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Cogswell.i
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Cogswell.i
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#
# Modified CH according to Cogswell and Carter (2011).
#
[Mesh]
type = GeneratedMesh
dim = 2
elem_type = QUAD4
nx = 100
ny = 100
nz = 0
xmin = 0
xmax = 25.0#e-9
ymin = 0
ymax = 25.0#e-9
zmin = 0
zmax = 0
uniform_refine = 2
# type = GeneratedMesh
# dim = 1
# elem_type = EDGE2#QUAD4
# nx = 1000
# ny = 0
# nz = 0
# xmin = 0
# xmax = 100
# ymin = 0
# ymax = 0
# zmin = 0
# zmax = 0
# uniform_refine = 2
[]
[Variables]
#[./T] # Temperature
# order = FIRST
# family = LAGRANGE
#[../]
[./c1] # Mole fraction of species 1 (unitless)
order = FIRST
family = LAGRANGE
# scaling = 1e-7
[../]
[./c2] # Mole fraction of species 2 (unitless)
order = FIRST
family = LAGRANGE
# scaling = 1e-7
[../]
[./mu1] # Variational derivative for diffusion of species 1. Maybe in eV/mol
order = FIRST
family = LAGRANGE
# scaling = 1.0e15
[../]
[./mu2] # Variational derivative for diffusion of species 1. Maybe in eV/mol
order = FIRST
family = LAGRANGE
# scaling = 1.0e15
[../]
[]
[AuxVariables]
[./c3]
order = FIRST
family = MONOMIAL
[../]
[./T]
order = FIRST
family = MONOMIAL
[../]
[./ctot]
order = FIRST
family = MONOMIAL
[../]
[]
[AuxKernels]
[./c3]
type = ParsedAux
args = 'c1 c2'
execute_on = timestep_end
variable = c3
function = '1-c1-c2'
[../]
[./ctot]
type = ParsedAux
args = 'c1 c2 c3'
execute_on = timestep_end
variable = ctot
function = 'c1+c2+c3'
[../]
[]
#NEEDS CHANGED
[ICs]
[./c1IC] # 46.774 mol% with variations
# type = RandomIC
# min = 0.45
# max = 0.50
# seed = 25
# variable = c1
# type = BoundingBoxIC
# x1 = 5.0
# x2 = 20.0
# y1 = 11.0
# y2 = 14.0
# variable = c1
# inside = 0.6
# outside = 0.3
# type = RampIC
# variable = c1
# value_left = 0.6
# value_right = 0.3
type = MultiBoundingBoxIC
corners = '11.0 11.0 0 5.0 11.0 0 14.0 11.0 0 0.0 14.0 0 0.0 0.0 0 0.0 11.0 0 20.0 11.0 0'
opposite_corners = '14.0 14.0 0 11.0 14.0 0 20.0 14.0 0 25.0 25.0 0 25.0 11.0 0 5.0 14.0 0 25.0 14.0 0'
inside = '0.6 0.3 0.3 0.3 0.3 0.3 0.3'
# corners = '44.0e-9 44.0e-9 0 20.0e-9 44.0e-9 0 56.0e-9 44.0e-9 0 0.0 56.0e-9 0 0.0 0.0 0 0.0 44.0e-9 0 80.0e-9 44.0e-9 0'
# opposite_corners = '56.0e-9 56.0e-9 0 44.0e-9 56.0e-9 0 80.0e-9 56.0e-9 0 100.0e-9 100.0e-9 0 100.0e-9 44.0e-9 0 20.0e-9 56.0e-9 0 100.0e-9 56.0e-9 0'
# inside = '0.6 0.3 0.3 0.3 0.3 0.3 0.3'
# corners = '0.11 0.11 0 0.05 0.11 0 0.14 0.11 0 0.0 0.14 0 0.0 0.0 0 0.0 0.11 0 0.2 0.11 0'
# opposite_corners = '0.14 0.14 0 0.11 0.14 0 0.2 0.14 0 0.25 0.25 0 0.25 0.11 0 0.05 0.14 0 0.25 0.14 0'
# inside = '0.6 0.3 0.3 0.3 0.3 0.3 0.3'
#outside = 0.1
variable = c1
[../]
[./c2IC] # 25.0 mol% with variations
# type = RandomIC
# min = 0.22
# max = 0.28
# seed = 30
# variable = c2
# type = BoundingBoxIC
# x1 = 11.0
# x2 = 14.0
# y1 = 11.0
# y2 = 14.0
# variable = c2
# inside = 0.3
# outside = 0.6
# type = RampIC
# variable = c2
# value_left = 0.3
# value_right = 0.2
# type = SmoothCircleIC
# variable = c2
# invalue = 0.3
# radius = 1.5
# outvalue = 0.6
# x1 = 12.5
# y1 = 12.5
type = MultiBoundingBoxIC
corners = '11.0 11.0 0 5.0 11.0 0 14.0 11.0 0 0.0 14.0 0 0.0 0.0 0 0.0 11.0 0 20.0 11.0 0'
opposite_corners = '14.0 14.0 0 11.0 14.0 0 20.0 14.0 0 25.0 25.0 0 25.0 11.0 0 5.0 14.0 0 25.0 14.0 0'
inside = '0.3 0.6 0.6 0.3 0.3 0.3 0.3'
# corners = '44.0e-9 44.0e-9 0 20.0e-9 44.0e-9 0 56.0e-9 44.0e-9 0 0.0 56.0e-9 0 0.0 0.0 0 0.0 44.0e-9 0 80.0e-9 44.0e-9 0'
# opposite_corners = '56.0e-9 56.0e-9 0 44.0e-9 56.0e-9 0 80.0e-9 56.0e-9 0 100.0e-9 100.0e-9 0 100.0e-9 44.0e-9 0 20.0e-9 56.0e-9 0 100.0e-9 56.0e-9 0'
# inside = '0.3 0.6 0.6 0.3 0.3 0.3 0.3'
# corners = '0.11 0.11 0 0.05 0.11 0 0.14 0.11 0 0.0 0.14 0 0.0 0.0 0 0.0 0.11 0 0.2 0.11 0'
# opposite_corners = '0.14 0.14 0 0.11 0.14 0 0.2 0.14 0 0.25 0.25 0 0.25 0.11 0 0.05 0.14 0 0.25 0.14 0'
# inside = '0.3 0.6 0.6 0.3 0.3 0.3 0.3'
#outside = 0.1
variable = c2
[../]
[./TIC] # Temperature IC
type = ConstantIC
variable = T
value = 1000.0
[../]
[]
[BCs]
# periodic BC as is usually done on phase-field models
[./Periodic]
[./cx_bcs]
auto_direction = 'x y'
[../]
[../]
[]
[Kernels]
[./c1_dot]
variable = mu1
v = c1
type = CoupledTimeDerivative
[../]
[./coupled_res_c1_Prim]
variable = mu1
type = SplitCHWRes#Prim
mob_name = M1
c_i = c1
c_j = c2
mu_j = mu2
[../]
# [./coupled_res_c1_Second]
# variable = mu1
# type = SplitCHWResSecond
# mob_name = M
# c_i = c1
# c_j = c2
# mu_j = mu2
# [../]
[./coupled_parsed_c1]
variable = c1
type = SplitCHParsed
f_name = f_loc
kappa_name = kappa_c
# mols_in_sys = sys_mols
w = mu1
c_j = c2
[../]
[./c2_dot]
variable = mu2
v = c2
type = CoupledTimeDerivative
[../]
[./coupled_res_c2_Prim]
variable = mu2
type = SplitCHWRes#Prim
mob_name = M2
c_i = c2
c_j = c1
mu_j = mu1
[../]
# [./coupled_res_c2_Second]
# variable = mu2
# type = SplitCHWResSecond
# mob_name = M
# c_i = c2
# c_j = c1
# mu_j = mu1
# [../]
[./coupled_parsed_c2]
variable = c2
type = SplitCHParsed
f_name = f_loc
kappa_name = kappa_c
# mols_in_sys = sys_mols
c_j = c1
w = mu2
[../]
[]
#NEEDS CHANGED
[Materials]
[./mobility_1] # Mobility (nm^2 mol/eV/s)
type = DerivativeParsedMaterial
f_name = M1
args = 'c1 T'
constant_names = 'R'
constant_expressions = '8314.0'
function = '(16.0)*c1/(8314.0*T)'
derivative_order = 1
outputs = exodus
[../]
[./mobility_2] # Mobility (nm^2 mol/eV/s)
type = DerivativeParsedMaterial
f_name = M2
args = 'c2 T'
constant_names = 'R'
constant_expressions = '8314.0'
function = '(16.0)*c2/(8314.0*T)'
derivative_order = 1
outputs = exodus
[../]
[./kappa] # Gradient energy coefficient (eV nm^2/mol)
type = GenericFunctionMaterial
prop_names = 'kappa11 kappa22 kappa12'
prop_values = '8.0 8.0 8.0'
# prop_names = 'kappa_c'
# prop_values = '8.0'
# kappa_c*eV_J*nm_m^2*d
[../]
# d is a scaling factor that makes it easier for the solution to converge
# without changing the results. It is defined in each of the materials and
# must have the same value in each one.
# [./constants]
# # Define constant values kappa_c and M. Eventually M will be replaced with
# # an equation rather than a constant.
# type = GenericFunctionMaterial
# prop_names = 'kappa_c sys_mols'
# # length_scale = 1e-9, time_scale = 1e-9, energy_scale = 8314 J/mol
# # REALISTIC PROPS
# # prop_values = ' 6.6512e-9/1e+27
# # (1.0e-8)*0.5*(1e+27)/(8314.0*1000.0)
# # 1.0'#(1.0e-9)*(25.0e-9)*(25.0e-9)/(1.0e-5)
# # prop_values = ' 6.6512e-8*1e-30
# # ((1.0e-8)*((1.0e+9)^2)*0.5/(6.242e+18*8314.0*1000.0))/1e-30
# # (1.0)*(25.0)*(25.0)/(1.0e+22)'
# # prop_values = '6.6512e-9
# # (1.0*10.0^-8)*0.5/(8314.0*1000.0)
# # 1.0'
# # prop_values = '6.512e-2
# # (1.0*10.0^-2)*0.5/(8314.0*1000.0)
# # 1.0'
# # prop_values = '6.6512*10^(-17.0)
# # 10.0^(10.0)*0.46774/(8314.0*1000.0)
# # 25.0*25.0/(10.0^(22.0))'#x1*x2*(c1/Vm1+c2/Vm2+(1-c1-c2)/vm3)'
# # kappa_c*eV_J*nm_m^2*d
# # M*nm_m^2/eV_J/d
# # prop_values = '6.512e-2
# # (1.0*10.0^-2)*0.5/(8314.0*1000.0)
# # 1.0'
# # REALISTIC NORMALISED PROPS
# prop_values = '8.0 1.0'
# # OTHER MATERIAL PROPS
# # prop_values = ' VALUE
# # VALUE
# # VALUE'#(1.0e-9)*(25.0e-9)*(25.0e-9)/(1.0e-5)
# [../]
[./local_energy]
# Defines the function for the local free energy density as given in the
# problem, then converts units and adds scaling factor.
type = DerivativeParsedMaterial
f_name = f_loc
args = 'c1 c2 T'#c3
# WORKING
constant_names = 'Omega12 Omega13 Omega23 R'
constant_expressions = '-10.0 -10.0 -10 8314'
function = '(Omega12*c1*c2 + Omega13*c1*(1.0-c1-c2) + Omega23*c2*(1.0-c1-c2) + T*(c1*log(c1) + c2*log(c2) + (1.0-c1-c2)*log(1.0-c1-c2)))'
# constant_expressions = '25.0*25.0/(10.0^22.0) -10.0*8314.0 -10.0*8314.0 -10.0*8314.0 8314.0'
# function = '(1/n)*(Omega12*c1*c2 + Omega13*c1*c3 + Omega23*c2*c3 + R*T*(c1*log(c1) + c2*log(c2) + c3*log(c3)))'
# WORKING
# constant_expressions = '1.0 -10.0*8314.0 -10.0*8314.0 -10.0*8314.0 8314.0'
# function = '(1.0/n)*(Omega12*c1*c2 + Omega13*c1*(1.0-c1-c2) + Omega23*c2*(1.0-c1-c2) + R*T*(c1*log(c1) + c2*log(c2) + (1.0-c1-c2)*log(1.0-c1-c2)))/1e+27'#(Omega12*c1*c2 + Omega13*c1*c3 + Omega23*c2*c3 + R*T*(c1*log(c1) + c2*log(c2) + c3*log(c3)))
# NOT WORKING, UNNORMALISED
# constant_names = 'Nmols Omega12 Omega13 Omega23 R'
# constant_expressions = '(1.0e-9)*(25.0e-9)*(25.0e-9)/(1.0e-5) -10.0*8314.0 -10.0*8314.0 -10.0*8314.0 8314.0'
# function = '(1.0/Nmols)*(Omega12*c1*c2 + Omega13*c1*(1.0-c1-c2) + Omega23*c2*(1.0-c1-c2) + R*T*(c1*log(c1) + c2*log(c2) + (1.0-c1-c2)*log(1.0-c1-c2)))'
# constant_names = 'Nmols Omega12 Omega13 Omega23 R'
# constant_expressions = '(1.0)*(25.0)*(25.0)/(1.0e+22) -10.0*8314.0 -10.0*8314.0 -10.0*8314.0 8314.0'
# function = '((1e-30)*(6.242e+18)/Nmols)*(Omega12*c1*c2 + Omega13*c1*(1.0-c1-c2) + Omega23*c2*(1.0-c1-c2) + R*(c1*log(c1) + c2*log(c2) + (1.0-c1-c2)*log(1.0-c1-c2)))'
# OTHER PROPS
# constant_names = 'n Omega12 Omega13 Omega23 R'
# constant_expressions = '1.0 -10.0*8314.0 -10.0*8314.0 -10.0*8314.0 8314.0'
# function = '(1/n)*(Omega12*c1*c2 + Omega13*c1*c3 + Omega23*c2*c3 + R*T*(c1*log(c1) + c2*log(c2) + c3*log(c3)))'
# OTHER MATERIAL PROPS
# constant_expressions = 'VALUE VALUE VALUE VALUE VALUE'
# function = '(1.0/n)*(Omega12*c1*c2 + Omega13*c1*c3 + Omega23*c2*c3 + R*T*(c1*log(c1) + c2*log(c2) + c3*log(c3)))/8314.0'
derivative_order = 2
[../]
[]
[Postprocessors]
[./step_size] # Size of the time step
type = TimestepSize
[../]
[./iterations] # Number of iterations needed to converge timestep
type = NumNonlinearIterations
[../]
[./nodes] # Number of nodes in mesh
type = NumNodes
[../]
[./evaluations] # Cumulative residual calculations for simulation
type = NumResidualEvaluations
[../]
[./active_time] # Time computer spent on simulation
type = PerformanceData
event = ALIVE#ACTIVE
[../]
[]
# [Preconditioning]
# [./coupled]
# type = SMP
# full = true
# [../]
# # [./FDP]
# # type = FDP
# # full = true
# # [../]
# []
# [Executioner]
# type = Transient
# solve_type = NEWTON#PJFNK
# l_max_its = 100
# l_tol = 1e-6
# nl_max_its = 50
# # nl_rel_tol = 1e-8
# nl_abs_tol = 1e-9
# # line_search = none
# end_time = 600.0#7200 # seconds
# petsc_options = '-ksp_converged_reason -ksp_monitor_true_residual -snes_converged_reason -snes_linesearch_monitor' #-snes_check_jacobian -pc_svd_monitor -snes_check_jacobian_view -snes_view -log_view -snes_fd - -snes_error_if_not_converged -ksp_error_if_not_converged'
# petsc_options_iname = '-snes_linesearch_type -pc_type'#-pc_factor_mat_solver_package
# petsc_options_value = 'basic lu'#svd lu mumps
# # petsc_options_iname = '-pc_type -ksp_gmres_restart -sub_ksp_type
# # -sub_pc_type -pc_asm_overlap'
# # petsc_options_value = 'asm 31 preonly
# # ilu 1'
# [./TimeStepper]
# type = IterationAdaptiveDT
# dt = 0.1
# cutback_factor = 0.7
# growth_factor = 1.5
# optimal_iterations = 15
# [../]
# [./Adaptivity]
# coarsen_fraction = 0.1
# refine_fraction = 0.7
# max_h_level = 2
# [../]
# []
# [Debug]
# show_var_residual_norms = true
# []
# [Outputs]
# exodus = true
# console = true
# # csv = true
# [./console]
# type = Console
# max_rows = 10
# [../]
# []
[Preconditioning]
[./coupled]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
solve_type = NEWTON#PJFNK
l_max_its = 30
l_tol = 1e-6
nl_max_its = 50
nl_abs_tol = 1e-9
# nl_rel_tol = 1e-3
end_time = 600.0 # seconds.
# automatic_scaling = true
petsc_options_iname = '-pc_type -ksp_gmres_restart -sub_ksp_type
-sub_pc_type -pc_asm_overlap'
petsc_options_value = 'asm 31 preonly
ilu 1'
# petsc_options_iname = '-pc_type'
# petsc_options_value = 'lu'
[./TimeStepper]
type = IterationAdaptiveDT
dt = 0.1
cutback_factor = 0.7
growth_factor = 1.5
optimal_iterations = 15
[../]
[./Adaptivity]
coarsen_fraction = 0.1
refine_fraction = 0.7
max_h_level = 2
[../]
[]
[Debug]
show_var_residual_norms = true
[]
[Outputs]
exodus = true
console = true
#csv = true
[./console]
type = Console
max_rows = 10
[../]
[]