[CPMD-list] Geometry optimization and misrepresentation of the x-ray data...

[Pedro Nuno Simões]

Dear Axel

I accept your criticism. But as I firstly said, I am a beginner both in 
CPMD code and CPMD mailing list, and I assume my lack of experience in 
the field. Obviously, I had no intention to make things difficult. The 
complete input is attached.

Thank you for your guidelines.
Sincerely,
Pedro.

Axel Kohlmeyer escreveu:
> On Fri, 25 Apr 2008, Pedro Nuno Simões wrote:
>
> dear pedro,
>
> how do you expect people to investigate you problem,
> if you do not give them a chance to reproduce it???
>
> it has become a _very_ bad habit that people post 
> incomplete inputs. please keep in mind, that the
> chances to get help are the higher the easier you
> make it to answer. i for myself am getting increasingly
> tired of having to play 20 questions with people to
> get out the full story, and i noticed similar trends
> with other people on other mailing lists. it is also
> important to note that the ratio of people asking to
> people answering is changing toward the asking side
> and not only because of more people asking...
>
> if you think it would be too much of a bother, 
> just put your file(s) up for download somewhere.
>
> based on the little information you are providing,
> it looks like you have one or a combination of the 
> following problems (in decreasing order of 
> likelyhood, but remember this is pure speculation!):
>
> - you made a mistake entering your coordinates
> - the structure of your system is dominated by
>   dispersion interactions.
> - you have incomplete k-point sampling
>
> PNS> Dear Ewald
> PNS> 
> PNS> Thank you for you prompt reply. Here it goes the input (hope enough). 
> PNS> All coordinates came from X-ray data (CIF file). I should say that the 
> PNS> single point calculation (OPTIMIZE WAVEFUNCTION) has run without problems.
>
> this does not mean a lot. if you plot the charge density,
> do you get something reasonable?
>
> BTW: how do you come to expect to get reliable phonons
> when your structure is not fully minimized??
> please check the literature about what a vibrational
> analysis actually does.
>
> cheers,
>     axel.
>
> PNS> Thanks again,
> PNS> Pedro.
> PNS> 
> PNS> -----------------------------------
> PNS> !  Sample LD01
> PNS> !
> PNS>  &CPMD
> PNS>     OPTIMIZE GEOMETRY XYZ
> PNS>     RESTART WAVEFUNCTION COORDINATES LATEST
> PNS>     LBFGS
> PNS>     CONVERGENCE ADAPT
> PNS>      0.02
> PNS>     CONVERGENCE ENERGY
> PNS>      0.05
> PNS>     HESSIAN DISCO
> PNS>  &END
> PNS>  &DFT
> PNS>  FUNCTIONAL BLYP
> PNS>  &END
> PNS>  &SYSTEM
> PNS>    ANGSTROM
> PNS>    CELL ABSOLUTE VECTORS
> PNS>      9.304 0.0 -6.10537904 0.0 6.6665 0.0 0.0 0.0 10.07482858
> PNS>    CUTOFF
> PNS>      120
> PNS>    POINT GROUP
> PNS>      5
> PNS>  &END
> PNS>  &ATOMS
> PNS> *C_SG_BLYP
> PNS>  LMAX=D
> PNS>  12
> PNS> (...)
> PNS> *N_SG_BLYP
> PNS>  LMAX=D
> PNS>  4
> PNS> (...)
> PNS> *O_SG_BLYP
> PNS>  LMAX=D
> PNS>  12
> PNS> (...)
> PNS> *Cl_SG_BLYP
> PNS>  LMAX=D
> PNS>  4
> PNS> (...)
> PNS> *H_SG_BLYP
> PNS>  LMAX=S
> PNS>  32
> PNS> (...)
> PNS>    CONSTRAINTS
> PNS>      FIX SEQUENCE
> PNS>        1 32
> PNS>    END CONSTRAINTS
> PNS>  &END
> PNS> -----------------------------------
> PNS> 
> PNS> Ewald Pauwels escreveu:
> PNS> > Dear Pedro,
> PNS> >
> PNS> > It looks like you might have made some mistakes in defining the 
> PNS> > periodicity of your crystal.
> PNS> > But please include your inputfile in your post, otherwise people won't 
> PNS> > be able to help you.
> PNS> >
> PNS> > Sincerely,
> PNS> > Ewald.
> PNS> >
> PNS> >
> PNS> >
> PNS> > Pedro Nuno Simões wrote:
> PNS> >> Dear CPMD users.
> PNS> >>
> PNS> >> I am a beginner, with a basic experience in CPMD. Now, I am trying to 
> PNS> >> further expand my capabilities in using the code.
> PNS> >> For now I am using CPMD toward the vibrational analysis of organic 
> PNS> >> crystalline systems, based on X-ray data. The main problem I am 
> PNS> >> facing occurs in geometry optimizations. I was expecting that 
> PNS> >> optimization essentially resulted in the correction of protonic 
> PNS> >> positions. This was not the case, preventing any reliable comparison 
> PNS> >> with experimental vibrational data.
> PNS> >>
> PNS> >> I have tried several approaches summarized below for a representative 
> PNS> >> system.
> PNS> >> (1) A cell including 4 complete cations and 4 chlorine anions was 
> PNS> >> created based on x-ray information.
> PNS> >> Looking to the "trajectory" corresponding to the optimization steps, 
> PNS> >> a dramatic structural change was observed, involving 
> PNS> >> cleavage/formation of protonic bonds.
> PNS> >> (2) I repeated the procedure describe in (1) but by fixing the heavy 
> PNS> >> atoms according to a CONSTRAINTS|FIX SEQUENCE specification. The same 
> PNS> >> problem was encountered.
> PNS> >> (3) I decided to repeat the above scheme by defining the initial 
> PNS> >> geometrical parameters directly from CIF data (i.e., without any 
> PNS> >> reconstruction of complete fragments within the cell, as attempted in 
> PNS> >> (1) and (2). The result was identical to those from the previous cases.
> PNS> >> (4) Finally I tried the same as in (3) but using POINT GROUP=5 
> PNS> >> (according to X-ray data) instead of POINT GROUP=AUTO in the SYSTEM 
> PNS> >> section. In this case, I allowed the optimization to be finished and 
> PNS> >> after vibrational analysis has been performed. The results are quite 
> PNS> >> doubtful.
> PNS> >>
> PNS> >> I look forward to any kind of  help.
> PNS> >> Thanks in advance,
> PNS> >> Pedro.
> PNS> >>
> PNS> >>   
> PNS> >
> PNS> >
> PNS> 
> PNS> 
> PNS> 
>
>   


-- 
----------------------
Pedro Nuno N.L. Simões

Departamento de Engenharia Química
FCTUC-Pólo II
Rua Sílvio Lima
3030-790 Coimbra
Portugal

Telef.: +351 239 798 732
   Fax: +351 239 798 703

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