README

Synthesized compositions search from cif database.

Installation via PyPI

[In progress] cifcombo can be obtained from PyPI

pip install cifcombo

Installation from source

If you prefer to install from source, instead follow the procedures below.

git clone https://github.com/kousuke-nakano/cifcombo.git
cd cifcombo
pip install -e .

Quick use

Preparation of a CIF data file (from CIF files)

You should prepare a CIF data file from your cif files

cifcombo -m cif_dir1 cif_dir2 ....

The generation process is parallelized using joblib library. Nevertheless, it takes a very long time if the specified CIF database is huge (e.g., It takes ~ 2 days for the entire COD/Crystallography Open Database [http://www.crystallography.net/cod/] CIF files with 256 cores of Intel(R) Xeon Phi(TM) CPU 7210 @ 1.30GHz).

If one wants to use a prepared CIF database, plz. contact to the developer Kosuke Nakano [[email protected]].

Using a prepared CIF database

You can use CIF database that has been already generated

To copy a prepared the CIF database:

%cifcombo -cc cif_data    # A prepared CIF database
%cifcombo -cd cif_dir     # The directory containing the CIF files used for generating the CIF database

or to make symbolic links to the CIF database:

%cifcombo -lc cif_data    # A prepared CIF database
%cifcombo -ld cif_dir     # The directory containing the CIF files used for generating the CIF database

Search a CIF file from the generated database

You should search a CIF that can be sum of the input compositions from the generated database.

%cifcombo -s CaO TiO2
1*Ca1 Ti1 O3 = 1*Ca1O1 + 1*Ti1O2, cifid=1000022, SG=Pnma
...

Get a CIF file from the generated database

You should copy a CIF with an ID in the generated database.

cifcombo -g 1000022
# copying 1000022.cif to the current directory.

Decompose an input composition

You can decompose a target composition with the input compositions

%cifcombo -s CaO TiO2 -t CaTiO3
1*CaTiO3 = 1*CaO + 1*TiO2

If you do not specify the input compositions, cifcombo searches for possible decompositions based on the CIF files registered in the CIF database. You can also specify the number of decomposition by the option -nd (default is 2).

%cifcombo -t CaTiO3 -nd 2

target composition = Ca1 Ti1 O3
The num. possible decomposition = 2
1*CaTiO3 = 1*CaO + 1*TiO2
...

Additional information

For additional information, you can use the help command:

cifcombo -h

or you can refer to the documentation.

How to release

Work on the devel or on a new branch

git merge <new branch> devel # if you work on a new branch.
git push origin devel # A GitHub Action triggers pytests.

Check the next-version version

# Confirm the version number via `setuptools-scm`
python -m setuptools_scm
e.g., 1.1.4.dev28+gceef293.d20221123 -> <next-version> = v1.1.4 or v1.1.4-alpha(for pre-release)

Add and push with the new tag

# Push with tag
git tag <next-version>  # e.g., git tag v1.1.4  # Do not forget "v" before the version number!
git push origin devel --tags  # or to the new branch

Send a pull request to the master branch on GitHub. After the pull request is approved and the devel branch is merged to the master, a GitHub Action checks if the automatic deploy works using test-pyPI (if the commit is tagged correctly, e.g., v1.1.0).

Finally, do a new release with a release note on GitHub. The new release trigggers an implemented GitHub Action that automatically uploads the package to PyPI (if the commit is tagged correctly, e.g., v1.1.0).

Contributing to the project

If you want to contribute to the project, report a bug, or ask for a new feature, please raise an issue.