[Pw_forum] Atomic positions for Black Phosphorus calculations

[Elio Physics]

Thanks for your help once again.  I do not have XCrysDen and I have been having problems installing it. This is weird as with Crystal builder the atoms were well separated and different.  One more thing: Where can I find the ccorect coordinates? any idea how to form the atomic positions?


Thanks


________________________________
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 9:53 PM
To: PWSCF Forum
Subject: Re: [Pw_forum] Atomic positions for Black Phosphorus calculations

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<mailto:pw_forum-bounces at pwscf.org> <pw_forum-bounces at pwscf.org><mailto:pw_forum-bounces at pwscf.org> on behalf of Duc-Long NGUYEN <longnguyenqtr at gmail.com><mailto: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



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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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