Merge pull request #1537 from ghutchis/fix-density-color-crash

Fix electron density calculation (and crash)

avogadro/qtplugins/meshes/meshes.cpp

@@ -15,8 +15,8 @@
 
 #include <QtCore/QDebug>
 #include <QtCore/QSettings>
-#include <QtWidgets/QSlider>
 #include <QtWidgets/QFormLayout>
+#include <QtWidgets/QSlider>
 #include <QtWidgets/QVBoxLayout>
 
 #include <algorithm>
@@ -36,17 +36,15 @@ Meshes::Meshes(QObject* p) : ScenePlugin(p), m_setupWidget(nullptr)
   // out of 255
   m_opacity = settings.value("meshes/opacity", 150).toUInt();
 
-  auto color =
-    settings.value("meshes/color1", QColor(Qt::red)).value<QColor>();
+  auto color = settings.value("meshes/color1", QColor(Qt::red)).value<QColor>();
   m_color1[0] = static_cast<unsigned char>(color.red());
   m_color1[1] = static_cast<unsigned char>(color.green());
   m_color1[2] = static_cast<unsigned char>(color.blue());
 
-  color =
-    settings.value("meshes/color2", QColor(Qt::blue)).value<QColor>();
+  color = settings.value("meshes/color2", QColor(Qt::blue)).value<QColor>();
   m_color2[0] = static_cast<unsigned char>(color.red());
   m_color2[1] = static_cast<unsigned char>(color.green());
-  m_color2[2] = static_cast<unsigned char>(color.blue());  
+  m_color2[2] = static_cast<unsigned char>(color.blue());
 }
 
 Meshes::~Meshes() {}
@@ -67,7 +65,7 @@ void Meshes::process(const QtGui::Molecule& mol, GroupNode& node)
   if (mol.meshCount()) {
     auto* geometry = new GeometryNode;
     node.addChild(geometry);
- 
+
     const Mesh* mesh = mol.mesh(0);
 
     /// @todo Allow use of MeshGeometry without an index array when all vertices
@@ -84,20 +82,19 @@ void Meshes::process(const QtGui::Molecule& mol, GroupNode& node)
     mesh1->setOpacity(m_opacity);
 
     if (hasColors) {
-    auto colors = mesh->colors();
-    Core::Array<Vector3ub> colorsRGB(colors.size());
-    for (size_t i = 0; i < colors.size(); i++)
-      colorsRGB[i] = Vector3ub(
-        colors[i].red() * 255, colors[i].green() * 255, colors[i].blue() * 255
-      );
-    mesh1->addVertices(mesh->vertices(), mesh->normals(), colorsRGB);
+      auto colors = mesh->colors();
+      Core::Array<Vector3ub> colorsRGB(colors.size());
+      for (size_t i = 0; i < colors.size(); i++)
+        colorsRGB[i] = Vector3ub(colors[i].red() * 255, colors[i].green() * 255,
+                                 colors[i].blue() * 255);
+      mesh1->addVertices(mesh->vertices(), mesh->normals(), colorsRGB);
     } else { // probably a molecular orbital
       mesh1->setColor(m_color1);
       mesh1->addVertices(mesh->vertices(), mesh->normals());
     }
     mesh1->addTriangles(indices);
     mesh1->setRenderPass(m_opacity == 255 ? Rendering::SolidPass
-                                        : Rendering::TranslucentPass);
+                                          : Rendering::TranslucentPass);
 
     if (mol.meshCount() >= 2) { // it's a molecular orbital, two parts
       auto* mesh2 = new MeshGeometry;
@@ -115,7 +112,7 @@ void Meshes::process(const QtGui::Molecule& mol, GroupNode& node)
       mesh2->addVertices(mesh->vertices(), mesh->normals());
       mesh2->addTriangles(indices);
       mesh2->setRenderPass(m_opacity == 255 ? Rendering::SolidPass
-                                          : Rendering::TranslucentPass);
+                                            : Rendering::TranslucentPass);
     }
   }
 }
@@ -189,4 +186,4 @@ QWidget* Meshes::setupWidget()
   return m_setupWidget;
 }
 
-} // namespace Avogadro
+} // namespace Avogadro::QtPlugins

avogadro/qtplugins/propertytables/propertyview.h

@@ -24,15 +24,15 @@ class PropertyView : public QTableView
   explicit PropertyView(PropertyType type, QWidget* parent = 0);
 
   void selectionChanged(const QItemSelection& selected,
-                        const QItemSelection& previous);
+                        const QItemSelection& previous) override;
   void setMolecule(QtGui::Molecule* molecule);
   void setSourceModel(PropertyModel* model) { m_model = model; }
-  void hideEvent(QHideEvent* event);
+  void hideEvent(QHideEvent* event) override;
   void contextMenuEvent(QContextMenuEvent* event) override;
 
 protected:
   // copy the selected properties to the clipboard
-  void keyPressEvent(QKeyEvent* event);
+  void keyPressEvent(QKeyEvent* event) override;
 
 private:
   PropertyType m_type;

avogadro/qtplugins/spacegroup/spacegroup.h

@@ -21,18 +21,18 @@ class SpaceGroup : public Avogadro::QtGui::ExtensionPlugin
   explicit SpaceGroup(QObject* parent_ = nullptr);
   ~SpaceGroup();
 
-  QString name() const { return tr("SpaceGroup"); }
-  QString description() const;
-  QList<QAction*> actions() const;
-  QStringList menuPath(QAction*) const;
+  QString name() const override { return tr("SpaceGroup"); }
+  QString description() const override;
+  QList<QAction*> actions() const override;
+  QStringList menuPath(QAction*) const override;
 
   bool handleCommand(const QString& command,
                      const QVariantMap& options) override;
 
   void registerCommands() override;
 
 public slots:
-  void setMolecule(QtGui::Molecule* mol);
+  void setMolecule(QtGui::Molecule* mol) override;
 
   void moleculeChanged(unsigned int changes);
 

avogadro/qtplugins/surfaces/surfacedialog.cpp

@@ -52,8 +52,12 @@ void SurfaceDialog::surfaceComboChanged(int n)
   if (type == Surfaces::Type::MolecularOrbital ||
       type == Surfaces::Type::FromFile) {
     m_ui->orbitalCombo->setEnabled(true);
+    m_ui->propertyCombo->setEnabled(false);
+    m_ui->propertyCombo->setCurrentIndex(0); // None
+    m_ui->colormapCombo->setEnabled(false);
   } else {
     m_ui->orbitalCombo->setEnabled(false);
+    m_ui->propertyCombo->setEnabled(true);
   }
 }
 

avogadro/qtplugins/surfaces/surfaces.cpp

@@ -129,8 +129,6 @@ bool Surfaces::handleCommand(const QString& command, const QVariantMap& options)
   if (m_molecule == nullptr)
     return false; // No molecule to handle the command.
 
-  qDebug() << "handle surface cmd:" << command << options;
-
   // Set up some defaults for the options.
   int index = -1;
   int homo = -1;
@@ -593,7 +591,7 @@ void Surfaces::calculateQM(Type type, int index, bool beta, float isoValue,
     } else {
       m_slaterConcurrent->calculateElectronDensity(m_cube);
     }
-  } else if (type == ElectronDensity) {
+  } else if (type == SpinDensity) {
     progressText = tr("Calculating spin density");
     m_cube->setName("Spin Density");
     m_cube->setCubeType(Core::Cube::Type::SpinDensity);
@@ -693,8 +691,6 @@ void Surfaces::displayMesh()
   if (!m_cube)
     return;
 
-  // qDebug() << " running displayMesh";
-
   if (m_dialog != nullptr)
     m_smoothingPasses = m_dialog->smoothingPassesValue();
   else
@@ -706,7 +702,7 @@ void Surfaces::displayMesh()
     m_meshGenerator1 = new QtGui::MeshGenerator;
     connect(m_meshGenerator1, SIGNAL(finished()), SLOT(meshFinished()));
   }
-  m_meshGenerator1->initialize(m_cube, m_mesh1, -m_isoValue, m_smoothingPasses);
+  m_meshGenerator1->initialize(m_cube, m_mesh1, m_isoValue, m_smoothingPasses);
 
   bool isMO = false;
   // if it's from a file we should "play it safe"
@@ -722,8 +718,8 @@ void Surfaces::displayMesh()
       m_meshGenerator2 = new QtGui::MeshGenerator;
       connect(m_meshGenerator2, SIGNAL(finished()), SLOT(meshFinished()));
     }
-    m_meshGenerator2->initialize(m_cube, m_mesh2, m_isoValue, m_smoothingPasses,
-                                 true);
+    m_meshGenerator2->initialize(m_cube, m_mesh2, -m_isoValue,
+                                 m_smoothingPasses, true);
   }
 
   // Start the mesh generation - this needs an improved mutex with a read lock
@@ -797,6 +793,9 @@ void Surfaces::colorMeshByPotential()
   const auto colormap = getColormapFromString(m_dialog->colormapName());
 
   const auto positionsf = m_mesh1->vertices();
+  if (positionsf.empty())
+    return;
+
   Core::Array<Vector3> positions(positionsf.size());
   std::transform(positionsf.begin(), positionsf.end(), positions.begin(),
                  [](const Vector3f& pos) { return pos.cast<double>(); });