*Rcl, "pc"))
# These are the coordinates of all triangle vertices in the surface
triangles = surf.triangles
# construct triange normal vectors
w1 = surf.triangles[:,1] - surf.triangles[:,0]
w2 = surf.triangles[:,1] - surf.triangles[:,2]
# calculate triangle areas
vector_area = np.cross(w1, w2)/2*(yu.pc**2).to('cm**2')
scalar_area = np.linalg.norm(vector_area, axis=1)
surf_area = scalar_area.sum()
# idx for neutral cloud within sphere
idx = (sph['xHI'] + 2.0*sph['xH2'] > xneu_min) & (sph[xCL] > xCL_min)
# Surface integral
if mhd:
rdotTM = np.column_stack([surf['rdotTM_{0:s}'.format(x)] \
for x in 'xyz'])*(yu.erg/yu.cm**2)
rdotPi_kin = np.column_stack([surf['rdotPi_kin_{0:s}'.format(x)] \
for x in 'xyz'])*(yu.erg/yu.cm**2)
rdotPi_thm = np.column_stack([surf['rdotPi_thm_{0:s}'.format(x)] \
for x in 'xyz'])*(yu.erg/yu.cm**2)
rhovrsq = np.column_stack([surf['rhovrsq_{0:s}'.format(x)] \
for x in 'xyz'])*(yu.g/yu.s)
# Velocity dispersion
for ax in ('x','y','z'):
r[f'vmean_{ax}_cl'] = ((sph['density']*sph[f'velocity_{ax}'])[idx].sum()/
(sph['density'][idx]).sum()).to('km/s')
r[f'vrms_{ax}_cl'] =\
(sph['density'][idx]*((sph[f'velocity_{ax}'])[idx] -
r[f'vmean_{ax}_cl'])**2).sum()/\
(sph['density'][idx].sum())
r[f'vrms_{ax}_cl'] = np.sqrt(r[f'vrms_{ax}_cl']).to('km/s')
r[f'vmean_{ax}_cl_all'] = ((da['density']*da[f'velocity_{ax}'])[idx_neu_cl].sum()/
(da['density'][idx_neu_cl]).sum()).to('km/s')
r[f'vrms_{ax}_cl_all'] =\
(da['density'][idx_neu_cl]*((da[f'velocity_{ax}'])[idx_neu_cl] -
r[f'vmean_{ax}_cl_all'])**2).sum()/\
(da['density'][idx_neu_cl].sum())
r[f'vrms_{ax}_cl_all'] = np.sqrt(r[f'vrms_{ax}_cl_all']).to('km/s')
# (Neutral cloud) mass within sphere
r['Mgas'] = ((sph['cell_volume']*sph['density']).sum()).to('Msun')
r['Mgas_cl'] = ((sph['cell_volume'][idx]*sph['density'][idx]).sum()).to('Msun')
r['Mgas_all'] = ((da['cell_volume']*da['density']).sum()).to('Msun')
r['Mgas_cl_all'] = ((da['cell_volume'][idx_neu_cl]*da['density'][idx_neu_cl]).sum()).to('Msun')
# Moment of inertia
r['I_E'] = ((sph['cell_volume']*sph['rho_rsq']).sum()).to('g*cm**2')
r['I_E_cl'] = ((sph['cell_volume'][idx]*sph['rho_rsq'][idx]).sum()).to('g*cm**2')
r['I_E_all'] = ((da['cell_volume']*da['rho_rsq']).sum()).to('g*cm**2')
r['I_E_cl_all'] = ((da['cell_volume'][idx_neu_cl]*da['rho_rsq'][idx_neu_cl]).sum()).to('g*cm**2')
# Volume
r['V'] = ((sph['cell_volume']).sum()).to('pc**3')
r['V_cl'] = ((sph['cell_volume'][idx]).sum()).to('pc**3')
r['V_all'] = ((da['cell_volume']).sum()).to('pc**3')
r['V_cl_all'] = ((da['cell_volume'][idx_neu_cl]).sum()).to('pc**3')
# Effective radius
r['R_rms'] = np.sqrt(5.0/3.0*r['I_E']/r['Mgas']).to('pc')
r['R_rms_cl'] = np.sqrt(5.0/3.0*r['I_E_cl']/r['Mgas_cl']).to('pc')
r['R_rms_cl_all'] = np.sqrt(5.0/3.0*r['I_E_cl_all']/r['Mgas_cl_all']).to('pc')
# Flux of momentum of inertia
r['S_surf'] = 0.5*np.sum(vector_area*rhovrsq)
# Surface integral of kinetic energy
r['T_surf_kin'] = 0.5*np.sum(vector_area*rdotPi_kin)
# Surface integral of thermal energy
r['T_surf_thm'] = 0.5*np.sum(vector_area*rdotPi_thm)
# Volume integral of thermal/kinetic energy
r['T_thm'] = 1.5*((sph['cell_volume']*sph['pressure']).sum()).to('erg')
r['T_kin'] = 0.5*((sph['cell_volume']*sph['density']*
sph['velocity_magnitude']**2).sum()).to('erg')
r['T_thm_cl'] = 1.5*((sph['cell_volume'][idx]*sph['pressure'][idx]).sum()).to('erg')
r['T_kin_cl'] = 0.5*((sph['cell_volume'][idx]*sph['density'][idx]*
sph['velocity_magnitude'][idx]**2).sum()).to('erg')
r['T_thm_all'] = 1.5*((da['cell_volume']*da['pressure']).sum()).to('erg')
r['T_kin_all'] = 0.5*((da['cell_volume']*da['density']*
da['velocity_magnitude']**2).sum()).to('erg')
r['T_thm_cl_all'] = 1.5*((da['cell_volume'][idx_neu_cl]*
da['pressure'][idx_neu_cl]).sum()).to('erg')
r['T_kin_cl_all'] = 0.5*((da['cell_volume'][idx_neu_cl]*
da['density'][idx_neu_cl]*
da['velocity_magnitude'][idx_neu_cl]**2).sum()).to('erg')
# Surface integral of Maxwell stress
if mhd:
# Surface integral of Maxwell tensor
r['B_surf'] = np.sum(vector_area*rdotTM)
# Equivalent method
# r['M_surf_'] = surf.calculate_flux('rdotTM_x', 'rdotTM_y', 'rdotTM_z',
# fluxing_field="ones")
# Volume integral of magnetic energy density
r['B'] = (sph['cell_volume']*sph['magnetic_energy']).sum().to('erg')
r['B_cl'] = (sph['cell_volume'][idx]*sph['magnetic_energy'][idx]).sum().to('erg')
r['B_all'] = (da['cell_volume']*da['magnetic_energy']).sum().to('erg')
r['B_cl_all'] = (da['cell_volume'][idx_neu_cl]*da['magnetic_energy'][idx_neu_cl]).sum().to('erg')
# Define average magnetic field on surface
r['B_surf_avg_x'] = (surf['magnetic_field_x']*scalar_area).sum()/surf_area
r['B_surf_avg_y'] = (surf['magnetic_field_y']*scalar_area).sum()/surf_area
r['B_surf_avg_z'] = (surf['magnetic_field_z']*scalar_area).sum()/surf_area
r['B_surf_avg_mag'] = np.sqrt(r['B_surf_avg_x']**2 +
r['B_surf_avg_y']**2 +
r['B_surf_avg_z']**2)
# Magnetic energy as obtaind by volume integral of B^2 - B_avg^2
r['B_alt'] = (((sph['magnetic_field_magnitude']**2 - r['B_surf_avg_mag']**2)*
sph['cell_volume']).sum()).to('erg') / (8.0*np.pi)
r['B_cl_alt'] = (((sph['magnetic_field_magnitude'][idx]**2 - r['B_surf_avg_mag']**2)*
sph['cell_volume'][idx]).sum()).to('erg') / (8.0*np.pi)
r['B_cl_alt_all'] = (((da['magnetic_field_magnitude'][idx_neu_cl]**2 - r['B_surf_avg_mag']**2)*
da['cell_volume'][idx_neu_cl]).sum()).to('erg') / (8.0*np.pi)
else:
r['B'] = 0.0
r['B_surf'] = 0.0
r['B_cl'] = 0.0
r['B_cl_all'] = 0.0
r['B_surf_avg_x'] = 0.0
r['B_surf_avg_y'] = 0.0
r['B_surf_avg_z'] = 0.0
r['B_surf_avg_mag'] = 0.0
r['B_alt'] = 0.0
r['B_cl_alt'] = 0.0
r['B_cl_alt_all'] = 0.0
# Gravitational term (gravitational energy in the absence of external potential)
r['W'] = (sph['density']*\
(sph['x']*sph['gravitational_potential_gradient_x'] +\
sph['y']*sph['gravitational_potential_gradient_y'] +\
sph['z']*sph['gravitational_potential_gradient_z'])*
sph['cell_volume']).sum().to('erg')
r['W_cl'] = (sph['density'][idx]*\
(sph['x'][idx]*sph['gravitational_potential_gradient_x'][idx] +\
sph['y'][idx]*sph['gravitational_potential_gradient_y'][idx] +\
sph['z'][idx]*sph['gravitational_potential_gradient_z'][idx])*
sph['cell_volume'][idx]).sum().to('erg')
r['W_cl_all'] = (da['density'][idx_neu_cl]*\
(da['x'][idx_neu_cl]*da['gravitational_potential_gradient_x'][idx_neu_cl] +\
da['y'][idx_neu_cl]*da['gravitational_potential_gradient_y'][idx_neu_cl] +\
da['z'][idx_neu_cl]*da['gravitational_potential_gradient_z'][idx_neu_cl])*
da['cell_volume'][idx_neu_cl]).sum().to('erg')
return r
import numpy as np
import matplotlib.pyplot as plt
from matplotlib import cm
from matplotlib.colors import ListedColormap
import yt
from yt.units import dimensions
import trident as tri
from mpl_toolkits.axes_grid1 import AxesGrid
from massFracs import *
from yt.funcs import mylog
mylog.setLevel(40) # This sets the log level to "ERROR"
kpc = 3.086e21 #cm
#define the runs and ions
run1 = {'Name': 'M1-v480-T1-chem', 'times': ['0041']}
run2 = {'Name': 'M6.2-v3000-T1-chem', 'times': ['0117']}
run3 = {'Name': 'M3.6-v3000-T3-chem', 'times': ['0143']}
runList = []
runList.append(run1)
runList.append(run2)
runList.append(run3)
ion1 = {
'atom': 'H',
'ion': 'I',
'name': 'HI',
'chem': 'fracHI_chem',
'tri': 'fracHI_tri',
'ionfolder': '/HI/',
'rest_wave': 1215.67,
def _get_data(self, fields):
"""
Get a list of fields to include in the trajectory collection.
The trajectory collection itself is a dict of 2D numpy arrays,
with shape (num_indices, num_steps)
"""
missing_fields = [
field for field in fields if field not in self.field_data
]
if not missing_fields:
return
if self.suppress_logging:
old_level = int(ytcfg.get("yt", "loglevel"))
mylog.setLevel(40)
ds_first = self.data_series[0]
dd_first = ds_first.all_data()
fds = {}
new_particle_fields = []
for field in missing_fields:
fds[field] = dd_first._determine_fields(field)[0]
if field not in self.particle_fields:
if self.data_series[0]._get_field_info(
*fds[field]).particle_type:
self.particle_fields.append(field)
new_particle_fields.append(field)
grid_fields = [
field for field in missing_fields
if field not in self.particle_fields
]
step = int(0)
pbar = get_pbar(
f"Generating [{', '.join(missing_fields)}] fields in trajectories",
self.num_steps,
)
my_storage = {}
for i, (sto,
ds) in enumerate(self.data_series.piter(storage=my_storage)):
mask = self.masks[i]
sort = self.sorts[i]
pfield = {}
if new_particle_fields: # there's at least one particle field
dd = ds.all_data()
for field in new_particle_fields:
# This is easy... just get the particle fields
pfield[field] = dd[fds[field]].d[mask][sort]
if grid_fields:
# This is hard... must loop over grids
for field in grid_fields:
pfield[field] = np.zeros(self.num_indices)
x = self["particle_position_x"][:, step].d
y = self["particle_position_y"][:, step].d
z = self["particle_position_z"][:, step].d
particle_grids, particle_grid_inds = ds.index._find_points(
x, y, z)
# This will fail for non-grid index objects
for grid in particle_grids:
cube = grid.retrieve_ghost_zones(1, grid_fields)
for field in grid_fields:
CICSample_3(
x,
y,
z,
pfield[field],
self.num_indices,
cube[fds[field]],
np.array(grid.LeftEdge).astype(np.float64),
np.array(grid.ActiveDimensions).astype(np.int32),
grid.dds[0],
)
sto.result_id = ds.parameter_filename
sto.result = (self.array_indices[i], pfield)
pbar.update(step)
step += 1
pbar.finish()
output_field = np.empty((self.num_indices, self.num_steps))
output_field.fill(np.nan)
for field in missing_fields:
fd = fds[field]
for i, (_fn, (indices,
pfield)) in enumerate(sorted(my_storage.items())):
output_field[indices, i] = pfield[field]
self.field_data[field] = array_like_field(dd_first,
output_field.copy(), fd)
if self.suppress_logging:
mylog.setLevel(old_level)
#comm.Barrier()
#t_start = MPI.Wtime()
time = np.array([])
rad_dens =np.zeros([p_res, nfiles])
#center = [0.0, 0.0, 0.5]
for i in range(start, end):
if i > 9 and i <= 99:
file = fname + "00" + str(i)
elif i > 99 and i <= 999:
file = fname + "0" + str(i)
elif i > 999 :
file = fname + str(i)
else :
file = fname + "000" + str(i)
mylog.setLevel(40)
ds = yt.load(file)
print("Reading", file)
# Create a 4cm-radius sphere
center = ds.domain_left_edge#-(0.45,0.45,0.)
sp = ds.sphere(center, r_max)
profile = yt.create_profile(sp, 'radius', ['pressure'], n_bins=p_res,
units = {'radius': 'cm', "pressure": "dyn/cm**2"},
logs = {'radius': False, "pressure": True})
# Transform the profile from a dictionary to a numpy array
profVal = list(profile.field_data.values())
for k in profVal:
d = k
rad_dens[:,i] = d
time = np.append(time, float(ds.current_time))
rad = np.array(profile.x)/r_tar
def __call__(self, parser, namespace, values, option_string=None):
param, val = values.split("=")
mylog.debug("Overriding config: %s = %s", param, val)
ytcfg["yt", param] = val
if param == "log_level": # special case
mylog.setLevel(int(val))
norm_L1_error(ds_ref,
ds,
comparison_fields,
Nx=dim_length,
Ny=dim_length,
Nz=dim_length))
if __name__ == '__main__':
args = parser.parse_args()
verbose = args.v
if not verbose:
from yt.funcs import mylog
mylog.setLevel(30)
# load the target data to be analyzed
target_file = get_block_list(args.target_path)
ds = yt_load(target_file)
specified_fields = args.fields
if args.ref_type == 'sim':
sim_comp = True
unexpected_args = [("std", False), ("median", False),
("permute", None), ("reverse", False),
("offset_soln", 0.), ('bkg_velocity', [])]
for name, default_val in unexpected_args:
if hasattr(args, name) and getattr(args, name) != default_val: