[Pw_forum] Atomic positions for Black Phosphorus calculations

[Duc-Long NGUYEN]

Dear Elio,

ATOMIC_POSITIONS crystal
P  -0.89832 0.89832 0.91944
P  -0.39832 0.39832 0.58056
_P  -0.10168 0.10168 0.08056_
P   0.10168 0.89832 0.91944
_P  -0.10168 1.10168 0.08056_
P  -0.60168 0.60168 0.41944
P  -0.39832 1.39832 0.58056
P   0.39832 0.60168 0.41944
These two atom positions have the same coordinate. This could be the 
problem.

Duc-Long

On 1/12/2016 6:44 AM, Elio Physics wrote:
>
> Dear all,
>
>
> I am trying to perform some calculations on Black Phosphorus (BP).  To 
> get the atomic positions I used the Crystal Builder, where I have 
> chosen the lattice type to be base centered orthorhombic.  The 
> "builder" produced a set of cartesian and fractional  (in terms of the 
> primitive cell vectors) . I have used the fractional ones and I have 
> also used ibrav=0 with the CELL_PARAMETERS defined as in the builder 
> (a/2, -b/2, 0), (a/2, b/2,0), (0,0,c). However I have got the 
> following error:
>
>
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      from check_atoms : error #         1
>      atoms #   1 and #   4 overlap!
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> Doing the same calculation with ibrav=8 and using the coordinates 
> produced by the Crystal builder for a simple orthorhombic does not 
> produce any errors. Can anyone please tell me what is wrong with atoms 
> (1) and (4). Is BP simple or base centered orthorhombic..Where can I 
> find the coorect atomic position of bulk BP? The scf input is below:
>
>
> &CONTROL
>     prefix='bp',
>     calculation='scf',
>     restart_mode='from_scratch',
>     wf_collect=.true.,
>     forc_conv_thr=1.D-4
>     etot_conv_thr=1.D-5
>     tstress=.true.,
>     tprnfor=.true.,
>     pseudo_dir ='/home_cluster/fis718/elio/espresso-4.1.3/pseudo',
> outdir='/home_cluster/fis718/elio/espresso-4.1.3/BP/OUT'
>  /
>  &SYSTEM
>     ibrav=0,celldm(1)=6.26179,nat=8, ntyp= 1, ecutwfc=10, ecutrho=40, 
> occupations='smearing', london=.true., smearing='mp', 
> degauss=0.035,nbnd=32
> /
>  &ELECTRONS
>     conv_thr=1.D-8,
>     mixing_beta=0.1
> /
> &IONS
> ion_dynamics='bfgs'
> /
> &CELL
> cell_dynamics='bfgs'
> press=0.0
> /
> ATOMIC_SPECIES
> P 30.97376  P.pbe-n-van.UPF
> ATOMIC_POSITIONS crystal
> P  -0.89832 0.89832 0.91944
> P  -0.39832 0.39832 0.58056
> P  -0.10168 0.10168 0.08056
> P   0.10168 0.89832 0.91944
> P  -0.10168 1.10168 0.08056
> P  -0.60168 0.60168 0.41944
> P  -0.39832 1.39832 0.58056
> P   0.39832 0.60168 0.41944
>
> K_POINTS automatic
>  2 2 2 0 0 0
>
> CELL_PARAMETERS alat
> 0.5000 -1.58106 0.0000
> 0.500 1.58106 0.0000
> 0.0000 0.00000 4.3763
>
>
> thanks
>
> Elio Arbid
> University of Nottingham
> UK
>
>
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-- 
Duc-Long Nguyen
Graduate Student, Molecular Science and Technology Program, TIGP
Institute of Atomic and Molecular Sciences,
Academia Sinica, Taipei 106, Taiwan
Phone +886 979279073

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