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Made a number of improvements to the handling of encounters. time and…
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… id dimensions are now limited, which significantly reduces the file sizes of the individual encounter data files
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@daminton
daminton committed Dec 7, 2022
1 parent f4fec1e commit d09d8c5
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Showing 3 changed files with 66 additions and 36 deletions.
12 changes: 6 additions & 6 deletions src/modules/symba_classes.f90
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Original file line number Diff line number Diff line change
Expand Up @@ -182,12 +182,12 @@ module symba_classes

!! NetCDF dimension and variable names for the enounter save object
type, extends(netcdf_parameters) :: symba_io_encounter_parameters
integer(I4B) :: COLLIDER_DIM_SIZE = 2 !! Size of collider dimension
integer(I4B) :: ienc_frame = 1 !! Current frame number for the encounter history
character(STRMAX) :: enc_file = "encounter.nc" !! Encounter output file name

character(NAMELEN) :: level_varname = "level" !! Recursion depth
integer(I4B) :: ienc_frame = 1 !! Current frame number for the encounter history
character(STRMAX) :: enc_file = "encounter.nc" !! Encounter output file name
character(NAMELEN) :: level_varname = "level" !! Recursion depth
integer(I4B) :: level_varid !! ID for the recursion level variable
integer(I4B) :: time_dimsize = 0 !! Number of time values in snapshot
integer(I4B) :: id_dimsize = 0 !! Number of potential id values in snapshot
contains
procedure :: initialize => symba_io_encounter_initialize_output !! Initialize a set of parameters used to identify a NetCDF output object
end type symba_io_encounter_parameters
Expand Down Expand Up @@ -230,7 +230,7 @@ module symba_classes


type, extends(symba_nbody_system) :: symba_encounter_snapshot
integer(I4B) :: tslot !! The index for the time array in the final NetCDF file
integer(I4B) :: tslot !! The index for the time array in the final NetCDF file
contains
procedure :: write_encounter_frame => symba_io_encounter_write_frame !! Writes a frame of encounter data to file
generic :: write_frame => write_encounter_frame
Expand Down
79 changes: 55 additions & 24 deletions src/symba/symba_io.f90
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,8 @@ module subroutine symba_io_encounter_dump(self, param)
self%nc%ienc_frame = i
call snapshot%write_frame(self%nc,param)
end select
else
exit
end if
end do

Expand All @@ -57,7 +59,6 @@ module subroutine symba_io_encounter_initialize_output(self, param)
character(len=STRMAX) :: errmsg
integer(I4B) :: ndims


associate(nc => self)
dfill = ieee_value(dfill, IEEE_QUIET_NAN)
sfill = ieee_value(sfill, IEEE_QUIET_NAN)
Expand All @@ -69,7 +70,6 @@ module subroutine symba_io_encounter_initialize_output(self, param)
self%out_type = NF90_DOUBLE
end select


! Check if the file exists, and if it does, delete it
inquire(file=nc%enc_file, exist=fileExists)
if (fileExists) then
Expand All @@ -80,9 +80,9 @@ module subroutine symba_io_encounter_initialize_output(self, param)
call check( nf90_create(nc%enc_file, NF90_NETCDF4, nc%id), "symba_io_encounter_initialize_output nf90_create" )

! Dimensions
call check( nf90_def_dim(nc%id, nc%time_dimname, NF90_UNLIMITED, nc%time_dimid), "symba_io_encounter_initialize_output nf90_def_dim time_dimid" ) ! Simulation time dimension
call check( nf90_def_dim(nc%id, nc%space_dimname, NDIM, nc%space_dimid), "symba_io_encounter_initialize_output nf90_def_dim space_dimid" ) ! 3D space dimension
call check( nf90_def_dim(nc%id, nc%id_dimname, NF90_UNLIMITED, nc%id_dimid), "symba_io_encounter_initialize_output nf90_def_dim id_dimid" ) ! dimension to store particle id numbers
call check( nf90_def_dim(nc%id, nc%time_dimname, nc%time_dimsize, nc%time_dimid), "symba_io_encounter_initialize_output nf90_def_dim time_dimid" ) ! Simulation time dimension
call check( nf90_def_dim(nc%id, nc%space_dimname, NDIM , nc%space_dimid), "symba_io_encounter_initialize_output nf90_def_dim space_dimid" ) ! 3D space dimension
call check( nf90_def_dim(nc%id, nc%id_dimname, param%maxid, nc%id_dimid), "symba_io_encounter_initialize_output nf90_def_dim id_dimid" ) ! dimension to store particle id numbers
call check( nf90_def_dim(nc%id, nc%str_dimname, NAMELEN, nc%str_dimid), "symba_io_encounter_initialize_output nf90_def_dim str_dimid" ) ! Dimension for string variables (aka character arrays)

! Dimension coordinates
Expand Down Expand Up @@ -141,37 +141,58 @@ module subroutine symba_io_encounter_write_frame(self, nc, param)
use netcdf
implicit none
! Arguments
class(symba_encounter_snapshot), intent(in) :: self !! Swiftest encounter structure
class(symba_io_encounter_parameters), intent(inout) :: nc !! Parameters used to identify a particular encounter io NetCDF dataset
class(swiftest_parameters), intent(inout) :: param !! Current run configuration parameters
class(symba_encounter_snapshot), intent(in) :: self !! Swiftest encounter structure
class(symba_io_encounter_parameters), intent(inout) :: nc !! Parameters used to identify a particular encounter io NetCDF dataset
class(swiftest_parameters), intent(inout) :: param !! Current run configuration parameters
! Internals
integer(I4B) :: i, tslot, idslot, old_mode, n
character(len=NAMELEN) :: charstring
integer(I4B) :: i, tslot, idslot, old_mode, npl, ntp
character(len=NAMELEN) :: charstring

tslot = self%tslot
call check( nf90_set_fill(nc%id, nf90_nofill, old_mode), "symba_io_encounter_write_frame nf90_set_fill" )

tslot = self%tslot
call check( nf90_put_var(nc%id, nc%time_varid, self%t, start=[tslot]), "symba_io_encounter_write_frame nf90_put_var time_varid" )

select type(pl => self%pl)
class is (symba_pl)
n = size(pl%id(:))
do i = 1, n
npl = pl%nbody
do i = 1, npl
idslot = pl%id(i)
call check( nf90_put_var(nc%id, nc%time_varid, self%t, start=[tslot]), "symba_io_encounter_write_frame nf90_put_var time_varid" )
call check( nf90_put_var(nc%id, nc%id_varid, pl%id(i), start=[idslot]), "symba_io_encounter_write_frame nf90_put_var id_varid" )
call check( nf90_put_var(nc%id, nc%rh_varid, pl%rh(:,i), start=[1,idslot,tslot], count=[NDIM,1,1]), "symba_io_encounter_write_frame nf90_put_var rh_varid" )
call check( nf90_put_var(nc%id, nc%vh_varid, pl%vh(:,i), start=[1,idslot,tslot], count=[NDIM,1,1]), "symba_io_encounter_write_frame nf90_put_var vh_varid" )
call check( nf90_put_var(nc%id, nc%Gmass_varid, pl%Gmass(i), start=[idslot, tslot]), "symba_io_encounter_write_frame nf90_put_var body Gmass_varid" )
if (param%lclose) call check( nf90_put_var(nc%id, nc%radius_varid, pl%radius(i), start=[idslot, tslot]), "symba_io_encounter_write_frame nf90_put_var body radius_varid" )
call check( nf90_put_var(nc%id, nc%id_varid, pl%id(i), start=[idslot]), "symba_io_encounter_write_frame nf90_put_var pl id_varid" )
call check( nf90_put_var(nc%id, nc%rh_varid, pl%rh(:,i), start=[1,idslot,tslot], count=[NDIM,1,1]), "symba_io_encounter_write_frame nf90_put_var pl rh_varid" )
call check( nf90_put_var(nc%id, nc%vh_varid, pl%vh(:,i), start=[1,idslot,tslot], count=[NDIM,1,1]), "symba_io_encounter_write_frame nf90_put_var pl vh_varid" )
call check( nf90_put_var(nc%id, nc%Gmass_varid, pl%Gmass(i), start=[idslot, tslot]), "symba_io_encounter_write_frame nf90_put_var pl Gmass_varid" )

if (param%lclose) call check( nf90_put_var(nc%id, nc%radius_varid, pl%radius(i), start=[idslot, tslot]), "symba_io_encounter_write_frame nf90_put_var pl radius_varid" )

if (param%lrotation) then
call check( nf90_put_var(nc%id, nc%Ip_varid, pl%Ip(:,i), start=[1, idslot, tslot], count=[NDIM,1,1]), "symba_io_encounter_write_frame nf90_put_var body Ip_varid" )
call check( nf90_put_var(nc%id, nc%rot_varid, pl%rot(:,i), start=[1,idslot, tslot], count=[NDIM,1,1]), "symba_io_encounter_write_frame nf90_put_var body rotx_varid" )
call check( nf90_put_var(nc%id, nc%Ip_varid, pl%Ip(:,i), start=[1, idslot, tslot], count=[NDIM,1,1]), "symba_io_encounter_write_frame nf90_put_var pl Ip_varid" )
call check( nf90_put_var(nc%id, nc%rot_varid, pl%rot(:,i), start=[1,idslot, tslot], count=[NDIM,1,1]), "symba_io_encounter_write_frame nf90_put_var pl rotx_varid" )
end if

charstring = trim(adjustl(pl%info(i)%name))
call check( nf90_put_var(nc%id, nc%name_varid, charstring, start=[1, idslot], count=[NAMELEN, 1]), "symba_io_encounter_write_frame nf90_put_var name_varid" )
call check( nf90_put_var(nc%id, nc%name_varid, charstring, start=[1, idslot], count=[NAMELEN, 1]), "symba_io_encounter_write_frame nf90_put_var pl name_varid" )
charstring = trim(adjustl(pl%info(i)%particle_type))
call check( nf90_put_var(nc%id, nc%ptype_varid, charstring, start=[1, idslot], count=[NAMELEN, 1]), "symba_io_encounter_write_frame nf90_put_var particle_type_varid" )
call check( nf90_put_var(nc%id, nc%ptype_varid, charstring, start=[1, idslot], count=[NAMELEN, 1]), "symba_io_encounter_write_frame nf90_put_var pl particle_type_varid" )
end do

end select

associate(tp => self%tp)
ntp = tp%nbody
do i = 1, ntp
idslot = tp%id(i)
call check( nf90_put_var(nc%id, nc%id_varid, tp%id(i), start=[idslot]), "symba_io_encounter_write_frame nf90_put_var tp id_varid" )
call check( nf90_put_var(nc%id, nc%rh_varid, tp%rh(:,i), start=[1,idslot,tslot], count=[NDIM,1,1]), "symba_io_encounter_write_frame nf90_put_var tp rh_varid" )
call check( nf90_put_var(nc%id, nc%vh_varid, tp%vh(:,i), start=[1,idslot,tslot], count=[NDIM,1,1]), "symba_io_encounter_write_frame nf90_put_var tp vh_varid" )

charstring = trim(adjustl(tp%info(i)%name))
call check( nf90_put_var(nc%id, nc%name_varid, charstring, start=[1, idslot], count=[NAMELEN, 1]), "symba_io_encounter_write_frame nf90_put_var tp name_varid" )
charstring = trim(adjustl(tp%info(i)%particle_type))
call check( nf90_put_var(nc%id, nc%ptype_varid, charstring, start=[1, idslot], count=[NAMELEN, 1]), "symba_io_encounter_write_frame nf90_put_var tp particle_type_varid" )
end do
end associate

call check( nf90_set_fill(nc%id, old_mode, old_mode) )

return
Expand Down Expand Up @@ -388,10 +409,20 @@ module subroutine symba_io_stop_encounter(self, param, t)
class(symba_parameters), intent(inout) :: param !! Current run configuration parameters
real(DP), intent(in) :: t !! Current simulation time
! Internals
!character(STRMAX)
integer(I4B) :: i

! Create and save the output file for this encounter

! Figure out how many time slots we need
do i = 1, self%encounter_history%nframes
if (self%t + param%dt <= self%encounter_history%tvals(i)) then
self%encounter_history%nc%time_dimsize = i
exit
end if
end do

write(self%encounter_history%nc%enc_file, '("encounter_",I0.6,".nc")') param%iloop

call self%encounter_history%nc%initialize(param)
call self%encounter_history%dump(param)
call self%encounter_history%nc%close()
Expand Down
11 changes: 5 additions & 6 deletions src/symba/symba_util.f90
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Original file line number Diff line number Diff line change
Expand Up @@ -1326,9 +1326,10 @@ module subroutine symba_util_take_encounter_snapshot(self, param, t)
associate(npl => self%pl%nbody, ntp => self%tp%nbody)

allocate(symba_encounter_snapshot :: snapshot)
snapshot%t = t

if (npl > 0) allocate(symba_pl :: snapshot%pl)
if (ntp > 0) allocate(symba_tp :: snapshot%tp)
allocate(symba_pl :: snapshot%pl)
allocate(symba_tp :: snapshot%tp)
if (npl + ntp == 0) return
npl_snap = npl
ntp_snap = ntp
Expand All @@ -1345,6 +1346,7 @@ module subroutine symba_util_take_encounter_snapshot(self, param, t)
tp%lmask(1:ntp) = tp%status(1:ntp) /= INACTIVE .and. tp%levelg(1:ntp) == self%irec
ntp_snap = count(tp%lmask(1:ntp))
end if
snapshot%pl%nbody = npl_snap

! Take snapshot of the currently encountering massive bodies
if (npl_snap > 0) then
Expand Down Expand Up @@ -1377,6 +1379,7 @@ module subroutine symba_util_take_encounter_snapshot(self, param, t)
end if

! Take snapshot of the currently encountering test particles
snapshot%tp%nbody = ntp_snap
if (ntp_snap > 0) then
allocate(snapshot%tp%id(ntp_snap))
allocate(snapshot%tp%info(ntp_snap))
Expand All @@ -1390,10 +1393,6 @@ module subroutine symba_util_take_encounter_snapshot(self, param, t)
end do
end if

if (npl_snap + ntp_snap == 0) return

snapshot%t = t

! Save the snapshot
self%encounter_history%iframe = self%encounter_history%iframe + 1
call self%resize_storage(self%encounter_history%iframe)
Expand Down

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