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Parse more MOPAC aux properties including coordinates #1843

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Dec 5, 2024
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Parse more MOPAC aux properties including coordinates #1843

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93 changes: 92 additions & 1 deletion avogadro/quantumio/mopacaux.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -87,6 +87,33 @@ bool MopacAux::read(std::istream& in, Core::Molecule& molecule)
molecule.setVibrationLx(normalModes);
}

// add charges and properties
molecule.setData("totalCharge", m_charge);
molecule.setData("totalSpinMultiplicity", m_spin);
molecule.setData("dipoleMoment", m_dipoleMoment);
molecule.setData("DeltaH", m_heatOfFormation);
molecule.setData("Area", m_area);
molecule.setData("Volume", m_volume);

if (m_partialCharges.size() > 0) {
MatrixX charges(m_partialCharges.size(), 1);
for (size_t i = 0; i < m_partialCharges.size(); ++i)
charges(i, 0) = m_partialCharges[i];
molecule.setPartialCharges("MOPAC", charges);
}

// if we have more than one coordinate set
if (m_coordSets.size() > 1) {
for (unsigned int i = 0; i < m_coordSets.size(); ++i) {
Core::Array<Vector3> positions;
positions.reserve(molecule.atomCount());
for (size_t j = 0; j < molecule.atomCount(); ++j) {
positions.push_back(m_coordSets[i][j]);
}
molecule.setCoordinate3d(positions, i);
}
}

return true;
}

Expand All @@ -104,6 +131,65 @@ void MopacAux::processLine(std::istream& in)
int tmp = Core::lexicalCast<int>(key.substr(key.find('[') + 1, 4));
cout << "Number of atoms = " << tmp << endl;
m_atomNums = readArrayElements(in, tmp);
} else if (Core::contains(key, "HEAT_OF_FORMATION:KCAL/MOL")) {
vector<string> list = Core::split(line, '=');
if (list.size() > 1) {
std::replace(list[1].begin(), list[1].end(), 'D', 'E');
m_heatOfFormation = Core::lexicalCast<double>(list[1]);
cout << "Heat of formation = " << m_heatOfFormation << " kcal/mol"
<< endl;
}
} else if (Core::contains(key, "AREA:SQUARE ANGSTROMS")) {
vector<string> list = Core::split(line, '=');
if (list.size() > 1) {
std::replace(list[1].begin(), list[1].end(), 'D', 'E');
m_area = Core::lexicalCast<double>(list[1]);
cout << "Area = " << m_area << " square Angstroms" << endl;
}
} else if (Core::contains(key, "VOLUME:CUBIC ANGSTROMS")) {
vector<string> list = Core::split(line, '=');
if (list.size() > 1) {
std::replace(list[1].begin(), list[1].end(), 'D', 'E');
m_volume = Core::lexicalCast<double>(list[1]);
cout << "Volume = " << m_volume << " cubic Angstroms" << endl;
}
} else if (Core::contains(key, "KEYWORDS=")) {
// parse for charge and spin
std::vector<std::string> list = Core::split(key, ' ');
for (size_t i = 0; i < list.size(); ++i) {
if (Core::contains(list[i], "CHARGE=")) {
m_charge = Core::lexicalCast<int>(list[i].substr(7));
} else if (Core::contains(list[i], "DOUBLET")) {
m_spin = 2;
} else if (Core::contains(list[i], "TRIPLET")) {
m_spin = 3;
} else if (Core::contains(list[i], "QUARTET")) {
m_spin = 4;
} else if (Core::contains(list[i], "QUINTET")) {
m_spin = 5;
} else if (Core::contains(list[i], "SEXTET")) {
m_spin = 6;
} else if (Core::contains(list[i], "SEPTET")) {
m_spin = 7;
} else if (Core::contains(list[i], "OCTET")) {
m_spin = 8;
} else if (Core::contains(list[i], "NONET")) {
m_spin = 9;
}
}
} else if (Core::contains(key, "DIP_VEC:DEBYE")) {
vector<string> list = Core::split(line, '=');
if (list.size() > 1) {
// split based on spaces
std::replace(list[1].begin(), list[1].end(), 'D', 'E');
vector<string> dipole = Core::split(list[1], ' ');
if (dipole.size() == 3) {
m_dipoleMoment = Vector3(Core::lexicalCast<double>(dipole[0]),
Core::lexicalCast<double>(dipole[1]),
Core::lexicalCast<double>(dipole[2]));
}
}
cout << "Dipole moment " << m_dipoleMoment.norm() << " Debye" << endl;
} else if (Core::contains(key, "AO_ATOMINDEX")) {
int tmp = Core::lexicalCast<int>(key.substr(key.find('[') + 1, 4));
cout << "Number of atomic orbitals = " << tmp << endl;
Expand All @@ -118,6 +204,10 @@ void MopacAux::processLine(std::istream& in)
int tmp = Core::lexicalCast<int>(key.substr(key.find('[') + 1, 4));
cout << "Number of zeta values = " << tmp << endl;
m_zeta = readArrayD(in, tmp);
} else if (Core::contains(key, "ATOM_CHARGES")) {
int tmp = Core::lexicalCast<int>(key.substr(key.find('[') + 1, 4));
cout << "Number of atomic charges = " << tmp << endl;
m_partialCharges = readArrayD(in, tmp);
} else if (Core::contains(key, "ATOM_PQN")) {
int tmp = Core::lexicalCast<int>(key.substr(key.find('[') + 1, 4));
cout << "Number of PQN values =" << tmp << endl;
Expand All @@ -128,10 +218,11 @@ void MopacAux::processLine(std::istream& in)
m_electrons = Core::lexicalCast<int>(list[1]);
cout << "Number of electrons = " << m_electrons << endl;
}
} else if (Core::contains(key, "ATOM_X_OPT:ANGSTROMS")) {
} else if (Core::contains(key, "ATOM_X")) {
int tmp = Core::lexicalCast<int>(key.substr(key.find('[') + 1, 4));
cout << "Number of atomic coordinates = " << tmp << endl;
m_atomPos = readArrayVec(in, tmp);
m_coordSets.push_back(m_atomPos);
} else if (Core::contains(key, "OVERLAP_MATRIX")) {
int tmp = Core::lexicalCast<int>(key.substr(key.find('[') + 1, 6));
cout << "Size of lower half triangle of overlap matrix = " << tmp << endl;
Expand Down
9 changes: 9 additions & 0 deletions avogadro/quantumio/mopacaux.h
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Original file line number Diff line number Diff line change
Expand Up @@ -64,6 +64,14 @@
bool readNormalModes(std::istream& in, unsigned int n);

int m_electrons;
int m_charge = 0;
int m_spin = 1;
Vector3 m_dipoleMoment;
std::vector<double> m_partialCharges;

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avogadro/quantumio/mopacaux.h#L70 

class member 'MopacAux::m_partialCharges' is never used.
double m_heatOfFormation;

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avogadro/quantumio/mopacaux.h#L71 

class member 'MopacAux::m_heatOfFormation' is never used.
double m_area;

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avogadro/quantumio/mopacaux.h#L72 

class member 'MopacAux::m_area' is never used.
double m_volume;

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avogadro/quantumio/mopacaux.h#L73 

class member 'MopacAux::m_volume' is never used.

std::vector<int> m_shellTypes;
std::vector<int> m_shellNums;
std::vector<int> m_shelltoAtom;
Expand All @@ -78,6 +86,7 @@
std::vector<double> m_zeta;
std::vector<int> m_pqn;
std::vector<Eigen::Vector3d> m_atomPos;
std::vector<std::vector<Eigen::Vector3d>> m_coordSets;

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avogadro/quantumio/mopacaux.h#L89 

class member 'MopacAux::m_coordSets' is never used.

std::vector<double> m_frequencies;
std::vector<double> m_irIntensities;
Expand Down
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