From owner-chemistry@ccl.net Sun Jul 17 00:11:00 2011 From: "Hyunbok Lee mutebeat*gmail.com" To: CCL Subject: CCL:G: molecular geometry visualization on GaussView Message-Id: <-45096-110717000922-1767-kG5VhhWi3X2YezC8xLlChw-x-server.ccl.net> X-Original-From: "Hyunbok Lee" Date: Sun, 17 Jul 2011 00:09:19 -0400 Sent to CCL by: "Hyunbok Lee" [mutebeat/./gmail.com] Dear all, I performed geometry optimization of a molecule with Gaussian 09. The output was visualized by GaussView 5.0 and I have two questions about it. 1. Cartesian coordinates varied with output file type, *.out or *.chk. Although the differences are very small, (~10^-7 A orders) it is possible? I think that they must have the exactly same geometry because both 'out' and 'chk' come from the same calculation. (An error was not found in my out file.) 2. How are 'bonds' determined in molecular geometry visualization on GaussView? Atomic bonds in the molecule were also not the same due to the above reason. What is the parameter whether two atoms bond or not? (atomic distance?) And can I modify the bond when I load 'chk' file? Thanks in advance. Hyunbok Lee From owner-chemistry@ccl.net Sun Jul 17 02:55:01 2011 From: "Utpal Sarkar utpalchemiitkgp,,gmail.com" To: CCL Subject: CCL: Free Crystal structure generator Message-Id: <-45097-110717025256-25326-fHCrGHo0rsawQxH2erEMuQ[a]server.ccl.net> X-Original-From: Utpal Sarkar Content-Type: multipart/alternative; boundary=bcaec5299a0bac045704a83e5496 Date: Sun, 17 Jul 2011 12:22:48 +0530 MIME-Version: 1.0 Sent to CCL by: Utpal Sarkar [utpalchemiitkgp*gmail.com] --bcaec5299a0bac045704a83e5496 Content-Type: text/plain; charset=ISO-8859-1 Dear CCL users, Can you please suggest me some free software using which I can generate ,say FCC (111) or BCC (100) plane with "M" atoms along x-direction, "N" atoms along Y and "L" along Z? Using this program I want to get the xyz-coordinate of the atoms. Thanking you in advance best regards Utpal --bcaec5299a0bac045704a83e5496 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear CCL users,
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 = Can you please suggest me some free software using which I can generate ,sa= y FCC (111) or BCC (100) plane with=A0"M" atoms along x-direction= ,=A0"N" atoms along Y and=A0"L" along Z? Using this pro= gram I want to get the xyz-coordinate of the atoms.
Thanking you in advance
best regards
Utpal
--bcaec5299a0bac045704a83e5496-- From owner-chemistry@ccl.net Sun Jul 17 13:11:01 2011 From: "Edmanuel Torres torresam]![ualberta.ca" To: CCL Subject: CCL: Free Crystal structure generator Message-Id: <-45098-110717051601-24113-n+xf6Lev23prQXSOGi/Z2A],[server.ccl.net> X-Original-From: Edmanuel Torres Content-Type: multipart/alternative; boundary=000e0cd3b0409077b604a8405399 Date: Sun, 17 Jul 2011 03:15:40 -0600 MIME-Version: 1.0 Sent to CCL by: Edmanuel Torres [torresam##ualberta.ca] --000e0cd3b0409077b604a8405399 Content-Type: text/plain; charset=ISO-8859-1 Try Aten http://www.projectaten.org/ http://www.projectaten.org/doc/Examples ET On Sun, Jul 17, 2011 at 12:52 AM, Utpal Sarkar utpalchemiitkgp,,gmail.com < owner-chemistry:_:ccl.net> wrote: > Dear CCL users, > Can you please suggest me some free software using > which I can generate ,say FCC (111) or BCC (100) plane with "M" atoms along > x-direction, "N" atoms along Y and "L" along Z? Using this program I want to > get the xyz-coordinate of the atoms. > Thanking you in advance > best regards > Utpal > --000e0cd3b0409077b604a8405399 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Try Aten

http://www.proj= ectaten.org/
htt= p://www.projectaten.org/doc/Examples

ET

On Sun, Jul 17, 2011 at 12:52 AM, Utpal Sarkar utpalchemiitkgp,,gmail.com <owner-chemistry:_:ccl.net> wrote:
Dear CCL users,
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 = Can you please suggest me some free software using which I can generate ,sa= y FCC (111) or BCC (100) plane with=A0"M" atoms along x-direction= ,=A0"N" atoms along Y and=A0"L" along Z? Using this pro= gram I want to get the xyz-coordinate of the atoms.
Thanking you in advance
best regards
Utpal


--000e0cd3b0409077b604a8405399-- From owner-chemistry@ccl.net Sun Jul 17 17:27:00 2011 From: "Jonathan Tennyson j.tennyson]~[ucl.ac.uk" To: CCL Subject: CCL: Longuet-Higgins sign change Message-Id: <-45099-110717144246-8173-0+5zWWo9Aubv52VzTicH5A..server.ccl.net> X-Original-From: "Jonathan Tennyson" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Sun, 17 Jul 2011 19:42:37 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: "Jonathan Tennyson" [j.tennyson:ucl.ac.uk] Dear Anita. I wrote my first paper on this topic, see: A.J.C. Varandas, J. Tennyson and J.N. Murrell, Chercher le Croisment, Chem. Phys. Letts., 61, 431-434 (1979). (No it's not in French just a joke from my supervisor). The issue is clouded by the fact that the sign of the wavefunction is arbitrary. What you need to do is establish some sort of phase convention. The best is probably to choose a starting point; choose the sign of the next point to maximize the overlap of the coefficients with the first point and so on round the circle. Should work OK provided your points are reasonably closely spaced. However I should add that my paper above is on the triatomic LiNaK. We originally tried HLiNa (as being simpler) and could not get it to work. Good luck, Jonathan > Dear all, > We know that according to Longuet-Higgins theorem, if the wave > function > changes sign when transported adiabatically around the loop in CS, then > there must be a point of degeneracy within this loop. I am doing the state > average MCSCF calculation in a system which has cs symmetry configuration > . > After detecting the position of conical Intersection(CI) between two A' > states, I tagged the largest coefficient vector of the MCSCF wave function > around the CI, but the coefficient vector changes sign several times.I am > very confused about the result. Am I doing something wrong? > > Any comments on this matter will be greatly appreciated. > Thanks in advance. > anita > > ** > -- Jonathan Tennyson, Department of Physics & Astronomy, mailto: j.tennyson _ ucl.ac.uk University College London, Tel (work): +(44) 20 7679 7155 Gower Street, Tel (home): +(44) 20 8341 0923 London WC1E 6BT, UK Fax (if you must): +(44) 20 7679 7145 http://www.ucl.ac.uk/phys/amopp/people/jonathan_tennyson/ The second edition of my book Astronomical Spectroscopy has just been published, see: http://www.worldscibooks.com/physics/7574.html