[Ifeffit] atoms crashes
Bruce Ravel
bravel at bnl.gov
Fri Jun 3 10:06:05 CDT 2016
Okee doke! I'll look into it.
B
On 06/03/2016 10:47 AM, Jesús Eduardo Vega Castillo wrote:
> Thanks for your answer Bruce,
>
> I had not read the instructions for reporting bugs and that is why I did
> not send the log file. I have found the datoms.log and dartemis.log files:
>
> datoms:
>
> Started at 2016-06-03T11:23:45
> Win7Home Premium (64-bit) Service Pack 1Service Pack 16176012107681
>
> PATH is:
> C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Users\Jesus\AppData\Roaming\DemeterPerl\c\bin;C:\Users\Jesus\AppData\Roaming\DemeterPerl\perl\site\bin;C:\Users\Jesus\AppData\Roaming\DemeterPerl\perl\bin;C:\Users\Jesus\AppData\Roaming\DemeterPerl\c\bin\gnuplot\bin
>
> perl version: v5.18.2
>
> @INC:
> C:/Users/Jesus/AppData/Roaming/DemeterPerl/perl/site/lib/MSWin32-x64-multi-thread
> C:/Users/Jesus/AppData/Roaming/DemeterPerl/perl/site/lib
> C:/Users/Jesus/AppData/Roaming/DemeterPerl/perl/vendor/lib
> C:/Users/Jesus/AppData/Roaming/DemeterPerl/perl/lib
> .
> Demeter version 0.9.24
>
> dartemis:
>
> Started at 2016-06-03T09:02:07
> Win7Home Premium (64-bit) Service Pack 1Service Pack 16176012107681
>
> PATH is:
> C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Users\Jesus\AppData\Roaming\DemeterPerl\c\bin;C:\Users\Jesus\AppData\Roaming\DemeterPerl\perl\site\bin;C:\Users\Jesus\AppData\Roaming\DemeterPerl\perl\bin;C:\Users\Jesus\AppData\Roaming\DemeterPerl\c\bin\gnuplot\bin
>
> perl version: v5.18.2
>
> backend: ifeffit
>
> @INC:
> C:/Users/Jesus/AppData/Roaming/DemeterPerl/perl/site/lib/MSWin32-x64-multi-thread
> C:/Users/Jesus/AppData/Roaming/DemeterPerl/perl/site/lib
> C:/Users/Jesus/AppData/Roaming/DemeterPerl/perl/vendor/lib
> C:/Users/Jesus/AppData/Roaming/DemeterPerl/perl/lib
> .
> Demeter version 0.9.24
>
> Attribute (a) does not pass the type constraint because: Num is not
> larger than or equal to 0 at
> C:\Users\Jesus\AppData\Roaming\DemeterPerl\perl\vendor\lib\Moose\Exception.pm
> line 37
> Moose::Exception::_build_trace('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x133b24c0)')
> called at reader Moose::Exception::trace (defined at
> C:\Users\Jesus\AppData\Roaming\DemeterPerl\perl\vendor\lib\Moose\Exception.pm
> line 9) line 7
> Moose::Exception::trace('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x133b24c0)')
> called at
> C:\Users\Jesus\AppData\Roaming\DemeterPerl\perl\vendor\lib\Moose\Exception.pm
> line 49
> Moose::Exception::BUILD('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x133b24c0)',
> 'HASH(0x13d93c48)') called at
> C:\Users\Jesus\AppData\Roaming\DemeterPerl\perl\vendor\lib\Class\MOP\Method.pm
> line 128
> Class::MOP::Method::execute('Moose::Meta::Method=HASH(0x13771368)',
> 'Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x133b24c0)',
> 'HASH(0x13d93c48)') called at
> C:\Users\Jesus\AppData\Roaming\DemeterPerl\perl\vendor\lib\Moose\Object.pm
> line 56
> Moose::Object::BUILDALL('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x133b24c0)',
> 'HASH(0x13d93c48)') called at
> C:\Users\Jesus\AppData\Roaming\DemeterPerl\perl\vendor\lib\Moose\Meta\Class.pm
> line 282
> Moose::Meta::Class::new_object('Moose::Meta::Class=HASH(0xe21e6e0)',
> 'HASH(0x13d93c48)') called at
> C:\Users\Jesus\AppData\Roaming\DemeterPerl\perl\vendor\lib\Moose\Object.pm
> line 27
> Moose::Object::new('Moose::Exception::ValidationFailedForInlineTypeConstraint',
> 'type_constraint_message', 'Num is not larger than or equal to 0',
> 'class_name', 'Demeter::Atoms', 'attribute_name', 'a', 'value',
> '3.839()') called at
> C:\Users\Jesus\AppData\Roaming\DemeterPerl\perl\vendor\lib\Moose\Util.pm
> line 51
> Moose::Util::throw_exception('ValidationFailedForInlineTypeConstraint',
> 'type_constraint_message', 'Num is not larger than or equal to 0',
> 'class_name', 'Demeter::Atoms', 'attribute_name', 'a', 'value',
> '3.839()') called at accessor Demeter::Atoms::a (defined at
> C:\Users\Jesus\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\Atoms.pm line
> 90) line 4
> Demeter::Atoms::a('Demeter::Atoms=HASH(0xec38948)', '3.839()') called at
> C:\Users\Jesus\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\Atoms\Cif.pm
> line 88
> Demeter::Atoms::Cif::read_cif('Demeter::Atoms=HASH(0xec38948)') called
> at
> C:\Users\Jesus\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\Atoms.pm line
> 208
> Demeter::Atoms::__ANON__('Demeter::Atoms=HASH(0xec38948)', 'F:\XAS
> 2016\XAS\K-Fe\LaSr3Fe3O10.cif', '') called at accessor
> Demeter::Atoms::cif (defined at
> C:\Users\Jesus\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\Atoms.pm line
> 211) line 10
> Demeter::Atoms::cif('Demeter::Atoms=HASH(0xec38948)', 'F:\XAS
> 2016\XAS\K-Fe\LaSr3Fe3O10.cif') called at
> C:\Users\Jesus\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\UI\Atoms\Xtal.pm
> line 650
> Demeter::UI::Atoms::Xtal::open_file('Demeter::UI::Atoms::Xtal=HASH(0x12b5b920)',
> 'F:\XAS 2016\XAS\K-Fe\LaSr3Fe3O10.cif') called at
> C:\Users\Jesus\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\UI\Artemis.pm
> line 1378
> Demeter::UI::Artemis::make_feff_frame('Wx::Frame=HASH(0x136d4ca0)',
> 'F:\XAS 2016\XAS\K-Fe\LaSr3Fe3O10.cif') called at
> C:\Users\Jesus\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\UI\Artemis\Import.pm
> line 177
> Demeter::UI::Artemis::Import::_feff(undef) called at
> C:\Users\Jesus\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\UI\Artemis\Import.pm
> line 39
> Demeter::UI::Artemis::Import::Import('feff') called at
> C:\Users\Jesus\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\UI\Artemis.pm
> line 358
> Demeter::UI::Artemis::__ANON__('Wx::Button=HASH(0x136d6a20)',
> 'Wx::CommandEvent=SCALAR(0x13c37730)') called at
> C:\Users\Jesus\AppData\Roaming\DemeterPerl\perl\site\bin\dartemis.bat
> line 47
> eval {...} at
> C:\Users\Jesus\AppData\Roaming\DemeterPerl\perl\site\bin\dartemis.bat
> line 47
>
> Surprisingly, now the inp file works in atoms. The only thing I did in
> between was to locate the log files. I tried many times before.
>
> Thank you again
>
>
>
>
> 2016-06-03 11:10 GMT-03:00 Bruce Ravel <bravel at bnl.gov
> <mailto:bravel at bnl.gov>>:
>
>
> Your atoms.inp file works for me.
>
> As I say *all* *the* *time* on this list and as I've explained
> clearly online
> (http://bruceravel.github.io/demeter/documents/SinglePage/bugs.html), you
> have to give me enough information to understand the problem.
>
> When something crashes, I need to see the log file that is written
> so I can diagnose the problem. Without that, I can't help.
>
> B
>
>
>
> On 06/03/2016 09:52 AM, Jesús Eduardo Vega Castillo wrote:
>
> Hello everyone,
>
> I have manually introduced the crystal structure of La4Fe3O10
> into Atoms
> and generated and .inp file. The structure contains 2 sites
> of La, 2
> sites of Fe and 4 sites of O.
> When I try to run Atoms from this file it crashes.
>
> This is the inp file:
>
> ## This Atoms file was generated by Demeter 0.9.24
> ## Demeter written by and copyright (c) Bruce Ravel, 2006-2015
>
> title = La4Fe3O10 (LSFC)
> space = I 4/m m m
> a = 3.83900 b = 3.83900 c = 27.87050
> alpha = 90.00000 beta = 90.00000 gamma = 90.00000
> rmax = 5.00000 core = Fe1
> # polarization = 0.0 0.0 0.0
> shift = 0.00000 0.00000 0.00000
> atoms
> # el. x y z tag
> La 0.00000 0.00000 0.56860 La1
> La 0.00000 0.00000 0.70130 La2
> Fe 0.00000 0.00000 0.00000 Fe1
> Fe 0.00000 0.00000 0.13840 Fe2
> O 0.00000 0.50000 0.13810 O1
> O 0.00000 0.00000 0.06980 O2
> O 0.00000 0.00000 0.21050 O3
> O 0.00000 0.50000 0.00000 O4
>
> Any help would be appreciated.
>
> Yours,
>
> Jesús
>
>
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> <mailto:Ifeffit at millenia.cars.aps.anl.gov>
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> Unsubscribe:
> http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
>
>
>
> --
> Bruce Ravel ------------------------------------ bravel at bnl.gov
> <mailto:bravel at bnl.gov>
>
> National Institute of Standards and Technology
> Synchrotron Science Group at NSLS-II
> Building 535A
> Upton NY, 11973
>
> Homepage: http://bruceravel.github.io/home/
> Software: https://github.com/bruceravel
> Demeter: http://bruceravel.github.io/demeter/
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> <mailto:Ifeffit at millenia.cars.aps.anl.gov>
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
>
>
>
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
>
--
Bruce Ravel ------------------------------------ bravel at bnl.gov
National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
Building 535A
Upton NY, 11973
Homepage: http://bruceravel.github.io/home/
Software: https://github.com/bruceravel
Demeter: http://bruceravel.github.io/demeter/
More information about the Ifeffit
mailing list