---------- note that address of Mike Whitbeck changed. It is now: whitbeck1@llnl.gov or whitbeck1@popcorn.llnl.gov From whitbeck@sanjuan.wrc.unr.edu Tue May 14 15:49:40 1991 Received: from equinox.unr.edu by oscsunb.ccl.net (5.64+IDA+kva.1/901126.13) id AA08361; Tue, 14 May 91 15:49:26 -0400 Received: from wheeler.wrc.unr.edu (wrc.unr.edu) by equinox.unr.edu (4.1/1.34) id AA15201; Tue, 14 May 91 12:45:38 PDT Received: from sanjuan.wrc.unr.edu by wheeler.wrc.unr.edu (4.1//06-07-88) id AA14047; Tue, 14 May 91 12:45:16 PDT Received: by sanjuan.wrc.unr.edu (4.1/SMI-4.1) id AA03303; Tue, 14 May 91 12:45:11 PDT Date: Tue, 14 May 91 12:45:11 PDT From: whitbeck@sanjuan.wrc.unr.edu (Mike Whitbeck) Message-Id: <9105141945.AA03303@sanjuan.wrc.unr.edu> To: aslam@sp63.csrd.uiuc.edu, bernie@ecr.mu.oz.au, dkent@ucsd.edu, eczam@clan.nottingham.ac.uk, edwards@cae.wisc.edu, emv@poe.aa.ox.com, huang@deakin.oz.au, jkl@ccl.net, jpensar@ra.abo.fi, kenr@peabody.iusb.indiana.edu, pc@kjemi.unit.no, peri@eng.buffalo.edu, probert%cs@hub.ucsb.edu, shankar@s1.msi.umn.edu Subject: ftp site Status: R An ftp site for REACT (chemical kinetics simulation) has been found at Ohio State. As soon as I get confirmation on its final resting place I'll let you know. In the meanwhile look for it at www.ccl.net (128.146.36.48) in pub/incoming/react.tar.Z get it in binary mode uncompress it and untar it zcat react.tar.Z | tar xvf - It should make a directory called REACT. If you are on a sun 3|4 cd REACT make libq.a cd reaction make react select extract NOTE: if you do not support -fswitch then change this in the makefiles and use whatever hard math you do have or just leave it off. If you are on a VAX, well errr what can I say? If you get it ported please let me know! If you are using a MSDOS, ATARI, AMIGA... the port should be fairly straight forward. Look in rxn.h for parameters that address the size of the systems that can be handled- reduce accordingly if your machine is shy on memory. The string functions are the most likely place for incompatibility between unix and these other systems- be especially attentative to fgets() and strtok() and mytok() [my copy of strtok()]. Let me know if you port it and I'll incorporate the changes with conditional compiler statements. MANY THANKS to Jan K. Labanowski, Ph.D., Senior Supercomputer Specialist for making an ftp site available. Jan will make an announcement to a computational chemistry list at the Ohio Supercomputer Center after he has checked it out. At that time it may/probably be moved to another directory. IN EUROPE: try (ugle.unit.no 129.241.1.97) incoming/react.tar.Z MANY THANKS here to Per Christer Lund Department of Chemical Engineering The Norwegian Institute of Technology Enjoy! ___________________________________________________________ |Mike Whitbeck | whitbeck@unssun.unr.edu | |Desert Research Inst. | whitbeck@wheeler.wrc.unr.edu | |POB 60220 | whitbeck@sanjuan.UUCP | |RENO, NV 89506 | 702-673-7348 | |__________________________|______________________________| All academics have the potential for being insatiable... but the chemists are the most expensive and insatiable among the expensive and insatiable. - J. Martin in "To Rise Above Principle" From whitbeck@sanjuan.wrc.unr.edu Tue May 14 15:59:28 1991 Received: from equinox.unr.edu by oscsunb.ccl.net (5.64+IDA+kva.1/901126.13) id AA08502; Tue, 14 May 91 15:59:04 -0400 Received: from wheeler.wrc.unr.edu (wrc.unr.edu) by equinox.unr.edu (4.1/1.34) id AA15856; Tue, 14 May 91 12:56:04 PDT Received: from sanjuan.wrc.unr.edu by wheeler.wrc.unr.edu (4.1//06-07-88) id AA14109; Tue, 14 May 91 12:55:41 PDT Received: by sanjuan.wrc.unr.edu (4.1/SMI-4.1) id AA03369; Tue, 14 May 91 12:55:37 PDT Date: Tue, 14 May 91 12:55:37 PDT From: whitbeck@sanjuan.wrc.unr.edu (Mike Whitbeck) Message-Id: <9105141955.AA03369@sanjuan.wrc.unr.edu> To: aslam@sp63.csrd.uiuc.edu, bernie@ecr.mu.oz.au, dkent@ucsd.edu, eczam@clan.nottingham.ac.uk, edwards@cae.wisc.edu, emv@poe.aa.ox.com, huang@deakin.oz.au, jkl@ccl.net, jpensar@ra.abo.fi, kenr@peabody.iusb.indiana.edu, pc@kjemi.unit.no, peri@eng.buffalo.edu, probert%cs@hub.ucsb.edu, shankar@s1.msi.umn.edu Subject: disclaimer Status: R Not being a lawyer I always forget these things. The software I am providing comes free and with no gurantees. Use at your own risk. I hope to here from some of you after you have had a chance to try it out. If I get feedback on bugs/enhancements I will try to keep the code current and notify users of such changes. If at anytime you want to be removed from this list just send mail. Mike Whitbeck, Desert Research Institute. From whitbeck@sanjuan.wrc.unr.edu Tue May 14 18:44:34 1991 Received: from equinox.unr.edu by oscsunb.ccl.net (5.64+IDA+kva.1/901126.13) id AA10869; Tue, 14 May 91 18:44:12 -0400 Received: from wheeler.wrc.unr.edu (wrc.unr.edu) by equinox.unr.edu (4.1/1.34) id AA26534; Tue, 14 May 91 15:41:10 PDT Received: from sanjuan.wrc.unr.edu by wheeler.wrc.unr.edu (4.1//06-07-88) id AA15324; Tue, 14 May 91 15:40:44 PDT Received: by sanjuan.wrc.unr.edu (4.1/SMI-4.1) id AA03528; Tue, 14 May 91 15:40:40 PDT Date: Tue, 14 May 91 15:40:40 PDT From: whitbeck@sanjuan.wrc.unr.edu (Mike Whitbeck) Message-Id: <9105142240.AA03528@sanjuan.wrc.unr.edu> To: aslam@sp63.csrd.uiuc.edu, bernie@ecr.mu.oz.au, dkent@ucsd.edu, eczam@clan.nottingham.ac.uk, edwards@cae.wisc.edu, emv@poe.aa.ox.com, huang@deakin.oz.au, jkl@ccl.net, jpensar@ra.abo.fi, kenr@peabody.iusb.indiana.edu, pc@kjemi.unit.no, peri@eng.buffalo.edu, probert%cs@hub.ucsb.edu, rcruz@paul.rutgers.edu, shankar@s1.msi.umn.edu Subject: some test data Status: R Here is a test problem a little larger than the example given in the distribution for REACT. ============================= problem.m=================================== .2500e-05 no2m -> no + om .5556e+10 om -> oh + ohm .1000e+10 oh + ohm -> om .1000e+10 oh + no2m -> no2 + ohm .2500e+09 om + no2m -> no2 + ohm + ohm .2500e+10 om + o2 -> o3m .5500e+04 o3m -> o2 + om .1000e+09 no2 + no2 -> n2o4 .1300e+04 n2o4 -> no2 + no2 .1200e+04 n2o4 -> no2m + no3m .3000e+03 no2 -> x .1000e+09 no2 + x -> no2m + no3m .1000e+09 no2 + no -> n2o3 .2000e+04 n2o3 -> no2 + no .2000e+04 n2o3 -> no2m + no2m .1000e-00 x + no -> no2m + no2m ============================= problem.m=================================== and here are the parameters. ============================= problem.p=================================== 0 .36e+04 .06e+04 1.0e-03 no2m 0.1e-0 1.0e-8 1.0e-03 o2 .3e-03 1.0e-8 1.0e-03 ohm .1e-06 1.0e-8 1.0e-03 ============================= problem.p=================================== The solution is found by ............................................................... %react problem 1) .2500e-05 no2m -> no + om 2) .5556e+10 om -> oh + ohm 3) .1000e+10 oh + ohm -> om 4) .1000e+10 oh + no2m -> no2 + ohm 5) .2500e+09 om + no2m -> no2 + ohm + ohm 6) .2500e+10 om + o2 -> o3m 7) .5500e+04 o3m -> o2 + om 8) .1000e+09 no2 + no2 -> n2o4 9) .1300e+04 n2o4 -> no2 + no2 10) .1200e+04 n2o4 -> no2m + no3m 11) .3000e+03 no2 -> x 12) .1000e+09 no2 + x -> no2m + no3m 13) .1000e+09 no2 + no -> n2o3 14) .2000e+04 n2o3 -> no2 + no 15) .2000e+04 n2o3 -> no2m + no2m 16) .1000e-00 x + no -> no2m + no2m ............................................................... 6.340u 0.340s 0:12.26 54% 0+22k 0+2io 0pf+0w (6.34 seconds run time) I can look at the results using select (here I have a file problem.e with only the words no2 no no3m rather than everything to reduce the amount of output) ............................................................... % select no2aq 16 reacions involving 12 species no2m no om oh ohm no2 o2 o3m n2o4 no3m x n2o3 time no2 no no3m 0.0000e+00 0.0000e+00 0.0000e+00 0.0000e+00 6.0000e+02 8.5578e-11 4.5160e-05 2.1075e-05 1.2000e+03 6.7257e-11 6.5957e-05 3.1552e-05 1.8000e+03 5.2981e-11 8.3997e-05 4.0644e-05 2.4000e+03 4.6293e-11 9.9261e-05 4.8192e-05 3.0000e+03 4.1795e-11 1.1373e-04 5.5295e-05 3.6000e+03 3.8639e-11 1.2502e-04 6.0946e-05 ............................................................... Now how do I know that the tolerance values are ok? I could rerun with smaller values and look for an effect. But in this case I was carefull to write reactions conserving all 'n' containing species (not so with o an h, in this sample I make OH- readily (ohm) but not H+ where I should!). If I add up all the 'n's in the result I should get what I started with (0.10 == no2m initial, see problem.p). Here is the problem.e file to extract all the species with 'n's: =============================problem.e=================================== no2m no no2 n2o4 n2o4 no3m x n2o3 n2o3 =============================problem.e=================================== notice n2o4 and n2o3 are in the list twice so they get counted twice! I just pipe the output to Gary Pearlman's dm to add them up! (recall that the first column is time) %extract problem | dm ' x2 + x3 + x4 + x5 + x6 + x7 + x8 + x9 + x10 ' to get: 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 You could also use an awk script % extract problem | awk '{a= $2+$3+$4+$5+$6+$7+$8+$9+$10; print a}' .1 .1 .1 .1 .1 .1 .1 ............................................................... You may have noticed that since I use '-' as a token in the reaction arrow I designate charge with a lowercase m or p appended to the name. Tokens parsed as word delimeters in the mechanism file are: "$,+;:(){}[]" and "->" That is [CH3] + (CH2) -> {stuff} is equivalent to CH3 + CH2 -> stuff In a future release I may remove the "(){}[]" from the token list after I decide what if anything I want to do with automated invocation of the steady state approximation (I was thinking about enclosing variables in {} if they could be approximated by ss). ___________________________________________________________ |Mike Whitbeck | whitbeck@unssun.unr.edu | |Desert Research Inst. | whitbeck@wheeler.wrc.unr.edu | |POB 60220 | whitbeck@sanjuan.UUCP | |RENO, NV 89506 | 702-673-7348 | |__________________________|______________________________| All academics have the potential for being insatiable... but the chemists are the most expensive and insatiable among the expensive and insatiable. - J. Martin in "To Rise Above Principle" From whitbeck@sanjuan.wrc.unr.edu Wed May 15 14:57:18 1991 Received: from equinox.unr.edu by oscsunb.ccl.net (5.64+IDA+kva.1/901126.13) id AA07543; Wed, 15 May 91 14:56:54 -0400 Received: from wheeler.wrc.unr.edu (wrc.unr.edu) by equinox.unr.edu (4.1/1.34) id AA03211; Wed, 15 May 91 11:46:47 PDT Received: from sanjuan.wrc.unr.edu by wheeler.wrc.unr.edu (4.1//06-07-88) id AA18235; Wed, 15 May 91 11:46:22 PDT Received: by sanjuan.wrc.unr.edu (4.1/SMI-4.1) id AA03993; Wed, 15 May 91 11:46:15 PDT Date: Wed, 15 May 91 11:46:15 PDT From: whitbeck@sanjuan.wrc.unr.edu (Mike Whitbeck) Message-Id: <9105151846.AA03993@sanjuan.wrc.unr.edu> To: aslam@sp63.csrd.uiuc.edu, beasockj@lonex.radc.af.mil, bernie@ecr.mu.oz.au, dkent@ucsd.edu, eczam@clan.nottingham.ac.uk, edwards@cae.wisc.edu, emv@poe.aa.ox.com, huang@deakin.oz.au, jkl@ccl.net, jpensar@ra.abo.fi, kenr@peabody.iusb.indiana.edu, klemm@msc.edu, mderksen@sci.kun.nl, nanis@llex.ll.mit.edu, pc@kjemi.unit.no, peri@eng.buffalo.edu, probert%cs@hub.ucsb.edu, rcruz@paul.rutgers.edu, shankar@s1.msi.umn.edu Subject: my error ! Status: R The response to the REACT software has been overwhelming! If I get a little behind in answering individual mail please have patience; I'll get to it! Here are some frequently asked questions: 1) fortran version There was ONCE a fortran version that was a very complete tool for the analysis of chemical kinetic problems. It is NO LONGER AVAILABLE (I lost it!). The computer center is checking an archive tape but there is little hope. I have a VERY LONG listing if there is interest I can make copies available. As time goes by I hope to add all the features that were in the fortran code to REACT. 2) example problem works, extract works but select fails To my chagrin I goofed in the test problem recently mailed. After running the problem I said enter select no2aq to view some results... but I told you to name the test files 'problem' so that should be select problem select then looks for problem.e for a list of species to tabulate vs time. If you entered select no2aq it looked for and failed to find no2aq.e for such a list. 3) port to DOS and DOS like critters I have started the port to the ATARI 1040ST. In the process I discovered a problem. I guess I am too use to the SUN on my desk because I have become lazy about checking for free memory. There are a lot of malloc's in the code so one of the next revisions will test each malloc for success/failure. This will help those who want to port to PC's or other memory stingy platforms. Programmers note: If you want you can replace the call to lsoda with your own integrater such as a Runge-Kutta routine. It will probably run much slower but will be much smaller code. ========== I'll try not to bother you with many more of these posting's. Please let me know if you have any problems etc. Thanks for the interest. ___________________________________________________________ |Mike Whitbeck | whitbeck@unssun.unr.edu | |Desert Research Inst. | whitbeck@wheeler.wrc.unr.edu | |POB 60220 | whitbeck@sanjuan.UUCP | |RENO, NV 89506 | 702-673-7348 | |__________________________|______________________________| All academics have the potential for being insatiable... but the chemists are the most expensive and insatiable among the expensive and insatiable. - J. Martin in "To Rise Above Principle" From whitbeck@sanjuan.wrc.unr.edu Fri May 17 20:53:10 1991 Received: from equinox.unr.edu by oscsunb.ccl.net (5.64+IDA+kva.1/901126.13) id AA23015; Fri, 17 May 91 20:52:11 -0400 Received: from wheeler.wrc.unr.edu (wrc.unr.edu) by equinox.unr.edu (4.1/1.34) id AA19670; Fri, 17 May 91 15:43:39 PDT Received: from sanjuan.wrc.unr.edu by wheeler.wrc.unr.edu (4.1//06-07-88) id AA24945; Fri, 17 May 91 15:43:14 PDT Received: by sanjuan.wrc.unr.edu (4.1/SMI-4.1) id AA05216; Fri, 17 May 91 15:43:09 PDT Date: Fri, 17 May 91 15:43:09 PDT From: whitbeck@sanjuan.wrc.unr.edu (Mike Whitbeck) Message-Id: <9105172243.AA05216@sanjuan.wrc.unr.edu> To: TTENSFELDT@eagle.wesleyan.edu, aslam@sp63.csrd.uiuc.edu, beasockj@lonex.radc.af.mil, bernie@ecr.mu.oz.au, dkent@ucsd.edu, dove@cats.ucsc.edu, eczam@clan.nottingham.ac.uk, edwards@cae.wisc.edu, emv@poe.aa.ox.com, huang@deakin.oz.au, jkl@ccl.net, jpensar@ra.abo.fi, kenr@peabody.iusb.indiana.edu, klemm@msc.edu, mderksen@sci.kun.nl, mgo@inel.gov, mr0183@usma2.usma.edu, nanis@llex.ll.mit.edu, pc@kjemi.unit.no, peri@eng.buffalo.edu, probert%cs@hub.ucsb.edu, rcruz@paul.rutgers.edu, shankar@s1.msi.umn.edu, water@u.washington.edu, yos@tasman.cc.utas.edu.au Subject: lsoda ... more than 500 steps Status: R IF in using REACT you should see a message like lsoda .... more than 500 steps taken....tout ... this is a complaint from the core integrater that it is having a difficult time achieving the desired accuracy. In a future release I will trap on this condition to stop the program. In my experience thus far this condition does not easily cure itself. For now I suggest that when you see this (or any message from lsoda) you kill the job. Take a look at the tolerance values that you specified. Typically they need to be numerically larger (lower tolerance) to correct this problem. === some of you have noticed that in the distribution there is a program called example.c in with the lsoda stuff. I hacked this from netlibs example.f for testing lsoda. If you want to be impressed by lsoda's abilities compile example.c and link in the library made with lsoda cc -o wow example.c -lq -lm -fswitch wow [leave off -fswitch if not supported at your site] The first column in the output is the independent variable (time); note the time steps!