Tutorial 3: Read a DNS dataset¶

Note

The complete code associated with this tutorial, including the original Jupyter notebook, is available here.

This exercise introduces the Field3D class, which highlights the main purpose of aPrioriDNS: providing a clean, memory-efficient interface for working with formatted DNS datasets.

From this point onward, the tutorials assume you are working with properly formatted DNS data (e.g., BlastNet). If you want to run the tutorial locally, download the dataset from the aPrioriDNS GitHub repository using the function ap.download(). If you already downloaded the data, simply comment out that line.

Import modules and define data path¶

Script header¶
import os
import aPriori as ap
import json

# Download data (comment this if already downloaded)
ap.download(dataset='h2_lifted')

# Adjust this path depending on where the DNS dataset is stored
directory = os.path.join('.', 'Lifted_H2_subdomain')

# BlastNet stores the global shape in info.json.
# Field3D will automatically parse everything, so we don't need to load it manually.
# The following lines check that the dataset is present in your system
with open(os.path.join(directory, 'info.json'), 'r') as file:
    info = json.load(file)
DNS_shape = info['global']['Nxyz']

Initialize the Field3D object¶

If your dataset follows the BlastNet format, you only need to provide the correct folder path. Field3D will automatically:

  • read the mesh,

  • load the chemistry mechanism,

  • detect all scalar/vector fields available,

  • create memory-light pointers to the data files.

DNS_field = ap.Field3D(directory)

Example console output¶

---------------------------------------------------------------
Initializing 3D Field

Checking files inside folder ../data/Lifted_H2_subdomain...

Folder structure OK

---------------------------------------------------------------
Building mesh attribute...
Mesh fields read correctly

---------------------------------------------------------------
Reading kinetic mechanism...
Kinetic mechanism file found: ../data/Lifted_H2_subdomain/chem_thermo_tran/li_h2.yaml
Species:
['H2', 'O2', 'H2O', 'H', 'O', 'OH', 'HO2', 'H2O2', 'N2']

---------------------------------------------------------------
Building scalar attributes...
Field attributes:
+-----------+------------------------------------------------------+
| Attribute |                         Path                         |
+-----------+------------------------------------------------------+
|     P     |   ../data/Lifted_H2_subdomain/data/P_Pa_id000.dat    |
|    RHO    | ../data/Lifted_H2_subdomain/data/RHO_kgm-3_id000.dat |
|     T     |    ../data/Lifted_H2_subdomain/data/T_K_id000.dat    |
|    U_X    |  ../data/Lifted_H2_subdomain/data/UX_ms-1_id000.dat  |
|    U_Y    |  ../data/Lifted_H2_subdomain/data/UY_ms-1_id000.dat  |
|    U_Z    |  ../data/Lifted_H2_subdomain/data/UZ_ms-1_id000.dat  |
|    YH2    |    ../data/Lifted_H2_subdomain/data/YH2_id000.dat    |
|    YO2    |    ../data/Lifted_H2_subdomain/data/YO2_id000.dat    |
|   YH2O    |   ../data/Lifted_H2_subdomain/data/YH2O_id000.dat    |
|    YH     |    ../data/Lifted_H2_subdomain/data/YH_id000.dat     |
|    YO     |    ../data/Lifted_H2_subdomain/data/YO_id000.dat     |
|    YOH    |    ../data/Lifted_H2_subdomain/data/YOH_id000.dat    |
|   YHO2    |   ../data/Lifted_H2_subdomain/data/YHO2_id000.dat    |
|   YH2O2   |   ../data/Lifted_H2_subdomain/data/YH2O2_id000.dat   |
|    YN2    |    ../data/Lifted_H2_subdomain/data/YN2_id000.dat    |
+-----------+------------------------------------------------------+

Using the Field3D object¶

Once initialized, the Field3D object exposes all field variables as Scalar3D objects.

Access a scalar field:¶

DNS_field.T

Example output:

<aPrioriDNS.DNS.Scalar3D at 0x14c36ab50>

Access the raw 3D data:¶

DNS_field.U_Y._3D

This returns the full NumPy array of the Y velocity component.

Filtering a field¶

You may apply any filtering operation (e.g., Gaussian, box, or Favre filtering):

filt_YO2 = DNS.filter_3D(DNS_field.YO2._3D, 8)

Plotting a midplane slice¶

DNS_field.plot_z_midplane('YH2O2')

3D visualisation and further examples will be covered in the next tutorials.