Tutorial on fold2bloch¶
Unfolding the electronic structure of a lattice of Hydrogen atoms.¶
Supercells are often used in electronic structure calculations in order to model compound alloys, defects, etc. The band structure obtained directly from these calculations is hard to interpret due to the Brillouin zone folding as a result of its reduced size for the supercell, compared to that for the unperturbed host unit cell. The unfolding technique used in Abinit is the one presented in [Rubel2014].
This tutorial aims at demonstrating how to unfold the band structure of a supercell and present it in the basis of conventional Bloch wave vectors inherent to the unperturbed unit cell. We will construct a supercell of 6 hydrogen atoms, perform self-consistent cycle and plot the corresponding band structure. At the end, we will recover the familiar dispersion relation using the fold2Bloch utility. See also the fold2bloch help file.
All the necessary input files to run the examples can be found in the ~abinit/tests/ directory where ~abinit is the absolute path of the abinit top-level directory.
To execute the tutorials, you are supposed to create a working directory (
copy there the input files and the files file of the lesson.
The files file ending with _x (e.g. tbase1_x.files) must be edited every time you start to use a new input file. You will discover more about the files file in section 1.1 of the help file.
To make things easier, we suggest to define some handy environment variables by executing the following lines in the terminal:
export ABI_HOME=Replace_with_the_absolute_path_to_the_abinit_top_level_dir export ABI_TESTS=$ABI_HOME/tests/ export ABI_TUTORIAL=$ABI_TESTS/tutorial/ # Files for base1-2-3-4, GW ... export ABI_TUTORESPFN=$ABI_TESTS/tutorespfn/ # Files specific to DFPT tutorials. export ABI_TUTOPARAL=$ABI_TESTS/tutoparal/ # Tutorials about parallel version export ABI_TUTOPLUGS=$ABI_TESTS/tutoplugs/ # Examples using external libraries. export ABI_PSPDIR=$ABI_TESTS/Psps_for_tests/ # Pseudos used in examples. export PATH=$ABI_HOME/src/98_main/:$PATH
The examples in this tutorial will use these shell variables so that one can easily copy and paste the code snippets into the terminal (remember to set ABI_HOME first!)
The last line adds the directory containing the executables to your PATH so that one can invoke the code by simply typing abinit in the terminal instead of providing the absolute path.
Finally, to run the examples in parallel with e.g. 2 MPI processes, use mpirun (mpiexec) and the syntax:
mpirun -n 2 abinit < files_file > log 2> err
The standard output of the application is redirected to
err collects the standard error
(runtime error messages, if any, are written here).
This tutorial should take about 1 hour.
Creating a Hydrogen supercell structure¶
Let’s begin with the simplest structure: a lattice of hydrogen atoms. It is a convenient starting point since the hybridization between s-orbitals results in a well known dispersion relation for the energy eigenvalues as a function of the wave vector k:
Here b is the lattice spacing and A reflects the strength of hybridization between adjacent s-orbitals. For more details please refer to the Feynman’s Lectures on Physics (vol 3, chapter 13).
Our model structure will be a cubic lattice of hydrogen atoms spaced 3 Bohr apart. The primitive cell contains only one atom. Here we chose to represent the same structure with a 6 atom supercell. Such a large cell is redundant in this case, since there is nothing that disturbs the original symmetry. However, we made this choice on purpose in order to observe the zone folding.
Since we are interested in the band structure, we need to select a path in the reciprocal space which will be used for plotting. The supercell was expanded in Y and Z directions. Accordingly, the reciprocal space shrinks along the same directions. We select those directions for the band structure plot as they will be affected by the zone folding.
Before beginning, you might consider to work in a different subdirectory as for the other tutorials. Why not Work_fold2Bloch?
In order to use the fold2Bloch, you need to first generate a wave function file (WFK file).
In the directory ~abinit/tests/tutorial/Input/Work_fold2Bloch, copy the files tests/tutorial/Input/tfold2bloch_1.files and tests/tutorial/Input/tfold2bloch_1.in.
cd $ABI_TUTORIAL/Input mkdir Work_fold2Bloch cd Work_fold2Bloch cp ../tfold2bloch_1.files . # You will need to edit this file. cp ../tfold2bloch_1.in .
tfold2Bloch_1.in tfold2Bloch_1.out tfold2Bloch_1i tfold2Bloch_1o tfold2Bloch_1 ../../../Psps_for_tests/H-LDA-uspp.paw
# H6 Supercell # Generates a 6 atom Hydrogen supercell with the multiplicity of 1:2:3 (x:y:z) prtcif 1 # If set to 1, a CIF file is output with the crystallographic data for the present run (cell size shape and atomic positions) ndtset 2 # There will be two datasets here: SCF run and the band structure # Dataset 2 : the band structure iscf2 -2 getden2 -1 # get charge density from the 1st run kptopt2 -5 # band structure plot with 5 intervals ndivk2 10 10 1 10 10 # number of divisors for each interval kptbounds2 0.0 -0.5 0.0 # Y point 0.0 0.0 0.0 # Gamma point 0.0 0.5 0.0 # Y point 0.0 0.0 -0.5 # Z point 0.0 0.0 0.0 # Gamma 0.0 0.0 0.5 # Z point tolwfr2 1.0d-12 enunit2 1 # Will output the eigenenergies in eV #Common input data ixc 2 # 2 => LDA #Starting approximation for the unit cell acell 3.0 6.0 9.0 # [Bohr] rprim 1 0 0 0 1 0 0 0 1 chkprim 0 # do not check for primitive cell #Definition of the atom types and atoms ntypat 1 znucl 1 natom 6 typat 1 1 1 1 1 1 #Atomic positions in REDUCED coordinates xred 0.0 0.0 0.0 0.0 0.0 1/3 0.0 0.0 2/3 0.0 0.5 0.0 0.0 0.5 1/3 0.0 0.5 2/3 # fband 0 # In case fband is 0.0d0, the code computes from the pseudopotential # files and the geometry data contained in the input file, the number # of electrons present in the system. Then, it computes the minimum # number of bands that can accomodate them, and use that value for _nband_ #Definition of the plane wave basis set ecut 10.0 # Maximum kinetic energy cutoff (Hartree) pawecutdg 25 # PAW - Energy CUToff for the Double Grid #Definition of the k-point grid ngkpt 3 2 1 # 3x2x1 Monkhorst-Pack grid nshiftk 1 # Use one copy of grid only (default) shiftk 0.0 0.0 0.0 # Unshifted K-mesh #Definition of the self-consistency procedure diemac 9.0 # Model dielectric preconditioner iscf 7 # PAW compatible Pulay mixing of the potential based on the npulayit previous iterations nstep 999 # Maxiumum number of SCF iterations tolvrs 1.0d-6 # tolerance for potential residual ## After modifying the following section, one might need to regenerate the pickle database with runtests.py -r #%%<BEGIN TEST_INFO> #%% [setup] #%% executable = abinit #%% test_chain = tfold2bloch_1.in, tfold2bloch_2.in #%% [files] #%% files_to_test = #%% tfold2bloch_1.out, tolnlines=35, tolabs=1.0e-5, tolrel=2.0e-02 #%% psp_files = H-LDA-uspp.paw #%% [paral_info] #%% max_nprocs = 2 #%% [extra_info] #%% authors = O. Rubel #%% keywords = FOLD2BLOCH #%% description = #%% H6 Supercell #%% Generates a 6 atom Hydrogen supercell with the multiplicity of 1:2:3 (x:y:z) #%% Produce WFK file to be analyzed with fold2bloch #%%<END TEST_INFO>
The input file has two datasets, the first to generate the WFK file, and the second to draw the band structure. Now you are ready to run Abinit. Issue the following:
abinit tfold2bloch_1.files > & tfold1bloch_1.log &
This will generate a self consistent charge density for the 6 Hydrogen atom supercell structure, and the wave function file, tfold2bloch_1o_WFK, which is needed for unfolding with fold2Bloch.
Folded band structure¶
Before we proceed with the unfolding, let’s plot the “standard” band structure of a supercell. We will be looking for signatures of the zone folding. In order to do this you will need the following scripts:
which are located at /abinit/doc/tutorial/fold2Bloch_assets/
Execute the energy_eig-avinit.sh script
This will generate an output file: tfold2bloch_1o_DS2_EIG.dat
Edit plot_band.m file and point to the newly created tfold2bloch_1o_DS2_EIG.dat file.
Then, run the plot_band.m script in MatLab
This will plot the band structure of the 6 atom Hydrogen supercell created.
Lastly, compare the image obtained to the band structure image below.
Here you can see that the band structure does not look like a cosine function along directions Y-Gamma and Z-Gamma. The band structure is folded according to the multiplicity along those directions used when constructing the supercell (Fig. 1b).
If AbiPy is installed on your machine, you can use the abiopen script
--expose option to visualize the band dispersion:
abiopen.py tfold2bloch_1o_DS2_GSR.nc --expose
Bloch spectral weights with fold2Bloch¶
Next step is to execute fold2Bloch using the wave function file from the 2nd dataset, and multiplicity in the corresponding directions, used when constructing the super-cell (x:y:z), included as part of the command line arguments. For this example the multiplicity used was (1:2:3)
Execute the following command:
fold2Bloch tfold2bloch_WFK 1:2:3
You should see the following:
*********************** ** Fold2Bloch V 1.0 ** **Build Oct 16, 2014** *********************** 2% Processing K point: 0.000000 -0.500000 0.000000 4% Processing K point: 0.000000 -0.450000 0.000000 6% Processing K point: 0.000000 -0.400000 0.000000 ... 95% Processing K point: 0.000000 0.000000 0.400000 97% Processing K point: 0.000000 0.000000 0.450000 100% Processing K point: 0.000000 0.000000 0.500000 Number of K points processed: 43 Data was written to: fold2Bloch.out Data format: KX, KY, KZ, Eigenvalue(Ha), Weight
That output tells us which K-point was processed, total number of K-points processed, output file, and the format that the data is written in.
Now take a look at the fold2Bloch.out. The first few lines should be as follows:
less fold2Bloch.out 0.000000 -0.250000 0.000000 -0.317960 0.579542 0.000000 -0.250000 0.333333 -0.317960 0.000000 0.000000 -0.250000 -0.333333 -0.317960 0.000000 0.000000 0.250000 0.000000 -0.317960 0.420458 0.000000 0.250000 0.333333 -0.317960 0.000000 0.000000 0.250000 -0.333333 -0.317960 0.000000 0.000000 -0.250000 0.000000 -0.317960 0.420458 0.000000 -0.250000 0.333333 -0.317960 0.000000 0.000000 -0.250000 -0.333333 -0.317960 0.000000 0.000000 0.250000 0.000000 -0.317960 0.579542 0.000000 0.250000 0.333333 -0.317960 0.000000 0.000000 0.250000 -0.333333 -0.317960 0.000000 0.000000 -0.250000 0.000000 -0.093527 0.000000 0.000000 -0.250000 0.333333 -0.093527 0.315820 0.000000 -0.250000 -0.333333 -0.093527 0.251111 0.000000 0.250000 0.000000 -0.093527 0.000000 0.000000 0.250000 0.333333 -0.093527 0.144884 0.000000 0.250000 -0.333333 -0.093527 0.288185 0.000000 -0.250000 0.000000 -0.093527 0.000000 0.000000 -0.250000 0.333333 -0.093527 0.494070 0.000000 -0.250000 -0.333333 -0.093527 0.103712 0.000000 0.250000 0.000000 -0.093527 0.000000 0.000000 0.250000 0.333333 -0.093527 0.386301 0.000000 0.250000 -0.333333 -0.093527 0.015917 ...
Let’s take a moment to analyse the output. Columns 1-3 correspond to kx, ky and kz of the unfolded bands; the 4th column is the energy eigenvalue in [Ha] and the 5th column corresponds to a spectral weight of the k-point after unfolding. Do not confuse it with k-point weight, which represents its multiplicity in the Brillouin zone. Since our supercell contains 6 unit cells (1 x 2 x 3), each eigenvalue in the solution contains information about 6 Bloch wave vectors, i.e., unfolded into 6 k-points. The relative contribution of these k-points is determined by the spectral weight.
Lines 1-6 represent unfolding of the 1st eigenvalue of -0.31796 Ha. This eigenvalue corresponds to the Bloch wave vectors of (0 ±½ 0) as they have a non-zero weight. The weights total 1 for normalization. This eigenvalue is degenerate, so lines 7-12 look very similar. When a disorder is present (in a form of defects, distortions, impurities) individual eigenstates may not express an exclusive Bloch character any longer. This can have some interesting consequences for transport or optical properties, which are not apparent from the folded band structure.
the whole output is much bigger than the sample provided above. For the band structure visualization proceed to the next step.
Unfolded band structure¶
Lets visualize the unfolded band structure. It is different from a regular band structure plot, though. Now we have one additional dimension – the Bloch spectral weight. There are several alternative visualization strategies. Here we use the scatter plot with the point size proportional to the spectral weight. The following MatLab script will help you build a graph for any fold2Bloch output: ubs_dots.m
Make sure the following parameters in ubs_dots.m are set as follows:
KPATH = [0 1/2 0; ... 0 0 0; ... 0 0 1/2]; finpt='tfold2bloch_1o.f2b';
G = [0.3333333 0.0000000 0.0000000; 0.000000 0.1666667 0.0000000; 0.000000 0.000000 0.1111111]; % Reciprocal latt. vect. [Bohr^-1] from *.out
Reciprocal lattice vector information must match that in tfold2bloch_1.out:
Real(R)+Recip(G) space primitive vectors, cartesian coordinates (Bohr,Bohr^-1): R(1)= 3.0000000 0.0000000 0.0000000 G(1)= 0.3333333 0.0000000 0.0000000 R(2)= 0.0000000 6.0000000 0.0000000 G(2)= 0.0000000 0.1666667 0.0000000 R(3)= 0.0000000 0.0000000 9.0000000 G(3)= 0.0000000 0.0000000 0.1111111 Unit cell volume ucvol= 1.6200000E+02 bohr^3 Angles (23,13,12)= 9.00000000E+01 9.00000000E+01 9.00000000E+01 degrees
For graphing any other fold2Bloch output, make sure that the “%%Init Parameters” are set accordingly to size of the supercell constructed.
After running the script you should see the following graph:
As you can see the unfolded band structure perfectly reproduces the anticipated dispersion relation E(k)=E_0 - 2A \cos(kb). We can even estimate the magnitude of the hopping matrix element between adjacent atoms VssG = -A. The band width is 4A = (-1) - (-12) = 11 eV which results in VssG = -2.75 eV.
To analyze the results with AbiPy use:
to open the file inside ipython and then type:
# Plot unfolded bands along the path defined by kbounds. In  kbounds = [0, 1/2, 0, 0, 0, 0, 0, 0, 1/2] In  klabels = ["Y", r"$\Gamma$", "X"] In  abifile.plot_unfolded(kbounds, klabels, title="Unfolded bands")
See also this example.