- functionfunction expression
C++ Type:FunctionExpression
Description:function expression
- variableThe name of the variable that this object applies to
C++ Type:AuxVariableName
Description:The name of the variable that this object applies to
ParsedAux
under construction:Undocumented Class
The ParsedAux has not been documented. The content listed below should be used as a starting point for documenting the class, which includes the typical automatic documentation associated with a MooseObject; however, what is contained is ultimately determined by what is necessary to make the documentation clear for users.
# ParsedAux
!syntax description /AuxKernels/ParsedAux
## Overview
!! Replace these lines with information regarding the ParsedAux object.
## Example Input File Syntax
!! Describe and include an example of how to use the ParsedAux object.
!syntax parameters /AuxKernels/ParsedAux
!syntax inputs /AuxKernels/ParsedAux
!syntax children /AuxKernels/ParsedAux
Parsed function AuxKernel.
Input Parameters
- argscoupled variables
C++ Type:std::vector
Options:
Description:coupled variables
- 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
- 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
- constant_expressionsVector of values for the constants in constant_names (can be an FParser expression)
C++ Type:std::vector
Options:
Description:Vector of values for the constants in constant_names (can be an FParser expression)
- constant_namesVector of constants used in the parsed function (use this for kB etc.)
C++ Type:std::vector
Options:
Description:Vector of constants used in the parsed function (use this for kB etc.)
- 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.
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.
- disable_fpoptimizerFalseDisable the function parser algebraic optimizer
Default:False
C++ Type:bool
Options:
Description:Disable the function parser algebraic optimizer
- enableTrueSet the enabled status of the MooseObject.
Default:True
C++ Type:bool
Options:
Description:Set the enabled status of the MooseObject.
- enable_ad_cacheTrueEnable cacheing of function derivatives for faster startup time
Default:True
C++ Type:bool
Options:
Description:Enable cacheing of function derivatives for faster startup time
- enable_auto_optimizeTrueEnable automatic immediate optimization of derivatives
Default:True
C++ Type:bool
Options:
Description:Enable automatic immediate optimization of derivatives
- enable_jitTrueEnable just-in-time compilation of function expressions for faster evaluation
Default:True
C++ Type:bool
Options:
Description:Enable just-in-time compilation of function expressions for faster evaluation
- fail_on_evalerrorFalseFail fatally if a function evaluation returns an error code (otherwise just pass on NaN)
Default:False
C++ Type:bool
Options:
Description:Fail fatally if a function evaluation returns an error code (otherwise just pass on NaN)
- 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/combined/test/tests/poro_mechanics/borehole_highres.i
- modules/porous_flow/test/tests/chemistry/dissolution.i
- modules/tensor_mechanics/test/tests/notched_plastic_block/cmc_planar.i
- modules/combined/examples/mortar/mortar_gradient.i
- modules/fluid_properties/test/tests/water/water.i
- modules/porous_flow/test/tests/poro_elasticity/mandel_fully_saturated.i
- modules/tensor_mechanics/test/tests/notched_plastic_block/biaxial_planar.i
- modules/functional_expansion_tools/test/tests/standard_use/volume_coupling_custom_norm_sub.i
- modules/functional_expansion_tools/examples/2D_volumetric_Cartesian/sub.i
- modules/functional_expansion_tools/examples/1D_volumetric_Cartesian/sub.i
- test/tests/auxkernels/linear_combination/test.i
- modules/combined/examples/phase_field-mechanics/kks_mechanics_KHS.i
- modules/functional_expansion_tools/examples/3D_volumetric_Cartesian_direct/sub.i
- modules/functional_expansion_tools/test/tests/standard_use/multiapp_sub.i
- modules/porous_flow/test/tests/pressure_pulse/pressure_pulse_1d_MD.i
- modules/porous_flow/test/tests/chemistry/precipitation_2phase.i
- modules/porous_flow/test/tests/chemistry/precipitation.i
- modules/porous_flow/examples/tutorial/11.i
- modules/combined/test/tests/poro_mechanics/borehole_lowres.i
- test/tests/auxkernels/parsed_aux/parsed_aux_test.i
- modules/functional_expansion_tools/examples/3D_volumetric_cylindrical/sub.i
- modules/functional_expansion_tools/examples/3D_volumetric_cylindrical_subapp_mesh_refine/sub.i
- modules/porous_flow/test/tests/poro_elasticity/mandel_constM.i
- modules/porous_flow/examples/tutorial/11_2D.i
- modules/combined/examples/phase_field-mechanics/kks_mechanics_VTS.i
- modules/functional_expansion_tools/examples/3D_volumetric_Cartesian_different_submesh/sub.i
- modules/porous_flow/test/tests/poro_elasticity/mandel_fully_saturated_volume.i
- modules/porous_flow/test/tests/chemistry/dissolution_limited.i
- modules/porous_flow/examples/reservoir_model/field_model.i
- modules/combined/test/tests/poro_mechanics/mandel.i
- modules/porous_flow/test/tests/poro_elasticity/mandel_basicthm.i
- modules/porous_flow/examples/reservoir_model/regular_grid.i
- modules/functional_expansion_tools/test/tests/standard_use/volume_sub.i
- modules/porous_flow/test/tests/poro_elasticity/mandel.i
- test/tests/functions/piecewise_multilinear/twoD_const.i
- modules/phase_field/examples/interfacekernels/interface_fluxbc.i
- modules/functional_expansion_tools/examples/3D_volumetric_Cartesian/sub.i
- modules/porous_flow/test/tests/chemistry/dissolution_limited_2phase.i
- test/tests/outputs/png/wedge.i
- modules/functional_expansion_tools/test/tests/errors/multiapp_sub.i
modules/combined/test/tests/poro_mechanics/borehole_highres.i
# Poroelastic response of a borehole.
#
# HIGHRES VERSION: this version gives good agreement with the analytical solution, but it takes a while so is a "heavy" test
#
# A fully-saturated medium contains a fluid with a homogeneous porepressure,
# but an anisitropic insitu stress. A infinitely-long borehole aligned with
# the $$z$$ axis is instanteously excavated. The borehole boundary is
# stress-free and allowed to freely drain. This problem is analysed using
# plane-strain conditions (no $$z$$ displacement).
#
# The solution in Laplace space is found in E Detournay and AHD Cheng "Poroelastic response of a borehole in a non-hydrostatic stress field". International Journal of Rock Mechanics and Mining Sciences and Geomechanics Abstracts 25 (1988) 171-182. In the small-time limit, the Laplace transforms may be performed. There is one typo in the paper. Equation (A4)'s final term should be -(a/r)\sqrt(4ct/(a^2\pi)), and not +(a/r)\sqrt(4ct/(a^2\pi)).
#
# Because realistic parameters are chosen (below),
# the residual for porepressure is much smaller than
# the residuals for the displacements. Therefore the
# scaling parameter is chosen. Also note that the
# insitu stresses are effective stresses, not total
# stresses, but the solution in the above paper is
# expressed in terms of total stresses.
#
# Here are the problem's parameters, and their values:
# Borehole radius. a = 1
# Rock's Lame lambda. la = 0.5E9
# Rock's Lame mu, which is also the Rock's shear modulus. mu = G = 1.5E9
# Rock bulk modulus. K = la + 2*mu/3 = 1.5E9
# Drained Poisson ratio. nu = (3K - 2G)/(6K + 2G) = 0.125
# Rock bulk compliance. 1/K = 0.66666666E-9
# Fluid bulk modulus. Kf = 0.7171315E9
# Fluid bulk compliance. 1/Kf = 1.39444444E-9
# Rock initial porosity. phi0 = 0.3
# Biot coefficient. alpha = 0.65
# Biot modulus. M = 1/(phi0/Kf + (alpha - phi0)(1 - alpha)/K) = 2E9
# Undrained bulk modulus. Ku = K + alpha^2*M = 2.345E9
# Undrained Poisson ratio. nuu = (3Ku - 2G)/(6Ku + 2G) = 0.2364
# Skempton coefficient. B = alpha*M/Ku = 0.554
# Fluid mobility (rock permeability/fluid viscosity). k = 1E-12
[Mesh]
type = FileMesh
file = borehole_highres_input.e
[]
[GlobalParams]
displacements = 'disp_x disp_y disp_z'
porepressure = porepressure
block = 1
[]
[Variables]
[./disp_x]
[../]
[./disp_y]
[../]
[./disp_z]
[../]
[./porepressure]
scaling = 1E9 # Notice the scaling, to make porepressure's kernels roughly of same magnitude as disp's kernels
[../]
[]
[GlobalParams]
volumetric_locking_correction=true
[]
[ICs]
[./initial_p]
type = ConstantIC
variable = porepressure
value = 1E6
[../]
[]
[BCs]
[./fixed_outer_x]
type = DirichletBC
variable = disp_x
value = 0
boundary = outer
[../]
[./fixed_outer_y]
type = DirichletBC
variable = disp_y
value = 0
boundary = outer
[../]
[./plane_strain]
type = DirichletBC
variable = disp_z
value = 0
boundary = 'zmin zmax'
[../]
[./borehole_wall]
type = DirichletBC
variable = porepressure
value = 0
boundary = bh_wall
[../]
[]
[AuxVariables]
[./stress_yy]
order = CONSTANT
family = MONOMIAL
[../]
[./tot_yy]
order = CONSTANT
family = MONOMIAL
[../]
[]
[AuxKernels]
[./stress_yy]
type = RankTwoAux
rank_two_tensor = stress
variable = stress_yy
index_i = 1
index_j = 1
[../]
[./tot_yy]
type = ParsedAux
args = 'stress_yy porepressure'
execute_on = timestep_end
variable = tot_yy
function = 'stress_yy-0.65*porepressure'
[../]
[]
[Kernels]
[./grad_stress_x]
type = StressDivergenceTensors
variable = disp_x
component = 0
[../]
[./grad_stress_y]
type = StressDivergenceTensors
variable = disp_y
component = 1
[../]
[./grad_stress_z]
type = StressDivergenceTensors
variable = disp_z
component = 2
[../]
[./poro_x]
type = PoroMechanicsCoupling
variable = disp_x
component = 0
[../]
[./poro_y]
type = PoroMechanicsCoupling
variable = disp_y
component = 1
[../]
[./poro_z]
type = PoroMechanicsCoupling
variable = disp_z
component = 2
[../]
[./poro_timederiv]
type = PoroFullSatTimeDerivative
variable = porepressure
[../]
[./darcy_flow]
type = CoefDiffusion
variable = porepressure
coef = 1E-12
[../]
[]
[Materials]
[./elasticity_tensor]
type = ComputeElasticityTensor
C_ijkl = '0.5E9 1.5E9'
# bulk modulus is lambda + 2*mu/3 = 0.5 + 2*1.5/3 = 1.5E9
fill_method = symmetric_isotropic
[../]
[./strain]
type = ComputeFiniteStrain
displacements = 'disp_x disp_y disp_z'
eigenstrain_names = ini_stress
[../]
[./ini_stress]
type = ComputeEigenstrainFromInitialStress
initial_stress = '-1.35E6 0 0 0 -3.35E6 0 0 0 0' # remember this is the effective stress
eigenstrain_name = ini_stress
[../]
[./no_plasticity]
type = ComputeFiniteStrainElasticStress
[../]
[./poro_material]
type = PoroFullSatMaterial
porosity0 = 0.3
biot_coefficient = 0.65
solid_bulk_compliance = 0.6666666666667E-9
fluid_bulk_compliance = 1.3944444444444E-9
constant_porosity = false
[../]
[]
[Postprocessors]
[./p00]
type = PointValue
variable = porepressure
point = '1.00 0 0'
outputs = csv_p
[../]
[./p01]
type = PointValue
variable = porepressure
point = '1.01 0 0'
outputs = csv_p
[../]
[./p02]
type = PointValue
variable = porepressure
point = '1.02 0 0'
outputs = csv_p
[../]
[./p03]
type = PointValue
variable = porepressure
point = '1.03 0 0'
outputs = csv_p
[../]
[./p04]
type = PointValue
variable = porepressure
point = '1.04 0 0'
outputs = csv_p
[../]
[./p05]
type = PointValue
variable = porepressure
point = '1.05 0 0'
outputs = csv_p
[../]
[./p06]
type = PointValue
variable = porepressure
point = '1.06 0 0'
outputs = csv_p
[../]
[./p07]
type = PointValue
variable = porepressure
point = '1.07 0 0'
outputs = csv_p
[../]
[./p08]
type = PointValue
variable = porepressure
point = '1.08 0 0'
outputs = csv_p
[../]
[./p09]
type = PointValue
variable = porepressure
point = '1.09 0 0'
outputs = csv_p
[../]
[./p10]
type = PointValue
variable = porepressure
point = '1.10 0 0'
outputs = csv_p
[../]
[./p11]
type = PointValue
variable = porepressure
point = '1.11 0 0'
outputs = csv_p
[../]
[./p12]
type = PointValue
variable = porepressure
point = '1.12 0 0'
outputs = csv_p
[../]
[./p13]
type = PointValue
variable = porepressure
point = '1.13 0 0'
outputs = csv_p
[../]
[./p14]
type = PointValue
variable = porepressure
point = '1.14 0 0'
outputs = csv_p
[../]
[./p15]
type = PointValue
variable = porepressure
point = '1.15 0 0'
outputs = csv_p
[../]
[./p16]
type = PointValue
variable = porepressure
point = '1.16 0 0'
outputs = csv_p
[../]
[./p17]
type = PointValue
variable = porepressure
point = '1.17 0 0'
outputs = csv_p
[../]
[./p18]
type = PointValue
variable = porepressure
point = '1.18 0 0'
outputs = csv_p
[../]
[./p19]
type = PointValue
variable = porepressure
point = '1.19 0 0'
outputs = csv_p
[../]
[./p20]
type = PointValue
variable = porepressure
point = '1.20 0 0'
outputs = csv_p
[../]
[./p21]
type = PointValue
variable = porepressure
point = '1.21 0 0'
outputs = csv_p
[../]
[./p22]
type = PointValue
variable = porepressure
point = '1.22 0 0'
outputs = csv_p
[../]
[./p23]
type = PointValue
variable = porepressure
point = '1.23 0 0'
outputs = csv_p
[../]
[./p24]
type = PointValue
variable = porepressure
point = '1.24 0 0'
outputs = csv_p
[../]
[./p25]
type = PointValue
variable = porepressure
point = '1.25 0 0'
outputs = csv_p
[../]
[./s00]
type = PointValue
variable = disp_x
point = '1.00 0 0'
outputs = csv_s
[../]
[./s01]
type = PointValue
variable = disp_x
point = '1.01 0 0'
outputs = csv_s
[../]
[./s02]
type = PointValue
variable = disp_x
point = '1.02 0 0'
outputs = csv_s
[../]
[./s03]
type = PointValue
variable = disp_x
point = '1.03 0 0'
outputs = csv_s
[../]
[./s04]
type = PointValue
variable = disp_x
point = '1.04 0 0'
outputs = csv_s
[../]
[./s05]
type = PointValue
variable = disp_x
point = '1.05 0 0'
outputs = csv_s
[../]
[./s06]
type = PointValue
variable = disp_x
point = '1.06 0 0'
outputs = csv_s
[../]
[./s07]
type = PointValue
variable = disp_x
point = '1.07 0 0'
outputs = csv_s
[../]
[./s08]
type = PointValue
variable = disp_x
point = '1.08 0 0'
outputs = csv_s
[../]
[./s09]
type = PointValue
variable = disp_x
point = '1.09 0 0'
outputs = csv_s
[../]
[./s10]
type = PointValue
variable = disp_x
point = '1.10 0 0'
outputs = csv_s
[../]
[./s11]
type = PointValue
variable = disp_x
point = '1.11 0 0'
outputs = csv_s
[../]
[./s12]
type = PointValue
variable = disp_x
point = '1.12 0 0'
outputs = csv_s
[../]
[./s13]
type = PointValue
variable = disp_x
point = '1.13 0 0'
outputs = csv_s
[../]
[./s14]
type = PointValue
variable = disp_x
point = '1.14 0 0'
outputs = csv_s
[../]
[./s15]
type = PointValue
variable = disp_x
point = '1.15 0 0'
outputs = csv_s
[../]
[./s16]
type = PointValue
variable = disp_x
point = '1.16 0 0'
outputs = csv_s
[../]
[./s17]
type = PointValue
variable = disp_x
point = '1.17 0 0'
outputs = csv_s
[../]
[./s18]
type = PointValue
variable = disp_x
point = '1.18 0 0'
outputs = csv_s
[../]
[./s19]
type = PointValue
variable = disp_x
point = '1.19 0 0'
outputs = csv_s
[../]
[./s20]
type = PointValue
variable = disp_x
point = '1.20 0 0'
outputs = csv_s
[../]
[./s21]
type = PointValue
variable = disp_x
point = '1.21 0 0'
outputs = csv_s
[../]
[./s22]
type = PointValue
variable = disp_x
point = '1.22 0 0'
outputs = csv_s
[../]
[./s23]
type = PointValue
variable = disp_x
point = '1.23 0 0'
outputs = csv_s
[../]
[./s24]
type = PointValue
variable = disp_x
point = '1.24 0 0'
outputs = csv_s
[../]
[./s25]
type = PointValue
variable = disp_x
point = '1.25 0 0'
outputs = csv_s
[../]
[./t00]
type = PointValue
variable = tot_yy
point = '1.00 0 0'
outputs = csv_t
[../]
[./t01]
type = PointValue
variable = tot_yy
point = '1.01 0 0'
outputs = csv_t
[../]
[./t02]
type = PointValue
variable = tot_yy
point = '1.02 0 0'
outputs = csv_t
[../]
[./t03]
type = PointValue
variable = tot_yy
point = '1.03 0 0'
outputs = csv_t
[../]
[./t04]
type = PointValue
variable = tot_yy
point = '1.04 0 0'
outputs = csv_t
[../]
[./t05]
type = PointValue
variable = tot_yy
point = '1.05 0 0'
outputs = csv_t
[../]
[./t06]
type = PointValue
variable = tot_yy
point = '1.06 0 0'
outputs = csv_t
[../]
[./t07]
type = PointValue
variable = tot_yy
point = '1.07 0 0'
outputs = csv_t
[../]
[./t08]
type = PointValue
variable = tot_yy
point = '1.08 0 0'
outputs = csv_t
[../]
[./t09]
type = PointValue
variable = tot_yy
point = '1.09 0 0'
outputs = csv_t
[../]
[./t10]
type = PointValue
variable = tot_yy
point = '1.10 0 0'
outputs = csv_t
[../]
[./t11]
type = PointValue
variable = tot_yy
point = '1.11 0 0'
outputs = csv_t
[../]
[./t12]
type = PointValue
variable = tot_yy
point = '1.12 0 0'
outputs = csv_t
[../]
[./t13]
type = PointValue
variable = tot_yy
point = '1.13 0 0'
outputs = csv_t
[../]
[./t14]
type = PointValue
variable = tot_yy
point = '1.14 0 0'
outputs = csv_t
[../]
[./t15]
type = PointValue
variable = tot_yy
point = '1.15 0 0'
outputs = csv_t
[../]
[./t16]
type = PointValue
variable = tot_yy
point = '1.16 0 0'
outputs = csv_t
[../]
[./t17]
type = PointValue
variable = tot_yy
point = '1.17 0 0'
outputs = csv_t
[../]
[./t18]
type = PointValue
variable = tot_yy
point = '1.18 0 0'
outputs = csv_t
[../]
[./t19]
type = PointValue
variable = tot_yy
point = '1.19 0 0'
outputs = csv_t
[../]
[./t20]
type = PointValue
variable = tot_yy
point = '1.20 0 0'
outputs = csv_t
[../]
[./t21]
type = PointValue
variable = tot_yy
point = '1.21 0 0'
outputs = csv_t
[../]
[./t22]
type = PointValue
variable = tot_yy
point = '1.22 0 0'
outputs = csv_t
[../]
[./t23]
type = PointValue
variable = tot_yy
point = '1.23 0 0'
outputs = csv_t
[../]
[./t24]
type = PointValue
variable = tot_yy
point = '1.24 0 0'
outputs = csv_t
[../]
[./t25]
type = PointValue
variable = tot_yy
point = '1.25 0 0'
outputs = csv_t
[../]
[./dt]
type = FunctionValuePostprocessor
outputs = console
function = 2*t
[../]
[]
[Preconditioning]
[./andy]
type = SMP
full = true
petsc_options = '-snes_monitor -snes_linesearch_monitor'
petsc_options_iname = '-ksp_type -pc_type -snes_atol -snes_rtol -snes_max_it -ksp_max_it -sub_pc_type -sub_pc_factor_shift_type'
petsc_options_value = 'gmres asm 1E0 1E-10 200 500 lu NONZERO'
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
start_time = 0
end_time = 0.3
dt = 0.1
#[./TimeStepper]
# type = PostprocessorDT
# postprocessor = dt
# dt = 0.003
#[../]
[]
[Outputs]
execute_on = 'timestep_end'
file_base = borehole_highres
exodus = true
sync_times = '0.003 0.3'
[./csv_p]
file_base = borehole_highres_p
type = CSV
[../]
[./csv_s]
file_base = borehole_highres_s
type = CSV
[../]
[./csv_t]
file_base = borehole_highres_t
type = CSV
[../]
[]
modules/porous_flow/test/tests/chemistry/dissolution.i
# The dissolution reaction
#
# a <==> mineral
#
# produces "mineral". Using mineral_density = fluid_density, theta = 1 = eta, the DE is
#
# a' = -(mineral / porosity)' = rate * surf_area * molar_vol (1 - (1 / eqm_const) * (act_coeff * a)^stoi)
#
# The following parameters are used
#
# T_ref = 0.5 K
# T = 1 K
# activation_energy = 3 J/mol
# gas_constant = 6 J/(mol K)
# kinetic_rate_at_ref_T = 0.60653 mol/(m^2 s)
# These give rate = 0.60653 * exp(1/2) = 1 mol/(m^2 s)
#
# surf_area = 0.5 m^2/L
# molar_volume = 2 L/mol
# These give rate * surf_area * molar_vol = 1 s^-1
#
# equilibrium_constant = 0.5 (dimensionless)
# primary_activity_coefficient = 2 (dimensionless)
# stoichiometry = 1 (dimensionless)
# This means that 1 - (1 / eqm_const) * (act_coeff * a)^stoi = 1 - 4 a, which is positive for a < 0.25, ie dissolution for a(t=0) < 0.25
#
# The solution of the DE is
# a = eqm_const / act_coeff + (a(t=0) - eqm_const / act_coeff) exp(-rate * surf_area * molar_vol * act_coeff * t / eqm_const)
# = 0.25 + (a(t=0) - 0.25) exp(-4 * t)
# c = c(t=0) - (a - a(t=0)) * porosity
#
# This test checks that (a + c / porosity) is time-independent, and that a follows the above solution
#
# Aside:
# The exponential curve is not followed exactly because moose actually solves
# (a - a_old)/dt = rate * surf_area * molar_vol (1 - (1 / eqm_const) * (act_coeff * a)^stoi)
# which does not give an exponential exactly, except in the limit dt->0
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./a]
initial_condition = 0.05
[../]
[]
[AuxVariables]
[./eqm_k]
initial_condition = 0.5
[../]
[./pressure]
[../]
[./ini_mineral_conc]
initial_condition = 0.3
[../]
[./mineral]
family = MONOMIAL
order = CONSTANT
[../]
[./should_be_static]
family = MONOMIAL
order = CONSTANT
[../]
[]
[AuxKernels]
[./mineral]
type = PorousFlowPropertyAux
property = mineral_concentration
mineral_species = 0
variable = mineral
[../]
[./should_be_static]
type = ParsedAux
args = 'mineral a'
function = 'a + mineral / 0.1'
variable = should_be_static
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./mass_a]
type = PorousFlowMassTimeDerivative
fluid_component = 0
variable = a
[../]
[./pre_dis]
type = PorousFlowPreDis
variable = a
mineral_density = 1000
stoichiometry = 1
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = a
number_fluid_phases = 1
number_fluid_components = 2
number_aqueous_kinetic = 1
[../]
[]
[Modules]
[./FluidProperties]
[./simple_fluid]
type = SimpleFluidProperties
bulk_modulus = 2e9 # huge, so mimic chemical_reactions
density0 = 1000
thermal_expansion = 0
viscosity = 1e-3
[../]
[../]
[]
[Materials]
[./temperature]
type = PorousFlowTemperature
temperature = 1
[../]
[./ppss]
type = PorousFlow1PhaseFullySaturated
porepressure = pressure
[../]
[./mass_frac]
type = PorousFlowMassFraction
mass_fraction_vars = a
[../]
[./predis]
type = PorousFlowAqueousPreDisChemistry
primary_concentrations = a
num_reactions = 1
equilibrium_constants = eqm_k
primary_activity_coefficients = 2
reactions = 1
specific_reactive_surface_area = 0.5
kinetic_rate_constant = 0.6065306597126334
activation_energy = 3
molar_volume = 2
gas_constant = 6
reference_temperature = 0.5
[../]
[./mineral_conc]
type = PorousFlowAqueousPreDisMineral
initial_concentrations = ini_mineral_conc
[../]
[./simple_fluid]
type = PorousFlowSingleComponentFluid
fp = simple_fluid
phase = 0
[../]
[./porosity]
type = PorousFlowPorosityConst
porosity = 0.1
[../]
[]
[Preconditioning]
[./smp]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
nl_abs_tol = 1E-10
dt = 0.01
end_time = 1
[]
[Postprocessors]
[./a]
type = PointValue
point = '0 0 0'
variable = a
[../]
[./should_be_static]
type = PointValue
point = '0 0 0'
variable = should_be_static
[../]
[]
[Outputs]
interval = 10
csv = true
perf_graph = true
[]
modules/tensor_mechanics/test/tests/notched_plastic_block/cmc_planar.i
# Uses an unsmoothed version of capped-Mohr-Coulomb (via ComputeMultiPlasticityStress with TensorMechanicsPlasticTensileMulti and TensorMechanicsPlasticMohrCoulombMulti) to simulate the following problem.
# A cubical block is notched around its equator.
# All of its outer surfaces have roller BCs, but the notched region is free to move as needed
# The block is initialised with a high hydrostatic tensile stress
# Without the notch, the BCs do not allow contraction of the block, and this stress configuration is admissible
# With the notch, however, the interior parts of the block are free to move in order to relieve stress, and this causes plastic failure
# The top surface is then pulled upwards (the bottom is fixed because of the roller BCs)
# This causes more failure
[Mesh]
[generated_mesh]
type = GeneratedMeshGenerator
dim = 3
nx = 9
ny = 9
nz = 9
xmin = 0
xmax = 0.1
ymin = 0
ymax = 0.1
zmin = 0
zmax = 0.1
[]
[block_to_remove_xmin]
type = SubdomainBoundingBoxGenerator
bottom_left = '-0.01 -0.01 0.045'
top_right = '0.01 0.11 0.055'
location = INSIDE
block_id = 1
input = generated_mesh
[]
[block_to_remove_xmax]
type = SubdomainBoundingBoxGenerator
bottom_left = '0.09 -0.01 0.045'
top_right = '0.11 0.11 0.055'
location = INSIDE
block_id = 1
input = block_to_remove_xmin
[]
[block_to_remove_ymin]
type = SubdomainBoundingBoxGenerator
bottom_left = '-0.01 -0.01 0.045'
top_right = '0.11 0.01 0.055'
location = INSIDE
block_id = 1
input = block_to_remove_xmax
[]
[block_to_remove_ymax]
type = SubdomainBoundingBoxGenerator
bottom_left = '-0.01 0.09 0.045'
top_right = '0.11 0.11 0.055'
location = INSIDE
block_id = 1
input = block_to_remove_ymin
[]
[remove_block]
type = BlockDeletionGenerator
block_id = 1
input = block_to_remove_ymax
[]
[]
[GlobalParams]
displacements = 'disp_x disp_y disp_z'
[]
[Modules/TensorMechanics/Master]
[./all]
add_variables = true
incremental = true
generate_output = 'max_principal_stress mid_principal_stress min_principal_stress stress_zz'
eigenstrain_names = ini_stress
[../]
[]
[Postprocessors]
[./uz]
type = PointValue
point = '0 0 0.1'
use_displaced_mesh = false
variable = disp_z
[../]
[./s_zz]
type = ElementAverageValue
use_displaced_mesh = false
variable = stress_zz
[../]
[./num_res]
type = NumResidualEvaluations
[../]
[./nr_its]
type = ElementAverageValue
variable = num_iters
[../]
[./max_nr_its]
type = ElementExtremeValue
variable = num_iters
[../]
[./runtime]
type = PerfGraphData
data_type = TOTAL
section_name = 'Root'
[../]
[]
[BCs]
# back=zmin, front=zmax, bottom=ymin, top=ymax, left=xmin, right=xmax
[./xmin_xzero]
type = DirichletBC
variable = disp_x
boundary = left
value = 0.0
[../]
[./xmax_xzero]
type = DirichletBC
variable = disp_x
boundary = right
value = 0.0
[../]
[./ymin_yzero]
type = DirichletBC
variable = disp_y
boundary = bottom
value = 0.0
[../]
[./ymax_yzero]
type = DirichletBC
variable = disp_y
boundary = top
value = 0.0
[../]
[./zmin_zzero]
type = DirichletBC
variable = disp_z
boundary = back
value = '0'
[../]
[./zmax_disp]
type = FunctionDirichletBC
variable = disp_z
boundary = front
function = '1E-6*max(t,0)'
[../]
[]
[AuxVariables]
[./mc_int]
order = CONSTANT
family = MONOMIAL
[../]
[./plastic_strain]
order = CONSTANT
family = MONOMIAL
[../]
[./num_iters]
order = CONSTANT
family = MONOMIAL
[../]
[./yield_fcn]
order = CONSTANT
family = MONOMIAL
[../]
[]
[AuxKernels]
[./mc_int_auxk]
type = MaterialStdVectorAux
index = 0
property = plastic_internal_parameter
variable = mc_int
[../]
[./plastic_strain_aux]
type = MaterialRankTwoTensorAux
i = 2
j = 2
property = plastic_strain
variable = plastic_strain
[../]
[./num_iters_auxk] # cannot use plastic_NR_iterations directly as this is zero, since no NR iterations are actually used, since we use a custom algorithm to do the return
type = ParsedAux
args = plastic_strain
function = 'if(plastic_strain>0,1,0)'
variable = num_iters
[../]
[./yield_fcn_auxk]
type = MaterialStdVectorAux
index = 0
property = plastic_yield_function
variable = yield_fcn
[../]
[]
[UserObjects]
[./ts]
type = TensorMechanicsHardeningConstant
value = 3E6
[../]
[./tensile]
type = TensorMechanicsPlasticTensileMulti
tensile_strength = ts
yield_function_tolerance = 1
internal_constraint_tolerance = 1.0E-6
#shift = 1
use_custom_returnMap = false
use_custom_cto = false
[../]
[./mc_coh]
type = TensorMechanicsHardeningConstant
value = 5E6
[../]
[./mc_phi]
type = TensorMechanicsHardeningConstant
value = 35
convert_to_radians = true
[../]
[./mc_psi]
type = TensorMechanicsHardeningConstant
value = 10
convert_to_radians = true
[../]
[./mc]
type = TensorMechanicsPlasticMohrCoulombMulti
cohesion = mc_coh
friction_angle = mc_phi
dilation_angle = mc_psi
yield_function_tolerance = 1E-5
internal_constraint_tolerance = 1E-11
use_custom_returnMap = false
[../]
[]
[Materials]
[./elasticity_tensor]
type = ComputeIsotropicElasticityTensor
youngs_modulus = 16E9
poissons_ratio = 0.25
[../]
[./mc]
type = ComputeMultiPlasticityStress
ep_plastic_tolerance = 1E-6
plastic_models = 'tensile mc'
max_NR_iterations = 50
specialIC = rock
deactivation_scheme = safe_to_dumb
debug_fspb = crash
[../]
[./strain_from_initial_stress]
type = ComputeEigenstrainFromInitialStress
initial_stress = '2.5E6 0 0 0 2.5E6 0 0 0 2.5E6'
eigenstrain_name = ini_stress
[../]
[]
[Preconditioning]
[./andy]
type = SMP
full = true
[../]
[]
[Executioner]
start_time = -1
end_time = 10
dt = 1
solve_type = NEWTON
type = Transient
l_tol = 1E-2
nl_abs_tol = 1E-5
nl_rel_tol = 1E-7
l_max_its = 200
nl_max_its = 400
petsc_options_iname = '-pc_type -pc_asm_overlap -sub_pc_type -ksp_type -ksp_gmres_restart'
petsc_options_value = ' asm 2 lu gmres 200'
[]
[Outputs]
file_base = cmc_planar
perf_graph = true
exodus = false
csv = true
[]
modules/combined/examples/mortar/mortar_gradient.i
#
# Compare a diffusion equation with (c) and without (v) periodic gradient
# constraints and a ramped sloped initial condition and value-periodic diffusion (p)
# without a slope.
#
[Mesh]
[gen]
type = GeneratedMeshGenerator
dim = 2
nx = 40
ny = 40
[]
[slave_x]
input = gen
type = LowerDBlockFromSidesetGenerator
sidesets = '3'
new_block_id = 10
new_block_name = "slave_x"
[]
[master_x]
input = slave_x
type = LowerDBlockFromSidesetGenerator
sidesets = '1'
new_block_id = 12
new_block_name = "master_x"
[]
[slave_y]
input = master_x
type = LowerDBlockFromSidesetGenerator
sidesets = '0'
new_block_id = 11
new_block_name = "slave_y"
[]
[master_y]
input = slave_y
type = LowerDBlockFromSidesetGenerator
sidesets = '2'
new_block_id = 13
new_block_name = "master_y"
[]
[]
[Functions]
[./init_slope]
# slope with a concentration spike close to the lower interface
type = ParsedFunction
value = 'if(x>0.4 & x<0.6 & y>0.1 & y<0.3, 3+y, y)'
[../]
[./init_flat]
# no-slope and the same spike
type = ParsedFunction
value = 'if(x>0.4 & x<0.6 & y>0.1 & y<0.3, 3, 0)'
[../]
[]
[Variables]
# gradient constrained concentration
[./c]
order = FIRST
family = LAGRANGE
block = 0
[./InitialCondition]
type = FunctionIC
function = init_slope
[../]
[../]
# unconstrained concentrarion
[./v]
order = FIRST
family = LAGRANGE
block = 0
[./InitialCondition]
type = FunctionIC
function = init_slope
[../]
[../]
# flat value periodic diffusion
[./p]
order = FIRST
family = LAGRANGE
block = 0
[./InitialCondition]
type = FunctionIC
function = init_flat
[../]
[../]
# Lagrange multipliers for gradient component in the horizontal directon
[./lm_left_right_x]
order = FIRST
family = LAGRANGE
block = "slave_x"
[../]
[./lm_left_right_y]
order = FIRST
family = LAGRANGE
block = "slave_x"
[../]
# Lagrange multipliers for gradient component in the vertical directon
[./lm_up_down_x]
order = FIRST
family = LAGRANGE
block = "slave_y"
[../]
[./lm_up_down_y]
order = FIRST
family = LAGRANGE
block = "slave_y"
[../]
[]
[Kernels]
# the gradient constrained concentration
[./diff]
type = Diffusion
variable = c
block = 0
[../]
[./dt]
type = TimeDerivative
variable = c
block = 0
[../]
# the un-constrained concentration
[./diff2]
type = Diffusion
variable = v
block = 0
[../]
[./dt2]
type = TimeDerivative
variable = v
block = 0
[../]
# the value periodic concentration
[./diff3]
type = Diffusion
variable = p
block = 0
[../]
[./dt3]
type = TimeDerivative
variable = p
block = 0
[../]
[]
[Constraints]
[./equaly_grad_x]
type = EqualGradientConstraint
variable = lm_up_down_x
component = 0
slave_variable = c
slave_boundary = bottom
master_boundary = top
slave_subdomain = slave_y
master_subdomain = master_y
periodic = true
[../]
[./equaly_grad_y]
type = EqualGradientConstraint
variable = lm_up_down_y
component = 1
slave_variable = c
slave_boundary = bottom
master_boundary = top
slave_subdomain = slave_y
master_subdomain = master_y
periodic = true
[../]
[./equalx_grad_x]
type = EqualGradientConstraint
variable = lm_left_right_x
component = 0
slave_variable = c
slave_boundary = left
master_boundary = right
slave_subdomain = slave_x
master_subdomain = master_x
periodic = true
[../]
[./equalx_grad_y]
type = EqualGradientConstraint
variable = lm_left_right_y
component = 1
slave_variable = c
slave_boundary = left
master_boundary = right
slave_subdomain = slave_x
master_subdomain = master_x
periodic = true
[../]
[]
[BCs]
# DiffusionFluxBC is the surface term in the weak form of the Diffusion equation
[./surface]
type = DiffusionFluxBC
boundary = 'top bottom left right'
variable = c
[../]
[./surface2]
type = DiffusionFluxBC
boundary = 'top bottom left right'
variable = v
[../]
# for the value periodic diffusion we skip the surface term and apply value PBCs
[./Periodic]
[./up_down]
variable = p
primary = 0
secondary = 2
translation = '0 1 0'
[../]
[./left_right]
variable = p
primary = 1
secondary = 3
translation = '-1 0 0'
[../]
[../]
[]
[AuxVariables]
[./diff_constraint]
block = 0
[../]
[./diff_periodic]
block = 0
[../]
[./diff_slope]
block = 0
[../]
[./slope]
block = 0
[./InitialCondition]
type = FunctionIC
function = y
[../]
[../]
[]
[AuxKernels]
# difference between the constrained and unconstrained sloped diffusions
[./diff_constraint]
type = ParsedAux
variable = diff_constraint
function = 'c-v'
args = 'c v'
block = 0
[../]
# difference between the periodic gradient constrained diffusion and the flat
# value period diffusien with a constant slope added. This should be the same,
# but they aren't quite because the gradient constraint affects the gradient in
# the entire elements (i.e. a larger volume is affected by the gradient constraint
# compared to the nodal value periodicity)
[./diff_periodic]
type = ParsedAux
variable = diff_periodic
function = 'c-p-slope'
args = 'c p slope'
block = 0
[../]
# subtract the constant slope from the gradient periodic simulation (should yield
# almost p - per the argument above)
[./diff_slope]
type = ParsedAux
variable = diff_slope
function = 'c-slope'
args = 'c slope'
block = 0
[../]
[]
[Preconditioning]
[./smp]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
solve_type = NEWTON
# the shift is necessary to facilitate the solve. The Lagrange multipliers
# introduce zero-on diaginal blocks, which make the matrix hard to invert.
petsc_options_iname = '-pc_type -pc_factor_shift_type -pc_factor_shift_amount'
petsc_options_value = ' lu NONZERO 1e-10'
nl_rel_tol = 1e-11
nl_abs_tol = 1e-10
l_tol = 1e-10
dt = 0.01
num_steps = 20
[]
[Outputs]
exodus = true
[]
modules/fluid_properties/test/tests/water/water.i
# Example of using Water97FluidProperties module in Region 1 by recovering the values
# in Table 5 of Revised Release on the IAPWS Industrial Formulation 1997 for the
# Thermodynamic Properties of Water and Steam
[Mesh]
type = GeneratedMesh
dim = 2
nx = 3
xmax = 3
# This test uses ElementalVariableValue postprocessors on specific
# elements, so element numbering needs to stay unchanged
allow_renumbering = false
[]
[Variables]
[./dummy]
[../]
[]
[AuxVariables]
[./pressure]
order = CONSTANT
family = MONOMIAL
[../]
[./temperature]
order = CONSTANT
family = MONOMIAL
[../]
[./rho]
family = MONOMIAL
order = CONSTANT
[../]
[./v]
family = MONOMIAL
order = CONSTANT
[../]
[./e]
family = MONOMIAL
order = CONSTANT
[../]
[./h]
family = MONOMIAL
order = CONSTANT
[../]
[./s]
family = MONOMIAL
order = CONSTANT
[../]
[./cp]
family = MONOMIAL
order = CONSTANT
[../]
[./cv]
family = MONOMIAL
order = CONSTANT
[../]
[./c]
family = MONOMIAL
order = CONSTANT
[../]
[./mu]
family = MONOMIAL
order = CONSTANT
[../]
[./k]
family = MONOMIAL
order = CONSTANT
[../]
[]
[Functions]
[./tic]
type = ParsedFunction
value = 'if(x<2, 300, 500)'
[../]
[./pic]
type = ParsedFunction
value = 'if(x<1,3e6, if(x<2, 80e6, 3e6))'
[../]
[]
[ICs]
[./p_ic]
type = FunctionIC
function = pic
variable = pressure
[../]
[./t_ic]
type = FunctionIC
function = tic
variable = temperature
[../]
[]
[AuxKernels]
[./rho]
type = MaterialRealAux
variable = rho
property = density
[../]
[./v]
type = ParsedAux
args = rho
function = 1/rho
variable = v
[../]
[./e]
type = MaterialRealAux
variable = e
property = e
[../]
[./h]
type = MaterialRealAux
variable = h
property = h
[../]
[./s]
type = MaterialRealAux
variable = s
property = s
[../]
[./cp]
type = MaterialRealAux
variable = cp
property = cp
[../]
[./cv]
type = MaterialRealAux
variable = cv
property = cv
[../]
[./c]
type = MaterialRealAux
variable = c
property = c
[../]
[./mu]
type = MaterialRealAux
variable = mu
property = viscosity
[../]
[./k]
type = MaterialRealAux
variable = k
property = k
[../]
[]
[Modules]
[./FluidProperties]
[./water]
type = Water97FluidProperties
[../]
[../]
[]
[Materials]
[./fp_mat]
type = FluidPropertiesMaterialPT
pressure = pressure
temperature = temperature
fp = water
[../]
[]
[Kernels]
[./diff]
type = Diffusion
variable = dummy
[../]
[]
[Postprocessors]
[./density0]
type = ElementalVariableValue
variable = rho
elementid = 0
[../]
[./density1]
type = ElementalVariableValue
variable = rho
elementid = 1
[../]
[./density2]
type = ElementalVariableValue
variable = rho
elementid = 2
[../]
[./v0]
type = ElementalVariableValue
variable = v
elementid = 0
[../]
[./v1]
type = ElementalVariableValue
variable = v
elementid = 1
[../]
[./v2]
type = ElementalVariableValue
variable = v
elementid = 2
[../]
[./e0]
type = ElementalVariableValue
variable = e
elementid = 0
[../]
[./e1]
type = ElementalVariableValue
variable = e
elementid = 1
[../]
[./e2]
type = ElementalVariableValue
variable = e
elementid = 2
[../]
[./h0]
type = ElementalVariableValue
variable = h
elementid = 0
[../]
[./h1]
type = ElementalVariableValue
variable = h
elementid = 1
[../]
[./h2]
type = ElementalVariableValue
variable = h
elementid = 2
[../]
[./s0]
type = ElementalVariableValue
variable = s
elementid = 0
[../]
[./s1]
type = ElementalVariableValue
variable = s
elementid = 1
[../]
[./s2]
type = ElementalVariableValue
variable = s
elementid = 2
[../]
[./cp0]
type = ElementalVariableValue
variable = cp
elementid = 0
[../]
[./cp1]
type = ElementalVariableValue
variable = cp
elementid = 1
[../]
[./cp2]
type = ElementalVariableValue
variable = cp
elementid = 2
[../]
[./cv0]
type = ElementalVariableValue
variable = cv
elementid = 0
[../]
[./cv1]
type = ElementalVariableValue
variable = cv
elementid = 1
[../]
[./cv2]
type = ElementalVariableValue
variable = cv
elementid = 2
[../]
[./c0]
type = ElementalVariableValue
variable = c
elementid = 0
[../]
[./c1]
type = ElementalVariableValue
variable = c
elementid = 1
[../]
[./c2]
type = ElementalVariableValue
variable = c
elementid = 2
[../]
[./mu0]
type = ElementalVariableValue
variable = mu
elementid = 0
[../]
[./mu1]
type = ElementalVariableValue
variable = mu
elementid = 1
[../]
[./mu2]
type = ElementalVariableValue
variable = mu
elementid = 2
[../]
[./k0]
type = ElementalVariableValue
variable = k
elementid = 0
[../]
[./k1]
type = ElementalVariableValue
variable = k
elementid = 1
[../]
[./k2]
type = ElementalVariableValue
variable = k
elementid = 2
[../]
[]
[Executioner]
type = Steady
solve_type = NEWTON
[]
[Outputs]
csv = true
[]
modules/porous_flow/test/tests/poro_elasticity/mandel_fully_saturated.i
# Mandel's problem of consolodation of a drained medium
# Using the FullySaturatedDarcyBase and FullySaturatedMassTimeDerivative kernels
# Note the use of consistent_with_displaced_mesh = false in the calculation of volumetric strain
#
# A sample is in plane strain.
# -a <= x <= a
# -b <= y <= b
# It is squashed with constant force by impermeable, frictionless plattens on its top and bottom surfaces (at y=+/-b)
# Fluid is allowed to leak out from its sides (at x=+/-a)
# The porepressure within the sample is monitored.
#
# As is common in the literature, this is simulated by
# considering the quarter-sample, 0<=x<=a and 0<=y<=b, with
# impermeable, roller BCs at x=0 and y=0 and y=b.
# Porepressure is fixed at zero on x=a.
# Porepressure and displacement are initialised to zero.
# Then the top (y=b) is moved downwards with prescribed velocity,
# so that the total force that is inducing this downwards velocity
# is fixed. The velocity is worked out by solving Mandel's problem
# analytically, and the total force is monitored in the simulation
# to check that it indeed remains constant.
#
# Here are the problem's parameters, and their values:
# Soil width. a = 1
# Soil height. b = 0.1
# Soil's Lame lambda. la = 0.5
# Soil's Lame mu, which is also the Soil's shear modulus. mu = G = 0.75
# Soil bulk modulus. K = la + 2*mu/3 = 1
# Drained Poisson ratio. nu = (3K - 2G)/(6K + 2G) = 0.2
# Soil bulk compliance. 1/K = 1
# Fluid bulk modulus. Kf = 8
# Fluid bulk compliance. 1/Kf = 0.125
# Soil initial porosity. phi0 = 0.1
# Biot coefficient. alpha = 0.6
# Biot modulus. M = 1/(phi0/Kf + (alpha - phi0)(1 - alpha)/K) = 4.705882
# Undrained bulk modulus. Ku = K + alpha^2*M = 2.694118
# Undrained Poisson ratio. nuu = (3Ku - 2G)/(6Ku + 2G) = 0.372627
# Skempton coefficient. B = alpha*M/Ku = 1.048035
# Fluid mobility (soil permeability/fluid viscosity). k = 1.5
# Consolidation coefficient. c = 2*k*B^2*G*(1-nu)*(1+nuu)^2/9/(1-nuu)/(nuu-nu) = 3.821656
# Normal stress on top. F = 1
#
# The solution for porepressure and displacements is given in
# AHD Cheng and E Detournay "A direct boundary element method for plane strain poroelasticity" International Journal of Numerical and Analytical Methods in Geomechanics 12 (1988) 551-572.
# The solution involves complicated infinite series, so I shall not write it here
[Mesh]
type = GeneratedMesh
dim = 3
nx = 10
ny = 1
nz = 1
xmin = 0
xmax = 1
ymin = 0
ymax = 0.1
zmin = 0
zmax = 1
[]
[GlobalParams]
displacements = 'disp_x disp_y disp_z'
PorousFlowDictator = dictator
block = 0
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = 'porepressure disp_x disp_y disp_z'
number_fluid_phases = 1
number_fluid_components = 1
[../]
[]
[Variables]
[./disp_x]
[../]
[./disp_y]
[../]
[./disp_z]
[../]
[./porepressure]
[../]
[]
[BCs]
[./roller_xmin]
type = DirichletBC
variable = disp_x
value = 0
boundary = 'left'
[../]
[./roller_ymin]
type = DirichletBC
variable = disp_y
value = 0
boundary = 'bottom'
[../]
[./plane_strain]
type = DirichletBC
variable = disp_z
value = 0
boundary = 'back front'
[../]
[./xmax_drained]
type = DirichletBC
variable = porepressure
value = 0
boundary = right
[../]
[./top_velocity]
type = FunctionDirichletBC
variable = disp_y
function = top_velocity
boundary = top
[../]
[]
[Functions]
[./top_velocity]
type = PiecewiseLinear
x = '0 0.002 0.006 0.014 0.03 0.046 0.062 0.078 0.094 0.11 0.126 0.142 0.158 0.174 0.19 0.206 0.222 0.238 0.254 0.27 0.286 0.302 0.318 0.334 0.35 0.366 0.382 0.398 0.414 0.43 0.446 0.462 0.478 0.494 0.51 0.526 0.542 0.558 0.574 0.59 0.606 0.622 0.638 0.654 0.67 0.686 0.702'
y = '-0.041824842 -0.042730269 -0.043412712 -0.04428867 -0.045509181 -0.04645965 -0.047268246 -0.047974749 -0.048597109 -0.0491467 -0.049632388 -0.050061697 -0.050441198 -0.050776675 -0.051073238 -0.0513354 -0.051567152 -0.051772022 -0.051953128 -0.052113227 -0.052254754 -0.052379865 -0.052490464 -0.052588233 -0.052674662 -0.052751065 -0.052818606 -0.052878312 -0.052931093 -0.052977751 -0.053018997 -0.053055459 -0.053087691 -0.053116185 -0.053141373 -0.05316364 -0.053183324 -0.053200724 -0.053216106 -0.053229704 -0.053241725 -0.053252351 -0.053261745 -0.053270049 -0.053277389 -0.053283879 -0.053289615'
[../]
[]
[AuxVariables]
[./stress_yy]
order = CONSTANT
family = MONOMIAL
[../]
[./tot_force]
order = CONSTANT
family = MONOMIAL
[../]
[]
[AuxKernels]
[./stress_yy]
type = RankTwoAux
rank_two_tensor = stress
variable = stress_yy
index_i = 1
index_j = 1
[../]
[./tot_force]
type = ParsedAux
args = 'stress_yy porepressure'
execute_on = timestep_end
variable = tot_force
function = '-stress_yy+0.6*porepressure'
[../]
[]
[Kernels]
[./grad_stress_x]
type = StressDivergenceTensors
variable = disp_x
component = 0
[../]
[./grad_stress_y]
type = StressDivergenceTensors
variable = disp_y
component = 1
[../]
[./grad_stress_z]
type = StressDivergenceTensors
variable = disp_z
component = 2
[../]
[./poro_x]
type = PorousFlowEffectiveStressCoupling
biot_coefficient = 0.6
variable = disp_x
component = 0
[../]
[./poro_y]
type = PorousFlowEffectiveStressCoupling
biot_coefficient = 0.6
variable = disp_y
component = 1
[../]
[./poro_z]
type = PorousFlowEffectiveStressCoupling
biot_coefficient = 0.6
component = 2
variable = disp_z
[../]
[./mass0]
type = PorousFlowFullySaturatedMassTimeDerivative
biot_coefficient = 0.6
coupling_type = HydroMechanical
variable = porepressure
[../]
[./flux]
type = PorousFlowFullySaturatedDarcyBase
variable = porepressure
gravity = '0 0 0'
[../]
[]
[Modules]
[./FluidProperties]
[./simple_fluid]
type = SimpleFluidProperties
bulk_modulus = 8
density0 = 1
thermal_expansion = 0
viscosity = 1
[../]
[../]
[]
[Materials]
[./temperature]
type = PorousFlowTemperature
[../]
[./elasticity_tensor]
type = ComputeElasticityTensor
C_ijkl = '0.5 0.75'
# bulk modulus is lambda + 2*mu/3 = 0.5 + 2*0.75/3 = 1
fill_method = symmetric_isotropic
[../]
[./strain]
type = ComputeSmallStrain
[../]
[./stress]
type = ComputeLinearElasticStress
[../]
[./eff_fluid_pressure_qp]
type = PorousFlowEffectiveFluidPressure
[../]
[./vol_strain]
type = PorousFlowVolumetricStrain
consistent_with_displaced_mesh = false
[../]
[./ppss]
type = PorousFlow1PhaseFullySaturated
porepressure = porepressure
[../]
[./massfrac]
type = PorousFlowMassFraction
[../]
[./simple_fluid_qp]
type = PorousFlowSingleComponentFluid
fp = simple_fluid
phase = 0
[../]
[./porosity]
type = PorousFlowPorosityConst # only the initial value of this is ever used
porosity = 0.1
[../]
[./biot_modulus]
type = PorousFlowConstantBiotModulus
biot_coefficient = 0.6
solid_bulk_compliance = 1
fluid_bulk_modulus = 8
[../]
[./permeability]
type = PorousFlowPermeabilityConst
permeability = '1.5 0 0 0 1.5 0 0 0 1.5'
[../]
[]
[Postprocessors]
[./p0]
type = PointValue
outputs = csv
point = '0.0 0 0'
variable = porepressure
[../]
[./p1]
type = PointValue
outputs = csv
point = '0.1 0 0'
variable = porepressure
[../]
[./p2]
type = PointValue
outputs = csv
point = '0.2 0 0'
variable = porepressure
[../]
[./p3]
type = PointValue
outputs = csv
point = '0.3 0 0'
variable = porepressure
[../]
[./p4]
type = PointValue
outputs = csv
point = '0.4 0 0'
variable = porepressure
[../]
[./p5]
type = PointValue
outputs = csv
point = '0.5 0 0'
variable = porepressure
[../]
[./p6]
type = PointValue
outputs = csv
point = '0.6 0 0'
variable = porepressure
[../]
[./p7]
type = PointValue
outputs = csv
point = '0.7 0 0'
variable = porepressure
[../]
[./p8]
type = PointValue
outputs = csv
point = '0.8 0 0'
variable = porepressure
[../]
[./p9]
type = PointValue
outputs = csv
point = '0.9 0 0'
variable = porepressure
[../]
[./p99]
type = PointValue
outputs = csv
point = '1 0 0'
variable = porepressure
[../]
[./xdisp]
type = PointValue
outputs = csv
point = '1 0.1 0'
variable = disp_x
[../]
[./ydisp]
type = PointValue
outputs = csv
point = '1 0.1 0'
variable = disp_y
[../]
[./total_downwards_force]
type = ElementAverageValue
outputs = csv
variable = tot_force
[../]
[./dt]
type = FunctionValuePostprocessor
outputs = console
function = if(0.15*t<0.01,0.15*t,0.01)
[../]
[]
[Preconditioning]
[./andy]
type = SMP
full = true
petsc_options_iname = '-ksp_type -pc_type -sub_pc_type -snes_atol -snes_rtol -snes_max_it'
petsc_options_value = 'gmres asm lu 1E-14 1E-10 10000'
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
start_time = 0
end_time = 0.7
[./TimeStepper]
type = PostprocessorDT
postprocessor = dt
dt = 0.001
[../]
[]
[Outputs]
execute_on = 'timestep_end'
file_base = mandel_fully_saturated
[./csv]
interval = 3
type = CSV
[../]
[]
modules/tensor_mechanics/test/tests/notched_plastic_block/biaxial_planar.i
# Uses non-smoothed Mohr-Coulomb (via ComputeMultiPlasticityStress and TensorMechanicsPlasticMohrCoulombMulti) to simulate the following problem.
# A cubical block is notched around its equator.
# All of its outer surfaces have roller BCs, but the notched region is free to move as needed
# The block is initialised with a high hydrostatic tensile stress
# Without the notch, the BCs do not allow contraction of the block, and this stress configuration is admissible
# With the notch, however, the interior parts of the block are free to move in order to relieve stress, and this causes plastic failure
# The top surface is then pulled upwards (the bottom is fixed because of the roller BCs)
# This causes more failure
[Mesh]
[generated_mesh]
type = GeneratedMeshGenerator
dim = 3
nx = 9
ny = 9
nz = 9
xmin = 0
xmax = 0.1
ymin = 0
ymax = 0.1
zmin = 0
zmax = 0.1
[]
[block_to_remove_xmin]
type = SubdomainBoundingBoxGenerator
bottom_left = '-0.01 -0.01 0.045'
top_right = '0.01 0.11 0.055'
location = INSIDE
block_id = 1
input = generated_mesh
[]
[block_to_remove_xmax]
type = SubdomainBoundingBoxGenerator
bottom_left = '0.09 -0.01 0.045'
top_right = '0.11 0.11 0.055'
location = INSIDE
block_id = 1
input = block_to_remove_xmin
[]
[block_to_remove_ymin]
type = SubdomainBoundingBoxGenerator
bottom_left = '-0.01 -0.01 0.045'
top_right = '0.11 0.01 0.055'
location = INSIDE
block_id = 1
input = block_to_remove_xmax
[]
[block_to_remove_ymax]
type = SubdomainBoundingBoxGenerator
bottom_left = '-0.01 0.09 0.045'
top_right = '0.11 0.11 0.055'
location = INSIDE
block_id = 1
input = block_to_remove_ymin
[]
[remove_block]
type = BlockDeletionGenerator
block_id = 1
input = block_to_remove_ymax
[]
[]
[GlobalParams]
displacements = 'disp_x disp_y disp_z'
[]
[Modules/TensorMechanics/Master]
[./all]
add_variables = true
incremental = true
generate_output = 'max_principal_stress mid_principal_stress min_principal_stress stress_zz'
eigenstrain_names = ini_stress
[../]
[]
[Postprocessors]
[./uz]
type = PointValue
point = '0 0 0.1'
use_displaced_mesh = false
variable = disp_z
[../]
[./s_zz]
type = ElementAverageValue
use_displaced_mesh = false
variable = stress_zz
[../]
[./num_res]
type = NumResidualEvaluations
[../]
[./nr_its]
type = ElementAverageValue
variable = num_iters
[../]
[./max_nr_its]
type = ElementExtremeValue
variable = num_iters
[../]
[./runtime]
type = PerfGraphData
data_type = TOTAL
section_name = 'Root'
[../]
[]
[BCs]
# back=zmin, front=zmax, bottom=ymin, top=ymax, left=xmin, right=xmax
[./xmin_xzero]
type = DirichletBC
variable = disp_x
boundary = left
value = 0.0
[../]
[./xmax_xzero]
type = DirichletBC
variable = disp_x
boundary = right
value = 0.0
[../]
[./ymin_yzero]
type = DirichletBC
variable = disp_y
boundary = bottom
value = 0.0
[../]
[./ymax_yzero]
type = DirichletBC
variable = disp_y
boundary = top
value = 0.0
[../]
[./zmin_zzero]
type = DirichletBC
variable = disp_z
boundary = back
value = '0'
[../]
[./zmax_disp]
type = FunctionDirichletBC
variable = disp_z
boundary = front
function = '1E-6*max(t,0)'
[../]
[]
[AuxVariables]
[./mc_int]
order = CONSTANT
family = MONOMIAL
[../]
[./plastic_strain]
order = CONSTANT
family = MONOMIAL
[../]
[./num_iters]
order = CONSTANT
family = MONOMIAL
[../]
[./yield_fcn]
order = CONSTANT
family = MONOMIAL
[../]
[]
[AuxKernels]
[./mc_int_auxk]
type = MaterialStdVectorAux
index = 0
property = plastic_internal_parameter
variable = mc_int
[../]
[./plastic_strain_aux]
type = MaterialRankTwoTensorAux
i = 2
j = 2
property = plastic_strain
variable = plastic_strain
[../]
[./num_iters_auxk] # cannot use plastic_NR_iterations directly as this is zero, since no NR iterations are actually used, since we use a custom algorithm to do the return
type = ParsedAux
args = plastic_strain
function = 'if(plastic_strain>0,1,0)'
variable = num_iters
[../]
[./yield_fcn_auxk]
type = MaterialStdVectorAux
index = 0
property = plastic_yield_function
variable = yield_fcn
[../]
[]
[UserObjects]
[./mc_coh]
type = TensorMechanicsHardeningConstant
value = 5E6
[../]
[./mc_phi]
type = TensorMechanicsHardeningConstant
value = 35
convert_to_radians = true
[../]
[./mc_psi]
type = TensorMechanicsHardeningConstant
value = 10
convert_to_radians = true
[../]
[./mc]
type = TensorMechanicsPlasticMohrCoulombMulti
cohesion = mc_coh
friction_angle = mc_phi
dilation_angle = mc_psi
yield_function_tolerance = 1E-5
internal_constraint_tolerance = 1E-11
[../]
[]
[Materials]
[./elasticity_tensor]
type = ComputeIsotropicElasticityTensor
youngs_modulus = 16E9
poissons_ratio = 0.25
[../]
[./mc]
type = ComputeMultiPlasticityStress
ep_plastic_tolerance = 1E-11
plastic_models = mc
max_NR_iterations = 1000
debug_fspb = crash
[../]
[./strain_from_initial_stress]
type = ComputeEigenstrainFromInitialStress
initial_stress = '6E6 0 0 0 6E6 0 0 0 6E6'
eigenstrain_name = ini_stress
[../]
[]
[Preconditioning]
[./andy]
type = SMP
full = true
[../]
[]
[Executioner]
start_time = -1
end_time = 10
dt = 1
solve_type = NEWTON
type = Transient
l_tol = 1E-2
nl_abs_tol = 1E-5
nl_rel_tol = 1E-7
l_max_its = 200
nl_max_its = 400
petsc_options_iname = '-pc_type -pc_asm_overlap -sub_pc_type -ksp_type -ksp_gmres_restart'
petsc_options_value = ' asm 2 lu gmres 200'
[]
[Outputs]
file_base = biaxial_planar
perf_graph = true
exodus = false
csv = true
[]
modules/functional_expansion_tools/test/tests/standard_use/volume_coupling_custom_norm_sub.i
[Mesh]
type = GeneratedMesh
dim = 1
xmin = 0.0
xmax = 10.0
nx = 15
[]
[Variables]
[./empty]
[../]
[]
[AuxVariables]
[./s]
order = FIRST
family = LAGRANGE
[../]
[./m_in]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
[./null_kernel]
type = NullKernel
variable = empty
[../]
[]
[AuxKernels]
[./reconstruct_m_in]
type = FunctionSeriesToAux
function = FX_Basis_Value_Sub
variable = m_in
[../]
[./calculate_s]
type = ParsedAux
variable = s
args = m_in
function = '2*exp(-m_in/0.8)'
[../]
[]
[Functions]
[./FX_Basis_Value_Sub]
type = FunctionSeries
series_type = Cartesian
orders = '3'
physical_bounds = '0.0 10.0'
x = Legendre
generation_type = 'sqrt_mu'
expansion_type = 'sqrt_mu'
[../]
[]
[UserObjects]
[./FX_Value_UserObject_Sub]
type = FXVolumeUserObject
function = FX_Basis_Value_Sub
variable = s
[../]
[]
[Executioner]
type = Transient
num_steps = 10
dt = 0.5
solve_type = PJFNK
petsc_options_iname = '-pc_type -pc_hypre_type'
petsc_options_value = 'hypre boomeramg'
[]
modules/functional_expansion_tools/examples/2D_volumetric_Cartesian/sub.i
# Basic example coupling a master and sub app in a 2D Cartesian volume.
#
# The master app provides field values to the sub app via Functional Expansions, which then performs
# its calculations. The sub app's solution field values are then transferred back to the master app
# and coupled into the solution of the master app solution.
#
# This example couples Functional Expansions via AuxVariable.
[Mesh]
type = GeneratedMesh
dim = 2
xmin = 0.0
xmax = 10.0
nx = 15
ymin = 1.0
ymax = 11.0
ny = 25
[]
# Non-copy transfers only work with AuxVariable, but nothing will be solved without a variable
# defined. The solution is to define an empty variable tha does nothing, but causes MOOSE to solve
# the AuxKernels that we need.
[Variables]
[./empty]
[../]
[]
[AuxVariables]
[./s]
order = FIRST
family = LAGRANGE
[../]
[./m_in]
order = FIRST
family = LAGRANGE
[../]
[]
# We must have a kernel for every variable, hence this null kernel to match the variable 'empty'
[Kernels]
[./null_kernel]
type = NullKernel
variable = empty
[../]
[]
[AuxKernels]
[./reconstruct_m_in]
type = FunctionSeriesToAux
function = FX_Basis_Value_Sub
variable = m_in
[../]
[./calculate_s] # Something to make 's' change each time, but allow a converging solution
type = ParsedAux
variable = s
args = m_in
function = '2*exp(-m_in/0.8)'
[../]
[]
[Functions]
[./FX_Basis_Value_Sub]
type = FunctionSeries
series_type = Cartesian
orders = '3 4'
physical_bounds = '0.0 10.0 1.0 11.0'
x = Legendre
y = Legendre
[../]
[]
[UserObjects]
[./FX_Value_UserObject_Sub]
type = FXVolumeUserObject
function = FX_Basis_Value_Sub
variable = s
[../]
[]
[Executioner]
type = Transient
num_steps = 10
dt = 0.5
solve_type = PJFNK
petsc_options_iname = '-pc_type -pc_hypre_type'
petsc_options_value = 'hypre boomeramg'
[]
modules/functional_expansion_tools/examples/1D_volumetric_Cartesian/sub.i
# Basic example coupling a master and sub app in a 1D Cartesian volume.
#
# The master app provides field values to the sub app via Functional Expansions, which then performs
# its calculations. The sub app's solution field values are then transferred back to the master app
# and coupled into the solution of the master app solution.
#
# This example couples Functional Expansions via AuxVariable.
[Mesh]
type = GeneratedMesh
dim = 1
xmin = 0.0
xmax = 10.0
nx = 15
[]
# Non-copy transfers only work with AuxVariable, but nothing will be solved without a variable
# defined. The solution is to define an empty variable tha does nothing, but causes MOOSE to solve
# the AuxKernels that we need.
[Variables]
[./empty]
[../]
[]
[AuxVariables]
[./s]
order = FIRST
family = LAGRANGE
[../]
[./m_in]
order = FIRST
family = LAGRANGE
[../]
[]
# We must have a kernel for every variable, hence this null kernel to match the variable 'empty'
[Kernels]
[./null_kernel]
type = NullKernel
variable = empty
[../]
[]
[AuxKernels]
[./reconstruct_m_in]
type = FunctionSeriesToAux
function = FX_Basis_Value_Sub
variable = m_in
[../]
[./calculate_s] # Something to make 's' change each time, but allow a converging solution
type = ParsedAux
variable = s
args = m_in
function = '2*exp(-m_in/0.8)'
[../]
[]
[Functions]
[./FX_Basis_Value_Sub]
type = FunctionSeries
series_type = Cartesian
orders = '3'
physical_bounds = '0.0 10.0'
x = Legendre
[../]
[]
[UserObjects]
[./FX_Value_UserObject_Sub]
type = FXVolumeUserObject
function = FX_Basis_Value_Sub
variable = s
[../]
[]
[Executioner]
type = Transient
num_steps = 10
dt = 0.5
solve_type = PJFNK
petsc_options_iname = '-pc_type -pc_hypre_type'
petsc_options_value = 'hypre boomeramg'
[]
test/tests/auxkernels/linear_combination/test.i
# All tested logic is in the aux system
# The non-linear problem is unrelated
[Mesh]
type = GeneratedMesh
dim = 1
xmin = -1
xmax = 1
nx = 10
[]
[Functions]
[./v1_func]
type = ParsedFunction
value = (1-x)/2
[../]
[./v2_func]
type = ParsedFunction
value = (1+x)/2
[../]
[]
[Variables]
[./u]
order = FIRST
family = LAGRANGE
[../]
[]
[AuxVariables]
[./lc]
[../]
[./v1]
[../]
[./v2]
[../]
[./w1]
[../]
[./w2]
[../]
[]
[ICs]
[./v1_ic]
type = FunctionIC
variable = v1
function = v1_func
[../]
[./v2_ic]
type = FunctionIC
variable = v2
function = v2_func
[../]
[./w1_ic]
type = ConstantIC
variable = w1
value = 0.3
[../]
[./w2_ic]
type = ConstantIC
variable = w2
value = 0.5
[../]
[]
[AuxKernels]
[./lc-aux]
type = ParsedAux
variable = lc
function = 'v1*w1+v2*w2'
args = 'v1 w1 v2 w2'
execute_on = 'timestep_end'
[../]
[]
[Kernels]
[./diff]
type = Diffusion
variable = u
[../]
[]
[BCs]
[./left]
type = DirichletBC
variable = u
boundary = left
value = 1
[../]
[./right]
type = DirichletBC
variable = u
boundary = right
value = 2
[../]
[]
[Executioner]
type = Steady
solve_type = 'PJFNK'
[]
[Outputs]
[./out]
type = Exodus
[../]
[]
modules/combined/examples/phase_field-mechanics/kks_mechanics_KHS.i
# KKS phase-field model coupled with elasticity using Khachaturyan's scheme as
# described in L.K. Aagesen et al., Computational Materials Science, 140, 10-21 (2017)
# Original run #170403a
[Mesh]
type = GeneratedMesh
dim = 3
nx = 640
ny = 1
nz = 1
xmin = -10
xmax = 10
ymin = 0
ymax = 0.03125
zmin = 0
zmax = 0.03125
elem_type = HEX8
[]
[Variables]
# order parameter
[./eta]
order = FIRST
family = LAGRANGE
[../]
# solute concentration
[./c]
order = FIRST
family = LAGRANGE
[../]
# chemical potential
[./w]
order = FIRST
family = LAGRANGE
[../]
# solute phase concentration (matrix)
[./cm]
order = FIRST
family = LAGRANGE
[../]
# solute phase concentration (precipitate)
[./cp]
order = FIRST
family = LAGRANGE
[../]
[./disp_x]
order = FIRST
family = LAGRANGE
[../]
[./disp_y]
order = FIRST
family = LAGRANGE
[../]
[./disp_z]
order = FIRST
family = LAGRANGE
[../]
[]
[ICs]
[./eta_ic]
variable = eta
type = FunctionIC
function = ic_func_eta
block = 0
[../]
[./c_ic]
variable = c
type = FunctionIC
function = ic_func_c
block = 0
[../]
[./w_ic]
variable = w
type = ConstantIC
value = 0.00991
block = 0
[../]
[./cm_ic]
variable = cm
type = ConstantIC
value = 0.131
block = 0
[../]
[./cp_ic]
variable = cp
type = ConstantIC
value = 0.236
block = 0
[../]
[]
[Functions]
[./ic_func_eta]
type = ParsedFunction
value = '0.5*(1.0+tanh((x)/delta_eta/sqrt(2.0)))'
vars = 'delta_eta'
vals = '0.8034'
[../]
[./ic_func_c]
type = ParsedFunction
value = '0.2389*(0.5*(1.0+tanh(x/delta/sqrt(2.0))))^3*(6*(0.5*(1.0+tanh(x/delta/sqrt(2.0))))^2-15*(0.5*(1.0+tanh(x/delta/sqrt(2.0))))+10)+0.1339*(1-(0.5*(1.0+tanh(x/delta/sqrt(2.0))))^3*(6*(0.5*(1.0+tanh(x/delta/sqrt(2.0))))^2-15*(0.5*(1.0+tanh(x/delta/sqrt(2.0))))+10))'
vars = 'delta'
vals = '0.8034'
[../]
[./psi_eq_int]
type = ParsedFunction
value = 'volume*psi_alpha'
vars = 'volume psi_alpha'
vals = 'volume psi_alpha'
[../]
[./gamma]
type = ParsedFunction
value = '(psi_int - psi_eq_int) / dy / dz'
vars = 'psi_int psi_eq_int dy dz'
vals = 'psi_int psi_eq_int 0.03125 0.03125'
[../]
[]
[AuxVariables]
[./sigma11]
order = CONSTANT
family = MONOMIAL
[../]
[./sigma22]
order = CONSTANT
family = MONOMIAL
[../]
[./sigma33]
order = CONSTANT
family = MONOMIAL
[../]
[./e11]
order = CONSTANT
family = MONOMIAL
[../]
[./e12]
order = CONSTANT
family = MONOMIAL
[../]
[./e22]
order = CONSTANT
family = MONOMIAL
[../]
[./e33]
order = CONSTANT
family = MONOMIAL
[../]
[./e_el11]
order = CONSTANT
family = MONOMIAL
[../]
[./e_el12]
order = CONSTANT
family = MONOMIAL
[../]
[./e_el22]
order = CONSTANT
family = MONOMIAL
[../]
[./f_el]
order = CONSTANT
family = MONOMIAL
[../]
[./eigen_strain00]
order = CONSTANT
family = MONOMIAL
[../]
[./Fglobal]
order = CONSTANT
family = MONOMIAL
[../]
[./psi]
order = CONSTANT
family = MONOMIAL
[../]
[]
[AuxKernels]
[./matl_sigma11]
type = RankTwoAux
rank_two_tensor = stress
index_i = 0
index_j = 0
variable = sigma11
[../]
[./matl_sigma22]
type = RankTwoAux
rank_two_tensor = stress
index_i = 1
index_j = 1
variable = sigma22
[../]
[./matl_sigma33]
type = RankTwoAux
rank_two_tensor = stress
index_i = 2
index_j = 2
variable = sigma33
[../]
[./matl_e11]
type = RankTwoAux
rank_two_tensor = total_strain
index_i = 0
index_j = 0
variable = e11
[../]
[./f_el]
type = MaterialRealAux
variable = f_el
property = f_el_mat
execute_on = timestep_end
[../]
[./GlobalFreeEnergy]
variable = Fglobal
type = KKSGlobalFreeEnergy
fa_name = fm
fb_name = fp
w = 0.0264
kappa_names = kappa
interfacial_vars = eta
[../]
[./psi_potential]
variable = psi
type = ParsedAux
args = 'Fglobal w c f_el sigma11 e11'
function = 'Fglobal - w*c + f_el - sigma11*e11'
[../]
[]
[BCs]
[./left_x]
type = DirichletBC
variable = disp_x
boundary = left
value = 0
[../]
[./right_x]
type = DirichletBC
variable = disp_x
boundary = right
value = 0
[../]
[./front_y]
type = DirichletBC
variable = disp_y
boundary = front
value = 0
[../]
[./back_y]
type = DirichletBC
variable = disp_y
boundary = back
value = 0
[../]
[./top_z]
type = DirichletBC
variable = disp_z
boundary = top
value = 0
[../]
[./bottom_z]
type = DirichletBC
variable = disp_z
boundary = bottom
value = 0
[../]
[]
[Materials]
# Chemical free energy of the matrix
[./fm]
type = DerivativeParsedMaterial
f_name = fm
args = 'cm'
function = '6.55*(cm-0.13)^2'
[../]
# Chemical Free energy of the precipitate phase
[./fp]
type = DerivativeParsedMaterial
f_name = fp
args = 'cp'
function = '6.55*(cp-0.235)^2'
[../]
# Elastic energy of the precipitate
[./elastic_free_energy_p]
type = ElasticEnergyMaterial
f_name = f_el_mat
args = 'eta'
outputs = exodus
[../]
# h(eta)
[./h_eta]
type = SwitchingFunctionMaterial
h_order = HIGH
eta = eta
[../]
# 1- h(eta), putting in function explicitly
[./one_minus_h_eta_explicit]
type = DerivativeParsedMaterial
f_name = one_minus_h_explicit
args = eta
function = 1-eta^3*(6*eta^2-15*eta+10)
outputs = exodus
[../]
# g(eta)
[./g_eta]
type = BarrierFunctionMaterial
g_order = SIMPLE
eta = eta
[../]
# constant properties
[./constants]
type = GenericConstantMaterial
prop_names = 'M L kappa misfit'
prop_values = '0.7 0.7 0.01704 0.00377'
[../]
#Mechanical properties
[./Stiffness_matrix]
type = ComputeElasticityTensor
base_name = C_matrix
C_ijkl = '103.3 74.25 74.25 103.3 74.25 103.3 46.75 46.75 46.75'
fill_method = symmetric9
[../]
[./Stiffness_ppt]
type = ComputeElasticityTensor
C_ijkl = '100.7 71.45 71.45 100.7 71.45 100.7 50.10 50.10 50.10'
base_name = C_ppt
fill_method = symmetric9
[../]
[./C]
type = CompositeElasticityTensor
args = eta
tensors = 'C_matrix C_ppt'
weights = 'one_minus_h_explicit h'
[../]
[./stress]
type = ComputeLinearElasticStress
[../]
[./strain]
type = ComputeSmallStrain
displacements = 'disp_x disp_y disp_z'
eigenstrain_names = 'eigenstrain_ppt'
[../]
[./eigen_strain]
type = ComputeVariableEigenstrain
eigen_base = '0.00377 0.00377 0.00377 0 0 0'
prefactor = h
args = eta
eigenstrain_name = 'eigenstrain_ppt'
[../]
[]
[Kernels]
[./TensorMechanics]
displacements = 'disp_x disp_y disp_z'
[../]
# enforce c = (1-h(eta))*cm + h(eta)*cp
[./PhaseConc]
type = KKSPhaseConcentration
ca = cm
variable = cp
c = c
eta = eta
[../]
# enforce pointwise equality of chemical potentials
[./ChemPotVacancies]
type = KKSPhaseChemicalPotential
variable = cm
cb = cp
fa_name = fm
fb_name = fp
[../]
#
# Cahn-Hilliard Equation
#
[./CHBulk]
type = KKSSplitCHCRes
variable = c
ca = cm
fa_name = fm
w = w
[../]
[./dcdt]
type = CoupledTimeDerivative
variable = w
v = c
[../]
[./ckernel]
type = SplitCHWRes
mob_name = M
variable = w
[../]
#
# Allen-Cahn Equation
#
[./ACBulkF]
type = KKSACBulkF
variable = eta
fa_name = fm
fb_name = fp
w = 0.0264
args = 'cp cm'
[../]
[./ACBulkC]
type = KKSACBulkC
variable = eta
ca = cm
cb = cp
fa_name = fm
[../]
[./ACBulk_el] #This adds df_el/deta for strain interpolation
type = AllenCahn
variable = eta
f_name = f_el_mat
[../]
[./ACInterface]
type = ACInterface
variable = eta
kappa_name = kappa
[../]
[./detadt]
type = TimeDerivative
variable = eta
[../]
[]
[Executioner]
type = Transient
solve_type = 'PJFNK'
petsc_options_iname = '-pc_type -sub_pc_type -sub_pc_factor_shift_type'
petsc_options_value = 'asm ilu nonzero'
l_max_its = 30
nl_max_its = 10
l_tol = 1.0e-4
nl_rel_tol = 1.0e-8
nl_abs_tol = 1.0e-11
num_steps = 200
[./TimeStepper]
type = SolutionTimeAdaptiveDT
dt = 0.5
[../]
[]
[Postprocessors]
[./f_el_int]
type = ElementIntegralMaterialProperty
mat_prop = f_el_mat
[../]
[./c_alpha]
type = SideAverageValue
boundary = left
variable = c
[../]
[./c_beta]
type = SideAverageValue
boundary = right
variable = c
[../]
[./e11_alpha]
type = SideAverageValue
boundary = left
variable = e11
[../]
[./e11_beta]
type = SideAverageValue
boundary = right
variable = e11
[../]
[./s11_alpha]
type = SideAverageValue
boundary = left
variable = sigma11
[../]
[./s22_alpha]
type = SideAverageValue
boundary = left
variable = sigma22
[../]
[./s33_alpha]
type = SideAverageValue
boundary = left
variable = sigma33
[../]
[./s11_beta]
type = SideAverageValue
boundary = right
variable = sigma11
[../]
[./s22_beta]
type = SideAverageValue
boundary = right
variable = sigma22
[../]
[./s33_beta]
type = SideAverageValue
boundary = right
variable = sigma33
[../]
[./f_el_alpha]
type = SideAverageValue
boundary = left
variable = f_el
[../]
[./f_el_beta]
type = SideAverageValue
boundary = right
variable = f_el
[../]
[./f_c_alpha]
type = SideAverageValue
boundary = left
variable = Fglobal
[../]
[./f_c_beta]
type = SideAverageValue
boundary = right
variable = Fglobal
[../]
[./chem_pot_alpha]
type = SideAverageValue
boundary = left
variable = w
[../]
[./chem_pot_beta]
type = SideAverageValue
boundary = right
variable = w
[../]
[./psi_alpha]
type = SideAverageValue
boundary = left
variable = psi
[../]
[./psi_beta]
type = SideAverageValue
boundary = right
variable = psi
[../]
[./total_energy]
type = ElementIntegralVariablePostprocessor
variable = Fglobal
[../]
# Get simulation cell size from postprocessor
[./volume]
type = ElementIntegralMaterialProperty
mat_prop = 1
[../]
[./psi_eq_int]
type = FunctionValuePostprocessor
function = psi_eq_int
[../]
[./psi_int]
type = ElementIntegralVariablePostprocessor
variable = psi
[../]
[./gamma]
type = FunctionValuePostprocessor
function = gamma
[../]
[./int_position]
type = FindValueOnLine
start_point = '-10 0 0'
end_point = '10 0 0'
v = eta
target = 0.5
[../]
[]
#
# Precondition using handcoded off-diagonal terms
#
[Preconditioning]
[./full]
type = SMP
full = true
[../]
[]
[Outputs]
[./exodus]
type = Exodus
interval = 20
[../]
checkpoint = true
[./csv]
type = CSV
execute_on = 'final'
[../]
[]
modules/functional_expansion_tools/examples/3D_volumetric_Cartesian_direct/sub.i
# Derived from the example '3D_volumetric_Cartesian' with the following differences:
#
# 1) The coupling is performed via BodyForce instead of the
# FunctionSeriesToAux+CoupledForce approach
[Mesh]
type = GeneratedMesh
dim = 3
xmin = 0.0
xmax = 10.0
nx = 15
ymin = 1.0
ymax = 11.0
ny = 25
zmin = 2.0
zmax = 12.0
nz = 35
[]
# Non-copy transfers only work with AuxVariable, but nothing will be solved without a variable
# defined. The solution is to define an empty variable tha does nothing, but causes MOOSE to solve
# the AuxKernels that we need.
[Variables]
[./empty]
[../]
[]
[AuxVariables]
[./s]
order = FIRST
family = LAGRANGE
[../]
[./m_in]
order = FIRST
family = LAGRANGE
[../]
[]
# We must have a kernel for every variable, hence this null kernel to match the variable 'empty'
[Kernels]
[./null_kernel]
type = NullKernel
variable = empty
[../]
[]
[AuxKernels]
[./reconstruct_m_in]
type = FunctionSeriesToAux
function = FX_Basis_Value_Sub
variable = m_in
[../]
[./calculate_s] # Something to make 's' change each time, but allow a converging solution
type = ParsedAux
variable = s
args = m_in
function = '2*exp(-m_in/0.8)'
[../]
[]
[Functions]
[./FX_Basis_Value_Sub]
type = FunctionSeries
series_type = Cartesian
orders = '3 4 5'
physical_bounds = '0.0 10.0 1.0 11.0 2.0 12.0'
x = Legendre
y = Legendre
z = Legendre
[../]
[]
[UserObjects]
[./FX_Value_UserObject_Sub]
type = FXVolumeUserObject
function = FX_Basis_Value_Sub
variable = s
[../]
[]
[Executioner]
type = Transient
num_steps = 10
dt = 0.5
solve_type = PJFNK
petsc_options_iname = '-pc_type -pc_hypre_type'
petsc_options_value = 'hypre boomeramg'
[]
modules/functional_expansion_tools/test/tests/standard_use/multiapp_sub.i
[Mesh]
type = GeneratedMesh
dim = 1
xmin = 0.0
xmax = 10.0
nx = 15
[]
[Variables]
[./empty]
[../]
[]
[AuxVariables]
[./s]
order = FIRST
family = LAGRANGE
[../]
[./m_in]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
[./null_kernel]
type = NullKernel
variable = empty
[../]
[]
[AuxKernels]
[./reconstruct_m_in]
type = FunctionSeriesToAux
function = FX_Basis_Value_Sub
variable = m_in
[../]
[./calculate_s]
type = ParsedAux
variable = s
args = m_in
function = '2*exp(-m_in/0.8)'
[../]
[]
[Functions]
[./FX_Basis_Value_Sub]
type = FunctionSeries
series_type = Cartesian
orders = '3'
physical_bounds = '0.0 10.0'
x = Legendre
[../]
[]
[UserObjects]
[./FX_Value_UserObject_Sub]
type = FXVolumeUserObject
function = FX_Basis_Value_Sub
variable = s
[../]
[]
[Executioner]
type = Transient
num_steps = 10
dt = 0.5
solve_type = PJFNK
petsc_options_iname = '-pc_type -pc_hypre_type'
petsc_options_value = 'hypre boomeramg'
[]
modules/porous_flow/test/tests/pressure_pulse/pressure_pulse_1d_MD.i
# Pressure pulse in 1D with 1 phase - transient
# Using the "MD" formulation (where primary variable is log(mass-density
[Mesh]
type = GeneratedMesh
dim = 1
nx = 10
xmin = 0
xmax = 100
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Variables]
[./md]
# initial porepressure = 2E6
# so initial md = log(density_P0) + porepressure/bulk_modulus =
initial_condition = 6.90875527898214
[../]
[]
[Kernels]
[./mass0]
type = PorousFlowMassTimeDerivative
fluid_component = 0
variable = md
[../]
[./flux]
type = PorousFlowAdvectiveFlux
variable = md
gravity = '0 0 0'
fluid_component = 0
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = 'md'
number_fluid_phases = 1
number_fluid_components = 1
[../]
[]
[Modules]
[./FluidProperties]
[./simple_fluid]
type = SimpleFluidProperties
bulk_modulus = 2e9
density0 = 1000
thermal_expansion = 0
viscosity = 1e-3
[../]
[../]
[]
[Materials]
[./temperature]
type = PorousFlowTemperature
[../]
[./ppss]
type = PorousFlow1PhaseMD_Gaussian
mass_density = md
al = 1E-6 # this is irrelevant in this example
density_P0 = 1000
bulk_modulus = 2E9
[../]
[./massfrac]
type = PorousFlowMassFraction
[../]
[./simple_fluid]
type = PorousFlowSingleComponentFluid
fp = simple_fluid
phase = 0
[../]
[./porosity]
type = PorousFlowPorosityConst
porosity = 0.1
[../]
[./permeability]
type = PorousFlowPermeabilityConst
permeability = '1E-15 0 0 0 1E-15 0 0 0 1E-15'
[../]
[./relperm]
type = PorousFlowRelativePermeabilityCorey
n = 0
phase = 0
[../]
[]
[BCs]
[./left]
type = DirichletBC
boundary = left
# BC porepressure = 3E6
# so boundary md = log(density_P0) + porepressure/bulk_modulus =
value = 6.90925527898214
variable = md
[../]
[]
[Preconditioning]
[./andy]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
dt = 1E3
end_time = 1E4
[]
[AuxVariables]
[./pp]
[../]
[]
[AuxKernels]
[./pp]
type = ParsedAux
function = '(md-6.9077552789821)*2.0E9'
args = 'md'
variable = pp
[../]
[]
[Postprocessors]
[./p000]
type = PointValue
variable = pp
point = '0 0 0'
execute_on = 'initial timestep_end'
[../]
[./p010]
type = PointValue
variable = pp
point = '10 0 0'
execute_on = 'initial timestep_end'
[../]
[./p020]
type = PointValue
variable = pp
point = '20 0 0'
execute_on = 'initial timestep_end'
[../]
[./p030]
type = PointValue
variable = pp
point = '30 0 0'
execute_on = 'initial timestep_end'
[../]
[./p040]
type = PointValue
variable = pp
point = '40 0 0'
execute_on = 'initial timestep_end'
[../]
[./p050]
type = PointValue
variable = pp
point = '50 0 0'
execute_on = 'initial timestep_end'
[../]
[./p060]
type = PointValue
variable = pp
point = '60 0 0'
execute_on = 'initial timestep_end'
[../]
[./p070]
type = PointValue
variable = pp
point = '70 0 0'
execute_on = 'initial timestep_end'
[../]
[./p080]
type = PointValue
variable = pp
point = '80 0 0'
execute_on = 'initial timestep_end'
[../]
[./p090]
type = PointValue
variable = pp
point = '90 0 0'
execute_on = 'initial timestep_end'
[../]
[./p100]
type = PointValue
variable = pp
point = '100 0 0'
execute_on = 'initial timestep_end'
[../]
[]
[Outputs]
file_base = pressure_pulse_1d_MD
print_linear_residuals = false
csv = true
[]
modules/porous_flow/test/tests/chemistry/precipitation_2phase.i
# Using a two-phase system (see precipitation.i for the single-phase)
# The saturation and porosity are chosen so that the results are identical to precipitation.i
#
# The precipitation reaction
#
# a <==> mineral
#
# produces "mineral". Using mineral_density = fluid_density, theta = 1 = eta, the DE is
#
# a' = -(mineral / (porosity * saturation))' = rate * surf_area * molar_vol (1 - (1 / eqm_const) * (act_coeff * a)^stoi)
#
# The following parameters are used
#
# T_ref = 0.5 K
# T = 1 K
# activation_energy = 3 J/mol
# gas_constant = 6 J/(mol K)
# kinetic_rate_at_ref_T = 0.60653 mol/(m^2 s)
# These give rate = 0.60653 * exp(1/2) = 1 mol/(m^2 s)
#
# surf_area = 0.5 m^2/L
# molar_volume = 2 L/mol
# These give rate * surf_area * molar_vol = 1 s^-1
#
# equilibrium_constant = 0.5 (dimensionless)
# primary_activity_coefficient = 2 (dimensionless)
# stoichiometry = 1 (dimensionless)
# This means that 1 - (1 / eqm_const) * (act_coeff * a)^stoi = 1 - 4 a, which is negative for a > 0.25, ie precipitation for a(t=0) > 0.25
#
# The solution of the DE is
# a = eqm_const / act_coeff + (a(t=0) - eqm_const / act_coeff) exp(-rate * surf_area * molar_vol * act_coeff * t / eqm_const)
# = 0.25 + (a(t=0) - 0.25) exp(-4 * t)
# c = c(t=0) - (a - a(t=0)) * (porosity * saturation)
#
# This test checks that (a + c / (porosity * saturation)) is time-independent, and that a follows the above solution
#
# Aside:
# The exponential curve is not followed exactly because moose actually solves
# (a - a_old)/dt = rate * surf_area * molar_vol (1 - (1 / eqm_const) * (act_coeff * a)^stoi)
# which does not give an exponential exactly, except in the limit dt->0
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./a]
initial_condition = 0.9
[../]
[]
[AuxVariables]
[./eqm_k]
initial_condition = 0.5
[../]
[./pressure0]
[../]
[./saturation1]
initial_condition = 0.25
[../]
[./b]
initial_condition = 0.123
[../]
[./ini_mineral_conc]
initial_condition = 0.2
[../]
[./mineral]
family = MONOMIAL
order = CONSTANT
[../]
[./should_be_static]
family = MONOMIAL
order = CONSTANT
[../]
[]
[AuxKernels]
[./mineral]
type = PorousFlowPropertyAux
property = mineral_concentration
mineral_species = 0
variable = mineral
[../]
[./should_be_static]
type = ParsedAux
args = 'mineral a'
function = 'a + mineral / 0.1'
variable = should_be_static
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./mass_a]
type = PorousFlowMassTimeDerivative
fluid_component = 0
variable = a
[../]
[./pre_dis]
type = PorousFlowPreDis
variable = a
mineral_density = 1000
stoichiometry = 1
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = a
number_fluid_phases = 2
number_fluid_components = 2
number_aqueous_kinetic = 1
aqueous_phase_number = 1
[../]
[./pc]
type = PorousFlowCapillaryPressureConst
[../]
[]
[Modules]
[./FluidProperties]
[./simple_fluid]
type = SimpleFluidProperties
bulk_modulus = 2e9 # huge, so mimic chemical_reactions
density0 = 1000
thermal_expansion = 0
viscosity = 1e-3
[../]
[../]
[]
[Materials]
[./temperature]
type = PorousFlowTemperature
temperature = 1
[../]
[./ppss]
type = PorousFlow2PhasePS
capillary_pressure = pc
phase0_porepressure = pressure0
phase1_saturation = saturation1
[../]
[./mass_frac]
type = PorousFlowMassFraction
mass_fraction_vars = 'b a'
[../]
[./predis]
type = PorousFlowAqueousPreDisChemistry
primary_concentrations = a
num_reactions = 1
equilibrium_constants = eqm_k
primary_activity_coefficients = 2
reactions = 1
specific_reactive_surface_area = 0.5
kinetic_rate_constant = 0.6065306597126334
activation_energy = 3
molar_volume = 2
gas_constant = 6
reference_temperature = 0.5
[../]
[./mineral_conc]
type = PorousFlowAqueousPreDisMineral
initial_concentrations = ini_mineral_conc
[../]
[./simple_fluid0]
type = PorousFlowSingleComponentFluid
fp = simple_fluid
phase = 0
[../]
[./simple_fluid1]
type = PorousFlowSingleComponentFluid
fp = simple_fluid
phase = 1
[../]
[./porosity]
type = PorousFlowPorosityConst
porosity = 0.4
[../]
[]
[Preconditioning]
[./smp]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
nl_abs_tol = 1E-10
dt = 0.01
end_time = 1
[]
[Postprocessors]
[./a]
type = PointValue
point = '0 0 0'
variable = a
[../]
[./should_be_static]
type = PointValue
point = '0 0 0'
variable = should_be_static
[../]
[]
[Outputs]
interval = 10
csv = true
perf_graph = true
[]
modules/porous_flow/test/tests/chemistry/precipitation.i
# The precipitation reaction
#
# a <==> mineral
#
# produces "mineral". Using mineral_density = fluid_density, theta = 1 = eta, the DE is
#
# a' = -(mineral / porosity)' = rate * surf_area * molar_vol (1 - (1 / eqm_const) * (act_coeff * a)^stoi)
#
# The following parameters are used
#
# T_ref = 0.5 K
# T = 1 K
# activation_energy = 3 J/mol
# gas_constant = 6 J/(mol K)
# kinetic_rate_at_ref_T = 0.60653 mol/(m^2 s)
# These give rate = 0.60653 * exp(1/2) = 1 mol/(m^2 s)
#
# surf_area = 0.5 m^2/L
# molar_volume = 2 L/mol
# These give rate * surf_area * molar_vol = 1 s^-1
#
# equilibrium_constant = 0.5 (dimensionless)
# primary_activity_coefficient = 2 (dimensionless)
# stoichiometry = 1 (dimensionless)
# This means that 1 - (1 / eqm_const) * (act_coeff * a)^stoi = 1 - 4 a, which is negative for a > 0.25, ie precipitation for a(t=0) > 0.25
#
# The solution of the DE is
# a = eqm_const / act_coeff + (a(t=0) - eqm_const / act_coeff) exp(-rate * surf_area * molar_vol * act_coeff * t / eqm_const)
# = 0.25 + (a(t=0) - 0.25) exp(-4 * t)
# c = c(t=0) - (a - a(t=0)) * porosity
#
# This test checks that (a + c / porosity) is time-independent, and that a follows the above solution
#
# Aside:
# The exponential curve is not followed exactly because moose actually solves
# (a - a_old)/dt = rate * surf_area * molar_vol (1 - (1 / eqm_const) * (act_coeff * a)^stoi)
# which does not give an exponential exactly, except in the limit dt->0
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./a]
initial_condition = 0.9
[../]
[]
[AuxVariables]
[./pressure]
[../]
[./ini_mineral_conc]
initial_condition = 0.2
[../]
[./k]
initial_condition = 0.5
[../]
[./mineral]
family = MONOMIAL
order = CONSTANT
[../]
[./should_be_static]
family = MONOMIAL
order = CONSTANT
[../]
[]
[AuxKernels]
[./mineral]
type = PorousFlowPropertyAux
property = mineral_concentration
mineral_species = 0
variable = mineral
[../]
[./should_be_static]
type = ParsedAux
args = 'mineral a'
function = 'a + mineral / 0.1'
variable = should_be_static
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./mass_a]
type = PorousFlowMassTimeDerivative
fluid_component = 0
variable = a
[../]
[./pre_dis]
type = PorousFlowPreDis
variable = a
mineral_density = 1000
stoichiometry = 1
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = a
number_fluid_phases = 1
number_fluid_components = 2
number_aqueous_kinetic = 1
[../]
[]
[Modules]
[./FluidProperties]
[./simple_fluid]
type = SimpleFluidProperties
bulk_modulus = 2e9 # huge, so mimic chemical_reactions
density0 = 1000
thermal_expansion = 0
viscosity = 1e-3
[../]
[../]
[]
[Materials]
[./temperature]
type = PorousFlowTemperature
temperature = 1
[../]
[./ppss]
type = PorousFlow1PhaseFullySaturated
porepressure = pressure
[../]
[./mass_frac]
type = PorousFlowMassFraction
mass_fraction_vars = a
[../]
[./predis]
type = PorousFlowAqueousPreDisChemistry
primary_concentrations = a
num_reactions = 1
equilibrium_constants = k
primary_activity_coefficients = 2
reactions = 1
specific_reactive_surface_area = 0.5
kinetic_rate_constant = 0.6065306597126334
activation_energy = 3
molar_volume = 2
gas_constant = 6
reference_temperature = 0.5
[../]
[./mineral_conc]
type = PorousFlowAqueousPreDisMineral
initial_concentrations = ini_mineral_conc
[../]
[./simple_fluid]
type = PorousFlowSingleComponentFluid
fp = simple_fluid
phase = 0
[../]
[./porosity]
type = PorousFlowPorosityConst
porosity = 0.1
[../]
[]
[Preconditioning]
[./smp]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
nl_abs_tol = 1E-10
dt = 0.01
end_time = 1
[]
[Postprocessors]
[./a]
type = PointValue
point = '0 0 0'
variable = a
[../]
[./should_be_static]
type = PointValue
point = '0 0 0'
variable = should_be_static
[../]
[]
[Outputs]
interval = 10
csv = true
perf_graph = true
[]
modules/porous_flow/examples/tutorial/11.i
# Two-phase borehole injection problem
[Mesh]
[annular]
type = AnnularMeshGenerator
nr = 10
rmin = 1.0
rmax = 10
growth_r = 1.4
nt = 4
dmin = 0
dmax = 90
[]
[./make3D]
input = annular
type = MeshExtruderGenerator
extrusion_vector = '0 0 12'
num_layers = 3
bottom_sideset = 'bottom'
top_sideset = 'top'
[../]
[./shift_down]
type = TransformGenerator
transform = TRANSLATE
vector_value = '0 0 -6'
input = make3D
[../]
[./aquifer]
type = SubdomainBoundingBoxGenerator
block_id = 1
bottom_left = '0 0 -2'
top_right = '10 10 2'
input = shift_down
[../]
[./injection_area]
type = ParsedGenerateSideset
combinatorial_geometry = 'x*x+y*y<1.01'
included_subdomain_ids = 1
new_sideset_name = 'injection_area'
input = 'aquifer'
[../]
[./rename]
type = RenameBlockGenerator
old_block_id = '0 1'
new_block_name = 'caps aquifer'
input = 'injection_area'
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = 'pwater pgas T disp_x disp_y'
number_fluid_phases = 2
number_fluid_components = 2
[../]
[./pc]
type = PorousFlowCapillaryPressureVG
alpha = 1E-6
m = 0.6
[../]
[]
[GlobalParams]
displacements = 'disp_x disp_y disp_z'
gravity = '0 0 0'
biot_coefficient = 1.0
PorousFlowDictator = dictator
[]
[Variables]
[./pwater]
initial_condition = 20E6
[../]
[./pgas]
initial_condition = 20.1E6
[../]
[./T]
initial_condition = 330
scaling = 1E-5
[../]
[./disp_x]
scaling = 1E-5
[../]
[./disp_y]
scaling = 1E-5
[../]
[]
[Kernels]
[./mass_water_dot]
type = PorousFlowMassTimeDerivative
fluid_component = 0
use_displaced_mesh = false
variable = pwater
[../]
[./flux_water]
type = PorousFlowAdvectiveFlux
fluid_component = 0
use_displaced_mesh = false
variable = pwater
[../]
[./vol_strain_rate_water]
type = PorousFlowMassVolumetricExpansion
fluid_component = 0
use_displaced_mesh = false
variable = pwater
[../]
[./mass_co2_dot]
type = PorousFlowMassTimeDerivative
fluid_component = 1
use_displaced_mesh = false
variable = pgas
[../]
[./flux_co2]
type = PorousFlowAdvectiveFlux
fluid_component = 1
use_displaced_mesh = false
variable = pgas
[../]
[./vol_strain_rate_co2]
type = PorousFlowMassVolumetricExpansion
fluid_component = 1
use_displaced_mesh = false
variable = pgas
[../]
[./energy_dot]
type = PorousFlowEnergyTimeDerivative
use_displaced_mesh = false
variable = T
[../]
[./advection]
type = PorousFlowHeatAdvection
use_displaced_mesh = false
variable = T
[../]
[./conduction]
type = PorousFlowHeatConduction
use_displaced_mesh = false
variable = T
[../]
[./vol_strain_rate_heat]
type = PorousFlowHeatVolumetricExpansion
use_displaced_mesh = false
variable = T
[../]
[./grad_stress_x]
type = StressDivergenceTensors
temperature = T
variable = disp_x
thermal_eigenstrain_name = thermal_contribution
use_displaced_mesh = false
component = 0
[../]
[./poro_x]
type = PorousFlowEffectiveStressCoupling
variable = disp_x
use_displaced_mesh = false
component = 0
[../]
[./grad_stress_y]
type = StressDivergenceTensors
temperature = T
variable = disp_y
thermal_eigenstrain_name = thermal_contribution
use_displaced_mesh = false
component = 1
[../]
[./poro_y]
type = PorousFlowEffectiveStressCoupling
variable = disp_y
use_displaced_mesh = false
component = 1
[../]
[]
[AuxVariables]
[./disp_z]
[../]
[./effective_fluid_pressure]
family = MONOMIAL
order = CONSTANT
[../]
[./mass_frac_phase0_species0]
initial_condition = 1 # all water in phase=0
[../]
[./mass_frac_phase1_species0]
initial_condition = 0 # no water in phase=1
[../]
[./sgas]
family = MONOMIAL
order = CONSTANT
[../]
[./swater]
family = MONOMIAL
order = CONSTANT
[../]
[./stress_rr]
family = MONOMIAL
order = CONSTANT
[../]
[./stress_tt]
family = MONOMIAL
order = CONSTANT
[../]
[./stress_zz]
family = MONOMIAL
order = CONSTANT
[../]
[./porosity]
family = MONOMIAL
order = CONSTANT
[../]
[]
[AuxKernels]
[./effective_fluid_pressure]
type = ParsedAux
args = 'pwater pgas swater sgas'
function = 'pwater * swater + pgas * sgas'
variable = effective_fluid_pressure
[../]
[./swater]
type = PorousFlowPropertyAux
variable = swater
property = saturation
phase = 0
execute_on = timestep_end
[../]
[./sgas]
type = PorousFlowPropertyAux
variable = sgas
property = saturation
phase = 1
execute_on = timestep_end
[../]
[./stress_rr]
type = RankTwoScalarAux
variable = stress_rr
rank_two_tensor = stress
scalar_type = RadialStress
point1 = '0 0 0'
point2 = '0 0 1'
execute_on = timestep_end
[../]
[./stress_tt]
type = RankTwoScalarAux
variable = stress_tt
rank_two_tensor = stress
scalar_type = HoopStress
point1 = '0 0 0'
point2 = '0 0 1'
execute_on = timestep_end
[../]
[./stress_zz]
type = RankTwoAux
variable = stress_zz
rank_two_tensor = stress
index_i = 2
index_j = 2
execute_on = timestep_end
[../]
[./porosity]
type = PorousFlowPropertyAux
variable = porosity
property = porosity
execute_on = timestep_end
[../]
[]
[BCs]
[./roller_tmax]
type = DirichletBC
variable = disp_x
value = 0
boundary = dmax
[../]
[./roller_tmin]
type = DirichletBC
variable = disp_y
value = 0
boundary = dmin
[../]
[./pinned_top_bottom_x]
type = DirichletBC
variable = disp_x
value = 0
boundary = 'top bottom'
[../]
[./pinned_top_bottom_y]
type = DirichletBC
variable = disp_y
value = 0
boundary = 'top bottom'
[../]
[./cavity_pressure_x]
type = Pressure
boundary = injection_area
variable = disp_x
component = 0
postprocessor = constrained_effective_fluid_pressure_at_wellbore
use_displaced_mesh = false
[../]
[./cavity_pressure_y]
type = Pressure
boundary = injection_area
variable = disp_y
component = 1
postprocessor = constrained_effective_fluid_pressure_at_wellbore
use_displaced_mesh = false
[../]
[./cold_co2]
type = DirichletBC
boundary = injection_area
variable = T
value = 290 # injection temperature
use_displaced_mesh = false
[../]
[./constant_co2_injection]
type = PorousFlowSink
boundary = injection_area
variable = pgas
fluid_phase = 1
flux_function = -1E-4
use_displaced_mesh = false
[../]
[./outer_water_removal]
type = PorousFlowPiecewiseLinearSink
boundary = rmax
variable = pwater
fluid_phase = 0
pt_vals = '0 1E9'
multipliers = '0 1E8'
PT_shift = 20E6
use_mobility = true
use_relperm = true
use_displaced_mesh = false
[../]
[./outer_co2_removal]
type = PorousFlowPiecewiseLinearSink
boundary = rmax
variable = pgas
fluid_phase = 1
pt_vals = '0 1E9'
multipliers = '0 1E8'
PT_shift = 20.1E6
use_mobility = true
use_relperm = true
use_displaced_mesh = false
[../]
[]
[Modules]
[./FluidProperties]
[./true_water]
type = Water97FluidProperties
[../]
[./tabulated_water]
type = TabulatedFluidProperties
fp = true_water
temperature_min = 275
pressure_max = 1E8
interpolated_properties = 'density viscosity enthalpy internal_energy'
fluid_property_file = water97_tabulated_11.csv
[../]
[./true_co2]
type = CO2FluidProperties
[../]
[./tabulated_co2]
type = TabulatedFluidProperties
fp = true_co2
temperature_min = 275
pressure_max = 1E8
interpolated_properties = 'density viscosity enthalpy internal_energy'
fluid_property_file = co2_tabulated_11.csv
[../]
[../]
[]
[Materials]
[./temperature]
type = PorousFlowTemperature
temperature = T
[../]
[./saturation_calculator]
type = PorousFlow2PhasePP
phase0_porepressure = pwater
phase1_porepressure = pgas
capillary_pressure = pc
[../]
[./massfrac]
type = PorousFlowMassFraction
mass_fraction_vars = 'mass_frac_phase0_species0 mass_frac_phase1_species0'
[../]
[./water]
type = PorousFlowSingleComponentFluid
fp = tabulated_water
phase = 0
[../]
[./co2]
type = PorousFlowSingleComponentFluid
fp = tabulated_co2
phase = 1
[../]
[./relperm_water]
type = PorousFlowRelativePermeabilityCorey
n = 4
s_res = 0.1
sum_s_res = 0.2
phase = 0
[../]
[./relperm_co2]
type = PorousFlowRelativePermeabilityBC
nw_phase = true
lambda = 2
s_res = 0.1
sum_s_res = 0.2
phase = 1
[../]
[./porosity]
type = PorousFlowPorosity
fluid = true
mechanical = true
thermal = true
porosity_zero = 0.1
reference_temperature = 330
reference_porepressure = 20E6
thermal_expansion_coeff = 15E-6 # volumetric
solid_bulk = 8E9 # unimportant since biot = 1
[../]
[./permeability_aquifer]
type = PorousFlowPermeabilityKozenyCarman
block = aquifer
poroperm_function = kozeny_carman_phi0
phi0 = 0.1
n = 2
m = 2
k0 = 1E-12
[../]
[./permeability_caps]
type = PorousFlowPermeabilityKozenyCarman
block = caps
poroperm_function = kozeny_carman_phi0
phi0 = 0.1
n = 2
m = 2
k0 = 1E-15
k_anisotropy = '1 0 0 0 1 0 0 0 0.1'
[../]
[./rock_thermal_conductivity]
type = PorousFlowThermalConductivityIdeal
dry_thermal_conductivity = '2 0 0 0 2 0 0 0 2'
[../]
[./rock_internal_energy]
type = PorousFlowMatrixInternalEnergy
specific_heat_capacity = 1100
density = 2300
[../]
[./elasticity_tensor]
type = ComputeIsotropicElasticityTensor
youngs_modulus = 5E9
poissons_ratio = 0.0
[../]
[./strain]
type = ComputeSmallStrain
eigenstrain_names = 'thermal_contribution initial_stress'
[../]
[./thermal_contribution]
type = ComputeThermalExpansionEigenstrain
temperature = T
thermal_expansion_coeff = 5E-6 # this is the linear thermal expansion coefficient
eigenstrain_name = thermal_contribution
stress_free_temperature = 330
[../]
[./initial_strain]
type = ComputeEigenstrainFromInitialStress
initial_stress = '20E6 0 0 0 20E6 0 0 0 20E6'
eigenstrain_name = initial_stress
[../]
[./stress]
type = ComputeLinearElasticStress
[../]
[./effective_fluid_pressure]
type = PorousFlowEffectiveFluidPressure
[../]
[./volumetric_strain]
type = PorousFlowVolumetricStrain
[../]
[]
[Postprocessors]
[./effective_fluid_pressure_at_wellbore]
type = PointValue
variable = effective_fluid_pressure
point = '1 0 0'
execute_on = timestep_begin
use_displaced_mesh = false
[../]
[./constrained_effective_fluid_pressure_at_wellbore]
type = FunctionValuePostprocessor
function = constrain_effective_fluid_pressure
execute_on = timestep_begin
[../]
[]
[Functions]
[./constrain_effective_fluid_pressure]
type = ParsedFunction
vars = effective_fluid_pressure_at_wellbore
vals = effective_fluid_pressure_at_wellbore
value = 'max(effective_fluid_pressure_at_wellbore, 20E6)'
[../]
[]
[Preconditioning]
active = basic
[./basic]
type = SMP
full = true
petsc_options = '-ksp_diagonal_scale -ksp_diagonal_scale_fix'
petsc_options_iname = '-pc_type -sub_pc_type -sub_pc_factor_shift_type -pc_asm_overlap'
petsc_options_value = ' asm lu NONZERO 2'
[../]
[./preferred_but_might_not_be_installed]
type = SMP
full = true
petsc_options_iname = '-pc_type -pc_factor_mat_solver_package'
petsc_options_value = ' lu mumps'
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
end_time = 1E3
[./TimeStepper]
type = IterationAdaptiveDT
dt = 1E3
growth_factor = 1.2
optimal_iterations = 10
[../]
nl_abs_tol = 1E-7
[]
[Outputs]
exodus = true
[]
modules/combined/test/tests/poro_mechanics/borehole_lowres.i
# Poroelastic response of a borehole.
#
# LOWRES VERSION: this version does not give perfect agreement with the analytical solution
#
# A fully-saturated medium contains a fluid with a homogeneous porepressure,
# but an anisitropic insitu stress. A infinitely-long borehole aligned with
# the $$z$$ axis is instanteously excavated. The borehole boundary is
# stress-free and allowed to freely drain. This problem is analysed using
# plane-strain conditions (no $$z$$ displacement).
#
# The solution in Laplace space is found in E Detournay and AHD Cheng "Poroelastic response of a borehole in a non-hydrostatic stress field". International Journal of Rock Mechanics and Mining Sciences and Geomechanics Abstracts 25 (1988) 171-182. In the small-time limit, the Laplace transforms may be performed. There is one typo in the paper. Equation (A4)'s final term should be -(a/r)\sqrt(4ct/(a^2\pi)), and not +(a/r)\sqrt(4ct/(a^2\pi)).
#
# Because realistic parameters are chosen (below),
# the residual for porepressure is much smaller than
# the residuals for the displacements. Therefore the
# scaling parameter is chosen. Also note that the
# insitu stresses are effective stresses, not total
# stresses, but the solution in the above paper is
# expressed in terms of total stresses.
#
# Here are the problem's parameters, and their values:
# Borehole radius. a = 1
# Rock's Lame lambda. la = 0.5E9
# Rock's Lame mu, which is also the Rock's shear modulus. mu = G = 1.5E9
# Rock bulk modulus. K = la + 2*mu/3 = 1.5E9
# Drained Poisson ratio. nu = (3K - 2G)/(6K + 2G) = 0.125
# Rock bulk compliance. 1/K = 0.66666666E-9
# Fluid bulk modulus. Kf = 0.7171315E9
# Fluid bulk compliance. 1/Kf = 1.39444444E-9
# Rock initial porosity. phi0 = 0.3
# Biot coefficient. alpha = 0.65
# Biot modulus. M = 1/(phi0/Kf + (alpha - phi0)(1 - alpha)/K) = 2E9
# Undrained bulk modulus. Ku = K + alpha^2*M = 2.345E9
# Undrained Poisson ratio. nuu = (3Ku - 2G)/(6Ku + 2G) = 0.2364
# Skempton coefficient. B = alpha*M/Ku = 0.554
# Fluid mobility (rock permeability/fluid viscosity). k = 1E-12
[Mesh]
type = FileMesh
file = borehole_lowres_input.e
[]
[GlobalParams]
displacements = 'disp_x disp_y disp_z'
porepressure = porepressure
block = 1
[]
[GlobalParams]
volumetric_locking_correction=true
[]
[Variables]
[./disp_x]
[../]
[./disp_y]
[../]
[./disp_z]
[../]
[./porepressure]
scaling = 1E9 # Notice the scaling, to make porepressure's kernels roughly of same magnitude as disp's kernels
[../]
[]
[ICs]
[./initial_p]
type = ConstantIC
variable = porepressure
value = 1E6
[../]
[]
[BCs]
[./fixed_outer_x]
type = DirichletBC
variable = disp_x
value = 0
boundary = outer
[../]
[./fixed_outer_y]
type = DirichletBC
variable = disp_y
value = 0
boundary = outer
[../]
[./plane_strain]
type = DirichletBC
variable = disp_z
value = 0
boundary = 'zmin zmax'
[../]
[./borehole_wall]
type = DirichletBC
variable = porepressure
value = 0
boundary = bh_wall
[../]
[]
[AuxVariables]
[./stress_yy]
order = CONSTANT
family = MONOMIAL
[../]
[./tot_yy]
order = CONSTANT
family = MONOMIAL
[../]
[]
[AuxKernels]
[./stress_yy]
type = RankTwoAux
rank_two_tensor = stress
variable = stress_yy
index_i = 1
index_j = 1
[../]
[./tot_yy]
type = ParsedAux
args = 'stress_yy porepressure'
execute_on = timestep_end
variable = tot_yy
function = 'stress_yy-0.65*porepressure'
[../]
[]
[Kernels]
[./grad_stress_x]
type = StressDivergenceTensors
variable = disp_x
component = 0
[../]
[./grad_stress_y]
type = StressDivergenceTensors
variable = disp_y
component = 1
[../]
[./grad_stress_z]
type = StressDivergenceTensors
variable = disp_z
component = 2
[../]
[./poro_x]
type = PoroMechanicsCoupling
variable = disp_x
component = 0
[../]
[./poro_y]
type = PoroMechanicsCoupling
variable = disp_y
component = 1
[../]
[./poro_z]
type = PoroMechanicsCoupling
variable = disp_z
component = 2
[../]
[./poro_timederiv]
type = PoroFullSatTimeDerivative
variable = porepressure
[../]
[./darcy_flow]
type = CoefDiffusion
variable = porepressure
coef = 1E-12
[../]
[]
[Materials]
[./elasticity_tensor]
type = ComputeElasticityTensor
C_ijkl = '0.5E9 1.5E9'
# bulk modulus is lambda + 2*mu/3 = 0.5 + 2*1.5/3 = 1.5E9
fill_method = symmetric_isotropic
[../]
[./strain]
type = ComputeFiniteStrain
displacements = 'disp_x disp_y disp_z'
eigenstrain_names = ini_stress
[../]
[./ini_stress]
type = ComputeEigenstrainFromInitialStress
initial_stress = '-1.35E6 0 0 0 -3.35E6 0 0 0 0' # remember this is the effective stress
eigenstrain_name = ini_stress
[../]
[./no_plasticity]
type = ComputeFiniteStrainElasticStress
[../]
[./poro_material]
type = PoroFullSatMaterial
porosity0 = 0.3
biot_coefficient = 0.65
solid_bulk_compliance = 0.6666666666667E-9
fluid_bulk_compliance = 1.3944444444444E-9
constant_porosity = false
[../]
[]
[Postprocessors]
[./p00]
type = PointValue
variable = porepressure
point = '1.00 0 0'
outputs = csv_p
[../]
[./p01]
type = PointValue
variable = porepressure
point = '1.01 0 0'
outputs = csv_p
[../]
[./p02]
type = PointValue
variable = porepressure
point = '1.02 0 0'
outputs = csv_p
[../]
[./p03]
type = PointValue
variable = porepressure
point = '1.03 0 0'
outputs = csv_p
[../]
[./p04]
type = PointValue
variable = porepressure
point = '1.04 0 0'
outputs = csv_p
[../]
[./p05]
type = PointValue
variable = porepressure
point = '1.05 0 0'
outputs = csv_p
[../]
[./p06]
type = PointValue
variable = porepressure
point = '1.06 0 0'
outputs = csv_p
[../]
[./p07]
type = PointValue
variable = porepressure
point = '1.07 0 0'
outputs = csv_p
[../]
[./p08]
type = PointValue
variable = porepressure
point = '1.08 0 0'
outputs = csv_p
[../]
[./p09]
type = PointValue
variable = porepressure
point = '1.09 0 0'
outputs = csv_p
[../]
[./p10]
type = PointValue
variable = porepressure
point = '1.10 0 0'
outputs = csv_p
[../]
[./p11]
type = PointValue
variable = porepressure
point = '1.11 0 0'
outputs = csv_p
[../]
[./p12]
type = PointValue
variable = porepressure
point = '1.12 0 0'
outputs = csv_p
[../]
[./p13]
type = PointValue
variable = porepressure
point = '1.13 0 0'
outputs = csv_p
[../]
[./p14]
type = PointValue
variable = porepressure
point = '1.14 0 0'
outputs = csv_p
[../]
[./p15]
type = PointValue
variable = porepressure
point = '1.15 0 0'
outputs = csv_p
[../]
[./p16]
type = PointValue
variable = porepressure
point = '1.16 0 0'
outputs = csv_p
[../]
[./p17]
type = PointValue
variable = porepressure
point = '1.17 0 0'
outputs = csv_p
[../]
[./p18]
type = PointValue
variable = porepressure
point = '1.18 0 0'
outputs = csv_p
[../]
[./p19]
type = PointValue
variable = porepressure
point = '1.19 0 0'
outputs = csv_p
[../]
[./p20]
type = PointValue
variable = porepressure
point = '1.20 0 0'
outputs = csv_p
[../]
[./p21]
type = PointValue
variable = porepressure
point = '1.21 0 0'
outputs = csv_p
[../]
[./p22]
type = PointValue
variable = porepressure
point = '1.22 0 0'
outputs = csv_p
[../]
[./p23]
type = PointValue
variable = porepressure
point = '1.23 0 0'
outputs = csv_p
[../]
[./p24]
type = PointValue
variable = porepressure
point = '1.24 0 0'
outputs = csv_p
[../]
[./p25]
type = PointValue
variable = porepressure
point = '1.25 0 0'
outputs = csv_p
[../]
[./s00]
type = PointValue
variable = disp_x
point = '1.00 0 0'
outputs = csv_s
[../]
[./s01]
type = PointValue
variable = disp_x
point = '1.01 0 0'
outputs = csv_s
[../]
[./s02]
type = PointValue
variable = disp_x
point = '1.02 0 0'
outputs = csv_s
[../]
[./s03]
type = PointValue
variable = disp_x
point = '1.03 0 0'
outputs = csv_s
[../]
[./s04]
type = PointValue
variable = disp_x
point = '1.04 0 0'
outputs = csv_s
[../]
[./s05]
type = PointValue
variable = disp_x
point = '1.05 0 0'
outputs = csv_s
[../]
[./s06]
type = PointValue
variable = disp_x
point = '1.06 0 0'
outputs = csv_s
[../]
[./s07]
type = PointValue
variable = disp_x
point = '1.07 0 0'
outputs = csv_s
[../]
[./s08]
type = PointValue
variable = disp_x
point = '1.08 0 0'
outputs = csv_s
[../]
[./s09]
type = PointValue
variable = disp_x
point = '1.09 0 0'
outputs = csv_s
[../]
[./s10]
type = PointValue
variable = disp_x
point = '1.10 0 0'
outputs = csv_s
[../]
[./s11]
type = PointValue
variable = disp_x
point = '1.11 0 0'
outputs = csv_s
[../]
[./s12]
type = PointValue
variable = disp_x
point = '1.12 0 0'
outputs = csv_s
[../]
[./s13]
type = PointValue
variable = disp_x
point = '1.13 0 0'
outputs = csv_s
[../]
[./s14]
type = PointValue
variable = disp_x
point = '1.14 0 0'
outputs = csv_s
[../]
[./s15]
type = PointValue
variable = disp_x
point = '1.15 0 0'
outputs = csv_s
[../]
[./s16]
type = PointValue
variable = disp_x
point = '1.16 0 0'
outputs = csv_s
[../]
[./s17]
type = PointValue
variable = disp_x
point = '1.17 0 0'
outputs = csv_s
[../]
[./s18]
type = PointValue
variable = disp_x
point = '1.18 0 0'
outputs = csv_s
[../]
[./s19]
type = PointValue
variable = disp_x
point = '1.19 0 0'
outputs = csv_s
[../]
[./s20]
type = PointValue
variable = disp_x
point = '1.20 0 0'
outputs = csv_s
[../]
[./s21]
type = PointValue
variable = disp_x
point = '1.21 0 0'
outputs = csv_s
[../]
[./s22]
type = PointValue
variable = disp_x
point = '1.22 0 0'
outputs = csv_s
[../]
[./s23]
type = PointValue
variable = disp_x
point = '1.23 0 0'
outputs = csv_s
[../]
[./s24]
type = PointValue
variable = disp_x
point = '1.24 0 0'
outputs = csv_s
[../]
[./s25]
type = PointValue
variable = disp_x
point = '1.25 0 0'
outputs = csv_s
[../]
[./t00]
type = PointValue
variable = tot_yy
point = '1.00 0 0'
outputs = csv_t
[../]
[./t01]
type = PointValue
variable = tot_yy
point = '1.01 0 0'
outputs = csv_t
[../]
[./t02]
type = PointValue
variable = tot_yy
point = '1.02 0 0'
outputs = csv_t
[../]
[./t03]
type = PointValue
variable = tot_yy
point = '1.03 0 0'
outputs = csv_t
[../]
[./t04]
type = PointValue
variable = tot_yy
point = '1.04 0 0'
outputs = csv_t
[../]
[./t05]
type = PointValue
variable = tot_yy
point = '1.05 0 0'
outputs = csv_t
[../]
[./t06]
type = PointValue
variable = tot_yy
point = '1.06 0 0'
outputs = csv_t
[../]
[./t07]
type = PointValue
variable = tot_yy
point = '1.07 0 0'
outputs = csv_t
[../]
[./t08]
type = PointValue
variable = tot_yy
point = '1.08 0 0'
outputs = csv_t
[../]
[./t09]
type = PointValue
variable = tot_yy
point = '1.09 0 0'
outputs = csv_t
[../]
[./t10]
type = PointValue
variable = tot_yy
point = '1.10 0 0'
outputs = csv_t
[../]
[./t11]
type = PointValue
variable = tot_yy
point = '1.11 0 0'
outputs = csv_t
[../]
[./t12]
type = PointValue
variable = tot_yy
point = '1.12 0 0'
outputs = csv_t
[../]
[./t13]
type = PointValue
variable = tot_yy
point = '1.13 0 0'
outputs = csv_t
[../]
[./t14]
type = PointValue
variable = tot_yy
point = '1.14 0 0'
outputs = csv_t
[../]
[./t15]
type = PointValue
variable = tot_yy
point = '1.15 0 0'
outputs = csv_t
[../]
[./t16]
type = PointValue
variable = tot_yy
point = '1.16 0 0'
outputs = csv_t
[../]
[./t17]
type = PointValue
variable = tot_yy
point = '1.17 0 0'
outputs = csv_t
[../]
[./t18]
type = PointValue
variable = tot_yy
point = '1.18 0 0'
outputs = csv_t
[../]
[./t19]
type = PointValue
variable = tot_yy
point = '1.19 0 0'
outputs = csv_t
[../]
[./t20]
type = PointValue
variable = tot_yy
point = '1.20 0 0'
outputs = csv_t
[../]
[./t21]
type = PointValue
variable = tot_yy
point = '1.21 0 0'
outputs = csv_t
[../]
[./t22]
type = PointValue
variable = tot_yy
point = '1.22 0 0'
outputs = csv_t
[../]
[./t23]
type = PointValue
variable = tot_yy
point = '1.23 0 0'
outputs = csv_t
[../]
[./t24]
type = PointValue
variable = tot_yy
point = '1.24 0 0'
outputs = csv_t
[../]
[./t25]
type = PointValue
variable = tot_yy
point = '1.25 0 0'
outputs = csv_t
[../]
[./dt]
type = FunctionValuePostprocessor
outputs = console
function = 2*t
[../]
[]
[Preconditioning]
[./andy]
type = SMP
full = true
petsc_options = '-snes_monitor -snes_linesearch_monitor'
petsc_options_iname = '-ksp_type -pc_type -snes_atol -snes_rtol -snes_max_it -ksp_max_it -sub_pc_type -sub_pc_factor_shift_type'
petsc_options_value = 'gmres asm 1E0 1E-10 200 500 lu NONZERO'
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
start_time = 0
end_time = 0.3
dt = 0.3
#[./TimeStepper]
# type = PostprocessorDT
# postprocessor = dt
# dt = 0.003
#[../]
[]
[Outputs]
execute_on = 'timestep_end'
file_base = borehole_lowres
exodus = true
sync_times = '0.003 0.3'
[./csv_p]
file_base = borehole_lowres_p
type = CSV
[../]
[./csv_s]
file_base = borehole_lowres_s
type = CSV
[../]
[./csv_t]
file_base = borehole_lowres_t
type = CSV
[../]
[]
test/tests/auxkernels/parsed_aux/parsed_aux_test.i
[Mesh]
type = GeneratedMesh
dim = 2
xmin = 0
xmax = 1
ymin = 0
ymax = 1
nx = 10
ny = 10
[]
[Variables]
[./u]
order = FIRST
family = LAGRANGE
[../]
[./v]
order = FIRST
family = LAGRANGE
[../]
[]
[AuxVariables]
[./parsed]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
[./diff_u]
type = Diffusion
variable = u
[../]
[./diff_v]
type = Diffusion
variable = v
[../]
[]
[BCs]
[./left_u]
type = DirichletBC
variable = u
boundary = 2
value = 0
[../]
[./right_u]
type = DirichletBC
variable = u
boundary = 0
value = 1
[../]
[./left_v]
type = DirichletBC
variable = v
boundary = 3
value = 0
[../]
[./right_v]
type = DirichletBC
variable = v
boundary = 1
value = 1
[../]
[]
[Bounds]
[./u_bounds]
type = ParsedAux
variable = parsed
args = 'u v'
function = '(u-0.5)^3*v'
[../]
[]
[Executioner]
type = Steady
solve_type = 'PJFNK'
[]
[Outputs]
file_base = out
exodus = true
[]
modules/functional_expansion_tools/examples/3D_volumetric_cylindrical/sub.i
# Basic example coupling a master and sub app in a 3D cylindrical mesh from an input file
#
# The master app provides field values to the sub app via Functional Expansions, which then performs
# its calculations. The sub app's solution field values are then transferred back to the master app
# and coupled into the solution of the master app solution.
#
# This example couples Functional Expansions via AuxVariable, the recommended approach.
#
# Note: this problem is not light, and may take a few minutes to solve.
[Mesh]
type = FileMesh
file = cyl-tet.e
[]
# Non-copy transfers only work with AuxVariable, but nothing will be solved without a variable
# defined. The solution is to define an empty variable tha does nothing, but causes MOOSE to solve
# the AuxKernels that we need.
[Variables]
[./empty]
[../]
[]
[AuxVariables]
[./s]
order = FIRST
family = LAGRANGE
[../]
[./m_in]
order = FIRST
family = LAGRANGE
[../]
[]
# We must have a kernel for every variable, hence this null kernel to match the variable 'empty'
[Kernels]
[./null_kernel]
type = NullKernel
variable = empty
[../]
[]
[AuxKernels]
[./reconstruct_m_in]
type = FunctionSeriesToAux
function = FX_Basis_Value_Sub
variable = m_in
[../]
[./calculate_s] # Something to make 's' change each time, but allow a converging solution
type = ParsedAux
variable = s
args = m_in
function = '2*exp(-m_in/0.8)'
[../]
[]
[Functions]
[./FX_Basis_Value_Sub]
type = FunctionSeries
series_type = CylindricalDuo
orders = '5 3' # Axial first, then (r, t) FX
physical_bounds = '-2.5 2.5 0 0 1' # z_min z_max x_center y_center radius
z = Legendre # Axial in z
disc = Zernike # (r, t) default to unit disc in x-y plane
[../]
[]
[UserObjects]
[./FX_Value_UserObject_Sub]
type = FXVolumeUserObject
function = FX_Basis_Value_Sub
variable = s
[../]
[]
[Executioner]
type = Transient
num_steps = 10
dt = 0.5
solve_type = PJFNK
petsc_options_iname = '-pc_type -pc_hypre_type'
petsc_options_value = 'hypre boomeramg'
[]
modules/functional_expansion_tools/examples/3D_volumetric_cylindrical_subapp_mesh_refine/sub.i
# Derived from the example '3D_volumetric_cylindrical' with the following differences:
#
# 1) The model mesh is refined in the MasterApp by 1
# 2) Mesh adaptivity is enabled for the SubApp
# 3) Output from the SubApp is enabled so that the mesh changes can be visualized
[Mesh]
type = FileMesh
file = cyl-tet.e
[]
[Adaptivity]
marker = errorfrac
steps = 2
[./Indicators]
[./error]
type = GradientJumpIndicator
variable = s
outputs = none
[../]
[../]
[./Markers]
[./errorfrac]
type = ErrorFractionMarker
refine = 0.4
coarsen = 0.1
indicator = error
outputs = none
[../]
[../]
[]
# Non-copy transfers only work with AuxVariable, but nothing will be solved without a variable
# defined. The solution is to define an empty variable tha does nothing, but causes MOOSE to solve
# the AuxKernels that we need.
[Variables]
[./empty]
[../]
[]
[AuxVariables]
[./s]
order = FIRST
family = LAGRANGE
[../]
[./m_in]
order = FIRST
family = LAGRANGE
[../]
[]
# We must have a kernel for every variable, hence this null kernel to match the variable 'empty'
[Kernels]
[./null_kernel]
type = NullKernel
variable = empty
[../]
[]
[AuxKernels]
[./reconstruct_m_in]
type = FunctionSeriesToAux
function = FX_Basis_Value_Sub
variable = m_in
[../]
[./calculate_s] # Something to make 's' change each time, but allow a converging solution
type = ParsedAux
variable = s
args = m_in
function = '2*exp(-m_in/0.8)'
[../]
[]
[Functions]
[./FX_Basis_Value_Sub]
type = FunctionSeries
series_type = CylindricalDuo
orders = '5 3' # Axial first, then (r, t) FX
physical_bounds = '-2.5 2.5 0 0 1' # z_min z_max x_center y_center radius
z = Legendre # Axial in z
disc = Zernike # (r, t) default to unit disc in x-y plane
[../]
[]
[UserObjects]
[./FX_Value_UserObject_Sub]
type = FXVolumeUserObject
function = FX_Basis_Value_Sub
variable = s
[../]
[]
[Executioner]
type = Transient
num_steps = 10
dt = 0.5
solve_type = PJFNK
petsc_options_iname = '-pc_type -pc_hypre_type'
petsc_options_value = 'hypre boomeramg'
[]
[Outputs]
exodus = true
file_base = sub
[]
modules/porous_flow/test/tests/poro_elasticity/mandel_constM.i
# Mandel's problem of consolodation of a drained medium
#
# A sample is in plane strain.
# -a <= x <= a
# -b <= y <= b
# It is squashed with constant force by impermeable, frictionless plattens on its top and bottom surfaces (at y=+/-b)
# Fluid is allowed to leak out from its sides (at x=+/-a)
# The porepressure within the sample is monitored.
#
# As is common in the literature, this is simulated by
# considering the quarter-sample, 0<=x<=a and 0<=y<=b, with
# impermeable, roller BCs at x=0 and y=0 and y=b.
# Porepressure is fixed at zero on x=a.
# Porepressure and displacement are initialised to zero.
# Then the top (y=b) is moved downwards with prescribed velocity,
# so that the total force that is inducing this downwards velocity
# is fixed. The velocity is worked out by solving Mandel's problem
# analytically, and the total force is monitored in the simulation
# to check that it indeed remains constant.
#
# Here are the problem's parameters, and their values:
# Soil width. a = 1
# Soil height. b = 0.1
# Soil's Lame lambda. la = 0.5
# Soil's Lame mu, which is also the Soil's shear modulus. mu = G = 0.75
# Soil bulk modulus. K = la + 2*mu/3 = 1
# Drained Poisson ratio. nu = (3K - 2G)/(6K + 2G) = 0.2
# Soil bulk compliance. 1/K = 1
# Fluid bulk modulus. Kf = 8
# Fluid bulk compliance. 1/Kf = 0.125
# Soil initial porosity. phi0 = 0.1
# Biot coefficient. alpha = 0.6
# Biot modulus. M = 1/(phi0/Kf + (alpha - phi0)(1 - alpha)/K) = 4.705882
# Undrained bulk modulus. Ku = K + alpha^2*M = 2.694118
# Undrained Poisson ratio. nuu = (3Ku - 2G)/(6Ku + 2G) = 0.372627
# Skempton coefficient. B = alpha*M/Ku = 1.048035
# Fluid mobility (soil permeability/fluid viscosity). k = 1.5
# Consolidation coefficient. c = 2*k*B^2*G*(1-nu)*(1+nuu)^2/9/(1-nuu)/(nuu-nu) = 3.821656
# Normal stress on top. F = 1
#
# The solution for porepressure and displacements is given in
# AHD Cheng and E Detournay "A direct boundary element method for plane strain poroelasticity" International Journal of Numerical and Analytical Methods in Geomechanics 12 (1988) 551-572.
# The solution involves complicated infinite series, so I shall not write it here
[Mesh]
type = GeneratedMesh
dim = 3
nx = 10
ny = 1
nz = 1
xmin = 0
xmax = 1
ymin = 0
ymax = 0.1
zmin = 0
zmax = 1
[]
[GlobalParams]
displacements = 'disp_x disp_y disp_z'
PorousFlowDictator = dictator
block = 0
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = 'porepressure disp_x disp_y disp_z'
number_fluid_phases = 1
number_fluid_components = 1
[../]
[./pc]
type = PorousFlowCapillaryPressureVG
m = 0.8
alpha = 1e-5
[../]
[]
[Variables]
[./disp_x]
[../]
[./disp_y]
[../]
[./disp_z]
[../]
[./porepressure]
[../]
[]
[BCs]
[./roller_xmin]
type = DirichletBC
variable = disp_x
value = 0
boundary = 'left'
[../]
[./roller_ymin]
type = DirichletBC
variable = disp_y
value = 0
boundary = 'bottom'
[../]
[./plane_strain]
type = DirichletBC
variable = disp_z
value = 0
boundary = 'back front'
[../]
[./xmax_drained]
type = DirichletBC
variable = porepressure
value = 0
boundary = right
[../]
[./top_velocity]
type = FunctionDirichletBC
variable = disp_y
function = top_velocity
boundary = top
[../]
[]
[Functions]
[./top_velocity]
type = PiecewiseLinear
x = '0 0.002 0.006 0.014 0.03 0.046 0.062 0.078 0.094 0.11 0.126 0.142 0.158 0.174 0.19 0.206 0.222 0.238 0.254 0.27 0.286 0.302 0.318 0.334 0.35 0.366 0.382 0.398 0.414 0.43 0.446 0.462 0.478 0.494 0.51 0.526 0.542 0.558 0.574 0.59 0.606 0.622 0.638 0.654 0.67 0.686 0.702'
y = '-0.041824842 -0.042730269 -0.043412712 -0.04428867 -0.045509181 -0.04645965 -0.047268246 -0.047974749 -0.048597109 -0.0491467 -0.049632388 -0.050061697 -0.050441198 -0.050776675 -0.051073238 -0.0513354 -0.051567152 -0.051772022 -0.051953128 -0.052113227 -0.052254754 -0.052379865 -0.052490464 -0.052588233 -0.052674662 -0.052751065 -0.052818606 -0.052878312 -0.052931093 -0.052977751 -0.053018997 -0.053055459 -0.053087691 -0.053116185 -0.053141373 -0.05316364 -0.053183324 -0.053200724 -0.053216106 -0.053229704 -0.053241725 -0.053252351 -0.053261745 -0.053270049 -0.053277389 -0.053283879 -0.053289615'
[../]
[]
[AuxVariables]
[./stress_yy]
order = CONSTANT
family = MONOMIAL
[../]
[./tot_force]
order = CONSTANT
family = MONOMIAL
[../]
[]
[AuxKernels]
[./stress_yy]
type = RankTwoAux
rank_two_tensor = stress
variable = stress_yy
index_i = 1
index_j = 1
[../]
[./tot_force]
type = ParsedAux
args = 'stress_yy porepressure'
execute_on = timestep_end
variable = tot_force
function = '-stress_yy+0.6*porepressure'
[../]
[]
[Kernels]
[./grad_stress_x]
type = StressDivergenceTensors
variable = disp_x
component = 0
[../]
[./grad_stress_y]
type = StressDivergenceTensors
variable = disp_y
component = 1
[../]
[./grad_stress_z]
type = StressDivergenceTensors
variable = disp_z
component = 2
[../]
[./poro_x]
type = PorousFlowEffectiveStressCoupling
biot_coefficient = 0.6
variable = disp_x
component = 0
[../]
[./poro_y]
type = PorousFlowEffectiveStressCoupling
biot_coefficient = 0.6
variable = disp_y
component = 1
[../]
[./poro_z]
type = PorousFlowEffectiveStressCoupling
biot_coefficient = 0.6
component = 2
variable = disp_z
[../]
[./poro_vol_exp]
type = PorousFlowMassVolumetricExpansion
variable = porepressure
fluid_component = 0
[../]
[./mass0]
type = PorousFlowMassTimeDerivative
fluid_component = 0
variable = porepressure
[../]
[./flux]
type = PorousFlowAdvectiveFlux
variable = porepressure
gravity = '0 0 0'
fluid_component = 0
[../]
[]
[Modules]
[./FluidProperties]
[./simple_fluid]
type = SimpleFluidProperties
bulk_modulus = 8
density0 = 1
thermal_expansion = 0
viscosity = 1
[../]
[../]
[]
[Materials]
[./temperature]
type = PorousFlowTemperature
[../]
[./elasticity_tensor]
type = ComputeElasticityTensor
C_ijkl = '0.5 0.75'
# bulk modulus is lambda + 2*mu/3 = 0.5 + 2*0.75/3 = 1
fill_method = symmetric_isotropic
[../]
[./strain]
type = ComputeSmallStrain
[../]
[./stress]
type = ComputeLinearElasticStress
[../]
[./eff_fluid_pressure]
type = PorousFlowEffectiveFluidPressure
[../]
[./vol_strain]
type = PorousFlowVolumetricStrain
[../]
[./ppss]
type = PorousFlow1PhaseP
porepressure = porepressure
capillary_pressure = pc
[../]
[./massfrac]
type = PorousFlowMassFraction
[../]
[./simple_fluid]
type = PorousFlowSingleComponentFluid
fp = simple_fluid
phase = 0
[../]
[./porosity]
type = PorousFlowPorosityHMBiotModulus
porosity_zero = 0.1
biot_coefficient = 0.6
solid_bulk = 1
constant_fluid_bulk_modulus = 8
constant_biot_modulus = 4.7058823529
[../]
[./permeability]
type = PorousFlowPermeabilityConst
permeability = '1.5 0 0 0 1.5 0 0 0 1.5'
[../]
[./relperm]
type = PorousFlowRelativePermeabilityCorey
n = 0 # unimportant in this fully-saturated situation
phase = 0
[../]
[]
[Postprocessors]
[./p0]
type = PointValue
outputs = csv
point = '0.0 0 0'
variable = porepressure
[../]
[./p1]
type = PointValue
outputs = csv
point = '0.1 0 0'
variable = porepressure
[../]
[./p2]
type = PointValue
outputs = csv
point = '0.2 0 0'
variable = porepressure
[../]
[./p3]
type = PointValue
outputs = csv
point = '0.3 0 0'
variable = porepressure
[../]
[./p4]
type = PointValue
outputs = csv
point = '0.4 0 0'
variable = porepressure
[../]
[./p5]
type = PointValue
outputs = csv
point = '0.5 0 0'
variable = porepressure
[../]
[./p6]
type = PointValue
outputs = csv
point = '0.6 0 0'
variable = porepressure
[../]
[./p7]
type = PointValue
outputs = csv
point = '0.7 0 0'
variable = porepressure
[../]
[./p8]
type = PointValue
outputs = csv
point = '0.8 0 0'
variable = porepressure
[../]
[./p9]
type = PointValue
outputs = csv
point = '0.9 0 0'
variable = porepressure
[../]
[./p99]
type = PointValue
outputs = csv
point = '1 0 0'
variable = porepressure
[../]
[./xdisp]
type = PointValue
outputs = csv
point = '1 0.1 0'
variable = disp_x
[../]
[./ydisp]
type = PointValue
outputs = csv
point = '1 0.1 0'
variable = disp_y
[../]
[./total_downwards_force]
type = ElementAverageValue
outputs = csv
variable = tot_force
[../]
[./dt]
type = FunctionValuePostprocessor
outputs = console
function = if(0.15*t<0.01,0.15*t,0.01)
[../]
[]
[Preconditioning]
[./andy]
type = SMP
full = true
petsc_options_iname = '-ksp_type -pc_type -sub_pc_type -snes_atol -snes_rtol -snes_max_it'
petsc_options_value = 'gmres asm lu 1E-14 1E-10 10000'
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
start_time = 0
end_time = 0.7
[./TimeStepper]
type = PostprocessorDT
postprocessor = dt
dt = 0.001
[../]
[]
[Outputs]
execute_on = 'timestep_end'
file_base = mandel_constM
[./csv]
interval = 3
type = CSV
[../]
[]
modules/porous_flow/examples/tutorial/11_2D.i
# Two-phase borehole injection problem in RZ coordinates
[Mesh]
[gen]
type = GeneratedMeshGenerator
dim = 2
nx = 10
xmin = 1.0
xmax = 10
bias_x = 1.4
ny = 3
ymin = -6
ymax = 6
[]
[./aquifer]
input = gen
type = SubdomainBoundingBoxGenerator
block_id = 1
bottom_left = '0 -2 0'
top_right = '10 2 0'
[../]
[./injection_area]
type = ParsedGenerateSideset
combinatorial_geometry = 'x<1.0001'
included_subdomain_ids = 1
new_sideset_name = 'injection_area'
input = 'aquifer'
[../]
[./rename]
type = RenameBlockGenerator
old_block_id = '0 1'
new_block_name = 'caps aquifer'
input = 'injection_area'
[../]
[]
[Problem]
coord_type = RZ
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = 'pwater pgas T disp_r'
number_fluid_phases = 2
number_fluid_components = 2
[../]
[./pc]
type = PorousFlowCapillaryPressureVG
alpha = 1E-6
m = 0.6
[../]
[]
[GlobalParams]
displacements = 'disp_r disp_z'
gravity = '0 0 0'
biot_coefficient = 1.0
PorousFlowDictator = dictator
[]
[Variables]
[./pwater]
initial_condition = 20E6
[../]
[./pgas]
initial_condition = 20.1E6
[../]
[./T]
initial_condition = 330
scaling = 1E-5
[../]
[./disp_r]
scaling = 1E-5
[../]
[]
[Kernels]
[./mass_water_dot]
type = PorousFlowMassTimeDerivative
fluid_component = 0
use_displaced_mesh = false
variable = pwater
[../]
[./flux_water]
type = PorousFlowAdvectiveFlux
fluid_component = 0
use_displaced_mesh = false
variable = pwater
[../]
[./vol_strain_rate_water]
type = PorousFlowMassVolumetricExpansion
fluid_component = 0
use_displaced_mesh = false
variable = pwater
[../]
[./mass_co2_dot]
type = PorousFlowMassTimeDerivative
fluid_component = 1
use_displaced_mesh = false
variable = pgas
[../]
[./flux_co2]
type = PorousFlowAdvectiveFlux
fluid_component = 1
use_displaced_mesh = false
variable = pgas
[../]
[./vol_strain_rate_co2]
type = PorousFlowMassVolumetricExpansion
fluid_component = 1
use_displaced_mesh = false
variable = pgas
[../]
[./energy_dot]
type = PorousFlowEnergyTimeDerivative
use_displaced_mesh = false
variable = T
[../]
[./advection]
type = PorousFlowHeatAdvection
use_displaced_mesh = false
variable = T
[../]
[./conduction]
type = PorousFlowHeatConduction
use_displaced_mesh = false
variable = T
[../]
[./vol_strain_rate_heat]
type = PorousFlowHeatVolumetricExpansion
use_displaced_mesh = false
variable = T
[../]
[./grad_stress_r]
type = StressDivergenceRZTensors
temperature = T
variable = disp_r
thermal_eigenstrain_name = thermal_contribution
use_displaced_mesh = false
component = 0
[../]
[./poro_r]
type = PorousFlowEffectiveStressCoupling
variable = disp_r
use_displaced_mesh = false
component = 0
[../]
[]
[AuxVariables]
[./disp_z]
[../]
[./effective_fluid_pressure]
family = MONOMIAL
order = CONSTANT
[../]
[./mass_frac_phase0_species0]
initial_condition = 1 # all water in phase=0
[../]
[./mass_frac_phase1_species0]
initial_condition = 0 # no water in phase=1
[../]
[./sgas]
family = MONOMIAL
order = CONSTANT
[../]
[./swater]
family = MONOMIAL
order = CONSTANT
[../]
[./stress_rr]
family = MONOMIAL
order = CONSTANT
[../]
[./stress_tt]
family = MONOMIAL
order = CONSTANT
[../]
[./stress_zz]
family = MONOMIAL
order = CONSTANT
[../]
[./porosity]
family = MONOMIAL
order = CONSTANT
[../]
[]
[AuxKernels]
[./effective_fluid_pressure]
type = ParsedAux
args = 'pwater pgas swater sgas'
function = 'pwater * swater + pgas * sgas'
variable = effective_fluid_pressure
[../]
[./swater]
type = PorousFlowPropertyAux
variable = swater
property = saturation
phase = 0
execute_on = timestep_end
[../]
[./sgas]
type = PorousFlowPropertyAux
variable = sgas
property = saturation
phase = 1
execute_on = timestep_end
[../]
[./stress_rr_aux]
type = RankTwoAux
variable = stress_rr
rank_two_tensor = stress
index_i = 0
index_j = 0
[../]
[./stress_tt]
type = RankTwoAux
rank_two_tensor = stress
variable = stress_tt
index_i = 2
index_j = 2
[../]
[./stress_zz]
type = RankTwoAux
rank_two_tensor = stress
variable = stress_zz
index_i = 1
index_j = 1
[../]
[./porosity]
type = PorousFlowPropertyAux
variable = porosity
property = porosity
execute_on = timestep_end
[../]
[]
[BCs]
[./pinned_top_bottom_r]
type = DirichletBC
variable = disp_r
value = 0
boundary = 'top bottom'
[../]
[./cavity_pressure_r]
type = Pressure
boundary = injection_area
variable = disp_r
component = 0
postprocessor = constrained_effective_fluid_pressure_at_wellbore
use_displaced_mesh = false
[../]
[./cold_co2]
type = DirichletBC
boundary = injection_area
variable = T
value = 290 # injection temperature
use_displaced_mesh = false
[../]
[./constant_co2_injection]
type = PorousFlowSink
boundary = injection_area
variable = pgas
fluid_phase = 1
flux_function = -1E-4
use_displaced_mesh = false
[../]
[./outer_water_removal]
type = PorousFlowPiecewiseLinearSink
boundary = right
variable = pwater
fluid_phase = 0
pt_vals = '0 1E9'
multipliers = '0 1E8'
PT_shift = 20E6
use_mobility = true
use_relperm = true
use_displaced_mesh = false
[../]
[./outer_co2_removal]
type = PorousFlowPiecewiseLinearSink
boundary = right
variable = pgas
fluid_phase = 1
pt_vals = '0 1E9'
multipliers = '0 1E8'
PT_shift = 20.1E6
use_mobility = true
use_relperm = true
use_displaced_mesh = false
[../]
[]
[Modules]
[./FluidProperties]
[./true_water]
type = Water97FluidProperties
[../]
[./tabulated_water]
type = TabulatedFluidProperties
fp = true_water
temperature_min = 275
pressure_max = 1E8
fluid_property_file = water97_tabulated_11.csv
[../]
[./true_co2]
type = CO2FluidProperties
[../]
[./tabulated_co2]
type = TabulatedFluidProperties
fp = true_co2
temperature_min = 275
pressure_max = 1E8
fluid_property_file = co2_tabulated_11.csv
[../]
[../]
[]
[Materials]
[./temperature]
type = PorousFlowTemperature
temperature = T
[../]
[./saturation_calculator]
type = PorousFlow2PhasePP
phase0_porepressure = pwater
phase1_porepressure = pgas
capillary_pressure = pc
[../]
[./massfrac]
type = PorousFlowMassFraction
mass_fraction_vars = 'mass_frac_phase0_species0 mass_frac_phase1_species0'
[../]
[./water]
type = PorousFlowSingleComponentFluid
fp = tabulated_water
phase = 0
[../]
[./co2]
type = PorousFlowSingleComponentFluid
fp = tabulated_co2
phase = 1
[../]
[./relperm_water]
type = PorousFlowRelativePermeabilityCorey
n = 4
s_res = 0.1
sum_s_res = 0.2
phase = 0
[../]
[./relperm_co2]
type = PorousFlowRelativePermeabilityBC
nw_phase = true
lambda = 2
s_res = 0.1
sum_s_res = 0.2
phase = 1
[../]
[./porosity]
type = PorousFlowPorosity
fluid = true
mechanical = true
thermal = true
porosity_zero = 0.1
reference_temperature = 330
reference_porepressure = 20E6
thermal_expansion_coeff = 15E-6 # volumetric
solid_bulk = 8E9 # unimportant since biot = 1
[../]
[./permeability_aquifer]
type = PorousFlowPermeabilityKozenyCarman
block = aquifer
poroperm_function = kozeny_carman_phi0
phi0 = 0.1
n = 2
m = 2
k0 = 1E-12
[../]
[./permeability_caps]
type = PorousFlowPermeabilityKozenyCarman
block = caps
poroperm_function = kozeny_carman_phi0
phi0 = 0.1
n = 2
m = 2
k0 = 1E-15
k_anisotropy = '1 0 0 0 1 0 0 0 0.1'
[../]
[./rock_thermal_conductivity]
type = PorousFlowThermalConductivityIdeal
dry_thermal_conductivity = '2 0 0 0 2 0 0 0 2'
[../]
[./rock_internal_energy]
type = PorousFlowMatrixInternalEnergy
specific_heat_capacity = 1100
density = 2300
[../]
[./elasticity_tensor]
type = ComputeIsotropicElasticityTensor
youngs_modulus = 5E9
poissons_ratio = 0.0
[../]
[./strain]
type = ComputeAxisymmetricRZSmallStrain
eigenstrain_names = 'thermal_contribution initial_stress'
[../]
[./thermal_contribution]
type = ComputeThermalExpansionEigenstrain
temperature = T
thermal_expansion_coeff = 5E-6 # this is the linear thermal expansion coefficient
eigenstrain_name = thermal_contribution
stress_free_temperature = 330
[../]
[./initial_strain]
type = ComputeEigenstrainFromInitialStress
initial_stress = '20E6 0 0 0 20E6 0 0 0 20E6'
eigenstrain_name = initial_stress
[../]
[./stress]
type = ComputeLinearElasticStress
[../]
[./effective_fluid_pressure]
type = PorousFlowEffectiveFluidPressure
[../]
[./volumetric_strain]
type = PorousFlowVolumetricStrain
[../]
[]
[Postprocessors]
[./effective_fluid_pressure_at_wellbore]
type = PointValue
variable = effective_fluid_pressure
point = '1 0 0'
execute_on = timestep_begin
use_displaced_mesh = false
[../]
[./constrained_effective_fluid_pressure_at_wellbore]
type = FunctionValuePostprocessor
function = constrain_effective_fluid_pressure
execute_on = timestep_begin
[../]
[]
[Functions]
[./constrain_effective_fluid_pressure]
type = ParsedFunction
vars = effective_fluid_pressure_at_wellbore
vals = effective_fluid_pressure_at_wellbore
value = 'max(effective_fluid_pressure_at_wellbore, 20E6)'
[../]
[]
[Preconditioning]
active = basic
[./basic]
type = SMP
full = true
petsc_options = '-ksp_diagonal_scale -ksp_diagonal_scale_fix'
petsc_options_iname = '-pc_type -sub_pc_type -sub_pc_factor_shift_type -pc_asm_overlap'
petsc_options_value = ' asm lu NONZERO 2'
[../]
[./preferred_but_might_not_be_installed]
type = SMP
full = true
petsc_options_iname = '-pc_type -pc_factor_mat_solver_package'
petsc_options_value = ' lu mumps'
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
end_time = 1E3
[./TimeStepper]
type = IterationAdaptiveDT
dt = 1E3
growth_factor = 1.2
optimal_iterations = 10
[../]
nl_abs_tol = 1E-7
[]
[Outputs]
exodus = true
[]
modules/combined/examples/phase_field-mechanics/kks_mechanics_VTS.i
# KKS phase-field model coupled with elasticity using the Voigt-Taylor scheme as
# described in L.K. Aagesen et al., Computational Materials Science, 140, 10-21 (2017)
# Original run #170329e
[Mesh]
type = GeneratedMesh
dim = 3
nx = 640
ny = 1
nz = 1
xmin = -10
xmax = 10
ymin = 0
ymax = 0.03125
zmin = 0
zmax = 0.03125
elem_type = HEX8
[]
[Variables]
# order parameter
[./eta]
order = FIRST
family = LAGRANGE
[../]
# solute concentration
[./c]
order = FIRST
family = LAGRANGE
[../]
# chemical potential
[./w]
order = FIRST
family = LAGRANGE
[../]
# solute phase concentration (matrix)
[./cm]
order = FIRST
family = LAGRANGE
[../]
# solute phase concentration (precipitate)
[./cp]
order = FIRST
family = LAGRANGE
[../]
[./disp_x]
order = FIRST
family = LAGRANGE
[../]
[./disp_y]
order = FIRST
family = LAGRANGE
[../]
[./disp_z]
order = FIRST
family = LAGRANGE
[../]
[]
[ICs]
[./eta_ic]
variable = eta
type = FunctionIC
function = ic_func_eta
block = 0
[../]
[./c_ic]
variable = c
type = FunctionIC
function = ic_func_c
block = 0
[../]
[./w_ic]
variable = w
type = ConstantIC
value = 0.00991
block = 0
[../]
[./cm_ic]
variable = cm
type = ConstantIC
value = 0.131
block = 0
[../]
[./cp_ic]
variable = cp
type = ConstantIC
value = 0.236
block = 0
[../]
[]
[Functions]
[./ic_func_eta]
type = ParsedFunction
value = '0.5*(1.0+tanh((x)/delta_eta/sqrt(2.0)))'
vars = 'delta_eta'
vals = '0.8034'
[../]
[./ic_func_c]
type = ParsedFunction
value = '0.2388*(0.5*(1.0+tanh(x/delta/sqrt(2.0))))^3*(6*(0.5*(1.0+tanh(x/delta/sqrt(2.0))))^2-15*(0.5*(1.0+tanh(x/delta/sqrt(2.0))))+10)+0.1338*(1-(0.5*(1.0+tanh(x/delta/sqrt(2.0))))^3*(6*(0.5*(1.0+tanh(x/delta/sqrt(2.0))))^2-15*(0.5*(1.0+tanh(x/delta/sqrt(2.0))))+10))'
vars = 'delta'
vals = '0.8034'
[../]
[./psi_eq_int]
type = ParsedFunction
value = 'volume*psi_alpha'
vars = 'volume psi_alpha'
vals = 'volume psi_alpha'
[../]
[./gamma]
type = ParsedFunction
value = '(psi_int - psi_eq_int) / dy / dz'
vars = 'psi_int psi_eq_int dy dz'
vals = 'psi_int psi_eq_int 0.03125 0.03125'
[../]
[]
[AuxVariables]
[./sigma11]
order = CONSTANT
family = MONOMIAL
[../]
[./sigma22]
order = CONSTANT
family = MONOMIAL
[../]
[./sigma33]
order = CONSTANT
family = MONOMIAL
[../]
[./e11]
order = CONSTANT
family = MONOMIAL
[../]
[./e12]
order = CONSTANT
family = MONOMIAL
[../]
[./e22]
order = CONSTANT
family = MONOMIAL
[../]
[./e33]
order = CONSTANT
family = MONOMIAL
[../]
[./e_el11]
order = CONSTANT
family = MONOMIAL
[../]
[./e_el12]
order = CONSTANT
family = MONOMIAL
[../]
[./e_el22]
order = CONSTANT
family = MONOMIAL
[../]
[./f_el]
order = CONSTANT
family = MONOMIAL
[../]
[./eigen_strain00]
order = CONSTANT
family = MONOMIAL
[../]
[./Fglobal]
order = CONSTANT
family = MONOMIAL
[../]
[./psi]
order = CONSTANT
family = MONOMIAL
[../]
[]
[AuxKernels]
[./matl_sigma11]
type = RankTwoAux
rank_two_tensor = stress
index_i = 0
index_j = 0
variable = sigma11
[../]
[./matl_sigma22]
type = RankTwoAux
rank_two_tensor = stress
index_i = 1
index_j = 1
variable = sigma22
[../]
[./matl_sigma33]
type = RankTwoAux
rank_two_tensor = stress
index_i = 2
index_j = 2
variable = sigma33
[../]
[./matl_e11]
type = RankTwoAux
rank_two_tensor = total_strain
index_i = 0
index_j = 0
variable = e11
[../]
[./matl_e12]
type = RankTwoAux
rank_two_tensor = total_strain
index_i = 0
index_j = 1
variable = e12
[../]
[./matl_e22]
type = RankTwoAux
rank_two_tensor = total_strain
index_i = 1
index_j = 1
variable = e22
[../]
[./matl_e33]
type = RankTwoAux
rank_two_tensor = total_strain
index_i = 2
index_j = 2
variable = e33
[../]
[./f_el]
type = MaterialRealAux
variable = f_el
property = f_el_mat
execute_on = timestep_end
[../]
[./GlobalFreeEnergy]
variable = Fglobal
type = KKSGlobalFreeEnergy
fa_name = fm
fb_name = fp
w = 0.0264
kappa_names = kappa
interfacial_vars = eta
[../]
[./psi_potential]
variable = psi
type = ParsedAux
args = 'Fglobal w c f_el sigma11 e11'
function = 'Fglobal - w*c + f_el - sigma11*e11'
[../]
[]
[BCs]
[./left_x]
type = DirichletBC
variable = disp_x
boundary = left
value = 0
[../]
[./right_x]
type = DirichletBC
variable = disp_x
boundary = right
value = 0
[../]
[./front_y]
type = DirichletBC
variable = disp_y
boundary = front
value = 0
[../]
[./back_y]
type = DirichletBC
variable = disp_y
boundary = back
value = 0
[../]
[./top_z]
type = DirichletBC
variable = disp_z
boundary = top
value = 0
[../]
[./bottom_z]
type = DirichletBC
variable = disp_z
boundary = bottom
value = 0
[../]
[]
[Materials]
# Chemical free energy of the matrix
[./fm]
type = DerivativeParsedMaterial
f_name = fm
args = 'cm'
function = '6.55*(cm-0.13)^2'
[../]
# Elastic energy of the matrix
[./elastic_free_energy_m]
type = ElasticEnergyMaterial
base_name = matrix
f_name = fe_m
args = ' '
outputs = exodus
[../]
# Total free energy of the matrix
[./Total_energy_matrix]
type = DerivativeSumMaterial
f_name = f_total_matrix
sum_materials = 'fm fe_m'
args = 'cm'
[../]
# Free energy of the precipitate phase
[./fp]
type = DerivativeParsedMaterial
f_name = fp
args = 'cp'
function = '6.55*(cp-0.235)^2'
[../]
# Elastic energy of the precipitate
[./elastic_free_energy_p]
type = ElasticEnergyMaterial
base_name = ppt
f_name = fe_p
args = ' '
outputs = exodus
[../]
# Total free energy of the precipitate
[./Total_energy_ppt]
type = DerivativeSumMaterial
f_name = f_total_ppt
sum_materials = 'fp fe_p'
args = 'cp'
[../]
# Total elastic energy
[./Total_elastic_energy]
type = DerivativeTwoPhaseMaterial
eta = eta
f_name = f_el_mat
fa_name = fe_m
fb_name = fe_p
outputs = exodus
W = 0
[../]
# h(eta)
[./h_eta]
type = SwitchingFunctionMaterial
h_order = HIGH
eta = eta
[../]
# g(eta)
[./g_eta]
type = BarrierFunctionMaterial
g_order = SIMPLE
eta = eta
[../]
# constant properties
[./constants]
type = GenericConstantMaterial
prop_names = 'M L kappa misfit'
prop_values = '0.7 0.7 0.01704 0.00377'
[../]
#Mechanical properties
[./Stiffness_matrix]
type = ComputeElasticityTensor
C_ijkl = '103.3 74.25 74.25 103.3 74.25 103.3 46.75 46.75 46.75'
base_name = matrix
fill_method = symmetric9
[../]
[./Stiffness_ppt]
type = ComputeElasticityTensor
C_ijkl = '100.7 71.45 71.45 100.7 71.45 100.7 50.10 50.10 50.10'
base_name = ppt
fill_method = symmetric9
[../]
[./stress_matrix]
type = ComputeLinearElasticStress
base_name = matrix
[../]
[./stress_ppt]
type = ComputeLinearElasticStress
base_name = ppt
[../]
[./strain_matrix]
type = ComputeSmallStrain
displacements = 'disp_x disp_y disp_z'
base_name = matrix
[../]
[./strain_ppt]
type = ComputeSmallStrain
displacements = 'disp_x disp_y disp_z'
base_name = ppt
eigenstrain_names = 'eigenstrain_ppt'
[../]
[./eigen_strain]
type = ComputeEigenstrain
base_name = ppt
eigen_base = '1 1 1 0 0 0'
prefactor = misfit
eigenstrain_name = 'eigenstrain_ppt'
[../]
[./global_stress]
type = TwoPhaseStressMaterial
base_A = matrix
base_B = ppt
[../]
[./global_strain]
type = ComputeSmallStrain
displacements = 'disp_x disp_y disp_z'
[../]
[]
[Kernels]
[./TensorMechanics]
displacements = 'disp_x disp_y disp_z'
[../]
# enforce c = (1-h(eta))*cm + h(eta)*cp
[./PhaseConc]
type = KKSPhaseConcentration
ca = cm
variable = cp
c = c
eta = eta
[../]
# enforce pointwise equality of chemical potentials
[./ChemPotVacancies]
type = KKSPhaseChemicalPotential
variable = cm
cb = cp
fa_name = f_total_matrix
fb_name = f_total_ppt
[../]
#
# Cahn-Hilliard Equation
#
[./CHBulk]
type = KKSSplitCHCRes
variable = c
ca = cm
fa_name = f_total_matrix
w = w
[../]
[./dcdt]
type = CoupledTimeDerivative
variable = w
v = c
[../]
[./ckernel]
type = SplitCHWRes
mob_name = M
variable = w
[../]
#
# Allen-Cahn Equation
#
[./ACBulkF]
type = KKSACBulkF
variable = eta
fa_name = f_total_matrix
fb_name = f_total_ppt
w = 0.0264
args = 'cp cm'
[../]
[./ACBulkC]
type = KKSACBulkC
variable = eta
ca = cm
cb = cp
fa_name = f_total_matrix
[../]
[./ACInterface]
type = ACInterface
variable = eta
kappa_name = kappa
[../]
[./detadt]
type = TimeDerivative
variable = eta
[../]
[]
[Executioner]
type = Transient
solve_type = 'PJFNK'
petsc_options_iname = '-pc_type -sub_pc_type -sub_pc_factor_shift_type'
petsc_options_value = 'asm ilu nonzero'
l_max_its = 30
nl_max_its = 10
l_tol = 1.0e-4
nl_rel_tol = 1.0e-8
nl_abs_tol = 1.0e-11
num_steps = 200
[./TimeStepper]
type = SolutionTimeAdaptiveDT
dt = 0.5
[../]
[]
[VectorPostprocessors]
#[./eta]
# type = LineValueSampler
# start_point = '-10 0 0'
# end_point = '10 0 0'
# variable = eta
# num_points = 321
# sort_by = id
#[../]
#[./eta_position]
# type = FindValueOnLineSample
# vectorpostprocessor = eta
# variable_name = eta
# search_value = 0.5
#[../]
# [./f_el]
# type = LineMaterialRealSampler
# start = '-20 0 0'
# end = '20 0 0'
# sort_by = id
# property = f_el
# [../]
# [./f_el_a]
# type = LineMaterialRealSampler
# start = '-20 0 0'
# end = '20 0 0'
# sort_by = id
# property = fe_m
# [../]
# [./f_el_b]
# type = LineMaterialRealSampler
# start = '-20 0 0'
# end = '20 0 0'
# sort_by = id
# property = fe_p
# [../]
# [./h_out]
# type = LineMaterialRealSampler
# start = '-20 0 0'
# end = '20 0 0'
# sort_by = id
# property = h
# [../]
# [./fm_out]
# type = LineMaterialRealSampler
# start = '-20 0 0'
# end = '20 0 0'
# sort_by = id
# property = fm
# [../]
[]
[Postprocessors]
[./f_el_int]
type = ElementIntegralMaterialProperty
mat_prop = f_el_mat
[../]
[./c_alpha]
type = SideAverageValue
boundary = left
variable = c
[../]
[./c_beta]
type = SideAverageValue
boundary = right
variable = c
[../]
[./e11_alpha]
type = SideAverageValue
boundary = left
variable = e11
[../]
[./e11_beta]
type = SideAverageValue
boundary = right
variable = e11
[../]
[./s11_alpha]
type = SideAverageValue
boundary = left
variable = sigma11
[../]
[./s22_alpha]
type = SideAverageValue
boundary = left
variable = sigma22
[../]
[./s33_alpha]
type = SideAverageValue
boundary = left
variable = sigma33
[../]
[./s11_beta]
type = SideAverageValue
boundary = right
variable = sigma11
[../]
[./s22_beta]
type = SideAverageValue
boundary = right
variable = sigma22
[../]
[./s33_beta]
type = SideAverageValue
boundary = right
variable = sigma33
[../]
[./f_el_alpha]
type = SideAverageValue
boundary = left
variable = f_el
[../]
[./f_el_beta]
type = SideAverageValue
boundary = right
variable = f_el
[../]
[./f_c_alpha]
type = SideAverageValue
boundary = left
variable = Fglobal
[../]
[./f_c_beta]
type = SideAverageValue
boundary = right
variable = Fglobal
[../]
[./chem_pot_alpha]
type = SideAverageValue
boundary = left
variable = w
[../]
[./chem_pot_beta]
type = SideAverageValue
boundary = right
variable = w
[../]
[./psi_alpha]
type = SideAverageValue
boundary = left
variable = psi
[../]
[./psi_beta]
type = SideAverageValue
boundary = right
variable = psi
[../]
[./total_energy]
type = ElementIntegralVariablePostprocessor
variable = Fglobal
[../]
# Get simulation cell size from postprocessor
[./volume]
type = ElementIntegralMaterialProperty
mat_prop = 1
[../]
[./psi_eq_int]
type = FunctionValuePostprocessor
function = psi_eq_int
[../]
[./psi_int]
type = ElementIntegralVariablePostprocessor
variable = psi
[../]
[./gamma]
type = FunctionValuePostprocessor
function = gamma
[../]
[]
#
# Precondition using handcoded off-diagonal terms
#
[Preconditioning]
[./full]
type = SMP
full = true
[../]
[]
[Outputs]
[./exodus]
type = Exodus
interval = 20
[../]
[./csv]
type = CSV
execute_on = 'final'
[../]
#[./console]
# type = Console
# output_file = true
# [../]
[]
modules/functional_expansion_tools/examples/3D_volumetric_Cartesian_different_submesh/sub.i
# Derived from the example '3D_volumetric_Cartesian' with the following differences:
#
# 1) The number of x and y divisions in the sub app is not the same as the master app
# 2) The subapp mesh is skewed in x and z
[Mesh]
type = GeneratedMesh
dim = 3
xmin = 0.0
xmax = 10.0
nx = 23
bias_x = 1.2
ymin = 1.0
ymax = 11.0
ny = 33
zmin = 2.0
zmax = 12.0
nz = 35
bias_z = 0.8
[]
# Non-copy transfers only work with AuxVariable, but nothing will be solved without a variable
# defined. The solution is to define an empty variable tha does nothing, but causes MOOSE to solve
# the AuxKernels that we need.
[Variables]
[./empty]
[../]
[]
[AuxVariables]
[./s]
order = FIRST
family = LAGRANGE
[../]
[./m_in]
order = FIRST
family = LAGRANGE
[../]
[]
# We must have a kernel for every variable, hence this null kernel to match the variable 'empty'
[Kernels]
[./null_kernel]
type = NullKernel
variable = empty
[../]
[]
[AuxKernels]
[./reconstruct_m_in]
type = FunctionSeriesToAux
function = FX_Basis_Value_Sub
variable = m_in
[../]
[./calculate_s] # Something to make 's' change each time, but allow a converging solution
type = ParsedAux
variable = s
args = m_in
function = '2*exp(-m_in/0.8)'
[../]
[]
[Functions]
[./FX_Basis_Value_Sub]
type = FunctionSeries
series_type = Cartesian
orders = '3 4 5'
physical_bounds = '0.0 10.0 1.0 11.0 2.0 12.0'
x = Legendre
y = Legendre
z = Legendre
[../]
[]
[UserObjects]
[./FX_Value_UserObject_Sub]
type = FXVolumeUserObject
function = FX_Basis_Value_Sub
variable = s
[../]
[]
[Executioner]
type = Transient
num_steps = 10
dt = 0.5
solve_type = PJFNK
petsc_options_iname = '-pc_type -pc_hypre_type'
petsc_options_value = 'hypre boomeramg'
[]
modules/porous_flow/test/tests/poro_elasticity/mandel_fully_saturated_volume.i
# Mandel's problem of consolodation of a drained medium
# Using the FullySaturatedDarcyBase and FullySaturatedFullySaturatedMassTimeDerivative kernels
# with multiply_by_density = false, so that this problem becomes linear
# Note the use of consistent_with_displaced_mesh = false in the calculation of volumetric strain
#
# A sample is in plane strain.
# -a <= x <= a
# -b <= y <= b
# It is squashed with constant force by impermeable, frictionless plattens on its top and bottom surfaces (at y=+/-b)
# Fluid is allowed to leak out from its sides (at x=+/-a)
# The porepressure within the sample is monitored.
#
# As is common in the literature, this is simulated by
# considering the quarter-sample, 0<=x<=a and 0<=y<=b, with
# impermeable, roller BCs at x=0 and y=0 and y=b.
# Porepressure is fixed at zero on x=a.
# Porepressure and displacement are initialised to zero.
# Then the top (y=b) is moved downwards with prescribed velocity,
# so that the total force that is inducing this downwards velocity
# is fixed. The velocity is worked out by solving Mandel's problem
# analytically, and the total force is monitored in the simulation
# to check that it indeed remains constant.
#
# Here are the problem's parameters, and their values:
# Soil width. a = 1
# Soil height. b = 0.1
# Soil's Lame lambda. la = 0.5
# Soil's Lame mu, which is also the Soil's shear modulus. mu = G = 0.75
# Soil bulk modulus. K = la + 2*mu/3 = 1
# Drained Poisson ratio. nu = (3K - 2G)/(6K + 2G) = 0.2
# Soil bulk compliance. 1/K = 1
# Fluid bulk modulus. Kf = 8
# Fluid bulk compliance. 1/Kf = 0.125
# Soil initial porosity. phi0 = 0.1
# Biot coefficient. alpha = 0.6
# Biot modulus. M = 1/(phi0/Kf + (alpha - phi0)(1 - alpha)/K) = 4.705882
# Undrained bulk modulus. Ku = K + alpha^2*M = 2.694118
# Undrained Poisson ratio. nuu = (3Ku - 2G)/(6Ku + 2G) = 0.372627
# Skempton coefficient. B = alpha*M/Ku = 1.048035
# Fluid mobility (soil permeability/fluid viscosity). k = 1.5
# Consolidation coefficient. c = 2*k*B^2*G*(1-nu)*(1+nuu)^2/9/(1-nuu)/(nuu-nu) = 3.821656
# Normal stress on top. F = 1
#
# The solution for porepressure and displacements is given in
# AHD Cheng and E Detournay "A direct boundary element method for plane strain poroelasticity" International Journal of Numerical and Analytical Methods in Geomechanics 12 (1988) 551-572.
# The solution involves complicated infinite series, so I shall not write it here
[Mesh]
type = GeneratedMesh
dim = 3
nx = 10
ny = 1
nz = 1
xmin = 0
xmax = 1
ymin = 0
ymax = 0.1
zmin = 0
zmax = 1
[]
[GlobalParams]
displacements = 'disp_x disp_y disp_z'
PorousFlowDictator = dictator
block = 0
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = 'porepressure disp_x disp_y disp_z'
number_fluid_phases = 1
number_fluid_components = 1
[../]
[]
[Variables]
[./disp_x]
[../]
[./disp_y]
[../]
[./disp_z]
[../]
[./porepressure]
[../]
[]
[BCs]
[./roller_xmin]
type = DirichletBC
variable = disp_x
value = 0
boundary = 'left'
[../]
[./roller_ymin]
type = DirichletBC
variable = disp_y
value = 0
boundary = 'bottom'
[../]
[./plane_strain]
type = DirichletBC
variable = disp_z
value = 0
boundary = 'back front'
[../]
[./xmax_drained]
type = DirichletBC
variable = porepressure
value = 0
boundary = right
[../]
[./top_velocity]
type = FunctionDirichletBC
variable = disp_y
function = top_velocity
boundary = top
[../]
[]
[Functions]
[./top_velocity]
type = PiecewiseLinear
x = '0 0.002 0.006 0.014 0.03 0.046 0.062 0.078 0.094 0.11 0.126 0.142 0.158 0.174 0.19 0.206 0.222 0.238 0.254 0.27 0.286 0.302 0.318 0.334 0.35 0.366 0.382 0.398 0.414 0.43 0.446 0.462 0.478 0.494 0.51 0.526 0.542 0.558 0.574 0.59 0.606 0.622 0.638 0.654 0.67 0.686 0.702'
y = '-0.041824842 -0.042730269 -0.043412712 -0.04428867 -0.045509181 -0.04645965 -0.047268246 -0.047974749 -0.048597109 -0.0491467 -0.049632388 -0.050061697 -0.050441198 -0.050776675 -0.051073238 -0.0513354 -0.051567152 -0.051772022 -0.051953128 -0.052113227 -0.052254754 -0.052379865 -0.052490464 -0.052588233 -0.052674662 -0.052751065 -0.052818606 -0.052878312 -0.052931093 -0.052977751 -0.053018997 -0.053055459 -0.053087691 -0.053116185 -0.053141373 -0.05316364 -0.053183324 -0.053200724 -0.053216106 -0.053229704 -0.053241725 -0.053252351 -0.053261745 -0.053270049 -0.053277389 -0.053283879 -0.053289615'
[../]
[]
[AuxVariables]
[./stress_yy]
order = CONSTANT
family = MONOMIAL
[../]
[./tot_force]
order = CONSTANT
family = MONOMIAL
[../]
[]
[AuxKernels]
[./stress_yy]
type = RankTwoAux
rank_two_tensor = stress
variable = stress_yy
index_i = 1
index_j = 1
[../]
[./tot_force]
type = ParsedAux
args = 'stress_yy porepressure'
execute_on = timestep_end
variable = tot_force
function = '-stress_yy+0.6*porepressure'
[../]
[]
[Kernels]
[./grad_stress_x]
type = StressDivergenceTensors
variable = disp_x
component = 0
[../]
[./grad_stress_y]
type = StressDivergenceTensors
variable = disp_y
component = 1
[../]
[./grad_stress_z]
type = StressDivergenceTensors
variable = disp_z
component = 2
[../]
[./poro_x]
type = PorousFlowEffectiveStressCoupling
biot_coefficient = 0.6
variable = disp_x
component = 0
[../]
[./poro_y]
type = PorousFlowEffectiveStressCoupling
biot_coefficient = 0.6
variable = disp_y
component = 1
[../]
[./poro_z]
type = PorousFlowEffectiveStressCoupling
biot_coefficient = 0.6
component = 2
variable = disp_z
[../]
[./mass0]
type = PorousFlowFullySaturatedMassTimeDerivative
biot_coefficient = 0.6
multiply_by_density = false
coupling_type = HydroMechanical
variable = porepressure
[../]
[./flux]
type = PorousFlowFullySaturatedDarcyBase
multiply_by_density = false
variable = porepressure
gravity = '0 0 0'
[../]
[]
[Modules]
[./FluidProperties]
[./simple_fluid]
type = SimpleFluidProperties
bulk_modulus = 8
density0 = 1
thermal_expansion = 0
viscosity = 1
[../]
[../]
[]
[Materials]
[./temperature]
type = PorousFlowTemperature
[../]
[./elasticity_tensor]
type = ComputeElasticityTensor
C_ijkl = '0.5 0.75'
# bulk modulus is lambda + 2*mu/3 = 0.5 + 2*0.75/3 = 1
fill_method = symmetric_isotropic
[../]
[./strain]
type = ComputeSmallStrain
[../]
[./stress]
type = ComputeLinearElasticStress
[../]
[./eff_fluid_pressure_qp]
type = PorousFlowEffectiveFluidPressure
[../]
[./vol_strain]
type = PorousFlowVolumetricStrain
consistent_with_displaced_mesh = false
[../]
[./ppss]
type = PorousFlow1PhaseFullySaturated
porepressure = porepressure
[../]
[./massfrac]
type = PorousFlowMassFraction
[../]
[./simple_fluid_qp]
type = PorousFlowSingleComponentFluid
fp = simple_fluid
phase = 0
[../]
[./porosity]
type = PorousFlowPorosityConst # only the initial value of this is ever used
porosity = 0.1
[../]
[./biot_modulus]
type = PorousFlowConstantBiotModulus
biot_coefficient = 0.6
solid_bulk_compliance = 1
fluid_bulk_modulus = 8
[../]
[./permeability]
type = PorousFlowPermeabilityConst
permeability = '1.5 0 0 0 1.5 0 0 0 1.5'
[../]
[]
[Postprocessors]
[./p0]
type = PointValue
outputs = csv
point = '0.0 0 0'
variable = porepressure
[../]
[./p1]
type = PointValue
outputs = csv
point = '0.1 0 0'
variable = porepressure
[../]
[./p2]
type = PointValue
outputs = csv
point = '0.2 0 0'
variable = porepressure
[../]
[./p3]
type = PointValue
outputs = csv
point = '0.3 0 0'
variable = porepressure
[../]
[./p4]
type = PointValue
outputs = csv
point = '0.4 0 0'
variable = porepressure
[../]
[./p5]
type = PointValue
outputs = csv
point = '0.5 0 0'
variable = porepressure
[../]
[./p6]
type = PointValue
outputs = csv
point = '0.6 0 0'
variable = porepressure
[../]
[./p7]
type = PointValue
outputs = csv
point = '0.7 0 0'
variable = porepressure
[../]
[./p8]
type = PointValue
outputs = csv
point = '0.8 0 0'
variable = porepressure
[../]
[./p9]
type = PointValue
outputs = csv
point = '0.9 0 0'
variable = porepressure
[../]
[./p99]
type = PointValue
outputs = csv
point = '1 0 0'
variable = porepressure
[../]
[./xdisp]
type = PointValue
outputs = csv
point = '1 0.1 0'
variable = disp_x
[../]
[./ydisp]
type = PointValue
outputs = csv
point = '1 0.1 0'
variable = disp_y
[../]
[./total_downwards_force]
type = ElementAverageValue
outputs = csv
variable = tot_force
[../]
[./dt]
type = FunctionValuePostprocessor
outputs = console
function = if(0.15*t<0.01,0.15*t,0.01)
[../]
[]
[Preconditioning]
[./andy]
type = SMP
full = true
petsc_options_iname = '-ksp_type -pc_type -sub_pc_type -snes_atol -snes_rtol -snes_max_it'
petsc_options_value = 'gmres asm lu 1E-14 1E-10 10000'
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
start_time = 0
end_time = 0.7
[./TimeStepper]
type = PostprocessorDT
postprocessor = dt
dt = 0.001
[../]
[]
[Outputs]
execute_on = 'timestep_end'
file_base = mandel_fully_saturated_volume
[./csv]
interval = 3
type = CSV
[../]
[]
modules/porous_flow/test/tests/chemistry/dissolution_limited.i
# The dissolution reaction, with limited initial mineral concentration
#
# a <==> mineral
#
# produces "mineral". Using mineral_density = fluid_density, theta = 1 = eta, the DE is
#
# a' = -(mineral / porosity)' = rate * surf_area * molar_vol (1 - (1 / eqm_const) * (act_coeff * a)^stoi)
#
# The following parameters are used
#
# T_ref = 0.5 K
# T = 1 K
# activation_energy = 3 J/mol
# gas_constant = 6 J/(mol K)
# kinetic_rate_at_ref_T = 0.60653 mol/(m^2 s)
# These give rate = 0.60653 * exp(1/2) = 1 mol/(m^2 s)
#
# surf_area = 0.5 m^2/L
# molar_volume = 2 L/mol
# These give rate * surf_area * molar_vol = 1 s^-1
#
# equilibrium_constant = 0.5 (dimensionless)
# primary_activity_coefficient = 2 (dimensionless)
# stoichiometry = 1 (dimensionless)
# This means that 1 - (1 / eqm_const) * (act_coeff * a)^stoi = 1 - 4 a, which is positive for a < 0.25, ie dissolution for a(t=0) < 0.25
#
# The solution of the DE is
# a = eqm_const / act_coeff + (a(t=0) - eqm_const / act_coeff) exp(-rate * surf_area * molar_vol * act_coeff * t / eqm_const)
# = 0.25 + (a(t=0) - 0.25) exp(-4 * t)
# c = c(t=0) - (a - a(t=0)) * porosity
#
# However, c(t=0) is small, so that the reaction only works until c=0, then a and c both remain fixed
#
# This test checks that (a + c / porosity) is time-independent, and that a follows the above solution, until c=0 and thereafter remains fixed.
#
# Aside:
# The exponential curve is not followed exactly because moose actually solves
# (a - a_old)/dt = rate * surf_area * molar_vol (1 - (1 / eqm_const) * (act_coeff * a)^stoi)
# which does not give an exponential exactly, except in the limit dt->0
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./a]
initial_condition = 0.05
[../]
[]
[AuxVariables]
[./eqm_k]
initial_condition = 0.5
[../]
[./pressure]
[../]
[./ini_mineral_conc]
initial_condition = 0.015
[../]
[./mineral]
family = MONOMIAL
order = CONSTANT
[../]
[./should_be_static]
family = MONOMIAL
order = CONSTANT
[../]
[]
[AuxKernels]
[./mineral]
type = PorousFlowPropertyAux
property = mineral_concentration
mineral_species = 0
variable = mineral
[../]
[./should_be_static]
type = ParsedAux
args = 'mineral a'
function = 'a + mineral / 0.1'
variable = should_be_static
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./mass_a]
type = PorousFlowMassTimeDerivative
fluid_component = 0
variable = a
[../]
[./pre_dis]
type = PorousFlowPreDis
variable = a
mineral_density = 1000
stoichiometry = 1
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = a
number_fluid_phases = 1
number_fluid_components = 2
number_aqueous_kinetic = 1
[../]
[]
[Modules]
[./FluidProperties]
[./simple_fluid]
type = SimpleFluidProperties
bulk_modulus = 2e9 # huge, so mimic chemical_reactions
density0 = 1000
thermal_expansion = 0
viscosity = 1e-3
[../]
[../]
[]
[Materials]
[./temperature]
type = PorousFlowTemperature
temperature = 1
[../]
[./ppss]
type = PorousFlow1PhaseFullySaturated
porepressure = pressure
[../]
[./mass_frac]
type = PorousFlowMassFraction
mass_fraction_vars = a
[../]
[./predis]
type = PorousFlowAqueousPreDisChemistry
primary_concentrations = a
num_reactions = 1
equilibrium_constants = eqm_k
primary_activity_coefficients = 2
reactions = 1
specific_reactive_surface_area = 0.5
kinetic_rate_constant = 0.6065306597126334
activation_energy = 3
molar_volume = 2
gas_constant = 6
reference_temperature = 0.5
[../]
[./mineral_conc]
type = PorousFlowAqueousPreDisMineral
initial_concentrations = ini_mineral_conc
[../]
[./simple_fluid]
type = PorousFlowSingleComponentFluid
fp = simple_fluid
phase = 0
[../]
[./porosity]
type = PorousFlowPorosityConst
porosity = 0.1
[../]
[]
[Preconditioning]
[./smp]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
nl_abs_tol = 1E-10
dt = 0.01
end_time = 1
[]
[Postprocessors]
[./a]
type = PointValue
point = '0 0 0'
variable = a
[../]
[./should_be_static]
type = PointValue
point = '0 0 0'
variable = should_be_static
[../]
[]
[Outputs]
interval = 10
csv = true
perf_graph = true
[]
modules/porous_flow/examples/reservoir_model/field_model.i
# Field model generated using geophysical modelling tool
[Mesh]
type = FileMesh
file = field.e
[]
[GlobalParams]
PorousFlowDictator = dictator
gravity = '0 0 -9.81'
temperature_unit = Celsius
[]
[Variables]
[porepressure]
initial_condition = 20e6
[]
[]
[AuxVariables]
[temperature]
initial_condition = 50
[]
[xnacl]
initial_condition = 0.1
[]
[porosity]
family = MONOMIAL
order = CONSTANT
initial_from_file_var = poro
[]
[permx_md]
family = MONOMIAL
order = CONSTANT
initial_from_file_var = permX
[]
[permy_md]
family = MONOMIAL
order = CONSTANT
initial_from_file_var = permY
[]
[permz_md]
family = MONOMIAL
order = CONSTANT
initial_from_file_var = permZ
[]
[permx]
family = MONOMIAL
order = CONSTANT
[]
[permy]
family = MONOMIAL
order = CONSTANT
[]
[permz]
family = MONOMIAL
order = CONSTANT
[]
[]
[AuxKernels]
[permx]
type = ParsedAux
variable = permx
args = permx_md
function = '9.869233e-16*permx_md'
execute_on = initial
[]
[permy]
type = ParsedAux
variable = permy
args = permy_md
function = '9.869233e-16*permy_md'
execute_on = initial
[]
[permz]
type = ParsedAux
variable = permz
args = permz_md
function = '9.869233e-16*permz_md'
execute_on = initial
[]
[]
[Kernels]
[mass0]
type = PorousFlowMassTimeDerivative
variable = porepressure
[]
[flux0]
type = PorousFlowFullySaturatedDarcyFlow
variable = porepressure
[]
[]
[UserObjects]
[dictator]
type = PorousFlowDictator
porous_flow_vars = porepressure
number_fluid_phases = 1
number_fluid_components = 1
[]
[]
[Modules]
[FluidProperties]
[water]
type = Water97FluidProperties
[]
[watertab]
type = TabulatedFluidProperties
fp = water
save_file = false
[]
[]
[]
[Materials]
[temperature]
type = PorousFlowTemperature
temperature = temperature
[]
[ps]
type = PorousFlow1PhaseFullySaturated
porepressure = porepressure
[]
[massfrac]
type = PorousFlowMassFraction
[]
[brine]
type = PorousFlowBrine
compute_enthalpy = false
compute_internal_energy = false
xnacl = xnacl
phase = 0
water_fp = watertab
[]
[porosity]
type = PorousFlowPorosityConst
porosity = porosity
[]
[permeability]
type = PorousFlowPermeabilityConstFromVar
perm_xx = permx
perm_yy = permy
perm_zz = permz
[]
[]
[Preconditioning]
[smp]
type = SMP
full = true
[]
[]
[Executioner]
type = Transient
solve_type = Newton
dt = 1e2
end_time = 1e2
[]
[Outputs]
execute_on = 'initial timestep_end'
exodus = true
perf_graph = true
[]
modules/combined/test/tests/poro_mechanics/mandel.i
# Mandel's problem of consolodation of a drained medium
#
# A sample is in plane strain.
# -a <= x <= a
# -b <= y <= b
# It is squashed with constant force by impermeable, frictionless plattens on its top and bottom surfaces (at y=+/-b)
# Fluid is allowed to leak out from its sides (at x=+/-a)
# The porepressure within the sample is monitored.
#
# As is common in the literature, this is simulated by
# considering the quarter-sample, 0<=x<=a and 0<=y<=b, with
# impermeable, roller BCs at x=0 and y=0 and y=b.
# Porepressure is fixed at zero on x=a.
# Porepressure and displacement are initialised to zero.
# Then the top (y=b) is moved downwards with prescribed velocity,
# so that the total force that is inducing this downwards velocity
# is fixed. The velocity is worked out by solving Mandel's problem
# analytically, and the total force is monitored in the simulation
# to check that it indeed remains constant.
#
# Here are the problem's parameters, and their values:
# Soil width. a = 1
# Soil height. b = 0.1
# Soil's Lame lambda. la = 0.5
# Soil's Lame mu, which is also the Soil's shear modulus. mu = G = 0.75
# Soil bulk modulus. K = la + 2*mu/3 = 1
# Drained Poisson ratio. nu = (3K - 2G)/(6K + 2G) = 0.2
# Soil bulk compliance. 1/K = 1
# Fluid bulk modulus. Kf = 8
# Fluid bulk compliance. 1/Kf = 0.125
# Soil initial porosity. phi0 = 0.1
# Biot coefficient. alpha = 0.6
# Biot modulus. M = 1/(phi0/Kf + (alpha - phi0)(1 - alpha)/K) = 4.705882
# Undrained bulk modulus. Ku = K + alpha^2*M = 2.694118
# Undrained Poisson ratio. nuu = (3Ku - 2G)/(6Ku + 2G) = 0.372627
# Skempton coefficient. B = alpha*M/Ku = 1.048035
# Fluid mobility (soil permeability/fluid viscosity). k = 1.5
# Consolidation coefficient. c = 2*k*B^2*G*(1-nu)*(1+nuu)^2/9/(1-nuu)/(nuu-nu) = 3.821656
# Normal stress on top. F = 1
#
# The solution for porepressure and displacements is given in
# AHD Cheng and E Detournay "A direct boundary element method for plane strain poroelasticity" International Journal of Numerical and Analytical Methods in Geomechanics 12 (1988) 551-572.
# The solution involves complicated infinite series, so I shall not write it here
[Mesh]
type = GeneratedMesh
dim = 3
nx = 10
ny = 1
nz = 1
xmin = 0
xmax = 1
ymin = 0
ymax = 0.1
zmin = 0
zmax = 1
[]
[GlobalParams]
displacements = 'disp_x disp_y disp_z'
porepressure = porepressure
block = 0
[]
[Variables]
[./disp_x]
[../]
[./disp_y]
[../]
[./disp_z]
[../]
[./porepressure]
[../]
[]
[BCs]
[./roller_xmin]
type = DirichletBC
variable = disp_x
value = 0
boundary = 'left'
[../]
[./roller_ymin]
type = DirichletBC
variable = disp_y
value = 0
boundary = 'bottom'
[../]
[./plane_strain]
type = DirichletBC
variable = disp_z
value = 0
boundary = 'back front'
[../]
[./xmax_drained]
type = DirichletBC
variable = porepressure
value = 0
boundary = right
[../]
[./top_velocity]
type = FunctionDirichletBC
variable = disp_y
function = top_velocity
boundary = top
[../]
[]
[Functions]
[./top_velocity]
type = PiecewiseLinear
x = '0 0.002 0.006 0.014 0.03 0.046 0.062 0.078 0.094 0.11 0.126 0.142 0.158 0.174 0.19 0.206 0.222 0.238 0.254 0.27 0.286 0.302 0.318 0.334 0.35 0.366 0.382 0.398 0.414 0.43 0.446 0.462 0.478 0.494 0.51 0.526 0.542 0.558 0.574 0.59 0.606 0.622 0.638 0.654 0.67 0.686 0.702'
y = '-0.041824842 -0.042730269 -0.043412712 -0.04428867 -0.045509181 -0.04645965 -0.047268246 -0.047974749 -0.048597109 -0.0491467 -0.049632388 -0.050061697 -0.050441198 -0.050776675 -0.051073238 -0.0513354 -0.051567152 -0.051772022 -0.051953128 -0.052113227 -0.052254754 -0.052379865 -0.052490464 -0.052588233 -0.052674662 -0.052751065 -0.052818606 -0.052878312 -0.052931093 -0.052977751 -0.053018997 -0.053055459 -0.053087691 -0.053116185 -0.053141373 -0.05316364 -0.053183324 -0.053200724 -0.053216106 -0.053229704 -0.053241725 -0.053252351 -0.053261745 -0.053270049 -0.053277389 -0.053283879 -0.053289615'
[../]
[]
[AuxVariables]
[./stress_yy]
order = CONSTANT
family = MONOMIAL
[../]
[./tot_force]
order = CONSTANT
family = MONOMIAL
[../]
[]
[AuxKernels]
[./stress_yy]
type = RankTwoAux
rank_two_tensor = stress
variable = stress_yy
index_i = 1
index_j = 1
[../]
[./tot_force]
type = ParsedAux
args = 'stress_yy porepressure'
execute_on = timestep_end
variable = tot_force
function = '-stress_yy+0.6*porepressure'
[../]
[]
[Kernels]
[./grad_stress_x]
type = StressDivergenceTensors
variable = disp_x
component = 0
[../]
[./grad_stress_y]
type = StressDivergenceTensors
variable = disp_y
component = 1
[../]
[./grad_stress_z]
type = StressDivergenceTensors
variable = disp_z
component = 2
[../]
[./poro_x]
type = PoroMechanicsCoupling
variable = disp_x
component = 0
[../]
[./poro_y]
type = PoroMechanicsCoupling
variable = disp_y
component = 1
[../]
[./poro_z]
type = PoroMechanicsCoupling
variable = disp_z
component = 2
[../]
[./poro_timederiv]
type = PoroFullSatTimeDerivative
variable = porepressure
[../]
[./darcy_flow]
type = CoefDiffusion
variable = porepressure
coef = 1.5
[../]
[]
[Materials]
[./elasticity_tensor]
type = ComputeElasticityTensor
C_ijkl = '0.5 0.75'
# bulk modulus is lambda + 2*mu/3 = 0.5 + 2*0.75/3 = 1
fill_method = symmetric_isotropic
[../]
[./strain]
type = ComputeSmallStrain
displacements = 'disp_x disp_y disp_z'
[../]
[./stress]
type = ComputeLinearElasticStress
[../]
[./poro_material]
type = PoroFullSatMaterial
porosity0 = 0.1
biot_coefficient = 0.6
solid_bulk_compliance = 1
fluid_bulk_compliance = 0.125
constant_porosity = true
[../]
[]
[Postprocessors]
[./p0]
type = PointValue
outputs = csv
point = '0.0 0 0'
variable = porepressure
[../]
[./p1]
type = PointValue
outputs = csv
point = '0.1 0 0'
variable = porepressure
[../]
[./p2]
type = PointValue
outputs = csv
point = '0.2 0 0'
variable = porepressure
[../]
[./p3]
type = PointValue
outputs = csv
point = '0.3 0 0'
variable = porepressure
[../]
[./p4]
type = PointValue
outputs = csv
point = '0.4 0 0'
variable = porepressure
[../]
[./p5]
type = PointValue
outputs = csv
point = '0.5 0 0'
variable = porepressure
[../]
[./p6]
type = PointValue
outputs = csv
point = '0.6 0 0'
variable = porepressure
[../]
[./p7]
type = PointValue
outputs = csv
point = '0.7 0 0'
variable = porepressure
[../]
[./p8]
type = PointValue
outputs = csv
point = '0.8 0 0'
variable = porepressure
[../]
[./p9]
type = PointValue
outputs = csv
point = '0.9 0 0'
variable = porepressure
[../]
[./p99]
type = PointValue
outputs = csv
point = '1 0 0'
variable = porepressure
[../]
[./xdisp]
type = PointValue
outputs = csv
point = '1 0.1 0'
variable = disp_x
[../]
[./ydisp]
type = PointValue
outputs = csv
point = '1 0.1 0'
variable = disp_y
[../]
[./total_downwards_force]
type = ElementAverageValue
outputs = csv
variable = tot_force
[../]
[./dt]
type = FunctionValuePostprocessor
outputs = console
function = if(0.15*t<0.01,0.15*t,0.01)
[../]
[]
[Preconditioning]
[./andy]
type = SMP
full = true
petsc_options_iname = '-ksp_type -pc_type -snes_atol -snes_rtol -snes_max_it'
petsc_options_value = 'bcgs bjacobi 1E-14 1E-10 10000'
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
start_time = 0
end_time = 0.7
[./TimeStepper]
type = PostprocessorDT
postprocessor = dt
dt = 0.001
[../]
[]
[Outputs]
execute_on = 'timestep_end'
file_base = mandel
[./csv]
interval = 3
type = CSV
[../]
[]
modules/porous_flow/test/tests/poro_elasticity/mandel_basicthm.i
# using a BasicTHM Action
#
# Mandel's problem of consolodation of a drained medium
# Using the FullySaturatedDarcyBase and FullySaturatedFullySaturatedMassTimeDerivative kernels
# with multiply_by_density = false, so that this problem becomes linear
# Note the use of consistent_with_displaced_mesh = false in the calculation of volumetric strain
#
# A sample is in plane strain.
# -a <= x <= a
# -b <= y <= b
# It is squashed with constant force by impermeable, frictionless plattens on its top and bottom surfaces (at y=+/-b)
# Fluid is allowed to leak out from its sides (at x=+/-a)
# The porepressure within the sample is monitored.
#
# As is common in the literature, this is simulated by
# considering the quarter-sample, 0<=x<=a and 0<=y<=b, with
# impermeable, roller BCs at x=0 and y=0 and y=b.
# Porepressure is fixed at zero on x=a.
# Porepressure and displacement are initialised to zero.
# Then the top (y=b) is moved downwards with prescribed velocity,
# so that the total force that is inducing this downwards velocity
# is fixed. The velocity is worked out by solving Mandel's problem
# analytically, and the total force is monitored in the simulation
# to check that it indeed remains constant.
#
# Here are the problem's parameters, and their values:
# Soil width. a = 1
# Soil height. b = 0.1
# Soil's Lame lambda. la = 0.5
# Soil's Lame mu, which is also the Soil's shear modulus. mu = G = 0.75
# Soil bulk modulus. K = la + 2*mu/3 = 1
# Drained Poisson ratio. nu = (3K - 2G)/(6K + 2G) = 0.2
# Soil bulk compliance. 1/K = 1
# Fluid bulk modulus. Kf = 8
# Fluid bulk compliance. 1/Kf = 0.125
# Soil initial porosity. phi0 = 0.1
# Biot coefficient. alpha = 0.6
# Biot modulus. M = 1/(phi0/Kf + (alpha - phi0)(1 - alpha)/K) = 4.705882
# Undrained bulk modulus. Ku = K + alpha^2*M = 2.694118
# Undrained Poisson ratio. nuu = (3Ku - 2G)/(6Ku + 2G) = 0.372627
# Skempton coefficient. B = alpha*M/Ku = 1.048035
# Fluid mobility (soil permeability/fluid viscosity). k = 1.5
# Consolidation coefficient. c = 2*k*B^2*G*(1-nu)*(1+nuu)^2/9/(1-nuu)/(nuu-nu) = 3.821656
# Normal stress on top. F = 1
#
# The solution for porepressure and displacements is given in
# AHD Cheng and E Detournay "A direct boundary element method for plane strain poroelasticity" International Journal of Numerical and Analytical Methods in Geomechanics 12 (1988) 551-572.
# The solution involves complicated infinite series, so I shall not write it here
[Mesh]
type = GeneratedMesh
dim = 3
nx = 10
ny = 1
nz = 1
xmin = 0
xmax = 1
ymin = 0
ymax = 0.1
zmin = 0
zmax = 1
[]
[GlobalParams]
displacements = 'disp_x disp_y disp_z'
PorousFlowDictator = dictator
block = 0
[]
[Variables]
[./disp_x]
[../]
[./disp_y]
[../]
[./disp_z]
[../]
[./porepressure]
[../]
[]
[BCs]
[./roller_xmin]
type = DirichletBC
variable = disp_x
value = 0
boundary = 'left'
[../]
[./roller_ymin]
type = DirichletBC
variable = disp_y
value = 0
boundary = 'bottom'
[../]
[./plane_strain]
type = DirichletBC
variable = disp_z
value = 0
boundary = 'back front'
[../]
[./xmax_drained]
type = DirichletBC
variable = porepressure
value = 0
boundary = right
[../]
[./top_velocity]
type = FunctionDirichletBC
variable = disp_y
function = top_velocity
boundary = top
[../]
[]
[Functions]
[./top_velocity]
type = PiecewiseLinear
x = '0 0.002 0.006 0.014 0.03 0.046 0.062 0.078 0.094 0.11 0.126 0.142 0.158 0.174 0.19 0.206 0.222 0.238 0.254 0.27 0.286 0.302 0.318 0.334 0.35 0.366 0.382 0.398 0.414 0.43 0.446 0.462 0.478 0.494 0.51 0.526 0.542 0.558 0.574 0.59 0.606 0.622 0.638 0.654 0.67 0.686 0.702'
y = '-0.041824842 -0.042730269 -0.043412712 -0.04428867 -0.045509181 -0.04645965 -0.047268246 -0.047974749 -0.048597109 -0.0491467 -0.049632388 -0.050061697 -0.050441198 -0.050776675 -0.051073238 -0.0513354 -0.051567152 -0.051772022 -0.051953128 -0.052113227 -0.052254754 -0.052379865 -0.052490464 -0.052588233 -0.052674662 -0.052751065 -0.052818606 -0.052878312 -0.052931093 -0.052977751 -0.053018997 -0.053055459 -0.053087691 -0.053116185 -0.053141373 -0.05316364 -0.053183324 -0.053200724 -0.053216106 -0.053229704 -0.053241725 -0.053252351 -0.053261745 -0.053270049 -0.053277389 -0.053283879 -0.053289615'
[../]
[]
[AuxVariables]
[./tot_force]
order = CONSTANT
family = MONOMIAL
[../]
[]
[AuxKernels]
[./tot_force]
type = ParsedAux
args = 'stress_yy porepressure'
execute_on = timestep_end
variable = tot_force
function = '-stress_yy+0.6*porepressure'
[../]
[]
[Modules]
[./FluidProperties]
[./the_simple_fluid]
type = SimpleFluidProperties
thermal_expansion = 0.0
bulk_modulus = 8.0
viscosity = 1.0
density0 = 1.0
[../]
[../]
[]
[PorousFlowBasicTHM]
coupling_type = HydroMechanical
displacements = 'disp_x disp_y disp_z'
multiply_by_density = false
porepressure = porepressure
biot_coefficient = 0.6
gravity = '0 0 0'
fp = the_simple_fluid
[]
[Materials]
[./elasticity_tensor]
type = ComputeElasticityTensor
C_ijkl = '0.5 0.75'
# bulk modulus is lambda + 2*mu/3 = 0.5 + 2*0.75/3 = 1
fill_method = symmetric_isotropic
[../]
[./strain]
type = ComputeSmallStrain
[../]
[./stress]
type = ComputeLinearElasticStress
[../]
[./porosity]
type = PorousFlowPorosityConst # only the initial value of this is ever used
porosity = 0.1
[../]
[./biot_modulus]
type = PorousFlowConstantBiotModulus
biot_coefficient = 0.6
solid_bulk_compliance = 1
fluid_bulk_modulus = 8
[../]
[./permeability]
type = PorousFlowPermeabilityConst
permeability = '1.5 0 0 0 1.5 0 0 0 1.5'
[../]
[]
[Postprocessors]
[./p0]
type = PointValue
outputs = csv
point = '0.0 0 0'
variable = porepressure
[../]
[./p1]
type = PointValue
outputs = csv
point = '0.1 0 0'
variable = porepressure
[../]
[./p2]
type = PointValue
outputs = csv
point = '0.2 0 0'
variable = porepressure
[../]
[./p3]
type = PointValue
outputs = csv
point = '0.3 0 0'
variable = porepressure
[../]
[./p4]
type = PointValue
outputs = csv
point = '0.4 0 0'
variable = porepressure
[../]
[./p5]
type = PointValue
outputs = csv
point = '0.5 0 0'
variable = porepressure
[../]
[./p6]
type = PointValue
outputs = csv
point = '0.6 0 0'
variable = porepressure
[../]
[./p7]
type = PointValue
outputs = csv
point = '0.7 0 0'
variable = porepressure
[../]
[./p8]
type = PointValue
outputs = csv
point = '0.8 0 0'
variable = porepressure
[../]
[./p9]
type = PointValue
outputs = csv
point = '0.9 0 0'
variable = porepressure
[../]
[./p99]
type = PointValue
outputs = csv
point = '1 0 0'
variable = porepressure
[../]
[./xdisp]
type = PointValue
outputs = csv
point = '1 0.1 0'
variable = disp_x
[../]
[./ydisp]
type = PointValue
outputs = csv
point = '1 0.1 0'
variable = disp_y
[../]
[./total_downwards_force]
type = ElementAverageValue
outputs = csv
variable = tot_force
[../]
[./dt]
type = FunctionValuePostprocessor
outputs = console
function = if(0.15*t<0.01,0.15*t,0.01)
[../]
[]
[Preconditioning]
[./andy]
type = SMP
full = true
petsc_options_iname = '-ksp_type -pc_type -sub_pc_type -snes_atol -snes_rtol -snes_max_it'
petsc_options_value = 'gmres asm lu 1E-14 1E-10 10000'
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
start_time = 0
end_time = 0.7
[./TimeStepper]
type = PostprocessorDT
postprocessor = dt
dt = 0.001
[../]
[]
[Outputs]
execute_on = 'timestep_end'
file_base = mandel_basicthm
[./csv]
interval = 3
type = CSV
[../]
[]
modules/porous_flow/examples/reservoir_model/regular_grid.i
# SPE 10 comparative problem - model 1
# Data and description from https://www.spe.org/web/csp/datasets/set01.htm
# Simple input file that just establishes gravity equilibrium in the model
#
# Heterogeneous permeability is included by reading data from an external file
# using the PiecewiseMultilinear function, and saving that data to an elemental
# AuxVariable that is then used in PorousFlowPermeabilityConstFromVar
[Mesh]
type = GeneratedMesh
dim = 2
nx = 100
ny = 20
xmax = 762
ymax = 15.24
[]
[GlobalParams]
PorousFlowDictator = dictator
gravity = '0 -9.81 0'
temperature_unit = Celsius
[]
[Variables]
[porepressure]
initial_condition = 20e6
[]
[]
[Functions]
[perm_md_fcn]
type = PiecewiseMultilinear
data_file = spe10_case1.data
[]
[]
[BCs]
[top]
type = DirichletBC
variable = porepressure
value = 20e6
boundary = top
[]
[]
[AuxVariables]
[temperature]
initial_condition = 50
[]
[xnacl]
initial_condition = 0.1
[]
[porosity]
family = MONOMIAL
order = CONSTANT
initial_condition = 0.2
[]
[perm_md]
family = MONOMIAL
order = CONSTANT
[]
[perm]
family = MONOMIAL
order = CONSTANT
[]
[]
[Kernels]
[mass0]
type = PorousFlowMassTimeDerivative
variable = porepressure
[]
[flux0]
type = PorousFlowFullySaturatedDarcyFlow
variable = porepressure
[]
[]
[AuxKernels]
[perm_md]
type = FunctionAux
function = perm_md_fcn
variable = perm_md
execute_on = initial
[]
[perm]
type = ParsedAux
variable = perm
args = perm_md
function = '9.869233e-16*perm_md'
execute_on = initial
[]
[]
[UserObjects]
[dictator]
type = PorousFlowDictator
porous_flow_vars = porepressure
number_fluid_phases = 1
number_fluid_components = 1
[]
[]
[Modules]
[FluidProperties]
[water]
type = Water97FluidProperties
[]
[watertab]
type = TabulatedFluidProperties
fp = water
save_file = false
[]
[]
[]
[Materials]
[temperature]
type = PorousFlowTemperature
temperature = temperature
[]
[ps]
type = PorousFlow1PhaseFullySaturated
porepressure = porepressure
[]
[massfrac]
type = PorousFlowMassFraction
[]
[brine]
type = PorousFlowBrine
compute_enthalpy = false
compute_internal_energy = false
xnacl = xnacl
phase = 0
water_fp = watertab
[]
[porosity]
type = PorousFlowPorosityConst
porosity = porosity
[]
[permeability]
type = PorousFlowPermeabilityConstFromVar
perm_xx = perm
perm_yy = perm
perm_zz = perm
[]
[]
[Preconditioning]
[smp]
type = SMP
full = true
[]
[]
[Executioner]
type = Transient
solve_type = Newton
end_time = 1e5
nl_abs_tol = 1e-12
nl_rel_tol = 1e-06
steady_state_detection = true
steady_state_tolerance = 1e-12
[TimeStepper]
type = IterationAdaptiveDT
dt = 1e2
[]
[]
[Outputs]
execute_on = 'initial timestep_end'
exodus = true
perf_graph = true
[]
modules/functional_expansion_tools/test/tests/standard_use/volume_sub.i
[Mesh]
type = GeneratedMesh
dim = 1
xmin = 0.0
xmax = 10.0
nx = 15
[]
[Variables]
[./empty]
[../]
[]
[AuxVariables]
[./s]
order = FIRST
family = LAGRANGE
[../]
[./m_in]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
[./null_kernel]
type = NullKernel
variable = empty
[../]
[]
[AuxKernels]
[./reconstruct_m_in]
type = FunctionSeriesToAux
function = FX_Basis_Value_Sub
variable = m_in
[../]
[./calculate_s]
type = ParsedAux
variable = s
args = m_in
function = '2*exp(-m_in/0.8)'
[../]
[]
[Functions]
[./FX_Basis_Value_Sub]
type = FunctionSeries
series_type = Cartesian
orders = '3'
physical_bounds = '0.0 10.0'
x = Legendre
[../]
[]
[UserObjects]
[./FX_Value_UserObject_Sub]
type = FXVolumeUserObject
function = FX_Basis_Value_Sub
variable = s
[../]
[]
[Executioner]
type = Transient
num_steps = 10
dt = 0.5
solve_type = PJFNK
petsc_options_iname = '-pc_type -pc_hypre_type'
petsc_options_value = 'hypre boomeramg'
[]
modules/porous_flow/test/tests/poro_elasticity/mandel.i
# Mandel's problem of consolodation of a drained medium
#
# A sample is in plane strain.
# -a <= x <= a
# -b <= y <= b
# It is squashed with constant force by impermeable, frictionless plattens on its top and bottom surfaces (at y=+/-b)
# Fluid is allowed to leak out from its sides (at x=+/-a)
# The porepressure within the sample is monitored.
#
# As is common in the literature, this is simulated by
# considering the quarter-sample, 0<=x<=a and 0<=y<=b, with
# impermeable, roller BCs at x=0 and y=0 and y=b.
# Porepressure is fixed at zero on x=a.
# Porepressure and displacement are initialised to zero.
# Then the top (y=b) is moved downwards with prescribed velocity,
# so that the total force that is inducing this downwards velocity
# is fixed. The velocity is worked out by solving Mandel's problem
# analytically, and the total force is monitored in the simulation
# to check that it indeed remains constant.
#
# Here are the problem's parameters, and their values:
# Soil width. a = 1
# Soil height. b = 0.1
# Soil's Lame lambda. la = 0.5
# Soil's Lame mu, which is also the Soil's shear modulus. mu = G = 0.75
# Soil bulk modulus. K = la + 2*mu/3 = 1
# Drained Poisson ratio. nu = (3K - 2G)/(6K + 2G) = 0.2
# Soil bulk compliance. 1/K = 1
# Fluid bulk modulus. Kf = 8
# Fluid bulk compliance. 1/Kf = 0.125
# Soil initial porosity. phi0 = 0.1
# Biot coefficient. alpha = 0.6
# Biot modulus. M = 1/(phi0/Kf + (alpha - phi0)(1 - alpha)/K) = 4.705882
# Undrained bulk modulus. Ku = K + alpha^2*M = 2.694118
# Undrained Poisson ratio. nuu = (3Ku - 2G)/(6Ku + 2G) = 0.372627
# Skempton coefficient. B = alpha*M/Ku = 1.048035
# Fluid mobility (soil permeability/fluid viscosity). k = 1.5
# Consolidation coefficient. c = 2*k*B^2*G*(1-nu)*(1+nuu)^2/9/(1-nuu)/(nuu-nu) = 3.821656
# Normal stress on top. F = 1
#
# The solution for porepressure and displacements is given in
# AHD Cheng and E Detournay "A direct boundary element method for plane strain poroelasticity" International Journal of Numerical and Analytical Methods in Geomechanics 12 (1988) 551-572.
# The solution involves complicated infinite series, so I shall not write it here
#
# FINAL NOTE: The above solution assumes constant Biot Modulus.
# In porous_flow this is not true. Therefore the solution is
# a little different than in the paper. This test was therefore
# validated against MOOSE's poromechanics, which can choose either
# a constant Biot Modulus (which has been shown to agree with
# the analytic solution), or a non-constant Biot Modulus (which
# gives the same results as porous_flow).
[Mesh]
type = GeneratedMesh
dim = 3
nx = 10
ny = 1
nz = 1
xmin = 0
xmax = 1
ymin = 0
ymax = 0.1
zmin = 0
zmax = 1
[]
[GlobalParams]
displacements = 'disp_x disp_y disp_z'
PorousFlowDictator = dictator
block = 0
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = 'porepressure disp_x disp_y disp_z'
number_fluid_phases = 1
number_fluid_components = 1
[../]
[./pc]
type = PorousFlowCapillaryPressureVG
m = 0.8
alpha = 1e-5
[../]
[]
[Variables]
[./disp_x]
[../]
[./disp_y]
[../]
[./disp_z]
[../]
[./porepressure]
[../]
[]
[BCs]
[./roller_xmin]
type = DirichletBC
variable = disp_x
value = 0
boundary = 'left'
[../]
[./roller_ymin]
type = DirichletBC
variable = disp_y
value = 0
boundary = 'bottom'
[../]
[./plane_strain]
type = DirichletBC
variable = disp_z
value = 0
boundary = 'back front'
[../]
[./xmax_drained]
type = DirichletBC
variable = porepressure
value = 0
boundary = right
[../]
[./top_velocity]
type = FunctionDirichletBC
variable = disp_y
function = top_velocity
boundary = top
[../]
[]
[Functions]
[./top_velocity]
type = PiecewiseLinear
x = '0 0.002 0.006 0.014 0.03 0.046 0.062 0.078 0.094 0.11 0.126 0.142 0.158 0.174 0.19 0.206 0.222 0.238 0.254 0.27 0.286 0.302 0.318 0.334 0.35 0.366 0.382 0.398 0.414 0.43 0.446 0.462 0.478 0.494 0.51 0.526 0.542 0.558 0.574 0.59 0.606 0.622 0.638 0.654 0.67 0.686 0.702'
y = '-0.041824842 -0.042730269 -0.043412712 -0.04428867 -0.045509181 -0.04645965 -0.047268246 -0.047974749 -0.048597109 -0.0491467 -0.049632388 -0.050061697 -0.050441198 -0.050776675 -0.051073238 -0.0513354 -0.051567152 -0.051772022 -0.051953128 -0.052113227 -0.052254754 -0.052379865 -0.052490464 -0.052588233 -0.052674662 -0.052751065 -0.052818606 -0.052878312 -0.052931093 -0.052977751 -0.053018997 -0.053055459 -0.053087691 -0.053116185 -0.053141373 -0.05316364 -0.053183324 -0.053200724 -0.053216106 -0.053229704 -0.053241725 -0.053252351 -0.053261745 -0.053270049 -0.053277389 -0.053283879 -0.053289615'
[../]
[]
[AuxVariables]
[./stress_yy]
order = CONSTANT
family = MONOMIAL
[../]
[./tot_force]
order = CONSTANT
family = MONOMIAL
[../]
[]
[AuxKernels]
[./stress_yy]
type = RankTwoAux
rank_two_tensor = stress
variable = stress_yy
index_i = 1
index_j = 1
[../]
[./tot_force]
type = ParsedAux
args = 'stress_yy porepressure'
execute_on = timestep_end
variable = tot_force
function = '-stress_yy+0.6*porepressure'
[../]
[]
[Kernels]
[./grad_stress_x]
type = StressDivergenceTensors
variable = disp_x
component = 0
[../]
[./grad_stress_y]
type = StressDivergenceTensors
variable = disp_y
component = 1
[../]
[./grad_stress_z]
type = StressDivergenceTensors
variable = disp_z
component = 2
[../]
[./poro_x]
type = PorousFlowEffectiveStressCoupling
biot_coefficient = 0.6
variable = disp_x
component = 0
[../]
[./poro_y]
type = PorousFlowEffectiveStressCoupling
biot_coefficient = 0.6
variable = disp_y
component = 1
[../]
[./poro_z]
type = PorousFlowEffectiveStressCoupling
biot_coefficient = 0.6
component = 2
variable = disp_z
[../]
[./poro_vol_exp]
type = PorousFlowMassVolumetricExpansion
variable = porepressure
fluid_component = 0
[../]
[./mass0]
type = PorousFlowMassTimeDerivative
fluid_component = 0
variable = porepressure
[../]
[./flux]
type = PorousFlowAdvectiveFlux
variable = porepressure
gravity = '0 0 0'
fluid_component = 0
[../]
[]
[Modules]
[./FluidProperties]
[./simple_fluid]
type = SimpleFluidProperties
bulk_modulus = 8
density0 = 1
thermal_expansion = 0
viscosity = 1
[../]
[../]
[]
[Materials]
[./temperature]
type = PorousFlowTemperature
[../]
[./elasticity_tensor]
type = ComputeElasticityTensor
C_ijkl = '0.5 0.75'
# bulk modulus is lambda + 2*mu/3 = 0.5 + 2*0.75/3 = 1
fill_method = symmetric_isotropic
[../]
[./strain]
type = ComputeSmallStrain
[../]
[./stress]
type = ComputeLinearElasticStress
[../]
[./eff_fluid_pressure]
type = PorousFlowEffectiveFluidPressure
[../]
[./vol_strain]
type = PorousFlowVolumetricStrain
[../]
[./ppss]
type = PorousFlow1PhaseP
porepressure = porepressure
capillary_pressure = pc
[../]
[./massfrac]
type = PorousFlowMassFraction
[../]
[./simple_fluid]
type = PorousFlowSingleComponentFluid
fp = simple_fluid
phase = 0
[../]
[./porosity]
type = PorousFlowPorosity
fluid = true
mechanical = true
ensure_positive = false
porosity_zero = 0.1
biot_coefficient = 0.6
solid_bulk = 1
[../]
[./permeability]
type = PorousFlowPermeabilityConst
permeability = '1.5 0 0 0 1.5 0 0 0 1.5'
[../]
[./relperm]
type = PorousFlowRelativePermeabilityCorey
n = 0 # unimportant in this fully-saturated situation
phase = 0
[../]
[]
[Postprocessors]
[./p0]
type = PointValue
outputs = csv
point = '0.0 0 0'
variable = porepressure
[../]
[./p1]
type = PointValue
outputs = csv
point = '0.1 0 0'
variable = porepressure
[../]
[./p2]
type = PointValue
outputs = csv
point = '0.2 0 0'
variable = porepressure
[../]
[./p3]
type = PointValue
outputs = csv
point = '0.3 0 0'
variable = porepressure
[../]
[./p4]
type = PointValue
outputs = csv
point = '0.4 0 0'
variable = porepressure
[../]
[./p5]
type = PointValue
outputs = csv
point = '0.5 0 0'
variable = porepressure
[../]
[./p6]
type = PointValue
outputs = csv
point = '0.6 0 0'
variable = porepressure
[../]
[./p7]
type = PointValue
outputs = csv
point = '0.7 0 0'
variable = porepressure
[../]
[./p8]
type = PointValue
outputs = csv
point = '0.8 0 0'
variable = porepressure
[../]
[./p9]
type = PointValue
outputs = csv
point = '0.9 0 0'
variable = porepressure
[../]
[./p99]
type = PointValue
outputs = csv
point = '1 0 0'
variable = porepressure
[../]
[./xdisp]
type = PointValue
outputs = csv
point = '1 0.1 0'
variable = disp_x
[../]
[./ydisp]
type = PointValue
outputs = csv
point = '1 0.1 0'
variable = disp_y
[../]
[./total_downwards_force]
type = ElementAverageValue
outputs = csv
variable = tot_force
[../]
[./dt]
type = FunctionValuePostprocessor
outputs = console
function = if(0.15*t<0.01,0.15*t,0.01)
[../]
[]
[Preconditioning]
[./andy]
type = SMP
full = true
petsc_options_iname = '-ksp_type -pc_type -sub_pc_type -snes_atol -snes_rtol -snes_max_it'
petsc_options_value = 'gmres asm lu 1E-14 1E-10 10000'
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
start_time = 0
end_time = 0.7
[./TimeStepper]
type = PostprocessorDT
postprocessor = dt
dt = 0.001
[../]
[]
[Outputs]
execute_on = 'timestep_end'
file_base = mandel
[./csv]
interval = 3
type = CSV
[../]
[]
test/tests/functions/piecewise_multilinear/twoD_const.i
# PiecewiseMultilinear function tests in 2D
# See [Functions] block for a description of the tests
# The functions are compared with ParsedFunctions using postprocessors
[Mesh]
type = GeneratedMesh
dim = 2
xmin = 0
xmax = 2
nx = 4
ymin = -1
ymax = 1
ny = 4
[]
[Variables]
[./dummy]
[../]
[]
[Kernels]
[./dummy_u]
type = TimeDerivative
variable = dummy
[../]
[]
[AuxVariables]
[./constant]
family = MONOMIAL
order = CONSTANT
[../]
[./constant_ref]
family = MONOMIAL
order = CONSTANT
[../]
[./diff]
family = MONOMIAL
order = CONSTANT
[../]
[]
[AuxKernels]
[./const_AuxK]
type = FunctionAux
variable = constant
function = const_fcn
[../]
[./const_ref_AuxK]
type = FunctionAux
variable = constant_ref
function = const_ref
[../]
[./diff]
type = ParsedAux
variable = diff
function = 'constant - constant_ref'
args = 'constant constant_ref'
[../]
[]
[Functions]
[./const_fcn]
type = PiecewiseMulticonstant
direction = 'left right'
data_file = twoD_const.txt
[../]
[./const_ref]
type = ParsedFunction
value = '
ix := if(x < 0.5, 0, if(x < 1, 1, 2));
iy := if(y > 0, 2, if(y > -0.5, 1, 0));
iy * 3 + ix
'
[../]
[]
[Postprocessors]
[./diff_pp]
type = ElementIntegralVariablePostprocessor
variable = diff
[../]
[]
[Executioner]
type = Transient
dt = 1
end_time = 1
[]
[Outputs]
execute_on = 'timestep_end'
file_base = twoD_const
hide = dummy
exodus = true
[]
modules/phase_field/examples/interfacekernels/interface_fluxbc.i
#
# This test demonstrates an InterfaceKernel (InterfaceDiffusionFlux) that can
# replace a pair of integrated DiffusionFluxBC boundary conditions.
#
# The AuxVariable 'diff' shows the difference between the BC and the InterfaceKernel
# approach.
#
[Mesh]
[gen]
type = GeneratedMeshGenerator
dim = 2
nx = 50
ny = 50
[]
[./box1]
input = gen
type = SubdomainBoundingBoxGenerator
block_id = 1
bottom_left = '0 0 0'
top_right = '0.51 1 0'
[../]
[./box2]
input = box1
type = SubdomainBoundingBoxGenerator
block_id = 2
bottom_left = '0.49 0 0'
top_right = '1 1 0'
[../]
[./iface_u]
type = SideSetsBetweenSubdomainsGenerator
master_block = 1
paired_block = 2
new_boundary = 10
input = box2
[../]
[./iface_v]
type = SideSetsBetweenSubdomainsGenerator
master_block = 2
paired_block = 1
new_boundary = 11
input = iface_u
[../]
[]
[Variables]
[./u1]
block = 1
[./InitialCondition]
type = FunctionIC
function = 'r:=sqrt((x-0.4)^2+(y-0.5)^2);if(r<0.05,5,1)'
[../]
[../]
[./v1]
block = 2
[./InitialCondition]
type = FunctionIC
function = 'r:=sqrt((x-0.7)^2+(y-0.5)^2);if(r<0.05,5,1)'
[../]
[../]
[./u2]
block = 1
[./InitialCondition]
type = FunctionIC
function = 'r:=sqrt((x-0.4)^2+(y-0.5)^2);if(r<0.05,5,1)'
[../]
[../]
[./v2]
block = 2
[./InitialCondition]
type = FunctionIC
function = 'r:=sqrt((x-0.7)^2+(y-0.5)^2);if(r<0.05,5,1)'
[../]
[../]
[]
[Kernels]
[./u1_diff]
type = Diffusion
variable = u1
block = 1
[../]
[./u1_dt]
type = TimeDerivative
variable = u1
block = 1
[../]
[./v1_diff]
type = Diffusion
variable = v1
block = 2
[../]
[./v1_dt]
type = TimeDerivative
variable = v1
block = 2
[../]
[./u2_diff]
type = Diffusion
variable = u2
block = 1
[../]
[./u2_dt]
type = TimeDerivative
variable = u2
block = 1
[../]
[./v2_diff]
type = Diffusion
variable = v2
block = 2
[../]
[./v2_dt]
type = TimeDerivative
variable = v2
block = 2
[../]
[]
[AuxVariables]
[./diff]
[../]
[]
[AuxKernels]
[./u_side]
type = ParsedAux
variable = diff
block = 1
args = 'u1 u2'
function = 'u1 - u2'
[../]
[./v_side]
type = ParsedAux
variable = diff
block = 2
args = 'v1 v2'
function = 'v1 - v2'
[../]
[]
[InterfaceKernels]
[./iface]
type = InterfaceDiffusionBoundaryTerm
boundary = 10
variable = u2
neighbor_var = v2
[../]
[]
[BCs]
[./u_boundary_term]
type = DiffusionFluxBC
variable = u1
boundary = 10
[../]
[./v_boundary_term]
type = DiffusionFluxBC
variable = v1
boundary = 11
[../]
[]
[Executioner]
type = Transient
dt = 0.001
num_steps = 20
[]
[Outputs]
exodus = true
print_linear_residuals = false
[]
modules/functional_expansion_tools/examples/3D_volumetric_Cartesian/sub.i
# Basic example coupling a master and sub app in a 3D Cartesian volume.
#
# The master app provides field values to the sub app via Functional Expansions, which then performs
# its calculations. The sub app's solution field values are then transferred back to the master app
# and coupled into the solution of the master app solution.
#
# This example couples Functional Expansions via AuxVariable.
#
# Note: this problem is not light, and may take a few minutes to solve.
[Mesh]
type = GeneratedMesh
dim = 3
xmin = 0.0
xmax = 10.0
nx = 15
ymin = 1.0
ymax = 11.0
ny = 25
zmin = 2.0
zmax = 12.0
nz = 35
[]
# Non-copy transfers only work with AuxVariable, but nothing will be solved without a variable
# defined. The solution is to define an empty variable tha does nothing, but causes MOOSE to solve
# the AuxKernels that we need.
[Variables]
[./empty]
[../]
[]
[AuxVariables]
[./s]
order = FIRST
family = LAGRANGE
[../]
[./m_in]
order = FIRST
family = LAGRANGE
[../]
[]
# We must have a kernel for every variable, hence this null kernel to match the variable 'empty'
[Kernels]
[./null_kernel]
type = NullKernel
variable = empty
[../]
[]
[AuxKernels]
[./reconstruct_m_in]
type = FunctionSeriesToAux
function = FX_Basis_Value_Sub
variable = m_in
[../]
[./calculate_s] # Something to make 's' change each time, but allow a converging solution
type = ParsedAux
variable = s
args = m_in
function = '2*exp(-m_in/0.8)'
[../]
[]
[Functions]
[./FX_Basis_Value_Sub]
type = FunctionSeries
series_type = Cartesian
orders = '3 4 5'
physical_bounds = '0.0 10.0 1.0 11.0 2.0 12.0'
x = Legendre
y = Legendre
z = Legendre
[../]
[]
[UserObjects]
[./FX_Value_UserObject_Sub]
type = FXVolumeUserObject
function = FX_Basis_Value_Sub
variable = s
[../]
[]
[Executioner]
type = Transient
num_steps = 10
dt = 0.5
solve_type = PJFNK
petsc_options_iname = '-pc_type -pc_hypre_type'
petsc_options_value = 'hypre boomeramg'
[]
modules/porous_flow/test/tests/chemistry/dissolution_limited_2phase.i
# Using a two-phase system (see dissolution_limited.i for the single-phase)
# The saturation and porosity are chosen so that the results are identical to dissolution_limited.i
#
# The dissolution reaction, with limited initial mineral concentration
#
# a <==> mineral
#
# produces "mineral". Using mineral_density = fluid_density, theta = 1 = eta, the DE is
#
# a' = -(mineral / (porosity * saturation))' = rate * surf_area * molar_vol (1 - (1 / eqm_const) * (act_coeff * a)^stoi)
#
# The following parameters are used
#
# T_ref = 0.5 K
# T = 1 K
# activation_energy = 3 J/mol
# gas_constant = 6 J/(mol K)
# kinetic_rate_at_ref_T = 0.60653 mol/(m^2 s)
# These give rate = 0.60653 * exp(1/2) = 1 mol/(m^2 s)
#
# surf_area = 0.5 m^2/L
# molar_volume = 2 L/mol
# These give rate * surf_area * molar_vol = 1 s^-1
#
# equilibrium_constant = 0.5 (dimensionless)
# primary_activity_coefficient = 2 (dimensionless)
# stoichiometry = 1 (dimensionless)
# This means that 1 - (1 / eqm_const) * (act_coeff * a)^stoi = 1 - 4 a, which is positive for a < 0.25, ie dissolution for a(t=0) < 0.25
#
# The solution of the DE is
# a = eqm_const / act_coeff + (a(t=0) - eqm_const / act_coeff) exp(-rate * surf_area * molar_vol * act_coeff * t / eqm_const)
# = 0.25 + (a(t=0) - 0.25) exp(-4 * t)
# c = c(t=0) - (a - a(t=0)) * porosity * saturation
#
# However, c(t=0) is small, so that the reaction only works until c=0, then a and c both remain fixed
#
# This test checks that (a + c / (porosity * saturation)) is time-independent, and that a follows the above solution, until c=0 and thereafter remains fixed.
#
# Aside:
# The exponential curve is not followed exactly because moose actually solves
# (a - a_old)/dt = rate * surf_area * molar_vol (1 - (1 / eqm_const) * (act_coeff * a)^stoi)
# which does not give an exponential exactly, except in the limit dt->0
[Mesh]
type = GeneratedMesh
dim = 1
[]
[Variables]
[./a]
initial_condition = 0.05
[../]
[]
[AuxVariables]
[./eqm_k]
initial_condition = 0.5
[../]
[./pressure0]
[../]
[./saturation1]
initial_condition = 0.25
[../]
[./b]
initial_condition = 0.123
[../]
[./ini_mineral_conc]
initial_condition = 0.015
[../]
[./mineral]
family = MONOMIAL
order = CONSTANT
[../]
[./should_be_static]
family = MONOMIAL
order = CONSTANT
[../]
[]
[AuxKernels]
[./mineral]
type = PorousFlowPropertyAux
property = mineral_concentration
mineral_species = 0
variable = mineral
[../]
[./should_be_static]
type = ParsedAux
args = 'mineral a'
function = 'a + mineral / 0.1'
variable = should_be_static
[../]
[]
[GlobalParams]
PorousFlowDictator = dictator
[]
[Kernels]
[./mass_a]
type = PorousFlowMassTimeDerivative
fluid_component = 0
variable = a
[../]
[./pre_dis]
type = PorousFlowPreDis
variable = a
mineral_density = 1000
stoichiometry = 1
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = a
number_fluid_phases = 2
number_fluid_components = 2
number_aqueous_kinetic = 1
aqueous_phase_number = 1
[../]
[./pc]
type = PorousFlowCapillaryPressureConst
[../]
[]
[Modules]
[./FluidProperties]
[./simple_fluid]
type = SimpleFluidProperties
bulk_modulus = 2e9 # huge, so mimic chemical_reactions
density0 = 1000
thermal_expansion = 0
viscosity = 1e-3
[../]
[../]
[]
[Materials]
[./temperature]
type = PorousFlowTemperature
temperature = 1
[../]
[./ppss]
type = PorousFlow2PhasePS
capillary_pressure = pc
phase0_porepressure = pressure0
phase1_saturation = saturation1
[../]
[./mass_frac]
type = PorousFlowMassFraction
mass_fraction_vars = 'b a'
[../]
[./predis]
type = PorousFlowAqueousPreDisChemistry
primary_concentrations = a
num_reactions = 1
equilibrium_constants = eqm_k
primary_activity_coefficients = 2
reactions = 1
specific_reactive_surface_area = 0.5
kinetic_rate_constant = 0.6065306597126334
activation_energy = 3
molar_volume = 2
gas_constant = 6
reference_temperature = 0.5
[../]
[./mineral_conc]
type = PorousFlowAqueousPreDisMineral
initial_concentrations = ini_mineral_conc
[../]
[./simple_fluid0]
type = PorousFlowSingleComponentFluid
fp = simple_fluid
phase = 0
[../]
[./simple_fluid1]
type = PorousFlowSingleComponentFluid
fp = simple_fluid
phase = 1
[../]
[./porosity]
type = PorousFlowPorosityConst
porosity = 0.4
[../]
[]
[Preconditioning]
[./smp]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
solve_type = Newton
nl_abs_tol = 1E-10
dt = 0.01
end_time = 1
[]
[Postprocessors]
[./a]
type = PointValue
point = '0 0 0'
variable = a
[../]
[./should_be_static]
type = PointValue
point = '0 0 0'
variable = should_be_static
[../]
[]
[Outputs]
interval = 10
csv = true
perf_graph = true
[]
test/tests/outputs/png/wedge.i
[Mesh]
file = wedge.e
uniform_refine = 1
[]
[Functions]
active = 'tr_x tr_y'
[./tr_x]
type = ParsedFunction
value = -x
[../]
[./tr_y]
type = ParsedFunction
value = y
[../]
[]
[AuxVariables]
[two_u]
[]
[]
[AuxKernels]
[two_u]
type = ParsedAux
variable = two_u
args = 'u'
function = '2*u'
[]
[]
[Variables]
active = 'u'
[./u]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
active = 'diff forcing dot'
[./diff]
type = Diffusion
variable = u
[../]
[./forcing]
type = GaussContForcing
variable = u
x_center = -0.5
y_center = 3.0
x_spread = 0.2
y_spread = 0.2
[../]
[./dot]
type = TimeDerivative
variable = u
[../]
[]
[BCs]
#active = ' '
[./Periodic]
[./x]
primary = 1
secondary = 2
transform_func = 'tr_x tr_y'
inv_transform_func = 'tr_x tr_y'
[../]
[../]
[]
[Executioner]
type = Transient
dt = 0.5
num_steps = 6
solve_type = NEWTON
[]
[Outputs]
[png]
type = PNGOutput
resolution = 25
color = RWB
variable = 'two_u'
[]
[]
modules/functional_expansion_tools/test/tests/errors/multiapp_sub.i
[Mesh]
type = GeneratedMesh
dim = 1
xmin = 0.0
xmax = 10.0
nx = 15
[]
[Variables]
[./empty]
[../]
[]
[AuxVariables]
[./s]
order = FIRST
family = LAGRANGE
[../]
[./m_in]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
[./null_kernel]
type = NullKernel
variable = empty
[../]
[]
[AuxKernels]
[./reconstruct_m_in]
type = FunctionSeriesToAux
function = FX_Basis_Value_Sub
variable = m_in
[../]
[./calculate_s]
type = ParsedAux
variable = s
args = m_in
function = '2*exp(-m_in/0.8)'
[../]
[]
[Functions]
[./FX_Basis_Value_Sub]
type = FunctionSeries
series_type = Cartesian
orders = '3'
physical_bounds = '0.0 10.0'
x = Legendre
[../]
[]
[UserObjects]
[./FX_Value_UserObject_Sub]
type = FXVolumeUserObject
function = FX_Basis_Value_Sub
variable = s
[../]
[]
[Executioner]
type = Transient
num_steps = 10
dt = 0.5
solve_type = PJFNK
petsc_options_iname = '-pc_type -pc_hypre_type'
petsc_options_value = 'hypre boomeramg'
[]