The link below downloads "Kinetica98b" which is a
rough beta version of a kinetics simulation program based on the Hichem
FORTRAN program developed at NBS (now NIST) and kindly provided by Professor
R. Hanrahan. It allows simulations of mechanisms (i.e., concentrations/pressures
vs. time) to be run as well as the fitting of experimental data to a mechanism
by a simplex optimization of the rate constants. The latter function
is not available in other easy to use kinetics programs (such as IBM's
excellent Chemical Kinetics
Simulator package).
Select the kin98b.zip link below to download. Unzip the downloaded file into an empty, temporary directory and run the Setup program there. Follow instructions on the screen. This is a 32 bit program ---Windows 95/98/NT only!
NOTE: Accept the default install directory (c:\Kinfit) or use X:\Kinfit, where X is another drive letter.
The program here is a rough beta. I will not provide support for it. A 1.0 version with a help file and fixes will be posted when available. No documentation is available now. Mechanisms can be created using the program. Examine the sample files included for syntax for mechanism files and standard data files. Any problems in the input files for the hichem dynamic link library will cause the program to crash. Beware! Bug reports and suggestions are welcome (Email: der@chem.ufl.edu ).
An icon appears for "Kinfit" on the Start|Programs menu in Windows.
The program can be uninstalled via the Add/Remove Programs dialog in Control
Panel. The kinetics program is listed as "KINETICA98."
Setup
Use File|Setup to change default parameters and enter program locations. Under Spreadsheet Executable enter the exe filename for your spreadsheet if you want to export results for plotting and analysis.
Mechanisms
Use File|Open Mechanism File to open saved mechanism files. "New2.mec" is included in the installation as an example. The program will check your mechanism for some syntax errors such as blanks and warn you to save the modified, corrected version of the *.mec file.
Alternatively, use Mechanism|Create New Mechanism to enter a new mechanism. Reaction steps should be entered as, for example, A+B=C or X1 + X2 = X3 + X4, etc., where any alphanumeric symbols can be used to represent the reactants and products. The program assigns the first compound encountered as "1", the second as "2", and so on. Concentrations are entered as "A, 1.23" or "X1, 0.003", for example, and can be expressed in M units, pressure units, mM, or any convenient units. Times do not have explicit units and can be entered as ns, min, years or whatever (just be sure your rate constants on the reaction steps are expressed in the correct form according to your choice for concentration and time!) .
Finally, mechanisms can be edited directly in the text box of the application or using any text editor. Mechanisms that are modified can be saved by using File|Save Mechanism File. A mechanism can be cleared by using Mechanism|Clear Mechanism.
IMPORTANT: When naming reactants and products do not use the same combination of letters and numbers in two or more names. For example, do not use "h2o" and "o2h" for two different species.
Analyze
To run a simulation choose Analyze|Run Simulation. The results appear in a separate form and can be exported using Export|Export Simulation...
Optimize
To optimize the rate constants for your trial mechanism by comparison to experimental data, first choose a mechanism as described above. Next, Use File|Read Std Data to read in your experimental results. See the new.dat example file (with Notepad, for example) for syntax of this file. (Read IonSpec Data is a special function for our instrument and is not used normally).
It is important that every species in the mechanism has a column in the data file in the order the species appear in the mechanism. If you don't know the concentrations of one or more species, just enter a column of zeros and use Analyze|Optimize Options|Select Species to Fit to exclude that species from the fit.
If desired, one or more rate constants in the mechanism can be fixed to a constant by using Analyze|Optimize Options|Fix Rate Constants.
To initiate an optimization, select Analyze|Optimize|Simplex Method (the Powell method has not been implemented in this version). After saving and/or selecting file names, you are asked to enter a convergence limit. Smaller limits lead to more iterations and a better fit. The optimization progress is then followed with a listing of the convergence tests in the lower left textbox and a list of the rate constants in order to the right. After completion or cancellation of the fit, a form appears comparing the fit to the experiment. The results can be exported by using Export|Export Optimization... The exported text file arranges the data in a useful way and is highly recommended for examination of the results in a spreadsheet.
To see the optimizer in action load the new2.mec mechanism and the new.dat data file, then select Analyze|Optimize|Simplex Method accepting the default limit.
Note that the fits are done for normalized concentrations (i.e., the sum of the normalized concentrations at any time point is 1). Your starting concentrations must reflect the distribution of species in the time = 0 entry in the data file to yield a good fit.
Also note that the optimizer is an unsophisticated simplex routine and
suffers the shortcomings of all such methods. It is helpful to start
with good guesses for the rate constants. Restarts are sometimes
useful, especially if increasingly small convergence limits are used.
Kinetica98 was produced using Visual Basic 5.
D. E. Richardson, Dept of Chemistry