flyft documentation

.gitignore

@@ -1,3 +1,5 @@
 .DS_Store
-/build
+build
 __pycache__
+doc/source/generated
+*.egg-info

.readthedocs.yml

@@ -0,0 +1,17 @@
+version: 2
+
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.11"
+
+sphinx:
+  configuration: doc/source/conf.py
+  fail_on_warning: true
+
+python:
+  install:
+    - requirements: requirements.txt
+    - requirements: doc/requirements.txt
+    - method: pip
+      path: .

CMakeLists.txt

@@ -34,6 +34,23 @@ if(FLYFT_TESTING)
 endif()
 
 add_subdirectory(src)
+
 if(FLYFT_PYTHON)
     add_subdirectory(python)
+    # set(PYTHON_SITE_INSTALL_DIR "${_python_site_package_rel}/flyft" CACHE PATH "Python site-packages directory (relative to CMAKE_INSTALL_PREFIX)" FORCE)
 endif()
+
+find_package(Python REQUIRED COMPONENTS Interpreter Development)
+execute_process(
+    COMMAND ${Python_EXECUTABLE} -c "import site; print(site.getsitepackages()[0])"
+    OUTPUT_VARIABLE _python_site_packages
+    OUTPUT_STRIP_TRAILING_WHITESPACE
+    ERROR_VARIABLE _error
+)
+
+if(_error)
+    message(FATAL_ERROR "Failed to find Python site-packages: ${_error}")
+endif()
+
+set(CMAKE_INSTALL_PREFIX ${_python_site_packages} CACHE PATH "Install prefix" FORCE)
+message(STATUS "Setting CMAKE_INSTALL_PREFIX to Python site-packages: ${CMAKE_INSTALL_PREFIX}")

LICENSE

@@ -0,0 +1,26 @@
+Copyright (c) 2021-2025, Auburn University
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright
+  notice, this list of conditions and the following disclaimer.
+* Redistributions in binary form must reproduce the above copyright
+  notice, this list of conditions and the following disclaimer in the
+  documentation and/or other materials provided with the distribution.
+* Neither the name of the copyright holder nor the
+  names of its contributors may be used to endorse or promote products
+  derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER BE LIABLE FOR ANY
+DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

doc/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)

doc/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

doc/requirements.txt

@@ -0,0 +1,7 @@
+furo
+ipython==9.3.0
+MyST-Parser
+nbsphinx==0.9.7
+sphinx==8.1.3
+sphinx_design==0.6.1
+sphinx_favicon==1.0.1

doc/source/_templates/autosummary/class.rst

@@ -0,0 +1,29 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+
+   {% block methods %}
+   {% if methods %}
+   .. rubric:: {{ _('Methods:') }}
+
+   .. autosummary::
+   {% for item in methods %}
+      {%- if not item in ['__init__'] %}
+      ~{{ name }}.{{ item }}
+      {%- endif -%}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: {{ _('Attributes:') }}
+
+   .. autosummary::
+   {% for item in attributes %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}

doc/source/api.rst

@@ -0,0 +1,67 @@
+API
+---
+
+Free-energy models for hard-sphere fluids
+-----------------------------------------
+
+Free-energy functionals is an important component of the dynamic density functional functional
+theory (DDFT) framework. Free-energy functional has three components: ideal-gas, excess, and external
+potential contributions. ``flyft`` package provides several built-in free-energy
+functionals for hard-sphere fluids to model the different excess and external contributions.
+
+Excess free-energy functional
+=============================
+
+Depending on the required accuracy and density of the system, different
+free-energy functionals can be employed.
+
+.. autosummary::
+    :nosignatures:
+    :toctree: generated/
+
+        flyft.functional.IdealGas
+        flyft.functional.VirialExpansion
+        flyft.functional.BoublikHardSphere
+        flyft.functional.RosenfeldFMT
+
+External free-energy functional
+===============================
+
+We also provide several built-in external potential models to represent
+various confinement geometries and external fields for hard-sphere fluids.
+
+.. autosummary::
+    :nosignatures:
+    :toctree: generated/
+
+        flyft.external.LinearPotential
+        flyft.external.HardWall
+        flyft.external.HarmonicWall
+
+Mobility tensor for hard-sphere fluids
+--------------------------------------
+
+In addition to free-energy functionals, flux models are also a key component of the DDFT
+framework. Mobility tensor define how particles move in response to gradients in chemical potential
+and external forces. The ``flyft`` package provides several built-in flux models for hard-sphere
+fluids. These include:
+
+.. autosummary::
+    :nosignatures:
+    :toctree: generated/
+
+        flyft.dynamics.BrownianDiffusiveFlux
+        flyft.dynamics.CompositeFlux
+        flyft.dynamics.RPYDiffusiveFlux
+
+Iterative solvers
+-----------------
+
+The ``flyft`` package also provides iterative solvers to find equilibrium density profiles
+for hard-sphere fluids under various free-energy functionals and external potentials.
+
+.. autosummary::
+    :nosignatures:
+    :toctree: generated/
+
+        flyft.solver.PicardIteration

doc/source/conf.py

@@ -0,0 +1,73 @@
+# 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
+
+import datetime
+
+project = "flyft"
+year = datetime.date.today().year
+copyright = f"2021-{year}, Auburn University"
+author = "Michael P. Howard"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "IPython.sphinxext.ipython_console_highlighting",
+    "nbsphinx",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.napoleon",
+    "sphinx_design",
+    "sphinx_favicon",
+    "myst_parser",
+]
+
+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 = "furo"
+html_static_path = []
+html_theme_options = {
+    "navigation_with_keys": True,
+    "top_of_page_buttons": [],
+    "dark_css_variables": {
+        "color-brand-primary": "#ef904d",
+        "color-brand-content": "#ef904d",
+        "color-admonition-background": "#ef904d",
+    },
+    "light_css_variables": {
+        "color-brand-primary": "#e86100",
+        "color-brand-content": "#e86100",
+        "color-admonition-background": "#e86100",
+    },
+    "sidebar_hide_name": True,
+}
+html_logo = "_images/flyft_logo.svg"
+# html_favicon = "_images/flyft_icon.svg"
+
+# -- Options for autodoc & autosummary ---------------------------------------
+
+autosummary_generate = True
+
+autodoc_member_order = "bysource"
+
+autodoc_default_options = {"inherited-members": None, "special-members": False}
+autodoc_typehints = "none"
+
+# -- Options for intersphinx -------------------------------------------------
+
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+    "numpy": ("https://numpy.org/doc/stable", None),
+}

doc/source/index.rst

@@ -0,0 +1,30 @@
+.. flyft documentation master file, created by
+   sphinx-quickstart on Thu Dec  4 19:14:04 2025.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+flyft documentation
+===================
+
+flyft is a Python package for conducting dynamic density functional theory (DDFT)
+simulations of hard-sphere fluids. It provides a flexible framework for defining
+free-energy functionals, external potentials, and numerical solvers to study the
+time evolution of density profiles in various geometries.
+
+.. toctree::
+    :maxdepth: 1
+    :caption: Getting started
+
+    ./install
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Reference
+
+   ./api
+
+.. toctree::
+    :maxdepth: 1
+    :caption: Additional information
+
+    ./license