surf_react ID style args
global args = pdelete pcreate pdelete = probability that surface collision removes the incident particle pcreate = probability that surface collision clones the incident particle prob args = infile infile = file with list of surface chemistry reactions
surf_react global 0.2 0.15 surf_react prob air.surf
Define a model for surface chemistry reactions to perform when particles collide with surface elements or the global boundaries of the simulation box. One or more models can be defined and assigned to different surfaces or simulation box boundaries via the surf_modify or bound_modify commands. See Section 6.9 for more details of how SPARTA defines surfaces as collections of geometric elements, triangles in 3d and line segments in 2d. Also see the react command for specification of a gas-phase chemistry reaction model.
The ID for a surface reaction model is used to identify it in other commands. Each surface reaction model ID must be unique. The ID can only contain alphanumeric characters and underscores.
The surface reaction models for the various styles are described below. When a a particle collides with a surface element or boundary. the list of all reactions possible with that species as the reactant is looped over. A probability for each reaction is calculated, using the formulas discussed below, and a random number is used to decide which reaction (if any) takes place. A check is made that the sum of probabilities for all possible reactions is <= 1.0, which should normally be the case if reasonable reaction coefficients are defined.
IMPORTANT NOTE: A surface reaction model can only be specified for surfaces whose surface collision model is diffuse. This is partly because reactions do not make physical sense with the other current surface collision models. And because the diffuse model defines a surface temperature, which is used to initialize the rotational and vibrational energies of new particles appearing due to dissociation reactions. Note that the diffuse model can effectively perform specular reflections if its acc parameter is set to 0.0. This is a way to to perform surface reactions with specular reflection, which you cannot do directly using the surf_collide specular model. See the surf_collide doc page for details.
The global style is a simple model that can be used to test whether surface reactions are occurring as expected. There is no list of raactions for different species; all species are treated the same.
The global style takes two paramters, pdelete and pcreate. The first is the probability that a "deletion" reaction takes place when a collision occurs. If it does, the particle is deleted. The second is the probablity that a "creation" reaction occurs, which clones the particle, so that one particle becomes two. The two particles leave the surface according to whatever surface collision model is defined by the surf_collide command, and is assigned to that surface/boundary by the surf_modify collide command.
The sum of pdelete and pcreate must be <= 1.0.
Note that if you simply wish to delete all particles which hit the surface, you can use the surf_collide vanish command, which is simpler.
For the prob style, a file is specified which contains a list of surface chemical reactions, with their associated parameters. The reactions are read into SPARTA and stored in a list. Each time a simulation is run via the run command, the list is scanned. Only reactions for which all the reactants and all the products are currently defined as species-IDs will be active for the simulation. Thus the file can contain more reactions than are used in a particular simulation. See the species command for how species IDs are defined.
As explained below each reaction has a specified probability between 0.0 and 1.0. That probability is used to choose which reaction (if any) is performed.
The format of the input surface reaction file is as follows. Comments or blank lines are allowed in the file. Comment lines start with a "#" character. All other entries must come in 2-line pairs with values separated by whitespace in the following format
R1 --> P1 + P2 type style C1 C2 ...
The first line is a text-based description of a single reaction. R1 is a single reactant for the particle that collides with the surface/boundary, listed as a species IDs. P1 and P2 are one or two products, also listed as species IDs. The number of reactants is always 1. The number of allowed products depends on the reaction type, as discussed below. Individual reactants and products must be separated by whitespace and a "+" sign. The left-hand and right-hand sides of the equation must be separated by whitespace and "-->".
The type of each reaction is a single character (upper or lower case) with the following meaning. The type determines how many reactants and products can be specified in the first line.
D = dissociation = 1 reactant and 2 products E = exchange = 1 reactant and 1 product R = recombination = 1 reactant and 1 product named NULL
A dissociation reaction means that R1 dissociates into P1 and P2 when it collides with the surface/boundary. There is no restriction on the species involved in the reaction.
An exchange reaction is a collision where R1 becomes a new product P1. There is no restriction on the species involved in the reaction.
A recombination reaction is a collision where R1 is absorbed by the surface, so that the particle disappears. There are no products which is indicated in the file by listing a single product as NULL. There is no restriction on the species involved in the reaction.
The style of each reaction is a single character (upper or lower case) with the following meaning:
The style determines how many reaction coefficients are listed as C1, C2, etc, and how they are interpreted by SPARTA.
For S = Surface style, there is a single coefficient:
If the ambipolar approximation is being used, via the fix ambipolar command, then reactions which involve either ambipolar ions or the ambipolar electron have more restricitve rules about the ordering of reactants and products, than those described in the preceeding section for the prob style.
The first is an "exchange" reaction which converts an ambipolar ion into a neutral species. Internally this removes the ambipolar electron associated with the ion. In the file of reactions this is done by having the reactant be an ambipolar ion, and the product not be an ambipolar ion.
The second is a "dissociation" reaction where a neutral species is ionized by colliding with the surface/boundary, creating an ambipolar ion and ambipolar electron. In the file of reactions this is done by having the reactant not be an ambipolar ion, the first product be an ambipolar ion, and the second product be an ambipolar electron. The two products must be specified in this order.
All the surface reaction models calculate a global vector of length 2. The values can be used by the stats_style command and by variables that define formulas. The latter means they can be used by any command that uses a variable as input, e.g. "the fix ave/time command. See Section 4.4 for an overview of SPARTA output options.
The first element of the vector is the count of particles that performed surface reactions for surface elements assigned to this reaction model during the current timestep. The second element is the cummulative count of particles that have performed reactions since the beginning of the current run.
react, surf_modify, bound_modify