Split spectra plot and vibrations extensions

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

avogadro/core/molecule.cpp

@@ -36,10 +36,11 @@ Molecule::Molecule()
 
 Molecule::Molecule(const Molecule& other)
   : m_data(other.m_data), m_partialCharges(other.m_partialCharges),
-    m_customElementMap(other.m_customElementMap), m_elements(other.m_elements),
-    m_positions2d(other.m_positions2d), m_positions3d(other.m_positions3d),
-    m_label(other.m_label), m_coordinates3d(other.m_coordinates3d),
-    m_timesteps(other.m_timesteps), m_hybridizations(other.m_hybridizations),
+    m_spectra(other.m_spectra), m_customElementMap(other.m_customElementMap),
+    m_elements(other.m_elements), m_positions2d(other.m_positions2d),
+    m_positions3d(other.m_positions3d), m_label(other.m_label),
+    m_coordinates3d(other.m_coordinates3d), m_timesteps(other.m_timesteps),
+    m_hybridizations(other.m_hybridizations),
     m_formalCharges(other.m_formalCharges), m_colors(other.m_colors),
     m_vibrationFrequencies(other.m_vibrationFrequencies),
     m_vibrationIRIntensities(other.m_vibrationIRIntensities),
@@ -92,6 +93,9 @@ void Molecule::readProperties(const Molecule& other)
     m_partialCharges[it->first] = it->second;
   }
 
+  // copy spectra
+  m_spectra = other.m_spectra;
+
   // copy orbital information
   SlaterSet* slaterSet = dynamic_cast<SlaterSet*>(other.m_basisSet);
   if (slaterSet != nullptr) {
@@ -127,6 +131,7 @@ void Molecule::readProperties(const Molecule& other)
 
 Molecule::Molecule(Molecule&& other) noexcept
   : m_data(other.m_data), m_partialCharges(std::move(other.m_partialCharges)),
+    m_spectra(other.m_spectra),
     m_customElementMap(std::move(other.m_customElementMap)),
     m_elements(other.m_elements), m_positions2d(other.m_positions2d),
     m_positions3d(other.m_positions3d), m_label(other.m_label),
@@ -166,6 +171,7 @@ Molecule& Molecule::operator=(const Molecule& other)
   if (this != &other) {
     m_data = other.m_data;
     m_partialCharges = other.m_partialCharges;
+    m_spectra = other.m_spectra;
     m_customElementMap = other.m_customElementMap;
     m_elements = other.m_elements;
     m_positions2d = other.m_positions2d;
@@ -227,6 +233,7 @@ Molecule& Molecule::operator=(Molecule&& other) noexcept
   if (this != &other) {
     m_data = other.m_data;
     m_partialCharges = std::move(other.m_partialCharges);
+    m_spectra = other.m_spectra;
     m_customElementMap = std::move(other.m_customElementMap);
     m_elements = other.m_elements;
     m_positions2d = other.m_positions2d;
@@ -322,6 +329,31 @@ std::set<std::string> Molecule::partialChargeTypes() const
   return types;
 }
 
+std::set<std::string> Molecule::spectraTypes() const
+{
+  std::set<std::string> types;
+  for (auto& it : m_spectra)
+    types.insert(it.first);
+  return types;
+}
+
+void Molecule::setSpectra(const std::string& type, const MatrixX& value)
+{
+  m_spectra[type] = value;
+}
+
+MatrixX Molecule::spectra(const std::string& type) const
+{
+  MatrixX value;
+
+  auto search = m_spectra.find(type);
+  if (search != m_spectra.end()) {
+    value = search->second; // value from the map
+  }
+
+  return value;
+}
+
 void Molecule::setFrozenAtom(Index atomId, bool frozen)
 {
   if (atomId >= m_atomicNumbers.size())

avogadro/core/molecule.h

@@ -100,6 +100,15 @@ class AVOGADROCORE_EXPORT Molecule
   /** \overload */
   VariantMap& dataMap();
 
+  /** @return a specific spectra entry */
+  MatrixX spectra(const std::string& name) const;
+
+  /** Sets the spectra value with @p name to @p value. */
+  void setSpectra(const std::string& name, const MatrixX& value);
+
+  /** @return the list of available spectra */
+  std::set<std::string> spectraTypes() const;
+
   /** Sets atomic partial charges with @p type to @p value. */
   void setPartialCharges(const std::string& type, const MatrixX& value);
 
@@ -764,6 +773,8 @@ class AVOGADROCORE_EXPORT Molecule
   VariantMap m_data;
   std::map<std::string, MatrixX>
     m_partialCharges; //!< Sets of atomic partial charges
+
+  std::map<std::string, MatrixX> m_spectra; //!< Sets of spectra
   CustomElementMap m_customElementMap;
   ElementMask m_elements; //!< Which elements this molecule contains (e.g., for
                           //!< force fields)

avogadro/qtplugins/CMakeLists.txt

@@ -113,12 +113,14 @@ add_subdirectory(hydrogens)
 add_subdirectory(importpqr)
 add_subdirectory(insertdna)
 add_subdirectory(label)
+add_subdirectory(lammpsinput)
 add_subdirectory(lineformatinput)
 add_subdirectory(manipulator)
 add_subdirectory(measuretool)
 add_subdirectory(navigator)
 add_subdirectory(networkdatabases)
 add_subdirectory(openbabel)
+add_subdirectory(openmminput)
 add_subdirectory(playertool)
 add_subdirectory(ply)
 add_subdirectory(povray)
@@ -130,36 +132,32 @@ if(USE_SPGLIB)
   add_subdirectory(spacegroup)
 endif()
 add_subdirectory(surfaces)
-add_subdirectory(lammpsinput)
-add_subdirectory(openmminput)
+add_subdirectory(templatetool)
+add_subdirectory(vibrations)
+add_subdirectory(vrml)
+
 if(QT_VERSION EQUAL 5)
   # This will need some work on the QRegExp migration
+  add_subdirectory(apbs)
   add_subdirectory(coordinateeditor)
+  add_subdirectory(cp2kinput)
+  add_subdirectory(gamessinput)
   add_subdirectory(insertfragment)
   add_subdirectory(molecularproperties)
   # The SVG library is not available in Qt 6
   add_subdirectory(svg)
 endif()
-add_subdirectory(spectra)
-add_subdirectory(templatetool)
-add_subdirectory(vrml)
 
 # Plugins that require VTK
 if(USE_VTK)
   add_subdirectory(coloropacitymap)
+  add_subdirectory(spectra)
   add_subdirectory(plotpdf)
   add_subdirectory(plotrmsd)
   add_subdirectory(plotxrd)
   add_subdirectory(yaehmop)
 endif()
 
-if(QT_VERSION EQUAL 5)
-  # QRegExp fixes needed in classes these depend on
-  add_subdirectory(apbs)
-  add_subdirectory(cp2kinput)
-  add_subdirectory(gamessinput)
-endif()
-
 # script plugins (input generators, etc.)
 if(QT_VERSION EQUAL 5)
   # QRegExp fixes needed in classes these depend on
@@ -186,8 +184,6 @@ add_subdirectory(licorice)
 add_subdirectory(meshes)
 add_subdirectory(noncovalent)
 add_subdirectory(vanderwaals)
-# redundant since there's universal AO
-# add_subdirectory(vanderwaalsao)
 add_subdirectory(wireframe)
 if (USE_OPENGL)
   # needs some raw OpenGL code

avogadro/qtplugins/spectra/CMakeLists.txt

@@ -1,19 +1,15 @@
 set(plugin_srcs
-  vibrationdialog.cpp
-  vibrationmodel.cpp
+  spectradialog.cpp
   spectra.cpp
 )
 
 avogadro_plugin(Spectra
-  "Spectra and Vibrations"
+  "Spectra Plots"
   ExtensionPlugin
   spectra.h
   Spectra
   "${plugin_srcs}"
-  "vibrationdialog.ui"
+  "spectradialog.ui"
 )
 
-if (USE_VTK)
-  add_definitions(-DUSE_VTK)
-  target_link_libraries(Spectra PRIVATE Avogadro::Vtk)
-endif()
+target_link_libraries(Spectra PRIVATE Avogadro::Vtk)