updated docs and scripts

Updated docs Changed tkgui.properties.XrayInteractionsGUI to run independantly. Added cli arguments to run xray properties gui and fdmnes gui.
DanPorter · Feb 9, 2025 · 4982192 · 4982192
1 parent f9c1a22
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diff --git a/Dans_Diffraction/__init__.py b/Dans_Diffraction/__init__.py
@@ -208,11 +208,14 @@ def doc_str():
 # tkGUI Activation
 def start_gui(xtl=None):
     """Start GUI window (requires tkinter)"""
-    try:
-        from .tkgui import CrystalGui
-        CrystalGui(xtl)
-    except ImportError:
-        print('GUI functionality not available, you need to install tkinter.')
+    from .tkgui import CrystalGui
+    CrystalGui(xtl)
+
+
+def start_properties_gui():
+    """Start XRay Interactions GUI"""
+    from .tkgui.properties import XrayInteractionsGui
+    XrayInteractionsGui()
 
 
 # FDMNES Activation
@@ -224,3 +227,9 @@ def activate_fdmnes(initial_dir=None, fdmnes_filename='fdmnes_win64.exe'):
     :return: None
     """
     fdmnes_checker(activate=True, fdmnes_filename=fdmnes_filename, initial_dir=initial_dir)
+
+
+def start_fdmnes_gui():
+    """Start GUI for FDMNES"""
+    from .tkgui.fdmnes import AnaFDMNESgui
+    AnaFDMNESgui()
diff --git a/Dans_Diffraction/__main__.py b/Dans_Diffraction/__main__.py
@@ -37,4 +37,10 @@
             print(xtl.info())
         elif 'gui' in arg.lower():
             xtl.start_gui()
+        elif 'properties' in arg.lower():
+            from Dans_Diffraction.tkgui.properties import XrayInteractionsGui
+            XrayInteractionsGui()
+        elif 'fdmnes' in arg.lower():
+            from Dans_Diffraction.tkgui.fdmnes import AnaFDMNESgui
+            AnaFDMNESgui()
 
diff --git a/Dans_Diffraction/tkgui/basic_widgets.py b/Dans_Diffraction/tkgui/basic_widgets.py
@@ -105,11 +105,14 @@ def topmenu(root, menu_dict):
     # 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)
+    for item, obj in menu_dict.items():
+        if isinstance(obj, dict):
+            men = tk.Menu(menubar, tearoff=0)
+            for label, function in obj.items():
+                men.add_command(label=label, command=function)
+            menubar.add_cascade(label=item, menu=men)
+        else:
+            menubar.add_command(label=item,command=obj)
     root.config(menu=menubar)
 
 

diff --git a/Dans_Diffraction/tkgui/properties.py b/Dans_Diffraction/tkgui/properties.py
@@ -8,7 +8,7 @@
 from .. import functions_general as fg
 from .. import functions_crystallography as fc
 from .. import functions_plotting as fp
-from .basic_widgets import tk, StringViewer, SelectionBox, messagebox
+from .basic_widgets import tk, StringViewer, SelectionBox, messagebox, topmenu
 from .basic_widgets import (TF, BF, SF, LF, HF,
                             bkg, ety, btn, opt, btn2,
                             btn_active, opt_active, txtcol,
@@ -312,9 +312,8 @@ class XrayInteractionsGui:
     Calculate X-Ray interactions with Matter
     """
 
-    def __init__(self, xtl):
+    def __init__(self, xtl=None):
         """Initialise"""
-        self.xtl = xtl
         # Create Tk inter instance
         self.root = tk.Tk()
         self.root.wm_title('X-Ray Interactions with Matter')
@@ -330,9 +329,9 @@ def __init__(self, xtl):
         frame.pack(side=tk.LEFT, anchor=tk.N)
 
         # Crystal info
-        name = xtl.name
-        formula = xtl.Properties.molname()
-        density = round(xtl.Properties.density(), 3)
+        name = xtl.name if xtl else 'Fe'
+        formula = xtl.Properties.molname() if xtl else 'Fe'
+        density = round(xtl.Properties.density(), 3) if xtl else 92.735
 
         # Variables
         self.chem_formula = tk.StringVar(frame, formula)
@@ -364,6 +363,14 @@ def __init__(self, xtl):
             'Wavelength (nm)': 'nm'
         }
 
+        # ---Menu---
+        menu = {
+            'Periodic Table': self.menu_info_table,
+            'Unit Converter': self.menu_converter,
+            'About': self.menu_about,
+        }
+        topmenu(self.root, menu)
+
         # ---Line 0---
         line = tk.Frame(frame)
         line.pack(side=tk.TOP, expand=tk.TRUE, fill=tk.X, pady=5)
@@ -460,6 +467,20 @@ def __init__(self, xtl):
                         activebackground=btn_active)
         var.pack(side=tk.LEFT)
 
+    def menu_info_table(self):
+        from .periodic_table import PeriodTableGui
+        PeriodTableGui()
+
+    def menu_converter(self):
+        """Open unit converter"""
+        from .converter import UnitConverter
+        UnitConverter()
+
+    def menu_about(self):
+        about = "Xray Interactions with Matter\nBy Dan Porter 2025\n\n"
+        about += "Inspired by CXRO: https://henke.lbl.gov/optical_constants/\n\n"
+        messagebox.showinfo('X-Ray Interactions with Matter', about)
+
     def get_scan(self):
         scan_type = self.scan_type.get()
         scan_min = self.scan_min.get()

diff --git a/docs/Dans_Diffraction.classes_crystal.html b/docs/Dans_Diffraction.classes_crystal.html
@@ -6,7 +6,7 @@
 <table width="100%" cellspacing=0 cellpadding=2 border=0 summary="heading">
 <tr bgcolor="#7799ee">
 <td valign=bottom>&nbsp;<br>
-<font color="#ffffff" face="helvetica, arial">&nbsp;<br><big><big><strong><a href="Dans_Diffraction.html"><font color="#ffffff">Dans_Diffraction</font></a>.classes_crystal</strong></big></big> (version 3.2.4)</font></td
+<font color="#ffffff" face="helvetica, arial">&nbsp;<br><big><big><strong><a href="Dans_Diffraction.html"><font color="#ffffff">Dans_Diffraction</font></a>.classes_crystal</strong></big></big> (version 3.3.0)</font></td
 ><td align=right valign=bottom
 ><font color="#ffffff" face="helvetica, arial"><a href=".">index</a><br><a href="file:c%3A%5Cusers%5Cgrp66007%5Conedrive%20-%20diamond%20light%20source%20ltd%5Cpythonprojects%5Cdans_diffraction%5Cdans_diffraction%5Cclasses_crystal.py">c:\users\grp66007\onedrive - diamond light source ltd\pythonprojects\dans_diffraction\dans_diffraction\classes_crystal.py</a></font></td></tr></table>
     <p><tt>classes_crystal.py<br>
@@ -34,8 +34,8 @@
 Diamond<br>
 2017<br>
 &nbsp;<br>
-Version&nbsp;3.2.4<br>
-Last&nbsp;updated:&nbsp;22/05/23<br>
+Version&nbsp;3.3.0<br>
+Last&nbsp;updated:&nbsp;06/02/25<br>
 &nbsp;<br>
 Version&nbsp;History:<br>
 27/07/17&nbsp;1.0&nbsp;&nbsp;&nbsp;&nbsp;Version&nbsp;History&nbsp;started.<br>
@@ -59,6 +59,7 @@
 15/11/21&nbsp;3.2.2&nbsp;&nbsp;Added&nbsp;<a href="#Cell">Cell</a>.orientation,&nbsp;updated&nbsp;<a href="#Cell">Cell</a>.UV()<br>
 12/01/21&nbsp;3.2.3&nbsp;&nbsp;Added&nbsp;<a href="#Symmetry">Symmetry</a>.axial_vector<br>
 22/05/23&nbsp;3.2.4&nbsp;&nbsp;Added&nbsp;<a href="#Symmetry">Symmetry</a>.wyckoff_label(),&nbsp;<a href="#Symmetry">Symmetry</a>.spacegroup_dict<br>
+06/05/25&nbsp;3.3.0&nbsp;&nbsp;<a href="#Symmetry">Symmetry</a>.from_cif&nbsp;now&nbsp;loads&nbsp;operations&nbsp;from&nbsp;find_spacegroup&nbsp;if&nbsp;not&nbsp;already&nbsp;loaded<br>
 &nbsp;<br>
 @author:&nbsp;DGPorter</tt></p>
 <p>
@@ -70,8 +71,9 @@
 <tr><td bgcolor="#aa55cc"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
 <td width="100%"><table width="100%" summary="list"><tr><td width="25%" valign=top><a href="Dans_Diffraction.functions_crystallography.html">Dans_Diffraction.functions_crystallography</a><br>
 </td><td width="25%" valign=top><a href="Dans_Diffraction.functions_general.html">Dans_Diffraction.functions_general</a><br>
+</td><td width="25%" valign=top><a href="Dans_Diffraction.functions_lattice.html">Dans_Diffraction.functions_lattice</a><br>
 </td><td width="25%" valign=top><a href="numpy.html">numpy</a><br>
-</td><td width="25%" valign=top></td></tr></table></td></tr></table><p>
+</td></tr></table></td></tr></table><p>
 <table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
 <tr bgcolor="#ee77aa">
 <td colspan=3 valign=bottom>&nbsp;<br>
@@ -293,7 +295,7 @@
 <dl><dt><a name="Cell-Bmatrix"><strong>Bmatrix</strong></a>(self)</dt><dd><tt>Calculate&nbsp;the&nbsp;Busing&nbsp;and&nbsp;Levy&nbsp;B&nbsp;matrix&nbsp;from&nbsp;a&nbsp;real&nbsp;space&nbsp;UV<br>
 &nbsp;"choose&nbsp;the&nbsp;x-axis&nbsp;parallel&nbsp;to&nbsp;a*,&nbsp;the&nbsp;y-axis&nbsp;in&nbsp;the&nbsp;plane&nbsp;of&nbsp;a*&nbsp;and&nbsp;b*,&nbsp;and&nbsp;the&nbsp;z-axis&nbsp;perpendicular&nbsp;to<br>
 &nbsp;that&nbsp;plane"<br>
-&nbsp;W.&nbsp;R.&nbsp;Busing&nbsp;&amp;&nbsp;H.&nbsp;A.&nbsp;Levy,&nbsp;Acta&nbsp;&nbsp;Cryst.&nbsp;&nbsp;(1967).&nbsp;22,&nbsp;&nbsp;457</tt></dd></dl>
+W.&nbsp;R.&nbsp;Busing&nbsp;&amp;&nbsp;H.&nbsp;A.&nbsp;Levy,&nbsp;Acta&nbsp;&nbsp;Cryst.&nbsp;&nbsp;(1967).&nbsp;22,&nbsp;&nbsp;457</tt></dd></dl>
 
 <dl><dt><a name="Cell-Qmag"><strong>Qmag</strong></a>(self, HKL)</dt><dd><tt>Returns&nbsp;the&nbsp;magnitude&nbsp;of&nbsp;wave-vector&nbsp;transfer&nbsp;of&nbsp;[h,k,l],&nbsp;in&nbsp;A-1<br>
 :param&nbsp;HKL:&nbsp;list&nbsp;of&nbsp;hkl&nbsp;reflections<br>
@@ -334,11 +336,17 @@
 <dl><dt><a name="Cell-calculateR"><strong>calculateR</strong></a>(self, UVW)</dt><dd><tt>Convert&nbsp;coordinates&nbsp;[u,v,w],&nbsp;in&nbsp;the&nbsp;basis&nbsp;of&nbsp;the&nbsp;unit&nbsp;cell,&nbsp;to<br>
 coordinates&nbsp;[x,y,z],&nbsp;in&nbsp;an&nbsp;orthogonal&nbsp;basis,&nbsp;in&nbsp;units&nbsp;of&nbsp;A<br>
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;R(x,y,z)&nbsp;=&nbsp;uA&nbsp;+&nbsp;vB&nbsp;+&nbsp;wC<br>
-&nbsp;<br>
 E.G.<br>
 &nbsp;&nbsp;&nbsp;&nbsp;R&nbsp;=&nbsp;<a href="#Cell">Cell</a>.<a href="#Cell-calculateR">calculateR</a>([0.1,0,0])&nbsp;#&nbsp;for&nbsp;a&nbsp;hexagonal&nbsp;system,&nbsp;a&nbsp;=&nbsp;2.85<br>
 &nbsp;&nbsp;&nbsp;&nbsp;&gt;&nbsp;R&nbsp;=&nbsp;array([[0.285,&nbsp;0,&nbsp;0]])</tt></dd></dl>
 
+<dl><dt><a name="Cell-choose_basis"><strong>choose_basis</strong></a>(self, option='default')</dt><dd><tt>Choose&nbsp;the&nbsp;basis&nbsp;function<br>
+Options:<br>
+&nbsp;&nbsp;&nbsp;&nbsp;1.&nbsp;c&nbsp;||&nbsp;z,&nbsp;b*&nbsp;||&nbsp;y&nbsp;-&nbsp;basis&nbsp;choice&nbsp;of&nbsp;Materials&nbsp;Project<br>
+&nbsp;&nbsp;&nbsp;&nbsp;2.&nbsp;a&nbsp;||&nbsp;x,&nbsp;c*&nbsp;||&nbsp;z&nbsp;-&nbsp;basis&nbsp;choice&nbsp;of&nbsp;Vesta<br>
+&nbsp;&nbsp;&nbsp;&nbsp;3.&nbsp;c&nbsp;||&nbsp;z,&nbsp;a*&nbsp;||&nbsp;x&nbsp;-&nbsp;basis&nbsp;choice&nbsp;of&nbsp;Busing&nbsp;&amp;&nbsp;Levy&nbsp;(Default)<br>
+:param&nbsp;option:&nbsp;name&nbsp;or&nbsp;number&nbsp;of&nbsp;basis</tt></dd></dl>
+
 <dl><dt><a name="Cell-diff6circle"><strong>diff6circle</strong></a>(self, delta=0, gamma=0, energy_kev=None, wavelength=1.0)</dt><dd><tt>Calcualte&nbsp;wavevector&nbsp;in&nbsp;diffractometer&nbsp;axis&nbsp;using&nbsp;detector&nbsp;angles<br>
 :param&nbsp;delta:&nbsp;float&nbsp;angle&nbsp;in&nbsp;degrees&nbsp;in&nbsp;vertical&nbsp;direction&nbsp;(about&nbsp;diff-z)<br>
 :param&nbsp;gamma:&nbsp;float&nbsp;angle&nbsp;in&nbsp;degrees&nbsp;in&nbsp;horizontal&nbsp;direction&nbsp;(about&nbsp;diff-x)<br>
@@ -420,7 +428,7 @@
 :param&nbsp;hkl:&nbsp;[3xn]&nbsp;array&nbsp;of&nbsp;(h,&nbsp;k,&nbsp;l)&nbsp;reciprocal&nbsp;lattice&nbsp;vectors<br>
 :return:&nbsp;[3xn]&nbsp;array&nbsp;of&nbsp;Q&nbsp;vectors&nbsp;in&nbsp;the&nbsp;lab&nbsp;coordinate&nbsp;system</tt></dd></dl>
 
-<dl><dt><a name="Cell-latt"><strong>latt</strong></a>(self, lattice_parameters=(), *args, **kwargs)</dt><dd><tt>Generate&nbsp;lattice&nbsp;parameters&nbsp;with&nbsp;list<br>
+<dl><dt><a name="Cell-latt"><strong>latt</strong></a>(self, *lattice_parameters, **kwargs)</dt><dd><tt>Generate&nbsp;lattice&nbsp;parameters&nbsp;with&nbsp;list<br>
 &nbsp;&nbsp;<a href="#Cell-latt">latt</a>(1)&nbsp;-&gt;&nbsp;a=b=c=1,alpha=beta=gamma=90<br>
 &nbsp;&nbsp;<a href="#Cell-latt">latt</a>([1,2,3])&nbsp;-&gt;&nbsp;a=1,b=2,c=3,alpha=beta=gamma=90<br>
 &nbsp;&nbsp;<a href="#Cell-latt">latt</a>([1,2,3,120])&nbsp;-&gt;&nbsp;a=1,b=2,c=3,alpha=beta=90,gamma=120<br>
@@ -444,7 +452,7 @@
 :param&nbsp;hkl:&nbsp;array&nbsp;:&nbsp;list&nbsp;of&nbsp;reflections<br>
 :return:&nbsp;correction</tt></dd></dl>
 
-<dl><dt><a name="Cell-reciprocal_space_plane"><strong>reciprocal_space_plane</strong></a>(self, x_axis=[1, 0, 0], y_axis=[0, 1, 0], centre=[0, 0, 0], q_max=4.0, cut_width=0.05)</dt><dd><tt>Returns&nbsp;positions&nbsp;within&nbsp;a&nbsp;reciprocal&nbsp;space&nbsp;plane<br>
+<dl><dt><a name="Cell-reciprocal_space_plane"><strong>reciprocal_space_plane</strong></a>(self, x_axis=(1, 0, 0), y_axis=(0, 1, 0), centre=(0, 0, 0), q_max=4.0, cut_width=0.05)</dt><dd><tt>Returns&nbsp;positions&nbsp;within&nbsp;a&nbsp;reciprocal&nbsp;space&nbsp;plane<br>
 &nbsp;&nbsp;x_axis&nbsp;=&nbsp;direction&nbsp;along&nbsp;x,&nbsp;in&nbsp;units&nbsp;of&nbsp;the&nbsp;reciprocal&nbsp;lattice&nbsp;(hkl)<br>
 &nbsp;&nbsp;y_axis&nbsp;=&nbsp;direction&nbsp;along&nbsp;y,&nbsp;in&nbsp;units&nbsp;of&nbsp;the&nbsp;reciprocal&nbsp;lattice&nbsp;(hkl)<br>
 &nbsp;&nbsp;centre&nbsp;=&nbsp;centre&nbsp;of&nbsp;the&nbsp;plot,&nbsp;in&nbsp;units&nbsp;of&nbsp;the&nbsp;reciprocal&nbsp;lattice&nbsp;(hkl)<br>
@@ -607,10 +615,19 @@
 :param&nbsp;mxmymz:&nbsp;array&nbsp;:&nbsp;atomic&nbsp;magnetic&nbsp;vectors&nbsp;[mu,mv,mw]<br>
 :return:&nbsp;None</tt></dd></dl>
 
-<dl><dt><a name="Crystal-new_cell"><strong>new_cell</strong></a>(self, lattice_parameters=(), *args, **kwargs)</dt><dd><tt>Replace&nbsp;the&nbsp;lattice&nbsp;parameters<br>
+<dl><dt><a name="Crystal-new_cell"><strong>new_cell</strong></a>(self, *lattice_parameters, **kwargs)</dt><dd><tt>Replace&nbsp;the&nbsp;lattice&nbsp;parameters<br>
 :param&nbsp;lattice_parameters:&nbsp;[a,b,c,alpha,beta,gamma]<br>
 :return:&nbsp;None</tt></dd></dl>
 
+<dl><dt><a name="Crystal-search_distances"><strong>search_distances</strong></a>(self, min_d=0.65, max_d=3.2, c_ele=None, elems=None, labels=None, simple=True)</dt><dd><tt>Calculated&nbsp;atoms&nbsp;interatomic&nbsp;distances&nbsp;form&nbsp;each&nbsp;label.<br>
+:param&nbsp;c_ele&nbsp;(list,string):&nbsp;only&nbsp;sites&nbsp;with&nbsp;noted&nbsp;elements<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;if&nbsp;None&nbsp;all&nbsp;site<br>
+:param&nbsp;elems&nbsp;(list,string):&nbsp;only&nbsp;distances&nbsp;with&nbsp;noted&nbsp;elements<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;if&nbsp;None&nbsp;all&nbsp;site<br>
+:param&nbsp;min_d:&nbsp;minimum&nbsp;distance&nbsp;<br>
+:param&nbsp;max_d:&nbsp;maximum&nbsp;distance<br>
+:return&nbsp;dictionary:</tt></dd></dl>
+
 <dl><dt><a name="Crystal-start_gui"><strong>start_gui</strong></a>(self)</dt><dd><tt>Start&nbsp;<a href="#Crystal">Crystal</a>&nbsp;GUI<br>
 :return:&nbsp;None</tt></dd></dl>
 
@@ -799,10 +816,19 @@
 :param&nbsp;mxmymz:&nbsp;array&nbsp;:&nbsp;atomic&nbsp;magnetic&nbsp;vectors&nbsp;[mu,mv,mw]<br>
 :return:&nbsp;None</tt></dd></dl>
 
-<dl><dt><a name="Superstructure-new_cell"><strong>new_cell</strong></a>(self, lattice_parameters=(), *args, **kwargs)</dt><dd><tt>Replace&nbsp;the&nbsp;lattice&nbsp;parameters<br>
+<dl><dt><a name="Superstructure-new_cell"><strong>new_cell</strong></a>(self, *lattice_parameters, **kwargs)</dt><dd><tt>Replace&nbsp;the&nbsp;lattice&nbsp;parameters<br>
 :param&nbsp;lattice_parameters:&nbsp;[a,b,c,alpha,beta,gamma]<br>
 :return:&nbsp;None</tt></dd></dl>
 
+<dl><dt><a name="Superstructure-search_distances"><strong>search_distances</strong></a>(self, min_d=0.65, max_d=3.2, c_ele=None, elems=None, labels=None, simple=True)</dt><dd><tt>Calculated&nbsp;atoms&nbsp;interatomic&nbsp;distances&nbsp;form&nbsp;each&nbsp;label.<br>
+:param&nbsp;c_ele&nbsp;(list,string):&nbsp;only&nbsp;sites&nbsp;with&nbsp;noted&nbsp;elements<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;if&nbsp;None&nbsp;all&nbsp;site<br>
+:param&nbsp;elems&nbsp;(list,string):&nbsp;only&nbsp;distances&nbsp;with&nbsp;noted&nbsp;elements<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;if&nbsp;None&nbsp;all&nbsp;site<br>
+:param&nbsp;min_d:&nbsp;minimum&nbsp;distance&nbsp;<br>
+:param&nbsp;max_d:&nbsp;maximum&nbsp;distance<br>
+:return&nbsp;dictionary:</tt></dd></dl>
+
 <dl><dt><a name="Superstructure-start_gui"><strong>start_gui</strong></a>(self)</dt><dd><tt>Start&nbsp;<a href="#Crystal">Crystal</a>&nbsp;GUI<br>
 :return:&nbsp;None</tt></dd></dl>
 

diff --git a/docs/Dans_Diffraction.classes_orientation.html b/docs/Dans_Diffraction.classes_orientation.html
@@ -31,11 +31,8 @@
 
 <tr><td bgcolor="#aa55cc"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
 <td width="100%"><table width="100%" summary="list"><tr><td width="25%" valign=top><a href="Dans_Diffraction.functions_crystallography.html">Dans_Diffraction.functions_crystallography</a><br>
-<a href="Dans_Diffraction.functions_general.html">Dans_Diffraction.functions_general</a><br>
+</td><td width="25%" valign=top><a href="Dans_Diffraction.functions_lattice.html">Dans_Diffraction.functions_lattice</a><br>
 </td><td width="25%" valign=top><a href="numpy.html">numpy</a><br>
-<a href="os.html">os</a><br>
-</td><td width="25%" valign=top><a href="re.html">re</a><br>
-<a href="sys.html">sys</a><br>
 </td><td width="25%" valign=top></td></tr></table></td></tr></table><p>
 <table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
 <tr bgcolor="#ee77aa">
@@ -59,7 +56,7 @@
 <font color="#000000" face="helvetica, arial"><a name="CrystalOrientation">class <strong>CrystalOrientation</strong></a>(<a href="builtins.html#object">builtins.object</a>)</font></td></tr>
 
 <tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
-<td colspan=2><tt><a href="#CrystalOrientation">CrystalOrientation</a>(lattice_parameters=(),&nbsp;*args,&nbsp;**kwargs)<br>
+<td colspan=2><tt><a href="#CrystalOrientation">CrystalOrientation</a>(*lattice_parameters,&nbsp;**kwargs)<br>
 &nbsp;<br>
 <a href="#CrystalOrientation">CrystalOrientation</a>&nbsp;Class<br>
 &nbsp;<br>
@@ -70,7 +67,7 @@
 &nbsp;&nbsp;y-axis&nbsp;:&nbsp;vector&nbsp;normal&nbsp;to&nbsp;x,z&nbsp;axes&nbsp;(parallel&nbsp;to&nbsp;beam&nbsp;(+z)&nbsp;in&nbsp;lab&nbsp;frame)<br>&nbsp;</tt></td></tr>
 <tr><td>&nbsp;</td>
 <td width="100%">Methods defined here:<br>
-<dl><dt><a name="CrystalOrientation-__init__"><strong>__init__</strong></a>(self, lattice_parameters=(), *args, **kwargs)</dt><dd><tt>Initialize&nbsp;self.&nbsp;&nbsp;See&nbsp;help(type(self))&nbsp;for&nbsp;accurate&nbsp;signature.</tt></dd></dl>
+<dl><dt><a name="CrystalOrientation-__init__"><strong>__init__</strong></a>(self, *lattice_parameters, **kwargs)</dt><dd><tt>Initialize&nbsp;self.&nbsp;&nbsp;See&nbsp;help(type(self))&nbsp;for&nbsp;accurate&nbsp;signature.</tt></dd></dl>
 
 <dl><dt><a name="CrystalOrientation-__repr__"><strong>__repr__</strong></a>(self)</dt><dd><tt>Return&nbsp;repr(self).</tt></dd></dl>
 
@@ -195,6 +192,5 @@
 <tr><td bgcolor="#eeaa77"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
 <td width="100%"><dl><dt><a name="-string_matrix"><strong>string_matrix</strong></a>(m)</dt><dd><tt>Convert&nbsp;[3*3]&nbsp;array&nbsp;to&nbsp;string</tt></dd></dl>
  <dl><dt><a name="-string_vector"><strong>string_vector</strong></a>(v)</dt><dd><tt>Convert&nbsp;[3]&nbsp;array&nbsp;to&nbsp;string</tt></dd></dl>
- <dl><dt><a name="-warn"><strong>warn</strong></a>(message, category=None, stacklevel=1, source=None)</dt><dd><tt>Issue&nbsp;a&nbsp;warning,&nbsp;or&nbsp;maybe&nbsp;ignore&nbsp;it&nbsp;or&nbsp;raise&nbsp;an&nbsp;exception.</tt></dd></dl>
 </td></tr></table>
 </body></html>