fargopy 0.4.0__py3-none-any.whl → 1.0.0__py3-none-any.whl

fargopy-1.0.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: fargopy
+Version: 1.0.0
+Summary: FARGO3D Wrapper
+Home-page: https://pypi.org/project/fargopy
+Author: Jorge Zuluaga, Alejandro Murillo-González, Matias Montesinos
+Author-email: jorge.zuluaga@udea.edu.co
+License: AGPL-3.0-only
+Keywords: astronomy MHD CFD
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Astronomy
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: scipy
+Requires-Dist: matplotlib
+Requires-Dist: PyQt5
+Requires-Dist: tqdm
+Requires-Dist: numpy
+Requires-Dist: ipython
+Requires-Dist: scikit-learn
+Requires-Dist: ipympl
+Requires-Dist: joblib
+Requires-Dist: celluloid
+Requires-Dist: psutil
+Requires-Dist: gdown
+Requires-Dist: pandas
+Requires-Dist: plotly
+Requires-Dist: pytest
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+<p></p>
+<div align="center">
+  <img src="https://raw.githubusercontent.com/seap-udea/fargopy/main/docs/fargopy_logo.webp" alt="FARGOpy Logo" width="600"/>
+</div>
+<p></p>
+
+<h2 align="center">A FARGO3D wrapper and more</h2>
+
+<!-- This are visual tags that you may add to your package at the beginning with useful information on your package -->
+[![version](https://img.shields.io/pypi/v/fargopy?color=blue)](https://pypi.org/project/fargopy/) 
+[![downloads](https://img.shields.io/pypi/dw/fargopy)](https://pypi.org/project/fargopy/) 
+[![License](https://img.shields.io/badge/License-AGPL%20v3-blue.svg)](https://github.com/seap-udea/fargopy/blob/master/LICENSE) 
+[![python](https://img.shields.io/badge/python-3-grey)](https://pypi.org/project/fargopy/) 
+[![Powered by FARGO3D](https://img.shields.io/badge/Powered%20by-FARGO3D-blue)](https://fargo3d.bitbucket.io/)
+<!--[![arXiv](https://img.shields.io/badge/arXiv-0000.00000-orange.svg?style=flat)](https://arxiv.org/abs/0000.00000)-->
+<a target="_blank" href="https://colab.research.google.com/github/seap-udea/fargopy/blob/main/README.ipynb">
+  <img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/>
+</a>
+
+<div align="center">
+  <img src="https://raw.githubusercontent.com/seap-udea/fargopy/main/gallery/pds-70c-disk_densiy-200_orbits_high_resolution.gif" alt="PDS 70c disk density" width="60%"/>
+  <!--<img src="https://raw.githubusercontent.com/seap-udea/fargopy/main/gallery/pds-70c-disk_densiy_vertical-200_orbits_high_resolution.gif" alt="PDS 70c disk density (vertical)" width="45%"/>-->
+</div>
+
+## Introducing FARGOpy
+
+`FARGOpy` is a Python wrapper and post-processing tool designed for `FARGO3D`, a widely used hydrodynamical code for simulating planet-disk interactions.
+
+With `FARGOpy`, you can easily:
+
+- Analyze and visualize simulation outputs.
+- Control and run `FARGO3D` simulations directly from Python (optional).
+- Generate complex initial conditions and diverse setups with minimal effort.
+
+It streamlines the workflow for researchers, allowing them to focus on the physics rather than the technicalities of setting up and processing simulations. 
+
+For instance, the animations above show the gas density of the circumstellar disk around the planet **PDS-70c** coming from a `FARGO3D` high resolution simulation. The reading of the simulation output and the generation of the animations, the interpolation of the fields, and the creation of the animations   with just a few lines of code. 
+
+For the code used to generate these animations, see the tutorial notebook [basics with FARGOpy](https://github.com/seap-udea/fargopy/blob/main/examples/fargopy-tutorial-basics.ipynb).
+
+## Resources
+
+A complete list of resources and further information about the package and the science relate to it can be found in the following links:
+
+- **GitHub Repository**: [https://github.com/seap-udea/fargopy](https://github.com/seap-udea/fargopy)
+- **Documentation**: [https://fargopy.readthedocs.io](https://fargopy.readthedocs.io)
+- **PyPI Page**: [https://pypi.org/project/fargopy/](https://pypi.org/project/fargopy/)
+
+## Installation
+
+### From PyPI
+
+`FARGOpy` is available at the `Python` package index and can be installed using:
+
+```bash
+$ pip install fargopy
+```
+as usual this command will install all dependencies (excluding `FARGO3D` which must be installed indepently as explained before) and download some useful data, scripts and constants.
+
+### From sources
+
+You can also install from the [GitHub repository](https://github.com/seap-udea/fargopy):
+
+```bash
+git clone https://github.com/seap-udea/fargopy
+cd fargopy
+pip install .
+```
+
+For development, use an editable installation:
+
+```bash
+cd fargopy
+pip install -e .
+```
+
+### In Google Colab
+
+Since `FARGOpy` is a python wrap for `FARGO3D` the ideal environment to work with the package is `IPython`/`Jupyter`. It works really fine in `Google Colab` ensuing training and demonstration purposes. This README, for instance, can be ran in `Google Colab`:
+
+<a target="_blank" href="https://colab.research.google.com/github/seap-udea/fargopy/blob/main/README.ipynb">
+  <img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/>
+</a>
+
+This code only works in Colab and it is intended to install the latest version of `FARGOpy`
+
+```python
+try:
+    from google.colab import drive
+    %pip install -Uq git+https://github.com/seap-udea/fargopy
+except ImportError:
+    print("Not running in Colab, skipping installation")
+```
+
+    Not running in Colab, skipping installation
+
+### Running in `IPython`
+
+If you are working on a remote Linux server, it is better to run the package using `IPython`. For this purpose, after installation, `FARGOpy` provides a special initialization command:
+
+```bash
+$ ifargopy
+```
+
+The first time you run this script, it will create a configuration directory `~/.fargopy` (with `~` the abbreviation for the home directory). This directory contains a set of basic configuration variables which are stored in the file `~/.fargopy/fargopyrc`. You may change this file if you want to customize the installation. The configuration directory also contains the `IPython` initialization script `~/.fargopy/ifargopy.py`.
+
+You may also use the commando `ifargopy` to run several interesting commands:
+
+- Verify the installation:
+
+    ```bash
+    $ ifargopy --verify
+    ```
+    ```
+    Running FARGOpy version X.Y.Z
+    fargopy X.Y.Z is successfully installed.
+    Location: /usr/local/lib/pythonX.X/site-packages/fargopy
+    ```
+
+- Run a battery of tests:
+
+    ```bash
+    $ ifargopy --test
+    ```
+
+## Quickstart
+
+Here is a quick example of how to use FARGOpy. For more examples, see the [examples](https://fargopy.readthedocs.io/en/latest/examples.html) directory in the documentation.
+
+Import the package:
+
+```python
+import fargopy as fp
+```
+
+### Density map
+
+Download a precomputed simulation to test the package:
+
+```python
+fp.Simulation.download_precomputed('fargo')
+```
+
+    Downloading fargo.tgz from cloud (compressed size around 55 MB) into /tmp
+
+    Downloading...
+    From: https://docs.google.com/uc?export=download&id=1YXLKlf9fCGHgLej2fSOHgStD05uFB2C3
+    To: /tmp/fargo.tgz
+    100%|██████████| 54.7M/54.7M [00:01<00:00, 46.5MB/s]
+
+    Uncompressing fargo.tgz into /tmp/fargo
+    Done.
+
+    '/tmp/fargo'
+
+Connect to the simulation output directory:
+
+```python
+sim = fp.Simulation(output_dir='/tmp/fargo')
+```
+
+    Your simulation is now connected with '/Users/jzuluaga/fargo3d/'
+    Now you are connected with output directory '/tmp/fargo'
+    Found a variables.par file in '/tmp/fargo', loading properties
+    Loading variables
+    84 variables loaded
+    Simulation in 2 dimensions
+    Loading domain in cylindrical coordinates:
+    	Variable phi: 384 [[0, np.float64(-3.1334114227210694)], [-1, np.float64(3.1334114227210694)]]
+    	Variable r: 128 [[0, np.float64(0.408203125)], [-1, np.float64(2.491796875)]]
+    	Variable z: 1 [[0, np.float64(0.0)], [-1, np.float64(0.0)]]
+    Number of snapshots in output directory: 51
+    Planets found in summary.dat:
+      Name: Jupiter, Initial pos: [1.0, 0.001, 0.0], Mass: 0.001
+
+Load a field (e.g., gas density) from a specific snapshot:
+
+```python
+gasdens = sim.load_field('gasdens', snapshot=20, interpolate=False)
+```
+
+Crate a 2D slice of a 3D field at $z=0$, 
+
+```python
+gasdens_plane, mesh = gasdens.meshslice(slice='z=0')
+```
+
+Plot the fields of the FARGO simulation using a `colormesh` plot:
+
+```python
+import matplotlib.pyplot as plt
+fig, ax = plt.subplots(figsize=(6,6))
+ax.pcolormesh(mesh.x, mesh.y, gasdens_plane, cmap='prism')
+ax.axis('equal')
+ax.set_xlabel('x [au]')
+ax.set_ylabel('y [au]')
+
+fp.Plot.fargopy_mark(ax)
+plt.savefig('gallery/readme-gasdens.png')
+plt.show()
+```
+
+<img src="https://raw.githubusercontent.com/seap-udea/fargopy/refactor/gallery/readme-gasdens.png" alt="png">
+
+### Streamlines
+
+We can visualize the streamlines of the fluid to observe the flow direction at a specific snapshot by interpolating the velocity field. This visualization provides a detailed representation of the velocity field, enabling us to analyze the fluid dynamics and identify key patterns such as vortices, flow separations, or other phenomena of interest. By combining this with contour plots of other fields, such as density or energy, we can gain deeper insights into the interactions and behavior of the simulated system.
+
+We will use the 3D simulation of a disk with a Jovian planet:
+
+```python
+fp.Simulation.download_precomputed('p3disoj')
+sim = fp.Simulation(output_dir='/tmp/p3disoj')
+```
+
+    Precomputed output directory '/tmp/p3disoj' already exist
+    Your simulation is now connected with '/Users/jzuluaga/fargo3d/'
+    Now you are connected with output directory '/tmp/p3disoj'
+    Found a variables.par file in '/tmp/p3disoj', loading properties
+    Loading variables
+    85 variables loaded
+    Simulation in 3 dimensions
+    Loading domain in spherical coordinates:
+    	Variable phi: 128 [[0, np.float64(-3.117048960983623)], [-1, np.float64(3.117048960983623)]]
+    	Variable r: 64 [[0, np.float64(0.5078125)], [-1, np.float64(1.4921875)]]
+    	Variable theta: 32 [[0, np.float64(1.4231400767948967)], [-1, np.float64(1.5684525767948965)]]
+    Number of snapshots in output directory: 11
+    Planets found in summary.dat:
+      Name: Jupiter, Initial pos: [1.0, 0.001, 0.0], Mass: 0.001
+
+First load the density and velocity fields at snapshot 6:
+
+```python
+data = sim.load_field(
+    fields=['gasv'],
+    slice="phi=0",
+    snapshot=(0,10)
+    )
+```
+
+Now is necesary create a regular mesh where the value of the field is interpolated:
+
+```python
+import numpy as np
+
+# This is the snapshot number where the streamplot will be computed
+time = 6
+
+# Get the minimum and maximum values of var1 and var3 (x and z coordinates)
+xmin=data.var1_mesh[time].min()
+xmax=data.var1_mesh[time].max()
+zmin=data.var3_mesh[time].min()
+zmax=data.var3_mesh[time].max()
+
+# Create a grid of points
+resolution = 120
+xs = np.linspace(xmin, xmax, resolution)
+zs = np.linspace(zmin, zmax, resolution)
+X, Z = np.meshgrid(xs, zs, indexing='ij')
+```
+
+Using the mesh we can evaluate the field at any point in space:
+
+```python
+vxs, vys, vzs = data.evaluate(field='gasv', time=6, var1=X, var3=Z)
+
+# Velocity magnitude at each mesh point
+v_mag = np.sqrt(vxs**2 + vzs**2).T *sim.UV / 1e5 
+```
+
+Now we can plot the streamlines of the gas velocity:
+
+```python
+fig,axs = plt.subplots(1,1,figsize=(6,6))
+
+cmap = 'Spectral_r'
+
+strm = axs.streamplot(X.T, Z.T, vxs.T, vzs.T,
+                       color=v_mag, linewidth=0.7, density=3.0, cmap='viridis')
+
+fig.colorbar(strm.lines, ax=axs, label="|v| [km/s]")
+
+axs.set_xlim(xmin, xmax)
+axs.set_ylim(zmin, zmax)
+axs.set_xlabel('$x$ [au]')
+axs.set_ylabel('$z$ [au]')
+
+fp.Plot.fargopy_mark(axs)
+plt.savefig('gallery/readme-streamlines.png') # Save figure
+```
+
+<img src="https://raw.githubusercontent.com/seap-udea/fargopy/refactor/gallery/readme-streamlines.png" alt="png">
+
+### Accretion rate (mass flux)
+
+We compute the mass flux through a closed surface S around the planet. The mass flux (accretion rate) is:\n
+$$\dot{M}=\int_S\rho(\mathbf{v}\cdot\hat{n})\,dS$$
+where $\rho$ is the density, $\mathbf{v}$ the velocity vector and $\hat{n}$ the outward normal to the surface. We evaluate this integral by interpolating fields at triangle centers and summing $\rho (\mathbf{v}dotat{n}) A_{i}$ over tessellation triangles.
+
+### Define Planet and Surface for Accretion Calculation
+
+Set up the planet and surface objects for the accretion rate calculation.
+
+For this example we will calculate the total flux going through a sphere with a radius equal to the planet's hill radius. For this purpose we need the location and the value of Hill radius of the planet at the snapchot we are interested in:
+
+```python
+snap = 10
+planet = sim.load_planets(snapshot=snap)[0]
+r_hill = planet.hill_radius
+print(f"Jupiter Hill Radius: {r_hill * sim.UL / fp.AU:.3f} AU")
+```
+
+    Jupiter Hill Radius: 0.068 AU
+
+Now we define the surface over which you want to compute the fluxes:
+
+```python
+sphere = fp.Surface(
+    type='sphere',
+    radius=r_hill,
+    subdivisions=6,
+)
+```
+
+The computation is performed with `follow_planet=True`, ensuring that the integration surface co-moves with the planet. This choice is required because the Hill radius evolves in time as a consequence of planetary migration, and therefore the associated control volume must be updated consistently to remain centered on the planet.
+
+```python
+acc_rate = sphere.mass_flux(sim=sim, snapshot=[0,snap], follow_planet=True) 
+```
+
+    Calculating mass flux: 100%|██████████| 11/11 [00:37<00:00,  3.44s/it]
+
+And we can plot it:
+
+```python
+snaps = np.linspace(0, snap, len(acc_rate))
+
+fig, ax = plt.subplots(figsize=(10, 6))
+ax.plot(snaps, acc_rate * sim.UM / sim.UT, color='dodgerblue')
+ax.set_xlabel('Planet Orbits', size=15)
+ax.set_ylabel(r'$\dot{M}$ [kg/s]', size=15)
+ax.legend(fontsize=12)
+fp.Plot.fargopy_mark(ax)
+plt.savefig('gallery/readme-accretion.png')
+
+```
+
+<img src="https://raw.githubusercontent.com/seap-udea/fargopy/refactor/gallery/readme-accretion.png" alt="png">
+
+## What's New
+
+For a detailed list of changes and new features in each version, please see the [WHATSNEW.md](https://github.com/seap-udea/fargopy/blob/main/WHATSNEW.md) file.
+
+## Authors and Licensing
+
+This project is developed by members the **Solar, Earth and Planetary Physics Group (SEAP)** at Universidad de Antioquia, Medellín, Colombia and the the **Department of Physics** of the Universidad Técnica Federico Santa María, Valdivia, Chile. The main developers are:
+
+- **Jorge I. Zuluaga** (SEAP/FACom/UdeA) - jorge.zuluaga@udea.edu.co
+- **Alejandro Murillo-González** (SEAP/FACom/UdeA) - alejandro.murillo1@udea.edu.co
+- **Matías Montesinos** (Physics/USM) - matias.montesinosa@usm.cl
+
+This project is licensed under the GNU Affero General Public License v3.0 (AGPL-3.0) - see the [LICENSE](LICENSE) file for details.
+
+## Contributing
+
+We welcome contributions! If you're interested in contributing to MultiNEAs, please:
+
+1. Fork the repository
+2. Create a feature branch
+3. Make your changes
+4. Submit a pull request
+
+Please read the [CONTRIBUTING.md](CONTRIBUTING.md) file for more information.
+
+---
+*Powered by fargopy*. For more examples see [fargopy GitHub repo](https://github.com/seap-udea/fargopy/tree/main/examples). 
+
+Jorge I. Zuluaga, Alejandro Murillo-González and Matías Montesinos © 2023-present
+

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{fargopy-0.4.0.dist-info → fargopy-1.0.0.dist-info}/WHEEL

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