Merge branch 'bugfix/kraichnan_checkpointing' into develop

cpp/full_code/kraichnan_field.cpp

@@ -104,26 +104,17 @@ int kraichnan_field<rnumber>::initialize(void)
     DEBUG_MSG("Coefficient: %g\n",
             this->spectrum_coefficient);
 
+    this->generate_random_velocity();
     // is this the first iteration?
     if ((this->iteration == 0) and (this->output_velocity == 1))
     {
         // if yes, generate random field and save it
-        this->generate_random_velocity();
         this->velocity->io(
                 this->get_current_fname(),
                 "velocity",
                 this->iteration,
                 false);
     }
-    else
-    {
-        // if not, read the random field that exists in the checkpoint file
-        this->velocity->io(
-                this->get_current_fname(),
-                "velocity",
-                this->iteration,
-                true);
-    }
 
     return EXIT_SUCCESS;
 }
@@ -336,14 +327,23 @@ void kraichnan_field<rnumber>::update_checkpoint()
             hsize_t fields_stored;
             hid_t fid, group_id;
             fid = H5Fopen(fname.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
-            group_id = H5Gopen(fid, "velocity/real", H5P_DEFAULT);
-            H5Gget_num_objs(
+            group_id = H5Gopen(fid, "tracers0/state", H5P_DEFAULT);
+            bool dset_exists;
+            if (group_id > 0)
+            {
+                H5Gget_num_objs(
                     group_id,
                     &fields_stored);
-            bool dset_exists = H5Lexists(
+                dset_exists = H5Lexists(
                     group_id,
                     std::to_string(this->iteration).c_str(),
                     H5P_DEFAULT);
+            }
+            else
+            {
+                fields_stored = 0;
+                dset_exists = false;
+            }
             H5Gclose(group_id);
             H5Fclose(fid);
             if ((int(fields_stored) >= this->checkpoints_per_file) &&
@@ -360,13 +360,13 @@ void kraichnan_field<rnumber>::update_checkpoint()
                     H5P_DEFAULT);
             hid_t gg = H5Gcreate(
                     fid,
-                    "velocity",
+                    "tracers0",
                     H5P_DEFAULT,
                     H5P_DEFAULT,
                     H5P_DEFAULT);
             hid_t ggg = H5Gcreate(
                     gg,
-                    "real",
+                    "state",
                     H5P_DEFAULT,
                     H5P_DEFAULT,
                     H5P_DEFAULT);

cpp/particles/particles_output_hdf5.hpp

@@ -29,6 +29,7 @@
 #include <memory>
 #include <vector>
 #include <hdf5.h>
+#include <sys/stat.h>
 
 #include "abstract_particles_output.hpp"
 #include "scope_timer.hpp"
@@ -140,10 +141,23 @@ public:
         if(Parent::isInvolved()){
             if (Parent::getMyRank() == 0)
             {
-                hid_t file_id = H5Fopen(
+                bool file_exists = false;
+                {
+                    struct stat file_buffer;
+                    file_exists = (stat(filename.c_str(), &file_buffer) == 0);
+                }
+                hid_t file_id;
+                if (file_exists)
+                    file_id = H5Fopen(
                         filename.c_str(),
                         H5F_ACC_RDWR | H5F_ACC_DEBUG,
                         H5P_DEFAULT);
+                else
+                    file_id = H5Fcreate(
+                        filename.c_str(),
+                        H5F_ACC_EXCL | H5F_ACC_DEBUG,
+                        H5P_DEFAULT,
+                        H5P_DEFAULT);
                 assert(file_id >= 0);
                 bool group_exists = H5Lexists(
                         file_id,