Skip to content

Commit

Permalink
deploy: 86fb5a4
Browse files Browse the repository at this point in the history
  • Loading branch information
JaGeo committed Feb 27, 2024
0 parents commit 0b36b7e
Show file tree
Hide file tree
Showing 367 changed files with 76,461 additions and 0 deletions.
4 changes: 4 additions & 0 deletions .buildinfo
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: e115b12a6e1950854652473c17e39d56
tags: 645f666f9bcd5a90fca523b33c5a78b7
Binary file added .doctrees/about/changelog.doctree
Binary file not shown.
Binary file added .doctrees/about/license.doctree
Binary file not shown.
Binary file added .doctrees/dev/contributing.doctree
Binary file not shown.
Binary file added .doctrees/dev/dev_installation.doctree
Binary file not shown.
Binary file added .doctrees/environment.pickle
Binary file not shown.
Binary file added .doctrees/fundamentals/index.doctree
Binary file not shown.
Binary file added .doctrees/index.doctree
Binary file not shown.
Binary file added .doctrees/installation/index.doctree
Binary file not shown.
Binary file added .doctrees/reference/cli.doctree
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file added .doctrees/reference/cli_subcommands/plot.doctree
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file added .doctrees/reference/index.doctree
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file added .doctrees/reference/lobsterpy.cohp.doctree
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file added .doctrees/reference/lobsterpy.featurize.doctree
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file added .doctrees/reference/lobsterpy.plotting.doctree
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file added .doctrees/tutorial/atomateauto.doctree
Binary file not shown.
Binary file added .doctrees/tutorial/commandlineinterface.doctree
Binary file not shown.
Binary file added .doctrees/tutorial/computingtimes.doctree
Binary file not shown.
Binary file added .doctrees/tutorial/index.doctree
Binary file not shown.
Binary file added .doctrees/tutorial/tutorial.doctree
Binary file not shown.
Empty file added .nojekyll
Empty file.
14 changes: 14 additions & 0 deletions _downloads/8f717a44707c0b40f1d30cb8055189c3/CdF2.html

Large diffs are not rendered by default.

14 changes: 14 additions & 0 deletions _downloads/bdff33f4f22a5d2dc65348c72950861a/CdF2_orb.html

Large diffs are not rendered by default.

Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/COHP.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/COHP_330.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/COOP_330.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/DOS_example.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/ICOHP.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/ICOHPs_distance_example.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/LobsterEnv_schema.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/bonding_percentage.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added _images/orbital_wise_illustration.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
491 changes: 491 additions & 0 deletions _modules/index.html

Large diffs are not rendered by default.

2,131 changes: 2,131 additions & 0 deletions _modules/lobsterpy/cohp/analyze.html

Large diffs are not rendered by default.

1,327 changes: 1,327 additions & 0 deletions _modules/lobsterpy/cohp/describe.html

Large diffs are not rendered by default.

1,322 changes: 1,322 additions & 0 deletions _modules/lobsterpy/featurize/batch.html

Large diffs are not rendered by default.

1,652 changes: 1,652 additions & 0 deletions _modules/lobsterpy/featurize/core.html

Large diffs are not rendered by default.

570 changes: 570 additions & 0 deletions _modules/lobsterpy/featurize/utils.html

Large diffs are not rendered by default.

1,666 changes: 1,666 additions & 0 deletions _modules/lobsterpy/plotting.html

Large diffs are not rendered by default.

659 changes: 659 additions & 0 deletions _modules/lobsterpy/structuregraph/graph.html

Large diffs are not rendered by default.

2 changes: 2 additions & 0 deletions _sources/about/changelog.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
```{include} ../../CHANGELOG.md
```
32 changes: 32 additions & 0 deletions _sources/about/license.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,32 @@
License
=======

BSD 3-Clause License

Copyright (c) 2021, LobsterPy Development Team
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.

3. Neither the name of the copyright holder nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
2 changes: 2 additions & 0 deletions _sources/dev/contributing.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
```{include} ../../CONTRIBUTING.md
```
53 changes: 53 additions & 0 deletions _sources/dev/dev_installation.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,53 @@
# Developer Installation

Install LobsterPy from source, by cloning the repository via [github](https://github.com/JaGeo/LobsterPy.git)

```bash
git clone https://github.com/JaGeo/LobsterPy.git
cd LobsterPy
pip install -e .[featurizer,docs,tests,dev]
```
This will install LobsterPy will all dependencies for tests, pre-commit and docs building.

## Running unit tests

Unit tests can be run from the source folder using `pytest`.

```bash
pytest
```
This will run all the tests.

To get a detailed report of test coverage you can use following command
```bash
pytest --cov=lobsterpy --cov-report term-missing --cov-append
```

If you feel test execution takes too long locally, you can speedup the execution using [pytest-xdist](https://pypi.org/project/pytest-xdist/). Install this in library in your environment using

```bash
pip install pytest-xdist
```

Once installed, you can now use multiple processors to run your tests. For example, if you want to use 8 processors to run tests in parallel, run

```bash
pytest -n 8
```

We rely on pytest-split to run tests in parallel on github workflow, thus it is necessary to update the test-durations files in the repository, incase you add new tests. To generate this file, use

```bash
pytest --cov=lobsterpy --cov-append --splits 1 --group 1 --durations-path ./tests/test_data/.pytest-split-durations --store-durations
```

## Building the documentation locally

The atomate2 documentation can be built using the sphinx package.

The docs can be built to the `_build` directory:

```bash
sphinx-build -W docs _build
```

306 changes: 306 additions & 0 deletions _sources/fundamentals/index.ipynb

Large diffs are not rendered by default.

84 changes: 84 additions & 0 deletions _sources/index.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,84 @@
```{toctree}
:caption: User Guide
:hidden:
installation/index
fundamentals/index
tutorial/index
```

```{toctree}
:caption: Reference
:hidden:
reference/index
reference/cli
```

```{toctree}
:caption: Contributing Guide
:hidden:
dev/contributing
dev/dev_installation
```

```{toctree}
:caption: About
:hidden:
about/changelog
about/license
```

# LobsterPy documentation

**Date**: {sub-ref}`today`

**Useful links**:
[Github Repository](https://github.com/JaGeo/LobsterPy) |
[PyPI](https://pypi.org/project/lobsterpy/) |
[Issues & Ideas](https://github.com/JaGeo/LobsterPy/issues) |

LobsterPy is a package that enables automatic analysis of LOBTSER outputs to get summarized bonding information and relevant bond plots. Additionally, one can also generate features for machine learning studies from LOBSTER outputs.

::::{grid} 1 1 2 2
:class-container: text-center
:gutter: 3


:::{grid-item-card}
:link: fundamentals/index
:link-type: doc
:class-header: bg-light
**Fundamental Aspects**
^^^
This guide contains a detailed explanation of the key functionalites on
which LobsterPy automatic analysis is based on.
:::

:::{grid-item-card}
:link: installation/index
:link-type: doc
:class-header: bg-light
**User Guide**
^^^
This guide provides in-depth information for getting started and tutorials for *LobsterPy*.
:::

:::{grid-item-card}
:link: https://materialsproject.github.io/atomate2/user/codes/vasp.html#lobster
:class-header: bg-light
**LOBSTER Workflow**
^^^
Here you can find how to use our completely automated workflow to perform bonding analysis with
LOBSTER and Lobsterpy via atomate2.
:::


:::{grid-item-card}
:link: dev/dev_installation
:link-type: doc
:class-header: bg-light
**Developer guide**
^^^
Do you want contribute or improve existing functionalities?
Check out the developer guide.
:::
::::
7 changes: 7 additions & 0 deletions _sources/installation/index.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
Getting started
================
```{include} ../../README.md
---
start-line: 5
---
```
14 changes: 14 additions & 0 deletions _sources/reference/cli.rst
Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
CLI Reference
==============

.. toctree::
:maxdepth: 1

cli_subcommands/createinputs
cli_subcommands/description
cli_subcommands/descriptionquality
cli_subcommands/plotauto
cli_subcommands/plotautoia
cli_subcommands/plotdos
cli_subcommands/ploticohpdistance
cli_subcommands/plot
16 changes: 16 additions & 0 deletions _sources/reference/cli_subcommands/createinputs.rst
Original file line number Diff line number Diff line change
@@ -0,0 +1,16 @@
create-inputs
==============

Create inputs for lobster computation. It works only with PBE POTCARs.

.. hint:: Aliases available

- createinputs


.. argparse::
:module: lobsterpy.cli
:func: get_parser
:prog: lobsterpy
:path: create-inputs

11 changes: 11 additions & 0 deletions _sources/reference/cli_subcommands/description.rst
Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
description
============

Deliver a text description of the COHPs or COBIS or COOP results from Lobster and VASP

.. argparse::
:module: lobsterpy.cli
:func: get_parser
:prog: lobsterpy
:path: description

10 changes: 10 additions & 0 deletions _sources/reference/cli_subcommands/descriptionquality.rst
Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
description-quality
===================

Deliver a text description of the LOBSTER calc quality analysis. Mandatory required files: POSCAR, POTCAR or POTCAR symbols, lobsterout, lobsterin. Optional files (BVA comparison): CHARGE.lobster, (DOS comparison): DOSCAR.lobster/ DOSCAR.LSO.lobster, Vasprun.xml.

.. argparse::
:module: lobsterpy.cli
:func: get_parser
:prog: lobsterpy
:path: description-quality
11 changes: 11 additions & 0 deletions _sources/reference/cli_subcommands/plot.rst
Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
plot
====

Plot specific COHPs/COBIs/COOPs based on bond numbers.

.. argparse::
:module: lobsterpy.cli
:func: get_parser
:prog: lobsterpy
:path: plot

19 changes: 19 additions & 0 deletions _sources/reference/cli_subcommands/plotauto.rst
Original file line number Diff line number Diff line change
@@ -0,0 +1,19 @@
plot-automatic
==============

Plot most important COHPs or COBIs or COOPs automatically. This option also includes an automatic description.

.. hint:: Aliases available

- plot-auto
- auto-plot
- autoplot
- automatic-plot
- automaticplot

.. argparse::
:module: lobsterpy.cli
:func: get_parser
:prog: lobsterpy
:path: plot-automatic

18 changes: 18 additions & 0 deletions _sources/reference/cli_subcommands/plotautoia.rst
Original file line number Diff line number Diff line change
@@ -0,0 +1,18 @@
plot-automatic-ia
==================

Creates an interactive plot of most important COHPs or COBIs or COOPs automatically.

.. hint:: Aliases available

- plot-auto-ia
- auto-plot-ia
- autoplotia
- automatic-plot-ia
- automaticplot-ia

.. argparse::
:module: lobsterpy.cli
:func: get_parser
:prog: lobsterpy
:path: plot-automatic-ia
11 changes: 11 additions & 0 deletions _sources/reference/cli_subcommands/plotdos.rst
Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
plot-dos
=========

Plots DOS from lobster computation.

.. argparse::
:module: lobsterpy.cli
:func: get_parser
:prog: lobsterpy
:path: plot-dos

15 changes: 15 additions & 0 deletions _sources/reference/cli_subcommands/ploticohpdistance.rst
Original file line number Diff line number Diff line change
@@ -0,0 +1,15 @@
plot-icohp-distance
====================

Plot ICOHPs or ICOOPs or ICOBIs with respect to bond lengths.

.. hint:: Aliases available

- ploticohpdistance

.. argparse::
:module: lobsterpy.cli
:func: get_parser
:prog: lobsterpy
:path: plot-icohp-distance

15 changes: 15 additions & 0 deletions _sources/reference/index.rst
Original file line number Diff line number Diff line change
@@ -0,0 +1,15 @@
Python API reference
====================


.. currentmodule:: lobsterpy

.. autosummary::
:recursive:
:toctree:
:nosignatures:

cohp
featurize
plotting
structuregraph
8 changes: 8 additions & 0 deletions _sources/reference/lobsterpy.cohp.analyze.Analysis.rst
Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
Analysis
========

.. currentmodule:: lobsterpy.cohp.analyze

.. autoclass:: Analysis
:show-inheritance:
:members:
45 changes: 45 additions & 0 deletions _sources/reference/lobsterpy.cohp.analyze.rst
Original file line number Diff line number Diff line change
@@ -0,0 +1,45 @@
lobsterpy.cohp.analyze
======================

.. automodule:: lobsterpy.cohp.analyze
























.. rubric:: Classes

.. autosummary::
:toctree:
:nosignatures:

Analysis










Loading

0 comments on commit 0b36b7e

Please sign in to comment.