Chemical properties file format (Draft)

These tables collect all the information necessary for the chemical stage of the simulation, comprising dissociation into, diffusion of and reaction between chemical species.
The file format is described below.

The usual file name extension is .chem. Example.
TRAX versions > 1808 come with a complete database of supported solvents in the CHEM subdirectory.

File version 20150519

   !filetype trxchem
   !fileversion <yyyymmdd>
   !filedate    <dow> <mmm> <dd> <hh>:<mm>:<ss> <yyyy>
   # 
   # Comment
   #
   !solvent <material>

   !dissociation <event_1>
   <decay_1_1_1> [ <decay_1_1_2> [...] ] <ratio_1_1>
   <decay_1_2_1> [ <decay_1_2_2> [...] ] <ratio_1_2>
   ...
   <decay_1_n_1> [ <decay_1_n_2> [...] ] <ratio_1_n>

   !dissociation <event_2>
   <decay_2_1_1> [ <decay_2_1_2> [...] ] <ratio_2_1>
   <decay_2_2_1> [ <decay_2_2_2> [...] ] <ratio_2_2>
   ...
   <decay_2_n_1> [ <decay_2_n_2> [...] ] <ratio_2_n>

   !dissociation <event_n>
   ...

   
   !diffusion
   <diffspecies_1> <diffconst_1>
   <diffspecies_2> <diffconst_2>
   ...
   <diffspecies_n> <diffconst_n>
      
   !reaction <reactant_1_1> <reactant_1_2> [ <reactant_1_3> [...] ]
   <product_1_1> <product_1_2> [ <product_1_3> [...] ] <rateconst_1>
   !reaction <reactant_2_1> <reactant_2_2> [ <reactant_2_3> [...] ]
   <product_2_1> <product_2_2> [ <product_2_3> [...] ] <rateconst_2>
   ... 
   !reaction <reactant_n_1> <reactant_n_2> [ <reactant_n_3> [...] ]
   <product_n_1> <product_n_2> [ <product_n_3> [...] ] <rateconst_n>

!filetype

Uniquely identifies this file as a chemical properties file.

!fileversion

Denotes the particular format version, at present 20150519. This allows the reader function to deal with changing syntax.

!filedate

This is for reference only, to record the date of creation of the file content. It is not parsed.

!solvent

Specifies the solvent to which the chemical properties pertain. <material> should be one of the loaded target materials.

!dissociation

Specifies the decay channels, <decay_i_j_k>, following particular physical events, <event_i>, with branching ratios <ratio_i_j> running from 0 to 1. Each event can have an arbitrary number of decay channels, and each decay channel can have an arbitrary number of chemical species.
At the time of this writing (Jan-2016), a physical event denotes an excited state, e.g. A1B1, associated with a shell specific partial cross section. If no such partial cross section exists, i.e. the shell number is undefined, generic physical events i, x and k may be specified for ionization, excitation and cutoff interactions, respectively.

!diffusion

Specifies the diffusion coefficients, <diffconst_i> [m2/s], for each species, <diffspecies_i>, to be considered in the simulation.

!reaction

Specifies the possible chemical reactions between chemical species, <reactant_i_j>, yielding products <product_i_k>, with reaction rate constants <rateconst_i> [liters/mol/s].
For each reaction, an arbitrary number of reactants can be specified, yielding an arbitrary number of products. The last entry in the products line is assumed to be the reaction rate constant.

File version 20180808

Supported from TRAX version 1808 onwards. Like file version 20150519, but adds electron thermalization and support for displacements in the pre-chemical phase as well as after reactions.

Electron thermalization table

This optional table may appear anywhere outside one of the other data blocks. It's purpose is to specify the displacement ("thermalization") of electrons whose energies have dropped below the cutoff energy. The displacement parameters are energy dependent and are interpolated linearly from the table. 
   !thermalization
   <E_1> <centre_1> <width_1>
   ...
   <E_n> <centre_n> <width_n>
<E_i>: electron energy [keV]
<centre_i>: centre [cm]
<width_i>: width [cm] (FWHM)
The electron displacement is sampled from a normal distribution with the interpolated centre and width parameters. Directions are isotropic.

Chemical species displacements

Chemical species displacements can occur at several stages of the simulation. They are sampled from a normal distribution. Directions are either isotropic or relative to another species in the same process.
For dissociation events, displacements may be specified for the individual dissociation products as well as a displacement of the molecule prior to dissociation, e.g. to account for charge transfer.
For reactions, displacements may be specified for the individual reaction products. 

   !dissociation <event>_i

   <decay>_i_1_1 [ <decay>_i_1_2 [...] ] <ratio>_i_1
   [
   !displacement [ <displ>_i_1 ]
   [ <displ>_i_1_1 [ <displ>_i_1_2 ] ... ]
   ]

   <decay>_i_2_1 [ <decay>_i_2_2 [...] ] <ratio>_i_2
   ...
   <decay>_i_n_1 [ <decay>_i_n_2 [...] ] <ratio>_i_n

      
   !reaction <reactant>_i_1 <reactant>_i_2 
   <product>_i_1 <product>_i_2 [ <product>_i_3 [...] ] <rateconst>_i
   [ <displ>_i_1_1 [ <displ>_i_1_2 ] ... ]
<displ>_i_1 specify displacements prior to a dissociation.
<displ>_i_1_j specify individual displacements for the products. They appear in the same order as the products.
Displacements are defined as follows: 
   <displ> = <centre> <width> <direction>
   <direction> = { isotropic | <relative> }
   <relative> = <species><modifier>
   <modifier> = *<factor>
Apart from isotropic displacements, directions may be specified relative to the direction of another species from the same product list. In this case, <species> denotes the reference species from the same product list,
<modifier>=*-1 specifies emission opposite to the reference.

References

Last updated: M.Kraemer,
$Id: traxfmtchem.html,v 1.4 2019/03/17 22:57:52 kraemer Exp $