From owner-chemistry@ccl.net Tue Apr 27 08:44:00 2010 From: "Andrew Dalke dalke/a\dalkescientific.com" To: CCL Subject: CCL: cheminformatics programming training courses Message-Id: <-41718-100427001532-11786-3Bjxq7+2oPwdyOjhL1hcBA() server.ccl.net> X-Original-From: Andrew Dalke Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Tue, 27 Apr 2010 05:15:19 +0200 Mime-Version: 1.0 (Apple Message framework v1078) Sent to CCL by: Andrew Dalke [dalke!^!dalkescientific.com] Last month I announced my upcoming course for cheminformatics web development. It will be in Leipzig, Germany on 18-20 May. Places are still available if you are interested. I have just now posted an updated outline of the course topics at http://tinyurl.com/35ulsoh The course will walk through building a web application which includes: JMol structure input, SQL database searching, molecular property calculations, interactive results, and personalized search history. The course is meant for a computational chemist who has some programming experience and who wants to get up to speed in developing web applications. Some of the technologies I'll cover are: - Django web application framework - OEChem for cheminformatics - handling CSV, SMILES and SD file - structure and substructure depictions - SQL databases and Excel - descriptor and fingerprint calculations - Javascript for AJAX and browser widgets - plotting, calling external binaries, and more. More details are available at http://dalkescientific.com/training/ or feel free to email me to reserve a spot or ask questions. Andrew dalke .. dalkescientific.com From owner-chemistry@ccl.net Tue Apr 27 15:36:01 2010 From: "DIEGOI GOMEZ darkego21 _ yahoo.com" To: CCL Subject: CCL:G: Error termination in NtrErr at MP2 calculation. Message-Id: <-41719-100427103728-2655-tj+775NnS7/RvPy7U9iqNg++server.ccl.net> X-Original-From: DIEGOI GOMEZ Content-Type: multipart/alternative; boundary="0-566014898-1272379037=:11399" Date: Tue, 27 Apr 2010 07:37:17 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: DIEGOI GOMEZ [darkego21-x-yahoo.com] --0-566014898-1272379037=:11399 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hi again...=0A=0AFirstly, thanks Ibrahim for your reply.=0A=0AWell, after r= emaking the imput (in this case in cartesians to avoid the ghost atoms), I = have fixed the problem but I don't have clear why it was the solution.=0A= =0AHere is the problematic imput file:=0A=0A-------------------------------= ---------------------------------------------------------------------------= ---------------=0A =0A=0A%chk=3D/data1/diego/GAU/metals/palladium/Pd1hcpx.c= hk=0A%mem=3D20GB=0A%nproc=3D8=0A# MP2/GENecp geom=3Dconnectivity scf=3D(max= cycle=3D500, qc) guess=3Dread counterpoise=3D2 maxdisk=3D50GB=0A=0ATitle Ca= rd Required=0A=0A0 1=0A Pd(Fragment=3D1) -0.08140700 0.03= 787500 -0.00549500=0A O(Fragment=3D1) -1.97461900 -0.99= 338100 -0.06543100=0A O(Fragment=3D1) 1.81180500 1.06= 913100 0.05444000=0A O(Fragment=3D1) 0.86489800 -1.70= 544900 0.09890800=0A O(Fragment=3D1) -1.02771300 1.78= 119900 -0.10989800=0A H(Fragment=3D1) -2.38699000 -1.26= 562000 -0.87355800=0A H(Fragment=3D1) -2.46575500 -1.21= 329400 0.71409400=0A H(Fragment=3D1) 2.30294000 1.28= 904400 -0.72508400=0A H(Fragment=3D1) 2.22417600 1.34= 137000 0.86256800=0A H(Fragment=3D1) 1.18280000 -1.98= 870600 0.95001100=0A H(Fragment=3D1) -1.42728100 2.11= 870900 0.68515200=0A H(Fragment=3D2) 3.82319200 -1.61= 126300 -0.66318300=0A H(Fragment=3D2) 3.09668700 -1.62= 449400 -0.52137500=0A=0A 1 4 1.0 5 1.0=0A 2 6 1.0 7 1.0=0A 3 8 1.0 9 1.0= =0A 4 10 1.0=0A 5 11 1.0=0A 6=0A 7=0A 8=0A 9=0A 10=0A 11=0A 12=0A 13=0A=0AO= H 0=0A6-31G**=0A****=0APd 0=0Alanl2dz=0A****=0A=0APd 0=0Alanl2dz=0A=0A=0A= =0A=0A=0A------------------------------------------------------------------= ----------------------------------------------------------=0A=0AAs mentione= d, the calculation starts without problems but after the first SCF cycle th= e process fail with "Error termination in NtrErr"=0A=0AThe problem was fixe= d by removing the "qc" keyword from the keywords line. But Why?=0AAre there= any inconsistency with the use of the QC algorithm and the counterpoise pr= ocedure?=0A=0AThanks again.=0A=0ARegards.=0A=0ADiego=0A=0AUPV-ITQ=0ASpain.*= ************=0A=0A=0A=0A=0A________________________________=0AFrom: Mahmoud= A. A. Ibrahim m.ibrahim|compchem.net =0ATo: "Gome= z, Diego Armando " =0ASent: Fri, April 23, 201= 0 11:43:39 PM=0ASubject: CCL:G: Error termination in NtrErr at MP2 calculat= ion.=0A=0ADear Diego=0AI read your complain about a NtrErr error. This typ= e of errors happens in different cases, one of them as Dave mentioned due t= o space issue, and in this case NMax information should be mentioned in las= t few lines, which is not available in the supported information you gave. = Another possibility is the checkpoint file, what happened is your checkpoin= t file has not be created, or optimization data (for first cycle) has not b= e saved in your checkpoint file. that is what you have got.=0AThere is no t= echnical solve for this error. Just, try to build up your input file again,= save checkpoint file (%chk=3Dfilename.chk) and change its path.=0AIf you g= ot the error again, you would send your input file and we can test it.=0ASi= ncerely;=0AM. Ibrahim=0A=0A=0AOn Thu, Apr 22, 2010 at 9:24 PM, DIEGOI GOMEZ= darkego21]_[yahoo.com wrote:=0A=0AHi Dave, =0A= >thanks for your reply!!=0A>=0A>I'm using Gaussian09 and my system is reall= y small, I'm doing a test with one Pd(II) atom in square planar stereo-chem= istry with two H2O molecules and two OH- groups as ligands interacting with= one H2 molecule.=0A>>-----------------------------------------------------= ---------------------------------------------------------------=0A> 118 b= asis functions, 217 primitive gaussians, 124 cartesian basis functions= =0A> 29 alpha electrons 29 beta electrons=0A>>--------------------= ---------------------------------------------------------------------------= --------------------=0A>Previously I did one MP2 optimization of the system= (without counterpoise) with no problems. So I don't believe=0A> that the E= rror is related with storage capacity (actually, I have done calculation on= bigger systems with more than 300 basis functions). I speculate that It se= ems to be related with the reading of some file or keyword when the second = step starts.=0A>=0A>I forgot to mention that in this particular case the Pd= cluster is fixed (opt=3Dz-matrix) an the optimization is only done on the = H2 coordinates.=0A>=0A>However I have not tried that option (%rwf), I'll gi= ve a look...=0A>=0A>Thanks again..=0A>=0A>=0A>Diego=0A>>UPV-ITQ=0A>>Spain.= =0A>=0A>=0A>=0A>=0A>=0A>=0A________________________________=0A From: "Close= , David M. CLOSED_._mail.etsu.edu" =0A>To: "Gome= z, Diego Armando " =0A>Sent: Thu, April 22, 2010 8:0= 2:19 PM=0A>Subject: CCL: Error termination in NtrErr at MP2 calculation.=0A= >=0A>=0A>>=0A>Diegoi:=0A> This is a common error that means you have excee= ded disc storage=0A>space. This happens with MP2 calculations that require= s a great deal of=0A>scratch disc space for storing integrals. There are c= ommon fixes to this=0A>problem, but it is necessary to tell us about the si= ze of the calculation you=0A>are doing. Like how many heavy atoms, and wha= t program you are=0A>using. Basically a 32 bit machine is limited to 16 Gb= ytes of storage. =0A>Have you tried simple fixes like %rwf=3D =E2=80=A6. = ?=0A> Regards, Dave Close.=0A> =0A>>=0A>>=0A>From:>owner-chemistry+closed= =3D=3Detsu.edu*ccl.net >[mailto:owner-chemistry+closed=3D=3Detsu.edu*ccl.ne= t] On Behalf Of DIEGOI=0A>GOMEZ darkego21 ~ yahoo.com=0A>Sent: Thursday, Ap= ril 22, 2010 9:56 AM=0A>To: Close, David M.=0A>Subject: CCL: Error terminat= ion in NtrErr at MP2 calculation.=0A> =0A>>=0A>Hello there.=0A>=0A>>I'm doi= ng an optimization of a pair of interacting molecules at MP2 level with=0A>= simultaneous counterpoise correction. I'm using two basis set (lanl2dz and= =0A>6-31G**) through the "GEN" keyword. The calculation starts=0A>without = problems, so the first SCF cycle and the second-order perturbation are=0A>a= ccomplished. However, when the next step starts the follow Error is reporte= d:=0A>=0A>>----------------------------------------------------------------= ---------------------------------------------------------------------------= --=0A>> ***** Axes restored to original set *****=0A>> Cartesian Forces: = Max 0.199455160=0A>RMS 0.055013514=0A>> Operation on file out of ra= nge.=0A>>FileIO: IOper=3D 2 IFilNo(1)=3D -522=0A>Len=3D 118=0A>IPo= s=3D 118 Q=3D =0A>47965310131088=0A>=0A>=0A>> dumping /fiocom/, un= it =3D 1 NFiles =3D 98 SizExt=0A>=3D 524288 WInBlk =3D 512=0A>>= =0A>defal =3D T LstWrd =3D 233431552 FType=3D2 FMxFil= =3D10000=0A>=0A>> Number =0A>0 =0A>0 =0A>0 = 0 =0A>0 =0A>0 =0A>0 0=0A>> Base 122= 03972 =0A>390144 495616 =0A>321536 12752384 10698752 =0A>2= 01216 365568=0A>> End 12204032 =0A>402432 527360 =0A>32= 2048 12818944 11614208 =0A>201728 372736=0A>> End1 12204032= =0A>402432 527360 =0A>322048 12818944 11614208 201728 = =0A>372736=0A>> Wr Pntr 12203972 =0A>388608 495616 =0A>321536 = 12533760 10698752 =0A>201216 365568=0A>> Rd Pntr 12203972 = =0A>388608 495616 =0A>321536 12533760 10698752 =0A>201216 = 365568=0A>> Length =0A>60 12288 =0A>31744 =0A>512 = 66560 =0A>915456 =0A>512 7168=0A>=0A>>(...)=0A>>=0A> Err= or termination in=0A>NtrErr:=0A>> NtrErr Called from FileIO.=0A>=0A>>------= ---------------------------------------------------------------------------= -------------------------------------------------------------=0A>=0A>>Thank= s in advance for any sugestion.=0A>=0A>>Diego=0A>>UPV-ITQ=0A>>Spain.=0A> = =0A>=0A=0A=0A-- =0A Mahmoud A. A. Ibrahim =0A = Current Address=0A 7.05, School of Chemistry= ,=0A The University of Manchester,=0A Oxford Road, Manch= ester, M13 9PL, =0A United Kingdom.=0A=0A = Home Address=0A Chemistry Department,=0A = Faculty of Science,=0A Minia University,= =0A Minia 61519,=0A = Egypt. =0A=0A Contact Information=0A Email: m.i= brahim,+,compchem.net=0A Website: www.compchem.net=0A = Fax No.: +20862342601=0A=0A=0A=0A --0-566014898-1272379037=:11399 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Hi again...

Firstly, thanks Ibrahim for your reply.

Well, = after remaking the imput (in this case in cartesians to avoid the ghost ato= ms), I have fixed the problem but I don't have clear why it was the solutio= n.

Here is the problematic imput file:

----------------------= ---------------------------------------------------------------------------= ------------------------
 
%chk=3D/data1/diego/GAU/metals/p= alladium/Pd1hcpx.chk
%mem=3D20GB
%nproc=3D8
# MP2/GENecp geom=3Dco= nnectivity scf=3D(maxcycle=3D500, qc) guess=3Dread counterpoise=3D2 maxdisk= =3D50GB

Title Card Required

0 1
 Pd(Fragment=3D1)&nbs= p;            &= nbsp;  -0.08140700    0.03787500   -0.00549500
 O(Fragment=3D1)      &n= bsp;          -1.97461900 = ;  -0.99338100   -0.06543100
 O(Fragment=3D1) &= nbsp;           &nbs= p;    1.81180500    1.06913100  &nb= sp; 0.05444000
 O(Fragment=3D1)      =             0.864898= 00   -1.70544900    0.09890800
 O(Fragment= =3D1)           &nbs= p;     -1.02771300    1.78119900 &n= bsp; -0.10989800
 H(Fragment=3D1)     &nbs= p;           -2.38699000&= nbsp;  -1.26562000   -0.87355800
 H(Fragment=3D1)      &n= bsp;          -2.46575500 = ;  -1.21329400    0.71409400
 H(Fragment=3D1)&n= bsp;            = ;     2.30294000    1.28904400 &nbs= p; -0.72508400
 H(Fragment=3D1)      =             2.224176= 00    1.34137000    0.86256800
 H(Fra= gment=3D1)           = ;       1.18280000   -1.98870600&nb= sp;   0.95001100
 H(Fragment=3D1)    =              -1= .42728100    2.11870900    0.68515200
 H(Fragment=3D2)      &nb= sp;           3.82319200&= nbsp;  -1.61126300   -0.66318300
 H(Fragment=3D2)&nb= sp;            =      3.09668700   -1.62449400   -0.= 52137500

 1 4 1.0 5 1.0
 2 6 1.0 7 1.0
 3 8 1.0= 9 1.0
 4 10 1.0
 5 11 1.0
 6
 7
 8=
 9
 10
 11
 12
 13

O H 06-31G**
****
Pd 0
lanl2dz
****

Pd 0
lanl2dz

<= /div>



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

As = mentioned, the calculation starts without problems but after the first SCF cycle the process fail with "Error termination in NtrErr"

The probl= em was fixed by removing the "qc" keyword from the keywords line. But Why?<= br>Are there any inconsistency with the use of the QC algorithm and the cou= nterpoise procedure?

Thanks again.

Regards.

Diego
<= div>

=0AUPV-ITQ
=0ASpain.

=0A= =0A
=0A=0A
=0A=0A*************


From= : Mahmoud A. A. Ibrahim m.ibrahim|compchem.net <owner-chemist= ry{=}ccl.net>
To: "Gom= ez, Diego Armando " <darkego21{=}yahoo.com>
Sent: Fri, April 23, 2010 11:43:39 PMSubject: CCL:G: Error ter= mination in NtrErr at MP2 calculation.

Dear Diego
I read your complain about a NtrErr  error. This type of errors happens in different cases= , one of them as Dave mentioned due to space issue, and in this case NMax i= nformation should be mentioned in last few lines, which is not available in= the supported information you gave. Another possibility is the checkpoint = file, what happened is your checkpoint file has not be created, or optimiza= tion data (for first cycle) has not be saved in your checkpoint file. that = is what you have got.
=0A
There is no technical solve for = this error. Just, try to build up your input file again, save checkpoint fi= le (%chk=3Dfilename.chk) and change its path.
=0A=
If you g= ot the error again, you would send your input file and we can test it.
=0A
Sincerely;
=0A
M. Ibrahim=
=0A

On Thu, Apr 22, 2010 at= 9:24 PM, DIEGOI GOMEZ darkego21]_[yahoo.com <owner-chemistry,+,ccl.net>= wrote:
=0A
= Hi Dave,
thanks for your reply!!

I'm using Gaussian09 and my sys= tem is really small, I'm doing a test with one Pd(II) atom in square planar= stereo-chemistry with two H2O molecules and two OH- groups as ligands inte= racting with one H2 molecule.
=0A---------------------------------------= ---------------------------------------------------------------------------= --
   118 basis functions,   217 primitive gaussians= ,   124 cartesian basis functions
    29 alpha = electrons       29 beta electrons
=0A-----= ---------------------------------------------------------------------------= -----------------------------------
Previously I did one MP2 optimizatio= n of the system (without counterpoise) with no problems. So I don't believe= =0A that the Error is related with storage capacity (actually, I have done = calculation on bigger systems with more than 300 basis functions). I specul= ate that It seems to be related with the reading of some file or keyword wh= en the second step starts.
=0A
I forgot to mention that in this parti= cular case the Pd cluster is fixed (opt=3Dz-matrix) an the optimization is = only done on the H2 coordinates.

However I have not tried that optio= n (%rwf), I'll give a look...
=0A
Thanks again..

Diego
=0AUPV-ITQ
=0ASpain.

=0A=0A=0A=0A
=0A=0A




=0AFrom: "Close, David M. CLOSED_._mail.etsu.edu" <owner-chem= istry]~[ccl.n= et>
=0ATo: "Gome= z, Diego Armando " <darkego21]~[yahoo.com>
Sent: Thu, April 22, 2010 8:02:19 PM
=0ASubject: CCL: Error termination in NtrE= rr at MP2 calculation.

=0A=0A=0A=0A =0A =0A=0A=0A=0A=0A
= =0A=0A

Diegoi:

=0A=0A

  This is a common error th= at means you have exceeded disc storage=0Aspace.  This happens with MP= 2 calculations that requires a great deal of=0Ascratch disc space for stori= ng integrals.  There are common fixes to this=0Aproblem, but it is nec= essary to tell us about the size of the calculation you=0Aare doing.  = Like how many heavy atoms, and what program you are=0Ausing.  Basicall= y a 32 bit machine is limited to 16 Gbytes of storage. =0AHave you tri= ed simple fixes like %rwf=3D   =E2=80=A6. ?

=0A=0A

 

=0A= =0A
=0A=0A
= =0A=0A

From:=0Aowner-chemistry+closed=3D=3Detsu.edu*ccl.net=0A[ma= ilto:owner-chemistry+closed= =3D=3Det= su.edu*cc= l.net] On Behalf Of DIEGOI=0AGOMEZ darkego21 ~ yahoo.com
=0ASent:= Thursday, April 22, 2010 9:56 AM
=0ATo: Close, David M.
= =0ASubject: CCL: Error termination in NtrErr at MP2 calculation.

=0A=0A
=0A=0A
=0A=0A

 

= =0A=0A
=0A=0A

Hello there.
=0A
=0AI'm do= ing an optimization of a pair of interacting molecules at MP2 level with=0A= simultaneous counterpoise correction. I'm using two basis set (lanl2dz and= =0A6-31G**) through the "GEN" keyword.  The calculation starts=0Awitho= ut problems, so the first SCF cycle and the second-order perturbation are= =0Aaccomplished. However, when the next step starts the follow Error is rep= orted:
=0A
=0A-------------------------------------------------------= ---------------------------------------------------------------------------= -----------
=0A  ***** Axes restored to original set *****
=0A&n= bsp;Cartesian Forces:  Max     0.199455160=0ARMS&n= bsp;    0.055013514
=0A Operation on file out of ran= ge.
=0AFileIO: IOper=3D 2 IFilNo(1)=3D  -522=0ALen=3D  &n= bsp;      118=0AIPos=3D    &nb= sp;    118 Q=3D  =0A47965310131088
=0A
=0A=0A dumping /fiocom/, unit =3D 1 NFiles =3D    98 Siz= Ext=0A=3D    524288 WInBlk =3D     =   512
=0A         &nbs= p;        =0Adefal =3D T LstWrd =3D=    233431552 FType=3D2 FMxFil=3D10000
=0A
=0A Number&n= bsp;         =0A0  &= nbsp;      =0A0     =     =0A0        = ;  0         =0A0 &n= bsp;       =0A0    &= nbsp;    =0A0       =    0
=0A Base      12203972 = ;   =0A390144     495616  &nbs= p; =0A321536   12752384   10698752  &nbs= p; =0A201216     365568
=0A End  = ;     12204032    =0A402432 &n= bsp;   527360    =0A322048   128189= 44   11614208    =0A201728   &= nbsp; 372736
=0A End1      12204032 &= nbsp;  =0A402432     527360   =  =0A322048   12818944   11614208   =   201728    =0A372736
=0A Wr Pntr &nb= sp; 12203972    =0A388608     49561= 6    =0A321536   12533760   1069875= 2    =0A201216     365568
=0A&nb= sp;Rd Pntr   12203972    =0A388608  = ;   495616    =0A321536   12533760&= nbsp;  10698752    =0A201216   &nbs= p; 365568
=0A Length        = ; =0A60      12288    &nb= sp;=0A31744       =0A512  &nbs= p;   66560    =0A915456   &nbs= p;   =0A512       7168
=0A<= br>=0A(...)

=0A=0A
=0A=0A

 Err= or termination in=0ANtrErr:
=0A NtrErr Called from FileIO.
=0A=0A----------------------------------------------------------------------= ------------------------------------------------------------------------=0A
=0AThanks in advance for any sugestion.
=0A
=0ADiego
=0AUP= V-ITQ
=0ASpain.

=0A=0A
=0A=0A
=0A=0A

 

=0A=0A
=0A=0A
=0A

=0A=0A =



--
    &n= bsp;            Mahmoud A. A. Ibrahim   =      
              =         Current Address
       =         7.05, School of Chemistry,
    &= nbsp;        The University of Manchester,
=0A  = ;       Oxford Road, Manchester, M13 9PL,
   =                   United King= dom.

                 =      Home Address
          &n= bsp;      Chemistry Department,
      &nb= sp;             Faculty of Science,
 = ;                     &nb= sp;Minia University,
=0A              = ;             Minia 61519,
    =                      = ;      Egypt.

          &n= bsp;         Contact Information
    &nbs= p;     Email: m.i= brahim,+,compchem.net
=0A             =  Website: www.compchem.net
          &nbs= p;       Fax No.: +20862342601
=0A
=0A
= =0A

=0A=0A --0-566014898-1272379037=:11399-- From owner-chemistry@ccl.net Tue Apr 27 19:08:00 2010 From: "Mahmoud A. A. Ibrahim m.ibrahim[]compchem.net" To: CCL Subject: CCL:G: Error termination in NtrErr at MP2 calculation. Message-Id: <-41720-100427170626-22282-vdBCH5+07ztIRJy5U6Cy9g+/-server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary=001485f1dc1875ae1c04853e4393 Date: Tue, 27 Apr 2010 22:06:13 +0100 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim(_)compchem.net] --001485f1dc1875ae1c04853e4393 Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Dear Diego I have run your input file (using G03) but without guess=3Dread (also I hav= e tested a couple of jobs for your input using guess=3Dread, with/without qc) and all of them gave me a normal termination: Counterpoise: corrected energy =3D -430.811138359266 Counterpoise: BSSE energy =3D 0.003915169173 As I told you before, the problem is returned to your checkpoint file, or something related to G09 where I haven't it here to check your job with it. Sincerely; M. Ibrahim On Tue, Apr 27, 2010 at 3:37 PM, DIEGOI GOMEZ darkego21 _ yahoo.com < owner-chemistry[A]ccl.net> wrote: > Hi again... > > Firstly, thanks Ibrahim for your reply. > > Well, after remaking the imput (in this case in cartesians to avoid the > ghost atoms), I have fixed the problem but I don't have clear why it was = the > solution. > > Here is the problematic imput file: > > > -------------------------------------------------------------------------= ------------------------------------------------ > > %chk=3D/data1/diego/GAU/metals/palladium/Pd1hcpx.chk > %mem=3D20GB > %nproc=3D8 > # MP2/GENecp geom=3Dconnectivity scf=3D(maxcycle=3D500, qc) guess=3Dread > counterpoise=3D2 maxdisk=3D50GB > > Title Card Required > > 0 1 > Pd(Fragment=3D1) -0.08140700 0.03787500 -0.00549500 > O(Fragment=3D1) -1.97461900 -0.99338100 -0.06543100 > O(Fragment=3D1) 1.81180500 1.06913100 0.05444000 > O(Fragment=3D1) 0.86489800 -1.70544900 0.09890800 > O(Fragment=3D1) -1.02771300 1.78119900 -0.10989800 > H(Fragment=3D1) -2.38699000 -1.26562000 -0.87355800 > H(Fragment=3D1) -2.46575500 -1.21329400 0.71409400 > H(Fragment=3D1) 2.30294000 1.28904400 -0.72508400 > H(Fragment=3D1) 2.22417600 1.34137000 0.86256800 > H(Fragment=3D1) 1.18280000 -1.98870600 0.95001100 > H(Fragment=3D1) -1.42728100 2.11870900 0.68515200 > H(Fragment=3D2) 3.82319200 -1.61126300 -0.66318300 > H(Fragment=3D2) 3.09668700 -1.62449400 -0.52137500 > > 1 4 1.0 5 1.0 > 2 6 1.0 7 1.0 > 3 8 1.0 9 1.0 > 4 10 1.0 > 5 11 1.0 > 6 > 7 > 8 > 9 > 10 > 11 > 12 > 13 > > O H 0 > 6-31G** > **** > Pd 0 > lanl2dz > **** > > Pd 0 > lanl2dz > > > > > > -------------------------------------------------------------------------= --------------------------------------------------- > > As mentioned, the calculation starts without problems but after the first > SCF cycle the process fail with "Error termination in NtrErr" > > The problem was fixed by removing the "qc" keyword from the keywords line= . > But Why? > Are there any inconsistency with the use of the QC algorithm and the > counterpoise procedure? > > Thanks again. > > Regards. > > Diego > > UPV-ITQ > Spain. > ************* > > > ------------------------------ > *From:* Mahmoud A. A. Ibrahim m.ibrahim|compchem.net ccl.net> > *To:* "Gomez, Diego Armando " > *Sent:* Fri, April 23, 2010 11:43:39 PM > *Subject:* CCL:G: Error termination in NtrErr at MP2 calculation. > > Dear Diego > I read your complain about a NtrErr error. This type of errors happens i= n > different cases, one of them as Dave mentioned due to space issue, and in > this case NMax information should be mentioned in last few lines, which i= s > not available in the supported information you gave. Another possibility = is > the checkpoint file, what happened is your checkpoint file has not be > created, or optimization data (for first cycle) has not be saved in your > checkpoint file. that is what you have got. > There is no technical solve for this error. Just, try to build up your > input file again, save checkpoint file (%chk=3Dfilename.chk) and change i= ts > path. > If you got the error again, you would send your input file and we can tes= t > it. > Sincerely; > M. Ibrahim > > On Thu, Apr 22, 2010 at 9:24 PM, DIEGOI GOMEZ darkego21]_[yahoo.com < > owner-chemistry,+,ccl.net> wrote: > >> Hi Dave, >> thanks for your reply!! >> >> I'm using Gaussian09 and my system is really small, I'm doing a test wit= h >> one Pd(II) atom in square planar stereo-chemistry with two H2O molecules= and >> two OH- groups as ligands interacting with one H2 molecule. >> >> ------------------------------------------------------------------------= -------------------------------------------- >> 118 basis functions, 217 primitive gaussians, 124 cartesian basis >> functions >> 29 alpha electrons 29 beta electrons >> >> ------------------------------------------------------------------------= ------------------------------------------- >> Previously I did one MP2 optimization of the system (without counterpois= e) >> with no problems. So I don't believe that the Error is related with stor= age >> capacity (actually, I have done calculation on bigger systems with more = than >> 300 basis functions). I speculate that It seems to be related with the >> reading of some file or keyword when the second step starts. >> >> I forgot to mention that in this particular case the Pd cluster is fixed >> (opt=3Dz-matrix) an the optimization is only done on the H2 coordinates. >> >> However I have not tried that option (%rwf), I'll give a look... >> >> Thanks again.. >> >> Diego >> UPV-ITQ >> Spain. >> >> >> >> >> ------------------------------ >> *From:* "Close, David M. CLOSED_._mail.etsu.edu" > ccl.net> >> *To:* "Gomez, Diego Armando " >> *Sent:* Thu, April 22, 2010 8:02:19 PM >> *Subject:* CCL: Error termination in NtrErr at MP2 calculation. >> >> Diegoi: >> >> This is a common error that means you have exceeded disc storage space= . >> This happens with MP2 calculations that requires a great deal of scratch >> disc space for storing integrals. There are common fixes to this proble= m, >> but it is necessary to tell us about the size of the calculation you are >> doing. Like how many heavy atoms, and what program you are using. >> Basically a 32 bit machine is limited to 16 Gbytes of storage. Have you >> tried simple fixes like %rwf=3D =85. ? >> >> Regards, Dave Close. >> >> >> >> *From:* owner-chemistry+closed=3D=3Detsu.edu*ccl.net [mailto: >> owner-chemistry+closed =3D=3Detsu.edu*ccl.net]= *On >> Behalf Of *DIEGOI GOMEZ darkego21 ~ yahoo.com >> *Sent:* Thursday, April 22, 2010 9:56 AM >> *To:* Close, David M. >> *Subject:* CCL: Error termination in NtrErr at MP2 calculation. >> >> >> >> Hello there. >> >> I'm doing an optimization of a pair of interacting molecules at MP2 leve= l >> with simultaneous counterpoise correction. I'm using two basis set (lanl= 2dz >> and 6-31G**) through the "GEN" keyword. The calculation starts without >> problems, so the first SCF cycle and the second-order perturbation are >> accomplished. However, when the next step starts the follow Error is >> reported: >> >> >> ------------------------------------------------------------------------= --------------------------------------------------------------------- >> ***** Axes restored to original set ***** >> Cartesian Forces: Max 0.199455160 RMS 0.055013514 >> Operation on file out of range. >> FileIO: IOper=3D 2 IFilNo(1)=3D -522 Len=3D 118 IPos=3D = 118 Q=3D >> 47965310131088 >> >> >> dumping /fiocom/, unit =3D 1 NFiles =3D 98 SizExt =3D 524288 WInB= lk >> =3D 512 >> defal =3D T LstWrd =3D 233431552 FType=3D2 FMxFil= =3D10000 >> >> Number 0 0 0 0 0 >> 0 0 0 >> Base 12203972 390144 495616 321536 12752384 >> 10698752 201216 365568 >> End 12204032 402432 527360 322048 12818944 >> 11614208 201728 372736 >> End1 12204032 402432 527360 322048 12818944 >> 11614208 201728 372736 >> Wr Pntr 12203972 388608 495616 321536 12533760 >> 10698752 201216 365568 >> Rd Pntr 12203972 388608 495616 321536 12533760 >> 10698752 201216 365568 >> Length 60 12288 31744 512 66560 >> 915456 512 7168 >> >> (...) >> >> Error termination in NtrErr: >> NtrErr Called from FileIO. >> >> >> ------------------------------------------------------------------------= ---------------------------------------------------------------------- >> >> Thanks in advance for any sugestion. >> >> Diego >> UPV-ITQ >> Spain. >> >> >> >> > > > -- > Mahmoud A. A. Ibrahim > Current Address > 7.05, School of Chemistry, > The University of Manchester, > Oxford Road, Manchester, M13 9PL, > United Kingdom. > > Home Address > Chemistry Department, > Faculty of Science, > Minia University, > Minia 61519, > Egypt. > > Contact Information > Email: m.ibrahim,+,compchem.net > Website: www.compchem.net > Fax No.: +20862342601 > > --=20 Mahmoud A. A. Ibrahim Current Address 7.05, School of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. Home Address Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt. Contact Information Email: m.ibrahim[A]compchem.net Website: www.compchem.net Fax No.: +20862342601 --001485f1dc1875ae1c04853e4393 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Dear Diego
I have run your input file (using G03) but without guess=3Dr= ead (also=A0I have tested a couple of jobs for your input using guess=3Drea= d, with/without qc)=A0and all of them gave me a normal termination:
Counterpoise: corrected energy =3D =A0 =A0-430.811138359266
Count= erpoise: BSSE energy =3D =A0 =A0 =A0 0.003915169173
As I told you= before, the problem is returned to your checkpoint file, or something rela= ted to G09 where I haven't it here to check your job with it.
Sincerely;
M. Ibrahim


On Tue, Apr 27, 2010 at 3:37 PM, DIEGOI GOMEZ darkego21 _ yahoo.com <owner-chemistry[A]ccl.net> wrote:<= br>
Hi again...

Firstly, thanks Ibrahim f= or your reply.

Well, after remaking the imput (in this case in cartesians to avoid the= ghost atoms), I have fixed the problem but I don't have clear why it w= as the solution.

Here is the problematic imput file:

--------= ---------------------------------------------------------------------------= --------------------------------------
=A0
%chk=3D/data1/diego/GAU/metals/palladium/Pd1hcpx.chk
%mem=3D= 20GB
%nproc=3D8
# MP2/GENecp geom=3Dconnectivity scf=3D(maxcycle=3D50= 0, qc) guess=3Dread counterpoise=3D2 maxdisk=3D50GB

Title Card Requi= red

0 1
=A0Pd(Fragment=3D1)=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 -0.0814070= 0=A0=A0=A0 0.03787500=A0=A0 -0.00549500
=A0O(Fragment=3D1)=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0 -1.97461900=A0=A0 -0.99338100=A0=A0 -0.06543100
=A0O(Fragment= =3D1)=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 1.81180500=A0=A0= =A0 1.06913100=A0=A0=A0 0.05444000
=A0O(Fragment=3D1)=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.86489800=A0=A0 -1.70544900=A0=A0=A0 0.0= 9890800
=A0O(Fragment=3D1)=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 -1.02771= 300=A0=A0=A0 1.78119900=A0=A0 -0.10989800
=A0H(Fragment=3D1)=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 -2.38699000=A0=A0 -1.26562000=A0=A0 -0.87355800
=A0H(Fragment=3D1)=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0 -2.46575500=A0=A0 -1.21329400=A0=A0=A0 0.71409400
=A0H(Fragmen= t=3D1)=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 2.30294000=A0=A0= =A0 1.28904400=A0=A0 -0.72508400
=A0H(Fragment=3D1)=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 2.22417600=A0=A0=A0 1.34137000=A0=A0=A0 0.86= 256800
=A0H(Fragment=3D1)=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 1.182= 80000=A0=A0 -1.98870600=A0=A0=A0 0.95001100
=A0H(Fragment=3D1)=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 -1.42728100=A0=A0=A0 2.11870900=A0= =A0=A0 0.68515200
=A0H(Fragment=3D2)=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0 3.82319200=A0=A0 -1.61126300=A0=A0 -0.66318300
=A0H(Fragment= =3D2)=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 3.09668700=A0=A0 -= 1.62449400=A0=A0 -0.52137500

=A01 4 1.0 5 1.0
=A02 6 1.0 7 1.0=A03 8 1.0 9 1.0
=A04 10 1.0
=A05 11 1.0
=A06
=A07
=A08
=A09
=A010
=A01= 1
=A012
=A013

O H 0
6-31G**
****
Pd 0
lanl2dz
*= ***

Pd 0
lanl2dz




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

As men= tioned, the calculation starts without problems but after the first SCF cycle the process fail with "Error termination in NtrErr"
The problem was fixed by removing the "qc" keyword from the keyw= ords line. But Why?
Are there any inconsistency with the use of the QC a= lgorithm and the counterpoise procedure?

Thanks again.

Regards.

Diego

UPV-ITQ
Spain.

=20
*************


From: Mahmoud A. A. Ibrahi= m m.ibrahim|compchem.net<= /a> <owner-chemistry|a|ccl.= net>
To: "Gomez, Diego Arman= do " <darkego21|a|ya= hoo.com>
Sent: Fri= , April 23, 2010 11:43:39 PM
Subject: CCL:G: Error termin= ation in NtrErr at MP2 calculation.

Dear=A0Diego
I read your complain about a=A0NtrErr =A0error. This type of errors happens in different cases, one of them as= Dave mentioned due to space issue, and in this case NMax information shoul= d be mentioned in last few lines, which is not available in the supported i= nformation you gave. Another possibility is the checkpoint file, what happe= ned is your checkpoint file has not be created, or optimization data (for f= irst cycle) has not be saved in your checkpoint file. that is what you have= got.
There is no technical so= lve for this error. Just, try to build up your input file again, save check= point file (%chk=3Dfilename.chk) and change its path.<= /div>
If you got the error aga= in, you would send your input file and we can test it.=
Sincerely;=
M. Ibrahim=

On Thu, Apr 22, 2010 at 9:24 PM, DIEGOI= GOMEZ darkego21]_[yahoo.com <owner-chemistry,+,ccl.net<= /a>> wrote:
Hi Dave,
thanks for = your reply!!

I'm using Gaussian09 and my system is really small, I'm doing a= test with one Pd(II) atom in square planar stereo-chemistry with two H2O m= olecules and two OH- groups as ligands interacting with one H2 molecule. ---------------------------------------------------------------------------= -----------------------------------------
=A0=A0 118 basis functions,=A0= =A0 217 primitive gaussians,=A0=A0 124 cartesian basis functions
=A0=A0= =A0 29 alpha electrons=A0=A0=A0=A0=A0=A0 29 beta electrons
---------------------------------------------------------------------------= ----------------------------------------
Previously I did one MP2 optimi= zation of the system (without counterpoise) with no problems. So I don'= t believe that the Error is related with storage capacity (actually, I have done cal= culation on bigger systems with more than 300 basis functions). I speculate= that It seems to be related with the reading of some file or keyword when = the second step starts.

I forgot to mention that in this particular case the Pd cluster is fixe= d (opt=3Dz-matrix) an the optimization is only done on the H2 coordinates.<= br>
However I have not tried that option (%rwf), I'll give a look...=

Thanks again..

Diego
UPV-ITQ
Spain.

=20




From: "Close, David M. = CLOSED_._mail.etsu.edu" <owner-chemistry]~[ccl.net>
To: "Gomez, Diego Arman= do " <darkego21]~[yahoo.com>
Sen= t: Thu, April 22, 2010 8:02:19 PM
Subject: CCL: Error terminat= ion in NtrErr at MP2 calculation.

=20 =20

From: owner-chemistry+closed=3D=3Detsu.edu*ccl.net [mailto:owner-chemistry+closed=3D=3Detsu.edu*ccl.net] On Behalf Of DIEGOI GOMEZ darkego21 ~ yahoo.com
Sent: Thursday, April 22, 2010 9:56 AM
To: Close, David M.
Subject: CCL: Error termination in NtrErr at MP2 calculation.=

=20

=A0

=20

Hello there.

I'm doing an optimization of a pair of interacting molecules at MP2 lev= el with simultaneous counterpoise correction. I'm using two basis set (lanl2dz = and 6-31G**) through the "GEN" keyword.=A0 The calculation starts without problems, so the first SCF cycle and the second-order perturbation = are accomplished. However, when the next step starts the follow Error is report= ed:

---------------------------------------------------------------------------= ------------------------------------------------------------------
=A0 ***** Axes restored to original set *****
=A0Cartesian Forces:=A0 Max=A0=A0=A0=A0 0.199455160 RMS=A0=A0=A0=A0 0.055013514
=A0Operation on file out of range.
FileIO: IOper=3D 2 IFilNo(1)=3D=A0 -522 Len=3D=A0=A0=A0=A0=A0=A0=A0=A0 118 IPos=3D=A0=A0=A0=A0=A0=A0=A0=A0 118 Q=3D=A0=A0 47965310131088


=A0dumping /fiocom/, unit =3D 1 NFiles =3D=A0=A0=A0 98 SizExt =3D=A0=A0=A0 524288 WInBlk =3D=A0=A0=A0=A0=A0=A0 512
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 defal =3D T LstWrd =3D=A0=A0 233431552 FType=3D2 FMxFil=3D10000

=A0Number=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0
=A0Base=A0=A0=A0=A0=A0 12203972=A0=A0=A0=A0 390144=A0=A0=A0=A0 495616=A0=A0=A0=A0 321536=A0=A0 12752384=A0=A0 10698752=A0=A0=A0=A0 201216=A0=A0=A0=A0 365568
=A0End=A0=A0=A0=A0=A0=A0 12204032=A0=A0=A0=A0 402432=A0=A0=A0=A0 527360=A0=A0=A0=A0 322048=A0=A0 12818944=A0=A0 11614208=A0=A0=A0=A0 201728=A0=A0=A0=A0 372736
=A0End1=A0=A0=A0=A0=A0 12204032=A0=A0=A0=A0 402432=A0=A0=A0=A0 527360=A0=A0=A0=A0 322048=A0=A0 12818944=A0=A0 11614208=A0=A0=A0=A0 201728=A0=A0=A0=A0 372736
=A0Wr Pntr=A0=A0 12203972=A0=A0=A0=A0 388608=A0=A0=A0=A0 495616=A0=A0=A0=A0 321536=A0=A0 12533760=A0=A0 10698752=A0=A0=A0=A0 201216=A0=A0=A0=A0 365568
=A0Rd Pntr=A0=A0 12203972=A0=A0=A0=A0 388608=A0=A0=A0=A0 495616=A0=A0=A0=A0 321536=A0=A0 12533760=A0=A0 10698752=A0=A0=A0=A0 201216=A0=A0=A0=A0 365568
=A0Length=A0=A0=A0=A0=A0=A0=A0=A0=A0 60=A0=A0=A0=A0=A0 12288=A0=A0=A0=A0=A0 31744=A0=A0=A0=A0=A0=A0=A0 512=A0=A0=A0=A0=A0 66560=A0=A0=A0=A0 915456=A0=A0=A0=A0=A0=A0=A0 512=A0=A0=A0=A0=A0=A0 7168

(...)

=20

=A0Error termination in NtrErr:
=A0NtrErr Called from FileIO.

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

Thanks in advance for any sugestion.

Diego
UPV-ITQ
Spain.

=20

=A0

=20




--
=A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0Mahmoud A. A. Ibrahim =A0 =A0 =A0 =A0
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Current Address
=A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 7.05, School of Chemistry,
=A0 =A0 =A0 =A0 =A0 =A0 =A0= The University of Manchester,
=A0 =A0 =A0 =A0 Oxford Road, Manchester, M13 9PL,
=A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 United Kingdom.

=A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0Home Address
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= Chemistry Department,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Faculty o= f Science,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Minia University,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Minia 61519,
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Egypt.

= =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Contact Information
=A0 =A0 =A0= =A0 =A0 Email: m.ibrahim,+,compchem.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0Website: www.compchem.net
=A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 Fax No.: +20862342601




--
=A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0Mahmoud A. A. Ibrahim =A0 =A0 =A0 =A0
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Current Address
=A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 7.05, School of Chemistry,
=A0 =A0 =A0 =A0 =A0 =A0 =A0= The University of Manchester,
=A0 =A0 =A0 =A0 Oxford Road, Manchester, M13 9PL,
=A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 United Kingdom.

=A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0Home Address
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= Chemistry Department,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Faculty o= f Science,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Minia Univers= ity,
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