yb66

Upgrade XOPPY/CRYSTAL and SHADOW with any crystal, in particular YB66. This repo contains workspaces and scripts.

Paper

Yu, X. J., Chi, X., Smulders, T., Wee, A. T. S., Rusydi, A., Sanchez del Rio, M. & Breese, M. B. H. "Beamline simulations using monochromators with high d-spacing crystals" (2022). J. Synchrotron Rad. 29. https://doi.org/10.1107/S160057752200707X

Oasys workspaces

There are a OASYS workspaces with YB66 examples and calculations for the paper in this repository (https://github.com/91902078/yb66/tree/main/workspaces/), in files:

• https://raw.githubusercontent.com/91902078/yb66/main/workspaces/yb66_paper.ows
• https://raw.githubusercontent.com/91902078/yb66/main/workspaces/JUMBO_YB66.ows
• https://raw.githubusercontent.com/91902078/yb66/main/workspaces/YB66_VS_GRATING.ows

If loading from OASYS, please use the link after pressing the "raw" button in github.

FIGURES AND TABLES

Figures and Tables for the paper used these scripts and worspaces:

• Table 1 use https://github.com/91902078/yb66/paper_figs_and_tables/table1_explore.py https://github.com/91902078/yb66/paper_figs_and_tables/table1.py and *txt
• Table 3 use https://github.com/91902078/yb66/paper_figs_and_tables/table3.py
• Fig. 1 use https://github.com/91902078/yb66/paper_figs_and_tables/figure1.py
• Fig. 4,5 use the Oasys workspace https://github.com/91902078/yb66/workspaces/yb66_paper.ows
• Fig. 6 use https://github.com/91902078/yb66/paper_figs_and_tables/figure6.py
• Fig. 7,8 use the Oasys workspace https://github.com/91902078/yb66/workspaces/yb66_paper.ows and https://raw.githubusercontent.com/91902078/yb66/main/workspaces/JUMBO_YB66.ows

Summary of changes

XOPPY

XOPPY/CRYSTAL and also XOPPY/FH read a preprocessor file xcrystal.bra

This file was prepared with (now obsolete)

    from orangecontrib.xoppy.util.xoppy_xraylib_util import bragg_calc
    from orangecontrib.xoppy.util.xoppy_xraylib_util import crystal_fh

The file (or dictionary) created by bragg_calc() is used:

• in python crystal_fh() to calculate structure factors in XOPPY/FH
• in fortran diff_patt to calculate diffraction profiles in XOPPY/CRYSTAL

The new tools for creating the preprocessor file necessary for YB66 work using dabax instead of xraylib. They are integrated in a new package xoppylib.

The new bragg_calc is called bragg_calc2:

    from xoppylib.crystals.tools import bragg_calc2, crystal_fh

a typical run of bragg_calc2:

    from dabax.dabax_xraylib import DabaxXraylib # imports dabax decorated with interface like xraylib
    import xraylib
    
    ENERGY = 8040.0
    SCANFROM = 0  # in microradiants
    SCANTO = 100  # in microradiants
    SCANPOINTS = 200
    # if using DABAX for YB66:
    bragg_dictionary = bragg_calc2(descriptor=descr"YB66",
                                       hh=4, kk=0, ll=0,
                                       temper=1.0,
                                       emin=ENERGY - 100.0, emax=ENERGY + 100.0,
                                       estep=(SCANTO - SCANFROM) / SCANPOINTS, fileout="xcrystal.bra",
                                       material_constants_library=DabaxXraylib())
                                       
    # Example using xraylib (for Si)
    bragg_dictionary = bragg_calc2(descriptor=descr"Si",hh=1, kk=1, ll=1,temper=1.0,
                                       emin=ENERGY - 100.0, emax=ENERGY + 100.0,
                                       estep=(SCANTO - SCANFROM) / SCANPOINTS, fileout="xcrystal.bra",
                                       material_constants_library=xraylib)

In Oasys, one can use this dictionary to calculate the structure factors (using crystal_fh) or the diffraction pattern (using run_diff_pat):

from xoppylib.crystals.tools import run_diff_pat, crystal_fh

    run_diff_pat(
        bragg_dictionary,
        preprocessor_file="xcrystal.bra",
        MOSAIC=0,
        GEOMETRY=0,
        SCAN=2,
        UNIT=1,
        SCANFROM=SCANFROM,
        SCANTO=SCANTO,
        SCANPOINTS=SCANPOINTS,
        ENERGY=ENERGY,
        ASYMMETRY_ANGLE=0.0,
        THICKNESS=0.7)

    from srxraylib.plot.gol import plot

    data = numpy.loadtxt("diff_pat.dat", skiprows=5)
    plot(data[:, 0], data[:, -1])
    
    dic0b = crystal_fh(bragg_dictionary, 8000.0)
    print(dict0['info'])
    
        

Examples are in the directory https://github.com/91902078/yb66/yb66/new

SHADOW

the python tools in XOPPY allows to create the preprocessor file for shadow (the one created with bragg_calc2).

This new preprocessor file required important changes in the SHADOW fortran kernel. It accepts now both preprocessors file vesrions (v1 for the old one, v2 for the new one). The new code added for the v2 preprocessor.

ShadowOui

The bragg preprocessor widget has been upgraded. This includes Beryl, Muscovite and YB66 in the "bragg" "default" or traditional preprocessor (v1). In addition, it creates preprocessor file v2 with a crystal from two new lists: DABAX and XRayServer. It uses xoppylib as dependence, as it reuses the bragg_calc2 in xoppy.