pyfvtool 0.6.0__tar.gz

pyfvtool-0.6.0/AUTHORS

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+PyFVTool Authors
+================
+
+Ali A. Eftekhari <aliak@dtu.dk>
+Martinus H. V. Werts <martinus.werts@univ-angers.fr>

pyfvtool-0.6.0/LICENSE

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+MIT License
+
+Copyright (c) 2023-2025 Ali A. Eftekhari and Martinus H. V. Werts
+
+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.

pyfvtool-0.6.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: pyfvtool
+Version: 0.6.0
+Summary: Finite-volume toolbox in Python
+Author-email: "Ali A. Eftekhari" <aliak@dtu.dk>, "Martinus H. V. Werts" <martinus.werts@univ-angers.fr>
+Project-URL: Homepage, https://github.com/FiniteVolumeTransportPhenomena/PyFVTool
+Project-URL: Bug Tracker, https://github.com/FiniteVolumeTransportPhenomena/PyFVTool/issues
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: AUTHORS
+Requires-Dist: numpy>=2
+Requires-Dist: scipy
+Requires-Dist: matplotlib
+Dynamic: license-file
+
+# PyFVTool: Python toolbox for the finite volume method
+
+[![DOI](https://img.shields.io/badge/DOI-10.5281/zenodo.17904660-blue.svg)](https://doi.org/10.5281/zenodo.17904660)
+
+PyFVTool discretizes and numerically solves the conservative form of transient [convection-diffusion-reaction](https://en.wikipedia.org/wiki/Convection%E2%80%93diffusion_equation) equations with variable velocity field/diffusion coefficients and source terms. PyFVTool uses the [finite volume method](https://en.wikipedia.org/wiki/Finite_volume_method) (FVM) to do this. 
+
+The partial differential equations that can be solved numerically with PyFVTool have the general form
+
+```math
+\underbrace{\alpha\frac{\partial\phi}{\partial t}}_{\textrm{Transient term}}+\underbrace{\vec{\nabla} \cdot \left(\vec{u}\phi\right)}_{\textrm{Advection term}}+\underbrace{\vec{\nabla} \cdot (-D\vec{\nabla}\phi)}_{\textrm{Diffusion term}}+\underbrace{\beta\phi}_{\textrm{Linear source term}}+\underbrace{\gamma}_{\textrm{Constant source term}}=0
+```
+with the following general form of boundary conditions (specified by constants $a$, $b$ and $c$, with $\hat{e}$ being the unit vector in the direction of the coordinate at the specific boundary):
+
+```math
+a(\vec{\nabla}\phi \cdot \hat{e})+b\phi=c
+```
+An important feature of PyFVTool is that it is 'pure scientific Python' (*i.e.* it needs only Python and the standard scientific computing libraries  `numpy`, `scipy` and `matplotlib` to run). Further optional dependencies may appear in the future, *e.g.*, for increasing the computational speed via optimised numerical libraries, but these will remain optional.
+
+PyFVTool is limited to calculations on structured meshes (regular grids). It is oriented to calculation of heat and mass transport phenomena (diffusion-advection-reaction) for the frequent cases where the flow velocity field is already known (or where flow is absent). It is not particularly suited for fluid dynamics (solving Navier-Stokes), which requires implementation of further numerical schemes on top of the current PyFVTool ([simulkade](https://github.com/simulkade) knows how).  For fluid dynamics, other specialized finite-volume codes exist.
+
+The [finite-volume](https://en.wikipedia.org/wiki/Finite_volume_method) discretization schemes in PyFVTool include:  
+  * 1D, 2D and 3D Cartesian, cylindrical and spherical grids
+  * Second order (central difference) [diffusion](https://en.wikipedia.org/wiki/Diffusion_equation) terms
+  * Second order (central difference), first order ([upwind](https://en.wikipedia.org/wiki/Upwind_scheme)), and [total variation diminishing](https://en.wikipedia.org/wiki/Total_variation_diminishing) (TVD) for advection terms
+  * Constant and linear source terms
+  * Backward and forward [Euler](https://en.wikipedia.org/wiki/Euler_method) for transient terms
+  * [Dirichlet](https://en.wikipedia.org/wiki/Dirichlet_boundary_condition), [Neumann](https://en.wikipedia.org/wiki/Neumann_boundary_condition), [Robin](https://en.wikipedia.org/wiki/Robin_boundary_condition), and [periodic](https://en.wikipedia.org/wiki/Periodic_boundary_conditions) boundary conditions
+  * (Relatively) easy linearization of nonlinear PDEs
+  * Averaging methods (linear, arithmetic, geometric, harmonic, upwind, TVD)
+  * Divergence and gradient terms
+
+PyFVTool is a Python implementation of [A. A. Eftekhari](https://github.com/simulkade)'s Matlab/Octave FVM solver [FVTool](https://github.com/FiniteVolumeTransportPhenomena/FVTool). It was strongly inspired by [FiPy](https://pages.nist.gov/fipy/en/latest/index.html), but it has only a fraction of FiPy's features. Boundary conditions, however, are more easily (and arguably more consistently) implemented in PyFVTool. 
+
+PyFVTool is under active development. Several test cases have been validated to match analytical solutionsn with more validation under way, in particular through the use of this toolbox in ongoing research projects. The documentation can be found at https://finitevolumetransportphenomena.github.io/PyFVTool/. It includes many [examples](https://finitevolumetransportphenomena.github.io/PyFVTool/examples/index.html) in the form of Jupyter notebooks. From these examples, it is easy to understand how to set up finite-volume solvers for heat and mass transfer.
+
+
+## Installation
+
+### Python environment
+
+We recommend to use PyFVTool with Python 3.12 (no more, no less) and the most recent NumPy and SciPy versions. It is also highly recommended to use the [MiniForge](https://conda-forge.org/download/) / Anaconda / miniconda Python distributions and to set up a specific environment for PyFVTool (we'll call the environment `pyfvtool_user`).
+
+This requires two commands to be launched from the command-line prompt.
+```
+conda create --name pyfvtool_user python=3.12 numpy scipy matplotlib spyder jupyterlab tqdm
+
+conda activate pyfvtool_user
+```
+
+Of course, do not forget to  `conda activate pyfvtool_user`  the environment every time you run Python code that uses PyFVTool.
+
+### Installation of PyFVTool
+
+Install PyFVTool into your specific PyFVTool Conda environment using `pip`. You will need `Python 3.12` (or later) and `numpy` (version 2.0.0 or later), `scipy`, and `matplotlib`, which are provided for by the Conda `pyfvtool_user` environment. The current `pip` install sources PyFVTool directly from GitHub.
+
+```
+pip install git+https://github.com/FiniteVolumeTransportPhenomena/PyFVTool.git
+```
+
+If you'd like to use PyFVTool in [Google Colab](https://colab.research.google.com/), you can enter the following in the first cell of a Colab Notebook:
+
+```
+!pip install git+https://github.com/FiniteVolumeTransportPhenomena/PyFVTool.git
+```
+
+This will install PyFVTool in the current Colab instance, and make it available for import in the Notebook.
+
+
+
+
+### Development installation
+If you would like to work on the source code, it is possible to install a development version using `pip`. See [`CONTRIBUTING.md`](https://github.com/FiniteVolumeTransportPhenomena/PyFVTool/blob/main/CONTRIBUTING.md)
+
+
+
+
+## Example
+
+Here is a simple example of a 1D transient diffusion equation. Further [examples](https://finitevolumetransportphenomena.github.io/PyFVTool/examples/index.html) can be found in the [documentation](https://finitevolumetransportphenomena.github.io/PyFVTool/). These examples are also available as Jupyter notebook source files in [`./docs/source/notebook-examples/`](docs/source/notebook-examples/).
+
+
+```python
+import pyfvtool as pf
+import matplotlib.pyplot as plt
+
+# Solving a 1D diffusion equation with a fixed concentration 
+# at the left boundary and a closed boundary on the right side
+
+
+# Calculation parameters
+Nx = 100 # number of finite volume cells
+Lx = 1.0 # [m] length of the domain 
+c_left = 1.0 # left boundary concentration
+c_init = 0.0 # initial concentration
+D_val = 1e-5 # diffusion coefficient (gas phase)
+t_simulation = 7200.0 # [s] simulation time
+dt = 60.0 # [s] time step
+Nskip = 10 # plot every Nskip-th profile
+
+# Define mesh
+mesh = pf.Grid1D(Nx, Lx)
+
+# Create a cell variable with initial concentration
+# By default, 'no flux' boundary conditions are applied
+c = pf.CellVariable(mesh, c_init)
+
+# Switch the left boundary to Dirichlet: fixed concentration
+c.BCs.left.fixedValue(c_left)
+
+# Assign diffusivity: the diffusivity is needed at the interface between cells.
+# The required `pf.FaceVariable` is obtained here using the `pf.geometricMean`
+# averager.
+D_cell = pf.CellVariable(mesh, D_val)
+D_face = pf.geometricMean(D_cell)
+
+# Time loop (with integrated plotting)
+plt.figure(1)
+plt.clf()
+t = 0.0
+nplot = 0
+while t<t_simulation:
+    # Compose discretized terms for matrix equation
+    eqnterms = [ pf.transientTerm(c, dt),
+                -pf.diffusionTerm(D_face)]
+
+    # Solve PDE
+    pf.solvePDE(c, eqnterms)
+    t+=dt
+
+    if (nplot % Nskip == 0):
+        pf.visualizeCells(c)
+    nplot+=1
+plt.show()
+```

pyfvtool-0.6.0/README.md

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+# PyFVTool: Python toolbox for the finite volume method
+
+[![DOI](https://img.shields.io/badge/DOI-10.5281/zenodo.17904660-blue.svg)](https://doi.org/10.5281/zenodo.17904660)
+
+PyFVTool discretizes and numerically solves the conservative form of transient [convection-diffusion-reaction](https://en.wikipedia.org/wiki/Convection%E2%80%93diffusion_equation) equations with variable velocity field/diffusion coefficients and source terms. PyFVTool uses the [finite volume method](https://en.wikipedia.org/wiki/Finite_volume_method) (FVM) to do this. 
+
+The partial differential equations that can be solved numerically with PyFVTool have the general form
+
+```math
+\underbrace{\alpha\frac{\partial\phi}{\partial t}}_{\textrm{Transient term}}+\underbrace{\vec{\nabla} \cdot \left(\vec{u}\phi\right)}_{\textrm{Advection term}}+\underbrace{\vec{\nabla} \cdot (-D\vec{\nabla}\phi)}_{\textrm{Diffusion term}}+\underbrace{\beta\phi}_{\textrm{Linear source term}}+\underbrace{\gamma}_{\textrm{Constant source term}}=0
+```
+with the following general form of boundary conditions (specified by constants $a$, $b$ and $c$, with $\hat{e}$ being the unit vector in the direction of the coordinate at the specific boundary):
+
+```math
+a(\vec{\nabla}\phi \cdot \hat{e})+b\phi=c
+```
+An important feature of PyFVTool is that it is 'pure scientific Python' (*i.e.* it needs only Python and the standard scientific computing libraries  `numpy`, `scipy` and `matplotlib` to run). Further optional dependencies may appear in the future, *e.g.*, for increasing the computational speed via optimised numerical libraries, but these will remain optional.
+
+PyFVTool is limited to calculations on structured meshes (regular grids). It is oriented to calculation of heat and mass transport phenomena (diffusion-advection-reaction) for the frequent cases where the flow velocity field is already known (or where flow is absent). It is not particularly suited for fluid dynamics (solving Navier-Stokes), which requires implementation of further numerical schemes on top of the current PyFVTool ([simulkade](https://github.com/simulkade) knows how).  For fluid dynamics, other specialized finite-volume codes exist.
+
+The [finite-volume](https://en.wikipedia.org/wiki/Finite_volume_method) discretization schemes in PyFVTool include:  
+  * 1D, 2D and 3D Cartesian, cylindrical and spherical grids
+  * Second order (central difference) [diffusion](https://en.wikipedia.org/wiki/Diffusion_equation) terms
+  * Second order (central difference), first order ([upwind](https://en.wikipedia.org/wiki/Upwind_scheme)), and [total variation diminishing](https://en.wikipedia.org/wiki/Total_variation_diminishing) (TVD) for advection terms
+  * Constant and linear source terms
+  * Backward and forward [Euler](https://en.wikipedia.org/wiki/Euler_method) for transient terms
+  * [Dirichlet](https://en.wikipedia.org/wiki/Dirichlet_boundary_condition), [Neumann](https://en.wikipedia.org/wiki/Neumann_boundary_condition), [Robin](https://en.wikipedia.org/wiki/Robin_boundary_condition), and [periodic](https://en.wikipedia.org/wiki/Periodic_boundary_conditions) boundary conditions
+  * (Relatively) easy linearization of nonlinear PDEs
+  * Averaging methods (linear, arithmetic, geometric, harmonic, upwind, TVD)
+  * Divergence and gradient terms
+
+PyFVTool is a Python implementation of [A. A. Eftekhari](https://github.com/simulkade)'s Matlab/Octave FVM solver [FVTool](https://github.com/FiniteVolumeTransportPhenomena/FVTool). It was strongly inspired by [FiPy](https://pages.nist.gov/fipy/en/latest/index.html), but it has only a fraction of FiPy's features. Boundary conditions, however, are more easily (and arguably more consistently) implemented in PyFVTool. 
+
+PyFVTool is under active development. Several test cases have been validated to match analytical solutionsn with more validation under way, in particular through the use of this toolbox in ongoing research projects. The documentation can be found at https://finitevolumetransportphenomena.github.io/PyFVTool/. It includes many [examples](https://finitevolumetransportphenomena.github.io/PyFVTool/examples/index.html) in the form of Jupyter notebooks. From these examples, it is easy to understand how to set up finite-volume solvers for heat and mass transfer.
+
+
+## Installation
+
+### Python environment
+
+We recommend to use PyFVTool with Python 3.12 (no more, no less) and the most recent NumPy and SciPy versions. It is also highly recommended to use the [MiniForge](https://conda-forge.org/download/) / Anaconda / miniconda Python distributions and to set up a specific environment for PyFVTool (we'll call the environment `pyfvtool_user`).
+
+This requires two commands to be launched from the command-line prompt.
+```
+conda create --name pyfvtool_user python=3.12 numpy scipy matplotlib spyder jupyterlab tqdm
+
+conda activate pyfvtool_user
+```
+
+Of course, do not forget to  `conda activate pyfvtool_user`  the environment every time you run Python code that uses PyFVTool.
+
+### Installation of PyFVTool
+
+Install PyFVTool into your specific PyFVTool Conda environment using `pip`. You will need `Python 3.12` (or later) and `numpy` (version 2.0.0 or later), `scipy`, and `matplotlib`, which are provided for by the Conda `pyfvtool_user` environment. The current `pip` install sources PyFVTool directly from GitHub.
+
+```
+pip install git+https://github.com/FiniteVolumeTransportPhenomena/PyFVTool.git
+```
+
+If you'd like to use PyFVTool in [Google Colab](https://colab.research.google.com/), you can enter the following in the first cell of a Colab Notebook:
+
+```
+!pip install git+https://github.com/FiniteVolumeTransportPhenomena/PyFVTool.git
+```
+
+This will install PyFVTool in the current Colab instance, and make it available for import in the Notebook.
+
+
+
+
+### Development installation
+If you would like to work on the source code, it is possible to install a development version using `pip`. See [`CONTRIBUTING.md`](https://github.com/FiniteVolumeTransportPhenomena/PyFVTool/blob/main/CONTRIBUTING.md)
+
+
+
+
+## Example
+
+Here is a simple example of a 1D transient diffusion equation. Further [examples](https://finitevolumetransportphenomena.github.io/PyFVTool/examples/index.html) can be found in the [documentation](https://finitevolumetransportphenomena.github.io/PyFVTool/). These examples are also available as Jupyter notebook source files in [`./docs/source/notebook-examples/`](docs/source/notebook-examples/).
+
+
+```python
+import pyfvtool as pf
+import matplotlib.pyplot as plt
+
+# Solving a 1D diffusion equation with a fixed concentration 
+# at the left boundary and a closed boundary on the right side
+
+
+# Calculation parameters
+Nx = 100 # number of finite volume cells
+Lx = 1.0 # [m] length of the domain 
+c_left = 1.0 # left boundary concentration
+c_init = 0.0 # initial concentration
+D_val = 1e-5 # diffusion coefficient (gas phase)
+t_simulation = 7200.0 # [s] simulation time
+dt = 60.0 # [s] time step
+Nskip = 10 # plot every Nskip-th profile
+
+# Define mesh
+mesh = pf.Grid1D(Nx, Lx)
+
+# Create a cell variable with initial concentration
+# By default, 'no flux' boundary conditions are applied
+c = pf.CellVariable(mesh, c_init)
+
+# Switch the left boundary to Dirichlet: fixed concentration
+c.BCs.left.fixedValue(c_left)
+
+# Assign diffusivity: the diffusivity is needed at the interface between cells.
+# The required `pf.FaceVariable` is obtained here using the `pf.geometricMean`
+# averager.
+D_cell = pf.CellVariable(mesh, D_val)
+D_face = pf.geometricMean(D_cell)
+
+# Time loop (with integrated plotting)
+plt.figure(1)
+plt.clf()
+t = 0.0
+nplot = 0
+while t<t_simulation:
+    # Compose discretized terms for matrix equation
+    eqnterms = [ pf.transientTerm(c, dt),
+                -pf.diffusionTerm(D_face)]
+
+    # Solve PDE
+    pf.solvePDE(c, eqnterms)
+    t+=dt
+
+    if (nplot % Nskip == 0):
+        pf.visualizeCells(c)
+    nplot+=1
+plt.show()
+```

pyfvtool-0.6.0/pyproject.toml

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+# minimalist pyproject.toml for PyFVTool
+
+[project]
+name = "pyfvtool"
+dynamic = ["version"] # version will be read from pyfvtool/__init__.py
+authors = [
+    { name="Ali A. Eftekhari", email="aliak@dtu.dk" },
+    { name="Martinus H. V. Werts", email="martinus.werts@univ-angers.fr" }
+]
+description = "Finite-volume toolbox in Python"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Mathematics"
+]
+readme = "README.md"
+requires-python = ">=3.12"
+dependencies = [
+        "numpy>=2",
+        "scipy",
+		"matplotlib"
+        ]
+
+
+[project.urls]
+"Homepage" = "https://github.com/FiniteVolumeTransportPhenomena/PyFVTool"
+"Bug Tracker" = "https://github.com/FiniteVolumeTransportPhenomena/PyFVTool/issues"
+
+[build-system]
+requires = ["setuptools>=61.0", "numpy>=2", "scipy", "matplotlib"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.dynamic]
+ # version will be read from pyfvtool/__init__.py
+version = {attr = "pyfvtool.__version__"}

pyfvtool-0.6.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

pyfvtool-0.6.0/setup.py

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+# minimalist setup.py
+from setuptools import setup
+
+setup()

pyfvtool-0.6.0/src/pyfvtool/__init__.py

@@ -0,0 +1,32 @@
+__version__ = "0.6.0"
+
+__author__ = ["Ali A. Eftekhari", "Martinus H. V. Werts"]
+
+__email__ = ["aliak@dtu.dk", "martinus.werts@univ-angers.fr"]
+
+__copyright__ = "Copyright 2023-2026, The Authors"
+
+__license__ = "MIT License"
+
+
+
+from .mesh import Grid1D, CylindricalGrid1D, SphericalGrid1D
+from .mesh import Grid2D, CylindricalGrid2D, PolarGrid2D 
+from .mesh import Grid3D, CylindricalGrid3D, SphericalGrid3D
+from .advection import convectionTerm, convectionTVDupwindRHSTerm,\
+                       convectionUpwindTerm
+from .diffusion import diffusionTerm
+from .source import linearSourceTerm, constantSourceTerm, transientTerm
+from .boundary import BoundaryConditions, boundaryConditionsTerm
+from .utilities import fluxLimiter
+from .calculus import gradient, gradientFixedBC
+from .calculus import divergence, divergenceTerm
+from .averaging import linearMean, arithmeticMean, upwindMean,\
+                       harmonicMean, geometricMean, tvdMean
+from .pdesolver import solveMatrixPDE, solvePDE, solveExplicitPDE
+from .cell import CellVariable
+from .cell import funceval, celleval
+from .cell import cellLocations
+from .face import FaceVariable, faceeval
+from .face import faceLocations
+from .visualization import visualizeCells