[Pw_forum] Atomic positions for Black Phosphorus calculations

[Duc-Long NGUYEN]

Hi,

You could use xcrysden to check your input.
This is the result with your input:
Number of Atoms:  8
Number of Frames: 12
WARNING: Atom 1 and atom 3 overlap !!!   Atom 3 deleted !!!
WARNING: Atom 2 and atom 7 overlap !!!   Atom 7 deleted !!!
WARNING: Atom 4 and atom 8 overlap !!!   Atom 8 deleted !!!
WARNING: Atom 5 and atom 6 overlap !!!   Atom 6 deleted !!!
That was also why pwscf showed that error.

Duc-Long

On 1/12/2016 7:46 AM, Elio Physics wrote:
>
> Dear Duc-Long,
>
>
> thanks for your response. I do not think they have the same 
> coordinate. The "y" coordinate of one is *0.10168* while that of the 
> 2nd is *1.10168, * that is a difference of 1 ang.
>
>
> Elio
>
>
>
> ------------------------------------------------------------------------
> *From:* pw_forum-bounces at pwscf.org <pw_forum-bounces at pwscf.org> on 
> behalf of Duc-Long NGUYEN <longnguyenqtr at gmail.com>
> *Sent:* Monday, January 11, 2016 9:38 PM
> *To:* PWSCF Forum
> *Subject:* Re: [Pw_forum] Atomic positions for Black Phosphorus 
> calculations
> 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
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>
> -- 
> 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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