From owner-chemistry@ccl.net Fri Jun 13 01:20:01 2008 From: "Jerome Baffreau jerome.baffreau]*[umontreal.ca" To: CCL Subject: CCL:G: LanL2DZ for calculations on Ru complexes Message-Id: <-37148-080613011826-415-GepvH3PhACea5ij6Q6H3mQ^_^server.ccl.net> X-Original-From: "Jerome Baffreau" Date: Fri, 13 Jun 2008 01:18:22 -0400 Sent to CCL by: "Jerome Baffreau" [jerome.baffreau-,-umontreal.ca] > "Jerome Baffreau jerome.baffreau{:}umontreal.ca" wrote: > > Sent to CCL by: "Jerome Baffreau" [jerome.baffreau!^!umontreal.ca] > Hi all, > > I want to do calculations on Ru complexes with DFT using LanL2DZ for Ru and 6-31G(2d,p) for all the other atoms, but I get this error message(G03W): > > ############### > Leave Link 202 at Thu Jun 12 09:56:39 2008, MaxMem= 104857600 cpu: 0.0 > (Enter C:\G03W\l301.exe) > General basis read from cards: (5D, 7F) > WANTED AN INTEGER AS INPUT. > FOUND A FLOATING POINT NUMBER AS INPUT. > 1 3 1.5 2 1.5 38 1.0 > ############### > > Here is my route: > > ############### > %chk=job name > %mem=800MB > %nproc=2 > %rwf=piece1,490mw,piece2,490mw,-1 > #p b3lyp genecp opt > > 2 1 > atoms specs > > Sorry the end of my original message was missing, here is the end: C N H 0 6-31G(2d,p) **** Ru 0 LANL2DZ **** Ru 0 LANL2DZ I'm not confortable with this kind of calculations so it may be a very simple mistake... Thanks for your help. Jerome Baffreau, PhD University of Montreal, QC, Canada From owner-chemistry@ccl.net Fri Jun 13 02:11:00 2008 From: "Babarao Ravichandar ravichandar%%nus.edu.sg" To: CCL Subject: CCL:G: LanL2DZ for calculations on Ru complexes Message-Id: <-37149-080613020812-31053-13p+nQGW1Lzsg+fSkLjSBQ|-|server.ccl.net> X-Original-From: "Babarao Ravichandar" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Fri, 13 Jun 2008 14:07:55 +0800 MIME-Version: 1.0 Sent to CCL by: "Babarao Ravichandar" [ravichandar^nus.edu.sg] Hi Check the space at the end of the file, there should be two blank file after=20 C N H 0 6-31G(2d,p) **** Ru 0 LANL2DZ **** Ru 0 LANL2DZ -----Original Message----- > From: owner-chemistry]^[ccl.net [mailto:owner-chemistry]^[ccl.net]=20 Sent: Friday, June 13, 2008 1:18 PM To: Babarao Ravichandar Subject: CCL:G: LanL2DZ for calculations on Ru complexes Sent to CCL by: "Jerome Baffreau" [jerome.baffreau-,-umontreal.ca] > "Jerome Baffreau jerome.baffreau{:}umontreal.ca" wrote: >=20 > Sent to CCL by: "Jerome Baffreau" [jerome.baffreau!^!umontreal.ca] Hi > all, >=20 > I want to do calculations on Ru complexes with DFT using LanL2DZ for Ru and 6-31G(2d,p) for all the other atoms, but I get this error message(G03W): >=20 > ############### > Leave Link 202 at Thu Jun 12 09:56:39 2008, MaxMem=3D 104857600 cpu: 0.0 > (Enter C:\G03W\l301.exe) > General basis read from cards: (5D, 7F) > WANTED AN INTEGER AS INPUT. > FOUND A FLOATING POINT NUMBER AS INPUT. > 1 3 1.5 2 1.5 38 1.0 =20 > ############### >=20 > Here is my route: >=20 > ############### > %chk=3Djob name > %mem=3D800MB > %nproc=3D2 > %rwf=3Dpiece1,490mw,piece2,490mw,-1 > #p b3lyp genecp opt >=20 > 2 1 > atoms specs >=20 >=20 Sorry the end of my original message was missing, here is the end: C N H 0 6-31G(2d,p) **** Ru 0 LANL2DZ **** Ru 0 LANL2DZ I'm not confortable with this kind of calculations so it may be a very simple mistake... Thanks for your help. Jerome Baffreau, PhD University of Montreal, QC, Canada -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Jun 13 03:09:01 2008 From: "Vlad vvv900__anusf.anu.edu.au" To: CCL Subject: CCL:G: Java Molecular Editor 08 Released Message-Id: <-37150-080613030313-28367-BZ3ZruyQLjACxJ1vDIoyRw * server.ccl.net> X-Original-From: Vlad Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=WINDOWS-1251; format=flowed Date: Fri, 13 Jun 2008 15:26:01 +1000 MIME-Version: 1.0 Sent to CCL by: Vlad [vvv900- -anusf.anu.edu.au] Dear CCLers, We are pleased to announce the release of Java Molecular Editor (JMolEditor) 08. Java Molecular Editor (JMolEditor) is a program for displaying, analyzing, editing, and converting molecular systems. JMolEditor is written in Java, so it is a cross-platform application. It has intuitive interface and inbuilt help system. JMolEditor can be used also for the analysis to display molecular orbitals, electron densities and electrostatic potentials from the Gaussian. A full description of JMolEditor and its documentation are available via the JMolEditor WWW home page: http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.html System requirements: Java Virtual Machine (JVM) >= 1.5 and Java3d >= 1.4. Key features in JMolEditor include: - Molecular builder/editor - - (http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/manual/editing-molecule/index.html) - Ability to read and visualize popular Computational Chemistry formats - - (http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/input-files.html): - - Gaussian (input, output, cube, fragment, trajectory) - - ADF (input, output) - - Gamess (input and output) - - Mopac (input and output) - - QChem (input and output) - - VASP (input, vasprun.xml) - - Amber (prmtop files) - - Gromacs (gro files) - - GULP (input) - - Siesta input (in development) - - PDB, Tripos Mol2, MDL molfile, XMol XYZ - Output - - Gaussian input - - XMol XYZ - - Tripos Mol2 - - PDB - - Povray - Visualization of the OOGL off files - Ability to load and visualize Computational Chemistry files from SFTP server - Visualization of molecular orbitals, electron densities, electrostatic potentials and mapped surfaces from the Gaussian Cube files - Interactive Charting - - (http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/manual/charting/index.html) - - ability to display plots of energy and other quantities from calculations that produce multiple structures among their results - - ability to interact with a plot to view corresponding structure - - supported formats: gaussian and ADF output, Vasprun.xml files - Vibrational Analysis - - http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/manual/frequencies/index.html - - ability to display various spectra (Infrared, Raman, etc.) based on information from Gaussian frequency calculation - - ability to animate vibrations for selected frequency - - ability to show displacement vectors for selected frequency - Tools - - In-built SFTP browser (http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/manual/sftp-browser/index.html) - Tutorials - - Gaussian (http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/manual/tutorials/index.html) Future plans include support of periodic/crystal structures, writing documentation and tutorials, interfaces to additional computational packages, etc. JMolEditor is also a free, open source, cross-platform Computational Chemistry Toolkit which could be extended and/or used in other applications. Source code is provided under the Apache2, GPL, and LGPL licenses (http://sf.anu.edu.au/~vvv900/cct/api/index.html). So, the developers who like challenge and aggressive programming are welcome to contribute. Regards, Vlad =============== Dr. Vladislav Vasilyev Supercomputer Facility The Australian National University Canberra, ACT, 0200, Australia From owner-chemistry@ccl.net Fri Jun 13 17:13:00 2008 From: "shentan chen modigger~!~gmail.com" To: CCL Subject: CCL:G: LanL2DZ for calculations on Ru complexes Message-Id: <-37151-080613171029-20726-BCOM5bCjPFQzp5iPbhqvmQ{}server.ccl.net> X-Original-From: shentan chen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 13 Jun 2008 16:07:37 -0400 MIME-Version: 1.0 Sent to CCL by: shentan chen [modigger++gmail.com] It seems that the you may have problem with the input file. Check for space or blank line needed. Jerome Baffreau jerome.baffreau]*[umontreal.ca wrote: > Sent to CCL by: "Jerome Baffreau" [jerome.baffreau-,-umontreal.ca] > > >> "Jerome Baffreau jerome.baffreau{:}umontreal.ca" wrote: >> >> Sent to CCL by: "Jerome Baffreau" [jerome.baffreau!^!umontreal.ca] >> Hi all, >> >> I want to do calculations on Ru complexes with DFT using LanL2DZ for Ru and 6-31G(2d,p) for all the other atoms, but I get this error message(G03W): >> >> ############### >> Leave Link 202 at Thu Jun 12 09:56:39 2008, MaxMem= 104857600 cpu: 0.0 >> (Enter C:\G03W\l301.exe) >> General basis read from cards: (5D, 7F) >> WANTED AN INTEGER AS INPUT. >> FOUND A FLOATING POINT NUMBER AS INPUT. >> 1 3 1.5 2 1.5 38 1.0 >> ############### >> >> Here is my route: >> >> ############### >> %chk=job name >> %mem=800MB >> %nproc=2 >> %rwf=piece1,490mw,piece2,490mw,-1 >> #p b3lyp genecp opt >> >> 2 1 >> atoms specs >> >> >> > Sorry the end of my original message was missing, here is the end: > > C N H 0 > 6-31G(2d,p) > **** > Ru 0 > LANL2DZ > **** > Ru 0 > LANL2DZ > > I'm not confortable with this kind of calculations so it may be a very simple mistake... Thanks for your help. > > Jerome Baffreau, PhD > University of Montreal, QC, Canada> > > From owner-chemistry@ccl.net Fri Jun 13 20:56:00 2008 From: "Brian Salter-Duke brian.james.duke[A]gmail.com" To: CCL Subject: CCL:G: LanL2DZ for calculations on Ru complexes Message-Id: <-37152-080613202858-11046-akW1JZ8e2cyKTaQm3Aeieg|*|server.ccl.net> X-Original-From: Brian Salter-Duke Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sat, 14 Jun 2008 09:32:30 +1000 MIME-Version: 1.0 Sent to CCL by: Brian Salter-Duke [brian.james.duke__gmail.com] Blank lines are needed as shown below:- Babarao Ravichandar ravichandar%%nus.edu.sg wrote: > Sent to CCL by: "Babarao Ravichandar" [ravichandar^nus.edu.sg] > > Hi > Check the space at the end of the file, there should be two blank file > after > <-- and only one after atoms > C N H 0 > 6-31G(2d,p) > **** > Ru 0 > LANL2DZ > **** <-- one and only one here > Ru 0 > LANL2DZ <-- need **** <-- then at least one blank line > > -----Original Message----- >> From: owner-chemistry,+,ccl.net [mailto:owner-chemistry,+,ccl.net] > Sent: Friday, June 13, 2008 1:18 PM > To: Babarao Ravichandar > Subject: CCL:G: LanL2DZ for calculations on Ru complexes > > > Sent to CCL by: "Jerome Baffreau" [jerome.baffreau-,-umontreal.ca] > >> "Jerome Baffreau jerome.baffreau{:}umontreal.ca" wrote: >> >> Sent to CCL by: "Jerome Baffreau" [jerome.baffreau!^!umontreal.ca] Hi > >> all, >> >> I want to do calculations on Ru complexes with DFT using LanL2DZ for > Ru and 6-31G(2d,p) for all the other atoms, but I get this error > message(G03W): >> ############### >> Leave Link 202 at Thu Jun 12 09:56:39 2008, MaxMem= 104857600 cpu: > 0.0 >> (Enter C:\G03W\l301.exe) >> General basis read from cards: (5D, 7F) >> WANTED AN INTEGER AS INPUT. >> FOUND A FLOATING POINT NUMBER AS INPUT. >> 1 3 1.5 2 1.5 38 1.0 >> ############### >> >> Here is my route: >> >> ############### >> %chk=job name >> %mem=800MB >> %nproc=2 >> %rwf=piece1,490mw,piece2,490mw,-1 >> #p b3lyp genecp opt >> >> 2 1 >> atoms specs >> >> > Sorry the end of my original message was missing, here is the end: > > C N H 0 > 6-31G(2d,p) > **** > Ru 0 > LANL2DZ > **** > Ru 0 > LANL2DZ > > I'm not confortable with this kind of calculations so it may be a very > simple mistake... Thanks for your help. > > Jerome Baffreau, PhD > University of Montreal, QC, Canadahttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/spammers.txt > > > -=his is automatically added to each message by the mailing script =-> > > From owner-chemistry@ccl.net Fri Jun 13 23:23:01 2008 From: "Oluwakemi.Oloba+*+mail.uh.edu" To: CCL Subject: CCL:G: LanL2DZ for calculations on Ru complexes Message-Id: <-37153-080613164338-17933-te7fFhUSIj947bS90MeKBQ!=!server.ccl.net> X-Original-From: Oluwakemi.Oloba*mail.uh.edu Content-language: en Content-type: multipart/alternative; boundary="Boundary_(ID_Ysa5ZsEMOPCnlB6xZXOMhA)" Date: Fri, 13 Jun 2008 15:35:35 -0500 MIME-version: 1.0 Sent to CCL by: Oluwakemi.Oloba(!)mail.uh.edu This is a multi-part message in MIME format. --Boundary_(ID_Ysa5ZsEMOPCnlB6xZXOMhA) Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: QUOTED-PRINTABLE Content-disposition: inline there is an additional input in your file which might have been added= by the 'geom=3Dconnect' keyword. Do you thing you can send all your = input file. one more thing, there should be a line between the basis = and the ecp. ----- Original Message ----- =46rom: "Jerome Baffreau jerome.baffreau]*[umontreal.ca" Date: Friday, June 13, 2008 12:29 am Subject: CCL:G: LanL2DZ for calculations on Ru complexes To: "Oloba, Kemi A " >=20 > Sent to CCL by: "Jerome=A0 Baffreau" [jerome.baffreau-,- > umontreal.ca] > > "Jerome Baffreau jerome.baffreau{:}umontreal.ca"=A0 wrote: > >=20 > > Sent to CCL by: "Jerome=A0 Baffreau"=20 > [jerome.baffreau!^!umontreal.ca]> Hi all, > >=20 > > I want to do calculations on Ru complexes with DFT using=20 > LanL2DZ for Ru and 6-31G(2d,p) for all the other atoms, but I=20 > get this error message(G03W): > >=20 > > ############### > > Leave Link=A0 202 at Thu Jun 12 09:56:39 2008,=20 > MaxMem=3D=A0 104857600 cpu:=A0=A0=A0=A0=A0=A0 0.0 > >=A0 (Enter C:\G03W\l301.exe) > >=A0 General basis read from cards:=A0 (5D, 7F) > >=A0=A0 WANTED AN INTEGER AS INPUT. > >=A0=A0 FOUND A FLOATING POINT NUMBER AS INPUT. > >=A0=A0 1 3 1.5 2 1.5 38 1.0=A0=A0=20 > > ############### > >=20 > > Here is my route: > >=20 > > ############### > > %chk=3Djob name > > %mem=3D800MB > > %nproc=3D2 > > %rwf=3Dpiece1,490mw,piece2,490mw,-1 > > #p b3lyp genecp opt > >=20 > > 2 1 > > atoms specs > >=20 > >=20 > Sorry the end of my original message was missing, here is the end: >=20 > C N H 0 > 6-31G(2d,p) > **** > Ru 0 > LANL2DZ > **** > Ru 0 > LANL2DZ >=20 > I'm not confortable with this kind of calculations so it may be= =20 > a very simple mistake... Thanks for your help. >=20 > Jerome Baffreau, PhD > University of Montreal, QC, Canada >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing= =20 > script =3D- > To recover the email address of the author of the message,=20 > please change>=20> =A0=A0=A0=A0=A0 http://www.ccl.net/cgi- > bin/ccl/send_ccl_message> =A0=A0=A0=A0=A0 http://www.ccl.net/cgi- > bin/ccl/send_ccl_message > Subscribe/Unsubscribe:=20 > =A0=A0=A0=A0=A0=20>=20 > Job: http://www.ccl.net/jobs=20 > Conferences:=20 > http://server.ccl.net/chemistry/announcements/conferences/ > Search Messages: http://www.ccl.net/htdig=A0 (login: ccl,=20 > Password: search) >=20> =A0=A0=A0=A0=A0>=20>=20 >=20 > --Boundary_(ID_Ysa5ZsEMOPCnlB6xZXOMhA) Content-type: text/html; charset=us-ascii Content-transfer-encoding: QUOTED-PRINTABLE Content-disposition: inline there is an additional input in your file which might have been added= by the 'geom=3Dconnect' keyword. Do you thing you can send all your = input file. one more thing, there should be a line between the basis = and the ecp.

----- Original Message -----
From: "Jerome Baf= freau jerome.baffreau]*[umontreal.ca" <owner-chemistry]|[ccl.net>=
Date: Friday, June 13, 2008 12:29 am
Subject: CCL:G: LanL2DZ f= or calculations on Ru complexes
To: "Oloba, Kemi A " <o= oloba]|[uh.edu>

>
> Sent to CCL by: "Jerome  B= affreau" [jerome.baffreau-,-
> umontreal.ca]
> > "Jero= me Baffreau jerome.baffreau{:}umontreal.ca"  wrote:
> >=
> > Sent to CCL by: "Jerome  Baffreau"
> [jero= me.baffreau!^!umontreal.ca]> Hi all,
> >
> > I = want to do calculations on Ru complexes with DFT using
> LanL2= DZ for Ru and 6-31G(2d,p) for all the other atoms, but I
> get= this error message(G03W):
> >
> > ###############=
> > Leave Link  202 at Thu Jun 12 09:56:39 2008,
&= gt; MaxMem=3D  104857600 cpu:      = ; 0.0
> >  (Enter C:\G03W\l301.exe)
> >  = General basis read from cards:  (5D, 7F)
> >  = ; WANTED AN INTEGER AS INPUT.
> >   FOUND A FLOATI= NG POINT NUMBER AS INPUT.
> >   1 3 1.5 2 1.5 38 1= .0  
> > ###############
> >
> &g= t; Here is my route:
> >
> > ###############
&g= t; > %chk=3Djob name
> > %mem=3D800MB
> > %nproc= =3D2
> > %rwf=3Dpiece1,490mw,piece2,490mw,-1
> > #p= b3lyp genecp opt
> >
> > 2 1
> > atoms s= pecs
> >
> >
> Sorry the end of my original= message was missing, here is the end:
>
> C N H 0
&g= t; 6-31G(2d,p)
> ****
> Ru 0
> LANL2DZ
> ****=
> Ru 0
> LANL2DZ
>
> I'm not confortable wi= th this kind of calculations so it may be
> a very simple mist= ake... Thanks for your help.
>
> Jerome Baffreau, PhD> University of Montreal, QC, Canada
>
>
> > -=3D This is automatically added to each message by the mailin= g
> script =3D-
> To recover the email address of the au= thor of the message,
> please change
> the strange chara= cters on the top line to the ]|[ sign. You can also
> look up the= X-Original-From: line in the mail header.
>
> E-mail to= subscribers: CHEMISTRY]|[ccl.net or use:
>    &nb= sp;  http://www.ccl.net/cgi-
> bin/ccl/send_ccl_message>
&= gt;       http://www.ccl.net/cgi-
> bi= n/ccl/send_ccl_message
>
>  =     
> http://www.ccl.net/chemistry/sub_un= sub.shtml
> Before posting, check wait time at: http://www.ccl.= net
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>
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> Search Messages: http://www.ccl.net/htdig  (login: ccl= ,
> Password: search)
>
> If your mail bounces fr= om CCL with 5.7.1 error, check:
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> RTFI: http://www.c= cl.net/chemistry/aboutccl/instructions/
>
>
> --Boundary_(ID_Ysa5ZsEMOPCnlB6xZXOMhA)-- From owner-chemistry@ccl.net Fri Jun 13 23:58:01 2008 From: "Colin Kinz-Thompson ckinztho#%#mail.rochester.edu" To: CCL Subject: CCL:G: Cubegen Segfault Message-Id: <-37154-080613152725-9679-upwbb9TZarHH3+Dy6nmO8w(-)server.ccl.net> X-Original-From: "Colin Kinz-Thompson" Date: Fri, 13 Jun 2008 15:27:21 -0400 Sent to CCL by: "Colin Kinz-Thompson" [ckinztho:mail.rochester.edu] Hi, I'm using cubegen from Gaussian 2003 from a linux terminal to try and create a cube of the electron density of a molecule which is very large (~300 atoms). Originally, I performed a DFT calculation of the density using B3LYP as a hamiltonian and cc-pVDZ as a basis. This successfully generated a checkpoint file, which I succesfully formated using formchk but when I try and run cubegen I keep getting a segmentation fault. Specifically: forrtl: severe (174): SIGSEGV, segmentation fault occurred Stack trace terminated abnormally. I've tried using 0 as the memory flag, and also setting it to the max my system can take (~450mw) as well as other lower values, but al give me a segfault. I know the calculations that I'm doing are very large, but G03 was able to handle the molecule in the first place. Does anyone have any ideas as to how I can get a cube file or even better, the electron density? Is there anyway that I can extrapolate the information from the .fchk file? Thank You, Colin Kinz-Thompson University of Rochester