Merge pull request #631 from Xiangyu-Hu/fix/clarified_comment_on_comp…

…lex_shape

clarify the limitation of using complex shape

src/shared/geometries/base_geometry.h

@@ -21,9 +21,9 @@
  *                                                                           *
  * ------------------------------------------------------------------------- */
 /**
- * @file 	base_geometry.h
- * @brief 	Define the base classes Shape, BinaryShape and Edge,
- * 			which are the base classes for all geometries.
+ * @file base_geometry.h
+ * @brief Define the base classes Shape, BinaryShape and Edge,
+ * which are the base classes for all geometries.
  * @author	Chi Zhang, Yongchuan Yu and Xiangyu Hu
  */
 
@@ -92,11 +92,10 @@ class Shape
 using SubShapeAndOp = std::pair<Shape *, ShapeBooleanOps>;
 /**
  * @class BinaryShapes
- * @brief a collections of shapes with binary operations
+ * @brief A collections of shapes with binary operations.
  * This class has ownership of all shapes by using a unique pointer vector.
  * In this way, add or subtract a shape will call the shape's constructor other than
  * passing the shape pointer.
- * For now, partially overlapped the shapes are not allowed for binary operations.
  */
 class BinaryShapes : public Shape
 {
@@ -106,15 +105,15 @@ class BinaryShapes : public Shape
     virtual ~BinaryShapes(){};
 
     template <class SubShapeType, typename... Args>
-    void add(Args &&...args)
+    void add(Args &&... args)
     {
         Shape *sub_shape = sub_shape_ptrs_keeper_.createPtr<SubShapeType>(std::forward<Args>(args)...);
         SubShapeAndOp sub_shape_and_op(sub_shape, ShapeBooleanOps::add);
         sub_shapes_and_ops_.push_back(sub_shape_and_op);
     };
 
     template <class SubShapeType, typename... Args>
-    void subtract(Args &&...args)
+    void subtract(Args &&... args)
     {
         Shape *sub_shape = sub_shape_ptrs_keeper_.createPtr<SubShapeType>(std::forward<Args>(args)...);
         SubShapeAndOp sub_shape_and_op(sub_shape, ShapeBooleanOps::sub);

src/shared/geometries/complex_shape.h

@@ -21,10 +21,10 @@
  *                                                                           *
  * ------------------------------------------------------------------------- */
 /**
- * @file 	complex_shape.h
- * @brief 	Here, we define the a container of different type of shapes, which allow
- * 			the boolean operation between the different type of shapes. The shapes
- * 			can be defined previously and add to this complex shapes container.
+ * @file complex_shape.h
+ * @brief Here, we define the a container of different type of shapes, which allow
+ * the boolean operation between the different type of shapes. The shapes
+ * can be defined previously and add to this complex shapes container.
  */
 
 #ifndef COMPLEX_SHAPE_H
@@ -39,6 +39,15 @@ namespace SPH
 {
 class LevelSetShape;
 
+/**
+ * @class ComplexShape
+ * @brief  For now, if the level set shape (for particle relaxation) 
+ * will be generated from the complex shape, 
+ * partially overlapped shapes are not allowed for 3D problems. 
+ * However, if only the contain function
+ * is used, for example generating particles using lattice generator, 
+ * partially overlapped shapes are allowed.
+ **/
 class ComplexShape : public BinaryShapes
 {
   public:
@@ -47,7 +56,7 @@ class ComplexShape : public BinaryShapes
     virtual ~ComplexShape(){};
 
     template <typename... Args>
-    LevelSetShape *defineLevelSetShape(SPHBody &sph_body, const std::string &shape_name, Args &&...args)
+    LevelSetShape *defineLevelSetShape(SPHBody &sph_body, const std::string &shape_name, Args &&... args)
     {
         size_t index = getSubShapeIndexByName(shape_name);
         LevelSetShape *level_set_shape = sub_shape_ptrs_keeper_[index].createPtr<LevelSetShape>(
@@ -71,12 +80,12 @@ class AlignedBoxShape : public TransformShape<GeometricShapeBox>
   public:
     /** construct directly */
     template <typename... Args>
-    explicit AlignedBoxShape(int upper_bound_axis, const Transform &transform, Args &&...args)
+    explicit AlignedBoxShape(int upper_bound_axis, const Transform &transform, Args &&... args)
         : TransformShape<GeometricShapeBox>(transform, std::forward<Args>(args)...),
           alignment_axis_(upper_bound_axis){};
     /** construct from a shape already has aligned boundaries */
     template <typename... Args>
-    explicit AlignedBoxShape(int upper_bound_axis, const Shape &shape, Args &&...args)
+    explicit AlignedBoxShape(int upper_bound_axis, const Shape &shape, Args &&... args)
         : TransformShape<GeometricShapeBox>(
               Transform(Vecd(0.5 * (shape.bounding_box_.second_ + shape.bounding_box_.first_))),
               0.5 * (shape.bounding_box_.second_ - shape.bounding_box_.first_), std::forward<Args>(args)...),