[DFTB-Plus-User] MD in liquid water
Christopher Mark Maupin
cmaupin at hec.utah.edu
Wed Oct 7 22:54:10 CEST 2009
Paulo,
I am unable to comment on the parser. I removed all references to N
and C in my test case, and it originally did not converge. Only after I
changed the electronic temp did the system start to converge. So, on
this limited test I would say the electronic temp was the issue.
Generally speaking, if you are not using N then don't include
information on them in the input. It is cleaner and less confusing this
way.
Best wishes,
Mark
Paulo Cesar Piquini wrote:
> Dear Christopher and Ben,
>
> I implemented the suggested changes in my input file and it works!
> That is great
> Thanks a lot.
> Do you guys really think there is a bug in the parser?
>
> Yours
> Paulo Piquini
>
> On Wed, Oct 7, 2009 at 12:20 PM, Christopher Mark Maupin
> <cmaupin at hec.utah.edu <mailto:cmaupin at hec.utah.edu>> wrote:
>
> Paulo,
> I agree with Ben that having N terms in the file may be an issue. I
> took you file and striped out all the carbons leaving just the
> water. I
> then ran the code (with the H and O *.skf files) and the system
> did not
> converge. I then noticed you had your Filling = Fermi {
> Temperature[Kelvin] = 0}. I changed this this to be in agreement with
> the system temp of 300.0 K. The system then converged in 28
> cycles the
> first step, and 10 - 12 cycles for the next few steps.
> When I had question about this issue it was suggested that I use the
> same electronic temperature as MD temp in addition to
> AdaptFillingTemperature = Yes.
> I sure hope this helps
>
> Best wishes,
>
> Mark
> > Hello Paulo,
> >
> > the problem seems to be set of by the nitrogen atoms in the
> > input. Your structure doesn't actually have any N atoms, but
> there are
> > several places where there are settings for these, which when
> commented
> > out/removed should cure the problem:
> >
> > TypeNames = {"O" "H" "C"}# "N"}
> >
> > # N-H = "N-H.skf"
> > # H-N = "H-N.skf"
> > # C-N = "C-N.skf"
> > # N-C = "C-N.skf"
> > # N-N = "N-N.skf"
> > # O-N = "O-N.skf"
> > # N-O = "O-N.skf"
> >
> > # N = "p"
> >
> > it looks like you have found a bug in the parsing of the input in
> > this case.
> >
> > Regards
> >
> > Ben
> >
> > Paulo Cesar Piquini wrote:
> >
> >> Dear Mark,
> >>
> >> attached you will see the input and the output files of one of
> my tests.
> >> I played with some variables as timestep and others but the
> result was
> >> similar or worst.
> >> As you will see, the SCC cycle does not achieve convergence. If one
> >> increases the number of iterations, it goes well until some
> cycle and
> >> then the problem appears again.
> >> Thanks
> >>
> >> Yours
> >> Paulo
> >>
> >> On Tue, Oct 6, 2009 at 12:19 PM, Christopher Mark Maupin
> >> <cmaupin at hec.utah.edu <mailto:cmaupin at hec.utah.edu>
> <mailto:cmaupin at hec.utah.edu <mailto:cmaupin at hec.utah.edu>>> wrote:
> >>
> >> DEar Paulo Cesar Piquini,
> >> I have conducted several liquid water simulations and have
> not seen
> >> this issue. Can you please attach your input file and the
> output file.
> >>
> >> Best wishes,
> >>
> >> Mark
> >>
> >> Paulo Cesar Piquini wrote:
> >> > Dear users of DFTB+
> >> >
> >> > I am a new user of DFTB+ and Iam having difficulties to
> make the SCC
> >> > cycle to converge when I simulate a liquid water at 300 K.
> >> > Have someone already performed similar calculations
> successfully?
> >> >
> >> > Thanks
> >> > Paulo Piquini
> >> >
> >> > --
> >> > Paulo Cesar Piquini
> >> > Departamento de Física
> >> > Universidade Federal de Santa Maria
> >> > 97105-900
> >> > Santa Maria, RS
> >> > Brasil
> >> > Fax: 55 55 3220-8032
> >> > e-mail: ppiquini at gmail.com <mailto:ppiquini at gmail.com>
> <mailto:ppiquini at gmail.com <mailto:ppiquini at gmail.com>>
> >> <mailto:ppiquini at gmail.com <mailto:ppiquini at gmail.com>
> <mailto:ppiquini at gmail.com <mailto:ppiquini at gmail.com>>>;
> >> > ppiquini at smail.ufsm.br <mailto:ppiquini at smail.ufsm.br>
> <mailto:ppiquini at smail.ufsm.br <mailto:ppiquini at smail.ufsm.br>>
> >> <mailto:ppiquini at smail.ufsm.br
> <mailto:ppiquini at smail.ufsm.br> <mailto:ppiquini at smail.ufsm.br
> <mailto:ppiquini at smail.ufsm.br>>>
> >> > http://w3.ufsm.br/piquini
> >> >
> >> >
> >>
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> >> >
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> >>
> >>
> >> --
> >> Paulo Cesar Piquini
> >> Departamento de Física
> >> Universidade Federal de Santa Maria
> >> 97105-900
> >> Santa Maria, RS
> >> Brasil
> >> Fax: 55 55 3220-8032
> >> e-mail: ppiquini at gmail.com <mailto:ppiquini at gmail.com>
> <mailto:ppiquini at gmail.com <mailto:ppiquini at gmail.com>>;
> >> ppiquini at smail.ufsm.br <mailto:ppiquini at smail.ufsm.br>
> <mailto:ppiquini at smail.ufsm.br <mailto:ppiquini at smail.ufsm.br>>
> >> http://w3.ufsm.br/piquini
> >>
> >>
> >
> >
>
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>
>
> --
> Paulo Cesar Piquini
> Departamento de Física
> Universidade Federal de Santa Maria
> 97105-900
> Santa Maria, RS
> Brasil
> Fax: 55 55 3220-8032
> e-mail: ppiquini at gmail.com <mailto:ppiquini at gmail.com>;
> ppiquini at smail.ufsm.br <mailto:ppiquini at smail.ufsm.br>
> http://w3.ufsm.br/piquini
>
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