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Improvements to xml toolkit: 

- can read tags not in order, although only in some specific cases (luckily
  including those PP files that do have some tags not in the usual order)
- writes complex variables as two reals, not in fortran free format:
  it makes reading data from other languages (e.g., python) easy
This commit is contained in:
Paolo Giannozzi 2020-07-06 12:51:40 +02:00
parent 1767e45c90
commit 8a3e92febe
2 changed files with 265 additions and 127 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

69
upflib/read_upf_new.f90
View File

@ -87,7 +87,15 @@ CONTAINS
IF( .NOT. upf%tcoulombp) then
allocate ( upf%vloc(upf%mesh) )
CALL xmlr_readtag( capitalize_if_v2('pp_local'), &
upf%vloc(:) )
upf%vloc(:), ierr )
!
! existing PP files may have pp_nlcc first, pp_local later,
! but also the other way round - check that everything was right
!
if ( ierr /= 0 ) then
ierr = -81
return
end if
end if
!
CALL read_pp_semilocal ( upf )
@ -258,51 +266,32 @@ CONTAINS
allocate ( vnl(1:upf%mesh) )
CALL xmlr_opentag( capitalize_if_v2('pp_semilocal') )
!
IF ( v2 ) THEN
tag = 'PP_VNL.1'
ELSE
tag = 'vnl'
END IF
tag = 'vnl'
DO nb = 1,upf%nbeta
IF ( v2 ) THEN
! NOTA BENE: v2 format follows available PP files, written
! using original write_upf_v2; not FoX-based write_upf_v2
IF ( nb - 1 == upf%lloc ) CYCLE
tag = 'PP_VNL.'//i2c(nb-1)
END IF
CALL xmlr_readtag( tag, vnl, ierr )
if ( ierr /= 0 ) then
if ( v2 ) then
go to 10
else
call upf_error('read_pp_semilocal','error reading SL PPs',1)
end if
end if
if ( ierr /= 0 ) &
call upf_error('read_pp_semilocal','error reading SL PPs',1)
CALL get_attr ( 'l', l)
ind = 1
IF ( upf%has_so ) then
CALL get_attr ( 'j', j)
IF ( l > 0 .AND. ABS(j-l-0.5_dp) < 0.001_dp ) ind = 2
if ( v2 .and. ind == 2 ) &
call upf_error('read_pp_semilocal','inconsistency in SL',1)
! FIXME: what about spin-orbit case for v.2 upf?
if ( v2 ) &
call upf_error('read_pp_semilocal','check spin-orbit',1)
END IF
upf%vnl(:,l,ind) = vnl(:)
END DO
deallocate ( vnl )
!
CALL xmlr_closetag( ) ! end pp_semilocal
!
10 IF ( v2 .and. upf%has_so ) then
rewind ( iun )
CALL xmlr_opentag( capitalize_if_v2('pp_semilocal') )
ind = 2
tag = 'PP_VNL.2'
DO nb = 1,upf%nbeta
CALL xmlr_readtag( tag, vnl, ierr )
if ( ierr /= 0 ) exit
CALL get_attr ( 'l', l)
CALL get_attr ( 'j', j)
IF ( .not. (l > 0 .AND. ABS(j-l-0.5_dp) < 0.001_dp) ) ind = 1
if ( v2 .and. ind == 1 ) &
call upf_error('read_pp_semilocal','inconsistency in SL',2)
upf%vnl(:,l,ind) = vnl(:)
END DO
CALL xmlr_closetag( ) ! end pp_semilocal
END IF
deallocate ( vnl )
END IF
!
END SUBROUTINE read_pp_semilocal
@ -359,7 +348,7 @@ CONTAINS
CALL get_attr('cutoff_radius_index', upf%kbeta(nb))
CALL get_attr('cutoff_radius', upf%rcut(nb))
CALL get_attr('ultrasoft_cutoff_radius', upf%rcutus(nb))
!
END DO
!
! pp_dij (D_lm matrix)
@ -599,7 +588,7 @@ CONTAINS
!
IMPLICIT NONE
TYPE(pseudo_upf),INTENT(INOUT) :: upf ! the pseudo data
INTEGER :: nw, nb
INTEGER :: nw, nb, ierr
CHARACTER(LEN=1) :: dummy
!
IF ( .NOT. v2 .OR. .NOT. upf%has_so ) RETURN
@ -617,7 +606,15 @@ CONTAINS
ENDDO
!
DO nb = 1,upf%nbeta
CALL xmlr_readtag( 'PP_RELBETA.'//i2c(nb), dummy )
CALL xmlr_readtag( 'PP_RELBETA.'//i2c(nb), dummy, ierr )
!
! existing PP files may have pp_relbeta first, pp_relwfc later,
! but also the other way round - check that everything was right
!
if ( ierr /= 0 ) then
ierr = -81
return
end if
CALL get_attr( 'index' , nw )
IF ( nb /= nw ) CALL upf_error('read_pp_spinorb','mismatch',2)
CALL get_attr( 'lll', upf%lll(nb) )

323
upflib/xmltools.f90
View File

@ -16,23 +16,35 @@ MODULE xmltools
! * lines no more than 1024 characters long (see maxline parameter)
! * no more than 9 levels of tags (see maxlevel parameter)
! * length of tags no more than 80 characters (see maxlength parameter)
! Can read tags only in the correct order and in the following format:
! * tags holding a single value should begin and end in the same line
! * tags holding arrays of values should be opened in a single line,
! then the array in free format, then a single line with closing tag
! * can read tags only in the correct order. If a tag is not found, the
! file is rewound. If "ierr" is present, a second attempt to find the
! tag is done starting from the top of the file - may work if the searched
! tag is found only above the current position, and nowhere else
! * only single values (e.g. no vectors) in attributes
! * attributes should not contain commas or strange characters
! Unpredictable results may follow otherwise.
!
USE upf_kinds, ONLY : dp
IMPLICIT NONE
!
#undef __debug
!! define __debug to print information on opened and closed tags
LOGICAL, PARAMETER :: one_line_tags=.true.
!! if true, write tags with one value in a single line:
!! <tag attr1="val1" ... >value</tag>
!! otherwise, as in iotk:
!! <tag attr1="val1" ... >
!! value
!! </tag>
!! Only for single values; arrays are always written as in iotk
!
! internal variables for reading and writing
!
INTEGER :: xmlunit
INTEGER, PARAMETER :: maxline=1024
character(len=maxline) :: line
integer :: eot
integer :: nattr
CHARACTER(LEN=maxline) :: line
INTEGER :: eot
! eot points to the end of tag in line just scanned
INTEGER :: nattr
CHARACTER(LEN=:), ALLOCATABLE :: attrlist
!
! variables used keep track of open tags
@ -55,12 +67,18 @@ MODULE xmltools
!
INTERFACE xmlr_readtag
MODULE PROCEDURE readtag_c, readtag_r, readtag_l, readtag_i, &
readtag_rv, readtag_rm, readtag_rt, readtag_zv, readtag_zm
readtag_iv, readtag_rv, readtag_rm, readtag_rt, &
readtag_zv, readtag_zm
END INTERFACE xmlr_readtag
!
! IMPORTANT NOTICE: complex numbers, z=a+ib, are written as two reals:
! "a b", not in fortran free format as "(a,b)". Reason:
! make the file readable by non-fortran tools, e.g. python
!
INTERFACE xmlw_writetag
MODULE PROCEDURE writetag_c, writetag_r, writetag_l, writetag_i, &
writetag_rv, writetag_rm, writetag_rt, writetag_zv, writetag_zm
writetag_iv, writetag_rv, writetag_rm, writetag_rt, &
writetag_zv, writetag_zm
END INTERFACE xmlw_writetag
!
INTERFACE get_attr
@ -224,18 +242,22 @@ CONTAINS
xmlunit = iun
nlevel = 0
open_tags(nlevel) = 'root'
if ( allocated(attrlist) ) DEALLOCATE ( attrlist)
if ( allocated(attrlist) ) DEALLOCATE ( attrlist)
#if defined ( __debug )
print "('file ',a,' opened with unit ',i5)",trim(filexml),iun
#endif
!
END FUNCTION xml_openfile
!
SUBROUTINE xml_closefile ( )
!
CLOSE ( UNIT=xmlunit, STATUS='keep' )
#if defined ( __debug )
print "('unit ',i5,': file closed')", xmlunit
#endif
xmlunit = -1
IF ( nlevel > 0 ) THEN
print '("severe error: file closed at level ",i1," with tag ",A," open")', &
nlevel, trim(open_tags(nlevel))
END IF
IF (nlevel > 0) print '("warning: file closed at level ",i1,&
& " with tag ",A," open")', nlevel, trim(open_tags(nlevel))
nlevel = 0
!
END SUBROUTINE xml_closefile
@ -278,7 +300,7 @@ CONTAINS
! If cval=' ' write <name attr1="val1" attr2="val2" ... />
! If cval='?' write <?name attr1="val1" attr2="val2" ...?>
! otherwise, write <name attr1="val1" attr2="val2" ...>cval</name>
! (su di una stessa riga)
! (on a same line if one_line_tags=.true.)
! On output, same as xmlw_opentag
!
CHARACTER(LEN=*), INTENT(IN) :: name
@ -307,7 +329,11 @@ CONTAINS
CALL xmlw_closetag ( '?' )
ELSE
! write value (character)
WRITE (xmlunit, "('>',A)", ADVANCE='no') trim(cval)
IF (one_line_tags) THEN
WRITE (xmlunit, "('>',A)", ADVANCE='no') trim(cval)
ELSE
WRITE (xmlunit, "('>',/,A)") trim(cval)
ENDIF
! close here the tag
CALL xmlw_closetag ( name )
END IF
@ -317,7 +343,6 @@ CONTAINS
ierr = ier_
ELSE IF ( ier_ > 0 ) THEN
print '("Fatal error ",i2," in xmlw_writetag!")', ier_
stop
END IF
!
END SUBROUTINE writetag_c
@ -334,6 +359,20 @@ CONTAINS
!
END SUBROUTINE writetag_i
!
SUBROUTINE writetag_iv (name, ivec, ierr )
!
! As writetag_c, for integer value
!
CHARACTER(LEN=*), INTENT(IN) :: name
INTEGER, INTENT(IN) :: ivec(:)
INTEGER, INTENT(OUT),OPTIONAL :: ierr
!
CALL xmlw_opentag (name, ierr )
WRITE( xmlunit, *) ivec
CALL xmlw_closetag ( )
!
END SUBROUTINE writetag_iv
!
SUBROUTINE writetag_l (name, lval, ierr )
!
! As writetag_c, for logical value
@ -404,26 +443,50 @@ CONTAINS
!
! As writetag_c, for a vector of complex values
!
USE iso_c_binding
CHARACTER(LEN=*), INTENT(IN) :: name
COMPLEX(dp), INTENT(IN) :: zvec(:)
INTEGER, INTENT(OUT),OPTIONAL :: ierr
COMPLEX(dp), INTENT(IN), TARGET:: zvec(:)
INTEGER, INTENT(OUT), OPTIONAL :: ierr
!
! Casts a real pointer (rvec) to a complex array (zvec) via C pointer (!)
! in order to write complexes as two reals. Some compilers require that
! the argument of c_loc (zvec) is a pointer or has the "target" attribute
!
TYPE (c_ptr) :: cp
REAL(dp), POINTER :: rvec(:)
INTEGER :: n, ndim
!
NULLIFY (rvec)
cp = c_loc(zvec)
CALL c_f_pointer (cp, rvec, shape(zvec)*[2])
CALL xmlw_opentag (name, ierr )
WRITE( xmlunit, *) zvec
ndim = SIZE (zvec)
DO n=1,2*ndim,2
WRITE( xmlunit, *) rvec(n), rvec(n+1)
END DO
CALL xmlw_closetag ( )
!
END SUBROUTINE writetag_zv
!
SUBROUTINE writetag_zm (name, zmat, ierr )
!
! As writetag_c, for a matrix of complex values
! As writetag_c for a matrix of complex values - see comments in writetag_zv
!
USE iso_c_binding
CHARACTER(LEN=*), INTENT(IN) :: name
COMPLEX(dp), INTENT(IN) :: zmat(:,:)
INTEGER, INTENT(OUT),OPTIONAL :: ierr
COMPLEX(dp), INTENT(IN), TARGET:: zmat(:,:)
INTEGER, INTENT(OUT), OPTIONAL :: ierr
!
TYPE (c_ptr) :: cp
REAL(dp), POINTER :: rmat(:,:)
INTEGER :: n, nvec
!
NULLIFY (rmat)
cp = c_loc(zmat)
CALL c_f_pointer (cp, rmat, shape(zmat)*[2,1])
!
CALL xmlw_opentag (name, ierr )
WRITE( xmlunit, *) zmat
WRITE( xmlunit, *) rmat
CALL xmlw_closetag ( )
!
END SUBROUTINE writetag_zm
@ -455,7 +518,9 @@ CONTAINS
WRITE (xmlunit, "(' ')", ADVANCE="no", ERR=10)
END DO
WRITE (xmlunit, "('<',A)", ADVANCE="no", ERR=10) trim(name)
! print '("opened at level ",i1," tag ",A)', nlevel, trim(open_tags(nlevel))
#if defined ( __debug )
print '("opened (write) level-",i1," tag ",A)', nlevel, trim(open_tags(nlevel))
#endif
!
! attributes (if present)
!
@ -478,24 +543,35 @@ CONTAINS
CHARACTER(LEN=*), INTENT(IN), OPTIONAL :: tag
INTEGER :: i
!
IF ( nlevel < 0 ) &
print '("severe error: closing tag that was never opened")'
IF ( nlevel < 0 ) print "('severe error: closing tag that was never opened')"
IF ( .NOT.PRESENT(tag) ) THEN
DO i=2,nlevel
WRITE (xmlunit, '(" ")', ADVANCE='NO')
END DO
WRITE (xmlunit, '("</",A,">")') trim(open_tags(nlevel))
#if defined ( __debug )
print '("closed (write) level-",i1," tag ",A)', nlevel, trim(open_tags(nlevel))
#endif
ELSE
i = len_trim(tag)
IF ( i == 0 ) THEN
WRITE (xmlunit, '("/>")')
#if defined ( __debug )
print '("closed (write) level-",i1," tag ",A)', &
nlevel, trim(open_tags(nlevel))
#endif
ELSE IF ( i == 1 .AND. tag(1:1) == '?' ) THEN
WRITE (xmlunit, '("?>")')
#if defined ( __debug )
print '("closed (write) level-",i1," tag ",A)', nlevel, tag
#endif
ELSE
WRITE (xmlunit, '("</",A,">")') trim(tag)
#if defined ( __debug )
print '("closed (write) level-",i1," tag ",A)', nlevel, tag
#endif
END IF
END IF
!print '("closed at level ",i1," tag ",A)', nlevel, trim(open_tags(nlevel))
nlevel = nlevel-1
!
END SUBROUTINE xmlw_closetag
@ -586,6 +662,26 @@ CONTAINS
!
END SUBROUTINE readtag_i
!
SUBROUTINE readtag_iv (name, ivec, ierr)
!
! As readtag_c, for a vector of integer values
!
CHARACTER(LEN=*), INTENT(IN) :: name
INTEGER, INTENT(OUT) :: ivec(:)
INTEGER, INTENT(OUT),OPTIONAL :: ierr
INTEGER :: ier_
!
CALL xmlr_opentag (name, ier_)
if ( ier_ == 0 ) then
READ(xmlunit, *) ivec
CALL xmlr_closetag ( )
else
ivec = 0.0_dp
end if
IF ( present (ierr) ) ierr = ier_
!
END SUBROUTINE readtag_iv
!
SUBROUTINE readtag_l (name, lval, ierr )
!
! As readtag_c, for logical value
@ -684,16 +780,23 @@ CONTAINS
!
SUBROUTINE readtag_zv (name, zvec, ierr)
!
! As readtag_c, for a vector of complex values
! As readtag_c, for a vector of complex values - see comments in writetag_zv
!
USE iso_c_binding
CHARACTER(LEN=*), INTENT(IN) :: name
COMPLEX(dp), INTENT(OUT) :: zvec(:)
COMPLEX(dp), INTENT(OUT), target :: zvec(:)
INTEGER, INTENT(OUT),OPTIONAL :: ierr
!
TYPE (c_ptr) :: cp
REAL(dp), POINTER :: rvec(:)
INTEGER :: ier_
!
CALL xmlr_opentag (name, ier_)
if ( ier_ == 0 ) then
READ(xmlunit, *) zvec
NULLIFY (rvec)
cp = c_loc(zvec)
CALL c_f_pointer ( cp, rvec, shape(zvec)*[2])
READ( xmlunit, *) rvec
CALL xmlr_closetag ( )
else
zvec = 0.0_dp
@ -704,16 +807,22 @@ CONTAINS
!
SUBROUTINE readtag_zm (name, zmat, ierr)
!
! As readtag_c, for a matrix of complex values
! As readtag_c, for a matrix of complex values - see comments in writetag_zv
!
USE iso_c_binding
CHARACTER(LEN=*), INTENT(IN) :: name
COMPLEX(dp), INTENT(OUT) :: zmat(:,:)
COMPLEX(dp), INTENT(OUT), target :: zmat(:,:)
INTEGER, INTENT(OUT),OPTIONAL :: ierr
TYPE (c_ptr) :: cp
REAL(dp), POINTER :: rmat(:,:)
INTEGER :: ier_
!
CALL xmlr_opentag (name, ier_)
if ( ier_ == 0 ) then
READ(xmlunit, *) zmat
NULLIFY (rmat)
cp = c_loc(zmat)
CALL c_f_pointer (cp, rmat, shape(zmat)*[2,1])
READ(xmlunit, *) rmat
CALL xmlr_closetag ( )
else
zmat = 0.0_dp
@ -734,44 +843,64 @@ CONTAINS
! 1: error parsing file
! 2: error in arguments
!
integer :: i, j, lt
integer :: i, j, lt, ll
character(len=1) :: endtag
!
call xmlr_opentag ( tag, ierr )
!
if ( eot > 0 ) then
j = eot
lt = len_trim(tag)
! beginning of val at line(j:j): search for end tag
i = index ( line(j:), '</'//trim(tag) )
if ( i < 1 ) then
! </tag> not found on this line
! print *, 'tag </',trim(tag),'> not found'
ierr = 1
return
else
! maybe found end tag?
endtag = adjustl( line(j+i+1+lt:) )
if ( endtag /= '>' ) then
! print *, 'tag ',trim(tag),' not correctly closed'
if (present(ierr)) ierr = 1
else
! <tag ....>val</tag> found, exit
cval = adjustl(trim(line(j:j+i-2)))
! print *, 'value=',cval
end if
! print '("closed at level ",i1," tag ",A)', nlevel, trim(open_tags(nlevel))
nlevel = nlevel -1
!
return
!
endif
else if ( eot == 0 ) then
cval = ''
if ( eot < 0 ) then
! print *, 'end of file reached, tag not found'
if ( present(ierr) ) ierr =-1
else if ( eot < 0 ) then
return
else if ( eot == 0 ) then
! print *, 'tag found, no value to read on line'
cval = ''
return
else
! scan current line if there is something after the end of tag
! (variable "eot"); read a new line otherwise
do while(.true.)
if ( eot > len_trim(line) ) then
read(xmlunit,'(a)', end=10) line
j = 1
else
j = eot
end if
! beginning of val at line(j:j): search for end tag
i = index ( line(j:), '</'//trim(tag) )
if ( i < 1 ) then
! </tag> not found on this line: read value and continue
cval = trim(cval) // adjustl(trim(line(j:)))
else
! possible end tag found
lt = len_trim(tag)
endtag = adjustl( line(j+i+1+lt:) )
if ( endtag /= '>' ) then
! print *, 'tag ',trim(tag),' not correctly closed'
if (present(ierr)) ierr = 1
else
! end of tag found, read value (if any) and exit
if ( i > 1 ) cval = trim(cval) // adjustl(trim(line(j:j+i-2)))
! print *, 'value=',cval
end if
#if defined ( __debug )
print '("closed (read) level-",i1," tag ",A)', &
nlevel, trim(open_tags(nlevel))
#endif
nlevel = nlevel -1
!
return
!
endif
!
end do
!
end if
! print *, 'tag </',trim(tag),'> not found'
10 if ( present(ierr) ) then
ierr = 1
else
print *, 'end of file reached, tag </'//trim(tag)//'> not found'
end if
!
end subroutine readtag_c
@ -788,7 +917,7 @@ CONTAINS
! 2: line too long
! 3: too many levels of tags
!
integer :: stat, ll, lt, i, j, j0
integer :: stat, ntry, ll, lt, i, j, j0
! stat= 0: begin
! stat=-1: in comment
! stat=1 : tag found
@ -796,16 +925,18 @@ CONTAINS
character(len=1) :: quote
!
nattr=0
ntry =0
if ( allocated(attrlist) ) deallocate (attrlist)
!
lt = len_trim(tag)
!
1 ntry = ntry+1
stat=0
eot =0
eot =-1
do while (.true.)
read(xmlunit,'(a)', end=10) line
ll = len_trim(line)
if ( ll == maxline ) then
print *, 'line too long'
print *, 'severe error: line too long'
if (present(ierr)) ierr = 2
return
end if
@ -840,11 +971,12 @@ CONTAINS
! tag found? check what follows our would-be tag
j = j+i+lt
if ( j > ll ) then
print *, 'oops... opened tag not closed on same line'
stat = 1
! <tag continues in next line
exit parse
else if ( line(j:j) == ' ' .or. line(j:j) == '>' &
.or. line(j:j+1)=='/>') then
! print *, '<tag found'
! <tag or <tag> or <tag/> found
stat = 1
end if
end if
@ -859,29 +991,26 @@ CONTAINS
else if ( line(j:j+1) == '/>' ) then
! <tag ... /> found : return
if (present(ierr)) ierr = 0
! eot = -2: tag with no value found
eot = -2
! eot = 0: tag with no value found
eot = 0
!
return
!
else if ( line(j:j) == '>' ) then
! <tag ... > found
if ( j+1 > ll ) then
! eot = -1: tag found, line ends
eot = -1
else
! eot points to the rest of the line
eot = j+1
end if
! eot points to the rest of the line
eot = j+1
if (present(ierr)) ierr = 0
nlevel = nlevel+1
IF ( nlevel > maxlevel ) THEN
print *, ' too many levels'
print *, ' severe error: too many levels'
if (present(ierr)) ierr = 3
else
open_tags(nlevel) = trim(tag)
!print '("opened at level ",i1," tag ",A)', &
! nlevel, trim(open_tags(nlevel))
#if defined ( __debug )
print '("opened (read) level-",i1," tag ",A)',&
nlevel, trim(open_tags(nlevel))
#endif
end if
!
return
@ -923,11 +1052,16 @@ CONTAINS
10 if ( stat == 0 ) then
if ( present(ierr) ) then
ierr =-1
! quick-and-dirty pseudo-fix to deal with tags not found:
! rewind and try again - will work if the desired tag is
! found above the current position (and nowhere else)
rewind(xmlunit)
if ( ntry == 1 ) go to 1
else
print *, 'end of file reached, tag '//trim(tag)//' not found'
end if
else
print *, 'parsing error'
print *, 'severe parsing error'
if ( present(ierr) ) ierr = 1
end if
!
@ -948,16 +1082,22 @@ CONTAINS
! stat= 0: begin
! stat= 1: end
!
IF ( nlevel < 0 ) &
if ( nlevel < 0 ) &
print '("severe error: closing tag that was never opened")'
stat=0
!write(6,'("closing at level ",i1," tag ",A,"...")',advance='no') &
! nlevel,trim(open_tags(nlevel))
#if defined ( __debug )
if ( .not. present(tag) ) then
print '("closed (read) level-",i1," tag ",A)', &
nlevel, trim(open_tags(nlevel))
else
print '("closed (read) level-",i1," tag ",A)', nlevel, tag
end if
#endif
do while (.true.)
read(xmlunit,'(a)', end=10) line
ll = len_trim(line)
if ( ll == maxline ) then
print *, 'line too long'
print *, 'Fatal error: line too long'
if (present(ierr)) ierr = 1
return
end if
@ -996,10 +1136,11 @@ CONTAINS
! tag found? check what follows our would-be tag
j = j+i+1+lt
if ( j > ll ) then
print *, 'oops... opened tag not closed on same line'
stat = 1
! </tag continues in next line
exit parse
else if ( line(j:j) == ' ' .or. line(j:j) == '>') then
! print *, '</tag found'
! </tag or </tag> found
stat = 1
end if
end if