Backport fixes from PR #488

corelib/src/libs/SireBase/countflops.cpp

@@ -215,8 +215,10 @@ double FlopsMark::operator-(const FlopsMark &other) const
     return (1000.0 * dnflops) / dms;
 }
 
+#ifdef SIRE_TIME_ROUTINES
 Q_GLOBAL_STATIC_WITH_ARGS(double, benchmarkSum, (0.0))
 Q_GLOBAL_STATIC(QMutex, benchmarkMutex)
+#endif
 
 /** Perform a simple benchmark to work out what the realistic maximum
     FLOPS count for this processor (compiled with this compiler)

corelib/src/libs/SireBase/pagecache.cpp

@@ -30,18 +30,18 @@
 
 #include "SireError/errors.h"
 
-#include "SireBase/parallel.h"
-#include "SireBase/console.h"
 #include "SireBase/atexit.h"
+#include "SireBase/console.h"
+#include "SireBase/parallel.h"
 
+#include <QAtomicInt>
 #include <QDir>
-#include <QThread>
-#include <QQueue>
 #include <QHash>
 #include <QMutex>
-#include <QTemporaryFile>
+#include <QQueue>
 #include <QTemporaryDir>
-#include <QAtomicInt>
+#include <QTemporaryFile>
+#include <QThread>
 
 #include <boost/noncopyable.hpp>
 
@@ -1074,7 +1074,7 @@ void CacheData::run()
 
                 const unsigned int n_bytes = static_cast<unsigned int>(data.size());
 
-                if (n_bytes >= page_size)
+                if (n_bytes >= static_cast<unsigned int>(page_size))
                 {
                     // this is bigger than a page, so needs to have its
                     // own page!

corelib/src/libs/SireBase/process.cpp

@@ -194,7 +194,7 @@ Process::Process(const Process &other) : d(other.d)
 /** Destructor */
 Process::~Process()
 {
-    if (d.unique())
+    if (d.use_count() == 1)
     {
         this->kill();
     }

corelib/src/libs/SireBase/progressbar.cpp

@@ -28,9 +28,9 @@
 
 #include "progressbar.h"
 
+#include <QAtomicInteger>
 #include <QDateTime>
 #include <QThread>
-#include <QAtomicInteger>
 
 #include <boost/noncopyable.hpp>
 
@@ -450,7 +450,7 @@ namespace SireBase
             {
                 QMutexLocker lkr(&mutex);
 
-                if (not bar.d.unique())
+                if (bar.d.use_count() != 1)
                     bar.d = bar.d->clone();
 
                 if (has_finished)

corelib/src/libs/SireCAS/CMakeLists.txt

@@ -91,6 +91,11 @@ set ( SIRECAS_SOURCES
 
     )
 
+# NaN is used to mark missing values, so it must survive -ffast-math.
+if (NOT MSVC)
+  set_source_files_properties(lambdaschedule.cpp PROPERTIES COMPILE_OPTIONS "-fno-finite-math-only")
+endif()
+
 add_library (SireCAS ${SIRECAS_SOURCES})
 
 set_target_properties (SireCAS PROPERTIES

corelib/src/libs/SireCAS/lambdaschedule.cpp

@@ -185,8 +185,8 @@ LambdaSchedule::LambdaSchedule(const LambdaSchedule &other)
       lever_names(other.lever_names), stage_names(other.stage_names),
       default_equations(other.default_equations),
       stage_equations(other.stage_equations),
-      coupled_levers(other.coupled_levers),
-      stage_weights(other.stage_weights)
+      stage_weights(other.stage_weights),
+      coupled_levers(other.coupled_levers)
 {
 }
 

corelib/src/libs/SireCAS/symbol.h

@@ -112,6 +112,13 @@ namespace SireCAS
 
         bool operator==(const ExBase &other) const;
 
+        /** Exact match so C++20 doesn't find this ambiguous with the
+            reversed Expression overload */
+        bool operator==(const Symbol &other) const
+        {
+            return this->operator==(static_cast<const ExBase &>(other));
+        }
+
         bool operator<(const Symbol &other) const;
         bool operator>(const Symbol &other) const;
         bool operator<=(const Symbol &other) const;

corelib/src/libs/SireCluster/node.cpp

@@ -227,7 +227,7 @@ bool Node::release()
 
     d.reset();
 
-    return my_d.unique();
+    return my_d.use_count() == 1;
 }
 
 /** Force the release of this node. This aborts any running
@@ -243,7 +243,7 @@ void Node::forceRelease()
 
     d.reset();
 
-    if (my_d.unique())
+    if (my_d.use_count() == 1)
     {
         // just reset this pointer, and we are ok
         my_d.reset();

corelib/src/libs/SireCluster/nodes.cpp

@@ -180,7 +180,7 @@ Nodes::Nodes(const Nodes &other) : d(other.d)
 /** Destructor */
 Nodes::~Nodes()
 {
-    if (d.unique())
+    if (d.use_count() == 1)
     {
         this->removeAll();
     }

corelib/src/libs/SireIO/netcdffile.cpp

@@ -779,7 +779,7 @@ NetCDFDataInfo::NetCDFDataInfo(const NetCDFDataInfo &other, const NetCDFHyperSla
 
         for (int i = 0; i < dim_sizes.count(); ++i)
         {
-            if (slab.starts()[i] < 0 or slab.starts()[i] + slab.counts()[i] > dim_sizes[i])
+            if (slab.starts()[i] + slab.counts()[i] > static_cast<size_t>(dim_sizes[i]))
             {
                 throw SireError::invalid_index(QObject::tr(
                                                    "The slab for dimension %1 has the wrong shape (%2, %3) when the "

corelib/src/libs/SireIO/perturbationslibrary.cpp

@@ -1191,7 +1191,7 @@ Molecule PerturbationsLibrary::applyTemplate(const Molecule &molecule) const
             SireUnits::Dimension::Charge icharge = pert.getInitCharge(iname);
             atom.setProperty(initial_charge_property, icharge);
         }
-        catch (const SireError::invalid_key)
+        catch (const SireError::invalid_key &)
         {
             continue;
         }
@@ -1200,7 +1200,7 @@ Molecule PerturbationsLibrary::applyTemplate(const Molecule &molecule) const
             SireUnits::Dimension::Charge fcharge = pert.getFinalCharge(iname);
             atom.setProperty(final_charge_property, fcharge);
         }
-        catch (const SireError::invalid_key)
+        catch (const SireError::invalid_key &)
         {
             continue;
         }
@@ -1210,7 +1210,7 @@ Molecule PerturbationsLibrary::applyTemplate(const Molecule &molecule) const
             LJParameter ilj = pert.getInitLJ(iname);
             atom.setProperty(initial_LJ_property, ilj);
         }
-        catch (const SireError::invalid_key)
+        catch (const SireError::invalid_key &)
         {
             continue;
         }
@@ -1219,7 +1219,7 @@ Molecule PerturbationsLibrary::applyTemplate(const Molecule &molecule) const
             LJParameter flj = pert.getFinalLJ(iname);
             atom.setProperty(final_LJ_property, flj);
         }
-        catch (const SireError::invalid_key)
+        catch (const SireError::invalid_key &)
         {
             continue;
         }
@@ -1229,7 +1229,7 @@ Molecule PerturbationsLibrary::applyTemplate(const Molecule &molecule) const
             QString iatype = pert.getInitType(iname);
             atom.setProperty(initial_ambertype_property, iatype);
         }
-        catch (const SireError::invalid_key)
+        catch (const SireError::invalid_key &)
         {
             continue;
         }
@@ -1238,7 +1238,7 @@ Molecule PerturbationsLibrary::applyTemplate(const Molecule &molecule) const
             QString fatype = pert.getFinalType(iname);
             atom.setProperty(final_ambertype_property, fatype);
         }
-        catch (const SireError::invalid_key)
+        catch (const SireError::invalid_key &)
         {
             continue;
         }

corelib/src/libs/SireIO/third_party/xdrfile_trr.c

@@ -481,7 +481,7 @@ int read_trr_natoms(char *fn, int *natoms)
 int write_trr(XDRFILE *xd, int natoms, int step, float t, float lambda,
               matrix box, rvec *x, rvec *v, rvec *f)
 {
-  int *plcholder;
+  int *plcholder = NULL;
   return do_trn(xd, 0, &step, &t, &lambda, box, &natoms, x, v, f, plcholder);
 }
 

corelib/src/libs/SireIO/tinker.cpp

@@ -482,12 +482,8 @@ void Tinker::loadParameters(const QString &prmfile)
 
     QTextStream ts(&f);
 
-    int linenum = -1;
-
     while (not ts.atEnd())
     {
-        ++linenum;
-
         QString line = ts.readLine().simplified();
 
         if (line.isEmpty() or line.startsWith("#"))

corelib/src/libs/SireIO/zmatrixmaker.cpp

@@ -217,7 +217,7 @@ void ZmatrixTemplate::setDihedralDelta(const QString &atom, const QString &bond,
 // Implementation of ZmatrixResidue
 //
 
-ZmatrixResidue::ZmatrixResidue(const QString &name) : ZmatrixTemplate(name)
+ZmatrixResidue::ZmatrixResidue(const QString &name) : ZmatrixTemplate(name), rotate(0), translate(0)
 {
 }
 
@@ -593,7 +593,7 @@ Molecule ZmatrixMaker::applyTemplates(Molecule &molecule)
             {
                 linetemplate = restemplate.getZmatrixLineTemplate(atom.name().value());
             }
-            catch (SireError::invalid_key)
+            catch (const SireError::invalid_key &)
             {
                 /** If this fails, look also in the matching backbone zmatrix*/
                 ZmatrixTemplate chain = restemplate.getChain(position);

corelib/src/libs/SireMM/anglerestraints.cpp

@@ -85,7 +85,7 @@ QDataStream &operator>>(QDataStream &ds, AngleRestraint &angrest)
 /** Null constructor */
 AngleRestraint::AngleRestraint()
     : ConcreteProperty<AngleRestraint, Property>(),
-      _ktheta(0), _theta0(0)
+      _theta0(0), _ktheta(0)
 {
 }
 
@@ -253,8 +253,7 @@ QDataStream &operator>>(QDataStream &ds, AngleRestraints &angrests)
     {
         SharedDataStream sds(ds);
 
-        sds >> angrests.r >> angrests.use_pbc
-            >> static_cast<Restraints &>(angrests);
+        sds >> angrests.r >> angrests.use_pbc >> static_cast<Restraints &>(angrests);
     }
     else
         throw version_error(v, "1,2", r_angrests, CODELOC);

corelib/src/libs/SireMM/cljatoms.cpp

@@ -1638,13 +1638,13 @@ void CLJAtoms::append(const CLJAtoms &other, int n)
 
         if (n_whole > 0)
         {
-            std::memcpy(&(_x[start_idx]), &(other._x[0]), n_whole * sizeof(MultiFloat));
-            std::memcpy(&(_y[start_idx]), &(other._y[0]), n_whole * sizeof(MultiFloat));
-            std::memcpy(&(_z[start_idx]), &(other._z[0]), n_whole * sizeof(MultiFloat));
-            std::memcpy(&(_q[start_idx]), &(other._q[0]), n_whole * sizeof(MultiFloat));
-            std::memcpy(&(_sig[start_idx]), &(other._sig[0]), n_whole * sizeof(MultiFloat));
-            std::memcpy(&(_eps[start_idx]), &(other._eps[0]), n_whole * sizeof(MultiFloat));
-            std::memcpy(&(_id[start_idx]), &(other._id[0]), n_whole * sizeof(MultiInt));
+            std::memcpy(static_cast<void *>(&(_x[start_idx])), &(other._x[0]), n_whole * sizeof(MultiFloat));
+            std::memcpy(static_cast<void *>(&(_y[start_idx])), &(other._y[0]), n_whole * sizeof(MultiFloat));
+            std::memcpy(static_cast<void *>(&(_z[start_idx])), &(other._z[0]), n_whole * sizeof(MultiFloat));
+            std::memcpy(static_cast<void *>(&(_q[start_idx])), &(other._q[0]), n_whole * sizeof(MultiFloat));
+            std::memcpy(static_cast<void *>(&(_sig[start_idx])), &(other._sig[0]), n_whole * sizeof(MultiFloat));
+            std::memcpy(static_cast<void *>(&(_eps[start_idx])), &(other._eps[0]), n_whole * sizeof(MultiFloat));
+            std::memcpy(static_cast<void *>(&(_id[start_idx])), &(other._id[0]), n_whole * sizeof(MultiInt));
         }
 
         if (n_partial > 0)
@@ -1888,13 +1888,13 @@ void CLJAtoms::copyIn(const CLJAtoms &other)
 
     const int nelements = other._x.count();
 
-    std::memcpy(_x.data(), other._x.constData(), nelements * sizeof(MultiFloat));
-    std::memcpy(_y.data(), other._y.constData(), nelements * sizeof(MultiFloat));
-    std::memcpy(_z.data(), other._z.constData(), nelements * sizeof(MultiFloat));
-    std::memcpy(_q.data(), other._q.constData(), nelements * sizeof(MultiFloat));
-    std::memcpy(_sig.data(), other._sig.constData(), nelements * sizeof(MultiFloat));
-    std::memcpy(_eps.data(), other._eps.constData(), nelements * sizeof(MultiFloat));
-    std::memcpy(_id.data(), other._id.constData(), nelements * sizeof(MultiInt));
+    std::memcpy(static_cast<void *>(_x.data()), other._x.constData(), nelements * sizeof(MultiFloat));
+    std::memcpy(static_cast<void *>(_y.data()), other._y.constData(), nelements * sizeof(MultiFloat));
+    std::memcpy(static_cast<void *>(_z.data()), other._z.constData(), nelements * sizeof(MultiFloat));
+    std::memcpy(static_cast<void *>(_q.data()), other._q.constData(), nelements * sizeof(MultiFloat));
+    std::memcpy(static_cast<void *>(_sig.data()), other._sig.constData(), nelements * sizeof(MultiFloat));
+    std::memcpy(static_cast<void *>(_eps.data()), other._eps.constData(), nelements * sizeof(MultiFloat));
+    std::memcpy(static_cast<void *>(_id.data()), other._id.constData(), nelements * sizeof(MultiInt));
 }
 
 /** Return a copy of these CLJAtoms where the charge and LJ epsilon parameters

corelib/src/libs/SireMM/cljboxes.cpp

@@ -116,7 +116,7 @@ void CLJBox::findGaps()
 
     const QVector<MultiInt> &ids = atms.ID();
 
-    const quint32 dummy_id = CLJAtoms::idOfDummy()[0];
+    const qint32 dummy_id = CLJAtoms::idOfDummy()[0];
 
     for (int i = ids.count() - 1; i >= 0; --i)
     {

corelib/src/libs/SireMM/cljworkspace.cpp

@@ -108,7 +108,7 @@ namespace SireMM
                 {
                     // loop over the old and new atoms
                     {
-                        const QVector<MultiInt> &ids = deltas.constData()[i].newAtoms().ID();
+                        const QVector<MultiInt> ids = deltas.constData()[i].newAtoms().ID();
 
                         for (int j = 0; j < ids.count(); ++j)
                         {
@@ -131,7 +131,7 @@ namespace SireMM
 
                     // loop over the old and new atoms
                     {
-                        const QVector<MultiInt> &ids = deltas.constData()[i].oldAtoms().ID();
+                        const QVector<MultiInt> ids = deltas.constData()[i].oldAtoms().ID();
 
                         for (int j = 0; j < ids.count(); ++j)
                         {
@@ -516,7 +516,7 @@ void CLJWorkspace::returnToMemoryPool()
     if (d.get() == 0)
         return;
 
-    if (not d.unique())
+    if (d.use_count() != 1)
     {
         d.reset();
         return;
@@ -541,7 +541,7 @@ void CLJWorkspace::createFromMemoryPool()
 {
     if (d.get() != 0)
     {
-        if (d.unique())
+        if (d.use_count() == 1)
         {
             d->clear();
             return;
@@ -694,7 +694,7 @@ void CLJWorkspace::detach()
 {
     if (d.get() != 0)
     {
-        if (not d.unique())
+        if (d.use_count() != 1)
         {
             std::shared_ptr<detail::CLJWorkspaceData> d2 = d;
             d.reset();

corelib/src/libs/SireMM/cmapfunctions.cpp

@@ -32,11 +32,11 @@
 
 #include "SireBase/console.h"
 
+#include "SireMol/atommapping.h"
 #include "SireMol/atommatcher.h"
 #include "SireMol/atomselection.h"
-#include "SireMol/moleculeinfodata.h"
 #include "SireMol/moleculedata.h"
-#include "SireMol/atommapping.h"
+#include "SireMol/moleculeinfodata.h"
 
 #include "SireError/errors.h"
 
@@ -365,7 +365,7 @@ void CMAPFunctions::set(AtomIdx atom0, AtomIdx atom1, AtomIdx atom2,
     quint32 atm3 = atom3.map(info().nAtoms());
     quint32 atm4 = atom4.map(info().nAtoms());
 
-    if (atm0 == atm1 or atm0 == atm2 or atm0 == atm3 or atm0 == atom4 or
+    if (atm0 == atm1 or atm0 == atm2 or atm0 == atm3 or atm0 == atm4 or
         atm1 == atm2 or atm1 == atm3 or atm1 == atm4 or
         atm2 == atm3 or atm2 == atm4 or atm3 == atm4)
         throw SireMol::duplicate_atom(QObject::tr("You cannot add a function that acts between the same atoms! "