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improve POD // allow custom separators when reading from ascii file /…
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…/ add force computation from HDF5 files
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@tommy-engels
tommy-engels committed Jan 11, 2019
1 parent 5c910fc commit b3b39b9
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Showing 5 changed files with 524 additions and 279 deletions.
2 changes: 1 addition & 1 deletion Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ FFILES = rhs.f90 vis.f90 fluid_time_step.f90 init_fields.f90 \
sponge.f90 fft_unit_test.f90 draw_plate.f90 draw_sphere.f90 \
rotation_matrices.f90 add_channel.f90 add_cavity.f90 init_scalar.f90 dry_run.f90 \
noncircular_cylinder.f90 draw_flexible_plate.f90 \
runtime_backuping.f90 io_test.f90 POD.f90
runtime_backuping.f90 io_test.f90 POD.f90 post_force.f90

ifndef NOHDF5
# Case WITH HDF5 (all machines except earth simulator)
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220 changes: 136 additions & 84 deletions src/ini_files_parser.f90
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Original file line number Diff line number Diff line change
Expand Up @@ -59,110 +59,162 @@ module module_ini_files_parser
! note: array is assumed-shape and its size defines what we try to read
! --> MPI wrapper in the MPI parser module
!-----------------------------------------------------------------------------
subroutine read_array_from_ascii_file(file, array, n_header)
implicit none
character(len=*), intent(in) :: file
integer, intent(in) :: n_header
real(kind=pr), intent(inout) :: array (1:,1:)
integer :: nlines, ncols, i, io_error
character(len=maxcolumns) :: dummy
character(len=16) :: fmt
character(len=3) :: ncols_str

! check if the specified file exists
call check_file_exists( file )

nlines = size(array,1)
ncols = size(array,2)

write(*,'(80("-"))')
write(*,'("INFO: reading ",i8," lines with ",i8," colums from ",A)') nlines, ncols, file

! set up format string
write(ncols_str,'(i3.3)') ncols
fmt = '('//ncols_str//'(es12.4,1x))'

io_error = 0
i = 0

open(unit=14,file=trim(adjustl(file)),action='read',status='old')
do while (io_error==0)
! read a line from file
read (14,'(A)',iostat=io_error) dummy
i = i + 1
! if we're past the header AND the read worked (i.e. not end of file)
if (i > n_header .and. io_error==0) then
read(dummy,*) array(i-n_header,:)
subroutine read_array_from_ascii_file(file, array, n_header, user_separator)
implicit none
character(len=*), intent(in) :: file
integer, intent(in) :: n_header
real(kind=pr), intent(inout) :: array (1:,1:)
character(len=1), optional, intent(in) :: user_separator
integer :: nlines, ncols, i, io_error, k
character(len=maxcolumns) :: dummy
character(len=16) :: fmt
character(len=3) :: ncols_str
character(len=1) :: sep

! check if the specified file exists
call check_file_exists( file )

nlines = size(array,1)
ncols = size(array,2)

if (present(user_separator)) then
sep = user_separator
else
sep = " "
endif
enddo
close (14)

write(*,'("Done reading.")')
write(*,'(80("-"))')
write(*,'(80("-"))')
write(*,'("INFO: reading ",i8," lines with ",i8," colums from ",A)') nlines, ncols, file
write(*,'("INFO: separator is -->",A1,"<--")') sep

! set up format string
write(ncols_str,'(i3.3)') ncols
fmt = '('//ncols_str//'(es12.4,1x))'

io_error = 0
i = 0

open(unit=14,file=trim(adjustl(file)),action='read',status='old')
do while (io_error==0)
! read a line from file
read (14,'(A)',iostat=io_error) dummy
i = i + 1

! if we're past the header AND the read worked (i.e. not end of file)
if (i > n_header .and. io_error==0) then

k = count_seperators_in_line(dummy, sep)
if (k == ncols) then
dummy = adjustl(dummy)
read(dummy,*) array(i-n_header,:)
else
write(*,*) "ERROR in file ",trim(adjustl(file))," line ", i, "has wrong number of columns, skip"
! this module is not MPI aware so abort is not available
stop
endif
endif
enddo
close (14)

write(*,'("Done reading.")')
write(*,'(80("-"))')
end subroutine read_array_from_ascii_file


!-----------------------------------------------------------------------------
! count the number of lines in an ascii file, skip n_header lines
! --> MPI wrapper in the MPI parser module
!-----------------------------------------------------------------------------
subroutine count_lines_in_ascii_file(file, num_lines, n_header)
implicit none
character(len=*), intent(in) :: file
integer, intent(out) :: num_lines
integer, intent(in) :: n_header
integer :: io_error, i
character(len=maxcolumns) :: dummy

! check if the specified file exists
call check_file_exists( file )
subroutine count_lines_in_ascii_file(file, num_lines, n_header, user_separator)
implicit none
character(len=*), intent(in) :: file
integer, intent(out) :: num_lines
integer, intent(in) :: n_header
character(len=1), optional, intent(in) :: user_separator
integer :: io_error, i
character(len=maxcolumns) :: dummy
character(len=1) :: sep

! check if the specified file exists
call check_file_exists( file )

if (present(user_separator)) then
sep = user_separator
else
sep = " "
endif

! count the lines
io_error = 0
i = 0
open(unit=14,file=trim(adjustl(file)),action='read',status='old')
do while (io_error==0)
read (14,'(A)',iostat=io_error) dummy
if (io_error==0) i = i+1
enddo
close (14)
num_lines = i - n_header
! count the lines
io_error = 0
i = 0
open(unit=14,file=trim(adjustl(file)),action='read',status='old')
do while (io_error==0)
read (14,'(A)',iostat=io_error) dummy
if (io_error==0) i = i+1
enddo
close (14)
num_lines = i - n_header
end subroutine count_lines_in_ascii_file


subroutine count_cols_in_ascii_file(file, num_cols, n_header)
implicit none
character(len=*), intent(in) :: file
integer, intent(out) :: num_cols
integer, intent(in) :: n_header
integer :: io_error, i
character(len=maxcolumns) :: dummy
subroutine count_cols_in_ascii_file(file, num_cols, n_header, user_separator)
implicit none
character(len=*), intent(in) :: file
integer, intent(out) :: num_cols
integer, intent(in) :: n_header
character(len=1), optional, intent(in) :: user_separator
integer :: io_error, i
character(len=maxcolumns) :: dummy
character(len=1) :: sep

! check if the specified file exists
call check_file_exists( file )
! check if the specified file exists
call check_file_exists( file )

! count the lines
io_error = 0
i = 0
if (present(user_separator)) then
sep = user_separator
else
sep = " "
endif

open(unit=14,file=trim(adjustl(file)),action='read',status='old')
do while (io_error==0)
read (14,'(A)',iostat=io_error) dummy
if (io_error==0 .and. i>n_header) exit
i=i+1
enddo
close (14)
! count the lines
io_error = 0
i = 1

num_cols = 1
do i = 1, len_trim(adjustl(dummy))
! count elements in the line by counting the separating spaces
if ( dummy(i:i) == " " ) then
num_cols = num_cols + 1
end if
enddo
! just read first line....after the header
open(unit=14,file=trim(adjustl(file)),action='read',status='old')
do while (io_error==0)
read (14,'(A)',iostat=io_error) dummy
if (io_error==0 .and. i>n_header) exit
i = i+1
enddo
close (14)

num_cols = count_seperators_in_line(dummy, sep)
end subroutine count_cols_in_ascii_file



integer function count_seperators_in_line( line, sep )
implicit none
CHARACTER(len=*), intent(in) :: line, sep
character(len=maxcolumns) :: dummy
integer :: num_cols, i

num_cols = 1
! remove leading spaces
dummy = adjustl(line)

do i = 1, len_trim(dummy)
! count elements in the dummy by counting the separators
if ( dummy(i:i) == sep(1:1) ) then
num_cols = num_cols + 1
end if
enddo

count_seperators_in_line = num_cols
end function


!-------------------------------------------------------------------------------
! clean a previously read ini file, deallocate its string array, and reset
! verbosity to .true. (as a matter of precaution)
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31 changes: 25 additions & 6 deletions src/ini_files_parser_mpi.f90
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Original file line number Diff line number Diff line change
Expand Up @@ -24,11 +24,12 @@ module module_ini_files_parser_mpi
! read an array from an ascii file (SERIAL version, to be executed only on root)
! note: array is assumed-shape and its size defines what we try to read
!-----------------------------------------------------------------------------
subroutine read_array_from_ascii_file_mpi(file, array, n_header)
subroutine read_array_from_ascii_file_mpi(file, array, n_header, user_separator)
implicit none
character(len=*), intent(in) :: file
integer, intent(in) :: n_header
real(kind=pr), intent(inout) :: array (1:,1:)
character(len=1), optional, intent(in) :: user_separator
integer :: nlines, ncols, mpicode, mpirank

! fetch my process id
Expand All @@ -41,7 +42,12 @@ subroutine read_array_from_ascii_file_mpi(file, array, n_header)
ncols = size(array,2)

! only root reads from file...
if (mpirank==0) call read_array_from_ascii_file(file, array, n_header)
if (present(user_separator)) then
if (mpirank==0) call read_array_from_ascii_file(file, array, n_header, user_separator)
else
if (mpirank==0) call read_array_from_ascii_file(file, array, n_header)
endif

! ... then broadcast
call MPI_BCAST(array,nlines*ncols,MPI_DOUBLE_PRECISION,0,MPI_COMM_WORLD,mpicode)
end subroutine read_array_from_ascii_file_mpi
Expand All @@ -50,35 +56,48 @@ end subroutine read_array_from_ascii_file_mpi
!-----------------------------------------------------------------------------
! count the number of lines in an ascii file, skip n_header lines
!-----------------------------------------------------------------------------
subroutine count_lines_in_ascii_file_mpi(file, num_lines, n_header)
subroutine count_lines_in_ascii_file_mpi(file, num_lines, n_header, user_separator)
implicit none
character(len=*), intent(in) :: file
integer, intent(out) :: num_lines
integer, intent(in) :: n_header
character(len=1), optional, intent(in) :: user_separator
integer :: mpicode, mpirank

! fetch my process id
call MPI_Comm_rank(MPI_COMM_WORLD, mpirank, mpicode)

! only root reads from file...
if (mpirank==0) call count_lines_in_ascii_file(file, num_lines, n_header)
if (present(user_separator)) then
if (mpirank==0) call count_lines_in_ascii_file(file, num_lines, n_header, user_separator)
else
if (mpirank==0) call count_lines_in_ascii_file(file, num_lines, n_header)
endif

! ... then broadcast
call MPI_BCAST(num_lines,1,MPI_INTEGER,0,MPI_COMM_WORLD,mpicode)
end subroutine count_lines_in_ascii_file_mpi


subroutine count_cols_in_ascii_file_mpi(file, num_cols, n_header)
subroutine count_cols_in_ascii_file_mpi(file, num_cols, n_header, user_separator)
implicit none
character(len=*), intent(in) :: file
integer, intent(out) :: num_cols
integer, intent(in) :: n_header
character(len=1), optional, intent(in) :: user_separator
integer :: mpicode, mpirank

! fetch my process id
call MPI_Comm_rank(MPI_COMM_WORLD, mpirank, mpicode)

! only root reads from file...
if (mpirank==0) call count_cols_in_ascii_file(file, num_cols, n_header)
if (present(user_separator)) then
if (mpirank==0) call count_cols_in_ascii_file(file, num_cols, n_header, user_separator)
else
if (mpirank==0) call count_cols_in_ascii_file(file, num_cols, n_header)
endif


! ... then broadcast
call MPI_BCAST(num_cols,1,MPI_INTEGER,0,MPI_COMM_WORLD,mpicode)
end subroutine count_cols_in_ascii_file_mpi
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2 comments on commit b3b39b9

@Truong-Hung
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It seems to me that you forgot to submit the post_force.f90 file?

@tommy-engels
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sorry! added the file now.
thanks for noticing!

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