fargopy 0.1.3

FARGO3D Wrapping

FARGOpy

Wrapping FRAGO3D

FARGOpy is a python wrapping for FARGO3D., the well-knwon hydrodynamics and magnetohydrodynamics parallel code. This wrapping is intended to ensue the interaction with FARGO3D especially for those starting using the code, for instance for teaching and training purposes, but also provide functionalities for most advanced users in tasks related to the postprocessing of output files and plotting.

Download and install

For using FARGOpy you first need to download and install FARGO3D and all its prerequisites. For a detailed guide please see the FARGO documentation or the project repo at bitbucket. Still, FARGOpy provides some useful commands and tools to test the platform on which you are working and check if it is prepared to use the whole functionalities of the packages or part of them.

NOTE: 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 internal as well as public features of the packages are designed to work in a Linux environment. For working in another operating systems, for instance for teaching or training purposes, please consider to use virtual machines.

For installing FARGOpy run:

# Uncomment if you are in Google Colab
# !pip install -q fargopy

Once installed import it:

import fargopy as fp

# Set in True to see all messages
fp.Conf.VERBOSE = False

# For developing purpose. Remove during production
%load_ext autoreload
%autoreload 2

Running FARGOpy version 0.1.1

Install FARGO3D

For obvious reasons FARGO3D is not provided with FARGOpy. Get and set the package using:

fp.Conf.set_fargo3d()

> Checking for FARGO3D directroy:
FARGO3D source code is not available at './public/'
	Getting FARGO3D public repo...
	✓Package downloaded to './public/'
> Checking for FARGO3D normal binary:
FARGO3D binary with options '' not compiled at './public/'
	Compiling FARGO3D (it may take a while)...
	✓Binary in normal mode compiling correctly
> Checking for FARGO3D parallel binary:
FARGO3D binary with options 'PARALLEL=1' not compiled at './public/'
	✓Binary in parallel mode compiling correctly
> Checking for FARGO3D GPU binary:
FARGO3D binary with options 'GPU=1' not compiled at './public/'
	Compiling FARGO3D with GPU (it may take a while)...
	No GPU available

Once set, check configuration:

fp.Conf.show_fargo3d_configuration()

Is FARGO3D installed:  True
Is FARGO3D compiling:  True
Is FARGO3D compiling in parallel:  True
Is FARGO3D compiling in GPU:  False
FARGO3D clone repositoty command:  git clone https://bitbucket.org/fargo3d/public.git
FARGO3D directories: 
	Base directory:  ./
	Package directory:  public/
	Basic package header:  src/fargo3d.h
	Setups location:  setups/
	Setups location:  ./public/
Compile in parallel:  1
Compile in GPU:  0

If you already have a copy of FARGO3D you just need to set the configuration variables telling FARGOpy where the source code is located:

fp.Conf.configure_fargo3d(basedir='/tmp',packdir='public',parallel=1,gpu=0)

Once the variables has been set, you should set the package:

fp.Conf.set_fargo3d()
fp.Conf.show_fargo3d_configuration()

> Checking for FARGO3D directroy:
	✓FARGO3D source code is available in your system at '/tmp/public/'
> Checking for FARGO3D normal binary:
	✓Binary in normal mode compiling correctly
> Checking for FARGO3D parallel binary:
	✓Binary in parallel mode compiling correctly
> Checking for FARGO3D GPU binary:
FARGO3D binary with options 'GPU=1' not compiled at '/tmp/public/'
	Compiling FARGO3D with GPU (it may take a while)...
	No GPU available
Is FARGO3D installed:  True
Is FARGO3D compiling:  True
Is FARGO3D compiling in parallel:  True
Is FARGO3D compiling in GPU:  False
FARGO3D clone repositoty command:  git clone https://bitbucket.org/fargo3d/public.git
FARGO3D directories: 
	Base directory:  /tmp/
	Package directory:  public/
	Basic package header:  src/fargo3d.h
	Setups location:  setups/
	Setups location:  /tmp/public/
Compile in parallel:  1
Compile in GPU:  0

Quickstart

The first thing you need to run FARGOpy is to create a simulation:

sim = fp.Simulation()

FARGO3D comes along with several test simulations configured as setups. You may list which setups are available using:

sim.list_setups()

['binary',
 'fargo',
 'fargo_multifluid',
 'fargo_nu',
 'mri',
 'otvortex',
 'p3diso',
 'p3disof',
 'sod1d']

Once you select the setup, you may load it into the simulation:

sim.load_setup('fargo')

Alternatively, you may create the simulation from the beginning using the setup option:

sim = fp.Simulation(setup='fargo')

Before start, it's a good idea to clean all outputs (if they exists):

sim.clean_output()

Cleaning simulation outputs...
Done.

You may compile the simulation:

sim.compile(force=True)

Compiling FARGO3D with options 'SETUP=fargo PARALLEL=1 GPU=0 ' (it may take a while... go for a coffee)

Once you have loaded the setup we may proceed compiling and running the simulation:

sim.run()

Running asynchronously: mpirun -np 1 ./.fargo3d_SETUP-fargo_PARALLEL-1_GPU-0_ -m -t setups/fargo/fargo.par
Command is running in background

You can check the status:

sim.status(mode='isrunning')

################################################################################
Running status of the process:
	The process is running.

There are several status modes:

• Show progress of the simulation

sim.status(mode='progress')

OUTPUTS 0 at date t = 0.000000 OK [output pace = 0.1 secs]
OUTPUTS 1 at date t = 6.283185 OK [output pace = 0.1 secs]
OUTPUTS 2 at date t = 12.566371 OK [output pace = 1.5 secs]
OUTPUTS 3 at date t = 18.849556 OK [output pace = 3.0 secs]
OUTPUTS 4 at date t = 25.132741 OK [output pace = 3.0 secs]
OUTPUTS 5 at date t = 31.415927 OK [output pace = 3.0 secs]

• Check the latest lines of the logfile:

sim.status(mode='logfile')

################################################################################
Logfile content:
The latest 10 lines of the logfile:

..............
..............
..............
..............
..............
..............
..............
..............
..............
...

• Check (and return) the output files:

sim.status(mode='outputs')

################################################################################
Output content:

58 available datafiles:

bigplanet0.dat, dims.dat, domain_x.dat, domain_y.dat, domain_z.dat, gasdens0.dat, gasdens0_2d.dat, gasdens1.dat, gasdens2.dat, gasdens3.dat, 
gasdens4.dat, gasdens5.dat, gasdens6.dat, gasdens7.dat, gasdens8.dat, gasenergy0.dat, gasenergy1.dat, gasenergy2.dat, gasenergy3.dat, gasenergy4.dat, 
gasenergy5.dat, gasenergy6.dat, gasenergy7.dat, gasenergy8.dat, gasvx0.dat, gasvx0_2d.dat, gasvx1.dat, gasvx2.dat, gasvx3.dat, gasvx4.dat, 
gasvx5.dat, gasvx6.dat, gasvx7.dat, gasvx8.dat, gasvy0.dat, gasvy0_2d.dat, gasvy1.dat, gasvy2.dat, gasvy3.dat, gasvy4.dat, 
gasvy5.dat, gasvy6.dat, gasvy7.dat, gasvy8.dat, orbit0.dat, outputgas.dat, planet0.dat, summary0.dat, summary1.dat, summary2.dat, 
summary3.dat, summary4.dat, summary5.dat, summary6.dat, summary7.dat, summary8.dat, tqwk0.dat, used_rad.dat, 

• Check the available snapshots:

sim.status(mode='snapshots')

################################################################################
Snapshots:
	Number of available snapshots: 10
	Latest resumable snapshot: 8

You may also combine them:

sim.status(mode='isrunning snapshots')

################################################################################
Running status of the process:
	The process is running.

################################################################################
Snapshots:
	Number of available snapshots: 11
	Latest resumable snapshot: 9

Or ran all of them:

sim.status(mode='all')

################################################################################
Running status of the process:
	The process is running.

################################################################################
Logfile content:
The latest 10 lines of the logfile:

..............
..............
..............
..............
..............
..............
..............
..............
..............
..............

################################################################################
Output content:

68 available datafiles:

bigplanet0.dat, dims.dat, domain_x.dat, domain_y.dat, domain_z.dat, gasdens0.dat, gasdens0_2d.dat, gasdens1.dat, gasdens10.dat, gasdens2.dat, 
gasdens3.dat, gasdens4.dat, gasdens5.dat, gasdens6.dat, gasdens7.dat, gasdens8.dat, gasdens9.dat, gasenergy0.dat, gasenergy1.dat, gasenergy10.dat, 
gasenergy2.dat, gasenergy3.dat, gasenergy4.dat, gasenergy5.dat, gasenergy6.dat, gasenergy7.dat, gasenergy8.dat, gasenergy9.dat, gasvx0.dat, gasvx0_2d.dat, 
gasvx1.dat, gasvx10.dat, gasvx2.dat, gasvx3.dat, gasvx4.dat, gasvx5.dat, gasvx6.dat, gasvx7.dat, gasvx8.dat, gasvx9.dat, 
gasvy0.dat, gasvy0_2d.dat, gasvy1.dat, gasvy10.dat, gasvy2.dat, gasvy3.dat, gasvy4.dat, gasvy5.dat, gasvy6.dat, gasvy7.dat, 
gasvy8.dat, gasvy9.dat, orbit0.dat, outputgas.dat, planet0.dat, summary0.dat, summary1.dat, summary10.dat, summary2.dat, summary3.dat, 
summary4.dat, summary5.dat, summary6.dat, summary7.dat, summary8.dat, summary9.dat, tqwk0.dat, used_rad.dat, 

################################################################################
Snapshots:
	Number of available snapshots: 11
	Latest resumable snapshot: 9

You may stop the run at any time:

sim.stop()

The process is already running with pid '30287'
Stopping FARGO3D process (pid = 30287)

Before resuming get the latest resumable snapshot:

sim.status(mode='snapshots')

################################################################################
Snapshots:
	Number of available snapshots: 13
	Latest resumable snapshot: 11

And resume since the latest resumable snapshot:

sim.resume(since=sim.resumable_snapshot)

Resuming from snapshot 11
Running asynchronously: mpirun -np 1 ./.fargo3d_SETUP-fargo_PARALLEL-1_GPU-0_ -m -t -S 11 -t setups/fargo/fargo.par
Command is running in background

Check the status again:

sim.status(mode='snapshots')

################################################################################
Snapshots:
	Number of available snapshots: 16
	Latest resumable snapshot: 12

Once the running is finished you will get:

sim.status(mode='isrunning')

################################################################################
Running status of the process:
	The process has ended with termination code 0.

Postprocessing output

Let's run another setup:

sim = fp.Simulation(setup='p3diso')
sim.compile()

Compiling FARGO3D with options 'SETUP=p3diso PARALLEL=0 GPU=0 ' (it may take a while... go for a coffee)

And run it:

sim.run()

Running asynchronously: mpirun -np 1 ./.fargo3d_SETUP-p3diso_PARALLEL-1_GPU-0_ -m -t setups/p3diso/p3diso.par
Command is running in background

Check output:

sim.status('progress')

OUTPUTS 2 at date t = 6.283185 OK [output pace = 0.1 secs]
OUTPUTS 3 at date t = 9.424778 OK [output pace = 0.1 secs]
OUTPUTS 4 at date t = 12.566371 OK [output pace = 12.6 secs]
OUTPUTS 5 at date t = 15.707963 OK [output pace = 18.9 secs]

Stop it:

sim.stop()

The process is stopped.

Get the latest snapshot:

sim.get_resumable_snapshot()

6

You may load data items of the simulation:

• Domain:

sim.load_domain()

Loading domain...
Domain size:
	Variable 1 (periodic): 101
	Variable 2: 81
	Variable 3: 21
Problem in 3 dimensions
Building vargrids...
Done.

• Variables:

sim.load_variables()

Loading variables
85 variables load. See <sim>.vars

• Load a field:

dens = sim.load_field(fluid='gas',field='dens')

What's new

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!

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This package has been designed and written mostly by Jorge I. Zuluaga with advising and contributions by Matías Montesinos (C) 2023