Merge remote-tracking branch 'remotes/upstream/master'

Author: JRChreim

README.md

@@ -107,7 +107,7 @@ The weak scaling of MFC on this machine shows near-ideal utilization.
 ## What else can this thing do
 
 MFC has many features.
-They are organized below. Just click the drop-downs!
+They are organized below.
 
 ### Physics
 
@@ -158,7 +158,8 @@ They are organized below. Just click the drop-downs!
 * GPU compatible on NVIDIA ([P/V/A/H]100, GH200, etc.) and AMD (MI[1/2/3]00+) GPU and APU hardware
 * Ideal weak scaling to 100% of the largest GPU and superchip supercomputers
 	* \>10K NVIDIA GPUs on [OLCF Summit](https://www.olcf.ornl.gov/summit/) (NV V100-based)
-	* \>66K AMD GPUs on the first exascale computer, [OLCF Frontier](https://www.olcf.ornl.gov/frontier/) (AMD MI250X-based)
+	* \>66K AMD GPUs (MI250X) on the first exascale computer, [OLCF Frontier](https://www.olcf.ornl.gov/frontier/) (AMD MI250X-based)
+ 	* \>3K AMD APUs on [LLNL Tuolumne](https://hpc.llnl.gov/hardware/compute-platforms/tuolumne) (El Capitan family, AMD MI300A-based) 
 * Near compute roofline behavior
 * RDMA (remote data memory access; GPU-GPU direct communication) via GPU-aware MPI on NVIDIA (CUDA-aware MPI) and AMD GPU systems
 * Optional single-precision computation and storage

src/common/m_helper.fpp

@@ -315,10 +315,11 @@ contains
     !> This procedure creates a transformation matrix.
     !! @param  p Parameters for the transformation.
     !! @return Transformation matrix.
-    function f_create_transform_matrix(p) result(out_matrix)
+    function f_create_transform_matrix(p, center) result(out_matrix)
 
         type(ic_model_parameters), intent(in) :: p
-        t_mat4x4 :: sc, rz, rx, ry, tr, out_matrix
+        t_vec3, optional, intent(in) :: center
+        t_mat4x4 :: sc, rz, rx, ry, tr, t_back, t_to_origin, out_matrix
 
         sc = transpose(reshape([ &
                                p%scale(1), 0._wp, 0._wp, 0._wp, &
@@ -350,7 +351,25 @@ contains
                                0._wp, 0._wp, 1._wp, p%translate(3), &
                                0._wp, 0._wp, 0._wp, 1._wp], shape(tr)))
 
-        out_matrix = matmul(tr, matmul(ry, matmul(rx, matmul(rz, sc))))
+        if (present(center)) then
+            ! Translation matrix to move center to the origin
+            t_to_origin = transpose(reshape([ &
+                                            1._wp, 0._wp, 0._wp, -center(1), &
+                                            0._wp, 1._wp, 0._wp, -center(2), &
+                                            0._wp, 0._wp, 1._wp, -center(3), &
+                                            0._wp, 0._wp, 0._wp, 1._wp], shape(tr)))
+
+            ! Translation matrix to move center back to original position
+            t_back = transpose(reshape([ &
+                                       1._wp, 0._wp, 0._wp, center(1), &
+                                       0._wp, 1._wp, 0._wp, center(2), &
+                                       0._wp, 0._wp, 1._wp, center(3), &
+                                       0._wp, 0._wp, 0._wp, 1._wp], shape(tr)))
+
+            out_matrix = matmul(tr, matmul(t_back, matmul(ry, matmul(rx, matmul(rz, matmul(sc, t_to_origin))))))
+        else
+            out_matrix = matmul(ry, matmul(rx, rz))
+        end if
 
     end function f_create_transform_matrix
 
@@ -372,10 +391,10 @@ contains
     !> This procedure transforms a triangle by a matrix, one vertex at a time.
     !! @param triangle Triangle to transform.
     !! @param matrix   Transformation matrix.
-    subroutine s_transform_triangle(triangle, matrix)
+    subroutine s_transform_triangle(triangle, matrix, matrix_n)
 
         type(t_triangle), intent(inout) :: triangle
-        t_mat4x4, intent(in) :: matrix
+        t_mat4x4, intent(in) :: matrix, matrix_n
 
         integer :: i
 
@@ -385,20 +404,22 @@ contains
             call s_transform_vec(triangle%v(i, :), matrix)
         end do
 
+        call s_transform_vec(triangle%n(1:3), matrix_n)
+
     end subroutine s_transform_triangle
 
     !> This procedure transforms a model by a matrix, one triangle at a time.
     !! @param model  Model to transform.
     !! @param matrix Transformation matrix.
-    subroutine s_transform_model(model, matrix)
+    subroutine s_transform_model(model, matrix, matrix_n)
 
         type(t_model), intent(inout) :: model
-        t_mat4x4, intent(in) :: matrix
+        t_mat4x4, intent(in) :: matrix, matrix_n
 
         integer :: i
 
         do i = 1, size(model%trs)
-            call s_transform_triangle(model%trs(i), matrix)
+            call s_transform_triangle(model%trs(i), matrix, matrix_n)
         end do
 
     end subroutine s_transform_model

src/pre_process/m_patches.fpp

@@ -1978,18 +1978,18 @@ contains
 
         integer :: i, j, k !< Generic loop iterators
 
-        type(t_bbox) :: bbox
+        type(t_bbox) :: bbox, bbox_old
         type(t_model) :: model
         type(ic_model_parameters) :: params
 
-        t_vec3 :: point
+        t_vec3 :: point, model_center
 
         real(wp) :: grid_mm(1:3, 1:2)
 
         integer :: cell_num
         integer :: ncells
 
-        t_mat4x4 :: transform
+        t_mat4x4 :: transform, transform_n
 
         if (present(ib) .and. proc_rank == 0) then
             print *, " * Reading model: "//trim(patch_ib(patch_id)%model_filepath)
@@ -2017,9 +2017,17 @@ contains
             print *, " * Transforming model."
         end if
 
-        transform = f_create_transform_matrix(params)
-        call s_transform_model(model, transform)
+        ! Get the model center before transforming the model
+        bbox_old = f_create_bbox(model)
+        model_center(1:3) = (bbox_old%min(1:3) + bbox_old%max(1:3))/2._wp
 
+        ! Compute the transform matrices for vertices and normals
+        transform = f_create_transform_matrix(params, model_center)
+        transform_n = f_create_transform_matrix(params)
+
+        call s_transform_model(model, transform, transform_n)
+
+        ! Recreate the bounding box after transformation
         bbox = f_create_bbox(model)
 
         ! Show the number of vertices in the original STL model

src/simulation/m_start_up.fpp

@@ -665,7 +665,7 @@ contains
 
                         call MPI_FILE_SET_VIEW(ifile, disp, MPI_INTEGER, MPI_IO_IB_DATA%view, &
                                                'native', mpi_info_int, ierr)
-                        call MPI_FILE_READ(ifile, MPI_IO_IB_DATA%var%sf, data_size * num_ibs, &
+                        call MPI_FILE_READ(ifile, MPI_IO_IB_DATA%var%sf, data_size, &
                                            MPI_INTEGER, status, ierr)
 
                     else
@@ -834,7 +834,7 @@ contains
 
                         call MPI_FILE_SET_VIEW(ifile, disp, mpi_p, MPI_IO_levelset_DATA%view, &
                                                'native', mpi_info_int, ierr)
-                        call MPI_FILE_READ(ifile, MPI_IO_levelset_DATA%var%sf, data_size, &
+                        call MPI_FILE_READ(ifile, MPI_IO_levelset_DATA%var%sf, data_size * num_ibs, &
                                            mpi_p, status, ierr)
 
                     else