From chemistry-request@ccl.net Fri Jun 3 13:43:29 2005 Received: from mxsf02.cluster1.charter.net (mxsf02.cluster1.charter.net [209.225.28.202]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j53HhLww020805 for ; Fri, 3 Jun 2005 13:43:21 -0400 Received: from mxip11a.cluster1.charter.net (mxip11a.cluster1.charter.net [209.225.28.141]) by mxsf02.cluster1.charter.net (8.12.11/8.12.11) with ESMTP id j53HhJhg000594 for ; Fri, 3 Jun 2005 13:43:20 -0400 Received: from 24-247-172-122.dhcp.bycy.mi.charter.com (HELO inspiron9100) (24.247.172.122) by mxip11a.cluster1.charter.net with ESMTP; 03 Jun 2005 13:43:20 -0400 Message-Id: <4403cd$12a7kc9=at=mxip11a.cluster1.charter.net> X-IronPort-AV: i="3.93,166,1115006400"; d="scan'208"; a="1151586697:sNHT19675636" From: "Jim Kress" To: "'Gustavo, , Mercier'" , Subject: RE: W:gOpenMol and Gamess MO plotting Date: Fri, 3 Jun 2005 13:43:16 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Mailer: Microsoft Office Outlook, Build 11.0.6353 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 Thread-Index: AcVoSrJoDoR4/iAmRxOXc0+rLTioKAAGLOVw In-Reply-To: <200506030511.j535B9ba021246=at=server.ccl.net> X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Use: Chemcraft (www.chemcraftprog.com) It will compute and plot orbitals from the GAMESS output (log) file and will (optionally) generate a cube file Molekel will also import GAMESS log files and compute and plot orbitals from that log file. Jim > -----Original Message----- > From: Gustavo, , Mercier [mailto:gamercier=at=yahoo.com] > Sent: Friday, June 03, 2005 1:11 AM > To: chemistry=at=ccl.net > Subject: CCL:W:gOpenMol and Gamess MO plotting > > Hi! > > I am interested in plotting MO's computed using GAMESS-US. > I've tried several programs with limited succes (molden, > molekel, orbdraw) and now I am trying gOpenMol. > > Looking at the manual etc I need to generate a cube file that > will be converted to the plt format read by gOpenMol using a > plugin. However, it is not clear to me how to generate the > cube file using GAMESS-US. > > GAMESS-US can compute a variety of properties, ie. electron > density, electrostatic potential, etc. but I don't see an > option for MO's. Moreover, these are computed either a set of > user defined points (option POINTS), in a plane (option > GRID), and as multiples of the van der wall surface (option > PDC). There is no option for a 3D cube like gaussian's cube. > > Obviously, you can take the GRID or POINTS options and > generate a cube from these, but then you have to find out the > format expected by the plugin, i.e. what axis run fastest, etc. > > Any one willing to shed some light on how to proceed before I > engage in writing code to do some of this stuff? > > 1) How do you generate the 3D cube using GAMESS-US? > 2) Is it possible to plot GAMESS-US MO's using gOpenMoL? I do > have the MO's from running a SCF run, but I would like to > know if it is possible to "coax" GAMESS-US into computing the > cube data needed by gOpenMol. > > Thanks! > G. Mercier > gamercier=at=yahoo.com > gustavom=at=baylorhealth.edu > > > -= This is automatically added to each message by the mailing > script =- To send e-mail to subscribers of CCL put the string > CCL: on your Subject: line and send your message to: > CHEMISTRY=at=ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST=at=ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to spam > filters, please use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > > > > From chemistry-request@ccl.net Fri Jun 3 13:45:25 2005 Received: from mxsf20.cluster1.charter.net (mxsf20.cluster1.charter.net [209.225.28.220]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j53HjKKq020933 for ; Fri, 3 Jun 2005 13:45:21 -0400 Received: from mxip19a.cluster1.charter.net (mxip19a.cluster1.charter.net [209.225.28.149]) by mxsf20.cluster1.charter.net (8.12.11/8.12.11) with ESMTP id j53HjJXH018611 for ; Fri, 3 Jun 2005 13:45:19 -0400 Received: from 24-247-172-122.dhcp.bycy.mi.charter.com (HELO inspiron9100) (24.247.172.122) by mxip19a.cluster1.charter.net with ESMTP; 03 Jun 2005 13:45:19 -0400 Message-Id: <4404qh$1112fh6=at=mxip19a.cluster1.charter.net> X-IronPort-AV: i="3.93,166,1115006400"; d="scan'208"; a="1108426278:sNHT19374388" From: "Jim Kress" To: "'Gustavo, , Mercier'" , Subject: RE: W:gOpenMol and Gamess MO plotting Date: Fri, 3 Jun 2005 13:45:16 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Mailer: Microsoft Office Outlook, Build 11.0.6353 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 Thread-Index: AcVoSrJoDoR4/iAmRxOXc0+rLTioKAAGUCvA In-Reply-To: <200506030511.j535B9ba021246=at=server.ccl.net> X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Also, PCGAMESS will generate cube files. Jim > -----Original Message----- > From: Gustavo, , Mercier [mailto:gamercier=at=yahoo.com] > Sent: Friday, June 03, 2005 1:11 AM > To: chemistry=at=ccl.net > Subject: CCL:W:gOpenMol and Gamess MO plotting > > Hi! > > I am interested in plotting MO's computed using GAMESS-US. > I've tried several programs with limited succes (molden, > molekel, orbdraw) and now I am trying gOpenMol. > > Looking at the manual etc I need to generate a cube file that > will be converted to the plt format read by gOpenMol using a > plugin. However, it is not clear to me how to generate the > cube file using GAMESS-US. > > GAMESS-US can compute a variety of properties, ie. electron > density, electrostatic potential, etc. but I don't see an > option for MO's. Moreover, these are computed either a set of > user defined points (option POINTS), in a plane (option > GRID), and as multiples of the van der wall surface (option > PDC). There is no option for a 3D cube like gaussian's cube. > > Obviously, you can take the GRID or POINTS options and > generate a cube from these, but then you have to find out the > format expected by the plugin, i.e. what axis run fastest, etc. > > Any one willing to shed some light on how to proceed before I > engage in writing code to do some of this stuff? > > 1) How do you generate the 3D cube using GAMESS-US? > 2) Is it possible to plot GAMESS-US MO's using gOpenMoL? I do > have the MO's from running a SCF run, but I would like to > know if it is possible to "coax" GAMESS-US into computing the > cube data needed by gOpenMol. > > Thanks! > G. Mercier > gamercier=at=yahoo.com > gustavom=at=baylorhealth.edu > > > -= This is automatically added to each message by the mailing > script =- To send e-mail to subscribers of CCL put the string > CCL: on your Subject: line and send your message to: > CHEMISTRY=at=ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST=at=ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to spam > filters, please use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > > > > From chemistry-request@ccl.net Fri Jun 3 17:50:22 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j53LoLNC032047 for ; Fri, 3 Jun 2005 17:50:21 -0400 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j53LoLF7032046 for chemistry=at=ccl.net; Fri, 3 Jun 2005 17:50:21 -0400 Date: Fri, 3 Jun 2005 17:50:21 -0400 Message-Id: <200506032150.j53LoLF7032046=at=server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request=at=ccl.net using -f From: "Yiming, , Zhang" To: chemistry=at=ccl.net X-Web-Message-Number: 050603174948-31992 Subject: W:Gaussian 03 compilation on RH Xeon cluster HELP X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net We compiled Gaussian 03 source code using pgf77 on our Xeon Cluster(Red hat linux 8.0). The compilation (bldg03 with PGF77) ends succesfully, and when we run a single processor job, the output ends here: Leave Link 1 at Fri Jun 3 12:59:38 2005, MaxMem= 0 cpu: 0.1 (Enter /home/shemep//g03/l101.exe) There is no error message I am wondering if anybody met such situation before. Any suggestion will be appreciated. Thanks, YZ From chemistry-request@ccl.net Sat Jun 4 03:59:23 2005 Received: from web26808.mail.ukl.yahoo.com (web26808.mail.ukl.yahoo.com [217.146.176.84]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j547xJGd023502 for ; Sat, 4 Jun 2005 03:59:19 -0400 Received: (qmail 77657 invoked by uid 60001); 4 Jun 2005 07:59:17 -0000 Message-ID: <20050604075917.77655.qmail ## web26808.mail.ukl.yahoo.com> Received: from [213.140.56.83] by web26808.mail.ukl.yahoo.com via HTTP; Sat, 04 Jun 2005 09:59:17 CEST Date: Sat, 4 Jun 2005 09:59:17 +0200 (CEST) From: may abdelghani Subject: RE: CCL:Radical Dimerization To: Wai-To Chan Cc: ccl In-Reply-To: <200506010706.j5176qZ13341 ## curl.gkcl.yorku.ca> MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Hello,CCLers (Mr Wai-To Chan) Thank you very much Dr Wai-To Chan, for your reply (help) on my message (problem), What is the difference between the tow The problem in other world; what is the factors that difficult (or help) the polymer formation. > When you said 'dimerization is not *acceptable*' > did you mean that > dimerization is not desired for the purpose of the > synthesis of a > polymer or did you mean you cannot build a polymer > because the > radical monomers fail to dimerize? What is the difference between the tow ? or what is the factors that difficult (or help) the polymer formation. best regards may abdelghani _____________________________________________________________________________ Dicouvrez le nouveau Yahoo! Mail : 1 Go d'espace de stockage pour vos mails, photos et vidios ! Criez votre Yahoo! Mail sur http://fr.mail.yahoo.com From chemistry-request@ccl.net Sat Jun 4 17:17:51 2005 Received: from web53708.mail.yahoo.com (web53708.mail.yahoo.com [206.190.37.29]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j54LHloq021694 for ; Sat, 4 Jun 2005 17:17:47 -0400 Received: (qmail 86771 invoked by uid 60001); 4 Jun 2005 20:17:46 -0000 DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; h=Message-ID:Received:Date:From:Subject:To:MIME-Version:Content-Type:Content-Transfer-Encoding; b=w11q5396/EMbJXJujE/rrGyZ31SheeOSCtp+Gzj1bVtGOoqbkTSmFHeMsueumwTFiGmJ1+xCSFDdOYGDN8pzW+jmNdNO/ImyCrFXWiZX8mOw9YSAoP1pJEYzsDBv2yT6UI0LFQmhsYatQPrHw7Jayu82Iy+1yAmjz1VlMxbvcUM= ; Message-ID: <20050604201746.86769.qmail ^^^ web53708.mail.yahoo.com> Received: from [130.18.145.140] by web53708.mail.yahoo.com via HTTP; Sat, 04 Jun 2005 13:17:46 PDT Date: Sat, 4 Jun 2005 13:17:46 -0700 (PDT) From: Delwar Hossain Subject: How to plot/calculate Density of State (DOS)? To: chemistry ^^^ ccl.net MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-117557910-1117916266=:86740" Content-Transfer-Encoding: 8bit X-Spam-Status: No, score=2.3 required=5.0 tests=DNS_FROM_RFC_ABUSE, DNS_FROM_RFC_POST,FROM_ENDS_IN_NUMS,HTML_30_40,HTML_MESSAGE autolearn=no version=3.0.3 X-Spam-Level: ** X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net --0-117557910-1117916266=:86740 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear Respected Colleagues, I am trying to calculate/plot density of state (DOS) of metal cluster. I use Guassian 03 and '98. I would be grateful if anyone instruct me in detail how to plot DOS. Thank you . Sincerely yours, Delwar Hossain Hand Lab. Mississippi State University --------------------------------- Discover Yahoo! Get on-the-go sports scores, stock quotes, news & more. Check it out! --0-117557910-1117916266=:86740 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Dear Respected Colleagues,
I am trying to calculate/plot density of state (DOS) of metal cluster. I use Guassian 03 and '98.
I would be grateful if anyone  instruct me in detail how to plot DOS.
Thank you .
Sincerely yours,
Delwar Hossain
Hand Lab.
Mississippi State University

Discover Yahoo!
Get on-the-go sports scores, stock quotes, news & more. Check it out! --0-117557910-1117916266=:86740--