xrayutilities-users — User mailinglist for xrayutilities

[Xrayutilities-users] Importing CIF file gives interesting response

[Allen H. <aj...@gm...>]

Hi XrayUtilities Mailing list!!

Great python package!!

I'm attempting to use the CIF import to run an RS visualization on a 
substrate (for peak finding purposes), and I'm using the following for 
import:

import os

import numpy
import xrayutilities as xu

# create material
GaAs = xu.materials.Crystal.fromCIF(os.path.join("data", "gaas4.cif"))

The error:
XU.materials: element As used instead of As3-
Traceback (most recent call last):

   File "/Users/allenhall/Desktop/reciprocal 
space/xrayutilities-main/examples/GaAs RSM attempt.py", line 18, in <module>
     geom = xu.HXRD(GaAs.Q(1, 1, 1))

TypeError: __init__() missing 1 required positional argument: 'ndir'

To help in completeness, I'm adding the full text of the CIF file I have 
for GaAs here:

data_43359-ICSD
#©2003 by Fachinformationszentrum Karlsruhe, and the U.S. Secretary of
#Commerce on behalf of the United States.  All rights reserved.
_database_code_ICSD                43359
_audit_creation_date               2000/07/15
_chemical_name_systematic          'Gallium Arsenide'
_chemical_formula_structural       'Ga As'
_chemical_formula_sum              'As1 Ga1'
_publ_section_title
;
An X-ray study of some A(III) B(V) compounds which display deviataion
from stoichoimetry
;
loop_
_citation_id
_citation_journal_abbrev
_citation_year
_citation_journal_volume
_citation_page_first
_citation_page_last
_citation_journal_id_ASTM
primary Kristallografiya 1962 7 850 853 KRISAJ
loop_
_publ_author_name
'Ozolins, G.'
'Averkieva, G.K.'
'Ievins, A.'
'Goryunova, N.A.'
_cell_length_a                     5.65317(10)
_cell_length_b                     5.65317
_cell_length_c                     5.65317
_cell_angle_alpha                  90.
_cell_angle_beta                   90.
_cell_angle_gamma                  90.
_cell_volume                       180.67
_cell_formula_units_Z              4
_symmetry_space_group_name_H-M     'F -4 3 m'
_symmetry_Int_Tables_number        216
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
   1    '-z, -y, x'
   2    '-y, -x, z'
   3    '-x, -z, y'
   4    '-z, -x, y'
   5    '-y, -z, x'
   6    '-x, -y, z'
   7    '-z, y, -x'
   8    '-y, x, -z'
   9    '-x, z, -y'
  10    '-z, x, -y'
  11    '-y, z, -x'
  12    '-x, y, -z'
  13    'z, -y, -x'
  14    'y, -x, -z'
  15    'x, -z, -y'
  16    'z, -x, -y'
  17    'y, -z, -x'
  18    'x, -y, -z'
  19    'z, y, x'
  20    'y, x, z'
  21    'x, z, y'
  22    'z, x, y'
  23    'y, z, x'
  24    'x, y, z'
  25    '-z, -y+1/2, x+1/2'
  26    '-z+1/2, -y, x+1/2'
  27    '-z+1/2, -y+1/2, x'
  28    '-y, -x+1/2, z+1/2'
  29    '-y+1/2, -x, z+1/2'
  30    '-y+1/2, -x+1/2, z'
  31    '-x, -z+1/2, y+1/2'
  32    '-x+1/2, -z, y+1/2'
  33    '-x+1/2, -z+1/2, y'
  34    '-z, -x+1/2, y+1/2'
  35    '-z+1/2, -x, y+1/2'
  36    '-z+1/2, -x+1/2, y'
  37    '-y, -z+1/2, x+1/2'
  38    '-y+1/2, -z, x+1/2'
  39    '-y+1/2, -z+1/2, x'
  40    '-x, -y+1/2, z+1/2'
  41    '-x+1/2, -y, z+1/2'
  42    '-x+1/2, -y+1/2, z'
  43    '-z, y+1/2, -x+1/2'
  44    '-z+1/2, y, -x+1/2'
  45    '-z+1/2, y+1/2, -x'
  46    '-y, x+1/2, -z+1/2'
  47    '-y+1/2, x, -z+1/2'
  48    '-y+1/2, x+1/2, -z'
  49    '-x, z+1/2, -y+1/2'
  50    '-x+1/2, z, -y+1/2'
  51    '-x+1/2, z+1/2, -y'
  52    '-z, x+1/2, -y+1/2'
  53    '-z+1/2, x, -y+1/2'
  54    '-z+1/2, x+1/2, -y'
  55    '-y, z+1/2, -x+1/2'
  56    '-y+1/2, z, -x+1/2'
  57    '-y+1/2, z+1/2, -x'
  58    '-x, y+1/2, -z+1/2'
  59    '-x+1/2, y, -z+1/2'
  60    '-x+1/2, y+1/2, -z'
  61    'z, -y+1/2, -x+1/2'
  62    'z+1/2, -y, -x+1/2'
  63    'z+1/2, -y+1/2, -x'
  64    'y, -x+1/2, -z+1/2'
  65    'y+1/2, -x, -z+1/2'
  66    'y+1/2, -x+1/2, -z'
  67    'x, -z+1/2, -y+1/2'
  68    'x+1/2, -z, -y+1/2'
  69    'x+1/2, -z+1/2, -y'
  70    'z, -x+1/2, -y+1/2'
  71    'z+1/2, -x, -y+1/2'
  72    'z+1/2, -x+1/2, -y'
  73    'y, -z+1/2, -x+1/2'
  74    'y+1/2, -z, -x+1/2'
  75    'y+1/2, -z+1/2, -x'
  76    'x, -y+1/2, -z+1/2'
  77    'x+1/2, -y, -z+1/2'
  78    'x+1/2, -y+1/2, -z'
  79    'z, y+1/2, x+1/2'
  80    'z+1/2, y, x+1/2'
  81    'z+1/2, y+1/2, x'
  82    'y, x+1/2, z+1/2'
  83    'y+1/2, x, z+1/2'
  84    'y+1/2, x+1/2, z'
  85    'x, z+1/2, y+1/2'
  86    'x+1/2, z, y+1/2'
  87    'x+1/2, z+1/2, y'
  88    'z, x+1/2, y+1/2'
  89    'z+1/2, x, y+1/2'
  90    'z+1/2, x+1/2, y'
  91    'y, z+1/2, x+1/2'
  92    'y+1/2, z, x+1/2'
  93    'y+1/2, z+1/2, x'
  94    'x, y+1/2, z+1/2'
  95    'x+1/2, y, z+1/2'
  96    'x+1/2, y+1/2, z'
loop_
_atom_type_symbol
_atom_type_oxidation_number
As3-      -3
Ga3+      3
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_symmetry_multiplicity
_atom_site_Wyckoff_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
_atom_site_attached_hydrogens
Ga1 Ga3+ 4 a 0 0 0 1. 0
As2 As3- 4 c 0.25 0.25 0.25 1. 0

#End of data_43359-ICSD



-- 
Allen Hall
aj...@gm...
al...@il...

[Xrayutilities-users] xrayutilities-1.7.3 release notification

[Dominik K. <dom...@gm...>]

xrayutilities-1.7.3 is available.

The release was necessary since the previous version had some broken files
on PyPI [1]. It is otherwise equivalent with version 1.7.2. Python wheel
packages are now provided in an updated format for versions 3.6 to 3.10 [1].

If you encounter problems, please report them on Github [2] or on the
mailinglist [3]

[1] https://pypi.python.org/pypi/xrayutilities
[2] https://github.com/dkriegner/xrayutilities/
[3] https://sourceforge.net/p/xrayutilities/mailman/xrayutilities-users/

[Xrayutilities-users] xrayutilities 1.7.2 release notification

[Dominik K. <dom...@gm...>]

xrayutilities-1.7.2 is available.

This version is compatible with Python >3.6.

Version 1.7.2 contains some bug fixes and is compatible with matplotlib
3.5. Details can be found in the Changes.txt file [1].

In order to obtain the new version, go to SourceForge [2] or use PyPI [3].
Wheel packages for Windows, macOS and Linux are found on PyPI for 64-bit
Python in versions 3.6, 3.7, 3.8, and 3.9. Python 3.10 is also supported,
but currently no wheel packages can be provided. There is also a
conda-forge package [4] which should make installing for Conda users more
straightforward.
If you encounter problems, please report them on GitHub or on the
mailinglist [5].

[1] https://github.com/dkriegner/xrayutilities/blob/main/CHANGES.txt
[2] https://sourceforge.net/projects/xrayutilities
[3] https://pypi.python.org/pypi/xrayutilities
[4] https://github.com/conda-forge/xrayutilities-feedstock
[5] https://sourceforge.net/p/xrayutilities/mailman/xrayutilities-users/

[Xrayutilities-users] how to install the latest GIT version of xrayutilities

[Dominik K. <dom...@gm...>]

Dear xrayutilities users,

This is an updated version of how to install the latest GIT master [1] of
xrayutilities.

Upon questions and bug reports it is usually a good idea to reproduce your
problem with the latest GIT version. Since installation from source
requires a working C-compiler sometimes people have problems with this.
However, every change on GIT master triggers automatic building of Python
wheel files [2], hence obtaining the latest development version is rather
easy.

Just run:
pip install --user --upgrade xrayutilities --extra-index-url
https://pkgs.dev.azure.com/dominikkriegner/xrayutilities/_packaging/xrayutilities-dev/pypi/simple

Likely you want the '--user' option as included above to not interfere with
your system packages. But variations of this command are of course possible.

On systems with appropriate C-compiler (manual/alternative version) you
also can:

1) download the latest git version either by GIT or from the following link:
https://github.com/dkriegner/xrayutilities/archive/master.zip
2)  open a command line with access to your python executables and go to
the folder where you have the 'xrayutilities' source files.
3) run 'pip install .' or variants thereof outlined in the Readme [3].

cheers
dominik

[1] https://sourceforge.net/p/xrayutilities/mailman/message/36512225/
[2]
https://dev.azure.com/dominikkriegner/xrayutilities/_packaging?_a=feed&feed=xrayutilities-dev
[3] https://github.com/dkriegner/xrayutilities#installation-source

Re: [Xrayutilities-users] conversion of an image from an area detector

[Dominik K. <dom...@gm...>]

Dear Ruggero,

It seems to me everyone using xrayutilities for the first time has problems
with the directions. If somebody sees how one can explain this better in
some documentation I would appreciate suggestions for changes. From the
many discussions I have had so far it always turns out that different
people use different coordinate frames and not always all things are
adjusted according to their imagination and it's not always obvious what
everything is autoadjusted by xrayutilities.

One thing which is not clear to me from the pseudoscript you sent in your
first email is if you redefined the goniometer rotation directions?
FourC assumes the following which is in contrast to what you write in your
email with a detector rotation around z. If you deviate from this system
you have to specify a custom 'qconv' in the constructor of FourC:
sample geometry(3): x+y+z-
detector geometry(1): x+
primary beam direction: ( 0.00  1.00  0.00)
This could be a potential source of confusion because what you call surface
normal is likely determined by the detector rotation plane! The surface
normal is also configurable in xrayutilities by "sampleor" parameter to the
constructor of Experiment classes. I copied the relevant documentation to
the end of this email!

I can further not comment on the specific directions you write because all
obviously depends on your a,b,c, alpha,beta, gamma.

kind regards
Dominik

from the docstring of Experiment._set_transform:
        The sampleor variable determines the sample surface orientation with
        respect to the coordinate system in which the goniometer rotations
are
        given. You can use the [xyz][+-] syntax to specify the nominal
surface
        orientation (when all goniometer angles are zero). In addition two
        special values 'det' and 'sam' are available, which will let the
code
        determine the orientation from either the inner most detector or
sample
        rotation. 'det' means the surface is in the plane spanned by the
inner
        most detector rotation (rotation around primary beam is ignored) and
        perpendicular to the primary beam. 'sam' means the surface
orientation
        is along the innermost sample circles rotation direction (in this
case
        this should be the azimuth motor to yield the expected results).
        Default is 'det'.

On Sat, Dec 12, 2020 at 1:45 AM ruggero frison <rug...@uz...>
wrote:

> Dear Dominik,
>
> thanks for the explanation.
>
> I see.
> The Q2AngFit works but unfortunately not at best since with reasonable
> bounds the fit converges to values that do not match my experimental ones.
> This suggest me that one possibility is that the experimental parameters
> are not all correct.
>
> One thing I am not sure about is still the call to FourC, where the second
> direction should be the out of plane one. Setting such that
> hxrd = xu.FourC(sample.Q(1, 0, 0), sample.Q(0, 1, 0), en=energy)
> The normal to the scattering plane results in: (0.000000 0.000000
> -1.000000).
> But in my experiment the scattering plane is the a,c-plane, which is also
> the xy-plane of the reference system when the angles are at 0. The detector
> rotates with 2th around the z-axis, so in the xy-plane.
> So I would think that the second direction in FourC should be (0,0,1).
>
> In any case thank you for your help.
>
> Best
> Ruggero
>
>
>
> > On 11 Dec 2020, at 13:14, Dominik Kriegner <dom...@gm...>
> wrote:
> >
> > Dear Ruggero
> >
> > Actually using Q2Ang for consistency checks is not really feasible.
> > Let me explain why:
> > Q2Ang takes the orientation of the material from the definition of
> "hxrd" (in your case FourC).
> > This is somehow elaborate and likely by default fits best applications
> of thin film diffraction.
> > The two directions you specify in the constructor of FourC define the
> crystal axis which is along the primary beam (when all goniometer angles
> are at zero) and a second direction which for the thin film case
> corresponds to the out of plane direction. In fact the meaning of the
> second direction also depends on the setting of the optional 'sample_or'.
> So yes you can set the sample orientation. I see that somebody would want
> to set this directly using an orientation matrix. Maybe you could report an
> issue on github about this if you agree.
> >
> > But there is a more fundamental problem why Q2Ang likely will not be
> useful for you: You basically want to determine four goniometer angles from
> three reciprocal space coordinates/Miller indices. So the problem is
> overdetermined.
> > The implementation of Q2Ang in FourC (and HXRD) make some assumptions
> about how to angles are calculated (in fact they turn the sample to obtain
> a coplanar setting of incidence/diffracted and surface normal). There is
> also NonCOP which describes the same goniometer with a different Q2Ang
> implementation. For your 2D detector both will likely not help. There is an
> alternative, however, look at Q2AngFit. There you can define your own
> orientation matrix and other geometrical restrictions and the function by
> numerical optimization determines the diffraction angles. [1]
> >
> > cheers
> > dominik
> >
> > [1]
> https://xrayutilities.sourceforge.io/examples.html#calculation-of-diffraction-angles-for-a-general-geometry
> > ps: I realized now a major problem in the documentation (both online and
> in the pdf) which do not contain the docstrings of __init__ functions. I
> will fix this asap.
> >
> > On Fri, Dec 11, 2020 at 11:59 AM ruggero frison <rug...@uz...>
> wrote:
> > Dear Dominik,
> >
> > thank you.
> > That helped and things work thought the results are not fully consisten
> with the experiment, but it might be
> > some little error that I hope I will figure out myself with a more
> careful look at.
> >
> > One more thing. To check the results I understand that I could use Q2Ang.
> > I expect the return values of Q2Ang should match the experimental values.
> > Where from the Q2Ang gets the sample orientation?
> >
> > In the example xrayutilities_angular2hkl_conversion.py  there is:
> > [om, chi, phi, tt] = hxrd.Q2Ang(mat.Q(H, K, L))
> >
> > Is there a way to set the sample orientation?
> >
> > Thank you
> >
> > Best regards
> > Ruggero
> >
> >
> >
> > > On 11 Dec 2020, at 00:37, Dominik Kriegner <dom...@gm...>
> wrote:
> > >
> > > Dear Ruggero,
> > >
> > > I think you seemed to look more or less in the right places. I see
> three problems in the the dummy script you sent:
> > >
> > > 1) I am not sure which version or xrayutilities you are using but
> reasonable up to date versions the material definition would need to be
> > > sam = xu.materials.material.Crystal('sample1',
> xu.materials.SGLattice(1, *abcabg))
> > >
> > > 2) Since you say you are describing a four circle machine you should
> likely use FourC
> > > hxrd = xu.FourC(sam.Q(-2, 0, 0), sam.Q(0, 0, -4), en=energy)
> > > you then will need to specify chi and phi in your call to Ang2HKL
> > >
> > > 3) Ang2HKL takes an optional parameter dettype [1]. This should in
> your case likely be set to 'area'
> > > h,k,l = hxrd.Ang2HKL(omega, chi, phi, towtheta, U=ubmat,
> dettype='area')
> > >
> > > h,k,l should then be matrices of the shape (Nch1, Nch2) for every
> angular position you specify. If you specify arrays of angles h,k,l will be
> three dimensional arrays with according dimensions.
> > >
> > > I hope this helps.
> > >
> > > kind regards
> > > Dominik
> > >
> > > [1]
> https://xrayutilities.sourceforge.io/xrayutilities.html?highlight=ang2hkl#xrayutilities.experiment.Experiment.Ang2HKL
> > >
> > > On Thu, Dec 10, 2020 at 6:38 PM ruggero frison <rug...@uz...>
> wrote:
> > > >
> > > > Hello,
> > > >
> > > > I would need some help, I am trying to index a frame of an Area
> detector into hkl coordinateds following the example provided in Appendix B
> of the reference paper and in some scripts provided in the example folder
> of the distribution.
> > > >
> > > > I have some frames of an area detector with a 4-circles Eulerian
> cradle.
> > > >
> > > > I paste below a dummy script, which
> > > > I prepared a script building on the examples but it does not give
> results, I do not understand why.
> > > > I guess because I do not understand the underlying action of
> xrayutilities.
> > > >
> > > > I understand that Ang2HKL would create the arrays of hkl vlaues
> using the experimental angles.
> > > > Thus I could feed it with the scan parameters I retrieve from the
> scan files and the UB matrix determined during the sample alignment.
> > > >
> > > > Would that work or I am getting wrong?
> > > >
> > > > I paste below a dummy script to avoid useless details.
> > > >
> > > > Thanks
> > > >
> > > > Best regards
> > > >
> > > > Ruggero
> > > >
> > > >
> > > > ##__set the material
> > > > abcabg = [a,b,c,alpha, beta, gamma]
> > > > sam = xru.materials.material.Crystal(’sample1', abcabg)
> > > >
> > > > ##__the UB matrix is retrieved during the experiment
> > > > ubmat = np.array([[1.364,-0.131,0.270],[-0.044, 1.639,
> 0.083],[-0.950, -0.264, 0.384]])
> > > >
> > > >
> > > > ##__load the frame and associated parameter file to get scan
> parameters,
> > > > omega, twotheta, chi, phi, energy, detector_distance = ...
> > > >
> > > > ##__fix detector spec
> > > >
> > > > #__define experiment geometry
> > > > hxrd = xru.HXRD(sam.Q(-2, 0, 0), sam.Q(0, 0, -4), en=energy)
> > > >
> > > > ##__assign orientation matrix
> > > > hxrd.Ang2Q.init_area('z+','x+', cch1=cpix, cch2=cpiy, Nch1=npix,
> Nch2=npiy,
> > > >  pwidth1=xpix, pwidth2=ypix, distance=sam_det)
> > > >
> > > > ## conversion to h,k,l
> > > > h,k,l = hxrd.Ang2HKL(omega, towtheta, U=ubmat)
> > > >
> > > >
> > > >
> > > > ==================================================================
> > > > Ruggero Frison
> > > > University of Zurich, Physik Institut
> > > >
> > > > Winterthurerstrasse 190
> > > > CH-8057 Zurich, Switzerland
> > > > Office: Y36-H-76
> > > > Phone: +41 44 635 5780
> > > > ==================================================================
> > > >
> > > >
> > > >
> > > >
> > > > _______________________________________________
> > > > xrayutilities-users mailing list
> > > > xra...@li...
> > > > https://lists.sourceforge.net/lists/listinfo/xrayutilities-users
> >
>
>

Re: [Xrayutilities-users] conversion of an image from an area detector

[ruggero f. <rug...@uz...>]

Dear Dominik,

thanks for the explanation.

I see.
The Q2AngFit works but unfortunately not at best since with reasonable bounds the fit converges to values that do not match my experimental ones.
This suggest me that one possibility is that the experimental parameters are not all correct.

One thing I am not sure about is still the call to FourC, where the second direction should be the out of plane one. Setting such that
hxrd = xu.FourC(sample.Q(1, 0, 0), sample.Q(0, 1, 0), en=energy)
The normal to the scattering plane results in: (0.000000 0.000000 -1.000000).
But in my experiment the scattering plane is the a,c-plane, which is also the xy-plane of the reference system when the angles are at 0. The detector rotates with 2th around the z-axis, so in the xy-plane.
So I would think that the second direction in FourC should be (0,0,1).

In any case thank you for your help.

Best
Ruggero



> On 11 Dec 2020, at 13:14, Dominik Kriegner <dom...@gm...> wrote:
> 
> Dear Ruggero
> 
> Actually using Q2Ang for consistency checks is not really feasible.
> Let me explain why:
> Q2Ang takes the orientation of the material from the definition of "hxrd" (in your case FourC). 
> This is somehow elaborate and likely by default fits best applications of thin film diffraction.
> The two directions you specify in the constructor of FourC define the crystal axis which is along the primary beam (when all goniometer angles are at zero) and a second direction which for the thin film case corresponds to the out of plane direction. In fact the meaning of the second direction also depends on the setting of the optional 'sample_or'. So yes you can set the sample orientation. I see that somebody would want to set this directly using an orientation matrix. Maybe you could report an issue on github about this if you agree.
> 
> But there is a more fundamental problem why Q2Ang likely will not be useful for you: You basically want to determine four goniometer angles from three reciprocal space coordinates/Miller indices. So the problem is overdetermined.
> The implementation of Q2Ang in FourC (and HXRD) make some assumptions about how to angles are calculated (in fact they turn the sample to obtain a coplanar setting of incidence/diffracted and surface normal). There is also NonCOP which describes the same goniometer with a different Q2Ang implementation. For your 2D detector both will likely not help. There is an alternative, however, look at Q2AngFit. There you can define your own orientation matrix and other geometrical restrictions and the function by numerical optimization determines the diffraction angles. [1]
> 
> cheers
> dominik
> 
> [1] https://xrayutilities.sourceforge.io/examples.html#calculation-of-diffraction-angles-for-a-general-geometry
> ps: I realized now a major problem in the documentation (both online and in the pdf) which do not contain the docstrings of __init__ functions. I will fix this asap.
> 
> On Fri, Dec 11, 2020 at 11:59 AM ruggero frison <rug...@uz...> wrote:
> Dear Dominik,
> 
> thank you.
> That helped and things work thought the results are not fully consisten with the experiment, but it might be 
> some little error that I hope I will figure out myself with a more careful look at.
> 
> One more thing. To check the results I understand that I could use Q2Ang.
> I expect the return values of Q2Ang should match the experimental values.
> Where from the Q2Ang gets the sample orientation? 
> 
> In the example xrayutilities_angular2hkl_conversion.py  there is:
> [om, chi, phi, tt] = hxrd.Q2Ang(mat.Q(H, K, L))
> 
> Is there a way to set the sample orientation?
> 
> Thank you
> 
> Best regards
> Ruggero 
> 
> 
> 
> > On 11 Dec 2020, at 00:37, Dominik Kriegner <dom...@gm...> wrote:
> > 
> > Dear Ruggero,
> > 
> > I think you seemed to look more or less in the right places. I see three problems in the the dummy script you sent:
> > 
> > 1) I am not sure which version or xrayutilities you are using but reasonable up to date versions the material definition would need to be
> > sam = xu.materials.material.Crystal('sample1', xu.materials.SGLattice(1, *abcabg))
> > 
> > 2) Since you say you are describing a four circle machine you should likely use FourC
> > hxrd = xu.FourC(sam.Q(-2, 0, 0), sam.Q(0, 0, -4), en=energy)
> > you then will need to specify chi and phi in your call to Ang2HKL
> > 
> > 3) Ang2HKL takes an optional parameter dettype [1]. This should in your case likely be set to 'area'
> > h,k,l = hxrd.Ang2HKL(omega, chi, phi, towtheta, U=ubmat, dettype='area')
> > 
> > h,k,l should then be matrices of the shape (Nch1, Nch2) for every angular position you specify. If you specify arrays of angles h,k,l will be three dimensional arrays with according dimensions.
> > 
> > I hope this helps.
> > 
> > kind regards
> > Dominik
> > 
> > [1] https://xrayutilities.sourceforge.io/xrayutilities.html?highlight=ang2hkl#xrayutilities.experiment.Experiment.Ang2HKL
> > 
> > On Thu, Dec 10, 2020 at 6:38 PM ruggero frison <rug...@uz...> wrote:
> > >
> > > Hello,
> > >
> > > I would need some help, I am trying to index a frame of an Area detector into hkl coordinateds following the example provided in Appendix B of the reference paper and in some scripts provided in the example folder of the distribution.
> > >
> > > I have some frames of an area detector with a 4-circles Eulerian cradle.
> > >
> > > I paste below a dummy script, which
> > > I prepared a script building on the examples but it does not give results, I do not understand why.
> > > I guess because I do not understand the underlying action of xrayutilities.
> > >
> > > I understand that Ang2HKL would create the arrays of hkl vlaues using the experimental angles.
> > > Thus I could feed it with the scan parameters I retrieve from the scan files and the UB matrix determined during the sample alignment.
> > >
> > > Would that work or I am getting wrong?
> > >
> > > I paste below a dummy script to avoid useless details.
> > >
> > > Thanks
> > >
> > > Best regards
> > >
> > > Ruggero
> > >
> > >
> > > ##__set the material
> > > abcabg = [a,b,c,alpha, beta, gamma]
> > > sam = xru.materials.material.Crystal(’sample1', abcabg)
> > >
> > > ##__the UB matrix is retrieved during the experiment
> > > ubmat = np.array([[1.364,-0.131,0.270],[-0.044, 1.639, 0.083],[-0.950, -0.264, 0.384]])
> > >
> > >
> > > ##__load the frame and associated parameter file to get scan parameters,
> > > omega, twotheta, chi, phi, energy, detector_distance = ...
> > >
> > > ##__fix detector spec
> > >
> > > #__define experiment geometry
> > > hxrd = xru.HXRD(sam.Q(-2, 0, 0), sam.Q(0, 0, -4), en=energy)
> > >
> > > ##__assign orientation matrix
> > > hxrd.Ang2Q.init_area('z+','x+', cch1=cpix, cch2=cpiy, Nch1=npix, Nch2=npiy,
> > >  pwidth1=xpix, pwidth2=ypix, distance=sam_det)
> > >
> > > ## conversion to h,k,l
> > > h,k,l = hxrd.Ang2HKL(omega, towtheta, U=ubmat)
> > >
> > >
> > >
> > > ==================================================================
> > > Ruggero Frison
> > > University of Zurich, Physik Institut
> > >
> > > Winterthurerstrasse 190
> > > CH-8057 Zurich, Switzerland
> > > Office: Y36-H-76
> > > Phone: +41 44 635 5780
> > > ==================================================================
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > xrayutilities-users mailing list
> > > xra...@li...
> > > https://lists.sourceforge.net/lists/listinfo/xrayutilities-users
> 

Re: [Xrayutilities-users] conversion of an image from an area detector

[Dominik K. <dom...@gm...>]

Dear Ruggero

Actually using Q2Ang for consistency checks is not really feasible.
Let me explain why:
Q2Ang takes the orientation of the material from the definition of "hxrd"
(in your case FourC).
This is somehow elaborate and likely by default fits best applications of
thin film diffraction.
The two directions you specify in the constructor of FourC define the
crystal axis which is along the primary beam (when all goniometer angles
are at zero) and a second direction which for the thin film case
corresponds to the out of plane direction. In fact the meaning of
the second direction also depends on the setting of the optional
'sample_or'. So yes you can set the sample orientation. I see that somebody
would want to set this directly using an orientation matrix. Maybe you
could report an issue on github about this if you agree.

But there is a more fundamental problem why Q2Ang likely will not be useful
for you: You basically want to determine four goniometer angles from three
reciprocal space coordinates/Miller indices. So the problem is
overdetermined.
The implementation of Q2Ang in FourC (and HXRD) make some assumptions about
how to angles are calculated (in fact they turn the sample to obtain a
coplanar setting of incidence/diffracted and surface normal). There is also
NonCOP which describes the same goniometer with a different Q2Ang
implementation. For your 2D detector both will likely not help. There is an
alternative, however, look at Q2AngFit. There you can define your own
orientation matrix and other geometrical restrictions and the function by
numerical optimization determines the diffraction angles. [1]

cheers
dominik

[1]
https://xrayutilities.sourceforge.io/examples.html#calculation-of-diffraction-angles-for-a-general-geometry
ps: I realized now a major problem in the documentation (both online and in
the pdf) which do not contain the docstrings of __init__ functions. I will
fix this asap.

On Fri, Dec 11, 2020 at 11:59 AM ruggero frison <rug...@uz...>
wrote:

> Dear Dominik,
>
> thank you.
> That helped and things work thought the results are not fully consisten
> with the experiment, but it might be
> some little error that I hope I will figure out myself with a more careful
> look at.
>
> One more thing. To check the results I understand that I could use Q2Ang.
> I expect the return values of Q2Ang should match the experimental values.
> Where from the Q2Ang gets the sample orientation?
>
> In the example xrayutilities_angular2hkl_conversion.py  there is:
> [om, chi, phi, tt] = hxrd.Q2Ang(mat.Q(H, K, L))
>
> Is there a way to set the sample orientation?
>
> Thank you
>
> Best regards
> Ruggero
>
>
>
> > On 11 Dec 2020, at 00:37, Dominik Kriegner <dom...@gm...>
> wrote:
> >
> > Dear Ruggero,
> >
> > I think you seemed to look more or less in the right places. I see three
> problems in the the dummy script you sent:
> >
> > 1) I am not sure which version or xrayutilities you are using but
> reasonable up to date versions the material definition would need to be
> > sam = xu.materials.material.Crystal('sample1', xu.materials.SGLattice(1,
> *abcabg))
> >
> > 2) Since you say you are describing a four circle machine you should
> likely use FourC
> > hxrd = xu.FourC(sam.Q(-2, 0, 0), sam.Q(0, 0, -4), en=energy)
> > you then will need to specify chi and phi in your call to Ang2HKL
> >
> > 3) Ang2HKL takes an optional parameter dettype [1]. This should in your
> case likely be set to 'area'
> > h,k,l = hxrd.Ang2HKL(omega, chi, phi, towtheta, U=ubmat, dettype='area')
> >
> > h,k,l should then be matrices of the shape (Nch1, Nch2) for every
> angular position you specify. If you specify arrays of angles h,k,l will be
> three dimensional arrays with according dimensions.
> >
> > I hope this helps.
> >
> > kind regards
> > Dominik
> >
> > [1]
> https://xrayutilities.sourceforge.io/xrayutilities.html?highlight=ang2hkl#xrayutilities.experiment.Experiment.Ang2HKL
> >
> > On Thu, Dec 10, 2020 at 6:38 PM ruggero frison <rug...@uz...>
> wrote:
> > >
> > > Hello,
> > >
> > > I would need some help, I am trying to index a frame of an Area
> detector into hkl coordinateds following the example provided in Appendix B
> of the reference paper and in some scripts provided in the example folder
> of the distribution.
> > >
> > > I have some frames of an area detector with a 4-circles Eulerian
> cradle.
> > >
> > > I paste below a dummy script, which
> > > I prepared a script building on the examples but it does not give
> results, I do not understand why.
> > > I guess because I do not understand the underlying action of
> xrayutilities.
> > >
> > > I understand that Ang2HKL would create the arrays of hkl vlaues using
> the experimental angles.
> > > Thus I could feed it with the scan parameters I retrieve from the scan
> files and the UB matrix determined during the sample alignment.
> > >
> > > Would that work or I am getting wrong?
> > >
> > > I paste below a dummy script to avoid useless details.
> > >
> > > Thanks
> > >
> > > Best regards
> > >
> > > Ruggero
> > >
> > >
> > > ##__set the material
> > > abcabg = [a,b,c,alpha, beta, gamma]
> > > sam = xru.materials.material.Crystal(’sample1', abcabg)
> > >
> > > ##__the UB matrix is retrieved during the experiment
> > > ubmat = np.array([[1.364,-0.131,0.270],[-0.044, 1.639, 0.083],[-0.950,
> -0.264, 0.384]])
> > >
> > >
> > > ##__load the frame and associated parameter file to get scan
> parameters,
> > > omega, twotheta, chi, phi, energy, detector_distance = ...
> > >
> > > ##__fix detector spec
> > >
> > > #__define experiment geometry
> > > hxrd = xru.HXRD(sam.Q(-2, 0, 0), sam.Q(0, 0, -4), en=energy)
> > >
> > > ##__assign orientation matrix
> > > hxrd.Ang2Q.init_area('z+','x+', cch1=cpix, cch2=cpiy, Nch1=npix,
> Nch2=npiy,
> > >  pwidth1=xpix, pwidth2=ypix, distance=sam_det)
> > >
> > > ## conversion to h,k,l
> > > h,k,l = hxrd.Ang2HKL(omega, towtheta, U=ubmat)
> > >
> > >
> > >
> > > ==================================================================
> > > Ruggero Frison
> > > University of Zurich, Physik Institut
> > >
> > > Winterthurerstrasse 190
> > > CH-8057 Zurich, Switzerland
> > > Office: Y36-H-76
> > > Phone: +41 44 635 5780
> > > ==================================================================
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > xrayutilities-users mailing list
> > > xra...@li...
> > > https://lists.sourceforge.net/lists/listinfo/xrayutilities-users
>
>

Re: [Xrayutilities-users] conversion of an image from an area detector

[ruggero f. <rug...@uz...>]

Dear Dominik,

thank you.
That helped and things work thought the results are not fully consisten with the experiment, but it might be 
some little error that I hope I will figure out myself with a more careful look at.

One more thing. To check the results I understand that I could use Q2Ang.
I expect the return values of Q2Ang should match the experimental values.
Where from the Q2Ang gets the sample orientation? 

In the example xrayutilities_angular2hkl_conversion.py  there is:
[om, chi, phi, tt] = hxrd.Q2Ang(mat.Q(H, K, L))

Is there a way to set the sample orientation?

Thank you

Best regards
Ruggero 



> On 11 Dec 2020, at 00:37, Dominik Kriegner <dom...@gm...> wrote:
> 
> Dear Ruggero,
> 
> I think you seemed to look more or less in the right places. I see three problems in the the dummy script you sent:
> 
> 1) I am not sure which version or xrayutilities you are using but reasonable up to date versions the material definition would need to be
> sam = xu.materials.material.Crystal('sample1', xu.materials.SGLattice(1, *abcabg))
> 
> 2) Since you say you are describing a four circle machine you should likely use FourC
> hxrd = xu.FourC(sam.Q(-2, 0, 0), sam.Q(0, 0, -4), en=energy)
> you then will need to specify chi and phi in your call to Ang2HKL
> 
> 3) Ang2HKL takes an optional parameter dettype [1]. This should in your case likely be set to 'area'
> h,k,l = hxrd.Ang2HKL(omega, chi, phi, towtheta, U=ubmat, dettype='area')
> 
> h,k,l should then be matrices of the shape (Nch1, Nch2) for every angular position you specify. If you specify arrays of angles h,k,l will be three dimensional arrays with according dimensions.
> 
> I hope this helps.
> 
> kind regards
> Dominik
> 
> [1] https://xrayutilities.sourceforge.io/xrayutilities.html?highlight=ang2hkl#xrayutilities.experiment.Experiment.Ang2HKL
> 
> On Thu, Dec 10, 2020 at 6:38 PM ruggero frison <rug...@uz...> wrote:
> >
> > Hello,
> >
> > I would need some help, I am trying to index a frame of an Area detector into hkl coordinateds following the example provided in Appendix B of the reference paper and in some scripts provided in the example folder of the distribution.
> >
> > I have some frames of an area detector with a 4-circles Eulerian cradle.
> >
> > I paste below a dummy script, which
> > I prepared a script building on the examples but it does not give results, I do not understand why.
> > I guess because I do not understand the underlying action of xrayutilities.
> >
> > I understand that Ang2HKL would create the arrays of hkl vlaues using the experimental angles.
> > Thus I could feed it with the scan parameters I retrieve from the scan files and the UB matrix determined during the sample alignment.
> >
> > Would that work or I am getting wrong?
> >
> > I paste below a dummy script to avoid useless details.
> >
> > Thanks
> >
> > Best regards
> >
> > Ruggero
> >
> >
> > ##__set the material
> > abcabg = [a,b,c,alpha, beta, gamma]
> > sam = xru.materials.material.Crystal(’sample1', abcabg)
> >
> > ##__the UB matrix is retrieved during the experiment
> > ubmat = np.array([[1.364,-0.131,0.270],[-0.044, 1.639, 0.083],[-0.950, -0.264, 0.384]])
> >
> >
> > ##__load the frame and associated parameter file to get scan parameters,
> > omega, twotheta, chi, phi, energy, detector_distance = ...
> >
> > ##__fix detector spec
> >
> > #__define experiment geometry
> > hxrd = xru.HXRD(sam.Q(-2, 0, 0), sam.Q(0, 0, -4), en=energy)
> >
> > ##__assign orientation matrix
> > hxrd.Ang2Q.init_area('z+','x+', cch1=cpix, cch2=cpiy, Nch1=npix, Nch2=npiy,
> >  pwidth1=xpix, pwidth2=ypix, distance=sam_det)
> >
> > ## conversion to h,k,l
> > h,k,l = hxrd.Ang2HKL(omega, towtheta, U=ubmat)
> >
> >
> >
> > ==================================================================
> > Ruggero Frison
> > University of Zurich, Physik Institut
> >
> > Winterthurerstrasse 190
> > CH-8057 Zurich, Switzerland
> > Office: Y36-H-76
> > Phone: +41 44 635 5780
> > ==================================================================
> >
> >
> >
> >
> > _______________________________________________
> > xrayutilities-users mailing list
> > xra...@li...
> > https://lists.sourceforge.net/lists/listinfo/xrayutilities-users

Re: [Xrayutilities-users] conversion of an image from an area detector

[Dominik K. <dom...@gm...>]

Dear Ruggero,

I think you seemed to look more or less in the right places. I see three
problems in the the dummy script you sent:

1) I am not sure which version or xrayutilities you are using but
reasonable up to date versions the material definition would need to be
sam = xu.materials.material.Crystal('sample1', xu.materials.SGLattice(1,
*abcabg))

2) Since you say you are describing a four circle machine you should likely
use FourC
hxrd = xu.FourC(sam.Q(-2, 0, 0), sam.Q(0, 0, -4), en=energy)
you then will need to specify chi and phi in your call to Ang2HKL

3) Ang2HKL takes an optional parameter dettype [1]. This should in your
case likely be set to 'area'
h,k,l = hxrd.Ang2HKL(omega, chi, phi, towtheta, U=ubmat, dettype='area')

h,k,l should then be matrices of the shape (Nch1, Nch2) for every angular
position you specify. If you specify arrays of angles h,k,l will be three
dimensional arrays with according dimensions.

I hope this helps.

kind regards
Dominik

[1]
https://xrayutilities.sourceforge.io/xrayutilities.html?highlight=ang2hkl#xrayutilities.experiment.Experiment.Ang2HKL

On Thu, Dec 10, 2020 at 6:38 PM ruggero frison <rug...@uz...>
wrote:
>
> Hello,
>
> I would need some help, I am trying to index a frame of an Area detector
into hkl coordinateds following the example provided in Appendix B of the
reference paper and in some scripts provided in the example folder of the
distribution.
>
> I have some frames of an area detector with a 4-circles Eulerian cradle.
>
> I paste below a dummy script, which
> I prepared a script building on the examples but it does not give
results, I do not understand why.
> I guess because I do not understand the underlying action of
xrayutilities.
>
> I understand that Ang2HKL would create the arrays of hkl vlaues using the
experimental angles.
> Thus I could feed it with the scan parameters I retrieve from the scan
files and the UB matrix determined during the sample alignment.
>
> Would that work or I am getting wrong?
>
> I paste below a dummy script to avoid useless details.
>
> Thanks
>
> Best regards
>
> Ruggero
>
>
> ##__set the material
> abcabg = [a,b,c,alpha, beta, gamma]
> sam = xru.materials.material.Crystal(’sample1', abcabg)
>
> ##__the UB matrix is retrieved during the experiment
> ubmat = np.array([[1.364,-0.131,0.270],[-0.044, 1.639, 0.083],[-0.950,
-0.264, 0.384]])
>
>
> ##__load the frame and associated parameter file to get scan parameters,
> omega, twotheta, chi, phi, energy, detector_distance = ...
>
> ##__fix detector spec
>
> #__define experiment geometry
> hxrd = xru.HXRD(sam.Q(-2, 0, 0), sam.Q(0, 0, -4), en=energy)
>
> ##__assign orientation matrix
> hxrd.Ang2Q.init_area('z+','x+', cch1=cpix, cch2=cpiy, Nch1=npix,
Nch2=npiy,
>  pwidth1=xpix, pwidth2=ypix, distance=sam_det)
>
> ## conversion to h,k,l
> h,k,l = hxrd.Ang2HKL(omega, towtheta, U=ubmat)
>
>
>
> ==================================================================
> Ruggero Frison
> University of Zurich, Physik Institut
>
> Winterthurerstrasse 190
> CH-8057 Zurich, Switzerland
> Office: Y36-H-76
> Phone: +41 44 635 5780
> ==================================================================
>
>
>
>
> _______________________________________________
> xrayutilities-users mailing list
> xra...@li...
> https://lists.sourceforge.net/lists/listinfo/xrayutilities-users

[Xrayutilities-users] conversion of an image from an area detector

[ruggero f. <rug...@uz...>]

Hello,

I would need some help, I am trying to index a frame of an Area detector into hkl coordinateds following the example provided in Appendix B of the reference paper and in some scripts provided in the example folder of the distribution.

I have some frames of an area detector with a 4-circles Eulerian cradle.

I paste below a dummy script, which 
I prepared a script building on the examples but it does not give results, I do not understand why.
I guess because I do not understand the underlying action of xrayutilities.

I understand that Ang2HKL would create the arrays of hkl vlaues using the experimental angles.
Thus I could feed it with the scan parameters I retrieve from the scan files and the UB matrix determined during the sample alignment.

Would that work or I am getting wrong?

I paste below a dummy script to avoid useless details.

Thanks

Best regards

Ruggero


##__set the material
abcabg = [a,b,c,alpha, beta, gamma]
sam = xru.materials.material.Crystal(’sample1', abcabg)

##__the UB matrix is retrieved during the experiment
ubmat = np.array([[1.364,-0.131,0.270],[-0.044, 1.639, 0.083],[-0.950, -0.264, 0.384]])


##__load the frame and associated parameter file to get scan parameters, 
omega, twotheta, chi, phi, energy, detector_distance = ...

##__fix detector spec

#__define experiment geometry
hxrd = xru.HXRD(sam.Q(-2, 0, 0), sam.Q(0, 0, -4), en=energy)

##__assign orientation matrix
hxrd.Ang2Q.init_area('z+','x+', cch1=cpix, cch2=cpiy, Nch1=npix, Nch2=npiy,
 pwidth1=xpix, pwidth2=ypix, distance=sam_det)

## conversion to h,k,l 
h,k,l = hxrd.Ang2HKL(omega, towtheta, U=ubmat)



==================================================================
Ruggero Frison
University of Zurich, Physik Institut

Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Office: Y36-H-76
Phone: +41 44 635 5780
==================================================================

[Xrayutilities-users] xrayutilities 1.7.0 release notification

[Dominik K. <dom...@gm...>]

xrayutilities-1.7.0 is available.
This version is compatible with Python >3.6.

Version 1.7.0 contains several fixes and as usual every user is advised
to upgrade. In order to obtain the new version go to sourceforge [1] or
use PyPI [2]. Windows and MacOS wheel packages are found on PyPI for
64-bit Python in versions 3.6, 3.7, 3.8, and 3.9. There is also a
conda-forge package [3] which should make installing for Conda users
more straightforward. If you encounter problems please report them on
github or on the mailinglist.

Noteworthy changes are:
Dropped runtime dependency on setuptools, which results in significantly
faster import times.
Runtime dependencies are now:
* numpy>=1.9.2
* scipy>=0.11.0
* h5py
Recommended packages include
* matplotlib>=3.1.0
* lmfit>=1.0.1

X-ray reflectivity simulations can now be performed with Gaussian beam
shape of the primary beam. This is configurable via the 'beamshape'
parameter to xrayutilities.simpack.SpecularReflectivityModel.

Plotting of powder diffraction data can now indicate the line position
for the various components of a powder model. see
examples/xrayutilities_experiment_Powder_example_Iron.py for details.

Most work, however, went into new methods for material definition and
extraction of useful information from materials. The definition is now
more flexible. So far you had to specify the Wyckoff position labels for
every atom:

InP = xu.materials.Crystal("InP", xu.materials.SGLattice(216, 5.8687, atoms=[In, P],pos=['4a', '4c']),

Now you can also give just the position of one atom and the code will
determine this automatically:

InP = xu.materials.Crystal("InP", xu.materials.SGLattice(216, 5.8687, atoms=["In", "P"], pos=[(0,0,0), (1/4, 1/4, 1/4)]))

I do, however, recommend you to check the resulting Crystal object (use
print(InP)) to check that you obtained what you wanted! You can also use
the upgraded Crystal.show_unitcell() method to visualize the unit cell.
If you have mayavi installed I recommend to set the optional parameter
mode='mayavi' to get an accurate 3D visualization.

Crystal or more precisely speaking their associated SGLattice objects
now know more about themself: There are new get_allowed_hkl,
hkl_allowed, equivalent_hkls, isequivalent, iscentrosymmetric, findsym,
symops methods of SGLattice. See their docstrings for details [4]

You can now also transform a unit cell with a transformation matrix. See
[5] for details.

A more complete set of changes can be found in the CHANGES.txt file [6]
and the git log.

The test code coverage is now 76% [7]
[1] https://sourceforge.net/projects/xrayutilities
[2] https://pypi.python.org/pypi/xrayutilities
[3] https://github.com/conda-forge/xrayutilities-feedstock
[4] https://xrayutilities.sourceforge.io/xrayutilities.materials.html?highlight=sglattice#xrayutilities.materials.spacegrouplattice.SGLattice
[5] https://xrayutilities.sourceforge.io/examples.html#transformation-of-sglattice
[6] https://github.com/dkriegner/xrayutilities/blob/master/CHANGES.txt
[7] https://dev.azure.com/dominikkriegner/xrayutilities/_build/results?buildId=60&view=results

Re: [Xrayutilities-users] Pedestrian usage

[Dominik K. <dom...@gm...>]

Dear Jansen Dwan,

On Fri, Oct 2, 2020 at 10:08 AM Jansen A. Dwan <jan...@gm...>
wrote:

>
>
> Hello,
>
>
>
> I’m currently doing a master’s thesis at Leipzig University about
> multilayers of III-nitrides/ZnO to effect oxynitride band bending
> characteristics. Analysis of my completed films (mono and multilayer) has
> been done with XRD. As I am becoming more familiar with using Python and
> matplotlib as a plotting tool I am growing to like origin less and less. So
> to that end I searched out a xray library and ended up finding your work.
> It seems this is an exceptionally robust tool for X-ray analysis. In fact,
> so much so that I am having difficulty determining how to use it for more
> elementary purposes. Most, of what I have done has been simple rocking
> curve, 2th-om and phi scans. I thought rather than scour through the
> documentation for hours it might be more efficient to simply ask the
> authors what modules I might look at for these more rudimentary
> evaluations. Hopefully, you will not find this to presumptuous of me.
>
In my opinion that's what the mailing list is for! Unfortunately many
people send me private mails.

Generally I think xrayutilities can help you, but it will "not do the
thinking for you". I will outline below what I mean by that.


>
>
> Here is a short list of what I would like to accomplish:
>
>    - Analyze multiple data sets to determine peak position FWHM and plot
>    the results. This is most often for AlN on c-plane sapphire.
>
> It seems here you just need a general peak fitting algorithm. I usually
suggest to use lmfit for this [1] since it provides a nice interface and
works well.
But there is also a rudimentary function in xrayutilities.math named
peak_fit which you could use [2] and works fine for well separated peaks.


>
>    - Calculate crystallite size
>
> Here comes what I mentioned before: For calculation of the crystallite
size many factors play a role and I think it's almost impossible to provide
one solution which fits all possible cases. It's for example not even clear
from what kind of scan you want to determine it. The lateral crystallite
size is encoded in the rocking curves but also the mosaicity enters, and
likely multiple rocking curves of different Bragg peaks are needed to
disentangle the effects. The vertical crystallite size shows up in the
2th-om scans, but here of course also the various peaks from your
multilayer can interfere. (And all I wrote is strictly speaking only true
for symmetric peaks). So you will have to find your own way of analyzing
this in a way it fits for your system.

One thing which could help you understand the mosaicity and crystallite
size effects is the simulation function mosaicity_analytic [3]


>    - Calculate lattice constants
>
> The reason no function is provided is a bit similar here. In general
multiple Bragg peak positions (2th) are needed to determine all the lattice
parameters (a,b,c, alpha, beta, gamma). Usually, however, one measures just
the one peak one needs to get for example the out of plane spacing. If
determination of the peak position is not hindered by dynamic diffraction
effects or overlay of multiple peaks the calculation of the lattice
parameter is trivial. Xrayutilities.Experiment classes can be of some help
with getting reciprocal space coordinates. In case of peak overlaps one
might actually need simulations (see below).


>
>    - Simulate XRD results for ideal depositions to contrast with my
>    experimental results
>
> Simulation of radial 2th-om scans for symmetric Bragg peaks can be done
with several different models in the xrayutilities simpack model. I guess
here this page [4] gives some introduction. but you will also find full
examples in the examples folder [5]. Which model is the best for you again
depends on the particularities of your system.

kind regards
Dominik

[1] https://lmfit.github.io/lmfit-py/
[2]
https://xrayutilities.sourceforge.io/xrayutilities.math.html#xrayutilities.math.fit.peak_fit
[3]
https://xrayutilities.sourceforge.io/xrayutilities.simpack.html#xrayutilities.simpack.mosaicity.mosaic_analytic
[4] https://xrayutilities.sourceforge.io/simulations.html
[5] https://github.com/dkriegner/xrayutilities/tree/master/examples

ps: sorry for the broken formating in the online documentation. I need to
look into this. The pdf seems to be fine.

[Xrayutilities-users] Pedestrian usage

[Jansen A. D. <jan...@gm...>]

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--></style></head><body lang=EN-US><div class=WordSection1><p class=MsoNormal><o:p>&nbsp;</o:p></p><p class=MsoNormal>Hello, </p><p class=MsoNormal><o:p>&nbsp;</o:p></p><p class=MsoNormal>I’m currently doing a master’s thesis at Leipzig University about multilayers of III-nitrides/ZnO to effect oxynitride band bending characteristics. Analysis of my completed films (mono and multilayer) has been done with XRD. As I am becoming more familiar with using Python and matplotlib as a plotting tool I am growing to like origin less and less. So to that end I searched out a xray library and ended up finding your work. It seems this is an exceptionally robust tool for X-ray analysis. In fact, so much so that I am having difficulty determining how to use it for more elementary purposes. Most, of what I have done has been simple rocking curve, 2th-om and phi scans. I thought rather than scour through the documentation for hours it might be more efficient to simply ask the authors what modules I might look at for these more rudimentary evaluations. Hopefully, you will not find this to presumptuous of me. </p><p class=MsoNormal><o:p>&nbsp;</o:p></p><p class=MsoNormal>Here is a short list of what I would like to accomplish:</p><ul style='margin-top:0in' type=disc><li class=MsoListParagraph style='margin-left:0in;mso-list:l0 level1 lfo1'>Analyze multiple data sets to determine peak position FWHM and plot the results. This is most often for AlN on c-plane sapphire.</li><li class=MsoListParagraph style='margin-left:0in;mso-list:l0 level1 lfo1'>Calculate crystallite size</li><li class=MsoListParagraph style='margin-left:0in;mso-list:l0 level1 lfo1'>Calculate lattice constants</li><li class=MsoListParagraph style='margin-left:0in;mso-list:l0 level1 lfo1'>Simulate XRD results for ideal depositions to contrast with my experimental results</li></ul><p class=MsoNormal><o:p>&nbsp;</o:p></p><p class=MsoNormal>Obviously I understand I have to work out the particulars, but I would very much appreciate it if you would point me in the right direction. It seems most of the examples within the documentation are for far more advanced analysis than I need. Perhaps that even means that this isn’t quite the right tool for me which is, of course, good to know. I hope you aren’t too bothered by my inexperience here. </p><p class=MsoNormal><o:p>&nbsp;</o:p></p><p class=MsoNormal>All the best,</p><p class=MsoNormal>Jansen Dwan</p></div></body></html>

[Xrayutilities-users] xrayutilities 1.6.0 and 1.5.4 release notification

[Dominik K. <dom...@gm...>]

Today two version of xrayutilities were released. A bug fix update to the
1.5 series which is the Python2.7 compatible branch, and will likely not
see any further updates! Newer versions, including the 1.6.0 version
published today are only compatible with Python >3.3.

Version 1.6.0 contains several code rearrangements, minor fixes, and is
Python3 only. The element database is no longer shipped with the package
but is now created during the install process. Therefore the h5py, numpy,
and scipy are now already needed during the setup process. pip handles this
automatically so most users should not notice any difference!

A more complete set of changes can be found in the CHANGES.txt file [1] and
the git log.

As usual every user is advised to upgrade. In order to obtain the new
version go to sourceforge [2] or use PyPI [3]. Windows binaries and wheel
packages are found on PyPI for 32 and 64-bit Python in versions 3.5, 3.6,
and 3.7. There is also a conda-forge package [4] which should make
installing for Conda users more straightforward.
If you encounter problems please report them on github or on the
mailinglist.

[1] https://github.com/dkriegner/xrayutilities/blob/master/CHANGES.txt
[2] https://sourceforge.net/projects/xrayutilities
[3] https://pypi.python.org/pypi/xrayutilities
[4] https://github.com/conda-forge/xrayutilities-feedstock

[Xrayutilities-users] xrayutilities 1.5.3 release notification (2019-10-09)

[Dominik K. <dom...@gm...>]

xrayutilities 1.5.3 release notes

This is a bug-fix release. Several bugs in particular in file parsers and
simulation models were fixed.

Most notable is a change in PowderModel were a memory leak from
insufficient cleanup of the multiprocessing code should be fixed now.

Several improvements in the CIF and Spec file parsers were incorporated.
Thanks for reporting and corresponding pull requests!

(As a note to the future myself: The test coverage of this release is at
70%.)

A more complete set of changes can be found in the CHANGES.txt file [1].
As usual every user is advised to upgrade. In order to obtain the new
version go to sourceforge [2] or use PyPI [3]. Windows binaries and wheel
packages are found on PyPI for 32 and 64-bit Python in versions 2.7 and
3.5, 3.6, and 3.7. There is now also a conda-forge package [4] which should
make installing for Conda users more straightforward. The package should be
updated within the next days (I hope).
If you encounter problems please report them on github or on the
mailinglist.

[1] https://github.com/dkriegner/xrayutilities/blob/master/CHANGES.txt
[2] https://sourceforge.net/projects/xrayutilities
[3] https://pypi.python.org/pypi/xrayutilities
[4] https://github.com/conda-forge/xrayutilities-feedstock

Re: [Xrayutilities-users] pseudo-angles constraints in Q2AngFit

[Dominik K. <dom...@gm...>]

Dear Guilherme,

On Wed, Sep 25, 2019 at 2:41 PM Guilherme Calligaris via
xrayutilities-users <xra...@li...> wrote:

> Hi all,
>
> I'm having difficulties in progressing to make pseudo-angles like
> constraints for the Q2AngFit, under q2ang_fit module. I'm hoping that this
> mailing list is the right way to discuss matters like this.
>
You asked at the right place.


> It might be straightforward, but I am not an expert in python (I'm trying
> my best to reach a reasonable programming level). I did notice that inside
> the q2ang_fit.py, it has an exitAngleConst function that is supposed to
> guide users like me. However, I didn't quite get it how to use such
> constraints yet.
>
I added this functionality once very quickly because I needed it but its
not very well documented. I am afraid at the moment you have to read a bit
the code to understand how it works. The "contraints" argument to Q2AngFit
is in principle passed unchecked to scipy.optimize.minimize. Therefore the
documentation of this function (
https://docs.scipy.org/doc/scipy-1.3.0/reference/generated/scipy.optimize.minimize.html#scipy.optimize.minimize)
is your best reference. Note that the SLSQP algorithm is used.

I added an issue on Github to remind me that the documentation of this
needs improvement (https://github.com/dkriegner/xrayutilities/issues/85)
If you find issues when using this please report them also there!


> The plan is to make pseudo-angles constraints in a 4S+2D diffractometer
> such as the ones implemented in SPEC (Certified Scientific Software) and H.
> You (J. Appl. Cryst. (1999), 32, 614).
>
This should be possible. But be aware that a numerical procedure is used in
Q2AngFit which not always (depending on the starting values ->
"startvalues" agrument) find the correct solution. So this approach is
unfortunately not as stable as the implementation in SPEC. the advantage is
it works for any given goniometer as long as enough degrees of freedom are
fixed of course!


> I'm not sure, for instance, if the constraints need to be inserted like a
> function inside the q2ang_fit.py (somehow similar to the exitAngleConst
> function) or would I define the constraints in the same program that calls
> the Q2AngFit function, using its constraints parameter.
> Hope I made my self understandable.
>
I think you should find what you need at
https://docs.scipy.org/doc/scipy-1.3.0/reference/generated/scipy.optimize.minimize.html#scipy.optimize.minimize
But yes you have to define functions like the exitAngleConst function which
return 0 when your constraint is fulfilled and pass them to Q2AngFit as
explained in the scipy.optimize.minimize documentation.

kind regards
Dominik


> Any thoughts or examples regarding such an approach are welcome and much
> appreciated.
>
> Thanks in advance for your time,
>
> Guilherme
>
> _______________________________________________
> xrayutilities-users mailing list
> xra...@li...
> https://lists.sourceforge.net/lists/listinfo/xrayutilities-users
>

[Xrayutilities-users] pseudo-angles constraints in Q2AngFit

[Guilherme C. <g.a...@me...>]

Hi all,

I'm having difficulties in progressing to make pseudo-angles like constraints for the Q2AngFit, under q2ang_fit module. I'm hoping that this mailing list is the right way to discuss matters like this.
It might be straightforward, but I am not an expert in python (I'm trying my best to reach a reasonable programming level). I did notice that inside the q2ang_fit.py, it has an exitAngleConst function that is supposed to guide users like me. However, I didn't quite get it how to use such constraints yet.  
The plan is to make pseudo-angles constraints in a 4S+2D diffractometer such as the ones implemented in SPEC (Certified Scientific Software) and H. You (J. Appl. Cryst. (1999), 32, 614). 
I'm not sure, for instance, if the constraints need to be inserted like a function inside the q2ang_fit.py (somehow similar to the exitAngleConst function) or would I define the constraints in the same program that calls the Q2AngFit function, using its constraints parameter. 
Hope I made my self understandable. 
Any thoughts or examples regarding such an approach are welcome and much appreciated. 

Thanks in advance for your time,

Guilherme

[Xrayutilities-users] xrayutilities 1.5.2 release notification (2019-06-28)

[Dominik K. <dom...@gm...>]

xrayutilities 1.5.2 release notes

Several bugs were fixed and some changes were incorporated which might
cause script changes upon update.

The most important changes are:
*) fix bug in PowderDiffraction where the last Bragg peak before
`tt_cutoff` was ignored, other fixes in PowderDiffraction for the case when
`enable_simulation=False`

*) change of SMaterial.density to a unit of kg/m3. If you use XRR fitting
you will have to change the used parameters to an absolute density in kg/m3.

*) addition of an arbitrary line cut function which allows to extract a
line cut in an arbitrary direction from 2 and 3D data sets.

*) bug fixes in the spec parser enabling more flexible handling of empty
scans and NaN/inf values

*) the function geth5_map was removed. users should use geth5_scan instead

A more complete set of changes can be found in the CHANGES.txt file [1].
As usual every user is advised to upgrade. In order to obtain the new
version go to sourceforge [2] or use PyPI [3]. Windows binaries and wheel
packages are found on PyPI for 32 and 64-bit Python in versions 2.7 and
3.5, 3.6, and 3.7. If you encounter problems please report them on github
or on the mailinglist.

[1] https://github.com/dkriegner/xrayutilities/blob/master/CHANGES.txt
[2] https://sourceforge.net/projects/xrayutilities
[3] https://pypi.python.org/pypi/xrayutilities

[Xrayutilities-users] install latest GIT version of xrayutilities

[Dominik K. <dom...@gm...>]

Hi all,

Usually one of my first replies to questions/bugs reports I receive about
xrayutilities is to install the latest development version from the GIT
repository. I realize that many people have problems with this. Especially
on Windows the problems is that one needs a suitable C compiler to compile
the included library.

I outline below what should be the easiest way to get the this done in case
you want to work with the latest version or need some feature from it.

On windows (without C-compiler):

Actually for every change made in xrayutilities there is some automatic
testing done via travis-ci.org and appveyor.com. For that purpose
appveyor.com creates installable binaries for every supported python
version.

1) Download the appropriate xrayutilities version from:
https://ci.appveyor.com/project/dkriegner/xrayutilities -> Click on your
python version (e.g. "Environment: PYTHON=C:\Python36" (do not use the
miniconda versions since they have no artifacts!) -> click on "Artifacts"
and download the .whl file
2) open a command line with access to your python executables and go to the
folder where you have the 'xrayutilities*.whl' file
3) run "pip install filename.whl"

On systems with appropriate C-compiler (Linux/Unix/Windows):

1) download the latest git version either by GIT or from the following link:
https://github.com/dkriegner/xrayutilities/archive/master.zip
2)  open a command line with access to your python executables and go to
the folder where you have the 'xrayutilities' source files.
3) run 'python setup.py install' or variants thereof outlined in the Readme
[1] or Documentation [2].

if you have comments on this please reply on the mailinglist!

cheers
dominik

[1] https://github.com/dkriegner/xrayutilities#installation-source
[2] https://xrayutilities.sourceforge.io/#source-installation

[Xrayutilities-users] xrayutilities 1.5.1 release notification (2019-01-07)

[Dominik K. <dom...@gm...>]

xrayutilities 1.5.1 release notes

The new version contains several fixes and improvements from the last month.
Noteworthy are:

*) CIF exporter for Crystalline materials
Structures can now be exported to a CIF file:
  import xrayutilities as xu
  xu.materials.Si.toCIF('filename.cif')
also see [1]

*) new FourC experiment class with consistent Q2Ang and Ang2Q functions

*) rewrite of the line cut functions which now work faster and are more
versatile. These functions are intended to extract line cuts/scans along
Qx, Qy, Qz, omega, 2theta, radial directions from 2D and 3D reciprocal
space maps. Integration for line cuts can be performed along various
directions. See [2] for details.

*) simple unit cell visualization: since from the feedback I received I see
that several people make mistakes in the material definitions I added a
quick and dirty plot function to visualize the unit cell and allow for a
visual check of the definition. see the documentation for details [3].

A more complete set of changes can be found in the CHANGES.txt file [4].
As usual every user is advised to upgrade. In order to obtain the new
version go to sourceforge [5] or use PyPI [6]. Windows binaries and wheel
packages are found on PyPI for 32 and 64-bit Python in versions 2.7 and
3.5, 3.6, and 3.7. If you encounter problems please report them on github
or on the mailinglist.

[1]
https://xrayutilities.sourceforge.io/xrayutilities.materials.html?highlight=tocif#xrayutilities.materials.material.Crystal.toCIF
[2]
https://xrayutilities.sourceforge.io/examples.html#line-cuts-from-reciprocal-space-maps
[3]
https://xrayutilities.sourceforge.io/examples.html#using-the-material-class
[4] https://github.com/dkriegner/xrayutilities/blob/master/CHANGES.txt
[5] https://sourceforge.net/projects/xrayutilities
[6] https://pypi.python.org/pypi/xrayutilities

[Xrayutilities-users] xrayutilities 1.5.0 releases (2018-07-04)

[Dominik K. <dom...@gm...>]

xrayutilities 1.5.0 was released on 2018-07-04

It contains several bug fixes and improvements which are outlined in
detail in the CHANGES.txt file. 

Noteworthy are:

*) Another significant improvement of the CIF-file parser which should
   now is able to parse also files which do not have the symmetry
   operations included.  If you find a CIF file where this does not work
   please report it!

*) Compatibility with numpy 1.14. If you use this numpy version you will
   have to update to this version, otherwise you will experience errors
   when using file parsers.

*) New simulation code for diffuse X-ray reflectivity is now included in
   simpack.DiffuseReflectivityModel

*) The U/UB matrix is now compatible with the notation used in SPEC and
   it should be possible to transfer the orientation obtained in the
   experiment to xrayutilities.

As usual every user is advised to upgrade. In order to obtain the new
version go to sourceforge [1] or use PyPI [2]. Windows binaries and
wheel packages are found on PyPI for 32 and 64-bit Python in versions
2.7 and 3.5 and 3.6.

[1] https://sourceforge.net/projects/xrayutilities
[2] https://pypi.python.org/pypi/xrayutilities

[Xrayutilities-users] xrayutilities 1.4.2 released (2017-11-28)

[Dominik K. <dom...@gm...>]

xrayutilities 1.4.2 was released on 2017-11-28

It contains several bug fixes and improvements which are outlined in
detail in the CHANGES.txt file. Noteworthy is the vastly improved
CIF-file parser which should now be able to recognize correctly the
space group and Wyckoff position of atoms. If you find a CIF file where
this does not work please report it!

As usual every user is advised to upgrade. In order to obtain the new
version go to sourceforge [1] or use PyPI [2]. Windows binaries and
wheel packages are found on PyPI for 32 and 64-bit Python in versions
2.7 and 3.5 and 3.6.

[1] https://sourceforge.net/projects/xrayutilities
[2] https://pypi.python.org/pypi/xrayutilities

[Xrayutilities-users] xrayutilities 1.4.1 releases (2017-04-03)

[Dominik K. <dom...@gm...>]

xrayutilities 1.4.1 was released (2017-04-03)

This is a bug-fix release which fixes three annoying/important bugs:
1) the symmetry of tetragonal materials was wrong in 1.4.0
2) the PowderModel/PowderDiffraction classes did not work on Windows
3) fix in DarwinModel (caused first layer in a sequence to be treated wrong)

As usual every user is advised to upgrade. In order to obtain the new
version go to sourceforge [1] or use PyPI [2]. Windows binaries and wheel
packages are found on PyPI for Python in versions 3.5 and 3.6 in 32 and
64-bit versions.

Note that there are no packages for Python 2.7.X anymore. If you need such
packages and can not build it yourself please let me know.

[1] https://sourceforge.net/projects/xrayutilities
[2] https://pypi.python.org/pypi/xrayutilities

[Xrayutilities-users] xrayutilities 1.4.0 released (2017-02-09)

[Dominik K. <dom...@gm...>]

xrayutilities 1.4.0 was released (2017-02-09)

During the last month several important improvements, changes, and
additions were made to xrayutilities. As usual every user is advised to
upgrade. In order to obtain the new version go to sourceforge [1] or use
PyPI [2]. Windows binaries and wheel packages are found on PyPI for 64-bit
Python in versions 2.7 and 3.5 and 3.6.

With the change to version 1.4.0 there might be some code changes in your
scripts required. Please check the list of changes below and see if you are
likely to be affected.

New simulation capabilities were added to xrayutilities. Notable are a
dynamical multibeam formalism for symmetric crystal truncation rods and
powder diffraction code based on the fundamental parameters approach. The
core of the powder diffraction code was submitted by Marcus H. Mendenhall <
mar...@ni...> and is documented in Journal of Research of
NIST 120, 223 (2015) http://dx.doi.org/10.6028/jres.120.014 . Example
scripts for powder diffraction (simpack_powdermodel.py) and the new
dynamical diffraction simulation (simpack_xrd_Darwin_AlGaAs.py) can be
found in the example folder [3].

Further changes include a complete redesign of how materials or better
their lattices are defined. The new way of defining materials is more
flexible and closer to the way most other software treats lattices. A
crystalline material is now specified by its space group number and the
Wyckoff position of atoms within the unit cell.

For example a zincblende material one defines by:
import xrayutilities as xu
InP = xu.materials.Crystal("InP", xu.materials.SGLattice(216, 5.8687,
atoms=[xu.materials.elements.In, xu.materials.elements.P], pos=['4a',
'4c']))
InAs = xu.materials.Crystal("InAs", xu.materials.SGLattice(216, 6.0583,
atoms=['In', 'As'], pos=['4a', '4c']))

The definition of the lattice takes a variable number of parameters
depending on the symmetry of the given space group. A more complex
definition is for example used for ferroelectric GeTe which is rhombohedral
and its atomic positions have several degrees of freedom which need to be
specified:
GeTe = Crystal("GeTe",
SGLattice('160:R', 5.996, 88.18, atoms=[e.Ge, e.Ge, e.Te, e.Te],
pos=[('1a', -0.237), ('3b', (0.5-0.237, -0.237)),
('1a', 0.237), ('3b', (0.5+0.237, +0.237))]))

Many more examples of material definitions can be found seen in the list of
predefined materials [4].
With the new changes the definition of alloyed materials is much more
straight forward since alloying is now automatically performed also within
the unit cell. The only requirement is that both materials have the same
space group! To create an InAs_{1-x} P_x alloy whose lattice parameter
follows Vegard's rule one uses:

InAsP = xu.materials.Alloy(InAs, InP, 0.4)
print(InAsP)

Alloy: InAs(0.60)InP(0.40)
Lattice:
216 cubic F-43m: a = 5.9825, b = 5.9825 c= 5.9825
alpha = 90.000, beta = 90.000, gamma = 90.000
Lattice base:
0: In (49) 4a occ=0.600 b=0.000
1: As (33) 4c occ=0.600 b=0.000
2: In (49) 4a occ=0.400 b=0.000
3: P (15) 4c occ=0.400 b=0.000

Currently the old Lattice code is still included and can be used to make a
primitive conversion of your old materials and help you convert your
material definitions. If you for example had defined your own zincblende
lattice/material you can convert it with:
zb = xu.materials.ZincBlendeLattice(xu.materials.elements.In,
xu.materials.elements.P, 5.8687)
new_zb = xu.materials.SGLattice.fromLattice(zb)
print(new_zb)
...

As you will see from the output this conversion always uses the P1
space-group. This conversion code and all old Lattice definitions will be
removed in the next major release.

For a more exhaustive list of changes in version 1.4.0 see the CHANGES.txt
file or the GIT log. Test coverage of this version is at 60%.

[1] https://sourceforge.net/projects/xrayutilities
[2] https://pypi.python.org/pypi/xrayutilities
[3] https://github.com/dkriegner/xrayutilities/tree/master/examples
[4]
https://github.com/dkriegner/xrayutilities/blob/master/xrayutilities/materials/predefined_materials.py

[Xrayutilities-users] xrayutilities 1.3.3 released

[Dominik K. <dom...@gm...>]

xrayutilities 1.3.3 was released (2016-08-24)

This release cycle focused on fixing of several small bugs. The only
notable feature change is that the definition of Amorphous materials is now
easier: they can now be defined easily using the chemical formula in the
name and giving the density. An example is given below:
cofe = xu.materials.Amorphous('Co2Fe', rho_cofe)

See the CHANGES.txt file or the GIT log for a more complete list of changes.

As usual every user is advised to upgrade. In order to obtain the new
version go to sourceforge [1] or use PyPI [2]. Windows binaries and wheel
packages are found on PyPI for 64-bit Python in versions 2.7 and 3.5.

[1] https://sourceforge.net/projects/xrayutilities
[2] https://pypi.python.org/pypi/xrayutilities

ps: note that version 1.3.2 was skipped due to some packaging issues.