4
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I am running PBE defect calculations on InAs in Quantum Espresso. Whenever I run relax, the first 8 atoms stay fixed in place, while the rest displace by some amount. For example,

As            0.0000000000        0.0000000000        0.0000000000
In            0.0000000000        0.0000000000        0.5000000000
In            0.0000000000        0.5000000000        0.0000000000
In            0.0000000000        0.5000000000        0.5000000000
In            0.5000000000        0.0000000000        0.0000000000
In            0.5000000000        0.0000000000        0.5000000000
In            0.5000000000        0.5000000000        0.0000000000
In            0.5000000000        0.5000000000        0.5000000000
In            0.0006947837        0.2501563472        0.2501563472
In           -0.0006947837        0.2501563472        0.7498436528
In           -0.0006947837        0.7498436528        0.2501563472
In            0.0006947837        0.7498436528        0.7498436528
In            0.4998783164        0.2500438960        0.2500438960
In            0.5001216836        0.2500438960        0.7499561040

This is a snippet of the atomic coordinates after relaxing the ions.

Does anybody know why the first 8 atoms would stay fixed in place?

EDIT

Input file:

&control
prefix       = 'inas',
calculation  = 'relax',
verbosity    = 'high',
disk_io      = 'low',
pseudo_dir   = '/work/PP/',
outdir       = './temp',
/
&system
   ibrav = 1, celldm(1) = 22.853105188484857,
   nat = 64, ntyp = 2, nbnd=500,
   ecutwfc = 25, ecutrho = 100,
   occupations = 'smearing', smearing = 'gauss', degauss = 0.005,
   nspin = 2,
   starting_magnetization(1) = 0.0,
   starting_magnetization(2) = 0.0,
/
&electrons
   diagonalization = 'david',
   conv_thr        =  1.0D-7,
   mixing_beta     =  0.7,
   startingwfc     = 'random',
/
&ions
/
&cell
/
ATOMIC_SPECIES
   In   114.818   in_pbesol_v1.4.uspp.F.UPF
   As   74.9216   as_pbesol_v1.uspp.F.UPF

ATOMIC_POSITIONS crystal
 As     0.000000000         0.000000000         0.000000000
 In     0.000000000         0.000000000         0.500000000
 In     0.000000000         0.500000000         0.000000000
 In     0.000000000         0.500000000         0.500000000
 In     0.500000000         0.000000000         0.000000000
 In     0.500000000         0.000000000         0.500000000
 In     0.500000000         0.500000000         0.000000000
 In     0.500000000         0.500000000         0.500000000
 In     0.000000000         0.250000000         0.250000000
 In     0.000000000         0.250000000         0.750000000
 In     0.000000000         0.750000000         0.250000000
 In     0.000000000         0.750000000         0.750000000
 In     0.500000000         0.250000000         0.250000000
 In     0.500000000         0.250000000         0.750000000
 In     0.500000000         0.750000000         0.250000000
 In     0.500000000         0.750000000         0.750000000
 In     0.250000000         0.000000000         0.250000000
 In     0.250000000         0.000000000         0.750000000
 In     0.250000000         0.500000000         0.250000000
 In     0.250000000         0.500000000         0.750000000
 In     0.750000000         0.000000000         0.250000000
 In     0.750000000         0.000000000         0.750000000
 In     0.750000000         0.500000000         0.250000000
 In     0.750000000         0.500000000         0.750000000
 In     0.250000000         0.250000000         0.000000000
 In     0.250000000         0.250000000         0.500000000
 In     0.250000000         0.750000000         0.000000000
 In     0.250000000         0.750000000         0.500000000
 In     0.750000000         0.250000000         0.000000000
 In     0.750000000         0.250000000         0.500000000
 In     0.750000000         0.750000000         0.000000000
 In     0.750000000         0.750000000         0.500000000
 As     0.375000000         0.375000000         0.375000000
 As     0.375000000         0.375000000         0.875000000
 As     0.375000000         0.875000000         0.375000000
 As     0.375000000         0.875000000         0.875000000
 As     0.875000000         0.375000000         0.375000000
 As     0.875000000         0.375000000         0.875000000
 As     0.875000000         0.875000000         0.375000000
 As     0.875000000         0.875000000         0.875000000
 As     0.375000000         0.125000000         0.125000000
 As     0.375000000         0.125000000         0.625000000
 As     0.375000000         0.625000000         0.125000000
 As     0.375000000         0.625000000         0.625000000
 As     0.875000000         0.125000000         0.125000000
 As     0.875000000         0.125000000         0.625000000
 As     0.875000000         0.625000000         0.125000000
 As     0.875000000         0.625000000         0.625000000
 As     0.125000000         0.375000000         0.125000000
 As     0.125000000         0.375000000         0.625000000
 As     0.125000000         0.875000000         0.125000000
 As     0.125000000         0.875000000         0.625000000
 As     0.625000000         0.375000000         0.125000000
 As     0.625000000         0.375000000         0.625000000
 As     0.625000000         0.875000000         0.125000000
 As     0.625000000         0.875000000         0.625000000
 As     0.125000000         0.125000000         0.375000000
 As     0.125000000         0.125000000         0.875000000
 As     0.125000000         0.625000000         0.375000000
 As     0.125000000         0.625000000         0.875000000
 As     0.625000000         0.125000000         0.375000000
 As     0.625000000         0.125000000         0.875000000
 As     0.625000000         0.625000000         0.375000000
 As     0.625000000         0.625000000         0.875000000
K_POINTS automatic
   2 2 2  0  0  0
$\endgroup$
5
  • $\begingroup$ +1 but please include an input/output file. $\endgroup$ Commented May 17 at 1:55
  • $\begingroup$ @NikeDattani-NoFreeTime I included the input file, but the output file is 11626 lines. $\endgroup$
    – Austin
    Commented May 17 at 2:29
  • 1
    $\begingroup$ Please put it on Modeling Matters along with all the other long output files there: mattermodeling.meta.stackexchange.com/q/393/5 $\endgroup$ Commented May 17 at 3:32
  • $\begingroup$ @NikeDattani-NoFreeTime Forgive me, I am a bit of a novice when it comes to Github. I attempted to make a pull request and paste the contents of the output file into the description, but it says the body is too long and exceeds the maximum of 65536 characters. $\endgroup$
    – Austin
    Commented May 19 at 19:23
  • $\begingroup$ You would need to add the file to the GitHub folder using a command line interface (e.g. git commit, and git push), rather than using the GitHub website. $\endgroup$ Commented May 19 at 21:26

1 Answer 1

2
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Usually this happens when the forces on atoms are fixed by symmetry. Consider e.g. the CO2 molecule. If you change the bond-length on both sides of the C atom so that the molecule is still symmetric, there are forces on each O atom that cause them to displace, but the reciprocal forces on the C atom from each O exactly cancel each other so that the C atom stays fixed.

I am not looking carefully at your structure, but I assume this is the case.

If you want those atoms to move for some reason, you can break the symmetry by applying small random displacements. Note, this will lower the symmetry of the crystal as a whole, resulting in a more expensive calculation since you will have to explicitly calculate more k-points etc.

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