Loading of data

The most convinient way of working with EMC3 data is from netcdf files. This way all metadata and all available fields are known, and are loaded into memory as needed.

Netcdf files are also beneficial for sharing simulation results, as they contain metadata and are thus easy to use. While xemc3 only exists for python, netcdf library implementation are present in most languages, so you can easily do your analysis in your preferred language.

import xemc3

import xarray as xr
import numpy as np

# Matplotlib setup
import setup_plt

%%time

ds = xr.open_dataset("../../example-data/emc3_example.nc")

CPU times: user 38.2 ms, sys: 10 ms, total: 48.2 ms
Wall time: 51.2 ms

Checking the present data

xarray is nicely integrated in jupyter notebook and many IDEs, so it is easy to check what quantities are included as well as units and so on.

Note that for this view the data does not need to recide in memory, which is especially beneficial for high-resolution grids or large parameter scans.

ds

<xarray.Dataset> Size: 2GB
Dimensions:                       (r: 139, theta: 512, phi: 36, delta_r: 2,
                                   delta_theta: 2, delta_phi: 2,
                                   iteration: 1000, plate_ind: 22,
                                   plate_phi_plus1: 57, r_plus1: 140,
                                   theta_plus1: 513, phi_plus1: 37,
                                   plate_phi: 560, plate_x: 100,
                                   plate_x_plus1: 50, delta_plate_phi: 2,
                                   delta_plate_x: 2)
Coordinates:
    R_bounds                      (r, theta, phi, delta_r, delta_theta, delta_phi) float64 164MB ...
    z_bounds                      (r, theta, phi, delta_r, delta_theta, delta_phi) float64 164MB ...
    phi_bounds                    (phi, delta_phi) float64 576B ...
  * iteration                     (iteration) int64 8kB -999 -998 -997 ... -1 0
    plate_phi                     (plate_ind, plate_phi_plus1) float64 10kB ...
    plate_z                       (plate_ind, plate_phi_plus1, plate_x_plus1) float64 502kB ...
    plate_R                       (plate_ind, plate_phi_plus1, plate_x_plus1) float64 502kB ...
    plate_z_bounds                (plate_ind, plate_phi, plate_x, delta_plate_phi, delta_plate_x) float64 39MB ...
    plate_phi_bounds              (plate_ind, plate_phi, plate_x, delta_plate_phi, delta_plate_x) float64 39MB ...
    plate_R_bounds                (plate_ind, plate_phi, plate_x, delta_plate_phi, delta_plate_x) float64 39MB ...
Dimensions without coordinates: r, theta, phi, delta_r, delta_theta, delta_phi,
                                plate_ind, plate_phi_plus1, r_plus1,
                                theta_plus1, phi_plus1, plate_x, plate_x_plus1,
                                delta_plate_phi, delta_plate_x
Data variables: (12/93)
    _plasma_map                   (r, theta, phi) int64 20MB ...
    ne                            (r, theta, phi) float64 20MB ...
    nZ1                           (r, theta, phi) float64 20MB ...
    nZ2                           (r, theta, phi) float64 20MB ...
    nZ3                           (r, theta, phi) float64 20MB ...
    nZ4                           (r, theta, phi) float64 20MB ...
    ...                            ...
    f_E                           (plate_ind, plate_phi, plate_x) float64 10MB ...
    avg_n                         (plate_ind, plate_phi, plate_x) float64 10MB ...
    avg_Te                        (plate_ind, plate_phi, plate_x) float64 10MB ...
    avg_Ti                        (plate_ind, plate_phi, plate_x) float64 10MB ...
    tot_n                         (plate_ind) float64 176B ...
    tot_P                         (plate_ind) float64 176B ...
Attributes:
    title:             EMC3-EIRENE Simulation data
    software_name:     xemc3
    software_version:  0.2.2.dev5+g7311151
    date_created:      2022-10-27T13:16:46.836400
    id:                9bda9808-55f9-11ed-9228-00001029fe80
    references:        https://doi.org/10.5281/zenodo.5562265

xarray.Dataset

• Dimensions:
  • r: 139
  • theta: 512
  • phi: 36
  • delta_r: 2
  • delta_theta: 2
  • delta_phi: 2
  • iteration: 1000
  • plate_ind: 22
  • plate_phi_plus1: 57
  • r_plus1: 140
  • theta_plus1: 513
  • phi_plus1: 37
  • plate_phi: 560
  • plate_x: 100
  • plate_x_plus1: 50
  • delta_plate_phi: 2
  • delta_plate_x: 2
• Coordinates: (10)
  • R_bounds
    (r, theta, phi, delta_r, delta_theta, delta_phi)
    float64
    ...

    xemc3_type :

    geom

    units :

    m

    [20496384 values with dtype=float64]

  • z_bounds
    (r, theta, phi, delta_r, delta_theta, delta_phi)
    float64
    ...

    xemc3_type :

    geom

    units :

    m

    [20496384 values with dtype=float64]

  • phi_bounds
    (phi, delta_phi)
    float64
    ...

    xemc3_type :

    geom

    units :

    radian

    [72 values with dtype=float64]

  • iteration
    (iteration)
    int64
    -999 -998 -997 -996 ... -3 -2 -1 0

    array([-999, -998, -997, ...,   -2,   -1,    0], shape=(1000,))

  • plate_phi
    (plate_ind, plate_phi_plus1)
    float64
    ...

    [1254 values with dtype=float64]

  • plate_z
    (plate_ind, plate_phi_plus1, plate_x_plus1)
    float64
    ...

    [62700 values with dtype=float64]

  • plate_R
    (plate_ind, plate_phi_plus1, plate_x_plus1)
    float64
    ...

    [62700 values with dtype=float64]

  • plate_z_bounds
    (plate_ind, plate_phi, plate_x, delta_plate_phi, delta_plate_x)
    float64
    ...

    [4928000 values with dtype=float64]

  • plate_phi_bounds
    (plate_ind, plate_phi, plate_x, delta_plate_phi, delta_plate_x)
    float64
    ...

    [4928000 values with dtype=float64]

  • plate_R_bounds
    (plate_ind, plate_phi, plate_x, delta_plate_phi, delta_plate_x)
    float64
    ...

    [4928000 values with dtype=float64]

• Data variables: (93)
  • _plasma_map
    (r, theta, phi)
    int64
    ...

    numcells :

    2562048

    plasmacells :

    379649

    other :

    780311

    [2562048 values with dtype=int64]

  • ne
    (r, theta, phi)
    float64
    ...

    print_before :

    1

    xemc3_type :

    mapped

    long_name :

    Electron density

    units :

    m$^{-3}$

    [2562048 values with dtype=float64]

  • nZ1
    (r, theta, phi)
    float64
    ...

    print_before :

    2

    xemc3_type :

    mapped

    units :

    m$^{-3}$

    [2562048 values with dtype=float64]

  • nZ2
    (r, theta, phi)
    float64
    ...

    print_before :

    3

    xemc3_type :

    mapped

    units :

    m$^{-3}$

    [2562048 values with dtype=float64]

  • nZ3
    (r, theta, phi)
    float64
    ...

    print_before :

    4

    xemc3_type :

    mapped

    units :

    m$^{-3}$

    [2562048 values with dtype=float64]

  • nZ4
    (r, theta, phi)
    float64
    ...

    print_before :

    5

    xemc3_type :

    mapped

    units :

    m$^{-3}$

    [2562048 values with dtype=float64]

  • nZ5
    (r, theta, phi)
    float64
    ...

    print_before :

    6

    xemc3_type :

    mapped

    units :

    m$^{-3}$

    [2562048 values with dtype=float64]

  • nZ6
    (r, theta, phi)
    float64
    ...

    print_before :

    7

    xemc3_type :

    mapped

    units :

    m$^{-3}$

    [2562048 values with dtype=float64]

  • M
    (r, theta, phi)
    float64
    ...

    xemc3_type :

    mapped

    long_name :

    Mach number

    [2562048 values with dtype=float64]

  • Te
    (r, theta, phi)
    float64
    ...

    xemc3_type :

    mapped

    long_name :

    Electron temperature

    units :

    eV

    [2562048 values with dtype=float64]

  • Ti
    (r, theta, phi)
    float64
    ...

    xemc3_type :

    mapped

    long_name :

    Ion temperature

    units :

    eV

    [2562048 values with dtype=float64]

  • Lc
    (r, theta, phi)
    float64
    ...

    xemc3_type :

    mapped

    long_name :

    Connection length

    units :

    m

    [2562048 values with dtype=float64]

  • nH
    (r, theta, phi)
    float64
    ...

    xemc3_type :

    mapped

    long_name :

    Atomic deuterium density

    units :

    m$^{-3}$

    [2562048 values with dtype=float64]

  • nH2
    (r, theta, phi)
    float64
    ...

    xemc3_type :

    mapped

    long_name :

    D_2 density

    units :

    m$^{-3}$

    [2562048 values with dtype=float64]

  • nH2+
    (r, theta, phi)
    float64
    ...

    xemc3_type :

    mapped

    long_name :

    D_2^+ density

    units :

    m$^{-3}$

    [2562048 values with dtype=float64]

  • TH
    (r, theta, phi)
    float64
    ...

    xemc3_type :

    mapped

    long_name :

    Atomic hydrogen temperature

    units :

    eV

    [2562048 values with dtype=float64]

  • bf_bounds
    (r, theta, phi, delta_r, delta_theta, delta_phi)
    float64
    ...

    xemc3_type :

    full

    long_name :

    Magnetic field strength

    units :

    T

    [20496384 values with dtype=float64]

  • PLATES_MAG
    (r, theta, phi)
    bool
    ...

    xemc3_type :

    plates_mag

    long_name :

    Cells that are within or behind plates

    [2562048 values with dtype=bool]

  • TEMPERATURE_I_0
    (r, theta, phi)
    float64
    ...

    xemc3_type :

    mapped

    [2562048 values with dtype=float64]

  • DENSITY_E_A_0
    (r, theta, phi)
    float64
    ...

    xemc3_type :

    mapped

    [2562048 values with dtype=float64]

  • DENSITY_E_I_0
    (r, theta, phi)
    float64
    ...

    xemc3_type :

    mapped

    [2562048 values with dtype=float64]

  • DENSITY_E_M_0
    (r, theta, phi)
    float64
    ...

    xemc3_type :

    mapped

    [2562048 values with dtype=float64]

  • fort.1
    ()
    <U1410
    ...

    xemc3_type :

    raw

    long_name :

    Geometry input file

    [1 values with dtype=<U1410]

  • fort.2
    ()
    <U1969
    ...

    xemc3_type :

    raw

    long_name :

    Plasma parameters, boundary and initial conditions input file

    [1 values with dtype=<U1969]

  • fort.3
    ()
    <U301
    ...

    xemc3_type :

    raw

    long_name :

    Control flow input file

    [1 values with dtype=<U301]

  • fort.4
    ()
    <U3567
    ...

    xemc3_type :

    raw

    long_name :

    Neutrals input file for EIRENE

    [1 values with dtype=<U3567]

  • fort.40_0
    (r, theta, phi)
    float64
    ...

    xemc3_type :

    mapped

    [2562048 values with dtype=float64]

  • fort.42_0
    (r, theta, phi)
    float64
    ...

    xemc3_type :

    mapped

    [2562048 values with dtype=float64]

  • fort.43_0
    (r, theta, phi)
    float64
    ...

    xemc3_type :

    mapped

    [2562048 values with dtype=float64]

  • fort.46_0
    (r, theta, phi)
    float64
    ...

    xemc3_type :

    mapped

    [2562048 values with dtype=float64]

  • fort.47_0
    (r, theta, phi)
    float64
    ...

    xemc3_type :

    mapped

    [2562048 values with dtype=float64]

  • fort.47_1
    (r, theta, phi)
    float64
    ...

    xemc3_type :

    mapped

    [2562048 values with dtype=float64]

  • IMPURITY_IONIZATION_SOURCE_0
    (r, theta, phi)
    float64
    ...

    xemc3_type :

    mapped

    [2562048 values with dtype=float64]

  • IMPURITY_IONIZATION_SOURCE_1
    (r, theta, phi)
    float64
    ...

    xemc3_type :

    mapped

    [2562048 values with dtype=float64]

  • IMPURITY_NEUTRAL_0
    (r, theta, phi)
    float64
    ...

    xemc3_type :

    mapped

    [2562048 values with dtype=float64]

  • IMP_RADIATION_0
    (r, theta, phi)
    float64
    ...

    xemc3_type :

    mapped

    [2562048 values with dtype=float64]

  • FLUX_CONSERVATION_0
    (r, theta, phi)
    float64
    ...

    xemc3_type :

    mapped

    [2562048 values with dtype=float64]

  • LG_CELL_0
    (r, theta, phi)
    float64
    ...

    xemc3_type :

    mapped

    [2562048 values with dtype=float64]

  • dens_change
    (iteration)
    float64
    ...

    xemc3_type :

    info

    long_name :

    Relative change in density

    units :

    notes :

    Unlike in EMC3/pymc3 this is not percent.

    [1000 values with dtype=float64]

  • flow_change
    (iteration)
    float64
    ...

    xemc3_type :

    info

    long_name :

    Change in Flow

    notes :

    Not scaled

    [1000 values with dtype=float64]

  • part_balance
    (iteration)
    float64
    ...

    xemc3_type :

    info

    long_name :

    Global particle balance

    units :

    A

    [1000 values with dtype=float64]

  • dens_upstream
    (iteration)
    float64
    ...

    xemc3_type :

    info

    long_name :

    Upstream Density

    units :

    m$^{-3}$

    [1000 values with dtype=float64]

  • dens_down_back
    (iteration)
    float64
    ...

    xemc3_type :

    info

    long_name :

    Downstream Density (backward direction)

    units :

    m$^{-3}$

    [1000 values with dtype=float64]

  • dens_down_mean
    (iteration)
    float64
    ...

    xemc3_type :

    info

    long_name :

    Downstream Density (averaged)

    units :

    m$^{-3}$

    [1000 values with dtype=float64]

  • dens_down_fwd
    (iteration)
    float64
    ...

    xemc3_type :

    info

    long_name :

    Downstream Density (forward direction)

    units :

    m$^{-3}$

    [1000 values with dtype=float64]

  • Te_change
    (iteration)
    float64
    ...

    xemc3_type :

    info

    long_name :

    Relative change in el. temperature

    units :

    notes :

    Unlike in EMC3/pymc3 this is not percent.

    [1000 values with dtype=float64]

  • Te_upstream
    (iteration)
    float64
    ...

    xemc3_type :

    info

    long_name :

    Upstream el. temperature

    units :

    eV

    [1000 values with dtype=float64]

  • Te_down_back
    (iteration)
    float64
    ...

    xemc3_type :

    info

    long_name :

    Downstream el. temperature (backward direction)

    units :

    eV

    [1000 values with dtype=float64]

  • Te_down_mean
    (iteration)
    float64
    ...

    xemc3_type :

    info

    long_name :

    Downstream el. temperature (averaged)

    units :

    eV

    [1000 values with dtype=float64]

  • Te_down_fwd
    (iteration)
    float64
    ...

    xemc3_type :

    info

    long_name :

    Downstream el. temperature (forward direction)

    units :

    eV

    [1000 values with dtype=float64]

  • Ti_change
    (iteration)
    float64
    ...

    xemc3_type :

    info

    long_name :

    Change in ion temperature

    units :

    notes :

    Unlike in EMC3/pymc3 this is not percent.

    [1000 values with dtype=float64]

  • Ti_upstream
    (iteration)
    float64
    ...

    xemc3_type :

    info

    long_name :

    Upstream ion temperature

    units :

    eV

    [1000 values with dtype=float64]

  • Ti_down_back
    (iteration)
    float64
    ...

    xemc3_type :

    info

    long_name :

    Downstream ion temperature (backward direction)

    units :

    eV

    [1000 values with dtype=float64]

  • Ti_down_mean
    (iteration)
    float64
    ...

    xemc3_type :

    info

    long_name :

    Downstream ion temperature (averaged)

    units :

    eV

    [1000 values with dtype=float64]

  • Ti_down_fwd
    (iteration)
    float64
    ...

    xemc3_type :

    info

    long_name :

    Downstream ion temperature (forward direction)

    units :

    eV

    [1000 values with dtype=float64]

  • P_loss_gas
    (iteration)
    float64
    ...

    xemc3_type :

    info

    long_name :

    Power losses (neutral gas)

    units :

    W

    [1000 values with dtype=float64]

  • P_loss_imp
    (iteration)
    float64
    ...

    xemc3_type :

    info

    long_name :

    Power losses (impurities)

    units :

    W

    [1000 values with dtype=float64]

  • P_loss_target
    (iteration)
    float64
    ...

    xemc3_type :

    info

    long_name :

    Power losses (target)

    units :

    W

    [1000 values with dtype=float64]

  • ionization_core
    (iteration)
    float64
    ...

    xemc3_type :

    info

    long_name :

    Core ionization

    [1000 values with dtype=float64]

  • ionization_edge
    (iteration)
    float64
    ...

    xemc3_type :

    info

    long_name :

    Edge ionization

    [1000 values with dtype=float64]

  • ionization_electron
    (iteration)
    float64
    ...

    xemc3_type :

    info

    long_name :

    Electron energy source / ionization

    units :

    eV

    [1000 values with dtype=float64]

  • ionization_ion
    (iteration)
    float64
    ...

    xemc3_type :

    info

    long_name :

    Ion energy source / ionization

    units :

    eV

    [1000 values with dtype=float64]

  • ionization_moment_fwd
    (iteration)
    float64
    ...

    xemc3_type :

    info

    long_name :

    Forward momentum source/ ionization

    [1000 values with dtype=float64]

  • ionization_moment_bwk
    (iteration)
    float64
    ...

    xemc3_type :

    info

    long_name :

    Backward momentum source/ ionization

    [1000 values with dtype=float64]

  • TOTAL_FLX
    (iteration)
    float64
    ...

    xemc3_type :

    info

    long_name :

    Total impurity flux

    [1000 values with dtype=float64]

  • TOTAL_RAD
    (iteration)
    float64
    ...

    xemc3_type :

    info

    long_name :

    Total radiation

    units :

    W

    [1000 values with dtype=float64]

  • _plate_phi_plus1_dims
    (plate_ind)
    int64
    ...

    [22 values with dtype=int64]

  • _plate_x_plus1_dims
    (plate_ind)
    int64
    ...

    [22 values with dtype=int64]

  • surftype_ne
    (r_plus1, theta_plus1, phi_plus1)
    bool
    ...

    xemc3_type :

    depo

    description :

    True means +1, False means -1

    [2657340 values with dtype=bool]

  • flux_ne
    (r_plus1, theta_plus1, phi_plus1)
    float64
    ...

    xemc3_type :

    depo

    long_name :

    Outflux of particles

    units :

    s^-1

    [2657340 values with dtype=float64]

  • PARTICLE_DEPO_2
    (r_plus1, theta_plus1, phi_plus1)
    float64
    ...

    xemc3_type :

    depo

    [2657340 values with dtype=float64]

  • PARTICLE_DEPO_3
    (r_plus1, theta_plus1, phi_plus1)
    float64
    ...

    xemc3_type :

    depo

    [2657340 values with dtype=float64]

  • PARTICLE_DEPO_4
    (r_plus1, theta_plus1, phi_plus1)
    float64
    ...

    xemc3_type :

    depo

    [2657340 values with dtype=float64]

  • PARTICLE_DEPO_5
    (r_plus1, theta_plus1, phi_plus1)
    float64
    ...

    xemc3_type :

    depo

    [2657340 values with dtype=float64]

  • PARTICLE_DEPO_6
    (r_plus1, theta_plus1, phi_plus1)
    bool
    ...

    xemc3_type :

    depo

    [2657340 values with dtype=bool]

  • PARTICLE_DEPO_7
    (r_plus1, theta_plus1, phi_plus1)
    float64
    ...

    xemc3_type :

    depo

    [2657340 values with dtype=float64]

  • surftype_Te
    (r_plus1, theta_plus1, phi_plus1)
    bool
    ...

    xemc3_type :

    depo

    description :

    True means +1, False means -1

    [2657340 values with dtype=bool]

  • flux_P
    (r_plus1, theta_plus1, phi_plus1)
    float64
    ...

    xemc3_type :

    depo

    long_name :

    Outflux of energy

    units :

    W

    [2657340 values with dtype=float64]

  • ENERGY_DEPO_2
    (r_plus1, theta_plus1, phi_plus1)
    float64
    ...

    xemc3_type :

    depo

    [2657340 values with dtype=float64]

  • ENERGY_DEPO_3
    (r_plus1, theta_plus1, phi_plus1)
    float64
    ...

    xemc3_type :

    depo

    [2657340 values with dtype=float64]

  • ENERGY_DEPO_4
    (r_plus1, theta_plus1, phi_plus1)
    float64
    ...

    xemc3_type :

    depo

    [2657340 values with dtype=float64]

  • ENERGY_DEPO_5
    (r_plus1, theta_plus1, phi_plus1)
    float64
    ...

    xemc3_type :

    depo

    [2657340 values with dtype=float64]

  • ENERGY_DEPO_6
    (r_plus1, theta_plus1, phi_plus1)
    bool
    ...

    xemc3_type :

    depo

    [2657340 values with dtype=bool]

  • ENERGY_DEPO_7
    (r_plus1, theta_plus1, phi_plus1)
    float64
    ...

    xemc3_type :

    depo

    [2657340 values with dtype=float64]

  • _plate_phi_dims
    (plate_ind)
    int64
    ...

    [22 values with dtype=int64]

  • _plate_x_dims
    (plate_ind)
    int64
    ...

    [22 values with dtype=int64]

  • f_n
    (plate_ind, plate_phi, plate_x)
    float64
    ...

    long_name :

    Particle flux

    [1232000 values with dtype=float64]

  • f_E
    (plate_ind, plate_phi, plate_x)
    float64
    ...

    units :

    W/m²

    scale :

    10000.0

    long_name :

    Energy flux

    [1232000 values with dtype=float64]

  • avg_n
    (plate_ind, plate_phi, plate_x)
    float64
    ...

    units :

    m^-3

    scale :

    1000000.0

    long_name :

    Averge density

    [1232000 values with dtype=float64]

  • avg_Te
    (plate_ind, plate_phi, plate_x)
    float64
    ...

    units :

    eV

    long_name :

    Average electron temperature

    [1232000 values with dtype=float64]

  • avg_Ti
    (plate_ind, plate_phi, plate_x)
    float64
    ...

    units :

    eV

    long_name :

    Average ion temperature

    [1232000 values with dtype=float64]

  • tot_n
    (plate_ind)
    float64
    ...

    [22 values with dtype=float64]

  • tot_P
    (plate_ind)
    float64
    ...

    [22 values with dtype=float64]

• Attributes: (6)

  title :

  EMC3-EIRENE Simulation data

  software_name :

  xemc3

  software_version :

  0.2.2.dev5+g7311151

  date_created :

  2022-10-27T13:16:46.836400

  id :

  9bda9808-55f9-11ed-9228-00001029fe80

  references :

  https://doi.org/10.5281/zenodo.5562265

Quantities can be accessed either by the [] operator like ["nZ3"] or by .nZ3. Note that assigning new quantities is only possible with the [] notation.

ds.nZ3

<xarray.DataArray 'nZ3' (r: 139, theta: 512, phi: 36)> Size: 20MB
[2562048 values with dtype=float64]
Dimensions without coordinates: r, theta, phi
Attributes:
    print_before:             4\n
    xemc3_type:    mapped
    units:         m$^{-3}$

xarray.DataArray

'nZ3'

• r: 139
• theta: 512
• phi: 36

• ...

  [2562048 values with dtype=float64]

• Attributes: (3)

  print_before :

  4

  xemc3_type :

  mapped

  units :

  m$^{-3}$

ds.nZ3.isel(r=-2).plot()

<matplotlib.collections.QuadMesh at 0x7ac960b47620>

ds.emc3.plot_rz("nZ3", phi=np.pi / 5)

<matplotlib.collections.QuadMesh at 0x7ac960bf3d10>