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Allow for reading imaginary vibrational frequencies in ORCA outputs. #1398

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Oct 24, 2023
Merged

Allow for reading imaginary vibrational frequencies in ORCA outputs. #1398

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35 changes: 28 additions & 7 deletions avogadro/quantumio/orca.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -301,7 +301,11 @@ void ORCAOutput::processLine(std::istream& in, GaussianSet* basis)
break;
list = Core::split(key, ' ');
while (!key.empty()) {
if (list.size() != 3) {
// imaginary frequencies can have an additional comment:
// ***imaginary mode***
if (list.size() != 3 &&
(list.size() != 5 || list[3] != "***imaginary" ||
list[4] != "mode***")) {
break;
}
// e.g. 0: 0.00 cm**-1
Expand Down Expand Up @@ -331,14 +335,24 @@ void ORCAOutput::processLine(std::istream& in, GaussianSet* basis)
if (key.empty())
break;
list = Core::split(key, ' ');
vector<int> modeIndex;
vector<std::size_t> modeIndex;
bool invalid_index = false;
while (!key.empty()) {
// first we get a set of column numbers
// e.g. 1 2 3 4 5 6 7 8 9 10
modeIndex.clear();
for (unsigned int i = 0; i < list.size(); i++) {
modeIndex.push_back(Core::lexicalCast<int>(list[i]));
for (const auto& index_str : list) {
auto index = Core::lexicalCast<std::size_t>(index_str);
if (index >= m_frequencies.size()) {
invalid_index = true;
break;
}
modeIndex.push_back(index);
}
// invalid column index
if (invalid_index)
break;

// now we read the displacements .. there should be 3N lines
// x,y,z for each atom
getline(in, key);
Expand Down Expand Up @@ -373,7 +387,11 @@ void ORCAOutput::processLine(std::istream& in, GaussianSet* basis)
}
// the first entry might be 5 or 6 because of removed rotations /
// translations
int index = Core::lexicalCast<int>(list[0]);
auto index = Core::lexicalCast<std::size_t>(list[0]);
// invalid index
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if (index >= m_frequencies.size())
break;

double intensity = Core::lexicalCast<double>(list[3]);
m_IRintensities[index] = intensity;

Expand All @@ -396,8 +414,11 @@ void ORCAOutput::processLine(std::istream& in, GaussianSet* basis)
}
// the first entry might be 5 or 6 because of removed rotations /
// translations
int index = Core::lexicalCast<int>(list[0]);
if (m_RamanIntensities.size() == 0 && index > 0) {
auto index = Core::lexicalCast<std::size_t>(list[0]);
// invalid index
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if (index >= m_frequencies.size())
break;
if (m_RamanIntensities.empty()) {
while (m_RamanIntensities.size() < index) {
m_RamanIntensities.push_back(0.0);
}
Expand Down