From owner-chemistry@ccl.net Fri Mar 9 01:57:00 2012 From: "Jun Zhang coolrainbow##yahoo.cn" To: CCL Subject: CCL: Some confusions about indices of two-electron integrals in programming Message-Id: <-46448-120309015542-10486-9r1Y+vL3PgZ/UEXvHUivEw(_)server.ccl.net> X-Original-From: Jun Zhang Content-Type: multipart/alternative; boundary="1292221969-890095745-1331276133=:97701" Date: Fri, 9 Mar 2012 14:55:33 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: Jun Zhang [coolrainbow(!)yahoo.cn] --1292221969-890095745-1331276133=:97701 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hello Everyone:=0A=0AWe know that in quantum chemistry programming the two-= electron integrals (ERI) are computed in batch (e.g., ,, at the same time) to make efficient use of the common immediate quan= tities. But what confused me is the index fetching. That is, when = is to calculate, how to determine the indices of the 3 integrals ,<= ss|spy>, in memory? And then, how to make the following subroutine= s know that and have been calculated? =0A=0AIt will be be= tter if you can recommend me=A0some codes to read.=A0 Thank you in advance.= =0A----------------------------------------------------------------=0AJun Z= hang (coolrainbow _ yahoo.cn)=0AComputational Chemistry Group=0ANo.94, Weijin= lu=0ANankai University =0ATianjin, China --1292221969-890095745-1331276133=:97701 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hello Ever= yone:
We know that in quantum chemistry programming the tw= o-electron integrals (ERI) are computed in batch (e.g., <ss|spx>,<= ss|spy>, <ss|spz> at the same time) to make efficient use of the c= ommon immediate quantities. But what confused me is the index fetching. Tha= t is, when <ss|spx> is to calculate, how to determine the indices of = the 3 integrals <ss|spx>,<ss|spy>, <ss|spz> in memory? An= d then, how to make the following subroutines know that <ss|spy> and = <ss|spz> have been calculated?
 
It will be= better if you can recommend me some codes to read.  Thank you in= advance.
-----------------------= -----------------------------------------
Jun Zhang (coolrainbow _ yahoo.cn)
Computational Chemistry Group
No.94, Weijinlu=
Nankai University
Tianjin, China
--1292221969-890095745-1331276133=:97701-- From owner-chemistry@ccl.net Fri Mar 9 03:16:01 2012 From: "Jussi Lehtola jussi.lehtola=-=helsinki.fi" To: CCL Subject: CCL: Some confusions about indices of two-electron integrals in programming Message-Id: <-46449-120309031253-13702-sSf71vWAguoQUUQXXAHEzw- -server.ccl.net> X-Original-From: Jussi Lehtola Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Fri, 9 Mar 2012 10:12:45 +0200 Mime-Version: 1.0 Sent to CCL by: Jussi Lehtola [jussi.lehtola[#]helsinki.fi] On Fri, 9 Mar 2012 14:55:33 +0800 (CST) "Jun Zhang coolrainbow##yahoo.cn" wrote: > Hello Everyone: > > We know that in quantum chemistry programming the two-electron > integrals (ERI) are computed in batch (e.g., ,, > at the same time) to make efficient use of the common > immediate quantities. But what confused me is the index fetching. > That is, when is to calculate, how to determine the indices > of the 3 integrals ,, in memory? And then, > how to make the following subroutines know that and > have been calculated? > > It will be better if you can recommend me some codes to read.  Thank > you in advance. The indexing with two-electron integrals is rather nontrivial. Even more nontrivial would be writing a two-electron integral code, as there are many possible paths to the wanted target integral. Fortunately, Ed Valeev has written libint, which uses Obara-Saika and Head-Gordon-Pople recursion relations to automatically generate optimal code to obtain the wanted integral. http://sourceforge.net/p/libint/ What you get out of libint is just the target integrals. From the libint programmer's manual: "Shell-sets of integrals contain integrals in “row major” order.For exam- ple, if the number of functions in each shell is na , nb , nc , and nd , respectively, then the integral (ab|cd) is found at position abcd = ((a*nb + b)*nc + c)*nd + d." -- -------------------------------------------------------- Mr. Jussi Lehtola, M. Sc. Doctoral Student jussi.lehtola(0)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(0)helsinki.fi Fysiikan laitos http://www.helsinki.fi/~jzlehtol Helsingin Yliopisto Työpuhelin: (0)9 191 50 632 -------------------------------------------------------- From owner-chemistry@ccl.net Fri Mar 9 06:03:00 2012 From: "Vera Cathrine vera.cathrine^^^yahoo.com" To: CCL Subject: CCL:G: G09: ONIOM error Message-Id: <-46450-120309060130-13066-6hgIRLTauDmQzBOHDi/flQ-#-server.ccl.net> X-Original-From: "Vera Cathrine" Date: Fri, 9 Mar 2012 06:01:28 -0500 Sent to CCL by: "Vera Cathrine" [vera.cathrine||yahoo.com] Dear CCLers. I like to do an ONIOM(QM/MM) geometry optimization. I don't freeze any atom during optimization. I start the model chemistry with oniom(blyp/3-21g:amber) The optimization was terminated normally with this method. Then, to extend the calculation to oniom(blyp/6-31g:amber) I build a new input file from out file of previous calculation using Gaussview. All the set up is the same and I just want to extend my basis set to a larger one. However I run into problem with missing parameters as following: Include all MM classes Bondstretch undefined between atoms 599 600 C-OM [H,H] * Bondstretch undefined between atoms 1002 1003 CM-HC [H,H] * Bondstretch undefined between atoms 1002 1004 CM-HC [H,H] * Bondstretch undefined between atoms 1914 1915 C1-OM [H,H] * Bondstretch undefined between atoms 1914 1916 C1-CM [H,H] * Bondstretch undefined between atoms 1916 1917 CM-HC [H,H] * Bondstretch undefined between atoms 1918 1919 CM-HC [H,H] * Bondstretch undefined between atoms 1925 1926 C-OM [H,H] * Angle bend undefined between atoms 597 599 600 CA-C-OM [H,H,H] * Angle bend undefined between atoms 600 599 602 OM-C-CA [H,H,H] * Angle bend undefined between atoms 998 1000 1002 N-CT-CM [H,H,H] * Angle bend undefined between atoms 1000 1002 1003 CT-CM-HC [H,H,H] * Angle bend undefined between atoms 1000 1002 1004 CT-CM-HC [H,H,H] * Angle bend undefined between atoms 1001 1000 1002 H1-CT-CM [H,H,H] * Angle bend undefined between atoms 1002 1000 1006 CM-CT-C [H,H,L] Angle bend undefined between atoms 1003 1002 1004 HC-CM-HC [H,H,H] * Angle bend undefined between atoms 1914 1916 1917 C1-CM-HC [H,H,H] * Angle bend undefined between atoms 1914 1916 1918 C1-CM-CM [H,H,H] * Angle bend undefined between atoms 1915 1914 1916 OM-C1-CM [H,H,H] * Angle bend undefined between atoms 1916 1918 1919 CM-CM-HC [H,H,H] * Angle bend undefined between atoms 1917 1916 1918 HC-CM-CM [H,H,H] * Angle bend undefined between atoms 1918 1920 1921 CM-CA-CA [H,H,H] * Angle bend undefined between atoms 1918 1920 1929 CM-CA-CM [H,H,H] * Angle bend undefined between atoms 1919 1918 1920 HC-CM-CA [H,H,H] * Angle bend undefined between atoms 1921 1920 1929 CA-CA-CM [H,H,H] * Angle bend undefined between atoms 1923 1925 1926 CA-C-OM [H,H,H] * Angle bend undefined between atoms 1923 1925 1927 CA-C-CM [H,H,H] * Angle bend undefined between atoms 1926 1925 1927 OM-C-CM [H,H,H] * * These undefined terms cancel in the ONIOM expression. MM function not complete Error termination via Lnk1e in /usr/local/gaussian/g09/l101.exe at Fri Mar 9 10:57:34 2012. I understand now that error shows some missing parameters. But my questions are : 1-why I had no such a problem in my previous calculation? whtehr Gaussview removes some parameters? I compared the input file and they are quite the same. 2-These missing parameter all are related to higher level, why Gaussian should complain about them? 3-I have a proton which is bound to an atom in my QM layer but its distance with connected atom (oxygen) increases during the first optimization. It seems that this hydrogen is not bound to that oxygen any more but with a new atom. Should I change the atom type for the second optimization? or should I keep the same atom type? I would appreciate any help. Best wishes, Vera From owner-chemistry@ccl.net Fri Mar 9 08:02:00 2012 From: "Paulo E. Abreu paulo.abreu ~ ci.uc.pt" To: CCL Subject: CCL:G: Ring pseudorotation Message-Id: <-46451-120309024842-1343-gxum/g0bXVv1C40mLZ/ekg::server.ccl.net> X-Original-From: "Paulo E. Abreu" Content-Type: multipart/alternative; boundary=bcaec52c6abba392e604baca9eff Date: Fri, 9 Mar 2012 07:48:04 +0000 MIME-Version: 1.0 Sent to CCL by: "Paulo E. Abreu" [paulo.abreu[a]ci.uc.pt] --bcaec52c6abba392e604baca9eff Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hiya, I cant remember when I read the term "automagically" for the first time, but I am sure it was a long time ago. But I always associate it with Arthur C. Clarke's third law : "Any sufficiently advanced technology is indistinguishable from magic." (quote from http://en.wikipedia.org/wiki/Clarke's_three_laws) Here they cite printed works which contain the word: http://en.wiktionary.org/wiki/Citations:automagical#English and the first reference dates back to 1987. --=20 Paulo E. Abreu Professor Auxiliar Departamento de Qu=EDmica Faculdade de Ci=EAncias e Tecnologia da Universidade de Coimbra Portugal On Thu, Mar 8, 2012 at 7:26 PM, Daniel Fernando Coimbra danielfcoimbra_+_ gmail.com wrote: > > Sent to CCL by: Daniel Fernando Coimbra [danielfcoimbra*|*gmail.com] > As far as I know this term was first used by the authors of the (now > discontinued) brazillian Linux distribution Kurumin. They created sets of > BASH scripts that automated lots of installation proccess so that a novic= e > user could configure non-trivial hardware with just a click on a menu ite= m. > There were said to so "automagicamente" (automagically), as it looked eve= n > easyer than simpler automatic task available at the time. > > Em 08-03-2012 11:40, John McKelvey jmmckel%%gmail.com escreveu: > >> I do not know how to answer this query but I do find something quite >> interesting in the use of the word 'automagic.' This could be a >> delightful word if deliberately used, even if simply a typo.. Either >> way it is a delightful coinage of a very useful word. >> >> John McKelvey >> >> On Thu, Mar 8, 2012 at 6:49 AM, Alcides Simao alsimao^^^gmail.com >> > >> >> >> wrote: >> >> Hello all! >> >> I'm trying to study a pseudorotation of a substituted pyrrolidine >> ring using GAUSSIAN 03. Although literature exists on the theme, I >> haven't come across any input example of it,so I'm trying to compute >> it in a way that I dislike particulary, which is to set a plane made >> of four atoms, and set one of the atoms off-plane, which is quite >> unrealistic. I would ask if anyone could kindly tell me what is your >> way of computing pseudorotation, and if you happen to have an >> 'automagic' way of doing so, if you would be so kind as to share it. >> >> Best, >> >> Alcides >> >> >> >> >> -- >> John McKelvey >> 10819 Middleford Pl >> Ft Wayne, IN 46818 >> 260-489-2160 >> jmmckel%%gmail.com >> > > -- > Daniel Fernando Coimbra > Grupo de Estrutura Eletr=F4nica Molecular > Departamento de Qu=EDmica > Universidade Federal de Santa Catarina > > > > -=3D This is automatically added to each message by the mailing script = =3D-> http://www.ccl.net/cgi-bin/**ccl/send_ccl_message http://www.ccl.net/cgi-bin/**ccl/send_ccl_message chemistry/announcements/**conferences/ > > Search Messages: http://www.ccl.net/chemistry/**searchccl/index.shtml http://www.ccl.net/spammers.**txt > > RTFI: http://www.ccl.net/chemistry/**aboutccl/instructions/ > > > --bcaec52c6abba392e604baca9eff Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hiya,

I cant remember when I read the term &q= uot;automagically" for the first time, but I am sure it was a long tim= e ago.
But I always associate it with Arthur C. Clarke's thir= d law : "Any sufficiently advanced technology is indistinguishable fro= m magic."

Here they cite printed works which contain= the word:
http://en.wiktionary.org/wiki/Citations:automagical#English<= /a>
and the first reference dates back to 1987.

--=A0
Paulo E. Abreu
Professor Auxiliar
Departamento de Qu=EDmica<= br>Faculdade de Ci=EAncias e Tecnologia da Universidade de CoimbraPortugal

On Thu, Mar 8, 2012 at 7:26 PM, Daniel Ferna= ndo Coimbra danielfcoimbra_+_gmail.com <owner-chemistry[#]ccl.net> wrote:

Sent to CCL by: Daniel Fernando Coimbra [danielfcoimbra*|*gmail.com]
As far as I know this term was first used by the authors of the (now discon= tinued) brazillian Linux distribution Kurumin. They created sets of BASH sc= ripts that automated lots of installation proccess so that a novice user co= uld configure non-trivial hardware with just a click on a menu item. There = were said to so "automagicamente" (automagically), as it looked e= ven easyer than simpler automatic task available at the time.

Em 08-03-2012 11:40, John McKelvey jmmckel%%gmail.com escreveu:
I do not know how to answer this query but I do find something quite
interesting in the use of the word 'automagic.' =A0This could be a<= br> delightful word if deliberately used, even if simply a typo.. =A0Either
way it is a delightful coinage of a very useful word.

John McKelvey

On Thu, Mar 8, 2012 at 6:49 AM, Alcides Simao alsimao^^^gmail.com
<http://gmail.com>= <owner-chemistry%%ccl.net<= /a>

<mailto:owner-chemistry%%ccl.net>> wrote:

=A0 =A0Hello all!

=A0 =A0I'm trying to study a pseudorotation of a substituted pyrrolidi= ne
=A0 =A0ring using GAUSSIAN 03. Although literature exists on the theme, I<= br> =A0 =A0haven't come across any input example of it,so I'm trying t= o compute
=A0 =A0it in a way that I dislike particulary, which is to set a plane mad= e
=A0 =A0of four atoms, and set one of the atoms off-plane, which is quite =A0 =A0unrealistic. I would ask if anyone could kindly tell me what is you= r
=A0 =A0way of computing pseudorotation, and if you happen to have an
=A0 =A0'automagic' way of doing so, if you would be so kind as to = share it.

=A0 =A0Best,

=A0 =A0Alcides




--
John McKelvey
10819 Middleford Pl
Ft Wayne, IN 46818
260-4= 89-2160
jmmckel%%gmail.com <m= ailto:jmmckel%%= gmail.com>

--
Daniel Fernando Coimbra
Grupo de Estrutura Eletr=F4nica Molecular
Departamento de Qu=EDmica
Universidade Federal de Santa Catarina



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--bcaec52c6abba392e604baca9eff-- From owner-chemistry@ccl.net Fri Mar 9 11:00:00 2012 From: "Ravi Kumar Venkatraman ravi.ipc.iisc]^[gmail.com" To: CCL Subject: CCL: Optimisation along normal coordinate Message-Id: <-46452-120309070433-1058-P8kL3WMZvVRsvCjv3vv8LA_-_server.ccl.net> X-Original-From: Ravi Kumar Venkatraman Content-Type: multipart/alternative; boundary=20cf3079bc9ea5afe304bace1714 Date: Fri, 9 Mar 2012 17:27:09 +0530 MIME-Version: 1.0 Sent to CCL by: Ravi Kumar Venkatraman [ravi.ipc.iisc^_^gmail.com] --20cf3079bc9ea5afe304bace1714 Content-Type: text/plain; charset=ISO-8859-1 Dear All, Could anybody help me carry out the optimisation along Normal Coordinate using G09. I have seen some paper in which they have carried out the same using qgrad.f, a fortran code. Is there any other software packages do it by default. Please help me in this regard. Thank you. * ** With Regards, * * Ravi Kumar Venkatraman,* *c/o Prof. Siva Umapathy,*** *IPC Dept., IISc.,* *Bangalore, INDIA,* *Phone No: +91-9686933963* > --20cf3079bc9ea5afe304bace1714 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear All, =A0=A0
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Could anybody hel= p me carry out the optimisation along Normal Coordinate using G09. I have s= een some paper in which they have carried out the same using qgrad.f, a for= tran code. Is there any other software packages do it by default. Please he= lp me in this regard.

Thank you.

 With Regar= ds,
=A0Ravi Kumar Venkatraman,
=A0c/o Prof. Siva Umapa= thy,
=A0IPC Dept., IISc.,
=A0Banga= lore, INDIA,
=A0Phone No: +91-9686933963

--20cf3079bc9ea5afe304bace1714-- From owner-chemistry@ccl.net Fri Mar 9 15:24:01 2012 From: "M. Nicklaus mn1,helix.nih.gov" To: CCL Subject: CCL:G: Ring pseudorotation Message-Id: <-46453-120309141021-28611-M95F/OB8WrmoBhIMhf+GmA:-:server.ccl.net> X-Original-From: "M. Nicklaus" Content-Type: multipart/mixed; boundary="13439187-20076-1331320178=:5108" Date: Fri, 9 Mar 2012 14:09:38 -0500 MIME-Version: 1.0 Sent to CCL by: "M. Nicklaus" [mn1*helix.nih.gov] --13439187-20076-1331320178=:5108 Content-Type: text/plain; charset="ISO-8859-1"; format=flowed Content-Transfer-Encoding: 8BIT Alcides, There are two ways of interpreting "computing pseudorotation." One is to compute the pseudorotation parameters from an existing structure (for which you have the 3D coordinates); the other is to generate a specific "pseudorotation conformation" for a molecule for your values of interest of the pseudorotation angle P and the amplitude nu_max. The former you can do with our web service PROSIT at http://cactus.nci.nih.gov/prosit/. The latter is implicitly done in PROSIT's ancillary tool Pseudorotation Visualization (http://cactus.nci.nih.gov/pseudo-visual/). The algorithm we used for it could probably be adapted for your needs. Some more background (mostly about PROSIT) is given in: Guangyu Sun, Johannes H. Voigt, Igor V. Filippov, Victor E. Marquez, Marc C. Nicklaus, "PROSIT: Pseudo-Rotational Online Service and Interactive Tool, Applied to a Conformational Survey of Nucleosides and Nucleotides", J. Chem. Inf. Comput. Sci., 2004, 44 (5), pp 17521762. Hope this helps, Marc ------------------------------------------------------------------------ Marc C. Nicklaus, Ph.D. Frederick National Lab E-mail: mn1*o*helix.nih.gov Bldg 376, Rm 207 Phone: (301) 846-5903 376 Boyles Street Fax: (301) 846-6033 FREDERICK, MD 21702 USA Head, Computer-Aided Drug Design (CADD) Group Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health Frederick National Laboratory for Cancer Research http://ccr.cancer.gov/Staff/Staff.asp?profileid=6282 CADD Group Web Server: http://cactus.nci.nih.gov ------------------------------------------------------------------------ On Thu, 8 Mar 2012, Alcides Simao alsimao^^^gmail.com wrote: > Hello all! > > I'm trying to study a pseudorotation of a substituted pyrrolidine ring > using GAUSSIAN 03. Although literature exists on the theme, I haven't come > across any input example of it,so I'm trying to compute it in a way that I > dislike particulary, which is to set a plane made of four atoms, and set > one of the atoms off-plane, which is quite unrealistic. I would ask if > anyone could kindly tell me what is your way of computing pseudorotation, > and if you happen to have an 'automagic' way of doing so, if you would be > so kind as to share it. > > Best, > > Alcides > --13439187-20076-1331320178=:5108--