The best viewer for SIESTA output is still GDIS. A bit out of date (certainly a
few SIESTA versions behind), and sometimes it shows something totally wrong (I
have yet to find out the trigger for this), but 90% of the time it gets things
right. You can use it to measure distances and angles between individual atoms.
You can also watch an optimisation or MD run as a movie. Available on
sourceforge; it's also in the usual repositories for Ubuntu or Mint ("sudo
apt-get install gdis" should work).
Alternatively, I have written a utility to translate between a few periodic
input and output formats, so you can get the final geometry out of a SIESTA
output in fdf format (with which GDIS has no problem at all). I's open source
and in Fortran if somebody wants it.
Herbert
On 24/04/13 10:28, roz _gh wrote:
thanks for your regard,
I know atomic coordinates of atoms are in the block of
AtomicCoordinatesAndAtomicSpecies, but after SW defect's effect, location of
atom change. I don't have xcrysden,but befor using it we have towrite atoms'
location, I want to know these location, for example new angles and new bonds'
lengh and location of atoms in unit-cell.
Thanks.
*From:* Yunpeng Wang <[email protected]>
*To:* roz _gh <[email protected]>
*Sent:* Tuesday, April 23, 2013 8:12 PM
*Subject:* RE: [SIESTA-L] defect in graphene
1. atomic coordinates of atoms are in the block of
AtomicCoordinatesAndAtomicSpecies. You can change any or all of them as you
wish. After changing the coordinates, you can use xcrysden or vesta to visualize
the atomic structure to make sure it is the structure you want.
2. What is the difference between big unit-cell and super cell? In order to
eliminate the interaction between the defects, a convergence test of defect
formation energy as a function of size of unit cell is necessary.
hope this helps
best,
Yun-Peng Wang
PhD Candidate
State Key Laboratory of Magnetism
Institute of Physics, Chinese Academy of Science
No.8 Nansan Street, Zhongguancun
P.O. Box 603, Beijing 100190, China
Date: Tue, 23 Apr 2013 08:15:03 -0700
From: [email protected]
To: [email protected]
Subject: [SIESTA-L] defect in graphene
dear siesta users
i work with siesta 2.0.2. i want to investigate Stone-Wales defect on graphene,
but
1. I dont know how do atomic coordinates change?
2.can I consider a big unit-cell instead of a super cell? I want to create
unit-cell that involves about 40 atoms, are the 40 atoms suitable?
please help me, thanks...
--
Herbert Fruchtl
Senior Scientific Computing Officer
School of Chemistry, School of Mathematics and Statistics
University of St Andrews
--
The University of St Andrews is a charity registered in Scotland:
No SC013532
