gospl_extensions

1. gospl_tectonics_ext - Data-driven tectonics extension
2. gospl_model_ext - Enhanced model with granular time control
3. cpp_interface - C++ interface to goSPL extensions

Prerequisites

Important: All extensions require the gospl conda environment to be activated:

conda activate gospl

The extensions depend on goSPL and its Fortran extensions, which are typically installed via conda.

Additional Requirements for C++ Interface

For the cpp_interface, you'll also need C++ build tools:

# On Ubuntu/Debian:
sudo apt install build-essential python3-dev python3-numpy

# On CentOS/RHEL:
sudo yum install gcc-c++ python3-devel python3-numpy

gospl_tectonics_ext: Data-driven tectonics for goSPL

This out-of-tree extension adds a way to drive horizontal and vertical tectonic velocities from an external dataset (positions + 3-component velocities) whose sampling points don’t coincide with the model mesh. Velocities are interpolated to mesh nodes via k-nearest-neighbor inverse-distance weighting and then applied using goSPL’s existing advection machinery.

• Core goSPL code remains untouched.
• Import path: from gospl_tectonics_ext import DataDrivenTectonics.

Install or make importable

Option A — Add to PYTHONPATH (quickest):

• Ensure path/to/gospl_extensions is on PYTHONPATH so Python can find gospl_tectonics_ext.

Option B — Editable install (recommended):

• Use the provided pyproject.toml and run an editable install.

Usage

from gospl.model import Model
from gospl_tectonics_ext import DataDrivenTectonics

m = Model("input-escarpment.yml", verbose=True)

# Bind the methods to this instance without modifying Model inheritance
m.apply_velocity_data = DataDrivenTectonics.apply_velocity_data.__get__(m, type(m))
m.interpolate_elevation_to_points = DataDrivenTectonics.interpolate_elevation_to_points.__get__(m, type(m))

veldata = {
    "coords": coords_np_array,  # shape (N, 3)
    "vel":    vel_np_array,     # shape (N, 3)
}

# Interpolate and apply external velocities
m.apply_velocity_data(veldata, timer=None, k=3, power=1.0)

# Interpolate current elevation field to external points
external_points = np.array([[x1, y1, z1], [x2, y2, z2], ...])  # shape (N, 3)
elevations = m.interpolate_elevation_to_points(external_points, k=3, power=1.0)

Behavior by advection scheme:

• advscheme == 0 (semi-Lagrangian): builds interpolation to advected positions and schedules plate advection at tNow + timer.
• advscheme > 0 (finite-volume IIOE/upwind): computes face velocities and advects immediately.

Methods

apply_velocity_data(veldata, timer=None, k=3, power=1.0)

• Interpolates external velocity data to mesh nodes and applies it using goSPL's advection machinery
• veldata: dict or object with 'coords' (N,3) and 'vel' (N,3) arrays
• timer: time interval for semi-Lagrangian scheme (defaults to model dt)
• k: number of nearest neighbors for interpolation
• power: inverse distance weighting power

interpolate_elevation_to_points(src_pts, k=3, power=1.0)

• Interpolates current elevation field (hGlobal) to external points
• src_pts: target coordinates array of shape (N,3)
• Returns: numpy array of interpolated elevations (N,)
• Useful for data extraction, analysis, or coupling with other models

Notes:

• Requires goSPL to be importable and its Fortran extensions available (gospl._fortran.getfacevelocity).
• Handles coincident nodes robustly; respects flat vs spherical mode.
• MPI safe: interpolation built on global coordinates; locals are sliced to locIDs.

Files

• gospl_tectonics_ext/data_driven_tectonics.py: the extension implementation.
• gospl_tectonics_ext/__init__.py: re-exports DataDrivenTectonics.

Testing

The extension includes a comprehensive test suite to ensure reliability:

# Run tests using pytest (recommended)
pytest tests/

# Or use the built-in test runner (no pytest required)
python run_tests.py

Test coverage includes:

• Input validation and error handling
• Interpolation accuracy with different parameters (both velocity and elevation)
• Both advection schemes (semi-Lagrangian and finite-volume)
• Edge cases (coincident nodes, empty data, etc.)
• Elevation interpolation with various k and power values
• Mock testing that doesn't require goSPL installation

Examples

Several example scripts demonstrate different use cases:

DataDrivenTectonics Basic Example

cd examples
python data_driven_tectonics_basic.py

Shows basic usage with synthetic velocity data and elevation interpolation.

DataDrivenTectonics Advanced Example

cd examples
python data_driven_tectonics_advanced.py

Demonstrates:

• Loading velocity data from CSV files
• Time-dependent velocity fields
• Comparing interpolation parameters
• Elevation field interpolation and sampling
• Monitoring velocity field effects

Sample Data

• examples/velocity_data.csv: Sample velocity data for testing
• examples/input-escarpment.yml: Working goSPL configuration file

Packaging (optional)

A pyproject.toml is included for proper Python packaging. To install in editable mode:

pip install -e path/to/gospl_extensions

This will also install required dependencies (numpy, scipy) and make the extension importable from anywhere.

Development Installation

For development with testing dependencies:

pip install -e "path/to/gospl_extensions[dev]"

After this, from gospl_tectonics_ext import DataDrivenTectonics will work from anywhere.

gospl_model_ext: Enhanced Model with Granular Time Control

This extension provides an EnhancedModel class that extends the goSPL Model class with additional methods for granular time control.

Features

• runProcessesForDt: Run processes for a specific time step 'dt'
• runProcessesForSteps: Run processes for a specified number of time steps
• runProcessesUntilTime: Run processes until a target time is reached

Usage

from gospl_model_ext import EnhancedModel

# Create enhanced model
model = EnhancedModel("config.yml")

# Run for specific dt
model.runProcessesForDt(dt=1000.0)

# Run for multiple steps with specific dt
model.runProcessesForSteps(num_steps=10, dt=1000.0)

# Run until target time is reached
model.runProcessesUntilTime(target_time=50000.0, dt=1000.0)

Files

• gospl_model_ext/enhanced_model.py: the extension implementation.
• gospl_model_ext/__init__.py: re-exports EnhancedModel.

Examples

EnhancedModel Basic Example

cd examples
python enhanced_model_basic.py

Shows controlled time-stepping with the EnhancedModel class, including demonstrations of all three new methods.

EnhancedModel Advanced Example

cd examples
python enhanced_model_advanced.py

Demonstrates:

• Elevation tracking at velocity sampling points
• Updating velocity coordinates based on evolving topography
• Analyzing elevation changes before and after each time step
• Advanced coupling between tectonics and topographic evolution

cpp_interface: C++ Interface to goSPL Extensions

This directory provides a C++ interface to the goSPL extensions through Python C API bindings, allowing external C++ simulation codes to use the EnhancedModel and DataDrivenTectonics functionality.

Features

• C++ API: Full C++ interface to EnhancedModel and DataDrivenTectonics
• Time Control: Run goSPL simulations with granular time control from C++
• Velocity Data: Apply time-dependent velocity fields from C++ code
• Integration Ready: Easy integration with existing C++ simulation frameworks

Quick Start

# Build the interface
cd cpp_interface
make

# Install locally for external C++ integration (e.g., DynEarthSol)
make install-local

# Run basic tests
make test

# Run with goSPL simulation
make test-gospl

DynEarthSol Integration

The C++ interface includes special support for integration with DynEarthSol, a finite element geodynamic modeling code. After building with make install-local, the library and headers are placed in gospl_extensions/lib/ and gospl_extensions/include/ directories, which can be used by external build systems.

Building for DynEarthSol Integration

1. Build gospl_extensions for local installation:

   cd cpp_interface
   make install-local

   This creates:

   • ../lib/libgospl_extensions.so - Shared library
   • ../include/gospl_extensions.h - C++ header file

2. Integration with DynEarthSol:

   • Clone gospl_extensions in your DynEarthSol directory
   • Set use_gospl = 1 in DynEarthSol's Makefile
   • Build DynEarthSol normally - it will automatically link with gospl_extensions

3. Usage in DynEarthSol:

   • Configure surface processes with surface_process_option = 11
   • Specify GoSPL config file with surface_process_gospl_config_file
   • DynEarthSol will automatically initialize and use GoSPL for landscape evolution

Directory Structure After Local Installation

gospl_extensions/
├── lib/
│   └── libgospl_extensions.so        # Shared library for linking
├── include/
│   └── gospl_extensions.h            # Header for C++ integration
└── cpp_interface/
    ├── Makefile                      # Build system with install-local target
    └── ...                          # Source files

Basic Usage

#include "gospl_extensions.h"

// Initialize and create model
initialize_gospl_extensions();
ModelHandle model = create_enhanced_model("config.yml");

// Run simulation with time control
double elapsed = run_processes_for_dt(model, 1000.0, 1);

// Apply velocity data
apply_velocity_data(model, coords, velocities, num_points, 1.0, 3, 1.0);

// Cleanup
destroy_model(model);
finalize_gospl_extensions();

For detailed documentation, API reference, build instructions, and examples, see cpp_interface/README.md.

Project Structure

gospl_extensions/
├── README.md
├── pyproject.toml                    # Python packaging configuration
├── run_tests.py                      # Standalone test runner
├── gospl_tectonics_ext/
│   ├── __init__.py
│   └── data_driven_tectonics.py      # Main implementation
├── gospl_model_ext/
│   ├── __init__.py
│   └── enhanced_model.py             # Enhanced Model implementation
├── cpp_interface/
│   ├── README.md                     # Detailed C++ interface documentation
│   ├── gospl_extensions.h            # C++ header file
│   ├── gospl_extensions.cpp          # C++ implementation
│   ├── gospl_python_interface.py     # Python bridge module
│   ├── enhanced_model_driver.cpp     # C++ driver example
│   ├── test_interface.cpp            # Basic interface tests
│   ├── Makefile                      # Build system
│   └── CMakeLists.txt                # CMake configuration
├── tests/
│   ├── __init__.py
│   ├── test_data_driven_tectonics.py # Comprehensive test suite
│   └── test_enhanced_model.py        # Enhanced Model tests
└── examples/
    ├── __init__.py
    ├── data_driven_tectonics_basic.py    # DataDrivenTectonics basic usage
    ├── data_driven_tectonics_advanced.py # DataDrivenTectonics advanced features
    ├── enhanced_model_basic.py           # EnhancedModel basic usage
    ├── enhanced_model_advanced.py        # EnhancedModel with elevation tracking
    ├── velocity_data.csv             # Sample velocity data
    └── input-escarpment.yml          # Working goSPL config

Dependencies

Required Python Packages

• numpy: Numerical computations
• scipy: Spatial indexing and interpolation

Optional Python Packages

• pytest: For running the full test suite
• pandas: For CSV data loading in examples
• matplotlib: For visualization in examples

Contributing

To contribute to this extension:

1. Clone the repository
2. Install in development mode: pip install -e ".[dev]"
3. Run tests: pytest tests/ or python run_tests.py
4. Make your changes and ensure tests pass
5. Add tests for new functionality

Acknowledgments

This extension was developed with assistance from GitHub Copilot, an AI-powered coding assistant. The comprehensive test suite, documentation, examples, and project structure were collaboratively created to ensure robustness and usability.