[Ifeffit] atoms crashes

Jesús Eduardo Vega Castillo jevecas at gmail.com
Fri Jun 3 09:47:17 CDT 2016


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 1 Service 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 1 Service 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 en 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 en 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/
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