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 :

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

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 http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

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 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

_______________________________________________ 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

-- 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/

Thank you 2016-06-03 12:24 GMT-03:00 Bruce Ravel :

After a bit more investigation, it seems that the Atoms GUI does, in fact, check that hings like A are interpretable as numbers.

However, the part of the code that attempts to import an atoms.inp or CIF file does not make that same check properly.

So, you have uncovered something that is certainly a bug. Thanks!

For the time being, you need to be sure that the crystal data files you are attempting to read do not have things like "a = 3.839()".

Cheers, B

On 06/03/2016 11:12 AM, Bruce Ravel wrote:

...

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.

-- 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/ _______________________________________________ Ifeffit mailing list 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