Update Final time in the print statement to match performance_expectations.md and add benchmark case to examples/

[sbryngelson]

Update Final time in the print statement in simulation to match performance_expectations.md as ns/gp/rhs-evaluation.

Add benchmark case to examples/ which is apparently:

#!/usr/bin/env python3

import json

# Configuring case dictionary
print(json.dumps({
    # Logistics ================================================================
    'run_time_info'                : 'T',
    # ==========================================================================

    # Computational Domain Parameters ==========================================
    # For these computations, the bubble is placed at the (0,0,0)
    # domain origin. Only one octant of a full spherical bubble is
    # used, with reflecting BC's at octant boundaries acting
    # as the other bubble regions.
    'x_domain%beg'                 : 0.E+00,
    'x_domain%end'                 : 4.E-03/1.E-03,
    'y_domain%beg'                 : 0.E+00,
    'y_domain%end'                 : 4.E-03/1.E-03,
    'z_domain%beg'                 : 0.E+00,
    'z_domain%end'                 : 4.E-03/1.E-03,
    # Grid stretching is used in the all coordinate directions 
    # to minimize computational costs. The grid is coarsened
    # away from the bubble / origin
    'stretch_x'                    : 'T',
    'a_x'                          : 4.E+00,
    'x_a'                          : -1.5E-03/1.E-03,
    'x_b'                          : 1.5E-03/1.E-03,
    'stretch_y'                    : 'T',
    'a_y'                          : 4.E+00,
    'y_a'                          : -1.5E-03/1.E-03,
    'y_b'                          : 1.5E-03/1.E-03,
    'stretch_z'                    : 'T',
    'a_z'                          : 4.E+00,
    'z_a'                          : -1.5E-03/1.E-03,
    'z_b'                          : 1.5E-03/1.E-03,
    'cyl_coord'                    : 'F',
    'm'                            : 99,
    'n'                            : 99,
    'p'                            : 99,
    'dt'                           : 0.2E-09,
    't_step_start'                 : 0,
    't_step_stop'                  : 100,
    't_step_save'                  : 100,
    # ==========================================================================
    
    # Simulation Algorithm Parameters ==========================================
    # Only two patches are necesssary, the background liquid and the
    # gas bubble
    'num_patches'                  : 2,
    # Use the 6 equation model
    'model_eqns'                   : 2  ,
    # 6 equations model does not need the K \div(u) term                    
    'alt_soundspeed'               : 'F',
    # Two fluids: water and air
    'num_fluids'                   : 2,
    # Advect both volume fractions
    'adv_alphan'                   : 'T',
    # Ensure the volume fractions sum to unity at the end of each
    # time step
    'mpp_lim'                      : 'T',
    # Correct errors when computing speed of sound
    'mixture_err'                  : 'T',
    # Use TVD RK3 for time marching
    'time_stepper'                 : 3,
    # Use WENO5
    'weno_order'                   : 5,
    'weno_eps'                     : 1.E-16,
    'weno_Re_flux'                 : 'F',  
    'weno_avg'                     : 'F',
    'avg_state'                    : 2,
    # Use the mapped WENO weights to maintain monotinicity
    'mapped_weno'                  : 'T',
    'null_weights'                 : 'F',
    'mp_weno'                      : 'F',
    # Use the HLLC  Riemann solver
    'riemann_solver'               : 2,
    'wave_speeds'                  : 1,
    # We use reflective boundary conditions at octant edges and 
    # non-reflective boundary conditions at the domain edges
    'bc_x%beg'                     : -2,
    'bc_x%end'                     : -6,
    'bc_y%beg'                     : -2,
    'bc_y%end'                     : -6,
    'bc_z%beg'                     : -2,
    'bc_z%end'                     : -6,
    # ==========================================================================

    # Formatted Database Files Structure Parameters ============================
    # Export primitive variables in double precision with parallel
    # I/O to minimize I/O computational time during large simulations
    'format'                       : 1,
    'precision'                    : 2,
    'prim_vars_wrt'                :'T',
    'parallel_io'                  :'T',
    # ==========================================================================

    # Patch 1: High pressured water ============================================
    # Specify the cubic water background grid geometry
    'patch_icpp(1)%geometry'       : 9,
    'patch_icpp(1)%x_centroid'     : 80.E-03/1.E-03,
    'patch_icpp(1)%y_centroid'     : 80.E-03/1.E-03,
    'patch_icpp(1)%z_centroid'     : 80.E-03/1.E-03,
    'patch_icpp(1)%length_x'       : 160.E-03/1.E-03,
    'patch_icpp(1)%length_y'       : 160.E-03/1.E-03,
    'patch_icpp(1)%length_z'       : 160.E-03/1.E-03,
    # Specify the patch primitive variables
    'patch_icpp(1)%vel(1)'         : 0.E+00,
    'patch_icpp(1)%vel(2)'         : 0.E+00,
    'patch_icpp(1)%vel(3)'         : 0.E+00,
    'patch_icpp(1)%pres'           : 1.E+05,
    'patch_icpp(1)%alpha_rho(1)'   : 1000.E+00,
    'patch_icpp(1)%alpha_rho(2)'   : 0.1E+00,
    'patch_icpp(1)%alpha(1)'       : 0.9E+00,
    'patch_icpp(1)%alpha(2)'       : 0.1E+00,
    # ==========================================================================

    # Patch 3: Air bubble ======================================================
    # Specify the spherical gas bubble grid geometry
    'patch_icpp(2)%geometry'       : 8,
    'patch_icpp(2)%smoothen'       : 'T',
    'patch_icpp(2)%smooth_patch_id' : 1,
    'patch_icpp(2)%smooth_coeff'   : 0.5E+00,
    'patch_icpp(2)%x_centroid'     : 0.E+00,
    'patch_icpp(2)%y_centroid'     : 0.E+00,
    'patch_icpp(2)%z_centroid'     : 0.E+00,
    'patch_icpp(2)%radius'         : 1.E-03/1.E-03,
    'patch_icpp(2)%alter_patch(1)' : 'T',
    # Specify the patch primitive variables 
    'patch_icpp(2)%vel(1)'         : 0.E+00,
    'patch_icpp(2)%vel(2)'         : 0.E+00,
    'patch_icpp(2)%vel(3)'         : 0.E+00,
    'patch_icpp(2)%pres'           : 1.E+03,
    'patch_icpp(2)%alpha_rho(1)'   : 100.E+00,
    'patch_icpp(2)%alpha_rho(2)'   : 0.9E+00,
    'patch_icpp(2)%alpha(1)'       : 0.1E+00,
    'patch_icpp(2)%alpha(2)'       : 0.9E+00,
    # ==========================================================================

    # Fluids Physical Parameters ===============================================
    'fluid_pp(1)%gamma'            : 1.E+00/(4.4E+00-1.E+00),
    'fluid_pp(1)%pi_inf'           : 4.4E+00*6.E+08/(4.4E+00-1.E+00),
    'fluid_pp(2)%gamma'            : 1.E+00/(1.4E+00-1.E+00),
    'fluid_pp(2)%pi_inf'           : 0.E+00,
    # ==========================================================================
}))

# ==============================================================================

[sbryngelson]

Update: Probably want to switch both the code and the .md file in the docs to be ns per grid-point per equation per rhs evaluation (I updated the docs to have this already but without the "per-equation" part).

[sbryngelson]

Closed by #411