Merge pull request #1 from ionuorah/master

Added example Fe_bcc

.gitignore

@@ -4,6 +4,7 @@ __pycache__
 *.bz2
 .coverage
 dist
+*.DS_Store
 MANIFEST
 build
 muesr/engines/LFCExt/oldstuff

examples/Fe_bcc/Fe.cif

@@ -0,0 +1,39 @@
+#------------------------------------------------------------------------------
+#$Date: 2016-06-30 18:40:41 +0300 (Thu, 30 Jun 2016) $
+#$Revision: 184081 $
+#$URL: file:///home/coder/svn-repositories/cod/cif/1/10/01/1100108.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_1100108
+_publ_section_title              Fe-5Al-20Ni(5to)0.1
+_chemical_formula_sum            Fe
+_chemical_name_common            alfa-Fe
+_symmetry_cell_setting           cubic
+_symmetry_space_group_name_H-M   Im-3m
+_audit_update_record             'Last update Sat Feb 14 17:27:25 MSK 2004'
+_cell_angle_alpha                90
+_cell_angle_beta                 90
+_cell_angle_gamma                90
+_cell_formula_units_Z            2
+_cell_length_a                   2.8680182
+_cell_length_b                   2.8680182
+_cell_length_c                   2.8680182
+_refine_ls_goodness_of_fit_all   1.1737101
+_refine_ls_R_factor_all          0.04816144
+_refine_ls_wR_factor_all         0.06062723
+_cod_database_code               1100108
+loop_
+_atom_site_label
+_atom_site_type_symbol
+_atom_site_occupancy
+_atom_site_fract_x
+_atom_site_fract_y
+_atom_site_fract_z
+_atom_site_B_iso_or_equiv
+Fe1 Fe 1 0 0 0 -0.21(3)

examples/Fe_bcc/run_example.py

@@ -0,0 +1,148 @@
+# coding: utf-8
+
+#   This is an example to calculate the muon local field at the tetrahedral site(s) in bcc-Fe.
+
+
+import numpy as np
+from muesr.core.sample import Sample                   # Retains all the sample info.
+from muesr.io.cif.cif import load_cif                  # For loading the structure from cif files
+from muesr.io.xsf.xsf import load_xsf                  # For loading the structure from xsf files
+from muesr.io.xsf.xsf import show_supercell, show_cell # For visualisation with xcrysden (http://www.xcrysden.org/)
+from muesr.utilities.ms import mago_add                # For magnetic structure description
+from muesr.engines.clfc import locfield                # Does the sum and returns the local field in its diff. contributions
+from muesr.engines.clfc import find_largest_sphere     # Aids in the calculation of the sphere's radius for the lattice sum.
+from muesr.utilities.muon import muon_find_equiv       # For finding and including the symmetry equivalent muon positions in the calculation 
+
+
+#    Declare  and load sample 
+fe= Sample()                          
+load_cif(fe,"./Fe.cif")
+
+#    To add the muon position
+fe.add_muon([0.50,0.25,0.0])    
+
+
+#   Finds and includes the symmetry equivalent positions of the above defined muon.
+#   For this example there are 12 sites "print fe.muons" will show their positions.
+muon_find_equiv(fe)  
+
+
+#   Description of the propagation vector k and fourier components fc with a new magnetic structure declared with fe.new_mm()
+fe.new_mm()     
+fe.mm.k=np.array([0.0,0.0,0.0])
+fe.mm.fc= np.array([[0.0+0.j, 0.0+0.j, 2.22+0.j],
+                     [0.0+0.j, 0.0+0.j, 2.22+0.j]])
+
+
+"""
+- This is another way to define the magnetic structure especially when using the interactive session
+
+mago_add(fe)
+0.0 0.0 0.0
+Fe
+0.00 0.00 2.22 
+0.00 0.00 2.22 
+
+
+-It should appear like this on the interactive screen 
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+mago_add(fe)
+	 Propagation vector (w.r.t. conv. rec. cell): 0.0 0.0 0.0
+	 Magnetic moments in bohr magnetons and cartesian coordinates.
+	 Which atom? (enter for all)Fe
+	 Lattice vectors:
+	   a    2.868018200000000    0.000000000000000    0.000000000000000
+	   b    0.000000000000000    2.868018200000000    0.000000000000000
+	   c    0.000000000000000    0.000000000000000    2.868018200000000
+	 Atomic positions (fractional):
+	     1 Fe  0.00000000000000  0.00000000000000  0.00000000000000  55.845
+	     2 Fe  0.50000000000000  0.50000000000000  0.50000000000000  55.845
+	 FC for atom 1 Fe (3 real, [3 imag]): 0.00 0.00 2.22 
+	 FC for atom 2 Fe (3 real, [3 imag]): 0.00 0.00 2.22 
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+- 2.22 is the Fe experimental magnetic moment in Bohr magneton
+
+-Both commands below can be used for visualization on interactive session with xcrysden 
+show_cell(fe)                        
+show_supercell(fe,[2,2,2]) 
+
+"""
+
+
+
+radius=find_largest_sphere(fe,[100, 100, 100])  
+r=locfield(fe, 's', [100, 100, 100] ,radius) 
+
+"""
+- The find_largest_sphere func. is an experimental function.This func. must not be used, see documentation. 
+-  s is for the summation method used. For help type 'help(locfield)' on the interactive python session after the locfield  must have been imported
+-  [100, 100, 100] defines the supercell for the calculation
+-  radius is the sphere radius
+-  All the local fied contributions are contained in r, Bdipolar in r[i].D, BLorentz in r[i].L, BContact in r[i].C, Btotal in r[i].T
+-  If r[i].Acont(Contact field term) is not defined r[i].C is all zero.
+-  For Acont and its unit, see the documentation (http://muesr.readthedocs.io/en/latest/ContactTerm.html)  
+
+"""
+
+
+B_dip=np.zeros([len(fe.muons),3])
+B_Lor=np.zeros([len(fe.muons),3])
+B_Cont=np.zeros([len(fe.muons),3])
+B_Tot=np.zeros([len(fe.muons),3])
+for i in range(len(fe.muons)):
+	B_dip[i]=r[i].D
+	B_Lor[i]=r[i].L
+	r[i].ACont = 0.0644
+	B_Cont[i]=r[i].C
+	B_Tot[i]=r[i].T
+
+
+print("Dipolar Field for all the 12 tetrahedral equivalent sites")
+print(B_dip) 
+
+# This is and should be same for all the equivalent sites
+print("The Lorentz field is {}".format(B_Lor[0]))   
+
+print("The contact field is {} T".format(np.linalg.norm(B_Cont[0]))) 
+
+
+
+"""
+Quick look on the description of the muon jumps between the tetrahedral sites as 
+discussed in the reference below. "The field contribution at each equivalent site
+ is either parallel or antiparallel to the magnetization of the domains" such that
+ B_dip(parallel)=-2B_dip(antiparallel) "the average of the dipolar field at these three sites vanishes "
+
+Reference:  M. Schmolz et.al, Hyperfine Interactions 31 (1986) 199-204 
+
+"""
+
+print("Dipolar average of 1 parallel site and 2 antiparallel sites is {} T".format(np.linalg.norm(B_dip[3]+B_dip[10]+B_dip[11])))
+
+
+
+
+
+"""
+- Result on standard output should appear like this:
+Using internal LFC library
+Dipolar Field for all the 12 tetrahedral equivalent sites
+[[  5.92276907e-18   3.82211885e-17   2.64976810e-01]
+ [ -2.69848666e-17  -7.10720260e-18   2.64976810e-01]
+ [ -1.86130196e-17   4.90398830e-16  -5.29953619e-01]
+ [  7.49570991e-16   4.25793961e-16  -5.29953619e-01]
+ [  2.85341954e-17   1.46870359e-17   2.64976810e-01]
+ [ -9.54449012e-17  -3.56696222e-17   2.64976810e-01]
+ [  2.32510025e-17  -9.21149791e-18   2.64976810e-01]
+ [ -2.55973467e-17  -3.03263233e-17   2.64976810e-01]
+ [  4.74017137e-16   4.22061112e-16  -5.29953619e-01]
+ [  4.95076670e-16   4.00493505e-16  -5.29953619e-01]
+ [ -2.89631243e-17   4.75531976e-19   2.64976810e-01]
+ [ -1.58672778e-17  -1.93742009e-17   2.64976810e-01]]
+The Lorentz field is [ 0.          0.          0.73108635]
+The contact field is 1.11077214797 T
+Dipolar average of 1 parallel site and 2 antiparallel sites is 9.30957573598e-14 T 
+
+"""
+