DFT Preparation¶
This section discusses steps to perform DFT calculations to obtain data required to run PyProcar for post-processing. Examples of these are available in the examples directory of the Github repository. Features that require non-collinear spin calculations such as 2D spin texture plots and 3D Fermi surfaces with spin texture is currently only supported for VASP calculations. Band unfolding is also limited to VASP calculations since the phase of the wavefunctions is only parsed from the VASP PROCAR file. Support for these features in other DFT codes will be available in the future.
The flag is to be set in PyProcar functions to select the DFT code.
E.g.:
pyprocar.bandsplot(code='elk', elimit=[-5,5], mode='plain')
1. VASP¶
Required files : PROCAR, OUTCAR (optional), KPOINTS (optional)
flag : code=’vasp’ (default)
In the VASP code, the wavefunction projection information is written into the PROCAR file when LORBIT=11 is set in the INCAR file. For band unfolding, set LORBIT=12 to include phase projections of the wave functions.
An OUTCAR file is required to extract the Fermi-energy and reciprocal lattice vectors. If a KPOINTS file is provided, the \(k\)-path will automatically be labeled in the band structure.
To perform spin colinear calculations set ISPIN = 2 in the INCAR.
To perform spin non-colinear calculations set ISPIN = 2 and LNONCOLLINEAR = .TRUE..
First perform a self-consistent calculation with a \(k\)-mesh grid. Then set ICHARG=11 in the INCAR and create a KPOINTS file containing the :math:-k-path. This can be done with the Generating a k-path feature in PyProcar.
2. Elk¶
Required files : elk.in, BANDLINES.OUT, EFERMI.OUT, LATTICE.OUT, BAND_S*_A*.OUT files
flag : code=’elk’
To obtain the required files for Elk, set the following tasks in elk.in:
tasks
0
22
Additionally, for spin colinear calculations set:
spinpol
.true.
A \(k\)-path can be specified in elk.in as follows:
! These are the vertices to be joined for the band structure plot
plot1d
6 40
0.0 0.0 0.0 : \Gamma
0.5 0.0 0.0 : X
0.5 0.5 0.0 : M
0.0 0.0 0.0 : \Gamma
0.5 0.5 0.5 : R
0.5 0.0 0.0 : X
First, complete the Elk calculation and then run PyProcar in the same directory as the Elk calculations were performed.
3. Quantum Espresso¶
Required files : bands.in, kpdos.in, pdos.in,scf.in, atomic_proj.xml
flag : code=’qe’
Quantum Espresso v6.5+ is supported.
To use Pyprocar with QE, one has to run various calculations in independent directories. Here, we will show examples for the different calculations
Band Structure
Create directory called
bands.Run
pw.xon yourscf.infile.Run
pw.xon yourbands.infile. (Read kpoints section on how to add labels)Run
projwfc.xon yourkpdos.infile (Make sure kresolveddos=.true.).Make sure to copy the atomic_proj.xml file that is found in the .save directory into the main directory
Run pyprocar.bandsplot(dirname = ‘bands’ ,mode = ‘plain’, code = ‘qe’)
Density of States
Create directory called
dos.Run
pw.xon yourscf.infile.Run
pw.xon yournscf.infile.Run
projwfc.xon yourpdos.infile (Make sure kresolveddos=.false.).Make sure to copy the atomic_proj.xml file that is found in the .save directory into the main directory
Run pyprocar.dosplot(dirname = ‘bands’ ,mode = ‘plain’, code = ‘qe’)
Band Structure and Density of States
Run the band structure and dos calculation as stated above
Run pyprocar.bandsdosplot(bands_dirname = ‘bands’, dos_dirname = ‘dos’, bands_mode = ‘plain’, dos_mode = ‘plain’, code = ‘qe’)
Fermi
Create directory called
fermi.Run
pw.xon yourscf.infile.Run
pw.xon yournscf.infile.Run
projwfc.xon yourkpdos.infile (Make sure kresolveddos=.true.).Make sure to copy the atomic_proj.xml file that is found in the .save directory into the main directory
Run pyprocar.fermi3D
K-Points Format
The \(k\)-path can be specified in bands.in which is used for the band structure calculation as one of the following:
K_POINTS {crystal_b}
8
0.0000000000 0.0000000000 0.0000000000 30 !G
0.5000000000 0.0000000000 0.5000000000 30 !X
0.6250000000 0.2500000000 0.6250000000 1 !U
0.3750000000 0.3750000000 0.7500000000 30 !K
0.0000000000 0.0000000000 0.0000000000 30 !G
0.5000000000 0.5000000000 0.5000000000 30 !L
0.5000000000 0.2500000000 0.7500000000 30 !W
0.5000000000 0.0000000000 0.5000000000 30 !X
Where the one occurs is at the place of a discontinuity.
Explicit:
K_POINTS {crystal}
269
0.0000000000 0.0000000000 0.0000000000 1.0 !G
0.0083333333 0.0000000000 0.0083333333 1.0
0.0166666667 0.0000000000 0.0166666667 1.0
0.0250000000 0.0000000000 0.0250000000 1.0
0.0333333333 0.0000000000 0.0333333333 1.0
0.0416666667 0.0000000000 0.0416666667 1.0
.
.
.
0.4916666667 0.0000000000 0.4916666667 1.0
0.5000000000 0.0000000000 0.5000000000 1.0 !X
0.5062500000 0.0125000000 0.5062500000 1.0
.
.
.
0.6125000000 0.2250000000 0.6125000000 1.0
0.6187500000 0.2375000000 0.6187500000 1.0
0.6250000000 0.2500000000 0.6250000000 1.0 !U
0.3750000000 0.3750000000 0.7500000000 1.0 !K
0.3691406250 0.3691406250 0.7382812500 1.0
0.3632812500 0.3632812500 0.7265625000 1.0
0.3574218750 0.3574218750 0.7148437500 1.0
.
.
.
0.0058593750 0.0058593750 0.0117187500 1.0
0.0000000000 0.0000000000 0.0000000000 1.0 !G
Explicitly listing kpoints as ‘’!kpoint” is important for labels
To perform spincalcs set nspin = 2 and starting_magnetization(1)= 0.7
4. Lobster¶
Required files : scf.in, scf.out, lobsterin, lobsterout, FATBAND*.lobter files
flag : code=’lobster’, lobstercode=’qe’
Currently supported for Lobster with Quantum Espresso v6.3.
You must have the following settings for lobster:
wf_collect = .true. in CONTROL
nosym = .TRUE., noinv = .TRUE. in SYSTEM
The kpoints for a lobster file must be listed in the scf.in file as the following:
K_POINTS crystal
520
0.0000000 0.0000000 0.0000000 1.0
0.0000000 0.0000000 0.1428571 1.0
0.0000000 0.0000000 0.2857143 1.0
0.0000000 0.0000000 0.4285714 1.0
.
.
.
-0.1428571 -0.1428571 -0.2857143 1.0
-0.1428571 -0.1428571 -0.1428571 1.0
0.0000000000 0.0000000000 0.0000000000 0.0000 !G
0.0200000000 0.0200000000 0.0200000000 0.0000
.
.
.
0.4800000000 0.4800000000 0.4800000000 0.0000
0.5000000000 0.5000000000 0.5000000000 0.0000 !T
0.5110420726 0.4889579274 0.5000000000 0.0000
.
.
.
0.7539676705 0.2460323295 0.5000000000 0.0000
0.7650097432 0.2349902568 0.5000000000 0.0000 !H2
0.5000000000 -0.2349902568 0.2349902568 0.0000 !H0
0.5000000000 -0.2238002446 0.2238002446 0.0000
.
.
The k meth and kpath must be listed explicitly. kmesh gets a weight of 1, and the path gets a weight of 0.
Explicitly listing kpoints as ‘’!kpoint” on the k path is important for labels
To perform spincalcs set nspin = 2 and starting_magnetization(1)= 0.7
lobster_input_file must include explicit bands such as:
createFatband F 2p_x 2p_y 2p_z 2s
createFatband Li 1s 2s
Follow instructions on how to perform a Lobster analysis with Quantum Espresso. Also refer to the files in the relevant examples directory.
5. Abinit¶
Required files : PROCAR, <abinitoutput>.out
flag : code=’abinit’
Abinit version \(9.x^*\) generates a PROCAR similar to that of VASP when prtprocar is set in the input file.
To provide the Abinit output file, use the flag abinit_output=<nameofoutputfile> in PyProcar functions.
When running Abinit in parallel the PROCAR is split into multiple files. PyProcar’s cat function can merge these files together as explained in the section Concatenating multiple calculations. This also has an option to fix formatting issues in the Abinit PROCAR if needed.