From owner-chemistry@ccl.net Thu Jul 7 08:21:00 2011 From: "Eliac Brown Eliacbrown%yahoo.com" To: CCL Subject: CCL: SCF - Algorithm Message-Id: <-45042-110707081712-17993-WLKTcWMloimdmWILcHdCGA() server.ccl.net> X-Original-From: "Eliac Brown" Date: Thu, 7 Jul 2011 08:17:09 -0400 Sent to CCL by: "Eliac Brown" [Eliacbrown{}yahoo.com] Dear CCL During optimization and single point energy, some of the studied complexes suffered from SCF-Confused error. So, different SCF algorithms were used. I was wondering, energies of the optimized complexes using different SCF algorithms are comparable? If not, what kind of correction could be used? One more question, please, for some complexes, it gives DIIS SCF confused, so I changed the SCF algorithm into fermi (SCF=(Fermi)). But I got the same error "DIIS SCF confused". Why it is still calling the algorithm DIIS? Is that a bug? Thanks in advance Eliac From owner-chemistry@ccl.net Thu Jul 7 08:56:00 2011 From: "William F. Polik polik]_[hope.edu" To: CCL Subject: CCL:G: How to visualize molecular orbitals from Gaussian09 output file? Message-Id: <-45043-110707051243-10695-1olXXgSnJ5EOhBnTTITEyg]-[server.ccl.net> X-Original-From: "William F. Polik" Content-Type: multipart/alternative; boundary="------------060903070004060801080307" Date: Thu, 07 Jul 2011 05:12:31 -0400 MIME-Version: 1.0 Sent to CCL by: "William F. Polik" [polik_-_hope.edu] This is a multi-part message in MIME format. --------------060903070004060801080307 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Beyond creating, running, and visualizing Gaussian 03/09 jobs, WebMO (www.webmo.net) can import output files and visualize information contained therein. To view molecules orbitals in an imported file, be sure to include "GFINPUT POP=FULL" in the Gaussian route line so that the output file contains the relevant basis set and orbital information. WebMO runs on linux, mac, or windows, and is accessed from all platforms through a modern web-browser. No installation is needed to try WebMO -- just see the Working Demo at the website. On 7/6/11 9:46 AM, Gegham Galstyan gegham(a)chemie.fu-berlin.de wrote: > Sent to CCL by: "Gegham Galstyan" [gegham%%chemie.fu-berlin.de] > > Dear CCLers, > > do you know any good software for linux, mac or windows that can be used to visualize occupied molecular orbitals from gaussian03 output? I just want to quickly select the occupied pi-MOs among all MOs in a given molecule. > Thanks a lot beforehand for any help/suggestion. > > With best wishes, > Gegham > -- ------------------------------------------------------------------------ Dr. William F. Polik Hofma Professor of Chemistry Department of Chemistry Hope College 35 East 12th Street Holland, MI 49422-9000 USA polik * hope.edu http://www.chem.hope.edu/~polik tel: (616) 395-7639 fax: (616) 395-7118 ------------------------------------------------------------------------ --------------060903070004060801080307 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Beyond creating, running, and visualizing Gaussian 03/09 jobs, WebMO (www.webmo.net) can import output files and visualize information contained therein.

To view molecules orbitals in an imported file, be sure to include "GFINPUT POP=FULL" in the Gaussian route line so that the output file contains the relevant basis set and orbital information.

WebMO runs on linux, mac, or windows, and is accessed from all platforms through a modern web-browser.  No installation is needed to try WebMO --  just see the Working Demo at the website.

On 7/6/11 9:46 AM, Gegham Galstyan gegham(a)chemie.fu-berlin.de wrote:
Sent to CCL by: "Gegham  Galstyan" [gegham%%chemie.fu-berlin.de]

Dear CCLers,

do you know any good software for linux, mac or windows that can be used to visualize occupied molecular orbitals from gaussian03 output? I just want to quickly select the occupied pi-MOs among all MOs in a given molecule.
Thanks a lot beforehand for any help/suggestion.

With best wishes,
Gegham


--

Dr. William F. Polik
Hofma Professor of Chemistry

Department of Chemistry
Hope College
35 East 12th Street
Holland, MI  49422-9000
USA

polik * hope.edu
http://www.chem.hope.edu/~polik
tel: (616) 395-7639
fax: (616) 395-7118

--------------060903070004060801080307-- From owner-chemistry@ccl.net Thu Jul 7 09:30:00 2011 From: "Youzhao Lan lyzhao]-[zjnu.cn" To: CCL Subject: CCL: Request a algorithm to implement a coupled-cluster calculation Message-Id: <-45044-110707085213-4103-peijPlaOKHMmUHtwjNbSiw---server.ccl.net> X-Original-From: "Youzhao Lan" Date: Thu, 7 Jul 2011 08:52:09 -0400 Sent to CCL by: "Youzhao Lan" [lyzhao[]zjnu.cn] Dear all, I want to make a program to run a coupled-cluster(CC) calculation. Could you tell me the best algorithm I should use to solve the CC equation? Any references are welcome. Note that I have finished the HF and MP2 codes and the atomic and molecular orbitals based integrals can be obtained freely. The efficiency of calculation is temporarily not required for me. Any help will be appreciated. Best regards. ======================================================== -------------------------------------------------------- Youzhao Lan Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang, 321004, China. -------------------------------------------------------- 2011-07-07 ======================================================== From owner-chemistry@ccl.net Thu Jul 7 10:18:00 2011 From: "Gegham Galstyan gegham(!)zedat.fu-berlin.de" To: CCL Subject: CCL: How to visualize molecular orbitals from Gaussian output file? Message-Id: <-45045-110707101640-3139-1395kTmPino6/RGYr0lDVg^^^server.ccl.net> X-Original-From: Gegham Galstyan Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 07 Jul 2011 16:16:27 +0200 MIME-Version: 1.0 Sent to CCL by: Gegham Galstyan [gegham=-=zedat.fu-berlin.de] Many thanks to everyone, I tried with Chemcraft and Gaussview, both worked fine. Gegham From owner-chemistry@ccl.net Thu Jul 7 11:56:00 2011 From: "Gerald Knizia knizia(0)theochem.uni-stuttgart.de" To: CCL Subject: CCL: Request a algorithm to implement a coupled-cluster calculation Message-Id: <-45046-110707115402-7521-qwC6cT1GXHL44L9zY69Sig-,-server.ccl.net> X-Original-From: Gerald Knizia Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 07 Jul 2011 11:53:53 -0400 MIME-Version: 1.0 Sent to CCL by: Gerald Knizia [knizia^-^theochem.uni-stuttgart.de] Youzhao Lan lyzhao]-[zjnu.cn wrote: > Dear all, > I want to make a program to run a coupled-cluster(CC) calculation. > Could you tell me the best algorithm I should use to solve the CC equation? Any references are welcome. > Note that I have finished the HF and MP2 codes and the atomic and molecular orbitals based integrals can be obtained freely. The efficiency of calculation is temporarily not required for me. There we have for fast implementations on CCSD(T) level: o closed-shell CCSD in implementation-friendly formulation: Hampel, Peterson, Werner, Chem.Phys.Lett. 190 1 (1992) http://dx.doi.org/10.1016/0009-2614(92)86093-W o high-spin open-shell CCSD in similar fashion: Knowles, Hampel, Werner, J. Chem. Phys. 99 5219 (1993) http://dx.doi.org/10.1063/1.465990 o Perturbative (T) for closed-shell HF reference functions: Rendell, Lee, Komornicki, Chem. Phys. Lett. 178 462 (1991) http://dx.doi.org/10.1016/0009-2614(91)87003-T o Perturbative (T) for high-spin open-shell reference functions (incl. non-HF): Deegan, Knowles, Chem. Phys. Lett. 227 321 (1994) http://dx.doi.org/10.1016/0009-2614(94)00815-9 Note: These are the references on which the Molpro coupled cluster programs are based, which are widely regarded to be the most efficient available. If speed is not important for your application or you need higher excitations than CCSD(T), you might also want to consider making a string-based general coupled-cluster program like that: o general CC(n): Kállay, Surján, J. Chem. Phys. 115 2945 (2001) http://dx.doi.org/10.1063/1.1383290 o perturbative excitations: Kállay, Gauss, J. Chem. Phys. 123 214105 (2005) -- Gerald Knizia From owner-chemistry@ccl.net Thu Jul 7 12:30:00 2011 From: "Olasunkanmi Lukman Olawale walecomuk%a%yahoo.co.uk" To: CCL Subject: CCL: thermodynamic data for transition metal ions Message-Id: <-45047-110707120956-24973-Pe1f1CwbacbqxiJyirWugg]-[server.ccl.net> X-Original-From: Olasunkanmi Lukman Olawale Content-Type: multipart/alternative; boundary="0-311948970-1310054987=:7717" Date: Thu, 7 Jul 2011 17:09:47 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: Olasunkanmi Lukman Olawale [walecomuk . yahoo.co.uk] --0-311948970-1310054987=:7717 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hello everyone,=0ACan you=A0please refer me to a source=A0where I can get t= he thermodynamic data (H, =0AS, Heat of formation etc.) for transition meta= l ions (e.g. Ni2+, Pt2+, Pd2+, =0AFe2+, Ru2+, etc.). Thank you in anticipat= ion of your=A0contribution.=0A=A0Olasunkanmi Lukman Olawale=0A_____________= ___________________=0ACurrent Address:=0ADepartment of Chemistry,=0AObafemi= Awolowo University,=0AIle-Ife, Osun State.=0ANigeria.=0A=0A+234-0-80-52401= 564 Or +234-0-80-67161091=0A________________________________=0A --0-311948970-1310054987=:7717 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hello everyone,
=0A
Can you please refer= me to a source where I can get the thermodynamic data (H, S, Heat of = formation etc.) for transition metal ions (e.g. Ni2+, Pt2+, Pd2+, Fe2+, Ru2= +, etc.). Thank you in anticipation of your contribution.
 Olasunkanmi Lukma= n Olawale
=0A
=0ACurrent Address:
Department of Chemistry,
Obafemi Awolowo University,
Ile-Ife, Osun State.
Nig= eria.
=0A
+234-0-80-52401564 Or +234-0-80-67161091=
=0A
=0A
=0A
--0-311948970-1310054987=:7717-- From owner-chemistry@ccl.net Thu Jul 7 14:50:00 2011 From: "joseph.golab##ineos.com" To: CCL Subject: CCL:G: thermodynamic data for transition metal ions Message-Id: <-45048-110707144803-2305-KsleCb/7+1fwuB9rW2oAMw[*]server.ccl.net> X-Original-From: joseph.golab!^!ineos.com Content-Type: multipart/alternative; boundary="=_alternative 00674168862578C6_=" Date: Thu, 7 Jul 2011 13:47:48 -0500 MIME-Version: 1.0 Sent to CCL by: joseph.golab||ineos.com This is a multipart message in MIME format. --=_alternative 00674168862578C6_= Content-Type: text/plain; charset="US-ASCII" Hi Dr Olawale: The computational chemistry programs Gaussian, GAMESS, or NWCHEM are capable of calculating the data you are requesting ... whether for the cations or the various compounds the cations are contained in. There are also several papers in the (recent = post 1995) literature which summarize some of these data. I don't know of any good books (like CRC or TRC) for these systems. Regards, Joe ___________________________ Joseph T. Golab, PhD Molecular Modeling & Simulation Scientist Senior Research Associate INEOS Technologies, Nitriles R&D Phone: +1 (630) 420-5063 Cell: +1 (630) 336-0063 Email: Joseph.Golab_at_ineos.com > From: "Olasunkanmi Lukman Olawale walecomuk%a%yahoo.co.uk" To: Joseph Golab/US/TECHNOLOGIES/INEOS]_[INEOS Date: 07/07/2011 12:08 PM Subject: CCL: thermodynamic data for transition metal ions Sent by: owner-chemistry+joseph.golab==innovene.com]_[ccl.net Hello everyone, Can you please refer me to a source where I can get the thermodynamic data (H, S, Heat of formation etc.) for transition metal ions (e.g. Ni2+, Pt2+, Pd2+, Fe2+, Ru2+, etc.). Thank you in anticipation of your contribution. Olasunkanmi Lukman Olawale Current Address: Department of Chemistry, Obafemi Awolowo University, Ile-Ife, Osun State. Nigeria. +234-0-80-52401564 Or +234-0-80-67161091 --=_alternative 00674168862578C6_= Content-Type: text/html; charset="US-ASCII" Hi Dr Olawale:

The computational chemistry programs Gaussian, GAMESS, or NWCHEM are capable of calculating the data you are requesting ... whether for the cations or the various compounds the cations are contained in.

There are also several papers in the (recent = post 1995) literature which summarize some of these data.  I don't know of any good books (like CRC or TRC) for these systems.

Regards,

Joe
___________________________
Joseph T. Golab, PhD
Molecular Modeling & Simulation Scientist
Senior Research Associate
INEOS Technologies, Nitriles R&D
Phone: +1 (630) 420-5063
Cell:  +1 (630) 336-0063
Email: Joseph.Golab_at_ineos.com




From:        "Olasunkanmi Lukman Olawale walecomuk%a%yahoo.co.uk" <owner-chemistry]_[ccl.net>
To:        Joseph Golab/US/TECHNOLOGIES/INEOS]_[INEOS
Date:        07/07/2011 12:08 PM
Subject:        CCL: thermodynamic data for transition metal ions
Sent by:        owner-chemistry+joseph.golab==innovene.com]_[ccl.net




Hello everyone,
Can you please refer me to a source where I can get the thermodynamic data (H, S, Heat of formation etc.) for transition metal ions (e.g. Ni2+, Pt2+, Pd2+, Fe2+, Ru2+, etc.). Thank you in anticipation of your contribution.

Olasunkanmi Lukman Olawale

Current Address:
Department of Chemistry,
Obafemi Awolowo University,
Ile-Ife, Osun State.
Nigeria.

+234-0-80-52401564 Or +234-0-80-67161091


--=_alternative 00674168862578C6_=-- From owner-chemistry@ccl.net Thu Jul 7 21:20:00 2011 From: "Bennion, Brian Bennion1-x-llnl.gov" To: CCL Subject: CCL:G: How to visualize molecular orbitals from Gaussian output file? Message-Id: <-45049-110707113250-4058-W/XDt2QhANvMs54im7plXw(a)server.ccl.net> X-Original-From: "Bennion, Brian" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 7 Jul 2011 08:32:09 -0700 MIME-Version: 1.0 Sent to CCL by: "Bennion, Brian" [Bennion1++llnl.gov] Were you able to separate out the MOs that you wanted, with these to packages? Brian Bennion -----Original Message----- > From: owner-chemistry+bennion1==llnl.gov:ccl.net [mailto:owner-chemistry+bennion1==llnl.gov:ccl.net] On Behalf Of Gegham Galstyan gegham(!)zedat.fu-berlin.de Sent: Thursday, July 07, 2011 7:16 AM To: Bennion, Brian Subject: CCL: How to visualize molecular orbitals from Gaussian output file? Sent to CCL by: Gegham Galstyan [gegham=-=zedat.fu-berlin.de] Many thanks to everyone, I tried with Chemcraft and Gaussview, both worked fine. Geghamhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu Jul 7 23:03:00 2011 From: "Jun Zhang coolrainbow]-[yahoo.cn" To: CCL Subject: CCL: SCF - Algorithm Message-Id: <-45050-110707214946-16430-cGGj1xLM/NMeE68txuzLNg+*+server.ccl.net> X-Original-From: Jun Zhang Content-Type: multipart/alternative; boundary="0-1900052974-1310089775=:58472" Date: Fri, 8 Jul 2011 09:49:35 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: Jun Zhang [coolrainbow]|[yahoo.cn] --0-1900052974-1310089775=:58472 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Dear Eliac:=0A=C2=A0=0ADifferent algorithms (DIIS or not, Fermi or not) sho= uld converge to the same result as long as your system is near the equillib= rium geometry and the convergency threshold is the same.=0A=C2=A0=0AAccordi= ng to your description,=C2=A0 I guess your structure of complex is unreason= able, or your system is intrinct difficult to converge. You can use some lo= w level models to get a converged=C2=A0result (such as HF/3-21g), then use = this as initial guess to start an advanced computation. =0A=C2=A0=0AIf you = use G09, for your complex, fragmentation guess can be a choice.=0A=0A------= ----------------------------------------------------------=0AJun Zhang (coo= lrainbow]*[yahoo.ch)=0AComputational Chemistry Group=0ANo.94, Weijinlu=0ANank= ai University =0ATianjin, China=0A=0A=E5=8F=91=E4=BB=B6=E4=BA=BA=EF=BC=9A E= liac Brown Eliacbrown%yahoo.com =0A=E6=94=B6=E4=BB= =B6=E4=BA=BA=EF=BC=9A "Zhang, Jun " =0A=E5=8F= =91=E9=80=81=E6=97=A5=E6=9C=9F=EF=BC=9A 2011=E5=B9=B47=E6=9C=887=E6=97=A5, = =E6=98=9F=E6=9C=9F=E5=9B=9B, =E4=B8=8B=E5=8D=88 8:17=0A=E4=B8=BB=E9=A2=98: = CCL: SCF - Algorithm=0A=0A=0ASent to CCL by: "Eliac=C2=A0 Brown" [Eliacbrow= n{}yahoo.com]=0ADear CCL=0ADuring optimization and single point energy, som= e of the studied complexes =0Asuffered from SCF-Confused error. So, differe= nt SCF algorithms were used.=0AI was wondering, energies of the optimized c= omplexes using different SCF =0Aalgorithms are comparable?=0AIf not, what k= ind of correction could be used?=0AOne more question, please, for some comp= lexes, it gives DIIS SCF confused, so I =0Achanged the SCF algorithm into f= ermi (SCF=3D(Fermi)). But I got the same error =0A"DIIS SCF confused". Why = it is still calling the algorithm DIIS? Is that a bug?=0AThanks in advance= =0AEliac=0A=0A=0A=0A-=3D This is automatically added to each message by the= mailing script =3D-=0ATo recover the email address of the author of the me= ssage, please change=0Athe strange characters on the top line to the ]*[ sign= . You can also=0A=0A= =0A=0A=C2=A0 =C2=A0 =C2=A0 ==0A=0AE-mail to administrato= rs: CHEMISTRY-REQUEST]*[ccl.net or use=0A=C2=A0 =C2=A0 =C2=A0 http://www.ccl.= net/cgi-bin/ccl/send_ccl_message=0A=0A=0A=C2=A0 =C2= =A0 =C2=A0=0A=0ABefore posting= , check wait time at: http://www.ccl.net=0A=0A= =0A= =0A=0A= =0A=0A=0A=C2=A0 =C2= =A0 =C2=A0=0A=0ARTFI: http://www.ccl.net/ch= emistry/aboutccl/instructions/ --0-1900052974-1310089775=:58472 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Dear Eliac:
 
Different algorithms= (DIIS or not, Fermi or not) should converge to the same result as long as = your system is near the equillibrium geometry and the convergency threshold= is the same.
 
According to your de= scription,  I guess your structure of complex is unreasonable, or your= system is intrinct difficult to converge. You can use some low level model= s to get a converged result (such as HF/3-21g), then use this as initi= al guess to start an advanced computation.
 
If you use G09, for = your complex, fragmentation guess can be a choice.<= /VAR>
 
------------------------------------------------= ----------------
Jun Zhang (coolrainbow]*[yahoo.ch)
Computational Chemi= stry Group
No.94, Weijinlu
Nankai University
Tianjin, China
=E5= =8F=91=E4=BB=B6=E4=BA=BA=EF=BC=9A Eliac Brown Eliacbrown%yahoo.c= om <owner-chemistry]*[ccl.net>
= =E6=94=B6=E4=BB=B6=E4=BA=BA=EF=BC=9A "Zhang, Jun " <c= oolrainbow]*[yahoo.cn>
=E5=8F=91= =E9=80=81=E6=97=A5=E6=9C=9F=EF=BC=9A 2011=E5=B9=B47=E6=9C=887=E6= =97=A5, =E6=98=9F=E6=9C=9F=E5=9B=9B, =E4=B8=8B=E5=8D=88 8:17
=E4=B8=BB=E9=A2=98: CCL: SCF - Algorit= hm


Sent to CCL by: "Eliac  Brown" [Eliacbrown{}yahoo= .com]
Dear CCL
During optimization and single point energy, some of t= he studied complexes
suffered from SCF-Confused error. So, different SC= F algorithms were used.
I was wondering, energies of the optimized comple= xes using different SCF
algorithms are comparable?
If not, what kind= of correction could be used?
One more question, please, for some comple= xes, it gives DIIS SCF confused, so I
changed the SCF algorithm into fe= rmi (SCF=3D(Fermi)). But I got the same error
"DIIS SCF confused". Why = it is still calling the algorithm DIIS? Is that a bug?
Thanks in advance=
Eliac



-=3D This is automatically added to each message b= y the mailing script =3D-
To recover the email address of the author of = the message, please change
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--0-1900052974-1310089775=:58472--