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- ReactionModel:
Wiki Markup +rxn_expressions+ \- These expressions determine the elementary reaction, and are the most important part of the model. They must be defined unless the elementary_rxns, adsorbate_names, transition_state_names, and gas_names are all explicitly defined since the rxn_expressions are parsed into these 3 attributes. It is much easier to just define rxn_expressions, although it is important to note the syntax. There must be spaces between all elements of each expression (i.e. C*+O\* is not okay, but C\* + O\* is), and species ending with \_g are gasses by default. Adsorbed species may end with * or \_x where * designates adsorption at the "s" site (by default), while \_x designates adsorption at the "x" site (note that "x" may be any letter except "g", and that X* and X_s are equivalent). Transition-states should include a \-, and reactions with a transition-state are specified by 'IS <-> TS \-> FS' while reactions without a transition-state are defined as 'IS \-> FS' (where IS,TS,FS are expressions for the Initial/Transition/Final State). When the model initializes it checks the expressions for mass/site balances, and if it finds that they are not balanced it will raise an exception. \[list of strings\]. Instead of specifying rxn_expressions the following attributes may instead be defined:
Wiki Markup elementary_rxns - list version of rxn_expressions. These will be automatically populated if rxn_expressions are defined. \[list of lists of lists\]
Wiki Markup adsorbate_names - list of adsorbate names included in the analysis. Automatically populated if rxn_expressions are defined.\[list of strings\]
Wiki Markup transition_state_names\* - list of transition-state names included in the analysis. Automatically populated if rxn_expressions are defined. \[list of strings\]Wiki Markup +gas_names+ \- list of gas names included in the analysis. \[list of strings\]
Wiki Markup +surface_names+ \- list of surface names to be included in the analysis. \[list of strings\]
- species_definitions - This is a dictionary where all species-specific information is stored. The required information will vary depending on the scaler/thermo corrections/solver/mapper used, and the "parser" generally fills in most information. However, there are a few things which generally need to be supplied explicitly:
Wiki Markup +species_definitions\[\{site\}\]\['site_names'\]+ (where \{site\} is each site name in the model) - A list of "site names" which correspond to \{site\}. If the TableParser (default) is being used then the "site names" must also match the designations in the "site_name" column. For example, if you want the "s" site to correspond to the energetics of an adsorbate at a (211) site, and (211) sites are designated by '211' in the site_name column of the input_file, then this would be specified by: species_definitions\['s'\] = \{'site_names':\['211'\]\}. Similarly, if you wanted the 't' site to correspond to 'fcc' or 'bridge' sites then you could specify: species_definitions\['t'\] = \{'site_names':\['fcc','bridge'\]\}.Wiki Markup +species_definitions\[\{site\}\]\['total'\]+ (where \{site\} is each site name in the model) - A number to which the total coverage of \{site\} must sum. For example, if you wanted to have a total coverage of 1 with 10\% 's' sites and 90\% 't' sites (with the same site definitions as above) you would specify: species_definitions\['s'\] = \{'site_names':\['211'\],'total':0.1\} and species_definitions\['t'\] = \{'site_names':\['fcc','bridge'\],'total:0.9\}.Wiki Markup +species_definitions\[\{gas\}\]\['pressure'\]+ (where \{gas\} is each gas name in the model) - The pressure of each gas species in bar. For example, if you wanted a carbon monoxide pressure of 10 bar and hydrogen pressure of 20 bar you would specify: species_definitions\['CO_g'\]\['pressure'\] = 10 and species_definitions\['H2_g'\]\['pressure'\] = 20. Note that for some situations you may instead need to specify a 'concentration','approach_to_equilibrium', or some other key, but in almost every situation some method for obtaining the gas pressures must be specified for each gas in the model.
Wiki Markup +temperature+ \- temperature used for the analysis. May not be defined if ThermodynamicScaler is being used with temperature as a descriptor. \[number in Kelvin\]
Wiki Markup +descriptor_names+ \- names of variables to be used as descriptors. \[list of strings\]
Wiki Markup descriptor_ranges \- Used for mapping through descriptors space. Specify the limits of the descriptor values. Should be a list equal in length to the number of descriptors where each entry is a list of 2 floats (min and max for that descriptor). \[list of lists of floats\].
Wiki Markup resolution \- Used for mapping through descriptor space. Resolution used when discretizing over descriptor_range. \[int\]
Wiki Markup parser - name of class to use for solver. Defaults to TableParser. \[string\]
Wiki Markup mapper - name of class to use as a mapper. Defaults to MinResidMapper. \[string\]
Wiki Markup scaler - name of class to use for scaler. Defaults to GeneralizedLinearScaler. \[string\]
Wiki Markup solver - name of class to use for solver. Defaults to SteadyStateSolver. \[string\]
Wiki Markup thermodynamics - name of class to use for thermodynamic corrections. Defaults to ThermoCorrections. \[string\]
Wiki Markup data_file - file where large outputs will be saved as binary pickle files. Defaults to 'data.pkl' \[filepath string\]
Wiki Markup numerical_representation - determines how to store numbers as binary. Can be 'mpmath' for multiple precision or 'numpy' for normal floats. Note that 'numpy' rarely works. Defaults to 'mpmath'. \[string\]
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