Merge pull request #29 from DanPorter/polarised_neutrons

Polarised neutrons

Author: DanPorter

.github/workflows/pypi-publish.yml

@@ -16,7 +16,7 @@ jobs:
         run: pipx run build
 
       - name: Upload sdist and wheel as artifacts
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: dist
           path: dist
@@ -35,7 +35,7 @@ jobs:
 
     steps:
       # download sdist and wheel from dist job
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
 
       # publish to PyPI using trusted publishing
       - name: Publish to PyPI

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/Structures/MnO.mcif

@@ -0,0 +1,168 @@
+#\#CIF_2.0
+# Created by the Bilbao Crystallographic Server
+# http://www.cryst.ehu.es
+# Date: 11/19/2017 17:07:02
+# Database entry: 1.31 MnO
+# Cif-like file for the case 1.31
+
+
+data_5yOhtAoR
+_audit_creation_date            2017-11-19
+_audit_creation_method          "Bilbao Crystallographic Server"
+
+_chemical_name_systematic
+;
+;
+_chemical_name_common                    ?
+_chemical_formula_moiety                 ?
+_chemical_formula_structural             ?
+_chemical_formula_analytical             ?
+_chemical_formula_iupac                  ?
+_chemical_formula_sum                    'Mn O'
+_chemical_formula_weight                 ?
+_chemical_melting_point                  ?
+_chemical_compound_source                ?
+_chemical_absolute_configuration         .
+
+
+_citation_journal_abbrev        "PHYSICAL REVIEW LETTERS"
+_citation_journal_volume        96
+_citation_page_first            ?
+_citation_page_last             ?
+_citation_article_id            047209
+_citation_year                  2006
+_citation_DOI                   10.1103/physrevlett.96.047209
+
+loop_
+_citation_author_name
+"A.L. Goodwin"
+"M.G. Tucker"
+"M.T. Dove"
+"D.A. Keen"
+
+
+
+
+
+_atomic_positions_source_database_code_ICSD   9864
+_atomic_positions_source_other               .
+
+_transition_temperature     120
+_experiment_temperature     10
+
+loop_
+_irrep_id
+_irrep_dimension
+_irrep_small_dimension
+_irrep_direction_type
+_irrep_action
+_irrep_modes_number
+_irrep_presence
+mL3+ 8 2 special primary . .
+
+_exptl_crystal_magnetic_properties_details
+;
+NSD
+Additional modulation observed. Only average structure presented here
+Atomic positions used are of the parent phase (icsd 9864).
+The reference reports a C2 positional structure.
+Its deviations from from the parent structure used here smaller than 0.1 A.
+Modulus magnetic moment Mn: 5.65
+Other source: Phys. Rev. 83 (1951) 333
+The magnetic symmetry implies the space group C2/m as effective
+symmetry for the positional structure, higher than the symmetry C2
+proposed in the reference.
+;
+
+_active_magnetic_irreps_details
+;
+1k magnetic structure
+a secondary magnetic irrep possible but not present: mL2+
+;
+
+_parent_space_group.name_H-M_alt  'F  m  -3m'
+_parent_space_group.IT_number                       225
+_parent_space_group.transform_Pp_abc  'a,b,c;0,0,0'
+
+loop_
+_parent_propagation_vector.id
+_parent_propagation_vector.kxkykz
+k1 [0.5 0.5 0.5]
+
+_parent_space_group.child_transform_Pp_abc  '2a,2b,2c;0,0,0'
+_space_group_magn.transform_BNS_Pp_abc  'a/4+b/4-c/2,a/4-b/4,-a/2-b/2;0,0,0'
+
+
+_space_group_magn.number_BNS  15.90
+_space_group_magn.name_BNS  "C_c  2/c"
+_space_group_magn.point_group_name  "2/m1'"
+_space_group_magn.point_group_number  "5.2.13"
+_cell_length_a                 8.8920
+_cell_length_b                 8.8920
+_cell_length_c                 8.8920
+_cell_angle_alpha              90.0000
+_cell_angle_beta               90.0000
+_cell_angle_gamma              90.0000
+
+loop_
+_space_group_symop_magn_operation.id
+_space_group_symop_magn_operation.xyz
+1 x,y,z,+1
+2 -y+3/4,-x+3/4,-z,+1
+3 -x+1/4,-y+3/4,-z,+1
+4 y,x+1/2,z,+1
+
+loop_
+_space_group_symop_magn_centering.id
+_space_group_symop_magn_centering.xyz
+1 x,y,z,+1
+2 x,y+1/4,z+3/4,+1
+3 x,y+1/2,z+1/2,+1
+4 x,y+3/4,z+1/4,+1
+5 x+1/4,y,z+3/4,+1
+6 x+1/4,y+1/4,z+1/2,+1
+7 x+1/4,y+1/2,z+1/4,+1
+8 x+1/4,y+3/4,z,+1
+9 x+1/2,y,z+1/2,+1
+10 x+1/2,y+1/4,z+1/4,+1
+11 x+1/2,y+1/2,z,+1
+12 x+1/2,y+3/4,z+3/4,+1
+13 x+3/4,y,z+1/4,+1
+14 x+3/4,y+1/4,z,+1
+15 x+3/4,y+1/2,z+3/4,+1
+16 x+3/4,y+3/4,z+1/2,+1
+17 x+3/4,y+3/4,z,-1
+18 x+3/4,y,z+3/4,-1
+19 x+3/4,y+1/4,z+1/2,-1
+20 x+3/4,y+1/2,z+1/4,-1
+21 x,y+3/4,z+3/4,-1
+22 x,y,z+1/2,-1
+23 x,y+1/4,z+1/4,-1
+24 x,y+1/2,z,-1
+25 x+1/4,y+3/4,z+1/2,-1
+26 x+1/4,y,z+1/4,-1
+27 x+1/4,y+1/4,z,-1
+28 x+1/4,y+1/2,z+3/4,-1
+29 x+1/2,y+3/4,z+1/4,-1
+30 x+1/2,y,z,-1
+31 x+1/2,y+1/4,z+3/4,-1
+32 x+1/2,y+1/2,z+1/2,-1
+
+loop_
+_atom_site_label
+_atom_site_type_symbol
+_atom_site_fract_x
+_atom_site_fract_y
+_atom_site_fract_z
+_atom_site_occupancy
+Mn1 Mn 0.00000 0.00000 0.00000 1
+O1 O 0.75000 0.50000 0.00000 1
+
+loop_
+_atom_site_moment.label
+_atom_site_moment.crystalaxis_x
+_atom_site_moment.crystalaxis_y
+_atom_site_moment.crystalaxis_z
+_atom_site_moment.symmform
+Mn1 2.31 2.31 -4.62 mx,mx,mz
+

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.
@@ -83,6 +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
+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
@@ -109,6 +110,7 @@
     Aug 2024    Thanks to MaxPelly for spell checks in examples
     Sep 2024    Thanks to thamnos for suggestion to add complex neutron scattering lengths
     Oct 2024    Thanks to Lee Richter for pointing out the error in triclinic basis definition
+    Dec 2024    Thanks to dragonyanglong for pointing out the error with magnetic neutron scattering
 
 -----------------------------------------------------------------------------
    Copyright 2024 Diamond Light Source Ltd.
@@ -163,8 +165,8 @@
            'Structures', 'Fdmnes', 'FdmnesAnalysis']
 
 
-__version__ = '3.3.2'
-__date__ = '2024/11/20'
+__version__ = '3.3.3'
+__date__ = '2025/02/06'
 
 
 # Build