From owner-chemistry@ccl.net Fri May 1 07:22:01 2015 From: "Jan H Jensen jhjensen(-)chem.ku.dk" To: CCL Subject: CCL: Computational Chemistry Highlights: April issue Message-Id: <-51336-150501045356-2452-kA2U2+UB58vkw0xv7erUpw[#]server.ccl.net> X-Original-From: "Jan H Jensen" Date: Fri, 1 May 2015 04:53:55 -0400 Sent to CCL by: "Jan H Jensen" [jhjensen.{}.chem.ku.dk] The April issue of Computational Chemistry Highlights is out. http://www.compchemhighlights.org/2015_04_01_archive.html CCH is an overlay journal that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years. CCH is not affiliated with any publisher: it is a free resource run by scientists for scientists. Table of content for this issue features contributions from CCH editors Mario Barbatti, Steven Bachrach, and Jan Jensen: Big Data Meets Quantum Chemistry Approximations: The -Machine Learning Approach http://www.compchemhighlights.org/2015/04/big-data-meets-quantum-chemistry.html Electron-Driven Proton Transfer Along H2O Wires Enables Photorelaxation of * States in ChromophoreWater Clusters http://x.vindicosuite.com/click/fbfpc=1;v=5;m=3;l=401071;c=776283;b=3368032;dct=http%3A/ /www.compchemhighlights.org/2015/04/electron-driven-proton-transfer-along-h.html The Fluorenyl Cation http://www.compchemhighlights.org/2015/04/the-fluorenyl-cation.html The Nucleoside Uridine Isolated in the Gas Phase http://www.compchemhighlights.org/2015/04/the-nucleoside-uridine-isolated-in-gas.html Interested in more? There are many ways to subscribe to CCH updates. http://www.compchemhighlights.org/p/get-cch-updates.html Also, for your daily computational chemistry fix subscribe to Computational Chemistry Daily https://paper.li/janhjensen/1416314690 From owner-chemistry@ccl.net Fri May 1 11:02:01 2015 From: "Igors Mihailovs igors.mihailovs0::gmail.com" To: CCL Subject: CCL: Spin contamination increased by annihilation of the first-order contaminant Message-Id: <-51337-150501110125-32146-YbeXmPHP3SSRrtVJ5+XgZA _ server.ccl.net> X-Original-From: Igors Mihailovs Content-Type: multipart/alternative; boundary=001a11c33f0213daf10515067cb1 Date: Fri, 1 May 2015 18:00:58 +0300 MIME-Version: 1.0 Sent to CCL by: Igors Mihailovs [igors.mihailovs0_._gmail.com] --001a11c33f0213daf10515067cb1 Content-Type: text/plain; charset=UTF-8 Dear all, I was quite surprised when, during stability analysis of my wavefunction and subsequent reoptimization of it in unrestricted space, the spin contamination was not descreased by removal of the first-order contaminant: SCF Done: E(RHF) = -2277.17663511 A.U. after 1 cycles NFock= 1 Conv=0.39D-08 -V/T= 2.0012 [..] The wavefunction has an RHF -> UHF instability. The two search directions are symmetric. [..] SCF Done: E(UHF) = -2277.19705082 a.u. after 42 cycles Convg = 0.4967D-05 164 Fock formations. S**2 = 2.1080 -V/T = 2.0009 = 0.0000 = 0.0000 = 0.0000 = 2.1080 S= 1.0356 = 0.000000000000E+00 Annihilation of the first spin contaminant: S**2 before annihilation 2.1080, after 8.9661 Is there some way to interpret this result? Looking forward to Your help, Igors Mihailovs (engineer) Institute of Solid State Physics University of Latvia --001a11c33f0213daf10515067cb1 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear all,

I was quite surprised whe= n, during stability analysis of my wavefunction and subsequent reoptimizati= on of it in unrestricted space, the spin contamination was not descreased b= y removal of the first-order contaminant:


=C2=A0 SCF Done:=C2=A0= E(RHF) =3D=C2=A0 -2277.17663511=C2=A0=C2=A0=C2=A0=C2=A0 A.U. after=C2=A0= =C2=A0=C2=A0 1 cycles
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 NFoc= k=3D=C2=A0 1=C2=A0 Conv=3D0.39D-08=C2=A0=C2=A0=C2=A0=C2=A0 -V/T=3D 2.0012
=C2=A0[..]
=C2=A0The wavefunction has an RHF -> UHF instability.
=C2=A0The two search directions are symmetric.
=C2=A0[..]
=C2=A0SCF Done:=C2=A0 E(UHF) =3D=C2=A0 -2277.19705082=C2=A0=C2=A0=C2=A0= =C2=A0 a.u. after=C2=A0=C2=A0 42 cycles
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 Conv= g=C2=A0 =3D=C2=A0=C2=A0=C2=A0 0.4967D-05=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= 164 Fock formations.
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 S**2 =3D=C2=A0 2.1080=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 -V/T =3D=C2=A0= 2.0009
=C2=A0<Sx>=3D 0.0000 <Sy>=3D 0.0000 <Sz>=3D 0.0000 &l= t;S**2>=3D 2.1080 S=3D 1.0356
=C2=A0<L.S>=3D 0.000000000000E+00
=C2=A0Annihilation of the first spin contaminant:
=C2=A0S**2 before annihilation=C2=A0=C2=A0=C2=A0=C2=A0 2.1080,=C2=A0=C2= =A0 after=C2=A0=C2=A0=C2=A0=C2=A0 8.9661
=C2=A0

Is there some way to interpret this result?

Looking forward to Your help,
Igors Mihailovs (engineer)
Institute of Solid State Physics
University of L= atvia

--001a11c33f0213daf10515067cb1-- From owner-chemistry@ccl.net Fri May 1 12:48:01 2015 From: "Mariusz Radon mariusz.radon!A!gmail.com" To: CCL Subject: CCL: How to insert basic set manually in GAMES? Message-Id: <-51338-150430132521-18251-L/mQ0NfAWi3vlw8ssjhfsw-,-server.ccl.net> X-Original-From: Mariusz Radon Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 30 Apr 2015 19:25:02 +0200 MIME-Version: 1.0 Sent to CCL by: Mariusz Radon [mariusz.radon^-^gmail.com] On 04/30/2015 06:15 AM, Shawkat Islam sislam|,|swin.edu.au wrote: > Sent to CCL by: "Shawkat Islam" [sislam===swin.edu.au] > Hi, I want to use two different basic sets for my molecule, one of which is > not in the GAMES default basic set. How I can I insert that manually in the > input files? > > Thanks > Hi, take a look at this (from INPUT.DOC in GAMESS documentation): """ EXTFIL = a flag to read basis sets from an external file, defined by EXTBAS, rather than from $DATA. (default=.false.) """ You can download many basis sets in the GAMESS format from EMSL Basis Set Exachange. Best, Mariusz> > -- Dr Mariusz Radon, Ph.D. Coordination Chemistry Group Faculty of Chemistry Jagiellonian University ul. Ingardena 3, 30-060 Krakow, Poland http://www2.chemia.uj.edu.pl/~mradon From owner-chemistry@ccl.net Fri May 1 15:40:01 2015 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor * fluor.quimica.uniovi.es" To: CCL Subject: CCL: Spin contamination increased by annihilation of the first-order contaminant Message-Id: <-51339-150501153729-10229-fjDmGjwIwIqwH0UKaeFDTg . 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, 01 May 2015 21:29:20 +0200 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor%x%fluor.quimica.uniovi.es] On Fri, May 01, 2015 at 06:00:58PM +0300, Igors Mihailovs igors.mihailovs0::gmail.com wrote: > I was quite surprised when, during stability analysis of my wavefunction > and subsequent reoptimization of it in unrestricted space, the spin > contamination was not descreased by removal of the first-order contaminant: > The wavefunction has an RHF -> UHF instability. > The two search directions are symmetric. > Is there some way to interpret this result? Sorry, no simple to say without knowing any other thing about your problem, but a Jahn-Teller effect corresponds to the data available. Regards, Dr. Víctor Luaña -- . . "Research is to see what everybody else has seen, and to / `' \ think what nobody else has thought"-- Albert Szent-Gyorgi /(o)(o)\ /`. \/ .'\ "Lo mediocre es peor que lo bueno, pero también es peor / '`'` \ que lo malo, porque la mediocridad no es un grado, es una | \'`'`/ | actitud" -- Jorge Wasenberg, 2015 | |'`'`| | (Mediocre is worse than good, but it is also worse than \/`'`'`'\/ bad, because mediocrity is not a grade, it is an attitude) ===(((==)))==================================+========================= ! Dr.Víctor Luaña, in silico chemist & prof. ! ! Departamento de Química Física y Analítica ! ! Universidad de Oviedo, 33006-Oviedo, Spain ! ! e-mail: victor^^^fluor.quimica.uniovi.es ! ! phone: +34-985-103491 fax: +34-985-103125 ! +--------------------------------------------+ GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) From owner-chemistry@ccl.net Fri May 1 17:47:00 2015 From: "Mariusz Radon mariusz.radon::gmail.com" To: CCL Subject: CCL: Spin contamination increased by annihilation of the first-order contaminant Message-Id: <-51340-150501174523-12051-0awbFALzOQLh/ZN/IuMTng{:}server.ccl.net> X-Original-From: Mariusz Radon Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8 Date: Fri, 01 May 2015 23:45:15 +0200 MIME-Version: 1.0 Sent to CCL by: Mariusz Radon [mariusz.radon]_[gmail.com] On 05/01/2015 05:00 PM, Igors Mihailovs igors.mihailovs0::gmail.com wrote: > Dear all, > > the spin > contamination was not descreased by removal of the first-order contaminant: > (...) > Annihilation of the first spin contaminant: > S**2 before annihilation 2.1080, after 8.9661 > > > Is there some way to interpret this result? > Dear Igors: Yes, this could happen if your wave function is contaminated by higher spin states (not only S+1, but also S+2, S+3, etc; where S = M_S is the desired spin state; zero in your case). Take a look at the following paper: Davidson, E. R. & Clark, A. E. "Spin Polarization and Annihilation for Radicals and Diradicals" Int. J. Quantum Chem., 2005, 103, 1-9. The most relevant conclusion: "The annihilation procedure greatly increases the weights on the higher spin states and can easily lead to an increase, rather than a decrease, in ." You have probably a biradical or multiradical system. In such case, analysis of natural orbitals (eigenvectors of the density matrix) or natural spin density orbitals (eigenvectors of the spin density matrix), or Amos-Hall corresponding orbitals can be useful to identify the pairs of weakly coupled electrons in your system. Best regards, Mariusz -- Dr Mariusz Radon, Ph.D. Coordination Chemistry Group Faculty of Chemistry Jagiellonian University ul. Ingardena 3, 30-060 Krakow, Poland http://www2.chemia.uj.edu.pl/~mradon