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Updated MESA-H5 #1

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8d1a8ff
Update mesa_hdf5_params.inc
bamunson Feb 28, 2022
ee4ed17
Update mesa_hdf5_routines.inc
bamunson Feb 28, 2022
d04a824
Update run_star_extras.f
bamunson Feb 28, 2022
5bb843e
Add files via upload
bamunson Feb 28, 2022
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13 changes: 13 additions & 0 deletions src/extra_history_cols.inc
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Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
integer function how_many_extra_history_columns(id)
integer, intent(in) :: id
end function how_many_extra_history_columns

subroutine data_for_extra_history_columns( &
id, n, names, vals, ierr)
use const_def, only: dp
use star_def, only: maxlen_history_column_name
integer, intent(in) :: id, n
character (len=maxlen_history_column_name) :: names(n)
real(dp) :: vals(n)
integer, intent(out) :: ierr
end subroutine data_for_extra_history_columns
13 changes: 13 additions & 0 deletions src/extra_profile_cols.inc
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@@ -0,0 +1,13 @@
integer function how_many_extra_profile_columns(id)
integer, intent(in) :: id
end function how_many_extra_profile_columns

subroutine data_for_extra_profile_columns( &
id, n, nz, names, vals, ierr)
use const_def, only: dp
use star_def, only: maxlen_profile_column_name
integer, intent(in) :: id, n, nz
character (len=maxlen_profile_column_name) :: names(n)
real(dp) :: vals(nz,n)
integer, intent(out) :: ierr
end subroutine data_for_extra_profile_columns
8 changes: 4 additions & 4 deletions src/mesa_hdf5_params.inc
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Expand Up @@ -14,19 +14,19 @@
!!!!!!! format_cycle -> suffix format in the cycle name
!!!!!!! hdf5_num_mod_output -> number of cycles per HDF5 file
!!!!!!! change_names -> whether you want to change the name of some quantities,
!!!!!!! for instance 'star_mass' into 'stellar_mass'.
!!!!!!! See subroutines change_history_names and change_profile_names
!!!!!!! for instance 'star_mass' into 'stellar_mass'.
!!!!!!! See subroutines change_history_names and change_profile_names
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

! If left as empty strings, these parameters will take default values
! If left as empty strings, these parameters will take default values
! determined at runtime (see header).
character (len=256) :: hdf5_prefix = ''
character (len=256) :: hdf5_codev = ''
character(len=256), parameter :: hdf5_modname = 'HDF5'
character(len=256), parameter :: hdf5_profile_list = 'hdf5_profile_columns.list'

character(len=*), parameter :: head_cycle_name = 'cycle'
character(len=*), parameter :: head_cycle_name = 'cycle'
character(len=*), parameter :: dataset_cycle_name = 'SE_DATASET'
character(len=*), parameter :: dataset_cycle_name2 = 'ISO_MASSF'

Expand Down
6 changes: 3 additions & 3 deletions src/mesa_hdf5_routines.inc
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Expand Up @@ -225,15 +225,15 @@
call add_attribute_dbl(file_id, 1, "zini", value_dbl)
call scalar_to_rank1_dbl(0.d0, value_dbl)
call add_attribute_dbl(file_id, 1, "rotini", value_dbl)
call scalar_to_rank1_dbl(s% overshoot_f_above_burn_h_core, value_dbl)
call scalar_to_rank1_dbl(s% overshoot_f(1), value_dbl)
call add_attribute_dbl(file_id, 1, "overini", value_dbl)
call scalar_to_rank1_dbl(secyer, value_dbl)
call add_attribute_dbl(file_id, 1, "age_unit", value_dbl)
call scalar_to_rank1_dbl(secyer, value_dbl)
call add_attribute_dbl(file_id, 1, "one_year", value_dbl)
call scalar_to_rank1_dbl(msol, value_dbl)
call scalar_to_rank1_dbl(Msun, value_dbl)
call add_attribute_dbl(file_id, 1, "mass_unit", value_dbl)
call scalar_to_rank1_dbl(rsol, value_dbl)
call scalar_to_rank1_dbl(Rsun, value_dbl)
call add_attribute_dbl(file_id, 1, "radius_unit", value_dbl)
call scalar_to_rank1_dbl(1.d0, value_dbl)
call add_attribute_dbl(file_id, 1, "rho_unit", value_dbl)
Expand Down
47 changes: 24 additions & 23 deletions src/run_star_extras.f
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Expand Up @@ -25,7 +25,7 @@ module run_star_extras
use star_lib
use star_def
use const_def
use crlibm_lib
use math_lib
use chem_def
use run_star_support, only: failed
use utils_lib, only: utils_OMP_GET_MAX_THREADS
Expand Down Expand Up @@ -92,7 +92,7 @@ end subroutine extras_controls
! None of the following functions are called unless you set their
! function point in extras_control.

integer function extras_startup(id, restart, ierr)
subroutine extras_startup(id, restart, ierr)
integer, intent(in) :: id
logical, intent(in) :: restart
integer, intent(out) :: ierr
Expand All @@ -110,7 +110,7 @@ integer function extras_startup(id, restart, ierr)

call star_ptr(id, s, ierr)
if (ierr /= 0) return
extras_startup = 0
!extras_startup = 0
if (.not. restart) then
call alloc_extra_info(s)
else ! it is a restart
Expand Down Expand Up @@ -146,20 +146,20 @@ integer function extras_startup(id, restart, ierr)
call system("mkdir -p "//hdf5_modname)

! Get names and values for history
call get_data_for_history_columns(s, id_extra, ierr)
call get_data_for_history_columns(s, ierr)
num_history_columns = s% number_of_history_columns

! Get names and values for profiles
! We do not use the same for the profiles files and the HDF5
! HDF5 profiles are a subset of the profiles files
num_profile_columns_logs = num_standard_profile_columns(s) + how_many_extra_profile_columns(id, id_extra)
num_profile_columns_logs = num_standard_profile_columns(s) + how_many_extra_profile_columns(id)
allocate( &
profile_names_logs(num_profile_columns_logs), &
profile_vals_logs(s% nz,num_profile_columns_logs), &
profile_is_int_logs(num_profile_columns_logs), &
stat=ierr)

call get_data_for_profile_columns(s, id_extra, s% nz, &
call get_data_for_profile_columns(s , s% nz, &
profile_names_logs, profile_vals_logs, profile_is_int_logs,ierr)

! Parse the hdf5_profile_columns.list to get number of HDF5 profiles
Expand Down Expand Up @@ -210,7 +210,7 @@ integer function extras_startup(id, restart, ierr)
! Deallocate only profile_vals (because nz changes during the evolution)
deallocate(profile_vals)

end function extras_startup
end subroutine extras_startup

subroutine get_profile_index(index, index_logs, ierr)

Expand All @@ -232,18 +232,18 @@ subroutine get_profile_index(index, index_logs, ierr)

end subroutine get_profile_index

subroutine get_data_for_profile_columns_hfd5(s, id_extra, nz, ierr)
subroutine get_data_for_profile_columns_hfd5(s, nz, ierr)

type (star_info), pointer :: s
integer, intent(in) :: id_extra, nz
integer, intent(in) :: nz
integer, intent(out) :: ierr

integer i, j, index

ierr = 0

! Call for the logs
call get_data_for_profile_columns(s, id_extra, nz, &
call get_data_for_profile_columns(s, nz, &
profile_names_logs, profile_vals_logs, profile_is_int_logs, ierr)
if (ierr /= 0) return

Expand Down Expand Up @@ -289,8 +289,8 @@ integer function extras_check_model(id, id_extra)
end function extras_check_model


integer function how_many_extra_history_columns(id, id_extra)
integer, intent(in) :: id, id_extra
integer function how_many_extra_history_columns(id)
integer, intent(in) :: id
integer :: ierr
type (star_info), pointer :: s
ierr = 0
Expand All @@ -300,8 +300,8 @@ integer function how_many_extra_history_columns(id, id_extra)
end function how_many_extra_history_columns


subroutine data_for_extra_history_columns(id, id_extra, n, names, vals, ierr)
integer, intent(in) :: id, id_extra, n
subroutine data_for_extra_history_columns(id, n, names, vals, ierr)
integer, intent(in) :: id, n
character (len=maxlen_history_column_name) :: names(n)
real(dp) :: vals(n)
integer, intent(out) :: ierr
Expand All @@ -323,9 +323,9 @@ subroutine data_for_extra_history_columns(id, id_extra, n, names, vals, ierr)
end subroutine data_for_extra_history_columns


integer function how_many_extra_profile_columns(id, id_extra)
integer function how_many_extra_profile_columns(id)
use star_def, only: star_info
integer, intent(in) :: id, id_extra
integer, intent(in) :: id
integer :: ierr
type (star_info), pointer :: s
ierr = 0
Expand All @@ -335,10 +335,10 @@ integer function how_many_extra_profile_columns(id, id_extra)
end function how_many_extra_profile_columns


subroutine data_for_extra_profile_columns(id, id_extra, n, nz, names, vals, ierr)
subroutine data_for_extra_profile_columns(id, n, nz, names, vals, ierr)
use star_def, only: star_info, maxlen_profile_column_name
use const_def, only: dp
integer, intent(in) :: id, id_extra, n, nz
integer, intent(in) :: id, n, nz
character (len=maxlen_profile_column_name) :: names(n)
real(dp) :: vals(nz,n)
integer, intent(out) :: ierr
Expand All @@ -363,7 +363,7 @@ subroutine data_for_extra_profile_columns(id, id_extra, n, nz, names, vals, ierr
names(2) = 'rho'
names(3) = 'dcoeff'
do k = 1, nz
vals(k,1) = s% mstar * s% dq(k) / msol
vals(k,1) = s% mstar * s% dq(k) / Msun
vals(k,2) = s% rho(k)
vals(k,3) = s% D_mix(k)
end do
Expand All @@ -373,8 +373,8 @@ 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(id, id_extra)
integer, intent(in) :: id, id_extra
integer function extras_finish_step(id)
integer, intent(in) :: id
integer :: ierr
integer :: ios, line
character(len=100) :: buffer
Expand All @@ -392,12 +392,13 @@ integer function extras_finish_step(id, id_extra)
! s% need_to_update_history_now = .true.

! Get names and values for history
call get_data_for_history_columns(s, id_extra, ierr)
!call get_data_for_history_columns(s, id_extra, ierr)
call get_data_for_history_columns(s, ierr)

allocate(profile_vals_logs(s% nz,num_profile_columns_logs), &
profile_vals(s% nz,num_profile_columns), &
stat=ierr)
call get_data_for_profile_columns_hfd5(s, id_extra, s% nz, ierr)
call get_data_for_profile_columns_hfd5(s, s% nz, ierr)

! Main function call
call hdf5_finish_step(s, change_names, &
Expand Down