Model module

The left panel displays the current values of the project’s parameters (initialized from the control.dat file present in the project’s folder or the chosen template for new projects).

The right panel contains a series of tabs for the different parts of the model.

Chemistry tab

This is where the chemical scheme/network is set-up.

• Generate: generate the list of reactions corresponding to the initial mixture.

  • the Species and Compo. boxes enable to define the composition of the initial gaz mixture.

  • when the composition is typed in, hit the Generate Reactions button. The code reads the chemistry databases and elaborates iteratively a set of reactions specific to the species present in the initial gaz mixture.

    Note: if a file reacScheme.Rda exists in the Run directory, it is downloaded and the reaction scheme is initialized automatically, without the need to hit Generate Reactions.

  • the results of the Volpert analysis used to generate the reaction network are proveded in the right panel, showing the new species added at each iteration. The Volpert index (VlpI) is the number of steps separating a species from the initial mixture.

      # Pseudocode for the 'Volpert' generation of reaction scheme
      # Inputs: 
      # - the initial mixture of the gaz
      # - a database of reactions (including photoprocesses)
      # Outputs:
      # - a reduced and consistent list of reactions
      # - a list of accessible species
        
      1. VlpI = 0 : initialize species list with initial mixture
        
      2. VlPI = 1 :
         a. search and list photoprocess for species in the list
         b. augment the list with the photoprocess products
             (new species are tagged with VlpI = 1)
        
      3. VlpI = VlpI +1 
         a. search and list photoprocess and reactions involving 
            species in the list as reactants
         b. augment the list with the products of these reactions
            (new species are tagged with VlpI)
         c. if (no new species) 
              stop 
            else 
              iterate at 3. 
    

• Simplify offers options to reduce the initial reaction scheme:

  • Remove ions ! enables to keep a purely neutral network. This can be used to estimate the impact of ions chemistry on neutral species…

  • Species to remove enables to enter a list of comma separated species names. All the reactions in which the species participate, either as reactants or products, are removed from the scheme.

  • Dummify sinks ! transforms all loss-less species, if any, into a dummy ‘Products’ species. Other dummy species are not affected. This has no impact on the reactions scheme.

• Network presents a zoomable and active graphical view of the network. Two controls are available:

  • Nodes attraction controls the strength of the forces in the network representation.

  • Max Volpert Index enables to see the iterative building of the reactions network, from the initial mixture, to the final scheme. The species appearing at each Volpert iteration are color coded.

  • Coloring/Clustering offers a choice of options to color the nodes of the graph:

    • volpert colors by the value of the volpert index

    • charge colors by the charge of the species

    • edge_betweeneness, louvain, fast_greedy and leading_eigen are community detection algorithms proposed by the igraph package (experimental; might be very slow for large networks)

• Reactions lists the reactions.

  • The list can be copied to the clipboard or downloaded to disk.

  • Typing a species name into the Target sp. textbox on the left selects the subset of reactions involving this species.

• Checks lists the species for which no loss reactions have been found. These will act as sinks.

• Sample is used to assemble Monte-Carlo samples from the generated network. The data are gathered from ChemDBPublic, a repository of database samples generated from MC-ChemDB (see https://github.com/ppernot/MC-ChemDB).

  • #MC samples enables to define the desired number (N, currently 500 max).

  • Generate Samples starts the generation of MC samples.

  N+1 samples are generated, with numbers from 0 to N, where 0 is the nominal sample, containing the unperturbed reference values for the chemistry parameters.

  The generated files are stored in the MC_Input subfolder of the project’s folder. They will overwrite existing files with the same sample numbers.

Irradiation tab

The spectrum, intensity and cross-section of the irradiation beam are defined here.

• Beam spectrum file is used to choose a spectrum file on disk.

  Note the spectral resolution has to be conform to the one declared for the photolysis cross-sections in the ChemDB Versions tab.

• Predefined files proposes a set of spectra.

• Spectrum Range enables to define the irradiation spectral range (by default the range of the spectrum file, in nanometers)

• Beam intensity (ph.cm^-2.s^-1) defines the intensity of the beam. If negative, the intensities in the spectrum file are used.

• Beam Section (cm^2) defines the beam’s cross-section.

A summary is provided at the bottom of the controls column, and a figure of the model spectrum is shown on the right.

Reactor tab

The reactor is considered as a tube in which a gaz flow is maintained.

The dimensions of the tube (length, cross-section), the working temperatures (gaz and electrons), the properties of the gaz flow (total pressure, reactants pressure and reactants flux) and the duration of the experiment are managed here.

ChemDB Versions tab

By default, the latest versions of the chemmistry databases (Photoprocs, Neutrals and Ions) are used, but the user can control specific versions through this tab.

The resolution of the photoprocesses cross-sections can be switched between 1 nm (default) and 0.1 nm (high resolution).