From owner-chemistry@ccl.net Thu Jan 22 00:20:01 2015 From: "Samer Gozem sgozem|,|usc.edu" To: CCL Subject: CCL: ezDyson v.3.0 Message-Id: <-50949-150121233025-20656-psMgBoIupoJh4Rqybl692g-x-server.ccl.net> X-Original-From: "Samer Gozem" Date: Wed, 21 Jan 2015 23:30:23 -0500 Sent to CCL by: "Samer Gozem" [sgozem-,-usc.edu] Dear Colleague, A new release of ezDyson is available for download: http://iopenshell.usc.edu/downloads/ezdyson/ ezDyson is a C++ code that calculates absolute photodetachment/photoionization cross sections, photoelectron angular distributions, and anisotropy parameters using Dyson orbitals computed by an ab initio program. The calculation is based on the following approximations: (1) weak field limit, i.e., the photodetachment or photoionization is treated in a perturbative regime; (2) dipole approximation, i.e., assuming that the wavelength of the radiation field is longer than the size of the molecule and that the process is one-photon (first order in perturbation theory); (3) sudden approximation, i.e., we ignore the interactions between the ejected photoelectron and the remaining core electrons; (4) strong orthogonality condition, i.e., the continuum orbital is orthogonal to all states of initial system. We use plane waves to describe the continuum state of the photoelectron. Version 3.0 of ezDyson introduces a number of important bug fixes and improvements. Please refer to the updated manual for detailed theoretical background, instructions on running ezDyson, and a description of ezDyson input and output files. Samer Gozem, Ph.D Postdoctoral Researcher Department of Chemistry University of Southern California Los Angeles, CA 90089 From owner-chemistry@ccl.net Thu Jan 22 09:01:01 2015 From: "Anjali B anjaliamutha|,|gmail.com" To: CCL Subject: CCL:G: Change in coordinates after Single point energy calculation Message-Id: <-50950-150122061117-27988-NBTie02xENxy5wgCkryF1w-$-server.ccl.net> X-Original-From: Anjali B Content-Type: multipart/alternative; boundary=047d7bf0c58ed1f0eb050d3bba67 Date: Thu, 22 Jan 2015 16:41:12 +0530 MIME-Version: 1.0 Sent to CCL by: Anjali B [anjaliamutha~~gmail.com] --047d7bf0c58ed1f0eb050d3bba67 Content-Type: text/plain; charset=UTF-8 Hello everyone Can anyone tell me the difference between input orientation and standard orientation in gaussian 09 output. I got different coordinates after single point energy calculation in solvent. I used optimized geometry in the input. Thank you --047d7bf0c58ed1f0eb050d3bba67 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hello everyone

Can anyone tell me the d= ifference between input orientation and standard orientation in gaussian 09= output.
I got different coordinates after single point energ= y calculation in solvent.
I used optimized geometry in the input.=

Thank you=C2=A0
--047d7bf0c58ed1f0eb050d3bba67-- From owner-chemistry@ccl.net Thu Jan 22 09:36:01 2015 From: "Steve Williams willsd{=}appstate.edu" To: CCL Subject: CCL: CAUTION..Not science: Welcome to the 15th International Congress of Quantum Chemistry ! Message-Id: <-50951-150122075746-14746-Gd1Sc2wf+Tw5PmKMPvo9fA-#-server.ccl.net> X-Original-From: Steve Williams Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Thu, 22 Jan 2015 07:51:56 -0500 MIME-Version: 1.0 Sent to CCL by: Steve Williams [willsd a appstate.edu] Je suis sycophant. Steve Williams, ASU Chemistry On 01/21/2015 03:22 PM, Daniel Roe daniel.r.roe##gmail.com wrote: > Sent to CCL by: Daniel Roe [daniel.r.roe(!)gmail.com] > Mr. Kress, > > I would like to bring to your attention two quotes written by you from > an e-mail you sent February 16, 2014 (in response to another e-mail > with the subject 'CCL: ICQC shame'): > >> If people want to discuss "gender inequality" they should start a forum on LinkedIn or Facebook or any of the many Social Media sites... >> If you INSIST on discussing this on CCL, the please place an identifying header on all your emails so that those of us who care about SCIENCE... > Kindly follow your own advice if you intended to send such unkind and > non-science-related e-mails to the list. Thank you, > > -Dan > > On Wed, Jan 21, 2015 at 9:42 AM, Jim Kress jimkress35{=}gmail.com > wrote: >> Sent to CCL by: "Jim Kress" [jimkress35,+,gmail.com] >> Did you make sure the feminist quota has been met or exceeded? You wouldn't >> want the Feminist harpies and their male sycophants descending upon you >> again, with threats and boycotts. >> >> Jim Kress >> >> -----Original Message----- >>> From: owner-chemistry+jimkress35==gmail.com::ccl.net >> [mailto:owner-chemistry+jimkress35==gmail.com::ccl.net] On Behalf Of Vincent >> lee to_wenqiangli|a|163.com >> Sent: Tuesday, January 20, 2015 11:29 AM >> To: Kress, Jim >> Subject: CCL: Welcome to the 15th International Congress of Quantum >> Chemistry ! >> >> >> Sent to CCL by: "Vincent lee" [to_wenqiangli_-_163.com] Dear Colleagues, >> The 15th International Congress of Quantum Chemistry (ICQC) will take place >> in Beijing, June 8-13, 2015. The registration will be opened by Oct 1, 2014. >> >> Please browse http://www.icqc2015.org/. The following eminent theoretical >> chemists have accepted the invitation for lectures: >> >> Millard Alexander (U Maryland), Yuriko Aoki (Kyushu U), Paul Ayers (McMaster >> U), Joel Bowman (Emory U), Ria Broer-Braam (Groningen U), Filipp Furche (UC >> Irvine), Jiali Gao (U Minnesota), Yiqin Gao (Peking U), Stefan Grimme (U >> Bonn), Sharon Hammes-Schiffer (UIUC), Martin Head-Gordon (UC Berkeley), >> Dudley Herschbach (Harvard, Nobel Laureate), Roald Hoffmann (Cornell U, >> Nobel Laureate), Kendall Houk (UCLA), Denis Jacquemin (U Nantes), Poul >> Jrgensen (U Aarhus), Kwang S. Kim (Ulsan), Wanzhen Liang (Xiamen U), Carmay >> Lim (Acad Sinica), Yi Luo (KTH), Rudolf Marcus (Caltech, Nobel Laureate), >> Benedetta Mennucci (U Pisa), Josef Michl (U Colorado), Keiji Morokuma (U >> Kyoto), Hiroshi Nakatsuji (QCRI), Jozef Noga (Comenius U), Oleg Prezhdo (U >> So Calif), Leo Radom (U Sydney), Lucia Reining(Ecole Polytech), Andreas >> Savin (UPMC), George Schatz (Northwester U), H. Bernhard Schlegel (Wayne >> State U), Tamar Seideman (Northwestern U), Juha Vaara (U Oulu), Xin Xu >> (Fudan U), Yijing Yan (Hong Kong UST), Xueming Yang (DICP), Donghui Zhang >> (DICP) >> >> The registration fee is 350 EUROs (regular) and 175 EUROs (student), which >> covers (i) conference and reception, coffee breaks, all the lunches; (ii) >> tour to the Great Wall; (iii) refreshments in the four poster sessions. >> >> The conference venue will be in the Tsinghua University Campus (ranked by >> Forbes as one of the 14 most beautiful University Campuses in the world, >> only one from Asia), easy connected by subways and other public transport. >> Many hotels, restaurants, supermarkets, cafes are within the distance of >> 20-minute walk. You may also easily rent a bicycle for one week or even one >> month for less than 10 EUROs. Beijing is a fantastic place to see. And this >> is the very first ICQC in China. >> >> Please check the air quality of Beijing in http://aqicn.org/city/beijing/ : >> >> Beijing is not much worse than other megacities like Tokyo or New York on >> average. The air quality in the first half of June will be satisfactory and >> it is sure that you will enjoy the sunshine and the cosy temperature. >> >> There will be eight satellite meetings featuring on specialized directions >> of theoretical and computational chemistry. Please consult the website. >> >> Please mark your calendar. We look forward to welcoming you in China! >> >> Sincerely, >> >> Zhigang Shuai, Weihai Fang, Wenjian Liu, Weitao Yang Organizing Committee of >> the 15th ICQC http://www.icqc2015.org/http://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 Jan 22 15:34:01 2015 From: "Jason Swails jason.swails{:}gmail.com" To: CCL Subject: CCL: Welcome to the 15th International Congress of Quantum Chemistry ! Message-Id: <-50952-150122111157-536-A66yDsMjOIy3+3674TvTkA-*-server.ccl.net> X-Original-From: Jason Swails Content-Type: multipart/alternative; boundary=001a11331f9a2160ff050d3fee96 Date: Thu, 22 Jan 2015 11:11:52 -0500 MIME-Version: 1.0 Sent to CCL by: Jason Swails [jason.swails .. gmail.com] --001a11331f9a2160ff050d3fee96 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable On Wed, Jan 21, 2015 at 3:07 PM, Jim Kress jimkress35^^^gmail.com < owner-chemistry[a]ccl.net> wrote: > > People need to be reminded of their malice and pernicious attempt to squa= sh > dissent and impose their agenda on others who they attempted, in the best > Stalinist style, to intimidate and silence. > =E2=80=8BDuty calls! =E2=80=8Bhttp://xkcd.com/386/ Jason --=20 Jason M. Swails BioMaPS, Rutgers University Postdoctoral Researcher --001a11331f9a2160ff050d3fee96 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

On Wed, J= an 21, 2015 at 3:07 PM, Jim Kress jimkress35^^^gmail.com <owner-chemistry[a]ccl.net> wrote:

People need to be reminded of their malice and pernicious attempt to squash=
dissent and impose their agenda on others who they attempted, in the best Stalinist style, to intimidate and silence.

=
=E2=80=8BDuty calls! =E2=80=8Bhttp://xkcd= .com/386/

<troll calls troll a troll>= ;

Jason

--
Jason M. Swails
BioMaPS= ,
Rutgers University
Postdoctoral Researcher
--001a11331f9a2160ff050d3fee96-- From owner-chemistry@ccl.net Thu Jan 22 16:09:01 2015 From: "Mehboob Alam mehboob.cu__gmail.com" To: CCL Subject: CCL:G: Change in coordinates after Single point energy calculation Message-Id: <-50953-150122114541-5577-mpnnPQq8pbjI8iPlhYI9kA()server.ccl.net> X-Original-From: Mehboob Alam Content-Type: multipart/alternative; boundary=089e0158b7e4bf04fa050d4066c7 Date: Thu, 22 Jan 2015 17:45:36 +0100 MIME-Version: 1.0 Sent to CCL by: Mehboob Alam [mehboob.cu]_[gmail.com] --089e0158b7e4bf04fa050d4066c7 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi, For calculation, the program puts the molecule in such a way that the centre of mass (COM) coincides with the origin of the Cartesian axes. The standard orientation represents this orientation. So, input orientation is what you provided to the program and Standard orientation is the one where COM is origin. Hope it helps. Regards, Mehboob Dr. Md. Mehboob Alam Post-Doctoral Researcher Institut de Chimie de Strasbourg Laboratoire de Chimie Quantique Universit=E9 de Strasbourg PostDoc Supervisor - Dr. Emmanuel Fromager On Thu, Jan 22, 2015 at 12:11 PM, Anjali B anjaliamutha|,|gmail.com < owner-chemistry::ccl.net> wrote: > Hello everyone > > Can anyone tell me the difference between input orientation and standard > orientation in gaussian 09 output. > I got different coordinates after single point energy calculation in > solvent. > I used optimized geometry in the input. > > Thank you > --089e0158b7e4bf04fa050d4066c7 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi,

For calculation, the program puts the mol= ecule in such a way that the centre of mass (COM) coincides with the origin= of the Cartesian axes. The standard orientation represents this orientatio= n. So, input orientation is what you provided to the program and Standard o= rientation is the one where COM is origin.

Hope it= helps.

Regards,
Mehboob

Dr. Md. Mehboob Alam
<= /div>Post-Doctoral Researcher
Institut de Chimie de Strasbourg
Laboratoire de Chimie Quantique
Universit=E9 de Strasbourg<= br>
PostDoc Supervisor - Dr. Emmanuel Fromager

On Thu, Jan 22, 2015 at 12:11 PM, Anjali B a= njaliamutha|,|gmail.com = <owner-chem= istry::ccl.net> wrote:
Hello everyone

Can anyone tell me the differ= ence between input orientation and standard orientation in gaussian 09 outp= ut.
I got different coordinates after single point energy cal= culation in solvent.
I used optimized geometry in the input.

Thank you=A0

--089e0158b7e4bf04fa050d4066c7-- From owner-chemistry@ccl.net Thu Jan 22 18:07:01 2015 From: "Igors Mihailovs igors.mihailovs0:-:gmail.com" To: CCL Subject: CCL:G: Change in coordinates after Single point energy calculation Message-Id: <-50954-150122171027-15031-n/XrxpcDMUv96OIXyET2mg.@.server.ccl.net> X-Original-From: Igors Mihailovs Content-Type: multipart/alternative; boundary=089e0158c78a2db93b050d44f050 Date: Fri, 23 Jan 2015 00:10:01 +0200 MIME-Version: 1.0 Sent to CCL by: Igors Mihailovs [igors.mihailovs0:-:gmail.com] --089e0158c78a2db93b050d44f050 Content-Type: text/plain; charset=UTF-8 Dear Anjali, Gaussian simply rotates the molecule before the calculation, to make use of the symmetry of Your molecule (if it detects some). Thus it is reducing computational costs. Symmetry could be even very low, as Cs (one mirror plane, planar molecule). To restrict Gaussian from doing this rotation (e. g., if You want to compare geometries before and after the optimization), You should add "NoSymm" keyword to the route section (#) of Your job. But in any case, the rotation of molecule does not change its geometry. If You check every bond length, angles and dihedrals, they should be the same. With best wishes, Igors Mihailovs (engineer) Institute of Solid State Physics University of Latvia 2015-01-22 13:11 GMT+02:00 Anjali B anjaliamutha|,|gmail.com < owner-chemistry-$-ccl.net>: > Hello everyone > > Can anyone tell me the difference between input orientation and standard > orientation in gaussian 09 output. > I got different coordinates after single point energy calculation in > solvent. > I used optimized geometry in the input. > > Thank you > --089e0158c78a2db93b050d44f050 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Anjali,

Gaussian simply rotates the= molecule before the calculation, to make use of the symmetry of Your molec= ule (if it detects some). Thus it is reducing computational costs. Symmetry= could be even very low, as Cs (one mirror plane, planar molecule). To rest= rict Gaussian from doing this rotation (e. g., if You want to compare geome= tries before and after the optimization), You should add "NoSymm"= keyword to the route section (#) of Your job. But in any case, the rotatio= n of molecule does not change its geometry. If You check every bond length,= angles and dihedrals, they should be the same.

With best wishes,
Igors Mihailovs (engineer)
Institute of Solid Stat= e Physics
University of Latvia

=

2015-01-22 13:11 GMT+02:00 Anjali B anjaliam= utha|,|gmail.com <owner-chemistry-$-c= cl.net>:
H= ello everyone

Can anyone tell me the difference between = input orientation and standard orientation in gaussian 09 output.
=
I got different coordinates after single point energy calculation in s= olvent.
I used optimized geometry in the input.

Thank you=C2=A0

--089e0158c78a2db93b050d44f050-- From owner-chemistry@ccl.net Thu Jan 22 18:42:00 2015 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor(~)fluor.quimica.uniovi.es" To: CCL Subject: CCL:G: Change in coordinates after Single point energy calculation Message-Id: <-50955-150122182551-21108-RSfF1FVInX/bKweCTc2DOA||server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-disposition: inline Content-transfer-encoding: 8BIT Content-type: text/plain; charset=iso-8859-1 Date: Fri, 23 Jan 2015 00:05:46 +0100 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor\a/fluor.quimica.uniovi.es] On Thu, Jan 22, 2015 at 05:45:36PM +0100, Mehboob Alam mehboob.cu__gmail.com wrote: > Hi, > > For calculation, the program puts the molecule in such a way that the > centre of mass (COM) coincides with the origin of the Cartesian axes. The > standard orientation represents this orientation. So, input orientation is > what you provided to the program and Standard orientation is the one where > COM is origin. Some more details can be found on and I didn't check ALL the details in the last document so I can't ensure that everything is correct, but what I examined clearly is! Regards, Dr. Víctor Luaña -- . . "La suma de la mediocridad y de la creatividad es / `' \ constante: a más de la una menos de la otra" /(o)(o)\ (Jorge Wasenberg, 2015) /`. \/ .'\ "mediocrity+creativity=constant" / '`'` \ (First Principle of thermodynamics,Universal version) | \'`'`/ | "Lo mediocre es peor que lo bueno, pero también es peor | |'`'`| | que lo malo, porque la mediocridad no es un grado, es una \/`'`'`'\/ actitud" ===(((==)))==================================+========================= ! Dr.Víctor Luaña ! Mediocre is worse than ! Departamento de Química Física y Analítica ! good, but it is also ! Universidad de Oviedo, 33006-Oviedo, Spain ! worse than bad, because ! e-mail: victor!^!fluor.quimica.uniovi.es ! mediocrity is not a grade, ! phone: +34-985-103491 fax: +34-985-103125 ! it is an attitude +--------------------------------------------+ GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) From owner-chemistry@ccl.net Thu Jan 22 20:55:01 2015 From: "Kaushik Hatua kaushikhatua:-:yahoo.in" To: CCL Subject: CCL: regarding spin densities Message-Id: <-50956-150122125532-9493-ozbKPj+hPPU8JvLVWHrDrQ]*[server.ccl.net> X-Original-From: Kaushik Hatua Content-Type: multipart/alternative; boundary="_77718843-89BC-43F9-8294-9DD134DEECDC_" Date: Thu, 22 Jan 2015 23:25:17 +0530 MIME-Version: 1.0 Sent to CCL by: Kaushik Hatua [kaushikhatua|a|yahoo.in] --_77718843-89BC-43F9-8294-9DD134DEECDC_ Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" I use Gabedit but it need some input in the route section before to run. Sent from Nokia Lumia=20 -----Original Message----- > From: "Hemlata Agarwala cclhemlata]|[gmail.com" Sent: =E2=80=8E21-=E2=80=8E01-=E2=80=8E2015 10:23 PM To: "Hatua, Kaushik " Subject: CCL: regarding spin densities Hi everyone I have done geometry optimization of a transition metal complex using UB3LY= P since it contains unpaired electrons. I have also included the keyword PO= P=3D(NBO,Full) in the input route so that I get the spin densities on the a= toms too. But when I am opening the output file in a graphical visualisation software= like chemcraft I do not get any option to see the spin density values on i= ndividual atoms. Could you please help me out=20 Thanking you Regards Hemlata= --_77718843-89BC-43F9-8294-9DD134DEECDC_ Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset="utf-8"
I use Gabedit but it need some input in the route section= before to run.

Sent from Nokia Lumia
<= hr>From: Hemlata Agarwal= a cclhemlata]|[gmail.com
Sent: =E2=80=8E21-=E2=80= =8E01-=E2=80=8E2015 10:23 PM
To: Hatua, Kaushik
Subject: <= /span>CCL= : regarding spin densities

Hi everyone=

I have done geometry optimization of a transition metal= complex using UB3LYP since it contains unpaired electrons. I have also inc= luded the keyword POP=3D(NBO,Full) in the input route so that I get the spi= n densities on the atoms too.

But when I am openin= g the output file in a graphical visualisation software like chemcraft I do= not get any option to see the spin density values on individual atoms.

Could you please help me out 

Thanking you

Regards
Hemlata
=0A= = --_77718843-89BC-43F9-8294-9DD134DEECDC_--