From owner-chemistry@ccl.net Thu Jan 30 01:23:00 2014 From: "Bradley K Welch bwelch5[*]slu.edu" To: CCL Subject: CCL:G: B97D functional optimization with a small imaginary frequency Message-Id: <-49617-140130012200-5535-HOJV7llBnpjLB91k3jRRRA.@.server.ccl.net> X-Original-From: "Bradley K Welch" Date: Thu, 30 Jan 2014 01:21:58 -0500 Sent to CCL by: "Bradley K Welch" [bwelch5!^!slu.edu] Dear all, I recently optimized a buckyholder complex with B97D/def2-svp/auto (density fitting) and a ultrafine integration grid in gaussian 09 v.a02. def2-svp was taken from emsl. I ran a frequency calculation and it gave a small imaginary frequency of -12.8996. All other frequencies were real. I adjusted the structure slightly based upon the imaginary mode, and reran the calculation and did another frequency calculation. It gave a mode of -7.8843. I repeated process again, and got a different frequency of -9.1011. At this point could I ignore the imaginary frequency due to it being so small? Bradley Welch From owner-chemistry@ccl.net Thu Jan 30 09:49:01 2014 From: "Parag Agarwal paragagarwal.2008^^gmail.com" To: CCL Subject: CCL: chekpoint file conversion Message-Id: <-49618-140130034438-30610-COmjWFLZ3IKrUuLc0CO1gw^^^server.ccl.net> X-Original-From: "Parag Agarwal" Date: Thu, 30 Jan 2014 03:44:37 -0500 Sent to CCL by: "Parag Agarwal" [paragagarwal.2008*_*gmail.com] Hello Sir, I have to change .chk files to .fchk file. Please tell me, how to do it. Yours Sincerely, Parag Agarwal From owner-chemistry@ccl.net Thu Jan 30 10:24:00 2014 From: "Fedor Goumans goumans{=}scm.com" To: CCL Subject: CCL: Open-shell TDDFT in ADF & transition density Message-Id: <-49619-140130082615-3971-Z14ZLPry3+EE7fzEMGp6rw^-^server.ccl.net> X-Original-From: Fedor Goumans Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 30 Jan 2014 14:25:51 +0100 MIME-Version: 1.0 Sent to CCL by: Fedor Goumans [goumans=scm.com] Dear Radoslaw, At the moment, transition densities are not implemented for open-shell TDDFT in ADF. Best wishes, Fedor On 1/30/2014 4:57 AM, Radoslaw Kaminski rkaminski.rk]=[gmail.com wrote: > Sent to CCL by: "Radoslaw Kaminski" [rkaminski.rk=-=gmail.com] > Dear All, > > I performed a TDDFT computation on the open-shell molecule in ADF. Some of the most relevant keywords are listed below: > > Relativistic Scalar ZORA > Symmetry NoSym > Unrestricted > Charge 0 4 > ExactDensity > Excitations > Lowest 100 > End > Save TAPE21 > > The output file looks fine, all requested transitions were computed, the spectrum is nicely visualized with adfpectra program etc. I then used the TAPE21 file in the densf utility to produce transition densities with the keywords: > > Density Fit Trans > > However, the resultant TAPE41 file does not contain any information about the transition densities. Any other density or orbitals looks OK if computed with densf. Am I missing some additional keyword or something like that? > > Thanks in advance, > > Radek> > -- Dr. T. P. M. (Fedor) Goumans Business Developer Scientific Computing & Modelling NV (SCM) Vrije Universiteit, FEW, Theoretical Chemistry De Boelelaan 1083 1081 HV Amsterdam, The Netherlands T +31 20 598 7625 F +31 20 598 7629 E-mail: goumans+*+scm.com http://www.scm.com ADF mailing list: http://lists.scm.com/pipermail/adflist/ From owner-chemistry@ccl.net Thu Jan 30 10:59:00 2014 From: "Sandhya Rai sandhyachemistry30[]gmail.com" To: CCL Subject: CCL: chekpoint file conversion Message-Id: <-49620-140130102021-863-7sPiFVvmRd63Dc49rb2IFw ~ server.ccl.net> X-Original-From: Sandhya Rai Content-Type: multipart/alternative; boundary=047d7b2e3d0026215804f131981b Date: Thu, 30 Jan 2014 20:50:15 +0530 MIME-Version: 1.0 Sent to CCL by: Sandhya Rai [sandhyachemistry30-x-gmail.com] --047d7b2e3d0026215804f131981b Content-Type: text/plain; charset=ISO-8859-1 Use the command formchk formchk filename.chk filename.fchk This will give you the .fchk file. Regards, Sandhya On 30 Jan 2014 20:46, "Parag Agarwal paragagarwal.2008^^gmail.com" < owner-chemistry|-|ccl.net> wrote: > > Sent to CCL by: "Parag Agarwal" [paragagarwal.2008*_*gmail.com] > Hello Sir, > I have to change .chk files to .fchk file. Please tell me, how > to do it. > > Yours Sincerely, > Parag Agarwal> > > --047d7b2e3d0026215804f131981b Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Use the command formchk
formchk filename.chk filename.fchk
This will give you the .fchk file.

Regards,
Sandhya

On 30 Jan 2014 20:46, "Parag Agarwal paraga= garwal.2008^^gmail.com" <owner-chemistry|-|ccl.net> wrote:<= br type=3D"attribution">

Sent to CCL by: "Parag =A0Agarwal" [paragagarwal.2008*_*gmail.com]
Hello Sir,
=A0 =A0 =A0 =A0 =A0 I have to change .chk files to .fchk file. Please tell = me, how to do it.

Yours Sincerely,
Parag Agarwal



-=3D This is automatically added to each message by the mailing script =3D-=
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--047d7b2e3d0026215804f131981b-- From owner-chemistry@ccl.net Thu Jan 30 11:34:00 2014 From: "=?ISO-8859-1?Q?Francisco_Nu=F1ez_Zarur?= franuz21#,#gmail.com" To: CCL Subject: CCL:G: chekpoint file conversion Message-Id: <-49621-140130103855-13689-/CHfpVkiIlGe7Xr2zdI6bg!A!server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Francisco_Nu=F1ez_Zarur?= Content-Type: multipart/alternative; boundary=001a11334c38591d4f04f131dadc Date: Thu, 30 Jan 2014 16:38:45 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Francisco_Nu=F1ez_Zarur?= [franuz21-#-gmail.com] --001a11334c38591d4f04f131dadc Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable It=B4s quite straightforward. Just be sure you have loaded the gaussian module in your terminal: module load g0X Then type in the terminal: formchk name.chk name.fchk where 'name' is the name of your checkpoint file. I hope this helps you Francisco 2014-01-30 Parag Agarwal paragagarwal.2008^^gmail.com < owner-chemistry(!)ccl.net>: > > Sent to CCL by: "Parag Agarwal" [paragagarwal.2008*_*gmail.com] > Hello Sir, > I have to change .chk files to .fchk file. Please tell me, how > to do it. > > Yours Sincerely, > Parag Agarwal > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --001a11334c38591d4f04f131dadc Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
It=B4s quite straightforward. Just be sure you have loaded= the gaussian module in your terminal: module load g0X

T= hen type in the terminal:

formchk name.chk name.fc= hk

where 'name' is the name of your checkpoint fil= e.


I hope this helps you
=


Francisco=A0


2014-01-30 Parag Agarwal paragagarwal.20= 08^^gmail.com <owner-chemistry(!)ccl.= net>:

Sent to CCL by: "Parag =A0Agarwal" [paragagarwal.2008*_*gmail.com]
Hello Sir,
=A0 =A0 =A0 =A0 =A0 I have to change .chk files to .fchk file. Please tell = me, how to do it.

Yours Sincerely,
Parag Agarwal



-=3D This is automatically added to each message by the mailing script =3D-=
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--001a11334c38591d4f04f131dadc-- From owner-chemistry@ccl.net Thu Jan 30 12:09:01 2014 From: "Adam Tenderholt atenderholt===gmail.com" To: CCL Subject: CCL:G: chekpoint file conversion Message-Id: <-49622-140130105552-27592-Xz6VXRcPom54T6vxWSY95g[#]server.ccl.net> X-Original-From: Adam Tenderholt Content-Type: multipart/alternative; boundary=047d7b342d302b91c304f13217b8 Date: Thu, 30 Jan 2014 07:55:26 -0800 MIME-Version: 1.0 Sent to CCL by: Adam Tenderholt [atenderholt{}gmail.com] --047d7b342d302b91c304f13217b8 Content-Type: text/plain; charset=ISO-8859-1 Hi Parag, You need to use the formchk utility: http://www.gaussian.com/g_tech/g_ur/u_formchk.htm. Adam On Thu, Jan 30, 2014 at 12:44 AM, Parag Agarwal paragagarwal.2008^^gmail.com wrote: > > Sent to CCL by: "Parag Agarwal" [paragagarwal.2008*_*gmail.com] > Hello Sir, > I have to change .chk files to .fchk file. Please tell me, how > to do it. > > Yours Sincerely, > Parag Agarwal> > > --047d7b342d302b91c304f13217b8 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi Parag,

You need to use the formchk u= tility:=A0htt= p://www.gaussian.com/g_tech/g_ur/u_formchk.htm.

Adam



On Thu, Jan 30, 2014 at 12:44 AM, Parag Agarwal paragagarwal.2008^^= gmail.com <owner-chemistry__ccl.net<= /a>> wrote:

Sent to CCL by: "Parag =A0Agarwal" [paragagarwal.2008*_*gmail.com]
Hello Sir,
=A0 =A0 =A0 =A0 =A0 I have to change .chk files to .fchk file. Please tell = me, how to do it.

Yours Sincerely,
Parag Agarwal



-=3D This is automatically added to each message by the mailing script =3D-=
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--047d7b342d302b91c304f13217b8-- From owner-chemistry@ccl.net Thu Jan 30 12:44:00 2014 From: "Dr. Vitaly Chaban vvchaban^^^gmail.com" To: CCL Subject: CCL:G: chekpoint file conversion Message-Id: <-49623-140130110349-2631-aJeq1lbrZLMLtbyzuefOHA!^!server.ccl.net> X-Original-From: "Dr. Vitaly Chaban" Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 30 Jan 2014 17:02:57 +0100 MIME-Version: 1.0 Sent to CCL by: "Dr. Vitaly Chaban" [vvchaban()gmail.com] Using gaussian utilities clearly described on their website. Dr. Vitaly V. Chaban On Thu, Jan 30, 2014 at 9:44 AM, Parag Agarwal paragagarwal.2008^^gmail.com wrote: > > Sent to CCL by: "Parag Agarwal" [paragagarwal.2008*_*gmail.com] > Hello Sir, > I have to change .chk files to .fchk file. Please tell me, how to do it. > > Yours Sincerely, > Parag Agarwal> > From owner-chemistry@ccl.net Thu Jan 30 13:19:00 2014 From: "Jissy AK jissy a iisertvm.ac.in" To: CCL Subject: CCL: chekpoint file conversion Message-Id: <-49624-140130112218-18835-EYqXH5q29MT+r7VVkf+EGQ[]server.ccl.net> X-Original-From: Jissy AK Content-Type: multipart/alternative; boundary=001a113470d2a89df004f13275e1 Date: Thu, 30 Jan 2014 10:22:11 -0600 MIME-Version: 1.0 Sent to CCL by: Jissy AK [jissy- -iisertvm.ac.in] --001a113470d2a89df004f13275e1 Content-Type: text/plain; charset=ISO-8859-1 Hi Parag Use the formchk command. Jissy On Thu, Jan 30, 2014 at 2:44 AM, Parag Agarwal paragagarwal.2008^^gmail.com wrote: > > Sent to CCL by: "Parag Agarwal" [paragagarwal.2008*_*gmail.com] > Hello Sir, > I have to change .chk files to .fchk file. Please tell me, how > to do it. > > Yours Sincerely, > Parag Agarwal> > > -- Jissy AK PhD Student IISER-TVM "Logic will get you from A to B, Imagination will take you everywhere"-- Albert Einstein --001a113470d2a89df004f13275e1 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi Parag

=A0=A0=A0 Use the formchk comm= and.

Jissy


On Thu, Jan 30, 2014 at 2:44 AM, Parag Agarwal paragagarwal.2008= ^^gmail.com <owner-chemistry]^[ccl.n= et> wrote:

Sent to CCL by: "Parag =A0Agarwal" [paragagarwal.2008*_*gmail.com]
Hello Sir,
=A0 =A0 =A0 =A0 =A0 I have to change .chk files to .fchk file. Please tell = me, how to do it.

Yours Sincerely,
Parag Agarwal



-=3D This is automatically added to each message by the mailing script =3D-=
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--
Jissy AK
PhD Student=
IISER-TVM

"Logic will get you from A to B, Imagination will= take you everywhere"-- Albe= rt Einstein
--001a113470d2a89df004f13275e1-- From owner-chemistry@ccl.net Thu Jan 30 13:54:00 2014 From: "Ambrish K Srivastava ambrishphysics{=}gmail.com" To: CCL Subject: CCL:G: chekpoint file conversion Message-Id: <-49625-140130120255-23258-mkdTDpJ+yx3AP29l7XFeTQ%a%server.ccl.net> X-Original-From: Ambrish K Srivastava Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 30 Jan 2014 22:32:48 +0530 MIME-Version: 1.0 Sent to CCL by: Ambrish K Srivastava [ambrishphysics() gmail.com] Dear Parag, Go to Gaussian--Utilities--FormChk ..and locate your ".chk" file you will get a ".fch" file in the same folder as that of ".chk".. Cheers, Ambrish K. Srivastava CSIR Research Fellow Department of Physics University of Lucknow On 1/30/14, Parag Agarwal paragagarwal.2008^^gmail.com wrote: > > Sent to CCL by: "Parag Agarwal" [paragagarwal.2008*_*gmail.com] > Hello Sir, > I have to change .chk files to .fchk file. Please tell me, how to > do it. > > Yours Sincerely, > Parag Agarwal> > > -- *Ambrish K. Srivastava CSIR Junior Research Fellow Department of Physics University of Lucknow Lucknow, India-226007* From owner-chemistry@ccl.net Thu Jan 30 14:49:00 2014 From: "Guenter Grethe ggrethe_+_att.net" To: CCL Subject: CCL: 2014 CINF-RSC Scholarships Message-Id: <-49626-140130141258-9575-XunOmlIblBAHoklGfeC3+g%x%server.ccl.net> X-Original-From: "Guenter Grethe" Date: Thu, 30 Jan 2014 14:12:57 -0500 Sent to CCL by: "Guenter Grethe" [ggrethe[A]att.net] 2014 CINF Scholarship for Scientific Excellence Sponsored by the Royal Society of Chemistry The scholarship program of the Division of Chemical Information (CINF) of the American Chemical Society (ACS) funded by the Royal Society of Chemistry (RSC) is designed to reward graduate and postdoctoral students in chemical information and related sciences for scientific excellence and to foster their involvement in CINF. Up to four scholarships valued at $1,000 each will be presented at the 248th ACS National Meeting in San Francisco, CA, August 10 August 14, 2014. Applicants must be enrolled at a certified college or university, and they will present a poster during the Welcoming Reception of the Division on Sunday evening at the National Meeting. Additionally, they will have the option to also show their poster at the Sci-Mix session on Monday night. Abstracts for the poster must be submitted electronically through PACS, the abstract submission system of ACS. To apply, please inform the Chair of the selection committee, Guenter Grethe at ggrethe_._att.net that you are applying for a scholarship. Submit your abstract to http://abstracts.acs.org using your ACS ID. If you do not have an ACS ID, follow the registration instructions and submit your abstract in the CINF program for the session CINF Scholarship for Scientific Excellence. PACS will be open for abstract submissions from January 13 to March 10, 2014. Additionally, please send a 2,000-word abstract describing the work to be presented in electronic form to the Chair of the selection committee by June 20, 2014. Any questions related to applying for one of the scholarships should be directed to the same e-mail address. Winners will be chosen based on contents, presentation and relevance of the poster and they will be announced during the reception. The contents shall reflect upon the students work and describe research in the field of cheminformatics and related sciences. Guenter Grethe