from festim.reaction import Reaction as _Reaction
from festim.species import ImplicitSpecies as _ImplicitSpecies
from festim.species import Species as _Species
[docs]
class Trap(_Species):
"""Trap species class for H transport simulation.
This class only works for 1 mobile species and 1 trapping level and is
for convenience, for more details see notes.
Args:
name (str, optional): a name given to the trap. Defaults to None.
mobile_species (_Species): the mobile species to be trapped
k_0 (float): the trapping rate constant pre-exponential factor (m3 s-1)
E_k (float): the trapping rate constant activation energy (eV)
p_0 (float): the detrapping rate constant pre-exponential factor (s-1)
E_p (float): the detrapping rate constant activation energy (eV)
volume (F.VolumeSubdomain1D): The volume subdomain where the trap is.
Attributes:
name (str, optional): a name given to the trap. Defaults to None.
mobile_species (_Species): the mobile species to be trapped
k_0 (float): the trapping rate constant pre-exponential factor (m3 s-1)
E_k (float): the trapping rate constant activation energy (eV)
p_0 (float): the detrapping rate constant pre-exponential factor (s-1)
E_p (float): the detrapping rate constant activation energy (eV)
volume (F.VolumeSubdomain1D): The volume subdomain where the trap is.
trapped_concentration (_Species): The immobile trapped concentration
trap_reaction (_Reaction): The reaction for trapping the mobile conc.
empty_trap_sites (F.ImplicitSpecies): The implicit species for the
empty trap sites
Examples:
.. testsetup:: Trap
from festim import Trap, Species, VolumeSubdomain, Material
from festim import HydrogenTransportProblem
my_mat = Material(D_0=1, E_D=1, name="test_mat")
my_vol = VolumeSubdomain(id=1, material=my_mat)
H = Species(name="H")
.. testcode:: Trap
trap = Trap(name="Trap", mobile_species=H, k_0=1.0, E_k=0.2,
p_0=0.1, E_p=0.3, n=100, volume=my_vol)
my_model = HydrogenTransportProblem()
my_model.traps = [trap]
Notes:
This convenience class replaces the need to specify an implicit species and
the associated reaction, thus:
.. code:: python
cm = _Species("mobile")
my_trap = F.Trap(
name="trapped",
mobile_species=cm,
k_0=1,
E_k=1,
p_0=1,
E_p=1,
n=1,
volume=my_vol,
)
my_model.species = [cm]
my_model.traps = [my_trap]
is equivalent to:
.. code:: python
cm = _Species("mobile")
ct = _Species("trapped")
trap_sites = F.ImplicitSpecies(n=1, others=[ct])
trap_reaction = _Reaction(
reactant=[cm, trap_sites],
product=ct,
k_0=1,
E_k=1,
p_0=1,
E_p=1,
volume=my_vol,
)
my_model.species = [cm, ct]
my_model.reactions = [trap_reaction]
"""
def __init__(
self, name: str, mobile_species, k_0, E_k, p_0, E_p, n, volume
) -> None:
super().__init__(name)
self.mobile_species = mobile_species
self.k_0 = k_0
self.E_k = E_k
self.p_0 = p_0
self.E_p = E_p
self.n = n
self.volume = volume
self.trapped_concentration = None
self.reaction = None
[docs]
def create_species_and_reaction(self):
"""Create the immobile trapped species object and the reaction for trapping."""
self.trapped_concentration = _Species(name=self.name, mobile=False)
self.empty_trap_sites = _ImplicitSpecies(
n=self.n, others=[self.trapped_concentration]
)
self.reaction = _Reaction(
reactant=[self.mobile_species, self.empty_trap_sites],
product=self.trapped_concentration,
k_0=self.k_0,
E_k=self.E_k,
p_0=self.p_0,
E_p=self.E_p,
volume=self.volume,
)
