The ABINIT Users Mailing List ( CLOSED )

["Amancherla, Sundar (CORP, GEITC)" <Sundar.Amancherla@geind.ge.com>]

Dear users,

I am stuck at trying to display the xml file using prtcml option. The
visualizers that I have used do not read the fractional co-ordinates! I
have tried converting it from xml to xyz using openbabel and that does
not read fractional coordinates. Even jmol is showing me all coordinates
to be 0,0,0 after reading the data.

Here is the xml file
==============================================================
<?xml version="1.0" encoding="iso-8859-1"?>
<!DOCTYPE molecule SYSTEM "CML-1999-05-15.dtd" []>
<molecule class="3d">
 <crystal>
  <!--
   "ITC" refers to the space group number
   in the International Tables for Crystallography
   -->
  <string builtin="spacegroup" convention="ITC">167</string>
  <float builtin="acell" units="angstrom">5.129685104098</float>
  <float builtin="bcell" units="angstrom">5.129685104098</float>
  <float builtin="ccell" units="angstrom">5.129685104098</float>
  <float builtin="alpha" units="degrees">55.330000000000</float>
  <float builtin="beta"  units="degrees">55.330000000000</float>
  <float builtin="gamma" units="degrees">55.330000000000</float>
 </crystal>
 <symmetry>
  <floatMatrix builtin="symOp" rows="4" columns="3">
    1 0 0 0.000000000000
    0 1 0 0.000000000000
    0 0 1 0.000000000000
  </floatMatrix>
  <floatMatrix builtin="symOp" rows="4" columns="3">
    0 0 1 0.000000000000
    1 0 0 0.000000000000
    0 1 0 0.000000000000
  </floatMatrix>
  <floatMatrix builtin="symOp" rows="4" columns="3">
    0 1 0 0.000000000000
    0 0 1 0.000000000000
    1 0 0 0.000000000000
  </floatMatrix>
  <floatMatrix builtin="symOp" rows="4" columns="3">
    0 1 0 0.500000000000
    1 0 0 0.500000000000
    0 0 1 0.500000000000
  </floatMatrix>
  <floatMatrix builtin="symOp" rows="4" columns="3">
    0 0 1 0.500000000000
    0 1 0 0.500000000000
    1 0 0 0.500000000000
  </floatMatrix>
  <floatMatrix builtin="symOp" rows="4" columns="3">
    1 0 0 0.500000000000
    0 0 1 0.500000000000
    0 1 0 0.500000000000
  </floatMatrix>
  <floatMatrix builtin="symOp" rows="4" columns="3">
    -1 0 0 0.000000000000
    0 -1 0 0.000000000000
    0 0 -1 0.000000000000
  </floatMatrix>
  <floatMatrix builtin="symOp" rows="4" columns="3">
    0 0 -1 0.000000000000
    -1 0 0 0.000000000000
    0 -1 0 0.000000000000
  </floatMatrix>
  <floatMatrix builtin="symOp" rows="4" columns="3">
    0 -1 0 0.000000000000
    0 0 -1 0.000000000000
    -1 0 0 0.000000000000
  </floatMatrix>
  <floatMatrix builtin="symOp" rows="4" columns="3">
    0 -1 0 0.500000000000
    -1 0 0 0.500000000000
    0 0 -1 0.500000000000
  </floatMatrix>
  <floatMatrix builtin="symOp" rows="4" columns="3">
    0 0 -1 0.500000000000
    0 -1 0 0.500000000000
    -1 0 0 0.500000000000
  </floatMatrix>
  <floatMatrix builtin="symOp" rows="4" columns="3">
    -1 0 0 0.500000000000
    0 0 -1 0.500000000000
    0 -1 0 0.500000000000
  </floatMatrix>
 </symmetry>
 <atomArray>
  <stringArray builtin="elementType">
    AL O O O AL O O O AL AL
  </stringArray>
  <stringArray builtin="xFract">
    0.352000000000 0.556000000000 0.250000000000 0.944000000000
0.852000000000
    0.444000000000 0.750000000000 0.056000000000 0.648000000000
0.148000000000
  </stringArray>
  <stringArray builtin="yFract">
    0.352000000000 0.944000000000 0.556000000000 0.250000000000
0.852000000000
    0.056000000000 0.444000000000 0.750000000000 0.648000000000
0.148000000000
  </stringArray>
  <stringArray builtin="zFract">
    0.352000000000 0.250000000000 0.944000000000 0.556000000000
0.852000000000
    0.750000000000 0.056000000000 0.444000000000 0.648000000000
0.148000000000
  </stringArray>
 </atomArray>
</molecule>
============================================================

I will be grateful to any pointers in visualizing the data to look at
the unit cell.

Thanks very much in advance...

--
  Aman


-----Original Message-----
From: Xavier Gonze [mailto:gonze@pcpm.ucl.ac.be]
Sent: Friday, August 29, 2003 7:45 PM
To: forum@abinit.org
Subject: Re: [abinit-forum] Question on crystal building


Dear Sundar Amancher,

sundar.amancherla@geind.ge.com wrote:
> Hello
> 
> I am a new user of ABINIT and also electronic structure calculations.
I need a little help in constructing a crystal of alpha-alumina. If I do
not have all the atomic positions (10 atoms) considering a primitive
rhombohedral cell, would it be difficult to create the crystal.
> 
> I have gone through the tutorial and examples' input files, and could
not get how to use the spgroup,brvlatt,natom combination.
> 
> I have these info -
> 
> Spacegroup 167 (R-3c)
> a = 3.621A; b = 0.257A
> 
> Do I need any other info? Could you point me towards an example.
Thanks very much in advance for the help...

There is an example of the setting up of crystallographic
data for Al2O3 (four different possibilities are set up !)
in ~ABINIT/Test_v1/t96.in .
Be careful : this is an example ONLY for the setting of the
crystallographic data. The ecut is much too small ...
Other parameters might have to be adjusted ...

Good continuation,
Xavier