Hollowconical Frustum with cutout

doc/sphinx/constraints.rst

@@ -440,14 +440,20 @@ HollowConicalFrustum
 
 :class:`espressomd.shapes.HollowConicalFrustum`
 
-A hollow cone with round corners. The specific parameters
+A hollow cone with round corners.
+Can include an opening in the side (see figures below). The specific parameters
 are described in the shape's class :class:`espressomd.shapes.HollowConicalFrustum`.
 
 .. figure:: figures/shape-conical_frustum.png
    :alt: Visualization of a constraint with a HollowConicalFrustum shape.
    :align: center
    :height: 6.00000cm
 
+.. figure:: figures/shape-hollowconicalfrustum_central_angle.png
+   :alt: Visualization a HollowConicalFrustum shape with central angle
+   :align: center
+   :height: 6.00000cm
+
 .. figure:: figures/conical_frustum.png
    :alt: Schematic for the HollowConicalFrustum shape with labeled geometrical parameters.
    :align: center

doc/tutorials/active_matter/exercises/rectification_geometry.py

@@ -30,7 +30,7 @@
 from espressomd import lb
 from espressomd.lbboundaries import LBBoundary
 import espressomd.shapes
-
+import espressomd.math
 
 # Setup constants
 
@@ -90,9 +90,12 @@
 ORAD = (DIAMETER - IRAD) / np.sin(ANGLE)
 SHIFT = 0.25 * ORAD * np.cos(ANGLE)
 
+ctp = espressomd.math.CylindricalTransformationParameters(
+    axis=[-1, 0, 0], center=[BOX_L[0] / 2.0 - 1.3 * SHIFT, BOX_L[1] / 2.0, BOX_L[2] / 2.0])
+
 hollow_cone = LBBoundary(shape=espressomd.shapes.HollowConicalFrustum(
-    center=[BOX_L[0] / 2.0 - 1.3 * SHIFT, BOX_L[1] / 2.0, BOX_L[2] / 2.0],
-    axis=[-1, 0, 0], r1=ORAD, r2=IRAD, thickness=2.0, length=18,
+    cyl_transform_params=ctp,
+    r1=ORAD, r2=IRAD, thickness=2.0, length=18,
     direction=1))
 system.lbboundaries.add(hollow_cone)
 

doc/tutorials/active_matter/exercises/rectification_simulation.py

@@ -29,6 +29,7 @@
 import espressomd
 from espressomd import assert_features
 import espressomd.shapes
+import espressomd.math
 
 
 assert_features(["ENGINE", "LENNARD_JONES", "ROTATION", "MASS"])
@@ -119,6 +120,7 @@ def a2quat(phi, theta):
 system.constraints.add(shape=wall, particle_type=1)
 
 # Setup cone
+ctp = espressomd.math.CylindricalTransformationParameters(...)
 hollow_cone = espressomd.shapes.HollowConicalFrustum(...)
 system.constraints.add(shape=hollow_cone, particle_type=1)
 

doc/tutorials/active_matter/solutions/rectification_geometry.py

@@ -30,6 +30,7 @@
 from espressomd import lb
 from espressomd.lbboundaries import LBBoundary
 import espressomd.shapes
+import espressomd.math
 
 
 # Setup constants
@@ -91,9 +92,12 @@
 ORAD = (DIAMETER - IRAD) / np.sin(ANGLE)
 SHIFT = 0.25 * ORAD * np.cos(ANGLE)
 
+ctp = espressomd.math.CylindricalTransformationParameters(
+    axis=[-1, 0, 0], center=[BOX_L[0] / 2.0 - 1.3 * SHIFT, BOX_L[1] / 2.0, BOX_L[2] / 2.0])
+
 hollow_cone = LBBoundary(shape=espressomd.shapes.HollowConicalFrustum(
-    center=[BOX_L[0] / 2.0 - 1.3 * SHIFT, BOX_L[1] / 2.0, BOX_L[2] / 2.0],
-    axis=[-1, 0, 0], r1=ORAD, r2=IRAD, thickness=2.0, length=18,
+    cyl_transform_params=ctp,
+    r1=ORAD, r2=IRAD, thickness=2.0, length=18,
     direction=1))
 system.lbboundaries.add(hollow_cone)
 

doc/tutorials/active_matter/solutions/rectification_simulation.py

@@ -29,6 +29,7 @@
 import espressomd
 from espressomd import assert_features
 import espressomd.shapes
+import espressomd.math
 
 
 assert_features(["ENGINE", "LENNARD_JONES", "ROTATION", "MASS"])
@@ -118,9 +119,12 @@ def a2quat(phi, theta):
 ORAD = (DIAMETER - IRAD) / np.sin(ANGLE)
 SHIFT = 0.25 * ORAD * np.cos(ANGLE)
 
+ctp = espressomd.math.CylindricalTransformationParameters(
+    axis=[-1, 0, 0], center=[BOX_L[0] / 2.0 - 1.3 * SHIFT, BOX_L[1] / 2.0, BOX_L[2] / 2.0])
+
 hollow_cone = espressomd.shapes.HollowConicalFrustum(
-    center=[BOX_L[0] / 2.0 - 1.3 * SHIFT, BOX_L[1] / 2.0, BOX_L[2] / 2.0],
-    axis=[-1, 0, 0], r1=ORAD, r2=IRAD, thickness=2.0, length=18,
+    cyl_transform_params=ctp,
+    r1=ORAD, r2=IRAD, thickness=2.0, length=18,
     direction=1)
 system.constraints.add(shape=hollow_cone, particle_type=1)
 

samples/visualization_constraints.py

@@ -22,6 +22,7 @@
 import argparse
 
 import espressomd
+import espressomd.math
 import espressomd.shapes
 import espressomd.visualization_opengl
 
@@ -96,9 +97,11 @@
         particle_type=0, penetrable=True)
 
 elif args.shape == "HollowConicalFrustum":
+    ctp = espressomd.math.CylindricalTransformationParameters(
+        axis=1 / np.sqrt(2) * np.array([0.0, 1.0, 1.0]), center=[25, 25, 25], orientation=[1, 0, 0])
     system.constraints.add(shape=espressomd.shapes.HollowConicalFrustum(
         r1=12, r2=8, length=15.0, thickness=3,
-        axis=[0.0, 1.0, 1.0], center=[25, 25, 25], direction=1),
+        cyl_transform_params=ctp, direction=1, central_angle=np.pi / 2),
         particle_type=0, penetrable=True)
 
 elif args.shape == "Torus":

src/python/espressomd/math.py

@@ -32,5 +32,10 @@ class CylindricalTransformationParameters(ScriptInterfaceHelper):
         Orientation vector of the ``z``-axis of the cylindrical coordinate system.
     orientation: (3,) array_like of :obj:`float`, default = [1, 0, 0]
         The axis on which ``phi = 0``.
+
+    Notes
+    -----
+    If you provide no arguments, the defaults above are set.
+    If you provide only a ``center`` and an ``axis``, an ``orientation`` will be automatically generated that is orthogonal to ``axis``.
     """
     _so_name = "CylindricalTransformationParameters"

src/python/espressomd/shapes.py

@@ -231,16 +231,21 @@ class HollowConicalFrustum(Shape, ScriptInterfaceHelper):
 
     Attributes
     ----------
+    cyl_transform_params : :class:`espressomd.math.CylindricalTransformationParameters`, 
+        Parameters of the spacial orientation of the frustum. Contained must be parameters for ``center`` and ``axis``. ``orientation`` has no effect, unless ``central_angle != 0``
     r1: :obj:`float`
         Radius r1.
     r2: :obj:`float`
         Radius r2.
     length: :obj:`float`
         Length of the conical frustum along ``axis``.
-    axis: (3,) array_like of :obj:`float`
-        Symmetry axis.
-    center: (3,) array_like of :obj:`float`
-        Position of the center.
+    thickness: float
+        The thickness of the frustum. Also determines the rounding radius of the edges
+    direction: :obj:`int`, optional
+        Surface orientation, for +1 the normal points
+        out of the mantel, for -1 it points inside of the shape. Defaults to 1
+    cantral_angle: :obj:`float`, optional
+        A ``central_angle`` creates an opening in the frustum along the side, centered symmetrically around the ``direction`` of ``cyl_transform_params``. Must be between ``0`` and ``2 pi``. Defaults to 0.
 
 
     .. image:: figures/conical_frustum.png

src/python/espressomd/visualization_opengl.py

@@ -1977,20 +1977,23 @@ def __init__(self, shape, particle_type, color, material,
                  quality, box_l, rasterize_resolution, rasterize_pointsize):
         super().__init__(shape, particle_type, color, material,
                          quality, box_l, rasterize_resolution, rasterize_pointsize)
-        self.center = np.array(self.shape.get_parameter('center'))
-        self.radius_1 = np.array(self.shape.get_parameter('r1'))
-        self.radius_2 = np.array(self.shape.get_parameter('r2'))
-        self.length = np.array(self.shape.get_parameter('length'))
-        self.thickness = np.array(self.shape.get_parameter('thickness'))
-        self.axis = np.array(self.shape.get_parameter('axis'))
+        ctp = self.shape.get_parameter('cyl_transform_params')
+        self.center = np.array(ctp.center)
+        self.axis = np.array(ctp.axis)
+        self.orientation = np.array(ctp.orientation)
+        self.radius_1 = self.shape.get_parameter('r1')
+        self.radius_2 = self.shape.get_parameter('r2')
+        self.length = self.shape.get_parameter('length')
+        self.thickness = self.shape.get_parameter('thickness')
+        self.central_angle = self.shape.get_parameter('central_angle')
 
     def draw(self):
         """
         Draw using OpenGL Extrusion library, if available.
         Use rasterization of base class, otherwise.
 
         """
-        if bool(OpenGL.GLE.gleSpiral):
+        if bool(OpenGL.GLE.gleSpiral) and self.central_angle == 0.:
             self._draw_using_gle()
         else:
             super().draw()

src/script_interface/CylindricalTransformationParameters.hpp

@@ -22,6 +22,8 @@
 #ifndef SCRIPT_INTERFACE_CYL_TRANSFORM_PARAMS_HPP
 #define SCRIPT_INTERFACE_CYL_TRANSFORM_PARAMS_HPP
 
+#include <stdexcept>
+
 #include "script_interface/ScriptInterface.hpp"
 
 #include "utils/math/cylindrical_transformation_parameters.hpp"
@@ -44,14 +46,29 @@ class CylindricalTransformationParameters
     return m_transform_params;
   }
   void do_construct(VariantMap const &params) override {
-    m_transform_params =
-        std::make_shared<Utils::CylindricalTransformationParameters>(
-            get_value_or<Utils::Vector3d>(params, "center",
-                                          Utils::Vector3d{{0, 0, 0}}),
-            get_value_or<Utils::Vector3d>(params, "axis",
-                                          Utils::Vector3d{{0, 0, 1}}),
-            get_value_or<Utils::Vector3d>(params, "orientation",
-                                          Utils::Vector3d{{1, 0, 0}}));
+    auto n_params = params.size();
+    switch (n_params) {
+    case 0:
+      m_transform_params =
+          std::make_shared<Utils::CylindricalTransformationParameters>();
+      break;
+    case 2:
+      m_transform_params =
+          std::make_shared<Utils::CylindricalTransformationParameters>(
+              get_value<Utils::Vector3d>(params, "center"),
+              get_value<Utils::Vector3d>(params, "axis"));
+      break;
+    case 3:
+      m_transform_params =
+          std::make_shared<Utils::CylindricalTransformationParameters>(
+              get_value<Utils::Vector3d>(params, "center"),
+              get_value<Utils::Vector3d>(params, "axis"),
+              get_value<Utils::Vector3d>(params, "orientation"));
+      break;
+    default:
+      throw std::runtime_error("Provide either no arguments, center and axis, "
+                               "or center and axis and orientation");
+    }
   }
 
 private:

src/script_interface/shapes/HollowConicalFrustum.hpp

@@ -20,26 +20,17 @@
 #ifndef ESPRESSO_HOLLOW_CONICAL_FRUSTUM_HPP
 #define ESPRESSO_HOLLOW_CONICAL_FRUSTUM_HPP
 #include "Shape.hpp"
+#include <script_interface/CylindricalTransformationParameters.hpp>
 #include <shapes/HollowConicalFrustum.hpp>
 
 namespace ScriptInterface {
 namespace Shapes {
 
 class HollowConicalFrustum : public Shape {
 public:
-  HollowConicalFrustum()
-      : m_hollow_conical_frustum(new ::Shapes::HollowConicalFrustum()) {
+  HollowConicalFrustum() {
     add_parameters(
-        {{"center",
-          [this](Variant const &v) {
-            m_hollow_conical_frustum->set_center(get_value<Utils::Vector3d>(v));
-          },
-          [this]() { return m_hollow_conical_frustum->center(); }},
-         {"axis",
-          [this](Variant const &v) {
-            m_hollow_conical_frustum->set_axis(get_value<Utils::Vector3d>(v));
-          },
-          [this]() { return m_hollow_conical_frustum->axis(); }},
+        {{"cyl_transform_params", m_cyl_transform_params},
          {"r1",
           [this](Variant const &v) {
             m_hollow_conical_frustum->set_r1(get_value<double>(v));
@@ -64,7 +55,28 @@ class HollowConicalFrustum : public Shape {
           [this](Variant const &v) {
             m_hollow_conical_frustum->set_direction(get_value<int>(v));
           },
-          [this]() { return m_hollow_conical_frustum->direction(); }}});
+          [this]() { return m_hollow_conical_frustum->direction(); }},
+         {"central_angle",
+          [this](Variant const &v) {
+            m_hollow_conical_frustum->set_central_angle(get_value<double>(v));
+          },
+          [this]() { return m_hollow_conical_frustum->central_angle(); }}});
+  }
+
+  void do_construct(VariantMap const &params) override {
+    set_from_args(m_cyl_transform_params, params, "cyl_transform_params");
+
+    if (m_cyl_transform_params)
+      m_hollow_conical_frustum =
+          std::make_shared<::Shapes::HollowConicalFrustum>(
+              get_value<double>(params, "r1"), get_value<double>(params, "r2"),
+              get_value<double>(params, "length"),
+              get_value_or<double>(params, "thickness", 0.),
+              get_value_or<int>(params, "direction", 1),
+              get_value_or<double>(params, "central_angle", 0.),
+              m_cyl_transform_params->cyl_transform_params()
+
+          );
   }
 
   std::shared_ptr<::Shapes::Shape> shape() const override {
@@ -73,6 +85,7 @@ class HollowConicalFrustum : public Shape {
 
 private:
   std::shared_ptr<::Shapes::HollowConicalFrustum> m_hollow_conical_frustum;
+  std::shared_ptr<CylindricalTransformationParameters> m_cyl_transform_params;
 };
 
 } /* namespace Shapes */

src/shapes/include/shapes/HollowConicalFrustum.hpp

@@ -21,10 +21,12 @@
 #define SHAPES_CONICAL_FRUSTUM_HPP
 
 #include "Shape.hpp"
+#include "utils/math/cylindrical_transformation_parameters.hpp"
 #include <utils/Vector.hpp>
-#include <utils/math/orthonormal_vec.hpp>
 
 #include <list>
+#include <memory>
+#include <utility>
 
 namespace Shapes {
 
@@ -48,40 +50,37 @@ namespace Shapes {
  */
 class HollowConicalFrustum : public Shape {
 public:
-  HollowConicalFrustum()
-      : m_r1(0.0), m_r2(0.0), m_length(0.0), m_thickness(0.0),
-        m_direction(1), m_center{Utils::Vector3d{}}, m_axis{Utils::Vector3d{
-                                                         0., 0., 1.}},
-        m_orientation{Utils::Vector3d{1., 0., 0.}} {}
+  HollowConicalFrustum(
+      double const r1, double const r2, double const length,
+      double const thickness, int const direction, double const central_angle,
+      std::shared_ptr<Utils::CylindricalTransformationParameters>
+          cyl_transform_params)
+      : m_r1(r1), m_r2(r2), m_length(length), m_thickness(thickness),
+        m_direction(direction), m_central_angle(central_angle),
+        m_cyl_transform_params(std::move(cyl_transform_params)) {}
 
   void set_r1(double const radius) { m_r1 = radius; }
   void set_r2(double const radius) { m_r2 = radius; }
   void set_length(double const length) { m_length = length; }
   void set_thickness(double const thickness) { m_thickness = thickness; }
   void set_direction(int const dir) { m_direction = dir; }
-  void set_axis(Utils::Vector3d const &axis) {
-    m_axis = axis;
-    // Even though the HCF is cylinder-symmetric, it needs a well defined phi=0
-    // orientation for the coordinate transformation.
-    m_orientation = Utils::calc_orthonormal_vector(axis);
+  void set_central_angle(double const central_angle) {
+    m_central_angle = central_angle;
   }
-  void set_center(Utils::Vector3d const &center) { m_center = center; }
 
   /// Get radius 1 perpendicular to axis.
   double radius1() const { return m_r1; }
   /// Get radius 2 perpendicular to axis.
   double radius2() const { return m_r2; }
-  /// Get length of the frustum (modulo thickness).
+  /// Get length of the frustum (without thickness).
   double length() const { return m_length; }
   /// Get thickness of the frustum.
   double thickness() const { return m_thickness; }
-  /// Get the direction of the shape. If -1, distance is positive within the
-  /// enclosed volume of the frustum.
+  /// Get direction
   int direction() const { return m_direction; }
-  /// Get center of symmetry.
-  Utils::Vector3d const &center() const { return m_center; }
-  /// Get symmetry axis.
-  Utils::Vector3d const &axis() const { return m_axis; }
+  /// Get central angle
+  double central_angle() const { return m_central_angle; }
+
   /**
    * @brief Calculate the distance vector and its norm between a given position
    * and the cone.
@@ -98,9 +97,9 @@ class HollowConicalFrustum : public Shape {
   double m_length;
   double m_thickness;
   int m_direction;
-  Utils::Vector3d m_center;
-  Utils::Vector3d m_axis;
-  Utils::Vector3d m_orientation;
+  double m_central_angle;
+  std::shared_ptr<Utils::CylindricalTransformationParameters>
+      m_cyl_transform_params;
 };
 } // namespace Shapes