# Explanation of files
## `PDWF_export_20230314.aiida`
This is an AiiDA archive file that contains all the calculations for the paper.
It is exported with AiiDA v2.2.2.
One can import it by using the command:
```bash
verdi archive import -- PDWF_export_20230314.aiida
```
For how to install and use AiiDA, please refer to
- [AiiDA website](https://www.aiida.net/)
- [AiiDA tutorial](https://aiida.readthedocs.io/projects/aiida-core/en/latest/intro/tutorial.html)
- [AiiDA documentation](https://aiida.readthedocs.io/en/latest/)
## `aiida_stashed_files-20230726.tar`
This file contains the AiiDA stashed files of all the calculations, including
- charge densities files for Quantum ESPRESSO scf calculations, that were used
to restart Wannierizations
- Wannier tight-binding Hamiltonians and shape of Wannier functions, i.e., the
`tb.dat`, `wsvec.dat` and `cube` files generated by Wannier90.
They can be used to compute band structures, DOS, etc.
In addition, the `aiida_stashed_files.json` file serves as a table of contents
for the stashed files, it contains the AiiDA UUIDs of the calculations, chemical
formulae, and the file names and file paths inside the tar file.
## `list_of_calculations_for_test_structures.txt`
This file contains a list of all the calculations that were performed for the
4 test structures: graphene, silicon, copper, and SrVO3. Note for completeness,
I exported all the calculations, including the testing ones that are not used
in the paper.
For example, the line 4 to line 12 in the file are:
```
paper/pwbands/test
Si2 5e8fdec5-312d-4f81-aa1e-e3e4615bc99d ProjwfcBandsWorkChain
Cu 6043ef65-9672-4a51-a4bf-ac0682ef8475 ProjwfcBandsWorkChain
O3SrV 7822fa73-ff22-4d1a-a5a5-c5461f4b8096 ProjwfcBandsWorkChain
C2 6e9405a3-df81-4d22-bc30-51d9881e9151 ProjwfcBandsWorkChain nbnd=20
Si2 30a47730-da92-4879-8674-819ec4578920 ProjwfcBandsWorkChain nbnd=40
C2 2366a1d4-e1ef-4973-b3e2-6ef6f3021850 ProjwfcBandsWorkChain nbnd=60
Au 016517d3-7e50-46bf-bcb2-41248eef45ea ProjwfcBandsWorkChain
Si2 2182f4a7-8a2b-4fd0-a790-8c120ced645a ProjwfcBandsWorkChain nbnd=40;custom_pseudo_with_3d
```
Here, the `paper/pwbands/test` is the AiiDA group label that contains all the
workflows under this line. The `Si2` is the formula of the structure, and the
`5e8fdec5-312d-4f81-aa1e-e3e4615bc99d` is the UUID of the workflow. The
`ProjwfcBandsWorkChain` is the AiiDA workflow class name. The `nbnd=20` is a
short description of the workflow.
### `paper/pwbands/test`
This group contains pw.x band structure calculations, the description can be:
- `nbnd=20`: the number of bands for pw.x nscf step is set to 20
- `custom_pseudo_with_3d`: for a `ProjwfcBandsWorkChain` workflow, this is using
a custom generated pseudo with a different 3d projector. However, please
note that this is only a reference: actually the PW band structure are not
good, since the new 3d projector replaces one of the old 3d projector, actually
degrading the transferability of the pseudo for conduction bands! DO NOT use
this pseudo for pw.x calculations!
### `paper/wannier/test/analytic`
This group contains Wannierizations using standard hydrogenic projectors, the
description can be:
- `remove-O:2s`: remove oxygen s orbitals from the Wannierization
- `add-Sr:4p`: add strontium p orbitals to the Wannierization
- `add-Sr:4p:r=2`: add strontium p orbitals that have two radial nodes (`r=2`
in the wannier90 input projection block) to the Wannierization
### `paper/wannier/test/scdm`
This group contains Wannierizations using SCDM method, the rule for description
is the same as previous one.
### `paper/wannier/test/scdm_custom_pseudo/more_proj`
The group contains Wannierizations using SCDM method with custom `scdm_mu` and
`scdm_sigma` for the `pw2wannier90.x` input parameters, however I am still using
the standard SSSP pseudo so that the nscf calculation is still correct!
There is only one calculation for silicon:
```
Si2 edc1d7b2-0526-4b7b-88b5-3f994710127d Wannier90BandsWorkChain nbnd=40;use_custom_pseudo_with_3d_to_compute_scdm_mu_sigma
```
The description `use_custom_pseudo_with_3d_to_compute_scdm_mu_sigma` means that
the `scdm_mu` and `scdm_sigma` are computed using the projectabilities on silicon
2s, 2p, and 3d orbitals from the custom pseudo with 3d projectors. Thus, the
`scdm_mu` is higher than default one, so that we can Wannierize the 3d orbitals
(instead of only 2s and 2p orbitals with the default SCDM protocol).
### `paper/wannier/test/atomproj_qe`
This group contains Wannierizations using PDWF method, the description can be:
- `proj+win-DIS`: using projectability plus energy window disentanglement (PD+ED)
- `proj-DIS`: using projectability disentanglement (PD)
- `win-DIS`: using energy window disentanglement (ED)
- `full_optimization`: I explicitly set the `optimize_bands_distance_threshold`
input of `Wannier90OptimizeWorkChain` to 0, so that the workflow will exhaust
all the possible combinations of `dis_proj_min` and `dis_proj_max` for the
projectability disentanglement
### `paper/wannier/test/atomproj_openmx`
This group contains Wannierizations using PDWF method with OpenMX PAOs, the rule
for description is the same as previous one.
### `paper/wannier/test/atomproj_openmx/more_proj`
This group contains Wannierizations using PDWF method with OpenMX PAOs, and with
additional PAOs (e.g., including also 3d for silicon), the description can be:
- `dis_froz_max=Ef+12`: the `dis_froz_max` of Wannier90 input is set to 12 eV
above the Fermi energy, to freeze more conduction states
### `paper/wannier/test/atomproj_custom_pseudo/more_proj`
This group contains Wannierizations using PDWF method with custom pseudo, there
is only calculation:
```
Si2 a05bd92f-66bd-42c2-8c6a-96223346849b Wannier90OptimizeWorkChain nbnd=40;full_optimization;proj-DIS;add-Si:3d
```
This calculation uses projectability disentanglement (PD) method, use a custom
pseudo to project also on 3d orbitals, and run a full optimization of `dis_proj_min`
and `dis_proj_max`.
## `list_of_calculations_for_200_structures.txt`
This file contains the list of all the calculations for the 200 reference
structures, there are four groups:
1. `paper/structure/scdm200`: the 200 structures
2. `paper/pwbands/scdm200`: QE band structure calculations for the 200 structures
3. `paper/wannier/scdm200/scdm`: Wannierizations using SCDM for the 200 structures
4. `paper/wannier/scdm200/atomproj_qe`: Wannierizations using PDWF for the 200
structures
## miscellaneous
There are some additional groups that are exported:
- `paper/structure/scdm200`: this group contains the 200 reference structures
- `paper/structure/test`: this group contains the 4 test structures