From tone.kokalj at ijs.si  Fri Dec  5 17:26:01 2008
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Fri, 05 Dec 2008 17:26:01 +0100
Subject: [xcrysden] finally new xcrysden version
Message-ID: <1228494361.5096.47.camel@walk.ijs.si>

Hello everybody,

After far too long a period of time a new version of XCrySDen is about
to be ready. It will have several new features, and many bug fixes. 

Today I put on-line the 1.5.17 version (aka 1.6 pre-release).
Those of you who might be interested, can download the package from 

www.xcrysden.org/Download.html

In particular:

http://www.xcrysden.org/download/xc-1.5.17-linux_x86_64-semishared.tar.gz
(64bit linux version)

http://www.xcrysden.org/download/xc-1.5.17-src.tar.gz
http://www.xcrysden.org/download/xc-1.5.17-src-all.tar.gz
(two flavors of source package)

Best regards, Tone

PS: I would appreciate potential reports about the encountered problems.
-- 
Tone Kokalj <tone.kokalj at ijs.si>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)


From ahboufelfel at gmail.com  Sat Dec  6 19:34:02 2008
From: ahboufelfel at gmail.com (Ahmed Boufelfel)
Date: Sat, 6 Dec 2008 19:34:02 +0100
Subject: [xcrysden] XCrySDen Digest, Vol 12, Issue 1
In-Reply-To: <mailman.7.1228548742.6584.xcrysden@democritos.it>
References: <mailman.7.1228548742.6584.xcrysden@democritos.it>
Message-ID: <ec0e59120812061034tefbc33cw3d0038f7d3ec7471@mail.gmail.com>

thank you

On Sat, Dec 6, 2008 at 8:32 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. finally new xcrysden version (Tone Kokalj)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 05 Dec 2008 17:26:01 +0100
> From: Tone Kokalj <tone.kokalj at ijs.si>
> Subject: [xcrysden] finally new xcrysden version
> To: XCrySDen mailing list <xcrysden at democritos.it>
> Message-ID: <1228494361.5096.47.camel at walk.ijs.si>
> Content-Type: text/plain
>
> Hello everybody,
>
> After far too long a period of time a new version of XCrySDen is about
> to be ready. It will have several new features, and many bug fixes.
>
> Today I put on-line the 1.5.17 version (aka 1.6 pre-release).
> Those of you who might be interested, can download the package from
>
> www.xcrysden.org/Download.html
>
> In particular:
>
> http://www.xcrysden.org/download/xc-1.5.17-linux_x86_64-semishared.tar.gz
> (64bit linux version)
>
> http://www.xcrysden.org/download/xc-1.5.17-src.tar.gz
> http://www.xcrysden.org/download/xc-1.5.17-src-all.tar.gz
> (two flavors of source package)
>
> Best regards, Tone
>
> PS: I would appreciate potential reports about the encountered problems.
> --
> Tone Kokalj <tone.kokalj at ijs.si>
> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
> +386-1-477-3523 // fax:+386-1-477-3822)
>
>
>
> ------------------------------
>
> _______________________________________________
> XCrySDen mailing list
> XCrySDen at democritos.it
> http://www.democritos.it/mailman/listinfo/xcrysden
>
>
> End of XCrySDen Digest, Vol 12, Issue 1
> ***************************************
>



-- 
Ahmed Boufelfel
Professor of Physics
University of Guelma
BP401 24000
Guelma, Algeria
Phone + 213 37 20 77 95
cell phone +213 668 49 45 75
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From mpei at uni-bonn.de  Sun Dec  7 10:27:25 2008
From: mpei at uni-bonn.de (Michael F. Peintinger)
Date: Sun, 7 Dec 2008 10:27:25 +0100
Subject: [xcrysden] XCrySDen Digest, Vol 12, Issue 1
In-Reply-To: <mailman.7.1228548742.6584.xcrysden@democritos.it>
References: <mailman.7.1228548742.6584.xcrysden@democritos.it>
Message-ID: <200812071027.26283.mpei@uni-bonn.de>

Hi Tone,

thank you very much! I can report it works perfectly on my three Intel EM64 / 
amd64 machines. I use Kubuntu 8.10 Intrepid. I used the precompiled semishared 
binaries.

Regards

Michael

Am Samstag, 6. Dezember 2008 08:32:22 schrieb xcrysden-request at democritos.it:
> 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. finally new xcrysden version (Tone Kokalj)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 05 Dec 2008 17:26:01 +0100
> From: Tone Kokalj <tone.kokalj at ijs.si>
> Subject: [xcrysden] finally new xcrysden version
> To: XCrySDen mailing list <xcrysden at democritos.it>
> Message-ID: <1228494361.5096.47.camel at walk.ijs.si>
> Content-Type: text/plain
>
> Hello everybody,
>
> After far too long a period of time a new version of XCrySDen is about
> to be ready. It will have several new features, and many bug fixes.
>
> Today I put on-line the 1.5.17 version (aka 1.6 pre-release).
> Those of you who might be interested, can download the package from
>
> www.xcrysden.org/Download.html
>
> In particular:
>
> http://www.xcrysden.org/download/xc-1.5.17-linux_x86_64-semishared.tar.gz
> (64bit linux version)
>
> http://www.xcrysden.org/download/xc-1.5.17-src.tar.gz
> http://www.xcrysden.org/download/xc-1.5.17-src-all.tar.gz
> (two flavors of source package)
>
> Best regards, Tone
>
> PS: I would appreciate potential reports about the encountered problems.

-- 
Institut f?r Physikalische
und Theoretische Chemie

Wegelerstr.12
D-53115 Bonn

Telefon: 0228/73-2998
E-Mail: mpei at uni-bonn.de

From zhaohscas at yahoo.com.cn  Mon Dec  8 11:48:05 2008
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Mon, 8 Dec 2008 18:48:05 +0800
Subject: [xcrysden] finally new xcrysden version
In-Reply-To: <1228494361.5096.47.camel@walk.ijs.si>
References: <1228494361.5096.47.camel@walk.ijs.si>
Message-ID: <772688764.20081208184805@yahoo.com.cn>

On Saturday, December 6, 2008 at 0:26, tone.kokalj at ijs.si wrote:
> Hello everybody,

> After far too long a period of time a new version of XCrySDen is about
> to be ready. It will have several new features, and many bug fixes. 

> Today I put on-line the 1.5.17 version (aka 1.6 pre-release).
> Those of you who might be interested, can download the package from 

> www.xcrysden.org/Download.html

> In particular:

> http://www.xcrysden.org/download/xc-1.5.17-linux_x86_64-semishared.tar.gz
> (64bit linux version)

> http://www.xcrysden.org/download/xc-1.5.17-src.tar.gz
> http://www.xcrysden.org/download/xc-1.5.17-src-all.tar.gz
> (two flavors of source package)

The above latest versions doesn't include the pre-compiled one for
cygwin, why?

Regards,
-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn> 
Xinjiang Technical Institute of Physics and Chemistry
Chinese Academy of Sciences 
GnuPG DSA: 0xD108493
2008-12-8

__________________________________________________
?????????????????????????????
http://cn.mail.yahoo.com


From tasaka at affinity-science.com  Mon Dec  8 12:41:55 2008
From: tasaka at affinity-science.com (Tomohiko Tasaka)
Date: Mon, 8 Dec 2008 20:41:55 +0900
Subject: [xcrysden] finally new xcrysden version
In-Reply-To: <1228494361.5096.47.camel@walk.ijs.si>
References: <1228494361.5096.47.camel@walk.ijs.si>
Message-ID: <003b01c95929$f90c16a0$eb2443e0$@com>

Hello,

I can build new xcrysden on Intel-based Mac OS X 10.5.5 and have no problem until now.

Below is my Make.sys:

eta:XCrySDen-1.5.17-src-all tasaka$ grep -v ^# Make.sys

MAKE = make

CFLAGS = -ansi -fwritable-strings  -funroll-loops -fPIC -DUSE_FONTS
CC     = gcc
MATH   = -lm
FFLAGS = -O2
FC     = g77

DARWIN_X11_PREFIX = /usr/X11
X_LIB     = -L$(DARWIN_X11_PREFIX)/lib -lXmu -lX11 -lXext
X_INCDIR  = -I$(DARWIN_X11_PREFIX)/include

COMPILE_TCLTK = no
COMPILE_MESA  = no

TCLTK_OPTIONS      = --disable-shared
MESA_OPTIONS       = --disable-shared --disable-3dnow

CoreFoundation=/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
TCL_LIB      = /sw/lib/libtcl8.4.dylib $(CoreFoundation)
TK_LIB      = /sw/lib/libtk8.4.dylib

GLU_LIB     = /sw/lib/mesa/libGLU.a
GL_LIB      = /sw/lib/mesa/libGL.a


eta:XCrySDen-1.5.17-src-all tasaka$ otool -L bin/xcrys
bin/xcrys:
        /sw/lib/libtk8.4.dylib (compatibility version 8.4.0, current version 8.4.13)
        /sw/lib/libtcl8.4.dylib (compatibility version 8.4.0, current version 8.4.13)
        /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version
150.0.0, current version 476.15.0)
        /usr/X11/lib/libXmu.6.dylib (compatibility version 9.0.0, current version 9.0.0)
        /usr/X11/lib/libX11.6.dylib (compatibility version 9.0.0, current version 9.0.0)
        /usr/X11/lib/libXext.6.dylib (compatibility version 11.0.0, current version 11.0.0)
        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 111.1.1)
        /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
eta:XCrySDen-1.5.17-src-all tasaka$


HTH

Regards,
Tomohiko


-----Original Message-----
From: xcrysden-bounces at democritos.it [mailto:xcrysden-bounces at democritos.it] On Behalf Of Tone Kokalj
Sent: Saturday, December 06, 2008 1:26 AM
To: XCrySDen mailing list
Subject: [xcrysden] finally new xcrysden version

Hello everybody,

After far too long a period of time a new version of XCrySDen is about
to be ready. It will have several new features, and many bug fixes. 

Today I put on-line the 1.5.17 version (aka 1.6 pre-release).
Those of you who might be interested, can download the package from 

www.xcrysden.org/Download.html

In particular:

http://www.xcrysden.org/download/xc-1.5.17-linux_x86_64-semishared.tar.gz
(64bit linux version)

http://www.xcrysden.org/download/xc-1.5.17-src.tar.gz
http://www.xcrysden.org/download/xc-1.5.17-src-all.tar.gz
(two flavors of source package)

Best regards, Tone

PS: I would appreciate potential reports about the encountered problems.
-- 
Tone Kokalj <tone.kokalj at ijs.si>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)

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


From lanhaiping at gmail.com  Mon Dec  8 13:41:43 2008
From: lanhaiping at gmail.com (lan haiping)
Date: Mon, 8 Dec 2008 20:41:43 +0800
Subject: [xcrysden] finally new xcrysden version
In-Reply-To: <003b01c95929$f90c16a0$eb2443e0$@com>
References: <1228494361.5096.47.camel@walk.ijs.si>
	<003b01c95929$f90c16a0$eb2443e0$@com>
Message-ID: <c92002fa0812080441i6d00e247xa6d26fc2f1fed34c@mail.gmail.com>

Anyone has a make.sys for x86-32 configuration ?

thanks

On Mon, Dec 8, 2008 at 7:41 PM, Tomohiko Tasaka <tasaka at affinity-science.com
> wrote:

> Hello,
>
> I can build new xcrysden on Intel-based Mac OS X 10.5.5 and have no problem
> until now.
>
> Below is my Make.sys:
>
> eta:XCrySDen-1.5.17-src-all tasaka$ grep -v ^# Make.sys
>
> MAKE = make
>
> CFLAGS = -ansi -fwritable-strings  -funroll-loops -fPIC -DUSE_FONTS
> CC     = gcc
> MATH   = -lm
> FFLAGS = -O2
> FC     = g77
>
> DARWIN_X11_PREFIX = /usr/X11
> X_LIB     = -L$(DARWIN_X11_PREFIX)/lib -lXmu -lX11 -lXext
> X_INCDIR  = -I$(DARWIN_X11_PREFIX)/include
>
> COMPILE_TCLTK = no
> COMPILE_MESA  = no
>
> TCLTK_OPTIONS      = --disable-shared
> MESA_OPTIONS       = --disable-shared --disable-3dnow
>
>
> CoreFoundation=/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
> TCL_LIB      = /sw/lib/libtcl8.4.dylib $(CoreFoundation)
> TK_LIB      = /sw/lib/libtk8.4.dylib
>
> GLU_LIB     = /sw/lib/mesa/libGLU.a
> GL_LIB      = /sw/lib/mesa/libGL.a
>
>
> eta:XCrySDen-1.5.17-src-all tasaka$ otool -L bin/xcrys
> bin/xcrys:
>        /sw/lib/libtk8.4.dylib (compatibility version 8.4.0, current version
> 8.4.13)
>        /sw/lib/libtcl8.4.dylib (compatibility version 8.4.0, current
> version 8.4.13)
>
>  /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
> (compatibility version
> 150.0.0, current version 476.15.0)
>        /usr/X11/lib/libXmu.6.dylib (compatibility version 9.0.0, current
> version 9.0.0)
>        /usr/X11/lib/libX11.6.dylib (compatibility version 9.0.0, current
> version 9.0.0)
>        /usr/X11/lib/libXext.6.dylib (compatibility version 11.0.0, current
> version 11.0.0)
>        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
> version 111.1.1)
>        /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current
> version 1.0.0)
> eta:XCrySDen-1.5.17-src-all tasaka$
>
>
> HTH
>
> Regards,
> Tomohiko
>
>
> -----Original Message-----
> From: xcrysden-bounces at democritos.it [mailto:
> xcrysden-bounces at democritos.it] On Behalf Of Tone Kokalj
> Sent: Saturday, December 06, 2008 1:26 AM
> To: XCrySDen mailing list
> Subject: [xcrysden] finally new xcrysden version
>
> Hello everybody,
>
> After far too long a period of time a new version of XCrySDen is about
> to be ready. It will have several new features, and many bug fixes.
>
> Today I put on-line the 1.5.17 version (aka 1.6 pre-release).
> Those of you who might be interested, can download the package from
>
> www.xcrysden.org/Download.html
>
> In particular:
>
> http://www.xcrysden.org/download/xc-1.5.17-linux_x86_64-semishared.tar.gz
> (64bit<http://www.xcrysden.org/download/xc-1.5.17-linux_x86_64-semishared.tar.gz%2864bit>linux version)
>
> http://www.xcrysden.org/download/xc-1.5.17-src.tar.gz
> http://www.xcrysden.org/download/xc-1.5.17-src-all.tar.gz
> (two flavors of source package)
>
> Best regards, Tone
>
> PS: I would appreciate potential reports about the encountered problems.
> --
> Tone Kokalj <tone.kokalj at ijs.si>
> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
> +386-1-477-3523 // fax:+386-1-477-3822)
>
> _______________________________________________
> XCrySDen mailing list
> XCrySDen at democritos.it
> http://www.democritos.it/mailman/listinfo/xcrysden
>
> _______________________________________________
> XCrySDen mailing list
> XCrySDen at democritos.it
> http://www.democritos.it/mailman/listinfo/xcrysden
>



-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From psbishtphyjiwaji at yahoo.co.in  Mon Dec  8 14:14:42 2008
From: psbishtphyjiwaji at yahoo.co.in (pradeep bisht)
Date: Mon, 8 Dec 2008 18:44:42 +0530 (IST)
Subject: [xcrysden] warning appear
Message-ID: <769183.92154.qm@web94207.mail.in2.yahoo.com>

Respected Xcrysden users,
I have install the xcrysden latest release. during compilation few warning appears

xcAppInit.c:511: warning
meso not found

But when I run the xcrysden script it works fine 

Please suggest me is this type warning will create the problem

With regard
Pradeep






      Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/
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From tone.kokalj at ijs.si  Tue Dec  9 00:24:53 2008
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Tue, 09 Dec 2008 00:24:53 +0100
Subject: [xcrysden] finally new xcrysden version
In-Reply-To: <772688764.20081208184805@yahoo.com.cn>
References: <1228494361.5096.47.camel@walk.ijs.si>
	<772688764.20081208184805@yahoo.com.cn>
Message-ID: <1228778693.4759.6.camel@walk.ijs.si>

On Mon, 2008-12-08 at 18:48 +0800, Hongsheng Zhao wrote:
> On Saturday, December 6, 2008 at 0:26, tone.kokalj at ijs.si wrote:
> > In particular:
> 
> > http://www.xcrysden.org/download/xc-1.5.17-linux_x86_64-semishared.tar.gz
> > (64bit linux version)
> 
> > http://www.xcrysden.org/download/xc-1.5.17-src.tar.gz
> > http://www.xcrysden.org/download/xc-1.5.17-src-all.tar.gz
> > (two flavors of source package)
> 
> The above latest versions doesn't include the pre-compiled one for
> cygwin, why?


Because, I am not familiar with MS Windows / Cygwin / ... 

Today I got access to a computer running MS-Vista and I installed
cygwin. After a struggle I succeeded to compile xcrysden. Basic
functionality is working, but not yet all the features. I am working on
it. Please wait a few days more. 

Regards, Tone

-- 
Tone Kokalj <tone.kokalj at ijs.si>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)


From tone.kokalj at ijs.si  Tue Dec  9 00:35:11 2008
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Tue, 09 Dec 2008 00:35:11 +0100
Subject: [xcrysden] finally new xcrysden version
In-Reply-To: <003b01c95929$f90c16a0$eb2443e0$@com>
References: <1228494361.5096.47.camel@walk.ijs.si>
	<003b01c95929$f90c16a0$eb2443e0$@com>
Message-ID: <1228779311.4759.15.camel@walk.ijs.si>

On Mon, 2008-12-08 at 20:41 +0900, Tomohiko Tasaka wrote:
> Hello,
> 
> I can build new xcrysden on Intel-based Mac OS X 10.5.5 and have no problem until now.

Very good!!! 

I would much appreciate if you could make your compiled version
available also to other mac-osx users (myself, I don't have mac and I
cannot create it)? The recipe would go as follows: run "make bindist"
and email me the so-created tar.gz file. I will put it on the download
page.

Regards, Tone
-- 
Tone Kokalj <tone.kokalj at ijs.si>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)


From tone.kokalj at ijs.si  Tue Dec  9 00:53:45 2008
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Tue, 09 Dec 2008 00:53:45 +0100
Subject: [xcrysden] warning appear
In-Reply-To: <769183.92154.qm@web94207.mail.in2.yahoo.com>
References: <769183.92154.qm@web94207.mail.in2.yahoo.com>
Message-ID: <1228780425.4759.26.camel@walk.ijs.si>

On Mon, 2008-12-08 at 18:44 +0530, pradeep bisht wrote:
> Respected Xcrysden users,
> I have install the xcrysden latest release. during compilation few
> warning appears
> 
> xcAppInit.c:511: warning
> meso not found
> 

Strange warning! There is no "meso" string in the whole C-code of
xcrysden, not even at line xcAppInit.c:511

It's only warning, so if the program runs well, don't mind about it ...

Regards, Tone
-- 
Tone Kokalj <tone.kokalj at ijs.si>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)



From tone.kokalj at ijs.si  Tue Dec  9 01:12:20 2008
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Tue, 09 Dec 2008 01:12:20 +0100
Subject: [xcrysden] finally new xcrysden version
In-Reply-To: <c92002fa0812080441i6d00e247xa6d26fc2f1fed34c@mail.gmail.com>
References: <1228494361.5096.47.camel@walk.ijs.si>
	<003b01c95929$f90c16a0$eb2443e0$@com>
	<c92002fa0812080441i6d00e247xa6d26fc2f1fed34c@mail.gmail.com>
Message-ID: <1228781540.4759.38.camel@walk.ijs.si>

On Mon, 2008-12-08 at 20:41 +0800, lan haiping wrote:
> Anyone has a make.sys for x86-32 configuration ?

You may use with some editing those in system/Make.linux*

For x86_32 compilation. I have used these two (attached).

Regards, Tone

PS: linux_x86 (32bit) binaries are now available on the download page.

http://www.xcrysden.org/download/xc-1.5.17-linux_x86-semishared.tar.gz
http://www.xcrysden.org/download/xc-1.5.17-linux_x86-shared.tar.gz

-- 
Tone Kokalj <tone.kokalj at ijs.si>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)
-------------- next part --------------
########################################################################
#
# System-dependent definitions for Linux.
# Edit according to your own needs.
#
########################################################################

#------------------------------------------------------------------------
# if you have a GNU make it is better to set the MAKE variable to point
# to gnu make
#------------------------------------------------------------------------
MAKE   = make

#------------------------------------------------------------------------
# compilers & flags
#------------------------------------------------------------------------
# static:
#----------------------------
CFLAGS  = -ansi -ffast-math -funroll-loops -DUSE_FONTS -pedantic -Wall -O2
LDFLAGS =
LDLIB   = -ldl 
MATH    = -lm
CC      = gcc


FC      = gfortran
FFLAGS  = -O2


#------------------------------------------------------------------------
# X-libraries & include files
#------------------------------------------------------------------------
X_LIB     = -lXmu -lX11
X_INCDIR  = 

COMPILE_TCLTK = no
COMPILE_MESA  = no

#
# Libraries
#
TK_LIB      = -ltk8.5
TCL_LIB     = -ltcl8.5
GLU_LIB     = -lGLU
GL_LIB      = -lGL

#
# Include directories
#
TCL_INCDIR  = -I/usr/include/tcl8.5
TK_INCDIR   = -I/usr/include/tk8.5
GL_INCDIR   = 
-------------- next part --------------
#########################################################################
#
# System-dependent definitions for Linux.
#
# EDIT ACCORDING TO YOUR OWN NEEDS !!!
#
########################################################################

#------------------------------------------------------------------------
# if you have a GNU make it is better to set the MAKE variable to point
# to gnu make
#------------------------------------------------------------------------
MAKE = make

#------------------------------------------------------------------------
# compilers & flags
#------------------------------------------------------------------------
CFLAGS = -ansi -ffast-math -funroll-loops -fPIC -DUSE_FONTS -O2
CC     = gcc
#LDLIB  = -ldl
MATH   = -lm

# we use  a static libgfortran not to depend on gfortran version
FFLAGS = -O2 -static-libgfortran
FC     = gfortran 

#-------------------------------------------
#debug options
#CFLAGS = -ansi -g -fPIC
#-------------------------------------------


#------------------------------------------------------------------------
# X-libraries & include files
#
# for STATIC compilation one should add: -lpthread
#------------------------------------------------------------------------
X_LIB     = -lXmu -lX11 -lXext
X_INCDIR  = 


###
### use EITHER THIS:
###

#-Possibility-1----------------------------------------------------------
#
# If you want to use your own libraries and include files,
# then set *_LIB and *_INCDIR variables below accordingly:
#
#------------------------------------------------------------------------

# COMPILE_TCLTK = no
# COMPILE_MESA  = no
# 
# #
# # Libraries
# #
# TK_LIB      = -ltk8.5
# TCL_LIB     = -ltcl8.5
# GLU_LIB     = -lGLU
# GL_LIB      = -lGL
# 
# #
# # Include directories
# #
# TCL_INCDIR  = 
# TK_INCDIR   = 
# GL_INCDIR   = 

#------------------------------------------------------------------------

###
### or THAT:
###


#-Possibility-2----------------------------------------------------------- 
#
# XCRYSDEN package may contain the tcl, tk & Mesa sources !!!
# If you would like to compile and use these then uncomment below lines and
# comment lines "Possibility-1" (see above).
#
#------------------------------------------------------------------------

COMPILE_TCLTK = yes
COMPILE_MESA  = yes

#
# Do we want a shared library version of Tcl/Tk/Mesa or static?
# If we want shared then set the following flags to: --enable-shared
# else set the following flag to: --disable-shared
#
TCLTK_OPTIONS      = --enable-shared
MESA_TARGET        = linux

#
# Libraries (dynamic loading)
#           for shared linking the libraries postfix should be .so
#           for static linking the libraries postfix should be .a
#
TCL_LIB     = -L$(TOPDIR)/external/lib -ltcl$(TCL_VER2)
TK_LIB      = -ltk$(TCL_VER2)
GLU_LIB     = -lGLU
GL_LIB      = -lGL

#
# Include directories
#
TCL_INCDIR  = -I$(TOPDIR)/external/src/tcl$(TCL_VER3)/generic
TK_INCDIR   = -I$(TOPDIR)/external/src/tk$(TCL_VER3)/generic
GL_INCDIR   = -I$(TOPDIR)/external/include 

#------------------------------------------------------------------------

From zhaohscas at yahoo.com.cn  Tue Dec  9 05:33:28 2008
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Tue, 9 Dec 2008 12:33:28 +0800
Subject: [xcrysden] finally new xcrysden version
In-Reply-To: <1228778693.4759.6.camel@walk.ijs.si>
References: <1228494361.5096.47.camel@walk.ijs.si>
	<772688764.20081208184805@yahoo.com.cn>
	<1228778693.4759.6.camel@walk.ijs.si>
Message-ID: <505369562.20081209123328@yahoo.com.cn>

On Tuesday, December 9, 2008 at 7:24, tone.kokalj at ijs.si wrote:
> Today I got access to a computer running MS-Vista and I installed
> cygwin. After a struggle I succeeded to compile xcrysden. Basic
> functionality is working, but not yet all the features. I am working on
> it. Please wait a few days more.

Thanks a lot, I just stay tuned!

Regards,
--
Hongsheng Zhao <zhaohscas at yahoo.com.cn> 
Xinjiang Technical Institute of Physics and Chemistry
Chinese Academy of Sciences 
GnuPG DSA: 0xD108493
2008-12-9


From hongyi.zhao at gmail.com  Tue Dec  9 11:29:04 2008
From: hongyi.zhao at gmail.com (hongyi.zhao at gmail.com)
Date: Tue, 9 Dec 2008 18:29:04 +0800
Subject: [xcrysden] Want to extract the 2D charge density based on a 3d
	Charge density datagrid by using XCrySDen automatically.
In-Reply-To: <1228780425.4759.26.camel@walk.ijs.si>
References: <769183.92154.qm@web94207.mail.in2.yahoo.com>
	<1228780425.4759.26.camel@walk.ijs.si>
Message-ID: <66680366.20081209182904@gmail.com>

Dear Tone,

In my case, I can easily get the 3d Charge density datagrid for  XCrySDen, but currently, the XCrySDen can only give me the iso-surfaces of Charge density on three basal cystal planes.  If I can let XCrySDen extract a specific 2D charge density alone a specific plane based on a 3d Charge density datagrid used by XCrySDen, it should be a wonderful thing for me.  Would you like give me some hints on this? 

Regards,
-- 
Hongyi Zhao <hongyi.zhao at gmail.com> 
Xinjiang Technical Institute of Physics and Chemistry
Chinese Academy of Sciences 
GnuPG DSA: 0xD108493
2008-12-9


From tone.kokalj at ijs.si  Wed Dec 10 00:19:43 2008
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Wed, 10 Dec 2008 00:19:43 +0100
Subject: [xcrysden] Want to extract the 2D charge density based on a
	3d	Charge density datagrid by using XCrySDen automatically.
In-Reply-To: <66680366.20081209182904@gmail.com>
References: <769183.92154.qm@web94207.mail.in2.yahoo.com>
	<1228780425.4759.26.camel@walk.ijs.si>
	<66680366.20081209182904@gmail.com>
Message-ID: <1228864783.4650.31.camel@walk.ijs.si>

On Tue, 2008-12-09 at 18:29 +0800, hongyi.zhao at gmail.com wrote:
> Dear Tone,
> 
> In my case, I can easily get the 3d Charge density datagrid for  XCrySDen, but currently, 
> the XCrySDen can only give me the iso-surfaces of Charge density on three basal cystal planes. 
> If I can let XCrySDen extract a specific 2D charge density alone a specific plane based on a 3d 
> Charge density datagrid used by XCrySDen, it should be a wonderful thing for me.  
> Would you like give me some hints on this? 

This is currently not possible. But it would be a very useful feature.
I will think about it for the future releases.

In the meantime, perhaps the easiest thing would be to write, say, a
standalone fotran program that reads the 3D XSF datagrid and interpolate
a 2D datagrid on the specified plane, then you load this 2D datagrid
into xcrysden.

Regards, Tone
-- 
Tone Kokalj <tone.kokalj at ijs.si>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)


From zhaohscas at yahoo.com.cn  Wed Dec 10 03:54:08 2008
From: zhaohscas at yahoo.com.cn (Hongsheng Zhao)
Date: Wed, 10 Dec 2008 10:54:08 +0800
Subject: [xcrysden] Want to extract the 2D charge density based on a 3d
	Charge density datagrid by using XCrySDen automatically.
In-Reply-To: <1228864783.4650.31.camel@walk.ijs.si>
References: <769183.92154.qm@web94207.mail.in2.yahoo.com>
	<1228780425.4759.26.camel@walk.ijs.si>
	<66680366.20081209182904@gmail.com>
	<1228864783.4650.31.camel@walk.ijs.si>
Message-ID: <451473193.20081210105408@yahoo.com.cn>

On Wednesday, December 10, 2008 at 7:19, tone.kokalj at ijs.si wrote:
> On Tue, 2008-12-09 at 18:29 +0800, hongyi.zhao at gmail.com wrote:
>> Dear Tone,
>> 
>> In my case, I can easily get the 3d Charge density datagrid for  XCrySDen, but currently, 
>> the XCrySDen can only give me the iso-surfaces of Charge density on three basal cystal planes. 
>> If I can let XCrySDen extract a specific 2D charge density alone a specific plane based on a 3d 
>> Charge density datagrid used by XCrySDen, it should be a wonderful thing for me.  
>> Would you like give me some hints on this? 

> This is currently not possible. But it would be a very useful feature.
> I will think about it for the future releases.

> In the meantime, perhaps the easiest thing would be to write, say, a
> standalone fotran program that reads the 3D XSF datagrid and interpolate
> a 2D datagrid on the specified plane, then you load this 2D datagrid
> into xcrysden.

Would you kindly do so some basic job on this subroutine only in the
form of standalone fotran program?   If so, I can then test it for you
and this will be the first step for its integrate into the
xcrysden.

Regards,
-- 
Hongsheng Zhao <zhaohscas at yahoo.com.cn> 
Xinjiang Technical Institute of Physics and Chemistry
Chinese Academy of Sciences 
GnuPG DSA: 0xD108493
2008-12-10


From tasaka at affinity-science.com  Wed Dec 10 15:21:32 2008
From: tasaka at affinity-science.com (Tomohiko Tasaka)
Date: Wed, 10 Dec 2008 23:21:32 +0900
Subject: [xcrysden] finally new xcrysden version
In-Reply-To: <1228779311.4759.15.camel@walk.ijs.si>
References: <1228494361.5096.47.camel@walk.ijs.si>	<003b01c95929$f90c16a0$eb2443e0$@com>
	<1228779311.4759.15.camel@walk.ijs.si>
Message-ID: <001801c95ad2$9a648240$cf2d86c0$@com>

Hello Tone,

Sorry for the delay in response.
I was out of office and not able to access my Mac.

I find updated version on your web(thanks to Marino ;-),
but I can built xcrys linked with tcl/tk 8.5.5 now.

Here is new Make.sys.

eta:XCrySDen-1.5.17-src-all tasaka$ grep -v ^# Make.sys

MAKE = make

CFLAGS = -ansi -fwritable-strings  -funroll-loops -fPIC -DUSE_FONTS
CC     = gcc
MATH   = -lm
FFLAGS = -O2
FC     = g77


DARWIN_X11_PREFIX = /usr/X11
X_LIB     = -L$(DARWIN_X11_PREFIX)/lib -lXmu -lX11 -lXext -lXss -lfontconfig -lXft
X_INCDIR  = -I$(DARWIN_X11_PREFIX)/include


COMPILE_TCLTK = yes
COMPILE_MESA  = no

TCLTK_OPTIONS      = --disable-shared
MESA_OPTIONS       = --disable-shared --disable-3dnow

CoreFoundation=/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
TCL_LIB      = $(TOPDIR)/external/lib/libtcl8.5.a $(CoreFoundation)
TK_LIB      = $(TOPDIR)/external/lib/libtk8.5.a

GLU_LIB     = /sw/lib/mesa/libGLU.a
GL_LIB      = /sw/lib/mesa/libGL.a

TCL_INCDIR  = -I$(TOPDIR)/external/src/tcl$(TCL_VER3)/generic
TK_INCDIR   = -I$(TOPDIR)/external/src/tk$(TCL_VER3)/generic


eta:XCrySDen-1.5.17-src-all tasaka$ otool -L ./bin/xcrys
./bin/xcrys:
        /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version
150.0.0, current version 476.15.0)
        /usr/X11/lib/libXmu.6.dylib (compatibility version 9.0.0, current version 9.0.0)
        /usr/X11/lib/libX11.6.dylib (compatibility version 9.0.0, current version 9.0.0)
        /usr/X11/lib/libXext.6.dylib (compatibility version 11.0.0, current version 11.0.0)
        /usr/X11/lib/libXss.1.dylib (compatibility version 2.0.0, current version 2.0.0)
        /usr/X11/lib/libfontconfig.1.dylib (compatibility version 5.0.0, current version 5.0.0)
        /usr/X11/lib/libXft.2.dylib (compatibility version 4.0.0, current version 4.2.0)
        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 111.1.1)
        /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
eta:XCrySDen-1.5.17-src-all tasaka$


If you need this tar ball, I will send it to you via email.


regards,
Tomohiko

-----Original Message-----
From: xcrysden-bounces at democritos.it [mailto:xcrysden-bounces at democritos.it] On Behalf Of Tone Kokalj
Sent: Tuesday, December 09, 2008 8:35 AM
To: XCrySDen mailing list
Subject: Re: [xcrysden] finally new xcrysden version

On Mon, 2008-12-08 at 20:41 +0900, Tomohiko Tasaka wrote:
> Hello,
> 
> I can build new xcrysden on Intel-based Mac OS X 10.5.5 and have no problem until now.

Very good!!! 

I would much appreciate if you could make your compiled version
available also to other mac-osx users (myself, I don't have mac and I
cannot create it)? The recipe would go as follows: run "make bindist"
and email me the so-created tar.gz file. I will put it on the download
page.

Regards, Tone
-- 
Tone Kokalj <tone.kokalj at ijs.si>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)

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


From tone.kokalj at ijs.si  Wed Dec 10 15:29:53 2008
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Wed, 10 Dec 2008 15:29:53 +0100
Subject: [xcrysden] finally new xcrysden version
In-Reply-To: <001801c95ad2$9a648240$cf2d86c0$@com>
References: <1228494361.5096.47.camel@walk.ijs.si>
	<003b01c95929$f90c16a0$eb2443e0$@com>
	<1228779311.4759.15.camel@walk.ijs.si>
	<001801c95ad2$9a648240$cf2d86c0$@com>
Message-ID: <1228919393.4816.6.camel@walk.ijs.si>

On Wed, 2008-12-10 at 23:21 +0900, Tomohiko Tasaka wrote:
> Hello Tone,
> 
> Sorry for the delay in response.
> I was out of office and not able to access my Mac.
> 
> I find updated version on your web(thanks to Marino ;-),
> but I can built xcrys linked with tcl/tk 8.5.5 now.

If it works, sure!

Based on your Make.sys file, you may say "make bindist-static" to create
the appropriate distribution tarball. (the bindist-static target will
include the required external/lib/tcl8.5 and external/lib/tk8.5
directories into the package).

Regards, Tone
-- 
Tone Kokalj <tone.kokalj at ijs.si>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)


From tone.kokalj at ijs.si  Wed Dec 10 15:43:07 2008
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Wed, 10 Dec 2008 15:43:07 +0100
Subject: [xcrysden] finally new xcrysden version
In-Reply-To: <772688764.20081208184805@yahoo.com.cn>
References: <1228494361.5096.47.camel@walk.ijs.si>
	<772688764.20081208184805@yahoo.com.cn>
Message-ID: <1228920187.4816.12.camel@walk.ijs.si>

On Mon, 2008-12-08 at 18:48 +0800, Hongsheng Zhao wrote:
> 
> The above latest versions doesn't include the pre-compiled one for
> cygwin, why?

Dear Hongsheng Zhao,

In attition to the linux and macosx pre-compiled packages, also cygwin
package is avialable now on http://www.xcrysden.org/Download.html

Let me know how it works.

Regards, Tone
-- 
Tone Kokalj <tone.kokalj at ijs.si>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)


From juergen.spitaler at unileoben.ac.at  Wed Dec 10 16:09:17 2008
From: juergen.spitaler at unileoben.ac.at (Juergen Spitaler)
Date: Wed, 10 Dec 2008 16:09:17 +0100
Subject: [xcrysden] finally new xcrysden version
In-Reply-To: <1228920187.4816.12.camel@walk.ijs.si>
References: <1228494361.5096.47.camel@walk.ijs.si>	<772688764.20081208184805@yahoo.com.cn>
	<1228920187.4816.12.camel@walk.ijs.si>
Message-ID: <493FDB9D.9040104@unileoben.ac.at>

Dear Tone,
I have been using and appreciating XCrysden for several
years. I think it is a really great visualization tool, so I am very
happy about the new release!

I wanted to report some ideas for improvement:
- Currently, "Save current state and structure" does not save
 forces. It would be nice if they could be saved as well
- I would appreciate a possibility to "hide" selected atoms
 in order to produce print-outs that focus on specific parts
 or species of a structure.
- I would also appreciate a possibility to give the zoom factor
 and rotations directly as numbers; for example
    > Zoom=+25
    > RotX=+12
    > RotY=-3
    > RotZ=+47
(I think the order of the rotation matters, so this could be more tricky
...)
This way  one could reconstruct a certain perspective and size of the
structure
directly. This would be especially helpful for comparing structures
which slightly differ from each other, where the
"Save current state and structure" menu does not do the job one wants.

Best wishes,
Juergen



> Dear Hongsheng Zhao,
>
> In attition to the linux and macosx pre-compiled packages, also cygwin
> package is avialable now on http://www.xcrysden.org/Download.html
>
> Let me know how it works.
>
> Regards, Tone
>   


-- 
Dr. J?rgen Spitaler
Material Center Leoben and
Chair of Atomistic Modelling and Design of Materials, Leoben University
Franz-Josef-Stra?e 18    
8700 Leoben
Tel.: ++43 (0)3842 402 4404
E-Mail: juergen.spitaler at unileoben.ac.at



From pemryan at gmail.com  Wed Dec 10 17:01:16 2008
From: pemryan at gmail.com (Yan Ren)
Date: Thu, 11 Dec 2008 00:01:16 +0800
Subject: [xcrysden] Error in xcInit.tcl
Message-ID: <200812110001.16685.pemryan@gmail.com>

Dear all,

I downloaded a shared version of xcrysden (xc-1.5.17-linux_x86-shared.tar.gz) 
from the official website. After untargz and install, I met this error when 
executing xcrysden :

----------------
Running on platform: unix
Executing: /home/pem/XCrySDen-1.5.17-bin-shared/bin/ftnunit
./xcrysden: line 211: 22307 Aborted                 
${XCRYSDEN_TOPDIR}/bin/xcrys ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- 
$XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH $ARGS > /dev/null 
---------------

I looked up line 211 of xcrysden, and found it calls 
$XCRYSDEN_TOPDIR/Tcl/xcInit.tcl. So I tested with this command:

./${XCRYSDEN_TOPDIR}/bin/xcrys  ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl

and the error info is:

Error in startup script: couldn't open "/images/xcrysden_kpath.gif": no such 
file or directory                           
    while executing                                                                                                      
"image create photo kpath -format gif \                                                                                  
    -file $system(TOPDIR)/images/xcrysden_kpath.gif"                                                                     
    (file "/home/pem/XCrySDen-1.5.17-bin-shared/Tcl/xcInit.tcl" line 478)    

where my $HOME=/home/pem. But /home/pem/images/xcrysden_kpath.gif  exists. 
Thus I tested this:

tclsh  $system(TOPDIR)

this gives such a result: 

% $system(TOPDIR)
can't read "system(TOPDIR)": no such variable

I googled and found this form : $::env(TOPDIR), and it works,
% $::env(TOPDIR)
invalid command name "/home/pem/XCrySDen-1.5.17-bin-shared"

So I replaced $system(TOPDIR) with $::env(TOPDIR)  in this file and tried to 
run xcrysden again. this time the error was:

ERROR: SCRATCH directory "" does not exist

I export $XCRYSDEN_SCRATCH=/home/pem/XCrySDen-1.5.17-bin-shared/ and tried 
again and found this error:

Error in startup script: no such variable                               
    (read trace on "::env(SCRDIR)")                                     
    invoked from within                                                 
"file isdirectory $::env(SCRDIR)"                                       
    invoked from within                                                 
"if { ![file isdirectory $::env(SCRDIR)] } {                            
        puts stderr "ERROR: SCRATCH directory \"$::env(SCRDIR)\" does not 
exist"
        exit 0                                                                  
    }"                                                                          
    ("eval" body line 5)                                                        
    invoked from within                                                         
"eval [info body xcInit]"        

... ...

My computer is running Arch linux current, the version of tcl and tk are 8.5.
I don't konw where is the problem and need your help.  Hope the info above 
helps. Thank you in advance.

--------------------------
pem 
pemryan at gmail.com




From hongyi.zhao at gmail.com  Wed Dec 10 17:01:21 2008
From: hongyi.zhao at gmail.com (hongyi.zhao at gmail.com)
Date: Thu, 11 Dec 2008 00:01:21 +0800
Subject: [xcrysden] finally new xcrysden version
In-Reply-To: <1228920187.4816.12.camel@walk.ijs.si>
References: <1228494361.5096.47.camel@walk.ijs.si>
	<772688764.20081208184805@yahoo.com.cn>
	<1228920187.4816.12.camel@walk.ijs.si>
Message-ID: <1573807783.20081211000121@gmail.com>

On Wednesday, December 10, 2008 at 22:43, tone.kokalj at ijs.si wrote:
> Dear Hongsheng Zhao,

> In attition to the linux and macosx pre-compiled packages, also cygwin
> package is avialable now on http://www.xcrysden.org/Download.html

I've tested the cygwin package on my winxp sp3 32-bit os, it does
works smoothly.

Regards,
--
Hongyi Zhao <hongyi.zhao at gmail.com> 
Xinjiang Technical Institute of Physics and Chemistry
Chinese Academy of Sciences 
GnuPG DSA: 0xD108493
2008-12-10


From tone.kokalj at ijs.si  Wed Dec 10 22:16:15 2008
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Wed, 10 Dec 2008 22:16:15 +0100
Subject: [xcrysden] Error in xcInit.tcl
In-Reply-To: <200812110001.16685.pemryan@gmail.com>
References: <200812110001.16685.pemryan@gmail.com>
Message-ID: <1228943775.12621.15.camel@walk.ijs.si>

On Thu, 2008-12-11 at 00:01 +0800, Yan Ren wrote:
> Dear all,
> 
> I downloaded a shared version of xcrysden (xc-1.5.17-linux_x86-shared.tar.gz) 
> from the official website. After untargz and install, I met this error when 
> executing xcrysden :
> 
> ----------------
> Running on platform: unix
> Executing: /home/pem/XCrySDen-1.5.17-bin-shared/bin/ftnunit
> ./xcrysden: line 211: 22307 Aborted                 
> ${XCRYSDEN_TOPDIR}/bin/xcrys ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- 
> $XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH $ARGS > /dev/null 

The problem here is that xcrysden "crashes" (more precisely aborts). The
line 211 is the actuall "call" to launch xcrysden.

> ---------------
> 
> I looked up line 211 of xcrysden, and found it calls 
> $XCRYSDEN_TOPDIR/Tcl/xcInit.tcl. So I tested with this command:
> 
> ./${XCRYSDEN_TOPDIR}/bin/xcrys  ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl

Don't launch xcrysden like that. It will defenitely fail. The purpose of
"xcrysden" wrapper is to setup proper environment.

Your above printout may indicate that it is the ftnunit program that
gives the problem. Try to execute:

/home/pem/XCrySDen-1.5.17-bin-shared/bin/ftnunit

Does it work (it shoud create file fort.99)?

If it works, the reason is elsewhere. Run xcrysden as:

xcrysden -T >& log

and send me the log file.

Regards, Tone
-- 
Tone Kokalj <tone.kokalj at ijs.si>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)


From tone.kokalj at ijs.si  Wed Dec 10 22:17:53 2008
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Wed, 10 Dec 2008 22:17:53 +0100
Subject: [xcrysden] finally new xcrysden version
In-Reply-To: <493FDB9D.9040104@unileoben.ac.at>
References: <1228494361.5096.47.camel@walk.ijs.si>
	<772688764.20081208184805@yahoo.com.cn>
	<1228920187.4816.12.camel@walk.ijs.si>
	<493FDB9D.9040104@unileoben.ac.at>
Message-ID: <1228943873.12621.18.camel@walk.ijs.si>

On Wed, 2008-12-10 at 16:09 +0100, Juergen Spitaler wrote:
> Dear Tone,
> I have been using and appreciating XCrysden for several
> years. I think it is a really great visualization tool, so I am very
> happy about the new release!
> 
> I wanted to report some ideas for improvement:
> - Currently, "Save current state and structure" does not save
>  forces. It would be nice if they could be saved as well

Indeed! Thanks. Added to TODO list (priority=high). 

> - I would appreciate a possibility to "hide" selected atoms
>  in order to produce print-outs that focus on specific parts
>  or species of a structure.

Actually, it is on my wishlist to make kind of structure-builder
(but this is for several years so, can't promise when this will be
realized).

> - I would also appreciate a possibility to give the zoom factor
>  and rotations directly as numbers; for example
>     > Zoom=+25
>     > RotX=+12
>     > RotY=-3
>     > RotZ=+47
> (I think the order of the rotation matters, so this could be more tricky
> ...)

You may switch to discrete rotation-zooming mode, and then you can press
corresponding buttons in the sequence you want (is this what would you like to achieve?).

Regards, Tone

-- 
Tone Kokalj <tone.kokalj at ijs.si>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)


From pemryan at gmail.com  Thu Dec 11 09:28:02 2008
From: pemryan at gmail.com (Yan Ren)
Date: Thu, 11 Dec 2008 16:28:02 +0800
Subject: [xcrysden] Error in xcInit.tcl
In-Reply-To: <mailman.5.1228981078.5747.xcrysden@democritos.it>
References: <mailman.5.1228981078.5747.xcrysden@democritos.it>
Message-ID: <200812111628.02870.pemryan@gmail.com>

Hello Tone,

Thank you for your reply.

On Thursday 11 December 2008 15:37:58 xcrysden-request at democritos.it wrote:
> The problem here is that xcrysden "crashes" (more precisely aborts). The
> line 211 is the actuall "call" to launch xcrysden.
>
> Don't launch xcrysden like that. It will defenitely fail. The purpose of
> "xcrysden" wrapper is to setup proper environment.
>
> Your above printout may indicate that it is the ftnunit program that
> gives the problem. Try to execute:
>
> /home/pem/XCrySDen-1.5.17-bin-shared/bin/ftnunit
>
> Does it work (it shoud create file fort.99)?
it works.

bash-3.2$ rm fort.99 
bash-3.2$ /home/pem/XCrySDen-1.5.17-bin-shared/bin/ftnunit
bash-3.2$ cat fort.99 
 test


> If it works, the reason is elsewhere. Run xcrysden as:
>
> xcrysden -T >& log
>
> and send me the log file.
this command shows a splash of the xcrysden logo and exit.
I've attached the log file created by this command.


Regards,

pem


-------------- next part --------------

+----------------------------------------------------------------+
|****************************************************************|
|*								*|
|*  XCrySDen - (X-Window) CRYstalline Structures and DENsities  *|
|*		=         ===         =              ===        *|
|*--------------------------------------------------------------*|
|*								*|
|*    Anton Kokalj (Tone.Kokalj at ijs.si)                         *|
|*    Jozef Stefan Institute, Ljubljana, Slovenia               *|
|*								*|
|*    Copyright (c) 1996--2004 by Anton Kokalj                  *|
|*                                                              *|
|****************************************************************|
+----------------------------------------------------------------+

  Version: 1.5.17

  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=/home/pem/XCrySDen-1.5.17-bin-shared
XCRYSDEN_SCRATCH=/home/pem/xcrys_tmp

Running on platform: unix
centerWelcome .title ; level == 1
::tk_setPalette {{#e0dfde}} ; level == 1
::tk::RecolorTree . new ; level == 2
::tk::RecolorTree .#BWidget c ; level == 3
::tk::RecolorTree .#BWidget.#label c ; level == 4
::tk::RecolorTree .#BWidget.#Class#DynamicHelp c ; level == 4
::tk::RecolorTree .#BWidget.#button c ; level == 4
::tk::RecolorTree .#BWidget.#frame c ; level == 4
::tk::RecolorTree .#BWidget.#scrollbar c ; level == 4
::tk::RecolorTree .#BWidget.#entry c ; level == 4
::tk::RecolorTree .#BWidget.#canvas c ; level == 4
::tk::RecolorTree .#BWidget.#listbox c ; level == 4
::tk::RecolorTree .#BWidget.#message c ; level == 4
::tk::RecolorTree .title c ; level == 3
::tk::RecolorTree .title.f c ; level == 4
::tk::RecolorTree .title.f.l c ; level == 5
::tk::RecolorTree .title.f.l2 c ; level == 5
::tk::RecolorTree .___tk_set_palette c ; level == 3
::tk::RecolorTree .___tk_set_palette.button c ; level == 4
::tk::RecolorTree .___tk_set_palette.canvas c ; level == 4
::tk::RecolorTree .___tk_set_palette.checkbutton c ; level == 4
::tk::RecolorTree .___tk_set_palette.entry c ; level == 4
::tk::RecolorTree .___tk_set_palette.frame c ; level == 4
::tk::RecolorTree .___tk_set_palette.label c ; level == 4
::tk::RecolorTree .___tk_set_palette.labelframe c ; level == 4
::tk::RecolorTree .___tk_set_palette.listbox c ; level == 4
::tk::RecolorTree .___tk_set_palette.menubutton c ; level == 4
::tk::RecolorTree .___tk_set_palette.menu c ; level == 4
::tk::RecolorTree .___tk_set_palette.message c ; level == 4
::tk::RecolorTree .___tk_set_palette.radiobutton c ; level == 4
::tk::RecolorTree .___tk_set_palette.scale c ; level == 4
::tk::RecolorTree .___tk_set_palette.scrollbar c ; level == 4
::tk::RecolorTree .___tk_set_palette.spinbox c ; level == 4
::tk::RecolorTree .___tk_set_palette.text c ; level == 4
GetWidgetConfig button -disabledforeground ; level == 1
GetWidgetConfig scale -foreground ; level == 1
GetWidgetConfig button -background ; level == 1
ProbeResolution ; level == 1
ModifyFont TkDefaultFont .test_widget {-size -12 -default 1} ; level == 2
ModifyFont TkDefaultFont .test_widget {-size -14 -default 1} ; level == 2
ModifyFont TkDefaultFont .test_widget {-size -10 -default 1} ; level == 2
ModifyFont TkDefaultFont .test_widget {-size -12 -default 1} ; level == 2
ModifyFont TkTextFont .test_widget {-size -12 -default 1} ; level == 2
ModifyFont TkTextFont .test_widget {-size -14 -default 1} ; level == 2
ModifyFont TkDefaultFont .test_widget {-size -12 -default 1} ; level == 2
ModifyFont TkDefaultFont .test_widget {-size -12 -default 1} ; level == 2
ModifyFont TkMenuFont .test_widget {-size -12 -default 1} ; level == 2
ModifyFont TkDefaultFont .test_widget {-size -12 -default 1} ; level == 2
ModifyFont TkDefaultFont .test_widget {-size -12 -default 1} ; level == 2
ModifyFont TkDefaultFont .test_widget {-size -12 -default 1} ; level == 2
ModifyFont TkDefaultFont .test_widget {-size -12 -default 1} ; level == 2
ModifyFont TkFixedFont .test_widget {-size -12 -default 1} ; level == 2
xcDebug {Taking settings for 1440x900 screen-resolution !!!} {} ; level == 2
xcDebug ------------------- {} ; level == 2
xcDebug {Small  Font Size set to:   -14} {} ; level == 2
xcDebug {Normal Font Size set to:   -12} {} ; level == 2
SetImageSizes ; level == 1
check_package_awk ; level == 1
check_package_terminal ; level == 1
check_package_crystal ; level == 1
find_package_imagemagick ; level == 1
find_package convert xcMisc(ImageMagick.convert) query_imagemagick ; level == 2
check_package convert query_imagemagick ; level == 3
query_imagemagick /usr/bin/convert ; level == 4
find_package import xcMisc(ImageMagick.import) query_imagemagick ; level == 2
check_package import query_imagemagick ; level == 3
query_imagemagick /usr/bin/import ; level == 4
find_package_gifsicle ; level == 1
find_package gifsicle xcMisc(gifsicle) query_gifsicle ; level == 2
check_package gifsicle query_gifsicle ; level == 3
find_package_whirlgif ; level == 1
find_package whirlgif xcMisc(whirlgif) query_whirlgif ; level == 2
check_package whirlgif query_whirlgif ; level == 3
find_package_mencoder ; level == 1
find_package mencoder xcMisc(mencoder) query_mencoder ; level == 2
check_package mencoder query_mencoder ; level == 3
query_mencoder /usr/bin/mencoder ; level == 4
find_package_ppmtompeg ; level == 1
find_package ppmtompeg xcMisc(ppmtompeg) query_ppmtompeg ; level == 2
check_package ppmtompeg query_ppmtompeg ; level == 3
query_ppmtompeg /usr/bin/ppmtompeg ; level == 4
find_package_babel ; level == 1
find_package babel xcMisc(babel) query_babel ; level == 2
check_package babel query_babel ; level == 3
query_babel /usr/bin/babel ; level == 4
find_package_xwd ; level == 1
find_package xwd xcMisc(xwd) query_xwd ; level == 2
check_package xwd query_xwd ; level == 3
query_xwd /usr/bin/xwd ; level == 4
determine_movie_encoders ; level == 1
FtnName ; level == 1
xcCatchExecReturn /home/pem/XCrySDen-1.5.17-bin-shared/bin/ftnunit ; level == 2
destroyWelcome ; level == 3
xcDebug -stderr {{Executing: /home/pem/XCrySDen-1.5.17-bin-shared/bin/ftnunit}} ; level == 3
Executing: /home/pem/XCrySDen-1.5.17-bin-shared/bin/ftnunit
GetGengM3Arg ANGS none ; level == 2
ModConst ; level == 2
/home/pem/XCrySDen-1.5.17-bin-shared/xcrysden: line 211:  2861 Aborted                 ${XCRYSDEN_TOPDIR}/bin/xcrys ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH $ARGS > /dev/null

From tone.kokalj at ijs.si  Thu Dec 11 10:10:10 2008
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Thu, 11 Dec 2008 10:10:10 +0100
Subject: [xcrysden] Error in xcInit.tcl
In-Reply-To: <200812111628.02870.pemryan@gmail.com>
References: <mailman.5.1228981078.5747.xcrysden@democritos.it>
	<200812111628.02870.pemryan@gmail.com>
Message-ID: <1228986610.25820.11.camel@walk.ijs.si>

On Thu, 2008-12-11 at 16:28 +0800, Yan Ren wrote:
> > If it works, the reason is elsewhere. Run xcrysden as:
> >
> > xcrysden -T >& log
> >
> > and send me the log file.
> this command shows a splash of the xcrysden logo and exit.
> I've attached the log file created by this command.

OK, now I know where it chashes (in the first OpenGL call). 

I noticed that sometimes xcrysden doesn't work with the default 
system libGL.so library that the shared packages of xcrysden use
(but so far I only expirienced this for 64bit version).

The solution is to used the semishared xcrysden package instead, which has it's 
own-compiled libGL.so library that *should* work.

Regards, Tone
-- 
Tone Kokalj <tone.kokalj at ijs.si>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)


From psbishtphyjiwaji at yahoo.co.in  Thu Dec 11 12:44:33 2008
From: psbishtphyjiwaji at yahoo.co.in (pradeep bisht)
Date: Thu, 11 Dec 2008 17:14:33 +0530 (IST)
Subject: [xcrysden] Electron density
In-Reply-To: <mailman.5.1228981078.5747.xcrysden@democritos.it>
Message-ID: <383146.87736.qm@web94208.mail.in2.yahoo.com>

respect to all xcrysden users,

I am using wien2k for my project I want to know how I can calculate the electron density using xcrysden 
I have? Select 2D-plot
Specified a resolution of 100 points
Selected a plane by selecting 3 atoms and define these 3 atoms by
  clicking on them
Choose? rectangular parallelogram and enlarge the
  rectangular selection by 0.5 and updtate the display and submit 
Another? window appear
How to select the no of shell? what is the meaning of X shell and y and z
X shells
?y Shell
Z shell
I have make them default
as 
3
2
3
Select density fleg rho
unit flag Ang
norm flag val
and submit another window appear here degree of cubic supline is one chose the rainbow colour option.
select scale function? linear
and plot 
is this is write way to visulize the electron density

Thanking u
Pradeep





      Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/
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From juergen.spitaler at unileoben.ac.at  Thu Dec 11 14:41:46 2008
From: juergen.spitaler at unileoben.ac.at (Juergen Spitaler)
Date: Thu, 11 Dec 2008 14:41:46 +0100
Subject: [xcrysden] Primitive cell in scripting
In-Reply-To: <1228990011.25820.32.camel@walk.ijs.si>
References: <1228494361.5096.47.camel@walk.ijs.si>	
	<772688764.20081208184805@yahoo.com.cn>	
	<1228920187.4816.12.camel@walk.ijs.si>
	<493FDB9D.9040104@unileoben.ac.at>	
	<1228943114.12621.8.camel@walk.ijs.si>
	<4940E3CE.5090202@unileoben.ac.at>
	<1228990011.25820.32.camel@walk.ijs.si>
Message-ID: <4941189A.7040303@unileoben.ac.at>

Dear Tone,
following your advice I have started to use scripting
for displaying a structure with specified parameters
and it works fine!

I probably also found a small bug: I do not succeed
to switch to primitive cell mode within script.

I have used the following short script

==================== SCRIPT ======================
scripting::open --wien_struct str_prim_cell.struct
scripting::display on crystal-cells
scripting::display as cell-mode primitive
=======================================

where str_prim_cell.struct is a very simple WIEN2k struct file,
which is also attached to this email. Actually, if I execute the script
xcrysden shows the conventional cell, but in the "Display" menu
"Primitive Cell mode" is checked.

Regards,
Juergen



============= BEGIN str_prim_cell.struct =========================
Very simple rhombohedral test structure          
R                           
1167_R-3c                                        
            
RELA                                                             
 8.9894300
8.989430024.543200090.000000090.000000090.0000000                  
ATOM  -1: X=0.35192080 Y=0.35192080 Z=0.35192080
          MULT= 4          ISPLIT= 4
      -1: X=0.85192080 Y=0.85192080 Z=0.85192080
      -1: X=0.14807920 Y=0.14807920 Z=0.14807920
      -1: X=0.64807920 Y=0.64807920 Z=0.64807920
Al               781     .000500000 RMT=   1.57      Z:
13.00000              
LOCAL ROT MATRIX:    1.0000000 0.0000000 0.0000000
                     0.0000000 1.0000000 0.0000000
                     0.0000000 0.0000000 1.0000000
  0       NUMBER OF SYMMETRY OPERATIONS
================ END WIEN2k struct file ========================


-- 
Dr. J?rgen Spitaler
Material Center Leoben and
Chair of Atomistic Modelling and Design of Materials, Leoben University
Franz-Josef-Stra?e 18    
8700 Leoben
Tel.: ++43 (0)3842 402 4404
E-Mail: juergen.spitaler at unileoben.ac.at



From tone.kokalj at ijs.si  Thu Dec 11 14:53:57 2008
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Thu, 11 Dec 2008 14:53:57 +0100
Subject: [xcrysden] Primitive cell in scripting
In-Reply-To: <4941189A.7040303@unileoben.ac.at>
References: <1228494361.5096.47.camel@walk.ijs.si>
	<772688764.20081208184805@yahoo.com.cn>
	<1228920187.4816.12.camel@walk.ijs.si>
	<493FDB9D.9040104@unileoben.ac.at>
	<1228943114.12621.8.camel@walk.ijs.si>
	<4940E3CE.5090202@unileoben.ac.at>
	<1228990011.25820.32.camel@walk.ijs.si>
	<4941189A.7040303@unileoben.ac.at>
Message-ID: <1229003637.25820.36.camel@walk.ijs.si>

On Thu, 2008-12-11 at 14:41 +0100, Juergen Spitaler wrote:
> Dear Tone,
> following your advice I have started to use scripting
> for displaying a structure with specified parameters
> and it works fine!
> 
> I probably also found a small bug: I do not succeed
> to switch to primitive cell mode within script.

Indeed! Thanks. Bug fixed. (copy attached file into xcrysden's Tcl/
subdurectory and it should work).

Regards, Tone
-- 
Tone Kokalj <tone.kokalj at ijs.si>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)
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From dstrubbe at civet.berkeley.edu  Thu Dec 18 04:04:06 2008
From: dstrubbe at civet.berkeley.edu (David Strubbe)
Date: Wed, 17 Dec 2008 19:04:06 -0800
Subject: [xcrysden] Problem with MacOS version
Message-ID: <31110e0e0812171904i5a44d176u5bbd767cbb65676e@mail.gmail.com>

Tone,

I just installed from the website the following version for Mac OS:

Semistatic: xc-1.5.17-macosx.tar.gz (Courtesy of Tomohiko Tasaka)

After configuring, when I run it, it immediately terminates, saying it
cannot find the library /usr/X11/lib/libXmu.6.dylib
I have this file instead at /usr/X11R6/lib/libXmu.6.dylib
Is there a way to change the path where XCrySDen looks for the file?

Thanks,
David Strubbe

Here is the full output below:

+----------------------------------------------------------------+
|****************************************************************|
|*                                                              *|
|*  XCrySDen - (X-Window) CRYstalline Structures and DENsities  *|
|*              =         ===         =              ===        *|
|*--------------------------------------------------------------*|
|*                                                              *|
|*    Anton Kokalj (Tone.Kokalj at ijs.si)                         *|
|*    Jozef Stefan Institute, Ljubljana, Slovenia               *|
|*                                                              *|
|*    Copyright (c) 1996--2004 by Anton Kokalj                  *|
|*                                                              *|
|****************************************************************|
+----------------------------------------------------------------+

 Version: 1.5.17

 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=/Users/dstrubbe/XCrySDen-1.5.17-bin/external/lib/tcl8.5
XCRYSDEN_TOPDIR=/Users/dstrubbe/XCrySDen-1.5.17-bin
XCRYSDEN_SCRATCH=/Users/dstrubbe/XCrySDen-1.5.17-bin/xcrys_tmp

dyld: Library not loaded: /usr/X11/lib/libXmu.6.dylib
 Referenced from: /Users/dstrubbe/XCrySDen-1.5.17-bin/bin/xcrys
 Reason: image not found
/Users/dstrubbe/XCrySDen-1.5.17-bin/xcrysden: line 248:   100
Trace/BPT trap          ${XCRYSDEN_TOPDIR}/bin/xcrys
${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR
$XCRYSDEN_SCRATCH $ARGS >/dev/null
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From tasaka at affinity-science.com  Thu Dec 18 04:23:39 2008
From: tasaka at affinity-science.com (Tomohiko Tasaka)
Date: Thu, 18 Dec 2008 12:23:39 +0900
Subject: [xcrysden] Problem with MacOS version
In-Reply-To: <31110e0e0812171904i5a44d176u5bbd767cbb65676e@mail.gmail.com>
References: <31110e0e0812171904i5a44d176u5bbd767cbb65676e@mail.gmail.com>
Message-ID: <001401c960c0$056d5b50$104811f0$@com>

Hello,

 

Please try the following command from a terminal prompt.

 

for sh/bash user

export DYLD_FALLBACK_LIBRARY_PATH=/usr/X11R6/lib

 

for csh/tcsh user

setenv DYLD_FALLBACK_LIBRARY_PATH /usr/X11R6/lib

 

HTH

Tomo

 

 

From: xcrysden-bounces at democritos.it [mailto:xcrysden-bounces at democritos.it] On Behalf Of David Strubbe
Sent: Thursday, December 18, 2008 12:04 PM
To: xcrysden at democritos.it
Subject: [xcrysden] Problem with MacOS version

 

Tone,

I just installed from the website the following version for Mac OS:

Semistatic: xc-1.5.17-macosx.tar.gz (Courtesy of Tomohiko Tasaka)

After configuring, when I run it, it immediately terminates, saying it
cannot find the library /usr/X11/lib/libXmu.6.dylib
I have this file instead at /usr/X11R6/lib/libXmu.6.dylib
Is there a way to change the path where XCrySDen looks for the file?

Thanks,
David Strubbe

Here is the full output below:

+----------------------------------------------------------------+
|****************************************************************|
|*                                                              *|
|*  XCrySDen - (X-Window) CRYstalline Structures and DENsities  *|
|*              =         ===         =              ===        *|
|*--------------------------------------------------------------*|
|*                                                              *|
|*    Anton Kokalj (Tone.Kokalj at ijs.si)                         *|
|*    Jozef Stefan Institute, Ljubljana, Slovenia               *|
|*                                                              *|
|*    Copyright (c) 1996--2004 by Anton Kokalj                  *|
|*                                                              *|
|****************************************************************|
+----------------------------------------------------------------+

 Version: 1.5.17

 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. <http://www.xcrysden.org/> xcrysden.org/.

TCL_LIBRARY=/Users/dstrubbe/XCrySDen-1.5.17-bin/external/lib/tcl8.5
XCRYSDEN_TOPDIR=/Users/dstrubbe/XCrySDen-1.5.17-bin
XCRYSDEN_SCRATCH=/Users/dstrubbe/XCrySDen-1.5.17-bin/xcrys_tmp

dyld: Library not loaded: /usr/X11/lib/libXmu.6.dylib
 Referenced from: /Users/dstrubbe/XCrySDen-1.5.17-bin/bin/xcrys
 Reason: image not found
/Users/dstrubbe/XCrySDen-1.5.17-bin/xcrysden: line 248:   100
Trace/BPT trap          ${XCRYSDEN_TOPDIR}/bin/xcrys
${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR
$XCRYSDEN_SCRATCH $ARGS >/dev/null 

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From sarayazdani at yahoo.com  Thu Dec 18 09:16:57 2008
From: sarayazdani at yahoo.com (sara yazdani)
Date: Thu, 18 Dec 2008 00:16:57 -0800 (PST)
Subject: [xcrysden] xcrysden on opensuse
Message-ID: <881726.44269.qm@web52004.mail.re2.yahoo.com>

hi all,

I have tried installing different versions of xcrysden on opensuse 11. but I have encountered two problems:

1. it always gives the warning of "unknown -m" ?!?!
2. although Ialways check the correctness of the addresses of "babel" , "imagemagick" and ..., it still does not show up the xcrysden window!!!

I have installed it successfuly in Fedora and Centos, but on suse ?!?!?! please let me know what I should do.

Regards,
Sara





      
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From tone.kokalj at ijs.si  Thu Dec 18 11:02:35 2008
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Thu, 18 Dec 2008 11:02:35 +0100
Subject: [xcrysden] xcrysden on opensuse
In-Reply-To: <881726.44269.qm@web52004.mail.re2.yahoo.com>
References: <881726.44269.qm@web52004.mail.re2.yahoo.com>
Message-ID: <1229594555.24851.4.camel@walk.ijs.si>

On Thu, 2008-12-18 at 00:16 -0800, sara yazdani wrote:
> hi all,
> 
> I have tried installing different versions of xcrysden on opensuse 11.
> but I have encountered two problems:
> 
> 1. it always gives the warning of "unknown -m" ?!?!
> 2. although Ialways check the correctness of the addresses of "babel" , "imagemagick" and ..., it still does not show up the xcrysden window!!!

Have no idea what is "unknown -m". Moreover, the external programs such
as ImageMagick are optional not mandatory, so this is unlikely the
failure reason.

Please run xcrysden as: xcrysden -T >& log
and send me the log file.

Regards, Tone

-- 
Tone Kokalj <tone.kokalj at ijs.si>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)


From mpy at gmx.net  Thu Dec 18 11:29:54 2008
From: mpy at gmx.net (Manuel Presnitz)
Date: Thu, 18 Dec 2008 11:29:54 +0100
Subject: [xcrysden] xcrysden on opensuse
In-Reply-To: <881726.44269.qm@web52004.mail.re2.yahoo.com>
References: <881726.44269.qm@web52004.mail.re2.yahoo.com>
Message-ID: <20081218102954.301890@gmx.net>

> I have tried installing different versions of xcrysden on opensuse 11. but
> I have encountered two problems:

I can't confirm this problem, XCrysDen 1.5.17 works fine here on openSuSE 11.0,
so it could be an individual issue:

# cat /etc/SuSE-release
openSUSE 11.0 (X86-64)
VERSION = 11.0

# xcrysden

+----------------------------------------------------------------+
|****************************************************************|
|*								*|
|*  XCrySDen - (X-Window) CRYstalline Structures and DENsities  *|
|*		=         ===         =              ===        *|
|*--------------------------------------------------------------*|
|*								*|
|*    Anton Kokalj (Tone.Kokalj at ijs.si)                         *|
|*    Jozef Stefan Institute, Ljubljana, Slovenia               *|
|*								*|
|*    Copyright (c) 1996--2004 by Anton Kokalj                  *|
|*                                                              *|
|****************************************************************|
+----------------------------------------------------------------+

  Version: 1.5.17

  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=/usr/local/xcrysden_1.5.17/external/lib/tcl8.5
XCRYSDEN_TOPDIR=/usr/local/xcrysden_1.5.17
XCRYSDEN_SCRATCH=/tmp

Running on platform: unix
CRYSTAL VERSION: 06
Executing: /usr/local/xcrysden_1.5.17/bin/ftnunit
************************************************************************
Deleting directory /tmp/xc_19291 ; Please Wait !!!
************************************************************************
Directory deleted !


Regards,
Manuel.

-- 
Sensationsangebot verl?ngert: GMX FreeDSL - Telefonanschluss + DSL 
f?r nur 16,37 Euro/mtl.!* http://dsl.gmx.de/?ac=OM.AD.PD003K1308T4569a

From sarayazdani at yahoo.com  Thu Dec 18 12:17:59 2008
From: sarayazdani at yahoo.com (sara yazdani)
Date: Thu, 18 Dec 2008 03:17:59 -0800 (PST)
Subject: [xcrysden] xcrysden on opensuse
In-Reply-To: <1229594555.24851.4.camel@walk.ijs.si>
Message-ID: <150405.51498.qm@web52009.mail.re2.yahoo.com>

Dear all,

Thanks for replying me.

In order to have exact report I again downloaded xcrysden "xc-1.5.17-src-all.tar.gz" today.

after printing: ./xcConfigure I received:

more: unknown option "-m"
usage: more [-dflpcsu] [+linenum | +/pattern] name1 name2 ...

I entered down and printed "source ~/.bashrc" and xcrysden which was again an unknown command for it!!! This is while I have installed opensuse completely.

I have enclosed the log file you kindly asked me.

Sorry to take your time in busy time of christmas.
Regards,
Sara

--- On Thu, 18/12/08, Tone Kokalj <tone.kokalj at ijs.si> wrote:
From: Tone Kokalj <tone.kokalj at ijs.si>
Subject: Re: [xcrysden] xcrysden on opensuse
To: sarayazdani at yahoo.com, "XCrySDen mailing list" <xcrysden at democritos.it>
Date: Thursday, 18 December, 2008, 2:02 AM

On Thu, 2008-12-18 at 00:16 -0800, sara yazdani wrote:
> hi all,
> 
> I have tried installing different versions of xcrysden on opensuse 11.
> but I have encountered two problems:
> 
> 1. it always gives the warning of "unknown -m" ?!?!
> 2. although Ialways check the correctness of the addresses of
"babel" , "imagemagick" and ..., it still does not show up
the xcrysden window!!!

Have no idea what is "unknown -m". Moreover, the external programs
such
as ImageMagick are optional not mandatory, so this is unlikely the
failure reason.

Please run xcrysden as: xcrysden -T >& log
and send me the log file.

Regards, Tone

-- 
Tone Kokalj <tone.kokalj at ijs.si>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)




      
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From eyert at physik.uni-augsburg.de  Thu Dec 18 11:40:36 2008
From: eyert at physik.uni-augsburg.de (Volker Eyert)
Date: Thu, 18 Dec 2008 11:40:36 +0100
Subject: [xcrysden] xcrysden on opensuse
In-Reply-To: <20081218102954.301890@gmx.net>
References: <881726.44269.qm@web52004.mail.re2.yahoo.com>
	<20081218102954.301890@gmx.net>
Message-ID: <494A28A4.9020602@physik.uni-augsburg.de>

Manuel,

thanks a lot, I can confirm your statement. I have no problems
installing and running XCrysDen on openSuSE 11.0 at all.

Best wishes

Volker


Manuel Presnitz wrote:
>> I have tried installing different versions of xcrysden on opensuse 11. but
>> I have encountered two problems:
> 
> I can't confirm this problem, XCrysDen 1.5.17 works fine here on openSuSE 11.0,
> so it could be an individual issue:
> 
> # cat /etc/SuSE-release
> openSUSE 11.0 (X86-64)
> VERSION = 11.0
> 
> # xcrysden
> 
> +----------------------------------------------------------------+
> |****************************************************************|
> |*								*|
> |*  XCrySDen - (X-Window) CRYstalline Structures and DENsities  *|
> |*		=         ===         =              ===        *|
> |*--------------------------------------------------------------*|
> |*								*|
> |*    Anton Kokalj (Tone.Kokalj at ijs.si)                         *|
> |*    Jozef Stefan Institute, Ljubljana, Slovenia               *|
> |*								*|
> |*    Copyright (c) 1996--2004 by Anton Kokalj                  *|
> |*                                                              *|
> |****************************************************************|
> +----------------------------------------------------------------+
> 
>   Version: 1.5.17
> 
>   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=/usr/local/xcrysden_1.5.17/external/lib/tcl8.5
> XCRYSDEN_TOPDIR=/usr/local/xcrysden_1.5.17
> XCRYSDEN_SCRATCH=/tmp
> 
> Running on platform: unix
> CRYSTAL VERSION: 06
> Executing: /usr/local/xcrysden_1.5.17/bin/ftnunit
> ************************************************************************
> Deleting directory /tmp/xc_19291 ; Please Wait !!!
> ************************************************************************
> Directory deleted !
> 
> 
> Regards,
> Manuel.
> 

-- 

   ===================================================================
     Priv.-Doz. Dr. Volker Eyert
   -------------------------------------------------------------------
     Center for Electronic Correlations and Magnetism
     Institute for Physics, University of Augsburg
     86135 Augsburg, Germany
     email: eyert at physik.uni-augsburg.de,     volker at eyert.de
     http://www.physik.uni-augsburg.de/~eyert/,  www.eyert.de
   ===================================================================


From tone.kokalj at ijs.si  Thu Dec 18 13:03:14 2008
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Thu, 18 Dec 2008 13:03:14 +0100
Subject: [xcrysden] xcrysden on opensuse
In-Reply-To: <150405.51498.qm@web52009.mail.re2.yahoo.com>
References: <150405.51498.qm@web52009.mail.re2.yahoo.com>
Message-ID: <1229601794.24851.27.camel@walk.ijs.si>

On Thu, 2008-12-18 at 03:17 -0800, sara yazdani wrote:
> Dear all,
> 
> Thanks for replying me.
> 
> In order to have exact report I again downloaded xcrysden
> "xc-1.5.17-src-all.tar.gz" today.
> 
> after printing: ./xcConfigure I received:
> 
> more: unknown option "-m"
> usage: more [-dflpcsu] [+linenum | +/pattern] name1 name2 ...
> 
> I entered down and printed "source ~/.bashrc" and xcrysden which was
> again an unknown command for it!!! This is while I have installed
> opensuse completely.

You have downloaded the source package. Note that source package needs
to be compiled before you run "xcConfigure". From your description, I
would presume you didn't compile it. Moreover, the "xcConfigure" is
optional now. You don't need to run it, and xcrysden should still work.

I suggest you to download one of the linux precompiled packages (that
don't need compilation). Then:

> tar zxvf ****.tar.gz
> cd ****
> ./xcrysden

This should work (**** is the name of the package and the directory that
the package is expanded to).

Final note: your log file that you mailed contain:

bash: xcrysden: command not found

which means you don't have "." in your path. In this case you should run
as: "./xcrysden"

Regards, Tone

PS: the message "more: unknown option "-m"" is really awkward, as more
is never invoked with -m option in the xcConfigure script ...

-- 
Tone Kokalj <tone.kokalj at ijs.si>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)


From sarayazdani at yahoo.com  Fri Dec 19 13:16:17 2008
From: sarayazdani at yahoo.com (sara yazdani)
Date: Fri, 19 Dec 2008 04:16:17 -0800 (PST)
Subject: [xcrysden] XCrySDen Digest, Vol 12, Issue 10
In-Reply-To: <mailman.5.1229672753.29613.xcrysden@democritos.it>
Message-ID: <364407.57997.qm@web52004.mail.re2.yahoo.com>

I'm sorry to say that the problem still exists !!! 

using both compiled and pecompiled versions, when I write "./xcrysden" I received the ugly message of:

./xcrysden: line 129: /home/sara/XCrySDen-1.4.1s-all/scripts/xcLib.sh: No such file or directory

I know this goes back to compilation problem, but why does it occur for pre-compiled ones as well?



      
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From tone.kokalj at ijs.si  Fri Dec 19 13:53:18 2008
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Fri, 19 Dec 2008 13:53:18 +0100
Subject: [xcrysden] XCrySDen Digest, Vol 12, Issue 10
In-Reply-To: <364407.57997.qm@web52004.mail.re2.yahoo.com>
References: <364407.57997.qm@web52004.mail.re2.yahoo.com>
Message-ID: <1229691198.11372.21.camel@walk.ijs.si>

On Fri, 2008-12-19 at 04:16 -0800, sara yazdani wrote:
> I'm sorry to say that the problem still exists !!! 
> 
> using both compiled and pecompiled versions, when I write "./xcrysden"
> I received the ugly message of:
> 
> ./xcrysden: line 129: /home/sara/XCrySDen-1.4.1s-all/scripts/xcLib.sh:
> No such file or directory
> 
> I know this goes back to compilation problem, but why does it occur
> for pre-compiled ones as well?

No, it's not. Read thoroughly what the error message says:

.../XCrySDen-1.4.1s-all/...

Your XCRYSDEN_TOPDIR point to an old xcrysden v-1.4 installation. You
may either update the XCRYSDEN_TOPDIR definition in your profile, or
simply unset it. As a quick check you may do:

unset XCRYSDEN_TOPDIR
./xcrysden

Regards, Tone

-- 
Tone Kokalj <tone.kokalj at ijs.si>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)


From hana.milani at yahoo.com  Mon Dec 22 07:13:29 2008
From: hana.milani at yahoo.com (Hana Milani)
Date: Sun, 21 Dec 2008 22:13:29 -0800 (PST)
Subject: [xcrysden] H-passivation
Message-ID: <12777.58176.qm@web111213.mail.gq1.yahoo.com>

hello,

I would like to know if there's a way to find the "h" coordinates via xcrysden in passivated nanostructures.

If you have any manual about passivation, I would be grateful to have that.

Regards,
Hana



      
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From psbishtphyjiwaji at yahoo.co.in  Tue Dec 23 08:28:25 2008
From: psbishtphyjiwaji at yahoo.co.in (pradeep bisht)
Date: Tue, 23 Dec 2008 12:58:25 +0530 (IST)
Subject: [xcrysden] xcrysden for Siesta
In-Reply-To: <mailman.3.1229930872.4982.xcrysden@democritos.it>
Message-ID: <306790.1298.qm@web94202.mail.in2.yahoo.com>

Respected Xcrysden users,
Can we use the xcrysden to visulize the structure in Siesta if yes please help me.

Thanking you
Pradeep



      Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/
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From tone.kokalj at ijs.si  Tue Dec 23 08:59:53 2008
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Tue, 23 Dec 2008 08:59:53 +0100
Subject: [xcrysden] H-passivation
In-Reply-To: <12777.58176.qm@web111213.mail.gq1.yahoo.com>
References: <12777.58176.qm@web111213.mail.gq1.yahoo.com>
Message-ID: <1230019193.18465.14.camel@walk.ijs.si>

On Sun, 2008-12-21 at 22:13 -0800, Hana Milani wrote:
> hello,
> 
> I would like to know if there's a way to find the "h" coordinates via
> xcrysden in passivated nanostructures.

What do you mean by H-coordinates? xcrysden can visualize H bonds, and 
that's more or less all it can do in this respect (menus: Display->H-bonds, 
and Modify->H-bonds Settings).

Regards, Tone
-- 
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 Dec 23 09:09:19 2008
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Tue, 23 Dec 2008 09:09:19 +0100
Subject: [xcrysden] xcrysden for Siesta
In-Reply-To: <306790.1298.qm@web94202.mail.in2.yahoo.com>
References: <306790.1298.qm@web94202.mail.in2.yahoo.com>
Message-ID: <1230019759.18465.20.camel@walk.ijs.si>

On Tue, 2008-12-23 at 12:58 +0530, pradeep bisht wrote:
> Respected Xcrysden users,
> Can we use the xcrysden to visulize the structure in Siesta if yes please help me.


Well, I don't know Siesta, but googling "siesta xsf" will give you
useful info. The first hit is this one:

http://www.uam.es/departamentos/ciencias/fismateriac/siesta/Tutorials/Barcelona-2007/Postnikov-visual.pdf

Regards, Tone
-- 
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 rodrigo_oeiras at yahoo.com.br  Tue Dec 23 10:58:51 2008
From: rodrigo_oeiras at yahoo.com.br (Rodrigo Oeiras)
Date: Tue, 23 Dec 2008 01:58:51 -0800 (PST)
Subject: [xcrysden] two iso-surfaces
Message-ID: <928799.6288.qm@web55606.mail.re4.yahoo.com>

Hi, 
I can plot two iso-surfaces (with different values) at same molecule?
regards
oeiras



      Veja quais s?o os assuntos do momento no Yahoo! +Buscados
http://br.maisbuscados.yahoo.com
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From lanhaiping at gmail.com  Tue Dec 23 13:42:31 2008
From: lanhaiping at gmail.com (lan haiping)
Date: Tue, 23 Dec 2008 20:42:31 +0800
Subject: [xcrysden] two iso-surfaces
In-Reply-To: <928799.6288.qm@web55606.mail.re4.yahoo.com>
References: <928799.6288.qm@web55606.mail.re4.yahoo.com>
Message-ID: <c92002fa0812230442x379623fduabe42ba705b8aa6d@mail.gmail.com>

Hi,
As far as i know,  xcrysden cannot
plot two isosurfaces at the same plot.
But you may try to use vmd or other tools.
Another way you may try  is to write  some scripts to combine the data for
two iso-surface .
regards,



2008/12/23 Rodrigo Oeiras <rodrigo_oeiras at yahoo.com.br>

> Hi,
> I can plot two iso-surfaces (with different values) at same molecule?
> regards
> oeiras
>
> ------------------------------
> Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10<http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/>-
> Celebridades<http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/celebridades/>-
> M?sica<http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/m%C3%BAsica/>-
> Esportes<http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/esportes/>
>
> _______________________________________________
> XCrySDen mailing list
> XCrySDen at democritos.it
> http://www.democritos.it/mailman/listinfo/xcrysden
>
>


-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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From hansonr at stolaf.edu  Tue Dec 23 14:14:32 2008
From: hansonr at stolaf.edu (Robert Hanson)
Date: Tue, 23 Dec 2008 07:14:32 -0600
Subject: [xcrysden] two iso-surfaces
In-Reply-To: <c92002fa0812230442x379623fduabe42ba705b8aa6d@mail.gmail.com>
References: <928799.6288.qm@web55606.mail.re4.yahoo.com>
	<c92002fa0812230442x379623fduabe42ba705b8aa6d@mail.gmail.com>
Message-ID: <ba9c0bd60812230514k6223c777p1bc45942b199af66@mail.gmail.com>

Jmol will draw as many isosurfaces as you want.

On Tue, Dec 23, 2008 at 6:42 AM, lan haiping <lanhaiping at gmail.com> wrote:
> Hi,
> As far as i know,  xcrysden cannot
> plot two isosurfaces at the same plot.
> But you may try to use vmd or other tools.
> Another way you may try  is to write  some scripts to combine the data for
> two iso-surface .
> regards,
>
>
>
> 2008/12/23 Rodrigo Oeiras <rodrigo_oeiras at yahoo.com.br>
>>
>> Hi,
>> I can plot two iso-surfaces (with different values) at same molecule?
>> regards
>> oeiras
>>
>> ________________________________
>> Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10 -
>> Celebridades - M?sica - Esportes
>> _______________________________________________
>> XCrySDen mailing list
>> XCrySDen at democritos.it
>> http://www.democritos.it/mailman/listinfo/xcrysden
>>
>
>
>
> --
> Hai-Ping Lan
> Department of Electronics ,
> Peking University , Bejing, 100871
> lanhaiping at gmail.com, hplan at pku.edu.cn
>
> _______________________________________________
> XCrySDen mailing list
> XCrySDen at democritos.it
> http://www.democritos.it/mailman/listinfo/xcrysden
>
>



-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

From tone.kokalj at ijs.si  Tue Dec 23 14:22:59 2008
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Tue, 23 Dec 2008 14:22:59 +0100
Subject: [xcrysden] two iso-surfaces
In-Reply-To: <928799.6288.qm@web55606.mail.re4.yahoo.com>
References: <928799.6288.qm@web55606.mail.re4.yahoo.com>
Message-ID: <1230038579.27591.9.camel@walk.ijs.si>

On Tue, 2008-12-23 at 01:58 -0800, Rodrigo Oeiras wrote:
> Hi, 
> I can plot two iso-surfaces (with different values) at same molecule?

In general, xcrysden cannot. There is only one exception: you can plot +value and -value 
isosurface at once (there is a checkbutton Render +/- isovalue). Why? At the time I programmed it, 
I thought that more than one isosurface at once would be too much info and not very useful. 
Probably I was wrong.

Regards, Tone
-- 
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 rfaccio at fq.edu.uy  Tue Dec 23 14:53:21 2008
From: rfaccio at fq.edu.uy (Ricardo Faccio)
Date: Tue, 23 Dec 2008 10:53:21 -0300
Subject: [xcrysden] xcrysden for Siesta
References: <306790.1298.qm@web94202.mail.in2.yahoo.com>
Message-ID: <004d01c96505$d1f3d6b0$0602a8c0@ricardof>

Dear Pradeep
In the Postnikov's web page you can find a script called xv2xsf for a case.XV file and transforms it into case.XSF, that can easily be read by Xcrysden. This script is found with other tools in a collection called Sies2xsf (http://www.home.uni-osnabrueck.de/apostnik/download.html)
Regards
Ricardo
-------------------------------------------------------------------------
-----   Dr. Ricardo Faccio
 
  Mail: Cryssmat-Lab., C?tedra de F?sica, DETEMA
  Facultad de Qu?mica, Universidad de la Rep?blica
       Av. Gral. Flores 2124, C.C. 1157
       C.P. 11800, Montevideo, Uruguay.
  E-mail: rfaccio at fq.edu.uy
  Phone: 598 2 9249859
             598 2 9290705
  Fax:    598 2 9241906
  Web:  http://cryssmat.fq.edu.uy/ricardo/ricardo.htm
  ----- Original Message ----- 
  From: pradeep bisht 
  To: xcrysden at democritos.it 
  Sent: Tuesday, December 23, 2008 4:28 AM
  Subject: [xcrysden] xcrysden for Siesta


        Respected Xcrysden users,
        Can we use the xcrysden to visulize the structure in Siesta if yes please help me.

        Thanking you
        Pradeep
       


------------------------------------------------------------------------------
  Cricket on your mind? Visit the ultimate cricket website. Enter now!


------------------------------------------------------------------------------


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  XCrySDen mailing list
  XCrySDen at democritos.it
  http://www.democritos.it/mailman/listinfo/xcrysden
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From psbishtphyjiwaji at yahoo.co.in  Tue Dec 23 14:55:01 2008
From: psbishtphyjiwaji at yahoo.co.in (pradeep bisht)
Date: Tue, 23 Dec 2008 19:25:01 +0530 (IST)
Subject: [xcrysden] happy X mas day to all xcrysden users
In-Reply-To: <mailman.808.1230038787.15655.xcrysden@democritos.it>
Message-ID: <86339.60922.qm@web94202.mail.in2.yahoo.com>






???????????HAPPY? ?CHRISTMAS? DAY?To ALL????????? XCRYSDEN USERS






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From hana.milani at yahoo.com  Tue Dec 23 16:20:41 2008
From: hana.milani at yahoo.com (Hana Milani)
Date: Tue, 23 Dec 2008 07:20:41 -0800 (PST)
Subject: [xcrysden] XCrySDen Digest, Vol 12, Issue 13
References: <mailman.808.1230038787.15655.xcrysden@democritos.it>
Message-ID: <874913.18245.qm@web111209.mail.gq1.yahoo.com>

you should have .xyz file

you can have this file by having these terms written in your .fdf file

WriteCoorStep      .true.
WriteCoorXmol      .true.

this will make a .xyz file for you, then you can visualize it with xcrysden

Enjoy xcrysden




________________________________
From: "xcrysden-request at democritos.it" <xcrysden-request at democritos.it>
To: xcrysden at democritos.it
Sent: Tuesday, December 23, 2008 4:56:27 PM
Subject: XCrySDen Digest, Vol 12, Issue 13

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. xcrysden for Siesta (pradeep bisht)
   2. Re: H-passivation (Tone Kokalj)
   3. Re: xcrysden for Siesta (Tone Kokalj)
   4. two iso-surfaces (Rodrigo Oeiras)
   5. Re: two iso-surfaces (lan haiping)
   6. Re: two iso-surfaces (Robert Hanson)
   7. Re: two iso-surfaces (Tone Kokalj)
   8. Re: xcrysden for Siesta (Ricardo Faccio)


----------------------------------------------------------------------

Message: 1
Date: Tue, 23 Dec 2008 12:58:25 +0530 (IST)
From: pradeep bisht <psbishtphyjiwaji at yahoo.co.in>
Subject: [xcrysden] xcrysden for Siesta
To: xcrysden at democritos.it
Message-ID: <306790.1298.qm at web94202.mail.in2.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Respected Xcrysden users,
Can we use the xcrysden to visulize the structure in Siesta if yes please help me.

Thanking you
Pradeep



      Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/
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------------------------------

Message: 2
Date: Tue, 23 Dec 2008 08:59:53 +0100
From: Tone Kokalj <tone.kokalj at ijs.si>
Subject: Re: [xcrysden] H-passivation
To: XCrySDen mailing list <xcrysden at democritos.it>
Message-ID: <1230019193.18465.14.camel at walk.ijs.si>
Content-Type: text/plain

On Sun, 2008-12-21 at 22:13 -0800, Hana Milani wrote:
> hello,
> 
> I would like to know if there's a way to find the "h" coordinates via
> xcrysden in passivated nanostructures.

What do you mean by H-coordinates? xcrysden can visualize H bonds, and 
that's more or less all it can do in this respect (menus: Display->H-bonds, 
and Modify->H-bonds Settings).

Regards, Tone
-- 
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



------------------------------

Message: 3
Date: Tue, 23 Dec 2008 09:09:19 +0100
From: Tone Kokalj <tone.kokalj at ijs.si>
Subject: Re: [xcrysden] xcrysden for Siesta
To: psbishtphyjiwaji at yahoo.co.in,    XCrySDen mailing list
    <xcrysden at democritos.it>
Message-ID: <1230019759.18465.20.camel at walk.ijs.si>
Content-Type: text/plain

On Tue, 2008-12-23 at 12:58 +0530, pradeep bisht wrote:
> Respected Xcrysden users,
> Can we use the xcrysden to visulize the structure in Siesta if yes please help me.


Well, I don't know Siesta, but googling "siesta xsf" will give you
useful info. The first hit is this one:

http://www.uam.es/departamentos/ciencias/fismateriac/siesta/Tutorials/Barcelona-2007/Postnikov-visual.pdf

Regards, Tone
-- 
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



------------------------------

Message: 4
Date: Tue, 23 Dec 2008 01:58:51 -0800 (PST)
From: Rodrigo Oeiras <rodrigo_oeiras at yahoo.com.br>
Subject: [xcrysden] two iso-surfaces
To: xcrysden at democritos.it
Message-ID: <928799.6288.qm at web55606.mail.re4.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Hi, 
I can plot two iso-surfaces (with different values) at same molecule?
regards
oeiras



      Veja quais s?o os assuntos do momento no Yahoo! +Buscados
http://br.maisbuscados.yahoo.com
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------------------------------

Message: 5
Date: Tue, 23 Dec 2008 20:42:31 +0800
From: "lan haiping" <lanhaiping at gmail.com>
Subject: Re: [xcrysden] two iso-surfaces
To: rodrigo_oeiras at yahoo.com.br,     "XCrySDen mailing list"
    <xcrysden at democritos.it>
Message-ID:
    <c92002fa0812230442x379623fduabe42ba705b8aa6d at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi,
As far as i know,  xcrysden cannot
plot two isosurfaces at the same plot.
But you may try to use vmd or other tools.
Another way you may try  is to write  some scripts to combine the data for
two iso-surface .
regards,



2008/12/23 Rodrigo Oeiras <rodrigo_oeiras at yahoo.com.br>

> Hi,
> I can plot two iso-surfaces (with different values) at same molecule?
> regards
> oeiras
>
> ------------------------------
> Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10<http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/>-
> Celebridades<http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/celebridades/>-
> M?sica<http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/m%C3%BAsica/>-
> Esportes<http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/esportes/>
>
> _______________________________________________
> XCrySDen mailing list
> XCrySDen at democritos.it
> http://www.democritos.it/mailman/listinfo/xcrysden
>
>


-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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------------------------------

Message: 6
Date: Tue, 23 Dec 2008 07:14:32 -0600
From: "Robert Hanson" <hansonr at stolaf.edu>
Subject: Re: [xcrysden] two iso-surfaces
To: "XCrySDen mailing list" <xcrysden at democritos.it>
Message-ID:
    <ba9c0bd60812230514k6223c777p1bc45942b199af66 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Jmol will draw as many isosurfaces as you want.

On Tue, Dec 23, 2008 at 6:42 AM, lan haiping <lanhaiping at gmail.com> wrote:
> Hi,
> As far as i know,  xcrysden cannot
> plot two isosurfaces at the same plot.
> But you may try to use vmd or other tools.
> Another way you may try  is to write  some scripts to combine the data for
> two iso-surface .
> regards,
>
>
>
> 2008/12/23 Rodrigo Oeiras <rodrigo_oeiras at yahoo.com.br>
>>
>> Hi,
>> I can plot two iso-surfaces (with different values) at same molecule?
>> regards
>> oeiras
>>
>> ________________________________
>> Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10 -
>> Celebridades - M?sica - Esportes
>> _______________________________________________
>> XCrySDen mailing list
>> XCrySDen at democritos.it
>> http://www.democritos.it/mailman/listinfo/xcrysden
>>
>
>
>
> --
> Hai-Ping Lan
> Department of Electronics ,
> Peking University , Bejing, 100871
> lanhaiping at gmail.com, hplan at pku.edu.cn
>
> _______________________________________________
> XCrySDen mailing list
> XCrySDen at democritos.it
> http://www.democritos.it/mailman/listinfo/xcrysden
>
>



-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900


------------------------------

Message: 7
Date: Tue, 23 Dec 2008 14:22:59 +0100
From: Tone Kokalj <tone.kokalj at ijs.si>
Subject: Re: [xcrysden] two iso-surfaces
To: rodrigo_oeiras at yahoo.com.br, XCrySDen mailing list
    <xcrysden at democritos.it>
Message-ID: <1230038579.27591.9.camel at walk.ijs.si>
Content-Type: text/plain

On Tue, 2008-12-23 at 01:58 -0800, Rodrigo Oeiras wrote:
> Hi, 
> I can plot two iso-surfaces (with different values) at same molecule?

In general, xcrysden cannot. There is only one exception: you can plot +value and -value 
isosurface at once (there is a checkbutton Render +/- isovalue). Why? At the time I programmed it, 
I thought that more than one isosurface at once would be too much info and not very useful. 
Probably I was wrong.

Regards, Tone
-- 
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



------------------------------

Message: 8
Date: Tue, 23 Dec 2008 10:53:21 -0300
From: "Ricardo Faccio" <rfaccio at fq.edu.uy>
Subject: Re: [xcrysden] xcrysden for Siesta
To: <psbishtphyjiwaji at yahoo.co.in>,    "XCrySDen mailing list"
    <xcrysden at democritos.it>
Message-ID: <004d01c96505$d1f3d6b0$0602a8c0 at ricardof>
Content-Type: text/plain; charset="utf-8"

Dear Pradeep
In the Postnikov's web page you can find a script called xv2xsf for a case.XV file and transforms it into case.XSF, that can easily be read by Xcrysden. This script is found with other tools in a collection called Sies2xsf (http://www.home.uni-osnabrueck.de/apostnik/download.html)
Regards
Ricardo
-------------------------------------------------------------------------
-----   Dr. Ricardo Faccio

  Mail: Cryssmat-Lab., C?tedra de F?sica, DETEMA
  Facultad de Qu?mica, Universidad de la Rep?blica
       Av. Gral. Flores 2124, C.C. 1157
       C.P. 11800, Montevideo, Uruguay.
  E-mail: rfaccio at fq.edu.uy
  Phone: 598 2 9249859
             598 2 9290705
  Fax:    598 2 9241906
  Web:  http://cryssmat.fq.edu.uy/ricardo/ricardo.htm
  ----- Original Message ----- 
  From: pradeep bisht 
  To: xcrysden at democritos.it 
  Sent: Tuesday, December 23, 2008 4:28 AM
  Subject: [xcrysden] xcrysden for Siesta


        Respected Xcrysden users,
        Can we use the xcrysden to visulize the structure in Siesta if yes please help me.

        Thanking you
        Pradeep
      


------------------------------------------------------------------------------
  Cricket on your mind? Visit the ultimate cricket website. Enter now!


------------------------------------------------------------------------------


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

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


End of XCrySDen Digest, Vol 12, Issue 13
****************************************



      
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From hana.milani at yahoo.com  Tue Dec 23 16:23:59 2008
From: hana.milani at yahoo.com (Hana Milani)
Date: Tue, 23 Dec 2008 07:23:59 -0800 (PST)
Subject: [xcrysden] XCrySDen Digest, Vol 12, Issue 13
References: <mailman.808.1230038787.15655.xcrysden@democritos.it>
Message-ID: <489815.20796.qm@web111215.mail.gq1.yahoo.com>

dear Tone,

I have put time to add h-bonds to a nanowire to saturate the dangling bonds, but after all I didn't get to good results.

I wanted to know if there's a way that I add the h-bonds via xcrysden and get the coordinates from xcrysden, then, I optimize the system!!!

I have gone through doing it via hyperchem, I got to awful results.

Any suggestions????




________________________________
From: "xcrysden-request at democritos.it" <xcrysden-request at democritos.it>
To: xcrysden at democritos.it
Sent: Tuesday, December 23, 2008 4:56:27 PM
Subject: XCrySDen Digest, Vol 12, Issue 13

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. xcrysden for Siesta (pradeep bisht)
   2. Re: H-passivation (Tone Kokalj)
   3. Re: xcrysden for Siesta (Tone Kokalj)
   4. two iso-surfaces (Rodrigo Oeiras)
   5. Re: two iso-surfaces (lan haiping)
   6. Re: two iso-surfaces (Robert Hanson)
   7. Re: two iso-surfaces (Tone Kokalj)
   8. Re: xcrysden for Siesta (Ricardo Faccio)


----------------------------------------------------------------------

Message: 1
Date: Tue, 23 Dec 2008 12:58:25 +0530 (IST)
From: pradeep bisht <psbishtphyjiwaji at yahoo.co.in>
Subject: [xcrysden] xcrysden for Siesta
To: xcrysden at democritos.it
Message-ID: <306790.1298.qm at web94202.mail.in2.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Respected Xcrysden users,
Can we use the xcrysden to visulize the structure in Siesta if yes please help me.

Thanking you
Pradeep



      Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/
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------------------------------

Message: 2
Date: Tue, 23 Dec 2008 08:59:53 +0100
From: Tone Kokalj <tone.kokalj at ijs.si>
Subject: Re: [xcrysden] H-passivation
To: XCrySDen mailing list <xcrysden at democritos.it>
Message-ID: <1230019193.18465.14.camel at walk.ijs.si>
Content-Type: text/plain

On Sun, 2008-12-21 at 22:13 -0800, Hana Milani wrote:
> hello,
> 
> I would like to know if there's a way to find the "h" coordinates via
> xcrysden in passivated nanostructures.

What do you mean by H-coordinates? xcrysden can visualize H bonds, and 
that's more or less all it can do in this respect (menus: Display->H-bonds, 
and Modify->H-bonds Settings).

Regards, Tone
-- 
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



------------------------------

Message: 3
Date: Tue, 23 Dec 2008 09:09:19 +0100
From: Tone Kokalj <tone.kokalj at ijs.si>
Subject: Re: [xcrysden] xcrysden for Siesta
To: psbishtphyjiwaji at yahoo.co.in,    XCrySDen mailing list
    <xcrysden at democritos.it>
Message-ID: <1230019759.18465.20.camel at walk.ijs.si>
Content-Type: text/plain

On Tue, 2008-12-23 at 12:58 +0530, pradeep bisht wrote:
> Respected Xcrysden users,
> Can we use the xcrysden to visulize the structure in Siesta if yes please help me.


Well, I don't know Siesta, but googling "siesta xsf" will give you
useful info. The first hit is this one:

http://www.uam.es/departamentos/ciencias/fismateriac/siesta/Tutorials/Barcelona-2007/Postnikov-visual.pdf

Regards, Tone
-- 
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



------------------------------

Message: 4
Date: Tue, 23 Dec 2008 01:58:51 -0800 (PST)
From: Rodrigo Oeiras <rodrigo_oeiras at yahoo.com.br>
Subject: [xcrysden] two iso-surfaces
To: xcrysden at democritos.it
Message-ID: <928799.6288.qm at web55606.mail.re4.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Hi, 
I can plot two iso-surfaces (with different values) at same molecule?
regards
oeiras



      Veja quais s?o os assuntos do momento no Yahoo! +Buscados
http://br.maisbuscados.yahoo.com
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------------------------------

Message: 5
Date: Tue, 23 Dec 2008 20:42:31 +0800
From: "lan haiping" <lanhaiping at gmail.com>
Subject: Re: [xcrysden] two iso-surfaces
To: rodrigo_oeiras at yahoo.com.br,     "XCrySDen mailing list"
    <xcrysden at democritos.it>
Message-ID:
    <c92002fa0812230442x379623fduabe42ba705b8aa6d at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi,
As far as i know,  xcrysden cannot
plot two isosurfaces at the same plot.
But you may try to use vmd or other tools.
Another way you may try  is to write  some scripts to combine the data for
two iso-surface .
regards,



2008/12/23 Rodrigo Oeiras <rodrigo_oeiras at yahoo.com.br>

> Hi,
> I can plot two iso-surfaces (with different values) at same molecule?
> regards
> oeiras
>
> ------------------------------
> Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10<http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/>-
> Celebridades<http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/celebridades/>-
> M?sica<http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/m%C3%BAsica/>-
> Esportes<http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/esportes/>
>
> _______________________________________________
> XCrySDen mailing list
> XCrySDen at democritos.it
> http://www.democritos.it/mailman/listinfo/xcrysden
>
>


-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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------------------------------

Message: 6
Date: Tue, 23 Dec 2008 07:14:32 -0600
From: "Robert Hanson" <hansonr at stolaf.edu>
Subject: Re: [xcrysden] two iso-surfaces
To: "XCrySDen mailing list" <xcrysden at democritos.it>
Message-ID:
    <ba9c0bd60812230514k6223c777p1bc45942b199af66 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Jmol will draw as many isosurfaces as you want.

On Tue, Dec 23, 2008 at 6:42 AM, lan haiping <lanhaiping at gmail.com> wrote:
> Hi,
> As far as i know,  xcrysden cannot
> plot two isosurfaces at the same plot.
> But you may try to use vmd or other tools.
> Another way you may try  is to write  some scripts to combine the data for
> two iso-surface .
> regards,
>
>
>
> 2008/12/23 Rodrigo Oeiras <rodrigo_oeiras at yahoo.com.br>
>>
>> Hi,
>> I can plot two iso-surfaces (with different values) at same molecule?
>> regards
>> oeiras
>>
>> ________________________________
>> Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10 -
>> Celebridades - M?sica - Esportes
>> _______________________________________________
>> XCrySDen mailing list
>> XCrySDen at democritos.it
>> http://www.democritos.it/mailman/listinfo/xcrysden
>>
>
>
>
> --
> Hai-Ping Lan
> Department of Electronics ,
> Peking University , Bejing, 100871
> lanhaiping at gmail.com, hplan at pku.edu.cn
>
> _______________________________________________
> XCrySDen mailing list
> XCrySDen at democritos.it
> http://www.democritos.it/mailman/listinfo/xcrysden
>
>



-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900


------------------------------

Message: 7
Date: Tue, 23 Dec 2008 14:22:59 +0100
From: Tone Kokalj <tone.kokalj at ijs.si>
Subject: Re: [xcrysden] two iso-surfaces
To: rodrigo_oeiras at yahoo.com.br, XCrySDen mailing list
    <xcrysden at democritos.it>
Message-ID: <1230038579.27591.9.camel at walk.ijs.si>
Content-Type: text/plain

On Tue, 2008-12-23 at 01:58 -0800, Rodrigo Oeiras wrote:
> Hi, 
> I can plot two iso-surfaces (with different values) at same molecule?

In general, xcrysden cannot. There is only one exception: you can plot +value and -value 
isosurface at once (there is a checkbutton Render +/- isovalue). Why? At the time I programmed it, 
I thought that more than one isosurface at once would be too much info and not very useful. 
Probably I was wrong.

Regards, Tone
-- 
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



------------------------------

Message: 8
Date: Tue, 23 Dec 2008 10:53:21 -0300
From: "Ricardo Faccio" <rfaccio at fq.edu.uy>
Subject: Re: [xcrysden] xcrysden for Siesta
To: <psbishtphyjiwaji at yahoo.co.in>,    "XCrySDen mailing list"
    <xcrysden at democritos.it>
Message-ID: <004d01c96505$d1f3d6b0$0602a8c0 at ricardof>
Content-Type: text/plain; charset="utf-8"

Dear Pradeep
In the Postnikov's web page you can find a script called xv2xsf for a case.XV file and transforms it into case.XSF, that can easily be read by Xcrysden. This script is found with other tools in a collection called Sies2xsf (http://www.home.uni-osnabrueck.de/apostnik/download.html)
Regards
Ricardo
-------------------------------------------------------------------------
-----   Dr. Ricardo Faccio

  Mail: Cryssmat-Lab., C?tedra de F?sica, DETEMA
  Facultad de Qu?mica, Universidad de la Rep?blica
       Av. Gral. Flores 2124, C.C. 1157
       C.P. 11800, Montevideo, Uruguay.
  E-mail: rfaccio at fq.edu.uy
  Phone: 598 2 9249859
             598 2 9290705
  Fax:    598 2 9241906
  Web:  http://cryssmat.fq.edu.uy/ricardo/ricardo.htm
  ----- Original Message ----- 
  From: pradeep bisht 
  To: xcrysden at democritos.it 
  Sent: Tuesday, December 23, 2008 4:28 AM
  Subject: [xcrysden] xcrysden for Siesta


        Respected Xcrysden users,
        Can we use the xcrysden to visulize the structure in Siesta if yes please help me.

        Thanking you
        Pradeep
      


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


End of XCrySDen Digest, Vol 12, Issue 13
****************************************



      
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From spbeckman at gmail.com  Tue Dec 23 16:47:56 2008
From: spbeckman at gmail.com (Scott Beckman)
Date: Tue, 23 Dec 2008 09:47:56 -0600
Subject: [xcrysden] XCrySDen Digest, Vol 12, Issue 13
In-Reply-To: <489815.20796.qm@web111215.mail.gq1.yahoo.com>
References: <mailman.808.1230038787.15655.xcrysden@democritos.it>
	<489815.20796.qm@web111215.mail.gq1.yahoo.com>
Message-ID: <BA94A796-196D-4061-B1DA-72C654ECB34D@gmail.com>


Explain what you mean by awful results.  Are the H atoms misplaced or  
do the calculations not work correctly?

Surface passivation isn't as simple as the literature makes is  
sound.  It might not be the placement that is a problem, but other  
issues in the calculation.


On Dec 23, 2008, at 9:23 AM, Hana Milani wrote:

> dear Tone,
>
> I have put time to add h-bonds to a nanowire to saturate the  
> dangling bonds, but after all I didn't get to good results.
>
> I wanted to know if there's a way that I add the h-bonds via  
> xcrysden and get the coordinates from xcrysden, then, I optimize  
> the system!!!
>
> I have gone through doing it via hyperchem, I got to awful results.
>
> Any suggestions????
>
> From: "xcrysden-request at democritos.it" <xcrysden- 
> request at democritos.it>
> To: xcrysden at democritos.it
> Sent: Tuesday, December 23, 2008 4:56:27 PM
> Subject: XCrySDen Digest, Vol 12, Issue 13
>
> 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. xcrysden for Siesta (pradeep bisht)
>   2. Re: H-passivation (Tone Kokalj)
>   3. Re: xcrysden for Siesta (Tone Kokalj)
>   4. two iso-surfaces (Rodrigo Oeiras)
>   5. Re: two iso-surfaces (lan haiping)
>   6. Re: two iso-surfaces (Robert Hanson)
>   7. Re: two iso-surfaces (Tone Kokalj)
>   8. Re: xcrysden for Siesta (Ricardo Faccio)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 23 Dec 2008 12:58:25 +0530 (IST)
> From: pradeep bisht <psbishtphyjiwaji at yahoo.co.in>
> Subject: [xcrysden] xcrysden for Siesta
> To: xcrysden at democritos.it
> Message-ID: <306790.1298.qm at web94202.mail.in2.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Respected Xcrysden users,
> Can we use the xcrysden to visulize the structure in Siesta if yes  
> please help me.
>
> Thanking you
> Pradeep
>
>
>
>       Add more friends to your messenger and enjoy! Go to http:// 
> messenger.yahoo.com/invite/
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://www.democritos.it/pipermail/xcrysden/attachments/ 
> 20081223/3edf4abf/attachment-0001.htm
>
> ------------------------------
>
> Message: 2
> Date: Tue, 23 Dec 2008 08:59:53 +0100
> From: Tone Kokalj <tone.kokalj at ijs.si>
> Subject: Re: [xcrysden] H-passivation
> To: XCrySDen mailing list <xcrysden at democritos.it>
> Message-ID: <1230019193.18465.14.camel at walk.ijs.si>
> Content-Type: text/plain
>
> On Sun, 2008-12-21 at 22:13 -0800, Hana Milani wrote:
> > hello,
> >
> > I would like to know if there's a way to find the "h" coordinates  
> via
> > xcrysden in passivated nanostructures.
>
> What do you mean by H-coordinates? xcrysden can visualize H bonds, and
> that's more or less all it can do in this respect (menus: Display- 
> >H-bonds,
> and Modify->H-bonds Settings).
>
> Regards, Tone
> -- 
> 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
>
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 23 Dec 2008 09:09:19 +0100
> From: Tone Kokalj <tone.kokalj at ijs.si>
> Subject: Re: [xcrysden] xcrysden for Siesta
> To: psbishtphyjiwaji at yahoo.co.in,    XCrySDen mailing list
>     <xcrysden at democritos.it>
> Message-ID: <1230019759.18465.20.camel at walk.ijs.si>
> Content-Type: text/plain
>
> On Tue, 2008-12-23 at 12:58 +0530, pradeep bisht wrote:
> > Respected Xcrysden users,
> > Can we use the xcrysden to visulize the structure in Siesta if  
> yes please help me.
>
>
> Well, I don't know Siesta, but googling "siesta xsf" will give you
> useful info. The first hit is this one:
>
> http://www.uam.es/departamentos/ciencias/fismateriac/siesta/ 
> Tutorials/Barcelona-2007/Postnikov-visual.pdf
>
> Regards, Tone
> -- 
> 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
>
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 23 Dec 2008 01:58:51 -0800 (PST)
> From: Rodrigo Oeiras <rodrigo_oeiras at yahoo.com.br>
> Subject: [xcrysden] two iso-surfaces
> To: xcrysden at democritos.it
> Message-ID: <928799.6288.qm at web55606.mail.re4.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
> I can plot two iso-surfaces (with different values) at same molecule?
> regards
> oeiras
>
>
>
>       Veja quais s?o os assuntos do momento no Yahoo! +Buscados
> http://br.maisbuscados.yahoo.com
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://www.democritos.it/pipermail/xcrysden/attachments/ 
> 20081223/679cd122/attachment-0001.htm
>
> ------------------------------
>
> Message: 5
> Date: Tue, 23 Dec 2008 20:42:31 +0800
> From: "lan haiping" <lanhaiping at gmail.com>
> Subject: Re: [xcrysden] two iso-surfaces
> To: rodrigo_oeiras at yahoo.com.br,     "XCrySDen mailing list"
>     <xcrysden at democritos.it>
> Message-ID:
>     <c92002fa0812230442x379623fduabe42ba705b8aa6d at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
> As far as i know,  xcrysden cannot
> plot two isosurfaces at the same plot.
> But you may try to use vmd or other tools.
> Another way you may try  is to write  some scripts to combine the  
> data for
> two iso-surface .
> regards,
>
>
>
> 2008/12/23 Rodrigo Oeiras <rodrigo_oeiras at yahoo.com.br>
>
> > Hi,
> > I can plot two iso-surfaces (with different values) at same  
> molecule?
> > regards
> > oeiras
> >
> > ------------------------------
> > Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top  
> 10<http://br.rd.yahoo.com/mail/taglines/mail/*http:// 
> br.maisbuscados.yahoo.com/>-
> > Celebridades<http://br.rd.yahoo.com/mail/taglines/mail/*http:// 
> br.maisbuscados.yahoo.com/celebridades/>-
> > M?sica<http://br.rd.yahoo.com/mail/taglines/mail/*http:// 
> br.maisbuscados.yahoo.com/m%C3%BAsica/>-
> > Esportes<http://br.rd.yahoo.com/mail/taglines/mail/*http:// 
> br.maisbuscados.yahoo.com/esportes/>
> >
> > _______________________________________________
> > XCrySDen mailing list
> > XCrySDen at democritos.it
> > http://www.democritos.it/mailman/listinfo/xcrysden
> >
> >
>
>
> -- 
> Hai-Ping Lan
> Department of Electronics ,
> Peking University , Bejing, 100871
> lanhaiping at gmail.com, hplan at pku.edu.cn
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://www.democritos.it/pipermail/xcrysden/attachments/ 
> 20081223/c42ac1c0/attachment-0001.htm
>
> ------------------------------
>
> Message: 6
> Date: Tue, 23 Dec 2008 07:14:32 -0600
> From: "Robert Hanson" <hansonr at stolaf.edu>
> Subject: Re: [xcrysden] two iso-surfaces
> To: "XCrySDen mailing list" <xcrysden at democritos.it>
> Message-ID:
>     <ba9c0bd60812230514k6223c777p1bc45942b199af66 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Jmol will draw as many isosurfaces as you want.
>
> On Tue, Dec 23, 2008 at 6:42 AM, lan haiping <lanhaiping at gmail.com>  
> wrote:
> > Hi,
> > As far as i know,  xcrysden cannot
> > plot two isosurfaces at the same plot.
> > But you may try to use vmd or other tools.
> > Another way you may try  is to write  some scripts to combine the  
> data for
> > two iso-surface .
> > regards,
> >
> >
> >
> > 2008/12/23 Rodrigo Oeiras <rodrigo_oeiras at yahoo.com.br>
> >>
> >> Hi,
> >> I can plot two iso-surfaces (with different values) at same  
> molecule?
> >> regards
> >> oeiras
> >>
> >> ________________________________
> >> Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top  
> 10 -
> >> Celebridades - M?sica - Esportes
> >> _______________________________________________
> >> XCrySDen mailing list
> >> XCrySDen at democritos.it
> >> http://www.democritos.it/mailman/listinfo/xcrysden
> >>
> >
> >
> >
> > --
> > Hai-Ping Lan
> > Department of Electronics ,
> > Peking University , Bejing, 100871
> > lanhaiping at gmail.com, hplan at pku.edu.cn
> >
> > _______________________________________________
> > XCrySDen mailing list
> > XCrySDen at democritos.it
> > http://www.democritos.it/mailman/listinfo/xcrysden
> >
> >
>
>
>
> -- 
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
> ------------------------------
>
> Message: 7
> Date: Tue, 23 Dec 2008 14:22:59 +0100
> From: Tone Kokalj <tone.kokalj at ijs.si>
> Subject: Re: [xcrysden] two iso-surfaces
> To: rodrigo_oeiras at yahoo.com.br, XCrySDen mailing list
>     <xcrysden at democritos.it>
> Message-ID: <1230038579.27591.9.camel at walk.ijs.si>
> Content-Type: text/plain
>
> On Tue, 2008-12-23 at 01:58 -0800, Rodrigo Oeiras wrote:
> > Hi,
> > I can plot two iso-surfaces (with different values) at same  
> molecule?
>
> In general, xcrysden cannot. There is only one exception: you can  
> plot +value and -value
> isosurface at once (there is a checkbutton Render +/- isovalue).  
> Why? At the time I programmed it,
> I thought that more than one isosurface at once would be too much  
> info and not very useful.
> Probably I was wrong.
>
> Regards, Tone
> -- 
> 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
>
>
>
> ------------------------------
>
> Message: 8
> Date: Tue, 23 Dec 2008 10:53:21 -0300
> From: "Ricardo Faccio" <rfaccio at fq.edu.uy>
> Subject: Re: [xcrysden] xcrysden for Siesta
> To: <psbishtphyjiwaji at yahoo.co.in>,    "XCrySDen mailing list"
>     <xcrysden at democritos.it>
> Message-ID: <004d01c96505$d1f3d6b0$0602a8c0 at ricardof>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Pradeep
> In the Postnikov's web page you can find a script called xv2xsf for  
> a case.XV file and transforms it into case.XSF, that can easily be  
> read by Xcrysden. This script is found with other tools in a  
> collection called Sies2xsf (http://www.home.uni-osnabrueck.de/ 
> apostnik/download.html)
> Regards
> Ricardo
> ---------------------------------------------------------------------- 
> ---
> -----  Dr. Ricardo Faccio
>
>   Mail: Cryssmat-Lab., C?tedra de F?sica, DETEMA
>   Facultad de Qu?mica, Universidad de la Rep?blica
>       Av. Gral. Flores 2124, C.C. 1157
>       C.P. 11800, Montevideo, Uruguay.
>   E-mail: rfaccio at fq.edu.uy
>   Phone: 598 2 9249859
>             598 2 9290705
>   Fax:    598 2 9241906
>   Web:  http://cryssmat.fq.edu.uy/ricardo/ricardo.htm
>   ----- Original Message -----
>   From: pradeep bisht
>   To: xcrysden at democritos.it
>   Sent: Tuesday, December 23, 2008 4:28 AM
>   Subject: [xcrysden] xcrysden for Siesta
>
>
>         Respected Xcrysden users,
>         Can we use the xcrysden to visulize the structure in Siesta  
> if yes please help me.
>
>         Thanking you
>         Pradeep
>
>
>
> ---------------------------------------------------------------------- 
> --------
>   Cricket on your mind? Visit the ultimate cricket website. Enter now!
>
>
> ---------------------------------------------------------------------- 
> --------
>
>
>   _______________________________________________
>   XCrySDen mailing list
>   XCrySDen at democritos.it
>   http://www.democritos.it/mailman/listinfo/xcrysden
> -------------- next part --------------
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> URL: http://www.democritos.it/pipermail/xcrysden/attachments/ 
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>
> ------------------------------
>
> _______________________________________________
> XCrySDen mailing list
> XCrySDen at democritos.it
> http://www.democritos.it/mailman/listinfo/xcrysden
>
>
> End of XCrySDen Digest, Vol 12, Issue 13
> ****************************************
>
> _______________________________________________
> XCrySDen mailing list
> XCrySDen at democritos.it
> http://www.democritos.it/mailman/listinfo/xcrysden


From tone.kokalj at ijs.si  Tue Dec 23 20:55:42 2008
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Tue, 23 Dec 2008 20:55:42 +0100
Subject: [xcrysden] XCrySDen Digest, Vol 12, Issue 13
In-Reply-To: <489815.20796.qm@web111215.mail.gq1.yahoo.com>
References: <mailman.808.1230038787.15655.xcrysden@democritos.it>
	<489815.20796.qm@web111215.mail.gq1.yahoo.com>
Message-ID: <1230062142.5793.15.camel@walk.ijs.si>

On Tue, 2008-12-23 at 07:23 -0800, Hana Milani wrote:
> dear Tone,
> 
> I wanted to know if there's a way that I add the h-bonds via xcrysden
> and get the coordinates from xcrysden, then, I optimize the system!!!

No, there isn't.

[well actually there is something via the AdvGeom menu that is activated
only for CRYSTAL package (because it uses crystal behind the scene); if
you have CRYSTAL program, then refer to crystal manual]


> I have put time to add h-bonds to a nanowire to saturate the dangling
> bonds, but after all I didn't get to good results. I have gone through
> doing it via hyperchem, I got to awful results.

I would presume that by visual examination of H-saturated dangling bonds 
one may estimate if the structure is reasonable, however, I have no 
experience with H-saturation ...

Regards, Tone
-- 
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