Merge branch 'master' into index

.github/workflows/actions.yml

@@ -0,0 +1,63 @@
+name: TREXIO CI
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+  
+jobs:
+  trexio_ubuntu:
+
+    runs-on: ubuntu-latest
+    name: x86 Ubuntu latest
+
+    steps:
+      - uses: actions/checkout@v2
+    
+      - name: install dependencies    
+        run: |
+          sudo add-apt-repository ppa:kelleyk/emacs
+          sudo apt-get install libhdf5-dev emacs26
+        
+      - name: configure with autotools
+        run: |
+          ./autogen.sh
+          TREXIO_DEVEL=1 ./configure --enable-silent-rules
+        
+      - name: compile TREXIO
+        run: make -j 2
+        
+      - name: check TREXIO
+        run: make check
+        
+      - name: clean
+        run: make clean
+
+  trexio_macos:
+
+    runs-on: macos-latest
+    name: x86 MacOS latest
+
+    steps:
+      - uses: actions/checkout@v2
+      
+      - name: install dependencies
+        run: |
+          brew install emacs
+          brew install hdf5
+          brew install automake
+        
+      - name: configure with autotools
+        run: |
+          ./autogen.sh
+          TREXIO_DEVEL=1 ./configure FC=gfortran-10 --enable-silent-rules
+        
+      - name: compile TREXIO
+        run: make -j 2
+        
+      - name: check TREXIO
+        run: make check
+        
+      - name: clean
+        run: make clean

Makefile.am

@@ -87,7 +87,7 @@ tests_test_f_SOURCES = $(test_trexio_f) tests/test_f.f90
 tests_test_f_LDADD   = src/libtrexio.la
 tests_test_f_LDFLAGS = -no-install
 
-$(test_trexio_f):
+$(test_trexio_f): $(trexio_f)
 	cp $(trexio_f) $(test_trexio_f)
 
 clean-local:

src/templates_front/templator_front.org

@@ -25,11 +25,12 @@ module trexio
   implicit none
 
   integer, parameter :: trexio_exit_code = 4
+  integer, parameter :: trexio_backend = 4
 
-  integer, parameter :: TREXIO_HDF5 = 0
+  integer(trexio_backend), parameter :: TREXIO_HDF5 = 0
-  integer, parameter :: TREXIO_TEXT = 1
+  integer(trexio_backend), parameter :: TREXIO_TEXT = 1
-! integer, parameter :: TREXIO_JSON = 2
+! integer(trexio_backend), parameter :: TREXIO_JSON = 2
-  integer, parameter :: TREXIO_INVALID_BACK_END = 2
+  integer(trexio_backend), parameter :: TREXIO_INVALID_BACK_END = 2
    #+end_src
 
   #+end_src
@@ -586,9 +587,10 @@ trexio_open(const char* file_name, const char mode,
 interface
    integer(8) function trexio_open_c (filename, mode, backend) bind(C, name="trexio_open")
      use, intrinsic :: iso_c_binding
-     character(kind=c_char), dimension(*)  :: filename
+     import
-     character, intent(in), value          :: mode
+     character(kind=c_char), dimension(*)       :: filename
-     integer, intent(in), value            :: backend
+     character, intent(in), value               :: mode
+     integer(trexio_backend), intent(in), value :: backend
    end function trexio_open_c
 end interface
    #+end_src
@@ -1560,10 +1562,9 @@ contains
    integer(8) function trexio_open (filename, mode, backend)
      use, intrinsic :: iso_c_binding
      implicit none
-     character(len=*)      :: filename
+     character(len=*)                             :: filename
-     character, intent(in), value :: mode
+     character, intent(in), value                 :: mode
-     integer, intent(in), value   :: backend
+     integer(trexio_backend), intent(in), value   :: backend
-
      character(len=len_trim(filename)+1) :: filename_c
      integer :: rc
 

src/templates_hdf5/templator_hdf5.org

@@ -332,7 +332,7 @@ trexio_hdf5_read_$group_dset$ (trexio_t* const file, $group_dset_dtype$* const $
  /* High-level H5LT API. No need to deal with dataspaces and datatypes */
   status = H5LTread_dataset(f->$group$_group,
 			    $GROUP_DSET$_NAME,
-			    H5T_NATIVE_$GROUP_DSET_H5_DTYPE$,
+			    H5T_$GROUP_DSET_H5_DTYPE$,
 			    $group_dset$);
   if (status < 0) return TREXIO_FAILURE;
 
@@ -362,7 +362,7 @@ trexio_hdf5_write_$group_dset$ (trexio_t* const file, const $group_dset_dtype$*
     const herr_t status = H5LTmake_dataset(f->$group$_group,
 					   $GROUP_DSET$_NAME,
 					   (int) rank, (const hsize_t*) dims,
-					   H5T_NATIVE_$GROUP_DSET_H5_DTYPE$,
+					   H5T_$GROUP_DSET_H5_DTYPE$,
 					   $group_dset$);
     if (status < 0) return TREXIO_FAILURE;
 
@@ -372,7 +372,7 @@ trexio_hdf5_write_$group_dset$ (trexio_t* const file, const $group_dset_dtype$*
     if (dset_id <= 0) return TREXIO_INVALID_ID;
 
     const herr_t status = H5Dwrite(dset_id,
-				   H5T_NATIVE_$GROUP_DSET_H5_DTYPE$,
+				   H5T_$GROUP_DSET_H5_DTYPE$,
 				   H5S_ALL, H5S_ALL, H5P_DEFAULT,
 				   $group_dset$);
 

tests/test.c

@@ -15,11 +15,15 @@ int main() {
   assert (rc == 0);
   test_write("test_write.h5", TREXIO_HDF5);
   test_read ("test_write.h5", TREXIO_HDF5);
+  rc = system("rm -rf test_write.h5");
+  assert (rc == 0);
 
   rc = system("rm -rf test_write.dir");
   assert (rc == 0);
   test_write("test_write.dir", TREXIO_TEXT);
   test_read ("test_write.dir", TREXIO_TEXT);
+  rc = system("rm -rf test_write.dir");
+  assert (rc == 0);
 
   return 0;
 }

tests/test_f.f90

@@ -1,21 +1,39 @@
 program test_trexio
+  use trexio
+  implicit none
 
-  call test_write()
+  call system('rm -rf trexio_test_fort')
-  call test_read()
+  print *, 'call test_write(''trexio_test_fort'', TREXIO_TEXT)'
+  call test_write('trexio_test_fort', TREXIO_TEXT)
+  print *, 'call test_read(''trexio_test_fort'', TREXIO_TEXT)'
+  call test_read('trexio_test_fort', TREXIO_TEXT)
+  call system('rm -rf trexio_test_fort')
+
+  call system('rm -rf trexio_test_fort')
+  print *, 'call test_write(''trexio_test_fort.h5'', TREXIO_HDF5)'
+  call test_write('trexio_test_fort.h5', TREXIO_HDF5)
+  print *, 'call test_read(''trexio_test_fort.h5'', TREXIO_HDF5)'
+  call test_read('trexio_test_fort.h5', TREXIO_HDF5)
+  call system('rm -rf trexio_test_fort.h5')
 
 end program test_trexio
 
-subroutine test_write()
+subroutine test_write(file_name, back_end)
 
 ! ============ Test write functionality =============== !
 
   use trexio
   implicit none
 
+  character*(*), intent(in) :: file_name
+  integer(trexio_backend), intent(in) :: back_end
+
   integer(8) :: trex_file
 
   integer :: rc = 1
   integer :: num
+  character*(128) :: str
+
 
   double precision :: charge(12)
   double precision :: coord(3,12)
@@ -39,33 +57,84 @@ subroutine test_write()
 
 ! ================= START OF TEST ===================== !
 
-  trex_file = trexio_open('trexio_test_fort', 'w', TREXIO_TEXT)
+  trex_file = trexio_open(file_name, 'w', back_end)
-!  trex_file = trexio_open('test_hdf5_fort.h5', 'w', TREXIO_HDF5)
 
   rc = trexio_has_nucleus_num(trex_file)
-  if (rc == TREXIO_HAS_NOT) write(*,*) 'SUCCESS HAS NOT 1'
+  if (rc == TREXIO_HAS_NOT) then
+    write(*,*) 'SUCCESS HAS NOT 1'
+  else
+    call trexio_string_of_error(TREXIO_READONLY,str)
+    print *, trim(str)
+    call exit(1)
+  endif
+
   rc = trexio_has_nucleus_charge(trex_file)
-  if (rc == TREXIO_HAS_NOT) write(*,*) 'SUCCESS HAS NOT 2'
+  if (rc == TREXIO_HAS_NOT) then
+    write(*,*) 'SUCCESS HAS NOT 2'
+  else
+    call trexio_string_of_error(TREXIO_READONLY,str)
+    print *, trim(str)
+    call exit(1)
+  endif
+
 
   rc = trexio_write_nucleus_num(trex_file, num)
-  if (rc == TREXIO_SUCCESS) write(*,*) 'SUCCESS WRITE NUM'
+  if (rc == TREXIO_SUCCESS) then
+    write(*,*) 'SUCCESS WRITE NUM'
+  else
+    call trexio_string_of_error(TREXIO_READONLY,str)
+    print *, trim(str)
+    call exit(1)
+  endif
 
   rc = trexio_write_nucleus_charge(trex_file, charge)
-  if (rc == TREXIO_SUCCESS) write(*,*) 'SUCCESS WRITE CHARGE'
+  if (rc == TREXIO_SUCCESS) then
+    write(*,*) 'SUCCESS WRITE CHARGE'
+  else
+    call trexio_string_of_error(TREXIO_READONLY,str)
+    print *, trim(str)
+    call exit(1)
+  endif
 
   rc = trexio_write_nucleus_coord(trex_file, coord)
-  if (rc == TREXIO_SUCCESS) write(*,*) 'SUCCESS WRITE COORD'
+  if (rc == TREXIO_SUCCESS) then
+    write(*,*) 'SUCCESS WRITE COORD'
+  else
+    call trexio_string_of_error(TREXIO_READONLY,str)
+    print *, trim(str)
+    call exit(1)
+  endif
 
   rc = trexio_has_nucleus_num(trex_file)
-  if (rc == TREXIO_SUCCESS) write(*,*) 'SUCCESS HAS 1'
+  if (rc == TREXIO_SUCCESS) then
+    write(*,*) 'SUCCESS HAS 1'
+  else
+    call trexio_string_of_error(TREXIO_READONLY,str)
+    print *, trim(str)
+    call exit(1)
+  endif
+
   rc = trexio_has_nucleus_coord(trex_file)
-  if (rc == TREXIO_SUCCESS) write(*,*) 'SUCCESS HAS 2'
+  if (rc == TREXIO_SUCCESS) then
+    write(*,*) 'SUCCESS HAS 2'
+  else
+    call trexio_string_of_error(TREXIO_READONLY,str)
+    print *, trim(str)
+    call exit(1)
+  endif
 
   rc = trexio_close(trex_file)
-  if (rc == TREXIO_SUCCESS) write(*,*) 'SUCCESS CLOSE'
+  if (rc == TREXIO_SUCCESS) then
+    write(*,*) 'SUCCESS CLOSE'
+  else
+    call trexio_string_of_error(TREXIO_READONLY,str)
+    print *, trim(str)
+    call exit(1)
+  endif
+
 
 ! ---------------------------------- !
-! to modify fiels of existing file:
+! to modify fields of existing file:
 ! text backend -> open with 'w'
 ! hdf5 backend -> open with 'a'
 ! ---------------------------------- !
@@ -85,13 +154,19 @@ subroutine test_write()
 
 end subroutine test_write
 
-subroutine test_read()
+
+
+
+subroutine test_read(file_name, back_end)
 
 ! ============ Test read functionality =============== !
 
   use trexio
   implicit none
 
+  character*(*), intent(in) :: file_name
+  integer(trexio_backend), intent(in) :: back_end
+
   integer(8) :: trex_file
 
   integer :: rc = 1
@@ -106,26 +181,48 @@ subroutine test_read()
 
 ! ================= START OF TEST ===================== !
 
-  trex_file = trexio_open('trexio_test_fort', 'r', TREXIO_TEXT)
+  trex_file = trexio_open(file_name, 'r', back_end)
-!  trex_file = trexio_open('test_hdf5_fort.h5', 'r', TREXIO_HDF5)
 
   rc = trexio_read_nucleus_num(trex_file, num_read)
 
-  if (rc == TREXIO_SUCCESS .and. num_read == num) write(*,*) 'SUCCESS READ NUM'
+  if (rc == TREXIO_SUCCESS .and. num_read == num) then
+    write(*,*) 'SUCCESS READ NUM'
+  else
+    call trexio_string_of_error(TREXIO_READONLY,str)
+    print *, trim(str)
+    call exit(1)
+  endif
+
 
   rc = trexio_read_nucleus_charge(trex_file, charge)
 
-  if (rc == TREXIO_SUCCESS .and. (abs(charge(11) - 1.0) < 1.0D-8) ) write(*,*) 'SUCCESS READ CHARGE'
+  if (rc == TREXIO_SUCCESS .and. (dabs(charge(11) - 1.d0) < 1.0D-8) ) then
+    write(*,*) 'SUCCESS READ CHARGE'
+  else
+    call trexio_string_of_error(TREXIO_READONLY,str)
+    print *, trim(str)
+    call exit(-1)
+  endif
 
   rc = trexio_read_nucleus_coord(trex_file, coord)
 
-  if (rc == TREXIO_SUCCESS .and. (abs(coord(2,1) - 1.39250319d0) < 1.0D-8) ) write(*,*) 'SUCCESS READ COORD'
+  if (rc == TREXIO_SUCCESS .and. (dabs(coord(2,1) - 1.39250319d0) < 1.0D-8) ) then
+    write(*,*) 'SUCCESS READ COORD'
+  else
+    call trexio_string_of_error(TREXIO_READONLY,str)
+    print *, trim(str)
+    call exit(-1)
+  endif
 
   rc = trexio_close(trex_file)
-  if (rc == TREXIO_SUCCESS) write(*,*) 'SUCCESS CLOSE'
+  if (rc == TREXIO_SUCCESS) then
+    write(*,*) 'SUCCESS CLOSE'
+  else
+    call trexio_string_of_error(TREXIO_READONLY,str)
+    print *, trim(str)
+    call exit(1)
+  endif
 
-  call trexio_string_of_error(TREXIO_READONLY,str)
-  write(*,*) str
 
 ! ================= END OF TEST ===================== !
 

tools/generator_tools.py

@@ -462,7 +462,7 @@ def split_dset_dict_detailed (datasets: dict) -> tuple:
         # specify details required to replace templated variables later
         if v[0] == 'float':
             datatype = 'double'
-            group_dset_h5_dtype       = 'double'
+            group_dset_h5_dtype       = 'native_double'
             group_dset_f_dtype_default= 'real(8)'
             group_dset_f_dtype_double = 'real(8)'
             group_dset_f_dtype_single = 'real(4)'
@@ -474,7 +474,7 @@ def split_dset_dict_detailed (datasets: dict) -> tuple:
             group_dset_std_dtype_in = 'lf'
         elif v[0] == 'int':
             datatype = 'int64_t'
-            group_dset_h5_dtype = 'int64'
+            group_dset_h5_dtype = 'native_int64'
             group_dset_f_dtype_default= 'integer(4)'
             group_dset_f_dtype_double = 'integer(8)'
             group_dset_f_dtype_single = 'integer(4)'

trex.json

@@ -37,17 +37,18 @@
 } ,
 
 "basis": {
-              "type" : [ "str"  , []                    ]
+                 "type" : [ "str"  , []                   ]
-  ,      "shell_num" : [ "int"  , []                    ]
+  ,               "num" : [ "int"  , []                   ]
-  ,   "shell_center" : [ "index", [ "basis.shell_num" ] ]
+  ,          "prim_num" : [ "int"  , []                   ]
-  ,  "shell_ang_mom" : [ "int"  , [ "basis.shell_num" ] ]
+  ,     "nucleus_index" : [ "index"  , [ "nucleus.num" ]    ]
-  , "shell_prim_num" : [ "int"  , [ "basis.shell_num" ] ]
+  , "nucleus_shell_num" : [ "int"  , [ "nucleus.num" ]    ]
-  ,   "shell_factor" : [ "float", [ "basis.shell_num" ] ]
+  ,     "shell_ang_mom" : [ "int"  , [ "basis.num" ]      ]
-  ,     "prim_index" : [ "index", [ "basis.shell_num" ] ]
+  ,    "shell_prim_num" : [ "int"  , [ "basis.num" ]      ]
-  ,       "prim_num" : [ "int"  , []                    ]
+  ,      "shell_factor" : [ "float", [ "basis.num" ]      ]
-  ,       "exponent" : [ "float", [ "basis.prim_num" ]  ]
+  ,  "shell_prim_index" : [ "index"  , [ "basis.num" ]      ]
-  ,    "coefficient" : [ "float", [ "basis.prim_num" ]  ]
+  ,          "exponent" : [ "float", [ "basis.prim_num" ] ]
-  ,    "prim_factor" : [ "float", [ "basis.prim_num" ]  ]
+  ,       "coefficient" : [ "float", [ "basis.prim_num" ] ]
+  ,       "prim_factor" : [ "float", [ "basis.prim_num" ] ]
 } ,
 
 "ao": {

trex.org

@@ -162,8 +162,8 @@ arrays are 0-base. Hence, we introduce the ~index~ type which is an
 * 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
@@ -189,25 +189,28 @@ arrays are 0-base. Hence, we introduce the ~index~ type which is an
   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"                |
+  | ~type~              | ~str~   |                    | Type of basis set: "Gaussian" or "Slater"                |
-  | ~shell_num~      | ~int~   |                     | Total Number of shells                                   |
+  | ~num~               | ~int~   |                    | Total Number of shells                                   |
-  | ~shell_center~   | ~index~ | ~(basis.shell_num)~ | Nucleus on which the shell is centered ($A$)             |
+  | ~prim_num~          | ~int~   |                    | Total number of primitives                               |
-  | ~shell_ang_mom~  | ~int~   | ~(basis.shell_num)~ | Angular momentum ~0:S, 1:P, 2:D, ...~                    |
+  | ~nucleus_index~     | ~index~ | ~(nucleus.num)~    | Index of the first shell of each nucleus ($A$)           |
-  | ~shell_prim_num~ | ~int~   | ~(basis.shell_num)~ | Number of primitives in the shell ($N_{\text{prim}}$)    |
+  | ~nucleus_shell_num~ | ~int~   | ~(nucleus.num)~    | Number of shells for each nucleus                        |
-  | ~shell_factor~   | ~float~ | ~(basis.shell_num)~ | Normalization factor of the shell ($\mathcal{N}_s$)      |
+  | ~shell_ang_mom~     | ~int~   | ~(basis.num)~      | Angular momentum ~0:S, 1:P, 2:D, ...~                    |
-  | ~prim_index~     | ~index~ | ~(basis.shell_num)~ | Index of the first primitive in the complete list        |
+  | ~shell_prim_num~    | ~int~   | ~(basis.num)~      | Number of primitives in the shell ($N_{\text{prim}}$)    |
-  | ~prim_num~       | ~int~   |                     | Total number of primitives                               |
+  | ~shell_factor~      | ~float~ | ~(basis.num)~      | Normalization factor of the shell ($\mathcal{N}_s$)      |
-  | ~exponent~       | ~float~ | ~(basis.prim_num)~  | Exponents of the primitives ($\gamma_{ks})               |
+  | ~shell_prim_index~  | ~index~ | ~(basis.num)~      | Index of the first primitive in the complete list        |
-  | ~coefficient~    | ~float~ | ~(basis.prim_num)~  | Coefficients of the primitives ($a_{ks}$)                |
+  | ~exponent~          | ~float~ | ~(basis.prim_num)~ | Exponents of the primitives ($\gamma_{ks})               |
-  | ~prim_factor~    | ~float~ | ~(basis.prim_num)~  | Normalization coefficients for the primitives ($f_{ks}$) |
+  | ~coefficient~       | ~float~ | ~(basis.prim_num)~ | Coefficients of the primitives ($a_{ks}$)                |
+  | ~prim_factor~       | ~float~ | ~(basis.prim_num)~ | Normalization coefficients for the primitives ($f_{ks}$) |
     
   #+CALL: json(data=basis, title="basis")
 
@@ -215,21 +218,78 @@ arrays are 0-base. Hence, we introduce the ~index~ type which is an
   :results:
   #+begin_src python :tangle trex.json
       "basis": {
-                    "type" : [ "str"  , []                    ]
+                       "type" : [ "str"  , []                   ]
-        ,      "shell_num" : [ "int"  , []                    ]
+        ,               "num" : [ "int"  , []                   ]
-        ,   "shell_center" : [ "index", [ "basis.shell_num" ] ]
+        ,          "prim_num" : [ "int"  , []                   ]
-        ,  "shell_ang_mom" : [ "int"  , [ "basis.shell_num" ] ]
+        ,     "nucleus_index" : [ "index"  , [ "nucleus.num" ]    ]
-        , "shell_prim_num" : [ "int"  , [ "basis.shell_num" ] ]
+        , "nucleus_shell_num" : [ "int"  , [ "nucleus.num" ]    ]
-        ,   "shell_factor" : [ "float", [ "basis.shell_num" ] ]
+        ,     "shell_ang_mom" : [ "int"  , [ "basis.num" ]      ]
-        ,     "prim_index" : [ "index", [ "basis.shell_num" ] ]
+        ,    "shell_prim_num" : [ "int"  , [ "basis.num" ]      ]
-        ,       "prim_num" : [ "int"  , []                    ]
+        ,      "shell_factor" : [ "float", [ "basis.num" ]      ]
-        ,       "exponent" : [ "float", [ "basis.prim_num" ]  ]
+        ,  "shell_prim_index" : [ "index"  , [ "basis.num" ]      ]
-        ,    "coefficient" : [ "float", [ "basis.prim_num" ]  ]
+        ,          "exponent" : [ "float", [ "basis.prim_num" ] ]
-        ,    "prim_factor" : [ "float", [ "basis.prim_num" ]  ]
+        ,       "coefficient" : [ "float", [ "basis.prim_num" ] ]
+        ,       "prim_factor" : [ "float", [ "basis.prim_num" ] ]
       } ,
   #+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
@@ -254,7 +314,8 @@ arrays are 0-base. Hence, we introduce the ~index~ type which is an
   \chi_i (\mathbf{r}) = \mathcal{N}_i\, P_{\eta(i)}(\mathbf{r})\, R_{\theta(i)} (\mathbf{r})
   \]
 
-  where $i$ is the atomic orbital index, $P$ encodes for either the
+  where $i$ is the atomic orbital index,
+  $P$ 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.