Add index in files

configure.ac

@@ -56,7 +56,7 @@ 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

@@ -49,11 +49,12 @@ 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"
 /*
@@ -70,6 +71,7 @@ typedef int32_t trexio_exit_code;
 #include "trexio.h"
 #include <pthread.h>
 #include <assert.h>
+#include <stdbool.h>
   #+end_src
 
 * Coding conventions
@@ -421,11 +423,12 @@ 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
@@ -458,11 +461,13 @@ 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);
@@ -509,16 +514,15 @@ 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);
 
@@ -545,7 +549,6 @@ trexio_open(const char* file_name, const char mode,
   }
 
   if (rc != TREXIO_SUCCESS) {
-    free(result->file_name);
     free(result);
     return NULL;
   }
@@ -571,7 +574,6 @@ trexio_open(const char* file_name, const char mode,
   }
 
   if (rc != TREXIO_SUCCESS) {
-    free(result->file_name);
     free(result);
     return NULL;
   }
@@ -591,6 +593,25 @@ 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
+
 ** File closing
 
  ~trexio_close~ closes an existing ~trexio_t~ file.
@@ -634,7 +655,6 @@ trexio_close (trexio_t* file)
   }
 
   if (rc != TREXIO_SUCCESS) {
-    FREE(file->file_name);
     FREE(file);
     return rc;
   }
@@ -661,8 +681,6 @@ trexio_close (trexio_t* file)
 
  /* Terminate front end */
 
-  FREE(file->file_name);
-
   int irc = pthread_mutex_destroy( &(file->thread_lock) );
 
   free(file);

trex.json

@@ -39,11 +39,11 @@
 "basis": {
               "type" : [ "str"  , []                    ]
   ,      "shell_num" : [ "int"  , []                    ]
-  ,   "shell_center" : [ "int"  , [ "basis.shell_num" ] ]
+  ,   "shell_center" : [ "index", [ "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_index" : [ "index", [ "basis.shell_num" ] ]
   ,       "prim_num" : [ "int"  , []                    ]
   ,       "exponent" : [ "float", [ "basis.prim_num" ]  ]
   ,    "coefficient" : [ "float", [ "basis.prim_num" ]  ]
@@ -53,7 +53,7 @@
 "ao": {
         "cartesian" : [ "int"  , []           ]
   ,           "num" : [ "int"  , []           ]
-  ,         "shell" : [ "int"  , [ "ao.num" ] ]
+  ,         "shell" : [ "index", [ "ao.num" ] ]
   , "normalization" : [ "float", [ "ao.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
@@ -195,11 +199,11 @@ written in C.
   #+NAME: basis
   | ~type~           | ~str~   |                     | Type of basis set: "Gaussian" or "Slater"                |
   | ~shell_num~      | ~int~   |                     | Total Number of shells                                   |
-  | ~shell_center~   | ~int~   | ~(basis.shell_num)~ | Nucleus on which the shell is centered ($A$)             |
+  | ~shell_center~   | ~index~ | ~(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_index~     | ~index~ | ~(basis.shell_num)~ | Index of the first primitive in the complete list        |
   | ~prim_num~       | ~int~   |                     | Total number of primitives                               |
   | ~exponent~       | ~float~ | ~(basis.prim_num)~  | Exponents of the primitives ($\gamma_{ks})               |
   | ~coefficient~    | ~float~ | ~(basis.prim_num)~  | Coefficients of the primitives ($a_{ks}$)                |
@@ -213,11 +217,11 @@ written in C.
       "basis": {
                     "type" : [ "str"  , []                    ]
         ,      "shell_num" : [ "int"  , []                    ]
-        ,   "shell_center" : [ "int"  , [ "basis.shell_num" ] ]
+        ,   "shell_center" : [ "index", [ "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_index" : [ "index", [ "basis.shell_num" ] ]
         ,       "prim_num" : [ "int"  , []                    ]
         ,       "exponent" : [ "float", [ "basis.prim_num" ]  ]
         ,    "coefficient" : [ "float", [ "basis.prim_num" ]  ]
@@ -250,8 +254,7 @@ written in C.
   \chi_i (\mathbf{r}) = \mathcal{N}_i\, P_{\eta(i)}(\mathbf{r})\, R_{\theta(i)} (\mathbf{r})
   \]
 
-  where $i$ is the atomic orbital index,
+  where $i$ is the atomic orbital index, $P$ encodes for either the
-  $P$ encodes for either the
   polynomials or the spherical harmonics, $\theta(i)$ returns the
   shell on which the AO is expanded, and $\eta(i)$ denotes which
   angular function is chosen.
@@ -273,7 +276,7 @@ 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 +287,7 @@ written in C.
       "ao": {
               "cartesian" : [ "int"  , []           ]
         ,           "num" : [ "int"  , []           ]
-        ,         "shell" : [ "int"  , [ "ao.num" ] ]
+        ,         "shell" : [ "index", [ "ao.num" ] ]
         , "normalization" : [ "float", [ "ao.num" ] ]
       } ,
   #+end_src