Merge branch 'master' into frontier-CI2

Author: sbryngelson

.typos.toml

@@ -17,6 +17,7 @@ gam = "gam"
 Gam = "Gam"
 strang = "strang"
 Strang = "Strang"
+TKE = "TKE"
 
 [files]
 extend-exclude = ["docs/documentation/references*", "tests/", "toolchain/cce_simulation_workgroup_256.sh"]

benchmarks/ibm/case.py

@@ -23,7 +23,7 @@
 
 dx = 1.0 / (1.0 * (Nx + 1))
 
-Tend = 64e-06
+Tend = 1e-4
 Nt = 200
 mydt = Tend / (1.0 * Nt)
 
@@ -48,21 +48,21 @@
             "t_step_stop": int(20 * (95 * size + 5)),
             "t_step_save": int(20 * (95 * size + 5)),
             # Simulation Algorithm Parameters
-            "num_patches": 2,
+            "num_patches": 1,
             "model_eqns": 2,
             "alt_soundspeed": "F",
-            "num_fluids": 1,
+            "num_fluids": 2,
             "mpp_lim": "F",
             "mixture_err": "F",
             "time_stepper": 3,
             "weno_order": 5,
             "weno_eps": 1.0e-16,
-            "weno_Re_flux": "F",
-            "weno_avg": "F",
-            "mapped_weno": "F",
+            "weno_Re_flux": "T",
+            "weno_avg": "T",
+            "mapped_weno": "T",
             "null_weights": "F",
             "mp_weno": "F",
-            "riemann_solver": 1,
+            "riemann_solver": 2,
             "wave_speeds": 1,
             "avg_state": 2,
             "bc_x%beg": -3,
@@ -71,48 +71,45 @@
             "bc_y%end": -3,
             "bc_z%beg": -3,
             "bc_z%end": -3,
-            # Turning on Hypoelasticity
-            "hypoelasticity": "T",
-            "fd_order": 4,
+            # Turn on IBM
+            "ib": "T",
+            "num_ibs": 1,
+            "viscous": "T",
             # Formatted Database Files Structure Parameters
             "format": 1,
             "precision": 2,
             "prim_vars_wrt": "T",
             "parallel_io": "T",
             # Patch 1 L
             "patch_icpp(1)%geometry": 9,
-            "patch_icpp(1)%x_centroid": 0.25,
+            "patch_icpp(1)%x_centroid": 0.5,
             "patch_icpp(1)%y_centroid": 0.25,
             "patch_icpp(1)%z_centroid": 0.25,
-            "patch_icpp(1)%length_x": 0.5,
+            "patch_icpp(1)%length_x": 1.0,
             "patch_icpp(1)%length_y": 0.5,
             "patch_icpp(1)%length_z": 0.5,
-            "patch_icpp(1)%vel(1)": 0.0,
+            "patch_icpp(1)%vel(1)": 0.1,
             "patch_icpp(1)%vel(2)": 0,
             "patch_icpp(1)%vel(3)": 0,
-            "patch_icpp(1)%pres": 1.0e8,
-            "patch_icpp(1)%alpha_rho(1)": 1000,
-            "patch_icpp(1)%alpha(1)": 1.0,
-            "patch_icpp(1)%tau_e(1)": 0.0,
-            # Patch 2 R
-            "patch_icpp(2)%geometry": 9,
-            "patch_icpp(2)%x_centroid": 0.75,
-            "patch_icpp(2)%y_centroid": 0.25,
-            "patch_icpp(2)%z_centroid": 0.25,
-            "patch_icpp(2)%length_x": 0.5,
-            "patch_icpp(2)%length_y": 0.5,
-            "patch_icpp(2)%length_z": 0.5,
-            "patch_icpp(2)%vel(1)": 0,
-            "patch_icpp(2)%vel(2)": 0,
-            "patch_icpp(2)%vel(3)": 0,
-            "patch_icpp(2)%pres": 1.0e05,
-            "patch_icpp(2)%alpha_rho(1)": 1000,
-            "patch_icpp(2)%alpha(1)": 1.0,
-            "patch_icpp(2)%tau_e(1)": 0.0,
+            "patch_icpp(1)%pres": 1.0,
+            "patch_icpp(1)%alpha_rho(1)": 0.8e00,
+            "patch_icpp(1)%alpha(1)": 0.8e00,
+            "patch_icpp(1)%alpha_rho(2)": 0.2e00,
+            "patch_icpp(1)%alpha(2)": 0.2e00,
+            # Patch: Sphere Immersed Boundary
+            "patch_ib(1)%geometry": 8,
+            "patch_ib(1)%x_centroid": 0.25,
+            "patch_ib(1)%y_centroid": 0.25,
+            "patch_ib(1)%z_centroid": 0.25,
+            "patch_ib(1)%radius": 0.1,
             # Fluids Physical Parameters
-            "fluid_pp(1)%gamma": 1.0e00 / (4.4e00 - 1.0e00),
-            "fluid_pp(1)%pi_inf": 4.4e00 * 6.0e08 / (4.4e00 - 1.0e00),
-            "fluid_pp(1)%G": 10e09,
+            # Specify 2 fluids
+            "fluid_pp(1)%gamma": 1.0e00 / (1.4 - 1.0e00),
+            "fluid_pp(1)%pi_inf": 0,
+            "fluid_pp(1)%Re(1)": 54000,
+            "fluid_pp(2)%gamma": 1.0e00 / (1.4 - 1.0e00),
+            "fluid_pp(2)%pi_inf": 0,
+            "fluid_pp(2)%Re(1)": 54000,
         }
     )
 )

docs/documentation/case.md

@@ -825,7 +825,6 @@ When ``polytropic = 'F'``, the gas compression is modeled as non-polytropic due
 | `mixlayer_vel_profile` | Logical | Set the mean streamwise velocity to hyperbolic tangent profile |
 | `mixlayer_vel_coef`    | Real    | Coefficient for the hyperbolic tangent profile of a mixing layer |
 | `mixlayer_perturb`     | Logical | Perturb the initial velocity field by instability waves |
-| `mixlayer_domain`      | Real    | Domain size of a mixing layer for the linear stability analysis |
 
 The table lists velocity field parameters.
 The parameters are optionally used to define initial velocity profiles and perturbations.
@@ -840,15 +839,13 @@ The parameters are optionally used to define initial velocity profiles and pertu
 
 - `perturb_sph_fluid` specifies the fluid component whose partial density is to be perturbed.
 
-- `mixlayer_vel_profile` activates setting the mean streamwise velocity to a hyperbolic tangent profile. This option works only for 2D and 3D cases.
+- `mixlayer_vel_profile` activates setting the mean streamwise velocity to a hyperbolic tangent profile. This option works only for `n > 0`.
 
 - `mixlayer_vel_coef` is a parameter for the hyperbolic tangent profile of a mixing layer when `mixlayer_vel_profile = 'T'`. The mean streamwise velocity profile is given as:
 
-$$ u = patch\_icpp(1)\%vel(1) * tanh(y\_cc * mixlayer\_vel\_profile) $$
+$$ u = \mbox{patch\_icpp(1)\%vel(1)} * \tanh( y_{cc} * \mbox{mixlayer\_vel\_coef}) $$
 
-- `mixlayer_perturb` activates the perturbation of initial velocity by instability waves obtained from linear stability analysis for a mixing layer with hyperbolic tangent mean streamwise velocity profile. This option only works for `n > 0`, `bc_y%[beg,end] = -6`, `num_fluids = 1`, `model_eqns = 2` and `mixlayer_vel_profile = 'T'`.
-
-- `mixlayer_domain` defines the domain size to compute spatial eigenvalues of the linear instability analysis when `mixlayer_perturb = 'T'`. For example, the spatial eigenvalue in `x` direction in 2D problem will be $2 \pi \alpha / (mixlayer\_domain*patch\_icpp(1)\%length\_y)$ for $\alpha = 1$, $2$ and $4$.
+- `mixlayer_perturb` activates the velocity perturbation for a temporal mixing layer with hyperbolic tangent mean streamwise velocity profile, using an inverter version of the spectrum-based synthetic turbulence generation method proposed by Guo et al. (2023, JFM). This option only works for `p > 0` and `mixlayer_vel_profile = 'T'`.
 
 ### 11. Phase Change Model
 | Parameter              | Type    | Description                                    |

docs/documentation/references.md

@@ -20,6 +20,8 @@
 
 - <a id="Gottlieb98">Gottlieb, S. and Shu, C.-W. (1998). Total variation diminishing runge-kutta schemes. Mathematics of computation of the American Mathematical Society, 67(221):73–85.</a>
 
+- <a id="Guo23">Guo, H., Jiang, P., Ye, L., & Zhu, Y. (2023). An efficient and low-divergence method for generating inhomogeneous and anisotropic turbulence with arbitrary spectra. Journal of Fluid Mechanics, 970, A2.</a>
+
 - <a id="Henrick05">Henrick, A. K., Aslam, T. D., and Powers, J. M. (2005). Mapped weighted essentially nonoscillatory schemes: achieving optimal order near critical points. Journal of Computational Physics, 207(2):542–567.</a>
 
 - <a id="Borges08">Borges, R., Carmona, M., Costa, B., and Don, W. S. (2008). An improved weighted essentially non-oscillatory scheme for hyperbolic conservation laws. Journal of computational physics, 227(6):3191–3211.</a>
@@ -34,6 +36,8 @@
 
 - <a id="Meng16">Meng, J. C. C. (2016). Numerical simulations of droplet aerobreakup. PhD thesis, California Institute of Technology.</a>
 
+- <a id="Michalke64"> Michalke, A. (1964). On the inviscid instability of the hyperbolictangent velocity profile. Journal of Fluid Mechanics, 19(4), 543-556.</a>
+
 - <a id="Pirozzoli13">Pirozzoli, S., and Colonius, T. (2013). Generalized characteristic relaxation boundary conditions for unsteady compressible flow simulations. Journal of Computational Physics, 248:109-126.</a>
 
 - <a id="Preston07">Preston, A., Colonius, T., and Brennen, C. (2007). A reduced-order model of diffusive effects on the dynamics of bubbles. Physics of Fluids, 19(12):123302.</a>

examples/2D_mixing_artificial_Ma/case.py

@@ -108,8 +108,6 @@
             # Mixing layer
             "mixlayer_vel_profile": "T",
             "mixlayer_vel_coef": 1.0,
-            "mixlayer_domain": 1.0,
-            "mixlayer_perturb": "T",
             # Artificial Mach number
             "pi_fac": pi_fac,
             # Fluids Physical Parameters

examples/3D_turb_mixing/case.py

@@ -4,39 +4,38 @@
 
 # SURROUNDING FLOW
 # Nondimensional parameters
-Re0 = 50.0  # Reynolds number
+Re0 = 320.0  # Reynolds number
 M0 = 0.2  # Mach number
 
 # Fluid properties
 gamma = 1.4
-pi_inf = 0.0
 
 # Free stream velocity & pressure
 u0 = 1.0
 pres0 = 1.0 / (gamma * M0**2)
 
 # Domain size
-Lx = 59.0
-Ly = 59.0
-Lz = 59.0
+Lx = 160.0
+Ly = 160.0
+Lz = 80.0
 
 # Number of grid cells
-Nx = 191
-Ny = 191
-Nz = 191
+Nx = 1023
+Ny = 1023
+Nz = 511
 
 # Grid spacing
 dx = Lx / float(Nx)
 dy = Ly / float(Ny)
 dz = Lz / float(Nz)
 
 # Time advancement
-cfl = 0.1
-T = 100.0
-dt = cfl * dx / u0
+cfl = 0.5
+T = 150.0
+dt = cfl * dx / (u0 / M0 + 1)
 Ntfinal = int(T / dt)
 Ntstart = 0
-Nfiles = 100
+Nfiles = 30
 t_save = int(math.ceil((Ntfinal - 0) / float(Nfiles)))
 Nt = t_save * Nfiles
 t_step_start = Ntstart
@@ -53,6 +52,11 @@
             "x_domain%end": Lx,
             "y_domain%beg": -Ly / 2.0,
             "y_domain%end": Ly / 2.0,
+            "stretch_y": "T",
+            "a_y": 2,
+            "y_a": -0.3 * Ly,
+            "y_b": 0.3 * Ly,
+            "loops_y": 2,
             "z_domain%beg": 0.0,
             "z_domain%end": Lz,
             "m": Nx,
@@ -68,10 +72,9 @@
             "num_fluids": 1,
             "time_stepper": 3,
             "weno_order": 5,
-            "weno_eps": 1.0e-16,
-            "weno_Re_flux": "T",
-            "weno_avg": "T",
-            "mapped_weno": "T",
+            "weno_eps": 1.0e-40,
+            "weno_Re_flux": "F",
+            "wenoz": "T",
             "riemann_solver": 2,
             "wave_speeds": 1,
             "avg_state": 2,
@@ -85,7 +88,7 @@
             # Formatted Database Files Structure Parameters
             "format": 1,
             "precision": 2,
-            "cons_vars_wrt": "T",
+            "cons_vars_wrt": "F",
             "prim_vars_wrt": "T",
             "parallel_io": "T",
             "fd_order": 1,
@@ -99,7 +102,7 @@
             "patch_icpp(1)%y_centroid": 0.0,
             "patch_icpp(1)%z_centroid": Lz / 2.0,
             "patch_icpp(1)%length_x": Lx,
-            "patch_icpp(1)%length_y": Ly,
+            "patch_icpp(1)%length_y": 1e6,
             "patch_icpp(1)%length_z": Lz,
             "patch_icpp(1)%alpha_rho(1)": 1.0,
             "patch_icpp(1)%alpha(1)": 1.0,
@@ -109,8 +112,6 @@
             "patch_icpp(1)%pres": pres0,
             # Mixing layer
             "mixlayer_vel_profile": "T",
-            "mixlayer_vel_coef": 1.0,
-            "mixlayer_domain": 1.0,
             "mixlayer_perturb": "T",
             # Fluids Physical Parameters
             # Surrounding liquid

examples/3D_turb_mixing/turbulence_stat/README.md

@@ -0,0 +1,23 @@
+# Temporally evolving turbulent mixing layer (3D)
+
+Reference:
+> Bell, J. H., & Mehta, R. D. (1990). Development of a two-stream mixing layer from tripped and untripped boundary layers. AIAA Journal, 28(12), 2034-2042.
+> Rogers, M. M., & Moser, R. D. (1994). Direct simulation of a self‐similar turbulent mixing layer. Physics of Fluids, 6(2), 903-923.
+> Pantano, C., & Sarkar, S. (2002). A study of compressibility effects in the high-speed turbulent shear layer using direct simulation. Journal of Fluid Mechanics, 451, 329-371.
+> Vaghefi, S. N. S. (2014). Simulation and modeling of compressible turbulent mixing layer. State University of New York at Buffalo.
+> Wang, X., Wang, J., & Chen, S. (2022). Compressibility effects on statistics and coherent structures of compressible turbulent mixing layers. Journal of Fluid Mechanics, 947, A38.
+
+## Description
+This directory (`turbulence_stat`) contains sub-directories and Matlab scripts for computing turbulence statistics of 3D temporally evolving turbulent mixing layer as described below:
+
+Files:
+- `set_user_inputs.m`: User input parameters are defined in this file.
+- `run_turbulence.m`: Turbulence statistics (growth rate, Reynolds stress, TKE budget) are computed and plots are generated in this file.
+- `average_tke_over_self_similar.m`: Averaging over self-similar period of TKE budget is performed in this file.
+- `submit_batch_job_*.sh`: Example scripts for batch job submission on DoD Carpenter (PBS system) and NCSA Delta (Slurm system)
+
+Directories:
+- `log`: Log files from batch job are stored in this directory.
+- `reference_data`: Data from reference papers are provided in this directory.
+- `variables`: User inputs from `set_user_inputs.m` are saved as Matlab data (`user_inputs.mat`) in this directory.
+- `results`: Outputs are stored in sub-directories in the directory.