Microkinetic Modeling Panel

Predict and understand rates of catalytic reactions of interest.

To display this panel: click the Tasks button and browse to Materials → Quantum Mechanics → Surface Science → Microkinetic Modeling

The following licenses are required to use this panel: MS Maestro, MS Microkinetics

Using
Features
Additional Resources

Using the Microkinetic Modeling Panel

The Microkinetic Modeling Panel is intended to simulate rates of reactions under various conditions (e.g. temperature, pressure, reactor setup) via numerical solutions of rate equations for a given series of elementary reactions and their corresponding energetics.

The panel takes a reaction network and corresponding forward and reverse activation free energies as inputs. Activation free energies for elementary reactions of interest can be extracted from literature data or calculated by performing physics-based simulations using tools such as the Nudged Elastic Band Calculations Panel. It is suggested that the contributions from entropy and heat capacity to the activation free energies used should be calculated at the temperature specified in the Temperature text box. These contributions are usually significant for adsorption/desorption gas-surface reactions, but less significant for surface-surface reactions.

The Microkinetic Modeling Panel can be used to predict the overall kinetics of catalytic reactions within minutes. Due to the short simulation time, modifications can be made to the reaction network, species involved, and energies used to understand reactivity, selectivity, competing reactions, rate limiting steps, etc.

Output files for each stage of the calculation are written by the panel and can be used to troubleshoot and restart failed jobs. For example, if a calculation is converging but reaches the maximum wall clock time, a CSV file with the coverages is written at the end of the simulation. These coverages can be loaded into the panel to resume the calculation from the stopping point. This in effect acts as a restart mechanism to achieve steady state.

This workflow is not an atomistic model and therefore does not interact with the workspace. An empty entry is added to the entry list for each successful microkinetic modeling job, and all resulting data is placed in the job directory.

To visualize the results, you can use the Microkinetic Modeling Viewer Panel (click the Tasks button and browse to Materials → Quantum Mechanics → Surface Science → Microkinetic Viewer).

To write out the input file and a script for running the job from the command line, click the arrow next to the Settings button and choose Write. For information on command usage and options, see mean_field_driver.py Command Help.

Load Model button

Load a previously saved JSON file with microkinetic modeling input data and model settings. Click to open the Open File data dialog box, where you can navigate to the file. Typically, this JSON file is written from the Microkinetic Modeling Panel using the Save Model button.

Save Model button

Save input data and model settings from all tabs in the panel to a JSON file. Opens the Save File dialog box so you can navigate to a location and name the file. This allows you to save a typical reaction set up and later on load it into the panel again using the Load Model button for easy access and modification.

Load Model from Workspace button

Load the JSON file for a completed microkinetic modeling run from the corresponding entry that is in the Workspace. The entry name is shown to the right of the button.

Reactor Settings tab

Specify the physical conditions of a model reactor as well as the catalyst(s) and optionally bulk materials within.

Physical conditions section

Set the reactor conditions for the microkinetic modeling calculation.

Temperature text box: Specify the temperature to be used in Kelvin.; It is suggested that this temperature value should also be used to compute the contributions from entropy and heat capacity to the activation free energies of the reaction network. These contributions are usually significant for adsorption/desorption gas-surface reactions, but less significant for surface-surface reactions.
Volume text box: Specify the volume of the reactor in liters.
Fluid flowrate text box: Specify the flowrate of fluid in and out of the reactor in liters per second.

Catalysts table

Specify information for each catalyst you want to model. The mass, specific surface area, and site density provided here allows the solver to calculate the number of empty sites on a catalyst. Click on the trash icon to delete the row.

Catalysts with multiple active sites (e.g. Rh111 and Rh101) are considered separate and require unique entries to the table. The catalysts are modeled as multiple site types present in the same reactor.

Name—Specify the name of the catalyst.
Loading (g)—Specify the mass of catalyst present in the reactor in grams.
Specific Surface Area (m²/g)—Specify the specific surface area of the catalyst in meter² per gram. This value can be determined from experiment. If no experimental value is available, the default value is sufficient for making comparisons among different catalysts.
Site Density (sites/cm²)—Specify the adsorption site density of the catalyst in sites per centimeter². This value can be determined from experiment. If no experimental value is available, the default value is sufficient for making comparisons among different catalysts.

Add button: Add a row to the Catalysts table for the specified catalyst. Opens the Define Catalyst Name dialog box so you can name the catalyst.

Bulks table

Optionally specify information for each bulk material you want to model. Bulk materials with multiple active site types are considered separate and require unique entries to the table. Since bulk materials have unlimited active sites, the rates of reactions involving them are zeroth order in the empty site and/or absorbed species coverage. Click on the trash icon to delete the row.

Add button: Add a row to the Bulk table for the specified bulk material. Opens the Define Bulk Name dialog box so you can name the bulk material.

Reaction Network tab

Specify the species involved in the reaction network, as well as the set of elementary reactions and their corresponding energetics.

Load Network button

Load a previously saved CSV file with the reaction network. Click to open the Open File data dialog box, where you can navigate to the file. Typically, this CSV file is written from the Microkinetic Modeling Panel using the Save Network button. This is helpful in cases where you want to make modifications to previous network such as changing the free energy barriers for a calculation at a new temperature or changing the stoichiometry of a reaction network.

Save Network button

Save all of the information in the Reaction Network tab to a CSV file. Opens the Save File dialog box so you can navigate to a location and name the file. This allows you to save a typical reaction set up and later on load it into the panel again using the Load Network button for easy access and modification.

Load Network from Workspace button

Load the CSV file for the reaction network of a completed microkinetic modeling run from the corresponding entry that is in the Workspace. The entry name is shown to the right of the button.

Species section

Provide information for species that are adsorbed onto catalysts, absorbed into bulks, or are in the gas or solution phase.

Adsorbed intermediates table

Specify information for each species adsorbed onto a catalyst surface. The information provided here populates the Reaction table.

Name—The name of the adsorbate and the catalyst it is on is displayed as Adsorbate:Catalyst. This is identical to the commonly used nomenclature of Adsorbate*.
Initial Coverage—Specify the initial fractional coverages of empty sites and adsorbates on catalysts. The defaults are 1.0 for empty sites and 0.0 for adsorbates. The coverages must sum to 1.0 for each catalyst with individual coverages between 0.0 and 1.0.
Lateral Scaling Parameter (eV)—Specify scaling parameters used to calculate the lateral interaction corrections to the reaction energies. Parameters for adsorbate pairs are calculated using the geometric mean combination rule. Only present when Simple quadratic is selected in the Adsorbate-adsorbate interactions option menu.

Add Adsorbate button

Add a row to the Adsorbed intermediates table for the specified adsorbate. Opens the Define Adsorbate Name dialog box so you can name the adsorbate, add an optional description, and specify the catalyst it is on. It is highly recommended to use a chemical formula (e.g. ZnC4H10) for the adsorbate name as this allows the reaction network to be checked for stoichiometric balance prior to calculation. If you choose to use other naming conventions, the reaction network is not checked.

Rename button

Change the name of an existing adsorbate in the Adsorbed intermediates table. Opens the Define Adsorbate Name dialog box so you can choose the name to update, rename the adsorbate, add an optional description, and specify the catalyst it is on. Click OK to update the name in the table.

Load Coverages button

Load a CSV file with coverages for the empty sites and adsorbates. Click to open the Open File dialog box, where you can navigate to the file. The name of the file you selected is displayed in the text box. Alternatively, manually enter coverages in the Adsorbed intermediates table.

The CSV file must contain the headers Species,Coverage to be compatible with the panel. The headers should be followed by a <species>,<coverage> row for each empty site or adsorbate.

This can be a useful feature when loading coverages from the steady state of a previous calculation or to restart a calculation if it didn’t fully converge.

Absorbed intermediates table

Optionally specify information for each species absorbed into a bulk material. The information provided here populates the Reaction table.

Name—The name of the absorbate and the bulk material containing it is displayed as Absorbate:Bulk. This is identical to the commonly used nomenclature of Absorbate*.

Add Absorbate button: Add a row to the Absorbed intermediates table for the specified absorbate. Opens the Define Absorbate Name dialog box so you can name the absorbate, add an optional description, and specify the bulk material containing it. It is highly recommended to use a chemical formula (e.g. H2O) for the absorbate name as this allows the reaction network to be checked for stoichiometric balance prior to calculation. If you choose to use other naming conventions, the reaction network is not checked.
Rename button: Change the name of an existing absorbate in the Absorbed intermediates table. Opens the Define Absorbate Name dialog box so you can choose the name to update, rename the absorbate, add an optional description, and specify the bulk material containing it. Click OK to update the name in the table.

Gas/solute species table

Specify information for each species in the gas or solution fluid phase. The information provided here populates the Reaction table.

Name—The name of the gas/solute is displayed.
Partial Pressure in Inlet Stream (bar)—Specify the initial partial pressure of the gas/solute in the inlet stream in bar. To allow these values to change during the course of the calculation, select the Microkinetic Modeling Panel; otherwise the pressures will be held constant.
Molecular Weight (g/mol)—Specify the molecular weight of the gas/solute. For valid molecular formulae, the molecular weight is automatically populated.
Variable Pressure—Select this option to allow gas or solute pressures to change from their specified initial values.

Add Gas/Solute button: Add a row to the Gas/solute species table for the specified gas or solute. Opens the Define Gas/Solute Name dialog box so you can name the gas or solute and add an optional description. It is highly recommended to use a chemical formula (e.g. CO2) for the gas/solute name as this allows the reaction network to be checked for stoichiometric balance prior to calculation. If you choose to use other naming conventions, the reaction network is not checked.
Rename button: Change the name of an existing gas/solute in the Gas/solute species table. Opens the Define Gas/Solute Name dialog box so you can choose the name to update, rename the gas/solute, and add an optional description. Click OK to update the name in the table.

Adsorbate-adsorbate interactions option menu

Specify the model for adsorbate-adsorbate interactions:

None—Adsorbate-adsorbate interactions are ignored in the calculation.
Simple quadratic—A simple second-order dependence on the coverage is specified for free energy barriers. Selecting this option adds the Lateral Scaling Parameter column to the Absorbed intermediates table and the TS Lateness Parameter column to the Free Energy Barriers section of the Reactions table.

Reactions section

Provide stoichiometric coefficients and activation free energies for all elementary reactions that make up the reaction of interest.

Reactions table

Specify information for all of the elementary reactions that make up the reaction of interest. The Reaction table is populated with all specified adsorbed intermediates, absorbed intermediates, gas/solute species, and empty sites from the Species section.

Name—The name of the reaction is displayed.
Stoichiometric Coefficients—Specify the stoichiometric coefficients of all elementary reactions participating in the reaction network. Negative numbers are used for reactants, positive numbers are used for products, and the quantities themselves are used for the coefficients.
Free Energy Barriers—Specify the forward and reverse activation free energies, in eV, the collision factor, and the TS lateness parameter for each reaction.

Activation free energies can be extracted from literature data or calculated by performing quantum mechanical calculations using tools such as the Nudged Elastic Band Calculations Panel and Phonon Density of States calculations. See the Microkinetic Modeling tutorial for an example. It is suggested that the activation free energies should be calculated at the temperature specified in the Temperature text box.

Choose a collision factor (Arrhenius prefactor) for computing the reaction rate constant from the option menu. The default is Auto. The Auto option applies the Hertz-Knudsen collision factor if there is a single, molecular adsorption or desorption process in the reaction; otherwise it applies the Eyring collision factor. It defines how the lateral correction to the reaction energy is partitioned into forward and reverse barriers

The TS Lateness Parameter column is only present when Simple quadratic is selected in the Adsorbate-adsorbate interactions option menu. A value of 0 means that the transition state resembles the reactants while a value of 1 means that it resembles the products. This parameter defines how the lateral correction to the reaction energy is partitioned into forward and reverse barriers.

New Reactions button

Add one or more new reaction(s) to the Reactions table. Opens the New Reactions Editor dialog box so you can enter the reaction. The dialog box has an example of the syntax and format to use when adding reactions. Add multiple reactions at once by using a new line for each reaction.

Add Reaction button

Add a row to the Reactions table for the specified reaction. Opens the Define Reaction Name dialog box so you can name the reaction.

Rename Reaction button

Change the name of an existing reaction in the Reactions table. Opens the Define Reaction Name dialog box so you can choose the name to update and rename the reaction. Click OK to update the name in the table.

View Reactions button

Opens the View Reactions dialog which displays a simplified version of the reaction network specified in this tab. This can be helpful in building or modifying a reaction network of interest. The Export as PNG button exports the complete contents of the Reaction Viewer (including all reactions, not just the visible portion) to a PNG image file for sharing or reporting.

Steady State tab

Choose to search for a steady state solution and specify additional related parameters.

Steady State option and section: Select this option to search for a steady state solution where the maximum time derivative of coverages, and if relevant, pressures, is below the specified Convergence tolerance. The ODE solver is stopped once the convergence tolerance is met. If the convergence tolerance is never met, then the job will fail but the results will still be returned. Do not use this option if no steady state is expected for the specified reaction network.
Convergence tolerance text box: Specify the acceptable rate of change of coverages and pressures to consider the system as having reached a steady state. Only available if the Steady State option is selected.
Calculate degree of rate control option: Calculate the degrees of rate control once steady state is reached. The degree of rate control is calculated by differentiating with respect to rate constants, and as a result can add significantly to the calculation time. Only available if the Steady State option is selected.
Calculate degree of selectivity control option: Calculate the degrees of selectivity control once steady state is reached. Only available if the Steady State option is selected.
Calculate reaction order option: Calculate the reaction order with respect to each gas-phase species once steady state is reached. Reaction orders are calculated by differentiating with respect to pressures, and as a result can add significantly to the calculation time. Only available if the Steady State option is selected.
Numerical derivative step size text box: Specify the relative magnitude of the perturbation used in the differentiation of rates by finite differences in order to calculate the degree of rate control or reaction order. Increasing the step size decreases the computation time but may lead to less accurate results. Only available when at least one of the Calculate degree of rate control or Calculate reaction order options are selected and the Steady State option is selected.

Solver Settings tab

Specify solver parameters for the microkinetic modeling calculation.

ODE solver option menu

Specify the ODE solver to use. Choose between RK45 [1], RK23 [2], DOP853 [3], Radau [4], BDF [5], LSODA [6, 7]. LSODA is used by default.

Jacobian options

Specify the Jacobian for the ODE solver to use:

Numerical—Use a finite difference numerical Jacobian.
Analytical—Use an analytical Jacobian. This is the default and recommended option.

Maximum integration time text box

Specify the maximum integration time in seconds.

Maximum integration time step text box

Specify the maximum integration time step in seconds.

Maximum integration wall clock time text box

Specify the maximum integration wall clock time in seconds.

Absolute Tolerance text box

Specify the absolute tolerance, the number of decimal places, to use in the ODE solver to minimize local error estimates. For more information on this parameter, see the SciPy documentation.

Relative Tolerance text box

Specify the relative tolerance, the number of digits, to use in the ODE solver to minimize local error estimates. For more information on this parameter, see the SciPy documentation.

Multistage tab

Optionally specify additional stages and related parameters for the microkinetic modeling calculation. Stage specific files, such as log files and .mae files compatible with the Microkinetic Modeling Viewer Panel can be found in the job directory under stagen.

This tab can be useful for a chemical processes influenced by changes in external conditions, such as temperature and pressure. An example of this is atomic layer deposition.

Initial Stage section

Displays a stage label, 0, and text for the initial stage which is defined in the Reactor Settings, Reaction Network, Steady State, and Solver Settings tabs. Noneditable.

Subsequent stages for a multistage run section

The tools in this section allow you to define additional microkinetic modeling stages and related parameters. The stages are run in the order they are listed.

Stage label

The label indicates the stage number and is updated if the stage is moved.

stage management buttons

These buttons perform display and ordering operations on the stage. They allow for easy duplication and rearrangement of stages.

	Show or hide the contents of the stage. When hidden, only the stage number, label (if any) and these buttons are displayed. This is useful when you have a number of stages and want to compare two separate stages, for example.
	Move the stage up or down one place in the list.
	Delete the stage.

General Options section

Specify coverage options for the additional microkinetic modeling stages. By default, all options in this section are selected.

Temperature from previous stage option: Select this option to use the same temperature as the previous stage. When this option is deselected, the Temperature text box is present.
Flowrate from previous stage option: Select this option to use the same flowrate as the previous stage. When this option is deselected, the Fluid flowrate text box is present.
Degree of rate control setting from previous stage option: Select this option to maintain the same degree of rate control selection as the previous stage. When this option is deselected, the Calculate degree of rate control option is present.
Degree of selectivity control from previous stage option: Select this option to maintain the same degree of selectivity control selection as the previous stage. When this option is deselected, the Calculate degree of selectivity control option is present.
Reaction order setting from previous stage option: Select this option to maintain the same reaction order selection as the previous stage. When this option is deselected, the Calculate reaction order option is present.
Maximum integration time from previous stage option: Select this option to use the same maximum integration time as the previous stage. When this option is deselected, the Maximum integration time text box is present.

Coverage Options section

Specify coverage options for the additional microkinetic modeling stages. By default, all options in this section are selected.

Coverage from final value of previous stage option: Select this option to use the final coverages from the previous stage. When this option is deselected, the Adsorbed intermediates table and Load Coverages button are present.

Pressure Options section

Specify coverage options for the additional microkinetic modeling stages. By default, all options in this section are selected.

Pressures from final value of previous stage option: Select this option to use the final pressures from the previous stage. When this option is deselected, the Gas/solute species table is present.

Append Stage button

Click this button to add another stage tool set at the end of the list.

Job toolbar

Manage job submission and settings. See Job Toolbar for a description of this toolbar.

The Job Settings button opens the Microkinetic Modeling - Job Settings Dialog Box, where you can make settings for running the job.

Status bar

Use the Reset button to reset the panel to its default settings and clear any data from the panel. If the panel has a Job toolbar, you can also reset the panel from the Settings button menu.

If you can submit a job from the panel, the status bar displays information about the current job settings and status for the panel. The settings include the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation.

The status bar also contains the Help button , which opens an option menu with choices to open the help topic for the panel (Documentation), launch Maestro Assistant, or if available, choose from an option menu of Tutorials. If the panel is used by one or more tutorials, hover over the Tutorials option to display a list of tutorials. Choosing a tutorial opens the tutorial topic.

Tutorials

Microkinetic Modeling Panel

Using the Microkinetic Modeling Panel

Microkinetic Modeling Panel Features

Related Topics