Made minor modifications to the NetCDF I/O so that files are only wri…

…tten to disk when a dump is called. Setting ISTEP_DUMP > ISTEP_OUT greatly increases the speed of a run

examples/rmvs_swifter_comparison/1pl_1tp_encounter/init_cond.py

@@ -18,7 +18,7 @@
 swiftest_pl    = "pl.swiftest.in"
 swiftest_tp    = "tp.swiftest.in"
 swiftest_cb    = "cb.swiftest.in"
-swiftest_bin   = "bin.swiftest.dat"
+swiftest_bin   = "bin.swiftest.nc"
 swiftest_enc   = "enc.swiftest.dat"
 
 MU2KG = swiftest.MSun
@@ -39,8 +39,8 @@
 rmax = 1000.0
 
 npl = 1
-plid = 2
-tpid = 100
+plid = 1
+tpid = 2
 
 radius = np.double(4.25875607065041e-05)
 Gmass = np.double(0.00012002693582795244940133) 
@@ -60,7 +60,7 @@
 #Make Swifter files
 plfile = open(swifter_pl, 'w')
 print(npl+1, f'! Planet input file generated using init_cond.py',file=plfile)
-print(1,GMSun,file=plfile)
+print(0,GMSun,file=plfile)
 print('0.0 0.0 0.0',file=plfile)
 print('0.0 0.0 0.0',file=plfile)
 print(plid,"{:.23g}".format(Gmass),rhill, file=plfile)
@@ -106,9 +106,19 @@
 sys.stdout = sys.__stdout__
 
 #Now make Swiftest files
+NAMELEN = 32
+cbname = "Sun"
+plname = "Planet"
+tpname = "TestParticle"
+
+cbname = cbname.ljust(NAMELEN)
+plname = plname.ljust(NAMELEN)
+tpname = tpname.ljust(NAMELEN)
+
 cbfile = FortranFile(swiftest_cb, 'w')
 Msun = np.double(1.0)
 cbfile.write_record(0)
+cbfile.write_record(cbname)
 cbfile.write_record(np.double(GMSun))
 cbfile.write_record(np.double(rmin))
 cbfile.write_record(np.double(swiftest.J2Sun))
@@ -119,6 +129,7 @@
 plfile.write_record(npl)
 
 plfile.write_record(plid)
+plfile.write_record(plname)
 plfile.write_record(p_pl[0])
 plfile.write_record(p_pl[1])
 plfile.write_record(p_pl[2])
@@ -133,6 +144,7 @@
 ntp = 1
 tpfile.write_record(ntp)
 tpfile.write_record(tpid)
+tpfile.write_record(tpname)
 tpfile.write_record(p_tp[0])
 tpfile.write_record(p_tp[1])
 tpfile.write_record(p_tp[2])
@@ -154,8 +166,8 @@
 print(f'ISTEP_OUT      {iout:d}')
 print(f'ISTEP_DUMP     {iout:d}')
 print(f'BIN_OUT        {swiftest_bin}')
-print(f'OUT_TYPE       REAL8')
-print(f'OUT_FORM       XV')
+print(f'OUT_TYPE       NETCDF_DOUBLE')
+print(f'OUT_FORM       XVEL')
 print(f'OUT_STAT       REPLACE')
 print(f'RHILL_PRESENT  yes')
 print(f'CHK_CLOSE      yes')

examples/rmvs_swifter_comparison/1pl_1tp_encounter/param.swiftest.in

@@ -7,10 +7,10 @@ PL_IN          pl.swiftest.in
 TP_IN          tp.swiftest.in
 IN_TYPE        REAL8
 ISTEP_OUT      1
-ISTEP_DUMP     1
-BIN_OUT        bin.swiftest.dat
-OUT_TYPE       REAL8
-OUT_FORM       XV
+ISTEP_DUMP     10
+BIN_OUT        bin.swiftest.nc
+OUT_TYPE       NETCDF_DOUBLE
+OUT_FORM       XVEL
 OUT_STAT       REPLACE
 RHILL_PRESENT  yes
 CHK_CLOSE      yes

examples/rmvs_swifter_comparison/1pl_1tp_encounter/pl.swifter.in

@@ -1,8 +1,8 @@
 2 ! Planet input file generated using init_cond.py
-1 39.476926408897625196
+0 39.476926408897625196
 0.0 0.0 0.0
 0.0 0.0 0.0
-2 0.00012002693582795244940133 0.010044724833237892
+1 0.00012002693582795244940133 0.010044724833237892
 4.25875607065041e-05
 1.0 0.0 0.0
 0.0 6.283185307179586 0.0

examples/rmvs_swifter_comparison/1pl_1tp_encounter/tp.swifter.in

@@ -1,4 +1,4 @@
 1
-100
+2
 1.01 0.0 0.0
 0.0 6.252003053624663 0.0

src/io/io.f90

@@ -73,11 +73,11 @@ module subroutine io_conservation_report(self, param, lterminal)
             if (abs(Merror) > 100 * epsilon(Merror)) then
                write(*,*) "Severe error! Mass not conserved! Halting!"
                call pl%xv2el(cb)
-               call param%nciu%open(param)
+               !call param%nciu%open(param)
                call self%write_hdr(param%nciu, param)
                call cb%write_frame(param%nciu, param)
                call pl%write_frame(param%nciu, param)
-               call param%nciu%close(param)
+               call param%nciu%close()
                call util_exit(FAILURE)
             end if
          end if
@@ -202,9 +202,7 @@ module subroutine io_dump_particle_info_base(self, param, idx)
          close(unit = LUN, err = 667, iomsg = errmsg)
       !else if ((param%out_type == NETCDF_FLOAT_TYPE) .or. (param%out_type == NETCDF_DOUBLE_TYPE)) then
       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
@@ -307,7 +305,9 @@ module subroutine io_dump_system(self, param)
          call self%cb%write_frame(dump_param%nciu, dump_param)
          call self%pl%write_frame(dump_param%nciu, dump_param)
          call self%tp%write_frame(dump_param%nciu, dump_param)
-         call dump_param%nciu%close(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()
       end if
 
       idx = idx + 1
@@ -1856,9 +1856,7 @@ module subroutine io_write_discard(self, param)
 
          ! Record the discarded body metadata information to file
          if ((param%out_type == NETCDF_FLOAT_TYPE) .or. (param%out_type == NETCDF_DOUBLE_TYPE)) then
-            call param%nciu%open(param) 
             call tp_discards%write_particle_info(param%nciu)
-            call param%nciu%close(param)
          end if
 
          if (param%discard_out == "") return
@@ -2176,7 +2174,7 @@ module subroutine io_write_frame_system(self, param)
 
             lfirst = .false.
          else
-            call param%nciu%open(param)
+            !call param%nciu%open(param)
          end if
       end if
 
@@ -2202,7 +2200,6 @@ module subroutine io_write_frame_system(self, param)
          call cb%write_frame(param%nciu, param)
          call pl%write_frame(param%nciu, param)
          call tp%write_frame(param%nciu, param)
-         call param%nciu%close(param)
       end if
 
       return

src/kick/kick.f90

@@ -19,15 +19,18 @@ module subroutine kick_getacch_int_pl(self, param)
       character(len=STRMAX) :: tstr, nstr, cstr, mstr, lstyle
       character(len=1) :: schar
 
-
       if (param%ladaptive_interactions) then
-         if (lfirst) then
-            write(itimer%loopname, *) "kick_getacch_int_pl"
-            write(itimer%looptype, *) "INTERACTION"
-            call itimer%time_this_loop(param, self, self%nplpl)
-            lfirst = .false.
+         if (self%nplpl > 0) then
+            if (lfirst) then
+               write(itimer%loopname, *) "kick_getacch_int_pl"
+               write(itimer%looptype, *) "INTERACTION"
+               call itimer%time_this_loop(param, self, self%nplpl)
+               lfirst = .false.
+            else
+               if (itimer%check(param, self%nplpl)) call itimer%time_this_loop(param, self, self%nplpl)
+            end if
          else
-            if (itimer%check(param, self%nplpl)) call itimer%time_this_loop(param, self, self%nplpl)
+            param%lflatten_interactions = .false.
          end if
       end if
 
@@ -37,7 +40,7 @@ module subroutine kick_getacch_int_pl(self, param)
          call kick_getacch_int_all_triangular_pl(self%nbody, self%nbody, self%xh, self%Gmass, self%radius, self%ah)
       end if
 
-      if (param%ladaptive_interactions) then 
+      if (param%ladaptive_interactions .and. self%nplpl > 0) then 
          if (itimer%is_on) call itimer%adapt(param, self, self%nplpl)
       end if
 

src/main/swiftest_driver.f90

@@ -106,6 +106,8 @@ program swiftest_driver
       end do
    end associate
 
+   call nbody_system%finalize(param)
+
    call util_exit(SUCCESS)
 
    stop

src/modules/swiftest_classes.f90

@@ -79,6 +79,7 @@ module swiftest_classes
       procedure :: close      => netcdf_close             !! Closes an open NetCDF file
       procedure :: initialize => netcdf_initialize_output !! Initialize a set of parameters used to identify a NetCDF output object
       procedure :: open       => netcdf_open              !! Opens a NetCDF file
+      procedure :: sync       => netcdf_sync              !! Syncrhonize the disk and memory buffer of the NetCDF file (e.g. commit the frame files stored in memory to disk) 
    end type netcdf_parameters
 
    !********************************************************************************************************************************
@@ -432,6 +433,7 @@ module swiftest_classes
       procedure :: read_particle_info      => io_read_particle_info_system           !! Read in particle metadata from file
       procedure :: write_discard           => io_write_discard                       !! Write out information about discarded test particles
       procedure :: obl_pot                 => obl_pot_system                         !! Compute the contribution to the total gravitational potential due solely to the oblateness of the central body
+      procedure :: finalize                => setup_finalize_system                  !! Runs any finalization subroutines when ending the simulation.
       procedure :: initialize              => setup_initialize_system                !! Initialize the system from input files
       procedure :: init_particle_info      => setup_initialize_particle_info_system  !! Initialize the system from input files
       procedure :: step_spin               => tides_step_spin_system                 !! Steps the spins of the massive & central bodies due to tides.
@@ -998,10 +1000,9 @@ module pure subroutine kick_getacch_int_one_tp(rji2, xr, yr, zr, Gmpl, ax, ay, a
          real(DP), intent(inout) :: ax, ay, az !! Acceleration vector components of test particle
       end subroutine kick_getacch_int_one_tp
 
-      module subroutine netcdf_close(self, param)
+      module subroutine netcdf_close(self)
          implicit none
          class(netcdf_parameters),   intent(inout) :: self   !! Parameters used to identify a particular NetCDF dataset
-         class(swiftest_parameters), intent(in)    :: param  !! Current run configuration parameters
       end subroutine netcdf_close
 
       module function netcdf_get_old_t_final_system(self, param) result(old_t_final)
@@ -1023,6 +1024,11 @@ module subroutine netcdf_open(self, param)
          class(swiftest_parameters), intent(in)    :: param  !! Current run configuration parameters
       end subroutine netcdf_open
 
+      module subroutine netcdf_sync(self)
+         implicit none
+         class(netcdf_parameters),   intent(inout) :: self !! Parameters used to identify a particular NetCDF dataset
+      end subroutine netcdf_sync
+
       module function netcdf_read_frame_base(self, iu, param) result(ierr)
          implicit none
          class(swiftest_base),       intent(inout) :: self  !! Swiftest base object
@@ -1157,6 +1163,12 @@ module subroutine setup_encounter(self, n)
          integer(I4B),              intent(in)    :: n    !! Number of encounters to allocate space for
       end subroutine setup_encounter
 
+      module subroutine setup_finalize_system(self, param)
+         implicit none
+         class(swiftest_nbody_system), intent(inout) :: self  !! Swiftest system object
+         class(swiftest_parameters),   intent(inout) :: param !! Current run configuration parameters 
+      end subroutine setup_finalize_system
+
       module subroutine setup_initialize_particle_info_system(self, param)
          implicit none
          class(swiftest_nbody_system), intent(inout) :: self  !! Swiftest nbody system object

src/netcdf/netcdf.f90

@@ -19,14 +19,13 @@ subroutine check(status)
       return
    end subroutine check
 
-   module subroutine netcdf_close(self, param)
+   module subroutine netcdf_close(self)
       !! author: Carlisle A. Wishard, Dana Singh, and David A. Minton
       !!
       !! Closes a NetCDF file
       implicit none
       ! Arguments
       class(netcdf_parameters),   intent(inout) :: self   !! Parameters used to identify a particular NetCDF dataset
-      class(swiftest_parameters), intent(in)    :: param  !! Current run configuration parameters
 
       call check( nf90_close(self%ncid) )
 
@@ -446,7 +445,7 @@ module function netcdf_read_frame_system(self, iu, param) result(ierr)
       call self%cb%read_in(param)
       call self%pl%read_in(param)
       call self%tp%read_in(param)
-      call iu%close(param)
+      call iu%close()
 
       ierr = 0
       return
@@ -500,6 +499,21 @@ module subroutine netcdf_read_hdr_system(self, iu, param)
       return
    end subroutine netcdf_read_hdr_system
 
+
+   module subroutine netcdf_sync(self)
+      !! author: David A. Minton
+      !!
+      !! Syncrhonize the disk and memory buffer of the NetCDF file (e.g. commit the frame files stored in memory to disk) 
+      !!    
+      implicit none
+      ! Arguments
+      class(netcdf_parameters),   intent(inout) :: self !! Parameters used to identify a particular NetCDF dataset
+
+      call check( nf90_sync(self%ncid) )
+
+      return
+   end subroutine netcdf_sync
+
    module subroutine netcdf_write_frame_base(self, iu, param)
       !! author: Carlisle A. Wishard, Dana Singh, and David A. Minton
       !!
@@ -610,13 +624,10 @@ module subroutine netcdf_write_frame_system(self, iu, param)
       class(netcdf_parameters),   intent(inout)   :: iu    !! Parameters used to identify a particular NetCDF dataset
       class(swiftest_parameters),   intent(in)    :: param !! Current run configuration parameters 
 
-      call iu%open(param)
-
       call self%write_hdr(iu, param)
       call self%cb%write_frame(iu, param)
       call self%pl%write_frame(iu, param)
       call self%tp%write_frame(iu, param)
-      call iu%close(param)
 
       return
    end subroutine netcdf_write_frame_system

src/setup/setup.f90

@@ -126,6 +126,27 @@ module subroutine setup_encounter(self, n)
    end subroutine setup_encounter
 
 
+   module subroutine setup_finalize_system(self, param)
+      !! author: David A. Minton
+      !!
+      !! Runs any finalization subroutines when ending the simulation.
+      !!
+      implicit none
+      ! Arguments
+      class(swiftest_nbody_system), intent(inout) :: self   !! Swiftest system object
+      class(swiftest_parameters),   intent(inout) :: param  !! Current run configuration parameters
+      integer(I4B)                                :: ierr
+
+      associate(system => self)
+         if ((param%out_type == NETCDF_FLOAT_TYPE) .or. (param%out_type == NETCDF_DOUBLE_TYPE)) then
+            call param%nciu%close()
+         end if
+      end associate
+
+      return
+   end subroutine setup_finalize_system
+
+
    module subroutine setup_initialize_particle_info_system(self, param)
       !! author: David A. Minton
       !!

src/symba/symba_io.f90

@@ -176,9 +176,7 @@ module subroutine symba_io_write_discard(self, param)
 
             ! Record the discarded body metadata information to file
             if ((param%out_type == NETCDF_FLOAT_TYPE) .or. (param%out_type == NETCDF_DOUBLE_TYPE)) then
-               call param%nciu%open(param) 
                call pl_discards%write_particle_info(param%nciu)
-               call param%nciu%close(param)
             end if
 
             if (param%discard_out == "") return