m_start_up.fpp.f90

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!>
!! @file
!! @brief Contains module m_start_up
 
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! Caution:
! This macro requires the use of a binding script to set CUDA_VISIBLE_DEVICES, such that we have one GPU device per MPI rank.
! That's because for both cudaMemAdvise (preferred location) and cudaMemPrefetchAsync we use location = device_id = 0.
! For an example see misc/nvidia_uvm/bind.sh.
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!> @brief Reads and validates user inputs, loads existing grid/IC data, and initializes pre-process modules
module m_start_up
 
    use m_derived_types         !< definitions of the derived types
 
    use m_global_parameters     !< global parameters for the code
 
    use m_mpi_proxy             !< message passing interface (mpi) module proxy
 
    use m_mpi_common
 
    use m_variables_conversion  !< subroutines to change the state variables from
                                !! one form to another
 
    use m_grid                  !< procedures to generate (non-)uniform grids
 
    use m_initial_condition     !< procedures to generate initial condition
 
    use m_data_output           !< procedures to write the grid data and the
                                !! conservative variables to files
 
    use m_compile_specific      !< compile-specific procedures
 
    use m_icpp_patches
 
    use m_assign_variables
 
    use m_phase_change          !< phase-change module
 
    use m_helper_basic          !< functions to compare floating point numbers
 
    use m_helper
 
#ifdef MFC_MPI
    use mpi                     !< message passing interface (mpi) module
#endif
 
    use m_check_patches
 
    use m_check_ib_patches
 
    use m_helper
 
    use m_checker_common
 
    use m_checker
 
    use m_boundary_common
 
    use m_boundary_conditions
 
    implicit none
 
    private; 
    public :: s_read_input_file, &
              s_check_input_file, &
              s_read_grid_data_files, &
              s_read_ic_data_files, &
              s_read_serial_grid_data_files, &
              s_read_serial_ic_data_files, &
              s_read_parallel_grid_data_files, &
              s_read_parallel_ic_data_files, &
              s_check_grid_data_files, &
              s_initialize_modules, &
              s_initialize_mpi_domain, &
              s_finalize_modules, &
              s_apply_initial_condition, &
              s_save_data, s_read_grid
 
    abstract interface
 
        !> @brief Abstract interface for reading grid data files in serial or parallel.
        impure subroutine s_read_abstract_grid_data_files
 
        end subroutine s_read_abstract_grid_data_files
 
        !> @brief Abstract interface for reading initial condition data files in serial or parallel.
        !! @param q_cons_vf Conservative variables
        impure subroutine s_read_abstract_ic_data_files(q_cons_vf_in)
 
            import :: scalar_field, integer_field, sys_size, pres_field
 
            type(scalar_field), &
                dimension(sys_size), &
                intent(inout) :: q_cons_vf_in
 
        end subroutine s_read_abstract_ic_data_files
 
    end interface
 
    character(LEN=path_len + name_len) :: proc_rank_dir !<
    !! Location of the folder associated with the rank of the local processor
 
    character(LEN=path_len + 2*name_len), private :: t_step_dir !<
    !! Possible location of time-step folder containing preexisting grid and/or
    !! conservative variables data to be used as starting point for pre-process
 
    procedure(s_read_abstract_grid_data_files), pointer :: s_read_grid_data_files => null()
    procedure(s_read_abstract_ic_data_files), pointer :: s_read_ic_data_files => null()
 
contains
 
    !>  Reads the configuration file pre_process.inp, in order to
        !!      populate the parameters in module m_global_parameters.f90
        !!      with the user provided inputs
    impure subroutine s_read_input_file
 
        character(LEN=name_len) :: file_loc  !<
            !! Generic string used to store the address of a particular file
 
        logical :: file_check !<
            !! Generic logical used for the purpose of asserting whether a file
            !! is or is not present in the designated location
 
        integer :: iostatus
            !! Integer to check iostat of file read
 
        character(len=1000) :: line
 
        ! Namelist for all of the parameters to be inputted by the user
        namelist /user_inputs/ case_dir, old_grid, old_ic, &
            t_step_old, t_step_start, m, n, p, x_domain, y_domain, z_domain, &
            stretch_x, stretch_y, stretch_z, a_x, a_y, &
            a_z, x_a, y_a, z_a, x_b, y_b, z_b, &
            model_eqns, num_fluids, mpp_lim, &
            weno_order, bc_x, bc_y, bc_z, num_patches, &
            hypoelasticity, mhd, patch_icpp, fluid_pp, bub_pp, &
            precision, parallel_io, mixlayer_vel_profile, mixlayer_vel_coef, &
            mixlayer_perturb, mixlayer_perturb_nk, mixlayer_perturb_k0, &
            pi_fac, perturb_flow, perturb_flow_fluid, perturb_flow_mag, &
            perturb_sph, perturb_sph_fluid, fluid_rho, &
            cyl_coord, loops_x, loops_y, loops_z, &
            rhoref, pref, bubbles_euler, r0ref, nb, &
            polytropic, thermal, ca, web, re_inv, &
            polydisperse, poly_sigma, qbmm, &
            sigr, sigv, dist_type, rhorv, &
            file_per_process, relax, relax_model, &
            palpha_eps, ptgalpha_eps, ib, num_ibs, patch_ib, &
            sigma, adv_n, cfl_adap_dt, cfl_const_dt, n_start, &
            n_start_old, surface_tension, hyperelasticity, pre_stress, &
            elliptic_smoothing, elliptic_smoothing_iters, &
            viscous, bubbles_lagrange, num_bc_patches, &
            patch_bc, bx0, relativity, cont_damage, igr, igr_order, &
            down_sample, recon_type, muscl_order, hyper_cleaning, &
            simplex_perturb, simplex_params, fft_wrt
 
        ! Inquiring the status of the pre_process.inp file
        file_loc = 'pre_process.inp'
        inquire (file=trim(file_loc), exist=file_check)
 
        ! Checking whether the input file is there. If it is, the input file
        ! is read. If not, the program is terminated.
        if (file_check) then
            open (1, file=trim(file_loc), form='formatted', &
                  status='old', action='read')
            read (1, nml=user_inputs, iostat=iostatus)
            if (iostatus /= 0) then
                backspace(1)
                read (1, fmt='(A)') line
                print *, 'Invalid line in namelist: '//trim(line)
                call s_mpi_abort('Invalid line in pre_process.inp. It is '// &
                                 'likely due to a datatype mismatch. Exiting.')
            end if
            close (1)
 
            call s_update_cell_bounds(cells_bounds, m, n, p)
 
            ! Store m,n,p into global m,n,p
            m_glb = m
            n_glb = n
            p_glb = p
 
            nglobal = int(m_glb + 1, kind=8)*int(n_glb + 1, kind=8)*int(p_glb + 1, kind=8)
 
            if (cfl_adap_dt .or. cfl_const_dt) cfl_dt = .true.
 
            if (any((/bc_x%beg, bc_x%end, bc_y%beg, bc_y%end, bc_z%beg, bc_z%end/) == bc_dirichlet) .or. &
                num_bc_patches > 0) then
                bc_io = .true.
            end if
 
        else
            call s_mpi_abort('File pre_process.inp is missing. Exiting.')
        end if
 
    end subroutine s_read_input_file
 
    !>  Checking that the user inputs make sense, i.e. that the
    !!      individual choices are compatible with the code's options
    !!      and that the combination of these choices results into a
    !!      valid configuration for the pre-process
    impure subroutine s_check_input_file
 
        character(LEN=len_trim(case_dir)) :: file_loc !<
            !! Generic string used to store the address of a particular file
 
        logical :: dir_check !<
            !! Logical variable used to test the existence of folders
 
        ! Checking the existence of the case folder
        case_dir = adjustl(case_dir)
 
        file_loc = trim(case_dir)//'/.'
 
        call my_inquire(file_loc, dir_check)
 
        if (dir_check .neqv. .true.) then
            print '(A)', 'WARNING: Ensure that compiler flags/choices in Makefiles match your compiler! '
            print '(A)', 'WARNING: Ensure that preprocessor flags are enabled! '
            call s_mpi_abort('Unsupported choice for the value of case_dir.'// &
                             'Exiting.')
        end if
 
        call s_check_inputs_common()
        call s_check_inputs()
 
        ! Check all the patch properties
        call s_check_patches()
 
        if (ib) call s_check_ib_patches()
 
    end subroutine s_check_input_file
 
    !> The goal of this subroutine is to read in any preexisting
        !!      grid data as well as based on the imported grid, complete
        !!      the necessary global computational domain parameters.
    impure subroutine s_read_serial_grid_data_files
 
        ! Generic string used to store the address of a particular file
        character(LEN=len_trim(case_dir) + 3*name_len) :: file_loc
 
        ! Logical variable used to test the existence of folders
        logical :: dir_check
 
        ! Generic logical used for the purpose of asserting whether a file
        ! is or is not present in the designated location
        logical :: file_check
 
        ! Setting address of the local processor rank and time-step directory
        write (proc_rank_dir, '(A,I0)') '/p_all/p', proc_rank
        proc_rank_dir = trim(case_dir)//trim(proc_rank_dir)
 
        write (t_step_dir, '(A,I0)') '/', t_step_start
        t_step_dir = trim(proc_rank_dir)//trim(t_step_dir)
 
        ! Inquiring as to the existence of the time-step directory
        file_loc = trim(t_step_dir)//'/.'
        call my_inquire(file_loc, dir_check)
 
        ! If the time-step directory is missing, the pre-process exits
        if (dir_check .neqv. .true.) then
            call s_mpi_abort('Time-step folder '//trim(t_step_dir)// &
                             ' is missing. Exiting.')
        end if
 
        ! Reading the Grid Data File for the x-direction
 
        ! Checking whether x_cb.dat exists
        file_loc = trim(t_step_dir)//'/x_cb.dat'
        inquire (file=trim(file_loc), exist=file_check)
 
        ! If it exists, x_cb.dat is read
        if (file_check) then
            open (1, file=trim(file_loc), form='unformatted', &
                  status='old', action='read')
            read (1) x_cb(-1:m)
            close (1)
        else
            call s_mpi_abort('File x_cb.dat is missing in '// &
                             trim(t_step_dir)//'. Exiting.')
        end if
 
        ! Computing cell-center locations
        x_cc(0:m) = (x_cb(0:m) + x_cb(-1:(m - 1)))/2._wp
 
        ! Computing minimum cell-width
        dx = minval(x_cb(0:m) - x_cb(-1:m - 1))
        if (num_procs > 1) call s_mpi_reduce_min(dx)
 
        ! Setting locations of domain bounds
        x_domain%beg = x_cb(-1)
        x_domain%end = x_cb(m)
 
        ! Reading the Grid Data File for the y-direction
 
        if (n > 0) then
 
            ! Checking whether y_cb.dat exists
            file_loc = trim(t_step_dir)//'/y_cb.dat'
            inquire (file=trim(file_loc), exist=file_check)
 
            ! If it exists, y_cb.dat is read
            if (file_check) then
                open (1, file=trim(file_loc), form='unformatted', &
                      status='old', action='read')
                read (1) y_cb(-1:n)
                close (1)
            else
                call s_mpi_abort('File y_cb.dat is missing in '// &
                                 trim(t_step_dir)//'. Exiting.')
            end if
 
            ! Computing cell-center locations
            y_cc(0:n) = (y_cb(0:n) + y_cb(-1:(n - 1)))/2._wp
 
            ! Computing minimum cell-width
            dy = minval(y_cb(0:n) - y_cb(-1:n - 1))
            if (num_procs > 1) call s_mpi_reduce_min(dy)
 
            ! Setting locations of domain bounds
            y_domain%beg = y_cb(-1)
            y_domain%end = y_cb(n)
 
            ! Reading the Grid Data File for the z-direction
            if (p > 0) then
 
                ! Checking whether z_cb.dat exists
                file_loc = trim(t_step_dir)//'/z_cb.dat'
                inquire (file=trim(file_loc), exist=file_check)
 
                ! If it exists, z_cb.dat is read
                if (file_check) then
                    open (1, file=trim(file_loc), form='unformatted', &
                          status='old', action='read')
                    read (1) z_cb(-1:p)
                    close (1)
                else
                    call s_mpi_abort('File z_cb.dat is missing in '// &
                                     trim(t_step_dir)//'. Exiting.')
                end if
 
                ! Computing cell-center locations
                z_cc(0:p) = (z_cb(0:p) + z_cb(-1:(p - 1)))/2._wp
 
                ! Computing minimum cell-width
                dz = minval(z_cb(0:p) - z_cb(-1:p - 1))
                if (num_procs > 1) call s_mpi_reduce_min(dz)
 
                ! Setting locations of domain bounds
                z_domain%beg = z_cb(-1)
                z_domain%end = z_cb(p)
 
            end if
 
        end if
 
        ! If only the preexisting grid data files are read in and there will
        ! not be any preexisting initial condition data files imported, then
        ! the directory associated with the rank of the local processor may
        ! be cleaned to make room for the new pre-process data. In addition,
        ! the time-step directory that will contain the new grid and initial
        ! condition data are also generated.
        if (old_ic .neqv. .true.) then
            call s_delete_directory(trim(proc_rank_dir)//'/*')
            call s_create_directory(trim(proc_rank_dir)//'/0')
        end if
 
    end subroutine s_read_serial_grid_data_files
 
    !> Cell-boundary data are checked for consistency by looking
        !!      at the (non-)uniform cell-width distributions for all the
        !!      active coordinate directions and making sure that all of
        !!      the cell-widths are positively valued
    impure subroutine s_check_grid_data_files
 
        ! Cell-boundary Data Consistency Check in x-direction
 
        if (any(x_cb(0:m) - x_cb(-1:m - 1) <= 0._wp)) then
            call s_mpi_abort('x_cb.dat in '//trim(t_step_dir)// &
                             ' contains non-positive cell-spacings. Exiting.')
        end if
 
        ! Cell-boundary Data Consistency Check in y-direction
 
        if (n > 0) then
 
            if (any(y_cb(0:n) - y_cb(-1:n - 1) <= 0._wp)) then
                call s_mpi_abort('y_cb.dat in '//trim(t_step_dir)// &
                                 ' contains non-positive cell-spacings. '// &
                                 'Exiting.')
            end if
 
            ! Cell-boundary Data Consistency Check in z-direction
 
            if (p > 0) then
 
                if (any(z_cb(0:p) - z_cb(-1:p - 1) <= 0._wp)) then
                    call s_mpi_abort('z_cb.dat in '//trim(t_step_dir)// &
                                     ' contains non-positive cell-spacings'// &
                                     ' .Exiting.')
                end if
 
            end if
 
        end if
 
    end subroutine s_check_grid_data_files
 
    !> The goal of this subroutine is to read in any preexisting
        !!      initial condition data files so that they may be used by
        !!      the pre-process as a starting point in the creation of an
        !!      all new initial condition.
        !! @param q_cons_vf_in Conservative variables
    impure subroutine s_read_serial_ic_data_files(q_cons_vf_in)
 
        type(scalar_field), &
            dimension(sys_size), &
            intent(inout) :: q_cons_vf_in
 
        character(LEN=len_trim(case_dir) + 3*name_len) :: file_loc !<
        ! Generic string used to store the address of a particular file
 
        character(len= &
                  int(floor(log10(real(sys_size, wp)))) + 1) :: file_num !<
            !! Used to store the variable position, in character form, of the
            !! currently manipulated conservative variable file
 
        logical :: file_check !<
            !! Generic logical used for the purpose of asserting whether a file
            !! is or is not present in the designated location
 
        integer :: i, r !< Generic loop iterator
 
        ! Reading the Conservative Variables Data Files
        do i = 1, sys_size
 
            ! Checking whether data file associated with variable position
            ! of the currently manipulated conservative variable exists
            write (file_num, '(I0)') i
            file_loc = trim(t_step_dir)//'/q_cons_vf'// &
                       trim(file_num)//'.dat'
            inquire (file=trim(file_loc), exist=file_check)
 
            ! If it exists, the data file is read
            if (file_check) then
                open (1, file=trim(file_loc), form='unformatted', &
                      status='old', action='read')
                read (1) q_cons_vf_in(i)%sf
                close (1)
            else
                call s_mpi_abort('File q_cons_vf'//trim(file_num)// &
                                 '.dat is missing in '//trim(t_step_dir)// &
                                 '. Exiting.')
            end if
 
        end do
 
        !Read bubble variables pb and mv for non-polytropic qbmm
        if (qbmm .and. .not. polytropic) then
            do i = 1, nb
                do r = 1, nnode
                    ! Checking whether data file associated with variable position
                    ! of the currently manipulated bubble variable exists
                    write (file_num, '(I0)') sys_size + r + (i - 1)*nnode
                    file_loc = trim(t_step_dir)//'/pb'// &
                               trim(file_num)//'.dat'
                    inquire (file=trim(file_loc), exist=file_check)
 
                    ! If it exists, the data file is read
                    if (file_check) then
                        open (1, file=trim(file_loc), form='unformatted', &
                              status='old', action='read')
                        read (1) pb%sf(:, :, :, r, i)
                        close (1)
                    else
                        call s_mpi_abort('File pb'//trim(file_num)// &
                                         '.dat is missing in '//trim(t_step_dir)// &
                                         '. Exiting.')
                    end if
                end do
 
            end do
 
            do i = 1, nb
                do r = 1, 4
                    ! Checking whether data file associated with variable position
                    ! of the currently manipulated bubble variable exists
                    write (file_num, '(I0)') sys_size + r + (i - 1)*4
                    file_loc = trim(t_step_dir)//'/mv'// &
                               trim(file_num)//'.dat'
                    inquire (file=trim(file_loc), exist=file_check)
 
                    ! If it exists, the data file is read
                    if (file_check) then
                        open (1, file=trim(file_loc), form='unformatted', &
                              status='old', action='read')
                        read (1) mv%sf(:, :, :, r, i)
                        close (1)
                    else
                        call s_mpi_abort('File mv'//trim(file_num)// &
                                         '.dat is missing in '//trim(t_step_dir)// &
                                         '. Exiting.')
                    end if
                end do
 
            end do
        end if
 
        ! Since the preexisting grid and initial condition data files have
        ! been read in, the directory associated with the rank of the local
        ! process may be cleaned out to make room for new pre-process data.
        ! In addition, the time-step folder that will contain the new grid
        ! and initial condition data are also generated.
        call s_create_directory(trim(proc_rank_dir)//'/*')
        call s_create_directory(trim(proc_rank_dir)//'/0')
 
    end subroutine s_read_serial_ic_data_files
 
    !> Cell-boundary data are checked for consistency by looking
        !!      at the (non-)uniform cell-width distributions for all the
        !!      active coordinate directions and making sure that all of
        !!      the cell-widths are positively valued
    impure subroutine s_read_parallel_grid_data_files
 
#ifdef MFC_MPI
 
        real(wp), allocatable, dimension(:) :: x_cb_glb, y_cb_glb, z_cb_glb
 
        integer :: ifile, ierr, data_size
        integer, dimension(MPI_STATUS_SIZE) :: status
 
        character(LEN=path_len + 2*name_len) :: file_loc
        logical :: file_exist
 
        allocate (x_cb_glb(-1:m_glb))
        allocate (y_cb_glb(-1:n_glb))
        allocate (z_cb_glb(-1:p_glb))
 
        ! Read in cell boundary locations in x-direction
        file_loc = trim(case_dir)//'/restart_data'//trim(mpiiofs)//'x_cb.dat'
        inquire (file=trim(file_loc), exist=file_exist)
 
        if (file_exist) then
            data_size = m_glb + 2
            call mpi_file_open(mpi_comm_world, file_loc, mpi_mode_rdonly, mpi_info_int, ifile, ierr)
            call mpi_file_read_all(ifile, x_cb_glb, data_size, mpi_p, status, ierr)
            call mpi_file_close(ifile, ierr)
        else
            call s_mpi_abort('File '//trim(file_loc)//' is missing. Exiting. ')
        end if
 
        ! Assigning local cell boundary locations
        x_cb(-1:m) = x_cb_glb((start_idx(1) - 1):(start_idx(1) + m))
        ! Computing cell center locations
        x_cc(0:m) = (x_cb(0:m) + x_cb(-1:(m - 1)))/2._wp
        ! Computing minimum cell width
        dx = minval(x_cb(0:m) - x_cb(-1:(m - 1)))
        if (num_procs > 1) call s_mpi_reduce_min(dx)
        ! Setting locations of domain bounds
        x_domain%beg = x_cb(-1)
        x_domain%end = x_cb(m)
 
        if (n > 0) then
            ! Read in cell boundary locations in y-direction
            file_loc = trim(case_dir)//'/restart_data'//trim(mpiiofs)//'y_cb.dat'
            inquire (file=trim(file_loc), exist=file_exist)
 
            if (file_exist) then
                data_size = n_glb + 2
                call mpi_file_open(mpi_comm_world, file_loc, mpi_mode_rdonly, mpi_info_int, ifile, ierr)
                call mpi_file_read_all(ifile, y_cb_glb, data_size, mpi_p, status, ierr)
                call mpi_file_close(ifile, ierr)
            else
                call s_mpi_abort('File '//trim(file_loc)//' is missing. Exiting. ')
            end if
 
            ! Assigning local cell boundary locations
            y_cb(-1:n) = y_cb_glb((start_idx(2) - 1):(start_idx(2) + n))
            ! Computing cell center locations
            y_cc(0:n) = (y_cb(0:n) + y_cb(-1:(n - 1)))/2._wp
            ! Computing minimum cell width
            dy = minval(y_cb(0:n) - y_cb(-1:(n - 1)))
            if (num_procs > 1) call s_mpi_reduce_min(dy)
            ! Setting locations of domain bounds
            y_domain%beg = y_cb(-1)
            y_domain%end = y_cb(n)
 
            if (p > 0) then
                ! Read in cell boundary locations in z-direction
                file_loc = trim(case_dir)//'/restart_data'//trim(mpiiofs)//'z_cb.dat'
                inquire (file=trim(file_loc), exist=file_exist)
 
                if (file_exist) then
                    data_size = p_glb + 2
                    call mpi_file_open(mpi_comm_world, file_loc, mpi_mode_rdonly, mpi_info_int, ifile, ierr)
                    call mpi_file_read_all(ifile, z_cb_glb, data_size, mpi_p, status, ierr)
                    call mpi_file_close(ifile, ierr)
                else
                    call s_mpi_abort('File '//trim(file_loc)//' is missing. Exiting. ')
                end if
 
                ! Assigning local cell boundary locations
                z_cb(-1:p) = z_cb_glb((start_idx(3) - 1):(start_idx(3) + p))
                ! Computing cell center locations
                z_cc(0:p) = (z_cb(0:p) + z_cb(-1:(p - 1)))/2._wp
                ! Computing minimum cell width
                dz = minval(z_cb(0:p) - z_cb(-1:(p - 1)))
                if (num_procs > 1) call s_mpi_reduce_min(dz)
                ! Setting locations of domain bounds
                z_domain%beg = z_cb(-1)
                z_domain%end = z_cb(p)
 
            end if
        end if
 
        deallocate (x_cb_glb, y_cb_glb, z_cb_glb)
 
#endif
 
    end subroutine s_read_parallel_grid_data_files
 
    !> The goal of this subroutine is to read in any preexisting
        !!      initial condition data files so that they may be used by
        !!      the pre-process as a starting point in the creation of an
        !!      all new initial condition.
        !! @param q_cons_vf_in Conservative variables
    impure subroutine s_read_parallel_ic_data_files(q_cons_vf_in)
 
        type(scalar_field), &
            dimension(sys_size), &
            intent(inout) :: q_cons_vf_in
 
#ifdef MFC_MPI
 
        integer :: ifile, ierr, data_size
        integer, dimension(MPI_STATUS_SIZE) :: status
        integer(KIND=MPI_OFFSET_KIND) :: disp
        integer(KIND=MPI_OFFSET_KIND) :: m_mok, n_mok, p_mok
        integer(KIND=MPI_OFFSET_KIND) :: wp_mok, var_mok, str_mok
        integer(KIND=MPI_OFFSET_KIND) :: nvars_mok
        integer(KIND=MPI_OFFSET_KIND) :: mok
 
        character(LEN=path_len + 2*name_len) :: file_loc
        logical :: file_exist
 
        integer :: i
 
        ! Open the file to read
        if (cfl_adap_dt) then
            write (file_loc, '(I0,A)') n_start, '.dat'
        else
            write (file_loc, '(I0,A)') t_step_start, '.dat'
        end if
        file_loc = trim(restart_dir)//trim(mpiiofs)//trim(file_loc)
        inquire (file=trim(file_loc), exist=file_exist)
 
        if (file_exist) then
            call mpi_file_open(mpi_comm_world, file_loc, mpi_mode_rdonly, mpi_info_int, ifile, ierr)
 
            call s_initialize_mpi_data(q_cons_vf_in)
 
            ! Size of local arrays
            data_size = (m + 1)*(n + 1)*(p + 1)
 
            ! Resize some integers so MPI can read even the biggest files
            m_mok = int(m_glb + 1, mpi_offset_kind)
            n_mok = int(n_glb + 1, mpi_offset_kind)
            p_mok = int(p_glb + 1, mpi_offset_kind)
            wp_mok = int(8._wp, mpi_offset_kind)
            mok = int(1._wp, mpi_offset_kind)
            str_mok = int(name_len, mpi_offset_kind)
            nvars_mok = int(sys_size, mpi_offset_kind)
 
            ! Read the data for each variable
            do i = 1, sys_size
                var_mok = int(i, mpi_offset_kind)
 
                ! Initial displacement to skip at beginning of file
                disp = m_mok*max(mok, n_mok)*max(mok, p_mok)*wp_mok*(var_mok - 1)
 
                call mpi_file_set_view(ifile, disp, mpi_p, mpi_io_data%view(i), &
                                       'native', mpi_info_int, ierr)
                call mpi_file_read(ifile, mpi_io_data%var(i)%sf, data_size, &
                                   mpi_p, status, ierr)
            end do
 
            if (qbmm .and. .not. polytropic) then
                do i = sys_size + 1, sys_size + 2*nb*4
                    var_mok = int(i, mpi_offset_kind)
 
                    ! Initial displacement to skip at beginning of file
                    disp = m_mok*max(mok, n_mok)*max(mok, p_mok)*wp_mok*(var_mok - 1)
 
                    call mpi_file_set_view(ifile, disp, mpi_p, mpi_io_data%view(i), &
                                           'native', mpi_info_int, ierr)
                    call mpi_file_read(ifile, mpi_io_data%var(i)%sf, data_size, &
                                       mpi_p, status, ierr)
                end do
            end if
 
            call s_mpi_barrier()
 
            call mpi_file_close(ifile, ierr)
 
        else
            call s_mpi_abort('File '//trim(file_loc)//' is missing. Exiting. ')
        end if
 
        call s_mpi_barrier()
 
#endif
 
    end subroutine s_read_parallel_ic_data_files
 
    !> @brief Initializes all pre-process modules, allocates data structures, and sets I/O procedure pointers.
    impure subroutine s_initialize_modules
        ! Computation of parameters, allocation procedures, and/or any other tasks
        ! needed to properly setup the modules
        call s_initialize_global_parameters_module()
        if (bubbles_euler .or. bubbles_lagrange) then
            call s_initialize_bubbles_model()
        end if
        call s_initialize_mpi_common_module()
        call s_initialize_data_output_module()
        call s_initialize_variables_conversion_module()
        call s_initialize_grid_module()
        call s_initialize_initial_condition_module()
        call s_initialize_perturbation_module()
        call s_initialize_assign_variables_module()
        call s_initialize_boundary_common_module()
        if (relax) call s_initialize_phasechange_module()
 
        ! Create the D directory if it doesn't exit, to store
        ! the serial data files
        call s_create_directory('D')
 
        ! Associate pointers for serial or parallel I/O
        if (parallel_io .neqv. .true.) then
            s_generate_grid => s_generate_serial_grid
            s_read_grid_data_files => s_read_serial_grid_data_files
            s_read_ic_data_files => s_read_serial_ic_data_files
            s_write_data_files => s_write_serial_data_files
        else
            s_generate_grid => s_generate_parallel_grid
            s_read_grid_data_files => s_read_parallel_grid_data_files
            s_read_ic_data_files => s_read_parallel_ic_data_files
            s_write_data_files => s_write_parallel_data_files
        end if
 
    end subroutine s_initialize_modules
 
    !> @brief Reads an existing grid from data files or generates a new grid from user inputs.
    impure subroutine s_read_grid()
 
        if (old_grid) then
            call s_read_grid_data_files()
            call s_check_grid_data_files()
        else
            if (parallel_io .neqv. .true.) then
                call s_generate_grid()
            else
                if (proc_rank == 0) call s_generate_grid()
                call s_mpi_barrier()
                call s_read_grid_data_files()
                call s_check_grid_data_files()
            end if
        end if
 
    end subroutine s_read_grid
 
    !> @brief Generates or reads the initial condition, applies relaxation if needed, and writes output data files.
    impure subroutine s_apply_initial_condition(start, finish)
 
        real(wp), intent(inout) :: start, finish
 
        integer :: j, k, l
        real(wp) :: r2
 
        ! Setting up the grid and the initial condition. If the grid is read in from
        ! preexisting grid data files, it is checked for consistency. If the grid is
        ! not read in, it is generated from scratch according to the inputs provided
        ! by the user. The initial condition may also be read in. It in turn is not
        ! checked for consistency since it WILL further be edited by the pre-process
        ! and also because it may be incomplete at the time it is read in. Finally,
        ! when the grid and initial condition are completely setup, they are written
        ! to their respective data files.
 
        ! Setting up grid and initial condition
        call cpu_time(start)
 
        if (old_ic) call s_read_ic_data_files(q_cons_vf)
 
        call s_generate_initial_condition()
 
        ! hard-coded psi
        if (hyper_cleaning) then
    if (.not. (psi_idx > 0)) then
# 793 "/home/runner/work/MFC/MFC/src/pre_process/m_start_up.fpp"
        call s_mpi_abort("m_start_up.fpp:793: "// &
# 793 "/home/runner/work/MFC/MFC/src/pre_process/m_start_up.fpp"
                         "Assertion failed: psi_idx > 0. " &
# 793 "/home/runner/work/MFC/MFC/src/pre_process/m_start_up.fpp"
                         //"hyper_cleaning requires psi_idx to be set")
# 793 "/home/runner/work/MFC/MFC/src/pre_process/m_start_up.fpp"
    end if
            do l = 0, p
                do k = 0, n
                    do j = 0, m
                        r2 = x_cc(j)**2
                        if (n > 0) r2 = r2 + y_cc(k)**2
                        if (p > 0) r2 = r2 + z_cc(l)**2
                        q_cons_vf(psi_idx)%sf(j, k, l) = 1.0e-2_wp*exp(-r2/(2.0_wp*0.05_wp**2))
                        q_prim_vf(psi_idx)%sf(j, k, l) = q_cons_vf(psi_idx)%sf(j, k, l)
                    end do
                end do
            end do
        end if
 
        if (relax) then
            if (proc_rank == 0) then
                print *, 'initial condition might have been altered due to enforcement of &
&                pTg-equilirium (relax = "T" activated)'
            end if
 
            call s_infinite_relaxation_k(q_cons_vf)
        end if
 
        call s_write_data_files(q_cons_vf, q_prim_vf, bc_type)
 
        call cpu_time(finish)
    end subroutine s_apply_initial_condition
 
    !> @brief Gathers processor timing data and writes elapsed wall-clock time to a summary file.
    impure subroutine s_save_data(proc_time, time_avg, time_final, file_exists)
 
        real(wp), dimension(:), intent(inout) :: proc_time
        real(wp), intent(inout) :: time_avg, time_final
        logical, intent(inout) :: file_exists
 
        call s_mpi_barrier()
 
        if (num_procs > 1) then
            call mpi_bcast_time_step_values(proc_time, time_avg)
        end if
 
        if (proc_rank == 0) then
            time_final = 0._wp
            if (num_procs == 1) then
                time_final = time_avg
                print *, "Elapsed Time", time_final
            else
                time_final = maxval(proc_time)
                print *, "Elapsed Time", time_final
            end if
            inquire (file='pre_time_data.dat', exist=file_exists)
            if (file_exists) then
                open (1, file='pre_time_data.dat', position='append', status='old')
                write (1, *) num_procs, time_final
                close (1)
            else
                open (1, file='pre_time_data.dat', status='new')
                write (1, *) num_procs, time_final
                close (1)
            end if
        end if
    end subroutine s_save_data
 
    !> @brief Initializes MPI, reads and validates user inputs on rank 0, and decomposes the computational domain.
    impure subroutine s_initialize_mpi_domain
        ! Initialization of the MPI environment
 
        call s_mpi_initialize()
 
        ! Rank 0 processor assigns default values to user inputs prior to reading
        ! those in from the input file. Next, the user inputs are read in and their
        ! consistency is checked. The detection of any inconsistencies automatically
        ! leads to the termination of the pre-process.
 
        if (proc_rank == 0) then
            call s_assign_default_values_to_user_inputs()
            call s_read_input_file()
            call s_check_input_file()
 
            print '(" Pre-processing a ", I0, "x", I0, "x", I0, " case on ", I0, " rank(s)")', m, n, p, num_procs
        end if
 
        ! Broadcasting the user inputs to all of the processors and performing the
        ! parallel computational domain decomposition. Neither procedure has to be
        ! carried out if pre-process is in fact not truly executed in parallel.
        call s_mpi_bcast_user_inputs()
        call s_initialize_parallel_io()
        call s_mpi_decompose_computational_domain()
    end subroutine s_initialize_mpi_domain
 
    !> @brief Finalizes all pre-process modules, deallocates resources, and shuts down MPI.
    impure subroutine s_finalize_modules
        ! Disassociate pointers for serial and parallel I/O
        s_generate_grid => null()
        s_read_grid_data_files => null()
        s_read_ic_data_files => null()
        s_write_data_files => null()
 
        ! Deallocation procedures for the modules
        call s_finalize_mpi_common_module()
        call s_finalize_grid_module()
        call s_finalize_variables_conversion_module()
        call s_finalize_data_output_module()
        call s_finalize_global_parameters_module()
        call s_finalize_assign_variables_module()
        call s_finalize_perturbation_module()
        call s_finalize_boundary_common_module()
        if (relax) call s_finalize_relaxation_solver_module()
        call s_finalize_initial_condition_module()
        ! Finalization of the MPI environment
        call s_mpi_finalize()
    end subroutine s_finalize_modules
 
end module m_start_up