PR: Feature lattice prim cell

doc/source/api/cuds.rst

@@ -38,6 +38,8 @@ Pure Python implementation
 
 .. autosummary::
 
+   ~primitive_cell.PrimitiveCell
+   ~primitive_cell.BravaisLattice
    ~lattice.Lattice
    ~lattice.LatticeNode
    ~particles.Particles
@@ -53,11 +55,20 @@ Pure Python implementation
 
 .. autosummary::
 
-   ~lattice.make_hexagonal_lattice
-   ~lattice.make_square_lattice
-   ~lattice.make_rectangular_lattice
    ~lattice.make_cubic_lattice
-   ~lattice.make_orthorombicp_lattice
+   ~lattice.make_body_centered_cubic_lattice
+   ~lattice.make_face_centered_cubic_lattice
+   ~lattice.make_rhombohedral_lattice
+   ~lattice.make_tetragonal_lattice
+   ~lattice.make_body_centered_tetragonal_lattice
+   ~lattice.make_hexagonal_lattice
+   ~lattice.make_orthorhombic_lattice
+   ~lattice.make_body_centered_orthorhombic_lattice
+   ~lattice.make_face_centered_orthorhombic_lattice
+   ~lattice.make_base_centered_orthorhombic_lattice
+   ~lattice.make_monoclinic_lattice
+   ~lattice.make_base_centered_monoclinic_lattice
+   ~lattice.make_triclinic_lattice
 
 .. rubric:: Implementation
 

doc/source/uml/h5lattice.txt

@@ -8,9 +8,9 @@ class H5Lattice as "H5Lattice(Group)" {
   lattice : Table = Nodes
   data : Table = ContainerData
   -- Node Attributes --
-  type: str
-  base_vect : float[3]
-  size : int[3]
+  prim_cell: array of float[3]
+  bravais_lattice: int
+  size: int[3]
   origin: float[3]
   cuds_version: int
 }

doc/source/uml/lattice.txt

@@ -1,16 +1,22 @@
 @startuml
 abstract class ABCLattice {
   name: str
-  type: str
-  base_vect: float[3]
+  prim_cell: PrimitiveCell
   size: int[3]
   origin: float[3]
   data: DataContainer
   {abstract} get_node(index: int[3]) LatticeNode
   {abstract} update_nodes(nodes: iterable of LatticeNode)
   {abstract} iter_nodes(indices: iterable of int[3] {optional}): iterator of LatticeNode
-  {abstract} get_coordinate((index: int[3]): float[3]
+  get_coordinate((index: int[3]): float[3]
 
   {abstract} count_of(key: CUDSItem): integer
 }
+
+class PrimitiveCell {
+  p1: float[3]
+  p2: float[3]
+  p3: float[3]
+  bravais_lattice: int
+}
 @enduml

simphony/cuds/abc_lattice.py

@@ -8,17 +8,14 @@ class ABCLattice(object):
     ----------
     name : str
         name of lattice
-    type : str
-        type of lattice
-    base_vect : float[3]
-        base vector of lattice
+    prim_cell : PrimitiveCell
+        primitive cell specifying the 3D Bravais lattice
     size : int[3]
         lattice dimensions
     origin : float[3]
         lattice origin
     data : DataContainer
         high level CUBA data assigned to lattice
-
     """
     __metaclass__ = ABCMeta
 
@@ -66,20 +63,28 @@ def iter_nodes(self, indices=None):  # pragma: no cover
 
         """
 
-    @abstractmethod
-    def get_coordinate(self, index):  # pragma: no cover
+    @property
+    def prim_cell(self):
+        return self._prim_cell
+
+    def get_coordinate(self, ind):
         """Get coordinate of the given index coordinate.
 
         Parameters
         ----------
-        index : int[3]
+        ind : int[3]
             node index coordinate
 
         Returns
         -------
         coordinates : float[3]
-
         """
+        p1 = self.prim_cell.p1
+        p2 = self.prim_cell.p2
+        p3 = self.prim_cell.p3
+        return (self.origin[0] + ind[0]*p1[0] + ind[1]*p2[0] + ind[2]*p3[0],
+                self.origin[1] + ind[0]*p1[1] + ind[1]*p2[1] + ind[2]*p3[1],
+                self.origin[2] + ind[0]*p1[2] + ind[1]*p2[2] + ind[2]*p3[2])
 
     @abstractmethod
     def count_of(self, item_type):  # pragma: no cover