KINTECUS: A powerful, versatile kinetics program.

James Ianni sg928ah5 at dunx1.ocs.drexel.edu
Mon Jan 22 16:17:40 EST 1996


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                  "The Ultimate Kinetics Program Module"


                 Kintecus (c) Copyright 1995 James C. Ianni.
                          All Rights Reserved.

For    :PC ( => MS-DOS 3.3, => '386 ) 
Subject:Chemistry, Physics, Biology & Engineering
Type   : DISABLED Shareware


[  Introduction  ]
=============================================================================

        Kintecus is a program to model the reactions of chemical, biological,
nuclear and atmospheric processes using two input spreadsheet files: a reaction
spreadsheet and a species description spreadsheet. Kintecus can model like no
other modeler can. Absolutely NO programming, compiling nor linking required.
 A quick overview of the main features are: 

     1) the ability to model over 2,000 reactions in less than 8 megabytes
of RAM running in pure high speed 32-bit under DOS! (And because the program is
*ENTIRELY* written in ANSI-FORTRAN 77, other platforms, AIX, Cray, Sun, Mac and
Amiga are coming...)

     2) the ability to use concentration profiles of any wave pattern for
any species or laser profile for any hv. This is very useful for studying very
complicated external perturbation affects or using your own experimentally
recorded concentration profile in your model.

     3) a powerful parser with mass & charge balance checker for those
reactions that the OCR or the graduate student "supposedly" entered in
correctly but the model is yielding incorrect results or is divergent. Do you
know a kinetics program that can completely parse and check for mass/charge
balance on a reaction like this:

#
# Rate Constants ,  REACTIONS:
#
1.234e-20        , CH3(((NO2)3(CO)93)3(CH2)9)23.30H2O+ + Co2 = A--- + B++++ 

Or how about this:

#
# Rate Constants ,  REACTIONS:
#
5.043e+20        , 3.43234 (CH4(N(PO342)43(CH3)3)34)(Os(S7)8)34++++ + 199.432
X++++5CH5+ ==>
5.434Some_Really_Funky_Enzyme_Name_But_I_Just_don't_Remember_IT_This_Name_Is_Ju
st_Too_Long_It_Seems_to_go_on_and_on_like_that_a n n o y i n g Rabbit???---- +
8 HCl + HCO3-

Kintecus is able to accurately check the above reaction for mass and charge
balance because you can create an optional name file containing common names
for species and then their mass representation. This smart mass balance can be
used for biological and nuclear reactions!
Also duplicate reaction and species checking.

     4) As you can see in the above reaction, *FRACTIONAL* coefficients for
species! Now you can finally model that last step in the Oregonator or crunch
100 elementary reaction steps in one reaction step!

     5) Quickly and easily hold one or more concentrations of any species
at a constant level just by typing the value in the field of the species.

     6) Built in support for photochemical reactions involving hv and
Loseschmidt's number. Current units supported are molecules/cm^3, moles/liter &
ppm.

     7) Model reactions from femtoseconds to years! A special switch in
Kintecus allows it to output the concentration of the species that are
displayed only if its concentration has changed significantly from its past
values. This may seem like no big deal, but if you model reactions that last
from days to years you can easily generate files that are dozens of megabytes
in size or more. Such a file is nearly impossible or extremely time consuming
to plot or print, but in Kintecus a special option turns a 100-multimeg file 
into a 100 kilobyte file without any loss in data!

     8) Automatic generation of the species spreadsheet file using the
reaction spreadsheet file.

     9) The ability to do reactions in a continuous stirred tank reactor
(CSTR) with multiple inlets and outlets!!

     10) Support for sensitivity analysis. The registered version now has 
full normalized sensitivity analysis (Just add -SENSIT:1 on the command 
line!)  Determine which reactions are important and which ones are not 
(ie. you can throw out reactions which are not important therefore, 
making mechanism determination easier, faster and much more accurate). 
Determine which reactions must have accurately calculated rate constants 
and which reactions can have approximated rate constants !

     11) The integration is carried out by an integration technique
superior to Gears with all internal matrices (reactions and jacobians) are
calculated analytically. There in NO SLOW AND USUALLY UNSTABLE
APPROXIMATION[1]. See references in .doc file...

     12) Checked against a number of published kinetics models.
         (See .doc file for references...)

     13) Support for Excel and Lotus spreadsheet programs.


A QUICK EXAMPLE OF ENTERING AND RUNNING A SAMPLE KINETICS SCHEME:
-----------------------------------------------------------------
Go into MS-DOS and create a file named MODEL.DAT. Enter your reactions
like so (using a spreadsheet to do this is highly recommended):

1.323e-4, A- +Widget-- + C ==> G+++ + F---+H20
3.2     , E+F = = > G + DNA_A_Replicated_Over_One_Day
54.34   , G = A
END  ( <==-- Make sure this END is here)

Run Kintecus: >Kintecus -c
Now copy the created ADDSPEC.TXT file as a SPECIES.DAT file
(ie. >COPY ADDSPEC.TXT SPECIES.DAT )
Edit the initial concentration fields in species.dat for your model and
type "Y" in the DISPLAY field for species' concentrations you want to save.
Run kintecus: >KINTECUS -ig:mass -ig:charge -show.

That's all.
-----------------------------------------------------------------
WHERE TO GET:

Using Netscape/Webrowser/Mosaic: 
===============================
http://ccl.osc.edu/chemistry.html
under Software/MS-DOS

Simtel:
ftp://ftp.coast.net/SimTel/msdos/chem/kintecus.zip

Using FTP:
==========
FTP ccl.osc.edu
under pub/chemistry/software/MS-DOS/kintecus
(remember to use the same exact case of the letters, and don't forget
to get it using binary transfer mode.)

example:

>FTP ccl.osc.edu
USER:anonymous
PASSWORD:(enter your E-mail address)
ftp>cd pub/chemistry/software/MS-DOS/kintecus
ftp>bi
ftp>mget *.*
ftp>bye

For Registered Users:
---------------------
By now you should have the new version which has full sensitivity analysis
and a bug fix related to KINTECUS accidently setting the step size 
to zero right before the end of the simulation and therefore breaking out 
with an underflow error. This bug showed up only once while performing my 
own simulations, I doubt anyone caught this. For the disabled sharewre 
version this bug can be fixed by changing the accuracy in the parameter 
desciption file. So far no other bugs reported! (which is still 
unbelievable...). If you are a registered user and have not received the 
update please email/phone me with your serial # ready, I will immediated 
send you the update.


(... END OF TEXT ...)





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