From owner-chemistry@ccl.net Thu Feb 7 03:02:00 2013 From: "Cina Foroutan-Nejad canyslopus!=!yahoo.co.uk" To: CCL Subject: CCL:G: Huzinaga Basis Set Message-Id: <-48181-130207030026-1754-VSuGHVlIiG+LOBqFUxVY6A*_*server.ccl.net> X-Original-From: Cina Foroutan-Nejad Content-Type: multipart/alternative; boundary="-1712059246-1013271434-1360224016=:66607" Date: Thu, 7 Feb 2013 08:00:16 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: Cina Foroutan-Nejad [canyslopus]~[yahoo.co.uk] ---1712059246-1013271434-1360224016=:66607 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi,=0A=0AYou can find Huzinaga basis set beside hundreds of other basis set= s for different atoms in the Periodic Table in this webpage:=0Ahttps://bse.= pnl.gov/bse/portal=0A=0AGood luck,=0ACina=0A-------------------------------= ---------------------------------------------------------------------------= -------------------------------------------------=0ACina Foroutan-Nejad, Ph= D=0Ahttp://muni.academia.edu/CinaForoutanNejad=0A=0A=0A=0A_________________= _______________=0A From: Arun Manna arun.manna17*gmail.com =0ATo: "Foroutan-Nejad, Cina " = =0ASent: Thursday, 7 February 2013, 4:35=0ASubject: CCL:G: Huzinaga Basis S= et=0A =0A=0A=A0Dear Cory C. Pye,=0A=0A=A0Thank you for your reply containin= g detained basis set description, which really helps me to understand certa= in things. =0A=A0But, still I have confusions in constructing basis sets fo= r my system, where, I have "Se" as chemical elements with few other=A0 =0A= =A0elements too. From literature, I have found that, the Huzinaga basis set= s, such as 14s10p5d & 17s13p6d are best for the Se=A0 =0A=A0atoms (although= they did not mention about the contraction pattern). So, I would like to u= se these two basis sets for my systems.=0A=A0I try to understand your basis= set description for the As element that described in your reply. I have fe= w queries for describing basis sets:=0A1) How to you get these coefficients= for each block? Is there any database which provides these coefficients? Y= ou have pointed out a book by S. Huzinaga for the extra polarization. Are t= hese coefficients are taken from this book. Unfortunately, I do not have ac= cess to this book. So, is there any alternative source which helps for cons= tructing these basis sets coefficients.=0A2) If I want to use your describe= d basis set for Se, what are the changes to be carried out in your basis se= t description of As element?=0A3) What would be the changes in the basis se= t description between 14s10p5d & 17s13p6d Huzinaga basis sets?=0A=0AIt woul= d be great help if you can provide me these basis sets for Se arom or helpi= ng me in constructing these basis sets from scratch.=0A=0AThank you once ag= ain for your help.=0A=0AWith best regards,=0AArun=0A=0A=0A=A0=0A=0AOn Thu, = Feb 7, 2013 at 6:53 AM, Cory Pye cpye_._ap.smu.ca wrote:=0A=0A=0A>Sent to CCL by: Cory Pye [cpye|a|ap.smu.ca]=0A>Arun,=0A>= =0A>The answer depends on how you want to contract the basis sets, and I do= n't have enough information to make this determination.=0A>=0A>Based on my = experience with these basis sets, you are probably trying to use=0A>the 14s= 10p5d primitive set. In a minimal basis set, the contraction pattern=0A>wou= ld be 5333/433/5, most likely. This tells me you are probably trying to=0A>= model an element between Sc-Kr. If you wanted to improve the basis set, you= =0A>could partially decontract it to make a split valence basis set, as=0A>= 53321/4321/41, where the exponents are arranged from largest to smallest.= =0A>Huzinaga also supplies a recommended set of exponents for polarization= =0A>functions in his book.=0A>=0A>For example, the 4333/433/4 As basis set = looks something like this.=0A>with for example B3LYP/gen in the route line.= =0A>=0A>AS =A0 0=0A>=A0S =A0 4 =A01.00=0A>=A0 =A0 =A0 =A0 15860.364 =A0 =A0= =A00.0171048=0A>=A0 =A0 =A0 =A0 2391.2232 =A0 =A0 =A00.1200249=0A>=A0 =A0 = =A0 =A0 542.23120 =A0 =A0 =A00.4378747=0A>=A0 =A0 =A0 =A0 146.00269 =A0 =A0= =A00.5576566=0A>=A0S =A0 3 =A01.00=0A>=A0 =A0 =A0 =A0 219.08007 =A0 =A0 = =A0-.1096535=0A>=A0 =A0 =A0 =A0 24.437631 =A0 =A0 =A00.6475717=0A>=A0 =A0 = =A0 =A0 10.206970 =A0 =A0 =A00.4248194=0A>=A0S =A0 3 =A01.00=0A>=A0 =A0 =A0= =A0 18.744848 =A0 =A0 =A0-.2334702=0A>=A0 =A0 =A0 =A0 3.1047892 =A0 =A0 = =A00.7294911=0A>=A0 =A0 =A0 =A0 1.2970598 =A0 =A0 =A00.4044278=0A>=A0S =A0 = 3 =A01.00=0A>=A0 =A0 =A0 =A0 1.8301844 =A0 =A0 =A0-.1924620=0A>=A0 =A0 =A0 = =A0 0.28147770 =A0 =A0 0.6866084=0A>=A0 =A0 =A0 =A0 0.10437810 =A0 =A0 ????= =0A>=A0P =A0 4 =A01.00=0A>=A0 =A0 =A0 =A0 670.45052 =A0 =A0 =A00.0275156=0A= >=A0 =A0 =A0 =A0 157.17065 =A0 =A0 =A00.1794001=0A>=A0 =A0 =A0 =A0 48.63953= 7 =A0 =A0 =A00.5052466=0A>=A0 =A0 =A0 =A0 16.532308 =A0 =A0 =A00.4576592=0A= >=A0P =A0 3 =A01.00=0A>=A0 =A0 =A0 =A0 7.4556466 =A0 =A0 =A00.3248901=0A>= =A0 =A0 =A0 =A0 2.9185276 =A0 =A0 =A00.5568808=0A>=A0 =A0 =A0 =A0 1.1701325= =A0 =A0 =A00.2280292=0A>=A0P =A0 3 =A01.00=0A>=A0 =A0 =A0 =A0 0.17189969 = =A0 =A0 0.5495546=0A>=A0 =A0 =A0 =A0 0.44648872 =A0 =A0 0.3297273=0A>=A0 = =A0 =A0 =A0 0.06621832 =A0 =A0 ????=0A>=A0D =A0 4 =A01.00=0A>=A0 =A0 =A0 = =A0 49.802186 =A0 =A0 =A00.0618851=0A>=A0 =A0 =A0 =A0 13.722924 =A0 =A0 =A0= 0.2858504=0A>=A0 =A0 =A0 =A0 4.3622725 =A0 =A0 =A00.5264330=0A>=A0 =A0 =A0 = =A0 1.3044304 =A0 =A0 =A00.4103582=0A>****=0A>=0A>where the ???? refers to = values that I don't have access to at the moment.=0A>After splitting and ad= ding an extra D-type function, it looks like=0A>=0A>=0A>AS =A0 0=0A>=A0S = =A0 4 =A01.00=0A>=A0 =A0 =A0 =A0 15860.364 =A0 =A0 =A00.0171048=0A>=A0 =A0 = =A0 =A0 2391.2232 =A0 =A0 =A00.1200249=0A>=A0 =A0 =A0 =A0 542.23120 =A0 =A0= =A00.4378747=0A>=A0 =A0 =A0 =A0 146.00269 =A0 =A0 =A00.5576566=0A>=A0S =A0= 3 =A01.00=0A>=A0 =A0 =A0 =A0 219.08007 =A0 =A0 =A0-.1096535=0A>=A0 =A0 =A0= =A0 24.437631 =A0 =A0 =A00.6475717=0A>=A0 =A0 =A0 =A0 10.206970 =A0 =A0 = =A00.4248194=0A>=A0S =A0 3 =A01.00=0A>=A0 =A0 =A0 =A0 18.744848 =A0 =A0 =A0= -.2334702=0A>=A0 =A0 =A0 =A0 3.1047892 =A0 =A0 =A00.7294911=0A>=A0 =A0 =A0 = =A0 1.2970598 =A0 =A0 =A00.4044278=0A>=A0S =A0 2 =A01.00 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 <----=0A>=A0 =A0 =A0 =A0 1.8301= 844 =A0 =A0 =A0-.1924620=0A>=A0 =A0 =A0 =A0 0.28147770 =A0 =A0 0.6866084=0A= >=A0S =A0 1 =A01.00 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= =A0 <----=0A>=A0 =A0 =A0 =A0 0.10437810 =A0 =A0 1.000000=0A>=A0P =A0 4 =A0= 1.00=0A>=A0 =A0 =A0 =A0 670.45052 =A0 =A0 =A00.0275156=0A>=A0 =A0 =A0 =A0 1= 57.17065 =A0 =A0 =A00.1794001=0A>=A0 =A0 =A0 =A0 48.639537 =A0 =A0 =A00.505= 2466=0A>=A0 =A0 =A0 =A0 16.532308 =A0 =A0 =A00.4576592=0A>=A0P =A0 3 =A01.0= 0=0A>=A0 =A0 =A0 =A0 7.4556466 =A0 =A0 =A00.3248901=0A>=A0 =A0 =A0 =A0 2.91= 85276 =A0 =A0 =A00.5568808=0A>=A0 =A0 =A0 =A0 1.1701325 =A0 =A0 =A00.228029= 2=0A>=A0P =A0 2 =A01.00 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= =A0 =A0 <----=0A>=A0 =A0 =A0 =A0 0.17189969 =A0 =A0 0.5495546=0A>=A0 =A0 = =A0 =A0 0.44648872 =A0 =A0 0.3297273=0A>=A0P =A0 1 =A01.00 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 <----=0A>=A0 =A0 =A0 =A0 0.0662= 1832 =A0 =A0 1.000000=0A>=A0SP =A01 =A01.00=0A>=A0 =A0 =A0 =A0 0.019 =A0 = =A0 =A0 =A0 =A01.000000 =A0 =A0 =A01.000000=0A>=A0D =A0 4 =A01.00=0A>=A0 = =A0 =A0 =A0 49.802186 =A0 =A0 =A00.0618851=0A>=A0 =A0 =A0 =A0 13.722924 =A0= =A0 =A00.2858504=0A>=A0 =A0 =A0 =A0 4.3622725 =A0 =A0 =A00.5264330=0A>=A0 = =A0 =A0 =A0 1.3044304 =A0 =A0 =A00.4103582=0A>=A0D =A0 1 =A01.00 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 <----=0A>=A0 =A0 =A0 = =A0 0.2930000 =A0 =A0 =A01.000000=0A>=0A>=0A>The <--- denotes areas that yo= u should pay particular attention to when=0A>splitting the basis set or add= inf the extra function.=0A>We don't bother to split the d-function as it is= considered part of the core,=0A>but you probably would split this for the = transition metals. We did add a=0A>d-type polarization function here. we al= so added an sp-type diffuse function as=0A>well. Note that the S and P cont= raction coefficients are specified in the same=0A>line.=0A>=0A>The whole in= put would look like, for example for arsine=0A>=0A>----=0A>%chk=3DAsH3=0A>#= n B3lyp/gen FOpt=3D(CalcFC,z-matrix) Freq=0A>=0A>AsH3=0A>=0A>=A00 1=0A>As= =0A>X*1 As 1.0=0A>H1 =A0As H1As =A0X*1 =A0 H1AsX=0A>H2 =A0As H1As =A0X*1 = =A0 H1AsX =A0 =A0H1 =A0 120.0=0A>H3 =A0As H1As =A0X*1 =A0 H1AsX =A0 =A0H1 = =A0-120.0=0A>=0A>H1As=3D1.3=0A>H1AsX=3D127.0=0A>=0A>=0A>****=0A>H 0=0A>6-31G =A0 <----if you are using the canned b= asis sets for H.=0A>****=0A>=0A>=0A>=0A>=0A>On Thu, 7 Feb 2013, Arun Manna = arun.manna17|-|gmail.com wrote:=0A>=0A>> Dear All,=0A>>=0A>> I want to use = the Huzinaga basis set in DFT code, gaussian09 for my system.=0A>> I would = like to use *14s10p5d & 17s13p6d* Huzinaga basis sets for=0A>=0A>> some spe= cific elements. Though I understand that, these numbers are the=0A>> number= of primitive basis functions, but, I do not know how to specify=0A>> these= in gaussian input file.=0A>> Would anyone help me in defining these two ba= sis sets for using in gaussian=0A>> input file?=0A>>=0A>> Thank you in adva= nce,=0A>>=0A>> With best regards,=0A>> Arun=0A>>=0A>> --=0A>> Arun K Manna= =0A>> PhD Student, TSU, JNCASR,=0A>> Bangalore - 560064, India=0A>>=0A>=0A>= =A0 =A0************* =A0 =A0! =A0Dr. Cory C. Pye=0A>=A0***************** = =A0! =A0Associate Professor=0A>*** =A0 ** =A0 =A0** =A0** =A0! =A0Theoretic= al and Computational Chemistry=0A>** =A0 * =A0**** =A0 =A0 =A0 =A0! =A0Depa= rtment of Chemistry, Saint Mary's University=0A>** =A0 =A0 =A0* =A0* =A0 = =A0 =A0 =A0! =A0923 Robie Street, Halifax, NS B3H 3C3=0A>** =A0 =A0 =A0* = =A0* =A0 =A0 =A0 =A0! =A0cpye,,crux.stmarys.ca =A0 http://apwww.stmarys.ca/= ~cpye=0A>*** =A0 =A0 * =A0* =A0 =A0** =A0! =A0Ph: (902)-420-5654 =A0FAX:(90= 2)-496-8104=0A>=A0***************** =A0!=0A>=A0 =A0************* =A0 =A0! = =A0Les Hartree-Focks (Apologies to Montreal Canadien Fans)=0A>=0A>=0A>=0A>-= =3D This is automatically added to each message by the mailing script =3D-= =0A>=0A>E-mail to subscribers: CHEMISTRY::ccl.net or use:=0A>=A0 =A0 =A0 ht= tp://www.ccl.net/cgi-bin/ccl/send_ccl_message=0A>=0A>E-mail to administrato= rs: CHEMISTRY-REQUEST::ccl.net or use=0A>=A0 =A0 =A0 http://www.ccl.net/cgi= -bin/ccl/send_ccl_message=0A>=0A>Subscribe/Unsubscribe:=0A>=A0 =A0 =A0 http= ://www.ccl.net/chemistry/sub_unsub.shtml=0A>=0A>Before posting, check wait = time at: http://www.ccl.net=0A>=0A>Job: http://www.ccl.net/jobs=0A>Conferen= ces: http://server.ccl.net/chemistry/announcements/conferences/=0A>=0A>Sear= ch Messages: http://www.ccl.net/chemistry/searchccl/index.shtml=0A>=0A>=A0 = =A0 =A0=0A>=0A>RTFI: http://www.ccl.net/che= mistry/aboutccl/instructions/=0A>=0A>=0A>=0A=0A=0A-- =0AArun K Manna=0APhD = Student, TSU, JNCASR, =0ABangalore - 560064, India ---1712059246-1013271434-1360224016=:66607 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hi,

You can find Huzinaga ba= sis set beside hundreds of other basis sets for different atoms in the Peri= odic Table in this webpage:
https://bse.pnl.gov/bs= e/portal

Good= luck,
Cina
-------------= ---------------------------------------------------------------------------= -------------------------------------------------------------------<= /div>
Cina Foroutan-Nejad, PhD
http://= muni.academia.edu/CinaForoutanNejad

From: Arun Manna a= run.manna17*gmail.com <owner-chemistry*|*ccl.net>
To: "Foroutan-Nejad, Cina " <can= yslopus*|*yahoo.co.uk>
Sent: Thursday, 7 February 2013, 4:35
Subject: CCL:G: Huzinaga Basis Set
 Dear Cory C. Pye,

 Thank you f= or your reply containing detained basis set description, which really helps me to unders= tand certain things.
 But, still I have confusions in constructing= basis sets for my system, where, I have "Se" as chemical elements with few= other 
=0A elements too. From literature, I have found that,= the Huzinaga basis sets, such as 14s10p5d & 17s13p6d are best for the = Se 
 atoms (although they did not mention about the contracti= on pattern). So, I would like to use these two basis sets for my systems.=0A I try to understand your basis set description for the As elemen= t that described in your reply. I have few queries for describing basis set= s:
1) How to you get these coefficients for each block? Is there any dat= abase which provides these coefficients? You have pointed out a book by S. = Huzinaga for the extra polarization. Are these coefficients are taken from = this book. Unfortunately, I do not have access to this book. So, is there a= ny alternative source which helps for constructing these basis sets coeffic= ients.
=0A2) If I want to use your described basis set for Se, what are = the changes to be carried out in your basis set description of As element?<= br>3) What would be the changes in the basis set description between 14s10p= 5d & 17s13p6d Huzinaga basis sets?
=0A
It would be great help if = you can provide me these basis sets for Se arom or helping me in constructi= ng these basis sets from scratch.

Thank you once again for your help= .

With best regards,
Arun

=0A
 
On Thu, Feb 7, 2013 at 6:53 AM, Cory Pye cpye_._ap.smu.ca= <owne= r-chemistry::ccl.net> wrote:
=0A

=0ASent to CCL by: Cory Pye [cpye|a|ap.smu.ca]
=0AArun,<= br>=0A
=0AThe answer depends on how you want to contract the basis sets,= and I don't have enough information to make this determination.
=0A
= =0ABased on my experience with these basis sets, you are probably trying to= use
=0Athe 14s10p5d primitive set. In a minimal basis set, the contract= ion pattern
=0Awould be 5333/433/5, most likely. This tells me you are p= robably trying to
=0Amodel an element between Sc-Kr. If you wanted to im= prove the basis set, you
=0Acould partially decontract it to make a spli= t valence basis set, as
=0A53321/4321/41, where the exponents are arrang= ed from largest to smallest.
=0AHuzinaga also supplies a recommended set= of exponents for polarization
=0Afunctions in his book.
=0A
=0AFo= r example, the 4333/433/4 As basis set looks something like this.
=0Awit= h for example B3LYP/gen in the route line.
=0A
=0AAS   0
=0A&= nbsp;S   4  1.00
=0A        15860.364 &nbs= p;    0.0171048
=0A        2391.2232  = ;    0.1200249
=0A        542.23120  =    0.4378747
=0A        146.00269   =    0.5576566
=0A S   3  1.00
=0A   = ;     219.08007      -.1096535
=0A   =     24.437631      0.6475717
=0A    =     10.206970      0.4248194
=0A S   = 3  1.00
=0A        18.744848     &nbs= p;-.2334702
=0A        3.1047892      = ;0.7294911
=0A        1.2970598      = 0.4044278
=0A S   3  1.00
=0A      &nbs= p; 1.8301844      -.1924620
=0A       = ; 0.28147770     0.6866084
=0A        0.10= 437810     ????
=0A P   4  1.00
=0A  &n= bsp;     670.45052      0.0275156
=0A  &nb= sp;     157.17065      0.1794001
=0A  &nbs= p;     48.639537      0.5052466
=0A   = ;     16.532308      0.4576592
=0A P  = ; 3  1.00
=0A        7.4556466     &n= bsp;0.3248901
=0A        2.9185276     &nb= sp;0.5568808
=0A        1.1701325     &nbs= p;0.2280292
=0A P   3  1.00
=0A      &n= bsp; 0.17189969     0.5495546
=0A        0= .44648872     0.3297273
=0A        0.06621= 832     ????
=0A D   4  1.00
=0A   = ;     49.802186      0.0618851
=0A   =     13.722924      0.2858504
=0A    =     4.3622725      0.5264330
=0A    &= nbsp;   1.3044304      0.4103582
=0A****
=0A
= =0Awhere the ???? refers to values that I don't have access to at the momen= t.
=0AAfter splitting and adding an extra D-type function, it looks like=
=0A
=0A
=0AAS   0
=0A S   4  1.00
=0A&n= bsp;       15860.364      0.0171048
=0A&nb= sp;       2391.2232      0.1200249
=0A&nbs= p;       542.23120      0.4378747
=0A = ;       146.00269      0.5576566
=0A = S   3  1.00
=0A        219.08007   &n= bsp;  -.1096535
=0A        24.437631   &nb= sp;  0.6475717
=0A        10.206970   &nbs= p;  0.4248194
=0A S   3  1.00
=0A    &n= bsp;   18.744848      -.2334702
=0A    &nb= sp;   3.1047892      0.7294911
=0A    &nbs= p;   1.2970598      0.4044278
=0A S   2 &n= bsp;1.00                   &nb= sp;           <----
=0A      =   1.8301844      -.1924620
=0A      &= nbsp; 0.28147770     0.6866084
=0A S   1  1.00 =                      = ;         <----
=0A        0.= 10437810     1.000000
=0A P   4  1.00
=0A&nb= sp;       670.45052      0.0275156
=0A&nbs= p;       157.17065      0.1794001
=0A = ;       48.639537      0.5052466
=0A =       16.532308      0.4576592
=0A P=   3  1.00
=0A        7.4556466   &nb= sp;  0.3248901
=0A        2.9185276   &nbs= p;  0.5568808
=0A        1.1701325    = ;  0.2280292
=0A P   2  1.00       &n= bsp;                     =   <----
=0A        0.17189969     = 0.5495546
=0A        0.44648872     0.3297= 273
=0A P   1  1.00           &n= bsp;                   <---= -
=0A        0.06621832     1.000000
= =0A SP  1  1.00
=0A        0.019 &nbs= p;        1.000000      1.000000
=0A&= nbsp;D   4  1.00
=0A        49.802186 &nbs= p;    0.0618851
=0A        13.722924  = ;    0.2858504
=0A        4.3622725  =    0.5264330
=0A        1.3044304   =    0.4103582
=0A D   1  1.00     &nbs= p;                     &n= bsp;   <----
=0A        0.2930000   &nb= sp;  1.000000
=0A
=0A
=0AThe <--- denotes areas that you s= hould pay particular attention to when
=0Asplitting the basis set or add= inf the extra function.
=0AWe don't bother to split the d-function as it= is considered part of the core,
=0Abut you probably would split this fo= r the transition metals. We did add a
=0Ad-type polarization function he= re. we also added an sp-type diffuse function as
=0Awell. Note that the = S and P contraction coefficients are specified in the same
=0Aline.
= =0A
=0AThe whole input would look like, for example for arsine
=0A=0A----
=0A%chk=3DAsH3
=0A#n B3lyp/gen FOpt=3D(CalcFC,z-matrix) Freq=
=0A
=0AAsH3
=0A
=0A 0 1
=0AAs
=0AX*1 As 1.0
=0AH= 1  As H1As  X*1   H1AsX
=0AH2  As H1As  X*1 &nb= sp; H1AsX    H1   120.0
=0AH3  As H1As  X*1 &nb= sp; H1AsX    H1  -120.0
=0A
=0AH1As=3D1.3
=0AH1AsX= =3D127.0
=0A
=0A<insert basis set for arsenic here>
=0A****<= br>=0AH 0
=0A6-31G   <----if you are using the canned basis sets= for H.
=0A****
=0A

=0A
=0A
= =0AOn Thu, 7 Feb 2013, Arun Manna arun.manna17|-|gmail.com wrote:
=0A
=0A&g= t; Dear All,
=0A>
=0A> I want to use the Huzinaga basis set in = DFT code, gaussian09 for my system.
=0A
> I would like to use *1= 4s10p5d & 17s13p6d* Huzinaga basis sets for
=0A
> some specific elements. Though I understand that, these numbe= rs are the
=0A> number of primitive basis functions, but, I do not kn= ow how to specify
=0A> these in gaussian input file.
=0A> Would= anyone help me in defining these two basis sets for using in gaussian
= =0A> input file?
=0A>
=0A> Thank you in advance,
=0A><= br>=0A> With best regards,
=0A> Arun
=0A>
=0A> --
= =0A> Arun K Manna
=0A> PhD Student, TSU, JNCASR,
=0A> Bangal= ore - 560064, India
=0A>
=0A
=0A
   ************= *    !  Dr. Cory C. Pye
=0A *****************  = !  Associate Professor
=0A***   **    **  ** &n= bsp;!  Theoretical and Computational Chemistry
=0A**   *  = ;****        !  Department of Chemistry, Saint Mar= y's University
=0A**      *  *       =  !  923 Robie Street, Halifax, NS B3H 3C3
=0A**     =  *  *        !  cpye,,crux.stmarys.ca &n= bsp; http://apwww.stmarys.ca/~cpye
=0A***     *  = *    **  !  Ph: (902)-420= -5654  FAX:(902)-496-8104
=0A=  *****************  !
=0A   *************   &nb= sp;!  Les Hartree-Focks (Apologies to Montreal Canadien Fans)
=0A=0A
=0A
=0A-=3D This is automatically added to each message by the = mailing script =3D-
=0A
=0AE-mail to subscribers: CHEMISTRY::ccl.net or use:
=0A      = http://www.ccl.net/cgi-bin/ccl/send_ccl_message
= =0A
=0AE-mail to administrators: CHEMISTRY-REQUEST::ccl.net or use
=0A    &nbs= p; http://www.ccl.net/cgi-bin/ccl/send_ccl_message<= br>=0A
=0ASubscribe/Unsubscribe:
=0A      http://www.ccl.net/chemistry/sub_unsub.shtml
=0A
=0ABefore p= osting, check wait time at: http://www.ccl.net
=0A
=0AJob: http://www.ccl.net= /jobs
=0AConferences: http://server.c= cl.net/chemistry/announcements/conferences/
=0A
=0ASearch Message= s: http://www.ccl.net/chemistry/searchccl/index.shtm= l
=0A
=0A      http://www.ccl.net/spammers.txt=
=0A
=0ARTFI: http://www.ccl.net/chemistr= y/aboutccl/instructions/
=0A
=0A
=0A


--
Arun K Manna
PhD Student, TSU, JNCASR,
Ban= galore - 560064, India
=0A


---1712059246-1013271434-1360224016=:66607-- From owner-chemistry@ccl.net Thu Feb 7 04:05:00 2013 From: "Frank Jensen frj(0)chem.au.dk" To: CCL Subject: CCL:G: Huzinaga Basis Set Message-Id: <-48182-130207040044-26378-7zxWW4preL+cmKa36ykqBw*o*server.ccl.net> X-Original-From: Frank Jensen Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_D5BC00C0FB9AC34D9C8F4DC965C516890A514177SRVUNIMBX07unia_" Date: Thu, 7 Feb 2013 09:00:28 +0000 MIME-Version: 1.0 Sent to CCL by: Frank Jensen [frj-#-chem.au.dk] --_000_D5BC00C0FB9AC34D9C8F4DC965C516890A514177SRVUNIMBX07unia_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable There is really nothing special about Se, and several modern basis sets, su= ch as cc-pVXZ, Def2-xxx and pc-n, are available for wide selection of eleme= nts, and these can be picked up at the EMSL web site. At the risk of offending several people, I consider the Huzinaga basis sets= as being of mainly historical interest. Furthermore, constructing well-balanced basis sets is somewhat of an art, a= nd I strongly suggest that inexperienced users stick to standard basis sets= from one of the basis set families designed for the specific method employ= ed. Frank Frank Jensen Assoc. Prof. Dept. of Chemistry Aarhus University http://old.chem.au.dk/~frj > From: owner-chemistry+frj=3D=3Dchem.au.dk!A!ccl.net [mailto:owner-chemistry+f= rj=3D=3Dchem.au.dk!A!ccl.net] On Behalf Of Cina Foroutan-Nejad canyslopus!=3D= !yahoo.co.uk Sent: 7. februar 2013 09:00 To: Frank Jensen Subject: CCL:G: Huzinaga Basis Set Hi, You can find Huzinaga basis set beside hundreds of other basis sets for dif= ferent atoms in the Periodic Table in this webpage: https://bse.pnl.gov/bse/portal Good luck, Cina ---------------------------------------------------------------------------= ---------------------------------------------------------------------------= ----- Cina Foroutan-Nejad, PhD http://muni.academia.edu/CinaForoutanNejad ________________________________ > From: Arun Manna arun.manna17*gmail.com To: "Foroutan-Nejad, Cina " Sent: Thursday, 7 February 2013, 4:35 Subject: CCL:G: Huzinaga Basis Set Dear Cory C. Pye, Thank you for your reply containing detained basis set description, which = really helps me to understand certain things. But, still I have confusions in constructing basis sets for my system, whe= re, I have "Se" as chemical elements with few other elements too. From literature, I have found that, the Huzinaga basis sets,= such as 14s10p5d & 17s13p6d are best for the Se atoms (although they did not mention about the contraction pattern). So, I= would like to use these two basis sets for my systems. I try to understand your basis set description for the As element that des= cribed in your reply. I have few queries for describing basis sets: 1) How to you get these coefficients for each block? Is there any database = which provides these coefficients? You have pointed out a book by S. Huzina= ga for the extra polarization. Are these coefficients are taken from this b= ook. Unfortunately, I do not have access to this book. So, is there any alt= ernative source which helps for constructing these basis sets coefficients. 2) If I want to use your described basis set for Se, what are the changes t= o be carried out in your basis set description of As element? 3) What would be the changes in the basis set description between 14s10p5d = & 17s13p6d Huzinaga basis sets? It would be great help if you can provide me these basis sets for Se arom o= r helping me in constructing these basis sets from scratch. Thank you once again for your help. With best regards, Arun On Thu, Feb 7, 2013 at 6:53 AM, Cory Pye cpye_._ap.smu.ca > wrote: Sent to CCL by: Cory Pye [cpye|a|ap.smu.ca] Arun, The answer depends on how you want to contract the basis sets, and I don't = have enough information to make this determination. Based on my experience with these basis sets, you are probably trying to us= e the 14s10p5d primitive set. In a minimal basis set, the contraction pattern would be 5333/433/5, most likely. This tells me you are probably trying to model an element between Sc-Kr. If you wanted to improve the basis set, you could partially decontract it to make a split valence basis set, as 53321/4321/41, where the exponents are arranged from largest to smallest. Huzinaga also supplies a recommended set of exponents for polarization functions in his book. For example, the 4333/433/4 As basis set looks something like this. with for example B3LYP/gen in the route line. AS 0 S 4 1.00 15860.364 0.0171048 2391.2232 0.1200249 542.23120 0.4378747 146.00269 0.5576566 S 3 1.00 219.08007 -.1096535 24.437631 0.6475717 10.206970 0.4248194 S 3 1.00 18.744848 -.2334702 3.1047892 0.7294911 1.2970598 0.4044278 S 3 1.00 1.8301844 -.1924620 0.28147770 0.6866084 0.10437810 ???? P 4 1.00 670.45052 0.0275156 157.17065 0.1794001 48.639537 0.5052466 16.532308 0.4576592 P 3 1.00 7.4556466 0.3248901 2.9185276 0.5568808 1.1701325 0.2280292 P 3 1.00 0.17189969 0.5495546 0.44648872 0.3297273 0.06621832 ???? D 4 1.00 49.802186 0.0618851 13.722924 0.2858504 4.3622725 0.5264330 1.3044304 0.4103582 **** where the ???? refers to values that I don't have access to at the moment. After splitting and adding an extra D-type function, it looks like AS 0 S 4 1.00 15860.364 0.0171048 2391.2232 0.1200249 542.23120 0.4378747 146.00269 0.5576566 S 3 1.00 219.08007 -.1096535 24.437631 0.6475717 10.206970 0.4248194 S 3 1.00 18.744848 -.2334702 3.1047892 0.7294911 1.2970598 0.4044278 S 2 1.00 <---- 1.8301844 -.1924620 0.28147770 0.6866084 S 1 1.00 <---- 0.10437810 1.000000 P 4 1.00 670.45052 0.0275156 157.17065 0.1794001 48.639537 0.5052466 16.532308 0.4576592 P 3 1.00 7.4556466 0.3248901 2.9185276 0.5568808 1.1701325 0.2280292 P 2 1.00 <---- 0.17189969 0.5495546 0.44648872 0.3297273 P 1 1.00 <---- 0.06621832 1.000000 SP 1 1.00 0.019 1.000000 1.000000 D 4 1.00 49.802186 0.0618851 13.722924 0.2858504 4.3622725 0.5264330 1.3044304 0.4103582 D 1 1.00 <---- 0.2930000 1.000000 The <--- denotes areas that you should pay particular attention to when splitting the basis set or addinf the extra function. We don't bother to split the d-function as it is considered part of the cor= e, but you probably would split this for the transition metals. We did add a d-type polarization function here. we also added an sp-type diffuse functio= n as well. Note that the S and P contraction coefficients are specified in the s= ame line. The whole input would look like, for example for arsine ---- %chk=3DAsH3 #n B3lyp/gen FOpt=3D(CalcFC,z-matrix) Freq AsH3 0 1 As X*1 As 1.0 H1 As H1As X*1 H1AsX H2 As H1As X*1 H1AsX H1 120.0 H3 As H1As X*1 H1AsX H1 -120.0 H1As=3D1.3 H1AsX=3D127.0 **** H 0 6-31G <----if you are using the canned basis sets for H. **** On Thu, 7 Feb 2013, Arun Manna arun.manna17|-|gmail.com = wrote: > Dear All, > > I want to use the Huzinaga basis set in DFT code, gaussian09 for my syste= m. > I would like to use *14s10p5d & 17s13p6d* Huzinaga basis sets for > some specific elements. Though I understand that, these numbers are the > number of primitive basis functions, but, I do not know how to specify > these in gaussian input file. > Would anyone help me in defining these two basis sets for using in gaussi= an > input file? > > Thank you in advance, > > With best regards, > Arun > > -- > Arun K Manna > PhD Student, TSU, JNCASR, > Bangalore - 560064, India > ************* ! Dr. Cory C. Pye ***************** ! Associate Professor *** ** ** ** ! Theoretical and Computational Chemistry ** * **** ! Department of Chemistry, Saint Mary's University ** * * ! 923 Robie Street, Halifax, NS B3H 3C3 ** * * ! cpye,,crux.stmarys.ca htt= p://apwww.stmarys.ca/~cpye *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104 ***************** ! ************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fa= ns) -=3D This is automatically added to each message by the mailing script =3D- E-mail to subscribers: CHEMISTRY::ccl.net or use= :E-mail to administrators: CHEMISTRY-REQUEST::ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtml

There is really nothing s= pecial about Se, and several modern basis sets, such as cc-pVXZ, Def2-xxx a= nd pc-n, are available for wide selection of elements, and these can be picked up at the EMSL web site.

At the risk of offending = several people, I consider the Huzinaga basis sets as being of mainly histo= rical interest.

Furthermore, constructing= well-balanced basis sets is somewhat of an art, and I strongly suggest tha= t inexperienced users stick to standard basis sets from one of the basis set families designed for the specific method employed.

 <= /p>

Frank

 <= /p>

Frank Jensen
Assoc. Prof.
Dept. of Chemistry
Aarhus University
http://old.chem.au= .dk/~frj

 <= /p>

From: owner-ch= emistry+frj=3D=3Dchem.au.dk!A!ccl.net [mailto:owner-chemistry+frj=3D= =3Dchem.au.dk!A!ccl.net] On Behalf Of Cina Foroutan-Nejad canyslopus!=3D!yahoo.co.uk
Sent: 7. februar 2013 09:00
To: Frank Jensen
Subject: CCL:G: Huzinaga Basis Set

 

Hi,

 

You can find Huzinaga basis set beside = hundreds of other basis sets for different atoms in the Periodic Table in t= his webpage:

 

Good luck,

Cina

---------------------------------------= ---------------------------------------------------------------------------= -----------------------------------------

Cina Foroutan-Nejad, PhD

 <= /o:p>

From: Arun Manna arun.manna17*gmail.com = <owner-chemistry..ccl.net>
To: "Foroutan-Nejad, Cina " <canyslopus..yahoo.co.uk>= ;
Sent: Thursday, 7 February 2013, 4:35
Subject: CCL:G: Huzinaga Basis Set

 

 Dear Cory C. Pye,

 Thank you for your reply containing detained basis set description, w= hich really helps me to understand certain things.
 But, still I have confusions in constructing basis sets for my system= , where, I have "Se" as chemical elements with few other 
 elements too. From literature, I have found that, the Huzinaga basis = sets, such as 14s10p5d & 17s13p6d are best for the Se 
 atoms (although they did not mention about the contraction pattern). = So, I would like to use these two basis sets for my systems.
 I try to understand your basis set description for the As element tha= t described in your reply. I have few queries for describing basis sets: 1) How to you get these coefficients for each block? Is there any database = which provides these coefficients? You have pointed out a book by S. Huzina= ga for the extra polarization. Are these coefficients are taken from this b= ook. Unfortunately, I do not have access to this book. So, is there any alternative source which helps for c= onstructing these basis sets coefficients.
2) If I want to use your described basis set for Se, what are the changes t= o be carried out in your basis set description of As element?
3) What would be the changes in the basis set description between 14s10p5d = & 17s13p6d Huzinaga basis sets?

It would be great help if you can provide me these basis sets for Se arom o= r helping me in constructing these basis sets from scratch.

Thank you once again for your help.

With best regards,
Arun


 

On Thu, Feb 7, 2013 at 6:53 AM, Cory Pye cpye_._ap.smu.ca <owner-chemistry::ccl.net> wrote:


Sent to CCL by: Cory Pye [cpye|a|ap.smu.ca]
Arun,

The answer depends on how you want to contract the basis sets, and I don't = have enough information to make this determination.

Based on my experience with these basis sets, you are probably trying to us= e
the 14s10p5d primitive set. In a minimal basis set, the contraction pattern=
would be 5333/433/5, most likely. This tells me you are probably trying to<= br> model an element between Sc-Kr. If you wanted to improve the basis set, you=
could partially decontract it to make a split valence basis set, as
53321/4321/41, where the exponents are arranged from largest to smallest. Huzinaga also supplies a recommended set of exponents for polarization
functions in his book.

For example, the 4333/433/4 As basis set looks something like this.
with for example B3LYP/gen in the route line.

AS   0
 S   4  1.00
        15860.364      0.0171048
        2391.2232      0.1200249
        542.23120      0.4378747
        146.00269      0.5576566
 S   3  1.00
        219.08007      -.1096535
        24.437631      0.6475717
        10.206970      0.4248194
 S   3  1.00
        18.744848      -.2334702
        3.1047892      0.7294911
        1.2970598      0.4044278
 S   3  1.00
        1.8301844      -.1924620
        0.28147770     0.6866084
        0.10437810     ????
 P   4  1.00
        670.45052      0.0275156
        157.17065      0.1794001
        48.639537      0.5052466
        16.532308      0.4576592
 P   3  1.00
        7.4556466      0.3248901
        2.9185276      0.5568808
        1.1701325      0.2280292
 P   3  1.00
        0.17189969     0.5495546
        0.44648872     0.3297273
        0.06621832     ????
 D   4  1.00
        49.802186      0.0618851
        13.722924      0.2858504
        4.3622725      0.5264330
        1.3044304      0.4103582
****

where the ???? refers to values that I don't have access to at the moment.<= br> After splitting and adding an extra D-type function, it looks like


AS   0
 S   4  1.00
        15860.364      0.0171048
        2391.2232      0.1200249
        542.23120      0.4378747
        146.00269      0.5576566
 S   3  1.00
        219.08007      -.1096535
        24.437631      0.6475717
        10.206970      0.4248194
 S   3  1.00
        18.744848      -.2334702
        3.1047892      0.7294911
        1.2970598      0.4044278
 S   2  1.00              = ;                 <----
        1.8301844      -.1924620
        0.28147770     0.6866084
 S   1  1.00              = ;                 <----
        0.10437810     1.000000
 P   4  1.00
        670.45052      0.0275156
        157.17065      0.1794001
        48.639537      0.5052466
        16.532308      0.4576592
 P   3  1.00
        7.4556466      0.3248901
        2.9185276      0.5568808
        1.1701325      0.2280292
 P   2  1.00              = ;                 <----
        0.17189969     0.5495546
        0.44648872     0.3297273
 P   1  1.00              = ;                 <----
        0.06621832     1.000000
 SP  1  1.00
        0.019          1.00000= 0      1.000000
 D   4  1.00
        49.802186      0.0618851
        13.722924      0.2858504
        4.3622725      0.5264330
        1.3044304      0.4103582
 D   1  1.00              = ;                 <----
        0.2930000      1.000000


The <--- denotes areas that you should pay particular attention to when<= br> splitting the basis set or addinf the extra function.
We don't bother to split the d-function as it is considered part of the cor= e,
but you probably would split this for the transition metals. We did add a d-type polarization function here. we also added an sp-type diffuse functio= n as
well. Note that the S and P contraction coefficients are specified in the s= ame
line.

The whole input would look like, for example for arsine

----
%chk=3DAsH3
#n B3lyp/gen FOpt=3D(CalcFC,z-matrix) Freq

AsH3

 0 1
As
X*1 As 1.0
H1  As H1As  X*1   H1AsX
H2  As H1As  X*1   H1AsX    H1   120.0
H3  As H1As  X*1   H1AsX    H1  -120.0

H1As=3D1.3
H1AsX=3D127.0

<insert basis set for arsenic here>
****
H 0
6-31G   <----if you are using the canned basis sets for H.
****




On Thu, 7 Feb 2013, Arun Manna arun.manna17|-|gmail.com wrote:

> Dear All,
>
> I want to use the Huzinaga basis set in DFT code, gaussian09 for my sy= stem.

> I would like to use *14s10p5d & 17s13p6d* Huzinaga basis sets f= or

> some specific elements. Though I understand th= at, these numbers are the
> number of primitive basis functions, but, I do not know how to specify=
> these in gaussian input file.
> Would anyone help me in defining these two basis sets for using in gau= ssian
> input file?
>
> Thank you in advance,
>
> With best regards,
> Arun
>
> --
> Arun K Manna
> PhD Student, TSU, JNCASR,
> Bangalore - 560064, India
>

   *************    !  Dr.= Cory C. Pye
 *****************  !  Associate Professor
***   **    **  **  !  Theoretical and Comput= ational Chemistry
**   *  ****        !  Department of Che= mistry, Saint Mary's University
**      *  *        !  923 Rob= ie Street, Halifax, NS B3H 3C3
**      *  *        !  cpye,,<= a href=3D"http://crux.stmarys.ca/" target=3D"_blank">crux.stmarys.ca &n= bsp; http://apwww.= stmarys.ca/~cpye
***     *  *    **  !  Ph: (902)-420-5654  FAX:(902)-496-8104
 *****************  !
   *************    !  Les Hartree-Focks (Apologie= s to Montreal Canadien Fans)



-=3D This is automatically added to each message by the mailing script =3D-=

E-mail to subscribers: CHEMISTRY::ccl.net or use:
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--
Arun K Manna
PhD Student, TSU, JNCASR,
Bangalore - 560064, India

 

--_000_D5BC00C0FB9AC34D9C8F4DC965C516890A514177SRVUNIMBX07unia_-- From owner-chemistry@ccl.net Thu Feb 7 04:40:01 2013 From: "benoit benoit bonoit_10###yahoo.fr" To: CCL Subject: CCL: 2nd derivative Message-Id: <-48183-130207041306-2117-jbt6CYuR7Vgm6wLysX0uOw:server.ccl.net> X-Original-From: "benoit benoit" Date: Thu, 7 Feb 2013 04:13:04 -0500 Sent to CCL by: "benoit benoit" [bonoit_10^^yahoo.fr] Dear CCLers, I'm writing to enquire about this question: why are analytical 2nd derivatives necessary for locating transition structures?" Any help is welcome and very appreciated Regards Benoit From owner-chemistry@ccl.net Thu Feb 7 05:14:01 2013 From: "benoit benoit bonoit_10[A]yahoo.fr" To: CCL Subject: CCL: Charge/Spin density Message-Id: <-48184-130207041554-4183-IT5yU+aQlyxYptlx98PlNA,,server.ccl.net> X-Original-From: "benoit benoit" Date: Thu, 7 Feb 2013 04:15:52 -0500 Sent to CCL by: "benoit benoit" [bonoit_10. _ .yahoo.fr] Dear CCLers, I'm writing to enquire about the the difference between the electronic charge and the spin density. Is there any thing common between them or they are totally different? I'll be very gratful if someone c'd clarify this point. Any help is welcome and very appreciated Regards Benoit From owner-chemistry@ccl.net Thu Feb 7 06:11:00 2013 From: "Vivek Sharma vivek.viv.sharma{}gmail.com" To: CCL Subject: CCL: Charge/Spin density Message-Id: <-48185-130207060953-20914-XbMpU7owIELDtdQTjohdrw-,-server.ccl.net> X-Original-From: Vivek Sharma Content-Type: multipart/alternative; boundary=e89a8ff1c73201f08404d5207be4 Date: Thu, 7 Feb 2013 13:09:46 +0200 MIME-Version: 1.0 Sent to CCL by: Vivek Sharma [vivek.viv.sharma{:}gmail.com] --e89a8ff1c73201f08404d5207be4 Content-Type: text/plain; charset=ISO-8859-1 Dear Benoit, I think there is a difference between the two. Spin density would correspond to the residual density that is either spin_UP - spin_DOWN or spin_DOWN - spin_UP. It will give you the contributions from the unpaired electrons for example, whereas charge density is the charge/volume. In case of total electron density, it would simply be the sum of two densities, spin_UP+spin_DOWN. Hope it helps, ViV On 7 February 2013 11:15, benoit benoit bonoit_10[A]yahoo.fr < owner-chemistry^^ccl.net> wrote: > > Sent to CCL by: "benoit benoit" [bonoit_10.^^.yahoo.fr] > Dear CCLers, > > I'm writing to enquire about the the difference between the electronic > charge and the spin density. > Is there any thing common between them or they are totally different? > I'll be very gratful if someone c'd clarify this point. > > Any help is welcome and very appreciated > > Regards > > Benoit> > > --e89a8ff1c73201f08404d5207be4 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Benoit,

I think ther= e is a difference between the two. Spin density would correspond to the res= idual density that is either spin_UP - spin_DOWN
=A0or spin_DOWN -= spin_UP. It will give you the contributions from the unpaired electrons fo= r example, whereas charge density is the charge/volume.
In case of total electron density, it would simply be the sum of= two densities, spin_UP+spin_DOWN.

Hope it helps,

ViV


On 7 = February 2013 11:15, benoit benoit bonoit_10[A]= yahoo.fr <owner-chemistry^^ccl.net> wrote:

Sent to CCL by: "benoit =A0benoit" [bonoit_10.^^.yahoo.fr]
Dear CCLers,

I'm writing to enquire about the the difference between the electronic = charge and the spin density.
Is there any thing common between them or they are totally different?
I'll be very gratful if someone c'd clarify this point.

Any help is welcome and very appreciated

Regards

Benoit



-=3D This is automatically added to each message by the mailing script =3D-=
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--e89a8ff1c73201f08404d5207be4-- From owner-chemistry@ccl.net Thu Feb 7 06:45:00 2013 From: "Amir Bernat bernat!^!post.bgu.ac.il" To: CCL Subject: CCL: 2nd derivative Message-Id: <-48186-130207061846-27764-vbH2zZ0RnbzORZ4KPmbKtg^server.ccl.net> X-Original-From: Amir Bernat Content-Type: multipart/alternative; boundary=047d7b6d9964cce3d804d5209a6e Date: Thu, 7 Feb 2013 13:18:39 +0200 MIME-Version: 1.0 Sent to CCL by: Amir Bernat [bernat**post.bgu.ac.il] --047d7b6d9964cce3d804d5209a6e Content-Type: text/plain; charset=ISO-8859-1 Hi Benoit, > From my understanding this is quite general, once one can derive analytically the 2nd derivatives it is possible to find the extremum and hessian of the function and thus the saddle points where the TS are found. It would also be possible to do this with a numeric function but it would be much more time consuming. There are many other properties related to the derivatives of the wavefunction which can be calculated faster (and some would say better) analytically. On Thu, Feb 7, 2013 at 11:13 AM, benoit benoit bonoit_10###yahoo.fr < owner-chemistry|,|ccl.net> wrote: > > Sent to CCL by: "benoit benoit" [bonoit_10^^yahoo.fr] > Dear CCLers, > > I'm writing to enquire about this question: > why are analytical 2nd derivatives necessary for locating transition > structures?" > > Any help is welcome and very appreciated > > Regards > > Benoit> > > -- -- Amir Bernat http://physweb.bgu.ac.il/~bernat/ --047d7b6d9964cce3d804d5209a6e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi=A0Benoit,

From my understanding this is quite general, once o= ne can derive=A0analytically the=A02nd deri= vatives it is possible to find the extremum and hessian of the function and= thus the saddle points where the TS are found. It would also be possible t= o do this with a numeric function but it would be much more time consuming.= There are many other properties related to the derivatives of the=A0wavefu= nction=A0which can be=A0calculated=A0faster (and some would say better) ana= lytically.=A0


On Thu,= Feb 7, 2013 at 11:13 AM, benoit benoit bonoit_10###yahoo.fr <owner-chemistry|,|ccl.net> wrote:

Sent to CCL by: "benoit =A0benoit" [bonoit_10^^yahoo.fr]
Dear CCLers,

I'm writing to enquire about this question:
why are analytical 2nd derivatives necessary for locating transition struct= ures?"

Any help is welcome and very appreciated

Regards

Benoit



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--

--=A0
Amir Bernat
http://physwe= b.bgu.ac.il/~bernat/

--047d7b6d9964cce3d804d5209a6e-- From owner-chemistry@ccl.net Thu Feb 7 07:21:00 2013 From: "Phil Hasnip phil.hasnip]*[york.ac.uk" To: CCL Subject: CCL: Charge/Spin density Message-Id: <-48187-130207063140-23966-jVsS3fzDDF9iyN1UjV6rsA/a\server.ccl.net> X-Original-From: Phil Hasnip Content-Type: multipart/alternative; boundary=20cf3074b54cc79c7b04d520c8c4 Date: Thu, 7 Feb 2013 11:31:30 +0000 MIME-Version: 1.0 Sent to CCL by: Phil Hasnip [phil.hasnip[A]york.ac.uk] --20cf3074b54cc79c7b04d520c8c4 Content-Type: text/plain; charset=ISO-8859-1 Dear Benoit, Within the collinear spin approximation, the charge density is the density of spin up electrons plus the density of spin down electrons; the spin density is the density of up electrons *minus* the density of down electrons. The two can normally be treated as independent quantities, indeed there are spintronics device applications based entirely around this concept. All the best, Phil Hasnip On 7 February 2013 09:15, benoit benoit bonoit_10[A]yahoo.fr < owner-chemistry===ccl.net> wrote: > > Sent to CCL by: "benoit benoit" [bonoit_10.===.yahoo.fr] > Dear CCLers, > > I'm writing to enquire about the the difference between the electronic > charge and the spin density. > Is there any thing common between them or they are totally different? > I'll be very gratful if someone c'd clarify this point. > > Any help is welcome and very appreciated > > Regards > > Benoit> > > -- ----------------------------------------------------------------------------- Dr Phil Hasnip Email: phil.hasnip===york.ac.uk Dept of Physics University of York Tel: +44 (0)1904 324624 York YO10 5DD --20cf3074b54cc79c7b04d520c8c4 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Benoit,

Within the collinear spin approximatio= n, the charge density is the density of spin up electrons plus the density = of spin down electrons; the spin density is the density of up electrons *mi= nus* the density of down electrons. The two can normally be treated as inde= pendent quantities, indeed there are spintronics device applications based = entirely around this concept.

All the best,

Phil Hasnip

On 7 February 2013 09:15, benoit benoit bo= noit_10[A]yahoo.fr <owner-chemistry==== ccl.net> wrote:

Sent to CCL by: "benoit =A0benoit" [bonoit_10.===.yahoo.fr]
Dear CCLers,

I'm writing to enquire about the the difference between the electronic = charge and the spin density.
Is there any thing common between them or they are totally different?
I'll be very gratful if someone c'd clarify this point.

Any help is welcome and very appreciated

Regards

Benoit



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--
-----------------------= ------------------------------------------------------
Dr Phil Hasnip = =A0 =A0 =A0 =A0 =A0 =A0Email: phil.hasnip===york.ac.uk
Dept of Physics
University of York =A0 =A0 =A0 =A0Tel: =A0+44 (0)1904 32= 4624
York YO10 5DD
--20cf3074b54cc79c7b04d520c8c4-- From owner-chemistry@ccl.net Thu Feb 7 07:56:00 2013 From: "sonam bhatia sonamalerts++gmail.com" To: CCL Subject: CCL: use of OCCUPATION key word in ADF Message-Id: <-48188-130207071317-2672-yG5DdpoVdA8JFolNT99mUw.@.server.ccl.net> X-Original-From: sonam bhatia Content-Type: multipart/alternative; boundary=20cf303a2f03a0798404d5215dbd Date: Thu, 7 Feb 2013 17:43:07 +0530 MIME-Version: 1.0 Sent to CCL by: sonam bhatia [sonamalerts~!~gmail.com] --20cf303a2f03a0798404d5215dbd Content-Type: text/plain; charset=ISO-8859-1 I am interested in performing Energy decomposition through ADF software. For specifying electronic states in moleuclar orbitals (MO) I have to use OCCUPATION keyword. Please suggest that how I can specify the electrons in MO if my compound is having C2V symmetry. In the ADF manual use of OCCUPATION key word is as OCCUPATIONS Options {irrep orbitalnumbers irrep orbitalnumbers ... End } I am confused that what is irrep. (I guess for C2V syymetry it is A1, A2, B1, B2) now suppose if my system is L-->C<--L. A carbon taking accepting electron density from two ligands. Then how can through OCCUPATION I can assign two lone pairs on central Carbon. --20cf303a2f03a0798404d5215dbd Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable I am interested in performing Energy decomposition=A0through=A0ADF software= .
For specifying electronic states in moleuclar orbitals (MO) I have to= use OCCUPATION keyword.=A0
Please suggest that how I can specify= the electrons in MO if my compound is having C2V symmetry.=A0
In the ADF manual =A0use of=A0OCCUPATION=A0key word is as=A0

OCCUPATIONS Options
{irrep orbitalnumbers
irrep orbitalnumbers
...
End }
=
I am confused that what is irrep. (I guess for C2V syymetry it i= s A1, A2, B1, B2) now suppose if my system is L-->C<--L. A carbon tak= ing accepting electron density from two ligands. Then how can through OCCUP= ATION I can assign two lone pairs on central Carbon.
--20cf303a2f03a0798404d5215dbd-- From owner-chemistry@ccl.net Thu Feb 7 08:30:00 2013 From: "Susi Lehtola susi.lehtola*_*alumni.helsinki.fi" To: CCL Subject: CCL: Charge/Spin density Message-Id: <-48189-130207062919-3079-0FoYjQPENpbYaMqwcRt87w]-[server.ccl.net> X-Original-From: Susi Lehtola Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Thu, 7 Feb 2013 13:29:11 +0200 Mime-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola a alumni.helsinki.fi] On Thu, 7 Feb 2013 04:15:52 -0500 "benoit benoit bonoit_10[A]yahoo.fr" wrote: > Sent to CCL by: "benoit benoit" [bonoit_10.~~.yahoo.fr] > Dear CCLers, > > I'm writing to enquire about the the difference between the > electronic charge and the spin density. Is there any thing common > between them or they are totally different? I'll be very gratful if > someone c'd clarify this point. > > Any help is welcome and very appreciated The electronic *charge* is simply the amount of electrons in the system (times the elementary charge). What you must be thinking about is the electron density, which is simply the sum of the densities of the spin up and spin down electrons rho(r) = rho_a(r) + rho_b(r) The spin density is a way of describing how the net spin in the system is distributed delta(r) = rho_a(r) - rho_b(r) Areas with positive spin density contain a surplus of spin up electrons, and those with negative spin density have a surplus of spin down electrons. -- -------------------------------------------------------- Mr. Susi Lehtola, M. Sc. Doctoral Student susi.lehtola~~alumni.helsinki.fi Department of Physics http://www.helsinki.fi/~jzlehtol University of Helsinki Office phone: +358 9 191 50 632 Finland -------------------------------------------------------- Susi Lehtola, FM Tohtorikoulutettava susi.lehtola~~alumni.helsinki.fi Fysiikan laitos http://www.helsinki.fi/~jzlehtol Helsingin Yliopisto Työpuhelin: (0)9 191 50 632 -------------------------------------------------------- From owner-chemistry@ccl.net Thu Feb 7 09:05:00 2013 From: "Esha Shah esha.physics,,gmail.com" To: CCL Subject: CCL:G: Problem running file in Gaussian 03W Message-Id: <-48190-130207045038-23669-Uvxl7lQWrqld6aYtJPq5ww{}server.ccl.net> X-Original-From: Esha Shah Content-Type: multipart/alternative; boundary=089e012280fc709b0f04d51f5f77 Date: Thu, 7 Feb 2013 01:50:28 -0800 MIME-Version: 1.0 Sent to CCL by: Esha Shah [esha.physics()gmail.com] --089e012280fc709b0f04d51f5f77 Content-Type: text/plain; charset=ISO-8859-1 This are the initial input lines followed by the dimensions of the unit cell structure in my input file: %mem=40mw # B3LYP/LANL2DZ SCF=(MAXCYCLE=2000) MaxDisk=4000MB FREQ(NR) TEMPERATURE=315.0 The execution of file aborts at (Computing 1-Electron Integral First or Second Derivatives) with severe error message as follows: The system cannot find the file specified CreateProcess C:\G03W\1702.exe returned with error code 2 What can be done to resolve this? Any help would be appreciated. -- Ms. Esha.Shah (esha.physics ) Department of Applied Physics National Institute of Technology, Surat Gujarat, India. www.svnit.ac.in --089e012280fc709b0f04d51f5f77 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
This are the initial input lines followed by the dime= nsions of the unit cell structure in my input file:


%mem=3D40mw
# B3LYP/LANL2DZ SCF=3D(MAXCYCLE= =3D2000) MaxDisk=3D4000MB FREQ(NR) TEMPERATURE=3D315.0


The execution of file aborts at (Computi= ng 1-Electron Integral First or Second Derivatives) with severe error messa= ge as follows:

The system cannot find the file spe= cified

CreateProcess
C:\G03W\1702.exe
retu= rned with error code 2


What can be = done to resolve this?

Any help would be appreciate= d.

--
Ms. Esha.Shah (esha.physics)
Department of Applie= d Physics
National Institute of Technology, Surat
Gujarat, India.
www.svnit.ac.in
--089e012280fc709b0f04d51f5f77-- From owner-chemistry@ccl.net Thu Feb 7 09:40:00 2013 From: "Fedor Goumans goumans-#-scm.com" To: CCL Subject: CCL: 2nd derivative Message-Id: <-48191-130207052647-21626-mQgbazzxsHxkiqSAsLLzkw_+_server.ccl.net> X-Original-From: Fedor Goumans Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 07 Feb 2013 11:25:58 +0100 MIME-Version: 1.0 Sent to CCL by: Fedor Goumans [goumans : scm.com] Dear Benoit, The answer is that they are not. However, depending on your optimization algorithm a good Hessian (2nd derivatives) will considerably improve your chances of locating any TS, and hopefully the correct TS. For saddle-point finding algorithms that only require forces you don't need second derivatives. For example: dimer, nudged-elastic band, growing string, Lanczcos, synchronous transit, transition state reaction coordinate are all methods that don't require a Hessian (2nd derivatives). However, for Hessian-based saddle point optimization algorithms (e.g. PRFO), you may greatly benefit from starting off with a good Hessian, especially so for the lowest few modes including the transition one. You may get a good starting Hessian with either analytical or numerical 2nd derivatives for your entire system or a part thereof. For a correct curvature of a partial Hessian you may use the so-called Mobile Block Hessian approach by Ann Ghysels and coworkers. Equally important is to start off with a geometry close to the anticipated transition structure, e.g. by first doing a quick linear transit run or by finding a TS for a smaller model system or with a smaller basis, etc. ... Good luck with hunting TSs! Best wishes, Fedor On 2/7/2013 10:13 AM, benoit benoit bonoit_10###yahoo.fr wrote: > Sent to CCL by: "benoit benoit" [bonoit_10^^yahoo.fr] > Dear CCLers, > > I'm writing to enquire about this question: > why are analytical 2nd derivatives necessary for locating transition structures?" > > Any help is welcome and very appreciated > > Regards > > Benoit> > -- Dr. T. P. M. Goumans Business Developer Scientific Computing & Modelling NV (SCM) Vrije Universiteit, FEW, Theoretical Chemistry De Boelelaan 1083 1081 HV Amsterdam, The Netherlands T +31 20 598 7625 F +31 20 598 7629 E-mail: goumans:_:scm.com http://www.scm.com From owner-chemistry@ccl.net Thu Feb 7 10:16:00 2013 From: "rocky walden rocky.walden19[]gmail.com" To: CCL Subject: CCL: Reg: computation of Delta H Message-Id: <-48192-130207095751-5719-tRgXAflzv7S5JD/CbiMXGg*o*server.ccl.net> X-Original-From: rocky walden Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 7 Feb 2013 20:27:41 +0530 MIME-Version: 1.0 Sent to CCL by: rocky walden [rocky.walden19[a]gmail.com] Hi, I have computed heat of formation for few compounds, ( cis butene & trans butene) and ( cis 1,2 dichloro ethene, & trans ( 1,2 dichloroethene). I see the Delta H formation for trans is greater than cis, but as far as I, know Heat of formation is inversely proportional to stability. Am I doing some thing wrong ? Or the application is behaving / throwing some value? Your suggestions much appreciated. Rocky M. Walden From owner-chemistry@ccl.net Thu Feb 7 10:50:00 2013 From: "Fedor Goumans goumans##scm.com" To: CCL Subject: CCL: use of OCCUPATION key word in ADF Message-Id: <-48193-130207103808-8784-Rg7AWE5wGrpbwAxLYO2/Jw**server.ccl.net> X-Original-From: Fedor Goumans Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 07 Feb 2013 16:37:20 +0100 MIME-Version: 1.0 Sent to CCL by: Fedor Goumans [goumans!A!scm.com] Dear Soniam, As our support team already replied this morning, presumably your mail was held for a bit at the CCL servers: "Best is to use a coordinate system, in which the closest ligand atoms are either on the x, y, and/or z-axis, and the C atom is at the origin. You should look in which irrep p:x, p:y, and p:z will be present in C(2v) symmetry (so perhaps it is better to use D(2h) symmetry instead? ), and use occupation numbers that match your requirements." Further to this note that with the natural orbital for chemical valence approach, ETS-NOCV, it is not necessary to adhere to a certain symmetry, as the orbital interactions are calculated for each orbital pair between the fragments. See http://www.scm.com/Products/Capabilities/ETS-NOCV.html for some links to recent papers that use this powerful chemical analysis method. I hope this helps, best wishes, Fedor On 2/7/2013 1:13 PM, sonam bhatia sonamalerts++gmail.com wrote: > I am interested in performing Energy decomposition through ADF software. > For specifying electronic states in moleuclar orbitals (MO) I have to > use OCCUPATION keyword. > Please suggest that how I can specify the electrons in MO if my > compound is having C2V symmetry. > In the ADF manual use of OCCUPATION key word is as > > OCCUPATIONS Options > {irrep orbitalnumbers > irrep orbitalnumbers > ... > End } > > I am confused that what is irrep. (I guess for C2V syymetry it is A1, > A2, B1, B2) now suppose if my system is L-->C<--L. A carbon taking > accepting electron density from two ligands. Then how can through > OCCUPATION I can assign two lone pairs on central Carbon. -- Dr. T. P. M. Goumans Business Developer Scientific Computing & Modelling NV (SCM) Vrije Universiteit, FEW, Theoretical Chemistry De Boelelaan 1083 1081 HV Amsterdam, The Netherlands T +31 20 598 7625 F +31 20 598 7629 E-mail: goumans!=!scm.com http://www.scm.com