[Pw_forum] Atomic positions for Black Phosphorus calculations

Tue Jan 12 01:13:47 CET 2016

You have set your atomic coordinates to the crystal coordinates:

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

You're positioning your atoms with reference to your lattice constant, 
with 0.0 begin on one end of a lattice vector and 1.0 on the other end. 
Atoms #2&7 and #3&5 differ by 1 lattice vector in the 2nd column, and 
are therefor in the same position. If you wanted units of angstroms, 
replace "crystal" with "angtrom" after ATOMIC_POSITIONS.

Check out the pw.x input guide:
http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html

Hope this helps,
Hank Seeley
University of Oregon, Chemistry

On 2016/01/11 16:03, Elio Physics wrote:
> 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 <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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> 
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