[CP2K-user] Calculating normal modes for a saddle point structure from NEB
Mohammad Momeni Taheri
mome... at ualberta.ca
Tue Oct 30 17:11:35 UTC 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
-------------------------------------------------------------------------------
-
-
- DBCSR STATISTICS
-
-
-
-------------------------------------------------------------------------------
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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