# Dataset for &ldquo;Native Defects and their Doping Response in Lithium Solid Electrolyte Li<sub>7</sub> La<sub>3</sub>Zr<sub>2</sub>O<sub>12</sub>&rdquo;

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[Alexander G. Squires]()
[David O. Scanlon](https://orcid.org/0000-0001-9174-8601)
[Benjamin J. Morgan.](http://orcid.org/0000-0002-3056-8233)

This repository contains the computational data for the paper [&ldquo;Native Defects and their Doping Response in Lithium Solid Electrolyte Li<sub>7</sub> La<sub>3</sub>Zr<sub>2</sub>O<sub>12</sub>&rdquo;][paper_link]\[1\].

The repository contains input and output files for the DFT calculations, performed using [VASP](https://www.vasp.at/). This is detailed below in the Data section.
generation of the metadata used to carry out analysis depends on the [`vasppy`](https://github.com/bjmorgan/vasppy) Python module \[2\].

## Data

The complete data set produced for this study.

### Directory structure

```
.
├── HSE
│   ├── defects (HSE06 defect calculations)
|   |    |
|   |    ├── neutral defect
|   |    |    |
|   |    |    ├── charge states
|   |    |    |   |
|   |    |    |   └── input/output/metadata
|   |    |    |
|   |    |    └── input/output/metadata
|   |    └── ...
|   |
│   ├── LOPTICS (High frequency dielectric response calculation)
|   |   |
|   |   └── input/output/metadata
|   |
│   ├── parchg  (oxygen vacancy partial charge calculations)
|   |   |
|   |   ├── PARCHG_V_O
|   |   |    └── input/output/metadata
|   |   ├── PARCHG_V_O_+
|   |   |    └── input/output/metadata
|   |   └── PARCHG_V_O_++
|   |        └── input/output/metadata
|   |
│   ├── ref (competing phases and elemental references)
|   |    |
|   |    ├── system
|   |    |   |
|   |    |   └── input/output/metadata
|   |    └── ...
|   |
│   └── vol_opt (equation of state fit for stoichiometric LLZO)
|       |
|       ├── scaling factor
|       |    |
|       |    └── input/output/metadata
|       |
|       └── opt (optimised volume relaxation)
|            |
|            └── input/output/metadata
└── PS
    ├── LEPSILON (low frequency dielectric)
    |   |
    │   └── input/output/metadata
    |
    └── o_mobility
        |
        ├── neb1
        |   ├── input/metadata
        |   └── images
        |       └──output
        ├── neb2
        |   ├── input/metadata
        |   └── images
        |       └──output
        ├── neb3
        |   ├── input/metadata
        |   └── images
        |       └──output
        ├── neb4
        |   ├── input/metadata
        |   └── images
        |       └──output
        ├── neb5
        |   ├── input/metadata
        |   └── images
        |       └──output
        └── neb6
            ├── input/metadata
            └── images
                └──output

```

Each bottom level directory contains the following VASP calculation files:
```
INCAR
POSCAR
KPOINTS
OUTCAR
vasprun.xml
vaspmeta.yaml
```

The `vaspmeta.yaml` file contains additional metadata for each calculation:
```
title: short description of the calculation
description: long description of the calculation
notes: any additional notes
status: describes the status of the calculation. This will be "finished" in all cases here to denote completed calculations
```

### summarised data

The various `.yaml` files contains relevant subsets of VASP calculations in the dataset formatted as YAML, including summarised input, output, and additional metadata.

e.g. for the La<sub>Li</sub> defect calculation, the summary is:
```
---
title: La_Li
status: finished
stoichiometry:
    - Li: 27
    - La: 13
    - Zr: 8
    - O: 48
potcar:
    - Li: PAW_PBE Li 17Jan2003
    - La: PAW_PBE La 06Sep2000
    - Zr: PAW_PBE Zr_sv 04Jan2005
    - O: PAW_PBE O 08Apr2002
energy: -832.53744678 eV
lreal: True
k-points:
    scheme: Monkhorst
    grid: 2 2 2
functional: screened hybrid. alpha=0.25, mu=0.207
encut: 520.0
ediffg: -0.01
ibrion: 2
vbm: 8.593
cbm: 9.6709
converged: True
version: vasp.5.4.4.18Apr17-6-g9f103f2a35
vasprun md5: 29e1ed97f168a70066ad2585a05a4af4
directory: ./La_Li/
```

To reproduce the analysis found at , metadata is should be collated using the `vasp_summary` script, which depends on the [`vasppy`](https://github.com/bjmorgan/vasppy) module \[2\]. For parsing the `vasprun.xml` files, this makes extensive use of the `Vasprun` object in [`pymatgen`](http://pymatgen.org/) \[3\].

```
vasp_summary --recursive > defects.yaml
```

## Citing this dataset
```
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```

### BibTeX

```
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```

## References

1. paper.
2. Benjamin J. Morgam. vasppy. doi:[10.5281/zenodo.801662](https://doi.org/10.5281/zenodo.801662).
3. Shyue Ping Ong <i>et al.</i> Python Materials Genomics (pymatgen) : A Robust, Open-Source Python Library for Materials Analysis. Computational Materials Science, 2013, 68, 314–319. doi:[10.1016/j.commatsci.2012.10.028](https://doi.org/10.1016/j.commatsci.2012.10.028).

[paper_link]: http://dx.doi.org/10.1038/nmat4976