Re: [Ifeffit] atoms crashes

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 mailto:bravel@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

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-- Bruce Ravel ------------------------------------ bravel@bnl.gov mailto:bravel@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@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

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-- Bruce Ravel ------------------------------------ bravel@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/