def test_mpi(verbose=False, plot=False, npoints=8, turn_mpi_off_after=True):
phoebe.reset_settings()
phoebe.mpi_on(4)
b = phoebe.Bundle.default_binary()
b.add_dataset('lc', times=np.linspace(0, 1, npoints))
if verbose: print("calling compute")
b.run_compute(irrad_method='none', ntriangles=1000, detach=True)
if verbose:
print("attaching to model")
print(b['model'].status)
b['model'].attach()
if verbose: print("model received")
if plot:
b.plot(show=True)
phoebe.reset_settings()
if turn_mpi_off_after:
# we need to turn this off for the next test in nosetests... but
# if running from python or mpirun, we don't want to release all the
# workers or they'll just pickup all the previous tasks
phoebe.mpi_off()
return b
def test_mpi(plot=False, npoints=8):
phoebe.reset_settings()
phoebe.mpi_on(4)
b = phoebe.Bundle.default_binary()
b.add_dataset('lc', times=np.linspace(0, 1, npoints))
if plot: print "calling compute"
b.run_compute(irrad_method='none', model='phoebe2model')
if plot: print "model received"
if plot:
b.plot(show=True)
phoebe.reset_settings()
phoebe.mpi_off()
return b
def test_mpi(plot=False, npoints=8):
phoebe.reset_settings()
phoebe.mpi_on(4)
b = phoebe.Bundle.default_binary()
b.add_dataset('lc', times=np.linspace(0,1,npoints))
if plot: print "calling compute"
b.run_compute(irrad_method='none', ntriangles=1000, detach=True)
if plot:
print "attaching to model"
print b['model'].status
b['model'].attach()
if plot: print "model received"
if plot:
b.plot(show=True)
phoebe.reset_settings()
phoebe.mpi_off()
return b
import phoebe
phoebe.mpi_off()
import numpy as np
import multiprocessing as mp
def compute_lc(values):
(q, r1, r2, tratio, incl, ecc, per0) = values
# b.set_value_all('atm', value='blackbody')
# b.set_value_all('ld_mode', value='manual')
b['q'] = q
b['requiv@primary'] = r1 * b['value@sma@binary']
b['requiv@secondary'] = r2 * b['value@sma@binary']
b['teff@secondary'] = tratio * b['teff@primary'].value
b['incl@binary'] = incl
b['ecc'] = ecc
b['per0'] = per0
try:
b.run_compute()
return b['value@fluxes@model']
except:
return np.zeros(len(phases))
phases = np.linspace(-0.5, 0.5, 100)
b = phoebe.default_binary()
b.add_dataset('lc', compute_phases=phases)
def binary_star_mesh(star1_params,
star2_params,
binary_params,
observation_times,
use_blackbody_atm=False,
make_mesh_plots=True,
mesh_temp=False,
mesh_temp_cmap=None,
plot_name=None,
print_diagnostics=False,
par_compute=False,
num_par_processes=8,
num_triangles=1500):
"""Compute the light curve for a binary system
Keyword arguments:
star1_params -- Tuple of parameters for the primary star
star2_params -- Tuple of parameters for the secondary star
binary_params -- Tuple of parameters for the binary system configuration
observation_times -- Tuple of observation times,
with numpy array of MJDs in each band
(kp_MJDs, h_MJDs, mesh_MJDs) = observation_times
use_blackbody_atm -- Use blackbody atmosphere
instead of default Castelli & Kurucz (default False)
make_mesh_plots -- Make a mesh plot of the binary system (default False)
plot_name
print_diagnostics
par_compute
num_par_processes
"""
if par_compute:
# TODO: Need to implement parallelization correctly
phoebe.mpi_on(nprocs=num_par_processes)
else:
phoebe.mpi_off()
# Read in the stellar parameters of the binary components
(star1_mass, star1_rad, star1_teff, star1_logg, star1_mag_Kp, star1_mag_H,
star1_pblum_Kp, star1_pblum_H) = star1_params
(star2_mass, star2_rad, star2_teff, star2_logg, star2_mag_Kp, star2_mag_H,
star2_pblum_Kp, star2_pblum_H) = star2_params
# Read in the parameters of the binary system
(binary_period, binary_ecc, binary_inc, t0) = binary_params
err_out = (np.array([-1.]), np.array([-1.]))
# Check for high temp ck2004 atmosphere limits
if not use_blackbody_atm:
# log g = 3.5, high temp bounds (above 31e3 K)
if star1_teff > (31000 * u.K) and (4.0 > star1_logg > 3.5):
star1_teff_round = 30995.0 * u.K
if print_diagnostics:
print('Star 1 out of C&K 2004 grid')
print('star1_logg = {0:.4f}'.format(star1_logg))
print('Rounding down star1_teff')
print('{0:.4f} -> {1:.4f}'.format(star1_teff,
star1_teff_round))
star1_teff = star1_teff_round
if star2_teff > (31000 * u.K) and (4.0 > star2_logg > 3.5):
star2_teff_round = 30995.0 * u.K
if print_diagnostics:
print('Star 2 out of C&K 2004 grid')
print('star2_logg = {0:.4f}'.format(star2_logg))
print('Rounding down star2_teff')
print('{0:.4f} -> {1:.4f}'.format(star2_teff,
star2_teff_round))
star2_teff = star2_teff_round
# log g = 4.0, high temp bounds (above 40e3 K)
if star1_teff > (40000 * u.K) and (4.5 > star1_logg > 4.0):
star1_teff_round = 39995.0 * u.K
print('Star 1 out of C&K 2004 grid')
print('star1_logg = {0:.4f}'.format(star1_logg))
print('Rounding down star1_teff')
print('{0:.4f} -> {1:.4f}'.format(star1_teff, star1_teff_round))
star1_teff = star1_teff_round
if star2_teff > (40000 * u.K) and (4.0 > star2_logg > 3.50):
star2_teff_round = 39995.0 * u.K
print('Star 2 out of C&K 2004 grid')
print('star2_logg = {0:.4f}'.format(star2_logg))
print('Rounding down star2_teff')
print('{0:.4f} -> {1:.4f}'.format(star2_teff, star2_teff_round))
star2_teff = star2_teff_round
# Set up binary model
b = phoebe.default_binary()
## Set a default distance
b.set_value('distance', 10 * u.pc)
## Set period, semimajor axis, and mass ratio (q)
binary_sma = ((binary_period**2. * const.G * (star1_mass + star2_mass)) /
(4. * np.pi**2.))**(1. / 3.)
binary_q = star2_mass / star1_mass
if print_diagnostics:
print('\nBinary orbit checks')
print('Binary SMA: {0}'.format(binary_sma.to(u.AU)))
print('Binary Mass Ratio (q): {0}'.format(binary_q))
b.set_value('period@orbit', binary_period)
b.set_value('sma@binary@component', binary_sma)
b.set_value('q@binary@component', binary_q)
## Inclination
b.set_value('incl@orbit', binary_inc)
# Check for overflow
## Variables to help store the non-detached binary cases
star1_semidetached = False
star2_semidetached = False
star1_overflow = False
star2_overflow = False
## Get the max radii for both component stars
star1_rad_max = b.get_value('requiv_max@primary@component') * u.solRad
star2_rad_max = b.get_value('requiv_max@secondary@component') * u.solRad
## Check for semidetached cases
if print_diagnostics:
print('\nSemidetached checks')
print('Star 1: {0}'.format(
np.abs((star1_rad - star1_rad_max) / star1_rad_max)))
print('Star 2: {0}'.format(
np.abs((star2_rad - star2_rad_max) / star2_rad_max)))
semidet_cut = 0.001 # (within 0.1% of max radii)
semidet_cut = 0.015 # (within 1.5% of max radii)
if np.abs((star1_rad - star1_rad_max) / star1_rad_max) < semidet_cut:
star1_semidetached = True
if np.abs((star2_rad - star2_rad_max) / star2_rad_max) < semidet_cut:
star2_semidetached = True
## Check for overflow
if (star1_rad > star1_rad_max) and not star1_semidetached:
star1_overflow = True
if (star2_rad > star2_rad_max) and not star2_semidetached:
star2_overflow = True
### Check for if both stars are overflowing; which star overflows more?
### Choose that star to be overflowing more
if star1_overflow and star2_overflow:
if (star1_rad - star1_rad_max) >= (star2_rad - star2_rad_max):
star2_overflow = False
else:
star1_overflow = False
if print_diagnostics:
print('\nOverflow Checks')
print('Star 1 Semidetached: {0}'.format(star1_semidetached))
print('Star 2 Semidetached: {0}'.format(star2_semidetached))
print('Star 1 Overflow: {0}'.format(star1_overflow))
print('Star 2 Overflow: {0}'.format(star2_overflow))
# If star 2 is overflowing, have to re set up model:
# Calling this same binary_star_lc function again,
# with star 2 as primary and star 1 as secondary.
# Change t0 = t0 - per/2 to make sure phase is correct,
# wrt stars 1 and 2 being in same respective position
if star2_overflow and not star1_overflow:
redo_binary_params = (binary_period, binary_ecc, binary_inc,
t0 - (binary_period.to(u.d).value / 2.))
return binary_star_lc(star2_params,
star1_params,
redo_binary_params,
observation_times,
use_blackbody_atm=use_blackbody_atm,
make_mesh_plots=make_mesh_plots,
mesh_temp=mesh_temp,
mesh_temp_cmap=mesh_temp_cmap,
plot_name=plot_name,
print_diagnostics=print_diagnostics,
par_compute=par_compute,
num_par_processes=num_par_processes,
num_triangles=num_triangles)
## If none of these overflow cases, set variable to store if binary is detached
binary_detached = (not star1_semidetached) and \
(not star2_semidetached) and \
(not star1_overflow) and \
(not star2_overflow)
### Set non-zero eccentricity only if binary is detached
if binary_detached:
b.set_value('ecc@binary@component', binary_ecc)
else:
b.set_value('ecc@binary@component', 0.)
## Change set up for contact or semidetached cases
if star1_overflow or star2_overflow:
b = phoebe.default_binary(contact_binary=True)
### Reset all necessary binary properties for contact system
b.set_value('distance', 10 * u.pc)
b.set_value('period@orbit', binary_period)
b.set_value('sma@binary@component', binary_sma)
b.set_value('q@binary@component', binary_q)
b.set_value('incl@orbit', binary_inc)
if star1_semidetached and not star2_overflow:
b.add_constraint('semidetached', 'primary')
if star2_semidetached and not star1_overflow:
b.add_constraint('semidetached', 'secondary')
# Set up compute
if use_blackbody_atm:
b.add_compute('phoebe',
compute='detailed',
irrad_method='wilson',
atm='blackbody')
else:
b.add_compute('phoebe', compute='detailed', irrad_method='wilson')
# Set the parameters of the component stars of the system
## Primary
b.set_value('teff@primary@component', star1_teff)
# b.set_value('logg@primary@component', star1_logg)
if (not star1_semidetached) and (not star2_overflow):
b.set_value('requiv@primary@component', star1_rad)
## Secondary
b.set_value('teff@secondary@component', star2_teff)
# b.set_value('logg@secondary@component', star2_logg)
if (not star2_semidetached) and (not star1_overflow) and (
not star2_overflow):
try:
b.set_value('requiv@secondary@component', star2_rad)
except:
print('\nOverflow Checks')
print('Star 1 Semidetached: {0}'.format(star1_semidetached))
print('Star 2 Semidetached: {0}'.format(star2_semidetached))
print('Star 1 Overflow: {0}'.format(star1_overflow))
print('Star 2 Overflow: {0}'.format(star2_overflow))
print("Cannot set secondary radius: {0}".format(sys.exc_info()[0]))
return err_out
# Set the number of triangles in the mesh
# Detached stars
if len(b.filter('ntriangles@primary@detailed@compute')) == 1:
b.set_value('ntriangles@primary@detailed@compute', num_triangles)
if len(b.filter('ntriangles@secondary@detailed@compute')) == 1:
b.set_value('ntriangles@secondary@detailed@compute', num_triangles)
# Contact envelope
if len(b.filter('ntriangles@contact_envelope@detailed@compute')) == 1:
if print_diagnostics:
print('Setting number of triangles for contact envelope')
b.set_value('ntriangles@contact_envelope@detailed@compute',
num_triangles * 2.)
# Phase the observation times
## Read in observation times
(kp_MJDs, h_MJDs, mesh_MJDs) = observation_times
## Phase the observation times
kp_phased_days = (
(kp_MJDs - t0) % binary_period.to(u.d).value) / binary_period.to(
u.d).value
h_phased_days = ((h_MJDs - t0) %
binary_period.to(u.d).value) / binary_period.to(u.d).value
mesh_phased_days = (
(mesh_MJDs - t0) % binary_period.to(u.d).value) / binary_period.to(
u.d).value
# Add light curve datasets
## Kp
kp_phases_sorted_inds = np.argsort(kp_phased_days)
kp_model_times = (kp_phased_days) * binary_period.to(u.d).value
kp_model_times = kp_model_times[kp_phases_sorted_inds]
# b.add_dataset(phoebe.dataset.lc, time=kp_model_times,
# dataset='mod_lc_Kp', passband='Keck_NIRC2:Kp')
if use_blackbody_atm:
b.add_dataset(phoebe.dataset.lc,
time=kp_model_times,
dataset='mod_lc_Kp',
passband='Keck_NIRC2:Kp')
b.set_value('ld_mode@primary@mod_lc_Kp', 'manual')
b.set_value('ld_mode@secondary@mod_lc_Kp', 'manual')
b.set_value('ld_func@primary@mod_lc_Kp', 'logarithmic')
b.set_value('ld_func@secondary@mod_lc_Kp', 'logarithmic')
else:
b.add_dataset(phoebe.dataset.lc,
time=kp_model_times,
dataset='mod_lc_Kp',
passband='Keck_NIRC2:Kp')
## H
h_phases_sorted_inds = np.argsort(h_phased_days)
h_model_times = (h_phased_days) * binary_period.to(u.d).value
h_model_times = h_model_times[h_phases_sorted_inds]
# b.add_dataset(phoebe.dataset.lc, times=h_model_times,
# dataset='mod_lc_H', passband='Keck_NIRC2:H')
if use_blackbody_atm:
b.add_dataset(phoebe.dataset.lc,
times=h_model_times,
dataset='mod_lc_H',
passband='Keck_NIRC2:H')
b.set_value('ld_mode@primary@mod_lc_H', 'manual')
b.set_value('ld_mode@secondary@mod_lc_H', 'manual')
b.set_value('ld_func@primary@mod_lc_H', 'logarithmic')
b.set_value('ld_func@secondary@mod_lc_H', 'logarithmic')
else:
b.add_dataset(phoebe.dataset.lc,
times=h_model_times,
dataset='mod_lc_H',
passband='Keck_NIRC2:H')
# Add mesh dataset if making mesh plot
mesh_phases_sorted_inds = np.argsort(mesh_phased_days)
mesh_model_times = (mesh_phased_days) * binary_period.to(u.d).value
mesh_model_times = mesh_model_times[mesh_phases_sorted_inds]
if make_mesh_plots:
b.add_dataset('mesh', times=mesh_model_times, dataset='mod_mesh')
if mesh_temp:
b['columns@mesh'] = ['teffs', 'loggs']
# Set the passband luminosities for the stars
b.set_value('pblum_mode@mod_lc_Kp', 'decoupled')
b.set_value('pblum_mode@mod_lc_H', 'decoupled')
b.set_value('pblum@primary@mod_lc_Kp', star1_pblum_Kp)
b.set_value('pblum@primary@mod_lc_H', star1_pblum_H)
b.set_value('pblum@secondary@mod_lc_Kp', star2_pblum_Kp)
b.set_value('pblum@secondary@mod_lc_H', star2_pblum_H)
# Run compute
# if print_diagnostics:
# print("Trying inital compute run")
# b.run_compute(compute='detailed', model='run',
# progressbar=False)
try:
b.run_compute(compute='detailed', model='run', progressbar=False)
except:
if print_diagnostics:
print("Error during primary binary compute: {0}".format(
sys.exc_info()[0]))
return err_out
# Save out mesh plot
if make_mesh_plots:
## Plot Nerdery
plt.rc('font', family='serif')
plt.rc('font', serif='Computer Modern Roman')
plt.rc('text', usetex=True)
plt.rc('text.latex', preamble=r"\usepackage{gensymb}")
plt.rc('xtick', direction='in')
plt.rc('ytick', direction='in')
# plt.rc('xtick', top = True)
# plt.rc('ytick', right = True)
suffix_str = ''
if plot_name is not None:
suffix_str = '_' + plot_name
## Mesh plot
mesh_plot_out = []
if mesh_temp:
b['mod_mesh@model'].plot(
fc='teffs',
fcmap=mesh_temp_cmap,
ec='face',
animate=True,
save='./binary_mesh{0}.gif'.format(suffix_str),
save_kwargs={'writer': 'imagemagick'})
for (mesh_model_time,
mesh_index) in zip(mesh_model_times,
range(len(mesh_model_times))):
plt.clf()
new_fig = plt.figure()
(mesh_af_fig, mesh_plt_fig) = b['mod_mesh@model'].plot(
fig=new_fig,
time=mesh_model_time,
fc='teffs',
fcmap=mesh_temp_cmap,
ec='face',
save='./binary_mesh_{0}.pdf'.format(mesh_index))
mesh_plot_out.append(mesh_plt_fig)
plt.close(new_fig)
else:
b['mod_mesh@model'].plot(
animate=True,
save='./binary_mesh{0}.gif'.format(suffix_str),
save_kwargs={'writer': 'imagemagick'})
for mesh_model_time in mesh_model_times:
mesh_plot_out.append(b['mod_mesh@model'].plot(
time=mesh_model_time,
save='./binary_mesh.pdf'.format(suffix_str)))
# Get fluxes
## Kp
model_fluxes_Kp = np.array(
b['fluxes@lc@mod_lc_Kp@model'].value) * u.W / (u.m**2.)
model_mags_Kp = -2.5 * np.log10(model_fluxes_Kp / flux_ref_Kp) + 0.03
## H
model_fluxes_H = np.array(
b['fluxes@lc@mod_lc_H@model'].value) * u.W / (u.m**2.)
model_mags_H = -2.5 * np.log10(model_fluxes_H / flux_ref_H) + 0.03
if print_diagnostics:
print('\nFlux Checks')
print('Fluxes, Kp: {0}'.format(model_fluxes_Kp))
print('Mags, Kp: {0}'.format(model_mags_Kp))
print('Fluxes, H: {0}'.format(model_fluxes_H))
print('Mags, H: {0}'.format(model_mags_H))
if make_mesh_plots:
return (model_mags_Kp, model_mags_H, mesh_plot_out)
else:
return (model_mags_Kp, model_mags_H)
def binary_star_lc(star1_params, star2_params, binary_params, observation_times,
use_blackbody_atm=False,
use_compact_object=False,
make_mesh_plots=False, mesh_temp=False, mesh_temp_cmap=None,
plot_name=None,
print_diagnostics=False, par_compute=False, num_par_processes=8,
num_triangles=1500):
"""Compute the light curve for a binary system
Keyword arguments:
star1_params -- Tuple of parameters for the primary star
star2_params -- Tuple of parameters for the secondary star
binary_params -- Tuple of parameters for the binary system configuration
observation_times -- Tuple of observation times,
with numpy array of MJDs in each band and for the RVs
(kp_MJDs, h_MJDs, rv_MJDs) = observation_times
use_blackbody_atm -- Use blackbody atmosphere
instead of default Castelli & Kurucz (default False)
use_compact_object -- Set eclipse_method to 'only_horizon',
necessary for compact companions without eclipses (default False)
make_mesh_plots -- Make a mesh plot of the binary system (default False)
plot_name
print_diagnostics
par_compute
num_par_processes
"""
if par_compute:
# TODO: Need to implement parallelization correctly
phoebe.mpi_on(nprocs=num_par_processes)
else:
phoebe.mpi_off()
# Read in the stellar parameters of the binary components
(star1_mass, star1_rad, star1_teff, star1_logg,
[star1_mag_Kp, star1_mag_H],
[star1_pblum_Kp, star1_pblum_H]) = star1_params
(star2_mass, star2_rad, star2_teff, star2_logg,
[star2_mag_Kp, star2_mag_H],
[star2_pblum_Kp, star2_pblum_H]) = star2_params
# Read in the parameters of the binary system
(binary_period, binary_ecc, binary_inc, t0) = binary_params
err_out = (np.array([-1.]), np.array([-1.]),
np.array([-1.]), np.array([-1.]))
if make_mesh_plots:
err_out = (np.array([-1.]), np.array([-1.]),
np.array([-1.]), np.array([-1.]),
np.array([-1.]))
# Check for high temp ck2004 atmosphere limits
if not use_blackbody_atm:
# log g = 3.5, high temp bounds (above 31e3 K)
if star1_teff > (31000 * u.K) and (4.0 > star1_logg > 3.5):
star1_teff_round = 30995.0 * u.K
if print_diagnostics:
print('Star 1 out of C&K 2004 grid')
print('star1_logg = {0:.4f}'.format(star1_logg))
print('Rounding down star1_teff')
print('{0:.4f} -> {1:.4f}'.format(star1_teff, star1_teff_round))
star1_teff = star1_teff_round
if star2_teff > (31000 * u.K) and (4.0 > star2_logg > 3.5):
star2_teff_round = 30995.0 * u.K
if print_diagnostics:
print('Star 2 out of C&K 2004 grid')
print('star2_logg = {0:.4f}'.format(star2_logg))
print('Rounding down star2_teff')
print('{0:.4f} -> {1:.4f}'.format(star2_teff, star2_teff_round))
star2_teff = star2_teff_round
# log g = 4.0, high temp bounds (above 40e3 K)
if star1_teff > (40000 * u.K) and (4.5 > star1_logg > 4.0):
star1_teff_round = 39995.0 * u.K
print('Star 1 out of C&K 2004 grid')
print('star1_logg = {0:.4f}'.format(star1_logg))
print('Rounding down star1_teff')
print('{0:.4f} -> {1:.4f}'.format(star1_teff, star1_teff_round))
star1_teff = star1_teff_round
if star2_teff > (40000 * u.K) and (4.0 > star2_logg > 3.50):
star2_teff_round = 39995.0 * u.K
print('Star 2 out of C&K 2004 grid')
print('star2_logg = {0:.4f}'.format(star2_logg))
print('Rounding down star2_teff')
print('{0:.4f} -> {1:.4f}'.format(star2_teff, star2_teff_round))
star2_teff = star2_teff_round
# Set up binary model
b = phoebe.default_binary()
## Set a default distance
b.set_value('distance', 10 * u.pc)
## Set period, semimajor axis, and mass ratio (q)
binary_sma = ((binary_period**2. * const.G * (star1_mass + star2_mass)) / (4. * np.pi**2.))**(1./3.)
binary_q = star2_mass / star1_mass
if print_diagnostics:
print('\nBinary orbit checks')
print('Binary SMA: {0}'.format(binary_sma.to(u.AU)))
print('Binary Mass Ratio (q): {0}'.format(binary_q))
b.set_value('period@orbit', binary_period)
b.set_value('sma@binary@component', binary_sma)
b.set_value('q@binary@component', binary_q)
## Inclination
b.set_value('incl@orbit', binary_inc)
# Check for overflow
## Variables to help store the non-detached binary cases
star1_semidetached = False
star2_semidetached = False
star1_overflow = False
star2_overflow = False
## Get the max radii for both component stars
star1_rad_max = b.get_value('requiv_max@primary@component') * u.solRad
star2_rad_max = b.get_value('requiv_max@secondary@component') * u.solRad
## Check for semidetached cases
if print_diagnostics:
print('\nSemidetached checks')
print('Star 1: {0}'.format(np.abs((star1_rad - star1_rad_max) / star1_rad_max)))
print('Star 2: {0}'.format(np.abs((star2_rad - star2_rad_max) / star2_rad_max)))
semidet_cut = 0.001 # (within 0.1% of max radii)
semidet_cut = 0.015 # (within 1.5% of max radii)
if np.abs((star1_rad - star1_rad_max) / star1_rad_max) < semidet_cut:
star1_semidetached = True
if np.abs((star2_rad - star2_rad_max) / star2_rad_max) < semidet_cut:
star2_semidetached = True
## Check for overflow
if (star1_rad > star1_rad_max) and not star1_semidetached:
star1_overflow = True
if (star2_rad > star2_rad_max) and not star2_semidetached:
star2_overflow = True
### Check for if both stars are overflowing; which star overflows more?
### Choose that star to be overflowing more
if star1_overflow and star2_overflow:
if (star1_rad - star1_rad_max) >= (star2_rad - star2_rad_max):
star2_overflow = False
else:
star1_overflow = False
if print_diagnostics:
print('\nOverflow Checks')
print('Star 1 Semidetached: {0}'.format(star1_semidetached))
print('Star 2 Semidetached: {0}'.format(star2_semidetached))
print('Star 1 Overflow: {0}'.format(star1_overflow))
print('Star 2 Overflow: {0}'.format(star2_overflow))
# If star 2 is overflowing, have to re set up model:
# Calling this same binary_star_lc function again,
# with star 2 as primary and star 1 as secondary.
# Change t0 = t0 - per/2 to make sure phase is correct,
# wrt stars 1 and 2 being in same respective position
if star2_overflow and not star1_overflow:
redo_binary_params = (binary_period, binary_ecc, binary_inc,
t0 - (binary_period.to(u.d).value/2.))
return binary_star_lc(star2_params, star1_params,
redo_binary_params,
observation_times,
use_blackbody_atm=use_blackbody_atm,
make_mesh_plots=make_mesh_plots,
mesh_temp=mesh_temp, mesh_temp_cmap=mesh_temp_cmap,
plot_name=plot_name,
print_diagnostics=print_diagnostics,
par_compute=par_compute, num_par_processes=num_par_processes,
num_triangles=num_triangles)
## If none of these overflow cases, set variable to store if binary is detached
binary_detached = (not star1_semidetached) and \
(not star2_semidetached) and \
(not star1_overflow) and \
(not star2_overflow)
### Set non-zero eccentricity only if binary is detached
if binary_detached:
b.set_value('ecc@binary@component', binary_ecc)
else:
b.set_value('ecc@binary@component', 0.)
## Change set up for contact or semidetached cases
if star1_overflow or star2_overflow:
b = phoebe.default_binary(contact_binary=True)
### Reset all necessary binary properties for contact system
b.set_value('distance', 10 * u.pc)
b.set_value('period@orbit', binary_period)
b.set_value('sma@binary@component', binary_sma)
b.set_value('q@binary@component', binary_q)
b.set_value('incl@orbit', binary_inc)
if star1_semidetached and not star2_overflow:
b.add_constraint('semidetached', 'primary')
if star2_semidetached and not star1_overflow:
b.add_constraint('semidetached', 'secondary')
# Set up compute
if use_blackbody_atm:
b.add_compute('phoebe', compute='detailed',
irrad_method='wilson', atm='blackbody')
b.set_value('atm@primary@detailed', 'blackbody')
b.set_value('atm@secondary@detailed', 'blackbody')
else:
b.add_compute('phoebe', compute='detailed', irrad_method='wilson')
# Set the parameters of the component stars of the system
## Primary
b.set_value('teff@primary@component', star1_teff)
# b.set_value('logg@primary@component', star1_logg)
if (not star1_semidetached) and (not star2_overflow):
b.set_value('requiv@primary@component', star1_rad)
## Secondary
b.set_value('teff@secondary@component', star2_teff)
# b.set_value('logg@secondary@component', star2_logg)
if (not star2_semidetached) and (not star1_overflow) and (not star2_overflow):
try:
b.set_value('requiv@secondary@component', star2_rad)
except:
print('\nOverflow Checks')
print('Star 1 Semidetached: {0}'.format(star1_semidetached))
print('Star 2 Semidetached: {0}'.format(star2_semidetached))
print('Star 1 Overflow: {0}'.format(star1_overflow))
print('Star 2 Overflow: {0}'.format(star2_overflow))
print("Cannot set secondary radius: {0}".format(sys.exc_info()[0]))
return err_out
# Set the number of triangles in the mesh
# Detached stars
if len(b.filter('ntriangles@primary@detailed@compute')) == 1:
b.set_value('ntriangles@primary@detailed@compute', num_triangles)
if len(b.filter('ntriangles@secondary@detailed@compute')) == 1:
b.set_value('ntriangles@secondary@detailed@compute', num_triangles)
# Contact envelope
if len(b.filter('ntriangles@contact_envelope@detailed@compute')) == 1:
if print_diagnostics:
print('Setting number of triangles for contact envelope')
b.set_value('ntriangles@contact_envelope@detailed@compute',
num_triangles * 2.)
# Phase the observation times
## Read in observation times
(kp_MJDs, h_MJDs, rv_MJDs) = observation_times
## Phase the observation times
kp_phased_days = ((kp_MJDs - t0) % binary_period.to(u.d).value) / binary_period.to(u.d).value
h_phased_days = ((h_MJDs - t0) % binary_period.to(u.d).value) / binary_period.to(u.d).value
rv_phased_days = ((rv_MJDs - t0) % binary_period.to(u.d).value) / binary_period.to(u.d).value
# Add light curve datasets
if use_blackbody_atm:
b.set_value_all('ld_mode_bol', 'manual')
b.set_value_all('ld_func_bol', 'linear')
b.set_value_all('ld_coeffs_bol', [0.0])
# Check for compact companion
if use_compact_object:
b.set_value('irrad_method@detailed', 'none')
## Kp
kp_phases_sorted_inds = np.argsort(kp_phased_days)
kp_model_times = (kp_phased_days) * binary_period.to(u.d).value
kp_model_times = kp_model_times[kp_phases_sorted_inds]
if use_blackbody_atm:
b.add_dataset(phoebe.dataset.lc, time=kp_model_times,
dataset='mod_lc_Kp', passband='Keck_NIRC2:Kp')
b.set_value_all('ld_mode@mod_lc_Kp', 'manual')
b.set_value_all('ld_func@mod_lc_Kp', 'linear')
b.set_value_all('ld_coeffs@mod_lc_Kp', [0.0])
else:
b.add_dataset(phoebe.dataset.lc, time=kp_model_times,
dataset='mod_lc_Kp', passband='Keck_NIRC2:Kp')
## H
h_phases_sorted_inds = np.argsort(h_phased_days)
h_model_times = (h_phased_days) * binary_period.to(u.d).value
h_model_times = h_model_times[h_phases_sorted_inds]
if use_blackbody_atm:
b.add_dataset(phoebe.dataset.lc, times=h_model_times,
dataset='mod_lc_H', passband='Keck_NIRC2:H')
b.set_value_all('ld_mode@mod_lc_H', 'manual')
b.set_value_all('ld_func@mod_lc_H', 'linear')
b.set_value_all('ld_coeffs@mod_lc_H', [0.0])
else:
b.add_dataset(phoebe.dataset.lc, times=h_model_times,
dataset='mod_lc_H', passband='Keck_NIRC2:H')
## RV
rv_phases_sorted_inds = np.argsort(rv_phased_days)
rv_model_times = (rv_phased_days) * binary_period.to(u.d).value
rv_model_times = rv_model_times[rv_phases_sorted_inds]
if use_blackbody_atm:
b.add_dataset(phoebe.dataset.rv, time=rv_model_times,
dataset='mod_rv', passband='Keck_NIRC2:Kp')
b.set_value_all('ld_mode@mod_rv', 'manual')
b.set_value_all('ld_func@mod_rv', 'linear')
b.set_value_all('ld_coeffs@mod_rv', [0.0])
else:
b.add_dataset(phoebe.dataset.rv, time=rv_model_times,
dataset='mod_rv', passband='Keck_NIRC2:Kp')
# Add mesh dataset if making mesh plot
if make_mesh_plots:
b.add_dataset('mesh', times=[(binary_period/4.).to(u.d).value],
dataset='mod_mesh')
if mesh_temp:
b['columns@mesh'] = ['teffs', 'loggs', 'areas',
'*@mod_lc_Kp', '*@mod_lc_H']
# Set the passband luminosities for the stars
b.set_value('pblum_mode@mod_lc_Kp', 'decoupled')
b.set_value('pblum_mode@mod_lc_H', 'decoupled')
b.set_value('pblum@primary@mod_lc_Kp', star1_pblum_Kp)
b.set_value('pblum@primary@mod_lc_H', star1_pblum_H)
b.set_value('pblum@secondary@mod_lc_Kp', star2_pblum_Kp)
b.set_value('pblum@secondary@mod_lc_H', star2_pblum_H)
# Run compute
# Determine eclipse method
if use_compact_object:
eclipse_method = 'only_horizon'
else:
eclipse_method = 'native'
if print_diagnostics:
print("Trying inital compute run")
b.run_compute(compute='detailed', model='run',
progressbar=False, eclipse_method=eclipse_method)
else:
try:
b.run_compute(compute='detailed', model='run',
progressbar=False, eclipse_method=eclipse_method)
except:
if print_diagnostics:
print("Error during primary binary compute: {0}".format(sys.exc_info()[0]))
return err_out
# Save out mesh plot
if make_mesh_plots:
## Plot Nerdery
plt.rc('font', family='serif')
plt.rc('font', serif='Computer Modern Roman')
plt.rc('text', usetex=True)
plt.rc('text.latex', preamble=r"\usepackage{gensymb}")
plt.rc('xtick', direction = 'in')
plt.rc('ytick', direction = 'in')
# plt.rc('xtick', top = True)
# plt.rc('ytick', right = True)
suffix_str = ''
if plot_name is not None:
suffix_str = '_' + plot_name
## Mesh plot
if mesh_temp:
mesh_plot_out = b['mod_mesh@model'].plot(save='./binary_mesh{0}.pdf'.format(suffix_str),
fc='teffs',
fcmap=mesh_temp_cmap,
ec='none')
# print(mesh_plot_out.axs)
# Extract and output mesh quantities
mesh_quant_names = ['teffs', 'loggs', 'areas', 'abs_intensities']
mesh_quant_do_filt = [False, False, False, True]
mesh_quant_units = [u.K, 1.0, u.solRad**2, u.W / (u.m**3)]
mesh_quant_filts = ['mod_lc_Kp', 'mod_lc_H']
mesh_quants_pri = {}
mesh_quants_sec = {}
for (quant, do_filt,
quant_unit) in zip(mesh_quant_names, mesh_quant_do_filt,
mesh_quant_units):
if do_filt:
for filt in mesh_quant_filts:
quant_pri = b['{0}@primary@{1}'.format(quant, filt)].value *\
quant_unit
quant_sec = b['{0}@secondary@{1}'.format(quant, filt)].value *\
quant_unit
mesh_quants_pri['{0}_{1}'.format(quant, filt)] = quant_pri
mesh_quants_sec['{0}_{1}'.format(quant, filt)] = quant_sec
else:
quant_pri = b['{0}@primary'.format(quant)].value * quant_unit
quant_sec = b['{0}@secondary'.format(quant)].value * quant_unit
mesh_quants_pri[quant] = quant_pri
mesh_quants_sec[quant] = quant_sec
# Construct mesh tables for each star and output
mesh_pri_table = Table(mesh_quants_pri)
mesh_pri_table.sort(['teffs'], reverse=True)
with open('mesh_pri.txt', 'w') as out_file:
for line in mesh_pri_table.pformat_all():
out_file.write(line + '\n')
mesh_pri_table.write('mesh_pri.h5', format='hdf5',
path='data', serialize_meta=True,
overwrite=True)
mesh_pri_table.write('mesh_pri.fits', format='fits',
overwrite=True)
mesh_sec_table = Table(mesh_quants_sec)
mesh_sec_table.sort(['teffs'], reverse=True)
with open('mesh_sec.txt', 'w') as out_file:
for line in mesh_sec_table.pformat_all():
out_file.write(line + '\n')
mesh_sec_table.write('mesh_sec.h5', format='hdf5',
path='data', serialize_meta=True,
overwrite=True)
mesh_sec_table.write('mesh_sec.fits', format='fits',
overwrite=True)
else:
mesh_plot_out = b['mod_mesh@model'].plot(save='./binary_mesh{0}.pdf'.format(suffix_str))
# Get fluxes
## Kp
model_fluxes_Kp = np.array(b['fluxes@lc@mod_lc_Kp@model'].value) * u.W / (u.m**2.)
model_mags_Kp = -2.5 * np.log10(model_fluxes_Kp / flux_ref_Kp) + 0.03
## H
model_fluxes_H = np.array(b['fluxes@lc@mod_lc_H@model'].value) * u.W / (u.m**2.)
model_mags_H = -2.5 * np.log10(model_fluxes_H / flux_ref_H) + 0.03
# Get RVs
model_RVs_pri = np.array(b['rvs@primary@run@rv@model'].value) * u.km / u.s
model_RVs_sec = np.array(b['rvs@secondary@run@rv@model'].value) * u.km / u.s
if print_diagnostics:
print("\nFlux Checks")
print("Fluxes, Kp: {0}".format(model_fluxes_Kp))
print("Mags, Kp: {0}".format(model_mags_Kp))
print("Fluxes, H: {0}".format(model_fluxes_H))
print("Mags, H: {0}".format(model_mags_H))
print("\nRV Checks")
print("RVs, Primary: {0}".format(model_RVs_pri))
print("RVs, Secondary: {0}".format(model_RVs_sec))
if make_mesh_plots:
return (model_mags_Kp, model_mags_H,
model_RVs_pri, model_RVs_sec,
mesh_plot_out)
else:
return (model_mags_Kp, model_mags_H,
model_RVs_pri, model_RVs_sec)
def binary_star_lc(star1_params,
star2_params,
binary_params,
observation_times,
use_blackbody_atm=False,
make_mesh_plots=False,
plot_name=None,
print_diagnostics=False,
par_compute=False,
num_par_processes=8,
num_triangles=1500):
"""Compute the light curve for a binary system
Keyword arguments:
star1_params -- Tuple of parameters for the primary star
star2_params -- Tuple of parameters for the secondary star
binary_params -- Tuple of parameters for the binary system configuration
observation_times -- Tuple of observation times,
with numpy array of MJDs in each band
(kp_MJDs, h_MJDs) = observation_times
use_blackbody_atm -- Use blackbody atmosphere
instead of default Castelli & Kurucz (default False)
make_mesh_plots -- Make a mesh plot of the binary system (default False)
plot_name
print_diagnostics
par_compute
num_par_processes
"""
if par_compute:
# TODO: Need to implement parallelization correctly
phoebe.mpi_on(nprocs=num_par_processes)
else:
phoebe.mpi_off()
# Read in the stellar parameters of the binary components
(star1_mass, star1_rad, star1_teff, star1_mag_Kp,
star1_mag_H) = star1_params
(star2_mass, star2_rad, star2_teff, star2_mag_Kp,
star2_mag_H) = star2_params
# Read in the parameters of the binary system
(binary_period, binary_ecc, binary_inc, t0) = binary_params
err_out = (np.array([-1.]), np.array([-1.]))
# Set up binary model
b = phoebe.default_binary()
## Set period, semimajor axis, and mass ratio (q)
binary_sma = ((binary_period**2. * const.G * (star1_mass + star2_mass)) /
(4. * np.pi**2.))**(1. / 3.)
binary_q = star2_mass / star1_mass
b.set_value('period@orbit', binary_period)
b.set_value('sma@binary@component', binary_sma)
b.set_value('q@binary@component', binary_q)
## Inclination
b.set_value('incl@orbit', binary_inc)
# Check for overflow
## Variables to help store the non-detached binary cases
star1_semidetached = False
star2_semidetached = False
star1_overflow = False
star2_overflow = False
## Get the max radii for both component stars
star1_rad_max = b.get_value('requiv_max@primary@component') * u.solRad
star2_rad_max = b.get_value('requiv_max@secondary@component') * u.solRad
## Check for semidetached cases
if print_diagnostics:
print('\nSemidetached checks')
print(np.abs((star1_rad - star1_rad_max) / star1_rad_max))
print(np.abs((star2_rad - star2_rad_max) / star2_rad_max))
semidet_cut = 0.001 # (within 0.1% of max radii)
semidet_cut = 0.015 # (within 1.5% of max radii)
if np.abs((star1_rad - star1_rad_max) / star1_rad_max) < semidet_cut:
star1_semidetached = True
if np.abs((star2_rad - star2_rad_max) / star2_rad_max) < semidet_cut:
star2_semidetached = True
## Check for overflow
if (star1_rad > star1_rad_max) and not star1_semidetached:
star1_overflow = True
if (star2_rad > star2_rad_max) and not star2_semidetached:
star2_overflow = True
### Check for if both stars are overflowing; which star overflows more?
### Choose that star to be overflowing more
if star1_overflow and star2_overflow:
if (star1_rad - star1_rad_max) >= (star2_rad - star2_rad_max):
star2_overflow = False
else:
star1_overflow = False
if print_diagnostics:
print('\nOverflow Checks')
print(star1_semidetached)
print(star2_semidetached)
print(star1_overflow)
print(star2_overflow)
## If none of these overflow cases, set variable to store if binary is detached
binary_detached = (not star1_semidetached) and (
not star2_semidetached) and (not star1_overflow) and (
not star2_overflow)
### Set non-zero eccentricity only if binary is detached
if binary_detached:
b.set_value('ecc@binary@component', binary_ecc)
else:
b.set_value('ecc@binary@component', 0.)
## Change set up for contact or semidetached cases
if star1_overflow or star2_overflow:
b = phoebe.default_binary(contact_binary=True)
b.set_value('period@orbit', binary_period)
b.set_value('sma@binary@component', binary_sma)
b.set_value('q@binary@component', binary_q)
b.set_value('incl@orbit', binary_inc)
if star1_semidetached and not star2_overflow:
b.add_constraint('semidetached', 'primary')
if star2_semidetached and not star1_overflow:
b.add_constraint('semidetached', 'secondary')
# Set up compute
if use_blackbody_atm:
b.add_compute('phoebe',
compute='detailed',
irrad_method='wilson',
atm='blackbody')
else:
b.add_compute('phoebe', compute='detailed', irrad_method='wilson')
# Set the parameters of the component stars of the system
## Primary
b.set_value('teff@primary@component', star1_teff)
if (not star1_semidetached) and (not star2_overflow):
b.set_value('requiv@primary@component', star1_rad)
## Secondary
b.set_value('teff@secondary@component', star2_teff)
if (not star2_semidetached) and (not star1_overflow):
b.set_value('requiv@secondary@component', star2_rad)
# Set the number of triangles in the mesh
b.set_value('ntriangles@primary@detailed@compute', num_triangles)
b.set_value('ntriangles@secondary@detailed@compute', num_triangles)
# Phase the observation times
## Read in observation times
(kp_MJDs, h_MJDs) = observation_times
## Phase the observation times
kp_phased_days = (
(kp_MJDs - t0) % binary_period.to(u.d).value) / binary_period.to(
u.d).value
h_phased_days = ((h_MJDs - t0) %
binary_period.to(u.d).value) / binary_period.to(u.d).value
# Add light curve datasets
## Kp
kp_phases_sorted_inds = np.argsort(kp_phased_days)
kp_model_times = (kp_phased_days) * binary_period.to(u.d).value
kp_model_times = kp_model_times[kp_phases_sorted_inds]
if use_blackbody_atm:
b.add_dataset(phoebe.dataset.lc,
time=kp_model_times,
dataset='mod_lc_Kp',
passband='Keck_NIRC2:Kp',
ld_func='linear',
ld_coeffs=[0.0])
else:
b.add_dataset(phoebe.dataset.lc,
time=kp_model_times,
dataset='mod_lc_Kp',
passband='Keck_NIRC2:Kp')
## H
h_phases_sorted_inds = np.argsort(h_phased_days)
h_model_times = (h_phased_days) * binary_period.to(u.d).value
h_model_times = h_model_times[h_phases_sorted_inds]
if use_blackbody_atm:
b.add_dataset(phoebe.dataset.lc,
times=h_model_times,
dataset='mod_lc_H',
passband='Keck_NIRC2:H',
ld_func='linear',
ld_coeffs=[0.0])
else:
b.add_dataset(phoebe.dataset.lc,
times=h_model_times,
dataset='mod_lc_H',
passband='Keck_NIRC2:H')
# Add mesh dataset if making mesh plot
if make_mesh_plots:
b.add_dataset('mesh', times=[binary_period / 4.], dataset='mod_mesh')
# Run compute
# b.run_compute(compute='detailed', model='run')
try:
b.run_compute(compute='detailed', model='run')
except:
if print_diagnostics:
print("Error during primary binary compute: {0}".format(
sys.exc_info()[0]))
return err_out
# Save out mesh plot
if make_mesh_plots:
## Plot Nerdery
plt.rc('font', family='serif')
plt.rc('font', serif='Computer Modern Roman')
plt.rc('text', usetex=True)
plt.rc('text.latex', preamble=r"\usepackage{gensymb}")
plt.rc('xtick', direction='in')
plt.rc('ytick', direction='in')
plt.rc('xtick', top=True)
plt.rc('ytick', right=True)
suffix_str = ''
if plot_name is not None:
suffix_str = '_' + plot_name
## Mesh plot
b['mod_mesh@model'].plot(
save='./binary_mesh{0}.pdf'.format(suffix_str))
# Get fluxes
## Kp
model_fluxes_Kp = np.array(
b['fluxes@lc@mod_lc_Kp@model'].value) * u.solLum / (
4 * np.pi * u.m**2) # * u.W / (u.m**2.)
model_mags_Kp = -2.5 * np.log10(model_fluxes_Kp / flux_ref_Kp) + 0.03
## H
model_fluxes_H = np.array(
b['fluxes@lc@mod_lc_H@model'].value) * u.solLum / (
4 * np.pi * u.m**2) # * u.W / (u.m**2.)
model_mags_H = -2.5 * np.log10(model_fluxes_H / flux_ref_H) + 0.03
return (model_mags_Kp, model_mags_H)