vaspup2.0

A collection of bash scripts to efficiently generate and analyse VASP convergence-testing calculations. The original vaspup was developed by Alex Ganose for ground-state energy convergence testing and POTCAR generation.

vaspup2.0 Functionality includes

• Convergence testing of ground-state energy with respect to ENCUT (plane wave kinetic energy cutoff) (i.e. basis set size) and k-point density (specified in the KPOINTS file).
• Convergence testing of atomic forces with respect to ENCUT (plane wave kinetic energy cutoff)(i.e. basis set size) and k-point density (specified in the KPOINTS file), which uses the checkforce script written by Dr Ben Morgan 🙌
• Convergence testing of $\epsilon_{Ionic}$ (ionic contribution to the static dielectric constant $\epsilon_0 = \epsilon_{Ionic} + \epsilon_{Optic}$) with respect to ENCUT and k-point density, calculated with Density Functional Perturbation Theory (DFPT).
• Convergence testing of $\epsilon_{Optic}$ (optical / high-frequency dielectric constant) with respect to NBANDS, calculated with using the method of Furthmüller et al. (LOPTICS = True).

Installation

Installation is quite simple, just clone this git repository and update your PATH to include the location of the bin folder.

git clone https://github.com/kavanase/vaspup2.0
echo "export PATH=\"${PWD}/vaspup2.0/bin:\${PATH}\"" >> ~/.bashrc
source ~/.bashrc  # Update the current shell

Implementation

Ground-State Energy Convergence

To quickly set up a ground-state energy convergence test, the following steps are required:

• Create a folder named input, containing INCAR, KPOINTS, POSCAR, and POTCAR VASP input files, a jobscript file (job) and a CONFIG file. Example CONFIG and INCAR files are provided in the input directory named CONFIG and energy_INCAR respectively. (Note: Rename energy_INCAR to INCAR, and set ISPIN = 1 if your system is non-magnetic for faster calculations). The directory structure should match the below:

./<Convergence Testing Directory (run script from here)>
    ./input
        /INCAR
        /KPOINTS
        /POSCAR
        /POTCAR
        /CONFIG
        /job

• Customise the CONFIG file as you wish (specifying ENCUT and k-point convergence parameters and (optionally) the name to append to each jobname).

• Run the generate-converge executable from the directory above the input directory. A series of folders will be created, with the folder names matching the calculation settings. For example, the cutoff_converge/e450 folder will contain the ENCUT = 450 eV calculation and the kpoint_converge/k664 folder will contain the calculation with a k-mesh of $6\times6\times4$.

Note that vaspup2.0 uses the SGE qsub job submission command by default, but this can easily be modified in the bash scripts.

• Once the calculations have finished running, the data-converge script can be used to extract the total energies from the VASP output. This script will print the convergence data to the terminal (as shown below) as well as saving to a file named Convergence_Data. The data-converge script should be run separately within the folders named kpoint_converge and cutoff_converge.

Example output from data-converge:

Note that, for semiconductor materials, a denser k-point mesh is typically required for accurate density of states and optical absorption spectra. See Density of States & Absorption Spectrum Convergence examples below.

Ionic Dielectric Constant (DFPT) Convergence

The calculated value for the ionic contribution to the static dielectric constant $\epsilon_{Ionic}$ ($\epsilon_0 = \epsilon_{Ionic} + \epsilon_{Optic}$) is quite sensitive to both the plane wave kinetic energy cutoff ENCUT and the k-point density, with more expensive parameter values necessary (relative to ground-state-energy-converged values) due to the requirement of accurate ionic forces. This is demonstrated in the Dielectric_Constants_Convergence Jupyter notebook. Thus, calculation of the $\epsilon_{Ionic}$ should be accompanied by convergence tests with respect to these parameters.

To quickly set up a convergence test for $\epsilon_{Ionic}$, the following steps are required (note similarity to ground-state energy convergence procedure):

• Create a folder named input, containing appropriate INCAR, KPOINTS, POSCAR, and POTCAR files, in addition to a CONFIG file. Example CONFIG and INCAR files are provided in the input directory named CONFIG and dfpt_INCAR respectively. (Note: Rename dfpt_INCAR to INCAR). The directory structure should match the below:

./<DFPT Convergence Testing Directory (run script from here)>
    ./input
        /INCAR
        /KPOINTS
        /POSCAR
        /POTCAR
        /CONFIG
        /job

• Customise the CONFIG file as you wish (specifying ENCUT and k-point convergence parameters and (optionally) the name to append to each jobname).

• Run the generate-converge executable from the directory above the input directory. A series of folders will be created, with the folder names matching the calculation settings.

• Once the calculations have finished running, the dfpt-data-converge script can be used to extract the values for the ionic contribution to the static dielectric constant $\epsilon_{Ionic}$ (specifically the diagonal terms from the MACROSCOPIC STATIC DIELECTRIC TENSOR IONIC CONTRIBUTION in the VASP OUTCAR files). This script will print the convergence data to the terminal (as shown below) as well as saving to a file named Convergence_Data. The data-converge script should be run separately within the folders named kpoint_converge and cutoff_converge.

Example output from dfpt-data-converge:

Beware Warning: PSMAXN too small for non-local potential (in OUTCAR and stdout files) at too high ENCUT! It has been observed that when too large an ENCUT is used (depending on the 'hardness' of the pseudopotentials - determined by ENMAX in the POTCAR files) VASP appears to run as normal (but with Warning: PSMAXN too small for non-local potential printed in the OUTCAR and stdout files), but the results for $\epsilon_{Ionic}$ begin to diverge. This is demonstrated in the Dielectric_Constants_Convergence Jupyter notebook ("Region of Shit" red-zones).

Note that this INCAR is for calculating the ionic contribution to the dielectric constant. If you want to calculate other properties such as the elastic constant, you will need to change INCAR tages (e.g. ISIF = 3 for elastic constants).

Optical Dielectric Constant Convergence

The calculated value for the optical dielectric constant $\epsilon_{Optic}$ ($\epsilon_0 = \epsilon_{Ionic} + \epsilon_{Optic}$) is quite sensitive to the number of electronic bands included in the calculation (NBANDS), with a large number of unoccupied bands required for convergence, as demonstrated in the Dielectric_Constants_Convergence Jupyter notebook. Thus, calculation of the $\epsilon_{Optic}$ should be accompanied by a convergence test with respect to this parameter. Note that the calculated value for $\epsilon_{Optic}$ is typically not sensitive to either the plane wave kinetic energy cutoff ENCUT or the k-point density, assuming you are using values that are well-converged with respect to the ground-state energy! Additionally, note that the_optical absorption spectrum_, as with the density of states, typically requires a denser k-point mesh to give a converged result, than for total energy or optical dielectric constant. See Density of States & Absorption Spectrum Convergence examples below.

To quickly set up an NBANDS convergence test for $\epsilon_{Optic}$, the following steps are required:

• Create a folder named input, containing appropriate INCAR, KPOINTS, POSCAR, and POTCAR files, in addition to a CONFIG file. Example CONFIG and INCAR files are provided in the input directory named nbands_CONFIG and nbands_INCAR respectively. (Note: Rename to CONFIG and INCAR). The directory structure should match the below:

./<NBANDS Convergence Testing Directory (run script from here)>
    ./input
        /INCAR
        /KPOINTS
        /POSCAR
        /POTCAR
        /CONFIG
        /job

• Customise the CONFIG file as you wish (specifying the NBANDS convergence parameters and (optionally) the name to append to each jobname).

• Run the nbands-generate-converge executable from the directory above the input directory. A series of folders will be created, with the folder names matching the calculation settings. For example, the nbands_converge/nbands_100 folder will contain the NBANDS = 100 calculation

• Once the calculations have finished running, the nbands-epsopt-data-converge script can be run in the nbands_converge directory to extract the values for the optical dielectric constant $\epsilon_{Optic}$ (specifically the X, Y and Z components of the frequency dependent REAL DIELECTRIC FUNCTION in the VASP OUTCAR files). This script will print the convergence data to the terminal (as shown below) as well as saving to a file named NBANDS_Convergence_Data.

Example output from nbands-epsopt-data-converge:

Note

For accurate calculations of the optical dielectric constant $\epsilon_{Optic}$, it is recommended to use Hybrid DFT (such as the HSE06 functional) or a similar level of theory. However, in the example nbands_INCAR file, the PBEsol GGA DFT functional is used for the purpose of efficient use of computational resources during convergence testing. It is advised to use this cheaper lower-level theory in order to obtain a good estimate of the required number of electronic bands (NBANDS) for a well-converged value of the optical dielectric constant. Once the required NBANDS has been determined from the GGA DFT convergence test, it can then be used in a single Hybrid DFT calculation of $\epsilon_{Optic}$.

This procedure assumes similar convergence behaviour (wrt NBANDS) within Hybrid DFT as for GGA DFT. This is a reasonable assumption in this case, as GGA DFT tends to underestimate band gaps, implying that it would require a larger number of electronic bands to cover the required energy range for convergence of $\epsilon_{Optic}$, than for Hybrid DFT. Hence, a well-converged value of NBANDS for GGA DFT should certainly correspond to a well-converged value for Hybrid DFT, as has been observed.

Additionally, it should be noted that VASP automatically rounds NBANDS to the nearest multiple of NPAR = # of cores / (NCORE * KPAR). So ideally these parameters should be set so that NPAR is a factor of the NBANDS increment in the CONFIG file.

syntax error

If data-converge gives the output (standard_in) 1: syntax error, then it means that vaspup2.0 is having trouble parsing some or all of the calculation results. Typically, this means that some or all of the calculations failed, and so the solution is to look at the output files of the calculations and decide what needs to be changed for the caculations to be successful (e.g. reduce NCORE in INCAR to avoid parallelisation errors, increase job CPU hours to allow calculation to converge in time etc.), then re-run generate-converge. Also, if only some of the calculations failed, it is usually obvious from the output of data-converge in this case (Hint: they're the ones with batshit crazy energies), now go fix those calculations!

integer expression expected

If you have both vaspup2.0 and the older vaspup on your $PATH, and are using the vaspup2.0 CONFIG files, you may encounter the following error:

/home/path/to/src/vaspup/bin/generate-converge: line 16: [: : integer expression expected

In this case, the advice is to remove the older vaspup commands from your $PATH and/or remove the vaspup folder from your system.

Alternatively, this error can occur if a required tag (conv_encut, conv_kpoint, run_vasp etc.) in the CONFIG file is commented out.

Tips

For k-point convergence testing (of ground-state energy or $\epsilon_{Ionic}$), the k-point meshes to be tested must be explicitly provided in the CONFIG file (to allow for non-cubic systems), as below:

kpoints="3 3 2,4 4 3,5 5 4,6 6 5,7 7 6,8 8 7,9 9 8" # All the kpoints meshes
# you want to try, separated by a comma

Instead for convenience, one can auto-generate the k-points using the kgs_gen_kpts script:

kgs_gen_kpts

This will auto-populate the CONFIG file with the k-point meshes corresponding to real-space cutoff distances between 5 Å and 25 Å (default values – typically good for semiconductors and insulators, may need to be increased for metals). These real-space cutoff distances can be specified as arguments to the script in the format kgs_gen_kpts {min_real_space_cutoff} {max_real_space_cutoff}, if they need to be changed.

kgs_gen_kpts -h  # "-h" shows help message

vaspup2.0 - Seán Kavanagh ([email protected]), 2023
Usage: in 'input' directory with POSCAR and CONFIG files present, and 'kpoints' mentioned in CONFIG file.
$ kgs_gen_kpts {min_real_space_cutoff} {max_real_space_cutoff}
(Default: min = 5, max = 25 – max likely needs to be increased for metals)

This script uses the excellent kgrid package developed by Adam Jackson to generate appropriate k-point meshes corresponding to a given real-space length cutoff (in Angstrom).

A general recommendation for DFT-calculated dielectric constants is to converge the predicted value to within 0.1, at least, though this of course depends on the target property! For example, this criterion typically gives a well-converged optical absorption spectrum, something which can be quickly verified visually, using:

for i in nbands_*; do cd $i; sumo-optplot --ymax 2e6 --xmax 4; cd ..; done

then look at the absorption.pdf files in each directory.

Density of States and Absorption Spectrum Convergence

While the total energy and high-frequency dielectric constant $\epsilon_{Optic}$ were converged to within 1 meV/atom and 0.1 respectively at a k-point mesh of 3x3x3, convergence of the density of states and absorption spectrum are not reached until much higher k-point densities of 6x6x6. Note that use of tetrahedron smearing (ISMEAR = -5) will typically give better convergence of the density of states (i.e. converged at lower k-point densities) than Gaussian smearing (ISMEAR = 0), and is absolutely essential for optical absorption calculations.

Citation

If you use vaspup2.0 in your work, please cite as: S. R. Kavanagh, vaspup2.0 Zenodo DOI: 10.5281/zenodo.8408542 2023.

Disclaimer

This program is not affiliated with VASP. This program is made available under the MIT License; you are free to modify and use the code, but do so at your own risk.