FAQ

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This page contains answers to common questions handled by our support staff, along with some tips and tricks that we have found useful and presented here as questions.

 

  1. How do I ... ?
  2. Where can I find ... ?
  3. Why doesn't ... ?
  4. Who is ... ?
  5. What is ... ?
  6. When is ... ?

How do I ... ?

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.

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Why doesn't ... ?

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.

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Who is ... ?

 

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What is ... ?

The History of Kintecus ?

Kintecus was first developed on Amiga Computers back in 1992. It was written on an Absoft Fortran compiler 900k diskette that also was the boot disk on an Amiga 500 with 1 floppy disk, no hard disk, 1 meg memory. It has evolved somewhat from 1992-1995 mainly to conversion to PC's with Microsoft's really lousy and buggy Fortran Powerstation. It was released as shareware back in 1995. It is now written in FORTRAN77 with FORTRAN-95 and some C (mainly for accessing Window’s registry).

The deal with the name "KINTECUS" ?

Kintecus was initially named, "KINETICUS" which is Latin for "movement". Molecules/atoms/particles have to move before they react, so hence the name. In 1995, Kineticus was moved from the Amiga to the DOS platform which only supports filenames of eight characters, so a letter will have to be hacked off the name. The letter, "E" was deleted and the "I" replaced to "E" so we get the current name "KINTECUS". The program was also Copyrighted in 1995 under "KINTECUS", so do to legal reasons that name has been kept.

 I get the following prompt/message:

 "ALERT:

 Please close any programs that have the CONC.txt file opened...or any

of these related kintecus files:

krun.tmp

kdone.out

kwarn.out

kerr.out

view.txt

addspec.txt"

 This seems to happen under Windows Vista/Windows 7. You probably have to install Kintecus into “C:\” and NOT “C:\Program Files\” as for some reason, Vista/Windows 7 will not allow Kintecus to write files into “C:\Program Files\”.  This can also happen if you do not have write permission in the directory Kintecus is installed in. Kintecus writes various temporary files and output files into the directory it is installed in. You MUST have write permissions in the directory Kintecus is stored.

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When is ... ?

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Questions or problems regarding this web site should be directed to jianni10[el atto]gmail.com .
Copyright 2017  James C. Ianni. All rights reserved. Kintecus is a registered trademark.