! ***********************************************************************
!
!   Copyright (C) 2010  Bill Paxton
!
!   this file is part of mesa.
!
!   mesa is free software; you can redistribute it and/or modify
!   it under the terms of the gnu general library public license as published
!   by the free software foundation; either version 2 of the license, or
!   (at your option) any later version.
!
!   mesa is distributed in the hope that it will be useful, 
!   but without any warranty; without even the implied warranty of
!   merchantability or fitness for a particular purpose.  see the
!   gnu library general public license for more details.
!
!   you should have received a copy of the gnu library general public license
!   along with this software; if not, write to the free software
!   foundation, inc., 59 temple place, suite 330, boston, ma 02111-1307 usa
!
! ***********************************************************************
 
      module run_star_extras

      use star_lib
      use star_def
      use const_def

      use alert_lib
      use mlt_def
      
      implicit none
      
      ! these routines are called by the standard run_star check_model
      contains
      
      ! include 'standard_run_star_extras.inc'
      
      subroutine extras_controls(s, ierr)
         type (star_info), pointer :: s
         integer, intent(out) :: ierr
         ierr = 0
         
         ! this is the place to set any procedure pointers you want to change
         ! e.g., other_wind, other_mixing, other_energy  (see star_data.inc)

         s % other_mixing => pavel_mixing_micro
         
         
      end subroutine extras_controls
      
      
      integer function extras_startup(s, id, restart, ierr)
         type (star_info), pointer :: s
         integer, intent(in) :: id
         logical, intent(in) :: restart
         integer, intent(out) :: ierr
         ierr = 0
         extras_startup = 0
         if (.not. restart) then
            call alloc_extra_info(s)
         else ! it is a restart
            call unpack_extra_info(s)
         end if
      end function extras_startup
      

      ! returns either keep_going, retry, backup, or terminate.
      integer function extras_check_model(s, id, id_extra)
         type (star_info), pointer :: s
         integer, intent(in) :: id, id_extra
         extras_check_model = keep_going         
         if (.false. .and. s% star_mass_h1 < 0.35d0) then
            ! stop when star hydrogen mass drops to specified level
            extras_check_model = terminate
            write(*, *) 'have reached desired hydrogen mass'
            return
         end if
      end function extras_check_model


      integer function how_many_extra_log_columns(s, id, id_extra)
         type (star_info), pointer :: s
         integer, intent(in) :: id, id_extra
         how_many_extra_log_columns = 0
      end function how_many_extra_log_columns
      
      
      subroutine data_for_extra_log_columns(s, id, id_extra, n, names, vals, ierr)
         type (star_info), pointer :: s
         integer, intent(in) :: id, id_extra, n
         character (len=maxlen_log_column_name) :: names(n)
         real(dp) :: vals(n)
         integer, intent(out) :: ierr
         
         !note: do NOT add these names to log_columns.list
         ! the log_columns.list is only for the built-in log column options.
         ! it must not include the new column names you are adding here.
         
         ierr = 0
      end subroutine data_for_extra_log_columns

      
      integer function how_many_extra_profile_columns(s, id, id_extra)
         type (star_info), pointer :: s
         integer, intent(in) :: id, id_extra
         how_many_extra_profile_columns = 0
      end function how_many_extra_profile_columns
      
      
      subroutine data_for_extra_profile_columns(s, id, id_extra, n, nz, names, vals, ierr)
         type (star_info), pointer :: s
         integer, intent(in) :: id, id_extra, n, nz
         character (len=maxlen_profile_column_name) :: names(n)
         real(dp) :: vals(nz,n)
         integer, intent(out) :: ierr
         integer :: k
         ierr = 0
         
         !note: do NOT add these names to profile_columns.list
         ! the profile_columns.list is only for the built-in profile column options.
         ! it must not include the new column names you are adding here.

         ! here is an example for adding a profile column
         !if (n /= 1) stop 'data_for_extra_profile_columns'
         !names(1) = 'beta'
         !do k = 1, nz
         !   vals(k,1) = s% Pgas(k)/s% P(k)
         !end do
         
      end subroutine data_for_extra_profile_columns
      

      ! returns either keep_going or terminate.
      ! note: cannot request retry or backup; extras_check_model can do that.
      integer function extras_finish_step(s, id, id_extra)
         type (star_info), pointer :: s
         integer, intent(in) :: id, id_extra
         integer :: ierr
         extras_finish_step = keep_going
         call store_extra_info(s)

         ! to save a profile, 
            ! s% need_to_save_profiles_now = .true.
         ! to update the star log,
            ! s% need_to_update_logfile_now = .true.
            
      end function extras_finish_step
      
      
      subroutine extras_after_evolve(s, id, id_extra, ierr)
         type (star_info), pointer :: s
         integer, intent(in) :: id, id_extra
         integer, intent(out) :: ierr
         ierr = 0
      end subroutine extras_after_evolve
      
      
      ! routines for saving and restoring extra data so can do restarts
         
         ! put these defs at the top and delete from the following routines
         !integer, parameter :: extra_info_alloc = 1
         !integer, parameter :: extra_info_get = 2
         !integer, parameter :: extra_info_put = 3
      
      
      subroutine alloc_extra_info(s)
         integer, parameter :: extra_info_alloc = 1
         type (star_info), pointer :: s
         call move_extra_info(s,extra_info_alloc)
      end subroutine alloc_extra_info
      
      
      subroutine unpack_extra_info(s)
         integer, parameter :: extra_info_get = 2
         type (star_info), pointer :: s
         call move_extra_info(s,extra_info_get)
      end subroutine unpack_extra_info
      
      
      subroutine store_extra_info(s)
         integer, parameter :: extra_info_put = 3
         type (star_info), pointer :: s
         call move_extra_info(s,extra_info_put)
      end subroutine store_extra_info
      
      
      subroutine move_extra_info(s,op)
         integer, parameter :: extra_info_alloc = 1
         integer, parameter :: extra_info_get = 2
         integer, parameter :: extra_info_put = 3
         type (star_info), pointer :: s
         integer, intent(in) :: op
         
         integer :: i, j, num_ints, num_dbls, ierr
         
         i = 0
         ! call move_int or move_flg    
         num_ints = i
         
         i = 0
         ! call move_dbl       
         
         num_dbls = i
         
         if (op /= extra_info_alloc) return
         if (num_ints == 0 .and. num_dbls == 0) return
         
         ierr = 0
         call star_alloc_extras(s% id, num_ints, num_dbls, ierr)
         if (ierr /= 0) then
            write(*,*) 'failed in star_alloc_extras'
            write(*,*) 'alloc_extras num_ints', num_ints
            write(*,*) 'alloc_extras num_dbls', num_dbls
            stop 1
         end if
         
         contains
         
         subroutine move_dbl(dbl)
            real(dp) :: dbl
            i = i+1
            select case (op)
            case (extra_info_get)
               dbl = s% extra_work(i)
            case (extra_info_put)
               s% extra_work(i) = dbl
            end select
         end subroutine move_dbl
         
         subroutine move_int(int)
            integer :: int
            i = i+1
            select case (op)
            case (extra_info_get)
               int = s% extra_iwork(i)
            case (extra_info_put)
               s% extra_iwork(i) = int
            end select
         end subroutine move_int
         
         subroutine move_flg(flg)
            logical :: flg
            i = i+1
            select case (op)
            case (extra_info_get)
               flg = (s% extra_iwork(i) /= 0)
            case (extra_info_put)
               if (flg) then
                  s% extra_iwork(i) = 1
               else
                  s% extra_iwork(i) = 0
               end if
            end select
         end subroutine move_flg
      
      end subroutine move_extra_info

      ! examples of other_mixing subroutines


      ! examples


      subroutine pavel_mixing_micro(id, ierr)

         use chem_def, only: ih1,in14,ihe4,ic12,io16,ic13

         integer, intent(in) :: id
         integer, intent(out) :: ierr
         integer :: k, nz, h1, n14, he4, c12, o16, c13
         double precision :: x, dq00, dqm1, dqsum, T, kap, rho, cp, &
           molecular_diffusivity, radiative_diffusivity, &
           micro_diffusivity
         type (star_info), pointer :: s
         ierr = 0
         call get_star_ptr(id, s, ierr)
         if (ierr /= 0) return

         nz = s% nz

         h1 = s% net_iso(ih1)
         c13 = s% net_iso(ic13)
         n14 = s% net_iso(in14)
         he4 = s% net_iso(ihe4)
         c12 = s% net_iso(ic12)
         o16 = s% net_iso(io16)

       ! add microscopic diffusivity to D_mix
       ! clip_D_limit = 1 ! zero mixing diffusion coeffs that are smaller than this
       ! in inlist controls make clip_D_limt = 0.0001

         do k = 2, nz ! start at 2 since no mixing across surface
           ! interpolate values at face
            x = s% xa(h1,k)
            dq00 = s% dq(k)
            dqm1 = s% dq(k-1)
            dqsum = dq00 + dqm1
            kap = (dqm1*s% opacity(k) + dq00*s% opacity(k-1))/dqsum
            rho = (dqm1*s% rho(k) + dq00*s% rho(k-1))/dqsum
            cp = (dqm1*s% cp(k) + dq00*s% cp(k-1))/dqsum
            T = (dqm1*s% T(k) + dq00*s% T(k-1))/dqsum
            radiative_diffusivity = 4*crad*T**4/(15*kap*clight*rho**2)
            molecular_diffusivity = 1.84d-17*(1+7*x)*(T**2.5/rho)
            micro_diffusivity = radiative_diffusivity + &
               molecular_diffusivity
            s% D_mix(k) = s% D_mix(k) + micro_diffusivity

!!!            if ((s% xa(n14,k)<0.000000000001).and.((s% xa(he4,k)>0.1& !!!! TO CHECK INTERSHELL
!!!            )).and.((s% xa(c12,k)>0.1)).and.((((s% xa(he4,k))+&       !!!! TO CHECK INTERSHELL
!!!            (s% xa(c12,k))+(s% xa(o16,k))>0.9)))) then                !!!! TO CHECK INTERSHELL

            if ((s% xa(n14,k)<(s% xa(c13,k)).and.((s% xa(c13,k)>0.001& !!!! TO CHECK C13-POCKET
            )))) then                                                  !!!! TO CHECK C13-POCKET
               print*, '**********************************************'
               print*, 'Dtot= ',s% D_mix(k),'Dmicro= ',micro_diffusivity
               print*, 'Drad= ',radiative_diffusivity
               print*, 'Dmol= ',molecular_diffusivity
               print*, '**********************************************'
            else
               radiative_diffusivity=radiative_diffusivity
            endif

            !!print*, 'PAVEL MIXING' !! For debugging
         end do

      end subroutine pavel_mixing_micro

      end module run_star_extras