Re: [Wien] XCrysDen

2018-08-29 Thread Gavin Abo 
I just tried and the xcrysden semishared binary package successfully ran 
on openSUSE 15.0 installed on a USB stick. So I would expect a full 
openSUSE install to be no different.


The installation process was very similar to CentOS, Fedora, and Ubuntu 
[ http://www.democritos.it/pipermail/xcrysden/2017-December/001902.html ].


1. Went to: http://download.opensuse.org/distribution/leap/15.0/live/
2. Downloaded: openSUSE-Leap-15.0-GNOME-Live-x86_64-Snapshot20.21-Media.iso
3. Went to: https://rufus.akeo.ie/
4. Downloaded Rufus 3.1 Portable: rufus-3.1p.exe
5. Used Rufus to burn the above iso to a USB stick
6. Booted from the USB stick
a. Selected openSUSE Leap 15.0 GNOME Live
b. Connected to the Internet
7. Opened a terminal and performed the following:

linux@localhost:~> wget 
http://www.xcrysden.org/download/xcrysden-1.5.60-linux_x86_64-semishared.tar.gz

...
linux@localhost:~> tar xvf xcrysden-1.5.60-linux_x86_64-semishared.tar.gz
...
linux@localhost:~> cd xcrysden-1.5.60-bin-semishared/scripts/
linux@localhost:~/xcrysden-1.5.60-bin-semishared/scripts> ./xcConfigure.sh
more: unknown option -more
Try 'more --help' for more information.

   Please specify XCRYSDEN_SCRATCH directory (default: 
/home/linux/xcrys_tmp):

   Do you have a CRYSTAL package ([y]es/[n]o): n
   Is this correct ([y]es/[n]o): y
...
   Would you like to add xcrysden icon to the desktop ([y]es/[n]o): y
...
Then type: xcrysden

linux@localhost:~/xcrysden-1.5.60-bin-semishared/scripts> source ~/.bashrc
linux@localhost:~/xcrysden-1.5.60-bin-semishared/scripts> xcrysden

Your problem sounds very similar to this old post:

http://www.democritos.it/pipermail/xcrysden/2010-March/000778.html

However, I don't know how they solved it.

Though, I did encounter the same error of can't read "xcrys(platform)": 
no such variable seen at that old post, but that was using KDE 
(openSUSE-Leap-15.0-KDE-Live-x86_64-Snapshot20.21-Media.iso) instead of 
GNOME. Though, it seemed to work fine after following the advice in bug 
report [ https://bugzilla.redhat.com/show_bug.cgi?id=1043686 ], i.e.:


~]$ xrdb -load /dev/null
~]$ xrdb -query
~]$ xcrysden

However, in your post, it is not clear to me how you are running 
xcrysden on the cluster node.  VNC connection to a GUI desktop on the 
cluster?  Or are you X11 forwarding the display from the cluster to have 
it display on another system [ 
https://lists.freedesktop.org/archives/xorg/2011-April/052647.html , 
https://users.wfu.edu/natalie/s11phy752/lecturenote/PHY752lectLAPW.pdf 
]?  Sometime X11 forwarding works fine, but it many cases I found 
xcrysden to be very slow or hang doing X11 forwarding.  Thus, I usually 
preferred either the VNC connection or using xcrysden on my local box 
(where I would just transfer necessary WIEN2k files from the cluster to 
the local computer, then display it using xcrysden). For latter local 
using files from the cluster, it can take some work to figure out files 
are needed, but it is doable.  I gave somewhat of an example when I 
mentioned that case.struct, case.klist, case.clmdn, case.outputkgen, and 
case.output1up (are needed) in one case for displaying a fermi surface 
in xcrysden:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17847.html

Hope that helps and good luck.

On 8/28/2018 5:29 PM, FonsPaul wrote:


I have installed the latest stable version of OpenSuse, version 15 on 
a node in a cluster and have found that the semi-shared binary I was 
using of XCrystDen no longer works. When I attempt to run XCrysDen, I 
see the splash window, but then an error window pops up without any 
indications of what the error is. I then downloaded the sourcecode to 
version 1.5 only to find that the make script is broken (it attempts 
to download dependent libraries and the links seem to be broken). Has 
anyone run into this problem before and is there a simple solution?




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Re: [Wien] a query about fold2Bloch

2018-08-29 Thread karima Physique 
Thank you for your replies

Le mer. 29 août 2018 à 12:56, Rubel, Oleg  a écrit :

> In addition to Gavin's comment, I would suggest trying octave as a free
> alternative to Matlab.
>
> Oleg
>
> On Aug 28, 2018, at 23:27, Gavin Abo  wrote:
>
> Regarding 2, fold2Bloch Guide [
> https://github.com/rubel75/fold2Bloch-Wien2k/wiki/fold2Bloch-Guide ] and
> Tutorial 1 [
> https://github.com/rubel75/fold2Bloch-Wien2k/wiki/Tutorial-1:-Lattice-of-Hydrogen-atoms
> ] show that eigenvalues are Ry in case.f2b.
>
> Regarding 1, the ubs_dots.m [
> https://github.com/rubel75/fold2Bloch-Wien2k/blob/master/Utils/ubs_dots.m
> ] in Tutorial 1 seems to use a scatter plot [
> https://www.mathworks.com/help/matlab/ref/scatter.html ].  You might be
> able to use the plot function in gnuplot [
> https://stackoverflow.com/questions/35075113/scatter-plot-with-different-size-for-each-point
> , http://gnuplot.sourceforge.net/docs_4.2/node100.html ] or Indexed Size
> (Bubble) and Color Map Graph in Origin [
> https://www.originlab.com/doc/Origin-Help/2DSym-Graph ].
> On 8/28/2018 11:40 AM, karima Physique wrote:
>
> Dear dr. Oleg Rubel and Wien2k users:
>
> 1- do you have any idea to how to plot the band strcture using gnuplot or
> Originlab (transform F2B file to dataplot file with X:Y columns).
> 2- the unit of energy is it eV or Ry in F2B file
>
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Re: [Wien] a query about fold2Bloch

2018-08-29 Thread Rubel, Oleg 




In addition to Gavin's comment, I would suggest trying octave as a free alternative to Matlab.


Oleg

On Aug 28, 2018, at 23:27, Gavin Abo  wrote:




Regarding 2, fold2Bloch Guide [ 
https://github.com/rubel75/fold2Bloch-Wien2k/wiki/fold2Bloch-Guide ] and Tutorial 1 [

https://github.com/rubel75/fold2Bloch-Wien2k/wiki/Tutorial-1:-Lattice-of-Hydrogen-atoms ] show that eigenvalues are Ry in case.f2b.
Regarding 1, the ubs_dots.m [ 
https://github.com/rubel75/fold2Bloch-Wien2k/blob/master/Utils/ubs_dots.m ] in Tutorial 1 seems to use a scatter plot [

https://www.mathworks.com/help/matlab/ref/scatter.html ].  You might be able to use the plot function in gnuplot [

https://stackoverflow.com/questions/35075113/scatter-plot-with-different-size-for-each-point ,

http://gnuplot.sourceforge.net/docs_4.2/node100.html ] or Indexed Size (Bubble) and Color Map Graph in Origin [

https://www.originlab.com/doc/Origin-Help/2DSym-Graph ].

On 8/28/2018 11:40 AM, karima Physique wrote:


Dear dr. Oleg Rubel and Wien2k
 users:


1- do you have any idea to how to plot the band strcture using gnuplot or  Originlab (transform F2B file to dataplot file with X:Y columns).
2- the unit of energy is it eV or Ry in F2B file





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