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added interface for logical attributes in hdf5 files, modified the interface for chararters. Logical attributes are now written directly without translation to integers 

git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@13402 c92efa57-630b-4861-b058-cf58834340f0
This commit is contained in:
pietrodelugas 2017-03-14 10:41:45 +00:00
parent dc74716e8b
commit af63d37fc6
5 changed files with 163 additions and 60 deletions
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191
Modules/hdf5_qe.f90
View File

@ -8,7 +8,7 @@
module hdf5_qe
!
USE HDF5
!USE, intrinsic :: ISO_C_binding
USE, intrinsic :: ISO_C_binding
USE Kinds, ONLY : DP
!
implicit none
@ -46,11 +46,12 @@ module hdf5_qe
INTERFACE add_attributes_hdf5
MODULE PROCEDURE add_attributes_hdf5_i, add_attributes_hdf5_r, &
add_attributes_hdf5_c
add_attributes_hdf5_c, add_attributes_hdf5_boolean
END INTERFACE
INTERFACE read_attributes_hdf5
MODULE PROCEDURE read_attributes_hdf5_i, read_attributes_hdf5_r
MODULE PROCEDURE read_attributes_hdf5_i, read_attributes_hdf5_r, read_attributes_hdf5_c, &
read_attributes_hdf5_boolean
END INTERFACE
@ -751,58 +752,105 @@ module hdf5_qe
END SUBROUTINE add_attributes_hdf5_r
SUBROUTINE add_attributes_hdf5_c(hdf5desc, attr_data, attr_name, kpoint)
implicit none
IMPLICIT NONE
TYPE(HDF5_type), intent(inout) :: hdf5desc
integer, intent(in), optional :: kpoint
!LOGICAL, intent(in) :: attr_data
CHARACTER(LEN=*), intent(in) :: attr_data
INTEGER, INTENT(IN), OPTIONAL :: kpoint
CHARACTER(LEN=*),TARGET, INTENT(IN) :: attr_data
CHARACTER(LEN=*), intent(in) :: attr_name
character*100 kstring
integer :: error
CHARACTER*100 kstring
INTEGER :: error
INTEGER :: arank = 1 ! Attribure rank
INTEGER(HID_T) :: aspace_id ! Attribute Dataspace identifier
INTEGER(HSIZE_T), DIMENSION(1) :: adims = (/1/) ! Attribute dimension
INTEGER(SIZE_T) :: attrlen ! Length of the attribute string
INTEGER(HSIZE_T) :: attrlen ! Length of the attribute string
INTEGER(HID_T) :: atype_id ! Attribute Dataspace identifier
INTEGER(HID_T) :: attr_id ! Attribute Dataspace identifier
INTEGER(HSIZE_T), DIMENSION(1) :: data_dims
!data_dims(1) = 1
data_dims(1) = len(attr_data)
if(present(kpoint)) then
write(kstring,'(I0)') kpoint
TYPE(C_PTR) :: buf
!
buf = C_LOC(attr_data)
attrlen = LEN(TRIM(attr_data) )
CALL H5Screate_f( H5S_SCALAR_F, aspace_id, error)
CALL H5Tcopy_f ( H5T_FORTRAN_S1, atype_id, error )
CALL H5Tset_size_f( atype_id, attrlen, error)
IF(PRESENT(kpoint)) THEN
WRITE(kstring,'(I0)') kpoint
kstring='KPOINT'//kstring
!write(attrdata,'(I0)') attr_data
CALL h5tcopy_f(H5T_NATIVE_CHARACTER, atype_id, error)
CALL h5gopen_f(hdf5desc%file_id,kstring,hdf5desc%group_id,error)
CALL h5screate_simple_f(arank, adims, aspace_id, error)
CALL h5acreate_f(hdf5desc%group_id, attr_name, H5T_NATIVE_CHARACTER, aspace_id, attr_id, error)
CALL h5awrite_f(attr_id, H5T_NATIVE_CHARACTER, attr_data, data_dims, error)
CALL h5acreate_f(hdf5desc%group_id, attr_name, atype_id, aspace_id, attr_id, error)
CALL h5awrite_f(attr_id, atype_id, buf, error)
CALL h5aclose_f(attr_id, error)
!
! Terminate access to the data space.
!
CALL h5sclose_f(aspace_id, error)
!
! End access to the dataset and release resources used by it.
!
CALL h5gclose_f(hdf5desc%group_id, error)
else
ELSE
!write(attrdata,'(I0)') attr_data
CALL h5tcopy_f(H5T_NATIVE_CHARACTER, atype_id, error)
CALL h5screate_simple_f(arank, adims, aspace_id, error)
CALL h5acreate_f(hdf5desc%file_id, attr_name, H5T_NATIVE_CHARACTER, aspace_id, attr_id, error)
CALL h5awrite_f(attr_id, H5T_NATIVE_CHARACTER, attr_data, data_dims, error)
CALL h5acreate_f(hdf5desc%file_id, attr_name, atype_id, aspace_id, attr_id, error)
CALL h5awrite_f(attr_id, atype_id, buf, error)
CALL h5aclose_f(attr_id, error)
!
! Terminate access to the data space.
!
CALL h5sclose_f(aspace_id, error)
endif
ENDIF
CALL H5Sclose_f(aspace_id, error)
CALL H5Tclose_f(atype_id, error )
END SUBROUTINE add_attributes_hdf5_c
!
SUBROUTINE add_attributes_hdf5_boolean(hdf5desc, attr_data, attr_name, kpoint)
IMPLICIT NONE
TYPE(HDF5_type), intent(inout) :: hdf5desc
INTEGER, INTENT(IN), OPTIONAL :: kpoint
LOGICAL,INTENT(IN) :: attr_data
CHARACTER(LEN=*), intent(in) :: attr_name
CHARACTER*100 kstring
INTEGER :: error
INTEGER :: arank = 1 ! Attribure rank
INTEGER(HID_T) :: aspace_id ! Attribute Dataspace identifier
INTEGER(HSIZE_T) :: attrlen ! Length of the attribute string
INTEGER(HID_T) :: atype_id ! Attribute Dataspace identifier
INTEGER(HID_T) :: attr_id ! Attribute Dataspace identifier
CHARACTER(LEN=7),TARGET :: string_data
TYPE(C_PTR) :: buf
!
IF (attr_data) THEN
string_data = '.TRUE.'
ELSE
string_data ='.FALSE.'
END IF
buf = C_LOC(string_data)
attrlen = LEN(TRIM(string_data) )
CALL H5Screate_f( H5S_SCALAR_F, aspace_id, error)
CALL H5Tcopy_f ( H5T_FORTRAN_S1, atype_id, error )
CALL H5Tset_size_f( atype_id, attrlen, error)
IF(PRESENT(kpoint)) THEN
WRITE(kstring,'(I0)') kpoint
kstring='KPOINT'//kstring
!write(attrdata,'(I0)') attr_data
CALL h5gopen_f(hdf5desc%file_id,kstring,hdf5desc%group_id,error)
CALL h5acreate_f(hdf5desc%group_id, attr_name, atype_id, aspace_id, attr_id, error)
CALL h5awrite_f(attr_id, atype_id, buf, error)
CALL h5aclose_f(attr_id, error)
!
! End access to the dataset and release resources used by it.
!
CALL h5gclose_f(hdf5desc%group_id, error)
ELSE
!write(attrdata,'(I0)') attr_data
CALL h5acreate_f(hdf5desc%file_id, attr_name, atype_id, aspace_id, attr_id, error)
CALL h5awrite_f(attr_id, atype_id, buf, error)
CALL h5aclose_f(attr_id, error)
!
! Terminate access to the data space.
!
ENDIF
CALL H5Sclose_f(aspace_id, error)
CALL H5Tclose_f(atype_id, error )
END SUBROUTINE add_attributes_hdf5_boolean
SUBROUTINE read_attributes_hdf5_i(hdf5desc, attr_data, attr_name, kpoint, debug)
@ -840,6 +888,77 @@ module hdf5_qe
END SUBROUTINE read_attributes_hdf5_i
SUBROUTINE read_attributes_hdf5_c(hdf5desc, attr_data, attr_name, kpoint, debug)
implicit none
TYPE(HDF5_type), intent(inout) :: hdf5desc
integer, intent(in), optional :: kpoint, debug
CHARACTER(LEN=*),INTENT(OUT) :: attr_data
CHARACTER(LEN=*), intent(in) :: attr_name
character*12 kstring
integer :: error
INTEGER(HID_T) :: aspace_id ! Attribute Dataspace identifier
INTEGER(HSIZE_T) :: attrlen ! Length of the attribute string
INTEGER(HID_T) :: atype_id ! Attribute Dataspace identifier
INTEGER(HID_T) :: attr_id ! Attribute Dataspace identifier
CHARACTER,TARGET,ALLOCATABLE :: chars(:)
TYPE(C_PTR) :: buf
IF(PRESENT( kpoint )) THEN
WRITE(kstring,'(I0)') kpoint
kstring='KPOINT'//kstring
CALL H5Gopen_f(hdf5desc%file_id,kstring,hdf5desc%group_id,error)
CALL H5Aopen_by_name_f(hdf5desc%group_id,'.', TRIM(attr_name) , attr_id, error)
CALL extract_string
CALL H5Aclose_f(attr_id, error)
CALL H5Gclose_f(hdf5desc%group_id, error)
ELSE
CALL h5aopen_by_name_f(hdf5desc%file_id,'.',TRIM(attr_name), attr_id, error)
CALL extract_string
CALL h5aclose_f(attr_id, error)
ENDIF
CALL H5Tclose_f( atype_id, error )
CONTAINS
SUBROUTINE extract_string
IMPLICIT NONE
INTEGER :: i
CALL H5Aget_type_f (attr_id , atype_id, error )
CALL H5Tget_size_f (atype_id, attrlen, error )
IF ( attrlen .GT. LEN(attr_data) ) CALL infomsg ('read_attributes_hdf5',&
'string attribute on file too long, it will be truncated on reading')
ALLOCATE ( chars(attrlen) )
buf = C_LOC (chars)
CALL H5Aread_f( attr_id, atype_id, buf, error )
DO i =1, attrlen
IF ( i .GT. LEN( attr_data) ) EXIT
attr_data(i:i) = chars(i)
END DO
DEALLOCATE(chars)
buf = C_NULL_PTR
END SUBROUTINE extract_string
END SUBROUTINE read_attributes_hdf5_c
SUBROUTINE read_attributes_hdf5_boolean( hdf5desc, attr_data, attr_name, kpoint, debug)
IMPLICIT NONE
TYPE(HDF5_type), intent(inout) :: hdf5desc
INTEGER, INTENT(IN), OPTIONAL :: kpoint, debug
LOGICAL,INTENT(OUT) :: attr_data
CHARACTER(LEN=*), intent(in) :: attr_name
!
CHARACTER(LEN=10) :: attr_string
CALL read_attributes_hdf5_c( hdf5desc, attr_string, attr_name, kpoint, debug)
SELECT CASE (TRIM( attr_string) )
CASE ('.TRUE.' )
attr_data = .TRUE.
CASE ('.FALSE.')
attr_data = .FALSE.
CASE DEFAULT
attr_data = .FALSE.
CALL infomsg ( 'read_attributes_hdf5' , 'error reading attribute '//TRIM(attr_name)//' value set to .FALSE.')
END SELECT
END SUBROUTINE read_attributes_hdf5_boolean
SUBROUTINE read_attributes_hdf5_r(hdf5desc, attr_data, attr_name, kpoint)
implicit none
TYPE(HDF5_type), intent(inout) :: hdf5desc
@ -889,10 +1008,8 @@ module hdf5_qe
LOGICAL, INTENT(IN) :: gamma_only
INTEGER, INTENT(IN) :: nbnd, ngw, igwx
TYPE(HDF5_type), intent(inout) :: hdf5desc
integer :: gammaonly = 0
CALL add_attributes_hdf5(hdf5desc,ngw,"ngw",ik)
IF ( gamma_only) gammaonly = 1
CALL add_attributes_hdf5(evc_hdf5_write,gammaonly,"gamma_only",ik)
CALL add_attributes_hdf5(evc_hdf5_write,gamma_only,"gamma_only",ik)
CALL add_attributes_hdf5(evc_hdf5_write,igwx,"igwx",ik)
CALL add_attributes_hdf5(evc_hdf5_write,nbnd,"nbnd",ik)
CALL add_attributes_hdf5(evc_hdf5_write,ik,"ik",ik)

5
Modules/io_base.f90
View File

@ -63,7 +63,6 @@ MODULE io_base
INTEGER :: me_in_group, nproc_in_group, my_group
COMPLEX(DP), ALLOCATABLE :: wtmp(:)
!
INTEGER :: gammaonly
#if defined(__HDF5)
TYPE (hdf5_type),ALLOCATABLE :: h5_write_desc
!
@ -86,9 +85,7 @@ MODULE io_base
CALL prepare_for_writing_final ( h5_write_desc, 0, &
TRIM(filename)//'.hdf5',ik, ADD_GROUP = .false.)
CALL add_attributes_hdf5(h5_write_desc, ngw,"ngw",ik)
gammaonly = 0
IF (gamma_only) gammaonly = 1
CALL add_attributes_hdf5(h5_write_desc, gammaonly,"gamma_only",ik)
CALL add_attributes_hdf5(h5_write_desc, gamma_only,"gamma_only",ik)
CALL add_attributes_hdf5(h5_write_desc, igwx,"igwx",ik)
CALL add_attributes_hdf5(h5_write_desc, nbnd,"nbnd",ik)
CALL add_attributes_hdf5(h5_write_desc, ik,"ik",ik)

9
Modules/qexml.f90
View File

@ -1078,8 +1078,6 @@ CONTAINS
CHARACTER(*), INTENT(in) :: cutoff_units
#if defined __HDF5
CHARACTER(LEN=256) :: filename_hdf5
CHARACTER :: gammaonly
!integer :: gammaonly, ierr
integer :: ierr
#endif
@ -1091,12 +1089,7 @@ CONTAINS
CALL add_attributes_hdf5(g_hdf5_write,ecutwfc,"WFC_CUTOFF")
CALL add_attributes_hdf5(g_hdf5_write,ecutrho,"RHO_CUTOFF")
CALL add_attributes_hdf5(g_hdf5_write,npwx,"MAX_NUMBER_OF_GK-VECTORS")
IF ( gamma_only) THEN
write(gammaonly,'(I1)') 1
ELSE
write(gammaonly,'(I1)') 0
END IF
CALL add_attributes_hdf5(g_hdf5_write,gammaonly,"GAMMA_ONLY")
CALL add_attributes_hdf5(g_hdf5_write,gamma_only,"GAMMA_ONLY")
CALL add_attributes_hdf5(g_hdf5_write,trim(cutoff_units),"UNITS_FOR_CUTOFF")
CALL add_attributes_hdf5(g_hdf5_write,nr1,"nr1")
CALL add_attributes_hdf5(g_hdf5_write,nr2,"nr2")

4
Modules/xml_io_base.f90
View File

@ -763,7 +763,6 @@ MODULE xml_io_base
INTEGER :: me_in_group, nproc_in_group, io_in_parent, nproc_in_parent, me_in_parent, my_group, io_group
#if defined __HDF5
CHARACTER(LEN=256) :: filename_hdf5
INTEGER :: gammaonly = 0
#endif
COMPLEX(DP), ALLOCATABLE :: wtmp(:)
!
@ -795,8 +794,7 @@ MODULE xml_io_base
filename_hdf5=trim(tmp_dir) //"evc.hdf5"
CALL prepare_for_writing_final(evc_hdf5_write,inter_pool_comm,filename_hdf5,ik)
CALL add_attributes_hdf5(evc_hdf5_write,ngw,"ngw",ik)
IF ( gamma_only ) gammaonly = 1
CALL add_attributes_hdf5(evc_hdf5_write,gammaonly,"gamma_only",ik)
CALL add_attributes_hdf5(evc_hdf5_write,gamma_only,"gamma_only",ik)
CALL add_attributes_hdf5(evc_hdf5_write,igwx,"igwx",ik)
CALL add_attributes_hdf5(evc_hdf5_write,nbnd,"nbnd",ik)
CALL add_attributes_hdf5(evc_hdf5_write,ik,"ik",ik)

14
PW/src/pw_restart_new.f90
View File

@ -266,6 +266,7 @@ MODULE pw_restart_new
CALL qexsd_init_symmetries(output%symmetries, nsym, nrot, spacegroup,&
s, ft, sname, t_rev, nat, irt,symop_2_class(1:nrot), verbosity, &
noncolin)
output%symmetries_ispresent=.TRUE.
!
!-------------------------------------------------------------------------------
! ... BASIS SET
@ -649,10 +650,8 @@ MODULE pw_restart_new
INTEGER,INTENT(IN) :: nr1, nr2, nr3, ngm, mill(:,:)
LOGICAL,INTENT(IN) :: gamma_only
!
INTEGER :: gammaonly_ = 0
CALL prepare_for_writing_final(h5_desc,0,filename)
IF ( gamma_only) gammaonly_ =1
CALL add_attributes_hdf5(h5_desc, gammaonly_, "gamma_only")
CALL prepare_for_writing_final(h5_desc,0,filename)
CALL add_attributes_hdf5(h5_desc, gamma_only, "gamma_only")
CALL add_attributes_hdf5(h5_desc, nr1, "nr1s")
CALL add_attributes_hdf5(h5_desc, nr2, "nr2s")
CALL add_attributes_hdf5(h5_desc, nr3, "nr3s")
@ -677,7 +676,7 @@ MODULE pw_restart_new
!
INTEGER, ALLOCATABLE :: igwk(:)
INTEGER, ALLOCATABLE :: itmp(:)
INTEGER :: ierr, gammaonly_ = 0
INTEGER :: ierr
#if defined (__HDF5)
TYPE (hdf5_type),ALLOCATABLE :: h5_desc
!
@ -716,9 +715,8 @@ MODULE pw_restart_new
CALL prepare_for_writing_final ( h5_desc, 0,&
TRIM(filename)//'.hdf5',ik_g, ADD_GROUP = .false.)
CALL add_attributes_hdf5(h5_desc, ngk_g(ik_g), "number_of_gk_vectors")
CALL add_attributes_hdf5(h5_desc, npwx_g, "max_number_of_gk_vectors")
IF (gamma_only) gammaonly_ = 1
CALL add_attributes_hdf5(h5_desc, gammaonly_, "gamma_only")
CALL add_attributes_hdf5(h5_desc, npwx_g, "max_number_of_gk_vectors")
CALL add_attributes_hdf5(h5_desc, gamma_only, "gamma_only")
CALL add_attributes_hdf5(h5_desc, "2pi/a", "units")
CALL write_gkhdf5(h5_desc,xk(:,ik),igwk(1:ngk_g(ik)), &
mill_g(1:3,igwk(1:ngk_g(ik_g))),ik_g)