From d2efb67a9d7b102f6d7b65343da35ba3b81b71e5 Mon Sep 17 00:00:00 2001
From: q-posev <posenitskiy@irsamc.ups-tlse.fr>
Date: Wed, 3 Mar 2021 15:59:30 +0100
Subject: [PATCH 1/8] stupid but working implementation of read/write_dset
 decoupled from read_group

---
 src/trexio_hdf5.c   | 80 ++++++++++++++++++++++++++++++++++++++++++---
 src/trexio_hdf5.org | 80 ++++++++++++++++++++++++++++++++++++++++++---
 2 files changed, 150 insertions(+), 10 deletions(-)

diff --git a/src/trexio_hdf5.c b/src/trexio_hdf5.c
index d99d341..dec5604 100644
--- a/src/trexio_hdf5.c
+++ b/src/trexio_hdf5.c
@@ -411,10 +411,28 @@ trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* co
   assert (file != NULL);
   assert (coord != NULL);
 
-  h5nucleus_t* nucleus = trexio_hdf5_read_nucleus((trexio_hdf5_t*) file);
-
+  /*h5nucleus_t* nucleus = trexio_hdf5_read_nucleus((trexio_hdf5_t*) file);
   if (nucleus == NULL) return TREXIO_FAILURE;
+  assert (nucleus->coord != NULL);*/
+
+  /* Allocate and read nucleus_coord array */
+  h5nucleus_t* nucleus = (h5nucleus_t*) malloc(sizeof(h5nucleus_t));
+  assert (nucleus != NULL);
+
+  trexio_exit_code rc = trexio_hdf5_read_nucleus_num(file, &(nucleus->num));
+  assert (rc == TREXIO_SUCCESS);
+  assert (nucleus->num > 0L);
+
+  nucleus->coord = (double*) calloc(3 * nucleus->num, sizeof(double));
   assert (nucleus->coord != NULL);
+ 
+  trexio_hdf5_t* f = (trexio_hdf5_t*) file; 
+  herr_t status;
+  /* High-level H5LT API. No need to deal with dataspaces and datatypes */
+  status = H5LTread_dataset_double(f->nucleus_group, 
+                                    NUCLEUS_COORD_NAME, 
+				    nucleus->coord);
+  assert (status >= 0);
   
   for (size_t i=0 ; i<3*nucleus->num ; i++) {
     coord[i] = nucleus->coord[i];
@@ -430,17 +448,69 @@ trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const dou
   assert (file != NULL);
   assert (coord != NULL);
   
-  h5nucleus_t* nucleus = trexio_hdf5_read_nucleus((trexio_hdf5_t*) file);
-
+  /*h5nucleus_t* nucleus = trexio_hdf5_read_nucleus((trexio_hdf5_t*) file);
   if (nucleus == NULL) return TREXIO_FAILURE;
-  assert (nucleus->coord != NULL); 
+  assert (nucleus->coord != NULL);
  
   for (size_t i=0 ; i<3*nucleus->num ; i++) {
     nucleus->coord[i] = coord[i];
   }
   
   trexio_exit_code rc = trexio_hdf5_write_nucleus((trexio_hdf5_t*) file, nucleus);
+  assert (rc == TREXIO_SUCCESS);*/
+  
+  h5nucleus_t* nucleus = (h5nucleus_t*) malloc(sizeof(h5nucleus_t));
+  assert (nucleus != NULL);
+
+  trexio_exit_code rc = trexio_hdf5_read_nucleus_num(file, &(nucleus->num));
   assert (rc == TREXIO_SUCCESS);
+  assert (nucleus->num > 0L);
+
+  nucleus->coord = (double*) calloc(3 * nucleus->num, sizeof(double));
+  assert (nucleus->coord != NULL);
+
+  for (size_t i=0 ; i<3*nucleus->num ; i++) {
+    nucleus->coord[i] = coord[i];
+  }
+
+  trexio_hdf5_t* f = (trexio_hdf5_t*) file; 
+
+  hid_t dset_id, dspace, dtype;
+  herr_t status;
+  int coord_rank = 2;
+  const hsize_t coord_dims[2] = {nucleus->num, 3};
+  if ( H5LTfind_dataset(f->nucleus_group, NUCLEUS_COORD_NAME) != 1) { 
+    
+    status = H5LTmake_dataset_double (f->nucleus_group, NUCLEUS_COORD_NAME, 
+                                    coord_rank, coord_dims, nucleus->coord);
+    assert (status >= 0);
+
+  } else {   
+
+    dset_id = H5Dopen(f->nucleus_group, NUCLEUS_COORD_NAME, H5P_DEFAULT);
+    assert (dset_id > 0);
+    dspace = H5Dget_space(dset_id);
+    assert (dspace > 0);
+    dtype = H5Dget_type(dset_id);
+    assert (dtype > 0);
+    
+    int rrank;
+    hsize_t dims[2] = {0, 0};
+    rrank = H5Sget_simple_extent_dims(dspace,
+                                    dims, NULL);
+    assert (rrank == coord_rank);
+    for (int i=0; i<rrank; i++){
+      assert (dims[i] == coord_dims[i]);
+    }
+
+    status = H5Dwrite(dset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, nucleus->coord);
+    assert (status >= 0);
+
+    H5Sclose(dspace);
+    H5Tclose(dtype);
+    H5Dclose(dset_id);
+
+  }
 
   trexio_hdf5_free_nucleus(nucleus);
   
diff --git a/src/trexio_hdf5.org b/src/trexio_hdf5.org
index 97d2b91..a1d979a 100644
--- a/src/trexio_hdf5.org
+++ b/src/trexio_hdf5.org
@@ -574,10 +574,28 @@ trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* co
   assert (file != NULL);
   assert (coord != NULL);
 
-  h5nucleus_t* nucleus = trexio_hdf5_read_nucleus((trexio_hdf5_t*) file);
-
+  /*h5nucleus_t* nucleus = trexio_hdf5_read_nucleus((trexio_hdf5_t*) file);
   if (nucleus == NULL) return TREXIO_FAILURE;
+  assert (nucleus->coord != NULL);*/
+
+  /* Allocate and read nucleus_coord array */
+  h5nucleus_t* nucleus = (h5nucleus_t*) malloc(sizeof(h5nucleus_t));
+  assert (nucleus != NULL);
+
+  trexio_exit_code rc = trexio_hdf5_read_nucleus_num(file, &(nucleus->num));
+  assert (rc == TREXIO_SUCCESS);
+  assert (nucleus->num > 0L);
+
+  nucleus->coord = (double*) calloc(3 * nucleus->num, sizeof(double));
   assert (nucleus->coord != NULL);
+ 
+  trexio_hdf5_t* f = (trexio_hdf5_t*) file; 
+  herr_t status;
+  /* High-level H5LT API. No need to deal with dataspaces and datatypes */
+  status = H5LTread_dataset_double(f->nucleus_group, 
+                                    NUCLEUS_COORD_NAME, 
+				    nucleus->coord);
+  assert (status >= 0);
   
   for (size_t i=0 ; i<3*nucleus->num ; i++) {
     coord[i] = nucleus->coord[i];
@@ -593,17 +611,69 @@ trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const dou
   assert (file != NULL);
   assert (coord != NULL);
   
-  h5nucleus_t* nucleus = trexio_hdf5_read_nucleus((trexio_hdf5_t*) file);
-
+  /*h5nucleus_t* nucleus = trexio_hdf5_read_nucleus((trexio_hdf5_t*) file);
   if (nucleus == NULL) return TREXIO_FAILURE;
-  assert (nucleus->coord != NULL); 
+  assert (nucleus->coord != NULL);
  
   for (size_t i=0 ; i<3*nucleus->num ; i++) {
     nucleus->coord[i] = coord[i];
   }
   
   trexio_exit_code rc = trexio_hdf5_write_nucleus((trexio_hdf5_t*) file, nucleus);
+  assert (rc == TREXIO_SUCCESS);*/
+  
+  h5nucleus_t* nucleus = (h5nucleus_t*) malloc(sizeof(h5nucleus_t));
+  assert (nucleus != NULL);
+
+  trexio_exit_code rc = trexio_hdf5_read_nucleus_num(file, &(nucleus->num));
   assert (rc == TREXIO_SUCCESS);
+  assert (nucleus->num > 0L);
+
+  nucleus->coord = (double*) calloc(3 * nucleus->num, sizeof(double));
+  assert (nucleus->coord != NULL);
+
+  for (size_t i=0 ; i<3*nucleus->num ; i++) {
+    nucleus->coord[i] = coord[i];
+  }
+
+  trexio_hdf5_t* f = (trexio_hdf5_t*) file; 
+
+  hid_t dset_id, dspace, dtype;
+  herr_t status;
+  int coord_rank = 2;
+  const hsize_t coord_dims[2] = {nucleus->num, 3};
+  if ( H5LTfind_dataset(f->nucleus_group, NUCLEUS_COORD_NAME) != 1) { 
+    
+    status = H5LTmake_dataset_double (f->nucleus_group, NUCLEUS_COORD_NAME, 
+                                    coord_rank, coord_dims, nucleus->coord);
+    assert (status >= 0);
+
+  } else {   
+
+    dset_id = H5Dopen(f->nucleus_group, NUCLEUS_COORD_NAME, H5P_DEFAULT);
+    assert (dset_id > 0);
+    dspace = H5Dget_space(dset_id);
+    assert (dspace > 0);
+    dtype = H5Dget_type(dset_id);
+    assert (dtype > 0);
+    
+    int rrank;
+    hsize_t dims[2] = {0, 0};
+    rrank = H5Sget_simple_extent_dims(dspace,
+                                    dims, NULL);
+    assert (rrank == coord_rank);
+    for (int i=0; i<rrank; i++){
+      assert (dims[i] == coord_dims[i]);
+    }
+
+    status = H5Dwrite(dset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, nucleus->coord);
+    assert (status >= 0);
+
+    H5Sclose(dspace);
+    H5Tclose(dtype);
+    H5Dclose(dset_id);
+
+  }
 
   trexio_hdf5_free_nucleus(nucleus);
   

From 88d280820067d5983b8039a2c2c987d2e3d0d7cc Mon Sep 17 00:00:00 2001
From: q-posev <posenitskiy@irsamc.ups-tlse.fr>
Date: Thu, 4 Mar 2021 14:00:56 +0100
Subject: [PATCH 2/8] missing mode in rdm

---
 src/trexio_text.c   | 2 +-
 src/trexio_text.org | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/trexio_text.c b/src/trexio_text.c
index 5b795f0..b27eef5 100644
--- a/src/trexio_text.c
+++ b/src/trexio_text.c
@@ -438,7 +438,7 @@ rdm_t* trexio_text_read_rdm(trexio_text_t* file) {
   if (file->parent.mode == 'w') {
     rdm->file = fopen(file_name,"a");  
   } else {
-    rdm->file = fopen(file_name,"");  
+    rdm->file = fopen(file_name,"r");  
   }
   free(file_name);
   file->rdm = rdm ;
diff --git a/src/trexio_text.org b/src/trexio_text.org
index 208cd5e..3a91064 100644
--- a/src/trexio_text.org
+++ b/src/trexio_text.org
@@ -99,6 +99,7 @@ typedef struct trexio_text_s {
 
     #+end_src
 
+*** Init/deinit functions
 
     #+begin_src c :tangle trexio_text.h
 trexio_exit_code trexio_text_init(trexio_t* file);
@@ -611,7 +612,7 @@ rdm_t* trexio_text_read_rdm(trexio_text_t* file) {
   if (file->parent.mode == 'w') {
     rdm->file = fopen(file_name,"a");  
   } else {
-    rdm->file = fopen(file_name,"");  
+    rdm->file = fopen(file_name,"r");  
   }
   free(file_name);
   file->rdm = rdm ;

From aee737fa23753c8ef928ec6bc28ef31d287176e3 Mon Sep 17 00:00:00 2001
From: q-posev <posenitskiy@irsamc.ups-tlse.fr>
Date: Thu, 4 Mar 2021 14:03:34 +0100
Subject: [PATCH 3/8] provide dimensions and decouple dataset read/write from
 parent group

---
 src/trexio.c        |  10 +++-
 src/trexio.org      |  10 +++-
 src/trexio_hdf5.c   | 111 +++++++++++++++---------------------------
 src/trexio_hdf5.h   |   4 +-
 src/trexio_hdf5.org | 115 ++++++++++++++++----------------------------
 5 files changed, 100 insertions(+), 150 deletions(-)

diff --git a/src/trexio.c b/src/trexio.c
index 627f8e6..afe98d1 100644
--- a/src/trexio.c
+++ b/src/trexio.c
@@ -183,6 +183,9 @@ trexio_exit_code trexio_read_nucleus_coord(trexio_t* file, double* coord) {
   int64_t dim_coord = nucleus_num*3;
   if (dim_coord < 0) return TREXIO_FAILURE;
 
+  int rank = 2;
+  uint64_t dims[2] = {nucleus_num, 3}; 
+
   switch (file->back_end) {
 
   case TREXIO_TEXT:
@@ -190,7 +193,7 @@ trexio_exit_code trexio_read_nucleus_coord(trexio_t* file, double* coord) {
     break;
 
   case TREXIO_HDF5:
-    return trexio_hdf5_read_nucleus_coord(file, coord);
+    return trexio_hdf5_read_nucleus_coord(file, coord, rank, dims);
     break;
 /*
   case TREXIO_JSON:
@@ -213,6 +216,9 @@ trexio_exit_code trexio_write_nucleus_coord(trexio_t* file, const double* coord)
   int64_t dim_coord = nucleus_num*3;
   if (dim_coord < 0) return TREXIO_FAILURE;
 
+  int rank = 2;
+  uint64_t dims[2] = {nucleus_num, 3};
+ 
   switch (file->back_end) {
 
   case TREXIO_TEXT:
@@ -220,7 +226,7 @@ trexio_exit_code trexio_write_nucleus_coord(trexio_t* file, const double* coord)
     break;
 
   case TREXIO_HDF5:
-    return trexio_hdf5_write_nucleus_coord(file, coord);
+    return trexio_hdf5_write_nucleus_coord(file, coord, rank, dims);
     break;
 /*
   case TREXIO_JSON:
diff --git a/src/trexio.org b/src/trexio.org
index 050df1c..c0e35fb 100644
--- a/src/trexio.org
+++ b/src/trexio.org
@@ -345,6 +345,9 @@ trexio_exit_code trexio_read_nucleus_coord(trexio_t* file, double* coord) {
   int64_t dim_coord = nucleus_num*3;
   if (dim_coord < 0) return TREXIO_FAILURE;
 
+  int rank = 2;
+  uint64_t dims[2] = {nucleus_num, 3}; 
+
   switch (file->back_end) {
 
   case TREXIO_TEXT:
@@ -352,7 +355,7 @@ trexio_exit_code trexio_read_nucleus_coord(trexio_t* file, double* coord) {
     break;
 
   case TREXIO_HDF5:
-    return trexio_hdf5_read_nucleus_coord(file, coord);
+    return trexio_hdf5_read_nucleus_coord(file, coord, rank, dims);
     break;
 /*
   case TREXIO_JSON:
@@ -375,6 +378,9 @@ trexio_exit_code trexio_write_nucleus_coord(trexio_t* file, const double* coord)
   int64_t dim_coord = nucleus_num*3;
   if (dim_coord < 0) return TREXIO_FAILURE;
 
+  int rank = 2;
+  uint64_t dims[2] = {nucleus_num, 3};
+ 
   switch (file->back_end) {
 
   case TREXIO_TEXT:
@@ -382,7 +388,7 @@ trexio_exit_code trexio_write_nucleus_coord(trexio_t* file, const double* coord)
     break;
 
   case TREXIO_HDF5:
-    return trexio_hdf5_write_nucleus_coord(file, coord);
+    return trexio_hdf5_write_nucleus_coord(file, coord, rank, dims);
     break;
 /*
   case TREXIO_JSON:
diff --git a/src/trexio_hdf5.c b/src/trexio_hdf5.c
index dec5604..b5e5bdd 100644
--- a/src/trexio_hdf5.c
+++ b/src/trexio_hdf5.c
@@ -406,113 +406,82 @@ trexio_exit_code trexio_hdf5_write_nucleus_num(const trexio_t* file, const uint6
   return TREXIO_SUCCESS;
 }
 
-trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* coord) {
+trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* coord, const int rank, const uint64_t* dims) {
 
   assert (file != NULL);
   assert (coord != NULL);
-
-  /*h5nucleus_t* nucleus = trexio_hdf5_read_nucleus((trexio_hdf5_t*) file);
-  if (nucleus == NULL) return TREXIO_FAILURE;
-  assert (nucleus->coord != NULL);*/
-
-  /* Allocate and read nucleus_coord array */
-  h5nucleus_t* nucleus = (h5nucleus_t*) malloc(sizeof(h5nucleus_t));
-  assert (nucleus != NULL);
-
-  trexio_exit_code rc = trexio_hdf5_read_nucleus_num(file, &(nucleus->num));
-  assert (rc == TREXIO_SUCCESS);
-  assert (nucleus->num > 0L);
-
-  nucleus->coord = (double*) calloc(3 * nucleus->num, sizeof(double));
-  assert (nucleus->coord != NULL);
- 
-  trexio_hdf5_t* f = (trexio_hdf5_t*) file; 
-  herr_t status;
-  /* High-level H5LT API. No need to deal with dataspaces and datatypes */
-  status = H5LTread_dataset_double(f->nucleus_group, 
-                                    NUCLEUS_COORD_NAME, 
-				    nucleus->coord);
-  assert (status >= 0);
   
-  for (size_t i=0 ; i<3*nucleus->num ; i++) {
-    coord[i] = nucleus->coord[i];
+  uint64_t nucleus_num;
+  trexio_exit_code rc = trexio_hdf5_read_nucleus_num(file, &(nucleus_num));
+  assert (rc == TREXIO_SUCCESS);
+  assert (nucleus_num > 0L);
+  
+  uint64_t ddims[2] = {nucleus_num, 3};
+  for (int i=0; i<rank; i++){
+      assert (ddims[i] == dims[i]);
   }
 
-  trexio_hdf5_free_nucleus(nucleus);
+  double* nucleus_coord = (double*) calloc(3 * nucleus_num, sizeof(double));
+  assert (nucleus_coord != NULL);
+
+  trexio_hdf5_t* f = (trexio_hdf5_t*) file;
+  
+  /* High-level H5LT API. No need to deal with dataspaces and datatypes */
+  herr_t status = H5LTread_dataset_double(f->nucleus_group,
+                                    NUCLEUS_COORD_NAME,
+                                    nucleus_coord);
+				   
+  assert (status >= 0);
+
+  for (size_t i=0 ; i<3*nucleus_num ; i++) {
+    coord[i] = nucleus_coord[i];
+  }
+
+  free(nucleus_coord);
+
   return TREXIO_SUCCESS;
 }
 
  
-trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const double* coord) {
+trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const double* coord, const int rank, const uint64_t* dims) {
 
   assert (file != NULL);
   assert (coord != NULL);
-  
-  /*h5nucleus_t* nucleus = trexio_hdf5_read_nucleus((trexio_hdf5_t*) file);
-  if (nucleus == NULL) return TREXIO_FAILURE;
-  assert (nucleus->coord != NULL);
- 
-  for (size_t i=0 ; i<3*nucleus->num ; i++) {
-    nucleus->coord[i] = coord[i];
-  }
-  
-  trexio_exit_code rc = trexio_hdf5_write_nucleus((trexio_hdf5_t*) file, nucleus);
-  assert (rc == TREXIO_SUCCESS);*/
-  
-  h5nucleus_t* nucleus = (h5nucleus_t*) malloc(sizeof(h5nucleus_t));
-  assert (nucleus != NULL);
-
-  trexio_exit_code rc = trexio_hdf5_read_nucleus_num(file, &(nucleus->num));
+    
+  uint64_t nucleus_num;
+  trexio_exit_code rc = trexio_hdf5_read_nucleus_num(file, &(nucleus_num));
   assert (rc == TREXIO_SUCCESS);
-  assert (nucleus->num > 0L);
+  assert (nucleus_num > 0L);
 
-  nucleus->coord = (double*) calloc(3 * nucleus->num, sizeof(double));
-  assert (nucleus->coord != NULL);
+  double* nucleus_coord = (double*) calloc(3 * nucleus_num, sizeof(double));
+  assert (nucleus_coord != NULL);
 
-  for (size_t i=0 ; i<3*nucleus->num ; i++) {
-    nucleus->coord[i] = coord[i];
+  for (size_t i=0 ; i<3*nucleus_num ; i++) {
+    nucleus_coord[i] = coord[i];
   }
 
   trexio_hdf5_t* f = (trexio_hdf5_t*) file; 
 
-  hid_t dset_id, dspace, dtype;
   herr_t status;
-  int coord_rank = 2;
-  const hsize_t coord_dims[2] = {nucleus->num, 3};
   if ( H5LTfind_dataset(f->nucleus_group, NUCLEUS_COORD_NAME) != 1) { 
     
     status = H5LTmake_dataset_double (f->nucleus_group, NUCLEUS_COORD_NAME, 
-                                    coord_rank, coord_dims, nucleus->coord);
+                                      rank, (hsize_t*) dims, nucleus_coord);
     assert (status >= 0);
 
   } else {   
 
-    dset_id = H5Dopen(f->nucleus_group, NUCLEUS_COORD_NAME, H5P_DEFAULT);
+    hid_t dset_id = H5Dopen(f->nucleus_group, NUCLEUS_COORD_NAME, H5P_DEFAULT);
     assert (dset_id > 0);
-    dspace = H5Dget_space(dset_id);
-    assert (dspace > 0);
-    dtype = H5Dget_type(dset_id);
-    assert (dtype > 0);
     
-    int rrank;
-    hsize_t dims[2] = {0, 0};
-    rrank = H5Sget_simple_extent_dims(dspace,
-                                    dims, NULL);
-    assert (rrank == coord_rank);
-    for (int i=0; i<rrank; i++){
-      assert (dims[i] == coord_dims[i]);
-    }
-
-    status = H5Dwrite(dset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, nucleus->coord);
+    status = H5Dwrite(dset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, nucleus_coord);
     assert (status >= 0);
 
-    H5Sclose(dspace);
-    H5Tclose(dtype);
     H5Dclose(dset_id);
 
   }
 
-  trexio_hdf5_free_nucleus(nucleus);
+  free(nucleus_coord);
   
   return TREXIO_SUCCESS;
 }
diff --git a/src/trexio_hdf5.h b/src/trexio_hdf5.h
index 1689cf8..596b486 100644
--- a/src/trexio_hdf5.h
+++ b/src/trexio_hdf5.h
@@ -91,7 +91,7 @@ typedef struct four_index_s {
 trexio_exit_code trexio_hdf5_read_nucleus_num(const trexio_t* file, uint64_t* num);
 trexio_exit_code trexio_hdf5_write_nucleus_num(const trexio_t* file, const uint64_t num);
 
-trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* coord);
-trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const double* coord);
+trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* coord, const int rank, const uint64_t* dims);
+trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const double* coord, const int rank, const uint64_t* dims);
 
 #endif
diff --git a/src/trexio_hdf5.org b/src/trexio_hdf5.org
index a1d979a..0ad87a0 100644
--- a/src/trexio_hdf5.org
+++ b/src/trexio_hdf5.org
@@ -564,118 +564,87 @@ trexio_exit_code trexio_hdf5_write_nucleus_num(const trexio_t* file, const uint6
     The ~coord~ array is assumed allocated with the appropriate size.
     
    #+begin_src c :tangle trexio_hdf5.h
-trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* coord);
-trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const double* coord);
+trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* coord, const int rank, const uint64_t* dims);
+trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const double* coord, const int rank, const uint64_t* dims);
   #+end_src
 
    #+begin_src c :tangle trexio_hdf5.c
-trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* coord) {
+trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* coord, const int rank, const uint64_t* dims) {
 
   assert (file != NULL);
   assert (coord != NULL);
-
-  /*h5nucleus_t* nucleus = trexio_hdf5_read_nucleus((trexio_hdf5_t*) file);
-  if (nucleus == NULL) return TREXIO_FAILURE;
-  assert (nucleus->coord != NULL);*/
-
-  /* Allocate and read nucleus_coord array */
-  h5nucleus_t* nucleus = (h5nucleus_t*) malloc(sizeof(h5nucleus_t));
-  assert (nucleus != NULL);
-
-  trexio_exit_code rc = trexio_hdf5_read_nucleus_num(file, &(nucleus->num));
-  assert (rc == TREXIO_SUCCESS);
-  assert (nucleus->num > 0L);
-
-  nucleus->coord = (double*) calloc(3 * nucleus->num, sizeof(double));
-  assert (nucleus->coord != NULL);
- 
-  trexio_hdf5_t* f = (trexio_hdf5_t*) file; 
-  herr_t status;
-  /* High-level H5LT API. No need to deal with dataspaces and datatypes */
-  status = H5LTread_dataset_double(f->nucleus_group, 
-                                    NUCLEUS_COORD_NAME, 
-				    nucleus->coord);
-  assert (status >= 0);
   
-  for (size_t i=0 ; i<3*nucleus->num ; i++) {
-    coord[i] = nucleus->coord[i];
+  uint64_t nucleus_num;
+  trexio_exit_code rc = trexio_hdf5_read_nucleus_num(file, &(nucleus_num));
+  assert (rc == TREXIO_SUCCESS);
+  assert (nucleus_num > 0L);
+  
+  uint64_t ddims[2] = {nucleus_num, 3};
+  for (int i=0; i<rank; i++){
+      assert (ddims[i] == dims[i]);
   }
 
-  trexio_hdf5_free_nucleus(nucleus);
+  double* nucleus_coord = (double*) calloc(3 * nucleus_num, sizeof(double));
+  assert (nucleus_coord != NULL);
+
+  trexio_hdf5_t* f = (trexio_hdf5_t*) file;
+  
+  /* High-level H5LT API. No need to deal with dataspaces and datatypes */
+  herr_t status = H5LTread_dataset_double(f->nucleus_group,
+                                    NUCLEUS_COORD_NAME,
+                                    nucleus_coord);
+				   
+  assert (status >= 0);
+
+  for (size_t i=0 ; i<3*nucleus_num ; i++) {
+    coord[i] = nucleus_coord[i];
+  }
+
+  free(nucleus_coord);
+
   return TREXIO_SUCCESS;
 }
 
  
-trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const double* coord) {
+trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const double* coord, const int rank, const uint64_t* dims) {
 
   assert (file != NULL);
   assert (coord != NULL);
-  
-  /*h5nucleus_t* nucleus = trexio_hdf5_read_nucleus((trexio_hdf5_t*) file);
-  if (nucleus == NULL) return TREXIO_FAILURE;
-  assert (nucleus->coord != NULL);
- 
-  for (size_t i=0 ; i<3*nucleus->num ; i++) {
-    nucleus->coord[i] = coord[i];
-  }
-  
-  trexio_exit_code rc = trexio_hdf5_write_nucleus((trexio_hdf5_t*) file, nucleus);
-  assert (rc == TREXIO_SUCCESS);*/
-  
-  h5nucleus_t* nucleus = (h5nucleus_t*) malloc(sizeof(h5nucleus_t));
-  assert (nucleus != NULL);
-
-  trexio_exit_code rc = trexio_hdf5_read_nucleus_num(file, &(nucleus->num));
+    
+  uint64_t nucleus_num;
+  trexio_exit_code rc = trexio_hdf5_read_nucleus_num(file, &(nucleus_num));
   assert (rc == TREXIO_SUCCESS);
-  assert (nucleus->num > 0L);
+  assert (nucleus_num > 0L);
 
-  nucleus->coord = (double*) calloc(3 * nucleus->num, sizeof(double));
-  assert (nucleus->coord != NULL);
+  double* nucleus_coord = (double*) calloc(3 * nucleus_num, sizeof(double));
+  assert (nucleus_coord != NULL);
 
-  for (size_t i=0 ; i<3*nucleus->num ; i++) {
-    nucleus->coord[i] = coord[i];
+  for (size_t i=0 ; i<3*nucleus_num ; i++) {
+    nucleus_coord[i] = coord[i];
   }
 
   trexio_hdf5_t* f = (trexio_hdf5_t*) file; 
 
-  hid_t dset_id, dspace, dtype;
   herr_t status;
-  int coord_rank = 2;
-  const hsize_t coord_dims[2] = {nucleus->num, 3};
   if ( H5LTfind_dataset(f->nucleus_group, NUCLEUS_COORD_NAME) != 1) { 
     
     status = H5LTmake_dataset_double (f->nucleus_group, NUCLEUS_COORD_NAME, 
-                                    coord_rank, coord_dims, nucleus->coord);
+                                      rank, (hsize_t*) dims, nucleus_coord);
     assert (status >= 0);
 
   } else {   
 
-    dset_id = H5Dopen(f->nucleus_group, NUCLEUS_COORD_NAME, H5P_DEFAULT);
+    hid_t dset_id = H5Dopen(f->nucleus_group, NUCLEUS_COORD_NAME, H5P_DEFAULT);
     assert (dset_id > 0);
-    dspace = H5Dget_space(dset_id);
-    assert (dspace > 0);
-    dtype = H5Dget_type(dset_id);
-    assert (dtype > 0);
     
-    int rrank;
-    hsize_t dims[2] = {0, 0};
-    rrank = H5Sget_simple_extent_dims(dspace,
-                                    dims, NULL);
-    assert (rrank == coord_rank);
-    for (int i=0; i<rrank; i++){
-      assert (dims[i] == coord_dims[i]);
-    }
-
-    status = H5Dwrite(dset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, nucleus->coord);
+    status = H5Dwrite(dset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, nucleus_coord);
     assert (status >= 0);
 
-    H5Sclose(dspace);
-    H5Tclose(dtype);
     H5Dclose(dset_id);
 
   }
 
-  trexio_hdf5_free_nucleus(nucleus);
+  free(nucleus_coord);
   
   return TREXIO_SUCCESS;
 }

From e52cfbafea9865d1243c0f621e7364e6fdd88a6d Mon Sep 17 00:00:00 2001
From: q-posev <posenitskiy@irsamc.ups-tlse.fr>
Date: Thu, 4 Mar 2021 15:02:23 +0100
Subject: [PATCH 4/8] dummy write and smart read

---
 src/trexio_hdf5.c   | 52 +++++++++++++++++++------------------------
 src/trexio_hdf5.org | 54 ++++++++++++++++++++-------------------------
 2 files changed, 47 insertions(+), 59 deletions(-)

diff --git a/src/trexio_hdf5.c b/src/trexio_hdf5.c
index b5e5bdd..586ab67 100644
--- a/src/trexio_hdf5.c
+++ b/src/trexio_hdf5.c
@@ -411,34 +411,37 @@ trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* co
   assert (file != NULL);
   assert (coord != NULL);
   
-  uint64_t nucleus_num;
-  trexio_exit_code rc = trexio_hdf5_read_nucleus_num(file, &(nucleus_num));
-  assert (rc == TREXIO_SUCCESS);
-  assert (nucleus_num > 0L);
+  trexio_hdf5_t* f = (trexio_hdf5_t*) file;
   
-  uint64_t ddims[2] = {nucleus_num, 3};
+  herr_t status;
+  int rrank;
+  status = H5LTget_dataset_ndims (f->nucleus_group, NUCLEUS_COORD_NAME, 
+                                  &rrank);
+  assert (status >= 0);
+  assert (rrank == rank);
+
+  hsize_t* ddims = (hsize_t*) calloc(rrank, sizeof(hsize_t));
+  
+  hid_t dset_id = H5Dopen(f->nucleus_group, NUCLEUS_COORD_NAME, H5P_DEFAULT);
+  assert (dset_id > 0);
+
+  status = H5LDget_dset_dims(dset_id, ddims);
+  assert (status >= 0);
+  
+  H5Dclose(dset_id);
+
+  //uint64_t ddims[2] = {nucleus_num, 3};
   for (int i=0; i<rank; i++){
       assert (ddims[i] == dims[i]);
   }
 
-  double* nucleus_coord = (double*) calloc(3 * nucleus_num, sizeof(double));
-  assert (nucleus_coord != NULL);
-
-  trexio_hdf5_t* f = (trexio_hdf5_t*) file;
-  
   /* High-level H5LT API. No need to deal with dataspaces and datatypes */
-  herr_t status = H5LTread_dataset_double(f->nucleus_group,
+  status = H5LTread_dataset_double(f->nucleus_group,
                                     NUCLEUS_COORD_NAME,
-                                    nucleus_coord);
+                                    coord);
 				   
   assert (status >= 0);
 
-  for (size_t i=0 ; i<3*nucleus_num ; i++) {
-    coord[i] = nucleus_coord[i];
-  }
-
-  free(nucleus_coord);
-
   return TREXIO_SUCCESS;
 }
 
@@ -453,20 +456,13 @@ trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const dou
   assert (rc == TREXIO_SUCCESS);
   assert (nucleus_num > 0L);
 
-  double* nucleus_coord = (double*) calloc(3 * nucleus_num, sizeof(double));
-  assert (nucleus_coord != NULL);
-
-  for (size_t i=0 ; i<3*nucleus_num ; i++) {
-    nucleus_coord[i] = coord[i];
-  }
-
   trexio_hdf5_t* f = (trexio_hdf5_t*) file; 
 
   herr_t status;
   if ( H5LTfind_dataset(f->nucleus_group, NUCLEUS_COORD_NAME) != 1) { 
     
     status = H5LTmake_dataset_double (f->nucleus_group, NUCLEUS_COORD_NAME, 
-                                      rank, (hsize_t*) dims, nucleus_coord);
+                                      rank, (hsize_t*) dims, coord);
     assert (status >= 0);
 
   } else {   
@@ -474,14 +470,12 @@ trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const dou
     hid_t dset_id = H5Dopen(f->nucleus_group, NUCLEUS_COORD_NAME, H5P_DEFAULT);
     assert (dset_id > 0);
     
-    status = H5Dwrite(dset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, nucleus_coord);
+    status = H5Dwrite(dset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, coord);
     assert (status >= 0);
 
     H5Dclose(dset_id);
 
   }
-
-  free(nucleus_coord);
   
   return TREXIO_SUCCESS;
 }
diff --git a/src/trexio_hdf5.org b/src/trexio_hdf5.org
index 0ad87a0..382592f 100644
--- a/src/trexio_hdf5.org
+++ b/src/trexio_hdf5.org
@@ -36,7 +36,7 @@
 #include "trexio_hdf5.h"
   #+end_src
 
-
+  
 * HDF5 Back end
 
 ** HDF5 definitions
@@ -574,34 +574,37 @@ trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* co
   assert (file != NULL);
   assert (coord != NULL);
   
-  uint64_t nucleus_num;
-  trexio_exit_code rc = trexio_hdf5_read_nucleus_num(file, &(nucleus_num));
-  assert (rc == TREXIO_SUCCESS);
-  assert (nucleus_num > 0L);
+  trexio_hdf5_t* f = (trexio_hdf5_t*) file;
   
-  uint64_t ddims[2] = {nucleus_num, 3};
+  herr_t status;
+  int rrank;
+  status = H5LTget_dataset_ndims (f->nucleus_group, NUCLEUS_COORD_NAME, 
+                                  &rrank);
+  assert (status >= 0);
+  assert (rrank == rank);
+
+  hsize_t* ddims = (hsize_t*) calloc(rrank, sizeof(hsize_t));
+  
+  hid_t dset_id = H5Dopen(f->nucleus_group, NUCLEUS_COORD_NAME, H5P_DEFAULT);
+  assert (dset_id > 0);
+
+  status = H5LDget_dset_dims(dset_id, ddims);
+  assert (status >= 0);
+  
+  H5Dclose(dset_id);
+
+  //uint64_t ddims[2] = {nucleus_num, 3};
   for (int i=0; i<rank; i++){
       assert (ddims[i] == dims[i]);
   }
 
-  double* nucleus_coord = (double*) calloc(3 * nucleus_num, sizeof(double));
-  assert (nucleus_coord != NULL);
-
-  trexio_hdf5_t* f = (trexio_hdf5_t*) file;
-  
   /* High-level H5LT API. No need to deal with dataspaces and datatypes */
-  herr_t status = H5LTread_dataset_double(f->nucleus_group,
+  status = H5LTread_dataset_double(f->nucleus_group,
                                     NUCLEUS_COORD_NAME,
-                                    nucleus_coord);
+                                    coord);
 				   
   assert (status >= 0);
 
-  for (size_t i=0 ; i<3*nucleus_num ; i++) {
-    coord[i] = nucleus_coord[i];
-  }
-
-  free(nucleus_coord);
-
   return TREXIO_SUCCESS;
 }
 
@@ -616,20 +619,13 @@ trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const dou
   assert (rc == TREXIO_SUCCESS);
   assert (nucleus_num > 0L);
 
-  double* nucleus_coord = (double*) calloc(3 * nucleus_num, sizeof(double));
-  assert (nucleus_coord != NULL);
-
-  for (size_t i=0 ; i<3*nucleus_num ; i++) {
-    nucleus_coord[i] = coord[i];
-  }
-
   trexio_hdf5_t* f = (trexio_hdf5_t*) file; 
 
   herr_t status;
   if ( H5LTfind_dataset(f->nucleus_group, NUCLEUS_COORD_NAME) != 1) { 
     
     status = H5LTmake_dataset_double (f->nucleus_group, NUCLEUS_COORD_NAME, 
-                                      rank, (hsize_t*) dims, nucleus_coord);
+                                      rank, (hsize_t*) dims, coord);
     assert (status >= 0);
 
   } else {   
@@ -637,14 +633,12 @@ trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const dou
     hid_t dset_id = H5Dopen(f->nucleus_group, NUCLEUS_COORD_NAME, H5P_DEFAULT);
     assert (dset_id > 0);
     
-    status = H5Dwrite(dset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, nucleus_coord);
+    status = H5Dwrite(dset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, coord);
     assert (status >= 0);
 
     H5Dclose(dset_id);
 
   }
-
-  free(nucleus_coord);
   
   return TREXIO_SUCCESS;
 }

From db1f1d69800ae83ce523615cc17c024cfd3567c5 Mon Sep 17 00:00:00 2001
From: q-posev <posenitskiy@irsamc.ups-tlse.fr>
Date: Thu, 4 Mar 2021 18:53:13 +0100
Subject: [PATCH 5/8] fix leaking memory

---
 src/trexio.c        |  8 ++++++--
 src/trexio_hdf5.c   | 11 ++++-------
 src/trexio_hdf5.org | 11 ++++-------
 3 files changed, 14 insertions(+), 16 deletions(-)

diff --git a/src/trexio.c b/src/trexio.c
index afe98d1..b5860fb 100644
--- a/src/trexio.c
+++ b/src/trexio.c
@@ -74,8 +74,12 @@ trexio_t* trexio_open(const char* file_name, const char mode, const back_end_t b
     break;
 */      
   }
-  if (rc != TREXIO_SUCCESS) return NULL;
-  
+  if (rc != TREXIO_SUCCESS) {
+    free(result->file_name);
+    free(result);
+    return NULL;
+  }
+
   return result;
 }
 
diff --git a/src/trexio_hdf5.c b/src/trexio_hdf5.c
index 586ab67..9959deb 100644
--- a/src/trexio_hdf5.c
+++ b/src/trexio_hdf5.c
@@ -94,9 +94,9 @@ trexio_exit_code trexio_hdf5_init(trexio_t* file) {
 
     switch (file->mode) {
     case 'r': 
+    case 'a': 
       // reading non-existing file -> error
       return TREXIO_FAILURE;
-    case 'a': 
     case 'w': 
       // appending or writing non-existing file -> create it
       f->file_id = H5Fcreate(file->file_name, H5F_ACC_EXCL, H5P_DEFAULT, H5P_DEFAULT);
@@ -109,13 +109,8 @@ trexio_exit_code trexio_hdf5_init(trexio_t* file) {
   switch (file->mode) {
     case 'r':
     case 'a': 
-      if (f_exists == 1) {
-        f->nucleus_group = H5Gopen(f->file_id, NUCLEUS_GROUP_NAME, H5P_DEFAULT);
+      f->nucleus_group = H5Gopen(f->file_id, NUCLEUS_GROUP_NAME, H5P_DEFAULT);
       //f->electron_group = H5Gopen(f->file_id, ELECTRON_GROUP_NAME, H5P_DEFAULT);   
-      } else {
-        f->nucleus_group = H5Gcreate(f->file_id, NUCLEUS_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
-      //f->electron_group = H5Gcreate(f->file_id, ELECTRON_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
-      }
       break;
     case 'w':
       f->nucleus_group = H5Gcreate(f->file_id, NUCLEUS_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
@@ -442,6 +437,8 @@ trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* co
 				   
   assert (status >= 0);
 
+  free(ddims);
+
   return TREXIO_SUCCESS;
 }
 
diff --git a/src/trexio_hdf5.org b/src/trexio_hdf5.org
index 382592f..a31c709 100644
--- a/src/trexio_hdf5.org
+++ b/src/trexio_hdf5.org
@@ -185,9 +185,9 @@ trexio_exit_code trexio_hdf5_init(trexio_t* file) {
 
     switch (file->mode) {
     case 'r': 
+    case 'a': 
       // reading non-existing file -> error
       return TREXIO_FAILURE;
-    case 'a': 
     case 'w': 
       // appending or writing non-existing file -> create it
       f->file_id = H5Fcreate(file->file_name, H5F_ACC_EXCL, H5P_DEFAULT, H5P_DEFAULT);
@@ -200,13 +200,8 @@ trexio_exit_code trexio_hdf5_init(trexio_t* file) {
   switch (file->mode) {
     case 'r':
     case 'a': 
-      if (f_exists == 1) {
-        f->nucleus_group = H5Gopen(f->file_id, NUCLEUS_GROUP_NAME, H5P_DEFAULT);
+      f->nucleus_group = H5Gopen(f->file_id, NUCLEUS_GROUP_NAME, H5P_DEFAULT);
       //f->electron_group = H5Gopen(f->file_id, ELECTRON_GROUP_NAME, H5P_DEFAULT);   
-      } else {
-        f->nucleus_group = H5Gcreate(f->file_id, NUCLEUS_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
-      //f->electron_group = H5Gcreate(f->file_id, ELECTRON_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
-      }
       break;
     case 'w':
       f->nucleus_group = H5Gcreate(f->file_id, NUCLEUS_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
@@ -605,6 +600,8 @@ trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* co
 				   
   assert (status >= 0);
 
+  free(ddims);
+
   return TREXIO_SUCCESS;
 }
 

From 05d55028c4ea6be0ce976ee97b9098ffef004565 Mon Sep 17 00:00:00 2001
From: q-posev <posenitskiy@irsamc.ups-tlse.fr>
Date: Thu, 4 Mar 2021 19:36:32 +0100
Subject: [PATCH 6/8] add error codes for invalid returns

---
 src/trexio.h | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/trexio.h b/src/trexio.h
index d00c1ff..fcf2de8 100644
--- a/src/trexio.h
+++ b/src/trexio.h
@@ -21,6 +21,8 @@ typedef int32_t trexio_exit_code;
 #define TREXIO_INVALID_ARG_5 ( (trexio_exit_code)  5 )
 #define TREXIO_END           ( (trexio_exit_code) 10 )
 #define TREXIO_READONLY      ( (trexio_exit_code) 11 )
+#define TREXIO_INVALID_ID    ( (trexio_exit_code) 20 )
+#define TREXIO_INVALID_NUM   ( (trexio_exit_code) 21 )
 
 typedef int32_t back_end_t;
 

From 1df9cd7177e2a7534bf0d2599b84cb0e7a9925c5 Mon Sep 17 00:00:00 2001
From: q-posev <posenitskiy@irsamc.ups-tlse.fr>
Date: Thu, 4 Mar 2021 19:39:06 +0100
Subject: [PATCH 7/8] uint32 rank and better error handling

---
 src/trexio.c        | 13 +++++----
 src/trexio.org      | 23 +++++++++-------
 src/trexio_hdf5.c   | 60 ++++++++++++++++++++++++------------------
 src/trexio_hdf5.h   |  4 +--
 src/trexio_hdf5.org | 64 ++++++++++++++++++++++++++-------------------
 5 files changed, 94 insertions(+), 70 deletions(-)

diff --git a/src/trexio.c b/src/trexio.c
index b5860fb..9d5cdf2 100644
--- a/src/trexio.c
+++ b/src/trexio.c
@@ -74,6 +74,7 @@ trexio_t* trexio_open(const char* file_name, const char mode, const back_end_t b
     break;
 */      
   }
+
   if (rc != TREXIO_SUCCESS) {
     free(result->file_name);
     free(result);
@@ -107,17 +108,15 @@ trexio_exit_code trexio_close(trexio_t* file) {
     assert (1 == 0);  /* Impossible case */
   }
 
-  if (rc != TREXIO_SUCCESS) {
-    return TREXIO_FAILURE;
-  }
-  
   free(file->file_name);
   file->file_name = NULL;
   
   int irc = pthread_mutex_destroy( &(file->thread_lock) );
   assert (irc == 0);
 
-  free(file);
+  free(file); 
+
+  if (rc != TREXIO_SUCCESS) return rc;
   
   return TREXIO_SUCCESS;
 }
@@ -187,7 +186,7 @@ trexio_exit_code trexio_read_nucleus_coord(trexio_t* file, double* coord) {
   int64_t dim_coord = nucleus_num*3;
   if (dim_coord < 0) return TREXIO_FAILURE;
 
-  int rank = 2;
+  uint32_t rank = 2;
   uint64_t dims[2] = {nucleus_num, 3}; 
 
   switch (file->back_end) {
@@ -220,7 +219,7 @@ trexio_exit_code trexio_write_nucleus_coord(trexio_t* file, const double* coord)
   int64_t dim_coord = nucleus_num*3;
   if (dim_coord < 0) return TREXIO_FAILURE;
 
-  int rank = 2;
+  uint32_t rank = 2;
   uint64_t dims[2] = {nucleus_num, 3};
  
   switch (file->back_end) {
diff --git a/src/trexio.org b/src/trexio.org
index c0e35fb..a1fe8fa 100644
--- a/src/trexio.org
+++ b/src/trexio.org
@@ -78,6 +78,8 @@ typedef int32_t trexio_exit_code;
 #define TREXIO_INVALID_ARG_5 ( (trexio_exit_code)  5 )
 #define TREXIO_END           ( (trexio_exit_code) 10 )
 #define TREXIO_READONLY      ( (trexio_exit_code) 11 )
+#define TREXIO_INVALID_ID    ( (trexio_exit_code) 20 )
+#define TREXIO_INVALID_NUM   ( (trexio_exit_code) 21 )
    #+end_src
    
 ** Back ends
@@ -211,8 +213,13 @@ trexio_t* trexio_open(const char* file_name, const char mode, const back_end_t b
     break;
 ,*/      
   }
-  if (rc != TREXIO_SUCCESS) return NULL;
-  
+
+  if (rc != TREXIO_SUCCESS) {
+    free(result->file_name);
+    free(result);
+    return NULL;
+  }
+
   return result;
 }
    #+end_src
@@ -248,17 +255,15 @@ trexio_exit_code trexio_close(trexio_t* file) {
     assert (1 == 0);  /* Impossible case */
   }
 
-  if (rc != TREXIO_SUCCESS) {
-    return TREXIO_FAILURE;
-  }
-  
   free(file->file_name);
   file->file_name = NULL;
   
   int irc = pthread_mutex_destroy( &(file->thread_lock) );
   assert (irc == 0);
 
-  free(file);
+  free(file); 
+
+  if (rc != TREXIO_SUCCESS) return rc;
   
   return TREXIO_SUCCESS;
 }
@@ -345,7 +350,7 @@ trexio_exit_code trexio_read_nucleus_coord(trexio_t* file, double* coord) {
   int64_t dim_coord = nucleus_num*3;
   if (dim_coord < 0) return TREXIO_FAILURE;
 
-  int rank = 2;
+  uint32_t rank = 2;
   uint64_t dims[2] = {nucleus_num, 3}; 
 
   switch (file->back_end) {
@@ -378,7 +383,7 @@ trexio_exit_code trexio_write_nucleus_coord(trexio_t* file, const double* coord)
   int64_t dim_coord = nucleus_num*3;
   if (dim_coord < 0) return TREXIO_FAILURE;
 
-  int rank = 2;
+  uint32_t rank = 2;
   uint64_t dims[2] = {nucleus_num, 3};
  
   switch (file->back_end) {
diff --git a/src/trexio_hdf5.c b/src/trexio_hdf5.c
index 9959deb..4f54dd2 100644
--- a/src/trexio_hdf5.c
+++ b/src/trexio_hdf5.c
@@ -401,7 +401,7 @@ trexio_exit_code trexio_hdf5_write_nucleus_num(const trexio_t* file, const uint6
   return TREXIO_SUCCESS;
 }
 
-trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* coord, const int rank, const uint64_t* dims) {
+trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* coord, const uint32_t rank, const uint64_t* dims) {
 
   assert (file != NULL);
   assert (coord != NULL);
@@ -410,48 +410,58 @@ trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* co
   
   herr_t status;
   int rrank;
+  // get the rank of the dataset in a file
   status = H5LTget_dataset_ndims (f->nucleus_group, NUCLEUS_COORD_NAME, 
                                   &rrank);
-  assert (status >= 0);
-  assert (rrank == rank);
 
-  hsize_t* ddims = (hsize_t*) calloc(rrank, sizeof(hsize_t));
-  
+  if (status < 0) return TREXIO_FAILURE;
+
+  if (rrank != (int) rank) return TREXIO_INVALID_ARG_3;
+
+  // open the dataset to get its dimensions  
   hid_t dset_id = H5Dopen(f->nucleus_group, NUCLEUS_COORD_NAME, H5P_DEFAULT);
-  assert (dset_id > 0);
+  if (dset_id <= 0) return TREXIO_INVALID_ID; 
 
+  // allocate space for the dimensions to be read
+  hsize_t* ddims = (hsize_t*) calloc( (int) rank, sizeof(hsize_t));
+  if (ddims == NULL) return TREXIO_FAILURE;
+
+  // read dimensions from the existing dataset
   status = H5LDget_dset_dims(dset_id, ddims);
-  assert (status >= 0);
-  
-  H5Dclose(dset_id);
 
-  //uint64_t ddims[2] = {nucleus_num, 3};
-  for (int i=0; i<rank; i++){
-      assert (ddims[i] == dims[i]);
+  H5Dclose(dset_id);
+  if (status < 0) {
+    free(ddims);
+    return TREXIO_FAILURE;
   }
 
+  for (uint32_t i=0; i<rank; i++){
+     if (ddims[i] != dims[i]) {
+       free(ddims);
+       return TREXIO_INVALID_ARG_4;
+     }
+  }
+  free(ddims);
+
   /* High-level H5LT API. No need to deal with dataspaces and datatypes */
   status = H5LTread_dataset_double(f->nucleus_group,
                                     NUCLEUS_COORD_NAME,
-                                    coord);
-				   
-  assert (status >= 0);
-
-  free(ddims);
+                                    coord);				   
+  if (status < 0) return TREXIO_FAILURE;
 
   return TREXIO_SUCCESS;
 }
 
  
-trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const double* coord, const int rank, const uint64_t* dims) {
+trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const double* coord, const uint32_t rank, const uint64_t* dims) {
 
   assert (file != NULL);
   assert (coord != NULL);
     
   uint64_t nucleus_num;
   trexio_exit_code rc = trexio_hdf5_read_nucleus_num(file, &(nucleus_num));
-  assert (rc == TREXIO_SUCCESS);
-  assert (nucleus_num > 0L);
+  if (rc != TREXIO_SUCCESS) return rc;
+  if (nucleus_num <= 0L) return TREXIO_INVALID_NUM;
 
   trexio_hdf5_t* f = (trexio_hdf5_t*) file; 
 
@@ -459,18 +469,18 @@ trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const dou
   if ( H5LTfind_dataset(f->nucleus_group, NUCLEUS_COORD_NAME) != 1) { 
     
     status = H5LTmake_dataset_double (f->nucleus_group, NUCLEUS_COORD_NAME, 
-                                      rank, (hsize_t*) dims, coord);
-    assert (status >= 0);
+                                      (int) rank, (hsize_t*) dims, coord);
+    if (status < 0) return TREXIO_FAILURE;
 
   } else {   
 
     hid_t dset_id = H5Dopen(f->nucleus_group, NUCLEUS_COORD_NAME, H5P_DEFAULT);
-    assert (dset_id > 0);
+    if (dset_id <= 0) return TREXIO_INVALID_ID;
     
     status = H5Dwrite(dset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, coord);
-    assert (status >= 0);
-
+    
     H5Dclose(dset_id);
+    if (status < 0) return TREXIO_FAILURE;
 
   }
   
diff --git a/src/trexio_hdf5.h b/src/trexio_hdf5.h
index 596b486..f71360c 100644
--- a/src/trexio_hdf5.h
+++ b/src/trexio_hdf5.h
@@ -91,7 +91,7 @@ typedef struct four_index_s {
 trexio_exit_code trexio_hdf5_read_nucleus_num(const trexio_t* file, uint64_t* num);
 trexio_exit_code trexio_hdf5_write_nucleus_num(const trexio_t* file, const uint64_t num);
 
-trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* coord, const int rank, const uint64_t* dims);
-trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const double* coord, const int rank, const uint64_t* dims);
+trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* coord, const uint32_t rank, const uint64_t* dims);
+trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const double* coord, const uint32_t rank, const uint64_t* dims);
 
 #endif
diff --git a/src/trexio_hdf5.org b/src/trexio_hdf5.org
index a31c709..1f57adf 100644
--- a/src/trexio_hdf5.org
+++ b/src/trexio_hdf5.org
@@ -559,12 +559,12 @@ trexio_exit_code trexio_hdf5_write_nucleus_num(const trexio_t* file, const uint6
     The ~coord~ array is assumed allocated with the appropriate size.
     
    #+begin_src c :tangle trexio_hdf5.h
-trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* coord, const int rank, const uint64_t* dims);
-trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const double* coord, const int rank, const uint64_t* dims);
+trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* coord, const uint32_t rank, const uint64_t* dims);
+trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const double* coord, const uint32_t rank, const uint64_t* dims);
   #+end_src
 
    #+begin_src c :tangle trexio_hdf5.c
-trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* coord, const int rank, const uint64_t* dims) {
+trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* coord, const uint32_t rank, const uint64_t* dims) {
 
   assert (file != NULL);
   assert (coord != NULL);
@@ -573,48 +573,58 @@ trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* co
   
   herr_t status;
   int rrank;
+  // get the rank of the dataset in a file
   status = H5LTget_dataset_ndims (f->nucleus_group, NUCLEUS_COORD_NAME, 
                                   &rrank);
-  assert (status >= 0);
-  assert (rrank == rank);
 
-  hsize_t* ddims = (hsize_t*) calloc(rrank, sizeof(hsize_t));
-  
+  if (status < 0) return TREXIO_FAILURE;
+
+  if (rrank != (int) rank) return TREXIO_INVALID_ARG_3;
+
+  // open the dataset to get its dimensions  
   hid_t dset_id = H5Dopen(f->nucleus_group, NUCLEUS_COORD_NAME, H5P_DEFAULT);
-  assert (dset_id > 0);
+  if (dset_id <= 0) return TREXIO_INVALID_ID; 
 
+  // allocate space for the dimensions to be read
+  hsize_t* ddims = (hsize_t*) calloc( (int) rank, sizeof(hsize_t));
+  if (ddims == NULL) return TREXIO_FAILURE;
+
+  // read dimensions from the existing dataset
   status = H5LDget_dset_dims(dset_id, ddims);
-  assert (status >= 0);
-  
-  H5Dclose(dset_id);
 
-  //uint64_t ddims[2] = {nucleus_num, 3};
-  for (int i=0; i<rank; i++){
-      assert (ddims[i] == dims[i]);
+  H5Dclose(dset_id);
+  if (status < 0) {
+    free(ddims);
+    return TREXIO_FAILURE;
   }
 
+  for (uint32_t i=0; i<rank; i++){
+     if (ddims[i] != dims[i]) {
+       free(ddims);
+       return TREXIO_INVALID_ARG_4;
+     }
+  }
+  free(ddims);
+
   /* High-level H5LT API. No need to deal with dataspaces and datatypes */
   status = H5LTread_dataset_double(f->nucleus_group,
                                     NUCLEUS_COORD_NAME,
-                                    coord);
-				   
-  assert (status >= 0);
-
-  free(ddims);
+                                    coord);				   
+  if (status < 0) return TREXIO_FAILURE;
 
   return TREXIO_SUCCESS;
 }
 
  
-trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const double* coord, const int rank, const uint64_t* dims) {
+trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const double* coord, const uint32_t rank, const uint64_t* dims) {
 
   assert (file != NULL);
   assert (coord != NULL);
     
   uint64_t nucleus_num;
   trexio_exit_code rc = trexio_hdf5_read_nucleus_num(file, &(nucleus_num));
-  assert (rc == TREXIO_SUCCESS);
-  assert (nucleus_num > 0L);
+  if (rc != TREXIO_SUCCESS) return rc;
+  if (nucleus_num <= 0L) return TREXIO_INVALID_NUM;
 
   trexio_hdf5_t* f = (trexio_hdf5_t*) file; 
 
@@ -622,18 +632,18 @@ trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const dou
   if ( H5LTfind_dataset(f->nucleus_group, NUCLEUS_COORD_NAME) != 1) { 
     
     status = H5LTmake_dataset_double (f->nucleus_group, NUCLEUS_COORD_NAME, 
-                                      rank, (hsize_t*) dims, coord);
-    assert (status >= 0);
+                                      (int) rank, (hsize_t*) dims, coord);
+    if (status < 0) return TREXIO_FAILURE;
 
   } else {   
 
     hid_t dset_id = H5Dopen(f->nucleus_group, NUCLEUS_COORD_NAME, H5P_DEFAULT);
-    assert (dset_id > 0);
+    if (dset_id <= 0) return TREXIO_INVALID_ID;
     
     status = H5Dwrite(dset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, coord);
-    assert (status >= 0);
-
+    
     H5Dclose(dset_id);
+    if (status < 0) return TREXIO_FAILURE;
 
   }
   

From b964b73bbe6deacf230abe0b8a205b2e8d10a263 Mon Sep 17 00:00:00 2001
From: Evgeny Posenitskiy <45995097+q-posev@users.noreply.github.com>
Date: Thu, 4 Mar 2021 20:43:44 +0100
Subject: [PATCH 8/8] removed bracket

---
 src/trexio.org | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/trexio.org b/src/trexio.org
index d803907..874585f 100644
--- a/src/trexio.org
+++ b/src/trexio.org
@@ -329,8 +329,6 @@ trexio_exit_code trexio_close(trexio_t* file) {
   if (rc != TREXIO_SUCCESS) return TREXIO_FAILURE;
     
   return TREXIO_SUCCESS;
-}
-
 }
    #+end_src
 ** Reading/writing data