Loading simulations

Loading data from simulations is the central function plutoplot serves.

The central object to interact with a PLUTO simulation is the plutoplot.Simulation object. In loads the simulation metadata, the grid and creates the objects for the individual output files.

Simulation

To load a simulation from disk create a plutoplot.Simulation object:

import plutoplot as pp

sim = pp.Simulation("path/to/simulation", format="flt")

Additionally the coordinates system and indexing can be set manually. If no format is given, the first existing format is used (in the order dbl, flt, vtk, dbl.h5, flt.h5).

The coordinate system will be read from the gridfile if not specified. More information on the coordinate system can be found in the Grid section.

plutoplot.Simulation initialization reference

`plutoplot.simulation.Simulation.init(self, path='.', format=None, coordinates=None, indexing='ijk')` `special`

Create Simulation object from PLUTO output directory

Parameters:

Name	Type	Description	Default
`path`	`Path or str`	Path to simulation directory / data directory	`'.'`
`format`	`str`	PLUTO output format to load. Currently supported: 'dbl', 'flt', 'vtk', 'dbl.h5', 'flt.h5'. By default uses the first {format}.out file found.	`None`
`coordinates`	`str`	name of coordinates system of simulation. Will be read from gridfile by default Supported: (')	`None`
`indexing`	`str`	Array index convention. Supports ("ijk", "kji").	`'ijk'`

Exceptions:

Type	Description
`FileNotFoundError`	if no metadata or grid files are found.
`NotImplementedError`	if unsupported format is requested

After loading the Simulation-object has the following attributes:

Simulation attributes

`plutoplot.simulation.Simulation`

Container class for PLUTO (http://plutocode.ph.unito.it/) output. Reads the metadata of all files in working directory (wdir), and loads individual files when needed. Simulation is subscriptable and iterable.

Attributes:

Name	Type	Description
`path`	`pathlib.Path`	Path to simulation directory (directory with `pluto.ini`, `definitions.h`, etc)
`data_path`	`pathlib.Path`	path to data directory (with `*.out` and data files)
`format`	`str`	simulation format
`metadata`	`plutoplot.io.SimulationMetadata`	Simulation metadata
`grid`	`plutoplot.grid.Grid`	Simulation grid

To show information about the simulation, just use the string representation:

Example

print(sim)

PLUTO Simulation: path: 'path/to/simulation', data directory '$sim_path/.'
Data vars: rho, vx1, vx2, vx3
Data files: Format `flt`: 2 files, last time 1.0, data timestep 1.00e+00  
PLUTO Grid Dimensions: (128, 1, 384), spherical coordinate system
r: 0.40..2.50, Lx1=2.10, N1=128
theta: 1.45..1.57, Lx1=0.12, N1=1
phi: 0.00..6.28, Lx1=6.28, N1=384

or use the Jupyter Notebook formatting

sim

PLUTO Simulation path: /home/simeon/masterproject/PLUTO/test-problems/HD/Disk_Planet/03_0, data directory $sim_path/.
Data vars: rho vx1 vx2 vx3
Data files: Format flt: 2 files,last time 1.0, data timestep 1.00e+00
PLUTO Grid Dimensions (128, 1, 384), spherical coordinate system

L N

$r$ 0.40 2.50 2.10 128

$\theta$ 1.45 1.57 0.12 1

$\phi$ 0.00 6.28 6.28 384

Slicing simulations

Accessing simulation steps

Each simulation output step is represented by a PlutoData object, which will be generated on demand by the Simulation. The PlutoData-object then gives access to the actual data arrays. The data from the simulation output steps can be accessed from the Simulation-object with:

direct access using the []-operator or get() functions

step_data = sim[10]
step_data = sim.get(10, keep=False)

iteration
```
for step in sim:
    # process data
```
reduced data with reduce() and reduce_parallel() (over each time step)
```
mean_density = sim.reduce(lambda step: step.rho.mean())
```

More details in Data Access

Grid

The Grid object contains all the information of the simulation grid.

Grid reference

`plutoplot.grid.Grid`

Grid datastructure to be initialized from gridfile

Attributes:

Name	Type	Description
`gridfile_path`	`Path`	Path to gridfile
`coordinates`	`str`	Name of coordinate system
`mapping_grid`		obj:`dict` of :obj:`str`): mapping from coordinate system variable name to PLUTO variable names. (e.g. for spherical coordinates `r`->`x1`, `theta`->`x2`, `phi`->`x3`, )
`mapping_vars`		obj:`dict` of :obj:`str`): mapping from coordinate system variable attribute name to PLUTO variable names. (e.g. for spherical coordinates `vr`->`vx1`, `vtheta`->`vx2`, `vphi`->`vx3`)
`mapping_tex`		obj:`dict` of :obj:`str`): mapping from variable name to LaTeX names.
`dims`		obj:`tuple` of :obj:`int`): domain dimensions
`size`	`int`	total size of data arrays (product of dims)
`x1,`	`x2, x3 (numpy.ndarray`	cell centered grid (1d, not as mesh)
`x1i,`	`x2i, x3i (numpy.ndarray`	cell interface coordinates (1d, not as mesh)
`dx1,`	`dx2, dx3 (numpy.ndarray`	cell sizes (1d, not as mesh)
`r,`	`z (numpy.ndarray`	available if `coordinates == 'cylindrical'`, maps to x1, x2
`ri,`	`zi (numpy.ndarray`	available if `coordinates == 'cylindrical'`, maps to x1i, x2i
`dr,`	`dz (numpy.ndarray`	available if `coordinates == 'cylindrical'`, maps to dx1, dx2
`r,`	`phi, z (numpy.ndarray`	available if `coordinates == 'polar'`, maps to x1, x2, x3
`ri,`	`phii, zi (numpy.ndarray`	available if `coordinates == 'polar'`, maps to x1i, x2i, x3i
`dr,`	`dphi, dz (numpy.ndarray`	available if `coordinates == 'polar'`, maps to dx1, dx2, dx3
`r,`	`theta, phi (numpy.ndarray`	available if `coordinates == 'spherical'`, maps to x1, x2, x3
`ri,`	`thetai, phii (numpy.ndarray`	available if `coordinates == 'spherical'`, maps to x1i, x2i, x3i
`dr,`	`dtheta, dphi (numpy.ndarray`	available if `coordinates == 'spherical'`, maps to dx1, dx2, dx3

Todo

Generalize and document meshgrid functions

`init(self, gridfile, coordinates=None, indexing='ijk')` `special`

Initialize Grid from gridfile

Parameters:

Name	Description	Default
`gridfile`	obj:`str` or :obj:`Pathlike`): path to gridfile	required
`coordinates`	obj:`str`, optional): name of coordinate system (cartesian, polar, cylindrical, spherical). If not set this will be read from gridfile.	`None`
`indexing`	obj:`str`, optional): index order for arrays. 'ijk' or 'kji'	`'ijk'`

`read_gridfile(self, gridfile_path, coordinates=None)`

Read and parse gridfile

Parameters:

Name	Type	Description	Default
`gridfile_path`		obj:`str` or :obj:`Pathlike`): Path to PLUTO gridfile `grid.out`	required
`coordinates`		obj:`str`, optional): coordinate system name If not set this will be read from gridfile	`None`

Sets Attributes: x1, x2, x3 (numpy.ndarray): cell centered grid (1d, not as mesh) x1i, x2i, x3i (numpy.ndarray): cell interfaces (1d, not as mesh) dx1, dx2, dx3 (numpy.ndarray): cell sizes (1d, not as mesh) Lx1, Lx2, Lx3 (numpy.ndarray): Domain width dims (:obj:tuple of :obj:int): domain dimensions data_shape (:obj:tuple of :obj:int): shape of data array. Depends on index order size (int): total size of data arrays (product of dims)

`set_coordinate_system(self, coordinates)`

Set coordinate system of grid and get name mapping

Parameters:

Name	Type	Description	Default
`coordinates`	`str`	name of coordinate system (cartesian, polar, cylindrical, spherical)	required

			L	N
\(r\)	0.40	2.50	2.10	128
\(\theta\)	1.45	1.57	0.12	1
\(\phi\)	0.00	6.28	6.28	384

Loading simulations

Simulation

plutoplot.simulation.Simulation.__init__(self, path='.', format=None, coordinates=None, indexing='ijk') special

plutoplot.simulation.Simulation

Slicing simulations

Accessing simulation steps

Grid

plutoplot.grid.Grid

__init__(self, gridfile, coordinates=None, indexing='ijk') special

read_gridfile(self, gridfile_path, coordinates=None)

set_coordinate_system(self, coordinates)

`plutoplot.simulation.Simulation.init(self, path='.', format=None, coordinates=None, indexing='ijk')` `special`

`plutoplot.simulation.Simulation`

`plutoplot.grid.Grid`

`init(self, gridfile, coordinates=None, indexing='ijk')` `special`

`read_gridfile(self, gridfile_path, coordinates=None)`

`set_coordinate_system(self, coordinates)`