From owner-chemistry@ccl.net Sat Apr 18 02:06:01 2009 From: "Nathaniel Swenson nswenson###gustavus.edu" To: CCL Subject: CCL: Webmo Kills my jobs every six hours Message-Id: <-39109-090417171655-12797-d3ON+6g66LYFSR1o1IzR9g~~server.ccl.net> X-Original-From: Nathaniel Swenson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 17 Apr 2009 15:44:37 -0500 MIME-Version: 1.0 Sent to CCL by: Nathaniel Swenson [nswenson]_[gustavus.edu] When I was setting up WebMO, I had a few quirks too, but I solved all of them. Here's a couple things to check: 1) What are the time limit / job limit quotas set on your WebMO account? If you are running out of your alloted time, this is a likely reason why WebMO would kill your job. 2) Does the WebMO user account on your server have administrative access to your PBS queue (or whatever resource manager you are using)? This is what solved the problems I was having. In my case, I included the following lines in my TORQUE (PBS) configuration (assuming your webmo account is 'webmo' and the dns suffix of the computers in your cluster is '.cluster'): set server managers += webmo{:}*.cluster set server operators += webmo{:}*.cluster 3) You may also want to check the settings & limits for your account in your job scheduler (we use MAUI). WebMO might not be killing your jobs - it might be your PBS job scheduler, and your jobs may be getting killed because you are exceeding the amount of time you are allowed to use (as defined in the scheduler config files). Good luck! Nathaniel Swenson nswenson*at*gustavus.edu Yong Yan yyan(-)tulane.edu wrote: > Sent to CCL by: "Yong Yan" [yyan!A!tulane.edu] > Hi, All; > I used the webmo with the account by my university (Tulane university). In previous days, everything goes on pretty well, but I do not know why in recent days, they are going to kill my jobs every six hours, no matter what job it is. > Did anyone has the similar experience before? How can I improve it. > Thank you very much! > > Best Wishes! > Yong Yan > yyan * tulane.edu> > > From owner-chemistry@ccl.net Sat Apr 18 03:19:01 2009 From: "Jerome Kieffer jerome.Kieffer,+,terre-adelie.org" To: CCL Subject: CCL: structure from hkl Miller index Message-Id: <-39110-090418024952-16440-TSDWckBdIQD+18WJ0711Mw|-|server.ccl.net> X-Original-From: Jerome Kieffer Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-15 Date: Sat, 18 Apr 2009 08:46:11 +0200 Mime-Version: 1.0 Sent to CCL by: Jerome Kieffer [jerome.Kieffer:_:terre-adelie.org] Have a look at direct methods like SIR .... http://scripts.iucr.org/cgi-bin/paper?S0021889803012585 --=20 J=E9r=F4me KIEFFER =20 http://www.terre-adelie.org From owner-chemistry@ccl.net Sat Apr 18 05:06:01 2009 From: "Pablo Vitoria Garcia pablo.vitoria . ehu.es" To: CCL Subject: CCL: structure from hkl Miller index Message-Id: <-39111-090418050019-5450-awZ5rdvj64/YFBWLUi5GWA**server.ccl.net> X-Original-From: Pablo Vitoria Garcia Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Sat, 18 Apr 2009 10:59:24 +0200 MIME-Version: 1.0 Sent to CCL by: Pablo Vitoria Garcia [pablo.vitoria . ehu.es] Dear David, There are lots of free software that can solve a crystal structure =20 > from the data collected using X-ray diffraction, either on a single =20 crystal or a powder specimen. See, for example, the CCP14 site =20 (http://www.ccp14.ac.uk/tutorial/tutorial.htm) which although a bit =20 outdated can be a helpful starting point. Anyway, I would advise you to contact a crystallographer, since the =20 training for the task can be quite demanding (specially for powder =20 samples). But first of all, if you know the formula of the compound you are =20 interested in, I would check the crystallographic databases to see if =20 its structure is already know: ICSD for inorganic compounds, CSD for =20 (metalo)organic ones, PDF4,... If you don not have access to these, I =20 can help you if you give me the details of the compound. Best regards Pablo ******************************** Pablo Vitoria Garcia Research Services Technician, X-ray Diffraction Unit Web: http://www.ehu.es/SGIker/es/rayos_x/ Universidad del Pa=EDs Vasco (UPV/EHU) Fac. Ciencia y Tecnolog=EDa, Edificio CD3 c/ Barrio Sarriena s/n, 48940 Leioa (Bizkaia) Tfno. +34 946015334 Fax +34 946013500 ******************************** "David Santos david++fq.uh.cu" ha escrito: > > Sent to CCL by: "David Santos" [david::fq.uh.cu] > Is there any (free) software that propose the structure of a solid =20 > from the hkl Miller index obtained from X-ray diffraction? > Actually I want to know the parameters of the atoms in the unit cell =20 > for a salt of known molecular formula. > I accept any other sugerence. > Thanks in advance, > > David Santos Carballal > Departamento de Qumica-Fsica > Facultad de Qumica-Universidad de la Habana. > Zapata s/n entre G y Carlitos Aguirre. > Prncipe. Plaza de la Revolucin. > Cdigo Postal 10400. Cuba > e-mail: david]-[fq.uh.cu phone: 878-0684 > url: http://www.fq.uh.cu/investig/gqf/e/dsc.htm > > > > -=3D This is automatically added to each message by the mailing script =3D= -> > > --=20 ******************************** Pablo Vitoria Garcia Servicios Generales de Rayos X Universidad del Pa=EDs Vasco (UPV/EHU) Fac. Ciencia y Tecnolog=EDa, Edificio CD3 c/ Barrio Sarriena s/n, 48940 Leioa (Bizkaia) Tfno. +34 946015334 Fax +34 946013500 ******************************** From owner-chemistry@ccl.net Sat Apr 18 06:24:00 2009 From: "Peter Bladon cbas25,,strath.ac.uk" To: CCL Subject: CCL: Monitors for molecular Modelling Message-Id: <-39112-090418061921-6676-d+AWwi+JC4K7+KPGADzFbQ:_:server.ccl.net> X-Original-From: "Peter Bladon" Date: Sat, 18 Apr 2009 06:19:17 -0400 Sent to CCL by: "Peter Bladon" [cbas25(~)strath.ac.uk] With regard to the hand-held stereoviewers that were sold by VCH. VCH was I think the marketting arm of the German Chemical Society, but was aquired by Wiley some time between 1993 and 2003 (my vagueness here is because I am looking at the imprints of books published on these dates). Whether Wiley are still selling the viewers is another matter. There were two models (I got both of them when the Royal Society of Chemistry was selling them). With regard to monitors, Mitsubishi-Electric advertised their Diamond 1080p DLP HDTV as being capable of stereo viewing using shutter glasses. It came in three models 57, 65 and 73 inches. They have sockets for connection to computers, and resolutions up to 1280 x 1024 and 1920 x 1080. I do not know how much they cost. They were announced in North America, and I recollect that MItsubishi in the UK had no record of them I have always thought that using twin projectors was a better solution for viewing stereo when more than one person is involved. But projectors with native resolution of 1280 x 1024 (which I regard as a standard) are rather rare. Peter Bladon Interprobe Chemical Services Gallowhill House, Larch Avenue Lenzie, Kirkintilloch Glasgow G66 4HX From owner-chemistry@ccl.net Sat Apr 18 23:35:01 2009 From: "mi Yang shabbir . nenu.edu.cn" To: CCL Subject: CCL:G: First hyperpolarizability Vs intrisic First hyperpolarizabilty with FF Message-Id: <-39113-090418030658-26861-ot6J4rFeXFC3oqHCHwQR0A-.-server.ccl.net> X-Original-From: "mi Yang" Date: Sat, 18 Apr 2009 03:06:55 -0400 Sent to CCL by: "mi Yang" [shabbir(!)nenu.edu.cn] Dear CCL users! Last time I posted the question but did not get any satisfactory answer. I have calculated the first hyperpolarizability (beta) by finite field method (Polar=Enonly). I used all the default criteria in G03. I have not applied any field. I read many papers some use the field value of 0.0010 and some did not mention at all about field value during calculation of first hyperpolarizability with G03. Now my question is Can I report this value of beta as static first hyperpolarizability or I must have to give some field to calculate beta value? Also confusing between intrinsic first hyperpolarizability and first hyperpolarizability in a way of calculating it with FF method in G03. Highly appriciating for answer! Regards Miyang