From owner-chemistry@ccl.net Sat Mar 10 12:16:01 2012 From: "Kalaivanan Nagarajan kalaichemis,gmail.com" To: CCL Subject: CCL: Amber Calculation Message-Id: <-46454-120310121447-2647-WS5oSwDEm5oVnQ30WBzhUw**server.ccl.net> X-Original-From: "Kalaivanan Nagarajan" Date: Sat, 10 Mar 2012 12:14:45 -0500 Sent to CCL by: "Kalaivanan Nagarajan" [kalaichemis[A]gmail.com] Dear All, I am performing Amber calculation using macromodel. I am looking for pi pi interaction between two different structures. I am doing the calculation for both structures under same conditions. I dont know how to get the required result from the output file generated. Can anyone of you help me to solve this? From owner-chemistry@ccl.net Sat Mar 10 17:34:00 2012 From: "Anatoli Korkin a_korkin=-=yahoo.com" To: CCL Subject: CCL: Education resources at the Internet Message-Id: <-46455-120310173252-30621-NCClskVcKmBrfACOX/VCYA,server.ccl.net> X-Original-From: "Anatoli Korkin" Date: Sat, 10 Mar 2012 17:32:51 -0500 Sent to CCL by: "Anatoli Korkin" [a_korkin*o*yahoo.com] Dear CCLers, I am updating the "education" links at the ASDN.NET web site and will appreciate, if you send me the references to your own or your favorite web sources to be added to the list: http://asdn.net/asdn/links/education.shtml If you replay to this message to the list, I will appreciate a copy of your message to anatoli.korkin/at/asu.edu Thank you, Anatoli Korkin From owner-chemistry@ccl.net Sat Mar 10 20:10:00 2012 From: "Jun Zhang coolrainbow###yahoo.cn" To: CCL Subject: CCL: Some confusions about indices of two-electron integrals in programming Message-Id: <-46456-120310200315-16105-3vaqPnbq5WNCZfQkWGszWA#,#server.ccl.net> X-Original-From: Jun Zhang Content-Type: multipart/alternative; boundary="-1418736516-216597423-1331427784=:99434" Date: Sun, 11 Mar 2012 09:03:04 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: Jun Zhang [coolrainbow=-=yahoo.cn] ---1418736516-216597423-1331427784=:99434 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hi Jussi:=0A=0AYour suggestion is very useful for me. Thank you!=0A=0A-----= -----------------------------------------------------------=0AJun Zhang (co= olrainbow^^yahoo.cn)=0AComputational Chemistry Group=0ANo.94, Weijinlu=0ANan= kai University =0ATianjin, China=0A =0A=0A________________________________= =0A =E5=8F=91=E4=BB=B6=E4=BA=BA=EF=BC=9A Jussi Lehtola jussi.lehtola=3D-=3D= helsinki.fi =0A=E6=94=B6=E4=BB=B6=E4=BA=BA=EF=BC= =9A "Zhang, Jun " =0A=E5=8F=91=E9=80=81=E6= =97=A5=E6=9C=9F=EF=BC=9A 2012=E5=B9=B43=E6=9C=889=E6=97=A5, =E6=98=9F=E6=9C= =9F=E4=BA=94, =E4=B8=8B=E5=8D=88 4:12=0A=E4=B8=BB=E9=A2=98: CCL: Some confu= sions about indices of two-electron integrals in programming=0A =0A=0ASent= to CCL by: Jussi Lehtola [jussi.lehtola[#]helsinki.fi]=0AOn Fri, 9 Mar 201= 2 14:55:33 +0800 (CST)=0A"Jun Zhang coolrainbow##yahoo.cn" wrote:=0A> Hello Everyone:=0A> =0A> We know that in quantum che= mistry programming the two-electron=0A> integrals (ERI) are computed in bat= ch (e.g., ,,=0A> at the same time) to make efficie= nt use of the common=0A> immediate quantities. But what confused me is the = index fetching.=0A> That is, when is to calculate, how to determin= e the indices=0A> of the 3 integrals ,, in memory?= And then,=0A> how to make the following subroutines know that and= =0A> have been calculated? =0A> =0A> It will be better if you can = recommend me=C2=A0some codes to read.=C2=A0 Thank=0A> you in advance.=0A=0A= The indexing with two-electron integrals is rather nontrivial. Even=0Amore = nontrivial would be writing a two-electron integral code, as there=0Aare ma= ny possible paths to the wanted target integral.=0A=0AFortunately, Ed Valee= v has written libint, which uses Obara-Saika and=0AHead-Gordon-Pople recurs= ion relations to automatically generate optimal=0Acode to obtain the wanted= integral. http://sourceforge.net/p/libint/=0A=0AWhat you get out of libint= is just the target integrals. From the=0Alibint programmer's manual:=0A=0A= "Shell-sets of integrals contain integrals in =E2=80=9Crow major=E2=80=9D o= rder.For=0Aexam- ple, if the number of functions in each shell is na , nb ,= nc ,=0Aand nd , respectively, then the integral (ab|cd) is found at positi= on=0Aabcd =3D ((a*nb + b)*nc + c)*nd + d."=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 Tohtorikoulute= ttava=0Ajussi.lehtola:-:helsinki.fi=C2=A0 =C2=A0 =C2=A0 =C2=A0 Fysiikan la= itos=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 script =3D-=0ATo recover the email address of the author of the= message, please change=0Athe strange characters on the top line to the ^^ s= ign. You can also=0A= =0A=0A=0A=C2=A0 =C2=A0 =C2= =A0=0A=0AE-mail to administ= rators: CHEMISTRY-REQUEST^^ccl.net or use=0A=C2=A0 =C2=A0 =C2=A0 http://www.= ccl.net/cgi-bin/ccl/send_ccl_message=0A=0A=0A=C2=A0 = =C2=A0 =C2=A0=0A=0ABefore post= ing, check wait time at: http://www.ccl.net=0A=0AJob: http://www.ccl.net/jo= bs =0AConferences: http://server.ccl.net/chemistry/announcements/conference= s/=0A=0A= =0A=0A=0A=C2=A0 =C2= =A0 =C2=A0=0A=0ARTFI: http://www.ccl.net/ch= emistry/aboutccl/instructions/ ---1418736516-216597423-1331427784=:99434 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Hi Jussi:<= /span>
Your suggestion is very useful for me. Thank you!
 
--------------------------------------------------------= --------
Jun Zhang (coolrainbow^^yahoo.cn)
Computational Chemistry Gro= up
No.94, Weijinlu
Nankai University
Tianjin, China
=E5=8F=91=E4=BB=B6=E4=BA=BA=EF=BC=9A Jussi Lehtola jussi.le= htola=3D-=3Dhelsinki.fi <owner-chemistry^^ccl.net>
= =E6=94=B6=E4=BB=B6=E4=BA=BA=EF=BC=9A "Zhang, Jun " <c= oolrainbow^^yahoo.cn>
=E5=8F= =91=E9=80=81=E6=97=A5=E6=9C=9F=EF=BC=9A 2012=E5=B9=B43=E6=9C=889= =E6=97=A5, =E6=98=9F=E6=9C=9F=E4=BA=94, =E4=B8=8B=E5=8D=88 4:12
=E4=B8=BB=E9=A2=98: CCL: Some con= fusions about indices of two-electron integrals in programming
 =


Sent to CCL by: Jussi Lehtola [jussi.lehtola[#]helsinki.fi]<= br>On Fri, 9 Mar 2012 14:55:33 +0800 (CST)
"Jun Zhang coolrainbow##yahoo= .cn" <owner-chemistry:-:ccl.net> wrote:
> Hello Everyone:
&g= t;
> We know that in quantum chemistry programming the two-electron<= br>> integrals (ERI) are computed in batch (e.g., <ss|spx>,<ss|= spy>,
> <ss|spz> at the same time) to make efficient use of = the common
> immediate quantities. But what confused me is the index = fetching.
> That is, when <ss|spx> is to calculate, how to determine the indices
> of th= e 3 integrals <ss|spx>,<ss|spy>, <ss|spz> in memory? And = then,
> how to make the following subroutines know that <ss|spy>= ; and <ss|spz>
> have been calculated?
>
> It wil= l be better if you can recommend me some codes to read.  Thank> you in advance.

The indexing with two-electron integrals is ra= ther nontrivial. Even
more nontrivial would be writing a two-electron in= tegral code, as there
are many possible paths to the wanted target integ= ral.

Fortunately, Ed Valeev has written libint, which uses Obara-Sai= ka and
Head-Gordon-Pople recursion relations to automatically generate o= ptimal
code to obtain the wanted integral. http://sourceforge.net/p/libint/
<= br>What you get out of libint is just the target integrals. From the
libint programmer's manual:

"Shell-sets of integrals contain= integrals in =E2=80=9Crow major=E2=80=9D order.For
exam- ple, if the nu= mber of functions in each shell is na , nb , nc ,
and nd , respectively,= then the integral (ab|cd) is found at position
abcd =3D ((a*nb + b)*nc = + c)*nd + d."
--
---------------------------------------------------= -----
Mr. Jussi Lehtola, M. Sc.        Doctoral Stu= dent
jussi.lehtola:-:helsinki.fi        Department = of Physics
http://www.helsinki.fi/~jzlehtol  University of Helsinki
Offi= ce phone: +358 9 191 50 632  Finland
-----------------------------= ---------------------------
Jussi Lehtola, FM       =         Tohtorikoulutettava
jussi.lehtola:-:helsin= ki.fi        Fysiikan laitos
http://www.hel= sinki.fi/~jzlehtol  Helsingin Yliopisto
Ty=C3=B6puhelin: (0)9 1= 91 50 632
--------------------------------------------------------


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