Added _Examples folder

AMReX-FHD · Mar 13, 2024 · cb206a0 · cb206a0
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diff --git a/exec/multispec/_Examples/README b/exec/multispec/_Examples/README
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+This directory contains the inputs files which can be used to study propagation of ice front in a supercooled liquid.
+
+General instructions:
+1. Remember to change the values of thermophysical properties according to the table given within.
+2. You can turn stochasticity on/off by setting variance_coef_* to 1/0.
+
+In ./
+inputs_slab_3d:         inputs to measure the propagation speed of ice/water interface at various temperatures.
+inputs_nucleus_3d:      inputs for simulationg growth of an ice nucleus at various temperatures.
+
+In ./_Examples/
+inputs_laplace:         to measure laplace pressure inside an ice nucleus in a deterministic setting.
+inputs_spectrum:        to measure the spectral energy in a long slab and compare with theory.
diff --git a/exec/multispec/_Examples/_Validation/inputs_laplace b/exec/multispec/_Examples/_Validation/inputs_laplace
@@ -0,0 +1,152 @@
+  #----------------------
+  # Problem specification
+  #----------------------
+  prob_lo               = 0.      0.      # physical lo coordinate
+  prob_hi               = 48e-7   48e-7   # physical hi coordinate
+
+  cell_depth            = 1.0e-7
+
+  # refer to Init.cpp
+  prob_type             = 8
+  chk_base_name         = chk
+  plot_base_name        = plt
+
+  # number of cells in domain. IMP: 0.5 nm or less for deterministic simulations
+  n_cells               = 192 192
+  # max number of cells in a box
+  max_grid_size         = 96 96
+
+  # Time-step control
+  fixed_dt              = 1.e-13
+
+  # Controls for number of steps between actions
+  max_step              = 1000000
+  plot_int              = 10000
+  chk_int               = 100000
+  restart               = -1
+
+  use_ice_nucleation    = 1
+
+  #----------------------
+  # Thermodynamic and transport properties:
+  #------------------------------------------------------------------------------------------------------------------------------------
+  # Temperature (K)	    | 230           235         240         245         250         255         260         265         270
+  #------------------------------------------------------------------------------------------------------------------------------------
+  # c0_water            | 0.1099 	    0.0957 	    0.082  	    0.0687 	    0.0558 	    0.0431 	    0.0308 	    0.0186 	    0.0066 
+  # c0_ice              | 1.0637 	    1.0591 	    1.0539 	    1.048       1.0415 	    1.0341 	    1.0259 	    1.0167 	    1.0064 
+  # mu_water (Poise)    | 0.9124  	    0.2588      0.1279      0.0782      0.0536      0.0394      0.0304      0.0243      0.0200 
+  # fh_chi              | 2.6194        2.5637      2.5103      2.4591      2.4099      2.3626      2.3172      2.2735      2.2314
+  # fh_kappa            | 2.563e-15	    2.508e-15   2.456e-15   2.406e-15   2.358e-15	2.311e-15	2.267e-15	2.224e-15	2.183e-15
+  # rho (g/cm^3)        | 0.9453	    0.9676	    0.9789	    0.9862	    0.9912	    0.9946	    0.997	    0.9986	    0.9995
+  #------------------------------------------------------------------------------------------------------------------------------------
+
+  k_B                   = 1.3806488e-16                     # Boltzmann's constant [units: cm2*g*s-2*K-1]
+  T_init                = 255.0  	                        # [units: K] IMP: Change visc_coef, rho, fh_chi, fh_kappa, c_init_1, c_init_2 accordingly.
+
+  # Viscous friction L phi operator
+  # if abs(visc_type) = 1, L = div beta grad
+  # if abs(visc_type) = 2, L = div [ beta (grad + grad^T) ]
+  # if abs(visc_type) = 3, L = div [ beta (grad + grad^T) + I (gamma - (2/3)*beta) div ]
+  # positive = assume constant coefficients
+  # negative = assume spatially-varying coefficients
+  visc_coef             = 0.0394                            # [units: g*cm-1*s-1] dynamic (shear) viscosity of water at T_init
+  visc_type             = 1
+
+  nspecies              = 2
+  #molmass              = 2.98e-23 2.98e-23                 # molecular masses for nspecies (mass per molecule, *not* molar mass)
+  use_flory_huggins     = 1
+
+  fh_monomers           = 1. 1.
+  monomer_mass          = 2.98e-23
+  rho0                  = 0.9946
+  rhobar                = 0.9946 0.9946                     # pure component densities for all species. Same for ice and water for now.
+  fh_chi                = 0. 2.3626     2.3626      0.      # = 2.79e09/(rhobar*k_B*T_init/monomer_mass) ~ 602.478/T_init. Off-diagonal terms should be identical.
+  fh_kappa              = 0. 2.311e-15  2.311e-15   0.      # = 2.73e-6/(rhobar*k_B*T_init/monomer_mass) ~ 5.895e-13/T_init. Off-diagonal terms should be identical.
+
+  is_ideal_mixture      = 0
+
+  # initial values for c
+  c_init_1              = 1.0341 0.0431                     # ice   ~ -1.605e-05*T_init^2+0.006603*T_init+0.3938
+  c_init_2              = 0.0431 1.0341                     # water ~ -0.002575*T_init+0.7005
+  smoothing_width       = 0.0
+  radius_cyl            = 6.e-7
+
+  # These are lower-triangules of symmetric matrices represented as vectors
+  # Number of elements is (nspecies*(nspecies-1)/2)
+  # The values are red row by row starting from top going down
+  # (this allows easy addition/deletion of new species/rows)
+  # So D_12; D_13, D_23; D_14, D_24, D_34; ...
+  Dbar                  = 5.e-5 # Maxwell-Stefan diffusion constant  
+
+  use_charged_fluid     = 0
+  dielectric_const      = 9.2e-20
+  charge_per_mass       = 0. 0.
+
+  mg_verbose            = 0                  # multigrid verbosity
+  algorithm_type        = 6
+
+  #----------------------
+  # Stochastic parameters
+  #----------------------
+  seed                  = 1
+  variance_coef_mom     = 0.
+  variance_coef_mass    = 0.
+  initial_variance_mom  = 0.
+
+  struct_fact_int       = -1
+  n_steps_skip          = 0
+
+  #----------------------
+  # Boundary conditions
+  # ----------------------
+  # BC specifications:
+  # -1 = periodic
+  #  1 = slip
+  #  2 = no-slip
+  bc_vel_lo             = -1 -1 -1
+  bc_vel_hi             = -1 -1 -1
+
+  # -1 = periodic
+  #  1 = wall
+  #  2 = reservoir (Dirichlet values must be suppled by other means)
+  bc_mass_lo            = -1 -1 -1
+  bc_mass_hi            = -1 -1 -1
+
+  # -1 = periodic
+  #  1 = Dirichlet
+  #  2 = Neumann
+  bc_es_lo              = -1 -1 -1
+  bc_es_hi              = -1 -1 -1
+
+  potential_lo          = 0. 0. 0.
+  potential_hi          = 0. 0. 0.
+
+  #----------------------
+  # Staggered multigrid solver parameters
+  #----------------------
+  stag_mg_verbosity     = 0          # verbosity
+  stag_mg_max_vcycles   = 1         # max number of v-cycles
+  stag_mg_minwidth      = 2            # length of box at coarsest multigrid level
+  stag_mg_bottom_solver = 0       # bottom solver type
+  # 0 = smooths only, controlled by mg_nsmooths_bottom
+  # 4 = Fancy bottom solve that coarsens additionally
+  #     and then applies stag_mg_nsmooths_bottom smooths
+  stag_mg_nsmooths_down = 2  # number of smooths at each level on the way down
+  stag_mg_nsmooths_up   = 2    # number of smooths at each level on the way up
+  stag_mg_nsmooths_bottom = 8     # number of smooths at the bottom
+  stag_mg_max_bottom_nlevels = 10 # for stag_mg_bottom_solver 4, number of additional levels of multigrid
+  stag_mg_omega         = 1.e0            # weighted-jacobi omega coefficient
+  stag_mg_smoother      = 1            # 0 = jacobi; 1 = 2*dm-color Gauss-Seidel
+  stag_mg_rel_tol       = 1.e-9         # relative tolerance stopping criteria
+
+
+  #----------------------
+  # GMRES solver parameters
+  #----------------------
+  gmres_rel_tol         = 1.e-12                # relative tolerance stopping criteria
+  gmres_abs_tol         = 0                     # absolute tolerance stopping criteria
+  gmres_verbose         = 1                     # gmres verbosity; if greater than 1, more residuals will be printed out
+  gmres_max_outer       = 20                  # max number of outer iterations
+  gmres_max_inner       = 5                   # max number of inner iterations, or restart number
+  gmres_max_iter        = 100                  # max number of gmres iterations
+  gmres_min_iter        = 1                    # min number of gmres iterations
diff --git a/exec/multispec/_Examples/_Validation/inputs_spectrum b/exec/multispec/_Examples/_Validation/inputs_spectrum
@@ -0,0 +1,152 @@
+  #----------------------
+  # Problem specification
+  #----------------------
+  prob_lo               = 0.        0.      # physical lo coordinate
+  prob_hi               = 256e-7    64e-7   # physical hi coordinate
+
+  cell_depth            = 1.0e-7
+
+  # refer to Init.cpp
+  prob_type             = 16
+  chk_base_name         = chk
+  plot_base_name        = plt
+
+  # number of cells in domain. IMP: 0.5 nm for deterministic simulations
+  n_cells               = 256 64
+  # max number of cells in a box
+  max_grid_size         = 32 64
+
+  # Time-step control
+  fixed_dt              = 1.e-13
+
+  # Controls for number of steps between actions
+  max_step              = 1000000
+  plot_int              = 1000
+  chk_int               = 100000
+  restart               = -1
+
+  use_ice_nucleation    = 1
+
+  #----------------------
+  # Thermodynamic and transport properties:
+  #------------------------------------------------------------------------------------------------------------------------------------
+  # Temperature (K)	    | 230           235         240         245         250         255         260         265         270
+  #------------------------------------------------------------------------------------------------------------------------------------
+  # c0_water            | 0.1099 	    0.0957 	    0.082  	    0.0687 	    0.0558 	    0.0431 	    0.0308 	    0.0186 	    0.0066 
+  # c0_ice              | 1.0637 	    1.0591 	    1.0539 	    1.048       1.0415 	    1.0341 	    1.0259 	    1.0167 	    1.0064 
+  # mu_water (Poise)    | 0.9124  	    0.2588      0.1279      0.0782      0.0536      0.0394      0.0304      0.0243      0.0200 
+  # fh_chi              | 2.6194        2.5637      2.5103      2.4591      2.4099      2.3626      2.3172      2.2735      2.2314
+  # fh_kappa            | 2.563e-15	    2.508e-15   2.456e-15   2.406e-15   2.358e-15	2.311e-15	2.267e-15	2.224e-15	2.183e-15
+  # rho (g/cm^3)        | 0.9453	    0.9676	    0.9789	    0.9862	    0.9912	    0.9946	    0.997	    0.9986	    0.9995
+  #------------------------------------------------------------------------------------------------------------------------------------
+
+  k_B                   = 1.3806488e-16                     # Boltzmann's constant [units: cm2*g*s-2*K-1]
+  T_init                = 255.0  	                        # [units: K] IMP: Change visc_coef, rho, fh_chi, fh_kappa, c_init_1, c_init_2 accordingly.
+
+  # Viscous friction L phi operator
+  # if abs(visc_type) = 1, L = div beta grad
+  # if abs(visc_type) = 2, L = div [ beta (grad + grad^T) ]
+  # if abs(visc_type) = 3, L = div [ beta (grad + grad^T) + I (gamma - (2/3)*beta) div ]
+  # positive = assume constant coefficients
+  # negative = assume spatially-varying coefficients
+  visc_coef             = 0.0394                            # [units: g*cm-1*s-1] dynamic (shear) viscosity of water at T_init
+  visc_type             = 1
+
+  nspecies              = 2
+  #molmass              = 2.98e-23 2.98e-23                 # molecular masses for nspecies (mass per molecule, *not* molar mass)
+  use_flory_huggins     = 1
+
+  fh_monomers           = 1. 1.
+  monomer_mass          = 2.98e-23
+  rho0                  = 0.9946
+  rhobar                = 0.9946 0.9946                     # pure component densities for all species. Same for ice and water for now.
+  fh_chi                = 0. 2.3626     2.3626      0.      # = 2.79e09/(rhobar*k_B*T_init/monomer_mass) ~ 602.478/T_init. Off-diagonal terms should be identical.
+  fh_kappa              = 0. 2.311e-15  2.311e-15   0.      # = 2.73e-6/(rhobar*k_B*T_init/monomer_mass) ~ 5.895e-13/T_init. Off-diagonal terms should be identical.
+
+  is_ideal_mixture      = 0
+
+  # initial values for c
+  c_init_1              = 1.0341 0.0431                     # ice   ~ -1.605e-05*T_init^2+0.006603*T_init+0.3938
+  c_init_2              = 0.0431 1.0341                     # water ~ -0.002575*T_init+0.7005
+  smoothing_width       = 0.75
+  film_thickness        = 32.e-7
+
+  # These are lower-triangules of symmetric matrices represented as vectors
+  # Number of elements is (nspecies*(nspecies-1)/2)
+  # The values are red row by row starting from top going down
+  # (this allows easy addition/deletion of new species/rows)
+  # So D_12; D_13, D_23; D_14, D_24, D_34; ...
+  Dbar                  = 5.e-5 # Maxwell-Stefan diffusion constant  
+
+  use_charged_fluid     = 0
+  dielectric_const      = 9.2e-20
+  charge_per_mass       = 0. 0.
+
+  mg_verbose            = 0                  # multigrid verbosity
+  algorithm_type        = 6
+
+  #----------------------
+  # Stochastic parameters
+  #----------------------
+  seed                  = 1
+  variance_coef_mom     = 1.
+  variance_coef_mass    = 1.
+  initial_variance_mom  = 0.
+
+  struct_fact_int       = -1
+  n_steps_skip          = 0
+
+  #----------------------
+  # Boundary conditions
+  # ----------------------
+  # BC specifications:
+  # -1 = periodic
+  #  1 = slip
+  #  2 = no-slip
+  bc_vel_lo             = -1 -1 -1
+  bc_vel_hi             = -1 -1 -1
+
+  # -1 = periodic
+  #  1 = wall
+  #  2 = reservoir (Dirichlet values must be suppled by other means)
+  bc_mass_lo            = -1 -1 -1
+  bc_mass_hi            = -1 -1 -1
+
+  # -1 = periodic
+  #  1 = Dirichlet
+  #  2 = Neumann
+  bc_es_lo              = -1 -1 -1
+  bc_es_hi              = -1 -1 -1
+
+  potential_lo          = 0. 0. 0.
+  potential_hi          = 0. 0. 0.
+
+  #----------------------
+  # Staggered multigrid solver parameters
+  #----------------------
+  stag_mg_verbosity     = 0          # verbosity
+  stag_mg_max_vcycles   = 1         # max number of v-cycles
+  stag_mg_minwidth      = 2            # length of box at coarsest multigrid level
+  stag_mg_bottom_solver = 0       # bottom solver type
+  # 0 = smooths only, controlled by mg_nsmooths_bottom
+  # 4 = Fancy bottom solve that coarsens additionally
+  #     and then applies stag_mg_nsmooths_bottom smooths
+  stag_mg_nsmooths_down = 2  # number of smooths at each level on the way down
+  stag_mg_nsmooths_up   = 2    # number of smooths at each level on the way up
+  stag_mg_nsmooths_bottom = 8     # number of smooths at the bottom
+  stag_mg_max_bottom_nlevels = 10 # for stag_mg_bottom_solver 4, number of additional levels of multigrid
+  stag_mg_omega         = 1.e0            # weighted-jacobi omega coefficient
+  stag_mg_smoother      = 1            # 0 = jacobi; 1 = 2*dm-color Gauss-Seidel
+  stag_mg_rel_tol       = 1.e-9         # relative tolerance stopping criteria
+
+
+  #----------------------
+  # GMRES solver parameters
+  #----------------------
+  gmres_rel_tol         = 1.e-12                # relative tolerance stopping criteria
+  gmres_abs_tol         = 0                     # absolute tolerance stopping criteria
+  gmres_verbose         = 1                     # gmres verbosity; if greater than 1, more residuals will be printed out
+  gmres_max_outer       = 20                  # max number of outer iterations
+  gmres_max_inner       = 5                   # max number of inner iterations, or restart number
+  gmres_max_iter        = 100                  # max number of gmres iterations
+  gmres_min_iter        = 1                    # min number of gmres iterations