Elementary Reaction / Mechanism¶
ElementaryReaction
class allows to define reversible and/or irreversible elementary steps for adsorption
of molecules on surface sites, desorption from there, diffusion from one site to a neighboring site, or reactions
between adsorbed particles and gas species. ElementaryReaction
class has a one-to-one relation with the
sections steps
and reversible_step
in Zacros’ input files.
For our example (see use case system), we need to create three irreversible events:
Non-dissociative adsorption of CO:
CO(g) + * 🠒 CO*
Dissociative adsorption of O2:
O2(g) + * + * 🠒 O* + O*
Fast reaction between an O adatom and a CO adsorbate to produce CO2:
O* + CO* 🠒 * + * + CO2(g)
This can be achieved by using the lines 1-10 of following code:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | # Elementary Reactions
CO_ads = pz.ElementaryReaction( initial=[s0, CO_g], final=[CO_s],
reversible=False, pre_expon=10.0,
label="CO_adsorption" )
O2_ads = pz.ElementaryReaction( initial=[s0, s0, O2_g], final=[O_s, O_s],
neighboring=[(0,1)],
reversible=False, pre_expon=2.5,
label="O2_adsorption" )
CO_oxi = pz.ElementaryReaction( initial=[CO_s, O_s], final=[s0, s0, CO2_g],
neighboring=[(0,1)],
reversible=False, pre_expon=1.0e+20,
label="CO_oxidation")
mech = pz.Mechanism([O2_ads, CO_ads, CO_oxi])
print(mech)
|
Here, we have also introduced the class Mechanism
, which is formally a list of ElementaryReaction
objects
(see line 16). But, it allows looking at the Zacros code that will be generated by using the print()
function (see line 18).
The execution of the previous lines show the following on the standard output:
mechanism
step O2_adsorption
gas_reacs_prods O2 -1
sites 2
neighboring 1-2
initial
1 * 1
2 * 1
final
1 O* 1
2 O* 1
site_types 1 1
pre_expon 2.50000e+00
activ_eng 0.00000e+00
end_step
step CO_adsorption
gas_reacs_prods CO -1
sites 1
initial
1 * 1
final
1 CO* 1
site_types 1
pre_expon 1.00000e+01
activ_eng 0.00000e+00
end_step
step CO_oxidation
gas_reacs_prods CO2 1
sites 2
neighboring 1-2
initial
1 CO* 1
2 O* 1
final
1 * 1
2 * 1
site_types 1 1
pre_expon 1.00000e+20
activ_eng 0.00000e+00
end_step
end_mechanism
Please consult Zacros’ user guide ($AMSHOME/scripting/scm/pyzacros/doc/ZacrosManual.pdf
) for more details about the specific meaning of the keywords used in the previous lines.
API¶
-
class
ElementaryReaction
(initial, final, site_types=None, initial_entity_number=None, final_entity_number=None, neighboring=None, reversible=True, pre_expon=0.0, pe_ratio=0.0, activation_energy=0.0, prox_factor=None, label=None)¶ Creates a new ElementaryReaction object
initial
– List of species bound to the sites in the initial state, e.g.[ Species("H*",1), Species("H*",1) ]
. Gas species have to be added at the end of the list.final
– Same asinitial
but for the final state.site_types
– Specifies the name of the sites in the graph pattern, e.g.['fcc','hcp']
. Notice that the order is essential and it should agree with theinitial
andfinal
options.initial_entity_number
– List of the molecular entities ids bound to each site. For example, if a bidentate species is bound to sites 1 and 2 (species=[ Species("H**",2), Species("H**",2) ]
), both of these sites will have the same entity numbers, i.e.entity_number=[0,0]
. By default, the list of entity numbers is created by assuming that species with the same symbol belong to the same entity.final_entity_number
– Same asinitial_entity_number
but for the final state.neighboring
– Specifies the neighboring between sites, if more than one sites appear in the graph pattern, e.g. [ (0,1) ]reversible
– Sets the reaction as a reversible step.pre_expon
– Specifies the pre-exponential in the Arrhenius formula giving the rate constant of that elementary step. Units: 1/s or Hz.pe_ratio
– Sets the ratio of forward over reverse pre-exponential terms if the reaction is reversible.activation_energy
– Sets the activation energy at the zero coverage limit. Units eV.prox_factor
– The proximity factor used in the BEP relationship to calculate the forward (and also reverse, if applicable) activation energy.label
– If None, a unique label is generated based on the label of its initial and final states.
-
label
()¶ Returns the label of the cluster
-
site_types_set
()¶ Returns the set of the sites types
-
replace_site_types
(site_types_old, site_types_new)¶ Replaces the site types names
site_types_old
– List of strings containing the old site_types to be replacedsite_types_new
– List of strings containing the new site_types which would replace old site_types_old.
-
class
Mechanism
(data=[], fileName=None, gas_species=None, surface_species=None)¶ Creates a new Mechanism object. If no argument is given, the constructor creates a new empty mechanism.
data
– List of elementary reactions to initialize the mechanism.fileName
– Path to the zacros file name to load the mechanism, typicallymechanism_input.dat
gas_species
– Gas species. It is required if the optionfileName
was used.surface_species
– Surface species. It is required if the optionfileName
was used.
-
__fromZacrosFile
(fileName, gas_species, surface_species)¶ Creates a Mechanism from a Zacros input file mechanism_input.dat
-
append
(item)¶ Append item to the end of the sequence
-
extend
(other)¶ Extend sequence by appending elements from the iterable
-
insert
(i, item)¶ Insert value before index
-
surface_species
()¶ Returns the surface species list.
-
gas_species
()¶ Returns the gas species list.
-
species
()¶ Returns the adsorbed species.
-
site_types_set
()¶ Returns the set of the sites types
-
replace_site_types
(site_types_old, site_types_new)¶ Replaces the site types names
site_types_old
– List of strings containing the old site_types to be replacedsite_types_new
– List of strings containing the new site_types which would replace old site_types_old.
-
find
(label)¶ Returns the list of reactions where the substring
label
is found in the reactions’ label
-
find_one
(label)¶ Returns the first reaction where the substring
label
is found in the reaction’s label