Version 2.3.0

Merged pull request for non-integer hkl option on SF and electron form factors.
Thanks Prestipino!
Added menu with various options to GUI.
Updated docs and examples.

Dans_Diffraction/__init__.py

@@ -31,8 +31,8 @@
 Diamond
 2017
 
-Version 2.2.3
-Last updated: 14/01/23
+Version 2.3.0
+Last updated: 08/05/23
 
 Version History:
 02/03/18 1.0    Version History started.
@@ -66,6 +66,7 @@
 23/07/22 2.2.1  Fixed error in MultiCrystal.Scatter
 06/01/23 2.2.2  Removed redundent references to np.float
 14/01/23 2.2.3  Corrected background error in xtl.Scatter.powder
+08/05/23 2.3.0  Merged pull request for non-integer hkl option on SF and electron form factors. Thanks Prestipino!
 
 -----------------------------------------------------------------------------
    Copyright 2023 Diamond Light Source Ltd.
@@ -119,8 +120,8 @@
     from .classes_fdmnes import Fdmnes, FdmnesAnalysis
 
 
-__version__ = '2.2.3'
-__date__ = '14/01/23'
+__version__ = '2.3.0'
+__date__ = '08/05/23'
 
 
 # Build
@@ -155,6 +156,10 @@ def module_info():
     return out
 
 
+def doc_str():
+    return __doc__
+
+
 # tkGUI Activation
 def start_gui(xtl=None):
     """Start GUI window (requires tkinter)"""

Dans_Diffraction/__main__.py

@@ -15,7 +15,7 @@
 
 By Dan Porter, PhD
 Diamond
-2017
+2023
 """
 if __name__ == '__main__':
 
@@ -32,6 +32,9 @@
         if 'cif' in arg.lower():
             xtl = dif.Crystal(arg)
             print(xtl.info())
+        elif arg in dif.structure_list.list:
+            xtl = getattr(dif.structure_list, arg)()
+            print(xtl.info())
         elif 'gui' in arg.lower():
             xtl.start_gui()
 

Dans_Diffraction/classes_crystal.py

@@ -1826,11 +1826,11 @@ def print_symmetric_coordinate_operations(self, UVW, remove_identical=True):
             unique_uvw, uniqueidx, matchidx = fg.unique_vector(sym_uvw, tol=0.01)
 
             out += ' (%1.3g, %1.3g, %1.3g)\n' % (u, v, w)
-            out += '  n       u       v       w             Symmetry    Magnetic Symmetry\n'
+            out += '  n       u       v       w   Symmetry                        Magnetic Symmetry\n'
             if remove_identical:
                 # Only display distict positions
                 for n in range(len(unique_uvw)):
-                    out += '%3d %7.4f %7.4f %7.4f %20s %20s\n' % (
+                    out += '%3d %7.4f %7.4f %7.4f %30s %20s\n' % (
                         uniqueidx[n], unique_uvw[n, 0], unique_uvw[n, 1], unique_uvw[n, 2],
                         self.symmetry_operations[uniqueidx[n]], self.symmetry_operations_magnetic[uniqueidx[n]])
             else:

Dans_Diffraction/classes_scattering.py

@@ -7,8 +7,8 @@
 Diamond
 2017
 
-Version 2.1.1
-Last updated: 14/01/23
+Version 2.2.0
+Last updated: 06/05/23
 
 Version History:
 10/09/17 0.1    Program created
@@ -31,6 +31,7 @@
 08/02/22 2.0.3  Corrected error in powder of wrong tth values. Thanks Mirko!
 14/03/22 2.1.0   powder() updated for new inputs and outputs for pVoight and custom peak shapes. Thanks yevgenyr!
 14/01/23 2.1.1  Corrected background error in xtl.Scatter.powder
+06/05/23 2.0.0  Merged pull request for non-integer hkl option on SF and electron form factors. Thanks Prestipino!
 
 @author: DGPorter
 """
@@ -45,7 +46,7 @@
 from . import multiple_scattering as ms
 # from . import tensor_scattering as ts  # Removed V1.7
 
-__version__ = '2.1.1'
+__version__ = '2.2.0'
 __scattering_types__ = {'xray': ['xray', 'x', 'x-ray', 'thomson', 'charge'],
                         'neutron': ['neutron', 'n', 'nuclear'],
                         'xray magnetic': ['xray magnetic', 'magnetic xray', 'spin xray', 'xray spin'],
@@ -356,6 +357,7 @@ def structure_factor(self, hkl=None, scattering_type=None, int_hkl=True, **kwarg
 
         :param hkl: array[n,3] : reflection indexes (h, k, l)
         :param scattering_type: str : one of ['xray','neutron','xray magnetic','neutron magnetic','xray resonant']
+        :param int_hkl: Bool : when True, hkl values are converted to integer.
         :param kwargs: additional options to pass to scattering function
         :return: complex array[n] : structure factors
         """
@@ -365,9 +367,9 @@ def structure_factor(self, hkl=None, scattering_type=None, int_hkl=True, **kwarg
         if scattering_type is None:
             scattering_type = self._scattering_type
         if int_hkl:
-            hkl = np.asarray(np.rint(hkl), dtype=np.float).reshape([-1, 3])
+            hkl = np.asarray(np.rint(hkl), dtype=float).reshape([-1, 3])
         else:
-            hkl = np.asarray(hkl, dtype=np.float).reshape([-1, 3])
+            hkl = np.asarray(hkl, dtype=float).reshape([-1, 3])
         uvw, atom_type, label, occ, uiso, mxmymz = self.xtl.Structure.get()
 
         q = self.xtl.Cell.calculateQ(hkl)
@@ -424,14 +426,14 @@ def structure_factor(self, hkl=None, scattering_type=None, int_hkl=True, **kwarg
                     # Scattering factors
                     if scattering_type in fs.SCATTERING_TYPES['neutron']:
                         ff = fc.atom_properties(atom_type, 'Coh_b')
+                    elif scattering_type in fs.SCATTERING_TYPES['electron']:
+                        ff = fc.electron_scattering_factor(atom_type, qmag)
                     elif scattering_type in fs.SCATTERING_TYPES['xray fast']:
                         ff = fc.atom_properties(atom_type, 'Z')
                     elif scattering_type in fs.SCATTERING_TYPES['xray dispersion']:
                         ff = fc.xray_scattering_factor_resonant(atom_type, qmag, enval)
                     elif self._use_waaskirf_scattering_factor:
                         ff = fc.xray_scattering_factor_WaasKirf(atom_type, qmag)
-                    elif scattering_type in fs.SCATTERING_TYPES['electron']:
-                        ff = fc.electron_scattering_factor(atom_type, qmag)
                     else:
                         ff = fc.xray_scattering_factor(atom_type, qmag)
 
@@ -474,10 +476,12 @@ def structure_factor(self, hkl=None, scattering_type=None, int_hkl=True, **kwarg
 
     def intensity(self, hkl=None, scattering_type=None, int_hkl=True, **options):
         """
-
-        :param hkl:
-        :param scattering_type: str : one of ['xray','neutron','xray magnetic','neutron magnetic','xray resonant']
-        :return:
+        Return the structure factor squared
+        :param hkl: array[n,3] : reflection indexes (h, k, l)
+        :param scattering_type: str : one of ['xray','neutron', 'electron', 'xray magnetic','neutron magnetic','xray resonant']
+        :param int_hkl: Bool : when True, hkl values are converted to integer.
+        :param kwargs: additional options to pass to scattering function
+        :return: float array[n] : array of |SF|^2
         """
         return fs.intensity(self.new_structure_factor(hkl, scattering_type, int_hkl, **options))
     new_intensity = intensity
@@ -623,7 +627,7 @@ def x_ray(self, HKL):
 
         # Calculate structure factor
         # Broadcasting used on 2D ff
-        SF =  np.sum(ff*dw*occ*np.exp(1j*2*np.pi*dot_KR),axis=1)
+        SF =  np.sum(ff*dw*occ*np.exp(1j*2*np.pi*dot_KR), axis=1)
         #SF = np.zeros(Nref,dtype=complex)
         #for ref in range(Nref):
         #    for at in range(Nat): 
@@ -723,7 +727,16 @@ def xray_dispersion(self, HKL, energy_kev):
         # Calculate intensity
         I = sf * np.conj(sf)
         return np.real(I)
-
+
+    def electron(self, HKL):
+        """
+        Calculate the squared structure factor for the given HKL, using electron form factors
+          Scattering.electron([1,0,0])
+          Scattering.electron([[1,0,0],[2,0,0],[3,0,0])
+        Returns an array with the same length as HKL, giving the real intensity at each reflection.
+        """
+        return self.intensity(HKL, scattering_type='electron')
+
     def neutron(self, HKL):
         """
         Calculate the squared structure factor for the given HKL, using neutron scattering length

Dans_Diffraction/functions_crystallography.py

@@ -11,8 +11,8 @@
     OR
     - from Dans_Diffraction import functions_crystallography as fc
 
-Version 3.7.2
-Last updated: 23/04/22
+Version 3.8.0
+Last updated: 07/05/23
 
 Version History:
 09/07/15 0.1    Version History started.
@@ -40,9 +40,11 @@
 15/11/21 3.7    Added diffractometer orientation commands from Busing & Levy, H. You
 12/01/22 3.7.1  Added gen_sym_axial_vector
 23/04/22 3.7.2  Corrected magnitude of Q in magnetic_structure_factors
+07/05/23 3.8.0  Added electron_scattering_factors and electron wavelength formula
 
 Acknoledgements:
     April 2020  Thanks to ChunHai Wang for helpful suggestions in readcif!
+    May 2023    Thanks to Carmelo Prestipino for adding electron scattering factors
 
 @author: DGPorter
 """
@@ -966,6 +968,7 @@ def xray_scattering_factor(element, Qmag=0):
         Qff[:, n] = f
     return Qff
 
+
 def electron_scattering_factor(element, Qmag=0):
     """
     Read X-ray scattering factor table, calculate f(|Q|)
@@ -982,12 +985,10 @@ def electron_scattering_factor(element, Qmag=0):
     Qmag = np.asarray(Qmag).reshape(-1)
 
     try:
-        data = np.genfromtxt(PENGFILE, skip_header=0, dtype=None, names=True, 
-                             encoding='ascii', delimiter=',')
+        data = np.genfromtxt(PENGFILE, skip_header=0, dtype=None, names=True, encoding='ascii', delimiter=',')
     except TypeError:
         # Numpy version < 1.14
-        data = np.genfromtxt(PENGFILE, skip_header=0, dtype=None, names=True,
-                             delimiter=',')
+        data = np.genfromtxt(PENGFILE, skip_header=0, dtype=None, names=True, delimiter=',')
     # elements must be a list e.g. ['Co','O']
     elements_l = np.asarray(element).reshape(-1)
     all_elements = [el for el in data['Element']]
@@ -3104,6 +3105,16 @@ def wavevector(energy_kev=None, wavelength=None):
     return 2 * np.pi / wavelength
 
 
+def electron_wavelenth(energy_ev):
+    """
+    Calcualte the electron wavelength in Angstroms using DeBroglie's formula
+      lambda [nm] ~ sqrt( 1.5 / E [eV] )
+    :param energy_ev: electron energy in eV
+    :return: wavelength in Anstroms
+    """
+    return fg.h / np.sqrt(2 * fg.me * energy_ev * fg.e) / fg.A
+
+
 def biso2uiso(biso):
     """
     Convert B isotropic thermal parameters to U isotropic thermal parameters

Dans_Diffraction/functions_scattering.py

@@ -67,7 +67,8 @@
     'xray magnetic': ['xray magnetic', 'magnetic xray', 'spin xray', 'xray spin'],
     'neutron magnetic': ['neutron magnetic', 'magnetic neutron', 'magnetic'],
     'xray resonant': ['xray resonant', 'resonant', 'resonant xray', 'rxs'],
-    'xray dispersion': ['dispersion', 'xray dispersion']
+    'xray dispersion': ['dispersion', 'xray dispersion'],
+    'electron': ['electron', 'ele', 'e'],
 }
 
 
@@ -812,6 +813,8 @@ def get_scattering_function(scattering_type):
         return sf_xray_dispersion
     if scattering_type in SCATTERING_TYPES['neutron']:
         return sf_atom
+    if scattering_type in SCATTERING_TYPES['electron']:
+        return sf_atom
     if scattering_type in SCATTERING_TYPES['xray magnetic']:
         return sf_magnetic_xray
     if scattering_type in SCATTERING_TYPES['neutron magnetic']:

Dans_Diffraction/tkgui/basic_widgets.py

@@ -3,11 +3,14 @@
 """
 
 import sys
+import re
 
 if sys.version_info[0] < 3:
     import Tkinter as tk
+    import tkMessageBox as messagebox
 else:
     import tkinter as tk
+    from tkinter import messagebox
 
 # Fonts
 TF = ["Times", 12]
@@ -35,6 +38,66 @@
 TTFG = 'red'
 
 
+def popup_message(parent, title, message):
+    """Create a message box"""
+    root = tk.Toplevel(parent)
+    root.title(title)
+    #frame = tk.Frame(root)
+    tk.Label(root, text=message, padx=20, pady=20).pack()
+    #root.after(2000, root.destroy)
+    return root
+
+
+def popup_about():
+    """Create about message"""
+    from Dans_Diffraction import version_info, module_info
+    msg = "%s\n\n" \
+          "A Python package for loading crystal structures from " \
+          "cif files and calculating diffraction information.\n\n" \
+          "Module Info:\n%s\n\n" \
+          "By Dan Porter, Diamond Light Source Ltd" % (version_info(), module_info())
+    messagebox.showinfo('About', msg)
+
+
+def popup_help():
+    """Create help message"""
+    from Dans_Diffraction import doc_str
+    return StringViewer(doc_str(), 'Dans_Diffraction Help', width=121)
+
+
+def topmenu(root, menu_dict):
+    """
+    Add a menubar to tkinter frame
+    :param root: tkinter root
+    :param menu_dict: {Menu name: {Item name: function}}
+    :return: None
+    """
+    # Setup menubar
+    menubar = tk.Menu(root)
+
+    for item in menu_dict:
+        men = tk.Menu(menubar, tearoff=0)
+        for label, function in menu_dict[item].items():
+            men.add_command(label=label, command=function)
+        menubar.add_cascade(label=item, menu=men)
+    root.config(menu=menubar)
+
+
+def menu_docs():
+    """Open local docs"""
+    import os
+    import webbrowser
+    docs_dir = os.path.join(os.path.split(__file__)[0], '../../docs/Dans_Diffraction.html')
+    docs_dir = os.path.abspath(docs_dir)
+    webbrowser.open_new_tab(docs_dir)
+
+
+def menu_github():
+    """Open GitHub page"""
+    import webbrowser
+    webbrowser.open_new_tab("https://github.com/DanPorter/Dans_Diffraction#dans_diffaction")
+
+
 class StringViewer:
     """
     Simple GUI that displays strings