From 864b02da4ed811f69c428159bf9d227a30c585da Mon Sep 17 00:00:00 2001
From: David A Minton <daminton@purdue.edu>
Date: Thu, 1 Dec 2022 11:32:41 -0500
Subject: [PATCH] Added the storage of nbody_system snapshots between output
 dumps

---
 src/main/swiftest_driver.f90     | 35 ++++++++++++++++++++------------
 src/modules/swiftest_classes.f90 |  9 +-------
 src/util/util_copy.f90           |  2 ++
 3 files changed, 25 insertions(+), 21 deletions(-)

diff --git a/src/main/swiftest_driver.f90 b/src/main/swiftest_driver.f90
index 6bee4374b..42dfcd059 100644
--- a/src/main/swiftest_driver.f90
+++ b/src/main/swiftest_driver.f90
@@ -27,6 +27,7 @@ program swiftest_driver
    integer(I8B)                               :: iout             !! Output cadence counter
    integer(I8B)                               :: istart           !! Starting index for loop counter
    integer(I8B)                               :: nloops           !! Number of steps to take in the simulation
+   integer(I8B)                               :: iframe           !! System history frame cindex
    real(DP)                                   :: old_t_final = 0.0_DP !! Output time at which writing should start, in order to prevent duplicate lines being written for restarts
    type(walltimer)                            :: integration_timer !! Object used for computing elapsed wall time
    real(DP)                                   :: tfrac
@@ -78,12 +79,19 @@ program swiftest_driver
              display_unit    => param%display_unit)
 
       call nbody_system%initialize(param)
+
+      ! Set up loop and output cadence variables
       t = tstart
       iout = istep_out
-      idump = dump_cadence
       nloops = ceiling((tstop - t0) / dt, kind=I8B)
-      istart =  ceiling((tstart - t0) / dt, kind=I8B)
+      istart =  ceiling((tstart - t0) / dt + 1, kind=I8B)
       ioutput = int(istart / istep_out, kind=I8B)
+
+      ! Set up system storage for intermittent file dumps
+      if (dump_cadence == 0) dump_cadence = nloops
+      allocate(swiftest_storage(dump_cadence) :: system_history)
+      idump = dump_cadence
+
       ! Prevent duplicate frames from being written if this is a restarted run
       if (param%lrestart) then
          old_t_final = nbody_system%get_old_t_final(param)
@@ -119,9 +127,18 @@ program swiftest_driver
          if (istep_out > 0) then
             iout = iout - 1
             if (iout == 0) then
-               ioutput = int(iloop / istep_out, kind=I8B)
-               call nbody_system%write_frame(param)
-
+               idump = idump - 1
+               iframe = dump_cadence - idump 
+               system_history%frame(iframe) = nbody_system
+
+               if (idump == 0) then
+                  call nbody_system%dump(param)
+                  do iframe = 1_I8B, dump_cadence
+                     ioutput = int((iloop - dump_cadence - 1_I8B + iframe) / istep_out, kind=I8B)
+                     call system_history%frame(iframe)%system%write_frame(param)
+                  end do
+                  idump = dump_cadence
+               end if
 
                tfrac = (param%t - param%t0) / (param%tstop - param%t0)
 
@@ -147,14 +164,6 @@ program swiftest_driver
             end if
          end if
 
-         !> If the loop counter is at the dump cadence value, dump the state of the system to a file in case it needs to be restarted
-         if (dump_cadence > 0) then
-            idump = idump - 1
-            if (idump == 0) then
-               call nbody_system%dump(param)
-               idump = dump_cadence
-            end if
-         end if
       end do
       if (display_style == "COMPACT") write(*,*) "SWIFTEST STOP" // trim(adjustl(param%integrator))
    end associate
diff --git a/src/modules/swiftest_classes.f90 b/src/modules/swiftest_classes.f90
index 7952b28ac..5883adc44 100644
--- a/src/modules/swiftest_classes.f90
+++ b/src/modules/swiftest_classes.f90
@@ -425,11 +425,10 @@ module swiftest_classes
    end type
 
    type, extends(swiftest_base) :: swiftest_storage(nframes)
-      integer(I4B), len :: nframes
+      integer(I8B), len :: nframes
       !! A class that that is used to store simulation history data between file output 
       type(storage_frame), dimension(nframes) :: frame
    contains
-      procedure :: initialize => setup_initialize_storage 
    end type swiftest_storage
 
    abstract interface
@@ -1046,12 +1045,6 @@ module subroutine setup_initialize_particle_info_system(self, param)
          class(swiftest_parameters),   intent(inout) :: param !! Current run configuration parameters
       end subroutine setup_initialize_particle_info_system
 
-      module subroutine setup_initialize_storage(self, param)
-         implicit none
-         class(swiftest_storage(*)), intent(inout) :: self  !! Swiftest storage object
-         class(swiftest_parameters), intent(inout) :: param !! Current run configuration parameters 
-      end subroutine setup_initialize_storage
-
       module subroutine setup_initialize_system(self, param)
          implicit none
          class(swiftest_nbody_system), intent(inout) :: self  !! Swiftest system object
diff --git a/src/util/util_copy.f90 b/src/util/util_copy.f90
index fed2f0604..51e210787 100644
--- a/src/util/util_copy.f90
+++ b/src/util/util_copy.f90
@@ -86,7 +86,9 @@ module subroutine util_copy_store_system(self, system)
       class(storage_frame),         intent(inout) :: self   !! Swiftest storage frame object
       class(swiftest_nbody_system), intent(in)    :: system !! Swiftest n-body system object
 
+      if (allocated(self%system)) deallocate(self%system)
       allocate(self%system, source=system)
+      return
 
    end subroutine util_copy_store_system