Atoms are not relaxing, but successful optimization

Matt W MattWa... at gmail.com
Wed Mar 21 21:13:00 CET 2012


Is you system perfect fluorite structure obtained from converting a crystal 
structure in fractional coords?

If so it basically can't/won't move due to symmetry. 

Matt

On Wednesday, March 21, 2012 6:45:47 PM UTC, Nathaniel Swenson wrote:
>
> Hello, 
>
> My greatest apologies if you have already checked this, but this is a 
> simple point of clarification: 
>
> The cell_d-pos-1.xyz file typically should contain not just ONE set of 
> coordinates, but it should have sets of coordinates from ALL the 
> geometry optimization steps, all in one file.  Typically, the first 
> set of coordinates that appear in this file are your input 
> coordinates, so if you are simply opening this file with a 
> visualization program, this could explain why you are only getting 
> your input coordinates back.  On the contrary, the last set of 
> coordinates in the file should be your optimized coordinates. 
>
> How many sets of coordinates are showing up in your cell_d-pos-1.xyz 
> file? 
>
> Best wishes, 
> Nathaniel Swenson 
> Northwestern University 
>
>
> On Mar 21, 12:12 pm, Samuel Lamphier <samuell... at gmail.com> wrote: 
> > Hello all, I am modeling cerium oxide nano particles. I have prepared 
> > input file with high cutoffs, however, I have had good luck with 
> > optimizations. Then I discovered a problem, my atoms are not relaxing, 
> > is there something I am doing incorrectly? 
> > 
> > &GLOBAL 
> >    PRINT_LEVEL  LOW 
> >    PROJECT_NAME cell_d 
> >    RUN_TYPE  CELL_OPT 
> >    FLUSH_SHOULD_FLUSH  T 
> >  &END GLOBAL 
> >  &MOTION 
> >    &GEO_OPT 
> >      TYPE  MINIMIZATION 
> >      OPTIMIZER  BFGS 
> >      MAX_ITER             5000 
> >      MAX_DR     2.9999999999999997E-05 
> >      MAX_FORCE     5.0000000000000003E-06 
> >      RMS_DR     1.4999999999999999E-05 
> >      RMS_FORCE     5.0000000000000001E-06 
> >      STEP_START_VAL               1 
> >      &PRINT 
> >        &PROGRAM_RUN_INFO 
> >        &END PROGRAM_RUN_INFO 
> >      &END PRINT 
> >    &END GEO_OPT 
> >    &CELL_OPT 
> >      OPTIMIZER  CG 
> >      MAX_ITER             3000 
> >      MAX_DR     3.0000000000000001E-05 
> >      MAX_FORCE     5.0000000000000000E-06 
> >      RMS_DR     1.5000000000000000E-05 
> >      RMS_FORCE     2.9999999999999997E-06 
> >      STEP_START_VAL              1 
> >      TYPE  GEO_OPT 
> >      PRESSURE_TOLERANCE     1.0000000000000000E-01 
> >      &CG 
> >        MAX_STEEP_STEPS               0 
> >        RESTART_LIMIT     9.4999999999999996E-01 
> >        &LINE_SEARCH 
> >          TYPE  2PNT 
> >        &END LINE_SEARCH 
> >      &END CG 
> >    &END CELL_OPT 
> >  &END MOTION 
> >  &FORCE_EVAL 
> >    METHOD  QS 
> >    STRESS_TENSOR  ANALYTICAL 
> >    &DFT 
> >      CHARGE               0 
> >      PLUS_U_METHOD MULLIKEN 
> >      &SCF 
> >        MAX_SCF              1000 
> >        EPS_SCF     9.9999999999999995E-08 
> >        SCF_GUESS  ATOMIC 
> >        &OT  T 
> >          MINIMIZER  DIIS 
> >          PRECONDITIONER  FULL_ALL 
> >          ENERGY_GAP     1.0000000000000000E-03 
> >        &END OT 
> >        &OUTER_SCF  T 
> >          EPS_SCF     9.9999999999999995E-08 
> >        &END OUTER_SCF 
> >      &END SCF 
> >      &QS 
> >        EPS_DEFAULT     9.9999999999999998E-13 
> >      &END QS 
> >      &MGRID 
> >        CUTOFF     3.0000000000000000E+02 
> >      &END MGRID 
> >      &XC 
> >        DENSITY_CUTOFF     1.0000000000000000E-10 
> >        GRADIENT_CUTOFF     1.0000000000000000E-10 
> >        TAU_CUTOFF     1.0000000000000000E-10 
> >        &XC_GRID 
> >          XC_SMOOTH_RHO  NONE 
> >          XC_DERIV  SPLINE2_SMOOTH 
> >        &END XC_GRID 
> >        &XC_FUNCTIONAL  NO_SHORTCUT 
> >          &PADE  T 
> >          &END PADE 
> >        &END XC_FUNCTIONAL 
> >      &END XC 
> >     &PRINT 
> >        &MO_CUBES  SILENT 
> >          STRIDE               1              1              1 
> >          NLUMO               0 
> >          NHOMO               1 
> >          &EACH 
> >            GEO_OPT               1 
> >          &END EACH 
> >        &END MO_CUBES 
> >        &E_DENSITY_CUBE  SILENT 
> >          STRIDE               1              1              1 
> >          &EACH 
> >            GEO_OPT               1 
> >          &END EACH 
> >        &END E_DENSITY_CUBE 
> >        &TOT_DENSITY_CUBE  SILENT 
> >          STRIDE               1              1              1 
> >          &EACH 
> >            GEO_OPT               1 
> >          &END EACH 
> >        &END TOT_DENSITY_CUBE 
> >        &PDOS  SILENT 
> >          &EACH 
> >            GEO_OPT               1 
> >          &END EACH 
> >        &END PDOS 
> >        &MULLIKEN 
> >          &EACH 
> >            GEO_OPT               1 
> >          &END EACH 
> >        &END MULLIKEN 
> >        &LOWDIN 
> >          &EACH 
> >            GEO_OPT               1 
> >          &END EACH 
> >        &END LOWDIN 
> >       &DFT_CONTROL_PARAMETERS 
> >       &END DFT_CONTROL_PARAMETERS 
> >       &PLUS_U 
> >       &END PLUS_U 
> >     &END PRINT 
> >    &END DFT 
> >    &SUBSYS 
> >      &CELL 
> > A  16.23402000   0.000000000    0.0000000000 
> > B  0.000000000   16.23402000    0.0000000000 
> > C  0.000000000   0.000000000    16.234020000 
> >        PERIODIC XYZ 
> >      &END CELL 
> >      &COORD 
> > Ce           0.00000    14.88119     14.88119 
> > Ce           0.00000    14.88119    9.46985 
> > Ce           0.00000    14.88119   4.05851 
> > Ce           0.00000    9.46985     14.88119 
> > Ce           0.00000    9.46985    9.46985 
> > Ce           0.00000    9.46985   4.05851 
> > Ce           0.00000   4.05851     14.88119 
> > Ce           0.00000   4.05851    9.46985 
> > Ce           0.00000   4.05851   4.05851 
> > Ce           5.41134    14.88119     14.88119 
> > Ce           5.41134    14.88119    9.46985 
> > Ce           5.41134    14.88119   4.05851 
> > Ce           5.41134    9.46985     14.88119 
> > Ce           5.41134    9.46985    9.46985 
> > Ce           5.41134    9.46985   4.05851 
> > Ce           5.41134   4.05851     14.88119 
> > Ce           5.41134   4.05851    9.46985 
> > Ce           5.41134   4.05851   4.05851 
> > Ce          10.82268    14.88119     14.88119 
> > Ce          10.82268    14.88119    9.46985 
> > Ce          10.82268    14.88119   4.05851 
> > Ce          10.82268    9.46985     14.88119 
> > Ce          10.82268    9.46985    9.46985 
> > Ce          10.82268    9.46985   4.05851 
> > Ce          10.82268   4.05851     14.88119 
> > Ce          10.82268   4.05851    9.46985 
> > Ce          10.82268   4.05851   4.05851 
> > Ce           0.00000    12.17552    12.17552 
> > Ce           0.00000    12.17552    6.76418 
> > Ce           0.00000    12.17552   1.35284 
> > Ce           0.00000    6.76418    12.17552 
> > Ce           0.00000    6.76418    6.76418 
> > Ce           0.00000    6.76418   1.35284 
> > Ce           0.00000   1.35284    12.17552 
> > Ce           0.00000   1.35284    6.76418 
> > Ce           0.00000   1.35284   1.35284 
> > Ce           5.41134    12.17552    12.17552 
> > Ce           5.41134    12.17552    6.76418 
> > Ce           5.41134    12.17552   1.35284 
> > Ce           5.41134    6.76418    12.17552 
> > Ce           5.41134    6.76418    6.76418 
> > Ce           5.41134    6.76418   1.35284 
> > Ce           5.41134   1.35284    12.17552 
> > Ce           5.41134   1.35284    6.76418 
> > Ce           5.41134   1.35284   1.35284 
> > Ce          10.82268    12.17552    12.17552 
> > Ce          10.82268    12.17552    6.76418 
> > Ce          10.82268    12.17552   1.35284 
> > Ce          10.82268    6.76418    12.17552 
> > Ce          10.82268    6.76418    6.76418 
> > Ce          10.82268    6.76418   1.35284 
> > Ce          10.82268   1.35284    12.17552 
> > Ce          10.82268   1.35284    6.76418 
> > Ce          10.82268   1.35284   1.35284 
> > Ce           2.70567    12.17552     14.88119 
> > Ce           2.70567    12.17552    9.46985 
> > Ce           2.70567    12.17552   4.05851 
> > Ce           2.70567    6.76418     14.88119 
> > Ce           2.70567    6.76418    9.46985 
> > Ce           2.70567    6.76418   4.05851 
> > Ce           2.70567   1.35284     14.88119 
> > Ce           2.70567   1.35284    9.46985 
> > Ce           2.70567   1.35284   4.05851 
> > Ce           8.11701    12.17552     14.88119 
> > Ce           8.11701    12.17552    9.46985 
> > Ce           8.11701    12.17552   4.05851 
> > Ce           8.11701    6.76418     14.88119 
> > Ce           8.11701    6.76418    9.46985 
> > Ce           8.11701    6.76418   4.05851 
> > Ce           8.11701   1.35284     14.88119 
> > Ce           8.11701   1.35284    9.46985 
> > Ce           8.11701   1.35284   4.05851 
> > Ce          13.52835    12.17552     14.88119 
> > Ce          13.52835    12.17552    9.46985 
> > Ce          13.52835    12.17552   4.05851 
> > Ce          13.52835    6.76418     14.88119 
> > Ce          13.52835    6.76418    9.46985 
> > Ce          13.52835    6.76418   4.05851 
> > Ce          13.52835   1.35284     14.88119 
> > Ce          13.52835   1.35284    9.46985 
> > Ce          13.52835   1.35284   4.05851 
> > Ce           2.70567    14.88119    12.17552 
> > Ce           2.70567    14.88119    6.76418 
> > Ce           2.70567    14.88119   1.35284 
> > Ce           2.70567    9.46985    12.17552 
> > Ce           2.70567    9.46985    6.76418 
> > Ce           2.70567    9.46985   1.35284 
> > Ce           2.70567   4.05851    12.17552 
> > Ce           2.70567   4.05851    6.76418 
> > Ce           2.70567   4.05851   1.35284 
> > Ce           8.11701    14.88119    12.17552 
> > Ce           8.11701    14.88119    6.76418 
> > Ce           8.11701    14.88119   1.35284 
> > Ce           8.11701    9.46985    12.17552 
> > Ce           8.11701    9.46985    6.76418 
> > Ce           8.11701    9.46985   1.35284 
> > Ce           8.11701   4.05851    12.17552 
> > Ce           8.11701   4.05851    6.76418 
> > Ce           8.11701   4.05851   1.35284 
> > Ce          13.52835    14.88119    12.17552 
> > Ce          13.52835    14.88119    6.76418 
> > Ce          13.52835    14.88119   1.35284 
> > Ce          13.52835    9.46985    12.17552 
> > Ce          13.52835    9.46985    6.76418 
> > Ce          13.52835    9.46985   1.35284 
> > Ce          13.52835   4.05851    12.17552 
> > Ce          13.52835   4.05851    6.76418 
> > Ce          13.52835   4.05851   1.35284 
> > #O            1.35284    13.52836    13.52836 
> > O            1.35284    13.52836    8.11702 
> > O            1.35284    13.52836   2.70567 
> > O            1.35284    8.11702    13.52836 
> > O            1.35284    8.11702    8.11702 
> > O            1.35284    8.11702   2.70567 
> > O            1.35284   2.70567    13.52836 
> > O            1.35284   2.70567    8.11702 
> > O            1.35284   2.70567   2.70567 
> > O            6.76417    13.52836    13.52836 
> > O            6.76417    13.52836    8.11702 
> > O            6.76417    13.52836   2.70567 
> > O            6.76417    8.11702    13.52836 
> > O            6.76417    8.11702    8.11702 
> > O            6.76417    8.11702   2.70567 
> > O            6.76417   2.70567    13.52836 
> > O            6.76417   2.70567    8.11702 
> > O            6.76417   2.70567   2.70567 
> > O           12.17552    13.52836    13.52836 
> > O           12.17552    13.52836    8.11702 
> > O           12.17552    13.52836   2.70567 
> > O           12.17552    8.11702    13.52836 
> > O           12.17552    8.11702    8.11702 
> > O           12.17552    8.11702   2.70567 
> > O           12.17552   2.70567    13.52836 
> > O           12.17552   2.70567    8.11702 
> > O           12.17552   2.70567   2.70567 
> > O            1.35284    10.82268    10.82268 
> > O            1.35284    10.82268    5.41135 
> > O            1.35284    10.82268   0.00000 
> > O            1.35284    5.41135    10.82268 
> > O            1.35284    5.41135    5.41135 
> > O            1.35284    5.41135   0.00000 
> > O            1.35284   0.00000    10.82268 
> > O            1.35284   0.00000    5.41135 
> > O            1.35284   0.00000   0.00000 
> > O            6.76417    10.82268    10.82268 
> > O            6.76417    10.82268    5.41135 
> > O            6.76417    10.82268   0.00000 
> > O            6.76417    5.41135    10.82268 
> > O            6.76417    5.41135    5.41135 
> > O            6.76417    5.41135   0.00000 
> > O            6.76417   0.00000    10.82268 
> > O            6.76417   0.00000    5.41135 
> > O            6.76417   0.00000   0.00000 
> > O           12.17552    10.82268    10.82268 
> > O           12.17552    10.82268    5.41135 
> > O           12.17552    10.82268   0.00000 
> > O           12.17552    5.41135    10.82268 
> > O           12.17552    5.41135    5.41135 
> > O           12.17552    5.41135   0.00000 
> > O           12.17552   0.00000    10.82268 
> > O           12.17552   0.00000    5.41135 
> > O           12.17552   0.00000   0.00000 
> > O            4.05851    10.82268    13.52836 
> > O            4.05851    10.82268    8.11702 
> > O            4.05851    10.82268   2.70567 
> > O            4.05851    5.41135    13.52836 
> > O            4.05851    5.41135    8.11702 
> > O            4.05851    5.41135   2.70567 
> > O            4.05851   0.00000    13.52836 
> > O            4.05851   0.00000    8.11702 
> > O            4.05851   0.00000   2.70567 
> > O            9.46984    10.82268    13.52836 
> > O            9.46984    10.82268    8.11702 
> > O            9.46984    10.82268   2.70567 
> > O            9.46984    5.41135    13.52836 
> > O            9.46984    5.41135    8.11702 
> > O            9.46984    5.41135   2.70567 
> > O            9.46984   0.00000    13.52836 
> > O            9.46984   0.00000    8.11702 
> > O            9.46984   0.00000   2.70567 
> > O           14.88119    10.82268    13.52836 
> > O           14.88119    10.82268    8.11702 
> > O           14.88119    10.82268   2.70567 
> > O           14.88119    5.41135    13.52836 
> > O           14.88119    5.41135    8.11702 
> > O           14.88119    5.41135   2.70567 
> > O           14.88119   0.00000    13.52836 
> > O           14.88119   0.00000    8.11702 
> > O           14.88119   0.00000   2.70567 
> > O            4.05851    13.52836    10.82268 
> > O            4.05851    13.52836    5.41135 
> > O            4.05851    13.52836   0.00000 
> > O            4.05851    8.11702    10.82268 
> > O            4.05851    8.11702    5.41135 
> > O            4.05851    8.11702   0.00000 
> > O            4.05851   2.70567    10.82268 
> > O            4.05851   2.70567    5.41135 
> > O            4.05851   2.70567   0.00000 
> > O            9.46984    13.52836    10.82268 
> > O            9.46984    13.52836    5.41135 
> > O            9.46984    13.52836   0.00000 
> > O            9.46984    8.11702    10.82268 
> > O            9.46984    8.11702    5.41135 
> > O            9.46984    8.11702   0.00000 
> > O            9.46984   2.70567    10.82268 
> > O            9.46984   2.70567    5.41135 
> > O            9.46984   2.70567   0.00000 
> > O           14.88119    13.52836    10.82268 
> > O           14.88119    13.52836    5.41135 
> > O           14.88119    13.52836   0.00000 
> > O           14.88119    8.11702    10.82268 
> > O           14.88119    8.11702    5.41135 
> > O           14.88119    8.11702   0.00000 
> > O           14.88119   2.70567    10.82268 
> > O           14.88119   2.70567    5.41135 
> > O           14.88119   2.70567   0.00000 
> > O            1.35284    13.52836    10.82268 
> > O            1.35284    13.52836    5.41135 
> > O            1.35284    13.52836   0.00000 
> > O            1.35284    8.11702    10.82268 
> > O            1.35284    8.11702    5.41135 
> > O            1.35284    8.11702   0.00000 
> > O            1.35284   2.70567    10.82268 
> > O            1.35284   2.70567    5.41135 
> > O            1.35284   2.70567   0.00000 
> > O            6.76417    13.52836    10.82268 
> > O            6.76417    13.52836    5.41135 
> > O            6.76417    13.52836   0.00000 
> > O            6.76417    8.11702    10.82268 
> > O            6.76417    8.11702    5.41135 
> > O            6.76417    8.11702   0.00000 
> > O            6.76417   2.70567    10.82268 
> > O            6.76417   2.70567    5.41135 
> > O            6.76417   2.70567   0.00000 
> > O           12.17552    13.52836    10.82268 
> > O           12.17552    13.52836    5.41135 
> > O           12.17552    13.52836   0.00000 
> > O           12.17552    8.11702    10.82268 
> > O           12.17552    8.11702    5.41135 
> > O           12.17552    8.11702   0.00000 
> > O           12.17552   2.70567    10.82268 
> > O           12.17552   2.70567    5.41135 
> > O           12.17552   2.70567   0.00000 
> > O            1.35284    10.82268    13.52836 
> > O            1.35284    10.82268    8.11702 
> > O            1.35284    10.82268   2.70567 
> > O            1.35284    5.41135    13.52836 
> > O            1.35284    5.41135    8.11702 
> > O            1.35284    5.41135   2.70567 
> > O            1.35284   0.00000    13.52836 
> > O            1.35284   0.00000    8.11702 
> > O            1.35284   0.00000   2.70567 
> > O            6.76417    10.82268    13.52836 
> > O            6.76417    10.82268    8.11702 
> > O            6.76417    10.82268   2.70567 
> > O            6.76417    5.41135    13.52836 
> > O            6.76417    5.41135    8.11702 
> > O            6.76417    5.41135   2.70567 
> > O            6.76417   0.00000    13.52836 
> > O            6.76417   0.00000    8.11702 
> > O            6.76417   0.00000   2.70567 
> > O           12.17552    10.82268    13.52836 
> > O           12.17552    10.82268    8.11702 
> > O           12.17552    10.82268   2.70567 
> > O           12.17552    5.41135    13.52836 
> > O           12.17552    5.41135    8.11702 
> > O           12.17552    5.41135   2.70567 
> > O           12.17552   0.00000    13.52836 
> > O           12.17552   0.00000    8.11702 
> > O           12.17552   0.00000   2.70567 
> > O            4.05851    10.82268    10.82268 
> > O            4.05851    10.82268    5.41135 
> > O            4.05851    10.82268   0.00000 
> > O            4.05851    5.41135    10.82268 
> > O            4.05851    5.41135    5.41135 
> > O            4.05851    5.41135   0.00000 
> > O            4.05851   0.00000    10.82268 
> > O            4.05851   0.00000    5.41135 
> > O            4.05851   0.00000   0.00000 
> > O            9.46984    10.82268    10.82268 
> > O            9.46984    10.82268    5.41135 
> > O            9.46984    10.82268   0.00000 
> > O            9.46984    5.41135    10.82268 
> > O            9.46984    5.41135    5.41135 
> > O            9.46984    5.41135   0.00000 
> > O            9.46984   0.00000    10.82268 
> > O            9.46984   0.00000    5.41135 
> > O            9.46984   0.00000   0.00000 
> > O           14.88119    10.82268    10.82268 
> > O           14.88119    10.82268    5.41135 
> > O           14.88119    10.82268   0.00000 
> > O           14.88119    5.41135    10.82268 
> > O           14.88119    5.41135    5.41135 
> > O           14.88119    5.41135   0.00000 
> > O           14.88119   0.00000    10.82268 
> > O           14.88119   0.00000    5.41135 
> > O           14.88119   0.00000   0.00000 
> > O            4.05851    13.52836    13.52836 
> > O            4.05851    13.52836    8.11702 
> > O            4.05851    13.52836   2.70567 
> > O            4.05851    8.11702    13.52836 
> > O            4.05851    8.11702    8.11702 
> > O            4.05851    8.11702   2.70567 
> > O            4.05851   2.70567    13.52836 
> > O            4.05851   2.70567    8.11702 
> > O            4.05851   2.70567   2.70567 
> > O            9.46984    13.52836    13.52836 
> > O            9.46984    13.52836    8.11702 
> > O            9.46984    13.52836   2.70567 
> > O            9.46984    8.11702    13.52836 
> > O            9.46984    8.11702    8.11702 
> > O            9.46984    8.11702   2.70567 
> > O            9.46984   2.70567    13.52836 
> > O            9.46984   2.70567    8.11702 
> > O            9.46984   2.70567   2.70567 
> > O           14.88119    13.52836    13.52836 
> > O           14.88119    13.52836    8.11702 
> > O           14.88119    13.52836   2.70567 
> > O           14.88119    8.11702    13.52836 
> > O           14.88119    8.11702    8.11702 
> > O           14.88119    8.11702   2.70567 
> > O           14.88119   2.70567    13.52836 
> > O           14.88119   2.70567    8.11702 
> > O           14.88119   2.70567   2.70567 
> > &END COORD 
> > &KIND Ce 
> >   BASIS_SET DZVP-GTH-PADE 
> >   POTENTIAL GTH-PADE-q12 
> >        &DFT_PLUS_U 
> >          L 3 
> >          U_MINUS_J [eV] 5 
> >        &END DFT_PLUS_U 
> > &END KIND 
> > &KIND O 
> >   BASIS_SET DZVP-GTH-PADE 
> >   POTENTIAL GTH-PADE-q6 
> > &END KIND 
> >    &END SUBSYS 
> >  &END FORCE_EVAL 
> > 
> > The output cell_d-pos-1.xyz is the same as the initial starting 
> > coordinates

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