From owner-chemistry@ccl.net Thu Sep 13 01:24:00 2012 From: "Ronald Cook cookrl^tda.com" To: CCL Subject: CCL: regarding negative fukui function Message-Id: <-47579-120911233749-10702-4Tp7HZ5ilwgcBnFeeMA/3g- -server.ccl.net> X-Original-From: Ronald Cook Content-Type: multipart/alternative; boundary=f46d0447f2ced140c904c978e926 Date: Tue, 11 Sep 2012 21:37:42 -0600 MIME-Version: 1.0 Sent to CCL by: Ronald Cook [cookrl:+:tda.com] --f46d0447f2ced140c904c978e926 Content-Type: text/plain; charset=ISO-8859-1 Ambrish Most likely your problem is the use of the Mullikin charges. They give unrealistic and incorrect values for charges.Take a look at Condensation of Frontier Molecular Orbital Fukui Functions by Bulat et al. J. Phys. Chem. A 2004, 108, 342-349 aper "Possible negative values for the Fukui indexes have been discussed in the literature and considered as artifacts coming > from the condensation procedure12 or due to strong structural distortions14 (see also refs 13 and 15-17). Thanikaivelan et al.18 have thoroughly studied the effects of the population scheme and the basis set dependency of the Fukui indexes within the finite difference approximation eqs 9-11. *The most stable schemes upon basis set modification turn out to be the Atoms in Molecules (AIM)19 and the CHELPG (charges from electrostatic potentials, using a grid-based method),*20 this last one being based on the molecular electrostatic potential (MESP) to derive the atomic charges. Interestingly enough, these two schemes provide also very similar Fukui indexes and they both predict appropriate reactivity sites for all kinds of attacks (nucleophilic, electrophilic, and radical). Although they note that Hirshfeld partitioning provides in all studied cases nonnegative Fukui indexes, as also stated by Roy et al.,12 this fact cannot be generally extended since the allowance of negative values is in part a consequence of the finite difference approximation. Indeed, eqs 3-5 might be negative at some points since FN+1(r) might be smaller than FN(r) and FN(r) might be smaller than FN-1(r). Hence, regardless of the condensation scheme chosen negative Fukui indexes might appear. Furthermore, Hirshfeld partitioning fails to predict the correct reactivity trends in some cases.12,18" and their references On Tue, Sep 11, 2012 at 11:39 AM, AMBRISH KUMAR SRIVASTAVA ambrishphysics]^[ gmail.com wrote: > > Sent to CCL by: "AMBRISH KUMAR SRIVASTAVA" [ambrishphysics_._gmail.com] > Respected all, > During calculation on fukui fn using mullikan atomic charges, i got a > number of negative values for e.g. f0 values are given below: > -0.82305 > -0.90080 > 0.22285 > -0.14005 > 0.32460 > -0.12940 > 0.58775 > -0.13240 > -0.45095 > -0.12075 > 0.95505 > -0.12835 > -0.13485 > 0.36405 > -0.03600 > -0.24670 > -0.15305 > -0.05770 > how to interpret these values?? how can i extract any useful info with > this data set?? > any kind of help will be highly appreciated! > thanking you in advance.. > Ambrish K. Srivastava > ambrishphysics]~[gmail.com> > > -- Ronald L Cook Principal Scientist TDA Research, Inc. cookrl[A]tda.com 303-940-2302 --f46d0447f2ced140c904c978e926 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Ambrish

Most likely your problem is the use of the Mullikin charges.= =A0 They give unrealistic and incorrect values for charges.Take a look at <= br>
Condensation of Frontier Molecular Orbital Fukui Functions by Bulat = et al. J. Phys. Chem. A 2004, 108, 342-349
aper

"Possible negative values for the Fukui indexes have been<= br>discussed in the literature and considered as artifacts coming
from t= he condensation procedure12 or due to strong structural
distortions14 (s= ee also refs 13 and 15-17).
Thanikaivelan et al.18 have thoroughly studied the effects of
the popula= tion scheme and the basis set dependency of the Fukui
indexes within the= finite difference approximation eqs 9-11.
The most stable schemes up= on basis set modification turn out
to be the Atoms in Molecules (AIM)19 and the CHELPG
(charges from electr= ostatic potentials, using a grid-based
method),20 this last one bein= g based on the molecular electrostatic
potential (MESP) to derive the at= omic charges. Interestingly
enough, these two schemes provide also very similar Fukui
indexes and th= ey both predict appropriate reactivity sites for
all kinds of attacks (n= ucleophilic, electrophilic, and radical).
Although they note that Hirshf= eld partitioning provides in all
studied cases nonnegative Fukui indexes, as also stated by Roy
et al.,12= this fact cannot be generally extended since the
allowance of negative = values is in part a consequence of the
finite difference approximation. = Indeed, eqs 3-5 might be
negative at some points since FN+1(r) might be smaller than
FN(r) and FN= (r) might be smaller than FN-1(r). Hence, regardless
of the condensation= scheme chosen negative Fukui indexes
might appear. Furthermore, Hirshfe= ld partitioning fails to predict
the correct reactivity trends in some cases.12,18"

and their re= ferences

On Tue, Sep 11, 2012 at 11:39 AM= , AMBRISH KUMAR SRIVASTAVA ambrishphysics]^[gm= ail.com <owner-chemistry[A]ccl.net> wrote:

Sent to CCL by: "AMBRISH KUMAR SRIVASTAVA" [ambrishphysics_._gmail.com]
Respected all,
During calculation on fukui fn using mullikan atomic charges, i got a numbe= r of negative values for e.g. f0 values are given below:
-0.82305
-0.90080
=A00.22285
-0.14005
=A00.32460
-0.12940
=A00.58775
-0.13240
-0.45095
-0.12075
=A00.95505
-0.12835
-0.13485
=A00.36405
-0.03600
-0.24670
-0.15305
-0.05770
how to interpret these values?? how can i extract any useful info with this= data set??
any kind of help will be highly appreciated!
thanking you in advance..
Ambrish K. Srivastava
ambrishphysics]~[gmail.com



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY[A]ccl.n= et or use:
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--
Ronald L Cook
Princi= pal Scientist
TDA Research, Inc.
cookrl[A]tda.com
303-940-2302

--f46d0447f2ced140c904c978e926-- From owner-chemistry@ccl.net Thu Sep 13 03:13:00 2012 From: "Sergio Manzetti sergio.manzetti%%gmx.com" To: CCL Subject: CCL: Basis set Message-Id: <-47580-120913030844-5396-te7fFhUSIj947bS90MeKBQ:-:server.ccl.net> X-Original-From: "Sergio Manzetti" Content-Type: multipart/alternative; boundary="========GMXBoundary167041347520113209944" Date: Thu, 13 Sep 2012 09:08:32 +0200 MIME-Version: 1.0 Sent to CCL by: "Sergio Manzetti" [sergio.manzetti%x%gmx.com] --========GMXBoundary167041347520113209944 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 8bit SDD basis set, accordingly to default. However there are more accurate basis sets at: http://www.emsl.pnl.gov/forms/basisform.html Best wishes Sergio ----- Original Message ----- > From: quantum chem qchem66++gmail.com Sent: 09/13/12 04:36 AM To: Manzetti, Sergio Subject: CCL: Basis set Sent to CCL by: "quantum chem" [qchem66!A!gmail.com] Dear members, I would very much appreciate if anyone can let me know the exact/correct way of choosing a basis set for a DFT calculation.The system for study involves monomers/dimners of Ge/Se/As. regards thanks in advance to all qchttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--========GMXBoundary167041347520113209944 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: quoted-printable SDD basi= s set, accordingly to default. However there are more accurate basis sets a= t:
=20
=20 http://www.emsl.pnl.gov/forms/basisform.html
=20
=20 Best wishes
=20
=20 Sergio
=20
=20

=20 =C2=A0

=20
=20

=20 ----- = Original Message -----

=20

=20 From: = quantum chem qchem66++gmail.com

=20

=20 Sent: = 09/13/12 04:36 AM

=20

=20 To: Ma= nzetti, Sergio

=20

=20 Subjec= t: CCL: Basis set

=20
=20
=20
=20 
=20
Sent to CCL by: "quantum  chem" [qchem66!A!gmail.com]=20
Dear members,=20
               I would very much appreciate if anyone can let me know the=
=20
exact/correct way of choosing a basis set for a DFT calculation.The system =
for=20
study involves monomers/dimners of Ge/Se/As.=20
regards=20
thanks in advance to all=20
qc=20



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=20 --========GMXBoundary167041347520113209944-- From owner-chemistry@ccl.net Thu Sep 13 08:17:01 2012 From: "Patrick Bultinck patrick.bultinck^_^ugent.be" To: CCL Subject: CCL: regarding negative fukui function Message-Id: <-47581-120913024049-2440-2wRwpJ7st8wW+FLlbl6Vtg[*]server.ccl.net> X-Original-From: Patrick Bultinck Content-Type: multipart/alternative; boundary=Apple-Mail-1--155949529 Date: Thu, 13 Sep 2012 07:40:37 +0100 Mime-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: Patrick Bultinck [patrick.bultinck!A!ugent.be] --Apple-Mail-1--155949529 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=windows-1252 Colleagues, I think this is of enough general interest to allow for a CCL wide = reply. Negative Fukui functions have been a main focus in my work and = there is a lot of nonsense being written on it too. Let me summarize the = following points. 1. Fukui functions through space (not atom condensed) - Fukui functions can be negative and probably always are in some parts = of space. There is nothing strange there and I have proven it both = through observation and through a closed analytical mathematical proof. = There is nothing fancy there. If you extend the function to a matrix = form and diagonalize that, you see that negative eigenvalues MUST exist. = If they would at some point not be there at Hartree-Fock or DFT level, = your calculation is simply wrong. Whether you will actually see it in a = plot is another matter and depends on the eigenvectors (or rather their = mutual shape). - Same thing: do not use a frontier MO approximation. You miss the = physics of the business if you want to get into the details of negative = Fukui functions. There is, however, a simple explanation why FMO theory = works if you want to see only a big picture. Take a look at:=20 Bultinck, P.; Clarisse, D.; Ayers, P.W., Carbo-Dorca, R. The Fukui = matrix: a simple approach to the analysis of the Fukui function and its = positive character. Phys. Chem. Chem. Phys., 2011, 13, 6110=966115. Bultinck, P.; Van Neck, D.; Acke, G.; Ayers, P.W. Influence of electron = correlation on the Fukui matrix and extension of frontier molecular = orbital theory to correlated quantum chemical methods. Phys. Chem. Chem. = Phys., 2012, 14, 2408 - 2416. 2. Atom condensed Fukui functions - There are two ways to compute atom condensed Fukui functions that both = can be argumented for. There is a way in which you do not take into = account the change in atomic weights upon the change in number of = electrons and there is the way you do allow for it. This has been = discussed in detail in Bultinck, P.; Van Alsenoy, C.; Ayers, P.W.; = Carb=F3-Dorca, R. A critical analysis of the Hirshfeld atom in a = molecule. J. Chem. Phys., 2007, 126, 144111. - In general, I am reluctant to use the scheme that you say that the = atom condensed Fukui function is a difference in atomic charges. You = need to do the integral numerically (most often) yourself! Read the = original work of Yang and Mortier on atom condensed Fukui functions and = you will see that they say something like "provided atom condensing and = taking the derivative commute, ...". This is usually not the case, so = you should carefully consider what you do! I tend to be very wary of = charge difference based atom condensing. Actually; Mulliken is probably = the only scheme where this IS allowed!!! I agree with the late Richard = Bader that for atom condensing you need to condens the molecular = response and not compute the response of an atom in the molecule. Check = the above reference for details. - There have been lots of claims that stockholder/Hirshfeld atom = condensed Fukui functions would be "best" because they give fewest = negative values. This is wrong and a consequence of the fact that the = Hirshfeld method is arbitrary. You should use a Hirshfeld-I model which = is much closer in philosophy to the Bader scheme. If then you use the = right method (not difference in charges); you will get different = results. See Bultinck, P.; Van Alsenoy, C.; Ayers, P.W.; Carb=F3-Dorca, = R. A critical analysis of the Hirshfeld atom in a molecule. J. Chem. = Phys., 2007, 126, 144111. =20 3. Your calculations - It is hard to say anything on your results if you do not give a basis = set. Mulliken MAY be problematic but not necessarily. Too many people = just repeat what they read and never personally checked the properties = of the overlap matrix of their basis functions. - You may have found a very interesting case of oxidation of an atom = under global reduction. They ARE known to exist (check work by Melin and = Ayers)!!! - Your Fukui functions sum to minus 1 instead of 1, so try to sort that = out. There may be another error somewhere if you were a bit too careless = with checking whether your data fulfill the requirements for Fukui = functions. Feel free to contact me for more information personally. Patrick Bultinck On 11 Sep 2012, at 18:39, AMBRISH KUMAR SRIVASTAVA = ambrishphysics]^[gmail.com wrote: >=20 > Sent to CCL by: "AMBRISH KUMAR SRIVASTAVA" = [ambrishphysics_._gmail.com] > Respected all, > During calculation on fukui fn using mullikan atomic charges, i got a = number of negative values for e.g. f0 values are given below: > -0.82305 > -0.90080 > 0.22285 > -0.14005 > 0.32460 > -0.12940 > 0.58775 > -0.13240 > -0.45095 > -0.12075 > 0.95505 > -0.12835 > -0.13485 > 0.36405 > -0.03600 > -0.24670 > -0.15305 > -0.05770 > how to interpret these values?? how can i extract any useful info with = this data set?? > any kind of help will be highly appreciated! > thanking you in advance.. > Ambrish K. Srivastava > ambrishphysics]~[gmail.com >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please = change>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20 > Job: http://www.ccl.net/jobs=20 > Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20>=20 >=20 --Apple-Mail-1--155949529 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=windows-1252 Bultinck, P.; Clarisse, D.; Ayers, P.W., Carbo-Dorca, R. The Fukui matrix: a = simple approach to the analysis of the Fukui function and its positive character. Phys. = Chem. Chem. Phys., 2011, 13, 6110=966115.
Bultinck, P.; Van Neck, D.; Acke, G.; Ayers, P.W. Influence of electron = correlation on the Fukui matrix and extension of frontier molecular orbital theory to correlated quantum chemical methods. Phys. Chem. Chem. Phys., 2012, = 14, 2408 - = 2416.

2. Atom condensed Fukui functions
- There are two ways to compute atom condensed Fukui functions that = both can be argumented for. There is a way in which you do not take into = account the change in atomic weights upon the change in number of = electrons and there is the way you do allow for it. This has been = discussed in detail in Bultinck, P.; Van Alsenoy, C.; Ayers, P.W.; Carb=F3-Dorca, R. A critical analysis = of the Hirshfeld atom in a molecule. J. Chem. Phys., 2007, 126, 144111.
 - In general, I am reluctant to use the = scheme that you say that the atom condensed Fukui function is a = difference in atomic charges. You need to do the integral numerically = (most often) yourself! Read the original work of Yang and Mortier on = atom condensed Fukui functions and you will see that they say something = like "provided atom condensing and taking the derivative commute, ...". = This is usually not the case, so you should carefully consider what you = do! I tend to be very wary of charge difference based atom condensing. = Actually; Mulliken is probably the only scheme where this IS allowed!!! = I agree with the late Richard Bader that for atom condensing you need to = condens the molecular response and not compute the response of an atom = in the molecule. Check the above reference for = details.
- There have = been lots of claims that stockholder/Hirshfeld atom condensed Fukui = functions would be "best" because they give fewest negative values. This = is wrong and a consequence of the fact that the Hirshfeld method is = arbitrary. You should use a Hirshfeld-I model which is much closer in = philosophy to the Bader scheme. If then you use the right method (not = difference in charges); you will get different results. = See Bultinck, P.; Van Alsenoy, C.; Ayers, P.W.; Carb=F3-Dorca, R. A critical analysis = of the Hirshfeld atom in a molecule. J. = Chem. Phys., 2007, 126, 144111.
 
3. Your calculations
- It is hard to say anything on your = results if you do not give a basis set. Mulliken MAY be problematic but = not necessarily. Too many people just repeat what they read and never = personally checked the properties of the overlap matrix of their basis = functions.
- You may have found a very interesting case of = oxidation of an atom under global reduction. They ARE known to exist = (check work by Melin and Ayers)!!!
- Your Fukui functions sum = to minus 1 instead of 1, so try to sort that out. There may be another = error somewhere if you were a bit too careless with checking whether = your data fulfill the requirements for Fukui = functions.

Feel free to contact me for more = information personally.

Patrick = Bultinck

On 11 Sep 2012, at 18:39, AMBRISH KUMAR = SRIVASTAVA ambrishphysics]^[gmail.com wrote:


Sent to CCL by: "AMBRISH KUMAR SRIVASTAVA" = [ambrishphysics_._gmail.com]
Respected all,
During calculation on = fukui fn using mullikan atomic charges, i got a number of negative = values for e.g. f0 values are given below:
-0.82305
-0.90080
= 0.22285
-0.14005
0.32460
-0.12940
= 0.58775
-0.13240
-0.45095
-0.12075
= 0.95505
-0.12835
-0.13485
= 0.36405
-0.03600
-0.24670
-0.15305
-0.05770
how to = interpret these values?? how can i extract any useful info with this = data set??
any kind of help will be highly appreciated!
thanking = you in advance..
Ambrish K. = Srivastava
ambrishphysics]~[gmail.com



-=3D This is = automatically added to each message by the mailing script =3D-
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<= /div>
= --Apple-Mail-1--155949529-- From owner-chemistry@ccl.net Thu Sep 13 08:52:01 2012 From: "polosan silviu spol68(a)yahoo.com" To: CCL Subject: CCL: Basis set Message-Id: <-47582-120913041034-30836-EkwzxNliklKAj+VI0E2/vw-$-server.ccl.net> X-Original-From: polosan silviu Content-Type: multipart/alternative; boundary="-230932972-1832546562-1347523828=:62172" Date: Thu, 13 Sep 2012 01:10:28 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: polosan silviu [spol68(-)yahoo.com] ---230932972-1832546562-1347523828=:62172 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Colleagues, =A0 How it=A0looks the input file for adiabatic TD-DFT? Thank you. Dr. Silviu POLOSAN National Institute of Materials Physics e-mails: silv*_*infim.ro --- On Thu, 9/13/12, Sergio Manzetti sergio.manzetti%%gmx.com wrote: > From: Sergio Manzetti sergio.manzetti%%gmx.com Subject: CCL: Basis set To: "Polosan, Silviu Pavel " Date: Thursday, September 13, 2012, 10:08 AM SDD basis set, accordingly to default. However there are more accurate basi= s sets at: http://www.emsl.pnl.gov/forms/basisform.html Best wishes Sergio ----- Original Message ----- > From: quantum chem qchem66++gmail.com Sent: 09/13/12 04:36 AM To: Manzetti, Sergio=20 Subject: CCL: Basis set Sent to CCL by: "quantum chem" [qchem66!A!gmail.com] Dear members, I would = very much appreciate if anyone can let me know the exact/correct way of cho= osing a basis set for a DFT calculation.The system for study involves monom= ers/dimners of Ge/Se/As. regards thanks in advance to all qchttp://www.ccl.= net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtm= lhttp://www.ccl.net/spammers.txt--=3D=3D=3D=3D=3D=3D=3D=3DGMXBoundary167041= 347520113209944 Content-Type: text/html; charset=3D"utf-8" Content-Transfer-Encoding: quoted-printable SDD = basi=3D s set, accordingly to default. However there are more accurate basis sets a= =3D t:
=3D20
=3D20 http://www.emsl.pnl.gov/forms/basisform.html
=3D20
=3D20 Best wishes
=3D20
=3D20 Sergio
=3D20
=3D20

=3D20 =A0=A0=A0 =3DC2=3DA0

=3D20
=3D20 =A0=A0=A0

=3D20 =A0=A0=A0 =A0=A0=A0 ----- =3D Original Message -----

=3D20 =A0=A0=A0

=3D20 =A0=A0=A0 =A0=A0=A0 From: =3D quantum chem qchem66++gmail.com

=3D20 =A0=A0=A0

=3D20 =A0=A0=A0 =A0=A0=A0 Sent: =3D 09/13/12 04:36 AM

=3D20 =A0=A0=A0

=3D20 =A0=A0=A0 =A0=A0=A0 To: Ma=3D nzetti, Sergio

=3D20 =A0=A0=A0

=3D20 =A0=A0=A0 =A0=A0=A0 Subjec=3D t: CCL: Basis set

=3D20 =A0=A0=A0
=3D20 =A0=A0=A0
=3D20 =A0=A0=A0 =A0=A0=A0
=3D20 =A0=A0=A0 =A0=A0=A0 =A0=A0=A0 
=3D20
Sent to CCL by: "quantum=A0 chem" [qchem66!A!gmail.com]=3D20
Dear members,=3D20
=A0 =A0 =A0 =A0 =A0 =A0 =A0=A0=A0I would very much appreciate if anyone can=
 let me know the=3D
=3D20
exact/correct way of choosing a basis set for a DFT calculation.The system =
=3D
for=3D20
study involves monomers/dimners of Ge/Se/As.=3D20
regards=3D20
thanks in advance to all=3D20
qc=3D20



-=3D3D This is automatically added to each message by the mailing script =
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Job: http://www.ccl.net/jobs=3D20=3D20=3D20=3D20=3D20=3D20
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=3D20 ---230932972-1832546562-1347523828=:62172 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Colleagues,
 
How it looks the input file for adiabatic TD-DFT?
Thank you.

Dr. Silviu POLOSAN
National Institute of Material= s Physics
e-mails: silv*_*infim.ro

--- On Thu, 9/13/12, Sergio M= anzetti sergio.manzetti%%gmx.com <owner-chemistry*_*ccl.net>= wrote:

From: Sergio Manzetti sergio.manzetti%%gmx.com &l= t;owner-chemistry*_*ccl.net>
Subject: CCL: Basis set
To: "Polosan, S= ilviu Pavel " <spol68*_*yahoo.com>
Date: Thursday, September= 13, 2012, 10:08 AM

SDD basis set, accordingly to default. However there= are more accurate basis sets at:

http://www.emsl.pnl.gov/forms/basisf= orm.html

Best wishes

Sergio

----- Original Message= -----
> From: quantum chem qchem66++gmail.com
Sent: 09/13/12 04:3= 6 AM
To: Manzetti, Sergio
Subject: CCL: Basis set

Sent to CCL= by: "quantum chem" [qchem66!A!gmail.com] Dear members, I would very much a= ppreciate if anyone can let me know the exact/correct way of choosing a bas= is set for a DFT calculation.The system for study involves monomers/dimners= of Ge/Se/As. regards thanks in advance to all qchttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.= ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--=3D=3D=3D= =3D=3D=3D=3D=3DGMXBoundary167041347520113209944
Content-Type: text/h= tml; charset=3D"utf-8"
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<span style=3D3D'font-family:Verdana'><span style=3D3D'font-size= :12px'>SDD basi=3D
s set, accordingly to default. However there are m= ore accurate basis sets a=3D
t:<br />=3D20
<br />=3D20h= ttp://www.emsl.pnl.gov/forms/basisform.html<br />=3D20
<br = />=3D20
Best wishes<br />=3D20
<br />=3D20
Sergio&l= t;br />=3D20
<br />=3D20
<p style=3D3D"margin:0px; paddin= g:0px;" >=3D20
    =3DC2=3DA0</p>=3D20
<bl= ockquote style=3D3D"border-left: 1px solid #CCC; padding-left: 5px; margin= =3D
-left: 5px; margin-bottom: 0px; margin-top: 0px; margin-right: 0px;" type=3D
=3D3D"cite">=3D20
    = <p style=3D3D"margin:0px; padding:0px;" >=3D20
    =     <span style=3D3D"font-family:Verdana"><span sty= le=3D3D"font-size:12px">----- =3D
Original Message -----</span>= </span></p>=3D20
    <p style=3D3D"margin:= 0px; padding:0px;" >=3D20
        <s= pan style=3D3D"font-family:Verdana"><span style=3D3D"font-size:12px"&= gt;From: =3D
quantum chem qchem66++gmail.com</span></span>&l= t;/p>=3D20
    <p style=3D3D"margin:0px; padding:0p= x;" >=3D20
        <span style=3D3D"= font-family:Verdana"><span style=3D3D"font-size:12px">Sent: =3D09/13/12 04:36 AM</span></span></p>=3D20
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  =       <span style=3D3D"font-family:Verdana"><span style=3D3D"font-size:12px">= To: Ma=3D
nzetti, Sergio </span></span></p>=3D20
&n= bsp;   <p style=3D3D"margin:0px; padding:0px;" >=3D20
&n= bsp;       <span style=3D3D"font-family:Verdana= "><span style=3D3D"font-size:12px">Subjec=3D
t: CCL: Basis set&= lt;/span></span></p>=3D20
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         =    <pre style=3D3D"white-space: pre-wrap; word-wrap: break-wor= d; font-size:11=3D
;pre">=3D20
Sent to CCL by: "quantum  chem= " [qchem66!A!gmail.com]=3D20
Dear members,=3D20
      =          I would very much appreciate if anyo= ne can let me know the=3D
=3D20
exact/correct way of choosing a basis= set for a DFT calculation.The system =3D
for=3D20
study involves monomers/dimners of Ge/Se/As.=3D2= 0
regards=3D20
thanks in advance to all=3D20
qc=3D20


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---230932972-1832546562-1347523828=:62172-- From owner-chemistry@ccl.net Thu Sep 13 11:29:00 2012 From: "Trohalaki, Steven CTR USAF AFMC AFRL/RXPJE Steven.Trohalaki.ctr\a/wpafb.af.mil" To: CCL Subject: CCL: can't open PDB with TINKER GUI Message-Id: <-47583-120913100049-16588-tOdoSaJWM2tTwT+CjKzFxA#,#server.ccl.net> X-Original-From: "Trohalaki, Steven CTR USAF AFMC AFRL/RXPJE" Content-class: urn:content-classes:message Content-Type: multipart/signed; protocol="application/x-pkcs7-signature"; micalg=SHA1; boundary="----=_NextPart_000_0026_01CD9196.8C3D6C50" Date: Thu, 13 Sep 2012 10:00:09 -0400 MIME-Version: 1.0 Sent to CCL by: "Trohalaki, Steven CTR USAF AFMC AFRL/RXPJE" [Steven.Trohalaki.ctr-#-wpafb.af.mil] This is a multi-part message in MIME format. ------=_NextPart_000_0026_01CD9196.8C3D6C50 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit It appears that the tinker utility pdbxyz.x read the atom names from the Materials Studio PDB file and wrote them to the tinker.xyz file as it. This screwed up the formatting (tinker.xyz files are fixed format) because the atom names in the MS PDB contain the atom number, e.g., C123. Using the unix commands cut and paste, I was able to correct the format of my tinker.xyz files. FFE still wouldn't read it, however, until I replaced the atom types (pdbxyz.x wrote them all as zero) with non-zero integers. Now, I'm trying to use MOLDEN to assign atom types but I'm not having any luck; MOLDEN replaces my non-zero atom-type integers with zeros! It looks like I'll have to do it manually. Luckily, I get paid by the hour (although maybe not for long). Steve T -----Original Message----- > From: owner-chemistry+steven.trohalaki==wpafb.af.mil(-)ccl.net [mailto:owner-chemistry+steven.trohalaki==wpafb.af.mil(-)ccl.net] On Behalf Of Steven Trohalaki steven.trohalaki###wpafb.af.mil Sent: Monday, September 10, 2012 11:39 AM To: Trohalaki, Steven CTR USAF AFMC AFRL/RXPJE Subject: CCL: can't open PDB with TINKER GUI Sent to CCL by: "Steven Trohalaki" [steven.trohalaki[*]wpafb.af.mil] Im trying to import into FFE (TINKERs GUI) a structure I made with Materials Studio. I saved the Materials Studio structure as a PDB file. If I use the TINKER utility pdbxyz.x, I get a tinker.xyz file but when I try to open it in FFE, I get a blank screen and no Structural Hierarchy on the left side of the FFE display. Making up a tinker.key file before I try opening the tinker.xyz file doesnt help. I can open my PDB file directly with FFE. I am prompted to select a force field, I see a structure, and I see a Structural Hierarchy. Clicking on Keyword Editor allows me to select keywords and values for the keywords. However, when I click on Modeling Commands, the only commands I see are NUCEIC, PDBXYZ, and PROTEIN, i.e., I dont see Optimize, Dynamics, etc. I do see all of the Modeling Commands if I open one of the example files provided for TINKER, e.g., alkane.xyz. Id be obliged if anyone can tell me if Im doing anything wrong or if they have a work-around. Thanks. Steve Thttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt------=_NextPart_000_0026_01CD9196.8C3D6C50 Content-Type: application/x-pkcs7-signature; name="smime.p7s" Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="smime.p7s" MIAGCSqGSIb3DQEHAqCAMIACAQExCzAJBgUrDgMCGgUAMIAGCSqGSIb3DQEHAQAAoIISnzCCA3Aw ggJYoAMCAQICAQUwDQYJKoZIhvcNAQEFBQAwWzELMAkGA1UEBhMCVVMxGDAWBgNVBAoTD1UuUy4g R292ZXJubWVudDEMMAoGA1UECxMDRG9EMQwwCgYDVQQLEwNQS0kxFjAUBgNVBAMTDURvRCBSb290 IENBIDIwHhcNMDQxMjEzMTUwMDEwWhcNMjkxMjA1MTUwMDEwWjBbMQswCQYDVQQGEwJVUzEYMBYG A1UEChMPVS5TLiBHb3Zlcm5tZW50MQwwCgYDVQQLEwNEb0QxDDAKBgNVBAsTA1BLSTEWMBQGA1UE AxMNRG9EIFJvb3QgQ0EgMjCCASIwDQYJKoZIhvcNAQEBBQADggEPADCCAQoCggEBAMAswfaNO6z/ PzzWcb64dCIH7HBBFfyrQOMHqsHD2J/+2kw6vz/I2Ch7SzYBwKxFJcPSDgqPhRhkED0aE3Aqb47X 3I2Ts0EPOCHNravCPSoF01cRNw3NjFH5k+PMRkkhjhS0zcsUPjjNcjHuqxLyZeo0LlZd/+5jdctt 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owner-chemistry@ccl.net Thu Sep 13 12:04:00 2012 From: "Nicolas Grimblat nicogreen6---gmail.com" To: CCL Subject: CCL: Frequency Calculation Problem Message-Id: <-47584-120913101358-20353-g+3iEiTj97mLdIi6YyzI3Q~~server.ccl.net> X-Original-From: "Nicolas Grimblat" Date: Thu, 13 Sep 2012 10:13:40 -0400 Sent to CCL by: "Nicolas Grimblat" [nicogreen6()gmail.com] Dear All, Mi name is Nicolas and im having problems with a frequency calculation (B3LYP/6-311+G**). It is TS with 55 heavy atoms. The opt went fine, though the frequency gives me this error, not mem nor Disk space. I try splitting the RWF and the same. Every time i restart the job it take less than 20 minutes to stop. This is the last part of the log Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. Requested convergence on MAX density matrix=1.00D-06. Requested convergence on energy=1.00D-06. No special actions if energy rises. SCF Done: E(RB3LYP) = -2017.79900374 A.U. after 5 cycles Convg = 0.5751D-08 -V/T = 2.0041 Range of M.O.s used for correlation: 1 1166 NBasis= 1176 NAE= 158 NBE= 158 NFC= 0 NFV= 0 NROrb= 1166 NOA= 158 NOB= 158 NVA= 1008 NVB= 1008 **** Warning!!: The largest alpha MO coefficient is 0.11183179D+03 **** Warning!!: The smallest alpha delta epsilon is 0.96445386D-01 PrsmSu: requested number of processors reduced to: 2 ShMem 1 Linda. Symmetrizing basis deriv contribution to polar: IMax=3 JMax=2 DiffMx= 0.00D+00 G2DrvN: will do 39 centers at a time, making 2 passes doing MaxLOS=2. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. FoFDir/FoFCou used for L=0 through L=2. End of G2Drv Frequency-dependent properties file 721 does not exist. End of G2Drv Frequency-dependent properties file 722 does not exist. IDoAtm=11111111111111111111111111111111111111111111111111 IDoAtm=11111111111111111111111111 Differentiating once with respect to electric field. with respect to dipole field. Differentiating once with respect to nuclear coordinates. There are 231 degrees of freedom in the 1st order CPHF. IDoFFX=5. 231 vectors produced by pass 0 Test12= 1.59D-13 1.00D-09 XBig12= 9.19D+02 2.16D+01. AX will form 72 AO Fock derivatives at one time. 231 vectors produced by pass 1 Test12= 1.59D-13 1.00D-09 XBig12= 1.99D+02 1.76D+00. 228 vectors produced by pass 2 Test12= 1.59D-13 1.00D-09 XBig12= 1.83D+00 1.32D-01. 228 vectors produced by pass 3 Test12= 1.59D-13 1.00D-09 XBig12= 7.57D- 03 7.43D-03. 228 vectors produced by pass 4 Test12= 1.59D-13 1.00D-09 XBig12= 1.92D- 05 2.86D-04. 228 vectors produced by pass 5 Test12= 1.59D-13 1.00D-09 XBig12= 3.40D- 08 1.26D-05. 228 vectors produced by pass 6 Test12= 1.59D-13 1.00D-09 XBig12= 9.44D- 11 7.42D-07. 221 vectors produced by pass 7 Test12= 1.59D-13 1.00D-09 XBig12= 5.41D- 12 8.45D-08. 197 vectors produced by pass 8 Test12= 1.59D-13 1.00D-09 XBig12= 2.09D- 13 1.63D-08. 189 vectors produced by pass 9 Test12= 1.59D-13 1.00D-09 XBig12= 1.97D- 13 1.28D-08. 181 vectors produced by pass 10 Test12= 1.59D-13 1.00D-09 XBig12= 2.21D- 13 1.42D-08. 169 vectors produced by pass 11 Test12= 1.59D-13 1.00D-09 XBig12= 2.06D- 13 1.39D-08. 166 vectors produced by pass 12 Test12= 1.59D-13 1.00D-09 XBig12= 1.99D- 13 1.23D-08. 163 vectors produced by pass 13 Test12= 1.59D-13 1.00D-09 XBig12= 2.15D- 13 1.46D-08. 160 vectors produced by pass 14 Test12= 1.59D-13 1.00D-09 XBig12= 2.40D- 13 1.60D-08. 153 vectors produced by pass 15 Test12= 1.59D-13 1.00D-09 XBig12= 1.52D- 13 1.10D-08. 143 vectors produced by pass 16 Test12= 1.59D-13 1.00D-09 XBig12= 1.20D- 13 1.00D-08. 140 vectors produced by pass 17 Test12= 1.59D-13 1.00D-09 XBig12= 1.73D- 13 1.20D-08. 128 vectors produced by pass 18 Test12= 1.59D-13 1.00D-09 XBig12= 6.11D- 14 6.27D-09. 125 vectors produced by pass 19 Test12= 1.59D-13 1.00D-09 XBig12= 1.61D- 13 1.02D-08. 122 vectors produced by pass 20 Test12= 1.59D-13 1.00D-09 XBig12= 8.38D- 14 8.19D-09. 119 vectors produced by pass 21 Test12= 1.59D-13 1.00D-09 XBig12= 1.04D- 13 8.74D-09. 116 vectors produced by pass 22 Test12= 1.59D-13 1.00D-09 XBig12= 1.11D- 13 8.05D-09. 106 vectors produced by pass 23 Test12= 1.59D-13 1.00D-09 XBig12= 1.13D- 13 9.33D-09. 103 vectors produced by pass 24 Test12= 1.59D-13 1.00D-09 XBig12= 8.44D- 14 7.37D-09. 100 vectors produced by pass 25 Test12= 1.59D-13 1.00D-09 XBig12= 9.25D- 14 7.94D-09. 97 vectors produced by pass 26 Test12= 1.59D-13 1.00D-09 XBig12= 7.03D- 14 7.25D-09. 77 vectors produced by pass 27 Test12= 1.59D-13 1.00D-09 XBig12= 4.23D- 14 4.95D-09. 72 vectors produced by pass 28 Test12= 1.59D-13 1.00D-09 XBig12= 5.22D- 14 6.32D-09. 72 vectors produced by pass 29 Test12= 1.59D-13 1.00D-09 XBig12= 2.55D- 14 4.00D-09. 72 vectors produced by pass 30 Test12= 1.59D-13 1.00D-09 XBig12= 3.07D- 14 4.27D-09. 72 vectors produced by pass 31 Test12= 1.59D-13 1.00D-09 XBig12= 5.50D- 14 6.24D-09. 72 vectors produced by pass 32 Test12= 1.59D-13 1.00D-09 XBig12= 3.93D- 14 4.71D-09. 72 vectors produced by pass 33 Test12= 1.59D-13 1.00D-09 XBig12= 3.14D- 14 4.15D-09. 72 vectors produced by pass 34 Test12= 1.59D-13 1.00D-09 XBig12= 3.70D- 14 4.81D-09. 65 vectors produced by pass 35 Test12= 1.59D-13 1.00D-09 XBig12= 2.29D- 14 3.51D-09. 63 vectors produced by pass 36 Test12= 1.59D-13 1.00D-09 XBig12= 2.53D- 14 3.72D-09. 63 vectors produced by pass 37 Test12= 1.59D-13 1.00D-09 XBig12= 2.95D- 14 3.94D-09. 63 vectors produced by pass 38 Test12= 1.59D-13 1.00D-09 XBig12= 3.01D- 14 4.02D-09. 56 vectors produced by pass 39 Test12= 1.59D-13 1.00D-09 XBig12= 2.14D- 14 3.62D-09. 56 vectors produced by pass 40 Test12= 1.59D-13 1.00D-09 XBig12= 2.67D- 14 3.63D-09. 54 vectors produced by pass 41 Test12= 1.59D-13 1.00D-09 XBig12= 2.36D- 14 3.52D-09. 54 vectors produced by pass 42 Test12= 1.59D-13 1.00D-09 XBig12= 2.44D- 14 3.53D-09. 54 vectors produced by pass 43 Test12= 1.59D-13 1.00D-09 XBig12= 3.22D- 14 4.90D-09. 52 vectors produced by pass 44 Test12= 1.59D-13 1.00D-09 XBig12= 2.29D- 14 3.68D-09. 48 vectors produced by pass 45 Test12= 1.59D-13 1.00D-09 XBig12= 2.11D- 14 3.09D-09. 32 vectors produced by pass 46 Test12= 1.59D-13 1.00D-09 XBig12= 1.28D- 14 2.61D-09. 32 vectors produced by pass 47 Test12= 1.59D-13 1.00D-09 XBig12= 1.79D- 14 2.81D-09. 24 vectors produced by pass 48 Test12= 1.59D-13 1.00D-09 XBig12= 1.35D- 14 2.45D-09. 24 vectors produced by pass 49 Test12= 1.59D-13 1.00D-09 XBig12= 3.11D- 14 4.08D-09. 24 vectors produced by pass 50 Test12= 1.59D-13 1.00D-09 XBig12= 1.88D- 14 2.97D-09. 24 vectors produced by pass 51 Test12= 1.59D-13 1.00D-09 XBig12= 3.07D- 14 3.81D-09. 24 vectors produced by pass 52 Test12= 1.59D-13 1.00D-09 XBig12= 1.80D- 14 2.88D-09. 24 vectors produced by pass 53 Test12= 1.59D-13 1.00D-09 XBig12= 2.54D- 14 3.87D-09. 21 vectors produced by pass 54 Test12= 1.59D-13 1.00D-09 XBig12= 1.85D- 14 3.46D-09. 21 vectors produced by pass 55 Test12= 1.59D-13 1.00D-09 XBig12= 2.56D- 14 3.68D-09. 21 vectors produced by pass 56 Test12= 1.59D-13 1.00D-09 XBig12= 3.29D- 14 3.80D-09. 9 vectors produced by pass 57 Test12= 1.59D-13 1.00D-09 XBig12= 8.17D- 15 2.36D-09. 9 vectors produced by pass 58 Test12= 1.59D-13 1.00D-09 XBig12= 2.91D- 14 4.46D-09. 9 vectors produced by pass 59 Test12= 1.59D-13 1.00D-09 XBig12= 7.03D- 15 2.01D-09. 9 vectors produced by pass 60 Test12= 1.59D-13 1.00D-09 XBig12= 2.16D- 14 3.52D-09. 9 vectors produced by pass 61 Test12= 1.59D-13 1.00D-09 XBig12= 2.01D- 14 3.70D-09. 9 vectors produced by pass 62 Test12= 1.59D-13 1.00D-09 XBig12= 1.27D- 14 3.02D-09. 9 vectors produced by pass 63 Test12= 1.59D-13 1.00D-09 XBig12= 1.52D- 14 2.98D-09. 9 vectors produced by pass 64 Test12= 1.59D-13 1.00D-09 XBig12= 2.72D- 14 4.11D-09. 9 vectors produced by pass 65 Test12= 1.59D-13 1.00D-09 XBig12= 1.04D- 14 2.39D-09. 9 vectors produced by pass 66 Test12= 1.59D-13 1.00D-09 XBig12= 1.63D- 14 3.22D-09. 9 vectors produced by pass 67 Test12= 1.59D-13 1.00D-09 XBig12= 1.38D- 14 2.73D-09. 9 vectors produced by pass 68 Test12= 1.59D-13 1.00D-09 XBig12= 2.09D- 14 3.07D-09. 9 vectors produced by pass 69 Test12= 1.59D-13 1.00D-09 XBig12= 1.59D- 14 2.71D-09. 7 vectors produced by pass 70 Test12= 1.59D-13 1.00D-09 XBig12= 8.67D- 15 2.09D-09. 7 vectors produced by pass 71 Test12= 1.59D-13 1.00D-09 XBig12= 1.53D- 14 2.73D-09. 7 vectors produced by pass 72 Test12= 1.59D-13 1.00D-09 XBig12= 3.39D- 14 3.84D-09. 7 vectors produced by pass 73 Test12= 1.59D-13 1.00D-09 XBig12= 1.40D- 14 2.62D-09. 7 vectors produced by pass 74 Test12= 1.59D-13 1.00D-09 XBig12= 1.48D- 14 3.07D-09. 5 vectors produced by pass 75 Test12= 1.59D-13 1.00D-09 XBig12= 5.66D- 15 2.01D-09. Applied DIIS recursively to reduced A of dimension 6137. Erroneous write. Write 1407176 instead of 2454800. fd = 4 orig len = 2454800 left = 2454800 g_write Any suggestions would be fine =D Thank you all From owner-chemistry@ccl.net Thu Sep 13 12:39:00 2012 From: "Uwe Huniar huniar() cosmologic.de" To: CCL Subject: CCL:G: Basis set Message-Id: <-47585-120913105201-23977-l0o1/zYzWwGvVfzY6L4t+Q()server.ccl.net> X-Original-From: Uwe Huniar Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 13 Sep 2012 16:51:45 +0200 MIME-Version: 1.0 Sent to CCL by: Uwe Huniar [huniar~~cosmologic.de] Hello, > How it looks the input file for adiabatic TD-DFT? then some diffuse basis functions should be included. An optimized set of double-, triple- and quadruple-zeta quality for such purposes has been published (for example) here: "Property-optimized Gaussian basis sets for molecular response calculations", D. Rappoport and F. Furche, J. Chem. Phys. 133, 134105 (2010) (http://dx.doi.org/10.1063/1.3484283) on the EMSL Basis Set Exchange web site just select Def2-SVPD, Def2-TZVPD, Def2-TZVPPD, Def2-QZVPD or Def2-QZVPPD. Regards, Uwe > > Dr. Silviu POLOSAN > National Institute of Materials Physics > e-mails: silv]^[infim.ro > > --- On Thu, 9/13/12, Sergio Manzetti sergio.manzetti%%gmx.com wrote: > > >> From: Sergio Manzetti sergio.manzetti%%gmx.com > Subject: CCL: Basis set > To: "Polosan, Silviu Pavel " > Date: Thursday, September 13, 2012, 10:08 AM > > > SDD basis set, accordingly to default. However there are more accurate basis sets at: > > http://www.emsl.pnl.gov/forms/basisform.html > > Best wishes > > Sergio > > ----- Original Message ----- >> From: quantum chem qchem66++gmail.com > Sent: 09/13/12 04:36 AM > To: Manzetti, Sergio > Subject: CCL: Basis set > > Sent to CCL by: "quantum chem" [qchem66!A!gmail.com] Dear members, I would very much appreciate if anyone can let me know the exact/correct way of choosing a basis set for a DFT calculation.The system for study involves monomers/dimners of Ge/Se/As. regards thanks in advance to all qchttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--========GMXBoundary167041347520113209944 > Content-Type: text/html; charset="utf-8" > Content-Transfer-Encoding: quoted-printable > > SDD basi= > s set, accordingly to default. However there are more accurate basis sets a= > t:
=20 >
=20 > http://www.emsl.pnl.gov/forms/basisform.html
=20 >
=20 > Best wishes
=20 >
=20 > Sergio
=20 >
=20 >

=20 > =C2=A0

=20 >
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=20 > ----- = > Original Message -----

=20 >

=20 > From: = > quantum chem qchem66++gmail.com

=20 >

=20 > Sent: = > 09/13/12 04:36 AM

=20 >

=20 > To: Ma= > nzetti, Sergio

=20 >

=20 > Subjec= > t: CCL: Basis set

=20 >
=20 >
=20 >
=20 > 
 ;pre">=20
> Sent to CCL by: "quantum  chem" [qchem66!A!gmail.com]=20
> Dear members,=20
>                 I would very much appreciate if anyone can let me know the=
> =20
> exact/correct way of choosing a basis set for a DFT calculation.The system =
> for=20
> study involves monomers/dimners of Ge/Se/As.=20
> regards=20
> thanks in advance to all=20
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=20 > > -- ------------------------------------------------------------------------------ Dr. Uwe Huniar COSMOlogic GmbH & Co. KG Burscheider Strasse 515 D-51381 Leverkusen, Germany phone +49-2171-363665 fax +49-2171-731689 e-mail huniar_._cosmologic.de turbomole_._cosmologic.de info_._turbomole.com web www.cosmologic.de HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt Join us at the 4th-COSMO-RS-Symposium April 2013 Details at www.cosmologic.de/symposium2013 From owner-chemistry@ccl.net Thu Sep 13 13:13:00 2012 From: "Adam Tenderholt atenderholt(~)gmail.com" To: CCL Subject: CCL:G: how to calculate CDA using QMForge Message-Id: <-47586-120913120117-16108-5Y/agRz78fFWEI5k3pXuMA^^^server.ccl.net> X-Original-From: Adam Tenderholt Content-Type: multipart/alternative; boundary=e89a8f8398710d873f04c9976a3e Date: Thu, 13 Sep 2012 09:00:41 -0700 MIME-Version: 1.0 Sent to CCL by: Adam Tenderholt [atenderholt|*|gmail.com] --e89a8f8398710d873f04c9976a3e Content-Type: text/plain; charset=ISO-8859-1 Hi, Sorry that using QMForge for CDA isn't clear. The steps are: 1) Open the entire molecule log file. 2) Choose Calculate->Fragment Analysis->Charge Decomposition... from the menu. 3) Select your fragment log files. Keep in mind that the atom order and coordinates of the fragment files need to match the molecule file. You can find example Gaussian logfiles for BH3CO at http://cclib.svn.sourceforge.net/viewvc/cclib/trunk/data/Gaussian/CDA/. Hope that helps, Adam On Wed, Sep 12, 2012 at 11:15 AM, R V solo rvsolo*o*gmail.com < owner-chemistry[a]ccl.net> wrote: > > Sent to CCL by: "R V solo" [rvsolo]*[gmail.com] > Dear CCLers, > > I would like to do Charge Decomposition Analysis (CDA)using > QMForge and i am using G09. Can any one tell the procedure to do CDA? > Looking forward for your answers... > > yours > > rvsolo> > > --e89a8f8398710d873f04c9976a3e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,

Sorry that using QMForge for CDA isn't clear. Th= e steps are:

1) Open the entire molecule log file.=
2) Choose Calculate->Fragment Analysis->Charge Decompositi= on... from the menu.
3) Select your fragment log files.

Keep in mi= nd that the atom order and coordinates of the fragment files need to match = the molecule file. You can find example Gaussian logfiles for BH3CO at=A0http://cclib.svn.sourceforge.net/viewvc/cclib/trunk/data/Gaussian/CDA= /.

Hope that helps,

Adam

On Wed, Sep 12, 2012 at 11:15 AM, R V solo= rvsolo*o*gmail.com <= owner-chemistr= y[a]ccl.net> wrote:

Sent to CCL by: "R V solo" [rvsolo]*[gmail.com]
Dear CCLers,

=A0 =A0 =A0 =A0 =A0 =A0 =A0I would like to do Charge Decomposition Analysis= (CDA)using QMForge and i am using G09. Can any one tell the procedure to d= o CDA?
Looking forward for your answers...

yours

rvsolo



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--e89a8f8398710d873f04c9976a3e-- From owner-chemistry@ccl.net Thu Sep 13 13:48:00 2012 From: "Amy Austin amy_jean_austin^^^yahoo.com" To: CCL Subject: CCL: Frequency Calculation Problem Message-Id: <-47587-120913130710-11051-E3WtGHbaLEH05xV9upREtA|server.ccl.net> X-Original-From: Amy Austin Content-Type: multipart/alternative; boundary="-244526598-550607804-1347556019=:4492" Date: Thu, 13 Sep 2012 10:06:59 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Amy Austin [amy_jean_austin-,-yahoo.com] ---244526598-550607804-1347556019=:4492 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi Nicolas,=0A=A0=0AAre you setting your disk (MaxDisk) and memory (%mem) h= igh enough? Unless you use %mem the default is only 256MB. =0A=A0=0AOn a si= de note, if you can afford the CPU time, you may want to reconsider using a= DFT for transition state studies. The geometries are good, but the energie= s are underestimated which will affect the quality of barrier height predic= tions.=0A=A0=0AHope this helps!=0A=A0=0AAmy=0A=0A=0A_______________________= _________=0AFrom: Nicolas Grimblat nicogreen6---gmail.com =0ATo: "Austin, Amy J " =0ASent= : Thursday, September 13, 2012 10:13 AM=0ASubject: CCL: Frequency Calculati= on Problem=0A=0A=0ASent to CCL by: "Nicolas=A0 Grimblat" [nicogreen6()gmail= .com]=0ADear All,=0A=0AMi name is Nicolas and im having problems with a fre= quency calculation =0A(B3LYP/6-311+G**). It is TS with 55 heavy atoms. The = opt went fine, though =0Athe frequency gives me this error, not mem nor Dis= k space. I try splitting =0Athe RWF and the same. Every time i restart the = job it take less than 20 =0Aminutes to stop.=0AThis is the last part of the= log=0A=0ARequested convergence on RMS density matrix=3D1.00D-08 within 128= cycles.=0ARequested convergence on MAX density matrix=3D1.00D-06.=0AReques= ted convergence on=A0 =A0 =A0 =A0 =A0 =A0 energy=3D1.00D-06.=0ANo special a= ctions if energy rises.=0ASCF Done:=A0 E(RB3LYP) =3D=A0 -2017.79900374=A0 = =A0 A.U. after=A0 =A0 5 cycles=0A=A0 =A0 =A0 =A0 =A0 =A0 Convg=A0 =3D=A0 = =A0 0.5751D-08=A0 =A0 =A0 =A0 =A0 =A0 -V/T =3D=A0 2.0041=0ARange of M.O.s u= sed for correlation:=A0 =A0 1=A0 1166=0ANBasis=3D=A0 1176 NAE=3D=A0 158 NBE= =3D=A0 158 NFC=3D=A0 =A0 0 NFV=3D=A0 =A0 0=0ANROrb=3D=A0 1166 NOA=3D=A0 158= NOB=3D=A0 158 NVA=3D=A0 1008 NVB=3D=A0 1008=0A=0A**** Warning!!: The large= st alpha MO coefficient is=A0 0.11183179D+03=0A=0A=0A**** Warning!!: The sm= allest alpha delta epsilon is=A0 0.96445386D-01=0A=0APrsmSu:=A0 requested n= umber of processors reduced to:=A0 2 ShMem=A0 1 Linda.=0ASymmetrizing basis= deriv contribution to polar:=0AIMax=3D3 JMax=3D2 DiffMx=3D 0.00D+00=0AG2Dr= vN: will do=A0 =A0 39 centers at a time, making=A0 =A0 2 passes doing MaxLO= S=3D2.=0ACalling FoFCou, ICntrl=3D=A0 3107 FMM=3DT I1Cent=3D=A0 0 AccDes=3D= 0.00D+00.=0ACalling FoFCou, ICntrl=3D=A0 3107 FMM=3DT I1Cent=3D=A0 0 AccDe= s=3D 0.00D+00.=0AFoFDir/FoFCou used for L=3D0 through L=3D2.=0AEnd of G2Drv= Frequency-dependent properties file=A0 721 does not exist.=0AEnd of G2Drv = Frequency-dependent properties file=A0 722 does not exist.=0A=A0 =A0 =A0 = =A0 =A0 IDoAtm=3D11111111111111111111111111111111111111111111111111=0A=A0 = =A0 =A0 =A0 =A0 IDoAtm=3D11111111111111111111111111=0A=A0 =A0 =A0 =A0 =A0 D= ifferentiating once with respect to electric field.=0A=A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 with respect to dipole field.=0A=A0 =A0 =A0 =A0 =A0 Differentia= ting once with respect to nuclear coordinates.=0A=A0 =A0 =A0 =A0 =A0 There = are=A0 231 degrees of freedom in the 1st order CPHF.=A0 =0AIDoFFX=3D5.=0A= =A0 =A0 231 vectors produced by pass=A0 0 Test12=3D 1.59D-13 1.00D-09 XBig1= 2=3D =0A9.19D+02 2.16D+01.=0AAX will form=A0 =A0 72 AO Fock derivatives at = one time.=0A=A0 =A0 231 vectors produced by pass=A0 1 Test12=3D 1.59D-13 1.= 00D-09 XBig12=3D =0A1.99D+02 1.76D+00.=0A=A0 =A0 228 vectors produced by pa= ss=A0 2 Test12=3D 1.59D-13 1.00D-09 XBig12=3D =0A1.83D+00 1.32D-01.=0A=A0 = =A0 228 vectors produced by pass=A0 3 Test12=3D 1.59D-13 1.00D-09 XBig12=3D= 7.57D-=0A03 7.43D-03.=0A=A0 =A0 228 vectors produced by pass=A0 4 Test12= =3D 1.59D-13 1.00D-09 XBig12=3D 1.92D-=0A05 2.86D-04.=0A=A0 =A0 228 vectors= produced by pass=A0 5 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 3.40D-=0A08 1.= 26D-05.=0A=A0 =A0 228 vectors produced by pass=A0 6 Test12=3D 1.59D-13 1.00= D-09 XBig12=3D 9.44D-=0A11 7.42D-07.=0A=A0 =A0 221 vectors produced by pass= =A0 7 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 5.41D-=0A12 8.45D-08.=0A=A0 =A0= 197 vectors produced by pass=A0 8 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 2.= 09D-=0A13 1.63D-08.=0A=A0 =A0 189 vectors produced by pass=A0 9 Test12=3D 1= .59D-13 1.00D-09 XBig12=3D 1.97D-=0A13 1.28D-08.=0A=A0 =A0 181 vectors prod= uced by pass 10 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 2.21D-=0A13 1.42D-08.= =0A=A0 =A0 169 vectors produced by pass 11 Test12=3D 1.59D-13 1.00D-09 XBig= 12=3D 2.06D-=0A13 1.39D-08.=0A=A0 =A0 166 vectors produced by pass 12 Test1= 2=3D 1.59D-13 1.00D-09 XBig12=3D 1.99D-=0A13 1.23D-08.=0A=A0 =A0 163 vector= s produced by pass 13 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 2.15D-=0A13 1.4= 6D-08.=0A=A0 =A0 160 vectors produced by pass 14 Test12=3D 1.59D-13 1.00D-0= 9 XBig12=3D 2.40D-=0A13 1.60D-08.=0A=A0 =A0 153 vectors produced by pass 15= Test12=3D 1.59D-13 1.00D-09 XBig12=3D 1.52D-=0A13 1.10D-08.=0A=A0 =A0 143 = vectors produced by pass 16 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 1.20D-=0A= 13 1.00D-08.=0A=A0 =A0 140 vectors produced by pass 17 Test12=3D 1.59D-13 1= .00D-09 XBig12=3D 1.73D-=0A13 1.20D-08.=0A=A0 =A0 128 vectors produced by p= ass 18 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 6.11D-=0A14 6.27D-09.=0A=A0 = =A0 125 vectors produced by pass 19 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 1= .61D-=0A13 1.02D-08.=0A=A0 =A0 122 vectors produced by pass 20 Test12=3D 1.= 59D-13 1.00D-09 XBig12=3D 8.38D-=0A14 8.19D-09.=0A=A0 =A0 119 vectors produ= ced by pass 21 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 1.04D-=0A13 8.74D-09.= =0A=A0 =A0 116 vectors produced by pass 22 Test12=3D 1.59D-13 1.00D-09 XBig= 12=3D 1.11D-=0A13 8.05D-09.=0A=A0 =A0 106 vectors produced by pass 23 Test1= 2=3D 1.59D-13 1.00D-09 XBig12=3D 1.13D-=0A13 9.33D-09.=0A=A0 =A0 103 vector= s produced by pass 24 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 8.44D-=0A14 7.3= 7D-09.=0A=A0 =A0 100 vectors produced by pass 25 Test12=3D 1.59D-13 1.00D-0= 9 XBig12=3D 9.25D-=0A14 7.94D-09.=0A=A0 =A0 97 vectors produced by pass 26 = Test12=3D 1.59D-13 1.00D-09 XBig12=3D 7.03D-=0A14 7.25D-09.=0A=A0 =A0 77 ve= ctors produced by pass 27 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 4.23D-=0A14= 4.95D-09.=0A=A0 =A0 72 vectors produced by pass 28 Test12=3D 1.59D-13 1.00= D-09 XBig12=3D 5.22D-=0A14 6.32D-09.=0A=A0 =A0 72 vectors produced by pass = 29 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 2.55D-=0A14 4.00D-09.=0A=A0 =A0 72= vectors produced by pass 30 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 3.07D-= =0A14 4.27D-09.=0A=A0 =A0 72 vectors produced by pass 31 Test12=3D 1.59D-13= 1.00D-09 XBig12=3D 5.50D-=0A14 6.24D-09.=0A=A0 =A0 72 vectors produced by = pass 32 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 3.93D-=0A14 4.71D-09.=0A=A0 = =A0 72 vectors produced by pass 33 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 3.= 14D-=0A14 4.15D-09.=0A=A0 =A0 72 vectors produced by pass 34 Test12=3D 1.59= D-13 1.00D-09 XBig12=3D 3.70D-=0A14 4.81D-09.=0A=A0 =A0 65 vectors produced= by pass 35 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 2.29D-=0A14 3.51D-09.=0A= =A0 =A0 63 vectors produced by pass 36 Test12=3D 1.59D-13 1.00D-09 XBig12= =3D 2.53D-=0A14 3.72D-09.=0A=A0 =A0 63 vectors produced by pass 37 Test12= =3D 1.59D-13 1.00D-09 XBig12=3D 2.95D-=0A14 3.94D-09.=0A=A0 =A0 63 vectors = produced by pass 38 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 3.01D-=0A14 4.02D= -09.=0A=A0 =A0 56 vectors produced by pass 39 Test12=3D 1.59D-13 1.00D-09 X= Big12=3D 2.14D-=0A14 3.62D-09.=0A=A0 =A0 56 vectors produced by pass 40 Tes= t12=3D 1.59D-13 1.00D-09 XBig12=3D 2.67D-=0A14 3.63D-09.=0A=A0 =A0 54 vecto= rs produced by pass 41 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 2.36D-=0A14 3.= 52D-09.=0A=A0 =A0 54 vectors produced by pass 42 Test12=3D 1.59D-13 1.00D-0= 9 XBig12=3D 2.44D-=0A14 3.53D-09.=0A=A0 =A0 54 vectors produced by pass 43 = Test12=3D 1.59D-13 1.00D-09 XBig12=3D 3.22D-=0A14 4.90D-09.=0A=A0 =A0 52 ve= ctors produced by pass 44 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 2.29D-=0A14= 3.68D-09.=0A=A0 =A0 48 vectors produced by pass 45 Test12=3D 1.59D-13 1.00= D-09 XBig12=3D 2.11D-=0A14 3.09D-09.=0A=A0 =A0 32 vectors produced by pass = 46 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 1.28D-=0A14 2.61D-09.=0A=A0 =A0 32= vectors produced by pass 47 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 1.79D-= =0A14 2.81D-09.=0A=A0 =A0 24 vectors produced by pass 48 Test12=3D 1.59D-13= 1.00D-09 XBig12=3D 1.35D-=0A14 2.45D-09.=0A=A0 =A0 24 vectors produced by = pass 49 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 3.11D-=0A14 4.08D-09.=0A=A0 = =A0 24 vectors produced by pass 50 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 1.= 88D-=0A14 2.97D-09.=0A=A0 =A0 24 vectors produced by pass 51 Test12=3D 1.59= D-13 1.00D-09 XBig12=3D 3.07D-=0A14 3.81D-09.=0A=A0 =A0 24 vectors produced= by pass 52 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 1.80D-=0A14 2.88D-09.=0A= =A0 =A0 24 vectors produced by pass 53 Test12=3D 1.59D-13 1.00D-09 XBig12= =3D 2.54D-=0A14 3.87D-09.=0A=A0 =A0 21 vectors produced by pass 54 Test12= =3D 1.59D-13 1.00D-09 XBig12=3D 1.85D-=0A14 3.46D-09.=0A=A0 =A0 21 vectors = produced by pass 55 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 2.56D-=0A14 3.68D= -09.=0A=A0 =A0 21 vectors produced by pass 56 Test12=3D 1.59D-13 1.00D-09 X= Big12=3D 3.29D-=0A14 3.80D-09.=0A=A0 =A0 =A0 9 vectors produced by pass 57 = Test12=3D 1.59D-13 1.00D-09 XBig12=3D 8.17D-=0A15 2.36D-09.=0A=A0 =A0 =A0 9= vectors produced by pass 58 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 2.91D-= =0A14 4.46D-09.=0A=A0 =A0 =A0 9 vectors produced by pass 59 Test12=3D 1.59D= -13 1.00D-09 XBig12=3D 7.03D-=0A15 2.01D-09.=0A=A0 =A0 =A0 9 vectors produc= ed by pass 60 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 2.16D-=0A14 3.52D-09.= =0A=A0 =A0 =A0 9 vectors produced by pass 61 Test12=3D 1.59D-13 1.00D-09 XB= ig12=3D 2.01D-=0A14 3.70D-09.=0A=A0 =A0 =A0 9 vectors produced by pass 62 T= est12=3D 1.59D-13 1.00D-09 XBig12=3D 1.27D-=0A14 3.02D-09.=0A=A0 =A0 =A0 9 = vectors produced by pass 63 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 1.52D-=0A= 14 2.98D-09.=0A=A0 =A0 =A0 9 vectors produced by pass 64 Test12=3D 1.59D-13= 1.00D-09 XBig12=3D 2.72D-=0A14 4.11D-09.=0A=A0 =A0 =A0 9 vectors produced = by pass 65 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 1.04D-=0A14 2.39D-09.=0A= =A0 =A0 =A0 9 vectors produced by pass 66 Test12=3D 1.59D-13 1.00D-09 XBig1= 2=3D 1.63D-=0A14 3.22D-09.=0A=A0 =A0 =A0 9 vectors produced by pass 67 Test= 12=3D 1.59D-13 1.00D-09 XBig12=3D 1.38D-=0A14 2.73D-09.=0A=A0 =A0 =A0 9 vec= tors produced by pass 68 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 2.09D-=0A14 = 3.07D-09.=0A=A0 =A0 =A0 9 vectors produced by pass 69 Test12=3D 1.59D-13 1.= 00D-09 XBig12=3D 1.59D-=0A14 2.71D-09.=0A=A0 =A0 =A0 7 vectors produced by = pass 70 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 8.67D-=0A15 2.09D-09.=0A=A0 = =A0 =A0 7 vectors produced by pass 71 Test12=3D 1.59D-13 1.00D-09 XBig12=3D= 1.53D-=0A14 2.73D-09.=0A=A0 =A0 =A0 7 vectors produced by pass 72 Test12= =3D 1.59D-13 1.00D-09 XBig12=3D 3.39D-=0A14 3.84D-09.=0A=A0 =A0 =A0 7 vecto= rs produced by pass 73 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 1.40D-=0A14 2.= 62D-09.=0A=A0 =A0 =A0 7 vectors produced by pass 74 Test12=3D 1.59D-13 1.00= D-09 XBig12=3D 1.48D-=0A14 3.07D-09.=0A=A0 =A0 =A0 5 vectors produced by pa= ss 75 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 5.66D-=0A15 2.01D-09.=0AApplied= DIIS recursively to reduced A of dimension=A0 6137.=0AErroneous write. Wri= te 1407176 instead of 2454800.=0Afd =3D 4=0Aorig len =3D 2454800 left =3D 2= 454800=0Ag_write=0A=0A=0AAny suggestions would be fine =3DD=0A=0AThank you = all=0A=0A=0A=0A-=3D This is automatically added to each message by the mail= ing script =3D-=0ATo recover the email address of the author of the message= , please change=0Athe strange characters on the top line to the +*+ sign. You= can also=0A=0A=0AE-ma= il to subscribers: CHEMISTRY+*+ccl.net or use:=0A=A0 =A0 =A0 http://www.ccl.n= et/cgi-bin/ccl/send_ccl_message=0A=0AE-mail to administrators: CHEMISTRY-RE= QUEST+*+ccl.net or use=0A=A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_= message=0A=0A=0A=A0 =A0 =A0 http://www.ccl.net/chemi= stry/sub_unsub.shtml=0A=0ABefore posting, check wait time at: http://www.cc= l.net/=0A=0A=0AConferences: http://server.ccl.= net/chemistry/announcements/conferences/=0A=0ASearch Messages: http://www.c= cl.net/chemistry/searchccl/index.shtml=0A=0AIf your mail bounces from CCL w= ith 5.7.1 error, check:=0A=A0 =A0 =A0=0A=0A=---244526598-550607804-1347556019=:4492 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hi Nicolas,
 
Are you setting your= disk (MaxDisk) and memory (%mem) high enough? Unless you use %mem the defa= ult is only 256MB.
 
On a side note, if you can af= ford the CPU time, you may want to reconsider using a DFT for transition st= ate studies. The geometries are good, but the energies are underestimated w= hich will affect the quality of barrier height predictions.
 
Hope this helps!
 
Amy

From:= Nicolas Grimblat nicogreen6---gmail.com <owner-chemistry+*+ccl= .net>
To: "Austin, Am= y J " <amy_jean_austin+*+yahoo.com>
Sent: Thursday, September 13, 2012 10:13 AM
= Subject: CCL: Frequency Calcul= ation Problem


Sent to CCL by: "Nicolas  Grimbl= at" [nicogreen6()gmail.com]
Dear All,

Mi name is Nicolas and im h= aving problems with a frequency calculation
(B3LYP/6-311+G**). It is TS= with 55 heavy atoms. The opt went fine, though
the frequency gives me this err= or, not mem nor Disk space. I try splitting
the RWF and the same. Every= time i restart the job it take less than 20
minutes to stop.
This i= s the last part of the log

Requested convergence on RMS density matr= ix=3D1.00D-08 within 128 cycles.
Requested convergence on MAX density ma= trix=3D1.00D-06.
Requested convergence on        &nb= sp;   energy=3D1.00D-06.
No special actions if energy rises.
SCF= Done:  E(RB3LYP) =3D  -2017.79900374    A.U. after&nbs= p;   5 cycles
            Convg = =3D    0.5751D-08            -V/T = =3D  2.0041
Range of M.O.s used for correlation:    1&nbs= p; 1166
NBasis=3D  1176 NAE=3D  158 NBE=3D  158 NFC=3D&nb= sp;   0 NFV=3D    0
NROrb=3D  1166 NOA=3D  158 = NOB=3D  158 NVA=3D  1008 NVB=3D  1008

**** Warning!!: The largest alp= ha MO coefficient is  0.11183179D+03


**** Warning!!: The sm= allest alpha delta epsilon is  0.96445386D-01

PrsmSu:  req= uested number of processors reduced to:  2 ShMem  1 Linda.
Sym= metrizing basis deriv contribution to polar:
IMax=3D3 JMax=3D2 DiffMx=3D= 0.00D+00
G2DrvN: will do    39 centers at a time, making = ;   2 passes doing MaxLOS=3D2.
Calling FoFCou, ICntrl=3D  3107= FMM=3DT I1Cent=3D  0 AccDes=3D 0.00D+00.
Calling FoFCou, ICntrl=3D=   3107 FMM=3DT I1Cent=3D  0 AccDes=3D 0.00D+00.
FoFDir/FoFCou = used for L=3D0 through L=3D2.
End of G2Drv Frequency-dependent propertie= s file  721 does not exist.
End of G2Drv Frequency-dependent proper= ties file  722 does not exist.
          I= DoAtm=3D11111111111111111111111111111111111111111111111111
   =       IDoAtm=3D11111111111111111111111111
          = Differentiating once with respect to electric field.
     = ;           with respect to dipole field.
 = ;         Differentiating once with respect to nuclear = coordinates.
          There are  231 degr= ees of freedom in the 1st order CPHF. 
IDoFFX=3D5.
   = ; 231 vectors produced by pass  0 Test12=3D 1.59D-13 1.00D-09 XBig12= =3D
9.19D+02 2.16D+01.
AX will form    72 AO Fock derivati= ves at one time.
    231 vectors produced by pass  1 Test= 12=3D 1.59D-13 1.00D-09 XBig12=3D
1.99D+02 1.76D+00.
    2= 28 vectors produced by pass  2 Test12=3D 1.59D-13 1.00D-09 XBig12=3D <= BR>1.83D+00 1.32D-01.
    228 vectors produced by pass  3= Test12=3D 1.59D-13 1.00D-09 XBig12=3D 7.57D-
03 7.43D-03.
  &nb= sp; 228 vectors produced by pass  4 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 1.92D-
0= 5 2.86D-04.
    228 vectors produced by pass  5 Test12=3D= 1.59D-13 1.00D-09 XBig12=3D 3.40D-
08 1.26D-05.
    228 ve= ctors produced by pass  6 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 9.44D-=
11 7.42D-07.
    221 vectors produced by pass  7 Test= 12=3D 1.59D-13 1.00D-09 XBig12=3D 5.41D-
12 8.45D-08.
    1= 97 vectors produced by pass  8 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 2= .09D-
13 1.63D-08.
    189 vectors produced by pass  9= Test12=3D 1.59D-13 1.00D-09 XBig12=3D 1.97D-
13 1.28D-08.
  &nb= sp; 181 vectors produced by pass 10 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 2= .21D-
13 1.42D-08.
    169 vectors produced by pass 11 Test= 12=3D 1.59D-13 1.00D-09 XBig12=3D 2.06D-
13 1.39D-08.
    1= 66 vectors produced by pass 12 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 1.99D-=
13 1.23D-08.
    163 vectors produced by pass 13 Test12=3D 1.59D-13 1.00D-09 XBig12= =3D 2.15D-
13 1.46D-08.
    160 vectors produced by pass 14= Test12=3D 1.59D-13 1.00D-09 XBig12=3D 2.40D-
13 1.60D-08.
  &nb= sp; 153 vectors produced by pass 15 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 1= .52D-
13 1.10D-08.
    143 vectors produced by pass 16 Test= 12=3D 1.59D-13 1.00D-09 XBig12=3D 1.20D-
13 1.00D-08.
    1= 40 vectors produced by pass 17 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 1.73D-=
13 1.20D-08.
    128 vectors produced by pass 18 Test12=3D= 1.59D-13 1.00D-09 XBig12=3D 6.11D-
14 6.27D-09.
    125 ve= ctors produced by pass 19 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 1.61D-
1= 3 1.02D-08.
    122 vectors produced by pass 20 Test12=3D 1.59= D-13 1.00D-09 XBig12=3D 8.38D-
14 8.19D-09.
    119 vectors= produced by pass 21 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 1.04D-
13 8.7= 4D-09.
    116 vectors produced by pass 22 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 1.11D-13 8.05D-09.
    106 vectors produced by pass 23 Test12=3D 1= .59D-13 1.00D-09 XBig12=3D 1.13D-
13 9.33D-09.
    103 vect= ors produced by pass 24 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 8.44D-
14 = 7.37D-09.
    100 vectors produced by pass 25 Test12=3D 1.59D-= 13 1.00D-09 XBig12=3D 9.25D-
14 7.94D-09.
    97 vectors pr= oduced by pass 26 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 7.03D-
14 7.25D-= 09.
    77 vectors produced by pass 27 Test12=3D 1.59D-13 1.00= D-09 XBig12=3D 4.23D-
14 4.95D-09.
    72 vectors produced = by pass 28 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 5.22D-
14 6.32D-09.
=     72 vectors produced by pass 29 Test12=3D 1.59D-13 1.00D-09 XB= ig12=3D 2.55D-
14 4.00D-09.
    72 vectors produced by pass= 30 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 3.07D-
14 4.27D-09.
  =   72 vectors produced by pass 31 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 5.50D-
14 6.24D-09.
&n= bsp;   72 vectors produced by pass 32 Test12=3D 1.59D-13 1.00D-09 XBig= 12=3D 3.93D-
14 4.71D-09.
    72 vectors produced by pass 3= 3 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 3.14D-
14 4.15D-09.
  &n= bsp; 72 vectors produced by pass 34 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 3= .70D-
14 4.81D-09.
    65 vectors produced by pass 35 Test1= 2=3D 1.59D-13 1.00D-09 XBig12=3D 2.29D-
14 3.51D-09.
    63= vectors produced by pass 36 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 2.53D-14 3.72D-09.
    63 vectors produced by pass 37 Test12=3D 1.= 59D-13 1.00D-09 XBig12=3D 2.95D-
14 3.94D-09.
    63 vector= s produced by pass 38 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 3.01D-
14 4.= 02D-09.
    56 vectors produced by pass 39 Test12=3D 1.59D-13 = 1.00D-09 XBig12=3D 2.14D-
14 3.62D-09.
    56 vectors produ= ced by pass 40 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 2.67D-
14 3.63D-09.
    54 vec= tors produced by pass 41 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 2.36D-
14= 3.52D-09.
    54 vectors produced by pass 42 Test12=3D 1.59D-= 13 1.00D-09 XBig12=3D 2.44D-
14 3.53D-09.
    54 vectors pr= oduced by pass 43 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 3.22D-
14 4.90D-= 09.
    52 vectors produced by pass 44 Test12=3D 1.59D-13 1.00= D-09 XBig12=3D 2.29D-
14 3.68D-09.
    48 vectors produced = by pass 45 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 2.11D-
14 3.09D-09.
=     32 vectors produced by pass 46 Test12=3D 1.59D-13 1.00D-09 XB= ig12=3D 1.28D-
14 2.61D-09.
    32 vectors produced by pass= 47 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 1.79D-
14 2.81D-09.
  =   24 vectors produced by pass 48 Test12=3D 1.59D-13 1.00D-09 XBig12=3D= 1.35D-
14 2.45D-09.
    24 vectors produced by pass 49 Tes= t12=3D 1.59D-13 1.00D-09 XBig12=3D 3.11D-
14 4.08D-09.
    24 vectors produced by p= ass 50 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 1.88D-
14 2.97D-09.
&nbs= p;   24 vectors produced by pass 51 Test12=3D 1.59D-13 1.00D-09 XBig12= =3D 3.07D-
14 3.81D-09.
    24 vectors produced by pass 52 = Test12=3D 1.59D-13 1.00D-09 XBig12=3D 1.80D-
14 2.88D-09.
  &nbs= p; 24 vectors produced by pass 53 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 2.5= 4D-
14 3.87D-09.
    21 vectors produced by pass 54 Test12= =3D 1.59D-13 1.00D-09 XBig12=3D 1.85D-
14 3.46D-09.
    21 = vectors produced by pass 55 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 2.56D-14 3.68D-09.
    21 vectors produced by pass 56 Test12=3D 1.5= 9D-13 1.00D-09 XBig12=3D 3.29D-
14 3.80D-09.
      9 v= ectors produced by pass 57 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 8.17D-
= 15 2.36D-09.
      9 vectors produced by pass 58 Test12= =3D 1.59D-13 1.00D-09 XBig12=3D 2.91D-
14 4.46D-09.
      9 vectors produced by pass = 59 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 7.03D-
15 2.01D-09.
  &= nbsp;   9 vectors produced by pass 60 Test12=3D 1.59D-13 1.00D-09 XBig= 12=3D 2.16D-
14 3.52D-09.
      9 vectors produced by = pass 61 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 2.01D-
14 3.70D-09.
&nb= sp;     9 vectors produced by pass 62 Test12=3D 1.59D-13 1.00D-09= XBig12=3D 1.27D-
14 3.02D-09.
      9 vectors produce= d by pass 63 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 1.52D-
14 2.98D-09.      9 vectors produced by pass 64 Test12=3D 1.59D-13 1.0= 0D-09 XBig12=3D 2.72D-
14 4.11D-09.
      9 vectors pr= oduced by pass 65 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 1.04D-
14 2.39D-= 09.
      9 vectors produced by pass 66 Test12=3D 1.59D-1= 3 1.00D-09 XBig12=3D 1.63D-
14 3.22D-09.
      9 vecto= rs produced by pass 67 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 1.38D-
14 2.73D-09.
  &nb= sp;   9 vectors produced by pass 68 Test12=3D 1.59D-13 1.00D-09 XBig12= =3D 2.09D-
14 3.07D-09.
      9 vectors produced by pa= ss 69 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 1.59D-
14 2.71D-09.
 = ;     7 vectors produced by pass 70 Test12=3D 1.59D-13 1.00D-09 X= Big12=3D 8.67D-
15 2.09D-09.
      7 vectors produced = by pass 71 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 1.53D-
14 2.73D-09.
=       7 vectors produced by pass 72 Test12=3D 1.59D-13 1.00D= -09 XBig12=3D 3.39D-
14 3.84D-09.
      7 vectors prod= uced by pass 73 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 1.40D-
14 2.62D-09= .
      7 vectors produced by pass 74 Test12=3D 1.59D-13 = 1.00D-09 XBig12=3D 1.48D-
14 3.07D-09.
      5 vectors= produced by pass 75 Test12=3D 1.59D-13 1.00D-09 XBig12=3D 5.66D-
15 2.0= 1D-09.
Applied DIIS recursively to reduced A of dimension  6137.
Erroneous write. Writ= e 1407176 instead of 2454800.
fd =3D 4
orig len =3D 2454800 left =3D = 2454800
g_write


Any suggestions would be fine =3DD

Tha= nk you all



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---244526598-550607804-1347556019=:4492-- From owner-chemistry@ccl.net Thu Sep 13 14:23:00 2012 From: "Close, David M. CLOSED[A]mail.etsu.edu" To: CCL Subject: CCL: Frequency Calculation Problem Message-Id: <-47588-120913134254-9594-GxAs7yNsYw0YFX3BvRkP1g-x-server.ccl.net> X-Original-From: "Close, David M." Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 13 Sep 2012 17:42:46 +0000 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED]-[mail.etsu.edu] Nicolas: I believe that in spite of your attempting to split up the rwf files, you are still out of memory. Of course the error message is very cryptic, but the important part is at the bottom, "erroneous write". Most likely the program has read data from the check file, and is attempting to write more temporary files, but cannot find the space. You don't say what computer you are using, and how much file space you have access to. As a quick test, run the job at 6-31G just to see if execution proceeds beyond the 20 minutes you indicate. Regards, Dave Close. -----Original Message----- > From: owner-chemistry+closed==etsu.edu=-=ccl.net [mailto:owner-chemistry+closed==etsu.edu=-=ccl.net] On Behalf Of Nicolas Grimblat nicogreen6---gmail.com Sent: Thursday, September 13, 2012 10:14 AM To: Close, David M. Subject: CCL: Frequency Calculation Problem Sent to CCL by: "Nicolas Grimblat" [nicogreen6()gmail.com] Dear All, Mi name is Nicolas and im having problems with a frequency calculation (B3LYP/6-311+G**). It is TS with 55 heavy atoms. The opt went fine, though the frequency gives me this error, not mem nor Disk space. I try splitting the RWF and the same. Every time i restart the job it take less than 20 minutes to stop. This is the last part of the log Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. Requested convergence on MAX density matrix=1.00D-06. Requested convergence on energy=1.00D-06. No special actions if energy rises. SCF Done: E(RB3LYP) = -2017.79900374 A.U. after 5 cycles Convg = 0.5751D-08 -V/T = 2.0041 Range of M.O.s used for correlation: 1 1166 NBasis= 1176 NAE= 158 NBE= 158 NFC= 0 NFV= 0 NROrb= 1166 NOA= 158 NOB= 158 NVA= 1008 NVB= 1008 **** Warning!!: The largest alpha MO coefficient is 0.11183179D+03 **** Warning!!: The smallest alpha delta epsilon is 0.96445386D-01 PrsmSu: requested number of processors reduced to: 2 ShMem 1 Linda. Symmetrizing basis deriv contribution to polar: IMax=3 JMax=2 DiffMx= 0.00D+00 G2DrvN: will do 39 centers at a time, making 2 passes doing MaxLOS=2. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. FoFDir/FoFCou used for L=0 through L=2. End of G2Drv Frequency-dependent properties file 721 does not exist. End of G2Drv Frequency-dependent properties file 722 does not exist. IDoAtm=11111111111111111111111111111111111111111111111111 IDoAtm=11111111111111111111111111 Differentiating once with respect to electric field. with respect to dipole field. Differentiating once with respect to nuclear coordinates. There are 231 degrees of freedom in the 1st order CPHF. IDoFFX=5. 231 vectors produced by pass 0 Test12= 1.59D-13 1.00D-09 XBig12= 9.19D+02 2.16D+01. AX will form 72 AO Fock derivatives at one time. 231 vectors produced by pass 1 Test12= 1.59D-13 1.00D-09 XBig12= 1.99D+02 1.76D+00. 228 vectors produced by pass 2 Test12= 1.59D-13 1.00D-09 XBig12= 1.83D+00 1.32D-01. 228 vectors produced by pass 3 Test12= 1.59D-13 1.00D-09 XBig12= 7.57D- 03 7.43D-03. 228 vectors produced by pass 4 Test12= 1.59D-13 1.00D-09 XBig12= 1.92D- 05 2.86D-04. 228 vectors produced by pass 5 Test12= 1.59D-13 1.00D-09 XBig12= 3.40D- 08 1.26D-05. 228 vectors produced by pass 6 Test12= 1.59D-13 1.00D-09 XBig12= 9.44D- 11 7.42D-07. 221 vectors produced by pass 7 Test12= 1.59D-13 1.00D-09 XBig12= 5.41D- 12 8.45D-08. 197 vectors produced by pass 8 Test12= 1.59D-13 1.00D-09 XBig12= 2.09D- 13 1.63D-08. 189 vectors produced by pass 9 Test12= 1.59D-13 1.00D-09 XBig12= 1.97D- 13 1.28D-08. 181 vectors produced by pass 10 Test12= 1.59D-13 1.00D-09 XBig12= 2.21D- 13 1.42D-08. 169 vectors produced by pass 11 Test12= 1.59D-13 1.00D-09 XBig12= 2.06D- 13 1.39D-08. 166 vectors produced by pass 12 Test12= 1.59D-13 1.00D-09 XBig12= 1.99D- 13 1.23D-08. 163 vectors produced by pass 13 Test12= 1.59D-13 1.00D-09 XBig12= 2.15D- 13 1.46D-08. 160 vectors produced by pass 14 Test12= 1.59D-13 1.00D-09 XBig12= 2.40D- 13 1.60D-08. 153 vectors produced by pass 15 Test12= 1.59D-13 1.00D-09 XBig12= 1.52D- 13 1.10D-08. 143 vectors produced by pass 16 Test12= 1.59D-13 1.00D-09 XBig12= 1.20D- 13 1.00D-08. 140 vectors produced by pass 17 Test12= 1.59D-13 1.00D-09 XBig12= 1.73D- 13 1.20D-08. 128 vectors produced by pass 18 Test12= 1.59D-13 1.00D-09 XBig12= 6.11D- 14 6.27D-09. 125 vectors produced by pass 19 Test12= 1.59D-13 1.00D-09 XBig12= 1.61D- 13 1.02D-08. 122 vectors produced by pass 20 Test12= 1.59D-13 1.00D-09 XBig12= 8.38D- 14 8.19D-09. 119 vectors produced by pass 21 Test12= 1.59D-13 1.00D-09 XBig12= 1.04D- 13 8.74D-09. 116 vectors produced by pass 22 Test12= 1.59D-13 1.00D-09 XBig12= 1.11D- 13 8.05D-09. 106 vectors produced by pass 23 Test12= 1.59D-13 1.00D-09 XBig12= 1.13D- 13 9.33D-09. 103 vectors produced by pass 24 Test12= 1.59D-13 1.00D-09 XBig12= 8.44D- 14 7.37D-09. 100 vectors produced by pass 25 Test12= 1.59D-13 1.00D-09 XBig12= 9.25D- 14 7.94D-09. 97 vectors produced by pass 26 Test12= 1.59D-13 1.00D-09 XBig12= 7.03D- 14 7.25D-09. 77 vectors produced by pass 27 Test12= 1.59D-13 1.00D-09 XBig12= 4.23D- 14 4.95D-09. 72 vectors produced by pass 28 Test12= 1.59D-13 1.00D-09 XBig12= 5.22D- 14 6.32D-09. 72 vectors produced by pass 29 Test12= 1.59D-13 1.00D-09 XBig12= 2.55D- 14 4.00D-09. 72 vectors produced by pass 30 Test12= 1.59D-13 1.00D-09 XBig12= 3.07D- 14 4.27D-09. 72 vectors produced by pass 31 Test12= 1.59D-13 1.00D-09 XBig12= 5.50D- 14 6.24D-09. 72 vectors produced by pass 32 Test12= 1.59D-13 1.00D-09 XBig12= 3.93D- 14 4.71D-09. 72 vectors produced by pass 33 Test12= 1.59D-13 1.00D-09 XBig12= 3.14D- 14 4.15D-09. 72 vectors produced by pass 34 Test12= 1.59D-13 1.00D-09 XBig12= 3.70D- 14 4.81D-09. 65 vectors produced by pass 35 Test12= 1.59D-13 1.00D-09 XBig12= 2.29D- 14 3.51D-09. 63 vectors produced by pass 36 Test12= 1.59D-13 1.00D-09 XBig12= 2.53D- 14 3.72D-09. 63 vectors produced by pass 37 Test12= 1.59D-13 1.00D-09 XBig12= 2.95D- 14 3.94D-09. 63 vectors produced by pass 38 Test12= 1.59D-13 1.00D-09 XBig12= 3.01D- 14 4.02D-09. 56 vectors produced by pass 39 Test12= 1.59D-13 1.00D-09 XBig12= 2.14D- 14 3.62D-09. 56 vectors produced by pass 40 Test12= 1.59D-13 1.00D-09 XBig12= 2.67D- 14 3.63D-09. 54 vectors produced by pass 41 Test12= 1.59D-13 1.00D-09 XBig12= 2.36D- 14 3.52D-09. 54 vectors produced by pass 42 Test12= 1.59D-13 1.00D-09 XBig12= 2.44D- 14 3.53D-09. 54 vectors produced by pass 43 Test12= 1.59D-13 1.00D-09 XBig12= 3.22D- 14 4.90D-09. 52 vectors produced by pass 44 Test12= 1.59D-13 1.00D-09 XBig12= 2.29D- 14 3.68D-09. 48 vectors produced by pass 45 Test12= 1.59D-13 1.00D-09 XBig12= 2.11D- 14 3.09D-09. 32 vectors produced by pass 46 Test12= 1.59D-13 1.00D-09 XBig12= 1.28D- 14 2.61D-09. 32 vectors produced by pass 47 Test12= 1.59D-13 1.00D-09 XBig12= 1.79D- 14 2.81D-09. 24 vectors produced by pass 48 Test12= 1.59D-13 1.00D-09 XBig12= 1.35D- 14 2.45D-09. 24 vectors produced by pass 49 Test12= 1.59D-13 1.00D-09 XBig12= 3.11D- 14 4.08D-09. 24 vectors produced by pass 50 Test12= 1.59D-13 1.00D-09 XBig12= 1.88D- 14 2.97D-09. 24 vectors produced by pass 51 Test12= 1.59D-13 1.00D-09 XBig12= 3.07D- 14 3.81D-09. 24 vectors produced by pass 52 Test12= 1.59D-13 1.00D-09 XBig12= 1.80D- 14 2.88D-09. 24 vectors produced by pass 53 Test12= 1.59D-13 1.00D-09 XBig12= 2.54D- 14 3.87D-09. 21 vectors produced by pass 54 Test12= 1.59D-13 1.00D-09 XBig12= 1.85D- 14 3.46D-09. 21 vectors produced by pass 55 Test12= 1.59D-13 1.00D-09 XBig12= 2.56D- 14 3.68D-09. 21 vectors produced by pass 56 Test12= 1.59D-13 1.00D-09 XBig12= 3.29D- 14 3.80D-09. 9 vectors produced by pass 57 Test12= 1.59D-13 1.00D-09 XBig12= 8.17D- 15 2.36D-09. 9 vectors produced by pass 58 Test12= 1.59D-13 1.00D-09 XBig12= 2.91D- 14 4.46D-09. 9 vectors produced by pass 59 Test12= 1.59D-13 1.00D-09 XBig12= 7.03D- 15 2.01D-09. 9 vectors produced by pass 60 Test12= 1.59D-13 1.00D-09 XBig12= 2.16D- 14 3.52D-09. 9 vectors produced by pass 61 Test12= 1.59D-13 1.00D-09 XBig12= 2.01D- 14 3.70D-09. 9 vectors produced by pass 62 Test12= 1.59D-13 1.00D-09 XBig12= 1.27D- 14 3.02D-09. 9 vectors produced by pass 63 Test12= 1.59D-13 1.00D-09 XBig12= 1.52D- 14 2.98D-09. 9 vectors produced by pass 64 Test12= 1.59D-13 1.00D-09 XBig12= 2.72D- 14 4.11D-09. 9 vectors produced by pass 65 Test12= 1.59D-13 1.00D-09 XBig12= 1.04D- 14 2.39D-09. 9 vectors produced by pass 66 Test12= 1.59D-13 1.00D-09 XBig12= 1.63D- 14 3.22D-09. 9 vectors produced by pass 67 Test12= 1.59D-13 1.00D-09 XBig12= 1.38D- 14 2.73D-09. 9 vectors produced by pass 68 Test12= 1.59D-13 1.00D-09 XBig12= 2.09D- 14 3.07D-09. 9 vectors produced by pass 69 Test12= 1.59D-13 1.00D-09 XBig12= 1.59D- 14 2.71D-09. 7 vectors produced by pass 70 Test12= 1.59D-13 1.00D-09 XBig12= 8.67D- 15 2.09D-09. 7 vectors produced by pass 71 Test12= 1.59D-13 1.00D-09 XBig12= 1.53D- 14 2.73D-09. 7 vectors produced by pass 72 Test12= 1.59D-13 1.00D-09 XBig12= 3.39D- 14 3.84D-09. 7 vectors produced by pass 73 Test12= 1.59D-13 1.00D-09 XBig12= 1.40D- 14 2.62D-09. 7 vectors produced by pass 74 Test12= 1.59D-13 1.00D-09 XBig12= 1.48D- 14 3.07D-09. 5 vectors produced by pass 75 Test12= 1.59D-13 1.00D-09 XBig12= 5.66D- 15 2.01D-09. Applied DIIS recursively to reduced A of dimension 6137. Erroneous write. Write 1407176 instead of 2454800. fd = 4 orig len = 2454800 left = 2454800 g_write Any suggestions would be fine =D Thank you allhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu Sep 13 14:58:00 2012 From: "Beneberu, Habtamu hbeneberu(a)udc.edu" To: CCL Subject: CCL:G: Extended Huckel for Band structure calculation on Gaussian Message-Id: <-47589-120913102137-22212-jnjn5afkBRYy4lU3AjrqzQ(!)server.ccl.net> X-Original-From: "Beneberu, Habtamu" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 13 Sep 2012 10:20:38 -0400 MIME-Version: 1.0 Sent to CCL by: "Beneberu, Habtamu" [hbeneberu-*-udc.edu] I am trying to do Extended Huckel band structure calculation using Gaussian 09. I keep getting the error message: RdIPBC - cell file has zero length Error termination via Lnk1e in /share/apps/gaussian/g09/l402.exe Here is my route line: #p Huckel PBC=NKPoint=12 IOP(5/103=5) My question are 1) Can one do band structure calculation using Extended Huckel with Gaussian, if so how can I solve the error message? 2) What alternative software do you recommend Thank you H. Z. Beneberu From owner-chemistry@ccl.net Thu Sep 13 15:33:01 2012 From: "Jorge Ricardo Quintero jsaumeth.jorge-x-gmail.com" To: CCL Subject: CCL:G: POLYRATE + SOLVENT EFFECTS Message-Id: <-47590-120913114806-9931-IdwwST7Z5mJR9wy+WDCrRQ~!~server.ccl.net> X-Original-From: "Jorge Ricardo Quintero" Date: Thu, 13 Sep 2012 11:48:05 -0400 Sent to CCL by: "Jorge Ricardo Quintero" [jsaumeth.jorge#%#gmail.com] Dear CCL users, I'm trying to calculate constant rate using interpolated variational transition state theory by mapping (IVTST-M) in conjunction with Conventional transition state theory (CVT) with semi-classical tunneling (e.g. ZCT and SCT) with polyrate software + Gaussian 09 kit. Taking into account solvent effects, literature suggests to do Single point energy calculations using any solvation model at the gas-phase geometry (previously optimized) and Gibbs free energy is equal to: G(cond) = G(gas) + G(solv). According to the above, and reading polyrate manual, IVTST-M works constructing a fu31 file which contains gradient and hessian info for each point at minimum energy path (MEP) So, what vibrational contributions should I use: gas-phase or condensed phase? Thanks for your help!!!! From owner-chemistry@ccl.net Thu Sep 13 16:08:00 2012 From: "Jorge Ricardo Quintero jsaumeth.jorge*o*gmail.com" To: CCL Subject: CCL:G: POLYRATE + SOLVENT EFFECTS Message-Id: <-47591-120913115112-11100-xwMcvbc3ko8VbWvc/WvZtQ- -server.ccl.net> X-Original-From: "Jorge Ricardo Quintero" Date: Thu, 13 Sep 2012 11:51:11 -0400 Sent to CCL by: "Jorge Ricardo Quintero" [jsaumeth.jorge]|[gmail.com] Dear CCL users, I'm trying to calculate constant rate using interpolated variational transition state theory by mapping (IVTST-M) in conjunction with Conventional transition state theory (CVT) with semi-classical tunneling (e.g. ZCT and SCT) with polyrate software + Gaussian 09 kit. Taking into account solvent effects, literature suggests to do Single point energy calculations using any solvation model at the gas-phase geometry (previously optimized) and Gibbs free energy is equal to: G(cond) = G(gas) + G(solv). According to the above, and reading polyrate manual, IVTST-M works constructing a fu31 file which contains gradient and hessian info for each point at minimum energy path (MEP) So, what vibrational contributions should I use: gas-phase or condensed phase? Thanks for your help!!!! From owner-chemistry@ccl.net Thu Sep 13 16:43:00 2012 From: "Geoffrey Hutchison geoffh#%#pitt.edu" To: CCL Subject: CCL: Extended Huckel for Band structure calculation on Gaussian Message-Id: <-47592-120913160219-31454-9ah6FTAGxNhUASNuchiZYQ a server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=us-ascii Date: Thu, 13 Sep 2012 16:02:09 -0400 MIME-version: 1.0 (Apple Message framework v1278) Sent to CCL by: Geoffrey Hutchison [geoffh ~ pitt.edu] > 2) What alternative software do you recommend Use YAeHMOP, formerly from Roald Hoffmann's group: http://yaehmop.sourceforge.net It's an older program and not really maintained anymore, but it works and has software for processing the band structure results. Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh*|*pitt.edu web: http://hutchison.chem.pitt.edu/ From owner-chemistry@ccl.net Thu Sep 13 17:20:00 2012 From: "Paolo Tosco paolo.tosco===unito.it" To: CCL Subject: CCL: can't open PDB with TINKER GUI Message-Id: <-47593-120913122629-1736-MQ8vBICDUxb679QdFnncjw/./server.ccl.net> X-Original-From: Paolo Tosco Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Thu, 13 Sep 2012 19:26:09 +0300 Mime-Version: 1.0 (1.0) Sent to CCL by: Paolo Tosco [paolo.tosco++unito.it] Dear Steven, if MMFF94 atom typing is what you are looking for, you might want to use SDF2XYZ2SDF: http://sdf2xyz2sdf.sourceforge.net/ If you look at the examples on the website docs you'll see how to directly convert a PDB file to TINKER XYZ. In case of trouble, just drop me an e-mail. Cheers, Paolo -- ========================================================== Paolo Tosco, Ph.D. Department of Drug Science and Technology Via Pietro Giuria, 9 - 10125 Torino (Italy) Tel: +39 011 670 7680 | Mob: +39 348 5537206 Fax: +39 011 670 7687 | E-mail: paolo.tosco|,|unito.it http://open3dqsar.org | http://open3dalign.org ========================================================== On 13 Sep 2012, at 17:00, "Trohalaki, Steven CTR USAF AFMC AFRL/RXPJE Steven.Trohalaki.ctr\a/wpafb.af.mil" wrote: > > It appears that the tinker utility pdbxyz.x read the atom names from the > Materials Studio PDB file and wrote them to the tinker.xyz file as it. This > screwed up the formatting (tinker.xyz files are fixed format) because the > atom names in the MS PDB contain the atom number, e.g., C123. > > Using the unix commands cut and paste, I was able to correct the format of > my tinker.xyz files. FFE still wouldn't read it, however, until I replaced > the atom types (pdbxyz.x wrote them all as zero) with non-zero integers. > > Now, I'm trying to use MOLDEN to assign atom types but I'm not having any > luck; MOLDEN replaces my non-zero atom-type integers with zeros! It looks > like I'll have to do it manually. Luckily, I get paid by the hour (although > maybe not for long). > > Steve T > > > -----Original Message----- >> From: owner-chemistry+steven.trohalaki==wpafb.af.mil-,-ccl.net > [mailto:owner-chemistry+steven.trohalaki==wpafb.af.mil-,-ccl.net] On Behalf Of > Steven Trohalaki steven.trohalaki###wpafb.af.mil > Sent: Monday, September 10, 2012 11:39 AM > To: Trohalaki, Steven CTR USAF AFMC AFRL/RXPJE > Subject: CCL: can't open PDB with TINKER GUI > > > Sent to CCL by: "Steven Trohalaki" [steven.trohalaki[*]wpafb.af.mil] > > Im trying to import into FFE (TINKERs GUI) a structure I made with Materials > Studio. > > I saved the Materials Studio structure as a PDB file. If I use the TINKER > utility pdbxyz.x, I get a tinker.xyz file but when I try to open it in FFE, > I get a blank screen and no Structural Hierarchy on the left side of the FFE > display. Making up a tinker.key file before I try opening the tinker.xyz > file doesnt help. > > I can open my PDB file directly with FFE. I am prompted to select a force > field, I see a structure, and I see a Structural Hierarchy. Clicking on > Keyword Editor allows me to select keywords and values for the keywords. > However, when I click on Modeling Commands, the only commands I see are > NUCEIC, PDBXYZ, and PROTEIN, i.e., I dont see Optimize, Dynamics, etc. I do > see all of the Modeling Commands if I open one of the example files provided > for TINKER, e.g., alkane.xyz. > > Id be obliged if anyone can tell me if Im doing anything wrong or if they > have a work-around. > > Thanks. > > Steve Thttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt------=_NextPart_000_0026_01CD9196.8C3D6C50 > Content-Type: application/x-pkcs7-signature; > name="smime.p7s" > Content-Transfer-Encoding: base64 > Content-Disposition: attachment; > filename="smime.p7s" > > MIAGCSqGSIb3DQEHAqCAMIACAQExCzAJBgUrDgMCGgUAMIAGCSqGSIb3DQEHAQAAoIISnzCCA3Aw > ggJYoAMCAQICAQUwDQYJKoZIhvcNAQEFBQAwWzELMAkGA1UEBhMCVVMxGDAWBgNVBAoTD1UuUy4g > 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19:27:00 2012 From: "Nuno A. G. Bandeira nuno.bandeira(0)ist.utl.pt" To: CCL Subject: CCL:G: Extended Huckel for Band structure calculation on Gaussian Message-Id: <-47594-120913192101-922-qlcZUYMqvyBN8ftngHamMw|a|server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="ISO-8859-1"; format=flowed Date: Fri, 14 Sep 2012 00:20:47 +0100 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira#ist.utl.pt] On 13/09/2012 15:20, Beneberu, Habtamu hbeneberu(a)udc.edu wrote: > > My question are > 1) Can one do band structure calculation using Extended Huckel with Gaussian, if so how can I solve the error message? > You can't do any PBC calculations in Gaussian other than with DFT or HF. Try either MOPAC2012 (with PM7) or Yaehmop from sourceforge. -- Nuno A. G. Bandeira, AMRSC C8 - Centro de Química e Bioquímica FCUL, Campo Grande Lisbon 1749-016 PORTUGAL http://www.researcherid.com/rid/B-6399-2012 http://pt.linkedin.com/pub/nuno-a-g-bandeira/47/55a/2aa --