diff --git a/.gitignore b/.gitignore index c73a9d35..8308629e 100644 --- a/.gitignore +++ b/.gitignore @@ -4,5 +4,5 @@ __pycache__ *.pyc build* doc/build -doc/source/reference/api +doc/env **-checkpoint.ipynb diff --git a/.readthedocs.yml b/.readthedocs.yml new file mode 100644 index 00000000..f9274fe1 --- /dev/null +++ b/.readthedocs.yml @@ -0,0 +1,13 @@ +version: 2 + +sphinx: + configuration: doc/source/conf.py + fail_on_warning: true + +build: + os: "ubuntu-20.04" + tools: + python: "mambaforge-4.10" + +conda: + environment: doc/environment.yml diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 3baebf83..1f3dda2f 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -1,8 +1,8 @@ Release notes ============= -Unreleased ----------- +Upcoming +-------- *Other changes* * Add a code of conduct for contributors. @@ -11,14 +11,18 @@ Unreleased * The default git branch is renamed ``main``. More `information `_ is available. -v0.10.1 (12 Jan 2021) ---------------------- +v0.10.1 +------- +Released 12 Jan 2021 + *Bug fixes* * Fix normalization of velocity in ``flow.FlowProfiler``. -v0.10.0 (27 Jul 2020) ---------------------- +v0.10.0 +------- +Released 27 Jul 2020 + This is the first release of azplugins to include compilable documentation. The ``docs`` can be built using sphinx. Currently, only the APIs are thoroughly documented, but we will be expanding the rest of the documentation in future releases with examples @@ -38,8 +42,10 @@ and tutorials. * The python unit tests have been updated to remove ``import *``. -v0.9.2 (3 Mar 2020) -------------------- +v0.9.2 +------ +Released 3 Mar 2020 + *Bug fixes* * Fix a compilation error on MacOS clang builds. @@ -48,14 +54,18 @@ v0.9.2 (3 Mar 2020) * Update copyright to 2020. -v0.9.1 (18 Dec 2019) --------------------- +v0.9.1 +------ +Released 18 Dec 2019 + *Bug fixes* * Fix a compilation error in CUDA-enabled builds. -v0.9.0 (15 Dec 2019) --------------------- +v0.9.0 +------ +Released 15 Dec 2019 + *New features* * ``flow.constant`` implements a constant flow along a vector. @@ -71,8 +81,10 @@ v0.9.0 (15 Dec 2019) New pair potential evaluators should derive from one of the convenience base classes. * CI testing has been added for HOOMD 2.8.0 in addition to 2.6.0. -v0.8.0 (5 Nov 2019) -------------------- +v0.8.0 +------ +Released 5 Nov 2019 + *New features* * ``evaporate.implicit`` now supports evaporation in both film and droplet @@ -80,15 +92,19 @@ v0.8.0 (5 Nov 2019) * ``restrain.plane`` allows particles to be harmonically restrained by their distance relative to a plane. -v0.7.1 (20 Aug 2019) --------------------- +v0.7.1 +------ +Released 20 Aug 2019 + *Bug fixes* * Silence a warning in CMake >= 3.12. * Fix a link error in compiled unit tests. -v0.7.0 (24 Jun 2019) --------------------- +v0.7.0 +------ +Released 24 Jun 2019 + This version of the plugin **requires** HOOMD-blue v2.6.0 for compatibility with the new streaming geometries in its MPCD component. HOOMD-blue **must** be built with the MPCD component. @@ -104,8 +120,10 @@ be built with the MPCD component. numbers drawn for a given seed will change. New features using random numbers should add a unique 32-bit identifier to ``RNGIdentifiers.h``. -v0.6.2 (25 Apr 2019) --------------------- +v0.6.2 +------ +Released 25 Apr 2019 + All commits and pull requests are now automatically tested against HOOMD 2.5.1 on CircleCI. Unit tests are run for CPU-only build configurations. CUDA-enabled builds are tested for compilation, but their unit tests cannot be run on CircleCI. @@ -118,14 +136,18 @@ and tests for new code should be run locally on a GPU. * Fix HOOMD version parsing in CMake for external builds. * Fix CMake errors in testing for certain build configurations. -v0.6.1 (28 Mar 2019) --------------------- +v0.6.1 +------ +Released 28 Mar 2019 + *Bug fixes* * Fix thrust template parameters in ``mpcd.reverse_perturbation`` for CUDA 9 & 10. -v0.6.0 (25 Feb 2019) --------------------- +v0.6.0 +------ +Released 25 Feb 2019 + This version of the plugin **requires** HOOMD-blue v2.3.0 for compatibility with the embedded pybind11 library. Be sure to update your git submodules when recompiling and installing HOOMD-blue. @@ -145,8 +167,10 @@ GitHub (https://github.com/mphoward/azplugins). * ``FindHOOMD.cmake`` has been improved to support ``find_package`` and detect the installed version of HOOOMD. -v0.5.0 (11 Jun 2018) --------------------- +v0.5.0 +------ +Released 11 Jun 2018 + This version of the plugin **requires** HOOMD-blue v2.2.2 in order to ensure all necessary header files are available. @@ -164,8 +188,10 @@ ensure all necessary header files are available. external flow fields. Currently, the supported fields are ``flow.quiescent`` and ``flow.parabolic``, but additional fields can be included by templating. -v0.4.0 (16 Nov 2017) --------------------- +v0.4.0 +------ +Released 16 Nov 2017 + This version of the plugin **requires** HOOMD-blue v2.2.1 in order to ensure all necessary header files are available. @@ -194,8 +220,10 @@ to ensure all necessary header files are available. * CMake exits gracefully when the MD component is not available from hoomd. * Plugins now compile with debug flags. -v0.3.0 (22 Aug 2017) --------------------- +v0.3.0 +------ +Released 22 Aug 2017 + This version of the plugin is now tested against HOOMD-blue v2.1.9. Users running older versions of HOOMD-blue are recommended to upgrade their installations in order to ensure compatibility and the latest @@ -218,8 +246,10 @@ bug fixes on the main code paths. compilation errors with newer versions of hoomd where the header was removed. -v0.2.0 (28 Feb 2017) --------------------- +v0.2.0 +------ +Released 28 Feb 2017 + *New features* * ``analyze.rdf`` implements a radial distribution function calculator @@ -234,8 +264,10 @@ v0.2.0 (28 Feb 2017) * Source code guidelines and a pull request checklist are discussed in a new ``CONTRIBUTING.md``. -v0.1.0 (9 Feb 2017) -------------------- +v0.1.0 +------ +Released 9 Feb 2017 + *New features* * A framework is configured for developing pair potentials. diff --git a/azplugins/_azplugins.py b/azplugins/_azplugins.py deleted file mode 100644 index 6920ff8d..00000000 --- a/azplugins/_azplugins.py +++ /dev/null @@ -1,5 +0,0 @@ -# Copyright (c) 2018-2020, Michael P. Howard -# Copyright (c) 2021, Auburn University -# This file is part of the azplugins project, released under the Modified BSD License. - -"""This file is only for mock imports during doc generation.""" diff --git a/azplugins/analyze.py b/azplugins/analyze.py index 334f4327..6cb79289 100644 --- a/azplugins/analyze.py +++ b/azplugins/analyze.py @@ -1,7 +1,18 @@ # Copyright (c) 2018-2020, Michael P. Howard # Copyright (c) 2021, Auburn University # This file is part of the azplugins project, released under the Modified BSD License. +""" +Analyzers +========= +.. autosummary:: + :nosignatures: + + rdf + +.. autoclass:: rdf + +""" import numpy import hoomd diff --git a/azplugins/bond.py b/azplugins/bond.py index ff900aa3..ca1b8323 100644 --- a/azplugins/bond.py +++ b/azplugins/bond.py @@ -1,6 +1,22 @@ # Copyright (c) 2018-2020, Michael P. Howard # Copyright (c) 2021, Auburn University # This file is part of the azplugins project, released under the Modified BSD License. +""" +Bond potentials +=============== + +.. autosummary:: + :nosignatures: + + double_well + fene + fene24 + +.. autoclass:: double_well +.. autoclass:: fene +.. autoclass:: fene24 + +""" import math diff --git a/azplugins/dpd.py b/azplugins/dpd.py index a7c5ed8c..8d5a17a1 100644 --- a/azplugins/dpd.py +++ b/azplugins/dpd.py @@ -1,6 +1,18 @@ # Copyright (c) 2018-2020, Michael P. Howard # Copyright (c) 2021, Auburn University # This file is part of the azplugins project, released under the Modified BSD License. +""" +DPD potentials +============== + +.. autosummary:: + :nosignatures: + + general + +.. autoclass:: general + +""" import hoomd from hoomd import _hoomd diff --git a/azplugins/evaporate.py b/azplugins/evaporate.py index 08cbce16..f7165942 100644 --- a/azplugins/evaporate.py +++ b/azplugins/evaporate.py @@ -1,7 +1,20 @@ # Copyright (c) 2018-2020, Michael P. Howard # Copyright (c) 2021, Auburn University # This file is part of the azplugins project, released under the Modified BSD License. +""" +Evaporation +=========== +.. autosummary:: + :nosignatures: + + implicit + particles + +.. autoclass:: implicit +.. autoclass:: particles + +""" import hoomd from . import _azplugins diff --git a/azplugins/flow.py b/azplugins/flow.py index b96891f9..e9497fe7 100644 --- a/azplugins/flow.py +++ b/azplugins/flow.py @@ -1,6 +1,38 @@ # Copyright (c) 2018-2020, Michael P. Howard # Copyright (c) 2021, Auburn University # This file is part of the azplugins project, released under the Modified BSD License. +""" +Flow +==== + +Flow fields and profilers + +.. autosummary:: + :nosignatures: + + quiescent + constant + parabolic + reverse_perturbation + FlowProfiler + +Flow integrators + +.. autosummary:: + :nosignatures: + + brownian + langevin + +.. autoclass:: quiescent +.. autoclass:: constant +.. autoclass:: parabolic +.. autoclass:: reverse_perturbation +.. autoclass:: FlowProfiler +.. autoclass:: brownian +.. autoclass:: langevin + +""" import numpy as np import hoomd diff --git a/azplugins/integrate.py b/azplugins/integrate.py index b93e21be..8cba16aa 100644 --- a/azplugins/integrate.py +++ b/azplugins/integrate.py @@ -1,6 +1,20 @@ # Copyright (c) 2018-2020, Michael P. Howard # Copyright (c) 2021, Auburn University # This file is part of the azplugins project, released under the Modified BSD License. +""" +Integrators +=========== + +Bounce-back integrators + +.. autosummary:: + :nosignatures: + + slit + +.. autoclass:: slit + +""" import hoomd from hoomd.mpcd import _mpcd diff --git a/azplugins/mpcd.py b/azplugins/mpcd.py index 2e7a9639..00e1b05b 100644 --- a/azplugins/mpcd.py +++ b/azplugins/mpcd.py @@ -1,6 +1,19 @@ # Copyright (c) 2018-2020, Michael P. Howard # Copyright (c) 2021, Auburn University # This file is part of the azplugins project, released under the Modified BSD License. +""" +MPCD methods +============ + +.. autosummary:: + :nosignatures: + + reverse_perturbation + +.. autoclass:: reverse_perturbation + +""" + import hoomd diff --git a/azplugins/pair.py b/azplugins/pair.py index 9d042cae..c6287473 100644 --- a/azplugins/pair.py +++ b/azplugins/pair.py @@ -1,7 +1,34 @@ # Copyright (c) 2018-2020, Michael P. Howard # Copyright (c) 2021, Auburn University # This file is part of the azplugins project, released under the Modified BSD License. - +""" +Pair potentials +=============== + +.. autosummary:: + :nosignatures: + + ashbaugh + ashbaugh24 + colloid + hertz + lj124 + lj96 + slj + spline + two_patch_morse + +.. autoclass:: ashbaugh +.. autoclass:: ashbaugh24 +.. autoclass:: colloid +.. autoclass:: hertz +.. autoclass:: lj124 +.. autoclass:: lj96 +.. autoclass:: slj +.. autoclass:: spline +.. autoclass:: two_patch_morse + +""" import math import hoomd diff --git a/azplugins/restrain.py b/azplugins/restrain.py index b4da9656..41d229ef 100644 --- a/azplugins/restrain.py +++ b/azplugins/restrain.py @@ -2,7 +2,9 @@ # Copyright (c) 2021, Auburn University # This file is part of the azplugins project, released under the Modified BSD License. -r""" Restraining forces. +r""" +Restraints +========== Restraints are harmonic forces that are applied to particle groups with the goal of holding them to a region of space. Depending on the type of restraint, @@ -16,6 +18,21 @@ to each restraint and the restraint types are initialized properly and are compatible. +.. autosummary:: + :nosignatures: + + cylinder + plane + sphere + position + orientation + +.. autoclass:: cylinder +.. autoclass:: plane +.. autoclass:: sphere +.. autoclass:: position +.. autoclass:: orientation + """ import numpy diff --git a/azplugins/special_pair.py b/azplugins/special_pair.py index dce3d8fe..3fe42a4b 100644 --- a/azplugins/special_pair.py +++ b/azplugins/special_pair.py @@ -1,6 +1,18 @@ # Copyright (c) 2018-2020, Michael P. Howard # Copyright (c) 2021, Auburn University # This file is part of the azplugins project, released under the Modified BSD License. +""" +Special pair potentials +======================= + +.. autosummary:: + :nosignatures: + + lj96 + +.. autoclass:: lj96 + +""" import math diff --git a/azplugins/update.py b/azplugins/update.py index f6578741..d1f80d96 100644 --- a/azplugins/update.py +++ b/azplugins/update.py @@ -1,7 +1,18 @@ # Copyright (c) 2018-2020, Michael P. Howard # Copyright (c) 2021, Auburn University # This file is part of the azplugins project, released under the Modified BSD License. +""" +Updaters +======== +.. autosummary:: + :nosignatures: + + types + +.. autoclass:: types + +""" import hoomd from . import _azplugins diff --git a/azplugins/variant.py b/azplugins/variant.py index 8dc80ba0..e1007e7d 100644 --- a/azplugins/variant.py +++ b/azplugins/variant.py @@ -1,7 +1,18 @@ # Copyright (c) 2018-2020, Michael P. Howard # Copyright (c) 2021, Auburn University # This file is part of the azplugins project, released under the Modified BSD License. +""" +Variants +======== +.. autosummary:: + :nosignatures: + + sphere_area + +.. autoclass:: sphere_area + +""" import hoomd from . import _azplugins diff --git a/azplugins/wall.py b/azplugins/wall.py index a1246baa..e65df4fc 100644 --- a/azplugins/wall.py +++ b/azplugins/wall.py @@ -1,7 +1,20 @@ # Copyright (c) 2018-2020, Michael P. Howard # Copyright (c) 2021, Auburn University # This file is part of the azplugins project, released under the Modified BSD License. +""" +Wall potentials +=============== +.. autosummary:: + :nosignatures: + + colloid + lj93 + +.. autoclass:: colloid +.. autoclass:: lj93 + +""" import hoomd from hoomd import _hoomd diff --git a/doc/environment.yml b/doc/environment.yml new file mode 100644 index 00000000..2f30979a --- /dev/null +++ b/doc/environment.yml @@ -0,0 +1,13 @@ +name: rtd +channels: + - conda-forge + - defaults +dependencies: + - python=3.7 + - sphinx==4.3.2 + - sphinx_rtd_theme==1.0.0 + - numpy + - ipython + - pandoc + - nbsphinx + - hoomd=2.9 diff --git a/doc/requirements.txt b/doc/requirements.txt deleted file mode 100644 index e06f7d82..00000000 --- a/doc/requirements.txt +++ /dev/null @@ -1,3 +0,0 @@ -sphinx==4.2.0 -sphinx_rtd_theme==1.0.0 -nbsphinx==0.8.8 diff --git a/doc/source/_templates/shortclass.rst b/doc/source/_templates/shortclass.rst deleted file mode 100644 index 6a3c578f..00000000 --- a/doc/source/_templates/shortclass.rst +++ /dev/null @@ -1,5 +0,0 @@ -{{ fullname | escape | underline }} - -.. currentmodule:: {{ module }} - -.. autoclass :: {{ objname }} diff --git a/doc/source/api/analyze.rst b/doc/source/api/analyze.rst new file mode 100644 index 00000000..09567842 --- /dev/null +++ b/doc/source/api/analyze.rst @@ -0,0 +1 @@ +.. automodule:: azplugins.analyze diff --git a/doc/source/api/evaporate.rst b/doc/source/api/evaporate.rst new file mode 100644 index 00000000..3e5d3285 --- /dev/null +++ b/doc/source/api/evaporate.rst @@ -0,0 +1 @@ +.. automodule:: azplugins.evaporate diff --git a/doc/source/api/flow.rst b/doc/source/api/flow.rst new file mode 100644 index 00000000..48948ae6 --- /dev/null +++ b/doc/source/api/flow.rst @@ -0,0 +1 @@ +.. automodule:: azplugins.flow diff --git a/doc/source/api/integrate.rst b/doc/source/api/integrate.rst new file mode 100644 index 00000000..9f82ee67 --- /dev/null +++ b/doc/source/api/integrate.rst @@ -0,0 +1 @@ +.. automodule:: azplugins.integrate diff --git a/doc/source/api/mpcd.rst b/doc/source/api/mpcd.rst new file mode 100644 index 00000000..787735ee --- /dev/null +++ b/doc/source/api/mpcd.rst @@ -0,0 +1 @@ +.. automodule:: azplugins.mpcd diff --git a/doc/source/api/potentials/bond.rst b/doc/source/api/potentials/bond.rst new file mode 100644 index 00000000..87a81988 --- /dev/null +++ b/doc/source/api/potentials/bond.rst @@ -0,0 +1 @@ +.. automodule:: azplugins.bond diff --git a/doc/source/api/potentials/dpd.rst b/doc/source/api/potentials/dpd.rst new file mode 100644 index 00000000..09038188 --- /dev/null +++ b/doc/source/api/potentials/dpd.rst @@ -0,0 +1 @@ +.. automodule:: azplugins.dpd diff --git a/doc/source/api/potentials/index.rst b/doc/source/api/potentials/index.rst new file mode 100644 index 00000000..a561e775 --- /dev/null +++ b/doc/source/api/potentials/index.rst @@ -0,0 +1,11 @@ +Potentials +========== + +.. toctree:: + :maxdepth: 1 + + bond + dpd + pair + specialpair + wall diff --git a/doc/source/api/potentials/pair.rst b/doc/source/api/potentials/pair.rst new file mode 100644 index 00000000..7eaef14b --- /dev/null +++ b/doc/source/api/potentials/pair.rst @@ -0,0 +1 @@ +.. automodule:: azplugins.pair diff --git a/doc/source/api/potentials/specialpair.rst b/doc/source/api/potentials/specialpair.rst new file mode 100644 index 00000000..65d92256 --- /dev/null +++ b/doc/source/api/potentials/specialpair.rst @@ -0,0 +1 @@ +.. automodule:: azplugins.special_pair diff --git a/doc/source/api/potentials/wall.rst b/doc/source/api/potentials/wall.rst new file mode 100644 index 00000000..85c39b33 --- /dev/null +++ b/doc/source/api/potentials/wall.rst @@ -0,0 +1 @@ +.. automodule:: azplugins.wall diff --git a/doc/source/api/restrain.rst b/doc/source/api/restrain.rst new file mode 100644 index 00000000..e5bfe9c9 --- /dev/null +++ b/doc/source/api/restrain.rst @@ -0,0 +1 @@ +.. automodule:: azplugins.restrain diff --git a/doc/source/api/update.rst b/doc/source/api/update.rst new file mode 100644 index 00000000..bdbe7e63 --- /dev/null +++ b/doc/source/api/update.rst @@ -0,0 +1 @@ +.. automodule:: azplugins.update diff --git a/doc/source/api/variant.rst b/doc/source/api/variant.rst new file mode 100644 index 00000000..4fdf880d --- /dev/null +++ b/doc/source/api/variant.rst @@ -0,0 +1 @@ +.. automodule:: azplugins.variant diff --git a/doc/source/conf.py b/doc/source/conf.py index 4b196921..6a4befd6 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -2,12 +2,6 @@ # Copyright (c) 2021, Auburn University # This file is part of the azplugins project, released under the Modified BSD License. -# Configuration file for the Sphinx documentation builder. -# -# This file only contains a selection of the most common options. For a full -# list see the documentation: -# https://www.sphinx-doc.org/en/master/usage/configuration.html - # -- Path setup -------------------------------------------------------------- import os @@ -52,18 +46,17 @@ # -- Options for autodoc & autosummary --------------------------------------- autodoc_default_options = { - 'inherited-members': True, - 'show-inheritance': True + 'inherited-members': False } -autodoc_mock_imports = ['hoomd'] +autodoc_mock_imports = ['azplugins._azplugins'] -autosummary_generate = True +autosummary_generate = False # -- Options for intersphinx ------------------------------------------------- intersphinx_mapping = { 'python': ('https://docs.python.org/3', None), - 'numpy': ('https://docs.scipy.org/doc/numpy', None), + 'numpy': ('https://numpy.org/doc/stable', None), 'hoomd': ('https://hoomd-blue.readthedocs.io/en/stable', None) } diff --git a/doc/source/credits.rst b/doc/source/credits.rst index b7bf1de5..86813ae7 100644 --- a/doc/source/credits.rst +++ b/doc/source/credits.rst @@ -4,55 +4,15 @@ Credits Maintainers ----------- -**Michael P. Howard** (`@mphoward `_) - -- Original software design and plugin frameworks. -- ``analyze.rdf``: Radial distribution function calculator. -- ``dpd.general``: Generalized DPD pair potential. -- ``evaporate.implicit``: Moving harmonic potential to simulate drying in films and droplets. -- ``evaporate.particles``: Particle type changer to simulate explicit drying. -- ``flow.brownian`` / ``flow.langevin`` and imposed flow framework. -- ``flow.constant``, ``flow.parabolic``, and ``flow.quiescent`` flows fields. -- ``integrate.slit`` and bounce-back integrator framework. -- ``pair.ashbaugh``: Ashbaugh-Hatch pair potential. -- ``pair.colloid``: Integrated Lennard-Jones pair potential. -- ``pair.slj``: Modified core-shifted Lennard-Jones pair potential. -- ``restrain.plane``, ``restrain.cylinder``, and ``restrain.sphere`` : Harmonic restraints - to planes, cylinders, and spheres. -- ``update.types``: Type changer by region. -- ``wall.colloid``: Integrated Lennard-Jones wall potential. -- ``wall.lj93``: 9-3 Lennard-Jones wall potential. - - -**Antonia Statt** (`@astatt `_) - -- ``bond.double_well``: two-well bond potential. -- ``bond.fene``: modified FENE bond evaluator. -- ``bond.fene24``: FENE bond evaluator with Ashbaugh-Hatch 48-24 pair potential. -- ``flow.FlowProfiler``: 1d density / velocity averaging. -- ``flow.reverse_perturbation``: reverse perturbation shear flow. -- ``mpcd.reverse_perturbation``: reverse perturbation shear flow for MPCD. -- ``pair.ashbaugh24``: 48-24 Ashbaugh-Hatch pair potential. -- ``pair.spline``: Spline polynomial pair potential. +* Michael P. Howard (`@mphoward `_) +* Antonia Statt (`@astatt `_) Contributors ------------ -**Arjun Goswami** (`@arjungoswami `_) - -- ``pair.hertz``: Hertz pair potential. - -**Sally Jiao** - -- ``pair.lj124``: 12-4 Lennard-Jones pair potential. -- ``pair.lj96``: 9-6 Lennard-Jones pair potential. -- ``SpecialPairEvaluator``: Template class for special pair evaluators. - -**Wes Reinhart** (`@wfreinhart `_) - -- ``pair.two_patch_morse``: Anisotropic two-patch Morse potential. -- ``restrain.position``: Harmonic position restraints. -- ``restrain.orientation``: Harmonic orientation restraints. +* Arjun Goswami (`@arjungoswami `_) +* Sally Jiao +* Wes Reinhart (`@wfreinhart `_) Source code ----------- diff --git a/doc/source/develop/index.rst b/doc/source/develop/index.rst deleted file mode 100644 index 5834f20d..00000000 --- a/doc/source/develop/index.rst +++ /dev/null @@ -1,4 +0,0 @@ -Developer guide -=============== - -Developer topics. (How do I add a X?) diff --git a/doc/source/example/index.rst b/doc/source/example/index.rst deleted file mode 100644 index 0db942da..00000000 --- a/doc/source/example/index.rst +++ /dev/null @@ -1,4 +0,0 @@ -Examples -======== - -This has working examples, perhaps from papers. diff --git a/doc/source/index.rst b/doc/source/index.rst index 0281a806..d30cbf29 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -6,15 +6,26 @@ azplugins :caption: Getting started installation - reference/index tutorial/index - example/index + +.. toctree:: + :maxdepth: 1 + :caption: API + + api/analyze + api/evaporate + api/flow + api/integrate + api/mpcd + api/potentials/index + api/restrain + api/update + api/variant .. toctree:: :maxdepth: 1 :caption: Reference - develop/index release license credits diff --git a/doc/source/reference/analyze.rst b/doc/source/reference/analyze.rst deleted file mode 100644 index fc00d3f5..00000000 --- a/doc/source/reference/analyze.rst +++ /dev/null @@ -1,11 +0,0 @@ -Analyzers -========= - -.. automodule:: azplugins.analyze -.. currentmodule:: azplugins -.. autosummary:: - :toctree: api - :template: shortclass.rst - :nosignatures: - - analyze.rdf diff --git a/doc/source/reference/index.rst b/doc/source/reference/index.rst deleted file mode 100644 index e257b60e..00000000 --- a/doc/source/reference/index.rst +++ /dev/null @@ -1,12 +0,0 @@ -Features -======== -.. toctree:: - :maxdepth: 2 - - intro - potentials - restraints - noneq - analyze - update - variant diff --git a/doc/source/reference/intro.rst b/doc/source/reference/intro.rst deleted file mode 100644 index 1d44191a..00000000 --- a/doc/source/reference/intro.rst +++ /dev/null @@ -1,4 +0,0 @@ -Introduction -============ - -This explains azplugins in big terms. diff --git a/doc/source/reference/noneq.rst b/doc/source/reference/noneq.rst deleted file mode 100644 index d453a32b..00000000 --- a/doc/source/reference/noneq.rst +++ /dev/null @@ -1,49 +0,0 @@ -Nonequilibrium methods -====================== - -Flow fields ------------ -.. currentmodule:: azplugins -.. autosummary:: - :toctree: api - :template: shortclass.rst - :nosignatures: - - flow.quiescent - flow.constant - flow.parabolic - flow.FlowProfiler - -Flow integrators ----------------- -.. currentmodule:: azplugins -.. autosummary:: - :toctree: api - :template: shortclass.rst - :nosignatures: - - flow.brownian - flow.langevin - integrate.slit - -Evaporation ------------ -.. automodule:: azplugins.evaporate -.. currentmodule:: azplugins -.. autosummary:: - :toctree: api - :template: shortclass.rst - :nosignatures: - - evaporate.implicit - evaporate.particles - -Reverse perturbation --------------------- -.. autosummary:: - :toctree: api - :template: shortclass.rst - :nosignatures: - - flow.reverse_perturbation - mpcd.reverse_perturbation diff --git a/doc/source/reference/potentials.rst b/doc/source/reference/potentials.rst deleted file mode 100644 index f9d834a6..00000000 --- a/doc/source/reference/potentials.rst +++ /dev/null @@ -1,68 +0,0 @@ -Potentials -========== - -Bond potentials ---------------- -.. automodule:: azplugins.bond -.. currentmodule:: azplugins -.. autosummary:: - :toctree: api - :template: shortclass.rst - :nosignatures: - - bond.double_well - bond.fene - bond.fene24 - -DPD potentials --------------- -.. automodule:: azplugins.dpd -.. currentmodule:: azplugins -.. autosummary:: - :toctree: api - :template: shortclass.rst - :nosignatures: - - dpd.general - -Pair potentials ---------------- -.. automodule:: azplugins.pair -.. currentmodule:: azplugins -.. autosummary:: - :toctree: api - :template: shortclass.rst - :nosignatures: - - pair.ashbaugh - pair.ashbaugh24 - pair.colloid - pair.hertz - pair.lj124 - pair.lj96 - pair.slj - pair.spline - pair.two_patch_morse - -Special pair potentials ------------------------ -.. automodule:: azplugins.special_pair -.. currentmodule:: azplugins -.. autosummary:: - :toctree: api - :template: shortclass.rst - :nosignatures: - - special_pair.lj96 - -Wall potentials ---------------- -.. automodule:: azplugins.wall -.. currentmodule:: azplugins -.. autosummary:: - :toctree: api - :template: shortclass.rst - :nosignatures: - - wall.colloid - wall.lj93 diff --git a/doc/source/reference/restraints.rst b/doc/source/reference/restraints.rst deleted file mode 100644 index 7849cc20..00000000 --- a/doc/source/reference/restraints.rst +++ /dev/null @@ -1,27 +0,0 @@ -Restraints -========== - -.. automodule:: azplugins.restrain - -Regions -------- -.. currentmodule:: azplugins -.. autosummary:: - :toctree: api - :template: shortclass.rst - :nosignatures: - - restrain.cylinder - restrain.plane - restrain.sphere - -Particles ---------- -.. currentmodule:: azplugins -.. autosummary:: - :toctree: api - :template: shortclass.rst - :nosignatures: - - restrain.position - restrain.orientation diff --git a/doc/source/reference/update.rst b/doc/source/reference/update.rst deleted file mode 100644 index d368ca2c..00000000 --- a/doc/source/reference/update.rst +++ /dev/null @@ -1,11 +0,0 @@ -Updaters -======== - -.. automodule:: azplugins.update -.. currentmodule:: azplugins -.. autosummary:: - :toctree: api - :template: shortclass.rst - :nosignatures: - - update.types diff --git a/doc/source/reference/variant.rst b/doc/source/reference/variant.rst deleted file mode 100644 index 5dbb98f1..00000000 --- a/doc/source/reference/variant.rst +++ /dev/null @@ -1,11 +0,0 @@ -Variants -======== - -.. automodule:: azplugins.variant -.. currentmodule:: azplugins -.. autosummary:: - :toctree: api - :template: shortclass.rst - :nosignatures: - - variant.sphere_area