Merge branch 'master' of github.com:danieljvickers/MFC-Dan

Author: Daniel Vickers

.github/workflows/test.yml

@@ -149,7 +149,7 @@ jobs:
         continue-on-error: true
 
   github:
-    name: ${{ matrix.nvhpc && format('NVHPC {0} ({1})', matrix.nvhpc, matrix.target) || format('Github ({0}, {1}, {2}, intel={3})', matrix.os, matrix.mpi, matrix.debug, matrix.intel) }}
+    name: ${{ matrix.nvhpc && format('NVHPC {0} ({1})', matrix.nvhpc, matrix.target) || format('Github ({0}, {1}, {2}, {3})', matrix.os, matrix.mpi, matrix.debug, matrix.intel && 'intel' || 'GNU') }}
     needs: [lint-gate, file-changes, rebuild-cache]
     if: >-
       !cancelled() &&

CMakeLists.txt

@@ -636,7 +636,7 @@ exit 0
                     target_compile_options(${a_target} PRIVATE -fopenmp)
                     target_link_options(${a_target} PRIVATE -fopenmp)
                 elseif(CMAKE_Fortran_COMPILER_ID STREQUAL "LLVMFlang")
-                    target_compile_options(${a_target} PRIVATE -fopenmp --offload-arch=gfx90a)
+                    target_compile_options(${a_target} PRIVATE -fopenmp --offload-arch=gfx90a -fopenmp-target-fast -fopenmp-assume-threads-oversubscription -fopenmp-assume-teams-oversubscription)
                     target_link_options(${a_target} PRIVATE -fopenmp --offload-arch=gfx90a)
                 endif()
             endif()
@@ -1026,4 +1026,4 @@ site_name(SITE_NAME)
 
 configure_file(
     "${CMAKE_CURRENT_SOURCE_DIR}/toolchain/cmake/configuration.cmake.in"
-    "${CMAKE_CURRENT_BINARY_DIR}/configuration.txt")
+    "${CMAKE_CURRENT_BINARY_DIR}/configuration.txt")

docs/documentation/case.md

@@ -445,6 +445,7 @@ See @ref equations "Equations" for the mathematical models these parameters cont
 | `mp_weno`                  | Logical | Monotonicity preserving WENO |
 | `muscl_order`              | Integer | MUSCL order [1,2] |
 | `muscl_lim`                | Integer | MUSCL Slope Limiter: [1] minmod; [2] monotonized central; [3] Van Albada; [4] Van Leer; [5] SUPERBEE |
+| `muscl_eps`                | Real    | MUSCL limiter slope-product threshold (default: hard-coded thresholds; set to 0 for textbook behavior) |
 | `flux_lim`                 | Integer | Flux limiter for post-process: [1] minmod; [2] MUSCL; [3] OSPRE; [4] SUPERBEE |
 | `int_comp`                 | Logical | THINC Interface Compression |
 | `ic_eps`                   | Real    | Interface compression threshold (default: 1e-4) |
@@ -542,6 +543,10 @@ It is recommended to set `weno_eps` to $10^{-6}$ for WENO-JS, and to $10^{-40}$
 - `muscl_lim` specifies the slope limiter that is used in 2nd order MUSCL Reconstruction by an integer from 1 through 5.
 `muscl_lim = 1`, `2`, `3`, `4`, and `5` correspond to minmod, monotonized central, Van Albada, Van Leer, and SUPERBEE, respectively.
 
+- `muscl_eps` controls the slope-product activation threshold for all MUSCL limiters.
+When not set (default), the threshold is 1e-9 for minmod/MC, and 1e-6 for others.
+Setting `muscl_eps = 0` gives textbook limiter behavior where limiters activate whenever both slopes have the same sign.
+
 - `int_comp` activates interface compression using THINC used in MUSCL Reconstruction, with control parameters (`ic_eps`, and `ic_beta`).
 
 - `riemann_solver` specifies the choice of the Riemann solver that is used in simulation by an integer from 1 through 4.
@@ -1068,8 +1073,20 @@ When ``cyl_coord = 'T'`` is set in 2D the following constraints must be met:
 
 - `cantera_file` specifies the chemical mechanism file. If the file is part of the standard Cantera library, only the filename is required. Otherwise, the file must be located in the same directory as your `case.py` file
 
+### 18. Chemistry-Specific Boundary Conditions
+
+| Parameter          | Type    | Description                                                                 |
+| ---:               | :----:  | :---                                                                        |
+| `bc_[x,y,z]%%isothermal_in`    | Logical | Enable isothermal wall at the domain entrance (minimum coordinate).         |
+| `bc_[x,y,z]%%isothermal_out`   | Logical | Enable isothermal wall at the domain exit (maximum coordinate).             |
+| `bc_[x,y,z]%%Twall_in`         | Real    | Temperature [K] of the entrance isothermal wall.                            |
+| `bc_[x,y,z]%%Twall_out`        | Real    | Temperature [K] of the exit isothermal wall.                                |
+
+This boundary condition can be used for fixed-temperature (isothermal) walls at the domain extremities. It is exclusively available for reacting flows and requires chemistry to be enabled. It properly evaluates heat and species fluxes at the interface when ``chemistry = 'T'``, ``chem_params%%diffusion = 'T'``, and the corresponding domain boundary is set to a slip wall (`bc_[x,y,z]%%[beg,end]` = -15) or a no-slip wall (`bc_[x,y,z]%%[beg,end]` = -16).
+
+
 
-### 18. GPU Performance (NVIDIA UVM)
+### 19. GPU Performance (NVIDIA UVM)
 
 | Parameter                  | Type    | Description                                              |
 | ---:                       | :---:   | :---                                                     |

docs/documentation/visualization.md

@@ -205,7 +205,7 @@ Post-processed data in Silo-HDF5 format (`format=1`) can be opened directly in P
 Paraview 5.11.0 has been confirmed to work with the MFC databases for some parallel environments.
 Nevertheless, the installation and configuration of Paraview can be environment-dependent and are left to the user.
 
-The user can launch Paraview and open the index files under `/silo_hdf5/root`.
+The user can launch Paraview and open the series file `/silo_hdf5/collection.silo.series`.
 Once the database is loaded, flow field variables contained in the database can be added to the render view.
 Further information on Paraview can be found in its [documentation](https://docs.paraview.org/en/latest/).
 The figure below shows the iso-contour of the liquid void fraction (`alpha1`) in the database generated by the example case `3D_sphbubcollapse`.

docs/index.html

@@ -58,6 +58,7 @@
             { name: "Mach 0.3 flow over a corgi (2M STL)", image: "res/simulations/u.png", computer: "HiPerGator", computerUrl: "https://www.rc.ufl.edu/about/hipergator/",                                     accelerators: "2 GPUs",    walltime: "80s",  source: "https://www.youtube.com/watch?v=O8dSRqHLp_o" },
             // Shock-droplet
             { name: "Shedding water droplet",              image: "res/simulations/a.png", computer: "Summit",     computerUrl: "https://www.olcf.ornl.gov/summit/",                                            accelerators: "960 V100s", walltime: "4h",   source: "https://www.youtube.com/watch?v=Gjj-qZkXcrg" },
+            { name: "1K resolved particles",               image: "res/simulations/x.jpg", computer: "Phoenix",    computerUrl: "https://www.pace.gatech.edu/",                                                 accelerators: "4 A100s",   walltime: "~1.5h", source: "https://www.youtube.com/watch?v=ufisHG0KkOU" },
             // Biomedical & acoustics
             { name: "Burstwave lithotripsy",               image: "res/simulations/k.png", computer: "Delta",      computerUrl: "https://www.ncsa.illinois.edu/research/project-highlights/delta/",              accelerators: "128 A100s", walltime: "30m",  source: "https://www.youtube.com/watch?v=XWsUTaJXGF8" },
             { name: "Cavitation fragments kidney stone",   image: "res/simulations/d.png", computer: "Summit",     computerUrl: "https://www.olcf.ornl.gov/summit/",                                            accelerators: "576 V100s", walltime: "30m",  source: "https://doi.org/10.48550/arXiv.2305.09163" },
@@ -74,6 +75,7 @@
             { name: "Breakup of vibrated interface",       image: "res/simulations/f.png", computer: "Summit",     computerUrl: "https://www.olcf.ornl.gov/summit/",                                            accelerators: "128 V100s", walltime: "4h",   source: "https://www.youtube.com/watch?v=XQ3g1oSg8mc" },
             { name: "Viscous Taylor-Green vortex",         image: "res/simulations/h.png", computer: "Delta",      computerUrl: "https://www.ncsa.illinois.edu/research/project-highlights/delta/",              accelerators: "128 A100s", walltime: "17h",  source: "https://www.youtube.com/watch?v=7i2h08dlDQw" },
             { name: "Mach 1.5 shock-helium bubble",        image: "res/simulations/t.png", computer: "Phoenix",    computerUrl: "https://www.pace.gatech.edu/",                                                 accelerators: "1 A100",    walltime: "1h",   source: "https://www.youtube.com/watch?v=zDJoe0NYZsQ" },
+            { name: "Sphere collision and wall rebound",   image: "res/simulations/w.jpg", computer: "Phoenix",    computerUrl: "https://www.pace.gatech.edu/",                                                 accelerators: "4 A100s",   walltime: "~2h",   source: "https://www.youtube.com/watch?v=5ugLuDtV0C0" },
         ];
 
         const scalings = [

docs/res/simulations/w.jpg

@@ -0,0 +1,76 @@
+#!/usr/bin/env python3
+import json
+import math
+
+import cantera as ct
+
+Lx = 0.05
+Ly = 0.05
+
+ctfile = "h2o2.yaml"
+sol_L = ct.Solution(ctfile)
+sol_L.TPY = 1125, ct.one_atm, "O2:0.21,N2:0.79"
+# Configuring case dictionary
+case = {
+    "run_time_info": "T",
+    "x_domain%beg": 0.0,
+    "x_domain%end": Lx,
+    "y_domain%beg": 0.0,
+    "y_domain%end": Ly,
+    "m": 699,
+    "n": 699,
+    "p": 0,
+    "dt": 4.0e-08,
+    "t_step_start": 0,
+    "t_step_stop": 75000,
+    "t_step_save": 4500,
+    "num_patches": 1,
+    "model_eqns": 2,
+    "alt_soundspeed": "F",
+    "num_fluids": 1,
+    "mpp_lim": "F",
+    "mixture_err": "T",
+    "time_stepper": 3,
+    "mp_weno": "F",
+    "weno_order": 5,
+    "weno_eps": 1e-16,
+    "riemann_solver": 2,
+    "wave_speeds": 1,
+    "avg_state": 2,
+    "bc_x%beg": -7,
+    "bc_x%end": -3,
+    "bc_y%beg": -16,
+    "bc_y%end": -3,
+    "bc_y%isothermal_in": "T",
+    "bc_y%Twall_in": 600.0,
+    "format": 1,
+    "precision": 2,
+    "prim_vars_wrt": "T",
+    "parallel_io": "T",
+    "chemistry": "T",
+    "chem_params%diffusion": "T",
+    "chem_params%reactions": "F",
+    "cantera_file": ctfile,
+    "chem_wrt_T": "T",
+    "patch_icpp(1)%geometry": 3,
+    "patch_icpp(1)%hcid": 291,
+    "patch_icpp(1)%x_centroid": Lx / 2,
+    "patch_icpp(1)%y_centroid": Ly / 2,
+    "patch_icpp(1)%length_x": Lx,
+    "patch_icpp(1)%length_y": Ly,
+    "patch_icpp(1)%vel(1)": 0,
+    "patch_icpp(1)%vel(2)": 0,
+    "patch_icpp(1)%pres": 101325,
+    "patch_icpp(1)%alpha_rho(1)": 1.00,
+    "patch_icpp(1)%alpha(1)": 1,
+    "fluid_pp(1)%gamma": 1.0e00 / (1.4e00 - 1.0e00),
+    "fluid_pp(1)%pi_inf": 0.0e00,
+    "viscous": "T",
+    "fluid_pp(1)%Re(1)": 100000,
+}
+for i in range(len(sol_L.Y)):
+    case[f"chem_wrt_Y({i + 1})"] = "T"
+    case[f"patch_icpp(1)%Y({i + 1})"] = sol_L.Y[i]
+
+if __name__ == "__main__":
+    print(json.dumps(case))

docs/res/simulations/x.jpg

@@ -0,0 +1,114 @@
+import json
+import math
+
+# Free stream
+p_inf = 16281
+rho_inf = 0.416
+c_inf = math.sqrt(1.4 * p_inf / rho_inf)
+vel_inf = 2.5 * c_inf
+
+# Jet inlet conditions
+p_J = 1.0 * p_inf
+vel_J = 41.0
+rho_J = 1000.0
+
+# Viscosities
+mu_inf = 1.85e-5
+mu_J = 2.67e-3
+
+d_jet = 1.2e-3
+
+# Simulation parameters
+Ny = 3999
+Nx = 11999
+time_end = 5e-4
+cfl = 0.6
+eps = 1e-8
+
+# Case dictionary
+
+print(
+    json.dumps(
+        {
+            # Logistics
+            "run_time_info": "T",
+            # Computational domain parameters
+            "x_domain%beg": -40 * d_jet,
+            "x_domain%end": 60 * d_jet,
+            "y_domain%beg": 0.0,
+            "y_domain%end": 35 * d_jet,
+            "m": int(Nx),
+            "n": int(Ny),
+            "p": 0,
+            "cfl_adap_dt": "T",
+            "t_stop": time_end,
+            "t_save": time_end / 50,
+            "n_start": 0,
+            "cfl_target": cfl,
+            # Simulation algorithm parameters
+            "num_patches": 2,
+            "model_eqns": 3,
+            "alt_soundspeed": "F",
+            "num_fluids": 2,
+            "mpp_lim": "T",
+            "mixture_err": "F",
+            "time_stepper": 3,
+            "recon_type": 2,
+            "muscl_order": 2,
+            "muscl_lim": 1,
+            "riemann_solver": 2,
+            "wave_speeds": 1,
+            "avg_state": 2,
+            "elliptic_smoothing": "T",
+            "elliptic_smoothing_iters": 10,  # 50,
+            "bc_x%beg": -17,
+            "bc_x%end": -12,
+            "bc_y%beg": -17,
+            "bc_y%end": -3,
+            "num_bc_patches": 0,
+            # Formatted Database File Structures
+            "format": 1,
+            "precision": 2,
+            "prim_vars_wrt": "T",
+            "parallel_io": "T",
+            # Patch 1: Free stream
+            "patch_icpp(1)%geometry": 3,
+            "patch_icpp(1)%x_centroid": 0.0,
+            "patch_icpp(1)%y_centroid": 50 * d_jet,
+            "patch_icpp(1)%length_x": 1000 * d_jet,
+            "patch_icpp(1)%length_y": 1000 * d_jet,
+            "patch_icpp(1)%vel(1)": f"{vel_inf} * tanh(y / {d_jet / 4})",
+            "patch_icpp(1)%vel(2)": 0.0,
+            "patch_icpp(1)%pres": p_inf,
+            "patch_icpp(1)%alpha_rho(1)": rho_inf * (1.0 - eps),
+            "patch_icpp(1)%alpha(1)": 1.0 - eps,
+            "patch_icpp(1)%alpha_rho(2)": eps,
+            "patch_icpp(1)%alpha(2)": eps,
+            # Patch 2: Jet
+            "patch_icpp(2)%geometry": 3,
+            "patch_icpp(2)%alter_patch(1)": "T",
+            "patch_icpp(2)%x_centroid": 0.0,
+            "patch_icpp(2)%y_centroid": 0.0,
+            "patch_icpp(2)%length_x": d_jet,
+            "patch_icpp(2)%length_y": d_jet,
+            "patch_icpp(2)%vel(1)": 0.0,
+            "patch_icpp(2)%vel(2)": vel_J,
+            "patch_icpp(2)%pres": p_J,
+            "patch_icpp(2)%alpha_rho(1)": eps,
+            "patch_icpp(2)%alpha(1)": eps,
+            "patch_icpp(2)%alpha_rho(2)": (1.0 - eps) * rho_J,
+            "patch_icpp(2)%alpha(2)": 1.0 - eps,
+            # Fluid properties
+            "fluid_pp(1)%gamma": 1.00 / (1.4 - 1.0),
+            "fluid_pp(1)%pi_inf": 0.0,
+            "fluid_pp(2)%gamma": 1.0 / (6.12 - 1.0),
+            "fluid_pp(2)%pi_inf": 6.12 * 3.43e8 / (6.12 - 1),
+            "viscous": "T",
+            "fluid_pp(1)%Re(1)": 1 / mu_inf,
+            "fluid_pp(2)%Re(1)": 1 / mu_J,
+            "surface_tension": "T",
+            "cf_wrt": "T",
+            "sigma": 0.072,
+        }
+    )
+)

examples/2D_Thermal_Flatplate/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,