[Pw_forum] Fwd: Atoms moving into Vacuum

Guido Fratesi fratesi at mater.unimib.it
Fri Dec 23 15:10:55 CET 2011


Dear Dipak Thakur,

I don't know about the system and have not fully understood your 
problem, nor seen any figure, but I would recommend you to double check 
the input coordinates: you are plenty of O atoms very close to each 
other, see for example atom number 84 and 85 (76pm!).

And, the input file you sent us does not correspond to a slab.

You might want to use "K_POINTS Gamma".

HTH
Guido

Il 12/23/2011 02:53 PM, Dipak Thakur ha scritto:
> Dear All,
>
> I am trying to optimize hydroxyapatite 1x1x2 and 1x1x1.
> However, the atoms in the unit cell move into vacuum above the slab. See
> the figure below.
>
> That is while optimization [scf] all the atoms move such that they
> occupy the vacuum above.
> I have worked with graphene but never faced such problems.
>
> Can any one help me understanding why this might be happening.
> Below is my input file.
>
> ----------------------------------------------------------------------------------------------------------------------------------------------
> &CONTROL
>             Calculation = "relax" ,
>                   restart_mode = 'from_scratch' ,
>                 outdir ='/usr/espresso-4.3.2/',
>                     pseudo_dir = '/usr/espresso-4.3.2/pseudo/',
>                        disk_io = 'default' ,
>                      verbosity = 'default' ,
>                  etot_conv_thr = 1.D-4 ,
>                  forc_conv_thr = 1.D-3 ,
>                          nstep = 500 ,
>                             dt = 40 ,
> /
> &SYSTEM
>                          ibrav = 0,
>                            nat = 96,
>                           ntyp = 4,
>                        ecutwfc = 10 ,
>                        ecutrho = 80 ,
>                    occupations = 'smearing' ,
>                        degauss = 0.02 ,
> /
> &ELECTRONS
>               electron_maxstep = 300,
>                       Conv_thr = 1.0d-8 ,
>                    mixing_mode = 'plain' ,
>                    mixing_beta = 0.5 ,
>                diagonalization = 'cg' ,
>               diago_cg_maxiter = 50,
> /
> &IONS
> /
> CELL_PARAMETERS
>     17.80868385387    0.00000000000    0.00000000000
>     -8.90434192693    15.42277262532    0.00000000000
>     0.00000000000    0.00000000000    25.99871311373
> ATOMIC_SPECIES
>   Ca  40.07800  Ca.pz-n-vbc.UPF
>   P   39.09830  P.pz-van_ak.UPF
>   O   15.99940  O.pz-van_ak.UPF
>   H   1.007940  H.pz-van_ak.UPF
> ATOMIC_POSITIONS angstrom
> Ca -0.4710847875E-11   5.440920259      0.1031844561E-01
> Ca -0.4710847875E-11   5.440920259       6.889282188
> Ca   4.711975164       2.720460129       13.74760904
> Ca   4.711975164       2.720460129       6.868645296
> Ca   4.711975164       2.720460129       3.449800317
> Ca   4.711975164       2.720460129       10.32876406
> Ca  0.4713197894E-11   5.440920259       3.429163425
> Ca  0.4713197894E-11   5.440920259       10.30812717
> Ca  -2.355045187       8.107515277       1.719740935
> Ca  -2.355045187       8.107515277       8.598704677
> Ca   7.067020351      0.5386511056E-01   12.03818655
> Ca   7.067020351      0.5386511056E-01   5.159222806
> Ca   1.225113543       2.014228680       5.159222806
> Ca   1.225113543       2.014228680       12.03818655
> Ca   3.486861621       6.147151708       1.719740935
> Ca   3.486861621       6.147151708       8.598704677
> Ca  -1.131816434       2.068093790       1.719740935
> Ca  -1.131816434       2.068093790       8.598704677
> Ca   5.843791598       6.093286598       12.03818655
> Ca   5.843791598       6.093286598       5.159222806
> P   2.020966148       3.007468673       1.719740935
> P   2.020966148       3.007468673       8.598704677
> P   2.691009016       5.153911715       12.03818655
> P   2.691009016       5.153911715       5.159222806
> P  -1.594061198       3.253942361       5.159222806
> P  -1.594061198       3.253942361       12.03818655
> P   6.306036362       4.907438027       1.719740935
> P   6.306036362       4.907438027       8.598704677
> P   5.808922982      0.2464736877       1.719740935
> P   5.808922982      0.2464736877       8.598704677
> P  -1.096947818       7.914906700       12.03818655
> P  -1.096947818       7.914906700       5.159222806
> O  0.8104597282       3.956637212       1.719740935
> O  0.8104597282       3.956637212       8.598704677
> O   3.901515436       4.204743176       12.03818655
> O   3.901515436       4.204743176       5.159222806
> O   6.402631853       2.680197319       5.159222806
> O   6.402631853       2.680197319       12.03818655
> O  -1.690656689       5.481183068       1.719740935
> O  -1.690656689       5.481183068       8.598704677
> O  0.8801969606       6.884940495       1.719740935
> O  0.8801969606       6.884940495       8.598704677
> O   3.831778203       1.276439893       12.03818655
> O   3.831778203       1.276439893       5.159222806
> O   3.343146379       3.795858018       1.719740935
> O   3.343146379       3.795858018       8.598704677
> O   1.368828785       4.365522369       12.03818655
> O   1.368828785       4.365522369       5.159222806
> O  -1.615736284       4.793178702       5.159222806
> O  -1.615736284       4.793178702       12.03818655
> O   6.327711448       3.368201686       1.719740935
> O   6.327711448       3.368201686       8.598704677
> O   4.465067665      0.9973206834       1.719740935
> O   4.465067665      0.9973206834       8.598704677
> O  0.2469074986       7.164059704       12.03818655
> O  0.2469074986       7.164059704       5.159222806
> O   2.023793333       2.104820002      0.4829032547
> O   2.023793333       2.104820002       7.361866997
> O   2.688181831       6.056560386       13.27502423
> O   2.688181831       6.056560386       6.396060487
> O -0.8109309257       2.805066439       3.922385126
> O -0.8109309257       2.805066439       10.80134887
> O   5.522906090       5.356313949       2.956578616
> O   5.522906090       5.356313949       9.835542358
> O   6.589226069      0.7002464373      0.4829032547
> O   6.589226069      0.7002464373       7.361866997
> O  -1.877250905       7.461133951       13.27502423
> O  -1.877250905       7.461133951       6.396060487
> O   2.688181831       6.056560386       3.922385126
> O   2.688181831       6.056560386       10.80134887
> O   2.023793333       2.104820002       2.956578616
> O   2.023793333       2.104820002       9.835542358
> O   5.522906090       5.356313949      0.4829032547
> O   5.522906090       5.356313949       7.361866997
> O -0.8109309257       2.805066439       13.27502423
> O -0.8109309257       2.805066439       6.396060487
> O  -1.877250905       7.461133951       3.922385126
> O  -1.877250905       7.461133951       10.80134887
> O   6.589226069      0.7002464373       2.956578616
> O   6.589226069      0.7002464373       9.835542358
> O   0.000000000       0.000000000       1.341397930
> O   0.000000000       0.000000000       8.220361672
> O   0.000000000       0.000000000       12.41652955
> O   0.000000000       0.000000000       5.537565812
> O   0.000000000       0.000000000       4.780879801
> O   0.000000000       0.000000000       11.65984354
> O   0.000000000       0.000000000       2.098083941
> O   0.000000000       0.000000000       8.977047683
> H   0.000000000       0.000000000      0.4182409955
> H   0.000000000       0.000000000       7.297204737
> H   0.000000000       0.000000000       13.33968649
> H   0.000000000       0.000000000       6.460722746
> H   0.000000000       0.000000000       3.857722866
> H   0.000000000       0.000000000       10.73668661
> H   0.000000000       0.000000000       3.021240875
> H   0.000000000       0.000000000       9.900204617
> K_POINTS automatic
>     1 1 1   0 0 0
> ----------------------------------------------------------------------------------------------------------------------------------------------
>
>
>
>
>
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-- 
Guido Fratesi

Dipartimento di Scienza dei Materiali
Universita` degli Studi di Milano-Bicocca
via Cozzi 53, 20125 Milano, Italy



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