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
TYPE	The type of MKMCXX run. SEQUENCERUN : Normal MKMCXX run. Compute a series of single runs at different temperatures. SSITKA : Like SEQUENCERUN, but each single run is run a second time with a different input gas concentration. TPD : Do a single run where temperature is linearly changing during the run. REACTOR : Simple PFR implementation. Only uses first &runs entry and does not support sensitivity analysis.	string	SEQUENCERUN, SSITKA, TPD, REACTOR
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
CSTR_RES	Residence time of the gas phase in seconds. Defined as the reactor volume divided by the volumetric flow rate into the reactor. This parameter effectively sets the input flow rate. The actual residence time may differ if the overall reaction includes expansion or contraction of the gas volume. <=0 : Gas-phase concentrations are fixed. >0 : Model the gas-phase concentrations as in an isobaric CSTR with in- and outflow. Setting CSTR_RES = 1 is often a good start.	-1 (Fixed gas phase)	float > 0 or negative value
CSTR_LOAD	Sets the amount of sites (in mole) in the open reactor volume (in m^3). Reasonable values differ very much depending on the system. Often 10^-2 < CSTR_LOAD < 10^2. Increase CSTR_LOAD if conversion is too low. Decrease if conversion is too high.	1e-4	float > 0
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. - Requires KEYCOMPONENTS - Requires REAGENTS 0 : off 1 : on	0	0 or 1
EACT	Whether to calculate the apparent activation energy. - Requires KEYCOMPONENTS 0 : off 1 : on	0	0 or 1
DRC	Whether to perform a degree of rate control analysis. - Requires KEYCOMPONENTS 0 : off 1 : on - without drc groups 2 : on - with drc groups	0	0-2 (int)
TDRC	Whether to perform a thermodynamic degree of rate control analysis. - Requires KEYCOMPONENTS 0 : off 1 : on	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>},...
PDRC	Whether to include DRC results for every selectivity-component. - Requires DRC = 2 - Requires selectivity block 0 : Only output DRC results for KEYCOMPONENTS. 1 : Also output DRC results per component in selectivity blocks.	1	0 or 1
DSC	Whether to include DSC results for every selectivity-component. - Requires DRC > 0 - Requires selectivity block 0 : No DSC output. 1 : Output DSC results per component in selectivity blocks.	1	0 or 1
DCGC	Whether to include DCGC results for every ASF block. - Requires DRC = 2 - Requires ASF block 0 : No DCGC output. 1 : Output DCGC results per ASF block.	1	0 or 1
NPAR	Maximum number of CPU threads to use (if available). 0-1 : Single-threaded. >=2 : Multi-threaded SEQUENCERUN and sensitivity analysis.	0	int >= 0
TRANSIENT	Define the level of detail at which transient results should be stored. 0 : Do not write any transient SEQUENCERUN data. 1 : Write transient concentration and derivative data. 2 : Write transient concentration and derivative data. Also include transient sensitivity/selectivity data.	1	int >= 0
GRAPHDATA	Include data files that contain all data points that are plotted in the graphs. 0 : no 1 : yes	0	0 or 1
GRAPHFILTER	Apply a filter to graph data that omits small values. 0 : no 1 : yes	1	0 or 1

List of less 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)
CSTR_REPLACE	Replaces starting gas-phase compounds by some other component. E.g. "{He};{CO},{H2}" replaces CO and H2 with He. This does not change inflow concentrations.	NULL	{<ReplaceCmp>};{<Cmp1>},{<Cmp2>}
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
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
DRCBIN	Store binary data of sequencerun to allow re-plotting data. 0 : Don't store binary data. 1 : Store binary data.	0	0 or 1
MAKEPLOTS	Whether to create .png and .pdf files of plots. 0 : no 1 : yes	1	0 or 1
HEATMAP	Whether to create heatmap graphs for DRC/DSC results. 0 : no 1 : yes	1	0 or 1
COLORBLIND	Change the order of the graph-coloring for (slightly) improved readability. 0 : no 1 : yes	0	0 or 1
PRINTLIST	Generate some extra debug lines with the initial and final concentrations. - Requires DEBUG > 1 0 : no 1 : yes	1	0 or 1
WERROR	Interpret input warnings as errors. 0 : no 1 : yes	0	0 or 1
RELDERIV	Plot relative derivatives 0 : no 1 : yes	0	0 or 1
SELECTIVITY_CAP	Force upper limit for selectivity data to prevent unreadable selectivity graphs.	NULL	float > 0

List of networkplot-specific keywords and their meaning

Keyword	Explanation	Default value	Possible values
NETWORK	Allow creation of network graphs. 0 : no 1 : yes	1	0 or 1
NETWORK_RATES	Also print forward and backward rates in the network graphs. 0 : no 1 : yes	0	0 or 1
NETWORK_STRICT	Merge multiple edges between nodes into one edge. 0 : no 1 : yes	1	0 or 1
NETWORK_FLUX	Generate dedicated flux output. 0 : no 1 : yes	0	0 or 1
NETWORK_NODAL_PROD	Show connected products in nodal-recall chain. - Requires setting NODAL parameters in &networkplot 0 : no 1 : yes	0	0 or 1

List of TPD-specific keywords and their meaning

Keyword	Explanation	Default value	Possible values
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
TIME	Set the simulation time for a TPD run.	NULL	float > 0
TSTART	Starting temperature for a TPD run.	NULL	float > 0
TEND	Temperature reached at the end of the TPD run.	NULL	float > 0
TPD_EQ	Try to equilibrate the system before starting the TPD run. 0 : no 1 : yes	0	0 or 1

List of REACTOR-specific keywords and their meaning

Keyword	Explanation	Default value	Possible values
F_MOLE	In-flow of a PFR type reactor.	NULL	float > 0
A_REAC	Cross-sectional area of a PFR type reactor in m^2.	NULL	float > 0
L_REAC	Length of a PFR type reactor in m.	NULL	float > 0
RHO_SITES	Site density in mole sites / m^2	NULL	float > 0
BET	Surface area in m^2 / g	NULL	float > 0
CATALYST_LOADING	Ratio of active catalyst material on support kg/kg	NULL	float > 0
CATALYST_DENSITY	Density of the catalyst bed in kg / m^3	NULL	float > 0
VOID_FRACTION	Void fraction of the reactor	NULL	float > 0
REACNRSTEPS	Number of discrete slabs in the PFR.	30	int > 0

List of deprecated keywords and their meaning

Keyword	Explanation
GNUPLOT	Whether to output GNUPlot-style graphs.
CSTR	Whether to use the CSTR module or not. The CSTR functionality now fully depends on the value of CSTR_RES.
JACOBIAN	Whether to use the custom MKMCXX JACOBIAN. 0 : use default SUNDIALS jacobian (default) 1 : use custom MKMCXX jacobian (discontinued)
DAMPENING	Whether to enable dampening to old implementation of lateral interactions. 0 : no (default) 1 : yes
DAMPENING	Lower coverage bound for old implementation of lateral interactions. 0.0 (float) by default
DEFAULT_LAT	Allows old lateral repulsion parameters A and B to be set for all compounds. <float>;<float>

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}