Add in kvec isodistort tutorial (#4)

* first draft

* finalize the k-vector talk to isodistort tutorial

Author: Kvieta1990

MDtutorials/k_vec_isodistort/data/STO_Parent.cif

@@ -0,0 +1,132 @@
+#------------------------------------------------------------------------------
+#$Date: 2016-02-14 06:40:26 +0200 (Sun, 14 Feb 2016) $
+#$Revision: 176432 $
+#$URL: svn://www.crystallography.net/cod/cif/1/51/21/1512124.cif $
+#------------------------------------------------------------------------------
+#
+# This file is available in the Crystallography Open Database (COD),
+# http://www.crystallography.net/
+#
+# All data on this site have been placed in the public domain by the
+# contributors.
+#
+data_1512124
+loop_
+_publ_author_name
+'Natheer B. Mahmood'
+'Emad K. Al-Shakarchi'
+'Brahim Elouadi'
+_publ_section_title
+;
+ Three Techniques Used to Produce BaTiO3 Fine Powder
+;
+_journal_name_full               'Journal of Modern Physics'
+_journal_page_first              1420
+_journal_page_last               1428
+_journal_paper_doi               10.4236/jmp.2011.211175
+_journal_volume                  2
+_journal_year                    2011
+_chemical_formula_analytical     SrTiO3
+_chemical_formula_structural     SrTiO3
+_chemical_formula_sum            'O3 Sr Ti'
+_chemical_formula_weight_meas    183.490
+_chemical_name_structure_type
+;
+Perovskite
+;
+_chemical_name_systematic
+;
+strontium titanate
+;
+_space_group_IT_number           221
+_symmetry_Int_Tables_number      221
+_symmetry_space_group_name_Hall  '-P 4 2 3'
+_symmetry_space_group_name_H-M   'P m -3 m'
+_audit_creation_date             2013-07-23
+_audit_creation_method           ' Natheer'
+_audit_update_record             2013-07-23
+_cell_angle_alpha                90.000
+_cell_angle_beta                 90.000
+_cell_angle_gamma                90.000
+_cell_formula_units_Z            1
+_cell_length_a                   3.8990
+_cell_length_b                   3.8990
+_cell_length_c                   3.8990
+_cell_volume                     59.273
+_exptl_crystal_density_meas      5.140
+_cod_data_source_file            ST.cif
+_cod_data_source_block           ST
+_cod_original_cell_volume        59.3
+_cod_original_sg_symbol_Hall     -P_4_2_3
+_cod_original_formula_sum        'Sr Ti O3'
+_cod_database_code               1512124
+loop_
+_symmetry_equiv_pos_site_id
+_symmetry_equiv_pos_as_xyz
+1 x,y,z
+2 -y,x,z
+3 -x,-y,z
+4 y,-x,z
+5 x,-z,y
+6 x,-y,-z
+7 x,z,-y
+8 z,y,-x
+9 -x,y,-z
+10 -z,y,x
+11 z,x,y
+12 y,z,x
+13 -y,-z,x
+14 z,-x,-y
+15 -y,z,-x
+16 -z,-x,y
+17 -z,x,-y
+18 y,-z,-x
+19 y,x,-z
+20 -y,-x,-z
+21 -x,z,y
+22 -x,-z,-y
+23 z,-y,x
+24 -z,-y,-x
+25 -x,-y,-z
+26 y,-x,-z
+27 x,y,-z
+28 -y,x,-z
+29 -x,z,-y
+30 -x,y,z
+31 -x,-z,y
+32 -z,-y,x
+33 x,-y,z
+34 z,-y,-x
+35 -z,-x,-y
+36 -y,-z,-x
+37 y,z,-x
+38 -z,x,y
+39 y,-z,x
+40 z,x,-y
+41 z,-x,y
+42 -y,z,x
+43 -y,-x,z
+44 y,x,z
+45 x,-z,-y
+46 x,z,y
+47 -z,y,-x
+48 z,y,x
+loop_
+_atom_site_label
+_atom_site_type_symbol
+_atom_site_fract_x
+_atom_site_fract_y
+_atom_site_fract_z
+_atom_site_occupancy
+_atom_site_symmetry_multiplicity
+_atom_site_Wyckoff_symbol
+_atom_site_calc_flag
+sr Sr 0.5000 0.5000 0.5000 1.000 1 b d
+ti Ti 0.0000 0.0000 0.0000 1.000 1 a d
+o O 0.5000 0.0000 0.0000 1.000 3 d d
+loop_
+_atom_type_symbol
+_atom_type_radius_bond
+Sr 1.200
+Ti 1.200
+O 1.200

MDtutorials/k_vec_isodistort/data/STO_Subgroup.cif

@@ -0,0 +1,194 @@
+# This file was generated by ISODISTORT, version 6.12.2
+# Harold T. Stokes, Branton J. Campbell, David Tanner, Dorian M. Hatch
+# Brigham Young University, Provo, Utah, USA
+#
+# Space Group: 221 Pm-3m      Oh-1
+# 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= 3.89900, b= 3.89900, c= 3.89900, alpha= 90.00000, beta= 90.00000, gamma= 90.00000
+# sr 1b (1/2,1/2,1/2)
+# ti 1a (0,0,0)
+# o 3d (1/2,0,0)
+# Include strain, displacive ALL distortions
+# k point: X, k10 (0,1/2,0)
+# IR: X1+, k10t1
+# P1      (a;0;0) 123 P4/mmm, basis={(1,0,0),(0,0,1),(0,-2,0)}, origin=(0,0,0), s=2, i=6, k-active= (0,1/2,0)
+# Order parameter values:
+#  Pm-3m[0,1/2,0]X1+(a;0;0) 123 P4/mmm s=2 i=6
+#     [sr:b:dsp]T1u(a):  0.10000
+#     [o:d:dsp]A2u(a): -0.30000
+#  Pm-3m[0,0,0]GM1+(a) 221 Pm-3m s=1 i=1
+#     strain(a):  0.00000
+#  Pm-3m[0,0,0]GM3+(a,-1.732a) 123 P4/mmm s=1 i=3
+#     strain(a):  0.00000
+
+data_isodistort-output
+
+_cell_length_a     3.89900
+_cell_length_b     3.89900
+_cell_length_c     7.79800
+_cell_angle_alpha  90.00000
+_cell_angle_beta   90.00000
+_cell_angle_gamma  90.00000
+_cell_volume       118.54676
+
+_symmetry_space_group_name_H-M "P 4/m 2/m 2/m"
+_symmetry_Int_Tables_number 123
+_space_group.reference_setting '123:-P 4 2'
+_space_group.transform_Pp_abc a,b,c;0,0,0
+
+loop_
+_space_group_symop_id
+_space_group_symop_operation_xyz
+1 x,y,z
+2 x,-y,-z
+3 -x,y,-z
+4 -x,-y,z
+5 -y,-x,-z
+6 -y,x,z
+7 y,-x,z
+8 y,x,-z
+9 -x,-y,-z
+10 -x,y,z
+11 x,-y,z
+12 x,y,-z
+13 y,x,z
+14 y,-x,-z
+15 -y,x,-z
+16 -y,-x,z
+
+loop_
+_atom_type_symbol
+Sr    
+Ti    
+O     
+
+loop_
+_atom_site_label
+_atom_site_type_symbol
+_atom_site_symmetry_multiplicity
+_atom_site_Wyckoff_symbol
+_atom_site_fract_x
+_atom_site_fract_y
+_atom_site_fract_z
+_atom_site_occupancy
+_atom_site_fract_symmform
+sr_1 Sr   2 h  0.50000  0.50000  0.74093  1.00000 0,0,Dz 
+ti_1 Ti   1 a  0.00000  0.00000  0.00000  1.00000 0,0,0  
+ti_2 Ti   1 b  0.00000  0.00000  0.50000  1.00000 0,0,0  
+o_1  O    2 f  0.00000  0.50000  0.00000  1.00000 0,0,0  
+o_2  O    2 e  0.00000  0.50000  0.50000  1.00000 0,0,0  
+o_3  O    2 g  0.00000  0.00000  0.77720  1.00000 0,0,Dz 
+
+_iso_displacivemode_number    2
+
+loop_
+_iso_displacivemode_ID
+_iso_displacivemode_label
+_iso_displacivemode_value
+   1 Pm-3m[0,1/2,0]X1+(a;0;0)[sr:b:dsp]T1u(a)  0.10000
+   2 Pm-3m[0,1/2,0]X1+(a;0;0)[o:d:dsp]A2u(a) -0.30000
+
+loop_
+_iso_displacivemodenorm_ID
+_iso_displacivemodenorm_value
+   1  0.09068
+   2  0.09068
+
+loop_
+_iso_deltacoordinate_ID
+_iso_deltacoordinate_label
+_iso_deltacoordinate_value
+   1 sr_1_dz  -0.00907
+   2 o_3_dz   0.02720
+
+loop_
+_iso_coordinate_label
+_iso_coordinate_formula
+sr_1_x                  "1/2"
+sr_1_y                  "1/2"
+sr_1_z                  "3/4 + sr_1_dz"
+ti_1_x                  "0"
+ti_1_y                  "0"
+ti_1_z                  "0 + ti_1_dz"
+ti_2_x                  "0"
+ti_2_y                  "0"
+ti_2_z                  "1/2 + ti_2_dz"
+o_1_x                   "0"
+o_1_y                   "1/2"
+o_1_z                   "0 + o_1_dz"
+o_2_x                   "0"
+o_2_y                   "1/2"
+o_2_z                   "1/2 + o_2_dz"
+o_3_x                   "0"
+o_3_y                   "0"
+o_3_z                   "3/4 + o_3_dz"
+
+# matrix conversion: deltacoords(lattice units) = matrix.(modeamplitudes*modenormfactors)
+# Square matrix with _iso_displacivemode_number rows and columns
+
+loop_
+_iso_displacivemodematrix_row
+_iso_displacivemodematrix_col
+_iso_displacivemodematrix_value
+    1    1  -1.00000
+    2    2  -1.00000
+
+_iso_magneticmode_number    0
+
+
+_iso_rotationalmode_number    0
+
+
+_iso_occupancymode_number    0
+
+_iso_strainmode_number    2
+
+loop_
+_iso_strainmode_ID
+_iso_strainmode_label
+_iso_strainmode_value
+   1 Pm-3m[0,0,0]GM1+(a)strain(a)  0.00000
+   2 Pm-3m[0,0,0]GM3+(a,-1.732a)strain(a)  0.00000
+
+loop_
+_iso_strainmodenorm_ID
+_iso_strainmodenorm_value
+   1  0.57735
+   2  0.81650
+
+loop_
+_iso_strain_ID
+_iso_strain_label
+_iso_strain_value
+   1 E_1   0.00000
+   2 E_2   0.00000
+   3 E_3   0.00000
+   4 E_4   0.00000
+   5 E_5   0.00000
+   6 E_6   0.00000
+
+# matrix conversion: strains(parent) = matrix * modeamplitudes
+# Rectangular matrix with 6 rows and _iso_strainmode_number columns
+
+loop_
+_iso_strainmodematrix_row
+_iso_strainmodematrix_col
+_iso_strainmodematrix_value
+    1    1   1.00000
+    1    2  -0.50000
+    2    1   1.00000
+    2    2   1.00000
+    3    1   1.00000
+    3    2  -0.50000
+
+_iso_parentcell_length_a     3.89900
+_iso_parentcell_length_b     3.89900
+_iso_parentcell_length_c     3.89900
+_iso_parentcell_angle_alpha  90.00000
+_iso_parentcell_angle_beta   90.00000
+_iso_parentcell_angle_gamma  90.00000
+_iso_parentcell_volume       59.27338
+_iso_parent-to-child.transform_Pp_abc a,c,-2b;0,2,0
+
+# end of structure file
+# end of cif

MDtutorials/k_vec_isodistort/data/powgen_profile_lwf.instprm

@@ -0,0 +1,21 @@
+#GSAS-II instrument parameter file; do not add/delete items!
+Type:PNT
+Z:0.0
+fltPath:63.183
+alpha:0.19637459518597117
+sig-q:-115.671
+2-theta:90.0
+sig-1:-150.877831643885
+sig-0:223.89502267695218
+sig-2:74.40379758682252
+Zero:0.0
+difA:0.0
+difB:5.3599226472337405
+Azimuth:0.0
+Y:0.0
+X:0.0
+beta-q:0.1307895343792446
+beta-0:0.002606568983582579
+difC:22583.929270280536
+beta-1:-0.07551370867534292
+Bank:3.0