Merge branch 'debug'

src/discard/discard.f90

@@ -76,9 +76,9 @@ module subroutine discard_tp(self, system, param)
       integer(I4B) :: npl, ntp
 
       associate(tp => self, cb => system%cb, pl => system%pl)
-         if ((ntp == 0) .or. (npl ==0)) return 
          ntp = tp%nbody
          npl = pl%nbody
+         if ((ntp == 0) .or. (npl ==0)) return 
 
          if ((param%rmin >= 0.0_DP) .or. (param%rmax >= 0.0_DP) .or. &
              (param%rmaxu >= 0.0_DP) .or. ((param%qmin >= 0.0_DP) .and. (param%qmin_coord == "BARY"))) then

src/drift/drift.f90

@@ -39,6 +39,8 @@ module subroutine drift_body(self, system, param, dt)
          end if
       end associate
 
+      deallocate(iflag)
+
       return
    end subroutine drift_body
 
@@ -77,12 +79,15 @@ module subroutine drift_all(mu, x, v, n, param, dt, lmask, iflag)
       else
          where(lmask(1:n)) dtp(1:n) = dt
       end if 
+
       !$omp simd
       do i = 1, n
          if (lmask(i)) call drift_one(mu(i), x(1,i), x(2,i), x(3,i), v(1,i), v(2,i), v(3,i), dtp(i), iflag(i))
       end do
       !$omp end simd
 
+      deallocate(dtp)
+
       return
    end subroutine drift_all
 

src/encounter/encounter_check.f90

@@ -403,6 +403,7 @@ subroutine encounter_check_all_sort_and_sweep_plpl(npl, x, v, renc, dt, lvdotr,
          call encounter_check_all(nenc, index1, index2, x, v, x, v, renc, renc, dt, lencounter, lvdotr)
 
          call encounter_check_reduce_broadphase(npl, nenc, index1, index2, lencounter, lvdotr)
+         deallocate(lencounter)
       end if
 
       return
@@ -837,7 +838,6 @@ module subroutine encounter_check_collapse_ragged_list(ragged_list, n1, nenc, in
       end associate
       if (nenc == 0) return
 
-
       allocate(index1(nenc))
       allocate(index2(nenc))
       if (present(lvdotr)) allocate(lvdotr(nenc))

src/encounter/encounter_util.f90

@@ -62,6 +62,74 @@ module subroutine encounter_util_copy_list(self, source)
    end subroutine encounter_util_copy_list
 
 
+   module subroutine encounter_util_dealloc_aabb(self)
+      !! author: David A. Minton
+      !!
+      !! Deallocates all allocatables
+      implicit none
+      ! Arguments
+      class(encounter_bounding_box_1D), intent(inout) :: self
+
+      if (allocated(self%ind)) deallocate(self%ind)
+      if (allocated(self%ibeg)) deallocate(self%ibeg)
+      if (allocated(self%iend)) deallocate(self%iend)
+
+      return
+   end subroutine encounter_util_dealloc_aabb
+
+
+   module subroutine encounter_util_dealloc_list(self)
+      !! author: David A. Minton
+      !!
+      !! Deallocates all allocatables
+      implicit none
+      ! Arguments
+      class(encounter_list), intent(inout) :: self
+
+      if (allocated(self%lvdotr)) deallocate(self%lvdotr)
+      if (allocated(self%status)) deallocate(self%status)
+      if (allocated(self%index1)) deallocate(self%index1)
+      if (allocated(self%index2)) deallocate(self%index2)
+      if (allocated(self%id1)) deallocate(self%id1)
+      if (allocated(self%id2)) deallocate(self%id2)
+      if (allocated(self%x1)) deallocate(self%x1)
+      if (allocated(self%x2)) deallocate(self%x2)
+      if (allocated(self%v1)) deallocate(self%v1)
+      if (allocated(self%v2)) deallocate(self%v2)
+      if (allocated(self%t)) deallocate(self%t)
+
+      return
+   end subroutine encounter_util_dealloc_list
+
+
+   module subroutine encounter_util_final_aabb(self)
+      !! author: David A. Minton
+      !!
+      !! Finalize the axis aligned bounding box (1D) - deallocates all allocatables
+      implicit none
+      ! Arguments
+      type(encounter_bounding_box_1D), intent(inout) :: self
+
+      call self%dealloc()
+
+      return
+   end subroutine encounter_util_final_aabb
+
+
+   module subroutine encounter_util_final_list(self)
+      !! author: David A. Minton
+      !!
+      !! Finalize the encounter list - deallocates all allocatables
+      implicit none
+      ! Arguments
+      type(encounter_list), intent(inout) :: self
+
+      call self%dealloc()
+
+      return
+   end subroutine encounter_util_final_list
+
+
    module subroutine encounter_util_resize_list(self, nnew)
       !! author: David A. Minton
       !!

src/helio/helio_drift.f90

@@ -19,7 +19,7 @@ module subroutine helio_drift_body(self, system, param, dt)
       integer(I4B) :: i !! Loop counter
       real(DP) :: rmag, vmag2, energy
       integer(I4B), dimension(:),allocatable :: iflag !! Vectorized error code flag
-      real(DP), dimension(:), allocatable    :: dtp, mu
+      real(DP), dimension(:), allocatable    :: mu
 
       if (self%nbody == 0) return
 
@@ -37,6 +37,7 @@ module subroutine helio_drift_body(self, system, param, dt)
          end if
       end associate
 
+      deallocate(iflag, mu)
       return
    end subroutine helio_drift_body
 

src/helio/helio_util.f90

@@ -0,0 +1,46 @@
+submodule(helio_classes) s_helio_util
+   use swiftest
+contains
+
+   module subroutine helio_util_final_pl(self)
+      !! author: David A. Minton
+      !!
+      !! Finalize the Helio massive body object - deallocates all allocatables
+      implicit none
+      ! Arguments
+      type(helio_pl),  intent(inout) :: self !! Helio massive body object
+
+      call self%dealloc()
+
+      return
+   end subroutine helio_util_final_pl
+
+
+   module subroutine helio_util_final_system(self)
+      !! author: David A. Minton
+      !!
+      !! Finalize the Helio nbody system object - deallocates all allocatables
+      implicit none
+      ! Arguments
+      type(helio_nbody_system),  intent(inout) :: self !! Helio nbody system object
+
+      call self%dealloc()
+
+      return
+   end subroutine helio_util_final_system
+
+
+   module subroutine helio_util_final_tp(self)
+      !! author: David A. Minton
+      !!
+      !! Finalize the Helio test particle object - deallocates all allocatables
+      implicit none
+      ! Arguments
+      type(helio_tp),  intent(inout) :: self !! Helio test particle object
+
+      call self%dealloc()
+
+      return
+   end subroutine helio_util_final_tp
+
+end submodule s_helio_util

src/io/io.f90

@@ -304,7 +304,7 @@ module subroutine io_dump_system(self, param)
          call self%tp%write_frame(dump_param%nciu, dump_param)
          call dump_param%nciu%close()
          ! Syncrhonize the disk and memory buffer of the NetCDF file (e.g. commit the frame files stored in memory to disk) 
-         call param%nciu%sync()
+         call param%nciu%flush(param)
       end if
 
       idx = idx + 1
@@ -2130,8 +2130,6 @@ module subroutine io_write_frame_system(self, param)
             end select
 
             lfirst = .false.
-         else
-            !call param%nciu%open(param)
          end if
       end if
 

src/modules/encounter_classes.f90

@@ -23,12 +23,14 @@ module encounter_classes
       real(DP),     dimension(:,:), allocatable :: v2     !! the velocity of body 2 in the encounter
       real(DP),     dimension(:),   allocatable :: t      !! Time of encounter
    contains
-      procedure :: setup  => encounter_setup_list       !! A constructor that sets the number of encounters and allocates and initializes all arrays  
-      procedure :: append => encounter_util_append_list !! Appends elements from one structure to another
-      procedure :: copy   => encounter_util_copy_list   !! Copies elements from the source encounter list into self.
-      procedure :: spill  => encounter_util_spill_list  !! "Spills" bodies from one object to another depending on the results of a mask (uses the PACK intrinsic)
-      procedure :: resize => encounter_util_resize_list !! Checks the current size of the encounter list against the required size and extends it by a factor of 2 more than requested if it is too small.
-      procedure :: write  => encounter_io_write_list    !! Write close encounter data to output binary file
+      procedure :: setup   => encounter_setup_list        !! A constructor that sets the number of encounters and allocates and initializes all arrays  
+      procedure :: append  => encounter_util_append_list  !! Appends elements from one structure to another
+      procedure :: copy    => encounter_util_copy_list    !! Copies elements from the source encounter list into self.
+      procedure :: dealloc => encounter_util_dealloc_list !! Deallocates all allocatables
+      procedure :: spill   => encounter_util_spill_list   !! "Spills" bodies from one object to another depending on the results of a mask (uses the PACK intrinsic)
+      procedure :: resize  => encounter_util_resize_list  !! Checks the current size of the encounter list against the required size and extends it by a factor of 2 more than requested if it is too small.
+      procedure :: write   => encounter_io_write_list     !! Write close encounter data to output binary file
+      final     :: encounter_util_final_list            !! Finalize the encounter list - deallocates all allocatables
    end type encounter_list
 
    type encounter_bounding_box_1D
@@ -38,6 +40,8 @@ module encounter_classes
       integer(I4B), dimension(:), allocatable :: iend !! Ending index for box
    contains
       procedure :: sort  => encounter_check_sort_aabb_1D !! Sorts the bounding box extents along a single dimension prior to the sweep phase
+      procedure :: dealloc => encounter_util_dealloc_aabb !! Deallocates all allocatables
+      final     :: encounter_util_final_aabb             !! Finalize the axis-aligned bounding box (1D) - deallocates all allocatables
    end type
 
    type encounter_bounding_box
@@ -209,10 +213,30 @@ module subroutine encounter_util_copy_list(self, source)
          class(encounter_list), intent(in)    :: source !! Source object to copy into
       end subroutine encounter_util_copy_list
 
+      module subroutine encounter_util_dealloc_aabb(self)
+         implicit none
+         class(encounter_bounding_box_1D), intent(inout) :: self !!Bounding box structure along a single dimension
+      end subroutine encounter_util_dealloc_aabb
+
+      module subroutine encounter_util_dealloc_list(self)
+         implicit none
+         class(encounter_list), intent(inout) :: self !! Swiftest encounter list object
+      end subroutine encounter_util_dealloc_list
+
+      module subroutine encounter_util_final_aabb(self)
+         implicit none
+         type(encounter_bounding_box_1D), intent(inout) :: self !!Bounding box structure along a single dimension
+      end subroutine encounter_util_final_aabb
+
+      module subroutine encounter_util_final_list(self)
+         implicit none
+         type(encounter_list), intent(inout) :: self !! Swiftest encounter list object
+      end subroutine encounter_util_final_list
+
       module subroutine encounter_util_resize_list(self, nnew)
          implicit none
          class(encounter_list), intent(inout) :: self !! Swiftest encounter list 
-         integer(I4B),          intent(in)    :: nnew !! New size of list needed
+         integer(I4B),         intent(in)    :: nnew !! New size of list needed
       end subroutine encounter_util_resize_list
 
       module subroutine encounter_util_spill_list(self, discards, lspill_list, ldestructive)

src/modules/helio_classes.f90

@@ -17,6 +17,7 @@ module helio_classes
    contains
       procedure :: step       => helio_step_system             !! Advance the Helio nbody system forward in time by one step
       procedure :: initialize => helio_setup_initialize_system !! Performs Helio-specific initilization steps, including converting to DH coordinates
+      final     :: helio_util_final_system                     !! Finalizes the Helio system object - deallocates all allocatables 
    end type helio_nbody_system
 
    !********************************************************************************************************************************
@@ -43,6 +44,7 @@ module helio_classes
       procedure :: accel       => helio_kick_getacch_pl    !! Compute heliocentric accelerations of massive bodies
       procedure :: kick        => helio_kick_vb_pl         !! Kicks the barycentric velocities
       procedure :: step        => helio_step_pl            !! Steps the body forward one stepsize
+      final     :: helio_util_final_pl                     !! Finalizes the Helio massive body object - deallocates all allocatables
    end type helio_pl
 
    !********************************************************************************************************************************
@@ -59,6 +61,7 @@ module helio_classes
       procedure :: accel       => helio_kick_getacch_tp    !! Compute heliocentric accelerations of massive bodies
       procedure :: kick        => helio_kick_vb_tp         !! Kicks the barycentric velocities
       procedure :: step        => helio_step_tp            !! Steps the body forward one stepsize
+      final     :: helio_util_final_tp                     !! Finalizes the Helio test particle object - deallocates all allocatables
    end type helio_tp
 
    interface
@@ -213,6 +216,21 @@ module subroutine helio_step_tp(self, system, param, t, dt)
          real(DP),                     intent(in)    :: dt     !! Stepsizee
       end subroutine helio_step_tp
 
+      module subroutine helio_util_final_pl(self)
+         implicit none
+         type(helio_pl),  intent(inout) :: self !! Helio massive body object
+      end subroutine helio_util_final_pl
+
+      module subroutine helio_util_final_system(self)
+         implicit none
+         type(helio_nbody_system),  intent(inout) :: self !! Helio nbody system object
+      end subroutine helio_util_final_system
+
+      module subroutine helio_util_final_tp(self)
+         implicit none
+         type(helio_tp),  intent(inout) :: self !! Helio test particle object
+      end subroutine helio_util_final_tp
+
    end interface
 
 end module helio_classes