Re: [Wien] Optical gap

2016-03-11 Thread Gavin Abo 
Absorption coefficient can be used to make Tauc plot and tangent method 
gives Tauc gap [ https://en.wikipedia.org/wiki/Tauc_plot ].


Optical gap is determined from the plot of epsilon2 (the imaginary part 
of the dielectric function) using the tangent method.


To visualize what Xavier describes in the posts at

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg08951.html

see for example Figure 7 in the article titled "Band Gap Determination 
from Diffuse Reflectance Measurements of Irradiated Lead Borate Glass 
System Doped with TiO2 by Using Diffuse Reflectance Technique" by S. 
Ebraheem and A. El-Saied [ 
http://file.scirp.org/Html/8-7701026_31475.htm ].  This article also 
describes how r might be determined for the Tauc plot.


On 3/7/2016 3:05 PM, said chibani wrote:

Dear Wien Users ,
how to determineoptical gapfromthe graph of opticalproperties ? is 
determine from the graph of absorption coefficient? and how ?
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Re: [Wien] berrypi missing -c case (in automatic)

2016-03-11 Thread Laurence Marks 
You are right, I missed that.

---
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think what nobody
else has thought", Albert Szent-Gyorgi
http://www.numis.northwestern.edu
Corrosion in 4D http://MURI4D.numis.northwestern.edu
Partner of the CFW 100% gender equity project, www.cfw.org/100-percent
Co-Editor, Acta Cryst A

On Mar 11, 2016 18:31, "Oleg Rubel"  wrote:

> The necessity for the ‘-c’ option is not obvious. Would you please give a
> hint?
>
> BerryPI executes ‘x lapw1’ and then ‘x w2w’. I both cases, ‘x’ script is
> used that identifies complex calculation. There is no need to be more
> specific and call for ‘x lapw1 -c’ or ‘x w2w -c’ (please correct me, if I
> am wrong). Do you have a case where the complex calculation is not properly
> identified? I can take a look into that.
>
> Also, I think that there is no need to run BerryPI for a system with
> inversion symmetry explicitly present in the structure file. All electronic
> phases will be zero. Sometimes, centrosymmetric structure is a reference
> structure, whereas a perturbed structure lacks the inversion symmetry. In
> this case, I would recommend to run both calculations using identical low
> symmetry settings.
>
> Oleg
>
> > On Mar 11, 2016, at 4:04 PM, Laurence Marks 
> wrote:
> >
> > berrypi seems to need a "-c" option for the complex case, presumably can
> be hacked around.
> >
> > Similarly needed for the call of w2w that it makes (I think).
> >
> > --
> > Professor Laurence Marks
> > "Research is to see what everybody else has seen, and to think what
> nobody else has thought", Albert Szent-Gyorgi
> > www.numis.northwestern.edu ; Corrosion in 4D:
> MURI4D.numis.northwestern.edu
> > Partner of the CFW 100% program for gender equity,
> www.cfw.org/100-percent
> > Co-Editor, Acta Cryst A
>
>
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Re: [Wien] Problem with k-parallel

2016-03-11 Thread Guo-ping Zhang 

Dear Maciej,

I think Peter's suggestion is correct.

I encountered the same problem last year and it took me several days to 
figure it out. The problem is that the wien script deletes those temp 
files after each run. If you have two or more jobs running on the same 
node, you will have one job killing another job's tmp files.  You can see 
at the end of lapw2para ... that the script removes those tmp files which 
are still needed by other jobs. My solution is let tmp_dir point to your 
local working directory, not /tmp.



Best regards,

Guoping


On Thu, 10 Mar 2016, Maciej Polak wrote:


Dear Prof. Blaha,

Thank you very much for your support. I changed the code according to your 
suggestions and it seems to work better now. I will be testing it though and 
let you know if any other issues arise.


Thanks again,

Best regards,

Maciej Polak



On 03/09/2016 05:06 PM, Peter Blaha wrote:

Just put it to /tmp.

(There was a suggestion in the mailing list that someone wanted to change 
/tmp to some other directory, which is tedious in the old versions. With a 
variable $tmp_dir  this is "easy" to change and will be active in the next 
release.



On 03/09/2016 04:27 PM, Maciej Polak wrote:

Dear Prof. Blaha,

Thank you for your answer. I found the appropriate part of my lapw2para 
and substituted it with what you suggested.
However, one of the changes that I notice here is that you changed tmp for 
$tmp_dir. This $tmp_dir is a new variable which is not recognized by my 
script (tmp_dir: Undefined variable.). What is the meaning of this 
variable?


Thank you again for finding the time to reply to my email.

Best regards,

Maciej Polak

P.S In case you need it, I post the unmodified part of my code:


set i = 1
while ($i <= $maxproc)
# if ($debug > 0) echo -n "$i "
  cp $def.def /tmp/.tmp.$user.$$
  #subsituting in files:
  cat  /tmp/.tmp1.$user.$$
  sed "s/vector_${i}dn_$i/vectordn_$i/" 
/tmp/.tmp1.$user.$$>/tmp/.tmp2.$user.$$
  sed "s/vector_${i}up_$i/vectorup_$i/" 
/tmp/.tmp2.$user.$$>/tmp/.tmp1.$user.$$
  sed "s/vector_${i}so_$i/vectorso_$i/" 
/tmp/.tmp1.$user.$$>/tmp/.tmp2.$user.$$
  sed "s/energy_${i}up_$i/energyup_$i/" 
/tmp/.tmp2.$user.$$>/tmp/.tmp1.$user.$$
  sed "s/energy_${i}dn_$i/energydn_$i/" 
/tmp/.tmp1.$user.$$>/tmp/.tmp2.$user.$$
  sed "s/energy_${i}so_$i/energyso_$i/" 
/tmp/.tmp2.$user.$$>/tmp/.tmp1.$user.$$
  sed "s/energyso_${i}dn_$i/energysodn_${i}/" 
/tmp/.tmp1.$user.$$>/tmp/.tmp2.$u$
  sed "s/energy_${i}dum_$i/energydum_$i/" 
/tmp/.tmp2.$user.$$>/tmp/.tmp1.$user.$
  sed "s/vector_${i}so_${i}dn_$i/vectorsodn_$i/" 
/tmp/.tmp1.$user.$$>/tmp/.tmp2$
  sed "s/vector_${i}dum_${i}dn_$i/vectordumdn_$i/" 
/tmp/.tmp2.$user.$$>"$def"_$$

  @ i ++
end


W dniu 09/03/16 13:45 Peter Blaha  napisał:


Hi,

Yes, we had have recently also such a problem. It comes from slow disk 
I/O.


A fie like /tmp/.tmp2.mpolak.50255

is a temporary file created by lapw2para and is used when we modify the 
lapw2_xx.def files by a couple of sed commands.


Because of this I've reduced the sed commands in my version of lapw2para. 
Unfortunately, I cannot post the script because it will not be compatible 
with your WIEN2k version, but I can tell you what we did and since then 
these errors did not show up anymore.


Please identify the following lines in your lapw2para and modify it like 
shown below:

...
#creating def files
set i = 1
while ($i <= $maxproc)
# if ($debug > 0) echo -n "$i "
cp $def.def $tmp_dir/.tmp.$user.$$
#subsituting in files:
cat <$tmp_dir/.script.$user.$$
s/vectorso$dnup/&_$i/w $tmp_dir/.mist.$user.$$
s/vectorso$updn/&_$i/w $tmp_dir/.mist.$user.$$
s/vectordum$dnup/&_$i/w $tmp_dir/.mist.$user.$$
s/vectordum$updn/&_$i/w $tmp_dir/.mist.$user.$$
s/vector$dnup'/vector${dnup}_$i'/w $tmp_dir/.mist.$user.$$
s/vector$updn'/vector${updn}_$i'/w $tmp_dir/.mist.$user.$$
s/energyso$dnup/&_$i/w $tmp_dir/.mist.$user.$$

Re: [Wien] berrypi missing -c case (in automatic)

2016-03-11 Thread Oleg Rubel 
The necessity for the ‘-c’ option is not obvious. Would you please give a hint?

BerryPI executes ‘x lapw1’ and then ‘x w2w’. I both cases, ‘x’ script is used 
that identifies complex calculation. There is no need to be more specific and 
call for ‘x lapw1 -c’ or ‘x w2w -c’ (please correct me, if I am wrong). Do you 
have a case where the complex calculation is not properly identified? I can 
take a look into that.

Also, I think that there is no need to run BerryPI for a system with inversion 
symmetry explicitly present in the structure file. All electronic phases will 
be zero. Sometimes, centrosymmetric structure is a reference structure, whereas 
a perturbed structure lacks the inversion symmetry. In this case, I would 
recommend to run both calculations using identical low symmetry settings.

Oleg

> On Mar 11, 2016, at 4:04 PM, Laurence Marks  wrote:
> 
> berrypi seems to need a "-c" option for the complex case, presumably can be 
> hacked around.
> 
> Similarly needed for the call of w2w that it makes (I think).
> 
> -- 
> Professor Laurence Marks
> "Research is to see what everybody else has seen, and to think what nobody 
> else has thought", Albert Szent-Gyorgi
> www.numis.northwestern.edu ; Corrosion in 4D: MURI4D.numis.northwestern.edu
> Partner of the CFW 100% program for gender equity, www.cfw.org/100-percent
> Co-Editor, Acta Cryst A

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[Wien] berrypi missing -c case (in automatic)

2016-03-11 Thread Laurence Marks 
berrypi seems to need a "-c" option for the complex case, presumably can be
hacked around.

Similarly needed for the call of w2w that it makes (I think).

-- 
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think what nobody
else has thought", Albert Szent-Gyorgi
www.numis.northwestern.edu ; Corrosion in 4D: MURI4D.numis.northwestern.edu
Partner of the CFW 100% program for gender equity, www.cfw.org/100-percent
Co-Editor, Acta Cryst A
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Re: [Wien] Crystal structure that XCrySDen cannot visualize

2016-03-11 Thread Lyudmila Dobysheva 

11.03.2016 00:29, delamora wrote:

I am using the XCrySDen-1.5.25, and maybe it is why I am having this problem.


Mine is Version: 1.4.1

Best wishes
  Lyudmila Dobysheva
--
Phys.-Techn. Institute of Ural Br. of Russian Ac. of Sci.
426001 Izhevsk, ul.Kirova 132
RUSSIA
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