Remove Stomatocyte shape

doc/sphinx/constraints.rst

@@ -49,7 +49,6 @@ Available shapes are listed below.
     - :class:`espressomd.shapes.Slitpore`
     - :class:`espressomd.shapes.Sphere`
     - :class:`espressomd.shapes.SpheroCylinder`
-    - :class:`espressomd.shapes.Stomatocyte`
     - :class:`espressomd.shapes.Torus`
     - :class:`espressomd.shapes.HollowConicalFrustum`
     - :class:`espressomd.shapes.Union`
@@ -334,57 +333,6 @@ the smooth pore openings will be rendered using a sliced torus. You can safely
 ignore this visual artifact, it has no impact on the force/energy calculation.
 
 
-Stomatocyte
-"""""""""""
-
-.. note::
-
-    Requires ``EXPERIMENTAL_FEATURES``.
-
-:class:`espressomd.shapes.Stomatocyte`
-
-A stomatocyte-shaped boundary surface.
-This command should be used with care.
-The position can be any point in the simulation box and is set via the (3,) array_like parameter ``center``.
-The orientation of the (cylindrically symmetric) stomatocyte is given by an ``axis`` (a (3,) array_like of :obj:`float`),
-which points in the direction of the symmetry axis and does not need to be normalized.
-Parameters ``outer_radius``, ``inner_radius``, and ``layer_width`` specify the
-shape of the stomatocyte. Here inappropriate choices of parameters can yield
-undesired results, such as discontinuous shapes or NaN values. Always use
-values greater than 1 for ``inner_radius`` to avoid NaN values.
-The width ``layer_width`` is used as a scaling parameter.
-That is, a stomatocyte given by ``outer_radius:inner_radius:layer_width`` = 7:3:1
-is half the size of the stomatocyte given by 7:3:2.
-
-Not all choices of parameters give reasonable values for the shape of the stomatocyte,
-but the combination 7:3:1 is a good point to start from when trying to modify the shape.
-If you observe jumps in forces for particles inside the stomatocyte cavity,
-your parameters are most likely wrong, in which case the OpenGL visualizer
-will typically fail to draw dots inside the stomatocyte cavity.
-
-
-.. figure:: figures/shape-stomatocyte1.png
-   :alt: Visualization of a constraint with a Stomatocyte shape.
-   :align: center
-   :height: 6.00000cm
-
-.. figure:: figures/shape-stomatocyte2.png
-   :alt: Close-up view of the internal Stomatocyte structure.
-   :align: center
-   :height: 6.00000cm
-
-
-Pictured is an example constraint with a ``Stomatocyte`` shape (with a closeup of the internal structure) created with ::
-
-    stomatocyte = Stomatocyte(inner_radius=3,
-                              outer_radius=7,
-                              axis=[1.0, 0.0, 0.0],
-                              center=[25, 25, 25],
-                              layer_width=3,
-                              direction=1)
-    system.constraints.add(shape=stomatocyte, particle_type=0, penetrable=True)
-
-
 Slitpore
 """"""""
 

samples/visualization_constraints.py

@@ -30,15 +30,13 @@
 group.add_argument("--wall", action="store_const", dest="shape", const="Wall",
                    default="Wall")
 for shape in ("Sphere", "Ellipsoid", "Cylinder", "SpheroCylinder", "Torus",
-              "Stomatocyte", "SimplePore", "Slitpore", "HollowConicalFrustum"):
+              "SimplePore", "Slitpore", "HollowConicalFrustum"):
     group.add_argument("--" + shape.lower(), action="store_const",
                        dest="shape", const=shape)
 args = parser.parse_args()
 
 
 required_features = ["LENNARD_JONES"]
-if args.shape == "Stomatocyte":
-    required_features.append("EXPERIMENTAL_FEATURES")
 espressomd.assert_features(required_features)
 
 box_l = 50.0
@@ -86,11 +84,6 @@
         particle_type=0,
         penetrable=True)
 
-elif args.shape == "Stomatocyte":
-    system.constraints.add(shape=espressomd.shapes.Stomatocyte(
-        inner_radius=3, outer_radius=7, axis=[1.0, 0.0, 0.0], center=[25] * 3,
-        layer_width=3, direction=1), particle_type=0, penetrable=True)
-
 elif args.shape == "SimplePore":
     system.constraints.add(shape=espressomd.shapes.SimplePore(
         center=[25, 25, 25], axis=[1, 0, 0], length=15, radius=12.5,

src/python/espressomd/shapes.py

@@ -18,7 +18,6 @@
 import collections.abc
 
 from .script_interface import ScriptInterfaceHelper, script_interface_register, ScriptObjectRegistry
-from .utils import requires_experimental_features
 
 
 class Shape:
@@ -162,31 +161,6 @@ class SpheroCylinder(Shape, ScriptInterfaceHelper):
     _so_name = "Shapes::SpheroCylinder"
 
 
-@script_interface_register
-@requires_experimental_features("No test coverage")
-class Stomatocyte(Shape, ScriptInterfaceHelper):
-    """
-    Attributes
-    ----------
-    inner_radius : :obj:`float`
-        Inner radius of the stomatocyte.
-    outer_radius : :obj:`float`
-        Outer radius of the stomatocyte.
-    axis : (3,) array_like of :obj:`float`
-        Symmetry axis, prescribing the orientation of the stomatocyte.
-    center : (3,) array_like of :obj:`float`
-        Position of the stomatocyte.
-    layer_width : :obj:`float`
-        Scaling parameter.
-    direction : :obj:`int`
-        Surface orientation, for +1 the normal points
-        out of the mantel, for -1 it points inward.
-
-    """
-
-    _so_name = "Shapes::Stomatocyte"
-
-
 @script_interface_register
 class Torus(Shape, ScriptInterfaceHelper):
     """

src/script_interface/shapes/initialize.cpp

@@ -27,7 +27,6 @@
 #include "Slitpore.hpp"
 #include "Sphere.hpp"
 #include "SpheroCylinder.hpp"
-#include "Stomatocyte.hpp"
 #include "Torus.hpp"
 #include "Union.hpp"
 #include "Wall.hpp"
@@ -55,8 +54,6 @@ void initialize() {
       "Shapes::Rhomboid");
   ScriptInterface::register_new<ScriptInterface::Shapes::Slitpore>(
       "Shapes::Slitpore");
-  ScriptInterface::register_new<ScriptInterface::Shapes::Stomatocyte>(
-      "Shapes::Stomatocyte");
   ScriptInterface::register_new<ScriptInterface::Shapes::SimplePore>(
       "Shapes::SimplePore");
   ScriptInterface::register_new<ScriptInterface::Shapes::Torus>(

src/shapes/CMakeLists.txt

@@ -1,7 +1,7 @@
 set(SOURCE_FILES
     src/HollowConicalFrustum.cpp src/Cylinder.cpp src/Ellipsoid.cpp
     src/Rhomboid.cpp src/SimplePore.cpp src/Slitpore.cpp src/Sphere.cpp
-    src/SpheroCylinder.cpp src/Stomatocyte.cpp src/Torus.cpp src/Wall.cpp)
+    src/SpheroCylinder.cpp src/Torus.cpp src/Wall.cpp)
 
 add_library(shapes SHARED ${SOURCE_FILES})
 target_link_libraries(shapes PUBLIC utils PRIVATE Boost::boost cxx_interface)