Added new to_hoomd method

ChangeLog.rst

@@ -13,6 +13,7 @@ Added
 - ``simplices``, ``equations``, and ``face_centroids`` properties for the
   ConvexPolyhedron class.
 - Additional pytests for surface area, volume, centroid, moment of inertia, and equations properties.
+- Added ``to_hoomd`` export method for use with simulation tools
 
 Changed
 ~~~~~~~

Credits.rst

@@ -123,6 +123,7 @@ Jen Bradley
 * Added ``simplices``, ``equations``, and ``face_centroids`` properties to the
   ConvexPolyhedron class.
 * Optimized pytest configurations for more efficient use of local and remote resources.
+* Added ``to_hoomd`` export method for use with simulation tools.
 
 Domagoj Fijan
 

coxeter/__init__.py

@@ -21,4 +21,4 @@
 
 __all__ = ["families", "shapes", "from_gsd_type_shapes"]
 
-__version__ = "0.7.0"
+__version__ = "0.8.0"

coxeter/shapes/convex_spheropolygon.py

@@ -267,3 +267,42 @@ def _plato_primitive(self, backend):
             vertices=verts[:, :2],
             radius=self.radius,
         )
+
+    def to_hoomd(self):
+        """Get a json-serializable subset of ConvexSpheropolygon properties.
+
+        The json-serializable output of the to_hoomd method can be directly imported
+        into data management tools like Signac. This data can then be queried for use in
+        HOOMD simulations. Key naming matches HOOMD integrators: for example, the
+        moment_inertia key links to data from coxeter's inertia_tensor.
+
+        For a ConvexSpheropolygon, the following properties are stored:
+
+        * vertices (list(list)):
+            The vertices of the shape.
+        * centroid (list(float))
+            The centroid of the shape.
+            This is set to [0,0,0] to improve HOOMD performance.
+        * sweep_radius (float):
+            The rounding radius of the shape.
+        * area (float)
+            The area of the shape.
+        * moment_inertia (list(list))
+            The shape's inertia tensor.
+
+        Returns
+        -------
+        dict
+            Dict containing a subset of shape properties.
+        """
+        old_centroid = self.centroid
+        self.centroid = np.array([0, 0, 0])
+        hoomd_dict = {
+            "vertices": self.vertices.tolist(),
+            "centroid": self.centroid.tolist(),
+            "sweep_radius": self.radius,
+            "area": self.area,
+            "moment_inertia": self.inertia_tensor.tolist(),
+        }
+        self.centroid = old_centroid
+        return hoomd_dict

coxeter/shapes/convex_spheropolyhedron.py

@@ -304,3 +304,39 @@ def _plato_primitive(self, backend):
             vertices=self.vertices,
             radius=self.radius,
         )
+
+    def to_hoomd(self):
+        """Get a json-serializable subset of ConvexSpheropolyhedron properties.
+
+        The json-serializable output of the to_hoomd method can be directly imported
+        into data management tools like Signac. This data can then be queried for use in
+        HOOMD simulations. Key naming matches HOOMD integrators: for example, the
+        moment_inertia key links to data from coxeter's inertia_tensor.
+
+        For a ConvexSpheropolyhedron, the following properties are stored:
+
+        * vertices (list(list)):
+            The vertices of the shape.
+        * centroid (list(float))
+            The centroid of the shape.
+            This is set to [0,0,0] to improve HOOMD performance.
+        * sweep_radius (float):
+            The rounding radius of the shape.
+        * volume (float)
+            The volume of the shape.
+
+        Returns
+        -------
+        dict
+            Dict containing a subset of shape properties.
+        """
+        old_centroid = self._polyhedron.centroid
+        self._polyhedron.centroid = np.array([0, 0, 0])
+        hoomd_dict = {
+            "vertices": self.vertices.tolist(),
+            "centroid": self._polyhedron.centroid.tolist(),
+            "sweep_radius": self.radius,
+            "volume": self.volume,
+        }
+        self._polyhedron.centroid = old_centroid
+        return hoomd_dict

coxeter/shapes/ellipsoid.py

@@ -225,3 +225,45 @@ def __repr__(self):
             f"coxeter.shapes.Ellipsoid(a={self.a}, b={self.b}, c={self.c}, "
             f"center={self.centroid.tolist()})"
         )
+
+    def to_hoomd(self):
+        """Get a json-serializable subset of Ellipsoid properties.
+
+        The json-serializable output of the to_hoomd method can be directly imported
+        into data management tools like Signac. This data can then be queried for use in
+        HOOMD simulations. Key naming matches HOOMD integrators: for example, the
+        moment_inertia key links to data from coxeter's inertia_tensor.
+
+        For an Ellipsoid, the following properties are stored:
+
+        * a (float):
+            half axis of ellipsoid in the x direction
+        * b (float):
+            half axis of ellipsoid in the y direction
+        * c (float):
+            half axis of ellipsoid in the z direction
+        * centroid (list(float))
+            The centroid of the shape.
+            This is set to [0,0,0] to improve HOOMD performance.
+        * volume (float)
+            The volume of the shape.
+        * moment_inertia (list(list))
+            The shape's inertia tensor.
+
+        Returns
+        -------
+        dict
+            Dict containing a subset of shape properties.
+        """
+        old_centroid = self.centroid
+        self.centroid = np.array([0, 0, 0])
+        hoomd_dict = {
+            "a": self.a,
+            "b": self.b,
+            "c": self.c,
+            "centroid": self.centroid.tolist(),
+            "volume": self.volume,
+            "moment_inertia": self.inertia_tensor.tolist(),
+        }
+        self.centroid = old_centroid
+        return hoomd_dict

coxeter/shapes/polygon.py

@@ -761,3 +761,42 @@ def _plato_primitive(self, backend):
             colors=np.array([[0.5, 0.5, 0.5, 1]]),
             vertices=verts[:, :2],
         )
+
+    def to_hoomd(self):
+        """Get a json-serializable subset of Polygon properties.
+
+        The json-serializable output of the to_hoomd method can be directly imported
+        into data management tools like Signac. This data can then be queried for use in
+        HOOMD simulations. Key naming matches HOOMD integrators: for example, the
+        moment_inertia key links to data from coxeter's inertia_tensor.
+
+        For a Polygon or ConvexPolygon, the following properties are stored:
+
+        * vertices (list(list)):
+            The vertices of the shape.
+        * centroid (list(float))
+            The centroid of the shape.
+            This is set to [0,0,0] to improve HOOMD performance.
+        * sweep_radius (float):
+            The rounding radius of the shape (0.0).
+        * area (float)
+            The area of the shape.
+        * moment_inertia (list(list))
+            The shape's inertia tensor.
+
+        Returns
+        -------
+        dict
+            Dict containing a subset of shape properties.
+        """
+        old_centroid = self.centroid
+        self.centroid = np.array([0, 0, 0])
+        hoomd_dict = {
+            "vertices": self.vertices.tolist(),
+            "centroid": self.centroid.tolist(),
+            "sweep_radius": 0.0,
+            "area": self.area,
+            "moment_inertia": self.inertia_tensor.tolist(),
+        }
+        self.centroid = old_centroid
+        return hoomd_dict

coxeter/shapes/polyhedron.py

@@ -973,3 +973,45 @@ def _plato_primitive(self, backend):
             indices=self.faces,
             shape_colors=np.array([[0.5, 0.5, 0.5, 1]]),
         )
+
+    def to_hoomd(self):
+        """Get a json-serializable subset of Polyhedron properties.
+
+        The json-serializable output of the to_hoomd method can be directly imported
+        into data management tools like Signac. This data can then be queried for use in
+        HOOMD simulations. Key naming matches HOOMD integrators: for example, the
+        moment_inertia key links to data from coxeter's inertia_tensor.
+
+        For a Polyhedron or ConvexPolyhedron, the following properties are stored:
+
+        * vertices (list(list)):
+            The vertices of the shape.
+        * faces (list(list)):
+            The faces of the shape.
+        * centroid (list(float))
+            The centroid of the shape.
+            This is set to [0,0,0] to improve HOOMD performance.
+        * sweep_radius (float):
+            The rounding radius of the shape (0.0).
+        * volume (float)
+            The volume of the shape.
+        * moment_inertia (list(list))
+            The shape's inertia tensor.
+
+        Returns
+        -------
+        dict
+            Dict containing a subset of shape properties.
+        """
+        old_centroid = self.centroid
+        self.centroid = np.array([0, 0, 0])
+        hoomd_dict = {
+            "vertices": self.vertices.tolist(),
+            "faces": [face.tolist() for face in self.faces],
+            "centroid": self.centroid.tolist(),
+            "sweep_radius": 0.0,
+            "volume": self.volume,
+            "moment_inertia": self.inertia_tensor.tolist(),
+        }
+        self.centroid = old_centroid
+        return hoomd_dict

coxeter/shapes/sphere.py

@@ -202,3 +202,39 @@ def _plato_primitive(self, backend):
             colors=np.array([[0.5, 0.5, 0.5, 1]]),
             radii=[self.radius],
         )
+
+    def to_hoomd(self):
+        """Get a dict of json-serializable subset of Sphere properties.
+
+        The json-serializable output of the to_hoomd method can be directly imported
+        into data management tools like Signac. This data can then be queried for use in
+        HOOMD simulations. Key naming matches HOOMD integrators: for example, the
+        moment_inertia key links to data from coxeter's inertia_tensor.
+
+        For a Sphere, the following properties are stored:
+
+        * diameter (float):
+            The diameter of the sphere, equal to twice the radius.
+        * centroid (list(float))
+            The centroid of the shape.
+            This is set to [0,0,0] to improve HOOMD performance.
+        * volume (float)
+            The volume of the shape.
+        * moment_inertia (list(list))
+            The shape's inertia tensor.
+
+        Returns
+        -------
+        dict
+            Dict containing a subset of shape properties.
+        """
+        old_centroid = self.centroid
+        self.centroid = np.array([0, 0, 0])
+        hoomd_dict = {
+            "diameter": self.radius * 2,
+            "centroid": self.centroid.tolist(),
+            "volume": self.volume,
+            "moment_inertia": self.inertia_tensor.tolist(),
+        }
+        self.centroid = old_centroid
+        return hoomd_dict

doc/source/conf.py

@@ -22,8 +22,8 @@
 author = "Vyas Ramasubramani"
 
 # The full version, including alpha/beta/rc tags
-version = "0.7.0"
-release = "0.7.0"
+version = "0.8.0"
+release = "0.8.0"
 
 
 # -- General configuration ---------------------------------------------------