# Si supercell with a displaced atom
Below is a step-by-step guide for unfolding the electronic structure of a `2x2x2` supercell of
crystalline silicon (Si) which contains a displaced atom, breaking symmetry.
## Generate the project file (`easyunfold.json`) and _k_-points for supercell calculation
:::{note}
The files needed for this example are provided in the
[examples/Si222](https://github.com/SMTG-Bham/easyunfold/tree/main/examples/Si222) folder. This
guide assumes the current working directory is located at the root of that folder.
:::
First, generate the supercell _k_-points:
```bash
easyunfold generate Si/POSCAR Si_super_deformed/POSCAR Si/KPOINTS_band
```
Here, `KPOINTS_band` is the `KPOINTS` file corresponding to the band structure path for the primitive
unit cell, which in this case was generated using `sumo-kgen` (see [Step 1](
https://smtg-Bham.github.io/easyunfold/guide.html#step-1-generate-the-kpoints-path-of-the-primitive-cell)
of the tutorial docs page).
This generates an `easyunfold.json` file in the current direction containing information about the
unfolding. The output name of this file can be modified with the `--out-file` commandline argument.
Information stored in this file can be inspected with the `easyunfold unfold status` command:
```bash
$ easyunfold unfold status
Loaded data from easyunfold.json
Primitive cell information:
Space group number: 160
International symbol: R3m
Point group: 3m
Supercell cell information:
Space group number: 227
International symbol: Fd-3m
Point group: m-3m
No. of k points in the primitive cell : 73
No. of supercell k points : 103
No. of primitive cell symmetry operations : 48
No. of supercell symmetry operations : 6
Path in the primitive cell:
\Gamma : 1
L : 21
W : 38
X : 50
\Gamma : 73
Please run the supercell band structure calculation and run `unfold calculate`.
```
Copy the _k_-points to the supercell calculation folder:
```bash
cp KPOINTS_easyunfold Si_supercell_deformed
```
## Perform the supercell band structure calculation
Semi-local (GGA) DFT band structure calculations in VASP normally involve two steps. First, a normal
single point calculation is performed to obtain the self-consistent (SCF) charge density. Following
this, a non-self-consistent calculation is carried out to compute the eigenvalues of the _k_-points
along the defined band structure path.
First, we run our single point SCF supercell calculation, ensuring to use the appropriate converged SCF
_k_-point mesh for the supercell. The `ICHARG = 11` tag must not be set or be commented out in the `INCAR`
file for this single point calculation:
```bash
cd Si_supercell_deformed
cp KPOINTS_scf KPOINTS # SCF kpoint mesh
sed -i 's/^ICHARG = 11/!ICHARG = 11/g' INCAR # comment out ICHARG = 11
mpirun -np 4 vasp_std # run the calculation
```
Now, with our converged SCF charge density, we run the GGA band structure calculation with `ICHARG = 11`,
and the _k_-points mapped to the supercell from the primitive cell path:
```bash
sed -i 's/.*ICHARG = 11/ICHARG = 11/g' INCAR # set ICARG = 11
cp KPOINTS_easyunfold KPOINTS # supercell band structure kpoint path
mpirun -np 4 vasp_std # run the calculation
```
Alternatively, there is a `run.sh` script in the
[examples/Si222/Si_super_deformed](https://github.com/SMTG-Bham/easyunfold/tree/main/examples/Si222/Si_super_deformed)
folder that can be used to perform these two steps above.
## Perform band unfolding
Unfold the supercell wave function (`WAVECAR`) and calculate the spectral weights:
```
cd ../
easyunfold unfold calculate Si_super_deformed/WAVECAR
```
:::{note}
If you don't want to run the VASP calculation by yourself, the calculated `WAVECAR` and `vasprun.xml`
for this example can be downloaded with:
```
wget -O Si_super_deformed/WAVECAR https://www.dropbox.com/s/3cmn2epw7d290jd/WAVECAR?dl=1
```
:::
Plot the unfolded band structure:
```bash
easyunfold unfold plot
```
Output:
```{figure} ../../examples/Si222/unfold.png
:alt: Spectral function
:width: 400px
Spectral function of the unfolded bands.
```
:::{tip}
See the [NaBiS_{2} example](https://smtg-Bham.github.io/easyunfold/examples/example_nabis2.html) for tips on
customising and prettifying the unfolded band structure plot. Here we have also actually used the `--intensity 3.5`
option to increase the spectral function intensity.
:::
Note the appearance of extra branches compared to the band structure of the primitive cell (below), due
to symmetry breaking from the displaced atom.
```{figure} ../../examples/Si222/band.png
:alt: Primitive cell band structure
:width: 400px
Primitive cell band structure of Si.
```
## What happens if symmetry is not properly taken into account?
It is quite common that the supercell has lower symmetry compared to the primitive cell.
By default, `easyunfold` takes account of such symmetry breaking effect by including
additional _k_-points that no longer equivalent under the symmetry of the supercell cell.
In this example, we show what happens if we **do not** include the additional kpoints.
We can create a new unfolding project (`json` data file) using the following command:
```bash
easyunfold generate Si/POSCAR Si_super_deformed/POSCAR Si/KPOINTS_band --no-expand --out-file no-expand.json
```
Swap the `KPOINTS` to the new file, non-expanded `KPOINTS` file:
```bash
cp KPOINTS_no-expand Si_super_deformed/KPOINTS
cd Si_super_deformed
mpirun -np 4 vasp_std
cd ../
easyunfold unfold --data-file no-expand.json calculate Si_super_deformed/WAVECAR
easyunfold unfold --data-file no-expand.json plot --out-file unfold_no-expand.png --intensity 3.5
```
output:
```{figure} ../../examples/Si222/unfold_no-expand.png
:alt: Spectral function
:width: 400px
Spectral function of the unfolded bands with out additional kpoints due to reduced symmetry.
```
Comparing this plot with the one above, we see that we get spurious band breaking (e.g. along $\Gamma - L$)
and some branches are missing (near the $\Gamma$ point).
Nevertheless, by not expanding the _k_-point paths, fewer supercell _k_-points need to be calculated:
```bash
$ easyunfold unfold --data-file no-expand.json plot --out-file unfold_no-expand.png
Loaded data from no-expand.json
Using a reference energy of 5.284 eV
Unfolded band structure saved to unfold_no-expand.png
$ easyunfold unfold --data-file no-expand.json status
Loaded data from no-expand.json
Supercell cell information:
Space group number: 160
International symbol: R3m
Point group: 3m
Primitive cell information:
Space group number: 227
International symbol: Fd-3m
Point group: m-3m
No. of k points in the primitive cell : 73
No. of supercell k points : 70
No. of primitive cell symmetry operations : 48
No. of supercell symmetry operations : 6
Path in the primitive cell:
\Gamma : 1
L : 21
W : 38
X : 50
\Gamma : 73
Unfolding had been performed - use `unfold plot` to plot the spectral function.
```
Note that in most cases one would always want to include the additional kpoints to correctly capture the effect of symmetry breaking.
The `--no-expand` option should be used with care and **only when there is no alternative**,
for example,
when the expansion gives too many kpoints for very large supercells of special quasi-random structures.
:::{note}
One can always split the workload into multiple calculations with `--nk-per-split` to fit the computational resources available for individual calculations.
:::