Bug in the cell-optimization

xujroman leit... at matcalc.de
Mon Sep 7 15:30:27 CEST 2009


Dear Teo,

Thank you very much for your quick response.
I have to apologize for the uncomplete description of the problem.
And you are complete right that the CP2K-code performes the coordinate
transformation correctly with the multiple_uni_cell option. However,
with the multiple_unit_cell option this is not the case. Here is my
complete example inputfile:

&FORCE_EVAL
  METHOD Quickstep
  STRESS_TENSOR ANALYTICAL
  &DFT
    &MGRID
      CUTOFF 400
    &END MGRID
    &QS
      WF_INTERPOLATION PS
      EXTRAPOLATION_ORDER 3
    &END QS
    &SCF
      SCF_GUESS ATOMIC
      MAX_SCF 500
      &OT
        PRECONDITIONER FULL_ALL
      &END OT
    &END SCF
    &XC
      &XC_FUNCTIONAL Pade
      &END XC_FUNCTIONAL
    &END XC
  &END DFT
  &SUBSYS
    &CELL
       MULTIPLE_UNIT_CELL 2 2 2
       PERIODIC XYZ
         A 2.7 0.0 2.7
         B 0.0 2.7 2.7
         C 2.7 2.7 0.0
    &END CELL
    &TOPOLOGY
       MULTIPLE_UNIT_CELL 2 2 2
    &END TOPOLOGY
    &COORD
    Si                   0.00 0.00 0.00
    Si                   1.35 1.35 1.35
    &END COORD
    &KIND Si
      BASIS_SET DZVP-MOLOPT-SR-GTH
      POTENTIAL GTH-PADE-q4
    &END KIND
  &END SUBSYS
&END FORCE_EVAL
&GLOBAL
  PROJECT Bulk_Si
  RUN_TYPE CELL_OPT
  PRINT_LEVEL MEDIUM
&END GLOBAL
&MOTION
  &CELL_OPT
    OPTIMIZER CG
    KEEP_ANGLES .TRUE.
    &CG
      &LINE_SEARCH
        TYPE 2PNT
      &END LINE_SEARCH
    &END CG
  &END CELL_OPT
  &GEO_OPT
  OPTIMIZER CG
   &CG
     &LINE_SEARCH
       TYPE 2PNT
     &END LINE_SEARCH
   &END CG
  &END GEO_OPT
&END MOTION


Than CP2K produces the following restart file for the first geometry
optimization:

"Bulk_Si-GEO_OPT-0-1.restart"

&GLOBAL
   PRINT_LEVEL  MEDIUM
   PROJECT_NAME Bulk_Si-GEO_OPT-0
   RUN_TYPE  GEO_OPT
 &END GLOBAL
 &MOTION
   &GEO_OPT
     OPTIMIZER  CG
     STEP_START_VAL               4
     &CG
       &LINE_SEARCH
         TYPE  2PNT
       &END LINE_SEARCH
     &END CG
   &END GEO_OPT
   &CELL_OPT
     OPTIMIZER  CG
     KEEP_ANGLES  T
     &CG
       &LINE_SEARCH
         TYPE  2PNT
       &END LINE_SEARCH
     &END CG
   &END CELL_OPT
 &END MOTION
 &FORCE_EVAL
   METHOD  QS
   STRESS_TENSOR  ANALYTICAL
   &DFT
     &SCF
       MAX_SCF             500
       SCF_GUESS  ATOMIC
       &OT  T
         PRECONDITIONER  FULL_ALL
       &END OT
     &END SCF
     &QS
       EXTRAPOLATION  PS
       EXTRAPOLATION_ORDER               3
     &END QS
     &MGRID
       CUTOFF     4.0000000000000000E+02
     &END MGRID
     &XC
       DENSITY_CUTOFF     1.0000000000000000E-10
       GRADIENT_CUTOFF     1.0000000000000000E-10
       TAU_CUTOFF     1.0000000000000000E-10
       &XC_FUNCTIONAL  NO_SHORTCUT
         &PADE  T
         &END PADE
       &END XC_FUNCTIONAL
     &END XC
   &END DFT
   &SUBSYS
     &CELL
       A     7.6367532368147142E+00    0.0000000000000000E+00
0.0000000000000000E+00
       B     3.8183766184073580E+00    6.6136223055145820E+00
0.0000000000000000E+00
       C     3.8183766184073580E+00    2.2045407685048608E+00
6.2353829072479581E+00
       PERIODIC  XYZ
       MULTIPLE_UNIT_CELL               1              1
1
     &END CELL
     &COORD
Si    3.0639514919983863E-02   -2.8242821460592239E-02
1.2131623166612593E-01
Si    1.3193495751433768E+00    1.3782624207317524E+00
1.2286957353427554E+00
Si    3.8490798181990464E+00   -2.8320697084029275E-02
1.2126783349051763E-01
Si    5.1376820476818041E+00    1.3783083847899655E+00
1.2287240811324363E+00
Si    1.9398877629734372E+00    3.2785123111400014E+00
1.2127224020316246E-01
Si    3.2284938259833087E+00    4.6851396455951750E+00
1.2287292059456105E+00
Si    5.7582126739877406E+00    3.2785351488380750E+00
1.2131193923098339E-01
Si    7.0469084002716542E+00    4.6850408392785452E+00
1.2286951015890237E+00
Si    1.9398313145352879E+00    1.0740001965920085E+00
3.2390111451643167E+00
Si    3.2285203779859857E+00    2.4805201365770992E+00
4.3463762721786576E+00
Si    5.7582729781511999E+00    1.0739700719830776E+00
3.2389492368130282E+00
Si    7.0468843476696410E+00    2.4805953782967070E+00
4.3464148788581944E+00
Si    3.8490558773340240E+00    4.3807727795452909E+00
3.2389587712566126E+00
Si    5.1376813917952999E+00    5.7873852648962050E+00
4.3464231864196980E+00
Si    7.6674155348390309E+00    4.3808259988106144E+00
3.2390115121197063E+00
Si    8.9561123418762545E+00    5.7873380179790690E+00
4.3463760808472580E+00
       UNIT angstrom
       SCALED  F
     &END COORD
     &KIND Si
       BASIS_SET DZVP-MOLOPT-SR-GTH
       POTENTIAL GTH-PADE-q4
       &BASIS
 1
 2 0 2 4 2 2 1
  0.1256767641387000E+01  0.2277184666000000E+00 -0.1025748084300000E
+01  0.6777626750000000E-01  0.9978562
880000000E-01  0.1590266803000000E+00
  0.5063941224780000E+00 -0.2432359930000000E-01  0.6942830333000000E
+00 -0.2137167702000000E+00 -0.4119852
298000000E+00  0.3923304368000000E+00
  0.2388838456620000E+00 -0.5586397789000001E+00
0.5816256160000000E-01 -0.4098937266000000E+00 -0.5718312
630000000E-01  0.3930851518000000E+00
  0.8733688383600000E-01 -0.2072725022000000E+00 -0.2581810090000000E
+00 -0.3539223027000000E+00  0.7003078
694000000E+00  0.5503371190000000E+00
         # Basis set name:  DZVP-MOLOPT-SR-GTH  for symbol:  SI
         # Basis set read from the basis set filename: BASIS_SET
       &END BASIS
       &POTENTIAL
 2 2
  0.4400000000000000E+00 1 -0.7336102970000000E+01
 2
  0.4227381300000000E+00 2  0.5906928310000000E+01 -0.1261893970000000E
+01
  0.3258196220000000E+01
  0.4842784200000000E+00 1  0.2727013460000000E+01
         # Potential name:  GTH-PADE-Q4  for symbol:  SI
         # Potential read from the potential filename: POTENTIAL
       &END POTENTIAL
     &END KIND
     &TOPOLOGY
       MULTIPLE_UNIT_CELL               1              1
1
     &END TOPOLOGY
   &END SUBSYS
 &END FORCE_EVAL


Unfortunately the coordinates of the Si atoms are not correct with
respect to the transformed unit cell vectors A, B, and C. The correct
coordinates should look like this:


Si   -1.0974014519825657E-04   -1.7676012019053982E-03
-1.2247900828984469E-04
Si    1.9088000735955255E+00    1.0944726640717317E+00
7.7893023499684144E-01
Si    3.8183059956121781E+00   -1.7779368613748551E-03
-1.1357811744934891E-04
Si    5.7271759294263447E+00    1.0944547185135503E+00
7.7890654502406864E-01
Si    1.9090749183411335E+00    3.3050573189720218E+00
-1.5157491350578401E-04
Si    3.8179628211673160E+00    4.4012778324505941E+00
7.7892967187829554E-01
Si    5.7274934267539006E+00    3.3050361130777244E+00
-1.3821143796487556E-04
Si    7.6363617347003778E+00    4.4012824684472971E+00
7.7891991655355786E-01
Si    1.9091055301673019E+00    1.1005059638846280E+00
3.1175911749541818E+00
Si    3.8179649967213978E+00    2.1967404071085168E+00
3.8966155940247806E+00
Si    5.7274452451871918E+00    1.1005178548571481E+00
3.1175479694808246E+00
Si    7.6363591558557724E+00    2.1967134353509921E+00
3.8966375352308700E+00
Si    3.8182995220292710E+00    4.4073191096446083E+00
3.1175900344650893E+00
Si    5.7271689960387739E+00    5.5035538456743192E+00
3.8966033344321609E+00
Si    7.6366707112344292E+00    4.4073206445445692E+00
3.1175597801613035E+00
Si    9.5455465773110539E+00    5.5035454488461228E+00
3.8966256806012440E+00


Regarsds,
Roman







On 7 Sep., 12:32, Teodoro Laino <teodor... at gmail.com> wrote:
> Roman,
>
> there is a bunch of missing information. The CELL_UC is printed only
> when you use multiple_unit_cell, which is by
> far not he default.
> Is this maybe the case? Are you using multiple_unit_cell option?  If
> yes.. don't you think that maybe this could be an important thing to say ?
> What is the reason why all the time people are measuring out carefully
> information from their input file?
> Why not sending directly the input?
>
> Just to make the point of the situation clear enough:
> - without multiple_unit_cell there are no bugs (optimization is
> completed in 5 steps)
> - I checked as well the multiple_unit_cell and there are no bugs (your
> coordinates works perfectly) (optimization is completed in 11 steps with
> a  2 2 2 repetition).
>
> since I have no idea why have CELL_UC in your output file, I cannot say
> anything else than just confirming that the coordinates are properly
> adapted to the rotation of the cell and there is no evidence for bugs.
> (Keep in mind that the major printing of the coordinates that look like
> the thing you've pasted in the message is done long time before the
> rotation of the matrix).
>
> If you still want to claim to have found a bug please attach a complete
> input file.
> A code updated to the lastest CVS version may help as well the
> communication in order to avoid to see different things.
>
> Regards,
> Teo
>
> xujroman wrote:
> > Dear Teo,
>
> > the following part of the input file ndescribes my unit cell:
>
> >    &CELL
> >        PERIODIC XYZ
> >          A 2.7 0.0 2.7
> >          B 0.0 2.7 2.7
> >          C 2.7 2.7 0.0
> >     &END CELL
> >     &TOPOLOGY
> >     &END TOPOLOGY
> >     &COORD
> >     Si                   0.00 0.00 0.00
> >     Si                   1.35 1.35 1.35
> >     &END COORD
>
> > Than CP2K performes a coordinat transformation:
>
> >  CELL_UC| Volume
> > [angstrom^3]:                                            39.366
> >  CELL_UC| Vector a [angstrom]     3.818     0.000     0.000    |a|
> > =       3.818
> >  CELL_UC| Vector b [angstrom]     1.909     3.307     0.000    |b|
> > =       3.818
> >  CELL_UC| Vector c [angstrom]     1.909     1.102     3.118    |c|
> > =       3.818
> >  CELL_UC| Angle (b,c), alpha
> > [degree]:                                    60.000
> >  CELL_UC| Angle (a,c), beta
> > [degree]:                                    60.000
> >  CELL_UC| Angle (a,b), gamma [degree]:
> > 60.000
>
> > However the Si coordinates remain at the positions:
>
> >      1    1   Si   14    0.000000    0.000000    0.000000
> > 4.00      28.0860
> >      2    1   Si   14    1.350000    1.350000    0.350000
> > 4.00      28.0860
>
> > And this is of course not correct, because the periodic images are now
> > arranged in a wong way.
>
> > Regards,
> > Roman
>
> > On 7 Sep., 11:50, Teodoro Laino <teodor... at gmail.com> wrote:
>
> >> Dear Xujroman,
>
> >> what do you call "atomar basis". When the cell is rotated and aligned
> >> along the X,Y and Z axis the atomic coordinates are too...
> >> I don't see any evidence for the bug you're claiming to have found.
>
> >> Of course fee free to attach an input file that reproduces this error.
> >> Regards,
> >> Teo
>
> >> xujroman wrote:
>
> >>> Dear CP2K users,
>
> >>> I am performing a cell optimization using Cell_Opt and Geo_Opt for
> >>> bulk Si.
> >>> However, I recognized a bug during the setup of the unit cell.
>
> >>> If the starting cell vectors are given along arbitrary directions,
> >>> CP2K performes a coodinate transformation so that the first cell
> >>> vector (A) points along the x-axis. However, the atomar basis in the
> >>> unit cell is not transformed. That leads to a completely different
> >>> (wrong) atomic structure taking the periodic boundary conditions into
> >>> account.
>
> >>> The most simple way to avoid this bug, is to use cell vectors in such
> >>> a way that the A vector is parallel to the x-axis.


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