Keywords and settings new

Settings block

The list below is an overview of all the keywords that can be placed inside the &settings block. All keywords have a default value, so if these are not specified within the block, then the default value is used.

List of common keywords and their meaning

Keyword	Explanation	Default value	Possible values
DEBUG	Output additional debug statements. 0 : no debug statements 1-4 : various levels of debug statements	0	0-4 (int)
PRESSURE	The total pressure in the gas phase. <0 : Calculate the total pressure from the sum of the starting pressure of the compounds. >0 : Set this total pressure in bar and scale starting pressures proportionately.	-1 (Take starting pressures)	float > 0 or negative value
USETIMESTAMP	Whether to place the output in a new folder which name is based on the current time stamp. 0 = Place all output in a folder called 'run' 1 = Generate a folder following the format '<RUNTYPE>_<yyyy>_<mm>_ _<hhmm>'	1	0 or 1
ORDERS	Whether to calculate the reaction orders. 0 = off 1 = on (if KEYCOMPONENTS and REAGENTS are set)	0	0 or 1
EACT	Whether to calculate the apparent activation energy. 0 = off 1 = on (if KEYCOMPONENTS is set)	0	0 or 1
DRC	Whether to perform a degree of rate control analysis. 0 = off 1 = on (if KEYCOMPONENTS is set)	0	0-2 (int)
TDRC	Whether to perform a thermodynamic degree of rate control analysis. 0 = off 1 = on (if KEYCOMPONENTS is set)	0	0 or 1
REAGENTS	List of reagents for which the reaction orders will be calculated	NULL	{<Cmp1>},{<Cmp2>},...
KEYCOMPONENTS	List of compounds on which the reaction orders, apparent activation energy, DRC, DSC and/or TDRC analysis should be based	NULL	x{<Cmp1>},x{<Cmp2>},...

List of less common keywords and their meaning

Keyword	Explanation	Default value	Possible values
RERUN_OUTPUT	Define the folder used for re-running sensitivity analysis and graphs	run	string
RERUN_GRAPH	Whether to re-run graphs from the RERUN_OUTPUT folder 0 : Regular mkmcxx run 1 : Re-run graphs	0	0 or 1
ABSTOL	Set the absolute tolerance for a TPD run	1e-12	float > 0
RELTOL	Set the relative tolerance for a TPD run	1e-8	float > 0
CACHE_WORKPOINT	Reuse the sequencerun results as a workpoint in additional routines like DRC. 0 : Do not reuse. Rerun workpoint with zero perturbation. 1 : Reuse the sequencerun results and skip the zero perturbation workpoint.	1	0 or 1
NUMDIFF	Resolution of perturbations at each side of the workpoint.	2	int >= 1
ORDERSDIFF	Step size used in the linear fitting of reaction orders (fractional pressure) Example values: Wide = 0.1 | Normal = 0.01 | Tight = 0.001	0.01	float > 0
EACTDIFF	Step size used in the linear fitting of the apparent activation energy (fractional temperature) Example values: Wide = 0.001 | Normal = 0.0001 | Tight = 0.00001	0.0001	float > 0
DRCDIFF	Step size used in the linear fitting for the degree of rate control analysis (fractional k) Example values: Wide = 0.1 | Normal = 0.01 | Tight = 0.001	0.01	float > 0
TDRCDIFF	Step size used in the linear fitting for the thermodynamic DRC analysis (absolute dG in J/mol) Example values: Wide = 10 | Normal = 1 | Tight = 0.1	1	float > 0
BOOSTER	Multiplier used to speed-up reaction rates; sometimes leads to faster convergence towards the steady-state solution (time is scaled inversely to compensate)	1.0 (regular speed)	float > 0
SOLVERTYPE	Type of integration method to use for solving the system of ordinary differential equations 1 = BDF 2 = ADAMS	1 (BDF)	1 or 2 (int)
SOLSTOPTIME	Specificies when the solver should force re-evaluation of dydt/jac. 0 = never; use interpolated results for all t-out 1 = force re-evaluation only for the final t-out 2 = force re-evaluation at every t-out	2	0-2 (int)
SOLMAXSTEP	Maximum number of internal steps the solver is allowed to take.	5000	int > 0
SOLTESTFAIL	Maximum number of test failures before the solver gives up	70	int > 0
SOLCONVFAIL	Maximum number of convergence failures before the solver gives up	100	int > 0
PRECISION	Amount of significant digits to use in output.	10	int > 0
SEQAL	Use the output concentrations from completed runs as input for new runs. 0 = Start all runs using specified starting concentrations. 1 = Get starting concentrations from previous completed run.	0	0 or 1	GNUPLOT	Whether to output GNUPlot-style graphs	0
MAKEPLOTS	Whether to create plots	1

Graphs block

Inside the graphs block, you can set the colors used in the non-GNUPLOT graphs for specific components. On each line, you place the compound between curly brackets followed by the RGB color code. For example:

&graphs
# fix colors for particular compounds
{A*} #E74C3D
{B*} #F29C1F
{C*} #287FB9
{*}  #15A086

Selectivity block

Inside the selectivity block, you can specify mole balances on which basis you calculate selectivity and degree of selectivity control graphs. You need to specify a name, a key component and one or more products (typically more than one, else the concept of selectivity is rather trivial). The name will be used in the generation of the corresponding graph file, so please use a safe name (i.e. no spaces and no special characters!)

&selectivity
species_balance; {A}; {E},{F}

In the above example, the name of the mole balance block is "species_balance", the key component is A and the products of interest are E and F. A detailed example on how to use this block is explained here.

Stoichiometry

Often, the stoichiometry of the key component and the products is not simply a 1:1 ratio. To account for this difference, you need to put the stoichiometric coefficient in front the compound. The stoichiometric coefficient is simply the number of key components which need to be consumed to produce one product. To illustrate this, below an example for CO hydrogenation towards C1-C3 hydrocarbons is provided.

&selectivity
carbon_balance; {CO}; {CH4}, 2{CH2CH2}, 2{CH3CH3}, 3{CH3CH2CH3}, 3{CH2CHCH3}