Ensure energies for each frame is reserved

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

avogadro/io/xyzformat.cpp

@@ -37,22 +37,22 @@ using Core::trimmed;
 using std::isalpha;
 #endif
 
-bool findEnergy(std::string buffer, double energyValue)
+bool findEnergy(const std::string& buffer, double& energyValue)
 {
   // Check for energy in the comment line
   // orca uses  E -680.044112849966 (with spaces)
   // xtb uses energy: -680.044112849966
   // Open Babel uses Energy: -680.044112849966
   std::size_t energyStart = buffer.find("energy:");
   std::size_t offset = 7;
-  std::vector<double> energies;
   if (energyStart == std::string::npos) {
     energyStart = buffer.find("Energy:");
   }
   if (energyStart == std::string::npos) {
     energyStart = buffer.find(" E ");
     offset = 3;
   }
+
   if (energyStart != std::string::npos) {
     // find the next whitespace or end of the string
     std::size_t energyEnd = buffer.find_first_of(" \t", energyStart + offset);
@@ -62,7 +62,7 @@ bool findEnergy(std::string buffer, double energyValue)
     energyValue = lexicalCast<double>(energy);
     return true;
   }
-  return false; // didn't find an energy
+  return false;
 }
 
 bool XyzFormat::read(std::istream& inStream, Core::Molecule& mol)

avogadro/quantumio/orca.cpp

@@ -106,15 +106,16 @@ bool ORCAOutput::read(std::istream& in, Core::Molecule& molecule)
     molecule.setSpectra("NMR", nmrData);
   }
 
+  // this should be the final coordinate set (e.g. the optimized geometry)
   molecule.setCoordinate3d(molecule.atomPositions3d(), 0);
   if (m_coordSets.size() > 1) {
-    for (unsigned int i = 1; i < m_coordSets.size(); i++) {
+    for (unsigned int i = 0; i < m_coordSets.size(); i++) {
       Array<Vector3> positions;
       positions.reserve(molecule.atomCount());
       for (size_t j = 0; j < molecule.atomCount(); ++j) {
-        positions.push_back(m_atomPos[j] * BOHR_TO_ANGSTROM);
+        positions.push_back(m_coordSets[i][j] * BOHR_TO_ANGSTROM);
       }
-      molecule.setCoordinate3d(positions, i);
+      molecule.setCoordinate3d(positions, i + 1);
     }
   }
 
@@ -145,6 +146,9 @@ bool ORCAOutput::read(std::istream& in, Core::Molecule& molecule)
   molecule.setData("totalCharge", m_charge);
   molecule.setData("totalSpinMultiplicity", m_spin);
   molecule.setData("dipoleMoment", m_dipoleMoment);
+  molecule.setData("totalEnergy", m_totalEnergy);
+  if (m_energies.size() > 1)
+    molecule.setData("energies", m_energies);
 
   return true;
 }
@@ -213,6 +217,11 @@ void ORCAOutput::processLine(std::istream& in, GaussianSet* basis)
     list = Core::split(key, ' ');
     if (list.size() > 3)
       m_spin = Core::lexicalCast<int>(list[3]);
+  } else if (Core::contains(key, "FINAL SINGLE POINT ENERGY")) {
+    list = Core::split(key, ' ');
+    if (list.size() > 4)
+      m_totalEnergy = Core::lexicalCast<double>(list[4]);
+    m_energies.push_back(m_totalEnergy);
   } else if (Core::contains(key, "TOTAL NUMBER OF BASIS SET")) {
     m_currentMode = NotParsing; // no longer reading GTOs
   } else if (Core::contains(key, "NUMBER OF CARTESIAN GAUSSIAN BASIS")) {

avogadro/quantumio/orca.h

@@ -105,6 +105,7 @@ class AVOGADROQUANTUMIO_EXPORT ORCAOutput : public Io::FileFormat
   int m_homo;
   int m_charge;
   int m_spin;
+  double m_totalEnergy;
 
   int m_currentAtom;
   unsigned int m_numBasisFunctions;