From owner-nwchem-users@emsl.pnl.gov Sun Apr 27 14:37:57 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 m3RLbuDp020272 for ; Sun, 27 Apr 2008 14:37:57 -0700 (PDT) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.14.1/8.14.1/Submit) id m3RLbu4v020271 for nwchem-users-outgoing-0915; Sun, 27 Apr 2008 14:37:56 -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: 5.4 X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: ArwAAMmOFEigWwR3mmdsb2JhbACRWgEBAQEBCAUIBxEFRJYsAQ X-IronPort-AV: E=Sophos;i="4.25,713,1199692800"; d="scan'208";a="74743345" Date: Sun, 27 Apr 2008 17:37:55 -0400 From: "Robert J. Harrison" Subject: Re: [NWCHEM] Does the MO use 3p or 4p functions? In-reply-to: To: Eric Yezdimer Cc: nwchem-users@emsl.pnl.gov Message-id: <4814F233.3050200@ornl.gov> Organization: UT/ORNL MIME-version: 1.0 Content-type: text/plain; format=flowed; charset=us-ascii Content-transfer-encoding: 7bit User-Agent: Thunderbird 2.0.0.12 (X11/20080227) References: Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk My original input had a couple of typos ... here is a tested version. geometry; Be 0 0 0; end basis spherical; * library cc-pvtz; end scf; print "basis labels"; end task scf The output will include this Basis function labels --------------------- No. Atm El Type --- --- -- ---- 1 1 Be s 2 1 Be s 3 1 Be s 4 1 Be s 5 1 Be px 6 1 Be py 7 1 Be pz 8 1 Be px 9 1 Be py 10 1 Be pz 11 1 Be px 12 1 Be py 13 1 Be pz 14 1 Be d -2 15 1 Be d -1 16 1 Be d 0 17 1 Be d 1 18 1 Be d 2 19 1 Be d -2 20 1 Be d -1 21 1 Be d 0 22 1 Be d 1 23 1 Be d 2 24 1 Be f -3 25 1 Be f -2 26 1 Be f -1 27 1 Be f 0 28 1 Be f 1 29 1 Be f 2 30 1 Be f 3 Note that in a "spherical harmonic" basis real linear combinations of the actual complex spherical harmonics are used. Eric Yezdimer wrote: > Yup. There are commands to print the GTO's in basis set, but I can't find > one that prints exactly the basis functions used to compose each molecular > orbital outputted. > > Bfn. Coefficient Atom+Function > ------ --------------- ----------------------- > 24 0.357199 2 C pz > 119 -0.357199 11 C pz > 139 0.237984 13 C pz > 99 -0.237984 9 C pz > 21 0.231430 2 C pz > > The cc-pVDZ basis set has 2 P like functions (one labeled #4 and one labeled > #5). I have not found an output option that will tell me which P like > function is given by Bfn. 24 and Bfn. 21. These two functions are both on > the #2 atom site but I can't match the #4 and #5 GTO to the MO coefficients > because the output is not clear on this point. > > I really want a command to print out what GTOs are composing the functions > referenced by the term "Bfn." > > Eric > > >> -----Original Message----- >> From: Govind, Niri [mailto:niri.govind@pnl.gov] >> Sent: Sunday, April 27, 2008 10:13 AM >> To: Eric Yezdimer; nwchem-users@emsl.pnl.gov >> Subject: [SPAM-MAIL] RE: [NWCHEM] Does the MO use 3p or 4p functions? >> >> Hi Eric, >> >> Have you tried the print options described in Tables 10.1 and 11.7 ? >> >> -Niri >> >> ________________________________ >> >> From: owner-nwchem-users@emsl.pnl.gov on behalf of Eric Yezdimer >> Sent: Sun 4/27/2008 5:01 AM >> To: nwchem-users@emsl.pnl.gov >> Subject: RE: [NWCHEM] Does the MO use 3p or 4p functions? >> >> >> >> 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 >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>> >>>>>> >>>> >>>> >>> >>> >> >> >> >> >