I have settled this question. That is, to add more "\n" in the data grid. I think the problem is when xcrysden read one line of the data grid, the length of one line is limited to shorter than, say, 1000 numbers. <br>
<br>YP<br><br><br><div class="gmail_quote">On Wed, May 5, 2010 at 7:11 AM, <span dir="ltr"><<a href="mailto:xcrysden-request@democritos.it">xcrysden-request@democritos.it</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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Today's Topics:<br>
<br>
1. Error in plotting 3D scalar field, maybe a bug (Yunpeng Wang)<br>
2. Re: [Pw_forum] Error with Xcryden for view input and output<br>
of pwscf file (Tone Kokalj)<br>
3. Re: [Pw_forum] Error with Xcryden for view input and output<br>
of pwscf file (Tone Kokalj)<br>
4. Re: [Pw_forum] Error with Xcryden for view input and output<br>
of pwscf file (<a href="mailto:josepht@chips.ncsu.edu">josepht@chips.ncsu.edu</a>)<br>
5. Re: Error in plotting 3D scalar field, maybe a bug (Tone Kokalj)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Tue, 4 May 2010 05:44:40 -0400<br>
From: Yunpeng Wang <<a href="mailto:yunpengwang85@gmail.com">yunpengwang85@gmail.com</a>><br>
Subject: [xcrysden] Error in plotting 3D scalar field, maybe a bug<br>
To: <a href="mailto:xcrysden@democritos.it">xcrysden@democritos.it</a><br>
Message-ID:<br>
<<a href="mailto:k2l82b890711005040244q7e2dbd10g6152acd66a518d5d@mail.gmail.com">k2l82b890711005040244q7e2dbd10g6152acd66a518d5d@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hello all,<br>
<br>
I want to plot a 3D scalar field by XCrySDen. If the number of data-points<br>
is small (<10), I succeed to plot the scalar field and plot the isovalued<br>
surfaces. However, if I use larger (>10) value of number of data-points, the<br>
program will crash and gives error message like "child killed: segmentation<br>
violation".<br>
<br>
My xcrysden version is 1.5.21.<br>
The following is my .xsf file, in which there is only one DATAGRID_3D<br>
section:<br>
<br>
--------------------------------------------------------<br>
BEGIN_BLOCK_DATAGRID_3D<br>
whatever<br>
BEGIN_DATAGRID_3D_this_is_it<br>
10 10 10<br>
-3 -3 -3<br>
6 0 0<br>
0 6 0<br>
0 0 6<br>
...(totally 1000 numbers)<br>
END_DATAGRID_3D<br>
END_BLOCK_DATAGRID_3D<br>
-----------------------------------------------------------<br>
<br>
Thanks very much!<br>
<br>
--<br>
Yunpeng Wang<br>
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<br>
Message: 2<br>
Date: Wed, 05 May 2010 10:31:54 +0200<br>
From: Tone Kokalj <<a href="mailto:tone.kokalj@ijs.si">tone.kokalj@ijs.si</a>><br>
Subject: Re: [xcrysden] [Pw_forum] Error with Xcryden for view input<br>
and output of pwscf file<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Cc: <a href="mailto:xcrysden@democritos.it">xcrysden@democritos.it</a><br>
Message-ID: <<a href="mailto:1273048314.9405.60.camel@walk.ijs.si">1273048314.9405.60.camel@walk.ijs.si</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
On Tue, 2010-05-04 at 11:15 -0400, <a href="mailto:josepht@chips.ncsu.edu">josepht@chips.ncsu.edu</a> wrote:<br>
> Instead, the error occurs<br>
> when any parent directory containing the input file has been given a name with<br>
> spaces.<br>
><br>
> e.g. load attempt of output file located in:<br>
><br>
> /HOME/JT/QE/QUANTUM\ ESPRESSO\ TESTING/postproc/uroporphyrinogen3/scf1p2r3.out<br>
> vs<br>
> /HOME/JT/QE/QUANTUM__ESPRESSO__TESTING/postproc/uroporphyrinogen3/scf1p2r3.out<br>
><br>
> where the first case leads to load failure, and the second is successful. This<br>
> occurs with the xc-1.5.17-linux_x86-semishared.tar.gz package; untested for others.<br>
<br>
I believe having a whitespace in directory name is not a very smart idea<br>
under Unix. It may break many scripts.<br>
<br>
Nevertheless I adapted xcrysden script, and now it seems to be able to<br>
deal with it (at least it works on my computer). You may try it<br>
yourself. The script is attached to this email, you need to copy it to<br>
your $XCRYSDEN_TOPDIR.<br>
<br>
Regards, Tone<br>
--<br>
Anton Kokalj<br>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia<br>
(tel: +386-1-477-3523 // fax:+386-1-477-3822)<br>
<br>
Please, if possible, avoid sending me Word or PowerPoint attachments.<br>
See: <a href="http://www.gnu.org/philosophy/no-word-attachments.html" target="_blank">http://www.gnu.org/philosophy/no-word-attachments.html</a><br>
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<br>
Message: 3<br>
Date: Wed, 05 May 2010 10:41:43 +0200<br>
From: Tone Kokalj <<a href="mailto:tone.kokalj@ijs.si">tone.kokalj@ijs.si</a>><br>
Subject: Re: [xcrysden] [Pw_forum] Error with Xcryden for view input<br>
and output of pwscf file<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Cc: <a href="mailto:xcrysden@democritos.it">xcrysden@democritos.it</a><br>
Message-ID: <<a href="mailto:1273048903.9405.63.camel@walk.ijs.si">1273048903.9405.63.camel@walk.ijs.si</a>><br>
Content-Type: text/plain; charset="UTF-8"<br>
<br>
On Wed, 2010-05-05 at 10:31 +0200, Tone Kokalj wrote:<br>
> I believe having a whitespace in directory name is not a very smart idea<br>
> under Unix. It may break many scripts.<br>
><br>
> Nevertheless I adapted xcrysden script, and now it seems to be able to<br>
> deal with it (at least it works on my computer). You may try it<br>
> yourself. The script is attached to this email, you need to copy it to<br>
> your $XCRYSDEN_TOPDIR.<br>
<br>
Well, actually I just realized that the patch works for XSF files, but<br>
not for the PWscf files. The latter is too much involved to be adapted<br>
(and it would become a mass).<br>
<br>
Hence may recommendation is: don't use the spaces in the directory<br>
names.<br>
<br>
Regards, Tone<br>
--<br>
Anton Kokalj<br>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia<br>
(tel: +386-1-477-3523 // fax:+386-1-477-3822)<br>
<br>
Please, if possible, avoid sending me Word or PowerPoint attachments.<br>
See: <a href="http://www.gnu.org/philosophy/no-word-attachments.html" target="_blank">http://www.gnu.org/philosophy/no-word-attachments.html</a><br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Tue, 4 May 2010 11:15:47 -0400 (EDT)<br>
From: <a href="mailto:josepht@chips.ncsu.edu">josepht@chips.ncsu.edu</a><br>
Subject: Re: [xcrysden] [Pw_forum] Error with Xcryden for view input<br>
and output of pwscf file<br>
To: <a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a><br>
Cc: <a href="mailto:xcrysden@democritos.it">xcrysden@democritos.it</a><br>
Message-ID: <<a href="mailto:58446.152.14.192.32.1272986147.squirrel@chips.ncsu.edu">58446.152.14.192.32.1272986147.squirrel@chips.ncsu.edu</a>><br>
Content-Type: text/plain;charset=iso-8859-1<br>
<br>
Hello,<br>
<br>
I am resurrecting this thread - through spring cleaning, I observed the same<br>
behavior of xcrysden reported last year by Loc Duong Dinh. The source of the error,<br>
at least for my case, was actually unrelated to the format/content of the pwscf<br>
input/output file one attempts to read into xcrysden. Instead, the error occurs<br>
when any parent directory containing the input file has been given a name with<br>
spaces.<br>
<br>
e.g. load attempt of output file located in:<br>
<br>
/HOME/JT/QE/QUANTUM\ ESPRESSO\ TESTING/postproc/uroporphyrinogen3/scf1p2r3.out<br>
vs<br>
/HOME/JT/QE/QUANTUM__ESPRESSO__TESTING/postproc/uroporphyrinogen3/scf1p2r3.out<br>
<br>
where the first case leads to load failure, and the second is successful. This<br>
occurs with the xc-1.5.17-linux_x86-semishared.tar.gz package; untested for others.<br>
<br>
<br>
Joe Turnbull<br>
North Carolina State University<br>
<br>
<br>
On Sun, 2009-02-02 at 16:08 -0800, Tone Kokalj wrote:<br>
>You will need to provide more info!<br>
>How did you load the file (i.e. sequence of steps), what is the actual file (mail<br>
it as attachement)? Only then there is a change to help. Regards, Tone<br>
>--<br>
>Anton Kokalj<br>
>J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia<br>
>(tel: +386-1-477-3523 // fax:+386-1-477-3822)<br>
>Please, if possible, avoid sending me Word or PowerPoint attachments. See:<br>
<a href="http://www.gnu.org/philosophy/no-word-attachments.html" target="_blank">http://www.gnu.org/philosophy/no-word-attachments.html</a><br>
>On Sun, 2009-02-01 at 18:53 -0800, loc duong ding wrote:<br>
>> Dear all user,<br>
>><br>
>>I have a problem when using Xcrysden to view input and output file of pwscf. The<br>
error i got was:<br>
>>wrong # args: should be "pwInputPreset file"<br>
>>wrong # args: should be "pwInputPreset file"<br>
>> while executing<br>
>>"pwInputPreset /cygdrive/g/Research/MODELLING/output_model2"<br>
>> ("eval" body line 1)<br>
>> invoked from within<br>
>>"eval $preset $file"<br>
>> (procedure "openExtStruct" line 106)<br>
>> invoked from within<br>
>>"openExtStruct 3 crystal external {sh<br>
>>/home/cuteo/XCrySDen-1.5.18-bin-shared/scripts/pwi2xsf.sh} pwi2xsf.xsf_out {PWSCF<br>
Input File} ANGS -preset pwInpu..."<br>
>> (menu invoke)<br>
>><br>
>>I did not see this error before.<br>
>>I great appreciate all your instructions.<br>
>>-----------------------------------------------<br>
>>Loc Duong Dinh<br>
>>Ms-Ph.D Student<br>
>>Sungkyunkwan Advanced Institute of Nanotechnology,<br>
>>Sungkyunkwan University,<br>
>>Suwon, 440-746, Korea<br>
>>Email: mambom1902 at <a href="http://yahoo.com" target="_blank">yahoo.com</a><br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Wed, 05 May 2010 12:39:52 +0200<br>
From: Tone Kokalj <<a href="mailto:tone.kokalj@ijs.si">tone.kokalj@ijs.si</a>><br>
Subject: Re: [xcrysden] Error in plotting 3D scalar field, maybe a bug<br>
To: XCrySDen mailing list <<a href="mailto:xcrysden@democritos.it">xcrysden@democritos.it</a>><br>
Message-ID: <<a href="mailto:1273055992.9405.83.camel@walk.ijs.si">1273055992.9405.83.camel@walk.ijs.si</a>><br>
Content-Type: text/plain; charset="UTF-8"<br>
<br>
On Tue, 2010-05-04 at 05:44 -0400, Yunpeng Wang wrote:<br>
> Hello all,<br>
><br>
> I want to plot a 3D scalar field by XCrySDen. If the number of<br>
> data-points is small (<10), I succeed to plot the scalar field and<br>
> plot the isovalued surfaces. However, if I use larger (>10) value of<br>
> number of data-points, the program will crash and gives error message<br>
> like "child killed: segmentation violation".<br>
><br>
> My xcrysden version is 1.5.21.<br>
> The following is my .xsf file, in which there is only one DATAGRID_3D<br>
> section:<br>
<br>
To be able to help, please send me the whole XSF file (to my personal<br>
email).<br>
<br>
The number of points > 10 is still a very small number. Xcrysden can<br>
display datagrids with million points or more ...<br>
<br>
Regards, Tone<br>
--<br>
Anton Kokalj<br>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia<br>
(tel: +386-1-477-3523 // fax:+386-1-477-3822)<br>
<br>
Please, if possible, avoid sending me Word or PowerPoint attachments.<br>
See: <a href="http://www.gnu.org/philosophy/no-word-attachments.html" target="_blank">http://www.gnu.org/philosophy/no-word-attachments.html</a><br>
<br>
<br>
<br>
------------------------------<br>
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End of XCrySDen Digest, Vol 28, Issue 1<br>
***************************************<br>
<br>
</blockquote></div><br><br clear="all"><br>-- <br>Yunpeng Wang<br>