Rewrote comments describing input parameters. Started process of addi…

…ng system to the step method for bodies to make it more generalizable across all integrators. I'm doing this so that the system object always gets passed down, rather than pulling out individual components for each method

Makefile.Defines

@@ -65,8 +65,8 @@ GPAR = -fopenmp -ftree-parallelize-loops=4
 GMEM = -fsanitize=undefined -fsanitize=address -fsanitize=leak 
 GWARNINGS = -Wall -Warray-bounds  -Wimplicit-interface -Wextra -Warray-temporaries
 
-#FFLAGS  = $(IDEBUG) $(HEAPARR)
-FFLAGS  = -init=snan,arrays -no-wrap-margin -O3 $(STRICTREAL) $(SIMDVEC) $(PAR) 
+FFLAGS  = $(IDEBUG) $(HEAPARR)
+#FFLAGS  = -init=snan,arrays -no-wrap-margin -O3 $(STRICTREAL) $(SIMDVEC) $(PAR) 
 FORTRAN = ifort
 #AR     = xiar
 

src/discard/discard.f90

@@ -10,7 +10,7 @@ module subroutine discard_system(self, param)
       !! Adapted from Hal Levison's Swift routine discard.f
       implicit none
       class(swiftest_nbody_system),  intent(inout) :: self    !! Swiftest system object
-      class(swiftest_parameters), intent(in)    :: param  !! Input collection of  parameters parameters
+      class(swiftest_parameters), intent(in)    :: param  !! Current run configuration parameters of parameters
 
       if (self%tp%nbody == 0) return 
       select type(self)
@@ -51,7 +51,7 @@ module subroutine discard_sun_tp(self, cb, param, t, msys)
       ! Arguments
       class(swiftest_tp),            intent(inout) :: self   !! Swiftest test particle object
       class(swiftest_cb),            intent(inout) :: cb     !! Swiftest central body object
-      class(swiftest_parameters), intent(in)    :: param !!  parameters parameters
+      class(swiftest_parameters), intent(in)    :: param !! parameters
       real(DP),                      intent(in)    :: t      !! Current simulation tim
       real(DP),                      intent(in)    :: msys   !! Total system mass
       ! Internals
@@ -102,7 +102,7 @@ module subroutine discard_peri_tp(self, cb, pl, param, t, msys)
       class(swiftest_tp),            intent(inout) :: self   !! Swiftest test particle object
       class(swiftest_cb),            intent(inout) :: cb     !! Swiftest central body object
       class(swiftest_pl),            intent(inout) :: pl     !! Swiftest massive body object
-      class(swiftest_parameters), intent(in)    :: param !!  parameters parameters
+      class(swiftest_parameters), intent(in)    :: param !! parameters
       real(DP),                      intent(in)    :: t      !! Current simulation tim
       real(DP),                      intent(in)    :: msys   !! Total system mass 
       ! Internals

src/helio/helio_drift.f90

@@ -13,7 +13,7 @@ module subroutine helio_drift_pl(self, cb, param, dt)
       ! Arguments
       class(helio_pl),               intent(inout) :: self   !! Helio test particle data structure
       class(swiftest_cb),            intent(inout) :: cb     !! Helio central body particle data structuree
-      class(swiftest_parameters), intent(in)    :: param !! Input collection of 
+      class(swiftest_parameters), intent(in)    :: param !! Current run configuration parameters of 
       real(DP),                      intent(in)    :: dt     !! Stepsize
       ! Internals
       integer(I4B) :: i !! Loop counter
@@ -105,7 +105,7 @@ module subroutine helio_drift_tp(self, cb, param, dt)
       ! Arguments
       class(helio_tp),               intent(inout) :: self   !! Helio test particle data structure
       class(swiftest_cb),            intent(inout) :: cb     !! Helio central body particle data structuree
-      class(swiftest_parameters), intent(in)    :: param !! Input collection of 
+      class(swiftest_parameters), intent(in)    :: param !! Current run configuration parameters of 
       real(DP),                      intent(in)    :: dt     !! Stepsize
       ! Internals
       integer(I4B) :: i !! Loop counter

src/helio/helio_getacch.f90

@@ -12,7 +12,7 @@ module subroutine helio_getacch_pl(self, cb, param, t)
       ! Arguments
       class(helio_pl),               intent(inout) :: self     !! Helio massive body particle data structure
       class(swiftest_cb),            intent(inout) :: cb       !! Swiftest central body particle data structure
-      class(swiftest_parameters), intent(in)    :: param   !! Input collection of 
+      class(swiftest_parameters), intent(in)    :: param   !! Current run configuration parameters of 
       real(DP),                      intent(in)    :: t        !! Current time
       ! Internals
       logical, save                    :: lmalloc = .true.
@@ -48,7 +48,7 @@ module subroutine helio_getacch_tp(self, cb, pl, param, t, xh)
          class(helio_tp),               intent(inout) :: self   !! Helio test particle data structure
          class(swiftest_cb),                 intent(inout) :: cb     !! Swiftest central body particle data structuree 
          class(whm_pl),                 intent(inout) :: pl     !! WHM massive body particle data structure. 
-         class(swiftest_parameters), intent(in)    :: param !! Input collection of 
+         class(swiftest_parameters), intent(in)    :: param !! Current run configuration parameters of 
          real(DP),                      intent(in)    :: t      !! Current time
          real(DP), dimension(:,:),      intent(in)    :: xh     !! Heliocentric positions of planets
          ! Internals

src/helio/helio_step.f90

@@ -11,7 +11,7 @@ module subroutine helio_step_system(self, param)
       implicit none
       ! Arguments
       class(helio_nbody_system),     intent(inout) :: self    !! Helio nbody system object
-      class(swiftest_parameters), intent(in)    :: param  !! Input collection of on parameters 
+      class(swiftest_parameters), intent(in)    :: param  !! Current run configuration parameters of on parameters 
 
       select type(cb => self%cb)
       class is (helio_cb)
@@ -45,7 +45,7 @@ module subroutine helio_step_pl(self, cb, param, t, dt)
       ! Arguments
       class(helio_pl),               intent(inout) :: self   !! WHM massive body particle data structure
       class(swiftest_cb),            intent(inout) :: cb     !! Helio central body particle data structure
-      class(swiftest_parameters), intent(in)    :: param !! Input collection of 
+      class(swiftest_parameters), intent(in)    :: param !! Current run configuration parameters of 
       real(DP),                      intent(in)    :: t      !! Current time
       real(DP),                      intent(in)    :: dt     !! Stepsize
       ! Internals 
@@ -63,6 +63,7 @@ module subroutine helio_step_pl(self, cb, param, t, dt)
       call self%lindrift(cb, dth, ptbeg)
       call self%getacch(cb, param, t)
       call self%kickvb(dth)
+
       call self%drift(cb, param, dt)
       call self%getacch(cb, param, t + dt)
       call self%kickvb(dth)
@@ -85,7 +86,7 @@ module subroutine helio_step_tp(self, cb, pl, param, t, dt)
       class(helio_tp),                 intent(inout) :: self !! Helio test particle data structure
       class(swiftest_cb),            intent(inout) :: cb     !! Swiftest central body particle data structure
       class(whm_pl),                 intent(inout) :: pl     !! WHM massive body data structure
-      class(swiftest_parameters), intent(in)    :: param !! Input collection of 
+      class(swiftest_parameters), intent(in)    :: param !! Current run configuration parameters of 
       real(DP),                      intent(in)    :: t      !! Current time
       real(DP),                      intent(in)    :: dt     !! Stepsize
       ! Internals

src/io/io.f90

@@ -13,7 +13,7 @@ module subroutine io_param_reader(self, unit, iotype, v_list, iostat, iomsg)
       !! Adapted from Martin Duncan's Swift routine io_init_param.f
       implicit none
       ! Arguments
-      class(swiftest_parameters), intent(inout) :: self       !! Collection of  parameters parameters
+      class(swiftest_parameters), intent(inout) :: self       !! Collection of parameters
       integer, intent(in)                          :: unit       !! File unit number
       character(len=*), intent(in)                 :: iotype     !! Dummy argument passed to the  input/output procedure contains the text from the char-literal-constant, prefixed with DT. 
                                                                  !!    If you do not include a char-literal-constant, the iotype argument contains only DT.
@@ -316,7 +316,7 @@ module subroutine io_param_writer(self, unit, iotype, v_list, iostat, iomsg)
       !! Adapted from Martin Duncan's Swift routine io_dump_param.f
       implicit none
       ! Arguments
-      class(swiftest_parameters),intent(in)     :: self         !! Collection of  parameters parameters
+      class(swiftest_parameters),intent(in)     :: self         !! Collection of parameters
       integer, intent(in)                          :: unit       !! File unit number
       character(len=*), intent(in)                 :: iotype     !! Dummy argument passed to the  input/output procedure contains the text from the char-literal-constant, prefixed with DT. 
                                                                !!    If you do not include a char-literal-constant, the iotype argument contains only DT.
@@ -405,7 +405,7 @@ module subroutine io_dump_param(self, param_file_name, t, dt)
       !! Adapted from Martin Duncan's Swift routine io_dump_param.f
       implicit none
       ! Arguments
-      class(swiftest_parameters),intent(in) :: self    !! Output collection of  parameters
+      class(swiftest_parameters),intent(in) :: self    !! Output collection of parameters
       character(len=*), intent(in)             :: param_file_name !! Parameter input file name (i.e. param.in)
       real(DP),intent(in)                      :: t       !! Current simulation time
       real(DP),intent(in)                      :: dt      !! Step size
@@ -444,7 +444,7 @@ module subroutine io_dump_swiftest(self, param, t, dt, msg)
       implicit none
       ! Arguments
       class(swiftest_base),          intent(inout) :: self   !! Swiftest base object
-      class(swiftest_parameters), intent(in)    :: param !! Input collection of  parameters parameters 
+      class(swiftest_parameters), intent(in)    :: param !! Current run configuration parameters of parameters 
       real(DP),                      intent(in)    :: t      !! Current simulation time
       real(DP),                      intent(in)    :: dt     !! Stepsize
       character(*), optional,        intent(in)    :: msg  !! Message to display with dump operation
@@ -483,7 +483,7 @@ module subroutine io_dump_system(self, param, t, dt, msg)
       implicit none
       ! Arguments
       class(swiftest_nbody_system),  intent(inout) :: self    !! Swiftest system object
-      class(swiftest_parameters), intent(in)    :: param  !! Input collection of  parameters parameters 
+      class(swiftest_parameters), intent(in)    :: param  !! Current run configuration parameters of parameters 
       real(DP),                      intent(in)    :: t       !! Current simulation time
       real(DP),                      intent(in)    :: dt      !! Stepsize
       character(*), optional,        intent(in)    :: msg  !! Message to display with dump operation
@@ -636,7 +636,7 @@ module subroutine io_read_body_in(self, param)
       implicit none
       ! Arguments
       class(swiftest_body),          intent(inout) :: self   !! Swiftest particle object
-      class(swiftest_parameters), intent(inout) :: param !! Input collection of  parameters parameters
+      class(swiftest_parameters), intent(inout) :: param !! Current run configuration parameters of parameters
       ! Internals
       integer(I4B), parameter       :: LUN = 7              !! Unit number of input file
       integer(I4B)                  :: iu = LUN
@@ -776,7 +776,7 @@ module subroutine io_read_param_in(self, param_file_name)
       !! Adapted from Martin Duncan's Swift routine io_init_param.f
       implicit none
       ! Arguments
-      class(swiftest_parameters),intent(out) :: self             !! Input collection of  parameters parameters
+      class(swiftest_parameters),intent(out) :: self             !! Current run configuration parameters of parameters
       character(len=*), intent(in)              :: param_file_name !! Parameter input file name (i.e. param.in)
       ! Internals
       integer(I4B), parameter :: LUN = 7                 !! Unit number of input file
@@ -870,7 +870,7 @@ module subroutine io_read_frame_body(self, iu, param, form, t, ierr)
       ! Arguments
       class(swiftest_body),          intent(inout) :: self    !! Swiftest particle object
       integer(I4B),                  intent(inout) :: iu      !! Unit number for the output file to write frame to
-      class(swiftest_parameters), intent(inout) :: param  !! Input collection of  parameters parameters 
+      class(swiftest_parameters), intent(inout) :: param  !! Current run configuration parameters of parameters 
       character(*),                  intent(in)    :: form    !! Input format code ("XV" or "EL")
       real(DP),                      intent(out)   :: t       !! Simulation time
       integer(I4B),                  intent(out)   :: ierr    !! Error code
@@ -932,7 +932,7 @@ module subroutine io_read_frame_cb(self, iu, param, form, t, ierr)
       ! Arguments
       class(swiftest_cb),            intent(inout) :: self     !! Swiftest central body object
       integer(I4B),                  intent(inout) :: iu       !! Unit number for the output file to write frame to
-      class(swiftest_parameters), intent(inout) :: param   !! Input collection of  parameters parameters 
+      class(swiftest_parameters), intent(inout) :: param   !! Current run configuration parameters of parameters 
       character(*),                  intent(in)    :: form     !! Input format code ("XV" or "EL")
       real(DP),                      intent(out)   :: t        !! Simulation time
       integer(I4B),                  intent(out)   :: ierr     !! Error cod
@@ -966,7 +966,7 @@ module subroutine io_read_frame_system(self, iu, param, form, t, ierr)
       ! Arguments
       class(swiftest_nbody_system),  intent(inout) :: self   !! Swiftest system object
       integer(I4B),                  intent(inout) :: iu     !! Unit number for the output file to write frame to
-      class(swiftest_parameters), intent(inout) :: param !! Input collection of  parameters parameters 
+      class(swiftest_parameters), intent(inout) :: param !! Current run configuration parameters of parameters 
       character(*),                  intent(in)    :: form   !! Input format code ("XV" or "EL")
       real(DP),                      intent(out)   :: t      !! Current simulation time
       integer(I4B),                  intent(out)   :: ierr   !! Error code
@@ -1042,7 +1042,7 @@ module subroutine io_read_initialize_system(self, param)
       implicit none
       ! Arguments
       class(swiftest_nbody_system),  intent(inout) :: self    !! Swiftest system object
-      class(swiftest_parameters), intent(inout) :: param  !! Input collection of  parameters parameters
+      class(swiftest_parameters), intent(inout) :: param  !! Current run configuration parameters of parameters
 
       call self%cb%initialize(param)
       call self%pl%initialize(param)
@@ -1063,7 +1063,7 @@ module subroutine io_write_discard(self, param, discards)
       implicit none
       ! Arguments
       class(swiftest_nbody_system),  intent(inout) :: self     !! Swiftest system object
-      class(swiftest_parameters), intent(in)    :: param   !! Input collection of  parameters parameters 
+      class(swiftest_parameters), intent(in)    :: param   !! Current run configuration parameters of parameters 
       class(swiftest_body),          intent(inout) :: discards !! Swiftest discard object 
       ! Internals
       integer(I4B), parameter   :: LUN = 40
@@ -1196,7 +1196,7 @@ module subroutine io_write_frame_body(self, iu, param, t, dt)
       ! Arguments
       class(swiftest_body),          intent(in)    :: self   !! Swiftest particle object
       integer(I4B),                  intent(inout) :: iu     !! Unit number for the output file to write frame to
-      class(swiftest_parameters), intent(in)    :: param !! Input collection of  parameters parameters 
+      class(swiftest_parameters), intent(in)    :: param !! Current run configuration parameters of parameters 
       real(DP),                      intent(in)    :: t      !! Current simulation time
       real(DP),                      intent(in)    :: dt     !! Step size
 
@@ -1252,7 +1252,7 @@ module subroutine io_write_frame_cb(self, iu, param, t, dt)
       ! Arguments
       class(swiftest_cb),            intent(in)    :: self   !! Swiftest central body object 
       integer(I4B),                  intent(inout) :: iu     !! Unit number for the output file to write frame to
-      class(swiftest_parameters), intent(in)    :: param !! Input collection of  parameters parameters 
+      class(swiftest_parameters), intent(in)    :: param !! Current run configuration parameters of parameters 
       real(DP),                      intent(in)    :: t      !! Current simulation time
       real(DP),                      intent(in)    :: dt     !! Step size
 
@@ -1288,7 +1288,7 @@ module subroutine io_write_frame_system(self, iu, param, t, dt)
       ! Arguments
       class(swiftest_nbody_system),  intent(in)    :: self   !! Swiftest system object
       integer(I4B),                  intent(inout) :: iu     !! Unit number for the output file to write frame to
-      class(swiftest_parameters), intent(in)    :: param !! Input collection of  parameters parameters 
+      class(swiftest_parameters), intent(in)    :: param !! Current run configuration parameters of parameters 
       real(DP),                      intent(in)    :: t      !! Current simulation time
       real(DP),                      intent(in)    :: dt     !! Step size
       ! Internals

src/main/swiftest_driver.f90

@@ -12,7 +12,7 @@ program swiftest_driver
    class(swiftest_nbody_system), allocatable  :: nbody_system     !! Polymorphic object containing the nbody system to be integrated
    type(swiftest_parameters)               :: param
    integer(I4B)                               :: integrator       !! Integrator type code (see swiftest_globals for symbolic names)
-   character(len=:),allocatable               :: param_file_name !! Name of the file containing user-defined parameters parameters
+   character(len=:),allocatable               :: param_file_name !! Name of the file containing user-defined parameters
    integer(I4B)                               :: ierr             !! I/O error code 
    logical                                    :: lfirst           !! Flag indicating that this is the first time through the main loop
    integer(I8B)                               :: iloop            !! Loop counter