From devendranegi at jncasr.ac.in Tue Feb 3 04:29:22 2015 From: devendranegi at jncasr.ac.in (Devendra Singh Negi) Date: Tue, 3 Feb 2015 08:59:22 +0530 (IST) Subject: [xcrysden] Error in xcryden In-Reply-To: <1622360377.489272.1422933924126.JavaMail.root@jncasr.ac.in> Message-ID: <865594217.489314.1422934162836.JavaMail.root@jncasr.ac.in> Dear xcrysden user, I am trying to plot the charge density map in xcrysden from WIEN2K calculation. After choosing 2D map and intended plane for charge density mapping and with Rainbow basis, at the end of submit it is showing the error of : " Domain error Argument not in valid range" Kindly suggest me the solution Thanks Devendra Singh Negi SRF,ICMS, JNCASR,Banglore India From martin at ruby.chemie.uni-freiburg.de Tue Feb 3 08:56:13 2015 From: martin at ruby.chemie.uni-freiburg.de (Martin Kroeker) Date: Tue, 3 Feb 2015 08:56:13 +0100 (CET) Subject: [xcrysden] Error in xcryden In-Reply-To: <865594217.489314.1422934162836.JavaMail.root@jncasr.ac.in> Message-ID: <20150203075613.F202C801B3@ruby.chemie.uni-freiburg.de> Can you post more of the error message (I expect it will contain some backtrace into the code module where the error occured), and of what exactly you were trying to plot ? "Domain error" generally means that an argument to a function was outside its mathematically defined range, e.g. taking the square root, or - more likely in your case - the logarithm of a negative number. Possibly your charge density map contains huge spikes, or even "NaN" ("not a number") entries from earlier errors. -- Dr. Martin Kroeker martin at ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg From muthu.physicsmath at gmail.com Thu Feb 5 06:42:42 2015 From: muthu.physicsmath at gmail.com (Muthu V) Date: Thu, 5 Feb 2015 11:12:42 +0530 Subject: [xcrysden] Band structure plotting -reg., Message-ID: Dear all users I am Working in DFT simulation and using Quantum Espresso. also Xcrysden is being more useful. I want to draw Band structure using Xcrysden like plotting charge density. it is possible with is ? if yes then how to do it. if no then what are other tools that can be used for this purpose. I look forward to your valuable suggestions Thank you ********************************* *Muthu.V?Project Fellow? Madurai Kamaraj Universit**y* ********************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20150205/58adf107/attachment.htm From tone.kokalj at ijs.si Thu Feb 5 07:40:34 2015 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 05 Feb 2015 07:40:34 +0100 Subject: [xcrysden] Band structure plotting -reg., In-Reply-To: References: Message-ID: <1423118434.1803.2.camel@ijs.si> On Thu, 2015-02-05 at 11:12 +0530, Muthu V wrote: > Dear all users > > I am Working in DFT simulation and using Quantum Espresso. also > Xcrysden is being more useful. I want to draw Band structure using > Xcrysden like plotting charge density. If you want to plot a band-structure spaghetti plot, then a program like gnuplot is all you need. 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 nityasagarjena at gmail.com Thu Feb 19 15:49:24 2015 From: nityasagarjena at gmail.com (Nityasagar Jena) Date: Thu, 19 Feb 2015 20:19:24 +0530 Subject: [xcrysden] xcrysden with VASP Message-ID: Dear Sir, I am Nityasagar, a student in theoretical nanoscience from INDIA. Dear sir, I am facing lots of problem to run VASP 5.3 output files in Xcrysden(version-1.5.53) in ubuntu platform. I am not getting K-path selection option and many options too. Please help me to fix it. Consider me a beginner to vasp, Linux, XCrySDen. step by step please guide me. I will wait for your reply. Thank you so much for your time to look into my problems. with warm regards, yours sincerely, Nityasagar Jena INST, INDIA From gsabo at crimson.ua.edu Thu Feb 19 19:47:45 2015 From: gsabo at crimson.ua.edu (Gavin Abo) Date: Thu, 19 Feb 2015 11:47:45 -0700 Subject: [xcrysden] xcrysden with VASP In-Reply-To: References: Message-ID: <54E62FD1.2050908@crimson.ua.edu> Dear Nityasagar, did you open the structure file (File->Open Structure->Open XSF)? I see that the Tools->k-path Selection is not available until after having opened an XSF file. Dear Tone, links to the xsfConvert utility, which is used to convert VASP output to xcrysden xsf format, on the XCrySDen website seem to be broken. The http://www.columbia.edu/~jk3610/software.html is not working for me, but http://theory.chm.tu-dresden.de/~jk/software.html is. On 2/19/2015 7:49 AM, Nityasagar Jena wrote: > Dear Sir, > > I am Nityasagar, a student in theoretical nanoscience from INDIA. Dear > sir, I am facing lots of problem to run VASP 5.3 output files in > Xcrysden(version-1.5.53) in ubuntu platform. I am not getting K-path > selection option and many options too. Please help me to fix it. > Consider me a beginner to vasp, Linux, XCrySDen. step by step please > guide me. > > I will wait for your reply. Thank you so much for your time to look > into my problems. > > with warm regards, > > yours sincerely, > Nityasagar Jena > INST, INDIA From mulwawinfred at gmail.com Sat Feb 21 06:39:47 2015 From: mulwawinfred at gmail.com (Winfred Mulwa) Date: Sat, 21 Feb 2015 07:39:47 +0200 Subject: [xcrysden] How to get k-path labels in xcrysden-1.5.60 Message-ID: Dear all, I am trying to get k-path points in xcrysden-1.5.60, when i click on the point, only reciprocal coordinates are displayed, no labels (GAM, X, W, K) displayed. Please assist, what can i do to get the labels displayed. Regards Mulwa Winfred. D Phil Student, Computational Material Science Group, University of the Free State - QwaQwa, South Africa. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20150221/d0b74a39/attachment.htm From martin at ruby.chemie.uni-freiburg.de Sat Feb 21 16:35:42 2015 From: martin at ruby.chemie.uni-freiburg.de (Martin Kroeker) Date: Sat, 21 Feb 2015 16:35:42 +0100 (CET) Subject: [xcrysden] How to get k-path labels in xcrysden-1.5.60 Message-ID: <20150221153542.8686A801B3@ruby.chemie.uni-freiburg.de> See the "K point selection HOWTO" in the "HOWTO" section of the webpage. Automatic labeling is provided for some Bravais lattices only, but you can always add your own in the label column - the k vector tool on the Bilbao Crystallographic Server at http://www.cryst.ehu.es/cryst/get_kvec.html may be of assistance here. -- Dr. Martin Kroeker martin at ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg From bogus@does.not.exist.com Mon Feb 2 10:44:46 2015 From: bogus@does.not.exist.com () Date: Mon, 02 Feb 2015 09:44:46 -0000 Subject: No subject Message-ID: http://www.xcrysden.org/News.html If you haven't installed fink in your mac yet, this is how you do it: http://www.finkproject.org/doc/bundled/install-first.php Once you have fink in your mac you just execute the following command: fink install xcrysden Hope that helps. Ryky On Sat, May 23, 2015 at 3:32 AM, Mirko Pieropan wrote: > Hello everybody, > I'm having troubles installing XCrysDen on my Mac Os X. > I've successfully untarred the download file and then I've attempted to > run the xcrysden file. > Maybe I'm doing something wrong but it seems there is no bin/xcrys folder! > I get the following in my terminal: > > MBP-di-Mirko:xcrysden-1.5.60 mirko$ ./xcrysden > > > +-----------------------------------------------------------------+ > > |*****************************************************************| > > |* *| > > |* XCrySDen -- (X-Window) CRYstalline Structures and DENsities *| > > |* = === = === *| > > |*---------------------------------------------------------------*| > > |* *| > > |* Anton Kokalj (tone.kokalj at ijs.si) *| > > |* Jozef Stefan Institute, Ljubljana, Slovenia *| > > |* *| > > |* Copyright (c) 1996--2014 by Anton Kokalj *| > > |* *| > > |*****************************************************************| > > +-----------------------------------------------------------------+ > > > Version: 1.5.60 > > > 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, J. Mol. Graph. Model., Vol. 17, pp. 176-179, 1999. > > Code available from http://www.xcrysden.org/. > > > XCRYSDEN_TOPDIR=/Users/mirko/Desktop/xcrysden-1.5.60 > > XCRYSDEN_SCRATCH=/var/folders/g8/2m80kqls4m750q_phtmbmwxc0000gn/T/ > > > ./xcrysden: line 257: /Users/mirko/Desktop/xcrysden-1.5.60/bin/xcrys: No > such file or directory > > > Can anybody help? > > Thank you very much in advance. > > > Mirko > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > --047d7b3a81fe6e85c00516c3e0f3 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
From my experience it's easier= to install xcrysden in mac via fink:

=

If you haven't installed fink in your mac ye= t, this is how you do it:

<= div class=3D"gmail_default" style=3D"font-family:'times new roman',= serif;font-size:large">
Once you have fink= in your mac you just execute the following command:

fink install xcrysden
<= /div>

Hope that = helps.=C2=A0

Ryky

= On Sat, May 23, 2015 at 3:32 AM, Mirko Pieropan <mirkopan91 at hotmail.it= > wrote:
Hello everybody,
I'm having troubles installi= ng XCrysDen on my Mac Os X.
I've successfully untarred the do= wnload file and then I've attempted to run the xcrysden file.
Maybe I'm doing something wrong but it seems there is no=C2=A0bin/xcrys folder!
I get the following in my terminal:

MBP-di-Mirko:xcrysden-1.5.60 mirko$ ./xcrysden=C2=A0


+----------------------------= -------------------------------------+

|****************************= *************************************|

|* =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 *|

|*=C2=A0 XCrySDen -- (X-Windo= w) CRYstalline Structures and DENsities=C2=A0 *|

|* =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =3D =C2=A0 =C2=A0 =C2=A0 =C2=A0 =3D=3D=3D =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =3D=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =3D=3D=3D=C2=A0 =C2=A0 =C2=A0 =C2=A0 *|

|*---------------------------= ------------------------------------*|

|* =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 *|

|*=C2=A0 =C2=A0 Anton Kokalj = (tone.kokalj at ijs.si= )=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 *|

|*=C2=A0 =C2=A0 Jozef Stefan = Institute, Ljubljana, Slovenia=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 *|

|* =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 *|

|*=C2=A0 =C2=A0 Copyright (c)= 1996--2014 by Anton Kokalj =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 *|

|* =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 *|

|****************************= *************************************|

+----------------------------= -------------------------------------+


=C2=A0 Version: 1.5.60


=C2=A0 Please report bugs to:= tone.kokalj at ijs.si=



=C2=A0 TERMS OF USE:

=C2=A0 -------------

=C2=A0 XCRYSDEN is released u= nder the GNU General Public License.


=C2=A0 Whenever graphics gene= rated by XCRYSDEN are used in scientific

=C2=A0 publications, it shall= be greatly appreciated to include an explicit

=C2=A0 reference. The preferr= ed form is the following:


=C2=A0 [ref] A. Kokalj, J. Mo= l. Graph. Model., Vol. 17, pp. 176-179, 1999.

=C2=A0 =C2=A0 =C2=A0 =C2=A0 C= ode available from h= ttp://www.xcrysden.org/.


XCRYSDEN_TOPDIR=3D/Users/mirk= o/Desktop/xcrysden-1.5.60

XCRYSDEN_SCRATCH=3D/var/folde= rs/g8/2m80kqls4m750q_phtmbmwxc0000gn/T/


./xcrysden: line 257: /Users/= mirko/Desktop/xcrysden-1.5.60/bin/xcrys: No such file or directory


Can anybody help?

Thank you very much in advance.


Mirko

=

_______________________________________________
XCrySDen mailing list
XCrySDen at democritos.it
http://www.democritos.it/mailman/listinfo/xcrysden


--047d7b3a81fe6e85c00516c3e0f3-- From bogus@does.not.exist.com Mon Feb 2 10:44:46 2015 From: bogus@does.not.exist.com () Date: Mon, 02 Feb 2015 09:44:46 -0000 Subject: No subject Message-ID: http://www.xcrysden.org/News.html If you haven't installed fink in your mac yet=2C this is how you do it: http://www.finkproject.org/doc/bundled/install-first.php Once you have fink in your mac you just execute the following command: fink install xcrysden Hope that helps.=20 Ryky On Sat=2C May 23=2C 2015 at 3:32 AM=2C Mirko Pieropan wrote: =0A= =0A= =0A= Hello everybody=2CI'm having troubles installing XCrysDen on my Mac Os X.I'= ve successfully untarred the download file and then I've attempted to run t= he xcrysden file.Maybe I'm doing something wrong but it seems there is no b= in/xcrys folder!I get the following in my terminal:MBP-di-Mirko:xcrysden-1.= 5.60 mirko$ ./xcrysden =0A= =0A= +-----------------------------------------------------------------+=0A= |*****************************************************************|=0A= |* *|=0A= |* XCrySDen -- (X-Window) CRYstalline Structures and DENsities *|=0A= |* =3D =3D=3D=3D =3D =3D=3D=3D = *|=0A= |*---------------------------------------------------------------*|=0A= |* *|=0A= |* Anton Kokalj (tone.kokalj at ijs.si) *|=0A= |* Jozef Stefan Institute=2C Ljubljana=2C Slovenia *|=0A= |* *|=0A= |* Copyright (c) 1996--2014 by Anton Kokalj *|=0A= |* *|=0A= |*****************************************************************|=0A= +-----------------------------------------------------------------+=0A= =0A= Version: 1.5.60=0A= =0A= Please report bugs to: tone.kokalj at ijs.si=0A= =0A= =0A= TERMS OF USE:=0A= -------------=0A= XCRYSDEN is released under the GNU General Public License.=0A= =0A= Whenever graphics generated by XCRYSDEN are used in scientific=0A= publications=2C it shall be greatly appreciated to include an explicit=0A= reference. The preferred form is the following:=0A= =0A= [ref] A. Kokalj=2C J. Mol. Graph. Model.=2C Vol. 17=2C pp. 176-179=2C 199= 9.=0A= Code available from http://www.xcrysden.org/.=0A= =0A= XCRYSDEN_TOPDIR=3D/Users/mirko/Desktop/xcrysden-1.5.60=0A= XCRYSDEN_SCRATCH=3D/var/folders/g8/2m80kqls4m750q_phtmbmwxc0000gn/T/=0A= =0A= ./xcrysden: line 257: /Users/mirko/Desktop/xcrysden-1.5.60/bin/xcrys: No su= ch file or directory Can anybody help?Thank you very much in advance. Mirko =0A= _______________________________________________ =0A= XCrySDen mailing list =0A= XCrySDen at democritos.it =0A= http://www.democritos.it/mailman/listinfo/xcrysden =0A= =0A= _______________________________________________=0A= XCrySDen mailing list=0A= XCrySDen at democritos.it=0A= http://www.democritos.it/mailman/listinfo/xcrysden = --_91149b7f-be5b-4617-ad41-13b03275e73d_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Thank you=2C
now=2C after ha= ving installed fink=2C I get stuck. I get the following:

MBP-di-Mirko:/= mirko$ fink install xcrysden

=0A=

Information about 112= 42 packages read in 0 seconds.

=0A=

<= br>

=0A=

fink needs help picki= ng an alternative to satisfy a virtual dependency. The

=0A=

candidates:

=0A=

<= br>

=0A=

(1) automake1.14: GNU Standards-= compliant Makefile generator

=0A=

(2) automake1.13: GNU Standards-= compliant Makefile generator

=0A=

(3) automake1.12: GNU Standards-= compliant Makefile generator

=0A=

<= br>

=0A=

Pick one: [1] 1

= =0A=

The following package= will be installed or updated:

=0A=

 =3Bxcrysden

= =0A=

The following 39 addi= tional packages will be installed:

=0A=

 =3Bautoconf2.6 a= utomake1.14 automake1.14-core cloog-org2 cloog-org2-shlibs

=0A=

 =3Bcoreutils exp= at1 fftw3 fink-buildenv-modules fink-package-precedence

=0A=

 =3Bfontconfig2-d= ev freetype219 gcc49-compiler gcc5-compiler gettext-tools gmp5

=0A=

 =3Bhelp2man-perl= 5182 isl isl-shlibs isl2 isl2-shlibs libgmpxx5-shlibs libmpc3

=0A=

 =3Blibmpc3-shlib= s libmpfr4 libmpfr4-shlibs libpng16 libsigsegv2

=0A=

 =3Blibsigsegv2-s= hlibs libtool2 locale-gettext-pm5182 m4 mesa mesa-shlibs

=0A=

 =3Btcltk-dev tex= i2html texinfo xft2-dev xz

=0A=

Default answer will b= e chosen in 60 seconds...

=0A=

Do you want to contin= ue? [Y/n] y

=0A=

curl --connect-timeou= t 30 -f -L -A 'fink/0.38.5' -O ftp://ftp.debian.org/debian/pool/main/f/free= type/freetype_2.5.2-2.diff.gz

=0A=

 =3B % Total = =3B  =3B % Received % Xferd =3B Average Speed  =3B Time =3B=  =3B Time  =3B  =3B Time =3B Current

=0A=

 =3B =3B &nbs= p=3B  =3B  =3B  =3B  =3B  =3B  =3B  =3B  = =3B  =3B  =3B  =3B  =3B  =3B  =3B Dload =3B Upl= oad  =3B Total  =3B Spent =3B  =3B Left =3B Speed

= =0A=

 =3B 0  =3B &= nbsp=3B 0 =3B  =3B 0  =3B  =3B 0 =3B  =3B 0  = =3B  =3B 0 =3B  =3B  =3B 0 =3B  =3B  =3B 0 --:-= -:-- =3B 0:00:01 --:--:--  =3B  =3B 0

=0A=

curl: (78) RETR respo= nse: 550

=0A=

### execution of curl= failed=2C exit code 78

=0A=

Downloading the file = "freetype_2.5.2-2.diff.gz" failed.

=0A=

<= br>

=0A=

(1) Give up

=0A=

(2) Retry the same mirror

=0A=

(3) Retry another mirror from yo= ur country

=0A=

(4) Retry another mirror from yo= ur continent

=0A=

(5) Retry another mirror

=0A=

<= br>

=0A=

Default answer will b= e chosen in 120 seconds...

=0A=

How do you want to pr= oceed? [3] =3B


What should = I do? I tried all the options many times.

Thanks again in advance.


Mirko



From: nelson.ry= ky at gmail.com
Date: Sat=2C 23 May 2015 13:23:22 -0500
To: xcrysden at dem= ocritos.it
Subject: Re: [xcrysden] troubles installing xcrysden

<= div dir=3D"ltr">
From my experience it's easier to= install xcrysden in mac via fink:

<= /div>

If you haven't installe= d fink in your mac yet=2C this is how you do it:


<= /div>
Once you have fink in your mac you just exec= ute the following command:

fink install xcrysden

Hope = that helps. =3B

Ryky

On Sat=2C May 23=2C 2015 at 3:32 AM=2C Mirko Pieropan <=3Bmirkopan91 at hotmail.it>=3B wrote:
= =0A= =0A= =0A=
Hello everybody=2C
I'm having troubles installing= XCrysDen on my Mac Os X.
I've successfully untarred the download= file and then I've attempted to run the xcrysden file.
Maybe I'm= doing something wrong but it seems there is no =3Bbin/xcrys folder!
I get = the following in my terminal:

MBP-di-Mirko:xcrysden-1.5.60 mirko$ ./xcrysden =3B

= =0A=


=0A=

+-----------------------= ------------------------------------------+

=0A=

|***********************= ******************************************|

=0A=

|*  =3B  =3B &nb= sp=3B  =3B  =3B  =3B  =3B  =3B  =3B  =3B  = =3B  =3B  =3B  =3B  =3B  =3B  =3B  =3B  =3B=  =3B  =3B  =3B  =3B  =3B  =3B  =3B  =3B &n= bsp=3B  =3B  =3B  =3B *|

=0A=

|* =3B XCrySDen -- (= X-Window) CRYstalline Structures and DENsities =3B *|

=0A=

|*  =3B  =3B &nb= sp=3B  =3B  =3B  =3B  =3B =3D  =3B  =3B  =3B &n= bsp=3B =3D=3D=3D  =3B  =3B  =3B  =3B =3D =3B  =3B &= nbsp=3B  =3B  =3B  =3B  =3B =3D=3D=3D =3B  =3B &nbs= p=3B  =3B *|

=0A=

|*----------------------= -----------------------------------------*|

=0A=

|*  =3B  =3B &nb= sp=3B  =3B  =3B  =3B  =3B  =3B  =3B  =3B  = =3B  =3B  =3B  =3B  =3B  =3B  =3B  =3B  =3B=  =3B  =3B  =3B  =3B  =3B  =3B  =3B  =3B &n= bsp=3B  =3B  =3B  =3B *|

=0A=

|* =3B  =3B Anto= n Kokalj (tone.koka= lj at ijs.si) =3B  =3B  =3B  =3B  =3B  =3B  = =3B  =3B  =3B  =3B  =3B  =3B  =3B *|

=0A=

|* =3B  =3B Joze= f Stefan Institute=2C Ljubljana=2C Slovenia =3B  =3B  =3B  = =3B  =3B  =3B  =3B  =3B *|

=0A=

|*  =3B  =3B &nb= sp=3B  =3B  =3B  =3B  =3B  =3B  =3B  =3B  = =3B  =3B  =3B  =3B  =3B  =3B  =3B  =3B  =3B=  =3B  =3B  =3B  =3B  =3B  =3B  =3B  =3B &n= bsp=3B  =3B  =3B  =3B *|

=0A=

|* =3B  =3B Copy= right (c) 1996--2014 by Anton Kokalj  =3B  =3B  =3B  =3B &n= bsp=3B  =3B  =3B  =3B  =3B *|

=0A=

|*  =3B  =3B &nb= sp=3B  =3B  =3B  =3B  =3B  =3B  =3B  =3B  = =3B  =3B  =3B  =3B  =3B  =3B  =3B  =3B  =3B=  =3B  =3B  =3B  =3B  =3B  =3B  =3B  =3B &n= bsp=3B  =3B  =3B  =3B *|

=0A=

|***********************= ******************************************|

=0A=

+-----------------------= ------------------------------------------+

=0A=


=0A=

 =3B Version: 1.5.60=

=0A=


=0A=

 =3B Please report b= ugs to: tone.kokalj= @ijs.si

=0A=


=0A=


=0A=

 =3B TERMS OF USE:=0A=

 =3B -------------=0A=

 =3B XCRYSDEN is rel= eased under the GNU General Public License.

=0A=


=0A=

 =3B Whenever graphi= cs generated by XCRYSDEN are used in scientific

=0A=

 =3B publications=2C= it shall be greatly appreciated to include an explicit

=0A=

 =3B reference. The = preferred form is the following:

=0A=


=0A=

 =3B [ref] A. Kokalj= =2C J. Mol. Graph. Model.=2C Vol. 17=2C pp. 176-179=2C 1999.

=0A=

 =3B  =3B  = =3B  =3B Code available from http://www.xcrysden.org/.

=0A=


=0A=

XCRYSDEN_TOPDIR=3D/Users= /mirko/Desktop/xcrysden-1.5.60

=0A=

XCRYSDEN_SCRATCH=3D/var/= folders/g8/2m80kqls4m750q_phtmbmwxc0000gn/T/

=0A=


=0A=

./xcrysden: line 257: /U= sers/mirko/Desktop/xcrysden-1.5.60/bin/xcrys: No such file or directory

=


Can anybody help?

Thank you very much in advance.


Mirko

=0A=
_______________________________________________
=0A= XCrySDen mailing list
=0A= XCrySDen at democritos.it
=0A= http://www.democritos.it/mailman/listinfo/xcrysden
=0A=

=0A=
_______________________________________________=0A= XCrySDen mailing list=0A= XCrySDen at democritos.it=0A= http://www.democritos.it/mailman/listinfo/xcrysden
<= /div> = --_91149b7f-be5b-4617-ad41-13b03275e73d_-- From bogus@does.not.exist.com Mon Feb 2 10:44:46 2015 From: bogus@does.not.exist.com () Date: Mon, 02 Feb 2015 09:44:46 -0000 Subject: No subject Message-ID: *case.output1* file. So I tried renaming the case.output1_1 file from mpi outputs but the error persists. How shall I overcome this problem? Thanks, Fermin --001a1141ecb0fe179b051fd51a1e Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear developer= s and users,

I want to plot t= he 3D fermi surface using Xcrysden after the calculation in wien2k with mpi= parallelization. The following error occurs:
"=
ERROR: while executing exec ~/XCrySDen/bin/wn_readbakgen bakg=
en.def"
in more info it says "child killed. S=
egmentation violation"
From the mailing list, I learn=
t that Xcrysden only recognizes the case.output1 file. So I tried re=
naming the case.output1_1 file from mpi outputs but the error persists.
How shall I overcome this problem?
Thanks,
Fermin
--001a1141ecb0fe179b051fd51a1e-- From bogus@does.not.exist.com Mon Feb 2 10:44:46 2015 From: bogus@does.not.exist.com () Date: Mon, 02 Feb 2015 09:44:46 -0000 Subject: No subject Message-ID: and for some reason it wants to open a datagrid, but I really can't tell more without the input. Maybe try pwi2xsf.sh in the terminal by itself: pwi2xsf.sh in-Ti-OV and try to see if there are any errors in the xsf file it produces. Hope this helps, best regards, Matic Matic Poberznik J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia On 08/25/2016 07:27 AM, mohaddeseh abbasnejad wrote: > Dear users, > > It is about a few days I have faced a strange problem. > Actually, xcrysden is working for visualising all the input files of PWscf. > Unfortunately, after I updated one of the input files ( obtained from > the vc-relax calculations), it stops and give me such an error: > ERROR: an error occurred while trying to update a structure; Error > reading file /tmp/xc_3330/xc_struc.3330. > However, the PWscf is running well with the updated structure. > I used the following command: > > mohaddeseh at mohaddeseh-Vostro1310:~/Desktop$ xcrysden --pwi in-Ti-OV > > +-----------------------------------------------------------------+ > |*****************************************************************| > |* *| > |* XCrySDen -- (X-Window) CRYstalline Structures and DENsities *| > |* = === = === *| > |*---------------------------------------------------------------*| > |* *| > |* Anton Kokalj (tone.kokalj at ijs.si > ) *| > |* Jozef Stefan Institute, Ljubljana, Slovenia *| > |* *| > |* Copyright (c) 1996--2012 by Anton Kokalj *| > |* *| > |*****************************************************************| > +-----------------------------------------------------------------+ > > 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=/opt/exp_softs/tools/xcrysden-1.5.53/share/xcrysden-1.5.53 > XCRYSDEN_SCRATCH=/tmp > > Running on platform : unix > Operating system : Linux > Package ImageMagick's convert: /usr/bin/convert > Package ImageMagick's import: /usr/bin/import > Package Ppmtompeg: /usr/bin/ppmtompeg > Package Babel: /usr/bin/babel > Package Xwd: /usr/bin/xwd > Executing: /opt/exp_softs/tools/xcrysden-1.5.53/lib/xcrysden-1.5.53/ftnunit > TEXT-WIDGET: .a1.f1.t > Executing: sh > /opt/exp_softs/tools/xcrysden-1.5.53/share/xcrysden-1.5.53/scripts/pwi2xsf.sh > /home/mohaddeseh/Desktop/in-Ti-OV > reading PRIMCOORD > Number of Atoms: 0 > Number of Frames: 0 > Estimated number of bonds = 0 > sInfo(dim) = 3; periodic(dim) = 3 > Executing: > /opt/exp_softs/tools/xcrysden-1.5.53/lib/xcrysden-1.5.53/gengeom 0 1 11 > 1 1 1 1 xc_gengeom.3330 /tmp/xc_3330/pwi2xsf.xsf_out.raw > Executing: > /opt/exp_softs/tools/xcrysden-1.5.53/lib/xcrysden-1.5.53/gengeom 2 1 11 > 1 1 1 1 /tmp/xc_3330/xc_struc.3330 /tmp/xc_3330/pwi2xsf.xsf_out.raw > reading PRIMCOORD > reading CONVCOORD > "/tmp/xc_3330/xc_struc.3330" > Error in startup script: can't read "sInfo(ldatagrid2D)": no such variable > while executing > "if { $sInfo(ldatagrid2D) || $sInfo(ldatagrid3D) } { > $m.menu entryconfig "Data Grid" -state normal > } else { > $m.menu entryconfig "Data Grid" -stat..." > (procedure "Get_sInfoArray" line 13) > invoked from within > "Get_sInfoArray" > (procedure "xsfOpen" line 92) > invoked from within > "xsfOpen $program_output .mesa" > (procedure "openExtStruct" line 183) > 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(TOPDIR)/scripts/pwi2xsf.sh] pwi2xsf..." > (procedure "parseComLinArg" line 89) > invoked from within > "parseComLinArg [lrange $argv 2 end]" > invoked from within > "if { [llength $argv] > 2 } { > parseComLinArg [lrange $argv 2 end] > } else { > ViewMol . > }" > (file > "/opt/exp_softs/tools/xcrysden-1.5.53/share/xcrysden-1.5.53/Tcl/xcInit.tcl" > line 609) > > Any help would be appreciated. > Thanks in advance. > Regards, > Mohaddeseh > > > -- > --------------------------------------------------------- > > Mohaddeseh Abbasnejad, > Room No. 323, Department of Physics, > University of Tehran, North Karegar Ave., > Tehran, P.O. Box: 14395-547- IRAN > Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 > Cellphone: +98 917 731 7514 > E-Mail: m.abbasnejad at gmail.com > Website: http://physics.ut.ac.ir > > --------------------------------------------------------- > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > From bogus@does.not.exist.com Mon Feb 2 10:44:46 2015 From: bogus@does.not.exist.com () Date: Mon, 02 Feb 2015 09:44:46 -0000 Subject: No subject Message-ID: ,
and for some reason it wants to open a datagrid, but I really can't tel= l
more without the input.

Maybe try pwi2xsf.sh in the terminal by itself:

pwi2xsf.sh in-Ti-OV

and try to see if there are any errors in the xsf file it produces. Hope this helps,

best regards,

Matic

Matic Poberznik
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia

On 08/25/2016 07:27 AM, mohaddeseh abbasnejad wrote:
> Dear users,
>
> It is about a few days I have faced a strange problem.
> Actually, xcrysden is working for visualising all the input files of P= Wscf.
> Unfortunately, after I updated one of the input files ( obtained from<= br> > the vc-relax calculations), it stops and give me such an error:
> ERROR: an error occurred while trying to update a structure; Error
> reading file /tmp/xc_3330/xc_struc.3330.
> However, the PWscf is running well with the updated structure.
> I used the following command:
>
> mohaddeseh at mohaddeseh-Vostro1310:~/Desktop$ xcrysden --pwi in-Ti-= OV
>
> +-----------------------------------------------------------= ------+
> |***********************************************************= ******|
> |*=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0*|
> |*=C2=A0 XCrySDen -- (X-Window) CRYstalline Structures and DENsities= =C2=A0 *|
> |*=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=3D=C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0=3D=3D=3D=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=3D=C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =3D=3D=3D=C2=A0 =C2=A0 =C2=A0= =C2=A0 *|
> |*----------------------------------------------------------= -----*|
> |*=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0*|
> |*=C2=A0 =C2=A0 Anton Kokalj (to= ne.kokalj at ijs.si
> <mailto:tone.kokalj at ij= s.si>)=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A0 *|
> |*=C2=A0 =C2=A0 Jozef Stefan Institute, Ljubljana, Sl= ovenia=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 *|
> |*=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0*|
> |*=C2=A0 =C2=A0 Copyright (c) 1996--2012 by Anton Kokalj=C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0*|
> |*=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0*|
> |***********************************************************= ******|
> +-----------------------------------------------------------= ------+
>
>=C2=A0 =C2=A0Version: 1.5.53
>
>=C2=A0 =C2=A0Please report bugs to: tone.kokalj at ijs.si <mailto:tone.kokalj at ijs.si>
>
>
>=C2=A0 =C2=A0TERMS OF USE:
>=C2=A0 =C2=A0-------------
>=C2=A0 =C2=A0XCRYSDEN is released under the GNU General Public License.=
>
>=C2=A0 =C2=A0Whenever graphics generated by XCRYSDEN are used in scient= ific
>=C2=A0 =C2=A0publications, it shall be greatly appreciated to include a= n explicit
>=C2=A0 =C2=A0reference. The preferred form is the following:
>
>=C2=A0 =C2=A0[ref] A. Kokalj, Comp. Mater. Sci., Vol. 28, p. 155, 2003.=
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Code available from http://www.xcrysde= n.org/.
>
> XCRYSDEN_TOPDIR=3D/opt/exp_softs/tools/xcrysden-1.5.53/share= /xcrysden-1.5.53
> XCRYSDEN_SCRATCH=3D/tmp
>
> Running on platform : unix
>=C2=A0 =C2=A0 Operating system : Linux
> Package ImageMagick's convert: /usr/bin/convert
> Package ImageMagick's import: /usr/bin/import
> Package Ppmtompeg: /usr/bin/ppmtompeg
> Package Babel: /usr/bin/babel
> Package Xwd: /usr/bin/xwd
> Executing: /opt/exp_softs/tools/xcrysden-1.5.53/lib/xcrysden-1.5.= 53/ftnunit
> TEXT-WIDGET: .a1.f1.t
> Executing: sh
> /opt/exp_softs/tools/xcrysden-1.5.53/share/xcrysden-1.5.53/s= cripts/pwi2xsf.sh
> /home/mohaddeseh/Desktop/in-Ti-OV
> reading PRIMCOORD
> Number of Atoms:=C2=A0 0
> Number of Frames: 0
> Estimated number of bonds =3D 0
> sInfo(dim) =3D 3; periodic(dim) =3D 3
> Executing:
> /opt/exp_softs/tools/xcrysden-1.5.53/lib/xcrysden-1.5.53/gen= geom 0 1 11
> 1 1 1 1 xc_gengeom.3330 /tmp/xc_3330/pwi2xsf.xsf_out.raw
> Executing:
> /opt/exp_softs/tools/xcrysden-1.5.53/lib/xcrysden-1.5.53/gen= geom 2 1 11
> 1 1 1 1 /tmp/xc_3330/xc_struc.3330 /tmp/xc_3330/pwi2xsf.xsf_out.r= aw
> reading PRIMCOORD
> reading CONVCOORD
> "/tmp/xc_3330/xc_struc.3330"
> Error in startup script: can't read "sInfo(ldatagrid2D)"= : no such variable
>=C2=A0 =C2=A0 =C2=A0while executing
> "if { $sInfo(ldatagrid2D) || $sInfo(ldatagrid3D) } {
>=C2=A0 =C2=A0 =C2=A0$m.menu entryconfig "Data Grid" -state no= rmal
>=C2=A0 =C2=A0 =C2=A0} else {
>=C2=A0 =C2=A0 =C2=A0$m.menu entryconfig "Data Grid" -stat...&= quot;
>=C2=A0 =C2=A0 =C2=A0(procedure "Get_sInfoArray" line 13)
>=C2=A0 =C2=A0 =C2=A0invoked from within
> "Get_sInfoArray"
>=C2=A0 =C2=A0 =C2=A0(procedure "xsfOpen" line 92)
>=C2=A0 =C2=A0 =C2=A0invoked from within
> "xsfOpen $program_output .mesa"
>=C2=A0 =C2=A0 =C2=A0(procedure "openExtStruct" line 183)
>=C2=A0 =C2=A0 =C2=A0invoked from within
> "openExtStruct 3 crystal external=C2=A0 [list sh
> $system(TOPDIR)/scripts/pwi2xsf.sh]=C2=A0 pwi2xsf.xsf_out=C2=A0 {= PWSCF Input File}
> ANGS=C2=A0 -file $filedir=C2=A0 -preset pwIn..."
>=C2=A0 =C2=A0 =C2=A0invoked from within
> "if [file exists $filedir] {
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0# pop-up Viewer
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0ViewMol .
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0openExtStruct 3 crystal= external=C2=A0 [list sh
> $system(TOPDIR)/scripts/pwi2xsf.sh]=C2=A0 pwi2xsf..."
>=C2=A0 =C2=A0 =C2=A0(procedure "parseComLinArg" line 89)
>=C2=A0 =C2=A0 =C2=A0invoked from within
> "parseComLinArg [lrange $argv 2 end]"
>=C2=A0 =C2=A0 =C2=A0invoked from within
> "if { [llength $argv] > 2 } {
>=C2=A0 =C2=A0 =C2=A0parseComLinArg [lrange $argv 2 end]
> } else {
>=C2=A0 =C2=A0 =C2=A0ViewMol .
> }"
>=C2=A0 =C2=A0 =C2=A0(file
> "/opt/exp_softs/tools/xcrysden-1.5.53/share/xcrysden-1.= 5.53/Tcl/xcInit.tcl"
> line 609)
>
> Any help would be appreciated.
> Thanks in advance.
> Regards,
> Mohaddeseh
>
>
> --
> ---------------------------------------------------------
>
> Mohaddeseh Abbasnejad,
> Room No. 323, Department of Physics,
> University of Tehran, North Karegar Ave.,
> Tehran, P.O. Box: 14395-547- IRAN
> Tel. No.: +98 21 6111 8634=C2=A0 & Fax No.: +98 21 8800 4781
> Cellphone: +98 917 731 7514
> E-Mail:=C2=A0 =C2=A0 =C2=A0m.abbasnejad at gmail.com <mailto:m.abbasnejad at gmail.com>
> Website:=C2=A0 http://physics.ut.ac.ir
>
> ---------------------------------------------------------
>
>
> _______________________________________________
> XCrySDen mailing list
> XCrySDen at democritos.it > http://www.democritos.it/mailman/listinf= o/xcrysden
>
_______________________________________________
XCrySDen mailing list
XCrySDen at democritos.it
http://www.democritos.it/mailman/listinfo/xcr= ysden



--
--------------------------------= -------------------------

Mohaddeseh Abbasnejad,
Room No. 323, D= epartment of Physics,
University of Tehran, North Karegar Ave.,
Tehr= an, P.O. Box: 14395-547- IRAN
Tel. No.: +98 21 6111 8634=C2=A0 & Fa= x No.: +98 21 8800 4781
Cellphone: +98 917 731 7514
E-Mail:=C2=A0 =C2= =A0=C2=A0 m.abb= asnejad at gmail.com
Website:=C2=A0 http://physics.ut.ac.ir

---------------------= ------------------------------------
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