Merge branch 'master' into add-strings

README.md

@@ -5,9 +5,10 @@ TREX library fo efficient I/O.
 
 ## Minimal requirements (for users):
 
-- Autoconf
+- Autotools             (autoconf, automake, libtool)
 - C compiler            (gcc/icc/clang)
-- Fortran compiler 	(gfortran/ifort/flang)
+- Fortran compiler      (gfortran/ifort)
+- HDF5 library          (>= 1.8)
 
 
 ## Installation procedure from the tarball (for users):
@@ -26,9 +27,8 @@ TREX library fo efficient I/O.
 
 ## Additional requirements (for developers):
 
-- Automake
+- python3       (>= 3.6)
-- python3 	(>=3.6)
+- Emacs         (>= 26.0)
-- Emacs		(>=26.0)
 
 
 ## Installation procedure from the GitHub repo clone (for developers):
@@ -36,7 +36,7 @@ TREX library fo efficient I/O.
 1. `git clone https://github.com/TREX-CoE/trexio.git`
 2. `cd trexio`
 3. `./autogen.sh`
-4. `./configure`
+4. `TREXIO_DEVEL=1 ./configure`
 5. `make`
 6. `make check`
 7. `sudo make install`

configure.ac

@@ -55,7 +55,7 @@ AC_PROG_LN_S
 ## ---------
 
 # Checks for basic header files.
-AC_CHECK_HEADERS([fcntl.h inttypes.h stdint.h stdlib.h string.h unistd.h])
+AC_CHECK_HEADERS([fcntl.h inttypes.h stdint.h stdbool.h stdlib.h string.h unistd.h])
 
 
 ### HDF5

src/templates_front/templator_front.org

@@ -52,11 +52,12 @@ typedef int32_t trexio_exit_code;
 #include <pthread.h>
 #include <assert.h>
 #include <stdlib.h>
+#include <stdbool.h>
 #include <string.h>
 
 #include "trexio.h"
-#include "trexio_s.h"
 #include "trexio_private.h"
+#include "trexio_s.h"
 #include "trexio_text.h"
 #include "trexio_hdf5.h"
 /*
@@ -73,6 +74,7 @@ typedef int32_t trexio_exit_code;
 #include "trexio.h"
 #include <pthread.h>
 #include <assert.h>
+#include <stdbool.h>
   #+end_src
 
 * Coding conventions
@@ -429,11 +431,12 @@ typedef struct trexio_s trexio_t;
 
    #+begin_src c :tangle prefix_s_front.h
 struct trexio_s {
-  char*             file_name;
+  char              file_name[TREXIO_MAX_FILENAME_LENGTH];
   pthread_mutex_t   thread_lock;
   back_end_t        back_end;
   char              mode;
-  char              padding[7]; /* Ensures the proper alignment of back ends */
+  bool              one_based;
+  char              padding[6]; /* Ensures the proper alignment of back ends */
 };
    #+end_src
 ** Polymorphism of the file handle
@@ -466,11 +469,13 @@ struct trexio_back_end_s {
    output:
  ~trexio_t~ file handle
 
-   Note: the ~file_name~ in TEXT back end actually corresponds to the name of the folder where ~.txt~
+   Note: the ~file_name~ in TEXT back end actually corresponds to the
-   data files are stored. The actual name of each ~.txt~ file corresponds to the group name provided in
+   name of the directory where ~.txt~ data files are stored. The
- ~trex.config~ (e.g. ~nucleus.txt~ for nuclei-related data).
+   actual name of each ~.txt~ file corresponds to the group name
-   These names are populated by the generator.py (i.e. they are hard-coded), which is why the user
+   provided in ~trex.config~ (e.g. ~nucleus.txt~ for nuclei-related
-   should tend to avoid renaming the ~.txt~ data files.
+   data).  These names are populated by the generator.py (i.e. they
+   are hard-coded), which is why the user should tend to avoid
+   renaming the ~.txt~ data files.
 
    #+begin_src c :tangle prefix_front.h :exports none
 trexio_t* trexio_open(const char* file_name, const char mode, const back_end_t back_end);
@@ -517,16 +522,15 @@ trexio_open(const char* file_name, const char mode,
 
  /* Data for the parent type */
 
-  result->file_name   = CALLOC(TREXIO_MAX_FILENAME_LENGTH, char);
   strncpy(result->file_name, file_name, TREXIO_MAX_FILENAME_LENGTH);
   if (result->file_name[TREXIO_MAX_FILENAME_LENGTH-1] != '\0') {
-    free(result->file_name);
     free(result);
     return NULL;
   }
 
   result->back_end    = back_end;
   result->mode        = mode;
+  result->one_based   = false;  // Need to be flipped in Fortran interface
   int irc = pthread_mutex_init ( &(result->thread_lock), NULL);
   assert (irc == 0);
 
@@ -553,7 +557,6 @@ trexio_open(const char* file_name, const char mode,
   }
 
   if (rc != TREXIO_SUCCESS) {
-    free(result->file_name);
     free(result);
     return NULL;
   }
@@ -579,7 +582,6 @@ trexio_open(const char* file_name, const char mode,
   }
 
   if (rc != TREXIO_SUCCESS) {
-    free(result->file_name);
     free(result);
     return NULL;
   }
@@ -600,6 +602,34 @@ interface
 end interface
    #+end_src
 
+   Because arrays are zero-based in Fortran, we need to set a flag to
+   know if we need to shift by 1 arrays of indices.
+
+   #+begin_src c :tangle prefix_front.h :exports none
+trexio_exit_code trexio_set_one_based(trexio_t* file);
+   #+end_src
+
+   #+begin_src c :tangle prefix_front.c
+trexio_exit_code trexio_set_one_based(trexio_t* file)
+{
+  if (file == NULL)
+    return TREXIO_FILE_ERROR;
+
+  file->one_based = true;
+
+  return TREXIO_SUCCESS;
+}
+   #+end_src
+
+   #+begin_src f90 :tangle prefix_fortran.f90
+interface
+   integer function trexio_set_one_based(trex_file) bind(C)
+     use, intrinsic :: iso_c_binding
+     integer(8), intent(in), value :: trex_file
+   end function trexio_set_one_based
+end interface
+   #+end_src
+
 ** File closing
 
  ~trexio_close~ closes an existing ~trexio_t~ file.
@@ -643,7 +673,6 @@ trexio_close (trexio_t* file)
   }
 
   if (rc != TREXIO_SUCCESS) {
-    FREE(file->file_name);
     FREE(file);
     return rc;
   }
@@ -670,8 +699,6 @@ trexio_close (trexio_t* file)
 
  /* Terminate front end */
 
-  FREE(file->file_name);
-
   int irc = pthread_mutex_destroy( &(file->thread_lock) );
 
   free(file);
@@ -1081,6 +1108,7 @@ trexio_read_$group_dset$_64 (trexio_t* const file, $group_dset_dtype_double$* co
 
  /* Error handling for this call is added by the generator */
   rc = trexio_read_$group_dset_dim$_64(file, &($group_dset_dim$));
+  if (rc != TREXIO_SUCCESS) return rc;
 
   if ($group_dset_dim$ == 0L) return TREXIO_INVALID_NUM;
 
@@ -1089,22 +1117,36 @@ trexio_read_$group_dset$_64 (trexio_t* const file, $group_dset_dtype_double$* co
 
   assert(file->back_end < TREXIO_INVALID_BACK_END);
 
+  rc = TREXIO_FAILURE;
   switch (file->back_end) {
     
   case TREXIO_TEXT:
-    return trexio_text_read_$group_dset$(file, $group_dset$, rank, dims);
+    rc = trexio_text_read_$group_dset$(file, $group_dset$, rank, dims);
     break;
 
   case TREXIO_HDF5:
-    return trexio_hdf5_read_$group_dset$(file, $group_dset$, rank, dims);
+    rc = trexio_hdf5_read_$group_dset$(file, $group_dset$, rank, dims);
     break;
 /*
   case TREXIO_JSON:
-    return trexio_json_read_$group_dset$(file, $group_dset$, rank, dims);
+    rc = trexio_json_read_$group_dset$(file, $group_dset$, rank, dims);
     break;
 ,*/
   }
-  return TREXIO_FAILURE;
+  if (rc != TREXIO_SUCCESS) return rc;
+  
+ /* Handle index type */
+  if ($is_index$) {
+    uint64_t dim_size = 1;
+    for (uint32_t i=0; i<rank; ++i){
+        dim_size *= dims[i];
+    }
+    for (uint64_t i=0; i<dim_size; ++i){
+       $group_dset$[i] += ($group_dset_dtype_single$) 1;
+    }
+  }
+  
+  return TREXIO_SUCCESS;
 }
      #+end_src
 
@@ -1122,30 +1164,56 @@ trexio_write_$group_dset$_64 (trexio_t* const file, const $group_dset_dtype_doub
 
  /* Error handling for this call is added by the generator */
   rc = trexio_read_$group_dset_dim$_64(file, &($group_dset_dim$));
+  if (rc != TREXIO_SUCCESS) return rc;
 
   if ($group_dset_dim$ == 0L) return TREXIO_INVALID_NUM;
 
   uint32_t rank = $group_dset_rank$;
   uint64_t dims[$group_dset_rank$] = {$group_dset_dim_list$};
 
+  $group_dset_dtype_double$* $group_dset$_p = $group_dset$;
+
+ /* Handle index type */
+  if ($is_index$) {
+
+    uint64_t dim_size = 1;
+    for (uint32_t i=0; i<rank; ++i){
+        dim_size *= dims[i];
+    }
+
+    $group_dset$_p = CALLOC(dim_size, $group_dset_dtype_double$);
+    if ($group_dset$_p == NULL) return TREXIO_ALLOCATION_FAILED;
+
+    for (uint64_t i=0; i<dim_size; ++i){
+       $group_dset$_p[i] = $group_dset$_p[i] - ($group_dset_dtype_single$) 1;
+    }
+  }
+
   assert(file->back_end < TREXIO_INVALID_BACK_END);
 
+  rc = TREXIO_FAILURE;
   switch (file->back_end) {
 
   case TREXIO_TEXT:
-    return trexio_text_write_$group_dset$(file, $group_dset$, rank, dims);
+    rc = trexio_text_write_$group_dset$(file, $group_dset$_p, rank, dims);
     break;
 
   case TREXIO_HDF5:
-    return trexio_hdf5_write_$group_dset$(file, $group_dset$, rank, dims);
+    rc = trexio_hdf5_write_$group_dset$(file, $group_dset$_p, rank, dims);
     break;
 /*
   case TREXIO_JSON:
-    return trexio_json_write_$group_dset$(file, $group_dset$, rank, dims);
+    rc = trexio_json_write_$group_dset$(file, $group_dset$_p, rank, dims);
     break;
 ,*/
   }
-  return TREXIO_FAILURE;
+
+ /* Handle index type */
+  if ($is_index$) {
+    FREE($group_dset$_p);
+  }
+
+  return rc;
 }
      #+end_src
 
@@ -1169,7 +1237,7 @@ trexio_read_$group_dset$_32 (trexio_t* const file, $group_dset_dtype_single$* co
   uint64_t dims[$group_dset_rank$] = {$group_dset_dim_list$};
 
   uint64_t dim_size = 1;
-  for (unsigned int i=0; i<rank; ++i){
+  for (uint32_t i=0; i<rank; ++i){
     dim_size *= dims[i];
   }
 
@@ -1201,9 +1269,15 @@ trexio_read_$group_dset$_32 (trexio_t* const file, $group_dset_dtype_single$* co
     return rc;
   }
 
+  if ($is_index$) {
+    for (uint64_t i=0; i<dim_size; ++i){
+      $group_dset$[i] = ($group_dset_dtype_single$) $group_dset$_64[i] + ($group_dset_dtype_single$) 1;
+    }
+  } else {
     for (uint64_t i=0; i<dim_size; ++i){
       $group_dset$[i] = ($group_dset_dtype_single$) $group_dset$_64[i];
     }
+  }
 
   FREE($group_dset$_64);
   return TREXIO_SUCCESS;
@@ -1231,7 +1305,7 @@ trexio_write_$group_dset$_32 (trexio_t* const file, const $group_dset_dtype_sing
   uint64_t dims[$group_dset_rank$] = {$group_dset_dim_list$};
 
   uint64_t dim_size = 1;
-  for (unsigned int i=0; i<rank; ++i){
+  for (uint32_t i=0; i<rank; ++i){
     dim_size *= dims[i];
   }
 
@@ -1239,9 +1313,15 @@ trexio_write_$group_dset$_32 (trexio_t* const file, const $group_dset_dtype_sing
   if ($group_dset$_64 == NULL) return TREXIO_ALLOCATION_FAILED;
 
  /* A type conversion from single precision to double reqired since back end only accepts 64-bit data */
+  if ($is_index$) {
+    for (uint64_t i=0; i<dim_size; ++i){
+      $group_dset$_64[i] = ($group_dset_dtype_double$) $group_dset$[i] - ($group_dset_dtype_double$) 1;
+    }
+  } else {
     for (uint64_t i=0; i<dim_size; ++i){
       $group_dset$_64[i] = ($group_dset_dtype_double$) $group_dset$[i];
     }
+  }
 
   assert(file->back_end < TREXIO_INVALID_BACK_END);
 
@@ -2036,9 +2116,18 @@ contains
      character, intent(in), value                 :: mode
      integer(trexio_backend), intent(in), value   :: backend
      character(len=len_trim(filename)+1) :: filename_c
+     integer :: rc
 
      filename_c = trim(filename) // c_null_char
      trexio_open = trexio_open_c(filename_c, mode, backend)
+     if (trexio_open == 0_8) then
+       return
+     endif
+     rc = trexio_set_one_based(trexio_open)
+     if (rc /= TREXIO_SUCCESS) then
+        rc = trexio_close(trexio_open)
+        trexio_open = 0_8
+     endif
    end function trexio_open
   #+end_src
 

tests/test_f.f90

@@ -35,6 +35,8 @@ subroutine test_write(file_name, back_end)
   integer :: rc = 1
 
   integer :: num
+
+  integer :: basis_nucleus_index(12)
   double precision :: charge(12)
   double precision :: coord(3,12)
 
@@ -58,6 +60,8 @@ subroutine test_write(file_name, back_end)
                        0.00000000d0,  2.47304151d0 ,  0.00000000d0 /), &
                        shape(coord) )
 
+  basis_nucleus_index = (/ 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 /)
+
   label = [character(len=8) :: 'C', 'Na','C', 'C 66', 'C','C', 'H 99', 'Ru', 'H', 'H',  'H', 'H' ]
 
   sym_str = 'B3U with some comments'
@@ -89,6 +93,11 @@ subroutine test_write(file_name, back_end)
   deallocate(sym_str)
   call trexio_assert(rc, TREXIO_SUCCESS, 'SUCCESS WRITE POINT GROUP')
 
+
+  rc = trexio_write_basis_nucleus_index(trex_file, basis_nucleus_index)
+  call trexio_assert(rc, TREXIO_SUCCESS, 'SUCCESS WRITE INDEX')
+
+
   rc = trexio_has_nucleus_num(trex_file)
   call trexio_assert(rc, TREXIO_SUCCESS, 'SUCCESS HAS 1')
 
@@ -119,6 +128,7 @@ subroutine test_read(file_name, back_end)
   integer :: rc = 1
   integer :: num, num_read
 
+  integer :: basis_nucleus_index(12)
   double precision :: charge(12)
   double precision :: coord(3,12)
 
@@ -177,6 +187,16 @@ subroutine test_read(file_name, back_end)
   endif
 
 
+  rc = trexio_read_basis_nucleus_index(trex_file, basis_nucleus_index)
+  call trexio_assert(rc, TREXIO_SUCCESS)
+  if (basis_nucleus_index(12) == 12) then
+    write(*,*) 'SUCCESS READ INDEX'
+  else
+    print *, 'FAILURE INDEX CHECK'
+    call exit(-1)
+  endif
+
+
   rc = trexio_read_nucleus_point_group(trex_file, sym_str, 10)
   call trexio_assert(rc, TREXIO_SUCCESS)
   if (sym_str(1:3) == 'B3U') then
@@ -186,6 +206,7 @@ subroutine test_read(file_name, back_end)
     call exit(-1)
   endif
 
+
   rc = trexio_close(trex_file)
   call trexio_assert(rc, TREXIO_SUCCESS)
 

tools/generator_tools.py

@@ -100,7 +100,7 @@ def recursive_populate_file(fname: str, paths: dict, detailed_source: dict) -> N
     fname_new = join('populated',f'pop_{fname}')
     templ_path = get_template_path(fname, paths)
 
-    triggers = ['group_dset_dtype', 'group_dset_h5_dtype', 'default_prec',
+    triggers = ['group_dset_dtype', 'group_dset_h5_dtype', 'default_prec', 'is_index', 
                 'group_dset_f_dtype_default', 'group_dset_f_dtype_double', 'group_dset_f_dtype_single', 
                 'group_dset_dtype_default', 'group_dset_dtype_double', 'group_dset_dtype_single', 
                 'group_dset_rank', 'group_dset_dim_list', 'group_dset_f_dims',
@@ -542,7 +542,7 @@ def split_dset_dict_detailed (datasets: dict) -> tuple:
             default_prec   = '64'
             group_dset_std_dtype_out = '24.16e'
             group_dset_std_dtype_in = 'lf'
-        elif v[0] == 'int':
+        elif v[0] in ['int', 'index']:
             datatype = 'int64_t'
             group_dset_h5_dtype = 'native_int64'
             group_dset_f_dtype_default= 'integer(4)'
@@ -564,6 +564,11 @@ def split_dset_dict_detailed (datasets: dict) -> tuple:
         
         # add the dset name for templates
         tmp_dict['group_dset'] = k
+        # add flag to detect index types
+        if 'index' == v[0]:
+            tmp_dict['is_index'] = 'file->one_based'
+        else:
+            tmp_dict['is_index'] = 'false'
         # add the datatypes for templates
         tmp_dict['dtype'] = datatype
         tmp_dict['group_dset_dtype'] = datatype

trex.json

@@ -1,104 +0,0 @@
-{
-
-"metadata": {
-       "code_num" : [ "int", []                        ]
-  ,        "code" : [ "str", [ "metadata.code_num" ]   ]
-  ,  "author_num" : [ "int", []                        ]
-  ,      "author" : [ "str", [ "metadata.author_num" ] ]
-  , "description" : [ "str", []                        ]
-} ,
-
-"electron": {
-    "up_num" : [ "int", []  ]
-  , "dn_num" : [ "int", []  ]
-} ,
-
-"nucleus": {
-            "num" : [ "int"  , []                     ]
-  ,      "charge" : [ "float", [ "nucleus.num" ]      ]
-  ,       "coord" : [ "float", [ "nucleus.num", "3" ] ]
-  ,       "label" : [ "str"  , [ "nucleus.num" ]      ]
-  , "point_group" : [ "str"  , []                     ]
-} ,
-
-"ecp": {
-            "lmax_plus_1" : [ "int"  , [ "nucleus.num" ]                            ]
-  ,              "z_core" : [ "float", [ "nucleus.num" ]                            ]
-  ,             "local_n" : [ "int"  , [ "nucleus.num" ]                            ]
-  ,     "local_num_n_max" : [ "int"  , []                                           ]
-  ,      "local_exponent" : [ "float", [ "nucleus.num", "ecp.local_num_n_max" ]     ]
-  ,          "local_coef" : [ "float", [ "nucleus.num", "ecp.local_num_n_max" ]     ]
-  ,         "local_power" : [ "int"  , [ "nucleus.num", "ecp.local_num_n_max" ]     ]
-  ,         "non_local_n" : [ "int"  , [ "nucleus.num" ]                            ]
-  , "non_local_num_n_max" : [ "int"  , []                                           ]
-  ,  "non_local_exponent" : [ "float", [ "nucleus.num", "ecp.non_local_num_n_max" ] ]
-  ,      "non_local_coef" : [ "float", [ "nucleus.num", "ecp.non_local_num_n_max" ] ]
-  ,     "non_local_power" : [ "int"  , [ "nucleus.num", "ecp.non_local_num_n_max" ] ]
-} ,
-
-"basis": {
-              "type" : [ "str"  , []                    ]
-  ,      "shell_num" : [ "int"  , []                    ]
-  ,   "shell_center" : [ "int"  , [ "basis.shell_num" ] ]
-  ,  "shell_ang_mom" : [ "int"  , [ "basis.shell_num" ] ]
-  , "shell_prim_num" : [ "int"  , [ "basis.shell_num" ] ]
-  ,   "shell_factor" : [ "float", [ "basis.shell_num" ] ]
-  ,     "prim_index" : [ "int"  , [ "basis.shell_num" ] ]
-  ,       "prim_num" : [ "int"  , []                    ]
-  ,       "exponent" : [ "float", [ "basis.prim_num" ]  ]
-  ,    "coefficient" : [ "float", [ "basis.prim_num" ]  ]
-  ,    "prim_factor" : [ "float", [ "basis.prim_num" ]  ]
-} ,
-
-"ao": {
-        "cartesian" : [ "int"  , []           ]
-  ,           "num" : [ "int"  , []           ]
-  ,         "shell" : [ "int"  , [ "ao.num" ] ]
-  , "normalization" : [ "float", [ "ao.num" ] ]
-} ,
-
-"ao_1e_int": {
-             "overlap" : [ "float", [ "ao.num", "ao.num" ] ]
-  ,          "kinetic" : [ "float", [ "ao.num", "ao.num" ] ]
-  ,    "potential_n_e" : [ "float", [ "ao.num", "ao.num" ] ]
-  ,        "ecp_local" : [ "float", [ "ao.num", "ao.num" ] ]
-  ,    "ecp_non_local" : [ "float", [ "ao.num", "ao.num" ] ]
-  , "core_hamiltonian" : [ "float", [ "ao.num", "ao.num" ] ]
-} ,
-
-"ao_2e_int": {
-       "eri" : [ "float sparse", [ "ao.num", "ao.num", "ao.num", "ao.num" ] ]
-  , "eri_lr" : [ "float sparse", [ "ao.num", "ao.num", "ao.num", "ao.num" ] ]
-} ,
-
-"mo": {
-           "type" : [ "str"  , []                     ]
-  ,         "num" : [ "int"  , []                     ]
-  , "coefficient" : [ "float", [ "mo.num", "ao.num" ] ]
-  ,       "class" : [ "str"  , [ "mo.num" ]           ]
-  ,    "symmetry" : [ "str"  , [ "mo.num" ]           ]
-  ,  "occupation" : [ "float", [ "mo.num" ]           ]
-} ,
-
-"mo_1e_int": {
-             "overlap" : [ "float", [ "mo.num", "mo.num" ] ]
-  ,          "kinetic" : [ "float", [ "mo.num", "mo.num" ] ]
-  ,    "potential_n_e" : [ "float", [ "mo.num", "mo.num" ] ]
-  ,        "ecp_local" : [ "float", [ "mo.num", "mo.num" ] ]
-  ,    "ecp_non_local" : [ "float", [ "mo.num", "mo.num" ] ]
-  , "core_hamiltonian" : [ "float", [ "mo.num", "mo.num" ] ]
-} ,
-
-"mo_2e_int": {
-       "eri" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
-  , "eri_lr" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
-} ,
-
-"rdm": {
-       "one_e" : [ "float"       , [ "mo.num", "mo.num" ]                     ]
-  , "one_e_up" : [ "float"       , [ "mo.num", "mo.num" ]                     ]
-  , "one_e_dn" : [ "float"       , [ "mo.num", "mo.num" ]                     ]
-  ,    "two_e" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
-}
-
-}

trex.org

@@ -7,6 +7,10 @@ column-major order (as in Fortran), and the ordering of the dimensions
 is reversed in the produces JSON configuration file as the library is
 written in C.
 
+In Fortran, the arrays are 1-based and in most other languages the
+arrays are 0-base. Hence, we introduce the ~index~ type which is an
+1-based ~int~ in the Fortran interface and 0-based otherwise.
+
   #+begin_src python :tangle trex.json 
 {
   #+end_src
@@ -158,8 +162,8 @@ written in C.
 * Basis set
 
   We consider here basis functions centered on nuclei. Hence, we enable
-  the possibility to define \emph{dummy atoms} to place basis functions
+  the possibility to define /dummy atoms/ to place basis functions in
-  in random positions.
+  random positions.
 
   The atomic basis set is defined as a list of shells. Each shell $s$ is
   centered on a center $A$, possesses a given angular momentum $l$ and a
@@ -185,22 +189,25 @@ written in C.
   Some codes assume that the contraction coefficients are for a linear
   combination of /normalized/ primitives. This implies that a normalization
   constant for the primitive $ks$ needs to be computed and stored. If
-  this normalization factor is not required, set $f_{ks}$ to one.
+  this normalization factor is not required, $f_{ks}=1$.
   
   Some codes assume that the basis function are normalized. This
   implies the computation of an extra normalization factor, $\mathcal{N}_s$.
-  If the the basis function is not normalized, set $\mathcal{N}_s=1$.
+  If the the basis function is not considered normalized, $\mathcal{N}_s=1$.
 
 
+  All the basis set parameters are stored in one-dimensional arrays:
+
   #+NAME: basis
   | ~type~              | ~str~   |                    | Type of basis set: "Gaussian" or "Slater"                |
-  | ~shell_num~      | ~int~   |                     | Total Number of shells                                   |
+  | ~num~               | ~int~   |                    | Total Number of shells                                   |
-  | ~shell_center~   | ~int~   | ~(basis.shell_num)~ | Nucleus on which the shell is centered ($A$)             |
-  | ~shell_ang_mom~  | ~int~   | ~(basis.shell_num)~ | Angular momentum ~0:S, 1:P, 2:D, ...~                    |
-  | ~shell_prim_num~ | ~int~   | ~(basis.shell_num)~ | Number of primitives in the shell ($N_{\text{prim}}$)    |
-  | ~shell_factor~   | ~float~ | ~(basis.shell_num)~ | Normalization factor of the shell ($\mathcal{N}_s$)      |
-  | ~prim_index~     | ~int~   | ~(basis.shell_num)~ | Index of the first primitive in the complete list        |
   | ~prim_num~          | ~int~   |                    | Total number of primitives                               |
+  | ~nucleus_index~     | ~index~ | ~(nucleus.num)~    | Index of the first shell of each nucleus ($A$)           |
+  | ~nucleus_shell_num~ | ~int~   | ~(nucleus.num)~    | Number of shells for each nucleus                        |
+  | ~shell_ang_mom~     | ~int~   | ~(basis.num)~      | Angular momentum ~0:S, 1:P, 2:D, ...~                    |
+  | ~shell_prim_num~    | ~int~   | ~(basis.num)~      | Number of primitives in the shell ($N_{\text{prim}}$)    |
+  | ~shell_factor~      | ~float~ | ~(basis.num)~      | Normalization factor of the shell ($\mathcal{N}_s$)      |
+  | ~shell_prim_index~  | ~index~ | ~(basis.num)~      | Index of the first primitive in the complete list        |
   | ~exponent~          | ~float~ | ~(basis.prim_num)~ | Exponents of the primitives ($\gamma_{ks})               |
   | ~coefficient~       | ~float~ | ~(basis.prim_num)~ | Coefficients of the primitives ($a_{ks}$)                |
   | ~prim_factor~       | ~float~ | ~(basis.prim_num)~ | Normalization coefficients for the primitives ($f_{ks}$) |
@@ -212,13 +219,14 @@ written in C.
   #+begin_src python :tangle trex.json
       "basis": {
                        "type" : [ "str"  , []                   ]
-        ,      "shell_num" : [ "int"  , []                    ]
+        ,               "num" : [ "int"  , []                   ]
-        ,   "shell_center" : [ "int"  , [ "basis.shell_num" ] ]
-        ,  "shell_ang_mom" : [ "int"  , [ "basis.shell_num" ] ]
-        , "shell_prim_num" : [ "int"  , [ "basis.shell_num" ] ]
-        ,   "shell_factor" : [ "float", [ "basis.shell_num" ] ]
-        ,     "prim_index" : [ "int"  , [ "basis.shell_num" ] ]
         ,          "prim_num" : [ "int"  , []                   ]
+        ,     "nucleus_index" : [ "index"  , [ "nucleus.num" ]    ]
+        , "nucleus_shell_num" : [ "int"  , [ "nucleus.num" ]    ]
+        ,     "shell_ang_mom" : [ "int"  , [ "basis.num" ]      ]
+        ,    "shell_prim_num" : [ "int"  , [ "basis.num" ]      ]
+        ,      "shell_factor" : [ "float", [ "basis.num" ]      ]
+        ,  "shell_prim_index" : [ "index"  , [ "basis.num" ]      ]
         ,          "exponent" : [ "float", [ "basis.prim_num" ] ]
         ,       "coefficient" : [ "float", [ "basis.prim_num" ] ]
         ,       "prim_factor" : [ "float", [ "basis.prim_num" ] ]
@@ -226,6 +234,62 @@ written in C.
   #+end_src
   :end:
 
+  For example, consider H_2 with the following basis set (in GAMESS
+  format), where both the AOs and primitives are considered normalized:
+
+   #+BEGIN_EXAMPLE
+HYDROGEN
+S   5
+1         3.387000E+01           6.068000E-03
+2         5.095000E+00           4.530800E-02
+3         1.159000E+00           2.028220E-01
+4         3.258000E-01           5.039030E-01
+5         1.027000E-01           3.834210E-01
+S   1
+1         3.258000E-01           1.000000E+00
+S   1
+1         1.027000E-01           1.000000E+00
+P   1
+1         1.407000E+00           1.000000E+00
+P   1
+1         3.880000E-01           1.000000E+00
+D   1
+1         1.057000E+00           1.0000000
+   #+END_EXAMPLE
+
+   we have:
+
+   #+BEGIN_EXAMPLE
+type     = "Gaussian"
+num      = 12
+prim_num = 20
+
+nucleus_index    = [0 , 6]
+shell_ang_mom    = [0 , 0 , 0 , 1 , 1 , 2 , 0 , 0 , 0 , 1 , 1 , 2 ]
+shell_prim_num   = [5 , 1 , 1 , 1 , 1 , 1 , 5 , 1 , 1 , 1 , 1 , 1 ]
+shell_prim_index = [0 , 5 , 6 , 7 , 8 , 9 , 10, 15, 16, 17, 18, 19]
+shell_factor     = [1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.]
+
+exponent =
+[ 33.87, 5.095, 1.159, 0.3258, 0.1027, 0.3258, 0.1027, 1.407,
+  0.388, 1.057, 33.87, 5.095, 1.159, 0.3258, 0.1027, 0.3258, 0.1027, 1.407,
+  0.388, 1.057]
+
+coefficient =
+[ 0.006068, 0.045308, 0.202822, 0.503903, 0.383421, 1.0, 1.0,
+  1.0, 1.0, 1.0, 0.006068, 0.045308, 0.202822, 0.503903, 0.383421, 1.0, 1.0,
+  1.0, 1.0, 1.0]
+
+prim_factor =
+[ 1.0006253235944540e+01, 2.4169531573445120e+00, 7.9610924849766440e-01
+  3.0734305383061117e-01, 1.2929684417481876e-01, 3.0734305383061117e-01,
+  1.2929684417481876e-01, 2.1842769845268308e+00, 4.3649547399719840e-01,
+  1.8135965626177861e+00, 1.0006253235944540e+01, 2.4169531573445120e+00,
+  7.9610924849766440e-01, 3.0734305383061117e-01, 1.2929684417481876e-01,
+  3.0734305383061117e-01, 1.2929684417481876e-01, 2.1842769845268308e+00,
+  4.3649547399719840e-01, 1.8135965626177861e+00 ]
+   #+END_EXAMPLE
+
 * Atomic orbitals
 
   Going from the atomic basis set to AOs implies a systematic
@@ -273,7 +337,7 @@ written in C.
   #+NAME: ao
   | ~cartesian~     | ~int~   |            | ~1~: true, ~0~: false           |
   | ~num~           | ~int~   |            | Total number of atomic orbitals |
-  | ~shell~         | ~int~   | ~(ao.num)~ | basis set shell for each AO     |
+  | ~shell~         | ~index~ | ~(ao.num)~ | basis set shell for each AO     |
   | ~normalization~ | ~float~ | ~(ao.num)~ | Normalization factors           |
 
   #+CALL: json(data=ao, title="ao")
@@ -284,7 +348,7 @@ written in C.
       "ao": {
               "cartesian" : [ "int"  , []           ]
         ,           "num" : [ "int"  , []           ]
-        ,         "shell" : [ "int"  , [ "ao.num" ] ]
+        ,         "shell" : [ "index", [ "ao.num" ] ]
         , "normalization" : [ "float", [ "ao.num" ] ]
       } ,
   #+end_src