From sramadugu at gmail.com  Wed Jun 18 20:50:30 2014
From: sramadugu at gmail.com (Sai Kumar Ramadugu)
Date: Wed, 18 Jun 2014 13:50:30 -0500
Subject: [xcrysden] Space Group 63,
	base centered Orthorhombic Structure Problem
Message-ID: <CAO6uzQUwBQZ9Y5zEtgmjMsQNbfSNMwMH2BhPkd_kX_ehf1YhqQ@mail.gmail.com>

Dear XCrysDen Users,

I am trying to run quantum espresso (QE) calculations on bulk
alpha-Uranium. It belongs to space group number 63 and is a base centered
orthorhobmic structure.
The paper by Barrett et al. Phys Rev 129, 625 (1963) has the coordinates
and the lattice constants (see below).

From sramadugu at gmail.com  Wed Jun 18 20:53:48 2014
From: sramadugu at gmail.com (Sai Kumar Ramadugu)
Date: Wed, 18 Jun 2014 13:53:48 -0500
Subject: [xcrysden] Space Group 63,
	base centered Orthorhombic Structure Problem
In-Reply-To: <CAO6uzQUwBQZ9Y5zEtgmjMsQNbfSNMwMH2BhPkd_kX_ehf1YhqQ@mail.gmail.com>
References: <CAO6uzQUwBQZ9Y5zEtgmjMsQNbfSNMwMH2BhPkd_kX_ehf1YhqQ@mail.gmail.com>
Message-ID: <CAO6uzQU5xp5RwB+KPBceNbANZSL9YsgejE2joHJqUMS=Z0Vvjg@mail.gmail.com>

Sorry for resending the same email, I forgot to add the attachments!


On Wed, Jun 18, 2014 at 1:50 PM, Sai Kumar Ramadugu <sramadugu at gmail.com>
wrote:

> Dear XCrysDen Users,
>
> I am trying to run quantum espresso (QE) calculations on bulk
> alpha-Uranium. It belongs to space group number 63 and is a base centered
> orthorhobmic structure.
> The paper by Barrett et al. Phys Rev 129, 625 (1963) has the coordinates
> and the lattice constants (see below).
> From QE's input description for this bravais lattice is 9 (ibrav=9).
> When I create an input file for PWSCF and view it in XCrysDen, it only
> shows two atoms (attached as figure1xsf.png), whereas if I create the
> structure file using Materials Studio or VESTA, I see 6 atoms (attached as
> figure2vesta.jpeg).
>
>
> Is my structure correct or am I not understanding the symmetry correctly
> or is there a problem with XCrysDen.
>
> The relevant part of the PWSCF input file:
>
> &SYSTEM
>   ibrav = 9,
>   celldm(1) = 5.392713591,
>   celldm(2) = 2.0568034482,
>   celldm(3) = 1.736272208,
>   nat = 1,
>   ntyp = 1,
>   ecutwfc = 35,
>   ecutrho = 280,
>   occupations = 'smearing',
>   smearing = 'mp',
>   degauss = 0.02,
> /
> &ELECTRONS
>   conv_thr = 1.D-7,
>   mixing_beta = 0.7D0,
> /
> &IONS
> /
> ATOMIC_SPECIES
> U  1.00  U.pbe-nd-rrkjus.UPF
> ATOMIC_POSITIONS {crystal}
> U      0.000     0.10239     0.25
> K_POINTS {automatic}
>  1 1 1 0 0 0
>
>
> Sorry if this is trivial but I could not get it correctly no matter what
> all options I tried.
>
> Regards
>
??
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From tone.kokalj at ijs.si  Thu Jun 19 09:03:04 2014
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Thu, 19 Jun 2014 09:03:04 +0200
Subject: [xcrysden] Space Group 63,
 base centered Orthorhombic Structure Problem
In-Reply-To: <CAO6uzQUwBQZ9Y5zEtgmjMsQNbfSNMwMH2BhPkd_kX_ehf1YhqQ@mail.gmail.com>
References: <CAO6uzQUwBQZ9Y5zEtgmjMsQNbfSNMwMH2BhPkd_kX_ehf1YhqQ@mail.gmail.com>
Message-ID: <1403161384.20896.9.camel@catalyst.ijs.si>

On Wed, 2014-06-18 at 13:50 -0500, Sai Kumar Ramadugu wrote:

> 
> When I create an input file for PWSCF and view it in XCrysDen, it only
> shows two atoms (attached as figure1xsf.png), 

To be more precise, it shows two atoms in the conventional cell and this
is correct. Why? Because you specified only one atom (for the primitive
cell) in the pw.x input file. This implies that for base-centered cells
there are two atoms in the conventional cell, i.e. (in crystal
coordinates):

atom1  x     y      z
atom2  x+0.5 y+0.5  z

> whereas if I create the structure file using Materials Studio or
> VESTA, I see 6 atoms (attached as figure2vesta.jpeg).

I guess the difference is that the VESTA and MS take advantage of the
space-group info and use corresponding symmetry operations to generate
other symmetry-equivalent atoms. The pw.x does not do this and you need
to specify all the atoms within the primitive unit cell.

You may do a check: run pw.x on your input and then display the
structure from the output: xcrysden should show only one atom (because
in this case xcrysden will display the primitive cell).

Regards,

-- 
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax:+386-1-477-3822)

Please, if possible, avoid sending me Word or PowerPoint attachments.
See:  http://www.gnu.org/philosophy/no-word-attachments.html


From 1009ukumar at gmail.com  Sat Jun 21 13:15:33 2014
From: 1009ukumar at gmail.com (Sonu Kumar)
Date: Sat, 21 Jun 2014 14:15:33 +0300
Subject: [xcrysden] Read POSCAR using Xcrysden
Message-ID: <CAHePdfAWOLEN=XZ5zPUn7gzzLXzxTx5ZZWecAyHSq--TwvAezQ@mail.gmail.com>

?Dear XCrysDen users,

?I tried to read POSCAR using xcrysden, but it seems it's not possible.
?
?Can this possibility be added in future ??


?with regards,
sonu?
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From tone.kokalj at ijs.si  Thu Jun 26 20:25:21 2014
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Thu, 26 Jun 2014 20:25:21 +0200
Subject: [xcrysden] Read POSCAR using Xcrysden
In-Reply-To: <CAHePdfAWOLEN=XZ5zPUn7gzzLXzxTx5ZZWecAyHSq--TwvAezQ@mail.gmail.com>
References: <CAHePdfAWOLEN=XZ5zPUn7gzzLXzxTx5ZZWecAyHSq--TwvAezQ@mail.gmail.com>
Message-ID: <1403807121.7053.21.camel@catalyst.ijs.si>

On Sat, 2014-06-21 at 14:15 +0300, Sonu Kumar wrote:

> ?I tried to read POSCAR using xcrysden, but it seems it's not
> possible.
> ?
> ?Can this possibility be added in future ??

Check the xsfConvert tool of Jens Kunstmann. I suppose it should be able
to convert POSCAR to xsf format. See:
http://www.columbia.edu/~jk3610/software.html

Regards,
-- 
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax:+386-1-477-3822)

Please, if possible, avoid sending me Word or PowerPoint attachments.
See:  http://www.gnu.org/philosophy/no-word-attachments.html


From 1009ukumar at gmail.com  Thu Jun 26 21:22:12 2014
From: 1009ukumar at gmail.com (Sonu Kumar)
Date: Thu, 26 Jun 2014 22:22:12 +0300
Subject: [xcrysden] Read POSCAR using Xcrysden
In-Reply-To: <1403807121.7053.21.camel@catalyst.ijs.si>
References: <CAHePdfAWOLEN=XZ5zPUn7gzzLXzxTx5ZZWecAyHSq--TwvAezQ@mail.gmail.com>
	<1403807121.7053.21.camel@catalyst.ijs.si>
Message-ID: <CAHePdfDkZkdRDQ58KjTsbk-XNcfbWEnw-+=3QLjOY0NBgA7ezA@mail.gmail.com>

Thank you very  much !!!


On Thu, Jun 26, 2014 at 9:25 PM, Tone Kokalj <tone.kokalj at ijs.si> wrote:

> On Sat, 2014-06-21 at 14:15 +0300, Sonu Kumar wrote:
>
> > ?I tried to read POSCAR using xcrysden, but it seems it's not
> > possible.
> > ?
> > ?Can this possibility be added in future ??
>
> Check the xsfConvert tool of Jens Kunstmann. I suppose it should be able
> to convert POSCAR to xsf format. See:
> http://www.columbia.edu/~jk3610/software.html
>
> Regards,
> --
> Anton Kokalj
> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
> (tel: +386-1-477-3523 // fax:+386-1-477-3822)
>
> Please, if possible, avoid sending me Word or PowerPoint attachments.
> See:  http://www.gnu.org/philosophy/no-word-attachments.html
>
> _______________________________________________
> XCrySDen mailing list
> XCrySDen at democritos.it
> http://www.democritos.it/mailman/listinfo/xcrysden
>
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