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Merge pull request #302 from mkelley/linkcheck-fix-20211004
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Address tox linkcheck failures
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@mkelley
mkelley committed Oct 20, 2021
2 parents c7920b5 + 0083589 commit e322b64
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Showing 3 changed files with 91 additions and 95 deletions.
164 changes: 79 additions & 85 deletions sbpy/activity/gas/core.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -669,22 +669,16 @@ class VectorialModel(GasComa):
Velocity of fragment resulting
from photodissociation of parent
q_t : function, optional
Parameters
----------
t : float
Time, in seconds ago (no astropy units)
q_t : callable, optional
Function yielding additional production beyond base_q at the
given time in units of inverse seconds:
Returns
-------
numpy.float64
Additional production beyond base_q at the given time, per
second, no astropy units
``q_t(t) -> float``
where ``t`` is lookback time in seconds as a float.
Notes
-----
If no time-dependence function is given, the model will run with
steady production at base_q stretching infinitely far into the
steady production at ``base_q`` stretching infinitely far into the
past.
radial_points: int, optional
Expand Down Expand Up @@ -794,9 +788,9 @@ def __init__(self, base_q, parent, fragment, q_t=None, radial_points=50,
# Make array of angles adjusted up away from zero, to keep from
# calculating a radial line's contribution to itself
self.vmodel['angular_grid'] = np.linspace(
0, self.vmodel['epsilon_max'], num=self.angular_points,
endpoint=False
)
0, self.vmodel['epsilon_max'], num=self.angular_points,
endpoint=False
)
# This maps addition over the whole array automatically
self.vmodel['angular_grid'] += self.vmodel['d_alpha']/2

Expand Down Expand Up @@ -968,8 +962,8 @@ def _setup_calculations(self):

# Eq. 5 of Festou 1981
self.vmodel['collision_sphere_radius'] = (
(self.parent['sigma'] * q * v_therm)/(vp * vp)
) * u.m
(self.parent['sigma'] * q * v_therm)/(vp * vp)
) * u.m

# Calculates the radius of the coma (parents only), given our input
# parameters
Expand All @@ -984,15 +978,15 @@ def _setup_calculations(self):
fragment_beta_r = -np.log(1.0 - self.fragment_destruction_level)

perm_flow_radius = (
self.vmodel['coma_radius'].value +
((vp + vf) * fragment_beta_r * self.fragment['tau_T'])
)
self.vmodel['coma_radius'].value +
((vp + vf) * fragment_beta_r * self.fragment['tau_T'])
)

t_secs = (
self.vmodel['coma_radius'].value/vp +
(perm_flow_radius - self.vmodel['coma_radius'].value)
/ (vp + vf)
)
self.vmodel['coma_radius'].value/vp +
(perm_flow_radius - self.vmodel['coma_radius'].value)
/ (vp + vf)
)
self.vmodel['t_perm_flow'] = (t_secs * u.s).to(u.day)

# This is the total radial size that parents & fragments occupy, beyond
Expand Down Expand Up @@ -1041,13 +1035,13 @@ def _make_radial_logspace_grid(self):
badly so don't do it, dear reader
"""
start_power = np.log10(
self.vmodel['collision_sphere_radius'].value * 2
)
self.vmodel['collision_sphere_radius'].value * 2
)
end_power = np.log10(self.vmodel['max_grid_radius'].value)
return np.logspace(
start_power, end_power,
num=self.radial_points, endpoint=True
)
start_power, end_power,
num=self.radial_points, endpoint=True
)

def _compute_fragment_density(self):
""" Computes the density of fragments as a function of radius
Expand Down Expand Up @@ -1089,9 +1083,9 @@ def _compute_fragment_density(self):
# Compute this once ahead of time
# More factors to fill out integral similar to eq. (36) Festou 1981
integration_factor = (
(1/(4 * np.pi * p_tau_d)) *
self.vmodel['d_alpha']/(4.0 * np.pi)
)
(1/(4 * np.pi * p_tau_d)) *
self.vmodel['d_alpha']/(4.0 * np.pi)
)

# Calculate the density contributions over the volume of the comet
# atmosphere due to one ejection axis
Expand All @@ -1108,8 +1102,8 @@ def _compute_fragment_density(self):
d_epsilon_steps = len(ejection_radii)
d_epsilon = (
(self.vmodel['epsilon_max'] - cur_angle)
/ d_epsilon_steps
)
/ d_epsilon_steps
)

# Maximum radius that contributes to point x,y when there is a
# a max ejection angle
Expand All @@ -1122,9 +1116,9 @@ def _compute_fragment_density(self):
# above, so it's d_epsilon_steps - 1
for dE in range(0, d_epsilon_steps-1):
ejection_radii[dE] = (
y -
x/np.tan((dE+1)*d_epsilon + cur_angle)
)
y -
x/np.tan((dE+1)*d_epsilon + cur_angle)
)

ejection_radii_start = 0
# Number of slices along the contributing axis for each step
Expand All @@ -1136,8 +1130,8 @@ def _compute_fragment_density(self):
# We are slicing up this axis into pieces
dr = (
(ejection_radii_end - ejection_radii_start) /
num_slices
)
num_slices
)

# Loop over tiny slices along this chunk
for m in range(0, num_slices):
Expand Down Expand Up @@ -1180,9 +1174,9 @@ def _compute_fragment_density(self):
# given by eq. 32, Festou 1981
prod_one = self.production_at_time(t_total_one)/vp
q_r_eps_one = (
(v_one * v_one * prod_one) /
(vf * np.abs(v_one - vp*cos_eject))
)
(v_one * v_one * prod_one) /
(vf * np.abs(v_one - vp*cos_eject))
)

# Parent extinction when traveling along to the
# dissociation site
Expand All @@ -1194,15 +1188,15 @@ def _compute_fragment_density(self):
# integrating along dr, similar to eq. (36) Festou
# 1981, due to the first velocity
n_r_one = (
(p_extinction*f_extinction_one*q_r_eps_one) /
(sep_dist**2 * v_one)
)
(p_extinction*f_extinction_one*q_r_eps_one) /
(sep_dist**2 * v_one)
)

# Add this contribution to the density grid
self.vmodel['density_grid'][i][j] = (
self.vmodel['density_grid'][i][j] +
n_r_one * dr
)
self.vmodel['density_grid'][i][j] +
n_r_one * dr
)

# Check if there is a second solution for the velocity
if vf > vp:
Expand All @@ -1217,18 +1211,18 @@ def _compute_fragment_density(self):
t_total_two = (cur_r/vp) + t_frag_two
prod_two = self.production_at_time(t_total_two)/vp
q_r_eps_two = (
(v_two * v_two * prod_two) /
(vf * np.abs(v_two - vp*cos_eject))
)
(v_two * v_two * prod_two) /
(vf * np.abs(v_two - vp*cos_eject))
)
f_extinction_two = np.e**(-t_frag_two/f_tau_T)
n_r_two = (
(p_extinction*f_extinction_two*q_r_eps_two) /
(v_two * sep_dist**2)
)
(p_extinction*f_extinction_two*q_r_eps_two) /
(v_two * sep_dist**2)
)
self.vmodel['density_grid'][i][j] = (
self.vmodel['density_grid'][i][j] +
n_r_two * dr
)
self.vmodel['density_grid'][i][j] +
n_r_two * dr
)

# Next starting radial point is the current end point
ejection_radii_start = ejection_radii_end
Expand Down Expand Up @@ -1265,15 +1259,15 @@ def _compute_fragment_density(self):
# Integration factors from angular part of integral, similar to
# eq. (36) Festou 1981
dens_contribution = (
2.0 * np.pi * np.sin(theta) *
self.vmodel['density_grid'][i][j]
)
2.0 * np.pi * np.sin(theta) *
self.vmodel['density_grid'][i][j]
)
self.vmodel['fast_radial_density'][i] += dens_contribution

# Tag with proper units
self.vmodel['radial_density'] = (
self.vmodel['fast_radial_density'] / (u.m**3)
)
self.vmodel['fast_radial_density'] / (u.m**3)
)

def _interpolate_radial_density(self):
""" Interpolate the radial density.
Expand All @@ -1287,10 +1281,10 @@ def _interpolate_radial_density(self):
# Interpolate this radial density grid with a cubic spline for lookup
# at non-grid radii, input in m, output in 1/m^3
self.vmodel['r_dens_interpolation'] = (
CubicSpline(self.vmodel['fast_radial_grid'],
self.vmodel['fast_radial_density'],
bc_type='natural')
)
CubicSpline(self.vmodel['fast_radial_grid'],
self.vmodel['fast_radial_density'],
bc_type='natural')
)

def _column_density_at_rho(self, rho):
""" Calculate the column density of fragments at a given impact parameter
Expand Down Expand Up @@ -1330,14 +1324,14 @@ def column_density_integrand(z):

if rho < (60 * self.vmodel['collision_sphere_radius'].value):
c_dens = (
quad(column_density_integrand,
-z_max, z_max, limit=3000)
)[0]
quad(column_density_integrand,
-z_max, z_max, limit=3000)
)[0]
else:
c_dens = (
2 * romberg(column_density_integrand,
0, z_max, rtol=0.0001, divmax=20)
)
2 * romberg(column_density_integrand,
0, z_max, rtol=0.0001, divmax=20)
)

# result is in 1/m^2
return c_dens
Expand Down Expand Up @@ -1369,12 +1363,12 @@ def _compute_column_density(self):
self.vmodel['column_densities'] = column_densities/(u.m**2)
# Interpolation gives column density in m^-2
self.vmodel['column_density_interpolation'] = (
CubicSpline(
column_density_grid,
column_densities,
bc_type='natural'
)
)
CubicSpline(
column_density_grid,
column_densities,
bc_type='natural'
)
)

def calc_num_fragments_theory(self):
""" The total number of fragment species we expect in the coma
Expand Down Expand Up @@ -1407,9 +1401,9 @@ def calc_num_fragments_theory(self):
max_r = self.vmodel['max_grid_radius'].value
last_density_element = len(self.vmodel['fast_radial_density'])-1
edge_adjust = (
(np.pi * max_r * max_r * (vf + vp) *
self.vmodel['fast_radial_density'][last_density_element])
)
(np.pi * max_r * max_r * (vf + vp) *
self.vmodel['fast_radial_density'][last_density_element])
)

num_time_slices = 10000
# array starting at tperm (farthest back in time we expect something to
Expand Down Expand Up @@ -1463,9 +1457,9 @@ def vol_integrand(r, r_func):
return (r_func(r) * r**2)

r_int = romberg(
vol_integrand, 0, max_r,
args=(self.vmodel['r_dens_interpolation'], ),
rtol=0.0001, divmax=20)
vol_integrand, 0, max_r,
args=(self.vmodel['r_dens_interpolation'], ),
rtol=0.0001, divmax=20)
return 4 * np.pi * r_int

def _column_density(self, rho):
Expand Down
1 change: 1 addition & 0 deletions sbpy/data/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@
``Conf.fieldnames_info`` is a list of dictionaries, one per field, with the
keys: `'description'`, `'fieldnames'`, `'provenance'`, `'dimension'`, and
`'equivalencies'`:
* description: text description of the field
* provenance: list of `~sbpy.DataClass` objects which use the field
* fieldnames: list of field names as strings, the first is considered the
Expand Down
21 changes: 11 additions & 10 deletions sbpy/data/phys.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -207,18 +207,19 @@ def from_jplspec(cls, temp_estimate, transition_freq, mol_tag):
Returns
-------
Molecular data : `~sbpy.data.Phys` instance
data : `~sbpy.data.Phys`
Quantities in the following order from JPL Spectral Molecular
Catalog:
| Transition frequency
| Temperature
| Integrated line intensity at 300 K
| Partition function at 300 K
| Partition function at designated temperature
| Upper state degeneracy
| Upper level energy in Joules
| Lower level energy in Joules
| Degrees of freedom
* Transition frequency
* Temperature
* Integrated line intensity at 300 K
* Partition function at 300 K
* Partition function at designated temperature
* Upper state degeneracy
* Upper level energy in Joules
* Lower level energy in Joules
* Degrees of freedom
"""

Expand Down

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