Nudged Elastic Band Monitor Panel

Monitor the convergence of a nudged elastic band calculation.

To display this panel: click the Tasks button and browse to Materials → Quantum Mechanics → Quantum ESPRESSO → Nudged Elastic Band Convergence Monitor

The following licenses are required to use this panel: MS Maestro, Quantum Espresso Interface

  • Using
  • Features
  • Additional Resources

Using the Nudged Elastic Band Monitor Panel

The Nudged Elastic Band (NEB) Monitor is intended to monitor the convergence of jobs submitted from the Nudged Elastic Band Calculations Panel. The progress of the jobs can be monitored as they are running or once they are completed, and action taken for problematic jobs. For example, if the calculation reaches the maximum number of optimization steps but convergence is not achieved, you may want to restart the job with a larger number of steps. Alternatively, if the energy profile shows two transition states, you may want to separate the calculation into two NEB jobs.

To see the progress of the NEB job while it is running, load the CSV file (jobname.csv) from the job directory into the panel. If you are using Job Server, the following command can be used to copy the current CSV file from the execution host to the directory of interest:

$SCHRODINGER/jsc tail-file <jobid> --name <jobname>.csv > <filename>.csv

For completed jobs, the CSV file is located in the job directory.

Warning

An error dialog pops up if an outdated CSV file is loaded into the panel. The outdated CSV file can be loaded into the panel after adding the following text as the first line of the file:

#{"path_thr": n, "nimages": i}

The values of path_thr and nimages can be found in the configuration file (jobname.cfg) from the job directory.

Nudged Elastic Band Monitor Panel Features

CSV file text box and Select button

Load a CSV file from an NEB calculation. Click Select to open the Select NEB CSV file dialog box, where you can navigate to the file. The name of the file you selected is displayed in the text box. For jobs that are still running and for completed jobs, the CSV file (jobname.csv) is located in the job directory. If you are using Job Server, please see the Using section to learn how to monitor calculations that are still running.

Number of images text box

Displays the total number of structures on the reaction path as set in the Nudged Elastic Band Calculations Panel. This includes the reactant, product, and structures in between. Noneditable.

Force norm threshold text box

Displays the convergence threshold as set in the Nudged Elastic Band Calculations Panel, in eV/Å. This value corresponds to the gray dashed line in the Error convergence tab. Noneditable.

Number of steps text box

Displays the number of optimization steps completed. Noneditable.

Error convergence tab

Plots the error as a function of optimization steps.

Plot toolbar

The toolbar has tools for manipulating the plot and for saving images. The buttons that are common to all plot toolbars are described in the Plot Toolbar topic.

Plot area

This area displays the plot of the error in eV/Å against the optimization step number for all images. The Force norm threshold corresponds to the gray dashed line. The reactant and product are not shown.

The Force norm threshold, or error convergence threshold, is defined as the norm of the force orthogonal to the path. The calculation stops and is considered converged when the norm is smaller than the Force norm threshold value for all images.

Activation energy tab

Plots the activation energy as a function of optimization steps.

Plot toolbar

The toolbar has tools for manipulating the plot and for saving images. The buttons that are common to all plot toolbars are described in the Plot Toolbar topic.

Plot area

This area displays the forward and reverse activation energy in eV at each step. If the energy is converging but the calculation is running out of optimization steps you may want to restart the job with a larger number of steps.

Energy profile tab

Plots the relative or absolute energy as a function of image. Relative energies are plotted by default. Alternatively, the Reaction Profile Viewer Panel can be used to look at NEB energy profiles.

Step option menu

Choose the optimization step to display in the plot. The last step is shown by default.

Plot absolute energy option

Choose to plot the absolute energy of each image in eV. When this option is selected, the y-axis label in the plot area updates to Absolute energy, eV.

Activation energy text boxes

Display the Forward and Reverse activation energies, in eV, for the selected Step. Noneditable.

Plot toolbar

The toolbar has tools for manipulating the plot and for saving images. The buttons that are common to all plot toolbars are described in the Plot Toolbar topic.

Plot area

This area displays the energy in eV of each structure in the reaction pathway, including the reactant and product. Display the energy profile for different optimization steps using the Step option menu. Relative energies are plotted by default. Select the Plot absolute energy option to update the plot to absolute energies. If the energy profile shows two transition states, you may want to separate the calculation into two NEB jobs.

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.

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