From sg928ah5@dunx1.ocs.drexel.edu Sun Sep 22 19:30:46 1996 Received: from dunx1.ocs.drexel.edu for sg928ah5@dunx1.ocs.drexel.edu by www.ccl.net (8.7.5/950822.1) id SAA10610; Sun, 22 Sep 1996 18:58:18 -0400 (EDT) Received: (from sg928ah5@localhost) by dunx1.ocs.drexel.edu (8.7.4/8.6.12) id SAA04423 for chemistry@www.ccl.net; Sun, 22 Sep 1996 18:55:21 -0400 (EDT) From: James Ianni Message-Id: <199609222255.SAA04423@dunx1.ocs.drexel.edu> Subject: KINTECUS, new version, pricing and features To: chemistry@www.ccl.net Date: Sun, 22 Sep 1996 18:55:20 -0400 (EDT) X-Mailer: ELM [version 2.4 PL25] Content-Type: text 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. name@foo.com ) 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