[xcrysden] Problem reading xsf file

lan haiping xcrysden@democritos.it
Wed, 6 Jun 2007 23:27:40 +0800


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hi , do you try the examples with XcrySDEN ?

i have came to some related errors , but i solved these problems by using
scripts..

Regards,

H.P

On 6/6/07, Abu Md. Asaduzzaman <ratan4321@yahoo.com> wrote:
>
> Hi
> I installed XCrysden (xc-1.4.1bin-linuxPC-static.tar.gz<http://www.xcrysden.org/download/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
>
> ------------------------------
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>



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

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hi , do you try the examples with XcrySDEN ?<br>&nbsp;<br>i have came to some related errors , but i solved these problems by using scripts..<br><br>Regards,<br><br>H.P<br><br><div><span class="gmail_quote">On 6/6/07, <b class="gmail_sendername">
Abu Md. Asaduzzaman</b> &lt;<a href="mailto:ratan4321@yahoo.com">ratan4321@yahoo.com</a>&gt; wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi<br> I installed XCrysden (<a href="http://www.xcrysden.org/download/xc-1.4.1bin-linuxPC-static.tar.gz" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">xc-1.4.1bin-linuxPC-static.tar.gz</a>) in my AMD64 machine with Suse 
10.2. It seems that installation is successful without any problem. Now, for .xsf&nbsp; file and even for .xyz file, the xcrysden gives some error message and can&#39;t visualize. Here is the whole message:<br> <span style="font-style: italic;">
Running on platform: unix</span><br style="font-style: italic;"> <span style="font-style: italic;">Executing: /home/abu/Desktop/XCrySDen-1.4.1bin-static/bin/ftnunit</span><br style="font-style: italic;"> <br style="font-style: italic;">
 <span style="font-style: italic;">*** the hardware does not support the stereo ***</span><br style="font-style: italic;"> <br style="font-style: italic;"> <span style="font-style: italic;">Number of Atoms:&nbsp; 0</span><br style="font-style: italic;">
 <span style="font-style: italic;">Number of Frames: 0</span><br style="font-style: italic;"> <span style="font-style: italic;">Estimated number of bonds = 0</span><br style="font-style: italic;"> <span style="font-style: italic;">
sInfo(dim) = 3; periodic(dim) = 0</span><br style="font-style: italic;"> <span style="font-style: italic;">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
</span><br style="font-style: italic;"> <span style="font-style: italic;">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
</span><br style="font-style: italic;"> <span style="font-style: italic;">Number of Atoms:&nbsp; 13</span><br style="font-style: italic;"> <span style="font-style: italic;">Number of Frames: 0</span><br style="font-style: italic;">
 <span style="font-style: italic;">ERROR: Error reading file &quot;/home/abu/xcrys_tmp/xc_28589/xc_struc.28589&quot;</span><br style="font-style: italic;"> <br style="font-style: italic;"> <br style="font-style: italic;">
 <span style="font-style: italic;">Error in startup script: can&#39;t read &quot;sInfo(ldatagrid2D)&quot;: no such variable</span><br style="font-style: italic;"> <span style="font-style: italic;">&nbsp;&nbsp;&nbsp; while executing</span>
<br style="font-style: italic;"> <span style="font-style: italic;">&quot;if { $sInfo(ldatagrid2D) || $sInfo(ldatagrid3D) } {</span><br style="font-style: italic;"> <span style="font-style: italic;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; $m.menu entryconfig &quot;Data Grid&quot; -state normal
</span><br style="font-style: italic;"> <span style="font-style: italic;">&nbsp;&nbsp;&nbsp; } else {</span><br style="font-style: italic;"> <span style="font-style: italic;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; $m.menu entryconfig &quot;Data Grid&quot; -stat...&quot;
</span><br style="font-style: italic;"> <span style="font-style: italic;">&nbsp;&nbsp;&nbsp; (procedure &quot;Get_sInfoArray&quot; line
 13)</span><br style="font-style: italic;"> <span style="font-style: italic;">&nbsp;&nbsp;&nbsp; invoked from within</span><br style="font-style: italic;"> <span style="font-style: italic;">&quot;Get_sInfoArray&quot;</span><br style="font-style: italic;">
 <span style="font-style: italic;">&nbsp;&nbsp;&nbsp; (procedure &quot;xsfOpen&quot; line 92)</span><br style="font-style: italic;"> <span style="font-style: italic;">&nbsp;&nbsp;&nbsp; invoked from within</span><br style="font-style: italic;"> <span style="font-style: italic;">
&quot;xsfOpen $filedir .mesa&quot;</span><br style="font-style: italic;"> <span style="font-style: italic;">&nbsp;&nbsp;&nbsp; (&quot;--xsf&quot; arm line 3)</span><br style="font-style: italic;"> <span style="font-style: italic;">&nbsp;&nbsp;&nbsp; invoked from within
</span><br style="font-style: italic;"> <span style="font-style: italic;">&quot;switch -glob -- $tag {</span><br style="font-style: italic;"> <span style="font-style: italic;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &quot;-a&quot; -</span><br style="font-style: italic;">
 <span style="font-style: italic;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &quot;--attrib*&quot; {</span><br style="font-style: italic;"> <span style="font-style: italic;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; set load_attributes 1</span><br style="font-style: italic;">
 <span style="font-style: italic;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; set file_attributes $filedir</span><br style="font-style: italic;"> <span style="font-style: italic;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; }</span><br style="font-style: italic;"> <br style="font-style: italic;">
 <span style="font-style: italic;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &quot;--xsf&quot; -</span><br style="font-style: italic;"> <span style="font-style: italic;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &quot;--xcr...&quot;</span><br style="font-style: italic;"> <span style="font-style: italic;">
&nbsp;&nbsp;&nbsp; (procedure &quot;parseComLinArg&quot; line 44)</span><br style="font-style: italic;"> <span style="font-style: italic;">&nbsp;&nbsp;&nbsp; invoked from within</span><br style="font-style: italic;"> <span style="font-style: italic;">
&quot;parseComLinArg [lrange $argv 2 end]&quot;</span><br style="font-style: italic;"> <span style="font-style: italic;">&nbsp;&nbsp;&nbsp; invoked from within</span><br style="font-style: italic;"> <span style="font-style: italic;">&quot;if { [llength $argv] &gt; 2 } {
</span><br style="font-style: italic;"> <span style="font-style: italic;">&nbsp;&nbsp;&nbsp; parseComLinArg [lrange $argv 2
 end]</span><br style="font-style: italic;"> <span style="font-style: italic;">} else {</span><br style="font-style: italic;"> <span style="font-style: italic;">&nbsp;&nbsp;&nbsp; ViewMol .</span><br style="font-style: italic;"> <span style="font-style: italic;">
}&quot;</span><br style="font-style: italic;"> <span style="font-style: italic;">&nbsp;&nbsp;&nbsp; (file &quot;/home/abu/Desktop/XCrySDen-1.4.1bin-static/Tcl/xcInit.tcl&quot; line </span><br style="font-style: italic;"> <br> The input file
<br> CRYSTAL<br> CONVVEC<br> &nbsp;&nbsp;&nbsp; 7.0000000000&nbsp;&nbsp;&nbsp; 0.0000000000&nbsp;&nbsp;&nbsp; 0.0000000000<br> &nbsp;&nbsp;&nbsp; 0.0000000000&nbsp;&nbsp;&nbsp; 3.0000000000&nbsp;&nbsp;&nbsp; 0.0000000000<br> &nbsp;&nbsp;&nbsp; 0.0000000000&nbsp;&nbsp;&nbsp; 0.0000000000&nbsp;&nbsp;&nbsp; 3.0000000000<br> PRIMCOORD<br> &nbsp; 6&nbsp;&nbsp;&nbsp; 2.325243&nbsp;&nbsp; -
0.115261&nbsp;&nbsp;&nbsp; 0.031711<br> &nbsp; 1&nbsp;&nbsp;&nbsp; 2.344577&nbsp;&nbsp;
 -0.363301&nbsp;&nbsp;&nbsp; 1.077589<br> &nbsp; 9&nbsp;&nbsp;&nbsp; 3.131708&nbsp;&nbsp; -0.909527&nbsp;&nbsp; -0.638930<br> &nbsp; 9&nbsp;&nbsp;&nbsp; 2.736189&nbsp;&nbsp;&nbsp; 1.130568&nbsp;&nbsp; -0.134093<br> &nbsp; 8&nbsp;&nbsp;&nbsp; 1.079338&nbsp;&nbsp; -0.265162&nbsp;&nbsp; -0.526351<br> &nbsp; 6&nbsp;&nbsp;&nbsp; 0.007719&nbsp;&nbsp; -0.041269&nbsp;&nbsp;&nbsp; 0.244204<br> &nbsp; 9&nbsp;&nbsp;&nbsp; 0.064656&nbsp;&nbsp;&nbsp; 
1.154700&nbsp;&nbsp;&nbsp; 0.824420<br> &nbsp; 9&nbsp;&nbsp; -0.042641&nbsp;&nbsp; -0.911850&nbsp;&nbsp;&nbsp; 1.255074<br> &nbsp; 8&nbsp;&nbsp; -1.071578&nbsp;&nbsp; -0.152842&nbsp;&nbsp; -0.539134<br> &nbsp; 6&nbsp;&nbsp; -2.310374&nbsp;&nbsp;&nbsp; 0.036537&nbsp;&nbsp;&nbsp; 0.022189<br> &nbsp; 1&nbsp;&nbsp; -2.267004&nbsp;&nbsp;&nbsp; 0.230694&nbsp;&nbsp;&nbsp; 1.077874<br> &nbsp; 9&nbsp;&nbsp; -2.890949&nbsp;&nbsp;&nbsp; 1.048938
&nbsp;&nbsp; -0.593940<br> &nbsp; 9&nbsp;&nbsp; -3.029540&nbsp;&nbsp; -1.046542&nbsp;&nbsp; -0.203665<br>
 <br> Any help will be highly appreciated.<br><span class="sg"> <br> Abu</span><p><span class="ad"> 
      <hr size="1">Fussy? Opinionated? Impossible to please? Perfect.  <a href="http://us.rd.yahoo.com/evt=48516/*http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7+" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
Join Yahoo!&#39;s user panel</a> and lay it on us.
</span></p></blockquote></div><br><br clear="all"><br>-- <br>Hai-Ping Lan <br>Department of Electronics ,<br>Peking University , Bejing, 100871<br><a href="mailto:lanhaiping@gmail.com">lanhaiping@gmail.com</a>, <a href="mailto:hplan@pku.edu.cn">
hplan@pku.edu.cn</a>

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