cannot get spacegroup to work

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Robert N (guest)
Date: 03 Jul 2013 01:46
Number of posts: 7

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cannot get spacegroup to work

Robert N (guest) 03 Jul 2013 01:46

Hello fellow DFTists. I am trying to utilize the spacegroup code that is included with exciting. At first I was following the instructions specified in the source code and manual; however, I later realized that it had been altered and now requires an xml file rather than a simple text .in file. So those corrections were made and I have generated what to me, appears to be an acceptable spacegroup.xml file. Unfortunately, the code does not appear to agree.

Here is my "spacegroup.xml" file.

<?xml version="1.0" encoding="UTF-8" ?>
<symmetries HermannMauguinSymbol="P63/m">
<title>Spacegroup hapf</title>
<lattice a="17.70673" b="17.70673" c="17.70673" ab="90" ac="90" bc="120" ncell="1 1 1" speciespath="links not allowed in posts" />
<WyckoffPositions>
<wspecies speciesfile="F.xml">
<wpos coord="0.000000 0.000000 0.250000" />
</wspecies>
<wspecies speciesfile="Ca.xml">
<wpos coord="0.333333 0.666667 0.000000" />
<wpos coord="0.237000 -0.01500 0.250000" />
</wspecies>
<wspecies speciesfile="P.xml">
<wpos coord="0.416000 0.361000 0.250000" />
</wspecies>
<wspecies speciesfile="O.xml">
<wpos coord="0.333333 0.500000 0.250000" />
<wpos coord="0.600000 0.250000 0.250000" />
<wpos coord="0.333333 0.250000 0.062000" />
</wspecies>
</WyckoffPositions>
</symmetries>

When I attempt to execute spacegroup as I would exciting I get this

[osu6811@oakley02 hapf]$ spacegroup
Type in cell parameters :

It does not recognize the spacegroup.xml file as being in the directory the program was executed from. I can fill in all the information as it is requested, the lattice parameters, space group, species, coordinates, but it will continue to ask for input and if I return an empty prompt, the program closes and nothing is generated.

Alternatively, If I direct the xml file into the program as an input file, I get a whole set of errors.

[osu6811@oakley02 hapf]$ spacegroup<spacegroup.xml
Type in cell parameters : Error - non-numerical character in the 1stitem of this line
Type in cell parameters : Error - non-numerical character in the 1stitem of this line
Type in cell parameters : Error - non-numerical character in the 1stitem of this line
Type in cell parameters : Error - non-numerical character in the 1stitem of this line
Type in cell parameters : Error - non-numerical character in the 1stitem of this line
Type in cell parameters : Error - non-numerical character in the 1stitem of this line
Type in cell parameters : Error - non-numerical character in the 1stitem of this line
Type in cell parameters : Error - non-numerical character in the 1stitem of this line
Type in cell parameters : Error - non-numerical character in the 1stitem of this line
Type in cell parameters : Error - non-numerical character in the 1stitem of this line
Type in cell parameters : Error - non-numerical character in the 1stitem of this line
Type in cell parameters : Error - non-numerical character in the 1stitem of this line
Type in cell parameters : Error - non-numerical character in the 1stitem of this line
Type in cell parameters : Error - non-numerical character in the 1stitem of this line
Type in cell parameters : Error - non-numerical character in the 1stitem of this line
Type in cell parameters : Error - non-numerical character in the 1stitem of this line
Type in cell parameters : Error - non-numerical character in the 1stitem of this line
Type in cell parameters : Error - non-numerical character in the 1stitem of this line
Type in cell parameters : Error - non-numerical character in the 1stitem of this line
Type in cell parameters : Error - non-numerical character in the 1stitem of this line
Type in cell parameters : Error - non-numerical character in the 1stitem of this line
Type in cell parameters : Error - non-numerical character in the 1stitem of this line
Type in cell parameters : forrtl: severe (24): end-of-file during read, unit 5, file stdin
Image PC Routine Line Source
spacegroup 000000000048ECDA Unknown Unknown Unknown
spacegroup 000000000048D7D6 Unknown Unknown Unknown
spacegroup 000000000045FDE0 Unknown Unknown Unknown
spacegroup 000000000044152F Unknown Unknown Unknown
spacegroup 0000000000440A37 Unknown Unknown Unknown
spacegroup 0000000000416F71 Unknown Unknown Unknown
spacegroup 000000000040A09C readreal_ 1129 spacegroup.f
spacegroup 00000000004034D3 MAIN__ 10 spacegroup.f
spacegroup 000000000040344C Unknown Unknown Unknown
libc.so.6 000000384421ECDD Unknown Unknown Unknown
spacegroup 0000000000403349 Unknown Unknown Unknown
[osu6811@oakley02 hapf]$

I'm sure there is something very simple I am missing. Can someone point it out?

Appreciatively,

Robert N.

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Robert N (guest), 03 Jul 2013 01:46

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Re: cannot get spacegroup to work

DmitriiNabok 03 Jul 2013 07:38

Hi,

Check first whether you're using right executable:
$ which spacegroup

I'm pretty sure that spacegroup program you try to run is from WIEN2k package. So the solution would be just to run exciting's spacegroup using full path, e.g.,
$ /(path_to_exciting_bin)/spacegroup

In addition, I've checked your example, it works fine.
Cheers,
Dmitrii

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DmitriiNabok, 03 Jul 2013 07:38

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Robert N (guest) 03 Jul 2013 18:50

Dmitrii,

Absolutely correct. I removed the WIEN2k root folder from the PATH variable since I am not currently utilizing it.

Unfortunately, I still get this error.

[osu6811@oakley02 hapf]$ spacegroup
### Could not open spacegroup.xml file.
### Check if file exists and if it is valid XML.

I noticed that you said you checked my example and it worked. So this causes me some concern.

When I first installed Exciting I had issues with the input.xml files producing the same error. I created them in gedit and vim first I believe, then I downloaded Eclipse and XML Copy Editor and continued to have problems. the following day I came in and did nothing different and one of the files I created seemed to work.

I looked over my work multiple times and XML offers a feature to check for well-formedness. No syntax errors were ever found and the mystery was never resolved. I have continued to use that input file as a template and had no problems since.

Now I am here having the same issue with this spacegroup.xml
I created it in gedit and was unable to get it to work. I then checked it in XML Copy Editor and all seemed well. I recreated the file in vim and still, I get the error.

Is there something about xml files that I am not understanding? This is my first encounter with xml language.

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Robert N (guest), 03 Jul 2013 18:50

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DmitriiNabok 04 Jul 2013 08:23

Hi Robert,

What about to try to convert your input (text) file from 'dos' format to 'unix' one.
There are many ways to do it. Either to use system utils like dos2unix (probably one has to install it from your linux distributive repositories),
or simply search in Google for "convert dos to unix text file" to find some other scripts.

The way I checked your input was simply to copy/past the input you posted above into a file (under linux). And than execute spacegroup.

Hope, it solves your problems with xml input.

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DmitriiNabok, 04 Jul 2013 08:23

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Robert N (guest) 05 Jul 2013 00:08

Dmitrii,

This is what I suspected was the problem; however, as I stated, I then recreated the spacegroup.xml file in a unix environment with "vi". In addition, when I used gedit on windows before transferring to the HPC environment, I selected the option "line ending -unix/linux."

I will try to copy and paste the input into another vi created file as you did.

Appreciatively,

Robert N

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Robert N (guest), 05 Jul 2013 00:08

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Robert N (guest) 05 Jul 2013 18:22

Dmitrii,

Oddly, copying and pasting the information into a new vi file did the trick.
Could using "tab" to create spacing be causing the issue? That is the only thing apparently different.

Best,

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Robert N (guest), 05 Jul 2013 18:22

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Re: cannot get spacegroup to work

kazem manzoor 30 Dec 2014 21:47

hi
i have same problem
i follow the instructions in Home » Documentation » 6. Structure generation and editing
copy the below example in gedit.
and when use
~/exciting/bin/spacegroup
see this error
### Could not open spacegroup.xml file.
### Check if file exists and if it is valid XML.

<?xml version="1.0" encoding="UTF-8" ?>
<symmetries HermannMauguinSymbol="Bmab">
<title>SpacegroupExample</title>
<lattice a="10.0605232" b="10.0605232" c="24.972729" ab="90"
ac="90" bc="90" ncell="1 1 1" />
<WyckoffPositions>
<wspecies speciesfile="La.xml">
<wpos coord="0.0000 0.0000 0.3608 " />
</wspecies>
<wspecies speciesfile="Cu.xml">
<wpos coord=" 0.0000 0.0000 0.0000" />
</wspecies>
<wspecies speciesfile="O.xml">
<wpos coord="0.2500 0.2500 0.0000" />
<wpos coord=" 0.0000 0.0000 0.1820" />
</wspecies>
</WyckoffPositions>
</symmetries>

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Unfold Re: cannot get spacegroup to work by

kazem manzoor, 30 Dec 2014 21:47

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