From 85904751 at qq.com Tue Apr 8 11:02:13 2014
From: 85904751 at qq.com (=?ISO-8859-1?B?SCpY?=)
Date: Tue, 8 Apr 2014 17:02:13 +0800
Subject: [xcrysden] error while executing
/xcrysden-1.5.53-bin-semishared/bin/ftnunit
Message-ID: <tencent_632FFC9E272B0F5F66C25FB3@qq.com>
Dear all,
After I finished installation of xcrysden-1.5.53-linux_x86_64-semishared.tar.gz, I typed ./xcrysden to launch the programme. The programme start but with the following error:
/xcrysden-1.5.53-bin-semishared/bin/ftnunit:error while loading shared libraries: libquadmath. so. 0: cannot open shared object file: No such file or directory.
I would be very appreciated if someone can help me to solve this problem.
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From mitulm at iitk.ac.in Wed Apr 9 13:36:35 2014
From: mitulm at iitk.ac.in (Mitul Mundra)
Date: Wed, 9 Apr 2014 17:06:35 +0530
Subject: [xcrysden] Problem in making NEB movie
Message-ID: <CAHaE1PMcLaBb4UZWZP6Ywd3tq8jKSQmfQbkZJ+_+nhk53=oKJA@mail.gmail.com>
Dear Xcrysden users,
I am a beginner in using Xcrysden. I am using Xcrysden to visualize my
files from Quantum Espresso. In the process, I am tyring to making a movie
using Xcrysden (Version 1.5.24) from the axsf ( Animation Xcrysden
Structure Format) file which I obtained by doing a NEB calculation in QE.
The dropbox link for my axsf file is
https://www.dropbox.com/s/d15wx1v9nasyrqy/Si_1_Li_within_neb.axsf . I am
getting an error in the execution of parameter-file (*/usr/bin/mencoder
mf://anim-0000.png, ...... -mf fps=10.0 -o /home/mitul/Desktop/movie.avi
-ovc lavc -lavcopts vcodec=mpeg4*) which says that the *number of files is
0*. Now I have a couple of doubts.
1. I have 7 images in my NEB calculation but in the parameter file, only 6
images are being displayed (anim-0000.png - anim-0005.png). What is it that
I am doing wrong here?
2. Is it possible to see my temporary image files which I am saving in my
Current working directory because I don't see any temporary image files
anywhere?
I would be extremely thankful if someone could help me figure out my
mistake in making the movie.
Thanks
Mitul Mundra
Final Year Dual Degree Student
Department of Chemical Engineering
IIT Kanpur
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From tone.kokalj at ijs.si Fri Apr 11 17:30:13 2014
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Fri, 11 Apr 2014 17:30:13 +0200
Subject: [xcrysden] error while executing
/xcrysden-1.5.53-bin-semishared/bin/ftnunit
In-Reply-To: <tencent_632FFC9E272B0F5F66C25FB3@qq.com>
References: <tencent_632FFC9E272B0F5F66C25FB3@qq.com>
Message-ID: <1397230213.25039.26.camel@catalyst.ijs.si>
On Tue, 2014-04-08 at 17:02 +0800, H*X wrote:
> xcrysden-1.5.53-linux_x86_64-semishared.tar.gz, I typed ./xcrysden to
> launch the programme. The programme start but with the following
> error:
> /xcrysden-1.5.53-bin-semishared/bin/ftnunit:error while loading
> shared libraries: libquadmath. so. 0: cannot open shared object file:
> No such file or directory.
You need to install libquadmath library. Depending on the linux distro
you use, you may try:
* for debian-based distros: apt-get install libquadmath0
* for fedora-based distros: yum install libquadmath
* etc.
> I would be very appreciated if someone can help me to solve this
> problem.
And I would much appreciate to know with whom I have the correspondence.
Please always sign your post (name and affiliation).
Regards,
--
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
(tel: +386-1-477-3523 // fax:+386-1-477-3822)
Please, if possible, avoid sending me Word or PowerPoint attachments.
See: http://www.gnu.org/philosophy/no-word-attachments.html
From tone.kokalj at ijs.si Fri Apr 11 17:41:40 2014
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Fri, 11 Apr 2014 17:41:40 +0200
Subject: [xcrysden] Problem in making NEB movie
In-Reply-To: <CAHaE1PMcLaBb4UZWZP6Ywd3tq8jKSQmfQbkZJ+_+nhk53=oKJA@mail.gmail.com>
References: <CAHaE1PMcLaBb4UZWZP6Ywd3tq8jKSQmfQbkZJ+_+nhk53=oKJA@mail.gmail.com>
Message-ID: <1397230900.25039.34.camel@catalyst.ijs.si>
On Wed, 2014-04-09 at 17:06 +0530, Mitul Mundra wrote:
> Dear Xcrysden users,
>
>
> I am a beginner in using Xcrysden. I am using Xcrysden to visualize my
> files from Quantum Espresso. In the process, I am tyring to making a
> movie using Xcrysden (Version 1.5.24) from the axsf ( Animation
> Xcrysden Structure Format) file which I obtained by doing a NEB
> calculation in QE. The dropbox link for my axsf file is
> https://www.dropbox.com/s/d15wx1v9nasyrqy/Si_1_Li_within_neb.axsf . I
> am getting an error in the execution of parameter-file
> (/usr/bin/mencoder mf://anim-0000.png, ...... -mf fps=10.0
> -o /home/mitul/Desktop/movie.avi -ovc lavc -lavcopts vcodec=mpeg4)
> which says that the number of files is 0. Now I have a couple of
> doubts.
At the bottom of the "Animation Control Center" window there is an
option "Edit flags or parameter-file before encoding". If this option is
"on", then you have the possibility to edit the "script" used for
encoding the movie. Read the man page of mencoder and try to figure out
what is incompatible between xcrysdem's used syntax and that of your
mencoder.
The other option is to make an animated-gif instead (you only have 7
images).
>
>
> 1. I have 7 images in my NEB calculation but in the parameter file,
> only 6 images are being displayed (anim-0000.png - anim-0005.png).
> What is it that I am doing wrong here?
The image is saved whenever the display changes, hence likely the first
image is skipped. Start recording with image-2 and as a first move go
backward from image-2 to image-1 (this will save the image-1), then go
forward to the last image.
>
>
> 2. Is it possible to see my temporary image files which I am saving in
> my Current working directory because I don't see any temporary image
> files anywhere?
Yes, tick the "current working directory" option in the "Animation
Control Center" window.
Regards, Tone
--
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
(tel: +386-1-477-3523 // fax:+386-1-477-3822)
Please, if possible, avoid sending me Word or PowerPoint attachments.
See: http://www.gnu.org/philosophy/no-word-attachments.html
From phoenix_1740 at yahoo.com Sun Apr 13 10:08:28 2014
From: phoenix_1740 at yahoo.com (Mostafa Abasi)
Date: Sun, 13 Apr 2014 01:08:28 -0700 (PDT)
Subject: [xcrysden] (no subject)
Message-ID: <1397376508.84764.YahooMailNeo@web161704.mail.bf1.yahoo.com>
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From masoodyousaf1 at yahoo.com Mon Apr 14 09:28:47 2014
From: masoodyousaf1 at yahoo.com (Masood Yousaf)
Date: Mon, 14 Apr 2014 00:28:47 -0700 (PDT)
Subject: [xcrysden] installed successfully but not able to view xcrystallden
in Fedora 16
Message-ID: <1397460527.11357.YahooMailNeo@web120302.mail.ne1.yahoo.com>
?
Dear Sir,
I have successfully embeded Xcrystalden in Wien2k but still fail to view
the structure. I have installed wien2k in root and tried Xcrystalden
installation both in root as well as in home. But both times, I am unable to view the structure. I can see the VIEW Structure option and I get the fallowing message below. Kindly have a look and help me to
resolve this issue.
View structure with XCrysDen
Requires X-Windows system ...
+----------------------------------------------------------------+
|****************************************************************|
|*??? ??? ??? ??? ??? ??? ??? ??? *|
|*? XCrySDen - (X-Window) CRYstalline Structures and DENsities? *|
|*??? ??? =???????? ===????????
=????????????? ===??????? *|
|*--------------------------------------------------------------*|
|*??? ??? ??? ??? ??? ??? ??? ??? *|
|*??? Anton Kokalj (Tone.Kokalj at ijs.si)???????????????????????? *|
|*??? Jozef Stefan Institute, Ljubljana, Slovenia?????????????? *|
|*??? ??? ??? ??? ??? ??? ??? ??? *|
|*??? Copyright (c) 1996--2009 by Anton
Kokalj????????????????? *|
|*????????????????????????????????????????????????????????????? *|
|****************************************************************|
+----------------------------------------------------------------+
? Version: 1.5.21
? Please report bugs to: Tone.Kokalj at 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, Comp. Mater. Sci., Vol. 28, p. 155, 2003.
??????? Code available from http://www.xcrysden.org/.
TCL_LIBRARY=/home/masood/xcrystal/XCrySDen-1.5.21-bin-semishared/external/lib/tcl8.5
XCRYSDEN_TOPDIR=/home/masood/xcrystal/XCrySDen-1.5.21-bin-semishared
XCRYSDEN_SCRATCH=/home/masood/xcrys_tmp
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From mohammedlawal08 at yahoo.com Wed Apr 16 06:41:27 2014
From: mohammedlawal08 at yahoo.com (Lawal Mohammed)
Date: Tue, 15 Apr 2014 21:41:27 -0700 (PDT)
Subject: [xcrysden] Need help
Message-ID: <1397623287.91715.YahooMailNeo@web125706.mail.ne1.yahoo.com>
Dear Developers and Users,
We got a problem installing the xcrysden on one of our system which have wien2k installed. We end up with this error
/usr/local/codes/wien/v.11/xcrysden-1.5.53-bin-semishared/bin/ftnunit: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory
After this we got a pop up of the xcrysden interface, then nothing happen.
Any help in this regard is welcome
With regards
Lawal Mohammed
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From saleemhasan at cox.net Wed Apr 16 13:36:28 2014
From: saleemhasan at cox.net (Saleem Hasan)
Date: Wed, 16 Apr 2014 6:36:28 -0500
Subject: [xcrysden] Need help
In-Reply-To: <qUhY1n01g0gB1Dv01UhasW>
Message-ID: <20140416073628.33KHX.117950.imail@eastrmwml208>
I am also very new to xcrysden so I am not sure if this will help. I got a similar error and I had to install fortran modules (cygfortran) in cygwin.
I am using cygwin to run xcrysden in Windows. If you are also using cygwin then, try searching and installing cygfort. I think, it is not able to find the cygfortran modules and that is why it gives this error.
Saleem Hasan
---- Lawal Mohammed <mohammedlawal08 at yahoo.com> wrote:
> Dear Developers and Users,
>
> We got a problem installing the xcrysden on one of our system which have wien2k installed. We end up with this error
>
> /usr/local/codes/wien/v.11/xcrysden-1.5.53-bin-semishared/bin/ftnunit: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory
>
> After this we got a pop up of the xcrysden interface, then nothing happen.
>
> Any help in this regard is welcome
> With regards
> Lawal Mohammed
From lorenzo.paulatto at impmc.upmc.fr Wed Apr 16 14:55:49 2014
From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Wed, 16 Apr 2014 14:55:49 +0200
Subject: [xcrysden] Need help
In-Reply-To: <20140416073628.33KHX.117950.imail@eastrmwml208>
References: <20140416073628.33KHX.117950.imail@eastrmwml208>
Message-ID: <534E7DD5.9000109@impmc.upmc.fr>
On 04/16/2014 01:36 PM, Saleem Hasan wrote:
> I am also very new to xcrysden so I am not sure if this will help. I got a similar error and I had to install fortran modules (cygfortran) in cygwin.
>
> I am using cygwin to run xcrysden in Windows. If you are also using cygwin then, try searching and installing cygfort. I think, it is not able to find the cygfortran modules and that is why it gives this error.
>
> Saleem Hasan
Dear Saleem,
just install gfortran inside cygwin (it should be explaiend in the
cygwin documentation)
In general, if the you get an error "cannot find libXXX.so" you'll have
to install XXX
cheers
--
Dr. Lorenzo Paulatto
IdR @ IMPMC -- CNRS & Universit? Paris 6
+33 (0)1 44 275 084 / skype: paulatz
http://www-int.impmc.upmc.fr/~paulatto/
23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05
From muthu.physicsmath at gmail.com Wed Apr 16 20:50:13 2014
From: muthu.physicsmath at gmail.com (Muthu V)
Date: Wed, 16 Apr 2014 20:50:13 +0200
Subject: [xcrysden] XCrySDen Digest, Vol 75, Issue 6
In-Reply-To: <mailman.1.1397626530.7356.xcrysden@democritos.it>
References: <mailman.1.1397626530.7356.xcrysden@democritos.it>
Message-ID: <CAPKCeTK-8Lf_oLQEMhGU1mMq_gPe3-zB=92jsOhY+g3bPriCow@mail.gmail.com>
HI all
Upto my knowledge this type error will occur when OS bit Configuration and
Xcrysden Bit not match each other. try to install xcrysden with bit that of
your os
*_________________________*
*Muthu.V ?Project Fellow ?Madurai Kamaraj Universit**y*
*__________________________*
On Wed, Apr 16, 2014 at 7:35 AM, <xcrysden-request at democritos.it> wrote:
> Send XCrySDen mailing list submissions to
> xcrysden at democritos.it
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://www.democritos.it/mailman/listinfo/xcrysden
> or, via email, send a message with subject or body 'help' to
> xcrysden-request at democritos.it
>
> You can reach the person managing the list at
> xcrysden-owner at democritos.it
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of XCrySDen digest..."
>
>
> Today's Topics:
>
> 1. Need help (Lawal Mohammed)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 15 Apr 2014 21:41:27 -0700 (PDT)
> From: Lawal Mohammed <mohammedlawal08 at yahoo.com>
> Subject: [xcrysden] Need help
> To: "xcrysden at democritos.it" <xcrysden at democritos.it>
> Message-ID:
> <1397623287.91715.YahooMailNeo at web125706.mail.ne1.yahoo.com>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear Developers and Users,
>
> We got a problem installing the xcrysden on one of our system which have
> wien2k installed. We end up with this error
>
> /usr/local/codes/wien/v.11/xcrysden-1.5.53-bin-semishared/bin/ftnunit:
> error while loading shared libraries: libgfortran.so.3: cannot open shared
> object file: No such file or directory
>
> After this we got a pop up of the xcrysden interface, then nothing happen.
>
> Any help in this regard is welcome
> With regards
> Lawal Mohammed
> -------------- next part --------------
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>
> ------------------------------
>
> _______________________________________________
> XCrySDen mailing list
> XCrySDen at democritos.it
> http://www.democritos.it/mailman/listinfo/xcrysden
>
>
> End of XCrySDen Digest, Vol 75, Issue 6
> ***************************************
>
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From deepika.goyal58 at gmail.com Wed Apr 16 22:42:37 2014
From: deepika.goyal58 at gmail.com (deepika goyal)
Date: Thu, 17 Apr 2014 02:12:37 +0530
Subject: [xcrysden] Isosurface plotting at particluar k point
Message-ID: <CAASgPXbwsoogxwNBJ-Q6djpeaJ70w4Y_xmO-=YH0mN8Hv9yKOQ@mail.gmail.com>
Dear XCrSDen Users,
I need your help for drawing spatial charge
distribution at one particular k-point from the output file ( CHGCAR) of
band structure calculation of VASP software.
I have converted CHGCAR to CHGCAR.xsf.gz file.
My CHGCAR file include information of charge density from gamma to X path,
and I need information of spacial charge distribution at gamma point only.
Looking forward for your reply
Thanks and regards
Deepika
--
Deepika
Research Scholar
Department of Physics
Indian Institute of Technology
Ropar, 140001
Punjab
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From mohammedlawal08 at yahoo.com Thu Apr 17 06:55:51 2014
From: mohammedlawal08 at yahoo.com (Lawal Mohammed)
Date: Wed, 16 Apr 2014 21:55:51 -0700 (PDT)
Subject: [xcrysden] Need help
In-Reply-To: <534E7DD5.9000109@impmc.upmc.fr>
References: <20140416073628.33KHX.117950.imail@eastrmwml208>
<534E7DD5.9000109@impmc.upmc.fr>
Message-ID: <1397710551.69543.YahooMailNeo@web125704.mail.ne1.yahoo.com>
Dear Users,
Thanks for your help.
We install the libgfortran.so.3, as suggested all is ok, that is no error. But, the xcrysden still not in the w2web with wien2k. We try the old version of the xcrysden and it works.
Regards
Lawal Mohammed
On Wednesday, April 16, 2014 8:56 PM, Lorenzo Paulatto <lorenzo.paulatto at impmc.upmc.fr> wrote:
On 04/16/2014 01:36 PM, Saleem Hasan wrote:
> I am also very new to xcrysden so I am not sure if this will help. I got a similar error and I had to install fortran modules (cygfortran) in cygwin.
>
> I am using cygwin to run xcrysden in Windows. If you are also using cygwin then, try searching and installing cygfort. I think, it is not able to find the cygfortran modules and that is why it gives this error.
>
> Saleem Hasan
Dear Saleem,
just install gfortran inside cygwin (it should be explaiend in the
cygwin documentation)
In general, if the you get an error "cannot find libXXX.so" you'll have
to install XXX
cheers
--
Dr. Lorenzo Paulatto
IdR @ IMPMC -- CNRS & Universit? Paris 6
+33 (0)1 44 275 084 / skype: paulatz
http://www-int.impmc.upmc.fr/~paulatto/
23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05
_______________________________________________
XCrySDen mailing list
XCrySDen at democritos.it
http://www.democritos.it/mailman/listinfo/xcrysden
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From tone.kokalj at ijs.si Fri Apr 18 08:57:39 2014
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Fri, 18 Apr 2014 08:57:39 +0200
Subject: [xcrysden] installed successfully but not able to view
xcrystallden in Fedora 16
In-Reply-To: <1397460527.11357.YahooMailNeo@web120302.mail.ne1.yahoo.com>
References: <1397460527.11357.YahooMailNeo@web120302.mail.ne1.yahoo.com>
Message-ID: <1397804259.4860.24.camel@catalyst.ijs.si>
On Mon, 2014-04-14 at 00:28 -0700, Masood Yousaf wrote:
> I have successfully embeded Xcrystalden in Wien2k but still fail to
> view the structure.
Does xcrysden works as standalone? If the answer is yes, then I suppose
you need to configure Wien2K properly to allow to use xcrysden (see the
Wien2K/w2web User Guide).
>
> View structure with XCrysDen
> Requires X-Windows system ...
This message seems to suggest you are trying to run xcrysden without
running X-window. This is not possible.
Regards,
--
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
(tel: +386-1-477-3523 // fax:+386-1-477-3822)
Please, if possible, avoid sending me Word or PowerPoint attachments.
See: http://www.gnu.org/philosophy/no-word-attachments.html
From tone.kokalj at ijs.si Fri Apr 18 09:05:15 2014
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Fri, 18 Apr 2014 09:05:15 +0200
Subject: [xcrysden] Isosurface plotting at particluar k point
In-Reply-To: <CAASgPXbwsoogxwNBJ-Q6djpeaJ70w4Y_xmO-=YH0mN8Hv9yKOQ@mail.gmail.com>
References: <CAASgPXbwsoogxwNBJ-Q6djpeaJ70w4Y_xmO-=YH0mN8Hv9yKOQ@mail.gmail.com>
Message-ID: <1397804715.4860.30.camel@catalyst.ijs.si>
On Thu, 2014-04-17 at 02:12 +0530, deepika goyal wrote:
> Dear XCrSDen Users,
>
> I need your help for drawing spatial
> charge distribution at one particular k-point from the output file
> ( CHGCAR) of band structure calculation of VASP software.
>
> I have converted CHGCAR to CHGCAR.xsf.gz file.
>
> My CHGCAR file include information of charge density from gamma to X
> path, and I need information of spacial charge distribution at gamma
> point only.
I frankly do not understand what is the problem, but it seems like a
VASP issue. You need to consult its User Guide as to determine how to
calculate charge density at a particular k-point.
Regards,
--
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
(tel: +386-1-477-3523 // fax:+386-1-477-3822)
Please, if possible, avoid sending me Word or PowerPoint attachments.
See: http://www.gnu.org/philosophy/no-word-attachments.html
From tone.kokalj at ijs.si Fri Apr 18 09:20:47 2014
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Fri, 18 Apr 2014 09:20:47 +0200
Subject: [xcrysden] Need help
In-Reply-To: <1397710551.69543.YahooMailNeo@web125704.mail.ne1.yahoo.com>
References: <20140416073628.33KHX.117950.imail@eastrmwml208>
<534E7DD5.9000109@impmc.upmc.fr>
<1397710551.69543.YahooMailNeo@web125704.mail.ne1.yahoo.com>
Message-ID: <1397805647.17093.5.camel@catalyst.ijs.si>
On Wed, 2014-04-16 at 21:55 -0700, Lawal Mohammed wrote:
> Dear Users,
> Thanks for your help.
>
> We install the libgfortran.so.3, as suggested all is ok, that is no
> error. But, the xcrysden still not in the w2web with wien2k. We try
> the old version of the xcrysden and it works.
Perhaps this will help:
http://lmgtfy.com/?q=w2web+xcrysden
You may also consult the Wien2K User's Guide (Sections 11.3 and 11.4).
Regards,
--
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
(tel: +386-1-477-3523 // fax:+386-1-477-3822)
Please, if possible, avoid sending me Word or PowerPoint attachments.
See: http://www.gnu.org/philosophy/no-word-attachments.html
From mohammedlawal08 at yahoo.com Sat Apr 19 04:38:43 2014
From: mohammedlawal08 at yahoo.com (Lawal Mohammed)
Date: Fri, 18 Apr 2014 19:38:43 -0700 (PDT)
Subject: [xcrysden] Need help
In-Reply-To: <1397805647.17093.5.camel@catalyst.ijs.si>
References: <20140416073628.33KHX.117950.imail@eastrmwml208> <534E7DD5.9000109@impmc.upmc.fr> <1397710551.69543.YahooMailNeo@web125704.mail.ne1.yahoo.com>
<1397805647.17093.5.camel@catalyst.ijs.si>
Message-ID: <1397875123.43306.YahooMailNeo@web125704.mail.ne1.yahoo.com>
Dear Anton Kokalj Sir,
Thank you, we will look at it.
Regards
Lawal Mohammed
On Friday, April 18, 2014 3:20 PM, Tone Kokalj <tone.kokalj at ijs.si> wrote:
On Wed, 2014-04-16 at 21:55 -0700, Lawal Mohammed wrote:
> Dear Users,
> Thanks for your help.
>
> We install the libgfortran.so.3, as suggested all is ok, that is no
> error. But, the xcrysden still not in the w2web with wien2k. We try
> the old version of the xcrysden and it works.
Perhaps this will help:
http://lmgtfy.com/?q=w2web+xcrysden
You may also consult the Wien2K User's Guide (Sections 11.3 and 11.4).
Regards,
--
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
(tel: +386-1-477-3523 // fax:+386-1-477-3822)
Please, if possible, avoid sending me Word or PowerPoint attachments.
See:? http://www.gnu.org/philosophy/no-word-attachments.html
_______________________________________________
XCrySDen mailing list
XCrySDen at democritos.it
http://www.democritos.it/mailman/listinfo/xcrysden
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From member at linkedin.com Sun Apr 20 18:47:32 2014
From: member at linkedin.com (Muthu V via LinkedIn)
Date: Sun, 20 Apr 2014 16:47:32 +0000 (UTC)
Subject: [xcrysden] =?utf-8?q?Andr=C3=A9_Pereira=2C_voc=C3=AA_poderia_me_a?=
=?utf-8?q?dicionar_=C3=A0_sua_rede_no_LinkedIn=3F?=
Message-ID: <909863912.23003835.1398012452495.JavaMail.app@ela4-app1550.prod>
LinkedIn
------------
Muthu V solicitou sua adi??o como uma conex?o no LinkedIn:
------------------------------------------
Eu gostaria de adicion?-lo ? minha rede profissional no LinkedIn.
Aceitar convite de Muthu V
http://www.linkedin.com/e/-fe5rcs-hu8kio3t-1n/V2kbc-S-ecaYaqU8y2MQlJBQAcaYZU7r_FU/blk/I578835056_125/3wOtCVFbmdxnSVFbm8JrnpKqlZJrmZzbmNJpjRQnOpBtn9QfmhBt71BoSd1p65Lr6lOfPkOclYSdj0RcPwUdPl9bSMThkpKhClAbPgMcPoQcjoQdPsMczAUdzcSe3kLrCBxbOYWrSlI/eml-comm_invm-b-in_ac-inv28/?hs=false&tok=0rZTdbNxpLy6c1
Visualizar perfil de Muthu V
http://www.linkedin.com/e/-fe5rcs-hu8kio3t-1n/rso/74900821/EeK-/name/128644874_I578835056_125/?hs=false&tok=3yEzThCj1Ly6c1
------------------------------------------
Voc? est? recebendo e-mails de convites.
Este e-mail era para Andr? Pereira XCrysden.
Saiba por que isto est? inclu?do: http://www.linkedin.com/e/-fe5rcs-hu8kio3t-1n/plh/http%3A%2F%2Fhelp%2Elinkedin%2Ecom%2Fapp%2Fanswers%2Fdetail%2Fa_id%2F4788/-GXI/?hs=false&tok=1XXd8-xchLy6c1
(c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043 - EUA.
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From mohammadmoaddeli at yahoo.com Fri Apr 25 16:40:32 2014
From: mohammadmoaddeli at yahoo.com (mohammad moaddeli)
Date: Fri, 25 Apr 2014 07:40:32 -0700 (PDT)
Subject: [xcrysden] installing Xcr on a 32 bit operating system
Message-ID: <1398436832.2956.YahooMailNeo@web140403.mail.bf1.yahoo.com>
Dear all,
?
I usually install Xcrysden on Fedora 64 bit operating
systems, but I have a few problems with installing it on 32 bit OS. Is there
any libraries I should install?
I tried all of these versions:
xc-1.4.1bin-linuxPC-static.tar
xc-1.5.24-src-all.tar
xcrysden-1.5.53-linux_x86_64-semishared.tar
xcrysden-1.5.53-linux_x86_64-shared.tar
?
Any help will be appreciated,
Mohammad
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From tone.kokalj at ijs.si Fri Apr 25 16:44:08 2014
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Fri, 25 Apr 2014 16:44:08 +0200
Subject: [xcrysden] installing Xcr on a 32 bit operating system
In-Reply-To: <1398436832.2956.YahooMailNeo@web140403.mail.bf1.yahoo.com>
References: <1398436832.2956.YahooMailNeo@web140403.mail.bf1.yahoo.com>
Message-ID: <1398437048.4512.3.camel@catalyst.ijs.si>
On Fri, 2014-04-25 at 07:40 -0700, mohammad moaddeli wrote:
> Dear all,
>
> I usually install Xcrysden on Fedora 64 bit operating systems, but I
> have a few problems with installing it on 32 bit OS. Is there any
> libraries I should install?
> I tried all of these versions:
>
> xc-1.4.1bin-linuxPC-static.tar
This one is very old.
> xcrysden-1.5.53-linux_x86_64-semishared.tar
> xcrysden-1.5.53-linux_x86_64-shared.tar
These two are 64bit.
Try this one:
http://www.xcrysden.org/download/xc-1.5.24-linux_x86-semishared.tar.gz
Regards, Tone
--
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
(tel: +386-1-477-3523 // fax:+386-1-477-3822)
Please, if possible, avoid sending me Word or PowerPoint attachments.
See: http://www.gnu.org/philosophy/no-word-attachments.html
From mohammadmoaddeli at yahoo.com Fri Apr 25 17:50:46 2014
From: mohammadmoaddeli at yahoo.com (mohammad moaddeli)
Date: Fri, 25 Apr 2014 08:50:46 -0700 (PDT)
Subject: [xcrysden] installing Xcr on a 32 bit operating system
In-Reply-To: <1398437048.4512.3.camel@catalyst.ijs.si>
References: <1398436832.2956.YahooMailNeo@web140403.mail.bf1.yahoo.com>
<1398437048.4512.3.camel@catalyst.ijs.si>
Message-ID: <1398441046.73168.YahooMailNeo@web140401.mail.bf1.yahoo.com>
Thanks,
I tried the version you recommended, but it failed:
/usr/local/xcrysden/XCrySDen-1.5.24-src-all/xcrysden: line 224: /usr/local/xcrysden/XCrySDen-1.5.24-src-all/bin/xcrys: No such file or directory
On Friday, April 25, 2014 7:14 PM, Tone Kokalj <tone.kokalj at ijs.si> wrote:
On Fri, 2014-04-25 at 07:40 -0700, mohammad moaddeli wrote:
> Dear all,
>?
> I usually install Xcrysden on Fedora 64 bit operating systems, but I
> have a few problems with installing it on 32 bit OS. Is there any
> libraries I should install?
> I tried all of these versions:
>
> xc-1.4.1bin-linuxPC-static.tar
This one is very old.
> xcrysden-1.5.53-linux_x86_64-semishared.tar
> xcrysden-1.5.53-linux_x86_64-shared.tar
These two are 64bit.
Try this one:
http://www.xcrysden.org/download/xc-1.5.24-linux_x86-semishared.tar.gz
Regards, Tone
--
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
(tel: +386-1-477-3523 // fax:+386-1-477-3822)
Please, if possible, avoid sending me Word or PowerPoint attachments.
See:? http://www.gnu.org/philosophy/no-word-attachments.html
_______________________________________________
XCrySDen mailing list
XCrySDen at democritos.it
http://www.democritos.it/mailman/listinfo/xcrysden
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From tone.kokalj at ijs.si Fri Apr 25 17:55:20 2014
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Fri, 25 Apr 2014 17:55:20 +0200
Subject: [xcrysden] installing Xcr on a 32 bit operating system
In-Reply-To: <1398441046.73168.YahooMailNeo@web140401.mail.bf1.yahoo.com>
References: <1398436832.2956.YahooMailNeo@web140403.mail.bf1.yahoo.com>
<1398437048.4512.3.camel@catalyst.ijs.si>
<1398441046.73168.YahooMailNeo@web140401.mail.bf1.yahoo.com>
Message-ID: <1398441320.4512.7.camel@catalyst.ijs.si>
On Fri, 2014-04-25 at 08:50 -0700, mohammad moaddeli wrote:
> Thanks,
> I tried the version you recommended, but it failed:
>
> /usr/local/xcrysden/XCrySDen-1.5.24-src-all/xcrysden: line
> 224: /usr/local/xcrysden/XCrySDen-1.5.24-src-all/bin/xcrys: No such
> file or directory
No, this is not the version I recommended. This is a source version
1.5.24.
Probably you have remnants of old xcrysden istallation in your ~/.bashrc
file. Clear the XCRYSDEN related files in the ~/.bashrc, then open a new
terminal window, cd into root directory of untarred
xc-1.5.24-linux_x86-semishared.tar.gz and try: ./xcrysden
Regards, Tone
From 85904751 at qq.com Sat Apr 26 13:16:09 2014
From: 85904751 at qq.com (=?ISO-8859-1?B?SCpY?=)
Date: Sat, 26 Apr 2014 19:16:09 +0800
Subject: [xcrysden] Error while opening a Pwscf input file
Message-ID: <tencent_5F30B52A04ED1BB954B80538@qq.com>
Dear all,
I am new to xcrysden and I try to open a Pwscf input file but failed.
[root at localhost asesma]# xcrysden --pwi Po.example.in
+----------------------------------------------------------------+
|****************************************************************|
|* *|
|* XCrySDen - (X-Window) CRYstalline Structures and DENsities *|
|* = === = === *|
|*--------------------------------------------------------------*|
|* *|
|* Anton Kokalj (Tone.Kokalj at ijs.si) *|
|* Jozef Stefan Institute, Ljubljana, Slovenia *|
|* *|
|* Copyright (c) 1996--2009 by Anton Kokalj *|
|* *|
|****************************************************************|
+----------------------------------------------------------------+
Version: 1.5.25
Please report bugs to: Tone.Kokalj at 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, Comp. Mater. Sci., Vol. 28, p. 155, 2003.
Code available from http://www.xcrysden.org/.
TCL_LIBRARY=/hexin/XCrySDen-1.5.25-bin-semishared/external/lib/tcl8.5
XCRYSDEN_TOPDIR=/hexin/XCrySDen-1.5.25-bin-semishared
XCRYSDEN_SCRATCH=/hexin/xcrys_tmp
Running on platform : unix
Operating system : Linux
CRYSTAL VERSION: 09
Executing: /hexin/XCrySDen-1.5.25-bin-semishared/bin/ftnunit
Error in startup script: wrong # args: should be "pwInputPreset file"
while executing
"pwInputPreset /hexin/ASESMA 2010/asesma/Po.example.in"
("eval" body line 1)
invoked from within
"eval $preset $file"
(procedure "openExtStruct" line 106)
invoked from within
"openExtStruct 3 crystal external [list sh $system(TOPDIR)/scripts/pwi2xsf.sh]
pwi2xsf.xsf_out {PWSCF Input File} ANGS -file $filedir -preset pwIn..."
invoked from within
"
if [file exists $filedir] {
# pop-up Viewer
ViewMol .
openExtStruct 3 crystal external [list sh $system(TOPDI
R)/scripts/pwi2xsf.sh] pwi2xsf..."
("--pwi" arm line 2)
invoked from within
"switch -glob -- $tag {
"-a" -
"--attrib*" {
set load_attributes 1
set file_attributes $filedir
}
"--xsf" -
"--xcr..."
(procedure "parseComLinArg" line 44)
invoked from within
"parseComLinArg [lrange $argv 2 end]"
invoked from within
"if { [llength $argv] > 2 } {
parseComLinArg [lrange $argv 2 end]
} else {
ViewMol .
}"
(file "/hexin/XCrySDen-1.5.25-bin-semishared/Tcl/xcInit.tcl" line 550)
/hexin/XCrySDen-1.5.25-bin-semishared/xcrysden: line 277: test: /hexin/ASESMA: binary operator expected
I would be very appreciated if you can help me to solve this problem.
Best regards,
Xin
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From flux_ray12 at 163.com Mon Apr 28 03:34:27 2014
From: flux_ray12 at 163.com (GAO Zhe)
Date: Mon, 28 Apr 2014 09:34:27 +0800 (CST)
Subject: [xcrysden] Cannot start xcrysden under Windows system
Message-ID: <361bd585.8013.145a5f80aa8.Coremail.flux_ray12@163.com>
Dear all,
I am trying to run XCrySDen (1.5.18, Cygwin shared) under Windows with Cygwin environment. Two Windows systems, Windows 7 32-bit and Windows 8 64-bit, were involved the tests. The installed Cygwin is with 64-bit libraries and binaries.
Under Win7 32bit, the XCrySDen showed "Segment Fault" after initialization step. Since I was not sure whether this problem was caused by the 64bit code running under 32bit system, I skipped Win7 32bit and reached to Win8 64bit.
Under Win8 64bit, I ran XServer at first, thereafter, the script xcrysden was performed after proper configuration by xcConfigue. However, even the initiallizing GUI was not appeared, and a error feedbacked through terminate:
Error in startup script: couldn't load file "~/Program/XCrySDen/bin/xcrys.dll": Exec format error
while executing
"load $system(TOPDIR)/bin/xcrys.dll"
invoked from within
"if { [file exists $system(TOPDIR)/bin/xcrys.dll] } {
load $system(TOPDIR)/bin/xcrys.dll
}"
(file "~/Program/XCrySDen/Tcl/xcInit.tcl" line 426)
Would any one help me out from this difficulty?
Thanks a lot.
Kind Regards,
--
GAO Zhe
Ceramic Metal Composite Lab,
Department of Materials Sci. & Eng.,
Seoul National University,
Daehak-dong, Gwanak-gu, Seoul, Public of Korea
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From tone.kokalj at ijs.si Mon Apr 28 11:30:09 2014
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Mon, 28 Apr 2014 11:30:09 +0200
Subject: [xcrysden] Error while opening a Pwscf input file
In-Reply-To: <tencent_5F30B52A04ED1BB954B80538@qq.com>
References: <tencent_5F30B52A04ED1BB954B80538@qq.com>
Message-ID: <1398677409.25432.6.camel@catalyst.ijs.si>
On Sat, 2014-04-26 at 19:16 +0800, H*X wrote:
> Dear all,
> I am new to xcrysden and I try to open a Pwscf input file but
> failed.
> [root at localhost asesma]# xcrysden --pwi Po.example.in
Please send me the Po.example.in so that I can see if I can reproduce
your error.
Regards,
--
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
(tel: +386-1-477-3523 // fax:+386-1-477-3822)
Please, if possible, avoid sending me Word or PowerPoint attachments.
See: http://www.gnu.org/philosophy/no-word-attachments.html
From tone.kokalj at ijs.si Mon Apr 28 11:32:54 2014
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Mon, 28 Apr 2014 11:32:54 +0200
Subject: [xcrysden] Cannot start xcrysden under Windows system
In-Reply-To: <361bd585.8013.145a5f80aa8.Coremail.flux_ray12@163.com>
References: <361bd585.8013.145a5f80aa8.Coremail.flux_ray12@163.com>
Message-ID: <1398677574.25432.8.camel@catalyst.ijs.si>
On Mon, 2014-04-28 at 09:34 +0800, GAO Zhe wrote:
> Dear all,
>
> I am trying to run XCrySDen (1.5.18, Cygwin shared) under Windows with
> Cygwin environment.
Consider trying newer version:
http://www.xcrysden.org/download/xcrysden-1.5.53-cygwin.tar.gz
Regards,
--
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
(tel: +386-1-477-3523 // fax:+386-1-477-3822)
Please, if possible, avoid sending me Word or PowerPoint attachments.
See: http://www.gnu.org/philosophy/no-word-attachments.html
From flux_ray12 at 163.com Mon Apr 28 16:24:06 2014
From: flux_ray12 at 163.com (GAO Zhe)
Date: Mon, 28 Apr 2014 22:24:06 +0800 (CST)
Subject: [xcrysden] Cannot start xcrysden under Windows system
In-Reply-To: <1398677574.25432.8.camel@catalyst.ijs.si>
References: <361bd585.8013.145a5f80aa8.Coremail.flux_ray12@163.com>
<1398677574.25432.8.camel@catalyst.ijs.si>
Message-ID: <4c7ac90d.14e7b.145a8b8af08.Coremail.flux_ray12@163.com>
Hi, Kokalj,
Thanks a lot for your kindly reply.
I tried XCrySDen 1.5.53 with cygwin under Win8 64-bit.
Once the script of xcrysden was run, I can only obtain the information shown below through terminate:
Version: 1.5.53
Please report bugs to: tone.kokalj at 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, Comp. Mater. Sci., Vol. 28, p. 155, 2003.
Code available from http://www.xcrysden.org/.
XCRYSDEN_TOPDIR=~/Program/XCrySDen
XCRYSDEN_SCRATCH=~/Program/XCrySDen/TEMP
Thereafter, the terminate return to "$" state. Would you give me any suggestion to figure out and solve this problem?
Thank you again,
Regards,
At 2014-04-28 17:32:54,"Tone Kokalj" <tone.kokalj at ijs.si> wrote:
>On Mon, 2014-04-28 at 09:34 +0800, GAO Zhe wrote:
>> Dear all,
>>
>> I am trying to run XCrySDen (1.5.18, Cygwin shared) under Windows with
>> Cygwin environment.
>
>Consider trying newer version:
>http://www.xcrysden.org/download/xcrysden-1.5.53-cygwin.tar.gz
>
>Regards,
>
>--
>Anton Kokalj
>J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
>(tel: +386-1-477-3523 // fax:+386-1-477-3822)
>
>Please, if possible, avoid sending me Word or PowerPoint attachments.
>See: http://www.gnu.org/philosophy/no-word-attachments.html
>
>_______________________________________________
>XCrySDen mailing list
>XCrySDen at democritos.it
>http://www.democritos.it/mailman/listinfo/xcrysden
--
GAO Zhe
Ceramic Metal Composite Lab,
Department of Materials Sci. & Eng.,
Seoul National University,
Daehak-dong, Gwanak-gu, Seoul, Public of Korea
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From tone.kokalj at ijs.si Tue Apr 29 20:10:40 2014
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Tue, 29 Apr 2014 20:10:40 +0200
Subject: [xcrysden] Cannot start xcrysden under Windows system
In-Reply-To: <4c7ac90d.14e7b.145a8b8af08.Coremail.flux_ray12@163.com>
References: <361bd585.8013.145a5f80aa8.Coremail.flux_ray12@163.com>
<1398677574.25432.8.camel@catalyst.ijs.si>
<4c7ac90d.14e7b.145a8b8af08.Coremail.flux_ray12@163.com>
Message-ID: <1398795040.6084.14.camel@catalyst.ijs.si>
On Mon, 2014-04-28 at 22:24 +0800, GAO Zhe wrote:
> Hi, Kokalj,
>
> Thanks a lot for your kindly reply.
> I tried XCrySDen 1.5.53 with cygwin under Win8 64-bit.
> Once the script of xcrysden was run, I can only obtain the information
> shown below through terminate:
I see. Unfortunately, I do not know what is the reason. There seems to
be some incompatibility. I also have no suggestion of how to solve this
issue, as I have almost zero experience with windows/cygwin.
Regards,
--
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
(tel: +386-1-477-3523 // fax:+386-1-477-3822)
Please, if possible, avoid sending me Word or PowerPoint attachments.
See: http://www.gnu.org/philosophy/no-word-attachments.html
From omamuyovwiakemu at yahoo.com Wed Apr 30 15:58:37 2014
From: omamuyovwiakemu at yahoo.com (Omamuyovwi Akemu)
Date: Wed, 30 Apr 2014 06:58:37 -0700 (PDT)
Subject: [xcrysden] Building a supercell
Message-ID: <1398866317.8680.YahooMailNeo@web121805.mail.ne1.yahoo.com>
Dear Xcrysden User,
I have searched through the archives on how to use xcrysden to build a supercell.?
From my search, It is possible based on some comments I got like:
XCrySDen can build simple {N}x{M}x{K} type of supercells.
To correctly extract the atoms within the supercell do the following:
1. generate the supercell via menu: Modify-->Number of units drawn
2. change unit of repetition to translational asymmetric unit via menu
Display-->Unit of repetition ...-->Translation asymmetric unit
3, save the XSF file via: File-->Save XSF structure
Then in the so generated file the atoms within the supercell are printed
in the "ATOMS" section.
However I have not been able to apply my findings to my work. I used cygwin as a platform for QE calculations and I have xcrysden installed.
I will really appreciate any comment that will help me resolve this.
Thank you all.
Akemu Rita
UNIBEN
Nigeria.
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