[xcrysden] Problem reading xsf file
Abu Md. Asaduzzaman
xcrysden@democritos.it
Wed, 6 Jun 2007 09:28:45 -0700 (PDT)
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Scott and H.P
Thanks for help.
I solved the problem (There was another error though).
abu
Scott Beckman <spbeckman@gmail.com> wrote: Abu,
The xsf file you included is missing the first line beneath the
keyword "PRIMCOORD". The first line following PRIMCOORD should be
(in this case):
13 1
The first number is the number of atoms in the second is always "1"
for PRIMCOORD.
This is all in the documentation located here:
http://www.xcrysden.org/doc/XSF.html#__toc__4
Scott
On Jun 6, 2007, at 10:48 AM, Abu Md. Asaduzzaman wrote:
> Hi
> I installed XCrysden (xc-1.4.1bin-linuxPC-static.tar.gz) in my
> AMD64 machine with Suse 10.2. It seems that installation is
> successful without any problem. Now, for .xsf file and even
> for .xyz file, the xcrysden gives some error message and can't
> visualize. Here is the whole message:
> Running on platform: unix
> Executing: /home/abu/Desktop/XCrySDen-1.4.1bin-static/bin/ftnunit
>
> *** the hardware does not support the stereo ***
>
> Number of Atoms: 0
> Number of Frames: 0
> Estimated number of bonds = 0
> sInfo(dim) = 3; periodic(dim) = 0
> Executing: /home/abu/Desktop/XCrySDen-1.4.1bin-static/bin/gengeom 0
> 1 11 1 1 1 1 xc_gengeom.28589 /home/abu/xcrys_tmp/xc_28589/
> exam.xsf.raw
> Executing: /home/abu/Desktop/XCrySDen-1.4.1bin-static/bin/gengeom 2
> 1 11 1 1 1 1 /home/abu/xcrys_tmp/xc_28589/xc_struc.28589 /home/abu/
> xcrys_tmp/xc_28589/exam.xsf.raw
> Number of Atoms: 13
> Number of Frames: 0
> ERROR: Error reading file "/home/abu/xcrys_tmp/xc_28589/xc_struc.
> 28589"
>
>
> Error in startup script: can't read "sInfo(ldatagrid2D)": no such
> variable
> while executing
> "if { $sInfo(ldatagrid2D) || $sInfo(ldatagrid3D) } {
> $m.menu entryconfig "Data Grid" -state normal
> } else {
> $m.menu entryconfig "Data Grid" -stat..."
> (procedure "Get_sInfoArray" line 13)
> invoked from within
> "Get_sInfoArray"
> (procedure "xsfOpen" line 92)
> invoked from within
> "xsfOpen $filedir .mesa"
> ("--xsf" arm line 3)
> invoked from within
> "switch -glob -- $tag {
> "-a" -
> "--attrib*" {
> set load_attributes 1
> set file_attributes $filedir
> }
>
> "--xsf" -
> "--xcr..."
> (procedure "parseComLinArg" line 44)
> invoked from within
> "parseComLinArg [lrange $argv 2 end]"
> invoked from within
> "if { [llength $argv] > 2 } {
> parseComLinArg [lrange $argv 2 end]
> } else {
> ViewMol .
> }"
> (file "/home/abu/Desktop/XCrySDen-1.4.1bin-static/Tcl/
> xcInit.tcl" line
>
> The input file
> CRYSTAL
> CONVVEC
> 7.0000000000 0.0000000000 0.0000000000
> 0.0000000000 3.0000000000 0.0000000000
> 0.0000000000 0.0000000000 3.0000000000
> PRIMCOORD
> 6 2.325243 -0.115261 0.031711
> 1 2.344577 -0.363301 1.077589
> 9 3.131708 -0.909527 -0.638930
> 9 2.736189 1.130568 -0.134093
> 8 1.079338 -0.265162 -0.526351
> 6 0.007719 -0.041269 0.244204
> 9 0.064656 1.154700 0.824420
> 9 -0.042641 -0.911850 1.255074
> 8 -1.071578 -0.152842 -0.539134
> 6 -2.310374 0.036537 0.022189
> 1 -2.267004 0.230694 1.077874
> 9 -2.890949 1.048938 -0.593940
> 9 -3.029540 -1.046542 -0.203665
>
> Any help will be highly appreciated.
>
> Abu
>
> Fussy? Opinionated? Impossible to please? Perfect. Join Yahoo!'s
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Scott and H.P<br>Thanks for help. <br>I solved the problem (There was another error though).<br><br>abu<br><b><i>Scott Beckman <spbeckman@gmail.com></i></b> wrote:<blockquote class="replbq" style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"> Abu,<br><br>The xsf file you included is missing the first line beneath the <br>keyword "PRIMCOORD". The first line following PRIMCOORD should be <br>(in this case):<br><br>13 1<br><br>The first number is the number of atoms in the second is always "1" <br>for PRIMCOORD.<br><br>This is all in the documentation located here:<br><br>http://www.xcrysden.org/doc/XSF.html#__toc__4<br><br>Scott<br><br><br><br><br>On Jun 6, 2007, at 10:48 AM, Abu Md. Asaduzzaman wrote:<br><br>> Hi<br>> I installed XCrysden (xc-1.4.1bin-linuxPC-static.tar.gz) in my <br>> AMD64 machine with Suse 10.2. It seems that installation is <br>> successful without any problem. Now, for .xsf file and even
<br>> for .xyz file, the xcrysden gives some error message and can't <br>> visualize. Here is the whole message:<br>> Running on platform: unix<br>> Executing: /home/abu/Desktop/XCrySDen-1.4.1bin-static/bin/ftnunit<br>><br>> *** the hardware does not support the stereo ***<br>><br>> Number of Atoms: 0<br>> Number of Frames: 0<br>> Estimated number of bonds = 0<br>> sInfo(dim) = 3; periodic(dim) = 0<br>> Executing: /home/abu/Desktop/XCrySDen-1.4.1bin-static/bin/gengeom 0 <br>> 1 11 1 1 1 1 xc_gengeom.28589 /home/abu/xcrys_tmp/xc_28589/ <br>> exam.xsf.raw<br>> Executing: /home/abu/Desktop/XCrySDen-1.4.1bin-static/bin/gengeom 2 <br>> 1 11 1 1 1 1 /home/abu/xcrys_tmp/xc_28589/xc_struc.28589 /home/abu/ <br>> xcrys_tmp/xc_28589/exam.xsf.raw<br>> Number of Atoms: 13<br>> Number of Frames: 0<br>> ERROR: Error reading file "/home/abu/xcrys_tmp/xc_28589/xc_struc. <br>> 28589"<br>><br>><br>> Error in startup
script: can't read "sInfo(ldatagrid2D)": no such <br>> variable<br>> while executing<br>> "if { $sInfo(ldatagrid2D) || $sInfo(ldatagrid3D) } {<br>> $m.menu entryconfig "Data Grid" -state normal<br>> } else {<br>> $m.menu entryconfig "Data Grid" -stat..."<br>> (procedure "Get_sInfoArray" line 13)<br>> invoked from within<br>> "Get_sInfoArray"<br>> (procedure "xsfOpen" line 92)<br>> invoked from within<br>> "xsfOpen $filedir .mesa"<br>> ("--xsf" arm line 3)<br>> invoked from within<br>> "switch -glob -- $tag {<br>> "-a" -<br>> "--attrib*" {<br>> set load_attributes 1<br>> set file_attributes $filedir<br>> }<br>><br>> "--xsf" -<br>> "--xcr..."<br>> (procedure "parseComLinArg" line 44)<br>> invoked from within<br>>
"parseComLinArg [lrange $argv 2 end]"<br>> invoked from within<br>> "if { [llength $argv] > 2 } {<br>> parseComLinArg [lrange $argv 2 end]<br>> } else {<br>> ViewMol .<br>> }"<br>> (file "/home/abu/Desktop/XCrySDen-1.4.1bin-static/Tcl/ <br>> xcInit.tcl" line<br>><br>> The input file<br>> CRYSTAL<br>> CONVVEC<br>> 7.0000000000 0.0000000000 0.0000000000<br>> 0.0000000000 3.0000000000 0.0000000000<br>> 0.0000000000 0.0000000000 3.0000000000<br>> PRIMCOORD<br>> 6 2.325243 -0.115261 0.031711<br>> 1 2.344577 -0.363301 1.077589<br>> 9 3.131708 -0.909527 -0.638930<br>> 9 2.736189 1.130568 -0.134093<br>> 8 1.079338 -0.265162 -0.526351<br>> 6 0.007719 -0.041269 0.244204<br>> 9 0.064656 1.154700 0.824420<br>> 9 -0.042641 -0.911850 1.255074<br>> 8 -1.071578 -0.152842
-0.539134<br>> 6 -2.310374 0.036537 0.022189<br>> 1 -2.267004 0.230694 1.077874<br>> 9 -2.890949 1.048938 -0.593940<br>> 9 -3.029540 -1.046542 -0.203665<br>><br>> Any help will be highly appreciated.<br>><br>> Abu<br>><br>> Fussy? Opinionated? Impossible to please? Perfect. Join Yahoo!'s <br>> user panel and lay it on us.<br><br>_______________________________________________<br>XCrySDen mailing list<br>XCrySDen@democritos.it<br>http://www.democritos.it/mailman/listinfo/xcrysden<br></blockquote><br><p> 
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