[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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