# Quickstart The following tutorial is intended for users who want a quick introduction to basic operations with the library. For a more thorough understanding and detailed explanations, please refer to the comprehensive tutorials available at [Fundamentals and Usage](/apriori-documentation-1/fundamentals-and-usage/apriori-fundamentals.md). This section assumes you have already installed the library. If you haven't installed it yet, please refer to the [previous page](/apriori-documentation-1/getting-started/installation.md) for instructions. aPriori uses a formatting that is coherent with many simulations on [Blastnet](https://blastnet.github.io) \[1, 2]. If you'd like to work with a different case than the one provided here, you can download a dataset directly from their website. The current version of the package is just able to handle one timeframe, so make sure to download a case that contains a single timestep. In alternative, in this tutorial we are going to use a built-in function to download a subset of this non-premixed hydrogen/air jet flame DNS, so no need to download anything to run the following code. The integral code of this tutorial is available at the [Github page](https://github.com/LorenzoPiu/aPrioriDNS/blob/main/tutorials/Quickstart.py). ### Dataset download As a first step we are going to download the dataset. Figure 1 shows a representation of the subdomain used in this tutorial.

Figure 1 - grafical representation of the DNS subset used in the tutorial

Run the following command to download the dataset: ```python >>> import aPrioriDNS as ap >>> # Download the dataset >>> ap.download() ``` This command should have downloaded from Github a folder with the following structure:

### Visualization After downloading the dataset, the following lines of code initialize a Field3D. After this, we can display the field leveraging the plotting utilities:

>>> # Initialize 3D DNS field
>>> field_DNS = ap.Field3D('Lifted_H2_subdomain')

>>> #----------------------------Visualize the dataset-----------------------------

>>> # Plot Temperature on the xy midplane (transposed as yx plane)
>>> field_DNS.plot_z_midplane('T',                 # plots the Temperature
...                           levels=[1400, 2000], # isocontours at 1400 and 2000
...                           vmin=1400,           # minimum temperature to plot
...                           title='T [K]',       # figure title
...                           linewidth=2,         # isocontour lines thickness
...                           transpose=True,      # inverts x and y axes
...                           x_name='y [mm]',     # x axis label
...                           y_name='x [mm]')     # y axis label
>>> # Plot Temperature on the xz midplane (transposed as zx plane)
>>> field_DNS.plot_y_midplane('T', 
...                           levels=[1400, 2000], 
...                           vmin=1400, 
...                           title='T [K]', 
...                           linewidth=2,
...                           transpose=True, 
...                           x_name='z [mm]', 
...                           y_name='x [mm]')
>>> # Plot Temperature on the yz midplane
>>> field_DNS.plot_x_midplane('T', levels=[1400, 2000], vmin=1400, 
...                           title='T [K]', linewidth=2)
>>> # Plot OH mass fraction on the transposed xy midplane
>>> field_DNS.plot_z_midplane('YOH', title=r'$Y_{OH}$', colormap='inferno',
...                           transpose=True, x_name='z [mm]', y_name='x [mm]')

Output plots:

Figure 3 - Temperature field on the x, y, and z midplanes

### Compute reaction rates on DNS field The reaction rates are computed using [Cantera](https://cantera.org). The method compute\_reaction\_rates() uses data chunking to allow large files to be read without causing memory issues. The optional input parameter n\_chunks defines in how many chunks the files to be read and to be written are divided. To compute the instantaneous rates the values of temperature, pressure, and species concentration are necessary. The chemical mechanism in the chem\_thermo\_tran directory is used to compute the rates in every cell. After the computation, new files in the folder 'data/' will be saved to store the reaction rates, for example, the hydrogen reaction rate will be named 'RH2\_DNS\_kgm-3s-1\_id000.dat'. The suffix DNS is used to distinguish the rates computed on the unfiltered grid to the ones computed on the filtered grid (that will be shown later on in the tutorial).

>>> #--------------------------Compute DNS reaction rates--------------------------
>>> field_DNS.compute_reaction_rates()

>>> # Plot reaction rates
>>> field_DNS.plot_z_midplane('RH2O_DNS', 
...                           title=r'$\dot{\omega}_{H2O}$ $[kg/m^3/s]$', 
...                           colormap='inferno',
...                           transpose=True, x_name='z [mm]', y_name='x [mm]')
>>> field_DNS.plot_z_midplane('ROH_DNS', 
...                           title=r'$\dot{\omega}_{OH}$ $[kg/m^3/s]$', 
...                           colormap='inferno',
...                           transpose=True, x_name='z [mm]', y_name='x [mm]')

>>> # compute kinetic energy
>>> field_DNS.compute_kinetic_energy()

>>> # Compute mixture fraction
>>> field_DNS.ox = 'O2'     # Defines the species to consider as oxydizer
>>> field_DNS.fuel = 'H2'   # Defines the species to consider as fuel
>>> Y_ox_2=0.233  # Oxygen mass fraction in the oxydizer stream (air)
>>> Y_f_1=0.65*2/(0.65*2+0.35*28) # Hydrogen mass fraction in the fuel stream
>>> # (the fuel stream is composed by X_H2=0.65 and X_N2=0.35)

>>> field_DNS.compute_mixture_fraction(Y_ox_2=Y_ox_2, Y_f_1=Y_f_1, s=2)

>>> # Scatter plot variables as functions of the mixture fraction Z
>>> field_DNS.scatter_Z('T', # the variable to plot on the y axis
...                     c=field_DNS.YOH.value, # set color of the points
...                     y_name='T [K]', 
...                     cbar_title=r'$Y_{OH}$'
...                     )

>>> field_DNS.scatter_Z('ROH_DNS',
...                     c=field_DNS.HRR_DNS.value, 
...                     y_name=r'$\dot{\omega}_{OH}$ $[kg/m^3/s]$', 
...                     cbar_title=r'$\dot{Q}_{DNS}$'
...                     )

Output plots:

Figure 5 - H2O and OH reaction rates plotted on the zx plane

Figure 6 - Variables scattered in the mixture fraction space

### Filtering The object's filtering function will create a secondary folder, with the same structure as the main folder containing the unfiltered data. The function returns a string with the folder name, that in this case is "Filter16FavreGauss". The filter size, the filter kernel (Box, Gaussian, etc...) are included in the folder name to define the filtering operation that was used to obtain the dataset. The word "Favre" appears in the folder's name if Favre filtering was used. All the files contained in the data folder when the command is launched will be automatically filtered by the filtering function.

>>> #-------------------------------Filter DNS field-------------------------------
>>> # perform favre filtering (high density gradients)
>>> # the output of the function is a string with the new folder's name, f_string
>>> f_string = field_DNS.filter_favre(filter_size=16, # filter amplitude
...                                         filter_type='Gauss') # 'Gauss' or 'Box'

>>> # The string with the folder's name is now used to initialize the filered field
>>> field_filtered = ap.Field3D(f_string)

>>> # Visualize the effect of filtering on the Heat Release Rate
>>> field_DNS.plot_z_midplane('HRR_DNS',
...                           title=r'$\dot{Q}_{DNS}$', 
...                           colormap='inferno',
...                           vmax=8*1e9,
...                           transpose=True, x_name='z [mm]', y_name='x [mm]')

>>> field_filtered.plot_z_midplane('HRR_DNS',
...                           title=r'$\overline{\dot{Q}_{DNS}}$', 
...                           colormap='inferno',
...                           vmax=8*1e9,
...                           transpose=True, x_name='z [mm]', y_name='x [mm]')

Output plots:

Figure 7 - original vs filtered heat release rates

### Model reaction rates on the filtered field The filtered field is what in *a priori* validation is considered to resemble an LES snapshot. From those values, it is possible to model the unclosed quantities, and then compare them with the DNS benchmark values. The simplest way to model the reaction rates is based on the so called Laminar Finite Rate (LFR) approximation. This approach directly computes the reaction rates from the filtered LES field: $$ \overline{\dot{\omega}}\_{LFR} = \dot{\omega}(\tilde{T}, \tilde{Y}\_k) $$ Where: * $$\overline{\dot{\omega}}\_{LFR}$$ represents the reaction rates, * $$\dot{\omega}(\tilde{T}, \tilde{Y}\_k)$$ is the computation of the instantaneous Arrhenius rates from the filtered temperature $$\tilde{T}$$ and the filtered species concentrations of species k, $$\tilde{Y}\_k$$. This code snippet computes $$\overline{\dot{\omega}}*{LFR}$$ and compares it with the filtered DNS values $$\overline{\dot{\omega}}*{DNS}$$. For more complex modeling approaches, see section [Machine Learning Tutorials](/apriori-documentation-1/fundamentals-and-usage/machine-learning-tutorials.md) at the paragraph 'Data-Driven Closure for Turbulence-Chemistry Interaction'.

>>> #-------------------------Compute reaction rates (LFR)-------------------------
>>> # Computing reaction rates directly from the filtered field (LFR approximation)
>>> field_filtered.compute_reaction_rates()

>>> # Compare visually the results 
>>> field_filtered.plot_z_midplane('RH2_DNS',
...                           title=r'$\overline{\dot{\omega}}_{H2,DNS}$', 
...                           vmax=-20,
...                           vmin=field_filtered.RH2_LFR.z_midplane.min(),
...                           levels=[-300, -50, -20],
...                           labels=True,
...                           colormap='inferno',
...                           transpose=True, x_name='z [mm]', y_name='x [mm]')

>>> # Compare visually the results in the z midplane
>>> field_filtered.plot_z_midplane('RH2_LFR',
...                           title=r'$\overline{\dot{\omega}}_{H2,LFR}$', 
...                           vmax=-20,
...                           vmin=field_filtered.RH2_LFR.z_midplane.min(),
...                           levels=[-300, -50, -20],
...                           labels=True,
...                           colormap='inferno',
...                           transpose=True, x_name='z [mm]', y_name='x [mm]')

>>> # Compare the heat release rate results with a parity plot
>>> f = ap.parity_plot(field_filtered.HRR_DNS.value,  # x
...                    field_filtered.HRR_LFR.value,  # y
...                    density=True,                  # KDE coloured
...                    x_name=r'$\overline{\dot{\omega}}_{H2,DNS}$',
...                    y_name=r'$\overline{\dot{\omega}}_{H2,LFR}$'
...                    )

Output plots:

Figure 8 - Hydrogen reaction rate DNS (on the left), and LFR (on the right).

Figure - Parity plot comparing the LFR rates with the benchmark
DNS values

--- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://apriori.gitbook.io/apriori-documentation-1/getting-started/quickstart.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.