Question regarding frequency analysis

[Sassy]

Dear Teo,

thanks for your reply. The fog starts to lift off and I can see
clearly now :-)

I have recompiled cp2k and I am running the calculation again.
Once I know which part of the molecule is causing the imaginary
frequency,
I get an idea of how to sort that problem out.

All the best

Jörg

On Mar 9, 6:09 pm, Teodoro Laino <teodor... at gmail.com> wrote:
> Jörg Saßmannshausen wrote:
> > Dear all,
>
> > I am fairly new to cp2k and after the workshop in Zurich I am beginning
> > slowly to find my way around the program. I thought I started off a bit
>
> Hi Joerg,
> > I assume that was ok?
>
> that's ok!
> > Ok, doing the same as I did above, ignoring the first 6 ones would still
> > leave me with the first one I am interested in. As I wanted to have the
> > output in the molden-format so I can actually find out which part of the
> > molecule is causing the negative frequency, I opened that file in
> > molden, only to find out that I am having the 19.68 as the lowest
> > frequency but not the -33.36.
>
> When CP2K prints the Internal Low-Frequencies, the rotations and
> translations have been already purified.
> This means that if you encounter the problem of having more negative
> frequencies than in the non-purified, either the geometry is not in a
> minimum or the DX is too small. In your case DX of 1.0E-3 is ok.. So
> there must be something wrong with the geometry.
>
> > So, now I am completly confused. Apparently, my molecule has not
> > converged to a minimum as I got negative frequencies, but they are not
> > in the molden file so how can I find out which part of the molecule is
> > causing the negative frequency?
> > Is there something I did wrong here?
>
> No.. that was a kind of "bug". In the output of molden only positive
> frequencies were dumped.
> It's fixed now in the CVS. Please update//recompile and you will find
> the right behavior.
> Only the purified frequencies are dumped anyway (this means that in the
> MOLDEN  file you will not
> find the translations and the rotations).
>
> Cheers
> Teo
>
> > I have attached input files (input, forceeval and subsys) at the end of
> > this email. I took the liberty to omit the coordinates and cut out some
> > part of the subsys.inc as they are not part of the problem. As I said,
> > the program runs ok, so there is more a confusion or a problem in the
> > input file. I can, if requested, provide them of cause.
>
> > Many thanks for you help!
>
> > Best wishes from Glasgow!
>
> > Jörg
>
> > input-file:
> > ! Possibly restart (if explicitly requested)
> > @IF 1
> > &EXT_RESTART ON
> >    RESTART_DEFAULT F
> >    RESTART_FILE_NAME FLUORGEOM-1.restart
> >    RESTART_POS T
> >    RESTART_COUNTERS T
> > &END EXT_RESTART
> > @ENDIF
>
> > &GLOBAL
> >    PROJECT  FLUORGEOM
> >    RUN_TYPE NORMAL_MODES
> >    PRINT_LEVEL LOW
> > &END GLOBAL
>
> > &VIBRATIONAL_ANALYSIS
> >     NPROC_REP 4
> >     DX 0.001
> > !   INTENSITIES
> >     &PRINT
> >       &PROGRAM_RUN_INFO ON
> >       &END
> >       &MOLDEN_VIB
> >        FILENAME=frequencies.mol
> >       &END
> >     &END
>
> > &END
>
> > @INCLUDE 'force_eval.inc'
>
> > force_eval.inc file:
>
> > @SET SCF_CONV   1.0E-6
> > @SET CUTOFF        450
> > @SET FUNCTIONAL    BLYP
> > @SET DECOUPLING     MT
> > @SET CHARGE          1
>
> > &FORCE_EVAL
> >    &PRINT
> >      &FORCES OFF
> >      &END
> >    &END
>
> >   &MIXED
> >    &PRINT
> >     &DIPOLE
> >     &END
> >    &END
> >   &END
>
> >    METHOD QS
>
> >    &DFT
> >      CHARGE ${CHARGE}
> >      &MGRID
> >        CUTOFF ${CUTOFF}
> >        NGRIDS 5
> >      &END MGRID
> >      &QS
> >        EPS_DEFAULT 1.0E-12
> >      &END QS
> >      &SCF
> >        SCF_GUESS ATOMIC
> >        EPS_SCF       ${SCF_CONV}
> >        MAX_SCF      30
> >        &PRINT
> >          &RESTART
> >            LOG_PRINT_KEY T
> >            FILENAME =./WFN_restart.wfn
> >            &EACH
> >              QS_SCF  0
> >            &END EACH
> >            ADD_LAST NUMERIC
> >            COMMON_ITERATION_LEVELS 1
> >          &END RESTART
> >        &END PRINT
> >        &OT ON
> >          MINIMIZER DIIS
> >             ! MINIMIZER CG
> >             ! PRECONDITIONER FULL_ALL
> >             ! PRECONDITIONER FULL_KINETIC
> >          PRECONDITIONER FULL_SINGLE_INVERSE
> >             !ENERGY_GAP  0.001
> >        &END OT
> >        &OUTER_SCF
> >          EPS_SCF ${SCF_CONV}
> >          MAX_SCF 5
> >        &END OUTER_SCF
> >      &END SCF
> >      &XC
> >        &XC_FUNCTIONAL ${FUNCTIONAL}
> >        &END XC_FUNCTIONAL
> >      &END XC
> > @IF ( ${DECOUPLING} == NONE )
> >      &POISSON
> >      &END
> > @ENDIF
> > @IF ( ${DECOUPLING} == MT )
> >      &POISSON
> >         POISSON_SOLVER MT
> >         PERIODIC NONE
> >         &MT
> >         &END
> >      &END
> > @ENDIF
> > @IF ( ${DECOUPLING} == WAVELET )
> >      &POISSON
> >         POISSON_SOLVER WAVELET
> >         PERIODIC NONE
> >         &WAVELET
> >           SCF_TYPE 60
> >         &END
> >      &END
> > @ENDIF
> >    &END DFT
>
> >    ! Include subsys
> > @INCLUDE 'subsys.inc'
> > &END FORCE_EVAL
>
> > subsys.inc file:
> >    &SUBSYS
> >      &CELL
> > #      ABC [angstrom] 23 15 10.0
> >        ABC [angstrom] 25 17 12
> >        PERIODIC NONE
> >      &END CELL
> >      &TOPOLOGY
> >        CONNECTIVITY OFF
> >        COORDINATE   XYZ
> >        COORD_FILE_NAME fluor.xyz
> >        CENTER_COORDINATES
> >      &END TOPOLOGY
> >      &KIND C
> >        POTENTIAL GTH
> >        &POTENTIAL
> >          # C GTH-BLYP-q4
> >      2    2
> >       0.33806609    2    -9.13626871     1.42925956
> >      2
> >       0.30232223    1     9.66551228
> >       0.28637912    0
> >        &END POTENTIAL
> >        &BASIS
> >          # C DZVP-GTH-BLYP
> >    2
> >    2  0  1  4  2  2
> >          4.3451975957   0.1511172750   0.0000000000  -0.0883417890
> > 0.0000000000
> >          1.2765552224  -0.0330272512   0.0000000000  -0.2797032766
> > 0.0000000000
> >          0.4047139801  -0.6994401873   0.0000000000  -0.4686400677
> > 0.0000000000
> >          0.1166096360  -0.3842706677   1.0000000000  -0.4085514115
> > 1.0000000000
> >    3  2  2  1  1
> >          0.6000000000   1.0000000000
> >        &END BASIS
> >      &END KIND
> >      &KIND F
> >        POTENTIAL GTH
> >        &POTENTIAL
> >          # F GTH-BLYP-q7
> >      2    5
> >       0.21384014    2   -21.90241518     3.27597572
> >      2
> >       0.19459028    1    23.79658295
> >       0.18786326    0
> >        &END POTENTIAL
> >        &BASIS
> >          # F DZVP-GTH-BLYP
> >    2
> >    2  0  1  4  2  2
> >         10.7284760684   0.1539953252   0.0000000000  -0.1034591141
> > 0.0000000000
> >          3.1496622427  -0.0503062083   0.0000000000  -0.3116781877
> > 0.0000000000
> >          0.9671794608  -0.7107682323   0.0000000000  -0.4776960745
> > 0.0000000000
> >          0.2640315133  -0.3648266470   1.0000000000  -0.3688578623
> > 1.0000000000
> >    3  2  2  1  1
> >          1.0000000000   1.0000000000
> >        &END BASIS
> >      &END KIND
> >      &KIND H
> >        POTENTIAL GTH
> >        &POTENTIAL
> >          # H GTH-BLYP-q1
> >      1
> >       0.20000000    2    -4.19596147     0.73049821
> >      0
> >        &END POTENTIAL
> >        &BASIS
> >          # H DZV-GTH-BLYP
> > [...]
>
> >        &END BASIS
> >      &END KIND
> >    &END SUBSYS