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Merge pull request #142 from 1041176461/develop
add some example for plotting PDOS and PBAND
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‎tools/plot-tools/README.md‎

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- [NumPy](https://numpy.org/)
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- [Matplotlib](https://matplotlib.org/)
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- [lxml](https://lxml.de/)
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- [setuptools](https://setuptools.pypa.io/en/latest/index.html)
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## Installation
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Use the following command to install this tool:
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## Usage
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There are two ways to use this tool:
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1. Specify parameters in `band.py` or `dos.py` directly, and then `python band.py` or `python dos.py`. And you can also import module in your own script e.g. `from abacus_plot.band import Band`
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2. Command-line tools are also supported in this tool. In this way, you need prepare an input file and execute some commands as follows
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1. Specify parameters in `band.py` or `dos.py` directly, and then `python band.py` or `python dos.py`. And you can also import module in your own script e.g. `from abacus_plot.band import Band`. (Recommend)
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2. Command-line tools are also supported in this tool. In this way, you need prepare an input file and execute some commands (see below). You can use `abacus-plot -h` to check command-line information
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### Band Structure
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First, prepare a json file e.g. band-input.json:
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First, prepare a file named 'config.json' in json format:
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```json
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{
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"bandfile" : "BANDS_1.dat",
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"efermi" : 10.39537843955395,
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"efermi" : 6.585653952007503,
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"energy_range" : [-1.5, 6],
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"kptfile" : "KPT"
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}
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```
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| Property | Type | Note |
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| :------------: | :----------------------: | :------------------------------------------------------------: |
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| *bandfile* | `str` or `List[str]` | Bands data file output from ABACUS |
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| *efermi* | `float` or `List[float]` | Fermi level in eV |
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| *energy_range* | `list` | Range of energy in eV |
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| *shift* | `bool` | If set `'true'`, it will evaluate band gap. Default: `'false'` |
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| *index* | `List[int]` or `Dict[int, List[int]]` or `Dict[int, Dict[int, List[int]]]]` | Extract PDOS of each atom e.g. [0, 1], {0:[0, 1], 1:[0]}, [0:{0:[0]}, 1:{1:[0, 1]}] |
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| *atom_index* | `List[int]` or `Dict[int, List[int]]` or `Dict[int, Dict[int, List[int]]]]` | Extract PDOS of each atom with same atom_index e.g. [0, 1], {0:[0, 1], 1:[0]}, [0:{0:[0]}, 1:{1:[0, 1]}] |
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| *species* | `List[str]` or `Dict[str, List[int]]` or `Dict[str, Dict[int, List[int]]]]` | Extract PDOS of each atom with same species e.g. ["C", "Si"], {"C":[0, 1], "Si":[0]}, ["C":{0:[0]}, "Si":{1:[0, 1]}] |
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| *kptfile* | `str` | K-points file in ABACUS format |
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| *label* | `str` or `List[str]` | Label of band structure |
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| *color* | `str` or `List[str]` | Color of band structure |
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| Property | Type | Note |
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| :------------: | :-------------------------------------------------------------------------: | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
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| *bandfile* | `str` or `List[str]` | Bands data file output from ABACUS. 'BANDS_*.dat' for band structure and 'PBANDS_*' for projected band structure |
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| *efermi* | `float` or `List[float]` | Fermi level in eV |
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| *energy_range* | `list` | Range of energy in eV |
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| *shift* | `bool` | If set `'true'`, it will evaluate band gap (only for semiconductors and insulators). Default: `'false'` |
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| *index* | `List[int]` or `Dict[str, List[int]]` or `Dict[str, Dict[int, List[int]]]]` | Extract PBANDS of each atom from 'PBANDS_*' file e.g. [index_0, index_1...] or {index_0:[l_0, l_1, ...], ...}, [index_0:{l_0:[m_0, m_1, ...], ...}, ...] |
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| *atom_index* | `List[int]` or `Dict[str, List[int]]` or `Dict[str, Dict[int, List[int]]]]` | Extract PBANDS of each atom with same atom_index from 'PBANDS_*' file e.g. [atom_index_0, atom_index_1...] or {atom_index_0:[l_0, l_1, ...], ...}, [atom_index_0:{l_0:[m_0, m_1, ...], ...}, ...] |
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| *species* | `List[str]` or `Dict[str, List[int]]` or `Dict[str, Dict[int, List[int]]]]` | Extract PBANDS of each atom with same species from 'PBANDS_*' file e.g. [elem_0, elem_1...] or {elem_0:[l_0, l_1, ...], ...}, [elem_0:{l_0:[m_0, m_1, ...], ...}, ...] |
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| *kptfile* | `str` | K-points file with `Line` mode in ABACUS format |
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| *label* | `str` or `List[str]` | Label of band structure |
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| *color* | `str` or `List[str]` | Color of band structure |
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If you want to plot band structure of `nspin=2` or compare two band structure on same k-path, you can set *bandfile*, *efermi*, *label*, *color* in `list` type.
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```
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Then, use the following command to plot band structure:
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```shell
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abacus-plot -b -f band-input.json
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abacus-plot -b
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```
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Then, the following command will plot projected band structure and figures output to directory `PBAND*_FIG` ($*=1$ for $nspin=1$, $*=2$ for $nspin=2$):
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```shell
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abacus-plot -d -p
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```
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Then, the following command will output parsed partial DOS to directory `PBAND*_FILE` ($*=1$ for $nspin=1$, $*=2$ for $nspin=2$):
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```shell
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abacus-plot -d -o
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```
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### DOS
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First, prepare a json file e.g. dos-input.json:
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First, prepare a file named 'config.json' in json format:
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```json
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{
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"pdosfile": "PDOS",
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"efermi": 10.39537843955395,
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"efermi": 6.585653952007503,
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"energy_range": [
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-5,
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],
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"species": {
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"C": {
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"0": [
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],
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"1": [
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]
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}
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```
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If you only want to plot total DOS, you can modify `pdosfile` to `tdosfile` and do not set `species` and `pdosfig`.
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| Property | Type | Note |
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| :------------: | :-------------------------------------------------------------------------: | :---------------------------------------------------------------------------------------------------------: |
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| *tdosfile* | `str` | Total DOS data file output from ABACUS |
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| *pdosfile* | `str` | Partial DOS data file output from ABACUS in xml format |
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| *efermi* | `float` | Fermi level in eV |
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| *energy_range* | `list` | Range of energy in eV |
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| *shift* | `bool` | If set `'true'`, it will evaluate band gap. Default: `'false'` |
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| *index* | `List[int]` or `Dict[int, List[int]]` or `Dict[int, Dict[int, List[int]]]]` | Extract PDOS of each atom e.g. [0, 1], {0:[0, 1], 1:[0]}, [0:{0:[0]}, 1:{1:[0, 1]}] |
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| *atom_index* | `List[int]` or `Dict[int, List[int]]` or `Dict[int, Dict[int, List[int]]]]` | Extract PDOS of each atom with same atom_index e.g. [0, 1], {0:[0, 1], 1:[0]}, [0:{0:[0]}, 1:{1:[0, 1]}] |
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| *species* | `List[str]` or `Dict[str, List[int]]` or `Dict[str, Dict[int, List[int]]]]` | Extract PDOS of each atom with same species e.g. ["C", "Si"], {"C":[0, 1], "Si":[0]}, ["C":{0:[0]}, "Si":{1:[0, 1]}] |
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| *tdosfig* | `str` | Output picture of total DOS |
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| *pdosfig* | `str` | Output picture of partial DOS |
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| Property | Type | Note |
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| :------------: | :-------------------------------------------------------------------------: | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
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| *tdosfile* | `str` | Total DOS data file output from ABACUS |
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| *pdosfile* | `str` | Partial DOS data file output from ABACUS in xml format |
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| *efermi* | `float` | Fermi level in eV |
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| *energy_range* | `list` | Range of energy in eV |
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| *shift* | `bool` | If set `'true'`, it will evaluate band gap. Default: `'false'` |
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| *index* | `List[int]` or `Dict[str, List[int]]` or `Dict[str, Dict[str, List[int]]]]` | Extract PDOS of each atom e.g. [index_0, index_1...] or {index_0:[l_0, l_1, ...], ...}, [index_0:{l_0:[m_0, m_1, ...], ...}, ...] |
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| *atom_index* | `List[int]` or `Dict[str, List[int]]` or `Dict[str, Dict[str, List[int]]]]` | Extract PDOS of each atom with same atom_index e.g. [atom_index_0, atom_index_1...] or {atom_index_0:[l_0, l_1, ...], ...}, [atom_index_0:{l_0:[m_0, m_1, ...], ...}, ...] |
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| *species* | `List[str]` or `Dict[str, List[int]]` or `Dict[str, Dict[str, List[int]]]]` | Extract PDOS of each atom with same species e.g. [elem_0, elem_1...] or {elem_0:[l_0, l_1, ...], ...}, [elem_0:{l_0:[m_0, m_1, ...], ...}, ...] |
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| *tdosfig* | `str` | Output picture of total DOS |
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| *pdosfig* | `str` | Output picture of partial DOS |
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Then, the following command will plot total DOS:
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```shell
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abacus-plot -t tdos-input.json
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abacus-plot -d
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```
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Then, the following command will plot partial DOS:
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```shell
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abacus-plot -p pdos-input.json
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abacus-plot -d -p
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```
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Then, the following command will output parsed partial DOS to directory `PDOS_FILE`:
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```shell
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abacus-plot -o pdos-input.json
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abacus-plot -d -o
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```

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