From 77d870e732883e621f418e59501a2627ec2be7cf Mon Sep 17 00:00:00 2001
From: Perminder <permindersingh089@gmail.com>
Date: Sat, 16 Nov 2024 16:35:24 +0530
Subject: [PATCH] fixes

Signed-off-by: Perminder <permindersingh089@gmail.com>
---
 avogadro/core/cube.h             | 22 +++++++++++++++-------
 avogadro/core/mesh.h             |  8 ++++++++
 avogadro/qtgui/meshgenerator.cpp |  6 ++++++
 avogadro/qtgui/meshgenerator.h   |  7 +++++++
 4 files changed, 36 insertions(+), 7 deletions(-)

diff --git a/avogadro/core/cube.h b/avogadro/core/cube.h
index 43775c345c..562d316fc5 100644
--- a/avogadro/core/cube.h
+++ b/avogadro/core/cube.h
@@ -24,7 +24,10 @@ class Mutex;
 /**
  * @class Cube cube.h <avogadro/core/cube.h>
  * @brief Provide a data structure for regularly spaced 3D grids.
+ * @author Marcus D. Hanwell
+ * @author Perminder Singh
  */
+
 class AVOGADROCORE_EXPORT Cube
 {
 public:
@@ -275,13 +278,18 @@ class AVOGADROCORE_EXPORT Cube
    */
   float getData(int i, int j, int k) const;
 
-  /**
-   * Get the positions of the eight corners of a cube defined by the indices (i, j, k).
-   * @param i x index
-   * @param j y index
-   * @param k z index
-   * @return Array of positions at the eight corners.
-   */
+/**
+ * Retrieves the positions of the eight corners of a cube at grid indices (i, j, k).
+ *
+ * The indices (i, j, k) are converted to real-space positions (xpos, ypos, zpos), mapping grid indices to physical coordinates.
+ * The method returns a cube that spans one step in each of the x, y, and z directions, with step sizes defined by `m_spacing`.
+ *
+ * @param i X-index.
+ * @param j Y-index.
+ * @param k Z-index.
+ * @return A `std::array` of eight `(x, y, z)` coordinates representing the cube's corners.
+ */
+
 std::array<std::array<float, 3>, 8> getPosCube(int i, int j, int k) const;
 
 protected:
diff --git a/avogadro/core/mesh.h b/avogadro/core/mesh.h
index 082006f283..596252aa6a 100644
--- a/avogadro/core/mesh.h
+++ b/avogadro/core/mesh.h
@@ -142,6 +142,14 @@ class AVOGADROCORE_EXPORT Mesh
    */
   const Core::Array<Vector3f>& normals() const;
 
+  /**
+   * @return The number of normals.
+   */
+  unsigned int numNormals() const
+  {
+    return static_cast<unsigned int>(m_normals.size());
+  }
+
   /**
    * @return Pointer to the first normal of the specified triangle.
    */
diff --git a/avogadro/qtgui/meshgenerator.cpp b/avogadro/qtgui/meshgenerator.cpp
index 3b39c233af..3bdce50599 100644
--- a/avogadro/qtgui/meshgenerator.cpp
+++ b/avogadro/qtgui/meshgenerator.cpp
@@ -593,6 +593,12 @@ unsigned char MeshGenerator::calcCaseEdge(bool const& prevEdge, bool const& curr
         return 3;
 }
 
+unsigned long MeshGenerator::duplicate(const Vector3i&, const Vector3f&)
+{
+  // FIXME Not implemented yet.
+  return 0;
+}
+
 void MeshGenerator::calcTrimValues(int& xl, int& xr, int const& j, int const& k) const
 {
 
diff --git a/avogadro/qtgui/meshgenerator.h b/avogadro/qtgui/meshgenerator.h
index 09935268f4..95a9a70a3a 100644
--- a/avogadro/qtgui/meshgenerator.h
+++ b/avogadro/qtgui/meshgenerator.h
@@ -26,6 +26,7 @@ namespace QtGui {
  * @class MeshGenerator meshgenerator.h <avogadro/qtgui/meshgenerator.h>
  * @brief Class that can generate Mesh objects from Cube objects.
  * @author Marcus D. Hanwell
+ * @author Perminder Singh
  *
  * This class implements a method of generating an isosurface Mesh from
  * volumetric data using the marching cubes algorithm. In the case of the
@@ -107,6 +108,12 @@ class AVOGADROQTGUI_EXPORT MeshGenerator : public QThread
         int zstart;
     };
 
+ /**
+ * Handles duplicate vertices (Not implemented). Placeholder for future functionality.
+ */
+  unsigned long duplicate(const Vector3i& c, const Vector3f& pos);
+
+
  /**
    * @name Flying Edges
    * Methods to implement the "flying edges" method for isosurface mesh generation.