[CP2K-user] Calculating normal modes for a saddle point structure from NEB

Jaap Louwen jaap.n... at gmail.com
Mon Oct 29 10:47:41 CET 2018


Hi Mohammad,

I have no experience with mode selective calculations, but if you just want 
to compute a partial Hessian over atoms directly involved in the TS, fixing 
all other atoms will work for you.
Your vibrational analysis namelist will just read something like:

&VIBRATIONAL_ANALYSIS
  NPROC_REP 28
  FULLY_PERIODIC
&END VIBRATIONAL_ANALYSIS

while within the &Motion namelist you include a constraint section like:
   &CONSTRAINT
      &FIXED_ATOMS
        COMPONENTS_TO_FIX XYZ
        LIST  1..12
        LIST  14..24
        LIST  26..65
        LIST  67..144
      &END FIXED_ATOMS
   &END CONSTRAINT

CP2K will simply skip the fixed atoms.

Regards, Jaap



Op zaterdag 27 oktober 2018 19:59:25 UTC+2 schreef Mohammad Momeni Taheri:
>
> Hi, I have problems in computing normal modes for a structure that I got 
> from NEB calculations. My smallest system has 476 atoms and therefore I 
> cannot perform a full numerical frequency calculations. However, when I use 
> the inout below it seems that CP2K still tries to diagonalize the entire 
> hessian matrix (the job fails after 48hrs; output file is attached). Is my 
> input correct if not could you please provide a sample input file for these 
> calculations?
>
> Thanks in advance,
> Mohammad
>
>
> Below is my input file:
>
> &GLOBAL
>   PROJECT test
>   RUN_TYPE NORMAL_MODES
>   PRINT_LEVEL MEDIUM
> &END GLOBAL
>
> &VIBRATIONAL_ANALYSIS
> NPROC_REP 28
> FULLY_PERIODIC TRUE
> &MODE_SELECTIVE
> ATOMS 450 451 452 446 468 434 445 413 398 99 447 448 449 457 453 454 455 
> 456 458 459 460 461 462 463 464 465 466 467
> LOWEST_FREQUENCY -500
> RANGE -500 100
> &INVOLVED_ATOMS 
> INVOLVED_ATOMS 450 451 452 446 468 434 445 413 398 99 447 448 449 457 453 
> 454 455 456 458 459 460 461 462 463 464 465 466 467
> RANGE -500 100
> &END INVOLVED_ATOMS
> &END MODE_SELECTIVE
> &END VIBRATIONAL_ANALYSIS
>
> &FORCE_EVAL
>   METHOD Quickstep
>   &SUBSYS
>     &KIND Zr
>       ELEMENT   Zr
>       BASIS_SET DZVP-MOLOPT-SR-GTH
>       POTENTIAL GTH-PBE-q12
>     &END
>     &KIND C
>       ELEMENT C
>       BASIS_SET DZVP-MOLOPT-GTH
>       POTENTIAL GTH-PBE-q4
>     &END 
>     &KIND O
>       ELEMENT O
>       BASIS_SET DZVP-MOLOPT-GTH
>       POTENTIAL GTH-PBE-q6
>     &END 
>     &KIND H
>       ELEMENT H
>       BASIS_SET DZVP-MOLOPT-GTH
>       POTENTIAL GTH-PBE-q1
>     &END 
>     &KIND F
>       ELEMENT F
>       BASIS_SET DZVP-MOLOPT-GTH
>       POTENTIAL GTH-PBE-q7
>     &END KIND
>     &KIND P
>       ELEMENT P
>       BASIS_SET DZVP-MOLOPT-GTH
>       POTENTIAL GTH-PBE-q5
>     &END KIND
>     &CELL
>  A [angstrom]                23.34964320    0.00000000    0.00000000
>  B [angstrom]               -11.67970624   20.19999013    0.00000000
>  C [angstrom]                -0.24143113    0.14997040   51.67634031
>    PERIODIC XYZ
>     &END CELL
>
> &TOPOLOGY                    ! Section used to center the atomic 
> coordinates in the given box. Useful for big molecules
> &CENTER_COORDINATES
> &END
> COORD_FILE_FORMAT xyz
> COORD_FILE_NAME  ./test.xyz
> &END
>
>   &END SUBSYS
>   &DFT
>     BASIS_SET_FILE_NAME  /opt/packages/CP2K/cp2k-5.1/data/BASIS_MOLOPT
>     POTENTIAL_FILE_NAME  /opt/packages/CP2K/cp2k-5.1/data/POTENTIAL
>
>     &POISSON
>      PERIODIC XYZ
>     &END POISSON
>     
>     &QS
>       EPS_DEFAULT 1.0E-12
>     &END QS
>   &XC
>   &XC_FUNCTIONAL PBE
>   &END XC_FUNCTIONAL
>       &vdW_POTENTIAL
>          DISPERSION_FUNCTIONAL PAIR_POTENTIAL
>          &PAIR_POTENTIAL
>             TYPE DFTD3(BJ)
>             CALCULATE_C9_TERM .TRUE.
>             REFERENCE_C9_TERM .TRUE.
>             LONG_RANGE_CORRECTION .TRUE.
>             PARAMETER_FILE_NAME ./dftd3.dat
>             REFERENCE_FUNCTIONAL PBE
>             R_CUTOFF 15
>     &END PAIR_POTENTIAL 
>       &END vdW_POTENTIAL
>     &END XC
>   &SCF
>       SCF_GUESS ATOMIC
>       EPS_SCF 1.0E-6
>       MAX_SCF 500
>      &OT
>      MINIMIZER CG
>      PRECONDITIONER FULL_ALL
>      ENERGY_GAP 0.001
>      &END OT
>     &END SCF
>   &END DFT
>   &END
>
>
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