Re: [Wien] query regarding opticplot

[Dr. K. C. Bhamu]

Thank you Gavin.
I got it.
I have some doubts for more details. First I will try and then inform you.
Like colour change, linewidth (this may be useful in case of doss)

Sincerely
Bhamu



On Mon, Sep 21, 2015 at 5:21 AM, Gavin Abo  wrote:

> Example in a bash ($) terminal:
>
> username@computername:~/test$ cat test.joint
> #2  Vol = 421.5088774080
> #  Energy  [eV] Im_eps_xx  Im_eps_zz
> #
>   0.0 0.2500E+00 0.E+00
>   1.0 0.5000E+00 0.5000E+00
>   2.0 0.7500E+00 1.E+00
> username@computername:~/test$ cp $WIENROOT/opticplot_lapw opticplot2
> username@computername:~/test$ chmod +x opticplot2
> username@computername:~/test$ gedit opticplot2
> Put a comment (#) in front of "rm $tmp1 $tmp2" on line 280 in
> opticplot2 of WIEN2k 14.2
> username@computername:~/test$ sed -n 280p opticplot2
> #rm $tmp1 $tmp2
> username@computername:~/test$ ./opticplot2
> ...
>File to plot:
> J
> ...
> Which column to plot?  2
> ...
>
> Do you want to set ranges? (y/N)N
> Do you want a hardcopy? (y/N)y
> ...
> Specify a filename (default is opticplot.ps)opticplot.ps
> ...
>File to plot:
> q
> username@computername:~/test$ gedit :opt2
> Edit the gnuplot file called :opt2 in text editor [
> 
> http://stackoverflow.com/questions/16073232/gnuplot-plotting-a-file-with-4-columns-all-on-y-axis
> ]
> username@computername:~/test$ cat :opt2
> set title 'test.joint'
> set style data lines
> set terminal png
> set output "opticplot2.png"
> set xrange [:]
> set yrange [:]
> set xlabel "Energy [eV]"
> set ylabel "Im_eps"
>
> plot ":opt1" using 1:2 title "Im_eps_xx", \
>  ":opt1" using 1:3 title "Im_eps_zz"
> username@computername:~/test$ gnuplot :opt2
>
>
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Re: [Wien] query regarding opticplot

[Víctor Luaña Cabal]

On Mon, Sep 21, 2015 at 03:48:29PM +0530, Dr. K. C. Bhamu wrote:
> Thank you Prof Blaha
> I usually do same as you suggested. I extract these files in excel and then
> used to plot in another softwares.
> I wanted through terminal just for new learning and really it also gives
> good plots.

Bhamu,

gnuplot is excellent, but it has some limitations. The veusz
(http://home.gna.org/veusz) follows a line very familiar for gnuplot
users and it represents a clear improvement on flexibility. You may
enjoy giving it a look.

It is also GPL like gnuplot. I would not mention it otherwise.

Best regards,
  V'ictor Lua~na
--
 .  ."In science a person can be convinced by a good argument.
/ `' \   That is almost impossible in politics or religion"
   /(o)(o)\  (Adapted from Carl Sagan)
  /`. \/ .'\  "Lo mediocre es peor que lo bueno, pero también es peor
 /   '`'`   \ que lo malo, porque la mediocridad no es un grado, es una
 |  \'`'`/  | actitud" -- Jorge Wasenberg, 2015
 |  |'`'`|  | (Mediocre is worse than good, but it is also worse than
  \/`'`'`'\/  bad, because mediocrity is not a grade, it is an attitude)
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist & prof. !"I have two kinds of problems,
! Departamento de Química Física y Analítica ! the urgent and the important.
! Universidad de Oviedo, 33006-Oviedo, Spain ! The urgent are not important,
! e-mail:   vic...@fluor.quimica.uniovi.es   ! and the important are never
! phone: +34-985-103491  fax: +34-985-103125 ! urgent.
++(Dwight D. Eisenhower)
 GroupPage : http://azufre.quimica.uniovi.es/ 
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Re: [Wien] query regarding opticplot

[Dr. K. C. Bhamu]

Thank you Prof Blaha
I usually do same as you suggested. I extract these files in excel and then
used to plot in another softwares.
I wanted through terminal just for new learning and really it also gives
good plots.

Sincerely

*Bhamu*

On Sun, Sep 20, 2015 at 9:33 PM, Peter Blaha 
wrote:

> You need to know GNUPLOT and csh syntax to do this.
>
> However, wh not plotting the text files (case.epsilon, sigma, ...) with
> your favorite program. You can for instance transfer these files to
> windows, import them into excel and plot there, .
>
> Am 20.09.2015 um 08:15 schrieb Dr. K. C. Bhamu:
>
>> Dear Prof Blaha and users
>> I want to plot optical properties directly from terminal. I am getting
>> plot with a single column but I want to plot two/three column
>> simultaneously (E vs XX together).
>> Is there any idea? I tried to change script of optic plot program but
>> could not succeeded.
>>
>>  set optic = J  # for JOINT DOS
>>= E  # for EPSILON
>>= S  # for SIGMAK
>>= I  # for SIGMA_INTRA
>>
>>  set col = "2"  # which column to plot, more than one
>> # column can be given
>>  set xmin = -15 # with xmin, xmax, ymin, ymax you
>>  set xmax = 15  # can specify plotting ranges
>>  set print = "file" # file to be used for plotting, or
>> # pipe directly to printer queue e.g. "|lpr"
>>  set noview # set to skip preview and directly print
>>
>> What I should I change in this script so that I get my desired columns
>> in a single plot?
>>
>> Sincerely
>> *K.C.Bhamu*
>>
>>
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>>
>>
> --
> Peter Blaha
> Inst.Materials Chemistry
> TU Vienna
> Getreidemarkt 9
> A-1060 Vienna
> Austria
> +43-1-5880115671
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Re: [Wien] time difference among nodes

[Luis Ogando]

Dear Prof. Marks,

   Many thanks for your help.
   The administrators said that everything is 0K, the software is the
problem (the easy answer) : no zombies, no other jobs in the node, ... !!
   Let me give you more information to see if you can imagine other
possibilities:

1) Intel Xeon Six Core 5680, 3.33GHz

2) Intel(R) Fortran/CC/OpenMPI Intel(R) 64 Compiler XE for applications
running on Intel(R) 64, Version 12.1.1.256 Build 20111011

3) OpenMPI 1.6.5

4) PBS Pro 11.0.2

5) OpenMPI built using  --with-tm  due to prohibited ssh among nodes  (
http://www.open-mpi.org/faq/?category=building#build-rte-tm )

6) Wien2k 14.2

7) The mystery : two weeks ago, everything was working properly !!

   Many thanks again !
   All the best,
   Luis

2015-09-18 23:24 GMT-03:00 Laurence Marks :

> Almost certainly one or more of:
> * Other jobs on the node
> * Zombie process(es)
> * Too many mpi
> * Bad memory
> * Full disc
> * Too hot
>
> If you have it use ganglia, if not ssh in and use top/ps or whatever SGI
> has. If you cannot sudo get help from someone who can.
> On Sep 18, 2015 8:58 PM, "Luis Ogando"  wrote:
>
>> Dear Wien2k community,
>>
>>I am using Wien2k in a SGI cluster with 32 nodes. My calculation is
>> running in 4 nodes that have the same characteristics and only my job is
>> running in these 4 nodes.
>>I noticed that one of these 4 nodes is spending more than 20 times the
>> time spent by the other 3 nodes in the run_lapw execution.
>>Could someone imagine a reason for this ? Any advice ?
>>All the best,
>> Luis
>>
>>
>
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> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
>
>
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Re: [Wien] time difference among nodes

[Peter Blaha]

a) Check your .machines file.  DFoes it meet your expectations, or has 
this node too large load.


b) Can you interactively login into these nodes while your job is running ?
If yes, login on 2 nodes (in two windows) and runtop

c) If nothing obvious is wrong so far, test the network by doing some 
bigger copying from/to these nodes from your $home (or $scratch) to see 
if file-io is killing you.



On 09/21/2015 02:51 PM, Luis Ogando wrote:

Dear Prof. Marks,

Many thanks for your help.
The administrators said that everything is 0K, the software is the
problem (the easy answer) : no zombies, no other jobs in the node, ... !!
Let me give you more information to see if you can imagine other
possibilities:

1) Intel Xeon Six Core 5680, 3.33GHz

2) Intel(R) Fortran/CC/OpenMPI Intel(R) 64 Compiler XE for applications
running on Intel(R) 64, Version 12.1.1.256 Build 20111011

3) OpenMPI 1.6.5

4) PBS Pro 11.0.2

5) OpenMPI built using  --with-tm  due to prohibited ssh among nodes  (
http://www.open-mpi.org/faq/?category=building#build-rte-tm )

6) Wien2k 14.2

7) The mystery : two weeks ago, everything was working properly !!

Many thanks again !
All the best,
Luis

2015-09-18 23:24 GMT-03:00 Laurence Marks >:

Almost certainly one or more of:
* Other jobs on the node
* Zombie process(es)
* Too many mpi
* Bad memory
* Full disc
* Too hot

If you have it use ganglia, if not ssh in and use top/ps or whatever
SGI has. If you cannot sudo get help from someone who can.

On Sep 18, 2015 8:58 PM, "Luis Ogando" > wrote:

Dear Wien2k community,

I am using Wien2k in a SGI cluster with 32 nodes. My
calculation is running in 4 nodes that have the same
characteristics and only my job is running in these 4 nodes.
I noticed that one of these 4 nodes is spending more than 20
times the time spent by the other 3 nodes in the run_lapw execution.
Could someone imagine a reason for this ? Any advice ?
All the best,
 Luis


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--

  P.Blaha
--
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
WWW:   http://www.imc.tuwien.ac.at/staff/tc_group_e.php
--
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[Wien] Need your help please

[sikander Azam]

Dear All
What is no shape approximation?
Regards
SIkander
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[Wien] partial DOS

[Seyyed Amir Abbas Emami]

​dear uses

I am trying to calculate DOS of  compound with stoichiometric  A 2  B 1-x C x 
by asist of supercell approach.The atom B, in first and end series have one 
position but in intermediate cases it split into two distinct positions.Now i 
want to calculate the partial DOS of d orbital of B atom for intermediate 
cases.Is there any way to calculate the contribution of two atoms 
simultaneously for d orbitals of B .

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Re: [Wien] partial DOS

[Gavin Abo]

See the posts:

http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg10872.html
http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg10873.html

On 9/21/2015 11:35 AM, Seyyed Amir Abbas Emami wrote:

​ dear uses

I am trying to calculate DOS of  compound with stoichiometric  A 2  B 
1-x C x by asist of supercell approach.The atom B, in first and end 
series have one position but in intermediate cases it split into two 
distinct positions.Now i want to calculate the partial DOS of d 
orbital of B atom for intermediate cases.Is there any way to calculate 
the contribution of two atoms simultaneously for d orbitals of B .
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Re: [Wien] time difference among nodes

[Luis Ogando]

Dear Professor Blaha,

   Thank you !
   My .machines file is 0K.
   I will ask the administrator to follow your other suggestions (users do
not have privileges).
   All the best,
   Luis


2015-09-21 10:22 GMT-03:00 Peter Blaha :

> a) Check your .machines file.  DFoes it meet your expectations, or has
> this node too large load.
>
> b) Can you interactively login into these nodes while your job is running ?
> If yes, login on 2 nodes (in two windows) and runtop
>
> c) If nothing obvious is wrong so far, test the network by doing some
> bigger copying from/to these nodes from your $home (or $scratch) to see if
> file-io is killing you.
>
>
> On 09/21/2015 02:51 PM, Luis Ogando wrote:
>
>> Dear Prof. Marks,
>>
>> Many thanks for your help.
>> The administrators said that everything is 0K, the software is the
>> problem (the easy answer) : no zombies, no other jobs in the node, ... !!
>> Let me give you more information to see if you can imagine other
>> possibilities:
>>
>> 1) Intel Xeon Six Core 5680, 3.33GHz
>>
>> 2) Intel(R) Fortran/CC/OpenMPI Intel(R) 64 Compiler XE for applications
>> running on Intel(R) 64, Version 12.1.1.256 Build 20111011
>>
>> 3) OpenMPI 1.6.5
>>
>> 4) PBS Pro 11.0.2
>>
>> 5) OpenMPI built using  --with-tm  due to prohibited ssh among nodes  (
>> http://www.open-mpi.org/faq/?category=building#build-rte-tm )
>>
>> 6) Wien2k 14.2
>>
>> 7) The mystery : two weeks ago, everything was working properly !!
>>
>> Many thanks again !
>> All the best,
>> Luis
>>
>> 2015-09-18 23:24 GMT-03:00 Laurence Marks > >:
>>
>> Almost certainly one or more of:
>> * Other jobs on the node
>> * Zombie process(es)
>> * Too many mpi
>> * Bad memory
>> * Full disc
>> * Too hot
>>
>> If you have it use ganglia, if not ssh in and use top/ps or whatever
>> SGI has. If you cannot sudo get help from someone who can.
>>
>> On Sep 18, 2015 8:58 PM, "Luis Ogando" > > wrote:
>>
>> Dear Wien2k community,
>>
>> I am using Wien2k in a SGI cluster with 32 nodes. My
>> calculation is running in 4 nodes that have the same
>> characteristics and only my job is running in these 4 nodes.
>> I noticed that one of these 4 nodes is spending more than 20
>> times the time spent by the other 3 nodes in the run_lapw
>> execution.
>> Could someone imagine a reason for this ? Any advice ?
>> All the best,
>>  Luis
>>
>>
>> ___
>> Wien mailing list
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>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>> SEARCH the MAILING-LIST at:
>>
>> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
>>
>>
>>
>>
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>> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
>>
>>
> --
>
>   P.Blaha
> --
> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
> Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
> Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
> WWW:   http://www.imc.tuwien.ac.at/staff/tc_group_e.php
> --
>
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Re: [Wien] Need your help please

[Fecher, Gerhard]

The assumption that a apple is not a sphere

Ciao
Gerhard

DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
"I think the problem, to be quite honest with you,
is that you have never actually known what the question is."


Dr. Gerhard H. Fecher
Institut of Inorganic and Analytical Chemistry
Johannes Gutenberg - University
55099 Mainz
and
Max Planck Institute for Chemical Physics of Solids
01187 Dresden

Von: wien-boun...@zeus.theochem.tuwien.ac.at 
[wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von sikander Azam 
[sikander.physi...@gmail.com]
Gesendet: Montag, 21. September 2015 13:40
An: A Mailing list for WIEN2k users
Betreff: [Wien] Need your help please

Dear All
What is no shape approximation?
Regards
SIkander
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