Input file

Overview

An input contains at least four mandatory sections, which are &compounds, &reactions, and &settings and &runs. In each of these sections, specific instructions for the microkinetic simulation need to be placed which are explained in more detail below. If you want to add comments to the input file, you can do so by placing a # before the text you want the input parser to ignore. Lines that start with a # or which are empty (i.e. have only white space characters), will be automatically ignored by the parser. Each section starts with a section header, which is simply the section keyword prepended by a &.

Compounds

For each compound in the system, you need to specify:

• the name of the compound
• whether this compound is a surface site or a gas species
• the starting concentration of the compound

(there is a fourth parameter, called the TDRC flag, but you can ignore this for the time being)

A simple compound header looks as follows:

&compounds
A;  		0;  1.0
B;  		0;  1.0
A*;  		1;  0.0
B*;  		1;  0.0
*;  		1;  1.0

Each line corresponds to a different compound. The first column is the name of each compound. The second and third columns correspond to whether the compound is a surface site (1=yes, 0=no) and the starting concentration, respectively. It is good practice to also put a * or some other character (but not #) behind every compound which is a surface site.

Reactions

&reactions
AR; {A} + {*} => {A*}; 1e8 ; 1e15;  0e3; 100e3
AR; {B} + {*} => {B*}; 1e8 ; 1e15;  0e3; 100e3
AR; {A*}      => {B*}; 1e13; 1e13; 90e3;  90e3

Settings

&settings
TYPE = SEQUENCERUN

Runs

For each simulation, you need to specify the following information in the columns

1. Simulation temperature in K 2. Simulation time in s 3. Absolute tolerance of the ODE solver 4. Relative tolerance of the ODE solver

&runs
600;	1e2;	1e-12;	1e-10
700;	1e1;	1e-12;	1e-10
800;	1e0;	1e-12;	1e-10