Merge pull request OpenChemistry#1284 from berquist/fix-compiled-warn…

…ings

Fix some compiler warnings not related to Qt

avogadro/core/ringperceiver.cpp

@@ -47,11 +47,6 @@ DistanceMatrix::~DistanceMatrix()
   delete[] m_values;
 }
 
-size_t DistanceMatrix::operator()(size_t i, size_t j) const
-{
-  return m_values[i * m_size + j];
-}
-
 size_t& DistanceMatrix::operator()(size_t i, size_t j)
 {
   return m_values[i * m_size + j];

avogadro/qtplugins/cp2kinput/cp2kinputdialog.cpp

@@ -759,13 +759,13 @@ void Cp2kInputDialog::updatePreviewText()
   file += "&END FORCE_EVAL\n";
 
   if (m_molecule) {
-    std::vector<int> atomList;
+    std::vector<unsigned int> atomList;
     bool inlist = true;
 
     for (size_t i = 0; i < m_molecule->atomCount(); ++i) {
       Core::Atom atom = m_molecule->atom(i);
-      for (int i : atomList) {
-        if (i == atom.atomicNumber()) {
+      for (unsigned iat : atomList) {
+        if (iat == atom.atomicNumber()) {
           inlist = false;
           break;
         } else {

avogadro/qtplugins/scriptcharges/scriptchargemodel.cpp

@@ -358,11 +358,11 @@ void ScriptChargeModel::processElementString(const QString& str)
   str2.replace(',', ' ');
   // then split on whitespace
   QStringList strList = str2.split(QRegExp("\\s+"), QString::SkipEmptyParts);
-  foreach (QString str, strList) {
+  foreach (QString sstr, strList) {
     // these should be numbers or ranges (e.g., 1-84)
-    if (str.contains('-')) {
+    if (sstr.contains('-')) {
       // range, so split on the dash
-      QStringList strList2 = str.split('-');
+      QStringList strList2 = sstr.split('-');
       if (strList2.size() != 2)
         return;
 
@@ -379,7 +379,7 @@ void ScriptChargeModel::processElementString(const QString& str)
     }
 
     bool ok;
-    int i = str.toInt(&ok);
+    int i = sstr.toInt(&ok);
     if (!ok || i < 1 || i > 119)
       return;
 

avogadro/qtplugins/symmetry/symmetry.cpp

@@ -183,15 +183,14 @@ void Symmetry::detectSymmetry()
   // interface with libmsym
   msym_error_t ret = MSYM_SUCCESS;
   msym_element_t* elements = nullptr;
-  const char* error = nullptr;
   char point_group[6];
-  double cm[3], radius = 0.0, symerr = 0.0;
+  double cm[3], radius = 0.0;
 
   /* Do not free these variables */
   const msym_symmetry_operation_t* msops = nullptr;
   const msym_subgroup_t* msg = nullptr;
   const msym_equivalence_set_t* mes = nullptr;
-  int mesl = 0, msgl = 0, msopsl = 0, mlength = 0;
+  int mesl = 0, msgl = 0, msopsl = 0;
 
   // initialize the c-style array of atom names and coordinates
   msym_element_t* a;

avogadro/qtplugins/symmetry/symmetrywidget.cpp

@@ -285,10 +285,10 @@ void SymmetryWidget::equivalenceSelectionChanged(
   if (a == nullptr)
     return;
 
-  unsigned int length = m_molecule->atomCount();
+  Index length = m_molecule->atomCount();
   // unselect all the atoms
-  for (Index i = 0; i < length; ++i) {
-    m_molecule->setAtomSelected(i, false);
+  for (Index iat = 0; iat < length; ++iat) {
+    m_molecule->setAtomSelected(iat, false);
   }
   // this is yucky, but libmsym uses <void*> for id
   auto selectedAtom = reinterpret_cast<Index>(a->id);

utilities/resdata/resdataparse.cxx

@@ -125,7 +125,7 @@ int main(int argc, char* argv[])
           output << "ResidueData " << currResidue << "Data(\"" << currResidue
                  << "\",\n"
                  << "// Atoms\n{";
-          int i = 0;
+          size_t i = 0;
           for (i = 0; i < atoms.size(); ++i) {
             output << "\"" << atoms[i] << "\"";
             if (i != atoms.size() - 1)
@@ -178,7 +178,7 @@ int main(int argc, char* argv[])
   }
 
   output << "std::map<std::string, ResidueData> residueDict = {\n";
-  for (int j = 0; j < residueClassNames.size(); ++j) {
+  for (size_t j = 0; j < residueClassNames.size(); ++j) {
     output << "{\"" << residueClassNames[j] << "\", " << residueClassNames[j]
            << "Data}";
     if (j != residueClassNames.size() - 1)