From 45b1064c09c68931e7b9816177b957690b8069c5 Mon Sep 17 00:00:00 2001
From: David A Minton <daminton@purdue.edu>
Date: Thu, 22 Dec 2022 20:08:16 -0500
Subject: [PATCH] Fixed bug that was causing the data.nc file to be closed
 before we were ready

---
 src/collision/collision_resolve.f90 | 7 ++-----
 src/fraggle/fraggle_generate.f90    | 6 +++---
 src/swiftest/swiftest_io.f90        | 5 +++--
 3 files changed, 8 insertions(+), 10 deletions(-)

diff --git a/src/collision/collision_resolve.f90 b/src/collision/collision_resolve.f90
index d7eff07eb..4dbfc4ea1 100644
--- a/src/collision/collision_resolve.f90
+++ b/src/collision/collision_resolve.f90
@@ -493,7 +493,6 @@ module subroutine collision_resolve_plpl(self, nbody_system, param, t, dt, irec)
       real(DP) :: Eorbit_before, Eorbit_after
       logical :: lplpl_collision
       character(len=STRMAX) :: timestr
-      class(swiftest_parameters), allocatable :: tmp_param
       integer(I4B), dimension(2) :: idx_parent       !! Index of the two bodies considered the "parents" of the collision
       logical  :: lgoodcollision
       integer(I4B) :: i, loop, ncollisions
@@ -533,7 +532,6 @@ module subroutine collision_resolve_plpl(self, nbody_system, param, t, dt, irec)
                                                             trim(adjustl(timestr)))
                   call swiftest_io_log_one_message(COLLISION_LOG_OUT, "***********************************************************" // &
                                                             "***********************************************************")
-                  allocate(tmp_param, source=param)
 
                   do i = 1, ncollisions
                      idx_parent(1) = pl%kin(idx1(i))%parent
@@ -555,15 +553,14 @@ module subroutine collision_resolve_plpl(self, nbody_system, param, t, dt, irec)
                   if ((nbody_system%pl_adds%nbody == 0) .and. (nbody_system%pl_discards%nbody == 0)) exit
 
                   ! Save the add/discard information to file
-                  call nbody_system%write_discard(tmp_param)
+                  call nbody_system%write_discard(param)
 
                   ! Rearrange the arrays: Remove discarded bodies, add any new bodies, resort, and recompute all indices and encounter lists
-                  call pl%rearray(nbody_system, tmp_param)
+                  call pl%rearray(nbody_system, param)
 
                   ! Destroy the add/discard list so that we don't append the same body multiple times if another collision is detected
                   call nbody_system%pl_discards%setup(0, param)
                   call nbody_system%pl_adds%setup(0, param)
-                  deallocate(tmp_param)
 
                   ! Check whether or not any of the particles that were just added are themselves in a collision state. This will generate a new plpl_collision 
                   call plpl_encounter%collision_check(nbody_system, param, t, dt, irec, lplpl_collision)
diff --git a/src/fraggle/fraggle_generate.f90 b/src/fraggle/fraggle_generate.f90
index d7d3766a0..fa3a9d2a6 100644
--- a/src/fraggle/fraggle_generate.f90
+++ b/src/fraggle/fraggle_generate.f90
@@ -25,7 +25,7 @@ module subroutine fraggle_generate_disruption(collider, nbody_system, param, t)
       !! 
       implicit none
       ! Arguments
-      class(collision_fraggle),        intent(inout) :: collider
+      class(collision_fraggle),     intent(inout) :: collider
       class(swiftest_nbody_system), intent(inout) :: nbody_system !! Swiftest nbody system object
       class(swiftest_parameters),   intent(inout) :: param        !! Current run configuration parameters with SyMBA additions
       real(DP),                     intent(in)    :: t            !! Time of collision
@@ -102,7 +102,7 @@ module subroutine fraggle_generate_hitandrun(collider, nbody_system, param, t)
       !! 
       implicit none
       ! Arguments
-      class(collision_fraggle),        intent(inout) :: collider !! Fraggle collision system object
+      class(collision_fraggle),     intent(inout) :: collider !! Fraggle collision system object
       class(swiftest_nbody_system), intent(inout) :: nbody_system     !! Swiftest nbody system object
       class(swiftest_parameters),   intent(inout) :: param            !! Current run configuration parameters with SyMBA additions
       real(DP),                     intent(in)    :: t                !! Time of collision
@@ -180,7 +180,7 @@ end subroutine fraggle_generate_hitandrun
 
    module subroutine fraggle_generate_system(self, nbody_system, param, t)
       implicit none
-      class(collision_fraggle),    intent(inout) :: self     !! Fraggle fragment nbody_system object 
+      class(collision_fraggle), intent(inout) :: self     !! Fraggle fragment nbody_system object 
       class(base_nbody_system), intent(inout) :: nbody_system    !! Swiftest nbody system object
       class(base_parameters),   intent(inout) :: param     !! Current run configuration parameters 
       real(DP),                 intent(in)    :: t         !! The time of the collision
diff --git a/src/swiftest/swiftest_io.f90 b/src/swiftest/swiftest_io.f90
index d3fbb229e..55360c7ca 100644
--- a/src/swiftest/swiftest_io.f90
+++ b/src/swiftest/swiftest_io.f90
@@ -2049,8 +2049,9 @@ module subroutine swiftest_io_param_reader(self, unit, iotype, v_list, iostat, i
          param%GU = GC / (param%DU2M**3 / (param%MU2KG * param%TU2S**2))
 
 
-         ! All reporting of collision information in SyMBA (including mergers) is now recorded in the Fraggle logfile
-         call swiftest_io_log_start(param, COLLISION_LOG_OUT, "Fraggle logfile")
+         ! A minimal log of collision outcomes is stored in the following log file
+         ! More complete data on collisions is stored in the NetCDF output files
+         call swiftest_io_log_start(param, COLLISION_LOG_OUT, "Collision logfile")
 
          if ((param%encounter_save /= "NONE")       .and. &
              (param%encounter_save /= "TRAJECTORY") .and. &