Dear Petra,
we encountered a similar problem a few weeks ago. I appears that Gaussian09
does sometimes automatically create link atoms or checks for atoms that should
be replaced by link atoms (although the online manual explicitly states that it
does not do that: "Note:
All link atoms must be specified by the user. Gaussian 09 does not define them
automatically or provide any defaults."). A possible workaround might be
using GaussView to set up the system.
In the case of diamond, however, since you probably require multivalent link
atoms (i.e., one link atom bound to two or more border carbons), you might need
to resort to more advanced schemes than simple hydrogen saturation. Just
visualise your problematic
model, the coordinates are given in the log file. You should be able to see
where the problem comes from.
Cheers,
Jan
>
> Sent to CCL by: "Petra Matunova"
[petra.matunova]|[seznam.cz]
> The surface is hydrogen-terminated and there where should be a
> continuation to the bulk are hydrogens too (it is a corner of a
> nanoparticle).
>
>
>> "zborowsk zborowsk[a]chemia.uj.edu.pl" wrote:
>>
>> Sent to CCL by: zborowsk [zborowsk%chemia.uj.edu.pl]
>>
>> I must say I am a bit suprised by presence of hydrogen in your
>> diamond....
>>
>>
>> W dniu 2015-11-04 12:06, Petra Matunova petra.matunova]![seznam.cz
>> napisa(a):
>> > Sent to CCL by: "Petra Matunova"
[petra.matunova%%seznam.cz]
>> > I am performing an ONIOM optimization calculation of a diamond
>> > nanoparticle, using b3lyp/6-31g(d):b3lyp/3-21g method. The
system
>> > contains 206 C atoms and 130 H atoms in the high level and 488
C
>> > atoms
>> > 188 H atoms in the low level. When I set the charge and
multiplicity
>> > as following: 0 1 0 1 0 1, the system do the low level SCF
>> > calculation
>> > without problems, but when starts with the high level
calculation on
>> > the model system, it ends with error:
>> >
>> > The combination of multiplicity 1 and 1455 electrons is
impossible.
>> >
>> > It only works when I set 0 1 0 2 0 2. In the high level
system there
>> > are 1366 electrons plus 89 link electrons from H atoms used as
link
>> > atoms.
>> >
>> > I had a problem with the specification of the link atoms on
the
>> > boundary between the low level and high level system. The low
level C
>> > atom close to the boundary has two bonds to another 2 high
level C
>> > atoms. I haven't known how to deal with that, as far as I know
>> > Gaussian allows to specify only one bond to for every low level
atom
>> > to a high level atom. So I specified for the low level C atom
linked
>> > to 2 high level C atoms only one link H atom and set the
>> > corresponding
>> > scale factor to 1, e.g.:
>> >
>> > C -1
3.953927 3.329465 3.558583 L H 18
1.
>> >
>> > Like this, I got only a following warning in output, e.g.:
>> >
>> > WARNING: Link atom host 21 is close to both atoms 18
and 123.
>> > Should it be oligovalent?
>> >
>> > Is there a way how to specify a link of the low level C to both
of
>> > the high level C to which it is bonded? Or how to solve that,
would
>> > it
>> > be right to leave the multiplicity to one?
>> >
>> > Thank you for your help!
>> > Best regards,
>> > Petra
>> >
>> >
>> >
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>> https://www.youtube.com/watch?v=IGyfx3Pmeyk
>> Krzysztof K. Zborowski
>> Faculty of Chemistry
>> Jagiellonian University
>> 3 Ingardena Street
>> 30-060 Krakow
>> Poland
>> phone: +48(12)663-2067
>> email: zborowsk]~[chemia.uj.edu.pl
>> gg 3817259
>> skype kzys70
>> www.chemia.uj.edu.pl/~zborowsk
>>
>>
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Jan Philipp Götze
School of Chemistry
University of St Andrews
North Haugh
St Andrews, Fife
KY16 9ST, Scotland, United Kingdom
Tel.: +44 (0)1334-464748 (ext. 14141)