def get_potential(log_M_h, log_r_s, log_M_n, log_a):
mw_potential = gp.CCompositePotential()
mw_potential['bulge'] = gp.HernquistPotential(m=5E9, c=1., units=galactic)
mw_potential['disk'] = gp.MiyamotoNagaiPotential(m=6.8E10 * u.Msun,
a=3 * u.kpc,
b=280 * u.pc,
units=galactic)
mw_potential['nucl'] = gp.HernquistPotential(m=np.exp(log_M_n),
c=np.exp(log_a) * u.pc,
units=galactic)
mw_potential['halo'] = gp.NFWPotential(m=np.exp(log_M_h),
r_s=np.exp(log_r_s),
units=galactic)
return mw_potential
def test_hernquist():
nmax = 6
lmax = 2
M = 1E10
r_s = 3.5
cos_coeff = np.zeros((nmax+1,lmax+1,lmax+1))
sin_coeff = np.zeros((nmax+1,lmax+1,lmax+1))
cos_coeff[0,0,0] = 1.
scf_potential = _bfe_class.SCFPotential(m=M, r_s=r_s,
Snlm=cos_coeff, Tnlm=sin_coeff,
units=galactic)
# scf_potential = HackPotential(m=10., units=galactic)
nbins = 128
rr = np.linspace(0.1,10.,nbins)
xyz = np.zeros((3,nbins))
xyz[0] = rr * np.cos(np.pi/4.) * np.sin(np.pi/4.)
xyz[1] = rr * np.sin(np.pi/4.) * np.sin(np.pi/4.)
xyz[2] = rr * np.cos(np.pi/4.)
hernquist = gp.HernquistPotential(m=M, c=r_s, units=galactic)
bfe_pot = scf_potential.energy(xyz).value
true_pot = hernquist.energy(xyz).value
np.testing.assert_allclose(bfe_pot, true_pot)
bfe_grad = scf_potential.gradient(xyz).value
true_grad = hernquist.gradient(xyz).value
np.testing.assert_allclose(bfe_grad, true_grad)
def get_potential(total_mass = 130.0075e10*u.Msun,\
r_scale = 18.927757889861788 * u.kpc,\
mw_conc = 9.39):
a_term = math.sqrt(2 * (math.log(1 + mw_conc) - mw_conc / (1 + mw_conc)))
mw_a = r_scale * a_term
return gp.HernquistPotential(m=total_mass, c=mw_a, units=galactic)
def test_staeckel_fudge_delta():
import galpy.potential as galpy_pot
from galpy.actionAngle import estimateDeltaStaeckel
ro = 8.1 * u.kpc
vo = 229 * u.km / u.s
paired_potentials = []
# Miyamoto-Nagai
potential = gp.MiyamotoNagaiPotential(m=6e10 * u.Msun,
a=3 * u.kpc,
b=0.3 * u.kpc,
units=galactic)
amp = (G * potential.parameters['m']).to_value(vo**2 * ro)
a = potential.parameters['a'].to_value(ro)
b = potential.parameters['b'].to_value(ro)
galpy_potential = galpy_pot.MiyamotoNagaiPotential(amp=amp,
a=a,
b=b,
ro=ro,
vo=vo)
paired_potentials.append((potential, galpy_potential))
# Hernquist
potential = gp.HernquistPotential(m=6e10 * u.Msun,
c=0.3 * u.kpc,
units=galactic)
amp = (G * potential.parameters['m']).to_value(vo**2 * ro)
a = potential.parameters['c'].to_value(ro)
galpy_potential = galpy_pot.HernquistPotential(amp=amp, a=a, ro=ro, vo=vo)
paired_potentials.append((potential, galpy_potential))
# NFW
potential = gp.NFWPotential(m=6e11 * u.Msun,
r_s=15.6 * u.kpc,
units=galactic)
amp = (G * potential.parameters['m']).to_value(vo**2 * ro)
a = potential.parameters['r_s'].to_value(ro)
galpy_potential = galpy_pot.NFWPotential(amp=amp, a=a, ro=ro, vo=vo)
paired_potentials.append((potential, galpy_potential))
# TEST:
N = 1024
rnd = np.random.default_rng(42)
w = PhaseSpacePosition(pos=rnd.uniform(-10, 10, size=(3, N)) * u.kpc,
vel=rnd.uniform(-100, 100, size=(3, N)) * u.km /
u.s)
R = w.cylindrical.rho.to_value(ro)
z = w.z.to_value(ro)
for p, galpy_p in paired_potentials:
galpy_deltas = estimateDeltaStaeckel(galpy_p, R, z, no_median=True)
gala_deltas = get_staeckel_fudge_delta(p, w).value
print(p, np.allclose(gala_deltas, galpy_deltas))
assert np.allclose(gala_deltas, galpy_deltas, atol=1e-6)
def integrate(w0,\
pot=gp.HernquistPotential(m=130.0075e10*u.Msun,c = 32.089, units=galactic),\
timestep = -10.67,\
ntimesteps = 250,\
verbose=False):
# TODO
orbit = None # define the orbit object in this scope
if verbose:
print('integrating ... ')
start_time = time.time()
orbit = gp.Hamiltonian(pot).integrate_orbit(w0,
dt=timestep,
n_steps=ntimesteps)
orbit_time = time.time() - start_time
print('done integrating')
print('Length of integration: %1.3f' % orbit_time)
else:
orbit = gp.Hamiltonian(pot).integrate_orbit(w0,
dt=timestep,
n_steps=ntimesteps)
return orbit, pot
a=1.9746 * 5 * u.kpc,
b=1 * u.kpc,
units=galactic)
pot['disk2'] = gp.MiyamotoNagaiPotential(m=10E10 * -1.2756 * u.Msun,
a=4.2333 * 5 * u.kpc,
b=1 * u.kpc,
units=galactic)
pot['disk3'] = gp.MiyamotoNagaiPotential(m=10E10 * 0.2153 * u.Msun,
a=0.6354 * 5 * u.kpc,
b=1 * u.kpc,
units=galactic)
pot['bulge'] = gp.HernquistPotential(m=3e10 * u.Msun,
c=0.5 * u.kpc,
units=galactic)
## Make grid (0.1 kpc resolution) for mock image
mock_image = np.zeros((61, 201))
## Calculate densities along line of sight in each x-z bin
temp_index = np.indices((1, 201, 1), dtype=float)
temp_index[1] = temp_index[1] / 2. - 50
# Not sure how to get properly shaped array of output from pot.density, hence for-loops
# Only run this once!!
for xind in range(0, 201):
for zind in range(0, 61):
xtemp = xind / 2. - 50
def hernquist_gradient(xyz, M, r_s):
import gala.potential as gp
p = gp.HernquistPotential(m=M, c=r_s,
units=[u.kpc, u.Myr, u.Msun, u.radian])
return p.gradient(xyz).value
Omega = ConfigItem(40., "Bar pattern speed [km/s/kpc]")
bar_mass = ConfigItem(1E10, "Bar mass [Msun]")
# TODO: add other tunable parameters once I decide on the potential...
# ==============================================================================
# Define the potential model up to the bar component
potential_no_bar = gp.CCompositePotential()
potential_no_bar['disk'] = gp.MiyamotoNagaiPotential(m=5E10 * u.Msun,
a=3 * u.kpc,
b=280 * u.pc,
units=galactic)
potential_no_bar['spheroid'] = gp.HernquistPotential(m=4E9 * u.Msun,
c=0.6 * u.kpc,
units=galactic)
potential_no_bar['halo'] = gp.NFWPotential(m=6E11,
r_s=18 * u.kpc,
units=galactic)
def get_hamiltonian(config_file=None):
c = Config()
c.load(config_file)
pot = potential_no_bar.copy()
pot['bar'] = get_bar_potential(config_file)
Om = [0., 0., c.Omega] * u.km / u.s / u.kpc
frame = gp.ConstantRotatingFrame(Omega=Om, units=galactic)
def integrate_dyn_fric(w0,\
sat_mass = 1e8,\
pot=gp.HernquistPotential(m=130.0075e10*u.Msun,c = 32.089, units=galactic),\
scale_radius = 18.927757889861788,\
timestep = -10.67,\
ntimesteps = 250,\
verbose=False):
def F_dyn_fric(t, w, msat, rs):
G_gal = 4.49850215e-12 # gravitational constant in galactic units (kpc^3 Msun^-1 Myr^-2)
accdf = 0.0
q = w[0:3]
p = w[3:6]
verf = np.vectorize(math.erf)
absr = np.linalg.norm(q, axis=0)
absv = np.linalg.norm(p, axis=0)
loglambda = np.maximum(0, np.log(absr / 3 / 1.6))
rhoh = pot.density(q).value
normalized_r = absr / rs
# 0.2199 kpc / Myr = 215 km/s
sigma = 0.2199 * (1.4393 * normalized_r**0.354 /
(1 + 1.1756 * normalized_r**0.725))
chand_x = absv / math.sqrt(2) / sigma
# k is the part of the equation with the erf and exp components
k = verf(chand_x) - 2 * chand_x * np.exp(
-np.square(chand_x)) / math.sqrt(math.pi)
accdf = (4 * math.pi * G_gal * G_gal * msat * loglambda * rhoh /
absv**3) * k * p
q_dot = p
p_dot = -pot.gradient(q).value + accdf
toreturn = np.concatenate((q_dot, p_dot))
return toreturn
integrator = gi.LeapfrogIntegrator(F_dyn_fric,
func_args=(sat_mass, scale_radius),
func_units=galactic)
orbit = None
if verbose:
print('integrating ... ')
start_time = time.time()
orbit = integrator.run(w0, dt=timestep, n_steps=ntimesteps)
orbit_time = time.time() - start_time
print('done integrating')
print('Length of integration: %1.3f' % orbit_time)
else:
orbit = integrator.run(w0, dt=timestep, n_steps=ntimesteps)
return orbit, pot
def get_potential(self, p):
"""pars is the unpacked pars dict"""
# HACK: TODO: allow other potentials
return gp.HernquistPotential(m=p['pot_m'],
c=np.exp(p['pot_log_rs']),
units=galactic)
# clockwise 1, widdershins -1, angular thing
c1 = 1.0
c2 = -1.0
w1 = 1.0
w2 = 1.0
# Milky Way and Andromeda
M_MW = 1.0E11 * u.Msun
M_AND = 1.23E12 * u.Msun
SIZE_MW = 36.8 # kpc
SIZE_AND = 33.7 # kpc
MW_AND_DIST = 778.0 / sqrt(3)
MW_AND_VEL = -110.0 / sqrt(3)
POT_MW = gp.MilkyWayPotential()
POT_AND = gp.HernquistPotential(M_AND.value, 0, units=galactic)
ICS_MW = gd.PhaseSpacePosition(pos=[0, 0, 0] * u.kpc,
vel=[0, 0, 0] * u.km / u.s)
ICS_AND = gd.PhaseSpacePosition(
pos=[MW_AND_DIST, MW_AND_DIST, MW_AND_DIST] * u.kpc,
vel=[MW_AND_VEL, MW_AND_VEL, MW_AND_VEL] * (u.km / u.s))
# Lörg and Smøl Magellanic Clouds
M_LORG = 1.0E10 * u.M_sun
SIZE_LORG = 4.3 # u.kpc
MW_LORG_DIST = 49.97 # wrt MW, in kpc
MW_LORG_VEL = 321.0 # wrt MW, in km/s
POT_LORG = gp.HernquistPotential(M_LORG.value, 0, units=galactic)
ICS_LORG = gd.PhaseSpacePosition(
pos=[MW_LORG_DIST, MW_LORG_DIST, MW_LORG_DIST] * u.kpc,
def run_gala_orbit(pos_sat, vel_sat, pos_tp, vel_tp):
"""
Specify units in ICs
"""
## GALA set up
# Design gala potential using Nbody and a test particle
# Present-day position/velocity in inertial frame moving with instantaneous
# Milky Way velocity:
w0_mw = gd.PhaseSpacePosition(
pos=[0, 0, 0] * u.kpc,
vel=[0, 0, 0] * u.km / u.s,
)
pot_mw = gp.HernquistPotential(m=Mhost * u.Msun,
c=1 * u.kpc,
units=galactic)
# Values from Vasiliev et al. 2020
w0_lmc = gd.PhaseSpacePosition(
pos=pos_sat,
vel=vel_sat,
)
w0_test = gd.PhaseSpacePosition(
pos=pos_tp,
vel=vel_tp,
)
pot_lmc = gp.HernquistPotential(m=Msat * u.Msun,
c=1 * u.kpc,
units=galactic)
w0 = gd.combine((w0_mw, w0_lmc, w0_test))
nbody = gd.DirectNBody(w0, [pot_mw, pot_lmc, None])
w1 = gd.combine((w0_lmc, w0_test))
isolated = gd.DirectNBody(w1, [pot_lmc, None])
# Full : Host - Satellite - test particle
orbits = nbody.integrate_orbit(dt=dt * u.Gyr,
t1=tmin * u.Gyr,
t2=tmax * u.Gyr)
# Orbit quantities full orbit
pos_halo = np.array([orbits.xyz[:, :, 0].to(u.kpc).value])[0]
pos_sat = np.array([orbits.xyz[:, :, 1].to(u.kpc).value])[0]
pos_tp = np.array([orbits.xyz[:, :, 2].to(u.kpc).value])[0]
vel_halo = np.array([orbits.v_xyz[:, :, 0].to(u.km / u.s).value])[0]
vel_sat = np.array([orbits.v_xyz[:, :, 1].to(u.km / u.s).value])[0]
vel_tp = np.array([orbits.v_xyz[:, :, 2].to(u.km / u.s).value])[0]
r_halo = (np.sum(orbits.xyz[:, :, 0]**2, axis=0))**0.5
r_sat = (np.sum(orbits.xyz[:, :, 1]**2, axis=0))**0.5
r_tp = (np.sum(orbits.xyz[:, :, 2]**2, axis=0))**0.5
v_halo = (np.sum(orbits.v_xyz[:, :, 0].to(u.km / u.s).value**2,
axis=0))**0.5
v_sat = (np.sum(orbits.v_xyz[:, :, 1].to(u.km / u.s).value**2,
axis=0))**0.5
v_tp = (np.sum(orbits.v_xyz[:, :, 2].to(u.km / u.s).value**2, axis=0))**0.5
rtp_r2_sat = np.sum((np.array(orbits.xyz[:, :, 2].to(u.kpc).value -
orbits.xyz[:, :, 1].to(u.kpc).value))**2,
axis=0)**0.5
vtp_r2_sat = np.sum(
(np.array(orbits.v_xyz[:, :, 2].to(u.km / u.s).value -
orbits.v_xyz[:, :, 1].to(u.km / u.s).value))**2,
axis=0)**0.5
return [pos_halo, vel_halo], [pos_sat, vel_sat], [pos_tp, vel_tp]
# coordinates (x, y, z) and returns the (scalar) value of the density at that
# location:
def density_func(x, y, z):
r = np.sqrt(x**2 + y**2 + z**2)
return 1 / (r**1.8 * (1 + r)**2.7)
# Let's visualize this density function. For comparison, let's also over-plot
# the Hernquist density distribution. The SCF expansion uses the Hernquist
# density for radial basis functions, so the similarity of the density we want
# to represent and the Hernquist function gives us a sense of how many radial
# terms we will need in the expansion:
hern = gp.HernquistPotential(m=1, c=1)
# +
x = np.logspace(-1, 1, 128)
plt.plot(x, density_func(x, 0, 0), marker='', label='custom density')
# need a 3D grid for the potentials in Gala
xyz = np.zeros((3, len(x)))
xyz[0] = x
plt.plot(x, hern.density(xyz), marker='', label='Hernquist')
plt.xscale('log')
plt.yscale('log')
plt.xlabel('$r$')
plt.ylabel(r'$\rho(r)$')