From owner-chemistry@ccl.net Wed Sep 23 00:40:00 2015 From: "Nico Green nicogreen6%x%gmail.com" To: CCL Subject: CCL: Constructive DFT suggestions appreciated Message-Id: <-51774-150922205745-3878-pkh4Q+TsxFUo46uGSni0Zw#%#server.ccl.net> X-Original-From: Nico Green Content-Type: multipart/alternative; boundary=001a11353a02ea3abb05205f9967 Date: Wed, 23 Sep 2015 00:57:30 +0000 MIME-Version: 1.0 Sent to CCL by: Nico Green [nicogreen6||gmail.com] --001a11353a02ea3abb05205f9967 Content-Type: text/plain; charset=UTF-8 While I think is the responsibility of each one of us to read, think and analyze when choosing the level of theory to use in any computational study we perform, the idea of what Alan meant was the idea of any discussion: If you are going to discredit something or someone, you should give a reason, not just because. That is my point of view of the subject, just don't say something isn't good (at a particular case) without justifying and if is possible give some thoughts of what should be a better choice. Nico On Tue, Sep 22, 2015 at 9:34 PM Susi Lehtola susi.lehtola!^! alumni.helsinki.fi wrote: > > Sent to CCL by: Susi Lehtola [susi.lehtola###alumni.helsinki.fi] > On 09/22/2015 02:31 PM, Alan Shusterman alan=-=reed.edu wrote: > > I have read several CCL messages over the past few weeks disparaging a > > correspondent's choice of DFT functional (usually B3LYP, but not always) > as > > being obsolete, useless, or both. > > > > These are perfectly fair opinions to share, but they are not > constructive. > > If you want to disparage a computational approach, fine with me, but > please > > recommend at least *one* better alternative. I would like to learn what > you > > think I should use, not just what I should not use. > > > > You don't need to cite publications or explain why you prefer a > particular > > functional. I can look that up once you tell me which functional(s) you > > think are worthy. > > This is certainly true. However, this *is* the computational chemistry > list, and most of the people here are scientists. The main duty of a > scientist is keep up to date with current methodology. Or, at least do a > literature search when someone tells you your method is outdated and > that you can get much better results with the same resources by using > more modern techniques, as has been pointed out (even with some > suggestions for alternatives) by many people on the forum. > > Unlike in the B3LYP/6-31G* days, where all you had was a hammer so every > problem started to look like nails, today there are specialized > methodologies for each field so general advice is harder to give, and so > the responsibility really rests on the researcher. > > [We wouldn't even be in the current jam if article reviewers were more > strict about the use of obsolete methodologies, but at that stage it is > somewhat too late. The reviewers might also not be computational chemists.] > -- > ----------------------------------------------------------------------- > Mr. Susi Lehtola, PhD Chemist Postdoctoral Fellow > susi.lehtola=alumni.helsinki.fi Lawrence Berkeley National Laboratory > http://www.helsinki.fi/~jzlehtol USA > -----------------------------------------------------------------------> > > --001a11353a02ea3abb05205f9967 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
While I think=C2=A0is the=C2=A0responsibility of each one = of us to read, think and analyze when choosing the level of theory to use i= n any computational study we perform, the idea of what Alan meant was the i= dea of any discussion:

If you are going to discredit som= ething or someone, you should give a reason, not just because.
That is my point of view of the subject, just don't say so= mething isn't good (at a particular case) without justifying and if is = possible give some thoughts of what should be a better choice.
Nico


=
On Tue, Sep 22, 2015 at 9:34 PM Susi Lehtola susi.lehtola!= ^!alumni.helsinki.fi <owner-chemistry:+:ccl.net> wrote:<= br>

Sent to CCL by: Susi Lehtola [susi.lehtola###alumni.helsinki.fi]
On 09/22/2015 02:31 PM, Alan Shusterman alan=3D-=3Dreed.edu wrote:
> I have read several CCL messages over the past few weeks disparaging a=
> correspondent's choice of DFT functional (usually B3LYP, but not a= lways) as
> being obsolete, useless, or both.
>
> These are perfectly fair opinions to share, but they are not construct= ive.
> If you want to disparage a computational approach, fine with me, but p= lease
> recommend at least *one* better alternative. I would like to learn wha= t you
> think I should use, not just what I should not use.
>
> You don't need to cite publications or explain why you prefer a pa= rticular
> functional. I can look that up once you tell me which functional(s) yo= u
> think are worthy.

This is certainly true. However, this *is* the computational chemistry
list, and most of the people here are scientists. The main duty of a
scientist is keep up to date with current methodology. Or, at least do a literature search when someone tells you your method is outdated and
that you can get much better results with the same resources by using
more modern techniques, as has been pointed out (even with some
suggestions for alternatives) by many people on the forum.

Unlike in the B3LYP/6-31G* days, where all you had was a hammer so every problem started to look like nails, today there are specialized
methodologies for each field so general advice is harder to give, and so the responsibility really rests on the researcher.

[We wouldn't even be in the current jam if article reviewers were more<= br> strict about the use of obsolete methodologies, but at that stage it is
somewhat too late. The reviewers might also not be computational chemists.]=
--
-----------------------------------------------------------------------
Mr. Susi Lehtola, PhD=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Chemis= t Postdoctoral Fellow
susi.lehtola=3Dalumni.helsinki.fi=C2=A0 =C2=A0Lawrence Berkeley Nationa= l Laboratory
http://www.helsinki.fi/~jzlehtol=C2=A0 USA
-----------------------------------------------------------------------



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--001a11353a02ea3abb05205f9967-- From owner-chemistry@ccl.net Wed Sep 23 07:15:01 2015 From: "Johannes Straub johannes.straub.:.aci.uni-heidelberg.de" To: CCL Subject: CCL:G: CMO Analysis of a roB3LYP calculation using Gaussian 09 and NBO 6 Message-Id: <-51775-150923040340-3409-1U52jl18zZpD/I4U4o7SQQ%%server.ccl.net> X-Original-From: "Johannes Straub" Date: Wed, 23 Sep 2015 04:03:39 -0400 Sent to CCL by: "Johannes Straub" [johannes.straub() aci.uni-heidelberg.de] Hey! I already posted this problem in the NBO forum, but still got no reply to my problem, so I thought I'll try it here on CCL. I'm working with Gaussian 09 D.01 and NBO 6.0. For my studies, I'd like to compare some particular orbital energies (d-Orbital set) of two isomeric Fe(IV)-oxo complexes, to see, if there are any significant differences. (The two isomers show different reactivity in HAT reactions.) We figured out that the CMO Analysis feature of NBO 6.0 might be very promising for this task, because I can see which MOs are the ones built up by the important Fe d- and O p-Orbitals. I started using a normal uB3LYP calculation with Gaussian "#p sp pop=(full,nbo6read) scrf=(pcm,solvent=acetonitrile) gfinput gfoldprint 5d 7f def2tzvp ub3lyp scf=(tight,xqc) .. $NBO plot print=3 file=L1Fe-e2-s1-bs3-nd-s-CMO-1 CMO archive $END" I get the .31 and .37 files containing the NBOs and the corresponding CMO output in the Gaussian output file, as expected. However, I was not able to completely identify the d-Orbital set for both alpha- and beta-spin orbitals. (They don't have the same MO number and are built up by NBOs very differently). So, I thought, a similar roB3LYP calculation might help, because I would get only one set of orbital eigenvalues and therefore only one set of NBO orbitals, which makes it more easy to assign the important orbitals. However, after the restricted oben shell SCF calculation, the NBO 6 module seems to split the MO eigenvalues again into a different set of alpha and beta spin orbitals having new, different eigenvalues. (At least I was able to identify all the d-orbitals both in alpha and beta spin now) What exactly is the NBO module doing in this step? Are the new eigenvalues reliable for the comparison of orbital energies between two isomeric complexes? Thank you! Johannes From owner-chemistry@ccl.net Wed Sep 23 12:12:01 2015 From: "KGP Mohan krishnamohan.gp-x-gmail.com" To: CCL Subject: CCL:G: Ortho-/ Para- H2 conversion Message-Id: <-51776-150923121004-8649-8qW4va+Oe/qbU1MzDUodJw_-_server.ccl.net> X-Original-From: "KGP Mohan" Date: Wed, 23 Sep 2015 12:10:03 -0400 Sent to CCL by: "KGP Mohan" [krishnamohan.gp() gmail.com] Dear List, A syllabus from an institution contains an interesting question: Find out the transition state of ortho H-H - para H-H inter-conversion reaction and determine the activation energy using HF/STO-3G basis set. And it is supposed to do the above task with Gaussian program. I really wonder How Can we really solve the above problem (even though if we try with higher quality basis set. ) with Gaussian/GAMESS? And before start to write to its author, I would like to discuss the relevance of the problem here: To the best of my knowledge nuclear-state does not play a major role in electronic structure calculation in Gaussian (may be exempted in nuclear shielding constant calculations etc.) I guess that there is NO transition state in the nuclear-spin involved reaction (unlike chemical reaction, where the TS on a PES is uniquely determined by the properties of its Hessian matrix). Interestingly, the Experimental Raman spectrum gives an indication of the ratio of the Ortho- / Para- H2 (Ref. 2). And I suppose that if we can simulate an ultra-fine Raman spectra with some high level ab initio methods one can deduce the ratio (rather than a TS!). For example at 0K only 100% para H2 will be presented in the sample (Ref. 1) and when T- >1000, a 1:3 ratio will be shown. Does anyone can give a hint on this part? May be I am TOTALLY incorrect on the above points, and if it is the case, please give me some direction/references to rectify the points... With thanks in advance, Mohan Ref: [1] Statistical Mechanics, By Norman Davidson, Chapter 9. [2] http://www.jascoinc.com/raman/determination-of-ortho-and-para- hydrogen-ratio-by-using-raman-spectroscopy-application-to-fuel-cell As a starter, when I tried 2 basic inputs in G03, the calculation was terminated with the following error < QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE. ISO=1, SPIN=1/2>. Please see below. INPUTS: ------------------ ---------------------- --------------------- --------- ------- From owner-chemistry@ccl.net Wed Sep 23 12:46:01 2015 From: "GPK Mohan krishnamohan.gp[]gmail.com" To: CCL Subject: CCL:G: Ortho-/ Para- H2 conversion Message-Id: <-51777-150923122653-15276-JNU1/6xLWGBbs9RrJAwGYg * server.ccl.net> X-Original-From: "GPK Mohan" Date: Wed, 23 Sep 2015 12:26:52 -0400 Sent to CCL by: "GPK Mohan" [krishnamohan.gp*o*gmail.com] Dear List, A syllabus from an institution contains an interesting question: Find out the transition state of ortho H-H - para H-H inter-conversion reaction and determine the activation energy using HF/STO-3G basis set. And it is supposed to do the above task with Gaussian program. I really wonder How Can we really solve the above problem (even if we try with higher quality basis set), with Gaussian/GAMESS? And before start to write to its author, I would like to discuss the relevance of the problem here: To the best of my knowledge nuclear-state does not play a major role in electronic structure calculation in Gaussian (may be exempted in nuclear shielding constant calculations etc.) I guess that there is NO transition state in the nuclear-spin involved reaction (unlike chemical reaction, where the TS on a PES is uniquely determined by the properties of its Hessian matrix). Interestingly, the Experimental Raman spectrum gives an indication of the ratio of the Ortho- / Para- H2 (Ref. 2). And I suppose that if we can simulate an ultra-fine Raman spectra with some high level ab initio methods one can deduce the ratio (rather than a TS!). For example at 0K only 100% para H2 will be presented in the sample (Ref. 1) and when T- >1000, a 1:3 ratio will be shown. Does anyone can give a hint on this part? May be I am TOTALLY incorrect on the above points, and if it is the case, please give me some direction/references to rectify the points... With thanks in advance, Mohan Ref: [1] Statistical Mechanics, By Norman Davidson, Chapter 9. [2] http://www.jascoinc.com/raman/determination-of-ortho-and-para- hydrogen-ratio-by- using-raman-spectroscopy-application-to-fuel-cell As a starter, when I tried 2 basic inputs in G03, the calculation was terminated with the following error < QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE. ISO=1, SPIN=1/2>. Please see below. INPUTS: ------------------ ---------------------- --------------------- --------- ------- From owner-chemistry@ccl.net Wed Sep 23 13:21:01 2015 From: "Arno Proeme aproeme++epcc.ed.ac.uk" To: CCL Subject: CCL: SC15 Workshop on Molecular Simulation Software Message-Id: <-51778-150923124009-6200-SoPr1Opz9ie536QCa4oIkw---server.ccl.net> X-Original-From: "Arno Proeme" Date: Wed, 23 Sep 2015 12:40:08 -0400 Sent to CCL by: "Arno Proeme" [aproeme%epcc.ed.ac.uk] This year's SC15 supercomputing conference features the following workshop: ==================================================================== Producing High-Performance and Sustainable Software for Molecular Simulation November 20th, 2015 Austin, Texas ==================================================================== This workshop aims to bring together developers and users of molecular simulation software, experts in high-performance computing, and researchers of numerical methods and algorithms to discuss the challenge of creating and maintaining high-performance sustainable software for molecular simulation. Invited Speakers ------------------ o Prof. Erik Lindahl (GROMACS) KTH Royal Institute of Technology and Stockholm University o James Phillips (Senior Research Programmer and NAMD Lead Developer) University of Illinois at Urbana-Champaign) Call for Abstracts ------------------- Abstracts are sought outlining proposed contributions (2-4 pages) to an open access workshop report / positional paper documenting state of the art developments, current bottlenecks, anticipated challenges, and priorities for future research and funding for molecular simulation software. Three of the accepted abstracts will be selected to give short talks at the workshop. The resulting joint paper will be made available online for free in an institutional repository in citable form with a unique and persistent location identifier. The deadline for abstract submission is October 5th (8:00 GMT). Authors will be notified October 12th. Abstracts can be submitted at https://easychair.org/conferences/? conf=sc15molsimsoftware We are especially seeking the following kinds of contributions: o Hot topics: recent work with (potential for) high impact on performance and / or sustainability of molecular simulation software (e.g. algorithms, forcefield models, parallelisation schemes and use of programming models, software development practices, exploiting new hardware). o Case studies: perspectives on achieving performance and / or sustainability based on experience in particular application areas, software development initiatives, etc. (e.g. interplay between optimisation and portability, analysis of goals and challenges, routes and barriers to success - technical, funding). Suggested Topics: Accelerators and heterogenous computing Algorithms Benchmarking and performance comparisons Computational models Data formats and interoperability of packages Libraries and APIs Numerical methods Parallelisation strategies and load balancing Portability Software development practices and collaborative models Testing Workflows More Information ------------------ http://www.apes-soft.org/sc15 http://sc15.supercomputing.org/schedule/event_detail?evid=wksp144 Questions about submissions: sc15molsimsoftware() easychair.org Any other questions about the workshop: aproeme() epcc.ed.ac.uk