Merge branch 'add-hard-coded-patched-for-tests' of github.com:danieljvickers/MFC into add-hard-coded-patched-for-tests

Author: danieljvickers

README.md

@@ -137,7 +137,6 @@ They are organized below.
 * Acoustic wave generation (one- and two-way sound sources)
 * Magnetohydrodynamics (MHD)
 * Relativistic Magnetohydrodynamics (RMHD)
-</details>
 
 ### Numerics
 
@@ -157,7 +156,6 @@ They are organized below.
 * RK4-5 operator splitting for Euler-Lagrange modeling
 * Interface sharpening (THINC-like)
 
-
 ### Large-scale and accelerated simulation
 
 * GPU compatible on NVIDIA ([P/V/A/H]100, GH200, etc.) and AMD (MI[1/2/3]00+) GPU and APU hardware
@@ -182,27 +180,20 @@ They are organized below.
 
 ## Citation
 
-If you use MFC, consider citing it as:
-
-<p align="center">
-  <a href="https://doi.org/10.1016/j.cpc.2020.107396">
-    S. H. Bryngelson, K. Schmidmayer, V. Coralic, K. Maeda, J. Meng, T. Colonius (2021) Computer Physics Communications <b>266</b>, 107396
-  </a>
-</p>
+If you use MFC, consider citing it as below.
+Ref. 1 includes all modern MFC features, including GPU acceleration and many new physics features.
+If referencing MFC's (GPU) performance, consider citing ref. 1 and 2, which describe the solver and how it was crafted.
+The original open-source release of MFC is ref. 3, which should be cited for provenance as appropriate.
 
 ```bibtex
-@article{Bryngelson_2021,
-  title   = {{MFC: A}n open-source high-order multi-component, multi-phase, and multi-scale compressible flow solver},
-  author  = {S. H. Bryngelson and K. Schmidmayer and V. Coralic and J. C. Meng and K. Maeda and T. Colonius},
-  journal = {Computer Physics Communications},
-  year    = {2021},
-  volume  = {266},
-  pages   = {107396},
-  doi     = {10.1016/j.cpc.2020.107396}
+@article{Wilfong_2025,
+  author = {Wilfong, Benjamin and {Le Berre}, Henry and Radhakrishnan, Anand and Gupta, Ansh and Vaca-Revelo, Diego and Adam, Dimitrios and Yu, Haocheng and Lee, Hyeoksu and Chreim, Jose Rodolfo and {Carcana Barbosa}, Mirelys and Zhang, Yanjun and Cisneros-Garibay, Esteban and Gnanaskandan, Aswin and {Rodriguez Jr.}, Mauro and Budiardja, Reuben D. and Abbott, Stephen and Colonius, Tim and Bryngelson, Spencer H.},
+  title = {{MFC 5.0: A}n exascale many-physics flow solver},
+  journal = {arXiv preprint arXiv:2503.07953},
+  year = {2025},
+  doi = {10.48550/arXiv.2503.07953}
 }
-```
 
-```bibtex
 @article{Radhakrishnan_2024,
   title   = {Method for portable, scalable, and performant {GPU}-accelerated simulation of multiphase compressible flow},
   author  = {A. Radhakrishnan and H. {Le Berre} and B. Wilfong and J.-S. Spratt and M. {Rodriguez Jr.} and T. Colonius and S. H. Bryngelson},
@@ -212,6 +203,16 @@ If you use MFC, consider citing it as:
   pages   = {109238},
   doi     = {10.1016/j.cpc.2024.109238}
 }
+
+@article{Bryngelson_2021,
+  title   = {{MFC: A}n open-source high-order multi-component, multi-phase, and multi-scale compressible flow solver},
+  author  = {S. H. Bryngelson and K. Schmidmayer and V. Coralic and J. C. Meng and K. Maeda and T. Colonius},
+  journal = {Computer Physics Communications},
+  year    = {2021},
+  volume  = {266},
+  pages   = {107396},
+  doi     = {10.1016/j.cpc.2020.107396}
+}
 ```
 
 ## License
@@ -225,12 +226,7 @@ Federal sponsors have supported MFC development, including the US Department of
 
 MFC computations have used many supercomputing systems. A partial list is below
   * OLCF Frontier and Summit, and testbeds Wombat, Crusher, and Spock (allocation CFD154, PI Bryngelson)
-  * LLNL Tuolumne and Lassen, El Capitan early access system Tioga
-  * PSC Bridges(1/2), NCSA Delta, SDSC Comet and Expanse, Purdue Anvil, TACC Stampede(1-3), and TAMU ACES via ACCESS-CI allocations from Bryngelson, Colonius, Rodriguez, and more.
-  * DOD systems Onyx, Carpenter, Nautilus, and Narwhal via the DOD HPCMP program
+  * LLNL El Capitan, Tuolumne, and Lassen; El Capitan early access system Tioga
+  * NCSA Delta and DeltaAI, PSC Bridges(1/2), SDSC Comet and Expanse, Purdue Anvil, TACC Stampede(1-3), and TAMU ACES via ACCESS-CI allocations from Bryngelson, Colonius, Rodriguez, and more.
+  * DOD systems Blueback, Onyx, Carpenter, Nautilus, and Narwhal via the DOD HPCMP program
   * Sandia National Labs systems Doom and Attaway and testbed systems Weaver and Vortex
-
-
-## Contributors
-
-[![Contributors](https://contributors-img.web.app/image?repo=mflowcode/mfc)](https://github.com/mflowcode/mfc/graphs/contributors)

src/common/m_derived_types.fpp

@@ -443,4 +443,10 @@ module m_derived_types
 
     end type bubbles_lagrange_parameters
 
+    !> Max and min number of cells in a direction of each combination of x-,y-, and z-
+    type cell_num_bounds
+        integer :: mn_max, np_max, mp_max, mnp_max
+        integer :: mn_min, np_min, mp_min, mnp_min
+    end type cell_num_bounds
+
 end module m_derived_types

src/common/m_helper_basic.fpp

@@ -16,7 +16,8 @@ module m_helper_basic
               f_is_default, &
               f_all_default, &
               f_is_integer, &
-              s_configure_coordinate_bounds
+              s_configure_coordinate_bounds, &
+              s_update_cell_bounds
 
 contains
 
@@ -146,4 +147,24 @@ contains
 
     end subroutine s_configure_coordinate_bounds
 
+    !> Updates the min and max number of cells in each set of axes
+    !! @param bounds Min ans max values to update
+    !! @param m Number of cells in x-axis
+    !! @param n Number of cells in y-axis
+    !! @param p Number of cells in z-axis
+    pure elemental subroutine s_update_cell_bounds(bounds, m, n, p)
+        type(cell_num_bounds), intent(out) :: bounds
+        integer, intent(in) :: m, n, p
+
+        bounds%mn_max = max(m, n)
+        bounds%np_max = max(n, p)
+        bounds%mp_max = max(m, p)
+        bounds%mnp_max = max(m, n, p)
+        bounds%mn_min = min(m, n)
+        bounds%np_min = min(n, p)
+        bounds%mp_min = min(m, p)
+        bounds%mnp_min = min(m, n, p)
+
+    end subroutine s_update_cell_bounds
+
 end module m_helper_basic

src/common/m_mpi_common.fpp

@@ -67,10 +67,10 @@ contains
                                          & (m + 2*buff_size + 1)* &
                                          & (n + 2*buff_size + 1)* &
                                          & (p + 2*buff_size + 1)/ &
-                                         & (min(m, n, p) + 2*buff_size + 1))
+                                         & (cells_bounds%mnp_min + 2*buff_size + 1))
             else
                 halo_size = -1 + buff_size*(v_size)* &
-                                         & (max(m, n) + 2*buff_size + 1)
+                                         & (cells_bounds%mn_max + 2*buff_size + 1)
             end if
         else
             halo_size = -1 + buff_size*(v_size)
@@ -1446,6 +1446,8 @@ contains
             end if
         end do
 
+        call s_update_cell_bounds(cells_bounds, m, n, p)
+
         ! Boundary condition at the beginning
         if (proc_coords(1) > 0 .or. (bc_x%beg == BC_PERIODIC .and. num_procs_x > 1)) then
             proc_coords(1) = proc_coords(1) - 1

src/common/m_variables_conversion.fpp

@@ -637,7 +637,7 @@ contains
 #ifdef MFC_SIMULATION
 
         if (viscous) then
-            @:ALLOCATE(Res(1:2, 1:maxval(Re_size)))
+            @:ALLOCATE(Res(1:2, 1:Re_size_max))
             do i = 1, 2
                 do j = 1, Re_size(i)
                     Res(i, j) = fluid_pp(Re_idx(i, j))%Re(i)

src/post_process/m_global_parameters.fpp

@@ -38,6 +38,9 @@ module m_global_parameters
     integer :: p
     !> @}
 
+    !> @name Max and min number of cells in a direction of each combination of x-,y-, and z-
+    type(cell_num_bounds) :: cells_bounds
+
     integer(8) :: nGlobal ! Total number of cells in global domain
 
     !> @name Cylindrical coordinates (either axisymmetric or full 3D)
@@ -336,6 +339,8 @@ contains
 
         ! Computational domain parameters
         m = dflt_int; n = 0; p = 0
+        call s_update_cell_bounds(cells_bounds, m, n, p)
+
         m_root = dflt_int
         cyl_coord = .false.
 

src/post_process/m_start_up.f90

@@ -111,6 +111,9 @@ impure subroutine s_read_input_file
             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

src/pre_process/m_global_parameters.fpp

@@ -40,6 +40,9 @@ module m_global_parameters
     integer :: n
     integer :: p
 
+    !> @name Max and min number of cells in a direction of each combination of x-,y-, and z-
+    type(cell_num_bounds) :: cells_bounds
+
     integer(8) :: nGlobal !< Global number of cells in the domain
 
     integer :: m_glb, n_glb, p_glb !< Global number of cells in each direction
@@ -306,6 +309,8 @@ contains
         ! Computational domain parameters
         m = dflt_int; n = 0; p = 0
 
+        call s_update_cell_bounds(cells_bounds, m, n, p)
+
         cyl_coord = .false.
 
         x_domain%beg = dflt_real

src/pre_process/m_patches.fpp

@@ -255,8 +255,8 @@ contains
         pi_inf = fluid_pp(1)%pi_inf
         gamma = fluid_pp(1)%gamma
         lit_gamma = (1._wp + gamma)/gamma
-        j = 0.0_wp
-        k = 0.0_wp
+        j = 0
+        k = 0
 
         ! Transferring the line segment's centroid and length information
         x_centroid = patch_icpp(patch_id)%x_centroid

src/pre_process/m_start_up.fpp

@@ -169,6 +169,9 @@ contains
                                  '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