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input files for DISCOS #2
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Daniel Ladiges committed Nov 10, 2020
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112 changes: 112 additions & 0 deletions exec/immersedIons/inputs_density_test_damp
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&common
! Problem specification
prob_lo(1:3) = 0.0 0.0 0.0 ! physical lo coordinate
prob_hi(1:3) = 8.284925963482451e-07 8.284925963482451e-07 8.284925963482451e-07 ! physical hi coordinate

n_cells(1:3) = 32 32 32
! max number of cells in a box
max_grid_size(1:3) = 16 32 16
max_particle_tile_size(1:3) = 256 256 256 ! set to zero to use max_grid_size, setting a very large number will also use max grid size, but will also ensure that refined es and particle grids will do the same.
! above settings are for fluid grid. EM and particle grid (the grid for finding neighbour lists) are coarsened or refined off these grids. <1 = refine, >1 = coarsen.
!Leave these on 1 until properly tested
particle_grid_refine = 0.25
es_grid_refine = 1
! Time-step control
fixed_dt = 1e-13
! Controls for number of steps between actions
max_step = 500000
plot_int = 10000
plot_ascii = 1
struct_fact_int = -1
n_steps_skip = 10000
! Toggles 0=off, 1=on

all_dry = 0
fluid_tog = 1 ! 0=Do nothing, 1=Do stokes solve, 2=Do low Mach solve
es_tog = 0 ! Do electrostatic solve 0=off, 1=Poisson, 2=Pairwise Coulomb (Doesn't work in parallel), 3=PPPM
drag_tog = 0 ! Apply drag force to fluid
rfd_tog = 1 ! Apply RFD force to fluid
move_tog = 2 ! ! Total particle move. 0 = off, 1 = single step, 2 = midpoint
dry_move_tog = 2 ! Dry particle move
sr_tog = 2 ! 1=WCA short range forces without walls, 2=with walls

! Fluid info
!--------------
! 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 = 1e-2
visc_type = 1
!particle initialization
! 1 = spread evenly per cell (not implemented yet), 2 = spread randomly over domain
particle_placement = 2
! -1 = calculate based on n0
particle_count = -100 -100
! real particles per simulator particle
particle_neff = 1
! ignore if particle_count is positive
!particle_n0 = 6.02e20 6.02e20
particle_n0 = 6.02e21 6.02e21
!Species info
!--------------
nspecies = 2
mass = 4e-23 4e-23
diameter = -2.488e-8 -2.488e-8
qval = 1.6e-19 -1.6e-19
diff = 1.33e-05 1.33e-05
!If diameter is negative, this value will be used. If diameter is positive, it will be ignored. This is the total wet+dry diffusion. The wet component arises from the grid size and peskin kernel, the dry component is set to recover the value entered here.

p_int_tog = 1 1 ! If zero, LJ/WCA forces will not be computed for this species with itself (different species always interact)
eepsilon = 5e-16 5e-16 !WCA potential---note that Aleks uses 10^-3 but we're not sure of the units in BDWoGF
sigma = 8e-8 8e-8 !Close range repulsion diameter*2
rmin = 1e-8 !Minimum range to prevent blow up of force. NOTE, THIS IS A RADIUS, THE OTHER VALUES ARE DIAMETER. YES THIS IS STUPID.
!Interaction parameters
!------------
permittivity = 692.96e-21
crange = 10 !cell depth when building neighbour lists USING PARTICLE GRID CELL SIZE
images = 0 !if pairwise Coulomb interactions have been selected, this is the number of periodic images to use
eamp = 0 0 0 !external electric field properties
efreq = 0 0 0
ephase = 0 0 0
! Poisson solver parameters -- there are more options which we can add to the namespace later
!-------------------
poisson_rel_tol = 1.e-6 ! relative tolerance stopping criteria
poisson_verbose = 1 ! multigrid verbosity
poisson_bottom_verbose = 0 ! base solver verbosity
poisson_max_iter = 100
!Peskin kernel (Currently 3, 4, & 6 implemented) (keep these the same for now)
!--------
pkernel_fluid = 4
pkernel_es = 4
! Stochastic parameters
seed = 0
k_B = 1.38064852e-16
T_init(1) = 295.00
variance_coef_mom = 1

! Boundary conditions
! ----------------------
! BC specifications:
! -1 = periodic, 2 = no slip stationary
bc_vel_lo(1:3) = -1 2 -1
bc_vel_hi(1:3) = -1 2 -1
! -1 = periodic, 1 = dirichlet, 2 = neumann
bc_es_lo(1:3) = -1 -1 -1
bc_es_hi(1:3) = -1 -1 -1
potential_lo(1:3) = 0 0 0
potential_hi(1:3) = 0 0 0 !

/
&gmres
! GMRES solver parameters
gmres_rel_tol = 1.e-7 ! 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 = 20 ! 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
/
112 changes: 112 additions & 0 deletions exec/immersedIons/inputs_density_test_dry
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&common
! Problem specification
prob_lo(1:3) = 0.0 0.0 0.0 ! physical lo coordinate
prob_hi(1:3) = 8.284925963482451e-07 8.284925963482451e-07 8.284925963482451e-07 ! physical hi coordinate

n_cells(1:3) = 64 64 64
! max number of cells in a box
max_grid_size(1:3) = 32 64 32
max_particle_tile_size(1:3) = 256 256 256 ! set to zero to use max_grid_size, setting a very large number will also use max grid size, but will also ensure that refined es and particle grids will do the same.
! above settings are for fluid grid. EM and particle grid (the grid for finding neighbour lists) are coarsened or refined off these grids. <1 = refine, >1 = coarsen.
!Leave these on 1 until properly tested
particle_grid_refine = 0.5
es_grid_refine = 1
! Time-step control
fixed_dt = 2.5e-14
! Controls for number of steps between actions
max_step = 500000
plot_int = 10000
plot_ascii = 1
struct_fact_int = -1
n_steps_skip = 40000
! Toggles 0=off, 1=on

all_dry = 1
fluid_tog = 0 ! 0=Do nothing, 1=Do stokes solve, 2=Do low Mach solve
es_tog = 0 ! Do electrostatic solve 0=off, 1=Poisson, 2=Pairwise Coulomb (Doesn't work in parallel), 3=PPPM
drag_tog = 0 ! Apply drag force to fluid
rfd_tog = 0 ! Apply RFD force to fluid
move_tog = 2 ! ! Total particle move. 0 = off, 1 = single step, 2 = midpoint
dry_move_tog = 2 ! Dry particle move
sr_tog = 2 ! 1=WCA short range forces without walls, 2=with walls

! Fluid info
!--------------
! 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 = 1e-2
visc_type = 1
!particle initialization
! 1 = spread evenly per cell (not implemented yet), 2 = spread randomly over domain
particle_placement = 2
! -1 = calculate based on n0
particle_count = -100 -100
! real particles per simulator particle
particle_neff = 1
! ignore if particle_count is positive
!particle_n0 = 6.02e20 6.02e20
particle_n0 = 6.02e21 6.02e21
!Species info
!--------------
nspecies = 2
mass = 4e-23 4e-23
diameter = -2.488e-8 -2.488e-8
qval = 1.6e-19 -1.6e-19
diff = 1.33e-05 1.33e-05
!If diameter is negative, this value will be used. If diameter is positive, it will be ignored. This is the total wet+dry diffusion. The wet component arises from the grid size and peskin kernel, the dry component is set to recover the value entered here.

p_int_tog = 1 1 ! If zero, LJ/WCA forces will not be computed for this species with itself (different species always interact)
eepsilon = 5e-16 5e-16 !WCA potential---note that Aleks uses 10^-3 but we're not sure of the units in BDWoGF
sigma = 8e-8 8e-8 !Close range repulsion diameter*2
rmin = 1e-8 !Minimum range to prevent blow up of force. NOTE, THIS IS A RADIUS, THE OTHER VALUES ARE DIAMETER. YES THIS IS STUPID.
!Interaction parameters
!------------
permittivity = 692.96e-21
crange = 10 !cell depth when building neighbour lists USING PARTICLE GRID CELL SIZE
images = 0 !if pairwise Coulomb interactions have been selected, this is the number of periodic images to use
eamp = 0 0 0 !external electric field properties
efreq = 0 0 0
ephase = 0 0 0
! Poisson solver parameters -- there are more options which we can add to the namespace later
!-------------------
poisson_rel_tol = 1.e-6 ! relative tolerance stopping criteria
poisson_verbose = 1 ! multigrid verbosity
poisson_bottom_verbose = 0 ! base solver verbosity
poisson_max_iter = 100
!Peskin kernel (Currently 3, 4, & 6 implemented) (keep these the same for now)
!--------
pkernel_fluid = 4
pkernel_es = 4
! Stochastic parameters
seed = 0
k_B = 1.38064852e-16
T_init(1) = 295.00
variance_coef_mom = 1

! Boundary conditions
! ----------------------
! BC specifications:
! -1 = periodic, 2 = no slip stationary
bc_vel_lo(1:3) = -1 2 -1
bc_vel_hi(1:3) = -1 2 -1
! -1 = periodic, 1 = dirichlet, 2 = neumann
bc_es_lo(1:3) = -1 -1 -1
bc_es_hi(1:3) = -1 -1 -1
potential_lo(1:3) = 0 0 0
potential_hi(1:3) = 0 0 0 !

/
&gmres
! GMRES solver parameters
gmres_rel_tol = 1.e-7 ! 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 = 20 ! 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
/
112 changes: 112 additions & 0 deletions exec/immersedIons/inputs_density_test_eo_wet
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Original file line number Diff line number Diff line change
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&common
! Problem specification
prob_lo(1:3) = 0.0 0.0 0.0 ! physical lo coordinate
prob_hi(1:3) = 8.284925963482451e-07 8.284925963482451e-07 8.284925963482451e-07 ! physical hi coordinate

n_cells(1:3) = 64 64 64
! max number of cells in a box
max_grid_size(1:3) = 32 32 64
max_particle_tile_size(1:3) = 256 256 256 ! set to zero to use max_grid_size, setting a very large number will also use max grid size, but will also ensure that refined es and particle grids will do the same.
! above settings are for fluid grid. EM and particle grid (the grid for finding neighbour lists) are coarsened or refined off these grids. <1 = refine, >1 = coarsen.
!Leave these on 1 until properly tested
particle_grid_refine = 0.5
es_grid_refine = 1
! Time-step control
fixed_dt = 0.5e-13
! Controls for number of steps between actions
max_step = 500000
plot_int = 10000
plot_ascii = 1
struct_fact_int = -1
n_steps_skip = 20000
! Toggles 0=off, 1=on

all_dry = 0
fluid_tog = 1 ! 0=Do nothing, 1=Do stokes solve, 2=Do low Mach solve
es_tog = 3 ! Do electrostatic solve 0=off, 1=Poisson, 2=Pairwise Coulomb (Doesn't work in parallel), 3=PPPM
drag_tog = 0 ! Apply drag force to fluid
rfd_tog = 1 ! Apply RFD force to fluid
move_tog = 2 ! ! Total particle move. 0 = off, 1 = single step, 2 = midpoint
dry_move_tog = 2 ! Dry particle move
sr_tog = 2 ! 1=WCA short range forces without walls, 2=WCA with walls, 3=Shifted repulsive-only LJ, 4=LJ with LJ walls

! Fluid info
!--------------
! 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 = 1e-2
visc_type = 1
!particle initialization
! 1 = spread evenly per cell (not implemented yet), 2 = spread randomly over domain
particle_placement = 2
! -1 = calculate based on n0
particle_count = -100 -100
! real particles per simulator particle
particle_neff = 1
! ignore if particle_count is positive
!particle_n0 = 6.02e20 6.02e20
particle_n0 = 6.02e20 6.02e20
!Species info
!--------------
nspecies = 2
mass = 4e-23 4e-23
diameter = -2.488e-8 -2.488e-8
qval = 1.6e-19 -1.6e-19
diff = 1.33e-05 2.03e-05
!If diameter is negative, this value will be used. If diameter is positive, it will be ignored. This is the total wet+dry diffusion. The wet component arises from the grid size and peskin kernel, the dry component is set to recover the value entered here.

p_int_tog = 1 1 ! If zero, LJ/WCA forces will not be computed for this species with itself (different species always interact)
eepsilon = 5e-16 5e-16 !WCA potential---note that Aleks uses 10^-3 but we're not sure of the units in BDWoGF
sigma = 8e-8 8e-8 !Close range repulsion diameter*2
rmin = 1e-8 !Minimum range to prevent blow up of force. NOTE, THIS IS A RADIUS, THE OTHER VALUES ARE DIAMETER. YES THIS IS STUPID.
!Interaction parameters
!------------
permittivity = 692.96e-21
crange = 10 !cell depth when building neighbour lists USING PARTICLE GRID CELL SIZE
images = 0 !if pairwise Coulomb interactions have been selected, this is the number of periodic images to use
eamp = 0 0 0 !external electric field properties
efreq = 0 0 0
ephase = 0 0 0
! Poisson solver parameters -- there are more options which we can add to the namespace later
!-------------------
poisson_rel_tol = 1.e-6 ! relative tolerance stopping criteria
poisson_verbose = 1 ! multigrid verbosity
poisson_bottom_verbose = 0 ! base solver verbosity
poisson_max_iter = 100
!Peskin kernel (Currently 3, 4, & 6 implemented) (keep these the same for now)
!--------
pkernel_fluid = 4
pkernel_es = 4
! Stochastic parameters
seed = 0
k_B = 1.38064852e-16
T_init(1) = 295.00
variance_coef_mom = 1

! Boundary conditions
! ----------------------
! BC specifications:
! -1 = periodic, 2 = no slip stationary
bc_vel_lo(1:3) = -1 2 -1
bc_vel_hi(1:3) = -1 2 -1
! -1 = periodic, 1 = dirichlet, 2 = neumann
bc_es_lo(1:3) = -1 2 -1
bc_es_hi(1:3) = -1 2 -1
potential_lo(1:3) = 0 0 0
potential_hi(1:3) = 0 0 0 !

/
&gmres
! GMRES solver parameters
gmres_rel_tol = 1.e-7 ! 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 = 20 ! 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
/
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