Version 3.3.3

Simplified input options for polarised neutron scattering for issue #27.

functions_scattering.py
 - added options 'neutron polarised' and 'xray polarised' to scattering types
 - Corrected error in sf_magnetic_neutron_polarised

classes_scattering.py
 - improved docs and setup_scatter

tkgui/scattering.py
 - added polarisation options

Added example_polarised_neutrons.py, MnO.mcif to example structures and additional tests

Author: DanPorter

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

@@ -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
+23/12/24 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__ = '2024/12/23'
 
 
 # Build

Dans_Diffraction/classes_scattering.py

@@ -7,8 +7,8 @@
 Diamond
 2017
 
-Version 2.3.4
-Last updated: 17/05/24
+Version 2.3.5
+Last updated: 23/12/24
 
 Version History:
 10/09/17 0.1    Program created
@@ -40,6 +40,7 @@
 15/05/24 2.3.4  Added "save" and "load" methods to structure factor calculation, improved powder for large calculations
 16/05/24 2.3.4  Added printed progress bar to generate_intensity_cut during convolusion
 17/05/24 2.3.4  Changed generate_intensity_cut to make it much faster
+23/12/24 2.3.5  Added polarised neutron options
 
 @author: DGPorter
 """
@@ -53,13 +54,7 @@
 from . import multiple_scattering as ms
 # from . import tensor_scattering as ts  # Removed V1.7
 
-__version__ = '2.3.4'
-__scattering_types__ = {'xray': ['xray', 'x', 'x-ray', 'thomson', 'charge'],
-                        'neutron': ['neutron', 'n', 'nuclear'],
-                        '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']}
+__version__ = '2.3.5'
 
 
 class Scattering:
@@ -119,14 +114,14 @@ class Scattering:
     # Polarisation Options
     _polarised = False
     _polarisation = 'sp'
-    _polarisation_vector_incident = [0, 1, 0]
+    _polarisation_vector_incident = (0, 1, 0)
 
     # Radiation energy
     _energy_kev = fg.Cu
 
     # Resonant X-ray Options
     _azimuthal_angle = 0
-    _azimuthal_reference = [1,0,0]
+    _azimuthal_reference = [1, 0, 0]
     _resonant_flm = (0, 1, 0)
     _resonant_approximation_e1e1 = True
     _resonant_approximation_e2e2 = False
@@ -137,7 +132,7 @@ def __init__(self, xtl):
         self.xtl = xtl
 
         # Initialise the scattering type container
-        self.Type = ScatteringTypes(self, __scattering_types__)
+        self.Type = ScatteringTypes(self, fs.SCATTERING_TYPES)
 
     def __repr__(self):
         return 'Scattering(%s, %s)' % (self.xtl.name, self._scattering_type)
@@ -195,7 +190,7 @@ def setup_scatter(self, scattering_type=None, energy_kev=None, wavelength_a=None
         """
         Simple way to set scattering parameters, each parameter is internal to xtl (self)
 
-        scattering_type: self._scattering type            :  'xray','neutron','xray magnetic','neutron magnetic','xray resonant', 'xray dispersion'
+        scattering_type: self._scattering type            :  'xray','neutron','xray magnetic','neutron magnetic','xray resonant', 'xray dispersion', 'neutron polarised', 'xray polarised'
         energy_kev  : self._energy_kev                    :  radiation energy in keV
         wavelength_a: self._wavelength_a                  :  radiation wavelength in Angstrom
         powder_units: self._powder_units                  :  units to use when displaying/ plotting ['twotheta', 'd',' 'q']
@@ -379,9 +374,11 @@ def structure_factor(self, hkl=None, scattering_type=None, int_hkl=True, **kwarg
           'xray'  - uses x-ray form factors
           'neutron' - uses neutron scattering lengths
           'xray magnetic' - calculates the magnetic (non-resonant) component of the x-ray scattering
-          'neutron magnetic' - calculates the magnetic component of neutron scattering
+          'neutron magnetic' - calculates the magnetic component of neutron scattering with average polarisation
           'xray resonant' - calculates magnetic resonant scattering
           'xray dispersion' - uses x-ray form factors including f'-if'' components
+          'neutron polarised' - calcualtes magnetic component with incident polarised neutrons
+          'xray polarised' - calcualtes magnetic component with incident polarised x-rays
 
         Notes:
         - Uses x-ray atomic form factors, calculated from approximated tables in the ITC
@@ -1088,7 +1085,7 @@ def magnetic_neutron(self, HKL):
         # Calculate intensity
         I = SF * np.conj(SF)
         return np.real(I)
-    
+
     def xray_magnetic(self, HKL):
         """
         Calculate the non-resonant magnetic component of the structure factor 
@@ -1102,51 +1099,53 @@ def xray_magnetic(self, HKL):
         No orbital component assumed
         magnetic moments assumed to be in the same reference frame as the polarisation
         """
-        
-        HKL = np.asarray(np.rint(HKL),dtype=float).reshape([-1,3])
+
+        HKL = np.asarray(np.rint(HKL), dtype=float).reshape([-1, 3])
         Nref = len(HKL)
-        
-        uvw,type,label,occ,uiso,mxmymz = self.xtl.Structure.get()
+
+        uvw, type, label, occ, uiso, mxmymz = self.xtl.Structure.get()
         Nat = len(uvw)
-        
+
         Qmag = self.xtl.Cell.Qmag(HKL)
-        
+
         # Get magnetic form factors
         if self._use_magnetic_form_factor:
-            ff = fc.magnetic_form_factor(type,Qmag)
+            ff = fc.magnetic_form_factor(type, Qmag)
         else:
-            ff = np.ones([len(HKL),Nat])
-        
+            ff = np.ones([len(HKL), Nat])
+
         # Calculate moment
-        momentmag = fg.mag(mxmymz).reshape([-1,1])
-        momentxyz = self.xtl.Cell.calculateR(mxmymz) # moment direction in cartesian reference frame
-        moment = momentmag*fg.norm(momentxyz) # broadcast n*1 x n*3 = n*3
+        momentmag = fg.mag(mxmymz).reshape([-1, 1])
+        momentxyz = self.xtl.Cell.calculateR(mxmymz)  # moment direction in cartesian reference frame
+        moment = momentmag * fg.norm(momentxyz)  # broadcast n*1 x n*3 = n*3
         moment[np.isnan(moment)] = 0.
-        
+
         # Calculate dot product
-        dot_KR = np.dot(HKL,uvw.T)
-        
+        dot_KR = np.dot(HKL, uvw.T)
+
         # Calculate structure factor
-        SF = np.zeros(Nref,dtype=complex)
+        SF = np.zeros(Nref, dtype=complex)
         for n in range(Nref):
             # Calculate vector structure factor
-            SFm = [0.,0.,0.]
-            for m,mom in enumerate(moment):
-                SFm = SFm + ff[n,m]*np.exp(1j*2*np.pi*dot_KR[n,m])*mom
-            
+            SFm = [0., 0., 0.]
+            for m, mom in enumerate(moment):
+                SFm = SFm + ff[n, m] * np.exp(1j * 2 * np.pi * dot_KR[n, m]) * mom
+
             # Calculate polarisation with incident x-ray
             # The reference frame of the x-ray and the crystal are assumed to be the same
             # i.e. pol=[1,0,0] || mom=[1,0,0] || (1,0,0)
             if self._polarised:
-                SF[n] = np.dot(SFm,self._polarisation_vector_incident)
+                SF[n] = np.dot(SFm, self._polarisation_vector_incident)
             else:
-                #SF[n] = np.dot(SFm,SFm) # maximum possible
-                SF[n] = (np.dot(SFm,[1,0,0]) + np.dot(SFm,[0,1,0]) + np.dot(SFm,[0,0,1]))/3 # average polarisation
-        
-        SF = SF/self.xtl.scale
-        
+                # SF[n] = np.dot(SFm,SFm) # maximum possible
+                SF[n] = (
+                                np.dot(SFm, [1, 0, 0]) + np.dot(SFm, [0, 1, 0]) + np.dot(SFm, [0, 0, 1])
+                        ) / 3  # average polarisation
+
+        SF = SF / self.xtl.scale
+
         if self._return_structure_factor: return SF
-        
+
         # Calculate intensity
         I = SF * np.conj(SF)
         return np.real(I)
@@ -1207,7 +1206,7 @@ def xray_resonant(self, HKL, energy_kev=None, polarisation='sp', F0=1, F1=1, F2=
 
             # Calculate structure factor
             # Broadcasting used on 2D fxres
-            SF[:,psival] = np.sum(fxres*dw*occ*np.exp(1j*2*np.pi*dot_KR),axis=1)
+            SF[:, psival] = np.sum(fxres*dw*occ*np.exp(1j*2*np.pi*dot_KR), axis=1)
 
         SF = SF/self.xtl.scale