So it is = useful to understand the parallel speedups of a code one has
already decided to use, but it is misleading to = compare parallel
speedups of different codes = without looking at the actual time to
solution = for representative calculations (being careful to compare
with similar accuracy settings, etc.)

Best = regards,
Gert von Helden

= --Apple-Mail-12-415981932-- From owner-chemistry@ccl.net Tue Oct 2 11:22:01 2007 From: "Tom FA de Greef t.f.a.d.greef!A!tue.nl" To: CCL Subject: CCL:G: TDDFT electric transition dipole moment plotting Message-Id: <-35287-071002092644-2120-3FuRLBhfMA/aBZSymkpT2g|a|server.ccl.net> X-Original-From: "Tom FA de Greef" Date: Tue, 2 Oct 2007 09:26:41 -0400 Sent to CCL by: "Tom FA de Greef" [t.f.a.d.greef#tue.nl] Dear all, Last week I asked if any programs are availabe to plot the ground to excited state transition electric dipole moment from gaussian TDDFT calculations (these vectors appear in the .log file). Due to the lack of response there are maybe no standard programs that can do the trick. However, maybe there are programs available that read the standard coordinates from the .log file and that give an option to plot a vector in terms of x,y,z coordinates. Does anyone know of such a program that can do this (windows or linux). best regards, tom From owner-chemistry@ccl.net Tue Oct 2 12:26:00 2007 From: "Herbert Fruchtl herbert.fruchtl .. st-andrews.ac.uk" To: CCL Subject: CCL:G: Gaussian parallelism and parallelism in general Message-Id: <-35288-071002122317-12271-YAdytCI983/r/Rr7y42Rzw|,|server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 02 Oct 2007 17:19:09 +0100 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl]~[st-andrews.ac.uk] PNNL used to do that, but their page looks like it's 10 years old: http://www.emsl.pnl.gov/docs/tms/abinitio/cover.html Nowadays many programs (including free ones) have clauses in their licenses that forbid publishing comparative benchmark results, at least without explicit permission from the owners. I have seen (and written) internal reports, but it is not as straight-forward as it looks on first sight. Results vary widely depending on lots of parameters: large basis set or large molecule? Symmetric or not? Integral cutoffs and convergence criteria. RI basis sets and other approximation methods. That's before you even look at parallelism (bandwidth? latency? local or shared I/O? memory contention?). And the fastest gradients don't help you if the geometry optimization doesn't converge (I know only two programs with a good, robust general purpose optimizer). Herbert Gert von Helden helden=fhi-berlin.mpg.de wrote: > > On Oct 2, 2007, at 1:41 AM, frisch[*]gaussian.com (Michael Frisch) wrote: > >> >> >> So it is useful to understand the parallel speedups of a code one has >> already decided to use, but it is misleading to compare parallel >> speedups of different codes without looking at the actual time to >> solution for representative calculations (being careful to compare >> with similar accuracy settings, etc.) >> >> > > Are there any benchmarks available that compare different codes? That > would be most useful, possibly avoiding a lot of wasted resources. > > Best regards, > Gert von Helden > -- Herbert Fruchtl EaStCHEM Fellow School of Chemistry University of St Andrews From owner-chemistry@ccl.net Tue Oct 2 13:01:00 2007 From: "John McKelvey jmmckel/./gmail.com" To: CCL Subject: CCL:G: TDDFT electric transition dipole moment plotting Message-Id: <-35289-071002124328-31258-Y5+oUadUOy67oy/c9PuRrg]=[server.ccl.net> X-Original-From: "John McKelvey" Content-Type: multipart/alternative; boundary="----=_Part_23117_12571168.1191343396544" Date: Tue, 2 Oct 2007 12:43:16 -0400 MIME-Version: 1.0 Sent to CCL by: "John McKelvey" [jmmckel ~ gmail.com] ------=_Part_23117_12571168.1191343396544 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline I would think that most programs can provide the x, y, and z components of the transition moment or dipole in addition to the vector total. Thus I would think any program that can plot a 3D vector should do as you wish. John McKelvey On 10/2/07, Tom FA de Greef t.f.a.d.greef!A!tue.nl wrote: > > > Sent to CCL by: "Tom FA de Greef" [t.f.a.d.greef#tue.nl] > Dear all, > Last week I asked if any programs are availabe to plot the ground to > excited state transition electric dipole moment from gaussian TDDFT > calculations (these vectors appear in the .log file). Due to the lack of > response there are maybe no standard programs that can do the trick. > However, maybe there are programs available that read the standard > coordinates from the .log file and that give an option to plot a vector in > terms of x,y,z coordinates. Does anyone know of such a program that can do > this (windows or linux). > > best regards, > > tom> > > > ------=_Part_23117_12571168.1191343396544 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline I would think that most programs can provide the x, y, and z components of the transition moment or dipole in addition to the vector total. Thus I would think any program that can plot a 3D vector should do as you wish.

John McKelvey

On 10/2/07, Tom FA de Greef t.f.a.d.greef!A!tue.nl <owner-chemistry**ccl.net> wrote:

Sent to CCL by: "Tom FA de Greef" [t.f.a.d.greef#tue.nl]
Dear all,
Last week I asked if any programs are availabe to plot the ground to excited state transition electric dipole moment from gaussian TDDFT calculations (these vectors appear in the .log file). Due to the lack of response there are maybe no standard programs that can do the trick. However, maybe there are programs available that read the standard coordinates from the .log file and that give an option to plot a vector in terms of x,y,z coordinates. Does anyone know of such a program that can do this (windows or linux).

best regards,

tom

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------=_Part_23117_12571168.1191343396544-- From owner-chemistry@ccl.net Tue Oct 2 15:13:01 2007 From: "Uwe Huniar uwe.huniar%x%cosmologic.de" To: CCL Subject: CCL: Gaussian 03 MP2 performance Message-Id: <-35290-071002093834-8353-G8zJQe1fF5fM8it41CrSKg,,server.ccl.net> X-Original-From: Uwe Huniar Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 02 Oct 2007 14:41:52 +0200 MIME-Version: 1.0 Sent to CCL by: Uwe Huniar [uwe.huniar~~cosmologic.de] the list of programs with RI-MP2 lacks of the one that has RI-MP2 energy and gradients since about 10 years: Turbomole RI-MP2 gradients have originally been published in 1997 (Theor. Chem. Acc. 97, 1997, 331) by Weigend and H�ser, and implemented in Turbomole. Meanwhile RI-MP2 calculations can also be done in parallel (based on MPI), here an example (taken from K�hn, H�ttig, Chem. Phys. Lett. 358, 2002, 350, and from a talk a bit later that used faster CPUs): Calicheamicin fragment, 39 atoms, cc-pVTZ basis, 924 basis functions, C1, MP2 energy, on (ancient) Athlon 1800 MP CPUs, 100MBit Ethernet: CPU Total wall time in minutes 1 60 7 18 13 11 A short note about the scaling: the N**5 step that is dominant for larger systems on 1, 7, 13 CPUs takes 34, 5.5, 3 minutes, resp. The MP2 energy was -4.26 Hartree, the error from RI 0.0005 Hartree when using the auxiliary basis sets of Weigend and H�ser (included in Turbomole and also available from the Turbomole ftp server). On a Core 2 machine an RI-MP2 single point calculation should take just a few minutes (and yes: that is shorter than the ground state Hartree-Fock calculation, but one can use RI-JK as pre-step for RI-MP2 with Turbomole). Regards, Uwe > MP2 does get expensive as the number of basis functions increases > (scaling as n**5). If it's only single-point calculations that you need, > you may want to look at "local" or "RI" implementations (you find them > in Q-Chem, NWChem, MOLPRO, ORCA, and probably several other programs > nowadays; some of them even have gradients, which used to be the problem > until lately). -- ------------------------------------------------------------------------------ Dr. Uwe Huniar COSMOlogic GmbH&Co.KG Burscheider Str. 515 D-51381 Leverkusen Germany Tel. +49 - 2171 - 36 36 65 Fax +49 - 2171 - 73 16 89 EMail: uwe.huniar,+,cosmologic.de turbomole,+,cosmologic.de info,+,turbomole.com From owner-chemistry@ccl.net Tue Oct 2 16:14:01 2007 From: "Rajarshi Guha rguha/./indiana.edu" To: CCL Subject: CCL: smi23d update Message-Id: <-35291-071002144324-22657-/g4lbIUpJUNpwVImvZRD1Q]~[server.ccl.net> X-Original-From: Rajarshi Guha Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Tue, 2 Oct 2007 14:43:05 -0400 Mime-Version: 1.0 (Apple Message framework v752.3) Sent to CCL by: Rajarshi Guha [rguha]_[indiana.edu] Hi, we've made a number of updates to the smi23d application for generating 3D coordinates from SMILES strings. * The code no longer uses stochastic proximity embedding * mengine has been modified so that by default it will not evaluate molecular properties like dipole moment and vibrational properties. This should provide a slight speed up in the optimization step. You can use command line switches to evaluate these if desired * We now provide a SOAP web service which accepts SMILES strings and returns an SDF with the 3D coordinates * A web form is provided (based on the above WS) which allows you to get 3D structures without having to use the program locally. It is limited to 200 molecules. The latest code is available from SVN and binaries for OS X and 64- bit Intel Linux are provided. smi23d - http://www.chembiogrid.org/cheminfo/smi23d/ web form - http://www.chembiogrid.org/cheminfo/threed/d3 ------------------------------------------------------------------- Rajarshi Guha GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- All science is either physics or stamp collecting. -- Ernest Rutherford