mGFD: Meshless Generalized Finite Differences 📐☁️

A high-performance Python ecosystem for Point Cloud Generation and PDE solving on highly irregular domains using Generalized Finite Differences.

---

📑 Table of Contents

• 🌟 Overview & The Mathematical Core
• 📦 Installation
• 🚀 End-to-End Workflow: Lake Pátzcuaro
• 📚 Python API Reference
• 🔬 Research & Datasets
• 🏗️ Repository Structure
• 🤝 Contributing & Citation

---

🌟 Overview & The Mathematical Core

mGFD is a complete meshless computational suite. Traditional methods (like Finite Elements or Finite Volumes) require complex and restrictive mesh generation. mGFD completely bypasses this limitation by solving Partial Differential Equations (PDEs) directly on unstructured point clouds.

This makes it exceptionally powerful for modeling physics in complex, real-world geometries such as natural lakes, islands, or custom engineering domains.

🧮 The Mathematical Core (El Operador Diferencial)

One of the most powerful features of mGFD is its ability to solve almost any second-order linear Partial Differential Equation by simply defining a 6-element mathematical vector.

Based on the theoretical formulation (Tinoco-Guerrero et al., 2025), a general second-order linear PDE operator ($L u$) can be expressed as:

$$ L u = A u_{xx} + B u_{xy} + C u_{yy} + D u_x + E u_y + F u $$

Using this exact nomenclature, mGFD can solve three main families of problems out-of-the-box. You just construct a 6-element Python array [D, E, A, B, C, F] and pass it to the solver:

1. Stationary Problems ($L u = f(x, y)$)

   • Poisson Equation: $u_{xx} + u_{yy} = f(x, y)$
   • In this case, $A = 1$ and $C = 1$. The operator is:

     # [D, E, 2*A, B, 2*C, F]
     L_poisson = np.vstack([[0], [0], [2], [0], [2], [0]])

2. First-Order Transients ($L u = u_t$)

   • Advection-Diffusion Equation: $\alpha_1 u_x + \alpha_2 u_y - \nu(u_{xx} + u_{yy}) = u_t$
   • Here $D = \alpha_1$, $E = \alpha_2$, $A = -\nu$, and $C = -\nu$. The operator is:

     # [D, E, 2*A, B, 2*C, F]
     L_adv_diff = np.vstack([[a1], [a2], [-2*nu], [0], [-2*nu], [0]])

3. Second-Order Transients ($L u = u_{tt}$)

   • Wave Equation: $c^2 u_{xx} + c^2 u_{yy} = u_{tt}$
   • Here $A = c^2$ and $C = c^2$. The operator is:

     # [D, E, 2*A, B, 2*C, F]
     L_wave = np.vstack([[0], [0], [2*c**2], [0], [2*c**2], [0]])

🚀 Key Features

• ☁️ Integrated Cloud Generator: A powerful engine to automatically generate 2D point clouds from geographic contour boundaries.
• 📐 Pure Meshless Solvers: Discretize and solve PDEs using only local neighbor stencils. No mesh required!
• 🏎️ High Performance: Fully optimized with Numba JIT compilation and parallelized with LLVM multithreading and KDTree C++ backends.
• 🧩 Modular Architecture: Highly professional PEP-8 compliant sub-package architecture.

---

📦 Installation

mGFD relies on a robust scientific stack (numpy, scipy, shapely, opencv-python-headless).

The easiest way to install the package is directly from PyPI:

pip install mGFD

To install the package from source (useful for development):

git clone https://github.com/gstinoco/mGFD.git
cd mGFD
pip install -e .

This will automatically install both the Python API and the mgfd-cloud command-line interface.

---

🚀 End-to-End Workflow: Lake Pátzcuaro

The true power of mGFD lies in its ability to go from a raw visual image to a solved PDE in a single, cohesive workflow. Here is a complete real-world scenario using Lake Pátzcuaro.

Step 1: Visual Contour Extraction

Instead of relying on idealized shapes (like circles or squares), mGFD excels at real geographic domains. We start by identifying our domain from a satellite map.

Before generating the computational point cloud, we must extract the geometric contours of the lake into a CSV file (Patzcuaro_contours.csv).

Tip

Visual Contour Extraction The easiest way to generate this contour file is by uploading your image to our interactive mGFD CloudGenerator Web Tool. You can manually trace the boundaries and export them directly to CSV!

Satellite Map	Extracted Contours (CSV Plot)

Step 2: Generate the Cloud (CLI)

Using the mgfd-cloud CLI, we fill the interior of these extracted contours with a computationally valid, Poisson-Disk distributed point cloud:

mgfd-cloud generate --input Patzcuaro_contours.csv --output Patzcuaro_cloud.csv --method natural --density 3

Step 3: Python Solution (API)

Create a script named solve_patzcuaro.py to load your new cloud, apply the meshless solver for the Poisson equation, and render the results using the built-in visualization utilities:

import numpy as np
from mGFD.io.io import load_points
from mGFD import Stationary
from mGFD.viz.graph import plot_stationary

# 1. Load the generated point cloud
p = load_points("Patzcuaro_cloud.csv")

# 2. Define the analytical boundary condition
phi = lambda x, y: np.exp(x + y)

# 3. Define the forcing function (RHS)
f_stat = lambda x, y: 2 * np.exp(x + y)

# 4. Define the differential operator for Poisson (Laplacian)
# Using [D, E, 2*A, B, 2*C, F]
L_stat = np.vstack([[0], [0], [2], [0], [2], [0]])

# 5. Execute the solver
print("Solving Poisson Equation for Lake Pátzcuaro...")
u_ap, vec = Stationary(p, phi, f_stat, operator=L_stat, verbose=True)

# 6. Visualize the numerical approximation
print("Rendering plot...")
plot_stationary(p, u_ap, save=False, title='Pátzcuaro Poisson Solution', verbose=True)

Run your script, and a Matplotlib 3D window will pop up showing the surface of your solution perfectly adapted to the irregular contours of the lake!

Step 4: Visualize Results

When running batch solvers or keeping save=True, mGFD automatically exports high-quality PNGs (for stationary problems) and animated GIFs (for transient problems).

Here are the actual simulation outputs for Lake Pátzcuaro using the exact cloud generated above:

Poisson (Stationary)	Heat (Transient)

---

📚 Python API Reference

mGFD provides a clean and modular Python API located in the mGFD module. Below is an exhaustive manual of the core functions available for point cloud generation, I/O operations, PDE solving, and visualization.

1. Core Solvers (mGFD.solvers)

These functions are the mathematical heart of mGFD. They compute spatial derivatives using generalized finite differences over local neighborhoods.

Stationary

Solves stationary problems (e.g., Poisson equation) with Dirichlet boundary conditions.

def Stationary(
    p: np.ndarray, 
    phi: Callable, 
    f: Callable, 
    operator: np.ndarray, 
    upwind: bool = False, 
    vec: Optional[np.ndarray] = None, 
    nvec: int = 12, 
    verbose: bool = False
) -> Tuple[np.ndarray, np.ndarray]:

• p (m x 3): Point cloud array with columns [x, y, flag]. Interior points have flag=0, boundary points have flag=1 or flag=2.
• phi: A Python lambda/function phi(x, y) representing the analytical Dirichlet boundary condition.
• f: A Python lambda/function f(x, y) representing the right-hand side (forcing term).
• operator (6 x 1): Differential operator vector [D, E, A, B, C, F].
• upwind: Set to True for advection-dominated problems to automatically bias the neighbor search against the velocity field.
• vec: Precomputed neighbor list. If None, it is computed automatically.
• nvec: The target number of neighbors to find for each point (default: 12). If instability is detected, the solver may dynamically retry with expanded neighborhoods (up to 30).
• Returns: (u_ap, vec), where u_ap is the computed numerical solution and vec is the neighborhood list.

TimeDerivative1

Solves first-order-in-time problems (e.g., Heat and Advection-Diffusion equations).

def TimeDerivative1(
    p: np.ndarray, 
    f: Callable, 
    t: int, 
    coef: List[float], 
    operator: np.ndarray, 
    implicit: bool = False, 
    lam: float = 0.5, 
    upwind: bool = False, 
    vec: Optional[np.ndarray] = None, 
    nvec: int = 12, 
    verbose: bool = False
) -> Tuple[np.ndarray, np.ndarray]:

• f: A time-dependent function f(x, y, T, coef) representing the exact solution (used for boundary conditions during time steps).
• t: The number of time steps. Transients use a normalized time grid T = np.linspace(0, 1, t).
• coef: A list of physical coefficients passed to f (e.g., [viscosity]).
• implicit: If True, uses a fully implicit matrix solve (SciPy bicgstab is required). Highly recommended for stability.
• lam: The interpolation factor $\lambda$ for time-stepping ($\lambda = 0.5$ implies a Crank-Nicolson scheme).

TimeDerivative2

Solves second-order-in-time problems (e.g., Wave equation).

def TimeDerivative2(
    p: np.ndarray, 
    f: Callable, 
    g: Callable, 
    t: int, 
    coef: List[float], 
    operator: np.ndarray, 
    implicit: bool = False, 
    lam: float = 0.5, 
    upwind: bool = False, 
    vec: Optional[np.ndarray] = None, 
    nvec: int = 12, 
    verbose: bool = False
) -> Tuple[np.ndarray, np.ndarray]:

• g: A function g(x, y, T, coef) representing the initial velocity of the system.

2. Cloud Generation (mGFD.cloud_generator)

Command-Line Interface (mgfd-cloud)

The mGFD installation includes a powerful CLI to rapidly generate and reduce computational domains.

mgfd-cloud generate -i INPUT -o OUTPUT -m {natural,regular} [-d DENSITY] [--inside-regions]

mgfd-cloud reduce -i INPUT -o OUTPUT -m MULTIPLIER

• generate: Fills a boundary contour with points.
  • -i / --input: Path to the boundary CSV file.
  • -o / --output: Path for the generated cloud CSV.
  • -m / --method: Use natural (Poisson-Disk) or regular (Grid).
  • -d / --density: Density multiplier. Higher values create denser, tighter clouds.
  • --inside-regions: If present, internal closed boundaries are treated as solid islands (holes in the domain).
• reduce: Reduces the density of an existing cloud.
  • -m / --multiplier: Scaling factor to space out points.

While the CLI (mgfd-cloud) is the easiest way to generate domains, you can invoke the generation directly via Python.

generate_cloud_natural / generate_cloud_regular

Generates an unstructured (Poisson-Disk) or regular (Grid) point cloud inside a contour.

def generate_cloud_natural(
    csv_file: str, 
    output_file: str, 
    inside_regions: bool = False, 
    verbose: bool = False
)

def generate_cloud_regular(
    csv_file: str, 
    output_file: str, 
    inside_regions: bool = False, 
    verbose: bool = False
)

• csv_file: Path to the input contour CSV file.
• output_file: Path where the generated cloud CSV will be saved.
• inside_regions: If True, interprets internal closed contours as solid islands (holes in the domain).

reduce_points_by_region

Reduces the point density of an existing cloud by a scaling factor.

def reduce_points_by_region(
    input_csv: str, 
    output_csv: str, 
    multiplier: int = 2
) -> Optional[List[Dict[str, Any]]]

• multiplier: A scaling factor for the distance between nodes. A multiplier of 2 significantly reduces the number of points.

3. I/O Operations (mGFD.io.io)

load_points

def load_points(
    file_path: str, 
    verbose: bool = False
) -> np.ndarray

• Reads a CSV file containing x, y, flag data and returns it as a standardized (m, 3) NumPy array ready for the solvers.

export_stationary_vtk / export_transient_vtk (mGFD.io.export_vtk)

Exports the numerical solutions directly to VTK format using PyVista, perfectly structured for advanced 3D analysis in Paraview.

def export_stationary_vtk(
    p: np.ndarray, 
    u_ap: np.ndarray, 
    out_dir: str, 
    basename: str = "Stationary_Solution", 
    cloud_path: Optional[str] = None
) -> None

def export_transient_vtk(
    p: np.ndarray, 
    u_ap: np.ndarray, 
    t: int, 
    T: np.ndarray, 
    out_dir: str, 
    basename: str = "Transient_Solution", 
    cloud_path: Optional[str] = None
) -> None

• u_ap: The computed numerical approximation array (or matrix for transients).
• out_dir: Directory where the .vtk files will be saved.
• cloud_path: (Optional) Passing the original cloud path allows mGFD to automatically locate and use the cached triangulation to build the PyVista mesh instantly.

4. Visualization Utilities (mGFD.viz.graph)

plot_stationary

def plot_stationary(
    p: np.ndarray, 
    u: np.ndarray, 
    save: bool = False, 
    nom: str = '', 
    title: str = 'Solution', 
    verbose: bool = True
) -> None

• Renders a 3D scatter surface of the solution over the point cloud. If save=True, it exports .png snapshots to the nom path.

plot_transient

def plot_transient(
    p: np.ndarray, 
    u: np.ndarray, 
    save: bool = False, 
    nom: str = '', 
    title: str = 'Solution', 
    verbose: bool = True
) -> None

• u (m x t): A matrix containing the solution at each node for every time step.
• Renders a 3D Matplotlib animation over time. If save=True, it exports an animated .gif to the nom path.

5. Core Utilities & Triangulations (mGFD.core.utils)

Because mGFD is a strictly meshless numerical method, the PDE solvers operate entirely on unstructured points and local distance-based neighborhoods (stencils). Meshes/triangles are never used during the numerical solution.

However, rendering 3D surfaces in Matplotlib and exporting meshes to Paraview (VTK) mathematically requires a triangulation to color the faces between points.

get_valid_triangulation

def get_valid_triangulation(p: np.ndarray, nom: Optional[str] = None) -> Optional[np.ndarray]

• What it does: Computes a constrained Delaunay triangulation of the point cloud, aggressively filtering out triangles that fall outside concave boundaries or inside holes (islands).
• Caching system: Computing Delaunay simplices on large clouds is extremely expensive. When mGFD computes a valid triangulation, it automatically caches the resulting simplices into a _triangulation.csv file next to your original cloud. Subsequent calls to plotting or VTK exports will load this cache, saving massive amounts of computation time.

---

🔬 Research & Datasets

Looking for the mathematical formulation, real-world geographic lake datasets (Lake Patzcuaro, Caspian Sea, etc.), or reproducible benchmarking scripts?

👉 Explore the Research Laboratory (/research/README.md)

The research/ directory contains our complete academic suite, including experimental data, geographic boundary files, VTK results, and the exact theoretical explanations associated with our scientific publications.

---

🏗️ Repository Structure

Understanding the layout of this project is helpful if you want to contribute or explore the underlying math:

mGFD/
├── docs/                     # Media assets for the README (images, gifs)
├── src/mGFD/                 # The core Python library (uploaded to PyPI)
│   ├── cloud_generator/      # PDE domain creation (natural, regular, etc.)
│   ├── core/                 # Krylov solvers, KDTree neighbors, stencils
│   ├── io/                   # CSV and VTK import/export operations
│   ├── solvers/              # The high-level PDE solvers (Stationary, TimeDerivative)
│   └── viz/                  # Matplotlib 3D and 2D rendering
├── research/                 # The academic reproducible suite
│   ├── codes/                # Batch benchmarking scripts (e.g. main.py)
│   ├── data/                 # Geographic boundaries (CSV files)
│   ├── results/              # Output GIFs, VTKs, PNGs, and metrics
│   └── README.md             # Detailed mathematical foundations
└── tests/                    # CI/CD Unit and Integration tests

---

🤝 Contributing & Citation

Contributing

We welcome contributions from the scientific and open-source community!

1. Fork the repository.
2. Clone your fork locally and create a new feature branch (git checkout -b feature-new-solver).
3. Develop your feature, ensuring all code strictly adheres to our PEP-8 standard (especially the inline # alignment at column 136).
4. Test your code (we run a comprehensive CI suite via GitHub Actions).
5. Open a Pull Request!

For major changes, please open an issue first to discuss what you would like to change.

Citation

This project is open-sourced under the MIT License.

If you use this library or the core mathematical methodology in your research, please cite our reference paper:

@article{tinoco2025mgfd,
  title={mGFD: A meshless generalized finite difference method},
  author={Tinoco-Guerrero, Gerardo and Domínguez-Mota, Francisco Javier and Guzmán-Torres, José Alberto and Pedraza-Jiménez, Gabriela and Tinoco-Ruiz, José Gerardo},
  journal={Computers & Mathematics with Applications},
  volume={195},
  pages={396--418},
  year={2025},
  publisher={Elsevier},
  doi={10.1016/j.camwa.2025.07.034}
}

Developed for the advancement of meshless numerical methods and scientific computing.

Dr. Gerardo Tinoco-Guerrero
Dr. Francisco Javier Domínguez-Mota
Dr. José Alberto Guzmán-Torres
Universidad Michoacana de San Nicolás de Hidalgo
gerardo.tinoco@umich.mx

Report a Bug | Contact Author