[srrietveld bug] limit in number of atoms?

[dif...@diffpy.org]

reporter: francesco...@unipr.it

summary: limit in number of atoms?

description: it looks like the program works (very well, congratulations!) for a number of atoms in the structure up to 9. Maybe the nature of the problem is different but troubles come out as I load a structure with 10 or more atoms, also without increasing the number of variables to be refined.

thank you in advance
best regards,
Francesco Mezzadri


component: srrietveld

version: 1.0beta-r6746-20110902

traceback:
Traceback (most recent call last):
File "D:\Uni\Programmi\DiffPy\Python26\lib\site-packages\diffpy.srrietveld-1.0beta_r6746_20110902-py2.6.egg\diffpy\srrietveld\gui\errorwrapper.py", line 61, in _f
return func(*args, **kwargs)
File "D:\Uni\Programmi\DiffPy\Python26\lib\site-packages\diffpy.srrietveld-1.0beta_r6746_20110902-py2.6.egg\diffpy\srrietveld\gui\mainframe.py", line 912, in loadExpPcr
fit = GLOBALS.project.importEngineFile(fullpath, name)
File "D:\Uni\Programmi\DiffPy\Python26\lib\site-packages\diffpy.srrietveld-1.0beta_r6746_20110902-py2.6.egg\diffpy\srrietveld\project.py", line 332, in importEngineFile
enginefit = loadFitFromEXP(fullpath)
File "D:\Uni\Programmi\DiffPy\Python26\lib\site-packages\diffpy.pygsas-1.0b_r6746_20110902-py2.6.egg\diffpy\pygsas\fitloader.py", line 42, in loadFitFromEXP
fit = loader(filename)
File "D:\Uni\Programmi\DiffPy\Python26\lib\site-packages\diffpy.pygsas-1.0b_r6746_20110902-py2.6.egg\diffpy\pygsas\fitloader.py", line 77, in __call__
self._importPhase(phidx1)
File "D:\Uni\Programmi\DiffPy\Python26\lib\site-packages\diffpy.pygsas-1.0b_r6746_20110902-py2.6.egg\diffpy\pygsas\fitloader.py", line 143, in _importPhase
self._importPhaseAtom(phidx1, aidx1)
File "D:\Uni\Programmi\DiffPy\Python26\lib\site-packages\diffpy.pygsas-1.0b_r6746_20110902-py2.6.egg\diffpy\pygsas\fitloader.py", line 164, in _importPhaseAtom
atom.set("Typ", expfile.getValue(akey('ATYP')))
File "D:\Uni\Programmi\DiffPy\Python26\lib\site-packages\diffpy.pygsas-1.0b_r6746_20110902-py2.6.egg\diffpy\pygsas\expfile.py", line 201, in getValue
key = self.getUniqueKey(*keywords)
File "D:\Uni\Programmi\DiffPy\Python26\lib\site-packages\diffpy.pygsas-1.0b_r6746_20110902-py2.6.egg\diffpy\pygsas\expfile.py", line 280, in getUniqueKey
raise KeyError(emsg)
KeyError: "Cannot find unique record for (('CRS1', 'AT10', 'ATYP'),)"

[Pavol Juhas]

Hi Francesco,

Thank you for your report, I will look into this.
Can you email me a GSAS EXP file that triggers this bug?

Best regards,

Pavol

On Nov 22, 5:02 am, dif...@diffpy.org wrote:
> reporter: francesco...@unipr.it
>
> summary: limit in number of atoms?
>
> description: it looks like the program works (very well, congratulations!) for a number of atoms in the structure up to 9. Maybe the nature of the problem is different but troubles come out as I load a structure with 10 or more atoms, also without increasing the number of variables to be refined.
>
> thank you in advance
> best regards,
> Francesco Mezzadri
>
> component: srrietveld
>
> version: 1.0beta-r6746-20110902
>
> traceback:
> Traceback (most recent call last):

>   File "D:\Uni\Programmi\DiffPy\Python26\lib\site-packages\diffpy.srrietveld-1.0be ta_r6746_20110902-py2.6.egg\diffpy\srrietveld\gui\errorwrapper.py", line 61, in _f
>     return func(*args, **kwargs)
>   File "D:\Uni\Programmi\DiffPy\Python26\lib\site-packages\diffpy.srrietveld-1.0be ta_r6746_20110902-py2.6.egg\diffpy\srrietveld\gui\mainframe.py", line 912, in loadExpPcr
>     fit = GLOBALS.project.importEngineFile(fullpath, name)
>   File "D:\Uni\Programmi\DiffPy\Python26\lib\site-packages\diffpy.srrietveld-1.0be ta_r6746_20110902-py2.6.egg\diffpy\srrietveld\project.py", line 332, in importEngineFile
>     enginefit = loadFitFromEXP(fullpath)
>   File "D:\Uni\Programmi\DiffPy\Python26\lib\site-packages\diffpy.pygsas-1.0b_r674 6_20110902-py2.6.egg\diffpy\pygsas\fitloader.py", line 42, in loadFitFromEXP
>     fit = loader(filename)
>   File "D:\Uni\Programmi\DiffPy\Python26\lib\site-packages\diffpy.pygsas-1.0b_r674 6_20110902-py2.6.egg\diffpy\pygsas\fitloader.py", line 77, in __call__
>     self._importPhase(phidx1)
>   File "D:\Uni\Programmi\DiffPy\Python26\lib\site-packages\diffpy.pygsas-1.0b_r674 6_20110902-py2.6.egg\diffpy\pygsas\fitloader.py", line 143, in _importPhase
>     self._importPhaseAtom(phidx1, aidx1)
>   File "D:\Uni\Programmi\DiffPy\Python26\lib\site-packages\diffpy.pygsas-1.0b_r674 6_20110902-py2.6.egg\diffpy\pygsas\fitloader.py", line 164, in _importPhaseAtom

>     atom.set("Typ", expfile.getValue(akey('ATYP')))

>   File "D:\Uni\Programmi\DiffPy\Python26\lib\site-packages\diffpy.pygsas-1.0b_r674 6_20110902-py2.6.egg\diffpy\pygsas\expfile.py", line 201, in getValue
>     key = self.getUniqueKey(*keywords)
>   File "D:\Uni\Programmi\DiffPy\Python26\lib\site-packages\diffpy.pygsas-1.0b_r674 6_20110902-py2.6.egg\diffpy\pygsas\expfile.py", line 280, in getUniqueKey

[Pavol Juhas]

On Wed, Nov 28, 2012 at 09:30:23AM +0100, Francesco Mezzadri wrote:
> Hi Pavol,
> as you ask me I enclose the exp file.
> thank you very much

Hi Francesco,

Unfortunately, it seems SrRietveld cannot handle your EXP file.
The first problem is that SrRietveld assumes sequential
labels for the atom sites, but the actual labels in your file
are AT1-9 followed by AT16-20. I guess this could happen after
removing some sites from the EXP file, but we did not expect such
situation. I tried to fix that bug, but then I hit another stumbling
block. Your project has constraints for spin components in the
magnetic scattering MX, MY, MZ, that are just not supported in
SrRietveld.

The bottom line is your project goes beyond what SrRietveld
can do and it would be too much work to add support for
magnetic refinements.

Sorry about the bad news. With best regards,

Pavol

--
Dr. Pavol Juhas
Condensed Matter Physics and Materials Science Department
building 510B
Brookhaven National Laboratory
P.O. Box 5000
Upton, NY 11973-5000