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Merge branch 'master' into add-inquire-functionality

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Evgeny Posenitskiy 2022-01-21 12:33:32 +01:00 committed by GitHub
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3 changed files with 151 additions and 104 deletions
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6
src/templates_front/build.sh
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@ -29,9 +29,9 @@ cat prefix_python.py > trexio.py
# append version string and attributes to the Fortran module file # append version string and attributes to the Fortran module file
echo "" >> trexio_f.f90 echo "" >> trexio_f.f90
echo "character(len = 12) :: TREXIO_PACKAGE_VERSION = ${VERSION_VAL:='0.0.0'}" >> trexio_f.f90 echo "character(len = 12) :: TREXIO_PACKAGE_VERSION = ${VERSION_VAL:='0.0.0'}" >> trexio_f.f90
echo "integer(4) :: TREXIO_VERSION_MAJOR = ${VERSION_MAJOR_VAL}" >> trexio_f.f90 echo "integer :: TREXIO_VERSION_MAJOR = ${VERSION_MAJOR_VAL}" >> trexio_f.f90
echo "integer(4) :: TREXIO_VERSION_MINOR = ${VERSION_MINOR_VAL}" >> trexio_f.f90 echo "integer :: TREXIO_VERSION_MINOR = ${VERSION_MINOR_VAL}" >> trexio_f.f90
echo "integer(4) :: TREXIO_VERSION_PATCH = ${VERSION_PATCH_VAL}" >> trexio_f.f90 echo "integer :: TREXIO_VERSION_PATCH = ${VERSION_PATCH_VAL}" >> trexio_f.f90
echo "character(len = 64) :: TREXIO_GIT_HASH = ${GIT_HASH_STR:='0000'}" >> trexio_f.f90 echo "character(len = 64) :: TREXIO_GIT_HASH = ${GIT_HASH_STR:='0000'}" >> trexio_f.f90
echo "" >> trexio_f.f90 echo "" >> trexio_f.f90

242
src/templates_front/templator_front.org
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@ -82,8 +82,9 @@ module trexio
use, intrinsic :: iso_c_binding use, intrinsic :: iso_c_binding
implicit none implicit none
integer, parameter :: trexio_exit_code = c_int32_t integer, parameter :: trexio_exit_code = c_int32_t
integer, parameter :: trexio_backend = c_int32_t integer, parameter :: trexio_back_end_t = c_int32_t
integer, parameter :: trexio_t = c_int64_t
character(kind=c_char), parameter :: TREXIO_DELIM = c_new_line character(kind=c_char), parameter :: TREXIO_DELIM = c_new_line
#+end_src #+end_src
@ -559,15 +560,16 @@ typedef int32_t back_end_t;
#define TREXIO_DELIM "\n" #define TREXIO_DELIM "\n"
#+end_src #+end_src
The helper function ~trexio_has_backend~ returns ~true~ if TREXIO compilation includes a back end provided as an argument; ~false~ otherwise. The helper function ~trexio_has_back_end~ returns ~true~ if TREXIO compilation includes a back end provided as an argument; ~false~ otherwise.
This is useful due to the fact that HDF5 back end can be disabled at configure step. This is useful due to the fact that HDF5 back end can be disabled at configure step.
#+begin_src c :tangle prefix_front.h #+begin_src c :tangle prefix_front.h
bool trexio_has_backend(back_end_t back_end); bool trexio_has_backend(back_end_t back_end);
bool trexio_has_back_end(back_end_t back_end);
#+end_src #+end_src
#+begin_src c :tangle prefix_front.c #+begin_src c :tangle prefix_front.c
bool trexio_has_backend(back_end_t back_end) { bool trexio_has_back_end(back_end_t back_end) {
switch (back_end) { switch (back_end) {
case TREXIO_TEXT: case TREXIO_TEXT:
return true; return true;
@ -580,28 +582,44 @@ bool trexio_has_backend(back_end_t back_end) {
} }
return false; return false;
} }
bool trexio_has_backend(back_end_t back_end) {
return trexio_has_back_end(back_end);
}
#+end_src #+end_src
*** Fortran *** Fortran
#+begin_src f90 :tangle prefix_fortran.f90 #+begin_src f90 :tangle prefix_fortran.f90
integer(trexio_backend), parameter :: TREXIO_HDF5 = 0 integer(trexio_back_end_t), parameter :: TREXIO_HDF5 = 0
integer(trexio_backend), parameter :: TREXIO_TEXT = 1 integer(trexio_back_end_t), parameter :: TREXIO_TEXT = 1
! integer(trexio_backend), parameter :: TREXIO_JSON = 2 ! integer(trexio_back_end_t), parameter :: TREXIO_JSON = 2
integer(trexio_backend), parameter :: TREXIO_INVALID_BACK_END = 2 integer(trexio_back_end_t), parameter :: TREXIO_INVALID_BACK_END = 2
#+end_src #+end_src
The function below is a Fortran interface for the aforementioned C-compatible ~trexio_has_backend~ function. The function below is a Fortran interface for the aforementioned C-compatible ~trexio_has_back_end~ function.
#+begin_src f90 :tangle prefix_fortran.f90 #+begin_src f90 :tangle prefix_fortran.f90
interface
logical(c_bool) function trexio_has_back_end (back_end) bind(C)
use, intrinsic :: iso_c_binding
import
integer(trexio_back_end_t), intent(in), value :: back_end
end function trexio_has_back_end
end interface
interface interface
logical(c_bool) function trexio_has_backend (back_end) bind(C) logical(c_bool) function trexio_has_backend (back_end) bind(C)
use, intrinsic :: iso_c_binding use, intrinsic :: iso_c_binding
integer(c_int32_t), intent(in), value :: back_end import
integer(trexio_back_end_t), intent(in), value :: back_end
end function trexio_has_backend end function trexio_has_backend
end interface end interface
#+end_src #+end_src
Originally, the function was named ~trexio_has_backend~. For
consistency, in version 2.2 it was renamed ~trexio_has_back_end~.
*** Python *** Python
#+begin_src python :tangle prefix_python.py #+begin_src python :tangle prefix_python.py
@ -966,13 +984,13 @@ trexio_open(const char* file_name, const char mode,
#+begin_src f90 :tangle prefix_fortran.f90 #+begin_src f90 :tangle prefix_fortran.f90
interface interface
integer(c_int64_t) function trexio_open_c (filename, mode, backend, rc_open) bind(C, name="trexio_open") integer(trexio_t) function trexio_open_c (filename, mode, back_end, rc_open) bind(C, name="trexio_open")
use, intrinsic :: iso_c_binding use, intrinsic :: iso_c_binding
import import
character(kind=c_char), dimension(*) :: filename character(kind=c_char), dimension(*) :: filename
character(kind=c_char), intent(in), value :: mode character(kind=c_char), intent(in), value :: mode
integer(trexio_backend), intent(in), value :: backend integer(trexio_back_end_t), intent(in), value :: back_end
integer(trexio_exit_code), intent(out) :: rc_open integer(trexio_exit_code), intent(out) :: rc_open
end function trexio_open_c end function trexio_open_c
end interface end interface
#+end_src #+end_src
@ -1044,8 +1062,9 @@ trexio_exit_code trexio_set_one_based(trexio_t* file)
#+begin_src f90 :tangle prefix_fortran.f90 #+begin_src f90 :tangle prefix_fortran.f90
interface interface
integer(c_int32_t) function trexio_set_one_based(trex_file) bind(C) integer(trexio_exit_code) function trexio_set_one_based(trex_file) bind(C)
use, intrinsic :: iso_c_binding use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file integer(c_int64_t), intent(in), value :: trex_file
end function trexio_set_one_based end function trexio_set_one_based
end interface end interface
@ -1147,8 +1166,9 @@ trexio_close (trexio_t* file)
#+begin_src f90 :tangle prefix_fortran.f90 #+begin_src f90 :tangle prefix_fortran.f90
interface interface
integer(c_int32_t) function trexio_close (trex_file) bind(C) integer(trexio_exit_code) function trexio_close (trex_file) bind(C)
use, intrinsic :: iso_c_binding use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file integer(c_int64_t), intent(in), value :: trex_file
end function trexio_close end function trexio_close
end interface end interface
@ -1231,7 +1251,7 @@ trexio_inquire (const char* file_name)
#+begin_src f90 :tangle prefix_fortran.f90 #+begin_src f90 :tangle prefix_fortran.f90
interface interface
integer function trexio_inquire_c (filename) bind(C, name="trexio_inquire") integer(trexio_exit_code) function trexio_inquire_c (filename) bind(C, name="trexio_inquire")
use, intrinsic :: iso_c_binding use, intrinsic :: iso_c_binding
import import
character(kind=c_char), dimension(*) :: filename character(kind=c_char), dimension(*) :: filename
@ -1356,7 +1376,7 @@ def _inquire(file_name: str) -> bool:
handle. Second parameter is the variable to be written/read handle. Second parameter is the variable to be written/read
to/from the ~TREXIO~ file (except for ~trexio_has_~ functions). to/from the ~TREXIO~ file (except for ~trexio_has_~ functions).
Suffixes ~_32~ and ~_64~ correspond to API calls dealing with Suffixes ~_32~ and ~_64~ correspond to API calls dealing with
single and double precision, respectively. The basic single and real(c_double), respectively. The basic
(non-suffixed) API call on dimensioning variables deals with single (non-suffixed) API call on dimensioning variables deals with single
precision (see Table above). precision (see Table above).
@ -1560,8 +1580,9 @@ trexio_has_$group_num$ (trexio_t* const file)
#+begin_src f90 :tangle write_attr_num_64_front_fortran.f90 #+begin_src f90 :tangle write_attr_num_64_front_fortran.f90
interface interface
integer(c_int32_t) function trexio_write_$group_num$_64 (trex_file, num) bind(C) integer(trexio_exit_code) function trexio_write_$group_num$_64 (trex_file, num) bind(C)
use, intrinsic :: iso_c_binding use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file integer(c_int64_t), intent(in), value :: trex_file
$group_num_f_dtype_double$, intent(in), value :: num $group_num_f_dtype_double$, intent(in), value :: num
end function trexio_write_$group_num$_64 end function trexio_write_$group_num$_64
@ -1570,8 +1591,9 @@ end interface
#+begin_src f90 :tangle read_attr_num_64_front_fortran.f90 #+begin_src f90 :tangle read_attr_num_64_front_fortran.f90
interface interface
integer(c_int32_t) function trexio_read_$group_num$_64 (trex_file, num) bind(C) integer(trexio_exit_code) function trexio_read_$group_num$_64 (trex_file, num) bind(C)
use, intrinsic :: iso_c_binding use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file integer(c_int64_t), intent(in), value :: trex_file
$group_num_f_dtype_double$, intent(out) :: num $group_num_f_dtype_double$, intent(out) :: num
end function trexio_read_$group_num$_64 end function trexio_read_$group_num$_64
@ -1580,8 +1602,9 @@ end interface
#+begin_src f90 :tangle write_attr_num_32_front_fortran.f90 #+begin_src f90 :tangle write_attr_num_32_front_fortran.f90
interface interface
integer(c_int32_t) function trexio_write_$group_num$_32 (trex_file, num) bind(C) integer(trexio_exit_code) function trexio_write_$group_num$_32 (trex_file, num) bind(C)
use, intrinsic :: iso_c_binding use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file integer(c_int64_t), intent(in), value :: trex_file
$group_num_f_dtype_single$, intent(in), value :: num $group_num_f_dtype_single$, intent(in), value :: num
end function trexio_write_$group_num$_32 end function trexio_write_$group_num$_32
@ -1590,8 +1613,9 @@ end interface
#+begin_src f90 :tangle read_attr_num_32_front_fortran.f90 #+begin_src f90 :tangle read_attr_num_32_front_fortran.f90
interface interface
integer(c_int32_t) function trexio_read_$group_num$_32 (trex_file, num) bind(C) integer(trexio_exit_code) function trexio_read_$group_num$_32 (trex_file, num) bind(C)
use, intrinsic :: iso_c_binding use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file integer(c_int64_t), intent(in), value :: trex_file
$group_num_f_dtype_single$, intent(out) :: num $group_num_f_dtype_single$, intent(out) :: num
end function trexio_read_$group_num$_32 end function trexio_read_$group_num$_32
@ -1600,8 +1624,9 @@ end interface
#+begin_src f90 :tangle write_attr_num_def_front_fortran.f90 #+begin_src f90 :tangle write_attr_num_def_front_fortran.f90
interface interface
integer(c_int32_t) function trexio_write_$group_num$ (trex_file, num) bind(C) integer(trexio_exit_code) function trexio_write_$group_num$ (trex_file, num) bind(C)
use, intrinsic :: iso_c_binding use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file integer(c_int64_t), intent(in), value :: trex_file
$group_num_f_dtype_default$, intent(in), value :: num $group_num_f_dtype_default$, intent(in), value :: num
end function trexio_write_$group_num$ end function trexio_write_$group_num$
@ -1610,8 +1635,9 @@ end interface
#+begin_src f90 :tangle read_attr_num_def_front_fortran.f90 #+begin_src f90 :tangle read_attr_num_def_front_fortran.f90
interface interface
integer(c_int32_t) function trexio_read_$group_num$ (trex_file, num) bind(C) integer(trexio_exit_code) function trexio_read_$group_num$ (trex_file, num) bind(C)
use, intrinsic :: iso_c_binding use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file integer(c_int64_t), intent(in), value :: trex_file
$group_num_f_dtype_default$, intent(out) :: num $group_num_f_dtype_default$, intent(out) :: num
end function trexio_read_$group_num$ end function trexio_read_$group_num$
@ -1620,8 +1646,9 @@ end interface
#+begin_src f90 :tangle has_attr_num_front_fortran.f90 #+begin_src f90 :tangle has_attr_num_front_fortran.f90
interface interface
integer(c_int32_t) function trexio_has_$group_num$ (trex_file) bind(C) integer(trexio_exit_code) function trexio_has_$group_num$ (trex_file) bind(C)
use, intrinsic :: iso_c_binding use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file integer(c_int64_t), intent(in), value :: trex_file
end function trexio_has_$group_num$ end function trexio_has_$group_num$
end interface end interface
@ -1729,7 +1756,7 @@ def has_$group_num$(trexio_file) -> bool:
First parameter is the ~TREXIO~ file handle. Second parameter is the variable to be written/read First parameter is the ~TREXIO~ file handle. Second parameter is the variable to be written/read
to/from the ~TREXIO~ file (except for ~trexio_has_~ functions). to/from the ~TREXIO~ file (except for ~trexio_has_~ functions).
Suffixes ~_32~ and ~_64~ correspond to API calls dealing with single and double precision, respectively. Suffixes ~_32~ and ~_64~ correspond to API calls dealing with single and double precision, respectively.
The basic (non-suffixed) API call on datasets deals with double precision (see Table above). The basic (non-suffixed) API call on datasets deals with real(c_double) (see Table above).
**** Function declarations **** Function declarations
@ -2013,7 +2040,7 @@ trexio_write_$group_dset$_32 (trexio_t* const file, const $group_dset_dtype_sing
$group_dset_dtype_double$* $group_dset$_64 = CALLOC(dim_size, $group_dset_dtype_double$); $group_dset_dtype_double$* $group_dset$_64 = CALLOC(dim_size, $group_dset_dtype_double$);
if ($group_dset$_64 == NULL) return TREXIO_ALLOCATION_FAILED; 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 */ /* A type conversion from single precision to double required since back end only accepts 64-bit data */
if ($is_index$) { if ($is_index$) {
for (uint64_t i=0; i<dim_size; ++i){ 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; $group_dset$_64[i] = ($group_dset_dtype_double$) $group_dset$[i] - ($group_dset_dtype_double$) 1;
@ -2223,8 +2250,9 @@ trexio_has_$group_dset$ (trexio_t* const file)
#+begin_src f90 :tangle write_dset_data_64_front_fortran.f90 #+begin_src f90 :tangle write_dset_data_64_front_fortran.f90
interface interface
integer(c_int32_t) function trexio_write_$group_dset$_64 (trex_file, dset) bind(C) integer(trexio_exit_code) function trexio_write_$group_dset$_64 (trex_file, dset) bind(C)
use, intrinsic :: iso_c_binding use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file integer(c_int64_t), intent(in), value :: trex_file
$group_dset_f_dtype_double$, intent(in) :: dset$group_dset_f_dims$ $group_dset_f_dtype_double$, intent(in) :: dset$group_dset_f_dims$
end function trexio_write_$group_dset$_64 end function trexio_write_$group_dset$_64
@ -2233,8 +2261,9 @@ end interface
#+begin_src f90 :tangle read_dset_data_64_front_fortran.f90 #+begin_src f90 :tangle read_dset_data_64_front_fortran.f90
interface interface
integer(c_int32_t) function trexio_read_$group_dset$_64 (trex_file, dset) bind(C) integer(trexio_exit_code) function trexio_read_$group_dset$_64 (trex_file, dset) bind(C)
use, intrinsic :: iso_c_binding use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file integer(c_int64_t), intent(in), value :: trex_file
$group_dset_f_dtype_double$, intent(out) :: dset$group_dset_f_dims$ $group_dset_f_dtype_double$, intent(out) :: dset$group_dset_f_dims$
end function trexio_read_$group_dset$_64 end function trexio_read_$group_dset$_64
@ -2243,8 +2272,9 @@ end interface
#+begin_src f90 :tangle write_dset_data_32_front_fortran.f90 #+begin_src f90 :tangle write_dset_data_32_front_fortran.f90
interface interface
integer(c_int32_t) function trexio_write_$group_dset$_32 (trex_file, dset) bind(C) integer(trexio_exit_code) function trexio_write_$group_dset$_32 (trex_file, dset) bind(C)
use, intrinsic :: iso_c_binding use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file integer(c_int64_t), intent(in), value :: trex_file
$group_dset_f_dtype_single$, intent(in) :: dset$group_dset_f_dims$ $group_dset_f_dtype_single$, intent(in) :: dset$group_dset_f_dims$
end function trexio_write_$group_dset$_32 end function trexio_write_$group_dset$_32
@ -2253,8 +2283,9 @@ end interface
#+begin_src f90 :tangle read_dset_data_32_front_fortran.f90 #+begin_src f90 :tangle read_dset_data_32_front_fortran.f90
interface interface
integer(c_int32_t) function trexio_read_$group_dset$_32 (trex_file, dset) bind(C) integer(trexio_exit_code) function trexio_read_$group_dset$_32 (trex_file, dset) bind(C)
use, intrinsic :: iso_c_binding use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file integer(c_int64_t), intent(in), value :: trex_file
$group_dset_f_dtype_single$, intent(out) :: dset$group_dset_f_dims$ $group_dset_f_dtype_single$, intent(out) :: dset$group_dset_f_dims$
end function trexio_read_$group_dset$_32 end function trexio_read_$group_dset$_32
@ -2263,8 +2294,9 @@ end interface
#+begin_src f90 :tangle write_dset_data_def_front_fortran.f90 #+begin_src f90 :tangle write_dset_data_def_front_fortran.f90
interface interface
integer(c_int32_t) function trexio_write_$group_dset$ (trex_file, dset) bind(C) integer(trexio_exit_code) function trexio_write_$group_dset$ (trex_file, dset) bind(C)
use, intrinsic :: iso_c_binding use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file integer(c_int64_t), intent(in), value :: trex_file
$group_dset_f_dtype_default$, intent(in) :: dset$group_dset_f_dims$ $group_dset_f_dtype_default$, intent(in) :: dset$group_dset_f_dims$
end function trexio_write_$group_dset$ end function trexio_write_$group_dset$
@ -2273,8 +2305,9 @@ end interface
#+begin_src f90 :tangle read_dset_data_def_front_fortran.f90 #+begin_src f90 :tangle read_dset_data_def_front_fortran.f90
interface interface
integer(c_int32_t) function trexio_read_$group_dset$ (trex_file, dset) bind(C) integer(trexio_exit_code) function trexio_read_$group_dset$ (trex_file, dset) bind(C)
use, intrinsic :: iso_c_binding use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file integer(c_int64_t), intent(in), value :: trex_file
$group_dset_f_dtype_default$, intent(out) :: dset$group_dset_f_dims$ $group_dset_f_dtype_default$, intent(out) :: dset$group_dset_f_dims$
end function trexio_read_$group_dset$ end function trexio_read_$group_dset$
@ -2283,8 +2316,9 @@ end interface
#+begin_src f90 :tangle has_dset_data_front_fortran.f90 #+begin_src f90 :tangle has_dset_data_front_fortran.f90
interface interface
integer(c_int32_t) function trexio_has_$group_dset$ (trex_file) bind(C) integer(trexio_exit_code) function trexio_has_$group_dset$ (trex_file) bind(C)
use, intrinsic :: iso_c_binding use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file integer(c_int64_t), intent(in), value :: trex_file
end function trexio_has_$group_dset$ end function trexio_has_$group_dset$
end interface end interface
@ -2833,10 +2867,11 @@ trexio_has_$group_dset$ (trexio_t* const file)
#+begin_src f90 :tangle write_dset_sparse_front_fortran.f90 #+begin_src f90 :tangle write_dset_sparse_front_fortran.f90
interface interface
integer(c_int32_t) function trexio_write_$group_dset$ (trex_file, & integer(trexio_exit_code) function trexio_write_$group_dset$ (trex_file, &
offset_file, buffer_size, & offset_file, buffer_size, &
index_sparse, value_sparse) bind(C) index_sparse, value_sparse) bind(C)
use, intrinsic :: iso_c_binding use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file integer(c_int64_t), intent(in), value :: trex_file
integer(c_int64_t), intent(in), value :: offset_file integer(c_int64_t), intent(in), value :: offset_file
integer(c_int64_t), intent(in), value :: buffer_size integer(c_int64_t), intent(in), value :: buffer_size
@ -2846,11 +2881,12 @@ interface
end interface end interface
interface interface
integer(c_int32_t) function trexio_write_safe_$group_dset$ (trex_file, & integer(trexio_exit_code) function trexio_write_safe_$group_dset$ (trex_file, &
offset_file, buffer_size, & offset_file, buffer_size, &
index_sparse, index_size, & index_sparse, index_size, &
value_sparse, value_size) bind(C) value_sparse, value_size) bind(C)
use, intrinsic :: iso_c_binding use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file integer(c_int64_t), intent(in), value :: trex_file
integer(c_int64_t), intent(in), value :: offset_file integer(c_int64_t), intent(in), value :: offset_file
integer(c_int64_t), intent(in), value :: buffer_size integer(c_int64_t), intent(in), value :: buffer_size
@ -2864,10 +2900,11 @@ end interface
#+begin_src f90 :tangle read_dset_sparse_front_fortran.f90 #+begin_src f90 :tangle read_dset_sparse_front_fortran.f90
interface interface
integer(c_int32_t) function trexio_read_$group_dset$ (trex_file, & integer(trexio_exit_code) function trexio_read_$group_dset$ (trex_file, &
offset_file, buffer_size, & offset_file, buffer_size, &
index_sparse, value_sparse) bind(C) index_sparse, value_sparse) bind(C)
use, intrinsic :: iso_c_binding use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file integer(c_int64_t), intent(in), value :: trex_file
integer(c_int64_t), intent(in), value :: offset_file integer(c_int64_t), intent(in), value :: offset_file
integer(c_int64_t), intent(inout) :: buffer_size integer(c_int64_t), intent(inout) :: buffer_size
@ -2877,11 +2914,12 @@ interface
end interface end interface
interface interface
integer(c_int32_t) function trexio_read_safe_$group_dset$ (trex_file, & integer(trexio_exit_code) function trexio_read_safe_$group_dset$ (trex_file, &
offset_file, buffer_size, & offset_file, buffer_size, &
index_sparse, index_size, & index_sparse, index_size, &
value_sparse, value_size) bind(C) value_sparse, value_size) bind(C)
use, intrinsic :: iso_c_binding use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file integer(c_int64_t), intent(in), value :: trex_file
integer(c_int64_t), intent(in), value :: offset_file integer(c_int64_t), intent(in), value :: offset_file
integer(c_int64_t), intent(inout) :: buffer_size integer(c_int64_t), intent(inout) :: buffer_size
@ -2895,19 +2933,21 @@ end interface
#+begin_src f90 :tangle read_dset_sparse_size_front_fortran.f90 #+begin_src f90 :tangle read_dset_sparse_size_front_fortran.f90
interface interface
integer(c_int32_t) function trexio_read_$group_dset$_size (trex_file, & integer(trexio_exit_code) function trexio_read_$group_dset$_size (trex_file, &
size_max) bind(C) size_max) bind(C)
use, intrinsic :: iso_c_binding use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file integer(c_int64_t), intent(in), value :: trex_file
integer(c_int64_t), intent(out) :: size_max integer(c_int64_t), intent(out) :: size_max
end function trexio_read_$group_dset$_size end function trexio_read_$group_dset$_size
end interface end interface
#+end_src #+end_src
#+begin_src f90 :tangle has_dset_sparse_front_fortran.f90 #+begin_src f90 :tangle has_dset_sparse_front_fortran.f90
interface interface
integer(c_int32_t) function trexio_has_$group_dset$ (trex_file) bind(C) integer(trexio_exit_code) function trexio_has_$group_dset$ (trex_file) bind(C)
use, intrinsic :: iso_c_binding use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file integer(c_int64_t), intent(in), value :: trex_file
end function trexio_has_$group_dset$ end function trexio_has_$group_dset$
end interface end interface
@ -3404,8 +3444,9 @@ trexio_has_$group_dset$ (trexio_t* const file)
#+begin_src f90 :tangle write_dset_str_front_fortran.f90 #+begin_src f90 :tangle write_dset_str_front_fortran.f90
interface interface
integer(c_int32_t) function trexio_write_$group_dset$_low (trex_file, dset, max_str_len) bind(C) integer(trexio_exit_code) function trexio_write_$group_dset$_low (trex_file, dset, max_str_len) bind(C)
use, intrinsic :: iso_c_binding use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file integer(c_int64_t), intent(in), value :: trex_file
character(kind=c_char), intent(in) :: dset(*) character(kind=c_char), intent(in) :: dset(*)
integer(c_int32_t), intent(in), value :: max_str_len integer(c_int32_t), intent(in), value :: max_str_len
@ -3415,8 +3456,9 @@ end interface
#+begin_src f90 :tangle read_dset_str_front_fortran.f90 #+begin_src f90 :tangle read_dset_str_front_fortran.f90
interface interface
integer(c_int32_t) function trexio_read_$group_dset$_low (trex_file, dset, max_str_len) bind(C) integer(trexio_exit_code) function trexio_read_$group_dset$_low (trex_file, dset, max_str_len) bind(C)
use, intrinsic :: iso_c_binding use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file integer(c_int64_t), intent(in), value :: trex_file
character(kind=c_char), intent(out) :: dset(*) character(kind=c_char), intent(out) :: dset(*)
integer(c_int32_t), intent(in), value :: max_str_len integer(c_int32_t), intent(in), value :: max_str_len
@ -3426,23 +3468,24 @@ end interface
#+begin_src f90 :tangle has_dset_str_front_fortran.f90 #+begin_src f90 :tangle has_dset_str_front_fortran.f90
interface interface
integer(c_int32_t) function trexio_has_$group_dset$ (trex_file) bind(C) integer(trexio_exit_code) function trexio_has_$group_dset$ (trex_file) bind(C)
use, intrinsic :: iso_c_binding use, intrinsic :: iso_c_binding
import
integer(c_int64_t), intent(in), value :: trex_file integer(c_int64_t), intent(in), value :: trex_file
end function trexio_has_$group_dset$ end function trexio_has_$group_dset$
end interface end interface
#+end_src #+end_src
#+begin_src f90 :tangle helper_read_dset_str_front_fortran.fh_90 #+begin_src f90 :tangle helper_read_dset_str_front_fortran.fh_90
integer function trexio_read_$group_dset$ (trex_file, dset, max_str_len) integer(trexio_exit_code) function trexio_read_$group_dset$ (trex_file, dset, max_str_len)
implicit none implicit none
integer(8), intent(in), value :: trex_file integer(c_int64_t), intent(in), value :: trex_file
integer(4), intent(in), value :: max_str_len integer(c_int32_t), intent(in), value :: max_str_len
character(len=*), intent(inout) :: dset(*) character(len=*), intent(inout) :: dset(*)
character, allocatable :: str_compiled(:) character, allocatable :: str_compiled(:)
integer(8) :: $group_dset_dim$ integer(c_int64_t) :: $group_dset_dim$
integer :: rc integer(trexio_exit_code) :: rc
rc = trexio_read_$group_dset_dim$_64(trex_file, $group_dset_dim$) rc = trexio_read_$group_dset_dim$_64(trex_file, $group_dset_dim$)
if (rc /= TREXIO_SUCCESS) trexio_read_$group_dset$ = rc if (rc /= TREXIO_SUCCESS) trexio_read_$group_dset$ = rc
@ -3463,15 +3506,15 @@ end interface
#+end_src #+end_src
#+begin_src f90 :tangle helper_write_dset_str_front_fortran.fh_90 #+begin_src f90 :tangle helper_write_dset_str_front_fortran.fh_90
integer function trexio_write_$group_dset$ (trex_file, dset, max_str_len) integer(trexio_exit_code) function trexio_write_$group_dset$ (trex_file, dset, max_str_len)
implicit none implicit none
integer(8), intent(in), value :: trex_file integer(c_int64_t), intent(in), value :: trex_file
integer(4), intent(in), value :: max_str_len integer(c_int32_t), intent(in), value :: max_str_len
character(len=*), intent(in) :: dset(*) character(len=*), intent(in) :: dset(*)
character(len=:), allocatable :: str_compiled character(len=:), allocatable :: str_compiled
integer(8) :: $group_dset_dim$ integer(c_int64_t) :: $group_dset_dim$
integer :: rc integer(trexio_exit_code) :: rc
rc = trexio_read_$group_dset_dim$_64(trex_file, $group_dset_dim$) rc = trexio_read_$group_dset_dim$_64(trex_file, $group_dset_dim$)
if (rc /= TREXIO_SUCCESS) then if (rc /= TREXIO_SUCCESS) then
@ -3720,10 +3763,11 @@ trexio_has_$group_str$ (trexio_t* const file)
#+begin_src f90 :tangle write_attr_str_front_fortran.f90 #+begin_src f90 :tangle write_attr_str_front_fortran.f90
interface interface
integer(c_int32_t) function trexio_write_$group_str$_c (trex_file, str, max_str_len) & integer(trexio_exit_code) function trexio_write_$group_str$_c (trex_file, str, max_str_len) &
bind(C, name="trexio_write_$group_str$") bind(C, name="trexio_write_$group_str$")
use, intrinsic :: iso_c_binding use, intrinsic :: iso_c_binding
integer(c_int64_t), intent(in), value :: trex_file import
integer(trexio_t), intent(in), value :: trex_file
character(kind=c_char), intent(in) :: str(*) character(kind=c_char), intent(in) :: str(*)
integer(c_int32_t), intent(in), value :: max_str_len integer(c_int32_t), intent(in), value :: max_str_len
end function trexio_write_$group_str$_c end function trexio_write_$group_str$_c
@ -3732,30 +3776,32 @@ end interface
#+begin_src f90 :tangle read_attr_str_front_fortran.f90 #+begin_src f90 :tangle read_attr_str_front_fortran.f90
interface interface
integer(c_int32_t) function trexio_read_$group_str$_c (trex_file, str, max_str_len) & integer(trexio_exit_code) function trexio_read_$group_str$_c (trex_file, str, max_str_len) &
bind(C, name="trexio_read_$group_str$") bind(C, name="trexio_read_$group_str$")
use, intrinsic :: iso_c_binding use, intrinsic :: iso_c_binding
integer(c_int64_t), intent(in), value :: trex_file import
integer(trexio_t), intent(in), value :: trex_file
character(kind=c_char), intent(out) :: str(*) character(kind=c_char), intent(out) :: str(*)
integer(c_int32_t), intent(in), value :: max_str_len integer(c_int32_t), intent(in), value :: max_str_len
end function trexio_read_$group_str$_c end function trexio_read_$group_str$_c
end interface end interface
#+end_src #+end_src
#+begin_src f90 :tangle has_attr_str_front_fortran.f90 #+begin_src f90 :tangle has_attr_str_front_fortran.f90
interface interface
integer(c_int32_t) function trexio_has_$group_str$ (trex_file) bind(C) integer(trexio_exit_code) function trexio_has_$group_str$ (trex_file) bind(C)
use, intrinsic :: iso_c_binding use, intrinsic :: iso_c_binding
integer(c_int64_t), intent(in), value :: trex_file import
integer(trexio_t), intent(in), value :: trex_file
end function trexio_has_$group_str$ end function trexio_has_$group_str$
end interface end interface
#+end_src #+end_src
#+begin_src f90 :tangle helper_read_attr_str_front_fortran.fh_90 #+begin_src f90 :tangle helper_read_attr_str_front_fortran.fh_90
integer function trexio_read_$group_str$ (trex_file, str, max_str_len) integer(trexio_exit_code) function trexio_read_$group_str$ (trex_file, str, max_str_len)
implicit none implicit none
integer(8), intent(in), value :: trex_file integer(trexio_t), intent(in), value :: trex_file
integer(4), intent(in), value :: max_str_len integer(c_int32_t), intent(in), value :: max_str_len
character, intent(out) :: str(*) character, intent(out) :: str(*)
trexio_read_$group_str$ = trexio_read_$group_str$_c(trex_file, str, max_str_len) trexio_read_$group_str$ = trexio_read_$group_str$_c(trex_file, str, max_str_len)
@ -3764,12 +3810,12 @@ end interface
#+end_src #+end_src
#+begin_src f90 :tangle helper_write_attr_str_front_fortran.fh_90 #+begin_src f90 :tangle helper_write_attr_str_front_fortran.fh_90
integer function trexio_write_$group_str$ (trex_file, str, max_str_len) integer(trexio_exit_code) function trexio_write_$group_str$ (trex_file, str, max_str_len)
use, intrinsic :: iso_c_binding, only : c_null_char use, intrinsic :: iso_c_binding, only : c_null_char
implicit none implicit none
integer(8), intent(in), value :: trex_file integer(trexio_t), intent(in), value :: trex_file
integer(4), intent(in), value :: max_str_len integer(c_int32_t), intent(in), value :: max_str_len
character(len=*), intent(in) :: str character(len=*), intent(in) :: str
character(len=len_trim(str)+1) :: str_c character(len=len_trim(str)+1) :: str_c
@ -3936,18 +3982,18 @@ def info():
#+begin_src f90 :tangle helper_fortran.f90 #+begin_src f90 :tangle helper_fortran.f90
contains contains
integer(8) function trexio_open (filename, mode, backend, rc_open) integer(trexio_t) function trexio_open (filename, mode, back_end, rc_open)
use, intrinsic :: iso_c_binding, only : c_null_char use, intrinsic :: iso_c_binding, only : c_null_char
implicit none implicit none
character(len=*), intent(in) :: filename character(len=*), intent(in) :: filename
character, intent(in), value :: mode character, intent(in), value :: mode
integer(trexio_backend), intent(in), value :: backend integer(trexio_back_end_t), intent(in), value :: back_end
integer(trexio_exit_code), intent(out) :: rc_open integer(trexio_exit_code), intent(out) :: rc_open
character(len=len_trim(filename)+1) :: filename_c character(len=len_trim(filename)+1) :: filename_c
integer(trexio_exit_code) :: rc integer(trexio_exit_code) :: rc
filename_c = trim(filename) // c_null_char filename_c = trim(filename) // c_null_char
trexio_open = trexio_open_c(filename_c, mode, backend, rc_open) trexio_open = trexio_open_c(filename_c, mode, back_end, rc_open)
if (trexio_open == 0_8 .or. rc_open /= TREXIO_SUCCESS) then if (trexio_open == 0_8 .or. rc_open /= TREXIO_SUCCESS) then
return return
endif endif
@ -3964,7 +4010,7 @@ contains
Note, that Fortran interface calls the main ~TREXIO~ API, which is written in C. Note, that Fortran interface calls the main ~TREXIO~ API, which is written in C.
#+begin_src f90 :tangle helper_fortran.f90 #+begin_src f90 :tangle helper_fortran.f90
integer function trexio_inquire (filename) integer(trexio_exit_code) function trexio_inquire (filename)
use, intrinsic :: iso_c_binding use, intrinsic :: iso_c_binding
implicit none implicit none
character(len=*), intent(in) :: filename character(len=*), intent(in) :: filename
@ -3985,11 +4031,11 @@ contains
use, intrinsic :: iso_c_binding, only : c_null_char use, intrinsic :: iso_c_binding, only : c_null_char
implicit none implicit none
integer(8), intent(in), value :: max_num_str ! number of elements in strign array integer(c_int64_t), intent(in), value :: max_num_str ! number of elements in strign array
integer, intent(in), value :: max_len_str ! maximum length of a string in an array integer, intent(in), value :: max_len_str ! maximum length of a string in an array
character(len=*), intent(in) :: str_array(*) character(len=*), intent(in) :: str_array(*)
character(len=:), allocatable, intent(out) :: str_res character(len=:), allocatable, intent(out) :: str_res
integer(8) :: i integer(c_int64_t) :: i
str_res = '' str_res = ''
do i = 1, max_num_str do i = 1, max_num_str
@ -4006,13 +4052,13 @@ contains
subroutine trexio_str2strarray(str_flat, max_num_str, max_len_str, str_array) subroutine trexio_str2strarray(str_flat, max_num_str, max_len_str, str_array)
implicit none implicit none
integer(8), intent(in), value :: max_num_str ! number of elements in strign array integer(c_int64_t), intent(in), value :: max_num_str ! number of elements in strign array
integer, intent(in), value :: max_len_str ! maximum length of a string in an array integer, intent(in), value :: max_len_str ! maximum length of a string in an array
character, intent(in) :: str_flat(*) character(kind=c_char), intent(in) :: str_flat(*)
character(len=*), intent(inout) :: str_array(*) character(len=*), intent(inout) :: str_array(*)
character(len=max_len_str) :: tmp_str character(len=max_len_str) :: tmp_str
integer(8) :: len_flat, i, j, k, ind integer(c_int64_t) :: i, j, k, ind, len_flat
len_flat = (max_len_str+1)*max_num_str + 1 len_flat = (max_len_str+1)*max_num_str + 1

7
trex.org
View File

@ -384,7 +384,7 @@ exponent =
coefficient = 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,
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 = prim_factor =
[ 1.0006253235944540e+01, 2.4169531573445120e+00, 7.9610924849766440e-01 [ 1.0006253235944540e+01, 2.4169531573445120e+00, 7.9610924849766440e-01
3.0734305383061117e-01, 1.2929684417481876e-01, 3.0734305383061117e-01, 3.0734305383061117e-01, 1.2929684417481876e-01, 3.0734305383061117e-01,
@ -401,8 +401,9 @@ prim_factor =
construction of all the angular functions of each shell. We construction of all the angular functions of each shell. We
consider two cases for the angular functions: the real-valued consider two cases for the angular functions: the real-valued
spherical harmonics, and the polynomials in Cartesian coordinates. spherical harmonics, and the polynomials in Cartesian coordinates.
In the case of spherical harmonics, the AOs are ordered as In the case of real spherical harmonics, the AOs are ordered as
$0, +1, -1, +2, -2, \dots, +m, -m$ and in the case of polynomials we $0, +1, -1, +2, -2, \dots, +m, -m$ (see [[https://en.wikipedia.org/wiki/Table_of_spherical_harmonics#Real_spherical_harmonics][Wikipedia]]).
In the case of polynomials we
impose the canonical (or alphabetical) ordering), i.e impose the canonical (or alphabetical) ordering), i.e
\begin{eqnarray} \begin{eqnarray}