Looking for zero frequencies

Satish Kumar satis... at gmail.com
Mon Dec 15 01:25:31 CET 2014


Hello CP2K users

Sorry about these basic questions. So, here the system was periodic in 3D. 
However if I have a 2D (surface slab) periodic system do I still have to 
set FULLY_PERIODIC keyword to True. What does "rotational motions are 
not projected out" mean? What is a translational invariant system (is any 
periodic system  translationally invariant?)? When should one use 
POISSON_SOLVER block? Also how should we interpret the frequencies in 
"Snippet output frequency run:" section.

So I tried to reproduce your results (just changed the basis set and the 
potentials to DZVP-MOLOPT-GTH and  GTH-PBE-q4 resp) and for 8 atom system, 
I get the following 21 normal modes while I should Ideally get 18 normal 
modes for 8 atoms (3N-6). So should the three (21-18) extra normal modes be 
equal to 0 ideally? Now, the normal modes are so close that I don't know 
which 18 I should consider as the actual normal modes. 

      250.512753
      319.954005
      399.465765
      405.037651
      422.843253
      435.761877
     1097.038334
     1117.184070
     1124.201100
     1127.137991
     1128.074863
     1128.868198
     1133.580152
     1136.804637
     1141.857240
     1142.663552
     1155.931539
     1163.319124
     1617.679412
     1624.770294
     1627.580761

I am thinking of using the following input file for my 2D surface slab for 
frequency calculations.

&VIBRATIONAL_ANALYSIS
    FULLY_PERIODIC T 
    DX 0.01
    NPROC_REP 8
  &MODE_SELECTIVE
     RESTART_FILE_NAME 4x4-VIBRATIONS-1.mol
      &INVOLVED_ATOMS
        INVOLVED_ATOMS 65 66
      &END INVOLVED_ATOMS
    ATOMS 65 66 
  &END MODE_SELECTIVE  
&END VIBRATIONAL_ANALYSIS

&FORCE_EVAL
  METHOD Quickstep
  STRESS_TENSOR ANALYTICAL
  &DFT
    BASIS_SET_FILE_NAME ./GTH_BASIS_SETS
    POTENTIAL_FILE_NAME ./GTH_POTENTIALS
    WFN_RESTART_FILE_NAME 4x4-RESTART.wfn 
    &MGRID
      CUTOFF 480
      NGRIDS 5
    &END MGRID
    &QS
      WF_INTERPOLATION ASPC
      EXTRAPOLATION_ORDER 3
    &END QS
   &SCF
     EPS_SCF 1.E-6
     SCF_GUESS RESTART
     MAX_SCF 100
     &OUTER_SCF
      EPS_SCF 1.E-6
      MAX_SCF 20
     &END OUTER_SCF
     &OT T
       PRECONDITIONER FULL_SINGLE_INVERSE
       MINIMIZER CG
       LINESEARCH 3PNT
     &END OT
    &END SCF
    &XC
      &XC_FUNCTIONAL PBE
      &END XC_FUNCTIONAL
    &END XC
  &PRINT
  &END PRINT
  &END DFT
  &SUBSYS
 &CELL
A      11.2005714139949148    0.0000000000000000    0.0000000000000000
B       5.6002857069974574    9.6999793814213842    0.0000000000000000
C       0.0000000000000000    0.0000000000000000   26.8589211979727551
&END CELL
&COORD
Pd    -0.0000061359210358 -0.0000222840946560  9.9880132312990213
Pd     2.8000908510293288  0.0000092115121854  9.9879695072021697
Pd     5.6002734938253287 -0.0000045647646310  9.9879245033445034
Pd     8.4004340473737855 -0.0000362027794058  9.9879677511115652
Pd     1.4000634784708132  2.4249744889860554  9.9880132682562639
Pd     4.2001617373702826  2.4250029632593546  9.9879685687298245
Pd     7.0003471689337546  2.4249881536022277  9.9879248470317670
Pd     9.8005050809925134  2.4249618882564654  9.9879671972427317
Pd     2.8001369378977943  4.8499691363190243  9.9880148797577206
Pd     5.6002312352107486  4.8499974956142475  9.9879690366522222
Pd     8.4004168005198139  4.8499832866277810  9.9879251120231469
Pd    11.2005770533358611  4.8499548963592893  9.9879640638995539
Pd     4.2002068480680155  7.2749634825025922  9.9880166024601085
Pd     7.0003058990547880  7.2749930185934337  9.9879692328558018
Pd     9.8004884696248684  7.2749791367862375  9.9879232637271596
Pd    12.6006459666106423  7.2749492464615217  9.9879647613984162
Pd     1.4002245368808004  0.8084157041067350 12.3012388137054103
Pd     4.2003558131593932  0.8084218859192664 12.3012418639169621
Pd     7.0005061178333099  0.8084332483716472 12.3012622163864087
Pd     9.8006578762588088  0.8084217487769948 12.3012772146045251
Pd     2.8002965326028924  3.2334107313122149 12.3012392548407323
Pd     5.6004272909567518  3.2334165217953741 12.3012418245909636
Pd     8.4005772468615536  3.2334291460788043 12.3012628426338733
Pd    11.2007297065823632  3.2334147570161607 12.3012750335016499
Pd     4.2003688965050028  5.6584053402129628 12.3012398254336990
Pd     7.0004993266283773  5.6584119088267411 12.3012414536964982
Pd     9.8006498524563774  5.6584251222740383 12.3012626779581495
Pd    12.6008005523876250  5.6584086848353445 12.3012752704691177
Pd     5.6004393945982400  8.0834002167787382 12.3012396637977126
Pd     8.4005708513076502  8.0834072604243818 12.3012409646385859
Pd    11.2007215403971241  8.0834195185537538 12.3012615384488573
Pd    14.0008718167863044  8.0834038420466356 12.3012780910986823
Pd     0.0000000000000000  1.6166632302368973 14.5726141319818385
Pd     2.8001428534987292  1.6166632302368973 14.5726141319818385
Pd     5.6002857069974583  1.6166632302368973 14.5726141319818385
Pd     8.4004285604961844  1.6166632302368973 14.5726141319818385
Pd     1.4000714267493641  4.0416580755922427 14.5726141319818385
Pd     4.2002142802480922  4.0416580755922427 14.5726141319818385
Pd     7.0003571337468218  4.0416580755922427 14.5726141319818385
Pd     9.8004999872455478  4.0416580755922427 14.5726141319818385
Pd     2.8001428534987287  6.4666529209475891 14.5726141319818385
Pd     5.6002857069974574  6.4666529209475891 14.5726141319818385
Pd     8.4004285604961844  6.4666529209475891 14.5726141319818385
Pd    11.2005714139949148  6.4666529209475891 14.5726141319818385
Pd     4.2002142802480922  8.8916477663029347 14.5726141319818385
Pd     7.0003571337468218  8.8916477663029347 14.5726141319818385
Pd     9.8004999872455496  8.8916477663029347 14.5726141319818385
Pd    12.6006428407442783  8.8916477663029347 14.5726141319818385
Pd     0.0000000000000000  0.0000000000000000 16.8589211979727551
Pd     2.8001428534987287  0.0000000000000000 16.8589211979727551
Pd     5.6002857069974574  0.0000000000000000 16.8589211979727551
Pd     8.4004285604961844  0.0000000000000000 16.8589211979727551
Pd     1.4000714267493644  2.4249948453553460 16.8589211979727551
Pd     4.2002142802480922  2.4249948453553460 16.8589211979727551
Pd     7.0003571337468218  2.4249948453553460 16.8589211979727551
Pd     9.8004999872455478  2.4249948453553460 16.8589211979727551
Pd     2.8001428534987287  4.8499896907106921 16.8589211979727551
Pd     5.6002857069974574  4.8499896907106921 16.8589211979727551
Pd     8.4004285604961844  4.8499896907106921 16.8589211979727551
Pd    11.2005714139949148  4.8499896907106921 16.8589211979727551
Pd     4.2002142802480922  7.2749845360660377 16.8589211979727551
Pd     7.0003571337468218  7.2749845360660377 16.8589211979727551
Pd     9.8004999872455478  7.2749845360660377 16.8589211979727551
Pd    12.6006428407442765  7.2749845360660377 16.8589211979727551
C     2.7695479032678416  1.5018869319588131  8.8099561225681224
O     2.7497835812269869  1.4846637516465382  7.6749430013606608
&END COORD
    &KIND Pd 
      BASIS_SET DZVP-MOLOPT-SR-GTH 
      POTENTIAL GTH-PBE-q18
    &END KIND
    &KIND O
      BASIS_SET DZVP-MOLOPT-GTH
      POTENTIAL GTH-PBE-q6
    &END KIND
    &KIND C
      BASIS_SET DZVP-MOLOPT-GTH
      POTENTIAL GTH-PBE-q4
    &END KIND
  &END SUBSYS
&END FORCE_EVAL
&GLOBAL
  PROJECT 4x4
  RUN_TYPE VIBRATIONAL_ANALYSIS
  PRINT_LEVEL LOW
&END GLOBAL
 &MOTION
  &GEO_OPT
    MAX_ITER 200 
    MAX_FORCE 0.0009725
    OPTIMIZER BFGS 
  &END GEO_OPT
  &CONSTRAINT
    &FIXED_ATOMS
     LIST 33..64
    &END FIXED_ATOMS
  &END CONSTRAINT
 &END MOTION

Thank you for any help.



On Friday, April 9, 2010 11:35:20 AM UTC-4, An Ghysels wrote:
>
> Dear forum users,
>
> I am calculating frequencies in periodic structures, from which I'd
> like to derive thermodynamic quantities like the entropy etc.
> Therefore I use the VIBRATIONAL_ANALYSIS keyword, where I have put the
> FULLY_PERIODIC keyword to True, such that rotational motions are not
> projected out.
>
> In principle, the second derivatives matrix should have 3 zero
> eigenvalues (even in non-optimized systems), because the system is
> translational invariant. However, this is not the case in my
> calculations. Even in a small test case like diamond with a cubic cell
> containing 8 atoms, the "zero" frequencies deviate largely from zero.
>
> (Between brackets: I'm much bothered by this bad performance, because
> it signals that the numerical accuracy of the frequencies is poor. I
> aim at studying larger unit cells (eg with 100 to 200 QM atoms) where
> I surely will encounter floppy modes, which are even more sensible to
> numerical errors. And those floppy modes play an essential role in the
> partition function/thermodynamics. Therefore, I wish to improve the
> accuracy of the calculated frequencies.)
>
> So my questions are mainly: why is the accuracy so bad? Is this
> directly related to the eggbox effect, and if so, how to remedy it? Is
> it something with interpolation grids? And what to do to improve it?
>
> I tried decreasing the EPS_DEFAULT (down to 10e-16), increasing the
> E_CUTOFF (up to 1400 Rydberg), increasing the REL_CUTOFF accordingly,
> adding the keyword COMMENSURATE, changing the interpolation grid (to
> spline3), but the improvements still do not get me close to "zero"
> frequencies (still of the order -70 to 50 cm-1).
>
> Looking forward to your comments and remarks,
>
> An
>
> Below: Information on version, input geometry optimization, input
> frequency run, snippets of output
> =====
> Version:
>  CP2K| version string:                  CP2K version 2.0.1
> (Development Version)
>  CP2K| is freely available from                          
> http://cp2k.berlios.de/
>  CP2K| Program compiled at
> Wed_Sep__9_15:48:59_CEST_2009
>  CP2K| Program compiled
> on                                               gengar1
>  CP2K| Program compiled for                                   Linux-
> x86-64-intel
> =====
> Input geomery optimization
> &GLOBAL
>   PRINT_LEVEL high
>   PROJECT_NAME vib
>   RUN_TYPE GEO_OPT
>   PREFERRED_FFT_LIBRARY FFTW
> &END GLOBAL
>
> &MOTION
>   &GEO_OPT
>     OPTIMIZER BFGS
>     MAX_ITER 300
>   &END GEO_OPT
> &END MOTION
>
> &VIBRATIONAL_ANALYSIS
>     FULLY_PERIODIC T
> &END VIBRATIONAL_ANALYSIS
>
> &FORCE_EVAL
>
>   METHOD QS
>   &DFT
>     BASIS_SET_FILE_NAME GTH_BASIS_SETS
>     POTENTIAL_FILE_NAME GTH_POTENTIALS
>     &MGRID
>       CUTOFF 100
>       REL_CUTOFF 23
>       COMMENSURATE
>     &END MGRID
>     &QS
>      EPS_DEFAULT 1.0E-10
>     &END QS
>     &SCF
>       EPS_SCF 1.0E-5
>       MAX_SCF 100
>       SCF_GUESS RESTART
>       &OUTER_SCF
>         EPS_SCF 1.0E-5
>         MAX_SCF 20
>       &END
>       &OT
>         ALGORITHM IRAC
>         MINIMIZER CG
>         PRECONDITIONER FULL_ALL
>         ENERGY_GAP 0.001
>       &END OT
>       &PRINT
>         &RESTART
>          BACKUP_COPIES 0
>         &END RESTART
>       &END PRINT
>     &END SCF
>     &XC
>       &XC_FUNCTIONAL PBE
>       &END XC_FUNCTIONAL
>     &END XC
>     &POISSON
>      POISSON_SOLVER PERIODIC
>      PERIODIC XYZ
>      &EWALD
>        EWALD_TYPE EWALD
>        ALPHA 0.3
>        GMAX 11
>        O_SPLINE 6
>      &END EWALD
>    &END POISSON
>   &PRINT
>   &END PRINT
>   &END DFT
>
>   &SUBSYS
>     &CELL
>       ABC 3.567 3.567 3.567
>       PERIODIC XYZ
>     &END CELL
>     &COORD
> C  -0.066491  -0.063731  -0.038851
> C   0.019572   1.759040   1.767428
> C   1.756129   0.023158   1.769616
> C   1.767376   1.770784   0.004363
> C   0.841267   0.843123   0.828198
> C   2.663349   0.903043   2.661920
> C   0.899007   2.665284   2.661387
> C   2.644659   2.648722   0.926362
>   &END COORD
>     &TOPOLOGY
>       &GENERATE
>         CREATE_MOLECULES
>       &END GENERATE
>     &END TOPOLOGY
>
>       &KIND C
>       BASIS_SET DZVP-GTH
>       POTENTIAL GTH-PBE-q4
>     &END KIND
>
>   &END SUBSYS
> &END FORCE_EVAL
> =====
> Input Frequency run
> &GLOBAL
>   PRINT_LEVEL high
>   PROJECT_NAME vib
>   RUN_TYPE VIBRATIONAL_ANALYSIS
>   PREFERRED_FFT_LIBRARY FFTW
> &END GLOBAL
>
> &MOTION
>   &GEO_OPT
>     OPTIMIZER BFGS
>     MAX_ITER 300
>   &END GEO_OPT
> &END MOTION
>
> &VIBRATIONAL_ANALYSIS
>     FULLY_PERIODIC T
> &END VIBRATIONAL_ANALYSIS
>
> &FORCE_EVAL
>
>   METHOD QS
>   &DFT
>     BASIS_SET_FILE_NAME GTH_BASIS_SETS
>     POTENTIAL_FILE_NAME GTH_POTENTIALS
>     &MGRID
>       CUTOFF 100
>       REL_CUTOFF 23
>       COMMENSURATE
>     &END MGRID
>     &QS
>      EPS_DEFAULT 1.0E-10
>     &END QS
>     &SCF
>       EPS_SCF 1.0E-5
>       MAX_SCF 100
>       SCF_GUESS RESTART
>       &OUTER_SCF
>         EPS_SCF 1.0E-5
>         MAX_SCF 20
>       &END
>       &OT
>         ALGORITHM IRAC
>         MINIMIZER CG
>         PRECONDITIONER FULL_ALL
>         ENERGY_GAP 0.001
>       &END OT
>       &PRINT
>         &RESTART
>          BACKUP_COPIES 0
>         &END RESTART
>       &END PRINT
>     &END SCF
>     &XC
>       &XC_FUNCTIONAL PBE
>       &END XC_FUNCTIONAL
>     &END XC
>     &POISSON
>      POISSON_SOLVER PERIODIC
>      PERIODIC XYZ
>      &EWALD
>        EWALD_TYPE EWALD
>        ALPHA 0.3
>        GMAX 11
>        O_SPLINE 6
>      &END EWALD
>    &END POISSON
>   &PRINT
>   &END PRINT
>   &END DFT
>   &SUBSYS
>     &CELL
>       ABC 3.567 3.567 3.567
>       PERIODIC XYZ
>     &END CELL
>     &COORD
>   C        -0.0393192769       -0.0522499977       -0.0007602780
>   C         0.0299677090        1.7769206120        1.7824574256
>   C         1.7642084626        0.0471181783        1.7911208859
>   C         1.7938452241        1.7853211459        0.0053883203
>   C         0.8664406756        0.8762954420        0.8435833733
>   C         2.6939879368        0.9029246308        2.6806928814
>   C         0.9092781460        2.6785011492        2.6771532650
>   C         2.6481574040        2.6661172907        0.9483093511
>   &END COORD
>     &TOPOLOGY
>       &GENERATE
>         CREATE_MOLECULES
>       &END GENERATE
>     &END TOPOLOGY
>
>       &KIND C
>       BASIS_SET DZVP-GTH
>       POTENTIAL GTH-PBE-q4
>     &END KIND
>
>   &END SUBSYS
> &END FORCE_EVAL
> =====
> Snippet output frequency run:
> If I look at the values with the lowest absolute value and I convert
> them to cm-1, it is poor accuracy:
>
>  VIB| Cartesian Low frequencies ----0.44072    -0.10876E-01
> 0.12458     0.69806
>  VIB| Cartesian Low frequencies --- 0.71490      1.4715
> 2.0898      3.8120
>  VIB| Cartesian Low frequencies ---  5.8007
>  VIB| Frequencies after removal of the rotations and translations
>  VIB| Internal  Low frequencies ----0.14095     0.50894
> 1.4072      2.0559
>  VIB| Internal  Low frequencies ---  3.6794      5.7900
> 25.027      25.504
>  VIB| Internal  Low frequencies ---  25.855      25.997
> 26.180      26.684
>  VIB| Internal  Low frequencies ---  26.818      26.970
> 27.202      27.461
>  VIB| Internal  Low frequencies ---  27.643      28.937
> 54.059      54.351
>  VIB| Internal  Low frequencies ---  54.817
>
>  VIB|                        NORMAL MODES - CARTESIAN DISPLACEMENTS
>  VIB|
>  VIB|                         1
> 2                    3
>  VIB|Frequency (cm^-1)   -82.399299           156.573040
> 260.352529
> ...
>  
>
> -------------------------------------------------------------------------------
>  ----                             MULTIGRID
> INFO                            ----
>  
>
> -------------------------------------------------------------------------------
>  count for grid        1:            868          cutoff
> [a.u.]           50.00
>  count for grid        2:            276          cutoff
> [a.u.]           12.50
>  count for grid        3:             80          cutoff
> [a.u.]            3.12
>  count for grid        4:              0          cutoff
> [a.u.]            0.78
>  total gridlevel count  :           1224
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20141214/15218b05/attachment.html>


More information about the CP2K-user mailing list