make dim an optional argument in read_ functions

if dim is None - the function read all necessary dimensions from the TREXIO file

python/test/test_api.py

@@ -53,7 +53,7 @@ charges_np = np.array(charges, dtype=np.float64)
 
 # function call below works with both lists and numpy arrays, dimension needed for memory-safety is derived 
 # from the size of the list/array by SWIG using typemaps from numpy.i
-rc = tr.write_nucleus_charge(test_file, charges_np)
+tr.write_nucleus_charge(test_file, charges_np)
 
 # initialize arrays of nuclear indices as a list and convert it to numpy array
 indices = [i for i in range(nucleus_num)]
@@ -64,6 +64,25 @@ indices_np = np.array(indices, dtype=np.int32)
 # from the size of the list/array by SWIG using typemacs from numpy.i
 tr.write_basis_nucleus_index(test_file, indices_np)
 
+# initialize a list of nuclear coordinates
+coords = [
+  0.00000000 ,  1.39250319 ,  0.00000000 ,
+ -1.20594314 ,  0.69625160 ,  0.00000000 ,
+ -1.20594314 , -0.69625160 ,  0.00000000 ,
+  0.00000000 , -1.39250319 ,  0.00000000 ,
+  1.20594314 , -0.69625160 ,  0.00000000 ,
+  1.20594314 ,  0.69625160 ,  0.00000000 ,
+ -2.14171677 ,  1.23652075 ,  0.00000000 ,
+ -2.14171677 , -1.23652075 ,  0.00000000 ,
+  0.00000000 , -2.47304151 ,  0.00000000 ,
+  2.14171677 , -1.23652075 ,  0.00000000 ,
+  2.14171677 ,  1.23652075 ,  0.00000000 ,
+  0.00000000 ,  2.47304151 ,  0.00000000 ,
+  ]
+
+# write coordinates in the file
+tr.write_nucleus_coord(test_file, coords)
+
 point_group = 'B3U'
 
 # write nucleus_point_group in the file
@@ -117,6 +136,10 @@ assert rindices_np.dtype is np.dtype(np.int32)
 for i in range(nucleus_num):
     assert rindices_np[i]==indices_np[i]
 
+# read nuclear coordinates without providing optional argument dim
+rcoords_np = tr.read_nucleus_coord(test_file2)
+assert rcoords_np.size==nucleus_num*3
+
 # read array of nuclear labels
 rlabels_2d = tr.read_nucleus_label(test_file2, dim=nucleus_num)
 print(rlabels_2d)

src/templates_front/templator_front.org

@@ -1860,7 +1860,7 @@ def write_$group_dset$(trexio_file, dset_w) -> None:
      #+end_src
 
      #+begin_src python :tangle read_dset_data_front.py
-def read_$group_dset$(trexio_file, dim: int): 
+def read_$group_dset$(trexio_file, dim = None): 
     """Read the $group_dset$ array of numbers from the TREXIO file.
 
     Parameters:
@@ -1868,8 +1868,9 @@ def read_$group_dset$(trexio_file, dim: int):
     trexio_file:
         TREXIO file handle.
 
-    dim: int
+    dim (Optional): int
         Size of the block to be read from the file (i.e. how many items of $group_dset$ will be returned)
+        If None, the function will read all necessary array dimensions from the file.
 
     Returns:
  ~dset_r~: numpy.ndarray
@@ -1881,6 +1882,16 @@ def read_$group_dset$(trexio_file, dim: int):
     """
 
     
+    # if dim is not specified, read dimensions from the TREXIO file
+    if dim is None:
+        $group_dset_dim$ = read_$group_dset_dim$(trexio_file) 
+        
+        dims_list = [$group_dset_dim_list$]
+        dim = 1
+        for i in range($group_dset_rank$):
+            dim *= dims_list[i]
+    
+
     try:
         rc, dset_r = trexio_read_safe_$group_dset$(trexio_file, dim)
         assert rc==TREXIO_SUCCESS
@@ -2381,7 +2392,7 @@ def write_$group_dset$(trexio_file, dset_w: list) -> None:
      #+end_src
 
      #+begin_src python :tangle read_dset_str_front.py
-def read_$group_dset$(trexio_file, dim: int) -> list: 
+def read_$group_dset$(trexio_file, dim = None) -> list: 
     """Read the $group_dset$ array of strings from the TREXIO file.
 
     Parameters:
@@ -2389,8 +2400,9 @@ def read_$group_dset$(trexio_file, dim: int) -> list:
     trexio_file:
         TREXIO file handle.
 
-    dim: int
+    dim (Optional): int
         Size of the block to be read from the file (i.e. how many items of $group_dset$ will be returned)
+        If None, the function will read all necessary array dimensions from the file.
 
     Returns:
  ~dset_r~: list
@@ -2401,6 +2413,17 @@ def read_$group_dset$(trexio_file, dim: int) -> list:
         - Exception from some other error (e.g. RuntimeError).
     """
 
+
+    # if dim is not specified, read dimensions from the TREXIO file
+    if dim is None:
+        $group_dset_dim$ = read_$group_dset_dim$(trexio_file) 
+        
+        dims_list = [$group_dset_dim_list$]
+        dim = 1
+        for i in range($group_dset_rank$):
+            dim *= dims_list[i]
+
+
     try:
         rc, dset_1d_r = trexio_read_$group_dset$_low(trexio_file, PYTREXIO_MAX_STR_LENGTH)
         assert rc==TREXIO_SUCCESS
@@ -2409,6 +2432,7 @@ def read_$group_dset$(trexio_file, dim: int) -> list:
     except:
         raise    
 
+
     try:
         dset_full = dset_1d_r.split(TREXIO_DELIM)
         dset_2d_r = [dset_full[i] for i in range(dim) if dset_full[i]]