option integer hkl

classes_scattering.py
 - added option for _integer_hkl, used in all scattering code.

classes_crystal.py
 - Symmetry now loads space group operations from tables if not in CIF

functions_general.py
 - change to norm, use np.squeeze on output

Tests
 - added tests for CIF output
 - all tests pass

Author: DanPorter

Dans_Diffraction/README.md

@@ -46,7 +46,7 @@ xtl.Cell.gamma
 
 Selected functions (see internal documentation for more):
  ```python
-xtl.Cell.latt([2.85,2.85,10.8,90,90,120]) # Define the lattice parameters from a list
+xtl.Cell.latt([2.85,2.85,10.8,90,90,120]) # Define the lattice parameters from a list or subset
 xtl.Cell.tth([0,0,12],energy_kev=8.0) # Calculate the two-theta of a reflection
 xtl.Cell.lp() # Returns the current lattice parameters
 xtl.Cell.volume() # Returns the calculated volume in A^3
@@ -111,16 +111,16 @@ xtl.Structrue contains all atomic positions in the unit cell.
 
 Each atom has properties:
 
-|   Property   |      |  
-| ------------- | ------------- |
-|   u   | Fractional atomic coordinates along direction of **a**  |
-|   v  | Fractional atomic coordinates along direction of **b**   |
-|   w   | Fractional atomic coordinates along direction of **c**   |
-|   type    | element species, given as element name, e.g. 'Fe'   |
-|   label   |   Name of atomic position, e.g. 'Fe1'   |
-|   occupancy   |   Occupancy of this atom at this atomic position   |
-|   uiso     |   atomic displacement factor (ADP) <u^2>   |
-|   mxmymz   |   magnetic moment direction [x,y,z]   |
+| Property  |                                                          |  
+|-----------|----------------------------------------------------------|
+| u         | Fractional atomic coordinates along direction of **a**   |
+| v         | Fractional atomic coordinates along direction of **b**   |
+| w         | Fractional atomic coordinates along direction of **c**   |
+| type      | element species, given as element name, e.g. 'Fe'        |
+| label     | Name of atomic position, e.g. 'Fe1'                      |
+| occupancy | Occupancy of this atom at this atomic position           |
+| uiso      | atomic displacement factor (ADP) <u^2>                   |
+| mxmymz    | magnetic moment direction [x,y,z]                        |
 
 Functions available:
 ```python
@@ -176,13 +176,14 @@ xtl.Plot.tensor_scattering_stokes # Return tensor scattering intensities for non
 ### Scattering
 Simulate diffraction from the crystal structure, for various scattering types, including:
 
-|   Name   |   Explanation   |
-|   ----   |   -----------    |
-| 'xray' | X-Ray diffraction, using atomic form factors |
-| 'neutron' | Neutron difraction, using neutron scattering lengths. |
-| 'neutron magnetic' | Magnetic neutron diffraction |
-| 'xray magnetic' | Non-resonant x-ray magnetic diffraction |
-| 'xray resonant' | Resonant x-ray magnetic diffraction |
+| Name               | Explanation                                              |
+|--------------------|----------------------------------------------------------|
+| 'xray'             | X-Ray diffraction, using atomic form factors             |
+| 'neutron'          | Neutron difraction, using neutron scattering lengths.    |
+| 'neutron magnetic' | Magnetic neutron diffraction                             |
+| 'xray magnetic'    | Non-resonant x-ray magnetic diffraction                  |
+| 'xray resonant'    | Resonant x-ray magnetic diffraction                      |
+| 'xray dispersion'  | X-Ray diffraction using energy dispersive form factors   |
 
 Functions calculate the complex structure factor based on the equation:
 
@@ -192,19 +193,27 @@ Scattering factors and scattering lengths for available elements are found in [d
 
 Setup the scattering attributes with the *xtl.Scatter.setup_scatter(parameter)* function:
 
-|   Parameter   |   Explanation   |
-|  ----------   |   -----------   |
-|    type         |  'xray','neutron','xray magnetic','neutron magnetic','xray resonant'  |
-|    energy_kev   |  radiation energy in keV  |
-|    wavelength_a |  radiation wavelength in Angstrom  |
-|    powder_units |  units to use when displaying/ plotting ['twotheta', 'd',' 'q']  |
-|    min_twotheta |  minimum detector (two-theta) angle  |
-|    max_twotheta |  maximum detector (two-theta) angle  |
-|    min_theta    |  minimum sample angle = -opening angle  |
-|    max_theta    |  maximum sample angle = opening angle  |
-|    theta_offset |  sample offset angle  |
-|    specular     | [h,k,l] : reflections normal to sample surface  |
-|    parallel     | [h,k,l] : reflections normal to sample surface  |
+| Parameter           | Explanation                                                                             |
+|---------------------|-----------------------------------------------------------------------------------------|
+| scattering_type     | 'xray','neutron','xray magnetic','neutron magnetic','xray resonant', 'xray dispersion'  |
+| energy_kev          | radiation energy in keV                                                                 |
+| wavelength_a        | radiation wavelength in Angstrom                                                        |
+| powder_units        | units to use when displaying/ plotting ['twotheta', 'd',' 'q']                          |
+| min_twotheta        | minimum detector (two-theta) angle                                                      |
+| max_twotheta        | maximum detector (two-theta) angle                                                      |
+| min_theta           | minimum sample angle = -opening angle                                                   |
+| max_theta           | maximum sample angle = opening angle                                                    |
+| theta_offset        | sample offset angle                                                                     |
+| specular            | [h,k,l] : reflections normal to sample surface                                          |
+| parallel            | [h,k,l] : reflections normal to sample surface                                          |
+| scattering_factors  | xray scattering factor, either 'waaskirf' or 'itc'                                      |
+| scattering_lengths  | neutron scattering lengths either 'sears' or 'default'                                  |
+| magnetic_formfactor | True/False magnetic form factor for magnetic SF                                         |
+| polarisation        | beam polarisation setting ['ss', 'sp'*, 'sp', 'pp']                                     |
+| polarisation_vector | [x,y,z] incident polarisation vector                                                    | 
+| azimuthal_reference | [h,k,l] direction of azimuthal zero angle                                               |
+| azimuth             | azimuthal angle in deg                                                                  |
+| flm                 | Resonant settings (flm1, flm2, flm3)                                                    |
 
 
 Selected functions (see internal documentation for more):

Dans_Diffraction/__init__.py

@@ -29,10 +29,10 @@
 
 By Dan Porter, PhD
 Diamond
-2017
+2017-2025
 
-Version 3.3.2
-Last updated: 20/11/2024
+Version 3.3.3
+Last updated: 06/02/2025
 
 Version History:
 02/03/18 1.0    Version History started.
@@ -83,7 +83,7 @@
 26/09/24 3.3.0  Added complex neutron scattering lengths for isotopes from package periodictable. Thanks thamnos!
 06/11/24 3.3.1  Fixed incorrect cell basis for triclinic cells. Added functions_lattice.py and tests. Thanks LeeRichter!
 20/11/24 3.3.2  Added alternate option for neutron scattering lengths
-23/12/24 3.3.3  Added scattering options for polarised neutron and x-ray scattering. Thanks dragonyanglong!
+06/02/25 3.3.3  Added scattering options for polarised neutron and x-ray scattering. Thanks dragonyanglong!
 
 Acknoledgements:
     2018        Thanks to Hepesu for help with Python3 support and ideas about breaking up calculations
@@ -166,7 +166,7 @@
 
 
 __version__ = '3.3.3'
-__date__ = '2024/12/23'
+__date__ = '2025/02/06'
 
 
 # Build

Dans_Diffraction/classes_crystal.py

@@ -24,8 +24,8 @@
 Diamond
 2017
 
-Version 3.2.4
-Last updated: 22/05/23
+Version 3.3.0
+Last updated: 06/02/25
 
 Version History:
 27/07/17 1.0    Version History started.
@@ -49,6 +49,7 @@
 15/11/21 3.2.2  Added Cell.orientation, updated Cell.UV()
 12/01/21 3.2.3  Added Symmetry.axial_vector
 22/05/23 3.2.4  Added Symmetry.wyckoff_label(), Symmetry.spacegroup_dict
+06/05/25 3.3.0  Symmetry.from_cif now loads operations from find_spacegroup if not already loaded
 
 @author: DGPorter
 """
@@ -67,7 +68,7 @@
 from .classes_multicrystal import MultiCrystal
 from .classes_plotting import Plotting, PlottingSuperstructure
 
-__version__ = '3.2.4'
+__version__ = '3.3.0'
 
 
 class Crystal:
@@ -227,13 +228,13 @@ def write_cif(self, filename=None, comments=None):
         else:
             fc.write_cif(cifvals, filename, comments)
 
-    def new_cell(self, lattice_parameters=(), *args, **kwargs):
+    def new_cell(self, *lattice_parameters, **kwargs):
         """
         Replace the lattice parameters
         :param lattice_parameters: [a,b,c,alpha,beta,gamma]
         :return: None
         """
-        self.Cell.latt(lattice_parameters, *args, **kwargs)
+        self.Cell.latt(*lattice_parameters, **kwargs)
 
     def new_atoms(self, u=[0], v=[0], w=[0], type=None,
                   label=None, occupancy=None, uiso=None, mxmymz=None):
@@ -468,8 +469,9 @@ def info(self):
         out += '{}\n'.format(self.name)
         out += 'Formula: {}\n'.format(self.Properties.molname())
         out += 'Magnetic: {}\n'.format(self.Structure.ismagnetic())
+        out += 'Spacegroup: %s\n' % repr(self.Symmetry)
         out += self.Cell.info()
-        out += '\nDensity: %6.3f g/cm\n' % self.Properties.density()
+        out += 'Density: %6.3f g/cm\n\n' % self.Properties.density()
         out += self.Structure.info()
         out += '\n'
         # print "To see the full list of structure positions, type Crystal.Structure.info()"
@@ -1157,7 +1159,7 @@ def fromcif(self, cifvals):
         :return: none
         """
         if not fc.cif_check(cifvals, self._required_cif):
-            warn('Atom site parameters cannot be read from cif')
+            warn('Atom site parameters cannot be read from cif')  # TODO: provide more details
             return
 
         keys = cifvals.keys()
@@ -1718,7 +1720,11 @@ def fromcif(self, cifvals):
             else:
                 self.spacegroup_dict = fc.spacegroup(1)
 
-        self.generate_matrices()
+        if len(self.symmetry_operations) == 1:
+            # use found spacegroup as none provided by CIF
+            self.load_spacegroup(sg_dict=self.spacegroup_dict)
+        else:
+            self.generate_matrices()
 
     def update_cif(self, cifvals):
         """