Made a number of structural improvements to the outputting as I work …

…on implementing a NetCDF-based fragmentation log file (take 2)

python/swiftest/swiftest/io.py

@@ -827,7 +827,8 @@ def process_netcdf_input(ds, param):
     if "id" in ds.dims:
         if len(np.unique(ds['name'])) == len(ds['name']):
             ds = ds.swap_dims({"id" : "name"})
-            ds = ds.reset_coords("id")
+            if "id" in ds:
+                ds = ds.reset_coords("id")
 
     return ds
 

python/swiftest/swiftest/simulation_class.py

@@ -2505,7 +2505,8 @@ def _combine_and_fix_dsnew(self,dsnew):
         if "id" not in self.data.dims:
             if len(np.unique(dsnew['name'])) == len(dsnew['name']):
                dsnew = dsnew.swap_dims({"id" : "name"})
-               dsnew = dsnew.reset_coords("id")
+               if "id" in dsnew:
+                   dsnew = dsnew.reset_coords("id")
             else:
                 msg = "Non-unique names detected for bodies. The Dataset will be dimensioned by integer id instead of name."
                 msg +="\nConsider using unique names instead."

src/encounter/encounter_io.f90

@@ -25,15 +25,14 @@ module subroutine encounter_io_dump(self, param)
 
       do i = 1, self%nframes
          if (allocated(self%frame(i)%item)) then
+            param%ioutput = self%tslot(i)
+
             select type(snapshot => self%frame(i)%item)
+            class is (fraggle_encounter_snapshot)
+               call snapshot%write_frame(self%ncc,param)
+               call snapshot%encounter_snapshot%write_frame(self%nce,param)
             class is (encounter_snapshot)
-               param%ioutput = self%tslot(i)
-               call snapshot%write_frame(self%nc,param)
-               select type(snapshot) ! Be sure to call the base class method to get the regular encounter data sved
-               class is (fraggle_encounter_snapshot)
-                  call snapshot%encounter_snapshot%write_frame(self%nc,param)
-            end select
-
+               call snapshot%write_frame(self%nce,param)
             end select
          else
             exit
@@ -56,12 +55,13 @@ module subroutine encounter_io_initialize(self, param)
       class(encounter_io_parameters), intent(inout) :: self    !! Parameters used to identify a particular NetCDF dataset
       class(swiftest_parameters),     intent(in)    :: param   !! Current run configuration parameters
       ! Internals
-      integer(I4B) :: i, nvar, varid, vartype
+      integer(I4B) :: nvar, varid, vartype
       real(DP) :: dfill
       real(SP) :: sfill
       logical :: fileExists
       character(len=STRMAX) :: errmsg
-      integer(I4B) :: ndims
+      integer(I4B) :: ndims, i
+      character(len=NAMELEN) :: charstring
 
       associate(nc => self)
          dfill = ieee_value(dfill, IEEE_QUIET_NAN)
@@ -75,13 +75,13 @@ module subroutine encounter_io_initialize(self, param)
          end select
 
          ! Check if the file exists, and if it does, delete it
-         inquire(file=nc%enc_file, exist=fileExists)
+         inquire(file=nc%file_name, exist=fileExists)
          if (fileExists) then
-            open(unit=LUN, file=nc%enc_file, status="old", err=667, iomsg=errmsg)
+            open(unit=LUN, file=nc%file_name, status="old", err=667, iomsg=errmsg)
             close(unit=LUN, status="delete")
          end if
 
-         call check( nf90_create(nc%enc_file, NF90_NETCDF4, nc%id), "encounter_io_initialize nf90_create" )
+         call check( nf90_create(nc%file_name, NF90_NETCDF4, nc%id), "encounter_io_initialize nf90_create" )
 
          ! Dimensions
          call check( nf90_def_dim(nc%id, nc%time_dimname, nc%time_dimsize, nc%time_dimid), "encounter_io_initialize nf90_def_dim time_dimid" ) ! Simulation time dimension
@@ -130,8 +130,7 @@ module subroutine encounter_io_initialize(self, param)
          ! Add in the space dimension coordinates
          call check( nf90_put_var(nc%id, nc%space_varid, nc%space_coords, start=[1], count=[NDIM]), "encounter_io_initialize nf90_put_var space"  )
 
-         ! Pre-fill id slots with ids
-
+         ! Pre-fill name slots with ids 
          call check( nf90_put_var(nc%id, nc%id_varid, [(-1,i=1,param%maxid)], start=[1], count=[param%maxid]), "encounter_io_initialize nf90_put_var pl id_varid"  )
       end associate
 
@@ -151,20 +150,20 @@ module subroutine encounter_io_write_frame(self, nc, param)
       implicit none
       ! Arguments
       class(encounter_snapshot),      intent(in)    :: self  !! Swiftest encounter structure
-      class(encounter_io_parameters), intent(inout) :: nc    !! Parameters used to identify a particular encounter io NetCDF dataset
+      class(encounter_io_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, npl, ntp
       character(len=NAMELEN) :: charstring
 
       tslot = param%ioutput
+      associate(pl => self%pl, tp => self%tp)
 
-      call check( nf90_set_fill(nc%id, nf90_nofill, old_mode), "encounter_io_write_frame nf90_set_fill"  )
-
-      call check( nf90_put_var(nc%id, nc%time_varid, self%t, start=[tslot]), "encounter_io_write_frame nf90_put_var time_varid"  )
-      call check( nf90_put_var(nc%id, nc%loop_varid, int(self%iloop,kind=I4B), start=[tslot]), "encounter_io_write_frame nf90_put_var pl loop_varid"  )
+         call check( nf90_set_fill(nc%id, nf90_nofill, old_mode), "encounter_io_write_frame nf90_set_fill"  )
+   
+         call check( nf90_put_var(nc%id, nc%time_varid, self%t, start=[tslot]), "encounter_io_write_frame nf90_put_var time_varid"  )
+         call check( nf90_put_var(nc%id, nc%loop_varid, int(self%iloop,kind=I4B), start=[tslot]), "encounter_io_write_frame nf90_put_var pl loop_varid"  )
 
-      associate(pl => self%pl, tp => self%tp)
          npl = pl%nbody
          do i = 1, npl
             idslot = pl%id(i)
@@ -198,9 +197,9 @@ module subroutine encounter_io_write_frame(self, nc, param)
             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]), "encounter_io_write_frame nf90_put_var tp particle_type_varid"  )
          end do
-      end associate
 
-      call check( nf90_set_fill(nc%id, old_mode, old_mode) )
+         call check( nf90_set_fill(nc%id, old_mode, old_mode) )
+      end associate
 
       return
    end subroutine encounter_io_write_frame

src/fraggle/fraggle_generate.f90

@@ -151,7 +151,6 @@ module subroutine fraggle_generate_fragments(self, colliders, system, param, lfa
          else
             call io_log_one_message(FRAGGLE_LOG_OUT, "Fraggle fragment generation succeeded after " // &
                                                        trim(adjustl(message)) // " tries")
-            call fraggle_io_log_generate(frag)
          end if
 
          call frag%set_original_scale(colliders)

src/io/io.f90

@@ -253,7 +253,7 @@ module subroutine io_dump_system(self, param)
       call dump_param%dump(param_file_name)
 
       dump_param%out_form = "XV"
-      dump_param%outfile = trim(adjustl(DUMP_NC_FILE(idx)))
+      dump_param%nc%file_name = trim(adjustl(DUMP_NC_FILE(idx)))
       dump_param%ioutput = 1 
       call dump_param%nc%initialize(dump_param)
       call self%write_frame(dump_param%nc, dump_param)
@@ -1312,7 +1312,7 @@ module subroutine io_read_in_system(self, param)
          self%Euntracked = param%Euntracked
       else
          allocate(tmp_param, source=param)
-         tmp_param%outfile = param%in_netcdf
+         tmp_param%nc%file_name = param%in_netcdf
          tmp_param%out_form = param%in_form
          if (.not. param%lrestart) then
             ! Turn off energy computation so we don't have to feed it into the initial conditions
@@ -1549,6 +1549,7 @@ module subroutine io_write_frame_system(self, param)
 
       param%nc%id_chunk = self%pl%nbody + self%tp%nbody
       param%nc%time_chunk = max(param%dump_cadence / param%istep_out, 1)
+      param%nc%file_name = param%outfile
       if (lfirst) then
          inquire(file=param%outfile, exist=fileExists)
 

src/modules/encounter_classes.f90

@@ -56,7 +56,6 @@ module encounter_classes
    !> NetCDF dimension and variable names for the enounter save object
    type, extends(netcdf_parameters) :: encounter_io_parameters
       integer(I4B)       :: ienc_frame    = 1        !! Current frame number for the encounter history
-      character(STRMAX)  :: enc_file                 !! Encounter output file name
       character(NAMELEN) :: loop_varname = "loopnum" !! Loop number for encounter
       integer(I4B)       :: loop_varid               !! ID for the recursion level variable
       integer(I4B)       :: time_dimsize = 0         !! Number of time values in snapshot
@@ -68,7 +67,8 @@ module encounter_classes
 
    !> A class that that is used to store simulation history data between file output
    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
+      class(encounter_io_parameters), allocatable :: nce  !! NetCDF parameter object containing the details about the encounter file attached to this storage object
+      class(encounter_io_parameters), allocatable :: ncc  !! NetCDF parameter object containing the details about the collision file attached to this storage object
    contains
       procedure :: dump   => encounter_io_dump !! Dumps contents of encounter history to file
       final     ::           encounter_util_final_storage
@@ -221,7 +221,7 @@ end subroutine encounter_io_initialize
       module subroutine encounter_io_write_frame(self, nc, param)
          implicit none
          class(encounter_snapshot),      intent(in)    :: self   !! Swiftest encounter structure
-         class(encounter_io_parameters), intent(inout) :: nc     !! Parameters used to identify a particular encounter io NetCDF dataset
+         class(encounter_io_parameters), intent(inout) :: nc    !! Parameters used to identify a particular encounter io NetCDF dataset
          class(swiftest_parameters),     intent(inout) :: param  !! Current run configuration parameters
       end subroutine encounter_io_write_frame
 

src/modules/fraggle_classes.f90

@@ -10,10 +10,10 @@
 module fraggle_classes
    !! author: The Purdue Swiftest Team - David A. Minton, Carlisle A. Wishard, Jennifer L.L. Pouplin, and Jacob R. Elliott
    !!
-   !! Definition of classes and methods specific to Fraggel: The Fragment Generation Model
+   !! Definition of classes and methods specific to Fraggle: *Frag*ment *g*eneration that conserves angular momentum (*L*) and energy (*E*)
    use swiftest_globals
    use swiftest_classes,  only : swiftest_parameters, swiftest_nbody_system, swiftest_cb, swiftest_pl, swiftest_storage, netcdf_parameters
-   use encounter_classes, only : encounter_snapshot, encounter_io_parameters
+   use encounter_classes, only : encounter_snapshot, encounter_io_parameters, encounter_storage
    implicit none
    public
 
@@ -111,7 +111,6 @@ module fraggle_classes
 
    !! NetCDF dimension and variable names for the enounter save object
    type, extends(encounter_io_parameters) :: fraggle_io_parameters
-      character(STRMAX)  :: frag_file                 !! Encounter output file name
       integer(I4B)       :: stage_dimid                                     !! ID for the name variable  
       integer(I4B)       :: stage_varid                                     !! ID for the name variable  
       character(NAMELEN) :: stage_dimname            = "stage"              !! name of the stage dimension (before/after)
@@ -155,15 +154,10 @@ end subroutine fraggle_io_initialize_output
       module subroutine fraggle_io_write_frame(self, nc, param)
          implicit none
          class(fraggle_encounter_snapshot), intent(in)    :: self   !! Swiftest encounter structure
-         class(encounter_io_parameters),    intent(inout) :: nc     !! Parameters used to identify a particular encounter io NetCDF dataset
+         class(encounter_io_parameters),    intent(inout) :: nc    !! Parameters used to identify a particular encounter io NetCDF dataset
          class(swiftest_parameters),        intent(inout) :: param  !! Current run configuration parameters
       end subroutine fraggle_io_write_frame
 
-      module subroutine fraggle_io_log_generate(frag)
-         implicit none
-         class(fraggle_fragments),   intent(in) :: frag
-      end subroutine fraggle_io_log_generate
-
       module subroutine fraggle_io_log_pl(pl, param)
          implicit none
          class(swiftest_pl),         intent(in) :: pl    !! Swiftest massive body object (only the new bodies generated in a collision)

src/modules/swiftest_classes.f90

@@ -20,6 +20,7 @@ module swiftest_classes
 
    !! This derived datatype stores the NetCDF ID values for each of the variables included in the NetCDF data file. This is used as the base class defined in swiftest_classes
    type :: netcdf_variables
+      character(STRMAX)  :: file_name                                   !! Name of the output file
       integer(I4B)       :: out_type                                    !! output type (will be assigned either NF90_DOUBLE or NF90_FLOAT, depending on the user parameter)
       integer(I4B)       :: id                                          !! ID for the output file
       integer(I4B)       :: discard_body_id_varid                       !! ID for the id of the other body involved in the discard

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_storage, encounter_snapshot
+   use encounter_classes, only : encounter_list, encounter_snapshot, encounter_storage
    implicit none
    public
 
@@ -184,13 +184,13 @@ module symba_classes
    !  symba_nbody_system class definitions and method interfaces
    !********************************************************************************************************************************
    type, extends(helio_nbody_system) :: symba_nbody_system
-      class(symba_merger),            allocatable :: pl_adds            !! List of added bodies in mergers or collisions
-      class(symba_pltpenc),           allocatable :: pltpenc_list       !! List of massive body-test particle encounters in a single step 
-      class(symba_plplenc),           allocatable :: plplenc_list       !! List of massive body-massive body encounters in a single step
-      class(symba_plplenc),           allocatable :: plplcollision_list !! List of massive body-massive body collisions in a single step
-      integer(I4B)                                :: irec               !! System recursion level
-      type(fraggle_colliders)                     :: colliders          !! Fraggle colliders object
-      type(fraggle_fragments)                     :: fragments          !! Fraggle fragmentation system object
+      class(symba_merger),            allocatable     :: pl_adds            !! List of added bodies in mergers or collisions
+      class(symba_pltpenc),           allocatable     :: pltpenc_list       !! List of massive body-test particle encounters in a single step 
+      class(symba_plplenc),           allocatable     :: plplenc_list       !! List of massive body-massive body encounters in a single step
+      class(symba_plplenc),           allocatable     :: plplcollision_list !! List of massive body-massive body collisions in a single step
+      integer(I4B)                                    :: irec               !! System recursion level
+      type(fraggle_colliders)                         :: colliders          !! Fraggle colliders object
+      type(fraggle_fragments)                         :: fragments          !! Fraggle fragmentation system object
       type(encounter_storage(nframes=:)), allocatable :: encounter_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

src/netcdf/netcdf.f90

@@ -172,14 +172,14 @@ module subroutine netcdf_initialize_output(self, param)
          end select
 
          ! Check if the file exists, and if it does, delete it
-         inquire(file=param%outfile, exist=fileExists)
+         inquire(file=nc%file_name, exist=fileExists)
          if (fileExists) then
-            open(unit=LUN, file=param%outfile, status="old", err=667, iomsg=errmsg)
+            open(unit=LUN, file=nc%file_name, status="old", err=667, iomsg=errmsg)
             close(unit=LUN, status="delete")
          end if
 
          ! Create the file
-         call check( nf90_create(param%outfile, NF90_NETCDF4, nc%id), "netcdf_initialize_output nf90_create" )
+         call check( nf90_create(nc%file_name, NF90_NETCDF4, nc%id), "netcdf_initialize_output nf90_create" )
 
          ! Dimensions
          call check( nf90_def_dim(nc%id, nc%time_dimname, NF90_UNLIMITED, nc%time_dimid), "netcdf_initialize_output nf90_def_dim time_dimid" ) ! Simulation time dimension
@@ -324,8 +324,8 @@ module subroutine netcdf_open(self, param, readonly)
 
       associate(nc => self)
 
-         write(errmsg,*) "netcdf_open nf90_open ",trim(adjustl(param%outfile))
-         call check( nf90_open(param%outfile, mode, nc%id), errmsg)
+         write(errmsg,*) "netcdf_open nf90_open ",trim(adjustl(nc%file_name))
+         call check( nf90_open(nc%file_name, mode, nc%id), errmsg)
 
          ! Dimensions
          call check( nf90_inq_dimid(nc%id, nc%time_dimname, nc%time_dimid), "netcdf_open nf90_inq_dimid time_dimid"  )
@@ -824,6 +824,9 @@ module subroutine netcdf_read_particle_info_system(self, nc, param, plmask, tpma
          cb%id = itemp(1)
          pl%id(:) = pack(itemp, plmask)
          tp%id(:) = pack(itemp, tpmask)
+         cb%id = 0
+         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

@@ -72,10 +72,12 @@ module subroutine setup_construct_system(system, param)
             select type(param)
             class is (symba_parameters)
                if (param%lencounter_save) then
-                  if (.not. allocated(system%encounter_history)) allocate(encounter_storage :: system%encounter_history)
-                  allocate(fraggle_io_parameters :: system%encounter_history%nc)
+                  allocate(encounter_storage :: system%encounter_history)
+                  allocate(encounter_io_parameters :: system%encounter_history%nce)
+                  allocate(fraggle_io_parameters :: system%encounter_history%ncc)
                   call system%encounter_history%reset()
-                  system%encounter_history%nc%file_number = param%iloop / param%dump_cadence
+                  system%encounter_history%nce%file_number = param%iloop / param%dump_cadence
+                  system%encounter_history%ncc%file_number = param%iloop / param%dump_cadence
                end if
             end select
          end select