Species / Species List

In a Zacros simulation, species are necessary to describe the chemistry involved in the system. If one atom is identical to another, we can say they are the same chemical species. In the same way, if one molecule is identical to another, we can say they are the same chemical species. Thus, we can highlight two essential kinds of species: 1) gas species and 2) surface or adsorbed species. A molecule in the gas phase is a species itself, but when it interacts with a catalytic surface, its properties generally change enough to be different from its gas counterpart. However, once it is adsorbed on the catalytic surface, its properties may not change enough to change its identity as it moves on the surface. In that sense, for example, for a CO molecule, we can identify two kinds of species: 1) CO in the gas phase and 2) CO adsorbed. Here, the CO is the same species independently if it is adsorbed, e.g., on an fcc or an hcp site.

For any kind of species, the only required parameter is the symbol (e.g., "CO"), and it can be created with the sentence pz.Species("CO"). The Species constructor allows specifying different parameters like denticity, gas energy, kind, and mass. By default, pyZacros parses the species symbol to get these parameters. If the symbol contains the character *, it assumes that the species is a surface species (kind=pz.Species.SURFACE) with a denticity given by the number of times that * is found in the symbol; i.e. pz.Species("O2**") is equivalent to pz.Species("O2**",denticity=2,kind=pz.Species.SURFACE). On the other hand, if the symbol doesn’t contain any *, it assumes that the species is a gas species (kind=pz.Species.GAS), with the mass calculated from the parsing of the symbol as a chemical formula string; i.e. pz.Species("O2") is equivalent to pz.Species("O2",kind=pz.Species.GAS,mass=31.9898).

For our example (see use case system), we need to create three gas species (CO, O2, and CO2), and three surface species (*, CO*, O*). This can be achieved by using the lines 1-10 of following code:

# Gas species
CO_g = pz.Species("CO")
O2_g = pz.Species("O2")
CO2_g = pz.Species("CO2", gas_energy=-2.337)

# Surface species
s0 = pz.Species("*")   # Empty adsorption site
CO_s = pz.Species("CO*")
O_s = pz.Species("O*", denticity=1)

# Species List
spl = pz.SpeciesList([CO_g,O2_g,CO2_g,s0,CO_s])
spl.append( O_s )

Notice that the species symbol * is reserved for the empty site species (or pseudo-species).

In this script, we have also introduced the class SpeciesList, which represents nothing more than a list of species (see lines 11-13). But, in particular, it is helpful to look at the Zacros code that will be generated based on it by using the print() function (see line 14). The execution of the previous script displays the following on the standard output:

n_gas_species    3
gas_specs_names              CO           O2          CO2
gas_energies        0.00000e+00  0.00000e+00 -2.33700e+00
gas_molec_weights   2.79949e+01  3.19898e+01  4.39898e+01
n_surf_species    2
surf_specs_names         CO*        O*
surf_specs_dent            1         1

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.


class Species(symbol, denticity=None, gas_energy=None, kind=None, mass=None)

Species class that represents a chemical species

  • symbol – Species’ symbol. If symbol contains the character ‘*’, it is considered an adsorbed species. Otherwise it is considered a gas species. e.g. H2*

  • denticity – Species’ denticity e.g. 2. If None, it is set as the number of times that the character ‘*’ is found in the symbol.

  • gas_energy – Species’ gas energy in eV. e.g. 0.0

  • kind – It can be Species.SURFACE (0), or Species.GAS (1). If None, it is selected from the symbol.

  • mass – Specifies the mass in Da. If None, the mass is calculated from the symbol interpreted as a chemical formula. The mass of the most abundant isotopes of composing atoms is used for this calculation. For example, if symbol='CH4', the mass will be 16.0312 (12.0000+4*1.0078).


Returns True if the name of the species has the character ‘*’.


Returns True if the name of the species has no the character ‘*’.


Returns a dictionary containing the number of atoms of each kind.


Returns the mass of the species in Da.

class SpeciesList(data=[])

Creates a new SpeciesList object which is formally a list of Species. It implements all python list operations.

  • data – List of Species to initially include.


Returns the gas species.


Returns the adsorbed species.


Returns the total mass as the sum of its all species in Da.

  • entity_numbers – Avoids double counting of the species if they belong to the same entity.


Updates the attribute ‘label’


Returns the label of the cluster


Removes duplicate species. Two species are considered the same if they have the same symbol.