From owner-chemistry@ccl.net Thu Dec 3 04:34:01 2009 From: "=?iso-8859-15?q?=D6d=F6n_Farkas?= farkas#chem.elte.hu" To: CCL Subject: CCL:G: Questions about linear dependence and basis set Message-Id: <-40857-091203042630-1559-Njo/6XoxRiYG9oO2LQCSqw^^^server.ccl.net> X-Original-From: =?iso-8859-15?q?=D6d=F6n_Farkas?= Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-15" Date: Thu, 3 Dec 2009 10:25:57 +0100 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-15?q?=D6d=F6n_Farkas?= [farkas~~chem.elte.hu] Hi Ron, I did not have the chance to see your input and make my own tests but I thi= nk=20 what you should try is "Guess=3DAlways". It may or may not help. Best wishes, =D6d=F6n Odon Farkas Associate Professor Laboratory of Chemical Informatics Institute of Chemistry E=F6tv=F6s Lor=E1nd University, Budapest 1/A P=E1zm=E1ny P=E9ter s=E9t=E1ny H-1117 Budapest, Hungary Cellphone: +36-30-2553111 On Wednesday 02 December 2009 22:47:49 Ronald C Bakus rbakus]*[chem.ucsb.ed= u=20 wrote: > Sent to CCL by: "Ronald C Bakus" [rbakus(_)chem.ucsb.edu] > Ol Ga, > For the input I gave you, it completes one SCF cycle, and then fails to > converge on the second, even with scf=3Dnosymm (and along with scf=3Dxqc)= and > ub3lyp. Im using G03 Rev E.01. > > Thanks, > Ron > > > "Ol Ga eurisco1:-:pochta.ru" wrote: > > > > Sent to CCL by: "Ol Ga" [eurisco1=3D=3D=3Dpochta.ru] > > Dear Ronald C. Bakus, > > > > I used geometry posted by you earlier but I changed slightly route - I > > changed method to unrestricted (Ub3lyp). Also, I recommend to add NoSym= m. > > I observed smooth SCF-convergence before XQC began to performe. > > > > Cycle 15 Pass 1 IDiag 1: > > RMSU=3D 6.17D-09 CP: 6.72D-01 7.68D-01 9.51D-01 5.80D-01 7.61= D-01 > > CP: 7.40D-01 9.08D-01 9.12D-01 8.16D-01 8.60D-= 01 > > CP: 8.93D-01 8.18D-01 7.10D-01 8.90D-01 > > E=3D -1117.18461578981 Delta-E=3D 0.000000000079 Rises=3DF = Damp=3DF > > DIIS: error=3D 1.15D-08 at cycle 15 NSaved=3D 15. > > NSaved=3D15 IEnMin=3D13 EnMin=3D -1117.18461578993 IErMin=3D15 Err= Min=3D > > 1.15D-08 ErrMax=3D 1.15D-08 EMaxC=3D 1.00D-01 BMatC=3D 2.74D-13 BMatP= =3D 2.88D-12 > > IDIUse=3D1 WtCom=3D 1.00D+00 WtEn=3D 0.00D+00 > > Coeff-Com: -0.140D-06 0.330D-06 0.303D-05 0.392D-05 0.829D-05 0.102D-04 > > Coeff-Com: -0.102D-03-0.495D-03-0.180D-02-0.238D-02 0.363D-02 0.175D-01 > > Coeff-Com: 0.164D+00 0.285D+00 0.535D+00 > > Coeff: -0.140D-06 0.330D-06 0.303D-05 0.392D-05 0.829D-05 0.102D-04 > > Coeff: -0.102D-03-0.495D-03-0.180D-02-0.238D-02 0.363D-02 0.175D-01 > > Coeff: 0.164D+00 0.285D+00 0.535D+00 > > Gap=3D 0.111 Goal=3D None Shift=3D 0.000 > > Gap=3D 0.111 Goal=3D None Shift=3D 0.000 > > RMSDP=3D4.49D-09 MaxDP=3D2.30D-07 DE=3D 7.87D-11 OVMax=3D 1.03D-07 > > > > SCF Done: E(UB3LYP) =3D -1117.18461579 A.U. after 15 cycles > > Convg =3D 0.4487D-08 -V/T =3D 2.0098 > > =3D 0.0000 =3D 0.0000 =3D 0.0000 =3D 0.0000 S=3D 0.0= 000 > > =3D 0.000000000000E+00 > > KE=3D 1.106300942892D+03 PE=3D-6.771451539404D+03 EE=3D 2.455058951308= D+03 > > Annihilation of the first spin contaminant: > > S**2 before annihilation 0.0000, after 0.0000 > > DiagDN has N=3D 672 LTot=3D 2048 but NE2=3D 3 cannot use DSYEVD. > > Leave Link 502 at Tue Dec 1 08:49:35 2009, MaxMem=3D 131072000 cpu:= =20 > > 7983.5 > > > > QCSCF skips out because SCF is already converged. > > > > > > What revision of Gaussian do you use? It is smart software. Thus, linear > > dependence can be observed very rarely. > > > > Sincerely, > > > > Ol Ga > > -=3D This is automatically added to each message by the mailing script = =3D- From owner-chemistry@ccl.net Thu Dec 3 05:32:01 2009 From: "Abhishek DuttaChowdhury abhishekdc],[chem.iitb.ac.in" To: CCL Subject: CCL:G: OPT problem Message-Id: <-40858-091203052826-30143-DoaHEffzPwSKE6uS41m7qA _ server.ccl.net> X-Original-From: "Abhishek DuttaChowdhury" Date: Thu, 3 Dec 2009 05:28:22 -0500 Sent to CCL by: "Abhishek DuttaChowdhury" [abhishekdc++chem.iitb.ac.in] Dear All, Following job is stopped after 1st cycle and at the end of output file following error is given: >>>>>>>>>> Convergence criterion not met. SCF Done: E(UB+HF-LYP) = -1958.29938401 A.U. after 129 cycles Convg = 0.9641D-06 -V/T = 2.0034 S**2 = 3.1271 KE= 1.951755250014D+03 PE=-1.443854351336D+04 EE= 5.590860464768D+03 Annihilation of the first spin contaminant: S**2 before annihilation 3.1271, after 2.2796 Convergence failure -- run terminated. Error termination via Lnk1e in /g03/l502.exe at Wed Dec 2 04:36:41 2009. Job cpu time: 1 days 5 hours 27 minutes 12.3 seconds. File lengths (MBytes): RWF= 285 Int= 0 D2E= 0 Chk= 10 Scr= 1 Following is my input file: %chk=cd_opt.chk %mem=500MB #P B3LYP GenECP opt Nosymm SCF=NoIncFock GFINPUT IOp(6/7=3) GFPRINT cd_opt 1 3 coordinates C H N O 0 6-31G* **** Si 0 LANL2DZ **** Si 0 LANL2DZ .............Please give me an indication again that what to do? Many thanks in advance. Sincerely, Abhishek From owner-chemistry@ccl.net Thu Dec 3 08:27:00 2009 From: "Soren Eustis soreneustis .. gmail.com" To: CCL Subject: CCL:G: OPT problem Message-Id: <-40859-091203075050-11939-jShlJeYtnjKXGtLCg6zBpQ _ server.ccl.net> X-Original-From: Soren Eustis Content-transfer-encoding: 7bit Content-type: text/plain; charset="US-ASCII" Date: Thu, 03 Dec 2009 12:54:52 +0100 Mime-version: 1.0 Sent to CCL by: Soren Eustis [soreneustis,+,gmail.com] You are having problems with the SCF convergence. One way to overcome this is to use the XQC term for the SCF job. This requests a quadratically convergent routing be used if the normal SCF convergence algorithm fails. Usually after one or two optimization cycles, the orbitals are sufficiently well defined that the SCF energy will converge normally and the job can proceed without the costly XQC procedure. Your input line would then be: #P B3LYP GenECP opt Nosymm SCF=(xqc,NoIncFock) GFINPUT IOp(6/7=3) GFPRINT This should work. If not, you can try a different guess method (i.e. Guess=indo). Regards, Soren On 12/3/09 11:28 AM, "Abhishek DuttaChowdhury abhishekdc],[chem.iitb.ac.in" wrote: > > Sent to CCL by: "Abhishek DuttaChowdhury" [abhishekdc++chem.iitb.ac.in] > Dear All, > Following job is stopped after 1st cycle and at the end of output file > following error is given: > >>>>>>>>>>> Convergence criterion not met. > SCF Done: E(UB+HF-LYP) = -1958.29938401 A.U. after 129 cycles > Convg = 0.9641D-06 -V/T = 2.0034 > S**2 = 3.1271 > KE= 1.951755250014D+03 PE=-1.443854351336D+04 EE= 5.590860464768D+03 > Annihilation of the first spin contaminant: > S**2 before annihilation 3.1271, after 2.2796 > Convergence failure -- run terminated. > Error termination via Lnk1e in /g03/l502.exe at Wed Dec 2 04:36:41 2009. > Job cpu time: 1 days 5 hours 27 minutes 12.3 seconds. > File lengths (MBytes): RWF= 285 Int= 0 D2E= 0 Chk= 10 > Scr= 1 > > > Following is my input file: > > %chk=cd_opt.chk > %mem=500MB > #P B3LYP GenECP opt Nosymm SCF=NoIncFock GFINPUT IOp(6/7=3) GFPRINT > > cd_opt > > 1 3 > coordinates > > C H N O 0 > 6-31G* > **** > Si 0 > LANL2DZ > **** > > Si 0 > LANL2DZ > > > > > .............Please give me an indication again that what to do? > > Many thanks in advance. > > Sincerely, > Abhishek> > From owner-chemistry@ccl.net Thu Dec 3 09:15:02 2009 From: "Mahmoud A. A. Ibrahim m.ibrahim%a%compchem.net" To: CCL Subject: CCL:G: OPT problem Message-Id: <-40860-091203091411-7045-59G+DNnuzv/WVZ3Bmt9D9A- -server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary=000e0cd6c9001d2b100479d39a4a Date: Thu, 3 Dec 2009 14:13:57 +0000 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim-,-compchem.net] --000e0cd6c9001d2b100479d39a4a Content-Type: text/plain; charset=ISO-8859-1 Sorry, this problem is originally returned to the fact that you have reached the maximum number of SCF cycles which is 129 by default, as be printed in your output: > SCF Done: E(UB+HF-LYP) = -1958.29938401 A.U. after 129 cycles You can overcome this problem by increasing the number of SCF cycles using MaxCycle=N keyword. If it didn't work , you would use what Soren suggested. Sincerely; M. Ibrahim On Thu, Dec 3, 2009 at 11:54 AM, Soren Eustis soreneustis .. gmail.com < owner-chemistry()ccl.net> wrote: > > Sent to CCL by: Soren Eustis [soreneustis,+,gmail.com] > You are having problems with the SCF convergence. One way to overcome this > is to use the XQC term for the SCF job. This requests a quadratically > convergent routing be used if the normal SCF convergence algorithm fails. > Usually after one or two optimization cycles, the orbitals are sufficiently > well defined that the SCF energy will converge normally and the job can > proceed without the costly XQC procedure. > > Your input line would then be: > > #P B3LYP GenECP opt Nosymm SCF=(xqc,NoIncFock) GFINPUT IOp(6/7=3) GFPRINT > > This should work. If not, you can try a different guess method (i.e. > Guess=indo). > > Regards, > > Soren > > > On 12/3/09 11:28 AM, "Abhishek DuttaChowdhury abhishekdc],[chem.iitb.ac.in > " > wrote: > > > > > Sent to CCL by: "Abhishek DuttaChowdhury" [abhishekdc++chem.iitb.ac.in] > > Dear All, > > Following job is stopped after 1st cycle and at the end of output file > > following error is given: > > > >>>>>>>>>>> Convergence criterion not met. > > SCF Done: E(UB+HF-LYP) = -1958.29938401 A.U. after 129 cycles > > Convg = 0.9641D-06 -V/T = 2.0034 > > S**2 = 3.1271 > > KE= 1.951755250014D+03 PE=-1.443854351336D+04 EE= 5.590860464768D+03 > > Annihilation of the first spin contaminant: > > S**2 before annihilation 3.1271, after 2.2796 > > Convergence failure -- run terminated. > > Error termination via Lnk1e in /g03/l502.exe at Wed Dec 2 04:36:41 > 2009. > > Job cpu time: 1 days 5 hours 27 minutes 12.3 seconds. > > File lengths (MBytes): RWF= 285 Int= 0 D2E= 0 Chk= 10 > > Scr= 1 > > > > > > Following is my input file: > > > > %chk=cd_opt.chk > > %mem=500MB > > #P B3LYP GenECP opt Nosymm SCF=NoIncFock GFINPUT IOp(6/7=3) GFPRINT > > > > cd_opt > > > > 1 3 > > coordinates > > > > C H N O 0 > > 6-31G* > > **** > > Si 0 > > LANL2DZ > > **** > > > > Si 0 > > LANL2DZ > > > > > > > > > > .............Please give me an indication again that what to do? > > > > Many thanks in advance. > > > > Sincerely, > > Abhishek> > > -- 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 --000e0cd6c9001d2b100479d39a4a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Sorry, this problem is originally returned to the fact that you have reache= d the maximum number of SCF cycles which is 129 by default, as be printed i= n your output:
> =A0SCF Done: =A0E(UB+HF-LYP) =3D =A0-1958.29938401 =A0 =A0 A.U. after = =A0129 cycles
You can overcome this problem by increasing the number of = SCF cycles using MaxCycle=3DN keyword.
If it didn't work , you would= use what Soren suggested.
Sincerely;
M. Ibrahim

On Thu, Dec 3, 2= 009 at 11:54 AM, Soren Eustis soreneustis .. g= mail.com <owner-chemistry()ccl.net> wrote:

Sent to CCL by: Soren Eustis [soreneustis,+,gmail.com]
You are having problems with the SCF convergence. =A0One way to overcome th= is
is to use the XQC term for the SCF job. =A0This requests a quadratically convergent routing be used if the normal SCF convergence algorithm fails. Usually after one or two optimization cycles, the orbitals are sufficiently=
well defined that the SCF energy will converge normally and the job can
proceed without the costly XQC procedure.

Your input line would then be:

#P B3LYP GenECP opt Nosymm SCF=3D(xqc,NoIncFock) GFINPUT IOp(6/7=3D3) GFPRI= NT

This should work. =A0If not, you can try a different guess method (i.e.
Guess=3Dindo).

Regards,

Soren


On 12/3/09 11:28 AM, "Abhishek DuttaChowdhury abhishekdc],[chem.iitb.ac.in"
<owner-chemistry[a]ccl.net<= /a>> wrote:

>
> Sent to CCL by: "Abhishek =A0DuttaChowdhury" [abhishekdc++chem.iitb.ac.in]
> Dear All,
> =A0 =A0Following job is stopped after 1st cycle and at the end of outp= ut file
> following error is given:
>
>>>>>>>>>>> Convergence criterion not met.=
> =A0SCF Done: =A0E(UB+HF-LYP) =3D =A0-1958.29938401 =A0 =A0 A.U. after = =A0129 cycles
> =A0 =A0 =A0 =A0 =A0 =A0 =A0Convg =A0=3D =A0 =A00.9641D-06 =A0 =A0 =A0 = =A0 =A0 =A0 -V/T =3D =A02.0034
> =A0 =A0 =A0 =A0 =A0 =A0 =A0S**2 =A0 =3D =A0 3.1271
> =A0KE=3D 1.951755250014D+03 PE=3D-1.443854351336D+04 EE=3D 5.590860464= 768D+03
> =A0Annihilation of the first spin contaminant:
> =A0S**2 before annihilation =A0 =A0 3.1271, =A0 after =A0 =A0 2.2796 > =A0Convergence failure -- run terminated.
> =A0Error termination via Lnk1e in /g03/l502.exe at Wed Dec =A02 04:36:= 41 2009.
> =A0Job cpu time: =A01 days =A05 hours 27 minutes 12.3 seconds.
> =A0File lengths (MBytes): =A0RWF=3D =A0 =A0285 Int=3D =A0 =A0 =A00 D2E= =3D =A0 =A0 =A00 Chk=3D =A0 =A0 10
> Scr=3D =A0 =A0 =A01
>
>
> Following is my input file:
>
> %chk=3Dcd_opt.chk
> %mem=3D500MB
> #P B3LYP GenECP opt Nosymm SCF=3DNoIncFock GFINPUT IOp(6/7=3D3) GFPRIN= T
>
> cd_opt
>
> 1 3
> coordinates
>
> C H N O 0
> 6-31G*
> ****
> Si 0
> LANL2DZ
> ****
>
> Si 0
> LANL2DZ
>
>
>
>
> .............Please give me an indication again that what to do?
>
> Many thanks in advance.
>
> Sincerely,
> Abhishek>
>



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--
=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 =A0The Universi= ty 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,
=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()compche= m.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0Website: ww= w.compchem.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Fax No.: +208623= 42601
--000e0cd6c9001d2b100479d39a4a-- From owner-chemistry@ccl.net Thu Dec 3 11:46:00 2009 From: "Ol Ga eurisco1===pochta.ru" To: CCL Subject: CCL:G: Questions about linear dependence and basis set Message-Id: <-40861-091203114511-22065-763Fwc+5a3NIk5Ahf+FWzQ]~[server.ccl.net> X-Original-From: "Ol Ga" Date: Thu, 3 Dec 2009 11:45:06 -0500 Sent to CCL by: "Ol Ga" [eurisco1##pochta.ru] Dear Ronald C. Bakus, First, try to add IOp(3/59=8) or add Guess=indo If it doesn't help, try IOp(3/32=3) If it doesn't help, try iop(3/32=2) or change basis set from split-palence basis sets to cc-pVxZ family. Sincerely, Ol Ga ********************** Sent to CCL by: =?iso-8859-15?q?dn_Farkas?= [farkas~~chem.elte.hu] Hi Ron, I did not have the chance to see your input and make my own tests but I think what you should try is "Guess=Always". It may or may not help. Best wishes, dn Odon Farkas Associate Professor Laboratory of Chemical Informatics Institute of Chemistry Etvs Lornd University, Budapest 1/A Pzmny Pter stny H-1117 Budapest, Hungary Cellphone: +36-30-2553111 On Wednesday 02 December 2009 22:47:49 Ronald C Bakus rbakus]*[chem.ucsb.edu wrote: > Sent to CCL by: "Ronald C Bakus" [rbakus(_)chem.ucsb.edu] > Ol Ga, > For the input I gave you, it completes one SCF cycle, and then fails to > converge on the second, even with scf=nosymm (and along with scf=xqc) and > ub3lyp. Im using G03 Rev E.01. > > Thanks, > Ron > > > "Ol Ga eurisco1:-:pochta.ru" wrote: > > > > Sent to CCL by: "Ol Ga" [eurisco1===pochta.ru] > > Dear Ronald C. Bakus, > > > > I used geometry posted by you earlier but I changed slightly route - I > > changed method to unrestricted (Ub3lyp). Also, I recommend to add NoSymm. > > I observed smooth SCF-convergence before XQC began to performe. > > > > Cycle 15 Pass 1 IDiag 1: > > RMSU= 6.17D-09 CP: 6.72D-01 7.68D-01 9.51D-01 5.80D-01 7.61D-01 > > CP: 7.40D-01 9.08D-01 9.12D-01 8.16D-01 8.60D-01 > > CP: 8.93D-01 8.18D-01 7.10D-01 8.90D-01 > > E= -1117.18461578981 Delta-E= 0.000000000079 Rises=F Damp=F > > DIIS: error= 1.15D-08 at cycle 15 NSaved= 15. > > NSaved=15 IEnMin=13 EnMin= -1117.18461578993 IErMin=15 ErrMin= > > 1.15D-08 ErrMax= 1.15D-08 EMaxC= 1.00D-01 BMatC= 2.74D-13 BMatP= 2.88D-12 > > IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 > > Coeff-Com: -0.140D-06 0.330D-06 0.303D-05 0.392D-05 0.829D-05 0.102D-04 > > Coeff-Com: -0.102D-03-0.495D-03-0.180D-02-0.238D-02 0.363D-02 0.175D-01 > > Coeff-Com: 0.164D+00 0.285D+00 0.535D+00 > > Coeff: -0.140D-06 0.330D-06 0.303D-05 0.392D-05 0.829D-05 0.102D-04 > > Coeff: -0.102D-03-0.495D-03-0.180D-02-0.238D-02 0.363D-02 0.175D-01 > > Coeff: 0.164D+00 0.285D+00 0.535D+00 > > Gap= 0.111 Goal= None Shift= 0.000 > > Gap= 0.111 Goal= None Shift= 0.000 > > RMSDP=4.49D-09 MaxDP=2.30D-07 DE= 7.87D-11 OVMax= 1.03D-07 > > > > SCF Done: E(UB3LYP) = -1117.18461579 A.U. after 15 cycles > > Convg = 0.4487D-08 -V/T = 2.0098 > > = 0.0000 = 0.0000 = 0.0000 = 0.0000 S= 0.0000 > > = 0.000000000000E+00 > > KE= 1.106300942892D+03 PE=-6.771451539404D+03 EE= 2.455058951308D+03 > > Annihilation of the first spin contaminant: > > S**2 before annihilation 0.0000, after 0.0000 > > DiagDN has N= 672 LTot= 2048 but NE2= 3 cannot use DSYEVD. > > Leave Link 502 at Tue Dec 1 08:49:35 2009, MaxMem= 131072000 cpu: > > 7983.5 > > > > QCSCF skips out because SCF is already converged. > > > > > > What revision of Gaussian do you use? It is smart software. Thus, linear > > dependence can be observed very rarely. > > > > Sincerely, > > > > Ol Ga- From owner-chemistry@ccl.net Thu Dec 3 13:35:01 2009 From: "Alex Allardyce aa]=[chemaxon.hu" To: CCL Subject: CCL: Tool or Software Module to retrieve unique molecules Message-Id: <-40862-091203095302-566-tFyHmGF6P5syLTyRSxJAtg[a]server.ccl.net> X-Original-From: Alex Allardyce Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 03 Dec 2009 15:52:45 +0100 MIME-Version: 1.0 Sent to CCL by: Alex Allardyce [aa-#-chemaxon.hu] Not so elegant but straightforward using JChemBase, JChem Cartridge (toolkit) or Instant JChem (desktop application) using these steps: 1. Set up a molecule database table with option that duplicates are not allowed. 2. Import molecules into the database table. (Duplicates will be skipped.) 3. Export the full table. For a python solution, jython could be used, or just call the jcman (JChem Manager) through the command-line. We also plan a simple script for exactly this task, but that won't happen in the short term. As usual all functionality is free for academic research/teaching (more info and sign up: http://www.chemaxon.com/acpack_conditions.html) and Instant JChem Personal is free for everyone's desktop (details and download/tryout here: http://www.chemaxon.com/product/ijc.html). Cheers Alex manoj kumar manojrudraraju*gmail.com wrote: > Hi All, > > Does anyone aware or has developed any tool to retrieve Unique > molecules from a large compound databases. > > if not what would be the challenges ahead to develop such script, I > wish to know the math behind such operation and want to develop in python. > > Thanks for read and time, > > regards > Manoj > > > >