Merge pull request #1648 from timfelle/fix/ibm_device

Fix bugs and update mesh preparation script

examples/immersed_bunny/.gitignore

@@ -3,5 +3,5 @@
 !.gitignore
 !*.case
 !readme.md
-!run.sh
+!prepare.sh
 !bunny.stl

examples/immersed_zones/run.sh → examples/immersed_bunny/prepare.sh

@@ -4,37 +4,34 @@
 # Define the help function
 
 function help() {
-    echo -e "run.sh case"
-    echo -e "  Generate a mesh and run all the desired case."
+    echo -e "prepare.sh case"
+    echo -e "  Generate a mesh to prepare for the desired case."
     echo -e "  The input arguments are the number of cells in the x, y, and z"
     echo -e "  directions, respectively."
     echo -e ""
     echo -e "  If no input arguments are provided, the default mesh size is"
     echo -e "  32x8x8."
     echo -e ""
     echo -e "  Example usage:"
-    echo -e "    run.sh -x32 -y8 -z8 case_name.case"
+    echo -e "    prepare.sh -x32 -y8 -z8"
     echo -e ""
     echo -e " Options:"
     echo -e "  -h, --help  Show this help message and exit."
     echo -e "  -x#         Number of cells in the x direction."
     echo -e "  -y#         Number of cells in the y direction."
     echo -e "  -z#         Number of cells in the z direction."
-    echo -e "  -a, --all   Run all cases."
     echo -e "  -q, --quiet Suppress output."
     echo -e ""
     echo -e "  See Readme for additional details."
     exit 0
 }
-if [ $# -eq 0 ]; then ALL=1; fi
 
 # Handle options
 Nx=32 && Ny=8 && Nz=8
 for arg in "$@"; do
     if [ "${arg:0:2}" == "--" ]; then
         case ${arg:2} in
         help) help ;;
-        all) ALL=1 ;;
         quiet) QUIET=1 ;;
         *) echo -e "Invalid option: $arg" >&2 && help ;;
         esac
@@ -44,7 +41,6 @@ for arg in "$@"; do
         x) Nx=${arg:2} ;;
         y) Ny=${arg:2} ;;
         z) Nz=${arg:2} ;;
-        a) ALL=1 ;;
         q) QUIET=1 ;;
         *) echo -e "Invalid option: ${arg:1}" >&2 && help ;;
         esac
@@ -53,38 +49,25 @@ for arg in "$@"; do
     fi
 done
 
-if [ "$ALL" ]; then
-    cases=$(find $(dirname $0) -name "*.case")
-fi
-
 # ============================================================================ #
 # Ensure Neko can be found and set default mesh size
 
 if [ "$NEKO_DIR" ]; then
     PATH=$NEKO_DIR/bin:$PATH
 fi
 
-if [[ -z $(which neko) ]]; then
+if [[ -z $(which genmeshbox) ]]; then
     echo -e "Neko not found." >&2
     echo -e "Please ensure Neko is installed and in your PATH." >&2
     echo -e "Alternatively, set the NEKO_DIR environment variable." >&2
     exit 1
 fi
 
 # ============================================================================ #
-# Generate mesh and run case
+# Generate mesh and prepare case
 
 echo "Generating mesh with dimensions: $Nx $Ny $Nz"
 genmeshbox 0 4 0 1 0 1 $Nx $Ny $Nz .false. .false. .false.
 
-for case in $cases; do
-    echo "Running case: $case"
-    if [ "$QUIET" ]; then
-        neko $case >/dev/null
-    else
-        neko $case >${case%.case}.log
-    fi
-done
-
 # End of file
 # ============================================================================ #

examples/immersed_zones/.gitignore

@@ -3,4 +3,4 @@
 !.gitignore
 !*.case
 !readme.md
-!run.sh
+!prepare.sh

examples/immersed_zones/prepare.sh

@@ -0,0 +1,73 @@
+#!/usr/bin/bash
+
+# ============================================================================ #
+# Define the help function
+
+function help() {
+    echo -e "prepare.sh case"
+    echo -e "  Generate a mesh to prepare for the desired case."
+    echo -e "  The input arguments are the number of cells in the x, y, and z"
+    echo -e "  directions, respectively."
+    echo -e ""
+    echo -e "  If no input arguments are provided, the default mesh size is"
+    echo -e "  32x8x8."
+    echo -e ""
+    echo -e "  Example usage:"
+    echo -e "    prepare.sh -x32 -y8 -z8"
+    echo -e ""
+    echo -e " Options:"
+    echo -e "  -h, --help  Show this help message and exit."
+    echo -e "  -x#         Number of cells in the x direction."
+    echo -e "  -y#         Number of cells in the y direction."
+    echo -e "  -z#         Number of cells in the z direction."
+    echo -e "  -q, --quiet Suppress output."
+    echo -e ""
+    echo -e "  See Readme for additional details."
+    exit 0
+}
+
+# Handle options
+Nx=32 && Ny=8 && Nz=8
+for arg in "$@"; do
+    if [ "${arg:0:2}" == "--" ]; then
+        case ${arg:2} in
+        help) help ;;
+        quiet) QUIET=1 ;;
+        *) echo -e "Invalid option: $arg" >&2 && help ;;
+        esac
+    elif [ "${arg:0:1}" == "-" ]; then
+        case ${arg:1:1} in
+        h) help ;;
+        x) Nx=${arg:2} ;;
+        y) Ny=${arg:2} ;;
+        z) Nz=${arg:2} ;;
+        q) QUIET=1 ;;
+        *) echo -e "Invalid option: ${arg:1}" >&2 && help ;;
+        esac
+    else
+        cases="$cases $arg"
+    fi
+done
+
+# ============================================================================ #
+# Ensure Neko can be found and set default mesh size
+
+if [ "$NEKO_DIR" ]; then
+    PATH=$NEKO_DIR/bin:$PATH
+fi
+
+if [[ -z $(which genmeshbox) ]]; then
+    echo -e "Neko not found." >&2
+    echo -e "Please ensure Neko is installed and in your PATH." >&2
+    echo -e "Alternatively, set the NEKO_DIR environment variable." >&2
+    exit 1
+fi
+
+# ============================================================================ #
+# Generate mesh and prepare case
+
+echo "Generating mesh with dimensions: $Nx $Ny $Nz"
+genmeshbox 0 4 0 1 0 1 $Nx $Ny $Nz .false. .false. .false.
+
+# End of file
+# ============================================================================ #

src/.depends

@@ -302,7 +302,7 @@ source_terms/boussinesq_source_term.lo : source_terms/boussinesq_source_term.f90
 source_terms/bcknd/cpu/boussinesq_source_term_cpu.lo : source_terms/bcknd/cpu/boussinesq_source_term_cpu.f90 math/math.lo field/field.lo field/field_list.lo config/num_types.lo 
 source_terms/bcknd/device/boussinesq_source_term_device.lo : source_terms/bcknd/device/boussinesq_source_term_device.f90 math/bcknd/device/device_math.lo field/field.lo field/field_list.lo config/num_types.lo 
 source_terms/source_term_fctry.lo : source_terms/source_term_fctry.f90 common/utils.lo common/json_utils.lo source_terms/coriolis_source_term.lo source_terms/brinkman_source_term.lo source_terms/boussinesq_source_term.lo source_terms/const_source_term.lo source_terms/source_term.lo 
-source_terms/brinkman_source_term.lo : source_terms/brinkman_source_term.f90 mesh/point_zone_registry.lo mesh/point_zone.lo mesh/search_tree/aabb.lo common/profiler.lo math/signed_distance.lo source_terms/brinkman/filters.lo device/device.lo mesh/tri_mesh.lo io/file.lo math/bcknd/device/device_math.lo math/math.lo math/field_math.lo common/utils.lo config/neko_config.lo sem/coef.lo source_terms/source_term.lo field/field_registry.lo common/json_utils.lo field/field_list.lo field/field.lo config/num_types.lo 
+source_terms/brinkman_source_term.lo : source_terms/brinkman_source_term.f90 common/utils.lo source_terms/source_term.lo math/signed_distance.lo common/profiler.lo mesh/point_zone_registry.lo mesh/point_zone.lo config/num_types.lo config/neko_config.lo mesh/tri_mesh.lo math/math.lo common/log.lo common/json_utils.lo io/file.lo source_terms/brinkman/filters.lo field/field_registry.lo math/field_math.lo field/field_list.lo field/field.lo math/bcknd/device/device_math.lo device/device.lo sem/coef.lo mesh/search_tree/aabb.lo 
 source_terms/brinkman/filters.lo : source_terms/brinkman/filters.f90 source_terms/bcknd/device/filters_device.lo source_terms/bcknd/cpu/filters_cpu.lo common/utils.lo config/num_types.lo config/neko_config.lo field/field.lo 
 source_terms/bcknd/cpu/filters_cpu.lo : source_terms/bcknd/cpu/filters_cpu.f90 config/num_types.lo 
 source_terms/bcknd/device/filters_device.lo : source_terms/bcknd/device/filters_device.F90 source_terms/bcknd/device/opencl/opencl_filters.lo source_terms/bcknd/device/hip/hip_filters.lo source_terms/bcknd/device/cuda/cuda_filters.lo common/utils.lo math/bcknd/device/device_math.lo config/num_types.lo 

src/source_terms/brinkman_source_term.f90

@@ -32,20 +32,29 @@
 !
 !> Implements the `brinkman_source_term_t` type.
 module brinkman_source_term
-  use num_types, only: rp, dp
+  use aabb, only : aabb_t, get_aabb
+  use coefs, only: coef_t
+  use device, only: device_memcpy, HOST_TO_DEVICE
+  use device_math, only: device_pwmax, device_cfill_mask
   use field, only: field_t
   use field_list, only: field_list_t
-  use json_module, only: json_file
-  use json_utils, only: json_get, json_get_or_default, json_extract_item
+  use field_math, only: field_subcol3
   use field_registry, only: neko_field_registry
-  use source_term, only: source_term_t
-  use coefs, only: coef_t
+  use filters, only: smooth_step_field, step_function_field, permeability_field
+  use file, only: file_t
+  use json_module, only: json_file, json_core, json_value
+  use json_utils, only: json_get, json_get_or_default, json_extract_item
+  use logger, only: neko_log, LOG_SIZE
+  use math, only: pwmax, cfill_mask
+  use tri_mesh, only: tri_mesh_t
   use neko_config, only: NEKO_BCKND_DEVICE
+  use num_types, only: rp, dp
+  use point_zone, only: point_zone_t
+  use point_zone_registry, only: neko_point_zone_registry
+  use profiler, only: profiler_start_region, profiler_end_region
+  use signed_distance, only: signed_distance_field
+  use source_term, only: source_term_t
   use utils, only: neko_error
-  use field_math, only: field_subcol3
-
-  use math, only: pwmax
-  use device_math, only: device_pwmax
   implicit none
   private
 
@@ -84,16 +93,6 @@ module brinkman_source_term
   !! @param fields A list of fields for adding the source values.
   !! @param coef The SEM coeffs.
   subroutine brinkman_source_term_init_from_json(this, json, fields, coef)
-    use file, only: file_t
-    use tri_mesh, only: tri_mesh_t
-    use device, only: device_memcpy, HOST_TO_DEVICE
-    use filters, only: smooth_step_field, step_function_field, &
-         permeability_field
-    use signed_distance, only: signed_distance_field
-    use profiler, only: profiler_start_region, profiler_end_region
-    use json_module, only: json_core, json_value
-    implicit none
-
     class(brinkman_source_term_t), intent(inout) :: this
     type(json_file), intent(inout) :: json
     type(field_list_t), intent(in), target :: fields
@@ -190,6 +189,7 @@ subroutine brinkman_source_term_free(this)
     call this%indicator%free()
     call this%brinkman%free()
     call this%free_base()
+
   end subroutine brinkman_source_term_free
 
   !> Computes the source term and adds the result to `fields`.
@@ -223,16 +223,6 @@ end subroutine brinkman_source_term_compute
 
   !> Initializes the source term from a boundary mesh.
   subroutine init_boundary_mesh(this, json)
-    use file, only: file_t
-    use tri_mesh, only: tri_mesh_t
-    use device, only: device_memcpy, HOST_TO_DEVICE
-    use filters, only: smooth_step_field, step_function_field, &
-         permeability_field
-    use signed_distance, only: signed_distance_field
-    use profiler, only: profiler_start_region, profiler_end_region
-    use aabb, only : aabb_t, get_aabb
-    implicit none
-
     class(brinkman_source_term_t), intent(inout) :: this
     type(json_file), intent(inout) :: json
 
@@ -256,6 +246,7 @@ subroutine init_boundary_mesh(this, json)
     type(field_t) :: temp_field
     type(aabb_t) :: mesh_box, target_box
     integer :: idx_p
+    character(len=LOG_SIZE) :: log_msg
 
     ! ------------------------------------------------------------------------ !
     ! Read the options for the boundary mesh
@@ -311,6 +302,14 @@ subroutine init_boundary_mesh(this, json)
                scaling * boundary_mesh%points(idx_p)%x + translation
        end do
 
+       ! Report the transformation applied
+       write(log_msg, '(A)') "The following transformation was applied:"
+       call neko_log%message(log_msg)
+       write(log_msg, '(A, 3F12.6)') "Scaling: ", scaling
+       call neko_log%message(log_msg)
+       write(log_msg, '(A, 3F12.6)') "Translation: ", translation
+       call neko_log%message(log_msg)
+
       case default
        call neko_error('Unknown mesh transform')
     end select
@@ -369,15 +368,6 @@ end subroutine init_boundary_mesh
 
   !> Initializes the source term from a point zone.
   subroutine init_point_zone(this, json)
-    use filters, only: smooth_step_field, step_function_field, &
-         permeability_field
-    use signed_distance, only: signed_distance_field
-    use profiler, only: profiler_start_region, profiler_end_region
-    use point_zone, only: point_zone_t
-    use device, only: device_memcpy, HOST_TO_DEVICE
-    use point_zone_registry, only: neko_point_zone_registry
-    implicit none
-
     class(brinkman_source_term_t), intent(inout) :: this
     type(json_file), intent(inout) :: json
 
@@ -400,9 +390,13 @@ subroutine init_point_zone(this, json)
 
     my_point_zone => neko_point_zone_registry%get_point_zone(zone_name)
 
-    do i = 1, my_point_zone%size
-       temp_field%x(my_point_zone%mask(i), 1, 1, 1) = 1.0_rp
-    end do
+    if (NEKO_BCKND_DEVICE .eq. 1) then
+       call device_cfill_mask(temp_field%x_d, 1.0_rp, temp_field%size(), &
+            my_point_zone%mask_d, my_point_zone%size)
+    else
+       call cfill_mask(temp_field%x, 1.0_rp, temp_field%size(), &
+            my_point_zone%mask, my_point_zone%size)
+    end if
 
     ! Run filter on the temporary indicator field to smooth it out.
 
@@ -414,7 +408,12 @@ subroutine init_point_zone(this, json)
     end select
 
     ! Update the global indicator field by max operator
-    this%indicator%x = max(this%indicator%x, temp_field%x)
+    if (NEKO_BCKND_DEVICE .eq. 1) then
+       call device_pwmax(this%indicator%x_d, temp_field%x_d, &
+            this%indicator%size())
+    else
+       this%indicator%x = max(this%indicator%x, temp_field%x)
+    end if
 
   end subroutine init_point_zone