&nbs= p; &= nbsp; &nbs= p; &= nbsp; &nbs= p; &= nbsp; &nbs= p; Sincerely,

&nbs= p; &= nbsp; &nbs= p; &= nbsp; &nbs= p; &= nbsp; &nbs= p; Z.J.

------=_Part_1175_10236925.1143032769052-- From xcrysden@democritos.it Wed Mar 22 14:51:15 2006 From: xcrysden@democritos.it (Mark Lusk) Date: Wed, 22 Mar 2006 07:51:15 -0700 Subject: [xcrysden] XCrySDens within Cygwin Message-ID: <200603221451.k2MEpK9g007779@incantation.Mines.EDU> This is a multi-part message in MIME format. ------=_NextPart_000_0017_01C64D85.65D513D0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear colleague, I noticed that you had posted a message to the XCrySDens group very similar to mine. I have since tried installing Tcl/TK on my Windows machine but have still not been able to get XCrySDens to run. Have you had any luck? Best, Mark Mark T. Lusk Professor and Chair Mechanical Engineering Program Colorado School of Mines Golden, CO 80401 Voice: 303-273-3675 mlusk@mines.edu http://egweb.mines.edu/mlusk/LuskWeb/mlusk.html http://egweb.mines.edu/research/mechanical/entrance.htm ------=_NextPart_000_0017_01C64D85.65D513D0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear colleague,

I noticed that you had posted a message to the = XCrySDens group very similar to mine. I have since tried installing Tcl/TK on my Windows machine but have still not been able to get XCrySDens to run. Have you = had any luck?

Best,

Mark

Mark T. Lusk

Professor and Chair

Mechanical Engineering = Program

Colorado School of = Mines

Golden, CO 80401

Voice: 303-273-3675

mlusk@mines.edu

http://egweb.mi= nes.edu/mlusk/LuskWeb/mlusk.html http://= egweb.mines.edu/research/mechanical/entrance.htm=

------=_NextPart_000_0017_01C64D85.65D513D0-- From xcrysden@democritos.it Wed Mar 22 15:04:00 2006 From: xcrysden@democritos.it (Tone Kokalj) Date: Wed, 22 Mar 2006 16:04:00 +0100 Subject: [xcrysden] XCrySDens within Cygwin In-Reply-To: <200603221451.k2MEpK9g007779@incantation.Mines.EDU> References: <200603221451.k2MEpK9g007779@incantation.Mines.EDU> Message-ID: <1143039841.6858.48.camel@localhost.localdomain> On Wed, 2006-03-22 at 07:51 -0700, Mark Lusk wrote: > Dear colleague, > > > > I noticed that you had posted a message to the XCrySDens group very > similar to mine. I have since tried installing Tcl/TK on my Windows > machine but have still not been able to get XCrySDens to run. One needs the Tcl/Tk provided by cygwin. Installing a Windows version of Tcl/Tk on the Windows OS will not do the job. Did you try with the cygwin Tcl/Tk? ( see http://cygwin.com/packages/ ; the proper package is tcltk ). Regards, Tone From xcrysden@democritos.it Wed Mar 22 18:09:11 2006 From: xcrysden@democritos.it (Wolfram Quester) Date: Wed, 22 Mar 2006 19:09:11 +0100 Subject: [xcrysden] Compile fixes for newer gcc In-Reply-To: <1142949922.6680.63.camel@localhost.localdomain> References: <20060301184635.GC22199@halley.zuhause> <1142949922.6680.63.camel@localhost.localdomain> Message-ID: <20060322180910.GC29648@halley.zuhause> --kfjH4zxOES6UT95V Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Hi Tone, thanks for reenabling the mailing list. On Tue, Mar 21, 2006 at 03:05:21PM +0100, Tone Kokalj wrote: > On Wed, 2006-03-01 at 19:46 +0100, Wolfram Quester wrote: > > Hi altogether! > >=20 > > I tried to compile XCrySDen here with gcc-4.0, but the compilation > > failed with > >=20 > > xcDisplayFunc.c:162: error: static declaration of =E2=80=98HandleDispla= y=E2=80=99 follows non-static declaration > > anaglyph.h:81: error: previous declaration of =E2=80=98HandleDisplay=E2= =80=99 was here > > xcDisplayFunc.c:164: error: static declaration of =E2=80=98CameraHome= =E2=80=99 follows non-static declaration > > anaglyph.h:82: error: previous declaration of =E2=80=98CameraHome=E2=80= =99 was here > > xcDisplayFunc.c:165: error: static declaration of =E2=80=98Normalise=E2= =80=99 follows non-static declaration > > anaglyph.h:83: error: previous declaration of =E2=80=98Normalise=E2=80= =99 was here > > xcDisplayFunc.c:166: error: static declaration of =E2=80=98CalcNormal= =E2=80=99 follows non-static declaration > > anaglyph.h:84: error: previous declaration of =E2=80=98CalcNormal=E2=80= =99 was here > > make[2]: *** [xcDisplayFunc.o] Error 1 > > make[2]: Leaving directory `/tmp/XC/C' > > make[1]: *** [compile] Error 2 > > make[1]: Leaving directory `/tmp/XC/C' > > make: *** [src-C] Error 2 > >=20 > >=20 > > The attached patch fixes this.=20 >=20 > Thank you very much for the patch. The even simpler solution is to > simply > delete these lines from anaglyph.h, as they are redundant. >=20 > void HandleDisplay(struct Togl *togl); > void CameraHome(); > void Normalise(XYZ *); > XYZ CalcNormal(XYZ,XYZ,XYZ); But shouldn't you remove them from the .c-file then? I think these are classical lines belonging into an .h file ;-). With best wishes, Wolfi >=20 > Regards, Tone >=20 > _______________________________________________ > XCrySDen mailing list > XCrySDen@democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden --kfjH4zxOES6UT95V Content-Type: application/pgp-signature; name="signature.asc" Content-Description: Digital signature Content-Disposition: inline -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) iD8DBQFEIZLGH0o2mefAfsQRAl3NAJ4jRyclxRfuR25sc5tgEzEHzxXLcwCfaMF1 oIKfI1gsu02hEhELKvku3BI= =C2Ax -----END PGP SIGNATURE----- --kfjH4zxOES6UT95V-- From xcrysden@democritos.it Wed Mar 22 20:19:43 2006 From: xcrysden@democritos.it (Tone Kokalj) Date: Wed, 22 Mar 2006 21:19:43 +0100 (CET) Subject: [xcrysden] Compile fixes for newer gcc In-Reply-To: <20060322180910.GC29648@halley.zuhause> References: <20060301184635.GC22199@halley.zuhause> <1142949922.6680.63.camel@localhost.localdomain> <20060322180910.GC29648@halley.zuhause> Message-ID: <51751.193.2.5.109.1143058783.squirrel@nabiralnik.ijs.si> > Hi Tone, > > thanks for reenabling the mailing list. Thanks to you for spotting the problem. >> void HandleDisplay(struct Togl *togl); >> void CameraHome(); >> void Normalise(XYZ *); >> XYZ CalcNormal(XYZ,XYZ,XYZ); > > But shouldn't you remove them from the .c-file then? I think these are > classical lines belonging into an .h file ;-). In principle you are right. However above functions are local [i.e. static void HandleDisplay(struct Togl *togl); etc...], used only in xcDisplayFunc.c. Therefore it is OK, if they are defined only in xcDisplayFunc.c. Regards, Tone From xcrysden@democritos.it Thu Mar 23 02:32:57 2006 From: xcrysden@democritos.it (Pan Zhijun) Date: Thu, 23 Mar 2006 10:32:57 +0800 Subject: [xcrysden] XCrySDens within Cygwin In-Reply-To: <200603221451.k2MEpK9g007779@incantation.Mines.EDU> References: <200603221451.k2MEpK9g007779@incantation.Mines.EDU> Message-ID: ------=_Part_14068_23811022.1143081177134 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline I have solved that problem after installing the tcl/tk. 2006/3/22, Mark Lusk : > > Dear colleague, > > > > I noticed that you had posted a message to the XCrySDens group very > similar to mine. I have since tried installing Tcl/TK on my Windows machi= ne > but have still not been able to get XCrySDens to run. Have you had any lu= ck? > > > > Best, > > > > Mark > > > > Mark T. Lusk > > Professor and Chair > > Mechanical Engineering Program > > Colorado School of Mines > > Golden, CO 80401 > > Voice: 303-273-3675 > > mlusk@mines.edu > > http://egweb.mines.edu/mlusk/LuskWeb/mlusk.html > http://egweb.mines.edu/research/mechanical/entrance.htm > > > ------=_Part_14068_23811022.1143081177134 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline I have solved that problem after installing the tcl/tk.

2006/3/22, Mark Lusk <mlusk@mines.edu>:

Dear colleague,

I noticed that you had posted a message to the XCrySDe= ns group very similar to mine. I have since tried installing Tcl/TK on my W= indows machine but have still not been able to get XCrySDens to run. Have y= ou had any luck?

Best,

Mark

Mark T. Lusk

Professor and Chair

Mechanical Engineering Program

Colorado School of Mines

Golden, CO 80401

Voice: 303-273-3675

mlusk@mines.edu

http://egwe= b.mines.edu/mlusk/LuskWeb/mlusk.html http://egweb.mines.e= du/research/mechanical/entrance.htm<= font color=3D"blue">

2006/3/23, Tone Kokalj <tone.kokalj@ijs.si>:
Pan Zhijun wrote:

> Hi= ,all users of xcrysden,
>     I want to install t= he software crystal98 on=20 cygwin.But I failed to
> do that.Who can do me a favor?Thank you very= much in advance.

Since crystal98 is written in fortran-77, I gu= ess that the compilation
of it
(or any other fortran-77 program) shou= ld be similar on cygwin as on linux,
provided that you have g77, gcc, make, and other possible shell utiliti= es
installed on cygwin.

For the specific case of crystal98 you ne= ed to edit the src/makefile,
and the platform specific src/Xmakes/$(ARCH= ).inc makefile's include file.
For the later I would start with Linux-g77.inc

Regards, Tone
= _______________________________________________
XCrySDen mailing listXCrySDen@democritos.it
http://www.d= emocritos.it/mailman/listinfo/xcrysden

------=_Part_3666_32207407.1143118488158-- From xcrysden@democritos.it Thu Mar 23 15:07:36 2006 From: xcrysden@democritos.it (Mark Lusk) Date: Thu, 23 Mar 2006 08:07:36 -0700 Subject: [xcrysden] RE:Success with XCrySDen on Cygwin In-Reply-To: <20060323023301.22205.9769.Mailman@democritos.sissa.it> Message-ID: <200603231507.k2NF7hNn028703@incantation.Mines.EDU> Dear colleagues, I have now gotten XCrySDens to run just fine on Cygwin. Great! I had not selected the proper package for TCL/TK when downloading cygwin the first time. (See note below.) http://cygwin.com/packages/ The proper package is tcltk Thanks very much for the help. Mark From xcrysden@democritos.it Fri Mar 24 09:26:52 2006 From: xcrysden@democritos.it (Pan Zhijun) Date: Fri, 24 Mar 2006 17:26:52 +0800 Subject: [xcrysden] How to install crystal 98 on cygwin? In-Reply-To: References: <44227089.7030601@ijs.si> Message-ID: ------=_Part_1871_17586363.1143192412443 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi,Tone, Thank you for your kind help. I have another problem to ask you for your help. How to activate the menus of AdvGeom and Properties of XcrySDen under the circumstance of no installing the Crystall98?Thank you. Best regards. Sincerely, Z.J. 2006/3/23, Pan Zhijun : > > Tone, > Thank you for your help. > Best regards! > Sincerely, > Z.J. > > > 2006/3/23, Tone Kokalj : > > > > Pan Zhijun wrote: > > > > > Hi,all users of xcrysden, > > > I want to install the software crystal98 on cygwin.But I failed t= o > > > do that.Who can do me a favor?Thank you very much in advance. > > > > > > Since crystal98 is written in fortran-77, I guess that the compilation > > of it > > (or any other fortran-77 program) should be similar on cygwin as on > > linux, > > provided that you have g77, gcc, make, and other possible shell > > utilities > > installed on cygwin. > > > > For the specific case of crystal98 you need to edit the src/makefile, > > and the platform specific src/Xmakes/$(ARCH).inc makefile's include > > file. > > For the later I would start with Linux-g77.inc > > > > Regards, Tone > > _______________________________________________ > > XCrySDen mailing list > > XCrySDen@democritos.it > > http://www.democritos.it/mailman/listinfo/xcrysden > > > > ------=_Part_1871_17586363.1143192412443 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
Hi,Tone,

     Thank you for your kind help. I have another = problem to ask you for your help. How to activate the menus of AdvGeom and = Properties of XcrySDen under the circumstance of no installing the Crystall= 98?Thank you.

      Best regards.

           &nbs= p;            &= nbsp;           &nbs= p;            &= nbsp; Sincerely,

           &nbs= p;            &= nbsp;           &nbs= p;            &= nbsp; Z.J.

2006/3/23, Pan Zhijun <panzhijun@gmail.com>:

Tone,

Thank you for your help.

Best regards!

           &nbs= p;            &= nbsp;           &nbs= p;           Sincerely,
           &nbs= p;            &= nbsp;           &nbs= p;           Z.J.

=

2006/3/23, Tone Kokalj <tone.kokalj@ijs.si>:=20

Pan Zhijun wrote:

> Hi= ,all users of xcrysden,
>     I want to install t= he software crystal98 on=20 cygwin.But I failed to
> do that.Who can do me a favor?Thank you very= much in advance.

Since crystal98 is written in fortran-77, I gu= ess that the compilation
of it
(or any other fortran-77 program) shou= ld be similar on cygwin as on linux,=20
provided that you have g77, gcc, make, and other possible shell utiliti= es
installed on cygwin.

For the specific case of crystal98 you ne= ed to edit the src/makefile,
and the platform specific src/Xmakes/$(ARCH= ).inc makefile's include file.=20
For the later I would start with Linux-g77.inc

Regards, Tone
= _______________________________________________
XCrySDen mailing list XCrySDen@democritos.it
http://www.democritos.it/mailman/listinfo/xcrysden

------=_Part_1871_17586363.1143192412443-- From xcrysden@democritos.it Fri Mar 24 13:21:34 2006 From: xcrysden@democritos.it (Ikutaro Hamada) Date: Fri, 24 Mar 2006 22:21:34 +0900 Subject: [xcrysden] mpeg-making with xcrysden on MacOSX In-Reply-To: <426d9c06a2dda6da8855fbbc2ae5de0c@rc.m-kagaku.co.jp> References: <426d9c06a2dda6da8855fbbc2ae5de0c@rc.m-kagaku.co.jp> Message-ID: 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 From xcrysden@democritos.it Mon Mar 27 07:35:17 2006 From: xcrysden@democritos.it (M. K. Singh) Date: Mon, 27 Mar 2006 12:05:17 +0530 (IST) Subject: [xcrysden] Re: XCrySDen Viewing of External format data of CRYSTAL03/98 In-Reply-To: <20060325063708.31544.15426.Mailman@democritos.sissa.it> References: <20060325063708.31544.15426.Mailman@democritos.sissa.it> Message-ID: <2082.10.11.0.2.1143441317.squirrel@10.11.0.2> Dear All, I would like to visualise CRYSTAL03/98 input with keyword EXTERNAL. The corresponding fort.34 file for EXTERNAL format is available in the same directory where input file exit but I can�t visualise it using Xcrysden code. Any help will be highly appreciated. Thank -- M. K. Singh From xcrysden@democritos.it Mon Mar 27 15:54:10 2006 From: xcrysden@democritos.it (Tone Kokalj) Date: Mon, 27 Mar 2006 16:54:10 +0200 Subject: [xcrysden] Re: XCrySDen Viewing of External format data of CRYSTAL03/98 In-Reply-To: <2082.10.11.0.2.1143441317.squirrel@10.11.0.2> References: <20060325063708.31544.15426.Mailman@democritos.sissa.it> <2082.10.11.0.2.1143441317.squirrel@10.11.0.2> Message-ID: <4427FC92.6060803@ijs.si> This is a multi-part message in MIME format. --------------010408070001000809040203 Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: 8bit M. K. Singh wrote: >Dear All, >I would like to visualise CRYSTAL03/98 input with keyword EXTERNAL. The >corresponding fort.34 file for EXTERNAL format is available in the same >directory where input file exit but I can�t visualise it using Xcrysden >code. >Any help will be highly appreciated. > > Indeed, the parsing of crystal03 input files with "EXTERNAL" keyword is not supported (I never thought about that). However the fix was quite simple. I attach the tar-gzipped file of four patched Tcl files. Please put them in $XCRYSDEN_TOPDIR/Tcl. Then the "EXTERNAL" feature should work. Regards, Tone --------------010408070001000809040203 Content-Type: application/x-gtar; name="c03_external_patch.tgz" Content-Transfer-Encoding: base64 Content-Disposition: inline; filename="c03_external_patch.tgz" H4sIABn2J0QAA+xc/3faSJKfX/FfUZZ5mfjemCAwycS7kzmCnYQLAT9wcsk4vjwBjdFYSKwk glmv//er6m/qFsJfJs7bnbvl+QUhVVdXd1VXV32qFW/89TWLZpV0FPzwvT5V/Dzd36dv91mj an7zJ/WG+4Nb3XfdZ0+f7lef/lB13aeNpz9A9btJZHwWSerFAD+kUchuorvt+Z/0s/OQn60d aC7SaRQfwLd/iNse/zwAM84NmiFqEd5GF17w++1NjmaeHxzACSq+Itr8p/97Ukl8ye2Qzb04 nbEwhWgCx9NV4o+8ALxwDL343Av9EbSmbOYnabwCfI58DuAS6j8/BRf2nz2DeqNW17L9V/R3 NoFByiZeCO0wSf10kbLN0r3yLnPcfnbdjJs3i756UH/+Ewzaey4uM+j8vhgGv3uhd/95G3R6 H4667ea9Wm7k9mAf4jaIFvEI57X8sdX/NDg86n456R0ftvtPTkbBEy9zbndk+eA214rmq9g/ n6bweLQL7vPnT/dq1Wodhqt7WiNxe9C1qof6IJ9C1TYPP3x5fdR7B73jk3avO6AO129unjw/ hHTqJzDxA1TxoNN8udZJq/N+cHLUh2ie+lGYgBcz8GfzgNG6ZOMHH+TDMkRux83+yY774oU5 slbzBJpr4/0f/dmaxxE6l0U6CLwhXF3D1RYRnAfREB3QG3gLHWgP3h9DtwOjRZog1SQaBeiJ 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text/plain; charset="windows-1250" Content-Transfer-Encoding: quoted-printable =20 Thank for your kind reply.=20 I have applied the patches Tcl files and my problem is solved. Now I can visualize CRYSTAL03 input with EXTERNAL Keyword using Xcrysden Graphics. = Now I can=92t visualize normal CRYSTAL03/98 file (i.e. No EXTERNAL Keyword) = with Xcrysden anymore.=20 How to correct it? Please help me. =20 Thank you, With best regards =20 Sincerely Yours M. K. Singh wrote: =20 >Dear All, >I would like to visualize CRYSTAL03/98 input with keyword EXTERNAL. The >corresponding fort.34 file for EXTERNAL format is available in the same >directory where input file exit but I can=92t visualize it using = Xcrysden >code. >Any help will be highly appreciated. > =20 >=20 =20 Indeed, the parsing of crystal03 input files with "EXTERNAL" keyword is not supported (I never thought about that). However the fix was quite simple. I attach the tar-gzipped file of four patched Tcl files. Please=20 put them in $XCRYSDEN_TOPDIR/Tcl. =20 Then the "EXTERNAL" feature should work. =20 Regards, Tone =20 M. K. Singh Scientific Officer Laser Materials Development and Device Division Centre for Advanced Technology PO: CAT Indore - 452 013 (MP) INDIA Phone No. +91-731-248-8677 (Office) Fax No. +91-731-248-8650 (Office) =20 --=20 No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.1.385 / Virus Database: 268.3.3/298 - Release Date: = 30/03/2006 =20 =20 ------=_NextPart_001_0001_01C654DF.3C6CC7C0 Content-Type: text/html; charset="windows-1250" Content-Transfer-Encoding: quoted-printable

Thank for your = kind reply.

I have applied = the patches Tcl files and my problem is solved. Now I can visualize CRYSTAL03 input = with EXTERNAL Keyword using Xcrysden Graphics. Now I can’t visualize = normal CRYSTAL03/98 file (i.e. No EXTERNAL Keyword) with Xcrysden anymore. =

How to correct = it?

Please help = me.

Thank = you,

With best = regards

Sincerely = Yours

M. K. Singh wrote:

>Dear All,

>I would like to visualize CRYSTAL03/98 input with = keyword EXTERNAL. The

>corresponding fort.34 file for EXTERNAL format is available in the same

>directory where input file exit but I can’t = visualize it using Xcrysden

>code.

>Any help will be highly = appreciated.

>

>

Indeed, the parsing of crystal03 input files with "EXTERNAL" keyword

is not supported (I never thought about that). However = the fix was quite

simple. I attach the tar-gzipped file of four patched = Tcl files. Please

put them in

$XCRYSDEN_TOPDIR/Tcl.

Then the "EXTERNAL" feature should = work.

Regards, Tone

M. K. Singh

Scientific = Officer

Laser Materials Development and Device = Division

Centre for Advanced = Technology

PO= : = CAT

Indore - 452 013 = (MP)

INDIA
Phone No. +91-731-248-8677 = (Office)

Fax     No. = +91-731-248-8650 (Office)

--
No virus found in this outgoing message.
Checked by AVG Free Edition.
Version: 7.1.385 / Virus Database: 268.3.3/298 - Release Date: = 30/03/2006

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Now I > can visualize CRYSTAL03 input with EXTERNAL Keyword using Xcrysden > Graphics. Now I can�t visualize normal CRYSTAL03/98 file (i.e. No > EXTERNAL Keyword) with Xcrysden anymore. > > How to correct it? > The last-time the patch was a bit too fast. Here is the correction (put the attached file into $XCRSDEN_TOPDIR/Tcl). Now both possibilities should work. Regards, Tone --------------080403080508020100040603 Content-Type: text/x-tcl; name="openInput.tcl" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="openInput.tcl" ############################################################################# # Author: # # ------ # # Anton Kokalj Email: Tone.Kokalj@ijs.si # # Department of Physical and Organic Chemistry Phone: x 386 1 477 3523 # # Jozef Stefan Institute Fax: x 386 1 477 3811 # # Jamova 39, SI-1000 Ljubljana # # SLOVENIA # # # # Source: $XCRYSDEN_TOPDIR/Tcl/openInput.tcl # ------ # # Copyright (c) 1996-2003 by Anton Kokalj # ############################################################################# proc OpenFile {{file {}}} { global fileselect distext Alist species speciesName \ type_group type_group1 job_title \ inp n_groupsel groupsel crdatom XCState system \ AdvGeom xcMisc crystalInput if { $system(c95_exist) == 0 } { ErrorDialog "can't open CRYSTAL-95/98/03 input File. CRYSTAL package is not installed !!!" return } # distext .... here go informations to be displayed in # information text widget if { $file == "" } { fileselect "Open CRYSTAL Input" } elseif { [file isdirectory $file]} { set fileselect(path) [tk_getOpenFile -defaultextension .r1 \ -filetypes { {{All Files} {.*} } {{CRYSTAL Input Files} {.r1}} } -initialdir $file \ -title "Open CRYSTAL Input"] if { $fileselect(path) == "" } { return } } else { set fileselect(path) $file } # maybe CANCEL button was pressed if { $fileselect(path) == "" } { xcDeleteState c95 xcDeleteState openinput xcUpdateState return } ################# # initialisation set XCState(state) c95_openinput xcUpdateState xcAdvGeomState reset # # reset the title of "." # wm title . "XCrySDen: [file tail $fileselect(path)]" set xcMisc(titlefile) [file tail $fileselect(path)] # OK button was pressed # check if selected file is Crystal95 file; # the best way for doing it is to go and check it with Crystal95 ######################################## # CD to $system(SCRDIR) cd $system(SCRDIR) ######################################## # test only geom part of the input file (this is quick) # xc_inp.$system(PID)...here just geom input will be stored xcCatchExecReturn $system(AWKDIR)/ginp.awk \ $fileselect(path) > $system(SCRDIR)/xc_inp.$system(PID) puts stdout "FILE: $fileselect(path)" puts stdout "FILTERED INPUT" catch {ReadFile $system(SCRDIR)/xc_inp.$system(PID)} # BEGIN t.k. # for EXTERNAL: copy also fort.34 if { [file exists $system(PWD)/$system(ftn_name).34 ] } { file copy -force $system(PWD)/$system(ftn_name).34 $system(SCRDIR)/external_unit34 file copy -force $system(SCRDIR)/external_unit34 $system(SCRDIR)/$system(ftn_name).34 } # END t.k. # if we catch error than selected file is of the right type, # but is corrupted if { [catch {exec $system(c95_integrals) < \ $system(SCRDIR)/xc_inp.$system(PID) >& \ $system(SCRDIR)/xc_tmp.$system(PID)} errmsg] } { set idx [tk_dialog .idx1 ERROR "Selected file seems to be \ Crystal95 input file, but is corrupted" error 0 OK Details] if { $idx == 1 } { #user want's to see details tk_dialog .errm Details "ERROR MESSAGE:\n$errmsg" {} 0 OK } catch {file delete $system(SCRDIR)/xc_tmp.$system(PID)} OpenFile return } else { # if Crystal95 find out that file is "bad", it has exited # nicely, but with ERROR message; grep ERROR --> if grep # doesn't find anything, we must catch the grep error #eval [list exec grep ERROR $system(SCRDIR)/xc_tmp.$system(PID)] if { ! [catch {exec grep ERROR $system(SCRDIR)/xc_tmp.$system(PID)}] } { puts stdout "grep ERROR catched" tk_dialog .idx2 ERROR "Selected file is bad !!" error 0 OK file delete $system(SCRDIR)/xc_tmp.$system(PID) OpenFile return } } # it Looks that Selected file is good !!! # READ THE FILE; "distext" variable collects a information to be displayed set input [open "$system(SCRDIR)/xc_inp.$system(PID)"] set job_title [gets $input] set distext "> TITLE::\n$job_title\n" append distext "--------------------------------------------------\n\n" # just in any case (lindex 0) if there is anything bisides the "$species" set species [string tolower [lindex [gets $input] 0]] append distext "> SPECIES:: $species\n" append distext "--------------------------------------------------\n\n" if { $species == "external" } { # EXTERNAL OPTION CalStru return } elseif { $species == "crystal" } { # ========================== # SPECIES == CRYSTAL # ========================== set type_group "space" set type_group1 "Space" set ifl [gets $input] set inp(IFLAG) [lindex $ifl 0] set inp(IFHR) [lindex $ifl 1] set inp(IFSO) [lindex $ifl 2] append distext "> CRYSTAL FLAGS::\n" append distext "IFLAG: $inp(IFLAG), IFHR: $inp(IFHR), IFSO: $inp(IFSO)\n" append distext "--------------------------------------------------\n\n" # =================================================== # WHAT ABOUT sequ. number or alfanum. code for "group" if { $inp(IFLAG) == 0 } { # n_groupsel is synonym for IGR; (lindex 0) is just in any case set n_groupsel [lindex [gets $input] 0] set groupsel [Igr2Agr $n_groupsel space_group] append distext "> SPACE GROUP::\n" append distext "IGR = $n_groupsel --> AGR = $groupsel\n" append distext "--------------------------------------------------\n\n" } else { # $groupsel & $AGR are synonyms set inp(AGR) [gets $input] set n_groupsel [Agr2Igr $inp(AGR)] set groupsel $inp(AGR); #gropusel & AGR are synonyms append distext "> SPACE GROUP::\n" append distext "AGR = $groupsel --> IGR = $n_groupsel\n\n" append distext "--------------------------------------------------\n\n" } if { $inp(IFSO) > 1} { # non-standard shift of the ORIGIN set ixyz [gets $input] set inp(IX) [lindex $ixyz 0] set inp(IY) [lindex $ixyz 1] set inp(IZ) [lindex $ixyz 2] append distext "> NON-STANDARD ORIGIN SHIFT::\n" append distext "IX = $inp(IX), IY = $inp(IY), IZ = $inp(IZ)\n" append distext "--------------------------------------------------\n\n" } # verify which unit-cell parameter must be read & read it !!! WhichPar2Read $input } elseif { $species == "slab" } { set type_group "plane" set type_group1 "Plane" # n_groupsel is synonym for IGR; (lindex 0) is just in any case set n_groupsel [lindex [gets $input] 0] set groupsel [Igr2Agr $n_groupsel plane_group] append distext "> LAYER GROUP::\n" append distext "IGR = $n_groupsel --> $groupsel\n" append distext "--------------------------------------------------\n\n" # verify which unit-cell parameter must be read & read it !!! WhichPar2Read $input } elseif { $species == "polymer" } { set type_group "line" set type_group1 "Line" # n_groupsel is synonym for IGR; (lindex 0) is just in any case set n_groupsel [lindex [gets $input] 0] set groupsel [Igr2Agr $n_groupsel line_group] append distext "> ROD GROUP::\n" append distext "IGR = $n_groupsel --> $groupsel\n" append distext "--------------------------------------------------\n\n" # for all polymers we must read just A parameter set inp(A) [gets $input] append distext "> UNIT CELL PARAMETER::\nA: $inp(A)\n" append distext "--------------------------------------------------\n\n" } elseif { $species == "molecule" } { set type_group "point" set type_group1 "Point" # n_groupsel is synonym for IGR; (lindex 0) is just in any case set n_groupsel [lindex [gets $input] 0] set groupsel [Igr2Agr $n_groupsel point_group] append distext "> POINT GROUP::\n" append distext "IGR = $n_groupsel --> $groupsel\n" append distext "--------------------------------------------------\n\n" } # =============================================== # THIS IS COMMON FOR ALL SPECIES # inp(NATR); (lindex 0) is just in any case to be save set inp(NATR) [lindex [gets $input] 0] # crdatom is used for checking the variables set crdatom 1 append distext "> NUMBER OF NON-EQUIVALENT ATOMS::\nNATR = $inp(NATR)\n\n" append distext "> ATOMIC NUMBERS & COORDINATES OF NON-EQUIVALENT ATOMS::\n" # read Nat,X,Y,Z for {set i 1} {$i <= $inp(NATR)} {incr i} { set natrx [gets $input] set inp(NAT,$i) [lindex $natrx 0] set inp(X,$i) [lindex $natrx 1] set inp(Y,$i) [lindex $natrx 2] set inp(Z,$i) [lindex $natrx 3] # this is to load atom names AtomNames append distext [format "%-3d %-4s %10.5f %10.5f %10.5f\n" \ $inp(NAT,$i) [Nat2Aname $inp(NAT,$i)] $inp(X,$i) $inp(Y,$i) $inp(Z,$i)] } append distext "--------------------------------------------------\n\n" set speciesName $species ####################################### # check for ADVANCE GEOMETRICAL INPUT # ####################################### set line [gets $input] if { $line != "STOP" } { ############################# # ADVANCE GEOMETRICAL INPUT # ############################# set AdvGeom(input) "$line\n" while { [set line [gets $input]] != "STOP" } { append AdvGeom(input) "$line\n" } xcDebug "\nADVANCE GEOMETRICAL INPUT FOUND::\n$AdvGeom(input)\n" append distext " #########################################\n" append distext " # GEOMETRY MANIPULATION INPUT was found #\n" append distext " #########################################\n\n" append distext "Geometry manipulation input::\n" append distext "$AdvGeom(input)\n" # chack if dimensionality of the system has changed during # the geometry manipulation foreach word $AdvGeom(input) { switch -glob -- $word { *SLAB* { set speciesName "slab" } *MOLECULE* { set speciesName "molecule" } *CLUSTER* { set speciesName "cluster" } } } } # ============================================================ # INPUT FILE HAS BEEN READ OUT !!!!!!!! # # make a toplevel where some information about selected file # will be printed out # # there will be text widget & OK button # for text widged there is a DispText procedure; # all will be displayed after the input file will be read out # # produce some toplevel where it will # be possible to modify different parameters # ============================================================= # StatusWidget creates Status Widget & return path of toplevel set tx [StatusWidget] # TOPLEVEL FOR DECISION (VIEWER,MODIFY) set td [xcToplevel .opfd "Open Crystal Input" "Open Crystal Input" \ . 50 100] set crystalInput(two_toplevels) {.opfd .opftx} AlwaysOnTopON . $crystalInput(two_toplevels) focus $td set l [label $td.lbl -text "What to do?" -relief raised -bd 2] set f [frame $td.frm] set b1 [button $f.but1 -text "Modify File" -command \ [list OpenFileModify $tx $td]] puts stdout "tx> $tx" set b2 [button $f.but2 -text "View $speciesName" -command \ [list OpFile2ViewMol $tx $td]] pack $l $f -side top -expand 1 -fill both -ipadx 10 -ipady 10 pack $b1 $b2 -side left -expand 1 -padx 7 } proc OpenFileModify {tx td} { global fileselect distext species type_group type_group1 \ inp n_groupsel groupsel XCState XCTrace CancelProc $td # MODIFY TOPLEVEL set t [xcToplevel .openfile "Modify" "Modify" \ . 50 100] # .opftx -- status widget AlwaysOnTopON . {.openfile .opftx} focus $t # because what ever I choose there will apper some new toplevel, that will # override AlwaysOnTop flag for .openfile & .opftx toplevels, # so we must set #set XCState(toplevel) {.openfile .opftx} puts stdout "species: $species" flush stdout # label goes on the top set l [label $t.lbl -text "MODIFY/CHANGE:" -relief groove -bd 2] pack $l -side top -expand 1 -fill x -padx 7 -pady 7 -ipady 7 -ipadx 10 # for every option/parameter make a button set spe [button $t.b1 -text "Species" \ -command ChooseSpecies] # if you will change $species you must change name of this button # this is possible throuh buutn-entry combination set igr [button $t.b4 -text "Group" \ -command [list ModGroup $t]] # Only for rhombohedral group is not meanningless to specify IHFR # so doit by CheckGroup proc set ifhr [button $t.b2 -text "Type of Cell for \n\ Rhombohedral Groups" -command CheckGroup] set ifso [button $t.b3 -text "Origin Setting" \ -command PreSetOrigin] set par [button $t.b5 -text "Cell Parameters" \ -command [list PreGeom_sym_input .opflgeom $t]] set coor [button $t.b6 -text "Atomic Coordinates &\n\ Atomic Numbers" -command atom_num_coord] set view [button $t.b8 -text "View Structure" \ -command [list OpFile2ViewMol $tx $t]] set close [button $t.b9 -text "Close" \ -command [list DestroyOpfl $t $tx]] if { $species == "crystal" } { pack $spe $igr $ifhr $ifso $par $coor $view $close \ -fill x -expand 1 -padx 5 -pady 3 -ipadx 0 -ipady 0 if { [lindex $groupsel 0] != "R" } { $ifhr config -state disabled set XCTrace(RHOMBO_TYPE_BUTTON) $ifhr trace variable groupsel w xcTrace } } elseif { $species == "slab" || $species == "polymer"} { pack $spe $igr $par $coor $view $close -fill x -expand 1 \ -padx 5 -pady 3 -ipadx 0 -ipady 0 } else { pack $spe $igr $coor $view $close -fill x -expand 1 \ -padx 5 -pady 3 -ipadx 0 -ipady 0 } } proc cxxManageExternal {} { global species system # if the species is external we need to copy # $system(SCRDIR)/external_unit34 to # $system(SCRDIR)/$system(ftn_name).34 # (see proc OpenFile) if { $species == "external" } { file copy -force $system(SCRDIR)/external_unit34 $system(SCRDIR)/$system(ftn_name).34 } } proc Agr2Igr {agr} { global group_list # "load" a $group_list space_group set n 1 # assign a sequ. number to $igr that correspond to $agr foreach word $group_list { # pure the $word set last [ string length $word ] set word [ string range $word 5 $last ] regexp {(([A-Z0-9] )|[A-Z0-9\/\-])+[A-Z0-9]} $word word if { $agr == $word } { set igr $n } incr n } puts stdout "Agr2Igr> agr = $agr" flush stdout # puts stdout " igr = $igr" # maybe "agr"symbol is not standard one if ![info exists igr] { return "\"$agr\" is not a standard space group" } return $igr } proc Igr2Agr {igr comm} { global group_list # "load" a $group_list eval $comm set n 1 # assign asymbol to $agr that correspond to $igr foreach word $group_list { # purify the $word if { $igr == $n } { set last [ string length $word ] set word [ string range $word 5 $last ] regexp {(([A-Z0-9] )|[A-Z0-9\/\-])+[A-Z0-9]} $word word set agr $word } incr n } return $agr } proc OpFile2ViewMol {tx td} { # there maybe trace on "groupsel" variable xcTraceDelete groupsel CancelProc $tx CancelProc $td # CHECK THE VARIABLES --> variables must be checked everytimes- # we do sometning in Modify; so if we are here everything is OK CalStru return } proc ModGroup {t} { global species if { $species == "molecule" } { # load point groups point_group geom_sym_input .opflmod $t } elseif { $species == "polymer" } { # load groups line_group geom_sym_input .opflmod $t } elseif { $species == "slab" } { # load groups plane_group crys_slab_sym .opflmod $t } elseif {$species == "crystal" } { # load groups space_group crys_slab_sym .opflmod $t } } proc UpdateStatus {t} { global fileselect distext Alist species type_group type_group1 job_title \ inp n_groupsel groupsel crdatom #t....text-widget-path # put updated information in $distext set distext "> TITLE::\n$job_title\n" append distext "--------------------------------------------------\n\n" append distext "> SPECIES:: $species\n" append distext "--------------------------------------------------\n\n" # ========================== # SPECIES == CRYSTAL # ========================== if { $species == "crystal" } { append distext "> CRYSTAL FLAGS::\n" append distext "IFLAG: $inp(IFLAG), IFHR: $inp(IFHR), IFSO: $inp(IFSO)\n" append distext "--------------------------------------------------\n\n" if { $n_groupsel == 999 } { set n_groupsel "\"$groupsel\" is not a standard space group" } if { $inp(IFLAG) == 0 } { append distext "> SPACE GROUP::\n" append distext "IGR = $n_groupsel --> AGR = $groupsel\n" append distext "--------------------------------------------------\n\n" } else { append distext "> SPACE GROUP::\n" append distext "AGR = $groupsel --> IGR = $n_groupsel\n\n" append distext "--------------------------------------------------\n\n" } if { $inp(IFSO) > 1} { append distext "> NON-STANDARD ORIGIN SHIFT::\n" append distext "IX = $inp(IX), IY = $inp(IY), IZ = $inp(IZ)\n" append distext "--------------------------------------------------\n\n" } # verify which unit-cell parameter must be read & read it !!! WhichPar2Print } elseif { $species == "slab" } { append distext "> LAYER GROUP::\n" append distext "IGR = $n_groupsel --> $groupsel\n" append distext "--------------------------------------------------\n\n" # verify which unit-cell parameter must be read & read it !!! WhichPar2Print } elseif { $species == "polymer" } { append distext "> ROD GROUP::\n" append distext "IGR = $n_groupsel --> $groupsel\n" append distext "--------------------------------------------------\n\n" append distext "> UNIT CELL PARAMETER::\nA: $inp(A)\n" append distext "--------------------------------------------------\n\n" } elseif { $species == "molecule" } { append distext "> POINT GROUP::\n" append distext "IGR = $n_groupsel --> $groupsel\n" append distext "--------------------------------------------------\n\n" } append distext "> NUMBER OF NON-EQUIVALENT ATOMS::\nNATR = $inp(NATR)\n\n" append distext "> ATOMIC NUMBERS & COORDINATES OF NON-EQUIVALENT ATOMS::\n" # read Nat,X,Y,Z for {set i 1} {$i <= $inp(NATR)} {incr i} { AtomNames append distext [format "%-3d %-4s %10.5f %10.5f %10.5f\n" \ $inp(NAT,$i) [Nat2Aname $inp(NAT,$i)] $inp(X,$i) $inp(Y,$i) $inp(Z,$i)] } append distext "--------------------------------------------------" # now display the updated information # first delete old text if nessecary if [winfo exists $t] { $t.t delete 1.0 end DispText $t $distext 50 25 } else { set t [StatusWidget] } } proc StatusWidget {} { global distext # TOPLEVEL WITH TEXT set tx [xcToplevel .opftx "Crystal Input: status" "Crystal Input" \ . 330 100] AlwaysOnTopON . .opftx DispText $tx.frm1 $distext 50 25 set frm [frame $tx.f -height 10] pack $frm -side bottom -before $tx.frm1 -fill x set ok [button $frm.ok -text "Close" -command "destroy $tx"] set updat [button $frm.upd -text "Update Status" \ -command [list UpdateStatus $tx.frm1]] pack $ok $updat -side left -expand 1 -ipadx 2 -ipady 2 -pady 10 return $tx } proc PreSetOrigin {} { global n_groupsel species inp # Origin settings is just for crystals & rhombohedral one; # if user has changed $species or group --> if origin settings become # meaningless, make a note to user if { $species != "crystal" } { set b [tk_dialog .preorgset WARNING "Species has been changed \ and is not any more a CRYSTAL, so Origin Setting is \ meaningless !!" warning 0 OK] return } set_origin } proc PreGeom_sym_input {w t} { global species set b 1 if { $species == "molecule" } { set b [tk_dialog .pregeom WARNING "Species has been changed to \ Molecule & for Molecules there is no Cell Parameters!!" \ warning 0 OK] } if { $b == 1 } { geom_sym_input .opflgeom $t } return } proc DestroyOpfl {t1 t2} { # delete trace on groupsel variable xcDeleteState c95 xcDeleteState openinput xcUpdateState xcTraceDelete groupsel CancelProc $t1 CancelProc $t2 return } --------------080403080508020100040603-- From xcrysden@democritos.it Wed Mar 1 08:04:17 2006 From: xcrysden@democritos.it (Pan Zhijun) Date: Wed, 1 Mar 2006 16:04:17 +0800 Subject: [xcrysden] How to install the xcrysden1.4 under the cygwin bash shell? Message-ID: ------=_Part_4200_31234637.1141200257282 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi,all users of xcrysden, I am a newer of xcrysden and want to install this software under the cygwin bash shell.After installing, when I perform the command xcrysden,errors come.The error information is the following:/home/Administrator/xcrysden/XCrySDen-1.4bin-shared/xcrysden:line 156: exec: wish: not found.How to solve the problem?Any hint is appreciated.Thank you very much in advance. Best regards! Yours sincerely, Zhijun ------=_Part_4200_31234637.1141200257282 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
Hi,all users of xcrysden,

    I am a newer of xcrysden and want to install this s= oftware under the cygwin bash shell.After installing, when I perform the co= mmand xcrysden,errors come.The error information is the following:/home/Adm= inistrator/xcrysden/XCrySDen- 1.4bin-shared/xcrysden:line 156: exec: wish: not found.How to solve the pro= blem?Any hint is appreciated.Thank you very much in advance.

   Best regards!

           &nbs= p;            &= nbsp;           &nbs= p;             = Yours sincerely,

           &nbs= p;            &= nbsp;           &nbs= p;             = Zhijun
------=_Part_4200_31234637.1141200257282-- From xcrysden@democritos.it Wed Mar 1 18:46:35 2006 From: xcrysden@democritos.it (Wolfram Quester) Date: Wed, 1 Mar 2006 19:46:35 +0100 Subject: [xcrysden] Compile fixes for newer gcc Message-ID: <20060301184635.GC22199@halley.zuhause> --7cm2iqirTL37Ot+N Content-Type: multipart/mixed; boundary="4Epv4kl9IRBfg3rk" Content-Disposition: inline --4Epv4kl9IRBfg3rk Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Hi altogether! I tried to compile XCrySDen here with gcc-4.0, but the compilation failed with xcDisplayFunc.c:162: error: static declaration of =E2=80=98HandleDisplay=E2= =80=99 follows non-static declaration anaglyph.h:81: error: previous declaration of =E2=80=98HandleDisplay=E2=80= =99 was here xcDisplayFunc.c:164: error: static declaration of =E2=80=98CameraHome=E2=80= =99 follows non-static declaration anaglyph.h:82: error: previous declaration of =E2=80=98CameraHome=E2=80=99 = was here xcDisplayFunc.c:165: error: static declaration of =E2=80=98Normalise=E2=80= =99 follows non-static declaration anaglyph.h:83: error: previous declaration of =E2=80=98Normalise=E2=80=99 w= as here xcDisplayFunc.c:166: error: static declaration of =E2=80=98CalcNormal=E2=80= =99 follows non-static declaration anaglyph.h:84: error: previous declaration of =E2=80=98CalcNormal=E2=80=99 = was here make[2]: *** [xcDisplayFunc.o] Error 1 make[2]: Leaving directory `/tmp/XC/C' make[1]: *** [compile] Error 2 make[1]: Leaving directory `/tmp/XC/C' make: *** [src-C] Error 2 The attached patch fixes this. The cleanest solution would probably be to move all the static declarations to the .h files. Shall I submit a patch that accomplishes this? With best regards, Wolfi --4Epv4kl9IRBfg3rk Content-Type: text/plain; charset=us-ascii Content-Disposition: attachment; filename="XCryS-compile.diff" Content-Transfer-Encoding: quoted-printable Index: C/anaglyph.h =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D --- C/anaglyph.h (revision 1) +++ C/anaglyph.h (working copy) @@ -78,10 +78,10 @@ int screenheight,screenwidth; } CAMERA; =20 -void HandleDisplay(struct Togl *togl); -void CameraHome(); -void Normalise(XYZ *); -XYZ CalcNormal(XYZ,XYZ,XYZ); +static void HandleDisplay(struct Togl *togl); +static void CameraHome(); +static void Normalise(XYZ *); +static XYZ CalcNormal(XYZ,XYZ,XYZ); =20 #define DTOR 0.0174532925 #define RTOD 57.2957795 Index: C/xcDisplayFunc.c =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D --- C/xcDisplayFunc.c (revision 1) +++ C/xcDisplayFunc.c (working copy) @@ -159,11 +159,11 @@ void xcSolidBond (GLdouble radius, GLdouble height, int bondFlag);=20 void xcSolidCone (GLdouble baseradius, GLdouble topradius, GLdouble height= );=20 static int CalcTessFactor(void); -static void HandleDisplay(struct Togl *togl); +void HandleDisplay(struct Togl *togl); static void draw_scene(void); -static void CameraHome(void); -static void Normalise(XYZ *p); -static XYZ CalcNormal(XYZ p, XYZ p1, XYZ p2); +void CameraHome(void); +void Normalise(XYZ *p); +XYZ CalcNormal(XYZ p, XYZ p1, XYZ p2); =20 /* --- extern function prototypes --- */ extern int MakeSticks1(int i, --4Epv4kl9IRBfg3rk-- --7cm2iqirTL37Ot+N Content-Type: application/pgp-signature; name="signature.asc" Content-Description: Digital signature Content-Disposition: inline -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2 (GNU/Linux) iD8DBQFEBewLH0o2mefAfsQRAturAJ9LqE4Vait6Hi+OfLgO9YKR4jlojwCeJ7b3 FW8NkLcr12EcItI14f2SCw4= =o5yO -----END PGP SIGNATURE----- --7cm2iqirTL37Ot+N-- From xcrysden@democritos.it Thu Mar 16 16:00:42 2006 From: xcrysden@democritos.it (Wolfram Quester) Date: Thu, 16 Mar 2006 17:00:42 +0100 Subject: [xcrysden] Test for ML and compile fix for gcc 4.0 Message-ID: <20060316160042.GK11018@halley.zuhause> --95CBLwa+io9O2zXc Content-Type: multipart/mixed; boundary="F7w+4yMapWozG0Ib" Content-Disposition: inline --F7w+4yMapWozG0Ib Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Dear XCrySDen community, two weeks ago I sent a patch to the list, but it never came through. So I resend the modified files and the patch to see what's going on. The compilation of XCrySDen with gcc-4.0 failed with xcDisplayFunc.c:162: error: static declaration of =E2=80=98HandleDisplay=E2= =80=99 follows non-static declaration anaglyph.h:81: error: previous declaration of =E2=80=98HandleDisplay=E2=80= =99 was here xcDisplayFunc.c:164: error: static declaration of =E2=80=98CameraHome=E2=80= =99 follows non-static declaration anaglyph.h:82: error: previous declaration of =E2=80=98CameraHome=E2=80=99 = was here xcDisplayFunc.c:165: error: static declaration of =E2=80=98Normalise=E2=80= =99 follows non-static declaration anaglyph.h:83: error: previous declaration of =E2=80=98Normalise=E2=80=99 w= as here xcDisplayFunc.c:166: error: static declaration of =E2=80=98CalcNormal=E2=80= =99 follows non-static declaration anaglyph.h:84: error: previous declaration of =E2=80=98CalcNormal=E2=80=99 = was here make[2]: *** [xcDisplayFunc.o] Error 1 make[2]: Leaving directory `/tmp/XC/C' make[1]: *** [compile] Error 2 make[1]: Leaving directory `/tmp/XC/C' make: *** [src-C] Error 2 With best regards, Wolfi --F7w+4yMapWozG0Ib Content-Type: text/plain; charset=us-ascii Content-Disposition: attachment; filename="XCryS-compile.diff" Content-Transfer-Encoding: quoted-printable Index: C/anaglyph.h =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D --- C/anaglyph.h (revision 1) +++ C/anaglyph.h (working copy) @@ -78,10 +78,10 @@ int screenheight,screenwidth; } CAMERA; =20 -void HandleDisplay(struct Togl *togl); -void CameraHome(); -void Normalise(XYZ *); -XYZ CalcNormal(XYZ,XYZ,XYZ); +static void HandleDisplay(struct Togl *togl); +static void CameraHome(); +static void Normalise(XYZ *); +static XYZ CalcNormal(XYZ,XYZ,XYZ); =20 #define DTOR 0.0174532925 #define RTOD 57.2957795 Index: C/xcDisplayFunc.c =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D --- C/xcDisplayFunc.c (revision 1) +++ C/xcDisplayFunc.c (working copy) @@ -159,11 +159,11 @@ void xcSolidBond (GLdouble radius, GLdouble height, int bondFlag);=20 void xcSolidCone (GLdouble baseradius, GLdouble topradius, GLdouble height= );=20 static int CalcTessFactor(void); -static void HandleDisplay(struct Togl *togl); +void HandleDisplay(struct Togl *togl); static void draw_scene(void); -static void CameraHome(void); -static void Normalise(XYZ *p); -static XYZ CalcNormal(XYZ p, XYZ p1, XYZ p2); +void CameraHome(void); +void Normalise(XYZ *p); +XYZ CalcNormal(XYZ p, XYZ p1, XYZ p2); =20 /* --- extern function prototypes --- */ extern int MakeSticks1(int i, --F7w+4yMapWozG0Ib Content-Type: application/x-gtar Content-Disposition: attachment; filename="XCrysDenCompile.tgz" Content-Transfer-Encoding: base64 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-----END PGP SIGNATURE----- --95CBLwa+io9O2zXc-- From xcrysden@democritos.it Sat Mar 18 12:48:27 2006 From: xcrysden@democritos.it (Mark Lusk) Date: Sat, 18 Mar 2006 05:48:27 -0700 Subject: [xcrysden] Installation on Windows via Cygwin Message-ID: <200603181248.k2ICmT1f018757@inspire.Mines.EDU> This is a multi-part message in MIME format. ------=_NextPart_000_0006_01C64A4F.949A4D90 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit Dear all, I am trying to install and run XCrysDen on my notebook (turion64 AMD in HP dv8000 case). The program unpacks okay, and I ran the configure routine with all of the defaults chosen. I am running it under Cygwin. However, when I run the software the many lines flash quickly by ended by Line 156: exec: wish: not found I have tried this with several variations on the configuration but to no avail. On the other hand, I have had no problem installing the software on my Linux workstation-also an AMD64 box. Any help would be greatly appreciated. Thanks, Mark Mark T. Lusk Professor and Chair Mechanical Engineering Program Colorado School of Mines Golden, CO 80401 Voice: 303-273-3675 mlusk@mines.edu http://egweb.mines.edu/mlusk/LuskWeb/mlusk.html http://egweb.mines.edu/research/mechanical/entrance.htm ------=_NextPart_000_0006_01C64A4F.949A4D90 Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable

Dear all,

I am trying to install and run XCrysDen on my = notebook (turion64 AMD in HP dv8000 case). The program unpacks okay, and I ran = the configure routine with all of the defaults chosen. I am running it under = Cygwin. However, when I run the software the many lines flash quickly by ended = by

Line 156: exec: wish: not = found

I have tried this with several variations on the configuration but to no avail. On the other hand, I have had no problem installing the software on my Linux workstation—also an AMD64 box. Any help would be greatly = appreciated.

Thanks,

Mark

Mark T. Lusk

Professor and Chair

Mechanical Engineering = Program

Colorado School of = Mines

Golden, CO 80401

Voice: 303-273-3675

mlusk@mines.edu

http://egweb.mi= nes.edu/mlusk/LuskWeb/mlusk.html http://= egweb.mines.edu/research/mechanical/entrance.htm=

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list had problems for few months: none of the messages appeared. I thought there are simply no messages. Thanks for Wolfram Quester for noticing that something is wrong. The problem has been removed now. Best regards, Tone Kokalj From xcrysden@democritos.it Tue Mar 21 13:21:00 2006 From: xcrysden@democritos.it (Tone Kokalj) Date: Tue, 21 Mar 2006 14:21:00 +0100 Subject: [xcrysden] how to display the output file of pwscf In-Reply-To: References: Message-ID: <1142947260.6680.23.camel@localhost.localdomain> On Sat, 2005-10-29 at 07:20 +0000, sun jason wrote: > Dear all, > > I've install xcrysden and it can display the input file of pwscf properly. > but I can not use it to open a output file of pwscf. neither the output > file of scf calculation and relax calculation. the error message said: > > error: while executing exec.sh > /home/sun/XCrysden-1.4.1bin-static/script/pwo2xsf.sh -- optcoor > /home/sun/esppresso/examples/example06/results/alas.scf.out > pwo2xsf.xsf It is likely that the problem is caused by locales. Some locales uses a comma (,) instead of dot (.) character for the decimal dilimiter character. You can try to execute the command manually, i.e.: /home/sun/XCrysden-1.4.1bin-static/script/pwo2xsf.sh --optcoor pwscf.out What is the output? Are there some nan-s or numbers with commas. If this is so then execute in the shell (for Bourne shells such as bash): LANG=C LC_ALL=C export LANG LC_ALL and retry the above pwo2xsf.sh command. Does this fix your problem. If so put these lines at the beggining of the pwo2xsf.sh script. In the incoming 1.5 version of xcrysden, all the scripts are patched so that locales is set to "C". Regards, Tone From xcrysden@democritos.it Tue Mar 21 13:25:45 2006 From: xcrysden@democritos.it (Tone Kokalj) Date: Tue, 21 Mar 2006 14:25:45 +0100 Subject: [xcrysden] (no subject) In-Reply-To: <000601c5e069$a2f3c600$d621748c@nian559f82dcc5> References: <000601c5e069$a2f3c600$d621748c@nian559f82dcc5> Message-ID: <1142947545.6680.26.camel@localhost.localdomain> On Thu, 2005-11-03 at 19:27 +0800, 粘駿楠 wrote: > > Cuprite- Cu2O > CRYSTAL > 0 0 0 > 208 (space group 208, P42 32, cubic) > 4.27 (angstrom) > 2 > 8 .0 .0 .0 > 29 .25 .25 .25 If you have a CRYSTAL program then add a STOP keyword to the end of the above file and execute: xcrysden --crystal_inp Cu2O.crystal (where Cu2O.crystal is the name of the file holding above information). Otherwise the corresponding XSF file would look as: CRYSTAL PRIMVEC 4.2700000000 0.0000000000 0.0000000000 0.0000000000 4.2700000000 0.0000000000 0.0000000000 0.0000000000 4.2700000000 PRIMCOORD 6 1 8 0.0000000000 0.0000000000 0.0000000000 29 1.0675000000 1.0675000000 1.0675000000 8 -2.1350000000 -2.1350000000 -2.1350000000 29 -1.0675000000 -1.0675000000 1.0675000000 29 1.0675000000 -1.0675000000 -1.0675000000 29 -1.0675000000 1.0675000000 -1.0675000000 Regards, Tone From xcrysden@democritos.it Tue Mar 21 13:29:26 2006 From: xcrysden@democritos.it (Tone Kokalj) Date: Tue, 21 Mar 2006 14:29:26 +0100 Subject: [xcrysden] Help-install XCrySDen In-Reply-To: <194798a80512131724x3dacf566i3bab19ac30034412@mail.gmail.com> References: <194798a80512131724x3dacf566i3bab19ac30034412@mail.gmail.com> Message-ID: <1142947767.6680.30.camel@localhost.localdomain> On Tue, 2005-12-13 at 18:24 -0700, Chang'e Weng wrote: > Hi all, > > I am new to xcrysden an not very familiar with Unix system. I followed > the instruction to compile the source package. But I couldnot find > "babel, convert ..." program in the util directory. I was wondering if > I did something wrong or I need to install those programs first. The babel is used by xcrysden to convert the Gaussian input files. Otherwise the babel is a converter for molecular modeling data files, see: http://openbabel.sourceforge.net/wiki/Main_Page Regards, Tone From xcrysden@democritos.it Tue Mar 21 13:32:01 2006 From: xcrysden@democritos.it (Tone Kokalj) Date: Tue, 21 Mar 2006 14:32:01 +0100 Subject: [xcrysden] Reading ELF file In-Reply-To: <194798a80512201730i464a68fl488d612f70790551@mail.gmail.com> References: <194798a80512201730i464a68fl488d612f70790551@mail.gmail.com> Message-ID: <1142947921.6680.34.camel@localhost.localdomain> On Tue, 2005-12-20 at 18:30 -0700, Chang'e Weng wrote: > Dear All, > > I was wondering if XCrySDen can display the electron pairs from ELF file. xcrysden can display whatever is in the XSF file. If the file (the DATAGRID section) contains the ELF (electron localization function), then the ELF will be displayed (as isosurface or contours, depends on your choice). Regards, Tone From xcrysden@democritos.it Tue Mar 21 13:37:27 2006 From: xcrysden@democritos.it (Tone Kokalj) Date: Tue, 21 Mar 2006 14:37:27 +0100 Subject: [xcrysden] awk-program not found In-Reply-To: <000001c60a4b$26affad0$14b2a8c0@mawa> References: <000001c60a4b$26affad0$14b2a8c0@mawa> Message-ID: <1142948247.6680.41.camel@localhost.localdomain> On Mon, 2005-12-26 at 19:35 +0100, Marco Walterfang wrote: > Hello Tone, > > > > I use XCrySDen with Cygwin and so far everything works fine. > But just after starting xcrysden the following warning appears: couldn�t find �awk� program. > But awk.exe and gawk.exe are in the cygwin/bin directory. So, what to do? If this is really so, then seems like xcrysden is not able to find it (don't know why). Edit the Tcl/check_package.tcl file and replace: proc check_package_awk {} { global system .... } with: proc check_package_awk {} { global system set system(awk) /path/to/awk/gawk.exe } Where /path/to/awk/ whould be replaced by real path. Regards, Tone From xcrysden@democritos.it Tue Mar 21 13:43:03 2006 From: xcrysden@democritos.it (Tone Kokalj) Date: Tue, 21 Mar 2006 14:43:03 +0100 Subject: [xcrysden] PWSCF 3.0 and XCrysDen 1.4.1 In-Reply-To: <6ac064b60601261425w473ed0ddl2e2538fe5969fb1d@mail.gmail.com> References: <6ac064b60601261425w473ed0ddl2e2538fe5969fb1d@mail.gmail.com> Message-ID: <1142948583.6680.45.camel@localhost.localdomain> On Thu, 2006-01-26 at 17:25 -0500, Nichols A. Romero wrote: > Hi, > > Is there a size limit on the PWSCF output files that XCrysDen can read > using the command? > > xcrysden --pw_out filename No, there is no size limit. > I was able to do this succesfully with a file which only had 30 or so > relaxation steps. This one has about 100. I see the awk script running > in the background when I type 'top'. For the output file which contain > only 30 relaxation steps, XCrysDen loaded the data in less than a > minute. In this latter case which has about 1000 relaxation steps, the > awk script has been running for 30 minutes. The reason is that your file is truncated in a very unfortunate way (the last line is): Forces acting on atoms (Ry/au): So the pwo2xsf.sh expects to read forces, but the forces are not there... Please remove this line, and then the pwo2xsf.sh will again take a fraction of the second (or at worst a few seconds if you really have a huge number of steps). Regards, Tone From xcrysden@democritos.it Tue Mar 21 13:51:26 2006 From: xcrysden@democritos.it (Sergio L. Palacios) Date: Tue, 21 Mar 2006 14:51:26 +0100 Subject: [xcrysden] Problems with xcrysden mailing list In-Reply-To: <1142946543.6680.16.camel@localhost.localdomain> References: <1142946543.6680.16.camel@localhost.localdomain> Message-ID: <442004DE.9010609@uniovi.es> This is a multi-part message in MIME format. --------------030704060807090302010501 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Since last November I was removed from the XCRYSDEN mailing list and now I am receiving the messages again. Please remove from the list. Thank you very much Prof. Sergio L. Palacios University of Oviedo. --------------030704060807090302010501 Content-Type: text/x-vcard; charset=utf-8; name="slpalacios.vcf" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="slpalacios.vcf" begin:vcard fn:Dr. Sergio L. Palacios n;quoted-printable:Palacios D=C3=ADaz;Dr. Sergio L. org;quoted-printable:Universidad de Oviedo;Dpto. de F=C3=ADsica adr:C/ Calvo Sotelo s/n;;Facultad de Ciencias;Oviedo;Asturias;33007;Spain email;internet:slpalacios@uniovi.es title;quoted-printable:Profesor Titular de F=C3=ADsica Aplicada tel;work:98 5 10 28 48 tel;fax:98 5 10 33 24 x-mozilla-html:TRUE version:2.1 end:vcard --------------030704060807090302010501-- From xcrysden@democritos.it Tue Mar 21 14:00:19 2006 From: xcrysden@democritos.it (Tone Kokalj) Date: Tue, 21 Mar 2006 15:00:19 +0100 Subject: [xcrysden] 2D cuts of the Fermi surface In-Reply-To: <8423EE75-ED14-4FD6-BCF0-55FB9BF643CB@physics.ubc.ca> References: <8423EE75-ED14-4FD6-BCF0-55FB9BF643CB@physics.ubc.ca> Message-ID: <1142949619.6680.58.camel@localhost.localdomain> On Tue, 2006-02-14 at 10:42 -0800, Suman Hossain wrote: > Dear Xcrysden Community, > > I've been using the nice Xcrysden Fermi surface viewer for a while > which is absolutely fantastic. It is meant to generate 3D surfaces. > But now I need to make certain 2D cuts of the Fermi surface I already > made. Unfortunately, xcrysden does not yet have this feature. But it would be possible to emulate it with some manual work: extract the correct slice from the 3D mesh and pretend you will plot something like charge density: i.e. in XSF file make a 2D DATAGRID instead of 3D BANDGRID. Note that XSF file should include at least one dummy atom. Then load the XSF file, switch off the display of atoms, and use the Tools->Data Grid menu. From this point on you pretend to render charge density: you have all the xcrysden contour features at disposal. The proper XSF should look as: SLAB PRIMVEC ax ay 0.0 bx by 0.0 0.0 0.0 1.0 PRIMCOORD 1 1 X 0.0 0.0 0.0 BEGIN_BLOCK_DATAGRID_2D a_sheet_of_eigenvalues DATAGRID_2D_bla_bla nx ny 0.0 0.0 0.0 ax ay 0.0 bx by 0.0 -8.632000e-11 -1.614379e-10 -2.793978e-10 -4.472420e-10 -6.637130e-10 -9.109040e-10 -1.153951e-09 ... (nx * ny values here) END_DATAGRID_2D END_BLOCK_DATAGRID_2D I guess it is clear what the ax, ay, bx, by, nx, and nz stand for, otherwise look at the XSF format specification ( http://www.xcrysden.org/doc/XSF.html#__toc__11 ) Regards, Tone From xcrysden@democritos.it Tue Mar 21 14:02:59 2006 From: xcrysden@democritos.it (Tone Kokalj) Date: Tue, 21 Mar 2006 15:02:59 +0100 Subject: [xcrysden] How to install the xcrysden1.4 under the cygwin bash shell? In-Reply-To: References: Message-ID: <1142949779.6680.60.camel@localhost.localdomain> On Wed, 2006-03-01 at 16:04 +0800, Pan Zhijun wrote: > Hi,all users of xcrysden, > I am a newer of xcrysden and want to install this software under > the cygwin bash shell.After installing, when I perform the command > xcrysden,errors come.The error information is the > following:/home/Administrator/xcrysden/XCrySDen- > 1.4bin-shared/xcrysden:line 156: exec: wish: not found.How to solve > the problem?Any hint is appreciated.Thank you very much in advance. You do not have Tcl/Tk package installed on your Cygwin. It is required by xcrysden. Here is a list of packagaes that are needed by xcrysden (most likely I miss to name a few): bash, bc, gawk, grep, gzip, less, more, opengl, tcltk, coreutils Best regards, Tone From xcrysden@democritos.it Tue Mar 21 14:05:21 2006 From: xcrysden@democritos.it (Tone Kokalj) Date: Tue, 21 Mar 2006 15:05:21 +0100 Subject: [xcrysden] Compile fixes for newer gcc In-Reply-To: <20060301184635.GC22199@halley.zuhause> References: <20060301184635.GC22199@halley.zuhause> Message-ID: <1142949922.6680.63.camel@localhost.localdomain> On Wed, 2006-03-01 at 19:46 +0100, Wolfram Quester wrote: > Hi altogether! > > I tried to compile XCrySDen here with gcc-4.0, but the compilation > failed with > > xcDisplayFunc.c:162: error: static declaration of �HandleDisplay� follows non-static declaration > anaglyph.h:81: error: previous declaration of �HandleDisplay� was here > xcDisplayFunc.c:164: error: static declaration of �CameraHome� follows non-static declaration > anaglyph.h:82: error: previous declaration of �CameraHome� was here > xcDisplayFunc.c:165: error: static declaration of �Normalise� follows non-static declaration > anaglyph.h:83: error: previous declaration of �Normalise� was here > xcDisplayFunc.c:166: error: static declaration of �CalcNormal� follows non-static declaration > anaglyph.h:84: error: previous declaration of �CalcNormal� was here > make[2]: *** [xcDisplayFunc.o] Error 1 > make[2]: Leaving directory `/tmp/XC/C' > make[1]: *** [compile] Error 2 > make[1]: Leaving directory `/tmp/XC/C' > make: *** [src-C] Error 2 > > > The attached patch fixes this. Thank you very much for the patch. The even simpler solution is to simply delete these lines from anaglyph.h, as they are redundant. void HandleDisplay(struct Togl *togl); void CameraHome(); void Normalise(XYZ *); XYZ CalcNormal(XYZ,XYZ,XYZ); Regards, Tone From xcrysden@democritos.it Tue Mar 21 14:08:00 2006 From: xcrysden@democritos.it (Tone Kokalj) Date: Tue, 21 Mar 2006 15:08:00 +0100 Subject: [xcrysden] Installation on Windows via Cygwin In-Reply-To: <200603181248.k2ICmT1f018757@inspire.Mines.EDU> References: <200603181248.k2ICmT1f018757@inspire.Mines.EDU> Message-ID: <1142950080.6680.66.camel@localhost.localdomain> On Sat, 2006-03-18 at 05:48 -0700, Mark Lusk wrote: > Dear all, > > > > I am trying to install and run XCrysDen on my notebook (turion64 AMD > in HP dv8000 case). The program unpacks okay, and I ran the configure > routine with all of the defaults chosen. I am running it under Cygwin. > However, when I run the software the many lines flash quickly by ended > by > > > > Line 156: exec: wish: not found A similar question has just been answered, see the message: Re: [xcrysden] How to install the xcrysden1.4 under the cygwin bash shell? Regards, Tone From xcrysden@democritos.it Tue Mar 21 14:32:27 2006 From: xcrysden@democritos.it (Tone Kokalj) Date: Tue, 21 Mar 2006 15:32:27 +0100 Subject: [xcrysden] Re: queston on Xcrysden In-Reply-To: References: Message-ID: <1142951548.6680.83.camel@localhost.localdomain> > Hi Dr. Kokalj, this is Newton Ooi here. I am using your Xcrysden software and > am trying to generate a figure like that shown in the screenshot on the site: > > http://www.xcrysden.org/img/xcrysden_molsurf2.png This particular picture has been made with "molecular surfaces" feature (i.e. "Display-->Molecular Surface", and "Modify-->Molecular Surface Setting") > > Specifically, I am trying to plot a structure where some of the atoms are > represented by solid spheres, and other atoms are represented by > wiremeshes. This is in general not possible in xcrysden, but with a simple trick. You can display the stucture in ball-and-sticks mode. The bond radius is set via the "Modify-->Ball/Stick Ratio". Then you can set the display radii for some atomic types to very large values ("Modify-->Atomic Radius"), while the other types to small values: you will end up with some atomic-types displayed as space-fills, while the other as "tubed" wireframe. Regards, Tone From xcrysden@democritos.it Wed Mar 22 07:06:17 2006 From: xcrysden@democritos.it (Michael Gurnett) Date: Wed, 22 Mar 2006 08:06:17 +0100 Subject: [xcrysden] Exciting dft package Message-ID: <1143011177.29962.5.camel@localhost.localdomain> Hello Would it be possible for xcrysden to be able to read geometry data from the exciting GEOMETRY.OUT file. Thanks Michael From xcrysden@democritos.it Wed Mar 22 10:27:40 2006 From: xcrysden@democritos.it (Tone Kokalj) Date: Wed, 22 Mar 2006 11:27:40 +0100 Subject: [xcrysden] Exciting dft package In-Reply-To: <1143011177.29962.5.camel@localhost.localdomain> References: <1143011177.29962.5.camel@localhost.localdomain> Message-ID: <1143023260.6858.15.camel@localhost.localdomain> --=-4htjfTFtoJC25ELApVWc Content-Type: text/plain Content-Transfer-Encoding: 7bit On Wed, 2006-03-22 at 08:06 +0100, Michael Gurnett wrote: > Hello > > Would it be possible for xcrysden to be able to read geometry data from > the exciting GEOMETRY.OUT file. This is a FAQ #8 ( http://www.xcrysden.org/doc/FAQ.html#Q6 ). Read also this: http://www.xcrysden.org/doc/custom.html#__toc__8 The GEOMETRY.OUT file needs to be tranformed to XSF file. This could be done easily as GEOMETRY.OUT is a simple file. I attach a fortran template, kind of myformat2xsf. You need to patch the first part of the file: the reading of the GEOMETRY.OUT. When the converter (filter) is working well you can add something as follows to the end of $HOME/.xcrysden/custom-definitions file: # Usage: # addOption option converterProgram description # # Arguments: # option ... option to add to XCRYSDEN options # # converterProgram ... program that converts from an "unknown" # to XSF format; this program must be # supplied by the user !!! # # description ... description of the options that will # appear in the help message # (i.e. xcrysden --help). # # addOption --exciting /path/to/exiting2xsf { load structure from Exciting GEOMETRY.OUT file format } # EOF Now you can do: xcrysden --exciting GEOMETRY.OUT When the exciting2xsf filter is well working, you can (if you wish so) send the filter to me and I will add it to xcrysden. Regards, Tone --=-4htjfTFtoJC25ELApVWc Content-Disposition: attachment; filename=myformat2xsf.f Content-Type: text/x-fortran; name=myformat2xsf.f; charset=us-ascii Content-Transfer-Encoding: 7bit c ****************************************************** program MyFormat2XSF c Usage: myformat2xsf myformat_file c c The program reads the myformat file from myformat_file c and writes the XSF file to standard output c ****************************************************** implicit none integer MAXATOMS PARAMETER (MAXATOMS = 1000) character*256 my_file real*8 $ primvec(3,3), ! primitive lattice vectors $ convvec(3,3), ! conventional lattice vectors $ coor(3,MAXATOMS) ! atomic coordinates integer $ iargc, $ nat(MAXATOMS), ! atomic numbers $ iat, i, j, len ! counters if (iargc().ne.1) $ stop 'Usage: myformat2xcr myformat_infile' call getarg(1,my_file) len = index(my_file,' ') - 1 open(unit=1, file=my_file(1:len), status='old') c *** c *** READ MyFormat file c *** ... insert code here ... c *** c *** WRITE XSF file c *** c *** lets suppose it is a CRYSTAL structure c *** other posibilites are (SLAB,POLYMER,MOLECULE) write(*,*) 'CRYSTAL' write(*,*) 'PRIMVEC' write(*,1000) primvec write(*,*) 'CONVVEC' write(*,1000) convvec write(*,*) 'PRIMCOORD' write(*,*) iat, 1 do i=1,iat write(*,1001) nat(i), (coor(j,i), j=1,3) enddo 1000 format(2(3(F15.9,2X),/),3(F15.9,2X)) 1001 format(I5,3(F15.9,2X)) END --=-4htjfTFtoJC25ELApVWc-- From xcrysden@democritos.it Wed Mar 22 13:06:09 2006 From: xcrysden@democritos.it (Pan Zhijun) Date: Wed, 22 Mar 2006 21:06:09 +0800 Subject: [xcrysden] How to install crystal 98 on cygwin? Message-ID: ------=_Part_1175_10236925.1143032769052 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi,all users of xcrysden, I want to install the software crystal98 on cygwin.But I failed to do that.Who can do me a favor?Thank you very much in advance. Best regards. Sincerely, Z.J. ------=_Part_1175_10236925.1143032769052 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
Hi,all users of xcrysden,

    I want to install the software crystal98 on cygwin.= But I failed to do that.Who can do me a favor?Thank you very much in advanc= e.

    Best regards.

           &nbs= p;            &= nbsp;           &nbs= p;            &= nbsp;           &nbs= p;            &= nbsp;           &nbs= p;           Sincerely,
           &nbs= p;            &= nbsp;           &nbs= p;            &= nbsp;           &nbs= p;            &= nbsp;           &nbs= p;           Z.J.
------=_Part_1175_10236925.1143032769052-- From xcrysden@democritos.it Wed Mar 22 14:51:15 2006 From: xcrysden@democritos.it (Mark Lusk) Date: Wed, 22 Mar 2006 07:51:15 -0700 Subject: [xcrysden] XCrySDens within Cygwin Message-ID: <200603221451.k2MEpK9g007779@incantation.Mines.EDU> This is a multi-part message in MIME format. ------=_NextPart_000_0017_01C64D85.65D513D0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear colleague, I noticed that you had posted a message to the XCrySDens group very similar to mine. I have since tried installing Tcl/TK on my Windows machine but have still not been able to get XCrySDens to run. Have you had any luck? Best, Mark Mark T. Lusk Professor and Chair Mechanical Engineering Program Colorado School of Mines Golden, CO 80401 Voice: 303-273-3675 mlusk@mines.edu http://egweb.mines.edu/mlusk/LuskWeb/mlusk.html http://egweb.mines.edu/research/mechanical/entrance.htm ------=_NextPart_000_0017_01C64D85.65D513D0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear colleague,

I noticed that you had posted a message to the = XCrySDens group very similar to mine. I have since tried installing Tcl/TK on my Windows machine but have still not been able to get XCrySDens to run. Have you = had any luck?

Best,

Mark

Mark T. Lusk

Professor and Chair

Mechanical Engineering = Program

Colorado School of = Mines

Golden, CO 80401

Voice: 303-273-3675

mlusk@mines.edu

http://egweb.mi= nes.edu/mlusk/LuskWeb/mlusk.html http://= egweb.mines.edu/research/mechanical/entrance.htm=

------=_NextPart_000_0017_01C64D85.65D513D0-- From xcrysden@democritos.it Wed Mar 22 15:04:00 2006 From: xcrysden@democritos.it (Tone Kokalj) Date: Wed, 22 Mar 2006 16:04:00 +0100 Subject: [xcrysden] XCrySDens within Cygwin In-Reply-To: <200603221451.k2MEpK9g007779@incantation.Mines.EDU> References: <200603221451.k2MEpK9g007779@incantation.Mines.EDU> Message-ID: <1143039841.6858.48.camel@localhost.localdomain> On Wed, 2006-03-22 at 07:51 -0700, Mark Lusk wrote: > Dear colleague, > > > > I noticed that you had posted a message to the XCrySDens group very > similar to mine. I have since tried installing Tcl/TK on my Windows > machine but have still not been able to get XCrySDens to run. One needs the Tcl/Tk provided by cygwin. Installing a Windows version of Tcl/Tk on the Windows OS will not do the job. Did you try with the cygwin Tcl/Tk? ( see http://cygwin.com/packages/ ; the proper package is tcltk ). Regards, Tone From xcrysden@democritos.it Wed Mar 22 18:09:11 2006 From: xcrysden@democritos.it (Wolfram Quester) Date: Wed, 22 Mar 2006 19:09:11 +0100 Subject: [xcrysden] Compile fixes for newer gcc In-Reply-To: <1142949922.6680.63.camel@localhost.localdomain> References: <20060301184635.GC22199@halley.zuhause> <1142949922.6680.63.camel@localhost.localdomain> Message-ID: <20060322180910.GC29648@halley.zuhause> --kfjH4zxOES6UT95V Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Hi Tone, thanks for reenabling the mailing list. On Tue, Mar 21, 2006 at 03:05:21PM +0100, Tone Kokalj wrote: > On Wed, 2006-03-01 at 19:46 +0100, Wolfram Quester wrote: > > Hi altogether! > >=20 > > I tried to compile XCrySDen here with gcc-4.0, but the compilation > > failed with > >=20 > > xcDisplayFunc.c:162: error: static declaration of =E2=80=98HandleDispla= y=E2=80=99 follows non-static declaration > > anaglyph.h:81: error: previous declaration of =E2=80=98HandleDisplay=E2= =80=99 was here > > xcDisplayFunc.c:164: error: static declaration of =E2=80=98CameraHome= =E2=80=99 follows non-static declaration > > anaglyph.h:82: error: previous declaration of =E2=80=98CameraHome=E2=80= =99 was here > > xcDisplayFunc.c:165: error: static declaration of =E2=80=98Normalise=E2= =80=99 follows non-static declaration > > anaglyph.h:83: error: previous declaration of =E2=80=98Normalise=E2=80= =99 was here > > xcDisplayFunc.c:166: error: static declaration of =E2=80=98CalcNormal= =E2=80=99 follows non-static declaration > > anaglyph.h:84: error: previous declaration of =E2=80=98CalcNormal=E2=80= =99 was here > > make[2]: *** [xcDisplayFunc.o] Error 1 > > make[2]: Leaving directory `/tmp/XC/C' > > make[1]: *** [compile] Error 2 > > make[1]: Leaving directory `/tmp/XC/C' > > make: *** [src-C] Error 2 > >=20 > >=20 > > The attached patch fixes this.=20 >=20 > Thank you very much for the patch. The even simpler solution is to > simply > delete these lines from anaglyph.h, as they are redundant. >=20 > void HandleDisplay(struct Togl *togl); > void CameraHome(); > void Normalise(XYZ *); > XYZ CalcNormal(XYZ,XYZ,XYZ); But shouldn't you remove them from the .c-file then? I think these are classical lines belonging into an .h file ;-). With best wishes, Wolfi >=20 > Regards, Tone >=20 > _______________________________________________ > XCrySDen mailing list > XCrySDen@democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden --kfjH4zxOES6UT95V Content-Type: application/pgp-signature; name="signature.asc" Content-Description: Digital signature Content-Disposition: inline -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) iD8DBQFEIZLGH0o2mefAfsQRAl3NAJ4jRyclxRfuR25sc5tgEzEHzxXLcwCfaMF1 oIKfI1gsu02hEhELKvku3BI= =C2Ax -----END PGP SIGNATURE----- --kfjH4zxOES6UT95V-- From xcrysden@democritos.it Wed Mar 22 20:19:43 2006 From: xcrysden@democritos.it (Tone Kokalj) Date: Wed, 22 Mar 2006 21:19:43 +0100 (CET) Subject: [xcrysden] Compile fixes for newer gcc In-Reply-To: <20060322180910.GC29648@halley.zuhause> References: <20060301184635.GC22199@halley.zuhause> <1142949922.6680.63.camel@localhost.localdomain> <20060322180910.GC29648@halley.zuhause> Message-ID: <51751.193.2.5.109.1143058783.squirrel@nabiralnik.ijs.si> > Hi Tone, > > thanks for reenabling the mailing list. Thanks to you for spotting the problem. >> void HandleDisplay(struct Togl *togl); >> void CameraHome(); >> void Normalise(XYZ *); >> XYZ CalcNormal(XYZ,XYZ,XYZ); > > But shouldn't you remove them from the .c-file then? I think these are > classical lines belonging into an .h file ;-). In principle you are right. However above functions are local [i.e. static void HandleDisplay(struct Togl *togl); etc...], used only in xcDisplayFunc.c. Therefore it is OK, if they are defined only in xcDisplayFunc.c. Regards, Tone From xcrysden@democritos.it Thu Mar 23 02:32:57 2006 From: xcrysden@democritos.it (Pan Zhijun) Date: Thu, 23 Mar 2006 10:32:57 +0800 Subject: [xcrysden] XCrySDens within Cygwin In-Reply-To: <200603221451.k2MEpK9g007779@incantation.Mines.EDU> References: <200603221451.k2MEpK9g007779@incantation.Mines.EDU> Message-ID: ------=_Part_14068_23811022.1143081177134 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline I have solved that problem after installing the tcl/tk. 2006/3/22, Mark Lusk : > > Dear colleague, > > > > I noticed that you had posted a message to the XCrySDens group very > similar to mine. I have since tried installing Tcl/TK on my Windows machi= ne > but have still not been able to get XCrySDens to run. Have you had any lu= ck? > > > > Best, > > > > Mark > > > > Mark T. Lusk > > Professor and Chair > > Mechanical Engineering Program > > Colorado School of Mines > > Golden, CO 80401 > > Voice: 303-273-3675 > > mlusk@mines.edu > > http://egweb.mines.edu/mlusk/LuskWeb/mlusk.html > http://egweb.mines.edu/research/mechanical/entrance.htm > > > ------=_Part_14068_23811022.1143081177134 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline I have solved that problem after installing the tcl/tk.

2006/3/22, Mark Lusk <mlusk@mines.edu>:

Dear colleague,

I noticed that you had posted a message to the XCrySDe= ns group very similar to mine. I have since tried installing Tcl/TK on my W= indows machine but have still not been able to get XCrySDens to run. Have y= ou had any luck?

Best,

Mark

Mark T. Lusk

Professor and Chair

Mechanical Engineering Program

Colorado School of Mines

Golden, CO 80401

Voice: 303-273-3675

mlusk@mines.edu

http://egwe= b.mines.edu/mlusk/LuskWeb/mlusk.html http://egweb.mines.e= du/research/mechanical/entrance.htm<= font color=3D"blue">

2006/3/23, Tone Kokalj <tone.kokalj@ijs.si>:
Pan Zhijun wrote:

> Hi= ,all users of xcrysden,
>     I want to install t= he software crystal98 on=20 cygwin.But I failed to
> do that.Who can do me a favor?Thank you very= much in advance.

Since crystal98 is written in fortran-77, I gu= ess that the compilation
of it
(or any other fortran-77 program) shou= ld be similar on cygwin as on linux,
provided that you have g77, gcc, make, and other possible shell utiliti= es
installed on cygwin.

For the specific case of crystal98 you ne= ed to edit the src/makefile,
and the platform specific src/Xmakes/$(ARCH= ).inc makefile's include file.
For the later I would start with Linux-g77.inc

Regards, Tone
= _______________________________________________
XCrySDen mailing listXCrySDen@democritos.it
http://www.d= emocritos.it/mailman/listinfo/xcrysden

------=_Part_3666_32207407.1143118488158-- From xcrysden@democritos.it Thu Mar 23 15:07:36 2006 From: xcrysden@democritos.it (Mark Lusk) Date: Thu, 23 Mar 2006 08:07:36 -0700 Subject: [xcrysden] RE:Success with XCrySDen on Cygwin In-Reply-To: <20060323023301.22205.9769.Mailman@democritos.sissa.it> Message-ID: <200603231507.k2NF7hNn028703@incantation.Mines.EDU> Dear colleagues, I have now gotten XCrySDens to run just fine on Cygwin. Great! I had not selected the proper package for TCL/TK when downloading cygwin the first time. (See note below.) http://cygwin.com/packages/ The proper package is tcltk Thanks very much for the help. Mark From xcrysden@democritos.it Fri Mar 24 09:26:52 2006 From: xcrysden@democritos.it (Pan Zhijun) Date: Fri, 24 Mar 2006 17:26:52 +0800 Subject: [xcrysden] How to install crystal 98 on cygwin? In-Reply-To: References: <44227089.7030601@ijs.si> Message-ID: ------=_Part_1871_17586363.1143192412443 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi,Tone, Thank you for your kind help. I have another problem to ask you for your help. How to activate the menus of AdvGeom and Properties of XcrySDen under the circumstance of no installing the Crystall98?Thank you. Best regards. Sincerely, Z.J. 2006/3/23, Pan Zhijun : > > Tone, > Thank you for your help. > Best regards! > Sincerely, > Z.J. > > > 2006/3/23, Tone Kokalj : > > > > Pan Zhijun wrote: > > > > > Hi,all users of xcrysden, > > > I want to install the software crystal98 on cygwin.But I failed t= o > > > do that.Who can do me a favor?Thank you very much in advance. > > > > > > Since crystal98 is written in fortran-77, I guess that the compilation > > of it > > (or any other fortran-77 program) should be similar on cygwin as on > > linux, > > provided that you have g77, gcc, make, and other possible shell > > utilities > > installed on cygwin. > > > > For the specific case of crystal98 you need to edit the src/makefile, > > and the platform specific src/Xmakes/$(ARCH).inc makefile's include > > file. > > For the later I would start with Linux-g77.inc > > > > Regards, Tone > > _______________________________________________ > > XCrySDen mailing list > > XCrySDen@democritos.it > > http://www.democritos.it/mailman/listinfo/xcrysden > > > > ------=_Part_1871_17586363.1143192412443 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
Hi,Tone,

     Thank you for your kind help. I have another = problem to ask you for your help. How to activate the menus of AdvGeom and = Properties of XcrySDen under the circumstance of no installing the Crystall= 98?Thank you.

      Best regards.

           &nbs= p;            &= nbsp;           &nbs= p;            &= nbsp; Sincerely,

           &nbs= p;            &= nbsp;           &nbs= p;            &= nbsp; Z.J.

2006/3/23, Pan Zhijun <panzhijun@gmail.com>:

Tone,

Thank you for your help.

Best regards!

           &nbs= p;            &= nbsp;           &nbs= p;           Sincerely,
           &nbs= p;            &= nbsp;           &nbs= p;           Z.J.

=

2006/3/23, Tone Kokalj <tone.kokalj@ijs.si>:=20

Pan Zhijun wrote:

> Hi= ,all users of xcrysden,
>     I want to install t= he software crystal98 on=20 cygwin.But I failed to
> do that.Who can do me a favor?Thank you very= much in advance.

Since crystal98 is written in fortran-77, I gu= ess that the compilation
of it
(or any other fortran-77 program) shou= ld be similar on cygwin as on linux,=20
provided that you have g77, gcc, make, and other possible shell utiliti= es
installed on cygwin.

For the specific case of crystal98 you ne= ed to edit the src/makefile,
and the platform specific src/Xmakes/$(ARCH= ).inc makefile's include file.=20
For the later I would start with Linux-g77.inc

Regards, Tone
= _______________________________________________
XCrySDen mailing list XCrySDen@democritos.it
http://www.democritos.it/mailman/listinfo/xcrysden

------=_Part_1871_17586363.1143192412443-- From xcrysden@democritos.it Fri Mar 24 13:21:34 2006 From: xcrysden@democritos.it (Ikutaro Hamada) Date: Fri, 24 Mar 2006 22:21:34 +0900 Subject: [xcrysden] mpeg-making with xcrysden on MacOSX In-Reply-To: <426d9c06a2dda6da8855fbbc2ae5de0c@rc.m-kagaku.co.jp> References: <426d9c06a2dda6da8855fbbc2ae5de0c@rc.m-kagaku.co.jp> Message-ID: 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 From xcrysden@democritos.it Mon Mar 27 07:35:17 2006 From: xcrysden@democritos.it (M. K. Singh) Date: Mon, 27 Mar 2006 12:05:17 +0530 (IST) Subject: [xcrysden] Re: XCrySDen Viewing of External format data of CRYSTAL03/98 In-Reply-To: <20060325063708.31544.15426.Mailman@democritos.sissa.it> References: <20060325063708.31544.15426.Mailman@democritos.sissa.it> Message-ID: <2082.10.11.0.2.1143441317.squirrel@10.11.0.2> Dear All, I would like to visualise CRYSTAL03/98 input with keyword EXTERNAL. The corresponding fort.34 file for EXTERNAL format is available in the same directory where input file exit but I can�t visualise it using Xcrysden code. Any help will be highly appreciated. Thank -- M. K. Singh From xcrysden@democritos.it Mon Mar 27 15:54:10 2006 From: xcrysden@democritos.it (Tone Kokalj) Date: Mon, 27 Mar 2006 16:54:10 +0200 Subject: [xcrysden] Re: XCrySDen Viewing of External format data of CRYSTAL03/98 In-Reply-To: <2082.10.11.0.2.1143441317.squirrel@10.11.0.2> References: <20060325063708.31544.15426.Mailman@democritos.sissa.it> <2082.10.11.0.2.1143441317.squirrel@10.11.0.2> Message-ID: <4427FC92.6060803@ijs.si> This is a multi-part message in MIME format. --------------010408070001000809040203 Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: 8bit M. K. Singh wrote: >Dear All, >I would like to visualise CRYSTAL03/98 input with keyword EXTERNAL. The >corresponding fort.34 file for EXTERNAL format is available in the same >directory where input file exit but I can�t visualise it using Xcrysden >code. >Any help will be highly appreciated. > > Indeed, the parsing of crystal03 input files with "EXTERNAL" keyword is not supported (I never thought about that). However the fix was quite simple. I attach the tar-gzipped file of four patched Tcl files. Please put them in $XCRYSDEN_TOPDIR/Tcl. Then the "EXTERNAL" feature should work. 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text/plain; charset="windows-1250" Content-Transfer-Encoding: quoted-printable =20 Thank for your kind reply.=20 I have applied the patches Tcl files and my problem is solved. Now I can visualize CRYSTAL03 input with EXTERNAL Keyword using Xcrysden Graphics. = Now I can=92t visualize normal CRYSTAL03/98 file (i.e. No EXTERNAL Keyword) = with Xcrysden anymore.=20 How to correct it? Please help me. =20 Thank you, With best regards =20 Sincerely Yours M. K. Singh wrote: =20 >Dear All, >I would like to visualize CRYSTAL03/98 input with keyword EXTERNAL. The >corresponding fort.34 file for EXTERNAL format is available in the same >directory where input file exit but I can=92t visualize it using = Xcrysden >code. >Any help will be highly appreciated. > =20 >=20 =20 Indeed, the parsing of crystal03 input files with "EXTERNAL" keyword is not supported (I never thought about that). However the fix was quite simple. I attach the tar-gzipped file of four patched Tcl files. Please=20 put them in $XCRYSDEN_TOPDIR/Tcl. =20 Then the "EXTERNAL" feature should work. =20 Regards, Tone =20 M. K. Singh Scientific Officer Laser Materials Development and Device Division Centre for Advanced Technology PO: CAT Indore - 452 013 (MP) INDIA Phone No. +91-731-248-8677 (Office) Fax No. +91-731-248-8650 (Office) =20 --=20 No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.1.385 / Virus Database: 268.3.3/298 - Release Date: = 30/03/2006 =20 =20 ------=_NextPart_001_0001_01C654DF.3C6CC7C0 Content-Type: text/html; charset="windows-1250" Content-Transfer-Encoding: quoted-printable

Thank for your = kind reply.

I have applied = the patches Tcl files and my problem is solved. Now I can visualize CRYSTAL03 input = with EXTERNAL Keyword using Xcrysden Graphics. Now I can’t visualize = normal CRYSTAL03/98 file (i.e. No EXTERNAL Keyword) with Xcrysden anymore. =

How to correct = it?

Please help = me.

Thank = you,

With best = regards

Sincerely = Yours

M. K. Singh wrote:

>Dear All,

>I would like to visualize CRYSTAL03/98 input with = keyword EXTERNAL. The

>corresponding fort.34 file for EXTERNAL format is available in the same

>directory where input file exit but I can’t = visualize it using Xcrysden

>code.

>Any help will be highly = appreciated.

>

>

Indeed, the parsing of crystal03 input files with "EXTERNAL" keyword

is not supported (I never thought about that). However = the fix was quite

simple. I attach the tar-gzipped file of four patched = Tcl files. Please

put them in

$XCRYSDEN_TOPDIR/Tcl.

Then the "EXTERNAL" feature should = work.

Regards, Tone

M. K. Singh

Scientific = Officer

Laser Materials Development and Device = Division

Centre for Advanced = Technology

PO= : = CAT

Indore - 452 013 = (MP)

INDIA
Phone No. +91-731-248-8677 = (Office)

Fax     No. = +91-731-248-8650 (Office)

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Checked by AVG Free Edition.
Version: 7.1.385 / Virus Database: 268.3.3/298 - Release Date: = 30/03/2006

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Now I > can visualize CRYSTAL03 input with EXTERNAL Keyword using Xcrysden > Graphics. Now I can�t visualize normal CRYSTAL03/98 file (i.e. No > EXTERNAL Keyword) with Xcrysden anymore. > > How to correct it? > The last-time the patch was a bit too fast. Here is the correction (put the attached file into $XCRSDEN_TOPDIR/Tcl). Now both possibilities should work. Regards, Tone --------------080403080508020100040603 Content-Type: text/x-tcl; name="openInput.tcl" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="openInput.tcl" ############################################################################# # Author: # # ------ # # Anton Kokalj Email: Tone.Kokalj@ijs.si # # Department of Physical and Organic Chemistry Phone: x 386 1 477 3523 # # Jozef Stefan Institute Fax: x 386 1 477 3811 # # Jamova 39, SI-1000 Ljubljana # # SLOVENIA # # # # Source: $XCRYSDEN_TOPDIR/Tcl/openInput.tcl # ------ # # Copyright (c) 1996-2003 by Anton Kokalj # ############################################################################# proc OpenFile {{file {}}} { global fileselect distext Alist species speciesName \ type_group type_group1 job_title \ inp n_groupsel groupsel crdatom XCState system \ AdvGeom xcMisc crystalInput if { $system(c95_exist) == 0 } { ErrorDialog "can't open CRYSTAL-95/98/03 input File. CRYSTAL package is not installed !!!" return } # distext .... here go informations to be displayed in # information text widget if { $file == "" } { fileselect "Open CRYSTAL Input" } elseif { [file isdirectory $file]} { set fileselect(path) [tk_getOpenFile -defaultextension .r1 \ -filetypes { {{All Files} {.*} } {{CRYSTAL Input Files} {.r1}} } -initialdir $file \ -title "Open CRYSTAL Input"] if { $fileselect(path) == "" } { return } } else { set fileselect(path) $file } # maybe CANCEL button was pressed if { $fileselect(path) == "" } { xcDeleteState c95 xcDeleteState openinput xcUpdateState return } ################# # initialisation set XCState(state) c95_openinput xcUpdateState xcAdvGeomState reset # # reset the title of "." # wm title . "XCrySDen: [file tail $fileselect(path)]" set xcMisc(titlefile) [file tail $fileselect(path)] # OK button was pressed # check if selected file is Crystal95 file; # the best way for doing it is to go and check it with Crystal95 ######################################## # CD to $system(SCRDIR) cd $system(SCRDIR) ######################################## # test only geom part of the input file (this is quick) # xc_inp.$system(PID)...here just geom input will be stored xcCatchExecReturn $system(AWKDIR)/ginp.awk \ $fileselect(path) > $system(SCRDIR)/xc_inp.$system(PID) puts stdout "FILE: $fileselect(path)" puts stdout "FILTERED INPUT" catch {ReadFile $system(SCRDIR)/xc_inp.$system(PID)} # BEGIN t.k. # for EXTERNAL: copy also fort.34 if { [file exists $system(PWD)/$system(ftn_name).34 ] } { file copy -force $system(PWD)/$system(ftn_name).34 $system(SCRDIR)/external_unit34 file copy -force $system(SCRDIR)/external_unit34 $system(SCRDIR)/$system(ftn_name).34 } # END t.k. # if we catch error than selected file is of the right type, # but is corrupted if { [catch {exec $system(c95_integrals) < \ $system(SCRDIR)/xc_inp.$system(PID) >& \ $system(SCRDIR)/xc_tmp.$system(PID)} errmsg] } { set idx [tk_dialog .idx1 ERROR "Selected file seems to be \ Crystal95 input file, but is corrupted" error 0 OK Details] if { $idx == 1 } { #user want's to see details tk_dialog .errm Details "ERROR MESSAGE:\n$errmsg" {} 0 OK } catch {file delete $system(SCRDIR)/xc_tmp.$system(PID)} OpenFile return } else { # if Crystal95 find out that file is "bad", it has exited # nicely, but with ERROR message; grep ERROR --> if grep # doesn't find anything, we must catch the grep error #eval [list exec grep ERROR $system(SCRDIR)/xc_tmp.$system(PID)] if { ! [catch {exec grep ERROR $system(SCRDIR)/xc_tmp.$system(PID)}] } { puts stdout "grep ERROR catched" tk_dialog .idx2 ERROR "Selected file is bad !!" error 0 OK file delete $system(SCRDIR)/xc_tmp.$system(PID) OpenFile return } } # it Looks that Selected file is good !!! # READ THE FILE; "distext" variable collects a information to be displayed set input [open "$system(SCRDIR)/xc_inp.$system(PID)"] set job_title [gets $input] set distext "> TITLE::\n$job_title\n" append distext "--------------------------------------------------\n\n" # just in any case (lindex 0) if there is anything bisides the "$species" set species [string tolower [lindex [gets $input] 0]] append distext "> SPECIES:: $species\n" append distext "--------------------------------------------------\n\n" if { $species == "external" } { # EXTERNAL OPTION CalStru return } elseif { $species == "crystal" } { # ========================== # SPECIES == CRYSTAL # ========================== set type_group "space" set type_group1 "Space" set ifl [gets $input] set inp(IFLAG) [lindex $ifl 0] set inp(IFHR) [lindex $ifl 1] set inp(IFSO) [lindex $ifl 2] append distext "> CRYSTAL FLAGS::\n" append distext "IFLAG: $inp(IFLAG), IFHR: $inp(IFHR), IFSO: $inp(IFSO)\n" append distext "--------------------------------------------------\n\n" # =================================================== # WHAT ABOUT sequ. number or alfanum. code for "group" if { $inp(IFLAG) == 0 } { # n_groupsel is synonym for IGR; (lindex 0) is just in any case set n_groupsel [lindex [gets $input] 0] set groupsel [Igr2Agr $n_groupsel space_group] append distext "> SPACE GROUP::\n" append distext "IGR = $n_groupsel --> AGR = $groupsel\n" append distext "--------------------------------------------------\n\n" } else { # $groupsel & $AGR are synonyms set inp(AGR) [gets $input] set n_groupsel [Agr2Igr $inp(AGR)] set groupsel $inp(AGR); #gropusel & AGR are synonyms append distext "> SPACE GROUP::\n" append distext "AGR = $groupsel --> IGR = $n_groupsel\n\n" append distext "--------------------------------------------------\n\n" } if { $inp(IFSO) > 1} { # non-standard shift of the ORIGIN set ixyz [gets $input] set inp(IX) [lindex $ixyz 0] set inp(IY) [lindex $ixyz 1] set inp(IZ) [lindex $ixyz 2] append distext "> NON-STANDARD ORIGIN SHIFT::\n" append distext "IX = $inp(IX), IY = $inp(IY), IZ = $inp(IZ)\n" append distext "--------------------------------------------------\n\n" } # verify which unit-cell parameter must be read & read it !!! WhichPar2Read $input } elseif { $species == "slab" } { set type_group "plane" set type_group1 "Plane" # n_groupsel is synonym for IGR; (lindex 0) is just in any case set n_groupsel [lindex [gets $input] 0] set groupsel [Igr2Agr $n_groupsel plane_group] append distext "> LAYER GROUP::\n" append distext "IGR = $n_groupsel --> $groupsel\n" append distext "--------------------------------------------------\n\n" # verify which unit-cell parameter must be read & read it !!! WhichPar2Read $input } elseif { $species == "polymer" } { set type_group "line" set type_group1 "Line" # n_groupsel is synonym for IGR; (lindex 0) is just in any case set n_groupsel [lindex [gets $input] 0] set groupsel [Igr2Agr $n_groupsel line_group] append distext "> ROD GROUP::\n" append distext "IGR = $n_groupsel --> $groupsel\n" append distext "--------------------------------------------------\n\n" # for all polymers we must read just A parameter set inp(A) [gets $input] append distext "> UNIT CELL PARAMETER::\nA: $inp(A)\n" append distext "--------------------------------------------------\n\n" } elseif { $species == "molecule" } { set type_group "point" set type_group1 "Point" # n_groupsel is synonym for IGR; (lindex 0) is just in any case set n_groupsel [lindex [gets $input] 0] set groupsel [Igr2Agr $n_groupsel point_group] append distext "> POINT GROUP::\n" append distext "IGR = $n_groupsel --> $groupsel\n" append distext "--------------------------------------------------\n\n" } # =============================================== # THIS IS COMMON FOR ALL SPECIES # inp(NATR); (lindex 0) is just in any case to be save set inp(NATR) [lindex [gets $input] 0] # crdatom is used for checking the variables set crdatom 1 append distext "> NUMBER OF NON-EQUIVALENT ATOMS::\nNATR = $inp(NATR)\n\n" append distext "> ATOMIC NUMBERS & COORDINATES OF NON-EQUIVALENT ATOMS::\n" # read Nat,X,Y,Z for {set i 1} {$i <= $inp(NATR)} {incr i} { set natrx [gets $input] set inp(NAT,$i) [lindex $natrx 0] set inp(X,$i) [lindex $natrx 1] set inp(Y,$i) [lindex $natrx 2] set inp(Z,$i) [lindex $natrx 3] # this is to load atom names AtomNames append distext [format "%-3d %-4s %10.5f %10.5f %10.5f\n" \ $inp(NAT,$i) [Nat2Aname $inp(NAT,$i)] $inp(X,$i) $inp(Y,$i) $inp(Z,$i)] } append distext "--------------------------------------------------\n\n" set speciesName $species ####################################### # check for ADVANCE GEOMETRICAL INPUT # ####################################### set line [gets $input] if { $line != "STOP" } { ############################# # ADVANCE GEOMETRICAL INPUT # ############################# set AdvGeom(input) "$line\n" while { [set line [gets $input]] != "STOP" } { append AdvGeom(input) "$line\n" } xcDebug "\nADVANCE GEOMETRICAL INPUT FOUND::\n$AdvGeom(input)\n" append distext " #########################################\n" append distext " # GEOMETRY MANIPULATION INPUT was found #\n" append distext " #########################################\n\n" append distext "Geometry manipulation input::\n" append distext "$AdvGeom(input)\n" # chack if dimensionality of the system has changed during # the geometry manipulation foreach word $AdvGeom(input) { switch -glob -- $word { *SLAB* { set speciesName "slab" } *MOLECULE* { set speciesName "molecule" } *CLUSTER* { set speciesName "cluster" } } } } # ============================================================ # INPUT FILE HAS BEEN READ OUT !!!!!!!! # # make a toplevel where some information about selected file # will be printed out # # there will be text widget & OK button # for text widged there is a DispText procedure; # all will be displayed after the input file will be read out # # produce some toplevel where it will # be possible to modify different parameters # ============================================================= # StatusWidget creates Status Widget & return path of toplevel set tx [StatusWidget] # TOPLEVEL FOR DECISION (VIEWER,MODIFY) set td [xcToplevel .opfd "Open Crystal Input" "Open Crystal Input" \ . 50 100] set crystalInput(two_toplevels) {.opfd .opftx} AlwaysOnTopON . $crystalInput(two_toplevels) focus $td set l [label $td.lbl -text "What to do?" -relief raised -bd 2] set f [frame $td.frm] set b1 [button $f.but1 -text "Modify File" -command \ [list OpenFileModify $tx $td]] puts stdout "tx> $tx" set b2 [button $f.but2 -text "View $speciesName" -command \ [list OpFile2ViewMol $tx $td]] pack $l $f -side top -expand 1 -fill both -ipadx 10 -ipady 10 pack $b1 $b2 -side left -expand 1 -padx 7 } proc OpenFileModify {tx td} { global fileselect distext species type_group type_group1 \ inp n_groupsel groupsel XCState XCTrace CancelProc $td # MODIFY TOPLEVEL set t [xcToplevel .openfile "Modify" "Modify" \ . 50 100] # .opftx -- status widget AlwaysOnTopON . {.openfile .opftx} focus $t # because what ever I choose there will apper some new toplevel, that will # override AlwaysOnTop flag for .openfile & .opftx toplevels, # so we must set #set XCState(toplevel) {.openfile .opftx} puts stdout "species: $species" flush stdout # label goes on the top set l [label $t.lbl -text "MODIFY/CHANGE:" -relief groove -bd 2] pack $l -side top -expand 1 -fill x -padx 7 -pady 7 -ipady 7 -ipadx 10 # for every option/parameter make a button set spe [button $t.b1 -text "Species" \ -command ChooseSpecies] # if you will change $species you must change name of this button # this is possible throuh buutn-entry combination set igr [button $t.b4 -text "Group" \ -command [list ModGroup $t]] # Only for rhombohedral group is not meanningless to specify IHFR # so doit by CheckGroup proc set ifhr [button $t.b2 -text "Type of Cell for \n\ Rhombohedral Groups" -command CheckGroup] set ifso [button $t.b3 -text "Origin Setting" \ -command PreSetOrigin] set par [button $t.b5 -text "Cell Parameters" \ -command [list PreGeom_sym_input .opflgeom $t]] set coor [button $t.b6 -text "Atomic Coordinates &\n\ Atomic Numbers" -command atom_num_coord] set view [button $t.b8 -text "View Structure" \ -command [list OpFile2ViewMol $tx $t]] set close [button $t.b9 -text "Close" \ -command [list DestroyOpfl $t $tx]] if { $species == "crystal" } { pack $spe $igr $ifhr $ifso $par $coor $view $close \ -fill x -expand 1 -padx 5 -pady 3 -ipadx 0 -ipady 0 if { [lindex $groupsel 0] != "R" } { $ifhr config -state disabled set XCTrace(RHOMBO_TYPE_BUTTON) $ifhr trace variable groupsel w xcTrace } } elseif { $species == "slab" || $species == "polymer"} { pack $spe $igr $par $coor $view $close -fill x -expand 1 \ -padx 5 -pady 3 -ipadx 0 -ipady 0 } else { pack $spe $igr $coor $view $close -fill x -expand 1 \ -padx 5 -pady 3 -ipadx 0 -ipady 0 } } proc cxxManageExternal {} { global species system # if the species is external we need to copy # $system(SCRDIR)/external_unit34 to # $system(SCRDIR)/$system(ftn_name).34 # (see proc OpenFile) if { $species == "external" } { file copy -force $system(SCRDIR)/external_unit34 $system(SCRDIR)/$system(ftn_name).34 } } proc Agr2Igr {agr} { global group_list # "load" a $group_list space_group set n 1 # assign a sequ. number to $igr that correspond to $agr foreach word $group_list { # pure the $word set last [ string length $word ] set word [ string range $word 5 $last ] regexp {(([A-Z0-9] )|[A-Z0-9\/\-])+[A-Z0-9]} $word word if { $agr == $word } { set igr $n } incr n } puts stdout "Agr2Igr> agr = $agr" flush stdout # puts stdout " igr = $igr" # maybe "agr"symbol is not standard one if ![info exists igr] { return "\"$agr\" is not a standard space group" } return $igr } proc Igr2Agr {igr comm} { global group_list # "load" a $group_list eval $comm set n 1 # assign asymbol to $agr that correspond to $igr foreach word $group_list { # purify the $word if { $igr == $n } { set last [ string length $word ] set word [ string range $word 5 $last ] regexp {(([A-Z0-9] )|[A-Z0-9\/\-])+[A-Z0-9]} $word word set agr $word } incr n } return $agr } proc OpFile2ViewMol {tx td} { # there maybe trace on "groupsel" variable xcTraceDelete groupsel CancelProc $tx CancelProc $td # CHECK THE VARIABLES --> variables must be checked everytimes- # we do sometning in Modify; so if we are here everything is OK CalStru return } proc ModGroup {t} { global species if { $species == "molecule" } { # load point groups point_group geom_sym_input .opflmod $t } elseif { $species == "polymer" } { # load groups line_group geom_sym_input .opflmod $t } elseif { $species == "slab" } { # load groups plane_group crys_slab_sym .opflmod $t } elseif {$species == "crystal" } { # load groups space_group crys_slab_sym .opflmod $t } } proc UpdateStatus {t} { global fileselect distext Alist species type_group type_group1 job_title \ inp n_groupsel groupsel crdatom #t....text-widget-path # put updated information in $distext set distext "> TITLE::\n$job_title\n" append distext "--------------------------------------------------\n\n" append distext "> SPECIES:: $species\n" append distext "--------------------------------------------------\n\n" # ========================== # SPECIES == CRYSTAL # ========================== if { $species == "crystal" } { append distext "> CRYSTAL FLAGS::\n" append distext "IFLAG: $inp(IFLAG), IFHR: $inp(IFHR), IFSO: $inp(IFSO)\n" append distext "--------------------------------------------------\n\n" if { $n_groupsel == 999 } { set n_groupsel "\"$groupsel\" is not a standard space group" } if { $inp(IFLAG) == 0 } { append distext "> SPACE GROUP::\n" append distext "IGR = $n_groupsel --> AGR = $groupsel\n" append distext "--------------------------------------------------\n\n" } else { append distext "> SPACE GROUP::\n" append distext "AGR = $groupsel --> IGR = $n_groupsel\n\n" append distext "--------------------------------------------------\n\n" } if { $inp(IFSO) > 1} { append distext "> NON-STANDARD ORIGIN SHIFT::\n" append distext "IX = $inp(IX), IY = $inp(IY), IZ = $inp(IZ)\n" append distext "--------------------------------------------------\n\n" } # verify which unit-cell parameter must be read & read it !!! WhichPar2Print } elseif { $species == "slab" } { append distext "> LAYER GROUP::\n" append distext "IGR = $n_groupsel --> $groupsel\n" append distext "--------------------------------------------------\n\n" # verify which unit-cell parameter must be read & read it !!! WhichPar2Print } elseif { $species == "polymer" } { append distext "> ROD GROUP::\n" append distext "IGR = $n_groupsel --> $groupsel\n" append distext "--------------------------------------------------\n\n" append distext "> UNIT CELL PARAMETER::\nA: $inp(A)\n" append distext "--------------------------------------------------\n\n" } elseif { $species == "molecule" } { append distext "> POINT GROUP::\n" append distext "IGR = $n_groupsel --> $groupsel\n" append distext "--------------------------------------------------\n\n" } append distext "> NUMBER OF NON-EQUIVALENT ATOMS::\nNATR = $inp(NATR)\n\n" append distext "> ATOMIC NUMBERS & COORDINATES OF NON-EQUIVALENT ATOMS::\n" # read Nat,X,Y,Z for {set i 1} {$i <= $inp(NATR)} {incr i} { AtomNames append distext [format "%-3d %-4s %10.5f %10.5f %10.5f\n" \ $inp(NAT,$i) [Nat2Aname $inp(NAT,$i)] $inp(X,$i) $inp(Y,$i) $inp(Z,$i)] } append distext "--------------------------------------------------" # now display the updated information # first delete old text if nessecary if [winfo exists $t] { $t.t delete 1.0 end DispText $t $distext 50 25 } else { set t [StatusWidget] } } proc StatusWidget {} { global distext # TOPLEVEL WITH TEXT set tx [xcToplevel .opftx "Crystal Input: status" "Crystal Input" \ . 330 100] AlwaysOnTopON . .opftx DispText $tx.frm1 $distext 50 25 set frm [frame $tx.f -height 10] pack $frm -side bottom -before $tx.frm1 -fill x set ok [button $frm.ok -text "Close" -command "destroy $tx"] set updat [button $frm.upd -text "Update Status" \ -command [list UpdateStatus $tx.frm1]] pack $ok $updat -side left -expand 1 -ipadx 2 -ipady 2 -pady 10 return $tx } proc PreSetOrigin {} { global n_groupsel species inp # Origin settings is just for crystals & rhombohedral one; # if user has changed $species or group --> if origin settings become # meaningless, make a note to user if { $species != "crystal" } { set b [tk_dialog .preorgset WARNING "Species has been changed \ and is not any more a CRYSTAL, so Origin Setting is \ meaningless !!" warning 0 OK] return } set_origin } proc PreGeom_sym_input {w t} { global species set b 1 if { $species == "molecule" } { set b [tk_dialog .pregeom WARNING "Species has been changed to \ Molecule & for Molecules there is no Cell Parameters!!" \ warning 0 OK] } if { $b == 1 } { geom_sym_input .opflgeom $t } return } proc DestroyOpfl {t1 t2} { # delete trace on groupsel variable xcDeleteState c95 xcDeleteState openinput xcUpdateState xcTraceDelete groupsel CancelProc $t1 CancelProc $t2 return } --------------080403080508020100040603--