probes.F90

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!
module probes
  use num_types, only: rp
  use matrix, only: matrix_t
  use logger, only: neko_log, log_size, neko_log_debug
  use utils, only: neko_error, nonlinear_index
  use field_list, only: field_list_t
  use time_state, only : time_state_t
  use simulation_component, only : simulation_component_t
  use field_registry, only : neko_field_registry
  use dofmap, only: dofmap_t
  use json_module, only : json_file, json_value, json_core
  use json_utils, only : json_get, json_extract_item, json_get_or_default
  use global_interpolation, only: global_interpolation_t
  use tensor, only: trsp
  use point_zone, only: point_zone_t
  use point_zone_registry, only: neko_point_zone_registry
  use file, only : file_t, file_free
  use csv_file, only : csv_file_t
  use case, only : case_t
  use, intrinsic :: iso_c_binding
  use comm, only : neko_comm, pe_rank, pe_size
  use neko_config, only : neko_bcknd_device
  use device, only : device_memcpy, device_to_host, device_map
  use mpi_f08, only : mpi_allreduce, mpi_integer, mpi_sum, mpi_double_precision
  implicit none
  private
 
  type, public, extends(simulation_component_t) :: probes_t
     real(kind=rp) :: start_time
     integer :: n_fields = 0
     type(global_interpolation_t) :: global_interp
     integer :: n_global_probes
     integer :: n_probes_offset
     real(kind=rp), allocatable :: xyz(:,:)
     real(kind=rp), allocatable :: out_values(:,:)
     type(c_ptr), allocatable :: out_values_d(:)
     real(kind=rp), allocatable :: out_vals_trsp(:,:)
     integer :: n_local_probes
     type(field_list_t) :: sampled_fields
     character(len=20), allocatable :: which_fields(:)
     integer, allocatable :: n_local_probes_tot_offset(:)
     integer, allocatable :: n_local_probes_tot(:)
     logical :: seq_io
     real(kind=rp), allocatable :: global_output_values(:,:)
     type(file_t) :: fout
     type(matrix_t) :: mat_out
   contains
     procedure, pass(this) :: init => probes_init_from_json
     ! Actual constructor
     procedure, pass(this) :: init_from_components => &
          probes_init_from_components
     procedure, pass(this) :: free => probes_free
     procedure, pass(this) :: setup_offset => probes_setup_offset
     procedure, pass(this) :: compute_ => probes_evaluate_and_write
 
     ! ----------------------------------------------------------------------- !
     ! Private methods
 
     procedure, private, pass(this) :: read_file
     procedure, private, pass(this) :: read_point
     procedure, private, pass(this) :: read_line
     procedure, private, pass(this) :: read_circle
     procedure, private, pass(this) :: read_point_zone
 
     procedure, private, pass(this) :: add_points
  end type probes_t
 
contains
 
  subroutine probes_init_from_json(this, json, case)
    class(probes_t), intent(inout), target :: this
    type(json_file), intent(inout) :: json
    class(case_t), intent(inout), target :: case
    character(len=:), allocatable :: output_file
    character(len=:), allocatable :: input_file
    integer :: i, ierr
 
    ! JSON variables
    character(len=:), allocatable :: point_type
    type(json_value), pointer :: json_point_list
    type(json_file) :: json_point
    type(json_core) :: core
    integer :: idx, n_point_children
 
    ! Initialize the base class
    call this%free()
    call this%init_base(json, case)
 
    call json%info('fields', n_children = this%n_fields)
    call json_get(json, 'fields', this%which_fields)
    call json_get(json, 'output_file', output_file)
    call json_get_or_default(json, 'start_time', this%start_time, -1.0_rp)
 
    call this%sampled_fields%init(this%n_fields)
    do i = 1, this%n_fields
 
       call this%sampled_fields%assign(i, &
       & neko_field_registry%get_field(trim(this%which_fields(i))))
    end do
 
    ! Setup the required arrays and initialize variables.
    this%n_local_probes = 0
    this%n_global_probes = 0
 
    ! Read the legacy point specification from the points file.
    if (json%valid_path('points_file')) then
 
       ! Todo: We should add a deprecation notice here
       call json_get(json, 'points_file', input_file)
 
       ! This is distributed as to make it similar to parallel file
       ! formats later, Reads all into rank 0
       call read_probe_locations(this, this%xyz, this%n_local_probes, &
            this%n_global_probes, input_file)
    end if
 
    ! Go through the points list and construct the probe list
    call json%get('points', json_point_list)
    call json%info('points', n_children = n_point_children)
 
    do idx = 1, n_point_children
       call json_extract_item(core, json_point_list, idx, json_point)
 
       call json_get_or_default(json_point, 'type', point_type, 'none')
       select case (point_type)
 
       case ('file')
          call this%read_file(json_point)
       case ('points')
          call this%read_point(json_point)
       case ('line')
          call this%read_line(json_point)
       case ('plane')
          call neko_error('Plane probes not implemented yet.')
       case ('circle')
          call this%read_circle(json_point)
       case ('point_zone')
          call this%read_point_zone(json_point, case%fluid%dm_Xh)
       case ('none')
          call json_point%print()
          call neko_error('No point type specified.')
       case default
          call neko_error('Unknown region type ' // point_type)
       end select
    end do
 
    call mpi_allreduce(this%n_local_probes, this%n_global_probes, 1, &
         mpi_integer, mpi_sum, neko_comm, ierr)
 
    call probes_show(this)
    call this%init_from_components(case%fluid%dm_Xh, output_file)
 
  end subroutine probes_init_from_json
 
  ! ========================================================================== !
  ! Readers for different point types
 
  subroutine read_file(this, json)
    class(probes_t), intent(inout) :: this
    type(json_file), intent(inout) :: json
    character(len=:), allocatable :: input_file
    real(kind=rp), dimension(:,:), allocatable :: point_list
 
    integer :: n_local, n_global
 
    if (pe_rank .ne. 0) return
 
    call json_get(json, 'file_name', input_file)
 
    call read_probe_locations(this, point_list, n_local, n_global, input_file)
 
    call this%add_points(point_list)
  end subroutine read_file
 
  subroutine read_point(this, json)
    class(probes_t), intent(inout) :: this
    type(json_file), intent(inout) :: json
 
    real(kind=rp), dimension(:,:), allocatable :: point_list
    real(kind=rp), dimension(:), allocatable :: rp_list_reader
 
    ! Ensure only rank 0 reads the coordinates.
    if (pe_rank .ne. 0) return
    call json_get(json, 'coordinates', rp_list_reader)
 
    if (mod(size(rp_list_reader), 3) /= 0) then
       call neko_error('Invalid number of coordinates.')
    end if
 
    ! Allocate list of points and reshape the input array
    allocate(point_list(3, size(rp_list_reader)/3))
    point_list = reshape(rp_list_reader, [3, size(rp_list_reader)/3])
 
    call this%add_points(point_list)
  end subroutine read_point
 
  subroutine read_line(this, json)
    class(probes_t), intent(inout) :: this
    type(json_file), intent(inout) :: json
 
    real(kind=rp), dimension(:,:), allocatable :: point_list
    real(kind=rp), dimension(:), allocatable :: start, end
    real(kind=rp), dimension(3) :: direction
    real(kind=rp) :: t
 
    integer :: n_points, i
 
    ! Ensure only rank 0 reads the coordinates.
    if (pe_rank .ne. 0) return
    call json_get(json, "start", start)
    call json_get(json, "end", end)
    call json_get(json, "amount", n_points)
 
    ! If either start or end is not of length 3, error out
    if (size(start) /= 3 .or. size(end) /= 3) then
       call neko_error('Invalid start or end coordinates.')
    end if
 
    ! Calculate the number of points
    allocate(point_list(3, n_points))
 
    ! Calculate the direction vector
    direction = end - start
    do i = 1, n_points
       t = real(i - 1, kind = rp) / real(n_points - 1, kind = rp)
       point_list(:, i) = start + direction * t
    end do
 
    call this%add_points(point_list)
  end subroutine read_line
 
  subroutine read_circle(this, json)
    class(probes_t), intent(inout) :: this
    type(json_file), intent(inout) :: json
 
    real(kind=rp), dimension(:,:), allocatable :: point_list
    real(kind=rp), dimension(:), allocatable :: center, normal
    real(kind=rp) :: radius
    real(kind=rp) :: angle
    integer :: n_points, i
    character(len=:), allocatable :: axis
 
    real(kind=rp), dimension(3) :: zero_line, cross_line, temp
    real(kind=rp) :: pi
 
    ! Ensure only rank 0 reads the coordinates.
    if (pe_rank .ne. 0) return
    call json_get(json, "center", center)
    call json_get(json, "normal", normal)
    call json_get(json, "radius", radius)
    call json_get(json, "amount", n_points)
    call json_get(json, "axis", axis)
 
    ! If either center or normal is not of length 3, error out
    if (size(center) /= 3 .or. size(normal) /= 3) then
       call neko_error('Invalid center or normal coordinates.')
    end if
    if (axis /= 'x' .and. axis /= 'y' .and. axis /= 'z') then
       call neko_error('Invalid axis.')
    end if
    if (radius <= 0) then
       call neko_error('Invalid radius.')
    end if
    if (n_points <= 0) then
       call neko_error('Invalid number of points.')
    end if
 
    ! Normalize the normal vector
    normal = normal / norm2(normal)
 
    ! Set the zero line
    if (axis .eq. 'x') zero_line = [1.0, 0.0, 0.0]
    if (axis .eq. 'y') zero_line = [0.0, 1.0, 0.0]
    if (axis .eq. 'z') zero_line = [0.0, 0.0, 1.0]
 
    if (1.0_rp - dot_product(zero_line, normal) .le. 1e-6) then
       call neko_error('Invalid axis and normal.')
    end if
 
    zero_line = zero_line - dot_product(zero_line, normal) * normal
    zero_line = zero_line / norm2(zero_line)
 
    cross_line(1) = normal(2) * zero_line(3) - normal(3) * zero_line(2)
    cross_line(2) = normal(3) * zero_line(1) - normal(1) * zero_line(3)
    cross_line(3) = normal(1) * zero_line(2) - normal(2) * zero_line(1)
 
    ! Calculate the number of points
    allocate(point_list(3, n_points))
 
    pi = 4.0_rp * atan(1.0_rp)
 
    ! Calculate the points
    do i = 1, n_points
       angle = 2.0_rp * pi * real(i - 1, kind = rp) / real(n_points, kind = rp)
       temp = cos(angle) * zero_line + sin(angle) * cross_line
 
       point_list(:, i) = center + radius * temp
    end do
 
    call this%add_points(point_list)
  end subroutine read_circle
 
  subroutine read_point_zone(this, json, dof)
    class(probes_t), intent(inout) :: this
    type(json_file), intent(inout) :: json
    type(dofmap_t), intent(in) :: dof
 
    real(kind=rp), dimension(:,:), allocatable :: point_list
    character(len=:), allocatable :: point_zone_name
    class(point_zone_t), pointer :: zone
    integer :: i, idx, lx, nlindex(4)
    real(kind=rp) :: x, y, z
 
    ! Ensure only rank 0 reads the coordinates.
    if (pe_rank .ne. 0) return
 
    call json_get(json, "name", point_zone_name)
    zone => neko_point_zone_registry%get_point_zone(point_zone_name)
 
    ! Allocate list of points and reshape the input array
    allocate(point_list(3, zone%size))
 
    lx = dof%Xh%lx
    do i = 1, zone%size
       idx = zone%mask%get(i)
 
       nlindex = nonlinear_index(idx, lx, lx, lx)
       x = dof%x(nlindex(1), nlindex(2), nlindex(3), nlindex(4))
       y = dof%y(nlindex(1), nlindex(2), nlindex(3), nlindex(4))
       z = dof%z(nlindex(1), nlindex(2), nlindex(3), nlindex(4))
 
       point_list(:, i) = [x, y, z]
    end do
 
    call this%add_points(point_list)
  end subroutine read_point_zone
 
  ! ========================================================================== !
  ! Supporting routines
 
  subroutine add_points(this, new_points)
    class(probes_t), intent(inout) :: this
    real(kind=rp), dimension(:,:), intent(in) :: new_points
 
    real(kind=rp), dimension(:,:), allocatable :: temp
    integer :: n_old, n_new
 
    ! Get the current number of points
    n_old = this%n_local_probes
    n_new = size(new_points, 2)
 
    ! Move current points to a temporary array
    if (allocated(this%xyz)) then
       call move_alloc(this%xyz, temp)
    end if
 
    ! Allocate the new array and copy the full list of points
    allocate(this%xyz(3, n_old + n_new))
    if (allocated(temp)) then
       this%xyz(:, 1:n_old) = temp
    end if
    this%xyz(:, n_old+1:n_old+n_new) = new_points
 
    this%n_local_probes = this%n_local_probes + n_new
  end subroutine add_points
 
  ! ========================================================================== !
  ! General initialization routine
 
  subroutine probes_init_from_components(this, dof, output_file)
    class(probes_t), intent(inout) :: this
    type(dofmap_t), intent(in) :: dof
    character(len=:), allocatable, intent(inout) :: output_file
    character(len=1024) :: header_line
    real(kind=rp), allocatable :: global_output_coords(:,:)
    integer :: i, ierr
    type(matrix_t) :: mat_coords
 
    call this%global_interp%init(dof)
 
    call this%global_interp%find_points_and_redist(this%xyz, &
         this%n_local_probes)
 
    allocate(this%out_values(this%n_local_probes, this%n_fields))
    allocate(this%out_values_d(this%n_fields))
    allocate(this%out_vals_trsp(this%n_fields, this%n_local_probes))
 
    if (neko_bcknd_device .eq. 1) then
       do i = 1, this%n_fields
          this%out_values_d(i) = c_null_ptr
          call device_map(this%out_values(:,i), this%out_values_d(i), &
               this%n_local_probes)
       end do
    end if
 
    call this%fout%init(trim(output_file))
 
    select type (ft => this%fout%file_type)
    type is (csv_file_t)
 
       this%seq_io = .true.
 
       ! Build the header
       write(header_line, '(I0,A,I0)') this%n_global_probes, ",", this%n_fields
       do i = 1, this%n_fields
          header_line = trim(header_line) // "," // trim(this%which_fields(i))
       end do
       call this%fout%set_header(header_line)
 
       allocate(this%n_local_probes_tot(pe_size))
       allocate(this%n_local_probes_tot_offset(pe_size))
       call this%setup_offset()
       if (pe_rank .eq. 0) then
          allocate(global_output_coords(3, this%n_global_probes))
          call this%mat_out%init(this%n_global_probes, this%n_fields)
          allocate(this%global_output_values(this%n_fields, &
               this%n_global_probes))
          call mat_coords%init(this%n_global_probes,3)
       end if
       call mpi_gatherv(this%xyz, 3*this%n_local_probes, &
            mpi_double_precision, global_output_coords, &
            3*this%n_local_probes_tot, &
            3*this%n_local_probes_tot_offset, &
            mpi_double_precision, 0, neko_comm, ierr)
       if (pe_rank .eq. 0) then
          call trsp(mat_coords%x, this%n_global_probes, &
               global_output_coords, 3)
          !! Write the data to the file
          call this%fout%write(mat_coords)
       end if
    class default
       call neko_error("Invalid data. Expected csv_file_t.")
    end select
 
  end subroutine probes_init_from_components
 
  subroutine probes_free(this)
    class(probes_t), intent(inout) :: this
 
    if (allocated(this%xyz)) then
       deallocate(this%xyz)
    end if
 
    if (allocated(this%out_values)) then
       deallocate(this%out_values)
    end if
 
    if (allocated(this%out_vals_trsp)) then
       deallocate(this%out_vals_trsp)
    end if
 
    call this%sampled_fields%free()
 
    if (allocated(this%n_local_probes_tot)) then
       deallocate(this%n_local_probes_tot)
    end if
 
    if (allocated(this%n_local_probes_tot_offset)) then
       deallocate(this%n_local_probes_tot_offset)
    end if
 
    if (allocated(this%global_output_values)) then
       deallocate(this%global_output_values)
    end if
 
    call this%global_interp%free()
 
  end subroutine probes_free
 
  subroutine probes_show(this)
    class(probes_t), intent(in) :: this
    character(len=LOG_SIZE) :: log_buf ! For logging status
    integer :: i
 
    ! Probes summary
    call neko_log%section('Probes')
    write(log_buf, '(A,I6)') "Number of probes: ", this%n_global_probes
    call neko_log%message(log_buf)
 
    call neko_log%message("xyz-coordinates:", lvl = neko_log_debug)
    do i = 1, this%n_local_probes
       write(log_buf, '("(",F10.6,",",F10.6,",",F10.6,")")') this%xyz(:,i)
       call neko_log%message(log_buf, lvl = neko_log_debug)
    end do
 
    ! Field summary
    write(log_buf, '(A,I6)') "Number of fields: ", this%n_fields
    call neko_log%message(log_buf)
    do i = 1, this%n_fields
       write(log_buf, '(A,I6,A,A)') &
            "Field: ", i, " ", trim(this%which_fields(i))
       call neko_log%message(log_buf, lvl = neko_log_debug)
    end do
    call neko_log%end_section()
    call neko_log%newline()
 
  end subroutine probes_show
 
  subroutine probes_debug(this)
    class(probes_t) :: this
 
    character(len=LOG_SIZE) :: log_buf ! For logging status
    integer :: i
 
    do i = 1, this%n_local_probes
       write (log_buf, *) pe_rank, "/", this%global_interp%proc_owner(i), &
            "/" , this%global_interp%el_owner(i), &
            "/", this%global_interp%error_code(i)
       call neko_log%message(log_buf)
       write(log_buf, '(A5,"(",F10.6,",",F10.6,",",F10.6,")")') &
            "rst: ", this%global_interp%rst(:,i)
       call neko_log%message(log_buf)
    end do
  end subroutine probes_debug
 
  subroutine probes_setup_offset(this)
    class(probes_t) :: this
    integer :: ierr
    this%n_local_probes_tot = 0
    this%n_local_probes_tot_offset = 0
    this%n_probes_offset = 0
    call mpi_gather(this%n_local_probes, 1, mpi_integer, &
         this%n_local_probes_tot, 1, mpi_integer, &
         0, neko_comm, ierr)
 
    call mpi_exscan(this%n_local_probes, this%n_probes_offset, 1, &
         mpi_integer, mpi_sum, neko_comm, ierr)
    call mpi_gather(this%n_probes_offset, 1, mpi_integer, &
         this%n_local_probes_tot_offset, 1, mpi_integer, &
         0, neko_comm, ierr)
 
 
 
  end subroutine probes_setup_offset
 
  subroutine probes_evaluate_and_write(this, time)
    class(probes_t), intent(inout) :: this
    type(time_state_t), intent(in) :: time
    integer :: i, ierr
 
    if (time%t .lt. this%start_time) return
 
    do i = 1, this%n_fields
       call this%global_interp%evaluate(this%out_values(:,i), &
            this%sampled_fields%items(i)%ptr%x)
    end do
 
    if (neko_bcknd_device .eq. 1) then
       do i = 1, this%n_fields
          call device_memcpy(this%out_values(:,i), this%out_values_d(i), &
               this%n_local_probes, device_to_host, sync = .true.)
       end do
    end if
 
    if (this%output_controller%check(time)) then
       ! Gather all values to rank 0
       ! If io is only done at root
       if (this%seq_io) then
          call trsp(this%out_vals_trsp, this%n_fields, &
               this%out_values, this%n_local_probes)
          call mpi_gatherv(this%out_vals_trsp, &
               this%n_fields*this%n_local_probes, &
               mpi_double_precision, this%global_output_values, &
               this%n_fields*this%n_local_probes_tot, &
               this%n_fields*this%n_local_probes_tot_offset, &
               mpi_double_precision, 0, neko_comm, ierr)
          if (pe_rank .eq. 0) then
             call trsp(this%mat_out%x, this%n_global_probes, &
                  this%global_output_values, this%n_fields)
             call this%fout%write(this%mat_out, time%t)
          end if
       else
          call neko_error('probes sim comp, parallel io need implementation')
       end if
 
       !! Register the execution of the activity
       call this%output_controller%register_execution()
    end if
 
  end subroutine probes_evaluate_and_write
 
  subroutine read_probe_locations(this, xyz, n_local_probes, n_global_probes, &
       points_file)
    class(probes_t), intent(inout) :: this
    character(len=:), allocatable :: points_file
    real(kind=rp), allocatable :: xyz(:,:)
    integer, intent(inout) :: n_local_probes, n_global_probes
 
    type(file_t) :: file_in
 
    call file_in%init(trim(points_file))
    select type (ft => file_in%file_type)
    type is (csv_file_t)
       call read_xyz_from_csv(xyz, n_local_probes, n_global_probes, ft)
       this%seq_io = .true.
    class default
       call neko_error("Invalid data. Expected csv_file_t.")
    end select
 
    call file_free(file_in)
 
  end subroutine read_probe_locations
 
  subroutine read_xyz_from_csv(xyz, n_local_probes, n_global_probes, f)
    type(csv_file_t), intent(inout) :: f
    real(kind=rp), allocatable :: xyz(:,:)
    integer, intent(inout) :: n_local_probes, n_global_probes
    type(matrix_t) :: mat_in, mat_in2
    integer :: n_lines
 
    n_lines = f%count_lines()
 
    ! Update the number of probes
    n_global_probes = n_lines
 
    ! Initialize the temporal array
    if (pe_rank .eq. 0) then
       n_local_probes = n_global_probes
       allocate(xyz(3, n_local_probes))
       call mat_in%init(n_global_probes,3)
       call mat_in2%init(3, n_global_probes)
       call f%read(mat_in)
       call trsp(xyz, 3, mat_in%x, n_global_probes)
    else
       n_local_probes = 0
       allocate(xyz(3, n_local_probes))
    end if
 
  end subroutine read_xyz_from_csv
end module probes