From owner-chemistry@ccl.net Sun Nov 18 01:49:01 2012 From: "Vincent Xianlong Wang xloongw%yahoo.com" To: CCL Subject: CCL:G: CC:: spherical Gaussian type orbitals Message-Id: <-47884-121118014808-2647-OuRVGla+UnjWOzBfzWcJqQ]^[server.ccl.net> X-Original-From: Vincent Xianlong Wang Content-Type: multipart/alternative; boundary="150314621-1089160191-1353221280=:53395" Date: Sat, 17 Nov 2012 22:48:00 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Vincent Xianlong Wang [xloongw . yahoo.com] --150314621-1089160191-1353221280=:53395 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Thanks for the answers, but they did not solve my question.=0AJan's introdu= ction about basis set as posted on CCL (http://www.ccl.net/cca/documents/ba= sis-sets/basis.html) only mentioned the Cartesian gaussian primitives=0Aexp= (-alpha r^2) x^l y^m x^n=C2=A0(without the normalization constant).=0AIn a = recent review (WIREs Comput Mol Sci 2012, 2: 290=E2=80=93303 doi: 10.1002/w= cms.78), the authors talk about the historical development of algorithms fo= r molecular integrals. Although the paper mentioned the spherical gaussian = orbitals, it actually refers to the s-type orbital only. The paper said tha= t the real-valued solid-harmonics Gaussian functions,=C2=A0exp(-alpha r^2) = Y_lm(r) ( Y is a solid harmonic, which is r^l times a spherical harmonic),= =C2=A0were expanded in Cartesian GTOs and all the algorithms were about Car= tesian GTOs.=C2=A0=0ASo there is no mention about using general spherical g= aussian orbitals, such as r^(2n) exp(-alpha r^2) Y_lm(r), as basis set and = this is what i am curious about.=0A=0AXianlong=0A=0A=0A____________________= ____________=0A From: Jussi Lehtola jussi.lehtola{}helsinki.fi =0ATo: "Wang, Xianlong " =0ASent: = Friday, November 16, 2012 7:36 PM=0ASubject: CCL:G: CC:: spherical Gaussian= type orbitals=0A =0A=0ASent to CCL by: Jussi Lehtola [jussi.lehtola-#-hels= inki.fi]=0AOn Fri, 16 Nov 2012 00:59:11 -0800 (PST)=0A"Vincent Xianlong Wan= g xloongw.,+,.yahoo.com" =0Awrote:=0A> Dear Coll= eagues,=C2=A0=0A> =0A> =0A> Spherical Gaussian-type orbitals are of the fol= lowing form:=0A> A f_n(r^2) exp(-alpha r^2) Y_lm(R)=0A> where A is the norm= alization constant, f_n is typical in the form of=0A> r^(2n) and Y_lm is th= e solid harmonic. I am interested to know if=0A> these orbitals are used in= some general purpose quantum chemical=0A> software packages? Thanks.=C2=A0= =0A=0AMost quantum chemistry software packages that use a Gaussian type bas= is=0Ause solid harmonics to represent the angular part, e.g. Gaussian,=0APS= I3, NWChem, cfour, etc. The basis functions are then of the form=0A=0Aphi(r= ) =3D N(alpha, l) r^l exp(-alpha r^2) Y_{lm} (r)=0A=0Awhere N is a normaliz= ation factor, alpha is the Gaussian exponent and=0Al and m are the angular = momentum and its z component.=0A-- =0A-------------------------------------= -------------------=0AMr. Jussi Lehtola, M. Sc.=C2=A0 =C2=A0 =C2=A0 =C2=A0 = Doctoral Student=0Ajussi.lehtola,+,helsinki.fi=C2=A0 =C2=A0 =C2=A0 =C2=A0 = Department of Physics=0Ahttp://www.helsinki.fi/~jzlehtol=C2=A0 University = of Helsinki=0AOffice phone: +358 9 191 50 632=C2=A0 Finland=0A------------= --------------------------------------------=0AJussi Lehtola, FM=C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Tohtorikoulutettava=0Ajussi.= lehtola,+,helsinki.fi=C2=A0 =C2=A0 =C2=A0 =C2=A0 Fysiikan laitos=0Ahttp://= www.helsinki.fi/~jzlehtol=C2=A0 Helsingin Yliopisto=0ATy=C3=B6puhelin: (0)9= 191 50 632=0A--------------------------------------------------------=0A= =0A=0A=0A-=3D This is automatically added to each message by the mailing sc= ript =3D-=0ATo recover the email address of the author of the message, plea= se change=0Athe strange characters on the top line to the ]_[ sign. You can a= lso=0A=0A=0AE-mail to = subscribers: CHEMISTRY]_[ccl.net or use:=0A=C2=A0 =C2=A0 =C2=A0 http://www.cc= l.net/cgi-bin/ccl/send_ccl_message=0A=0AE-mail to administrators: CHEMISTRY= -REQUEST]_[ccl.net or use=0A=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/c= cl/send_ccl_message=0A=0A=0A=C2=A0 =C2=A0 =C2=A0 htt= p://www.ccl.net/chemistry/sub_unsub.shtml=0A=0ABefore posting, check wait t= ime at: http://www.ccl.net=0A=0A=0AConferences= : http://server.ccl.net/chemistry/announcements/conferences/=0A=0ASearch Me= ssages: http://www.ccl.net/chemistry/searchccl/index.shtml=0A=0AIf your mai= l bounces from CCL with 5.7.1 error, check:=0A=C2=A0 =C2=A0 =C2=A0 http://w= ww.ccl.net/spammers.txt=0A=0ARTFI: http://www.ccl.net/chemistry/aboutccl/in= structions/ --150314621-1089160191-1353221280=:53395 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Thanks for the answers, b= ut they did not solve my question.
Jan's introduction about basis se= t as posted on CCL (http://www.ccl.net/cca/documents/basis-sets/basis.html)= only mentioned the Cartesian gaussian primitives
exp(-alpha r^2)= x^l y^m x^n (without the normalization constant).
In a rece= nt review (WIREs Comput Mol Sci 2012, 2: 290=E2=80=93303 doi: 10.1002/wcms.78<= /span>), the authors talk about the historical development of algorithms fo= r molecular integrals. Although the paper mentioned the spherical gaussian orbitals, it actually refers to the s-type orbital only. The paper said th= at the real-valued solid-harmonics Gaussian functions, exp(-alph= a r^2) Y_lm(r) ( Y is a solid harmonic, which is r^l times a spherical harm= onic), were expanded in Cartesian GTOs and all the algori= thms were about Cartesian GTOs. 
So there is no mention about using general s= pherical gaussian orbitals, such as r^(2n) exp(-alpha r^2) Y_lm(r), as basi= s set and this is what i am curious about.

Xianlong

From: Jussi Lehtola j= ussi.lehtola{}helsinki.fi <owner-chemistry]_[ccl.net>
To: "Wang, Xianlong " <xloon= gw]_[yahoo.com>
Sent: Friday, November 16, 2012 7:36 PM
Subject: CCL:G: CC:: spherical Gaussian type orbitals

=0ASent to CCL by: Jussi Lehtola [jussi.lehtola-#-helsinki.fi]
On Fri, 16 = Nov 2012 00:59:11 -0800 (PST)
"Vincent Xianlong Wang xloongw.,+,.yahoo.c= om" <owner-chemistry,+,ccl.net>
wrote:
> Dear Colleagues,&nb= sp;
>
>
> Spherical Gaussian-type orbitals are of the f= ollowing form:
> A f_n(r^2) exp(-alpha r^2) Y_lm(R)
> where A i= s the normalization constant, f_n is typical in the form of
> r^(2n) = and Y_lm is the solid harmonic. I am interested to know if
> these or= bitals are used in some general purpose quantum chemical
> software p= ackages? Thanks. 

Most quantum chemistry software packages that= use a Gaussian type basis
use solid harmonics to represent the angular = part, e.g. Gaussian,
PSI3, NWChem, cfour, etc. The basis functions are t= hen of the form

phi(r) =3D N(alpha, l) r^l exp(-alpha r^2) Y_{lm} (r= )

where N is a normalization factor, alpha is the Gaussian exponent and
l and m are the angular momentum and its z component.
-= -
--------------------------------------------------------
Mr. Jussi= Lehtola, M. Sc.        Doctoral Student
jussi.leht= ola,+,helsinki.fi        Department of Physics
http= ://www.helsinki.fi/~jzlehtol  University of Helsinki
Office phone: = +358 9 191 50 632  Finland
---------------------------------------= -----------------
Jussi Lehtola, FM          &n= bsp;     Tohtorikoulutettava
jussi.lehtola,+,helsinki.fi = ;       Fysiikan laitos
http://www.helsinki.fi/~jzlehtol  H= elsingin Yliopisto
Ty=C3=B6puhelin: (0)9 191 50 632
-----------------= ---------------------------------------



-=3D This is automat= ically added to each message by the mailing script =3D-
To recover the e= mail address of the author of the message, please change
the strange charact= ers on the top line to the ]_[ sign. You can also
look up the X-Original-F= rom: line in the mail header.

E-mail to subscribers: CHEMISTRY]_[ccl.ne= t or use:
      http://www.ccl.net/cgi-bin/ccl/send_c= cl_message

E-mail to administrators: CHEMISTRY-REQUES= T]_[ccl.net or use
      http://www.ccl.net/cgi-bin/= ccl/send_ccl_message
    &n= bsp;

Before posting, ch= eck wait time at: http://www.ccl.net

Search M= essages: http://www.ccl.net/chemistry/searchccl/index.shtml

If your = mail bounces from CCL with 5.7.1 error, check:
      http= ://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/about= ccl/instructions/




--150314621-1089160191-1353221280=:53395-- From owner-chemistry@ccl.net Sun Nov 18 05:23:00 2012 From: "Jussi Lehtola jussi.lehtola-x-helsinki.fi" To: CCL Subject: CCL:G: CC:: spherical Gaussian type orbitals Message-Id: <-47885-121118052042-21906-wzHwJ910l/xuGMiz83G3GA[#]server.ccl.net> X-Original-From: Jussi Lehtola Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Sun, 18 Nov 2012 12:20:32 +0200 Mime-Version: 1.0 Sent to CCL by: Jussi Lehtola [jussi.lehtola+/-helsinki.fi] On Sat, 17 Nov 2012 22:48:00 -0800 (PST) "Vincent Xianlong Wang xloongw%yahoo.com" wrote: > Thanks for the answers, but they did not solve my question. > Jan's introduction about basis set as posted on CCL > (http://www.ccl.net/cca/documents/basis-sets/basis.html) only > mentioned the Cartesian gaussian primitives exp(-alpha r^2) x^l y^m > x^n (without the normalization constant). In a recent review (WIREs > Comput Mol Sci 2012, 2: 290–303 doi: 10.1002/wcms.78), the authors > talk about the historical development of algorithms for molecular > integrals. Although the paper mentioned the spherical gaussian > orbitals, it actually refers to the s-type orbital only. The paper > said that the real-valued solid-harmonics Gaussian > functions, exp(-alpha r^2) Y_lm(r) ( Y is a solid harmonic, which is > r^l times a spherical harmonic), were expanded in Cartesian GTOs and > all the algorithms were about Cartesian GTOs. So there is no mention > about using general spherical gaussian orbitals, such as r^(2n) > exp(-alpha r^2) Y_lm(r), as basis set and this is what i am curious > about. No but the two approaches are equivalent. Although the integrals are calculated with regard to the cartesian functions, they are contracted so that you end up with proper spherical functions. See for instance [H. Bernhard Schlegel and Michael J. Frisch. Transformation between Cartesian and pure spherical harmonic Gaussians. Int. J. Quant. Chem., 54(2):83–87, April 1995.] The general form of a spherical harmonic Gaussian is phi(r;a,n,l) = N(a,n,l) r^{2n-l-2} exp(-a r^2) Y_{lm} (r) where N is again a normalization constant [see e.g. Molecular Electronic-Structure Theory by Helgaker, Jørgensen and Olsen]. You know that you can span a complete basis set either with a fixed exponent a and having all primary quantum numbers n present at all angular momenta ( n = 1 ... infinity, l = 0 ... n-1 ). Now, when you do the contraction and eliminate the contaminants of different angular momentum (e.g., the spherical s function on the cartesian d shell), what you end up with is functions of the form r^l exp(-a r^2) Y_{lm} (r) so n is constant on each shell, n=l+1. However, this is not a problem. Instead of using a fixed exponent and spanning all primary quantum numbers, you can just use a lot of exponents with the same primary quantum number and you end up with a complete basis set once again. The general spherical gaussian orbitals (spanning n instead of a) are not used, since they would result in a lot of computational overhead. For instance, the s type contaminant on the cartesian d shell is of the form r^2 exp(-a r^2) Y_{00} (r) which means n=2, l=0. Now, if you were to calculate integrals over this function, you would actually calculate the six integrals involving the cartesian functions, and then throw the 5 values corresponding to the spherical d functions (n=3, l=2) out... but the overhead is actually much larger, since the bulk of the work is in two-electron integrals, for which you would compute 6^4 = 1296 integrals and contract them to a single value, i.e., ( 2s 2s | 2s 2s ). I hope this has clarified the situation somewhat. -- -------------------------------------------------------- Mr. Jussi Lehtola, M. Sc. Doctoral Student jussi.lehtola{}helsinki.fi Department of Physics http://www.helsinki.fi/~jzlehtol University of Helsinki Office phone: +358 9 191 50 632 Finland -------------------------------------------------------- Jussi Lehtola, FM Tohtorikoulutettava jussi.lehtola{}helsinki.fi Fysiikan laitos http://www.helsinki.fi/~jzlehtol Helsingin Yliopisto Työpuhelin: (0)9 191 50 632 -------------------------------------------------------- From owner-chemistry@ccl.net Sun Nov 18 10:43:00 2012 From: "meishway linkon meishwaylinkon#%#yahoo.com" To: CCL Subject: CCL: p21/n space group Message-Id: <-47886-121118104141-7478-+Yghi6/82995dVNDTnYIqQ[-]server.ccl.net> X-Original-From: "meishway linkon" Date: Sun, 18 Nov 2012 10:41:38 -0500 Sent to CCL by: "meishway linkon" [meishwaylinkon : yahoo.com] hell to all ! I have found in literature,the crystal analysis of a compound have been done by using p21/n space group, so due to similar structure i also want to use this space group form my molecule for crystal structure pridiction calculations using material studio software but i have checked it in poly morph pridiction calculation box in the material studio , this space group is not present there , from internet i also found that p21/n and p21/c also same to some extent , then can i use p21/c instead of p21/n, by the way i have used p21/c but structure seems strange. so please guide me about this space group , also tell me how can i use this space group p21/n in material studio, that i need it . please urgent help me , i shall be grateful to you. From owner-chemistry@ccl.net Sun Nov 18 15:12:00 2012 From: "Jacco van de Streek jacco.vandestreek:sund.ku.dk" To: CCL Subject: CCL: p21/n space group Message-Id: <-47887-121118132520-18892-nA2fGerkjOFQAmTO1QDp4g _ server.ccl.net> X-Original-From: Jacco van de Streek Content-Language: en-GB Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Sun, 18 Nov 2012 18:25:07 +0000 MIME-Version: 1.0 Sent to CCL by: Jacco van de Streek [jacco.vandestreek[#]sund.ku.dk] > I have found in literature,the crystal analysis of a compound have been done by using p21/n space group, so due to similar structure i also want to use this space group form my molecule for crystal structure pridiction calculations using material studio software but i have checked it in poly morph pridiction calculation box in the material studio , this space group is not present there , from internet i also found that p21/n and p21/c also same to some extent , then can i use p21/c instead of p21/n, by the way i have used p21/c but structure seems strange. > so please guide me about this space group , also tell me how can i use this space group p21/n in material studio, that i need it . P21/c and P21/n are the same space group, just in different settings. Any crystal structure described in P21/c can also be described in P21/n and vice versa. P21/c is the standard setting and that is therefore the setting offered by the Polymorph Predictor in Materials Studio. "Predicting" a crystal structure by only searching in the experimental space group is not really a prediction. And from what you write, I get the impression that your molecule is only similar to, but not identical to, the other molecule, in which case there is no reason why they should have the same space group. And what does "structure seems strange" mean? After energy-minimisation with a force field (when done properly), a crystal structure should look acceptable. Best wishes, -- Dr Jacco van de Streek Department of Pharmacy University of Copenhagen