Port molecular orbital table from Avogadro v1 (#1888)

* Initial port of code from Avogadro v1

* Move energies and occupancies to BasisSet class, add const qualifiers
* Allow both beta and alpha symmetry labels
* Move Gaussian and Slater concurrent classes to qtgui for orbital table
* For now, skip the progress bar

Signed-off-by: Geoff Hutchison <[email protected]>

avogadro/core/basisset.h

@@ -103,7 +103,8 @@ class AVOGADROCORE_EXPORT BasisSet
   /**
    * @return The number of molecular orbitals in the BasisSet.
    */
-  virtual unsigned int molecularOrbitalCount(ElectronType type = Paired) = 0;
+  virtual unsigned int molecularOrbitalCount(
+    ElectronType type = Paired) const = 0;
 
   /**
    * Check if the given MO number is the HOMO or not.
@@ -134,6 +135,72 @@ class AVOGADROCORE_EXPORT BasisSet
    */
   virtual bool isValid() = 0;
 
+  /**
+   * @return the orbital symmetry labels (if they exist) for the MOs
+   */
+  std::vector<std::string> symmetryLabels(ElectronType type = Paired) const
+  {
+    if (type == Paired || type == Alpha)
+      return m_symmetryLabels[0];
+    else
+      return m_symmetryLabels[1];
+  }
+
+  /**
+   * Set the orbital symmetry labels (a1, t2g, etc.) for the molecular
+   * orbitals
+   */
+  void setSymmetryLabels(const std::vector<std::string>& labels,
+                         ElectronType type = Paired);
+
+  /**
+   * @brief Set the molecular orbital energies, expected in Hartrees.
+   * @param energies The vector containing energies for the MOs of type
+   * @param type The type of the electrons being set.
+   */
+  void setMolecularOrbitalEnergy(const std::vector<double>& energies,
+                                 ElectronType type = Paired);
+
+  /**
+   * @brief Set the molecular orbital occupancies.
+   * @param occ The occupancies for the MOs of type.
+   * @param type The type of the electrons being set.
+   */
+  void setMolecularOrbitalOccupancy(const std::vector<unsigned char>& occ,
+                                    ElectronType type = Paired);
+
+  std::vector<double>& moEnergy(ElectronType type = Paired)
+  {
+    if (type == Paired || type == Alpha)
+      return m_moEnergy[0];
+    else
+      return m_moEnergy[1];
+  }
+
+  std::vector<double> moEnergy(ElectronType type = Paired) const
+  {
+    if (type == Paired || type == Alpha)
+      return m_moEnergy[0];
+    else
+      return m_moEnergy[1];
+  }
+
+  std::vector<unsigned char>& moOccupancy(ElectronType type = Paired)
+  {
+    if (type == Paired || type == Alpha)
+      return m_moOccupancy[0];
+    else
+      return m_moOccupancy[1];
+  }
+
+  std::vector<unsigned char> moOccupancy(ElectronType type = Paired) const
+  {
+    if (type == Paired || type == Alpha)
+      return m_moOccupancy[0];
+    else
+      return m_moOccupancy[1];
+  }
+
 protected:
   /**
    * Total number of electrons, 0 is alpha electrons and 1 is beta electrons.
@@ -159,6 +226,22 @@ class AVOGADROCORE_EXPORT BasisSet
    * The name of the theory used for the calculation.
    */
   std::string m_theoryName;
+
+  /**
+   * The orbital symmetry labels (if they exist) for the MOs
+   */
+  std::vector<std::string> m_symmetryLabels[2];
+
+  /**
+   * @brief This block stores energies for the molecular orbitals (same
+   * convention as the molecular orbital coefficients).
+   */
+  std::vector<double> m_moEnergy[2];
+
+  /**
+   * @brief The occupancy of the molecular orbitals.
+   */
+  std::vector<unsigned char> m_moOccupancy[2];
 };
 
 inline void BasisSet::setElectronCount(unsigned int n, ElectronType type)
@@ -194,6 +277,33 @@ inline unsigned int BasisSet::electronCount(ElectronType type) const
   }
 }
 
+inline void BasisSet::setSymmetryLabels(const std::vector<std::string>& labels,
+                                        ElectronType type)
+{
+  if (type == Paired || type == Alpha)
+    m_symmetryLabels[0] = labels;
+  else
+    m_symmetryLabels[1] = labels;
+}
+
+inline void BasisSet::setMolecularOrbitalEnergy(
+  const std::vector<double>& energies, ElectronType type)
+{
+  if (type == Beta)
+    m_moEnergy[1] = energies;
+  else
+    m_moEnergy[0] = energies;
+}
+
+inline void BasisSet::setMolecularOrbitalOccupancy(
+  const std::vector<unsigned char>& occ, ElectronType type)
+{
+  if (type == Beta)
+    m_moOccupancy[1] = occ;
+  else
+    m_moOccupancy[0] = occ;
+}
+
 } // namespace Avogadro::Core
 
 #endif

avogadro/core/gaussianset.cpp

@@ -154,24 +154,6 @@ bool GaussianSet::setActiveSetStep(int index)
   return true;
 }
 
-void GaussianSet::setMolecularOrbitalEnergy(const vector<double>& energies,
-                                            ElectronType type)
-{
-  if (type == Beta)
-    m_moEnergy[1] = energies;
-  else
-    m_moEnergy[0] = energies;
-}
-
-void GaussianSet::setMolecularOrbitalOccupancy(const vector<unsigned char>& occ,
-                                               ElectronType type)
-{
-  if (type == Beta)
-    m_moOccupancy[1] = occ;
-  else
-    m_moOccupancy[0] = occ;
-}
-
 void GaussianSet::setMolecularOrbitalNumber(const vector<unsigned int>& nums,
                                             ElectronType type)
 {
@@ -195,7 +177,7 @@ bool GaussianSet::setSpinDensityMatrix(const MatrixX& m)
   return true;
 }
 
-unsigned int GaussianSet::molecularOrbitalCount(ElectronType type)
+unsigned int GaussianSet::molecularOrbitalCount(ElectronType type) const
 {
   size_t index(0);
   if (type == Beta)

avogadro/core/gaussianset.h

@@ -131,22 +131,6 @@ class AVOGADROCORE_EXPORT GaussianSet : public BasisSet
    */
   bool setActiveSetStep(int index);
 
-  /**
-   * @brief Set the molecular orbital energies, expected in Hartrees.
-   * @param energies The vector containing energies for the MOs of type
-   * @param type The type of the electrons being set.
-   */
-  void setMolecularOrbitalEnergy(const std::vector<double>& energies,
-                                 ElectronType type = Paired);
-
-  /**
-   * @brief Set the molecular orbital occupancies.
-   * @param occ The occupancies for the MOs of type.
-   * @param type The type of the electrons being set.
-   */
-  void setMolecularOrbitalOccupancy(const std::vector<unsigned char>& occ,
-                                    ElectronType type = Paired);
-
   /**
    * @brief This enables support of sparse orbital sets, and provides a mapping
    * from the index in memory to the actual molecular orbital number.
@@ -182,7 +166,7 @@ class AVOGADROCORE_EXPORT GaussianSet : public BasisSet
   /**
    * @return The number of molecular orbitals in the GaussianSet.
    */
-  unsigned int molecularOrbitalCount(ElectronType type = Paired) override;
+  unsigned int molecularOrbitalCount(ElectronType type = Paired) const override;
 
   /**
    * Debug routine, outputs all of the data in the GaussianSet.
@@ -260,38 +244,6 @@ class AVOGADROCORE_EXPORT GaussianSet : public BasisSet
       return m_moMatrix[1];
   }
 
-  std::vector<double>& moEnergy(ElectronType type = Paired)
-  {
-    if (type == Paired || type == Alpha)
-      return m_moEnergy[0];
-    else
-      return m_moEnergy[1];
-  }
-
-  std::vector<double> moEnergy(ElectronType type = Paired) const
-  {
-    if (type == Paired || type == Alpha)
-      return m_moEnergy[0];
-    else
-      return m_moEnergy[1];
-  }
-
-  std::vector<unsigned char>& moOccupancy(ElectronType type = Paired)
-  {
-    if (type == Paired || type == Alpha)
-      return m_moOccupancy[0];
-    else
-      return m_moOccupancy[1];
-  }
-
-  std::vector<unsigned char> moOccupancy(ElectronType type = Paired) const
-  {
-    if (type == Paired || type == Alpha)
-      return m_moOccupancy[0];
-    else
-      return m_moOccupancy[1];
-  }
-
   std::vector<unsigned int>& moNumber(ElectronType type = Paired)
   {
     if (type == Paired || type == Alpha)
@@ -337,17 +289,6 @@ class AVOGADROCORE_EXPORT GaussianSet : public BasisSet
    */
   std::vector<MatrixX> m_moMatrixSet[2];
 
-  /**
-   * @brief This block stores energies for the molecular orbitals (same
-   * convention as the molecular orbital coefficients).
-   */
-  std::vector<double> m_moEnergy[2];
-
-  /**
-   * @brief The occupancy of the molecular orbitals.
-   */
-  std::vector<unsigned char> m_moOccupancy[2];
-
   /**
    * @brief This stores the molecular orbital number (when they are sparse). It
    * is used to lookup the actual index of the molecular orbital data.

avogadro/core/slaterset.cpp

@@ -61,14 +61,12 @@ bool SlaterSet::addDensityMatrix(const Eigen::MatrixXd& d)
   return true;
 }
 
-unsigned int SlaterSet::molecularOrbitalCount(ElectronType)
+unsigned int SlaterSet::molecularOrbitalCount(ElectronType) const
 {
   return static_cast<unsigned int>(m_overlap.cols());
 }
 
-void SlaterSet::outputAll()
-{
-}
+void SlaterSet::outputAll() {}
 
 void SlaterSet::initCalculation()
 {
@@ -133,7 +131,7 @@ void SlaterSet::initCalculation()
     }
   }
   // Convert the exponents into Angstroms
-  for (double & m_zeta : m_zetas)
+  for (double& m_zeta : m_zetas)
     m_zeta = m_zeta / BOHR_TO_ANGSTROM_D;
 
   m_initialized = true;

avogadro/core/slaterset.h

@@ -116,7 +116,7 @@ class AVOGADROCORE_EXPORT SlaterSet : public BasisSet
   /**
    * @return The number of molecular orbitals in the BasisSet.
    */
-  unsigned int molecularOrbitalCount(ElectronType type = Paired) override;
+  unsigned int molecularOrbitalCount(ElectronType type = Paired) const override;
 
   /**
    * @return True of the basis set is valid, false otherwise.

avogadro/io/cjsonformat.cpp

@@ -417,6 +417,13 @@ bool CjsonFormat::deserialize(std::istream& file, Molecule& molecule,
           numArray.push_back(static_cast<unsigned int>(number));
         basis->setMolecularOrbitalNumber(numArray);
       }
+      json symmetryLabels = orbitals["symmetries"];
+      if (symmetryLabels.is_array()) {
+        std::vector<std::string> symArray;
+        for (auto& sym : symmetryLabels)
+          symArray.push_back(sym);
+        basis->setSymmetryLabels(symArray);
+      }
       json moCoefficients = orbitals["moCoefficients"];
       json moCoefficientsA = orbitals["alphaCoefficients"];
       json moCoefficientsB = orbitals["betaCoefficients"];

avogadro/qtgui/CMakeLists.txt

@@ -1,7 +1,7 @@
 if(QT_VERSION EQUAL 6)
-  find_package(Qt6 COMPONENTS Widgets REQUIRED)
+  find_package(Qt6 COMPONENTS Widgets Concurrent REQUIRED)
 else()
-  find_package(Qt5 COMPONENTS Widgets REQUIRED)
+  find_package(Qt5 COMPONENTS Widgets Concurrent REQUIRED)
 endif()
 
 # Provide some simple API to find the plugins, scripts, etc.
@@ -40,6 +40,7 @@ avogadro_headers(QtGui
   extensionplugin.h
   filebrowsewidget.h
   fileformatdialog.h
+  gaussiansetconcurrent.h
   generichighlighter.h
   hydrogentools.h
   insertfragmentdialog.h
@@ -62,6 +63,7 @@ avogadro_headers(QtGui
   sceneplugin.h
   scenepluginmodel.h
   scriptloader.h
+  slatersetconcurrent.h
   sortfiltertreeproxymodel.h
   toolplugin.h
   utilities.h
@@ -79,6 +81,7 @@ target_sources(QtGui PRIVATE
   extensionplugin.cpp
   filebrowsewidget.cpp
   fileformatdialog.cpp
+  gaussiansetconcurrent.cpp
   generichighlighter.cpp
   hydrogentools.cpp
   insertfragmentdialog.cpp
@@ -100,6 +103,7 @@ target_sources(QtGui PRIVATE
   sceneplugin.cpp
   scenepluginmodel.cpp
   scriptloader.cpp
+  slatersetconcurrent.cpp
   sortfiltertreeproxymodel.cpp
   toolplugin.cpp
   utilities.cpp
@@ -120,4 +124,4 @@ qt_add_resources(RC_SOURCES ${RCS})
 target_sources(QtGui PRIVATE ${RC_SOURCES})
 
 avogadro_add_library(QtGui)
-target_link_libraries(QtGui PUBLIC Avogadro::IO Qt::Widgets)
+target_link_libraries(QtGui PUBLIC Avogadro::IO Qt::Widgets Qt::Concurrent)

avogadro/qtplugins/surfaces/gaussiansetconcurrent.cpp → avogadro/qtgui/gaussiansetconcurrent.cpp

@@ -14,7 +14,7 @@
 
 #include <QtConcurrent/QtConcurrentMap>
 
-namespace Avogadro::QtPlugins {
+namespace Avogadro::QtGui {
 
 using Core::BasisSet;
 using Core::Cube;
@@ -147,4 +147,4 @@ void GaussianSetConcurrent::processSpinDensity(GaussianShell& shell)
   Vector3 pos = shell.tCube->position(shell.pos);
   shell.tCube->setValue(shell.pos, shell.tools->calculateSpinDensity(pos));
 }
-} // namespace Avogadro::QtPlugins
+} // namespace Avogadro::QtGui