- variableThe name of the variable that this object applies to
C++ Type:AuxVariableName
Description:The name of the variable that this object applies to
- sto_vThe stoichiometric coefficients of reactant species
C++ Type:std::vector
Description:The stoichiometric coefficients of reactant species
KineticDisPreConcAux
Concentration of secondary kinetic species
Calculates the concentration of mineral using the kinetic reaction rate (calculated using KineticDisPreRateAux),
(1)
Input Parameters
- sys_temp298.15System temperature, K
Default:298.15
C++ Type:std::vector
Options:
Description:System temperature, K
- e_act29100Activation energy, J/mol
Default:29100
C++ Type:double
Options:
Description:Activation energy, J/mol
- ref_temp298.15Reference temperature, K
Default:298.15
C++ Type:double
Options:
Description:Reference temperature, K
- gas_const8.31434Gas constant, in J/mol K
Default:8.31434
C++ Type:double
Options:
Description:Gas constant, in J/mol K
- log_kThe equilibrium constant of the dissolution reaction
C++ Type:std::vector
Options:
Description:The equilibrium constant of the dissolution reaction
- ref_kconst6.45654e-08Kinetic rate constant in mol/m^2 s
Default:6.45654e-08
C++ Type:double
Options:
Description:Kinetic rate constant in mol/m^2 s
- r_area0.1Specific reactive surface area in m^2/L solution
Default:0.1
C++ Type:double
Options:
Description:Specific reactive surface area in m^2/L solution
- vThe list of reactant species
C++ Type:std::vector
Options:
Description:The list of reactant species
- execute_onLINEAR TIMESTEP_ENDThe list of flag(s) indicating when this object should be executed, the available options include NONE, INITIAL, LINEAR, NONLINEAR, TIMESTEP_END, TIMESTEP_BEGIN, FINAL, CUSTOM, PRE_DISPLACE.
Default:LINEAR TIMESTEP_END
C++ Type:ExecFlagEnum
Options:NONE INITIAL LINEAR NONLINEAR TIMESTEP_END TIMESTEP_BEGIN FINAL CUSTOM PRE_DISPLACE
Description:The list of flag(s) indicating when this object should be executed, the available options include NONE, INITIAL, LINEAR, NONLINEAR, TIMESTEP_END, TIMESTEP_BEGIN, FINAL, CUSTOM, PRE_DISPLACE.
- boundaryThe list of boundary IDs from the mesh where this boundary condition applies
C++ Type:std::vector
Options:
Description:The list of boundary IDs from the mesh where this boundary condition applies
- blockThe list of block ids (SubdomainID) that this object will be applied
C++ Type:std::vector
Options:
Description:The list of block ids (SubdomainID) that this object will be applied
Optional Parameters
- control_tagsAdds user-defined labels for accessing object parameters via control logic.
C++ Type:std::vector
Options:
Description:Adds user-defined labels for accessing object parameters via control logic.
- enableTrueSet the enabled status of the MooseObject.
Default:True
C++ Type:bool
Options:
Description:Set the enabled status of the MooseObject.
- seed0The seed for the master random number generator
Default:0
C++ Type:unsigned int
Options:
Description:The seed for the master random number generator
- use_displaced_meshFalseWhether or not this object should use the displaced mesh for computation. Note that in the case this is true but no displacements are provided in the Mesh block the undisplaced mesh will still be used.
Default:False
C++ Type:bool
Options:
Description:Whether or not this object should use the displaced mesh for computation. Note that in the case this is true but no displacements are provided in the Mesh block the undisplaced mesh will still be used.
Advanced Parameters
Input Files
- modules/chemical_reactions/test/tests/solid_kinetics/2species_without_action.i
- modules/chemical_reactions/test/tests/parser/kinetic_without_action.i
- modules/chemical_reactions/test/tests/kinetic_rate/arrhenius.i
- modules/chemical_reactions/test/tests/exceptions/missing_sto3.i
- test/tests/restart/restart_refined_mesh/bad2.i
- test/tests/restart/restart_refined_mesh/bad1.i
modules/chemical_reactions/test/tests/solid_kinetics/2species_without_action.i
# Simple reaction-diffusion example without using the action.
# In this example, two primary species a and b diffuse towards each other from
# opposite ends of a porous medium, reacting when they meet to form a mineral
# precipitate
# This simulation is identical to 2species.i, but explicitly includes the AuxVariables,
# AuxKernels, and Kernels that the action in 2species.i adds
[Mesh]
type = GeneratedMesh
dim = 2
xmax = 1
ymax = 1
nx = 40
[]
[Variables]
[./a]
order = FIRST
family = LAGRANGE
initial_condition = 0
[../]
[./b]
order = FIRST
family = LAGRANGE
initial_condition = 0
[../]
[]
[AuxVariables]
[./mineral]
[../]
[]
[AuxKernels]
[./mineral_conc]
type = KineticDisPreConcAux
variable = mineral
e_act = 1.5e4
r_area = 1
log_k = -6
ref_kconst = 1e-8
gas_const = 8.314
ref_temp = 298.15
sys_temp = 298.15
sto_v = '1 1'
v = 'a b'
[../]
[]
[Kernels]
[./a_ie]
type = PrimaryTimeDerivative
variable = a
[../]
[./a_pd]
type = PrimaryDiffusion
variable = a
[../]
[./b_ie]
type = PrimaryTimeDerivative
variable = b
[../]
[./b_pd]
type = PrimaryDiffusion
variable = b
[../]
[./a_r]
type = CoupledBEKinetic
variable = a
v = mineral
weight = 1
[../]
[./b_r]
type = CoupledBEKinetic
variable = b
v = mineral
weight = 1
[../]
[]
[BCs]
[./a_left]
type = DirichletBC
variable = a
boundary = left
value = 1.0e-2
[../]
[./a_right]
type = DirichletBC
variable = a
boundary = right
value = 0
[../]
[./b_left]
type = DirichletBC
variable = b
boundary = left
value = 0
[../]
[./b_right]
type = DirichletBC
variable = b
boundary = right
value = 1.0e-2
[../]
[]
[Materials]
[./porous]
type = GenericConstantMaterial
prop_names = 'diffusivity conductivity porosity'
prop_values = '5e-4 4e-3 0.4'
[../]
[]
[Executioner]
type = Transient
solve_type = 'PJFNK'
end_time = 50
dt = 5
[]
[Preconditioning]
[./smp]
type = SMP
full = true
[../]
[]
[Outputs]
file_base = 2species_out
exodus = true
perf_graph = true
print_linear_residuals = true
[]
modules/chemical_reactions/test/tests/parser/kinetic_without_action.i
# Explicitly adds all Kernels and AuxKernels. Used to check that the
# SolidKineticReactions parser is working correctly
[Mesh]
type = GeneratedMesh
dim = 2
[]
[Variables]
[./a]
initial_condition = 0.1
[../]
[./b]
initial_condition = 0.1
[../]
[./c]
initial_condition = 0.1
[../]
[./d]
initial_condition = 0.1
[../]
[]
[AuxVariables]
[./m1]
[../]
[./m2]
[../]
[./m3]
[../]
[]
[AuxKernels]
[./m1]
type = KineticDisPreConcAux
variable = m1
v = 'a b'
sto_v = '1 1'
log_k = -8
r_area = 1
ref_kconst = 1e-8
e_act = 1e4
gas_const = 8.314
ref_temp = 298.15
sys_temp = 298.15
[../]
[./m2]
type = KineticDisPreConcAux
variable = m2
v = 'c d'
sto_v = '2 3'
log_k = -8
r_area = 2
ref_kconst = 2e-8
e_act = 2e4
gas_const = 8.314
ref_temp = 298.15
sys_temp = 298.15
[../]
[./m3]
type = KineticDisPreConcAux
variable = m3
v = 'a c'
sto_v = '1 -2'
log_k = -8
r_area = 3
ref_kconst = 3e-8
e_act = 3e4
gas_const = 8.314
ref_temp = 298.15
sys_temp = 298.15
[../]
[]
[Kernels]
[./a_ie]
type = PrimaryTimeDerivative
variable = a
[../]
[./b_ie]
type = PrimaryTimeDerivative
variable = b
[../]
[./c_ie]
type = PrimaryTimeDerivative
variable = c
[../]
[./d_ie]
type = PrimaryTimeDerivative
variable = d
[../]
[./a_kin]
type = CoupledBEKinetic
variable = a
v = 'm1 m3'
weight = '1 1'
[../]
[./b_kin]
type = CoupledBEKinetic
variable = b
v = m1
weight = 1
[../]
[./c_kin]
type = CoupledBEKinetic
variable = c
v = 'm2 m3'
weight = '2 -2'
[../]
[./d_kin]
type = CoupledBEKinetic
variable = d
v = m2
weight = 3
[../]
[]
[Materials]
[./porous]
type = GenericConstantMaterial
prop_names = porosity
prop_values = 0.1
[../]
[]
[Executioner]
type = Transient
solve_type = PJFNK
end_time = 1
l_tol = 1e-10
nl_rel_tol = 1e-10
[]
[Preconditioning]
[./smp]
type = SMP
full = true
[../]
[]
[Outputs]
file_base = kinetic_out
exodus = true
perf_graph = true
print_linear_residuals = true
[]
modules/chemical_reactions/test/tests/kinetic_rate/arrhenius.i
# Check the correct temperature dependence of the kinetic rate constant using
# the Arrhenius equation. Two kinetic reactions take place at different system
# temperatures. The Arrhenius equation states that the kinetic rate increases
# with temperature, so more mineral should be precipitated for the higher system
# temperature. In this case, the AuxVariables kinetic_rate1 and mineral1 should
# be larger than kinetic_rate0 and mineral0.
[Mesh]
type = GeneratedMesh
dim = 2
[]
[Variables]
[./a0]
initial_condition = 0.1
[../]
[./b0]
initial_condition = 0.1
[../]
[./a1]
initial_condition = 0.1
[../]
[./b1]
initial_condition = 0.1
[../]
[]
[AuxVariables]
[./mineral0]
[../]
[./mineral1]
[../]
[./kinetic_rate0]
[../]
[./kinetic_rate1]
[../]
[]
[AuxKernels]
[./kinetic_rate0]
type = KineticDisPreRateAux
variable = kinetic_rate0
e_act = 1.5e4
r_area = 1
log_k = -6
ref_kconst = 1e-8
gas_const = 8.31434
ref_temp = 298.15
sys_temp = 298.15
sto_v = '1 1'
v = 'a0 b0'
[../]
[./kinetic_rate1]
type = KineticDisPreRateAux
variable = kinetic_rate1
e_act = 1.5e4
r_area = 1
log_k = -6
ref_kconst = 1e-8
gas_const = 8.31434
ref_temp = 298.15
sys_temp = 323.15
sto_v = '1 1'
v = 'a1 b1'
[../]
[./mineral0_conc]
type = KineticDisPreConcAux
variable = mineral0
e_act = 1.5e4
r_area = 1
log_k = -6
ref_kconst = 1e-8
gas_const = 8.31434
ref_temp = 298.15
sys_temp = 298.15
sto_v = '1 1'
v = 'a0 b0'
[../]
[./mineral1_conc]
type = KineticDisPreConcAux
variable = mineral1
e_act = 1.5e4
r_area = 1
log_k = -6
ref_kconst = 1e-8
gas_const = 8.31434
ref_temp = 298.15
sys_temp = 323.15
sto_v = '1 1'
v = 'a1 b1'
[../]
[]
[Kernels]
[./a0_ie]
type = PrimaryTimeDerivative
variable = a0
[../]
[./b0_ie]
type = PrimaryTimeDerivative
variable = b0
[../]
[./a0_r]
type = CoupledBEKinetic
variable = a0
v = mineral0
weight = 1
[../]
[./b0_r]
type = CoupledBEKinetic
variable = b0
v = mineral0
weight = 1
[../]
[./a1_ie]
type = PrimaryTimeDerivative
variable = a1
[../]
[./b1_ie]
type = PrimaryTimeDerivative
variable = b1
[../]
[./a1_r]
type = CoupledBEKinetic
variable = a1
v = mineral1
weight = 1
[../]
[./b1_r]
type = CoupledBEKinetic
variable = b1
v = mineral1
weight = 1
[../]
[]
[Materials]
[./porous]
type = GenericConstantMaterial
prop_names = porosity
prop_values = 0.2
[../]
[]
[Executioner]
type = Transient
solve_type = PJFNK
end_time = 1
dt = 1
[]
[Preconditioning]
[./smp]
type = SMP
full = true
[../]
[]
[Outputs]
exodus = true
perf_graph = true
print_linear_residuals = true
[]
modules/chemical_reactions/test/tests/exceptions/missing_sto3.i
# Missing stoichiometric coefficient in AqueousEquilibriumRxnAux AuxKernel
# Simple reaction-diffusion example without using the action.
# In this example, two primary species a and b diffuse towards each other from
# opposite ends of a porous medium, reacting when they meet to form a mineral
# precipitate
# This simulation is identical to 2species.i, but explicitly includes the AuxVariables,
# AuxKernels, and Kernels that the action in 2species.i adds
[Mesh]
type = GeneratedMesh
dim = 2
[]
[Variables]
[./a]
[../]
[./b]
[../]
[]
[AuxVariables]
[./mineral]
[../]
[]
[AuxKernels]
[./mineral_conc]
type = KineticDisPreConcAux
variable = mineral
sto_v = 1
v = 'a b'
[../]
[]
[Kernels]
[./a_ie]
type = PrimaryTimeDerivative
variable = a
[../]
[./b_ie]
type = PrimaryTimeDerivative
variable = b
[../]
[]
[Materials]
[./porous]
type = GenericConstantMaterial
prop_names = porosity
prop_values = 0.2
[../]
[]
[Executioner]
type = Transient
end_time = 1
[]
test/tests/restart/restart_refined_mesh/bad2.i
[Mesh]
# dim = 2
file = 2d_stoch_aperture_caco3_pe1.5_64_mesh_out.e
# uniform_refine = 6
[]
[Variables]
active = 'pressure tracer ca2+ h+ hco3-'
[./pressure]
order = FIRST
family = LAGRANGE
initial_from_file_var = 'pressure'
initial_from_file_timestep = 51
# [./InitialCondition]
# type = BoundingBoxIC
# x1 = 0.0
# y1 = 0.0
# x2 = 1.0e-10
# y2 = 0.15
# inside = 60.0
# outside = 0.0
# [../]
[../]
[./tracer]
order = FIRST
family = LAGRANGE
initial_from_file_var = 'tracer'
initial_from_file_timestep = 51
# [./InitialCondition]
# type = BoundingBoxIC
# x1 = 0.0
# y1 = 0.0
# x2 = 1.0e-10
# y2 = 0.15
# inside = 1.0
# outside = 0.0
# [../]
[../]
[./ca2+]
order = FIRST
family = LAGRANGE
initial_from_file_var = 'ca2+'
initial_from_file_timestep = 51
# [./InitialCondition]
# type = BoundingBoxIC
# x1 = 0.0
# y1 = 0.0
# x2 = 1.0e-10
# y2 = 0.15
# inside = 1.0e-6
# outside = 5.0e-2
# [../]
[../]
[./h+]
order = FIRST
family = LAGRANGE
initial_from_file_var = 'h+'
initial_from_file_timestep = 51
# initial_condition = 1.0e-7
[../]
[./hco3-]
order = FIRST
family = LAGRANGE
initial_from_file_var = 'hco3-'
initial_from_file_timestep = 51
# initial_condition = 1.0e-6
# [./InitialCondition]
# type = BoundingBoxIC
# x1 = 0.0
# y1 = 0.0
# x2 = 1.0e-10
# y2 = 0.15
# inside = 5.0e-2
# outside = 1.0e-6
# [../]
[../]
[]
[AuxVariables]
active = 'conductivity caco3(s)'
[./conductivity]
order = CONSTANT
family = MONOMIAL
[../]
[./caco3(s)]
order = FIRST
family = LAGRANGE
initial_from_file_var = 'caco3(s)'
initial_from_file_timestep = 51
[../]
[]
[Kernels]
# active = 'pressure_ie pressure_diff
# tracer_ie tracer_pd tracer_conv
# ca2+_ie ca2+_pd ca2+_conv
# ca2+_caco3(aq)_sub ca2+_caco3(aq)_cd ca2+_caco3(aq)_conv
# ca2+_cahco3+_sub ca2+_cahco3+_cd ca2+_cahco3+_conv
# ca2+_caoh+_sub ca2+_caoh+_cd ca2+_caoh+_conv
# ca2+_calcite
# h+_ie h+_pd h+_conv
# h+_caco3(aq)_sub h+_caco3(aq)_cd h+_caco3(aq)_conv
# h+_caoh+_sub h+_caoh+_cd h+_caoh+_conv
# h+_co2(aq)_sub h+_co2(aq)_cd h+_co2(aq)_conv
# h+_co32-_sub h+_co32-_cd h+_co32-_conv
# h+_oh-_sub h+_oh-_cd h+_oh-_conv
# h+_calcite
# hco3-_ie hco3-_pd hco3-_conv
# hco3-_caco3(aq)_sub hco3-_caco3(aq)_cd hco3-_caco3(aq)_conv
# hco3-_cahco3+_sub hco3-_cahco3+_cd hco3-_cahco3+_conv
# hco3-_co2(aq)_sub hco3-_co2(aq)_cd hco3-_co2(aq)_conv
# hco3-_co32-_sub hco3-_co32-_cd hco3-_co32-_conv
# hco3-_calcite'
active = 'pressure_ie pressure_diff
tracer_ie tracer_pd tracer_conv
ca2+_ie ca2+_pd ca2+_conv
ca2+_caco3(aq)_sub ca2+_caco3(aq)_cd ca2+_caco3(aq)_conv
ca2+_cahco3+_sub ca2+_cahco3+_cd ca2+_cahco3+_conv
ca2+_calcite
h+_ie h+_pd h+_conv
h+_caco3(aq)_sub h+_caco3(aq)_cd h+_caco3(aq)_conv
h+_calcite
hco3-_ie hco3-_pd hco3-_conv
hco3-_caco3(aq)_sub hco3-_caco3(aq)_cd hco3-_caco3(aq)_conv
hco3-_cahco3+_sub hco3-_cahco3+_cd hco3-_cahco3+_conv
hco3-_calcite'
# Pressure
[./pressure_ie]
type = PressureImplicitEuler
variable = pressure
[../]
[./pressure_diff]
type = PressureDiffusion
variable = pressure
[../]
# tracer
[./tracer_ie]
type = PrimaryTimeDerivative
variable = tracer
[../]
[./tracer_pd]
type = PrimaryDiffusion
variable = tracer
[../]
[./tracer_conv]
type = PrimaryConvection
variable = tracer
p = 'pressure'
[../]
# ca2+
[./ca2+_ie]
type = PrimaryTimeDerivative
variable = ca2+
[../]
[./ca2+_pd]
type = PrimaryDiffusion
variable = ca2+
[../]
[./ca2+_conv]
type = PrimaryConvection
variable = ca2+
p = 'pressure'
[../]
[./ca2+_caco3(aq)_sub]
type = CoupledBEEquilibriumSub
variable = ca2+
weight = 1.0
log_k = -7.009
sto_u = 1.0
sto_v = '-1.0 1.0'
v = 'h+ hco3-'
# start_time = 1.0
[../]
[./ca2+_caco3(aq)_cd]
type = CoupledDiffusionReactionSub
variable = ca2+
weight = 1.0
log_k = -7.009
sto_u = 1.0
sto_v = '-1.0 1.0'
v = 'h+ hco3-'
# start_time = 1.0
[../]
[./ca2+_caco3(aq)_conv]
type = CoupledConvectionReactionSub
variable = ca2+
weight = 1.0
log_k = -7.009
sto_u = 1.0
sto_v = '-1.0 1.0'
v = 'h+ hco3-'
p = 'pressure'
# start_time = 1.0
[../]
[./ca2+_cahco3+_sub]
type = CoupledBEEquilibriumSub
variable = ca2+
weight = 1.0
log_k = 1.043
sto_u = 1.0
sto_v = 1.0
v = 'hco3-'
[../]
[./ca2+_cahco3+_cd]
type = CoupledDiffusionReactionSub
variable = ca2+
weight = 1.0
log_k = 1.043
sto_u = 1.0
sto_v = 1.0
v = 'hco3-'
[../]
[./ca2+_cahco3+_conv]
type = CoupledConvectionReactionSub
variable = ca2+
weight = 1.0
log_k = 1.043
sto_u = 1.0
sto_v = 1.0
v = 'hco3-'
p = 'pressure'
[../]
[./ca2+_caoh+_sub]
type = CoupledBEEquilibriumSub
variable = ca2+
weight = 1.0
log_k = -12.85
sto_u = 1.0
sto_v = -1.0
v = 'h+'
[../]
[./ca2+_caoh+_cd]
type = CoupledDiffusionReactionSub
variable = ca2+
weight = 1.0
log_k = -12.85
sto_u = 1.0
sto_v = -1.0
v = 'h+'
[../]
[./ca2+_caoh+_conv]
type = CoupledConvectionReactionSub
variable = ca2+
weight = 1.0
log_k = -12.85
sto_u = 1.0
sto_v = -1.0
v = 'h+'
p = 'pressure'
[../]
[./ca2+_calcite]
type = CoupledBEKinetic
variable = ca2+
weight = 1.0
v = 'caco3(s)'
# start_time = 1.0
[../]
# h+
[./h+_ie]
type = PrimaryTimeDerivative
variable = h+
[../]
[./h+_pd]
type = PrimaryDiffusion
variable = h+
[../]
[./h+_conv]
type = PrimaryConvection
variable = h+
p = 'pressure'
[../]
[./h+_caco3(aq)_sub]
type = CoupledBEEquilibriumSub
variable = h+
weight = -1.0
log_k = -7.009
sto_u = -1.0
sto_v = '1.0 1.0'
v = 'ca2+ hco3-'
# start_time = 1.0
[../]
[./h+_caco3(aq)_cd]
type = CoupledDiffusionReactionSub
variable = h+
weight = -1.0
log_k = -7.009
sto_u = -1.0
sto_v = '1.0 1.0'
v = 'ca2+ hco3-'
# start_time = 1.0
[../]
[./h+_caco3(aq)_conv]
type = CoupledConvectionReactionSub
variable = h+
weight = -1.0
log_k = -7.009
sto_u = -1.0
sto_v = '1.0 1.0'
v = 'ca2+ hco3-'
p = 'pressure'
# start_time = 1.0
[../]
[./h+_caoh+_sub]
type = CoupledBEEquilibriumSub
variable = h+
weight = -1.0
log_k = -12.85
sto_u = -1.0
sto_v = 1.0
v = 'ca2+'
[../]
[./h+_caoh+_cd]
type = CoupledDiffusionReactionSub
variable = h+
weight = -1.0
log_k = -12.85
sto_u = -1.0
sto_v = 1.0
v = 'ca2+'
[../]
[./h+_caoh+_conv]
type = CoupledConvectionReactionSub
variable = h+
weight = -1.0
log_k = -12.85
sto_u = -1.0
sto_v = 1.0
v = 'ca2+'
p = 'pressure'
[../]
[./h+_co2(aq)_sub]
type = CoupledBEEquilibriumSub
variable = h+
weight = 1.0
log_k = 6.341
sto_u = 1.0
sto_v = 1.0
v = 'hco3-'
[../]
[./h+_co2(aq)_cd]
type = CoupledDiffusionReactionSub
variable = h+
weight = 1.0
log_k = 6.341
sto_u = 1.0
sto_v = 1.0
v = 'hco3-'
[../]
[./h+_co2(aq)_conv]
type = CoupledConvectionReactionSub
variable = h+
weight = 1.0
log_k = 6.341
sto_u = 1.0
sto_v = 1.0
v = 'hco3-'
p = 'pressure'
[../]
[./h+_co32-_sub]
type = CoupledBEEquilibriumSub
variable = h+
weight = -1.0
log_k = -10.325
sto_u = -1.0
sto_v = 1.0
v = 'hco3-'
[../]
[./h+_co32-_cd]
type = CoupledDiffusionReactionSub
variable = h+
weight = -1.0
log_k = -10.325
sto_u = -1.0
sto_v = 1.0
v = 'hco3-'
[../]
[./h+_co32-_conv]
type = CoupledConvectionReactionSub
variable = h+
weight = -1.0
log_k = -10.325
sto_u = -1.0
sto_v = 1.0
v = 'hco3-'
p = 'pressure'
[../]
[./h+_oh-_sub]
type = CoupledBEEquilibriumSub
variable = h+
weight = -1.0
log_k = -13.991
sto_u = -1.0
sto_v = ' '
[../]
[./h+_oh-_cd]
type = CoupledDiffusionReactionSub
variable = h+
weight = -1.0
log_k = -13.991
sto_u = -1.0
sto_v = ' '
[../]
[./h+_oh-_conv]
type = CoupledConvectionReactionSub
variable = h+
weight = -1.0
log_k = -13.991
sto_u = -1.0
sto_v = ' '
p = 'pressure'
[../]
[./h+_calcite]
type = CoupledBEKinetic
variable = h+
weight = -1.0
v = 'caco3(s)'
# start_time = 1.0
[../]
# hco3-
[./hco3-_ie]
type = PrimaryTimeDerivative
variable = hco3-
[../]
[./hco3-_pd]
type = PrimaryDiffusion
variable = hco3-
[../]
[./hco3-_conv]
type = PrimaryConvection
variable = hco3-
p = 'pressure'
[../]
[./hco3-_caco3(aq)_sub]
type = CoupledBEEquilibriumSub
variable = hco3-
weight = 1.0
log_k = -7.009
sto_u = 1.0
sto_v = '1.0 -1.0'
v = 'ca2+ h+'
# start_time = 1.0
[../]
[./hco3-_caco3(aq)_cd]
type = CoupledDiffusionReactionSub
variable = hco3-
weight = 1.0
log_k = -7.009
sto_u = 1.0
sto_v = '1.0 -1.0'
v = 'ca2+ h+'
# start_time = 1.0
[../]
[./hco3-_caco3(aq)_conv]
type = CoupledConvectionReactionSub
variable = hco3-
weight = 1.0
log_k = -7.009
sto_u = 1.0
sto_v = '1.0 -1.0'
v = 'ca2+ h+'
p = 'pressure'
# start_time = 1.0
[../]
[./hco3-_cahco3+_sub]
type = CoupledBEEquilibriumSub
variable = hco3-
weight = 1.0
log_k = 1.043
sto_u = 1.0
sto_v = 1.0
v = 'ca2+'
[../]
[./hco3-_cahco3+_cd]
type = CoupledDiffusionReactionSub
variable = hco3-
weight = 1.0
log_k = 1.043
sto_u = 1.0
sto_v = 1.0
v = 'ca2+'
[../]
[./hco3-_cahco3+_conv]
type = CoupledConvectionReactionSub
variable = hco3-
weight = 1.0
log_k = 1.043
sto_u = 1.0
sto_v = 1.0
v = 'ca2+'
p = 'pressure'
[../]
[./hco3-_co2(aq)_sub]
type = CoupledBEEquilibriumSub
variable = hco3-
weight = 1.0
log_k = 6.341
sto_u = 1.0
sto_v = 1.0
v = 'h+'
[../]
[./hco3-_co2(aq)_cd]
type = CoupledDiffusionReactionSub
variable = hco3-
weight = 1.0
log_k = 6.341
sto_u = 1.0
sto_v = 1.0
v = 'h+'
[../]
[./hco3-_co2(aq)_conv]
type = CoupledConvectionReactionSub
variable = hco3-
weight = 1.0
log_k = 6.341
sto_u = 1.0
sto_v = 1.0
v = 'h+'
p = 'pressure'
[../]
[./hco3-_co32-_sub]
type = CoupledBEEquilibriumSub
variable = hco3-
weight = 1.0
log_k = -10.325
sto_u = 1.0
sto_v = -1.0
v = 'h+'
[../]
[./hco3-_co32-_cd]
type = CoupledDiffusionReactionSub
variable = hco3-
weight = 1.0
log_k = -10.325
sto_u = 1.0
sto_v = -1.0
v = 'h+'
[../]
[./hco3-_co32-_conv]
type = CoupledConvectionReactionSub
variable = hco3-
weight = 1.0
log_k = -10.325
sto_u = 1.0
sto_v = -1.0
v = 'h+'
p = 'pressure'
[../]
[./hco3-_calcite]
type = CoupledBEKinetic
variable = hco3-
weight = 1.0
v = 'caco3(s)'
# start_time = 1.0
[../]
[]
[AuxKernels]
active = 'aux_conductivity aux_caco3(s)'
# conductivity
[./aux_conductivity]
type = StochasticFieldAux
variable = conductivity
file_name = k_field.dat
[../]
# caco3(s)
[./aux_caco3(s)]
type = KineticDisPreConcAux
variable = caco3(s)
log_k = 1.8487
sto_v = '1.0 1.0 -1.0'
r_area = 4.61e-4
ref_kconst = 6.456542e-7
e_act = 1.5e4
gas_const = 8.314
ref_temp = 298.15
sys_temp = 298.15
v = 'ca2+ hco3- h+'
# start_time = 1.0
[../]
[]
[BCs]
active = 'pressure_left pressure_right
tracer_left tracer_right
ca2+_left ca2+_right
hco3-_left hco3-_right
h+_left h+_right'
# pressure
[./pressure_left]
type = DirichletBC
variable = pressure
boundary = 1
value = 60.0
[../]
[./pressure_right]
type = DirichletBC
variable = pressure
boundary = 2
value = 0.0
[../]
# tracer
[./tracer_left]
type = DirichletBC
variable = tracer
boundary = 1
value = 1.0
[../]
[./tracer_right]
type = OutFlowBC
variable = tracer
boundary = 2
porosity = 1.0
diffusivity = 7.5e-7
[../]
# ca2+
[./ca2+_left]
type = DirichletBC
variable = ca2+
boundary = 1
value = 1.0e-6
# type = SinDirichletBC
# variable = ca2+
# boundary = 1
# initial = 5.0e-2
# final = 1.0e-6
# duration = 1
[../]
[./ca2+_right]
type = OutFlowBC
variable = ca2+
boundary = 2
porosity = 1.0
diffusivity = 7.5e-7
[../]
# hco3-
[./hco3-_left]
type = DirichletBC
variable = hco3-
boundary = 1
value = 1.0e-2
# type = SinDirichletBC
# variable = hco3-
# boundary = 1
# initial = 1.0e-6
# final = 5.0e-2
# duration = 1
[../]
[./hco3-_right]
type = OutFlowBC
variable = hco3-
boundary = 2
porosity = 1.0
diffusivity = 7.5e-7
[../]
# h+
[./h+_left]
type = DirichletBC
variable = h+
boundary = 1
value = 1.0e-7
[../]
[./h+_right]
type = OutFlowBC
variable = h+
boundary = 2
porosity = 1.0
diffusivity = 7.5e-7
[../]
[]
[Materials]
active = 'stochastic'
[./stochastic]
type = StochasticMaterial
block = 1
diffusivity = 7.5e-7
storage = 1.0e-5
init_porosity = 1.0
conductivity = conductivity
mineral = 0.00
molecular_weight = 100.08
density = 2.7099
v = 'caco3(s)'
[../]
[]
[Executioner]
active = ' '
type = Transient
# type = SolutionTimeAdaptive
solve_type = 'PJFNK'
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart'
petsc_options_value = 'hypre boomeramg 51'
l_max_its = 50
l_tol = 1e-5
nl_max_its = 10
nl_rel_tol = 1e-5
start_time = 0.0
end_time = 2.0
num_steps = 10000000
dt = 0.02
dtmin = 0.0000001
dtmax = 0.1
# sol_time_adaptive_time_stepping = true
sync_times = '1.0 4.0 8.0 10.0'
[./Adaptivity]
# initial_adaptivity = 3
error_estimator = KellyErrorEstimator
refine_fraction = 0.85
coarsen_fraction = 0.05
# weight_names = 'urea nh4+'
# weight_values = '1.0e2 1.0e6'
max_h_level = 2
[../]
[]
[Outputs]
file_base = 2d_stoch_aperture_caco3_pe1.5_64_transient_out
exodus = true
[]
test/tests/restart/restart_refined_mesh/bad1.i
[Mesh]
dim = 2
file = 2d_aperture_field.e
uniform_refine = 6
[]
[Variables]
active = 'pressure tracer ca2+ h+ hco3-'
[./pressure]
order = FIRST
family = LAGRANGE
[./InitialCondition]
type = BoundingBoxIC
x1 = 0.0
y1 = 0.0
x2 = 1.0e-10
y2 = 0.15
inside = 60.0
outside = 0.0
[../]
[../]
[./tracer]
order = FIRST
family = LAGRANGE
[./InitialCondition]
type = BoundingBoxIC
x1 = 0.0
y1 = 0.0
x2 = 1.0e-10
y2 = 0.15
inside = 1.0
outside = 0.0
[../]
[../]
[./ca2+]
order = FIRST
family = LAGRANGE
[./InitialCondition]
type = BoundingBoxIC
x1 = 0.0
y1 = 0.0
x2 = 1.0e-10
y2 = 0.15
inside = 1.0e-6
outside = 5.0e-2
[../]
[../]
[./h+]
order = FIRST
family = LAGRANGE
initial_condition = 1.0e-7
[../]
[./hco3-]
order = FIRST
family = LAGRANGE
# initial_condition = 1.0e-6
[./InitialCondition]
type = BoundingBoxIC
x1 = 0.0
y1 = 0.0
x2 = 1.0e-10
y2 = 0.15
inside = 5.0e-2
outside = 1.0e-6
[../]
[../]
[]
[AuxVariables]
active = 'conductivity caco3(s)'
[./conductivity]
order = CONSTANT
family = MONOMIAL
[../]
[./caco3(s)]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
# active = 'pressure_ie pressure_diff
# tracer_ie tracer_pd tracer_conv
# ca2+_ie ca2+_pd ca2+_conv
# ca2+_caco3(aq)_sub ca2+_caco3(aq)_cd ca2+_caco3(aq)_conv
# ca2+_cahco3+_sub ca2+_cahco3+_cd ca2+_cahco3+_conv
# ca2+_caoh+_sub ca2+_caoh+_cd ca2+_caoh+_conv
# ca2+_calcite
# h+_ie h+_pd h+_conv
# h+_caco3(aq)_sub h+_caco3(aq)_cd h+_caco3(aq)_conv
# h+_caoh+_sub h+_caoh+_cd h+_caoh+_conv
# h+_co2(aq)_sub h+_co2(aq)_cd h+_co2(aq)_conv
# h+_co32-_sub h+_co32-_cd h+_co32-_conv
# h+_oh-_sub h+_oh-_cd h+_oh-_conv
# h+_calcite
# hco3-_ie hco3-_pd hco3-_conv
# hco3-_caco3(aq)_sub hco3-_caco3(aq)_cd hco3-_caco3(aq)_conv
# hco3-_cahco3+_sub hco3-_cahco3+_cd hco3-_cahco3+_conv
# hco3-_co2(aq)_sub hco3-_co2(aq)_cd hco3-_co2(aq)_conv
# hco3-_co32-_sub hco3-_co32-_cd hco3-_co32-_conv
# hco3-_calcite'
active = 'pressure_ie pressure_diff
tracer_ie tracer_pd tracer_conv
ca2+_ie ca2+_pd ca2+_conv
ca2+_caco3(aq)_sub ca2+_caco3(aq)_cd ca2+_caco3(aq)_conv
ca2+_cahco3+_sub ca2+_cahco3+_cd ca2+_cahco3+_conv
ca2+_calcite
h+_ie h+_pd h+_conv
h+_caco3(aq)_sub h+_caco3(aq)_cd h+_caco3(aq)_conv
h+_calcite
hco3-_ie hco3-_pd hco3-_conv
hco3-_caco3(aq)_sub hco3-_caco3(aq)_cd hco3-_caco3(aq)_conv
hco3-_cahco3+_sub hco3-_cahco3+_cd hco3-_cahco3+_conv
hco3-_calcite'
# Pressure
[./pressure_ie]
type = PressureImplicitEuler
variable = pressure
[../]
[./pressure_diff]
type = PressureDiffusion
variable = pressure
[../]
# tracer
[./tracer_ie]
type = PrimaryTimeDerivative
variable = tracer
[../]
[./tracer_pd]
type = PrimaryDiffusion
variable = tracer
[../]
[./tracer_conv]
type = PrimaryConvection
variable = tracer
p = 'pressure'
[../]
# ca2+
[./ca2+_ie]
type = PrimaryTimeDerivative
variable = ca2+
[../]
[./ca2+_pd]
type = PrimaryDiffusion
variable = ca2+
[../]
[./ca2+_conv]
type = PrimaryConvection
variable = ca2+
p = 'pressure'
[../]
[./ca2+_caco3(aq)_sub]
type = CoupledBEEquilibriumSub
variable = ca2+
weight = 1.0
log_k = -7.009
sto_u = 1.0
sto_v = '-1.0 1.0'
v = 'h+ hco3-'
start_time = 1.0
[../]
[./ca2+_caco3(aq)_cd]
type = CoupledDiffusionReactionSub
variable = ca2+
weight = 1.0
log_k = -7.009
sto_u = 1.0
sto_v = '-1.0 1.0'
v = 'h+ hco3-'
start_time = 1.0
[../]
[./ca2+_caco3(aq)_conv]
type = CoupledConvectionReactionSub
variable = ca2+
weight = 1.0
log_k = -7.009
sto_u = 1.0
sto_v = '-1.0 1.0'
v = 'h+ hco3-'
p = 'pressure'
start_time = 1.0
[../]
[./ca2+_cahco3+_sub]
type = CoupledBEEquilibriumSub
variable = ca2+
weight = 1.0
log_k = 1.043
sto_u = 1.0
sto_v = 1.0
v = 'hco3-'
[../]
[./ca2+_cahco3+_cd]
type = CoupledDiffusionReactionSub
variable = ca2+
weight = 1.0
log_k = 1.043
sto_u = 1.0
sto_v = 1.0
v = 'hco3-'
[../]
[./ca2+_cahco3+_conv]
type = CoupledConvectionReactionSub
variable = ca2+
weight = 1.0
log_k = 1.043
sto_u = 1.0
sto_v = 1.0
v = 'hco3-'
p = 'pressure'
[../]
[./ca2+_caoh+_sub]
type = CoupledBEEquilibriumSub
variable = ca2+
weight = 1.0
log_k = -12.85
sto_u = 1.0
sto_v = -1.0
v = 'h+'
[../]
[./ca2+_caoh+_cd]
type = CoupledDiffusionReactionSub
variable = ca2+
weight = 1.0
log_k = -12.85
sto_u = 1.0
sto_v = -1.0
v = 'h+'
[../]
[./ca2+_caoh+_conv]
type = CoupledConvectionReactionSub
variable = ca2+
weight = 1.0
log_k = -12.85
sto_u = 1.0
sto_v = -1.0
v = 'h+'
p = 'pressure'
[../]
[./ca2+_calcite]
type = CoupledBEKinetic
variable = ca2+
weight = 1.0
v = 'caco3(s)'
start_time = 1.0
[../]
# h+
[./h+_ie]
type = PrimaryTimeDerivative
variable = h+
[../]
[./h+_pd]
type = PrimaryDiffusion
variable = h+
[../]
[./h+_conv]
type = PrimaryConvection
variable = h+
p = 'pressure'
[../]
[./h+_caco3(aq)_sub]
type = CoupledBEEquilibriumSub
variable = h+
weight = -1.0
log_k = -7.009
sto_u = -1.0
sto_v = '1.0 1.0'
v = 'ca2+ hco3-'
start_time = 1.0
[../]
[./h+_caco3(aq)_cd]
type = CoupledDiffusionReactionSub
variable = h+
weight = -1.0
log_k = -7.009
sto_u = -1.0
sto_v = '1.0 1.0'
v = 'ca2+ hco3-'
start_time = 1.0
[../]
[./h+_caco3(aq)_conv]
type = CoupledConvectionReactionSub
variable = h+
weight = -1.0
log_k = -7.009
sto_u = -1.0
sto_v = '1.0 1.0'
v = 'ca2+ hco3-'
p = 'pressure'
start_time = 1.0
[../]
[./h+_caoh+_sub]
type = CoupledBEEquilibriumSub
variable = h+
weight = -1.0
log_k = -12.85
sto_u = -1.0
sto_v = 1.0
v = 'ca2+'
[../]
[./h+_caoh+_cd]
type = CoupledDiffusionReactionSub
variable = h+
weight = -1.0
log_k = -12.85
sto_u = -1.0
sto_v = 1.0
v = 'ca2+'
[../]
[./h+_caoh+_conv]
type = CoupledConvectionReactionSub
variable = h+
weight = -1.0
log_k = -12.85
sto_u = -1.0
sto_v = 1.0
v = 'ca2+'
p = 'pressure'
[../]
[./h+_co2(aq)_sub]
type = CoupledBEEquilibriumSub
variable = h+
weight = 1.0
log_k = 6.341
sto_u = 1.0
sto_v = 1.0
v = 'hco3-'
[../]
[./h+_co2(aq)_cd]
type = CoupledDiffusionReactionSub
variable = h+
weight = 1.0
log_k = 6.341
sto_u = 1.0
sto_v = 1.0
v = 'hco3-'
[../]
[./h+_co2(aq)_conv]
type = CoupledConvectionReactionSub
variable = h+
weight = 1.0
log_k = 6.341
sto_u = 1.0
sto_v = 1.0
v = 'hco3-'
p = 'pressure'
[../]
[./h+_co32-_sub]
type = CoupledBEEquilibriumSub
variable = h+
weight = -1.0
log_k = -10.325
sto_u = -1.0
sto_v = 1.0
v = 'hco3-'
[../]
[./h+_co32-_cd]
type = CoupledDiffusionReactionSub
variable = h+
weight = -1.0
log_k = -10.325
sto_u = -1.0
sto_v = 1.0
v = 'hco3-'
[../]
[./h+_co32-_conv]
type = CoupledConvectionReactionSub
variable = h+
weight = -1.0
log_k = -10.325
sto_u = -1.0
sto_v = 1.0
v = 'hco3-'
p = 'pressure'
[../]
[./h+_oh-_sub]
type = CoupledBEEquilibriumSub
variable = h+
weight = -1.0
log_k = -13.991
sto_u = -1.0
sto_v = ' '
[../]
[./h+_oh-_cd]
type = CoupledDiffusionReactionSub
variable = h+
weight = -1.0
log_k = -13.991
sto_u = -1.0
sto_v = ' '
[../]
[./h+_oh-_conv]
type = CoupledConvectionReactionSub
variable = h+
weight = -1.0
log_k = -13.991
sto_u = -1.0
sto_v = ' '
p = 'pressure'
[../]
[./h+_calcite]
type = CoupledBEKinetic
variable = h+
weight = -1.0
v = 'caco3(s)'
start_time = 1.0
[../]
# hco3-
[./hco3-_ie]
type = PrimaryTimeDerivative
variable = hco3-
[../]
[./hco3-_pd]
type = PrimaryDiffusion
variable = hco3-
[../]
[./hco3-_conv]
type = PrimaryConvection
variable = hco3-
p = 'pressure'
[../]
[./hco3-_caco3(aq)_sub]
type = CoupledBEEquilibriumSub
variable = hco3-
weight = 1.0
log_k = -7.009
sto_u = 1.0
sto_v = '1.0 -1.0'
v = 'ca2+ h+'
start_time = 1.0
[../]
[./hco3-_caco3(aq)_cd]
type = CoupledDiffusionReactionSub
variable = hco3-
weight = 1.0
log_k = -7.009
sto_u = 1.0
sto_v = '1.0 -1.0'
v = 'ca2+ h+'
start_time = 1.0
[../]
[./hco3-_caco3(aq)_conv]
type = CoupledConvectionReactionSub
variable = hco3-
weight = 1.0
log_k = -7.009
sto_u = 1.0
sto_v = '1.0 -1.0'
v = 'ca2+ h+'
p = 'pressure'
start_time = 1.0
[../]
[./hco3-_cahco3+_sub]
type = CoupledBEEquilibriumSub
variable = hco3-
weight = 1.0
log_k = 1.043
sto_u = 1.0
sto_v = 1.0
v = 'ca2+'
[../]
[./hco3-_cahco3+_cd]
type = CoupledDiffusionReactionSub
variable = hco3-
weight = 1.0
log_k = 1.043
sto_u = 1.0
sto_v = 1.0
v = 'ca2+'
[../]
[./hco3-_cahco3+_conv]
type = CoupledConvectionReactionSub
variable = hco3-
weight = 1.0
log_k = 1.043
sto_u = 1.0
sto_v = 1.0
v = 'ca2+'
p = 'pressure'
[../]
[./hco3-_co2(aq)_sub]
type = CoupledBEEquilibriumSub
variable = hco3-
weight = 1.0
log_k = 6.341
sto_u = 1.0
sto_v = 1.0
v = 'h+'
[../]
[./hco3-_co2(aq)_cd]
type = CoupledDiffusionReactionSub
variable = hco3-
weight = 1.0
log_k = 6.341
sto_u = 1.0
sto_v = 1.0
v = 'h+'
[../]
[./hco3-_co2(aq)_conv]
type = CoupledConvectionReactionSub
variable = hco3-
weight = 1.0
log_k = 6.341
sto_u = 1.0
sto_v = 1.0
v = 'h+'
p = 'pressure'
[../]
[./hco3-_co32-_sub]
type = CoupledBEEquilibriumSub
variable = hco3-
weight = 1.0
log_k = -10.325
sto_u = 1.0
sto_v = -1.0
v = 'h+'
[../]
[./hco3-_co32-_cd]
type = CoupledDiffusionReactionSub
variable = hco3-
weight = 1.0
log_k = -10.325
sto_u = 1.0
sto_v = -1.0
v = 'h+'
[../]
[./hco3-_co32-_conv]
type = CoupledConvectionReactionSub
variable = hco3-
weight = 1.0
log_k = -10.325
sto_u = 1.0
sto_v = -1.0
v = 'h+'
p = 'pressure'
[../]
[./hco3-_calcite]
type = CoupledBEKinetic
variable = hco3-
weight = 1.0
v = 'caco3(s)'
start_time = 1.0
[../]
[]
[AuxKernels]
active = 'aux_conductivity aux_caco3(s)'
# conductivity
[./aux_conductivity]
type = StochasticFieldAux
variable = conductivity
file_name = k_field.dat
[../]
# caco3(s)
[./aux_caco3(s)]
type = KineticDisPreConcAux
variable = caco3(s)
log_k = 1.8487
sto_v = '1.0 1.0 -1.0'
r_area = 4.61e-4
ref_kconst = 6.456542e-7
e_act = 1.5e4
gas_const = 8.314
ref_temp = 298.15
sys_temp = 298.15
v = 'ca2+ hco3- h+'
start_time = 1.0
[../]
[]
[BCs]
active = 'pressure_left pressure_right
tracer_left tracer_right
ca2+_left ca2+_right
hco3-_left hco3-_right
h+_left h+_right'
# pressure
[./pressure_left]
type = DirichletBC
variable = pressure
boundary = 1
value = 60.0
[../]
[./pressure_right]
type = DirichletBC
variable = pressure
boundary = 2
value = 0.0
[../]
# tracer
[./tracer_left]
type = DirichletBC
variable = tracer
boundary = 1
value = 1.0
[../]
[./tracer_right]
type = OutFlowBC
variable = tracer
boundary = 2
porosity = 1.0
diffusivity = 7.5e-7
[../]
# ca2+
[./ca2+_left]
# type = DirichletBC
# variable = ca2+
# boundary = 1
# value = 1.0e-6
type = SinDirichletBC
variable = ca2+
boundary = 1
initial = 5.0e-2
final = 1.0e-6
duration = 1
[../]
[./ca2+_right]
type = OutFlowBC
variable = ca2+
boundary = 2
porosity = 1.0
diffusivity = 7.5e-7
[../]
# hco3-
[./hco3-_left]
# type = DirichletBC
# variable = hco3-
# boundary = 1
# value = 1.0e-2
type = SinDirichletBC
variable = hco3-
boundary = 1
initial = 1.0e-6
final = 5.0e-2
duration = 1
[../]
[./hco3-_right]
type = OutFlowBC
variable = hco3-
boundary = 2
porosity = 1.0
diffusivity = 7.5e-7
[../]
# h+
[./h+_left]
type = DirichletBC
variable = h+
boundary = 1
value = 1.0e-7
[../]
[./h+_right]
type = OutFlowBC
variable = h+
boundary = 2
porosity = 1.0
diffusivity = 7.5e-7
[../]
[]
[Materials]
active = 'stochastic'
[./stochastic]
type = StochasticMaterial
block = 1
diffusivity = 7.5e-7
storage = 1.0e-5
init_porosity = 1.0
conductivity = conductivity
mineral = 0.00
molecular_weight = 100.08
density = 2.7099
v = 'caco3(s)'
[../]
[]
[Executioner]
active = ' '
type = Transient
# type = SolutionTimeAdaptive
solve_type = 'PJFNK'
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart'
petsc_options_value = 'hypre boomeramg 51'
l_max_its = 50
l_tol = 1e-5
nl_max_its = 10
nl_rel_tol = 1e-5
start_time = 0.0
end_time = 1.0
num_steps = 10000000
dt = 0.02
dtmin = 0.0000001
dtmax = 0.1
# sol_time_adaptive_time_stepping = true
sync_times = '1.0'
[./Adaptivity]
# initial_adaptivity = 3
error_estimator = KellyErrorEstimator
refine_fraction = 0.85
coarsen_fraction = 0.05
# weight_names = 'urea nh4+'
# weight_values = '1.0e2 1.0e6'
max_h_level = 2
[../]
[]
[Outputs]
file_base = 2d_stoch_aperture_caco3_pe1.5_64_mesh_out
exodus = true
[]