Fixed issues related to gaps in the id record that were causing the p…

…rocessing code to fail because of empty string values if idslots were not filled between writes. Now particle info is dumped to the bin file in NetCDF mode after a rearray operation to catch all newly created bodies and fill all id slots.

src/io/io.f90

@@ -145,7 +145,7 @@ module subroutine io_dump_particle_info_base(self, param, idx)
       implicit none
       ! Arguments
       class(swiftest_base),                 intent(inout) :: self  !! Swiftest base object (can be cb, pl, or tp)
-      class(swiftest_parameters),           intent(in)    :: param !! Current run configuration parameters 
+      class(swiftest_parameters),           intent(inout) :: param !! Current run configuration parameters 
       integer(I4B), dimension(:), optional, intent(in)    :: idx   !! Array of test particle indices to append to the particle file
 
       ! Internals
@@ -154,41 +154,47 @@ module subroutine io_dump_particle_info_base(self, param, idx)
       integer(I4B)              :: i
       character(STRMAX)         :: errmsg
 
-      if (lfirst) then
-         select case(param%out_stat)
-         case('APPEND')
-            open(unit = LUN, file = param%particle_out, status = 'OLD', position = 'APPEND', form = 'UNFORMATTED', err = 667, iomsg = errmsg)
-         case('NEW', 'UNKNOWN', 'REPLACE')
-            open(unit = LUN, file = param%particle_out, status = param%out_stat, form = 'UNFORMATTED', err = 667, iomsg = errmsg)
-         case default
-            write(*,*) 'Invalid status code',trim(adjustl(param%out_stat))
-            call util_exit(FAILURE)
-         end select
-
-         lfirst = .false.
-      else
-         open(unit = LUN, file = param%particle_out, status = 'OLD', position =  'APPEND', form = 'UNFORMATTED', err = 667, iomsg = errmsg)
-      end if
+      if ((param%out_type == REAL4_TYPE) .or. (param%out_type == REAL8_TYPE)) then
+         if (lfirst) then
+            select case(param%out_stat)
+            case('APPEND')
+               open(unit = LUN, file = param%particle_out, status = 'OLD', position = 'APPEND', form = 'UNFORMATTED', err = 667, iomsg = errmsg)
+            case('NEW', 'UNKNOWN', 'REPLACE')
+               open(unit = LUN, file = param%particle_out, status = param%out_stat, form = 'UNFORMATTED', err = 667, iomsg = errmsg)
+            case default
+               write(*,*) 'Invalid status code',trim(adjustl(param%out_stat))
+               call util_exit(FAILURE)
+            end select
 
-      select type(self)
-      class is (swiftest_cb)
-         write(LUN, err = 667, iomsg = errmsg) self%id
-         call self%info%dump(LUN)
-      class is (swiftest_body)
-         if (present(idx)) then
-            do i = 1, size(idx)
-               write(LUN, err = 667, iomsg = errmsg) self%id(idx(i))
-               call self%info(idx(i))%dump(LUN) 
-            end do
+            lfirst = .false.
          else
-            do i = 1, self%nbody
-               write(LUN, err = 667, iomsg = errmsg) self%id(i)
-               call self%info(i)%dump(LUN) 
-            end do
+            open(unit = LUN, file = param%particle_out, status = 'OLD', position =  'APPEND', form = 'UNFORMATTED', err = 667, iomsg = errmsg)
          end if
-      end select
 
-      close(unit = LUN, err = 667, iomsg = errmsg)
+         select type(self)
+         class is (swiftest_cb)
+            write(LUN, err = 667, iomsg = errmsg) self%id
+            call self%info%dump(LUN)
+         class is (swiftest_body)
+            if (present(idx)) then
+               do i = 1, size(idx)
+                  write(LUN, err = 667, iomsg = errmsg) self%id(idx(i))
+                  call self%info(idx(i))%dump(LUN) 
+               end do
+            else
+               do i = 1, self%nbody
+                  write(LUN, err = 667, iomsg = errmsg) self%id(i)
+                  call self%info(i)%dump(LUN) 
+               end do
+            end if
+         end select
+
+         close(unit = LUN, err = 667, iomsg = errmsg)
+      else if ((param%out_type == NETCDF_FLOAT_TYPE) .or. (param%out_type == NETCDF_DOUBLE_TYPE)) then
+         call param%nciu%open(param) 
+         call self%write_particle_info(param%nciu)
+         call param%nciu%close(param)
+      end if
 
       return
 

src/modules/swiftest_classes.f90

@@ -179,10 +179,12 @@ module swiftest_classes
       !! An abstract superclass for a generic Swiftest object
    contains
       !! The minimal methods that all systems must have
-      procedure :: dump               => io_dump_base                 !! Dump contents to file
-      procedure :: dump_particle_info => io_dump_particle_info_base   !! Dump contents of particle information metadata to file
-      procedure :: write_frame_netcdf => netcdf_write_frame_base      !! I/O routine for writing out a single frame of time-series data for all bodies in the system in NetCDF format  
-      generic   :: write_frame        => write_frame_netcdf           !! Set up generic procedure that will switch between NetCDF or Fortran binary depending on arguments
+      procedure :: dump                       => io_dump_base                 !! Dump contents to file
+      procedure :: dump_particle_info         => io_dump_particle_info_base   !! Dump contents of particle information metadata to file
+      procedure :: write_frame_netcdf         => netcdf_write_frame_base      !! I/O routine for writing out a single frame of time-series data for all bodies in the system in NetCDF format  
+      procedure :: write_particle_info_netcdf => netcdf_write_particle_info_base !! Writes out the particle information metadata to NetCDF file
+      generic   :: write_frame                => write_frame_netcdf           !! Set up generic procedure that will switch between NetCDF or Fortran binary depending on arguments
+      generic   :: write_particle_info        => write_particle_info_netcdf
    end type swiftest_base
 
    !********************************************************************************************************************************
@@ -652,7 +654,7 @@ end subroutine io_dump_param
       module subroutine io_dump_particle_info_base(self, param, idx)
          implicit none
          class(swiftest_base),                 intent(inout) :: self  !! Swiftest base object (can be cb, pl, or tp)
-         class(swiftest_parameters),           intent(in)    :: param !! Current run configuration parameters 
+         class(swiftest_parameters),           intent(inout) :: param !! Current run configuration parameters 
          integer(I4B), dimension(:), optional, intent(in)    :: idx   !! Array of test particle indices to append to the particle file
       end subroutine io_dump_particle_info_base
 
@@ -913,6 +915,12 @@ module subroutine netcdf_write_hdr_system(self, iu, param)
          class(swiftest_parameters),   intent(in)    :: param !! Current run configuration parameters
       end subroutine netcdf_write_hdr_system
 
+      module subroutine netcdf_write_particle_info_base(self, iu)
+         implicit none
+         class(swiftest_base),       intent(in)    :: self   !! Swiftest particle object
+         class(netcdf_parameters),   intent(inout) :: iu     !! Parameters used to identify a particular NetCDF dataset
+      end subroutine netcdf_write_particle_info_base
+
       module subroutine obl_acc_body(self, system)
          implicit none
          class(swiftest_body),         intent(inout) :: self   !! Swiftest body object 

src/modules/symba_classes.f90

@@ -571,7 +571,7 @@ module subroutine symba_util_rearray_pl(self, system, param)
          implicit none
          class(symba_pl),           intent(inout) :: self   !! SyMBA massive body object
          class(symba_nbody_system), intent(inout) :: system !! SyMBA nbody system object
-         class(symba_parameters),   intent(in)    :: param  !! Current run configuration parameters with SyMBA additions
+         class(symba_parameters),   intent(inout) :: param  !! Current run configuration parameters with SyMBA additions
       end subroutine symba_util_rearray_pl
    end interface
 

src/netcdf/netcdf.f90

@@ -238,26 +238,22 @@ module subroutine netcdf_write_frame_base(self, iu, param)
       integer(I4B), dimension(:), allocatable   :: ind
       character(len=:), allocatable             :: charstring
 
+      call self%write_particle_info(iu)
+
       tslot = int(param%ioutput, kind=I4B) + 1
 
       select type(self)
          class is (swiftest_body)
          associate(n => self%nbody)
             if (n == 0) return
+
+
             allocate(ind(n))
             call util_sort(self%id(1:n), ind)
 
             do i = 1, n
                j = ind(i)
                idslot = self%id(j) + 1
-               call check( nf90_put_var(iu%ncid, iu%id_varid, self%id(j), start=[idslot]) )
-               charstring = trim(adjustl(self%info(j)%name))
-               strlen = len(charstring)
-               call check( nf90_put_var(iu%ncid, iu%name_varid, charstring, start=[1, idslot], count=[strlen, 1]) )
-
-               charstring = trim(adjustl(self%info(j)%particle_type))
-               strlen = len(charstring)
-               call check( nf90_put_var(iu%ncid, iu%ptype_varid, charstring, start=[1, idslot], count=[strlen, 1]) )
 
                if ((param%out_form == XV) .or. (param%out_form == XVEL)) then
                   call check( nf90_put_var(iu%ncid, iu%xhx_varid, self%xh(1, j), start=[idslot, tslot]) )
@@ -277,19 +273,6 @@ module subroutine netcdf_write_frame_base(self, iu, param)
                   call check( nf90_put_var(iu%ncid, iu%capm_varid, self%capm(j), start=[idslot, tslot]) ) 
                end if
 
-               if (iu%ltrack_origin) then
-                  charstring = trim(adjustl(self%info(j)%origin_type))
-                  strlen = len(charstring)
-                  call check( nf90_put_var(iu%ncid, iu%origin_type_varid, charstring, start=[1, idslot], count=[strlen, 1]) )
-                  call check( nf90_put_var(iu%ncid, iu%origin_time_varid, self%info(j)%origin_time, start=[idslot]) )
-                  call check( nf90_put_var(iu%ncid, iu%origin_xhx_varid, self%info(j)%origin_xh(1), start=[idslot]) )
-                  call check( nf90_put_var(iu%ncid, iu%origin_xhy_varid, self%info(j)%origin_xh(2), start=[idslot]) )
-                  call check( nf90_put_var(iu%ncid, iu%origin_xhz_varid, self%info(j)%origin_xh(3), start=[idslot]) )
-                  call check( nf90_put_var(iu%ncid, iu%origin_vhx_varid, self%info(j)%origin_vh(1), start=[idslot]) )
-                  call check( nf90_put_var(iu%ncid, iu%origin_vhy_varid, self%info(j)%origin_vh(2), start=[idslot]) )
-                  call check( nf90_put_var(iu%ncid, iu%origin_vhz_varid, self%info(j)%origin_vh(3), start=[idslot]) )
-               end if
-
                select type(self)  
                class is (swiftest_pl)  ! Additional output if the passed polymorphic object is a massive body
                   call check( nf90_put_var(iu%ncid, iu%Gmass_varid, self%Gmass(j), start=[idslot, tslot]) )
@@ -342,23 +325,85 @@ module subroutine netcdf_write_frame_base(self, iu, param)
             call check( nf90_put_var(iu%ncid, iu%Q_varid, self%Q, start=[idslot, tslot]) )
          end if
 
-         if (iu%ltrack_origin) then
-            charstring = trim(adjustl(self%info%origin_type))
-            strlen = len(charstring)
-            call check( nf90_put_var(iu%ncid, iu%origin_type_varid, charstring, start=[1, idslot], count=[strlen, 1]) )
-            call check( nf90_put_var(iu%ncid, iu%origin_time_varid, self%info%origin_time, start=[idslot]) )
-            call check( nf90_put_var(iu%ncid, iu%origin_xhx_varid, self%info%origin_xh(1), start=[idslot]) )
-            call check( nf90_put_var(iu%ncid, iu%origin_xhy_varid, self%info%origin_xh(2), start=[idslot]) )
-            call check( nf90_put_var(iu%ncid, iu%origin_xhz_varid, self%info%origin_xh(3), start=[idslot]) )
-            call check( nf90_put_var(iu%ncid, iu%origin_vhx_varid, self%info%origin_vh(1), start=[idslot]) )
-            call check( nf90_put_var(iu%ncid, iu%origin_vhy_varid, self%info%origin_vh(2), start=[idslot]) )
-            call check( nf90_put_var(iu%ncid, iu%origin_vhz_varid, self%info%origin_vh(3), start=[idslot]) )
-         end if
       end select
 
       return
    end subroutine netcdf_write_frame_base
 
+
+   module subroutine netcdf_write_particle_info_base(self, iu)
+      !! author: Carlisle A. Wishard, Dana Singh, and David A. Minton
+      !!
+      !! Write all current particle to file
+      implicit none
+      ! Arguments
+      class(swiftest_base),       intent(in)    :: self   !! Swiftest particle object
+      class(netcdf_parameters),   intent(inout) :: iu     !! Parameters used to identify a particular NetCDF dataset
+      ! Internals
+      integer(I4B)                              :: i, j, tslot, strlen, idslot
+      integer(I4B), dimension(:), allocatable   :: ind
+      character(len=:), allocatable             :: charstring
+
+
+      select type(self)
+         class is (swiftest_body)
+         associate(n => self%nbody)
+            if (n == 0) return
+            allocate(ind(n))
+            call util_sort(self%id(1:n), ind)
+
+            do i = 1, n
+               j = ind(i)
+               idslot = self%id(j) + 1
+               call check( nf90_put_var(iu%ncid, iu%id_varid, self%id(j), start=[idslot]) )
+               charstring = trim(adjustl(self%info(j)%name))
+               strlen = len(charstring)
+               call check( nf90_put_var(iu%ncid, iu%name_varid, charstring, start=[1, idslot], count=[strlen, 1]) )
+
+               charstring = trim(adjustl(self%info(j)%particle_type))
+               strlen = len(charstring)
+               call check( nf90_put_var(iu%ncid, iu%ptype_varid, charstring, start=[1, idslot], count=[strlen, 1]) )
+
+               charstring = trim(adjustl(self%info(j)%origin_type))
+               strlen = len(charstring)
+               call check( nf90_put_var(iu%ncid, iu%origin_type_varid, charstring, start=[1, idslot], count=[strlen, 1]) )
+               call check( nf90_put_var(iu%ncid, iu%origin_time_varid, self%info(j)%origin_time, start=[idslot]) )
+               call check( nf90_put_var(iu%ncid, iu%origin_xhx_varid, self%info(j)%origin_xh(1), start=[idslot]) )
+               call check( nf90_put_var(iu%ncid, iu%origin_xhy_varid, self%info(j)%origin_xh(2), start=[idslot]) )
+               call check( nf90_put_var(iu%ncid, iu%origin_xhz_varid, self%info(j)%origin_xh(3), start=[idslot]) )
+               call check( nf90_put_var(iu%ncid, iu%origin_vhx_varid, self%info(j)%origin_vh(1), start=[idslot]) )
+               call check( nf90_put_var(iu%ncid, iu%origin_vhy_varid, self%info(j)%origin_vh(2), start=[idslot]) )
+               call check( nf90_put_var(iu%ncid, iu%origin_vhz_varid, self%info(j)%origin_vh(3), start=[idslot]) )
+            end do
+         end associate
+
+      class is (swiftest_cb)
+         idslot = self%id + 1
+         call check( nf90_put_var(iu%ncid, iu%id_varid, self%id, start=[idslot]) )
+
+         charstring = trim(adjustl(self%info%name))
+         strlen = len(charstring)
+         call check( nf90_put_var(iu%ncid, iu%name_varid, charstring, start=[1, idslot], count=[strlen, 1]) )
+
+         charstring = trim(adjustl(self%info%particle_type))
+         strlen = len(charstring)
+         call check( nf90_put_var(iu%ncid, iu%ptype_varid, charstring, start=[1, idslot], count=[strlen, 1]) )
+
+         charstring = trim(adjustl(self%info%origin_type))
+         strlen = len(charstring)
+         call check( nf90_put_var(iu%ncid, iu%origin_type_varid, charstring, start=[1, idslot], count=[strlen, 1]) )
+         call check( nf90_put_var(iu%ncid, iu%origin_time_varid, self%info%origin_time, start=[idslot]) )
+         call check( nf90_put_var(iu%ncid, iu%origin_xhx_varid, self%info%origin_xh(1), start=[idslot]) )
+         call check( nf90_put_var(iu%ncid, iu%origin_xhy_varid, self%info%origin_xh(2), start=[idslot]) )
+         call check( nf90_put_var(iu%ncid, iu%origin_xhz_varid, self%info%origin_xh(3), start=[idslot]) )
+         call check( nf90_put_var(iu%ncid, iu%origin_vhx_varid, self%info%origin_vh(1), start=[idslot]) )
+         call check( nf90_put_var(iu%ncid, iu%origin_vhy_varid, self%info%origin_vh(2), start=[idslot]) )
+         call check( nf90_put_var(iu%ncid, iu%origin_vhz_varid, self%info%origin_vh(3), start=[idslot]) )
+      end select
+
+      return
+   end subroutine netcdf_write_particle_info_base
+
 
    module subroutine netcdf_write_hdr_system(self, iu, param) 
       !! author: David A. Minton

src/setup/setup.f90

@@ -175,15 +175,8 @@ module subroutine setup_initialize_particle_info_system(self, param)
          end if
 
          cb%info%particle_type = CB_TYPE_NAME
-         call cb%dump_particle_info(param)
-         if (npl > 0) then
-            pl%info(1:npl)%particle_type = PL_TYPE_NAME
-            call pl%dump_particle_info(param)
-         end if
-         if (ntp > 0) then
-            tp%info(1:ntp)%particle_type = TP_TYPE_NAME
-            call tp%dump_particle_info(param)
-         end if
+         if (npl > 0) pl%info(1:npl)%particle_type = PL_TYPE_NAME
+         if (ntp > 0) tp%info(1:ntp)%particle_type = TP_TYPE_NAME
 
       end associate
 

src/symba/symba_collision.f90

@@ -907,7 +907,6 @@ subroutine symba_collision_mergeaddsub(system, param, family, id_frag, Ip_frag,
 
                ! Copy over identification, information, and physical properties of the new bodies from the fragment list
                plnew%id(1:nfrag) = id_frag(1:nfrag) 
-               param%maxid = param%maxid + nfrag
                plnew%xb(:, 1:nfrag) = xb_frag(:, 1:nfrag) 
                plnew%vb(:, 1:nfrag) = vb_frag(:, 1:nfrag)
                do i = 1, nfrag