Clean up code based on compiler warnings

scripts/build_ubuntu22_openmpi.sh

@@ -25,7 +25,7 @@ cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_DIR} \
       -DMPIEXEC_PREFLAGS="--oversubscribe" \
       -DMGMOL_WITH_CLANG_FORMAT=ON \
       -DCMAKE_PREFIX_PATH=${HOME}/bin \
-      -D CMAKE_CXX_FLAGS="-Wall -pedantic -Wextra" \
+      -D CMAKE_CXX_FLAGS="-Wall -pedantic -Wextra -Wno-cast-function-type" \
       ..
 
 # call make install

src/Control.cc

@@ -31,23 +31,6 @@ float Control::total_spin_     = 0.;
 std::string Control::run_directory_(".");
 bool Control::with_spin_ = false;
 
-static void finishRead(std::ifstream& tfile)
-{
-    // while( tfile.get()!='\n');
-    // string str;
-    // getline(tfile,str);
-    char str[256];
-    tfile.getline(str, 256);
-
-    char cc = (char)tfile.peek();
-    while (cc == ('#') || (cc == '\n') || cc == ' ')
-    {
-        while (tfile.get() != '\n')
-            ;
-        cc = (char)tfile.peek(); // look at next character
-    }
-}
-
 Control::Control()
 {
     assert(comm_global_ != MPI_COMM_NULL);

src/DistributedIonicData.cc

@@ -12,7 +12,6 @@
 #include "tools.h"
 
 #include <string.h>
-using namespace std;
 
 DistributedIonicData::DistributedIonicData(
     const std::vector<std::string>& local_names,
@@ -31,16 +30,16 @@ DistributedIonicData::DistributedIonicData(
 
 int DistributedIonicData::pack(char* cbuff, double* dbuff)
 {
-    vector<double>::iterator itf = data_.begin();
-    double* dptr                 = dbuff;
+    std::vector<double>::iterator itf = data_.begin();
+    double* dptr                      = dbuff;
 
     int idx = 0;
-    for (vector<std::string>::iterator it = ion_names_.begin();
+    for (std::vector<std::string>::iterator it = ion_names_.begin();
          it != ion_names_.end(); ++it)
     {
-        string s(*it);
+        std::string s(*it);
         FixedLengthString t;
-        strncpy(t.mystring, s.c_str(), IonData_MaxStrLength);
+        strncpy(t.mystring, s.c_str(), IonData_MaxStrLength - 1);
         memcpy(&cbuff[idx], t.mystring, IonData_MaxStrLength);
         idx += IonData_MaxStrLength;
 
@@ -58,7 +57,7 @@ void DistributedIonicData::unpack(char*& cptr, double*& dptr, const short ndata)
     for (short i = 0; i < ndata; i++)
     {
         // get name
-        string name(cptr, IonData_MaxStrLength);
+        std::string name(cptr, IonData_MaxStrLength);
         stripLeadingAndTrailingBlanks(name);
         ion_names_.push_back(name);
         cptr += IonData_MaxStrLength;

src/HDFrestart.cc

@@ -428,7 +428,7 @@ void HDFrestart::addReleaseNumber2File(const char* release)
         // if( onpe0 )
         {
             HDF_FixedLengthString t;
-            strncpy(t.mystring, release, MyHDFStrLength);
+            strncpy(t.mystring, release, MyHDFStrLength - 1);
             herr_t status = H5Awrite(attribute_id, strtype, &t);
             if (status < 0)
             {

src/HamiltonianMVP_DMStrategy.cc

@@ -57,7 +57,7 @@ HamiltonianMVP_DMStrategy<MatrixType, ProjMatrixType,
 
 template <class MatrixType, class ProjMatrixType, class OrbitalsType>
 void HamiltonianMVP_DMStrategy<MatrixType, ProjMatrixType,
-    OrbitalsType>::initialize(OrbitalsType& orbitals)
+    OrbitalsType>::initialize(OrbitalsType&)
 {
 }
 

src/IonData.cc

@@ -10,12 +10,11 @@
 #include "IonData.h"
 #include "tools.h"
 #include <string.h>
-using namespace std;
 
 void IonData::unpack(char*& cptr, int*& iptr, double*& dptr)
 {
     // get name
-    string name(cptr, IonData_MaxStrLength);
+    std::string name(cptr, IonData_MaxStrLength);
     stripLeadingAndTrailingBlanks(name);
     ion_name = name;
     cptr += IonData_MaxStrLength;
@@ -52,25 +51,25 @@ void IonData::unpack(char*& cptr, int*& iptr, double*& dptr)
 
 // pack Ions data for communication
 void IonData::packIonData(
-    char* cbuff, int* ibuff, double* dbuff, vector<IonData>& data)
+    char* cbuff, int* ibuff, double* dbuff, std::vector<IonData>& data)
 {
     // pack ion_names buffer
     int idx = 0;
-    for (vector<IonData>::iterator idata = data.begin(); idata != data.end();
-         ++idata)
+    for (std::vector<IonData>::iterator idata = data.begin();
+         idata != data.end(); ++idata)
     {
-        string s = (*idata).ion_name;
+        std::string s = (*idata).ion_name;
         FixedLengthString t;
-        strncpy(t.mystring, s.c_str(), IonData_MaxStrLength);
+        strncpy(t.mystring, s.c_str(), IonData_MaxStrLength - 1);
         memcpy(&cbuff[idx], t.mystring, IonData_MaxStrLength);
         idx += IonData_MaxStrLength;
     }
 
     // pack integer datatypes
     int* iptr = &ibuff[0];
     // first pack local data size
-    *(iptr++)                       = data.size();
-    vector<IonData>::iterator idata = data.begin();
+    *(iptr++)                            = data.size();
+    std::vector<IonData>::iterator idata = data.begin();
     while (idata != data.end())
     {
         // pack atomic_num

src/Ions.cc

@@ -1608,7 +1608,6 @@ int Ions::readAtomsFromXYZ(
     const std::string& filename, const bool cell_relative)
 {
     MGmol_MPI& mmpi(*(MGmol_MPI::instance()));
-    Control& ct(*(Control::instance()));
 
     // set up list boundaries
     // get radius of projectors
@@ -1698,9 +1697,6 @@ int Ions::readAtomsFromXYZ(
 int Ions::setAtoms(
     const std::vector<double>& crds, const std::vector<short>& spec)
 {
-    MGmol_MPI& mmpi(*(MGmol_MPI::instance()));
-    Control& ct(*(Control::instance()));
-
     const int natoms = crds.size() / 3;
 
     double velocity[3] = { 0., 0., 0. };
@@ -1748,8 +1744,6 @@ int Ions::setAtoms(
 
         addIonToList(species_[isp], aname, &crds[3 * ia], velocity, locked);
     }
-    //    std::cout<<mmpi.mype()<<"...list size = "<<list_ions_.size()<<" local
-    //    ions size = "<<local_ions_.size()<<endl;
 
     return natoms;
 }

src/MGmol.cc

@@ -1499,6 +1499,8 @@ double MGmol<OrbitalsType>::evaluateDMandEnergyAndForces(Orbitals* orbitals,
 
     force(*dorbitals, *ions_);
 
+    ions_->getForces(forces);
+
     return eks;
 }
 

src/MVP_DMStrategy.h

@@ -48,7 +48,7 @@ class MVP_DMStrategy : public DMStrategy<OrbitalsType>
         const std::vector<std::vector<int>>& overlappingGids,
         ProjectedMatricesInterface* proj_matrices, const bool use_old_dm);
 
-    void initialize(OrbitalsType& orbitals) override{};
+    void initialize(OrbitalsType&) override{};
     int update(OrbitalsType& orbitals) override;
 
     // H is updated with MVP loop, so no need to compute it outside

src/Potentials.cc

@@ -37,9 +37,8 @@ Potentials::~Potentials()
 #endif
 }
 
-Potentials::Potentials(const bool vh_frozen)
+Potentials::Potentials()
 {
-    //(*MPIdata::sout)<<"Potentials::setup()"<<endl;
     diel_            = false; // default: no dielectric
     itindex_vxc_     = -1;
     itindex_vh_      = -1;

src/Potentials.h

@@ -96,7 +96,7 @@ class Potentials
         const Vector3D& position, const Species& sp);
 
 public:
-    Potentials(const bool vh_frozen = false);
+    Potentials();
 
     ~Potentials();
 

src/hdf_tools.cc

@@ -22,6 +22,18 @@
 
 namespace mgmol_tools
 {
+void string2fixedlength(
+    std::vector<std::string>& data, std::vector<FixedLengthString>& tc)
+{
+    tc.clear();
+    for (auto& d : data)
+    {
+        FixedLengthString t;
+        strncpy(t.mystring, d.c_str(), IonData_MaxStrLength - 1);
+        tc.push_back(t);
+    }
+}
+
 void write1d(hid_t file_id, const std::string& datasetname,
     std::vector<int>& data, size_t length)
 {
@@ -235,14 +247,7 @@ void write2d(hid_t file_id, const std::string& datasetname,
 
     // First copy the contents of the vector into a temporary container
     std::vector<FixedLengthString> tc;
-    for (std::vector<std::string>::const_iterator i   = data.begin(),
-                                                  end = data.end();
-         i != end; ++i)
-    {
-        FixedLengthString t;
-        strncpy(t.mystring, i->c_str(), IonData_MaxStrLength);
-        tc.push_back(t);
-    }
+    string2fixedlength(data, tc);
 
     std::string attname("String_Length");
     hsize_t dimsA[1]    = { 1 };
@@ -583,14 +588,7 @@ void parallelWrite2d(hid_t file_id, const std::string& datasetname,
 
     // First copy the contents of the vector into a temporary container
     std::vector<FixedLengthString> tc;
-    for (std::vector<std::string>::const_iterator i   = data.begin(),
-                                                  end = data.end();
-         i != end; ++i)
-    {
-        FixedLengthString t;
-        strncpy(t.mystring, i->c_str(), IonData_MaxStrLength);
-        tc.push_back(t);
-    }
+    string2fixedlength(data, tc);
     status = H5Dwrite(dset_id, strtype, memspace, filespace, plist_id, &tc[0]);
     if (status < 0)
     {

src/mgmol_run.cc

@@ -91,7 +91,6 @@ int mgmol_check()
     Control& ct              = *(Control::instance());
     Mesh* mymesh             = Mesh::instance();
     const pb::PEenv& myPEenv = mymesh->peenv();
-    MGmol_MPI& mmpi          = *(MGmol_MPI::instance());
 
     if (myPEenv.color() > 0)
     {

tests/testSetGhostValues.cc

@@ -18,8 +18,6 @@ TEST_CASE("Set ghost values", "[set ghosts")
     const double ll         = 1.;
     const double lattice[3] = { ll, ll, ll };
 
-    const int nfunc = 10;
-
     MGmol_MPI::setup(MPI_COMM_WORLD, std::cout);
 
     MGmol_MPI& mmpi = *(MGmol_MPI::instance());
@@ -101,8 +99,6 @@ TEST_CASE("Set ghost values", "[set ghosts")
             gf.assign(inner_data.data(), 'd');
             gf.set_updated_boundaries(false);
 
-            double norm_before = gf.norm2();
-
             // fill ghost values
             const bool direction[3] = { true, true, true };
             gf.defaultTrade_boundaries();