From hobina@dmu.ac.uk Sat Jun 15 09:54:19 1996 Received: from macondo.dmu.ac.uk for hobina@dmu.ac.uk by www.ccl.net (8.7.5/950822.1) id JAA14113; Sat, 15 Jun 1996 09:00:39 -0400 (EDT) Received: from brains.eng.dmu.ac.uk (brains.eng.dmu.ac.uk [146.227.22.1]) by macondo.dmu.ac.uk (8.6.12/8.6.11) with ESMTP id OAA07240; Sat, 15 Jun 1996 14:04:45 +0100 Received: from shore.dmu.ac.uk (shore [146.227.22.9]) by brains.eng.dmu.ac.uk (8.6.12/8.6.12) with ESMTP id NAA22128; Sat, 15 Jun 1996 13:59:50 +0100 Received: from shore by shore.dmu.ac.uk (SMI-8.6/SMI-SVR4) id OAA20545; Sat, 15 Jun 1996 14:00:44 +0100 Sender: hobina@dmu.ac.uk Message-ID: <31C2B3FC.6C5E@dmu.ac.uk> Date: Sat, 15 Jun 1996 14:00:44 +0100 From: Hobina Rajakaruna X-Mailer: Mozilla 2.0 (X11; I; SunOS 5.5 sun4m) MIME-Version: 1.0 To: chemistry@www.ccl.net CC: hobina@dmu.ac.uk Subject: equation to calculate viscosity Of a liquid-gas mixture X-URL: http://www.ccl.net/ccl/welcome.html#3 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello Everybody; I am looking for a method to calculate viscosity of a gas-liquid mixture. i.e. a mixture containing a samll amount of liquid fuel, vapour of the same fuel and air. If there is a method please e-mail the details or just inform me from where to obtain the info. Thanks in advance; ************************************** * Hobina Rajakaruna * * Research Student * * De Montfort University * * Dept. of Mech. and Manf. Eng. * * Queens Building * * Leicester u.k * * E-mail: hobina@dmu.ac.uk * ************************************** From vam@kon.icp.ac.ru Sat Jun 15 11:54:17 1996 Received: from kon.icp.ac.ru for vam@kon.icp.ac.ru by www.ccl.net (8.7.5/950822.1) id LAA14702; Sat, 15 Jun 1996 11:47:47 -0400 (EDT) Received: (root@localhost) by kon.icp.ac.ru (8.6.12/8.6.5) id TAA02866 for chemistry@www.ccl.net; Sat, 15 Jun 1996 19:39:30 +0400 Date: Sat, 15 Jun 1996 19:39:30 +0400 From: Victor Anisimov Message-Id: <199606151539.TAA02866@kon.icp.ac.ru> To: chemistry@www.ccl.net Subject: Summary on MOPAC memory requirement Dear netters, Some weeks ago I posted a message with a problem I've encountered. My letter was: =Does someone have experience compiling MOPAC-93 for big =dimensions, 100x100, 200x200 heavy and light atoms, for =example. How much virtual space they will reqire? = =I'm getting "can't allocate memory" message on FreeBSD =with 400Mbyte of virtual space on hard disk for 100x100 =one. = =What is this, low virtual space or Fortran compiler error, =does someone know? = =Thanks for any idea. =Victor. ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ I'm very thankful to everyone who responced Pedro A M Vazquez Georg Ostertag David E. Bernholdt A J Turner Rainer Koch Serge Pachkovsky Mao My summary consist of three parts, first one have deal with virtual memory size required by MOPAC, compilled with fixed number of heavy and light atoms, second and third parts are concerned with resolving of the problem I had and will spetially interested only those who use MOPAC on PC with FreeBSD UNIX or considering to use FreeBSD may be in future. Third part gives a FreeBSD user a very usefull advice how increase your swap capabilities without reformatting your hard disk partitions. >>>>>>>>>>>>>>>>>>>>>>>>>>> 1-st part >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Here is a summary table of virtual memory requirements (in Mb) for MOPAC with different number of Heavy and Light atoms on some platforms: 30x30 50x50 60x60 70x70 80x80 90x90 100x100 150x150 200x200 ----------------------------------------------------------------------- DEC Alpha 27 39 - 83 - 127 - - - IBM RS/6000 - - - - 76 - 130 243 - SGI R8000 - - - - 65 - - 208 - FreeBSD 16 - 37 - - - - - - All the values I get from respondents, whom I'm very appreciated. Unfortunately I don't know author's MOPAC configurations, so to complete the picture and eliminate possible inconsistences I report virtual memory requirements of MOPAC-93 tested (except 200x200, sorry for lack of resources) and compilled on my i486/FreeBSD with 8Mb RAM FreeBSD* 13 30 - 75 96 120 147 320 578 These space requirements were derived with: Ford's ESP Yes Merz's ESP Yes Green Function corr. to IP No COSMO Yes Polarizability Yes MECI No CI No Pulay's SCF DIIS converger Yes Comparing the results from the table I have to agree with my respondents, that the size of mopac virtual memory requirements shows minor dependence from Operational System and hardware. Of course, those data can be used only as a rough guide if one will use different configurations, especially with CI or without COSMO or ESP, nevetheless they can be surtanly useful for evaluation goals. As an interesting result of capabilities to run big configured MOPAC on FreeBSD you can see successful test of 150x150 job on PC with only 8Mb RAM and with sufficient swap, of course. So you see there is no obligatory requirements to fit job in RAM to make a smooth execution. Testing molecule had 20 atoms but because MOPAC does static memory allocation I suppose it is sufficient test. One reason of such success could be advanced memory allocation kernel support from FreeBSD 2.1.0 that used instead of standart buggy malloc library. If it's right it will need new tests with big molecule to be true. >>>>>>>>>>>>>>>>>>>>>>>>>>> 2-nd part >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Second part is concerned with solving a problem I had. Many thanks to Gary Palmer , Joe Greco and espetially to David Greenman , who is a Core-team/Principal Architect of The FreeBSD Project. As a short resume I was simply out of resources. Gary Palmer explained that there is a per-process limit in FreeBSD to prevent a single process creating denial-of-service type attacks. Those limits can be easy unlocked and to do it he recommends Depending on your shell, try: csh/tcsh: limit datasize unlimited limit stacksize unlimited limit memoryuse unlimited sh/bash: ulimit -d unlimited ulimit -s unlimited ulimit -v unlimited David Greenman recommended me to look on /sys/i386/include/vmparam.h where default limits are located. There is a reason don't rely on "limit" command at all and to edit your vmparam.h and recompile a kernel. You can see that vmparam has not only default limit values but their maximum possible values too. I experienced that you can not get unlimited resources via "limit" command, the maximum you can have is described if vmparam.h. So I recommend you to edit your vmparam.h and set new values for some parameters. Here you see defaults sufficient to run MOPAC 200x200 and not only on your FreeBSD 2.1.0. * from: @(#)vmparam.h 5.9 (Berkeley) 5/12/91 /* * Virtual memory related constants, all in bytes */ #define MAXTSIZ (64UL*1024*1024) /* max text size */ #ifndef DFLDSIZ #define DFLDSIZ (512UL*1024*1024) /* initial data size limit */ #endif #ifndef MAXDSIZ #define MAXDSIZ (512UL*1024*1024) /* max data size */ #endif #ifndef DFLSSIZ #define DFLSSIZ (64UL*1024*1024) /* initial stack size limit */ #endif #ifndef MAXSSIZ #define MAXSSIZ (256UL*1024*1024) /* max stack size */ #endif #ifndef SGROWSIZ #define SGROWSIZ (128UL*1024) /* amount to grow stack */ #endif >>>>>>>>>>>>>>>>>>>>>>>>>>> 3-rd part >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Pedro A M Vazquez recommend to use very nice FreeBSD UNIX feature to add specially prepared continous file as swap device, that can increase swap without reformatting disk. It is really very powerful capability for quick management of swap space. It requires kernel support for /dev/vn* pseudo devices, to do it simply add next line to kernel config on desired number of swap files (2 swap files, for example) and recompile the kernel: pseudo-device vn 2 After rebooting with new kernel type the commands cd /dev; MAKEDEV vn0 vn1 dd if=/dev/zero of=/home/swap bs=1k count=100k vnconfig -c /dev/vn0c /home/swap swapon /dev/vn0c You are adding so additional 100Kb of swap space. Now swapinfo will report something like this: Device 1K-blocks Used Avail Capacity Type /dev/sd0s1b 51200 4504 46632 9% Interleaved /dev/vn0c 102400 48 102288 0% Interleaved Total 153472 4552 148920 3% Thanks if you could read this short ;-) summary. I'd like to expect it will be useful for someone. Victor. ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ *** Institute of Chemical Physics in Chernogolovka *** * Russian Academy of Sciences * * Dr. Victor M. Anisimov * * senior chemist and head of Networking & IT Dept. * *** vam@kon.icp.ac.ru *** ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ From katagiri@nightmare.qub.ac.uk Sat Jun 15 17:54:21 1996 Received: from Nzambi.qub.ac.uk for katagiri@nightmare.qub.ac.uk by www.ccl.net (8.7.5/950822.1) id RAA16490; Sat, 15 Jun 1996 17:03:43 -0400 (EDT) Received: from grumpy (actually host grumpy.qub.ac.uk) by Nzambi.qub.ac.uk with SMTP (PP); Sat, 15 Jun 1996 21:04:00 +0000 Received: from nightmare.qub.ac.uk ([143.117.7.36]) by grumpy (4.1/SMI-4.1) id AA12453; Sat, 15 Jun 96 22:04:41 BST Received: by nightmare.qub.ac.uk (950413.SGI.8.6.12/931108.SGI.AUTO.ANONFTP) for chemistry@www.ccl.net id WAA08659; Sat, 15 Jun 1996 22:02:58 +0100 Date: Sat, 15 Jun 1996 22:02:58 +0100 From: katagiri@nightmare.qub.ac.uk (katagiri) Message-Id: <199606152102.WAA08659@nightmare.qub.ac.uk> To: chemistry@www.ccl.net Subject: AFM Hi there, I would like to simulate atomic force microscopy. During the simulation, I'd like to keep the force which is perpendicular to the surface constant. Does anyone know any good algorithm or reference? Any information will be appreciated. regards, Masa Katagiri ----------------------------------------------------------------------- Masa Katagiri Queen's University of Belfast Atomistic Simulation Group http://titus.phy.qub.ac.uk School of Mathematics and Physics Tel:+44 1232 245133 ext.3528 Belfast BT7 1NN Fax:+44 1232 241958 Northern Ireland E-mail:katagiri@nightmare.qub.ac.uk -----------------------------------------------------------------------