From owner-chemistry@ccl.net Tue Nov 16 18:26:00 2010 From: "Joaquin Barroso Flores joaco_barroso[A]yahoo.com" To: CCL Subject: CCL:G: Error using SaveNBOs in Gaussian for NBO Calculations Message-Id: <-43174-101116181211-29214-Mif6ZI/QvI0XIWDpybNvxw##server.ccl.net> X-Original-From: Joaquin Barroso Flores Content-Type: multipart/alternative; boundary="0-1638770158-1289949122=:13555" Date: Tue, 16 Nov 2010 15:12:02 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Joaquin Barroso Flores [joaco_barroso!^!yahoo.com] --0-1638770158-1289949122=:13555 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Actually it is possible to visualize NBO's with GaussView or Molekel withou= t =0Asaving them (see: =0Ahttp://joaquinbarroso.wordpress.com/2009/09/24/nb= o-visualization/ ). Do you get =0Athe same error if the keyword "savenbos" = is not present? My guess is that this =0Aerror is related to something othe= r than the keyword, in other words it relates =0Ato some problem in your mo= lecule. Try optimizing it first but at a different =0Alevel of theory. What= I see in your output file is a lot of RY* (Rydberg) type =0Aorbitals and f= rom your input I see you are using polarization functions; =0Aprobably this= makes it difficult for the NBO program to re-orthogonalize your =0Awavefun= ction and by the way, I think there are some issues to the use of NBO =0Awi= th certain density functionals (it may be the case for PBEPBE). In short I = =0Awould reconsider the level of theory and the input geometry, unless you = have =0Astrong arguments for using them. =0A=0A=0A =0ABest wishes=0A=0A=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=0AJoaquin Barroso-Flores, Ph. D.=0ACentro Conjunto de Investig= acion en Quimica Sustentable=0AInstituto de Quimica=0AUNAM=0A=0A=0A-> http:= //joaquinbarroso.wordpress.com=0A=0A=0Ajoaquin.barroso''a''gmail.com =0A=0A= =0A"Blogastronom=EDa": http://joaquinbarroso.blogspot.com =0A=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=0A=0A=0A=0A=0A________________________________=0ADe: Jamin Krinsky krin= sky.jamin||gmail.com =0APara: "Flores, Joaquin Bar= roso " =0AEnviado: martes, 16 de noviembre= , 2010 11:45:13=0AAsunto: CCL:G: Error using SaveNBOs in Gaussian for NBO C= alculations=0A=0A=0ASent to CCL by: Jamin Krinsky [krinsky.jamin#gmail.com]= =0AHi Pritha,=0A=0AI have not heard of being able to visualize NBOs without= using the=0Asavenbos keyword. I think the error message you got is due to = the=0Aprogram having a built-in limit of the number of orbitals that can be= =0Asaved. It is built into the NBO3.1 program and I think it's 500 in=0AG03= , so 88 atoms with a fairly large basis will probably surpass the=0Alimit. = If you have the source code you can change that and recompile=0AG03 with th= e modified NBO code, see the NBO manual for discussion of=0Athat. Or you co= uld buy NBO5 and compile that with G03 or G09 (again=0Aassuming you have th= e Gaussian source code).=0A=0AJamin=0A=0A=0A=0AOn Sat, Nov 13, 2010 at 7:59= PM, Pritha Ghosh kunti33 * yahoo.com=0A wrote:= =0A>=0A> Sent to CCL by: "Pritha Ghosh" [kunti33*yahoo.com]=0A> I have not= had any success visualizing NBOs from only the .log file. I'd =0A>appreci= ate any further guidance you could provide.=0A>=0A> Thank you,=0A> Pritha= =0A>=0A>> "Jean Jules FIFEN julesfifen[a]gmail.com" wrote:=0A>>=0A>> Sent = to CCL by: Jean Jules FIFEN [julesfifen^^gmail.com]=0A>> --001636284c1c48e1= 850494f578e4=0A>> Content-Type: text/plain; charset=3DISO-8859-1=0A>>=0A>> = I think that, to visualize NBO results, you don't need to save it in the=0A= >> checkpoint file. All essential results are within the .log or the .out f= ile.=0A>> So, just do pop=3D(nbo,full) without the key word savenbos.=0A>>= =0A>> Best regards,=0A>> Jules.=0A>>=0A>>=0A>>=0A>>=0A>> On 13 November 201= 0 07:09, Pritha Ghosh kunti33(_)yahoo.com <=0A>> owner-chemistry|,|ccl.net>= wrote:=0A>>=0A>> >=0A>> > Sent to CCL by: "Pritha Ghosh" [kunti33(~)yahoo= .com]=0A>> > Hello CCL,=0A>> >=0A>> > I am currently using Gaussian09 to ca= lculate NBOs. However, whenever I try=0A>> > to save the NBOs to the chk f= ile for visualization, I get this error, which=0A>> > I have not seen anywh= ere else on the internet:=0A>> >=0A>> > Labels of output orbitals: RY* RY*= RY* RY* RY* RY* RY* RY* RY* RY* RY* RY*=0A>> > RY* RY* RY* RY* RY* RY* RY*= RY*=0A>> > Failed in SchOr1 in NBStor.=0A>> > Error termination via Lnk1= e in /act/apps/Gaussian09/g09/l607.exe at Fri=0A>> > Oct 29 03:53:21 2010.= =0A>> >=0A>> > My route section looks like this: # pbepbe/6-31+g(d)=0A>> > = pop=3D(nbo,full,savenbos) scf=3D(tight,maxcycle=3D4000)=0A>> >=0A>> > I hav= e successfully used this exact input file for the methylamine example=0A>> = > on the NBO website with no error. However, when I instead try to run the= =0A>> > calculation on my system of 88 atoms, I get the above error. If yo= u've =0Aseen=0A>> > this error before, or have some possible ideas as to wh= at might be the=0A>> > issue, please let me know!=0A>> >=0A>> > Thank you,= =0A>> >=0A>> > Pritha Ghosh>=0A>> >=0A>> >=0A>>=0A>>=0A>> --=0A>> Jean Jule= s FIFEN,=0A>> +237 75 21 61 39=0A>> +237 94 67 65 05=0A>> University of Nga= oundere,=0A>> PO.BOX 454 Ngaoundere=0A>>=0A>> --001636284c1c48e1850494f578e= 4=0A>> Content-Type: text/html; charset=3DISO-8859-1=0A>> Content-Transfer-= Encoding: quoted-printable=0A>>=0A>>
I think that, to vi= sualize NBO results, you don't need=3D=0A>> to save it in the checkpoint f= ile. All essential results are within the .l=3D=0A>> og or the .out file. S= o, just do pop=3D3D(nbo,full) without the key word save=3D=0A>> nbos.
= =0A>>
Best regards,
Jules.


=
=3D=0A>>


On 13 N= ovember 2010 07:0=3D=0A>> 9, Pritha Ghosh kunti33(_)yahoo.com > dir=3D3D"ltr"><>href=3D3D"ma= ilto:owner-chemistry|,|ccl.net">owner-chemistry|,|=3D=0A>> ccl.net><= /span> wrote:
=0A>>
> x #ccc solid;padding-left:1ex;">
=0A= >> Sent to CCL by: "Pritha =3DA0Ghosh" [kunti33(~)> hoo.com" target=3D3D"_blank">yahoo.com]
=0A>> Hello = CCL,
=0A>>
=0A>> I am currently using Gaussian09 to calculate NBOs. = =3DA0However, whenever I t=3D=0A>> ry to save the NBOs to the chk file for = visualization, I get this error, wh=3D=0A>> ich I have not seen anywhere el= se on the internet:
=0A>>
=0A>> Labels of output orbitals: =3DA0RY* = RY* RY* RY* RY* RY* RY* RY* RY* RY* RY* R=3D=0A>> Y* RY* RY* RY* RY* RY* RY= * RY* RY*
=0A>> =3DA0Failed in SchOr1 in NBStor.
=0A>> =3DA0Error ter= mination via Lnk1e in /act/apps/Gaussian09/g09/l607.exe at Fri =3D=0A>> Oct= 29 03:53:21 2010.
=0A>>
=0A>> My route section looks like this: # p= bepbe/6-31+g(d) pop=3D3D(nbo,full,savenb=3D=0A>> os) scf=3D3D(tight,maxcycl= e=3D3D4000)
=0A>>
=0A>> I have successfully used this exact input fi= le for the methylamine example =3D=0A>> on the NBO website with no error. = =3DA0However, when I instead try to run the=3D=0A>> calculation on my syst= em of 88 atoms, I get the above error. =3DA0If you'=3D=0A>> ;ve seen thi= s error before, or have some possible ideas as to what might be=3D=0A>> th= e issue, please let me know!
=0A>>=0A>>
=0A>> Thank you,
=0A>> =0A>> Pritha Ghosh
=0A>>
=0A>>
=0A>>
=0A>> -=3D3D This is = automatically added to each message by the mailing script =3D3D-=3D=0A>> =0A>>
=0A>> E-mail to subscribers: >href=3D3D"mail= to:CHEMISTRY|,|ccl.net">CHEMISTRY|,|ccl.n=3D=0A>> et or use:
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=0A>>



--
Jean Jules FIFEN,
+2=3D=0A>> 37 75 21 61 39
+237 94= 67 65 05
University of Ngaoundere,
PO.BOX 4=3D=0A>> 54 Ngaoundere=0A>>
=0A>>=0A>> --001636284c1c48e1850494f578e4--> =0A>> h= ttp://www.ccl.net/cgi-bin/ccl/send_ccl_message> =0A>> http://www.ccl.ne= t/cgi-bin/ccl/send_ccl_message> =0A>> http://www.ccl.net/chemistry/sub_= unsub.shtml> =0A>=0A>=0A>=0A=0A=0A=0A= -=3D This is automatically added to each message by the mailing script =3D-= =0A= =0A=0Aloo= k up the X-Original-From: line in the mail header.=0A=0AE-mail to subscribe= rs: CHEMISTRY-x-ccl.net or use:=0A http://www.ccl.net/cgi-bin/ccl/send_c= cl_message=0A=0A= =0A=0A=0ASubscribe/Uns= ubscribe: =0A=0A=0ABefore= posting, check wait time at: http://www.ccl.net=0A=0AJob: http://www.ccl.n= et/jobs =0AConferences: http://server.ccl.net/chemistry/announcements/confe= rences/=0A=0ASearch Messages: http://www.ccl.net/chemistry/searchccl/index.= shtml=0A=0A=0A h= ttp://www.ccl.net/spammers.txt=0A=0ARTFI: http://www.ccl.net/chemistry/abou= tccl/instructions/=0A=0A=0A --0-1638770158-1289949122=:13555 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Actually it is possible to visualize NBO's with GaussView or M= olekel without saving them (see: htt= p://joaquinbarroso.wordpress.com/2009/09/24/nbo-visualiz= ation/ ). Do you get the same error if the keyword "savenbos" is not= present? My guess is that this error is related to something other than th= e keyword, in other words it relates to some problem in your molecule. Try = optimizing it first but at a different level of theory. What I see in your = output file is a lot of RY* (Rydberg) type orbitals and from your input I s= ee you are using polarization functions; probably this makes it difficult f= or the NBO program to re-orthogonalize your wavefunction and by the way, I think = there are some issues to the use of NBO with certain density functionals (i= t may be the case for PBEPBE). In short I would reconsider the level of the= ory and the input geometry, unless you have strong arguments for using them= .
 
Best wishes

=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Jo= aquin Barroso-Flores, Ph. D.
Centro Conjunto de Investigacion en Quimica= Sustentable
Instituto de Quimica
UNAM



joaquin.barroso''a''gmai= l.com


"Blogastronom=EDa": http://joaquinbarroso.blogspot.com=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D


De: Jamin Krinsky krinsky.jamin||gmail.com <owner-chemistry-x-ccl.ne= t>
Para: "Flores, Jo= aquin Barroso " <joaco_barroso-x-yahoo.com>
Enviado: martes, 16 de noviembre, 2010 1= 1:45:13
Asunto: CCL:G: = Error using SaveNBOs in Gaussian for NBO Calculations


Sen= t to CCL by: Jamin Krinsky [krinsky.jamin#gmail.com]
Hi Pritha,

I= have not heard of being able to visualize NBOs without using the
savenb= os keyword. I think the error message you got is due to the
program havi= ng a built-in limit of the number of orbitals that can be
saved. It is b= uilt into the NBO3.1 program and I think it's 500 in
G03, so 88 atoms with a fair= ly large basis will probably surpass the
limit. If you have the source c= ode you can change that and recompile
G03 with the modified NBO code, se= e the NBO manual for discussion of
that. Or you could buy NBO5 and compi= le that with G03 or G09 (again
assuming you have the Gaussian source cod= e).

Jamin



On Sat, Nov 13, 2010 at 7:59 PM, Pritha Gho= sh kunti33 * yahoo.com
<owner-chemistry..ccl.net> wrote:
>> Sent to CCL by: "Pritha  Ghosh" [kunti33*yahoo.com]
> I h= ave not had any success visualizing NBOs from only the .log file.  I'd= appreciate any further guidance you could provide.
>
> Thank y= ou,
> Pritha
>
>> "Jean Jules FIFEN julesfifen[a]gmail= .com"  wrote:
>>
>> Sent to CCL by: Jean Jules FIFEN= [julesfifen^^gmail.com]
>> --001636284c1c48e1850494f578e4
>> Content-Type: text/plain; chars= et=3DISO-8859-1
>>
>> I think that, to visualize NBO resu= lts, you don't need to save it in the
>> checkpoint file. All esse= ntial results are within the .log or the .out file.
>> So, just do= pop=3D(nbo,full) without the key word savenbos.
>>
>> Be= st regards,
>> Jules.
>>
>>
>>
>&= gt;
>> On 13 November 2010 07:09, Pritha Ghosh kunti33(_)yahoo.com= <
>> owner-chemistry|,|ccl.net> wrote:
>>
>&= gt; >
>> > Sent to CCL by: "Pritha  Ghosh" [kunti33(~)y= ahoo.com]
>> > Hello CCL,
>> >
>> > I a= m currently using Gaussian09 to calculate NBOs.  However, whenever I t= ry
>> > to save the NBOs to the chk file for visualization, I g= et this error, which
>> > I have not seen anywhere else on the internet:
>> >
>> > Labels of output orbitals:=  RY* RY* RY* RY* RY* RY* RY* RY* RY* RY* RY* RY*
>> > RY*= RY* RY* RY* RY* RY* RY* RY*
>> >  Failed in SchOr1 in NBS= tor.
>> >  Error termination via Lnk1e in /act/apps/Gaussi= an09/g09/l607.exe at Fri
>> > Oct 29 03:53:21 2010.
>>= >
>> > My route section looks like this: # pbepbe/6-31+g(d)=
>> > pop=3D(nbo,full,savenbos) scf=3D(tight,maxcycle=3D4000)>> >
>> > I have successfully used this exact input = file for the methylamine example
>> > on the NBO website with n= o error.  However, when I instead try to run the
>> > calc= ulation on my system of 88 atoms, I get the above error.  If you've se= en
>> > this error before, or have some possible ideas as to wh= at might be the
>> > issue, please let me know!
>> >
>> > Thank you,
>> >
>> > Pritha = Ghosh>
>> >
>> >
>>
>>
>= > --
>> Jean Jules FIFEN,
>> +237 75 21 61 39
>&= gt; +237 94 67 65 05
>> University of Ngaoundere,
>> PO.B= OX 454 Ngaoundere
>>
>> --001636284c1c48e1850494f578e4>> Content-Type: text/html; charset=3DISO-8859-1
>> Content= -Transfer-Encoding: quoted-printable
>>
>> <div dir=3D= 3D"ltr">I think that, to visualize NBO results, you don't need=3D
>= ;>  to save it in the checkpoint file. All essential results are wi= thin the .l=3D
>> og or the .out file. So, just do pop=3D3D(nbo,fu= ll) without the key word save=3D
>> nbos.<br>
>> &l= t;br><div>Best regards,</div><div>Jules.</div>&l= t;div><br></div><div><br></div>=3D
>= > <div><br></div><div><br><div class=3D3D"g= mail_quote">On 13 November 2010 07:0=3D
>> 9, Pritha Ghosh kunt= i33(_)<a href=3D3D"http:/= /yahoo.com">yahoo.com</a> <span =3D
>> dir=3D3D"lt= r">&lt;<a href=3D3D"mailto:owner-chemistry|,|ccl.net">owner-ch= emistry|,|=3D
>> ccl.net</a>&gt;</span> wrote:<= br>
>> <blockquote class=3D3D"gmail_quote" style=3D3D"margin= :0 0 0 .8ex;border-left:1p=3D
>> x #ccc solid;padding-left:1ex;"&g= t;<br>
>> Sent to CCL by: &quot;Pritha =3DA0Ghosh&qu= ot; [kunti33(~)<a href=3D3D"h= ttp://ya=3D
>> hoo.com" target=3D3D"_blank">yahoo.com</a= >]<br>
>> Hello CCL,<br>
>> <br>
= >> I am currently using Gaussian09 to calculate NBOs. =3DA0However, w= henever I t=3D
>> ry to save the NBOs to the chk file for visualization, I get this error, wh=3D>> ich I have not seen anywhere else on the internet:<br>
= >> <br>
>> Labels of output orbitals: =3DA0RY* RY* RY*= RY* RY* RY* RY* RY* RY* RY* RY* R=3D
>> Y* RY* RY* RY* RY* RY* RY= * RY* RY*<br>
>> =3DA0Failed in SchOr1 in NBStor.<br><= br>>> =3DA0Error termination via Lnk1e in /act/apps/Gaussian09/g09/l6= 07.exe at Fri =3D
>> Oct 29 03:53:21 2010.<br>
>> &= lt;br>
>> My route section looks like this: # pbepbe/6-31+g(d) = pop=3D3D(nbo,full,savenb=3D
>> os) scf=3D3D(tight,maxcycle=3D3D400= 0)<br>
>> <br>
>> I have successfully used th= is exact input file for the methylamine example =3D
>> on the NBO = website with no error. =3DA0However, when I instead try to run the=3D
&g= t;>  calculation on my system of 88 atoms, I get the above error. = =3DA0If you&#39=3D
>> ;ve seen this error before, or have some possib= le ideas as to what might be=3D
>>  the issue, please let me = know!<br>
>>
>> <br>
>> Thank you,&l= t;br>
>> <br>
>> Pritha Ghosh<br>
>&= gt; <br>
>> <br>
>> <br>
>> -= =3D3D This is automatically added to each message by the mailing script =3D= 3D-=3D
>> <br<br=3D<br<br>
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