sim_base.conf

# General config

# Communication backend.
# local: shared-memory
# cubismnc: distrubuted with MPI using Cubism, 3D only
# native:  distrubited with MPI using native implementation, 2D and 3D
set string backend cubismnc
set int openmp 0
set int mpi_compress_msg 0

set int CHECKNAN 0
set int fill_halo_nan 0
set double fill_halo_nan_value 1e100

# Ranks in each direction.
# The total number of cells is the product `px * bx * bsx` etc.
set int px 2
set int py 2
set int pz 1

# Blocks per rank in each direction.
set int bx 1
set int by 1
set int bz 2

# Cells per block in each direction.
set int bsx 16
set int bsy 16
set int bsz 16

# Domain.
set double extent 1. # Maximum domain length over all directions.
set int spacedim 3 # Solver dimensionality (size of vectors).
set int dim 3 # Effective dimensionality (no computations in unused directions).
set int hypre_periodic_x 0 # 1 if domain is periodic in x
set int hypre_periodic_y 0 # 1 if domain is periodic in y
set int hypre_periodic_z 0 # 1 if domain is periodic in z


# Time step.
set double tmax 1e10
set double dt0 1e-6
set double dtmax 1e10
set double cfl 0.8
set double cfla 0.8
set double cflst 2
set int max_step 1000000

# Solvers.
set int enable_advection 1
set int enable_bc 0
set int enable_electro 0
set int enable_embed 0
set int enable_erasevf 0
set int enable_fluid 1
set int enable_surftens 1
set int enable_tracer 0
set int enable_stepwise_body 0

# Box to erase volume fraction from.
set vect erasevf_rect_x0 0 0 0
set vect erasevf_rect_x1 1 1 1
set double erasevf_t0 0
set double erasevf_per 1

# Tracers.
set int tracer_layers 2
set double cfl_tracer_advection 0.25
set double cfl_tracer_diffusion 0.125
set string tracer_scheme superbee
set int tracer_override_mixture 0
set int tracer_use_termvel 0
set vect tracer_spawn_sphere_c 0 0 0
set double tracer_spawn_sphere_r 0
set vect tracer_density 1 1
set vect tracer_viscosity 0 0
set vect tracer_termvel 0 0
set vect tracer_diameter 0 0
set int tracer_override_mixture 0
set double tracer_interface_diffusion_factor 0
set string tracer0_list_path inline
set string tracer1_list_path inline
set string tracer0_init zero
set string tracer1_init zero
set string tracer0_slip none
set string tracer1_slip none
set double tracer0_factor 1
set double tracer1_factor 1

# Electro.
set int enable_electro_control 0 # Controller of potential for given current.
set double resist1 1
set double resist2 1000
set double flux_from_current 0
set double electro_control_current 0 # Controller target current.
set double electro_control_rate 0 # Controller rate, [potential/current].
set double electro_control_initial_potential 0

# Nucleation through cells.
set int enable_nucleation 0
set double nucleation_cmax0 0.4 # critical concentration of tracer 0
set double nucleation_rate0 1 # nucleation rate from tracer 0
set double nucleation_cmax1 0.4 # critical concentration of tracer 1
set double nucleation_rate1 1 # nucleation rate from tracer 1

# Nucleation through points.
set int enable_nucleation_points 0
set double nucleation_number_density 0

# Bubble growth from tracers.
set double growth_rate_tracer0 0
set double growth_rate_tracer1 0

# Particles.
set int enable_particles 0
set int dump_particles 1
set vect particles_spawn_sphere_c 0 0 0
set double particles_spawn_sphere_r 0
set vect particles_spawn_rate 10 # particles per unit time
set vect particles_termvel 0
set string particles_mode tracer
set vect particles_spawn_velocity 0 0 0
set vect particles_radius 0
set double particles_density 1
set string particles_init_csv # path to csv file
set string particles_dumplist id x y z vx vy vz r
set int particles_dumpvtk 0 # Dump in VTK format (1) or CSV format (0).
set int particles_to_vof 0
set double particles_to_vof_radius 2
set int particles_coal 0
set double particles_growth_diffusion_factor 0
set double particles_growth_rate 8

# Embedded boundaries.
set string eb_init list
set string eb_list_path body.dat
set string eb_model_path model.ply
set vect eb_model_center 0.5 0.5 0.5
set vect eb_model_rotation 0 0 0
set double eb_model_extent 1
set int eb_init_inverse 1
set double embed_gradlim 0.5
set string bc_path bc.dat
set int embed_smoothen_iters 0

# Use stepwise approximation for complex boundaries.
set int dump_stepwise_body 0
set string body_list_path body.dat
#set string body_init list
set string body_init zero
set int body_init_inverse 0
set double stepwise_threshold 0.5 # Minimum volume fraction for inner cell.

# Convergence parameters.
set double tol 1e-3
set int max_iter 1
set int min_iter 1
set double abortvel 1e10     # abort if exceeded by velocity magnitude
set double stop_diff -1

# Numerical parameters.
# Fluid solver: Bell-Colella-Glaz (proj), SIMPLE (simple).
set string fluid_solver proj
# Bell-Colella-Glaz scheme in projection if true, else upwind scheme
set int proj_bcg 1
set int proj_redistr_adv 0
set int proj_diffusion_iters 1
set int proj_diffusion_consistent_guess 1
set double prelax 0.9
set double vrelax 0.8
set double rhie 1.
set int second_order 1
set int vfsmooth 0
set int vfsmooth_extrapolate_cut 0
set int vfsmoothnode 0
set int inletflux_numid 1
set double inletpressure_factor 0
set double stdiag 1.
set string conv imp
set string convsc quick
set double convdf 1.
set double kslip 0
set double penalslip 0
set double slipnormal 0
#set double slipnormal 10
set double slipnormal_dist 1
set vect slipvel 1 0 0
set int stokes 0
set int convsymm 0
set int explconv 0
set int explviscous 1 # enable explicit part of viscous terms
set double outlet_relax 1

# Advection solver.
# vof: standard VOF, vofm: Multi-VOF for coalescence prevention
set string advection_solver vof
set string vof_scheme weymouth
set int vof_verb 0
set double clipth 1e-10 # set volume fractions within this threshold to 0 or 1
set double filterth 0 # remove orphan fragments without neighbors above threshold

set int sharpen 0 # use forward-backward PLIC sharpening
set double sharpen_cfl 0.1

# Algorithm for connected component labeling (propagation, unionfind).
# propagation: iterative label propagation on blocks and between blocks
# unionfind: union-find on blocks, iterative between blocks
set string labeling unionfind
set int vof_recolor_unionfind 1
set int vof_recolor_verbose 0
set int vof_recolor_reduce 1
set int vof_recolor_grid 1
set double clfixed -1
set vect clfixed_x 1e10 1e10 1e10
# Coalescence is triggered the sum of volume fractions exceeds this value:
set double vofm_coalth 1e10

# Curvature estimation using particles.
set string curvature particles
set double part_h 4
set double part_relax 0.5
set int part_np 7
set double part_segcirc 0 # factor for circular segment
set int part_dn 0  # normal displacement
set int part_ns 3
set double part_tol 1e-5
set int part_itermax 20
set int part_verb 0

# Parameters of Multi-VOF.
set double avgnorm0 1
set double avgnorm1 1
set int vofm_layers 4
set int vof_extrapolate_boundaries 0

# Physical parameters.
set double rho1 1
set double rho2 1
set double mu1 0.01
set double mu2 0.01
set vect force 0 0 0
set vect gravity 0 0 0

# Surface tension.
set string surftens kn
set double zerostx0 1e10   # decay of surface tension withing range [x0,x1]
set double zerostx1 1e10
# initial surface tension sigma field
set string init_sig uniform
set double sigma 0
set double sig_k 1.25
set int marangoni 0
set int youngbc 0

set int bcc_reflectpoly 1   # reflect at boundaries for DumpPolyMarch
set double bcc_fill 0
set double bcc_clear0 0      # range for clipping vf near walls
set double bcc_clear1 1      # value set to 0 or 1 if outside the range
set double inletcl 1          # inlet color

# Point with fixed pressure.
#set double pfixed 0
#set vect pfixed_x 0. 0. 0.

# Initial velocity.
set string vel_init zero
set string vellist_path vel.dat

# Initial contact angle.
set string init_contang uniform
set double contang -1

# Initial volume fraction.
set string init_vf zero
set int vf_init_sm 0
set string list_path b.dat
set string init_vf_hdf_path vf.h5
set int init_vf_load_state 0
set string init_vf_state_dir state
set int list_ls 1

# Lamb wave.
set int wavelamb_vort 0
#set string init_vf wavelamb
#set double wavelamb_a0 0.1
#set double wavelamb_xc 0.5
#set double wavelamb_h 0.5
#set double wavelamb_k 6.28
#set double wavelamb_delta 0.01
#set double wavelamb_omk 1
#set int wavelamb_vort 1
#set string vel_init wavelamb_vort
#set int initvort 1

# Noise added to initial velocity.
set int vel_init_noise 0
# Disturbance vector.
set vect noise_vel0 1 0 0
set vect noise_vel1 1 0 0
set vect noise_vel2 1 0 0
# Wavelength relative to cell size.
set vect noise_per0 0 0 1
set vect noise_per1 0 0 1
set vect noise_per2 0 0 1

# Random initial force.
set int vel_init_random 0
set double random_amp 1
set vect random_vel 1 0 0

# Source from volume fraction.
set double source_mag 0.   # magnitude [1/time]
#set double source_freq 1.   # frequency [1/time]
#set double source_wly 1.   # wavelength in y [length]
set double source_mag0 0.   # magnitude, constant component [1/time]
set double source_mexp 0   # exponent for factor (m2/m20)^mexp
set double source_mexp0 0   # exponent for factor (m2/m20)^mexp0

# Force from volume fraction.
set double force_mag 0.   # magnitude [1/time]
#set double force_freq 1.   # frequency [1/time]
#set double force_wly 1.   # wavelength in y [length]

# Vortex force.
set double force_vort_g 0
set double force_vort_r 0
set vect force_vort_c 0

# Moving force.
set vect force_mov 0 0 0
set vect force_mov2 0 0 0

# Kolmogorov forcing.
set int force_kolm 0
set int force_kolm_accel 0

# Vortex ring.
set int initvort 0 # Interpret initial velocity as vorticity.
#set string vel_init vortexring
set vect ring_c 0.5 0.5 0.5
set vect ring_n 1. 0. 0.
set double ring_om 0.01
set double ring_r0 0.2
set double ring_r1 0.4

set int vort_report 1
set int linreport 0
set int check_symmetry 0
set double check_symmetry_dump_threshold 1e10

# Bubble generation.
set int enable_bubgen 0
set string bubgen_path bg.dat
set double bubgen_t0 0
set double bubgen_dt 1
set int bubgen_max 1000000

# Communication.
set int hl 2 # Number of halo cells.

# Parameters of local backend.
set int loc_maxcomm 16
set int loc_periodic_x 1
set int loc_periodic_y 1
set int loc_periodic_z 1


# Bubble tracker.
set int enable_color 0
set double color_th 0.5
set double color_maxr 1e10
# shell averaging around bubbles
# requires enable_color=true
# shell total radius: rr * req + r
set int enable_shell 0
set double shell_h 3    # shell thickness in cells
set double shell_rr 2   # shell inner radius relative to equivalent radius
set double shell_r 0    # shell inner radius absolute

# Linear solver.
# General.
set string linsolver_gen hypre
set string hypre_gen_solver gmres
set int hypre_gen_maxiter 30
set double hypre_gen_tol 1e-3
set int linsolver_gen_maxnorm 0
# Symmetric.
set string linsolver_symm hypre
set string hypre_symm_solver pcg
#set string hypre_symm_solver pcg+smg
#set string hypre_symm_solver smg
set int hypre_symm_maxiter 100
set int hypre_symm_miniter 10
set double hypre_symm_tol 1e-3
set int linsolver_symm_maxnorm 0
# Vorticity.
set string linsolver_vort hypre
set string hypre_vort_solver smg
set int hypre_vort_maxiter 1000
set double hypre_vort_tol 1e-6
set int linsolver_vort_maxnorm 0
# Common parameters.
set int hypre_print 0

set string bc_xm wall 0 0 0
set string bc_xp wall 0 0 0
set string bc_ym wall 0 0 0
set string bc_yp wall 0 0 0
set string bc_zm wall 0 0 0
set string bc_zp wall 0 0 0

set int enable_bc 0
set string BOX_X0 "box 0 0 0  1e-10 10 10"
set string BOX_X1 "box 1 0 0  1e-10 10 10"
set string BOX_Y0 "box 0 0 0  10 1e-10 10"
set string BOX_Y1 "box 0 1 0  10 1e-10 10"
set string BOX_Z0 "box 0 0 0  10 10 1e-10"
set string BOX_Z1 "box 0 0 1  10 10 1e-10"
set string BOX_ALL "box 0 0 0  1e6 1e6 1e6"

set int bc_wall_init_vel 0

set vect overwrite_inlet_times
set vect overwrite_inlet_factors
set vect overwrite_inletpressure_times
set vect overwrite_inletpressure_pressure
set int enable_inlet_periodic 0

# Body velocity.
set vect bodyvel_times
set vect bodyvel_x
set vect bodyvel_y
set vect bodyvel_z

# Initial velocity as Poiseuille flow in rectangular duct.
set int poiswym 1
set int poiswyp 1
set int poiswzm 1
set int poiswzp 1

# Field output.
set int output 1
set string dumpformat default # Field output format (default, hdf, raw, plain).
set int dumpmerge 0 # Merge fields into one file with many attributes.
set double dump_field_t0 0 # Time of the first dump.
set double dump_field_dt 1 # Time interval between dumps.
set int dump_field_max 10000
set int dumpinit 0 # Dump initial conditions.
set int dumplast 0 # Dump final state before termination.
set string dumplist vx vy vz p vf cl # List of fields to dump.
set int dumpbc 0  # Dump boundary conditions on faces to `bc.vtk`.

# Timing report, timings of stages written to files `trep_*.log`.
set double dump_trep_t0 1e10 # Time of first timing report.
set double dump_trep_dt 1 # Interval between timing reports.
set int dump_trep_max 10000

# Debug output.
set int report_knan 0  # nan curvature
set int report_stat 0  # field statistics
set int histogram 0    # collect statistics on each rank [ap.histbin -h]
                       # may generate large data in the case of many ranks and
                       # steps

# Output with bubble trajectories.
set double dump_traj_t0 0
set double dump_traj_dt 1
set int dump_traj_max 10000

# VOF output.
set int dumppoly 1 # Write `s_*.vtk` with PLIC interface fragments.
set int dumppolymarch 1 # Write `sm_*.vtk` with interface from marching cubes.
set double dumppolymarch_fill -1  # value to fill halo cells, applied if >=0
set int cloverride 0
set int vtkbin 1 # VTK format: binary (1) or ASCII (0).
set int vtkmerge 1 # Merge close points.
set double vtkiso 0.5 # Isovalue for marching cubes.

# Output from curvature estimation using particles.
set int dumppart 0 # Write particles `partit_*.csv`.
set int dumppartinter 0 # Write interface lines to `sp_*.vtk`.
set double dump_part_t0 0.
set double dump_part_dt 1
set int dump_part_max 10000
set int part_dump_fr 1
set int part_report_fr 1

# Statistics and text output.
set int dump_stat_max 1000000
set double dump_stat_dt 0
set int report_sysinfo 1
set int verbose 0 # Write the name of current stage (will print hundreds of lines per time step), use for debugging.
set int verbose_stages 1 # Write timings of stages after finishing simulation.
set int verbose_time 1
set int verbose_openmp 0
set int verbose_conf_reads 0
set int verbose_conf_unused 1
set string conf_unused_ignore_path base.conf
set int statvel 0
set int enstrophy 0
set int stat_area 0
set int stat_dissip 0
set int stat_vofm 0
set int report_step_every 1 # Interval in steps for printing statistics.
set int stat_step_every 1 # Interval in steps for writing to `stat.dat`.