From chemistry-request@ccl.net Fri Jun 20 16:36:43 2003 Received: from sims.csuohio.edu (csu-mail0.csuohio.edu [137.148.5.58]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5KKad5u013171 for ; Fri, 20 Jun 2003 16:36:43 -0400 Received: from dhcp.csuohio.edu (scifac137-148-208-146.dhcp.csuohio.edu [137.148.208.146]) by sims.csuohio.edu (Sun Internet Mail Server sims.4.0.1999.09.28.17.31.p2) with ESMTP id <0HGS0071FS0V42)at(sims.csuohio.edu> for chemistry)at(ccl.net; Fri, 20 Jun 2003 16:38:56 -0400 (EDT) Date: Fri, 20 Jun 2003 16:39:20 -0400 From: "David W. Ball" Subject: cml and svg X-Sender: d.ball)at(popmail.csuohio.edu To: chemistry)at(ccl.net Message-id: <5.1.0.14.0.20030620163715.04c6fb00)at(popmail.csuohio.edu> MIME-version: 1.0 X-Mailer: QUALCOMM Windows Eudora Version 5.1 Content-type: text/plain; format=flowed; charset=us-ascii Content-transfer-encoding: 7BIT Does anyone have any experience in chemical markup language? Are there programs that one can use to draw a molecule and save it as CML? In addition, I'm ultimately wanting to save the molecule as an SVG (scalable vector graphics) image. Again, anyone have experience in that? Will post a summary if replies warrant. Thanks in advance! David ************************************* David W. Ball, Ph.D. Professor of Chemistry President, Cleveland Technical Societies Council Councilor, Cleveland Section of the American Chemical Society Department of Chemistry Cleveland State University Cleveland OH 44115 d.ball)at(csuohio.edu 216-687-2456, fax 216-687-9298 www.csuohio.edu/chemistry/dwb.html Personal web pages: academic.csuohio.edu/ball (CAUTION! Includes lots of baby pictures!) "There is more stupidity than hydrogen in the universe, and it has a longer shelf-life" - Frank Zappa ************************************* From chemistry-request@ccl.net Fri Jun 20 09:48:11 2003 Received: from gaya.if.ufrgs.br ([143.54.2.77]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5KDmA5u002606 for ; Fri, 20 Jun 2003 09:48:11 -0400 Received: from pclap3.if.ufrgs.br (IDENT:perott@pclap3 [143.54.2.124]) by gaya.if.ufrgs.br (8.11.4/S-200206181) with SMTP id h5KDl3g29921 for ; Fri, 20 Jun 2003 10:47:04 -0300 (EST) Content-Type: text/plain; charset="iso-8859-1" From: Claudio Perottoni Reply-To: perott~at~if.ufrgs.br To: CHEMISTRY~at~ccl.net Subject: CCL: hydrogen molecule binding energy Date: Fri, 20 Jun 2003 10:54:35 -0300 X-Mailer: KMail [version 1.2] MIME-Version: 1.0 Message-Id: <03062010543500.00741~at~pclap3.if.ufrgs.br> Content-Transfer-Encoding: 8bit Hi, I am looking for the best experimental values available for the binding energy, interatomic distance and vibrational frequency for the hydrogen molecule. Could someone help me with this? Thanks, Claudio. -- ****************************************************************** Dr. Claudio A. Perottoni Universidade de Caxias do Sul Centro de Cijncias Exatas e Tecnologia Departamento de Fmsica e Qummica Rua Francisco Getzlio Vargas, 1130 95070-560 Caxias do Sul - RS - BRASIL e-mail: caperott~at~ucs.br Tel: +55 54 218 2100 ext. 2449 Associated Researcher Universidade Federal do Rio Grande do Sul Instituto de Fmsica - Lab. de Altas Pressues e Materiais Avangados Av. Bento Gongalves, 9500 CAIXA POSTAL 15051 91501-970 PORTO ALEGRE - RS - BRASIL e-mail: perott~at~if.ufrgs.br PHONE:+55-51-3316-6500 FAX :+55-51-3316-7286 http://www.if.ufrgs.br/~perott/index.html ****************************************************************** From chemistry-request@ccl.net Sun Jun 22 12:26:07 2003 Received: from bfp.cc.purdue.edu (bfp.cc.purdue.edu [128.210.189.30]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5MGQ75u023010 for ; Sun, 22 Jun 2003 12:26:07 -0400 Received: from bfp.cc.purdue.edu (localhost [127.0.0.1]) by bfp.cc.purdue.edu (8.12.9/8.12.9) with ESMTP id h5MGQ5bi005145 for ; Sun, 22 Jun 2003 11:26:05 -0500 (EST) Received: from localhost (bfp@localhost) by bfp.cc.purdue.edu (8.12.9/8.12.9/Submit) with ESMTP id h5MGQ51T005142 for ; Sun, 22 Jun 2003 11:26:05 -0500 (EST) X-Authentication-Warning: bfp.cc.purdue.edu: bfp owned process doing -bs Date: Sun, 22 Jun 2003 11:26:05 -0500 (EST) From: Bryan Putnam X-X-Sender: bfp/at/bfp.cc.purdue.edu To: CCL Subject: g03 and RedHat 7.3 on Pentium Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Greetings, Has anyone had success building Gaussian 03 (g03-B.03) on a Pentium II or III, using RedHat Linux 7.3, and Portland Group compiler 4.0-2 ? I see in the installation notes that Gaussian, Inc. says it will "NOT work" with versions of RedHat earlier than 8.0, but I don't know if that's the issue or not. g03 seems to compile OK, but when the build gets to the point where the executables are linked, for example, pgf77 -mp -O2 -tp p7 -Mreentrant -Mrecursive -Mnosave -Minfo \ -Mneginfo -time -fast -Munroll \ -Mvect=assoc,recog,cachesize:524288,prefetch,sse \ -fastsse -Mscalarsse -g -o g03 ml0.o util.so -lm -lc I get many undefined references of the form, /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_msync@GLIBC_2.0' I've reproduced the entire horrible list of them below. I've tried various things, building statically, dynamically, adding additional libraries, using the Portland version of pgcc, trying various versions of gcc, etc., but nothing seems to work. Any help or suggestions appreciated! Thanks, Bryan -- Bryan F. Putnam http://www-rcd.cc.purdue.edu/~bfp/ Young Hall bfp/at/purdue.edu ITaP Research Computing Services http://www.itap.purdue.edu/rcs/ 151 South Grant Street Voice: 765.496.8225 West Lafayette, IN 47906-3560 Fax: 765.494.0566 /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_msync@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_pwrite@GLIBC_2.1.3' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_system@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_pause@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_lseek@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_connect@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_open64@GLIBC_2.1.3' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_close@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_lseek64@GLIBC_2.1.3' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_accept@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_recvmsg@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_sendto@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_pread@GLIBC_2.1.3' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_pwrite64@GLIBC_2.1.3' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__rpc_thread_destroy@GLIBC_2.2.3' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_tcdrain@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_send@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_write@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__on_exit@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_longjmp@GLIBC_2.1' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_read@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_sigaction@GLIBC_2.2' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_fsync@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_nanosleep@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_fcntl@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_pread64@GLIBC_2.1.3' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_sendmsg@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_recvfrom@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_siglongjmp@GLIBC_2.1' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_open@GLIBC_2.0' /usr/pgi/linux86/lib/libpgthread.so: undefined reference to `__libc_recv@GLIBC_2.0' From chemistry-request@ccl.net Sun Jun 22 08:22:01 2003 Received: from web15214.mail.bjs.yahoo.com (web15214.mail.bjs.yahoo.com [202.3.77.144]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h5MCLx5u020190 for ; Sun, 22 Jun 2003 08:22:00 -0400 Message-ID: <20030622122158.77636.qmail$at$web15214.mail.bjs.yahoo.com> Received: from [218.30.18.116] by web15214.mail.bjs.yahoo.com via HTTP; Sun, 22 Jun 2003 20:21:58 CST Date: Sun, 22 Jun 2003 20:21:58 +0800 (CST) From: =?gb2312?q?Jinsong=20Zhao?= Subject: CCL: AIMPAC running with gcc 3.2 or higher To: CCL MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit Dear all, Does anyone here have a version of AIMPAC (source code) that could be run under RH8.0 with gcc 3.2 or higher? I have gotten very kindly help from Dr. Jeffrey D. Saxe and Dr. Julia Metzker concerning AIMPAC codes. There are no any errors when I compiled them, but when I run it, I got "segmentation fault". I was told it may due to I have a higher version of gcc. Does anyone here have the similar experience, and what's your solutions? Any help will be very appreciated. Thanks in advance. Regards, Jinsong _________________________________________________________ Do You Yahoo!? MxA55DZ9JM#:UfGi;9JG7EW]#? http://cn.rd.yahoo.com/mail_cn/tag/?http://cn.surveys.yahoo.com/netlove From chemistry-request@ccl.net Sun Jun 22 07:20:27 2003 Received: from wn1.sci.kun.nl (wn1.sci.kun.nl [131.174.8.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5MBKQ5u019579 for ; Sun, 22 Jun 2003 07:20:26 -0400 Received: from zeef.sci.kun.nl by wn1.sci.kun.nl via zeef.sci.kun.nl [131.174.8.13] with ESMTP id h5MBKPpT007282 (8.12.9/3.58); Sun, 22 Jun 2003 13:20:25 +0200 (MEST) Received: by zeef.sci.kun.nl via www@localhost id h5MBKP5a006426 (8.12.9/1.3); Sun, 22 Jun 2003 13:20:25 +0200 (MEST) X-Authentication-Warning: zeef.sci.kun.nl: www set sender to egonw$at$sci.kun.nl using -f Received: from f8117.upc-f.chello.nl (f8117.upc-f.chello.nl [80.56.8.117]) by webmail.sci.kun.nl (IMP) with HTTP for ; Sun, 22 Jun 2003 13:20:25 +0200 Message-ID: <1056280825.3ef590f930eea$at$webmail.sci.kun.nl> Date: Sun, 22 Jun 2003 13:20:25 +0200 From: egonw$at$sci.kun.nl To: "David W. Ball" Cc: chemistry$at$ccl.net Subject: Re: CCL:cml and svg References: <5.1.0.14.0.20030620163715.04c6fb00$at$popmail.csuohio.edu> In-Reply-To: <5.1.0.14.0.20030620163715.04c6fb00$at$popmail.csuohio.edu> MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.1 X-Originating-IP: 80.56.8.117 Quoting "David W. Ball" : > Does anyone have any experience in chemical markup language? Are there > programs that one can use to draw a molecule and save it as CML? In > addition, I'm ultimately wanting to save the molecule as an SVG (scalable > vector graphics) image. Again, anyone have experience in that? JChemPaint.sourceforge.net can do this (version 1.9.x) both. It's written in Java and will run on any system with a J2SE 1.4.1 Java system. In addition, it is OpenSource, so that you can customize it for specific needs. Or, you can post your feature requests which are often implemented in a next release. kind regards, Egon Willighagen