122338

10111213

Table of Contents

Table of ContentsUsing QuantumATK to work with Nudged Elastic Band calculations in VASP

IntroductionCreating the initial and final configurationsSetting up the VASP input for optimizing the bulk PtCreating and optimizing the end-pointsConstructing the NEB pathSetting up the NEB calculationAnalyzing the resultsReferences

Downloads & LinksDownloads & Links

PDF version VASP website

Docs » Tutorials » QuantumATK as GUI for VASP »Using QuantumATK to work with Nudged Elast ic Band calculat ions in VASP

Using QuantumATK to work with Nudged Elast icUsing QuantumATK to work with Nudged Elast icBand calculat ions in VASPBand calculat ions in VASP

In this tutorial, you will learn how to set up a Nudged Elast ic BandNudged Elast ic Band (NEB) calculat ion for VASPVASP and how toanalyze the output f iles by using Quant umAT KQuant umAT K, your graphical user interface for VASPVASP!

At t ent ionAt t ent ion

In part icular, you will benefit from a new method for the creat ion of high quality init ial react ion paths.This method is based on image- dependent pair pot ent ials (IDPP)image- dependent pair pot ent ials (IDPP) [SPSJ14] and it is nowimplemented in Quant umAT KQuant umAT K. Using this can reduce the total computat ional t ime by a factor of 2 to10, compared to the most commonly used technique of linear interpolat ion!

Not eNot e

If you are not familiar with the VASP Script erVASP Script er, f irst check out the more general Set up and analyzeVASP calculat ions with QuantumATK for a full descript ion of how to set up and analyze VASPVASPcalculat ions with Quant umAT KQuant umAT K.

In t roduct ionIn t roduct ion

This tutorial closely follows the NEB tutorial for Quant umAT KQuant umAT K/AT KAT K Pt diffusion on Pt surfaces using NEBcalculat ions. and covers the following steps:

opt imize the bulk Pt from scratch using VASP;construct the end-points for the “exchange diffusion” process of a Pt adatom on Pt (100) usingQuant umAT KQuant umAT K and opt imize them with VASP;construct the init ial guess for the NEB path for the same process;set up and run the NEB calculat ions with VASP;analyze the VASP output f iles with Quant umAT KQuant umAT K.

Quant umAT KQuant umAT K

Try it !

QuantumATK

Contact

The tutorial covers the same topic discussed in the VASP tutorial “Collect ive jumps of a Pt adatom onfcc-Pt (001): Nudged Elast ic Band Calculat ion”, although here the system geometry is slight ly different .There you can f ind more informat ions about VASP keywords and other input f iles.

Not eNot e

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

Not eNot e

To use the advanced VASP funct ionalit ies in Quant umAT KQuant umAT K you need a specif ic “ATKVASP” licensefeature. If the POSCAR icons are greyed out on the LabFloorLabFloor, it means you are missing this feature inyour license f ile - in this case, contact us for opt ions using this link.

Creat ing t he in it ial and f inal conf igurat ionsCreat ing t he in it ial and f inal conf igurat ions

To create the init ial and f inal configurat ions, you can follow similar steps as those described in the NEBtutorial for Quant umAT KQuant umAT K/AT KAT K ” Pt diffusion on Pt surfaces using NEB calculat ions. Thus, here we will bebrief and just focus on the differeces due to the use of VASP instead of AT K- classicalAT K- classical as calculat ionengine.

Set t ing up t he VASP input for opt im izing t he bu lk PtSet t ing up t he VASP input for opt im izing t he bu lk Pt

1. Once you have created the bulk st ructure of Pt as described in the tutorial Pt diffusion on Pt surfacesusing NEB calculat ions, click on Tools ‣ Custom Scripter in the main Quant umAT KQuant umAT K window. TheCust om script erCust om script er panel will open up. Select Scripters ‣ VASP scripter. The VASP script erVASP script er windowwill show up.

Drag and drop the init ial configurat ion from the St ashSt ash direct ly into the VASP Script erVASP Script er.

2. If it is not already selected, in the Set upSet up tab select :

Task: St ructural Opt imizat ion

3. In the AccuracyAccuracy tab select :

General precision: Accurate

4. In the Elect ronsElect rons tab select :

Smearing algorithm: 2nd order Methfessel-Paxton methodCriterion for energy change: 0.01 meV

5. In the IonsIons tab, t ick on the Cell shape and Volume opt ions to allow for the st ructural opt imizat ion ofthe cell.

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

Creat ing and opt im izing t he end- poin t sCreat ing and opt im izing t he end- poin t s

1. Once the bulk opt imizat ion is f inished, the VASP output f iles will appear in the LabFloorLabFloor main window.Select the CONTCAR file containing the opt imized configurat ion, and drag and drop it into the BuilderBuilderto construct the geometries of the init ial and f inal end-points start ing from bulk Pt as discussed in thetutorial Pt diffusion on Pt surfaces using NEB calculat ions.

2. Once you have constructed the two configurat ions, open again the VASP Script erVASP Script er and drag and dropthe init ial configurat ion into the scripter.

3. In the Set upSet up tab select :

Task: St ructural Opt imizat ion

4. In the AccuracyAccuracy tab select :

General precision: AccurateK-point mesh: 3x3x1

5. In the Elect ronsElect rons tab select :

Smearing algorithm: 2nd order Methfessel-Paxton method

6. In the IonsIons tag, select Edit Cont rainsEdit Cont rains and constrain the coordinates of the Pt (100) bot tomost twolayers as follows (see also the f igure below):

Select the bot tomost two layers;Click Add t ag f rom select ionAdd t ag f rom select ion;Change the constrain of the tagged atoms to “Fixed”.

Once you are done, save the f iles and run VASP. Then, repeat the same steps for the f inal end-point .

Const ruct ing t he NEB pat hConst ruct ing t he NEB pat h

1. Drag and drop the opt imized configurat ions of the init ial and f inal end-point contained in the respect iveCONTCAR files into the BuilderBuilder.

2. In the BuilderBuilder, use the Nudged Elast ic BandNudged Elast ic Band plugin to setup the init ial guess for the NEB path usingthe IDPP method [SPSJ14]. Set the maximum distance to have 7 images. For more details about theopt ions available in the NEB plugin and how to modify your NEB object check the Pt diffusion on Ptsurfaces using NEB calculat ions tutorial.

Not eNot e

In order to be consistent with the constrain set t ings, remember to constrain the two bot tommostlayers also during the generat ion of the NEB path guess! You can do it by clicking on the Const rainConst rainbut ton (see the image above) in the Nudged Elast ic BandNudged Elast ic Band plugin.

3. Once the init ial guess for the NEB path has been created, select the newly created NEB configurat ion inthe St ashSt ash. The sequence of images will show up in the BuilderBuilder main window. Select the f irst imageand click on the icon on the top bar of the BuilderBuilder to ext ract the selected image from thesequence. Repeat the procedure also for the last image of the sequence.

Set t ing up t he NEB calcu lat ionSet t ing up t he NEB calcu lat ion

1. Drag and drop the NEB configurat ion object from the St ashSt ash to the VASP Script erVASP Script er.

2. In the Set upSet up tab, the only available task is NEB.3. In the PrecisionPrecision tab, select :

General precision: AccurateK-point mesh: 3x3x1

4. In the Elect ronsElect rons 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 savethe VASP input f iles. Press SaveSave 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 Script erVASP Script er window open and go back to the BuilderBuilder. Drag and drop the configurat ionof the f irst image of the NEB path that you ext racted previously from the St ashSt ash to the VASPVASPScript erScript er.

7. In the Set upSet up tab select :Task: Stat ic run (SC)

8. Save the INCAR, KPOINTS, POTCAR and POSCAR files in the 00 directory of the NEB path. The programwill ask if you want to overwrite the exist ing input f iles. Press Yes.

9. Repeat steps 6-8 for the configurat ion of the last image of the NEB path that you ext racted previouslyand save the f iles in the 06 directory.

10. Run the VASP calculat ion in the directory of the INCAR file.11. Go to the 00 directory and run the VASP calcualt ion in there. Then do the same in the 06 directory.

Analyzing t he resu lt sAnalyzing t he resu lt s

1. When all the VASP calculat ions are done, the output f iles in each of the image directories will appear onthe LabFloor, and can be analyzed as usual with the various tools in Quant umAT KQuant umAT K.

2. In the LabFloorLabFloor, select the INCAR file of the NEB calculat ion. Two configurat ions are now present ,corresponding to the init ial guess (init ial) and the opt imized path (f inal) of the NEB calculat ion.

3. To visualize the opt imized NEB path, select the f inal configurat ion and click on the Movie T oolMovie T ool in thePanel pluginsPanel plugins on the right -hand side of the LabFloorLabFloor. The following windows will show up showing theNEB path. The calculated barrier is in good agreement with the results published in the literature [Fei01].

Next

T ipT ip

The window on the right side of the Movie T oolMovie T ool is interact ive! It is possible to export the selectedimage for further analysis by left -clicking on it with the mouse and using the icon in the menuthat appears.

ReferencesReferences

[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 init ial guess for minimumenergy path calculat ions. J. Chem. Phys., 140:214106, 2014. doi:10.1063/1.4878664.

Previous

© Copyright 2020 Synopsys, Inc. All Rights Reserved.