From de7ffa35bae624162a73bb475bca27628f0c316c Mon Sep 17 00:00:00 2001 From: wolearyc Date: Thu, 3 Oct 2024 15:21:41 -0700 Subject: [PATCH] updated docs to emphasize pymatgen integration --- README.md | 8 +++++++- docs/coverage-badge.svg | 2 +- docs/source/conf.py | 1 + docs/source/io.rst | 19 ++++++++++++------- docs/tests-badge.svg | 2 +- 5 files changed, 22 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index 81641ac..523993e 100644 --- a/README.md +++ b/README.md @@ -45,7 +45,13 @@ $ pip install torch-scatter torch-sparse -f https://data.pyg.org/whl/torch-2.4.0 $ pip install ramannoodle[torch] ``` -## Documentation +Ramannoodle includes interfaces with [pymatgen](https://pymatgen.org/). To use these interfaces, ramannoodle should be installed with the `[pymatgen]` option: + +``` +$ pip install ramannoodle[pymatgen] +``` + +## Tutorials and docs [https://ramannoodle.readthedocs.io/](https://ramannoodle.readthedocs.io/) diff --git a/docs/coverage-badge.svg b/docs/coverage-badge.svg index 6c95a77..3eb607c 100644 --- a/docs/coverage-badge.svg +++ b/docs/coverage-badge.svg @@ -1 +1 @@ -coverage: 94.32%coverage94.32% +coverage: 93.69%coverage93.69% diff --git a/docs/source/conf.py b/docs/source/conf.py index bdbee6f..11e06c2 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -52,6 +52,7 @@ # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output html_theme = 'furo' +html_title = 'ramannoodle' html_static_path = ['_static'] html_theme_options = { "light_logo": "logo.png", diff --git a/docs/source/io.rst b/docs/source/io.rst index 207885f..100ccb1 100644 --- a/docs/source/io.rst +++ b/docs/source/io.rst @@ -1,10 +1,10 @@ -Interfacing with first-principles software -========================================== +IO +==== -Ramannoodle includes functions for reading and writing files used by quantum chemistry software. Currently, ramannoodle only supports VASP. We hope to include community-contributed interfaces with other codes in future versions. +Ramannoodle includes functions for reading and writing files used by quantum chemistry software. Currently, ramannoodle includes build-in interfaces with VASP. Ramannoodle also includes an interface with `pymatgen `_, allowing spectra to be calculated using `a wide array of DFT packages `_. -IO ---- +File IO +------- IO operations are implemented in ramannoodle as functions. These are organized into packages and modules under :mod:`ramannoodle.io`. For example, VASP POSCAR IO functions are contained in :mod:`ramannoodle.io.vasp.poscar` while OUTCAR files can be read with functions in :mod:`ramannoodle.io.vasp.outcar`. Using this structure, files of various types can be interacted with in an intuitive and readable way: @@ -37,8 +37,8 @@ These generic functions are less flexible than those first mentioned, and theref .. _Supported formats: -Supported formats ------------------ +Supported file formats +---------------------- The following table reviews which file types and properties are currently supported by ramannoodle's IO functions: @@ -56,3 +56,8 @@ The following table reviews which file types and properties are currently suppor :sup:`1` Uses initial structure. :sup:`2` Not available in :mod:`ramannoodle.io.generic` + +Pymatgen integration +-------------------- + +Ramannoodle includes interfaces with `pymatgen `_. By taking advantage of pymatgen's IO functionality, one can use ramannoodle with a wide variety of popular DFT software packages. :mod:`ramannoodle.io.pymatgen` contains various useful functions for loading pymatgen data into ramannoodle. In addition :class:`InterpolationModel` and :class:`ARTModel` implement :meth:`.add_dof_from_pymatgen` and :meth:`.add_art_from_pymatgen` methods, allowing one to build up these models using pymatgen objects. diff --git a/docs/tests-badge.svg b/docs/tests-badge.svg index 811b707..9f5e908 100644 --- a/docs/tests-badge.svg +++ b/docs/tests-badge.svg @@ -1 +1 @@ -tests: 194tests194 +tests: 201tests201