completed scherrer example

crystalpy/util/calc_xcrystal.py

@@ -19,6 +19,7 @@ def get_diffraction_setup(
         miller_l=1,
         geometry_type_index=0,
         asymmetry_angle=0.0,
+        dabax=None, # only used if material_constants_library_flag > 0
         ):
 
     # Create a diffraction setup.
@@ -50,7 +51,9 @@ def get_diffraction_setup(
                                                    miller_k               = miller_k,           # int
                                                    miller_l               = miller_l,           # int
                                                    asymmetry_angle        = asymmetry_angle,    # radians
-                                                   azimuthal_angle        = 0.0)                # radians
+                                                   azimuthal_angle        = 0.0,                # radians
+                                                   dabax                  = dabax,
+                                                   )
 
     return diffraction_setup
 
@@ -73,6 +76,7 @@ def calc_xcrystal_angular_scan(
         use_transfer_matrix=0,
         do_plot=0,
         calculation_strategy_flag=0,  # 0=mpmath 1=numpy 2=numpy-truncated
+        dabax=None, # only used if material_constants_library_flag > 0
         ):
 
     print("material_constants_library_flag    = ", material_constants_library_flag)
@@ -91,6 +95,10 @@ def calc_xcrystal_angular_scan(
     print("is_thick                           = ", is_thick)
     print("use_transfer_matrix                = ", use_transfer_matrix)
     print("geometry_type_index                = ", geometry_type_index)
+    if dabax is None:
+        print("dabax                              = ", dabax)
+    else:
+        print("dabax                              = \n", dabax.info())
 
     # Create a diffraction setup.
     diffraction_setup = get_diffraction_setup(
@@ -102,6 +110,7 @@ def calc_xcrystal_angular_scan(
         asymmetry_angle=asymmetry_angle,
         geometry_type_index=geometry_type_index,
         material_constants_library_flag=material_constants_library_flag,
+        dabax=dabax,
         )
 
 
@@ -166,6 +175,7 @@ def calc_xcrystal_alphazachariasen_scan(
         use_transfer_matrix=0,
         do_plot=0,
         calculation_strategy_flag=0,  # 0=mpmath 1=numpy 2=numpy-truncated
+        dabax=None, # only used if material_constants_library_flag > 0
         ):
 
     print("material_constants_library_flag    = ", material_constants_library_flag)
@@ -183,6 +193,10 @@ def calc_xcrystal_alphazachariasen_scan(
     print("is_thick                           = ", is_thick)
     print("use_transfer_matrix                = ", use_transfer_matrix)
     print("geometry_type_index                = ", geometry_type_index)
+    if dabax is None:
+        print("dabax                              = ", dabax)
+    else:
+        print("dabax                              = \n", dabax.info())
 
     # Create a diffraction setup.
     diffraction_setup = get_diffraction_setup(
@@ -194,6 +208,7 @@ def calc_xcrystal_alphazachariasen_scan(
         asymmetry_angle=asymmetry_angle,
         geometry_type_index=geometry_type_index,
         material_constants_library_flag=material_constants_library_flag,
+        dabax=dabax,
         )
 
 
@@ -262,6 +277,7 @@ def calc_xcrystal_energy_scan(
         use_transfer_matrix=0,
         do_plot=0,
         calculation_strategy_flag=0,  # 0=mpmath 1=numpy 2=numpy-truncated
+        dabax=None, # only used if material_constants_library_flag > 0
         ):
 
     print("material_constants_library_flag    = ", material_constants_library_flag)
@@ -279,6 +295,10 @@ def calc_xcrystal_energy_scan(
     print("is_thick                           = ", is_thick)
     print("use_transfer_matrix                = ", use_transfer_matrix)
     print("geometry_type_index                = ", geometry_type_index)
+    if dabax is None:
+        print("dabax                              = ", dabax)
+    else:
+        print("dabax                              = \n", dabax.info())
 
     # Create a diffraction setup.
     diffraction_setup = get_diffraction_setup(
@@ -290,6 +310,7 @@ def calc_xcrystal_energy_scan(
         asymmetry_angle=asymmetry_angle,
         geometry_type_index=geometry_type_index,
         material_constants_library_flag=material_constants_library_flag,
+        dabax=dabax,
         )
 
     if theta is None:
@@ -354,6 +375,7 @@ def calc_xcrystal_double_scan(
         geometry_type_index=0,
         do_plot=0,
         calculation_strategy_flag=0,  # 0=mpmath 1=numpy 2=numpy-truncated
+        dabax=None,  # only used if material_constants_library_flag > 0
 ):
 
 
@@ -375,7 +397,10 @@ def calc_xcrystal_double_scan(
     print("is_thick                           = ", is_thick)
     print("use_transfer_matrix                = ", use_transfer_matrix)
     print("geometry_type_index                = ", geometry_type_index)
-
+    if dabax is None:
+        print("dabax                              = ", dabax)
+    else:
+        print("dabax                              = \n", dabax.info())
 
     # Create a diffraction setup.
     diffraction_setup = get_diffraction_setup(
@@ -387,6 +412,7 @@ def calc_xcrystal_double_scan(
         asymmetry_angle=asymmetry_angle,
         geometry_type_index=geometry_type_index,
         material_constants_library_flag=material_constants_library_flag,
+        dabax=dabax,
         )
 
     if energy_points == 1:

examples/scherrer/Readme.rst

@@ -0,0 +1,48 @@
+==============================================================
+Test of test Scherrer equation vs dynamical diffracion results
+==============================================================
+
+The dynamical diffraction profile is calculated for several cases of hkl reflections and crystal thickness, and
+the results are compared with the Scherrer equation for two crystals LaB6 and Tripalmitin.
+
+----
+LaB6
+----
+
+For LaB6 the results are calculated using the scripts:
+
+- scherrer_LaB6.py : comparison as a function of 2theta.
+
+.. image:: ./scherrer_LaB6.png
+
+- scherrer_vs_xtal_thickness_LaB6.py : comparison vs crystal thickness.
+
+.. image:: ./scherrer_vs_xtal_thickness_LaB6.png
+
+-----------
+Tripalmitin
+-----------
+
+Tripalmitin crystal is not available in the standard crystalpy material libraries (xraylib and dabax).
+To include it, a new entry has been created in the dabax data file ./dabax/Crystals.dat, that is used for calculations
+in the scripts
+
+- scherrer_Tripalmitin.py : comparison as a function of 2theta.
+
+.. image:: ./scherrer_Tripalmitin.png
+
+- scherrer_vs_xtal_thickness_tripalmitin.py : comparison vs crystal thickness.
+
+.. image:: ./scherrer_vs_xtal_thickness_Tripalmitin.png
+
+This new entry in dabax has been created:
+
+- using the cif file from: https://www.ccdc.cam.ac.uk/structures/Search?Compound=tripalmitin&DatabaseToSearch=Published
+
+- calculating the 1x1x1 supercell using cif2cell (files here: https://github.com/srio/shadow3-scripts/tree/master/cif131755 )
+
+- copying this structure to Crystals.dat
+
+The selected [intense] reflections are obtained making a powder diffraction simulation runing oasys/powder with the cif
+file (files: https://github.com/srio/shadow3-scripts/tree/master/cif131755 ).
+

examples/scherrer/crystal_check.py

@@ -0,0 +1,41 @@
+#
+# crystal tests
+#
+import numpy
+from dabax.dabax_xraylib import DabaxXraylib
+
+dx = DabaxXraylib(dabax_repository='./dabax/')
+print(dx.info())
+# dx.set_verbose()
+
+print("DABAX crystal list: \n", dx.Crystal_GetCrystalsList())
+
+crystal = 'Tripalmitin'
+siD = dx.Crystal_GetCrystal(crystal)
+
+print("DABAX crystal: \n", siD)
+
+print("%s 111 d-spacing: DABAX: %g" % \
+      (crystal, dx.Crystal_dSpacing(siD, 1, 1, 1)))
+
+print("%s 111 bragg angle at 10 keV [deg]: DABAX: %g" % ( crystal, \
+    180 / numpy.pi * dx.Bragg_angle(siD, 10, 1, 1, 1), ))
+
+# F0 = dx.Crystal_F_H_StructureFactor(siD,8.0,0,0,0,1.0,ratio_theta_thetaB=1.0)
+dabax_all_F = dx.Crystal_F_0_F_H_F_H_bar_StructureFactor(siD, 8.0, 1, 1, 1, 1.0, rel_angle=1.0)
+
+print("F0 dabax: ",
+      dx.Crystal_F_H_StructureFactor(siD, 8.0, 0, 0, 0, 1.0, 1.0), dabax_all_F[0],
+      )
+
+print("F111 dabax: ",
+      dx.Crystal_F_H_StructureFactor(siD, 8.1, 1, 1, 1, 1.0, 1.0), dabax_all_F[1],
+      )
+
+print("F-1-1-1 dabax: ",
+      dx.Crystal_F_H_StructureFactor(siD, 8.1, -1, -1, -1, 1.0, 1.0), dabax_all_F[2],
+      )
+
+print("F001 dabax F2: ", numpy.abs(dx.Crystal_F_H_StructureFactor(siD, 8.1, 0, 0, 1, 1.0, 1.0))**2)
+print("F002 dabax F2: ", numpy.abs(dx.Crystal_F_H_StructureFactor(siD, 8.1, 0, 0, 2, 1.0, 1.0))**2)
+print("F003 dabax F2: ", numpy.abs(dx.Crystal_F_H_StructureFactor(siD, 8.1, 0, 0, 3, 1.0, 1.0))**2)