Version 1.8.2

Magnetic spacegroup positions added, write_mcif added, various improvements. Tensor_Scattering removed.

Author: DanPorter

Dans_Diffraction/README.md

@@ -18,8 +18,8 @@ The *Crystal* object has the structure:
 xtl = dif.Crystal('file.cif')
 xtl.Cell # Cell properties - lattice parameters, generation of direct and recriprocal lattice
 xtl.Symmetry # Symmetry properties - contains symmetry operations and functions to apply symmetry to positions & reflections.
-xtl.Atoms # Atomic site properties - describes atoms at symmetric sites
-xtl.Structure # Atomic site properties - describes atoms at all positions in unit cell
+xtl.Atoms # Symmetically unique Atomic sites - describes atoms at symmetric sites
+xtl.Structure # All Atomic sites - describes atoms at all positions in unit cell
 xtl.Plot  # Plot functions - Various Plotting methods to produce graphed output
 xtl.Scatter # Scattering & Diffraction functions - calculate various types of scattering based on the crystal structure.
 xtl.Properties # Various functions - calculate various crystal properties

Dans_Diffraction/Structures/Sr3LiRuO6_C2'c'.mcif

@@ -1,62 +1,62 @@
-# This file was generated by ISODISTORT, version 6.3.1
+# This file was generated by ISODISTORT, version 6.3.4
 # Harold T. Stokes, Branton J. Campbell, David Tanner, Dorian M. Hatch
 # Brigham Young University, Provo, Utah, USA
 #
 # Space Group: 167 R-3c       D3d-6
 # Default space-group preferences: monoclinic axes a(b)c, monoclinic cell choice 1, orthorhombic axes abc, origin choice 2, hexagonal axes, SSG standard setting
-# Lattice parameters: a=9.63320, b=9.63320, c=11.09710, alpha=90.00000, beta=90.00000, gamma=120.00000
+# Lattice parameters: a=9.62020, b=9.62020, c=11.08130, alpha=90.00000, beta=90.00000, gamma=120.00000
 # Ru1 6b (0,0,0)
-# Sr1 18e (x,0,1/4), x=-0.35868
-# O1 36f (x,y,z), x=0.49243, y=0.18049, z=0.22873
-# Li 6a (0,0,1/4)
+# Sr1 18e (x,0,1/4), x=-0.35893
+# O1 36f (x,y,z), x=-0.02190, y=-0.17430, z=0.10501
+# Li1 6a (0,0,1/4)
 # k point: GM, k7 (0,0,0)
 # IR: mGM3+, mk7t5
 # P2      (a,0.577a) 15.89 C2'/c', basis={(-2/3,-1/3,2/3),(0,-1,0),(2/3,1/3,1/3)}, origin=(-1/6,-1/3,1/6), s=1, i=6, k-active= (0,0,0)
+# Note that this file uses an alternate (possibly nonstandard) setting of the subgroup chosen by the user:
+#     basis={(1,0,0),(0,1,0),(0,0,1)}, origin=(0.00000,0.00000,0.00000) with respect to the parent space group
 # Order parameter values:
 #  R-3c[0,0,0]mGM3+(a,0.577a) 15.89 C2'/c' s=1 i=6
-#     [Ru1:b:mag]Eg*_1(a): 3.45000
-#     [Ru1:b:mag]Eg*_2(a): -2.15000
+#     [Ru1:b:mag]Eg*_1(a): 3.00000
+#     [Ru1:b:mag]Eg*_2(a): -1.73100
 #  R-3c[0,0,0]mGM2+(a) 167.107 R-3c' s=1 i=2
-#     [Ru1:b:mag]Ag(a): 1.20000
+#     [Ru1:b:mag]Ag(a): 1.00000
 
 data_isodistort-output
 
-_cell_length_a    9.25550
-_cell_length_b    9.63320
-_cell_length_c    6.67950
+_cell_length_a    9.62020
+_cell_length_b    9.62020
+_cell_length_c    11.08130
 _cell_angle_alpha 90.00000
-_cell_angle_beta  93.30782
-_cell_angle_gamma 90.00000
+_cell_angle_beta  90.00000
+_cell_angle_gamma 120.00000
 
-_space_group.magn_number_BNS "15.89"
-_space_group.magn_name_BNS "C2'/c'"
-_space_group.magn_point_group "2'/m'"
+_space_group_magn.number_BNS "15.89"
+_space_group_magn.name_BNS "C2'/c'"
+_space_group_magn.number_OG "15.5.96"
+_space_group_magn.name_OG "C2'/c'"
+_space_group_magn.point_group "2'/m'"
 
 loop_
-_space_group_transform_id
-_space_group_transform_Pp_abc
-_space_group_transform_description
-1 a,b,c;0,0,0 "to magnetic BNS, standard ISO C2'/c' setting"
-2 a,b,c;0,0,0 "to magnetic OG, standard Litvin C2'/c' setting"
+_space_group_magn_transforms.id
+_space_group_magn_transforms.Pp_abc
+_space_group_magn_transforms.source
+1 -2/3a-1/3b+2/3c,-b,2/3a+1/3b+1/3c;1/2,1,-1/2 "BNS"
+2 -2/3a-1/3b+2/3c,-b,2/3a+1/3b+1/3c;1/2,1,-1/2 "OG"
 
 loop_
-_space_group_symop.magn_id
-_space_group_symop.magn_operation_xyz
-_space_group_symop.magn_operation_mxmymz
-1 x,y,z,+1 mx,my,mz  
-2 -x,-y,-z,+1 mx,my,mz  
-3 -x,y,-z+1/2,-1 mx,-my,mz  
-4 x,-y,z+1/2,-1 mx,-my,mz  
-5 x+1/2,y+1/2,z,+1 mx,my,mz  
-6 -x+1/2,-y+1/2,-z,+1 mx,my,mz  
-7 -x+1/2,y+1/2,-z+1/2,-1 mx,-my,mz  
-8 x+1/2,-y+1/2,z+1/2,-1 mx,-my,mz  
+_space_group_symop_magn_operation.id
+_space_group_symop_magn_operation.xyz
+1 x,y,z,+1 
+2 -x,-y,-z,+1 
+3 -x+1/3,-x+y+2/3,-z+1/6,-1 
+4 x+1/3,x-y+2/3,z+1/6,-1 
 
 loop_
-_space_group_symop.magn_centering_id
-_space_group_symop.magn_centering_xyz
-_space_group_symop.magn_centering_mxmymz
-1 x,y,z,+1 mx,my,mz
+_space_group_symop_magn_centering.id
+_space_group_symop_magn_centering.xyz
+1 x,y,z,+1 
+2 x+1/3,y+2/3,z+2/3,+1 
+3 x+2/3,y+1/3,z+1/3,+1 
 
 loop_
 _atom_site_label
@@ -67,20 +67,21 @@ _atom_site_fract_x
 _atom_site_fract_y
 _atom_site_fract_z
 _atom_site_occupancy
-Ru1_1 Ru   4 c  0.25000  0.25000  0.00000  1.00000
-Sr1_1 Sr   8 f  0.67934  0.07066  0.89132  1.00000
-Sr1_2 Sr   4 e  0.00000  0.10868  0.25000  1.00000
-O1_1  O    8 f  0.23252  0.31572  0.72116  1.00000
-O1_2  O    8 f  0.06898  0.34782  0.04824  1.00000
-O1_3  O    8 f  0.13470  0.08646  0.91680  1.00000
-Li_1  Li   4 e  0.00000  0.75000  0.25000  1.00000
+Ru1_1 Ru  24 c 0.33333 0.66667  0.66667 1.00000
+Sr1_1 Sr  48 f 0.64107 0.00000  0.25000 1.00000
+Sr1_2 Sr  24 e 0.66667 -0.02560 0.58333 1.00000
+O1_1  O   48 f 0.31143 0.49237  0.77168 1.00000
+O1_2  O   48 f 0.50763 0.81907  0.77168 1.00000
+O1_3  O   48 f 0.18093 0.68857  0.77168 1.00000
+Li1_1 Li  24 e 0.66667 0.33333  0.58333 1.00000
 
 loop_
-_atom_site_moment_label
-_atom_site_moment_crystalaxis_x
-_atom_site_moment_crystalaxis_y
-_atom_site_moment_crystalaxis_z
-Ru1_1  0.76143  -2.87282  0.43320  
+_atom_site_moment.label
+_atom_site_moment.crystalaxis_x
+_atom_site_moment.crystalaxis_y
+_atom_site_moment.crystalaxis_z
+_atom_site_moment.symmform
+Ru1_1 0.00074 2.44949 0.70711 mx,my,mz
 
 _iso_displacivemode_number    0
 
@@ -91,31 +92,31 @@ loop_
 _iso_magneticmode_ID
 _iso_magneticmode_label
 _iso_magneticmode_value
-   1 R-3c[0,0,0]mGM3+(a,0.577a)[Ru1:b:mag]Eg*_1(a) 3.45000
-   2 R-3c[0,0,0]mGM3+(a,0.577a)[Ru1:b:mag]Eg*_2(a) -2.15000
-   3 R-3c[0,0,0]mGM2+(a)[Ru1:b:mag]Ag(a) 1.20000
+   1 R-3c[0,0,0]mGM3+(a,0.577a)[Ru1:b:mag]Eg*_1(a) 3.00000
+   2 R-3c[0,0,0]mGM3+(a,0.577a)[Ru1:b:mag]Eg*_2(a) -1.73100
+   3 R-3c[0,0,0]mGM2+(a)[Ru1:b:mag]Ag(a) 1.00000
 
 loop_
 _iso_magneticmodenorm_ID
 _iso_magneticmodenorm_value
-   1 0.06357
-   2 0.07340
-   3 0.06372
+   1 0.06365
+   2 0.07350
+   3 0.06381
 
 loop_
 _iso_deltamoment_ID
 _iso_deltamoment_label
 _iso_deltamoment_value
-   1 Ru1_1_dmx   0.76143
-   2 Ru1_1_dmy  -2.87282
-   3 Ru1_1_dmz   0.43320
+   1 Ru1_1_dmy   2.44949
+   2 Ru1_1_dmy   2.44949
+   3 Ru1_1_dmy   2.44949
 
 loop_
 _iso_moment_label
 _iso_moment_formula
-Ru1_1_mx            "0 + Ru1_1_dmx"
-Ru1_1_my            "0 + Ru1_1_dmy"
-Ru1_1_mz            "0 + Ru1_1_dmz"
+Ru1_1_mx            "0 + 2*Ru1_1_dmy + 2*Ru1_1_dmy"
+Ru1_1_my            "0 + Ru1_1_dmy + Ru1_1_dmy + Ru1_1_dmy"
+Ru1_1_mz            "0 - 2*Ru1_1_dmy + Ru1_1_dmy"
 Sr1_1_mx            "0"
 Sr1_1_my            "0"
 Sr1_1_mz            "0"
@@ -131,9 +132,9 @@ O1_2_mz             "0"
 O1_3_mx             "0"
 O1_3_my             "0"
 O1_3_mz             "0"
-Li_1_mx             "0"
-Li_1_my             "0"
-Li_1_mz             "0"
+Li1_1_mx            "0"
+Li1_1_my            "0"
+Li1_1_mz            "0"
 
 # matrix conversion: deltamoments(lattice units) = matrix.(modeamplitudes*modenormfactors)
 # Note that deltamoment_i(crystalaxis units) = deltamoment_i(lattice units)*strained_cell_length_i
@@ -143,14 +144,9 @@ loop_
 _iso_magneticmodematrix_row
 _iso_magneticmodematrix_col
 _iso_magneticmodematrix_value
-    1    1  -0.33333
-    1    2  -0.50000
-    1    3   1.00000
-    2    1  -1.00000
-    2    2   0.50000
-    3    1   0.66667
-    3    2   1.00000
-    3    3   1.00000
+    1    1   1.33333
+    2    1   1.33333
+    3    1   1.33333
 
 _iso_rotationalmode_number    0
 

Dans_Diffraction/__init__.py

@@ -17,8 +17,8 @@
 Diamond
 2017
 
-Version 1.8.1
-Last updated: 12/05/20
+Version 1.8.2
+Last updated: 26/05/20
 
 Version History:
 02/03/18 1.0    Version History started.
@@ -29,9 +29,10 @@
 13/12/19 1.5    Multiple Scattering added, tkGUI refactored, Startgui changed to start_gui
 20/02/20 1.6    Tensor Scattering added
 31/03/20 1.7    Refactored multicrystal methods, other minor changes, improved powder diffraction
-19/04/20 1.7.1  Added writecif + spacegroup file + functions
+19/04/20 1.7.1  Added write_cif + spacegroup file + functions
 02/05/20 1.8    Updated readcif, added heavy atom properties, added magnetic spacegroups
 12/05/20 1.8.1  Updated readcif, added atomic_scattering_factors and classes_orbitals
+26/05/20 1.8.2  Updated copyright, removed tensor scattering. Updated magnetic spacegroups
 
 -----------------------------------------------------------------------------
    Copyright 2020 Diamond Light Source Ltd.
@@ -85,8 +86,8 @@
     from .classes_fdmnes import Fdmnes, FdmnesAnalysis
 
 
-__version__ = '1.8.1'
-__date__ = '12/05/20'
+__version__ = '1.8.2'
+__date__ = '26/05/20'
 
 
 # Build