Message-ID: <1146151519.6568.18.camel@localhost.localdomain>
On Wed, 2006-04-26 at 13:24 -0400, Ling Miao wrote:
> I have a question regarding the criteria
> of drawing a bond between two atoms. I noticed that in my system,
> some bonds are drawn between Pd and C
> atoms, some are not, although the bond length difference is only about
> 0.1A between those drawn and not drawn.
There are two parameters that determine the bond drawing.
One is chemical connectivity factor, the other is the covalent radius.
The former is a general parameter, while the latter is set to each
individual atomic type (not atom). Both can be set via the
"Modify-->Atomic radii" menu entry.
The bond between two atoms is drawn, when their distance is smaller than
the sum of their covalent radius times the connectivity factor.
If this is not sufficient to draw (or delete) given set of bonds, then
you can substitute some atoms by different atomic types manually in the
structure file. When displaying the structure assign to them different
covalent radii yet use (set) the same atomic color....
Regards, Tone
From xcrysden@democritos.it Sat Apr 29 13:32:58 2006
From: xcrysden@democritos.it (Saeid Jalali)
Date: Sat, 29 Apr 2006 05:32:58 -0700 (PDT)
Subject: [xcrysden] Surface structure
Message-ID: <20060429123258.269.qmail@web54302.mail.yahoo.com>
--0-1691686114-1146313978=:98522
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: 8bit
Dear xcrysden users,
I am a user of wien2k and xcrysden packages. I would study quantum size effects constructing surfaces along arbitrary directions, e.g. (111) of Si. It is not hard to imagine and hence construct surface of a simple cubic along (111) direction, however, this is not the case for more complicated structures. It will be great to find out that whether xcrysden can help us to construct the surfaces of a known complicated unit cell or not. In the former case I appreciate if someone can tell us how we can use xcrysden to construct the surfaces. In the later case any other information will be deeply thankful, say introducing other tools for this purpose.
Thank you in advance,
Sincerely yours,
S. Jalali.
Sincerely yours,
S. Jalali.
/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
Saeid Jalali Asadabadi,
Department of Physics, Faculty of Science,
University of Isfahan (UI), Hezar Gerib Avenue,
81744 Isfahan, Iran.
Phones:
Dep. of Phys. :+98-0311-793 2435
Office :+98-0311-793 2430
Fax No. :+98-0311-793 2409
E-mail :s_jalali_a@yahoo.com
www :http://www.ui.ac.ir
/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
---------------------------------
Yahoo! Messenger with Voice. PC-to-Phone calls for ridiculously low rates.
--0-1691686114-1146313978=:98522
Content-Type: text/html; charset=iso-8859-1
Content-Transfer-Encoding: 8bit
Dear xcrysden users,
I am a user of wien2k and xcrysden packages. I would study quantum size effects constructing surfaces along arbitrary directions, e.g. (111) of Si. It is not hard to imagine and hence construct surface of a simple cubic along (111) direction, however, this is not the case for more complicated structures. It will be great to find out that whether xcrysden can help us to construct the surfaces of a known complicated unit cell or not. In the former case I appreciate if someone can tell us how we can use xcrysden to construct the surfaces. In the later case any other information will be deeply thankful, say introducing other tools for this purpose.
Thank you in advance,
Sincerely yours,
S. Jalali.
Sincerely yours,
S. Jalali.
/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
Saeid Jalali Asadabadi,
Department of Physics, Faculty of Science,
University of Isfahan (UI), Hezar Gerib Avenue,
81744 Isfahan, Iran.
Phones:
Dep. of Phys. :+98-0311-793 2435
Office :+98-0311-793 2430
Fax No. :+98-0311-793 2409
E-mail :s_jalali_a@yahoo.com
www :http://www.ui.ac.ir
/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
Yahoo! Messenger with Voice. PC-to-Phone calls for ridiculously low rates.
--0-1691686114-1146313978=:98522--
From xcrysden@democritos.it Mon Apr 3 06:55:46 2006
From: xcrysden@democritos.it (mksingh)
Date: Mon, 3 Apr 2006 12:55:46 +0700
Subject: [xcrysden] this is regarding showing of Hydrogen bonding
In-Reply-To: <20060331114401.26805.86694.Mailman@democritos.sissa.it>
Message-ID: <20060403072650.70437112883@democritos.sissa.it>
Thank for your reply.
I have one more problem and this is related with Hydrogen bond
representation in Xcrysden Graphics.
I have generated a slab of urea crystal of (hkl) orientation and water
molecules were docked on the generated surface of orientation (hkl). Now I
would like to know/view where hydrogen bonding took place. It only show the
hydrogen bonding in urea slab but water molecule are 2.1 A apart from
Hydrogen atom of urea molecules in slab and I expect a hydrogen bond should
be there. But it not views the H-bond. Though I change the setting
Hydrogen Bond setting, but not able to show these H-bond.
Thank you,
Regards,
I am
M. K. Singh
--
No virus found in this outgoing message.
Checked by AVG Free Edition.
Version: 7.1.385 / Virus Database: 268.3.4/299 - Release Date: 31/03/2006
From xcrysden@democritos.it Mon Apr 3 09:10:54 2006
From: xcrysden@democritos.it (Raouf Bennaceur)
Date: Mon, 3 Apr 2006 09:10:54 +0100
Subject: [xcrysden] XcrySden on SunOS
Message-ID: <001801c656f6$216839a0$87b9cbc4@CPQ11380704345>
This is a multi-part message in MIME format.
------=_NextPart_000_0015_01C656FE.8314D3E0
Content-Type: text/plain;
charset="windows-1256"
Content-Transfer-Encoding: quoted-printable
Dear all,
I could not compile the XcrySden programs on sunSpark ( =
biprocessor).Please find the following transcript:
cc -Xa -O -DSOLARIS_BUG _DUSE_FONTS -I/usr/sfw/include =
-I/usr/sfw/include -I/usr/include -I/usr/X11R6/include=20
-c togle.r
ucbcc: warning:"-Xa" redefines compatibility mode from "Sun C =
transition" to "ANSI"=20
compilor(iropt):GCALL with no root
*** Error code 1
make: fatal error: Command failed for target 'togl.o'
Thank you
Regards.
Raouf Bennaceur
Laboratoire de Physique de la Mati=E8re Condens=E9e
Facult=E9 des Sciences de Tunis. Tunisia
------=_NextPart_000_0015_01C656FE.8314D3E0
Content-Type: text/html;
charset="windows-1256"
Content-Transfer-Encoding: quoted-printable
Dear all,
I could not compile the =
XcrySden programs=20
on sunSpark ( biprocessor).Please find the following =
transcript:
cc -Xa -O -DSOLARIS_BUG =
_DUSE_FONTS =20
-I/usr/sfw/include -I/usr/sfw/include -I/usr/include =
-I/usr/X11R6/include=20
-c togle.r
ucbcc: warning:"-Xa" redefines =
compatibility mode=20
from "Sun C transition" to "ANSI"
compilor(iropt):GCALL with no =
root
*** Error code 1
make: fatal error: Command failed for =
target=20
'togl.o'
Thank you
Regards.
Raouf Bennaceur
Laboratoire de Physique de la Mati=E8re =
Condens=E9e
Facult=E9 des Sciences de Tunis.=20
Tunisia
------=_NextPart_000_0015_01C656FE.8314D3E0--
From xcrysden@democritos.it Thu Apr 6 05:38:28 2006
From: xcrysden@democritos.it (Masayoshi Mikami)
Date: Thu, 6 Apr 2006 13:38:28 +0900
Subject: [xcrysden] mpeg-making with xcrysden on MacOSX
In-Reply-To:
References: <426d9c06a2dda6da8855fbbc2ae5de0c@rc.m-kagaku.co.jp>
Message-ID: <7fd0910c18e5e5923cb1ca14d57d689a@rc.m-kagaku.co.jp>
Dear Hamada-san,
I had been away from here, so my response was later than you might
expected.
O.K. it worked on MacOSX 10.3.9 as well. I appreciate your help very
much !
(NB: the comment (3) is related to "libpnmrw.c", just for others'
reference)
In passing, I had another question at that time:
"Otherwise, I would appreciate the method "how to convert animation gif
to mpeg", because I was able to make animation gif file using
"Animation Control Center" (whirlgif304.tar.gz was successfully
installed on the MacOSX). Is there a freeware for such purpose ?"
It was also solved already; try with "GraphicConverter" that accepts
Animation GIF.
Yours truly,
Masayoshi Mikami
On 2006/03/24, at 22:21, Ikutaro Hamada wrote:
> Dear Mikami-san,
>
>> I would appreciate very much, if someone could tell me how to make
>> mpeg file using "Animation Control Center" in xcrysden (v.1.4.1) on
>> MacOSX.
>>
>> I tried to compile the mpeg_encode "mpeg_encode-1.5b-src.tar.gz" on
>> the MacOSX (10.3.9), but I have not yet succeeded... Someone could
>> compile it on MacOSX ?
>> (the mpeg_encode seems quite old, so other encoders might be
>> available for this purpose ? I would like to know ...)
>
> I have succeeded to compile mpeg_encode (mpeg_encode-1.5b-src.tar.gz)
> on Mac OSX (10.4.5) in the following way:
>
>
> (1) Add a path to the header file (malloc.h) in Makefile
>
> #################
> # INCLUDE FILES #
> #################
> INCLUDEDIR = -Iheaders -I/usr/include -I/usr/include/malloc $(JPEG_DIR)
>
> (depending on the path to malloc.h)
>
>
> (2) comment out the following line (line 24) in headers/libpnmrw.h as
>
> /* extern char* malloc();*/
>
> (this can be avoided to add an appropriate cpp flag in Makefile)
>
>
> (3) finally, comment out the declaration of sys_errlist (line 129) as
> follows
>
> /*extern char* sys_errlist[];*/
>
> then "Make" and "Make test" work fine. Mpeg_encode works fine with
> XCrySDen.
>
>
> Hope this helps
>
> Regard,
>
> Ikutaro Hamada
>
> _______________________________________________
> XCrySDen mailing list
> XCrySDen@democritos.it
> http://www.democritos.it/mailman/listinfo/xcrysden
From xcrysden@democritos.it Mon Apr 10 14:47:24 2006
From: xcrysden@democritos.it (lyw1983)
Date: Mon, 10 Apr 2006 21:47:24 +0800 (CST)
Subject: [xcrysden] A question for AdvGeom
Message-ID: <443A61EC.000012.06950@bj163app60.163.com>
--Boundary-=_SQPJjuONBmHtxyrRmntVLYwulyUJ
Content-Type: text/plain; charset="gb2312"
Content-Transfer-Encoding: 7bit
Dear all:
I am a new user of xcrysden, I use the version1.4.1, after
instal it I found some tools can't be used, such as AdvGeom and
Properties and so on, I think if it needs some software to support it
,and what and where could I download it?
please help me, thanks very much!
--Boundary-=_SQPJjuONBmHtxyrRmntVLYwulyUJ
Content-Type: text/html; charset="gb2312"
Content-Transfer-Encoding: quoted-printable
Dear all:
I am a new user of xcrysden, I use the version1.4.1, after
instal it I found some tools can't be used, such as AdvGeom and
Properties and so on, I think if it needs some software to support it
,and what and where could I download it?
please help me, thanks very much!
=09=D6=D0 =B9=FA =C3=BF =
=C4=EA =D3=C3 =B5=F4 =B6=E0 =C9=D9 =CB=AB =D2=BB =B4=CE =D0=D4 =BF=EA =D7=
=D3 =A3=BF
=09
=09 450=D2=DA=CB=
=AB=A1=A3=D5=E2=BB=E1=BA=C4=B7=D1170=CD=F2=C1=A2=B7=BD=C3=D7=B5=C4=C4=BE=B2=
=C4=A3=AC=D0=E8=D2=AA=BF=B3=B7=A5=B4=F3=D4=BC2500=CD=F2=BF=C3=B4=F3=CA=F7=
=A3=A1 <=CD=F8=D2=D7=D3=CA=CF=E4=B9=AB=
=D2=E6=D0=FB=B4=AB>
--Boundary-=_SQPJjuONBmHtxyrRmntVLYwulyUJ--
From xcrysden@democritos.it Mon Apr 10 19:45:44 2006
From: xcrysden@democritos.it (Chang'e Weng)
Date: Mon, 10 Apr 2006 11:45:44 -0700
Subject: [xcrysden] Conventional Unit Cell
Message-ID: <194798a80604101145m5485174eg74ebd0796b1a8557@mail.gmail.com>
------=_Part_241_16527266.1144694744573
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable
Content-Disposition: inline
Dear All,
I have been trying to visualize conventional unit cell through xcrysden. I
did LMTO (ELF) calculation and used
xsfConvert
to
convert to xcrysden file. However, I can only get primitive unit cell and I
am not able to visualize conventional unit cell by using the button in
Display menu. I would be appreciate if you could give me some suggestion on
it.
Thanks,
Chang'e Weng
------=_Part_241_16527266.1144694744573
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable
Content-Disposition: inline
Dear All,
I have been trying to visualize conventional unit cell through xcrysde=
n. I did LMTO (ELF) calculation and used
xsfConvert to convert to xcr=
ysden file. However, I can only get primitive unit cell and I am not able t=
o visualize conventional unit cell by using the button in Display menu. I w=
ould be appreciate if you could give me some suggestion on it.
Thanks,
Chang'e Weng
------=_Part_241_16527266.1144694744573--
From xcrysden@democritos.it Fri Apr 14 15:22:04 2006
From: xcrysden@democritos.it (Tone Kokalj)
Date: Fri, 14 Apr 2006 16:22:04 +0200
Subject: [xcrysden] this is regarding showing of Hydrogen bonding
In-Reply-To: <20060403072650.70437112883@democritos.sissa.it>
References: <20060403072650.70437112883@democritos.sissa.it>
Message-ID: <1145024524.5906.7.camel@localhost.localdomain>
> I have generated a slab of urea crystal of (hkl) orientation and water
> molecules were docked on the generated surface of orientation (hkl). Now I
> would like to know/view where hydrogen bonding took place. It only show the
> hydrogen bonding in urea slab but water molecule are 2.1 A apart from
> Hydrogen atom of urea molecules in slab and I expect a hydrogen bond should
> be there. But it not views the H-bond. Though I change the setting
> Hydrogen Bond setting, but not able to show these H-bond.
There are several empirical paramemers controling the display of
H-bonds. The H...X bond distance is juct one among them: i.e. it is the
required but not sufficent condition for drawing the H-bonds. The other
important parameter is the bond-angle between: R-H....X. All these is
desribed here:
http://www.xcrysden.org/doc/modify.html#__toc__7
If you still have the problems, please send me your structure file, and
I can check what is going on.
Regards, Tone
From xcrysden@democritos.it Fri Apr 14 15:35:12 2006
From: xcrysden@democritos.it (Tone Kokalj)
Date: Fri, 14 Apr 2006 16:35:12 +0200
Subject: [xcrysden] A question for AdvGeom
In-Reply-To: <443A61EC.000012.06950@bj163app60.163.com>
References: <443A61EC.000012.06950@bj163app60.163.com>
Message-ID: <1145025312.5906.18.camel@localhost.localdomain>
On Mon, 2006-04-10 at 21:47 +0800, lyw1983 wrote:
> Dear all:
> I am a new user of xcrysden, I use the version1.4.1, after instal it
> I found some tools can't be used, such as AdvGeom and Properties and
> so on, I think if it needs some software to support it ,and what and
> where could I download it?
The "AdvGeom" and "Properties" menu buttons are active only when some
CRYSTAL file is loaded. This is the xcrysden's interface to CRYSTAL
program.
In adition the CRYSTAL package should be present for these two menu
buttons to work.
If you do not have the CRYSTAL program, then those menu buttons are
disabled.
Best regards, Tone
>
From xcrysden@democritos.it Fri Apr 14 15:44:41 2006
From: xcrysden@democritos.it (Tone Kokalj)
Date: Fri, 14 Apr 2006 16:44:41 +0200
Subject: [xcrysden] Conventional Unit Cell
In-Reply-To: <194798a80604101145m5485174eg74ebd0796b1a8557@mail.gmail.com>
References: <194798a80604101145m5485174eg74ebd0796b1a8557@mail.gmail.com>
Message-ID: <1145025881.5906.26.camel@localhost.localdomain>
On Mon, 2006-04-10 at 11:45 -0700, Chang'e Weng wrote:
> Dear All,
>
> I have been trying to visualize conventional unit cell through
> xcrysden. I did LMTO (ELF) calculation and used xsfConvert to convert
> to xcrysden file. However, I can only get primitive unit cell and I am
> not able to visualize conventional unit cell by using the button in
> Display menu. I would be appreciate if you could give me some
> suggestion on it.
xcrysden can show conventional cells only when the CONVVEC section is
present in the XSF file. ( see
http://www.xcrysden.org/doc/XSF.html#__toc__4 )
Please see your XSF file: if the CONVVEC section is missing in your XSF
file, and you know some suitable/compatible convetional lattice vectors,
then you can add them to XSF file. By doing this xcrysden can show the
structure in both primitive and convetional settings. Note that the
property (ELF is your case) will be displayed only in the "box" for
which the property has been calculated (as defined by the
***_DATAGRID_*** section of XSF file).
Regards, Tone
From xcrysden@democritos.it Fri Apr 14 15:47:27 2006
From: xcrysden@democritos.it (Tone Kokalj)
Date: Fri, 14 Apr 2006 16:47:27 +0200
Subject: [xcrysden] XcrySden on SunOS
In-Reply-To: <001801c656f6$216839a0$87b9cbc4@CPQ11380704345>
References: <001801c656f6$216839a0$87b9cbc4@CPQ11380704345>
Message-ID: <1145026047.5906.30.camel@localhost.localdomain>
> I could not compile the XcrySden programs on sunSpark
> ( biprocessor).Please find the following transcript:
>
> cc -Xa -O -DSOLARIS_BUG _DUSE_FONTS -I/usr/sfw/include
> -I/usr/sfw/include -I/usr/include -I/usr/X11R6/include
> -c togle.r
> ucbcc: warning:"-Xa" redefines compatibility mode from "Sun C
> transition" to "ANSI"
> compilor(iropt):GCALL with no root
> *** Error code 1
> make: fatal error: Command failed for target 'togl.o'
Unfortunately, I cannot say nor know what is the problem just from above
description. Try to figure out which lines in togl.c are problematic ...
Regards, Tone
From xcrysden@democritos.it Wed Apr 19 06:25:21 2006
From: xcrysden@democritos.it (Mustafa Uludogan)
Date: Tue, 18 Apr 2006 22:25:21 -0700 (PDT)
Subject: [xcrysden] brillouin zone of R3m space group
Message-ID: <20060419052521.8412.qmail@web33508.mail.mud.yahoo.com>
--0-169230604-1145424321=:4541
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: 8bit
Hi,
I am using Abinit and VASP and I would like to plot (electronic+phonon) band structure of R3m point group (160) Is there any possiblity with Xcrysden that I can get the detailed view of the first BZ for rhombohedral BaTiO3. I have checked the example of Wien code (bi.struct) but it seems it has slightly different BZ.
Is there any suggestions?
Yours Sincerely
Mustafa Uludogan
Chemical Engineering Department
Texas A&M University
College Station, TX 77843
---------------------------------
Love cheap thrills? Enjoy PC-to-Phone calls to 30+ countries for just 2¢/min with Yahoo! Messenger with Voice.
--0-169230604-1145424321=:4541
Content-Type: text/html; charset=iso-8859-1
Content-Transfer-Encoding: 8bit
Hi,
I am using Abinit and VASP and I would like to plot (electronic+phonon) band structure of R3m point group (160) Is there any possiblity with Xcrysden that I can get the detailed view of the first BZ for rhombohedral BaTiO3. I have checked the example of Wien code (bi.struct) but it seems it has slightly different BZ.
Is there any suggestions?
Yours Sincerely
Mustafa Uludogan
Chemical Engineering Department
Texas A&M University
College Station, TX 77843
Love cheap thrills? Enjoy PC-to-Phone calls to 30+ countries for just 2¢/min with Yahoo! Messenger with Voice.
--0-169230604-1145424321=:4541--
From xcrysden@democritos.it Thu Apr 27 16:15:07 2006
From: xcrysden@democritos.it (Tone Kokalj)
Date: Thu, 27 Apr 2006 17:15:07 +0200
Subject: [xcrysden] brillouin zone of R3m space group
In-Reply-To: <20060419052521.8412.qmail@web33508.mail.mud.yahoo.com>
References: <20060419052521.8412.qmail@web33508.mail.mud.yahoo.com>
Message-ID: <1146150907.6568.7.camel@localhost.localdomain>
--=-35ZNRSQs/oejHhKMVT7w
Content-Type: text/plain
Content-Transfer-Encoding: 7bit
On Tue, 2006-04-18 at 22:25 -0700, Mustafa Uludogan wrote:
> Hi,
> I am using Abinit and VASP and I would like to plot (electronic
> +phonon) band structure of R3m point group (160)
> Is there any possiblity with Xcrysden that I can get the detailed view
> of the first BZ for rhombohedral BaTiO3.
If you have the structure file of BaTiO3 (say XSF formatted), then you
can see the corresponding BZ via: "Tools-->k-path Selection" menu entry.
You can even select k-points and get their coordinates.
> I have checked the example of Wien code (bi.struct) but it seems it
> has slightly different BZ.
There can be hexagonal or rhombohedral setting for this space group. The
details of the BZ for hexagonal settings will depend on C vs. A ratio,
while the details for rhombohedral settings on the alpha angle.
I attach XSF files for the four cases (two for each settings).
Regards, Tone
--=-35ZNRSQs/oejHhKMVT7w
Content-Disposition: attachment; filename=R3M_hexa_aC.xsf
Content-Type: text/plain; name=R3M_hexa_aC.xsf; charset=us-ascii
Content-Transfer-Encoding: 7bit
DIM-GROUP
3 7
PRIMVEC
1.1547005384 0.0000000000 1.0000000000
-0.5773502692 1.0000000000 1.0000000000
-0.5773502692 -1.0000000000 1.0000000000
CONVVEC
1.7320508076 -1.0000000000 0.0000000000
0.0000000000 2.0000000000 0.0000000000
0.0000000000 0.0000000000 3.0000000000
PRIMCOORD
1 1
1 0.0000000000 0.0000000000 0.0000000000
--=-35ZNRSQs/oejHhKMVT7w
Content-Disposition: attachment; filename=R3M_hexa_Ac.xsf
Content-Type: text/plain; name=R3M_hexa_Ac.xsf; charset=us-ascii
Content-Transfer-Encoding: 7bit
DIM-GROUP
3 7
PRIMVEC
1.1547005384 0.0000000000 0.3333333333
-0.5773502692 1.0000000000 0.3333333333
-0.5773502692 -1.0000000000 0.3333333333
CONVVEC
1.7320508076 -1.0000000000 0.0000000000
0.0000000000 2.0000000000 0.0000000000
0.0000000000 0.0000000000 1.0000000000
PRIMCOORD
1 1
H 0.0000000000 0.0000000000 0.0000000000
--=-35ZNRSQs/oejHhKMVT7w
Content-Disposition: attachment; filename=R3M_rhomb60.xsf
Content-Type: text/plain; name=R3M_rhomb60.xsf; charset=us-ascii
Content-Transfer-Encoding: 7bit
DIM-GROUP
3 7
PRIMVEC
1.1547005384 0.0000000000 1.6329931619
-0.5773502692 1.0000000000 1.6329931619
-0.5773502692 -1.0000000000 1.6329931619
CONVVEC
1.7320508076 -1.0000000000 0.0000000000
0.0000000000 2.0000000000 0.0000000000
0.0000000000 0.0000000000 4.8989794856
PRIMCOORD
1 1
1 0.0000000000 0.0000000000 0.0000000000
--=-35ZNRSQs/oejHhKMVT7w
Content-Disposition: attachment; filename=R3M_rhomb75.xsf
Content-Type: text/plain; name=R3M_rhomb75.xsf; charset=us-ascii
Content-Transfer-Encoding: 7bit
DIM-GROUP
3 7
PRIMVEC
1.4058742996 0.0000000000 1.4225039380
-0.7029371498 1.2175228580 1.4225039380
-0.7029371498 -1.2175228580 1.4225039380
CONVVEC
2.1088114495 -1.2175228580 0.0000000000
0.0000000000 2.4350457160 0.0000000000
0.0000000000 0.0000000000 4.2675118140
PRIMCOORD
1 1
1 0.0000000000 0.0000000000 0.0000000000
--=-35ZNRSQs/oejHhKMVT7w--
From xcrysden@democritos.it Thu Apr 27 16:25:18 2006
From: xcrysden@democritos.it (Tone Kokalj)
Date: Thu, 27 Apr 2006 17:25:18 +0200
Subject: [xcrysden] Re: Xcrysden bond drawing criteria
In-Reply-To:
References:
Message-ID: <1146151519.6568.18.camel@localhost.localdomain>
On Wed, 2006-04-26 at 13:24 -0400, Ling Miao wrote:
> I have a question regarding the criteria
> of drawing a bond between two atoms. I noticed that in my system,
> some bonds are drawn between Pd and C
> atoms, some are not, although the bond length difference is only about
> 0.1A between those drawn and not drawn.
There are two parameters that determine the bond drawing.
One is chemical connectivity factor, the other is the covalent radius.
The former is a general parameter, while the latter is set to each
individual atomic type (not atom). Both can be set via the
"Modify-->Atomic radii" menu entry.
The bond between two atoms is drawn, when their distance is smaller than
the sum of their covalent radius times the connectivity factor.
If this is not sufficient to draw (or delete) given set of bonds, then
you can substitute some atoms by different atomic types manually in the
structure file. When displaying the structure assign to them different
covalent radii yet use (set) the same atomic color....
Regards, Tone
From xcrysden@democritos.it Sat Apr 29 13:32:58 2006
From: xcrysden@democritos.it (Saeid Jalali)
Date: Sat, 29 Apr 2006 05:32:58 -0700 (PDT)
Subject: [xcrysden] Surface structure
Message-ID: <20060429123258.269.qmail@web54302.mail.yahoo.com>
--0-1691686114-1146313978=:98522
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Dear xcrysden users,
I am a user of wien2k and xcrysden packages. I would study quantum size effects constructing surfaces along arbitrary directions, e.g. (111) of Si. It is not hard to imagine and hence construct surface of a simple cubic along (111) direction, however, this is not the case for more complicated structures. It will be great to find out that whether xcrysden can help us to construct the surfaces of a known complicated unit cell or not. In the former case I appreciate if someone can tell us how we can use xcrysden to construct the surfaces. In the later case any other information will be deeply thankful, say introducing other tools for this purpose.
Thank you in advance,
Sincerely yours,
S. Jalali.
Sincerely yours,
S. Jalali.
/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
Saeid Jalali Asadabadi,
Department of Physics, Faculty of Science,
University of Isfahan (UI), Hezar Gerib Avenue,
81744 Isfahan, Iran.
Phones:
Dep. of Phys. :+98-0311-793 2435
Office :+98-0311-793 2430
Fax No. :+98-0311-793 2409
E-mail :s_jalali_a@yahoo.com
www :http://www.ui.ac.ir
/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
---------------------------------
Yahoo! Messenger with Voice. PC-to-Phone calls for ridiculously low rates.
--0-1691686114-1146313978=:98522
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Dear xcrysden users,
I am a user of wien2k and xcrysden packages. I would study quantum size effects constructing surfaces along arbitrary directions, e.g. (111) of Si. It is not hard to imagine and hence construct surface of a simple cubic along (111) direction, however, this is not the case for more complicated structures. It will be great to find out that whether xcrysden can help us to construct the surfaces of a known complicated unit cell or not. In the former case I appreciate if someone can tell us how we can use xcrysden to construct the surfaces. In the later case any other information will be deeply thankful, say introducing other tools for this purpose.
Thank you in advance,
Sincerely yours,
S. Jalali.
Sincerely yours,
S. Jalali.
/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
Saeid Jalali Asadabadi,
Department of Physics, Faculty of Science,
University of Isfahan (UI), Hezar Gerib Avenue,
81744 Isfahan, Iran.
Phones:
Dep. of Phys. :+98-0311-793 2435
Office :+98-0311-793 2430
Fax No. :+98-0311-793 2409
E-mail :s_jalali_a@yahoo.com
www :http://www.ui.ac.ir
/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
Yahoo! Messenger with Voice. PC-to-Phone calls for ridiculously low rates.
--0-1691686114-1146313978=:98522--