[xcrysden] XCrySDen Digest, Vol 95, Issue 2
Muthu V
muthu.physicsmath at gmail.com
Mon Jan 18 18:56:43 CET 2016
Adding to my previous mail, if the concern is to get back the structure as
input file 1 then the mistake is at atomic coordinate conversion from
angstrom to crystal. here is the solution.
as the atomic coordinates are defined in primitive cell one should use
primitive lattice vectors to go to crystal units from angstrom. open
anatase pw input file in xcrysden then one can find the primitive vectors
for anatase is
PRIMVEC
1.8879977010 -1.8879977010 4.7429900630
1.8879977010 1.8879977010 4.7429900630
-1.8879977010 -1.8879977010 4.7429900630
now define atomic coordinate as matrix a and above as b
a =
0.00000 0.00000 0.00000
0.00000 1.88800 2.37150
0.00000 0.00000 -1.98310
0.00000 0.00000 1.98310
0.00000 1.88800 0.38780
0.00000 1.88800 4.35520
b =
1.8880 -1.8880 4.7430
1.8880 1.8880 4.7430
-1.8880 -1.8880 4.7430
now find a/b as a*b-1
0.00000 0.00000 -0.00000
-0.50000 0.75000 0.25000
0.00000 -0.20906 -0.20906
0.00000 0.20906 0.20906
-0.50000 0.54088 0.04088
-0.50000 0.95912 0.45912
so use this atomic coordinates then you will get the structure as expected.
note that make sure of getting correct bond length. if it is not so then
make sure that you are at correct precision of atomic coordinates as
pointed out by Gavin Abo in his reply.
find out the attachment for input file 2 which gives correct structure.
*---------------------------------------------*
*Muthu VSri Paramakalyani college,Alwarkruichi,
India---------------------------------------------*
On Mon, Jan 18, 2016 at 12:05 PM, <xcrysden-request at democritos.it> wrote:
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> Today's Topics:
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> 1. Re: Anatase primitive cell: Regarding (Gavin Abo)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 17 Jan 2016 18:09:25 -0700
> From: Gavin Abo <gsabo at crimson.ua.edu>
> Subject: Re: [xcrysden] Anatase primitive cell: Regarding
> To: xcrysden at democritos.it
> Message-ID: <569C3B45.5010601 at crimson.ua.edu>
> Content-Type: text/plain; charset="windows-1252"
>
> Regarding Inputfile 1, keep in mind that you might have to increase the
> precision of the atomic positions as described in the post at the
> following link:
>
> http://qe-forge.org/pipermail/pw_forum/2006-August/079340.html
>
> Regarding Inputfile 2, it seems like you can get XCrySDen to show the
> same structure as Inputfile 1 if you change ibrav from 7 to 6, nat from
> 6 to 12, and add the atomic positions for the other 6 atoms (for a total
> of 12 atoms) in Inputfile 2. Refer to the anatase.in file attached at
> the bottom of the post at the following link:
>
> https://www.mail-archive.com/pw_forum@pwscf.org/msg27155.html
>
> On 1/15/2016 11:48 PM, Suresh A wrote:
> > Dear Friends,
> > I have prepared primitive cell input file for
> > quantum espresso.I have included those files below. The problem is
> > XCRYSDEN shows two different structure for a same file where one is in
> > crystal coordinates and other one in angstrom.
> >
> > Inputfile number 1: This file shows correct strucutre in XCRYSDEN
> >
> >
> > &CONTROL
> > title = 'TiO2' ,
> > calculation = 'scf',
> > outdir ='$TMP_DIR/'
> > prefix = 'anatase',
> > pseudo_dir = '$PSEUDO_DIR/',
> > /
> >
> > &SYSTEM
> > ibrav = 7,
> > celldm(1) = 7.1356,
> > celldm(3) = 2.51218,
> > nat = 6 ,
> > ntyp = 2 ,
> > ecutwfc = 30.0000000000 ,
> > ecutrho = 300,
> >
> >
> > /
> >
> > &ELECTRONS
> >
> > conv_thr = 1.0d-09,
> >
> > /
> > ATOMIC_SPECIES
> > O 15.999 O.pw91-van_ak.UPF
> > Ti 47.867 Ti.pw91-nsp-van.UPF
> > ATOMIC_POSITIONS angstrom
> > Ti 0.000000000 0.000000000 0.000000000
> > Ti 0.000000000 1.888000000 2.371500000
> > O 0.000000000 0.000000000 -1.983097630
> > O 0.000000000 0.000000000 1.983097630
> > O 0.000000000 1.888000000 0.387796645
> > O 0.000000000 1.888000000 4.355203355
> > K_POINTS automatic
> > 4 4 4 0 0 0
> >
> >
> > /Inputfile number 2:
> > &CONTROL
> > title = 'anatase' ,
> > calculation = 'scf' ,
> > restart_mode = 'from_scratch' ,
> > pseudo_dir = '/home/suresh/GN2/',
> > outdir ='/home/suresh/Desktop/primitivecell/tmp/',
> > prefix = 'anatase' ,
> > tstress = .true. ,
> > tprnfor = .true. ,
> >
> >
> >
> > /
> > &SYSTEM
> > ibrav = 7,
> > celldm(1) = 7.153,
> > celldm(3) = 2.513,
> > nat = 6,
> > ntyp = 2,
> > ecutwfc = 60 ,
> > exxdiv_treatment = 'none' ,
> >
> >
> >
> > /
> > &ELECTRONS
> >
> >
> > /
> > &IONS
> >
> >
> > /
> > &CELL
> >
> >
> >
> > /
> > ATOMIC_SPECIES
> > Ti 47.86700 Ti.pz-mt_fhi.UPF
> > O 15.99940 O.pz-mt_fhi.UPF
> > ATOMIC_POSITIONS (crystal)
> > Ti 0.0000000 0.0000000 0.0000000
> > Ti 0.0000000 0.5000000 0.2500000
> > O 0.0000000 0.0000000 0.2080000
> > O 0.0000000 0.0000000 -0.208000
> > O 0.0000000 0.5000000 0.4580000
> > O 0.0000000 0.5000000 -0.042000
> > K_POINTS automatic
> > 4 4 2 1 1 1
> >
> > /
> > /Will you please pointout where the problem i?
> > /
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > With Regards,
> > A.Suresh,
> > Research Scholar,
> > Madurai Kamaraj University,
> > Madurai.
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