Added new to_hoomd method (#212)

* Added new to_hoomd method

* Updated changelog and credits

* Removed working tempfiles and rolled back bumpversion

* Added to_json method to base class

* Added mapping functions to utils

* Migrated to_hoomd functions to use internal to_json method

* Updated tests

* Fixed capitalization errors

* Added more detail to return descriptor

* Updated credits

* Updated explanation for centering shapes in to_hoomd

Author: janbridley

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_json`` and ``to_hoomd`` export methods.
 
 Domagoj Fijan
 

coxeter/shapes/base_classes.py

@@ -197,6 +197,30 @@ def to_plato_scene(self, backend="matplotlib", scene=None, scene_kwargs=None):
             scene.add_primitive(prim)
         return scene
 
+    def to_json(self, attributes: list):
+        """Get a JSON-serializable subset of shape properties.
+
+        Args:
+            attributes (list):
+                List of attributes to export. Each element must be a valid attribute
+                of the class.
+
+        Returns
+        -------
+           dict
+                A dict containing the requested attributes.
+
+        Raises
+        ------
+            AttributeError:
+                If any keys in the input list are invalid.
+        """
+        export = {}
+        for attribute in attributes:
+            # If an invalid key is passed, this will raise an attribute error
+            export.update({attribute: getattr(self, attribute)})
+        return export
+
 
 class Shape2D(Shape):
     """An abstract representation of a shape in 2 dimensions."""

coxeter/shapes/convex_spheropolygon.py

@@ -12,6 +12,7 @@
 from .base_classes import Shape2D
 from .convex_polygon import ConvexPolygon, _is_convex
 from .polygon import _align_points_by_normal
+from .utils import _hoomd_dict_mapping, _map_dict_keys
 
 
 class ConvexSpheropolygon(Shape2D):
@@ -267,3 +268,37 @@ 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. Stored values
+        are based on the shape with its centroid at the origin.
+
+        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] per HOOMD's spec.
+        * sweep_radius (float):
+            The rounding radius of the shape.
+        * area (float)
+            The area of the shape.
+
+        Returns
+        -------
+        dict
+            Dict containing a subset of shape properties required for HOOMD function.
+        """
+        old_centroid = self._polygon.centroid
+        data = self.to_json(["vertices", "radius", "area"])
+        hoomd_dict = _map_dict_keys(data, key_mapping=_hoomd_dict_mapping)
+        hoomd_dict["centroid"] = [0, 0, 0]
+
+        self._polygon.centroid = old_centroid
+        return hoomd_dict

coxeter/shapes/convex_spheropolyhedron.py

@@ -11,6 +11,7 @@
 
 from .base_classes import Shape3D
 from .convex_polyhedron import ConvexPolyhedron
+from .utils import _hoomd_dict_mapping, _map_dict_keys
 
 
 class ConvexSpheropolyhedron(Shape3D):
@@ -328,3 +329,38 @@ 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. Stored values
+        are based on the shape with its centroid at the origin.
+
+        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] per HOOMD's spec.
+        * 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 required for HOOMD function.
+        """
+        old_centroid = self._polyhedron.centroid
+        self._polyhedron.centroid = np.array([0, 0, 0])
+        data = self.to_json(["vertices", "radius", "volume"])
+        hoomd_dict = _map_dict_keys(data, key_mapping=_hoomd_dict_mapping)
+        hoomd_dict["centroid"] = [0, 0, 0]
+
+        self._polyhedron.centroid = old_centroid
+        return hoomd_dict

coxeter/shapes/ellipsoid.py

@@ -8,7 +8,7 @@
 
 from .base_classes import Shape3D
 from .sphere import Sphere
-from .utils import translate_inertia_tensor
+from .utils import _hoomd_dict_mapping, _map_dict_keys, translate_inertia_tensor
 
 
 class Ellipsoid(Shape3D):
@@ -225,3 +225,41 @@ 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. Stored values
+        are based on the shape with its centroid at the origin.
+
+        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] per HOOMD's spec.
+        * 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 required for HOOMD function.
+        """
+        old_centroid = self.centroid
+        self.centroid = np.array([0, 0, 0])
+        data = self.to_json(["a", "b", "c", "centroid", "volume", "inertia_tensor"])
+        hoomd_dict = _map_dict_keys(data, key_mapping=_hoomd_dict_mapping)
+
+        self.centroid = old_centroid
+        return hoomd_dict

coxeter/shapes/polygon.py

@@ -12,7 +12,13 @@
 from ..extern.polytri import polytri
 from .base_classes import Shape2D
 from .circle import Circle
-from .utils import _generate_ax, rotate_order2_tensor, translate_inertia_tensor
+from .utils import (
+    _generate_ax,
+    _hoomd_dict_mapping,
+    _map_dict_keys,
+    rotate_order2_tensor,
+    translate_inertia_tensor,
+)
 
 try:
     import miniball
@@ -761,3 +767,40 @@ 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. Stored values
+        are based on the shape with its centroid at the origin.
+
+        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] per HOOMD's spec.
+        * 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 required for HOOMD function.
+        """
+        old_centroid = self.centroid
+        self.centroid = np.array([0, 0, 0])
+        data = self.to_json(["vertices", "centroid", "area", "inertia_tensor"])
+        hoomd_dict = _map_dict_keys(data, key_mapping=_hoomd_dict_mapping)
+        hoomd_dict["sweep_radius"] = 0.0
+
+        self.centroid = old_centroid
+        return hoomd_dict

coxeter/shapes/polyhedron.py

@@ -15,7 +15,13 @@
 from .convex_polygon import ConvexPolygon, _is_convex
 from .polygon import Polygon, _is_simple
 from .sphere import Sphere
-from .utils import _generate_ax, _set_3d_axes_equal, translate_inertia_tensor
+from .utils import (
+    _generate_ax,
+    _hoomd_dict_mapping,
+    _map_dict_keys,
+    _set_3d_axes_equal,
+    translate_inertia_tensor,
+)
 
 try:
     import miniball
@@ -973,3 +979,44 @@ 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. Stored values
+        are based on the shape with its centroid at the origin.
+
+        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] per HOOMD's spec.
+        * 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 required for HOOMD function.
+        """
+        old_centroid = self.centroid
+        self.centroid = np.array([0, 0, 0])
+        data = self.to_json(
+            ["vertices", "faces", "centroid", "volume", "inertia_tensor"]
+        )
+        hoomd_dict = _map_dict_keys(data, key_mapping=_hoomd_dict_mapping)
+        hoomd_dict["sweep_radius"] = 0.0
+
+        self.centroid = old_centroid
+        return hoomd_dict

coxeter/shapes/sphere.py

@@ -6,7 +6,7 @@
 import numpy as np
 
 from .base_classes import Shape3D
-from .utils import translate_inertia_tensor
+from .utils import _hoomd_dict_mapping, _map_dict_keys, translate_inertia_tensor
 
 
 class Sphere(Shape3D):
@@ -68,6 +68,18 @@ def radius(self, value):
         else:
             raise ValueError("Radius must be greater than zero.")
 
+    @property
+    def diameter(self):
+        """float: Get or set the radius of the sphere."""
+        return 2 * self._radius
+
+    @diameter.setter
+    def diameter(self, value):
+        if value > 0:
+            self._radius = value / 2
+        else:
+            raise ValueError("Diameter must be greater than zero.")
+
     def _rescale(self, scale):
         """Multiply length scale.
 
@@ -202,3 +214,37 @@ 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. Stored values
+        are based on the shape with its centroid at the origin.
+
+        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] per HOOMD's spec.
+        * 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 required for HOOMD function.
+        """
+        old_centroid = self.centroid
+        self.centroid = np.array([0, 0, 0])
+        data = self.to_json(["diameter", "centroid", "volume", "inertia_tensor"])
+        hoomd_dict = _map_dict_keys(data, key_mapping=_hoomd_dict_mapping)
+
+        self.centroid = old_centroid
+        return hoomd_dict