Merge e8d408b into d06f4af

core/docs/INPUT.md

@@ -139,6 +139,10 @@ A lattice constant can be used for scaling:
 ### Scaling constant
 lattice_constant 1.0
 ```
+Note that it scales the Bravais vectors and therefore the
+translations, atom positions in the basis cell and potentially
+-- if you specified them in terms of the Bravais vectors --
+also the anisotropy and DM vectors.
 
 
 Heisenberg Hamiltonian <a name="Heisenberg"></a>

core/docs/c-api/Geometry.md

@@ -52,7 +52,7 @@ void Geometry_Set_Cell_Atoms(State *state, int n_atoms, float ** atoms)
 ```
 
 Set the number and positions of atoms in a basis cell.
-Positions are in units of the bravais vectors.
+Positions are in units of the bravais vectors (scaled by the lattice constant).
 
 
 
@@ -175,16 +175,6 @@ Get bravais vectors ta, tb, tc.
 
 
 
-### Geometry_Get_Translation_Vectors
-
-```C
-void Geometry_Get_Translation_Vectors(State *state, float ta[3], float tb[3], float tc[3], int idx_image=-1, int idx_chain=-1)
-```
-
-Get translation vectors ta, tb, tc.
-
-
-
 ### Geometry_Get_Dimensionality
 
 ```C
@@ -245,7 +235,7 @@ Get number of atoms in a basis cell.
 int Geometry_Get_Cell_Atoms(State *state, scalar ** atoms, int idx_image=-1, int idx_chain=-1)
 ```
 
-Get basis cell atoms.
+Get basis cell atom positions in units of the bravais vectors (scaled by the lattice constant).
 
 
 

core/include/Spirit/Geometry.h

@@ -57,7 +57,7 @@ PREFIX void Geometry_Set_N_Cells(State * state, int n_cells[3]) SUFFIX;
 
 /*
 Set the number and positions of atoms in a basis cell.
-Positions are in units of the bravais vectors.
+Positions are in units of the bravais vectors (scaled by the lattice constant).
 */
 PREFIX void Geometry_Set_Cell_Atoms(State *state, int n_atoms, float ** atoms) SUFFIX;
 
@@ -126,11 +126,6 @@ Get bravais vectors ta, tb, tc.
 */
 PREFIX void Geometry_Get_Bravais_Vectors(State *state, float a[3], float b[3], float c[3], int idx_image=-1, int idx_chain=-1) SUFFIX;
 
-/*
-Get translation vectors ta, tb, tc.
-*/
-PREFIX void Geometry_Get_Translation_Vectors(State *state, float ta[3], float tb[3], float tc[3], int idx_image=-1, int idx_chain=-1) SUFFIX;
-
 /*
 Retrieve dimensionality of the system (0, 1, 2, 3).
 */
@@ -161,7 +156,7 @@ Get number of atoms in a basis cell.
 PREFIX int Geometry_Get_N_Cell_Atoms(State *state, int idx_image=-1, int idx_chain=-1) SUFFIX;
 
 /*
-Get basis cell atoms.
+Get basis cell atom positions in units of the bravais vectors (scaled by the lattice constant).
 */
 PREFIX int Geometry_Get_Cell_Atoms(State *state, scalar ** atoms, int idx_image=-1, int idx_chain=-1) SUFFIX;
 

core/python/spirit/geometry.py

@@ -131,7 +131,7 @@ def get_bravais_lattice_type(p_state, idx_image=-1, idx_chain=-1):
                                ctypes.c_int, ctypes.c_int]
 _Get_Bravais_Vectors.restype  = None
 def get_bravais_vectors(p_state, idx_image=-1, idx_chain=-1):
-    """Get the bravais vectors.
+    """Get the Bravais vectors.
 
     Returns three arrays of shape (3).
     """
@@ -154,23 +154,6 @@ def get_n_cells(p_state, idx_image=-1, idx_chain=-1):
     _Get_N_Cells(ctypes.c_void_p(p_state), n_cells, ctypes.c_int(idx_image), ctypes.c_int(idx_chain))
     return [n for n in n_cells]
 
-_Get_Translation_Vectors          = _spirit.Geometry_Get_Translation_Vectors
-_Get_Translation_Vectors.argtypes = [ctypes.c_void_p, ctypes.POINTER(ctypes.c_float),
-                                     ctypes.POINTER(ctypes.c_float), ctypes.POINTER(ctypes.c_float),
-                                     ctypes.c_int, ctypes.c_int]
-_Get_Translation_Vectors.restype  = None
-def get_translation_vectors(p_state, idx_image=-1, idx_chain=-1):
-    """Get the translation vectors in global coordinates.
-
-    Returns three arrays of shape (3).
-    """
-    ta = (3*ctypes.c_float)()
-    tb = (3*ctypes.c_float)()
-    tc = (3*ctypes.c_float)()
-    _Get_Translation_Vectors(ctypes.c_void_p(p_state), ta, tb, tc,
-                             ctypes.c_int(idx_image), ctypes.c_int(idx_chain))
-    return [a for a in ta], [b for b in tb], [c for c in tc]
-
 _Get_Dimensionality          = _spirit.Geometry_Get_Dimensionality
 _Get_Dimensionality.argtypes = [ctypes.c_void_p, ctypes.c_int, ctypes.c_int]
 _Get_Dimensionality.restype  = ctypes.c_int

core/python/test/geometry.py

@@ -16,13 +16,13 @@
 p_state = state.setup(cfgfile)                  # State setup
 
 class TestParameters(unittest.TestCase):
-    
+
     def setUp(self):
         ''' Setup a p_state and copy it to Clipboard'''
         self.p_state = p_state
-        
+
 class Geometry(TestParameters):
-    
+
     def test_bounds(self):
         minb, maxb = geometry.get_bounds(self.p_state)
         # From the api.cfg the space is 2:2:1 particles
@@ -32,14 +32,14 @@ def test_bounds(self):
         self.assertEqual(maxb[0], 1)
         self.assertEqual(maxb[1], 1)
         self.assertEqual(maxb[2], 0)
-    
+
     def test_center(self):
         center = geometry.get_center(self.p_state)
         # From the api.cfg the space is 2:2:1 particles
         self.assertEqual(center[0], 0.5)
         self.assertEqual(center[1], 0.5)
         self.assertEqual(center[2], 0)
-    
+
     def test_bravais_vector(self):
         a, b, c = geometry.get_bravais_vectors(self.p_state)
         # From the api.cfg the bravais vectors are (1,0,0), (0,1,0), (0,0,1)
@@ -48,24 +48,17 @@ def test_bravais_vector(self):
         # Check also that the bravais lattice type matches simple cubic
         lattice_type = geometry.get_bravais_lattice_type(self.p_state)
         self.assertEqual(lattice_type, geometry.BRAVAIS_LATTICE_SC)
-    
+
     def test_N_cells(self):
         ncells = geometry.get_n_cells(self.p_state)
         self.assertEqual(ncells[0], 2)
         self.assertEqual(ncells[1], 2)
         self.assertEqual(ncells[2], 1)
-
-    def test_translational_vector(self):
-        ta, tb, tc = geometry.get_translation_vectors(self.p_state)
-        # From the api.cfg the tvec are (1,0,0), (0,1,0), (0,0,1)
-        self.assertEqual(ta[0], tb[1])
-        self.assertEqual(ta[1], tb[2])
-
-
+
     def test_dimensionality(self):
         dim = geometry.get_dimensionality(self.p_state)
         self.assertEqual(dim, 2)
-    
+
     def test_positions(self):
         positions = geometry.get_positions(self.p_state)
         # spin at (0,0,0)
@@ -84,7 +77,7 @@ def test_positions(self):
         self.assertAlmostEqual(positions[3][0], 1)
         self.assertAlmostEqual(positions[3][1], 1)
         self.assertAlmostEqual(positions[3][2], 0)
-    
+
     def test_atom_types(self):
         types = geometry.get_atom_types(self.p_state)
         self.assertEqual(len(types), 4)