perf: Start using cells for bonding calculation

src/classes/atom.cpp

@@ -150,3 +150,9 @@ void AtomBase::deserialise(const SerialisedValue &node)
     set(Deserialisable::deser<Elements::Element>(node.at("z")), Deserialisable::deser<Vector3>(node.at("r")),
         Deserialisable::deser_or<double>(node, "q", 0));
 }
+
+// Set cell in which the atom exists
+void AtomBase::setCell(Cell *cell) { cell_ = cell; }
+
+// Return cell in which the atom exists
+Cell *AtomBase::cell() const { return cell_; }

src/classes/atom.h

@@ -9,6 +9,8 @@
 #include "data/elements.h"
 #include "math/vector3.h"
 
+class Cell;
+
 // Atom Base
 class AtomBase
 {
@@ -26,6 +28,8 @@ class AtomBase
     int index_{-1};
     // Atom type index in parent object
     int atomTypeIndex_{AtomConstants::TypeIndex::Ignore};
+    // Cell in which the atom exists
+    Cell *cell_{nullptr};
 
     public:
     // Set basic properties
@@ -52,6 +56,10 @@ class AtomBase
     void setAtomTypeIndex(int id);
     // Return associated atom type index
     int atomTypeIndex() const;
+    // Set cell in which the atom exists
+    void setCell(Cell *cell);
+    // Return cell in which the atom exists
+    Cell *cell() const;
 
     /*
      * General Connectivity

src/classes/cell.cpp

@@ -35,14 +35,14 @@ const Vector3 &Cell::centre() const { return centre_; }
  */
 
 // Return vector of contained Atoms
-std::vector<ConfigurationAtom *> &Cell::atoms() { return atoms_; }
-const std::vector<ConfigurationAtom *> &Cell::atoms() const { return atoms_; }
+std::vector<AtomBase *> &Cell::atoms() { return atoms_; }
+const std::vector<AtomBase *> &Cell::atoms() const { return atoms_; }
 
 // Return number of Atoms in list
 int Cell::nAtoms() const { return atoms_.size(); }
 
 // Add atom to Cell
-void Cell::addAtom(ConfigurationAtom *atom)
+void Cell::addAtom(AtomBase *atom)
 {
     assert(atom);
     assert(!atom->cell());
@@ -52,7 +52,7 @@ void Cell::addAtom(ConfigurationAtom *atom)
 }
 
 // Remove Atom from Cell
-void Cell::removeAtom(ConfigurationAtom *atom)
+void Cell::removeAtom(AtomBase *atom)
 {
     auto it = std::find(atoms_.begin(), atoms_.end(), atom);
     assert(it != atoms_.end());

src/classes/cell.h

@@ -47,18 +47,18 @@ class Cell
      */
     private:
     // Vector of Atoms contained in this Cell
-    std::vector<ConfigurationAtom *> atoms_;
+    std::vector<AtomBase *> atoms_;
 
     public:
     // Return array of contained Atoms
-    std::vector<ConfigurationAtom *> &atoms();
-    const std::vector<ConfigurationAtom *> &atoms() const;
+    std::vector<AtomBase *> &atoms();
+    const std::vector<AtomBase *> &atoms() const;
     // Return number of Atoms in array
     int nAtoms() const;
     // Add atom to Cell
-    void addAtom(ConfigurationAtom *atom);
+    void addAtom(AtomBase *atom);
     // Remove Atom from Cell
-    void removeAtom(ConfigurationAtom *atom);
+    void removeAtom(AtomBase *atom);
     // Clear all atoms from cell
     void clearAtoms();
 };

src/classes/cellArray.cpp

@@ -165,6 +165,16 @@ const std::vector<CellNeighbour> &CellArray::neighbours(const Cell &cell) const
 // Return vector of all unique cell neighbour pairs
 const std::vector<CellNeighbourPair> &CellArray::getCellNeighbourPairs() const { return neighbourPairs_; }
 
+// Return vector of all unique cell neighbour pairs with self cell pairs
+const std::vector<CellNeighbourPair> CellArray::getCellNeighbourPairsWithSelf() const
+{
+    auto result = neighbourPairs_;
+    for (auto &cell : cells_)
+        result.emplace_back(cell, cell, false);
+
+    return result;
+}
+
 // Return whether minimum image calculation is required between the supplied cells
 bool CellArray::minimumImageRequired(const Cell &a, const Cell &b) const
 {

src/classes/cellArray.h

@@ -110,6 +110,8 @@ class CellArray
     const std::vector<CellNeighbour> &neighbours(const Cell &cell) const;
     // Return vector of all unique cell neighbour pairs
     const std::vector<CellNeighbourPair> &getCellNeighbourPairs() const;
+    // Return vector of all unique cell neighbour pairs with self cell pairs
+    const std::vector<CellNeighbourPair> getCellNeighbourPairsWithSelf() const;
     // Return whether minimum image calculation is required between the supplied cells
     bool minimumImageRequired(const Cell &a, const Cell &b) const;
 

src/classes/configurationAtom.cpp

@@ -23,12 +23,6 @@ void ConfigurationAtom::setMolecule(std::shared_ptr<Molecule> mol) { molecule_ =
 // Return Molecule in which this Atom exists
 const std::shared_ptr<Molecule> &ConfigurationAtom::molecule() const { return molecule_; }
 
-// Set cell in which the atom exists
-void ConfigurationAtom::setCell(Cell *cell) { cell_ = cell; }
-
-// Return cell in which the atom exists
-Cell *ConfigurationAtom::cell() const { return cell_; }
-
 /*
  * Intramolecular Information
  */

src/classes/configurationAtom.h

@@ -24,8 +24,6 @@ class ConfigurationAtom : public Atom<SpeciesBond>
     const SpeciesAtom *speciesAtom_{nullptr};
     // Molecule in which this Atom exists
     std::shared_ptr<Molecule> molecule_{nullptr};
-    // Cell in which the atom exists
-    Cell *cell_{nullptr};
 
     public:
     // Set SpeciesAtom that this Atom represents
@@ -36,10 +34,6 @@ class ConfigurationAtom : public Atom<SpeciesBond>
     void setMolecule(std::shared_ptr<Molecule> mol);
     // Return Molecule in which this Atom exists
     const std::shared_ptr<Molecule> &molecule() const;
-    // Set cell in which the atom exists
-    void setCell(Cell *cell);
-    // Return cell in which the atom exists
-    Cell *cell() const;
 
     /*
      * Intramolecular Information

src/gui2/qml/DissolveMain.qml

@@ -19,20 +19,13 @@ import "../../Dissolve"
 ApplicationWindow {
     id: dissolveWindow
 
+    property Dialog quickRunDialog: null
     property vector3d scale: Qt.vector3d(Math.min(graphView.width / 2.5, graphView.height / 2.5), Math.min(graphView.width / 2.5, graphView.height / 2.5), 200)
 
     height: Screen.height
-    width: Screen.width
     title: "Dissolve"
     visible: true
-
-    property Dialog quickRunDialog: null
-    Component {
-        id: quickRunDialogComponent
-
-        QuickRunDialog {
-        }
-    }
+    width: Screen.width
 
     /*
      * Dissolve2 Main Menu
@@ -50,51 +43,45 @@ ApplicationWindow {
             title: "&File"
 
             MenuItem {
-                text: "&New project"
-
-                ToolTip.visible: hovered
                 ToolTip.delay: Application.styleHints.mousePressAndHoldInterval
                 ToolTip.text: "Create a new Dissolve project"
+                ToolTip.visible: hovered
+                text: "&New project"
             }
             MenuItem {
+                ToolTip.delay: Application.styleHints.mousePressAndHoldInterval
+                ToolTip.text: "Load an existing Dissolve graph from a TOML file"
+                ToolTip.visible: hovered
                 //shortcut: "Ctrl+O"
                 text: "&Load project from TOML"
 
                 onTriggered: openDialog.open()
-
-                ToolTip.visible: hovered
-                ToolTip.delay: Application.styleHints.mousePressAndHoldInterval
-                ToolTip.text: "Load an existing Dissolve graph from a TOML file"
             }
             MenuItem {
+                ToolTip.delay: Application.styleHints.mousePressAndHoldInterval
+                ToolTip.text: "Save the current Dissolve graph to a TOML file"
+                ToolTip.visible: hovered
                 //shortcut: "Ctrl+S"
                 text: "&Save project to TOML"
 
                 onTriggered: saveDialog.open()
-
-                ToolTip.visible: hovered
-                ToolTip.delay: Application.styleHints.mousePressAndHoldInterval
-                ToolTip.text: "Save the current Dissolve graph to a TOML file"
             }
-
-            MenuSeparator {}
-
+            MenuSeparator {
+            }
             MenuItem {
                 text: "Load Restart Point..."
             }
             MenuItem {
                 text: "Save Restart Point..."
             }
-
-            MenuSeparator {}
-
+            MenuSeparator {
+            }
             MenuItem {
                 //shortcut: "Ctrl+X"
                 text: "Close project"
             }
-
-            MenuSeparator {}
-
+            MenuSeparator {
+            }
             MenuItem {
                 //shortcut: "Ctrl+Q"
                 text: "&Quit Dissolve"
@@ -112,35 +99,33 @@ ApplicationWindow {
             title: "&Graph"
 
             DissolveMenuItem {
+                iconPath: "qrc:/DissolveIconsModule/play.svg"
+
                 dissolveAction: Action {
-                    text: "&Run"
                     shortcut: "Ctrl+Enter"
+                    text: "&Run"
+
                     onTriggered: dissolveWindow.quickRunDialog.open()
                 }
-                iconPath: "qrc:/DissolveIconsModule/play.svg"
             }
-
-            MenuSeparator{}
-
+            MenuSeparator {
+            }
             MenuItem {
-                //shortcut: "Ctrl+A"
-                text: "&Add Node"
-
-                ToolTip.visible: hovered
                 ToolTip.delay: Application.styleHints.mousePressAndHoldInterval
                 ToolTip.text: "Search the Node registry by node name, and add the selection to the graph"
 
                 //onTriggered: dissolveWindow.nodeSearchDialog.open()
+                ToolTip.visible: hovered
+                //shortcut: "Ctrl+A"
+                text: "&Add Node"
+            }
+            MenuSeparator {
             }
-
-            MenuSeparator{}
-
             MenuItem {
-                text: "&EPSR"
-
-                ToolTip.visible: hovered
                 ToolTip.delay: Application.styleHints.mousePressAndHoldInterval
                 ToolTip.text: "Open the EPSR Manager"
+                ToolTip.visible: hovered
+                text: "&EPSR"
             }
         }
 
@@ -153,24 +138,30 @@ ApplicationWindow {
             title: "&View"
 
             MenuItem {
-                //shortcut: "Ctrl+N"
-                text: "&Nodes"
-
-                ToolTip.visible: hovered
                 ToolTip.delay: Application.styleHints.mousePressAndHoldInterval
                 ToolTip.text: "View all available Nodes"
+                ToolTip.visible: hovered
+                //shortcut: "Ctrl+N"
+                text: "&Nodes"
             }
         }
     }
 
+    Component {
+        id: quickRunDialogComponent
+
+        QuickRunDialog {
+        }
+    }
+
     /*
      * TabBar
      */
     TabBar {
         id: tabBar
 
-        width: parent.width
         currentIndex: 2
+        width: parent.width
 
         // DEFAULT TABS
         TabButton {
@@ -193,6 +184,7 @@ ApplicationWindow {
      */
     StackLayout {
         id: applicationTabStack
+
         anchors.bottom: parent.bottom
         anchors.top: tabBar.bottom
         currentIndex: tabBar.currentIndex
@@ -226,7 +218,10 @@ ApplicationWindow {
                 id: graphModel
 
                 graph: dissolve.graph
-                Component.onCompleted: dissolveWindow.quickRunDialog = quickRunDialogComponent.createObject(dissolveWindow, {graphModel : graphModel})
+
+                Component.onCompleted: dissolveWindow.quickRunDialog = quickRunDialogComponent.createObject(dissolveWindow, {
+                    graphModel: graphModel
+                })
             }
             Pane {
                 id: toolBar
@@ -291,8 +286,13 @@ ApplicationWindow {
                 parameterEndPointsModel: graphModel.parameterEndPoints
                 rootGraphModel: graphModel
 
+                Component.onCompleted: {
+                    graphModel.canvasDimensions = Qt.size(graph.width, graph.height);
+                }
+
                 Repeater {
                     id: graphDelegateRepeater
+
                     model: graph.nodeModel
 
                     delegate: Component {
@@ -308,10 +308,6 @@ ApplicationWindow {
                         }
                     }
                 }
-
-                Component.onCompleted: {
-                    graphModel.canvasDimensions = Qt.size(graph.width, graph.height)
-                }
             }
         }
     }