Fix build with HDF5P on

CMakeLists.txt

@@ -62,7 +62,6 @@ else() #search for HDF5
   if(MGMOL_USE_HDF5P)
     message(STATUS "Use HDF5 parallel capability")
     set(HDF5_PREFER_PARALLEL True)
-    add_definitions(-DMGMOL_USE_HDF5P)
   endif()
   message(STATUS "HDF5_ROOT: ${HDF5_ROOT}")
   find_package(HDF5 REQUIRED COMPONENTS C HL)
@@ -73,6 +72,10 @@ else() #search for HDF5
     message(FATAL_ERROR "Required HDF5 package not found.")
   endif (${HDF5_FOUND})
 endif()
+if(MGMOL_USE_HDF5P)
+  add_definitions(-DMGMOL_USE_HDF5P)
+endif()
+
 
 set(MGMOL_WITH_LIBXC FALSE CACHE BOOL "Compile with LIBXC")
 if(${MGMOL_WITH_LIBXC})

scripts/build_condo-mod.sh

@@ -21,6 +21,7 @@ cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_DIR} \
       -DCMAKE_CXX_COMPILER=mpiCC \
       -DCMAKE_Fortran_COMPILER=mpif77 \
       -DBLA_VENDOR=${BLAS_VENDOR} \
+      -DMGMOL_USE_HDF5P=OFF \
       -DMGMOL_WITH_CLANG_FORMAT=ON \
       -DCMAKE_PREFIX_PATH=${HOME}/bin \
       -DSCALAPACK_LIBRARY="${SCALAPACK_DIR}/lib/libscalapack.a;/lib64/libgfortran.so.3" \

src/Ions.cc

@@ -47,9 +47,10 @@ double Ions::max_Vl_radius_  = -1.;
 double Ions::max_Vnl_radius_ = -1.;
 
 template <typename T>
-void writeData2d(hid_t file_id, std::string datasetname, std::vector<T>& data,
-    const int n, T element)
+void writeData2d(HDFrestart& h5f_file, std::string datasetname,
+    std::vector<T>& data, const size_t n, T element)
 {
+    hid_t file_id = h5f_file.file_id();
 #ifdef MGMOL_USE_HDF5P
     if (h5f_file.useHdf5p())
     {
@@ -67,7 +68,7 @@ void writeData2d(hid_t file_id, std::string datasetname, std::vector<T>& data,
     else
 #endif
     {
-        size_t dims[2] = { data.size()/n, n };
+        size_t dims[2] = { data.size() / n, n };
         mgmol_tools::write2d(file_id, datasetname, data, dims);
     }
 }
@@ -753,7 +754,7 @@ void Ions::writeAtomicNumbers(HDFrestart& h5f_file)
     if (file_id >= 0)
     {
         std::string datasetname("/Atomic_numbers");
-        writeData2d(file_id, datasetname, data, 1, -1);
+        writeData2d(h5f_file, datasetname, data, 1, -1);
     }
 }
 
@@ -788,12 +789,11 @@ void Ions::writeAtomNames(HDFrestart& h5f_file)
 
     // write data
     hid_t file_id = h5f_file.file_id();
-
     if (file_id >= 0)
     {
         std::string datasetname("/Atomic_names");
         std::string empty;
-        writeData2d(file_id, datasetname, data, 1, empty);
+        writeData2d(h5f_file, datasetname, data, 1, empty);
     }
 }
 
@@ -864,7 +864,7 @@ void Ions::writeLockedAtomNames(HDFrestart& h5f_file)
     {
         std::string datasetname("/LockedAtomsNames");
         std::string empty;
-        writeData2d(file_id, datasetname, data, 1, empty);
+        writeData2d(h5f_file, datasetname, data, 1, empty);
     }
 }
 
@@ -900,7 +900,7 @@ void Ions::writeAtomicIDs(HDFrestart& h5f_file)
     if (file_id >= 0)
     {
         std::string datasetname("/Atomic_IDs");
-        writeData2d(file_id, datasetname, data, 1, -1);
+        writeData2d(h5f_file, datasetname, data, 1, -1);
     }
 }
 
@@ -937,7 +937,7 @@ void Ions::writeAtomicNLprojIDs(HDFrestart& h5f_file)
     if (file_id >= 0)
     {
         std::string datasetname("/AtomicNLproj_IDs");
-        writeData2d(file_id, datasetname, data, 1, -1);
+        writeData2d(h5f_file, datasetname, data, 1, -1);
     }
 }
 
@@ -975,7 +975,7 @@ void Ions::writePositions(HDFrestart& h5f_file)
     if (file_id >= 0)
     {
         std::string datasetname("/Ionic_positions");
-        writeData2d(file_id, datasetname, data, 3, 1.e32);
+        writeData2d(h5f_file, datasetname, data, 3, 1.e32);
     }
 }
 
@@ -1138,7 +1138,7 @@ void Ions::writeVelocities(HDFrestart& h5f_file)
     if (file_id >= 0)
     {
         std::string datasetname("/Ionic_velocities");
-        writeData2d(file_id, datasetname, data, 3, 1.e32);
+        writeData2d(h5f_file, datasetname, data, 3, 1.e32);
     }
 }
 
@@ -1184,7 +1184,7 @@ void Ions::writeRandomStates(HDFrestart& h5f_file)
     if (file_id >= 0)
     {
         std::string datasetname("/Ionic_RandomStates");
-        writeData2d(file_id, datasetname, data, 3, (unsigned short)0);
+        writeData2d(h5f_file, datasetname, data, 3, (unsigned short)0);
     }
 }
 
@@ -1343,7 +1343,7 @@ void Ions::writeForces(HDFrestart& h5f_file)
     if (file_id >= 0)
     {
         std::string datasetname("/Ionic_forces");
-        writeData2d(file_id, datasetname, data, 3, 1.e32);
+        writeData2d(h5f_file, datasetname, data, 3, 1.e32);
     }
 }