Subject: KINTECUS, new version, pricing and features

From: James Ianni <[email-masked]>
Date: Sun, 22 Sep 1996 18:55:20 -0400 (EDT)

immi  mmmi mmmi mmi    mm mmmmmmmmmi immmmmmmmmi   ,mmm_ I mmm     mm   gmms . 
 @[   iP    @[  ]YW.   ]  P  ]@[   [  '@@      ` ,Z!    V[ ]@      ]  ,A    V[ 
 @[  gf     @[  ]'@b   ]     ]@[       @@       ]@`      ! ]@      ]  W      ! 
 @[ gf      @[  ] Y@.  ]     ]@[       @@       W@         ]@      ]  MW.      
 @[d!       @[  ] !@W  ]     ]@[       @@   ,   @A         ]@      ]  !M@s_    
 @@b        @[  ]  ]@I ]     ]@[       @@mmmW   @[         ]@      ]    VM@W.  
 @PMm       @[  ]  '@W ]     ]@[       @@   '   @[         ]@      ]      ~M@m 
 @['MW.     @[  ]   V@I]     ]@[       @@       M@         ]@      ]        Y@I
 @[  M@.    @[  ]    M@]     ]@[       @@       ]@.        !@.     ]         @[
 @[   Y@.   @[  ]    ]@@     ]@[       @@        ]b     I`  MW     [  ]      @ 
,@b.  ,@W_ mmmi d_    M@    ,d@b.    ,g@@______I  V+___=/   '*+___/   !=c___/f 

          "The Kinetics Program Module for the Ultimate Lazy Scientist"

                 Kintecus V1.6 (c) Copyright 1995,96 James C. Ianni.
                              All Rights Reserved.

        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 has been 
designed with ease of use in mind. Absolutely no compiling nor linking 
required.
 A quick overview of the main features: 

        0) Extremely fast. On a 4DX2-66 Mhz PC the time required for a 
100 second simulation of the Cesium Flare Model (at an accuracy of 
1.0e-8) requires the popular program React32 that uses the famous
Hindmarsh and Cohen's CVODE algorithm to integrate the model in 1 minute 
and 36 seconds, while Kintecus integrated the same exact model in 6 
seconds and outputted more points. That's 16 times faster with higher 
curve resolution.

	1) the ability to model over 4,000 reactions (over 8,000 in the 
workstation versions) in less than 8 megabytes of RAM running in pure high 
speed 32-bit under DOS! Also, because of the incredible demand, Kintecus is 
*NOW* available for many popular workstations and supercomputers: Sun 
Sparcstations, IBM RISC/6000 series, Silicon Graphics, Cray YMP/J90's.

	2) Full output of normalized sensitivity coefficients selectable at 
any specified time or times. Normalized sensitivity coefficients are used in 
accurate mechanism reduction, determining which reactions are the main sources 
and sinks (network analysis) and which can also show which reactions require 
accurate rate constants and which ones can have essentially guessed rate 
constants. 

	3) 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 use your own experimentally 
recorded concentration profile in your model.

	4) 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_J
ust_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.

	5) 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!

	6) 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.

	7) Built in support for photochemical reactions involving hv and 
Loseschmidt's number.

	8) 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!

	9) Automatic generation of the species spreadsheet file using the 
reaction spreadsheet file. Why waste time finding, entering and initializing 
all the different species in your kinetic scheme?

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

	11) A switch that computes all internal Jacobians analytically. This 
is very useful for simulating very large kinetic mechanisms (more than 1,000). 
Finite difference methods can cause underflow or overflow errors in 
approximately such large Jacobians during the simulation

	12) Support for Excel and Lotus spreadsheet programs.

[ Running Kintecus ]
==========================================================================
Go into MS-DOS and create a file named MODEL.DAT. Enter your reactions
like so (using a spreadsheet 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 Obtain Program
==========================================================================

There are various versions of Kintecus for different 
workstations/supercomputers make sure you get the correct binary 
version for your computer.

HTML Sites (use your favorite WebBrowser to download Kintecus)
----------
http://www.coast.net/SimTel/msdos/chemstry.html 
(this site only has the 32-bit MSDOS/Windows version )

gopher://www.ccl.net:73/11/software
(this site has versions of Kintecus for SUN, SGI, RS6000, MSDOS/WINDOWS )

FTP Sites:
----------
ftp  www.ccl.net (go in /pub/chemistry  and then pick your platform...)
ftp  144.118.44.40
ftp  ftp.bio.indiana.edu
(these above sites have versions for SGI, Suns, RS/6000s,
 Crays, Macs and PC's) 

ftp  ftp.coast.net  (go in:  pub/SimTel/msdos/chemstry )
(this site only has the 32-bit msdos version)

How to FTP files
----------------
Here's how to ftp a file from site ftp.coast.net. This example will work 
with any ftp site except for the cd command in which case you will have to 
find out where the file is located.

$ ftp ftp.coast.net

Logon Name:anonymous
Password:(you put your own email address here! ie. [email-masked] )

ftp> cd pub/SimTel/msdos/chemstry

(since these are Unix sites, make sure you type the path above exactly 
the way it appears including the case, note the chemstry with no 'i')

ftp> binary
ftp> get kintecus.zip
ftp> bye

at the MS-DOS prompt:
> pkunzip kintecus.zip

for the workstations (SUN, SGI and so on) you use uncompress then tar:

$ uncompress kintecus_SUN.tar.Z 
$ tar -xvf kintecus_SUN.tar