https://github.com/zhubonan/res2desc
Computing descriptors for AIRSS style SHELX files.
https://github.com/zhubonan/res2desc
airss materials-science structure-prediction
Last synced: 2 months ago
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Computing descriptors for AIRSS style SHELX files.
- Host: GitHub
- URL: https://github.com/zhubonan/res2desc
- Owner: zhubonan
- License: mit
- Created: 2020-04-22T11:16:18.000Z (about 5 years ago)
- Default Branch: master
- Last Pushed: 2020-07-07T09:53:38.000Z (almost 5 years ago)
- Last Synced: 2025-02-05T11:52:51.493Z (4 months ago)
- Topics: airss, materials-science, structure-prediction
- Language: Python
- Size: 51.8 KB
- Stars: 3
- Watchers: 2
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# res2desc
Compute descriptors for AIRSS style SHELX files
## Installation
```text
git clone https://github.com/zhubonan/res2desc.git
pip install -e ./res2desc
```
Note, it is best to install inside a python virtual environment, such as those managed by [conda](https://docs.conda.io/en/latest/index.html).
## Usage
Invoke by `cat *.res | res2desc soap`.
You can get a list of options by passing `--help` flag.
```text
Usage: res2desc [OPTIONS] COMMAND [ARGS]...
Commandline tool for converting SHELX files to descriptors
Options:
-in, --input_source FILENAME [default: (STDIN)]
-out, --output FILENAME [default: (STDOUT)]
--cryan / --no-cryan Call cryan internally to obtain fully
compatible output. Should be disabled if cryan
is not avaliable. [default: True]
--cryan-style-in [1|2] Style of the cryan input, 1 for 3 lines for
structure, 2 for 2 lines per structure.
Automatically fallback to 1 if 2 does not
work. [default: 2]
--cryan-style-out [1|2] Style of the cryan output, 1 for 3 lines for
structure, 2 for 2 lines per structure.
Default to 3 lines for compatibility with
SHEAP [default: 1]
--cryan-args TEXT A string of the arges that should be passed to
cryan, as if in the shell [default: -v -dr 0]
--help Show this message and exit.
Commands:
soap Compute SOAP descriptors
xyz Create concatenated xyz files
```
Note that `input-source` and `output` default to STDIN and STDOUT by default, but you can still
specify file names.
### SOAP descriptors
Again, help can be obtained using the `echo '' | res2desc soap --help` flag.
Note that by default, `res2desc` take input from STDIN, so you have to use `echo`
to obtain the help string (subject to change in the future).
```text
Usage: res2desc soap [OPTIONS]
Compute SOAP descriptors
Options:
-np, --nprocs INTEGER Number of processes for parallelisation.
--l-max INTEGER [default: 4]
--n-max INTEGER [default: 8]
--cutoff INTEGER [default: 5]
--atom-sigma FLOAT [default: 0.1]
--crossover / --no-crossover Whether do the crossover for multiple species
[default: True]
-sn, --species-names TEXT Symbols of all species to be considered,
should be a list
-cn, --centres-name TEXT Centres where the descriptor should be
computed. If not specified, defaults to all
atomic sites. NOT IMPLEMENTED FOR NOW
--average / --no-average Averaging descriptors for each structrure,
rather than output those for individual sites.
[default: True]
--periodic / --no-periodic Whether assuming periodic boundary conditions
or not [default: True]
--help Show this message and exit.
```
### xyz output
Concatenate all structures in the xyz format, and write the labels in separate files.
This can be used when using [ASAP](https://github.com/BingqingCheng/ASAP) for analysing AIRSS search results.
```text
Usage: res2desc xyz [OPTIONS]
Create concatenated xyz files
Options:
--label-file TEXT Filename for writing out the labels
--label-style [label|short_label|short_symm|symm|enthalpy|volume|spin|spin_abs|pressure]
Style of the labels
--help Show this message and exit.
```
### Tab completion
Source the script in `scripts/res2desc_active.sh` to enable tab-completion. It can be place the file at
`$CONDA_PREFIX/etc/conda/activate.d/` to have it sourced upon environment activation. You may have to
create the direction if it does not exit.
## Requirement
* `DScribe` for computing descriptors
* `click` for commandline interface
## Testing
```text
git clone [email protected]:zhubonan/res2desc.git
pytest ./res2desc
```
## Limitations
* Only SOAP is implemented at the moment
* Filtering species is not avaliable for now
* Descripters are only computed once all files are read, this could cause problems for large number of input structures
## TODO
* Allow computing more types of descriptors other than SOAP
* Allow buffering input structures and avoid stressing the memory