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Adding diameter dependence of deposition factor

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This commit is contained in:
Nicolas Mounet 2021-09-22 14:35:19 +02:00
parent 4c33766e59
commit de0b0b4b10
1 changed files with 56 additions and 7 deletions
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63
cara/models.py
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@ -781,10 +781,12 @@ class ConcentrationModel:
# Equilibrium velocity of particle motion toward the floor
if (isinstance(self.infected, InfectedPopulation)
and isinstance(self.infected.expiration, Expiration)):
d = self.infected.expiration.diameter
vg = 1.88e-4 * (d*self.evaporation_factor / 2.5)**2
d = self.infected.expiration.diameter * self.evaporation_factor
vg = 1.88e-4 * (d / 2.5)**2 # see CERN-OPEN-2021-04
# (velocity of 1.88e-4 corresponds to diameter of 2.5 microns)
else:
# no diameter is defined - we choose a velocity value
# model is not evaluated for specific values of aerosol
# diameters - we choose a single velocity value
# corresponding to that obtained with a diameter of 2.5 microns
# (geometric average of the breathing expiration distribution,
# taking evaporation into account, see CERN-OPEN-2021-04)
@ -966,8 +968,26 @@ class ExposureModel:
#: The number of times the exposure event is repeated (default 1).
repeats: int = 1
#: The fraction of viruses actually deposited in the respiratory tract
fraction_deposited: _VectorisedFloat = 0.6
def fraction_deposited(self):
"""
The fraction of viruses actually deposited in the respiratory tract.
From W. C. Hinds, New York, Wiley, 1999 (pp. 233 – 259).
"""
if not (isinstance(self.concentration_model.infected,InfectedPopulation)
and isinstance(self.concentration_model.infected.expiration,Expiration)):
# model is not evaluated for specific values of aerosol
# diameters - we choose a single "average" deposition factor,
# as in CERN-OPEN-2021-04.
fdep = 0.6
else:
# deposition factor depends on aerosol particle diameter.
d = (self.concentration_model.infected.expiration.diameter
* self.concentration_model.evaporation_factor)
IFrac = 1 - 0.5 * (1 - (1 / (1 + (0.00076*(d**2.8)))))
fdep = IFrac * (0.0587
+ (0.911/(1 + np.exp(4.77 + 1.485 * np.log(d))))
+ (0.943/(1 + np.exp(0.508 - 2.58 * np.log(d)))))
return fdep
def _normed_exposure(self) -> _VectorisedFloat:
"""
@ -1006,15 +1026,44 @@ class ExposureModel:
return (np.array(self._normed_exposure()*aerosols).mean() *
emission_rate/aerosols)
def _deposited_exposure(self) -> _VectorisedFloat:
"""
The number of virus per meter^3 deposited on the respiratory
tract. As in the exposure method, with sampled diameters the
aerosol volume and the deposited fraction, have to be put
in the deposited exposure before taking the mean, to obtain the
proper result (which corresponds to an integration on diameters).
"""
emission_rate = self.concentration_model.infected.emission_rate_when_present()
if (not isinstance(self.concentration_model.infected,InfectedPopulation)
or not isinstance(self.concentration_model.infected.expiration,Expiration)
or np.isscalar(self.concentration_model.infected.expiration.diameter)
):
# in all these cases, there is no distribution of
# diameters that need to be integrated over
return (self._normed_exposure() *
self.fraction_deposited() *
emission_rate)
else:
# the mean of the diameter-dependent exposure (including
# aerosols volume, but NOT the other factors) has to be
# taken first (this is equivalent to integrating over the
# diameters)
mask = self.concentration_model.infected.mask
aerosols = self.concentration_model.infected.expiration.aerosols(mask)
return (np.array(self._normed_exposure() * aerosols *
self.fraction_deposited()).mean() *
emission_rate/aerosols)
def infection_probability(self) -> _VectorisedFloat:
exposure = self.exposure()
deposited_exposure = self._deposited_exposure()
f_inf = self.concentration_model.infected.fraction_of_infectious_virus()
inf_aero = (
self.exposed.activity.inhalation_rate *
(1 - self.exposed.mask.inhale_efficiency()) *
exposure * self.fraction_deposited * f_inf
deposited_exposure * f_inf
)
# oneoverln2 multiplied by ID_50 corresponds to ID_63.