Fixed issues with character variables not overwriting old data in Net…

…CDF files. Also added more helfpul information to the collision log file and rearranged the pl vs plm order in the swiftest log file

src/collision/collision_io.f90

@@ -15,7 +15,7 @@
    module subroutine collision_io_collider_message(pl, collidx, collider_message)
       !! author: David A. Minton
       !!
-      !! Prints a nicely formatted message about which bodies collided, including their names and ids.
+      !! Prints a nicely formatted message about which bodies collided, including their names
       !! This subroutine appends the body names and ids to an input message.
       implicit none
       ! Arguments
@@ -25,7 +25,6 @@ module subroutine collision_io_collider_message(pl, collidx, collider_message)
       ! Internals
       integer(I4B) :: i, n
       character(len=STRMAX) :: idstr
-
 
       n = size(collidx)
       if (n == 0) return
@@ -366,7 +365,7 @@ module subroutine collision_io_netcdf_write_frame_snapshot(self, history, param)
       class(base_parameters),      intent(inout) :: param   !! Current run configuration parameters
       ! Internals
       integer(I4B)           :: i, idslot, old_mode, npl, stage
-      character(len=:), allocatable :: charstring
+      character(len=NAMELEN) :: charstring
       class(swiftest_pl), allocatable :: pl
 
       select type(nc => history%nc)
@@ -378,7 +377,7 @@ module subroutine collision_io_netcdf_write_frame_snapshot(self, history, param)
             call netcdf_io_check( nf90_put_var(nc%id, nc%time_varid, self%t,                   start=[eslot]), "collision_io_netcdf_write_frame_snapshot nf90_put_var time_varid" )
 
             charstring = trim(adjustl(REGIME_NAMES(impactors%regime)))
-            call netcdf_io_check( nf90_put_var(nc%id, nc%regime_varid, charstring,             start=[1, eslot], count=[len(charstring), 1]), "collision_io_netcdf_write_frame_snapshot nf90_put_var regime_varid" )
+            call netcdf_io_check( nf90_put_var(nc%id, nc%regime_varid, charstring,             start=[1, eslot], count=[NAMELEN, 1]), "collision_io_netcdf_write_frame_snapshot nf90_put_var regime_varid" )
             call netcdf_io_check( nf90_put_var(nc%id, nc%Qloss_varid, impactors%Qloss,         start=[eslot] ), "collision_io_netcdf_write_frame_snapshot nf90_put_var Qloss_varid" )
 
             select type(before =>self%collider%before)
@@ -398,9 +397,9 @@ module subroutine collision_io_netcdf_write_frame_snapshot(self, history, param)
                      idslot = findloc(history%idvals,pl%id(i),dim=1)
                      call netcdf_io_check( nf90_put_var(nc%id, nc%id_varid,     pl%id(i),     start=[   idslot              ]), "collision_io_netcdf_write_frame_snapshot nf90_put_var id_varid"  )
                      charstring = trim(adjustl(pl%info(i)%name))
-                     call netcdf_io_check( nf90_put_var(nc%id, nc%name_varid,   charstring,   start=[1, idslot              ], count=[len(charstring), 1]), "collision_io_netcdf_write_frame_snapshot nf90_put_var name_varid"  )
+                     call netcdf_io_check( nf90_put_var(nc%id, nc%name_varid,   charstring,   start=[1, idslot              ], count=[NAMELEN, 1]), "collision_io_netcdf_write_frame_snapshot nf90_put_var name_varid"  )
                      charstring = trim(adjustl(pl%info(i)%particle_type))
-                     call netcdf_io_check( nf90_put_var(nc%id, nc%ptype_varid,  charstring,   start=[1, idslot, stage, eslot], count=[len(charstring), 1, 1]), "collision_io_netcdf_write_frame_snapshot nf90_put_var particle_type_varid"  )
+                     call netcdf_io_check( nf90_put_var(nc%id, nc%ptype_varid,  charstring,   start=[1, idslot, stage, eslot], count=[NAMELEN, 1, 1]), "collision_io_netcdf_write_frame_snapshot nf90_put_var particle_type_varid"  )
                      call netcdf_io_check( nf90_put_var(nc%id, nc%rh_varid,     pl%rh(:,i),   start=[1, idslot, stage, eslot], count=[NDIM,1,1,1]), "collision_io_netcdf_write_frame_snapshot nf90_put_var rh_varid"  )
                      call netcdf_io_check( nf90_put_var(nc%id, nc%vh_varid,     pl%vh(:,i),   start=[1, idslot, stage, eslot], count=[NDIM,1,1,1]), "collision_io_netcdf_write_frame_snapshot nf90_put_var vh_varid"  )
                      call netcdf_io_check( nf90_put_var(nc%id, nc%Gmass_varid,  pl%Gmass(i),  start=[   idslot, stage, eslot]), "collision_io_netcdf_write_frame_snapshot nf90_put_var Gmass_varid"  )

src/collision/collision_resolve.f90

@@ -325,6 +325,7 @@ module subroutine collision_resolve_mergeaddsub(nbody_system, param, t, status)
       integer(I4B) :: merge_text_length 
       character(len=NAMELEN) :: merge_text
       character(len=NAMELEN) :: newname, origin_type
+      character(len=STRMAX)  :: message
       real(DP) :: volume
 
       select type(nbody_system)
@@ -472,7 +473,7 @@ module subroutine collision_resolve_mergeaddsub(nbody_system, param, t, status)
 
             call pl_discards%append(plsub, lsource_mask=[(.true., i = 1, nimpactors)])
 
-            ! Log the properties of the old and new bodies
+            ! Save the before/after snapshots
             select type(before => collider%before)
             class is (swiftest_nbody_system)
                call move_alloc(plsub, before%pl)
@@ -597,7 +598,7 @@ module subroutine collision_resolve_plpl(self, nbody_system, param, t, dt, irec)
 
                   if (.not.lplpl_collision) exit
                   if (loop == MAXCASCADE) then
-                     call swiftest_io_log_one_message(COLLISION_LOG_OUT,"An runaway collisional cascade has been detected in collision_resolve_plpl.")
+                     call swiftest_io_log_one_message(COLLISION_LOG_OUT,"A runaway collisional cascade has been detected in collision_resolve_plpl.")
                      call swiftest_io_log_one_message(COLLISION_LOG_OUT,"Consider reducing the step size or changing the parameters in the collisional model to reduce the number of fragments.")
                      call base_util_exit(FAILURE)
                   end if

src/collision/collision_util.f90

@@ -122,6 +122,8 @@ module subroutine collision_util_construct_constraint_system(collider, nbody_sys
                end associate
 
                call collision_resolve_mergeaddsub(tmpsys, param, nbody_system%t, status)
+               deallocate(tmpsys%collider%before)
+               deallocate(tmpsys%collider%after)
                call tmpsys%pl%rearray(tmpsys, param)
             end if
             call move_alloc(tmpsys, constraint_system)
@@ -682,7 +684,8 @@ module subroutine collision_util_snapshot(self, param, nbody_system, t, arg)
       ! Arguments
       class(collision_snapshot), allocatable, save :: snapshot
       character(len=:), allocatable :: stage
-      integer(I4B) :: phase_val
+      integer(I4B) :: i,phase_val
+      character(len=STRMAX) :: message
 
       if (present(arg)) then
          stage = arg
@@ -724,17 +727,38 @@ module subroutine collision_util_snapshot(self, param, nbody_system, t, arg)
             class is (swiftest_nbody_system)
             select type(before_orig => nbody_system%collider%before)
             class is (swiftest_nbody_system)
+            select type(plsub => before_orig%pl)
+            class is (swiftest_pl)
+               ! Log the properties of the old and new bodies
+               call swiftest_io_log_one_message(COLLISION_LOG_OUT, "Removing bodies:")
+               do i = 1, plsub%nbody
+                  write(message,*) trim(adjustl(plsub%info(i)%name)), " (", trim(adjustl(plsub%info(i)%particle_type)),")"
+                  call swiftest_io_log_one_message(COLLISION_LOG_OUT, message)
+               end do
+
                call move_alloc(before_orig%pl, before_snap%pl)
             end select
             end select
+            end select
 
             select type(after_snap => snapshot%collider%after )
             class is (swiftest_nbody_system)
             select type(after_orig => nbody_system%collider%after)
             class is (swiftest_nbody_system)
+            select type(plnew => after_orig%pl)
+            class is (swiftest_pl)
+               call swiftest_io_log_one_message(COLLISION_LOG_OUT, "Adding bodies:")
+               do i = 1, plnew%nbody
+                  write(message,*) trim(adjustl(plnew%info(i)%name)), " (", trim(adjustl(plnew%info(i)%particle_type)),")"
+                  call swiftest_io_log_one_message(COLLISION_LOG_OUT, message)
+               end do
+               call swiftest_io_log_one_message(COLLISION_LOG_OUT, "***********************************************************" // &
+                                                                  "***********************************************************")
+
                call move_alloc(after_orig%pl, after_snap%pl)
             end select
             end select
+            end select
 
             ! Save the snapshot for posterity
             call self%save(snapshot)

src/encounter/encounter_io.f90

@@ -263,9 +263,9 @@ module subroutine encounter_io_netcdf_write_frame_snapshot(self, history, param)
                end if
 
                charstring = trim(adjustl(pl%info(i)%name))
-               call netcdf_io_check( nf90_put_var(nc%id, nc%name_varid, charstring, start=[1, idslot], count=[len(charstring), 1]), "encounter_io_netcdf_write_frame_snapshot nf90_put_var pl name_varid"  )
+               call netcdf_io_check( nf90_put_var(nc%id, nc%name_varid, charstring, start=[1, idslot], count=[NAMELEN, 1]), "encounter_io_netcdf_write_frame_snapshot nf90_put_var pl name_varid"  )
                charstring = trim(adjustl(pl%info(i)%particle_type))
-               call netcdf_io_check( nf90_put_var(nc%id, nc%ptype_varid, charstring, start=[1, idslot], count=[len(charstring), 1]), "encounter_io_netcdf_write_frame_snapshot nf90_put_var pl particle_type_varid"  )
+               call netcdf_io_check( nf90_put_var(nc%id, nc%ptype_varid, charstring, start=[1, idslot], count=[NAMELEN, 1]), "encounter_io_netcdf_write_frame_snapshot nf90_put_var pl particle_type_varid"  )
             end do
 
             ntp = tp%nbody
@@ -276,9 +276,9 @@ module subroutine encounter_io_netcdf_write_frame_snapshot(self, history, param)
                call netcdf_io_check( nf90_put_var(nc%id, nc%vh_varid, tp%vh(:,i), start=[1,idslot,tslot], count=[NDIM,1,1]), "encounter_io_netcdf_write_frame_snapshot nf90_put_var tp vh_varid"  )
 
                charstring = trim(adjustl(tp%info(i)%name))
-               call netcdf_io_check( nf90_put_var(nc%id, nc%name_varid, charstring, start=[1, idslot], count=[len(charstring), 1]), "encounter_io_netcdf_write_frame_snapshot nf90_put_var tp name_varid"  )
+               call netcdf_io_check( nf90_put_var(nc%id, nc%name_varid, charstring, start=[1, idslot], count=[NAMELEN, 1]), "encounter_io_netcdf_write_frame_snapshot nf90_put_var tp name_varid"  )
                charstring = trim(adjustl(tp%info(i)%particle_type))
-               call netcdf_io_check( nf90_put_var(nc%id, nc%ptype_varid, charstring, start=[1, idslot], count=[len(charstring), 1]), "encounter_io_netcdf_write_frame_snapshot nf90_put_var tp particle_type_varid"  )
+               call netcdf_io_check( nf90_put_var(nc%id, nc%ptype_varid, charstring, start=[1, idslot], count=[NAMELEN, 1]), "encounter_io_netcdf_write_frame_snapshot nf90_put_var tp particle_type_varid"  )
             end do
 
             call netcdf_io_check( nf90_set_fill(nc%id, old_mode, old_mode) )

src/swiftest/swiftest_io.f90

@@ -219,7 +219,7 @@ module subroutine swiftest_io_display_run_information(self, param, integration_t
       character(*), parameter :: statusfmt = '("Time = ", ES12.5, "; fraction done = ", F6.3, ' // & 
                                              '"; Number of active pl, tp = ", I6, ", ", I6)'
       character(*), parameter :: symbastatfmt = '("Time = ", ES12.5, "; fraction done = ", F6.3, ' // &
-                                                '"; Number of active plm, pl, tp = ", I6, ", ", I6, ", ", I6)'
+                                                '"; Number of active pl, plm, tp = ", I6, ", ", I6, ", ", I6)'
       character(*), parameter :: pbarfmt = '("Time = ", ES12.5," of ",ES12.5)'
 
       phase_val = 1
@@ -254,7 +254,7 @@ module subroutine swiftest_io_display_run_information(self, param, integration_t
       end if
 
       if (self%pl%nplm > 0) then
-         write(param%display_unit, symbastatfmt) self%t, tfrac, self%pl%nplm, self%pl%nbody, self%tp%nbody
+         write(param%display_unit, symbastatfmt) self%t, tfrac, self%pl%nbody, self%pl%nplm, self%tp%nbody
       else
          write(param%display_unit, statusfmt) self%t, tfrac, self%pl%nbody, self%tp%nbody
       end if
@@ -1728,14 +1728,14 @@ module subroutine swiftest_io_netcdf_write_info_body(self, nc, param)
                call netcdf_io_check( nf90_put_var(nc%id, nc%status_varid, self%status(j), start=[idslot,tslot]), "netcdf_io_write_info_body nf90_put_var status_varid"  )
 
                charstring = trim(adjustl(self%info(j)%name))
-               call netcdf_io_check( nf90_put_var(nc%id, nc%name_varid, charstring, start=[1, idslot], count=[len(charstring), 1]), "netcdf_io_write_info_body nf90_put_var name_varid"  )
+               call netcdf_io_check( nf90_put_var(nc%id, nc%name_varid, charstring, start=[1, idslot], count=[NAMELEN, 1]), "netcdf_io_write_info_body nf90_put_var name_varid"  )
 
                charstring = trim(adjustl(self%info(j)%particle_type))
-               call netcdf_io_check( nf90_put_var(nc%id, nc%ptype_varid, charstring, start=[1, idslot], count=[len(charstring), 1]), "netcdf_io_write_info_body nf90_put_var particle_type_varid"  )
+               call netcdf_io_check( nf90_put_var(nc%id, nc%ptype_varid, charstring, start=[1, idslot], count=[NAMELEN, 1]), "netcdf_io_write_info_body nf90_put_var particle_type_varid"  )
 
                if (param%lclose) then
                   charstring = trim(adjustl(self%info(j)%origin_type))
-                  call netcdf_io_check( nf90_put_var(nc%id, nc%origin_type_varid, charstring, start=[1, idslot], count=[len(charstring), 1]), "netcdf_io_write_info_body nf90_put_var origin_type_varid"  )
+                  call netcdf_io_check( nf90_put_var(nc%id, nc%origin_type_varid, charstring, start=[1, idslot], count=[NAMELEN, 1]), "netcdf_io_write_info_body nf90_put_var origin_type_varid"  )
                   call netcdf_io_check( nf90_put_var(nc%id, nc%origin_time_varid,  self%info(j)%origin_time,  start=[idslot]), "netcdf_io_write_info_body nf90_put_var origin_time_varid"  )
                   call netcdf_io_check( nf90_put_var(nc%id, nc%origin_rh_varid,    self%info(j)%origin_rh(:), start=[1,idslot], count=[NDIM,1]), "netcdf_io_write_info_body nf90_put_var origin_rh_varid"  )
                   call netcdf_io_check( nf90_put_var(nc%id, nc%origin_vh_varid,    self%info(j)%origin_vh(:), start=[1,idslot], count=[NDIM,1]), "netcdf_io_write_info_body nf90_put_var origin_vh_varid"  )
@@ -1765,7 +1765,7 @@ module subroutine swiftest_io_netcdf_write_info_cb(self, nc, param)
       class(swiftest_parameters),           intent(inout) :: param !! Current run configuration parameters
       ! Internals
       integer(I4B)                              :: idslot, old_mode
-      character(len=:), allocatable             :: charstring
+      character(len=NAMELEN) :: charstring
 
       ! This string of spaces of length NAMELEN is used to clear out any old data left behind inside the string variables
       call netcdf_io_check( nf90_set_fill(nc%id, NF90_NOFILL, old_mode), "netcdf_io_write_info_cb nf90_set_fill NF90_NOFILL"  )
@@ -1774,14 +1774,14 @@ module subroutine swiftest_io_netcdf_write_info_cb(self, nc, param)
       call netcdf_io_check( nf90_put_var(nc%id, nc%id_varid, self%id, start=[idslot]), "netcdf_io_write_info_cb nf90_put_var id_varid"  )
 
       charstring = trim(adjustl(self%info%name))
-      call netcdf_io_check( nf90_put_var(nc%id, nc%name_varid, charstring, start=[1, idslot], count=[len(charstring), 1]), "netcdf_io_write_info_cb nf90_put_var name_varid"  )
+      call netcdf_io_check( nf90_put_var(nc%id, nc%name_varid, charstring, start=[1, idslot], count=[NAMELEN, 1]), "netcdf_io_write_info_cb nf90_put_var name_varid"  )
 
       charstring = trim(adjustl(self%info%particle_type))
-      call netcdf_io_check( nf90_put_var(nc%id, nc%ptype_varid, charstring, start=[1, idslot], count=[len(charstring), 1]), "netcdf_io_write_info_cb nf90_put_var ptype_varid"  )
+      call netcdf_io_check( nf90_put_var(nc%id, nc%ptype_varid, charstring, start=[1, idslot], count=[NAMELEN, 1]), "netcdf_io_write_info_cb nf90_put_var ptype_varid"  )
 
       if (param%lclose) then
          charstring = trim(adjustl(self%info%origin_type))
-         call netcdf_io_check( nf90_put_var(nc%id, nc%origin_type_varid, charstring, start=[1, idslot], count=[len(charstring), 1]), "netcdf_io_write_info_body nf90_put_var cb origin_type_varid"  )
+         call netcdf_io_check( nf90_put_var(nc%id, nc%origin_type_varid, charstring, start=[1, idslot], count=[NAMELEN, 1]), "netcdf_io_write_info_body nf90_put_var cb origin_type_varid"  )
 
          call netcdf_io_check( nf90_put_var(nc%id, nc%origin_time_varid, self%info%origin_time, start=[idslot]), "netcdf_io_write_info_body nf90_put_var cb origin_time_varid"  )
          call netcdf_io_check( nf90_put_var(nc%id, nc%origin_rh_varid, self%info%origin_rh(:), start=[1, idslot], count=[NDIM,1]), "netcdf_io_write_info_body nf90_put_var cb origin_rh_varid"  )
@@ -1797,6 +1797,7 @@ module subroutine swiftest_io_netcdf_write_info_cb(self, nc, param)
       return
    end subroutine swiftest_io_netcdf_write_info_cb
 
+
    module subroutine swiftest_io_remove_nul_char(string)
       !! author: David A. Minton
       !!

src/swiftest/swiftest_util.f90

@@ -2681,7 +2681,6 @@ module subroutine swiftest_util_setup_construct_system(nbody_system, param)
       class(swiftest_nbody_system), allocatable, intent(inout) :: nbody_system !! Swiftest nbody_system object
       class(swiftest_parameters),                intent(inout) :: param  !! Current run configuration parameters
 
-
       select case(param%integrator)
       case (INT_BS)
          write(*,*) 'Bulirsch-Stoer integrator not yet enabled'