# FARGOpy
## Wrapping FRAGO3D
<!-- This are visual tags that you may add to your package at the beginning with useful information on your package -->
[](https://pypi.org/project/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 0.3.*:
- 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 with advising and contributions by Matías Montesinos (C) 2023
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"description": "# FARGOpy\n## Wrapping FRAGO3D\n\n<!-- This are visual tags that you may add to your package at the beginning with useful information on your package --> \n[](https://pypi.org/project/fargopy/)\n[](https://pypi.org/project/fargopy/)\n<a target=\"_blank\" href=\"https://colab.research.google.com/github/seap-udea/fargopy/blob/main/README.ipynb\">\n <img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/>\n</a>\n\n`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.\n\nThis is an animation created with a few lines of code using `FARGOpy`. \n<p align=\"center\"><img src=\"https://github.com/seap-udea/fargopy/blob/main/gallery/fargo-animation.gif?raw=true\" alt=\"Animation\"\"/></p>\n\nFor 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).\n\n## Installing `FARGOpy` \n\n`FARGOpy` is available at the `Python` package index and can be installed using:\n\n```bash\n$ sudo pip install fargopy\n```\nas 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.\n\n\n\n> **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`\n\nSince `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`:\n\n<a target=\"_blank\" href=\"https://colab.research.google.com/github/seap-udea/fargopy/blob/main/README.ipynb\">\n <img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/>\n</a>\n\nThis code only works in Colab and it is intended to install the latest version of `FARGOpy`\n\n\n```python\nimport sys\nif 'google.colab' in sys.modules:\n !sudo pip install -Uq fargopy\n```\n\nIf 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:\n\n\n```python\nimport fargopy as fp\n\n# These lines are intented for developing purposes; drop them in your code\n%load_ext autoreload \n%autoreload 2\n```\n\n Running FARGOpy version 0.3.6\n\n\nIf 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:\n\n```bash\n$ ifargopy\n```\n\nThe 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`.\n\n## Downloading and installing FARGO3D\n\nIt 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.\n\nBeing 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). \n\nStill `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/`. \n\n> **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`\n\nTo download the `FARGO3D` source code execute:\n\n\n```python\nfp.initialize('download',force=True)\n```\n\n Downloading FARGOpy...\n Directory '/home/jzuluaga/fargo3d/' already exists. Removing it...\n\n\n Cloning into 'fargo3d'...\n\n\n \tFARGO3D downloaded to /home/jzuluaga/fargo3d/\n Header file for FARGO3D found in the fargo directory /home/jzuluaga/fargo3d/\n\n\nOnce download it you may check if the source code is compiling in your machine. For that purpose run:\n\n\n```python\nfp.initialize('check',regular=1,gpu=0,parallel=0)\n```\n\n Test compilation of FARGO3D\n \tChecking normal compilation.\n \tRunning 'make -C /home/jzuluaga/fargo3d/ clean mrproper all PARALLEL=0 GPU=0 2>&1 |tee /tmp/fargo_regular.log':\n \t\tCompilation in mode regular successful.\n \tSkipping gpu compilation\n \tSkipping parallel compilation\n Summary of compilation modes:\n \tRegular: 1\n \tGPU: 0\n \tParallel: 0\n\n\nIf 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). \n\n## Quickstart\n\nHere 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. \n\nThere are two complimentary modes when using `FARGOpy`: \n\n- **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.\n\n- **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.\n\n### Control mode\n\nCreate a simulation:\n\n\n```python\nsim = fp.Simulation(setup='fargo')\n```\n\n Your simulation is now connected with '/home/jzuluaga/fargo3d/'\n Now your simulation setup is at '/home/jzuluaga/fargo3d/setups/fargo'\n\n\nCompile the `FARGO3D` binary to run the simulation:\n\n\n```python\nsim.compile(parallel=0,gpu=0)\n```\n\n Compiling fargo3d_SETUP-fargo_PARALLEL-0_GPU-0...\n Succesful compilation of FARGO3D binary fargo3d_SETUP-fargo_PARALLEL-0_GPU-0\n\n\nRun the simulation:\n\n\n```python\nsim.run(cleanrun=True)\n```\n\n Cleaning output directory /home/jzuluaga/fargo3d/outputs/fargo\n Running asynchronously (test = False): ./fargo3d_SETUP-fargo_PARALLEL-0_GPU-0 -m -t setups/fargo/fargo.par\n Now you are connected with output directory '/home/jzuluaga/fargo3d/outputs/fargo'\n Found a variables.par file in '/home/jzuluaga/fargo3d/outputs/fargo', loading properties\n Loading variables\n 84 variables loaded\n Simulation in 2 dimensions\n Loading domain in cylindrical coordinates:\n \tVariable phi: 384 [[0, -3.1334114227210694], [-1, 3.1334114227210694]]\n \tVariable r: 128 [[0, 0.408203125], [-1, 2.491796875]]\n \tVariable z: 1 [[0, 0.0], [-1, 0.0]]\n Number of snapshots in output directory: 1\n Configuration variables and domains load into the object. See e.g. <sim>.vars\n\n\nYou may check the status:\n\n\n```python\nsim.status()\n```\n\n \n ################################################################################\n Running status of the process:\n \tThe process is running.\n\n\nOr check the progress of the simulation:\n\n\n```python\nsim.status('progress')\n```\n\n Progress of the simulation (numstatus = 5, interrupting may stop the process):\n 1:OUTPUTS 3 at date t = 18.849556 OK [output pace = 0.1 secs]\n 2:OUTPUTS 4 at date t = 25.132741 OK [output pace = 0.1 secs]\n 3:OUTPUTS 5 at date t = 31.415927 OK [output pace = 0.9 secs]\n 4:OUTPUTS 6 at date t = 37.699112 OK [output pace = 1.8 secs]\n 5:OUTPUTS 7 at date t = 43.982297 OK [output pace = 1.9 secs]\n\n\nYou may stop the simulation at any time using:\n\n\n```python\nsim.stop()\n```\n\n Stopping FARGO3D process (pid = 26257)\n\n\nCheck the status of the simulation using:\n\n\n```python\nsim.status('summary')\n```\n\n The simulation has been ran for 9 time-steps (including the initial one).\n\n\nOnce stopped you may resume the simulation at any snapshot or at the latest resumable snapshot:\n\n\n```python\nsim.resume()\n```\n\n Resuming from snapshot 7...\n Running asynchronously (test = False): ./fargo3d_SETUP-fargo_PARALLEL-0_GPU-0 -m -t -S 7 -t setups/fargo/fargo.par\n Now you are connected with output directory '/home/jzuluaga/fargo3d/outputs/fargo'\n Found a variables.par file in '/home/jzuluaga/fargo3d/outputs/fargo', loading properties\n Loading variables\n 84 variables loaded\n Simulation in 2 dimensions\n Loading domain in cylindrical coordinates:\n \tVariable phi: 384 [[0, -3.1334114227210694], [-1, 3.1334114227210694]]\n \tVariable r: 128 [[0, 0.408203125], [-1, 2.491796875]]\n \tVariable z: 1 [[0, 0.0], [-1, 0.0]]\n Number of snapshots in output directory: 9\n Configuration variables and domains load into the object. See e.g. <sim>.vars\n\n\nOnce the simulation has been completed you will notice by ran:\n\n\n```python\nsim.stop()\n```\n\n The process has finished. Check logfile /home/jzuluaga/fargo3d/setups/fargo/fargo.log.\n\n\n### Postprocessing mode\n\nNow that you have some results to process, it is time to use the functionalities that `FARGOpy` provides for this purpose.\n\nCreate the simulation and connect it to the output directory:\n\n\n```python\nsim = fp.Simulation(output_dir = fp.Conf.FP_FARGO3D_DIR + '/outputs/fargo')\n```\n\n Your simulation is now connected with '/home/jzuluaga/fargo3d/'\n Now you are connected with output directory '/home/jzuluaga/fargo3d//outputs/fargo'\n Found a variables.par file in '/home/jzuluaga/fargo3d//outputs/fargo', loading properties\n Loading variables\n 84 variables loaded\n Simulation in 2 dimensions\n Loading domain in cylindrical coordinates:\n \tVariable phi: 384 [[0, -3.1334114227210694], [-1, 3.1334114227210694]]\n \tVariable r: 128 [[0, 0.408203125], [-1, 2.491796875]]\n \tVariable z: 1 [[0, 0.0], [-1, 0.0]]\n Number of snapshots in output directory: 21\n Configuration variables and domains load into the object. See e.g. <sim>.vars\n\n\n\n```python\nsim.load_properties()\n```\n\n Loading variables\n 84 variables loaded\n Simulation in 2 dimensions\n Loading domain in cylindrical coordinates:\n \tVariable phi: 384 [[0, -3.1334114227210694], [-1, 3.1334114227210694]]\n \tVariable r: 128 [[0, 0.408203125], [-1, 2.491796875]]\n \tVariable z: 1 [[0, 0.0], [-1, 0.0]]\n Number of snapshots in output directory: 22\n Configuration variables and domains load into the object. See e.g. <sim>.vars\n\n\nLoad gas density field from a given snapshot:\n\n\n```python\ngasdens = sim.load_field('gasdens',snapshot=20)\n```\n\nCreate a `meshslice` of the field:\n\n\n```python\ngasdens_r, mesh = gasdens.meshslice(slice='z=0,phi=0')\n```\n\nPlot the slice:\n\n\n```python\nimport matplotlib.pyplot as plt\nif not fp.IN_COLAB:plt.ioff() # Drop this out of this tutorial\nfig,ax = plt.subplots()\n\nax.semilogy(mesh.r,gasdens_r)\n\nax.set_xlabel(r\"$r$ [cu]\")\nax.set_ylabel(r\"$\\rho$ [cu]\")\nfp.Plot.fargopy_mark(ax)\nif not fp.IN_COLAB:fig.savefig('gallery/example-dens_r.png') # Drop this out of this tutorial\n```\n\n<p align=\"center\"><img src=\"https://github.com/seap-udea/fargopy/blob/main/gallery/example-dens_r.png?raw=true\" alt=\"Animation\"\"/></p>\n\nYou may also create a 2-dimensional `meshslice`:\n\n\n```python\ngasdens_plane, mesh = gasdens.meshslice(slice='z=0')\n```\n\nAnd plot it:\n\n\n```python\nif not fp.IN_COLAB:plt.ioff() # Drop this out of this tutorial\nfig,axs = plt.subplots(1,2,figsize=(12,6))\n\nax = axs[0]\n\nax.pcolormesh(mesh.phi,mesh.r,gasdens_plane,cmap='prism')\n\nax.set_xlabel('$\\phi$ [rad]')\nax.set_ylabel('$r$ [UL]')\nfp.Plot.fargopy_mark(ax)\n\nax = axs[1]\n\nax.pcolormesh(mesh.x,mesh.y,gasdens_plane,cmap='prism')\n\nax.set_xlabel('$x$ [UL]')\nax.set_ylabel('$y$ [UL]')\nfp.Plot.fargopy_mark(ax)\nax.axis('equal')\nif not fp.IN_COLAB:fig.savefig('gallery/example-dens_disk.png') # Drop this out of this tutorial\n```\n\n<p align=\"center\"><img src=\"https://github.com/seap-udea/fargopy/blob/main/gallery/example-dens_disk.png?raw=true\" alt=\"Animation\"\"/></p>\n\n### Working with precomputed simulations\n\nIf 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:\n\n\n```python\nfp.Simulation.download_precomputed(setup='fargo')\n```\n\n Downloading fargo.tgz from cloud (compressed size around 55 MB) into /tmp\n\n\n Downloading...\n From: https://docs.google.com/uc?export=download&id=1YXLKlf9fCGHgLej2fSOHgStD05uFB2C3\n To: /tmp/fargo.tgz\n 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 54.7M/54.7M [00:02<00:00, 19.1MB/s]\n\n\n Uncompressing fargo.tgz into /tmp/fargo\n Done.\n\n\nOnce downloaded you may connect with simulation using:\n\n\n```python\nsim = fp.Simulation(output_dir = '/tmp/fargo')\n```\n\n Your simulation is now connected with '/home/jzuluaga/fargo3d/'\n Now you are connected with output directory '/tmp/fargo'\n\n\nand perform the postprocessing as explained before.\n\nWe 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):\n\n\n```python\nfp.Simulation.list_precomputed()\n```\n\n fargo:\n \tDescription: Protoplanetary disk with a Jovian planet [2D]\n \tSize: 55 MB\n p3diso:\n \tDescription: Protoplanetary disk with a Super earth planet [3D]\n \tSize: 220 MB\n p3disoj:\n \tDescription: Protoplanetary disk with a Jovian planet [3D]\n \tSize: 84 MB\n fargo_multifluid:\n \tDescription: Protoplanetary disk with several fluids (dust) and a Jovian planet in 2D\n \tSize: 100 MB\n binary:\n \tDescription: Disk around a binary with the properties of Kepler-38 in 2D\n \tSize: 140 MB\n\n\nYou 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.\n\n## What's new\n\n\nVersion 0.3.*:\n\n- Refactoring of initializing routines.\n- Improvements in documentation of basic classes in `__init__.py`.\n- Precomputed simulations uploaded to FARGOpy Cloud Repository and available usnig `download_precomputed` static method.\n\nVersion 0.2.*:\n\n- First real applications tested with FARGOpy.\n- All basic routines for reading output created.\n- Major refactoring. \n\nVersion 0.1.*:\n\n- Package is now provided with a script 'ifargopy' to run 'ipython' with fargopy initialized.\n- A new 'progress' mode has been added to status method.\n- All the dynamics of loading/compiling/running/stopp\u00ecng/resuming FARGO3D has been developed.\n\nVersion 0.0.*:\n\n- First classes created.\n- The project is started!\n\n------------\n\nThis package has been designed and written mostly by Jorge I. Zuluaga with advising and contributions by Mat\u00edas Montesinos (C) 2023\n\n",
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