From owner-nwchem-users@emsl.pnl.gov Sun Apr 27 05:02:04 2008 Received: from odyssey.emsl.pnl.gov (localhost [127.0.0.1]) by odyssey.emsl.pnl.gov (8.14.1/8.14.1) with ESMTP id m3RC230c010365 for ; Sun, 27 Apr 2008 05:02:04 -0700 (PDT) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.14.1/8.14.1/Submit) id m3RC23KK010364 for nwchem-users-outgoing-0915; Sun, 27 Apr 2008 05:02:03 -0700 (PDT) X-Authentication-Warning: odyssey.emsl.pnl.gov: majordom set sender to owner-nwchem-users@emsl.pnl.gov using -f X-Ironport-SG: OK_Domains X-Ironport-SBRS: 6.3 X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: AnwAAGMHFEjbdtgHo2dsb2JhbACRWgEBAQEBAQcFCAcRlykB X-IronPort-AV: E=Sophos;i="4.25,712,1199692800"; d="scan'208";a="51824788" X-FD: True X-ASJ-Track-ID: <20080427120149.58656.qmail@xmx02.admiral.ne.jp> X-ASJ-Auth-ID: auth X-ASJ-Arrival-IP: 69.248.233.55 X-ASJ-SPF-Info: auth X-ASJ-Received-SPF: pass (send with smtp authentication by eric%istcorp.jp@69.248.233.55) From: "Eric Yezdimer" To: Subject: RE: [NWCHEM] Does the MO use 3p or 4p functions? Date: Sun, 27 Apr 2008 08:01:45 -0400 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Mailer: Microsoft Office Outlook, Build 11.0.5510 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2900.3198 Thread-Index: AcinvosiFFs4OhsNRaizGHNsRG+KIAAKcy8QAA3i4OgAD4T+kA== In-Reply-To: <003301c8a81f$e3619bf9$16015ba0@ornl.gov> X-Virus-Scanned: by ASJ VSCAN based on AMaViS perl-11-ASJ-ETHEL-04030800b-ML-SPEEDY58 Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk Exactly where in the manual is this information? I can not find the command and I have been looking for days. All the additional print commands I have tried do not do this. Eric > -----Original Message----- > From: owner-nwchem-users@emsl.pnl.gov > [mailto:owner-nwchem-users@emsl.pnl.gov] On Behalf Of > Harrison, Robert J. > Sent: Sunday, April 27, 2008 12:33 AM > To: Eric Yezdimer > Cc: nwchem-users@emsl.pnl.gov > Subject: [SPAM-MAIL] RE: [NWCHEM] Does the MO use 3p or 4p functions? > > This is correct and the manual describes how to print a > detailed list of the basis functions and their numbering > > > > RJ Harrison (from phone 865 274 8544) > > -----Original Message----- > From: Eric Yezdimer > Sent: Saturday, April 26, 2008 7:01 PM > To: nwchem-users@emsl.pnl.gov > Subject: Re: [NWCHEM] Does the MO use 3p or 4p functions? > > > Thank you very much for your answer Kirk. It was very helpful. > > I would like to ask everyone if there is someone else who can > "confirm" > Kirk's comment that the coefficients for the linear > combination of multiple GTOs, on the same atomic site, > outputted in the "NWChem vector analysis" > section appear in the order they are listed in the basis set > description. > > So for a basis set described by (this table is outputted by > NWChem as well): > > alpha coefficient > C 4 P 9.439*10^0 0.038109 > 2.002*10^0 0.209480 > 5.456*10^-1 0.508557 > > C 5 P 1.517*10^-1 1.00000 > > with a MO output of: > > Coeff Atom# AtomType Function > 0.302387 2 C pz > 0.267493 2 C pz > > means the MO is given by: > > phi(MO) = 0.302387 * GTO(atom 2, #4 P, pz) + 0.267493 * GTO > (atom 2, #5 P, > pz) + .... > > and not by > > phi(MO) = 0.302387 * GTO(atom 2, #5 P, pz) + 0.267493 * GTO > (atom 2, #4 P, > pz) + .... > > because 0.302387 2 C pz appears first in the basis set list > so it is a GTO(# > 4 P pz) and 0.267493 2 C pz is a GTO (#5 P pz) because it > appears second (where pz refers to the pz non radial > component of a 2 p orbital geometry) > > One other issue, as I think Kenneth was also describing, it > is possible the GTO's center might not even be localized to a > given atom site. I am assuming that since the NWChem output > is listing "some as yet 100% identified" GTOs being > associated with various atoms that the GTOs are centered on > that atom's nuclear position (and not on a bond bisector or > some other place). > But I do not know if this is true (or how to check for this > possibility in the NWChem output). > > David speaks of "print[ing] the basis out". This there a > command (beyond the normal NWChem output) that tells NWChem > to print out the "exact and complete" GTOs used to compose > each MO it uses? > > Cheers, > Eric > > PS> I know the difference between GTOs, MOs, and the exact > wave function > solution for H atom (which is only valid for that and maybe > the H2(+) or > He(+1) cases), so it would be more efficient if we could > restrict the discussion to the technical aspects of obtaining > more detailed MO information from the NWChem software. > > > > -----Original Message----- > > From: owner-nwchem-users@emsl.pnl.gov > > [mailto:owner-nwchem-users@emsl.pnl.gov] On Behalf Of Kirk Peterson > > Sent: Saturday, April 26, 2008 12:53 PM > > To: Eric Yezdimer > > Cc: nwchem-users@emsl.pnl.gov > > Subject: [SPAM-MAIL] Re: [NWCHEM] Does the MO use 3p or 4p > functions? > > > > Eric, > > > > admittedly I'm not much of a NWCHEM user so I can't say for > sure, but > > usually the basis functions in MO outputs are ordered > consecutively, > > so I would assume your first choice below is correct. > > > > -Kirk > > > > On Apr 26, 2008, at 9:47 AM, Eric Yezdimer wrote: > > > Kirk, > > > > > > Great. Now we are making progress. Okay now in the basis set > > > description outputted by NWChem there are two GTO functions > > with p for > > > a carbon atom. > > > They have the INDEX of 4 and 5. The functions are listed below. > > > > > >>>> alpha coefficient > > >>>> Carbon 4P 9.439*10^0 0.038109 > > >>>> 2.002*10^0 0.209480 > > >>>> 5.456*10^-1 0.508557 > > >>>> > > >>>> Carbon 5P 1.517*10^-1 1.00000 > > > > > > In the MO output I get > > > > > >>>> Coeff Atom# AtomType Function > > >>>> 0.302387 2 C pz > > >>>> -0.302387 11 C pz > > >>>> 0.267493 2 C pz > > >>>> -0.267493 17 C pz > > >>>> -0.199437 4 C pz > > >>>> 0.302387 7 C pz > > >>>> -0.302387 17 C pz > > >>>> 0.267493 7 C pz > > >>>> -0.267493 11 C pz > > >>>> -0.199437 9 C pz > > > > > > So my question is how should I combine the two p like > > orbitals, #4 or > > > #5, associated with atom #2. > > > > > >>>> phi(MO) = 0.302387 * GTO(atom 2, #4 P, pz) + 0.267493 * > > GTO (atom > > >>>> 2, #5 > > > P, pz) + .... or > > >>>> phi(MO) = 0.302387 * GTO(atom 2, #5 P, pz) + 0.267493 * > > GTO (atom > > >>>> 2, #4 > > > P, pz) + .... > > > > > > Or is my understanding of the output completely wrong. > > > > > > Eric > > > > > >> -----Original Message----- > > >> From: Kirk Peterson [mailto:kipeters@wsu.edu] > > >> Sent: Saturday, April 26, 2008 12:31 PM > > >> To: Eric Yezdimer > > >> Cc: nwchem-users@emsl.pnl.gov > > >> Subject: [SPAM-MAIL] Re: [NWCHEM] Does the MO use 3p or 4p > > functions? > > >> > > >> Dear Eric, > > >> > > >> All standard Gaussian basis sets only use basis functions of the > > >> following type: > > >> > > >> s: 1s > > >> p: 2p > > >> d: 3d > > >> f: 4f > > >> g: 5g > > >> etc. > > >> > > >> Multiple functions of the same angular momentum do not > > correspond to > > >> higher values of the principle quantum number as you > > assume, but only > > >> to different values of the Gaussian exponent (for the primitive > > >> functions) or different contractions of the primitive Gaussians. > > >> > > >> Hope that helps some. > > >> > > >> -Kirk > > >> > > >> On Apr 26, 2008, at 8:57 AM, Eric Yezdimer wrote: > > >>> Does anyone have a more informative and less superficial > > >> response that > > >>> could help me obtain the exact equation of the MO outputted > > >> by NWChem? > > >>> Any help > > >>> would be greatly appreciated. > > >>> > > >>> Thanks, > > >>> Eric > > >>> > > >>>> -----Original Message----- > > >>>> From: Dixon, David [mailto:dadixon@as.ua.edu] > > >>>> Sent: Saturday, April 26, 2008 11:36 AM > > >>>> To: Eric Yezdimer > > >>>> Subject: [SPAM-MAIL] RE: [NWCHEM] Does the MO use 3p or 4p > > >> functions? > > >>>> > > >>>> You are completely wrong. There is no such thing as a 4p or 5p > > >>>> orbital in the correlation consistent basis sets. You > > >> really need to > > >>>> read about Gaussian wave functions. > > >>>> > > >>>> -----Original Message----- > > >>>> From: owner-nwchem-users@emsl.pnl.gov > > >>>> [mailto:owner-nwchem-users@emsl.pnl.gov] On Behalf Of > > Eric Yezdimer > > >>>> Sent: Saturday, April 26, 2008 10:21 AM > > >>>> To: nwchem-users@emsl.pnl.gov > > >>>> Subject: Re: [NWCHEM] Does the MO use 3p or 4p functions? > > >>>> > > >>>> > > >>>> Thank you for the response. I will check out the visualization > > >>>> software. > > >>>> > > >>>> I understand that NWChem does not see 1 s and 2 s as in the > > >>>> traditional sense. However it does have several GTO to > > approximate > > >>>> these orbitals. I am using the cc-pVDZ basis set. > > >>>> For the carbon atom this basis set has descriptions of the > > >> 4P and 5P > > >>>> orbitals. > > >>>> > > >>>> alpha coefficient > > >>>> Carbon 4P 9.439*10^0 0.038109 > > >>>> 2.002*10^0 0.209480 > > >>>> 5.456*10^-1 0.508557 > > >>>> > > >>>> Carbon 5P 1.517*10^-1 1.00000 > > >>>> > > >>>> After I run NWChem several MO are reported. One > > antibonding pi MO, > > >>>> for example, is: > > >>>> > > >>>> Coeff Atom# AtomType Function > > >>>> 0.302387 2 C pz > > >>>> -0.302387 11 C pz > > >>>> 0.267493 2 C pz > > >>>> -0.267493 17 C pz > > >>>> -0.199437 4 C pz > > >>>> 0.302387 7 C pz > > >>>> -0.302387 17 C pz > > >>>> 0.267493 7 C pz > > >>>> -0.267493 11 C pz > > >>>> -0.199437 9 C pz > > >>>> > > >>>> In this MO the atoms 2, 11, 7 , and 17 appear to have 2 > > pz atomic > > >>>> orbitals on each atomic site. I assume one of the atomic > > >> orbitals is > > >>>> described by the GTO for 4P and one is described for the > > >> GTO for 5P. > > >>>> > > >>>> In this list however (outputted from NWChem) it does not > > >> tell me (as > > >>>> far as I can see) which is which. For example should I write > > >>>> > > >>>> phi(MO) = 0.302387 * GTO(atom 2, 4P, pz) + 0.267493 * > > GTO(atom 2, > > >>>> 5P, > > >>>> pz) + > > >>>> .... or > > >>>> phi(MO) = 0.302387 * GTO(atom 2, 5P, pz) + 0.267493 * > > GTO(atom 2, > > >>>> 4P, > > >>>> pz) + > > >>>> .... > > >>>> > > >>>> I am using Mathematica (a program like Matlab) to build > > >> out the all > > >>>> the MO for the molecules I am interested with so I can > > >> perform some > > >>>> non-standard calculations of molecular properties. This is > > >> why I need > > >>>> to know the "exact" > > >>>> functional form for the MO found by NWChem. > > >>>> > > >>>> Any additional insights you could provide would be helpful. > > >>>> > > >>>> Thanks, > > >>>> Eric > > >>>> > > >>>> > > >>>>> -----Original Message----- > > >>>>> From: JR Schmidt [mailto:jordan.schmidt@yale.edu] > > >>>>> Sent: Saturday, April 26, 2008 9:53 AM > > >>>>> To: Eric Yezdimer > > >>>>> Subject: [Norton AntiSpam] [SPAM-MAIL] Re: [NWCHEM] Does > > >>>> the MO use 3p > > >>>>> or 4p functions? > > >>>>> > > >>>>> > > >>>>>> The normal vector output display shows each molecular > > >>>>> orbital of course > > >>>>>> and each MO is given as a linear combination of basis > > >>>>> functions on the > > >>>>>> separate atoms. The output also gives the harmonics of > > >> each basis > > >>>>>> function (s, px, py, pz, etc) however it does not tell me if > > >>>>> it is a 2px or a 3px function. > > >>>>>> There is only a Bfn. value, that I assume is an internal > > >>>>> reference to > > >>>>>> the exact basis functions being used. > > >>>>> > > >>>>> NWChem (nor any other electronic structure program) knows > > >> anything > > >>>>> about 1s vs. 2s vs 2p 'shells'. These are simply > > >>>> approximations based > > >>>>> on hydrogen like orbitals. > > >>>>> > > >>>>> Most common basis sets include MANY sets of s,p,d,f > > >>>> functions, even if > > >>>>> you do a calculation on an isolated hydrogen atom. For > > >>>> example, you > > >>>>> would find that the 1s orbital of an H atoms would consist > > >>>> of a linear > > >>>>> combination of several 's'-like basis functions in the > > MO output. > > >>>>> This is necessary to increase accuracy (to approximate the > > >>>> exponential > > >>>>> decay of the 1s orbital with gaussian basis functions), > > >> because the > > >>>>> orbital exponent of H varies with its chemical > environment, etc. > > >>>>> > > >>>>> In practice, you will find that the calculation (on an > > >> atom) still > > >>>>> yields a shell-like structure, with identifiable > > >>>> 1s,2s,2p,3s orbitals. > > >>>>> However, as I mentioned, each of those orbitals will be > > >> composed of > > >>>>> several s or p type basis functions. The exception would > > >> be if you > > >>>>> use a minimal basis set (such as STO-3G) which contains > > >>>> only 1 basis > > >>>>> function per electron. In this case, one basis function > > >> represents > > >>>>> each orbital, and you will get results like you originally > > >>>> expected. > > >>>>> Unfortunately, the results will be quantitatively > terrible, and > > >>>>> possible also qualitatively poor! > > >>>>> > > >>>>> I hope that helps. Forgive me if I am simply telling > > you what I > > >>>>> already know. If not, I recommend the book 'Introduction to > > >>>>> Computational Chemistry', by Jenson. It is quite good, > > >> and an easy > > >>>>> read. > > >>>>> > > >>>>> JR Schmidt > > >>>>> > > >>>>> > > >>>>> > > >>>> > > >>>> > > >>>> > > >>> > > >> > > >> > > >> > > > > > > > > > > > >