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add Fortran interface for sparse data

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q-posev 2021-12-01 13:35:42 +01:00
parent 83c926fd6b
commit c30c3a532c
2 changed files with 109 additions and 22 deletions
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70
src/templates_front/templator_front.org
View File

@ -2396,10 +2396,8 @@ def has_$group_dset$(trexio_file) -> bool:
#+begin_src c :tangle hrw_dset_sparse_front.h :exports none
trexio_exit_code trexio_has_$group_sparse_dset$(trexio_t* const file);
trexio_exit_code trexio_read_$group_sparse_dset$(trexio_t* const file, const int64_t offset_file, const int64_t size, int32_t* const index_sparse, double* const value_sparse);
trexio_exit_code trexio_write_$group_sparse_dset$(trexio_t* const file, const int64_t offset_file, const int64_t size, const int32_t* index_sparse, const double* value_sparse);
//trexio_exit_code trexio_read_$group_sparse_dset$_value(trexio_t* const file, const uint64_t offset, const uint_64_t size, int32_t* const value_sparse);
//trexio_exit_code trexio_write_$group_sparse_dset$_value(trexio_t* const file, const uint64_t offset, const uint_64_t size, double* const value_sparse);
trexio_exit_code trexio_read_$group_sparse_dset$(trexio_t* const file, const int64_t offset_file, const int64_t buffer_size, int32_t* const index_sparse, double* const value_sparse);
trexio_exit_code trexio_write_$group_sparse_dset$(trexio_t* const file, const int64_t offset_file, const int64_t buffer_size, const int32_t* index_sparse, const double* value_sparse);
#+end_src
**** Source code for default functions
@ -2408,14 +2406,14 @@ trexio_exit_code trexio_write_$group_sparse_dset$(trexio_t* const file, const in
trexio_exit_code
trexio_read_$group_sparse_dset$(trexio_t* const file,
const int64_t offset_file,
const int64_t size,
const int64_t buffer_size,
int32_t* const index_sparse,
double* const value_sparse
)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
if (offset_file < 0L) return TREXIO_INVALID_ARG_2;
if (size <= 0L) return TREXIO_INVALID_ARG_3;
if (buffer_size <= 0L) return TREXIO_INVALID_ARG_3;
if (index_sparse == NULL) return TREXIO_INVALID_ARG_4;
if (value_sparse == NULL) return TREXIO_INVALID_ARG_5;
@ -2425,7 +2423,7 @@ trexio_read_$group_sparse_dset$(trexio_t* const file,
trexio_exit_code rc;
// temporary
size_max = size;
size_max = buffer_size;
/* TODO
rc = trexio_read_$group_sparse_dset$_num(file, &size_max);
if (rc != TREXIO_SUCCESS) return rc;
@ -2434,12 +2432,12 @@ trexio_read_$group_sparse_dset$(trexio_t* const file,
switch (file->back_end) {
case TREXIO_TEXT:
return trexio_text_read_$group_sparse_dset$(file, offset_file, size, size_max, index_sparse, value_sparse);
return trexio_text_read_$group_sparse_dset$(file, offset_file, buffer_size, size_max, index_sparse, value_sparse);
break;
case TREXIO_HDF5:
#ifdef HAVE_HDF5
return trexio_hdf5_read_$group_sparse_dset$(file, offset_file, size, size_max, index_sparse, value_sparse);
return trexio_hdf5_read_$group_sparse_dset$(file, offset_file, buffer_size, size_max, index_sparse, value_sparse);
break;
#else
return TREXIO_BACK_END_MISSING;
@ -2459,14 +2457,14 @@ trexio_read_$group_sparse_dset$(trexio_t* const file,
trexio_exit_code
trexio_write_$group_sparse_dset$(trexio_t* const file,
const int64_t offset_file,
const int64_t size,
const int64_t buffer_size,
const int32_t* index_sparse,
const double* value_sparse
)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
if (offset_file < 0L) return TREXIO_INVALID_ARG_2;
if (size <= 0L) return TREXIO_INVALID_ARG_3;
if (buffer_size <= 0L) return TREXIO_INVALID_ARG_3;
if (index_sparse == NULL) return TREXIO_INVALID_ARG_4;
if (value_sparse == NULL) return TREXIO_INVALID_ARG_5;
@ -2476,7 +2474,7 @@ trexio_write_$group_sparse_dset$(trexio_t* const file,
trexio_exit_code rc;
// temporary
size_max = size;
size_max = buffer_size;
/* TODO
rc = trexio_read_$group_sparse_dset$_num(file, &size_max);
if (rc != TREXIO_SUCCESS) return rc;
@ -2485,12 +2483,12 @@ trexio_write_$group_sparse_dset$(trexio_t* const file,
switch (file->back_end) {
case TREXIO_TEXT:
return trexio_text_write_$group_sparse_dset$(file, offset_file, size, size_max, index_sparse, value_sparse);
return trexio_text_write_$group_sparse_dset$(file, offset_file, buffer_size, size_max, index_sparse, value_sparse);
break;
case TREXIO_HDF5:
#ifdef HAVE_HDF5
return trexio_hdf5_write_$group_sparse_dset$(file, offset_file, size, size_max, index_sparse, value_sparse);
return trexio_hdf5_write_$group_sparse_dset$(file, offset_file, buffer_size, size_max, index_sparse, value_sparse);
break;
#else
return TREXIO_BACK_END_MISSING;
@ -2540,6 +2538,50 @@ trexio_has_$group_sparse_dset$ (trexio_t* const file)
}
#+end_src
*** Fortran templates for front end
The ~Fortran~ templates that provide an access to the ~C~ API calls from ~Fortran~.
These templates are based on the use of ~iso_c_binding~. Pointers have to be passed by value.
#+begin_src f90 :tangle write_dset_sparse_front_fortran.f90
interface
integer function trexio_write_$group_sparse_dset$ (trex_file, &
offset_file, buffer_size, &
index_sparse, value_sparse) bind(C)
use, intrinsic :: iso_c_binding
integer(8), intent(in), value :: trex_file
integer(8), intent(in), value :: offset_file
integer(8), intent(in), value :: buffer_size
integer(4), intent(in) :: index_sparse(*)
double precision, intent(in) :: value_sparse(*)
end function trexio_write_$group_sparse_dset$
end interface
#+end_src
#+begin_src f90 :tangle read_dset_sparse_front_fortran.f90
interface
integer function trexio_read_$group_sparse_dset$ (trex_file, &
offset_file, buffer_size, &
index_sparse, value_sparse) bind(C)
use, intrinsic :: iso_c_binding
integer(8), intent(in), value :: trex_file
integer(8), intent(in), value :: offset_file
integer(8), intent(in), value :: buffer_size
integer(4), intent(in) :: index_sparse(*)
double precision, intent(out) :: value_sparse(*)
end function trexio_read_$group_sparse_dset$
end interface
#+end_src
#+begin_src f90 :tangle has_dset_sparse_front_fortran.f90
interface
integer function trexio_has_$group_sparse_dset$ (trex_file) bind(C)
use, intrinsic :: iso_c_binding
integer(8), intent(in), value :: trex_file
end function trexio_has_$group_sparse_dset$
end interface
#+end_src
** Templates for front end has/read/write a dataset of strings
*** Introduction
This section concerns API calls related to datasets of strings.

61
tests/test_f.f90
View File

@ -2,14 +2,14 @@ program test_trexio
use trexio
use, intrinsic :: iso_c_binding
implicit none
logical :: have_hdf5
print * , "============================================"
print'(a,a)' , " TREXIO VERSION STRING : ", TREXIO_PACKAGE_VERSION
print * , "============================================"
print'(a,a)' , " TREXIO VERSION STRING : ", TREXIO_PACKAGE_VERSION
print'(a,i3)', " TREXIO MAJOR VERSION : ", TREXIO_VERSION_MAJOR
print'(a,i3)', " TREXIO MINOR VERSION : ", TREXIO_VERSION_MINOR
print * , "============================================"
print * , "============================================"
call system('rm -rf test_write_f.dir')
print *, 'call test_write(''test_write_f.dir'', TREXIO_TEXT)'
@ -20,7 +20,7 @@ program test_trexio
call test_read_void('test_write_f.dir', TREXIO_TEXT)
! No way to conditionally check whether compilation was done with HDF5
! No way to conditionally check whether compilation was done with HDF5
! So temporarily disable the test for HDF5 back end at the moment
have_hdf5 = trexio_has_backend(TREXIO_HDF5)
if (have_hdf5) then
@ -30,7 +30,7 @@ program test_trexio
print *, 'call test_read(''test_write_f.h5'', TREXIO_HDF5)'
call test_read('test_write_f.h5', TREXIO_HDF5)
call system('rm -f -- test_write_f.h5')
call test_read_void('test_write_f.h5', TREXIO_HDF5)
endif
@ -61,6 +61,22 @@ subroutine test_write(file_name, back_end)
character(len=:), allocatable :: sym_str
character(len=:), allocatable :: label(:)
! sparse data
integer(4) :: index_sparse_mo_2e_int_eri(400)
double precision :: value_sparse_mo_2e_int_eri(100)
integer :: i, n_buffers = 5
integer(8) :: buf_size, offset = 0
buf_size = 100/n_buffers
do i = 1, 100
index_sparse_mo_2e_int_eri(4*i-3) = 4*i - 3
index_sparse_mo_2e_int_eri(4*i+1-3) = 4*i+1 - 3
index_sparse_mo_2e_int_eri(4*i+2-3) = 4*i+2 - 3
index_sparse_mo_2e_int_eri(4*i+3-3) = 4*i+3 - 3
value_sparse_mo_2e_int_eri(i) = 3.14 + float(i)
enddo
! parameters to be written
num = 12
charge = (/ 6., 6., 6., 6., 6., 6., 1., 1., 1., 1., 1., 1. /)
@ -96,6 +112,9 @@ subroutine test_write(file_name, back_end)
rc = trexio_has_nucleus_charge(trex_file)
call trexio_assert(rc, TREXIO_HAS_NOT, 'SUCCESS HAS NOT 2')
rc = trexio_has_mo_2e_int_eri(trex_file)
call trexio_assert(rc, TREXIO_HAS_NOT, 'SUCCESS HAS NOT 3')
rc = trexio_write_nucleus_num(trex_file, num)
call trexio_assert(rc, TREXIO_SUCCESS, 'SUCCESS WRITE NUM')
@ -119,6 +138,13 @@ subroutine test_write(file_name, back_end)
rc = trexio_write_basis_nucleus_index(trex_file, basis_nucleus_index)
call trexio_assert(rc, TREXIO_SUCCESS, 'SUCCESS WRITE INDEX')
do i = 1, n_buffers
rc = trexio_write_mo_2e_int_eri(trex_file, offset, buf_size, &
index_sparse_mo_2e_int_eri(4*offset+1), &
value_sparse_mo_2e_int_eri(offset+1))
call trexio_assert(rc, TREXIO_SUCCESS, 'SUCCESS WRITE SPARSE')
offset = offset + buf_size
enddo
rc = trexio_has_nucleus_num(trex_file)
call trexio_assert(rc, TREXIO_SUCCESS, 'SUCCESS HAS 1')
@ -160,11 +186,20 @@ subroutine test_read(file_name, back_end)
character(len=32) :: sym_str
! sparse data
integer(4) :: index_sparse_mo_2e_int_eri(80)
double precision :: value_sparse_mo_2e_int_eri(20)
integer(8) :: read_buf_size = 10
integer(8) :: offset_read = 40
character*(128) :: str
num = 12
basis_shell_num = 24
index_sparse_mo_2e_int_eri = 0
value_sparse_mo_2e_int_eri = 0.0d0
! ================= START OF TEST ===================== !
trex_file = trexio_open(file_name, 'r', back_end, rc)
@ -199,7 +234,7 @@ subroutine test_read(file_name, back_end)
call exit(-1)
endif
rc = trexio_read_nucleus_label(trex_file, label, 2)
call trexio_assert(rc, TREXIO_SUCCESS)
if (trim(label(2)) == 'Na') then
@ -230,6 +265,17 @@ subroutine test_read(file_name, back_end)
endif
rc = trexio_read_mo_2e_int_eri(trex_file, offset_read, read_buf_size, &
index_sparse_mo_2e_int_eri(4*5+1), &
value_sparse_mo_2e_int_eri(5+1))
call trexio_assert(rc, TREXIO_SUCCESS)
if (index_sparse_mo_2e_int_eri(1) == 0 .and. index_sparse_mo_2e_int_eri(5*4+1) == offset_read*4+1) then
write(*,*) 'SUCCESS READ SPARSE DATA'
else
print *, 'FAILURE SPARSE DATA CHECK'
call exit(-1)
endif
rc = trexio_close(trex_file)
call trexio_assert(rc, TREXIO_SUCCESS)
@ -262,4 +308,3 @@ subroutine test_read_void(file_name, back_end)
! ================= END OF TEST ===================== !
end subroutine test_read_void