res2desc

Compute descriptors for AIRSS style SHELX files

Installation

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.

Usage

Invoke by cat *.res | res2desc soap.

You can get a list of options by passing --help flag.

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).

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 for analysing AIRSS search results.

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

git clone git@github.com: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

zhubonan / res2desc