Example case for 3D turbulent mixing layer

docs/documentation/case.md

@@ -66,8 +66,9 @@ There are multiple sets of parameters that must be specified in the python input
 6. [Formatted Database and Structure Parameters](#6-formatted-output)
 7. [(Optional) Acoustic Source Parameters](#7-acoustic-source)
 8. [(Optional) Ensemble-Averaged Bubble Model Parameters](#8-ensemble-averaged-bubble-model)
+9. [(Optional) Velocity Field Setup Parameters](#9-velocity-field-setup)
 
-Items 7 and 8 are optional sets of parameters that activate the acoustic source model and ensemble-averaged bubble model, respectively.
+Items 7, 8, and 9 are optional sets of parameters that activate the acoustic source model, ensemble-averaged bubble model, and initial velocity field setup, respectively.
 Definition of the parameters is described in the following subsections.
 
 ### 1. Runtime
@@ -295,10 +296,10 @@ Note that `time_stepper` $=$ 3 specifies the total variation diminishing (TVD),
 | `format`             | Integer | Output format. [1]: Silo-HDF5; [2] Binary	|
 | `precision`          | Integer | [1] Single; [2] Double	 |
 | `parallel_io`        | Logical | Parallel I/O	|
-| `cons_vars_wrt`      | Logical | Write conservative variables \|
+| `cons_vars_wrt`      | Logical | Write conservative variables |
 | `prim_vars_wrt`      | Logical | Write primitive variables	|
 | `fourier_decomp`     | Logical | Apply a spatial Fourier decomposition to the output variables	|
-| `alpha_rho_wrt(i)`   | Logical | Add the partial density of the fluid $i$ to the database \|
+| `alpha_rho_wrt(i)`   | Logical | Add the partial density of the fluid $i$ to the database |
 | `rho_wrt`            | Logical | Add the mixture density to the database	 |
 | `mom_wrt(i)`         | Logical | Add the $i$-direction momentum to the database	 |
 | `vel_wrt(i)`         | Logical | Add the $i$-direction velocity to the database	  |
@@ -307,11 +308,12 @@ Note that `time_stepper` $=$ 3 specifies the total variation diminishing (TVD),
 | `alpha_wrt(i)`       | Logical | Add the volume fraction of fluid $i$ to the database	|
 | `gamma_wrt`          | Logical | Add the specific heat ratio function to the database	|
 | `heat_ratio_wrt`     | Logical | Add the specific heat ratio to the database	|
-| `pi_inf_wrt`         | Logical | Add the liquid stiffness function to the database \|
+| `pi_inf_wrt`         | Logical | Add the liquid stiffness function to the database |
 | `pres_inf_wrt`       | Logical | Add the liquid stiffness to the formatted database	 |
 | `c_wrt`              | Logical | Add the sound speed to the database	 |
 | `omega_wrt(i)`       | Logical | Add the $i$-direction vorticity to the database	 |
 | `schlieren_wrt`      | Logical | Add the numerical schlieren to the database|
+| `qm_wrt`             | Logical | Add the Q-criterion to the database|
 | `fd_order`           | Integer | Order of finite differences for computing the vorticity and the numerical Schlieren function [1,2,4] |
 | `schlieren_alpha(i)` | Real    | Intensity of the numerical Schlieren computed via `alpha(i)` |
 | `probe_wrt`          | Logical | Write the flow chosen probes data files for each time step	|
@@ -433,6 +435,29 @@ When `polytropic` is set `False`, the gas compression is modeled as non-polytrop
 `gamma_v`, `M_v`, `mu_v`, and `k_v` specify the specific heat ratio, molecular weight, viscosity, and thermal conductivity of a chosen component.
 Implementation of the parameterse into the model follow [Ando (2010)](references.md#Ando10).
 
+### 9. Velocity Field Setup
+
+| Parameter      | Type    | Description                                    |
+| ---:           | :----:  |          :---                                  |
+| `perturb_flow` | Logical | Perturb the initlal velocity field by random noise |
+| `perturb_sph`  | Logical | Perturb the initial partial density by random noise |
+| `perturb_sph_fluid`  | Integer | Fluid component whose partial density to be perturbed |
+| `vel_profile`  | Logical  | Set the mean streamwise velocity to hyperbolic tangent profile |
+| `instability_wave` | Logical  | Perturb the initial velocity field by instability waves |
+
+The table lists velocity field parameters. The parameters are optionally used to define initial velocity profiles and perturbations.
+
+- `perturb_flow` activates the perturbation of initial velocity by random noise.
+
+- `perturb_sph` activates the perturbation of intial partial density by random noise. 
+
+- `perturb_sph_fluid` specifies the fluid component whose the partial density to be perturbed.
+
+- `vel_profile` activates setting the mean streamwise velocity to hyperbolic tangent profile. This option works only for 2D and 3D cases.
+
+- `instability_wave` 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 2D and 3D cases, together with `vel_profile`=TRUE.
+
+
 ## Enumerations
 
 ### Boundary conditions

examples/3D_turb_mixing/case.py

@@ -0,0 +1,136 @@
+#!/usr/bin/env python3
+
+import math
+import json
+
+# SURROUNDING FLOW =============================================================
+# Nondimensional parameters
+Re0     = 50.           # Reynolds number
+M0      = 0.2           # Mach number
+
+# Fluid properties
+gamma   = 1.4
+pi_inf  = 0.
+
+# Free stream velocity & pressure
+u0      = 1.
+pres0   = 1./(gamma*M0**2)
+
+# Domain size
+Lx = 59.0
+Ly = 59.0
+Lz = 59.0
+
+# Number of grid cells
+Nx = 255
+Ny = 255
+Nz = 255
+
+# Grid spacing
+dx      = Lx/float(Nx)
+dy      = Ly/float(Ny)
+dz      = Lz/float(Nz)
+
+# Time advancement
+cfl     = 0.1
+T       = 100.
+dt      = cfl*dx/u0
+Ntfinal = int(T/dt)
+Ntstart = 0
+Nfiles  = 100
+t_save  = int(math.ceil((Ntfinal-0)/float(Nfiles)))
+Nt      = t_save*Nfiles
+t_step_start    = Ntstart
+t_step_stop     = int(Nt)
+
+# ==============================================================================
+
+
+# Configuring case dictionary
+print(json.dumps({
+    # Logistics ================================================================
+    # 'case_dir'                      : '\'.\'',
+    'run_time_info'                 : 'T',
+    # ==========================================================================
+
+    # Computational Domain Parameters ==========================================
+    'x_domain%beg'                  :  0.,
+    'x_domain%end'                  :  Lx,
+    'y_domain%beg'                  : -Ly/2.,
+    'y_domain%end'                  :  Ly/2.,
+    'z_domain%beg'                  :  0.,
+    'z_domain%end'                  :  Lz,
+    'm'                             : Nx,
+    'n'                             : Ny,
+    'p'                             : Nz,
+    'dt'                            : dt,
+    't_step_start'                  : t_step_start,
+    't_step_stop'                   : t_step_stop,
+    't_step_save'                   : t_save,
+    # ==========================================================================
+
+    # Simulation Algorithm Parameters ==========================================
+    'num_patches'                   : 1,
+    'model_eqns'                    : 2,
+    'num_fluids'                    : 1,
+    'adv_alphan'                    : 'T',
+    'time_stepper'                  : 3,
+    'weno_vars'                     : 2,
+    'weno_order'                    : 5,
+    'weno_eps'                      : 1.E-16,
+    'weno_Re_flux'                  : 'T',
+    'mapped_weno'                   : 'T',
+    'riemann_solver'                : 2,
+    'wave_speeds'                   : 1,
+    'avg_state'                     : 2,
+    'bc_x%beg'                      : -1,
+    'bc_x%end'                      : -1,
+    'bc_y%beg'                      : -5,
+    'bc_y%end'                      : -5,
+    'bc_z%beg'                      : -1,
+    'bc_z%end'                      : -1,
+    # ==========================================================================
+
+    # Formatted Database Files Structure Parameters ============================
+    'format'                        : 1,
+    'precision'                     : 2,
+    'cons_vars_wrt'                 :'T',
+    'prim_vars_wrt'                 :'T',
+    'parallel_io'                   :'T',
+    'fd_order'                      : 1,
+    'omega_wrt(1)'                  :'T',
+    'omega_wrt(2)'                  :'T',
+    'omega_wrt(3)'                  :'T',
+    'qm_wrt'                        :'T',
+    # ==========================================================================
+
+    # Patch 1 ==================================================================
+    'patch_icpp(1)%geometry'        : 9,
+    'patch_icpp(1)%x_centroid'      : Lx/2.,
+    'patch_icpp(1)%y_centroid'      : 0.,
+    'patch_icpp(1)%z_centroid'      : Lz/2.,
+    'patch_icpp(1)%length_x'        : Lx,
+    'patch_icpp(1)%length_y'        : Ly,
+    'patch_icpp(1)%length_z'        : Lz,
+    'patch_icpp(1)%alpha_rho(1)'    : 1.,
+    'patch_icpp(1)%alpha(1)'        : 1.,
+    'patch_icpp(1)%vel(1)'          : u0,
+    'patch_icpp(1)%vel(2)'          : 0.,
+    'patch_icpp(1)%vel(3)'          : 0.,
+    'patch_icpp(1)%pres'            : pres0,
+    # ==========================================================================
+
+    # Mixing layer =============================================================
+    'vel_profile'                   : 'T',
+    'instability_wave'              : 'T',
+    # ==========================================================================
+
+    # Fluids Physical Parameters ===============================================
+    # Surrounding liquid
+    'fluid_pp(1)%gamma'             : 1./(gamma-1.),
+    'fluid_pp(1)%pi_inf'            : 0.,
+    'fluid_pp(1)%Re(1)'             : Re0,
+    # =========================================================================
+}))
+
+# ==============================================================================