[xcrysden] XCrySDen Digest, Vol 28, Issue 1
Yunpeng Wang
yunpengwang85 at gmail.com
Wed May 5 17:31:23 CEST 2010
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.
YP
On Wed, May 5, 2010 at 7:11 AM, <xcrysden-request at democritos.it> wrote:
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> Today's Topics:
>
> 1. Error in plotting 3D scalar field, maybe a bug (Yunpeng Wang)
> 2. Re: [Pw_forum] Error with Xcryden for view input and output
> of pwscf file (Tone Kokalj)
> 3. Re: [Pw_forum] Error with Xcryden for view input and output
> of pwscf file (Tone Kokalj)
> 4. Re: [Pw_forum] Error with Xcryden for view input and output
> of pwscf file (josepht at chips.ncsu.edu)
> 5. Re: Error in plotting 3D scalar field, maybe a bug (Tone Kokalj)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 4 May 2010 05:44:40 -0400
> From: Yunpeng Wang <yunpengwang85 at gmail.com>
> Subject: [xcrysden] Error in plotting 3D scalar field, maybe a bug
> To: xcrysden at democritos.it
> Message-ID:
> <k2l82b890711005040244q7e2dbd10g6152acd66a518d5d at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello all,
>
> I want to plot a 3D scalar field by XCrySDen. If the number of data-points
> is small (<10), I succeed to plot the scalar field and plot the isovalued
> surfaces. However, if I use larger (>10) value of number of data-points,
> the
> program will crash and gives error message like "child killed: segmentation
> violation".
>
> My xcrysden version is 1.5.21.
> The following is my .xsf file, in which there is only one DATAGRID_3D
> section:
>
> --------------------------------------------------------
> BEGIN_BLOCK_DATAGRID_3D
> whatever
> BEGIN_DATAGRID_3D_this_is_it
> 10 10 10
> -3 -3 -3
> 6 0 0
> 0 6 0
> 0 0 6
> ...(totally 1000 numbers)
> END_DATAGRID_3D
> END_BLOCK_DATAGRID_3D
> -----------------------------------------------------------
>
> Thanks very much!
>
> --
> Yunpeng Wang
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> ------------------------------
>
> Message: 2
> Date: Wed, 05 May 2010 10:31:54 +0200
> From: Tone Kokalj <tone.kokalj at ijs.si>
> Subject: Re: [xcrysden] [Pw_forum] Error with Xcryden for view input
> and output of pwscf file
> To: PWSCF Forum <pw_forum at pwscf.org>
> Cc: xcrysden at democritos.it
> Message-ID: <1273048314.9405.60.camel at walk.ijs.si>
> Content-Type: text/plain; charset="utf-8"
>
> On Tue, 2010-05-04 at 11:15 -0400, josepht at chips.ncsu.edu wrote:
> > Instead, the error occurs
> > when any parent directory containing the input file has been given a name
> with
> > spaces.
> >
> > e.g. load attempt of output file located in:
> >
> > /HOME/JT/QE/QUANTUM\ ESPRESSO\
> TESTING/postproc/uroporphyrinogen3/scf1p2r3.out
> > vs
> >
> /HOME/JT/QE/QUANTUM__ESPRESSO__TESTING/postproc/uroporphyrinogen3/scf1p2r3.out
> >
> > where the first case leads to load failure, and the second is successful.
> This
> > occurs with the xc-1.5.17-linux_x86-semishared.tar.gz package; untested
> for others.
>
> I believe having a whitespace in directory name is not a very smart idea
> under Unix. It may break many scripts.
>
> Nevertheless I adapted xcrysden script, and now it seems to be able to
> deal with it (at least it works on my computer). You may try it
> yourself. The script is attached to this email, you need to copy it to
> your $XCRYSDEN_TOPDIR.
>
> Regards, Tone
> --
> Anton Kokalj
> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
> (tel: +386-1-477-3523 // fax:+386-1-477-3822)
>
> Please, if possible, avoid sending me Word or PowerPoint attachments.
> See: http://www.gnu.org/philosophy/no-word-attachments.html
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> ------------------------------
>
> Message: 3
> Date: Wed, 05 May 2010 10:41:43 +0200
> From: Tone Kokalj <tone.kokalj at ijs.si>
> Subject: Re: [xcrysden] [Pw_forum] Error with Xcryden for view input
> and output of pwscf file
> To: PWSCF Forum <pw_forum at pwscf.org>
> Cc: xcrysden at democritos.it
> Message-ID: <1273048903.9405.63.camel at walk.ijs.si>
> Content-Type: text/plain; charset="UTF-8"
>
> On Wed, 2010-05-05 at 10:31 +0200, Tone Kokalj wrote:
> > I believe having a whitespace in directory name is not a very smart idea
> > under Unix. It may break many scripts.
> >
> > Nevertheless I adapted xcrysden script, and now it seems to be able to
> > deal with it (at least it works on my computer). You may try it
> > yourself. The script is attached to this email, you need to copy it to
> > your $XCRYSDEN_TOPDIR.
>
> Well, actually I just realized that the patch works for XSF files, but
> not for the PWscf files. The latter is too much involved to be adapted
> (and it would become a mass).
>
> Hence may recommendation is: don't use the spaces in the directory
> names.
>
> Regards, Tone
> --
> Anton Kokalj
> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
> (tel: +386-1-477-3523 // fax:+386-1-477-3822)
>
> Please, if possible, avoid sending me Word or PowerPoint attachments.
> See: http://www.gnu.org/philosophy/no-word-attachments.html
>
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 4 May 2010 11:15:47 -0400 (EDT)
> From: josepht at chips.ncsu.edu
> Subject: Re: [xcrysden] [Pw_forum] Error with Xcryden for view input
> and output of pwscf file
> To: pw_forum at pwscf.org
> Cc: xcrysden at democritos.it
> Message-ID: <58446.152.14.192.32.1272986147.squirrel at chips.ncsu.edu>
> Content-Type: text/plain;charset=iso-8859-1
>
> Hello,
>
> I am resurrecting this thread - through spring cleaning, I observed the
> same
> behavior of xcrysden reported last year by Loc Duong Dinh. The source of
> the error,
> at least for my case, was actually unrelated to the format/content of the
> pwscf
> input/output file one attempts to read into xcrysden. Instead, the error
> occurs
> when any parent directory containing the input file has been given a name
> with
> spaces.
>
> e.g. load attempt of output file located in:
>
> /HOME/JT/QE/QUANTUM\ ESPRESSO\
> TESTING/postproc/uroporphyrinogen3/scf1p2r3.out
> vs
>
> /HOME/JT/QE/QUANTUM__ESPRESSO__TESTING/postproc/uroporphyrinogen3/scf1p2r3.out
>
> where the first case leads to load failure, and the second is successful.
> This
> occurs with the xc-1.5.17-linux_x86-semishared.tar.gz package; untested for
> others.
>
>
> Joe Turnbull
> North Carolina State University
>
>
> On Sun, 2009-02-02 at 16:08 -0800, Tone Kokalj wrote:
> >You will need to provide more info!
> >How did you load the file (i.e. sequence of steps), what is the actual
> file (mail
> it as attachement)? Only then there is a change to help. Regards, Tone
> >--
> >Anton Kokalj
> >J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
> >(tel: +386-1-477-3523 // fax:+386-1-477-3822)
> >Please, if possible, avoid sending me Word or PowerPoint attachments. See:
> http://www.gnu.org/philosophy/no-word-attachments.html
> >On Sun, 2009-02-01 at 18:53 -0800, loc duong ding wrote:
> >> Dear all user,
> >>
> >>I have a problem when using Xcrysden to view input and output file of
> pwscf. The
> error i got was:
> >>wrong # args: should be "pwInputPreset file"
> >>wrong # args: should be "pwInputPreset file"
> >> while executing
> >>"pwInputPreset /cygdrive/g/Research/MODELLING/output_model2"
> >> ("eval" body line 1)
> >> invoked from within
> >>"eval $preset $file"
> >> (procedure "openExtStruct" line 106)
> >> invoked from within
> >>"openExtStruct 3 crystal external {sh
> >>/home/cuteo/XCrySDen-1.5.18-bin-shared/scripts/pwi2xsf.sh}
> pwi2xsf.xsf_out {PWSCF
> Input File} ANGS -preset pwInpu..."
> >> (menu invoke)
> >>
> >>I did not see this error before.
> >>I great appreciate all your instructions.
> >>-----------------------------------------------
> >>Loc Duong Dinh
> >>Ms-Ph.D Student
> >>Sungkyunkwan Advanced Institute of Nanotechnology,
> >>Sungkyunkwan University,
> >>Suwon, 440-746, Korea
> >>Email: mambom1902 at yahoo.com
>
>
>
>
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 05 May 2010 12:39:52 +0200
> From: Tone Kokalj <tone.kokalj at ijs.si>
> Subject: Re: [xcrysden] Error in plotting 3D scalar field, maybe a bug
> To: XCrySDen mailing list <xcrysden at democritos.it>
> Message-ID: <1273055992.9405.83.camel at walk.ijs.si>
> Content-Type: text/plain; charset="UTF-8"
>
> On Tue, 2010-05-04 at 05:44 -0400, Yunpeng Wang wrote:
> > Hello all,
> >
> > I want to plot a 3D scalar field by XCrySDen. If the number of
> > data-points is small (<10), I succeed to plot the scalar field and
> > plot the isovalued surfaces. However, if I use larger (>10) value of
> > number of data-points, the program will crash and gives error message
> > like "child killed: segmentation violation".
> >
> > My xcrysden version is 1.5.21.
> > The following is my .xsf file, in which there is only one DATAGRID_3D
> > section:
>
> To be able to help, please send me the whole XSF file (to my personal
> email).
>
> The number of points > 10 is still a very small number. Xcrysden can
> display datagrids with million points or more ...
>
> Regards, Tone
> --
> Anton Kokalj
> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
> (tel: +386-1-477-3523 // fax:+386-1-477-3822)
>
> Please, if possible, avoid sending me Word or PowerPoint attachments.
> See: http://www.gnu.org/philosophy/no-word-attachments.html
>
>
>
> ------------------------------
>
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>
> End of XCrySDen Digest, Vol 28, Issue 1
> ***************************************
>
>
--
Yunpeng Wang
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