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

Mohammad Momeni Taheri mome... at ualberta.ca
Tue Oct 30 18:11:35 CET 2018


Hi Jaap,

Thanks for your response. I fixed all the other atoms and it worked but the 
problem now is that CP2K doesn't print the imaginary frequency. I'm sure 
the structure I input should at least have one but CP2K apparently is only 
printing the positive ones. I thought putting the RANGE keyword will take 
care of this but it didn't. I have pasted the relevant sections of my input 
and output files below.

Thanks,
Mohammad

*Input:*
&GLOBAL
  PROJECT test
  RUN_TYPE NORMAL_MODES
  PRINT_LEVEL MEDIUM
&END GLOBAL

&MOTION
  &CONSTRAINT
    &FIXED_ATOMS
      COMPONENTS_TO_FIX XYZ
      LIST 1..7
      LIST 9..515
      LIST 517..521
      LIST 523..539
      LIST 541..545
      LIST 547..553
    &END FIXED_ATOMS
  &END CONSTRAINT
&END MOTION

&VIBRATIONAL_ANALYSIS
  NPROC_REP 24
  &MODE_SELECTIVE
    ATOMS 8 516 522 540 546 554 555 556 557 558 559 560 561 562 563 564 565 
566 567 568 569 570 571 572 573 574 575 576
    FREQUENCY -500
    RANGE -500 100
    &INVOLVED_ATOMS 
    INVOLVED_ATOMS 8 516 522 540 546 554 555 556 557 558 559 560 561 562 
563 564 565 566 567 568 569 570 571 572 573 574 575 576
      RANGE -500 100
    &END INVOLVED_ATOMS
  &END MODE_SELECTIVE
  &PRINT
    &MOLDEN_VIB
      FILENAME test
    &END MOLDEN_VIB
  &END PRINT
&END VIBRATIONAL_ANALYSIS

*Output:*
 REPLICA| layout of the replica grid, number of groups                     
    1
 REPLICA| layout of the replica grid, size of each group                   
   16
 REPLICA| MPI process to grid (group,rank) correspondence:
  (   0 :    0,   0)  (   1 :    0,   1)  (   2 :    0,   2)  (   3 :    0, 
  3)
  (   4 :    0,   4)  (   5 :    0,   5)  (   6 :    0,   6)  (   7 :    0, 
  7)
  (   8 :    0,   8)  (   9 :    0,   9)  (  10 :    0,  10)  (  11 :    0, 
 11)
  (  12 :    0,  12)  (  13 :    0,  13)  (  14 :    0,  14)  (  15 :    0, 
 15)
 MS| ITERATION STEP        1
 MS| TRACKED MODE     1067.402517cm-1  NOT  CONVERGED
 MS| ITERATION STEP        2
 MS| TRACKED MODE      629.589298cm-1  NOT  CONVERGED
 MS| ITERATION STEP        3
 MS| TRACKED MODE      516.249401cm-1  NOT  CONVERGED
 MS| ITERATION STEP        4
 MS| TRACKED MODE      297.969319cm-1  NOT  CONVERGED
 MS| ITERATION STEP        5
 MS| TRACKED MODE      274.303122cm-1  NOT  CONVERGED
 MS| ITERATION STEP        6
 MS| TRACKED MODE      197.889363cm-1  NOT  CONVERGED
 MS| ITERATION STEP        7
 MS| TRACKED MODE      177.282435cm-1  NOT  CONVERGED
 MS| ITERATION STEP        8
 MS| TRACKED MODE      150.074885cm-1  NOT  CONVERGED
 MS| ITERATION STEP        9
 MS| TRACKED MODE      125.450225cm-1  NOT  CONVERGED
 MS| ITERATION STEP       10
 MS| TRACKED MODE       98.399232cm-1  NOT  CONVERGED
 MS| ITERATION STEP       11
 MS| TRACKED MODE       81.644671cm-1  NOT  CONVERGED
 MS| DAVIDSON ALGORITHM CONVERGED
 MS| TRACKED FREQUENCY (1) IS:   11.618812   cm-1
 -------------------------------------------------------------------------------
                         FREQUENCY AND CONVERGENCE LIST
       FREQUENCY    MAXVAL CRITERIA    NORM CRITERIA    CONVERGENCE
  VIB|   451.221     0.127135E-05        0.451E-05           NO
  VIB|   826.941     0.177668E-05        0.712E-05           NO
  VIB|  1192.902     0.287789E-05        0.102E-04           NO
  VIB|  1405.678     0.172961E-05        0.694E-05           NO
  VIB|  1585.591     0.153388E-05        0.545E-05           NO
  VIB|  3001.268     0.126841E-05        0.450E-05           NO
  VIB|  3082.088     0.826133E-06        0.293E-05           NO
  VIB|  3131.784     0.131471E-05        0.467E-05           NO
  VIB|  3553.575     0.370080E-07        0.148E-06           YES
  VIB|  3706.396     0.161133E-07        0.646E-07           YES
  VIB|  3776.399     0.240125E-07        0.963E-07           YES

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On Monday, 29 October 2018 02:47:42 UTC-7, Jaap Louwen wrote:
>
> 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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