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F_POLAR=0 makes corrupted beam when running gen_source twice (or more times) in the same python session

In "Distances Summary" there is a warning:
Warning: SHADOW did not run, therefore autosetting angles are not consideredTotal deflection angle H = 0.000073 rad = 0.004 deg
Total deflection angle V = 0.000073 rad = 0.004 deg

I open an issue in shadow3

do it in python. Use macro_fresnelzoneplate.ws as template and test case

I have installed shadow3-18.5.30.tar.gz on anaconda python (anaconda version 1.7.2 python version 3.7.0) on redhat linux Entrerprise with gcc, g++ and gfortran 4.8.5-4 installed. during the of shadow 3 installation i need to install xraylib 4.0.0 and PyHamcrest-2.0.2.

Installation was successful but simple test program is not working

import os
import Shadow
beam = Shadow.Beam()
src = Shadow.Source()
beam.genSource(src)
oe1 = Shadow.OE()
beam.traceOE(oe1,1)

In the last line i got error
At line 416 of file src/fortran/stringio.f90
Internal Error: get_unit(): Bad internal unit KIND

Can not find solution from online resources

882530f is causing ShadowToolsPrivate.py to no longer run on Python 2. The print usage needs this line at the top of the file put back in:

from __future__ import print_function

Hello,

I am trying to install ShadowOui using OASYS and have encountered the following error when attempting to install shadow3:

"build\temp.win-amd64-3.8\shadow3c.lib : fatal error LNK1136: invalid or corrupt file"

From what I can tell, it appears like there is an issue with my C++ compiler that I am unaware how to fix. I am currently using VisualStudio build tools with the following installed:

MSVC v142 - VS 2019 C++ x64/86 build tools
Windows 10 SDK (10.0.18362.0) - but have also tried using v 10.0.14393.0
Windows Universal CRT SDK

I am using a Windows 10 machine with MinGW-W64 GCC-7.3.0 for the fortran compiler and the miniconda installer with python 3.8.5. I have also tried using other GCC versions (8.1, 6.4) but the newer version gives a different error like has been described in other issues.

Here is the full output during installation just in case it provides any useful information.
shadow3_lnk1136.txt

with gfortran 8 the compilation of shadow_variables.f90 (and others) fails with the following error:

Error: Component 'file_xxx' of BIND(C) type at (1) must have length one

This is a change of behaviour in the char C/Fortran interface. See:

https://gcc.gnu.org/bugzilla/show_bug.cgi?id=84885

See also this discussion:

https://sourceforge.net/p/wsjt/mailman/message/36262831/

@srio The footprint plot on the optical element does not work with the 'beam' instance, only via file.

This fails:
Shadow.ShadowTools.plotxy(beam, 1, 2, nbins=101, nolost=2, title="Footprint", ref=0)

This works:
Shadow.ShadowTools.plotxy('mirr.01', 1, 2, nbins=101, nolost=2, title="Footprint", ref=0)

This means that one is obliged to write files to look at the footprint.

@lucarebuffi it would be nice to have a 'footprint plot' tab in ShadowOui.

From: CARADOC-DAVIES, Tom
Sent: Saturday, September 5, 2020 4:08:23 PM
To: Rebuffi, Luca
Subject: Shadow bug? [SEC=UNCLASSIFIED]

Hi Luca,

I think I have found a minor bug. I am modelling CRLs in my beamline layout.

I am using the compound refractive lens widget to model 1D vertical and horizontal lenses.

This has the option for number of lenses and number of empty slots.

If I set number of lenses to zero on both CRL widgets in the Info widget distance summary table 4 CRLS are incorrectly listed (see attached).

They are not affecting the ray traced beam but seem to be incorrectly listed in the table? I would assume they should not be on the list as they are out of beam?

When I add lenses they appear as expected but I cannot get rid of the 4 “phantom” lenses.

I attached my model if you want to reproduce the error (apologies for the complex model).

Cheers,

Tom

MX3_CRL_defocus8.zip

Running Shadowoui, the "info" postprocessor does not show the top view and side view anymore.
In the output, the error is "Failed to append: object not understood: <class 'Shadow.ShadowLibExtensions.Source'>. "
Please help me out.
Thanks

Noticed by Xianbo, a screen/slit (empty element) modifies the beam in col 5.

See effect of oe3 (empty).
If suppressed, OK.
If col6 copied, OK.
otherwise NOT OK.

#
# Python script to run shadow3. Created automatically with ShadowTools.make_python_script_from_list().
#
import Shadow
import numpy

# write (1) or not (0) SHADOW files start.xx end.xx star.xx
iwrite = 0

#
# initialize shadow3 source (oe0) and beam
#
beam = Shadow.Beam()
oe0 = Shadow.Source()
oe1 = Shadow.OE()
oe2 = Shadow.OE()
oe3 = Shadow.OE()
oe4 = Shadow.OE()

#
# Define variables. See meaning of variables in: 
#  https://raw.githubusercontent.com/srio/shadow3/master/docs/source.nml 
#  https://raw.githubusercontent.com/srio/shadow3/master/docs/oe.nml
#

oe0.FDISTR = 3
oe0.F_PHOT = 0
oe0.HDIV1 = 0.0
oe0.HDIV2 = 0.0
oe0.ISTAR1 = 1001
oe0.NPOINT = 100000
oe0.PH1 = 25000.0
oe0.SIGDIX = 1e-10
oe0.SIGDIZ = 3.7e-06
oe0.SIGMAX = 0.0
oe0.SIGMAZ = 0.0046
oe0.VDIV1 = 0.0
oe0.VDIV2 = 0.0

oe1.DUMMY = 0.1
oe1.FCYL = 1
oe1.FHIT_C = 1
oe1.FMIRR = 2
oe1.RLEN1 = 200.0
oe1.RLEN2 = 200.0
oe1.RWIDX1 = 10.0
oe1.RWIDX2 = 10.0
oe1.T_IMAGE = 24700.0
oe1.T_INCIDENCE = 89.856761
oe1.T_REFLECTION = 89.856761
oe1.T_SOURCE = 35300.0

oe2.DUMMY = 0.1
oe2.F_REFRAC = 2
oe2.F_SCREEN = 1
oe2.I_SLIT = numpy.array([1, 0, 0, 0, 0, 0, 0, 0, 0, 0])
oe2.N_SCREEN = 1
oe2.RX_SLIT = numpy.array([1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0])
oe2.RZ_SLIT = numpy.array([0.002, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0])
oe2.T_IMAGE = 118695.0
oe2.T_INCIDENCE = 0.0
oe2.T_REFLECTION = 180.0
oe2.T_SOURCE = 0.0

oe3.DUMMY = 0.1
oe3.F_REFRAC = 2
oe3.F_SCREEN = 1
oe3.N_SCREEN = 1
oe3.T_IMAGE = 0.0
oe3.T_INCIDENCE = 0.0
oe3.T_REFLECTION = 180.0
oe3.T_SOURCE = 0.0

oe4.DUMMY = 0.1
oe4.FCYL = 1
oe4.FHIT_C = 1
oe4.FMIRR = 2
oe4.F_ANGLE = 1
oe4.F_DEFAULT = 0
oe4.RLEN1 = 150.0
oe4.RLEN2 = 150.0
oe4.RWIDX1 = 1.0
oe4.RWIDX2 = 1.0
oe4.SIMAG = 305.0
oe4.SSOUR = 119695.0
oe4.THETA = 89.856761
oe4.T_IMAGE = 305.0
oe4.T_INCIDENCE = 89.856761
oe4.T_REFLECTION = 89.856761
oe4.T_SOURCE = 1000.0



#Run SHADOW to create the source

if iwrite:
    oe0.write("start.00")

beam.genSource(oe0)

if iwrite:
    oe0.write("end.00")
    beam.write("begin.dat")


#
#run optical element 1
#
print("    Running optical element: %d"%(1))
if iwrite:
    oe1.write("start.01")
beam.traceOE(oe1,1)
if iwrite:
    oe1.write("end.01")
    beam.write("star.01")


#
#run optical element 2
#
print("    Running optical element: %d"%(2))
if iwrite:
    oe2.write("start.02")
beam.traceOE(oe2,2)
if iwrite:
    oe2.write("end.02")
    beam.write("star.02")


#
#run optical element 3
#
print("    Running optical element: %d"%(3))
if iwrite:
    oe3.write("start.03")
ray_before = beam.rays.copy()

beam.traceOE(oe3,3)


beam.rays[:,5]  = ray_before[:,5]
ray_after = beam.rays.copy()
for i in range(6):
    print(">>>>>>>>>>>>>>>>>>>>>",i,(ray_after-ray_before)[:,i])
if iwrite:
    oe3.write("end.03")
    beam.write("star.03")


#
#run optical element 4
#
print("    Running optical element: %d"%(4))
if iwrite:
    oe4.write("start.04")
beam.traceOE(oe4,4)
if iwrite:
    oe4.write("end.04")
    beam.write("star.04")


Shadow.ShadowTools.plotxy(beam,1,3,nbins=101,nolost=1,title="Real space")
# Shadow.ShadowTools.plotxy(beam,1,4,nbins=101,nolost=1,title="Phase space X")
# Shadow.ShadowTools.plotxy(beam,3,6,nbins=101,nolost=1,title="Phase space Z")

Dear Srio,
I want to raytrace the high energy laue monochromator, but how to set the anticlastic curvature optics? I think I can use a external file at the modified surface option. and I also found that there is pole location parameter for the torodal mirror , is that for a anticlastic curvature? and if so,how to use it? I try to set it but i don't know whether it is right or not. Thank you very much!

Best regards!
Yajun Tong
SSRF, China

Hello,

I have a problem when tracing a wiggler source using shadowoui. The sizes of source it gives are different from that of Spectra with the same parameters. It gives 118 micron x 35 micron with two distinct spots as shown below while the Spectra gives 1940 micron x 160 micron.

Is there a problem here in my settings?

Thank you for any help,
Zimeng Wang

On 8/13/22 1:41 AM, Samuel Gleason wrote:

Dear Manuel,

I have a small question about choosing the torus pole location.
I attach a file with two mirrors that represent different pieces of a bicycle-tire torus.
The first mirror is the 'bottom' of the tire, that is, a concave/concave surface.
The second mirror is the 'top' of the tire, that is, a convex/convex surface.

I've rotated the second mirror 180 degrees about its sagittal axis, expecting that this would make the two mirrors equivalent.
Instead, the beam now intersects the rotated mirror far away from the pole.

Are you able to explain why this is the case?
I asked Ruben Reininger, but he was also confused.

Thanks very much!
Sam Geason

torus_question.zip

Compound refractive lenses calculation present an image that is not centered at (0,0) as expected, but shifted vertically. This is more evident with a high number of lenses.

Effect of energy spread: it would be good to include energy spread in the calculation of divergence

Dear Sergey,

yes there is a problem in Laue symmetric, an undesirable switch that makes that it does not work correctly for symmetric Laue or asymmetric if angle is set at exactly 90.0 deg. The temporary solution is to set Laue asymmetric and set the angle near but not exactly at symmetric position, for example 90.001 deg.

I hope this answers your question.

Best regards,

Manuel

On 25.01.2020 10:08, Sergey Rashchenko wrote:

DEAR MANUEL,

Thank you for your efforts in developing Oasys!
Currently I am trying to study dispersion introduced into reflected
beam by Laue monochromator, and faced an unexpected behavior of SHADOW
(see attached workspace):
when I trace a parallel beam from a point source through symmetric
Laue crystal, no dispersion appears in the reflected beam in contrary
to theory (see also attached screenshots). I also checked symmetric
and asymmetric Bragg cases - they seem to give correct results. Is
this a bug, or just my misunderstanding of theory?

SINCERELY,
SERGEY V. RASHCHENKO, PH.D.

Budker Institute of Nuclear Physics
Novosibirsk, Russia

Running wigglers it may appear some error warning in interpolation routines.
This may originate non physical structures in the angular distributions, like:

Hello,

Trying to simulate simple angles scans in Bragg and Laue configurations for SI100, SI111 and SI220 crystals.
I have a ligth source (WIggler at 15 kEv with +/- 5ev distribution) connected to plane crystal set up in either Bragg or Lauer configuration. (Shown bellow)

I get expected results for SI111 and SI220, but for SI100 the intensity values explode (e.g. I get intensity >10000 at any incidence angle including computed Bragg/Laue configuration.

The crystal data is generated using Bragg tool. Is this a known issue? Or is there a solution/workaround I should try?

Configuration:

Result for SI100 at bragg angle

Result for SI111 at bragg angle

Thank you.

on the way...

It comes some confusions when I go through my simulation of paraboloid mirror. I will list them below.

1. The mirror
   I want the mirror could collimate the divergent beam in horizontal orientation, so I set the O.E. orientation angle of the mirror to 90 degrees.
   When I changed the angular divergence X(+ & -) of the source into a considerable value (e.g. 1 rad), the imaging results showed two light spots.
   I wonder whether two symmetrical mirrors have actually been set in the paraboloid module?
2. The orientation of center light
   An obvious question showed up If my presume above were true: I set up the incident angle, the source plane distance and the paraboloid parameter so that I can define the point “A” at which the center light acts with the parabolic collection mirror. Then I set up the dimensions of the mirror(X,Y half widths), so that I have construct the shape of one pair of dual parabolic mirrors. After I finish these steps, the another one pair of the dual parabolic mirrors would be created by symmetry through the axis of the parabola.
   Here comes the question: If I choose a gaussian source, the center light of the source is the ray that initiated from the center of gaussian spot to the point “A” which firstly defines the parabolic mirror that I construct, In the design of a spectrometer. It is hoped that the center light coincides with the parabolic mirrors symmetrical axis, the situation above makes the gaussian source plot somewhat asymmetric for parabolic symmetry axis.
   What could I attempt to make the center light coincide with the parabolic symmetry axis?
   
3. The movement of the source
   To be honest, I am so confused about those items in source movement. It seems that I could construct a polar coordinate system which the origin is at point “A”, then I could freely change the position of the source in the space. What confuse me is the item below.
   What would happen if I change those offsets in O.E. and SOURCE reference frames. after I have set up the angle of incidence, distance from O.E. and Z-rotation, i.e. whether there is a priority between the change of incident arm and angle with the change of the reference frame?
   

In my spectrometer layout design, I hope to make all the symmetry axes of meridional-oriental O.E. (e.g. focus mirror, grating) are coincident with the symmetry axis of the dual parabolic mirrors and the center light when the source is stable. However in the reference frame logic of SHADOW, when the source movement is taken into consideration, the layout seems to be so strange. In other words, I do not want my layout to be influenced by the movement of source. What parameter should I set extra to achieve my goal?

Thank you so much!
parabolic collimate mirror.zip

On 8/25/22 10:28 AM, Yu Xiaojiang wrote:

Dear Manuel

I test the reflectivity with graphite 002 and Si 111 for two configurations, finding the angles on the plane crystals of graphite are same in two configures, but reflectivity is difference, NOT expected.

For Si 111, angles are different, so the different reflectivity is just expected.

Do you think the problem is from Shadow code?

Please see the setup in the workspace attached (please check in CRYSTAL widget, graphite is chosen, my crystal list in the xraylib may be different from you).

Best regards
Xiaojian

graphite_reflectivity.zip

Request by Yasushi Kagoshima [email protected]:

Dear Dr. Manuel Sanchez del Rio

I am a professor in X-Ray physics.
I struggle to figure out how to simulate DuMond diagram by SHADOW.
In your paper
(http://www.esrf.eu/computing/scientific/people/srio/publications/SPIE98_rt-xtals.pdf
[1]), you said that

Du Mond diagram can be easily done with ray tracing.

I can not figure out how to simulate Du Mond diagram by SHADOW.

Could you please advise me?

Thank you very much for your help.

it seems that the calculated FWHM is a bit underestimated
Eg, Gaussian source 1umx1um 1e6 rays 501 bins gives 2.32, 2.29

Some great examples already given in the src/examples. And by using the functions of the C API we can create personalized scripts. But how can we use the subroutines in the shadow_preprocessors, like BRAGG or PreSURFACE in our C scripts？
This may be an old question already asked by others before, but it still keeps making me puzzled when I use the example01.c to simulate a Crystal diffraction.
Thanks, if there could be any tips~

It seems that "uniform" angular distribution for geometrical source is actually identical to "flat" one, and is not spherical as intended (see figure below). This is visible, however, only at very high angles, maybe not relevant for most calculations.

(Also reported in oasys-kit/ShadowOui)

When testing schemes with collimating lens installed before asymmetrically cut crystal, I found an unexpected behavior: lens widgets that use PreRefl data, followed by asymmetrically cut crystal produce a strange diagonal strike in beam cross-section, which I cannot explain physically. In addition, when using the 'ideal lens' widget instead (but with the same focal distance), the resulting beam cross-section is OK (see also .ows with example here: Test.zip).

see
oasys-kit/ShadowOui#166

Using python API, when shadow exit with stop because of some error, it crashes python and the user interface on top.

Bugs in OASYS / Shadow3, Jan 12, 2017 - Source and Optical Element Movement

Question by J. Dvorak. Answers in bold.

test: I set up a very simple geometric source, working in mm units using OASYS
point source, +H div = -H div = + V div = -V div = 0.001 rad, with a flat angular distribution
put a screen 1000 mm away, with a very short output plane, so that the OASYS plot shows the beam footprint at essentially the position of the screen

In this case, the beam footprint on the screen should appear as follows:

Test 1: Go under 'Optical Element Movement' and set it to 'Yes'
I find that none of the three translations or rotations have any effect.

It is normal. May be not logic. It has an explanation: the slit in ShadowOui, is in fact defined accompanying an “empty optical element” that you do not see in the interface. Moving an “empty element” does not make any effect.

Test 2: Go under 'Source Movement' and set it to 'Yes'. I set 'angle of incidence' to 0 (not quite sure what this does. angle relative to what?) and set the 'distance from OE' to +1000 mm. It is not explicitly stated in which reference frame this is, however, I assume this puts the source at -1000 mm in the OE reference frame, so I have reproduced the above configuration. I then get the same footprint on the screen as above.

It would be helpful if it explicitly says what reference frame the 'distance to OE' refers to.

The menu you refer to:

concerns the placement of the source (previous continuation plane) from the element itself. Therefore, in some way you should "copy" some information you already introduced (distance and incident angle).

Here there is a "complication" because you are using a slit as a testing element. In principle, one should use an optical element for that, with the referente frame as stated in the
Shadow3 primer

Therefore, you are applying the movements on an "empty element", and this is why you get weird effects. You should think in something like:

'z rotation' keeps image centered, but skews it. It acts like a rotation about the y axis. Furthermore, it does not act like a rotation of the source, it acts like a rotation of the OE reference frame.

in OE reference frame
x translation – seems to work correctly
y translation – should keep image centered, but make it larger or smaller, however, it acts as a z translation
z translation – acts like a y translation, making the image larger or smaller. Furthermore, if my interpretation of 'distance for OE' is correct, it has the
wrong sign. Moving +500 mm in the y direction in the OE reference frame should make the distance between the source and OE shorter,
and reduce the image size on the screen by 0.5 mm. It has the opposite effect.

in Source reference frame
x translation – seems to work correctly
y translation – in this very simple system, the +y direction in the source and OE reference frame are identical. In this case, if I set y offset to +500 mm,
the distance between the source and screen should decrease, and the image should be centered but smaller by 0.5 mm. This works correctly.
z translation – seems to work correctly

Please check the movements and you will see that it make sense now. I agree that is not trivial, the problem is that you have chosen a slit as your element, and we implemented it in ShadowOui linked to en empty element that you do not see. It is on top of this empty element that the movements are applied.

Hello @srio, what is the license for this project? Is it BSD 3-Clause or similar? Could you please kindly add the corresponding license file? Thank you!

from the two possible intersection of a ray with a conic, shadow selects one. It was explained here:
http://ftp.esrf.fr/pub/scisoft/shadow/user_contributions/hyperbola_fixes_2008-10-22.txt

In the case of highly demagnifying KBs, for example, p>>, and one solution is at -t1 and the other is at t2~p, so |-t1-p| < |t2-p| so it takes -t1 (wrong solution).

Temporary solution: place a screen close and upstream to the mirror.

Permanent solution: change the way of selecting t in
https://github.com/srio/shadow3/blob/master/src/fortran/shadow_kernel.f90

Change:

          IF ( ABS(TPAR1-T_SOURCE).LE.ABS(TPAR2-T_SOURCE)  ) THEN
             TPAR=TPAR1
          ELSE
             TPAR=TPAR2
          END IF

to:

          IF ( ABS( abs(TPAR1)-abs(T_SOURCE)).LE.ABS(abs(TPAR2)-abs(T_SOURCE))  ) THEN
             TPAR=TPAR1
          ELSE
             TPAR=TPAR2
          END IF

and make a lot of tests...

Hello.

Please help me with modeling the reflection from parabolic mirrors.

I take geometrical source with wavelenght 1.54A and try to focusing.

And i got good results for focusing by parabolic mirror with small distances. For example, source distance 14cm, Image 29 and paraboloid parameter 30 cm.

Are these results correct ? Can I use small distances ?
parabolic mirror.zip

And how I can set roughnes if I only have image from atomic-force microscope with some data like RMS, without any special files ?

ubuntu 20.04
python 3.8.8
pip 21.1.1
setuptools 56.1.0

python setup.py build

Traceback (most recent call last):
  File "setup.py", line 103, in <module>
    setup(
  File "...lib/python3.8/distutils/core.py", line 148, in setup
    dist.run_commands()
  File "...lib/python3.8/distutils/dist.py", line 966, in run_commands
    self.run_command(cmd)
  File "...lib/python3.8/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "...lib/python3.8/distutils/command/build.py", line 135, in run
    self.run_command(cmd_name)
  File "...lib/python3.8/distutils/cmd.py", line 313, in run_command
    self.distribution.run_command(command)
  File "...lib/python3.8/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "...lib/python3.8/site-packages/numpy/distutils/command/build_clib.py", line 122, in run
    dispatch_hpath = os.path.join(self.get_finalized_command("build_src").build_src, dispatch_hpath)
  File "...lib/python3.8/distutils/cmd.py", line 103, in __getattr__
    raise AttributeError(attr)
AttributeError: build_src

self.get_finalized_command("build_src") returns a NullCommand instance due to

    cmdclass={
        'build_clib': BuildClib,
        'build_src': NullCommand,
    },

In some LINUX installations of OASYS (using miniconda) the OASYS application bombs when running a system contaning source and at least one optical element:

Exit from SETSOUR
Call to IMREF
Exit from IMREF
Call to OPTAXIS
At line 416 of file src/fortran/stringio.f90
Internal Error: get_unit(): Bad internal unit KIND

The problem is related to using an old compiler for creating the shadow3 binaries.

For example, this is bad:

gurb:/nobackup/srio/OASYS1.1 % gfortran --version
GNU Fortran (Debian 4.9.2-10) 4.9.2
Copyright (C) 2014 Free Software Foundation, Inc.

GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of GNU Fortran
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING

This is good:

chac:~/OASYS1/shadow3/dist % gfortran --version
GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.4) 5.4.0 20160609
Copyright (C) 2015 Free Software Foundation, Inc.

Quick solution:
overwrite the installation with a working compiled version (wheel). For example:

pip install http://ftp.esrf.eu/pub/scisoft/shadow3/wheels/shadow3-18.5.30-cp36-cp36m-linux_x86_64.whl--upgrade

Developer solution:

Install shadow3 in your system, compile it and test it:

git clone http://github.com/oasys-kit/shadow3 
cd shadow3
python setup.py clean build
pip install . --upgrade
cd tests
python test_lens.py

If this fails, you need to upgrade your compiler.

Note that simple "pip install shadow3" may fail as it may download sources and build them in your system.

I am trying to upgrade the adds-on to OASYS-kit. The message reminds to upgrade pip. After upgrading the pip to the latest, the OASYS-kit still refuses to upgrade and keep warning.
Please help me out,
Thanks