muon_find_equiv -> find_equiv, and related tests and docs

docs/Tutorial.rst

@@ -89,12 +89,12 @@ can be specified as
 
 If proper symmetry of the sample is present in the sample definition, it
 is usually usefull to get symmetry equivalent sites.
-This can be done with the utility function :py:func:`~muesr.utilities.muon.muon_find_equiv`.
+This can be done with the utility function :py:func:`~muesr.utilities.muon.find_equiv`.
 
 .. code-block:: python
     
-    >>> from muesr.utilities.muon import muon_find_equiv
-    >>> muon_find_equiv(mysample)
+    >>> from muesr.utilities.muon import find_equiv
+    >>> find_equiv(mysample)
 
 
 Defining a magnetic structure

docs/Usage.rst

@@ -13,6 +13,7 @@ This is very easy! You just do: ::
 
 the :py:attr:`~muesr.core.sample.Sample.name` property is optional.
 
+
 Defining a lattice structure
 ----------------------------
 
@@ -224,6 +225,14 @@ Useful readings
  - http://www.neutron-sciences.org/articles/sfn/pdf/2014/01/sfn201402001.pdf
 
 
+Setting the muon position
+-------------------------
+
+The muon position can be easly set with the .
+
+If symmetry is defined, equivalent muon positions can be obtained with 
+the function :py:func:`~muesr.utilities.muon.find_equiv`
+
 Calculate local fields 
 ------------------------
 

examples/LaFeAsO/run_example.py

@@ -5,8 +5,8 @@
 
 from muesr.core.sample import Sample
 from muesr.io.cif.cif import load_mcif
-from muesr.utilities.symsearch import sym_search
-from muesr.utilities.muon import  muon_find_equiv
+from muesr.utilities.symsearch import symsearch
+from muesr.utilities.muon import  find_equiv
 from muesr.engines.clfc import locfield
 
 #define an empty sample.
@@ -24,12 +24,11 @@
 #  these are inspected from the structure rather than parsed from the cif.
 #  The reason for doing this is that structure may be read from files
 #  without symmetry informations.
-    sym_search(m)
+    symsearch(m)
 # Sets muon position in fractional coordinates
     m.add_muon([0.375,  0.375, 0.635])
-# Find crystalographically equivalent muon sites. Uses 3 decimal rounding
-#  to check if two positions are equivalent.
-    muon_find_equiv(m)
+# Find crystalographically equivalent muon sites. 
+    find_equiv(m)
     res=locfield(m, 's',[100,100,50],200)
     print('Structure in file: '+mcif)
     for e in res:

muesr/tests/utilities/test_muon.py

@@ -8,7 +8,7 @@
 
 from muesr.core.sampleErrors import CellError, MuonError
 from muesr.core.sample import Sample
-from muesr.utilities.muon import muon_set_frac, muon_find_equiv, muon_reset
+from muesr.utilities.muon import muon_set_frac, find_equiv, muon_reset
 from muesr.io.cif.cif import read_cif
 
 co_lattice = StringIO("""
@@ -314,7 +314,7 @@ def test_muon_reset(self):
         muon_set_frac(self._sample, "0.125 0.125 0.125")
         np.testing.assert_array_almost_equal(np.array([0.125,0.125,0.125]),self._sample.muons[1])
 
-    def test_muon_find_equiv(self):
+    def test_find_equiv(self):
         # ugly way to load a lattice with its symetry
         co_lattice.seek(0)
         atoms, sym = read_cif(co_lattice,0) # selectd index 0
@@ -328,10 +328,10 @@ def test_muon_find_equiv(self):
 
         #tests throw error if no muon positions defined
         with self.assertRaises(MuonError):
-            muon_find_equiv(self._sample)
+            find_equiv(self._sample)
 
         muon_set_frac(self._sample, "0 0 0")
-        muon_find_equiv(self._sample)
+        find_equiv(self._sample)
 
         muon_positions = self._sample.muons
 
@@ -342,7 +342,7 @@ def test_muon_find_equiv(self):
         self._sample._reset(muon=True)
 
         muon_set_frac(self._sample, "0.2 0.3 0.4")
-        muon_find_equiv(self._sample)
+        find_equiv(self._sample)
 
         muon_positions = self._sample.muons
         #positions calculated with VESTA

muesr/utilities/ms.py

@@ -52,10 +52,10 @@ def mago_set_k(sample, kvalue=None,mm=None):
             return
 
 
-def mago_add(sample, inputConvention='b-c'):
+def mago_add(sample, coordinates='b-c'):
     """
     Add a magnetic model (fourier components and K vector).
-    Fourier components are in CARTESIAN coordinates.
+    
     The order is automatically selected if succesfully added.
     
     
@@ -65,7 +65,7 @@ def mago_add(sample, inputConvention='b-c'):
     nmm = MM(sample.cell.get_number_of_atoms(),sample.cell.get_cell())
 
     mago_set_k(sample, mm=nmm)
-    mago_set_FC(sample, mm=nmm, inputConvention=inputConvention)
+    mago_set_FC(sample, mm=nmm, inputConvention=coordinates)
     sample.mm = nmm
 
 
@@ -94,7 +94,7 @@ def mago_set_FC(sample, fcs= None, atoms_types = None, mm=None, inputConvention=
         nprint('Magnetic moments in bohr magnetons and cartesian coordinates.')
         inputConvEnum = 0
 
-    elif inputConvention.lower() in ['bohr/angstrom-lattic', 'b/a-l']:
+    elif inputConvention.lower() in ['bohr/angstrom-lattice', 'b/a-l']:
         nprint('Magnetic moments in bohr magnetons/angstrom and lattice coordinates.')
         inputConvEnum = 1
 

muesr/utilities/muon.py

@@ -42,7 +42,7 @@ def muon_set_frac(sample, arg = None):
 
 
 
-def muon_find_equiv(sample, eps=1.e-3):
+def find_equiv(sample, eps=1.e-3):
     """
     Given the unit cell symmetry, finds the equivalent muon sites.
     Magnetic order is NOT considered