<div dir="ltr"><div class="gmail_default" style="font-family:comic sans ms,sans-serif;color:rgb(0,0,0)">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.<br><br></div><div class="gmail_default" style="font-family:comic sans ms,sans-serif;color:rgb(0,0,0)">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<br><br>PRIMVEC<br> 1.8879977010 -1.8879977010 4.7429900630<br> 1.8879977010 1.8879977010 4.7429900630<br> -1.8879977010 -1.8879977010 4.7429900630<br></div><div class="gmail_extra"><br><div class="gmail_default" style="font-family:comic sans ms,sans-serif;color:rgb(0,0,0)">now define atomic coordinate as matrix a and above as b<br>a =<br> 0.00000 0.00000 0.00000<br> 0.00000 1.88800 2.37150<br> 0.00000 0.00000 -1.98310<br> 0.00000 0.00000 1.98310<br> 0.00000 1.88800 0.38780<br> 0.00000 1.88800 4.35520<br></div><div class="gmail_default" style="font-family:comic sans ms,sans-serif;color:rgb(0,0,0)">b =<br> 1.8880 -1.8880 4.7430<br> 1.8880 1.8880 4.7430<br> -1.8880 -1.8880 4.7430<br></div><div class="gmail_default" style="font-family:comic sans ms,sans-serif;color:rgb(0,0,0)">now find a/b as a*b-1<br> 0.00000 0.00000 -0.00000<br> -0.50000 0.75000 0.25000<br> 0.00000 -0.20906 -0.20906<br> 0.00000 0.20906 0.20906<br> -0.50000 0.54088 0.04088<br> -0.50000 0.95912 0.45912<br></div><div class="gmail_default" style="font-family:comic sans ms,sans-serif;color:rgb(0,0,0)">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.<br></div><br><div class="gmail_default" style="font-family:comic sans ms,sans-serif;color:rgb(0,0,0)">find out the attachment for input file 2 which gives correct structure. <br></div><br><br clear="all"><div><div class="gmail_default" style="font-family:comic sans ms,sans-serif;color:rgb(0,0,0)"><span style="background-color:rgb(243,243,243)"><span style="font-family:georgia,serif"><span style="color:rgb(0,0,255)"><i><span style="font-size:12pt;line-height:115%"><b><span style="color:rgb(0,0,0)">---------------------------------------------</span><br></b></span></i></span><span style="font-family:comic sans ms,sans-serif"><span style="color:rgb(0,0,255)"><font size="2"><span style="line-height:115%"><b><span style="line-height:115%"><div class="gmail_default" style="font-family:comic sans ms,sans-serif;color:rgb(0,0,0);display:inline"><i>Muthu V</i></div></span><span style="line-height:150%"><br><div dir="ltr"><span style="background-color:rgb(243,243,243)"><span style="font-family:georgia,serif"><span style="font-family:comic sans ms,sans-serif"><span style="color:rgb(0,0,255)"><font size="2"><span style="line-height:115%"><b><span style="line-height:150%"><i><div class="gmail_default" style="font-family:comic sans ms,sans-serif;color:rgb(0,0,0);display:inline">Sri Paramakalyani colleg<font size="2">e,<br></font></div><div class="gmail_default" style="font-family:comic sans ms,sans-serif;color:rgb(0,0,0);display:inline"><font size="2">Alwarkruichi, India<br></font></div><div class="gmail_default" style="font-family:comic sans ms,sans-serif;color:rgb(0,0,0);display:inline"></div></i></span></b><span style="line-height:150%"></span></span></font></span></span></span></span><span style="color:rgb(0,0,0)"><b><span><span style="background-color:rgb(243,243,243)"><span style="font-family:georgia,serif"><i><span style="font-size:12pt;line-height:115%">---------------------------------------------</span></i></span></span></span></b></span></div></span></b></span></font></span></span></span></span></div><br></div>
<br><div class="gmail_quote">On Mon, Jan 18, 2016 at 12:05 PM, <span dir="ltr"><<a href="mailto:xcrysden-request@democritos.it" target="_blank">xcrysden-request@democritos.it</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Send XCrySDen mailing list submissions to<br>
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Today's Topics:<br>
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1. Re: Anatase primitive cell: Regarding (Gavin Abo)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Sun, 17 Jan 2016 18:09:25 -0700<br>
From: Gavin Abo <<a href="mailto:gsabo@crimson.ua.edu">gsabo@crimson.ua.edu</a>><br>
Subject: Re: [xcrysden] Anatase primitive cell: Regarding<br>
To: <a href="mailto:xcrysden@democritos.it">xcrysden@democritos.it</a><br>
Message-ID: <<a href="mailto:569C3B45.5010601@crimson.ua.edu">569C3B45.5010601@crimson.ua.edu</a>><br>
Content-Type: text/plain; charset="windows-1252"<br>
<br>
Regarding Inputfile 1, keep in mind that you might have to increase the<br>
precision of the atomic positions as described in the post at the<br>
following link:<br>
<br>
<a href="http://qe-forge.org/pipermail/pw_forum/2006-August/079340.html" rel="noreferrer" target="_blank">http://qe-forge.org/pipermail/pw_forum/2006-August/079340.html</a><br>
<br>
Regarding Inputfile 2, it seems like you can get XCrySDen to show the<br>
same structure as Inputfile 1 if you change ibrav from 7 to 6, nat from<br>
6 to 12, and add the atomic positions for the other 6 atoms (for a total<br>
of 12 atoms) in Inputfile 2. Refer to the <a href="http://anatase.in" rel="noreferrer" target="_blank">anatase.in</a> file attached at<br>
the bottom of the post at the following link:<br>
<br>
<a href="https://www.mail-archive.com/pw_forum@pwscf.org/msg27155.html" rel="noreferrer" target="_blank">https://www.mail-archive.com/pw_forum@pwscf.org/msg27155.html</a><br>
<br>
On 1/15/2016 11:48 PM, Suresh A wrote:<br>
> Dear Friends,<br>
> I have prepared primitive cell input file for<br>
> quantum espresso.I have included those files below. The problem is<br>
> XCRYSDEN shows two different structure for a same file where one is in<br>
> crystal coordinates and other one in angstrom.<br>
><br>
> Inputfile number 1: This file shows correct strucutre in XCRYSDEN<br>
><br>
><br>
> &CONTROL<br>
> title = 'TiO2' ,<br>
> calculation = 'scf',<br>
> outdir ='$TMP_DIR/'<br>
> prefix = 'anatase',<br>
> pseudo_dir = '$PSEUDO_DIR/',<br>
> /<br>
><br>
> &SYSTEM<br>
> ibrav = 7,<br>
> celldm(1) = 7.1356,<br>
> celldm(3) = 2.51218,<br>
> nat = 6 ,<br>
> ntyp = 2 ,<br>
> ecutwfc = 30.0000000000 ,<br>
> ecutrho = 300,<br>
><br>
><br>
> /<br>
><br>
> &ELECTRONS<br>
><br>
> conv_thr = 1.0d-09,<br>
><br>
> /<br>
> ATOMIC_SPECIES<br>
> O 15.999 O.pw91-van_ak.UPF<br>
> Ti 47.867 Ti.pw91-nsp-van.UPF<br>
> ATOMIC_POSITIONS angstrom<br>
> Ti 0.000000000 0.000000000 0.000000000<br>
> Ti 0.000000000 1.888000000 2.371500000<br>
> O 0.000000000 0.000000000 -1.983097630<br>
> O 0.000000000 0.000000000 1.983097630<br>
> O 0.000000000 1.888000000 0.387796645<br>
> O 0.000000000 1.888000000 4.355203355<br>
> K_POINTS automatic<br>
> 4 4 4 0 0 0<br>
><br>
><br>
> /Inputfile number 2:<br>
> &CONTROL<br>
> title = 'anatase' ,<br>
> calculation = 'scf' ,<br>
> restart_mode = 'from_scratch' ,<br>
> pseudo_dir = '/home/suresh/GN2/',<br>
> outdir ='/home/suresh/Desktop/primitivecell/tmp/',<br>
> prefix = 'anatase' ,<br>
> tstress = .true. ,<br>
> tprnfor = .true. ,<br>
><br>
><br>
><br>
> /<br>
> &SYSTEM<br>
> ibrav = 7,<br>
> celldm(1) = 7.153,<br>
> celldm(3) = 2.513,<br>
> nat = 6,<br>
> ntyp = 2,<br>
> ecutwfc = 60 ,<br>
> exxdiv_treatment = 'none' ,<br>
><br>
><br>
><br>
> /<br>
> &ELECTRONS<br>
><br>
><br>
> /<br>
> &IONS<br>
><br>
><br>
> /<br>
> &CELL<br>
><br>
><br>
><br>
> /<br>
> ATOMIC_SPECIES<br>
> Ti 47.86700 Ti.pz-mt_fhi.UPF<br>
> O 15.99940 O.pz-mt_fhi.UPF<br>
> ATOMIC_POSITIONS (crystal)<br>
> Ti 0.0000000 0.0000000 0.0000000<br>
> Ti 0.0000000 0.5000000 0.2500000<br>
> O 0.0000000 0.0000000 0.2080000<br>
> O 0.0000000 0.0000000 -0.208000<br>
> O 0.0000000 0.5000000 0.4580000<br>
> O 0.0000000 0.5000000 -0.042000<br>
> K_POINTS automatic<br>
> 4 4 2 1 1 1<br>
><br>
> /<br>
> /Will you please pointout where the problem i?<br>
> /<br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
> With Regards,<br>
> A.Suresh,<br>
> Research Scholar,<br>
> Madurai Kamaraj University,<br>
> Madurai.<br>
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</blockquote></div><br></div></div>