subject:"\"\\\[Wien\\\] XCrySDen\""

Re: [Wien] XCrySDen 1.6

2024-09-02 Thread Gavin Abo


You need to navigate to the file:


/home/Programas/xcrysden-1.6.2-bin-shared/Tcl/custom-definitions


In that file, there should be the line:


#set toglOpt(accum) false


That line needs changed to:


set toglOpt(accum) false


When I installed XCrySDen right after installing Fedora 40, it worked.  
However, after Fedora 40 push an update, it broke. However, I was able 
to get it working again after following the advice to use "set 
toglOpt(accum) false" in custom-definitions, which I found at:



https://unix.stackexchange.com/questions/702305/running-xcrysden-in-wayland


Kind Regards,

Gavin

WIEN2k & XCrySDen user


On 9/2/2024 12:07 PM, delamora wrote:

Gavin
Thanks for your reply, but it still does not work;
-

XCRYSDEN_SCRATCH=/home/pablo/xcrys_tmp

Running on platform : unix
   Operating system : Linux
Package ImageMagick's import: /usr/bin/import
Executing: /home/Programas/xcrysden-1.6.2-bin-shared/bin/ftnunit
Error in startup script: Can not set ident to a window path name
Couldn't configure togl widget
    while executing
"togl .mesa  -width          400  -height         400  -ident       
 .mesa  -rgba           $toglOpt(rgba)           -redsize       
 $toglOpt(redsize..."

    (procedure "PlaceGlobWin" line 107)
    invoked from within
"PlaceGlobWin 0 [expr round(670 * $fac1)] [expr round(670 * $fac1)]"
    (procedure "ViewMol" line 25)
    invoked from within
"ViewMol ."
    invoked from within
"if { [llength $argv] > 2 } {
    parseComLinArg [lrange $argv 2 end]
} else {
    ViewMol .
}"
    (file "/home/Programas/xcrysden-1.6.2-bin-shared/Tcl/xcInit.tcl" 
line 633)

-
Pablo

The libgfortran5 for example seems to be the wrong package name for 
Fedora 40. The package name gfortran can be used:


username@fedora:~$ sudo yum install gfortran
Last metadata expiration check: 0:00:05 ago on Mon 02 Sep 2024 
11:26:11 AM MDT.

Package gcc-gfortran-14.2.1-1.fc40.x86_64 is already installed.
Dependencies resolved.
Nothing to do.
Complete!

Regarding all the other Fedora 40 packages needed for XCrySDen 
(version 1.6.2), that was given in the XCrySDen mailing list post at:



http://www.democritos.it/pipermail/xcrysden/2024-August/002148.html 




Kind Regards,
Gavin
WIEN2k user


On 9/2/2024 11:17 AM, delamora wrote:

Dear WIEN2k users;
Now I have Linux Fedora 40 and I cannot use xcrysden 1.5
When I try to load the required packages;
--
dnf install tk libglu1-mesa libtogl2 libfftw3-3 libxmu6
 imagemagick openbabel libgfortran5
Última comprobación de caducidad de metadatos hecha hace 0:05:30,
el lun 02 sep 2024 09:38:00.
El paquete tk-1:8.6.13-3.fc40.x86_64 ya está instalado.
No hay coincidencias para el argumento: libglu1-mesa
No hay coincidencias para el argumento: libtogl2
No hay coincidencias para el argumento: libfftw3-3
No hay coincidencias para el argumento: libxmu6
No hay coincidencias para el argumento: imagemagick
  * Tal vez quiso decir: ImageMagick
No hay coincidencias para el argumento: libgfortran5
Error: No se pudo encontrar ningún resultado: libglu1-mesa
libtogl2 libfftw3-3 libxmu6 imagemagick libgfortran5
---
There were no results for
libglu1-mesa libtogl2 libfftw3-3 libxmu6 imagemagick libgfortran5
but
ImageMagick
is already installed.

So I cannot use xcrysden

Saludos

Pablo
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[Wien] XCrySDen 1.6

2024-09-02 Thread delamora

Gavin
Thanks for your reply, but it still does not work;
-

XCRYSDEN_SCRATCH=/home/pablo/xcrys_tmp

Running on platform : unix
   Operating system : Linux
Package ImageMagick's import: /usr/bin/import
Executing: /home/Programas/xcrysden-1.6.2-bin-shared/bin/ftnunit
Error in startup script: Can not set ident to a window path name
Couldn't configure togl widget
while executing
"togl .mesa  -width  400  -height 400  -ident  .mesa  
-rgba   $toglOpt(rgba)   -redsize$toglOpt(redsize..."
(procedure "PlaceGlobWin" line 107)
invoked from within
"PlaceGlobWin 0 [expr round(670 * $fac1)] [expr round(670 * $fac1)]"
(procedure "ViewMol" line 25)
invoked from within
"ViewMol ."
invoked from within
"if { [llength $argv] > 2 } {
parseComLinArg [lrange $argv 2 end]
} else {
ViewMol .
}"
(file "/home/Programas/xcrysden-1.6.2-bin-shared/Tcl/xcInit.tcl" line 633)
-
Pablo


The libgfortran5 for example seems to be the wrong package name for Fedora 40.  
The package name gfortran can be used:

username@fedora:~$ sudo yum install gfortran
Last metadata expiration check: 0:00:05 ago on Mon 02 Sep 2024 11:26:11 AM MDT.
Package gcc-gfortran-14.2.1-1.fc40.x86_64 is already installed.
Dependencies resolved.
Nothing to do.
Complete!


Regarding all the other Fedora 40 packages needed for XCrySDen (version 1.6.2), 
that was given in the XCrySDen mailing list post at:


http://www.democritos.it/pipermail/xcrysden/2024-August/002148.html


Kind Regards,
Gavin
WIEN2k user


On 9/2/2024 11:17 AM, delamora wrote:
Dear WIEN2k users;
Now I have Linux Fedora 40 and I cannot use xcrysden 1.5
When I try to load the required packages;
--
dnf install tk libglu1-mesa libtogl2 libfftw3-3 libxmu6  imagemagick openbabel 
libgfortran5
Última comprobación de caducidad de metadatos hecha hace 0:05:30, el lun 02 sep 
2024 09:38:00.
El paquete tk-1:8.6.13-3.fc40.x86_64 ya está instalado.
No hay coincidencias para el argumento: libglu1-mesa
No hay coincidencias para el argumento: libtogl2
No hay coincidencias para el argumento: libfftw3-3
No hay coincidencias para el argumento: libxmu6
No hay coincidencias para el argumento: imagemagick
  * Tal vez quiso decir: ImageMagick
No hay coincidencias para el argumento: libgfortran5
Error: No se pudo encontrar ningún resultado: libglu1-mesa libtogl2 libfftw3-3 
libxmu6 imagemagick libgfortran5
---
There were no results for
libglu1-mesa libtogl2 libfftw3-3 libxmu6 imagemagick libgfortran5
but
ImageMagick
is already installed.

So I cannot use xcrysden

Saludos

Pablo
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Re: [Wien] XCrySDen

2023-08-28 Thread delamora

Dear Tone,
You said;
"This annoying issue will be fixed in the next release"
I feel that this issue is not with XCrySDen but with "linux fedora 6.4.7"
Tanks again

Pablo

Thank you,
I updated my linux fedora;

with
linux fedora 6.2.15
there is no problem

but
with
linux fedora 6.4.7
the letters are quite small
-
Linux fedora 6.2.15-100.fc36.x86_64 #1 SMP PREEMPT_DYNAMIC Thu May 11 16:51:53 
UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

 > Linux fedora 6.4.7-100.fc37.x86_64 #1 SMP PREEMPT_DYNAMIC Thu Jul 27
> 19:56:37 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux


De: Wien  en nombre de Tone Kokalj 

Enviado: jueves, 17 de agosto de 2023 04:10 a. m.
Para: wien@zeus.theochem.tuwien.ac.at 
Asunto: Re: [Wien] XCrySDen

Dear Pablo,

You only upgraded the OS, or you got a new computer with a high screen
resolution, such as Quad HD (2,560×1,440) or Ultra HD (3,840×2,160).
For such high resolutions, xcrysden appearance is indeed awkward (too
small). This annoying issue will be fixed in the next release.

Best regards,
Tone
--
Jožef Stefan Institute, Ljubljana, Slovenia

On Wed, 2023-08-09 at 18:36 +, delamora wrote:
> I am having problems with XCrySDen; the figures and the letters are
> very small.
> I have the Fedora Linux;
> ---
> Linux fedora 6.4.7-100.fc37.x86_64 #1 SMP PREEMPT_DYNAMIC Thu Jul 27
> 19:56:37 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
> ---
> In earlier versions I did not have this problem
>
> Saludos
>
> Pablo
> ___
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[Wien] XCrySDen

2023-08-28 Thread delamora

Thank you,
I updated my linux fedora;

with
linux fedora 6.2.15
there is no problem

but
with
linux fedora 6.4.7
the letters are quite small
-
Linux fedora 6.2.15-100.fc36.x86_64 #1 SMP PREEMPT_DYNAMIC Thu May 11 16:51:53 
UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

 > Linux fedora 6.4.7-100.fc37.x86_64 #1 SMP PREEMPT_DYNAMIC Thu Jul 27
> 19:56:37 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux


De: Wien  en nombre de Tone Kokalj 

Enviado: jueves, 17 de agosto de 2023 04:10 a. m.
Para: wien@zeus.theochem.tuwien.ac.at 
Asunto: Re: [Wien] XCrySDen

Dear Pablo,

You only upgraded the OS, or you got a new computer with a high screen
resolution, such as Quad HD (2,560×1,440) or Ultra HD (3,840×2,160).
For such high resolutions, xcrysden appearance is indeed awkward (too
small). This annoying issue will be fixed in the next release.

Best regards,
Tone
--
Jožef Stefan Institute, Ljubljana, Slovenia

On Wed, 2023-08-09 at 18:36 +, delamora wrote:
> I am having problems with XCrySDen; the figures and the letters are
> very small.
> I have the Fedora Linux;
> ---
> Linux fedora 6.4.7-100.fc37.x86_64 #1 SMP PREEMPT_DYNAMIC Thu Jul 27
> 19:56:37 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
> ---
> In earlier versions I did not have this problem
>
> Saludos
>
> Pablo
> ___
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> Wien@zeus.theochem.tuwien.ac.at
> 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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Re: [Wien] XCrySDen

2023-08-17 Thread Tone Kokalj

Dear Pablo,

You only upgraded the OS, or you got a new computer with a high screen
resolution, such as Quad HD (2,560×1,440) or Ultra HD (3,840×2,160).
For such high resolutions, xcrysden appearance is indeed awkward (too
small). This annoying issue will be fixed in the next release.

Best regards,
Tone
-- 
Jožef Stefan Institute, Ljubljana, Slovenia

On Wed, 2023-08-09 at 18:36 +, delamora wrote:
> I am having problems with XCrySDen; the figures and the letters are
> very small.
> I have the Fedora Linux;
> ---
> Linux fedora 6.4.7-100.fc37.x86_64 #1 SMP PREEMPT_DYNAMIC Thu Jul 27
> 19:56:37 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
> ---
> In earlier versions I did not have this problem
> 
> Saludos
> 
> Pablo
> ___
> Wien mailing list
> Wien@zeus.theochem.tuwien.ac.at
> 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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[Wien] XCrySDen

2023-08-09 Thread delamora

I am having problems with XCrySDen; the figures and the letters are very small.
I have the Fedora Linux;
---
Linux fedora 6.4.7-100.fc37.x86_64 #1 SMP PREEMPT_DYNAMIC Thu Jul 27 19:56:37 
UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
---
In earlier versions I did not have this problem

Saludos

Pablo
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Re: [Wien] XCrySDen Version: 1.6.2

2023-03-25 Thread Gavin Abo

It might not work for other Linux distributions, but should it help, the 
following is what I did to install XCrySDen 1.6.2 for Ubuntu 22.04.2 LTS 
[1].



First, I checked if my system was set to Wayland or X11 [2]:


username@computername:~/Desktop$ grep Wayland /etc/gdm3/custom.conf
#WaylandEnable=false


The above shows that Ubuntu after installation was set to Wayland.


For using sudo commands, I had to be an administrator (or I had to ask 
my administrator to do those steps).



The custom.conf file was edited [3]:


username@computername:~/Desktop$ sudo gedit /etc/gdm3/custom.conf
...

username@computername:~/Desktop$ grep Wayland /etc/gdm3/custom.conf
WaylandEnable=false


The above shows the edit to custom.conf that removed the comment (#) for 
setting Wayland to false for enabling X11.



The computer was restarted to change Wayland to X11.


XCrySDen 1.6.2 was installed using:


username@computername:~/Desktop$ sudo apt install xcrysden
...


Since I wanted to use XCrySDen in w2web, XCRYSDEN_TOPDIR variable was 
set in the .basrhc using:



username@computername:~/Desktop$ gedit ~/.bashrc
username@computername:~/Desktop$ grep XCRYSDEN ~/.bashrc
export XCRYSDEN_TOPDIR=/usr/bin
username@computername:~/Desktop$ source ~/.bashrc


The w2web was started up:


username@computername:~/Desktop$ w2web
...


Then, I navigated to and clicked "view structure" in w2web. Then, the 
struct file was displayed [4].



[1] https://ubuntu.com/download/desktop

[2] 
https://unix.stackexchange.com/questions/202891/how-to-know-whether-wayland-or-x11-is-being-used


[3] 
https://askubuntu.com/questions/1410256/how-do-i-use-x-instead-of-wayland-on-22-04 



[4] 
https://raw.githubusercontent.com/gsabo/xcrysden-Patches/main/Ubuntu%2022.04.2%20XCrySDen%201.6.2.png 




Kind Regards,

Gavin

WIEN2k user


On 3/25/2023 1:47 AM, Peter Blaha wrote:


The semishared version has most libraries included and runs on almost 
any Linux system.


For the more recent version, the  developers provide only a "shared" 
version, i.e. most libraries are NOT included, but must be present on 
your Linux system.


On their website it is mentioned what libraries you need. At least you 
miss


libfftw3.so.3

but probably also others.


PS: I still use on most computers 1.5.60, as I do not want to install 
all  the necessary libraries on all my machines.




Am 25.03.2023 um 01:31 schrieb delamora:

The only difference is
semishared => shared


*De:* Wien  en nombre de 
delamora 

*Enviado:* viernes, 24 de marzo de 2023 06:28 p. m.
*Para:* A Mailing list for WIEN2k users 
*Asunto:* [Wien] XCrySDen Version: 1.6.2
Dear WIEN2k community
I am having trouble with XCrySDen, if I use;
xcrysden-1.5.60-bin-semishared
I have no problem, but if I use
  xcrysden-1.6.2-bin-shared

+-+
|*|
|*                                     *|
|*  XCrySDen -- (X-Window) CRYstalline Structures and DENsities  *|
|*               = ===         =              ===        *|
|*---*|
|*                                     *|
|*    Anton Kokalj (tone.kok...@ijs.si)                  *|
|*    Jozef Stefan Institute, Ljubljana, Slovenia                *|
|*                                     *|
|*    Copyright (c) 1996--2019 by Anton Kokalj                   *|
|*                                     *|
|*|
+-+

  Version: 1.6.2

  Please report bugs to: tone.kok...@ijs.si


  TERMS OF USE:
  -
  XCRYSDEN is released under the GNU General Public License.

  Whenever graphics generated by XCRYSDEN are used in scientific
  publications, it shall be greatly appreciated to include an explicit
  reference. The preferred form is the following:

  [ref] A. Kokalj, J. Mol. Graph. Model., Vol. 17, pp. 176-179, 1999.
        Code available from http://www.xcrysden.org/.

XCRYSDEN_TOPDIR=/home/Programas/xcrysden-1.6.2-bin-shared
XCRYSDEN_SCRATCH=/home/pablo/xcrys_tmp

/home/Programas/xcrysden-1.6.2-bin-shared/bin/xcrys: error while 
loading shared libraries: libfftw3.so.3: cannot open shared object 
file: No such file or directory


-
For the
xcrysden-1.5.60-bin-shared
I get the same answer, except for the line
 "Version: 1.6.2"

Saludos

Pablo



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Re: [Wien] XCrySDen Version: 1.6.2

2023-03-25 Thread Peter Blaha

The semishared version has most libraries included and runs on almost 
any Linux system.


For the more recent version, the  developers provide only a "shared" 
version, i.e. most libraries are NOT included, but must be present on 
your Linux system.


On their website it is mentioned what libraries you need. At least you miss

libfftw3.so.3

but probably also others.


PS: I still use on most computers 1.5.60, as I do not want to install 
all  the necessary libraries on all my machines.




Am 25.03.2023 um 01:31 schrieb delamora:

The only difference is
semishared => shared


*De:* Wien  en nombre de 
delamora 

*Enviado:* viernes, 24 de marzo de 2023 06:28 p. m.
*Para:* A Mailing list for WIEN2k users 
*Asunto:* [Wien] XCrySDen Version: 1.6.2
Dear WIEN2k community
I am having trouble with XCrySDen, if I use;
  xcrysden-1.5.60-bin-semishared
I have no problem, but if I use
  xcrysden-1.6.2-bin-shared

+-+
|*|
|*                                   *|
|*  XCrySDen -- (X-Window) CRYstalline Structures and DENsities  *|
|*               =         ===         =              ===        *|
|*---*|
|*                                   *|
|*    Anton Kokalj (tone.kok...@ijs.si)                          *|
|*    Jozef Stefan Institute, Ljubljana, Slovenia                *|
|*                                   *|
|*    Copyright (c) 1996--2019 by Anton Kokalj                   *|
|*                                   *|
|*|
+-+

  Version: 1.6.2

  Please report bugs to: tone.kok...@ijs.si


  TERMS OF USE:
  -
  XCRYSDEN is released under the GNU General Public License.

  Whenever graphics generated by XCRYSDEN are used in scientific
  publications, it shall be greatly appreciated to include an explicit
  reference. The preferred form is the following:

  [ref] A. Kokalj, J. Mol. Graph. Model., Vol. 17, pp. 176-179, 1999.
        Code available from http://www.xcrysden.org/.

XCRYSDEN_TOPDIR=/home/Programas/xcrysden-1.6.2-bin-shared
XCRYSDEN_SCRATCH=/home/pablo/xcrys_tmp

/home/Programas/xcrysden-1.6.2-bin-shared/bin/xcrys: error while 
loading shared libraries: libfftw3.so.3: cannot open shared object 
file: No such file or directory


-
For the
xcrysden-1.5.60-bin-shared
I get the same answer, except for the line
 "Version: 1.6.2"

Saludos

Pablo



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--
---
Peter Blaha,  Inst. f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-158801165300
Email:peter.bl...@tuwien.ac.at   
WWW:http://www.imc.tuwien.ac.at   WIEN2k:http://www.wien2k.at

-
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Re: [Wien] XCrySDen Version: 1.6.2

2023-03-24 Thread delamora

The only difference is
semishared => shared


De: Wien  en nombre de delamora 

Enviado: viernes, 24 de marzo de 2023 06:28 p. m.
Para: A Mailing list for WIEN2k users 
Asunto: [Wien] XCrySDen Version: 1.6.2

Dear WIEN2k community
I am having trouble with XCrySDen, if I use;
  xcrysden-1.5.60-bin-semishared
I have no problem, but if I use
  xcrysden-1.6.2-bin-shared

+-+
|*|
|*   *|
|*  XCrySDen -- (X-Window) CRYstalline Structures and DENsities  *|
|*   = === =  ===*|
|*---*|
|*   *|
|*Anton Kokalj (tone.kok...@ijs.si)  *|
|*Jozef Stefan Institute, Ljubljana, Slovenia*|
|*   *|
|*Copyright (c) 1996--2019 by Anton Kokalj   *|
|*   *|
|*|
+-+

  Version: 1.6.2

  Please report bugs to: tone.kok...@ijs.si


  TERMS OF USE:
  -
  XCRYSDEN is released under the GNU General Public License.

  Whenever graphics generated by XCRYSDEN are used in scientific
  publications, it shall be greatly appreciated to include an explicit
  reference. The preferred form is the following:

  [ref] A. Kokalj, J. Mol. Graph. Model., Vol. 17, pp. 176-179, 1999.
Code available from http://www.xcrysden.org/.

XCRYSDEN_TOPDIR=/home/Programas/xcrysden-1.6.2-bin-shared
XCRYSDEN_SCRATCH=/home/pablo/xcrys_tmp

/home/Programas/xcrysden-1.6.2-bin-shared/bin/xcrys: error while loading shared 
libraries: libfftw3.so.3: cannot open shared object file: No such file or 
directory

-
For the
  xcrysden-1.5.60-bin-shared
I get the same answer, except for the line
 "Version: 1.6.2"

Saludos

Pablo


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[Wien] XCrySDen Version: 1.6.2

2023-03-24 Thread delamora

Dear WIEN2k community
I am having trouble with XCrySDen, if I use;
  xcrysden-1.5.60-bin-semishared
I have no problem, but if I use
  xcrysden-1.6.2-bin-shared

+-+
|*|
|*   *|
|*  XCrySDen -- (X-Window) CRYstalline Structures and DENsities  *|
|*   = === =  ===*|
|*---*|
|*   *|
|*Anton Kokalj (tone.kok...@ijs.si)  *|
|*Jozef Stefan Institute, Ljubljana, Slovenia*|
|*   *|
|*Copyright (c) 1996--2019 by Anton Kokalj   *|
|*   *|
|*|
+-+

  Version: 1.6.2

  Please report bugs to: tone.kok...@ijs.si


  TERMS OF USE:
  -
  XCRYSDEN is released under the GNU General Public License.

  Whenever graphics generated by XCRYSDEN are used in scientific
  publications, it shall be greatly appreciated to include an explicit
  reference. The preferred form is the following:

  [ref] A. Kokalj, J. Mol. Graph. Model., Vol. 17, pp. 176-179, 1999.
Code available from http://www.xcrysden.org/.

XCRYSDEN_TOPDIR=/home/Programas/xcrysden-1.6.2-bin-shared
XCRYSDEN_SCRATCH=/home/pablo/xcrys_tmp

/home/Programas/xcrysden-1.6.2-bin-shared/bin/xcrys: error while loading shared 
libraries: libfftw3.so.3: cannot open shared object file: No such file or 
directory

-
For the
  xcrysden-1.5.60-bin-shared
I get the same answer, except for the line
 "Version: 1.6.2"

Saludos

Pablo


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Re: [Wien] Xcrysden issues with w2web

2020-06-22 Thread Gavin Abo

As was already hinted at in [1], if you need more help, you probably 
need describe better what you system(s) configuration is like such as 
are you only using w2web and xcrysden in Ubuntu locally (physical Linux 
box or in a virtual machine) or are you connecting to them remotely?



If you have defined $DISPLAY, w2web might just pick that up.  If you 
know Perl, I suggest you have a look at 
$WIENROOT/SRC_w2web/htdocs/util/viewcrys.pl.



The xserver that you mentioned, is it setup for X11 forwarding?  If you 
are not using w2web locally with an offline setup [2], but are instead 
using an online setup were w2web is connected to the internet (or a 
local network) and is unable to get xcrysden to open in w2web, are you 
able to get it to open instead using an ssh connection with X11 
forwarding?  Refer to [3,4].



[1] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20243.html


[2] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01124.html


[3] 
http://sites.science.oregonstate.edu/~tatej/COURSES/ph575/doku.php?id=xcrysden


[4] https://users.wfu.edu/natalie/s11phy752/lecturenote/PHY752lectLAPW.pdf


On 6/22/2020 2:21 PM, Johnathon Street wrote:
When typing echo $DISPLAY into the terminal I am seeing :0. I still 
continue to see "requires X-Windows System..." when I try to view the 
crystal in w2web. Is there a way to set the DISPLAY variable inside 
the w2web process so that it may work there as well. Where do you 
recommend I set DISPLAY?


Thank you

*From:* Wien  on behalf of 
Gavin Abo 

*Sent:* Saturday, June 13, 2020 4:55 PM
*To:* wien@zeus.theochem.tuwien.ac.at 
*Subject:* Re: [Wien] Xcrysden issues with w2web

Maybe there is still a problem with your XCRYSDEN_TOPDIR, refer to:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18555.html 
[mail-archive.com] 
<https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18555.html__;!!LNEL6vXnN3x8o9c!wOFlUzcyu_b8T0m5p3xrOisn5mqtXqTGifQSvDBIX9DI1D0YgI-CoKIpEkzRTEgp$>


http://www.democritos.it/pipermail/xcrysden/2020-January/001975.html 
[democritos.it] 
<https://urldefense.com/v3/__http://www.democritos.it/pipermail/xcrysden/2020-January/001975.html__;!!LNEL6vXnN3x8o9c!wOFlUzcyu_b8T0m5p3xrOisn5mqtXqTGifQSvDBIX9DI1D0YgI-CoKIpElJMWCG9$>



Regarding DISPLAY, maybe the following link to a xcrysden mailing list 
post can help:



http://www.democritos.it/pipermail/xcrysden/2020-May/001993.html 
[democritos.it] 
<https://urldefense.com/v3/__http://www.democritos.it/pipermail/xcrysden/2020-May/001993.html__;!!LNEL6vXnN3x8o9c!wOFlUzcyu_b8T0m5p3xrOisn5mqtXqTGifQSvDBIX9DI1D0YgI-CoKIpEmZACKf6$>



On 6/11/2020 2:51 PM, Johnathon Street wrote:
Thank you for the response. That did resolve the issue. I am now 
seeing "Requires X-windows system..." in the view struct portion of 
w2web. I do have an xserver runner, as I am running on Ubuntu. Is 
there a place where I need to set DISPLAY?



*From:* Wien  
<mailto:wien-boun...@zeus.theochem.tuwien.ac.at> on behalf of Gavin 
Abo  <mailto:gs...@crimson.ua.edu>

*Sent:* Saturday, June 6, 2020 11:05 AM
*To:* wien@zeus.theochem.tuwien.ac.at 
<mailto:wien@zeus.theochem.tuwien.ac.at> 
 
<mailto:wien@zeus.theochem.tuwien.ac.at>

*Subject:* Re: [Wien] Xcrysden issues with w2web

Most likely you just need to kill and restart w2web.


Refer to:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11246.html 
[mail-archive.com] 
<https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11246.html__;!!LNEL6vXnN3x8o9c!y3eR68_jwMy-ieFTucnQK_nzeOCOUwzEtSNG-uwkPO_yATLz4wAk2gM46Iqc3q-u$>


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01987.html 
[mail-archive.com] 
<https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01987.html__;!!LNEL6vXnN3x8o9c!y3eR68_jwMy-ieFTucnQK_nzeOCOUwzEtSNG-uwkPO_yATLz4wAk2gM46Lm0FwxV$>



On 6/6/2020 11:49 AM, Johnathon Street wrote:
I unable to view crystal with Xcrysden in w2web environment. 
However, I am able to view directly from terminal when typing 
Xcrysden in command line. I have found through the mailing list that 
XCRYSDEN_TOPDIR needs to be set, but I am unsure what it should be 
set to. Any help would be appreciated. I am running WIEN2k_19.2 and 
Xcrysden version 1.6.2.

Current Directory
 XCRYSDEN_TOPDIR=/usr/local/share/xcrysden-1.6.2
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[Wien] Xcrysden issues with w2web

2020-06-22 Thread Martin Kroeker

Is the w2web program running on the same system, and under the same user ID as 
the terminal you used
for the test ? If not, you could try setting "xhost localhost" (or if
you trust your firewall, even "xhost +") to allow connections to your
instance of the X server from other users/other systems on the network
-- 
Dr. Martin Kroekermar...@ruby.chemie.uni-freiburg.de
c/o Prof.Dr. Caroline Roehr
Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg

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Re: [Wien] Xcrysden issues with w2web

2020-06-22 Thread Johnathon Street

When typing echo $DISPLAY into the terminal I am seeing :0. I still continue to 
see "requires X-Windows System..." when I try to view the crystal in w2web. Is 
there a way to set the DISPLAY variable inside the w2web process so that it may 
work there as well. Where do you recommend I set DISPLAY?

Thank you

From: Wien  on behalf of Gavin Abo 

Sent: Saturday, June 13, 2020 4:55 PM
To: wien@zeus.theochem.tuwien.ac.at 
Subject: Re: [Wien] Xcrysden issues with w2web


Maybe there is still a problem with your XCRYSDEN_TOPDIR, refer to:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18555.html 
[mail-archive.com]<https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18555.html__;!!LNEL6vXnN3x8o9c!wOFlUzcyu_b8T0m5p3xrOisn5mqtXqTGifQSvDBIX9DI1D0YgI-CoKIpEkzRTEgp$>

http://www.democritos.it/pipermail/xcrysden/2020-January/001975.html 
[democritos.it]<https://urldefense.com/v3/__http://www.democritos.it/pipermail/xcrysden/2020-January/001975.html__;!!LNEL6vXnN3x8o9c!wOFlUzcyu_b8T0m5p3xrOisn5mqtXqTGifQSvDBIX9DI1D0YgI-CoKIpElJMWCG9$>


Regarding DISPLAY, maybe the following link to a xcrysden mailing list post can 
help:


http://www.democritos.it/pipermail/xcrysden/2020-May/001993.html 
[democritos.it]<https://urldefense.com/v3/__http://www.democritos.it/pipermail/xcrysden/2020-May/001993.html__;!!LNEL6vXnN3x8o9c!wOFlUzcyu_b8T0m5p3xrOisn5mqtXqTGifQSvDBIX9DI1D0YgI-CoKIpEmZACKf6$>


On 6/11/2020 2:51 PM, Johnathon Street wrote:
Thank you for the response. That did resolve the issue. I am now seeing 
"Requires X-windows system..." in the view struct portion of w2web. I do have 
an xserver runner, as I am running on Ubuntu. Is there a place where I need to 
set DISPLAY?


From: Wien 
<mailto:wien-boun...@zeus.theochem.tuwien.ac.at>
 on behalf of Gavin Abo <mailto:gs...@crimson.ua.edu>
Sent: Saturday, June 6, 2020 11:05 AM
To: wien@zeus.theochem.tuwien.ac.at<mailto:wien@zeus.theochem.tuwien.ac.at> 
<mailto:wien@zeus.theochem.tuwien.ac.at>
Subject: Re: [Wien] Xcrysden issues with w2web


Most likely you just need to kill and restart w2web.


Refer to:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11246.html 
[mail-archive.com]<https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11246.html__;!!LNEL6vXnN3x8o9c!y3eR68_jwMy-ieFTucnQK_nzeOCOUwzEtSNG-uwkPO_yATLz4wAk2gM46Iqc3q-u$>

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01987.html 
[mail-archive.com]<https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01987.html__;!!LNEL6vXnN3x8o9c!y3eR68_jwMy-ieFTucnQK_nzeOCOUwzEtSNG-uwkPO_yATLz4wAk2gM46Lm0FwxV$>


On 6/6/2020 11:49 AM, Johnathon Street wrote:
I unable to view crystal with Xcrysden in w2web environment. However, I am able 
to view directly from terminal when typing Xcrysden in command line. I have 
found through the mailing list that XCRYSDEN_TOPDIR needs to be set, but I am 
unsure what it should be set to. Any help would be appreciated. I am running 
WIEN2k_19.2 and Xcrysden version 1.6.2.
Current Directory
 XCRYSDEN_TOPDIR=/usr/local/share/xcrysden-1.6.2
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Re: [Wien] Xcrysden issues with w2web

2020-06-13 Thread Gavin Abo


Maybe there is still a problem with your XCRYSDEN_TOPDIR, refer to:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18555.html

http://www.democritos.it/pipermail/xcrysden/2020-January/001975.html


Regarding DISPLAY, maybe the following link to a xcrysden mailing list 
post can help:



http://www.democritos.it/pipermail/xcrysden/2020-May/001993.html


On 6/11/2020 2:51 PM, Johnathon Street wrote:
Thank you for the response. That did resolve the issue. I am now 
seeing "Requires X-windows system..." in the view struct portion of 
w2web. I do have an xserver runner, as I am running on Ubuntu. Is 
there a place where I need to set DISPLAY?



*From:* Wien  on behalf of 
Gavin Abo 

*Sent:* Saturday, June 6, 2020 11:05 AM
*To:* wien@zeus.theochem.tuwien.ac.at 
*Subject:* Re: [Wien] Xcrysden issues with w2web

Most likely you just need to kill and restart w2web.


Refer to:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11246.html 
[mail-archive.com] 
<https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11246.html__;!!LNEL6vXnN3x8o9c!y3eR68_jwMy-ieFTucnQK_nzeOCOUwzEtSNG-uwkPO_yATLz4wAk2gM46Iqc3q-u$>


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01987.html 
[mail-archive.com] 
<https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01987.html__;!!LNEL6vXnN3x8o9c!y3eR68_jwMy-ieFTucnQK_nzeOCOUwzEtSNG-uwkPO_yATLz4wAk2gM46Lm0FwxV$>



On 6/6/2020 11:49 AM, Johnathon Street wrote:
I unable to view crystal with Xcrysden in w2web environment. However, 
I am able to view directly from terminal when typing Xcrysden in 
command line. I have found through the mailing list that 
XCRYSDEN_TOPDIR needs to be set, but I am unsure what it should be 
set to. Any help would be appreciated. I am running WIEN2k_19.2 and 
Xcrysden version 1.6.2.

Current Directory
 XCRYSDEN_TOPDIR=/usr/local/share/xcrysden-1.6.2
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Re: [Wien] Xcrysden issues with w2web

2020-06-11 Thread Johnathon Street

Thank you for the response. That did resolve the issue. I am now seeing 
"Requires X-windows system..." in the view struct portion of w2web. I do have 
an xserver runner, as I am running on Ubuntu. Is there a place where I need to 
set DISPLAY?

From: Wien  on behalf of Gavin Abo 

Sent: Saturday, June 6, 2020 11:05 AM
To: wien@zeus.theochem.tuwien.ac.at 
Subject: Re: [Wien] Xcrysden issues with w2web

Most likely you just need to kill and restart w2web.

Refer to:

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11246.html 
[mail-archive.com]<https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11246.html__;!!LNEL6vXnN3x8o9c!y3eR68_jwMy-ieFTucnQK_nzeOCOUwzEtSNG-uwkPO_yATLz4wAk2gM46Iqc3q-u$>

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01987.html 
[mail-archive.com]<https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01987.html__;!!LNEL6vXnN3x8o9c!y3eR68_jwMy-ieFTucnQK_nzeOCOUwzEtSNG-uwkPO_yATLz4wAk2gM46Lm0FwxV$>

On 6/6/2020 11:49 AM, Johnathon Street wrote:
I unable to view crystal with Xcrysden in w2web environment. However, I am able 
to view directly from terminal when typing Xcrysden in command line. I have 
found through the mailing list that XCRYSDEN_TOPDIR needs to be set, but I am 
unsure what it should be set to. Any help would be appreciated. I am running 
WIEN2k_19.2 and Xcrysden version 1.6.2.
Current Directory
 XCRYSDEN_TOPDIR=/usr/local/share/xcrysden-1.6.2

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Re: [Wien] Xcrysden issues with w2web

2020-06-06 Thread Gavin Abo


Most likely you just need to kill and restart w2web.


Refer to:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11246.html

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01987.html


On 6/6/2020 11:49 AM, Johnathon Street wrote:
I unable to view crystal with Xcrysden in w2web environment. However, 
I am able to view directly from terminal when typing Xcrysden in 
command line. I have found through the mailing list that 
XCRYSDEN_TOPDIR needs to be set, but I am unsure what it should be set 
to. Any help would be appreciated. I am running WIEN2k_19.2 and 
Xcrysden version 1.6.2.

Current Directory
 XCRYSDEN_TOPDIR=/usr/local/share/xcrysden-1.6.2


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[Wien] Xcrysden issues with w2web

2020-06-06 Thread Johnathon Street

I unable to view crystal with Xcrysden in w2web environment. However, I am able 
to view directly from terminal when typing Xcrysden in command line. I have 
found through the mailing list that XCRYSDEN_TOPDIR needs to be set, but I am 
unsure what it should be set to. Any help would be appreciated. I am running 
WIEN2k_19.2 and Xcrysden version 1.6.2.
Current Directory
 XCRYSDEN_TOPDIR=/usr/local/share/xcrysden-1.6.2

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Re: [Wien] xcrysden installed but not able to integrate with wien2k interface

2018-10-27 Thread Gavin Abo

Sure, you can manually add/edit XCRYSDEN_TOPDIR according to the 
XCrySDen website:


http://www.xcrysden.org/doc/install.html

However, I installed XCrySDen on Fedora 28 starting with step 8 at

http://www.democritos.it/pipermail/xcrysden/2015-March/001697.html

and it installed just fine for me.  The ./xcConfigure.sh step was still 
able to automatically setup the XCrySDen environmental variables like 
XCRYSDEN_TOPDIR.


The w2web was running before I installed XCrySDen such that "view 
structure" was not working in w2web.  However, it started working fine 
after following previous advise in the mailing list to kill and restart 
w2web:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11246.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01987.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg04236.html

To use w2web offline, the system's hostname can be set to [ 
https://en.wikipedia.org/wiki/Localhost ]: localhost


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01124.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg15629.html

On 10/27/2018 12:43 PM, Ashwani Kumar wrote:

Hi,
i have installed xcrysden and know there some changes required in "TOP 
DIRECTORY" to integrate it into wien2k user interface. I tried 
changing it but remain unsuccessful. Browsed threads for the same 
problem, found plenty in wien2k mailing list but still could not 
understand how to do it.  I am using xcrysden offline. Please help 
with this.


thanks,
Ashwani Kumar


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[Wien] xcrysden installed but not able to integrate with wien2k interface

2018-10-27 Thread Ashwani Kumar

Hi,
i have installed xcrysden and know there some changes required in "TOP
DIRECTORY" to integrate it into wien2k user interface. I tried changing it
but remain unsuccessful. Browsed threads for the same problem, found plenty
in wien2k mailing list but still could not understand how to do it.  I am
using xcrysden offline. Please help with this.

thanks,
Ashwani Kumar
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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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[Wien] XCrysDen

2018-08-28 Thread FonsPaul

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] Xcrysden works for structure view, not for electron density display

2018-06-28 Thread Gavin Abo

After you click the "Calculate density with XCrysden" button, 1) the 
"Requires X-Windows system ... Calc" message appears immediately or 2) 
does the XCrySDen program open, the "Choose 2D/3D Density Plot" window 
appears (like that shown at 
http://www.xcrysden.org/doc/wien.html#__toc__6 ), then the "Requires 
X-Windows system ... Calc" message only shows up after you close XCrySDen.


If 2 above occurs, then that is normal and nothing is wrong.

If 1 above occurs, then there is a problem.  However, I'm not able to 
reproduce the error with the information you have provided.  I'm using 
the latest WIEN2k (17.1) and XCrySDen 
(xcrysden-1.5.60-linux_x86_64-semishared [ 
http://www.xcrysden.org/Download.html ]) as well and the "Calculate 
density with XCrysden" run locally in w2web seems to work fine for me.  
Without any additional hints you might have, the problem may go 
unresolved like what happened to a user before [ 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg15585.html 
].


If you try the same thing in the terminal, does it work or provide any 
additional information (like an error message).


For example, first navigate to the directory containing your case.struct 
file:


username@computername:~/Desktop$ cd ~/wiendata/test
username@computername:~/wiendata/test$ ls test.struct
test.struct

Back out of the directory so that you are in the directory containing 
your case folder and run the density calculation with XCrySDen [ 
http://www.xcrysden.org/doc/wien.html#__toc__1  ]:


username@computername:~/wiendata/test$ cd ..
username@computername:~/wiendata$ xcrysden --wien_density test

On 6/28/2018 8:17 AM, Luc Fruchter wrote:

Dear all,

Xcrysden works fine from the w2web interface (run locally), when 
viewing a structure. So, I think it is correctly installed and 
configured.


However, it displays "requires X-Windows system ... Calc" when trying 
to use the "Calculate density with Xcrysden" button, or "requires 
X-Windows system ... Render" when I use the "Preview density button".


When I use the "Rhoplot" button, the density is correctly displayed 
(so the density file must be ok).


( I use latest versions for Wien2k and Xcrysden).

Thanks for any help.

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[Wien] Xcrysden works for structure view, not for electron density display

2018-06-28 Thread Luc Fruchter


Dear all,

Xcrysden works fine from the w2web interface (run locally), when viewing 
a structure. So, I think it is correctly installed and configured.


However, it displays "requires X-Windows system ... Calc" when trying to 
use the "Calculate density with Xcrysden" button, or "requires X-Windows 
system ... Render" when I use the "Preview density button".


When I use the "Rhoplot" button, the density is correctly displayed (so 
the density file must be ok).


( I use latest versions for Wien2k and Xcrysden).

Thanks for any help.

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[Wien] XCrysDen problem in Wien2k16

2017-03-24 Thread Dr. K. Balamurugan


Dear Wien2k group,

I have one well known problem in working with XCrysDen in Wien2k. I  
recently updated to Wien2k16. Now while trying to plot Electron  
Density and selecting k-path for band structure using XCrySDen, I get  
"Requires X-Windows system ... Calc" and "Requires X-Windows system  
..." messages respectively.


I run Wine2k16 in openSUSE Linux installed in Windows10 system using  
Oracle Virtual Box. I am using 10 GB RAM for Linux with 2 cores from  
quad core processors. I tested with TiC case only; but getting the  
XCrySDen issues. I have properly installed X11 from X.org via openSUSE  
download site.


Please let me get some input to solve this issue.

Thanks.

With regards
K. Balamurugan
NIT Trichy, India.

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Re: [Wien] Xcrysden problem

2014-10-20 Thread delamora

I solved this problem for RED HAT;
In a terminal I tried to run
xcrysden
and there was a program missing, so I installed it, then another one, again I 
installed it.
With these two programs and their dependences XCrySDen worked.

Pablo

De: wien-boun...@zeus.theochem.tuwien.ac.at 
 en nombre de Peter Blaha 

Enviado: viernes, 10 de octubre de 2014 01:10 a.m.
Para: A Mailing list for WIEN2k users
Asunto: Re: [Wien] Xcrysden problem

After installation of xcrysden you must kill w2web
(ps -ef |grep w2web  and kill the corresponding processes).

Then make sure your environment is ok (eventually logout/login)
and restart w2web.

PS: before starting w2web, the environment variable XCRYSDEN_TOPDIR
must be set.


Am 10.10.2014 04:51, schrieb bayarr temuujin:
> Dear Wien2k users,
>
> I am new to Wien2k and i am running Wien2k version 13.1 on Ubuntu 14.04. LTS. 
> I have problem with Xcrysden not showing up when i run electron density 
> calculation. The
> button "Calculate density with XCrysden" doesnt show up. I have re-installed 
> Xcrysden and XCrysden is working fine. Please help me out.
> Best regards,
> Temuujin
>
>
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> SEARCH the MAILING-LIST at:  
> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
>

--
-
Peter Blaha
Inst. Materials Chemistry, TU Vienna
Getreidemarkt 9, A-1060 Vienna, Austria
Tel: +43-1-5880115671
Fax: +43-1-5880115698
email: pbl...@theochem.tuwien.ac.at
-
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Re: [Wien] Xcrysden problem

2014-10-09 Thread Peter Blaha


After installation of xcrysden you must kill w2web
(ps -ef |grep w2web  and kill the corresponding processes).

Then make sure your environment is ok (eventually logout/login)
and restart w2web.

PS: before starting w2web, the environment variable XCRYSDEN_TOPDIR
must be set.


Am 10.10.2014 04:51, schrieb bayarr temuujin:

Dear Wien2k users,

I am new to Wien2k and i am running Wien2k version 13.1 on Ubuntu 14.04. LTS. I 
have problem with Xcrysden not showing up when i run electron density 
calculation. The
button "Calculate density with XCrysden" doesnt show up. I have re-installed 
Xcrysden and XCrysden is working fine. Please help me out.
Best regards,
Temuujin


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--
-
Peter Blaha
Inst. Materials Chemistry, TU Vienna
Getreidemarkt 9, A-1060 Vienna, Austria
Tel: +43-1-5880115671
Fax: +43-1-5880115698
email: pbl...@theochem.tuwien.ac.at
-
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Re: [Wien] Xcrysden problem

2014-10-09 Thread delamora

Temuujin and WIEN2k users,


I want to add that this also happens with Fedora 19 and up.

XCrySDen works fine for Fedora 18 and down.


Pablo de la Mora


De: wien-boun...@zeus.theochem.tuwien.ac.at 
 en nombre de bayarr temuujin 

Enviado: jueves, 09 de octubre de 2014 09:51 p.m.
Para: wien@zeus.theochem.tuwien.ac.at
Asunto: [Wien] Xcrysden problem

Dear Wien2k users,

I am new to Wien2k and i am running Wien2k version 13.1 on Ubuntu 14.04. LTS. I 
have problem with Xcrysden not showing up when i run electron density 
calculation. The button "Calculate density with XCrysden" doesnt show up. I 
have re-installed Xcrysden and XCrysden is working fine. Please help me out.
Best regards,
Temuujin
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[Wien] Xcrysden problem

2014-10-09 Thread bayarr temuujin

Dear Wien2k users,
I am new to Wien2k and i am running Wien2k version 13.1 on Ubuntu 14.04. LTS. I 
have problem with Xcrysden not showing up when i run electron density 
calculation. The button "Calculate density with XCrysden" doesnt show up. I 
have re-installed Xcrysden and XCrysden is working fine. Please help me out.   
Best regards,Temuujin
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Re: [Wien] XCrySDen error

2014-01-18 Thread Michael Sluydts


Hello,

I think you forgot to replace "complete_path_to" in your 
XCRYSDEN_TOP_DIR variable. It should be your local install path.



Kind regards,

Michael Sluydts

ali betaouaf schreef op 1/18/2014 1:15 PM:

Dear members,
After installing XCrysden, and when I run, I see this message??

/home/ali13btf/Bureau/XCrySDen-1.5.17-bin-semishared/xcrysden: 160: .: 
Can't open /complete_path_to/XCrySDen-1.5.17-src-all/scripts/xcLib.sh


Where is the problem?!
Cordially


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[Wien] XCrySDen error

2014-01-18 Thread ali betaouaf

Dear members,
After installing XCrysden, and when I run, I see this message?? 

/home/ali13btf/Bureau/XCrySDen-1.5.17-bin-semishared/xcrysden: 160: .: Can't 
open 
/complete_path_to/XCrySDen-1.5.17-src-all/scripts/xcLib.sh

  Where is the problem?!Cordially ___
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[Wien] Xcrysden

2013-10-29 Thread swati chaudhury

Dear Anton Kokalj sir,
                   Is there any demo version of XCrysden available? Is it 
possible to install in windows 7 or windows 8 system?  If yes, then how to do, 
please guide me.
Warm regards
Dr Swati Chaudhury
Visiting Scientist
ICRISAT, India___
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[Wien] xcrysden

2013-08-01 Thread Oliver Albertini

Dear W2k,

I have been running W2k on an AIX server which does not have xcrysden
installed. I have been able to display 2d charge/spin density plots by
running lapw5 and then scp case.rho, case.struct, and case.output5 to my
local machine which has xcrysden.

However, to do 3d density plots locally (calculate & render), what
files/executables are needed? It seems like xcrysden runs 'x lapw5' for a
number of slices then builds the 3d image.

If anyone knows a solution or possible workaround for this, please let me
know.

Thanks,

Oliver Albertini
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[Wien] xcrysden large multipler k-points

2012-08-01 Thread محمد ارشد فرحان

actually, i used only 300 k-points and this specific problem arose when i
tried to select k-path for band structure calculations.
my system has monoclinic symmetry so there are a couple of special points
in k-path i wanted to adopt with coordinates like (0.64xxx, 0.32xxx, 0.5).
i selected the total number of divisions (k-points) of this path again 300.
the code insists on having an integer coordinate with a multiplier. for 300
k-points, the multiplier was quite large and the integer coordinates
printed in case.klist_band file were **.

Prof. Tone asked for my structure file and he too got into same error. Let
me copy - paste his reply:

"On Mon, 2012-07-16 at 17:37 +0900,   ? wrote:
> here are the .struct file and complete .klist_band file.
> i tried to solve this problem by making separate kpath klist files for
> every two points. the idea was to join them manually & use different
> multipliers for different path.

Yes, you are right. I could reproduce your problems. I believe that the
problem is due to Wien2K. Your case is a nasty case for Wien2K. Why?
Because it insist on representing the real number (rational number)
as the fraction p/q of two integers with a fixed format. As your case is
not a high symmetry case, the p & q numbers are simple too large and the
stars () are displayed.

As a work-around: you could use the coordinates of special k-points as
given by xcrysden, and then you need to construct out of that
semi-manually a klist file suitable for Wien2K (this would involve some
manual editing + some small scripting to interpolate points between
pairs of special k-points).

Regards. Tone

-- 
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
(tel: +386-1-477-3523 // fax:+386-1-477-3822)"

so, therefore i thought may be it is due to same problem you guys are
discussing, & just pushed my mail  . . . . ;D

any way, thnx. for ur reply.

M. Arshad Farhan

On Mon, Jul 30, 2012 at 3:32 PM, Gavin Abo  wrote:

>  What large values did you use in xcrysden for the multiplier and
> k-points?  Someone else might be able to comment on whether you can use
> smaller values and still get accurate results.
>
> I see your posts on the xcrysden mailing list:
>
> http://www.democritos.it/pipermail/xcrysden/2012-July/001215.html
> http://www.democritos.it/pipermail/xcrysden/2012-July/001223.html
>
> From the posts, it looks like the number of k-points you used is possibly
> greater than 99672.  You currently cannot use
>
> multipiler*k-points > 5-digits (i.e., 99,999)
>
> If the larger outputted values are really needed, it could probably be
> done by changing all the "4I5" to say "4I8" in F/kPath.f that is in the
> xcrysden source package (xcrysden-1.5.53.tar.gz).  However, you have to
> compile the xcrysden code.  There are some useful instructions on the web
> for compiling the xcrysden source in Debian or Ubuntu (
> https://sites.google.com/site/jamesanalytis/xcrysden-in-ubuntu-10-04),
> but have not seen for other Linux distributions if one wants to attempt it.
>
> Since your not quite a "linux guy", you will probably want to send your
> struct file (while providing also the multiplier and k-points value used)
> to Tone as requested on the xcrysden mailing list so that a linux binary
> package with changes can be provided if needed.
>
> On 7/29/2012 7:54 PM,   ? wrote:
>
> Dear Prof. Lawrance & Gavin-Abo,
>
> i've not tested the latest version of Wien2k but, let me mention one more
> place where real*4 are used that is in the creation of case.klist_band.
>
> for any complicated coordinate in the k-path (mainly in monoclinic
> systems) by using Xcrysden, the multiplier goes shooting high and
> coordinate value exceeds real*4 consequently printing ** in places of
> k-point coordinates in case.klist_band file.
>
> the XcrySden developers claim it to be on part of Wien2k where it insists
> on real value but restricts it to 4 digits.
>
> if possible, please also look into it and of-course suggest me a solution
> as i'm quite not a linux guy.
>
> regards,
>
>
>
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Pohang Univ of Sci & Tech
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[Wien] xcrysden large multipler k-points

2012-07-30 Thread Gavin Abo

What large values did you use in xcrysden for the multiplier and 
k-points?  Someone else might be able to comment on whether you can use 
smaller values and still get accurate results.

I see your posts on the xcrysden mailing list:

http://www.democritos.it/pipermail/xcrysden/2012-July/001215.html
http://www.democritos.it/pipermail/xcrysden/2012-July/001223.html

 From the posts, it looks like the number of k-points you used is 
possibly greater than 99672.  You currently cannot use

multipiler*k-points > 5-digits (i.e., 99,999)

If the larger outputted values are really needed, it could probably be 
done by changing all the "4I5" to say "4I8" in F/kPath.f that is in the 
xcrysden source package (xcrysden-1.5.53.tar.gz).  However, you have to 
compile the xcrysden code.  There are some useful instructions on the 
web for compiling the xcrysden source in Debian or Ubuntu 
(https://sites.google.com/site/jamesanalytis/xcrysden-in-ubuntu-10-04), 
but have not seen for other Linux distributions if one wants to attempt it.

Since your not quite a "linux guy", you will probably want to send your 
struct file (while providing also the multiplier and k-points value 
used) to Tone as requested on the xcrysden mailing list so that a linux 
binary package with changes can be provided if needed.

On 7/29/2012 7:54 PM,   ? wrote:
> Dear Prof. Lawrance & Gavin-Abo,
> i've not tested the latest version of Wien2k but, let me mention one 
> more place where real*4 are used that is in the creation of 
> case.klist_band.
> for any complicated coordinate in the k-path (mainly in monoclinic 
> systems) by using Xcrysden, the multiplier goes shooting high and 
> coordinate value exceeds real*4 consequently printing ** in places 
> of k-point coordinates in case.klist_band file.
> the XcrySden developers claim it to be on part of Wien2k where it 
> insists on real value but restricts it to 4 digits.
> if possible, please also look into it and of-course suggest me a 
> solution as i'm quite not a linux guy.
> regards,
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[Wien] xcrysden to plot Fermi surface

2012-04-14 Thread Peter Blaha

You are using an old version of xcrysden. The new version does not suggest 
these changes anymore.

You do not need to follow the steps listed in xcrysden, but can do all this 
(except the real plotting,
i.e. the last step) by hand.
You need:

A very dense UNSHIFTED  k-mesh.(x kgen)
run x lapw1with this mesh
x lapw2 -fermi
Now call xcrysden and just visualize the FS.

Am 13.04.2012 23:21, schrieb Yundi Quan:
> Dear Sir/Madam,
> My question may not be directly related to WIEN2k. When plotting Fermi
> surface using XCrysden, it says that case.in1 should be changed into
> unit 5. But if I change case.in1 to unit 5, I would always get an
> error message saying that kpoints in case.in1 is inconsistent with the
> kpoints in case.kgen. Should case.in1 be changed into unit 5?
> ___
> Wien mailing list
> Wien at zeus.theochem.tuwien.ac.at
> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien

-- 
-
Peter Blaha
Inst. Materials Chemistry, TU Vienna
Getreidemarkt 9, A-1060 Vienna, Austria
Tel: +43-1-5880115671
Fax: +43-1-5880115698
email: pblaha at theochem.tuwien.ac.at
-

[Wien] xcrysden to plot Fermi surface

2012-04-13 Thread Yundi Quan

Dear Sir/Madam,
My question may not be directly related to WIEN2k. When plotting Fermi
surface using XCrysden, it says that case.in1 should be changed into
unit 5. But if I change case.in1 to unit 5, I would always get an
error message saying that kpoints in case.in1 is inconsistent with the
kpoints in case.kgen. Should case.in1 be changed into unit 5?

[Wien] XCRYSDEN

2012-03-13 Thread Zhou Bing

Dear all,

I try to use XCRYSDEN to choose the plane for plotting electron density, thus, 
HPC installed XCRYSDEN (1.4.1) in my account so that I open XCrysDen using 
Xmanager on my PC. Here I have two questions concerning about it:

1. XCrysDen is extremely slow on the Xmanager window;

2. I do know how to choose and save a plane for plotting the electron density 
map using XCrysDen.

Any suggestions, comments and instructions are highly appreciated!

Thank you in advance!

Bing

 



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[Wien] XCrysDen in w2web?

2010-01-10 Thread Jian-Xin Zhu

Dear Prof. Blaha,

The suggested procedure works fine.
Thank you very much,

Jianxin

On Jan 9, 2010, at 7:05 AM, Peter Blaha wrote:

> At "localhost" issue:
>
> ssh -X hostname_where_w2web_runs(the -X option directs the X- 
> windows system to open screens on loc.host)
> ps -ef |grep w2web
> kill   (kill all pids with w2web)
> w2web
>
> now you can reconnect with your browser to w2web and xcrysden should  
> open on localhost.
>
> Alternatively xcrysden can always be called from a terminal:
>
> ssh -X w2web_host  (again -X is necessary!!!)
> cd case-directory
> xcrysden --wien_struct .
> (Try also   xcrysden --help  to see all options)
>
>
>> I have a problem using XCrysDen in w2web remotely.
>> From local host, I use the web-browser to connect to w2web in the  
>> remote machine, by
>> safari  http://hostname_where_w2web_runs:7890
>> and open a session successfully.
>> However, when I click "view structure" on the left panel, the  
>> Xcrysden utility is started on the screen
>> of the remote host instead of on my local machine.
>> One way I can think of: ssh to the remote host and start up  
>> xcrysden separately and open the structure file.
>> However, is there any other way (I mean within w2web) to have  
>> xcrysden display the picture on the local
>> machine?  Both of my machines (local and remote) are the Mac OSX  
>> systems.
>> Any help/suggestion would be appreciated.
>> Jianxin
>> ___
>> Wien mailing list
>> Wien at zeus.theochem.tuwien.ac.at
>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>
> -- 
> -
> Peter Blaha
> Inst. Materials Chemistry, TU Vienna
> Getreidemarkt 9, A-1060 Vienna, Austria
> Tel: +43-1-5880115671
> Fax: +43-1-5880115698
> email: pblaha at theochem.tuwien.ac.at
> -
> ___
> Wien mailing list
> Wien at zeus.theochem.tuwien.ac.at
> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien

[Wien] XCrysDen in w2web?

2010-01-09 Thread Peter Blaha

At "localhost" issue:

ssh -X hostname_where_w2web_runs(the -X option directs the X-windows system 
to open screens on loc.host)
ps -ef |grep w2web
kill   (kill all pids with w2web)
w2web

now you can reconnect with your browser to w2web and xcrysden should open on 
localhost.

Alternatively xcrysden can always be called from a terminal:

ssh -X w2web_host  (again -X is necessary!!!)
cd case-directory
xcrysden --wien_struct .
(Try also   xcrysden --help  to see all options)


> I have a problem using XCrysDen in w2web remotely.
> 
>  From local host, I use the web-browser to connect to w2web in the 
> remote machine, by
> safari  http://hostname_where_w2web_runs:7890
> and open a session successfully.
> 
> However, when I click "view structure" on the left panel, the Xcrysden 
> utility is started on the screen
> of the remote host instead of on my local machine.
> 
> One way I can think of: ssh to the remote host and start up xcrysden 
> separately and open the structure file.
> However, is there any other way (I mean within w2web) to have xcrysden 
> display the picture on the local
> machine?  Both of my machines (local and remote) are the Mac OSX systems.
> 
> Any help/suggestion would be appreciated.
> 
> Jianxin
> ___
> Wien mailing list
> Wien at zeus.theochem.tuwien.ac.at
> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien

-- 
-
Peter Blaha
Inst. Materials Chemistry, TU Vienna
Getreidemarkt 9, A-1060 Vienna, Austria
Tel: +43-1-5880115671
Fax: +43-1-5880115698
email: pblaha at theochem.tuwien.ac.at
-

[Wien] XCrysDen in w2web?

2010-01-08 Thread Jian-Xin Zhu

Dear Prof. Blaha and Wien2k users,

I have a problem using XCrysDen in w2web remotely.

 From local host, I use the web-browser to connect to w2web in the  
remote machine, by
safari  http://hostname_where_w2web_runs:7890
and open a session successfully.

However, when I click "view structure" on the left panel, the Xcrysden  
utility is started on the screen
of the remote host instead of on my local machine.

One way I can think of: ssh to the remote host and start up xcrysden  
separately and open the structure file.
However, is there any other way (I mean within w2web) to have xcrysden  
display the picture on the local
machine?  Both of my machines (local and remote) are the Mac OSX  
systems.

Any help/suggestion would be appreciated.

Jianxin

[Wien] xcrysden

2008-07-08 Thread Peter Blaha

The website for Xcrysden is reachable again !

http://www.xcrysden.org

Peter Blaha

[Wien] XCrysDen via w2web

2008-01-31 Thread Tomohiko Tasaka

Dear w2web users,

I tried to access xcrysden from w2web, but it's not started.
Only the following messages were displayed on w2web.

Requires X-Windows system ...

*Additionally, I had executed the command $xhost +"address of X client" on
ahead.

I think it's because the below line is comment out.
# $ENV{'DISPLAY'}="$ENV{'REMOTE_HOST'}:0.0";
included in bandxrys.pl, rhoxcrys.pl and viewxcrys.pl at
SRC_w2web/htdocs/util/.

If I remove a comment character(i.e. #), xcrysden starts normally.
Is this a reasonable solution? Could you please let me know what you think?

---
WIEN2k_08
X Server: Mac OS X 10.5.1
X Client: SUSE Linux Enterprise Desktop 10 SP1 

Thanks in advance.

With best regards,
Tomo Tasaka

[Wien] XCrysDen via w2web

2008-01-31 Thread Peter Blaha

If it works for you, it is fine.

It was in when using some years ago UNIX systems (or an early Linux),
but on the more recent platforms it was not necessary or even harms
sometimes). May depend on your X-server.

Tomohiko Tasaka schrieb:
> Dear w2web users,
> 
> I tried to access xcrysden from w2web, but it's not started.
> Only the following messages were displayed on w2web.
> 
> Requires X-Windows system ...
> 
> *Additionally, I had executed the command $xhost +"address of X client" on
> ahead.
> 
> I think it's because the below line is comment out.
> # $ENV{'DISPLAY'}="$ENV{'REMOTE_HOST'}:0.0";
> included in bandxrys.pl, rhoxcrys.pl and viewxcrys.pl at
> SRC_w2web/htdocs/util/.
> 
> If I remove a comment character(i.e. #), xcrysden starts normally.
> Is this a reasonable solution? Could you please let me know what you think?
> 
> ---
> WIEN2k_08
> X Server: Mac OS X 10.5.1
> X Client: SUSE Linux Enterprise Desktop 10 SP1 
> 
> Thanks in advance.
> 
> With best regards,
> Tomo Tasaka
> 
> 
> ___
> Wien mailing list
> Wien at zeus.theochem.tuwien.ac.at
> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien

-- 

   P.Blaha
--
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-15671 FAX: +43-1-58801-15698
Email: blaha at theochem.tuwien.ac.atWWW: http://info.tuwien.ac.at/theochem/
--

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