Descriptor based analysis is a powerful tool for understanding the trends across various catalysts. In general, the rate of a reaction over a given catalyst is a function of many parameters - reaction energies, activation barriers, thermodynamic conditions, etc. The high dimensionality of this problem makes it very difficult and expensive to solve completely and even a full solution would not give much insight into the rational design of new catalysts. The descriptor based approach seeks to determine a few "descriptors" upon which the other parameters are dependent. By doing this it is possible to reduce the dimensionality of the problem - preferably to 1 or 2 descriptors - thus greatly reducing computational efforts and simultaneously increasing the understanding of trends in catalysis.
The "kinetics" Python module seeks to standardize and automate many of the mathematical routines necessary to move from "descriptor space" to reaction rates. The module is designed to be both flexible and powerful. A "reaction model" can be fully defined by a configuration file, thus no new programming is necessary to change the complexity or assumptions of a model. Furthermore, various steps in the process of moving from descriptors to reaction rates have been abstracted into separate Python classes, making it easy to change the methods used or add new functionality. The downside of this approach is that it makes the code more complex. The purpose of this guide is to explain the general structure of the code, as well as its specific functions and how to begin using it.
Useful Definitions: (Note symbols may not appear in Safari/IE)
- descriptor - variable used to describe reaction kinetics at a high level. Most commonly these are the binding energies of atomic constituents in the adsorbates (e.g. carbon/nitrogen/oxygen adsorption energies) or other intermediates. However, in the general sense other variables such as electronic structure parameters (e.g. d-band center) or thermodynamic parameters (e.g. temperature/pressure) could also be descriptors.
- descriptor space ( D ) - the space spanned by the descriptors. Usually ℝ2.
- parameter space ( P ) - the space spanned by the full reaction parameters for the reaction model. Usually ℝ2n where where n is the number of elementary steps (one reaction energy and one reaction barrier per elementary step).
- reaction rates ( r ) - an n-vector of rates corresponding to each of the n elementary reactions.
- descriptor map - a map of some variable (rates,coverages,etc.) as a function of descriptor space.
- reaction model - a set of elementary steps and conditions which define the physics of the kinetic system, along with the mathematical methods and assumptions used to move from "descriptor space" to reaction rates.
- model definition - a file used to define the reaction model
- input file - a file used to store other data which is likely common to many reaction models (e.g. energetics data)
Code Structure:
- The interface to the code is handled through the the ReactionModel class class. This class acts as a messenger class which broadcasts all its attributes to the other classes used in the kinetics module. The class also handles common functions such as printing reactions/adsorbates or comparing/reversing elementary steps. The attributes of of ReactionModel are are automatically synchronized with the parser, scaler, solver, and mapper so it is useful to think of of ReactionModel as as a "toolbox" where all the necessary information and common functions are stored.
The The Parser class class serves to extend the "model definition" file by reading in various quantities from an "input file". Technically the use of a parser is optional, but in practice it is extremely helpful for reading in common data such as adsorption energies or vibrational frequencies rather than re-typing them for every reaction model.
The process of creating a "descriptor map" is abstracted into three general processes, which are handled by the following classes within the kinetics module:
Scaler: Projects Projects descriptor space into parameter space: ?? ? ?
Solver: Maps Maps parameter space into reaction rates: ? ? r?
Mapper: Moves Moves through descriptor space. This becomes important for practical reasons since it is often necessary to use a solution at one point in descriptor space as an initial guess for a nearby point.
The The ThermoCorrections class class is responsible for applying thermodynamic corrections to the electronic energies which are used as direct inputs. This includes the contributions of entropy/enthalpy and zero-point energy due to temperature, pressure, or other thermodynamic variables. There are also a variety of analysis classes which allow for automated analysis and visualization of the reaction model. These include the the RateAnalysis which which creates "volcano plot" (descriptor maps of the rate), CoverageAnalysis which which creates descriptor maps of the coverages of various intermediates, ScalingAnalysis which which can give a visual representation of how well the scaler projects descriptor space to parameter space, and several other useful tools.
Using the code:
Some examples can be found in the "demos" folder, and these should explain the syntax necessary and serve as a good starting point. The currently implemented features are also briefly described below in order to allow a better understanding of the demos and creating original reaction model definitions.
Using the kinetics module to conduct a descriptor analysis requires (at least) 2 files: the "model definition" which defines the reaction model, as well as another script to initialize the ReactionModel class and conduct analyses. The "model definition" is generally a static file (i.e. it is not a program) while the submission script will be an actual python program. Model definition files typically end in ".mkm" for micro-kinetic model (although this is not required) while submission scripts end in .py since they are just python scripts. In addition it is very useful to also have an "input file" which contains the raw data about the energetics of the reaction model. An example of such an input file is provided in "published_data.txt" in the demos folder.
Each class described in the the Code Structure section section will require some specialized parameters. Some of these parameters are common to all variants of these classes, while others are specific to certain implementations. The possible inputs for the currently implemented variants of each class are listed below. Required attributes are are underlined.
- 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, and transition_state_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. Adsorbed species may end with * or \_x where * designates adsorption at the "s" site, while \_x designates adsorption at the "x" site (note that "x" may be any letter except "g"). 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 prints a warning but does not raise an exception. \[list of strings\]
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 +surface_names+ \- list of surface names to be included in the analysis. \[list of strings\]
Wiki Markup +gas_names+ \- list of gas names included in the analysis. \[list of strings\]
Wiki Markup +gas_pressures+ \- list of gas pressures to be used for the analysis. May not be defined if ThermodynamicScaler is being used with pressure as a descriptor and gas_ratios is defined. \[list of numbers in bar\]
Wiki Markup gas_ratios - list of gas ratios to be used for the analysis. Only necessary if ThermodynamicScaler is being used to determine the overall pressure. \[list of dimensionless numbers\]
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 +site_definitions+ \- definitions for all sites used in rxn_expressions. Note that * defaults to 's' so 's' should always be defined. The values of the dictionary can be strings corresponding to the "site" field in the input file, or a list of strings if a site definition corresponds to multiple values of the "site" field. \[dictionary of string:(string OR list of strings)\]
Wiki Markup +site_totals+ \- dictionary of total which each site must sum to. \[dictionary of string:(floatable string OR dimensionless number)\]
Wiki Markup +descriptor_names+ \- names of variables to be used as descriptors. \[list of strings\]
Wiki Markup parser - name of class to use for solver. Defaults to KineticsParser. \[string\]
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 coverage_map_file - file to save coverage map data. \[filepath string\]
Wiki Markup rate_map_file - file to save rate map data. \[filepath string\]
- Parser:
- input_file - file where input data is stored. File must be in the correct format for the parser used.
- KineticsParser:
Wiki Markup estimate_frequencies - attempt to estimate frequencies when they are not listed in the input_file. First try to find adsorbates on different sites, then by using the frequencies of atomic species. If no frequencies are found for transition-states, use the combined frequencies of the dissociated state. Defaults to False. \[boolean\]
Wiki Markup adsorbate_definitions - dictionary which allows adsorbates to have a different name in the reaction model than in the input file e.g. \{'CH3O':'H3CO'\} if methoxy was called 'CH3O' in the reaction model but 'H3CO' in the input file. Defaults to \{\}. \[dictionary of string:string\]
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- Mapper:
- MinResidMapper:
Wiki Markup search_directions - list of "directions" to search for existing solutions. Defaults to \[\[0,0\],\[0,1\],\[1,0\],\[0,-1\],\[-1,0\],\[-1,1\],\[1,1\],\[1,-1\],\[-1,-1\]\] which are the nearest points on the orthogonals and diagonals plus the current point. More directions increase the chances of findinga good solution, but slow the mapper down considerably. Note that the current point corresponds to an initial guess coverage provided by the solver (i.e. Boltzmann coverages) and should always be included unless some solutions are already known. \[list of lists of integers\]
Wiki Markup max_bisections - maximum number of time to bisect descriptor space when moving from one point to the next. Note that this is actuall the number of iterations per bisection so that a total of 2{^}max_bisections^ points could be sampled between two points in descriptor space. Defaults to 3. \[integer\]Wiki Markup descriptor_decimal_precision - number of decimals to include when comparing two points in descriptor space. Defaults to 2. \[integer\]
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