[xcrysden] Cannot show multiple frame in out file

[Gabriele Sclauzero]

On 03/10/2011 07:22 PM, Yuelin Li wrote:
> Did that too. What I mean is that xcrysden did not start at all and is stuck at that line.
>
> Best,
>
> Yuelin
>

Ah, OK. Sorry, I did not understand at the first place. So this means 
that you can't run the newly installed version, right?
This might be a problem of libraries. I suggest you to try the 
semi-shared version or the binaries.


GS

>
> ----- Original Message -----
> From: Gabriele Sclauzero<sclauzer at sissa.it>
> To: XCrySDen mailing list<xcrysden at democritos.it>
> Sent: Thu, 10 Mar 2011 11:54:24 -0600 (CST)
> Subject: Re: [xcrysden] Cannot show multiple frame in out file
>
> Have you tried to correct the first problem, i.e. the call to pwo2xsf_old in pwo2xsh.sh?
>
> GS
>
> Il giorno 10/mar/2011, alle ore 18.38, Yuelin Li ha scritto:
>
>> Installed using the shared version, get the splash screen, then stopped at the famous line below
>>
>> Running on platform: unix
>> Executing: /home/ylli/XCrySDen-1.5.17-bin-shared/bin/ftnunit
>>
>> with try the source version.
>>
>> ----- Original Message -----
>> From: Yuelin Li<ylli at aps.anl.gov>
>> To: XCrySDen mailing list<xcrysden at democritos.it>
>> Sent: Thu, 10 Mar 2011 10:19:23 -0600 (CST)
>> Subject: Re: [xcrysden] Cannot show multiple frame in out file
>>
>> Thanks again.
>>
>> I did try the "latest coordinates" option. xcrysden did not complain, and there is nothing displayed.
>>
>> Looks like 1.5 is the solution.  I was not able to install it the last time. I will try again and let you know the result.
>>
>> Yuelin
>>
>>
>>
>> ----- Original Message -----
>> From: "Gabriele Sclauzero"<sclauzer at sissa.it>
>> To: "XCrySDen mailing list"<xcrysden at democritos.it>
>> Sent: Thursday, March 10, 2011 9:56:43 AM
>> Subject: Re: [xcrysden] Cannot show multiple frame in out file
>>
>>
>>
>>
>>
>>
>> Il giorno 10/mar/2011, alle ore 16.19, Yuelin Li ha scritto:
>>
>>
>>
>> Gabriele,
>>
>> thanks for the help. I commented the line you mentioned, but still got the same results. If I force it to read the optimised coordinate, a window pups up and say the following:
>>
>> ERROR: while executing exec sh
>> ..../scripts/pwo2xsf.sh --optcoor
>> ..../acetylene.out>  pwo2xsf.xsf
>>
>> I can only guess that pwo2xsf.xsf did not find the optcoor string in the out file.
>>
>>
>> I had a look to your input and it's a MD run, not a relaxation, so there are no "optimized" coordinates.
>> I tried to run your input and then open the output file with xcrysden 1.5.21 and it could read all the coordinates without any problem. Why are you using 1.4.1? I suggest you to upgrade to the latest version.
>>
>>
>> BTW, beware that even if you do a relaxation and use the "display optimized coordinates", it is not likely to work because the string which helped xcrysden identifying the optimized structure was changed in PWscf, but I suspect that the xcrysden has not been updated accordingly. However, if you select "latest coordinates" instead of "optimized coordinates" it works and you should get the same result (if the output file contains a converged relaxation run).
>>
>>
>>
>> HTH
>>
>>
>> GS
>>
>>
>>
>>
>>
>> I believe you are pointing to the right direction, must be some sort of mixing of versions.
>>
>> Any other thought?
>>
>> Best,
>>
>> Yuelin
>>
>>
>>
>> ----- Original Message -----
>> From: "Gabriele Sclauzero"<  sclauzer at sissa.it>
>> To: "XCrySDen mailing list"<  xcrysden at democritos.it>
>> Sent: Thursday, March 10, 2011 1:53:53 AM
>> Subject: Re: [xcrysden] Cannot show multiple frame in out file
>>
>>
>> I think I met the same problem some time ago. It comes from the fact that xcrysden checks the string of the PWscf version and, if it thinks that the version is an old one, it calls a different script to read the output file. Now, the problem is with the "a" in 4.3a which makes xcrysden think that's an old version.
>> If this is your problem you can solve it by commenting the calls to
>>
>> pwoCheckPWSCFVersion $option $input
>> in scripts/pwo2xsf.sh
>>
>>
>> Have fun with XCrysden! I also think it has very nice features.
>>
>>
>> Best regards,
>>
>>
>>
>>
>> GS
>>
>>
>>
>> Il giorno 09/mar/2011, alle ore 19.08, Yuelin Li ha scritto:
>>
>>
>>
>> was able to get xcrysden running - beautiful implementation!
>>
>> I do have a problem using it when look at out put with multiple atom positions. It looks like xcryden only sees the first frame not the others. If I force it, e.g., on the latest frame, the display is blank, xterm says.
>>
>> PWSCF version of the output: 4.3a
>> TEXT-WIDGET: .a1.f1.t
>> pwOutputPresetWhat: /home/ylli/XCrySDen-1.4.1s/scripts/pwo2xsf.sh --latestcoor /home/ylli/Documents/temp/acetylene.out
>> Executing: sh /home/ylli/XCrySDen-1.4.1s/scripts/pwo2xsf.sh --latestcoor /home/ylli/Documents/temp/acetylene.out>  pwo2xsf.xsf
>> Executing: sh /home/ylli/XCrySDen-1.4.1s/scripts/dummy.sh /home/ylli/Documents/temp/acetylene.out
>> Number of Atoms: 0
>> Number of Frames: 0
>> Estimated number of bonds = 0
>> sInfo(dim) = 0; periodic(dim) = 0
>>
>>
>> Attached is the in file directly from the tutorial pw examples.
>>
>> Please help. Thanks.
>>
>> Best,
>>
>> Yuelin<acetylene.in>  _______________________________________________
>> XCrySDen mailing list
>> XCrySDen at democritos.it
>> http://www.democritos.it/mailman/listinfo/xcrysden
>>
>>
>>
>>
>> § Gabriele Sclauzero, EPFL SB ITP CSEA
>> PH H2 462, Station 3, CH-1015 Lausanne
>>
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>>
>>
>>
>> § Gabriele Sclauzero, EPFL SB ITP CSEA
>> PH H2 462, Station 3, CH-1015 Lausanne
>>
>> _______________________________________________
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>
> § Gabriele Sclauzero, EPFL SB ITP CSEA
>     PH H2 462, Station 3, CH-1015 Lausanne
>
>
> _______________________________________________
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> XCrySDen at democritos.it
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-- 

Gabriele Sclauzero, EPFL SB ITP CSEA
PH H2 462, Station 3, CH-1015 Lausanne