Merge pull request #2282 from itischler/torus

Added a torus shape

src/core/shapes/CMakeLists.txt

@@ -9,6 +9,7 @@ set(Shapes_SRC
     Sphere.cpp
     SpheroCylinder.cpp
     Stomatocyte.cpp
+    Torus.cpp
     Wall.cpp
 )
 add_library(Shapes SHARED ${Shapes_SRC})

src/core/shapes/Torus.cpp

@@ -0,0 +1,24 @@
+#include "Torus.hpp"
+#include "utils.hpp"
+#include <cmath>
+
+namespace Shapes {
+
+int Torus::calculate_dist(const double *ppos, double *dist, double *vec) const {
+  /* Coordinate transform to cylinder coords
+     with origin at m_center. */
+  Vector3d const c_dist = Vector3d(ppos, ppos + 3) - m_center;
+  auto const z = e_z * c_dist;
+  auto const r_vec = c_dist - z * e_z;
+  auto const r = r_vec.norm();
+
+  *dist = (sqrt(Utils::sqr(r - m_rad) + z * z) - m_tube_rad) * m_direction;
+  Vector3d const dir_vec = c_dist - r_vec * m_rad / r;
+  auto const dir_vec_norm = dir_vec / dir_vec.norm();
+  vec[0] = dir_vec_norm[0] * m_direction;
+  vec[1] = dir_vec_norm[1] * m_direction;
+  vec[2] = dir_vec_norm[2] * m_direction;
+
+  return 0;
+}
+} // namespace Shapes

src/core/shapes/Torus.hpp

@@ -0,0 +1,59 @@
+#ifndef __TORUS_HPP
+#define __TORUS_HPP
+
+#include "Shape.hpp"
+#include "Vector.hpp"
+
+namespace Shapes {
+class Torus : public Shape {
+public:
+  /* center of the cylinder. */
+  Vector3d m_center;
+  /* Normal axis of the cylinder. */
+  Vector3d m_normal;
+  /* radius. */
+  double m_rad;
+  /* tube radius. */
+  double m_tube_rad;
+  /* direction -1: inside, +1 outside */
+  double m_direction;
+
+  /* Unit vector in z direction */
+  Vector3d e_z;
+
+  /** @brief Calculate derived parameters. */
+  void precalc() { e_z = m_normal / m_normal.norm(); }
+
+public:
+  Torus()
+      : m_center({0.0, 0.0, 0.0}), m_normal({1.0, 0.0, 0.0}), m_rad(0.0),
+        m_tube_rad(0.0), m_direction(1.0) {
+    precalc();
+  }
+
+  double radius() const { return m_rad; }
+  void set_radius(double const &radius) {
+    m_rad = radius;
+    precalc();
+  }
+
+  double tube_radius() const { return m_tube_rad; }
+  void set_tube_radius(double const &tube_rad) {
+    m_tube_rad = tube_rad;
+    precalc();
+  }
+
+  Vector3d const &normal() const { return m_normal; }
+  void set_normal(Vector3d const &normal) {
+    m_normal = normal;
+    precalc();
+  }
+
+  Vector3d &center() { return m_center; }
+  double &direction() { return m_direction; }
+
+  int calculate_dist(const double *ppos, double *dist,
+                     double *vec) const override;
+};
+} // namespace Shapes
+#endif

src/python/espressomd/shapes.py

@@ -231,6 +231,29 @@ class Stomatocyte(ScriptInterfaceHelper):
     _so_name = "Shapes::Stomatocyte"
 
 
+@script_interface_register
+class Torus(ScriptInterfaceHelper):
+
+    """
+    A torus shape.
+    Attributes
+    ----------
+    center : array_like :obj:`float`
+             Coordinates of the center of the torus.
+    normal : array_like :obj:`float`
+           Normal axis of the torus.
+    radius : :obj:`float`
+             Radius of the torus.
+    tube_radius : :obj:`float`
+             Radius of the tube.
+    direction : :obj:`int`
+                Surface orientation, for +1 the normal points
+                out of the mantel, for -1 it points inward.
+
+    """
+    _so_name = "Shapes::Torus"
+
+
 @script_interface_register
 class Wall(ScriptInterfaceHelper):
 

src/script_interface/shapes/Torus.hpp

@@ -0,0 +1,31 @@
+#ifndef SCRIPT_INTERFACE_TORUS_WALL_HPP
+#define SCRIPT_INTERFACE_TORUS_WALL_HPP
+
+#include "Shape.hpp"
+#include "core/shapes/Torus.hpp"
+
+namespace ScriptInterface {
+namespace Shapes {
+
+class Torus : public Shape {
+  using CoreShape = ::Shapes::Torus;
+  std::shared_ptr<::Shapes::Torus> m_torus;
+
+public:
+  Torus() : m_torus(new ::Shapes::Torus()) {
+    add_parameters(
+        {{"radius", m_torus, &CoreShape::set_radius, &CoreShape::radius},
+         {"tube_radius", m_torus, &CoreShape::set_tube_radius,
+          &CoreShape::tube_radius},
+         {"normal", m_torus, &CoreShape::set_normal, &CoreShape::normal},
+         {"center", m_torus, &CoreShape::center},
+         {"direction", m_torus, &CoreShape::direction}});
+  }
+
+  std::shared_ptr<::Shapes::Shape> shape() const override { return m_torus; }
+};
+
+} /* namespace Shapes */
+} /* namespace ScriptInterface */
+
+#endif

src/script_interface/shapes/initialize.cpp

@@ -30,6 +30,7 @@
 #include "Sphere.hpp"
 #include "SpheroCylinder.hpp"
 #include "Stomatocyte.hpp"
+#include "Torus.hpp"
 #include "Wall.hpp"
 
 namespace ScriptInterface {
@@ -57,6 +58,8 @@ void initialize() {
       "Shapes::Stomatocyte");
   ScriptInterface::register_new<ScriptInterface::Shapes::SimplePore>(
       "Shapes::SimplePore");
+  ScriptInterface::register_new<ScriptInterface::Shapes::Torus>(
+      "Shapes::Torus");
 }
 } /* namespace Shapes */
 } /* namespace ScriptInterface */