From 4273c849e8df48dd7ff2aa4ddf2dfd58f04f5ffc Mon Sep 17 00:00:00 2001 From: danieljvickers Date: Sun, 15 Mar 2026 07:51:06 -0400 Subject: [PATCH 01/11] Remove interior point conservative variable protection for stationary boundaries --- src/simulation/m_ibm.fpp | 22 ++++++++++------------ 1 file changed, 10 insertions(+), 12 deletions(-) diff --git a/src/simulation/m_ibm.fpp b/src/simulation/m_ibm.fpp index b87f5a1b19..d5eeb527cb 100644 --- a/src/simulation/m_ibm.fpp +++ b/src/simulation/m_ibm.fpp @@ -192,7 +192,7 @@ contains type(ghost_point) :: gp type(ghost_point) :: innerp - ! set the Moving IBM interior Pressure Values + ! set the Moving IBM interior conservative variables $:GPU_PARALLEL_LOOP(private='[i,j,k,patch_id,rho]', copyin='[E_idx,momxb]', collapse=3) do l = 0, p do k = 0, n @@ -200,18 +200,16 @@ contains patch_id = ib_markers%sf(j, k, l) if (patch_id /= 0) then q_prim_vf(E_idx)%sf(j, k, l) = 1._wp - if (patch_ib(patch_id)%moving_ibm > 0) then - rho = 0._wp - do i = 1, num_fluids - rho = rho + q_prim_vf(contxb + i - 1)%sf(j, k, l) - end do + rho = 0._wp + do i = 1, num_fluids + rho = rho + q_prim_vf(contxb + i - 1)%sf(j, k, l) + end do - ! Sets the momentum - do i = 1, num_dims - q_cons_vf(momxb + i - 1)%sf(j, k, l) = patch_ib(patch_id)%vel(i)*rho - q_prim_vf(momxb + i - 1)%sf(j, k, l) = patch_ib(patch_id)%vel(i) - end do - end if + ! Sets the momentum + do i = 1, num_dims + q_cons_vf(momxb + i - 1)%sf(j, k, l) = patch_ib(patch_id)%vel(i)*rho + q_prim_vf(momxb + i - 1)%sf(j, k, l) = patch_ib(patch_id)%vel(i) + end do end if end do end do From 89b8b976878f84df84354fe51c6ee9d1ed9c998b Mon Sep 17 00:00:00 2001 From: danieljvickers Date: Fri, 17 Apr 2026 18:03:55 -0400 Subject: [PATCH 02/11] Added parallel IB state writing --- src/simulation/m_data_output.fpp | 162 +++++++++++++++++++++++-------- 1 file changed, 120 insertions(+), 42 deletions(-) diff --git a/src/simulation/m_data_output.fpp b/src/simulation/m_data_output.fpp index 394882ef73..4a9f39b29e 100644 --- a/src/simulation/m_data_output.fpp +++ b/src/simulation/m_data_output.fpp @@ -24,15 +24,13 @@ module m_data_output private public :: s_initialize_data_output_module, s_open_run_time_information_file, s_open_com_files, s_open_probe_files, & - & s_open_ib_state_file, s_write_run_time_information, s_write_data_files, s_write_serial_data_files, & - & s_write_parallel_data_files, s_write_ib_data_file, s_write_com_files, s_write_probe_files, s_write_ib_state_file, & - & s_close_run_time_information_file, s_close_com_files, s_close_probe_files, s_close_ib_state_file, & - & s_finalize_data_output_module - - integer :: ib_state_unit = -1 !< I/O unit for IB state binary file - real(wp), allocatable, dimension(:,:,:) :: icfl_sf !< ICFL stability criterion - real(wp), allocatable, dimension(:,:,:) :: vcfl_sf !< VCFL stability criterion - real(wp), allocatable, dimension(:,:,:) :: Rc_sf !< Rc stability criterion + & s_write_run_time_information, s_write_data_files, s_write_serial_data_files, s_write_parallel_data_files, & + & s_write_ib_data_file, s_write_com_files, s_write_probe_files, s_write_ib_state_file, s_close_run_time_information_file, & + & s_close_com_files, s_close_probe_files, s_finalize_data_output_module + + real(wp), allocatable, dimension(:,:,:) :: icfl_sf !< ICFL stability criterion + real(wp), allocatable, dimension(:,:,:) :: vcfl_sf !< VCFL stability criterion + real(wp), allocatable, dimension(:,:,:) :: Rc_sf !< Rc stability criterion real(wp), public, allocatable, dimension(:,:) :: c_mass $:GPU_DECLARE(create='[icfl_sf, vcfl_sf, Rc_sf, c_mass]') @@ -161,26 +159,6 @@ contains end subroutine s_open_probe_files - !> Open the immersed boundary state file for binary output - impure subroutine s_open_ib_state_file - - character(len=path_len + 2*name_len) :: file_loc - integer :: ios - - call s_create_directory(trim(case_dir) // '/restart_data') - write (file_loc, '(A)') 'ib_state.dat' - file_loc = trim(case_dir) // '/restart_data/' // trim(file_loc) - if (t_step_start /= 0) then - ! On restart, append to existing file to preserve history - open (newunit=ib_state_unit, file=trim(file_loc), form='unformatted', access='stream', status='old', & - & position='append', iostat=ios) - else - open (newunit=ib_state_unit, file=trim(file_loc), form='unformatted', access='stream', status='replace', iostat=ios) - end if - if (ios /= 0) call s_mpi_abort('Cannot open IB state output file: ' // trim(file_loc)) - - end subroutine s_open_ib_state_file - !> Write stability criteria extrema to the run-time information file at the given time step impure subroutine s_write_run_time_information(q_prim_vf, t_step) @@ -918,16 +896,123 @@ contains end subroutine s_write_ib_data_file - !> @brief Writes IB state records to restart_data/ib_state.dat. Must be called only on rank 0. - impure subroutine s_write_ib_state_file() + !> Writes the IB state information out to file + subroutine s_write_parallel_ib_state(t_step) - integer :: i + integer, intent(in) :: t_step + + #ifdef MFC_MPI + character(LEN=path_len + 2*name_len) :: file_loc + integer(kind=MPI_OFFSET_KIND) :: disp + integer(kind=MPI_OFFSET_KIND) :: WP_MOK + integer :: ifile, ierr + integer, dimension(MPI_STATUS_SIZE) :: status + logical :: file_exist + integer :: i + integer, parameter :: NFIELDS_PER_IB = 19 + real(wp) :: ib_buf(NFIELDS_PER_IB) + + ! Partition IBs across ranks round-robin style + integer :: ib_start, ib_end, nibs_per_rank, remainder + + WP_MOK = int(storage_size(0._wp)/8, MPI_OFFSET_KIND) + + if (proc_rank == 0) then + call s_create_directory(trim(case_dir) // '/restart_data') + end if + call s_mpi_barrier() + + ! Divide num_ibs across num_procs + nibs_per_rank = num_ibs/num_procs + remainder = mod(num_ibs, num_procs) + + ! Ranks < remainder get one extra IB + if (proc_rank < remainder) then + ib_start = proc_rank*(nibs_per_rank + 1) + 1 + ib_end = ib_start + nibs_per_rank ! nibs_per_rank + 1 total + else + ib_start = remainder*(nibs_per_rank + 1) + (proc_rank - remainder)*nibs_per_rank + 1 + ib_end = ib_start + nibs_per_rank - 1 + end if + + write (file_loc, '(A,I0,A)') '/restart_data/ib_state_', t_step, '.dat' + file_loc = trim(case_dir) // trim(file_loc) + + inquire (FILE=trim(file_loc), EXIST=file_exist) + if (file_exist .and. proc_rank == 0) then + call MPI_FILE_DELETE(file_loc, mpi_info_int, ierr) + end if + call s_mpi_barrier() + + call MPI_FILE_OPEN(MPI_COMM_WORLD, file_loc, ior(MPI_MODE_WRONLY, MPI_MODE_CREATE), mpi_info_int, ifile, ierr) + + do i = ib_start, ib_end + ib_buf(1) = mytime + ib_buf(2:4) = patch_ib(i)%force(1:3) + ib_buf(5:7) = patch_ib(i)%torque(1:3) + ib_buf(8:10) = patch_ib(i)%vel(1:3) + ib_buf(11:13) = patch_ib(i)%angular_vel(1:3) + ib_buf(14:16) = patch_ib(i)%angles(1:3) + ib_buf(17) = patch_ib(i)%x_centroid + ib_buf(18) = patch_ib(i)%y_centroid + ib_buf(19) = patch_ib(i)%z_centroid + + ! Global IB index (i) determines position in file + disp = int(i - 1, MPI_OFFSET_KIND)*int(NFIELDS_PER_IB, MPI_OFFSET_KIND)*WP_MOK + + call MPI_FILE_WRITE_AT(ifile, disp, ib_buf, NFIELDS_PER_IB, mpi_p, status, ierr) + end do + + call MPI_FILE_CLOSE(ifile, ierr) + #endif + + end subroutine s_write_parallel_ib_state + + !> Write IB state data to a per-timestep serial (unformatted) file + subroutine s_write_serial_ib_state(t_step) + + integer, intent(in) :: t_step + character(LEN=path_len + 2*name_len) :: file_loc + integer :: i, ios, file_unit + integer, parameter :: NFIELDS_PER_IB = 19 + real(wp) :: ib_buf(NFIELDS_PER_IB) + + call s_create_directory(trim(case_dir) // '/restart_data') + + write (file_loc, '(A,I0,A)') '/restart_data/ib_state_', t_step, '.dat' + file_loc = trim(case_dir) // trim(file_loc) + + open (newunit=file_unit, file=trim(file_loc), form='unformatted', access='stream', status='replace', iostat=ios) + if (ios /= 0) call s_mpi_abort('Cannot open IB state output file: ' // trim(file_loc)) do i = 1, num_ibs - write (ib_state_unit) mytime, i, patch_ib(i)%force, patch_ib(i)%torque, patch_ib(i)%vel, patch_ib(i)%angular_vel, & - & patch_ib(i)%angles, patch_ib(i)%x_centroid, patch_ib(i)%y_centroid, patch_ib(i)%z_centroid + ib_buf(1) = mytime + ib_buf(2:4) = patch_ib(i)%force(1:3) + ib_buf(5:7) = patch_ib(i)%torque(1:3) + ib_buf(8:10) = patch_ib(i)%vel(1:3) + ib_buf(11:13) = patch_ib(i)%angular_vel(1:3) + ib_buf(14:16) = patch_ib(i)%angles(1:3) + ib_buf(17) = patch_ib(i)%x_centroid + ib_buf(18) = patch_ib(i)%y_centroid + ib_buf(19) = patch_ib(i)%z_centroid + + write (file_unit) ib_buf end do - flush (ib_state_unit) + + close (file_unit) + + end subroutine s_write_serial_ib_state + + !> @brief Writes IB state records to restart_data/ib_state.dat. Must be called only on rank 0. + impure subroutine s_write_ib_state_file(time_step) + + integer, intent(in) :: time_step + + if (parallel_io) then + call s_write_parallel_ib_state(time_step) + else + call s_write_serial_ib_state(time_step) + end if end subroutine s_write_ib_state_file @@ -1543,13 +1628,6 @@ contains end subroutine s_close_probe_files - !> Close the immersed boundary state file - impure subroutine s_close_ib_state_file - - close (ib_state_unit) - - end subroutine s_close_ib_state_file - !> Initialize the data output module impure subroutine s_initialize_data_output_module From ea12c518b54670f591d87df7554affce99ca9f2a Mon Sep 17 00:00:00 2001 From: danieljvickers Date: Fri, 17 Apr 2026 18:11:55 -0400 Subject: [PATCH 03/11] Now support restarting --- src/post_process/p_main.fpp | 4 --- src/simulation/m_start_up.fpp | 47 +++++++++++++++--------------- src/simulation/m_time_steppers.fpp | 10 ------- 3 files changed, 23 insertions(+), 38 deletions(-) diff --git a/src/post_process/p_main.fpp b/src/post_process/p_main.fpp index 64da30aa6b..20883a42a8 100644 --- a/src/post_process/p_main.fpp +++ b/src/post_process/p_main.fpp @@ -80,10 +80,6 @@ program p_main end do ! END: Time-Marching Loop - if (proc_rank == 0 .and. ib_state_wrt) then - call s_write_ib_state_files() - end if - close (11) call s_finalize_modules() diff --git a/src/simulation/m_start_up.fpp b/src/simulation/m_start_up.fpp index cf7a8a6ddd..52ddde10e1 100644 --- a/src/simulation/m_start_up.fpp +++ b/src/simulation/m_start_up.fpp @@ -914,7 +914,7 @@ contains if (model_eqns == 3) call s_initialize_internal_energy_equations(q_cons_ts(1)%vf) if (ib) then - if (t_step_start /= 0) call s_read_ib_restart_data() + if (t_step_start /= 0) call s_read_ib_restart_data(t_step_start) call s_ibm_setup() call s_write_ib_data_file(0) end if @@ -1135,38 +1135,37 @@ contains !> @brief Reads IB kinematic state from restart_data/ib_state.dat on restart. Rank 0 reads the last num_ibs records and !! broadcasts to all ranks. Overwrites patch_ib vel, angular_vel, angles, and centroid. - impure subroutine s_read_ib_restart_data() + impure subroutine s_read_ib_restart_data(t_step) + integer, intent(in) :: t_step character(len=path_len + 2*name_len) :: file_loc - integer :: i, ios, file_unit, ib_id, ierr - real(wp) :: time_read - real(wp), dimension(3) :: force_read, torque_read - real(wp), dimension(3) :: vel_read, angular_vel_read, angles_read - real(wp) :: xc_read, yc_read, zc_read + integer :: i, ios, file_unit, ierr + integer, parameter :: NFIELDS_PER_IB = 19 + real(wp) :: ib_buf(NFIELDS_PER_IB) logical :: file_exist + write (file_loc, '(A,I0,A)') '/restart_data/ib_state_', t_step, '.dat' + file_loc = trim(case_dir) // trim(file_loc) + if (proc_rank == 0) then - file_loc = trim(case_dir) // '/restart_data/ib_state.dat' inquire (FILE=trim(file_loc), EXIST=file_exist) - print *, "IB Restart File Exists: ", file_exist - if (file_exist) then - open (newunit=file_unit, file=trim(file_loc), form='unformatted', access='stream', status='old', iostat=ios) - print *, "iostat ", ios - else + if (.not. file_exist) then call s_mpi_abort('Cannot open IB state file for restart: ' // trim(file_loc)) end if - ! Read all records; the last num_ibs records are the final state - do - read (file_unit, iostat=ios) time_read, ib_id, force_read, torque_read, vel_read, angular_vel_read, angles_read, & - & xc_read, yc_read, zc_read - if (ios /= 0) exit - patch_ib(ib_id)%vel = vel_read - patch_ib(ib_id)%angular_vel = angular_vel_read - patch_ib(ib_id)%angles = angles_read - patch_ib(ib_id)%x_centroid = xc_read - patch_ib(ib_id)%y_centroid = yc_read - patch_ib(ib_id)%z_centroid = zc_read + open (newunit=file_unit, file=trim(file_loc), form='unformatted', access='stream', status='old', iostat=ios) + if (ios /= 0) call s_mpi_abort('Error opening IB state restart file: ' // trim(file_loc)) + + do i = 1, num_ibs + read (file_unit, iostat=ios) ib_buf + if (ios /= 0) call s_mpi_abort('Error reading IB state restart file') + + patch_ib(i)%vel = ib_buf(8:10) + patch_ib(i)%angular_vel = ib_buf(11:13) + patch_ib(i)%angles = ib_buf(14:16) + patch_ib(i)%x_centroid = ib_buf(17) + patch_ib(i)%y_centroid = ib_buf(18) + patch_ib(i)%z_centroid = ib_buf(19) end do close (file_unit) diff --git a/src/simulation/m_time_steppers.fpp b/src/simulation/m_time_steppers.fpp index 84a416c930..88d27cb975 100644 --- a/src/simulation/m_time_steppers.fpp +++ b/src/simulation/m_time_steppers.fpp @@ -394,11 +394,6 @@ contains call s_open_run_time_information_file() end if - ! Opening the ib state data file (used for restart and diagnostics) - if (proc_rank == 0 .and. ib) then - call s_open_ib_state_file() - end if - if (cfl_dt) then @:ALLOCATE(max_dt(0:m, 0:n, 0:p)) end if @@ -973,11 +968,6 @@ contains call s_close_run_time_information_file() end if - ! Closing the IB state data file - if (proc_rank == 0 .and. ib) then - call s_close_ib_state_file() - end if - end subroutine s_finalize_time_steppers_module end module m_time_steppers From cce3e5db92f5d84ac7b32c7adb549cb9bbc5c3a5 Mon Sep 17 00:00:00 2001 From: "Daniel J. Vickers" Date: Sun, 19 Apr 2026 17:57:46 -0400 Subject: [PATCH 04/11] Added subroutines for writing particle meshes from Ib states --- src/post_process/m_data_output.fpp | 137 +++++++++++++++++++++++++++++ 1 file changed, 137 insertions(+) diff --git a/src/post_process/m_data_output.fpp b/src/post_process/m_data_output.fpp index 3e7057ea09..cc6c8a1980 100644 --- a/src/post_process/m_data_output.fpp +++ b/src/post_process/m_data_output.fpp @@ -1341,6 +1341,143 @@ contains end subroutine s_write_energy_data_file + !> Read IB state from restart_data/ib_state_{t_step}.dat and write a Silo point mesh with per-body scalar fields. + impure subroutine s_write_ib_bodies_to_formatted_database_file(t_step) + + integer, intent(in) :: t_step + character(len=len_trim(case_dir) + 3*name_len) :: file_loc + +#ifdef MFC_MPI + integer, parameter :: NFIELDS_PER_IB = 19 + real(wp), dimension(:,:), allocatable :: ib_data ! (num_ibs, NFIELDS_PER_IB) + real(wp), dimension(:), allocatable :: px, py, pz + real(wp), dimension(:), allocatable :: fx, fy, fz + real(wp), dimension(:), allocatable :: tx, ty, tz + real(wp), dimension(:), allocatable :: vx, vy, vz + real(wp), dimension(:), allocatable :: ox, oy, oz + real(wp), dimension(:), allocatable :: ax, ay, az + real(wp), dimension(:), allocatable :: rad + real(wp) :: ib_buf(NFIELDS_PER_IB) + character(LEN=4*name_len), dimension(num_procs) :: meshnames + integer, dimension(num_procs) :: meshtypes + integer :: i, ios, file_unit, ierr + logical :: file_exist + + ! Build path to per-timestep IB state file + write (file_loc, '(A,I0,A)') '/restart_data/ib_state_', t_step, '.dat' + file_loc = trim(case_dir) // trim(file_loc) + + inquire (FILE=trim(file_loc), EXIST=file_exist) + if (.not. file_exist) then + ! No IB state file for this timestep - skip silently + return + end if + + allocate (ib_data(num_ibs, NFIELDS_PER_IB)) + + ! Rank 0 reads the entire file and broadcasts + if (proc_rank == 0) then + open (newunit=file_unit, file=trim(file_loc), form='unformatted', access='stream', status='old', iostat=ios) + if (ios /= 0) call s_mpi_abort('Cannot open IB state file: ' // trim(file_loc)) + + do i = 1, num_ibs + read (file_unit, iostat=ios) ib_buf + if (ios /= 0) call s_mpi_abort('Error reading IB state file at body ' // trim(file_loc)) + ib_data(i,:) = ib_buf(:) + end do + + close (file_unit) + end if + + call MPI_BCAST(ib_data, num_ibs*NFIELDS_PER_IB, mpi_p, 0, MPI_COMM_WORLD, ierr) + + ! Extract fields into per-variable arrays + allocate (px(num_ibs), py(num_ibs), pz(num_ibs)) + allocate (fx(num_ibs), fy(num_ibs), fz(num_ibs)) + allocate (tx(num_ibs), ty(num_ibs), tz(num_ibs)) + allocate (vx(num_ibs), vy(num_ibs), vz(num_ibs)) + allocate (ox(num_ibs), oy(num_ibs), oz(num_ibs)) + allocate (ax(num_ibs), ay(num_ibs), az(num_ibs)) + allocate (rad(num_ibs)) + + do i = 1, num_ibs + ! ib_buf layout: 1=mytime, 2:4=force, 5:7=torque, 8:10=vel, 11:13=angular_vel, 14:16=angles, 17=xc, 18=yc, 19=zc + fx(i) = ib_data(i, 2); fy(i) = ib_data(i, 3); fz(i) = ib_data(i, 4) + tx(i) = ib_data(i, 5); ty(i) = ib_data(i, 6); tz(i) = ib_data(i, 7) + vx(i) = ib_data(i, 8); vy(i) = ib_data(i, 9); vz(i) = ib_data(i, 10) + ox(i) = ib_data(i, 11); oy(i) = ib_data(i, 12); oz(i) = ib_data(i, 13) + ax(i) = ib_data(i, 14); ay(i) = ib_data(i, 15); az(i) = ib_data(i, 16) + px(i) = ib_data(i, 17); py(i) = ib_data(i, 18); pz(i) = ib_data(i, 19) + rad(i) = patch_ib(i)%radius + end do + + ! Write Silo point mesh - only rank 0 writes the multi-mesh entry + if (proc_rank == 0) then + do i = 1, num_procs + write (meshnames(i), '(A,I0,A,I0,A)') '../p', i - 1, '/', t_step, '.silo:ib_bodies' + meshtypes(i) = DB_POINTMESH + end do + err = DBSET2DSTRLEN(len(meshnames(1))) + err = DBPUTMMESH(dbroot, 'ib_bodies', 9, num_procs, meshnames, len_trim(meshnames), meshtypes, DB_F77NULL, ierr) + end if + + ! Every rank writes the same full set of IB bodies to its local silo file. This is consistent with how all ranks have + ! replicated IB state. + if (p > 0) then + err = DBPUTPM(dbfile, 'ib_bodies', 9, 3, px, py, pz, num_ibs, DB_DOUBLE, DB_F77NULL, ierr) + else + err = DBPUTPM(dbfile, 'ib_bodies', 9, 2, px, py, pz, num_ibs, DB_DOUBLE, DB_F77NULL, ierr) + end if + + ! Write per-body scalar variables + call s_write_ib_variable('ib_force_x', t_step, fx, num_ibs) + call s_write_ib_variable('ib_force_y', t_step, fy, num_ibs) + call s_write_ib_variable('ib_force_z', t_step, fz, num_ibs) + call s_write_ib_variable('ib_torque_x', t_step, tx, num_ibs) + call s_write_ib_variable('ib_torque_y', t_step, ty, num_ibs) + call s_write_ib_variable('ib_torque_z', t_step, tz, num_ibs) + call s_write_ib_variable('ib_vel_x', t_step, vx, num_ibs) + call s_write_ib_variable('ib_vel_y', t_step, vy, num_ibs) + call s_write_ib_variable('ib_vel_z', t_step, vz, num_ibs) + call s_write_ib_variable('ib_angular_vel_x', t_step, ox, num_ibs) + call s_write_ib_variable('ib_angular_vel_y', t_step, oy, num_ibs) + call s_write_ib_variable('ib_angular_vel_z', t_step, oz, num_ibs) + call s_write_ib_variable('ib_angle_x', t_step, ax, num_ibs) + call s_write_ib_variable('ib_angle_y', t_step, ay, num_ibs) + call s_write_ib_variable('ib_angle_z', t_step, az, num_ibs) + call s_write_ib_variable('ib_radius', t_step, rad, num_ibs) + + deallocate (ib_data, px, py, pz, fx, fy, fz, tx, ty, tz) + deallocate (vx, vy, vz, ox, oy, oz, ax, ay, az, rad) +#endif + + end subroutine s_write_ib_bodies_to_formatted_database_file + + !> Write a single IB point-variable to the Silo database slave and master files. + subroutine s_write_ib_variable(varname, t_step, data, nBodies) + + character(len=*), intent(in) :: varname + integer, intent(in) :: t_step + real(wp), dimension(:), intent(in) :: data + integer, intent(in) :: nBodies + character(len=4*name_len), dimension(num_procs) :: var_names + integer, dimension(num_procs) :: var_types + integer :: ierr, i + + if (proc_rank == 0) then + do i = 1, num_procs + write (var_names(i), '(A,I0,A,I0,A)') '../p', i - 1, '/', t_step, '.silo:' // trim(varname) + var_types(i) = DB_POINTVAR + end do + err = DBSET2DSTRLEN(len(var_names(1))) + err = DBPUTMVAR(dbroot, trim(varname), len_trim(varname), num_procs, var_names, len_trim(var_names), var_types, & + & DB_F77NULL, ierr) + end if + + err = DBPUTPV1(dbfile, trim(varname), len_trim(varname), 'ib_bodies', 9, data, nBodies, DB_DOUBLE, DB_F77NULL, ierr) + + end subroutine s_write_ib_variable + !> Close the formatted database slave file and, for the root process, the master file. impure subroutine s_close_formatted_database_file() From 0603f587636cc7363a8b45daebed6386e8a2cead Mon Sep 17 00:00:00 2001 From: "Daniel J. Vickers" Date: Sun, 19 Apr 2026 18:08:03 -0400 Subject: [PATCH 05/11] Finishing up mesh writing --- src/post_process/m_data_output.fpp | 4 ++-- src/post_process/m_start_up.fpp | 2 ++ toolchain/mfc/params/namelist_parser.py | 2 ++ 3 files changed, 6 insertions(+), 2 deletions(-) diff --git a/src/post_process/m_data_output.fpp b/src/post_process/m_data_output.fpp index cc6c8a1980..4743a4c2e0 100644 --- a/src/post_process/m_data_output.fpp +++ b/src/post_process/m_data_output.fpp @@ -19,8 +19,8 @@ module m_data_output & s_open_intf_data_file, s_open_energy_data_file, s_write_grid_to_formatted_database_file, & & s_write_variable_to_formatted_database_file, s_write_lag_bubbles_results_to_text, & & s_write_lag_bubbles_to_formatted_database_file, s_write_ib_state_files, s_write_intf_data_file, & - & s_write_energy_data_file, s_close_formatted_database_file, s_close_intf_data_file, s_close_energy_data_file, & - & s_finalize_data_output_module + & s_write_energy_data_file, s_write_ib_bodies_to_formatted_database_file, s_close_formatted_database_file, & + & s_close_intf_data_file, s_close_energy_data_file, s_finalize_data_output_module ! Include Silo-HDF5 interface library include 'silo_f9x.inc' diff --git a/src/post_process/m_start_up.fpp b/src/post_process/m_start_up.fpp index 48fe35abc1..b54e160fa3 100644 --- a/src/post_process/m_start_up.fpp +++ b/src/post_process/m_start_up.fpp @@ -746,6 +746,8 @@ contains if (lag_db_wrt) call s_write_lag_bubbles_to_formatted_database_file(t_step) ! silo file output end if + if (ib_state_wrt) call s_write_ib_bodies_to_formatted_database_file(t_step) + if (sim_data .and. proc_rank == 0) then call s_close_intf_data_file() call s_close_energy_data_file() diff --git a/toolchain/mfc/params/namelist_parser.py b/toolchain/mfc/params/namelist_parser.py index 8e4aa48c09..fdcb21d38a 100644 --- a/toolchain/mfc/params/namelist_parser.py +++ b/toolchain/mfc/params/namelist_parser.py @@ -174,6 +174,7 @@ "hyperelasticity", "hypoelasticity", "ib", + "ib_state_wrt", "ic_beta", "ic_eps", "igr", @@ -318,6 +319,7 @@ "hyperelasticity", "hypoelasticity", "ib", + "ib_state_wrt", "igr", "igr_order", "lag_betaC_wrt", From 4d25549a4a88e154b3e371b2b0ad3e94b0e60533 Mon Sep 17 00:00:00 2001 From: "Daniel J. Vickers" Date: Sun, 19 Apr 2026 18:40:04 -0400 Subject: [PATCH 06/11] Fixed compilation errors --- src/post_process/m_data_output.fpp | 6 +----- src/simulation/m_data_output.fpp | 4 ++-- src/simulation/m_start_up.fpp | 2 +- 3 files changed, 4 insertions(+), 8 deletions(-) diff --git a/src/post_process/m_data_output.fpp b/src/post_process/m_data_output.fpp index 4743a4c2e0..ea4cc18eb3 100644 --- a/src/post_process/m_data_output.fpp +++ b/src/post_process/m_data_output.fpp @@ -1356,7 +1356,6 @@ contains real(wp), dimension(:), allocatable :: vx, vy, vz real(wp), dimension(:), allocatable :: ox, oy, oz real(wp), dimension(:), allocatable :: ax, ay, az - real(wp), dimension(:), allocatable :: rad real(wp) :: ib_buf(NFIELDS_PER_IB) character(LEN=4*name_len), dimension(num_procs) :: meshnames integer, dimension(num_procs) :: meshtypes @@ -1398,7 +1397,6 @@ contains allocate (vx(num_ibs), vy(num_ibs), vz(num_ibs)) allocate (ox(num_ibs), oy(num_ibs), oz(num_ibs)) allocate (ax(num_ibs), ay(num_ibs), az(num_ibs)) - allocate (rad(num_ibs)) do i = 1, num_ibs ! ib_buf layout: 1=mytime, 2:4=force, 5:7=torque, 8:10=vel, 11:13=angular_vel, 14:16=angles, 17=xc, 18=yc, 19=zc @@ -1408,7 +1406,6 @@ contains ox(i) = ib_data(i, 11); oy(i) = ib_data(i, 12); oz(i) = ib_data(i, 13) ax(i) = ib_data(i, 14); ay(i) = ib_data(i, 15); az(i) = ib_data(i, 16) px(i) = ib_data(i, 17); py(i) = ib_data(i, 18); pz(i) = ib_data(i, 19) - rad(i) = patch_ib(i)%radius end do ! Write Silo point mesh - only rank 0 writes the multi-mesh entry @@ -1445,10 +1442,9 @@ contains call s_write_ib_variable('ib_angle_x', t_step, ax, num_ibs) call s_write_ib_variable('ib_angle_y', t_step, ay, num_ibs) call s_write_ib_variable('ib_angle_z', t_step, az, num_ibs) - call s_write_ib_variable('ib_radius', t_step, rad, num_ibs) deallocate (ib_data, px, py, pz, fx, fy, fz, tx, ty, tz) - deallocate (vx, vy, vz, ox, oy, oz, ax, ay, az, rad) + deallocate (vx, vy, vz, ox, oy, oz, ax, ay, az) #endif end subroutine s_write_ib_bodies_to_formatted_database_file diff --git a/src/simulation/m_data_output.fpp b/src/simulation/m_data_output.fpp index 4a9f39b29e..5c81137f63 100644 --- a/src/simulation/m_data_output.fpp +++ b/src/simulation/m_data_output.fpp @@ -901,7 +901,7 @@ contains integer, intent(in) :: t_step - #ifdef MFC_MPI +#ifdef MFC_MPI character(LEN=path_len + 2*name_len) :: file_loc integer(kind=MPI_OFFSET_KIND) :: disp integer(kind=MPI_OFFSET_KIND) :: WP_MOK @@ -964,7 +964,7 @@ contains end do call MPI_FILE_CLOSE(ifile, ierr) - #endif +#endif end subroutine s_write_parallel_ib_state diff --git a/src/simulation/m_start_up.fpp b/src/simulation/m_start_up.fpp index 52ddde10e1..4c5a87fe5c 100644 --- a/src/simulation/m_start_up.fpp +++ b/src/simulation/m_start_up.fpp @@ -818,7 +818,7 @@ contains end if ! Write IB kinematic state for restart - if (ib .and. proc_rank == 0) call s_write_ib_state_file() + if (ib) call s_write_ib_state_file(t_step) call nvtxEndRange call cpu_time(finish) From 100dc020fe77f59473f6a4624ba2d77064a81ee7 Mon Sep 17 00:00:00 2001 From: danieljvickers Date: Mon, 20 Apr 2026 12:35:07 -0400 Subject: [PATCH 07/11] Particle mesh writes successfully --- src/post_process/m_data_output.fpp | 152 ++++++++++++++--------------- src/simulation/m_data_output.fpp | 6 +- src/simulation/m_start_up.fpp | 1 + 3 files changed, 80 insertions(+), 79 deletions(-) diff --git a/src/post_process/m_data_output.fpp b/src/post_process/m_data_output.fpp index ea4cc18eb3..add1fe3768 100644 --- a/src/post_process/m_data_output.fpp +++ b/src/post_process/m_data_output.fpp @@ -1341,26 +1341,28 @@ contains end subroutine s_write_energy_data_file - !> Read IB state from restart_data/ib_state_{t_step}.dat and write a Silo point mesh with per-body scalar fields. + !> Read IB state and write a Silo point mesh with per-body scalar fields. impure subroutine s_write_ib_bodies_to_formatted_database_file(t_step) integer, intent(in) :: t_step character(len=len_trim(case_dir) + 3*name_len) :: file_loc #ifdef MFC_MPI - integer, parameter :: NFIELDS_PER_IB = 19 - real(wp), dimension(:,:), allocatable :: ib_data ! (num_ibs, NFIELDS_PER_IB) - real(wp), dimension(:), allocatable :: px, py, pz - real(wp), dimension(:), allocatable :: fx, fy, fz - real(wp), dimension(:), allocatable :: tx, ty, tz - real(wp), dimension(:), allocatable :: vx, vy, vz - real(wp), dimension(:), allocatable :: ox, oy, oz - real(wp), dimension(:), allocatable :: ax, ay, az + integer, parameter :: NFIELDS_PER_IB = 20 real(wp) :: ib_buf(NFIELDS_PER_IB) + real(wp), dimension(:,:), allocatable :: ib_data + logical :: file_exist character(LEN=4*name_len), dimension(num_procs) :: meshnames integer, dimension(num_procs) :: meshtypes - integer :: i, ios, file_unit, ierr - logical :: file_exist + integer :: i, ios, file_unit + integer :: ierr, nBodies + real(wp), dimension(:), allocatable :: px, py, pz + real(wp), dimension(:), allocatable :: force_x, force_y, force_z + real(wp), dimension(:), allocatable :: torque_x, torque_y, torque_z + real(wp), dimension(:), allocatable :: vel_x, vel_y, vel_z + real(wp), dimension(:), allocatable :: omega_x, omega_y, omega_z + real(wp), dimension(:), allocatable :: angle_x, angle_y, angle_z + real(wp), dimension(:), allocatable :: ib_radius ! Build path to per-timestep IB state file write (file_loc, '(A,I0,A)') '/restart_data/ib_state_', t_step, '.dat' @@ -1368,83 +1370,79 @@ contains inquire (FILE=trim(file_loc), EXIST=file_exist) if (.not. file_exist) then - ! No IB state file for this timestep - skip silently - return + call s_mpi_abort('Restart file ' // trim(file_loc) // ' does not exist!') end if - allocate (ib_data(num_ibs, NFIELDS_PER_IB)) - - ! Rank 0 reads the entire file and broadcasts - if (proc_rank == 0) then - open (newunit=file_unit, file=trim(file_loc), form='unformatted', access='stream', status='old', iostat=ios) - if (ios /= 0) call s_mpi_abort('Cannot open IB state file: ' // trim(file_loc)) + nBodies = num_ibs - do i = 1, num_ibs - read (file_unit, iostat=ios) ib_buf - if (ios /= 0) call s_mpi_abort('Error reading IB state file at body ' // trim(file_loc)) - ib_data(i,:) = ib_buf(:) - end do + if (nBodies > 0) then + allocate (ib_data(nBodies, NFIELDS_PER_IB)) + allocate (px(nBodies), py(nBodies), pz(nBodies)) + allocate (force_x(nBodies), force_y(nBodies), force_z(nBodies)) + allocate (torque_x(nBodies), torque_y(nBodies), torque_z(nBodies)) + allocate (vel_x(nBodies), vel_y(nBodies), vel_z(nBodies)) + allocate (omega_x(nBodies), omega_y(nBodies), omega_z(nBodies)) + allocate (angle_x(nBodies), angle_y(nBodies), angle_z(nBodies)) + allocate (ib_radius(nBodies)) - close (file_unit) - end if + if (proc_rank == 0) then + open (newunit=file_unit, file=trim(file_loc), form='unformatted', access='stream', status='old', iostat=ios) + if (ios /= 0) call s_mpi_abort('Cannot open IB state file: ' // trim(file_loc)) - call MPI_BCAST(ib_data, num_ibs*NFIELDS_PER_IB, mpi_p, 0, MPI_COMM_WORLD, ierr) + do i = 1, nBodies + read (file_unit, iostat=ios) ib_buf + if (ios /= 0) call s_mpi_abort('Error reading IB state file') + ib_data(i,:) = ib_buf(:) + end do - ! Extract fields into per-variable arrays - allocate (px(num_ibs), py(num_ibs), pz(num_ibs)) - allocate (fx(num_ibs), fy(num_ibs), fz(num_ibs)) - allocate (tx(num_ibs), ty(num_ibs), tz(num_ibs)) - allocate (vx(num_ibs), vy(num_ibs), vz(num_ibs)) - allocate (ox(num_ibs), oy(num_ibs), oz(num_ibs)) - allocate (ax(num_ibs), ay(num_ibs), az(num_ibs)) + close (file_unit) + end if - do i = 1, num_ibs - ! ib_buf layout: 1=mytime, 2:4=force, 5:7=torque, 8:10=vel, 11:13=angular_vel, 14:16=angles, 17=xc, 18=yc, 19=zc - fx(i) = ib_data(i, 2); fy(i) = ib_data(i, 3); fz(i) = ib_data(i, 4) - tx(i) = ib_data(i, 5); ty(i) = ib_data(i, 6); tz(i) = ib_data(i, 7) - vx(i) = ib_data(i, 8); vy(i) = ib_data(i, 9); vz(i) = ib_data(i, 10) - ox(i) = ib_data(i, 11); oy(i) = ib_data(i, 12); oz(i) = ib_data(i, 13) - ax(i) = ib_data(i, 14); ay(i) = ib_data(i, 15); az(i) = ib_data(i, 16) - px(i) = ib_data(i, 17); py(i) = ib_data(i, 18); pz(i) = ib_data(i, 19) - end do + call MPI_BCAST(ib_data, nBodies*NFIELDS_PER_IB, mpi_p, 0, MPI_COMM_WORLD, ierr) - ! Write Silo point mesh - only rank 0 writes the multi-mesh entry - if (proc_rank == 0) then - do i = 1, num_procs - write (meshnames(i), '(A,I0,A,I0,A)') '../p', i - 1, '/', t_step, '.silo:ib_bodies' - meshtypes(i) = DB_POINTMESH + do i = 1, nBodies + force_x(i) = ib_data(i, 2); force_y(i) = ib_data(i, 3); force_z(i) = ib_data(i, 4) + torque_x(i) = ib_data(i, 5); torque_y(i) = ib_data(i, 6); torque_z(i) = ib_data(i, 7) + vel_x(i) = ib_data(i, 8); vel_y(i) = ib_data(i, 9); vel_z(i) = ib_data(i, 10) + omega_x(i) = ib_data(i, 11); omega_y(i) = ib_data(i, 12); omega_z(i) = ib_data(i, 13) + angle_x(i) = ib_data(i, 14); angle_y(i) = ib_data(i, 15); angle_z(i) = ib_data(i, 16) + px(i) = ib_data(i, 17); py(i) = ib_data(i, 18); pz(i) = ib_data(i, 19) + ib_radius(i) = ib_data(i, 20) end do - err = DBSET2DSTRLEN(len(meshnames(1))) - err = DBPUTMMESH(dbroot, 'ib_bodies', 9, num_procs, meshnames, len_trim(meshnames), meshtypes, DB_F77NULL, ierr) - end if - ! Every rank writes the same full set of IB bodies to its local silo file. This is consistent with how all ranks have - ! replicated IB state. - if (p > 0) then - err = DBPUTPM(dbfile, 'ib_bodies', 9, 3, px, py, pz, num_ibs, DB_DOUBLE, DB_F77NULL, ierr) - else - err = DBPUTPM(dbfile, 'ib_bodies', 9, 2, px, py, pz, num_ibs, DB_DOUBLE, DB_F77NULL, ierr) - end if + if (proc_rank == 0) then + do i = 1, num_procs + write (meshnames(i), '(A,I0,A,I0,A)') '../p', i - 1, '/', t_step, '.silo:ib_bodies' + meshtypes(i) = DB_POINTMESH + end do + err = DBSET2DSTRLEN(len(meshnames(1))) + err = DBPUTMMESH(dbroot, 'ib_bodies', 16, num_procs, meshnames, len_trim(meshnames), meshtypes, DB_F77NULL, ierr) + end if - ! Write per-body scalar variables - call s_write_ib_variable('ib_force_x', t_step, fx, num_ibs) - call s_write_ib_variable('ib_force_y', t_step, fy, num_ibs) - call s_write_ib_variable('ib_force_z', t_step, fz, num_ibs) - call s_write_ib_variable('ib_torque_x', t_step, tx, num_ibs) - call s_write_ib_variable('ib_torque_y', t_step, ty, num_ibs) - call s_write_ib_variable('ib_torque_z', t_step, tz, num_ibs) - call s_write_ib_variable('ib_vel_x', t_step, vx, num_ibs) - call s_write_ib_variable('ib_vel_y', t_step, vy, num_ibs) - call s_write_ib_variable('ib_vel_z', t_step, vz, num_ibs) - call s_write_ib_variable('ib_angular_vel_x', t_step, ox, num_ibs) - call s_write_ib_variable('ib_angular_vel_y', t_step, oy, num_ibs) - call s_write_ib_variable('ib_angular_vel_z', t_step, oz, num_ibs) - call s_write_ib_variable('ib_angle_x', t_step, ax, num_ibs) - call s_write_ib_variable('ib_angle_y', t_step, ay, num_ibs) - call s_write_ib_variable('ib_angle_z', t_step, az, num_ibs) - - deallocate (ib_data, px, py, pz, fx, fy, fz, tx, ty, tz) - deallocate (vx, vy, vz, ox, oy, oz, ax, ay, az) + err = DBPUTPM(dbfile, 'ib_bodies', 9, 3, px, py, pz, nBodies, DB_DOUBLE, DB_F77NULL, ierr) + + call s_write_ib_variable('ib_force_x', t_step, force_x, nBodies) + call s_write_ib_variable('ib_force_y', t_step, force_y, nBodies) + call s_write_ib_variable('ib_force_z', t_step, force_z, nBodies) + call s_write_ib_variable('ib_torque_x', t_step, torque_x, nBodies) + call s_write_ib_variable('ib_torque_y', t_step, torque_y, nBodies) + call s_write_ib_variable('ib_torque_z', t_step, torque_z, nBodies) + call s_write_ib_variable('ib_vel_x', t_step, vel_x, nBodies) + call s_write_ib_variable('ib_vel_y', t_step, vel_y, nBodies) + call s_write_ib_variable('ib_vel_z', t_step, vel_z, nBodies) + call s_write_ib_variable('ib_omega_x', t_step, omega_x, nBodies) + call s_write_ib_variable('ib_omega_y', t_step, omega_y, nBodies) + call s_write_ib_variable('ib_omega_z', t_step, omega_z, nBodies) + call s_write_ib_variable('ib_angle_x', t_step, angle_x, nBodies) + call s_write_ib_variable('ib_angle_y', t_step, angle_y, nBodies) + call s_write_ib_variable('ib_angle_z', t_step, angle_z, nBodies) + call s_write_ib_variable('ib_radius', t_step, ib_radius, nBodies) + + deallocate (ib_data, px, py, pz, force_x, force_y, force_z) + deallocate (torque_x, torque_y, torque_z, vel_x, vel_y, vel_z) + deallocate (omega_x, omega_y, omega_z, angle_x, angle_y, angle_z) + deallocate (ib_radius) + end if #endif end subroutine s_write_ib_bodies_to_formatted_database_file diff --git a/src/simulation/m_data_output.fpp b/src/simulation/m_data_output.fpp index 5c81137f63..ca8a6c0677 100644 --- a/src/simulation/m_data_output.fpp +++ b/src/simulation/m_data_output.fpp @@ -909,7 +909,7 @@ contains integer, dimension(MPI_STATUS_SIZE) :: status logical :: file_exist integer :: i - integer, parameter :: NFIELDS_PER_IB = 19 + integer, parameter :: NFIELDS_PER_IB = 20 real(wp) :: ib_buf(NFIELDS_PER_IB) ! Partition IBs across ranks round-robin style @@ -956,6 +956,7 @@ contains ib_buf(17) = patch_ib(i)%x_centroid ib_buf(18) = patch_ib(i)%y_centroid ib_buf(19) = patch_ib(i)%z_centroid + ib_buf(20) = patch_ib(i)%radius ! Global IB index (i) determines position in file disp = int(i - 1, MPI_OFFSET_KIND)*int(NFIELDS_PER_IB, MPI_OFFSET_KIND)*WP_MOK @@ -974,7 +975,7 @@ contains integer, intent(in) :: t_step character(LEN=path_len + 2*name_len) :: file_loc integer :: i, ios, file_unit - integer, parameter :: NFIELDS_PER_IB = 19 + integer, parameter :: NFIELDS_PER_IB = 20 real(wp) :: ib_buf(NFIELDS_PER_IB) call s_create_directory(trim(case_dir) // '/restart_data') @@ -995,6 +996,7 @@ contains ib_buf(17) = patch_ib(i)%x_centroid ib_buf(18) = patch_ib(i)%y_centroid ib_buf(19) = patch_ib(i)%z_centroid + ib_buf(20) = patch_ib(i)%radius write (file_unit) ib_buf end do diff --git a/src/simulation/m_start_up.fpp b/src/simulation/m_start_up.fpp index 4c5a87fe5c..31a3270936 100644 --- a/src/simulation/m_start_up.fpp +++ b/src/simulation/m_start_up.fpp @@ -917,6 +917,7 @@ contains if (t_step_start /= 0) call s_read_ib_restart_data(t_step_start) call s_ibm_setup() call s_write_ib_data_file(0) + call s_write_ib_state_file(0) end if if (bodyForces) call s_initialize_body_forces_module() if (acoustic_source) call s_precalculate_acoustic_spatial_sources() From 3712069ad855f151231c6a4d734762ea16dea4c9 Mon Sep 17 00:00:00 2001 From: danieljvickers Date: Mon, 20 Apr 2026 14:34:23 -0400 Subject: [PATCH 08/11] Added ib state write to the shock cylinder example, so it is documented, and updated a mass value while I was at it. Regenerated golden files to handle IB state data output --- examples/2D_mibm_shock_cylinder/case.py | 3 ++- tests/7FA04E95/golden-metadata.txt | 23 ++++++++++++----------- tests/7FA04E95/golden.txt | 8 ++++---- 3 files changed, 18 insertions(+), 16 deletions(-) diff --git a/examples/2D_mibm_shock_cylinder/case.py b/examples/2D_mibm_shock_cylinder/case.py index 0ca5cbb635..69aca0cc9b 100644 --- a/examples/2D_mibm_shock_cylinder/case.py +++ b/examples/2D_mibm_shock_cylinder/case.py @@ -87,6 +87,7 @@ "precision": 2, "prim_vars_wrt": "T", "E_wrt": "T", + "ib_state_wrt": "T", "parallel_io": "T", # Patch: Constant Tube filled with air # Specify the cylindrical air tube grid geometry @@ -128,7 +129,7 @@ "patch_ib(1)%angular_vel(1)": 0.0, # x-axis rotational velocity in radians per second "patch_ib(1)%angular_vel(2)": 0.0, # y-axis rotation "patch_ib(1)%angular_vel(3)": 0.0, # z-axis rotation - "patch_ib(1)%mass": 0.5, # z-axis rotation + "patch_ib(1)%mass": 0.25, # z-axis rotation # Fluids Physical Parameters "fluid_pp(1)%gamma": 1.0e00 / (gam_a - 1.0e00), # 2.50(Not 1.40) "fluid_pp(1)%pi_inf": 0, diff --git a/tests/7FA04E95/golden-metadata.txt b/tests/7FA04E95/golden-metadata.txt index 5464c03831..f652d6d036 100644 --- a/tests/7FA04E95/golden-metadata.txt +++ b/tests/7FA04E95/golden-metadata.txt @@ -1,12 +1,12 @@ -This file was created on 2026-01-10 09:30:46.874399. +This file was created on 2026-04-20 14:32:49.351215. mfc.sh: - Invocation: test --generate -o 7FA04E95 - Lock: mpi=Yes & gpu=No & debug=No & gcov=No & unified=No & single=No & mixed=No & fastmath=No - Git: e262ef9387a432cc58ead795fa521c27e17e29be on viscous-stress-and-ellipse-ib (dirty) + Invocation: test --only 7FA04E95 --generate + Lock: mpi=Yes & gpu=No & debug=No & reldebug=No & gcov=No & unified=No & single=No & mixed=No & fastmath=No + Git: 100dc020fe77f59473f6a4624ba2d77064a81ee7 on parallel-state-write (dirty) -simulation: +post_process: CMake Configuration: @@ -16,8 +16,8 @@ simulation: Fortran : GNU v13.3.0 (/usr/bin/gfortran) PRE_PROCESS : OFF - SIMULATION : ON - POST_PROCESS : OFF + SIMULATION : OFF + POST_PROCESS : ON SYSCHECK : OFF DOCUMENTATION : OFF ALL : OFF @@ -74,7 +74,7 @@ pre_process: OMPI_CXX : OMPI_FC : -post_process: +simulation: CMake Configuration: @@ -84,8 +84,8 @@ post_process: Fortran : GNU v13.3.0 (/usr/bin/gfortran) PRE_PROCESS : OFF - SIMULATION : OFF - POST_PROCESS : ON + SIMULATION : ON + POST_PROCESS : OFF SYSCHECK : OFF DOCUMENTATION : OFF ALL : OFF @@ -160,7 +160,7 @@ CPU: Core(s) per socket: 12 Socket(s): 1 Stepping: 2 - CPU(s) scaling MHz: 29% + CPU(s) scaling MHz: 36% CPU max MHz: 5100.0000 CPU min MHz: 800.0000 BogoMIPS: 7219.20 @@ -180,6 +180,7 @@ CPU: Vulnerability Mds: Not affected Vulnerability Meltdown: Not affected Vulnerability Mmio stale data: Not affected + Vulnerability Old microcode: Not affected Vulnerability Reg file data sampling: Mitigation; Clear Register File Vulnerability Retbleed: Not affected Vulnerability Spec rstack 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1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 \ No newline at end of file From 77d51d5e35b390efeef81dbc7d472987e1c69412 Mon Sep 17 00:00:00 2001 From: danieljvickers Date: Mon, 20 Apr 2026 14:47:05 -0400 Subject: [PATCH 09/11] Changed output to use IB's diameter so mesh scaling is 1.0 --- src/post_process/m_data_output.fpp | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/post_process/m_data_output.fpp b/src/post_process/m_data_output.fpp index add1fe3768..aece31ff8d 100644 --- a/src/post_process/m_data_output.fpp +++ b/src/post_process/m_data_output.fpp @@ -1362,7 +1362,7 @@ contains real(wp), dimension(:), allocatable :: vel_x, vel_y, vel_z real(wp), dimension(:), allocatable :: omega_x, omega_y, omega_z real(wp), dimension(:), allocatable :: angle_x, angle_y, angle_z - real(wp), dimension(:), allocatable :: ib_radius + real(wp), dimension(:), allocatable :: ib_diameter ! Build path to per-timestep IB state file write (file_loc, '(A,I0,A)') '/restart_data/ib_state_', t_step, '.dat' @@ -1383,7 +1383,7 @@ contains allocate (vel_x(nBodies), vel_y(nBodies), vel_z(nBodies)) allocate (omega_x(nBodies), omega_y(nBodies), omega_z(nBodies)) allocate (angle_x(nBodies), angle_y(nBodies), angle_z(nBodies)) - allocate (ib_radius(nBodies)) + allocate (ib_diameter(nBodies)) if (proc_rank == 0) then open (newunit=file_unit, file=trim(file_loc), form='unformatted', access='stream', status='old', iostat=ios) @@ -1407,7 +1407,7 @@ contains omega_x(i) = ib_data(i, 11); omega_y(i) = ib_data(i, 12); omega_z(i) = ib_data(i, 13) angle_x(i) = ib_data(i, 14); angle_y(i) = ib_data(i, 15); angle_z(i) = ib_data(i, 16) px(i) = ib_data(i, 17); py(i) = ib_data(i, 18); pz(i) = ib_data(i, 19) - ib_radius(i) = ib_data(i, 20) + ib_diameter(i) = ib_data(i, 20)*2.0_wp end do if (proc_rank == 0) then @@ -1436,12 +1436,12 @@ contains call s_write_ib_variable('ib_angle_x', t_step, angle_x, nBodies) call s_write_ib_variable('ib_angle_y', t_step, angle_y, nBodies) call s_write_ib_variable('ib_angle_z', t_step, angle_z, nBodies) - call s_write_ib_variable('ib_radius', t_step, ib_radius, nBodies) + call s_write_ib_variable('ib_diameter', t_step, ib_diameter, nBodies) deallocate (ib_data, px, py, pz, force_x, force_y, force_z) deallocate (torque_x, torque_y, torque_z, vel_x, vel_y, vel_z) deallocate (omega_x, omega_y, omega_z, angle_x, angle_y, angle_z) - deallocate (ib_radius) + deallocate (ib_diameter) end if #endif From 90cfb5a4628331625f2e9be4346943b662860568 Mon Sep 17 00:00:00 2001 From: danieljvickers Date: Mon, 20 Apr 2026 15:07:08 -0400 Subject: [PATCH 10/11] Added protection so that restarts do not overwrite time-step 0 --- src/simulation/m_start_up.fpp | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/src/simulation/m_start_up.fpp b/src/simulation/m_start_up.fpp index 31a3270936..157b865464 100644 --- a/src/simulation/m_start_up.fpp +++ b/src/simulation/m_start_up.fpp @@ -914,10 +914,12 @@ contains if (model_eqns == 3) call s_initialize_internal_energy_equations(q_cons_ts(1)%vf) if (ib) then - if (t_step_start /= 0) call s_read_ib_restart_data(t_step_start) + if (t_step_start > 0) call s_read_ib_restart_data(t_step_start) call s_ibm_setup() - call s_write_ib_data_file(0) - call s_write_ib_state_file(0) + if (t_step_start == 0) then + call s_write_ib_data_file(0) + call s_write_ib_state_file(0) + end if end if if (bodyForces) call s_initialize_body_forces_module() if (acoustic_source) call s_precalculate_acoustic_spatial_sources() From 2fd5c084bb8f0c68e544493f02c45b1d6e6838b8 Mon Sep 17 00:00:00 2001 From: danieljvickers Date: Mon, 20 Apr 2026 15:39:37 -0400 Subject: [PATCH 11/11] Update restart data buff size --- src/simulation/m_start_up.fpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/simulation/m_start_up.fpp b/src/simulation/m_start_up.fpp index 157b865464..9ff90fbdd7 100644 --- a/src/simulation/m_start_up.fpp +++ b/src/simulation/m_start_up.fpp @@ -1143,7 +1143,7 @@ contains integer, intent(in) :: t_step character(len=path_len + 2*name_len) :: file_loc integer :: i, ios, file_unit, ierr - integer, parameter :: NFIELDS_PER_IB = 19 + integer, parameter :: NFIELDS_PER_IB = 20 real(wp) :: ib_buf(NFIELDS_PER_IB) logical :: file_exist