[Pw_forum] Atomic positions for Black Phosphorus calculations
Giuseppe Mattioli
giuseppe.mattioli at ism.cnr.it
Tue Jan 12 10:48:48 CET 2016
Dear Elio
> Thanks for reply. I can see where you are coming from. I did put "crystal" because those coordinates are the "fractional" coordinates given by
> the "Crystal builder". Isn't crystal (in terms of the primitive cells) in QE equivalent to fractional?
In *crystal* (as well as *fractional*) coordinates 0.10168*=*1.10168
the two atoms are not shifted by 1 A. They are shifted by 1 lattice vector so that they *fold on the same position in the unit cell and overlap*.
If you want to replicate a unit cell in crystal coordinates along a given direction you should double the corresponding lattice parameter and divide
by 2 the corresponding crystal coordinates.
HTH
Giuseppe
On Tuesday, January 12, 2016 12:22:54 AM Elio Physics wrote:
> Dear Henry,
>
> Thanks for reply. I can see where you are coming from. I did put "crystal" because those coordinates are the "fractional" coordinates given by
> the "Crystal builder". Isn't crystal (in terms of the primitive cells) in QE equivalent to fractional?
>
> Thanks
>
> ________________________________________
> From: pw_forum-bounces at pwscf.org <pw_forum-bounces at pwscf.org> on behalf of Henry J Seeley <hseeley at uoregon.edu>
> Sent: Monday, January 11, 2016 10:13 PM
> To: PWSCF Forum
> Subject: Re: [Pw_forum] Atomic positions for Black Phosphorus calculations
>
> 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
> >>
> >> _______________________________________________
> >> Pw_forum mailing list
> >> Pw_forum at pwscf.org
> >> http://pwscf.org/mailman/listinfo/pw_forum
> >
> > _______________________________________________
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Giuseppe Mattioli
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
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Tel + 39 06 90672836 - Fax +39 06 90672316
E-mail: <giuseppe.mattioli at ism.cnr.it>
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