Fix various bugs in HDF5 interface / MGXS code (found by valgrind)

include/openmc/hdf5_interface.h

@@ -193,13 +193,13 @@ read_attribute(hid_t obj_id, const char* name, std::vector<std::string>& vec)
 
   // Allocate a C char array to get strings
   auto n = attribute_typesize(obj_id, name);
-  char buffer[m][n+1];
+  char buffer[m][n];
 
   // Read char data in attribute
   read_attr_string(obj_id, name, n, buffer[0]);
 
   for (int i = 0; i < m; ++i) {
-    vec.emplace_back(&buffer[i][0]);
+    vec.emplace_back(&buffer[i][0], n);
   }
 }
 

src/hdf5_interface.cpp

@@ -392,7 +392,7 @@ object_name(hid_t obj_id)
 
   // Read and return name
   H5Iget_name(obj_id, buffer, size);
-  return {buffer, size};
+  return buffer;
 }
 
 
@@ -439,7 +439,9 @@ read_attr_string(hid_t obj_id, const char* name, size_t slen, char* buffer)
 {
   // Create datatype for a string
   hid_t datatype = H5Tcopy(H5T_C_S1);
-  H5Tset_size(datatype, slen + 1);
+  H5Tset_size(datatype, slen);
+  // numpy uses null-padding when writing fixed-length strings
+  H5Tset_strpad(datatype, H5T_STR_NULLPAD);
 
   // Read data into buffer
   read_attr(obj_id, name, datatype, buffer);
@@ -503,7 +505,9 @@ read_string(hid_t obj_id, const char* name, size_t slen, char* buffer, bool inde
 {
   // Create datatype for a string
   hid_t datatype = H5Tcopy(H5T_C_S1);
-  H5Tset_size(datatype, slen + 1);
+  H5Tset_size(datatype, slen);
+  // numpy uses null-padding when writing fixed-length strings
+  H5Tset_strpad(datatype, H5T_STR_NULLPAD);
 
   // Read data into buffer
   read_dataset(obj_id, name, datatype, buffer, indep);

src/mgxs_interface.cpp

@@ -208,7 +208,7 @@ void
 get_name_c(int index, int name_len, char* name)
 {
   // First blank out our input string
-  std::string str(name_len, ' ');
+  std::string str(name_len - 1, ' ');
   std::strcpy(name, str.c_str());
 
   // Now get the data and copy to the C-string