More cleanup

src/collision/collision_io.f90

@@ -191,7 +191,7 @@ module subroutine collision_io_initialize_output(self, param)
 
       667 continue
       write(*,*) "Error creating fragmentation output file. " // trim(adjustl(errmsg))
-      call util_exit(FAILURE)
+      call swiftest_util_exit(FAILURE)
    end subroutine collision_io_initialize_output
 
 

src/collision/collision_resolve.f90

@@ -635,7 +635,7 @@ subroutine collision_resolve_list(plpl_collision , system, param, t)
                   plpl_collision%status(i) = collision_resolve_merge(system, param, t)
                case default 
                   write(*,*) "Error in swiftest_collision, unrecognized collision regime"
-                  call util_exit(FAILURE)
+                  call swiftest_util_exit(FAILURE)
                end select
                call collision_history%take_snapshot(param,system, t, "after") 
                call impactors%reset()

src/collision/collision_util.f90

@@ -291,7 +291,7 @@ module subroutine collision_util_get_energy_momentum(self,  system, param, lbefo
                if (.not.allocated(tmpsys)) then
                   write(*,*) "Error in collision_util_get_energy_momentum. " // &
                            " This must be called with lbefore=.true. at least once before calling it with lbefore=.false."
-                  call util_exit(FAILURE)
+                  call swiftest_util_exit(FAILURE)
                end if
                select type(tmpsys)
                class is (swiftest_nbody_system)
@@ -345,7 +345,7 @@ module subroutine collision_util_index_map(self)
       call self%get_index_values(idvals, tvals)
 
       ! Consolidate ids to only unique values
-      call util_unique(idvals,self%idvals,self%idmap)
+      call swiftest_util_unique(idvals,self%idvals,self%idmap)
       self%nid = size(self%idvals)
 
       ! Don't consolidate time values (multiple collisions can happen in a single time step)
@@ -502,6 +502,7 @@ module subroutine collision_util_set_coordinate_system(self)
       return
    end subroutine collision_util_set_coordinate_system
 
+
    subroutine collision_util_save_snapshot(collision_history, snapshot)
       !! author: David A. Minton
       !!

src/encounter/encounter_check.f90

@@ -168,10 +168,10 @@ module subroutine encounter_check_all_plplm(param, nplm, nplt, xplm, vplm, xplt,
          call move_alloc(ltmp, lvdotr)
          nenc = nenc + plmplt_nenc
 
-         call util_sort(index1, ind)
-         call util_sort_rearrange(index1, ind, nenc)
-         call util_sort_rearrange(index2, ind, nenc)
-         call util_sort_rearrange(lvdotr, ind, nenc)
+         call swiftest_util_sort(index1, ind)
+         call swiftest_util_sort_rearrange(index1, ind, nenc)
+         call swiftest_util_sort_rearrange(index2, ind, nenc)
+         call swiftest_util_sort_rearrange(lvdotr, ind, nenc)
 
       end if
 
@@ -565,7 +565,7 @@ subroutine encounter_check_all_triangular_plpl(npl, x, v, renc, dt, nenc, index1
       integer(I4B), dimension(:), allocatable, save :: ind_arr
       type(collision_list_plpl), dimension(npl) :: lenc
 
-      call util_index_array(ind_arr, npl) 
+      call swiftest_util_index_array(ind_arr, npl) 
 
       !$omp parallel do default(private) schedule(static)&
       !$omp shared(x, v, renc, lenc, ind_arr) &
@@ -612,7 +612,7 @@ subroutine encounter_check_all_triangular_plplm(nplm, nplt, xplm, vplm, xplt, vp
       integer(I4B), dimension(:), allocatable, save :: ind_arr
       type(collision_list_plpl), dimension(nplm) :: lenc
 
-      call util_index_array(ind_arr, nplt)
+      call swiftest_util_index_array(ind_arr, nplt)
 
       !$omp parallel do default(private) schedule(dynamic)&
       !$omp shared(xplm, vplm, xplt, vplt, rencm, renct, lenc, ind_arr) &
@@ -659,7 +659,7 @@ subroutine encounter_check_all_triangular_pltp(npl, ntp, xpl, vpl, xtp, vtp, ren
       type(collision_list_pltp), dimension(npl) :: lenc
       real(DP), dimension(ntp) :: renct
 
-      call util_index_array(ind_arr, ntp)
+      call swiftest_util_index_array(ind_arr, ntp)
       renct(:) = 0.0_DP
 
       !$omp parallel do default(private) schedule(dynamic)&
@@ -807,10 +807,10 @@ subroutine encounter_check_remove_duplicates(n, nenc, index1, index2, lvdotr)
          return
       end if
 
-      call util_sort(index1, ind)
-      call util_sort_rearrange(index1, ind, nenc)
-      call util_sort_rearrange(index2, ind, nenc)
-      call util_sort_rearrange(lvdotr, ind, nenc)
+      call swiftest_util_sort(index1, ind)
+      call swiftest_util_sort_rearrange(index1, ind, nenc)
+      call swiftest_util_sort_rearrange(index2, ind, nenc)
+      call swiftest_util_sort_rearrange(lvdotr, ind, nenc)
 
       ! Get the bounds on the bodies in the first index
       ibeg(:) = n
@@ -836,7 +836,7 @@ subroutine encounter_check_remove_duplicates(n, nenc, index1, index2, lvdotr)
          khi = iend(i)
          nenci = khi - klo + 1_I8B
          if (allocated(ind)) deallocate(ind)
-         call util_sort(index2(klo:khi), ind)
+         call swiftest_util_sort(index2(klo:khi), ind)
          index2(klo:khi) = itmp(klo - 1_I8B + ind(:))
          do j = klo + 1_I8B, khi
             if (index2(j) == index2(j - 1_I8B)) lencounter(j) = .false. 
@@ -876,7 +876,7 @@ pure module subroutine encounter_check_sort_aabb_1D(self, n, extent_arr)
       ! Internals
       integer(I8B) :: i, k
 
-      call util_sort(extent_arr, self%ind)
+      call swiftest_util_sort(extent_arr, self%ind)
 
       do concurrent(k = 1_I8B:2_I8B * n)
          i = self%ind(k)
@@ -923,7 +923,7 @@ module subroutine encounter_check_sweep_aabb_double_list(self, n1, n2, r1, v1, r
       real(DP), dimension(2*(n1+n2)) :: xind, yind, zind, vxind, vyind, vzind, rencind
 
       ntot = n1 + n2
-      call util_index_array(ind_arr, ntot)
+      call swiftest_util_index_array(ind_arr, ntot)
 
       do concurrent(dim = 1:SWEEPDIM)
          loverlap_by_dimension(dim,:) = (self%aabb(dim)%ibeg(:) + 1_I8B) < (self%aabb(dim)%iend(:) - 1_I8B)
@@ -1035,7 +1035,7 @@ module subroutine encounter_check_sweep_aabb_single_list(self, n, x, v, renc, dt
       integer(I4B), dimension(:), allocatable, save :: ind_arr
       integer(I8B) :: ibeg, iend
 
-      call util_index_array(ind_arr, n)
+      call swiftest_util_index_array(ind_arr, n)
       dim = 1
 
       ! Sweep the intervals for each of the massive bodies along one dimension

src/encounter/encounter_io.f90

@@ -146,7 +146,7 @@ module subroutine encounter_io_initialize_output(self, param)
 
       667 continue
       write(*,*) "Error creating encounter output file. " // trim(adjustl(errmsg))
-      call util_exit(FAILURE)
+      call swiftest_util_exit(FAILURE)
    end subroutine encounter_io_initialize_output
 
 

src/encounter/encounter_setup.f90

@@ -84,6 +84,7 @@ module subroutine encounter_setup_list(self, n)
       allocate(self%r2(NDIM,n))
       allocate(self%v1(NDIM,n))
       allocate(self%v2(NDIM,n))
+      allocate(self%level(n))
 
       self%tcollision(:) = 0.0_DP
       self%lvdotr(:) = .false.
@@ -97,6 +98,7 @@ module subroutine encounter_setup_list(self, n)
       self%r2(:,:) = 0.0_DP
       self%v1(:,:) = 0.0_DP
       self%v2(:,:) = 0.0_DP
+      self%level(:) = 0
 
       return
    end subroutine encounter_setup_list

src/encounter/encounter_util.f90

@@ -26,17 +26,19 @@ module subroutine encounter_util_append_list(self, source, lsource_mask)
 
       nold = self%nenc
       nsrc = source%nenc
-      call util_append(self%lvdotr, source%lvdotr, nold, nsrc, lsource_mask)
-      call util_append(self%lclosest, source%lclosest, nold, nsrc, lsource_mask)
-      call util_append(self%status, source%status, nold, nsrc, lsource_mask)
-      call util_append(self%index1, source%index1, nold, nsrc, lsource_mask)
-      call util_append(self%index2, source%index2, nold, nsrc, lsource_mask)
-      call util_append(self%id1, source%id1, nold, nsrc, lsource_mask)
-      call util_append(self%id2, source%id2, nold, nsrc, lsource_mask)
-      call util_append(self%r1, source%r1, nold, nsrc, lsource_mask)
-      call util_append(self%r2, source%r2, nold, nsrc, lsource_mask)
-      call util_append(self%v1, source%v1, nold, nsrc, lsource_mask)
-      call util_append(self%v2, source%v2, nold, nsrc, lsource_mask)
+      call swiftest_util_append(self%tcollision, source%tcollision,   nold, nsrc, lsource_mask)
+      call swiftest_util_append(self%lclosest,   source%lclosest,     nold, nsrc, lsource_mask)
+      call swiftest_util_append(self%lvdotr,     source%lvdotr,       nold, nsrc, lsource_mask)
+      call swiftest_util_append(self%status,     source%status,       nold, nsrc, lsource_mask)
+      call swiftest_util_append(self%index1,     source%index1,       nold, nsrc, lsource_mask)
+      call swiftest_util_append(self%index2,     source%index2,       nold, nsrc, lsource_mask)
+      call swiftest_util_append(self%id1,        source%id1,          nold, nsrc, lsource_mask)
+      call swiftest_util_append(self%id2,        source%id2,          nold, nsrc, lsource_mask)
+      call swiftest_util_append(self%r1,         source%r1,           nold, nsrc, lsource_mask)
+      call swiftest_util_append(self%r2,         source%r2,           nold, nsrc, lsource_mask)
+      call swiftest_util_append(self%v1,         source%v1,           nold, nsrc, lsource_mask)
+      call swiftest_util_append(self%v2,         source%v2,           nold, nsrc, lsource_mask)
+      call swiftest_util_append(self%level,      source%level,        nold, nsrc, lsource_mask)
       self%nenc = nold + count(lsource_mask(1:nsrc))
 
       return
@@ -55,8 +57,10 @@ module subroutine encounter_util_copy_list(self, source)
       associate(n => source%nenc)
          self%nenc = n
          self%t = source%t
-         self%lvdotr(1:n) = source%lvdotr(1:n) 
+         self%lcollision = source%lcollision
+         self%tcollision(1:n) = source%tcollision(1:n) 
          self%lclosest(1:n) = source%lclosest(1:n) 
+         self%lvdotr(1:n)   = source%lvdotr(1:n) 
          self%status(1:n) = source%status(1:n) 
          self%index1(1:n) = source%index1(1:n)
          self%index2(1:n) = source%index2(1:n)
@@ -66,6 +70,7 @@ module subroutine encounter_util_copy_list(self, source)
          self%r2(:,1:n) = source%r2(:,1:n)
          self%v1(:,1:n) = source%v1(:,1:n)
          self%v2(:,1:n) = source%v2(:,1:n)
+         self%level(1:n) = source%level(1:n)
       end associate
 
       return
@@ -97,8 +102,8 @@ module subroutine encounter_util_dealloc_list(self)
       class(encounter_list), intent(inout) :: self
 
       if (allocated(self%tcollision)) deallocate(self%tcollision)
-      if (allocated(self%lvdotr)) deallocate(self%lvdotr)
       if (allocated(self%lclosest)) deallocate(self%lclosest)
+      if (allocated(self%lvdotr)) deallocate(self%lvdotr)
       if (allocated(self%status)) deallocate(self%status)
       if (allocated(self%index1)) deallocate(self%index1)
       if (allocated(self%index2)) deallocate(self%index2)
@@ -108,6 +113,7 @@ module subroutine encounter_util_dealloc_list(self)
       if (allocated(self%r2)) deallocate(self%r2)
       if (allocated(self%v1)) deallocate(self%v1)
       if (allocated(self%v2)) deallocate(self%v2)
+      if (allocated(self%level)) deallocate(self%level)
 
       return
    end subroutine encounter_util_dealloc_list
@@ -276,11 +282,11 @@ module subroutine encounter_util_index_map(self)
       call encounter_util_get_vals_storage(self, idvals, tvals)
 
       ! Consolidate ids to only unique values
-      call util_unique(idvals,self%idvals,self%idmap)
+      call swiftest_util_unique(idvals,self%idvals,self%idmap)
       self%nid = size(self%idvals)
 
       ! Consolidate time values to only unique values
-      call util_unique(tvals,self%tvals,self%tmap)
+      call swiftest_util_unique(tvals,self%tvals,self%tmap)
       self%nt = size(self%tvals)
 
       return
@@ -339,17 +345,19 @@ module subroutine encounter_util_spill_list(self, discards, lspill_list, ldestru
       integer(I8B) :: nenc_old
 
       associate(keeps => self)
-         call util_spill(keeps%lvdotr, discards%lvdotr, lspill_list, ldestructive)
-         call util_spill(keeps%lclosest, discards%lclosest, lspill_list, ldestructive)
-         call util_spill(keeps%status, discards%status, lspill_list, ldestructive)
-         call util_spill(keeps%index1, discards%index1, lspill_list, ldestructive)
-         call util_spill(keeps%index2, discards%index2, lspill_list, ldestructive)
-         call util_spill(keeps%id1, discards%id1, lspill_list, ldestructive)
-         call util_spill(keeps%id2, discards%id2, lspill_list, ldestructive)
-         call util_spill(keeps%r1, discards%r1, lspill_list, ldestructive)
-         call util_spill(keeps%r2, discards%r2, lspill_list, ldestructive)
-         call util_spill(keeps%v1, discards%v1, lspill_list, ldestructive)
-         call util_spill(keeps%v2, discards%v2, lspill_list, ldestructive)
+         call swiftest_util_spill(keeps%tcollision, discards%tcollision, lspill_list, ldestructive)
+         call swiftest_util_spill(keeps%lvdotr,     discards%lvdotr,     lspill_list, ldestructive)
+         call swiftest_util_spill(keeps%lclosest,   discards%lclosest,   lspill_list, ldestructive)
+         call swiftest_util_spill(keeps%status,     discards%status,     lspill_list, ldestructive)
+         call swiftest_util_spill(keeps%index1,     discards%index1,     lspill_list, ldestructive)
+         call swiftest_util_spill(keeps%index2,     discards%index2,     lspill_list, ldestructive)
+         call swiftest_util_spill(keeps%id1,        discards%id1,        lspill_list, ldestructive)
+         call swiftest_util_spill(keeps%id2,        discards%id2,        lspill_list, ldestructive)
+         call swiftest_util_spill(keeps%r1,         discards%r1,         lspill_list, ldestructive)
+         call swiftest_util_spill(keeps%r2,         discards%r2,         lspill_list, ldestructive)
+         call swiftest_util_spill(keeps%v1,         discards%v1,         lspill_list, ldestructive)
+         call swiftest_util_spill(keeps%v2,         discards%v2,         lspill_list, ldestructive)
+         call swiftest_util_spill(keeps%level,      discards%level,      lspill_list, ldestructive)
 
          nenc_old = keeps%nenc
 

src/fraggle/fraggle_generate.f90

@@ -401,7 +401,7 @@ subroutine fraggle_generate_tan_vel(collision_system, lfailure)
 
             tol = TOL_INIT
             do while(tol < TOL_MIN)
-               call util_minimize_bfgs(objective_function, nfrag-6, v_t_initial(7:nfrag), tol, MAXLOOP, lfailure, v_t_output)
+               call swiftest_util_minimize_bfgs(objective_function, nfrag-6, v_t_initial(7:nfrag), tol, MAXLOOP, lfailure, v_t_output)
                fragments%v_t_mag(7:nfrag) = v_t_output(:)
                ! Now that the KE-minimized values of the i>6 fragments are found, calculate the momentum-conserving solution for tangential velociteis
                v_t_initial(7:nfrag) = fragments%v_t_mag(7:nfrag)
@@ -495,7 +495,7 @@ function solve_fragment_tan_vel(lfailure, v_t_mag_input) result(v_t_mag_output)
                b(1:3) = -L_lin_others(:)
                b(4:6) = fragments%L_budget(:) - fragments%Lspin(:) - L_orb_others(:)
                allocate(v_t_mag_output(nfrag))
-               v_t_mag_output(1:6) = util_solve_linear_system(A, b, 6, lfailure)
+               v_t_mag_output(1:6) = swiftest_util_solve_linear_system(A, b, 6, lfailure)
                if (present(v_t_mag_input)) v_t_mag_output(7:nfrag) = v_t_mag_input(:)
             end associate
             end select
@@ -559,7 +559,7 @@ subroutine fraggle_generate_rad_vel(collision_system, lfailure)
       integer(I4B), parameter               :: MAXLOOP = 100
       real(DP)                              :: ke_radial, tol 
       integer(I4B)                          :: i
-      real(DP), dimension(:), allocatable   :: v_r_initial
+      real(DP), dimension(:), allocatable   :: v_r_initial, v_r_output
       real(DP), dimension(collision_system%fragments%nbody)       :: vnoise
       type(lambda_obj)                      :: objective_function
       character(len=STRMAX)                 :: message
@@ -584,7 +584,8 @@ subroutine fraggle_generate_rad_vel(collision_system, lfailure)
          objective_function = lambda_obj(radial_objective_function)
          tol = TOL_INIT
          do while(tol < TOL_MIN)
-            call util_minimize_bfgs(objective_function, nfrag, v_r_initial, tol, MAXLOOP, lfailure, fragments%v_r_mag)
+            call swiftest_util_minimize_bfgs(objective_function, nfrag, v_r_initial, tol, MAXLOOP, lfailure, v_r_output)
+            fragments%v_r_mag(1:nfrag) = v_r_output(1:nfrag) 
             if (.not.lfailure) exit
             tol = tol * 2 ! Keep increasing the tolerance until we converge on a solution
             v_r_initial(:) = fragments%v_r_mag(:)

src/main/swiftest_driver.f90

@@ -170,5 +170,5 @@ program swiftest_driver
       end associate
    end associate
 
-   call util_exit(SUCCESS)
+   call swiftest_util_exit(SUCCESS)
 end program swiftest_driver

src/modules/base.f90

@@ -387,7 +387,7 @@ subroutine netcdf_check(status, call_identifier)
          if(status /= nf90_noerr) then
             if (present(call_identifier)) write(*,*) "NetCDF error in ",trim(call_identifier)
             write(*,*) trim(nf90_strerror(status))
-            call util_exit(FAILURE)
+            call swiftest_util_exit(FAILURE)
          end if
 
          return

src/modules/collision.f90

@@ -7,6 +7,7 @@
 !! You should have received a copy of the GNU General Public License along with Swiftest. 
 !! If not, see: https://www.gnu.org/licenses. 
 
+
 module collision
    !! author: The Purdue Swiftest Team - David A. Minton, Carlisle A. Wishard, Jennifer L.L. Pouplin, and Jacob R. Elliott
    !!

src/modules/encounter.f90

@@ -22,7 +22,7 @@ module encounter
       integer(I8B)                              :: nenc = 0   !! Total number of encounters
       real(DP)                                  :: t          !! Time of encounter
       logical                                   :: lcollision !! Indicates if the encounter resulted in at least one collision
-      real(DP),     dimension(:),   allocatable :: tcollision!! Time of collision
+      real(DP),     dimension(:),   allocatable :: tcollision !! Time of collision
       logical,      dimension(:),   allocatable :: lclosest   !! indicates that thie pair of bodies is in currently at its closest approach point
       logical,      dimension(:),   allocatable :: lvdotr     !! relative vdotr flag
       integer(I4B), dimension(:),   allocatable :: status     !! status of the interaction
@@ -34,6 +34,7 @@ module encounter
       real(DP),     dimension(:,:), allocatable :: r2         !! the position of body 2 in the encounter
       real(DP),     dimension(:,:), allocatable :: v1         !! the velocity of body 1 in the encounter
       real(DP),     dimension(:,:), allocatable :: v2         !! the velocity of body 2 in the encounter
+      integer(I4B), dimension(:),   allocatable :: level      !! Recursion level (used in SyMBA)
    contains
       procedure :: setup       => encounter_setup_list        !! A constructor that sets the number of encounters and allocates and initializes all arrays  
       procedure :: append      => encounter_util_append_list  !! Appends elements from one structure to another