Pull Request with Dump File Changes

Makefile

@@ -45,7 +45,6 @@
 #******************************************************************************
 
 SWIFTEST_MODULES =   swiftest_globals.f90 \
-                     user.f90 \
                      swiftest_data_structures.f90 \
 							lambda_function.f90\
                      module_swifter.f90 \
@@ -135,11 +134,6 @@ lib:
 	  ln -s $(SWIFTEST_HOME)/Makefile.Defines .; \
 	  ln -s $(SWIFTEST_HOME)/Makefile .; \
 	  make libdir
-	cd $(SWIFTEST_HOME)/src/user; \
-	  rm -f Makefile.Defines Makefile; \
-	  ln -s $(SWIFTEST_HOME)/Makefile.Defines .; \
-	  ln -s $(SWIFTEST_HOME)/Makefile .; \
-	  make libdir2
 	cd $(SWIFTEST_HOME)/src/util; \
 	  rm -f Makefile.Defines Makefile; \
 	  ln -s $(SWIFTEST_HOME)/Makefile.Defines .; \
@@ -186,7 +180,6 @@ clean:
 	cd $(SWIFTEST_HOME)/src/rmvs;    rm -f Makefile.Defines Makefile *.gc*
 	cd $(SWIFTEST_HOME)/src/swiftest;   rm -f Makefile.Defines Makefile *.gc*
 	cd $(SWIFTEST_HOME)/src/symba;   rm -f Makefile.Defines Makefile *.gc*
-	cd $(SWIFTEST_HOME)/src/user;    rm -f Makefile.Defines Makefile *.gc*
 	cd $(SWIFTEST_HOME)/src/util;    rm -f Makefile.Defines Makefile *.gc*
 	cd $(SWIFTEST_HOME)/src/main;    rm -f Makefile.Defines Makefile *.gc*
 	cd $(SWIFTEST_HOME)/src/tool;    rm -f Makefile.Defines Makefile *.gc*

src/io/io_conservation_report.f90

@@ -12,7 +12,7 @@ module subroutine io_conservation_report(t, symba_plA, npl, j2rp2, j4rp4, param,
       type(symba_pl),              intent(inout) :: symba_plA    !! Swiftest planet data structure
       integer(I4B),                intent(in)    :: npl          !! Number of massive bodies
       real(DP),                    intent(in)    :: j2rp2, j4rp4 !! Central body oblateness terms
-      type(user_input_parameters), intent(inout)    :: param        !! Input colleciton of user-defined parameters
+      type(swiftest_parameters), intent(inout)    :: param        !! Input colleciton of user-defined parameters
       logical,                     intent(in)    :: lterminal    !! Indicates whether to output information to the terminal screen
       ! Internals
       real(DP), dimension(NDIM)       :: Ltot_now,  Lorbit_now,  Lspin_now

src/user/user_dump_param.f90 → src/io/io_dump_param.f90

@@ -1,21 +1,22 @@
-submodule(user) s_user_dump_param
+submodule(swiftest_data_structures) s_io_dump_param
 contains
-   module subroutine user_dump_param(param,t)
+   module subroutine io_dump_param(param, t, swiftest_plA)
       !! author: David A. Minton
       !!
       !! Dump integration parameters to file
       !!
       !! Adapted from David E. Kaufmann's Swifter routine io_dump_param.f90
       !! Adapted from Martin Duncan's Swift routine io_dump_param.f
-      use swiftest, except_this_one => user_dump_param
+      use swiftest, except_this_one => io_dump_param
       implicit none
 
       ! Arguments
-      class(user_input_parameters),intent(in)  :: param    !! Output collection of user-defined parameters
-      real(DP),intent(in)                 :: t        !! Current simulation tim
+      class(swiftest_parameters),intent(in)  :: param    !! Output collection of user-defined parameters
+      real(DP),intent(in)                      :: t        !! Current simulation tim
+      type(swiftest_pl), intent(inout)         :: swiftest_plA
 
       ! Internals
-      type(user_input_parameters)  :: param_dump !! Data type of dumped parameter file
+      type(swiftest_parameters)  :: param_dump !! Data type of dumped parameter file
       integer(I4B), parameter :: LUN = 7 !! Unit number of output file
       integer(I4B)            :: ierr     !! Error code
       integer(I4B), save      :: idx = 1  !! Index of current dump file. Output flips between 2 files for extra security
@@ -38,7 +39,7 @@ module subroutine user_dump_param(param,t)
       !! todo: Currently this procedure does not work in user-defined derived-type input mode 
       !!    due to compiler incompatabilities
       !write(LUN,'(DT)') param_dump
-      call param_dump%udio_writer(LUN, iotype="none",v_list=(/0/),iostat=ierr,iomsg=error_message)
+      call param_dump%udio_writer(LUN, iotype="none",v_list=(/0/),iostat=ierr,iomsg=error_message, swiftest_plA=swiftest_plA)
       call random_seed(put = param_dump%seed)
 
       if (idx == 2) then
@@ -51,5 +52,5 @@ module subroutine user_dump_param(param,t)
 
       return
 
-   end subroutine user_dump_param
-end submodule s_user_dump_param
+   end subroutine io_dump_param
+end submodule s_io_dump_param

src/io/io_dump_pl.f90

@@ -43,7 +43,7 @@ SUBROUTINE io_dump_pl(npl, swiftest_plA, param)
 ! Arguments
      INTEGER(I4B), INTENT(IN)         :: npl
      TYPE(swiftest_pl), INTENT(INOUT) :: swiftest_plA
-      type(user_input_parameters),intent(inout) :: param
+      type(swiftest_parameters),intent(inout) :: param
 
 ! Internals
    INTEGER(I4B)                     :: ierr

src/io/io_dump_pl_symba.f90

@@ -12,7 +12,7 @@ subroutine io_dump_pl_symba(npl, symba_plA, param)
 ! arguments
    integer(I4B), intent(in)         :: npl
    type(symba_pl), intent(inout) :: symba_plA
-   type(user_input_parameters),intent(inout) :: param
+   type(swiftest_parameters),intent(inout) :: param
 
 ! internals
    integer(I4B)                     :: ierr

src/user/user_get_token.f90 → src/io/io_get_token.f90

@@ -1,13 +1,13 @@
-submodule(user) s_user_get_token
+submodule(swiftest_data_structures) s_io_get_token
 contains
-   module function user_get_token(buffer, ifirst, ilast, ierr) result(token)
+   module function io_get_token(buffer, ifirst, ilast, ierr) result(token)
       !! author: David A. Minton
       !!
       !! Retrieves a character token from an input string. Here a token is defined as any set of contiguous non-blank characters not 
       !! beginning with or containing "!". If "!" is present, any remaining part of the buffer including the "!" is ignored
       !!
       !! Adapted from David E. Kaufmann's Swifter routine user_get_token.f90
-      use swiftest, except_this_one => user_get_token
+      use swiftest, except_this_one => io_get_token
       implicit none
 
       ! Arguments
@@ -49,5 +49,5 @@ module function user_get_token(buffer, ifirst, ilast, ierr) result(token)
 
       return
 
-   end function user_get_token
-end submodule s_user_get_token
+   end function io_get_token
+end submodule s_io_get_token

src/user/user_read_param_in.f90 → src/io/io_read_param_in.f90

@@ -1,19 +1,20 @@
-submodule (user) s_user_read_param_in
+submodule (swiftest_data_structures) s_io_read_param_in
 contains
-   module subroutine user_read_param_in(param,inparfile) 
+   module subroutine io_read_param_in(param, inparfile, swiftest_plA) 
       !! author: The Purdue Swiftest Team -  David A. Minton, Carlisle A. Wishard, Jennifer L.L. Pouplin, and Jacob R. Elliott
       !!
       !! Read in parameters for the integration
       !!
       !! Adapted from David E. Kaufmann's Swifter routine io_init_param.f90
       !! Adapted from Martin Duncan's Swift routine io_init_param.f
       !$ use omp_lib
-      use swiftest, except_this_one => user_read_param_in
+      use swiftest, except_this_one => io_read_param_in
       implicit none
 
       ! Arguments
-      class(user_input_parameters),intent(out) :: param         !! Input collection of user-defined parameters
-      character(*), intent(in)            :: inparfile     !! Parameter input file name (i.e. param.in)
+      class(swiftest_parameters),intent(out)   :: param         !! Input collection of user-defined parameters
+      character(*), intent(in)                 :: inparfile     !! Parameter input file name (i.e. param.in)
+      type(swiftest_pl), intent(inout)         :: swiftest_plA
 
       ! Internals
       integer(I4B), parameter :: LUN = 7                 !! Unit number of input file
@@ -35,7 +36,7 @@ module subroutine user_read_param_in(param,inparfile)
       !!    as the newline characters are ignored in the input file when compiled in ifort.
 
       !read(LUN,'(DT)', iostat= ierr, iomsg = error_message) param
-      call param%udio_reader(LUN,iotype="none",v_list=(/0/),iostat=ierr,iomsg=error_message)
+      call param%udio_reader(LUN,iotype="none",v_list=(/0/),iostat=ierr,iomsg=error_message, swiftest_plA=swiftest_plA)
       if (ierr /= 0) then
          write(*,*) 'Swiftest error reading ', trim(adjustl(inparfile))
          write(*,*) ierr,trim(adjustl(error_message))
@@ -117,6 +118,6 @@ module subroutine user_read_param_in(param,inparfile)
 
       return 
 
-   end subroutine user_read_param_in
+   end subroutine io_read_param_in
 
-end submodule s_user_read_param_in
+end submodule s_io_read_param_in

src/io/io_read_particle.f90

@@ -10,7 +10,7 @@ module subroutine io_read_particle_pl(swiftest_plA, param)
       implicit none
       ! Arguments
       class(swiftest_pl),          intent(inout) :: swiftest_plA   !! Swiftest massive body structure
-      type(user_input_parameters), intent(in) :: param   !! Input colleciton of user-defined parameters
+      type(swiftest_parameters), intent(in) :: param   !! Input colleciton of user-defined parameters
       ! Internals
       integer(I4B), parameter   :: lun = 22
       integer(I4B)              :: i, ierr, id, idx

src/user/user_udio_reader.f90 → src/io/io_udio_reader.f90

@@ -1,6 +1,6 @@
-submodule (user) s_user_udio_reader
+submodule (swiftest_data_structures) s_io_udio_reader
 contains
-   module subroutine user_udio_reader(param, unit, iotype, v_list, iostat, iomsg) 
+   module subroutine io_udio_reader(param, unit, iotype, v_list, iostat, iomsg, swiftest_plA) 
       !! author: The Purdue Swiftest Team -  David A. Minton, Carlisle A. Wishard, Jennifer L.L. Pouplin, and Jacob R. Elliott
       !!
       !! Read in parameters for the integration
@@ -12,16 +12,17 @@ module subroutine user_udio_reader(param, unit, iotype, v_list, iostat, iomsg)
       !! Adapted from Martin Duncan's Swift routine io_init_param.f
       !$ use omp_lib
       !use util, only: util_exit ! IMPLEMENTATION TBD
-      use swiftest, except_this_one => user_udio_reader
+      use swiftest, except_this_one => io_udio_reader
       implicit none
 
       ! Arguments
-      class(user_input_parameters),intent(inout)  :: param         !! Input collection of user-defined parameters
+      class(swiftest_parameters),intent(inout)  :: param         !! Input collection of user-defined parameters
       integer, intent(in)                    :: unit        
       character(len=*), intent(in)           :: iotype
       integer, intent(in)                    :: v_list(:)
       integer, intent(out)                   :: iostat
       character(len=*), intent(inout)        :: iomsg
+      type(swiftest_pl), intent(inout)       :: swiftest_plA
 
       ! Internals
       logical                 :: t0_set = .false.        !! Is the initial time set in the input file?
@@ -46,11 +47,11 @@ module subroutine user_udio_reader(param, unit, iotype, v_list, iostat, iomsg)
          if ((ilength /= 0)) then 
             ifirst = 1
             ! Read the pair of tokens. The first one is the parameter name, the second is the value.
-            param_name = user_get_token(line_trim, ifirst, ilast, iostat)
+            param_name = io_get_token(line_trim, ifirst, ilast, iostat)
             if (param_name == '') cycle ! No parameter name (usually because this line is commented out)
             call util_toupper(param_name)
             ifirst = ilast + 1
-            param_value = user_get_token(line_trim, ifirst, ilast, iostat)
+            param_value = io_get_token(line_trim, ifirst, ilast, iostat)
             select case (param_name)
             case ("T0")
                read(param_value, *) param%t0
@@ -106,7 +107,7 @@ module subroutine user_udio_reader(param, unit, iotype, v_list, iostat, iomsg)
             case ("CHK_QMIN_RANGE")
                read(param_value, *) param%qmin_alo
                ifirst = ilast + 1
-               param_value = user_get_token(line, ifirst, ilast, iostat)
+               param_value = io_get_token(line, ifirst, ilast, iostat)
                read(param_value, *) param%qmin_ahi
             case ("ENC_OUT")
                param%encounter_file = param_value
@@ -167,13 +168,13 @@ module subroutine user_udio_reader(param, unit, iotype, v_list, iostat, iomsg)
                   allocate(param%seed(nseeds))
                   do i = 1, nseeds
                      ifirst = ilast + 1
-                     param_value = user_get_token(line, ifirst, ilast, iostat) 
+                     param_value = io_get_token(line, ifirst, ilast, iostat) 
                      read(param_value, *) param%seed(i)
                   end do
                else ! Seed array in file is too small
                   do i = 1, nseeds_from_file
                      ifirst = ilast + 1
-                     param_value = user_get_token(line, ifirst, ilast, iostat) 
+                     param_value = io_get_token(line, ifirst, ilast, iostat) 
                      read(param_value, *) param%seed(i)
                   end do
                   param%seed(nseeds_from_file+1:nseeds) = [(param%seed(1) - param%seed(nseeds_from_file) + i, i=nseeds_from_file+1, nseeds)]
@@ -193,24 +194,59 @@ module subroutine user_udio_reader(param, unit, iotype, v_list, iostat, iomsg)
                read(param_value, *) param%Ltot_orig(1)
                do i = 2, NDIM
                   ifirst = ilast + 1
-                  param_value = user_get_token(line, ifirst, ilast, iostat) 
+                  param_value = io_get_token(line, ifirst, ilast, iostat) 
                   read(param_value, *) param%Ltot_orig(i)
                end do
                   param%Lmag_orig = norm2(param%Ltot_orig(:))
             case("LORBIT_ORIG")
                read(param_value, *) param%Lorbit_orig(1)
                do i = 2, NDIM
                   ifirst = ilast + 1
-                  param_value = user_get_token(line, ifirst, ilast, iostat) 
+                  param_value = io_get_token(line, ifirst, ilast, iostat) 
                   read(param_value, *) param%Lorbit_orig(i)
                end do
             case("LSPIN_ORIG")
                read(param_value, *) param%Lspin_orig(1)
                do i = 2, NDIM
                   ifirst = ilast + 1
-                  param_value = user_get_token(line, ifirst, ilast, iostat) 
+                  param_value = io_get_token(line, ifirst, ilast, iostat) 
                   read(param_value, *) param%Lspin_orig(i)
                end do
+            case("LCB_INITIAL")
+               read(param_value, *) swiftest_plA%Lcb_initial(1)
+               do i = 2, NDIM
+                  ifirst = ilast + 1
+                  param_value = io_get_token(line, ifirst, ilast, iostat) 
+                  read(param_value, *) swiftest_plA%Lcb_initial(i)
+               end do
+            case("DLCB")
+               read(param_value, *) swiftest_plA%dLcb(1)
+               do i = 2, NDIM
+                  ifirst = ilast + 1
+                  param_value = io_get_token(line, ifirst, ilast, iostat) 
+                  read(param_value, *) swiftest_plA%dLcb(i)
+               end do
+            case("LESCAPE")
+               read(param_value, *) swiftest_plA%Lescape(1)
+               do i = 2, NDIM
+                  ifirst = ilast + 1
+                  param_value = io_get_token(line, ifirst, ilast, iostat) 
+                  read(param_value, *) swiftest_plA%Lescape(i)
+               end do
+            case("MCB_INITIAL")
+               read(param_value, *) swiftest_plA%Mcb_initial 
+            case("DMCB")
+               read(param_value, *) swiftest_plA%dMcb
+            case("MESCAPE")
+               read(param_value, *) swiftest_plA%Mescape 
+            case("RCB_INITIAL")
+               read(param_value, *) swiftest_plA%Rcb_initial 
+            case("DRCB")
+               read(param_value, *) swiftest_plA%dRcb
+            case("ECOLLISIONS")
+               read(param_value, *) swiftest_plA%Ecollisions
+            case("EUNTRACKED")
+               read(param_value, *) swiftest_plA%Euntracked
             case default
                write(iomsg,*) "Unknown parameter -> ",param_name
                iostat = -1
@@ -299,6 +335,6 @@ module subroutine user_udio_reader(param, unit, iotype, v_list, iostat, iomsg)
 
       return 
 
-   end subroutine user_udio_reader
+   end subroutine io_udio_reader
 
-end submodule s_user_udio_reader
+end submodule s_io_udio_reader

src/user/user_udio_writer.f90 → src/io/io_udio_writer.f90

@@ -1,22 +1,23 @@
-submodule(user) s_user_udio_writer
+submodule(swiftest_data_structures) s_io_udio_writer
 contains
-   module subroutine user_udio_writer(param, unit, iotype, v_list, iostat, iomsg) 
+   module subroutine io_udio_writer(param, unit, iotype, v_list, iostat, iomsg, swiftest_plA) 
       !! author: David A. Minton
       !!
       !! Dump integration parameters to file
       !!
       !! Adapted from David E. Kaufmann's Swifter routine io_dump_param.f90
       !! Adapted from Martin Duncan's Swift routine io_dump_param.f
-      use swiftest, except_this_one => user_udio_writer
+      use swiftest, except_this_one => io_udio_writer
       implicit none
 
       ! Arguments
-      class(user_input_parameters),intent(in)  :: param         !! Output collection of user-defined parameters
+      class(swiftest_parameters),intent(in)  :: param         !! Output collection of user-defined parameters
       integer, intent(in)                 :: unit        
       character(len=*), intent(in)        :: iotype
       integer, intent(in)                 :: v_list(:)
       integer, intent(out)                :: iostat
       character(len=*), intent(inout)     :: iomsg
+      type(swiftest_pl), intent(inout)    :: swiftest_plA
 
       ! Internals
       character(*),parameter :: Ifmt  = '(I0)'         !! Format label for integer values
@@ -114,12 +115,23 @@ module subroutine user_udio_writer(param, unit, iotype, v_list, iostat, iomsg)
          write(unit, '("LTOT_ORIG  ",3(1X,ES25.17))') param%Ltot_orig(:)
          write(unit, '("LORBIT_ORIG",3(1X,ES25.17))') param%Lorbit_orig(:)
          write(unit, '("LSPIN_ORIG ",3(1X,ES25.17))') param%Lspin_orig(:)
+         write(unit, '("LCB_INITIAL ",3(1X,ES25.17))') swiftest_pLA%Lcb_initial(:)
+         write(unit, '("DLCB ",3(1X,ES25.17))') swiftest_pLA%dLcb(:)
+         write(unit, '("LESCAPE ",3(1X,ES25.17))') swiftest_pLA%Lescape(:)
+
+         write(param_name, Afmt) "MCB_INITIAL"; write(param_value, Rfmt) swiftest_pLA%Mcb_initial; write(unit, Afmt) adjustl(param_name), adjustl(param_value)
+         write(param_name, Afmt) "DMCB"; write(param_value, Rfmt) swiftest_pLA%dMcb; write(unit, Afmt) adjustl(param_name), adjustl(param_value)
+         write(param_name, Afmt) "MESCAPE"; write(param_value, Rfmt) swiftest_pLA%Mescape; write(unit, Afmt) adjustl(param_name), adjustl(param_value)
+         write(param_name, Afmt) "RCB_INITIAL"; write(param_value, Rfmt) swiftest_pLA%Rcb_initial; write(unit, Afmt) adjustl(param_name), adjustl(param_value)
+         write(param_name, Afmt) "DRCB"; write(param_value, Rfmt) swiftest_pLA%dRcb; write(unit, Afmt) adjustl(param_name), adjustl(param_value)   
+         write(param_name, Afmt) "ECOLLISIONS"; write(param_value, Rfmt) swiftest_pLA%Ecollisions; write(unit, Afmt) adjustl(param_name), adjustl(param_value)
+         write(param_name, Afmt) "EUNTRACKED"; write(param_value, Rfmt) swiftest_pLA%Euntracked; write(unit, Afmt) adjustl(param_name), adjustl(param_value)
       end if
       write(param_name, Afmt) "FIRSTKICK"; write(param_value, Lfmt) param%lfirstkick; write(unit, Afmt) adjustl(param_name), adjustl(param_value)
 
       iostat = 0
 
       return
 
-   end subroutine user_udio_writer
-end submodule s_user_udio_writer
+   end subroutine io_udio_writer
+end submodule s_io_udio_writer

src/io/io_write_particle.f90

@@ -11,7 +11,7 @@ module subroutine io_write_particle_pl(swiftest_plA, idx, param)
       ! Arguments
       class(swiftest_pl),          intent(in) :: swiftest_plA !! Swiftest massive body structure
       integer(I4B), dimension(:),  intent(in) :: idx       !! Array of particle indices to append to the particle file
-      type(user_input_parameters), intent(in) :: param     !! Input colleciton of user-defined parameters
+      type(swiftest_parameters), intent(in) :: param     !! Input colleciton of user-defined parameters
       ! Internals
       logical, save             :: lfirst = .true.
       integer(I4B), parameter   :: lun = 22