User`s manual
Contents
1. time concentration table These two methods modes are represented by the Sth and 6th menu items 6 1 Graph mode When the 5th menu item is chosen KINET will ask for a final reaction time i e the reaction time over which a calculation is to be performed A reaction time always starts at zero After the final reaction time input KINET will switch to graph mode with X and Y coordinate axes displayed The X axis scale will be determined by the given final reaction time the Y axis scale will be chosen from a maximal initial concentration KINET displays the kinetic curves during the computation run on this graph After the completion of the computation the points corresponding to experimental data will be shown as well if that data has been input To display and understand the colors corresponding to each particular substance and to change X and Y axis scales use the F1 F2 and F3 function keys Function key definitions are displayed on the information line at the bottom of the screen A computation may be interrupted at any time before its completion by pressing the ESC key To continue an interrupted computation is impossible but the parts of the kinetic curves already plotted may be used as if they were complete The interruption capability saves computation time if the curves show that the model s parameters and or the final reaction time were determined improperly On a color screen each curve is plotted in its own color To lea2. to be interrupted 6 2 Computation of time concentration table The 6th menu item facilitates the calculation of concentrations at a given moment of reaction time KINET asks for a time value and outputs the corresponding concentrations for all substances The results being printed on screen are simultaneously written to a file with the current filename and DAT extension If a file with the same name already exists its contents will be left intact the new data being appended to it This allows compilation of the table in several steps KINET makes it easy to create a time concentration table with a uniform time interval between consecutive reaction times by memorizing the interval between the two last moments of the reaction time for which the concentrations have been computed Simply press ENTER without inputting a value and KINET will assume the interval to be equal to the previous one For instance to compute a change of substance concentrations during 10 minutes of reaction time with an interval of 0 25 seconds enter the step value of 0 25 only once then press the ENTER key thirty nine times It is not necessary that the moments of reaction time be entered in ascending order however each time the new value is less than the previous one KINET will re start computation from a zero reaction time Therefore consecutively increasing values of reaction time is more profitable from the viewpoint of the total time of calculation To abort
3. A Software Package for the Numerical Modeling of Complicated Chemical Reaction Kinetics KINET version 1 2 5 User s manual 2 KINET User s Manual 1 AIMS AND CAPABILITIES OF KINET KINET is intended to provide help in studying chemical kinetics Given the description of a reaction mechanism as a set of equations KINET automatically draws a corresponding set of differential equations and calculates kinetic curves for all substances taking part in the reactions During the computation process the results are plotted on screen for detailed observation and examination and or printed as a table if desired Besides the simulation of the kinetics at given rate constants and initial concentrations i e solving the direct kinetic problem KINET makes it possible to solve so called reverse kinetic problems that deal with the determination of the rate constants of one or more elementary stages To tackle the reverse problem it is necessary to supply the experimental data on the concentrations of some substances at various consecutive moments in time KINET will optimize the constants to reach the best possible agreement between the calculated and experimentally measured concentrations When solving chemical kinetics problems the so called stiff systems of differential equations are often encountered These occur if the rates of the elementary stages differ by multiple orders of magnitude It is almost impossible to obtain a solution
4. ET User s Manual 5 Once a mechanism has been input KINET will proceed to the input for the initial concentrations For each substance a corresponding prompt will be displayed substance Input a numeric value as an answer to each prompt If ENTER is pressed and no value has been entered KINET will assume zero value This allows faster input since the concentration of a substance at the initial moment of a reaction most frequently equals zero Input errors will be treated exactly as described above After input of the initial concentrations KINET will ask whether experimental data will be entered The default is NO N to refuse entering experimental data simply press ENTER If it is necessary to enter experimental data KINET will ask a the name of the substance for which the kinetic curve is to be defined b number of the experimental data points for the curve c pairs of values time concentration for each point The values for the time and the concentration are divided with a space or comma After entry of the indicated number of data points KINET will display the input values for correction if necessary Any corrections required may only be made here because further corrections will be impossible After completing an experimental curve for one substance KINET will again ask for a substance name number of points and so on until it receives an empty line ENTER instead of a substance name In entering the data the
5. a computation and return to the menu press ESC when KINET asks for a new value of reaction time KINET will also return to the main menu if a void answer ENTER is given after a negative or Zero step 7 SOLVING THE REVERSE KINETIC PROBLEM If the 7th menu item is chosen the chemical reaction equations will be shown on the screen with their corresponding values of rate constants KINET will ask for the numbers of the constants to be optimized To enter these numbers type them on one line divided by commas or spaces The values assigned these constants while entering the reaction mechanism will be considered as their initial approximations KINET will vary these constants to reach a minimum sum of the squares of the deviations between the computed and the given experimental values of the concentrations To minimize the sum of the squared deviations the Powell method is employed To observe the optimization process KINET has the facility to output the results of each iteration i e the current values for the constants being varied and the sum of the squared deviations will be printed to screen If this option is not desired KINET will print only the final solution for the optimized rate constants Bear in mind the computation time may be lengthy After the completion of the rate constant optimization KINET offers viewing of the kinetic curves YES Y is the default KINET will solve the direct kinetic problem just as if the 5th menu item wa
6. e constants using the criteria of the best agreement between the experimental data and the kinetic curves calculated with a given mechanism choose the 7th menu item 4 DATA INPUT AND EDITING The initial data consist of three parts a a reaction mechanism i e a set of elementary reactions and corresponding rate constants b the initial concentrations of substances 4 KINET User s Manual c the experimental data i e the values of concentrations of one or more substances at various moments in reaction time The latter is mandatory only for solving the reverse problem if only the calculation of kinetic curves is desired the experimental data may be omitted 4 1 First time data input Data input 1st menu item begins with the determination of the reaction mechanism Each elementary reaction is presented as a common chemical equation To denote substances use arbitrary identifiers consisting of up to 8 symbols these must be letters or numbers but the first symbol must always be a letter These identifiers of substances are case sensitive that is KINET distinguishes lower case from upper case letters in substance names PRODUCT and product will be treated as different names The underscore sign _ is recognized as a letter The equal sign divides the leftmost and rightmost parts of an equation Substance identifiers are divided with the plus sign Example H Cl HCI A B Pr 1 As seen above s
7. er loaded and used for a new calculation altering if necessary the values for rate constants and initial concentrations as described above 6 KINET User s Manual Choose the 4th menu item to write current data to a file KINET will ask for a file name and automatically attach the file extension TXT The name of the file should meet the DOS format maximal length of name is 8 symbols maximal length of extension is 3 symbols The file is always created in the current directory To load data from a file 3rd menu item enter a filename minus the extension Data may be repeatedly written using different filenames or loaded from different files during one KINET session Choosing the Ist or 3rd menu item will delete the current data set from memory but leaving intact the data stored in files KINET considers the last file saved or read as the current data set name This name will be used in the case of a void answer to the next filename inquiry When the 6th menu item is chosen the current filename will be used as a label for the file containing results from the computations In this case the extension DAT will be added to the filename 6 SOLVING A DIRECT KINETICS PROBLEM There are two methods modes in solving the direct kinetics problem automatically creating and displaying kinetic curves and a concentrations calculation at given moments in reaction time The latter has the capability of recording its results in a file as a
8. h co processor to significantly increase computation speed otherwise calculation time for complex problems may take too long d color EGA or VGA for graphics capabilities to be fully realized monochrome EGA VGA CGA or Hercules are suitable as well but it may be difficult to identify graphics curves shown on the screen KINET User s Manual 3 3 OVERVIEW OF INSTRUCTIONS TO USERS KINET consists of two files KINET EXE and KINET BAN These must be in the same directory on floppy or hard disk During operation a 60 Kb temporary file will be created on disk make sure the disk has enough free space and it is addressable for writing To run KINET simply type KINET and press ENTER No command line parameters are necessary If the computer has a Hercules video card Microsoft s driver MSHERC COM should be installed before KINET is run otherwise it will be impossible to use the graphics mode When KINET comes up the KINET logo is shown Continue by pressing any key The following menu will be presented Choose the desired action by entering its corresponding number Enter new data View amp edit the data Load data from a file Save data in a file View kinetic curves Calculate concentrations at one point in time Optimize rate constants inverse problem Quit mMIANDANAWNHH SC Usually just after accessing KINET initial data needs to be entered using the keyboard the Ist menu item or downloading from a file the 3rd
9. item The latter choice is applicable if data saved from a previous session is desired Previous versions of the program used binary format for storing data so it was impossible to edit it with text editors The present version of KINET recognizes both binary files with kin extension and text formats files with txt extension To familiarize yourself with the syntax of data storage you can just view attached files of the demonstrational problems The data once entered can be saved in a file for later use 4th menu item or downloaded from a file viewed and edited 2nd menu item New data may also be viewed and edited employing this option as well With the initial data entered proceed to solving the direct or reverse kinetic problem To solve the direct problem select either the 5th or 6th menu item These items are independent and differ only in that the 5th item will initiate the calculation and graph representation of the kinetic curves up to the stated reaction time while the 6th selection will initiate the calculation of the concentrations of all substances at different given moments of reaction time the result being output to a file This selection facilitates obtaining a numerical representation of the results as a table that can be printed out This file can also be used as a source of future input data for some standard graph software packages MS Excel Origin To solve the reverse problem to optimize the values of the rat
10. nt has only a weak influence on some kinetic curves KINET cannot recognize these situations since the constant can be theoretically optimized but its found value may prove unreliable 8 DEMONSTRATIONAL PROBLEMS The KINET package includes 7 files with demonstrational problems CONSECUT TXT An ordinary consecutive reaction A B gt C There is also data for solving reverse kinetic problem MM TXT A Michaelis Menten kinetic scheme fermentative kinetics NO TXT A high temperature NO synthesis in N2 O2 mixture ET TXT A simplified scheme of ethane pyrolysis which adequately depicts the initial stage of the process OSCILL TXT An oscillating reaction a simplified scheme of Lotki Volterra BRUSSEL TXT A more complicated example of the oscillating reaction known as brusselator ORGNATOR TXT One more wide known example of oscillating reaction known as oregonator Examples on oscillating reactions were prepared by Kubasov A A
11. paces between the parts of an equation are not required however there must be no spaces in the names of substances There may be a stoichiometric coefficient before a substance name but no space is necessary The following equations are equivalent H H H2 2H H2 2 H H2 Only the numbers 1 2 or 3 can be the stoichiometric coefficients as only mono bi and trimolecular reactions are allowed that is no more than 3 molecules can take part in any one elementary reaction Fractional stoichiometric coefficients are obviously NOT allowed One can indicate a rate constant for an equation by ending the equation with a semicolon and k value Example H C1 HCI k 1 23e10 N204 2 NO2 K 125 As seen above both lower and uppercase letters k are allowed Equation input ends by pressing the ENTER key If the rate constant for the equation just entered is not indicated the cursor will move to the right of the screen KINET will ask that the rate constant be entered If a syntax error occurs in the input equation KINET will highlight the error found a corresponding diagnostic message will appear accompanied by a sound signal Press any key and repeat the input When a reaction mechanism definition is complete press ENTER just after KINET asks for the next elementary equation i e input a blank line instead of an equation After 20 elementary equations have been input the definition will be completed automatically KIN
12. re are no limitations imposed on the order of data points i e they need not necessarily go in the order of reaction time increase and the agreement between moments of reaction time for points that belong to different curves is not necessary 4 2 Editing initial data The 2nd menu item allows browsing and alteration of the initial data In the present KINET version editing capabilities are limited to changing rate constants and initial substance concentrations If the reaction mechanism requires alteration re enter the whole data set As stated above it is impossible to edit the experimental kinetic curves The current data will be shown again part by part After each part KINET will inquire whether changes need to be made The default is NO N If no alterations are needed simply press ENTER after each part is shown If alterations are needed type Y YES KINET will return to part one rate constants and ask for the number of each elementary equation where a rate constant needs changing The cursor goes to that line deleting the original value Type in a new rate constant To complete editing press the ENTER key without entering a value KINET will proceed to part two initial concentrations If alterations are needed enter as above except instead of the number of an equation KINET will ask the name of the substance 5 STORING INITIAL DATA IN A FILE After the initial data has been entered it can be written to a file and lat
13. rn which substance corresponds to which color press F1 the color legends will appear in the upper right hand corner Using a monochrome display may produce difficulties in identifying particular curves In this case it is recommended to first compute substance concentrations at several points using the 6th menu item in order to identify the curves later Since concentrations of different substances may vary by orders of magnitude some kinetic curves may be invisible i e lie just on the X axis or go beyond the limits of a chart Varying the Y scale with the F3 key allows easier examination of particular curves or their groups in greater detail During a run the computation results are written to a temporary file therefore consecutively changing the vertical Y scale does not require re computation and is relatively fast It is desirable that the temporary file is on a hard or virtual disk KINET User s Manual 7 The F2 key facilitates changing the horizontal X scale and giving another value for the final reaction time As a rule after altering the final time kinetic curves will be re computed Only if a new value for the final time is less than the previous one and it differs by less than 25 the curves will be plotted using the previous results If computations are complete pressing the ESC key switches KINET from graph mode returning it to the main menu If a computation is still running pressing the ESC key will cause it
14. s chosen see 6 1 above The new found rate constants will be substituted for the primary values in the initial data set for browsing use the 2nd menu item or save them by writing to a file using the 4th menu item When a reverse kinetics problem is formulated it should be taken into account that successful determination of a rate constant depends on which kinetic curves are presented in the experimental data For example in the case of a very simple kinetic scheme consisting of only two consecutive reactions 8 KINET User s Manual A gt B rate constant k1 B gt C rate constant k2 the kinetics of the consumption of substance A is determined only by the k1 constant and does not depend on k2 whereas the kinetics of the formation of the final product C depends on both constants If experimental results are known only for A then it is possible to calculate only k1 but not k2 since different values of k2 will produce the same kinetics curves for A if kl is fixed However if an experimental curve for only C is known it is possible to determine both the k1 and k2 constants KINET recognizes situations like the one above and on attempting to optimize values for constants not influencing given kinetic curves a warning message is published To proceed eliminate the indicated constant from the list of the optimizible constants It is necessary to bear in mind that cases may sometimes be encountered where the value of a rate consta
15. to a stiff differential equation system with common numerical methods such as Runge Kutta or Adams algorithms KINET employs Gear s algorithm that is especially suitable for integrating such systems and makes it possible to find solutions to chemical kinetics equations at almost any given rate constant value The abilities of KINET are limited to the following maximum number of elementary stages 20 maximum number of substances 15 maximum number of data points per experimental curve 20 total number of data points 50 The elementary stages can be mono bi and trimolecular up to 8 substances can participate in each elementary stage obviously quite enough for all realistic needs This version of KINET is intended for MS DOS operating system It can also work successfully in all Windows systems in a form of DOS window or console task But while working in Windows environment following restrictions exist 1 long file names are forbidden only 8 3 format is allowed i e maximal length of name is 8 symbols maximal length of extension is 3 symbols 2 graphical output is possible only in full screen mode and the standard VGA graphics is used resolution 640x480 16 colours Since the graph has been plotted the program can be switched to window mode by pressing Alt Enter However user can not interact with the program in this mode 2 EQUIPMENT NEEDED a IBM PC compatible computer with DOS 3 0 or higher b 640 K RAM c mat
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