Difference between revisions of "Keywords and settings new"

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{| class="wikitable"
 
{| class="wikitable"
−
|+List of common keywords and their meaning
+
|+List of common keywords and their meaning.
 
! Keyword
 
! Keyword
 
! Explanation
 
! Explanation
Line 14: Line 14:
 
| DEBUG
 
| DEBUG
 
| Output additional debug statements.
 
| Output additional debug statements.
−
* 0 : no debug statements
+
* 0 : No debug statements.
−
* 1-4 : various levels of debug statements
+
* 1-4 : Various levels of debug statements.
 
| 0
 
| 0
 
| 0-4 (int)
 
| 0-4 (int)
Line 28: Line 28:
 
| USETIMESTAMP
 
| USETIMESTAMP
 
| Whether to place the output in a new folder which name is based on the current time stamp.
 
| 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"
+
* 0 : Place all output in a folder called "run".
−
* 1 : Generate a folder following the format "<RUNTYPE>_<yyyy>_<mm>_<dd>_<hhmm>"
+
* 1 : Generate a folder following the format "<RUNTYPE>_<yyyy>_<mm>_<dd>_<hhmm>".
 
| 1
 
| 1
 
| 0 or 1
 
| 0 or 1
Line 68: Line 68:
 
|-
 
|-
 
| REAGENTS
 
| REAGENTS
−
| List of reagents for which the reaction orders will be calculated
+
| List of reagents for which the reaction orders will be calculated.
 
| ''NULL''
 
| ''NULL''
 
| {<Cmp1>},{<Cmp2>},...
 
| {<Cmp1>},{<Cmp2>},...
 
|-
 
|-
 
| KEYCOMPONENTS
 
| KEYCOMPONENTS
−
| List of compounds on which the reaction orders, apparent activation energy, DRC, DSC and/or TDRC analysis should be based
+
| List of compounds on which the reaction orders, apparent activation energy, DRC, DSC and/or TDRC analysis should be based.
 
| ''NULL''
 
| ''NULL''
 
| ''x''{<Cmp1>},''x''{<Cmp2>},...
 
| ''x''{<Cmp1>},''x''{<Cmp2>},...
 
|-
 
|-
 
| PDRC
 
| PDRC
−
| Whether to include DRC results for every selectivity-component
+
| Whether to include DRC results for every selectivity-component.
 
:- Requires DRC = 2
 
:- Requires DRC = 2
 
:- Requires selectivity block
 
:- Requires selectivity block
−
* 0 : Only output DRC results for KEYCOMPONENTS
+
* 0 : Only output DRC results for KEYCOMPONENTS.
−
* 1 : Also output DRC results per component in selectivity blocks
+
* 1 : Also output DRC results per component in selectivity blocks.
 
| 1
 
| 1
 
| 0 or 1
 
| 0 or 1
 
|-
 
|-
 
| DSC
 
| DSC
−
| Whether to include DSC results for every selectivity-component
+
| Whether to include DSC results for every selectivity-component.
 
:- Requires DRC > 0
 
:- Requires DRC > 0
 
:- Requires selectivity block
 
:- Requires selectivity block
−
* 0 : No DSC output
+
* 0 : No DSC output.
−
* 1 : Output DSC results per component in selectivity blocks
+
* 1 : Output DSC results per component in selectivity blocks.
 
| 1
 
| 1
 
| 0 or 1
 
| 0 or 1
Line 97: Line 97:
 
|-
 
|-
 
| DCGC
 
| DCGC
−
| Whether to include DCGC results for every ASF block
+
| Whether to include DCGC results for every ASF block.
 
:- Requires DRC = 2
 
:- Requires DRC = 2
 
:- Requires ASF block
 
:- Requires ASF block
−
* 0 : No DCGC output
+
* 0 : No DCGC output.
−
* 1 : Output DCGC results per ASF block
+
* 1 : Output DCGC results per ASF block.
 
| 1
 
| 1
 
| 0 or 1
 
| 0 or 1
Line 108: Line 108:
  
 
{| class="wikitable"
 
{| class="wikitable"
−
|+List of less common keywords and their meaning
+
|+List of less common keywords and their meaning.
 
! Keyword
 
! Keyword
 
! Explanation
 
! Explanation
Line 115: Line 115:
 
|-
 
|-
 
| RERUN_OUTPUT
 
| RERUN_OUTPUT
−
| Define the folder used for re-running sensitivity analysis and graphs
+
| Define the folder used for re-running sensitivity analysis and graphs.
 
| run
 
| run
 
| string
 
| string
 
|-  
 
|-  
 
| RERUN_GRAPH
 
| RERUN_GRAPH
−
| Whether to re-run graphs from the RERUN_OUTPUT folder
+
| Whether to re-run graphs from the RERUN_OUTPUT folder.
−
* 0 : Regular mkmcxx run
+
* 0 : Regular mkmcxx run.
−
* 1 : Re-run graphs
+
* 1 : Re-run graphs.
 
| 0
 
| 0
 
| 0 or 1
 
| 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
 
| CACHE_WORKPOINT
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|-
 
|-
 
| ORDERSDIFF
 
| ORDERSDIFF
−
| Step size used in the linear fitting of reaction orders (fractional pressure)
+
| Step size used in the linear fitting of reaction orders (fractional pressure).
 
* Example values: Wide = 0.1 | Normal = 0.01 | Tight = 0.001
 
* Example values: Wide = 0.1 | Normal = 0.01 | Tight = 0.001
 
| 0.01
 
| 0.01
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|-
 
|-
 
| EACTDIFF
 
| EACTDIFF
−
| Step size used in the linear fitting of the apparent activation energy (fractional temperature)
+
| 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
 
* Example values: Wide = 0.001 | Normal = 0.0001 | Tight = 0.00001
 
| 0.0001
 
| 0.0001
Line 161: Line 151:
 
|-
 
|-
 
| DRCDIFF
 
| DRCDIFF
−
| Step size used in the linear fitting for the degree of rate control analysis (fractional k)
+
| 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
 
* Example values: Wide = 0.1 | Normal = 0.01 | Tight = 0.001
 
| 0.01
 
| 0.01
Line 167: Line 157:
 
|-
 
|-
 
| TDRCDIFF
 
| TDRCDIFF
−
| Step size used in the linear fitting for the thermodynamic DRC analysis (absolute dG in J/mol)
+
| 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
 
* Example values: Wide = 10 | Normal = 1 | Tight = 0.1
 
| 1
 
| 1
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|-
 
|-
 
| BOOSTER
 
| BOOSTER
−
| Multiplier used to speed-up reaction rates; sometimes leads to faster convergence towards the steady-state solution (time is scaled inversely to compensate)
+
| 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)
 
| 1.0 (regular speed)
 
| float > 0
 
| float > 0
 
|-
 
|-
 
| SOLVERTYPE
 
| SOLVERTYPE
−
| Type of integration method to use for solving the system of ordinary differential equations
+
| Type of integration method to use for solving the system of ordinary differential equations.
 
* 1 : BDF
 
* 1 : BDF
 
* 2 : ADAMS
 
* 2 : ADAMS
Line 198: Line 188:
 
|-
 
|-
 
| SOLTESTFAIL
 
| SOLTESTFAIL
−
| Maximum number of test failures before the solver gives up
+
| Maximum number of test failures before the solver gives up.
 
| 70
 
| 70
 
| int > 0
 
| int > 0
 
|-
 
|-
 
| SOLCONVFAIL
 
| SOLCONVFAIL
−
| Maximum number of convergence failures before the solver gives up
+
| Maximum number of convergence failures before the solver gives up.
 
| 100
 
| 100
 
| int > 0
 
| int > 0
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|-
 
|-
 
| DRCBIN
 
| DRCBIN
−
| Store binary data of sequencerun to allow re-plotting data
+
| Store binary data of sequencerun to allow re-plotting data.
−
* 0 : Don't store binary data
+
* 0 : Don't store binary data.
−
* 1 : Store binary data
+
* 1 : Store binary data.
 
| 0
 
| 0
 
| 0 or 1
 
| 0 or 1
 
|-
 
|-
 
| MAKEPLOTS
 
| MAKEPLOTS
−
| Whether to create .png and .pdf files of plots
+
| Whether to create .png and .pdf files of plots.
 
* 0 : no
 
* 0 : no
 
* 1 : yes
 
* 1 : yes
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{| class="wikitable"
 
{| class="wikitable"
−
|+List of deprecated keywords and their meaning
+
|+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
 +
|-
 +
|}
 +
 
 +
{| class="wikitable"
 +
|+List of deprecated keywords and their meaning.
 
! Keyword
 
! Keyword
 
! Explanation
 
! Explanation
 
|-
 
|-
 
| GNUPLOT
 
| GNUPLOT
−
| Whether to output GNUPlot-style graphs
+
| Whether to output GNUPlot-style graphs.
 
|-
 
|-
 
|}
 
|}

Revision as of 13:59, 23 March 2020

Settings block

Mkmcxx2.15.3.png

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.
- 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
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
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
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
List of deprecated keywords and their meaning.
Keyword Explanation
GNUPLOT Whether to output GNUPlot-style graphs.

Graphs block

Mkmcxx 2 3 0.png

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

Mkmcxx 2 3 0.png

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}
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