Difference between revisions of "Methods"
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To make a supercell or a slab from the new unit cell you have just created VESTA you have to export the unit cell in a .vasp format. Open the vasp file in VESTA and then follow the same procedure for the creation of a supercell as has been explained above. | To make a supercell or a slab from the new unit cell you have just created VESTA you have to export the unit cell in a .vasp format. Open the vasp file in VESTA and then follow the same procedure for the creation of a supercell as has been explained above. | ||
| − | Finite-size correction for slab supercell calculations of materials with spontaneous polarization <ref> Yoo, SH., Todorova, M., Wickramaratne, D. et al. Finite-size correction for slab supercell calculations of materials with spontaneous polarization. npj Comput Mater 7, 58 (2021) http://dx.doi.org/10.1038/s41524-021-00529-1 </ref> | + | Finite-size correction for slab supercell calculations of materials with spontaneous polarization <ref>Yoo, SH., Todorova, M., Wickramaratne, D. et al. Finite-size correction for slab supercell calculations of materials with spontaneous polarization. npj Comput Mater 7, 58 (2021) http://dx.doi.org/10.1038/s41524-021-00529-1 </ref> |
===Grain boundaries and interfaces=== | ===Grain boundaries and interfaces=== | ||
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[[Software and resources#Materials project|Materials project]] provides a list of matching structures and terminations under the '''Substrates''' section for a selected structure. | [[Software and resources#Materials project|Materials project]] provides a list of matching structures and terminations under the '''Substrates''' section for a selected structure. | ||
| − | Special grain boundaries in perovskites <ref> B. M. Darinskiy, N. D. Efanova & D. S. Saiko (2020) Special grain boundaries in perovskite crystals, Ferroelectrics, 567:1, 13-19, https://doi.org/10.1080/00150193.2020.1791582 </ref> | + | Special grain boundaries in perovskites <ref>B. M. Darinskiy, N. D. Efanova & D. S. Saiko (2020) Special grain boundaries in perovskite crystals, Ferroelectrics, 567:1, 13-19, https://doi.org/10.1080/00150193.2020.1791582 </ref> |
| − | Machine learning sampling to determine rigid body translation <ref> Application of machine learning-based selective sampling to determine BaZrO3 grain boundary structures, Computational Materials Science, 164 (2019) 57-65. https://doi.org/10.1016/j.commatsci.2019.03.054 </ref> | + | Machine learning sampling to determine rigid body translation <ref>Application of machine learning-based selective sampling to determine BaZrO3 grain boundary structures, Computational Materials Science, 164 (2019) 57-65. https://doi.org/10.1016/j.commatsci.2019.03.054 </ref> |
===Disordered structures=== | ===Disordered structures=== | ||
| Line 52: | Line 52: | ||
===Charge correction=== | ===Charge correction=== | ||
| − | Self-Consistent Potential Correction for Charged Periodic Systems <ref> Mauricio Chagas da Silva, Michael Lorke, Bálint Aradi, Meisam Farzalipour Tabriz, Thomas Frauenheim, Angel Rubio, Dario Rocca, and Peter Deák | + | Self-Consistent Potential Correction for Charged Periodic Systems <ref>Mauricio Chagas da Silva, Michael Lorke, Bálint Aradi, Meisam Farzalipour Tabriz, Thomas Frauenheim, Angel Rubio, Dario Rocca, and Peter Deák |
Phys. Rev. Lett. 126, 076401. https://doi.org/10.1103/PhysRevLett.126.076401 </ref> | Phys. Rev. Lett. 126, 076401. https://doi.org/10.1103/PhysRevLett.126.076401 </ref> | ||
| − | CoFFEE: Corrections For Formation Energy and Eigenvalues for charged defect simulations <ref> Naik, Mit H., and Manish Jain. CoFFEE: corrections for formation energy and eigenvalues for charged defect simulations. Computer Physics Communications 226 (2018) 114-126. https://doi-org/10.1016/j.cpc.2018.01.011 </ref> | + | CoFFEE: Corrections For Formation Energy and Eigenvalues for charged defect simulations <ref>Naik, Mit H., and Manish Jain. CoFFEE: corrections for formation energy and eigenvalues for charged defect simulations. Computer Physics Communications 226 (2018) 114-126. https://doi-org/10.1016/j.cpc.2018.01.011 </ref> |
Limitations of empirical supercell extrapolation for calculations of point defects in bulk, at surfaces, and in two-dimensional materials <ref>Christoph Freysoldt, Jörg Neugebauer, Anne Marie Z. Tan, and Richard G. Hennig, Limitations of empirical supercell extrapolation for calculations of point defects in bulk, at surfaces, and in two-dimensional materials, Phys. Rev. B 105, 01410 http://dx.doi.org/10.1103/PhysRevB.105.014103 </ref> | Limitations of empirical supercell extrapolation for calculations of point defects in bulk, at surfaces, and in two-dimensional materials <ref>Christoph Freysoldt, Jörg Neugebauer, Anne Marie Z. Tan, and Richard G. Hennig, Limitations of empirical supercell extrapolation for calculations of point defects in bulk, at surfaces, and in two-dimensional materials, Phys. Rev. B 105, 01410 http://dx.doi.org/10.1103/PhysRevB.105.014103 </ref> | ||
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| + | The nudged elastic band (NEB) is a method for finding saddle points and minimum energy paths between known reactants and products. The method works by optimizing a number of intermediate images along the reaction path. Each image finds the lowest energy possible while maintaining equal spacing to neighboring images. This constrained optimization is done by adding spring forces along the band between images and by projecting out the component of the force due to the potential perpendicular to the band. | ||
| + | |||
| + | The climbing image method can be turned by setting '''LCLIMB''' = .TRUE. in the INCAR file. | ||
| + | |||
| + | For POSCAR, you can use '''nebmake.pl to t'''akes initial and final POSCAR files, and linearly interpolates the specified number of images between them. The interpolated files are written to the directories 00 to NI+1, where NI is the number of specified images. | ||
| + | |||
| + | '''nebmake.pl can be found''' https://theory.cm.utexas.edu/vtsttools/scripts.html | ||
==Polaron localization== | ==Polaron localization== | ||
| − | == | + | Normally polarons which are localized at d or p orbitals normally require DFT+U hybrid functionals. |
| + | |||
| + | The U value will determine the localization energy. | ||
| + | |||
| + | To determine the proper U value for this calculations, the a piecewise linear method is strongly recommended. | ||
| + | |||
| + | More detail can be found ''Physical Review B'', ''90''(3), 035204. | ||
| + | |||
| + | To visualize the polaron localization, you can generate the partial charge density, by set: | ||
| + | |||
| + | LPARD = T | ||
| + | |||
| + | IBAND = XX, the band where you localized polaron is. | ||
| + | |||
| + | The PARCHG will be generated after calculation, and it can be visualized in the VESTA. | ||
==Bader charge analysis== | ==Bader charge analysis== | ||
| − | + | INCAR | |
| + | |||
| + | PREC = A | ||
| + | |||
| + | LAECHG = T | ||
| + | |||
| + | The core charge is written to AECCAR0 and the valance charge to AECCAR2. These two charge density files can be summed using the chgsum.pl script; | ||
| + | chgsum.pl AECCAR0 AECCAR2 | ||
| + | |||
| + | The bader analysis can then be done on this total charge density file: | ||
| + | bader CHGCAR -ref CHGCAR_sum | ||
==Error messages== | ==Error messages== | ||
Revision as of 11:24, 28 February 2022
Contents
Methods
VASP Wiki and Support Forum
The VASP manual contains information on all INCAR tags and tutorials and guides to several types of calculations (www.vasp.at/wiki/).
The VASP Support Forum (www.vasp.at/forum/) allows users to troubleshoot and discuss technical and scientific topics. The VASP developers are also active in answering questions.
Convergence and Efficiency
Convergence tests
How to and relevant examples.
Benchmark
VASP efficiency on Saga (number of nodes/cores)
Computational cost: atoms vs kpoints vs functional etc.
General calculations and relaxation
NELM, NSW
Systems
Supercells
A supercell can be made in VESTA by going into Edit -> Edit data -> Unit Cell...
When the window for the unit cell has opened press Transform, change the numbers in the Transformation matrix to make a supercell of your choice.
Surfaces and slabs
Slabs can be constructed using ASE.
A specific surface can be exposed using VESTA, here is a youtube tutorial for exposing the (110) surface of a TiO2 rutile structure, tutorials for other structures can be found on the same youtube channel.
To make a supercell or a slab from the new unit cell you have just created VESTA you have to export the unit cell in a .vasp format. Open the vasp file in VESTA and then follow the same procedure for the creation of a supercell as has been explained above.
Finite-size correction for slab supercell calculations of materials with spontaneous polarization [1]
Grain boundaries and interfaces
Typically modeled as Coincident Site Lattice (CSL) structures that are optimized by rigid body translation.
Materials project provides a list of matching structures and terminations under the Substrates section for a selected structure.
Special grain boundaries in perovskites [2]
Machine learning sampling to determine rigid body translation [3]
Disordered structures
Site occupancy disorder program: https://github.com/gcmt-group/sod
TDEP code for generating special quasirandom structures
Defect calculations
Charge correction
Self-Consistent Potential Correction for Charged Periodic Systems [4]
CoFFEE: Corrections For Formation Energy and Eigenvalues for charged defect simulations [5]
Limitations of empirical supercell extrapolation for calculations of point defects in bulk, at surfaces, and in two-dimensional materials [6]
Defect configurations
Evolutionary computing and machine learning for discovering of low-energy defect configurations [7]
Phonon calculations
Nudged Elastic Band (NEB)
The nudged elastic band (NEB) is a method for finding saddle points and minimum energy paths between known reactants and products. The method works by optimizing a number of intermediate images along the reaction path. Each image finds the lowest energy possible while maintaining equal spacing to neighboring images. This constrained optimization is done by adding spring forces along the band between images and by projecting out the component of the force due to the potential perpendicular to the band.
The climbing image method can be turned by setting LCLIMB = .TRUE. in the INCAR file.
For POSCAR, you can use nebmake.pl to takes initial and final POSCAR files, and linearly interpolates the specified number of images between them. The interpolated files are written to the directories 00 to NI+1, where NI is the number of specified images.
nebmake.pl can be found https://theory.cm.utexas.edu/vtsttools/scripts.html
Polaron localization
Normally polarons which are localized at d or p orbitals normally require DFT+U hybrid functionals.
The U value will determine the localization energy.
To determine the proper U value for this calculations, the a piecewise linear method is strongly recommended.
More detail can be found Physical Review B, 90(3), 035204.
To visualize the polaron localization, you can generate the partial charge density, by set:
LPARD = T
IBAND = XX, the band where you localized polaron is.
The PARCHG will be generated after calculation, and it can be visualized in the VESTA.
Bader charge analysis
INCAR
PREC = A
LAECHG = T
The core charge is written to AECCAR0 and the valance charge to AECCAR2. These two charge density files can be summed using the chgsum.pl script;
chgsum.pl AECCAR0 AECCAR2
The bader analysis can then be done on this total charge density file:
bader CHGCAR -ref CHGCAR_sum
Error messages
References
- ↑ Yoo, SH., Todorova, M., Wickramaratne, D. et al. Finite-size correction for slab supercell calculations of materials with spontaneous polarization. npj Comput Mater 7, 58 (2021) http://dx.doi.org/10.1038/s41524-021-00529-1
- ↑ B. M. Darinskiy, N. D. Efanova & D. S. Saiko (2020) Special grain boundaries in perovskite crystals, Ferroelectrics, 567:1, 13-19, https://doi.org/10.1080/00150193.2020.1791582
- ↑ Application of machine learning-based selective sampling to determine BaZrO3 grain boundary structures, Computational Materials Science, 164 (2019) 57-65. https://doi.org/10.1016/j.commatsci.2019.03.054
- ↑ Mauricio Chagas da Silva, Michael Lorke, Bálint Aradi, Meisam Farzalipour Tabriz, Thomas Frauenheim, Angel Rubio, Dario Rocca, and Peter Deák Phys. Rev. Lett. 126, 076401. https://doi.org/10.1103/PhysRevLett.126.076401
- ↑ Naik, Mit H., and Manish Jain. CoFFEE: corrections for formation energy and eigenvalues for charged defect simulations. Computer Physics Communications 226 (2018) 114-126. https://doi-org/10.1016/j.cpc.2018.01.011
- ↑ Christoph Freysoldt, Jörg Neugebauer, Anne Marie Z. Tan, and Richard G. Hennig, Limitations of empirical supercell extrapolation for calculations of point defects in bulk, at surfaces, and in two-dimensional materials, Phys. Rev. B 105, 01410 http://dx.doi.org/10.1103/PhysRevB.105.014103
- ↑ Arrigoni, M., Madsen, G.K.H. Evolutionary computing and machine learning for discovering of low-energy defect configurations. npj Comput Mater 7, 71 (2021). https://doi.org/10.1038/s41524-021-00537-1
