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Fix a bug with parsing ORCA orbital coefficients #1910

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Jan 4, 2025
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Fix a bug with parsing ORCA orbital coefficients #1910

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36 changes: 21 additions & 15 deletions avogadro/quantumio/orca.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -869,7 +869,11 @@
numColumns = list.size();
columns.resize(numColumns);
while (list.size() > 0) {
orcaOrbitals.push_back(list[1]);
// get the '2s' or '1dx2y2' piece from the line
// so we can re-order the orbitals later
std::vector<std::string> pieces = Core::split(key, ' ');
orcaOrbitals.push_back(pieces[1]);

for (unsigned int i = 0; i < numColumns; ++i) {
columns[i].push_back(Core::lexicalCast<double>(list[i]));
}
Expand Down Expand Up @@ -945,31 +949,34 @@
getline(in, key); // skip -----------
getline(in, key); // now we've got coefficients

regex rx("[.][0-9]{6}[0-9-]");
regex rx("[-]?[0-9]{1,2}[.][0-9]{6}");
auto key_begin = std::sregex_iterator(key.begin(), key.end(), rx);
auto key_end = std::sregex_iterator();
list.clear();
for (std::sregex_iterator i = key_begin; i != key_end; ++i) {
key += i->str() + " ";
list.push_back(i->str());
}

list = Core::split(key, ' ');
numColumns = list.size() - 2;
numColumns = list.size();
columns.resize(numColumns);
while (list.size() > 2) {
orcaOrbitals.push_back(list[1]);
while (list.size() > 0) {
// get the '2s' or '1dx2y2' piece from the line
// so we can re-order the orbitals later
std::vector<std::string> pieces = Core::split(key, ' ');
orcaOrbitals.push_back(pieces[1]);

// columns.resize(numColumns);
for (unsigned int i = 0; i < numColumns; ++i) {
columns[i].push_back(Core::lexicalCast<double>(list[i + 2]));
columns[i].push_back(Core::lexicalCast<double>(list[i]));
}

getline(in, key);
key_begin = std::sregex_iterator(key.begin(), key.end(), rx);
key_end = std::sregex_iterator();
auto key_begin = std::sregex_iterator(key.begin(), key.end(), rx);

Check notice

Code scanning / CodeQL

Declaration hides variable Note

Variable key_begin hides another variable of the same name (on
line 953
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).
auto key_end = std::sregex_iterator();

Check notice

Code scanning / CodeQL

Declaration hides variable Note

Variable key_end hides another variable of the same name (on
line 954
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).
list.clear();
for (std::sregex_iterator i = key_begin; i != key_end; ++i) {
key += i->str() + " ";
list.push_back(i->str());
}
list = Core::split(key, ' ');
if (list.size() != numColumns + 2)
if (list.size() != numColumns)
break;

} // ok, we've finished one batch of MO coeffs
Expand Down Expand Up @@ -1001,7 +1008,6 @@
for (unsigned int i = 0; i < numColumns; ++i) {
numRows = columns[i].size();
for (unsigned int j = 0; j < numRows; ++j) {

m_BetaMOcoeffs.push_back(columns[i][j]);
}
}
Expand Down
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