flory 0.0.0__tar.gz

flory-0.0.0/.github/workflows/codecov.yml

@@ -0,0 +1,45 @@
+# This workflow will install Python dependencies, run tests and report code coverage to Codecov
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Codecov
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.12"]
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install pytest pytest-cov
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Test with pytest
+      env:
+        NUMBA_DISABLE_JIT: 1
+      run: |
+        python -m pytest --cov=flory --cov-report xml:.coverage_report.xml
+    - name: Upload coverage reports to Codecov
+      uses: codecov/codecov-action@v4.0.1
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        file: ./.coverage_report.xml
+        flags: Tests
+        name: codecov-flory
+        fail_ci_if_error: true

flory-0.0.0/.github/workflows/python-package.yml

@@ -0,0 +1,34 @@
+# This workflow will install Python dependencies, run tests with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Tests
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Test with pytest
+      run: |
+        python -m pytest

flory-0.0.0/.github/workflows/release.yml

@@ -0,0 +1,41 @@
+name: Upload Python Package
+
+on:
+  workflow_dispatch:
+  release:
+    types: [released]
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    strategy:
+      fail-fast: false
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.12
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build twine
+
+    - name: Prepare build
+      run: |
+        python -m build
+
+    - name: Check the package
+      run: twine check --strict dist/*
+
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: python -m twine upload dist/*

flory-0.0.0/.gitignore

@@ -0,0 +1,16 @@
+.vscode
+**/__pycache__
+**/*.pytest_cache
+
+.coverage*
+
+docs/build
+docs/source/_autosummary
+
+.DS_Store
+
+*.egg*
+build
+dist
+
+flory/_version.py

flory-0.0.0/.readthedocs.yaml

@@ -0,0 +1,32 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+    # You can also specify other tool versions:
+    # nodejs: "19"
+    # rust: "1.64"
+    # golang: "1.19"
+
+# Build documentation in the "docs/source" directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats:
+   - pdf
+   - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+   install:
+   - requirements: docs/rtd-requirements.txt

flory-0.0.0/CODE_OF_CONDUCT.md

@@ -0,0 +1,134 @@
+
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official email address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+[yicheng.qiang@ds.mpg.de].
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
+[https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations
+

flory-0.0.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Yicheng Qiang
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

flory-0.0.0/PKG-INFO

@@ -0,0 +1,82 @@
+Metadata-Version: 2.1
+Name: flory
+Version: 0.0.0
+Summary: Python package for finding coexisting phases in multicomponent mixtures
+Author-email: Yicheng Qiang <yicheng.qiang@ds.mpg.de>
+License: MIT License
+Project-URL: homepage, https://github.com/qiangyicheng/flory
+Project-URL: repository, https://github.com/qiangyicheng/flory
+Keywords: physics,phase-separation,free-energy
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numba>=0.57
+Requires-Dist: numpy>=1.22
+Requires-Dist: scipy>=1.7
+Requires-Dist: tqdm>=4.60
+Provides-Extra: dev
+Requires-Dist: pytest>=6.2; extra == "dev"
+Requires-Dist: pytest-cov>=4.0; extra == "dev"
+Requires-Dist: Sphinx>=4; extra == "dev"
+Requires-Dist: sphinx-autodoc-typehints>=2.2; extra == "dev"
+Requires-Dist: sphinx-paramlinks>=0.6; extra == "dev"
+Requires-Dist: sphinx-rtd-theme>=2.0; extra == "dev"
+
+# flory
+
+[![Tests](https://github.com/qiangyicheng/flory/actions/workflows/python-package.yml/badge.svg)](https://github.com/qiangyicheng/flory/actions/workflows/python-package.yml)
+[![Codecov](https://codecov.io/github/qiangyicheng/flory/graph/badge.svg?token=YF3K9ST8XQ)](https://codecov.io/github/qiangyicheng/flory)
+[![Documentation Status](https://readthedocs.org/projects/flory/badge/?version=latest)](https://flory.readthedocs.io/en/latest/?badge=latest)
+
+`flory` is a Python package for determining multiple coexisting phases in multicomponent mixtures.
+Although finding coexisting phases of binary mixture is simple, finding multiple coexisting phases in many-component mixtures is challenging, mainly due to the coupling of lots of nolinear equations.
+Currently `flory` supports finding coexisting phases of arbitrary multicomponent system with Flory-Huggins interactions in the canonical ensemble, whose average free energy density reads
+
+$$\bar{f}({N_\mathrm{p}}, \{J_\alpha\}, \{\phi_i^{(\alpha)}\}) = \sum_{\alpha=1}^{{N_\mathrm{p}}} J_\alpha f(\{\phi_i^{(\alpha)}\}) \; ,$$
+
+where $N_\mathrm{c}$ is the number of components, $N_\mathrm{p}$ is the number of phases, $J_\alpha$ is the volume fraction of the phase $\alpha$ and $\phi_i^{(\alpha)}$ is the volume fraction of the component $i$ in the phase $\alpha$.
+Each phase is considered to be homogeneous with a energy density
+
+$$f(\{\phi_i\}) = \frac{1}{2}\sum_{i,j=1}^{N_\mathrm{c}} \chi_{ij} \phi_i \phi_j + \sum_{i=1}^{N_\mathrm{c}} \frac{\phi_i}{l_i} \ln \phi_i \; ,$$
+
+where $\chi_{ij}$ is the Flory-Huggins interaction between component $i$ and $j$, and $l_i$ is the relative molecule size of the component $i$.
+With given interaction matrix $\chi_{ij}$, average volume fractions of all components across the system $\bar{\phi}_i$ and the relative molecule sizes $l_i$, `flory` provides tools to find the coexisting phases in equilibrium.
+
+Installation
+------------
+
+`flory` is available on `pypi`, so you should be able to install it through `pip`:
+
+```bash
+pip install flory
+```
+
+Usage
+-----
+
+A simple example finds the coexisting phases of a binary mixture:
+
+```python
+import flory
+
+chis = [[0, 4.0], [4.0, 0]]     # Set the \chi matrix
+phi_means = [0.5, 0.5]          # Set the average volume fractions
+
+volumes, phis = flory.find_coexisting_phases(chis, phi_means, 16)   # obtain the relative volumes and the compositions of the two coexisting phases
+```
+
+
+More information
+----------------
+* See examples in [examples folder](https://github.com/qiangyicheng/flory/tree/main/examples)
+* [Full documentation on readthedocs](https://flory.readthedocs.io/)
+

flory-0.0.0/README.md

@@ -0,0 +1,49 @@
+# flory
+
+[![Tests](https://github.com/qiangyicheng/flory/actions/workflows/python-package.yml/badge.svg)](https://github.com/qiangyicheng/flory/actions/workflows/python-package.yml)
+[![Codecov](https://codecov.io/github/qiangyicheng/flory/graph/badge.svg?token=YF3K9ST8XQ)](https://codecov.io/github/qiangyicheng/flory)
+[![Documentation Status](https://readthedocs.org/projects/flory/badge/?version=latest)](https://flory.readthedocs.io/en/latest/?badge=latest)
+
+`flory` is a Python package for determining multiple coexisting phases in multicomponent mixtures.
+Although finding coexisting phases of binary mixture is simple, finding multiple coexisting phases in many-component mixtures is challenging, mainly due to the coupling of lots of nolinear equations.
+Currently `flory` supports finding coexisting phases of arbitrary multicomponent system with Flory-Huggins interactions in the canonical ensemble, whose average free energy density reads
+
+$$\bar{f}({N_\mathrm{p}}, \{J_\alpha\}, \{\phi_i^{(\alpha)}\}) = \sum_{\alpha=1}^{{N_\mathrm{p}}} J_\alpha f(\{\phi_i^{(\alpha)}\}) \; ,$$
+
+where $N_\mathrm{c}$ is the number of components, $N_\mathrm{p}$ is the number of phases, $J_\alpha$ is the volume fraction of the phase $\alpha$ and $\phi_i^{(\alpha)}$ is the volume fraction of the component $i$ in the phase $\alpha$.
+Each phase is considered to be homogeneous with a energy density
+
+$$f(\{\phi_i\}) = \frac{1}{2}\sum_{i,j=1}^{N_\mathrm{c}} \chi_{ij} \phi_i \phi_j + \sum_{i=1}^{N_\mathrm{c}} \frac{\phi_i}{l_i} \ln \phi_i \; ,$$
+
+where $\chi_{ij}$ is the Flory-Huggins interaction between component $i$ and $j$, and $l_i$ is the relative molecule size of the component $i$.
+With given interaction matrix $\chi_{ij}$, average volume fractions of all components across the system $\bar{\phi}_i$ and the relative molecule sizes $l_i$, `flory` provides tools to find the coexisting phases in equilibrium.
+
+Installation
+------------
+
+`flory` is available on `pypi`, so you should be able to install it through `pip`:
+
+```bash
+pip install flory
+```
+
+Usage
+-----
+
+A simple example finds the coexisting phases of a binary mixture:
+
+```python
+import flory
+
+chis = [[0, 4.0], [4.0, 0]]     # Set the \chi matrix
+phi_means = [0.5, 0.5]          # Set the average volume fractions
+
+volumes, phis = flory.find_coexisting_phases(chis, phi_means, 16)   # obtain the relative volumes and the compositions of the two coexisting phases
+```
+
+
+More information
+----------------
+* See examples in [examples folder](https://github.com/qiangyicheng/flory/tree/main/examples)
+* [Full documentation on readthedocs](https://flory.readthedocs.io/)
+

flory-0.0.0/docs/Makefile

@@ -0,0 +1,24 @@
+# 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) $(O)
+
+cleanall:
+	@$(SPHINXBUILD) -M clean ${@:2} "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	rm -r $(SOURCEDIR)/_autosummary

flory-0.0.0/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

flory-0.0.0/docs/paper/flory.bib

@@ -0,0 +1,87 @@
+@article{zwicker2022Evolved,
+  title = {Evolved Interactions Stabilize Many Coexisting Phases in Multicomponent Liquids},
+  author = {Zwicker, David and Laan, Liedewij},
+  year = {2022},
+  month = jul,
+  journal = {Proc. Natl. Acad. Sci. U.S.A.},
+  volume = {119},
+  number = {28},
+  pages = {e2201250119},
+  publisher = {Proceedings of the National Academy of Sciences},
+  doi = {10.1073/pnas.2201250119},
+  urldate = {2023-06-21}
+}
+
+@incollection{panagiotopoulos1995Gibbs,
+  title = {Gibbs {{Ensemble Techniques}}},
+  booktitle = {Observation, {{Prediction}} and {{Simulation}} of {{Phase Transitions}} in {{Complex Fluids}}},
+  author = {Panagiotopoulos, Athanassios Z.},
+  editor = {Baus, Marc and Rull, Luis F. and Ryckaert, Jean-Paul},
+  year = {1995},
+  series = {Nato {{Science Series C}}},
+  pages = {463--501},
+  publisher = {Springer Netherlands},
+  address = {Dordrecht},
+  doi = {10.1007/978-94-011-0065-6_11},
+  urldate = {2024-03-01},
+  isbn = {978-94-011-0065-6},
+  langid = {english}
+}
+
+@article{mester2013Numerical,
+  title = {Numerical Self-Consistent Field Theory of Multicomponent Polymer Blends in the {{Gibbs}} Ensemble},
+  author = {Mester, Zoltan and A.~Lynd, Nathaniel and H.~Fredrickson, Glenn},
+  year = {2013},
+  journal = {Soft Matter},
+  volume = {9},
+  number = {47},
+  pages = {11288--11294},
+  publisher = {Royal Society of Chemistry},
+  doi = {10.1039/C3SM51893K},
+  urldate = {2024-03-01},
+  langid = {english}
+}
+
+@article{schmid1998Selfconsistentfield,
+  title = {Self-Consistent-Field Theories for Complex Fluids},
+  author = {Schmid, F.},
+  year = {1998},
+  month = sep,
+  journal = {J. Phys.: Condens. Matter},
+  volume = {10},
+  number = {37},
+  pages = {8105},
+  issn = {0953-8984},
+  doi = {10.1088/0953-8984/10/37/002},
+  urldate = {2024-03-26},
+  langid = {english}
+}
+
+@misc{qiang2024Scaling,
+  title = {Scaling of Phase Count in Multicomponent Liquids},
+  author = {Qiang, Yicheng and Luo, Chengjie and Zwicker, David},
+  year = {2024},
+  month = may,
+  number = {arXiv:2405.01138},
+  eprint = {2405.01138},
+  primaryclass = {cond-mat, physics:physics},
+  publisher = {arXiv},
+  urldate = {2024-08-12},
+  archiveprefix = {arXiv}
+}
+
+@inproceedings{lam2015Numba,
+  title = {Numba: A {{LLVM-based Python JIT}} Compiler},
+  shorttitle = {Numba},
+  booktitle = {Proceedings of the {{Second Workshop}} on the {{LLVM Compiler Infrastructure}} in {{HPC}}},
+  author = {Lam, Siu Kwan and Pitrou, Antoine and Seibert, Stanley},
+  year = {2015},
+  month = nov,
+  pages = {1--6},
+  publisher = {ACM},
+  address = {Austin Texas},
+  doi = {10.1145/2833157.2833162},
+  urldate = {2024-08-12},
+  isbn = {978-1-4503-4005-2},
+  langid = {english}
+}