Fixed and rearranged a bunch of stuff getting the collision history o…

…bject to work

src/CMakeLists.txt

@@ -78,7 +78,7 @@ SET(FAST_MATH_FILES
             ${SRC}/util/util_final.f90
             ${SRC}/util/util_flatten.f90
             ${SRC}/util/util_get_energy_momentum.f90
-            ${SRC}/util/util_index_array.f90
+            ${SRC}/util/util_index.f90
             ${SRC}/util/util_minimize_bfgs.f90
             ${SRC}/util/util_peri.f90
             ${SRC}/util/util_rescale.f90

src/encounter/encounter_io.f90

@@ -12,14 +12,14 @@
 contains
 
 
-   module subroutine encounter_io_dump(self, param)
+   module subroutine encounter_io_dump_collision_storage(self, param)
       !! author: David A. Minton
       !!
       !! Dumps the time history of an encounter to file.
       implicit none
       ! Arguments
-      class(encounter_storage(*)),  intent(inout)        :: self   !! Encounter storage object
-      class(swiftest_parameters),   intent(inout)        :: param  !! Current run configuration parameters 
+      class(collision_storage(*)),  intent(inout)        :: self   !! Encounter storage object
+      class(swiftest_parameters), intent(inout)        :: param  !! Current run configuration parameters 
       ! Internals
       integer(I4B) :: i
 
@@ -29,6 +29,30 @@ module subroutine encounter_io_dump(self, param)
             class is (fraggle_collision_snapshot)
                param%ioutput = i
                call snapshot%write_frame(self%nc,param)
+            end select
+         else
+            exit
+         end if
+      end do
+
+      return
+   end subroutine encounter_io_dump_collision_storage
+
+
+   module subroutine encounter_io_dump_storage(self, param)
+      !! author: David A. Minton
+      !!
+      !! Dumps the time history of an encounter to file.
+      implicit none
+      ! Arguments
+      class(encounter_storage(*)),  intent(inout)        :: self   !! Encounter storage object
+      class(swiftest_parameters),   intent(inout)        :: param  !! Current run configuration parameters 
+      ! Internals
+      integer(I4B) :: i
+
+      do i = 1, self%nframes
+         if (allocated(self%frame(i)%item)) then
+            select type(snapshot => self%frame(i)%item)
             class is (encounter_snapshot)
                param%ioutput = self%tslot(i)
                call snapshot%write_frame(self%nc,param)
@@ -40,7 +64,7 @@ module subroutine encounter_io_dump(self, param)
 
 
       return
-   end subroutine encounter_io_dump
+   end subroutine encounter_io_dump_storage
 
 
    module subroutine encounter_io_initialize(self, param)

src/encounter/encounter_util.f90

@@ -152,6 +152,20 @@ module subroutine encounter_util_final_snapshot(self)
    end subroutine encounter_util_final_snapshot
 
 
+   module subroutine encounter_util_final_collision_storage(self)
+      !! author: David A. Minton
+      !!
+      !! Finalizer will deallocate all allocatables
+      implicit none
+      ! Arguments
+      type(collision_storage(*)),  intent(inout) :: self !! SyMBA nbody system object
+
+      call util_final_storage(self%swiftest_storage)
+
+      return
+   end subroutine encounter_util_final_collision_storage
+
+
    module subroutine encounter_util_final_storage(self)
       !! author: David A. Minton
       !!
@@ -166,6 +180,33 @@ module subroutine encounter_util_final_storage(self)
    end subroutine encounter_util_final_storage
 
 
+   module subroutine encounter_util_index_map_storage(self)
+      !! author: David A. Minton
+      !!
+      !! Maps body id values to storage index values so we don't have to use unlimited dimensions for id
+      implicit none
+      ! Arguments
+      class(encounter_storage(*)), intent(inout) :: self !! Swiftest storage object
+      ! Internals
+
+      return
+   end subroutine encounter_util_index_map_storage
+
+
+
+   module subroutine encounter_util_index_map_collision_storage(self)
+      !! author: David A. Minton
+      !!
+      !! Maps body id values to storage index values so we don't have to use unlimited dimensions for id
+      implicit none
+      ! Arguments
+      class(collision_storage(*)), intent(inout) :: self !! Swiftest storage object
+      ! Internals
+
+      return
+   end subroutine encounter_util_index_map_collision_storage
+
+
    module subroutine encounter_util_resize_list(self, nnew)
       !! author: David A. Minton
       !!

src/fraggle/fraggle_io.f90

@@ -12,7 +12,6 @@
 
 contains
 
-
    module subroutine fraggle_io_initialize_output(self, param)
       !! author: David A. Minton
       !!

src/modules/encounter_classes.f90

@@ -68,10 +68,20 @@ module encounter_classes
    type, extends(swiftest_storage) :: encounter_storage
       class(encounter_io_parameters), allocatable :: nc  !! NetCDF parameter object containing the details about the file attached to this storage object
    contains
-      procedure :: dump   => encounter_io_dump !! Dumps contents of encounter history to file
-      final     ::           encounter_util_final_storage
+      procedure :: dump  => encounter_io_dump_storage        !! Dumps contents of encounter history to file
+      procedure :: mapid => encounter_util_index_map_storage !! Maps body id values to storage index values so we don't have to use unlimited dimensions for id
+      final     ::          encounter_util_final_storage
    end type encounter_storage
 
+   !> A class that that is used to store simulation history data between file output
+   type, extends(swiftest_storage) :: collision_storage
+      class(encounter_io_parameters), allocatable :: nc  !! NetCDF parameter object containing the details about the file attached to this storage object
+   contains
+      procedure :: dump  => encounter_io_dump_collision_storage        !! Dumps contents of encounter history to file
+      procedure :: mapid => encounter_util_index_map_collision_storage !! Maps body id values to storage index values so we don't have to use unlimited dimensions for id
+      final     ::          encounter_util_final_collision_storage
+   end type collision_storage
+
    type encounter_bounding_box_1D
       integer(I4B)                            :: n    !! Number of bodies with extents
       integer(I4B), dimension(:), allocatable :: ind  !! Sorted minimum/maximum extent indices (value > n indicates an ending index)
@@ -204,11 +214,17 @@ module subroutine encounter_check_sweep_aabb_single_list(self, n, x, v, renc, dt
          logical,      dimension(:), allocatable, intent(out)   :: lvdotr     !! Logical array indicating which pairs are approaching
       end subroutine encounter_check_sweep_aabb_single_list
 
-      module subroutine encounter_io_dump(self, param)
+      module subroutine encounter_io_dump_collision_storage(self, param)
+         implicit none
+         class(collision_storage(*)), intent(inout) :: self    !! Collision storage object
+         class(swiftest_parameters),  intent(inout) :: param !! Current run configuration parameters 
+      end subroutine encounter_io_dump_collision_storage
+
+      module subroutine encounter_io_dump_storage(self, param)
          implicit none
          class(encounter_storage(*)), intent(inout) :: self   !! Encounter storage object
          class(swiftest_parameters),  intent(inout) :: param  !! Current run configuration parameters 
-      end subroutine encounter_io_dump
+      end subroutine encounter_io_dump_storage
 
       module subroutine encounter_io_initialize(self, param)
          implicit none
@@ -264,6 +280,11 @@ module subroutine encounter_util_final_aabb(self)
          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_collision_storage(self)
+         implicit none
+         type(collision_storage(*)),  intent(inout) :: self !! SyMBA nbody system object
+      end subroutine encounter_util_final_collision_storage
+
       module subroutine encounter_util_final_list(self)
          implicit none
          type(encounter_list), intent(inout) :: self !! Swiftest encounter list object
@@ -279,6 +300,16 @@ module subroutine encounter_util_final_storage(self)
          type(encounter_storage(*)),  intent(inout) :: self !! SyMBA nbody system object
       end subroutine encounter_util_final_storage
 
+      module subroutine encounter_util_index_map_collision_storage(self)
+         implicit none
+         class(collision_storage(*)), intent(inout) :: self !! E
+      end subroutine encounter_util_index_map_collision_storage
+
+      module subroutine encounter_util_index_map_storage(self)
+         implicit none
+         class(encounter_storage(*)), intent(inout) :: self !! Swiftest storage object
+      end subroutine encounter_util_index_map_storage
+
       module subroutine encounter_util_resize_list(self, nnew)
          implicit none
          class(encounter_list), intent(inout) :: self !! Swiftest encounter list 

src/modules/fraggle_classes.f90

@@ -285,17 +285,17 @@ end subroutine fraggle_util_construct_temporary_system
 
       module subroutine fraggle_util_final_colliders(self)
          implicit none
-         type(fraggle_colliders),  intent(inout) :: self !! Fraggle encountar storage object
+         type(fraggle_colliders),  intent(inout) :: self !! Fraggle colliders object
       end subroutine fraggle_util_final_colliders
 
       module subroutine fraggle_util_final_fragments(self)
          implicit none
-         type(fraggle_fragments),  intent(inout) :: self !! Fraggle encountar storage object
+         type(fraggle_fragments),  intent(inout) :: self !! Fraggle frgments object
       end subroutine fraggle_util_final_fragments
 
       module subroutine fraggle_util_final_snapshot(self)
          implicit none
-         type(fraggle_collision_snapshot),  intent(inout) :: self !! Fraggle encountar storage object
+         type(fraggle_collision_snapshot),  intent(inout) :: self !! Fraggle storage snapshot object
       end subroutine fraggle_util_final_snapshot
 
       module subroutine fraggle_util_get_energy_momentum(self, colliders, system, param, lbefore)

src/modules/swiftest_classes.f90

@@ -153,14 +153,16 @@ module swiftest_classes
 
    type :: swiftest_storage(nframes)
       !! An class that establishes the pattern for various storage objects
-      integer(I4B), len                                :: nframes = 4096 !! Total number of frames that can be stored
-      type(swiftest_storage_frame), dimension(nframes) :: frame          !! Array of stored frames
-      integer(I4B)                                     :: iframe = 0     !! Index of the last frame stored in the system
-      integer(I4B),                 dimension(nframes) :: tslot          !! The value of the time dimension index associated with each frame
-      real(DP),                     dimension(nframes) :: tvals          !! Stored time values for snapshots
+      integer(I4B), len                                       :: nframes = 4096 !! Total number of frames that can be stored
+      type(swiftest_storage_frame), dimension(nframes)        :: frame          !! Array of stored frames
+      integer(I4B)                                            :: iframe = 0     !! Index of the last frame stored in the system
+      integer(I4B),                 dimension(nframes)        :: tslot          !! The value of the time dimension index associated with each frame
+      real(DP),                     dimension(nframes)        :: tvals          !! Stored time values for snapshots
+      integer(I4B),                 dimension(:), allocatable :: idmap          !! The id value -> index map  
    contains
-      procedure :: dump   => io_dump_storage     !! Dumps storage object contents to file
-      procedure :: reset  => util_reset_storage  !! Resets a storage object by deallocating all items and resetting the frame counter to 0
+      procedure :: dump  => io_dump_storage        !! Dumps storage object contents to file
+      procedure :: mapid => util_index_map_storage !! Maps body id values to storage index values so we don't have to use unlimited dimensions for id
+      procedure :: reset => util_reset_storage     !! Resets a storage object by deallocating all items and resetting the frame counter to 0
       final     :: util_final_storage
    end type swiftest_storage
 
@@ -1515,6 +1517,11 @@ module subroutine util_index_array(ind_arr, n)
          integer(I4B),                            intent(in)    :: n       !! The new size of the index array
       end subroutine util_index_array
 
+      module subroutine util_index_map_storage(self)
+         implicit none
+         class(swiftest_storage(*)), intent(inout) :: self !! Swiftest storage object
+      end subroutine util_index_map_storage
+
       module function util_minimize_bfgs(f, N, x0, eps, maxloop, lerr) result(x1)
          use lambda_function
          implicit none

src/modules/symba_classes.f90

@@ -16,7 +16,7 @@ module symba_classes
    use swiftest_classes,  only : swiftest_parameters, swiftest_base, swiftest_particle_info, swiftest_storage, netcdf_parameters
    use helio_classes,     only : helio_cb, helio_pl, helio_tp, helio_nbody_system
    use fraggle_classes,   only : fraggle_colliders, fraggle_fragments
-   use encounter_classes, only : encounter_list, encounter_snapshot, encounter_storage
+   use encounter_classes, only : encounter_list, encounter_snapshot, encounter_storage, collision_storage
    implicit none
    public
 
@@ -192,7 +192,7 @@ module symba_classes
       class(fraggle_colliders), allocatable           :: colliders          !! Fraggle colliders object
       class(fraggle_fragments), allocatable           :: fragments          !! Fraggle fragmentation system object
       type(encounter_storage(nframes=:)), allocatable :: encounter_history  !! Stores encounter history for later retrieval and saving to file
-      type(encounter_storage(nframes=:)), allocatable :: collision_history  !! Stores encounter history for later retrieval and saving to file
+      type(collision_storage(nframes=:)), allocatable :: collision_history  !! Stores encounter history for later retrieval and saving to file
    contains
       procedure :: write_discard    => symba_io_write_discard             !! Write out information about discarded and merged planets and test particles in SyMBA
       procedure :: initialize       => symba_setup_initialize_system      !! Performs SyMBA-specific initilization steps

src/netcdf/netcdf.f90

@@ -808,7 +808,7 @@ module subroutine netcdf_read_particle_info_system(self, nc, param, plmask, tpma
                call pl%info(i)%set_value(status="ACTIVE")
             end do
             allocate(plind(npl))
-            plind(:) = pack([(i, i = 0, idmax-1)], plmask(:))
+            plind(:) = pack([(i, i = 1, idmax)], plmask(:))
          end if
          if (ntp > 0) then
             tp%status(:) = ACTIVE
@@ -817,16 +817,16 @@ module subroutine netcdf_read_particle_info_system(self, nc, param, plmask, tpma
                call tp%info(i)%set_value(status="ACTIVE")
             end do
             allocate(tpind(ntp))
-            tpind(:) = pack([(i, i = 0, idmax-1)], tpmask(:))
+            tpind(:) = pack([(i, i = 1, idmax)], tpmask(:))
          end if
 
          call check( nf90_get_var(nc%id, nc%id_varid, itemp), "netcdf_read_particle_info_system nf90_getvar id_varid"  )
          cb%id = itemp(1)
          pl%id(:) = pack(itemp, plmask)
          tp%id(:) = pack(itemp, tpmask)
          cb%id = 0
-         pl%id(:) = pack([(i,i=0,idmax-1)],plmask)
-         tp%id(:) = pack([(i,i=0,idmax-1)],tpmask)
+         pl%id(:) = pack([(i,i=1,idmax)],plmask)
+         tp%id(:) = pack([(i,i=1,idmax)],tpmask)
 
          call check( nf90_get_var(nc%id, nc%name_varid, ctemp, count=[NAMELEN, idmax]), "netcdf_read_particle_info_system nf90_getvar name_varid"  )
          call cb%info%set_value(name=ctemp(1))

src/setup/setup.f90

@@ -82,7 +82,7 @@ module subroutine setup_construct_system(system, param)
                      end select
                   end associate
 
-                  allocate(encounter_storage :: system%collision_history)
+                  allocate(collision_storage :: system%collision_history)
                   associate (collision_history => system%collision_history)
                      allocate(fraggle_io_parameters :: collision_history%nc)
                      call collision_history%reset()

src/symba/symba_collision.f90

@@ -494,7 +494,6 @@ function symba_collision_consolidate_colliders(pl, cb, param, idx_parent, collid
          associate(idx_arr => parent_child_index_array(j)%idx, &
                    id_arr => parent_child_index_array(j)%id, &
                    ncj => nchild(j), &
-                   pl => pl, &
                    plkinj => pl%kin(idx_parent(j)))
             idx_arr(1) = idx_parent(j)
             if (ncj > 0) idx_arr(2:ncj + 1) = plkinj%child(1:ncj)

src/symba/symba_util.f90

@@ -881,7 +881,7 @@ subroutine symba_util_save_collision(system, snapshot)
       type(symba_nbody_system),  intent(inout) :: system   !! SyMBA nbody system object 
       class(encounter_snapshot), intent(in)    :: snapshot !! Encounter snapshot object
       ! Internals
-      type(encounter_storage(nframes=:)), allocatable :: tmp
+      type(collision_storage(nframes=:)), allocatable :: tmp
       integer(I4B) :: i, nnew, nold, nbig
 
       ! Advance the snapshot frame counter
@@ -896,7 +896,7 @@ subroutine symba_util_save_collision(system, snapshot)
          do while (nbig < nnew)
             nbig = nbig * 2
          end do
-         allocate(encounter_storage(nbig) :: tmp) 
+         allocate(collision_storage(nbig) :: tmp) 
          tmp%tvals(1:nold) = system%collision_history%tvals(1:nold)
          tmp%tvals(nold+1:nbig) = huge(1.0_DP)
          tmp%tslot(1:nold) = system%collision_history%tslot(1:nold)
@@ -1347,26 +1347,28 @@ module subroutine symba_util_take_collision_snapshot(self, param, t, stage)
       real(DP),                   intent(in)    :: t     !! current time
       character(*),               intent(in)    :: stage !! Either before or after
       ! Arguments
-      class(fraggle_collision_snapshot), allocatable:: snapshot
+      class(fraggle_collision_snapshot), allocatable :: snapshot
+      type(symba_pl)                                 :: pl
       integer(I4B) :: i,j
 
       select case(stage)
       case("before")
          ! Saves the states of the bodies involved in the collision before the collision is resolved
          associate (idx => self%colliders%idx, ncoll => self%colliders%ncoll)
-            allocate(symba_pl :: self%colliders%pl)
-            select type(pl => self%colliders%pl)
-            class is (symba_pl)
-               call pl%setup(ncoll, param)
-               pl%id(:) = self%pl%id(idx(:))
-               pl%Gmass(:) = self%pl%Gmass(idx(:))
-               pl%radius(:) = self%pl%radius(idx(:))
-               pl%rot(:,:) = self%pl%rot(:,idx(:))
-               pl%Ip(:,:) = self%pl%Ip(:,idx(:))
-               pl%rh(:,:) = self%pl%rh(:,idx(:))
-               pl%vh(:,:) = self%pl%vh(:,idx(:))
-               pl%info(:) = self%pl%info(idx(:))
-            end select
+            !allocate(symba_pl :: self%colliders%pl)
+            !select type(pl => self%colliders%pl)
+            !class is (symba_pl)
+            call pl%setup(ncoll, param)
+            pl%id(:) = self%pl%id(idx(:))
+            pl%Gmass(:) = self%pl%Gmass(idx(:))
+            pl%radius(:) = self%pl%radius(idx(:))
+            pl%rot(:,:) = self%pl%rot(:,idx(:))
+            pl%Ip(:,:) = self%pl%Ip(:,idx(:))
+            pl%rh(:,:) = self%pl%rh(:,idx(:))
+            pl%vh(:,:) = self%pl%vh(:,idx(:))
+            pl%info(:) = self%pl%info(idx(:))
+            !end select
+            allocate(self%colliders%pl, source=pl)
          end associate
       case("after")
          allocate(fraggle_collision_snapshot :: snapshot)