From owner-chemistry@ccl.net Tue Jul 10 07:06:00 2012 From: "Elham Abdolhamidi flight.66.ab ~~ gmail.com" To: CCL Subject: CCL: K-points in Gaussian Message-Id: <-47195-120710070437-20942-zuFBt9uH3taLXj6n3FserA~!~server.ccl.net> X-Original-From: "Elham Abdolhamidi" Date: Tue, 10 Jul 2012 07:04:36 -0400 Sent to CCL by: "Elham Abdolhamidi" [flight.66.ab.:.gmail.com] Dear members; I work with Gaussview and I have tried to find the band structure of polypyrrole, using GV.It calculated the energy related to each k-point.but the k points were in this way: K=0,0,0 k=1,1,1 k=2,1,1 k=3,1,1 .... while I need the energies of these points: k=0,0,0 k=1,0,0 k=2,0,0 k=3,0,0 ..... How can I find the energies related to this group of k-points? In other words, how can I control the K-points? From owner-chemistry@ccl.net Tue Jul 10 12:00:01 2012 From: "Nuno A. G. Bandeira nuno.bandeira[a]ist.utl.pt" To: CCL Subject: CCL:G: K-points in Gaussian Message-Id: <-47196-120710114707-11972-JU47sYTc63iuPXMcFSVQEw_-_server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="ISO-8859-1"; format=flowed Date: Tue, 10 Jul 2012 16:46:51 +0100 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira~~ist.utl.pt] Dear Elham, The short answer is you can't. Gaussian has an automatic k-point generation algorithm. Your only option will be to increase the k-point grid with PBC(NKPoint=xx). On 10/07/2012 12:04, Elham Abdolhamidi flight.66.ab ~~ gmail.com wrote: > Sent to CCL by: "Elham Abdolhamidi" [flight.66.ab.:.gmail.com] > Dear members; > I work with Gaussview and I have tried to find the band structure of polypyrrole, using GV.It calculated the energy related to each k-point.but the k points were in this way: K=0,0,0 > k=1,1,1 > k=2,1,1 > k=3,1,1 > .... > while I need the energies of these points: k=0,0,0 > k=1,0,0 > k=2,0,0 > k=3,0,0 > ..... > How can I find the energies related to this group of k-points? In other words, how can I control the K-points? > -- Nuno A. G. Bandeira, AMRSC C8 - Centro de Química e Bioquímica FCUL, Campo Grande Lisbon 1749-016 PORTUGAL http://www.researcherid.com/rid/B-6399-2012 http://pt.linkedin.com/pub/nuno-a-g-bandeira/47/55a/2aa -- From owner-chemistry@ccl.net Tue Jul 10 12:34:01 2012 From: "Joseph Han jhh3851]~[yahoo.com" To: CCL Subject: CCL: Question Message-Id: <-47197-120709165157-15732-VVg2ZQuYO5Iz+Qjb3jCCxw:server.ccl.net> X-Original-From: Joseph Han Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Mon, 9 Jul 2012 13:51:48 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Joseph Han [jhh3851**yahoo.com] Depending upon the system, could you push the check to the shell called by the system command and include a 'wait' in the system call? "call system(cmd1&cmd2&cmd3&cmd4&wait)" I think this should work for bash on linux. Joseph --- On Mon, 7/9/12, John McKelvey jmmckel:+:gmail.com wrote: > From: John McKelvey jmmckel:+:gmail.com > Subject: CCL: Question > To: "Han, Joseph " > Date: Monday, July 9, 2012, 6:51 AM > > Sent to CCL by: John McKelvey [jmmckel{=}gmail.com] > Hello... > > I'm trying to get 4 processes to run simultaneously on a 4 > processor > box and wait until they are all finished before > proceeding.  Don't > have "fork" , "wait" or "sleep" available in free ftn > compiler... > > I think I can do a "call > system(cmd1&cmd2&cmd3&cmd4)" to get the 4 > processes running at the same time, but I then need to wait > till all 4 > are finished before proceeding to the next step.  I > could do a "grep > *.out > wclist" and check the value of wclist in an > "infinite loop" > until satisfied, i.e. wclist=4, but would this eat a lot of > cycles? > > Would be happy to check out forums for this... > > > Many thanks.. > > John > > > > -- > John McKelvey > 10819 Middleford Pl > Ft Wayne, IN 46818 > 260-489-2160 > jmmckel ~ gmail.com > > > > -= This is automatically added to each message by the > mailing script =- > To recover the email address of the author of the message, > please change > the strange characters on the top line to the [#] sign. You > can also> > E-mail to subscribers: CHEMISTRY[#]ccl.net > or use: >      > > E-mail to administrators: CHEMISTRY-REQUEST[#]ccl.net > or use >      >      >      > > > From owner-chemistry@ccl.net Tue Jul 10 14:53:01 2012 From: "Ronald C Bakus II rbakus~!~chem.ucsb.edu" To: CCL Subject: CCL:G: Plotting ground to excited state transition dipoles Message-Id: <-47198-120710145236-1961-aaDUj9UZEfjEkzLElTdzkQ!=!server.ccl.net> X-Original-From: "Ronald C Bakus II" Date: Tue, 10 Jul 2012 14:52:35 -0400 Sent to CCL by: "Ronald C Bakus II" [rbakus###chem.ucsb.edu] Does anyone know of a program that allows you to plot the transition electric dipole moment from gaussian TDDFT calculations? There was a thread on this in '07, and I have tried the software mentioned (CCP1GUI), but it refuses to run on any of the machines I have tried. As such, I'd appreciate suggestions for other software that has this capability. Thanks, Ron From owner-chemistry@ccl.net Tue Jul 10 15:53:00 2012 From: "Gregorio =?iso-8859-1?Q?Garc=EDa_Moreno?= gjgarcia{=}ujaen.es" To: CCL Subject: CCL:G: Plotting ground to excited state transition dipoles Message-Id: <-47199-120710155115-27658-WoMYcoEwn/qIriXhAHGkhg^^^server.ccl.net> X-Original-From: Gregorio =?iso-8859-1?Q?Garc=EDa_Moreno?= Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Tue, 10 Jul 2012 21:50:50 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: Gregorio =?iso-8859-1?Q?Garc=EDa_Moreno?= [gjgarcia^^^ujaen.es] Try to look for a paper of T. LeBaher, C. Adamo et. al pusblised in JCTC 2011 about charge transfer index. > > Sent to CCL by: "Ronald C Bakus II" [rbakus###chem.ucsb.edu] > Does anyone know of a program that allows you to plot the transition > electric dipole moment from gaussian TDDFT calculations? There was a > thread on this in '07, and I have tried the software mentioned (CCP1GUI), > but it refuses to run on any of the machines I have tried. As such, I'd > appreciate suggestions for other software that has this capability. > > Thanks, > Ron> > From owner-chemistry@ccl.net Tue Jul 10 16:58:00 2012 From: "Joy Ku joyku||stanford.edu" To: CCL Subject: CCL: Workshop: Rapid Molecular Dynamics Prototyping and Simulations on GPU Message-Id: <-47200-120710155344-28878-JU47sYTc63iuPXMcFSVQEw:server.ccl.net> X-Original-From: "Joy Ku" Date: Tue, 10 Jul 2012 15:53:43 -0400 Sent to CCL by: "Joy Ku" [joyku%stanford.edu] Simbios invites you to join us at its next Open Molecular Mechanics (OpenMM) workshop. OpenMM (http://simtk.org/home/openmm) is open-source software that enables molecular dynamics (MD) simulations to be accelerated on high performance computer architectures. It has demonstrated speed ups for both implicit solvent[1] and explicit solvent simulations[2] on graphics processing units (GPUs) [see benchmarks at http://wiki.simtk.org/openmm/Benchmarks]. And with the new application layer in its recent release, OpenMM will allow non-programmers to easily and quickly run MD simulations and develop custom algorithms on GPUs, while continuing to enable programmers to integrate OpenMM into their own programs. ***WORKSHOP: RAPID MOLECULAR DYNAMICS PROTOTYPING AND SIMULATIONS ON GPUS *** Where: Stanford University When: September 6-7, 2012 Description: During the workshop, you will gain hands-on experience using OpenMMs new application layer and application programming interface (API). Learn to: * Set up and run an MD simulation on your GPU using both PDB and AMBER files * Create a custom force to apply to your simulations * Customize the simulation through Python scripting You will also have time to work with the OpenMM development team on your own research project. This workshop is designed for those interested in accelerating MD simulations on GPUs and/or developing new MD algorithms that can automatically be implemented and accelerated on GPUs. No programming background is required, though programming topics will also be covered for those who are interested in them. Registration: Registration is free but required and spaces are limited. To register or for more information, visit http://simbios.stanford.edu/MDWorkshop.htm. ________________________________________ OpenMM is supported by Simbios, an NIH National Center for Physics-Based Simulation of Biological Structures. To learn more about Simbios and its research and software tools, visit http://simbios.stanford.edu. [1] OpenMM accelerated code running on NVIDIA GeForce GTX 280 GPU vs. conventional code with Amber9 running on Intel Xenon 2.66 GHz CPU. MS Friedrichs, et al., "Accelerating Molecular Dynamic Simulation on Graphics Processing Units," J. Comp. Chem., 2009, 30(6):864-872. [2]Eastman, P. and Pande, V.S., Efficient Nonbonded Interactions for Molecular Dynamics on a Graphics Processing Unit, J. Comp. Chem., 2010, 31(6):1268-1272.