[Ifeffit] atoms crashes
Bruce Ravel
bravel at bnl.gov
Fri Jun 3 10:12:08 CDT 2016
It seems as though the crystal data you gave to atoms was slightly
different from what you sent in your first email.
The stack trace suggests that you gave '3.839()' as the value for the A
lattice constant. That is, you included the open and close parentheses,
even though what you sent in your earlier email does not have the parens.
It seems that the mistake is that Atoms allows you to put a string that
is not interpretable as a number in the little box for the value of A.
I had thought I checked against that, but perhaps not. I'll investigate.
The work-around is to be careful that things that are supposed to be
numbers actually are numbers.
The solution is for me to make sure that Atoms checks that the input
data are syntactically correct before it gets used. I will put that on
my to do list.
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