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Fix a bug when supercell k-points lie on periodic boundary (#62)
* Fix unfold kpoint wrap problem Fix a bug in find_K_from_k function where wrapping of the k point is not taken into account when computing the G0 (lattice vector in reciprocal space), which causes problem when the supercell k-point lies on the edge of the reciprocal space. * Fix --no-expand and update the documentation * Updated docs * Add .lfsconfig file * Fix * Update and add file to lfs * Fix doc strings * Update doc string * Update docs * Update docs/examples/example_si222.md Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> * Minor docs cleanup * Fix changed figure and update example command * Typo fix * Minor updates * Update examples * Remove old KPOINTS file * Add missing png file * Update no_expand.png --------- Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> Co-authored-by: Sean Kavanagh <s.kavanagh19@imperial.ac.uk>
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‎.lfsconfig‎

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[lfs]
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fetchexclude="examples/Si222/Si_super_deformed/WAVECAR,examples/Si222/Si_super_deformed/vasprun.xml"

‎docs/examples/example_mgo.md‎

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@@ -35,7 +35,7 @@ when plotting the unfolded band structure:
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```bash
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easyunfold unfold plot-projections --procar MgO_super/PROCAR.gz --atoms="Mg,O" --combined --emin=-6 \
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--emax=20 --intensity 6.5
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--emax=20 --intensity 6.5 --poscar MgO_super/POSCAR
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```
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Note that the path of the `PROCAR(.gz)` is passed along with the desired atom projections (`Mg` and `O` here).

‎docs/examples/example_si222.md‎

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@@ -99,17 +99,28 @@ folder that can be used to perform these two steps above.
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Unfold the supercell wave function (`WAVECAR`) and calculate the spectral weights:
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```
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```bash
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cd ../
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easyunfold unfold calculate Si_super_deformed/WAVECAR
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```
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:::{note}
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If you don't want to run the VASP calculation by yourself, the calculated `WAVECAR` and `vasprun.xml`
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for this example can be downloaded with:
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for this example can be downloaded using `git-lfs`:
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If `git-lfs` was not installed when you cloned the repository, install it via:
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```bash
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sudo apt install git-lfs
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git lfs install
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```
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wget -O Si_super_deformed/WAVECAR https://www.dropbox.com/s/3cmn2epw7d290jd/WAVECAR?dl=1
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(or `brew install git-lfs` on macOS; see [here](https://docs.github.com/en/repositories/working-with-files/managing-large-files/installing-git-large-file-storage) for full instructions).
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Then download the files:
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```bash
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git lfs pull -I examples/Si222/Si_super_deformed/WAVECAR,examples/Si222/Si_super_deformed/vasprun.xml --exclude=""
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```
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:::
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:::{tip}
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See the [NaBiS<sub>2</sub> example](https://smtg-Bham.github.io/easyunfold/examples/example_nabis2.html) for tips on
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customising and prettifying the unfolded band structure plot. Here we have also actually used the `--intensity 3.5`
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option to increase the spectral function intensity.
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customising and prettifying the unfolded band structure plot. For example, you can use the `--intensity 3.5` option to increase the spectral function intensity.
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:::
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Note the appearance of extra branches compared to the band structure of the primitive cell (below), due
@@ -161,12 +171,12 @@ easyunfold generate Si/POSCAR Si_super_deformed/POSCAR Si/KPOINTS_band --no-expa
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Swap the `KPOINTS` to the new file, non-expanded `KPOINTS` file:
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```bash
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cp KPOINTS_no-expand Si_super_deformed/KPOINTS
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cd Si_super_deformed
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cp KPOINTS_no-expand Si_super_deformed_no_expand/KPOINTS
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cd Si_super_deformed_no_expand
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mpirun -np 4 vasp_std
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cd ../
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easyunfold unfold --data-file no-expand.json calculate Si_super_deformed/WAVECAR
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easyunfold unfold --data-file no-expand.json plot --out-file unfold_no-expand.png --intensity 3.5
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easyunfold unfold --data-file no-expand.json calculate Si_super_deformed_no_expand/WAVECAR
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easyunfold unfold --data-file no-expand.json plot --out-file unfold_no-expand.png
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```
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output:

‎easyunfold/unfold.py‎

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@@ -53,11 +53,9 @@ def find_K_from_k(k: np.ndarray, M: np.ndarray):
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"""
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M = np.array(M)
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Kc = np.dot(k, M.T)
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G = np.array(np.round(Kc), dtype=int)
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# Wrap to -0.5, 0.5
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KG = wrap_kpoints(Kc)
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Kc = np.dot(k, M.T) # Primitive cell kpoint in supercell fractional coordinates
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KG = wrap_kpoints(Kc) # Wrap to the 1st BZ
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G = np.array(Kc - KG, dtype=int) # Compute the G vector in supercell fractional coordinates
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return KG, G
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kset, weights = expand_K_by_symmetry(kpt, self.pc_opts, self.sc_opts, time_reversal=self.time_reversal)
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else:
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# Just take the original point and set the weight to be unity
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kset = [kpt]
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kset = [wrap_kpoints(kpt)]
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weights = np.array([1.0])
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expended_k.append(kset)
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expended_weights.append(weights)

‎examples/MgO/KPOINTS_easyunfold‎

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‎examples/MgO/easyunfold.json‎

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‎examples/MgO/unfold.png‎

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‎examples/MgO/unfold_project.png‎

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