Perturb/Alter the _____ of the system during a simulation run?
Temperature (program temperature runs), species
concentrations (simulating diffusion of oxygen into a solution, pH quenching, induction of
current, external concentration alterations) and volume changes (for various piston
compressions) can all be simulated using the "Temperature (K) or Filename" in
the PARM spreadsheet, the "Constant File?" field in the SPECIES description
spreadsheet or the "Volume Profile" field in the PARM spreadsheet respectively.
You can see an animation of how this is done if you point your web browser to
www.kintecus.org and look under the
Animations.
Specify the mass flow rates "in and out" to compute a
continuous flow reactor?
In the species flowsheet there are two columns:
"Residence Time in CSTR(s)" and "External
Concentration". "The Residence Time in CSTR", is the total time a species
stays in the CSTR from once it enters the CSTR (the in part) and the time it exits (out
part). I leave it up to the modeler to figure this part out. If the flow is laminar than a
simple time=distance/velocity can be used, but if there is some turbulence than a more
detailed method to calculated the average Residence time will be needed. The
"External Concentration" is the concentration of the species once it enters the
CSTR and NOT the concentration of the species in the pre-mix tank, i.e. if a 5 MOLAR
concentration of species A enters a CSTR tank that will dilute it by 10:1, then the
"External Concentration" will be 0.5 Molar entering the tank. The
Oregonator_in_CSTR Excel Spreadsheet demonstrates this, you might also want to get the
paper it references the model and experimental data from. A side note, you might ask
yourself, "Shouldn't all the species have the SAME "Residence Time in
CSTR(s)" since all the species are being "pushed" out the CSTR at the same
time?" and the answer is "YES". Kintecus allows different Residence Times
in the CSTR for "special" instances of where zeolites, surfaces or other species
inhibitor might slow the average flow of one species against another.
Specify a constant Pressure system ?
As specified by the "Pressure Constant
(YES/NO)" field in the PARM spreadsheet. Specifying "NO" in this field
selects a variable pressure (constant volume) run.
Register Kintecus ?
Kintecus is not freeware but shareware. Please view the
Registration Section in the Kintecus documentation (see the Download
Webpage or the zip file) for full registration forms. Education Institutions and/or
Students can register here: Register.
Reference Kintecus ?
Ianni, James C., Kintecus , Windows Version
6.01, 2017, www.kintecus.com.
OR
There are some journals that do not allow a reference
to anything as an Internet address. I suppose they fear the reference is much
too "soft" and can easily point to other unrelated sites in the future. If you
have a paper excepted in such a journal and cannot use www.kintecus.com in
your reference, then please use the following "hard" citation:
Ianni, J. C. , "A Comparison of the Bader-Deuflhard
and the Cash-Karp Runge-Kutta Integrators for the GRI-MECH 3.0 Model Based on
the Chemical Kinetics Code Kintecus", pg.1368-1372, Computational Fluid and
Solid Mechanics 2003, K.J. Bathe editor, Elsevier Science Ltd., Oxford, UK.,
2003.
Enter in a gas pressure that is much larger than the gas reactant pressure ?
Go in the species description spreadsheet and enter in a
non-reactive gaseous species such as Ar (Argon) or Nitrogen (N2). The additional gaseous
species does not have to be in any chemical reaction. Now, in the Initial Concentration
field enter in a sufficiently high concentration to raise the pressure of the system. The
ideal gas equation can be used as an approximation for the initial concentration [
Concentration=n/V=P/(R*T) ]. Remember that the additional gaseous presence will contribute
to the overall heat capacity of the system and any equations containing [M] or pressure
fall-off equations.
This is an early Excel problem and not a problem with
Kintecus. Kintecus has no limit. You can go way beyond 255 columns of data
to plot if you have Excel2010 or later. Excel 2010 goes out to 16,000+
columns. However, there is a small trick though to get it to work.
To get Excel2010 (or higher) to plot more than 256
columns of data:
A) Save your Kintecus-Excel workbook as an “Excel
Macro-Enabled Workbook”. Your file should have an extension of “.xlsm”
appended to the end of it.
B) Close your Workbook.
C) Load the just saved Excel Macro-Enabled Workbook.
D) Replot your data. (click the PLOT button located on
the CONTROL worksheet)
E) You should now go beyond column IV (which is the
256th column) up to XXD (16,380th column).
On Linux:
---------------------
If you have access to a linux system, you can extract
specific columns of data via the cut command. For example to cut column one,
columns 260-270 and columns 290 to the end, you can type this (without the
quotes)
“cat conc.dat | cut –f1,260-270,290- > new_conc.txt”
The cut command assumes TABs as the data delimiter, if
you using commas then the command would be
“cat conc.dat | cut –d, –f1,260-270,290- > new_conc.txt”
If colons, then change “-d,” to “-d:”, etc.
In the species flowsheet there are two columns:
"Residence Time in CSTR(s)" and "External Concentration". "The Residence
Time in CSTR", is the total time a species stays in the CSTR from once it
enters the CSTR (the in part) and the time it exits (out part). I leave it
up to the modeler to figure this part out. If the flow is laminar than a
simple time=distance/velocity can be used, but if there is some turbulence
than a more detailed method to calculated the average Residence time will be
needed. The "External Concentration" is the concentration of the species
once it enters the CSTR and NOT the concentration of the species in the
pre-mix tank, i.e. if a 5 MOLAR concentration of species A enters a CSTR
tank that will dilute it by 10:1, then the "External Concentration" will be
0.5 Molar entering the tank. The Oregonator_in_CSTR Excel Spreadsheet
demonstrates this, you might also want to get the paper it references the
model and experimental data from. A side note, you might ask yourself,
"Shouldn't all the species have the SAME "Residence Time in CSTR(s)" since
all the species are being "pushed" out the CSTR at the same time?" and the
answer is "YES". Kintecus allows different Residence Times in the CSTR for
"special" instances of where zeolites, surfaces or other species inhibitor
might slow the average flow of one species against another.
As specified by the "Pressure Constant (YES/NO)" field
in the PARM spreadsheet. Specifying "NO" in this field selects a variable
pressure (constant volume) run.
Go in the species description spreadsheet and enter in
a non-reactive gaseous species such as Ar (Argon) or Nitrogen (N2). The
additional gaseous species does not have to be in any chemical reaction.
Now, go in the “Initial Concentration” field and enter in a sufficiently
high concentration to raise the pressure of the system. The ideal gas
equation can be used as an approximation for the initial concentration [
Concentration=n/V=P/(R*T) ]. Remember that the additional gaseous presence
will contribute to the overall heat capacity of the system and any equations
containing [M] or pressure fall-off equations.
This part explains how to run Kintecus using the
MODEL/SPECIES/PARM/FITDATA/etc worksheets in Excel without having Excel
constantly open up, waste cpu cycles and constantly annoy you as your
Kintecus simulation runs.
Click the Windows Start Button in the button, left hand
corner of the screen and type “cmd” or "command" and press enter. A console
window should pop up on the screen. Alternatively, hold the Windows key
(usually the key is at the bottom left of the keyboard, in between the CTRL
and ALT keys) and tap the "x" key. A menu will pop up, select or "Command"
or "run" (and type “cmd” or “command”), a new console should pop up.
1) Once you are in the console window (or PowerShell
window), type "cd C:\Kintecus" or where ever you have Kintecus installed.
2) In the Excel Window, click on "CONTROL" tab, click
"RUN", once Kintecus starts, stop it with "ctrl-c" (hold ctrl key and tap
the "c" key) or ctrl-break (hold ctrl key and tap the Pause/Break key). The
reason for this step is that once you press the RUN button, the
Kintecus-Excel VBA macros will output all your worksheets as input files for
Kintecus.
3) In the same "CONTROL" worksheet, click on the
contents of the "Kintecus Switches" cell (A12) and select COPY (right click,
select Copy)
4) Click in the console/command line window, in
PowerShell/command type "./kintecus". In command console, just type "kintecus"
(don’t press enter yet!)
5) Hold down the CTRL key and type "V" (for paste) and
press ENTER. This should paste your Kintecus switches from cell A12 on the
CONTROL worksheet into the command line.
6) Kintecus is now running outside of Excel using all
your inputs from the Excel Worksheet. Once Kintecus is finished, click the
“Plot Results” button located on the CONTROL worksheet. Also, note that you
can copy the entire Kintecus folder into a new directory (C:\Kintecus2\),
change the “Kintecus Path” located on the CONTROL worksheet, then change one
or two parameters in the Kintecus-Excel worksheet and perform the same steps
above. You will be running two different Kintecus simulations/optimizations
at the same time. Repeat as much as necessary assuming you have enough cores
on your cpu.
Go in the species description spreadsheet and enter in
a non-reactive gaseous species such as Ar (Argon) or Nitrogen (N2). The
additional gaseous species does not have to be in any chemical reaction.
Now, go in the “Initial Concentration” field and enter in a sufficiently
high concentration to raise the pressure of the system. The ideal gas
equation can be used as an approximation for the initial concentration [
Concentration=n/V=P/(R*T) ]. Remember that the additional gaseous presence
will contribute to the overall heat capacity of the system and any equations
containing [M] or pressure fall-off equations.
the Graphical Interface Appear When I Run Kintecus.exe ?
The graphical interface for Kintecus is encoded inside the Excel
spreadsheet files that end in ".xls" such as
"Enzyme_Regression_Fitting.xls", "GRI_MECH_30.xls" or the blank xls
file "Kintecus_workbook.xls". Naturally, you need Excel or a program capable of
running the xls files such as SUN Microsystems' STAR OFFICE.
the results from my Excel model DO NOT exactly match the Kintecus model run
from the COMMAND line ?
Some users have notice this, and its mainly due to Excel saving
"What you see on the screen"
numbers to the temporary Kintecus files and not exactly what the cell value holds.
Example: you entered in 3.14159265E+10 in an Excel cell. After pressing <ENTER>
Excel shows 3.14E+10 in the cell, but if you click the cell, Excel now shows the full
number 3.14159265E+10 in the command line up above. You click the "RUN" button,
and temporary Kintecus files are saved, the cell holding 3.14159265E+10 is written as
3.14E+10 and NOT the full number! For some models, this is OK, but keep that in mind. If
you need Excel to write the entire value out to the last decimal place BE SURE
to first select the rows, columns or sheets containing those numbers, then under the
FORMAT menu, select the sub-menu item "Cells". A prompt will pop-open. In
the Category, select Scientific and increase the decimal places to 6, 8 or 10. Click OK.
Done.
This seems to be happening to users who convert their
model from one of those "other" expensive simulation packages to Kintecus
and are running under thermodynamics mode (the –THERM switch is given on the
command line). The solution(s) is/are to re-check your units given in the
parameters worksheet (the worksheet named, "PARM") and double check the
"Arrhenius Units" field is set to the same units for the Arrhenius
parameters given in your reaction set (the MODEL worksheet). Having a
mismatch of this units will most certainly cause NaN's. Please check for the
same thing for the concentration Units and the concentrations given on the
SPECIES worksheet, make sure they match! If you are quite sure your units
are consistent, be sure to change to the fifth integrator (-INT:5) and set
the Accuracy to 1e-4 to 1e-9. This can solve the rest of the integration
problems. If that doesn't help, you can set the "Starting Minimum
Integration" and the "Maximum Integration Time" to 1e-8 to 1e-11 and give
the "-obeymaxint" Kintecus flag. This will force Kintecus to integrate
taking very small time steps. This will cause a significant delay to get to
the final integration time.
Please be sure you have access to the "ipconfig"
command under Windows or the "ifconfig" command for Linux. If you do not
have access or permissions to these commands, ask the administrator to give
you access and/or copy the command into the directory where Kintecus is
located (i.e. for Windows, it may be ("C:\Kintecus" or "C:\Program
Files\Kintecus" ) .
Note that the regressed Kintecus values and statistics
outputted by Kintecus are not affected. This is an Excel only issue. If you
don’t use the Kintecus-Excel fitted plots then you can ignore this part.
Some users have noticed that if you are
regressing/fitting less than 60 points of data with Kintecus, and you plot
your data against the Kintecus fit, the x-axis may not overlap correctly.
This only happens with less than 60 points of data and with different
starting time steps. You can manually produce a correct regressed plot by
overlapping your experimental data with the Kintecus fit. Please see below:
A) Click on the “FDATA” worksheet and delete your
columns of experimental data. Your experimental data will have column names
that do NOT start with “FIT(“ near the top and they will always be the last
columns.
B) We now must delete non-Excel numbers from your
“fitdata” worksheet. Click on the “fitdata” worksheet that has your
experimental data. You might want to work with a copy of the worksheet
(right click on the worksheet tab, select Move or Copy). Keep in mind to
(1) delete all excel rows that have a “#” prefixed (2) Search and replace
all “N” or “NaN” to blanks (3) delete any “END” or “ED” (a search and
replace on “N” to blank will change the “END” keyword to “ED”) keywords in
the first column (4) delete any standard deviations that are suffixed to any
values. If you fail to delete the items above, then part (C) below will NOT
work.
C) Once you are sure all non-Excel related values are
removed from “fitdata”. Click on the FITPLOT worksheet tab, click on the
graph (the graph should highlight or be surrounded by eight small, black
squares in each corner) , select “Paste Special” from Edit==>”Paste Special”
or click on the “Paste Special” button located on the “Home” tab. A small
window will appear in the middle of the screen. Make sure the buttons “New
series” and “Columns” are clicked on (they are usually are on by default, so
you might not have to click on them). Also make sure “Series Names in First
Row” and “Categories (X Values) in First Column” are check marked, click
“OK”. Your experimental data should now be aligned with the regressed/fitted
data.
Again, if you have more than 60 points or you don’t
use graphical plots from Excel, then you can ignore this.
