Merge branch 'master' of git://github.com/materialsproject/pymatgen

pymatgen/symmetry/finder.py

@@ -273,7 +273,6 @@ def get_symmetry_operations(self, cartesian=False):
             symmops.append(op)
         return symmops
 
-
     def get_point_group_operations(self, cartesian=False):
         """
         Return symmetry operations as a list of SymmOp objects.
@@ -287,10 +286,10 @@ def get_point_group_operations(self, cartesian=False):
         for rot, trans in zip(rotation, translation):
             if cartesian:
                 rot = np.dot(mat, np.dot(rot, invmat))
-                trans = np.dot(trans, self._structure.lattice.matrix)
-            op = SymmOp.from_rotation_and_translation(rot, np.array([0,0,0]))
+            op = SymmOp.from_rotation_and_translation(rot, np.array([0, 0, 0]))
             symmops.append(op)
         return symmops
+
     def get_symmetrized_structure(self):
         """
         Get a symmetrized structure. A symmetrized structure is one where the
@@ -351,8 +350,8 @@ def find_primitive(self):
         species = [self._unique_species[i - 1] for i in zs]
 
         if num_atom_prim > 0:
-            return Structure(lattice.T, species, positions[:num_atom_prim],to_unit_cell=True)\
-                .get_reduced_structure()
+            return Structure(lattice.T, species, positions[:num_atom_prim],
+                             to_unit_cell=True).get_reduced_structure()
         else:
             #Not sure if we should return None or just return the full
             #structure.

pymatgen/transformations/standard_transformations.py

@@ -301,14 +301,17 @@ def __init__(self, species_map):
         """
         Args:
             species_map:
-                A dict containing the species mapping in string-string pairs.
-                E.g., { "Li":"Na"} or {"Fe2+","Mn2+"}. Multiple substitutions
-                can be done. Overloaded to accept sp_and_occu dictionary
-                E.g. {"Si: {"Ge":0.75, "C":0.25} }, which substitutes a single
-                species with multiple species to generate a disordered
-                structure.
-        """
-        self._species_map = species_map
+                A dict or list of tuples containing the species mapping in 
+                string-string pairs. E.g., {"Li":"Na"} or [("Fe2+","Mn2+")]. 
+                Multiple substitutions can be done. Overloaded to accept 
+                sp_and_occu dictionary E.g. {"Si: {"Ge":0.75, "C":0.25}}, 
+                which substitutes a single species with multiple species to 
+                generate a disordered structure.
+        """        
+        self._species_map = dict(species_map)
+        for k, v in self._species_map.iteritems():
+            if isinstance(v, (tuple, list)):
+                self._species_map[k] = dict(v)
 
     def apply_transformation(self, structure):
         species_map = {}
@@ -341,7 +344,15 @@ def is_one_to_many(self):
 
     @property
     def to_dict(self):
-        sp_map = {str(k):str(v) for k, v in self._species_map.iteritems()}
+        #convert sp_map to tuple representation to work with Mongo
+        #which doesn't allow '.' in key names
+        sp_map = []
+        for k, v in self._species_map.iteritems():
+            if isinstance(v, dict):
+                v = [(str(k2), v2) for k2, v2 in v.iteritems()]
+                sp_map.append((str(k), v))
+            else:
+                sp_map.append((str(k), v))
         return {"name": self.__class__.__name__, "version": __version__,
                 "init_args": {"species_map": sp_map},
                 "@module": self.__class__.__module__,

pymatgen/transformations/tests/test_standard_transformations.py

@@ -94,6 +94,8 @@ def test_apply_transformation(self):
     def test_fractional_substitution(self):
         t = SubstitutionTransformation({"Li+": "Na+",
                                         "O2-": {"S2-": 0.5, "Se2-": 0.5}})
+        #test the to and from dict on the nested dictionary
+        t = SubstitutionTransformation.from_dict(t.to_dict)
         coords = list()
         coords.append([0, 0, 0])
         coords.append([0.75, 0.75, 0.75])

pymatgen/vis/structure_vtk.py

@@ -437,7 +437,9 @@ def add_line(self, start, end, color=(0.5, 0.5, 0.5), width=1):
         actor.GetProperty().SetLineWidth(width)
         self.ren.AddActor(actor)
 
-    def add_polyhedron(self, neighbors, center, color):
+    def add_polyhedron(self, neighbors, center, color, opacity=0.4,
+                       draw_edges=False, edges_color=[0.0, 0.0, 0.0],
+                       edges_linewidth=2):
         """
         Adds a polyhedron.
 
@@ -448,6 +450,14 @@ def add_polyhedron(self, neighbors, center, color):
                 The atom in the center of the polyhedron.
             color:
                 Color for text as RGB.
+            opacity:
+                Opacity of the polyhedron
+            draw_edges:
+                If set to True, the a line will be drawn at each edge
+            edges_color:
+                Color of the line for the edges
+            edges_linewidth:
+                Width of the line drawn for the edges
         """
         points = vtk.vtkPoints()
         conv = vtk.vtkConvexPointSet()
@@ -464,15 +474,99 @@ def add_polyhedron(self, neighbors, center, color):
         polysites = [center]
         polysites.extend(neighbors)
         self.mapper_map[dsm] = polysites
-        dsm.SetInputData(grid)
+        if vtk.VTK_MAJOR_VERSION <= 5:
+            dsm.SetInputConnection(grid.GetProducerPort())
+        else:
+            dsm.SetInputData(grid)
         ac = vtk.vtkActor()
         #ac.SetMapper(mapHull)
         ac.SetMapper(dsm)
-        ac.GetProperty().SetOpacity(0.4)
-        ac.GetProperty().SetColor(color)
+        ac.GetProperty().SetOpacity(opacity)
+        if color == 'element':
+            # If partial occupations are involved, the color of the specie with
+            # the highest occupation is used
+            myoccu = 0.0
+            for specie, occu in center.species_and_occu.items():
+                if occu > myoccu:
+                    myspecie = specie
+                    myoccu = occu
+            color = [i / 255 for i in self.el_color_mapping[myspecie.symbol]]
+            ac.GetProperty().SetColor(color)
+        else:
+            ac.GetProperty().SetColor(color)
+        if draw_edges:
+            ac.GetProperty().SetEdgeColor(edges_color)
+            ac.GetProperty().SetLineWidth(edges_linewidth)
+            ac.GetProperty().EdgeVisibilityOn()
         self.ren.AddActor(ac)
 
-    def add_bonds(self, neighbors, center):
+    def add_triangle(self, neighbors, color, center=None, opacity=0.4,
+                     draw_edges=False, edges_color=[0.0, 0.0, 0.0],
+                     edges_linewidth=2):
+        """
+        Adds a triangular surface between three atoms.
+
+        Args:
+            atoms:
+                Atoms between which a triangle will be drawn.
+            color:
+                Color for triangle as RGB.
+            center:
+                The "central atom" of the triangle
+            opacity:
+                opacity of the triangle
+            draw_edges:
+                If set to True, the a line will be drawn at each edge
+            edges_color:
+                Color of the line for the edges
+            edges_linewidth:
+                Width of the line drawn for the edges
+        """
+        points = vtk.vtkPoints()
+        triangle = vtk.vtkTriangle()
+        for ii in range(3):
+            points.InsertNextPoint(neighbors[ii].x, neighbors[ii].y,
+                                   neighbors[ii].z)
+            triangle.GetPointIds().SetId(ii,ii)
+        triangles = vtk.vtkCellArray()
+        triangles.InsertNextCell(triangle)
+
+        # polydata object
+        trianglePolyData = vtk.vtkPolyData()
+        trianglePolyData.SetPoints( points )
+        trianglePolyData.SetPolys( triangles )
+
+        # mapper
+        mapper = vtk.vtkPolyDataMapper()
+        mapper.SetInput(trianglePolyData)
+
+        ac = vtk.vtkActor()
+        ac.SetMapper(mapper)
+        ac.GetProperty().SetOpacity(opacity)
+        if color == 'element':
+            if center is None:
+                raise ValueError(
+                    'Color should be chosen according to the central atom, '
+                    'and central atom is not provided')
+            # If partial occupations are involved, the color of the specie with
+            # the highest occupation is used
+            myoccu = 0.0
+            for specie, occu in center.species_and_occu.items():
+                if occu > myoccu:
+                    myspecie = specie
+                    myoccu = occu
+            color = [i / 255 for i in self.el_color_mapping[myspecie.symbol]]
+            ac.GetProperty().SetColor(color)
+        else:
+            ac.GetProperty().SetColor(color)
+        if draw_edges:
+            ac.GetProperty().SetEdgeColor(edges_color)
+            ac.GetProperty().SetLineWidth(edges_linewidth)
+            ac.GetProperty().EdgeVisibilityOn()
+        self.ren.AddActor(ac)
+
+    def add_bonds(self, neighbors, center, color=None, opacity=None,
+                  radius=0.1):
         """
         Adds bonds for a site.
 
@@ -481,6 +575,12 @@ def add_bonds(self, neighbors, center):
                 Neighbors of the site.
             center:
                 The site in the center for all bonds.
+            color:
+                Color of the tubes representing the bonds
+            opacity:
+                Opacity of the tubes representing the bonds
+            radius:
+                radius of tube s representing the bonds
         """
         points = vtk.vtkPoints()
         points.InsertPoint(0, center.x, center.y, center.z)
@@ -497,13 +597,17 @@ def add_bonds(self, neighbors, center):
 
         tube = vtk.vtkTubeFilter()
         tube.SetInput(pd)
-        tube.SetRadius(0.1)
+        tube.SetRadius(radius)
 
         mapper = vtk.vtkPolyDataMapper()
         mapper.SetInputConnection(tube.GetOutputPort())
 
         actor = vtk.vtkActor()
         actor.SetMapper(mapper)
+        if opacity is not None:
+            actor.GetProperty().SetOpacity(opacity)
+        if color is not None:
+            actor.GetProperty().SetColor(color)
         self.ren.AddActor(actor)
 
     def add_picker_fixed(self):