Using Virtual NanoLab to work with Nudged Elastic Band calculations in VASP


In this tutorial, you will learn how to set up a Nudged Elastic Band (NEB) calculation for VASP and how to analyze the output files by using Virtual NanoLab, your graphical user interface for VASP!

Attention

In particular, you will benefit from a new method for the creation of high quality initial reaction paths. This method is based on image-dependent pair potentials (IDPP) [SPSJ14] and it is now implemented in VNL. Using this can reduce the total computational time by a factor of 2 to 10, compared to the most commonly used technique of linear interpolation!

Note

If you are not familiar with the VASP Scripter, first check out the more general VASP interface tutorials for a full description of how to set up and analyze VASP calculations with VNL.

Introduction

This tutorial closely follows the NEB tutorial for VNL/ATK Pt diffusion on Pt surfaces using NEB calculations. and covers the following steps:

  • optimize the bulk Pt from scratch using VASP;
  • construct the end-points for the “exchange diffusion” process of a Pt adatom on Pt(100) using VNL and optimize them with VASP;
  • construct the initial guess for the NEB path for the same process;
  • set up and run the NEB calculations with VASP;
  • analyze the VASP output files with VNL.

The tutorial covers the same topic discussed in the VASP tutorial “Collective jumps of a Pt adatom on fcc-Pt (001): Nudged Elastic Band Calculation”, although here the system geometry is slightly different. There you can find more informations about VASP keywords and other input files.

Note

This tutorial is not a guide to VASP, nor does QuantumWise provide access to the VASP code. It is assumed that you have already obtained and installed VASP from its official source (www.vasp.at) and that you are familiar with the code.

Note

To use the advanced VASP functionalities in VNL you need a specific “ATKVASP” license feature. If the POSCAR icons are greyed out on the LabFloor, it means you are missing this feature in your license file - in this case, contact us for options using this link.

Creating the initial and final configurations

To create the initial and final configurations, you can follow similar steps as those described in the NEB tutorial for VNL/ATKPt diffusion on Pt surfaces using NEB calculations. Thus, here we will be brief and just focus on the differeces due to the use of VASP instead of ATK-classical as calculation engine.

Setting up the VASP input for optimizing the bulk Pt

  1. Once you have created the bulk structure of Pt as described in the tutorial Pt diffusion on Pt surfaces using NEB calculations, click on Tools ‣ Custom Scripter in the main VNL window. The Custom scripter panel will open up. Select Scripters ‣ VASP scripter. The VASP scripter window will show up.

    ../../_images/113.png

    Drag and drop the initial configuration from the Stash directly into the VASP Scripter.


  2. If it is not already selected, in the Setup tab select:

    • Task: Structural Optimization

    ../../_images/210.png

  3. In the Accuracy tab select:

    • General precision: Accurate

    ../../_images/34.png

  4. In the Electrons tab select:

    • Smearing algorithm: 2nd order Methfessel-Paxton method
    • Criterion for energy change: 0.01 meV

    ../../_images/114.png

  5. In the Ions tab, tick on the Cell shape and Volume options to allow for the structural optimization of the cell.


    ../../_images/123.png

  6. Once you are done, press the Save icon (see the image below) to save the four input files INCAR, POSCAR, KPOINTS and POTCAR in the selected directory. Then, run VASP and wait for the output files.


    ../../_images/43.png

Creating and optimizing the end-points

  1. Once the bulk optimization is finished, the VASP output files will appear in the LabFloor main window. Select the CONTCAR file containing the optimized configuration, and drag and drop it into the Builder to construct the geometries of the initial and final end-points starting from bulk Pt as discussed in the tutorial Pt diffusion on Pt surfaces using NEB calculations.


    ../../_images/53.png

  2. Once you have constructed the two configurations, open again the VASP Scripter and drag and drop the initial configuration into the scripter.

  3. In the Setup tab select:

    • Task: Structural Optimization

  4. In the Accuracy tab select:

    • General precision: Accurate
    • K-point mesh: 3x3x1

    ../../_images/63.png

  5. In the Electrons tab select:

    • Smearing algorithm: 2nd order Methfessel-Paxton method

  6. In the Ions tag, select Edit Contrains and constrain the coordinates of the Pt(100) bottomost two layers as follows (see also the figure below):

    • Select the bottomost two layers;
    • Click Add tag from selection;
    • Change the constrain of the tagged atoms to “Fixed”.

    ../../_images/73.png

    Once you are done, save the files and run VASP. Then, repeat the same steps for the final end-point.

Constructing the NEB path

  1. Drag and drop the optimized configurations of the initial and final end-point contained in the respective CONTCAR files into the Builder.


    ../../_images/83.png

  2. In the Builder, use the Nudged Elastic Band plugin to setup the initial guess for the NEB path using the IDPP method [SPSJ14]. Set the maximum distance to have 7 images. For more details about the options available in the NEB plugin and how to modify your NEB object check the Pt diffusion on Pt surfaces using NEB calculations tutorial.

    ../../_images/133.png

    Note

    In order to be consistent with the constrain settings, remember to constrain the two bottommost layers also during the generation of the NEB path guess! You can do it by clicking on the Constrain button (see the image above) in the Nudged Elastic Band plugin.

  3. Once the initial guess for the NEB path has been created, select the newly created NEB configuration in the Stash. The sequence of images will show up in the Builder main window. Select the first image and click on the ExtractImageIcon_icon icon on the top bar of the Builder to extract the selected image from the sequence. Repeat the procedure also for the last image of the sequence.

    ../../_images/142.png

Setting up the NEB calculation

  1. Drag and drop the NEB configuration object from the Stash to the VASP Scripter.
  2. In the Setup tab, the only available task is NEB.
  3. In the Precision tab, select:
    • General precision: Accurate
    • K-point mesh: 3x3x1
  4. In the Electrons tab select:
    • Smearing algorithm: 2nd order Methfessel-Paxton method
  5. Create a new, empty directory inside the current project, and select this for the path where to save the VASP input files. Press Save to generate the INCAR, KPOINTS, POTCAR files and the 00, 01, 02, 03, 04, 05 and 06 directories, each one containing the POSCAR file of the corresponding image.
  6. Leave the VASP Scripter window open and go back to the Builder. Drag and drop the configuration of the first image of the NEB path that you extracted previously from the Stash to the VASP Scripter.
  7. In the Setup tab select:
    • Task: Static run (SC)
  8. Save the INCAR, KPOINTS, POTCAR and POSCAR files in the 00 directory of the NEB path. The program will ask if you want to overwrite the existing input files. Press Yes.
  9. Repeat steps 6-8 for the configuration of the last image of the NEB path that you extracted previously and save the files in the 06 directory.
  10. Run the VASP calculation in the directory of the INCAR file.
  11. Go to the 00 directory and run the VASP calcualtion in there. Then do the same in the 06 directory.

Analyzing the results

  1. When all the VASP calculations are done, the output files in each of the image directories will appear on the LabFloor, and can be analyzed as usual with the various tools in VNL.

  2. In the LabFloor, select the INCAR file of the NEB calculation. Two configurations are now present, corresponding to the initial guess (initial) and the optimized path (final) of the NEB calculation.


    ../../_images/93.png

  3. To visualize the optimized NEB path, select the final configuration and click on the Movie Tool in the Panel plugins on the right-hand side of the LabFloor. The following windows will show up showing the NEB path. The calculated barrier is in good agreement with the results published in the literature [Fei01].


    ../../_images/102.png

    ../../_images/movie.gif

    Tip

    The window on the right side of the Movie Tool is interactive! It is possible to export the selected image for further analysis by left-clicking on it with the mouse and using the sendto_icon icon in the menu that appears.

References

[Fei01]P. J. Feibelman. Surface diffusion mechanism versus electric field: Pt/pt(100). Phys. Rev. B, 64:125403, 2001. doi:10.1103/PhysRevB.64.125403.
[SPSJ14](1, 2) S. Smidstrup, A. Pedersen, K. Stokbro, and H. Jónsson. Improved initial guess for minimum energy path calculations. J. Chem. Phys., 140:214106, 2014. doi:10.1063/1.4878664.