From 76a44c59fc81704097bc6ef48bf0bdbd677830f6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Moritz=20R=2E=20Sch=C3=A4fer?= Date: Mon, 22 May 2023 22:39:12 +0200 Subject: [PATCH 01/35] documentation outline --- docs/Makefile | 20 +++++++++++ docs/make.bat | 35 +++++++++++++++++++ docs/source/_examples/index.rst | 7 ++++ docs/source/_get_started/index.rst | 15 ++++++++ docs/source/_get_started/installation.rst | 0 docs/source/_nodes/analysis.rst | 4 +++ docs/source/_nodes/bootstrap.rst | 4 +++ docs/source/_nodes/calculators.rst | 4 +++ .../_nodes/configuration_comparison.rst | 4 +++ .../_nodes/configuration_generation.rst | 4 +++ .../source/_nodes/configuration_selection.rst | 4 +++ docs/source/_nodes/data_loading.rst | 4 +++ docs/source/_nodes/geometry.rst | 4 +++ docs/source/_nodes/index.rst | 19 ++++++++++ docs/source/_nodes/models.rst | 4 +++ docs/source/conf.py | 28 +++++++++++++++ docs/source/index.rst | 33 +++++++++++++++++ index.rst | 20 +++++++++++ pyproject.toml | 4 +++ 19 files changed, 217 insertions(+) create mode 100644 docs/Makefile create mode 100644 docs/make.bat create mode 100644 docs/source/_examples/index.rst create mode 100644 docs/source/_get_started/index.rst create mode 100644 docs/source/_get_started/installation.rst create mode 100644 docs/source/_nodes/analysis.rst create mode 100644 docs/source/_nodes/bootstrap.rst create mode 100644 docs/source/_nodes/calculators.rst create mode 100644 docs/source/_nodes/configuration_comparison.rst create mode 100644 docs/source/_nodes/configuration_generation.rst create mode 100644 docs/source/_nodes/configuration_selection.rst create mode 100644 docs/source/_nodes/data_loading.rst create mode 100644 docs/source/_nodes/geometry.rst create mode 100644 docs/source/_nodes/index.rst create mode 100644 docs/source/_nodes/models.rst create mode 100644 docs/source/conf.py create mode 100644 docs/source/index.rst create mode 100644 index.rst diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 00000000..d0c3cbf1 --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,20 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build +SOURCEDIR = source +BUILDDIR = build + +# Put it first so that "make" without argument is like "make help". +help: + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + +.PHONY: help Makefile + +# Catch-all target: route all unknown targets to Sphinx using the new +# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). +%: Makefile + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/make.bat b/docs/make.bat new file mode 100644 index 00000000..747ffb7b --- /dev/null +++ b/docs/make.bat @@ -0,0 +1,35 @@ +@ECHO OFF + +pushd %~dp0 + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set SOURCEDIR=source +set BUILDDIR=build + +%SPHINXBUILD% >NUL 2>NUL +if errorlevel 9009 ( + echo. + echo.The 'sphinx-build' command was not found. Make sure you have Sphinx + echo.installed, then set the SPHINXBUILD environment variable to point + echo.to the full path of the 'sphinx-build' executable. Alternatively you + echo.may add the Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.https://www.sphinx-doc.org/ + exit /b 1 +) + +if "%1" == "" goto help + +%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% +goto end + +:help +%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% + +:end +popd diff --git a/docs/source/_examples/index.rst b/docs/source/_examples/index.rst new file mode 100644 index 00000000..d12863df --- /dev/null +++ b/docs/source/_examples/index.rst @@ -0,0 +1,7 @@ + + +.. _userdoc-examples: + +Examples +======== + diff --git a/docs/source/_get_started/index.rst b/docs/source/_get_started/index.rst new file mode 100644 index 00000000..1d51c41d --- /dev/null +++ b/docs/source/_get_started/index.rst @@ -0,0 +1,15 @@ + +.. _userdoc-get-started: + + +Getting Started +=============== + +TODO link to zntrack docs + + + +.. toctree:: + :maxdepth: 0 + + installation diff --git a/docs/source/_get_started/installation.rst b/docs/source/_get_started/installation.rst new file mode 100644 index 00000000..e69de29b diff --git a/docs/source/_nodes/analysis.rst b/docs/source/_nodes/analysis.rst new file mode 100644 index 00000000..5cb7d3d8 --- /dev/null +++ b/docs/source/_nodes/analysis.rst @@ -0,0 +1,4 @@ +Analysis +======== +.. automodule:: ipsuite.analysis + :members: \ No newline at end of file diff --git a/docs/source/_nodes/bootstrap.rst b/docs/source/_nodes/bootstrap.rst new file mode 100644 index 00000000..dceb0df1 --- /dev/null +++ b/docs/source/_nodes/bootstrap.rst @@ -0,0 +1,4 @@ +Bootstrap +========= +.. automodule:: ipsuite.bootstrap + :members: \ No newline at end of file diff --git a/docs/source/_nodes/calculators.rst b/docs/source/_nodes/calculators.rst new file mode 100644 index 00000000..0d53ec7b --- /dev/null +++ b/docs/source/_nodes/calculators.rst @@ -0,0 +1,4 @@ +Calculators +=========== +.. automodule:: ipsuite.calculators + :members: \ No newline at end of file diff --git a/docs/source/_nodes/configuration_comparison.rst b/docs/source/_nodes/configuration_comparison.rst new file mode 100644 index 00000000..64f86ab9 --- /dev/null +++ b/docs/source/_nodes/configuration_comparison.rst @@ -0,0 +1,4 @@ +Configuration Comparison +======================== +.. automodule:: ipsuite.configuration_comparison + :members: \ No newline at end of file diff --git a/docs/source/_nodes/configuration_generation.rst b/docs/source/_nodes/configuration_generation.rst new file mode 100644 index 00000000..a7a4c409 --- /dev/null +++ b/docs/source/_nodes/configuration_generation.rst @@ -0,0 +1,4 @@ +Configuration Generation +======================== +.. automodule:: ipsuite.configuration_generation + :members: \ No newline at end of file diff --git a/docs/source/_nodes/configuration_selection.rst b/docs/source/_nodes/configuration_selection.rst new file mode 100644 index 00000000..82136ac4 --- /dev/null +++ b/docs/source/_nodes/configuration_selection.rst @@ -0,0 +1,4 @@ +Configuration Selection +======================= +.. automodule:: ipsuite.configuration_selection + :members: \ No newline at end of file diff --git a/docs/source/_nodes/data_loading.rst b/docs/source/_nodes/data_loading.rst new file mode 100644 index 00000000..c99ad151 --- /dev/null +++ b/docs/source/_nodes/data_loading.rst @@ -0,0 +1,4 @@ +Data Loading +============ +.. automodule:: ipsuite.data_loading + :members: \ No newline at end of file diff --git a/docs/source/_nodes/geometry.rst b/docs/source/_nodes/geometry.rst new file mode 100644 index 00000000..0259f6b4 --- /dev/null +++ b/docs/source/_nodes/geometry.rst @@ -0,0 +1,4 @@ +Geometry +======== +.. automodule:: ipsuite.geometry + :members: \ No newline at end of file diff --git a/docs/source/_nodes/index.rst b/docs/source/_nodes/index.rst new file mode 100644 index 00000000..5b8cdf07 --- /dev/null +++ b/docs/source/_nodes/index.rst @@ -0,0 +1,19 @@ + + +.. _userdoc-modules: + +Nodes +===== + +.. toctree:: + :maxdepth: 2 + + data_loading + bootstrap + calculators + configuration_selection + models + analysis + configuration_comparison + configuration_generation + geometry diff --git a/docs/source/_nodes/models.rst b/docs/source/_nodes/models.rst new file mode 100644 index 00000000..70d7885a --- /dev/null +++ b/docs/source/_nodes/models.rst @@ -0,0 +1,4 @@ +Models +====== +.. automodule:: ipsuite.models + :members: \ No newline at end of file diff --git a/docs/source/conf.py b/docs/source/conf.py new file mode 100644 index 00000000..d4f57739 --- /dev/null +++ b/docs/source/conf.py @@ -0,0 +1,28 @@ +# Configuration file for the Sphinx documentation builder. +# +# For the full list of built-in configuration values, see the documentation: +# https://www.sphinx-doc.org/en/master/usage/configuration.html + +# -- Project information ----------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information + +project = 'IPSuite' +copyright = '2023, zincwarecode' +author = 'zincwarecode' +release = '0.1.0a2' + +# -- General configuration --------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration + +extensions = [] + +templates_path = ['_templates'] +exclude_patterns = [] + + + +# -- Options for HTML output ------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output + +html_theme = 'alabaster' +html_static_path = ['_static'] diff --git a/docs/source/index.rst b/docs/source/index.rst new file mode 100644 index 00000000..a7581673 --- /dev/null +++ b/docs/source/index.rst @@ -0,0 +1,33 @@ +.. IPSuite documentation master file, created by + sphinx-quickstart on Mon May 22 19:58:40 2023. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +IPS - The Inter Atomic Potential Suite +====================================== + +The Inter Atomic Potential Suite (IPS) allows for the fast construction and extension of atomistic machine learning workflows. +It is based on `ZnTrack `_ and thus allows for fully version controlled and reproducible workflows. +Within IPS, we provide numerous Nodes for creating atomistic data, training models, analyzing predictions and performing molecular dynamics. + + + +Example +======= + +Routine workflows are easy to set up and can be easily extended for more complex tasks. + +.. code-block:: python + + # TODO simple training example + print("hello") + + + +.. toctree:: + :hidden: + + _get_started/index + _examples/index + _nodes/index + diff --git a/index.rst b/index.rst new file mode 100644 index 00000000..d6428eab --- /dev/null +++ b/index.rst @@ -0,0 +1,20 @@ +.. IPSuite documentation master file, created by + sphinx-quickstart on Mon May 22 19:56:43 2023. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to IPSuite's documentation! +=================================== + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` diff --git a/pyproject.toml b/pyproject.toml index 7b2386a2..c6ee1b77 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -68,6 +68,10 @@ coverage = "^7.2.1" [tool.poetry.group.dev.dependencies] imageio = "^2.28.1" + +[tool.poetry.group.docs.dependencies] +sphinx = "^7.0.1" + [tool.poetry.extras] comparison = ["h5py", "tensorflow", "llvmlite", "numba", "dscribe"] gap = ["quippy-ase", "xmltodict"] From 5223e1c8ff4881f37f8f4091d2b39f4acbdff25d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Moritz=20R=2E=20Sch=C3=A4fer?= Date: Mon, 22 May 2023 22:39:53 +0200 Subject: [PATCH 02/35] updated poetry.lock --- poetry.lock | 6251 ++++++++++++++++++++++++++------------------------- 1 file changed, 3216 insertions(+), 3035 deletions(-) diff --git a/poetry.lock b/poetry.lock index 7abeb95b..23a4224b 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,5 +1,3 @@ -# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. - [[package]] name = "absl-py" version = "1.4.0" @@ -7,10 +5,6 @@ description = "Abseil Python Common Libraries, see https://github.com/abseil/abs category = "main" optional = true python-versions = ">=3.6" -files = [ - {file = "absl-py-1.4.0.tar.gz", hash = "sha256:d2c244d01048ba476e7c080bd2c6df5e141d211de80223460d5b3b8a2a58433d"}, - {file = "absl_py-1.4.0-py3-none-any.whl", hash = "sha256:0d3fe606adfa4f7db64792dd4c7aee4ee0c38ab75dfd353b7a83ed3e957fcb47"}, -] [[package]] name = "aiofiles" @@ -19,10 +13,6 @@ description = "File support for asyncio." category = "dev" optional = false python-versions = ">=3.7,<4.0" -files = [ - {file = "aiofiles-22.1.0-py3-none-any.whl", hash = "sha256:1142fa8e80dbae46bb6339573ad4c8c0841358f79c6eb50a493dceca14621bad"}, - {file = "aiofiles-22.1.0.tar.gz", hash = "sha256:9107f1ca0b2a5553987a94a3c9959fe5b491fdf731389aa5b7b1bd0733e32de6"}, -] [[package]] name = "aiohttp" @@ -31,95 +21,6 @@ description = "Async http client/server framework (asyncio)" category = "main" optional = false python-versions = ">=3.6" -files = [ - 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=?UTF-8?q?Moritz=20R=2E=20Sch=C3=A4fer?= Date: Mon, 22 May 2023 22:43:45 +0200 Subject: [PATCH 03/35] added sphinx autodoc --- docs/source/_get_started/installation.rst | 3 +++ docs/source/conf.py | 9 ++++++++- 2 files changed, 11 insertions(+), 1 deletion(-) diff --git a/docs/source/_get_started/installation.rst b/docs/source/_get_started/installation.rst index e69de29b..cd7a81df 100644 --- a/docs/source/_get_started/installation.rst +++ b/docs/source/_get_started/installation.rst @@ -0,0 +1,3 @@ +Installation +============ + diff --git a/docs/source/conf.py b/docs/source/conf.py index d4f57739..a6f44eb2 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -14,7 +14,14 @@ # -- General configuration --------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration -extensions = [] +extensions = [ + "sphinx.ext.autodoc", + "sphinx.ext.napoleon", + # "sphinx_copybutton", + # "nbsphinx", + # "nbsphinx_link", + "sphinx.ext.viewcode", +] templates_path = ['_templates'] exclude_patterns = [] From 4d659f46497216f078fb6476b6809d2b27bd78dc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Moritz=20R=2E=20Sch=C3=A4fer?= Date: Mon, 22 May 2023 22:48:25 +0200 Subject: [PATCH 04/35] added redthedocs config --- .readthedocs.yaml | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 .readthedocs.yaml diff --git a/.readthedocs.yaml b/.readthedocs.yaml new file mode 100644 index 00000000..70e262f3 --- /dev/null +++ b/.readthedocs.yaml @@ -0,0 +1,20 @@ +# .readthedocs.yaml +# Read the Docs configuration file +# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details + +version: 2 + +# Set the version of Python and other tools you might need +build: + os: ubuntu-22.04 + tools: + python: "3.11" + jobs: + post_install: + - pip install poetry + - poetry config virtualenvs.create false + - poetry install --with=docs + +# Build documentation in the docs/ directory with Sphinx +sphinx: + configuration: docs/source/conf.py \ No newline at end of file From 4953f31dacad6efeb1f172f9701868da1ef9dcb6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Moritz=20R=2E=20Sch=C3=A4fer?= Date: Mon, 22 May 2023 23:07:16 +0200 Subject: [PATCH 05/35] Added descriptions to models and bootstrap indices --- docs/source/_nodes/bootstrap.rst | 4 ++++ docs/source/_nodes/models.rst | 17 +++++++++++++++++ 2 files changed, 21 insertions(+) diff --git a/docs/source/_nodes/bootstrap.rst b/docs/source/_nodes/bootstrap.rst index dceb0df1..6dca29a7 100644 --- a/docs/source/_nodes/bootstrap.rst +++ b/docs/source/_nodes/bootstrap.rst @@ -1,4 +1,8 @@ Bootstrap ========= + +The Nodes provided by this submodule can be used to create an initial dataset with some structural diversity. +This can be useful when starting out from a single configuration and iteratively building datasets with learning on the fly. + .. automodule:: ipsuite.bootstrap :members: \ No newline at end of file diff --git a/docs/source/_nodes/models.rst b/docs/source/_nodes/models.rst index 70d7885a..a83ce071 100644 --- a/docs/source/_nodes/models.rst +++ b/docs/source/_nodes/models.rst @@ -1,4 +1,21 @@ Models ====== + +IPS allows for easy use and comparison of different machine learning interatomic potentials. +Below you can find all models currently interfaced with this framework. +A model's run method performs training on the provided data. +All models provide an ASE calculator, which can be used for inference and analysis of predictions. + +Note that each model is an extra dependency and needs to be installed accordingly. +See getting started for more information. +If you would like to add other models to IPS, please consider this guide. + + +.. TODO Add link to getting started + + +.. TODO example for implementing new model + + .. automodule:: ipsuite.models :members: \ No newline at end of file From 55353fef7f63076a08ce4e7d570dfc5783555989 Mon Sep 17 00:00:00 2001 From: Moritz Schaefer Date: Tue, 23 May 2023 10:55:35 +0200 Subject: [PATCH 06/35] added remaining module descriptions to docs --- docs/source/_nodes/analysis.rst | 7 +++++++ docs/source/_nodes/calculators.rst | 4 ++++ docs/source/_nodes/configuration_comparison.rst | 3 +++ docs/source/_nodes/configuration_generation.rst | 8 +++++++- docs/source/_nodes/configuration_selection.rst | 4 ++++ docs/source/_nodes/data_loading.rst | 4 ++++ docs/source/_nodes/geometry.rst | 6 ++++++ 7 files changed, 35 insertions(+), 1 deletion(-) diff --git a/docs/source/_nodes/analysis.rst b/docs/source/_nodes/analysis.rst index 5cb7d3d8..4a9f8ad5 100644 --- a/docs/source/_nodes/analysis.rst +++ b/docs/source/_nodes/analysis.rst @@ -1,4 +1,11 @@ Analysis ======== + +As in all ML applications, analysing both the dataset and model predictions are of paramount importance. +For dataset exploration it is often convenient to visualize the distribution of labels. +Most Nodes are concerned with analysing trained models and often compare to a reference calculator. +This ranges from simple prediction correlation plots to force decompositions and energy-volume curves. + + .. automodule:: ipsuite.analysis :members: \ No newline at end of file diff --git a/docs/source/_nodes/calculators.rst b/docs/source/_nodes/calculators.rst index 0d53ec7b..d7bad29c 100644 --- a/docs/source/_nodes/calculators.rst +++ b/docs/source/_nodes/calculators.rst @@ -1,4 +1,8 @@ Calculators =========== + +Calculators can be used for labeling a given set of data and running molecular dynamics. +For all cases, ASE calculators are used. + .. automodule:: ipsuite.calculators :members: \ No newline at end of file diff --git a/docs/source/_nodes/configuration_comparison.rst b/docs/source/_nodes/configuration_comparison.rst index 64f86ab9..43e0b2fe 100644 --- a/docs/source/_nodes/configuration_comparison.rst +++ b/docs/source/_nodes/configuration_comparison.rst @@ -1,4 +1,7 @@ Configuration Comparison ======================== + +Provides kernel based similarity measures for comparing configruations. + .. automodule:: ipsuite.configuration_comparison :members: \ No newline at end of file diff --git a/docs/source/_nodes/configuration_generation.rst b/docs/source/_nodes/configuration_generation.rst index a7a4c409..5171f998 100644 --- a/docs/source/_nodes/configuration_generation.rst +++ b/docs/source/_nodes/configuration_generation.rst @@ -1,4 +1,10 @@ Configuration Generation ======================== + +This module provides Nodes for creating molecular dynamics starting structures. +Workflows can be quickly created from just knowing the SMILES strings of the molecules within the simulation box. +The PACKMOL interface can then be used to create the actual starting configuration. + + .. automodule:: ipsuite.configuration_generation - :members: \ No newline at end of file + :members: diff --git a/docs/source/_nodes/configuration_selection.rst b/docs/source/_nodes/configuration_selection.rst index 82136ac4..28dc9e56 100644 --- a/docs/source/_nodes/configuration_selection.rst +++ b/docs/source/_nodes/configuration_selection.rst @@ -1,4 +1,8 @@ Configuration Selection ======================= + +The configuration selection submodule contains Nodes for splitting datasets. +A simple 80:20 random split can be achieved with a single Node, but multiple Nodes can be chained to create complex splittings. + .. automodule:: ipsuite.configuration_selection :members: \ No newline at end of file diff --git a/docs/source/_nodes/data_loading.rst b/docs/source/_nodes/data_loading.rst index c99ad151..ec439f0b 100644 --- a/docs/source/_nodes/data_loading.rst +++ b/docs/source/_nodes/data_loading.rst @@ -1,4 +1,8 @@ Data Loading ============ + +IPS can load datasets from ASE readable formats and HDF5 files. +Internally, atomistic data is represented by ASE's `Atoms` objects which are serialized to HDF5. + .. automodule:: ipsuite.data_loading :members: \ No newline at end of file diff --git a/docs/source/_nodes/geometry.rst b/docs/source/_nodes/geometry.rst index 0259f6b4..76a8dd5a 100644 --- a/docs/source/_nodes/geometry.rst +++ b/docs/source/_nodes/geometry.rst @@ -1,4 +1,10 @@ Geometry ======== + +This module contains Nodes and utilities for molecule mapping. +The Nodes provide `forward_mapping` and `backward_mapping` methods for applying and reversing the transformations. +Note that they do not implement `run` methods and are thus intended to be used as `zn.nodes()`. + + .. automodule:: ipsuite.geometry :members: \ No newline at end of file From 38a610da0b6fc11dff4e8ccc7bae469a2a8c06a6 Mon Sep 17 00:00:00 2001 From: Moritz Schaefer Date: Tue, 23 May 2023 11:04:39 +0200 Subject: [PATCH 07/35] Added furo theme and nbsphinx --- docs/source/conf.py | 14 +- poetry.lock | 7270 ++++++++++++++++++++++--------------------- 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"sha256:190f6424bb98fbc6f817d35c5714ada1239ee74db231d684dc57d04480b11619"}, {file = "znflow-0.1.11.tar.gz", hash = "sha256:9802f4604815aa64a1b42b6cdf4fcd042d277d21de800019c9040f7f35d0426f"}, ] -znh5md = [ + +[package.dependencies] +matplotlib = ">=3.6.3,<4.0.0" +networkx = ">=3.0,<4.0" + +[package.extras] +dask = ["bokeh (>=2.4.2,<3.0.0)", "dask (>=2022.12.1,<2023.0.0)", "dask-jobqueue (>=0.8.1,<0.9.0)", "distributed (>=2022.12.1,<2023.0.0)"] + +[[package]] +name = "znh5md" +version = "0.1.6" +description = "High Performance Interface for H5MD Trajectories" +category = "main" +optional = false +python-versions = ">=3.9,<4.0" +files = [ {file = "znh5md-0.1.6-py3-none-any.whl", hash = "sha256:9a5e2dbac74836992511f43eb6bd8f3879854d6107e70e3dfa9af2ac4c0766a7"}, {file = "znh5md-0.1.6.tar.gz", hash = "sha256:14b5fb3647a520fc120ed3fedf8374896895c248452390c9638b36aff952cc49"}, ] -zninit = [ + +[package.dependencies] +ase = ">=3.22.1,<4.0.0" +h5py = ">=3.7.0,<4.0.0" +tqdm = ">=4.65.0,<5.0.0" +typer = {version = ">=0.7.0,<0.8.0", extras = ["all"]} + +[package.extras] +dask = ["dask[array] (>=2022.11.1,<2023.0.0)"] + +[[package]] +name = "zninit" +version = "0.1.10" +description = "Descriptor based dataclass implementation" +category = "main" +optional = false +python-versions = ">=3.8,<4.0" +files = [ {file = "zninit-0.1.10-py3-none-any.whl", hash = "sha256:a019f47b33bb27822694f4c076dcb679f8e90c55712602508c42d99d84de0b37"}, {file = "zninit-0.1.10.tar.gz", hash = "sha256:c00366581901f3f73573c50d7396fadc781e94d70e4450e489e85939d4903c24"}, ] -znjson = [ + +[package.extras] +typeguard = ["typeguard (>=2.13.3,<3.0.0)"] + +[[package]] +name = "znjson" +version = "0.2.2" +description = "A Python Package to Encode/Decode some common file formats to json" +category = "main" +optional = false +python-versions = ">=3.8,<4.0" +files = [ {file = "znjson-0.2.2-py3-none-any.whl", hash = "sha256:ee29bb63716f66d1d259a8e3565fb66b9c8b79aee896dc231df990ad26e7fb6b"}, {file = "znjson-0.2.2.tar.gz", hash = "sha256:d421ff377d490d876ea016780ffd60a585949a29d6df28ae971da2a329f35b45"}, ] -zntrack = [ + +[[package]] +name = "zntrack" +version = "0.6.0a5" +description = "Create, Run and Benchmark DVC Pipelines in Python" +category = "main" +optional = false +python-versions = ">=3.8,<4.0.0" +files = [ {file = "zntrack-0.6.0a5-py3-none-any.whl", hash = "sha256:fbdfd9243af367ec1768d657e3a3482b4fc5d1febb2de33677890ceb7a4c76ff"}, {file = "zntrack-0.6.0a5.tar.gz", hash = "sha256:cf72850ee3a5785cb299b1d3197985d1b1cc1109aba5127b8ffb0a742923f5e3"}, ] + +[package.dependencies] +dot4dict = ">=0.1.1,<0.2.0" +dvc = ">=2.52.0,<2.53.0 || >2.53.0,<3.0.0" +pandas = ">=1.4.3,<2.0.0" +pyyaml = ">=6.0,<7.0" +tqdm = ">=4.64.0,<5.0.0" +typer = ">=0.7.0,<0.8.0" +znflow = ">=0.1.11,<0.2.0" +zninit = ">=0.1.9,<0.2.0" +znjson = ">=0.2.2,<0.3.0" + +[extras] +apax = ["apax"] +comparison = ["dscribe", "h5py", "llvmlite", "numba", "tensorflow"] +gap = ["quippy-ase", "xmltodict"] +nequip = ["nequip"] + +[metadata] +lock-version = "2.0" +python-versions = ">=3.10,<3.12" +content-hash = "3b1d9a32fc75a31b97c2df2f81c269e88feccaccaa159ce01fa4c75114b0af0a" diff --git a/pyproject.toml b/pyproject.toml index c6ee1b77..b38b0e12 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -71,6 +71,10 @@ imageio = "^2.28.1" [tool.poetry.group.docs.dependencies] sphinx = "^7.0.1" +furo = "^2023.5.20" +nbsphinx = "^0.9.1" +nbsphinx-link = "^1.3.0" +sphinx-copybutton = "^0.5.2" [tool.poetry.extras] comparison = ["h5py", "tensorflow", "llvmlite", "numba", "dscribe"] From 38fdca4d98e0f60ed0c19cab0fefb81d89179489 Mon Sep 17 00:00:00 2001 From: Moritz Schaefer Date: Tue, 23 May 2023 11:17:40 +0200 Subject: [PATCH 08/35] added show inheritacne to autodoc --- docs/source/_nodes/analysis.rst | 3 ++- docs/source/_nodes/bootstrap.rst | 3 ++- docs/source/_nodes/calculators.rst | 3 ++- docs/source/_nodes/configuration_comparison.rst | 3 ++- docs/source/_nodes/configuration_generation.rst | 1 + docs/source/_nodes/configuration_selection.rst | 3 ++- docs/source/_nodes/data_loading.rst | 3 ++- docs/source/_nodes/geometry.rst | 3 ++- docs/source/_nodes/models.rst | 3 ++- 9 files changed, 17 insertions(+), 8 deletions(-) diff --git a/docs/source/_nodes/analysis.rst b/docs/source/_nodes/analysis.rst index 4a9f8ad5..a3c8511e 100644 --- a/docs/source/_nodes/analysis.rst +++ b/docs/source/_nodes/analysis.rst @@ -8,4 +8,5 @@ This ranges from simple prediction correlation plots to force decompositions and .. automodule:: ipsuite.analysis - :members: \ No newline at end of file + :members: + :show-inheritance: \ No newline at end of file diff --git a/docs/source/_nodes/bootstrap.rst b/docs/source/_nodes/bootstrap.rst index 6dca29a7..491c1fb6 100644 --- a/docs/source/_nodes/bootstrap.rst +++ b/docs/source/_nodes/bootstrap.rst @@ -5,4 +5,5 @@ The Nodes provided by this submodule can be used to create an initial dataset wi This can be useful when starting out from a single configuration and iteratively building datasets with learning on the fly. .. automodule:: ipsuite.bootstrap - :members: \ No newline at end of file + :members: + :show-inheritance: \ No newline at end of file diff --git a/docs/source/_nodes/calculators.rst b/docs/source/_nodes/calculators.rst index d7bad29c..a5f7ed93 100644 --- a/docs/source/_nodes/calculators.rst +++ b/docs/source/_nodes/calculators.rst @@ -5,4 +5,5 @@ Calculators can be used for labeling a given set of data and running molecular d For all cases, ASE calculators are used. .. automodule:: ipsuite.calculators - :members: \ No newline at end of file + :members: + :show-inheritance: \ No newline at end of file diff --git a/docs/source/_nodes/configuration_comparison.rst b/docs/source/_nodes/configuration_comparison.rst index 43e0b2fe..ebdf322a 100644 --- a/docs/source/_nodes/configuration_comparison.rst +++ b/docs/source/_nodes/configuration_comparison.rst @@ -4,4 +4,5 @@ Configuration Comparison Provides kernel based similarity measures for comparing configruations. .. automodule:: ipsuite.configuration_comparison - :members: \ No newline at end of file + :members: + :show-inheritance: \ No newline at end of file diff --git a/docs/source/_nodes/configuration_generation.rst b/docs/source/_nodes/configuration_generation.rst index 5171f998..a59bcb2e 100644 --- a/docs/source/_nodes/configuration_generation.rst +++ b/docs/source/_nodes/configuration_generation.rst @@ -8,3 +8,4 @@ The PACKMOL interface can then be used to create the actual starting configurati .. automodule:: ipsuite.configuration_generation :members: + :show-inheritance: diff --git a/docs/source/_nodes/configuration_selection.rst b/docs/source/_nodes/configuration_selection.rst index 28dc9e56..42653921 100644 --- a/docs/source/_nodes/configuration_selection.rst +++ b/docs/source/_nodes/configuration_selection.rst @@ -5,4 +5,5 @@ The configuration selection submodule contains Nodes for splitting datasets. A simple 80:20 random split can be achieved with a single Node, but multiple Nodes can be chained to create complex splittings. .. automodule:: ipsuite.configuration_selection - :members: \ No newline at end of file + :members: + :show-inheritance: \ No newline at end of file diff --git a/docs/source/_nodes/data_loading.rst b/docs/source/_nodes/data_loading.rst index ec439f0b..6960ed10 100644 --- a/docs/source/_nodes/data_loading.rst +++ b/docs/source/_nodes/data_loading.rst @@ -5,4 +5,5 @@ IPS can load datasets from ASE readable formats and HDF5 files. Internally, atomistic data is represented by ASE's `Atoms` objects which are serialized to HDF5. .. automodule:: ipsuite.data_loading - :members: \ No newline at end of file + :members: + :show-inheritance: \ No newline at end of file diff --git a/docs/source/_nodes/geometry.rst b/docs/source/_nodes/geometry.rst index 76a8dd5a..05786634 100644 --- a/docs/source/_nodes/geometry.rst +++ b/docs/source/_nodes/geometry.rst @@ -7,4 +7,5 @@ Note that they do not implement `run` methods and are thus intended to be used a .. automodule:: ipsuite.geometry - :members: \ No newline at end of file + :members: + :show-inheritance: \ No newline at end of file diff --git a/docs/source/_nodes/models.rst b/docs/source/_nodes/models.rst index a83ce071..c11e0433 100644 --- a/docs/source/_nodes/models.rst +++ b/docs/source/_nodes/models.rst @@ -18,4 +18,5 @@ If you would like to add other models to IPS, please consider this guide. .. automodule:: ipsuite.models - :members: \ No newline at end of file + :members: + :show-inheritance: \ No newline at end of file From 71402ea4df05b63502d3e10c89162f50216e3411 Mon Sep 17 00:00:00 2001 From: Moritz Schaefer Date: Tue, 23 May 2023 11:28:42 +0200 Subject: [PATCH 09/35] added installation instructions --- docs/source/_get_started/installation.rst | 32 +++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/docs/source/_get_started/installation.rst b/docs/source/_get_started/installation.rst index cd7a81df..622c5858 100644 --- a/docs/source/_get_started/installation.rst +++ b/docs/source/_get_started/installation.rst @@ -1,3 +1,35 @@ Installation ============ +IPS is available on PyPI and can be installed using + +.. code-block:: bash + + pip install ipsuite + + +Note that a default installation does not come with any of the models. +These are available as extras and can be installed by specifying the models you would like to install. +For example, the following code snippets install the GAP model (via `quippy `_ ) and all available models respectively + +.. code-block:: bash + + pip install ipsuite[gap] + +.. code-block:: bash + + pip install ipsuite[all] + + + +Developer Installation +---------------------- + +IPS is devloped using `Poetry `_. +To install a developer verions of IPS, clone the repository and install it with poetry: + +.. code-block:: bash + + git clone https://github.com/zincware/IPSuite.git + cd IPSuite + poetry install From 17ffc6afc021dcfd7e73555c10e5394415760123 Mon Sep 17 00:00:00 2001 From: Moritz Schaefer Date: Tue, 23 May 2023 12:17:25 +0200 Subject: [PATCH 10/35] moved module docstrings to __init__ files --- docs/source/_nodes/analysis.rst | 7 --- docs/source/_nodes/bootstrap.rst | 4 -- docs/source/_nodes/calculators.rst | 4 -- .../_nodes/configuration_comparison.rst | 3 -- .../_nodes/configuration_generation.rst | 6 --- .../source/_nodes/configuration_selection.rst | 4 -- docs/source/_nodes/data_loading.rst | 4 -- docs/source/_nodes/geometry.rst | 6 --- docs/source/_nodes/models.rst | 17 ------- docs/source/conf.py | 4 +- docs/source/index.rst | 13 +++-- ipsuite/analysis/model/__init__.py | 5 ++ ipsuite/bootstrap/__init__.py | 3 ++ ipsuite/calculators/__init__.py | 3 ++ ipsuite/calculators/ase_geoopt.py | 47 +++++++++++++++++++ ipsuite/configuration_comparison/__init__.py | 2 +- ipsuite/configuration_generation/__init__.py | 4 +- ipsuite/configuration_selection/__init__.py | 3 +- ipsuite/data_loading/__init__.py | 3 +- ipsuite/geometry/__init__.py | 4 ++ ipsuite/models/__init__.py | 15 ++++++ 21 files changed, 97 insertions(+), 64 deletions(-) diff --git a/docs/source/_nodes/analysis.rst b/docs/source/_nodes/analysis.rst index a3c8511e..1d6d86ea 100644 --- a/docs/source/_nodes/analysis.rst +++ b/docs/source/_nodes/analysis.rst @@ -1,12 +1,5 @@ Analysis ======== - -As in all ML applications, analysing both the dataset and model predictions are of paramount importance. -For dataset exploration it is often convenient to visualize the distribution of labels. -Most Nodes are concerned with analysing trained models and often compare to a reference calculator. -This ranges from simple prediction correlation plots to force decompositions and energy-volume curves. - - .. automodule:: ipsuite.analysis :members: :show-inheritance: \ No newline at end of file diff --git a/docs/source/_nodes/bootstrap.rst b/docs/source/_nodes/bootstrap.rst index 491c1fb6..b089eee6 100644 --- a/docs/source/_nodes/bootstrap.rst +++ b/docs/source/_nodes/bootstrap.rst @@ -1,9 +1,5 @@ Bootstrap ========= - -The Nodes provided by this submodule can be used to create an initial dataset with some structural diversity. -This can be useful when starting out from a single configuration and iteratively building datasets with learning on the fly. - .. automodule:: ipsuite.bootstrap :members: :show-inheritance: \ No newline at end of file diff --git a/docs/source/_nodes/calculators.rst b/docs/source/_nodes/calculators.rst index a5f7ed93..467c417f 100644 --- a/docs/source/_nodes/calculators.rst +++ b/docs/source/_nodes/calculators.rst @@ -1,9 +1,5 @@ Calculators =========== - -Calculators can be used for labeling a given set of data and running molecular dynamics. -For all cases, ASE calculators are used. - .. automodule:: ipsuite.calculators :members: :show-inheritance: \ No newline at end of file diff --git a/docs/source/_nodes/configuration_comparison.rst b/docs/source/_nodes/configuration_comparison.rst index ebdf322a..f1916fb7 100644 --- a/docs/source/_nodes/configuration_comparison.rst +++ b/docs/source/_nodes/configuration_comparison.rst @@ -1,8 +1,5 @@ Configuration Comparison ======================== - -Provides kernel based similarity measures for comparing configruations. - .. automodule:: ipsuite.configuration_comparison :members: :show-inheritance: \ No newline at end of file diff --git a/docs/source/_nodes/configuration_generation.rst b/docs/source/_nodes/configuration_generation.rst index a59bcb2e..d4213157 100644 --- a/docs/source/_nodes/configuration_generation.rst +++ b/docs/source/_nodes/configuration_generation.rst @@ -1,11 +1,5 @@ Configuration Generation ======================== - -This module provides Nodes for creating molecular dynamics starting structures. -Workflows can be quickly created from just knowing the SMILES strings of the molecules within the simulation box. -The PACKMOL interface can then be used to create the actual starting configuration. - - .. automodule:: ipsuite.configuration_generation :members: :show-inheritance: diff --git a/docs/source/_nodes/configuration_selection.rst b/docs/source/_nodes/configuration_selection.rst index 42653921..80bcfaf8 100644 --- a/docs/source/_nodes/configuration_selection.rst +++ b/docs/source/_nodes/configuration_selection.rst @@ -1,9 +1,5 @@ Configuration Selection ======================= - -The configuration selection submodule contains Nodes for splitting datasets. -A simple 80:20 random split can be achieved with a single Node, but multiple Nodes can be chained to create complex splittings. - .. automodule:: ipsuite.configuration_selection :members: :show-inheritance: \ No newline at end of file diff --git a/docs/source/_nodes/data_loading.rst b/docs/source/_nodes/data_loading.rst index 6960ed10..0aa4ab68 100644 --- a/docs/source/_nodes/data_loading.rst +++ b/docs/source/_nodes/data_loading.rst @@ -1,9 +1,5 @@ Data Loading ============ - -IPS can load datasets from ASE readable formats and HDF5 files. -Internally, atomistic data is represented by ASE's `Atoms` objects which are serialized to HDF5. - .. automodule:: ipsuite.data_loading :members: :show-inheritance: \ No newline at end of file diff --git a/docs/source/_nodes/geometry.rst b/docs/source/_nodes/geometry.rst index 05786634..f427c578 100644 --- a/docs/source/_nodes/geometry.rst +++ b/docs/source/_nodes/geometry.rst @@ -1,11 +1,5 @@ Geometry ======== - -This module contains Nodes and utilities for molecule mapping. -The Nodes provide `forward_mapping` and `backward_mapping` methods for applying and reversing the transformations. -Note that they do not implement `run` methods and are thus intended to be used as `zn.nodes()`. - - .. automodule:: ipsuite.geometry :members: :show-inheritance: \ No newline at end of file diff --git a/docs/source/_nodes/models.rst b/docs/source/_nodes/models.rst index c11e0433..363b680f 100644 --- a/docs/source/_nodes/models.rst +++ b/docs/source/_nodes/models.rst @@ -1,22 +1,5 @@ Models ====== - -IPS allows for easy use and comparison of different machine learning interatomic potentials. -Below you can find all models currently interfaced with this framework. -A model's run method performs training on the provided data. -All models provide an ASE calculator, which can be used for inference and analysis of predictions. - -Note that each model is an extra dependency and needs to be installed accordingly. -See getting started for more information. -If you would like to add other models to IPS, please consider this guide. - - -.. TODO Add link to getting started - - -.. TODO example for implementing new model - - .. automodule:: ipsuite.models :members: :show-inheritance: \ No newline at end of file diff --git a/docs/source/conf.py b/docs/source/conf.py index b318c1f5..79d794f7 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -18,8 +18,8 @@ "sphinx.ext.autodoc", "sphinx.ext.napoleon", "sphinx_copybutton", - "nbsphinx", - "nbsphinx_link", + # "nbsphinx", + # "nbsphinx_link", "sphinx.ext.viewcode", ] diff --git a/docs/source/index.rst b/docs/source/index.rst index a7581673..0181b962 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -18,9 +18,16 @@ Example Routine workflows are easy to set up and can be easily extended for more complex tasks. .. code-block:: python - - # TODO simple training example - print("hello") + + import ipsuite as ips + + with ips.Project() as project: + data = ips.AddData(file="dataset.extxyz") + random_selection = ips.configuration_selection.RandomSelection( + data=data, n_configurations=100 + ) + + model = ips.models.GAP(data=random_selection) diff --git a/ipsuite/analysis/model/__init__.py b/ipsuite/analysis/model/__init__.py index eedeb08e..d7300b3b 100644 --- a/ipsuite/analysis/model/__init__.py +++ b/ipsuite/analysis/model/__init__.py @@ -1,3 +1,8 @@ +"""As in all ML applications, analysing both the dataset and model predictions are of paramount importance. +For dataset exploration it is often convenient to visualize the distribution of labels. +Most Nodes are concerned with analysing trained models and often compare to a reference calculator. +This ranges from simple prediction correlation plots to force decompositions and energy-volume curves. +""" from ipsuite.analysis.model.dynamics import ( BoxHeatUp, BoxScale, diff --git a/ipsuite/bootstrap/__init__.py b/ipsuite/bootstrap/__init__.py index de60a156..a9719f45 100644 --- a/ipsuite/bootstrap/__init__.py +++ b/ipsuite/bootstrap/__init__.py @@ -1,3 +1,6 @@ +"""The Nodes provided by this submodule can be used to create an initial dataset with some structural diversity. +This can be useful when starting out from a single configuration and iteratively building datasets with learning on the fly. +""" from ipsuite.bootstrap.random_displacements import ( RattleAtoms, RotateMolecules, diff --git a/ipsuite/calculators/__init__.py b/ipsuite/calculators/__init__.py index 62d86f77..f4bcd61a 100644 --- a/ipsuite/calculators/__init__.py +++ b/ipsuite/calculators/__init__.py @@ -1,3 +1,6 @@ +"""Calculators can be used for labeling a given set of data and running molecular dynamics. +For all cases, ASE calculators are used. +""" import lazy_loader as lazy __getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__) diff --git a/ipsuite/calculators/ase_geoopt.py b/ipsuite/calculators/ase_geoopt.py index 3432633d..ed4bb3b1 100644 --- a/ipsuite/calculators/ase_geoopt.py +++ b/ipsuite/calculators/ase_geoopt.py @@ -2,6 +2,7 @@ import pathlib import ase.io +from ase.io.trajectory import TrajectoryWriter import ase.optimize import zntrack @@ -44,3 +45,49 @@ def run(self): @property def atoms(self): return list(ase.io.iread(self.traj.as_posix())) + + +class BatchASEGeoOpt(base.ProcessAtoms): + """Class to run a geometry optimization with ASE. + + Parameters + ---------- + model: zntrack.Node + A node that implements 'get_calculator'. + """ + + model = zntrack.zn.deps() + model_outs = zntrack.dvc.outs(zntrack.nwd / "model_outs") + optimizer: str = zntrack.zn.params("FIRE") + traj: pathlib.Path = zntrack.dvc.outs(zntrack.nwd / "optim.traj") + optimized_structures: pathlib.Path = zntrack.dvc.outs(zntrack.nwd / "final.traj") + + repeat: list = zntrack.zn.params([1, 1, 1]) + run_kwargs: dict = zntrack.zn.params({"fmax": 0.05}) + init_kwargs: dict = zntrack.zn.params({}) + + def run(self): + self.model_outs.mkdir(parents=True, exist_ok=True) + (self.model_outs / "outs.txt").write_text("Lorem Ipsum") + calculator = self.model.get_calculator(directory=self.model_outs) + atoms_list = self.get_data() + + opt_structures = TrajectoryWriter(self.optimized_structures, mode="a") + + for atoms in atoms_list: + atoms = atoms.repeat(self.repeat) + if self.optimizer is not None: + atoms.calc = calculator + optimizer = getattr(ase.optimize, self.optimizer) + + dyn = optimizer(atoms, trajectory=self.traj.as_posix(), **self.init_kwargs) + dyn.run(**self.run_kwargs) + opt_structures.write(atoms) + + @property + def atoms(self): + return list(ase.io.iread(self.optimized_structures.as_posix())) + + @property + def trajectories(self): + return list(ase.io.iread(self.traj.as_posix())) diff --git a/ipsuite/configuration_comparison/__init__.py b/ipsuite/configuration_comparison/__init__.py index 5564415b..57b85a33 100644 --- a/ipsuite/configuration_comparison/__init__.py +++ b/ipsuite/configuration_comparison/__init__.py @@ -1,4 +1,4 @@ -"""Configuration Comparison Module.""" +"""Provides kernel based similarity measures for comparing configruations.""" import lazy_loader as lazy __getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__) diff --git a/ipsuite/configuration_generation/__init__.py b/ipsuite/configuration_generation/__init__.py index e36d8560..f55f3562 100644 --- a/ipsuite/configuration_generation/__init__.py +++ b/ipsuite/configuration_generation/__init__.py @@ -1,4 +1,6 @@ -"""Module for generating new configurations based on smiles.""" +"""This module provides Nodes for creating molecular dynamics starting structures. +Workflows can be quickly created from just knowing the SMILES strings of the molecules within the simulation box. +The PACKMOL interface can then be used to create the actual starting configuration.""" import lazy_loader as lazy __getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__) diff --git a/ipsuite/configuration_selection/__init__.py b/ipsuite/configuration_selection/__init__.py index 99330c2a..b0e121ba 100644 --- a/ipsuite/configuration_selection/__init__.py +++ b/ipsuite/configuration_selection/__init__.py @@ -1,4 +1,5 @@ -"""Configuration Selection Nodes.""" +"""The configuration selection submodule contains Nodes for splitting datasets. +A simple 80:20 random split can be achieved with a single Node, but multiple Nodes can be chained to create complex splittings..""" from ipsuite.configuration_selection.base import ConfigurationSelection from ipsuite.configuration_selection.index import IndexSelection from ipsuite.configuration_selection.kernel import KernelSelection diff --git a/ipsuite/data_loading/__init__.py b/ipsuite/data_loading/__init__.py index b65873f3..cf76f1c9 100644 --- a/ipsuite/data_loading/__init__.py +++ b/ipsuite/data_loading/__init__.py @@ -1,4 +1,5 @@ -"""ipsuite data loading module.""" +"""IPS can load datasets from ASE readable formats and HDF5 files. +Internally, atomistic data is represented by ASE's `Atoms` objects which are serialized to HDF5.""" from ipsuite.data_loading.add_data_ase import AddData from ipsuite.data_loading.add_data_h5md import AddDataH5MD diff --git a/ipsuite/geometry/__init__.py b/ipsuite/geometry/__init__.py index fb41ea59..74ca9601 100644 --- a/ipsuite/geometry/__init__.py +++ b/ipsuite/geometry/__init__.py @@ -1,3 +1,7 @@ +"""This module contains Nodes and utilities for molecule mapping. +The Nodes provide `forward_mapping` and `backward_mapping` methods for applying and reversing the transformations. +Note that they do not implement `run` methods and are thus intended to be used as `zn.nodes()`. +""" from ipsuite.geometry.mapping import BarycenterMapping __all__ = ["BarycenterMapping"] diff --git a/ipsuite/models/__init__.py b/ipsuite/models/__init__.py index 62d86f77..bc451df7 100644 --- a/ipsuite/models/__init__.py +++ b/ipsuite/models/__init__.py @@ -1,3 +1,18 @@ +"""IPS allows for easy use and comparison of different machine learning interatomic potentials. +Below you can find all models currently interfaced with this framework. +A model's run method performs training on the provided data. +All models provide an ASE calculator, which can be used for inference and analysis of predictions. + +Note that each model is an extra dependency and needs to be installed accordingly. +See getting started for more information. +If you would like to add other models to IPS, please consider this guide. + + +.. TODO Add link to getting started + + +.. TODO example for implementing new model +""" import lazy_loader as lazy __getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__) From ea600dbb1564802da2ea221a49d60f03452264b7 Mon Sep 17 00:00:00 2001 From: Moritz Schaefer Date: Tue, 23 May 2023 12:19:59 +0200 Subject: [PATCH 11/35] finished indes.rst example --- docs/source/index.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/source/index.rst b/docs/source/index.rst index 0181b962..cb724e62 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -16,6 +16,7 @@ Example ======= Routine workflows are easy to set up and can be easily extended for more complex tasks. +Training any of the interfaced models only requires a few lines of code: .. code-block:: python From 63a03fe8d1f89c9b45d3b23c9977855b4dc4ded1 Mon Sep 17 00:00:00 2001 From: Moritz Schaefer Date: Tue, 23 May 2023 14:54:27 +0200 Subject: [PATCH 12/35] example Notebook outlines --- .../01_Data_Loading_and_Selection.nblink | 3 + .../02_Bootstrapping_Datasets.nblink | 3 + .../03_Labeling_with_Calculators.nblink | 3 + ...litting_and_Configuration_Selection.nblink | 3 + .../_examples/05_Training_Models.nblink | 3 + ...sing_Datasets_and_Model_Predictions.nblink | 3 + ...Structure_Generation_and_Simulation.nblink | 3 + docs/source/_examples/index.rst | 21 +++++++ docs/source/conf.py | 4 +- examples/01_Data_Loading_and_Selection.ipynb | 58 +++++++++++++++++++ examples/02_Bootstrapping_Datasets.ipynb | 29 ++++++++++ examples/03_Labeling_with_Calculators.ipynb | 29 ++++++++++ ...plitting_and_Configuration_Selection.ipynb | 29 ++++++++++ examples/05_Training_Models.ipynb | 29 ++++++++++ ...ysing_Datasets_and_Model_Predictions.ipynb | 29 ++++++++++ ..._Structure_Generation_and_Simulation.ipynb | 29 ++++++++++ 16 files changed, 276 insertions(+), 2 deletions(-) create mode 100644 docs/source/_examples/01_Data_Loading_and_Selection.nblink create mode 100644 docs/source/_examples/02_Bootstrapping_Datasets.nblink create mode 100644 docs/source/_examples/03_Labeling_with_Calculators.nblink create mode 100644 docs/source/_examples/04_Data_Splitting_and_Configuration_Selection.nblink create mode 100644 docs/source/_examples/05_Training_Models.nblink create mode 100644 docs/source/_examples/06_Analysing_Datasets_and_Model_Predictions.nblink create mode 100644 docs/source/_examples/07_Molecular_Dynamics_Structure_Generation_and_Simulation.nblink create mode 100644 examples/01_Data_Loading_and_Selection.ipynb create mode 100644 examples/02_Bootstrapping_Datasets.ipynb create mode 100644 examples/03_Labeling_with_Calculators.ipynb create mode 100644 examples/04_Data_Splitting_and_Configuration_Selection.ipynb create mode 100644 examples/05_Training_Models.ipynb create mode 100644 examples/06_Analysing_Datasets_and_Model_Predictions.ipynb create mode 100644 examples/07_Molecular_Dynamics_Structure_Generation_and_Simulation.ipynb diff --git a/docs/source/_examples/01_Data_Loading_and_Selection.nblink b/docs/source/_examples/01_Data_Loading_and_Selection.nblink new file mode 100644 index 00000000..28b9a634 --- /dev/null +++ b/docs/source/_examples/01_Data_Loading_and_Selection.nblink @@ -0,0 +1,3 @@ +{ + "path": "../../../examples/01_Data_Loading_and_Selection.ipynb" +} \ No newline at end of file diff --git a/docs/source/_examples/02_Bootstrapping_Datasets.nblink b/docs/source/_examples/02_Bootstrapping_Datasets.nblink new file mode 100644 index 00000000..fd0880df --- /dev/null +++ b/docs/source/_examples/02_Bootstrapping_Datasets.nblink @@ -0,0 +1,3 @@ +{ + "path": "../../../examples/02_Bootstrapping_Datasets.ipynb" +} \ No newline at end of file diff --git a/docs/source/_examples/03_Labeling_with_Calculators.nblink b/docs/source/_examples/03_Labeling_with_Calculators.nblink new file mode 100644 index 00000000..4874f052 --- /dev/null +++ b/docs/source/_examples/03_Labeling_with_Calculators.nblink @@ -0,0 +1,3 @@ +{ + "path": "../../../examples/03_Labeling_with_Calculators.ipynb" +} \ No newline at end of file diff --git a/docs/source/_examples/04_Data_Splitting_and_Configuration_Selection.nblink b/docs/source/_examples/04_Data_Splitting_and_Configuration_Selection.nblink new file mode 100644 index 00000000..f589c5f5 --- /dev/null +++ b/docs/source/_examples/04_Data_Splitting_and_Configuration_Selection.nblink @@ -0,0 +1,3 @@ +{ + "path": "../../../examples/04_Data_Splitting_and_Configuration_Selection.ipynb" +} \ No newline at end of file diff --git a/docs/source/_examples/05_Training_Models.nblink b/docs/source/_examples/05_Training_Models.nblink new file mode 100644 index 00000000..682da3c6 --- /dev/null +++ b/docs/source/_examples/05_Training_Models.nblink @@ -0,0 +1,3 @@ +{ + "path": "../../../examples/05_Training_Models.ipynb" +} \ No newline at end of file diff --git a/docs/source/_examples/06_Analysing_Datasets_and_Model_Predictions.nblink b/docs/source/_examples/06_Analysing_Datasets_and_Model_Predictions.nblink new file mode 100644 index 00000000..4737d06e --- /dev/null +++ b/docs/source/_examples/06_Analysing_Datasets_and_Model_Predictions.nblink @@ -0,0 +1,3 @@ +{ + "path": "../../../examples/06_Analysing_Datasets_and_Model_Predictions.ipynb" +} \ No newline at end of file diff --git a/docs/source/_examples/07_Molecular_Dynamics_Structure_Generation_and_Simulation.nblink b/docs/source/_examples/07_Molecular_Dynamics_Structure_Generation_and_Simulation.nblink new file mode 100644 index 00000000..00a7d2a6 --- /dev/null +++ b/docs/source/_examples/07_Molecular_Dynamics_Structure_Generation_and_Simulation.nblink @@ -0,0 +1,3 @@ +{ + "path": "../../../examples/07_Molecular_Dynamics_Structure_Generation_and_Simulation.ipynb" +} \ No newline at end of file diff --git a/docs/source/_examples/index.rst b/docs/source/_examples/index.rst index d12863df..0b2f505e 100644 --- a/docs/source/_examples/index.rst +++ b/docs/source/_examples/index.rst @@ -2,6 +2,27 @@ .. _userdoc-examples: +The utility of IPS is best demonstrated by some worked examples. +This section starts out with some introductory notebooks demonstrating the cabailities of the Nodes from each submodule. +Later notebooks feature some more complex workflows which are closer to real world use case. +All notebooks can be found in `/examples/docs`. + + +.. image:: https://mybinder.org/badge_logo.svg + :alt: Binder + :target: https://mybinder.org/v2/gh/zincware/IPSuite/HEAD + + Examples ======== +.. toctree:: + :maxdepth: 0 + + 01_Data_Loading_and_Selection + 02_Bootstrapping_Datasets + 03_Labeling_with_Calculators + 04_Data_Splitting_and_Configuration_Selection + 05_Training_Models + 06_Analysing_Datasets_and_Model_Predictions + 07_Molecular_Dynamics_Structure_Generation_and_Simulation diff --git a/docs/source/conf.py b/docs/source/conf.py index 79d794f7..b318c1f5 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -18,8 +18,8 @@ "sphinx.ext.autodoc", "sphinx.ext.napoleon", "sphinx_copybutton", - # "nbsphinx", - # "nbsphinx_link", + "nbsphinx", + "nbsphinx_link", "sphinx.ext.viewcode", ] diff --git a/examples/01_Data_Loading_and_Selection.ipynb b/examples/01_Data_Loading_and_Selection.ipynb new file mode 100644 index 00000000..000f5ae2 --- /dev/null +++ b/examples/01_Data_Loading_and_Selection.ipynb @@ -0,0 +1,58 @@ +{ + "cells": [ + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Data Loading and Selection" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "2023-05-23 12:21:14,009 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n" + ] + } + ], + "source": [ + "import ipsuite as ips" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "ips2", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.9" + }, + "orig_nbformat": 4 + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/02_Bootstrapping_Datasets.ipynb b/examples/02_Bootstrapping_Datasets.ipynb new file mode 100644 index 00000000..54682195 --- /dev/null +++ b/examples/02_Bootstrapping_Datasets.ipynb @@ -0,0 +1,29 @@ +{ + "cells": [ + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Bootstrapping Datasets" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import ipsuite as ips" + ] + } + ], + "metadata": { + "language_info": { + "name": "python" + }, + "orig_nbformat": 4 + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/03_Labeling_with_Calculators.ipynb b/examples/03_Labeling_with_Calculators.ipynb new file mode 100644 index 00000000..707d18ca --- /dev/null +++ b/examples/03_Labeling_with_Calculators.ipynb @@ -0,0 +1,29 @@ +{ + "cells": [ + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Labeling with Calculators" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import ipsuite as ips" + ] + } + ], + "metadata": { + "language_info": { + "name": "python" + }, + "orig_nbformat": 4 + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/04_Data_Splitting_and_Configuration_Selection.ipynb b/examples/04_Data_Splitting_and_Configuration_Selection.ipynb new file mode 100644 index 00000000..17828e6f --- /dev/null +++ b/examples/04_Data_Splitting_and_Configuration_Selection.ipynb @@ -0,0 +1,29 @@ +{ + "cells": [ + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Data Splitting and Configuration Selection" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import ipsuite as ips" + ] + } + ], + "metadata": { + "language_info": { + "name": "python" + }, + "orig_nbformat": 4 + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/05_Training_Models.ipynb b/examples/05_Training_Models.ipynb new file mode 100644 index 00000000..c50d9dc1 --- /dev/null +++ b/examples/05_Training_Models.ipynb @@ -0,0 +1,29 @@ +{ + "cells": [ + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Training Models" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import ipsuite as ips" + ] + } + ], + "metadata": { + "language_info": { + "name": "python" + }, + "orig_nbformat": 4 + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/06_Analysing_Datasets_and_Model_Predictions.ipynb b/examples/06_Analysing_Datasets_and_Model_Predictions.ipynb new file mode 100644 index 00000000..8a7548c0 --- /dev/null +++ b/examples/06_Analysing_Datasets_and_Model_Predictions.ipynb @@ -0,0 +1,29 @@ +{ + "cells": [ + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Analysing Datasets and Model Predictions" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import ipsuite as ips" + ] + } + ], + "metadata": { + "language_info": { + "name": "python" + }, + "orig_nbformat": 4 + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/07_Molecular_Dynamics_Structure_Generation_and_Simulation.ipynb b/examples/07_Molecular_Dynamics_Structure_Generation_and_Simulation.ipynb new file mode 100644 index 00000000..5fceda42 --- /dev/null +++ b/examples/07_Molecular_Dynamics_Structure_Generation_and_Simulation.ipynb @@ -0,0 +1,29 @@ +{ + "cells": [ + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Molecular Dynamics Structure Generation and Simulation" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import ipsuite as ips" + ] + } + ], + "metadata": { + "language_info": { + "name": "python" + }, + "orig_nbformat": 4 + }, + "nbformat": 4, + "nbformat_minor": 2 +} From ba811737ff9cdfed4cae4a98c5807f4a0d16c5b2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Moritz=20R=2E=20Sch=C3=A4fer?= Date: Thu, 25 May 2023 10:46:09 +0200 Subject: [PATCH 13/35] data loading example outline --- docs/source/_examples/index.rst | 5 +- examples/01_Data_Loading_and_Selection.ipynb | 141 ++++++++++++++++++- 2 files changed, 144 insertions(+), 2 deletions(-) diff --git a/docs/source/_examples/index.rst b/docs/source/_examples/index.rst index 0b2f505e..6f2ee4ad 100644 --- a/docs/source/_examples/index.rst +++ b/docs/source/_examples/index.rst @@ -2,8 +2,11 @@ .. _userdoc-examples: +IPS is based on `ZnTrack `_, and we suggest working through the examples on the ZnTrack docs to understand how to construct version controlled workflows. +The notebooks contained in this section cover the functionality of IPS and assume familiarity with the basics of running workflows and experiments. + The utility of IPS is best demonstrated by some worked examples. -This section starts out with some introductory notebooks demonstrating the cabailities of the Nodes from each submodule. +This section starts out with some introductory notebooks demonstrating the capabilities of the Nodes from each submodule. Later notebooks feature some more complex workflows which are closer to real world use case. All notebooks can be found in `/examples/docs`. diff --git a/examples/01_Data_Loading_and_Selection.ipynb b/examples/01_Data_Loading_and_Selection.ipynb index 000f5ae2..f1fe23fc 100644 --- a/examples/01_Data_Loading_and_Selection.ipynb +++ b/examples/01_Data_Loading_and_Selection.ipynb @@ -8,6 +8,17 @@ "# Data Loading and Selection" ] }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Welcome to the first IPS example notebook!\n", + "Here we will demonstrate how to load existing datasets and perform some simple and more involved data splitting workflows.\n", + "\n", + "All examples are self-contained, and the data is created within the notebooks themselves." + ] + }, { "cell_type": "code", "execution_count": 1, @@ -22,7 +33,62 @@ } ], "source": [ - "import ipsuite as ips" + "import ipsuite as ips\n", + "\n", + "from ase import Atoms\n", + "from ase.visualize import view" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Data Creation\n", + "\n", + "First, we will create some sample data using ASE to perform a short molecular dynamics simulation.\n", + "\n", + "TODO make data and run MD\n", + "TODO combining multiple datasets" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# TODO" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Data Loading\n", + "\n", + "IPS uses ASE for many of its internals and datasets can be loaded from any ASE compatible format.\n", + "Here we are going to pretend that the above created sample data is some literature dataset that we have already downloaded." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "with ips.Project() as project:\n", + " data = ips.AddData(file=\"dataset.extxyz\", name=\"dataset\")\n", + "project.run()" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "The data is read from disk and is now available to both other Nodes in the project and for use in the notebook." ] }, { @@ -30,6 +96,79 @@ "execution_count": null, "metadata": {}, "outputs": [], + "source": [ + "trajectory = data.load() # requires the project to have been run\n", + "trajectory" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "We obtain a list of ASE Atoms, with which we can work in our notebook and use other ASE functionality, e.g.:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "view(trajectory)" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "The H5MD standard offers substantial size and I/O speed advantages.\n", + "For this reason H5MD is used by Nodes which serialize atomistic data, including `AddData`." + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Data Selection\n", + "\n", + "A common way to split data into training, validation and test splits is to randomly partition them into fractions like 75:15:10" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# TODO" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "While straightforward, this is not necessarily advisable for molecular dynamics data.\n", + "Trajectories are created sequentially, and a random split will result in validation samples that are drawn from between training samples.\n", + "By instead separating the dataset into fixed fraction first, we can ensure that the splits do not temporally overlap" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# TODO percentage split" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, "source": [] } ], From 96c4028c676c75bff4ad31e785ca6015c3355f8b Mon Sep 17 00:00:00 2001 From: Moritz Schaefer Date: Fri, 26 May 2023 14:24:40 +0200 Subject: [PATCH 14/35] notebook cleanup --- ...litting_and_Configuration_Selection.nblink | 3 - examples/01_Data_Loading_and_Selection.ipynb | 61 +++++++++++++++++- examples/02_Bootstrapping_Datasets.ipynb | 29 --------- examples/02_Training_Models.ipynb | 62 +++++++++++++++++++ ...sing_Datasets_and_Model_Predictions.ipynb} | 0 ...plitting_and_Configuration_Selection.ipynb | 29 --------- ...Structure_Generation_and_Simulation.ipynb} | 0 ...ynb => 05_Labeling_with_Calculators.ipynb} | 0 examples/05_Training_Models.ipynb | 29 --------- examples/06_Bootstrapping_Datasets.ipynb | 42 +++++++++++++ 10 files changed, 164 insertions(+), 91 deletions(-) delete mode 100644 docs/source/_examples/04_Data_Splitting_and_Configuration_Selection.nblink delete mode 100644 examples/02_Bootstrapping_Datasets.ipynb create mode 100644 examples/02_Training_Models.ipynb rename examples/{06_Analysing_Datasets_and_Model_Predictions.ipynb => 03_Analysing_Datasets_and_Model_Predictions.ipynb} (100%) delete mode 100644 examples/04_Data_Splitting_and_Configuration_Selection.ipynb rename examples/{07_Molecular_Dynamics_Structure_Generation_and_Simulation.ipynb => 04_Molecular_Dynamics_Structure_Generation_and_Simulation.ipynb} (100%) rename examples/{03_Labeling_with_Calculators.ipynb => 05_Labeling_with_Calculators.ipynb} (100%) delete mode 100644 examples/05_Training_Models.ipynb create mode 100644 examples/06_Bootstrapping_Datasets.ipynb diff --git a/docs/source/_examples/04_Data_Splitting_and_Configuration_Selection.nblink b/docs/source/_examples/04_Data_Splitting_and_Configuration_Selection.nblink deleted file mode 100644 index f589c5f5..00000000 --- a/docs/source/_examples/04_Data_Splitting_and_Configuration_Selection.nblink +++ /dev/null @@ -1,3 +0,0 @@ -{ - "path": "../../../examples/04_Data_Splitting_and_Configuration_Selection.ipynb" -} \ No newline at end of file diff --git a/examples/01_Data_Loading_and_Selection.ipynb b/examples/01_Data_Loading_and_Selection.ipynb index f1fe23fc..9f99aced 100644 --- a/examples/01_Data_Loading_and_Selection.ipynb +++ b/examples/01_Data_Loading_and_Selection.ipynb @@ -28,7 +28,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "2023-05-23 12:21:14,009 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n" + "2023-05-25 13:44:15,756 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n" ] } ], @@ -170,6 +170,65 @@ "cell_type": "markdown", "metadata": {}, "source": [] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Below is a list of all currently implemented selection methods.\n", + "Check out the API docs for more information about the methods not covered here." + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['ConfigurationSelection',\n", + " 'RandomSelection',\n", + " 'UniformEnergeticSelection',\n", + " 'UniformTemporalSelection',\n", + " 'UniformArangeSelection',\n", + " 'KernelSelection',\n", + " 'IndexSelection',\n", + " 'ThresholdSelection',\n", + " 'SplitSelection']" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ips.configuration_selection.__all__" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Kernel Based Selection Methods" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# TODO" + ] } ], "metadata": { diff --git a/examples/02_Bootstrapping_Datasets.ipynb b/examples/02_Bootstrapping_Datasets.ipynb deleted file mode 100644 index 54682195..00000000 --- a/examples/02_Bootstrapping_Datasets.ipynb +++ /dev/null @@ -1,29 +0,0 @@ -{ - "cells": [ - { - "attachments": {}, - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Bootstrapping Datasets" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "import ipsuite as ips" - ] - } - ], - "metadata": { - "language_info": { - "name": "python" - }, - "orig_nbformat": 4 - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/examples/02_Training_Models.ipynb b/examples/02_Training_Models.ipynb new file mode 100644 index 00000000..191cd41d --- /dev/null +++ b/examples/02_Training_Models.ipynb @@ -0,0 +1,62 @@ +{ + "cells": [ + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Training Models" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import ipsuite as ips" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Using the Trained Model\n", + "\n", + "Here we will briefly evaluate our model\"s predictions with a correlation plot of predicted and actual labels.\n", + "A more detailed presentation of the analysis capabilities contained in IPS can be found in the next notebook." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Transfer Learning\n", + "\n", + "TODO" + ] + } + ], + "metadata": { + "language_info": { + "name": "python" + }, + "orig_nbformat": 4 + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/06_Analysing_Datasets_and_Model_Predictions.ipynb b/examples/03_Analysing_Datasets_and_Model_Predictions.ipynb similarity index 100% rename from examples/06_Analysing_Datasets_and_Model_Predictions.ipynb rename to examples/03_Analysing_Datasets_and_Model_Predictions.ipynb diff --git a/examples/04_Data_Splitting_and_Configuration_Selection.ipynb b/examples/04_Data_Splitting_and_Configuration_Selection.ipynb deleted file mode 100644 index 17828e6f..00000000 --- a/examples/04_Data_Splitting_and_Configuration_Selection.ipynb +++ /dev/null @@ -1,29 +0,0 @@ -{ - "cells": [ - { - "attachments": {}, - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Data Splitting and Configuration Selection" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "import ipsuite as ips" - ] - } - ], - "metadata": { - "language_info": { - "name": "python" - }, - "orig_nbformat": 4 - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/examples/07_Molecular_Dynamics_Structure_Generation_and_Simulation.ipynb b/examples/04_Molecular_Dynamics_Structure_Generation_and_Simulation.ipynb similarity index 100% rename from examples/07_Molecular_Dynamics_Structure_Generation_and_Simulation.ipynb rename to examples/04_Molecular_Dynamics_Structure_Generation_and_Simulation.ipynb diff --git a/examples/03_Labeling_with_Calculators.ipynb b/examples/05_Labeling_with_Calculators.ipynb similarity index 100% rename from examples/03_Labeling_with_Calculators.ipynb rename to examples/05_Labeling_with_Calculators.ipynb diff --git a/examples/05_Training_Models.ipynb b/examples/05_Training_Models.ipynb deleted file mode 100644 index c50d9dc1..00000000 --- a/examples/05_Training_Models.ipynb +++ /dev/null @@ -1,29 +0,0 @@ -{ - "cells": [ - { - "attachments": {}, - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Training Models" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "import ipsuite as ips" - ] - } - ], - "metadata": { - "language_info": { - "name": "python" - }, - "orig_nbformat": 4 - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/examples/06_Bootstrapping_Datasets.ipynb b/examples/06_Bootstrapping_Datasets.ipynb new file mode 100644 index 00000000..c016e1cd --- /dev/null +++ b/examples/06_Bootstrapping_Datasets.ipynb @@ -0,0 +1,42 @@ +{ + "cells": [ + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Bootstrapping Datasets" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "In our last example we assumed that there was a pre-existing dataset available for us to use.\n", + "This is typically the case when working with literature datasets or if we perform the dataset aquisition with an external (molecular dyamics) program.\n", + "\n", + "However, in active learning scenarios one typically starts with a single (unlabeled) configuration. In these cases it is often convenient to bootstrap an initial training set in order to quickly obtain a stable force field with which to drive the sampling.\n", + "\n", + "A full active learning example can be found in a later notebook in this series." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import ipsuite as ips" + ] + } + ], + "metadata": { + "language_info": { + "name": "python" + }, + "orig_nbformat": 4 + }, + "nbformat": 4, + "nbformat_minor": 2 +} From 94fd15d56f808c5e0136210be4339fe729def9a2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Moritz=20R=2E=20Sch=C3=A4fer?= Date: Mon, 29 May 2023 13:01:06 +0200 Subject: [PATCH 15/35] notebook cleanup 2 --- .../02_Bootstrapping_Datasets.nblink | 3 - .../_examples/02_Training_Models.nblink | 3 + ...sing_Datasets_and_Model_Predictions.nblink | 3 + .../03_Labeling_with_Calculators.nblink | 3 - ...Structure_Generation_and_Simulation.nblink | 3 + .../05_Labeling_with_Calculators.nblink | 3 + .../_examples/05_Training_Models.nblink | 3 - ...sing_Datasets_and_Model_Predictions.nblink | 3 - .../06_Bootstrapping_Datasets.nblink | 3 + ...Structure_Generation_and_Simulation.nblink | 3 - examples/02_Training_Models.ipynb | 57 ++++++++++++++++++- 11 files changed, 69 insertions(+), 18 deletions(-) delete mode 100644 docs/source/_examples/02_Bootstrapping_Datasets.nblink create mode 100644 docs/source/_examples/02_Training_Models.nblink create mode 100644 docs/source/_examples/03_Analysing_Datasets_and_Model_Predictions.nblink delete mode 100644 docs/source/_examples/03_Labeling_with_Calculators.nblink create mode 100644 docs/source/_examples/04_Molecular_Dynamics_Structure_Generation_and_Simulation.nblink create mode 100644 docs/source/_examples/05_Labeling_with_Calculators.nblink delete mode 100644 docs/source/_examples/05_Training_Models.nblink delete mode 100644 docs/source/_examples/06_Analysing_Datasets_and_Model_Predictions.nblink create mode 100644 docs/source/_examples/06_Bootstrapping_Datasets.nblink delete mode 100644 docs/source/_examples/07_Molecular_Dynamics_Structure_Generation_and_Simulation.nblink diff --git a/docs/source/_examples/02_Bootstrapping_Datasets.nblink b/docs/source/_examples/02_Bootstrapping_Datasets.nblink deleted file mode 100644 index fd0880df..00000000 --- a/docs/source/_examples/02_Bootstrapping_Datasets.nblink +++ /dev/null @@ -1,3 +0,0 @@ -{ - "path": "../../../examples/02_Bootstrapping_Datasets.ipynb" -} \ No newline at end of file diff --git a/docs/source/_examples/02_Training_Models.nblink b/docs/source/_examples/02_Training_Models.nblink new file mode 100644 index 00000000..968dc697 --- /dev/null +++ b/docs/source/_examples/02_Training_Models.nblink @@ -0,0 +1,3 @@ +{ + "path": "../../../examples/02_Training_Models.ipynb" +} \ No newline at end of file diff --git a/docs/source/_examples/03_Analysing_Datasets_and_Model_Predictions.nblink b/docs/source/_examples/03_Analysing_Datasets_and_Model_Predictions.nblink new file mode 100644 index 00000000..c90b3b05 --- /dev/null +++ b/docs/source/_examples/03_Analysing_Datasets_and_Model_Predictions.nblink @@ -0,0 +1,3 @@ +{ + "path": "../../../examples/03_Analysing_Datasets_and_Model_Predictions.ipynb" +} \ No newline at end of file diff --git a/docs/source/_examples/03_Labeling_with_Calculators.nblink b/docs/source/_examples/03_Labeling_with_Calculators.nblink deleted file mode 100644 index 4874f052..00000000 --- a/docs/source/_examples/03_Labeling_with_Calculators.nblink +++ /dev/null @@ -1,3 +0,0 @@ -{ - "path": "../../../examples/03_Labeling_with_Calculators.ipynb" -} \ No newline at end of file diff --git a/docs/source/_examples/04_Molecular_Dynamics_Structure_Generation_and_Simulation.nblink b/docs/source/_examples/04_Molecular_Dynamics_Structure_Generation_and_Simulation.nblink new file mode 100644 index 00000000..f3f26703 --- /dev/null +++ b/docs/source/_examples/04_Molecular_Dynamics_Structure_Generation_and_Simulation.nblink @@ -0,0 +1,3 @@ +{ + "path": "../../../examples/04_Molecular_Dynamics_Structure_Generation_and_Simulation.ipynb" +} \ No newline at end of file diff --git a/docs/source/_examples/05_Labeling_with_Calculators.nblink b/docs/source/_examples/05_Labeling_with_Calculators.nblink new file mode 100644 index 00000000..07c10fcc --- /dev/null +++ b/docs/source/_examples/05_Labeling_with_Calculators.nblink @@ -0,0 +1,3 @@ +{ + "path": "../../../examples/05_Labeling_with_Calculators.ipynb" +} \ No newline at end of file diff --git a/docs/source/_examples/05_Training_Models.nblink b/docs/source/_examples/05_Training_Models.nblink deleted file mode 100644 index 682da3c6..00000000 --- a/docs/source/_examples/05_Training_Models.nblink +++ /dev/null @@ -1,3 +0,0 @@ -{ - "path": "../../../examples/05_Training_Models.ipynb" -} \ No newline at end of file diff --git a/docs/source/_examples/06_Analysing_Datasets_and_Model_Predictions.nblink b/docs/source/_examples/06_Analysing_Datasets_and_Model_Predictions.nblink deleted file mode 100644 index 4737d06e..00000000 --- a/docs/source/_examples/06_Analysing_Datasets_and_Model_Predictions.nblink +++ /dev/null @@ -1,3 +0,0 @@ -{ - "path": "../../../examples/06_Analysing_Datasets_and_Model_Predictions.ipynb" -} \ No newline at end of file diff --git a/docs/source/_examples/06_Bootstrapping_Datasets.nblink b/docs/source/_examples/06_Bootstrapping_Datasets.nblink new file mode 100644 index 00000000..a5aa23c0 --- /dev/null +++ b/docs/source/_examples/06_Bootstrapping_Datasets.nblink @@ -0,0 +1,3 @@ +{ + "path": "../../../examples/06_Bootstrapping_Datasets.ipynb" +} \ No newline at end of file diff --git a/docs/source/_examples/07_Molecular_Dynamics_Structure_Generation_and_Simulation.nblink b/docs/source/_examples/07_Molecular_Dynamics_Structure_Generation_and_Simulation.nblink deleted file mode 100644 index 00a7d2a6..00000000 --- a/docs/source/_examples/07_Molecular_Dynamics_Structure_Generation_and_Simulation.nblink +++ /dev/null @@ -1,3 +0,0 @@ -{ - "path": "../../../examples/07_Molecular_Dynamics_Structure_Generation_and_Simulation.ipynb" -} \ No newline at end of file diff --git a/examples/02_Training_Models.ipynb b/examples/02_Training_Models.ipynb index 191cd41d..cf1418ac 100644 --- a/examples/02_Training_Models.ipynb +++ b/examples/02_Training_Models.ipynb @@ -10,9 +10,17 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 2, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "2023-05-26 15:16:04,580 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n" + ] + } + ], "source": [ "import ipsuite as ips" ] @@ -24,6 +32,34 @@ "outputs": [], "source": [] }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "IPS is interfaced with a series of models. A complete list of available models is found below." + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['Apax', 'EnsembleModel', 'GAP', 'MACE', 'MLModel', 'Nequip']" + ] + }, + "execution_count": 3, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ips.models.__all__" + ] + }, { "attachments": {}, "cell_type": "markdown", @@ -36,6 +72,7 @@ ] }, { + "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [] @@ -52,8 +89,22 @@ } ], "metadata": { + "kernelspec": { + "display_name": "ips", + "language": "python", + "name": "python3" + }, "language_info": { - "name": "python" + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.11" }, "orig_nbformat": 4 }, From df8d71c47b920dcd8aef093469cc15f2cf4614a6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Moritz=20R=2E=20Sch=C3=A4fer?= Date: Mon, 29 May 2023 13:02:57 +0200 Subject: [PATCH 16/35] example index fix --- docs/source/_examples/index.rst | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/docs/source/_examples/index.rst b/docs/source/_examples/index.rst index 6f2ee4ad..5322e6c2 100644 --- a/docs/source/_examples/index.rst +++ b/docs/source/_examples/index.rst @@ -23,9 +23,8 @@ Examples :maxdepth: 0 01_Data_Loading_and_Selection - 02_Bootstrapping_Datasets - 03_Labeling_with_Calculators - 04_Data_Splitting_and_Configuration_Selection - 05_Training_Models - 06_Analysing_Datasets_and_Model_Predictions - 07_Molecular_Dynamics_Structure_Generation_and_Simulation + 02_Training_Models + 03_Analysing_Datasets_and_Model_Predictions + 04_Molecular_Dynamics_Structure_Generation_and_Simulation + 05_Labeling_with_Calculators + 06_Bootstrapping_Datasets From 46634b4300a6458f5cb6f939c34b1d25631ea23a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Moritz=20R=2E=20Sch=C3=A4fer?= Date: Tue, 30 May 2023 16:33:53 +0200 Subject: [PATCH 17/35] added bootstrapping example notebook --- examples/06_Bootstrapping_Datasets.ipynb | 535 ++++++++++++++++++++++- 1 file changed, 531 insertions(+), 4 deletions(-) diff --git a/examples/06_Bootstrapping_Datasets.ipynb b/examples/06_Bootstrapping_Datasets.ipynb index c016e1cd..17f53553 100644 --- a/examples/06_Bootstrapping_Datasets.ipynb +++ b/examples/06_Bootstrapping_Datasets.ipynb @@ -13,7 +13,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "In our last example we assumed that there was a pre-existing dataset available for us to use.\n", + "In previous examples we assumed that there was a pre-existing dataset available for us to use.\n", "This is typically the case when working with literature datasets or if we perform the dataset aquisition with an external (molecular dyamics) program.\n", "\n", "However, in active learning scenarios one typically starts with a single (unlabeled) configuration. In these cases it is often convenient to bootstrap an initial training set in order to quickly obtain a stable force field with which to drive the sampling.\n", @@ -21,19 +21,546 @@ "A full active learning example can be found in a later notebook in this series." ] }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "This notebook requires packmol for setting up the initial configuration and the xtb. \n", + "`xtb-python` and `packmol` are available from conda and can be installed via\n", + "\n", + "```bash\n", + "conda install -c conda-forge xtb-python\n", + "conda install -c conda-forge packmol\n", + "```" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "2023-05-30 16:18:18,325 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n" + ] + } + ], + "source": [ + "import ipsuite as ips\n", + "import znflow\n", + "import matplotlib.pyplot as plt\n", + "\n", + "from zntrack.utils import cwd_temp_dir\n", + "\n", + "temp_dir = cwd_temp_dir()" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "temp_dir" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "hint: Using 'master' as the name for the initial branch. This default branch name\n", + "hint: is subject to change. To configure the initial branch name to use in all\n", + "hint: of your new repositories, which will suppress this warning, call:\n", + "hint: \n", + "hint: \tgit config --global init.defaultBranch \n", + "hint: \n", + "hint: Names commonly chosen instead of 'master' are 'main', 'trunk' and\n", + "hint: 'development'. The just-created branch can be renamed via this command:\n", + "hint: \n", + "hint: \tgit branch -m \n", + "Initialized empty Git repository in /tmp/tmp8k077isy/.git/\n", + "Initialized DVC repository.\n", + "\n", + "You can now commit the changes to git.\n", + "\n", + "+---------------------------------------------------------------------+\n", + "| |\n", + "| DVC has enabled anonymous aggregate usage analytics. |\n", + "| Read the analytics documentation (and how to opt-out) here: |\n", + "| |\n", + "| |\n", + "+---------------------------------------------------------------------+\n", + "\n", + "What's next?\n", + "------------\n", + "- Check out the documentation: \n", + "- Get help and share ideas: \n", + "- Star us on GitHub: \n" + ] + } + ], + "source": [ + "!git init\n", + "!dvc init" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "We can use packmol to create an initial configuration.\n", + "Based on this, it is possible to bootstrap datasets using a combination of various methods.\n", + "Each of them is designed to probe a different seet of degrees of freedom.\n", + "Random atomic displacements will probe vibrations, while random translations and rotations of molecules, as well as box size scans probe slower degrees of freedom that depend on intermolecular interactions." + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Running DVC command: 'stage add --name SmilesToAtoms --force ...'\n", + "Running DVC command: 'stage add --name Packmol --force ...'\n", + "Running DVC command: 'stage add --name opt_calc --force ...'\n", + "Running DVC command: 'stage add --name ASEGeoOpt --force ...'\n", + "Running DVC command: 'stage add --name RattleAtoms --force ...'\n", + "Running DVC command: 'stage add --name RotateMolecules --force ...'\n", + "Running DVC command: 'stage add --name TranslateMolecules --force ...'\n", + "Running DVC command: 'stage add --name label_calc --force ...'\n", + "Running DVC command: 'stage add --name BoxScale --force ...'\n", + "Running DVC command: 'stage add --name BoxScale_mapping --force ...'\n", + "Could not create .gitignore entry in /tmp/tmp8k077isy/nodes/BoxScale_mapping/.gitignore. DVC will attempt to create .gitignore entry again when the stage is run.\n", + "Running DVC command: 'stage add --name EnergyHistogram --force ...'\n", + "Running DVC command: 'stage add --name ForcesHistogram --force ...'\n", + "Running DVC command: 'repro'\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "2023-05-30 16:18:20,899 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n", + "2023-05-30 16:18:22,115 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n", + "2023-05-30 16:18:22,296 (INFO): estimated box size: [6.6946734740471925, 6.6946734740471925, 6.6946734740471925]\n", + "\n", + "################################################################################\n", + "\n", + " PACKMOL - Packing optimization for the automated generation of\n", + " starting configurations for molecular dynamics simulations.\n", + " \n", + " Version 20.010 \n", + "\n", + "################################################################################\n", + "\n", + " Packmol must be run with: packmol < inputfile.inp \n", + "\n", + " Userguide at: http://m3g.iqm.unicamp.br/packmol \n", + "\n", + " Reading input file... (Control-C aborts)\n", + " Seed for random number generator: 1234567\n", + " Output file: mixture.xyz\n", + " Reading coordinate file: 0.xyz\n", + " Number of independent structures: 1\n", + " The structures are: \n", + " Structure 1 :Properties=species:S:1:pos:R:3 pbc=\"F F F\"( 3 atoms)\n", + " Maximum number of GENCAN loops for all molecule packing: 200\n", + " Total number of restrictions: 1\n", + " Distance tolerance: 2.0000000000000000 \n", + " Number of molecules of type 1 : 10\n", + " Total number of atoms: 30\n", + " Total number of molecules: 10\n", + " Number of fixed molecules: 0\n", + " Number of free molecules: 10\n", + " Number of variables: 60\n", + " Total number of fixed atoms: 0\n", + " Maximum internal distance of type 1 : 1.5660731739637310 \n", + " All atoms must be within these coordinates: \n", + " x: [ -998.39999999999998 , 1001.6000000000000 ] \n", + " y: [ -999.17727845236561 , 1000.8227215476344 ] \n", + " z: [ -1000.0000000000000 , 1000.0000000000000 ] \n", + " If the system is larger than this, increase the sidemax parameter. \n", + "\n", + "################################################################################\n", + "\n", + " Building initial approximation ... \n", + "\n", + "################################################################################\n", + "\n", + " Adjusting initial point to fit the constraints \n", + "\n", + "--------------------------------------------------------------------------------\n", + "\n", + "--------------------------------------------------------------------------------\n", + "\n", + " Molecules of type: 1\n", + "\n", + " Packing:|0 100%|\n", + " |*********************\n", + "\n", + " Restraint-only function value: 4.7908344210240500E-005\n", + " Maximum violation of the restraints: 3.3276214373314433E-005\n", + "\n", + "--------------------------------------------------------------------------------\n", + "\n", + " Rescaling maximum and minimum coordinates... \n", + " Computing size of patches... \n", + " Add fixed molecules to permanent arrays... \n", + " Reseting center of mass... \n", + "\n", + "--------------------------------------------------------------------------------\n", + "\n", + " Setting initial trial coordinates ... \n", + "\n", + "--------------------------------------------------------------------------------\n", + "\n", + "--------------------------------------------------------------------------------\n", + "\n", + " Molecules of type: 1\n", + " Adjusting random positions to fit the constraints. \n", + " Restraint-only function value: 0.0000000000000000 \n", + " Maximum violation of the restraints: 0.0000000000000000 \n", + "\n", + "################################################################################\n", + "\n", + " Objective function at initial point: 305.75852348958790 \n", + "\n", + "################################################################################\n", + "\n", + " Packing molecules of type: 1\n", + "\n", + "################################################################################\n", + "\n", + "\n", + "--------------------------------------------------------------------------------\n", + "\n", + " Starting GENCAN loop: 0\n", + " Scaling radii by: 1.1000000000000001 \n", + "\n", + " Packing:|0 100%|\n", + " |***********************************\n", + "\n", + " Function value from last GENCAN loop: f = .15568E-04\n", + " Best function value before: f = .30576E+03\n", + " Improvement from best function value: 99.99 %\n", + " Improvement from last loop: 99.99 %\n", + " Maximum violation of target distance: 0.000000\n", + " Maximum violation of the constraints: .15568E-04\n", + " Current structure written to file: mixture.xyz\n", + "--------------------------------------------------------------------------------\n", + " Packing solved for molecules of type 1\n", + " Objective function value: 1.5567789525860229E-005\n", + " Maximum violation of target distance: 0.0000000000000000 \n", + " Max. constraint violation: 1.5567789525860229E-005\n", + "--------------------------------------------------------------------------------\n", + "\n", + "################################################################################\n", + "\n", + " Packing all molecules together \n", + "\n", + "################################################################################\n", + "\n", + "\n", + " Initial approximation is a solution. Nothing to do. \n", + "\n", + " Solution written to file: mixture.xyz\n", + "\n", + "################################################################################\n", + "\n", + " Success! \n", + " Final objective function value: .31847E-01\n", + " Maximum violation of target distance: 0.000000\n", + " Maximum violation of the constraints: .15568E-04\n", + "\n", + "--------------------------------------------------------------------------------\n", + "\n", + " Please cite this work if Packmol was useful: \n", + "\n", + " L. Martinez, R. Andrade, E. G. Birgin, J. M. Martinez, \n", + " PACKMOL: A package for building initial configurations for\n", + " molecular dynamics simulations. \n", + " Journal of Computational Chemistry, 30:2157-2164,2009.\n", + "\n", + "################################################################################\n", + "\n", + " Running time: 5.92000026E-04 seconds. \n", + "\n", + "--------------------------------------------------------------------------------\n", + "\n", + "\n", + "2023-05-30 16:18:23,396 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "100%|██████████| 1/1 [00:00<00:00, 10.92it/s]\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "2023-05-30 16:18:24,687 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n", + " Step Time Energy fmax\n", + "BFGS: 0 16:18:24 -1452.227673 560.1183\n", + "BFGS: 1 16:18:25 -1525.179018 73.0175\n", + "BFGS: 2 16:18:25 -1541.432084 26.5437\n", + "BFGS: 3 16:18:25 -1548.847866 20.9261\n", + "BFGS: 4 16:18:25 -1553.041573 21.0507\n", + "BFGS: 5 16:18:25 -1557.985665 14.9412\n", + "BFGS: 6 16:18:25 -1560.632213 8.3526\n", + "BFGS: 7 16:18:25 -1562.409822 5.2405\n", + "BFGS: 8 16:18:25 -1563.889836 4.6672\n", + "BFGS: 9 16:18:26 -1565.320047 13.2885\n", + "BFGS: 10 16:18:26 -1566.448285 3.4639\n", + "BFGS: 11 16:18:26 -1567.953756 4.4025\n", + "BFGS: 12 16:18:26 -1568.948496 7.1006\n", + "BFGS: 13 16:18:26 -1569.550374 4.1206\n", + "BFGS: 14 16:18:26 -1570.227879 2.1917\n", + "BFGS: 15 16:18:26 -1570.532967 7.2313\n", + "BFGS: 16 16:18:26 -1570.847957 2.6559\n", + "BFGS: 17 16:18:27 -1571.138681 1.4818\n", + "BFGS: 18 16:18:27 -1571.662669 2.2882\n", + "BFGS: 19 16:18:27 -1571.800839 1.6854\n", + "BFGS: 20 16:18:27 -1571.956670 0.8907\n", + "2023-05-30 16:18:28,493 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n", + "2023-05-30 16:18:29,693 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n", + "2023-05-30 16:18:30,954 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n", + "2023-05-30 16:18:31,096 (WARNING): Setting maximum to 2 Pi.\n", + "2023-05-30 16:18:32,202 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n", + "2023-05-30 16:18:33,349 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "100%|██████████| 16/16 [00:01<00:00, 8.80it/s]\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "2023-05-30 16:18:36,564 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Could not load field atoms for node BoxScale_mapping.\n", + "100%|███████████████████████████████████| 5/5 [00:00<00:00, 8.29it/s]\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "2023-05-30 16:18:38,818 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n", + "2023-05-30 16:18:40,299 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n" + ] + } + ], + "source": [ + "mapping = ips.geometry.BarycenterMapping(data=None)\n", + "\n", + "with ips.Project(automatic_node_names=True) as project:\n", + " water = ips.configuration_generation.SmilesToAtoms(smiles=\"O\")\n", + " packmol = ips.configuration_generation.Packmol(\n", + " data=[water.atoms], count=[10], density=997\n", + " )\n", + "\n", + " opt_calc = ips.calculators.xTBSinglePoint(data=packmol, method=\"gfn1-xtb\", name=\"opt_calc\")\n", + "\n", + " geopt = ips.calculators.ASEGeoOpt(\n", + " model=opt_calc,\n", + " data=packmol.atoms,\n", + " optimizer=\"BFGS\",\n", + " run_kwargs={\"fmax\": 1.0},\n", + " )\n", + "\n", + " n_configs = 5\n", + " rattle = ips.bootstrap.RattleAtoms(\n", + " data=geopt.atoms,\n", + " data_id=-1,\n", + " n_configurations=n_configs,\n", + " maximum=0.08, # Ang max atomic displacement\n", + " include_original=True\n", + " )\n", + " rotate = ips.bootstrap.RotateMolecules(\n", + " data=geopt.atoms,\n", + " data_id=-1,\n", + " n_configurations=n_configs,\n", + " maximum=15, # deg max rotation\n", + " include_original=False\n", + " )\n", + " translate = ips.bootstrap.TranslateMolecules(\n", + " data=geopt.atoms,\n", + " data_id=-1,\n", + " n_configurations=n_configs,\n", + " maximum=0.3, # Ang max molecular displacement\n", + " include_original=False\n", + " )\n", + "\n", + " bootstrap_configurations = rattle.atoms + rotate.atoms + translate.atoms\n", + "\n", + " labeling_calc = ips.calculators.xTBSinglePoint(data=bootstrap_configurations, method=\"gfn1-xtb\", name=\"label_calc\")\n", + " volume_scan = ips.analysis.BoxScale(\n", + " data=rattle.atoms,\n", + " data_id=0,\n", + " model=labeling_calc,\n", + " mapping=mapping,\n", + " start=0.8,\n", + " stop=1.5,\n", + " num=5,\n", + " )\n", + " bootstrap_dataset = znflow.combine([labeling_calc, volume_scan], attribute=\"atoms\")\n", + "\n", + " energy_hist = ips.analysis.EnergyHistogram(data=bootstrap_dataset, bins=10)\n", + " forces_hist = ips.analysis.ForcesHistogram(data=bootstrap_dataset, bins=10)\n", + "\n", + "\n", + "project.run()" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Lets inspect the label distribution of our new dataset.\n", + "While they produce a plot in the respective `nodes` subdirectory, we will recreate them here to view them from within the notebook.\n", + "\n", + "In order to do that, we first have to load the histogram nodes.\n", + "Then we can create simple histogram with matplotlib.\n" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [], + "source": [ + "energy_hist.load()\n", + "forces_hist.load()" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "data": { + "image/png": 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", + "text/plain": [ + "
" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "counts, bin_edges = energy_hist.get_hist()\n", + "\n", + "plt.stairs(counts, bin_edges, fill=True)\n", + "plt.xlabel(energy_hist.xlabel)\n", + "plt.ylabel(energy_hist.ylabel)\n", + "plt.yscale(\"log\")\n", + "plt.show()\n" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "data": { + "image/png": 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", + "text/plain": [ + "
" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "counts, bin_edges = forces_hist.get_hist()\n", + "\n", + "plt.stairs(counts, bin_edges, fill=True)\n", + "plt.xlabel(forces_hist.xlabel)\n", + "plt.ylabel(forces_hist.ylabel)\n", + "plt.yscale(\"log\")\n", + "plt.show()" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "In both histograms we can see some outliers with fairly high energies / large forces.\n", + "While a few configurations like this are usually not detrimental to model performance, one should tune the displacement parameters such as to not obtain completely unphysical configurations.\n", + "\n", + "The data created here could now be supplied to a model Node and used for training." + ] + }, { "cell_type": "code", - "execution_count": null, + "execution_count": 9, "metadata": {}, "outputs": [], "source": [ - "import ipsuite as ips" + "temp_dir.cleanup()" ] } ], "metadata": { + "kernelspec": { + "display_name": "ips", + "language": "python", + "name": "python3" + }, "language_info": { - "name": "python" + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.11" }, "orig_nbformat": 4 }, From 8622edc5a5d7752f485416d3d5e539f8dd11636d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Moritz=20R=2E=20Sch=C3=A4fer?= Date: Wed, 31 May 2023 23:18:28 +0200 Subject: [PATCH 18/35] bootstrap example cleanup --- examples/06_Bootstrapping_Datasets.ipynb | 21 --------------------- 1 file changed, 21 deletions(-) diff --git a/examples/06_Bootstrapping_Datasets.ipynb b/examples/06_Bootstrapping_Datasets.ipynb index 17f53553..fd679462 100644 --- a/examples/06_Bootstrapping_Datasets.ipynb +++ b/examples/06_Bootstrapping_Datasets.ipynb @@ -58,26 +58,6 @@ "temp_dir = cwd_temp_dir()" ] }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "" - ] - }, - "execution_count": 2, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "temp_dir" - ] - }, { "cell_type": "code", "execution_count": 3, @@ -445,7 +425,6 @@ " energy_hist = ips.analysis.EnergyHistogram(data=bootstrap_dataset, bins=10)\n", " forces_hist = ips.analysis.ForcesHistogram(data=bootstrap_dataset, bins=10)\n", "\n", - "\n", "project.run()" ] }, From a0c5667784d63dd5807b302a17dd59ade55653ad Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Moritz=20R=2E=20Sch=C3=A4fer?= Date: Wed, 31 May 2023 23:19:00 +0200 Subject: [PATCH 19/35] added data loading example notebook --- examples/01_Data_Loading_and_Selection.ipynb | 353 +++++++++++++++++-- 1 file changed, 332 insertions(+), 21 deletions(-) diff --git a/examples/01_Data_Loading_and_Selection.ipynb b/examples/01_Data_Loading_and_Selection.ipynb index 9f99aced..fc7c4995 100644 --- a/examples/01_Data_Loading_and_Selection.ipynb +++ b/examples/01_Data_Loading_and_Selection.ipynb @@ -28,15 +28,71 @@ "name": "stdout", "output_type": "stream", "text": [ - "2023-05-25 13:44:15,756 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n" + "2023-05-31 23:10:07,791 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n" ] } ], "source": [ "import ipsuite as ips\n", + "from zntrack.utils import cwd_temp_dir\n", "\n", - "from ase import Atoms\n", - "from ase.visualize import view" + "temp_dir = cwd_temp_dir()\n", + "\n", + "import ipsuite as ips\n", + "\n", + "import os\n", + "from ase import units\n", + "from ase.calculators.emt import EMT\n", + "from ase.io.trajectory import TrajectoryWriter\n", + "from ase.lattice.cubic import FaceCenteredCubic\n", + "from ase.md.velocitydistribution import MaxwellBoltzmannDistribution\n", + "from ase.md.langevin import Langevin\n", + "from ase.visualize import view\n" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "hint: Using 'master' as the name for the initial branch. This default branch name\n", + "hint: is subject to change. To configure the initial branch name to use in all\n", + "hint: of your new repositories, which will suppress this warning, call:\n", + "hint: \n", + "hint: \tgit config --global init.defaultBranch \n", + "hint: \n", + "hint: Names commonly chosen instead of 'master' are 'main', 'trunk' and\n", + "hint: 'development'. The just-created branch can be renamed via this command:\n", + "hint: \n", + "hint: \tgit branch -m \n", + "Initialized empty Git repository in /tmp/tmpok_da3k5/.git/\n", + "Initialized DVC repository.\n", + "\n", + "You can now commit the changes to git.\n", + "\n", + "+---------------------------------------------------------------------+\n", + "| |\n", + "| DVC has enabled anonymous aggregate usage analytics. |\n", + "| Read the analytics documentation (and how to opt-out) here: |\n", + "| |\n", + "| |\n", + "+---------------------------------------------------------------------+\n", + "\n", + "What's next?\n", + "------------\n", + "- Check out the documentation: \n", + "- Get help and share ideas: \n", + "- Star us on GitHub: \n" + ] + } + ], + "source": [ + "!git init\n", + "!dvc init" ] }, { @@ -54,11 +110,53 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 3, "metadata": {}, "outputs": [], "source": [ - "# TODO" + "size = 3\n", + "\n", + "# Set up a crystal\n", + "atoms = FaceCenteredCubic(\n", + " directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],\n", + " symbol='Cu',\n", + " size=(size, size, size),\n", + " pbc=True\n", + ")\n" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "True" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "timestep = 5 * units.fs\n", + "steps = 100\n", + "temperature = 800\n", + "traj_path = os.path.join(temp_dir.name, \"trajectory.traj\")\n", + "\n", + "\n", + "atoms.calc = EMT()\n", + "MaxwellBoltzmannDistribution(atoms, temperature_K=temperature)\n", + "\n", + "dyn = Langevin(atoms, timestep, temperature_K=temperature, friction=0.002)\n", + "\n", + "writer = TrajectoryWriter(traj_path, \"w\", atoms=atoms)\n", + "dyn.attach(writer, interval=1)\n", + "\n", + "dyn.run(steps)" ] }, { @@ -74,12 +172,42 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 5, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "2023-05-31 23:10:17,739 (WARNING): Please run 'dvc add /tmp/tmpok_da3k5/trajectory.traj' to track the file with DVC. Otherwise, it might end up being git tracked.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Running DVC command: 'stage add --name trajectory --force ...'\n", + "Running DVC command: 'repro'\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "2023-05-31 23:10:19,001 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Reading File: 101it [00:00, 3355.28it/s]\n" + ] + } + ], "source": [ "with ips.Project() as project:\n", - " data = ips.AddData(file=\"dataset.extxyz\", name=\"dataset\")\n", + " trajectory = ips.AddData(file=traj_path, name=\"trajectory\")\n", "project.run()" ] }, @@ -93,12 +221,11 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 6, "metadata": {}, "outputs": [], "source": [ - "trajectory = data.load() # requires the project to have been run\n", - "trajectory" + "trajectory.load() # requires the project to have been run" ] }, { @@ -134,16 +261,100 @@ "source": [ "## Data Selection\n", "\n", - "A common way to split data into training, validation and test splits is to randomly partition them into fractions like 75:15:10" + "A common way to split data into training, validation and test splits is to randomly partition them into fractions like 75:15:10.\n", + "We can add the respective selection Nodes to our existing project." ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 7, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Running DVC command: 'stage add --name trajectory --force ...'\n", + "Running DVC command: 'stage add --name random_test_selection --force ...'\n", + "Running DVC command: 'stage add --name random_val_selection --force ...'\n", + "Running DVC command: 'stage add --name random_train_selection --force ...'\n", + "Running DVC command: 'repro'\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "2023-05-31 23:10:20,899 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n", + "2023-05-31 23:10:21,047 (DEBUG): Selecting from 101 configurations.\n", + "2023-05-31 23:10:22,301 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n", + "2023-05-31 23:10:22,491 (DEBUG): Selecting from 91 configurations.\n", + "2023-05-31 23:10:23,804 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n", + "2023-05-31 23:10:24,044 (DEBUG): Selecting from 76 configurations.\n" + ] + } + ], "source": [ - "# TODO" + "with project:\n", + " random_test_selection = ips.configuration_selection.RandomSelection(data=trajectory, n_configurations=10, name=\"random_test_selection\")\n", + " random_val_selection = ips.configuration_selection.RandomSelection(data=random_test_selection.excluded_atoms, n_configurations=15, name=\"random_val_selection\")\n", + " random_train_selection = ips.configuration_selection.RandomSelection(data=random_val_selection.excluded_atoms, n_configurations=75, name=\"random_train_selection\")\n", + "project.run()" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Selecting the testing data first means we can change our training and validation selection, e.g. by using a different selection method or a different number of configurations, without altering our test set.\n", + "Note that we had to give names to our selection nodes since we use multiple instances of that Node in our graph.\n", + "For convenience, it is also possible to assign numerical IDs by supplying `automatic_node_names=True` to the `Project`." + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "We can visualize our workflow at any time using" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + " +------------+ \n", + " | trajectory | \n", + " +------------+ \n", + " * \n", + " * \n", + " * \n", + "+-----------------------+ \n", + "| random_test_selection | \n", + "+-----------------------+ \n", + " * \n", + " * \n", + " * \n", + " +----------------------+ \n", + " | random_val_selection | \n", + " +----------------------+ \n", + " * \n", + " * \n", + " * \n", + "+------------------------+ \n", + "| random_train_selection | \n", + "+------------------------+ \n" + ] + } + ], + "source": [ + "!dvc dag" ] }, { @@ -153,23 +364,113 @@ "source": [ "While straightforward, this is not necessarily advisable for molecular dynamics data.\n", "Trajectories are created sequentially, and a random split will result in validation samples that are drawn from between training samples.\n", - "By instead separating the dataset into fixed fraction first, we can ensure that the splits do not temporally overlap" + "By instead separating the dataset into fixed fraction first, we can ensure that the splits do not temporally overlap.\n", + "\n", + "For demonstration purposes, we will delete the random splitting workflow we created above with `remove_existing_graph=True`." ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 9, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "2023-05-31 23:11:14,183 (WARNING): Please run 'dvc add /tmp/tmpok_da3k5/trajectory.traj' to track the file with DVC. Otherwise, it might end up being git tracked.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Running DVC command: 'stage add --name trajectory --force ...'\n", + "Running DVC command: 'stage add --name test_split --force ...'\n", + "Running DVC command: 'stage add --name val_split --force ...'\n", + "Running DVC command: 'stage add --name test_data --force ...'\n", + "Running DVC command: 'stage add --name val_data --force ...'\n", + "Running DVC command: 'stage add --name train_data --force ...'\n", + "Running DVC command: 'repro'\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "2023-05-31 23:11:15,722 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n", + "2023-05-31 23:11:15,915 (DEBUG): Selecting from 101 configurations.\n", + "2023-05-31 23:11:17,228 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n", + "2023-05-31 23:11:17,459 (DEBUG): Selecting from 91 configurations.\n", + "2023-05-31 23:11:18,780 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n", + "2023-05-31 23:11:19,031 (DEBUG): Selecting from 76 configurations.\n", + "2023-05-31 23:11:19,031 (WARNING): Running search for 80 to max 76\n", + "2023-05-31 23:11:20,350 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n", + "2023-05-31 23:11:20,561 (DEBUG): Selecting from 10 configurations.\n", + "2023-05-31 23:11:21,836 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n", + "2023-05-31 23:11:22,081 (DEBUG): Selecting from 15 configurations.\n" + ] + } + ], "source": [ - "# TODO percentage split" + "with ips.Project(remove_existing_graph=True) as project:\n", + " trajectory = ips.AddData(file=traj_path, name=\"trajectory\")\n", + " test_split = ips.configuration_selection.SplitSelection(data=trajectory, split=0.1, name=\"test_split\")\n", + " val_split = ips.configuration_selection.SplitSelection(data=test_split.excluded_atoms, split=0.17, name=\"val_split\") # 0.15 / 0.9 * 1.0 \\approx 0.17\n", + " train_split = val_split.excluded_atoms # 0.8 of the total data\n", + "\n", + " test_data = ips.configuration_selection.UniformTemporalSelection(data=test_split, n_configurations=10, name=\"test_data\")\n", + " val_data = ips.configuration_selection.UniformTemporalSelection(data=val_split, n_configurations=15, name=\"val_data\")\n", + " train_data = ips.configuration_selection.UniformEnergeticSelection(data=train_split, n_configurations=80, name=\"train_data\")\n", + "\n", + "project.run()" ] }, { "attachments": {}, "cell_type": "markdown", "metadata": {}, - "source": [] + "source": [ + "The selection methods here are purely for demonstration purposes.\n", + "Usually it makes sense to use all available test data and not perform a sub-selection since the test set should only be evaluated once which does not pose a performance bottleneck." + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + " +------------+ \n", + " | trajectory | \n", + " +------------+ \n", + " * \n", + " * \n", + " * \n", + " +------------+ \n", + " | test_split | \n", + " +------------+ \n", + " *** *** \n", + " * * \n", + " ** ** \n", + "+-----------+ +-----------+ \n", + "| test_data | | val_split | \n", + "+-----------+ +-----------+ \n", + " *** *** \n", + " * * \n", + " ** ** \n", + " +----------+ +------------+ \n", + " | val_data | | train_data | \n", + " +----------+ +------------+ \n" + ] + } + ], + "source": [ + "!dvc dag" + ] }, { "attachments": {}, @@ -217,6 +518,7 @@ ] }, { + "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [] @@ -229,6 +531,15 @@ "source": [ "# TODO" ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "temp_dir.cleanup()" + ] } ], "metadata": { @@ -247,7 +558,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.9" + "version": "3.10.10" }, "orig_nbformat": 4 }, From 78a6e578c39dd2707b24390b1e83d3f6c6ad6836 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Moritz=20R=2E=20Sch=C3=A4fer?= Date: Mon, 12 Jun 2023 17:04:03 +0200 Subject: [PATCH 20/35] analyse ds sketch --- examples/01_Data_Loading_and_Selection.ipynb | 2 +- ...ysing_Datasets_and_Model_Predictions.ipynb | 181 +++++++++++++++++- 2 files changed, 179 insertions(+), 4 deletions(-) diff --git a/examples/01_Data_Loading_and_Selection.ipynb b/examples/01_Data_Loading_and_Selection.ipynb index fc7c4995..723f56f0 100644 --- a/examples/01_Data_Loading_and_Selection.ipynb +++ b/examples/01_Data_Loading_and_Selection.ipynb @@ -558,7 +558,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.10" + "version": "3.10.11" }, "orig_nbformat": 4 }, diff --git a/examples/03_Analysing_Datasets_and_Model_Predictions.ipynb b/examples/03_Analysing_Datasets_and_Model_Predictions.ipynb index 8a7548c0..47afa1ec 100644 --- a/examples/03_Analysing_Datasets_and_Model_Predictions.ipynb +++ b/examples/03_Analysing_Datasets_and_Model_Predictions.ipynb @@ -8,19 +8,194 @@ "# Analysing Datasets and Model Predictions" ] }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "In the last example we already saw how to obtain a simple prediction-label correlation plot.\n", + "However, for most real-life applications, this alone would be insufficient to ascertain the reliability of the model across configuration space.\n", + "This notebook goes into more detail about how to use the various analysis tools implemented in IPS." + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Data Generation and Training\n", + "\n", + "We will once again create a simple dataset." + ] + }, { "cell_type": "code", - "execution_count": null, + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "2023-06-06 22:00:51,620 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n" + ] + } + ], + "source": [ + "import ipsuite as ips\n", + "from zntrack.utils import cwd_temp_dir\n", + "\n", + "temp_dir = cwd_temp_dir()\n", + "\n", + "import ipsuite as ips\n", + "\n", + "import os\n", + "from ase import units\n", + "from ase.calculators.emt import EMT\n", + "from ase.io.trajectory import TrajectoryWriter\n", + "from ase.lattice.cubic import FaceCenteredCubic\n", + "from ase.md.velocitydistribution import MaxwellBoltzmannDistribution\n", + "from ase.md.langevin import Langevin\n", + "from ase.visualize import view\n" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "hint: Using 'master' as the name for the initial branch. This default branch name\n", + "hint: is subject to change. To configure the initial branch name to use in all\n", + "hint: of your new repositories, which will suppress this warning, call:\n", + "hint: \n", + "hint: \tgit config --global init.defaultBranch \n", + "hint: \n", + "hint: Names commonly chosen instead of 'master' are 'main', 'trunk' and\n", + "hint: 'development'. The just-created branch can be renamed via this command:\n", + "hint: \n", + "hint: \tgit branch -m \n", + "Initialized empty Git repository in /tmp/tmpjx247w5h/.git/\n", + "Initialized DVC repository.\n", + "\n", + "You can now commit the changes to git.\n", + "\n", + "+---------------------------------------------------------------------+\n", + "| |\n", + "| DVC has enabled anonymous aggregate usage analytics. |\n", + "| Read the analytics documentation (and how to opt-out) here: |\n", + "| |\n", + "| |\n", + "+---------------------------------------------------------------------+\n", + "\n", + "What's next?\n", + "------------\n", + "- Check out the documentation: \n", + "- Get help and share ideas: \n", + "- Star us on GitHub: \n" + ] + } + ], + "source": [ + "!git init\n", + "!dvc init" + ] + }, + { + "cell_type": "code", + "execution_count": 3, "metadata": {}, "outputs": [], "source": [ - "import ipsuite as ips" + "size = 3\n", + "\n", + "# Set up a crystal\n", + "atoms = FaceCenteredCubic(\n", + " directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],\n", + " symbol='Cu',\n", + " size=(size, size, size),\n", + " pbc=True\n", + ")" ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "True" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "timestep = 5 * units.fs\n", + "steps = 100\n", + "temperature = 800\n", + "traj_path = os.path.join(temp_dir.name, \"trajectory.traj\")\n", + "\n", + "atoms.calc = EMT()\n", + "MaxwellBoltzmannDistribution(atoms, temperature_K=temperature)\n", + "\n", + "dyn = Langevin(atoms, timestep, temperature_K=temperature, friction=0.002)\n", + "\n", + "writer = TrajectoryWriter(traj_path, \"w\", atoms=atoms)\n", + "dyn.attach(writer, interval=1)\n", + "\n", + "dyn.run(steps)" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Dataset Analysis" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "This time around, we will explore the dataset a bit before training models on it.\n", + "It is often useful to visualize the distribution of labels " + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] } ], "metadata": { + "kernelspec": { + "display_name": "ips2", + "language": "python", + "name": "python3" + }, "language_info": { - "name": "python" + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.10" }, "orig_nbformat": 4 }, From ef45192859c8035a5694b2e82370d3d26dbb3f8e Mon Sep 17 00:00:00 2001 From: Julian Peters Date: Thu, 18 Apr 2024 10:58:37 +0200 Subject: [PATCH 21/35] add basic nodes List to docs --- .../ipsuite.analysis.bin_property.rst | 35 +++++++++++++ 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docs/source/_get_started/_autosummary/ipsuite.utils.combine.rst create mode 100644 docs/source/_get_started/_autosummary/ipsuite.utils.docs.rst create mode 100644 docs/source/_get_started/_autosummary/ipsuite.utils.helpers.rst create mode 100644 docs/source/_get_started/_autosummary/ipsuite.utils.logs.rst create mode 100644 docs/source/_get_started/_autosummary/ipsuite.utils.md.rst create mode 100644 docs/source/_get_started/_autosummary/ipsuite.utils.metrics.rst create mode 100644 docs/source/_get_started/_autosummary/ipsuite.utils.rst create mode 100644 docs/source/_get_started/nodes_list.rst diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.bin_property.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.bin_property.rst new file mode 100644 index 00000000..58a0eb6c --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.bin_property.rst @@ -0,0 +1,35 @@ +ipsuite.analysis.bin\_property +============================== + +.. automodule:: ipsuite.analysis.bin_property + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + DipoleHistogram + EnergyHistogram + EnergyUncertaintyHistogram + ForcesHistogram + ForcesUncertaintyHistogram + LabelHistogram + StressHistogram + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.bond_stretch.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.bond_stretch.rst new file mode 100644 index 00000000..aeb1ce96 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.bond_stretch.rst @@ -0,0 +1,29 @@ +ipsuite.analysis.bond\_stretch +============================== + +.. automodule:: ipsuite.analysis.bond_stretch + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + BondStretchAnalyses + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.ensemble.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.ensemble.rst new file mode 100644 index 00000000..d8779e0c --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.ensemble.rst @@ -0,0 +1,35 @@ +ipsuite.analysis.ensemble +========================= + +.. automodule:: ipsuite.analysis.ensemble + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + plot_with_uncertainty + + + + + + .. rubric:: Classes + + .. autosummary:: + + ModelEnsembleAnalysis + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.md.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.md.rst new file mode 100644 index 00000000..d85c609d --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.md.rst @@ -0,0 +1,29 @@ +ipsuite.analysis.md +=================== + +.. automodule:: ipsuite.analysis.md + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + AnalyseDensity + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics.rst new file mode 100644 index 00000000..2619720a --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics.rst @@ -0,0 +1,38 @@ +ipsuite.analysis.model.dynamics +=============================== + +.. automodule:: ipsuite.analysis.model.dynamics + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + run_stability_nve + + + + + + .. rubric:: Classes + + .. autosummary:: + + BoxHeatUp + BoxScale + MDStability + RattleAnalysis + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics_checks.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics_checks.rst new file mode 100644 index 00000000..2875ab96 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics_checks.rst @@ -0,0 +1,33 @@ +ipsuite.analysis.model.dynamics\_checks +======================================= + +.. automodule:: ipsuite.analysis.model.dynamics_checks + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + ConnectivityCheck + EnergySpikeCheck + NaNCheck + TemperatureCheck + ThresholdCheck + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.math.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.math.rst new file mode 100644 index 00000000..38988dc1 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.math.rst @@ -0,0 +1,33 @@ +ipsuite.analysis.model.math +=========================== + +.. automodule:: ipsuite.analysis.model.math + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + compute_intertia_tensor + compute_rot_forces + compute_trans_forces + decompose_stress_tensor + force_decomposition + + + + + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.plots.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.plots.rst new file mode 100644 index 00000000..05f858c5 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.plots.rst @@ -0,0 +1,32 @@ +ipsuite.analysis.model.plots +============================ + +.. automodule:: ipsuite.analysis.model.plots + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + density_scatter + get_figure + get_hist + get_histogram_figure + + + + + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.predict.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.predict.rst new file mode 100644 index 00000000..7666b23b --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.predict.rst @@ -0,0 +1,32 @@ +ipsuite.analysis.model.predict +============================== + +.. automodule:: ipsuite.analysis.model.predict + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + ForceAngles + ForceDecomposition + Prediction + PredictionMetrics + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.rst new file mode 100644 index 00000000..9a176f60 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.rst @@ -0,0 +1,35 @@ +ipsuite.analysis.model +====================== + +.. automodule:: ipsuite.analysis.model + + + + + + + + + + + + + + + + + + + +.. rubric:: Modules + +.. autosummary:: + :toctree: + :recursive: + + ipsuite.analysis.model.dynamics + ipsuite.analysis.model.dynamics_checks + ipsuite.analysis.model.math + ipsuite.analysis.model.plots + ipsuite.analysis.model.predict + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.rst new file mode 100644 index 00000000..92f626ea --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.rst @@ -0,0 +1,36 @@ +ipsuite.analysis +================ + +.. automodule:: ipsuite.analysis + + + + + + + + + + + + + + + + + + + +.. rubric:: Modules + +.. autosummary:: + :toctree: + :recursive: + + ipsuite.analysis.bin_property + ipsuite.analysis.bond_stretch + ipsuite.analysis.ensemble + ipsuite.analysis.md + ipsuite.analysis.model + ipsuite.analysis.sensitivity + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.sensitivity.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.sensitivity.rst new file mode 100644 index 00000000..8db8495d --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.sensitivity.rst @@ -0,0 +1,38 @@ +ipsuite.analysis.sensitivity +============================ + +.. automodule:: ipsuite.analysis.sensitivity + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + nonuniform_imshow + + + + + + .. rubric:: Classes + + .. autosummary:: + + AnalyseGlobalForceSensitivity + AnalyseSingleForceSensitivity + IsConstraintMD + MoveSingleParticle + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.base.base.rst b/docs/source/_get_started/_autosummary/ipsuite.base.base.rst new file mode 100644 index 00000000..ed4f51bb --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.base.base.rst @@ -0,0 +1,35 @@ +ipsuite.base.base +================= + +.. automodule:: ipsuite.base.base + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + AnalyseAtoms + AnalyseProcessAtoms + CheckBase + IPSNode + Mapping + ProcessAtoms + ProcessSingleAtom + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.base.protocol.rst b/docs/source/_get_started/_autosummary/ipsuite.base.protocol.rst new file mode 100644 index 00000000..446e1299 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.base.protocol.rst @@ -0,0 +1,31 @@ +ipsuite.base.protocol +===================== + +.. automodule:: ipsuite.base.protocol + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + HasAtoms + HasSelectedConfigurations + ProcessAtoms + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.base.rst b/docs/source/_get_started/_autosummary/ipsuite.base.rst new file mode 100644 index 00000000..6f3c0705 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.base.rst @@ -0,0 +1,32 @@ +ipsuite.base +============ + +.. automodule:: ipsuite.base + + + + + + + + + + + + + + + + + + + +.. rubric:: Modules + +.. autosummary:: + :toctree: + :recursive: + + ipsuite.base.base + ipsuite.base.protocol + diff --git a/docs/source/_get_started/_autosummary/ipsuite.bootstrap.random_displacements.rst b/docs/source/_get_started/_autosummary/ipsuite.bootstrap.random_displacements.rst new file mode 100644 index 00000000..8df9d95e --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.bootstrap.random_displacements.rst @@ -0,0 +1,32 @@ +ipsuite.bootstrap.random\_displacements +======================================= + +.. automodule:: ipsuite.bootstrap.random_displacements + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + Bootstrap + RattleAtoms + RotateMolecules + TranslateMolecules + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.bootstrap.rst b/docs/source/_get_started/_autosummary/ipsuite.bootstrap.rst new file mode 100644 index 00000000..54528569 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.bootstrap.rst @@ -0,0 +1,32 @@ +ipsuite.bootstrap +================= + +.. automodule:: ipsuite.bootstrap + + + + + + + + + + + + + + + + + + + +.. rubric:: Modules + +.. autosummary:: + :toctree: + :recursive: + + ipsuite.bootstrap.random_displacements + ipsuite.bootstrap.surface_mods + diff --git a/docs/source/_get_started/_autosummary/ipsuite.bootstrap.surface_mods.rst b/docs/source/_get_started/_autosummary/ipsuite.bootstrap.surface_mods.rst new file mode 100644 index 00000000..9651fc49 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.bootstrap.surface_mods.rst @@ -0,0 +1,36 @@ +ipsuite.bootstrap.surface\_mods +=============================== + +.. automodule:: ipsuite.bootstrap.surface_mods + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + plot_ture_vs_pred + + + + + + .. rubric:: Classes + + .. autosummary:: + + SurfaceRasterMetrics + SurfaceRasterScan + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.apax_jax_md.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.apax_jax_md.rst new file mode 100644 index 00000000..fc22c9c9 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.apax_jax_md.rst @@ -0,0 +1,29 @@ +ipsuite.calculators.apax\_jax\_md +================================= + +.. automodule:: ipsuite.calculators.apax_jax_md + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + ApaxJaxMD + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_geoopt.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_geoopt.rst new file mode 100644 index 00000000..a33a8dc7 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_geoopt.rst @@ -0,0 +1,30 @@ +ipsuite.calculators.ase\_geoopt +=============================== + +.. automodule:: ipsuite.calculators.ase_geoopt + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + ASEGeoOpt + BatchASEGeoOpt + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_md.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_md.rst new file mode 100644 index 00000000..60984016 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_md.rst @@ -0,0 +1,45 @@ +ipsuite.calculators.ase\_md +=========================== + +.. automodule:: ipsuite.calculators.ase_md + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + get_desc + update_metrics_dict + + + + + + .. rubric:: Classes + + .. autosummary:: + + ASEMD + BoxOscillatingRampModifier + FixedLayerConstraint + FixedSphereConstraint + LangevinThermostat + NPTThermostat + PressureRampModifier + RescaleBoxModifier + TemperatureOscillatingRampModifier + TemperatureRampModifier + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_standard.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_standard.rst new file mode 100644 index 00000000..82bd7ee7 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_standard.rst @@ -0,0 +1,31 @@ +ipsuite.calculators.ase\_standard +================================= + +.. automodule:: ipsuite.calculators.ase_standard + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + EMTCalculator + EMTSinglePoint + LJSinglePoint + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.cp2k.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.cp2k.rst new file mode 100644 index 00000000..0318deb3 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.cp2k.rst @@ -0,0 +1,30 @@ +ipsuite.calculators.cp2k +======================== + +.. automodule:: ipsuite.calculators.cp2k + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + CP2KSinglePoint + CP2KYaml + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.lammps.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.lammps.rst new file mode 100644 index 00000000..c7f44d55 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.lammps.rst @@ -0,0 +1,29 @@ +ipsuite.calculators.lammps +========================== + +.. automodule:: ipsuite.calculators.lammps + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + LammpsSimulator + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.mix.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.mix.rst new file mode 100644 index 00000000..8a7c8d11 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.mix.rst @@ -0,0 +1,30 @@ +ipsuite.calculators.mix +======================= + +.. automodule:: ipsuite.calculators.mix + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + CalculatorNode + MixCalculator + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.orca.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.orca.rst new file mode 100644 index 00000000..d37ccfa4 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.orca.rst @@ -0,0 +1,29 @@ +ipsuite.calculators.orca +======================== + +.. automodule:: ipsuite.calculators.orca + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + OrcaSinglePoint + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.rst new file mode 100644 index 00000000..8ee3eeb8 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.rst @@ -0,0 +1,40 @@ +ipsuite.calculators +=================== + +.. automodule:: ipsuite.calculators + + + + + + + + + + + + + + + + + + + +.. rubric:: Modules + +.. autosummary:: + :toctree: + :recursive: + + ipsuite.calculators.apax_jax_md + ipsuite.calculators.ase_geoopt + ipsuite.calculators.ase_md + ipsuite.calculators.ase_standard + ipsuite.calculators.cp2k + ipsuite.calculators.lammps + ipsuite.calculators.mix + ipsuite.calculators.orca + ipsuite.calculators.torch_d3 + ipsuite.calculators.xtb + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.xtb.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.xtb.rst new file mode 100644 index 00000000..4101c618 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.xtb.rst @@ -0,0 +1,29 @@ +ipsuite.calculators.xtb +======================= + +.. automodule:: ipsuite.calculators.xtb + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + xTBSinglePoint + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.MMKernel.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.MMKernel.rst new file mode 100644 index 00000000..00b16e08 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.MMKernel.rst @@ -0,0 +1,49 @@ +ipsuite.configuration\_comparison.MMKernel +========================================== + +.. currentmodule:: ipsuite.configuration_comparison + +.. autoclass:: MMKernel + + + .. automethod:: __init__ + + + .. rubric:: Methods + + .. autosummary:: + + ~MMKernel.__init__ + ~MMKernel.compare + ~MMKernel.convert_notebook + ~MMKernel.from_rev + ~MMKernel.load + ~MMKernel.run + ~MMKernel.save + ~MMKernel.save_representation + ~MMKernel.unlink_database + + + + + + .. rubric:: Attributes + + .. autosummary:: + + ~MMKernel.analyte + ~MMKernel.init_descriptors + ~MMKernel.init_subclass_basecls + ~MMKernel.memory + ~MMKernel.name + ~MMKernel.nwd + ~MMKernel.reference + ~MMKernel.result + ~MMKernel.similarities + ~MMKernel.soap + ~MMKernel.state + ~MMKernel.use_jit + ~MMKernel.use_repr + ~MMKernel.uuid + + \ No newline at end of file diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.REMatch.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.REMatch.rst new file mode 100644 index 00000000..f8e961b0 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.REMatch.rst @@ -0,0 +1,52 @@ +ipsuite.configuration\_comparison.REMatch +========================================= + +.. currentmodule:: ipsuite.configuration_comparison + +.. autoclass:: REMatch + + + .. automethod:: __init__ + + + .. rubric:: Methods + + .. autosummary:: + + ~REMatch.__init__ + ~REMatch.compare + ~REMatch.convert_notebook + ~REMatch.from_rev + ~REMatch.load + ~REMatch.run + ~REMatch.save + ~REMatch.save_representation + ~REMatch.unlink_database + + + + + + .. rubric:: Attributes + + .. autosummary:: + + ~REMatch.alpha + ~REMatch.analyte + ~REMatch.init_descriptors + ~REMatch.init_subclass_basecls + ~REMatch.memory + ~REMatch.metric + ~REMatch.name + ~REMatch.nwd + ~REMatch.reference + ~REMatch.result + ~REMatch.similarities + ~REMatch.soap + ~REMatch.state + ~REMatch.threshold + ~REMatch.use_jit + ~REMatch.use_repr + ~REMatch.uuid + + \ No newline at end of file diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.base.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.base.rst new file mode 100644 index 00000000..5598308b --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.base.rst @@ -0,0 +1,39 @@ +ipsuite.configuration\_comparison.base +====================================== + +.. automodule:: ipsuite.configuration_comparison.base + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + convert_to_df + create_dataset + write_dataset + + + + + + .. rubric:: Classes + + .. autosummary:: + + ConfigurationComparison + SOAPParameter + SOAPParameterConverter + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.rst new file mode 100644 index 00000000..8c33e3a6 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.rst @@ -0,0 +1,33 @@ +ipsuite.configuration\_comparison +================================= + +.. automodule:: ipsuite.configuration_comparison + + + + + + + + + + + + + + + + + + + +.. rubric:: Modules + +.. autosummary:: + :toctree: + :recursive: + + ipsuite.configuration_comparison.MMKernel + ipsuite.configuration_comparison.REMatch + ipsuite.configuration_comparison.base + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.packmol.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.packmol.rst new file mode 100644 index 00000000..561e5315 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.packmol.rst @@ -0,0 +1,30 @@ +ipsuite.configuration\_generation.packmol +========================================= + +.. automodule:: ipsuite.configuration_generation.packmol + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + MultiPackmol + Packmol + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.rst new file mode 100644 index 00000000..335cca0f --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.rst @@ -0,0 +1,32 @@ +ipsuite.configuration\_generation +================================= + +.. automodule:: ipsuite.configuration_generation + + + + + + + + + + + + + + + + + + + +.. rubric:: Modules + +.. autosummary:: + :toctree: + :recursive: + + ipsuite.configuration_generation.packmol + ipsuite.configuration_generation.smiles_to_atoms + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.smiles_to_atoms.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.smiles_to_atoms.rst new file mode 100644 index 00000000..8795be00 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.smiles_to_atoms.rst @@ -0,0 +1,30 @@ +ipsuite.configuration\_generation.smiles\_to\_atoms +=================================================== + +.. automodule:: ipsuite.configuration_generation.smiles_to_atoms + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + SmilesToAtoms + SmilesToConformers + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.base.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.base.rst new file mode 100644 index 00000000..ad9d34a8 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.base.rst @@ -0,0 +1,30 @@ +ipsuite.configuration\_selection.base +===================================== + +.. automodule:: ipsuite.configuration_selection.base + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + BatchConfigurationSelection + ConfigurationSelection + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.filter.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.filter.rst new file mode 100644 index 00000000..84e5db76 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.filter.rst @@ -0,0 +1,29 @@ +ipsuite.configuration\_selection.filter +======================================= + +.. automodule:: ipsuite.configuration_selection.filter + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + FilterOutlier + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.index.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.index.rst new file mode 100644 index 00000000..e24a4947 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.index.rst @@ -0,0 +1,29 @@ +ipsuite.configuration\_selection.index +====================================== + +.. automodule:: ipsuite.configuration_selection.index + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + IndexSelection + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.kernel.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.kernel.rst new file mode 100644 index 00000000..95ddf8b5 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.kernel.rst @@ -0,0 +1,29 @@ +ipsuite.configuration\_selection.kernel +======================================= + +.. automodule:: ipsuite.configuration_selection.kernel + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + KernelSelection + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.random.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.random.rst new file mode 100644 index 00000000..a0a278b2 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.random.rst @@ -0,0 +1,29 @@ +ipsuite.configuration\_selection.random +======================================= + +.. automodule:: ipsuite.configuration_selection.random + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + RandomSelection + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.rst new file mode 100644 index 00000000..030e6a6c --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.rst @@ -0,0 +1,40 @@ +ipsuite.configuration\_selection +================================ + +.. automodule:: ipsuite.configuration_selection + + + + + + + + + + + + + + + + + + + +.. rubric:: Modules + +.. autosummary:: + :toctree: + :recursive: + + ipsuite.configuration_selection.base + ipsuite.configuration_selection.filter + ipsuite.configuration_selection.index + ipsuite.configuration_selection.kernel + ipsuite.configuration_selection.random + ipsuite.configuration_selection.split + ipsuite.configuration_selection.threshold + ipsuite.configuration_selection.uniform_arange + ipsuite.configuration_selection.uniform_energetic + ipsuite.configuration_selection.uniform_temporal + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.split.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.split.rst new file mode 100644 index 00000000..b67b2254 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.split.rst @@ -0,0 +1,29 @@ +ipsuite.configuration\_selection.split +====================================== + +.. automodule:: ipsuite.configuration_selection.split + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + SplitSelection + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.threshold.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.threshold.rst new file mode 100644 index 00000000..2ba751a2 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.threshold.rst @@ -0,0 +1,37 @@ +ipsuite.configuration\_selection.threshold +========================================== + +.. automodule:: ipsuite.configuration_selection.threshold + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + check_dimension + max_reduction + mean_reduction + + + + + + .. rubric:: Classes + + .. autosummary:: + + ThresholdSelection + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_arange.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_arange.rst new file mode 100644 index 00000000..eb45287c --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_arange.rst @@ -0,0 +1,29 @@ +ipsuite.configuration\_selection.uniform\_arange +================================================ + +.. automodule:: ipsuite.configuration_selection.uniform_arange + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + UniformArangeSelection + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_energetic.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_energetic.rst new file mode 100644 index 00000000..d41e2d2e --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_energetic.rst @@ -0,0 +1,29 @@ +ipsuite.configuration\_selection.uniform\_energetic +=================================================== + +.. automodule:: ipsuite.configuration_selection.uniform_energetic + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + UniformEnergeticSelection + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_temporal.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_temporal.rst new file mode 100644 index 00000000..4833a013 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_temporal.rst @@ -0,0 +1,29 @@ +ipsuite.configuration\_selection.uniform\_temporal +================================================== + +.. automodule:: ipsuite.configuration_selection.uniform_temporal + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + UniformTemporalSelection + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_ase.rst b/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_ase.rst new file mode 100644 index 00000000..eb4384c7 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_ase.rst @@ -0,0 +1,36 @@ +ipsuite.data\_loading.add\_data\_ase +==================================== + +.. automodule:: ipsuite.data_loading.add_data_ase + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + load_data + + + + + + .. rubric:: Classes + + .. autosummary:: + + AddData + ReadData + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_h5md.rst b/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_h5md.rst new file mode 100644 index 00000000..5dad0ffc --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_h5md.rst @@ -0,0 +1,29 @@ +ipsuite.data\_loading.add\_data\_h5md +===================================== + +.. automodule:: ipsuite.data_loading.add_data_h5md + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + AddDataH5MD + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.data_loading.rst b/docs/source/_get_started/_autosummary/ipsuite.data_loading.rst new file mode 100644 index 00000000..dee0fd07 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.data_loading.rst @@ -0,0 +1,32 @@ +ipsuite.data\_loading +===================== + +.. automodule:: ipsuite.data_loading + + + + + + + + + + + + + + + + + + + +.. rubric:: Modules + +.. autosummary:: + :toctree: + :recursive: + + ipsuite.data_loading.add_data_ase + ipsuite.data_loading.add_data_h5md + diff --git a/docs/source/_get_started/_autosummary/ipsuite.fields.atoms.rst b/docs/source/_get_started/_autosummary/ipsuite.fields.atoms.rst new file mode 100644 index 00000000..3c4e1d82 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.fields.atoms.rst @@ -0,0 +1,29 @@ +ipsuite.fields.atoms +==================== + +.. automodule:: ipsuite.fields.atoms + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + Atoms + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.fields.rst b/docs/source/_get_started/_autosummary/ipsuite.fields.rst new file mode 100644 index 00000000..13d024e7 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.fields.rst @@ -0,0 +1,31 @@ +ipsuite.fields +============== + +.. automodule:: ipsuite.fields + + + + + + + + + + + + + + + + + + + +.. rubric:: Modules + +.. autosummary:: + :toctree: + :recursive: + + ipsuite.fields.atoms + diff --git a/docs/source/_get_started/_autosummary/ipsuite.geometry.barycenter_coarse_grain.rst b/docs/source/_get_started/_autosummary/ipsuite.geometry.barycenter_coarse_grain.rst new file mode 100644 index 00000000..f59fe34f --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.geometry.barycenter_coarse_grain.rst @@ -0,0 +1,30 @@ +ipsuite.geometry.barycenter\_coarse\_grain +========================================== + +.. automodule:: ipsuite.geometry.barycenter_coarse_grain + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + barycenter_backmapping + coarse_grain_to_barycenter + + + + + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.geometry.graphs.rst b/docs/source/_get_started/_autosummary/ipsuite.geometry.graphs.rst new file mode 100644 index 00000000..0c08f233 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.geometry.graphs.rst @@ -0,0 +1,32 @@ +ipsuite.geometry.graphs +======================= + +.. automodule:: ipsuite.geometry.graphs + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + atoms_to_graph + edges_from_atoms + identify_molecules + split_molecule + + + + + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.geometry.mapping.rst b/docs/source/_get_started/_autosummary/ipsuite.geometry.mapping.rst new file mode 100644 index 00000000..6899cfd7 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.geometry.mapping.rst @@ -0,0 +1,29 @@ +ipsuite.geometry.mapping +======================== + +.. automodule:: ipsuite.geometry.mapping + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + BarycenterMapping + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.geometry.rst b/docs/source/_get_started/_autosummary/ipsuite.geometry.rst new file mode 100644 index 00000000..2f89a858 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.geometry.rst @@ -0,0 +1,34 @@ +ipsuite.geometry +================ + +.. automodule:: ipsuite.geometry + + + + + + + + + + + + + + + + + + + +.. rubric:: Modules + +.. autosummary:: + :toctree: + :recursive: + + ipsuite.geometry.barycenter_coarse_grain + ipsuite.geometry.graphs + ipsuite.geometry.mapping + ipsuite.geometry.unwrap + diff --git a/docs/source/_get_started/_autosummary/ipsuite.geometry.unwrap.rst b/docs/source/_get_started/_autosummary/ipsuite.geometry.unwrap.rst new file mode 100644 index 00000000..2a4d6a60 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.geometry.unwrap.rst @@ -0,0 +1,33 @@ +ipsuite.geometry.unwrap +======================= + +.. automodule:: ipsuite.geometry.unwrap + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + closest_atom_to_center + displace_neighbors + sort_atomic_edges + unwrap + unwrap_system + + + + + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.apax.rst b/docs/source/_get_started/_autosummary/ipsuite.models.apax.rst new file mode 100644 index 00000000..ad68ba81 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.models.apax.rst @@ -0,0 +1,31 @@ +ipsuite.models.apax +=================== + +.. automodule:: ipsuite.models.apax + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + Apax + ApaxEnsemble + BatchKernelSelection + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.base.rst b/docs/source/_get_started/_autosummary/ipsuite.models.base.rst new file mode 100644 index 00000000..453bea26 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.models.base.rst @@ -0,0 +1,29 @@ +ipsuite.models.base +=================== + +.. automodule:: ipsuite.models.base + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + MLModel + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.ensemble.rst b/docs/source/_get_started/_autosummary/ipsuite.models.ensemble.rst new file mode 100644 index 00000000..3c0353c6 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.models.ensemble.rst @@ -0,0 +1,30 @@ +ipsuite.models.ensemble +======================= + +.. automodule:: ipsuite.models.ensemble + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + EnsembleCalculator + EnsembleModel + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.gap.rst b/docs/source/_get_started/_autosummary/ipsuite.models.gap.rst new file mode 100644 index 00000000..6b63bdc0 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.models.gap.rst @@ -0,0 +1,35 @@ +ipsuite.models.gap +================== + +.. automodule:: ipsuite.models.gap + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + DistanceNb + DistanceNbConverter + GAP + GapParameter + GapParameterConverter + SOAP + SOAPConverter + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.mace_model.rst b/docs/source/_get_started/_autosummary/ipsuite.models.mace_model.rst new file mode 100644 index 00000000..55cb0fe0 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.models.mace_model.rst @@ -0,0 +1,35 @@ +ipsuite.models.mace\_model +========================== + +.. automodule:: ipsuite.models.mace_model + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + execute + + + + + + .. rubric:: Classes + + .. autosummary:: + + MACE + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.nequip.rst b/docs/source/_get_started/_autosummary/ipsuite.models.nequip.rst new file mode 100644 index 00000000..bf109ce4 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.models.nequip.rst @@ -0,0 +1,29 @@ +ipsuite.models.nequip +===================== + +.. automodule:: ipsuite.models.nequip + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + Nequip + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.rst b/docs/source/_get_started/_autosummary/ipsuite.models.rst new file mode 100644 index 00000000..fba24c87 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.models.rst @@ -0,0 +1,36 @@ +ipsuite.models +============== + +.. automodule:: ipsuite.models + + + + + + + + + + + + + + + + + + + +.. rubric:: Modules + +.. autosummary:: + :toctree: + :recursive: + + ipsuite.models.apax + ipsuite.models.base + ipsuite.models.ensemble + ipsuite.models.gap + ipsuite.models.mace_model + ipsuite.models.nequip + diff --git a/docs/source/_get_started/_autosummary/ipsuite.nodes.rst b/docs/source/_get_started/_autosummary/ipsuite.nodes.rst new file mode 100644 index 00000000..5567e1c6 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.nodes.rst @@ -0,0 +1,23 @@ +ipsuite.nodes +============= + +.. automodule:: ipsuite.nodes + + + + + + + + + + + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.project.rst b/docs/source/_get_started/_autosummary/ipsuite.project.rst new file mode 100644 index 00000000..866148a5 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.project.rst @@ -0,0 +1,29 @@ +ipsuite.project +=============== + +.. automodule:: ipsuite.project + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + Project + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.rst b/docs/source/_get_started/_autosummary/ipsuite.rst new file mode 100644 index 00000000..2742a4d5 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.rst @@ -0,0 +1,45 @@ +ipsuite +======= + +.. automodule:: ipsuite + + + + + + + + + + + + + + + + + + + +.. rubric:: Modules + +.. autosummary:: + :toctree: + :recursive: + + ipsuite.analysis + ipsuite.base + ipsuite.bootstrap + ipsuite.calculators + ipsuite.configuration_comparison + ipsuite.configuration_generation + ipsuite.configuration_selection + ipsuite.data_loading + ipsuite.fields + ipsuite.geometry + ipsuite.models + ipsuite.nodes + ipsuite.project + ipsuite.static_data + ipsuite.utils + diff --git a/docs/source/_get_started/_autosummary/ipsuite.static_data.rst b/docs/source/_get_started/_autosummary/ipsuite.static_data.rst new file mode 100644 index 00000000..3ade5a4e --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.static_data.rst @@ -0,0 +1,23 @@ +ipsuite.static\_data +==================== + +.. automodule:: ipsuite.static_data + + + + + + + + + + + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.ase_sim.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.ase_sim.rst new file mode 100644 index 00000000..78b55805 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.ase_sim.rst @@ -0,0 +1,33 @@ +ipsuite.utils.ase\_sim +====================== + +.. automodule:: ipsuite.utils.ase_sim + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + freeze_copy_atoms + get_box_from_density + get_density_from_atoms + get_desc + get_energy + + + + + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.combine.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.combine.rst new file mode 100644 index 00000000..d7af5d2d --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.combine.rst @@ -0,0 +1,36 @@ +ipsuite.utils.combine +===================== + +.. automodule:: ipsuite.utils.combine + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + get_flat_data_from_dict + get_ids_per_key + + + + + + .. rubric:: Classes + + .. autosummary:: + + ExcludeIds + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.docs.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.docs.rst new file mode 100644 index 00000000..f0870ce3 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.docs.rst @@ -0,0 +1,29 @@ +ipsuite.utils.docs +================== + +.. automodule:: ipsuite.utils.docs + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + create_dvc_git_env_for_doctest + + + + + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.helpers.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.helpers.rst new file mode 100644 index 00000000..a2c70721 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.helpers.rst @@ -0,0 +1,31 @@ +ipsuite.utils.helpers +===================== + +.. automodule:: ipsuite.utils.helpers + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + check_duplicate_keys + get_deps_if_node + setup_ase + + + + + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.logs.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.logs.rst new file mode 100644 index 00000000..0a1e779d --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.logs.rst @@ -0,0 +1,29 @@ +ipsuite.utils.logs +================== + +.. automodule:: ipsuite.utils.logs + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + setup_logging + + + + + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.md.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.md.rst new file mode 100644 index 00000000..fbecdaa7 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.md.rst @@ -0,0 +1,29 @@ +ipsuite.utils.md +================ + +.. automodule:: ipsuite.utils.md + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + get_energy_terms + + + + + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.metrics.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.metrics.rst new file mode 100644 index 00000000..cf0e86b8 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.metrics.rst @@ -0,0 +1,37 @@ +ipsuite.utils.metrics +===================== + +.. automodule:: ipsuite.utils.metrics + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + calculate_l_p_norm + get_angles + get_full_metrics + get_u_vecs + maximum_error + mean_absolute_error + mean_squared_error + relative_rmse + root_mean_squared_error + + + + + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.rst new file mode 100644 index 00000000..0d9f5898 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.rst @@ -0,0 +1,37 @@ +ipsuite.utils +============= + +.. automodule:: ipsuite.utils + + + + + + + + + + + + + + + + + + + +.. rubric:: Modules + +.. autosummary:: + :toctree: + :recursive: + + ipsuite.utils.ase_sim + ipsuite.utils.combine + ipsuite.utils.docs + ipsuite.utils.helpers + ipsuite.utils.logs + ipsuite.utils.md + ipsuite.utils.metrics + diff --git a/docs/source/_get_started/nodes_list.rst b/docs/source/_get_started/nodes_list.rst new file mode 100644 index 00000000..56ee56ce --- /dev/null +++ b/docs/source/_get_started/nodes_list.rst @@ -0,0 +1,14 @@ +List of IPSuite Nodes +===================== + + + +.. autosummary:: + :toctree: _autosummary + :recursive: + + ipsuite.models + ipsuite.calculators + ipsuite.configuration_generation + ipsuite.configuration_comparison + diff --git a/docs/source/conf.py b/docs/source/conf.py index 53f30f9d..3b158f3f 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -25,8 +25,10 @@ "sphinx.ext.doctest", "sphinx_copybutton", "sphinx.ext.viewcode", + "sphinx.ext.autosummary", ] +autosummary_generate = True templates_path = ["_templates"] exclude_patterns = [] diff --git a/docs/source/index.rst b/docs/source/index.rst index 76bb3bf8..b5e3f479 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -16,8 +16,9 @@ Welcome to IPSuite's documentation! What is IPS? <_get_started/ips> Getting Started <_get_started/quickstart> - IPSuite <_nodes/ipsuite> - Modules <_nodes/modlules> + IPSuite <_nodes/modules> + Nodes List <_get_started/nodes_list> + Modules <_nodes/modules> Indices and tables From 7acaf02c1168a4bb9b917db6a62545191a9c8f6e Mon Sep 17 00:00:00 2001 From: Julian Peters Date: Thu, 18 Apr 2024 13:58:07 +0200 Subject: [PATCH 22/35] fix some things with the nodes list --- .../_autosummary/ipsuite.calculators.rst | 2 +- .../ipsuite.calculators.torch_d3.rst | 30 +++++++++++++++++++ .../ipsuite.configuration_comparison.rst | 2 +- .../ipsuite.configuration_generation.rst | 2 +- .../_autosummary/ipsuite.models.rst | 2 +- docs/source/_get_started/nodes_list.rst | 13 ++++++-- docs/source/index.rst | 1 - 7 files changed, 45 insertions(+), 7 deletions(-) create mode 100644 docs/source/_get_started/_autosummary/ipsuite.calculators.torch_d3.rst diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.rst index 8ee3eeb8..b18df547 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.rst @@ -1,4 +1,4 @@ -ipsuite.calculators +ipsuite.calculators =================== .. automodule:: ipsuite.calculators diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.torch_d3.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.torch_d3.rst new file mode 100644 index 00000000..7b1c0676 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.torch_d3.rst @@ -0,0 +1,30 @@ +ipsuite.calculators.torch\_d3 +============================= + +.. automodule:: ipsuite.calculators.torch_d3 + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + TorchD3 + TorchDFTD3CalculatorNL + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.rst index 8c33e3a6..4e63f973 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.rst @@ -1,4 +1,4 @@ -ipsuite.configuration\_comparison +ipsuite.configuration\_comparison ================================= .. automodule:: ipsuite.configuration_comparison diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.rst index 335cca0f..33089bee 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.rst @@ -1,4 +1,4 @@ -ipsuite.configuration\_generation +ipsuite.configuration\_generation ================================= .. automodule:: ipsuite.configuration_generation diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.rst b/docs/source/_get_started/_autosummary/ipsuite.models.rst index fba24c87..6b52f726 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.models.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.models.rst @@ -1,4 +1,4 @@ -ipsuite.models +ipsuite.models ============== .. automodule:: ipsuite.models diff --git a/docs/source/_get_started/nodes_list.rst b/docs/source/_get_started/nodes_list.rst index 56ee56ce..3015f55e 100644 --- a/docs/source/_get_started/nodes_list.rst +++ b/docs/source/_get_started/nodes_list.rst @@ -7,8 +7,17 @@ List of IPSuite Nodes :toctree: _autosummary :recursive: - ipsuite.models + ipsuite.analysis + ipsuite.base + ipsuite.bootstrap ipsuite.calculators ipsuite.configuration_generation + ipsuite.configuration_selection ipsuite.configuration_comparison - + ipsuite.data_loading + ipsuite.fields + ipsuite.geometry + ipsuite.models + ipsuite.project + ipsuite.static_data + ipsuite.utils \ No newline at end of file diff --git a/docs/source/index.rst b/docs/source/index.rst index b5e3f479..e0581908 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -16,7 +16,6 @@ Welcome to IPSuite's documentation! What is IPS? <_get_started/ips> Getting Started <_get_started/quickstart> - IPSuite <_nodes/modules> Nodes List <_get_started/nodes_list> Modules <_nodes/modules> From 2811b4ff66d45ea5667f8bba8942eb007954bcd9 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 18 Apr 2024 12:00:10 +0000 Subject: [PATCH 23/35] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- .../ipsuite.analysis.bin_property.rst | 25 +++++++--------- .../ipsuite.analysis.bond_stretch.rst | 25 +++++++--------- .../ipsuite.analysis.ensemble.rst | 29 +++++++++---------- .../_autosummary/ipsuite.analysis.md.rst | 25 +++++++--------- .../ipsuite.analysis.model.dynamics.rst | 29 +++++++++---------- ...ipsuite.analysis.model.dynamics_checks.rst | 25 +++++++--------- .../ipsuite.analysis.model.math.rst | 25 +++++++--------- .../ipsuite.analysis.model.plots.rst | 25 +++++++--------- .../ipsuite.analysis.model.predict.rst | 25 +++++++--------- .../_autosummary/ipsuite.analysis.model.rst | 25 ++++++++-------- .../_autosummary/ipsuite.analysis.rst | 25 ++++++++-------- .../ipsuite.analysis.sensitivity.rst | 29 +++++++++---------- .../_autosummary/ipsuite.base.base.rst | 25 +++++++--------- .../_autosummary/ipsuite.base.protocol.rst | 25 +++++++--------- .../_autosummary/ipsuite.base.rst | 25 ++++++++-------- ...ipsuite.bootstrap.random_displacements.rst | 25 +++++++--------- .../_autosummary/ipsuite.bootstrap.rst | 25 ++++++++-------- .../ipsuite.bootstrap.surface_mods.rst | 29 +++++++++---------- .../ipsuite.calculators.apax_jax_md.rst | 25 +++++++--------- .../ipsuite.calculators.ase_geoopt.rst | 25 +++++++--------- .../ipsuite.calculators.ase_md.rst | 29 +++++++++---------- .../ipsuite.calculators.ase_standard.rst | 25 +++++++--------- .../_autosummary/ipsuite.calculators.cp2k.rst | 25 +++++++--------- .../ipsuite.calculators.lammps.rst | 25 +++++++--------- .../_autosummary/ipsuite.calculators.mix.rst | 25 +++++++--------- .../_autosummary/ipsuite.calculators.orca.rst | 25 +++++++--------- .../_autosummary/ipsuite.calculators.rst | 25 ++++++++-------- .../ipsuite.calculators.torch_d3.rst | 25 +++++++--------- .../_autosummary/ipsuite.calculators.xtb.rst | 25 +++++++--------- ...uite.configuration_comparison.MMKernel.rst | 20 ++++++------- ...suite.configuration_comparison.REMatch.rst | 20 ++++++------- .../ipsuite.configuration_comparison.base.rst | 29 +++++++++---------- .../ipsuite.configuration_comparison.rst | 25 ++++++++-------- ...suite.configuration_generation.packmol.rst | 25 +++++++--------- .../ipsuite.configuration_generation.rst | 25 ++++++++-------- ...nfiguration_generation.smiles_to_atoms.rst | 25 +++++++--------- .../ipsuite.configuration_selection.base.rst | 25 +++++++--------- ...ipsuite.configuration_selection.filter.rst | 25 +++++++--------- .../ipsuite.configuration_selection.index.rst | 25 +++++++--------- ...ipsuite.configuration_selection.kernel.rst | 25 +++++++--------- ...ipsuite.configuration_selection.random.rst | 25 +++++++--------- .../ipsuite.configuration_selection.rst | 25 ++++++++-------- .../ipsuite.configuration_selection.split.rst | 25 +++++++--------- ...uite.configuration_selection.threshold.rst | 29 +++++++++---------- ...configuration_selection.uniform_arange.rst | 25 +++++++--------- ...figuration_selection.uniform_energetic.rst | 25 +++++++--------- ...nfiguration_selection.uniform_temporal.rst | 25 +++++++--------- .../ipsuite.data_loading.add_data_ase.rst | 29 +++++++++---------- .../ipsuite.data_loading.add_data_h5md.rst | 25 +++++++--------- .../_autosummary/ipsuite.data_loading.rst | 25 ++++++++-------- .../_autosummary/ipsuite.fields.atoms.rst | 25 +++++++--------- .../_autosummary/ipsuite.fields.rst | 25 ++++++++-------- ...suite.geometry.barycenter_coarse_grain.rst | 25 +++++++--------- .../_autosummary/ipsuite.geometry.graphs.rst | 25 +++++++--------- .../_autosummary/ipsuite.geometry.mapping.rst | 25 +++++++--------- .../_autosummary/ipsuite.geometry.rst | 25 ++++++++-------- .../_autosummary/ipsuite.geometry.unwrap.rst | 25 +++++++--------- .../_autosummary/ipsuite.models.apax.rst | 25 +++++++--------- .../_autosummary/ipsuite.models.base.rst | 25 +++++++--------- .../_autosummary/ipsuite.models.ensemble.rst | 25 +++++++--------- .../_autosummary/ipsuite.models.gap.rst | 25 +++++++--------- .../ipsuite.models.mace_model.rst | 29 +++++++++---------- .../_autosummary/ipsuite.models.nequip.rst | 25 +++++++--------- .../_autosummary/ipsuite.models.rst | 25 ++++++++-------- .../_autosummary/ipsuite.nodes.rst | 21 ++++++-------- .../_autosummary/ipsuite.project.rst | 25 +++++++--------- .../_get_started/_autosummary/ipsuite.rst | 25 ++++++++-------- .../_autosummary/ipsuite.static_data.rst | 21 ++++++-------- .../_autosummary/ipsuite.utils.ase_sim.rst | 25 +++++++--------- .../_autosummary/ipsuite.utils.combine.rst | 29 +++++++++---------- .../_autosummary/ipsuite.utils.docs.rst | 25 +++++++--------- .../_autosummary/ipsuite.utils.helpers.rst | 25 +++++++--------- .../_autosummary/ipsuite.utils.logs.rst | 25 +++++++--------- .../_autosummary/ipsuite.utils.md.rst | 25 +++++++--------- .../_autosummary/ipsuite.utils.metrics.rst | 25 +++++++--------- .../_autosummary/ipsuite.utils.rst | 25 ++++++++-------- docs/source/_get_started/nodes_list.rst | 2 +- 77 files changed, 865 insertions(+), 1059 deletions(-) diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.bin_property.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.bin_property.rst index 58a0eb6c..436d70e3 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.bin_property.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.bin_property.rst @@ -3,20 +3,20 @@ ipsuite.analysis.bin\_property .. automodule:: ipsuite.analysis.bin_property - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + DipoleHistogram EnergyHistogram EnergyUncertaintyHistogram @@ -24,12 +24,9 @@ ipsuite.analysis.bin\_property ForcesUncertaintyHistogram LabelHistogram StressHistogram - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.bond_stretch.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.bond_stretch.rst index aeb1ce96..6356a14f 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.bond_stretch.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.bond_stretch.rst @@ -3,27 +3,24 @@ ipsuite.analysis.bond\_stretch .. automodule:: ipsuite.analysis.bond_stretch - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + BondStretchAnalyses - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.ensemble.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.ensemble.rst index d8779e0c..8e4f4d53 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.ensemble.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.ensemble.rst @@ -3,33 +3,30 @@ ipsuite.analysis.ensemble .. automodule:: ipsuite.analysis.ensemble - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + plot_with_uncertainty - - - - + + + + .. rubric:: Classes .. autosummary:: - + ModelEnsembleAnalysis - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.md.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.md.rst index d85c609d..7d541465 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.md.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.md.rst @@ -3,27 +3,24 @@ ipsuite.analysis.md .. automodule:: ipsuite.analysis.md - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + AnalyseDensity - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics.rst index 2619720a..2d17f1ed 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics.rst @@ -3,36 +3,33 @@ ipsuite.analysis.model.dynamics .. automodule:: ipsuite.analysis.model.dynamics - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + run_stability_nve - - - - + + + + .. rubric:: Classes .. autosummary:: - + BoxHeatUp BoxScale MDStability RattleAnalysis - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics_checks.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics_checks.rst index 2875ab96..8c4a6de5 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics_checks.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics_checks.rst @@ -3,31 +3,28 @@ ipsuite.analysis.model.dynamics\_checks .. automodule:: ipsuite.analysis.model.dynamics_checks - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + ConnectivityCheck EnergySpikeCheck NaNCheck TemperatureCheck ThresholdCheck - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.math.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.math.rst index 38988dc1..52582ced 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.math.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.math.rst @@ -3,31 +3,28 @@ ipsuite.analysis.model.math .. automodule:: ipsuite.analysis.model.math - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + compute_intertia_tensor compute_rot_forces compute_trans_forces decompose_stress_tensor force_decomposition - - - - - - - - + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.plots.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.plots.rst index 05f858c5..9812305b 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.plots.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.plots.rst @@ -3,30 +3,27 @@ ipsuite.analysis.model.plots .. automodule:: ipsuite.analysis.model.plots - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + density_scatter get_figure get_hist get_histogram_figure - - - - - - - - + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.predict.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.predict.rst index 7666b23b..6bd20ed8 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.predict.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.predict.rst @@ -3,30 +3,27 @@ ipsuite.analysis.model.predict .. automodule:: ipsuite.analysis.model.predict - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + ForceAngles ForceDecomposition Prediction PredictionMetrics - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.rst index 9a176f60..8ee20ffd 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.rst @@ -3,21 +3,21 @@ ipsuite.analysis.model .. automodule:: ipsuite.analysis.model - - - - - - - - - - - - + + + + + + + + + + + + @@ -32,4 +32,3 @@ ipsuite.analysis.model ipsuite.analysis.model.math ipsuite.analysis.model.plots ipsuite.analysis.model.predict - diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.rst index 92f626ea..a5391f18 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.rst @@ -3,21 +3,21 @@ ipsuite.analysis .. automodule:: ipsuite.analysis - - - - - - - - - - - - + + + + + + + + + + + + @@ -33,4 +33,3 @@ ipsuite.analysis ipsuite.analysis.md ipsuite.analysis.model ipsuite.analysis.sensitivity - diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.sensitivity.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.sensitivity.rst index 8db8495d..1d5f221e 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.sensitivity.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.sensitivity.rst @@ -3,36 +3,33 @@ ipsuite.analysis.sensitivity .. automodule:: ipsuite.analysis.sensitivity - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + nonuniform_imshow - - - - + + + + .. rubric:: Classes .. autosummary:: - + AnalyseGlobalForceSensitivity AnalyseSingleForceSensitivity IsConstraintMD MoveSingleParticle - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.base.base.rst b/docs/source/_get_started/_autosummary/ipsuite.base.base.rst index ed4f51bb..4c83c56f 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.base.base.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.base.base.rst @@ -3,20 +3,20 @@ ipsuite.base.base .. automodule:: ipsuite.base.base - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + AnalyseAtoms AnalyseProcessAtoms CheckBase @@ -24,12 +24,9 @@ ipsuite.base.base Mapping ProcessAtoms ProcessSingleAtom - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.base.protocol.rst b/docs/source/_get_started/_autosummary/ipsuite.base.protocol.rst index 446e1299..56da7eda 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.base.protocol.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.base.protocol.rst @@ -3,29 +3,26 @@ ipsuite.base.protocol .. automodule:: ipsuite.base.protocol - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + HasAtoms HasSelectedConfigurations ProcessAtoms - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.base.rst b/docs/source/_get_started/_autosummary/ipsuite.base.rst index 6f3c0705..5e3b57a8 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.base.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.base.rst @@ -3,21 +3,21 @@ ipsuite.base .. automodule:: ipsuite.base - - - - - - - - - - - - + + + + + + + + + + + + @@ -29,4 +29,3 @@ ipsuite.base ipsuite.base.base ipsuite.base.protocol - diff --git a/docs/source/_get_started/_autosummary/ipsuite.bootstrap.random_displacements.rst b/docs/source/_get_started/_autosummary/ipsuite.bootstrap.random_displacements.rst index 8df9d95e..64c7512e 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.bootstrap.random_displacements.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.bootstrap.random_displacements.rst @@ -3,30 +3,27 @@ ipsuite.bootstrap.random\_displacements .. automodule:: ipsuite.bootstrap.random_displacements - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + Bootstrap RattleAtoms RotateMolecules TranslateMolecules - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.bootstrap.rst b/docs/source/_get_started/_autosummary/ipsuite.bootstrap.rst index 54528569..e00900b9 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.bootstrap.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.bootstrap.rst @@ -3,21 +3,21 @@ ipsuite.bootstrap .. automodule:: ipsuite.bootstrap - - - - - - - - - - - - + + + + + + + + + + + + @@ -29,4 +29,3 @@ ipsuite.bootstrap ipsuite.bootstrap.random_displacements ipsuite.bootstrap.surface_mods - diff --git a/docs/source/_get_started/_autosummary/ipsuite.bootstrap.surface_mods.rst b/docs/source/_get_started/_autosummary/ipsuite.bootstrap.surface_mods.rst index 9651fc49..cc1cbdc4 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.bootstrap.surface_mods.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.bootstrap.surface_mods.rst @@ -3,34 +3,31 @@ ipsuite.bootstrap.surface\_mods .. automodule:: ipsuite.bootstrap.surface_mods - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + plot_ture_vs_pred - - - - + + + + .. rubric:: Classes .. autosummary:: - + SurfaceRasterMetrics SurfaceRasterScan - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.apax_jax_md.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.apax_jax_md.rst index fc22c9c9..14a15959 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.apax_jax_md.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.apax_jax_md.rst @@ -3,27 +3,24 @@ ipsuite.calculators.apax\_jax\_md .. automodule:: ipsuite.calculators.apax_jax_md - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + ApaxJaxMD - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_geoopt.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_geoopt.rst index a33a8dc7..db5899ff 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_geoopt.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_geoopt.rst @@ -3,28 +3,25 @@ ipsuite.calculators.ase\_geoopt .. automodule:: ipsuite.calculators.ase_geoopt - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + ASEGeoOpt BatchASEGeoOpt - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_md.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_md.rst index 60984016..b154fc0e 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_md.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_md.rst @@ -3,27 +3,27 @@ ipsuite.calculators.ase\_md .. automodule:: ipsuite.calculators.ase_md - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + get_desc update_metrics_dict - - - - + + + + .. rubric:: Classes .. autosummary:: - + ASEMD BoxOscillatingRampModifier FixedLayerConstraint @@ -34,12 +34,9 @@ ipsuite.calculators.ase\_md RescaleBoxModifier TemperatureOscillatingRampModifier TemperatureRampModifier - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_standard.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_standard.rst index 82bd7ee7..25fe8744 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_standard.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_standard.rst @@ -3,29 +3,26 @@ ipsuite.calculators.ase\_standard .. automodule:: ipsuite.calculators.ase_standard - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + EMTCalculator EMTSinglePoint LJSinglePoint - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.cp2k.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.cp2k.rst index 0318deb3..60df164f 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.cp2k.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.cp2k.rst @@ -3,28 +3,25 @@ ipsuite.calculators.cp2k .. automodule:: ipsuite.calculators.cp2k - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + CP2KSinglePoint CP2KYaml - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.lammps.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.lammps.rst index c7f44d55..457d7499 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.lammps.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.lammps.rst @@ -3,27 +3,24 @@ ipsuite.calculators.lammps .. automodule:: ipsuite.calculators.lammps - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + LammpsSimulator - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.mix.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.mix.rst index 8a7c8d11..321d810b 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.mix.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.mix.rst @@ -3,28 +3,25 @@ ipsuite.calculators.mix .. automodule:: ipsuite.calculators.mix - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + CalculatorNode MixCalculator - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.orca.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.orca.rst index d37ccfa4..273def1d 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.orca.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.orca.rst @@ -3,27 +3,24 @@ ipsuite.calculators.orca .. automodule:: ipsuite.calculators.orca - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + OrcaSinglePoint - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.rst index b18df547..3e90e425 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.rst @@ -3,21 +3,21 @@ .. automodule:: ipsuite.calculators - - - - - - - - - - - - + + + + + + + + + + + + @@ -37,4 +37,3 @@ ipsuite.calculators.orca ipsuite.calculators.torch_d3 ipsuite.calculators.xtb - diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.torch_d3.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.torch_d3.rst index 7b1c0676..32352e84 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.torch_d3.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.torch_d3.rst @@ -3,28 +3,25 @@ .. automodule:: ipsuite.calculators.torch_d3 - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + TorchD3 TorchDFTD3CalculatorNL - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.xtb.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.xtb.rst index 4101c618..8c4efcd8 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.xtb.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.xtb.rst @@ -3,27 +3,24 @@ ipsuite.calculators.xtb .. automodule:: ipsuite.calculators.xtb - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + xTBSinglePoint - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.MMKernel.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.MMKernel.rst index 00b16e08..2ce1784c 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.MMKernel.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.MMKernel.rst @@ -5,14 +5,14 @@ ipsuite.configuration\_comparison.MMKernel .. autoclass:: MMKernel - + .. automethod:: __init__ - + .. rubric:: Methods .. autosummary:: - + ~MMKernel.__init__ ~MMKernel.compare ~MMKernel.convert_notebook @@ -22,15 +22,15 @@ ipsuite.configuration\_comparison.MMKernel ~MMKernel.save ~MMKernel.save_representation ~MMKernel.unlink_database - - - - + + + + .. rubric:: Attributes .. autosummary:: - + ~MMKernel.analyte ~MMKernel.init_descriptors ~MMKernel.init_subclass_basecls @@ -45,5 +45,5 @@ ipsuite.configuration\_comparison.MMKernel ~MMKernel.use_jit ~MMKernel.use_repr ~MMKernel.uuid - - \ No newline at end of file + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.REMatch.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.REMatch.rst index f8e961b0..d118569a 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.REMatch.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.REMatch.rst @@ -5,14 +5,14 @@ ipsuite.configuration\_comparison.REMatch .. autoclass:: REMatch - + .. automethod:: __init__ - + .. rubric:: Methods .. autosummary:: - + ~REMatch.__init__ ~REMatch.compare ~REMatch.convert_notebook @@ -22,15 +22,15 @@ ipsuite.configuration\_comparison.REMatch ~REMatch.save ~REMatch.save_representation ~REMatch.unlink_database - - - - + + + + .. rubric:: Attributes .. autosummary:: - + ~REMatch.alpha ~REMatch.analyte ~REMatch.init_descriptors @@ -48,5 +48,5 @@ ipsuite.configuration\_comparison.REMatch ~REMatch.use_jit ~REMatch.use_repr ~REMatch.uuid - - \ No newline at end of file + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.base.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.base.rst index 5598308b..c592fbe7 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.base.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.base.rst @@ -3,37 +3,34 @@ ipsuite.configuration\_comparison.base .. automodule:: ipsuite.configuration_comparison.base - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + convert_to_df create_dataset write_dataset - - - - + + + + .. rubric:: Classes .. autosummary:: - + ConfigurationComparison SOAPParameter SOAPParameterConverter - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.rst index 4e63f973..e3defe7d 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.rst @@ -3,21 +3,21 @@ .. automodule:: ipsuite.configuration_comparison - - - - - - - - - - - - + + + + + + + + + + + + @@ -30,4 +30,3 @@ ipsuite.configuration_comparison.MMKernel ipsuite.configuration_comparison.REMatch ipsuite.configuration_comparison.base - diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.packmol.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.packmol.rst index 561e5315..bb1d1e9c 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.packmol.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.packmol.rst @@ -3,28 +3,25 @@ ipsuite.configuration\_generation.packmol .. automodule:: ipsuite.configuration_generation.packmol - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + MultiPackmol Packmol - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.rst index 33089bee..7f6b21b7 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.rst @@ -3,21 +3,21 @@ .. automodule:: ipsuite.configuration_generation - - - - - - - - - - - - + + + + + + + + + + + + @@ -29,4 +29,3 @@ ipsuite.configuration_generation.packmol ipsuite.configuration_generation.smiles_to_atoms - diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.smiles_to_atoms.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.smiles_to_atoms.rst index 8795be00..9189801c 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.smiles_to_atoms.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.smiles_to_atoms.rst @@ -3,28 +3,25 @@ ipsuite.configuration\_generation.smiles\_to\_atoms .. automodule:: ipsuite.configuration_generation.smiles_to_atoms - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + SmilesToAtoms SmilesToConformers - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.base.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.base.rst index ad9d34a8..4148b404 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.base.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.base.rst @@ -3,28 +3,25 @@ ipsuite.configuration\_selection.base .. automodule:: ipsuite.configuration_selection.base - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + BatchConfigurationSelection ConfigurationSelection - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.filter.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.filter.rst index 84e5db76..2d8cd6be 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.filter.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.filter.rst @@ -3,27 +3,24 @@ ipsuite.configuration\_selection.filter .. automodule:: ipsuite.configuration_selection.filter - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + FilterOutlier - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.index.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.index.rst index e24a4947..e16a9186 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.index.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.index.rst @@ -3,27 +3,24 @@ ipsuite.configuration\_selection.index .. automodule:: ipsuite.configuration_selection.index - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + IndexSelection - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.kernel.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.kernel.rst index 95ddf8b5..cbe90c5e 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.kernel.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.kernel.rst @@ -3,27 +3,24 @@ ipsuite.configuration\_selection.kernel .. automodule:: ipsuite.configuration_selection.kernel - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + KernelSelection - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.random.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.random.rst index a0a278b2..e96f02fb 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.random.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.random.rst @@ -3,27 +3,24 @@ ipsuite.configuration\_selection.random .. automodule:: ipsuite.configuration_selection.random - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + RandomSelection - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.rst index 030e6a6c..1ea9b2ff 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.rst @@ -3,21 +3,21 @@ ipsuite.configuration\_selection .. automodule:: ipsuite.configuration_selection - - - - - - - - - - - - + + + + + + + + + + + + @@ -37,4 +37,3 @@ ipsuite.configuration\_selection ipsuite.configuration_selection.uniform_arange ipsuite.configuration_selection.uniform_energetic ipsuite.configuration_selection.uniform_temporal - diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.split.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.split.rst index b67b2254..23cf82ec 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.split.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.split.rst @@ -3,27 +3,24 @@ ipsuite.configuration\_selection.split .. automodule:: ipsuite.configuration_selection.split - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + SplitSelection - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.threshold.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.threshold.rst index 2ba751a2..ca606bb6 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.threshold.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.threshold.rst @@ -3,35 +3,32 @@ ipsuite.configuration\_selection.threshold .. automodule:: ipsuite.configuration_selection.threshold - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + check_dimension max_reduction mean_reduction - - - - + + + + .. rubric:: Classes .. autosummary:: - + ThresholdSelection - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_arange.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_arange.rst index eb45287c..c25038bd 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_arange.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_arange.rst @@ -3,27 +3,24 @@ ipsuite.configuration\_selection.uniform\_arange .. automodule:: ipsuite.configuration_selection.uniform_arange - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + UniformArangeSelection - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_energetic.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_energetic.rst index d41e2d2e..bb7f33ad 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_energetic.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_energetic.rst @@ -3,27 +3,24 @@ ipsuite.configuration\_selection.uniform\_energetic .. automodule:: ipsuite.configuration_selection.uniform_energetic - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + UniformEnergeticSelection - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_temporal.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_temporal.rst index 4833a013..227f6c93 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_temporal.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_temporal.rst @@ -3,27 +3,24 @@ ipsuite.configuration\_selection.uniform\_temporal .. automodule:: ipsuite.configuration_selection.uniform_temporal - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + UniformTemporalSelection - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_ase.rst b/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_ase.rst index eb4384c7..20e3c9f8 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_ase.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_ase.rst @@ -3,34 +3,31 @@ ipsuite.data\_loading.add\_data\_ase .. automodule:: ipsuite.data_loading.add_data_ase - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + load_data - - - - + + + + .. rubric:: Classes .. autosummary:: - + AddData ReadData - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_h5md.rst b/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_h5md.rst index 5dad0ffc..aeea8f87 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_h5md.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_h5md.rst @@ -3,27 +3,24 @@ ipsuite.data\_loading.add\_data\_h5md .. automodule:: ipsuite.data_loading.add_data_h5md - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + AddDataH5MD - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.data_loading.rst b/docs/source/_get_started/_autosummary/ipsuite.data_loading.rst index dee0fd07..bb6cd5a5 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.data_loading.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.data_loading.rst @@ -3,21 +3,21 @@ ipsuite.data\_loading .. automodule:: ipsuite.data_loading - - - - - - - - - - - - + + + + + + + + + + + + @@ -29,4 +29,3 @@ ipsuite.data\_loading ipsuite.data_loading.add_data_ase ipsuite.data_loading.add_data_h5md - diff --git a/docs/source/_get_started/_autosummary/ipsuite.fields.atoms.rst b/docs/source/_get_started/_autosummary/ipsuite.fields.atoms.rst index 3c4e1d82..d32ba900 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.fields.atoms.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.fields.atoms.rst @@ -3,27 +3,24 @@ ipsuite.fields.atoms .. automodule:: ipsuite.fields.atoms - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + Atoms - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.fields.rst b/docs/source/_get_started/_autosummary/ipsuite.fields.rst index 13d024e7..7b82b0b5 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.fields.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.fields.rst @@ -3,21 +3,21 @@ ipsuite.fields .. automodule:: ipsuite.fields - - - - - - - - - - - - + + + + + + + + + + + + @@ -28,4 +28,3 @@ ipsuite.fields :recursive: ipsuite.fields.atoms - diff --git a/docs/source/_get_started/_autosummary/ipsuite.geometry.barycenter_coarse_grain.rst b/docs/source/_get_started/_autosummary/ipsuite.geometry.barycenter_coarse_grain.rst index f59fe34f..f18a946b 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.geometry.barycenter_coarse_grain.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.geometry.barycenter_coarse_grain.rst @@ -3,28 +3,25 @@ ipsuite.geometry.barycenter\_coarse\_grain .. automodule:: ipsuite.geometry.barycenter_coarse_grain - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + barycenter_backmapping coarse_grain_to_barycenter - - - - - - - - + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.geometry.graphs.rst b/docs/source/_get_started/_autosummary/ipsuite.geometry.graphs.rst index 0c08f233..71c943a0 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.geometry.graphs.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.geometry.graphs.rst @@ -3,30 +3,27 @@ ipsuite.geometry.graphs .. automodule:: ipsuite.geometry.graphs - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + atoms_to_graph edges_from_atoms identify_molecules split_molecule - - - - - - - - + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.geometry.mapping.rst b/docs/source/_get_started/_autosummary/ipsuite.geometry.mapping.rst index 6899cfd7..25f9bdbd 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.geometry.mapping.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.geometry.mapping.rst @@ -3,27 +3,24 @@ ipsuite.geometry.mapping .. automodule:: ipsuite.geometry.mapping - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + BarycenterMapping - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.geometry.rst b/docs/source/_get_started/_autosummary/ipsuite.geometry.rst index 2f89a858..60b2e508 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.geometry.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.geometry.rst @@ -3,21 +3,21 @@ ipsuite.geometry .. automodule:: ipsuite.geometry - - - - - - - - - - - - + + + + + + + + + + + + @@ -31,4 +31,3 @@ ipsuite.geometry ipsuite.geometry.graphs ipsuite.geometry.mapping ipsuite.geometry.unwrap - diff --git a/docs/source/_get_started/_autosummary/ipsuite.geometry.unwrap.rst b/docs/source/_get_started/_autosummary/ipsuite.geometry.unwrap.rst index 2a4d6a60..79ac7f30 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.geometry.unwrap.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.geometry.unwrap.rst @@ -3,31 +3,28 @@ ipsuite.geometry.unwrap .. automodule:: ipsuite.geometry.unwrap - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + closest_atom_to_center displace_neighbors sort_atomic_edges unwrap unwrap_system - - - - - - - - + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.apax.rst b/docs/source/_get_started/_autosummary/ipsuite.models.apax.rst index ad68ba81..dd040a79 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.models.apax.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.models.apax.rst @@ -3,29 +3,26 @@ ipsuite.models.apax .. automodule:: ipsuite.models.apax - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + Apax ApaxEnsemble BatchKernelSelection - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.base.rst b/docs/source/_get_started/_autosummary/ipsuite.models.base.rst index 453bea26..da5cb4d6 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.models.base.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.models.base.rst @@ -3,27 +3,24 @@ ipsuite.models.base .. automodule:: ipsuite.models.base - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + MLModel - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.ensemble.rst b/docs/source/_get_started/_autosummary/ipsuite.models.ensemble.rst index 3c0353c6..af0ae522 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.models.ensemble.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.models.ensemble.rst @@ -3,28 +3,25 @@ ipsuite.models.ensemble .. automodule:: ipsuite.models.ensemble - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + EnsembleCalculator EnsembleModel - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.gap.rst b/docs/source/_get_started/_autosummary/ipsuite.models.gap.rst index 6b63bdc0..250cf917 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.models.gap.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.models.gap.rst @@ -3,20 +3,20 @@ ipsuite.models.gap .. automodule:: ipsuite.models.gap - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + DistanceNb DistanceNbConverter GAP @@ -24,12 +24,9 @@ ipsuite.models.gap GapParameterConverter SOAP SOAPConverter - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.mace_model.rst b/docs/source/_get_started/_autosummary/ipsuite.models.mace_model.rst index 55cb0fe0..2b7e8983 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.models.mace_model.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.models.mace_model.rst @@ -3,33 +3,30 @@ ipsuite.models.mace\_model .. automodule:: ipsuite.models.mace_model - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + execute - - - - + + + + .. rubric:: Classes .. autosummary:: - + MACE - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.nequip.rst b/docs/source/_get_started/_autosummary/ipsuite.models.nequip.rst index bf109ce4..35206b2c 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.models.nequip.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.models.nequip.rst @@ -3,27 +3,24 @@ ipsuite.models.nequip .. automodule:: ipsuite.models.nequip - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + Nequip - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.rst b/docs/source/_get_started/_autosummary/ipsuite.models.rst index 6b52f726..4bd01e37 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.models.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.models.rst @@ -3,21 +3,21 @@ .. automodule:: ipsuite.models - - - - - - - - - - - - + + + + + + + + + + + + @@ -33,4 +33,3 @@ ipsuite.models.gap ipsuite.models.mace_model ipsuite.models.nequip - diff --git a/docs/source/_get_started/_autosummary/ipsuite.nodes.rst b/docs/source/_get_started/_autosummary/ipsuite.nodes.rst index 5567e1c6..5f115004 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.nodes.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.nodes.rst @@ -3,21 +3,18 @@ ipsuite.nodes .. automodule:: ipsuite.nodes - - - - - - - - - - - - + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.project.rst b/docs/source/_get_started/_autosummary/ipsuite.project.rst index 866148a5..b4c711ee 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.project.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.project.rst @@ -3,27 +3,24 @@ ipsuite.project .. automodule:: ipsuite.project - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + Project - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.rst b/docs/source/_get_started/_autosummary/ipsuite.rst index 2742a4d5..5f8561aa 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.rst @@ -3,21 +3,21 @@ .. automodule:: ipsuite - - - - - - - - - - - - + + + + + + + + + + + + @@ -42,4 +42,3 @@ ipsuite.project ipsuite.static_data ipsuite.utils - diff --git a/docs/source/_get_started/_autosummary/ipsuite.static_data.rst b/docs/source/_get_started/_autosummary/ipsuite.static_data.rst index 3ade5a4e..832861d6 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.static_data.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.static_data.rst @@ -3,21 +3,18 @@ ipsuite.static\_data .. automodule:: ipsuite.static_data - - - - - - - - - - - - + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.ase_sim.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.ase_sim.rst index 78b55805..febb530c 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.utils.ase_sim.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.ase_sim.rst @@ -3,31 +3,28 @@ ipsuite.utils.ase\_sim .. automodule:: ipsuite.utils.ase_sim - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + freeze_copy_atoms get_box_from_density get_density_from_atoms get_desc get_energy - - - - - - - - + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.combine.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.combine.rst index d7af5d2d..3766a71d 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.utils.combine.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.combine.rst @@ -3,34 +3,31 @@ ipsuite.utils.combine .. automodule:: ipsuite.utils.combine - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + get_flat_data_from_dict get_ids_per_key - - - - + + + + .. rubric:: Classes .. autosummary:: - + ExcludeIds - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.docs.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.docs.rst index f0870ce3..7e1cba39 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.utils.docs.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.docs.rst @@ -3,27 +3,24 @@ ipsuite.utils.docs .. automodule:: ipsuite.utils.docs - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + create_dvc_git_env_for_doctest - - - - - - - - + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.helpers.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.helpers.rst index a2c70721..97f4d7d3 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.utils.helpers.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.helpers.rst @@ -3,29 +3,26 @@ ipsuite.utils.helpers .. automodule:: ipsuite.utils.helpers - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + check_duplicate_keys get_deps_if_node setup_ase - - - - - - - - + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.logs.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.logs.rst index 0a1e779d..5cd2e7c9 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.utils.logs.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.logs.rst @@ -3,27 +3,24 @@ ipsuite.utils.logs .. automodule:: ipsuite.utils.logs - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + setup_logging - - - - - - - - + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.md.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.md.rst index fbecdaa7..6ebfb0b1 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.utils.md.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.md.rst @@ -3,27 +3,24 @@ ipsuite.utils.md .. automodule:: ipsuite.utils.md - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + get_energy_terms - - - - - - - - + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.metrics.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.metrics.rst index cf0e86b8..2850ce41 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.utils.metrics.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.metrics.rst @@ -3,16 +3,16 @@ ipsuite.utils.metrics .. automodule:: ipsuite.utils.metrics - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + calculate_l_p_norm get_angles get_full_metrics @@ -22,16 +22,13 @@ ipsuite.utils.metrics mean_squared_error relative_rmse root_mean_squared_error - - - - - - - - + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.rst index 0d9f5898..485e1c55 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.utils.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.rst @@ -3,21 +3,21 @@ ipsuite.utils .. automodule:: ipsuite.utils - - - - - - - - - - - - + + + + + + + + + + + + @@ -34,4 +34,3 @@ ipsuite.utils ipsuite.utils.logs ipsuite.utils.md ipsuite.utils.metrics - diff --git a/docs/source/_get_started/nodes_list.rst b/docs/source/_get_started/nodes_list.rst index 3015f55e..5f245ee0 100644 --- a/docs/source/_get_started/nodes_list.rst +++ b/docs/source/_get_started/nodes_list.rst @@ -20,4 +20,4 @@ List of IPSuite Nodes ipsuite.models ipsuite.project ipsuite.static_data - ipsuite.utils \ No newline at end of file + ipsuite.utils From 3c437d89241b886eb00ef5547d5d15ddbff9c308 Mon Sep 17 00:00:00 2001 From: Julian Peters Date: Thu, 18 Apr 2024 14:05:12 +0200 Subject: [PATCH 24/35] idk --- .../ipsuite.analysis.bin_property.rst | 25 +++++++++------- .../ipsuite.analysis.bond_stretch.rst | 25 +++++++++------- .../ipsuite.analysis.ensemble.rst | 29 ++++++++++--------- .../_autosummary/ipsuite.analysis.md.rst | 25 +++++++++------- .../ipsuite.analysis.model.dynamics.rst | 29 ++++++++++--------- ...ipsuite.analysis.model.dynamics_checks.rst | 25 +++++++++------- .../ipsuite.analysis.model.math.rst | 25 +++++++++------- .../ipsuite.analysis.model.plots.rst | 25 +++++++++------- .../ipsuite.analysis.model.predict.rst | 25 +++++++++------- .../_autosummary/ipsuite.analysis.model.rst | 25 ++++++++-------- .../_autosummary/ipsuite.analysis.rst | 27 ++++++++--------- .../ipsuite.analysis.sensitivity.rst | 29 ++++++++++--------- .../_autosummary/ipsuite.base.base.rst | 25 +++++++++------- .../_autosummary/ipsuite.base.protocol.rst | 25 +++++++++------- .../_autosummary/ipsuite.base.rst | 27 ++++++++--------- ...ipsuite.bootstrap.random_displacements.rst | 25 +++++++++------- .../_autosummary/ipsuite.bootstrap.rst | 27 ++++++++--------- .../ipsuite.bootstrap.surface_mods.rst | 29 ++++++++++--------- .../ipsuite.calculators.apax_jax_md.rst | 25 +++++++++------- .../ipsuite.calculators.ase_geoopt.rst | 25 +++++++++------- .../ipsuite.calculators.ase_md.rst | 29 ++++++++++--------- .../ipsuite.calculators.ase_standard.rst | 25 +++++++++------- .../_autosummary/ipsuite.calculators.cp2k.rst | 25 +++++++++------- .../ipsuite.calculators.lammps.rst | 25 +++++++++------- .../_autosummary/ipsuite.calculators.mix.rst | 25 +++++++++------- .../_autosummary/ipsuite.calculators.orca.rst | 25 +++++++++------- .../_autosummary/ipsuite.calculators.rst | 25 ++++++++-------- .../ipsuite.calculators.torch_d3.rst | 27 +++++++++-------- .../_autosummary/ipsuite.calculators.xtb.rst | 25 +++++++++------- ...uite.configuration_comparison.MMKernel.rst | 20 ++++++------- ...suite.configuration_comparison.REMatch.rst | 20 ++++++------- .../ipsuite.configuration_comparison.base.rst | 29 ++++++++++--------- .../ipsuite.configuration_comparison.rst | 25 ++++++++-------- ...suite.configuration_generation.packmol.rst | 25 +++++++++------- .../ipsuite.configuration_generation.rst | 25 ++++++++-------- ...nfiguration_generation.smiles_to_atoms.rst | 25 +++++++++------- .../ipsuite.configuration_selection.base.rst | 25 +++++++++------- ...ipsuite.configuration_selection.filter.rst | 25 +++++++++------- .../ipsuite.configuration_selection.index.rst | 25 +++++++++------- ...ipsuite.configuration_selection.kernel.rst | 25 +++++++++------- ...ipsuite.configuration_selection.random.rst | 25 +++++++++------- .../ipsuite.configuration_selection.rst | 27 ++++++++--------- .../ipsuite.configuration_selection.split.rst | 25 +++++++++------- ...uite.configuration_selection.threshold.rst | 29 ++++++++++--------- ...configuration_selection.uniform_arange.rst | 25 +++++++++------- ...figuration_selection.uniform_energetic.rst | 25 +++++++++------- ...nfiguration_selection.uniform_temporal.rst | 25 +++++++++------- .../ipsuite.data_loading.add_data_ase.rst | 29 ++++++++++--------- .../ipsuite.data_loading.add_data_h5md.rst | 25 +++++++++------- .../_autosummary/ipsuite.data_loading.rst | 27 ++++++++--------- .../_autosummary/ipsuite.fields.atoms.rst | 25 +++++++++------- .../_autosummary/ipsuite.fields.rst | 27 ++++++++--------- ...suite.geometry.barycenter_coarse_grain.rst | 25 +++++++++------- .../_autosummary/ipsuite.geometry.graphs.rst | 25 +++++++++------- .../_autosummary/ipsuite.geometry.mapping.rst | 25 +++++++++------- .../_autosummary/ipsuite.geometry.rst | 27 ++++++++--------- .../_autosummary/ipsuite.geometry.unwrap.rst | 25 +++++++++------- .../_autosummary/ipsuite.models.apax.rst | 25 +++++++++------- .../_autosummary/ipsuite.models.base.rst | 25 +++++++++------- .../_autosummary/ipsuite.models.ensemble.rst | 25 +++++++++------- .../_autosummary/ipsuite.models.gap.rst | 25 +++++++++------- .../ipsuite.models.mace_model.rst | 29 ++++++++++--------- .../_autosummary/ipsuite.models.nequip.rst | 25 +++++++++------- .../_autosummary/ipsuite.models.rst | 25 ++++++++-------- .../_autosummary/ipsuite.nodes.rst | 23 ++++++++------- .../_autosummary/ipsuite.project.rst | 27 +++++++++-------- .../_autosummary/ipsuite.static_data.rst | 23 ++++++++------- .../_autosummary/ipsuite.utils.ase_sim.rst | 25 +++++++++------- .../_autosummary/ipsuite.utils.combine.rst | 29 ++++++++++--------- .../_autosummary/ipsuite.utils.docs.rst | 25 +++++++++------- .../_autosummary/ipsuite.utils.helpers.rst | 25 +++++++++------- .../_autosummary/ipsuite.utils.logs.rst | 25 +++++++++------- .../_autosummary/ipsuite.utils.md.rst | 25 +++++++++------- .../_autosummary/ipsuite.utils.metrics.rst | 25 +++++++++------- .../_autosummary/ipsuite.utils.rst | 27 ++++++++--------- 75 files changed, 1057 insertions(+), 864 deletions(-) diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.bin_property.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.bin_property.rst index 436d70e3..58a0eb6c 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.bin_property.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.bin_property.rst @@ -3,20 +3,20 @@ ipsuite.analysis.bin\_property .. automodule:: ipsuite.analysis.bin_property + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + DipoleHistogram EnergyHistogram EnergyUncertaintyHistogram @@ -24,9 +24,12 @@ ipsuite.analysis.bin\_property ForcesUncertaintyHistogram LabelHistogram StressHistogram + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.bond_stretch.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.bond_stretch.rst index 6356a14f..aeb1ce96 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.bond_stretch.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.bond_stretch.rst @@ -3,24 +3,27 @@ ipsuite.analysis.bond\_stretch .. automodule:: ipsuite.analysis.bond_stretch + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + BondStretchAnalyses + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.ensemble.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.ensemble.rst index 8e4f4d53..d8779e0c 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.ensemble.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.ensemble.rst @@ -3,30 +3,33 @@ ipsuite.analysis.ensemble .. automodule:: ipsuite.analysis.ensemble + + + - - - - - + + .. rubric:: Functions .. autosummary:: - + plot_with_uncertainty + + - - - - + + .. rubric:: Classes .. autosummary:: - + ModelEnsembleAnalysis + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.md.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.md.rst index 7d541465..d85c609d 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.md.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.md.rst @@ -3,24 +3,27 @@ ipsuite.analysis.md .. automodule:: ipsuite.analysis.md + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + AnalyseDensity + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics.rst index 2d17f1ed..2619720a 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics.rst @@ -3,33 +3,36 @@ ipsuite.analysis.model.dynamics .. automodule:: ipsuite.analysis.model.dynamics + + + - - - - - + + .. rubric:: Functions .. autosummary:: - + run_stability_nve + + - - - - + + .. rubric:: Classes .. autosummary:: - + BoxHeatUp BoxScale MDStability RattleAnalysis + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics_checks.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics_checks.rst index 8c4a6de5..2875ab96 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics_checks.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics_checks.rst @@ -3,28 +3,31 @@ ipsuite.analysis.model.dynamics\_checks .. automodule:: ipsuite.analysis.model.dynamics_checks + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + ConnectivityCheck EnergySpikeCheck NaNCheck TemperatureCheck ThresholdCheck + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.math.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.math.rst index 52582ced..38988dc1 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.math.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.math.rst @@ -3,28 +3,31 @@ ipsuite.analysis.model.math .. automodule:: ipsuite.analysis.model.math + + + - - - - - + + .. rubric:: Functions .. autosummary:: - + compute_intertia_tensor compute_rot_forces compute_trans_forces decompose_stress_tensor force_decomposition + + + + + - - - - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.plots.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.plots.rst index 9812305b..05f858c5 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.plots.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.plots.rst @@ -3,27 +3,30 @@ ipsuite.analysis.model.plots .. automodule:: ipsuite.analysis.model.plots + + + - - - - - + + .. rubric:: Functions .. autosummary:: - + density_scatter get_figure get_hist get_histogram_figure + + + + + - - - - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.predict.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.predict.rst index 6bd20ed8..7666b23b 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.predict.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.predict.rst @@ -3,27 +3,30 @@ ipsuite.analysis.model.predict .. automodule:: ipsuite.analysis.model.predict + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + ForceAngles ForceDecomposition Prediction PredictionMetrics + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.rst index 8ee20ffd..9a176f60 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.rst @@ -3,21 +3,21 @@ ipsuite.analysis.model .. automodule:: ipsuite.analysis.model + + + + + + + + + - - - - - - - - - - - - + + + @@ -32,3 +32,4 @@ ipsuite.analysis.model ipsuite.analysis.model.math ipsuite.analysis.model.plots ipsuite.analysis.model.predict + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.rst index a5391f18..b0c8214c 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.rst @@ -1,23 +1,23 @@ -ipsuite.analysis +ipsuite.analysis ================ .. automodule:: ipsuite.analysis + + + + + + + + + - - - - - - - - - - - - + + + @@ -33,3 +33,4 @@ ipsuite.analysis ipsuite.analysis.md ipsuite.analysis.model ipsuite.analysis.sensitivity + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.sensitivity.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.sensitivity.rst index 1d5f221e..8db8495d 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.sensitivity.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.sensitivity.rst @@ -3,33 +3,36 @@ ipsuite.analysis.sensitivity .. automodule:: ipsuite.analysis.sensitivity + + + - - - - - + + .. rubric:: Functions .. autosummary:: - + nonuniform_imshow + + - - - - + + .. rubric:: Classes .. autosummary:: - + AnalyseGlobalForceSensitivity AnalyseSingleForceSensitivity IsConstraintMD MoveSingleParticle + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.base.base.rst b/docs/source/_get_started/_autosummary/ipsuite.base.base.rst index 4c83c56f..ed4f51bb 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.base.base.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.base.base.rst @@ -3,20 +3,20 @@ ipsuite.base.base .. automodule:: ipsuite.base.base + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + AnalyseAtoms AnalyseProcessAtoms CheckBase @@ -24,9 +24,12 @@ ipsuite.base.base Mapping ProcessAtoms ProcessSingleAtom + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.base.protocol.rst b/docs/source/_get_started/_autosummary/ipsuite.base.protocol.rst index 56da7eda..446e1299 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.base.protocol.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.base.protocol.rst @@ -3,26 +3,29 @@ ipsuite.base.protocol .. automodule:: ipsuite.base.protocol + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + HasAtoms HasSelectedConfigurations ProcessAtoms + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.base.rst b/docs/source/_get_started/_autosummary/ipsuite.base.rst index 5e3b57a8..518ab6ea 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.base.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.base.rst @@ -1,23 +1,23 @@ -ipsuite.base +ipsuite.base ============ .. automodule:: ipsuite.base + + + + + + + + + - - - - - - - - - - - - + + + @@ -29,3 +29,4 @@ ipsuite.base ipsuite.base.base ipsuite.base.protocol + diff --git a/docs/source/_get_started/_autosummary/ipsuite.bootstrap.random_displacements.rst b/docs/source/_get_started/_autosummary/ipsuite.bootstrap.random_displacements.rst index 64c7512e..8df9d95e 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.bootstrap.random_displacements.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.bootstrap.random_displacements.rst @@ -3,27 +3,30 @@ ipsuite.bootstrap.random\_displacements .. automodule:: ipsuite.bootstrap.random_displacements + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + Bootstrap RattleAtoms RotateMolecules TranslateMolecules + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.bootstrap.rst b/docs/source/_get_started/_autosummary/ipsuite.bootstrap.rst index e00900b9..890eb009 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.bootstrap.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.bootstrap.rst @@ -1,23 +1,23 @@ -ipsuite.bootstrap +ipsuite.bootstrap ================= .. automodule:: ipsuite.bootstrap + + + + + + + + + - - - - - - - - - - - - + + + @@ -29,3 +29,4 @@ ipsuite.bootstrap ipsuite.bootstrap.random_displacements ipsuite.bootstrap.surface_mods + diff --git a/docs/source/_get_started/_autosummary/ipsuite.bootstrap.surface_mods.rst b/docs/source/_get_started/_autosummary/ipsuite.bootstrap.surface_mods.rst index cc1cbdc4..9651fc49 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.bootstrap.surface_mods.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.bootstrap.surface_mods.rst @@ -3,31 +3,34 @@ ipsuite.bootstrap.surface\_mods .. automodule:: ipsuite.bootstrap.surface_mods + + + - - - - - + + .. rubric:: Functions .. autosummary:: - + plot_ture_vs_pred + + - - - - + + .. rubric:: Classes .. autosummary:: - + SurfaceRasterMetrics SurfaceRasterScan + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.apax_jax_md.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.apax_jax_md.rst index 14a15959..fc22c9c9 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.apax_jax_md.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.apax_jax_md.rst @@ -3,24 +3,27 @@ ipsuite.calculators.apax\_jax\_md .. automodule:: ipsuite.calculators.apax_jax_md + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + ApaxJaxMD + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_geoopt.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_geoopt.rst index db5899ff..a33a8dc7 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_geoopt.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_geoopt.rst @@ -3,25 +3,28 @@ ipsuite.calculators.ase\_geoopt .. automodule:: ipsuite.calculators.ase_geoopt + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + ASEGeoOpt BatchASEGeoOpt + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_md.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_md.rst index b154fc0e..60984016 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_md.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_md.rst @@ -3,27 +3,27 @@ ipsuite.calculators.ase\_md .. automodule:: ipsuite.calculators.ase_md + + + - - - - - + + .. rubric:: Functions .. autosummary:: - + get_desc update_metrics_dict + + - - - - + + .. rubric:: Classes .. autosummary:: - + ASEMD BoxOscillatingRampModifier FixedLayerConstraint @@ -34,9 +34,12 @@ ipsuite.calculators.ase\_md RescaleBoxModifier TemperatureOscillatingRampModifier TemperatureRampModifier + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_standard.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_standard.rst index 25fe8744..82bd7ee7 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_standard.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_standard.rst @@ -3,26 +3,29 @@ ipsuite.calculators.ase\_standard .. automodule:: ipsuite.calculators.ase_standard + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + EMTCalculator EMTSinglePoint LJSinglePoint + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.cp2k.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.cp2k.rst index 60df164f..0318deb3 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.cp2k.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.cp2k.rst @@ -3,25 +3,28 @@ ipsuite.calculators.cp2k .. automodule:: ipsuite.calculators.cp2k + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + CP2KSinglePoint CP2KYaml + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.lammps.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.lammps.rst index 457d7499..c7f44d55 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.lammps.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.lammps.rst @@ -3,24 +3,27 @@ ipsuite.calculators.lammps .. automodule:: ipsuite.calculators.lammps + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + LammpsSimulator + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.mix.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.mix.rst index 321d810b..8a7c8d11 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.mix.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.mix.rst @@ -3,25 +3,28 @@ ipsuite.calculators.mix .. automodule:: ipsuite.calculators.mix + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + CalculatorNode MixCalculator + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.orca.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.orca.rst index 273def1d..d37ccfa4 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.orca.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.orca.rst @@ -3,24 +3,27 @@ ipsuite.calculators.orca .. automodule:: ipsuite.calculators.orca + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + OrcaSinglePoint + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.rst index 3e90e425..b18df547 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.rst @@ -3,21 +3,21 @@ .. automodule:: ipsuite.calculators + + + + + + + + + - - - - - - - - - - - - + + + @@ -37,3 +37,4 @@ ipsuite.calculators.orca ipsuite.calculators.torch_d3 ipsuite.calculators.xtb + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.torch_d3.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.torch_d3.rst index 32352e84..7fb63d12 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.torch_d3.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.torch_d3.rst @@ -1,27 +1,30 @@ -ipsuite.calculators.torch\_d3 +ipsuite.calculators.torch\_d3 ============================= .. automodule:: ipsuite.calculators.torch_d3 + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + TorchD3 TorchDFTD3CalculatorNL + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.xtb.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.xtb.rst index 8c4efcd8..4101c618 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.xtb.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.xtb.rst @@ -3,24 +3,27 @@ ipsuite.calculators.xtb .. automodule:: ipsuite.calculators.xtb + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + xTBSinglePoint + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.MMKernel.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.MMKernel.rst index 2ce1784c..00b16e08 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.MMKernel.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.MMKernel.rst @@ -5,14 +5,14 @@ ipsuite.configuration\_comparison.MMKernel .. autoclass:: MMKernel - + .. automethod:: __init__ - + .. rubric:: Methods .. autosummary:: - + ~MMKernel.__init__ ~MMKernel.compare ~MMKernel.convert_notebook @@ -22,15 +22,15 @@ ipsuite.configuration\_comparison.MMKernel ~MMKernel.save ~MMKernel.save_representation ~MMKernel.unlink_database + + - - - - + + .. rubric:: Attributes .. autosummary:: - + ~MMKernel.analyte ~MMKernel.init_descriptors ~MMKernel.init_subclass_basecls @@ -45,5 +45,5 @@ ipsuite.configuration\_comparison.MMKernel ~MMKernel.use_jit ~MMKernel.use_repr ~MMKernel.uuid - - + + \ No newline at end of file diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.REMatch.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.REMatch.rst index d118569a..f8e961b0 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.REMatch.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.REMatch.rst @@ -5,14 +5,14 @@ ipsuite.configuration\_comparison.REMatch .. autoclass:: REMatch - + .. automethod:: __init__ - + .. rubric:: Methods .. autosummary:: - + ~REMatch.__init__ ~REMatch.compare ~REMatch.convert_notebook @@ -22,15 +22,15 @@ ipsuite.configuration\_comparison.REMatch ~REMatch.save ~REMatch.save_representation ~REMatch.unlink_database + + - - - - + + .. rubric:: Attributes .. autosummary:: - + ~REMatch.alpha ~REMatch.analyte ~REMatch.init_descriptors @@ -48,5 +48,5 @@ ipsuite.configuration\_comparison.REMatch ~REMatch.use_jit ~REMatch.use_repr ~REMatch.uuid - - + + \ No newline at end of file diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.base.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.base.rst index c592fbe7..5598308b 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.base.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.base.rst @@ -3,34 +3,37 @@ ipsuite.configuration\_comparison.base .. automodule:: ipsuite.configuration_comparison.base + + + - - - - - + + .. rubric:: Functions .. autosummary:: - + convert_to_df create_dataset write_dataset + + - - - - + + .. rubric:: Classes .. autosummary:: - + ConfigurationComparison SOAPParameter SOAPParameterConverter + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.rst index e3defe7d..4e63f973 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.rst @@ -3,21 +3,21 @@ .. automodule:: ipsuite.configuration_comparison + + + + + + + + + - - - - - - - - - - - - + + + @@ -30,3 +30,4 @@ ipsuite.configuration_comparison.MMKernel ipsuite.configuration_comparison.REMatch ipsuite.configuration_comparison.base + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.packmol.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.packmol.rst index bb1d1e9c..561e5315 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.packmol.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.packmol.rst @@ -3,25 +3,28 @@ ipsuite.configuration\_generation.packmol .. automodule:: ipsuite.configuration_generation.packmol + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + MultiPackmol Packmol + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.rst index 7f6b21b7..33089bee 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.rst @@ -3,21 +3,21 @@ .. automodule:: ipsuite.configuration_generation + + + + + + + + + - - - - - - - - - - - - + + + @@ -29,3 +29,4 @@ ipsuite.configuration_generation.packmol ipsuite.configuration_generation.smiles_to_atoms + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.smiles_to_atoms.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.smiles_to_atoms.rst index 9189801c..8795be00 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.smiles_to_atoms.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.smiles_to_atoms.rst @@ -3,25 +3,28 @@ ipsuite.configuration\_generation.smiles\_to\_atoms .. automodule:: ipsuite.configuration_generation.smiles_to_atoms + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + SmilesToAtoms SmilesToConformers + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.base.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.base.rst index 4148b404..ad9d34a8 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.base.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.base.rst @@ -3,25 +3,28 @@ ipsuite.configuration\_selection.base .. automodule:: ipsuite.configuration_selection.base + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + BatchConfigurationSelection ConfigurationSelection + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.filter.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.filter.rst index 2d8cd6be..84e5db76 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.filter.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.filter.rst @@ -3,24 +3,27 @@ ipsuite.configuration\_selection.filter .. automodule:: ipsuite.configuration_selection.filter + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + FilterOutlier + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.index.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.index.rst index e16a9186..e24a4947 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.index.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.index.rst @@ -3,24 +3,27 @@ ipsuite.configuration\_selection.index .. automodule:: ipsuite.configuration_selection.index + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + IndexSelection + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.kernel.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.kernel.rst index cbe90c5e..95ddf8b5 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.kernel.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.kernel.rst @@ -3,24 +3,27 @@ ipsuite.configuration\_selection.kernel .. automodule:: ipsuite.configuration_selection.kernel + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + KernelSelection + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.random.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.random.rst index e96f02fb..a0a278b2 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.random.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.random.rst @@ -3,24 +3,27 @@ ipsuite.configuration\_selection.random .. automodule:: ipsuite.configuration_selection.random + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + RandomSelection + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.rst index 1ea9b2ff..732d2f88 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.rst @@ -1,23 +1,23 @@ -ipsuite.configuration\_selection +ipsuite.configuration\_selection ================================ .. automodule:: ipsuite.configuration_selection + + + + + + + + + - - - - - - - - - - - - + + + @@ -37,3 +37,4 @@ ipsuite.configuration\_selection ipsuite.configuration_selection.uniform_arange ipsuite.configuration_selection.uniform_energetic ipsuite.configuration_selection.uniform_temporal + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.split.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.split.rst index 23cf82ec..b67b2254 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.split.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.split.rst @@ -3,24 +3,27 @@ ipsuite.configuration\_selection.split .. automodule:: ipsuite.configuration_selection.split + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + SplitSelection + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.threshold.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.threshold.rst index ca606bb6..2ba751a2 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.threshold.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.threshold.rst @@ -3,32 +3,35 @@ ipsuite.configuration\_selection.threshold .. automodule:: ipsuite.configuration_selection.threshold + + + - - - - - + + .. rubric:: Functions .. autosummary:: - + check_dimension max_reduction mean_reduction + + - - - - + + .. rubric:: Classes .. autosummary:: - + ThresholdSelection + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_arange.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_arange.rst index c25038bd..eb45287c 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_arange.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_arange.rst @@ -3,24 +3,27 @@ ipsuite.configuration\_selection.uniform\_arange .. automodule:: ipsuite.configuration_selection.uniform_arange + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + UniformArangeSelection + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_energetic.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_energetic.rst index bb7f33ad..d41e2d2e 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_energetic.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_energetic.rst @@ -3,24 +3,27 @@ ipsuite.configuration\_selection.uniform\_energetic .. automodule:: ipsuite.configuration_selection.uniform_energetic + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + UniformEnergeticSelection + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_temporal.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_temporal.rst index 227f6c93..4833a013 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_temporal.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_temporal.rst @@ -3,24 +3,27 @@ ipsuite.configuration\_selection.uniform\_temporal .. automodule:: ipsuite.configuration_selection.uniform_temporal + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + UniformTemporalSelection + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_ase.rst b/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_ase.rst index 20e3c9f8..eb4384c7 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_ase.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_ase.rst @@ -3,31 +3,34 @@ ipsuite.data\_loading.add\_data\_ase .. automodule:: ipsuite.data_loading.add_data_ase + + + - - - - - + + .. rubric:: Functions .. autosummary:: - + load_data + + - - - - + + .. rubric:: Classes .. autosummary:: - + AddData ReadData + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_h5md.rst b/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_h5md.rst index aeea8f87..5dad0ffc 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_h5md.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_h5md.rst @@ -3,24 +3,27 @@ ipsuite.data\_loading.add\_data\_h5md .. automodule:: ipsuite.data_loading.add_data_h5md + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + AddDataH5MD + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.data_loading.rst b/docs/source/_get_started/_autosummary/ipsuite.data_loading.rst index bb6cd5a5..d921f903 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.data_loading.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.data_loading.rst @@ -1,23 +1,23 @@ -ipsuite.data\_loading +ipsuite.data\_loading ===================== .. automodule:: ipsuite.data_loading + + + + + + + + + - - - - - - - - - - - - + + + @@ -29,3 +29,4 @@ ipsuite.data\_loading ipsuite.data_loading.add_data_ase ipsuite.data_loading.add_data_h5md + diff --git a/docs/source/_get_started/_autosummary/ipsuite.fields.atoms.rst b/docs/source/_get_started/_autosummary/ipsuite.fields.atoms.rst index d32ba900..3c4e1d82 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.fields.atoms.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.fields.atoms.rst @@ -3,24 +3,27 @@ ipsuite.fields.atoms .. automodule:: ipsuite.fields.atoms + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + Atoms + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.fields.rst b/docs/source/_get_started/_autosummary/ipsuite.fields.rst index 7b82b0b5..933a1d5a 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.fields.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.fields.rst @@ -1,23 +1,23 @@ -ipsuite.fields +ipsuite.fields ============== .. automodule:: ipsuite.fields + + + + + + + + + - - - - - - - - - - - - + + + @@ -28,3 +28,4 @@ ipsuite.fields :recursive: ipsuite.fields.atoms + diff --git a/docs/source/_get_started/_autosummary/ipsuite.geometry.barycenter_coarse_grain.rst b/docs/source/_get_started/_autosummary/ipsuite.geometry.barycenter_coarse_grain.rst index f18a946b..f59fe34f 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.geometry.barycenter_coarse_grain.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.geometry.barycenter_coarse_grain.rst @@ -3,25 +3,28 @@ ipsuite.geometry.barycenter\_coarse\_grain .. automodule:: ipsuite.geometry.barycenter_coarse_grain + + + - - - - - + + .. rubric:: Functions .. autosummary:: - + barycenter_backmapping coarse_grain_to_barycenter + + + + + - - - - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.geometry.graphs.rst b/docs/source/_get_started/_autosummary/ipsuite.geometry.graphs.rst index 71c943a0..0c08f233 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.geometry.graphs.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.geometry.graphs.rst @@ -3,27 +3,30 @@ ipsuite.geometry.graphs .. automodule:: ipsuite.geometry.graphs + + + - - - - - + + .. rubric:: Functions .. autosummary:: - + atoms_to_graph edges_from_atoms identify_molecules split_molecule + + + + + - - - - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.geometry.mapping.rst b/docs/source/_get_started/_autosummary/ipsuite.geometry.mapping.rst index 25f9bdbd..6899cfd7 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.geometry.mapping.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.geometry.mapping.rst @@ -3,24 +3,27 @@ ipsuite.geometry.mapping .. automodule:: ipsuite.geometry.mapping + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + BarycenterMapping + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.geometry.rst b/docs/source/_get_started/_autosummary/ipsuite.geometry.rst index 60b2e508..f1ab65db 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.geometry.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.geometry.rst @@ -1,23 +1,23 @@ -ipsuite.geometry +ipsuite.geometry ================ .. automodule:: ipsuite.geometry + + + + + + + + + - - - - - - - - - - - - + + + @@ -31,3 +31,4 @@ ipsuite.geometry ipsuite.geometry.graphs ipsuite.geometry.mapping ipsuite.geometry.unwrap + diff --git a/docs/source/_get_started/_autosummary/ipsuite.geometry.unwrap.rst b/docs/source/_get_started/_autosummary/ipsuite.geometry.unwrap.rst index 79ac7f30..2a4d6a60 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.geometry.unwrap.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.geometry.unwrap.rst @@ -3,28 +3,31 @@ ipsuite.geometry.unwrap .. automodule:: ipsuite.geometry.unwrap + + + - - - - - + + .. rubric:: Functions .. autosummary:: - + closest_atom_to_center displace_neighbors sort_atomic_edges unwrap unwrap_system + + + + + - - - - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.apax.rst b/docs/source/_get_started/_autosummary/ipsuite.models.apax.rst index dd040a79..ad68ba81 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.models.apax.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.models.apax.rst @@ -3,26 +3,29 @@ ipsuite.models.apax .. automodule:: ipsuite.models.apax + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + Apax ApaxEnsemble BatchKernelSelection + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.base.rst b/docs/source/_get_started/_autosummary/ipsuite.models.base.rst index da5cb4d6..453bea26 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.models.base.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.models.base.rst @@ -3,24 +3,27 @@ ipsuite.models.base .. automodule:: ipsuite.models.base + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + MLModel + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.ensemble.rst b/docs/source/_get_started/_autosummary/ipsuite.models.ensemble.rst index af0ae522..3c0353c6 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.models.ensemble.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.models.ensemble.rst @@ -3,25 +3,28 @@ ipsuite.models.ensemble .. automodule:: ipsuite.models.ensemble + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + EnsembleCalculator EnsembleModel + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.gap.rst b/docs/source/_get_started/_autosummary/ipsuite.models.gap.rst index 250cf917..6b63bdc0 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.models.gap.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.models.gap.rst @@ -3,20 +3,20 @@ ipsuite.models.gap .. automodule:: ipsuite.models.gap + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + DistanceNb DistanceNbConverter GAP @@ -24,9 +24,12 @@ ipsuite.models.gap GapParameterConverter SOAP SOAPConverter + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.mace_model.rst b/docs/source/_get_started/_autosummary/ipsuite.models.mace_model.rst index 2b7e8983..55cb0fe0 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.models.mace_model.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.models.mace_model.rst @@ -3,30 +3,33 @@ ipsuite.models.mace\_model .. automodule:: ipsuite.models.mace_model + + + - - - - - + + .. rubric:: Functions .. autosummary:: - + execute + + - - - - + + .. rubric:: Classes .. autosummary:: - + MACE + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.nequip.rst b/docs/source/_get_started/_autosummary/ipsuite.models.nequip.rst index 35206b2c..bf109ce4 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.models.nequip.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.models.nequip.rst @@ -3,24 +3,27 @@ ipsuite.models.nequip .. automodule:: ipsuite.models.nequip + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + Nequip + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.rst b/docs/source/_get_started/_autosummary/ipsuite.models.rst index 4bd01e37..6b52f726 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.models.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.models.rst @@ -3,21 +3,21 @@ .. automodule:: ipsuite.models + + + + + + + + + - - - - - - - - - - - - + + + @@ -33,3 +33,4 @@ ipsuite.models.gap ipsuite.models.mace_model ipsuite.models.nequip + diff --git a/docs/source/_get_started/_autosummary/ipsuite.nodes.rst b/docs/source/_get_started/_autosummary/ipsuite.nodes.rst index 5f115004..24ef83d2 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.nodes.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.nodes.rst @@ -1,20 +1,23 @@ -ipsuite.nodes +ipsuite.nodes ============= .. automodule:: ipsuite.nodes + + + + + + + + + - - - - - - - - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.project.rst b/docs/source/_get_started/_autosummary/ipsuite.project.rst index b4c711ee..ee135e23 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.project.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.project.rst @@ -1,26 +1,29 @@ -ipsuite.project +ipsuite.project =============== .. automodule:: ipsuite.project + + + + + + - - - - - - - - + + .. rubric:: Classes .. autosummary:: - + Project + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.static_data.rst b/docs/source/_get_started/_autosummary/ipsuite.static_data.rst index 832861d6..0a5700c8 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.static_data.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.static_data.rst @@ -1,20 +1,23 @@ -ipsuite.static\_data +ipsuite.static\_data ==================== .. automodule:: ipsuite.static_data + + + + + + + + + - - - - - - - - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.ase_sim.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.ase_sim.rst index febb530c..78b55805 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.utils.ase_sim.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.ase_sim.rst @@ -3,28 +3,31 @@ ipsuite.utils.ase\_sim .. automodule:: ipsuite.utils.ase_sim + + + - - - - - + + .. rubric:: Functions .. autosummary:: - + freeze_copy_atoms get_box_from_density get_density_from_atoms get_desc get_energy + + + + + - - - - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.combine.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.combine.rst index 3766a71d..d7af5d2d 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.utils.combine.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.combine.rst @@ -3,31 +3,34 @@ ipsuite.utils.combine .. automodule:: ipsuite.utils.combine + + + - - - - - + + .. rubric:: Functions .. autosummary:: - + get_flat_data_from_dict get_ids_per_key + + - - - - + + .. rubric:: Classes .. autosummary:: - + ExcludeIds + + - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.docs.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.docs.rst index 7e1cba39..f0870ce3 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.utils.docs.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.docs.rst @@ -3,24 +3,27 @@ ipsuite.utils.docs .. automodule:: ipsuite.utils.docs + + + - - - - - + + .. rubric:: Functions .. autosummary:: - + create_dvc_git_env_for_doctest + + + + + - - - - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.helpers.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.helpers.rst index 97f4d7d3..a2c70721 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.utils.helpers.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.helpers.rst @@ -3,26 +3,29 @@ ipsuite.utils.helpers .. automodule:: ipsuite.utils.helpers + + + - - - - - + + .. rubric:: Functions .. autosummary:: - + check_duplicate_keys get_deps_if_node setup_ase + + + + + - - - - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.logs.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.logs.rst index 5cd2e7c9..0a1e779d 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.utils.logs.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.logs.rst @@ -3,24 +3,27 @@ ipsuite.utils.logs .. automodule:: ipsuite.utils.logs + + + - - - - - + + .. rubric:: Functions .. autosummary:: - + setup_logging + + + + + - - - - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.md.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.md.rst index 6ebfb0b1..fbecdaa7 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.utils.md.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.md.rst @@ -3,24 +3,27 @@ ipsuite.utils.md .. automodule:: ipsuite.utils.md + + + - - - - - + + .. rubric:: Functions .. autosummary:: - + get_energy_terms + + + + + - - - - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.metrics.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.metrics.rst index 2850ce41..cf0e86b8 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.utils.metrics.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.metrics.rst @@ -3,16 +3,16 @@ ipsuite.utils.metrics .. automodule:: ipsuite.utils.metrics + + + - - - - - + + .. rubric:: Functions .. autosummary:: - + calculate_l_p_norm get_angles get_full_metrics @@ -22,13 +22,16 @@ ipsuite.utils.metrics mean_squared_error relative_rmse root_mean_squared_error + + + + + - - - - - + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.rst index 485e1c55..81ecbfc0 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.utils.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.rst @@ -1,23 +1,23 @@ -ipsuite.utils +ipsuite.utils ============= .. automodule:: ipsuite.utils + + + + + + + + + - - - - - - - - - - - - + + + @@ -34,3 +34,4 @@ ipsuite.utils ipsuite.utils.logs ipsuite.utils.md ipsuite.utils.metrics + From 7aa3336c469b76d008be731824f0002fd85b0e17 Mon Sep 17 00:00:00 2001 From: Julian Peters Date: Thu, 18 Apr 2024 14:10:29 +0200 Subject: [PATCH 25/35] Add LAMMPS file docstring --- ipsuite/calculators/lammps.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/ipsuite/calculators/lammps.py b/ipsuite/calculators/lammps.py index 6e3227dd..25e5dc50 100644 --- a/ipsuite/calculators/lammps.py +++ b/ipsuite/calculators/lammps.py @@ -1,3 +1,6 @@ +"""LAMMPS interface for MD Simulations using LAMMPS +""" + import importlib.resources as pkg_resources import pathlib import subprocess @@ -12,7 +15,7 @@ class LammpsSimulator(base.ProcessSingleAtom): - """Can perform LAMMPS Simulations. + """Perform LAMMPS Simulations. Parameters ---------- From 5090e00e3722c2c9eb0cec19d586ef7b0c030041 Mon Sep 17 00:00:00 2001 From: Julian Peters Date: Thu, 18 Apr 2024 14:12:41 +0200 Subject: [PATCH 26/35] add Packmol docstring --- ipsuite/configuration_generation/packmol.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/ipsuite/configuration_generation/packmol.py b/ipsuite/configuration_generation/packmol.py index 21b4eca2..266815e4 100644 --- a/ipsuite/configuration_generation/packmol.py +++ b/ipsuite/configuration_generation/packmol.py @@ -18,7 +18,8 @@ class Packmol(base.IPSNode): """ - + Pack molecules in defined regions of space + Attributes ---------- data: list[list[ase.Atoms]] From 845813fe360693e8abc129d8e878d91d9dbc051b Mon Sep 17 00:00:00 2001 From: Julian Peters Date: Thu, 18 Apr 2024 14:23:48 +0200 Subject: [PATCH 27/35] add basic (actualy primitive) packmol docstring --- ipsuite/configuration_generation/smiles_to_atoms.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/ipsuite/configuration_generation/smiles_to_atoms.py b/ipsuite/configuration_generation/smiles_to_atoms.py index 5a29ddd4..a68a4e49 100644 --- a/ipsuite/configuration_generation/smiles_to_atoms.py +++ b/ipsuite/configuration_generation/smiles_to_atoms.py @@ -1,3 +1,4 @@ +""""Use RDKit to convert Smiles stings to atoms""" import pathlib import ase @@ -10,6 +11,8 @@ class SmilesToAtoms(base.IPSNode): + """Generate ase.atom object from smiles string + """ atoms = fields.Atoms() smiles: str = zntrack.params() @@ -45,6 +48,7 @@ def view(self) -> view: class SmilesToConformers(base.IPSNode): + """Generate random conformers of molecule from smiles string""" atoms = fields.Atoms() smiles: str = zntrack.params() From 4183163f7328ffaa151393e3b2397cbcdc7b445b Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 18 Apr 2024 12:24:25 +0000 Subject: [PATCH 28/35] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- .../ipsuite.analysis.bin_property.rst | 25 +++++++--------- .../ipsuite.analysis.bond_stretch.rst | 25 +++++++--------- .../ipsuite.analysis.ensemble.rst | 29 +++++++++---------- .../_autosummary/ipsuite.analysis.md.rst | 25 +++++++--------- .../ipsuite.analysis.model.dynamics.rst | 29 +++++++++---------- ...ipsuite.analysis.model.dynamics_checks.rst | 25 +++++++--------- .../ipsuite.analysis.model.math.rst | 25 +++++++--------- .../ipsuite.analysis.model.plots.rst | 25 +++++++--------- .../ipsuite.analysis.model.predict.rst | 25 +++++++--------- .../_autosummary/ipsuite.analysis.model.rst | 25 ++++++++-------- .../_autosummary/ipsuite.analysis.rst | 25 ++++++++-------- .../ipsuite.analysis.sensitivity.rst | 29 +++++++++---------- .../_autosummary/ipsuite.base.base.rst | 25 +++++++--------- .../_autosummary/ipsuite.base.protocol.rst | 25 +++++++--------- .../_autosummary/ipsuite.base.rst | 25 ++++++++-------- ...ipsuite.bootstrap.random_displacements.rst | 25 +++++++--------- .../_autosummary/ipsuite.bootstrap.rst | 25 ++++++++-------- .../ipsuite.bootstrap.surface_mods.rst | 29 +++++++++---------- .../ipsuite.calculators.apax_jax_md.rst | 25 +++++++--------- .../ipsuite.calculators.ase_geoopt.rst | 25 +++++++--------- .../ipsuite.calculators.ase_md.rst | 29 +++++++++---------- .../ipsuite.calculators.ase_standard.rst | 25 +++++++--------- .../_autosummary/ipsuite.calculators.cp2k.rst | 25 +++++++--------- .../ipsuite.calculators.lammps.rst | 25 +++++++--------- .../_autosummary/ipsuite.calculators.mix.rst | 25 +++++++--------- .../_autosummary/ipsuite.calculators.orca.rst | 25 +++++++--------- .../_autosummary/ipsuite.calculators.rst | 25 ++++++++-------- .../ipsuite.calculators.torch_d3.rst | 25 +++++++--------- .../_autosummary/ipsuite.calculators.xtb.rst | 25 +++++++--------- ...uite.configuration_comparison.MMKernel.rst | 20 ++++++------- ...suite.configuration_comparison.REMatch.rst | 20 ++++++------- .../ipsuite.configuration_comparison.base.rst | 29 +++++++++---------- .../ipsuite.configuration_comparison.rst | 25 ++++++++-------- ...suite.configuration_generation.packmol.rst | 25 +++++++--------- .../ipsuite.configuration_generation.rst | 25 ++++++++-------- ...nfiguration_generation.smiles_to_atoms.rst | 25 +++++++--------- .../ipsuite.configuration_selection.base.rst | 25 +++++++--------- ...ipsuite.configuration_selection.filter.rst | 25 +++++++--------- .../ipsuite.configuration_selection.index.rst | 25 +++++++--------- ...ipsuite.configuration_selection.kernel.rst | 25 +++++++--------- ...ipsuite.configuration_selection.random.rst | 25 +++++++--------- .../ipsuite.configuration_selection.rst | 25 ++++++++-------- .../ipsuite.configuration_selection.split.rst | 25 +++++++--------- ...uite.configuration_selection.threshold.rst | 29 +++++++++---------- ...configuration_selection.uniform_arange.rst | 25 +++++++--------- ...figuration_selection.uniform_energetic.rst | 25 +++++++--------- ...nfiguration_selection.uniform_temporal.rst | 25 +++++++--------- .../ipsuite.data_loading.add_data_ase.rst | 29 +++++++++---------- .../ipsuite.data_loading.add_data_h5md.rst | 25 +++++++--------- .../_autosummary/ipsuite.data_loading.rst | 25 ++++++++-------- .../_autosummary/ipsuite.fields.atoms.rst | 25 +++++++--------- .../_autosummary/ipsuite.fields.rst | 25 ++++++++-------- ...suite.geometry.barycenter_coarse_grain.rst | 25 +++++++--------- .../_autosummary/ipsuite.geometry.graphs.rst | 25 +++++++--------- .../_autosummary/ipsuite.geometry.mapping.rst | 25 +++++++--------- .../_autosummary/ipsuite.geometry.rst | 25 ++++++++-------- .../_autosummary/ipsuite.geometry.unwrap.rst | 25 +++++++--------- .../_autosummary/ipsuite.models.apax.rst | 25 +++++++--------- .../_autosummary/ipsuite.models.base.rst | 25 +++++++--------- .../_autosummary/ipsuite.models.ensemble.rst | 25 +++++++--------- .../_autosummary/ipsuite.models.gap.rst | 25 +++++++--------- .../ipsuite.models.mace_model.rst | 29 +++++++++---------- .../_autosummary/ipsuite.models.nequip.rst | 25 +++++++--------- .../_autosummary/ipsuite.models.rst | 25 ++++++++-------- .../_autosummary/ipsuite.nodes.rst | 21 ++++++-------- .../_autosummary/ipsuite.project.rst | 25 +++++++--------- .../_autosummary/ipsuite.static_data.rst | 21 ++++++-------- .../_autosummary/ipsuite.utils.ase_sim.rst | 25 +++++++--------- .../_autosummary/ipsuite.utils.combine.rst | 29 +++++++++---------- .../_autosummary/ipsuite.utils.docs.rst | 25 +++++++--------- .../_autosummary/ipsuite.utils.helpers.rst | 25 +++++++--------- .../_autosummary/ipsuite.utils.logs.rst | 25 +++++++--------- .../_autosummary/ipsuite.utils.md.rst | 25 +++++++--------- .../_autosummary/ipsuite.utils.metrics.rst | 25 +++++++--------- .../_autosummary/ipsuite.utils.rst | 25 ++++++++-------- ipsuite/configuration_generation/packmol.py | 2 +- .../smiles_to_atoms.py | 6 ++-- 77 files changed, 857 insertions(+), 1048 deletions(-) diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.bin_property.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.bin_property.rst index 58a0eb6c..436d70e3 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.bin_property.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.bin_property.rst @@ -3,20 +3,20 @@ ipsuite.analysis.bin\_property .. automodule:: ipsuite.analysis.bin_property - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + DipoleHistogram EnergyHistogram EnergyUncertaintyHistogram @@ -24,12 +24,9 @@ ipsuite.analysis.bin\_property ForcesUncertaintyHistogram LabelHistogram StressHistogram - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.bond_stretch.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.bond_stretch.rst index aeb1ce96..6356a14f 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.bond_stretch.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.bond_stretch.rst @@ -3,27 +3,24 @@ ipsuite.analysis.bond\_stretch .. automodule:: ipsuite.analysis.bond_stretch - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + BondStretchAnalyses - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.ensemble.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.ensemble.rst index d8779e0c..8e4f4d53 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.ensemble.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.ensemble.rst @@ -3,33 +3,30 @@ ipsuite.analysis.ensemble .. automodule:: ipsuite.analysis.ensemble - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + plot_with_uncertainty - - - - + + + + .. rubric:: Classes .. autosummary:: - + ModelEnsembleAnalysis - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.md.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.md.rst index d85c609d..7d541465 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.md.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.md.rst @@ -3,27 +3,24 @@ ipsuite.analysis.md .. automodule:: ipsuite.analysis.md - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + AnalyseDensity - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics.rst index 2619720a..2d17f1ed 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics.rst @@ -3,36 +3,33 @@ ipsuite.analysis.model.dynamics .. automodule:: ipsuite.analysis.model.dynamics - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + run_stability_nve - - - - + + + + .. rubric:: Classes .. autosummary:: - + BoxHeatUp BoxScale MDStability RattleAnalysis - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics_checks.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics_checks.rst index 2875ab96..8c4a6de5 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics_checks.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics_checks.rst @@ -3,31 +3,28 @@ ipsuite.analysis.model.dynamics\_checks .. automodule:: ipsuite.analysis.model.dynamics_checks - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + ConnectivityCheck EnergySpikeCheck NaNCheck TemperatureCheck ThresholdCheck - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.math.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.math.rst index 38988dc1..52582ced 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.math.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.math.rst @@ -3,31 +3,28 @@ ipsuite.analysis.model.math .. automodule:: ipsuite.analysis.model.math - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + compute_intertia_tensor compute_rot_forces compute_trans_forces decompose_stress_tensor force_decomposition - - - - - - - - + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.plots.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.plots.rst index 05f858c5..9812305b 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.plots.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.plots.rst @@ -3,30 +3,27 @@ ipsuite.analysis.model.plots .. automodule:: ipsuite.analysis.model.plots - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + density_scatter get_figure get_hist get_histogram_figure - - - - - - - - + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.predict.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.predict.rst index 7666b23b..6bd20ed8 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.predict.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.predict.rst @@ -3,30 +3,27 @@ ipsuite.analysis.model.predict .. automodule:: ipsuite.analysis.model.predict - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + ForceAngles ForceDecomposition Prediction PredictionMetrics - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.rst index 9a176f60..8ee20ffd 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.rst @@ -3,21 +3,21 @@ ipsuite.analysis.model .. automodule:: ipsuite.analysis.model - - - - - - - - - - - - + + + + + + + + + + + + @@ -32,4 +32,3 @@ ipsuite.analysis.model ipsuite.analysis.model.math ipsuite.analysis.model.plots ipsuite.analysis.model.predict - diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.rst index b0c8214c..345e9ded 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.rst @@ -3,21 +3,21 @@ .. automodule:: ipsuite.analysis - - - - - - - - - - - - + + + + + + + + + + + + @@ -33,4 +33,3 @@ ipsuite.analysis.md ipsuite.analysis.model ipsuite.analysis.sensitivity - diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.sensitivity.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.sensitivity.rst index 8db8495d..1d5f221e 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.sensitivity.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.sensitivity.rst @@ -3,36 +3,33 @@ ipsuite.analysis.sensitivity .. automodule:: ipsuite.analysis.sensitivity - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + nonuniform_imshow - - - - + + + + .. rubric:: Classes .. autosummary:: - + AnalyseGlobalForceSensitivity AnalyseSingleForceSensitivity IsConstraintMD MoveSingleParticle - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.base.base.rst b/docs/source/_get_started/_autosummary/ipsuite.base.base.rst index ed4f51bb..4c83c56f 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.base.base.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.base.base.rst @@ -3,20 +3,20 @@ ipsuite.base.base .. automodule:: ipsuite.base.base - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + AnalyseAtoms AnalyseProcessAtoms CheckBase @@ -24,12 +24,9 @@ ipsuite.base.base Mapping ProcessAtoms ProcessSingleAtom - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.base.protocol.rst b/docs/source/_get_started/_autosummary/ipsuite.base.protocol.rst index 446e1299..56da7eda 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.base.protocol.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.base.protocol.rst @@ -3,29 +3,26 @@ ipsuite.base.protocol .. automodule:: ipsuite.base.protocol - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + HasAtoms HasSelectedConfigurations ProcessAtoms - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.base.rst b/docs/source/_get_started/_autosummary/ipsuite.base.rst index 518ab6ea..d3507240 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.base.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.base.rst @@ -3,21 +3,21 @@ .. automodule:: ipsuite.base - - - - - - - - - - - - + + + + + + + + + + + + @@ -29,4 +29,3 @@ ipsuite.base.base ipsuite.base.protocol - diff --git a/docs/source/_get_started/_autosummary/ipsuite.bootstrap.random_displacements.rst b/docs/source/_get_started/_autosummary/ipsuite.bootstrap.random_displacements.rst index 8df9d95e..64c7512e 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.bootstrap.random_displacements.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.bootstrap.random_displacements.rst @@ -3,30 +3,27 @@ ipsuite.bootstrap.random\_displacements .. automodule:: ipsuite.bootstrap.random_displacements - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + Bootstrap RattleAtoms RotateMolecules TranslateMolecules - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.bootstrap.rst b/docs/source/_get_started/_autosummary/ipsuite.bootstrap.rst index 890eb009..a8850783 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.bootstrap.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.bootstrap.rst @@ -3,21 +3,21 @@ .. automodule:: ipsuite.bootstrap - - - - - - - - - - - - + + + + + + + + + + + + @@ -29,4 +29,3 @@ ipsuite.bootstrap.random_displacements ipsuite.bootstrap.surface_mods - diff --git a/docs/source/_get_started/_autosummary/ipsuite.bootstrap.surface_mods.rst b/docs/source/_get_started/_autosummary/ipsuite.bootstrap.surface_mods.rst index 9651fc49..cc1cbdc4 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.bootstrap.surface_mods.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.bootstrap.surface_mods.rst @@ -3,34 +3,31 @@ ipsuite.bootstrap.surface\_mods .. automodule:: ipsuite.bootstrap.surface_mods - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + plot_ture_vs_pred - - - - + + + + .. rubric:: Classes .. autosummary:: - + SurfaceRasterMetrics SurfaceRasterScan - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.apax_jax_md.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.apax_jax_md.rst index fc22c9c9..14a15959 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.apax_jax_md.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.apax_jax_md.rst @@ -3,27 +3,24 @@ ipsuite.calculators.apax\_jax\_md .. automodule:: ipsuite.calculators.apax_jax_md - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + ApaxJaxMD - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_geoopt.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_geoopt.rst index a33a8dc7..db5899ff 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_geoopt.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_geoopt.rst @@ -3,28 +3,25 @@ ipsuite.calculators.ase\_geoopt .. automodule:: ipsuite.calculators.ase_geoopt - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + ASEGeoOpt BatchASEGeoOpt - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_md.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_md.rst index 60984016..b154fc0e 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_md.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_md.rst @@ -3,27 +3,27 @@ ipsuite.calculators.ase\_md .. automodule:: ipsuite.calculators.ase_md - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + get_desc update_metrics_dict - - - - + + + + .. rubric:: Classes .. autosummary:: - + ASEMD BoxOscillatingRampModifier FixedLayerConstraint @@ -34,12 +34,9 @@ ipsuite.calculators.ase\_md RescaleBoxModifier TemperatureOscillatingRampModifier TemperatureRampModifier - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_standard.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_standard.rst index 82bd7ee7..25fe8744 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_standard.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_standard.rst @@ -3,29 +3,26 @@ ipsuite.calculators.ase\_standard .. automodule:: ipsuite.calculators.ase_standard - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + EMTCalculator EMTSinglePoint LJSinglePoint - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.cp2k.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.cp2k.rst index 0318deb3..60df164f 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.cp2k.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.cp2k.rst @@ -3,28 +3,25 @@ ipsuite.calculators.cp2k .. automodule:: ipsuite.calculators.cp2k - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + CP2KSinglePoint CP2KYaml - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.lammps.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.lammps.rst index c7f44d55..457d7499 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.lammps.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.lammps.rst @@ -3,27 +3,24 @@ ipsuite.calculators.lammps .. automodule:: ipsuite.calculators.lammps - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + LammpsSimulator - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.mix.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.mix.rst index 8a7c8d11..321d810b 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.mix.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.mix.rst @@ -3,28 +3,25 @@ ipsuite.calculators.mix .. automodule:: ipsuite.calculators.mix - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + CalculatorNode MixCalculator - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.orca.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.orca.rst index d37ccfa4..273def1d 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.orca.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.orca.rst @@ -3,27 +3,24 @@ ipsuite.calculators.orca .. automodule:: ipsuite.calculators.orca - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + OrcaSinglePoint - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.rst index b18df547..3e90e425 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.rst @@ -3,21 +3,21 @@ .. automodule:: ipsuite.calculators - - - - - - - - - - - - + + + + + + + + + + + + @@ -37,4 +37,3 @@ ipsuite.calculators.orca ipsuite.calculators.torch_d3 ipsuite.calculators.xtb - diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.torch_d3.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.torch_d3.rst index 7fb63d12..7fdd2ae2 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.torch_d3.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.torch_d3.rst @@ -3,28 +3,25 @@ ipsuite.calculators.torch\_d3 .. automodule:: ipsuite.calculators.torch_d3 - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + TorchD3 TorchDFTD3CalculatorNL - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.xtb.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.xtb.rst index 4101c618..8c4efcd8 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.xtb.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.xtb.rst @@ -3,27 +3,24 @@ ipsuite.calculators.xtb .. automodule:: ipsuite.calculators.xtb - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + xTBSinglePoint - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.MMKernel.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.MMKernel.rst index 00b16e08..2ce1784c 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.MMKernel.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.MMKernel.rst @@ -5,14 +5,14 @@ ipsuite.configuration\_comparison.MMKernel .. autoclass:: MMKernel - + .. automethod:: __init__ - + .. rubric:: Methods .. autosummary:: - + ~MMKernel.__init__ ~MMKernel.compare ~MMKernel.convert_notebook @@ -22,15 +22,15 @@ ipsuite.configuration\_comparison.MMKernel ~MMKernel.save ~MMKernel.save_representation ~MMKernel.unlink_database - - - - + + + + .. rubric:: Attributes .. autosummary:: - + ~MMKernel.analyte ~MMKernel.init_descriptors ~MMKernel.init_subclass_basecls @@ -45,5 +45,5 @@ ipsuite.configuration\_comparison.MMKernel ~MMKernel.use_jit ~MMKernel.use_repr ~MMKernel.uuid - - \ No newline at end of file + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.REMatch.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.REMatch.rst index f8e961b0..d118569a 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.REMatch.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.REMatch.rst @@ -5,14 +5,14 @@ ipsuite.configuration\_comparison.REMatch .. autoclass:: REMatch - + .. automethod:: __init__ - + .. rubric:: Methods .. autosummary:: - + ~REMatch.__init__ ~REMatch.compare ~REMatch.convert_notebook @@ -22,15 +22,15 @@ ipsuite.configuration\_comparison.REMatch ~REMatch.save ~REMatch.save_representation ~REMatch.unlink_database - - - - + + + + .. rubric:: Attributes .. autosummary:: - + ~REMatch.alpha ~REMatch.analyte ~REMatch.init_descriptors @@ -48,5 +48,5 @@ ipsuite.configuration\_comparison.REMatch ~REMatch.use_jit ~REMatch.use_repr ~REMatch.uuid - - \ No newline at end of file + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.base.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.base.rst index 5598308b..c592fbe7 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.base.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.base.rst @@ -3,37 +3,34 @@ ipsuite.configuration\_comparison.base .. automodule:: ipsuite.configuration_comparison.base - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + convert_to_df create_dataset write_dataset - - - - + + + + .. rubric:: Classes .. autosummary:: - + ConfigurationComparison SOAPParameter SOAPParameterConverter - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.rst index 4e63f973..e3defe7d 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.rst @@ -3,21 +3,21 @@ .. automodule:: ipsuite.configuration_comparison - - - - - - - - - - - - + + + + + + + + + + + + @@ -30,4 +30,3 @@ ipsuite.configuration_comparison.MMKernel ipsuite.configuration_comparison.REMatch ipsuite.configuration_comparison.base - diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.packmol.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.packmol.rst index 561e5315..bb1d1e9c 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.packmol.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.packmol.rst @@ -3,28 +3,25 @@ ipsuite.configuration\_generation.packmol .. automodule:: ipsuite.configuration_generation.packmol - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + MultiPackmol Packmol - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.rst index 33089bee..7f6b21b7 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.rst @@ -3,21 +3,21 @@ .. automodule:: ipsuite.configuration_generation - - - - - - - - - - - - + + + + + + + + + + + + @@ -29,4 +29,3 @@ ipsuite.configuration_generation.packmol ipsuite.configuration_generation.smiles_to_atoms - diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.smiles_to_atoms.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.smiles_to_atoms.rst index 8795be00..9189801c 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.smiles_to_atoms.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.smiles_to_atoms.rst @@ -3,28 +3,25 @@ ipsuite.configuration\_generation.smiles\_to\_atoms .. automodule:: ipsuite.configuration_generation.smiles_to_atoms - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + SmilesToAtoms SmilesToConformers - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.base.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.base.rst index ad9d34a8..4148b404 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.base.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.base.rst @@ -3,28 +3,25 @@ ipsuite.configuration\_selection.base .. automodule:: ipsuite.configuration_selection.base - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + BatchConfigurationSelection ConfigurationSelection - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.filter.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.filter.rst index 84e5db76..2d8cd6be 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.filter.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.filter.rst @@ -3,27 +3,24 @@ ipsuite.configuration\_selection.filter .. automodule:: ipsuite.configuration_selection.filter - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + FilterOutlier - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.index.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.index.rst index e24a4947..e16a9186 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.index.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.index.rst @@ -3,27 +3,24 @@ ipsuite.configuration\_selection.index .. automodule:: ipsuite.configuration_selection.index - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + IndexSelection - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.kernel.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.kernel.rst index 95ddf8b5..cbe90c5e 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.kernel.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.kernel.rst @@ -3,27 +3,24 @@ ipsuite.configuration\_selection.kernel .. automodule:: ipsuite.configuration_selection.kernel - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + KernelSelection - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.random.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.random.rst index a0a278b2..e96f02fb 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.random.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.random.rst @@ -3,27 +3,24 @@ ipsuite.configuration\_selection.random .. automodule:: ipsuite.configuration_selection.random - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + RandomSelection - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.rst index 732d2f88..fc04d6e8 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.rst @@ -3,21 +3,21 @@ .. automodule:: ipsuite.configuration_selection - - - - - - - - - - - - + + + + + + + + + + + + @@ -37,4 +37,3 @@ ipsuite.configuration_selection.uniform_arange ipsuite.configuration_selection.uniform_energetic ipsuite.configuration_selection.uniform_temporal - diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.split.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.split.rst index b67b2254..23cf82ec 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.split.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.split.rst @@ -3,27 +3,24 @@ ipsuite.configuration\_selection.split .. automodule:: ipsuite.configuration_selection.split - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + SplitSelection - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.threshold.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.threshold.rst index 2ba751a2..ca606bb6 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.threshold.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.threshold.rst @@ -3,35 +3,32 @@ ipsuite.configuration\_selection.threshold .. automodule:: ipsuite.configuration_selection.threshold - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + check_dimension max_reduction mean_reduction - - - - + + + + .. rubric:: Classes .. autosummary:: - + ThresholdSelection - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_arange.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_arange.rst index eb45287c..c25038bd 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_arange.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_arange.rst @@ -3,27 +3,24 @@ ipsuite.configuration\_selection.uniform\_arange .. automodule:: ipsuite.configuration_selection.uniform_arange - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + UniformArangeSelection - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_energetic.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_energetic.rst index d41e2d2e..bb7f33ad 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_energetic.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_energetic.rst @@ -3,27 +3,24 @@ ipsuite.configuration\_selection.uniform\_energetic .. automodule:: ipsuite.configuration_selection.uniform_energetic - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + UniformEnergeticSelection - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_temporal.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_temporal.rst index 4833a013..227f6c93 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_temporal.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_temporal.rst @@ -3,27 +3,24 @@ ipsuite.configuration\_selection.uniform\_temporal .. automodule:: ipsuite.configuration_selection.uniform_temporal - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + UniformTemporalSelection - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_ase.rst b/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_ase.rst index eb4384c7..20e3c9f8 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_ase.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_ase.rst @@ -3,34 +3,31 @@ ipsuite.data\_loading.add\_data\_ase .. automodule:: ipsuite.data_loading.add_data_ase - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + load_data - - - - + + + + .. rubric:: Classes .. autosummary:: - + AddData ReadData - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_h5md.rst b/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_h5md.rst index 5dad0ffc..aeea8f87 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_h5md.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_h5md.rst @@ -3,27 +3,24 @@ ipsuite.data\_loading.add\_data\_h5md .. automodule:: ipsuite.data_loading.add_data_h5md - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + AddDataH5MD - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.data_loading.rst b/docs/source/_get_started/_autosummary/ipsuite.data_loading.rst index d921f903..7a92b629 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.data_loading.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.data_loading.rst @@ -3,21 +3,21 @@ .. automodule:: ipsuite.data_loading - - - - - - - - - - - - + + + + + + + + + + + + @@ -29,4 +29,3 @@ ipsuite.data_loading.add_data_ase ipsuite.data_loading.add_data_h5md - diff --git a/docs/source/_get_started/_autosummary/ipsuite.fields.atoms.rst b/docs/source/_get_started/_autosummary/ipsuite.fields.atoms.rst index 3c4e1d82..d32ba900 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.fields.atoms.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.fields.atoms.rst @@ -3,27 +3,24 @@ ipsuite.fields.atoms .. automodule:: ipsuite.fields.atoms - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + Atoms - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.fields.rst b/docs/source/_get_started/_autosummary/ipsuite.fields.rst index 933a1d5a..ef4da94f 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.fields.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.fields.rst @@ -3,21 +3,21 @@ .. automodule:: ipsuite.fields - - - - - - - - - - - - + + + + + + + + + + + + @@ -28,4 +28,3 @@ :recursive: ipsuite.fields.atoms - diff --git a/docs/source/_get_started/_autosummary/ipsuite.geometry.barycenter_coarse_grain.rst b/docs/source/_get_started/_autosummary/ipsuite.geometry.barycenter_coarse_grain.rst index f59fe34f..f18a946b 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.geometry.barycenter_coarse_grain.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.geometry.barycenter_coarse_grain.rst @@ -3,28 +3,25 @@ ipsuite.geometry.barycenter\_coarse\_grain .. automodule:: ipsuite.geometry.barycenter_coarse_grain - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + barycenter_backmapping coarse_grain_to_barycenter - - - - - - - - + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.geometry.graphs.rst b/docs/source/_get_started/_autosummary/ipsuite.geometry.graphs.rst index 0c08f233..71c943a0 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.geometry.graphs.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.geometry.graphs.rst @@ -3,30 +3,27 @@ ipsuite.geometry.graphs .. automodule:: ipsuite.geometry.graphs - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + atoms_to_graph edges_from_atoms identify_molecules split_molecule - - - - - - - - + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.geometry.mapping.rst b/docs/source/_get_started/_autosummary/ipsuite.geometry.mapping.rst index 6899cfd7..25f9bdbd 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.geometry.mapping.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.geometry.mapping.rst @@ -3,27 +3,24 @@ ipsuite.geometry.mapping .. automodule:: ipsuite.geometry.mapping - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + BarycenterMapping - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.geometry.rst b/docs/source/_get_started/_autosummary/ipsuite.geometry.rst index f1ab65db..6dd258b8 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.geometry.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.geometry.rst @@ -3,21 +3,21 @@ .. automodule:: ipsuite.geometry - - - - - - - - - - - - + + + + + + + + + + + + @@ -31,4 +31,3 @@ ipsuite.geometry.graphs ipsuite.geometry.mapping ipsuite.geometry.unwrap - diff --git a/docs/source/_get_started/_autosummary/ipsuite.geometry.unwrap.rst b/docs/source/_get_started/_autosummary/ipsuite.geometry.unwrap.rst index 2a4d6a60..79ac7f30 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.geometry.unwrap.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.geometry.unwrap.rst @@ -3,31 +3,28 @@ ipsuite.geometry.unwrap .. automodule:: ipsuite.geometry.unwrap - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + closest_atom_to_center displace_neighbors sort_atomic_edges unwrap unwrap_system - - - - - - - - + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.apax.rst b/docs/source/_get_started/_autosummary/ipsuite.models.apax.rst index ad68ba81..dd040a79 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.models.apax.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.models.apax.rst @@ -3,29 +3,26 @@ ipsuite.models.apax .. automodule:: ipsuite.models.apax - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + Apax ApaxEnsemble BatchKernelSelection - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.base.rst b/docs/source/_get_started/_autosummary/ipsuite.models.base.rst index 453bea26..da5cb4d6 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.models.base.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.models.base.rst @@ -3,27 +3,24 @@ ipsuite.models.base .. automodule:: ipsuite.models.base - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + MLModel - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.ensemble.rst b/docs/source/_get_started/_autosummary/ipsuite.models.ensemble.rst index 3c0353c6..af0ae522 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.models.ensemble.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.models.ensemble.rst @@ -3,28 +3,25 @@ ipsuite.models.ensemble .. automodule:: ipsuite.models.ensemble - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + EnsembleCalculator EnsembleModel - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.gap.rst b/docs/source/_get_started/_autosummary/ipsuite.models.gap.rst index 6b63bdc0..250cf917 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.models.gap.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.models.gap.rst @@ -3,20 +3,20 @@ ipsuite.models.gap .. automodule:: ipsuite.models.gap - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + DistanceNb DistanceNbConverter GAP @@ -24,12 +24,9 @@ ipsuite.models.gap GapParameterConverter SOAP SOAPConverter - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.mace_model.rst b/docs/source/_get_started/_autosummary/ipsuite.models.mace_model.rst index 55cb0fe0..2b7e8983 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.models.mace_model.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.models.mace_model.rst @@ -3,33 +3,30 @@ ipsuite.models.mace\_model .. automodule:: ipsuite.models.mace_model - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + execute - - - - + + + + .. rubric:: Classes .. autosummary:: - + MACE - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.nequip.rst b/docs/source/_get_started/_autosummary/ipsuite.models.nequip.rst index bf109ce4..35206b2c 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.models.nequip.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.models.nequip.rst @@ -3,27 +3,24 @@ ipsuite.models.nequip .. automodule:: ipsuite.models.nequip - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + Nequip - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.rst b/docs/source/_get_started/_autosummary/ipsuite.models.rst index 6b52f726..4bd01e37 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.models.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.models.rst @@ -3,21 +3,21 @@ .. automodule:: ipsuite.models - - - - - - - - - - - - + + + + + + + + + + + + @@ -33,4 +33,3 @@ ipsuite.models.gap ipsuite.models.mace_model ipsuite.models.nequip - diff --git a/docs/source/_get_started/_autosummary/ipsuite.nodes.rst b/docs/source/_get_started/_autosummary/ipsuite.nodes.rst index 24ef83d2..a55c1629 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.nodes.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.nodes.rst @@ -3,21 +3,18 @@ .. automodule:: ipsuite.nodes - - - - - - - - - - - - + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.project.rst b/docs/source/_get_started/_autosummary/ipsuite.project.rst index ee135e23..8dcf6e3e 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.project.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.project.rst @@ -3,27 +3,24 @@ .. automodule:: ipsuite.project - - - - - - - - + + + + + + + + .. rubric:: Classes .. autosummary:: - + Project - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.static_data.rst b/docs/source/_get_started/_autosummary/ipsuite.static_data.rst index 0a5700c8..7eccd181 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.static_data.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.static_data.rst @@ -3,21 +3,18 @@ .. automodule:: ipsuite.static_data - - - - - - - - - - - - + + + + + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.ase_sim.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.ase_sim.rst index 78b55805..febb530c 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.utils.ase_sim.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.ase_sim.rst @@ -3,31 +3,28 @@ ipsuite.utils.ase\_sim .. automodule:: ipsuite.utils.ase_sim - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + freeze_copy_atoms get_box_from_density get_density_from_atoms get_desc get_energy - - - - - - - - + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.combine.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.combine.rst index d7af5d2d..3766a71d 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.utils.combine.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.combine.rst @@ -3,34 +3,31 @@ ipsuite.utils.combine .. automodule:: ipsuite.utils.combine - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + get_flat_data_from_dict get_ids_per_key - - - - + + + + .. rubric:: Classes .. autosummary:: - + ExcludeIds - - - - - + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.docs.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.docs.rst index f0870ce3..7e1cba39 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.utils.docs.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.docs.rst @@ -3,27 +3,24 @@ ipsuite.utils.docs .. automodule:: ipsuite.utils.docs - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + create_dvc_git_env_for_doctest - - - - - - - - + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.helpers.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.helpers.rst index a2c70721..97f4d7d3 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.utils.helpers.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.helpers.rst @@ -3,29 +3,26 @@ ipsuite.utils.helpers .. automodule:: ipsuite.utils.helpers - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + check_duplicate_keys get_deps_if_node setup_ase - - - - - - - - + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.logs.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.logs.rst index 0a1e779d..5cd2e7c9 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.utils.logs.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.logs.rst @@ -3,27 +3,24 @@ ipsuite.utils.logs .. automodule:: ipsuite.utils.logs - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + setup_logging - - - - - - - - + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.md.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.md.rst index fbecdaa7..6ebfb0b1 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.utils.md.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.md.rst @@ -3,27 +3,24 @@ ipsuite.utils.md .. automodule:: ipsuite.utils.md - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + get_energy_terms - - - - - - - - + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.metrics.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.metrics.rst index cf0e86b8..2850ce41 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.utils.metrics.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.metrics.rst @@ -3,16 +3,16 @@ ipsuite.utils.metrics .. automodule:: ipsuite.utils.metrics - - - - - + + + + + .. rubric:: Functions .. autosummary:: - + calculate_l_p_norm get_angles get_full_metrics @@ -22,16 +22,13 @@ ipsuite.utils.metrics mean_squared_error relative_rmse root_mean_squared_error - - - - - - - - + + + + + diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.rst index 81ecbfc0..ff838736 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.utils.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.rst @@ -3,21 +3,21 @@ .. automodule:: ipsuite.utils - - - - - - - - - - - - + + + + + + + + + + + + @@ -34,4 +34,3 @@ ipsuite.utils.logs ipsuite.utils.md ipsuite.utils.metrics - diff --git a/ipsuite/configuration_generation/packmol.py b/ipsuite/configuration_generation/packmol.py index 266815e4..d59ea802 100644 --- a/ipsuite/configuration_generation/packmol.py +++ b/ipsuite/configuration_generation/packmol.py @@ -19,7 +19,7 @@ class Packmol(base.IPSNode): """ Pack molecules in defined regions of space - + Attributes ---------- data: list[list[ase.Atoms]] diff --git a/ipsuite/configuration_generation/smiles_to_atoms.py b/ipsuite/configuration_generation/smiles_to_atoms.py index a68a4e49..15214c4f 100644 --- a/ipsuite/configuration_generation/smiles_to_atoms.py +++ b/ipsuite/configuration_generation/smiles_to_atoms.py @@ -1,4 +1,5 @@ """"Use RDKit to convert Smiles stings to atoms""" + import pathlib import ase @@ -11,8 +12,8 @@ class SmilesToAtoms(base.IPSNode): - """Generate ase.atom object from smiles string - """ + """Generate ase.atom object from smiles string""" + atoms = fields.Atoms() smiles: str = zntrack.params() @@ -49,6 +50,7 @@ def view(self) -> view: class SmilesToConformers(base.IPSNode): """Generate random conformers of molecule from smiles string""" + atoms = fields.Atoms() smiles: str = zntrack.params() From a542ca90e994a34efea581acaf98be3e1581982a Mon Sep 17 00:00:00 2001 From: Julian Peters Date: Thu, 18 Apr 2024 14:37:53 +0200 Subject: [PATCH 29/35] make water image in docs transparent (and fix minor error from previous commit) --- docs/source/images/water_packmol.png | Bin 56414 -> 47947 bytes .../smiles_to_atoms.py | 2 +- 2 files changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/images/water_packmol.png b/docs/source/images/water_packmol.png index e0604e5621d8fe503c9753ccc152f0a21718bcd0..fecc8ed9641b209b2e13798cc50772593b39969a 100644 GIT binary patch literal 47947 zcmeFYbx>T*wl_TZ;DdzV41*JNaJRvo5FiOQI0SchcXtRHAP^)#aQEOz2#^pwNFV`% 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b/ipsuite/configuration_generation/smiles_to_atoms.py @@ -1,4 +1,4 @@ -"""Use RDKit to convert Smiles stings to atoms""" +"""Use RDKit to convert Smiles strings to atoms""" import pathlib import ase From 2443472c22691d0ea1e406a911a670481a2374f8 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 18 Apr 2024 12:43:57 +0000 Subject: [PATCH 31/35] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- .../ipsuite.analysis.bin_property.rst | 6 ------ .../ipsuite.analysis.bond_stretch.rst | 6 ------ .../_autosummary/ipsuite.analysis.ensemble.rst | 6 ------ .../_autosummary/ipsuite.analysis.md.rst | 6 ------ .../ipsuite.analysis.model.dynamics.rst | 6 ------ .../ipsuite.analysis.model.dynamics_checks.rst | 6 ------ .../_autosummary/ipsuite.analysis.model.math.rst | 10 ---------- .../ipsuite.analysis.model.plots.rst | 10 ---------- .../ipsuite.analysis.model.predict.rst | 6 ------ .../ipsuite.analysis.sensitivity.rst | 6 ------ .../_autosummary/ipsuite.base.base.rst | 6 ------ .../_autosummary/ipsuite.base.protocol.rst | 6 ------ .../ipsuite.bootstrap.random_displacements.rst | 6 ------ .../ipsuite.bootstrap.surface_mods.rst | 6 ------ .../ipsuite.calculators.apax_jax_md.rst | 6 ------ .../ipsuite.calculators.ase_geoopt.rst | 6 ------ .../_autosummary/ipsuite.calculators.ase_md.rst | 6 ------ .../ipsuite.calculators.ase_standard.rst | 6 ------ .../_autosummary/ipsuite.calculators.cp2k.rst | 6 ------ .../_autosummary/ipsuite.calculators.lammps.rst | 6 ------ .../_autosummary/ipsuite.calculators.mix.rst | 6 ------ .../_autosummary/ipsuite.calculators.orca.rst | 6 ------ .../ipsuite.calculators.torch_d3.rst | 6 ------ .../_autosummary/ipsuite.calculators.xtb.rst | 6 ------ ...ipsuite.configuration_comparison.MMKernel.rst | 2 -- .../ipsuite.configuration_comparison.REMatch.rst | 2 -- .../ipsuite.configuration_comparison.base.rst | 6 ------ .../ipsuite.configuration_generation.packmol.rst | 6 ------ ....configuration_generation.smiles_to_atoms.rst | 6 ------ .../ipsuite.configuration_selection.base.rst | 6 ------ .../ipsuite.configuration_selection.filter.rst | 6 ------ .../ipsuite.configuration_selection.index.rst | 6 ------ .../ipsuite.configuration_selection.kernel.rst | 6 ------ .../ipsuite.configuration_selection.random.rst | 6 ------ .../ipsuite.configuration_selection.split.rst | 6 ------ ...ipsuite.configuration_selection.threshold.rst | 6 ------ ...te.configuration_selection.uniform_arange.rst | 6 ------ ...configuration_selection.uniform_energetic.rst | 6 ------ ....configuration_selection.uniform_temporal.rst | 6 ------ .../ipsuite.data_loading.add_data_ase.rst | 6 ------ .../ipsuite.data_loading.add_data_h5md.rst | 6 ------ .../_autosummary/ipsuite.fields.atoms.rst | 6 ------ .../ipsuite.geometry.barycenter_coarse_grain.rst | 10 ---------- .../_autosummary/ipsuite.geometry.graphs.rst | 10 ---------- .../_autosummary/ipsuite.geometry.mapping.rst | 6 ------ .../_autosummary/ipsuite.geometry.unwrap.rst | 10 ---------- .../_autosummary/ipsuite.models.apax.rst | 6 ------ .../_autosummary/ipsuite.models.base.rst | 6 ------ .../_autosummary/ipsuite.models.ensemble.rst | 6 ------ .../_autosummary/ipsuite.models.gap.rst | 6 ------ .../_autosummary/ipsuite.models.mace_model.rst | 6 ------ .../_autosummary/ipsuite.models.nequip.rst | 6 ------ .../_get_started/_autosummary/ipsuite.nodes.rst | 16 ---------------- .../_autosummary/ipsuite.project.rst | 6 ------ .../_autosummary/ipsuite.static_data.rst | 16 ---------------- .../_autosummary/ipsuite.utils.ase_sim.rst | 10 ---------- .../_autosummary/ipsuite.utils.combine.rst | 6 ------ .../_autosummary/ipsuite.utils.docs.rst | 10 ---------- .../_autosummary/ipsuite.utils.helpers.rst | 10 ---------- .../_autosummary/ipsuite.utils.logs.rst | 10 ---------- .../_autosummary/ipsuite.utils.md.rst | 10 ---------- .../_autosummary/ipsuite.utils.metrics.rst | 10 ---------- .../configuration_generation/smiles_to_atoms.py | 1 + 63 files changed, 1 insertion(+), 428 deletions(-) diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.bin_property.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.bin_property.rst index 436d70e3..a8116ab2 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.bin_property.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.bin_property.rst @@ -24,9 +24,3 @@ ipsuite.analysis.bin\_property ForcesUncertaintyHistogram LabelHistogram StressHistogram - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.bond_stretch.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.bond_stretch.rst index 6356a14f..b66183d5 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.bond_stretch.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.bond_stretch.rst @@ -18,9 +18,3 @@ ipsuite.analysis.bond\_stretch .. autosummary:: BondStretchAnalyses - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.ensemble.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.ensemble.rst index 8e4f4d53..55e9653f 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.ensemble.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.ensemble.rst @@ -24,9 +24,3 @@ ipsuite.analysis.ensemble .. autosummary:: ModelEnsembleAnalysis - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.md.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.md.rst index 7d541465..29166462 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.md.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.md.rst @@ -18,9 +18,3 @@ ipsuite.analysis.md .. autosummary:: AnalyseDensity - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics.rst index 2d17f1ed..ded615c5 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics.rst @@ -27,9 +27,3 @@ ipsuite.analysis.model.dynamics BoxScale MDStability RattleAnalysis - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics_checks.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics_checks.rst index 8c4a6de5..f09235c8 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics_checks.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics_checks.rst @@ -22,9 +22,3 @@ ipsuite.analysis.model.dynamics\_checks NaNCheck TemperatureCheck ThresholdCheck - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.math.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.math.rst index 52582ced..35998d9b 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.math.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.math.rst @@ -18,13 +18,3 @@ ipsuite.analysis.model.math compute_trans_forces decompose_stress_tensor force_decomposition - - - - - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.plots.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.plots.rst index 9812305b..88abaceb 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.plots.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.plots.rst @@ -17,13 +17,3 @@ ipsuite.analysis.model.plots get_figure get_hist get_histogram_figure - - - - - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.predict.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.predict.rst index 6bd20ed8..9357f2ac 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.predict.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.predict.rst @@ -21,9 +21,3 @@ ipsuite.analysis.model.predict ForceDecomposition Prediction PredictionMetrics - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.sensitivity.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.sensitivity.rst index 1d5f221e..9f95b8b9 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.analysis.sensitivity.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.analysis.sensitivity.rst @@ -27,9 +27,3 @@ ipsuite.analysis.sensitivity AnalyseSingleForceSensitivity IsConstraintMD MoveSingleParticle - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.base.base.rst b/docs/source/_get_started/_autosummary/ipsuite.base.base.rst index 4c83c56f..0ed40d88 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.base.base.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.base.base.rst @@ -24,9 +24,3 @@ ipsuite.base.base Mapping ProcessAtoms ProcessSingleAtom - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.base.protocol.rst b/docs/source/_get_started/_autosummary/ipsuite.base.protocol.rst index 56da7eda..720cbb0f 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.base.protocol.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.base.protocol.rst @@ -20,9 +20,3 @@ ipsuite.base.protocol HasAtoms HasSelectedConfigurations ProcessAtoms - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.bootstrap.random_displacements.rst b/docs/source/_get_started/_autosummary/ipsuite.bootstrap.random_displacements.rst index 64c7512e..fb43e7d5 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.bootstrap.random_displacements.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.bootstrap.random_displacements.rst @@ -21,9 +21,3 @@ ipsuite.bootstrap.random\_displacements RattleAtoms RotateMolecules TranslateMolecules - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.bootstrap.surface_mods.rst b/docs/source/_get_started/_autosummary/ipsuite.bootstrap.surface_mods.rst index cc1cbdc4..87ed5dbc 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.bootstrap.surface_mods.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.bootstrap.surface_mods.rst @@ -25,9 +25,3 @@ ipsuite.bootstrap.surface\_mods SurfaceRasterMetrics SurfaceRasterScan - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.apax_jax_md.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.apax_jax_md.rst index 14a15959..7a9298b6 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.apax_jax_md.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.apax_jax_md.rst @@ -18,9 +18,3 @@ ipsuite.calculators.apax\_jax\_md .. autosummary:: ApaxJaxMD - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_geoopt.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_geoopt.rst index db5899ff..4d87733f 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_geoopt.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_geoopt.rst @@ -19,9 +19,3 @@ ipsuite.calculators.ase\_geoopt ASEGeoOpt BatchASEGeoOpt - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_md.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_md.rst index b154fc0e..b829a446 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_md.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_md.rst @@ -34,9 +34,3 @@ ipsuite.calculators.ase\_md RescaleBoxModifier TemperatureOscillatingRampModifier TemperatureRampModifier - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_standard.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_standard.rst index 25fe8744..3effc4a2 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_standard.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_standard.rst @@ -20,9 +20,3 @@ ipsuite.calculators.ase\_standard EMTCalculator EMTSinglePoint LJSinglePoint - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.cp2k.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.cp2k.rst index 60df164f..16663e1f 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.cp2k.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.cp2k.rst @@ -19,9 +19,3 @@ ipsuite.calculators.cp2k CP2KSinglePoint CP2KYaml - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.lammps.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.lammps.rst index 457d7499..9e71f215 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.lammps.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.lammps.rst @@ -18,9 +18,3 @@ ipsuite.calculators.lammps .. autosummary:: LammpsSimulator - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.mix.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.mix.rst index 321d810b..9fc2a7de 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.mix.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.mix.rst @@ -19,9 +19,3 @@ ipsuite.calculators.mix CalculatorNode MixCalculator - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.orca.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.orca.rst index 273def1d..3135f426 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.orca.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.orca.rst @@ -18,9 +18,3 @@ ipsuite.calculators.orca .. autosummary:: OrcaSinglePoint - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.torch_d3.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.torch_d3.rst index 7fdd2ae2..128bf78d 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.torch_d3.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.torch_d3.rst @@ -19,9 +19,3 @@ ipsuite.calculators.torch\_d3 TorchD3 TorchDFTD3CalculatorNL - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.xtb.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.xtb.rst index 8c4efcd8..a40e989e 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.calculators.xtb.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.xtb.rst @@ -18,9 +18,3 @@ ipsuite.calculators.xtb .. autosummary:: xTBSinglePoint - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.MMKernel.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.MMKernel.rst index 2ce1784c..7adeab24 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.MMKernel.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.MMKernel.rst @@ -45,5 +45,3 @@ ipsuite.configuration\_comparison.MMKernel ~MMKernel.use_jit ~MMKernel.use_repr ~MMKernel.uuid - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.REMatch.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.REMatch.rst index d118569a..bbe8ea70 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.REMatch.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.REMatch.rst @@ -48,5 +48,3 @@ ipsuite.configuration\_comparison.REMatch ~REMatch.use_jit ~REMatch.use_repr ~REMatch.uuid - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.base.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.base.rst index c592fbe7..573796d3 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.base.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.base.rst @@ -28,9 +28,3 @@ ipsuite.configuration\_comparison.base ConfigurationComparison SOAPParameter SOAPParameterConverter - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.packmol.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.packmol.rst index bb1d1e9c..1c66af6b 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.packmol.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.packmol.rst @@ -19,9 +19,3 @@ ipsuite.configuration\_generation.packmol MultiPackmol Packmol - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.smiles_to_atoms.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.smiles_to_atoms.rst index 9189801c..fb6227d0 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.smiles_to_atoms.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.smiles_to_atoms.rst @@ -19,9 +19,3 @@ ipsuite.configuration\_generation.smiles\_to\_atoms SmilesToAtoms SmilesToConformers - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.base.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.base.rst index 4148b404..2db8513e 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.base.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.base.rst @@ -19,9 +19,3 @@ ipsuite.configuration\_selection.base BatchConfigurationSelection ConfigurationSelection - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.filter.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.filter.rst index 2d8cd6be..44fd9a9a 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.filter.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.filter.rst @@ -18,9 +18,3 @@ ipsuite.configuration\_selection.filter .. autosummary:: FilterOutlier - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.index.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.index.rst index e16a9186..9a4e32d0 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.index.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.index.rst @@ -18,9 +18,3 @@ ipsuite.configuration\_selection.index .. autosummary:: IndexSelection - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.kernel.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.kernel.rst index cbe90c5e..ecb538af 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.kernel.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.kernel.rst @@ -18,9 +18,3 @@ ipsuite.configuration\_selection.kernel .. autosummary:: KernelSelection - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.random.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.random.rst index e96f02fb..794a63fb 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.random.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.random.rst @@ -18,9 +18,3 @@ ipsuite.configuration\_selection.random .. autosummary:: RandomSelection - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.split.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.split.rst index 23cf82ec..23aa1dba 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.split.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.split.rst @@ -18,9 +18,3 @@ ipsuite.configuration\_selection.split .. autosummary:: SplitSelection - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.threshold.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.threshold.rst index ca606bb6..ac297e54 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.threshold.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.threshold.rst @@ -26,9 +26,3 @@ ipsuite.configuration\_selection.threshold .. autosummary:: ThresholdSelection - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_arange.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_arange.rst index c25038bd..ad5494bf 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_arange.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_arange.rst @@ -18,9 +18,3 @@ ipsuite.configuration\_selection.uniform\_arange .. autosummary:: UniformArangeSelection - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_energetic.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_energetic.rst index bb7f33ad..a58532cf 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_energetic.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_energetic.rst @@ -18,9 +18,3 @@ ipsuite.configuration\_selection.uniform\_energetic .. autosummary:: UniformEnergeticSelection - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_temporal.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_temporal.rst index 227f6c93..fc0f04f5 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_temporal.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_temporal.rst @@ -18,9 +18,3 @@ ipsuite.configuration\_selection.uniform\_temporal .. autosummary:: UniformTemporalSelection - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_ase.rst b/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_ase.rst index 20e3c9f8..2a5b6212 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_ase.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_ase.rst @@ -25,9 +25,3 @@ ipsuite.data\_loading.add\_data\_ase AddData ReadData - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_h5md.rst b/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_h5md.rst index aeea8f87..4586617f 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_h5md.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_h5md.rst @@ -18,9 +18,3 @@ ipsuite.data\_loading.add\_data\_h5md .. autosummary:: AddDataH5MD - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.fields.atoms.rst b/docs/source/_get_started/_autosummary/ipsuite.fields.atoms.rst index d32ba900..6f650f93 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.fields.atoms.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.fields.atoms.rst @@ -18,9 +18,3 @@ ipsuite.fields.atoms .. autosummary:: Atoms - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.geometry.barycenter_coarse_grain.rst b/docs/source/_get_started/_autosummary/ipsuite.geometry.barycenter_coarse_grain.rst index f18a946b..790d0303 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.geometry.barycenter_coarse_grain.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.geometry.barycenter_coarse_grain.rst @@ -15,13 +15,3 @@ ipsuite.geometry.barycenter\_coarse\_grain barycenter_backmapping coarse_grain_to_barycenter - - - - - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.geometry.graphs.rst b/docs/source/_get_started/_autosummary/ipsuite.geometry.graphs.rst index 71c943a0..e4e1cb6e 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.geometry.graphs.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.geometry.graphs.rst @@ -17,13 +17,3 @@ ipsuite.geometry.graphs edges_from_atoms identify_molecules split_molecule - - - - - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.geometry.mapping.rst b/docs/source/_get_started/_autosummary/ipsuite.geometry.mapping.rst index 25f9bdbd..fe850898 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.geometry.mapping.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.geometry.mapping.rst @@ -18,9 +18,3 @@ ipsuite.geometry.mapping .. autosummary:: BarycenterMapping - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.geometry.unwrap.rst b/docs/source/_get_started/_autosummary/ipsuite.geometry.unwrap.rst index 79ac7f30..87728056 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.geometry.unwrap.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.geometry.unwrap.rst @@ -18,13 +18,3 @@ ipsuite.geometry.unwrap sort_atomic_edges unwrap unwrap_system - - - - - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.apax.rst b/docs/source/_get_started/_autosummary/ipsuite.models.apax.rst index dd040a79..cab116c5 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.models.apax.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.models.apax.rst @@ -20,9 +20,3 @@ ipsuite.models.apax Apax ApaxEnsemble BatchKernelSelection - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.base.rst b/docs/source/_get_started/_autosummary/ipsuite.models.base.rst index da5cb4d6..674be800 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.models.base.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.models.base.rst @@ -18,9 +18,3 @@ ipsuite.models.base .. autosummary:: MLModel - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.ensemble.rst b/docs/source/_get_started/_autosummary/ipsuite.models.ensemble.rst index af0ae522..f42c02fe 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.models.ensemble.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.models.ensemble.rst @@ -19,9 +19,3 @@ ipsuite.models.ensemble EnsembleCalculator EnsembleModel - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.gap.rst b/docs/source/_get_started/_autosummary/ipsuite.models.gap.rst index 250cf917..3d3b7a85 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.models.gap.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.models.gap.rst @@ -24,9 +24,3 @@ ipsuite.models.gap GapParameterConverter SOAP SOAPConverter - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.mace_model.rst b/docs/source/_get_started/_autosummary/ipsuite.models.mace_model.rst index 2b7e8983..b77873f0 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.models.mace_model.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.models.mace_model.rst @@ -24,9 +24,3 @@ ipsuite.models.mace\_model .. autosummary:: MACE - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.nequip.rst b/docs/source/_get_started/_autosummary/ipsuite.models.nequip.rst index 35206b2c..508ee5f4 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.models.nequip.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.models.nequip.rst @@ -18,9 +18,3 @@ ipsuite.models.nequip .. autosummary:: Nequip - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.nodes.rst b/docs/source/_get_started/_autosummary/ipsuite.nodes.rst index a55c1629..79e2bca2 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.nodes.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.nodes.rst @@ -2,19 +2,3 @@ ============= .. automodule:: ipsuite.nodes - - - - - - - - - - - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.project.rst b/docs/source/_get_started/_autosummary/ipsuite.project.rst index 8dcf6e3e..39eac890 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.project.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.project.rst @@ -18,9 +18,3 @@ .. autosummary:: Project - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.static_data.rst b/docs/source/_get_started/_autosummary/ipsuite.static_data.rst index 7eccd181..cb98b831 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.static_data.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.static_data.rst @@ -2,19 +2,3 @@ ==================== .. automodule:: ipsuite.static_data - - - - - - - - - - - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.ase_sim.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.ase_sim.rst index febb530c..d860b798 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.utils.ase_sim.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.ase_sim.rst @@ -18,13 +18,3 @@ ipsuite.utils.ase\_sim get_density_from_atoms get_desc get_energy - - - - - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.combine.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.combine.rst index 3766a71d..8659aecd 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.utils.combine.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.combine.rst @@ -25,9 +25,3 @@ ipsuite.utils.combine .. autosummary:: ExcludeIds - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.docs.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.docs.rst index 7e1cba39..6c4606cd 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.utils.docs.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.docs.rst @@ -14,13 +14,3 @@ ipsuite.utils.docs .. autosummary:: create_dvc_git_env_for_doctest - - - - - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.helpers.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.helpers.rst index 97f4d7d3..8446b16e 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.utils.helpers.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.helpers.rst @@ -16,13 +16,3 @@ ipsuite.utils.helpers check_duplicate_keys get_deps_if_node setup_ase - - - - - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.logs.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.logs.rst index 5cd2e7c9..17b6c896 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.utils.logs.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.logs.rst @@ -14,13 +14,3 @@ ipsuite.utils.logs .. autosummary:: setup_logging - - - - - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.md.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.md.rst index 6ebfb0b1..16ab6dba 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.utils.md.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.md.rst @@ -14,13 +14,3 @@ ipsuite.utils.md .. autosummary:: get_energy_terms - - - - - - - - - - diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.metrics.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.metrics.rst index 2850ce41..5a6420b4 100644 --- a/docs/source/_get_started/_autosummary/ipsuite.utils.metrics.rst +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.metrics.rst @@ -22,13 +22,3 @@ ipsuite.utils.metrics mean_squared_error relative_rmse root_mean_squared_error - - - - - - - - - - diff --git a/ipsuite/configuration_generation/smiles_to_atoms.py b/ipsuite/configuration_generation/smiles_to_atoms.py index 8d2a2f50..1e9d73c9 100644 --- a/ipsuite/configuration_generation/smiles_to_atoms.py +++ b/ipsuite/configuration_generation/smiles_to_atoms.py @@ -1,4 +1,5 @@ """Use RDKit to convert Smiles strings to atoms""" + import pathlib import ase From 4c4ddf81369227bec7cefa38420819dafb4cd025 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 25 Jul 2024 14:52:35 +0000 Subject: [PATCH 32/35] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- ipsuite/calculators/lammps.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/ipsuite/calculators/lammps.py b/ipsuite/calculators/lammps.py index 25e5dc50..c51e5904 100644 --- a/ipsuite/calculators/lammps.py +++ b/ipsuite/calculators/lammps.py @@ -1,5 +1,4 @@ -"""LAMMPS interface for MD Simulations using LAMMPS -""" +"""LAMMPS interface for MD Simulations using LAMMPS""" import importlib.resources as pkg_resources import pathlib From a4e281cbe6b1ec19d25d5a8363a7430a69d553ab Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Moritz=20R=2E=20Sch=C3=A4fer?= Date: Thu, 5 Sep 2024 10:12:50 +0200 Subject: [PATCH 33/35] fixed pyproject --- poetry.lock | 2745 +++++++++++++++++++++++++++--------------------- pyproject.toml | 6 - 2 files changed, 1554 insertions(+), 1197 deletions(-) diff --git a/poetry.lock b/poetry.lock index 3180bd64..adaaabc8 100644 --- a/poetry.lock +++ b/poetry.lock @@ -24,25 +24,25 @@ files = [ [[package]] name = "aiobotocore" -version = "2.13.1" +version = "2.14.0" description = "Async client for aws services using botocore and aiohttp" optional = false python-versions = ">=3.8" files = [ - {file = "aiobotocore-2.13.1-py3-none-any.whl", hash = "sha256:1bef121b99841ee3cc788e4ed97c332ba32353b1f00e886d1beb3aae95520858"}, - {file = "aiobotocore-2.13.1.tar.gz", hash = "sha256:134f9606c2f91abde38cbc61c3241113e26ff244633e0c31abb7e09da3581c9b"}, + {file = "aiobotocore-2.14.0-py3-none-any.whl", hash = "sha256:721c52f5d1221daa4851cfa9ab5db14440477f33d763da9019691c4f67163873"}, + {file = "aiobotocore-2.14.0.tar.gz", hash = "sha256:680dcbcde9cb0dcefbcddc180d273c2d048940f87f2bdb0eebe0f4c30c1e39b9"}, ] [package.dependencies] aiohttp = ">=3.9.2,<4.0.0" aioitertools = ">=0.5.1,<1.0.0" -boto3 = {version = ">=1.34.70,<1.34.132", optional = true, markers = "extra == \"boto3\""} -botocore = ">=1.34.70,<1.34.132" +boto3 = {version = ">=1.35.0,<1.35.8", optional = true, markers = "extra == \"boto3\""} +botocore = ">=1.35.0,<1.35.8" wrapt = ">=1.10.10,<2.0.0" [package.extras] -awscli = ["awscli (>=1.32.70,<1.33.14)"] -boto3 = ["boto3 (>=1.34.70,<1.34.132)"] +awscli = ["awscli (>=1.34.0,<1.34.8)"] +boto3 = ["boto3 (>=1.35.0,<1.35.8)"] [[package]] name = "aiofiles" @@ -56,91 +56,118 @@ files = [ ] [[package]] -name = "aiohttp" -version = "3.9.5" -description = "Async http client/server framework (asyncio)" +name = "aiohappyeyeballs" +version = "2.4.0" +description = "Happy Eyeballs for asyncio" optional = false python-versions = ">=3.8" files = [ - {file = "aiohttp-3.9.5-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:fcde4c397f673fdec23e6b05ebf8d4751314fa7c24f93334bf1f1364c1c69ac7"}, - {file = "aiohttp-3.9.5-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:5d6b3f1fabe465e819aed2c421a6743d8debbde79b6a8600739300630a01bf2c"}, - {file = "aiohttp-3.9.5-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:6ae79c1bc12c34082d92bf9422764f799aee4746fd7a392db46b7fd357d4a17a"}, - {file = "aiohttp-3.9.5-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = 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-version = "3.53.1" ->>>>>>> main description = "Git for data scientists - manage your code and data together" optional = false python-versions = ">=3.9" files = [ -<<<<<<< HEAD {file = "dvc-3.55.2-py3-none-any.whl", hash = "sha256:1324e4a5471618a4300dd0a7c33ac877d5e057fbe48940812116494865d0e4e2"}, {file = "dvc-3.55.2.tar.gz", hash = "sha256:2fbb38385753d51b25967c80e672cf9dea046bdac182c159a2c1d1f246d15ce0"}, -======= - {file = "dvc-3.53.1-py3-none-any.whl", hash = "sha256:1294c390b107f119c58a168d9d74ffc3a1102a6e74fc931f6ba5e77a29df3a15"}, - {file = "dvc-3.53.1.tar.gz", hash = "sha256:8750b12055f5b505e60fe85010641c8a4d28fa0424c901adf745129fa6b3e5cf"}, ->>>>>>> main ] [package.dependencies] @@ -1860,22 +1616,13 @@ webhdfs-kerberos = ["dvc-webhdfs[kerberos] (>=3.1,<4)"] [[package]] name = "dvc-data" -<<<<<<< HEAD version = "3.16.5" -======= -version = "3.15.2" ->>>>>>> main description = "DVC's data management subsystem" optional = false python-versions = ">=3.9" files = [ -<<<<<<< HEAD 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false python-versions = "<4.0,>=3.10" files = [ -<<<<<<< HEAD {file = "znh5md-0.3.5-py3-none-any.whl", hash = "sha256:63199eb167a2c37df5cd40340c2665c894246eebd88aac8d0d39cb0fef351840"}, {file = "znh5md-0.3.5.tar.gz", hash = "sha256:94cc40518d7a78e8a9fc8742865928d0b7aee8c7421d3f42a9ad6820f138057e"}, -======= - {file = "znh5md-0.3.3-py3-none-any.whl", hash = "sha256:492d942057c461c67f4505ecbfc602d66c83409bb037f7d17efb8b478a1b4025"}, - {file = "znh5md-0.3.3.tar.gz", hash = "sha256:e1b2e8578c4bdac8f75c701d2b8c1a8324a0eef1658ace13d641e04c97a872e9"}, ->>>>>>> main ] [package.dependencies] @@ -8205,10 +7270,5 @@ gap = [] [metadata] lock-version = "2.0" -<<<<<<< HEAD -python-versions = ">=3.10,<3.12" -content-hash = "4fdd2ffb183ca84a325bc755d8231448ae8b251dec893202bf668a13dc1eb8ed" -======= python-versions = ">=3.10,<4.0.0" -content-hash = "cb5cdb0892be0bb7cdd7c42c06576dd330b71d8933c1baf3e854109cc3e5f988" ->>>>>>> main +content-hash = "abdec302cef669d143d3609d4804eb52891cf2ff50bd83b2757b7ef16f0bf83f" From 04cbc7c5ac5bada74066c664069b0000323dde62 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 5 Sep 2024 08:21:17 +0000 Subject: [PATCH 35/35] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- docs/source/_examples/01_Data_Loading_and_Selection.nblink | 2 +- docs/source/_examples/02_Training_Models.nblink | 2 +- .../03_Analysing_Datasets_and_Model_Predictions.nblink | 2 +- ...lecular_Dynamics_Structure_Generation_and_Simulation.nblink | 2 +- docs/source/_examples/05_Labeling_with_Calculators.nblink | 2 +- docs/source/_examples/06_Bootstrapping_Datasets.nblink | 2 +- docs/source/_examples/index.rst | 2 +- docs/source/_nodes/analysis.rst | 2 +- docs/source/_nodes/bootstrap.rst | 2 +- docs/source/_nodes/calculators.rst | 2 +- docs/source/_nodes/configuration_comparison.rst | 2 +- docs/source/_nodes/configuration_selection.rst | 2 +- docs/source/_nodes/data_loading.rst | 2 +- docs/source/_nodes/geometry.rst | 2 +- docs/source/_nodes/models.rst | 2 +- ipsuite/calculators/__init__.py | 3 ++- ipsuite/calculators/ase_geoopt.py | 1 - ipsuite/configuration_comparison/__init__.py | 1 + ipsuite/configuration_generation/__init__.py | 1 + ipsuite/configuration_selection/__init__.py | 1 + 20 files changed, 20 insertions(+), 17 deletions(-) diff --git a/docs/source/_examples/01_Data_Loading_and_Selection.nblink b/docs/source/_examples/01_Data_Loading_and_Selection.nblink index 28b9a634..4949dc69 100644 --- a/docs/source/_examples/01_Data_Loading_and_Selection.nblink +++ b/docs/source/_examples/01_Data_Loading_and_Selection.nblink @@ -1,3 +1,3 @@ { "path": "../../../examples/01_Data_Loading_and_Selection.ipynb" -} \ No newline at end of file +} diff --git a/docs/source/_examples/02_Training_Models.nblink b/docs/source/_examples/02_Training_Models.nblink index 968dc697..43debfed 100644 --- a/docs/source/_examples/02_Training_Models.nblink +++ b/docs/source/_examples/02_Training_Models.nblink @@ -1,3 +1,3 @@ { "path": "../../../examples/02_Training_Models.ipynb" -} \ No newline at end of file +} diff --git a/docs/source/_examples/03_Analysing_Datasets_and_Model_Predictions.nblink b/docs/source/_examples/03_Analysing_Datasets_and_Model_Predictions.nblink index c90b3b05..f73a3f83 100644 --- a/docs/source/_examples/03_Analysing_Datasets_and_Model_Predictions.nblink +++ b/docs/source/_examples/03_Analysing_Datasets_and_Model_Predictions.nblink @@ -1,3 +1,3 @@ { "path": "../../../examples/03_Analysing_Datasets_and_Model_Predictions.ipynb" -} \ No newline at end of file +} diff --git a/docs/source/_examples/04_Molecular_Dynamics_Structure_Generation_and_Simulation.nblink b/docs/source/_examples/04_Molecular_Dynamics_Structure_Generation_and_Simulation.nblink index f3f26703..48f1d5a1 100644 --- a/docs/source/_examples/04_Molecular_Dynamics_Structure_Generation_and_Simulation.nblink +++ b/docs/source/_examples/04_Molecular_Dynamics_Structure_Generation_and_Simulation.nblink @@ -1,3 +1,3 @@ { "path": "../../../examples/04_Molecular_Dynamics_Structure_Generation_and_Simulation.ipynb" -} \ No newline at end of file +} diff --git a/docs/source/_examples/05_Labeling_with_Calculators.nblink b/docs/source/_examples/05_Labeling_with_Calculators.nblink index 07c10fcc..56af6e18 100644 --- a/docs/source/_examples/05_Labeling_with_Calculators.nblink +++ b/docs/source/_examples/05_Labeling_with_Calculators.nblink @@ -1,3 +1,3 @@ { "path": "../../../examples/05_Labeling_with_Calculators.ipynb" -} \ No newline at end of file +} diff --git a/docs/source/_examples/06_Bootstrapping_Datasets.nblink b/docs/source/_examples/06_Bootstrapping_Datasets.nblink index a5aa23c0..56b6c559 100644 --- a/docs/source/_examples/06_Bootstrapping_Datasets.nblink +++ b/docs/source/_examples/06_Bootstrapping_Datasets.nblink @@ -1,3 +1,3 @@ { "path": "../../../examples/06_Bootstrapping_Datasets.ipynb" -} \ No newline at end of file +} diff --git a/docs/source/_examples/index.rst b/docs/source/_examples/index.rst index 5322e6c2..62bafde7 100644 --- a/docs/source/_examples/index.rst +++ b/docs/source/_examples/index.rst @@ -7,7 +7,7 @@ The notebooks contained in this section cover the functionality of IPS and assum The utility of IPS is best demonstrated by some worked examples. This section starts out with some introductory notebooks demonstrating the capabilities of the Nodes from each submodule. -Later notebooks feature some more complex workflows which are closer to real world use case. +Later notebooks feature some more complex workflows which are closer to real world use case. All notebooks can be found in `/examples/docs`. diff --git a/docs/source/_nodes/analysis.rst b/docs/source/_nodes/analysis.rst index 1d6d86ea..0e5fd368 100644 --- a/docs/source/_nodes/analysis.rst +++ b/docs/source/_nodes/analysis.rst @@ -2,4 +2,4 @@ Analysis ======== .. automodule:: ipsuite.analysis :members: - :show-inheritance: \ No newline at end of file + :show-inheritance: diff --git a/docs/source/_nodes/bootstrap.rst b/docs/source/_nodes/bootstrap.rst index b089eee6..08859e17 100644 --- a/docs/source/_nodes/bootstrap.rst +++ b/docs/source/_nodes/bootstrap.rst @@ -2,4 +2,4 @@ Bootstrap ========= .. automodule:: ipsuite.bootstrap :members: - :show-inheritance: \ No newline at end of file + :show-inheritance: diff --git a/docs/source/_nodes/calculators.rst b/docs/source/_nodes/calculators.rst index 467c417f..b6841898 100644 --- a/docs/source/_nodes/calculators.rst +++ b/docs/source/_nodes/calculators.rst @@ -2,4 +2,4 @@ Calculators =========== .. automodule:: ipsuite.calculators :members: - :show-inheritance: \ No newline at end of file + :show-inheritance: diff --git a/docs/source/_nodes/configuration_comparison.rst b/docs/source/_nodes/configuration_comparison.rst index f1916fb7..fc71452d 100644 --- a/docs/source/_nodes/configuration_comparison.rst +++ b/docs/source/_nodes/configuration_comparison.rst @@ -2,4 +2,4 @@ Configuration Comparison ======================== .. automodule:: ipsuite.configuration_comparison :members: - :show-inheritance: \ No newline at end of file + :show-inheritance: diff --git a/docs/source/_nodes/configuration_selection.rst b/docs/source/_nodes/configuration_selection.rst index 80bcfaf8..36dda743 100644 --- a/docs/source/_nodes/configuration_selection.rst +++ b/docs/source/_nodes/configuration_selection.rst @@ -2,4 +2,4 @@ Configuration Selection ======================= .. automodule:: ipsuite.configuration_selection :members: - :show-inheritance: \ No newline at end of file + :show-inheritance: diff --git a/docs/source/_nodes/data_loading.rst b/docs/source/_nodes/data_loading.rst index 0aa4ab68..824ebf0d 100644 --- a/docs/source/_nodes/data_loading.rst +++ b/docs/source/_nodes/data_loading.rst @@ -2,4 +2,4 @@ Data Loading ============ .. automodule:: ipsuite.data_loading :members: - :show-inheritance: \ No newline at end of file + :show-inheritance: diff --git a/docs/source/_nodes/geometry.rst b/docs/source/_nodes/geometry.rst index f427c578..8bdbc2c4 100644 --- a/docs/source/_nodes/geometry.rst +++ b/docs/source/_nodes/geometry.rst @@ -2,4 +2,4 @@ Geometry ======== .. automodule:: ipsuite.geometry :members: - :show-inheritance: \ No newline at end of file + :show-inheritance: diff --git a/docs/source/_nodes/models.rst b/docs/source/_nodes/models.rst index 363b680f..6f66ee98 100644 --- a/docs/source/_nodes/models.rst +++ b/docs/source/_nodes/models.rst @@ -2,4 +2,4 @@ Models ====== .. automodule:: ipsuite.models :members: - :show-inheritance: \ No newline at end of file + :show-inheritance: diff --git a/ipsuite/calculators/__init__.py b/ipsuite/calculators/__init__.py index f4bcd61a..4607f15b 100644 --- a/ipsuite/calculators/__init__.py +++ b/ipsuite/calculators/__init__.py @@ -1,6 +1,7 @@ """Calculators can be used for labeling a given set of data and running molecular dynamics. -For all cases, ASE calculators are used. +For all cases, ASE calculators are used. """ + import lazy_loader as lazy __getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__) diff --git a/ipsuite/calculators/ase_geoopt.py b/ipsuite/calculators/ase_geoopt.py index 4e8d06cd..20e3c634 100644 --- a/ipsuite/calculators/ase_geoopt.py +++ b/ipsuite/calculators/ase_geoopt.py @@ -3,7 +3,6 @@ import typing import ase.io -from ase.io.trajectory import TrajectoryWriter import ase.optimize import h5py import znh5md diff --git a/ipsuite/configuration_comparison/__init__.py b/ipsuite/configuration_comparison/__init__.py index 57b85a33..6ffc1cc8 100644 --- a/ipsuite/configuration_comparison/__init__.py +++ b/ipsuite/configuration_comparison/__init__.py @@ -1,4 +1,5 @@ """Provides kernel based similarity measures for comparing configruations.""" + import lazy_loader as lazy __getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__) diff --git a/ipsuite/configuration_generation/__init__.py b/ipsuite/configuration_generation/__init__.py index f55f3562..f421ba23 100644 --- a/ipsuite/configuration_generation/__init__.py +++ b/ipsuite/configuration_generation/__init__.py @@ -1,6 +1,7 @@ """This module provides Nodes for creating molecular dynamics starting structures. Workflows can be quickly created from just knowing the SMILES strings of the molecules within the simulation box. The PACKMOL interface can then be used to create the actual starting configuration.""" + import lazy_loader as lazy __getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__) diff --git a/ipsuite/configuration_selection/__init__.py b/ipsuite/configuration_selection/__init__.py index 69dcac91..2ce5de35 100644 --- a/ipsuite/configuration_selection/__init__.py +++ b/ipsuite/configuration_selection/__init__.py @@ -1,5 +1,6 @@ """The configuration selection submodule contains Nodes for splitting datasets. A simple 80:20 random split can be achieved with a single Node, but multiple Nodes can be chained to create complex splittings..""" + from ipsuite.configuration_selection.base import ConfigurationSelection from ipsuite.configuration_selection.filter import FilterOutlier from ipsuite.configuration_selection.index import IndexSelection