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

fargopy-0.4.0.dist-info/METADATA

@@ -1,492 +0,0 @@
-Metadata-Version: 2.4
-Name: fargopy
-Version: 0.4.0
-Summary: FARGO3D Wrapping
-Home-page: https://pypi.org/project/fargopy
-Author: Jorge Zuluaga, Alejandro Murillo-González, Matias Montesinos
-Author-email: jorge.zuluaga@gmail.com
-License: MIT
-Keywords: astronomy MHD CFD
-Classifier: Programming Language :: Python :: 3
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Operating System :: OS Independent
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: scipy
-Requires-Dist: matplotlib
-Requires-Dist: tqdm
-Requires-Dist: numpy
-Requires-Dist: ipython
-Requires-Dist: joblib
-Requires-Dist: celluloid
-Requires-Dist: psutil
-Requires-Dist: gdown
-Requires-Dist: pandas
-Requires-Dist: plotly
-Requires-Dist: ipywidgets
-Requires-Dist: nbformat
-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: summary
-
-# FARGOpy
-## Wrapping FRAGO3D
-
-<!-- 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/)
-<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>
-
-`FARGOpy` is a python wrapping for [`FARGO3D`](https://fargo3d.bitbucket.io/intro.html), the well-knwon hydrodynamics and magnetohydrodynamics parallel code. This wrapping is intended to facillitate the interaction with FARGO3D, especially for those starting using the code. `FARGOpy` may be also useful for teaching and training purposes. For advanced users, `FARGOpy` provides useful functionalities in the postprocessing of simulation results, derivative calculations and plots.
-
-This is an animation created with a few lines of code using `FARGOpy`. 
-<p align="center"><img src="https://github.com/seap-udea/fargopy/blob/main/gallery/fargo-animation.gif?raw=true" alt="Animation""/></p>
-
-For the code used to generate this animation see the tutorial notebook [animations with `FARGOpy`](https://github.com/seap-udea/fargopy/blob/main/examples/fargopy-tutorial-animations.ipynb). For other examples and a full tutorial see the [examples repository](https://github.com/seap-udea/fargopy/blob/main/examples).
-
-## Installing `FARGOpy` 
-
-`FARGOpy` is available at the `Python` package index and can be installed using:
-
-```bash
-$ sudo 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.
-
-
-
-> **NOTE**: If you don't have access to `sudo`, you can install `FARGOpy` in your local environmen (usually at `~/.local/`). In that case you need to add to your `PATH` environmental variable the location of the local python installation. Add to `~/.bashrc` the line `export PATH=$HOME/.local/bin:$PATH`
-
-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
-import sys
-if 'google.colab' in sys.modules:
-    !sudo pip install -Uq fargopy
-```
-
-If you are working in `Jupyter` or in `Google Colab`, the configuration directory and its content will be crated the first time you import the package:
-
-
-```python
-import fargopy as fp
-
-# These lines are intented for developing purposes; drop them in your code
-%load_ext autoreload 
-%autoreload 2
-```
-
-    Running FARGOpy version 0.3.6
-
-
-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`.
-
-## Downloading and installing FARGO3D
-
-It is important to understand that `FARGO3D` works especially well on Linux plaforms (including `MacOS`). The same condition applies for `FARGOpy`. Because of that, most of the internal as well as the public features of the packages are designed to work in a `Linux` environment. For working in other operating systems, especially on MS Windows, please consider using virtual machines ow WSL.
-
-Being an independent project, `FARGOpy` is not provided with a working version of `FARGO3D`. You need to download the C package and their prerequisites (compilers, third-party libraries, etc.) and configure them, by yourself. For a detailed guide please see the [FARGO3D documentation](https://fargo3d.bitbucket.io/index.html) or the [project repo at bitbucket](https://bitbucket.org/fargo3d/public/src/ae0fcdc67bb7c83aed85fc9a4d4a2d5061324597/?at=release%2Fpublic). 
-
-Still `FARGOpy` provides a simple way to get the latest version of the source code of `FARGO3D` from its public GitHub repository. The source code will be downloaded into the home directory and stored as `~/fargo3d/`. 
-
-> **WARNING**: If you want to change the final location of the source code or the name of the `FARGO3D` directory,  before executing the following command, please change the corresponding configuration variables in `~/.fargopy/fargopyrc`
-
-To download the `FARGO3D` source code execute:
-
-
-```python
-fp.initialize('download',force=True)
-```
-
-    Downloading FARGOpy...
-    Directory '/home/jzuluaga/fargo3d/' already exists. Removing it...
-
-
-    Cloning into 'fargo3d'...
-
-
-    	FARGO3D downloaded to /home/jzuluaga/fargo3d/
-    Header file for FARGO3D found in the fargo directory /home/jzuluaga/fargo3d/
-
-
-Once download it you may check if the source code is compiling in your machine. For that purpose run:
-
-
-```python
-fp.initialize('check',regular=1,gpu=0,parallel=0)
-```
-
-    Test compilation of FARGO3D
-    	Checking normal compilation.
-    	Running 'make -C /home/jzuluaga/fargo3d/ clean mrproper all PARALLEL=0 GPU=0 2>&1 |tee /tmp/fargo_regular.log':
-    		Compilation in mode regular successful.
-    	Skipping gpu compilation
-    	Skipping parallel compilation
-    Summary of compilation modes:
-    	Regular: 1
-    	GPU: 0
-    	Parallel: 0
-
-
-If you have some error at compiling `FARGO3D` in some of the possible modes (regular, gpu and/or parallel) please check the corresponding logfile and correct the problems. Compiling problems will normally arise because of a lacking of an important dependency, for instance a compiler, a driver (in the case of GPU) or a third-party library or tool (eg. openmpi). 
-
-## Quickstart
-
-Here we will illustrate the minimal commands you may run to test the package. A more detailed set of examples can be found exploring [the tutorial notebooks](https://github.com/seap-udea/fargopy/blob/main/examples). Other in depth examples are also available in the [examples repository](https://github.com/seap-udea/fargopy/tree/main/examples) of the `GitHub` repository. 
-
-There are two complimentary modes when using `FARGOpy`: 
-
-- **Control mode**: Using this mode you can run and control `FARGO3D` from your notebook.  This mode requires a working copy of `FARGO3D` ready to be compiled and run. This mode is ideal for training or testing purposes.
-
-- **Postprocessing mode**: Using `FARGOpy` in this mode allows you to process some of the output files produced by a `FARGO3D` simulation. This mode does not necesarily requires that a working copy of `FARGO3D` be installed in the machine where you are performing the postprocessing analysis. This mode is ideal for advanced users.
-
-### Control mode
-
-Create a simulation:
-
-
-```python
-sim = fp.Simulation(setup='fargo')
-```
-
-    Your simulation is now connected with '/home/jzuluaga/fargo3d/'
-    Now your simulation setup is at '/home/jzuluaga/fargo3d/setups/fargo'
-
-
-Compile the `FARGO3D` binary to run the simulation:
-
-
-```python
-sim.compile(parallel=0,gpu=0)
-```
-
-    Compiling fargo3d_SETUP-fargo_PARALLEL-0_GPU-0...
-    Succesful compilation of FARGO3D binary fargo3d_SETUP-fargo_PARALLEL-0_GPU-0
-
-
-Run the simulation:
-
-
-```python
-sim.run(cleanrun=True)
-```
-
-    Cleaning output directory /home/jzuluaga/fargo3d/outputs/fargo
-    Running asynchronously (test = False):  ./fargo3d_SETUP-fargo_PARALLEL-0_GPU-0 -m -t setups/fargo/fargo.par
-    Now you are connected with output directory '/home/jzuluaga/fargo3d/outputs/fargo'
-    Found a variables.par file in '/home/jzuluaga/fargo3d/outputs/fargo', loading properties
-    Loading variables
-    84 variables loaded
-    Simulation in 2 dimensions
-    Loading domain in cylindrical coordinates:
-    	Variable phi: 384 [[0, -3.1334114227210694], [-1, 3.1334114227210694]]
-    	Variable r: 128 [[0, 0.408203125], [-1, 2.491796875]]
-    	Variable z: 1 [[0, 0.0], [-1, 0.0]]
-    Number of snapshots in output directory: 1
-    Configuration variables and domains load into the object. See e.g. <sim>.vars
-
-
-You may check the status:
-
-
-```python
-sim.status()
-```
-
-    
-    ################################################################################
-    Running status of the process:
-    	The process is running.
-
-
-Or check the progress of the simulation:
-
-
-```python
-sim.status('progress')
-```
-
-    Progress of the simulation (numstatus = 5, interrupting may stop the process):
-    1:OUTPUTS 3 at date t = 18.849556 OK [output pace = 0.1 secs]
-    2:OUTPUTS 4 at date t = 25.132741 OK [output pace = 0.1 secs]
-    3:OUTPUTS 5 at date t = 31.415927 OK [output pace = 0.9 secs]
-    4:OUTPUTS 6 at date t = 37.699112 OK [output pace = 1.8 secs]
-    5:OUTPUTS 7 at date t = 43.982297 OK [output pace = 1.9 secs]
-
-
-You may stop the simulation at any time using:
-
-
-```python
-sim.stop()
-```
-
-    Stopping FARGO3D process (pid = 26257)
-
-
-Check the status of the simulation using:
-
-
-```python
-sim.status('summary')
-```
-
-    The simulation has been ran for 9 time-steps (including the initial one).
-
-
-Once stopped you may resume the simulation at any snapshot or at the latest resumable snapshot:
-
-
-```python
-sim.resume()
-```
-
-    Resuming from snapshot 7...
-    Running asynchronously (test = False):  ./fargo3d_SETUP-fargo_PARALLEL-0_GPU-0 -m -t -S 7 -t setups/fargo/fargo.par
-    Now you are connected with output directory '/home/jzuluaga/fargo3d/outputs/fargo'
-    Found a variables.par file in '/home/jzuluaga/fargo3d/outputs/fargo', loading properties
-    Loading variables
-    84 variables loaded
-    Simulation in 2 dimensions
-    Loading domain in cylindrical coordinates:
-    	Variable phi: 384 [[0, -3.1334114227210694], [-1, 3.1334114227210694]]
-    	Variable r: 128 [[0, 0.408203125], [-1, 2.491796875]]
-    	Variable z: 1 [[0, 0.0], [-1, 0.0]]
-    Number of snapshots in output directory: 9
-    Configuration variables and domains load into the object. See e.g. <sim>.vars
-
-
-Once the simulation has been completed you will notice by ran:
-
-
-```python
-sim.stop()
-```
-
-    The process has finished. Check logfile /home/jzuluaga/fargo3d/setups/fargo/fargo.log.
-
-
-### Postprocessing mode
-
-Now that you have some results to process, it is time to use the functionalities that `FARGOpy` provides for this purpose.
-
-Create the simulation and connect it to the output directory:
-
-
-```python
-sim = fp.Simulation(output_dir = fp.Conf.FP_FARGO3D_DIR + '/outputs/fargo')
-```
-
-    Your simulation is now connected with '/home/jzuluaga/fargo3d/'
-    Now you are connected with output directory '/home/jzuluaga/fargo3d//outputs/fargo'
-    Found a variables.par file in '/home/jzuluaga/fargo3d//outputs/fargo', loading properties
-    Loading variables
-    84 variables loaded
-    Simulation in 2 dimensions
-    Loading domain in cylindrical coordinates:
-    	Variable phi: 384 [[0, -3.1334114227210694], [-1, 3.1334114227210694]]
-    	Variable r: 128 [[0, 0.408203125], [-1, 2.491796875]]
-    	Variable z: 1 [[0, 0.0], [-1, 0.0]]
-    Number of snapshots in output directory: 21
-    Configuration variables and domains load into the object. See e.g. <sim>.vars
-
-
-
-```python
-sim.load_properties()
-```
-
-    Loading variables
-    84 variables loaded
-    Simulation in 2 dimensions
-    Loading domain in cylindrical coordinates:
-    	Variable phi: 384 [[0, -3.1334114227210694], [-1, 3.1334114227210694]]
-    	Variable r: 128 [[0, 0.408203125], [-1, 2.491796875]]
-    	Variable z: 1 [[0, 0.0], [-1, 0.0]]
-    Number of snapshots in output directory: 22
-    Configuration variables and domains load into the object. See e.g. <sim>.vars
-
-
-Load gas density field from a given snapshot:
-
-
-```python
-gasdens = sim.load_field('gasdens',snapshot=20)
-```
-
-Create a `meshslice` of the field:
-
-
-```python
-gasdens_r, mesh = gasdens.meshslice(slice='z=0,phi=0')
-```
-
-Plot the slice:
-
-
-```python
-import matplotlib.pyplot as plt
-if not fp.IN_COLAB:plt.ioff() # Drop this out of this tutorial
-fig,ax = plt.subplots()
-
-ax.semilogy(mesh.r,gasdens_r)
-
-ax.set_xlabel(r"$r$ [cu]")
-ax.set_ylabel(r"$\rho$ [cu]")
-fp.Plot.fargopy_mark(ax)
-if not fp.IN_COLAB:fig.savefig('gallery/example-dens_r.png') # Drop this out of this tutorial
-```
-
-<p align="center"><img src="https://github.com/seap-udea/fargopy/blob/main/gallery/example-dens_r.png?raw=true" alt="Animation""/></p>
-
-You may also create a 2-dimensional `meshslice`:
-
-
-```python
-gasdens_plane, mesh = gasdens.meshslice(slice='z=0')
-```
-
-And plot it:
-
-
-```python
-if not fp.IN_COLAB:plt.ioff() # Drop this out of this tutorial
-fig,axs = plt.subplots(1,2,figsize=(12,6))
-
-ax = axs[0]
-
-ax.pcolormesh(mesh.phi,mesh.r,gasdens_plane,cmap='prism')
-
-ax.set_xlabel('$\phi$ [rad]')
-ax.set_ylabel('$r$ [UL]')
-fp.Plot.fargopy_mark(ax)
-
-ax = axs[1]
-
-ax.pcolormesh(mesh.x,mesh.y,gasdens_plane,cmap='prism')
-
-ax.set_xlabel('$x$ [UL]')
-ax.set_ylabel('$y$ [UL]')
-fp.Plot.fargopy_mark(ax)
-ax.axis('equal')
-if not fp.IN_COLAB:fig.savefig('gallery/example-dens_disk.png') # Drop this out of this tutorial
-```
-
-<p align="center"><img src="https://github.com/seap-udea/fargopy/blob/main/gallery/example-dens_disk.png?raw=true" alt="Animation""/></p>
-
-### Working with precomputed simulations
-
-If you don't have the resources to compile or run `FARGO3D` and still you want to test the postprocessing functionalities of the package you may download a precomputed simulation:
-
-
-```python
-fp.Simulation.download_precomputed(setup='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 [00:02<00:00, 19.1MB/s]
-
-
-    Uncompressing fargo.tgz into /tmp/fargo
-    Done.
-
-
-Once downloaded you may connect with simulation using:
-
-
-```python
-sim = fp.Simulation(output_dir = '/tmp/fargo')
-```
-
-    Your simulation is now connected with '/home/jzuluaga/fargo3d/'
-    Now you are connected with output directory '/tmp/fargo'
-
-
-and perform the postprocessing as explained before.
-
-We have prepared a set of precomputed simulations covering some interesting scientific cases. You may see the list of precomputed simulations available in the `FARGOpy` [cloud repository](https://drive.google.com/drive/folders/1NRdNOcmxRK-pHv_8vR-aAAJGWXxIOY0J?usp=sharing):
-
-
-```python
-fp.Simulation.list_precomputed()
-```
-
-    fargo:
-    	Description: Protoplanetary disk with a Jovian planet [2D]
-    	Size: 55 MB
-    p3diso:
-    	Description: Protoplanetary disk with a Super earth planet [3D]
-    	Size: 220 MB
-    p3disoj:
-    	Description: Protoplanetary disk with a Jovian planet [3D]
-    	Size: 84 MB
-    fargo_multifluid:
-    	Description: Protoplanetary disk with several fluids (dust) and a Jovian planet in 2D
-    	Size: 100 MB
-    binary:
-    	Description: Disk around a binary with the properties of Kepler-38 in 2D
-    	Size: 140 MB
-
-
-You may find in the [examples directory](https://github.com/seap-udea/fargopy/tree/main/examples) of the `GitHub` repository, example notebooks illustrating how to use `FARGOpy` for processing the output of this precomputed simulations.
-
-## What's new
-
-Version 0.4.*:
-- Interpolation and flux computations.
-
-Version 0.3.*:
-
-- Refactoring of initializing routines.
-- Improvements in documentation of basic classes in `__init__.py`.
-- Precomputed simulations uploaded to FARGOpy Cloud Repository and available usnig `download_precomputed` static method.
-
-Version 0.2.*:
-
-- First real applications tested with FARGOpy.
-- All basic routines for reading output created.
-- Major refactoring. 
-
-Version 0.1.*:
-
-- Package is now provided with a script 'ifargopy' to run 'ipython' with fargopy initialized.
-- A new 'progress' mode has been added to status method.
-- All the dynamics of loading/compiling/running/stoppìng/resuming FARGO3D has been developed.
-
-Version 0.0.*:
-
-- First classes created.
-- The project is started!
-
-------------
-
-This package has been designed and written mostly by Jorge I. Zuluaga and Alejandro Murillo-González with advising and contributions by Matías Montesinos (C) 2023, 2024, 2025
-

fargopy-0.4.0.dist-info/RECORD

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fargopy-0.4.0.dist-info/licenses/LICENSE

@@ -1,21 +0,0 @@
-MIT License
-
-Copyright (c) 2023 Solar, Earth and Planetary Physics Group
-
-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.