From devan.umd at gmail.com  Wed Apr  3 03:37:14 2013
From: devan.umd at gmail.com (dev pe)
Date: Tue, 2 Apr 2013 21:37:14 -0400
Subject: [xcrysden] Error while opening PWscf output file
Message-ID: <CAG1HzpFknk+5hVq_2PPZ=RVV-xgMZsPo4p26+7fK5Eg=MEXdzQ@mail.gmail.com>

Dear XCrySDen users

I have concatenated many PWscf output files from a MD run. I am trying to
open the final file using Xcrysden 1.5.25-semishared. But I keep getting
the following error message:

ERROR: while executing exec
/home/user/XCrysden-1.5.25-bin-semishared/bin/gengeom 0 1111111
xcgengeom.10789
/home/user/xcrys_tmp/xc_10789/pwo2xsf.xsf.raw

I have fixed some ions during my MD run by specifying 0 against their
atomic location in the ATOMIC POSITIONS card in my PW input. They appear in
the output file too. Does Xcrysden ignore those 0's while reading the PW
output file?

Please let me know about the issue.
Any help is appreciated.

Thanks
Dev
PhD student
UMCP
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From tone.kokalj at ijs.si  Thu Apr  4 16:36:22 2013
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Thu, 04 Apr 2013 16:36:22 +0200
Subject: [xcrysden] Error while opening PWscf output file
In-Reply-To: <CAG1HzpFknk+5hVq_2PPZ=RVV-xgMZsPo4p26+7fK5Eg=MEXdzQ@mail.gmail.com>
References: <CAG1HzpFknk+5hVq_2PPZ=RVV-xgMZsPo4p26+7fK5Eg=MEXdzQ@mail.gmail.com>
Message-ID: <1365086182.25021.11.camel@catalyst.ijs.si>

On Tue, 2013-04-02 at 21:37 -0400, dev pe wrote:

> I have concatenated many PWscf output files from a MD run. I am trying
> to open the final file using Xcrysden 1.5.25-semishared. But I keep
> getting the following error message:
> 
> 
> ERROR: while executing
> exec /home/user/XCrysden-1.5.25-bin-semishared/bin/gengeom 0 1111111
> xcgengeom.10789
> /home/user/xcrys_tmp/xc_10789/pwo2xsf.xsf.raw

The problem is likely that in the pw-output to XSF conversion, the
number of animation-steps is wrongly assigned; 

Try a manual conversion, i.e.:

pwo2xsf.sh -a concatenated-pw-output-file > test.axsf

check that the ANIMSTEPS's number and the number of PRIMCOORD sections
in the axsf file matches (e.g., to facilitate the check you may grep the
PRIMCOORD and ANIMSTEPS keywords from the file). If you cannot fix the
problem, send me either the axsf or the pw-output-file.

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 devan.umd at gmail.com  Sat Apr  6 06:01:50 2013
From: devan.umd at gmail.com (dev pe)
Date: Sat, 6 Apr 2013 00:01:50 -0400
Subject: [xcrysden] XCrySDen Digest, Vol 63, Issue 2
In-Reply-To: <mailman.3.1365150547.14706.xcrysden@democritos.it>
References: <mailman.3.1365150547.14706.xcrysden@democritos.it>
Message-ID: <CAG1HzpE4aUYyCSLChtw54njKF3otK_NBy_NNfmMwSFo=XLEFtQ@mail.gmail.com>

Dear Dr. Anton Kokalj

Thank you for the reply.
I fixed the problem. For some reason, all the elements of my PRIMVEC matrix
was zero. When I manually assigned the values, it worked.
Thanks for the help.

Dev
PhD student
UMCP


On Fri, Apr 5, 2013 at 4:29 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. Re: Error while opening PWscf output file (Tone Kokalj)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 04 Apr 2013 16:36:22 +0200
> From: Tone Kokalj <tone.kokalj at ijs.si>
> Subject: Re: [xcrysden] Error while opening PWscf output file
> To: xcrysden at democritos.it
> Message-ID: <1365086182.25021.11.camel at catalyst.ijs.si>
> Content-Type: text/plain; charset="UTF-8"
>
> On Tue, 2013-04-02 at 21:37 -0400, dev pe wrote:
>
> > I have concatenated many PWscf output files from a MD run. I am trying
> > to open the final file using Xcrysden 1.5.25-semishared. But I keep
> > getting the following error message:
> >
> >
> > ERROR: while executing
> > exec /home/user/XCrysden-1.5.25-bin-semishared/bin/gengeom 0 1111111
> > xcgengeom.10789
> > /home/user/xcrys_tmp/xc_10789/pwo2xsf.xsf.raw
>
> The problem is likely that in the pw-output to XSF conversion, the
> number of animation-steps is wrongly assigned;
>
> Try a manual conversion, i.e.:
>
> pwo2xsf.sh -a concatenated-pw-output-file > test.axsf
>
> check that the ANIMSTEPS's number and the number of PRIMCOORD sections
> in the axsf file matches (e.g., to facilitate the check you may grep the
> PRIMCOORD and ANIMSTEPS keywords from the file). If you cannot fix the
> problem, send me either the axsf or the pw-output-file.
>
> 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
>
>
> End of XCrySDen Digest, Vol 63, Issue 2
> ***************************************
>
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From vjain045 at gmail.com  Sat Apr 13 07:13:39 2013
From: vjain045 at gmail.com (vishal jain)
Date: Sat, 13 Apr 2013 10:43:39 +0530
Subject: [xcrysden] Regarding Installation
Message-ID: <CAJsJeWTWkQp_m3zWNXh42X4VtDNbtJECJvF3JRpcMDK2AQrMrg@mail.gmail.com>

Good Morning Sir


I try to install XCRYSDEN in my intel Core 2 Duo OS Ubuntu 12.04
during compiling i get these errors

#------------------------------#
#                              #
#   Compiling XCRYSDEN C-code  #
#                              #
#------------------------------#

cd C; make "TOPDIR=/home/nrl/XCrySDen-1.5.24-src-all" compile
make[1]: Entering directory `/home/nrl/XCrySDen-1.5.24-src-all/C'
make  TOPDIR=/home/nrl/XCrySDen-1.5.24-src-all
make[2]: Entering directory `/home/nrl/XCrySDen-1.5.24-src-all/C'
gcc -ansi -funroll-loops -fPIC -DUSE_FONTS   -DUSE_FONTS
-I/home/nrl/XCrySDen-1.5.24-src-all/external/src/tcl8.5.9/generic
-I/home/nrl/XCrySDen-1.5.24-src-all/external/src/tk8.5.9/generic
-I/home/nrl/XCrySDen-1.5.24-src-all/external/include  -I/usr/X11R6/include
-c fft3d.c
fft3d.c:4:19: fatal error: fftw3.h: No such file or directory
compilation terminated.
make[2]: *** [fft3d.o] Error 1
make[2]: Leaving directory `/home/nrl/XCrySDen-1.5.24-src-all/C'
make[1]: *** [compile] Error 2
make[1]: Leaving directory `/home/nrl/XCrySDen-1.5.24-src-all/C'
make: *** [src-C] Error 2
nrl at nrl-Vostro-220s-Series:~/XCrySDen-1.5.24-src-all$
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From vjain045 at gmail.com  Sat Apr 13 11:21:50 2013
From: vjain045 at gmail.com (vishal jain)
Date: Sat, 13 Apr 2013 14:51:50 +0530
Subject: [xcrysden] Error in xcrysdens installation
Message-ID: <CAJsJeWS7aXv9NxpU_ZDuVHrs4Ur-KAaFELx288FiQvxULuDksA@mail.gmail.com>

fft3d.c:4:19: fatal error: fftw3.h: No such file or directory
compilation terminated.
make[2]: *** [fft3d.o] Error 1
make[2]: Leaving directory `/home/nrl/XCrySDen-1.5.24-src-all/C'
make[1]: *** [compile] Error 2
make[1]: Leaving directory `/home/nrl/XCrySDen-1.5.24-src-all/C'
make: *** [src-C] Error 2
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From pandey.bramha at gmail.com  Sat Apr 13 11:44:40 2013
From: pandey.bramha at gmail.com (Bramha Pandey)
Date: Sat, 13 Apr 2013 15:29:40 +0545
Subject: [xcrysden] Error in xcrysdens installation
In-Reply-To: <CAJsJeWS7aXv9NxpU_ZDuVHrs4Ur-KAaFELx288FiQvxULuDksA@mail.gmail.com>
References: <CAJsJeWS7aXv9NxpU_ZDuVHrs4Ur-KAaFELx288FiQvxULuDksA@mail.gmail.com>
Message-ID: <CAC2dNGG3VLzho6jDZU-YOh9nuOAtLkJsjPSXxE4iSfXvfKTcvA@mail.gmail.com>

Dear Vishal, As error messages told you what it required to run it properly.
So from symapatic pakages you have to installed the fft3d files and then
again start from begining.
Surely it will run if you feed him required meals :D


On Sat, Apr 13, 2013 at 3:06 PM, vishal jain <vjain045 at gmail.com> wrote:

> fft3d.c:4:19: fatal error: fftw3.h: No such file or directory
> compilation terminated.
> make[2]: *** [fft3d.o] Error 1
> make[2]: Leaving directory `/home/nrl/XCrySDen-1.5.24-src-all/C'
> make[1]: *** [compile] Error 2
> make[1]: Leaving directory `/home/nrl/XCrySDen-1.5.24-src-all/C'
> make: *** [src-C] Error 2
>
>
> _______________________________________________
> XCrySDen mailing list
> XCrySDen at democritos.it
> http://www.democritos.it/mailman/listinfo/xcrysden
>
>


-- 
Thanks and Regards
Bramha Prasad Pandey
Indian School of Mines(ISM)
Dhanbad, INDIA.
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From vjain045 at gmail.com  Sat Apr 13 13:55:29 2013
From: vjain045 at gmail.com (vishal jain)
Date: Sat, 13 Apr 2013 17:25:29 +0530
Subject: [xcrysden] Installation problem XcrySDen in Ubuntu 12.04
Message-ID: <CAJsJeWQ-jNzJjEiPhWzJ3adq2Lx=dMTLdczydXpRPcke+ArJFg@mail.gmail.com>

Dear sir

I downloaded xcrysden.deb file and try to install using ubuntu software
centre but its showing icon on desktop but cant open
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From pandey.bramha at gmail.com  Sat Apr 13 14:04:11 2013
From: pandey.bramha at gmail.com (Bramha Pandey)
Date: Sat, 13 Apr 2013 17:49:11 +0545
Subject: [xcrysden] Installation problem XcrySDen in Ubuntu 12.04
In-Reply-To: <CAJsJeWQ-jNzJjEiPhWzJ3adq2Lx=dMTLdczydXpRPcke+ArJFg@mail.gmail.com>
References: <CAJsJeWQ-jNzJjEiPhWzJ3adq2Lx=dMTLdczydXpRPcke+ArJFg@mail.gmail.com>
Message-ID: <CAC2dNGGWXwwzsR3W6q2DxgzwsWUT3XtFmkexcqsXba1MSP549Q@mail.gmail.com>

Here a link and do what the instruction are given in that for ubuntu
platform.
http://conquer-ur-computer.blogspot.in/2010/12/install-quantum-espresso-in-ubuntu.html


On Sat, Apr 13, 2013 at 5:40 PM, vishal jain <vjain045 at gmail.com> wrote:

> Dear sir
>
> I downloaded xcrysden.deb file and try to install using ubuntu software
> centre but its showing icon on desktop but cant open
>
> _______________________________________________
> XCrySDen mailing list
> XCrySDen at democritos.it
> http://www.democritos.it/mailman/listinfo/xcrysden
>
>


-- 
Thanks and Regards
Bramha Prasad Pandey
Indian School of Mines(ISM)
Dhanbad, INDIA.
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From pandey.bramha at gmail.com  Sat Apr 13 14:08:57 2013
From: pandey.bramha at gmail.com (Bramha Pandey)
Date: Sat, 13 Apr 2013 17:53:57 +0545
Subject: [xcrysden] Installation problem XcrySDen in Ubuntu 12.04
In-Reply-To: <CAC2dNGGWXwwzsR3W6q2DxgzwsWUT3XtFmkexcqsXba1MSP549Q@mail.gmail.com>
References: <CAJsJeWQ-jNzJjEiPhWzJ3adq2Lx=dMTLdczydXpRPcke+ArJFg@mail.gmail.com>
	<CAC2dNGGWXwwzsR3W6q2DxgzwsWUT3XtFmkexcqsXba1MSP549Q@mail.gmail.com>
Message-ID: <CAC2dNGH8ME=w+j+x1a-teQPh+ksY==rP6X=Bb8zfRA6=FxR-iQ@mail.gmail.com>

Sorry above link is not what you required here correct one is given ..
http://conquer-ur-computer.blogspot.in/2010/12/how-to-install-xcrysden-in-ubuntu-linux.html


On Sat, Apr 13, 2013 at 5:49 PM, Bramha Pandey <pandey.bramha at gmail.com>wrote:

> Here a link and do what the instruction are given in that for ubuntu
> platform.
>
> http://conquer-ur-computer.blogspot.in/2010/12/install-quantum-espresso-in-ubuntu.html
>
>
> On Sat, Apr 13, 2013 at 5:40 PM, vishal jain <vjain045 at gmail.com> wrote:
>
>> Dear sir
>>
>> I downloaded xcrysden.deb file and try to install using ubuntu software
>> centre but its showing icon on desktop but cant open
>>
>> _______________________________________________
>> XCrySDen mailing list
>> XCrySDen at democritos.it
>> http://www.democritos.it/mailman/listinfo/xcrysden
>>
>>
>
>
> --
> Thanks and Regards
> Bramha Prasad Pandey
> Indian School of Mines(ISM)
> Dhanbad, INDIA.
>



-- 
Thanks and Regards
Bramha Prasad Pandey
Indian School of Mines(ISM)
Dhanbad, INDIA.
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From tone.kokalj at ijs.si  Tue Apr 16 16:08:34 2013
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Tue, 16 Apr 2013 16:08:34 +0200
Subject: [xcrysden] Regarding Installation
In-Reply-To: <CAJsJeWTWkQp_m3zWNXh42X4VtDNbtJECJvF3JRpcMDK2AQrMrg@mail.gmail.com>
References: <CAJsJeWTWkQp_m3zWNXh42X4VtDNbtJECJvF3JRpcMDK2AQrMrg@mail.gmail.com>
Message-ID: <1366121314.9778.20.camel@catalyst.ijs.si>

On Sat, 2013-04-13 at 10:43 +0530, vishal jain wrote:1

> 
> I try to install XCRYSDEN in my intel Core 2 Duo OS Ubuntu 12.04 
> cd C; make "TOPDIR=/home/nrl/XCrySDen-1.5.24-src-all" compile

Please, use the newer xcrysden version, i.e.:

http://www.xcrysden.org/download/xcrysden-1.5.53.tar.gz


> -I/usr/X11R6/include  -c fft3d.c
> fft3d.c:4:19: fatal error: fftw3.h: No such file or directory

The 1.5.53 version will automatically download the needed software from
the internet (including the FFTW).

An even easier option is to use the pre-compiled package. If you are
using 32bit Ubuntu, download this:

http://www.xcrysden.org/download/xc-1.5.24-linux_x86-semishared.tar.gz

for 64bit you may try this instead:

http://www.xcrysden.org/download/xcrysden-1.5.53-linux_x86_64-semishared.tar.gz

Please also sign you posts with your 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  Tue Apr 16 16:09:43 2013
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Tue, 16 Apr 2013 16:09:43 +0200
Subject: [xcrysden] Installation problem XcrySDen in Ubuntu 12.04
In-Reply-To: <CAJsJeWQ-jNzJjEiPhWzJ3adq2Lx=dMTLdczydXpRPcke+ArJFg@mail.gmail.com>
References: <CAJsJeWQ-jNzJjEiPhWzJ3adq2Lx=dMTLdczydXpRPcke+ArJFg@mail.gmail.com>
Message-ID: <1366121383.9778.21.camel@catalyst.ijs.si>

On Sat, 2013-04-13 at 17:25 +0530, vishal jain wrote:
> Dear sir 
> 
> 
> I downloaded xcrysden.deb file and try to install using ubuntu
> software centre but its showing icon on desktop but cant open

Instead of clicking the icon, try to launch xcrysden from the terminal.
This way, you may see why it fails, because likely some error message
will be printed.

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 hgotsis67 at yahoo.com  Wed Apr 17 20:42:29 2013
From: hgotsis67 at yahoo.com (Harry Gotsis)
Date: Wed, 17 Apr 2013 11:42:29 -0700 (PDT)
Subject: [xcrysden] Error on viewing structure
Message-ID: <1366224149.25206.YahooMailNeo@web164004.mail.gq1.yahoo.com>

Dear All;

I'm trying to verify the geometry of a CRYSTAL09 input file (see
attached file) using XCrySDen. However, when I click the 'View Slab'
button on the Open Crystal Input window, I get an ERROR with the
following ErrorInfo:

At line 611 of file gengeom.f (unit = 34, file = 'fort.34')
Fortran runtime error: Bad integer for item 1 in list input

Thank you, looking forward to your answer at your earliest convenience.

Best Regards,
Harry Gotsis
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From max_bert at web.de  Thu Apr 18 18:43:29 2013
From: max_bert at web.de (Max Bert)
Date: Thu, 18 Apr 2013 18:43:29 +0200 (CEST)
Subject: [xcrysden] plot automatically DataGrid
Message-ID: <trinity-255dd4a2-8cda-46af-99c8-bcd6b77a0de3-1366303409469@3capp-webde-bs43>

Hello,

I'm working on a xcrysden script which can plot any sufficient isosurface of a molecular wavefunction, organized in a *.xsf-file as one DATAGRID_3D_orbital. Therefore I followed roughly http://www.xcrysden.org/doc/prog/plot_all_MO.sh.html, which does the job for two fixed wavefunctions. The general problem I encountered is that the minmum, maximum as well as the rangevalue for the isosurface-plot are varying quite a lot for different wavefunctions. Therefore numerical values are not sufficient. The onliest hint I encountered was given by Tone Kokalj in http://qe-forge.org/pipermail/pw_forum/2005-June/077156.html. However still the lines appended, are not working as expected. One problem arises from the fact that tcl/tk doesn't interpret the variables as numerical values, if the listing is done with {}-brakets, i.e.
"
array set isoControl {1,curr...}
".
But with the change to quotation marks for the listing (then variables are interpreted correctly right away), I get the following error code, which I was unable to figure out:

"
...
Estimated number of bonds = 208
Estimated number of bonds = 208
Estimated number of bonds = 208
------------------------------> ColorSchemeUpdate
coordinate system orientation is left
Error in startup script: list must have an even number of elements
    while executing
"array set isosurf "type_of_isosurf solid 3Dinterpl_degree 1 isovalue_entry .iso.fb1.f.left.f1.f3.1.entry1 1,2Dexpand_X 1 transparency off rangevalue  ..."
    (file "/home/birnbaum/hiwi/xcrys-script/xcrysden.script" line 541)
    invoked from within
"source [gunzipFile $scriptFile]"
    ("uplevel" body line 4)
    invoked from within
"uplevel \#0 {	
	cd $system(PWD)
	SetWatchCursor
	source [gunzipFile $scriptFile]
	ResetCursor
    }"
    (procedure "scripting::source" line 7)
    invoked from within
"scripting::source $filedir		    "
    (procedure "parseComLinArg" line 247)
    invoked from within
"parseComLinArg [lrange $argv 2 end]"
    invoked from within
"if { [llength $argv] > 2 } {
    parseComLinArg [lrange $argv 2 end]
} else {
    ViewMol .
}"
    (file "/usr/local/share/xcrysden-1.5.53/Tcl/xcInit.tcl" line 615)
"

Is there anyone who can help me out with an idea about that?

Greetings Max

APPENDIX:
"
DataGridOK
set minvalue [xc_iso minvalue]
set maxvalue [xc_iso maxvalue]
puts "min: $minvalue"
puts "max: $maxvalue"
set rangevalue [expr [xc_iso maxvalue] - [xc_iso minvalue]]

array set isoControl "1,current_slide 1 isoline_color monocolor datagridDim 3 3,cpl_thermoFont font17 1,cpl_thermoNTics 6 3,time_delay 100 2,cpl_thermoNTics 6 3,cpl_thermoNTics 6 3,2Dnisoline 15 cpl_thermoNTics 6 3,anim_step 1 3,cpl_basis MONOCHROME 1,isoline_monocolor #000000 1,isoline_width 2 2,cpl_thermoFont font17 3,cpl_thermoFmt %+8.4f 2,2Dlowvalue [xc_iso minvalue] 2,current_text_slide {Current slide:  1 / 89} 1,cpl_transparency 0 3,colorplane 0 blend_button .iso.fb1.f.right.f5.b3 3,isoline_color monocolor cbfn_apply_to_all 0 1,cpl_thermoFont font17 2,cpl_function LINEAR 1,time_delay 100 current_slide 1 revert_button1 .iso.fb1.f.right.f5.b12 1,2Dnisoline 15 revert_button2 .iso.fb1.f.right.f5.b10a 2Dlowvalue_entry .iso.fb2.f1.1.mf.r.f3.1.entry1 2,cpl_transparency 0 2Dnisoline_entry .iso.fb2.f1.1.mf.r.f5.1.entry1 2,isoline_monocolor #000000 1,2Dhighvalue [xc_iso maxvalue] cpl_basis MONOCHROME anim_step 1 1,isoline 0 2,isoline 0 3,2Dhighvalue [xc_iso maxvalue] 3,isoline 0 2,cpl_thermoFmt %+8.4f 2,colorplane_lighting 0 isoline_width 2 1,cpl_thermoLabel { Scale:   ? n(r)} 2,cpl_thermoLabel { Scale:   ? n(r)} isoline 0 3,cpl_thermoLabel { Scale:   ? n(r)} colorplane_lighting 0 cpl_thermoTplw 0 1,colorplane 0 cpl_thermoLabel { Scale:   ? n(r)} time_delay 100 3,cpl_transparency 0 2,isoline_color monocolor 2Dnisoline 15 3,current_slide 1 3,cpl_thermoTplw 0 max_allowed_2Dnisoline 100 3,2Dlowvalue [xc_iso minvalue] cpl_function LINEAR anim_apply_to_all 0 1,anim_step 1 1,cpl_basis MONOCHROME 3,current_text_slide {Current slide:  1 / 41} 3,nslide 41 colorplane 0 cpl_transparency 0 3,isoline_monocolor #000000 3,isoline_width 2 1,cpl_function LINEAR 1,cpl_thermoFmt %+8.4f 2Disolinewidth_entry .iso.fb2.f1.1.mf.i.3.f1.1.entry1 2,cpl_thermoTplw 0 2,time_delay 100 smooth_button .iso.fb1.f.right.f5.b2a 2,2Dnisoline 15 2,nslide 89 1,isoline_color monocolor disp_apply_to_all 0 plane {} 1,isoline_stipple {no stipple} 3Dinterpl_degree 1 2,isoline_stipple {no stipple} 2,current_slide 1 1,cpl_thermoTplw 0 3,isoline_stipple {no stipple} 1,2Dlowvalue [xc_iso minvalue] isoline_stipple {no stipple} 2Dhighvalue_entry .iso.fb2.f1.1.mf.r.f4.1.entry1 1,current_text_slide {Current slide:  1 / 93} 1,nslide 93 2,colorplane 0 2,anim_step 1 2,cpl_basis MONOCHROME 1,cpl_thermometer 0 2,isoline_width 2 2,cpl_thermometer 0 3,cpl_thermometer 0 2,2Dhighvalue [xc_iso maxvalue] 1,colorplane_lighting 0 bmc .iso.fb2.f1.1.mf.i.1.b color_button .iso.fb1.f.right.f5.b2 cpl_thermometer 0 isoline_monocolor #000000 isosurf 1 3,colorplane_lighting 0 3,cpl_function LINEAR 2Dhighvalue [xc_iso maxvalue] cpl_thermoFmt %+8.4f cpl_thermoFont font17 2Dlowvalue [xc_iso minvalue] current_text_slide {}"
array set prop {datagridDim 0 type_of_run RHF pm_isolevel 1 isolevel 0.2}
array set isosurf "type_of_isosurf solid 3Dinterpl_degree 1 isovalue_entry .iso.fb1.f.left.f1.f3.1.entry1 1,2Dexpand_X 1 transparency off rangevalue $rangevalue 1,2Dexpand_Y 1 1,2Dexpand none res_type angstroms 3,2Dexpand_X 1 1,2Dexpand_Z 1 twoside_lighting off 3,2Dexpand_Y 1 3,2Dexpand none 3,2Dexpand_Z 1 3Dinterpl_degree_old 1 space_sel whole_cell expand_X 1 tessellation_type cubes expand_Y 1 expand none expand_Z 1 minvalue [xc_iso minvalue] mb_angs/bohr Angstroms old_twoside_lighting off spin {} 2,2Dexpand_X 1 maxvalue [xc_iso maxvalue] 2,2Dexpand_Y 1 2,2Dexpand none Y_Sel centered 2,2Dexpand_Z 1 2Dexpand_X 1 normals_type gradient shade_model smooth Z_Sel centered 2Dexpand_Y 1 2Dexpand none 2Dexpand_Z 1"
"

From jxzhu at lanl.gov  Tue Apr 23 21:47:05 2013
From: jxzhu at lanl.gov (Zhu, Jianxin)
Date: Tue, 23 Apr 2013 19:47:05 +0000
Subject: [xcrysden] Xcrysden 1.5.53
In-Reply-To: <1358528326.3779.52.camel@catalyst.ijs.si>
Message-ID: <CD9C3FC4.1D367%jxzhu@lanl.gov>

Dear Tone and Xcrysden users,

I installed Xcrysden 1.5.53 on my linux box.
For some unknown reason, the generated k-path in "Open WIEN2k" for fcc
structure does not give me right band structure.
I can exclude all other possibilities in the bandstructure software itself
--- By replacing the k-path with the one generated from 1.5.24 on my mac
machine, the band structure comes up correctly.  I will do more tests by
also using 1.5.53 installed on my other Mac OSX machine.

Have you noticed this kind of problem?   Or does it mean I installed
Xcrysden 1.5.53 incorrectly on my linux box?

Thank you in advance for the help.

Best regards,

Jianxin



From tone.kokalj at ijs.si  Wed Apr 24 17:03:27 2013
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Wed, 24 Apr 2013 17:03:27 +0200
Subject: [xcrysden] Error on viewing structure
In-Reply-To: <1366224149.25206.YahooMailNeo@web164004.mail.gq1.yahoo.com>
References: <1366224149.25206.YahooMailNeo@web164004.mail.gq1.yahoo.com>
Message-ID: <1366815807.29834.2.camel@catalyst.ijs.si>

On Wed, 2013-04-17 at 11:42 -0700, Harry Gotsis wrote:
> Dear All;
> 
> I'm trying to verify the geometry of a CRYSTAL09 input file (see
> attached file) using XCrySDen. However, when I click the 'View Slab'
> button on the Open Crystal Input window, I get an ERROR with the
> following ErrorInfo:
> 
> At line 611 of file gengeom.f (unit = 34, file = 'fort.34')
> Fortran runtime error: Bad integer for item 1 in list input

I have no problem viewing your crystal input; works smoothly for me.
Are you able to see any CRYSTAL input file at all?

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  Wed Apr 24 17:06:16 2013
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Wed, 24 Apr 2013 17:06:16 +0200
Subject: [xcrysden] plot automatically DataGrid
In-Reply-To: <trinity-255dd4a2-8cda-46af-99c8-bcd6b77a0de3-1366303409469@3capp-webde-bs43>
References: <trinity-255dd4a2-8cda-46af-99c8-bcd6b77a0de3-1366303409469@3capp-webde-bs43>
Message-ID: <1366815976.29834.4.camel@catalyst.ijs.si>

On Thu, 2013-04-18 at 18:43 +0200, Max Bert wrote:
> Hello,
> 
> I'm working on a xcrysden script which can plot any sufficient isosurface of a molecular wavefunction, organized in a *.xsf-file as one DATAGRID_3D_orbital. Therefore I followed roughly http://www.xcrysden.org/doc/prog/plot_all_MO.sh.html, which does the job for two fixed wavefunctions. The general problem I encountered is that the minmum, maximum as well as the rangevalue for the isosurface-plot are varying quite a lot for different wavefunctions. Therefore numerical values are not sufficient. The onliest hint I encountered was given by Tone Kokalj in http://qe-forge.org/pipermail/pw_forum/2005-June/077156.html. However still the lines appended, are not working as expected. One problem arises from the fact that tcl/tk doesn't interpret the variables as numerical values, if the listing is done with {}-brakets, i.e.
> "
> array set isoControl {1,curr...}
> ".
> But with the change to quotation marks for the listing (then variables are interpreted correctly right away), I get the following error code, which I was unable to figure out:


Please send the whole script by email. Only then there is some change of
detecting the problem.

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 tone.kokalj at ijs.si  Wed Apr 24 17:07:49 2013
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Wed, 24 Apr 2013 17:07:49 +0200
Subject: [xcrysden] Xcrysden 1.5.53
In-Reply-To: <CD9C3FC4.1D367%jxzhu@lanl.gov>
References: <CD9C3FC4.1D367%jxzhu@lanl.gov>
Message-ID: <1366816069.29834.5.camel@catalyst.ijs.si>

On Tue, 2013-04-23 at 19:47 +0000, Zhu, Jianxin wrote:
> Dear Tone and Xcrysden users,
> 
> I installed Xcrysden 1.5.53 on my linux box.
> For some unknown reason, the generated k-path in "Open WIEN2k" for fcc
> structure does not give me right band structure.
> I can exclude all other possibilities in the bandstructure software itself
> --- By replacing the k-path with the one generated from 1.5.24 on my mac
> machine, the band structure comes up correctly.  I will do more tests by
> also using 1.5.53 installed on my other Mac OSX machine.

Have you compared the k-point coordinates between the two versions?
Do they differ?

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 jxzhu at lanl.gov  Wed Apr 24 17:34:23 2013
From: jxzhu at lanl.gov (Zhu, Jianxin)
Date: Wed, 24 Apr 2013 15:34:23 +0000
Subject: [xcrysden] Xcrysden 1.5.53
In-Reply-To: <1366816069.29834.5.camel@catalyst.ijs.si>
Message-ID: <CD9D5609.1D3D5%jxzhu@lanl.gov>

Hi Tone, 

I figured out the problem. The issue is not due to version 1.5.53 versus
1.5.24. 
I tested with the version 1.5.53 on my macbook, the generated k-path is
correct. 
The problem lies in that the version 1.5.53 on my linux box sets the value
of M (M*kx,M*ky,M*kz) to be 1 (rather than values like 4 for fcc Gamma -->
L --> W --> X --> Gamma as appropriately given on my macbook), which
causes the error. For this, I have manually correct M to be 4 and those
values of (M*kx,M*ky,M*kz) and then the generated k-path is identical to
those on my Mac OSX machines.

But I don't know why M is set to be 1 on my linux machine.

Regards, 

Jianxin 




-----Original Message-----
From: Tone Kokalj <tone.kokalj at ijs.si>
Organization: J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
(tel: +386-1-477-3523 // fax:+386-1-477-3822)
Reply-To: <tone.kokalj at ijs.si>, XCrySDen mailing list
<xcrysden at democritos.it>
Date: Wed, 24 Apr 2013 17:07:49 +0200
To: <xcrysden at democritos.it>
Subject: Re: [xcrysden] Xcrysden 1.5.53

>On Tue, 2013-04-23 at 19:47 +0000, Zhu, Jianxin wrote:
>> Dear Tone and Xcrysden users,
>> 
>> I installed Xcrysden 1.5.53 on my linux box.
>> For some unknown reason, the generated k-path in "Open WIEN2k" for fcc
>> structure does not give me right band structure.
>> I can exclude all other possibilities in the bandstructure software
>>itself
>> --- By replacing the k-path with the one generated from 1.5.24 on my mac
>> machine, the band structure comes up correctly.  I will do more tests by
>> also using 1.5.53 installed on my other Mac OSX machine.
>
>Have you compared the k-point coordinates between the two versions?
>Do they differ?
>
>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


From vjain045 at gmail.com  Thu Apr 25 14:08:14 2013
From: vjain045 at gmail.com (vishal jain)
Date: Thu, 25 Apr 2013 17:38:14 +0530
Subject: [xcrysden] Related to Software
Message-ID: <CAJsJeWRwGXY1pXSAp+VgiO5pg6AxMpD6Qz210+eOewH8+gnSdw@mail.gmail.com>

Dear Sir & Users

I want to know how to setup atoms name in crystal structure showing by
xcrysdens.
Exp like Fe, Co


Thanks & Regards
Vishal Jain
Research Scholar
Department of Physics
MLSU, udaipur
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From maofei at mail.bnu.edu.cn  Sat Apr 27 13:31:43 2013
From: maofei at mail.bnu.edu.cn (=?GBK?B?w6u3yQ==?=)
Date: Sat, 27 Apr 2013 19:31:43 +0800 (CST)
Subject: [xcrysden] Related to Software
In-Reply-To: <CAJsJeWRwGXY1pXSAp+VgiO5pg6AxMpD6Qz210+eOewH8+gnSdw@mail.gmail.com>
References: <CAJsJeWRwGXY1pXSAp+VgiO5pg6AxMpD6Qz210+eOewH8+gnSdw@mail.gmail.com>
Message-ID: <1238486.330231367062303399.JavaMail.coremail@mail>

Hi, vishal jain

 

It is easy to do that by choosing this sequence: Display-Atomic Symbols

Best

 

Fei Mao




-----????-----
???: "vishal jain" <vjain045 at gmail.com>
????: 2013?4?25? ???
???: "XCrySDen mailing list" <xcrysden at democritos.it>
??:
??: [xcrysden] Related to Software


Dear Sir & Users 


I want to know how to setup atoms name in crystal structure showing by xcrysdens.
Exp like Fe, Co 




Thanks & Regards 
Vishal Jain
Research Scholar
Department of Physics
MLSU, udaipur
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From maofei at mail.bnu.edu.cn  Sat Apr 27 13:45:03 2013
From: maofei at mail.bnu.edu.cn (=?GBK?B?w6u3yQ==?=)
Date: Sat, 27 Apr 2013 19:45:03 +0800 (CST)
Subject: [xcrysden] Electron density with different colors
Message-ID: <12877986.330361367063103335.JavaMail.coremail@mail>

Hi, Xcrysden users

 

I want to plot the electron density with different colors according to different density magnitudes. I do not know how to fix it.

 

Thank you in advance.

 

Fei Mao




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From amar.b.007 at gmail.com  Sun Apr 28 16:41:33 2013
From: amar.b.007 at gmail.com (Dr. Amar Bahadur)
Date: Sun, 28 Apr 2013 20:11:33 +0530
Subject: [xcrysden] reg xcysted compile
Message-ID: <CA+BUuFbq6CkqMy+Q+-9MQV0VnKWSaV9zYGDcxWVRgAD8fCYPOQ@mail.gmail.com>

Dear Users,
                  I compiled xcrysden in ubuntu, When i give the
command ./xcConfigure,
following message comes on terminal:

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

please suggest what should be written next.

-- 
Kind Regards.

==================
Dr. Amar Bahadur
(Department of Physics)
Kamla Nehru Institute of Physical and Social Sciences,
Sultanpur- 228 118 (U.P.) India
Email: amar.b.007 at gmail.com
Mob.-+91-9451431428, 9044160486
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From pandey.bramha at gmail.com  Sun Apr 28 18:26:06 2013
From: pandey.bramha at gmail.com (Bramha Pandey)
Date: Sun, 28 Apr 2013 22:11:06 +0545
Subject: [xcrysden] reg xcysted compile
In-Reply-To: <CA+BUuFbq6CkqMy+Q+-9MQV0VnKWSaV9zYGDcxWVRgAD8fCYPOQ@mail.gmail.com>
References: <CA+BUuFbq6CkqMy+Q+-9MQV0VnKWSaV9zYGDcxWVRgAD8fCYPOQ@mail.gmail.com>
Message-ID: <CAC2dNGGmtPokS7FFGXBZHRkJT+N=XswtPB5u7rFJdoT5sAktrw@mail.gmail.com>

Dear Dr. Amar,
It is simply saying that you can specify the XCRYSDEN_SCRATCH directory
manually otherwise it will create a xcrys_tmp  in your /home/amarbahadur/
directory.
If you don't bother or interest to create new directory (xcrys_tmp by
manually) then it is better to leave it as a default and then simply enter
and proceed the next step for installation.
I hope it will help you.


On Sun, Apr 28, 2013 at 8:26 PM, Dr. Amar Bahadur <amar.b.007 at gmail.com>wrote:

> Dear Users,
>                   I compiled xcrysden in ubuntu, When i give the command ./xcConfigure,
> following message comes on terminal:
>
> Please specify XCRYSDEN_SCRATCH directory (default:
> /home/amarbahadur/xcrys_tmp):
>
> please suggest what should be written next.
>
> --
> Kind Regards.
>
> ==================
> Dr. Amar Bahadur
> (Department of Physics)
> Kamla Nehru Institute of Physical and Social Sciences,
> Sultanpur- 228 118 (U.P.) India
> Email: amar.b.007 at gmail.com
> Mob.-+91-9451431428, 9044160486
>
> _______________________________________________
> XCrySDen mailing list
> XCrySDen at democritos.it
> http://www.democritos.it/mailman/listinfo/xcrysden
>
>


-- 
Thanks and Regards
Bramha Prasad Pandey
Indian School of Mines(ISM)
Dhanbad, INDIA.
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From amar.b.007 at gmail.com  Sun Apr 28 19:33:28 2013
From: amar.b.007 at gmail.com (Dr. Amar Bahadur)
Date: Sun, 28 Apr 2013 23:03:28 +0530
Subject: [xcrysden] reg: compiling error of xcrysden
Message-ID: <CA+BUuFZ0xEyizqu2FxvWLfqZbNt5FWwKrSc26OyFWed2BqHW8g@mail.gmail.com>

Dear Users,
                     I compiled xcrysden in ubuntu and got an error: Please
help.

amarbahadur at amarbahadur-G41T-M7:~/xcrys/XCrySDen-1.5.24-src-all$ xcrysden

+----------------------------------------------------------------+
|****************************************************************|
|*                                *|
|*  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: 1.5.24

  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/amarbahadur/xcrys/XCrySDen-1.5.24-src-all/external/lib/tcl8.5
XCRYSDEN_TOPDIR=/home/amarbahadur/xcrys/XCrySDen-1.5.24-src-all
XCRYSDEN_SCRATCH=/home/amarbahadur/xcrys_tmp

/home/amarbahadur/xcrys/XCrySDen-1.5.24-src-all/xcrysden: 223:
/home/amarbahadur/xcrys/XCrySDen-1.5.24-src-all/xcrysden:
/home/amarbahadur/xcrys/XCrySDen-1.5.24-src-all/bin/xcrys:
not found
amarbahadur at amarbahadur-G41T-M7:~/xcrys/XCrySDen-1.5.24-src-all$


-- 
Kind Regards.

==================
Dr. Amar Bahadur
(Department of Physics)
Kamla Nehru Institute of Physical and Social Sciences,
Sultanpur- 228 118 (U.P.) India
Email: amar.b.007 at gmail.com
Mob.-+91-9451431428, 9044160486
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From pandey.bramha at gmail.com  Sun Apr 28 19:46:21 2013
From: pandey.bramha at gmail.com (Bramha Pandey)
Date: Sun, 28 Apr 2013 23:31:21 +0545
Subject: [xcrysden] reg: compiling error of xcrysden
In-Reply-To: <CA+BUuFZ0xEyizqu2FxvWLfqZbNt5FWwKrSc26OyFWed2BqHW8g@mail.gmail.com>
References: <CA+BUuFZ0xEyizqu2FxvWLfqZbNt5FWwKrSc26OyFWed2BqHW8g@mail.gmail.com>
Message-ID: <CAC2dNGG9GsoH1GexdyeXhboRLE4epAY5E3wqNZcUFFAD-BkWnQ@mail.gmail.com>

In my opinion, the directory is some what wrong.
BTW try with making a folder name with xcrys in
/home/amarbahadur/xcrys/XCrySDen-1.5.24-src-all/bin/
and see what happened.


On Sun, Apr 28, 2013 at 11:18 PM, Dr. Amar Bahadur <amar.b.007 at gmail.com>wrote:

> Dear Users,
>                      I compiled xcrysden in ubuntu and got an error:
> Please help.
>
> amarbahadur at amarbahadur-G41T-M7:~/xcrys/XCrySDen-1.5.24-src-all$ xcrysden
>
> +----------------------------------------------------------------+
> |****************************************************************|
> |*                                *|
> |*  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: 1.5.24
>
>   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/amarbahadur/xcrys/XCrySDen-1.5.24-src-all/external/lib/tcl8.5
> XCRYSDEN_TOPDIR=/home/amarbahadur/xcrys/XCrySDen-1.5.24-src-all
> XCRYSDEN_SCRATCH=/home/amarbahadur/xcrys_tmp
>
> /home/amarbahadur/xcrys/XCrySDen-1.5.24-src-all/xcrysden: 223:
> /home/amarbahadur/xcrys/XCrySDen-1.5.24-src-all/xcrysden: /home/amarbahadur/xcrys/XCrySDen-1.5.24-src-all/bin/xcrys:
> not found
> amarbahadur at amarbahadur-G41T-M7:~/xcrys/XCrySDen-1.5.24-src-all$
>
>
> --
> Kind Regards.
>
> ==================
> Dr. Amar Bahadur
> (Department of Physics)
> Kamla Nehru Institute of Physical and Social Sciences,
> Sultanpur- 228 118 (U.P.) India
> Email: amar.b.007 at gmail.com
> Mob.-+91-9451431428, 9044160486
>
> _______________________________________________
> XCrySDen mailing list
> XCrySDen at democritos.it
> http://www.democritos.it/mailman/listinfo/xcrysden
>
>


-- 
Thanks and Regards
Bramha Prasad Pandey
Indian School of Mines(ISM)
Dhanbad, INDIA.
-------------- next part --------------
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From tone.kokalj at ijs.si  Mon Apr 29 23:07:33 2013
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Mon, 29 Apr 2013 23:07:33 +0200
Subject: [xcrysden] Xcrysden 1.5.53
In-Reply-To: <CD9D5609.1D3D5%jxzhu@lanl.gov>
References: <CD9D5609.1D3D5%jxzhu@lanl.gov>
Message-ID: <1367269653.24555.1.camel@catalyst.ijs.si>

On Wed, 2013-04-24 at 15:34 +0000, Zhu, Jianxin wrote:
> Hi Tone, 
> 
> I figured out the problem. The issue is not due to version 1.5.53 versus
> 1.5.24. 
> I tested with the version 1.5.53 on my macbook, the generated k-path is
> correct. 
> The problem lies in that the version 1.5.53 on my linux box sets the value
> of M (M*kx,M*ky,M*kz) to be 1 (rather than values like 4 for fcc Gamma -->
> L --> W --> X --> Gamma as appropriately given on my macbook), which
> causes the error. For this, I have manually correct M to be 4 and those
> values of (M*kx,M*ky,M*kz) and then the generated k-path is identical to
> those on my Mac OSX machines.
> 
> But I don't know why M is set to be 1 on my linux machine.

Neither do I; but there is the possibility to set it manually as you
did!

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 29 23:12:02 2013
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Mon, 29 Apr 2013 23:12:02 +0200
Subject: [xcrysden] Electron density with different colors
In-Reply-To: <12877986.330361367063103335.JavaMail.coremail@mail>
References: <12877986.330361367063103335.JavaMail.coremail@mail>
Message-ID: <1367269922.24555.5.camel@catalyst.ijs.si>

On Sat, 2013-04-27 at 19:45 +0800, ?? wrote:
> Hi, Xcrysden users
> 
>  
> 
> I want to plot the electron density with different colors according to
> different density magnitudes. I do not know how to fix it.


As for coloring of isosurfaces there is only one possibility: you can
color the negative and positive values (i.e. +isovalue and -isovalue),
but this is suitable only for charge density differences (i.e. formation
densities). For more details see:
http://www.xcrysden.org/doc/isocontrol.html

On the other hand if you want a colored-type of contour plots, then
follow this link:
http://www.xcrysden.org/doc/plane1control.html

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 29 23:15:20 2013
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Mon, 29 Apr 2013 23:15:20 +0200
Subject: [xcrysden] reg xcysted compile
In-Reply-To: <CA+BUuFbq6CkqMy+Q+-9MQV0VnKWSaV9zYGDcxWVRgAD8fCYPOQ@mail.gmail.com>
References: <CA+BUuFbq6CkqMy+Q+-9MQV0VnKWSaV9zYGDcxWVRgAD8fCYPOQ@mail.gmail.com>
Message-ID: <1367270120.24555.9.camel@catalyst.ijs.si>

On Sun, 2013-04-28 at 20:11 +0530, Dr. Amar Bahadur wrote:
> Dear Users,
>                   I compiled xcrysden in ubuntu, When i give the
> command ./xcConfigure, following message comes on terminal:

For the new versions of xcrysden  it is not required to run the
"./xcConfigure", hence you can skip it.

> Please specify XCRYSDEN_SCRATCH directory
> (default: /home/amarbahadur/xcrys_tmp): 
> 
> please suggest what should be written next.

Write the path of where would you like xcrysden to write the scratch
files. If you just press return, then the /home/amarbahadur/xcrys_tmp/
directory will be used. 

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 29 23:23:55 2013
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Mon, 29 Apr 2013 23:23:55 +0200
Subject: [xcrysden] reg: compiling error of xcrysden
In-Reply-To: <CA+BUuFZ0xEyizqu2FxvWLfqZbNt5FWwKrSc26OyFWed2BqHW8g@mail.gmail.com>
References: <CA+BUuFZ0xEyizqu2FxvWLfqZbNt5FWwKrSc26OyFWed2BqHW8g@mail.gmail.com>
Message-ID: <1367270635.24555.16.camel@catalyst.ijs.si>

On Sun, 2013-04-28 at 23:03 +0530, Dr. Amar Bahadur wrote:
> Dear Users,
>                      I compiled xcrysden in ubuntu and got an error:
> Please help.
> 
> amarbahadur at amarbahadur-G41T-M7:~/xcrys/XCrySDen-1.5.24-src-all$
> xcrysden ...
> TCL_LIBRARY=/home/amarbahadur/xcrys/XCrySDen-1.5.24-src-all/external/lib/tcl8.5
> XCRYSDEN_TOPDIR=/home/amarbahadur/xcrys/XCrySDen-1.5.24-src-all
> XCRYSDEN_SCRATCH=/home/amarbahadur/xcrys_tmp
> 
> /home/amarbahadur/xcrys/XCrySDen-1.5.24-src-all/xcrysden:
> 223: /home/amarbahadur/xcrys/XCrySDen-1.5.24-src-all/xcrysden: /home/amarbahadur/xcrys/XCrySDen-1.5.24-src-all/bin/xcrys: not found

You did not compile the source code; you may check
the /home/amarbahadur/xcrys/XCrySDen-1.5.24-src-all/bin/ directory and
you will either find it does not exists or that it is empty.

Why don't you use the pre-compiled version instead. Ubuntu is usually
32bit. In this case use:
http://www.xcrysden.org/download/xc-1.5.24-linux_x86-semishared.tar.gz

But if you have 64bit ubuntu, you may use:
http://www.xcrysden.org/download/xcrysden-1.5.53-linux_x86_64-semishared.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 jxzhu at lanl.gov  Mon Apr 29 23:26:33 2013
From: jxzhu at lanl.gov (Zhu, Jianxin)
Date: Mon, 29 Apr 2013 21:26:33 +0000
Subject: [xcrysden] Xcrysden 1.5.53
In-Reply-To: <1367269653.24555.1.camel@catalyst.ijs.si>
Message-ID: <CDA44157.1A348%jxzhu@lanl.gov>

Hi Tone, 

Thanks for the assuring message.
I will do it manually on the linux machine.

Regards,

Jianxin



-----Original Message-----
From: Tone Kokalj <tone.kokalj at ijs.si>
Organization: J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
(tel: +386-1-477-3523 // fax:+386-1-477-3822)
Reply-To: <tone.kokalj at ijs.si>, XCrySDen mailing list
<xcrysden at democritos.it>
Date: Mon, 29 Apr 2013 23:07:33 +0200
To: <xcrysden at democritos.it>
Subject: Re: [xcrysden] Xcrysden 1.5.53

>On Wed, 2013-04-24 at 15:34 +0000, Zhu, Jianxin wrote:
>> Hi Tone, 
>> 
>> I figured out the problem. The issue is not due to version 1.5.53 versus
>> 1.5.24. 
>> I tested with the version 1.5.53 on my macbook, the generated k-path is
>> correct. 
>> The problem lies in that the version 1.5.53 on my linux box sets the
>>value
>> of M (M*kx,M*ky,M*kz) to be 1 (rather than values like 4 for fcc Gamma
>>-->
>> L --> W --> X --> Gamma as appropriately given on my macbook), which
>> causes the error. For this, I have manually correct M to be 4 and those
>> values of (M*kx,M*ky,M*kz) and then the generated k-path is identical to
>> those on my Mac OSX machines.
>> 
>> But I don't know why M is set to be 1 on my linux machine.
>
>Neither do I; but there is the possibility to set it manually as you
>did!
>
>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


From amar.b.007 at gmail.com  Tue Apr 30 18:20:53 2013
From: amar.b.007 at gmail.com (Dr. Amar Bahadur)
Date: Tue, 30 Apr 2013 21:50:53 +0530
Subject: [xcrysden] XCrySDen Digest, Vol 63, Issue 13
In-Reply-To: <mailman.3.1367223719.19614.xcrysden@democritos.it>
References: <mailman.3.1367223719.19614.xcrysden@democritos.it>
Message-ID: <CA+BUuFb06MXK4xcdZy9=UUSCsr4KQ7rLkrZaBWszq_+EE7Ut=g@mail.gmail.com>

Many thanks sir.

On 29 April 2013 13:51, <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. reg xcysted compile (Dr. Amar Bahadur)
>    2. Re: reg xcysted compile (Bramha Pandey)
>    3. reg: compiling error of xcrysden (Dr. Amar Bahadur)
>    4. Re: reg: compiling error of xcrysden (Bramha Pandey)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 28 Apr 2013 20:11:33 +0530
> From: "Dr. Amar Bahadur" <amar.b.007 at gmail.com>
> Subject: [xcrysden] reg xcysted compile
> To: xcrysden at democritos.it
> Message-ID:
>         <
> CA+BUuFbq6CkqMy+Q+-9MQV0VnKWSaV9zYGDcxWVRgAD8fCYPOQ at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Users,
>                   I compiled xcrysden in ubuntu, When i give the
> command ./xcConfigure,
> following message comes on terminal:
>
> Please specify XCRYSDEN_SCRATCH directory (default:
> /home/amarbahadur/xcrys_tmp):
>
> please suggest what should be written next.
>
> --
> Kind Regards.
>
> ==================
> Dr. Amar Bahadur
> (Department of Physics)
> Kamla Nehru Institute of Physical and Social Sciences,
> Sultanpur- 228 118 (U.P.) India
> Email: amar.b.007 at gmail.com
> Mob.-+91-9451431428, 9044160486
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://www.democritos.it/pipermail/xcrysden/attachments/20130428/dac8e43a/attachment-0001.htm
>
> ------------------------------
>
> Message: 2
> Date: Sun, 28 Apr 2013 22:11:06 +0545
> From: Bramha Pandey <pandey.bramha at gmail.com>
> Subject: Re: [xcrysden] reg xcysted compile
> To: XCrySDen mailing list <xcrysden at democritos.it>
> Message-ID:
>         <CAC2dNGGmtPokS7FFGXBZHRkJT+N=
> XswtPB5u7rFJdoT5sAktrw at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Dr. Amar,
> It is simply saying that you can specify the XCRYSDEN_SCRATCH directory
> manually otherwise it will create a xcrys_tmp  in your /home/amarbahadur/
> directory.
> If you don't bother or interest to create new directory (xcrys_tmp by
> manually) then it is better to leave it as a default and then simply enter
> and proceed the next step for installation.
> I hope it will help you.
>
>
> On Sun, Apr 28, 2013 at 8:26 PM, Dr. Amar Bahadur <amar.b.007 at gmail.com
> >wrote:
>
> > Dear Users,
> >                   I compiled xcrysden in ubuntu, When i give the command
> ./xcConfigure,
> > following message comes on terminal:
> >
> > Please specify XCRYSDEN_SCRATCH directory (default:
> > /home/amarbahadur/xcrys_tmp):
> >
> > please suggest what should be written next.
> >
> > --
> > Kind Regards.
> >
> > ==================
> > Dr. Amar Bahadur
> > (Department of Physics)
> > Kamla Nehru Institute of Physical and Social Sciences,
> > Sultanpur- 228 118 (U.P.) India
> > Email: amar.b.007 at gmail.com
> > Mob.-+91-9451431428, 9044160486
> >
> > _______________________________________________
> > XCrySDen mailing list
> > XCrySDen at democritos.it
> > http://www.democritos.it/mailman/listinfo/xcrysden
> >
> >
>
>
> --
> Thanks and Regards
> Bramha Prasad Pandey
> Indian School of Mines(ISM)
> Dhanbad, INDIA.
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://www.democritos.it/pipermail/xcrysden/attachments/20130428/e42249be/attachment-0001.htm
>
> ------------------------------
>
> Message: 3
> Date: Sun, 28 Apr 2013 23:03:28 +0530
> From: "Dr. Amar Bahadur" <amar.b.007 at gmail.com>
> Subject: [xcrysden] reg: compiling error of xcrysden
> To: xcrysden-request at democritos.it, xcrysden at democritos.it
> Message-ID:
>         <
> CA+BUuFZ0xEyizqu2FxvWLfqZbNt5FWwKrSc26OyFWed2BqHW8g at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Users,
>                      I compiled xcrysden in ubuntu and got an error: Please
> help.
>
> amarbahadur at amarbahadur-G41T-M7:~/xcrys/XCrySDen-1.5.24-src-all$ xcrysden
>
> +----------------------------------------------------------------+
> |****************************************************************|
> |*                                *|
> |*  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: 1.5.24
>
>   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/amarbahadur/xcrys/XCrySDen-1.5.24-src-all/external/lib/tcl8.5
> XCRYSDEN_TOPDIR=/home/amarbahadur/xcrys/XCrySDen-1.5.24-src-all
> XCRYSDEN_SCRATCH=/home/amarbahadur/xcrys_tmp
>
> /home/amarbahadur/xcrys/XCrySDen-1.5.24-src-all/xcrysden: 223:
> /home/amarbahadur/xcrys/XCrySDen-1.5.24-src-all/xcrysden:
> /home/amarbahadur/xcrys/XCrySDen-1.5.24-src-all/bin/xcrys:
> not found
> amarbahadur at amarbahadur-G41T-M7:~/xcrys/XCrySDen-1.5.24-src-all$
>
>
> --
> Kind Regards.
>
> ==================
> Dr. Amar Bahadur
> (Department of Physics)
> Kamla Nehru Institute of Physical and Social Sciences,
> Sultanpur- 228 118 (U.P.) India
> Email: amar.b.007 at gmail.com
> Mob.-+91-9451431428, 9044160486
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://www.democritos.it/pipermail/xcrysden/attachments/20130428/4a0debca/attachment-0001.htm
>
> ------------------------------
>
> Message: 4
> Date: Sun, 28 Apr 2013 23:31:21 +0545
> From: Bramha Pandey <pandey.bramha at gmail.com>
> Subject: Re: [xcrysden] reg: compiling error of xcrysden
> To: XCrySDen mailing list <xcrysden at democritos.it>
> Message-ID:
>         <
> CAC2dNGG9GsoH1GexdyeXhboRLE4epAY5E3wqNZcUFFAD-BkWnQ at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> In my opinion, the directory is some what wrong.
> BTW try with making a folder name with xcrys in
> /home/amarbahadur/xcrys/XCrySDen-1.5.24-src-all/bin/
> and see what happened.
>
>
> On Sun, Apr 28, 2013 at 11:18 PM, Dr. Amar Bahadur <amar.b.007 at gmail.com
> >wrote:
>
> > Dear Users,
> >                      I compiled xcrysden in ubuntu and got an error:
> > Please help.
> >
> > amarbahadur at amarbahadur-G41T-M7:~/xcrys/XCrySDen-1.5.24-src-all$
> xcrysden
> >
> > +----------------------------------------------------------------+
> > |****************************************************************|
> > |*                                *|
> > |*  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: 1.5.24
> >
> >   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/amarbahadur/xcrys/XCrySDen-1.5.24-src-all/external/lib/tcl8.5
> > XCRYSDEN_TOPDIR=/home/amarbahadur/xcrys/XCrySDen-1.5.24-src-all
> > XCRYSDEN_SCRATCH=/home/amarbahadur/xcrys_tmp
> >
> > /home/amarbahadur/xcrys/XCrySDen-1.5.24-src-all/xcrysden: 223:
> > /home/amarbahadur/xcrys/XCrySDen-1.5.24-src-all/xcrysden:
> /home/amarbahadur/xcrys/XCrySDen-1.5.24-src-all/bin/xcrys:
> > not found
> > amarbahadur at amarbahadur-G41T-M7:~/xcrys/XCrySDen-1.5.24-src-all$
> >
> >
> > --
> > Kind Regards.
> >
> > ==================
> > Dr. Amar Bahadur
> > (Department of Physics)
> > Kamla Nehru Institute of Physical and Social Sciences,
> > Sultanpur- 228 118 (U.P.) India
> > Email: amar.b.007 at gmail.com
> > Mob.-+91-9451431428, 9044160486
> >
> > _______________________________________________
> > XCrySDen mailing list
> > XCrySDen at democritos.it
> > http://www.democritos.it/mailman/listinfo/xcrysden
> >
> >
>
>
> --
> Thanks and Regards
> Bramha Prasad Pandey
> Indian School of Mines(ISM)
> Dhanbad, INDIA.
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
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>
> ------------------------------
>
> _______________________________________________
> XCrySDen mailing list
> XCrySDen at democritos.it
> http://www.democritos.it/mailman/listinfo/xcrysden
>
>
> End of XCrySDen Digest, Vol 63, Issue 13
> ****************************************
>



-- 
Kind Regards.

==================
Dr. Amar Bahadur
(Department of Physics)
Kamla Nehru Institute of Physical and Social Sciences,
Sultanpur- 228 118 (U.P.) India
Email: amar.b.007 at gmail.com
Mob.-+91-9451431428, 9044160486
-------------- next part --------------
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