- vArray of coupled variables
C++ Type:std::vector<VariableName>
Description:Array of coupled variables
- variableThe name of the variable that this object applies to
C++ Type:AuxVariableName
Description:The name of the variable that this object applies to
BndsCalcAux
Calculate location of grain boundaries in a polycrystalline sample
This AuxKernel computes the value as
where is the variable the AuxKernel is acting on and (v) are a set of couple order parameters. When used with order parameters of the polycrystalline grain growth model, the resulting field for is in grain interiors and in grain boundaries ( along the mid plan of the grain boundaries).
Input Parameters
- blockThe list of block ids (SubdomainID) that this object will be applied
C++ Type:std::vector<SubdomainName>
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<BoundaryName>
Options:
Description:The list of boundary IDs from the mesh where this boundary condition applies
- check_boundary_restrictedTrueWhether to check for multiple element sides on the boundary in the case of a boundary restricted, element aux variable. Setting this to false will allow contribution to a single element's elemental value(s) from multiple boundary sides on the same element (example: when the restricted boundary exists on two or more sides of an element, such as at a corner of a mesh
Default:True
C++ Type:bool
Options:
Description:Whether to check for multiple element sides on the boundary in the case of a boundary restricted, element aux variable. Setting this to false will allow contribution to a single element's elemental value(s) from multiple boundary sides on the same element (example: when the restricted boundary exists on two or more sides of an element, such as at a corner of a mesh
- 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.
- op_numArray of coupled variables (num_name)
C++ Type:unsigned int
Options:
Description:Array of coupled variables (num_name)
- var_name_baseArray of coupled variables (base_name)
C++ Type:std::string
Options:
Description:Array of coupled variables (base_name)
Optional Parameters
- control_tagsAdds user-defined labels for accessing object parameters via control logic.
C++ Type:std::vector<std::string>
Options:
Description:Adds user-defined labels for accessing object parameters via control logic.
- enableTrueSet the enabled status of the MooseObject.
Default:True
C++ Type:bool
Options:
Description:Set the enabled status of the MooseObject.
- seed0The seed for the master random number generator
Default:0
C++ Type:unsigned int
Options:
Description:The seed for the master random number generator
- use_displaced_meshFalseWhether or not this object should use the displaced mesh for computation. Note that in the case this is true but no displacements are provided in the Mesh block the undisplaced mesh will still be used.
Default:False
C++ Type:bool
Options:
Description:Whether or not this object should use the displaced mesh for computation. Note that in the case this is true but no displacements are provided in the Mesh block the undisplaced mesh will still be used.
Advanced Parameters
Input Files
- (modules/phase_field/test/tests/rigidbodymotion/polycrystal_action.i)
- (modules/combined/test/tests/grain_texture/random_grain_orientation.i)
- (modules/combined/test/tests/grain_texture/EulerAngle2RGBAction.i)
- (modules/phase_field/test/tests/grain_growth/voronoi_adaptivity.i)
- (modules/phase_field/test/tests/grain_tracker_test/grain_tracker_ebsd.i)
- (modules/phase_field/test/tests/grain_growth/off-diagonal.i)
- (modules/phase_field/test/tests/rigidbodymotion/grain_maskedforce.i)
- (modules/phase_field/test/tests/grain_growth/test.i)
- (modules/phase_field/test/tests/initial_conditions/polycrystalcircles_fromvector.i)
- (modules/phase_field/test/tests/grain_growth/voronoi_adaptivity_ghost.i)
- (modules/phase_field/test/tests/grain_growth/boundingbox.i)
- (modules/phase_field/test/tests/grain_growth/explicit.i)
- (modules/phase_field/test/tests/initial_conditions/polycrystal_BndsCalcIC.i)
- (modules/phase_field/examples/grain_growth/grain_growth_2D_random.i)
- (modules/phase_field/test/tests/actions/gpm_kernel.i)
- (modules/phase_field/test/tests/grain_tracker_test/grain_tracker_volume_changing.i)
- (modules/phase_field/examples/grain_growth/grain_growth_3D.i)
- (modules/combined/examples/phase_field-mechanics/poly_grain_growth_2D_eldrforce.i)
- (modules/phase_field/examples/grain_growth/grain_growth_2D_voronoi_newadapt.i)
- (modules/phase_field/examples/ebsd_reconstruction/IN100-111grn.i)
- (modules/combined/examples/phase_field-mechanics/hex_grain_growth_2D_eldrforce.i)
- (modules/phase_field/test/tests/GrandPotentialPFM/GrandPotentialMultiphase.i)
- (modules/phase_field/test/tests/GrandPotentialPFM/GrandPotentialAnisotropy.i)
- (modules/phase_field/test/tests/grain_tracker_test/distributed_poly_ic.i)
- (modules/combined/test/tests/ACGrGrElasticDrivingForce/bicrystal.i)
- (modules/phase_field/test/tests/grain_tracker_test/grain_tracker_remapping_test.i)
- (modules/phase_field/test/tests/reconstruction/euler2rgb_no_grain_region.i)
- (modules/phase_field/test/tests/GrandPotentialPFM/GrandPotentialAnisotropyAntitrap.i)
- (modules/phase_field/test/tests/grain_tracker_test/grain_halo_over_bc.i)
- (modules/phase_field/test/tests/rigidbodymotion/grain_forcedensity.i)
- (modules/phase_field/test/tests/TotalFreeEnergy/TotalFreeEnergy_2var_test.i)
- (modules/phase_field/test/tests/DeformedGrain/DeformedGrain.i)
- (modules/phase_field/test/tests/grain_growth/hex.i)
- (modules/phase_field/test/tests/grain_growth/particle.i)
- (modules/phase_field/test/tests/grain_growth/constant_mobility.i)
- (modules/phase_field/test/tests/grain_growth/voronoi.i)
- (modules/phase_field/test/tests/grain_tracker_test/grain_tracker_test_elemental.i)
- (modules/phase_field/examples/rigidbodymotion/grain_forcedensity_ext.i)
- (modules/phase_field/examples/anisotropic_interfaces/GrandPotentialPlanarGrowth.i)
- (modules/phase_field/examples/grain_growth/grain_growth_2D_voronoi.i)
- (modules/phase_field/test/tests/rigidbodymotion/grain_motion_fauxGT.i)
- (modules/phase_field/test/tests/grain_growth/temperature_gradient.i)
- (modules/phase_field/test/tests/GBAnisotropy/test3.i)
- (modules/phase_field/examples/anisotropic_interfaces/GrandPotentialSolidification.i)
- (modules/phase_field/test/tests/grain_tracker_test/grain_tracker_nodal.i)
- (modules/phase_field/test/tests/grain_growth/thumb.i)
- (modules/phase_field/test/tests/grain_tracker_test/split_grain.i)
- (modules/phase_field/test/tests/grain_tracker_test/grain_tracker_advanced_op.i)
- (modules/phase_field/test/tests/GBAnisotropy/testwidth1.i)
- (modules/phase_field/examples/grain_growth/grain_growth_2D_graintracker.i)
- (modules/phase_field/test/tests/initial_conditions/TricrystalTripleJunctionIC.i)
- (modules/phase_field/examples/anisotropic_interfaces/GrandPotentialTwophaseAnisotropy.i)
- (modules/phase_field/test/tests/GBAnisotropy/test1.i)
- (modules/phase_field/test/tests/reconstruction/1phase_evolution.i)
- (modules/phase_field/examples/grain_growth/3D_6000_gr.i)
- (modules/misc/test/tests/dynamic_loading/dynamic_obj_registration/dynamic_syntax.i)
- (modules/phase_field/test/tests/GBAnisotropy/test2.i)
- (modules/combined/examples/phase_field-mechanics/grain_texture.i)
- (modules/phase_field/examples/rigidbodymotion/AC_CH_Multigrain.i)
- (modules/combined/examples/phase_field-mechanics/EBSD_reconstruction_grain_growth_mech.i)
- (modules/phase_field/test/tests/rigidbodymotion/grain_appliedforcedensity.i)
- (modules/phase_field/test/tests/grain_growth/evolution.i)
- (modules/phase_field/test/tests/reconstruction/euler2rgb_non_uniform_orientation.i)
- (modules/phase_field/examples/rigidbodymotion/grain_motion_GT.i)
- (modules/combined/test/tests/grain_texture/EulerAngleProvider2RGBAux_bicrystal.i)
- (modules/phase_field/test/tests/grain_growth/voronoi_columnar_3D.i)
References
(modules/phase_field/test/tests/rigidbodymotion/polycrystal_action.i)
# test file for showing reaction forces between particles
[GlobalParams]
var_name_base = eta
op_num = 2
[]
[Mesh]
type = GeneratedMesh
dim = 2
nx = 10
ny = 5
nz = 0
xmax = 50
ymax = 25
zmax = 0
elem_type = QUAD4
uniform_refine = 1
[]
[Variables]
[./c]
order = FIRST
family = LAGRANGE
[../]
[./w]
order = FIRST
family = LAGRANGE
[../]
[./PolycrystalVariables]
[../]
[]
[Kernels]
[./c_res]
type = SplitCHParsed
variable = c
f_name = F
kappa_name = kappa_c
args = 'eta0 eta1'
w = w
[../]
[./w_res]
type = SplitCHWRes
variable = w
mob_name = M
[../]
[./time]
type = CoupledTimeDerivative
variable = w
v = c
[../]
[./motion]
type = MultiGrainRigidBodyMotion
variable = w
c = c
v = 'eta0 eta1'
grain_force = grain_force
grain_tracker_object = grain_center
grain_volumes = grain_volumes
[../]
[./RigidBodyMultiKernel]
# Creates all of the necessary Allen Cahn kernels automatically
c = c
f_name = F
mob_name = M
kappa_name = kappa_eta
grain_force = grain_force
grain_tracker_object = grain_center
grain_volumes = grain_volumes
[../]
[]
[Materials]
[./pfmobility]
type = GenericConstantMaterial
prop_names = 'M kappa_c kappa_eta'
prop_values = '1.0 0.5 0.5'
[../]
[./free_energy]
type = DerivativeParsedMaterial
f_name = F
args = 'c eta0 eta1'
constant_names = 'barr_height cv_eq'
constant_expressions = '0.1 1.0e-2'
function = 16*barr_height*(c-cv_eq)^2*(1-cv_eq-c)^2+eta0*(1-eta0)*c+eta1*(1-eta1)*c
derivative_order = 2
[../]
[./force_density]
type = ForceDensityMaterial
c = c
etas ='eta0 eta1'
[../]
[]
[AuxVariables]
[./bnds]
[../]
[./MultiAuxVariables]
order = CONSTANT
family = MONOMIAL
variable_base = 'df'
data_type = 'RealGradient'
grain_num = 2
[../]
[./vadvx]
order = CONSTANT
family = MONOMIAL
[../]
[./vadvy]
order = CONSTANT
family = MONOMIAL
[../]
[./unique_grains]
order = CONSTANT
family = MONOMIAL
[../]
[./var_indices]
order = CONSTANT
family = MONOMIAL
[../]
[./centroids]
order = CONSTANT
family = MONOMIAL
[../]
[]
[AuxKernels]
[./bnds]
type = BndsCalcAux
variable = bnds
var_name_base = eta
op_num = 2
v = 'eta0 eta1'
[../]
[./MaterialVectorGradAuxKernel]
variable_base = 'df'
grain_num = 2
property = 'force_density'
[../]
[./vadv_x]
type = GrainAdvectionAux
component = x
grain_tracker_object = grain_center
grain_force = grain_force
grain_volumes = grain_volumes
variable = vadvx
[../]
[./vadv_y]
type = GrainAdvectionAux
component = y
grain_tracker_object = grain_center
grain_force = grain_force
grain_volumes = grain_volumes
variable = vadvy
[../]
[./unique_grains]
type = FeatureFloodCountAux
variable = unique_grains
flood_counter = grain_center
field_display = UNIQUE_REGION
execute_on = timestep_begin
[../]
[./var_indices]
type = FeatureFloodCountAux
variable = var_indices
flood_counter = grain_center
field_display = VARIABLE_COLORING
execute_on = timestep_begin
[../]
[./centroids]
type = FeatureFloodCountAux
variable = centroids
execute_on = timestep_begin
field_display = CENTROID
flood_counter = grain_center
[../]
[]
[ICs]
[./ic_eta0]
int_width = 1.0
x1 = 20.0
y1 = 0.0
radius = 14.0
outvalue = 0.0
variable = eta0
invalue = 1.0
type = SmoothCircleIC
[../]
[./IC_eta1]
int_width = 1.0
x1 = 30.0
y1 = 25.0
radius = 14.0
outvalue = 0.0
variable = eta1
invalue = 1.0
type = SmoothCircleIC
[../]
[./ic_c]
type = SpecifiedSmoothCircleIC
invalue = 1.0
outvalue = 0.1
int_width = 1.0
x_positions = '20.0 30.0 '
z_positions = '0.0 0.0 '
y_positions = '0.0 25.0 '
radii = '14.0 14.0'
3D_spheres = false
variable = c
block = 0
[../]
[]
[VectorPostprocessors]
[./forces]
type = GrainForcesPostprocessor
grain_force = grain_force
[../]
[./grain_volumes]
type = FeatureVolumeVectorPostprocessor
flood_counter = grain_center
execute_on = 'initial timestep_begin'
[../]
[]
[UserObjects]
[./grain_center]
type = GrainTracker
outputs = none
compute_var_to_feature_map = true
execute_on = 'initial timestep_begin'
[../]
[./grain_force]
type = ComputeGrainForceAndTorque
execute_on = 'initial linear nonlinear'
grain_data = grain_center
force_density = force_density
c = c
etas = 'eta0 eta1'
[../]
[]
[Preconditioning]
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = NEWTON
petsc_options_iname = '-pc_type -ksp_gmres_restart -sub_ksp_type -sub_pc_type -pc_asm_overlap'
petsc_options_value = 'asm 31 preonly lu 1'
l_max_its = 30
l_tol = 1.0e-4
nl_rel_tol = 1.0e-10
start_time = 0.0
num_steps = 1
dt = 0.1
[]
[Outputs]
exodus = true
csv = true
[]
(modules/combined/test/tests/grain_texture/random_grain_orientation.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 40
ny = 12
xmax = 1000
ymax = 300
elem_type = QUAD4
[]
[GlobalParams]
op_num = 2
var_name_base = gr
[]
[Variables]
[./PolycrystalVariables]
[../]
[]
[ICs]
[./PolycrystalICs]
[./BicrystalBoundingBoxIC]
x1 = 0
y1 = 0
x2 = 500
y2 = 1000
[../]
[../]
[]
[AuxVariables]
[./bnds]
order = FIRST
family = LAGRANGE
[../]
[./unique_grains]
order = CONSTANT
family = MONOMIAL
[../]
[./var_indices]
order = CONSTANT
family = MONOMIAL
[../]
[./active_bounds_elemental]
order = CONSTANT
family = MONOMIAL
[../]
[]
[Kernels]
[./PolycrystalKernel]
[../]
[]
[AuxKernels]
[./bnds_aux]
type = BndsCalcAux
variable = bnds
execute_on = timestep_end
[../]
[./unique_grains]
type = FeatureFloodCountAux
variable = unique_grains
flood_counter = grain_tracker
execute_on = 'initial timestep_begin'
field_display = UNIQUE_REGION
[../]
[./var_indices]
type = FeatureFloodCountAux
variable = var_indices
flood_counter = grain_tracker
execute_on = 'initial timestep_begin'
field_display = VARIABLE_COLORING
[../]
[./active_bounds_elemental]
type = FeatureFloodCountAux
variable = active_bounds_elemental
field_display = ACTIVE_BOUNDS
execute_on = 'initial timestep_begin'
flood_counter = grain_tracker
[../]
[]
[Modules]
[./PhaseField]
[./EulerAngles2RGB]
crystal_structure = cubic
euler_angle_provider = euler_angle_file
grain_tracker = grain_tracker
[../]
[../]
[]
[Materials]
[./Copper]
type = GBEvolution
block = 0
T = 500 # K
wGB = 75 # nm
GBmob0 = 2.5e-6 #m^4/(Js) from Schoenfelder 1997
Q = 0.23 #Migration energy in eV
GBenergy = 0.708 #GB energy in J/m^2
time_scale = 1.0e-6
[../]
[]
[UserObjects]
[./grain_tracker]
type = GrainTracker
flood_entity_type = elemental
outputs = none
compute_var_to_feature_map = true
execute_on = 'initial timestep_begin'
[../]
[./euler_angle_file]
type = RandomEulerAngleProvider
grain_tracker_object = grain_tracker
execute_on = 'initial timestep_begin'
[../]
[]
[Preconditioning]
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
solve_type = 'NEWTON'
dt = 0.2
num_steps = 3
[]
[Outputs]
exodus = true
perf_graph = true
[]
(modules/combined/test/tests/grain_texture/EulerAngle2RGBAction.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 40
ny = 12
xmax = 1000
ymax = 300
elem_type = QUAD4
[]
[GlobalParams]
op_num = 2
var_name_base = gr
[]
[Variables]
[./PolycrystalVariables]
[../]
[]
[ICs]
[./PolycrystalICs]
[./BicrystalBoundingBoxIC]
x1 = 0
y1 = 0
x2 = 500
y2 = 1000
[../]
[../]
[]
[AuxVariables]
[./bnds]
order = FIRST
family = LAGRANGE
[../]
[./unique_grains]
order = CONSTANT
family = MONOMIAL
[../]
[./var_indices]
order = CONSTANT
family = MONOMIAL
[../]
[./active_bounds_elemental]
order = CONSTANT
family = MONOMIAL
[../]
[]
[Kernels]
[./PolycrystalKernel]
[../]
[]
[AuxKernels]
[./bnds_aux]
type = BndsCalcAux
variable = bnds
execute_on = timestep_end
[../]
[./unique_grains]
type = FeatureFloodCountAux
variable = unique_grains
flood_counter = grain_tracker
execute_on = 'initial timestep_begin'
field_display = UNIQUE_REGION
[../]
[./var_indices]
type = FeatureFloodCountAux
variable = var_indices
flood_counter = grain_tracker
execute_on = 'initial timestep_begin'
field_display = VARIABLE_COLORING
[../]
[./active_bounds_elemental]
type = FeatureFloodCountAux
variable = active_bounds_elemental
field_display = ACTIVE_BOUNDS
execute_on = 'initial timestep_begin'
flood_counter = grain_tracker
[../]
[]
[Modules]
[./PhaseField]
[./EulerAngles2RGB]
crystal_structure = cubic
euler_angle_provider = euler_angle_file
grain_tracker = grain_tracker
[../]
[../]
[]
[Materials]
[./Copper]
type = GBEvolution
block = 0
T = 500 # K
wGB = 75 # nm
GBmob0 = 2.5e-6 #m^4/(Js) from Schoenfelder 1997
Q = 0.23 #Migration energy in eV
GBenergy = 0.708 #GB energy in J/m^2
time_scale = 1.0e-6
[../]
[]
[UserObjects]
[./grain_tracker]
type = FauxGrainTracker
connecting_threshold = 0.05
compute_var_to_feature_map = true
flood_entity_type = elemental
execute_on = 'initial timestep_begin'
outputs = none
[../]
[./euler_angle_file]
type = EulerAngleFileReader
file_name = test.tex
[../]
[]
[Postprocessors]
[./gr0_area]
type = ElementIntegralVariablePostprocessor
variable = gr0
[../]
[]
[Preconditioning]
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
solve_type = 'NEWTON'
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart -pc_hypre_boomeramg_strong_threshold'
petsc_options_value = 'hypre boomeramg 31 0.7'
l_max_its = 30
l_tol = 1e-4
nl_max_its = 30
nl_rel_tol = 1e-9
start_time = 0.0
num_steps = 3
dt = 0.2
[]
[Outputs]
execute_on = 'initial timestep_end'
exodus = true
perf_graph = true
[]
(modules/phase_field/test/tests/grain_growth/voronoi_adaptivity.i)
[Mesh]
[drmg]
type = DistributedRectilinearMeshGenerator
dim = 2
nx = 30
ny = 30
nz = 0
xmin = 0
xmax = 1000
ymin = 0
ymax = 1000
zmin = 0
zmax = 0
elem_type = QUAD4
[]
[]
[GlobalParams]
op_num = 4
var_name_base = gr
[]
[Variables]
[./PolycrystalVariables]
[../]
[]
[UserObjects]
[./voronoi]
type = FauxPolycrystalVoronoi
rand_seed = 105
grain_num = 4
coloring_algorithm = bt
[../]
[]
[ICs]
[./PolycrystalICs]
[./PolycrystalColoringIC]
polycrystal_ic_uo = voronoi
[../]
[../]
[]
[AuxVariables]
[./bnds]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
[./PolycrystalKernel]
[../]
[]
[AuxKernels]
[./BndsCalc]
type = BndsCalcAux
variable = bnds
execute_on = timestep_end
[../]
[]
[BCs]
[./Periodic]
[./All]
auto_direction = 'x y'
[../]
[../]
[]
[Materials]
[./Copper]
type = GBEvolution
T = 500 # K
wGB = 60 # nm
GBmob0 = 2.5e-6 #m^4/(Js) from Schoenfelder 1997
Q = 0.23 #Migration energy in eV
GBenergy = 0.708 #GB energy in J/m^2
[../]
[]
[Postprocessors]
active = ''
[./ngrains]
type = FeatureFloodCount
variable = bnds
threshold = 0.7
[../]
[]
[Preconditioning]
active = ''
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
scheme = 'bdf2'
solve_type = 'PJFNK'
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart'
petsc_options_value = 'hypre boomeramg 31'
l_tol = 1.0e-4
l_max_its = 30
nl_max_its = 20
nl_rel_tol = 1.0e-13
start_time = 0.0
num_steps = 2
dt = 80.0
[./Adaptivity]
initial_adaptivity = 2
refine_fraction = 0.7
coarsen_fraction = 0.1
max_h_level = 1
[../]
[]
[Outputs]
exodus = true
[]
(modules/phase_field/test/tests/grain_tracker_test/grain_tracker_ebsd.i)
[Mesh]
[ebsd_mesh]
type = EBSDMeshGenerator
filename = 'test.txt'
[]
[]
[GlobalParams]
op_num = 4
var_name_base = gr
[]
[UserObjects]
[ebsd_reader]
type = EBSDReader
[]
[ebsd]
type = PolycrystalEBSD
coloring_algorithm = bt
ebsd_reader = ebsd_reader
output_adjacency_matrix = true
[]
[grain_tracker]
type = GrainTracker
threshold = 0.2
connecting_threshold = 0.08
flood_entity_type = ELEMENTAL
compute_halo_maps = true # For displaying HALO fields
polycrystal_ic_uo = ebsd
execute_on = 'initial timestep_end'
[]
[]
[ICs]
[PolycrystalICs]
[PolycrystalColoringIC]
polycrystal_ic_uo = ebsd
[]
[]
[]
[Variables]
[PolycrystalVariables]
[]
[]
[AuxVariables]
[bnds]
[]
[unique_grains]
family = MONOMIAL
order = CONSTANT
[]
[var_indices]
family = MONOMIAL
order = CONSTANT
[]
[ebsd_grains]
family = MONOMIAL
order = CONSTANT
[]
[phi1]
family = MONOMIAL
order = CONSTANT
[]
[halo0]
order = CONSTANT
family = MONOMIAL
[]
[halo1]
order = CONSTANT
family = MONOMIAL
[]
[halo2]
order = CONSTANT
family = MONOMIAL
[]
[halo3]
order = CONSTANT
family = MONOMIAL
[]
[]
[Kernels]
[PolycrystalKernel]
[]
[]
[AuxKernels]
[BndsCalc]
type = BndsCalcAux
variable = bnds
execute_on = timestep_end
[]
[unique_grains]
type = FeatureFloodCountAux
variable = unique_grains
execute_on = 'initial timestep_end'
flood_counter = grain_tracker
field_display = UNIQUE_REGION
[]
[var_indices]
type = FeatureFloodCountAux
variable = var_indices
execute_on = 'initial timestep_end'
flood_counter = grain_tracker
field_display = VARIABLE_COLORING
[]
[grain_aux]
type = EBSDReaderPointDataAux
variable = ebsd_grains
ebsd_reader = ebsd_reader
data_name = 'feature_id'
execute_on = 'initial timestep_end'
[]
[phi1]
type = OutputEulerAngles
euler_angle_provider = ebsd_reader
output_euler_angle = phi1
grain_tracker = grain_tracker
variable = phi1
[]
[halo0]
type = FeatureFloodCountAux
variable = halo0
map_index = 0
field_display = HALOS
flood_counter = grain_tracker
[]
[halo1]
type = FeatureFloodCountAux
variable = halo1
map_index = 1
field_display = HALOS
flood_counter = grain_tracker
[]
[halo2]
type = FeatureFloodCountAux
variable = halo2
map_index = 2
field_display = HALOS
flood_counter = grain_tracker
[]
[halo3]
type = FeatureFloodCountAux
variable = halo3
map_index = 3
field_display = HALOS
flood_counter = grain_tracker
[]
[]
[Materials]
[CuGrGr]
type = GBEvolution
T = 500 #K
wGB = 0.75 #micron
length_scale = 1.0e-6
time_scale = 1.0e-4
GBmob0 = 2.5e-6
Q = 0.23
GBenergy = 0.708
molar_volume = 7.11e-6
[]
[]
[Postprocessors]
[n_nodes]
type = NumNodes
execute_on = timestep_end
[]
[DOFs]
type = NumDOFs
[]
[]
[Executioner]
type = Transient
scheme = 'bdf2'
#Preconditioned JFNK (default)
solve_type = 'PJFNK'
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart '
'-pc_hypre_boomeramg_strong_threshold'
petsc_options_value = 'hypre boomeramg 31 0.7'
l_tol = 1.0e-4
l_max_its = 20
nl_rel_tol = 1.0e-9
nl_max_its = 20
start_time = 0.0
num_steps = 1
dt = 0.05
[]
[Outputs]
execute_on = 'initial'
exodus = true
perf_graph = true
[]
(modules/phase_field/test/tests/grain_growth/off-diagonal.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 10
ny = 10
nz = 0
xmin = 0
xmax = 1000
ymin = 0
ymax = 1000
zmin = 0
zmax = 0
elem_type = QUAD4
uniform_refine = 2
[]
[GlobalParams]
op_num = 2
var_name_base = gr
[]
[Variables]
[./PolycrystalVariables]
[../]
[]
[ICs]
[./PolycrystalICs]
[./BicrystalCircleGrainIC]
radius = 333.333
x = 500
y = 500
int_width = 80
[../]
[../]
[]
[AuxVariables]
[./bnds]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
[./PolycrystalKernel]
[../]
[]
[AuxKernels]
[./BndsCalc]
type = BndsCalcAux
variable = bnds
[../]
[]
[BCs]
[./Periodic]
[./all]
auto_direction = 'x y'
[../]
[../]
[]
[Materials]
[./Copper]
type = GBEvolution
T = 500 # K
wGB = 60 # nm
GBmob0 = 2.5e-6 #m^4/(Js) from Schoenfelder 1997
Q = 0.23 #Migration energy in eV
GBenergy = 0.708 #GB energy in J/m^2
[../]
[]
[Postprocessors]
[./gr_area]
type = ElementIntegralVariablePostprocessor
variable = gr1
[../]
[]
[Preconditioning]
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = NEWTON
l_max_its = 30
nl_max_its = 20
start_time = 0.0
num_steps = 7
dt = 80.0
[./Adaptivity]
initial_adaptivity = 2
refine_fraction = 0.3
coarsen_fraction = 0.2
max_h_level = 2
[../]
[]
[Outputs]
exodus = true
[]
(modules/phase_field/test/tests/rigidbodymotion/grain_maskedforce.i)
# test file for showing pinning of grains
[GlobalParams]
var_name_base = eta
op_num = 2
[]
[Mesh]
type = GeneratedMesh
dim = 2
nx = 25
ny = 15
nz = 0
xmax = 50
ymax = 25
zmax = 0
elem_type = QUAD4
[]
[Variables]
[./c]
order = FIRST
family = LAGRANGE
[./InitialCondition]
type = SpecifiedSmoothCircleIC
invalue = 1.0
outvalue = 0.1
int_width = 4.0
x_positions = '20.0 30.0 '
z_positions = '0.0 0.0 '
y_positions = '0.0 25.0 '
radii = '10.0 10.0'
3D_spheres = false
variable = c
block = 0
[../]
[../]
[./w]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
[./c_res]
type = SplitCHParsed
variable = c
f_name = F
kappa_name = kappa_c
w = w
[../]
[./w_res]
type = SplitCHWRes
variable = w
mob_name = M
[../]
[./time]
type = CoupledTimeDerivative
variable = w
v = c
[../]
[./motion]
type = MultiGrainRigidBodyMotion
c = c
variable = w
v = 'eta0 eta1'
grain_tracker_object = grain_center
grain_force = grain_force
grain_volumes = grain_volumes
[../]
[]
[Materials]
[./pfmobility]
type = GenericConstantMaterial
block = 0
prop_names = 'M kappa_c kappa_eta'
prop_values = '5.0 2.0 0.1'
[../]
[./free_energy]
type = DerivativeParsedMaterial
block = 0
f_name = F
args = c
constant_names = 'barr_height cv_eq'
constant_expressions = '0.1 1.0e-2'
function = 16*barr_height*(c-cv_eq)^2*(1-cv_eq-c)^2
derivative_order = 2
[../]
[]
[AuxVariables]
[./eta0]
[../]
[./eta1]
[../]
[./bnds]
[../]
[]
[AuxKernels]
[./bnds]
type = BndsCalcAux
variable = bnds
var_name_base = eta
op_num = 2
v = 'eta0 eta1'
block = 0
[../]
[]
[ICs]
[./ic_eta0]
int_width = 4.0
x1 = 20.0
y1 = 0.0
radius = 10.0
outvalue = 0.0
variable = eta0
invalue = 1.0
type = SmoothCircleIC
[../]
[./IC_eta1]
int_width = 4.0
x1 = 30.0
y1 = 25.0
radius = 10.0
outvalue = 0.0
variable = eta1
invalue = 1.0
type = SmoothCircleIC
[../]
[]
[VectorPostprocessors]
[./forces_cosnt]
type = GrainForcesPostprocessor
grain_force = grain_force_const
[../]
[./forces_total]
type = GrainForcesPostprocessor
grain_force = grain_force
[../]
[./grain_volumes]
type = FeatureVolumeVectorPostprocessor
flood_counter = grain_center
execute_on = 'initial timestep_begin'
[../]
[]
[UserObjects]
[./grain_center]
type = GrainTracker
outputs = none
compute_var_to_feature_map = true
execute_on = 'initial timestep_begin'
[../]
[./grain_force_const]
type = ConstantGrainForceAndTorque
execute_on = 'linear nonlinear'
force = '5.0 10.0 0.0 1.0 0.0 0.0'
torque = '0.0 0.0 50.0 0.0 0.0 5.0'
[../]
[./grain_force]
type = MaskedGrainForceAndTorque
grain_force = grain_force_const
pinned_grains = 0
execute_on = 'linear nonlinear'
[../]
[]
[Preconditioning]
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = NEWTON
petsc_options_iname = '-pc_type -ksp_gmres_restart -sub_ksp_type -sub_pc_type -pc_asm_overlap'
petsc_options_value = 'asm 31 preonly lu 1'
l_max_its = 20
nl_max_its = 20
l_tol = 1.0e-4
nl_rel_tol = 1.0e-10
start_time = 0.0
num_steps = 1
dt = 1.0
[]
[Outputs]
exodus = true
csv = true
[]
(modules/phase_field/test/tests/grain_growth/test.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 10
ny = 10
nz = 0
xmin = 0
xmax = 400
ymin = 0
ymax = 400
zmin = 0
zmax = 0
elem_type = QUAD4
uniform_refine = 1
[]
[GlobalParams]
op_num = 2
var_name_base = gr
[]
[Variables]
[./PolycrystalVariables]
[../]
[]
[ICs]
[./PolycrystalICs]
[./BicrystalCircleGrainIC]
radius = 300
x = 400
y = 0
[../]
[../]
[]
[AuxVariables]
[./bnds]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
[./PolycrystalKernel]
[../]
[]
[AuxKernels]
[./BndsCalc]
type = BndsCalcAux
variable = bnds
[../]
[]
[Materials]
[./Copper]
type = GBEvolution
T = 500 # K
wGB = 60 # nm
GBmob0 = 2.5e-6 #m^4/(Js) from Schoenfelder 1997
Q = 0.23 #Migration energy in eV
GBenergy = 0.708 #GB energy in J/m^2
[../]
[]
[Postprocessors]
[./gr1area]
type = ElementIntegralVariablePostprocessor
variable = gr1
[../]
[]
[Preconditioning]
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = 'NEWTON'
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart'
petsc_options_value = 'hypre boomeramg 31'
l_tol = 1.0e-4
l_max_its = 30
nl_max_its = 20
nl_rel_tol = 1.0e-9
start_time = 0.0
num_steps = 5
dt = 80.0
[./Adaptivity]
initial_adaptivity = 2
refine_fraction = 0.8
coarsen_fraction = 0.05
max_h_level = 2
[../]
[]
[Outputs]
execute_on = 'timestep_end'
csv = true
exodus = true
[]
(modules/phase_field/test/tests/initial_conditions/polycrystalcircles_fromvector.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 100
ny = 56
nz = 0
xmin = 0
xmax = 200
ymin = 0
ymax = 112
zmin = 0
zmax = 0
[]
[GlobalParams]
op_num = 6
var_name_base = gr
[]
[Variables]
[./PolycrystalVariables]
[../]
[]
[AuxVariables]
[./bnds]
[../]
[]
[UserObjects]
[./circle_IC]
type = PolycrystalCircles
radii = '22 22 30 22 22 22 22 22 '
x_positions = '34 78 122 166 34 78 122 166'
y_positions = '34 34 34 34 78 78 78 78 '
z_positions = '0 0 0 0 0 0 0 0 '
execute_on = 'initial'
threshold = 0.2
connecting_threshold = 0.08
int_width = 8
[../]
[]
[ICs]
[./PolycrystalICs]
[./PolycrystalColoringIC]
polycrystal_ic_uo = circle_IC
[../]
[../]
[]
[Kernels]
[./dt_gr0]
type = TimeDerivative
variable = gr0
[../]
[./dt_gr1]
type = TimeDerivative
variable = gr1
[../]
[./dt_gr2]
type = TimeDerivative
variable = gr2
[../]
[./dt_gr3]
type = TimeDerivative
variable = gr3
[../]
[./dt_gr4]
type = TimeDerivative
variable = gr4
[../]
[./dt_gr5]
type = TimeDerivative
variable = gr5
[../]
[]
[AuxKernels]
[./bnds_aux]
type = BndsCalcAux
variable = bnds
execute_on = 'initial timestep_end'
[../]
[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = PJFNK
num_steps = 0
[]
[Outputs]
exodus = true
csv = false
[]
(modules/phase_field/test/tests/grain_growth/voronoi_adaptivity_ghost.i)
[Mesh]
[drmg]
type = DistributedRectilinearMeshGenerator
dim = 2
nx = 30
ny = 30
nz = 0
xmin = 0
xmax = 1000
ymin = 0
ymax = 1000
zmin = 0
zmax = 0
elem_type = QUAD4
partition = linear
[]
[]
[GlobalParams]
op_num = 4
var_name_base = gr
[]
[Variables]
[./PolycrystalVariables]
[../]
[]
[UserObjects]
[./voronoi]
type = PolycrystalVoronoi
rand_seed = 105
grain_num = 4
coloring_algorithm = bt
[../]
[]
[ICs]
[./PolycrystalICs]
[./PolycrystalColoringIC]
polycrystal_ic_uo = voronoi
[../]
[../]
[]
[AuxVariables]
[./bnds]
order = FIRST
family = LAGRANGE
[../]
[ghosting0]
order = CONSTANT
family = MONOMIAL
[]
[ghosting1]
order = CONSTANT
family = MONOMIAL
[]
[ghosting2]
order = CONSTANT
family = MONOMIAL
[]
[evaluable0]
order = CONSTANT
family = MONOMIAL
[]
[evaluable1]
order = CONSTANT
family = MONOMIAL
[]
[evaluable2]
order = CONSTANT
family = MONOMIAL
[]
[proc]
order = CONSTANT
family = MONOMIAL
[]
[]
[AuxKernels]
[ghosting0]
type = ElementUOAux
variable = ghosting0
element_user_object = ghosting_uo0
field_name = "ghosted"
execute_on = initial
[]
[ghosting1]
type = ElementUOAux
variable = ghosting1
element_user_object = ghosting_uo1
field_name = "ghosted"
execute_on = initial
[]
[ghosting2]
type = ElementUOAux
variable = ghosting2
element_user_object = ghosting_uo2
field_name = "ghosted"
execute_on = initial
[]
[evaluable0]
type = ElementUOAux
variable = evaluable0
element_user_object = ghosting_uo0
field_name = "evaluable"
execute_on = initial
[]
[evaluable1]
type = ElementUOAux
variable = evaluable1
element_user_object = ghosting_uo1
field_name = "evaluable"
execute_on = initial
[]
[evaluable2]
type = ElementUOAux
variable = evaluable2
element_user_object = ghosting_uo2
field_name = "evaluable"
execute_on = initial
[]
[proc]
type = ProcessorIDAux
variable = proc
execute_on = initial
[]
[]
[UserObjects]
[ghosting_uo0]
type = ElemSideNeighborLayersGeomTester
execute_on = initial
element_side_neighbor_layers = 2
rank = 0
[]
[ghosting_uo1]
type = ElemSideNeighborLayersGeomTester
execute_on = initial
element_side_neighbor_layers = 2
rank = 1
[]
[ghosting_uo2]
type = ElemSideNeighborLayersGeomTester
execute_on = initial
element_side_neighbor_layers = 2
rank = 2
[]
[]
[Kernels]
[./PolycrystalKernel]
[../]
[]
[AuxKernels]
[./BndsCalc]
type = BndsCalcAux
variable = bnds
execute_on = timestep_end
[../]
[]
[BCs]
[./Periodic]
[./All]
auto_direction = 'x y'
[../]
[../]
[]
[Materials]
[./Copper]
type = GBEvolution
T = 500 # K
wGB = 60 # nm
GBmob0 = 2.5e-6 #m^4/(Js) from Schoenfelder 1997
Q = 0.23 #Migration energy in eV
GBenergy = 0.708 #GB energy in J/m^2
[../]
[]
[Postprocessors]
active = ''
[./ngrains]
type = FeatureFloodCount
variable = bnds
threshold = 0.7
[../]
[]
[Preconditioning]
active = ''
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
scheme = 'bdf2'
solve_type = 'PJFNK'
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart'
petsc_options_value = 'hypre boomeramg 31'
l_tol = 1.0e-4
l_max_its = 30
nl_max_its = 20
nl_rel_tol = 1.0e-13
start_time = 0.0
num_steps = 2
dt = 80.0
[./Adaptivity]
initial_adaptivity = 2
refine_fraction = 0.7
coarsen_fraction = 0.1
max_h_level = 1
[../]
[]
[Outputs]
exodus = true
[]
(modules/phase_field/test/tests/grain_growth/boundingbox.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 10
ny = 10
nz = 0
xmin = 0
xmax = 1000
ymin = 0
ymax = 1000
zmin = 0
zmax = 0
elem_type = QUAD4
uniform_refine = 2
[]
[GlobalParams]
op_num = 2
var_name_base = gr
[]
[Variables]
[./PolycrystalVariables]
[../]
[]
[ICs]
[./PolycrystalICs]
[./BicrystalBoundingBoxIC]
x1 = 0
y1 = 0
x2 = 500
y2 = 1000
[../]
[../]
[]
[AuxVariables]
[./bnds]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
[./PolycrystalKernel]
[../]
[]
[AuxKernels]
[./BndsCalc]
type = BndsCalcAux
variable = bnds
[../]
[]
[Materials]
[./Copper]
type = GBEvolution
T = 500 # K
wGB = 60 # nm
GBmob0 = 2.5e-6 # m^4/(Js) from Schoenfelder 1997
Q = 0.23 # Migration energy in eV
GBenergy = 0.708 # GB energy in J/m^2
[../]
[]
[Postprocessors]
[./gr1area]
type = ElementIntegralVariablePostprocessor
variable = gr1
[../]
[]
[Preconditioning]
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = NEWTON
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart'
petsc_options_value = 'hypre boomeramg 31'
l_tol = 1.0e-4
l_max_its = 30
nl_max_its = 20
nl_rel_tol = 1.0e-9
start_time = 0.0
num_steps = 10
dt = 80.0
[./Adaptivity]
initial_adaptivity = 2
refine_fraction = 0.8
coarsen_fraction = 0.05
max_h_level = 2
[../]
[]
[Outputs]
execute_on = 'timestep_end'
csv = true
exodus = true
[]
(modules/phase_field/test/tests/grain_growth/explicit.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 10
ny = 10
nz = 0
xmin = 0
xmax = 400
ymin = 0
ymax = 400
zmin = 0
zmax = 0
elem_type = QUAD4
uniform_refine = 1
[]
[GlobalParams]
op_num = 2
var_name_base = gr
implicit = false
[]
[Variables]
[./PolycrystalVariables]
[../]
[]
[ICs]
[./PolycrystalICs]
[./BicrystalCircleGrainIC]
radius = 300
x = 400
y = 0
[../]
[../]
[]
[AuxVariables]
[./bnds]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
[./PolycrystalKernel]
[../]
[]
[AuxKernels]
[./BndsCalc]
type = BndsCalcAux
variable = bnds
execute_on = timestep_end
[../]
[]
[Materials]
[./Copper]
type = GBEvolution
T = 500 # K
wGB = 60 # nm
GBmob0 = 2.5e-6 #m^4/(Js) from Schoenfelder 1997
Q = 0.23 #Migration energy in eV
GBenergy = 0.708 #GB energy in J/m^2
[../]
[]
[Postprocessors]
[./gr1area]
type = ElementIntegralVariablePostprocessor
variable = gr1
execute_on = 'initial timestep_end'
[../]
[]
[Preconditioning]
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
scheme = explicit-euler
solve_type = NEWTON
# petsc_options_iname = '-pc_type'
# petsc_options_value = 'bjacobi'
#
l_tol = 1.0e-6
nl_rel_tol = 1.0e-10
num_steps = 61
dt = 0.08
[]
[Outputs]
execute_on = 'initial timestep_end final'
csv = true
interval = 20
exodus = true
[]
(modules/phase_field/test/tests/initial_conditions/polycrystal_BndsCalcIC.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 20
ny = 20
nz = 0
xmin = 0
xmax = 100
ymin = 0
ymax = 100
zmin = 0
zmax = 0
elem_type = QUAD4
[]
[GlobalParams]
op_num = 3
var_name_base = gr
int_width = 5 # int_width > 0 is required for initial adaptivity to work based on Bnds
[]
[Variables]
[./PolycrystalVariables]
[../]
[]
[UserObjects]
[./voronoi]
type = PolycrystalVoronoi
rand_seed = 105
grain_num = 3
[../]
[]
[ICs]
[./PolycrystalICs]
[./PolycrystalColoringIC]
polycrystal_ic_uo = voronoi
[../]
[../]
[./bnds]
type = BndsCalcIC # IC is created for activating the initial adaptivity
variable = bnds
[../]
[]
[AuxVariables]
[./bnds]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
[./PolycrystalKernel]
[../]
[]
[AuxKernels]
[./BndsCalc]
type = BndsCalcAux
variable = bnds
execute_on = timestep_end
[../]
[]
[BCs]
[./Periodic]
[./All]
auto_direction = 'x y'
[../]
[../]
[]
[Materials]
[./Copper]
type = GBEvolution
T = 500 # K
wGB = 6 # nm
GBmob0 = 2.5e-6 #m^4/(Js) from Schoenfelder 1997
Q = 0.23 #Migration energy in eV
GBenergy = 0.708 #GB energy in J/m^2
[../]
[]
[Postprocessors]
[./ngrains]
type = FeatureFloodCount
variable = bnds
threshold = 0.7
[../]
[]
[Preconditioning]
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
scheme = 'bdf2'
solve_type = 'PJFNK'
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart'
petsc_options_value = 'hypre boomeramg 31'
l_tol = 1.0e-4
l_max_its = 30
nl_max_its = 20
nl_rel_tol = 1.0e-9
start_time = 0.0
num_steps = 2
dt = 1.0
[]
[Adaptivity]
initial_steps = 1
max_h_level = 1
marker = err_bnds
[./Markers]
[./err_bnds]
type = ErrorFractionMarker
coarsen = 0.3
refine = 0.9
indicator = ind_bnds
[../]
[../]
[./Indicators]
[./ind_bnds]
type = GradientJumpIndicator
variable = bnds
[../]
[../]
[]
[Outputs]
exodus = true
perf_graph = true
[]
(modules/phase_field/examples/grain_growth/grain_growth_2D_random.i)
# This output simulations the shrinkage of a circular grain imbedded in a larger grain
# Simulation is 2-D
# Mesh adaptivity and time step adaptivity are used
# An AuxVariable is used to calculate the grain boundary locations
# Postprocessors are used to record time step and the area of the shrinking grain
[Mesh]
# Mesh block. Meshes can be read in or automatically generated
type = GeneratedMesh
dim = 2 # Problem dimension
nx = 10 # Number of elements in the x-direction
ny = 10 # Number of elements in the y-direction
nz = 0 # Number of elements in the z-direction
xmin = 0 # minimum x-coordinate of the mesh
xmax = 1000 # maximum x-coordinate of the mesh
ymin = 0 # minimum y-coordinate of the mesh
ymax = 1000 # maximum y-coordinate of the mesh
zmin = 0
zmax = 0
elem_type = QUAD4 # Type of elements used in the mesh
uniform_refine = 4 # Initial uniform refinement of the mesh
parallel_type = replicated # Periodic BCs
[]
[GlobalParams]
# Parameters used by several kernels that are defined globally to simplify input file
op_num = 10 # Number of grains
var_name_base = gr # Base name of grains
[]
[Variables]
# Variable block, where all variables in the simulation are declared
[./PolycrystalVariables]
# Custom action that created all of the grain variables and sets their initial condition
[../]
[]
[AuxVariables]
# Dependent variables
[./bnds]
# Variable used to visualize the grain boundaries in the simulation
order = FIRST
family = LAGRANGE
[../]
[]
[ICs]
[./PolycrystalICs]
[./PolycrystalRandomIC]
random_type = discrete
[../]
[../]
[]
[Kernels]
# Kernel block, where the kernels defining the residual equations are set up.
[./PolycrystalKernel]
# Custom action creating all necessary kernels for grain growth. All input parameters are up in GlobalParams
[../]
[]
[AuxKernels]
# AuxKernel block, defining the equations used to calculate the auxvars
[./bnds_aux]
# AuxKernel that calculates the GB term
type = BndsCalcAux
variable = bnds
execute_on = timestep_end
[../]
[]
[BCs]
# Boundary Condition block
[./Periodic]
[./top_bottom]
auto_direction = 'x y' # Makes problem periodic in the x and y directions
[../]
[../]
[]
[Materials]
[./CuGrGr]
# Material properties
type = GBEvolution # Quantitative material properties for copper grain growth. Dimensions are nm and ns
GBmob0 = 2.5e-6 # Mobility prefactor for Cu from Schonfelder1997
GBenergy = 0.708 # GB energy for Cu from Schonfelder1997
Q = 0.23 # Activation energy for grain growth from Schonfelder 1997
T = 450 # Constant temperature of the simulation (for mobility calculation)
wGB = 14 # Width of the diffuse GB
[../]
[]
[Postprocessors]
# Scalar postprocessors
[./dt]
# Outputs the current time step
type = TimestepSize
[../]
[./num_nodes]
type = NumNodes
[../]
[./num_grains]
type = FeatureFloodCount
variable = bnds
threshold = 0.7
[../]
[]
[Executioner]
type = Transient # Type of executioner, here it is transient with an adaptive time step
scheme = bdf2 # Type of time integration (2nd order backward euler), defaults to 1st order backward euler
solve_type = PJFNK
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart -mat_mffd_type'
petsc_options_value = 'hypre boomeramg 101 ds'
l_max_its = 30 # Max number of linear iterations
l_tol = 1e-5 # Relative tolerance for linear solves
nl_max_its = 40 # Max number of nonlinear iterations
nl_abs_tol = 1e-9 # Relative tolerance for nonlienar solves
nl_rel_tol = 1e-9 # Absolute tolerance for nonlienar solves
start_time = 0.0
end_time = 4000
[./TimeStepper]
type = IterationAdaptiveDT
dt = 5 # Initial time step. In this simulation it changes.
optimal_iterations = 8 # Time step will adapt to maintain this number of nonlinear iterations
growth_factor = 1.25
[../]
[./Adaptivity]
# Block that turns on mesh adaptivity. Note that mesh will never coarsen beyond initial mesh (before uniform refinement)
initial_adaptivity = 0 # Number of times mesh is adapted to initial condition
refine_fraction = 0.7 # Fraction of high error that will be refined
coarsen_fraction = 0.1 # Fraction of low error that will coarsened
max_h_level = 4 # Max number of refinements used, starting from initial mesh (before uniform refinement)
[../]
[]
[Outputs]
exodus = true
csv = true
[./console]
type = Console
max_rows = 20
[../]
[]
(modules/phase_field/test/tests/actions/gpm_kernel.i)
[Mesh]
type = GeneratedMesh
dim = 1
nx = 100
xmin = 0
xmax = 300
[]
[GlobalParams]
op_num = 1
var_name_base = eta
[]
[Variables]
[./w]
[../]
[./phi]
[../]
[./eta0]
[../]
[]
[AuxVariables]
[./bnds]
[../]
[]
[ICs]
[./IC_w]
type = BoundingBoxIC
variable = w
x1 = 150
x2 = 300
y1 = 0
y2 = 0
inside = 0.1
outside = 0
[../]
[./IC_phi]
type = BoundingBoxIC
variable = phi
x1 = 0
x2 = 150
y1 = 0
y2 = 0
inside = 1
outside = 0
[../]
[./IC_eta0]
type = BoundingBoxIC
variable = eta0
x1 = 150
x2 = 300
y1 = 0
y2 = 0
inside = 1
outside = 0
[../]
[]
[AuxKernels]
[./bnds_aux]
type = BndsCalcAux
variable = bnds
[../]
[]
[Modules]
[./PhaseField]
[./GrandPotential]
switching_function_names = 'hb hm'
chemical_potentials = 'w'
anisotropic = 'false'
mobilities = 'chiD'
susceptibilities = 'chi'
free_energies_w = 'rhob rhom'
gamma_gr = gamma
mobility_name_gr = L
kappa_gr = kappa
free_energies_gr = 'omegab omegam'
additional_ops = 'phi'
gamma_grxop = gamma
mobility_name_op = L_phi
kappa_op = kappa
free_energies_op = 'omegab omegam'
[../]
[../]
[]
[Materials]
#REFERENCES
[./constants]
type = GenericConstantMaterial
prop_names = 'Va cb_eq cm_eq kb km mu gamma L L_phi kappa kB'
prop_values = '0.04092 1.0 1e-5 1400 140 1.5 1.5 5.3e+3 2.3e+4 295.85 8.6173324e-5'
[../]
#SWITCHING FUNCTIONS
[./switchb]
type = SwitchingFunctionMultiPhaseMaterial
h_name = hb
all_etas = 'phi eta0'
phase_etas = 'phi'
[../]
[./switchm]
type = SwitchingFunctionMultiPhaseMaterial
h_name = hm
all_etas = 'phi eta0'
phase_etas = 'eta0'
[../]
[./omegab]
type = DerivativeParsedMaterial
f_name = omegab
args = 'w phi'
material_property_names = 'Va kb cb_eq'
function = '-0.5*w^2/Va^2/kb - w/Va*cb_eq'
derivative_order = 2
[../]
[./omegam]
type = DerivativeParsedMaterial
f_name = omegam
args = 'w eta0'
material_property_names = 'Va km cm_eq'
function = '-0.5*w^2/Va^2/km - w/Va*cm_eq'
derivative_order = 2
[../]
[./chi]
type = DerivativeParsedMaterial
f_name = chi
args = 'w'
material_property_names = 'Va hb hm kb km'
function = '(hm/km + hb/kb)/Va^2'
derivative_order = 2
[../]
#DENSITIES/CONCENTRATION
[./rhob]
type = DerivativeParsedMaterial
f_name = rhob
args = 'w'
material_property_names = 'Va kb cb_eq'
function = 'w/Va^2/kb + cb_eq/Va'
derivative_order = 1
[../]
[./rhom]
type = DerivativeParsedMaterial
f_name = rhom
args = 'w eta0'
material_property_names = 'Va km cm_eq(eta0)'
function = 'w/Va^2/km + cm_eq/Va'
derivative_order = 1
[../]
[./concentration]
type = ParsedMaterial
f_name = c
material_property_names = 'rhom hm rhob hb Va'
function = 'Va*(hm*rhom + hb*rhob)'
outputs = exodus
[../]
[./mobility]
type = DerivativeParsedMaterial
material_property_names = 'chi kB'
constant_names = 'T Em D0'
constant_expressions = '1400 2.4 1.25e2'
f_name = chiD
function = 'chi*D0*exp(-Em/kB/T)'
[../]
[]
[Preconditioning]
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = NEWTON
petsc_options_iname = '-pc_type -sub_pc_type -pc_asm_overlap -ksp_gmres_restart -sub_ksp_type'
petsc_options_value = ' asm lu 1 31 preonly'
nl_max_its = 20
l_max_its = 30
l_tol = 1e-4
nl_rel_tol = 1e-7
nl_abs_tol = 1e-7
start_time = 0
dt = 2e-5
num_steps = 3
[]
[Outputs]
exodus = true
[]
(modules/phase_field/test/tests/grain_tracker_test/grain_tracker_volume_changing.i)
# This simulation predicts GB migration of a 2D copper polycrystal with 100 grains represented with 18 order parameters
# Mesh adaptivity and time step adaptivity are used
# An AuxVariable is used to calculate the grain boundary locations
# Postprocessors are used to record time step and the number of grains
[Mesh]
# Mesh block. Meshes can be read in or automatically generated
type = GeneratedMesh
dim = 2 # Problem dimension
nx = 12 # Number of elements in the x-direction
ny = 12 # Number of elements in the y-direction
xmax = 1000 # maximum x-coordinate of the mesh
ymax = 1000 # maximum y-coordinate of the mesh
elem_type = QUAD4 # Type of elements used in the mesh
uniform_refine = 1 # Initial uniform refinement of the mesh
[]
[GlobalParams]
# Parameters used by several kernels that are defined globally to simplify input file
op_num = 8 # Number of order parameters used
var_name_base = gr # Base name of grains
order = CONSTANT
family = MONOMIAL
[]
[Variables]
# Variable block, where all variables in the simulation are declared
[./PolycrystalVariables]
order = FIRST
family = LAGRANGE
[../]
[]
[UserObjects]
[./voronoi]
type = PolycrystalVoronoi
grain_num = 12 # Number of grains
coloring_algorithm = jp
rand_seed = 15
output_adjacency_matrix = true
[../]
[./grain_tracker]
type = GrainTracker
threshold = 0.2
verbosity_level = 1
connecting_threshold = 0.08
compute_var_to_feature_map = true
compute_halo_maps = true # For displaying HALO fields
polycrystal_ic_uo = voronoi
execute_on = 'initial timestep_end'
[../]
[]
[ICs]
[./PolycrystalICs]
[./PolycrystalColoringIC]
polycrystal_ic_uo = voronoi
[../]
[../]
[]
[AuxVariables]
# Dependent variables
[./bnds]
# Variable used to visualize the grain boundaries in the simulation
order = FIRST
family = LAGRANGE
[../]
[./unique_grains]
[../]
[./var_indices]
[../]
[./ghost_regions]
[../]
[./halos]
[../]
[./halo0]
[../]
[./halo1]
[../]
[./halo2]
[../]
[./halo3]
[../]
[./halo4]
[../]
[./halo5]
[../]
[./halo6]
[../]
[./halo7]
[../]
[./centroids]
order = CONSTANT
family = MONOMIAL
[../]
[]
[Kernels]
# Kernel block, where the kernels defining the residual equations are set up.
[./PolycrystalKernel]
# Custom action creating all necessary kernels for grain growth. All input parameters are up in GlobalParams
[../]
[]
[AuxKernels]
# AuxKernel block, defining the equations used to calculate the auxvars
[./bnds_aux]
# AuxKernel that calculates the GB term
type = BndsCalcAux
variable = bnds
execute_on = 'initial timestep_end'
[../]
[./unique_grains]
type = FeatureFloodCountAux
variable = unique_grains
flood_counter = grain_tracker
field_display = UNIQUE_REGION
execute_on = 'initial timestep_end'
[../]
[./var_indices]
type = FeatureFloodCountAux
variable = var_indices
flood_counter = grain_tracker
field_display = VARIABLE_COLORING
execute_on = 'initial timestep_end'
[../]
[./ghosted_entities]
type = FeatureFloodCountAux
variable = ghost_regions
flood_counter = grain_tracker
field_display = GHOSTED_ENTITIES
execute_on = 'initial timestep_end'
[../]
[./halos]
type = FeatureFloodCountAux
variable = halos
flood_counter = grain_tracker
field_display = HALOS
execute_on = 'initial timestep_end'
[../]
[./halo0]
type = FeatureFloodCountAux
variable = halo0
map_index = 0
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo1]
type = FeatureFloodCountAux
variable = halo1
map_index = 1
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo2]
type = FeatureFloodCountAux
variable = halo2
map_index = 2
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo3]
type = FeatureFloodCountAux
variable = halo3
map_index = 3
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo4]
type = FeatureFloodCountAux
variable = halo4
map_index = 4
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo5]
type = FeatureFloodCountAux
variable = halo5
map_index = 5
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo6]
type = FeatureFloodCountAux
variable = halo6
map_index = 6
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo7]
type = FeatureFloodCountAux
variable = halo7
map_index = 7
field_display = HALOS
flood_counter = grain_tracker
[../]
[./centroids]
type = FeatureFloodCountAux
variable = centroids
execute_on = timestep_end
field_display = CENTROID
flood_counter = grain_tracker
[../]
[]
[BCs]
# Boundary Condition block
[]
[Materials]
[./CuGrGr]
# Material properties
type = GBEvolution
T = 450 # Constant temperature of the simulation (for mobility calculation)
wGB = 125 # Width of the diffuse GB
GBmob0 = 2.5e-6 # m^4(Js) for copper from Schoenfelder1997
Q = 0.23 # eV for copper from Schoenfelder1997
GBenergy = 0.708 # J/m^2 from Schoenfelder1997
[../]
[]
[Postprocessors]
# Scalar postprocessors
[./dt]
# Outputs the current time step
type = TimestepSize
[../]
[./avg_grain_volumes]
type = AverageGrainVolume
feature_counter = grain_tracker
execute_on = 'initial timestep_end'
[../]
[]
[Executioner]
# Uses newton iteration to solve the problem.
type = Transient # Type of executioner, here it is transient with an adaptive time step
scheme = bdf2 # Type of time integration (2nd order backward euler), defaults to 1st order backward euler
solve_type = PJFNK
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart -mat_mffd_type'
petsc_options_value = 'hypre boomeramg 101 ds'
l_max_its = 30 # Max number of linear iterations
l_tol = 1e-4 # Relative tolerance for linear solves
nl_max_its = 40 # Max number of nonlinear iterations
nl_rel_tol = 1e-10 # Absolute tolerance for nonlienar solves
start_time = 0.0
num_steps = 15
dt = 300
[]
[Problem]
type = FEProblem
[]
[Outputs]
csv = true
exodus = true
[]
(modules/phase_field/examples/grain_growth/grain_growth_3D.i)
# This simulation predicts GB migration of a 2D copper polycrystal with 100 grains represented with 18 order parameters
# Mesh adaptivity and time step adaptivity are used
# An AuxVariable is used to calculate the grain boundary locations
# Postprocessors are used to record time step and the number of grains
[Mesh]
# Mesh block. Meshes can be read in or automatically generated
type = GeneratedMesh
dim = 3 # Problem dimension
nx = 10 # Number of elements in the x-direction
ny = 10 # Number of elements in the y-direction
nz = 10
xmin = 0 # minimum x-coordinate of the mesh
xmax = 1000 # maximum x-coordinate of the mesh
ymin = 0 # minimum y-coordinate of the mesh
ymax = 1000 # maximum y-coordinate of the mesh
zmin = 0
zmax = 1000
uniform_refine = 1 # Initial uniform refinement of the mesh
parallel_type = distributed
[]
[GlobalParams]
# Parameters used by several kernels that are defined globally to simplify input file
op_num = 15 # Number of order parameters used
var_name_base = gr # Base name of grains
order = CONSTANT
family = MONOMIAL
[]
[Variables]
# Variable block, where all variables in the simulation are declared
[./PolycrystalVariables]
order = FIRST
family = LAGRANGE
[../]
[]
[UserObjects]
[./voronoi]
type = PolycrystalVoronoi
grain_num = 25 # Number of grains
rand_seed = 10
coloring_algorithm = jp
[../]
[./grain_tracker]
type = GrainTracker
threshold = 0.2
connecting_threshold = 0.08
compute_halo_maps = true # Only necessary for displaying HALOS
polycrystal_ic_uo = voronoi
[../]
[]
[ICs]
[./PolycrystalICs]
[./PolycrystalColoringIC]
polycrystal_ic_uo = voronoi
[../]
[../]
[]
[AuxVariables]
# Dependent variables
[./bnds]
# Variable used to visualize the grain boundaries in the simulation
order = FIRST
family = LAGRANGE
[../]
[./unique_grains]
[../]
[./var_indices]
[../]
[./ghost_regions]
[../]
[./halos]
[../]
[./halo0]
[../]
[./halo1]
[../]
[./halo2]
[../]
[./halo3]
[../]
[./halo4]
[../]
[./halo5]
[../]
[./halo6]
[../]
[./halo7]
[../]
[./halo8]
[../]
[./halo9]
[../]
[./halo10]
[../]
[./halo11]
[../]
[./halo12]
[../]
[./halo13]
[../]
[./halo14]
[../]
[./proc]
[../]
[]
[Kernels]
# Kernel block, where the kernels defining the residual equations are set up.
[./PolycrystalKernel]
# Custom action creating all necessary kernels for grain growth. All input parameters are up in GlobalParams
[../]
[]
[AuxKernels]
# AuxKernel block, defining the equations used to calculate the auxvars
[./bnds_aux]
# AuxKernel that calculates the GB term
type = BndsCalcAux
variable = bnds
execute_on = 'initial timestep_end'
[../]
[./unique_grains]
type = FeatureFloodCountAux
variable = unique_grains
flood_counter = grain_tracker
field_display = UNIQUE_REGION
execute_on = 'initial timestep_end'
[../]
[./var_indices]
type = FeatureFloodCountAux
variable = var_indices
flood_counter = grain_tracker
field_display = VARIABLE_COLORING
execute_on = 'initial timestep_end'
[../]
[./ghosted_entities]
type = FeatureFloodCountAux
variable = ghost_regions
flood_counter = grain_tracker
field_display = GHOSTED_ENTITIES
execute_on = 'initial timestep_end'
[../]
[./halos]
type = FeatureFloodCountAux
variable = halos
flood_counter = voronoi
field_display = HALOS
execute_on = 'initial timestep_end'
[../]
[./halo0]
type = FeatureFloodCountAux
variable = halo0
map_index = 0
field_display = HALOS
flood_counter = grain_tracker
execute_on = 'initial timestep_end'
[../]
[./halo1]
type = FeatureFloodCountAux
variable = halo1
map_index = 1
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo2]
type = FeatureFloodCountAux
variable = halo2
map_index = 2
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo3]
type = FeatureFloodCountAux
variable = halo3
map_index = 3
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo4]
type = FeatureFloodCountAux
variable = halo4
map_index = 4
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo5]
type = FeatureFloodCountAux
variable = halo5
map_index = 5
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo6]
type = FeatureFloodCountAux
variable = halo6
map_index = 6
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo7]
type = FeatureFloodCountAux
variable = halo7
map_index = 7
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo8]
type = FeatureFloodCountAux
variable = halo8
map_index = 8
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo9]
type = FeatureFloodCountAux
variable = halo9
map_index = 9
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo10]
type = FeatureFloodCountAux
variable = halo10
map_index = 10
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo11]
type = FeatureFloodCountAux
variable = halo11
map_index = 11
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo12]
type = FeatureFloodCountAux
variable = halo12
map_index = 12
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo13]
type = FeatureFloodCountAux
variable = halo13
map_index = 13
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo14]
type = FeatureFloodCountAux
variable = halo14
map_index = 14
field_display = HALOS
flood_counter = grain_tracker
[../]
[./proc]
type = ProcessorIDAux
variable = proc
execute_on = 'initial timestep_end'
[../]
[]
[Materials]
[./CuGrGr]
# Material properties
type = GBEvolution
T = 450 # Constant temperature of the simulation (for mobility calculation)
wGB = 125 # Width of the diffuse GB
GBmob0 = 2.5e-6 #m^4(Js) for copper from Schoenfelder1997
Q = 0.23 #eV for copper from Schoenfelder1997
GBenergy = 0.708 #J/m^2 from Schoenfelder1997
[../]
[]
[Postprocessors]
# Scalar postprocessors
[./dt]
# Outputs the current time step
type = TimestepSize
[../]
[]
[Executioner]
type = Transient # Type of executioner, here it is transient with an adaptive time step
scheme = bdf2 # Type of time integration (2nd order backward euler), defaults to 1st order backward euler
#Preconditioned JFNK (default)
solve_type = 'PJFNK'
# Uses newton iteration to solve the problem.
petsc_options_iname = '-pc_type'
petsc_options_value = 'asm'
l_max_its = 30 # Max number of linear iterations
l_tol = 1e-4 # Relative tolerance for linear solves
nl_max_its = 40 # Max number of nonlinear iterations
nl_rel_tol = 1e-10 # Absolute tolerance for nonlienar solves
start_time = 0.0
end_time = 4000
[./TimeStepper]
type = IterationAdaptiveDT
dt = 25 # Initial time step. In this simulation it changes.
optimal_iterations = 6 # Time step will adapt to maintain this number of nonlinear iterations
[../]
# [./Adaptivity]
# # Block that turns on mesh adaptivity. Note that mesh will never coarsen beyond initial mesh (before uniform refinement)
## initial_adaptivity = 2 # Number of times mesh is adapted to initial condition
# refine_fraction = 0.6 # Fraction of high error that will be refined
# coarsen_fraction = 0.1 # Fraction of low error that will coarsened
# max_h_level = 3 # Max number of refinements used, starting from initial mesh (before uniform refinement)
# [../]
[]
[Outputs]
exodus = true
csv = true
[./perf_graph]
type = PerfGraphOutput
execute_on = 'initial final' # Default is "final"
level = 2 # Default is 1
[../]
[]
(modules/combined/examples/phase_field-mechanics/poly_grain_growth_2D_eldrforce.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 20
ny = 20
nz = 0
xmax = 1000
ymax = 1000
zmax = 0
elem_type = QUAD4
uniform_refine = 2
[]
[GlobalParams]
op_num = 8
var_name_base = gr
grain_num = 36
[]
[Variables]
[./PolycrystalVariables]
[../]
[./disp_x]
order = FIRST
family = LAGRANGE
[../]
[./disp_y]
order = FIRST
family = LAGRANGE
[../]
[]
[UserObjects]
[./euler_angle_file]
type = EulerAngleFileReader
file_name = grn_36_rand_2D.tex
[../]
[./voronoi]
type = PolycrystalVoronoi
coloring_algorithm = bt
[../]
[./grain_tracker]
type = GrainTrackerElasticity
threshold = 0.2
compute_var_to_feature_map = true
execute_on = 'initial timestep_begin'
flood_entity_type = ELEMENTAL
C_ijkl = '1.27e5 0.708e5 0.708e5 1.27e5 0.708e5 1.27e5 0.7355e5 0.7355e5 0.7355e5'
fill_method = symmetric9
euler_angle_provider = euler_angle_file
[../]
[]
[ICs]
[./PolycrystalICs]
[./PolycrystalColoringIC]
polycrystal_ic_uo = voronoi
[../]
[../]
[]
[AuxVariables]
[./bnds]
order = FIRST
family = LAGRANGE
[../]
[./elastic_strain11]
order = CONSTANT
family = MONOMIAL
[../]
[./elastic_strain22]
order = CONSTANT
family = MONOMIAL
[../]
[./elastic_strain12]
order = CONSTANT
family = MONOMIAL
[../]
[./unique_grains]
order = CONSTANT
family = MONOMIAL
[../]
[./var_indices]
order = CONSTANT
family = MONOMIAL
[../]
[./vonmises_stress]
order = CONSTANT
family = MONOMIAL
[../]
[./C1111]
order = CONSTANT
family = MONOMIAL
[../]
[./euler_angle]
order = CONSTANT
family = MONOMIAL
[../]
[]
[Kernels]
[./PolycrystalKernel]
[../]
[./PolycrystalElasticDrivingForce]
[../]
[./TensorMechanics]
use_displaced_mesh = true
displacements = 'disp_x disp_y'
[../]
[]
[AuxKernels]
[./BndsCalc]
type = BndsCalcAux
variable = bnds
execute_on = timestep_end
[../]
[./elastic_strain11]
type = RankTwoAux
variable = elastic_strain11
rank_two_tensor = elastic_strain
index_i = 0
index_j = 0
execute_on = timestep_end
[../]
[./elastic_strain22]
type = RankTwoAux
variable = elastic_strain22
rank_two_tensor = elastic_strain
index_i = 1
index_j = 1
execute_on = timestep_end
[../]
[./elastic_strain12]
type = RankTwoAux
variable = elastic_strain12
rank_two_tensor = elastic_strain
index_i = 0
index_j = 1
execute_on = timestep_end
[../]
[./unique_grains]
type = FeatureFloodCountAux
variable = unique_grains
execute_on = timestep_end
flood_counter = grain_tracker
field_display = UNIQUE_REGION
[../]
[./var_indices]
type = FeatureFloodCountAux
variable = var_indices
execute_on = timestep_end
flood_counter = grain_tracker
field_display = VARIABLE_COLORING
[../]
[./C1111]
type = RankFourAux
variable = C1111
rank_four_tensor = elasticity_tensor
index_l = 0
index_j = 0
index_k = 0
index_i = 0
execute_on = timestep_end
[../]
[./vonmises_stress]
type = RankTwoScalarAux
variable = vonmises_stress
rank_two_tensor = stress
scalar_type = VonMisesStress
execute_on = timestep_end
[../]
[./euler_angle]
type = OutputEulerAngles
variable = euler_angle
euler_angle_provider = euler_angle_file
grain_tracker = grain_tracker
output_euler_angle = 'phi1'
execute_on = 'initial timestep_end'
[../]
[]
[BCs]
[./Periodic]
[./All]
auto_direction = 'x'
variable = 'gr0 gr1 gr2 gr3 gr4 gr5 gr6 gr7'
[../]
[../]
[./top_displacement]
type = DirichletBC
variable = disp_y
boundary = top
value = -50.0
[../]
[./x_anchor]
type = DirichletBC
variable = disp_x
boundary = 'left right'
value = 0.0
[../]
[./y_anchor]
type = DirichletBC
variable = disp_y
boundary = bottom
value = 0.0
[../]
[]
[Materials]
[./Copper]
type = GBEvolution
block = 0
T = 500 # K
wGB = 15 # nm
GBmob0 = 2.5e-6 # m^4/(Js) from Schoenfelder 1997
Q = 0.23 # Migration energy in eV
GBenergy = 0.708 # GB energy in J/m^2
[../]
[./ElasticityTensor]
type = ComputePolycrystalElasticityTensor
grain_tracker = grain_tracker
[../]
[./strain]
type = ComputeSmallStrain
block = 0
displacements = 'disp_x disp_y'
[../]
[./stress]
type = ComputeLinearElasticStress
block = 0
[../]
[]
[Postprocessors]
[./ngrains]
type = FeatureFloodCount
variable = bnds
threshold = 0.7
[../]
[./dofs]
type = NumDOFs
[../]
[./dt]
type = TimestepSize
[../]
[./run_time]
type = PerfGraphData
section_name = "Root"
data_type = total
[../]
[]
[Preconditioning]
[./SMP]
type = SMP
coupled_groups = 'disp_x,disp_y'
[../]
[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = PJFNK
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart -pc_hypre_boomeramg_strong_threshold'
petsc_options_value = 'hypre boomeramg 31 0.7'
l_tol = 1.0e-4
l_max_its = 30
nl_max_its = 25
nl_rel_tol = 1.0e-7
start_time = 0.0
num_steps = 50
[./TimeStepper]
type = IterationAdaptiveDT
dt = 1.5
growth_factor = 1.2
cutback_factor = 0.8
optimal_iterations = 8
[../]
[./Adaptivity]
initial_adaptivity = 2
refine_fraction = 0.8
coarsen_fraction = 0.05
max_h_level = 3
[../]
[]
[Outputs]
file_base = poly36_grtracker
exodus = true
[]
(modules/phase_field/examples/grain_growth/grain_growth_2D_voronoi_newadapt.i)
# This simulation predicts GB migration of a 2D copper polycrystal with 15 grains
# Mesh adaptivity (new system) and time step adaptivity are used
# An AuxVariable is used to calculate the grain boundary locations
# Postprocessors are used to record time step and the number of grains
# We are not using the GrainTracker in this example so the number
# of order paramaters must match the number of grains.
[Mesh]
# Mesh block. Meshes can be read in or automatically generated
type = GeneratedMesh
dim = 2 # Problem dimension
nx = 12 # Number of elements in the x-direction
ny = 12 # Number of elements in the y-direction
nz = 0 # Number of elements in the z-direction
xmin = 0 # minimum x-coordinate of the mesh
xmax = 1000 # maximum x-coordinate of the mesh
ymin = 0 # minimum y-coordinate of the mesh
ymax = 1000 # maximum y-coordinate of the mesh
zmin = 0
zmax = 0
elem_type = QUAD4 # Type of elements used in the mesh
uniform_refine = 3 # Initial uniform refinement of the mesh
parallel_type = replicated # Periodic BCs
[]
[GlobalParams]
# Parameters used by several kernels that are defined globally to simplify input file
op_num = 15 # Number of grains
var_name_base = gr # Base name of grains
[]
[UserObjects]
[./voronoi]
type = PolycrystalVoronoi
grain_num = 15
rand_seed = 42
coloring_algorithm = bt # We must use bt to force the UserObject to assign one grain to each op
[../]
[]
[ICs]
[./PolycrystalICs]
[./PolycrystalColoringIC]
polycrystal_ic_uo = voronoi
[../]
[../]
[]
[Variables]
# Variable block, where all variables in the simulation are declared
[./PolycrystalVariables]
# Custom action that created all of the grain variables and sets their initial condition
[../]
[]
[AuxVariables]
# Dependent variables
[./bnds]
# Variable used to visualize the grain boundaries in the simulation
[../]
[]
[Kernels]
# Kernel block, where the kernels defining the residual equations are set up.
[./PolycrystalKernel]
# Custom action creating all necessary kernels for grain growth. All input parameters are up in GlobalParams
[../]
[]
[AuxKernels]
# AuxKernel block, defining the equations used to calculate the auxvars
[./bnds_aux]
# AuxKernel that calculates the GB term
type = BndsCalcAux
variable = bnds
execute_on = timestep_end
[../]
[]
[BCs]
# Boundary Condition block
[./Periodic]
[./top_bottom]
auto_direction = 'x y' # Makes problem periodic in the x and y directions
[../]
[../]
[]
[Materials]
[./CuGrGr]
# Material properties
type = GBEvolution # Quantitative material properties for copper grain growth. Dimensions are nm and ns
GBmob0 = 2.5e-6 # Mobility prefactor for Cu from Schonfelder1997
GBenergy = 0.708 # GB energy for Cu from Schonfelder1997
Q = 0.23 # Activation energy for grain growth from Schonfelder 1997
T = 450 # Constant temperature of the simulation (for mobility calculation)
wGB = 14 # Width of the diffuse GB
[../]
[]
[Postprocessors]
# Scalar postprocessors
[./dt]
# Outputs the current time step
type = TimestepSize
[../]
[]
[Executioner]
type = Transient # Type of executioner, here it is transient with an adaptive time step
scheme = bdf2 # Type of time integration (2nd order backward euler), defaults to 1st order backward euler
#Preconditioned JFNK (default)
solve_type = 'PJFNK'
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart -mat_mffd_type'
petsc_options_value = 'hypre boomeramg 101 ds'
l_max_its = 30 # Max number of linear iterations
l_tol = 1e-4 # Relative tolerance for linear solves
nl_max_its = 40 # Max number of nonlinear iterations
nl_abs_tol = 1e-11 # Relative tolerance for nonlienar solves
nl_rel_tol = 1e-10 # Absolute tolerance for nonlienar solves
[./TimeStepper]
type = SolutionTimeAdaptiveDT
dt = 25 # Initial time step. In this simulation it changes.
[../]
start_time = 0.0
end_time = 4000
num_steps = 3
[]
[Adaptivity]
marker = errorfrac
max_h_level = 4
[./Indicators]
[./error]
type = GradientJumpIndicator
variable = bnds
[../]
[../]
[./Markers]
[./bound_adapt]
type = ValueThresholdMarker
third_state = DO_NOTHING
coarsen = 1.0
refine = 0.99
variable = bnds
invert = true
[../]
[./errorfrac]
type = ErrorFractionMarker
coarsen = 0.1
indicator = error
refine = 0.7
[../]
[../]
[]
[Outputs]
exodus = true
csv = true
[./console]
type = Console
max_rows = 20
[../]
[]
(modules/phase_field/examples/ebsd_reconstruction/IN100-111grn.i)
[Mesh]
[ebsd_mesh]
type = EBSDMeshGenerator
filename = IN100_120x120.txt
uniform_refine = 2
[]
[]
[GlobalParams]
op_num = 8
var_name_base = gr
[]
[UserObjects]
[ebsd_reader]
type = EBSDReader
[]
[ebsd]
type = PolycrystalEBSD
coloring_algorithm = bt
ebsd_reader = ebsd_reader
enable_var_coloring = true
[]
[grain_tracker]
type = GrainTracker
flood_entity_type = ELEMENTAL
compute_halo_maps = true # For displaying HALO fields
polycrystal_ic_uo = ebsd
[]
[]
[ICs]
[PolycrystalICs]
[PolycrystalColoringIC]
polycrystal_ic_uo = ebsd
[]
[]
[]
[Variables]
[PolycrystalVariables]
[]
[]
[AuxVariables]
[bnds]
[]
[unique_grains_ic]
order = CONSTANT
family = MONOMIAL
[]
[unique_grains]
order = CONSTANT
family = MONOMIAL
[]
[ghost_elements]
order = CONSTANT
family = MONOMIAL
[]
[halos]
order = CONSTANT
family = MONOMIAL
[]
[var_indices_ic]
order = CONSTANT
family = MONOMIAL
[]
[var_indices]
order = CONSTANT
family = MONOMIAL
[]
[ebsd_grains]
family = MONOMIAL
order = CONSTANT
[]
[]
[Kernels]
[PolycrystalKernel]
[]
[]
[AuxKernels]
[BndsCalc]
type = BndsCalcAux
variable = bnds
execute_on = 'initial timestep_end'
[]
[ghost_elements]
type = FeatureFloodCountAux
variable = ghost_elements
field_display = GHOSTED_ENTITIES
execute_on = 'initial timestep_end'
flood_counter = grain_tracker
[]
[halos]
type = FeatureFloodCountAux
variable = halos
field_display = HALOS
execute_on = 'initial timestep_end'
flood_counter = grain_tracker
[]
[var_indices_ic]
type = FeatureFloodCountAux
variable = var_indices_ic
execute_on = 'initial'
flood_counter = ebsd
field_display = VARIABLE_COLORING
[]
[unique_grains_ic]
type = FeatureFloodCountAux
variable = unique_grains_ic
execute_on = 'initial'
flood_counter = ebsd
field_display = UNIQUE_REGION
[]
[var_indices]
type = FeatureFloodCountAux
variable = var_indices
execute_on = 'initial timestep_end'
flood_counter = grain_tracker
field_display = VARIABLE_COLORING
[]
[unique_grains]
type = FeatureFloodCountAux
variable = unique_grains
execute_on = 'initial timestep_end'
flood_counter = grain_tracker
field_display = UNIQUE_REGION
[]
[grain_aux]
type = EBSDReaderPointDataAux
variable = ebsd_grains
ebsd_reader = ebsd_reader
data_name = 'feature_id'
execute_on = 'initial timestep_end'
[]
[]
[Modules]
[PhaseField]
[EulerAngles2RGB]
crystal_structure = cubic
euler_angle_provider = ebsd_reader
grain_tracker = grain_tracker
[]
[]
[]
[Materials]
[Copper]
# T = 500 # K
type = GBEvolution
T = 500
wGB = 0.6 # um
GBmob0 = 2.5e-6 # m^4/(Js) from Schoenfelder 1997
Q = 0.23 # Migration energy in eV
GBenergy = 0.708 # GB energy in J/m^2
molar_volume = 7.11e-6 # Molar volume in m^3/mol
length_scale = 1.0e-6
time_scale = 1.0e-6
[]
[]
[Postprocessors]
[dt]
type = TimestepSize
[]
[n_elements]
type = NumElems
execute_on = 'initial timestep_end'
[]
[n_nodes]
type = NumNodes
execute_on = 'initial timestep_end'
[]
[DOFs]
type = NumDOFs
[]
[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = PJFNK
petsc_options_iname = '-pc_type -pc_hypre_type -pc_hypre_boomeramg_strong_threshold'
petsc_options_value = 'hypre boomeramg 0.7'
l_tol = 1.0e-4
l_max_its = 20
nl_max_its = 20
nl_rel_tol = 1.0e-8
start_time = 0.0
num_steps = 30
[TimeStepper]
type = IterationAdaptiveDT
cutback_factor = 0.9
dt = 10.0
growth_factor = 1.1
optimal_iterations = 7
[]
[Adaptivity]
initial_adaptivity = 2
refine_fraction = 0.7
coarsen_fraction = 0.1
max_h_level = 2
[]
[]
[Outputs]
exodus = true
checkpoint = true
perf_graph = true
[]
(modules/combined/examples/phase_field-mechanics/hex_grain_growth_2D_eldrforce.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 20
ny = 17
nz = 0
xmax = 1000
ymax = 866
zmax = 0
elem_type = QUAD4
uniform_refine = 2
[]
[GlobalParams]
op_num = 3
var_name_base = gr
[]
[Variables]
[./PolycrystalVariables]
[../]
[./disp_x]
order = FIRST
family = LAGRANGE
[../]
[./disp_y]
order = FIRST
family = LAGRANGE
[../]
[]
[UserObjects]
[./hex_ic]
type = PolycrystalHex
coloring_algorithm = bt
grain_num = 36
x_offset = 0.0
output_adjacency_matrix = true
[../]
[./euler_angle_file]
type = EulerAngleFileReader
file_name = grn_36_test2_2D.tex
[../]
[./grain_tracker]
type = GrainTrackerElasticity
threshold = 0.2
compute_var_to_feature_map = true
execute_on = 'initial timestep_begin'
flood_entity_type = ELEMENTAL
fill_method = symmetric9
C_ijkl = '1.27e5 0.708e5 0.708e5 1.27e5 0.708e5 1.27e5 0.7355e5 0.7355e5 0.7355e5'
euler_angle_provider = euler_angle_file
[../]
[]
[ICs]
[./PolycrystalICs]
[./PolycrystalColoringIC]
polycrystal_ic_uo = hex_ic
[../]
[../]
[]
[AuxVariables]
[./bnds]
order = FIRST
family = LAGRANGE
[../]
[./elastic_strain11]
order = CONSTANT
family = MONOMIAL
[../]
[./elastic_strain22]
order = CONSTANT
family = MONOMIAL
[../]
[./elastic_strain12]
order = CONSTANT
family = MONOMIAL
[../]
[./unique_grains]
order = CONSTANT
family = MONOMIAL
[../]
[./var_indices]
order = CONSTANT
family = MONOMIAL
[../]
[./C1111]
order = CONSTANT
family = MONOMIAL
[../]
[./vonmises_stress]
order = CONSTANT
family = MONOMIAL
[../]
[./euler_angle]
order = CONSTANT
family = MONOMIAL
[../]
[]
[Kernels]
[./PolycrystalKernel]
[../]
[./PolycrystalElasticDrivingForce]
[../]
[./TensorMechanics]
displacements = 'disp_x disp_y'
[../]
[]
[AuxKernels]
[./BndsCalc]
type = BndsCalcAux
variable = bnds
execute_on = 'initial timestep_end'
[../]
[./elastic_strain11]
type = RankTwoAux
variable = elastic_strain11
rank_two_tensor = elastic_strain
index_i = 0
index_j = 0
execute_on = timestep_end
[../]
[./elastic_strain22]
type = RankTwoAux
variable = elastic_strain22
rank_two_tensor = elastic_strain
index_i = 1
index_j = 1
execute_on = timestep_end
[../]
[./elastic_strain12]
type = RankTwoAux
variable = elastic_strain12
rank_two_tensor = elastic_strain
index_i = 0
index_j = 1
execute_on = timestep_end
[../]
[./unique_grains]
type = FeatureFloodCountAux
variable = unique_grains
execute_on = timestep_end
flood_counter = grain_tracker
field_display = UNIQUE_REGION
[../]
[./var_indices]
type = FeatureFloodCountAux
variable = var_indices
execute_on = timestep_end
flood_counter = grain_tracker
field_display = VARIABLE_COLORING
[../]
[./C1111]
type = RankFourAux
variable = C1111
rank_four_tensor = elasticity_tensor
index_l = 0
index_j = 0
index_k = 0
index_i = 0
execute_on = timestep_end
[../]
[./vonmises_stress]
type = RankTwoScalarAux
variable = vonmises_stress
rank_two_tensor = stress
scalar_type = VonMisesStress
[../]
[./euler_angle]
type = OutputEulerAngles
variable = euler_angle
euler_angle_provider = euler_angle_file
grain_tracker = grain_tracker
output_euler_angle = 'phi1'
[../]
[]
[BCs]
[./Periodic]
[./All]
auto_direction = 'x y'
variable = 'gr0 gr1 gr2'
[../]
[../]
[./top_displacement]
type = DirichletBC
variable = disp_y
boundary = top
value = -50.0
[../]
[./x_anchor]
type = DirichletBC
variable = disp_x
boundary = 'left right'
value = 0.0
[../]
[./y_anchor]
type = DirichletBC
variable = disp_y
boundary = bottom
value = 0.0
[../]
[]
[Materials]
[./Copper]
type = GBEvolution
block = 0
T = 500 # K
wGB = 15 # nm
GBmob0 = 2.5e-6 # m^4/(Js) from Schoenfelder 1997
Q = 0.23 # Migration energy in eV
GBenergy = 0.708 # GB energy in J/m^2
[../]
[./ElasticityTensor]
type = ComputePolycrystalElasticityTensor
block = 0
grain_tracker = grain_tracker
[../]
[./strain]
type = ComputeSmallStrain
block = 0
displacements = 'disp_x disp_y'
[../]
[./stress]
type = ComputeLinearElasticStress
block = 0
[../]
[]
[Postprocessors]
[./dofs]
type = NumDOFs
[../]
[./dt]
type = TimestepSize
[../]
[./run_time]
type = PerfGraphData
section_name = "Root"
data_type = total
[../]
[./bnd_length]
type = GrainBoundaryArea
[../]
[]
[Preconditioning]
[./SMP]
type = SMP
off_diag_row = 'disp_x disp_y'
off_diag_column = 'disp_y disp_x'
[../]
[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = PJFNK
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart -pc_hypre_boomeramg_strong_threshold'
petsc_options_value = 'hypre boomeramg 31 0.7'
l_tol = 1.0e-4
l_max_its = 30
nl_max_its = 40
nl_rel_tol = 1.0e-7
start_time = 0.0
num_steps = 50
[./TimeStepper]
type = IterationAdaptiveDT
dt = 1.5
growth_factor = 1.2
cutback_factor = 0.8
optimal_iterations = 8
[../]
[./Adaptivity]
initial_adaptivity = 2
refine_fraction = 0.8
coarsen_fraction = 0.05
max_h_level = 3
[../]
[]
[Outputs]
exodus = true
[]
(modules/phase_field/test/tests/GrandPotentialPFM/GrandPotentialMultiphase.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 20
ny = 20
xmin = -20
xmax = 20
ymin = -20
ymax = 20
[]
[GlobalParams]
op_num = 2
var_name_base = etab
[]
[Variables]
[./w]
[../]
[./etaa0]
[../]
[./etab0]
[../]
[./etab1]
[../]
[]
[AuxVariables]
[./bnds]
order = FIRST
family = LAGRANGE
[../]
[]
[ICs]
[./IC_etaa0]
type = FunctionIC
variable = etaa0
function = ic_func_etaa0
[../]
[./IC_etab0]
type = FunctionIC
variable = etab0
function = ic_func_etab0
[../]
[./IC_etab1]
type = FunctionIC
variable = etab1
function = ic_func_etab1
[../]
[./IC_w]
type = ConstantIC
value = -0.05
variable = w
[../]
[]
[Functions]
[./ic_func_etaa0]
type = ParsedFunction
value = 'r:=sqrt(x^2+y^2);0.5*(1.0-tanh((r-10.0)/sqrt(2.0)))'
[../]
[./ic_func_etab0]
type = ParsedFunction
value = 'r:=sqrt(x^2+y^2);0.5*(1.0+tanh((r-10)/sqrt(2.0)))*0.5*(1.0+tanh((y)/sqrt(2.0)))'
[../]
[./ic_func_etab1]
type = ParsedFunction
value = 'r:=sqrt(x^2+y^2);0.5*(1.0+tanh((r-10)/sqrt(2.0)))*0.5*(1.0-tanh((y)/sqrt(2.0)))'
[../]
[]
[BCs]
[]
[Kernels]
# Order parameter eta_alpha0
[./ACa0_bulk]
type = ACGrGrMulti
variable = etaa0
v = 'etab0 etab1'
gamma_names = 'gab gab'
[../]
[./ACa0_sw]
type = ACSwitching
variable = etaa0
Fj_names = 'omegaa omegab'
hj_names = 'ha hb'
args = 'etab0 etab1 w'
[../]
[./ACa0_int]
type = ACInterface
variable = etaa0
kappa_name = kappa
[../]
[./ea0_dot]
type = TimeDerivative
variable = etaa0
[../]
# Order parameter eta_beta0
[./ACb0_bulk]
type = ACGrGrMulti
variable = etab0
v = 'etaa0 etab1'
gamma_names = 'gab gbb'
[../]
[./ACb0_sw]
type = ACSwitching
variable = etab0
Fj_names = 'omegaa omegab'
hj_names = 'ha hb'
args = 'etaa0 etab1 w'
[../]
[./ACb0_int]
type = ACInterface
variable = etab0
kappa_name = kappa
[../]
[./eb0_dot]
type = TimeDerivative
variable = etab0
[../]
# Order parameter eta_beta1
[./ACb1_bulk]
type = ACGrGrMulti
variable = etab1
v = 'etaa0 etab0'
gamma_names = 'gab gbb'
[../]
[./ACb1_sw]
type = ACSwitching
variable = etab1
Fj_names = 'omegaa omegab'
hj_names = 'ha hb'
args = 'etaa0 etab0 w'
[../]
[./ACb1_int]
type = ACInterface
variable = etab1
kappa_name = kappa
[../]
[./eb1_dot]
type = TimeDerivative
variable = etab1
[../]
#Chemical potential
[./w_dot]
type = SusceptibilityTimeDerivative
variable = w
f_name = chi
args = '' # in this case chi (the susceptibility) is simply a constant
[../]
[./Diffusion]
type = MatDiffusion
variable = w
diffusivity = Dchi
args = ''
[../]
[./coupled_etaa0dot]
type = CoupledSwitchingTimeDerivative
variable = w
v = etaa0
Fj_names = 'rhoa rhob'
hj_names = 'ha hb'
args = 'etaa0 etab0 etab1'
[../]
[./coupled_etab0dot]
type = CoupledSwitchingTimeDerivative
variable = w
v = etab0
Fj_names = 'rhoa rhob'
hj_names = 'ha hb'
args = 'etaa0 etab0 etab1'
[../]
[./coupled_etab1dot]
type = CoupledSwitchingTimeDerivative
variable = w
v = etab1
Fj_names = 'rhoa rhob'
hj_names = 'ha hb'
args = 'etaa0 etab0 etab1'
[../]
[]
[AuxKernels]
[./BndsCalc]
type = BndsCalcAux
variable = bnds
execute_on = timestep_end
[../]
[]
# enable_jit set to false in many materials to make this test start up faster.
# It is recommended to set enable_jit = true or just remove these lines for
# production runs with this model
[Materials]
[./ha]
type = SwitchingFunctionMultiPhaseMaterial
h_name = ha
all_etas = 'etaa0 etab0 etab1'
phase_etas = 'etaa0'
[../]
[./hb]
type = SwitchingFunctionMultiPhaseMaterial
h_name = hb
all_etas = 'etaa0 etab0 etab1'
phase_etas = 'etab0 etab1'
[../]
[./omegaa]
type = DerivativeParsedMaterial
args = 'w'
f_name = omegaa
material_property_names = 'Vm ka caeq'
function = '-0.5*w^2/Vm^2/ka-w/Vm*caeq'
derivative_order = 2
enable_jit = false
[../]
[./omegab]
type = DerivativeParsedMaterial
args = 'w'
f_name = omegab
material_property_names = 'Vm kb cbeq'
function = '-0.5*w^2/Vm^2/kb-w/Vm*cbeq'
derivative_order = 2
enable_jit = false
[../]
[./rhoa]
type = DerivativeParsedMaterial
args = 'w'
f_name = rhoa
material_property_names = 'Vm ka caeq'
function = 'w/Vm^2/ka + caeq/Vm'
derivative_order = 2
enable_jit = false
[../]
[./rhob]
type = DerivativeParsedMaterial
args = 'w'
f_name = rhob
material_property_names = 'Vm kb cbeq'
function = 'w/Vm^2/kb + cbeq/Vm'
derivative_order = 2
enable_jit = false
[../]
[./const]
type = GenericConstantMaterial
prop_names = 'kappa_c kappa L D chi Vm ka caeq kb cbeq gab gbb mu'
prop_values = '0 1 1.0 1.0 1.0 1.0 10.0 0.1 10.0 0.9 4.5 1.5 1.0'
[../]
[./Mobility]
type = DerivativeParsedMaterial
f_name = Dchi
material_property_names = 'D chi'
function = 'D*chi'
derivative_order = 2
enable_jit = false
[../]
[]
[Preconditioning]
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
scheme = bdf2
petsc_options_iname = '-pc_type -ksp_gmres_restart -sub_pc_type -pc_asm_overlap'
petsc_options_value = 'asm 31 lu 1'
l_tol = 1.0e-3
nl_rel_tol = 1.0e-8
nl_abs_tol = 1e-8
num_steps = 2
[./TimeStepper]
type = SolutionTimeAdaptiveDT
dt = 0.1
[../]
[]
[Outputs]
exodus = true
[]
(modules/phase_field/test/tests/GrandPotentialPFM/GrandPotentialAnisotropy.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 15
ny = 15
xmin = -2
xmax = 2
ymin = -2
ymax = 2
[]
# enable_jit set to false in many materials to make this test start up faster.
# It is recommended to set enable_jit = true or just remove these lines for
# production runs with this model
[GlobalParams]
radius = 1.0
int_width = 0.8
x1 = 0
y1 = 0
derivative_order = 2
enable_jit = false
[]
[Variables]
[./w]
[../]
[./etaa0]
[../]
[./etab0]
[../]
[]
[AuxVariables]
[./bnds]
[../]
[]
[AuxKernels]
[./bnds]
type = BndsCalcAux
variable = bnds
v = 'etaa0 etab0'
[../]
[]
[ICs]
[./w]
type = SmoothCircleIC
variable = w
# note w = A*(c-cleq), A = 1.0, cleq = 0.0 ,i.e., w = c (in the matrix/liquid phase)
outvalue = -4.0
invalue = 0.0
[../]
[./etaa0]
type = SmoothCircleIC
variable = etaa0
#Solid phase
outvalue = 0.0
invalue = 1.0
[../]
[./etab0]
type = SmoothCircleIC
variable = etab0
#Liquid phase
outvalue = 1.0
invalue = 0.0
[../]
[]
[BCs]
[./Periodic]
[./w]
variable = w
auto_direction = 'x y'
[../]
[./etaa0]
variable = etaa0
auto_direction = 'x y'
[../]
[./etab0]
variable = etab0
auto_direction = 'x y'
[../]
[../]
[]
[Kernels]
# Order parameter eta_alpha0
[./ACa0_bulk]
type = ACGrGrMulti
variable = etaa0
v = 'etab0'
gamma_names = 'gab'
[../]
[./ACa0_sw]
type = ACSwitching
variable = etaa0
Fj_names = 'omegaa omegab'
hj_names = 'ha hb'
args = 'etab0 w'
[../]
[./ACa0_int1]
type = ACInterface2DMultiPhase1
variable = etaa0
etas = 'etab0'
kappa_name = kappaa
dkappadgrad_etaa_name = dkappadgrad_etaa
d2kappadgrad_etaa_name = d2kappadgrad_etaa
[../]
[./ACa0_int2]
type = ACInterface2DMultiPhase2
variable = etaa0
kappa_name = kappaa
dkappadgrad_etaa_name = dkappadgrad_etaa
[../]
[./ea0_dot]
type = TimeDerivative
variable = etaa0
[../]
# Order parameter eta_beta0
[./ACb0_bulk]
type = ACGrGrMulti
variable = etab0
v = 'etaa0'
gamma_names = 'gab'
[../]
[./ACb0_sw]
type = ACSwitching
variable = etab0
Fj_names = 'omegaa omegab'
hj_names = 'ha hb'
args = 'etaa0 w'
[../]
[./ACb0_int1]
type = ACInterface2DMultiPhase1
variable = etab0
etas = 'etaa0'
kappa_name = kappab
dkappadgrad_etaa_name = dkappadgrad_etab
d2kappadgrad_etaa_name = d2kappadgrad_etab
[../]
[./ACb0_int2]
type = ACInterface2DMultiPhase2
variable = etab0
kappa_name = kappab
dkappadgrad_etaa_name = dkappadgrad_etab
[../]
[./eb0_dot]
type = TimeDerivative
variable = etab0
[../]
#Chemical potential
[./w_dot]
type = SusceptibilityTimeDerivative
variable = w
f_name = chi
[../]
[./Diffusion]
type = MatDiffusion
variable = w
diffusivity = Dchi
[../]
[./coupled_etaa0dot]
type = CoupledSwitchingTimeDerivative
variable = w
v = etaa0
Fj_names = 'rhoa rhob'
hj_names = 'ha hb'
args = 'etaa0 etab0'
[../]
[./coupled_etab0dot]
type = CoupledSwitchingTimeDerivative
variable = w
v = etab0
Fj_names = 'rhoa rhob'
hj_names = 'ha hb'
args = 'etaa0 etab0'
[../]
[]
[Materials]
[./ha]
type = SwitchingFunctionMultiPhaseMaterial
h_name = ha
all_etas = 'etaa0 etab0'
phase_etas = 'etaa0'
[../]
[./hb]
type = SwitchingFunctionMultiPhaseMaterial
h_name = hb
all_etas = 'etaa0 etab0'
phase_etas = 'etab0'
[../]
[./omegaa]
type = DerivativeParsedMaterial
args = 'w'
f_name = omegaa
material_property_names = 'Vm ka caeq'
function = '-0.5*w^2/Vm^2/ka-w/Vm*caeq'
[../]
[./omegab]
type = DerivativeParsedMaterial
args = 'w'
f_name = omegab
material_property_names = 'Vm kb cbeq'
function = '-0.5*w^2/Vm^2/kb-w/Vm*cbeq'
[../]
[./rhoa]
type = DerivativeParsedMaterial
args = 'w'
f_name = rhoa
material_property_names = 'Vm ka caeq'
function = 'w/Vm^2/ka + caeq/Vm'
[../]
[./rhob]
type = DerivativeParsedMaterial
args = 'w'
f_name = rhob
material_property_names = 'Vm kb cbeq'
function = 'w/Vm^2/kb + cbeq/Vm'
[../]
[./kappaa]
type = InterfaceOrientationMultiphaseMaterial
kappa_name = kappaa
dkappadgrad_etaa_name = dkappadgrad_etaa
d2kappadgrad_etaa_name = d2kappadgrad_etaa
etaa = etaa0
etab = etab0
outputs = exodus
output_properties = 'kappaa dkappadgrad_etaa'
[../]
[./kappab]
type = InterfaceOrientationMultiphaseMaterial
kappa_name = kappab
dkappadgrad_etaa_name = dkappadgrad_etab
d2kappadgrad_etaa_name = d2kappadgrad_etab
etaa = etab0
etab = etaa0
outputs = exodus
output_properties = 'kappab dkappadgrad_etab'
[../]
[./const]
type = GenericConstantMaterial
prop_names = 'L D chi Vm ka caeq kb cbeq gab mu'
prop_values = '1.0 1.0 0.1 1.0 10.0 0.1 10.0 0.9 4.5 10.0'
[../]
[./Mobility]
type = ParsedMaterial
f_name = Dchi
material_property_names = 'D chi'
function = 'D*chi'
[../]
[]
[Preconditioning]
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
scheme = bdf2
l_tol = 1.0e-5
nl_rel_tol = 1.0e-10
nl_abs_tol = 1e-12
num_steps = 2
dt = 0.001
[]
[Outputs]
exodus = true
[]
(modules/phase_field/test/tests/grain_tracker_test/distributed_poly_ic.i)
[Mesh]
# Mesh block. Meshes can be read in or automatically generated
type = GeneratedMesh
uniform_refine = 1 # Initial uniform refinement of the mesh
dim = 2 # Problem dimension
nx = 12 # Number of elements in the x-direction
ny = 12 # Number of elements in the y-direction
xmax = 1000 # maximum x-coordinate of the mesh
ymax = 1000 # maximum y-coordinate of the mesh
elem_type = QUAD4 # Type of elements used in the mesh
parallel_type = distributed
[]
[GlobalParams]
# Parameters used by several kernels that are defined globally to simplify input file
op_num = '8' # Number of order parameters used
var_name_base = 'gr' # Base name of grains
order = 'CONSTANT'
family = 'MONOMIAL'
[]
[Variables]
# Variable block, where all variables in the simulation are declared
[PolycrystalVariables]
order = FIRST
family = LAGRANGE
[]
[]
[UserObjects]
[voronoi]
type = PolycrystalVoronoi
grain_num = 12 # Number of grains
coloring_algorithm = jp
rand_seed = 10
[]
[grain_tracker]
type = GrainTracker
threshold = 0.2
verbosity_level = 1
connecting_threshold = 0.08
flood_entity_type = ELEMENTAL
compute_halo_maps = true # For displaying HALO fields
execute_on = 'initial timestep_end'
polycrystal_ic_uo = voronoi
[]
[]
[ICs]
[PolycrystalICs]
[PolycrystalColoringIC]
polycrystal_ic_uo = voronoi
[]
[]
[]
[AuxVariables]
# Dependent variables
[bnds]
# Variable used to visualize the grain boundaries in the simulation
order = FIRST
family = LAGRANGE
[]
[unique_grains]
[]
[var_indices]
[]
[ghost_regions]
[]
[halos]
[]
[halo0]
[]
[halo1]
[]
[halo2]
[]
[halo3]
[]
[halo4]
[]
[halo5]
[]
[halo6]
[]
[halo7]
[]
[centroids]
order = CONSTANT
family = MONOMIAL
[]
[proc_id]
[]
[voronoi_id]
[]
[evaluable_elems]
[]
[]
[Kernels]
# Kernel block, where the kernels defining the residual equations are set up.
[PolycrystalKernel]
# Custom action creating all necessary kernels for grain growth. All input parameters are up in GlobalParams
[]
[]
[AuxKernels]
# AuxKernel block, defining the equations used to calculate the auxvars
[bnds_aux]
# AuxKernel that calculates the GB term
type = BndsCalcAux
variable = bnds
execute_on = 'initial timestep_end'
[]
[unique_grains]
type = FeatureFloodCountAux
variable = unique_grains
flood_counter = grain_tracker
field_display = UNIQUE_REGION
execute_on = 'initial timestep_end'
[]
[var_indices]
type = FeatureFloodCountAux
variable = var_indices
flood_counter = grain_tracker
field_display = VARIABLE_COLORING
execute_on = 'initial timestep_end'
[]
[ghosted_entities]
type = FeatureFloodCountAux
variable = ghost_regions
flood_counter = grain_tracker
field_display = GHOSTED_ENTITIES
execute_on = 'initial timestep_end'
[]
[halos]
type = FeatureFloodCountAux
variable = halos
flood_counter = grain_tracker
field_display = HALOS
execute_on = 'initial timestep_end'
[]
[halo0]
type = FeatureFloodCountAux
variable = halo0
map_index = 0
field_display = HALOS
flood_counter = grain_tracker
[]
[halo1]
type = FeatureFloodCountAux
variable = halo1
map_index = 1
field_display = HALOS
flood_counter = grain_tracker
[]
[halo2]
type = FeatureFloodCountAux
variable = halo2
map_index = 2
field_display = HALOS
flood_counter = grain_tracker
[]
[halo3]
type = FeatureFloodCountAux
variable = halo3
map_index = 3
field_display = HALOS
flood_counter = grain_tracker
[]
[halo4]
type = FeatureFloodCountAux
variable = halo4
map_index = 4
field_display = HALOS
flood_counter = grain_tracker
[]
[halo5]
type = FeatureFloodCountAux
variable = halo5
map_index = 5
field_display = HALOS
flood_counter = grain_tracker
[]
[halo6]
type = FeatureFloodCountAux
variable = halo6
map_index = 6
field_display = HALOS
flood_counter = grain_tracker
[]
[halo7]
type = FeatureFloodCountAux
variable = halo7
map_index = 7
field_display = HALOS
flood_counter = grain_tracker
[]
[centroids]
type = FeatureFloodCountAux
variable = centroids
execute_on = 'timestep_end'
field_display = CENTROID
flood_counter = grain_tracker
[]
[proc_id]
type = ProcessorIDAux
variable = proc_id
execute_on = 'initial'
[]
[voronoi_id]
type = VoronoiICAux
variable = voronoi_id
execute_on = 'initial'
polycrystal_ic_uo = voronoi
[]
[]
[Materials]
[CuGrGr]
# Material properties
type = GBEvolution
T = '450' # Constant temperature of the simulation (for mobility calculation)
wGB = 125 # Width of the diffuse GB
GBmob0 = 2.5e-6 # m^4(Js) for copper from Schoenfelder1997
Q = 0.23 # eV for copper from Schoenfelder1997
GBenergy = 0.708 # J/m^2 from Schoenfelder1997
[]
[]
[Postprocessors]
# Scalar postprocessors
[dt]
# Outputs the current time step
type = TimestepSize
[]
[]
[Executioner]
# Uses newton iteration to solve the problem.
type = Transient # Type of executioner, here it is transient with an adaptive time step
scheme = bdf2 # Type of time integration (2nd order backward euler), defaults to 1st order backward euler
solve_type = PJFNK
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart -mat_mffd_type'
petsc_options_value = 'hypre boomeramg 101 ds'
l_max_its = 30 # Max number of linear iterations
l_tol = 1e-4 # Relative tolerance for linear solves
nl_max_its = 40 # Max number of nonlinear iterations
nl_rel_tol = 1e-10 # Absolute tolerance for nonlienar solves
start_time = 0.0
num_steps = 2
dt = 300
[]
[Outputs]
csv = true
[]
(modules/combined/test/tests/ACGrGrElasticDrivingForce/bicrystal.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 10
ny = 3
xmax = 1000
ymax = 1000
elem_type = QUAD4
uniform_refine = 2
[]
[GlobalParams]
op_num = 2
var_name_base = gr
[]
[Variables]
[./PolycrystalVariables]
[../]
[./disp_x]
[../]
[./disp_y]
[../]
[]
[ICs]
[./PolycrystalICs]
[./BicrystalBoundingBoxIC]
x1 = 0
y1 = 0
x2 = 500
y2 = 1000
[../]
[../]
[]
[AuxVariables]
[./bnds]
order = FIRST
family = LAGRANGE
[../]
[./elastic_strain11]
order = CONSTANT
family = MONOMIAL
[../]
[./elastic_strain22]
order = CONSTANT
family = MONOMIAL
[../]
[./elastic_strain12]
order = CONSTANT
family = MONOMIAL
[../]
[./unique_grains]
order = CONSTANT
family = MONOMIAL
[../]
[./var_indices]
order = CONSTANT
family = MONOMIAL
[../]
[./C1111]
order = CONSTANT
family = MONOMIAL
[../]
[./active_bounds_elemental]
order = CONSTANT
family = MONOMIAL
[../]
[./euler_angle]
order = CONSTANT
family = MONOMIAL
[../]
[]
[Kernels]
[./PolycrystalKernel]
[../]
[./PolycrystalElasticDrivingForce]
[../]
[./TensorMechanics]
displacements = 'disp_x disp_y'
[../]
[]
[AuxKernels]
[./bnds_aux]
type = BndsCalcAux
variable = bnds
execute_on = timestep_end
[../]
[./elastic_strain11]
type = RankTwoAux
variable = elastic_strain11
rank_two_tensor = elastic_strain
index_i = 0
index_j = 0
execute_on = timestep_end
[../]
[./elastic_strain22]
type = RankTwoAux
variable = elastic_strain22
rank_two_tensor = elastic_strain
index_i = 1
index_j = 1
execute_on = timestep_end
[../]
[./elastic_strain12]
type = RankTwoAux
variable = elastic_strain12
rank_two_tensor = elastic_strain
index_i = 0
index_j = 1
execute_on = timestep_end
[../]
[./unique_grains]
type = FeatureFloodCountAux
variable = unique_grains
flood_counter = grain_tracker
execute_on = 'initial timestep_begin'
field_display = UNIQUE_REGION
[../]
[./var_indices]
type = FeatureFloodCountAux
variable = var_indices
flood_counter = grain_tracker
execute_on = 'initial timestep_begin'
field_display = VARIABLE_COLORING
[../]
[./C1111]
type = RankFourAux
variable = C1111
rank_four_tensor = elasticity_tensor
index_l = 0
index_j = 0
index_k = 0
index_i = 0
execute_on = timestep_end
[../]
[./active_bounds_elemental]
type = FeatureFloodCountAux
variable = active_bounds_elemental
field_display = ACTIVE_BOUNDS
execute_on = 'initial timestep_begin'
flood_counter = grain_tracker
[../]
[./euler_angle]
type = OutputEulerAngles
variable = euler_angle
euler_angle_provider = euler_angle_file
grain_tracker = grain_tracker
output_euler_angle = 'phi1'
[../]
[]
[BCs]
[./top_displacement]
type = DirichletBC
variable = disp_y
boundary = top
value = -10.0
[../]
[./x_anchor]
type = DirichletBC
variable = disp_x
boundary = 'left right'
value = 0.0
[../]
[./y_anchor]
type = DirichletBC
variable = disp_y
boundary = bottom
value = 0.0
[../]
[]
[Materials]
[./Copper]
type = GBEvolution
block = 0
T = 500 # K
wGB = 75 # nm
GBmob0 = 2.5e-6 #m^4/(Js) from Schoenfelder 1997
Q = 0.23 #Migration energy in eV
GBenergy = 0.708 #GB energy in J/m^2
time_scale = 1.0e-6
[../]
[./ElasticityTensor]
type = ComputePolycrystalElasticityTensor
grain_tracker = grain_tracker
[../]
[./strain]
type = ComputeSmallStrain
block = 0
displacements = 'disp_x disp_y'
[../]
[./stress]
type = ComputeLinearElasticStress
block = 0
[../]
[]
[UserObjects]
[./euler_angle_file]
type = EulerAngleFileReader
file_name = test.tex
[../]
[./grain_tracker]
type = GrainTrackerElasticity
connecting_threshold = 0.05
compute_var_to_feature_map = true
flood_entity_type = elemental
execute_on = 'initial timestep_begin'
euler_angle_provider = euler_angle_file
fill_method = symmetric9
C_ijkl = '1.27e5 0.708e5 0.708e5 1.27e5 0.708e5 1.27e5 0.7355e5 0.7355e5 0.7355e5'
outputs = none
[../]
[]
[Postprocessors]
[./dt]
type = TimestepSize
[../]
[./gr0_area]
type = ElementIntegralVariablePostprocessor
variable = gr0
[../]
[]
[Preconditioning]
[./SMP]
type = SMP
coupled_groups = 'gr0,gr1 disp_x,disp_y'
[../]
[]
[Executioner]
type = Transient
solve_type = 'PJFNK'
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart -pc_hypre_boomeramg_strong_threshold'
petsc_options_value = 'hypre boomeramg 31 0.7'
l_max_its = 30
l_tol = 1e-4
nl_max_its = 30
nl_rel_tol = 1e-9
start_time = 0.0
num_steps = 3
dt = 0.2
[./Adaptivity]
initial_adaptivity = 2
refine_fraction = 0.7
coarsen_fraction = 0.1
max_h_level = 2
[../]
[]
[Outputs]
execute_on = 'timestep_end'
exodus = true
[]
(modules/phase_field/test/tests/grain_tracker_test/grain_tracker_remapping_test.i)
# This simulation predicts GB migration of a 2D copper polycrystal with 100 grains represented with 18 order parameters
# Mesh adaptivity and time step adaptivity are used
# An AuxVariable is used to calculate the grain boundary locations
# Postprocessors are used to record time step and the number of grains
[Mesh]
# Mesh block. Meshes can be read in or automatically generated
type = GeneratedMesh
dim = 2 # Problem dimension
nx = 12 # Number of elements in the x-direction
ny = 12 # Number of elements in the y-direction
xmax = 1000 # maximum x-coordinate of the mesh
ymax = 1000 # maximum y-coordinate of the mesh
elem_type = QUAD4 # Type of elements used in the mesh
uniform_refine = 1 # Initial uniform refinement of the mesh
[]
[GlobalParams]
# Parameters used by several kernels that are defined globally to simplify input file
op_num = 8 # Number of order parameters used
var_name_base = gr # Base name of grains
order = CONSTANT
family = MONOMIAL
[]
[Variables]
# Variable block, where all variables in the simulation are declared
[./PolycrystalVariables]
order = FIRST
family = LAGRANGE
[../]
[]
[UserObjects]
[./voronoi]
type = PolycrystalVoronoi
grain_num = 12 # Number of grains
coloring_algorithm = jp
rand_seed = 10
output_adjacency_matrix = true
[../]
[./grain_tracker]
type = GrainTracker
threshold = 0.2
verbosity_level = 1
connecting_threshold = 0.08
flood_entity_type = ELEMENTAL
compute_halo_maps = true # For displaying HALO fields
polycrystal_ic_uo = voronoi
error_on_grain_creation = true
execute_on = 'initial timestep_end'
[../]
[]
[ICs]
[./PolycrystalICs]
[./PolycrystalColoringIC]
polycrystal_ic_uo = voronoi
[../]
[../]
[]
[AuxVariables]
# Dependent variables
[./bnds]
# Variable used to visualize the grain boundaries in the simulation
order = FIRST
family = LAGRANGE
[../]
[./unique_grains]
[../]
[./var_indices]
[../]
[./ghost_regions]
[../]
[./halos]
[../]
[./halo0]
[../]
[./halo1]
[../]
[./halo2]
[../]
[./halo3]
[../]
[./halo4]
[../]
[./halo5]
[../]
[./halo6]
[../]
[./halo7]
[../]
[./centroids]
order = CONSTANT
family = MONOMIAL
[../]
[./proc_id]
[../]
[]
[Kernels]
# Kernel block, where the kernels defining the residual equations are set up.
[./PolycrystalKernel]
# Custom action creating all necessary kernels for grain growth. All input parameters are up in GlobalParams
[../]
[]
[AuxKernels]
# AuxKernel block, defining the equations used to calculate the auxvars
[./bnds_aux]
# AuxKernel that calculates the GB term
type = BndsCalcAux
variable = bnds
execute_on = 'initial timestep_end'
[../]
[./unique_grains]
type = FeatureFloodCountAux
variable = unique_grains
flood_counter = grain_tracker
field_display = UNIQUE_REGION
execute_on = 'initial timestep_end'
[../]
[./var_indices]
type = FeatureFloodCountAux
variable = var_indices
flood_counter = grain_tracker
field_display = VARIABLE_COLORING
execute_on = 'initial timestep_end'
[../]
[./ghosted_entities]
type = FeatureFloodCountAux
variable = ghost_regions
flood_counter = grain_tracker
field_display = GHOSTED_ENTITIES
execute_on = 'initial timestep_end'
[../]
[./halos]
type = FeatureFloodCountAux
variable = halos
flood_counter = grain_tracker
field_display = HALOS
execute_on = 'initial timestep_end'
[../]
[./halo0]
type = FeatureFloodCountAux
variable = halo0
map_index = 0
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo1]
type = FeatureFloodCountAux
variable = halo1
map_index = 1
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo2]
type = FeatureFloodCountAux
variable = halo2
map_index = 2
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo3]
type = FeatureFloodCountAux
variable = halo3
map_index = 3
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo4]
type = FeatureFloodCountAux
variable = halo4
map_index = 4
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo5]
type = FeatureFloodCountAux
variable = halo5
map_index = 5
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo6]
type = FeatureFloodCountAux
variable = halo6
map_index = 6
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo7]
type = FeatureFloodCountAux
variable = halo7
map_index = 7
field_display = HALOS
flood_counter = grain_tracker
[../]
[./centroids]
type = FeatureFloodCountAux
variable = centroids
execute_on = timestep_end
field_display = CENTROID
flood_counter = grain_tracker
[../]
[./proc_id]
type = ProcessorIDAux
variable = proc_id
execute_on = initial
[../]
[]
[BCs]
# Boundary Condition block
[]
[Materials]
[./CuGrGr]
# Material properties
type = GBEvolution
T = 450 # Constant temperature of the simulation (for mobility calculation)
wGB = 125 # Width of the diffuse GB
GBmob0 = 2.5e-6 # m^4(Js) for copper from Schoenfelder1997
Q = 0.23 # eV for copper from Schoenfelder1997
GBenergy = 0.708 # J/m^2 from Schoenfelder1997
[../]
[]
[Postprocessors]
# Scalar postprocessors
[./dt]
# Outputs the current time step
type = TimestepSize
[../]
[]
[Executioner]
# Uses newton iteration to solve the problem.
type = Transient # Type of executioner, here it is transient with an adaptive time step
scheme = bdf2 # Type of time integration (2nd order backward euler), defaults to 1st order backward euler
solve_type = PJFNK
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart -mat_mffd_type'
petsc_options_value = 'hypre boomeramg 101 ds'
l_max_its = 30 # Max number of linear iterations
l_tol = 1e-4 # Relative tolerance for linear solves
nl_max_its = 40 # Max number of nonlinear iterations
nl_rel_tol = 1e-10 # Absolute tolerance for nonlienar solves
start_time = 0.0
num_steps = 15
dt = 300
[]
[Problem]
type = FEProblem
[]
[Outputs]
csv = true
exodus = true
[./perf_graph]
type = PerfGraphOutput
level = 2 # Default is 1
[../]
[]
(modules/phase_field/test/tests/reconstruction/euler2rgb_no_grain_region.i)
[Mesh]
[ebsd_mesh]
type = EBSDMeshGenerator
filename = ebsd_small.txt
[]
[]
[GlobalParams]
op_num = 8
var_name_base = gr
[]
[UserObjects]
[ebsd_reader]
type = EBSDReader
execute_on = initial
[]
[ebsd]
type = PolycrystalEBSD
coloring_algorithm = bt
ebsd_reader = ebsd_reader
phase = 2
output_adjacency_matrix = true
[]
[grain_tracker]
type = GrainTracker
polycrystal_ic_uo = ebsd
[]
[]
[ICs]
[PolycrystalICs]
[PolycrystalColoringIC]
polycrystal_ic_uo = ebsd
[]
[]
[void_phase]
type = ReconPhaseVarIC
variable = c
ebsd_reader = ebsd_reader
phase = 1
[]
[]
[Variables]
[PolycrystalVariables]
[]
[]
[AuxVariables]
# active = 'c bnds'
[c]
[]
[bnds]
[]
[ebsd_numbers]
family = MONOMIAL
order = CONSTANT
[]
# Note: Not active
[unique_grains]
family = MONOMIAL
order = CONSTANT
[]
[var_indices]
family = MONOMIAL
order = CONSTANT
[]
[]
[Kernels]
[PolycrystalKernel]
c = c
[]
[]
[AuxKernels]
# active = 'BndsCalc'
[BndsCalc]
type = BndsCalcAux
variable = bnds
execute_on = 'initial timestep_end'
[]
[ebsd_numbers]
type = EBSDReaderAvgDataAux
data_name = feature_id
ebsd_reader = ebsd_reader
grain_tracker = grain_tracker
variable = ebsd_numbers
phase = 2
execute_on = 'initial timestep_end'
[]
# Note: Not active
[unique_grains]
type = FeatureFloodCountAux
variable = unique_grains
flood_counter = grain_tracker
field_display = UNIQUE_REGION
execute_on = 'initial timestep_end'
[]
[var_indices]
type = FeatureFloodCountAux
variable = var_indices
flood_counter = grain_tracker
field_display = VARIABLE_COLORING
execute_on = 'initial timestep_end'
[]
[]
[Modules]
[PhaseField]
[EulerAngles2RGB]
crystal_structure = cubic
grain_tracker = grain_tracker
euler_angle_provider = ebsd_reader
no_grain_color = '.1 .1 .1'
phase = 2
[]
[]
[]
[Materials]
[bulk]
type = GBEvolution
block = 0
T = 2273
wGB = 10.0
GBenergy = 1.58
GBmob0 = 9.2124e-9
Q = 2.77
length_scale = 1.0e-6
time_scale = 60.0
[]
[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = PJFNK
petsc_options_iname = '-pc_type -sub_pc_type -pc_asm_overlap -ksp_grmres_restart '
petsc_options_value = ' asm lu 1 21'
start_time = 0.0
dt = 0.2
num_steps = 1
[]
[Outputs]
csv = true
exodus = true
execute_on = 'INITIAL TIMESTEP_END'
perf_graph = true
[]
(modules/phase_field/test/tests/GrandPotentialPFM/GrandPotentialAnisotropyAntitrap.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 15
ny = 15
xmin = -2
xmax = 2
ymin = -2
ymax = 2
[]
[GlobalParams]
radius = 1.0
int_width = 0.8
x1 = 0
y1 = 0
enable_jit = true
derivative_order = 2
[]
[Variables]
[./w]
[../]
[./etaa0]
[../]
[./etab0]
[../]
[]
[AuxVariables]
[./bnds]
[../]
[]
[AuxKernels]
[./bnds]
type = BndsCalcAux
variable = bnds
v = 'etaa0 etab0'
[../]
[]
[ICs]
[./w]
type = SmoothCircleIC
variable = w
outvalue = -4.0
invalue = 0.0
[../]
[./etaa0]
type = SmoothCircleIC
variable = etaa0
#Solid phase
outvalue = 0.0
invalue = 1.0
[../]
[./etab0]
type = SmoothCircleIC
variable = etab0
#Liquid phase
outvalue = 1.0
invalue = 0.0
[../]
[]
[Kernels]
# Order parameter eta_alpha0
[./ACa0_bulk]
type = ACGrGrMulti
variable = etaa0
v = 'etab0'
gamma_names = 'gab'
[../]
[./ACa0_sw]
type = ACSwitching
variable = etaa0
Fj_names = 'omegaa omegab'
hj_names = 'ha hb'
args = 'etab0 w'
[../]
[./ACa0_int1]
type = ACInterface2DMultiPhase1
variable = etaa0
etas = 'etab0'
kappa_name = kappaa
dkappadgrad_etaa_name = dkappadgrad_etaa
d2kappadgrad_etaa_name = d2kappadgrad_etaa
[../]
[./ACa0_int2]
type = ACInterface2DMultiPhase2
variable = etaa0
kappa_name = kappaa
dkappadgrad_etaa_name = dkappadgrad_etaa
[../]
[./ea0_dot]
type = TimeDerivative
variable = etaa0
[../]
# Order parameter eta_beta0
[./ACb0_bulk]
type = ACGrGrMulti
variable = etab0
v = 'etaa0'
gamma_names = 'gab'
[../]
[./ACb0_sw]
type = ACSwitching
variable = etab0
Fj_names = 'omegaa omegab'
hj_names = 'ha hb'
args = 'etaa0 w'
[../]
[./ACb0_int1]
type = ACInterface2DMultiPhase1
variable = etab0
etas = 'etaa0'
kappa_name = kappab
dkappadgrad_etaa_name = dkappadgrad_etab
d2kappadgrad_etaa_name = d2kappadgrad_etab
[../]
[./ACb0_int2]
type = ACInterface2DMultiPhase2
variable = etab0
kappa_name = kappab
dkappadgrad_etaa_name = dkappadgrad_etab
[../]
[./eb0_dot]
type = TimeDerivative
variable = etab0
[../]
#Chemical potential
[./w_dot]
type = SusceptibilityTimeDerivative
variable = w
f_name = chi
args = '' # in this case chi (the susceptibility) is simply a constant
[../]
[./Diffusion]
type = MatDiffusion
variable = w
diffusivity = Dchi
args = ''
[../]
[./coupled_etaa0dot]
type = CoupledSwitchingTimeDerivative
variable = w
v = etaa0
Fj_names = 'rhoa rhob'
hj_names = 'ha hb'
args = 'etaa0 etab0'
[../]
[./coupled_etab0dot]
type = CoupledSwitchingTimeDerivative
variable = w
v = etab0
Fj_names = 'rhoa rhob'
hj_names = 'ha hb'
args = 'etaa0 etab0'
[../]
[./coupled_etaa0dot_int]
type = AntitrappingCurrent
variable = w
v = etaa0
f_name = rhodiff
[../]
[./coupled_etab0dot_int]
type = AntitrappingCurrent
variable = w
v = etab0
f_name = rhodiff
[../]
[]
[Materials]
[./ha]
type = SwitchingFunctionMultiPhaseMaterial
h_name = ha
all_etas = 'etaa0 etab0'
phase_etas = 'etaa0'
[../]
[./hb]
type = SwitchingFunctionMultiPhaseMaterial
h_name = hb
all_etas = 'etaa0 etab0'
phase_etas = 'etab0'
[../]
[./omegaa]
type = DerivativeParsedMaterial
args = 'w'
f_name = omegaa
material_property_names = 'Vm ka caeq'
function = '-0.5*w^2/Vm^2/ka-w/Vm*caeq'
[../]
[./omegab]
type = DerivativeParsedMaterial
args = 'w'
f_name = omegab
material_property_names = 'Vm kb cbeq'
function = '-0.5*w^2/Vm^2/kb-w/Vm*cbeq'
[../]
[./rhoa]
type = DerivativeParsedMaterial
args = 'w'
f_name = rhoa
material_property_names = 'Vm ka caeq'
function = 'w/Vm^2/ka + caeq/Vm'
[../]
[./rhob]
type = DerivativeParsedMaterial
args = 'w'
f_name = rhob
material_property_names = 'Vm kb cbeq'
function = 'w/Vm^2/kb + cbeq/Vm'
[../]
[./int]
type = DerivativeParsedMaterial
args = 'w'
f_name = rhodiff
material_property_names = 'rhoa rhob'
constant_names = 'int_width'
constant_expressions = '0.8'
function = 'int_width*(rhob-rhoa)'
[../]
[./kappaa]
type = InterfaceOrientationMultiphaseMaterial
kappa_name = kappaa
dkappadgrad_etaa_name = dkappadgrad_etaa
d2kappadgrad_etaa_name = d2kappadgrad_etaa
etaa = etaa0
etab = etab0
[../]
[./kappab]
type = InterfaceOrientationMultiphaseMaterial
kappa_name = kappab
dkappadgrad_etaa_name = dkappadgrad_etab
d2kappadgrad_etaa_name = d2kappadgrad_etab
etaa = etab0
etab = etaa0
[../]
[./const]
type = GenericConstantMaterial
prop_names = 'L D chi Vm ka caeq kb cbeq gab mu'
prop_values = '1.0 1.0 0.1 1.0 10.0 0.1 10.0 0.9 4.5 10.0'
[../]
[./Mobility]
type = ParsedMaterial
f_name = Dchi
material_property_names = 'D chi'
function = 'D*chi'
[../]
[]
[Preconditioning]
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
scheme = bdf2
petsc_options_iname = '-pc_type -ksp_gmres_restart -sub_pc_type -pc_asm_overlap'
petsc_options_value = 'asm 31 lu 1'
l_tol = 1.0e-3
nl_rel_tol = 1.0e-8
nl_abs_tol = 1e-8
num_steps = 3
[./TimeStepper]
type = IterationAdaptiveDT
dt = 0.001
[../]
[]
[Outputs]
exodus = true
[]
(modules/phase_field/test/tests/grain_tracker_test/grain_halo_over_bc.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 35
ny = 35
xmax = 1000
ymax = 1000
elem_type = QUAD4
parallel_type = replicated # Periodic BCs
[]
[GlobalParams]
op_num = 8 # Number of order parameters used
var_name_base = 'gr' # Base name of grains
[]
[Variables]
[./PolycrystalVariables]
[../]
[]
[UserObjects]
[./voronoi]
type = PolycrystalVoronoi
rand_seed = 12
grain_num = 15 # Number of grains
coloring_algorithm = bt
[../]
[./grain_tracker]
type = GrainTracker
threshold = 0.2
connecting_threshold = 0.08
flood_entity_type = ELEMENTAL
compute_halo_maps = true # Only necessary for displaying HALOS
[../]
[]
[ICs]
[./PolycrystalICs]
[./PolycrystalColoringIC]
polycrystal_ic_uo = voronoi
[../]
[../]
[]
[AuxVariables]
[./bnds]
[../]
[./unique_grains]
order = CONSTANT
family = MONOMIAL
[../]
[./var_indices]
order = CONSTANT
family = MONOMIAL
[../]
[./ghost_regions]
order = CONSTANT
family = MONOMIAL
[../]
[./halos]
order = CONSTANT
family = MONOMIAL
[../]
[./proc_id]
order = CONSTANT
family = MONOMIAL
[../]
[./halo0]
order = CONSTANT
family = MONOMIAL
[../]
[./halo1]
order = CONSTANT
family = MONOMIAL
[../]
[./halo2]
order = CONSTANT
family = MONOMIAL
[../]
[./halo3]
order = CONSTANT
family = MONOMIAL
[../]
[./halo4]
order = CONSTANT
family = MONOMIAL
[../]
[./halo5]
order = CONSTANT
family = MONOMIAL
[../]
[./halo6]
order = CONSTANT
family = MONOMIAL
[../]
[./halo7]
order = CONSTANT
family = MONOMIAL
[../]
[]
[Kernels]
[./PolycrystalKernel]
[../]
[]
[AuxKernels]
[./bnds_aux]
type = BndsCalcAux
variable = bnds
execute_on = 'initial timestep_end'
[../]
[./unique_grains]
type = FeatureFloodCountAux
variable = unique_grains
flood_counter = grain_tracker
field_display = UNIQUE_REGION
execute_on = 'initial timestep_end'
[../]
[./var_indices]
type = FeatureFloodCountAux
variable = var_indices
flood_counter = grain_tracker
field_display = VARIABLE_COLORING
execute_on = 'initial timestep_end'
[../]
[./ghosted_entities]
type = FeatureFloodCountAux
variable = ghost_regions
flood_counter = grain_tracker
field_display = GHOSTED_ENTITIES
execute_on = 'initial timestep_end'
[../]
[./halos]
type = FeatureFloodCountAux
variable = halos
flood_counter = grain_tracker
field_display = HALOS
execute_on = 'initial timestep_end'
[../]
[./proc_id]
type = ProcessorIDAux
variable = proc_id
[../]
[./halo0]
type = FeatureFloodCountAux
variable = halo0
map_index = 0
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo1]
type = FeatureFloodCountAux
variable = halo1
map_index = 1
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo2]
type = FeatureFloodCountAux
variable = halo2
map_index = 2
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo3]
type = FeatureFloodCountAux
variable = halo3
map_index = 3
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo4]
type = FeatureFloodCountAux
variable = halo4
map_index = 4
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo5]
type = FeatureFloodCountAux
variable = halo5
map_index = 5
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo6]
type = FeatureFloodCountAux
variable = halo6
map_index = 6
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo7]
type = FeatureFloodCountAux
variable = halo7
map_index = 7
field_display = HALOS
flood_counter = grain_tracker
[../]
[]
[BCs]
[./Periodic]
[./top_bottom]
auto_direction = 'x y'
[../]
[../]
[]
[Materials]
[./CuGrGr]
type = GBEvolution
T = '450'
wGB = 125
GBmob0 = 2.5e-6
Q = 0.23
GBenergy = 0.708
[../]
[]
[Postprocessors]
[./dt]
type = TimestepSize
[../]
[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = PJFNK
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart -mat_mffd_type'
petsc_options_value = 'hypre boomeramg 101 ds'
l_max_its = 30
l_tol = 1e-4
nl_max_its = 40
nl_rel_tol = 1e-10
dt = 25
num_steps = 1
[]
[Outputs]
exodus = true # Exodus file will be outputted
[]
(modules/phase_field/test/tests/rigidbodymotion/grain_forcedensity.i)
# test file for showing reaction forces between particles
[GlobalParams]
var_name_base = eta
op_num = 2
[]
[Mesh]
type = GeneratedMesh
dim = 2
nx = 10
ny = 5
nz = 0
xmax = 50
ymax = 25
zmax = 0
elem_type = QUAD4
uniform_refine = 1
[]
[Variables]
[./c]
order = FIRST
family = LAGRANGE
[../]
[./w]
order = FIRST
family = LAGRANGE
[../]
[./eta0]
[../]
[./eta1]
[../]
[]
[Kernels]
[./c_res]
type = SplitCHParsed
variable = c
f_name = F
kappa_name = kappa_c
args = 'eta0 eta1'
w = w
[../]
[./w_res]
type = SplitCHWRes
variable = w
mob_name = M
[../]
[./time]
type = CoupledTimeDerivative
variable = w
v = c
[../]
[./motion]
type = MultiGrainRigidBodyMotion
variable = w
c = c
v = 'eta0 eta1'
grain_force = grain_force
grain_tracker_object = grain_center
grain_volumes = grain_volumes
[../]
[./eta0_dot]
type = TimeDerivative
variable = eta0
[../]
[./vadv_eta]
type = SingleGrainRigidBodyMotion
variable = eta0
c = c
v = 'eta0 eta1'
grain_force = grain_force
grain_tracker_object = grain_center
grain_volumes = grain_volumes
op_index = 0
[../]
[./acint_eta0]
type = ACInterface
variable = eta0
mob_name = M
#args = c
kappa_name = kappa_eta
[../]
[./acbulk_eta0]
type = AllenCahn
variable = eta0
mob_name = M
f_name = F
args = 'c eta1'
[../]
[./eta1_dot]
type = TimeDerivative
variable = eta1
[../]
[./vadv_eta1]
type = SingleGrainRigidBodyMotion
variable = eta1
c = c
v = 'eta0 eta1'
op_index = 1
grain_force = grain_force
grain_tracker_object = grain_center
grain_volumes = grain_volumes
[../]
[./acint_eta1]
type = ACInterface
variable = eta1
mob_name = M
#args = c
kappa_name = kappa_eta
[../]
[./acbulk_eta1]
type = AllenCahn
variable = eta1
mob_name = M
f_name = F
args = 'c eta0'
[../]
[]
[Materials]
[./pfmobility]
type = GenericConstantMaterial
prop_names = 'M kappa_c kappa_eta'
prop_values = '1.0 0.5 0.5'
[../]
[./free_energy]
type = DerivativeParsedMaterial
f_name = F
args = 'c eta0 eta1'
constant_names = 'barr_height cv_eq'
constant_expressions = '0.1 1.0e-2'
function = 16*barr_height*(c-cv_eq)^2*(1-cv_eq-c)^2+eta0*(1-eta0)*c+eta1*(1-eta1)*c
derivative_order = 2
[../]
[./force_density]
type = ForceDensityMaterial
c = c
etas ='eta0 eta1'
[../]
[]
[AuxVariables]
[./bnds]
[../]
[./df00]
order = CONSTANT
family = MONOMIAL
[../]
[./df01]
order = CONSTANT
family = MONOMIAL
[../]
[./df10]
order = CONSTANT
family = MONOMIAL
[../]
[./df11]
order = CONSTANT
family = MONOMIAL
[../]
[./unique_grains]
order = CONSTANT
family = MONOMIAL
[../]
[./var_indices]
order = CONSTANT
family = MONOMIAL
[../]
[./centroids]
order = CONSTANT
family = MONOMIAL
[../]
[]
[AuxKernels]
[./bnds]
type = BndsCalcAux
variable = bnds
var_name_base = eta
op_num = 2
v = 'eta0 eta1'
[../]
[./df01]
type = MaterialStdVectorRealGradientAux
variable = df01
index = 0
component = 1
property = force_density
[../]
[./df11]
type = MaterialStdVectorRealGradientAux
variable = df11
index = 1
component = 1
property = force_density
[../]
[./df00]
type = MaterialStdVectorRealGradientAux
variable = df00
index = 0
component = 0
property = force_density
[../]
[./df10]
type = MaterialStdVectorRealGradientAux
variable = df10
index = 1
component = 0
property = force_density
[../]
[./unique_grains]
type = FeatureFloodCountAux
variable = unique_grains
flood_counter = grain_center
field_display = UNIQUE_REGION
execute_on = timestep_begin
[../]
[./var_indices]
type = FeatureFloodCountAux
variable = var_indices
flood_counter = grain_center
field_display = VARIABLE_COLORING
execute_on = timestep_begin
[../]
[./centroids]
type = FeatureFloodCountAux
variable = centroids
execute_on = timestep_begin
field_display = CENTROID
flood_counter = grain_center
[../]
[]
[ICs]
[./ic_eta0]
int_width = 1.0
x1 = 20.0
y1 = 0.0
radius = 14.0
outvalue = 0.0
variable = eta0
invalue = 1.0
type = SmoothCircleIC
[../]
[./IC_eta1]
int_width = 1.0
x1 = 30.0
y1 = 25.0
radius = 14.0
outvalue = 0.0
variable = eta1
invalue = 1.0
type = SmoothCircleIC
[../]
[./ic_c]
type = SpecifiedSmoothCircleIC
invalue = 1.0
outvalue = 0.1
int_width = 1.0
x_positions = '20.0 30.0 '
z_positions = '0.0 0.0 '
y_positions = '0.0 25.0 '
radii = '14.0 14.0'
3D_spheres = false
variable = c
block = 0
[../]
[]
[VectorPostprocessors]
[./forces]
type = GrainForcesPostprocessor
grain_force = grain_force
[../]
[./grain_volumes]
type = FeatureVolumeVectorPostprocessor
flood_counter = grain_center
execute_on = 'initial timestep_begin'
[../]
[]
[UserObjects]
[./grain_center]
type = GrainTracker
outputs = none
compute_var_to_feature_map = true
execute_on = 'initial timestep_begin'
[../]
[./grain_force]
type = ComputeGrainForceAndTorque
execute_on = 'linear nonlinear'
grain_data = grain_center
force_density = force_density
c = c
etas = 'eta0 eta1'
[../]
[]
[Preconditioning]
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = NEWTON
petsc_options_iname = '-pc_type -ksp_gmres_restart -sub_ksp_type -sub_pc_type -pc_asm_overlap'
petsc_options_value = 'asm 31 preonly lu 1'
l_max_its = 30
l_tol = 1.0e-4
nl_rel_tol = 1.0e-10
start_time = 0.0
num_steps = 1
dt = 0.1
[]
[Outputs]
exodus = true
csv = true
[]
(modules/phase_field/test/tests/TotalFreeEnergy/TotalFreeEnergy_2var_test.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 10
ny = 10
nz = 0
xmin = 0
xmax = 1000
ymin = 0
ymax = 1000
zmin = 0
zmax = 0
elem_type = QUAD4
uniform_refine = 2
[]
[GlobalParams]
op_num = 2
var_name_base = gr
[]
[Variables]
[./PolycrystalVariables]
[../]
[]
[ICs]
[./PolycrystalICs]
[./BicrystalCircleGrainIC]
radius = 333.333
x = 500
y = 500
int_width = 60
[../]
[../]
[]
[AuxVariables]
[./bnds]
order = FIRST
family = LAGRANGE
[../]
[./local_energy]
order = CONSTANT
family = MONOMIAL
[../]
[]
[Kernels]
[./gr0dot]
type = TimeDerivative
variable = gr0
[../]
[./gr0bulk]
type = AllenCahn
variable = gr0
f_name = F
args = gr1
[../]
[./gr0int]
type = ACInterface
variable = gr0
kappa_name = kappa_op
[../]
[./gr1dot]
type = TimeDerivative
variable = gr1
[../]
[./gr1bulk]
type = AllenCahn
variable = gr1
f_name = F
args = gr0
[../]
[./gr1int]
type = ACInterface
variable = gr1
kappa_name = kappa_op
[../]
[]
[AuxKernels]
[./BndsCalc]
type = BndsCalcAux
variable = bnds
[../]
[./local_free_energy]
type = TotalFreeEnergy
variable = local_energy
kappa_names = 'kappa_op kappa_op'
interfacial_vars = 'gr0 gr1'
[../]
[]
[BCs]
[./Periodic]
[./All]
auto_direction = 'x y'
[../]
[../]
[]
[Materials]
[./Copper]
type = GBEvolution
T = 500 # K
wGB = 60 # nm
GBmob0 = 2.5e-6 # m^4/(Js) from Schoenfelder 1997
Q = 0.23 # Migration energy in eV
GBenergy = 0.708 # GB energy in J/m^2
[../]
[./free_energy]
type = DerivativeParsedMaterial
args = 'gr0 gr1'
material_property_names = 'mu gamma_asymm'
function = 'mu*( gr0^4/4.0 - gr0^2/2.0 + gr1^4/4.0 - gr1^2/2.0 + gamma_asymm*gr0^2*gr1^2) + 1.0/4.0'
derivative_order = 2
enable_jit = true
[../]
[]
[Postprocessors]
[./total_energy]
type = ElementIntegralVariablePostprocessor
variable = local_energy
[../]
[]
[Preconditioning]
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = NEWTON
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart'
petsc_options_value = 'hypre boomeramg 31'
l_tol = 1.0e-4
l_max_its = 30
nl_max_its = 30
nl_rel_tol = 1.0e-9
start_time = 0.0
num_steps = 7
dt = 80.0
[./Adaptivity]
initial_adaptivity = 2
refine_fraction = 0.8
coarsen_fraction = 0.05
max_h_level = 2
[../]
[]
[Outputs]
execute_on = 'timestep_end'
csv = true
exodus = true
[]
(modules/phase_field/test/tests/DeformedGrain/DeformedGrain.i)
# This example tests the implementation of PolycrstalStoredEnergy kernels that assigns excess stored energy to grains with dislocation density
[Mesh]
type = GeneratedMesh
dim = 2
nx = 32
ny = 32
nz = 0
xmin = 0
xmax = 64
ymin = 0
ymax = 64
[]
[GlobalParams]
block = 0
op_num = 8
deformed_grain_num = 16
var_name_base = gr
grain_num = 18
grain_tracker = grain_tracker
time_scale = 1e-2
length_scale = 1e-8
[]
[Variables]
[./PolycrystalVariables]
[../]
[]
[AuxVariables]
[./bnds]
order = FIRST
family = LAGRANGE
[../]
[]
[UserObjects]
[./voronoi]
type = PolycrystalVoronoi
rand_seed = 81
coloring_algorithm = bt
[../]
[./grain_tracker]
type = GrainTracker
threshold = 0.2
connecting_threshold = 0.08
compute_var_to_feature_map = true
flood_entity_type = elemental
execute_on = ' initial timestep_begin'
outputs = none
[../]
[]
[ICs]
[./PolycrystalICs]
[./PolycrystalColoringIC]
polycrystal_ic_uo = voronoi
[../]
[../]
[]
[BCs]
[./Periodic]
[./all]
auto_direction = 'x y'
[../]
[../]
[]
[Kernels]
[./PolycrystalKernel]
[../]
[./PolycrystalStoredEnergy]
[../]
[]
[AuxKernels]
[./BndsCalc]
type = BndsCalcAux
variable = bnds
execute_on = timestep_end
[../]
[]
[Materials]
[./deformed]
type = DeformedGrainMaterial
int_width = 4.0
outputs = exodus
[../]
[]
[Preconditioning]
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
nl_max_its = 15
scheme = bdf2
solve_type = PJFNK
petsc_options_iname = -pc_type
petsc_options_value = asm
l_max_its = 15
l_tol = 1.0e-3
nl_rel_tol = 1.0e-8
start_time = 0.0
num_steps = 1
nl_abs_tol = 1e-8
dt = 0.20
[]
[Outputs]
exodus = true
interval = 1
show = bnds
perf_graph = true
[]
(modules/phase_field/test/tests/grain_growth/hex.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 40
ny = 40
nz = 0
xmin = 0
xmax = 1000
ymin = 0
ymax = 1000
zmin = 0
zmax = 0
elem_type = QUAD4
[]
[GlobalParams]
op_num = 4
var_name_base = gr
[]
[Variables]
[./PolycrystalVariables]
[../]
[]
[UserObjects]
[./hex_ic]
type = PolycrystalHex
coloring_algorithm = bt
x_offset = .5
grain_num = 4
[../]
[]
[ICs]
[./PolycrystalICs]
[./PolycrystalColoringIC]
polycrystal_ic_uo = hex_ic
[../]
[../]
[]
[AuxVariables]
[./bnds]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
[./PolycrystalKernel]
[../]
[]
[AuxKernels]
[./BndsCalc]
type = BndsCalcAux
variable = bnds
execute_on = timestep_end
[../]
[]
[BCs]
[./Periodic]
[./All]
auto_direction = 'x y'
[../]
[../]
[]
[Materials]
[./Copper]
type = GBEvolution
T = 500 # K
wGB = 60 # nm
GBmob0 = 2.5e-6 #m^4/(Js) from Schoenfelder 1997
Q = 0.23 #Migration energy in eV
GBenergy = 0.708 #GB energy in J/m^2
[../]
[]
[Preconditioning]
active = ''
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
scheme = 'bdf2'
solve_type = 'PJFNK'
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart'
petsc_options_value = 'hypre boomeramg 31'
l_tol = 1.0e-4
l_max_its = 30
nl_max_its = 20
nl_rel_tol = 1.0e-9
start_time = 0.0
num_steps = 2
dt = 80.0
[]
[Outputs]
exodus = true
[]
(modules/phase_field/test/tests/grain_growth/particle.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 10
ny = 10
nz = 0
xmin = 0
xmax = 1000
ymin = 0
ymax = 1000
zmin = 0
zmax = 0
elem_type = QUAD4
uniform_refine = 2
[]
[GlobalParams]
op_num = 2
var_name_base = gr
[]
[Variables]
[./PolycrystalVariables]
[../]
[]
[ICs]
[./PolycrystalICs]
[./BicrystalCircleGrainIC]
radius = 333.333
x = 500
y = 500
[../]
[../]
[]
[AuxVariables]
[./bnds]
order = FIRST
family = LAGRANGE
[../]
[./c]
[./InitialCondition]
int_width = 60
x1 = 167
y1 = 500
radius = 50
outvalue = 0
variable = c
invalue = 1
type = SmoothCircleIC
[../]
[../]
[]
[Kernels]
[./PolycrystalKernel]
c = c
[../]
[]
[AuxKernels]
[./BndsCalc]
type = BndsCalcAux
variable = bnds
[../]
[]
[BCs]
[./Periodic]
[./all]
auto_direction = 'x y'
[../]
[../]
[]
[Materials]
[./Copper]
type = GBEvolution
T = 500 # K
wGB = 60 # nm
GBmob0 = 2.5e-6 #m^4/(Js) from Schoenfelder 1997
Q = 0.23 #Migration energy in eV
GBenergy = 0.708 #GB energy in J/m^2
[../]
[]
[Postprocessors]
[./gr1area]
type = ElementIntegralVariablePostprocessor
variable = gr1
[../]
[]
[Preconditioning]
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = NEWTON
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart'
petsc_options_value = 'hypre boomeramg 31'
l_tol = 1.0e-4
l_max_its = 30
nl_max_its = 20
nl_rel_tol = 1.0e-9
start_time = 0.0
num_steps = 10
dt = 80.0
[./Adaptivity]
initial_adaptivity = 2
refine_fraction = 0.8
coarsen_fraction = 0.05
max_h_level = 2
[../]
[]
[Outputs]
execute_on = 'timestep_end'
csv = true
exodus = true
[]
(modules/phase_field/test/tests/grain_growth/constant_mobility.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 10
ny = 10
nz = 0
xmax = 1000
ymax = 1000
zmax = 0
elem_type = QUAD4
uniform_refine = 2
[]
[GlobalParams]
op_num = 4
var_name_base = 'gr'
[]
[Variables]
[./PolycrystalVariables]
[../]
[]
[UserObjects]
[./voronoi]
type = PolycrystalVoronoi
rand_seed = 6
grain_num = 4
coloring_algorithm = bt
[../]
[]
[ICs]
[./PolycrystalICs]
[./PolycrystalColoringIC]
polycrystal_ic_uo = voronoi
[../]
[../]
[]
[AuxVariables]
[./bnds]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
[./PolycrystalKernel]
[../]
[]
[AuxKernels]
[./BndsCalc]
type = BndsCalcAux
variable = bnds
execute_on = 'timestep_end'
[../]
[]
[BCs]
[./Periodic]
[./All]
auto_direction = 'x y'
[../]
[../]
[]
[Materials]
[./Moly_GB]
type = GBEvolution
time_scale = 1.0e-2
GBMobility = 1.88e-14 # m^4/J*s
T = '500' # K
wGB = 60 # nm
GBenergy = 1.4
[../]
[]
[Postprocessors]
[./gr1area]
type = ElementIntegralVariablePostprocessor
variable = gr1
execute_on = 'initial timestep_end'
[../]
[]
[Preconditioning]
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = 'NEWTON'
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart'
petsc_options_value = 'hypre boomeramg 31'
l_tol = 1.0e-4
l_max_its = 30
nl_max_its = 20
nl_rel_tol = 1.0e-9
start_time = 0.0
num_steps = 2
dt = 4
[]
[Outputs]
exodus = true
[]
(modules/phase_field/test/tests/grain_growth/voronoi.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 40
ny = 40
nz = 0
xmin = 0
xmax = 1000
ymin = 0
ymax = 1000
zmin = 0
zmax = 0
elem_type = QUAD4
[]
[GlobalParams]
op_num = 4
var_name_base = gr
[]
[Variables]
[./PolycrystalVariables]
[../]
[]
[UserObjects]
[./voronoi]
type = PolycrystalVoronoi
rand_seed = 105
grain_num = 4
coloring_algorithm = bt
[../]
[]
[ICs]
[./PolycrystalICs]
[./PolycrystalColoringIC]
polycrystal_ic_uo = voronoi
[../]
[../]
[]
[AuxVariables]
[./bnds]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
[./PolycrystalKernel]
[../]
[]
[AuxKernels]
[./BndsCalc]
type = BndsCalcAux
variable = bnds
execute_on = timestep_end
[../]
[]
[BCs]
[./Periodic]
[./All]
auto_direction = 'x y'
[../]
[../]
[]
[Materials]
[./Copper]
type = GBEvolution
T = 500 # K
wGB = 60 # nm
GBmob0 = 2.5e-6 #m^4/(Js) from Schoenfelder 1997
Q = 0.23 #Migration energy in eV
GBenergy = 0.708 #GB energy in J/m^2
[../]
[]
[Postprocessors]
active = ''
[./ngrains]
type = FeatureFloodCount
variable = bnds
threshold = 0.7
[../]
[]
[Preconditioning]
active = ''
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
scheme = 'bdf2'
solve_type = 'PJFNK'
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart'
petsc_options_value = 'hypre boomeramg 31'
l_tol = 1.0e-4
l_max_its = 30
nl_max_its = 20
nl_rel_tol = 1.0e-9
start_time = 0.0
num_steps = 2
dt = 80.0
[]
[Outputs]
exodus = true
[]
(modules/phase_field/test/tests/grain_tracker_test/grain_tracker_test_elemental.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 25
ny = 25
nz = 0
xmax = 1000
ymax = 1000
zmax = 0
elem_type = QUAD4
[]
[GlobalParams]
op_num = 12 # Should match grain_num so we can test with FauxGrainTracker too
var_name_base = gr
[]
[Variables]
[./PolycrystalVariables]
[../]
[]
[UserObjects]
[./voronoi]
type = PolycrystalVoronoi
grain_num = 12 # Number of grains
coloring_algorithm = bt # bt will assign one grain to each op if they are the same
rand_seed = 8675
[../]
[./grain_tracker]
type = GrainTracker
[../]
[]
[ICs]
[./PolycrystalICs]
[./PolycrystalColoringIC]
polycrystal_ic_uo = voronoi
[../]
[../]
[]
[AuxVariables]
[./bnds]
order = FIRST
family = LAGRANGE
[../]
[./unique_grains]
order = CONSTANT
family = MONOMIAL
[../]
[./var_indices]
order = CONSTANT
family = MONOMIAL
[../]
[]
[Kernels]
[./PolycrystalKernel]
[../]
[]
[AuxKernels]
[./BndsCalc]
type = BndsCalcAux
variable = bnds
[../]
[./unique_grains]
type = FeatureFloodCountAux
variable = unique_grains
flood_counter = grain_tracker
field_display = UNIQUE_REGION
[../]
[./var_indices]
type = FeatureFloodCountAux
variable = var_indices
flood_counter = grain_tracker
field_display = VARIABLE_COLORING
[../]
[]
[BCs]
[./Periodic]
[./all]
auto_direction = 'x y'
[../]
[../]
[]
[Materials]
[./CuGrGr]
type = GBEvolution
T = 500 # K
wGB = 100 # nm
GBmob0 = 2.5e-6
Q = 0.23
GBenergy = 0.708
molar_volume = 7.11e-6
[../]
[]
[Postprocessors]
[./DOFs]
type = NumDOFs
[../]
[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = PJFNK
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart'
petsc_options_value = 'hypre boomeramg 31'
l_tol = 1.0e-4
l_max_its = 30
nl_max_its = 20
nl_rel_tol = 1.0e-9
start_time = 0.0
num_steps = 2
dt = 100.0
[]
[Adaptivity]
marker = error_marker
max_h_level = 1
[./Markers]
active = 'error_marker'
[./bnds_marker]
type = ValueThresholdMarker
invert = true
refine = 0.85
coarsen = 0.975
third_state = DO_NOTHING
variable = bnds
[../]
[./error_marker]
type = ErrorFractionMarker
coarsen = 0.1
indicator = bnds_error
refine = 0.7
[../]
[../]
[./Indicators]
[./bnds_error]
type = GradientJumpIndicator
variable = bnds
[../]
[../]
[]
[Outputs]
exodus = true
[]
(modules/phase_field/examples/rigidbodymotion/grain_forcedensity_ext.i)
# example showing grain motion due to applied force density on grains
[GlobalParams]
var_name_base = eta
op_num = 2
[]
[Mesh]
type = GeneratedMesh
dim = 2
nx = 40
ny = 20
nz = 0
xmin = 0.0
xmax = 40.0
ymin = 0.0
ymax = 20.0
zmax = 0
elem_type = QUAD4
[]
[Variables]
[./c]
order = FIRST
family = LAGRANGE
[./InitialCondition]
type = SpecifiedSmoothCircleIC
invalue = 1.0
outvalue = 0.0
int_width = 6.0
x_positions = '20.0 30.0 '
z_positions = '0.0 0.0 '
y_positions = '0.0 25.0 '
radii = '14.0 14.0'
3D_spheres = false
variable = c
[../]
[../]
[./w]
order = FIRST
family = LAGRANGE
[../]
[]
[Functions]
[./load]
type = ConstantFunction
value = -0.01
[../]
[]
[Kernels]
[./c_res]
type = SplitCHParsed
variable = c
f_name = F
kappa_name = kappa_c
w = w
[../]
[./w_res]
type = SplitCHWRes
variable = w
mob_name = M
[../]
[./time]
type = CoupledTimeDerivative
variable = w
v = c
[../]
[./motion]
type = MultiGrainRigidBodyMotion
variable = w
c = c
v = 'eta0 eta1'
grain_tracker_object = grain_center
grain_force = grain_force
grain_volumes = grain_volumes
[../]
[]
[Materials]
[./pfmobility]
type = GenericConstantMaterial
prop_names = 'M kappa_c kappa_eta'
prop_values = '1.0 2.0 0.1'
[../]
[./free_energy]
type = DerivativeParsedMaterial
f_name = F
args = c
constant_names = 'barr_height cv_eq'
constant_expressions = '0.1 1.0e-2'
function = 16*barr_height*(c-cv_eq)^2*(1-cv_eq-c)^2
derivative_order = 2
[../]
[./force_density]
type = ExternalForceDensityMaterial
c = c
etas = 'eta0 eta1'
k = 1.0
force_y = load
[../]
[]
[AuxVariables]
[./eta0]
[../]
[./eta1]
[../]
[./bnds]
[../]
[./df00]
order = CONSTANT
family = MONOMIAL
[../]
[./df01]
order = CONSTANT
family = MONOMIAL
[../]
[./df10]
order = CONSTANT
family = MONOMIAL
[../]
[./df11]
order = CONSTANT
family = MONOMIAL
[../]
[]
[AuxKernels]
[./bnds]
type = BndsCalcAux
variable = bnds
var_name_base = eta
op_num = 2
v = 'eta0 eta1'
[../]
[./df01]
type = MaterialStdVectorRealGradientAux
variable = df01
component = 1
property = force_density_ext
[../]
[./df11]
type = MaterialStdVectorRealGradientAux
variable = df11
index = 1
component = 1
property = force_density_ext
[../]
[./df00]
type = MaterialStdVectorRealGradientAux
variable = df00
property = force_density_ext
[../]
[./df10]
type = MaterialStdVectorRealGradientAux
variable = df10
index = 1
property = force_density_ext
[../]
[]
[ICs]
[./ic_eta0]
int_width = 6.0
x1 = 20.0
y1 = 0.0
radius = 14.0
outvalue = 0.0
variable = eta0
invalue = 1.0
type = SmoothCircleIC
[../]
[./IC_eta1]
int_width = 6.0
x1 = 30.0
y1 = 25.0
radius = 14.0
outvalue = 0.0
variable = eta1
invalue = 1.0
type = SmoothCircleIC
[../]
[]
[VectorPostprocessors]
[./forces]
type = GrainForcesPostprocessor
grain_force = grain_force
[../]
[./grain_volumes]
type = FeatureVolumeVectorPostprocessor
flood_counter = grain_center
execute_on = 'initial timestep_begin'
[../]
[]
[UserObjects]
[./grain_center]
type = GrainTracker
outputs = none
compute_var_to_feature_map = true
execute_on = 'initial timestep_begin'
[../]
[./grain_force]
type = ComputeExternalGrainForceAndTorque
c = c
etas = 'eta0 eta1'
grain_data = grain_center
force_density = force_density_ext
execute_on = 'initial linear nonlinear'
[../]
[]
[Preconditioning]
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = NEWTON
petsc_options_iname = '-pc_type -ksp_gmres_restart -sub_ksp_type -sub_pc_type -pc_asm_overlap'
petsc_options_value = 'asm 31 preonly lu 1'
l_max_its = 30
l_tol = 1.0e-4
nl_rel_tol = 1.0e-10
start_time = 0.0
num_steps = 5
dt = 0.1
[./Adaptivity]
refine_fraction = 0.7
coarsen_fraction = 0.1
max_h_level = 2
initial_adaptivity = 1
[../]
[]
[Outputs]
exodus = true
[]
(modules/phase_field/examples/anisotropic_interfaces/GrandPotentialPlanarGrowth.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 10
ny = 10
xmin = -2
xmax = 2
ymin = -2
ymax = 2
uniform_refine = 2
[]
[GlobalParams]
x1 = -2
y1 = -2
x2 = 2
y2 = -1.5
derivative_order = 2
[]
[Variables]
[./w]
[../]
[./etaa0]
[../]
[./etab0]
[../]
[]
[AuxVariables]
[./bnds]
[../]
#Temperature
[./T]
[../]
[]
[AuxKernels]
[./bnds]
type = BndsCalcAux
variable = bnds
v = 'etaa0 etab0'
[../]
[./T]
type = FunctionAux
function = 95.0+2.0*(y-1.0*t)
variable = T
execute_on = 'initial timestep_begin'
[../]
[]
[ICs]
[./w]
type = BoundingBoxIC
variable = w
# note w = A*(c-cleq), A = 1.0, cleq = 0.0 ,i.e., w = c (in the matrix/liquid phase)
outside = -4.0
inside = 0.0
[../]
[./etaa0]
type = BoundingBoxIC
variable = etaa0
#Solid phase
outside = 0.0
inside = 1.0
[../]
[./etab0]
type = BoundingBoxIC
variable = etab0
#Liquid phase
outside = 1.0
inside = 0.0
[../]
[]
[Kernels]
# Order parameter eta_alpha0
[./ACa0_bulk]
type = ACGrGrMulti
variable = etaa0
v = 'etab0'
gamma_names = 'gab'
[../]
[./ACa0_sw]
type = ACSwitching
variable = etaa0
Fj_names = 'omegaa omegab'
hj_names = 'ha hb'
args = 'etab0 w'
[../]
[./ACa0_int1]
type = ACInterface2DMultiPhase1
variable = etaa0
etas = 'etab0'
kappa_name = kappaa
dkappadgrad_etaa_name = dkappadgrad_etaa
d2kappadgrad_etaa_name = d2kappadgrad_etaa
[../]
[./ACa0_int2]
type = ACInterface2DMultiPhase2
variable = etaa0
kappa_name = kappaa
dkappadgrad_etaa_name = dkappadgrad_etaa
[../]
[./ea0_dot]
type = TimeDerivative
variable = etaa0
[../]
# Order parameter eta_beta0
[./ACb0_bulk]
type = ACGrGrMulti
variable = etab0
v = 'etaa0'
gamma_names = 'gab'
[../]
[./ACb0_sw]
type = ACSwitching
variable = etab0
Fj_names = 'omegaa omegab'
hj_names = 'ha hb'
args = 'etaa0 w'
[../]
[./ACb0_int1]
type = ACInterface2DMultiPhase1
variable = etab0
etas = 'etaa0'
kappa_name = kappab
dkappadgrad_etaa_name = dkappadgrad_etab
d2kappadgrad_etaa_name = d2kappadgrad_etab
[../]
[./ACb0_int2]
type = ACInterface2DMultiPhase2
variable = etab0
kappa_name = kappab
dkappadgrad_etaa_name = dkappadgrad_etab
[../]
[./eb0_dot]
type = TimeDerivative
variable = etab0
[../]
#Chemical potential
[./w_dot]
type = SusceptibilityTimeDerivative
variable = w
f_name = chi
[../]
[./Diffusion]
type = MatDiffusion
variable = w
diffusivity = Dchi
[../]
[./coupled_etaa0dot]
type = CoupledSwitchingTimeDerivative
variable = w
v = etaa0
Fj_names = 'rhoa rhob'
hj_names = 'ha hb'
args = 'etaa0 etab0'
[../]
[./coupled_etab0dot]
type = CoupledSwitchingTimeDerivative
variable = w
v = etab0
Fj_names = 'rhoa rhob'
hj_names = 'ha hb'
args = 'etaa0 etab0'
[../]
[]
[Materials]
[./ha]
type = SwitchingFunctionMultiPhaseMaterial
h_name = ha
all_etas = 'etaa0 etab0'
phase_etas = 'etaa0'
[../]
[./hb]
type = SwitchingFunctionMultiPhaseMaterial
h_name = hb
all_etas = 'etaa0 etab0'
phase_etas = 'etab0'
[../]
[./omegaa]
type = DerivativeParsedMaterial
args = 'w'
f_name = omegaa
material_property_names = 'Vm ka caeq'
function = '-0.5*w^2/Vm^2/ka-w/Vm*caeq'
[../]
[./omegab]
type = DerivativeParsedMaterial
args = 'w T'
f_name = omegab
material_property_names = 'Vm kb cbeq S Tm'
function = '-0.5*w^2/Vm^2/kb-w/Vm*cbeq-S*(T-Tm)'
[../]
[./rhoa]
type = DerivativeParsedMaterial
args = 'w'
f_name = rhoa
material_property_names = 'Vm ka caeq'
function = 'w/Vm^2/ka + caeq/Vm'
[../]
[./rhob]
type = DerivativeParsedMaterial
args = 'w'
f_name = rhob
material_property_names = 'Vm kb cbeq'
function = 'w/Vm^2/kb + cbeq/Vm'
[../]
[./kappaa]
type = InterfaceOrientationMultiphaseMaterial
kappa_name = kappaa
dkappadgrad_etaa_name = dkappadgrad_etaa
d2kappadgrad_etaa_name = d2kappadgrad_etaa
etaa = etaa0
etab = etab0
outputs = exodus
output_properties = 'kappaa'
[../]
[./kappab]
type = InterfaceOrientationMultiphaseMaterial
kappa_name = kappab
dkappadgrad_etaa_name = dkappadgrad_etab
d2kappadgrad_etaa_name = d2kappadgrad_etab
etaa = etab0
etab = etaa0
outputs = exodus
output_properties = 'kappab'
[../]
[./const]
type = GenericConstantMaterial
prop_names = 'L D chi Vm ka caeq kb cbeq gab mu S Tm'
prop_values = '1.0 1.0 0.1 1.0 10.0 0.1 10.0 0.9 4.5 10.0 1.0 100.0'
[../]
[./Mobility]
type = ParsedMaterial
f_name = Dchi
material_property_names = 'D chi'
function = 'D*chi'
[../]
[]
[Preconditioning]
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = PJFNK
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart'
petsc_options_value = 'hypre boomeramg 31'
l_tol = 1.0e-3
l_max_its = 30
nl_max_its = 15
nl_rel_tol = 1.0e-8
nl_abs_tol = 1e-8
end_time = 2.0
[./TimeStepper]
type = IterationAdaptiveDT
dt = 0.0005
cutback_factor = 0.7
growth_factor = 1.2
[../]
[]
[Adaptivity]
initial_steps = 3
max_h_level = 3
initial_marker = err_eta
marker = err_bnds
[./Markers]
[./err_eta]
type = ErrorFractionMarker
coarsen = 0.3
refine = 0.95
indicator = ind_eta
[../]
[./err_bnds]
type = ErrorFractionMarker
coarsen = 0.3
refine = 0.95
indicator = ind_bnds
[../]
[../]
[./Indicators]
[./ind_eta]
type = GradientJumpIndicator
variable = etaa0
[../]
[./ind_bnds]
type = GradientJumpIndicator
variable = bnds
[../]
[../]
[]
[Outputs]
interval = 10
exodus = true
[]
(modules/phase_field/examples/grain_growth/grain_growth_2D_voronoi.i)
# This simulation predicts GB migration of a 2D copper polycrystal with 15 grains
# Mesh adaptivity and time step adaptivity are used
# An AuxVariable is used to calculate the grain boundary locations
# Postprocessors are used to record time step and the number of grains
# We are not using the GrainTracker in this example so the number
# of order paramaters must match the number of grains.
[Mesh]
# Mesh block. Meshes can be read in or automatically generated
type = GeneratedMesh
dim = 2 # Problem dimension
nx = 12 # Number of elements in the x-direction
ny = 12 # Number of elements in the y-direction
nz = 0 # Number of elements in the z-direction
xmin = 0 # minimum x-coordinate of the mesh
xmax = 1000 # maximum x-coordinate of the mesh
ymin = 0 # minimum y-coordinate of the mesh
ymax = 1000 # maximum y-coordinate of the mesh
zmin = 0
zmax = 0
elem_type = QUAD4 # Type of elements used in the mesh
uniform_refine = 3 # Initial uniform refinement of the mesh
parallel_type = replicated # Periodic BCs
[]
[GlobalParams]
# Parameters used by several kernels that are defined globally to simplify input file
op_num = 15 # Number of grains
var_name_base = gr # Base name of grains
[]
[UserObjects]
[./voronoi]
type = PolycrystalVoronoi
grain_num = 15
rand_seed = 42
coloring_algorithm = bt # We must use bt to force the UserObject to assign one grain to each op
[../]
[]
[ICs]
[./PolycrystalICs]
[./PolycrystalColoringIC]
polycrystal_ic_uo = voronoi
[../]
[../]
[]
[Variables]
# Variable block, where all variables in the simulation are declared
[./PolycrystalVariables]
# Custom action that created all of the grain variables
order = FIRST # element type used by each grain variable
family = LAGRANGE
[../]
[]
[AuxVariables]
#active = ''
# Dependent variables
[./bnds]
# Variable used to visualize the grain boundaries in the simulation
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
# Kernel block, where the kernels defining the residual equations are set up.
[./PolycrystalKernel]
# Custom action creating all necessary kernels for grain growth. All input parameters are up in GlobalParams
[../]
[]
[AuxKernels]
#active = ''
# AuxKernel block, defining the equations used to calculate the auxvars
[./bnds_aux]
# AuxKernel that calculates the GB term
type = BndsCalcAux
variable = bnds
execute_on = timestep_end
[../]
[]
[BCs]
# Boundary Condition block
[./Periodic]
[./top_bottom]
auto_direction = 'x y' # Makes problem periodic in the x and y directions
[../]
[../]
[]
[Materials]
[./CuGrGr]
# Material properties
type = GBEvolution # Quantitative material properties for copper grain growth. Dimensions are nm and ns
GBmob0 = 2.5e-6 #Mobility prefactor for Cu from Schonfelder1997
GBenergy = 0.708 #GB energy for Cu from Schonfelder1997
Q = 0.23 #Activation energy for grain growth from Schonfelder 1997
T = 450 # K #Constant temperature of the simulation (for mobility calculation)
wGB = 14 # nm #Width of the diffuse GB
[../]
[]
[Postprocessors]
active = 'dt '
# Scalar postprocessors
[./dt]
# Outputs the current time step
type = TimestepSize
[../]
[]
[Executioner]
type = Transient # Type of executioner, here it is transient with an adaptive time step
scheme = bdf2 # Type of time integration (2nd order backward euler), defaults to 1st order backward euler
#Preconditioned JFNK (default)
solve_type = 'PJFNK'
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart -mat_mffd_type'
petsc_options_value = 'hypre boomeramg 101 ds'
l_max_its = 30 # Max number of linear iterations
l_tol = 1e-4 # Relative tolerance for linear solves
nl_max_its = 40 # Max number of nonlinear iterations
nl_abs_tol = 1e-11 # Relative tolerance for nonlienar solves
nl_rel_tol = 1e-8 # Absolute tolerance for nonlienar solves
start_time = 0.0
end_time = 4000
[./TimeStepper]
type = IterationAdaptiveDT
dt = 25 # Initial time step. In this simulation it changes.
optimal_iterations = 6 #Time step will adapt to maintain this number of nonlinear iterations
[../]
[./Adaptivity]
# Block that turns on mesh adaptivity. Note that mesh will never coarsen beyond initial mesh (before uniform refinement)
initial_adaptivity = 2 # Number of times mesh is adapted to initial condition
refine_fraction = 0.7 # Fraction of high error that will be refined
coarsen_fraction = 0.1 # Fraction of low error that will coarsened
max_h_level = 4 # Max number of refinements used, starting from initial mesh (before uniform refinement)
[../]
[]
[Outputs]
exodus = true
csv = true
[./console]
type = Console
max_rows = 20
[../]
[]
(modules/phase_field/test/tests/rigidbodymotion/grain_motion_fauxGT.i)
# test file for showing reaction forces between particles
[GlobalParams]
var_name_base = eta
op_num = 2
[]
[Mesh]
type = GeneratedMesh
dim = 2
nx = 10
ny = 5
nz = 0
xmax = 50
ymax = 25
zmax = 0
elem_type = QUAD4
uniform_refine = 1
[]
[Variables]
[./c]
order = FIRST
family = LAGRANGE
[../]
[./w]
order = FIRST
family = LAGRANGE
[../]
[./eta0]
[../]
[./eta1]
[../]
[]
[Kernels]
[./c_res]
type = SplitCHParsed
variable = c
f_name = F
kappa_name = kappa_c
args = 'eta0 eta1'
w = w
[../]
[./w_res]
type = SplitCHWRes
variable = w
mob_name = M
[../]
[./time]
type = CoupledTimeDerivative
variable = w
v = c
[../]
[./motion]
type = MultiGrainRigidBodyMotion
variable = w
c = c
v = 'eta0 eta1'
grain_force = grain_force
grain_tracker_object = grain_center
grain_volumes = grain_volumes
[../]
[./eta0_dot]
type = TimeDerivative
variable = eta0
[../]
[./vadv_eta]
type = SingleGrainRigidBodyMotion
variable = eta0
c = c
v = 'eta0 eta1'
grain_force = grain_force
grain_tracker_object = grain_center
grain_volumes = grain_volumes
op_index = 0
[../]
[./acint_eta0]
type = ACInterface
variable = eta0
mob_name = M
#args = c
kappa_name = kappa_eta
[../]
[./acbulk_eta0]
type = AllenCahn
variable = eta0
mob_name = M
f_name = F
args = 'c eta1'
[../]
[./eta1_dot]
type = TimeDerivative
variable = eta1
[../]
[./vadv_eta1]
type = SingleGrainRigidBodyMotion
variable = eta1
c = c
v = 'eta0 eta1'
op_index = 1
grain_force = grain_force
grain_tracker_object = grain_center
grain_volumes = grain_volumes
[../]
[./acint_eta1]
type = ACInterface
variable = eta1
mob_name = M
#args = c
kappa_name = kappa_eta
[../]
[./acbulk_eta1]
type = AllenCahn
variable = eta1
mob_name = M
f_name = F
args = 'c eta0'
[../]
[]
[Materials]
[./pfmobility]
type = GenericConstantMaterial
prop_names = 'M kappa_c kappa_eta'
prop_values = '1.0 0.5 0.5'
[../]
[./free_energy]
type = DerivativeParsedMaterial
f_name = F
args = 'c eta0 eta1'
constant_names = 'barr_height cv_eq'
constant_expressions = '0.1 1.0e-2'
function = 16*barr_height*(c-cv_eq)^2*(1-cv_eq-c)^2+eta0*(1-eta0)*c+eta1*(1-eta1)*c
derivative_order = 2
[../]
[./force_density]
type = ForceDensityMaterial
c = c
etas ='eta0 eta1'
[../]
[]
[AuxVariables]
[./bnds]
[../]
[./df00]
order = CONSTANT
family = MONOMIAL
[../]
[./df01]
order = CONSTANT
family = MONOMIAL
[../]
[./df10]
order = CONSTANT
family = MONOMIAL
[../]
[./df11]
order = CONSTANT
family = MONOMIAL
[../]
[./unique_grains]
order = CONSTANT
family = MONOMIAL
[../]
[./var_indices]
order = CONSTANT
family = MONOMIAL
[../]
[./centroids]
order = CONSTANT
family = MONOMIAL
[../]
[]
[AuxKernels]
[./bnds]
type = BndsCalcAux
variable = bnds
var_name_base = eta
op_num = 2
v = 'eta0 eta1'
[../]
[./df01]
type = MaterialStdVectorRealGradientAux
variable = df01
index = 0
component = 1
property = force_density
[../]
[./df11]
type = MaterialStdVectorRealGradientAux
variable = df11
index = 1
component = 1
property = force_density
[../]
[./df00]
type = MaterialStdVectorRealGradientAux
variable = df00
index = 0
component = 0
property = force_density
[../]
[./df10]
type = MaterialStdVectorRealGradientAux
variable = df10
index = 1
component = 0
property = force_density
[../]
[./unique_grains]
type = FeatureFloodCountAux
variable = unique_grains
flood_counter = grain_center
field_display = UNIQUE_REGION
execute_on = 'initial timestep_end'
[../]
[./var_indices]
type = FeatureFloodCountAux
variable = var_indices
flood_counter = grain_center
field_display = VARIABLE_COLORING
execute_on = 'initial timestep_end'
[../]
[./centroids]
type = FeatureFloodCountAux
variable = centroids
execute_on = 'initial timestep_end'
field_display = CENTROID
flood_counter = grain_center
[../]
[]
[ICs]
[./ic_eta0]
int_width = 1.0
x1 = 20.0
y1 = 0.0
radius = 14.0
outvalue = 0.0
variable = eta0
invalue = 1.0
type = SmoothCircleIC
[../]
[./IC_eta1]
int_width = 1.0
x1 = 30.0
y1 = 25.0
radius = 14.0
outvalue = 0.0
variable = eta1
invalue = 1.0
type = SmoothCircleIC
[../]
[./ic_c]
type = SpecifiedSmoothCircleIC
invalue = 1.0
outvalue = 0.1
int_width = 1.0
x_positions = '20.0 30.0 '
z_positions = '0.0 0.0 '
y_positions = '0.0 25.0 '
radii = '14.0 14.0'
3D_spheres = false
variable = c
block = 0
[../]
[]
[VectorPostprocessors]
[./forces]
type = GrainForcesPostprocessor
grain_force = grain_force
[../]
[./grain_volumes]
type = FeatureVolumeVectorPostprocessor
flood_counter = grain_center
execute_on = 'initial timestep_begin'
[../]
[]
[UserObjects]
[./grain_center]
type = FauxGrainTracker
outputs = none
compute_var_to_feature_map = true
execute_on = 'initial timestep_begin'
variable = 'eta0 eta1'
[../]
[./grain_force]
type = ComputeGrainForceAndTorque
execute_on = 'linear nonlinear'
grain_data = grain_center
force_density = force_density
c = c
etas = 'eta0 eta1'
[../]
[]
[Preconditioning]
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = NEWTON
petsc_options_iname = '-pc_type -ksp_gmres_restart -sub_ksp_type -sub_pc_type -pc_asm_overlap'
petsc_options_value = 'asm 31 preonly lu 1'
l_max_its = 30
l_tol = 1.0e-4
nl_rel_tol = 1.0e-10
start_time = 0.0
num_steps = 1
dt = 0.1
[]
[Outputs]
exodus = true
csv = true
[]
(modules/phase_field/test/tests/grain_growth/temperature_gradient.i)
#
# This test ensures that a flat grain boundary does not move
# under a temperature gradient using the normal grain growth model
#
[Mesh]
type = GeneratedMesh
dim = 2
nx = 40
ny = 20
xmax = 1000
ymax = 500
elem_type = QUAD
[]
[GlobalParams]
op_num = 2
var_name_base = gr
[]
[Functions]
[./TGradient]
type = ParsedFunction
value = '450 + 0.1*x'
[../]
[]
[Variables]
[./PolycrystalVariables]
[../]
[]
[ICs]
[./PolycrystalICs]
[./BicrystalBoundingBoxIC]
x1 = 0.0
x2 = 500.0
y1 = 0.0
y2 = 500.0
[../]
[../]
[]
[AuxVariables]
[./bnds]
[../]
[./T]
[../]
[]
[Kernels]
[./PolycrystalKernel]
variable_mobility = true
args = 'T'
[../]
[]
[AuxKernels]
[./BndsCalc]
type = BndsCalcAux
variable = bnds
execute_on = timestep_end
[../]
[./Tgrad]
type = FunctionAux
variable = T
function = TGradient
[../]
[]
[Materials]
[./Copper]
type = GBEvolution
T = T # K
wGB = 60 # nm
GBmob0 = 2.5e-6 # m^4/(Js) from Schoenfelder 1997
Q = 0.23 # Migration energy in eV
GBenergy = 0.708 # GB energy in J/m^2
[../]
[]
[Postprocessors]
[./gr0_area]
type = ElementIntegralVariablePostprocessor
variable = gr0
execute_on = 'initial TIMESTEP_END'
[../]
[]
[Preconditioning]
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = NEWTON
l_max_its = 30
l_tol = 1.0e-4
nl_max_its = 20
nl_rel_tol = 1.0e-9
start_time = 0.0
num_steps = 10
dt = 100.0
[]
[Outputs]
exodus = true
[]
(modules/phase_field/test/tests/GBAnisotropy/test3.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 40
ny = 40
nz = 0
xmin = 0
xmax = 1000
ymin = 0
ymax = 1000
zmin = 0
zmax = 0
elem_type = QUAD4
[]
[GlobalParams]
op_num = 2
var_name_base = gr
wGB = 100
length_scale = 1.0e-9
time_scale = 1.0e-9
[]
[Variables]
[./PolycrystalVariables]
order = FIRST
family = LAGRANGE
[../]
[]
[ICs]
[./PolycrystalICs]
[./BicrystalCircleGrainIC]
radius = 333.33
x = 500
y = 500
[../]
[../]
[]
[AuxVariables]
[./bnds]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
[./PolycrystalKernel]
[../]
[]
[AuxKernels]
[./bnds_aux]
type = BndsCalcAux
variable = bnds
execute_on = timestep_end
[../]
[]
[BCs]
[./Periodic]
[./top_bottom]
auto_direction = 'x y'
[../]
[../]
[]
[Materials]
[./CuGrGranisotropic]
type = GBAnisotropy
T = 600 # K
# molar_volume_value = 7.11e-6 #Units:m^3/mol
Anisotropic_GB_file_name = anisotropy.txt
inclination_anisotropy = true
delta_sigma = 0.1
delta_mob = 0.0
[../]
[]
[Postprocessors]
[./dt]
# Outputs the current time step
type = TimestepSize
[../]
[./gr1_area]
type = ElementIntegralVariablePostprocessor
variable = gr1
[../]
[]
[Executioner]
type = Transient
scheme = bdf2
#Preconditioned JFNK (default)
solve_type = 'PJFNK'
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart'
petsc_options_value = 'hypre boomeramg 31'
l_max_its = 30
l_tol = 1e-4
nl_max_its = 40
nl_rel_tol = 1e-9
num_steps = 1
dt = 150.0
[]
[Outputs]
execute_on = 'timestep_end'
exodus = true
csv = true
[]
(modules/phase_field/examples/anisotropic_interfaces/GrandPotentialSolidification.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 28
ny = 28
xmin = -7
xmax = 7
ymin = -7
ymax = 7
uniform_refine = 2
[]
[GlobalParams]
radius = 0.2
int_width = 0.1
x1 = 0.0
y1 = 0.0
derivative_order = 2
[]
[Variables]
[./w]
[../]
[./etaa0]
[../]
[./etab0]
[../]
[./T]
[../]
[]
[AuxVariables]
[./bnds]
[../]
[]
[AuxKernels]
[./bnds]
type = BndsCalcAux
variable = bnds
v = 'etaa0 etab0'
[../]
[]
[ICs]
[./w]
type = SmoothCircleIC
variable = w
# note w = A*(c-cleq), A = 1.0, cleq = 0.0 ,i.e., w = c (in the matrix/liquid phase)
outvalue = -4.0
invalue = 0.0
[../]
[./etaa0]
type = SmoothCircleIC
variable = etaa0
#Solid phase
outvalue = 0.0
invalue = 1.0
[../]
[./etab0]
type = SmoothCircleIC
variable = etab0
#Liquid phase
outvalue = 1.0
invalue = 0.0
[../]
[]
[Kernels]
# Order parameter eta_alpha0
[./ACa0_bulk]
type = ACGrGrMulti
variable = etaa0
v = 'etab0'
gamma_names = 'gab'
[../]
[./ACa0_sw]
type = ACSwitching
variable = etaa0
Fj_names = 'omegaa omegab'
hj_names = 'ha hb'
args = 'etab0 w T'
[../]
[./ACa0_int1]
type = ACInterface2DMultiPhase1
variable = etaa0
etas = 'etab0'
kappa_name = kappaa
dkappadgrad_etaa_name = dkappadgrad_etaa
d2kappadgrad_etaa_name = d2kappadgrad_etaa
[../]
[./ACa0_int2]
type = ACInterface2DMultiPhase2
variable = etaa0
kappa_name = kappaa
dkappadgrad_etaa_name = dkappadgrad_etaa
[../]
[./ea0_dot]
type = TimeDerivative
variable = etaa0
[../]
# Order parameter eta_beta0
[./ACb0_bulk]
type = ACGrGrMulti
variable = etab0
v = 'etaa0'
gamma_names = 'gab'
[../]
[./ACb0_sw]
type = ACSwitching
variable = etab0
Fj_names = 'omegaa omegab'
hj_names = 'ha hb'
args = 'etaa0 w T'
[../]
[./ACb0_int1]
type = ACInterface2DMultiPhase1
variable = etab0
etas = 'etaa0'
kappa_name = kappab
dkappadgrad_etaa_name = dkappadgrad_etab
d2kappadgrad_etaa_name = d2kappadgrad_etab
[../]
[./ACb0_int2]
type = ACInterface2DMultiPhase2
variable = etab0
kappa_name = kappab
dkappadgrad_etaa_name = dkappadgrad_etab
[../]
[./eb0_dot]
type = TimeDerivative
variable = etab0
[../]
#Chemical potential
[./w_dot]
type = SusceptibilityTimeDerivative
variable = w
f_name = chi
[../]
[./Diffusion]
type = MatDiffusion
variable = w
diffusivity = Dchi
[../]
[./coupled_etaa0dot]
type = CoupledSwitchingTimeDerivative
variable = w
v = etaa0
Fj_names = 'rhoa rhob'
hj_names = 'ha hb'
args = 'etaa0 etab0'
[../]
[./coupled_etab0dot]
type = CoupledSwitchingTimeDerivative
variable = w
v = etab0
Fj_names = 'rhoa rhob'
hj_names = 'ha hb'
args = 'etaa0 etab0'
[../]
[./T_dot]
type = TimeDerivative
variable = T
[../]
[./CoefDiffusion]
type = Diffusion
variable = T
[../]
[./etaa0_dot_T]
type = CoefCoupledTimeDerivative
variable = T
v = etaa0
coef = -5.0
[../]
[]
[Materials]
[./ha]
type = SwitchingFunctionMultiPhaseMaterial
h_name = ha
all_etas = 'etaa0 etab0'
phase_etas = 'etaa0'
[../]
[./hb]
type = SwitchingFunctionMultiPhaseMaterial
h_name = hb
all_etas = 'etaa0 etab0'
phase_etas = 'etab0'
[../]
[./omegaa]
type = DerivativeParsedMaterial
args = 'w'
f_name = omegaa
material_property_names = 'Vm ka caeq'
function = '-0.5*w^2/Vm^2/ka-w/Vm*caeq'
[../]
[./omegab]
type = DerivativeParsedMaterial
args = 'w T'
f_name = omegab
material_property_names = 'Vm kb cbeq S Tm'
function = '-0.5*w^2/Vm^2/kb-w/Vm*cbeq-S*(T-Tm)'
[../]
[./rhoa]
type = DerivativeParsedMaterial
args = 'w'
f_name = rhoa
material_property_names = 'Vm ka caeq'
function = 'w/Vm^2/ka + caeq/Vm'
[../]
[./rhob]
type = DerivativeParsedMaterial
args = 'w'
f_name = rhob
material_property_names = 'Vm kb cbeq'
function = 'w/Vm^2/kb + cbeq/Vm'
[../]
[./kappaa]
type = InterfaceOrientationMultiphaseMaterial
kappa_name = kappaa
dkappadgrad_etaa_name = dkappadgrad_etaa
d2kappadgrad_etaa_name = d2kappadgrad_etaa
etaa = etaa0
etab = etab0
anisotropy_strength = 0.05
kappa_bar = 0.05
outputs = exodus
output_properties = 'kappaa'
[../]
[./kappab]
type = InterfaceOrientationMultiphaseMaterial
kappa_name = kappab
dkappadgrad_etaa_name = dkappadgrad_etab
d2kappadgrad_etaa_name = d2kappadgrad_etab
etaa = etab0
etab = etaa0
anisotropy_strength = 0.05
kappa_bar = 0.05
outputs = exodus
output_properties = 'kappab'
[../]
[./const]
type = GenericConstantMaterial
prop_names = 'L D chi Vm ka caeq kb cbeq gab mu S Tm'
prop_values = '33.33 1.0 0.1 1.0 10.0 0.1 10.0 0.9 4.5 10.0 1.0 5.0'
[../]
[./Mobility]
type = ParsedMaterial
f_name = Dchi
material_property_names = 'D chi'
function = 'D*chi'
[../]
[]
[Preconditioning]
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = PJFNK
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart'
petsc_options_value = 'hypre boomeramg 31'
l_tol = 1.0e-3
l_max_its = 30
nl_max_its = 15
nl_rel_tol = 1.0e-8
nl_abs_tol = 1e-10
end_time = 2.0
dtmax = 0.05
[./TimeStepper]
type = IterationAdaptiveDT
dt = 0.0005
cutback_factor = 0.7
growth_factor = 1.2
[../]
[]
[Adaptivity]
initial_steps = 5
max_h_level = 3
initial_marker = err_eta
marker = err_bnds
[./Markers]
[./err_eta]
type = ErrorFractionMarker
coarsen = 0.3
refine = 0.95
indicator = ind_eta
[../]
[./err_bnds]
type = ErrorFractionMarker
coarsen = 0.3
refine = 0.95
indicator = ind_bnds
[../]
[../]
[./Indicators]
[./ind_eta]
type = GradientJumpIndicator
variable = etaa0
[../]
[./ind_bnds]
type = GradientJumpIndicator
variable = bnds
[../]
[../]
[]
[Outputs]
interval = 5
exodus = true
[]
(modules/phase_field/test/tests/grain_tracker_test/grain_tracker_nodal.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 25
ny = 25
nz = 0
xmax = 1000
ymax = 1000
zmax = 0
elem_type = QUAD4
[]
[GlobalParams]
op_num = 10
var_name_base = gr
[]
[Variables]
[./PolycrystalVariables]
[../]
[]
[UserObjects]
[./voronoi]
type = PolycrystalVoronoi
grain_num = 10 # Number of grains
coloring_algorithm = bt # bt will assign one grain to each op if they are the same
rand_seed = 1
[../]
[./grain_tracker]
type = GrainTracker
threshold = 0.5
connecting_threshold = 0.2
# Note: This is here for demonstration purposes
# use elemental for most simulations
flood_entity_type = NODAL
[../]
[]
[ICs]
[./PolycrystalICs]
[./PolycrystalColoringIC]
polycrystal_ic_uo = voronoi
[../]
[../]
[]
[AuxVariables]
[./bnds]
order = FIRST
family = LAGRANGE
[../]
[./unique_grains]
order = FIRST
family = LAGRANGE
[../]
[./var_indices]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
[./PolycrystalKernel]
[../]
[]
[AuxKernels]
[./BndsCalc]
type = BndsCalcAux
variable = bnds
[../]
[./unique_grains]
type = FeatureFloodCountAux
variable = unique_grains
flood_counter = grain_tracker
field_display = UNIQUE_REGION
[../]
[./var_indices]
type = FeatureFloodCountAux
variable = var_indices
flood_counter = grain_tracker
field_display = VARIABLE_COLORING
[../]
[]
[BCs]
[]
[Materials]
[./CuGrGr]
type = GBEvolution
T = 500 # K
wGB = 100 # nm
GBmob0 = 2.5e-6
Q = 0.23
GBenergy = 0.708
molar_volume = 7.11e-6
[../]
[]
[Postprocessors]
[./DOFs]
type = NumDOFs
execute_on = 'initial timestep_end'
[../]
[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = PJFNK
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart'
petsc_options_value = 'hypre boomeramg 31'
l_tol = 1.0e-4
l_max_its = 30
nl_max_its = 20
nl_rel_tol = 1.0e-9
start_time = 0.0
num_steps = 2
dt = 100.0
[]
[Outputs]
exodus = true
[]
(modules/phase_field/test/tests/grain_growth/thumb.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 10
ny = 10
nz = 0
xmin = 0
xmax = 1000
ymin = 0
ymax = 1000
zmin = 0
zmax = 0
elem_type = QUAD4
uniform_refine = 2
[]
[GlobalParams]
op_num = 2
var_name_base = gr
v = 'gr0 gr1'
[]
[Variables]
[./gr0]
order = FIRST
family = LAGRANGE
[./InitialCondition]
type = ThumbIC
xcoord = 500.0
height = 600.0
width = 400.0
invalue = 0.0
outvalue = 1.0
[../]
[../]
[./gr1]
order = FIRST
family = LAGRANGE
[./InitialCondition]
type = ThumbIC
xcoord = 500.0
height = 600.0
width = 400.0
invalue = 1.0
outvalue = 0.0
[../]
[../]
[]
[AuxVariables]
[./bnds]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
[./PolycrystalKernel]
[../]
[]
[AuxKernels]
[./BndsCalc]
type = BndsCalcAux
variable = bnds
[../]
[]
[BCs]
active = ' '
[./Periodic]
[./left_right]
primary = 0
secondary = 2
translation = '0 1000 0'
[../]
[./top_bottom]
primary = 1
secondary = 3
translation = '-1000 0 0'
[../]
[../]
[]
[Materials]
[./Copper]
type = GBEvolution
T = 500 # K
wGB = 60 # nm
GBmob0 = 2.5e-6 #m^4/(Js) from Schoenfelder 1997
Q = 0.23 #Migration energy in eV
GBenergy = 0.708 #GB energy in J/m^2
[../]
[]
[Postprocessors]
[./gr_area]
type = ElementIntegralVariablePostprocessor
variable = gr1
[../]
[]
[Preconditioning]
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
scheme = 'bdf2'
solve_type = 'NEWTON'
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart'
petsc_options_value = 'hypre boomeramg 31'
l_tol = 1.0e-4
l_max_its = 30
nl_max_its = 20
nl_rel_tol = 1.0e-9
start_time = 0.0
num_steps = 10
dt = 80.0
[./Adaptivity]
initial_adaptivity = 2
refine_fraction = 0.8
coarsen_fraction = 0.05
max_h_level = 2
[../]
[]
[Outputs]
execute_on = 'timestep_end'
csv = true
exodus = true
[]
(modules/phase_field/test/tests/grain_tracker_test/split_grain.i)
[Mesh]
[ebsd_mesh]
type = EBSDMeshGenerator
filename = EBSD_split_grain.txt
[]
[]
[GlobalParams]
op_num = 4
var_name_base = gr
[]
[UserObjects]
[ebsd_reader]
type = EBSDReader
[]
[ebsd]
type = PolycrystalEBSD
coloring_algorithm = bt
ebsd_reader = ebsd_reader
enable_var_coloring = true
output_adjacency_matrix = true
[]
[grain_tracker]
type = GrainTracker
flood_entity_type = ELEMENTAL
compute_halo_maps = true # For displaying HALO fields
polycrystal_ic_uo = ebsd
[]
[]
[ICs]
[PolycrystalICs]
[PolycrystalColoringIC]
polycrystal_ic_uo = ebsd
[]
[]
[]
[Variables]
[PolycrystalVariables]
[]
[]
[AuxVariables]
[bnds]
[]
[unique_grains]
order = CONSTANT
family = MONOMIAL
[]
[ghost_elements]
order = CONSTANT
family = MONOMIAL
[]
[halos]
order = CONSTANT
family = MONOMIAL
[]
[var_indices]
order = CONSTANT
family = MONOMIAL
[]
[ebsd_grains]
family = MONOMIAL
order = CONSTANT
[]
[]
[Kernels]
[PolycrystalKernel]
[]
[]
[AuxKernels]
[BndsCalc]
type = BndsCalcAux
variable = bnds
execute_on = 'initial timestep_end'
[]
[ghost_elements]
type = FeatureFloodCountAux
variable = ghost_elements
field_display = GHOSTED_ENTITIES
execute_on = 'initial timestep_end'
flood_counter = grain_tracker
[]
[halos]
type = FeatureFloodCountAux
variable = halos
field_display = HALOS
execute_on = 'initial timestep_end'
flood_counter = grain_tracker
[]
[var_indices]
type = FeatureFloodCountAux
variable = var_indices
execute_on = 'initial timestep_end'
flood_counter = grain_tracker
field_display = VARIABLE_COLORING
[]
[unique_grains]
type = FeatureFloodCountAux
variable = unique_grains
execute_on = 'initial timestep_end'
flood_counter = grain_tracker
field_display = UNIQUE_REGION
[]
[grain_aux]
type = EBSDReaderPointDataAux
variable = ebsd_grains
ebsd_reader = ebsd_reader
data_name = 'feature_id'
execute_on = 'initial timestep_end'
[]
[]
[Modules]
[PhaseField]
[EulerAngles2RGB]
crystal_structure = cubic
euler_angle_provider = ebsd_reader
grain_tracker = grain_tracker
[]
[]
[]
[Materials]
[Copper]
# T = 500 # K
type = GBEvolution
T = 500
wGB = 0.6 # um
GBmob0 = 2.5e-6 # m^4/(Js) from Schoenfelder 1997
Q = 0.23 # Migration energy in eV
GBenergy = 0.708 # GB energy in J/m^2
molar_volume = 7.11e-6 # Molar volume in m^3/mol
length_scale = 1.0e-6
time_scale = 1.0e-6
[]
[]
[Postprocessors]
[n_elements]
type = NumElems
execute_on = 'initial timestep_end'
[]
[n_nodes]
type = NumNodes
execute_on = 'initial timestep_end'
[]
[DOFs]
type = NumDOFs
[]
[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = PJFNK
petsc_options_iname = '-pc_type -pc_hypre_type -pc_hypre_boomeramg_strong_threshold'
petsc_options_value = 'hypre boomeramg 0.7'
l_tol = 1.0e-4
l_max_its = 20
nl_max_its = 20
nl_rel_tol = 1.0e-8
start_time = 0.0
num_steps = 2
[TimeStepper]
type = IterationAdaptiveDT
cutback_factor = 0.9
dt = 10.0
growth_factor = 1.1
optimal_iterations = 7
[]
[]
[Outputs]
exodus = true
csv = true
perf_graph = true
[]
(modules/phase_field/test/tests/grain_tracker_test/grain_tracker_advanced_op.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 40
ny = 40
nz = 0
xmax = 1000
ymax = 1000
zmax = 0
elem_type = QUAD4
parallel_type = replicated # Periodic BCs
[]
[GlobalParams]
op_num = 8
var_name_base = gr
order = CONSTANT
family = MONOMIAL
[]
[Variables]
[./PolycrystalVariables]
order = FIRST
family = LAGRANGE
[../]
[]
[UserObjects]
[./voronoi]
type = PolycrystalVoronoi
rand_seed = 1
grain_num = 35
coloring_algorithm = bt
output_adjacency_matrix = true
[../]
[./grain_tracker]
type = GrainTracker
threshold = 0.5
connecting_threshold = 0.5
compute_halo_maps = true # For displaying HALO fields
remap_grains = false
[../]
[]
[ICs]
[./PolycrystalICs]
[./PolycrystalColoringIC]
polycrystal_ic_uo = voronoi
[../]
[../]
[]
[AuxVariables]
[./bnds]
order = FIRST
family = LAGRANGE
[../]
[./unique_grains]
[../]
[./var_indices]
[../]
[./halos]
[../]
[./halo0]
[../]
[./halo1]
[../]
[./halo2]
[../]
[./halo3]
[../]
[./halo4]
[../]
[./halo5]
[../]
[./halo6]
[../]
[./halo7]
[../]
[]
[Kernels]
[./PolycrystalKernel]
[../]
[]
[AuxKernels]
[./BndsCalc]
type = BndsCalcAux
variable = bnds
execute_on = 'initial timestep_end'
[../]
[./unique_grains]
type = FeatureFloodCountAux
variable = unique_grains
flood_counter = grain_tracker
field_display = UNIQUE_REGION
[../]
[./var_indices]
type = FeatureFloodCountAux
variable = var_indices
flood_counter = grain_tracker
field_display = VARIABLE_COLORING
[../]
[./halo0]
type = FeatureFloodCountAux
variable = halo0
map_index = 0
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo1]
type = FeatureFloodCountAux
variable = halo1
map_index = 1
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo2]
type = FeatureFloodCountAux
variable = halo2
map_index = 2
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo3]
type = FeatureFloodCountAux
variable = halo3
map_index = 3
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo4]
type = FeatureFloodCountAux
variable = halo4
map_index = 4
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo5]
type = FeatureFloodCountAux
variable = halo5
map_index = 5
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo6]
type = FeatureFloodCountAux
variable = halo6
map_index = 6
field_display = HALOS
flood_counter = grain_tracker
[../]
[./halo7]
type = FeatureFloodCountAux
variable = halo7
map_index = 7
field_display = HALOS
flood_counter = grain_tracker
[../]
[]
[BCs]
[./Periodic]
[./all]
auto_direction = 'x y'
[../]
[../]
[]
[Materials]
[./CuGrGr]
type = GBEvolution
T = 500 # K
wGB = 100 # nm
GBmob0 = 2.5e-6
Q = 0.23
GBenergy = 0.708
molar_volume = 7.11e-6
[../]
[]
[Postprocessors]
[./DOFs]
type = NumDOFs
execute_on = 'initial timestep_end'
[../]
[]
[Executioner]
type = Transient
num_steps = 0
dt = 100.0
[]
[Outputs]
csv = true
perf_graph = true
[]
[Problem]
solve = false
[]
(modules/phase_field/test/tests/GBAnisotropy/testwidth1.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 30
ny = 2
nz = 0
xmin = -500
xmax = 1000
ymin = 0
ymax = 100
zmin = 0
zmax = 0
elem_type = QUAD4
[]
[GlobalParams]
op_num = 3
var_name_base = gr
length_scale = 1.0e-9
time_scale = 1.0e-9
[]
[Variables]
[./PolycrystalVariables]
[../]
[]
[Functions]
[./ic_func_eta1]
type = ParsedFunction
value = '0.5*(1.0-tanh((x)*sqrt(m/kappa/2.0)))'
vars = 'm kappa'
vals = '0.26514 331.414'
[../]
[./ic_func_eta2]
type = ParsedFunction
value = '0.5*(1.0+tanh((x)*sqrt(m/kappa/2.0)))*0.5*(1.0-tanh((x-500)*sqrt(m/kappa/2.0)))'
vars = 'm kappa'
vals = '0.26514 331.414'
[../]
[./ic_func_eta3]
type = ParsedFunction
value = '0.5*(1.0+tanh((x-500)*sqrt(m/kappa/2.0)))'
vars = 'm kappa'
vals = '0.26514 331.414'
[../]
[]
[ICs]
[./eta1_ic]
variable = gr0
type = FunctionIC
function = ic_func_eta1
[../]
[./eta2_ic]
variable = gr1
type = FunctionIC
function = ic_func_eta2
[../]
[./eta3_ic]
variable = gr2
type = FunctionIC
function = ic_func_eta3
[../]
[]
[AuxVariables]
[./bnds]
order = FIRST
family = LAGRANGE
[../]
[./unique_grains]
order = FIRST
family = LAGRANGE
[../]
[./var_indices]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
[./PolycrystalKernel]
[../]
[]
[AuxKernels]
[./bnds_aux]
type = BndsCalcAux
variable = bnds
execute_on = timestep_end
[../]
[]
[Materials]
[./CuGrGranisotropic]
type = GBWidthAnisotropy
kappa = 331.414
mu = 0.26514
T = 600 # K
# molar_volume_value = 7.11e-6 #Units:m^3/mol
Anisotropic_GB_file_name = anisotropy_energy.txt
inclination_anisotropy = false # true
[../]
[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = 'PJFNK'
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart'
petsc_options_value = 'hypre boomeramg 31'
l_max_its = 30
l_tol = 1e-4
nl_max_its = 40
nl_rel_tol = 1e-10
nl_abs_tol = 1e-11
num_steps = 2
dt = 10
[]
[Outputs]
execute_on = 'timestep_end'
exodus = true
[]
(modules/phase_field/examples/grain_growth/grain_growth_2D_graintracker.i)
# This simulation predicts GB migration of a 2D copper polycrystal with 100 grains represented with 18 order parameters
# Mesh adaptivity and time step adaptivity are used
# An AuxVariable is used to calculate the grain boundary locations
# Postprocessors are used to record time step and the number of grains
[Mesh]
# Mesh block. Meshes can be read in or automatically generated
type = GeneratedMesh
dim = 2 # Problem dimension
nx = 11 # Number of elements in the x-direction
ny = 11 # Number of elements in the y-direction
xmin = 0 # minimum x-coordinate of the mesh
xmax = 1000 # maximum x-coordinate of the mesh
ymin = 0 # minimum y-coordinate of the mesh
ymax = 1000 # maximum y-coordinate of the mesh
elem_type = QUAD4 # Type of elements used in the mesh
uniform_refine = 3 # Initial uniform refinement of the mesh
parallel_type = replicated # Periodic BCs
[]
[GlobalParams]
# Parameters used by several kernels that are defined globally to simplify input file
op_num = 8 # Number of order parameters used
var_name_base = gr # Base name of grains
[]
[Variables]
# Variable block, where all variables in the simulation are declared
[./PolycrystalVariables]
[../]
[]
[UserObjects]
[./voronoi]
type = PolycrystalVoronoi
grain_num = 100 # Number of grains
rand_seed = 10
[../]
[./grain_tracker]
type = GrainTracker
threshold = 0.2
connecting_threshold = 0.08
compute_halo_maps = true # Only necessary for displaying HALOS
[../]
[]
[ICs]
[./PolycrystalICs]
[./PolycrystalColoringIC]
polycrystal_ic_uo = voronoi
[../]
[../]
[]
[AuxVariables]
# Dependent variables
[./bnds]
# Variable used to visualize the grain boundaries in the simulation
[../]
[./unique_grains]
order = CONSTANT
family = MONOMIAL
[../]
[./var_indices]
order = CONSTANT
family = MONOMIAL
[../]
[./ghost_regions]
order = CONSTANT
family = MONOMIAL
[../]
[./halos]
order = CONSTANT
family = MONOMIAL
[../]
[]
[Kernels]
# Kernel block, where the kernels defining the residual equations are set up.
[./PolycrystalKernel]
# Custom action creating all necessary kernels for grain growth. All input parameters are up in GlobalParams
[../]
[]
[AuxKernels]
# AuxKernel block, defining the equations used to calculate the auxvars
[./bnds_aux]
# AuxKernel that calculates the GB term
type = BndsCalcAux
variable = bnds
execute_on = 'initial timestep_end'
[../]
[./unique_grains]
type = FeatureFloodCountAux
variable = unique_grains
flood_counter = grain_tracker
field_display = UNIQUE_REGION
execute_on = 'initial timestep_end'
[../]
[./var_indices]
type = FeatureFloodCountAux
variable = var_indices
flood_counter = grain_tracker
field_display = VARIABLE_COLORING
execute_on = 'initial timestep_end'
[../]
[./ghosted_entities]
type = FeatureFloodCountAux
variable = ghost_regions
flood_counter = grain_tracker
field_display = GHOSTED_ENTITIES
execute_on = 'initial timestep_end'
[../]
[./halos]
type = FeatureFloodCountAux
variable = halos
flood_counter = grain_tracker
field_display = HALOS
execute_on = 'initial timestep_end'
[../]
[]
[BCs]
# Boundary Condition block
[./Periodic]
[./top_bottom]
auto_direction = 'x y' # Makes problem periodic in the x and y directions
[../]
[../]
[]
[Materials]
[./CuGrGr]
# Material properties
type = GBEvolution
T = 450 # Constant temperature of the simulation (for mobility calculation)
wGB = 14 # Width of the diffuse GB
GBmob0 = 2.5e-6 #m^4(Js) for copper from Schoenfelder1997
Q = 0.23 #eV for copper from Schoenfelder1997
GBenergy = 0.708 #J/m^2 from Schoenfelder1997
[../]
[]
[Postprocessors]
# Scalar postprocessors
[./dt]
# Outputs the current time step
type = TimestepSize
[../]
[]
[Executioner]
type = Transient # Type of executioner, here it is transient with an adaptive time step
scheme = bdf2 # Type of time integration (2nd order backward euler), defaults to 1st order backward euler
#Preconditioned JFNK (default)
solve_type = 'PJFNK'
# Uses newton iteration to solve the problem.
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart -mat_mffd_type'
petsc_options_value = 'hypre boomeramg 101 ds'
l_max_its = 30 # Max number of linear iterations
l_tol = 1e-4 # Relative tolerance for linear solves
nl_max_its = 40 # Max number of nonlinear iterations
nl_rel_tol = 1e-10 # Absolute tolerance for nonlienar solves
start_time = 0.0
end_time = 4000
[./TimeStepper]
type = IterationAdaptiveDT
dt = 25 # Initial time step. In this simulation it changes.
optimal_iterations = 6 # Time step will adapt to maintain this number of nonlinear iterations
[../]
[./Adaptivity]
# Block that turns on mesh adaptivity. Note that mesh will never coarsen beyond initial mesh (before uniform refinement)
initial_adaptivity = 2 # Number of times mesh is adapted to initial condition
refine_fraction = 0.7 # Fraction of high error that will be refined
coarsen_fraction = 0.1 # Fraction of low error that will coarsened
max_h_level = 4 # Max number of refinements used, starting from initial mesh (before uniform refinement)
[../]
[]
[Outputs]
exodus = true # Exodus file will be outputted
csv = true
[./console]
type = Console
max_rows = 20 # Will print the 20 most recent postprocessor values to the screen
[../]
[]
(modules/phase_field/test/tests/initial_conditions/TricrystalTripleJunctionIC.i)
# This simulation tests the TricrystalTripleJunctionIC
[Mesh]
# Mesh block. Meshes can be read in or automatically generated.
type = GeneratedMesh
dim = 2 # Problem dimension
nx = 11 # Number of elements in the x direction
ny = 11 # Number of elements in the y direction
xmax = 1001 # Maximum x-coordinate of mesh
xmin = 0 # Minimum x-coordinate of mesh
ymax = 1001 # Maximum y-coordinate of mesh
ymin = 0 # Minimum y-coordinate of mesh
elem_type = QUAD4 # Type of elements used in the mesh
uniform_refine = 3
[]
[GlobalParams]
# Parameters used by several kernels that are defined globally to simplify input file
op_num = 3 # Number of order parameters used
var_name_base = gr # base name of grains
v = 'gr0 gr1 gr2' # Names of the grains
theta1 = 135 # Angle the first grain makes at the triple junction
theta2 = 100 # Angle the second grain makes at the triple junction
length_scale = 1.0e-9 # Length scale in nm
time_scale = 1.0e-9 # Time scale in ns
[]
[Variables]
[./gr0]
order = FIRST
family = LAGRANGE
[./InitialCondition]
type = TricrystalTripleJunctionIC
op_index = 1
[../]
[../]
[./gr1]
order = FIRST
family = LAGRANGE
[./InitialCondition]
type = TricrystalTripleJunctionIC
op_index = 2
[../]
[../]
[./gr2]
order = FIRST
family = LAGRANGE
[./InitialCondition]
type = TricrystalTripleJunctionIC
op_index = 3
[../]
[../]
[]
[AuxVariables]
[./bnds]
# Variable used to visualize the grain boundaries in the simulation
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
# Kernels block where the kernels defining the residual equations are set up
[./PolycrystalKernel]
# Custom action creating all necessary kernels for grain growth. All input parameters are up in GlobalParams
[../]
[]
[AuxKernels]
# AuxKernel block, defining the equations used to calculate the auxvars
[./bnds_aux]
# AuxKernel that calculates the GB term
type = BndsCalcAux
variable = bnds
execute_on = 'initial timestep_end'
[../]
[]
[Materials]
[./material]
# Material properties
type = GBEvolution
T = 450 # Constant temperature of the simulation (for mobility calculation)
wGB = 14 # Width of the diffuse GB
GBmob0 = 2.5e-6 #m^4(Js) for copper from Schoenfelder1997
Q = 0.23 #eV for copper from Schoenfelder1997
GBenergy = 0.708 #J/m^2 from Schoenfelder1997
[../]
[]
[Postprocessors]
# Scalar postprocessors
[./grain_tracker]
type = FauxGrainTracker
[../]
[]
[Executioner]
type = Transient
num_steps = 1
[]
[Outputs]
exodus = true # Outputs to the Exodus file format
execute_on = 'final'
[]
[Problem]
solve = false
[]
(modules/phase_field/examples/anisotropic_interfaces/GrandPotentialTwophaseAnisotropy.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 10
ny = 10
xmin = -4
xmax = 4
ymin = -4
ymax = 4
uniform_refine = 2
[]
[GlobalParams]
radius = 0.5
int_width = 0.3
x1 = 0
y1 = 0
derivative_order = 2
[]
[Variables]
[./w]
[../]
[./etaa0]
[../]
[./etab0]
[../]
[]
[AuxVariables]
[./bnds]
[../]
[]
[AuxKernels]
[./bnds]
type = BndsCalcAux
variable = bnds
v = 'etaa0 etab0'
[../]
[]
[ICs]
[./w]
type = SmoothCircleIC
variable = w
# note w = A*(c-cleq), A = 1.0, cleq = 0.0 ,i.e., w = c (in the matrix/liquid phase)
outvalue = -4.0
invalue = 0.0
[../]
[./etaa0]
type = SmoothCircleIC
variable = etaa0
#Solid phase
outvalue = 0.0
invalue = 1.0
[../]
[./etab0]
type = SmoothCircleIC
variable = etab0
#Liquid phase
outvalue = 1.0
invalue = 0.0
[../]
[]
[BCs]
[./Periodic]
[./w]
variable = w
auto_direction = 'x y'
[../]
[./etaa0]
variable = etaa0
auto_direction = 'x y'
[../]
[./etab0]
variable = etab0
auto_direction = 'x y'
[../]
[../]
[]
[Kernels]
# Order parameter eta_alpha0
[./ACa0_bulk]
type = ACGrGrMulti
variable = etaa0
v = 'etab0'
gamma_names = 'gab'
[../]
[./ACa0_sw]
type = ACSwitching
variable = etaa0
Fj_names = 'omegaa omegab'
hj_names = 'ha hb'
args = 'etab0 w'
[../]
[./ACa0_int1]
type = ACInterface2DMultiPhase1
variable = etaa0
etas = 'etab0'
kappa_name = kappaa
dkappadgrad_etaa_name = dkappadgrad_etaa
d2kappadgrad_etaa_name = d2kappadgrad_etaa
[../]
[./ACa0_int2]
type = ACInterface2DMultiPhase2
variable = etaa0
kappa_name = kappaa
dkappadgrad_etaa_name = dkappadgrad_etaa
[../]
[./ea0_dot]
type = TimeDerivative
variable = etaa0
[../]
# Order parameter eta_beta0
[./ACb0_bulk]
type = ACGrGrMulti
variable = etab0
v = 'etaa0'
gamma_names = 'gab'
[../]
[./ACb0_sw]
type = ACSwitching
variable = etab0
Fj_names = 'omegaa omegab'
hj_names = 'ha hb'
args = 'etaa0 w'
[../]
[./ACb0_int1]
type = ACInterface2DMultiPhase1
variable = etab0
etas = 'etaa0'
kappa_name = kappab
dkappadgrad_etaa_name = dkappadgrad_etab
d2kappadgrad_etaa_name = d2kappadgrad_etab
[../]
[./ACb0_int2]
type = ACInterface2DMultiPhase2
variable = etab0
kappa_name = kappab
dkappadgrad_etaa_name = dkappadgrad_etab
[../]
[./eb0_dot]
type = TimeDerivative
variable = etab0
[../]
#Chemical potential
[./w_dot]
type = SusceptibilityTimeDerivative
variable = w
f_name = chi
[../]
[./Diffusion]
type = MatDiffusion
variable = w
diffusivity = Dchi
[../]
[./coupled_etaa0dot]
type = CoupledSwitchingTimeDerivative
variable = w
v = etaa0
Fj_names = 'rhoa rhob'
hj_names = 'ha hb'
args = 'etaa0 etab0'
[../]
[./coupled_etab0dot]
type = CoupledSwitchingTimeDerivative
variable = w
v = etab0
Fj_names = 'rhoa rhob'
hj_names = 'ha hb'
args = 'etaa0 etab0'
[../]
[]
[Materials]
[./ha]
type = SwitchingFunctionMultiPhaseMaterial
h_name = ha
all_etas = 'etaa0 etab0'
phase_etas = 'etaa0'
[../]
[./hb]
type = SwitchingFunctionMultiPhaseMaterial
h_name = hb
all_etas = 'etaa0 etab0'
phase_etas = 'etab0'
[../]
[./omegaa]
type = DerivativeParsedMaterial
args = 'w'
f_name = omegaa
material_property_names = 'Vm ka caeq'
function = '-0.5*w^2/Vm^2/ka-w/Vm*caeq'
[../]
[./omegab]
type = DerivativeParsedMaterial
args = 'w'
f_name = omegab
material_property_names = 'Vm kb cbeq'
function = '-0.5*w^2/Vm^2/kb-w/Vm*cbeq'
[../]
[./rhoa]
type = DerivativeParsedMaterial
args = 'w'
f_name = rhoa
material_property_names = 'Vm ka caeq'
function = 'w/Vm^2/ka + caeq/Vm'
[../]
[./rhob]
type = DerivativeParsedMaterial
args = 'w'
f_name = rhob
material_property_names = 'Vm kb cbeq'
function = 'w/Vm^2/kb + cbeq/Vm'
[../]
[./kappaa]
type = InterfaceOrientationMultiphaseMaterial
kappa_name = kappaa
dkappadgrad_etaa_name = dkappadgrad_etaa
d2kappadgrad_etaa_name = d2kappadgrad_etaa
etaa = etaa0
etab = etab0
outputs = exodus
output_properties = 'kappaa'
[../]
[./kappab]
type = InterfaceOrientationMultiphaseMaterial
kappa_name = kappab
dkappadgrad_etaa_name = dkappadgrad_etab
d2kappadgrad_etaa_name = d2kappadgrad_etab
etaa = etab0
etab = etaa0
outputs = exodus
output_properties = 'kappab'
[../]
[./const]
type = GenericConstantMaterial
prop_names = 'L D chi Vm ka caeq kb cbeq gab mu'
prop_values = '1.0 1.0 0.1 1.0 10.0 0.1 10.0 0.9 4.5 10.0'
[../]
[./Mobility]
type = ParsedMaterial
f_name = Dchi
material_property_names = 'D chi'
function = 'D*chi'
[../]
[]
[Preconditioning]
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = PJFNK
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart'
petsc_options_value = 'hypre boomeramg 31'
l_tol = 1.0e-3
l_max_its = 30
nl_max_its = 15
nl_rel_tol = 1.0e-8
nl_abs_tol = 1e-8
end_time = 10.0
[./TimeStepper]
type = IterationAdaptiveDT
dt = 0.0005
cutback_factor = 0.7
growth_factor = 1.2
[../]
[]
[Adaptivity]
initial_steps = 5
max_h_level = 3
initial_marker = err_eta
marker = err_bnds
[./Markers]
[./err_eta]
type = ErrorFractionMarker
coarsen = 0.3
refine = 0.95
indicator = ind_eta
[../]
[./err_bnds]
type = ErrorFractionMarker
coarsen = 0.3
refine = 0.95
indicator = ind_bnds
[../]
[../]
[./Indicators]
[./ind_eta]
type = GradientJumpIndicator
variable = etaa0
[../]
[./ind_bnds]
type = GradientJumpIndicator
variable = bnds
[../]
[../]
[]
[Outputs]
interval = 10
exodus = true
[]
(modules/phase_field/test/tests/GBAnisotropy/test1.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 60
ny = 30
nz = 0
xmin = 0
xmax = 1000
ymin = 0
ymax = 600
zmin = 0
zmax = 0
elem_type = QUAD4
[]
[GlobalParams]
op_num = 3
var_name_base = gr
wGB = 100
length_scale = 1.0e-9
time_scale = 1.0e-9
[]
[Variables]
[./PolycrystalVariables]
[../]
[]
[ICs]
[./PolycrystalICs]
[./Tricrystal2CircleGrainsIC]
[../]
[../]
[]
[AuxVariables]
[./bnds]
order = FIRST
family = LAGRANGE
[../]
[./unique_grains]
order = FIRST
family = LAGRANGE
[../]
[./var_indices]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
[./PolycrystalKernel]
[../]
[]
[AuxKernels]
[./bnds_aux]
type = BndsCalcAux
variable = bnds
execute_on = timestep_end
[../]
[]
[BCs]
[./Periodic]
[./top_bottom]
auto_direction = 'x y'
[../]
[../]
[]
[Materials]
[./CuGrGranisotropic]
type = GBAnisotropy
T = 600 # K
# molar_volume_value = 7.11e-6 #Units:m^3/mol
Anisotropic_GB_file_name = anisotropy_mobility.txt # anisotropy_energy.txt
inclination_anisotropy = false # true
[../]
[]
[Postprocessors]
[./dt]
# Outputs the current time step
type = TimestepSize
[../]
[./gr1_area]
type = ElementIntegralVariablePostprocessor
variable = gr1
[../]
[./gr2_area]
type = ElementIntegralVariablePostprocessor
variable = gr2
[../]
[]
[Executioner]
type = Transient
scheme = bdf2
#Preconditioned JFNK (default)
solve_type = 'PJFNK'
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart'
petsc_options_value = 'hypre boomeramg 31'
l_max_its = 30
l_tol = 1e-4
nl_max_its = 40
nl_rel_tol = 1e-9
num_steps = 1
dt = 10.0
[]
[Outputs]
execute_on = 'timestep_end'
exodus = true
csv = true
[]
(modules/phase_field/test/tests/reconstruction/1phase_evolution.i)
#
# In this test we set the initial condition of a set of order parameters
# by pulling out the grain data from given EBSD data file ignoring the phase completely.
#
[Mesh]
[ebsd_mesh]
type = EBSDMeshGenerator
filename = IN100_001_28x28_Marmot.txt
[]
[]
[GlobalParams]
op_num = 5
var_name_base = gr
[]
[UserObjects]
[ebsd_reader]
type = EBSDReader
[]
[ebsd]
type = PolycrystalEBSD
coloring_algorithm = bt
ebsd_reader = ebsd_reader
output_adjacency_matrix = true
[]
[grain_tracker]
type = GrainTracker
polycrystal_ic_uo = ebsd
[]
[]
[ICs]
[PolycrystalICs]
[PolycrystalColoringIC]
polycrystal_ic_uo = ebsd
[]
[]
[]
[Variables]
[PolycrystalVariables]
[]
[]
[Kernels]
[PolycrystalKernel]
[]
[]
[AuxVariables]
[feature]
family = MONOMIAL
order = CONSTANT
[]
[bnds]
[]
[]
[AuxKernels]
[feature]
type = EBSDReaderAvgDataAux
variable = feature
ebsd_reader = ebsd_reader
grain_tracker = grain_tracker
data_name = feature_id
execute_on = 'initial timestep_end'
[]
[bnds]
type = BndsCalcAux
variable = bnds
execute_on = 'initial timestep_end'
[]
[]
[Materials]
[CuGrGr]
# Material properties
type = GBEvolution # Quantitative material properties for copper grain growth. Dimensions are nm and ns
block = 0 # Block ID (only one block in this problem)
GBmob0 = 2.5e-6 #Mobility prefactor for Cu from Schonfelder1997
GBenergy = 0.708 # GB energy in J/m^2
Q = 0.23 #Activation energy for grain growth from Schonfelder 1997
T = 500 # K #Constant temperature of the simulation (for mobility calculation)
wGB = 1 # nm #Width of the diffuse GB
#outputs = exodus
length_scale = 1e-06
time_scale = 1e-6
[]
[]
[Executioner]
type = Transient
num_steps = 2
dt = 10
[]
[Outputs]
exodus = true
[]
(modules/phase_field/examples/grain_growth/3D_6000_gr.i)
[Mesh]
type = GeneratedMesh
dim = 3
nx = 180
ny = 180
nz = 180
xmin = 0
xmax = 180
ymin = 0
ymax = 180
zmin = 0
zmax = 180
elem_type = HEX8
[]
[GlobalParams]
op_num = 28
var_name_base = gr
[]
[Variables]
[./PolycrystalVariables]
order = FIRST
family = LAGRANGE
[../]
[]
[UserObjects]
[./voronoi]
type = PolycrystalVoronoi
grain_num = 6000 # Number of grains
rand_seed = 8675 # 301
coloring_algorithm = jp
[../]
[./term]
type = Terminator
expression = 'grain_tracker < 218'
[../]
[]
[ICs]
[./PolycrystalICs]
[./PolycrystalColoringIC]
polycrystal_ic_uo = voronoi
[../]
[../]
[]
[AuxVariables]
[./bnds]
order = FIRST
family = LAGRANGE
[../]
[./unique_grains]
order = CONSTANT
family = MONOMIAL
[../]
[./ghost_elements]
order = CONSTANT
family = MONOMIAL
[../]
[./halos]
order = CONSTANT
family = MONOMIAL
[../]
[./var_indices]
order = CONSTANT
family = MONOMIAL
[../]
[]
[Kernels]
[./PolycrystalKernel]
[../]
[]
[AuxKernels]
[./BndsCalc]
type = BndsCalcAux
variable = bnds
execute_on = 'initial timestep_end'
[../]
[./unique_grains]
type = FeatureFloodCountAux
variable = unique_grains
field_display = UNIQUE_REGION
execute_on = 'initial timestep_end'
flood_counter = grain_tracker
[../]
[./ghost_elements]
type = FeatureFloodCountAux
variable = ghost_elements
field_display = GHOSTED_ENTITIES
execute_on = 'initial timestep_end'
flood_counter = grain_tracker
[../]
[./halos]
type = FeatureFloodCountAux
variable = halos
field_display = HALOS
execute_on = 'initial timestep_end'
flood_counter = grain_tracker
[../]
[./var_indices]
type = FeatureFloodCountAux
variable = var_indices
field_display = VARIABLE_COLORING
execute_on = 'initial timestep_end'
flood_counter = grain_tracker
[../]
[]
#[BCs]
# [./Periodic]
# [./All]
# auto_direction = 'x y'
# [../]
# [../]
#[]
[Materials]
[./Copper]
type = GBEvolution
T = 500
wGB = 3 # um
GBmob0 = 2.5e-6 #m^4/(Js) from Schoenfelder 1997
Q = 0.23 #Migration energy in eV
GBenergy = 0.708 #GB energy in J/m^2
molar_volume = 7.11e-6 #Molar volume in m^3/mol
length_scale = 1.0e-6
time_scale = 1.0
[../]
[]
[Postprocessors]
[./dt]
type = TimestepSize
[../]
[./n_elements]
type = NumElems
execute_on = timestep_end
[../]
[./n_nodes]
type = NumNodes
execute_on = timestep_end
[../]
[./DOFs]
type = NumDOFs
[../]
[./grain_tracker]
type = GrainTracker
threshold = 0.1
compute_halo_maps = true
[../]
[]
#[Preconditioning]
# [./SMP]
# type = SMP
# full = true
# [../]
#[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = PJFNK #Preconditioned JFNK (default)
petsc_options_iname = '-pc_type'
petsc_options_value = 'asm'
l_tol = 1.0e-4
l_max_its = 30
nl_max_its = 20
nl_rel_tol = 1.0e-8
start_time = 0.0
num_steps = 500
dt = 0.0002
[./TimeStepper]
type = IterationAdaptiveDT
cutback_factor = 0.9
dt = 0.0002
growth_factor = 1.1
optimal_iterations = 8
[../]
#[./Adaptivity]
# initial_adaptivity = 4
# refine_fraction = 0.6
# coarsen_fraction = 0.1
# max_h_level = 4
# print_changed_info = true
#[../]
[]
[Outputs]
nemesis = true
checkpoint = true
csv = true
[./console]
type = Console
[../]
[]
(modules/misc/test/tests/dynamic_loading/dynamic_obj_registration/dynamic_syntax.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 10
ny = 10
nz = 0
xmin = 0
xmax = 1000
ymin = 0
ymax = 1000
zmin = 0
zmax = 0
elem_type = QUAD4
uniform_refine = 2
[]
[GlobalParams]
op_num = 2
var_name_base = gr
[]
[Variables]
[./PolycrystalVariables]
[../]
[]
[ICs]
[./PolycrystalICs]
[./BicrystalCircleGrainIC]
radius = 333.333
x = 500
y = 500
[../]
[../]
[]
[AuxVariables]
[./bnds]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
[./PolycrystalKernel]
[../]
[]
[AuxKernels]
[./BndsCalc]
type = BndsCalcAux
variable = bnds
[../]
[]
[BCs]
[./Periodic]
[./All]
auto_direction = 'x y'
[../]
[../]
[]
[Materials]
[./Copper]
type = GBEvolution
block = 0
T = 500 # K
wGB = 60 # nm
GBmob0 = 2.5e-6 #m^4/(Js) from Schoenfelder 1997
Q = 0.23 #Migration energy in eV
GBenergy = 0.708 #GB energy in J/m^2
[../]
[]
[Postprocessors]
[./gr1area]
type = ElementIntegralVariablePostprocessor
variable = gr1
[../]
[]
[Preconditioning]
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
# petsc_options_iname = '-pc_type'
# petsc_options_value = 'lu'
type = Transient
scheme = bdf2
solve_type = 'NEWTON'
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart'
petsc_options_value = 'hypre boomeramg 31'
l_tol = 1.0e-4
l_max_its = 30
nl_max_its = 20
nl_rel_tol = 1.0e-9
start_time = 0.0
num_steps = 1
dt = 80.0
[]
[Outputs]
execute_on = 'timestep_end'
exodus = true
[]
[Problem]
register_objects_from = 'PhaseFieldApp'
library_path = '../../../../../phase_field/lib'
[]
(modules/phase_field/test/tests/GBAnisotropy/test2.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 60
ny = 30
nz = 0
xmin = 0
xmax = 1000
ymin = 0
ymax = 600
zmin = 0
zmax = 0
elem_type = QUAD4
[]
[Variables] # produce smooth initial GB
[./gr0]
order = FIRST
family = LAGRANGE
[./InitialCondition]
type = SpecifiedSmoothCircleIC
x_positions = '250.0 750.0'
y_positions = '300.0 300.0'
z_positions = ' 0.0 0.0'
radii = '200.0 200.0'
invalue = 0.0
outvalue = 1.0
int_width = 50.0
[../]
[../]
[./gr1]
order = FIRST
family = LAGRANGE
[./InitialCondition]
type = SmoothCircleIC
x1 = 250.0
y1 = 300.0
radius = 200.0
invalue = 1.0
outvalue = 0.0
int_width = 50.0
[../]
[../]
[./gr2]
order = FIRST
family = LAGRANGE
[./InitialCondition]
type = SmoothCircleIC
x1 = 750.0
y1 = 300.0
radius = 200.0
invalue = 1.0
outvalue = 0.0
int_width = 50.0
[../]
[../]
[]
[AuxVariables]
[./bnds]
order = FIRST
family = LAGRANGE
[../]
[./unique_grains]
order = FIRST
family = LAGRANGE
[../]
[./var_indices]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
[./PolycrystalKernel]
var_name_base = gr
op_num = 3
[../]
[]
[AuxKernels]
[./bnds_aux]
type = BndsCalcAux
variable = bnds
execute_on = timestep_end
var_name_base = gr
op_num = 3
[../]
[]
[BCs]
[./Periodic]
[./top_bottom]
auto_direction = 'x y'
[../]
[../]
[]
[Materials]
[./CuGrGranisotropic]
type = GBAnisotropy
T = 600 # K
op_num = 3
var_name_base = gr
wGB = 100
length_scale = 1.0e-9
time_scale = 1.0e-9
# molar_volume_value = 7.11e-6 #Units:m^3/mol
Anisotropic_GB_file_name = anisotropy_mobility.txt
inclination_anisotropy = false
[../]
[]
[Postprocessors]
[./dt]
# Outputs the current time step
type = TimestepSize
[../]
[./gr1_area]
type = ElementIntegralVariablePostprocessor
variable = gr1
[../]
[./gr2_area]
type = ElementIntegralVariablePostprocessor
variable = gr2
[../]
[]
[Executioner]
type = Transient
scheme = bdf2
#Preconditioned JFNK (default)
solve_type = 'PJFNK'
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart'
petsc_options_value = 'hypre boomeramg 31'
l_max_its = 30
l_tol = 1e-4
nl_max_its = 40
nl_rel_tol = 1e-9
dt = 5.0
num_steps = 2
[]
[Outputs]
execute_on = 'timestep_end'
exodus = true
csv = true
[]
(modules/combined/examples/phase_field-mechanics/grain_texture.i)
# This simulation predicts GB migration of 8 grains and outputs grain texture information
# Mesh adaptivity is not used so that the VectorPostprocessor's output will be uniform
# Time step adaptivity is used
# An AuxVariable is used to calculate the grain boundary locations
# Postprocessors are used to record time step
[Mesh]
# Mesh block. Meshes can be read in or automatically generated
type = GeneratedMesh
dim = 2 # Problem dimension
nx = 100 # Number of elements in the x-direction
ny = 100 # Number of elements in the y-direction
xmin = 0 # minimum x-coordinate of the mesh
xmax = 1000 # maximum x-coordinate of the mesh
ymin = 0 # minimum y-coordinate of the mesh
ymax = 1000 # maximum y-coordinate of the mesh
elem_type = QUAD4 # Type of elements used in the mesh
[]
[GlobalParams]
# Parameters used by several kernels that are defined globally to simplify input file
op_num = 8 # Number of order parameters used
var_name_base = gr # Base name of grains
grain_num = 8 #Number of grains
[]
[Variables]
# Variable block, where all variables in the simulation are declared
[./PolycrystalVariables]
[../]
[]
[UserObjects]
[./voronoi]
type = PolycrystalVoronoi
coloring_algorithm = bt
[../]
[./grain_tracker]
type = GrainTracker
threshold = 0.2
connecting_threshold = 0.08
[../]
[]
[ICs]
[./PolycrystalICs]
[./PolycrystalColoringIC]
polycrystal_ic_uo = voronoi
[../]
[../]
[]
[AuxVariables]
# Dependent variables
[./bnds]
# Variable used to visualize the grain boundaries in the simulation
order = FIRST
family = LAGRANGE
[../]
[./unique_grains]
order = CONSTANT
family = MONOMIAL
[../]
[./var_indices]
order = CONSTANT
family = MONOMIAL
[../]
[]
[Kernels]
# Kernel block, where the kernels defining the residual equations are set up.
[./PolycrystalKernel]
# Custom action creating all necessary kernels for grain growth. All input parameters are up in GlobalParams
[../]
[]
[AuxKernels]
# AuxKernel block, defining the equations used to calculate the auxvars
[./bnds_aux]
# AuxKernel that calculates the GB term
type = BndsCalcAux
variable = bnds
execute_on = timestep_end
[../]
[./unique_grains]
type = FeatureFloodCountAux
variable = unique_grains
execute_on = timestep_end
flood_counter = grain_tracker
field_display = UNIQUE_REGION
[../]
[./var_indices]
type = FeatureFloodCountAux
variable = var_indices
execute_on = timestep_end
flood_counter = grain_tracker
field_display = VARIABLE_COLORING
[../]
[]
[BCs]
# Boundary Condition block
[./Periodic]
[./top_bottom]
auto_direction = 'x y' # Makes problem periodic in the x and y directions
[../]
[../]
[]
[Materials]
[./CuGrGr]
# Material properties
type = GBEvolution # Quantitative material properties for copper grain growth. Dimensions are nm and ns
block = 0 # Block ID (only one block in this problem)
GBmob0 = 2.5e-6 #Mobility prefactor for Cu from Schonfelder1997
GBenergy = 0.708 # GB energy in J/m^2
Q = 0.23 #Activation energy for grain growth from Schonfelder 1997
T = 450 # K #Constant temperature of the simulation (for mobility calculation)
wGB = 14 # nm #Width of the diffuse GB
outputs = exodus
[../]
[]
[UserObjects]
[./euler_angle_file]
type = EulerAngleFileReader
file_name = grn_8_rand_2D.tex
[../]
[]
[VectorPostprocessors]
[./gbInfo]
type = GrainTextureVectorPostprocessor
unique_grains = unique_grains
euler_angle_provider = euler_angle_file
sort_by = id # sort output by elem id
[../]
[]
[Executioner]
type = Transient # Type of executioner, here it is transient with an adaptive time step
scheme = bdf2 # Type of time integration (2nd order backward euler), defaults to 1st order backward euler
#Preconditioned JFNK (default)
solve_type = 'PJFNK'
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart -mat_mffd_type'
petsc_options_value = 'hypre boomeramg 101 ds'
l_max_its = 30 # Max number of linear iterations
l_tol = 1e-4 # Relative tolerance for linear solves
nl_max_its = 40 # Max number of nonlinear iterations
nl_abs_tol = 1e-11 # Relative tolerance for nonlinear solves
nl_rel_tol = 1e-10 # Absolute tolerance for nonlinear solves
start_time = 0.0
num_steps = 50
[./TimeStepper]
type = IterationAdaptiveDT
dt = 25 # Initial time step. In this simulation it changes.
optimal_iterations = 6 # Time step will adapt to maintain this number of nonlinear iterations
[../]
[]
[Outputs]
execute_on = 'INITIAL TIMESTEP_END'
exodus = true
csv = true
perf_graph = true
[./console]
type = Console
max_rows = 20
[../]
[]
(modules/phase_field/examples/rigidbodymotion/AC_CH_Multigrain.i)
# Tests the rigid body motion due to applied force of multiple particles.
# ***COPY AND PASTE THESE AS NEEDED***
# 'gr0 gr1 gr2 gr3 gr4 gr5 gr6 gr7 gr8 gr9 gr10 gr11 gr12 gr13 gr14 gr15 gr16 gr17 gr18 gr19'
# (gr0^2+gr1^2+gr2^2+gr3^2+gr4^2+gr5^2+gr6^2+gr7^2+gr8^2+gr9^2+gr10^2+gr11^2+gr12^2+gr13^2+gr14^2+gr15^2+gr16^2+gr17^2+gr18^2+gr19^2)
# (gr0^3+gr1^3+gr2^3+gr3^3+gr4^3+gr5^3+gr6^3+gr7^3+gr8^3+gr9^3+gr10^3+gr11^3+gr12^3+gr13^3+gr14^3+gr15^3+gr16^3+gr17^3+gr18^3+gr19^3)
[GlobalParams]
op_num = 4
var_name_base = gr
[]
[Mesh]
type = GeneratedMesh
dim = 2
nx = 15
ny = 15
xmin = 0
xmax = 600
ymin = 0
ymax = 600
elem_type = QUAD4
uniform_refine = 1
[]
[Variables]
[./c]
[../]
[./w]
[../]
[./PolycrystalVariables] # Automatically creates order parameter variables
[../]
[]
[AuxVariables]
[./bnds]
[../]
[./force]
order = CONSTANT
family = MONOMIAL
[../]
[./free_energy]
order = CONSTANT
family = MONOMIAL
[../]
[./unique_grains]
order = CONSTANT
family = MONOMIAL
[../]
[./var_indices]
order = CONSTANT
family = MONOMIAL
[../]
[./centroids]
order = CONSTANT
family = MONOMIAL
[../]
[]
[Functions]
[./load_x]
# Defines the force on the grains in the x-direction
type = ParsedFunction
value = 0.005*cos(x*pi/600)
[../]
[./load_y]
# Defines the force on the grains in the y-direction
type = ConstantFunction
value = 0.002
[../]
[]
[Kernels]
[./RigidBodyMultiKernel]
# Creates all of the necessary Allen Cahn kernels automatically
c = c
f_name = f_loc
mob_name = L
kappa_name = kappa_gr
grain_force = grain_force
grain_volumes = grain_volumes
grain_tracker_object = grain_center
[../]
# Cahn Hilliard kernels
[./dt_w]
type = CoupledTimeDerivative
variable = w
v = c
[../]
[./CH_wres]
type = SplitCHWRes
variable = w
mob_name = M
[../]
[./CH_Parsed]
type = SplitCHParsed
variable = c
f_name = f_loc
w = w
kappa_name = kappa_c
args = 'gr0 gr1 gr2 gr3' # Must be changed as op_num changes. Copy/paste from line 4
[../]
[./CH_RBM]
type = MultiGrainRigidBodyMotion
variable = w
c = c
v = 'gr0 gr1 gr2 gr3'
grain_force = grain_force
grain_volumes = grain_volumes
grain_tracker_object = grain_center
[../]
[]
[AuxKernels]
[./force_x]
type = FunctionAux
variable = force
function = load_x
[../]
[./force_y]
type = FunctionAux
variable = force
function = load_y
[../]
[./energy_density]
type = TotalFreeEnergy
variable = free_energy
f_name = f_loc
kappa_names = kappa_c
interfacial_vars = c
[../]
[./bnds]
type = BndsCalcAux
variable = bnds
[../]
[]
[BCs]
[./bcs]
#zero flux BC
type = NeumannBC
value = 0
variable = c
boundary = '0 1 2 3'
[../]
[]
[Materials]
[./constants]
type = GenericConstantMaterial
prop_names = 'kappa_gr kappa_c M L'
prop_values = '250 4000 4.5 60'
[../]
[./free_energy]
type = DerivativeParsedMaterial
f_name = f_loc
constant_names = 'A B'
constant_expressions = '450 1.5'
args = 'c gr0 gr1 gr2 gr3' #Must be changed as op_num changes. Copy/paste from line 4
function = 'A*c^2*(1-c)^2+B*(c^2+6*(1-c)*(gr0^2+gr1^2+gr2^2+gr3^2)
-4*(2-c)*(gr0^3+gr1^3+gr2^3+gr3^3)
+3*(gr0^2+gr1^2+gr2^2+gr3^2)^2)'
#Copy/paste from lines 5-6
derivative_order = 2
[../]
[./force_density]
type = ExternalForceDensityMaterial
c = c
k = 10.0
force_x = load_x
force_y = load_y
[../]
[]
[Postprocessors]
[./total_energy]
type = ElementIntegralVariablePostprocessor
variable = free_energy
execute_on = 'initial timestep_end'
[../]
[]
[VectorPostprocessors]
[./forces]
type = GrainForcesPostprocessor
grain_force = grain_force
[../]
[./grain_volumes]
type = FeatureVolumeVectorPostprocessor
flood_counter = grain_center
execute_on = 'initial timestep_begin'
[../]
[]
[UserObjects]
[./grain_center]
type = GrainTracker
outputs = none
compute_var_to_feature_map = true
execute_on = 'initial timestep_begin'
[../]
[./grain_force]
type = ComputeExternalGrainForceAndTorque
grain_data = grain_center
c = c
etas = 'gr0 gr1 gr2 gr3'
force_density = force_density_ext
execute_on = 'linear nonlinear'
[../]
[]
[Preconditioning]
[./coupled]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = NEWTON
petsc_options_iname = '-pc_type -ksp_gmres_restart -sub_ksp_type
-sub_pc_type -pc_asm_overlap'
petsc_options_value = 'asm 31 preonly
ilu 2'
l_tol = 1e-05
nl_max_its = 30
l_max_its = 30
nl_rel_tol = 1e-07
nl_abs_tol = 1e-09
start_time = 0.0
end_time = 4
dt = 0.05
[]
[Outputs]
exodus = true
perf_graph = true
[./display]
type = Console
max_rows = 12
[../]
[]
[ICs]
[./concentration_IC]
type = SpecifiedSmoothCircleIC
x_positions = '150 450 150 450'
y_positions = '150 150 450 450'
z_positions = '0 0 0 0'
radii = '120 120 120 120'
variable = c
invalue = 1.0
outvalue = 0.0
int_width = 25
[../]
[./gr0_IC]
type = SmoothCircleIC
variable = gr0
x1 = 150
y1 = 150
radius = 120
invalue = 1.0
outvalue = 0.0
int_width = 25
[../]
[./gr1_IC]
type = SmoothCircleIC
variable = gr1
x1 = 450
y1 = 150
radius = 120
invalue = 1.0
outvalue = 0.0
int_width = 25
[../]
[./gr2_IC]
type = SmoothCircleIC
variable = gr2
x1 = 150
y1 = 450
radius = 120
invalue = 1.0
outvalue = 0.0
int_width = 25
[../]
[./gr3_IC]
type = SmoothCircleIC
variable = gr3
x1 = 450
y1 = 450
radius = 120
invalue = 1.0
outvalue = 0.0
int_width = 25
[../]
[]
(modules/combined/examples/phase_field-mechanics/EBSD_reconstruction_grain_growth_mech.i)
# This example reconstructs the grain structure from an EBSD data file
# Then, an isotropic grain model is run with linear elasticity and an anisotropic
# elasticity tensor that uses the measured EBSD angles.
[Mesh]
[ebsd_mesh]
type = EBSDMeshGenerator
uniform_refine = 2 #Mesh can go two levels coarser than the EBSD grid
filename = IN100_128x128.txt
[]
[]
[GlobalParams]
op_num = 8
var_name_base = gr
displacements = 'disp_x disp_y'
[]
[Variables]
[PolycrystalVariables] #Polycrystal variable generation (30 order parameters)
[]
[disp_x]
[]
[disp_y]
[]
[]
[AuxVariables]
[bnds]
[]
[gt_indices]
order = CONSTANT
family = MONOMIAL
[]
[unique_grains]
order = CONSTANT
family = MONOMIAL
[]
[vonmises_stress]
order = CONSTANT
family = MONOMIAL
[]
[C1111]
order = CONSTANT
family = MONOMIAL
[]
[phi1]
order = CONSTANT
family = MONOMIAL
[]
[Phi]
order = CONSTANT
family = MONOMIAL
[]
[phi2]
order = CONSTANT
family = MONOMIAL
[]
[EBSD_grain]
family = MONOMIAL
order = CONSTANT
[]
[]
[ICs]
[PolycrystalICs]
[ReconVarIC]
ebsd_reader = ebsd
coloring_algorithm = bt
[]
[]
[]
[Kernels]
[PolycrystalKernel]
[]
[PolycrystalElasticDrivingForce]
[]
[TensorMechanics]
[]
[]
[AuxKernels]
[BndsCalc]
type = BndsCalcAux
variable = bnds
execute_on = 'initial timestep_end'
[]
[gt_indices]
type = FeatureFloodCountAux
variable = gt_indices
execute_on = 'initial timestep_end'
flood_counter = grain_tracker
field_display = VARIABLE_COLORING
[]
[unique_grains]
type = FeatureFloodCountAux
variable = unique_grains
execute_on = 'initial timestep_end'
flood_counter = grain_tracker
field_display = UNIQUE_REGION
[]
[C1111]
type = RankFourAux
variable = C1111
rank_four_tensor = elasticity_tensor
index_l = 0
index_j = 0
index_k = 0
index_i = 0
execute_on = timestep_end
[]
[vonmises_stress]
type = RankTwoScalarAux
variable = vonmises_stress
rank_two_tensor = stress
scalar_type = VonMisesStress
execute_on = timestep_end
[]
[phi1]
type = OutputEulerAngles
variable = phi1
euler_angle_provider = ebsd
grain_tracker = grain_tracker
output_euler_angle = 'phi1'
execute_on = 'initial'
[]
[Phi]
type = OutputEulerAngles
variable = Phi
euler_angle_provider = ebsd
grain_tracker = grain_tracker
output_euler_angle = 'Phi'
execute_on = 'initial'
[]
[phi2]
type = OutputEulerAngles
variable = phi2
euler_angle_provider = ebsd
grain_tracker = grain_tracker
output_euler_angle = 'phi2'
execute_on = 'initial'
[]
[grain_aux]
type = EBSDReaderPointDataAux
variable = EBSD_grain
ebsd_reader = ebsd
data_name = 'feature_id'
execute_on = 'initial'
[]
[]
[BCs]
[top_displacement]
type = DirichletBC
variable = disp_y
boundary = top
value = -2.0
[]
[x_anchor]
type = DirichletBC
variable = disp_x
boundary = 'left right'
value = 0.0
[]
[y_anchor]
type = DirichletBC
variable = disp_y
boundary = bottom
value = 0.0
[]
[]
[Modules]
[PhaseField]
[EulerAngles2RGB]
crystal_structure = cubic
euler_angle_provider = ebsd
grain_tracker = grain_tracker
[]
[]
[]
[Materials]
[Copper]
# T = 500 # K
type = GBEvolution
block = 0
T = 500
wGB = 0.6 # um
GBmob0 = 2.5e-6 # m^4/(Js) from Schoenfelder 1997
Q = 0.23 # Migration energy in eV
GBenergy = 0.708 # GB energy in J/m^2
molar_volume = 7.11e-6; # Molar volume in m^3/mol
length_scale = 1.0e-6
time_scale = 1.0e-6
[]
[ElasticityTensor]
type = ComputePolycrystalElasticityTensor
grain_tracker = grain_tracker
[]
[strain]
type = ComputeSmallStrain
block = 0
displacements = 'disp_x disp_y'
[]
[stress]
type = ComputeLinearElasticStress
block = 0
[]
[]
[Postprocessors]
[dt]
type = TimestepSize
[]
[n_elements]
type = NumElems
execute_on = 'initial timestep_end'
[]
[n_nodes]
type = NumNodes
execute_on = 'initial timestep_end'
[]
[DOFs]
type = NumDOFs
[]
[]
[UserObjects]
[ebsd]
type = EBSDReader
[]
[grain_tracker]
type = GrainTrackerElasticity
compute_var_to_feature_map = true
ebsd_reader = ebsd
fill_method = symmetric9
C_ijkl = '1.27e5 0.708e5 0.708e5 1.27e5 0.708e5 1.27e5 0.7355e5 0.7355e5 0.7355e5'
euler_angle_provider = ebsd
[]
[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = PJFNK
petsc_options_iname = '-pc_type -pc_hypre_type -pc_hypre_boomeramg_strong_threshold'
petsc_options_value = ' hypre boomeramg 0.7'
l_tol = 1.0e-4
l_max_its = 20
nl_max_its = 20
nl_rel_tol = 1.0e-8
start_time = 0.0
num_steps = 30
dt = 10
[Adaptivity]
initial_adaptivity = 0
refine_fraction = 0.7
coarsen_fraction = 0.1
max_h_level = 2
[]
[TimeStepper]
type = IterationAdaptiveDT
cutback_factor = 0.9
dt = 10.0
growth_factor = 1.1
optimal_iterations = 7
[]
[]
[Outputs]
csv = true
exodus = true
[]
(modules/phase_field/test/tests/rigidbodymotion/grain_appliedforcedensity.i)
# test file for showing grain motion due to applied force density on grains
[GlobalParams]
var_name_base = eta
op_num = 2
[]
[Mesh]
type = GeneratedMesh
dim = 2
nx = 25
ny = 10
nz = 0
xmax = 50
ymax = 25
zmax = 0
elem_type = QUAD4
[]
[Variables]
[./c]
order = FIRST
family = LAGRANGE
[./InitialCondition]
type = SpecifiedSmoothCircleIC
invalue = 1.0
outvalue = 0.1
int_width = 6.0
x_positions = '20.0 30.0 '
z_positions = '0.0 0.0 '
y_positions = '0.0 25.0 '
radii = '14.0 14.0'
3D_spheres = false
variable = c
[../]
[../]
[./w]
order = FIRST
family = LAGRANGE
[../]
[]
[Functions]
[./load]
type = ConstantFunction
value = 0.01
[../]
[]
[Kernels]
[./c_res]
type = SplitCHParsed
variable = c
f_name = F
kappa_name = kappa_c
w = w
[../]
[./w_res]
type = SplitCHWRes
variable = w
mob_name = M
[../]
[./time]
type = CoupledTimeDerivative
variable = w
v = c
[../]
[./motion]
type = MultiGrainRigidBodyMotion
variable = w
c = c
v = 'eta0 eta1'
grain_tracker_object = grain_center
grain_force = grain_force
grain_volumes = grain_volumes
[../]
[]
[Materials]
[./pfmobility]
type = GenericConstantMaterial
prop_names = 'M kappa_c kappa_eta'
prop_values = '5.0 2.0 0.1'
[../]
[./free_energy]
type = DerivativeParsedMaterial
f_name = F
args = c
constant_names = 'barr_height cv_eq'
constant_expressions = '0.1 1.0e-2'
function = 16*barr_height*(c-cv_eq)^2*(1-cv_eq-c)^2
derivative_order = 2
[../]
[./force_density_ext]
type = ExternalForceDensityMaterial
c = c
etas = 'eta0 eta1'
k = 1.0
force_y = load
[../]
[]
[AuxVariables]
[./eta0]
[../]
[./eta1]
[../]
[./bnds]
[../]
[]
[AuxKernels]
[./bnds]
type = BndsCalcAux
variable = bnds
var_name_base = eta
op_num = 2
v = 'eta0 eta1'
[../]
[]
[ICs]
[./ic_eta0]
int_width = 6.0
x1 = 20.0
y1 = 0.0
radius = 14.0
outvalue = 0.0
variable = eta0
invalue = 1.0
type = SmoothCircleIC
[../]
[./IC_eta1]
int_width = 6.0
x1 = 30.0
y1 = 25.0
radius = 14.0
outvalue = 0.0
variable = eta1
invalue = 1.0
type = SmoothCircleIC
[../]
[]
[VectorPostprocessors]
[./forces]
type = GrainForcesPostprocessor
grain_force = grain_force
[../]
[./grain_volumes]
type = FeatureVolumeVectorPostprocessor
flood_counter = grain_center
execute_on = 'initial timestep_begin'
[../]
[]
[UserObjects]
[./grain_center]
type = GrainTracker
outputs = none
compute_var_to_feature_map = true
execute_on = 'initial timestep_begin'
[../]
[./grain_force]
type = ComputeExternalGrainForceAndTorque
execute_on = 'linear nonlinear'
grain_data = grain_center
c = c
etas = 'eta0 eta1'
force_density = force_density_ext
[../]
[]
[Preconditioning]
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = PJFNK
petsc_options_iname = '-pc_type -ksp_gmres_restart -sub_ksp_type -sub_pc_type -pc_asm_overlap'
petsc_options_value = 'asm 31 preonly lu 1'
l_max_its = 30
l_tol = 1.0e-4
nl_rel_tol = 1.0e-10
start_time = 0.0
num_steps = 1
dt = 0.1
[]
[Outputs]
exodus = true
csv = true
[]
(modules/phase_field/test/tests/grain_growth/evolution.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 10
ny = 10
nz = 0
xmax = 1000
ymax = 1000
zmax = 0
elem_type = QUAD4
uniform_refine = 2
[]
[GlobalParams]
op_num = 4
var_name_base = 'gr'
[]
[Variables]
[./PolycrystalVariables]
[../]
[]
[UserObjects]
[./voronoi]
type = PolycrystalVoronoi
rand_seed = 102
grain_num = 4
coloring_algorithm = bt
[../]
[]
[ICs]
[./PolycrystalICs]
[./PolycrystalColoringIC]
polycrystal_ic_uo = voronoi
[../]
[../]
[]
[AuxVariables]
[./bnds]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
[./PolycrystalKernel]
[../]
[]
[AuxKernels]
[./BndsCalc]
type = BndsCalcAux
variable = bnds
execute_on = 'timestep_end'
[../]
[]
[BCs]
[./Periodic]
[./All]
auto_direction = 'x y'
[../]
[../]
[]
[Materials]
[./Moly_GB]
type = GBEvolution
time_scale = 1.0
GBmob0 = 3.986e-6
T = 500 # K
wGB = 60 # nm
Q = 1.0307
GBenergy = 2.4
[../]
[]
[Postprocessors]
[./gr1area]
type = ElementIntegralVariablePostprocessor
variable = gr1
execute_on = 'initial timestep_end'
[../]
[./avg_grain_vol]
type = AverageGrainVolume
grain_num = 4
execute_on = 'initial timestep_end'
[../]
[]
[Preconditioning]
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = 'NEWTON'
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart'
petsc_options_value = 'hypre boomeramg 31'
l_tol = 1.0e-4
l_max_its = 30
nl_max_its = 20
nl_rel_tol = 1.0e-9
start_time = 0.0
num_steps = 2
dt = 4
[]
[Outputs]
exodus = true
[]
(modules/phase_field/test/tests/reconstruction/euler2rgb_non_uniform_orientation.i)
[Mesh]
[ebsd_mesh]
type = EBSDMeshGenerator
filename = ebsd_scan.txt
[]
[]
[GlobalParams]
op_num = 10
var_name_base = gr
[]
[UserObjects]
[ebsd_reader]
type = EBSDReader
bins = 40
[]
[ebsd]
type = PolycrystalEBSD
coloring_algorithm = jp
ebsd_reader = ebsd_reader
enable_var_coloring = true
[]
[grain_tracker]
type = GrainTracker
flood_entity_type = ELEMENTAL
compute_halo_maps = true # For displaying HALO fields
polycrystal_ic_uo = ebsd
[]
[]
[ICs]
[PolycrystalICs]
[PolycrystalColoringIC]
polycrystal_ic_uo = ebsd
[]
[]
[]
[Variables]
[PolycrystalVariables]
[]
[]
[AuxVariables]
[bnds]
[]
[]
[Kernels]
[PolycrystalKernel]
[]
[]
[AuxKernels]
[BndsCalc]
type = BndsCalcAux
variable = bnds
execute_on = 'initial timestep_end'
[]
[]
[Modules]
[PhaseField]
[EulerAngles2RGB]
crystal_structure = cubic
euler_angle_provider = ebsd_reader
grain_tracker = grain_tracker
[]
[]
[]
[Materials]
[Copper]
# T = 500 # K
type = GBEvolution
T = 500
wGB = 0.6 # um
GBmob0 = 2.5e-6 # m^4/(Js) from Schoenfelder 1997
Q = 0.23 # Migration energy in eV
GBenergy = 0.708 # GB energy in J/m^2
molar_volume = 7.11e-6 # Molar volume in m^3/mol
length_scale = 1.0e-6
time_scale = 1.0e-6
[]
[]
[Postprocessors]
[dt]
type = TimestepSize
[]
[n_elements]
type = NumElems
execute_on = 'initial timestep_end'
[]
[n_nodes]
type = NumNodes
execute_on = 'initial timestep_end'
[]
[DOFs]
type = NumDOFs
[]
[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = Newton
petsc_options_iname = '-pc_type -pc_hypre_type -pc_hypre_boomeramg_strong_threshold'
petsc_options_value = 'hypre boomeramg 0.7'
l_tol = 1.0e-6
l_max_its = 100
nl_max_its = 20
nl_rel_tol = 1.0e-8
start_time = 0.0
num_steps = 0
[]
[Outputs]
exodus = true
perf_graph = true
[]
(modules/phase_field/examples/rigidbodymotion/grain_motion_GT.i)
# example showing grain motion due to applied force density on grains
[GlobalParams]
var_name_base = eta
op_num = 4
[]
[Mesh]
type = GeneratedMesh
dim = 2
nx = 80
ny = 40
nz = 0
xmin = 0.0
xmax = 40.0
ymin = 0.0
ymax = 20.0
zmax = 0
elem_type = QUAD4
[]
[Variables]
[./c]
[../]
[./w]
[../]
[./PolycrystalVariables]
[../]
[]
[Kernels]
[./c_res]
type = SplitCHParsed
variable = c
f_name = F
kappa_name = kappa_c
w = w
args = 'eta0 eta1 eta2 eta3'
[../]
[./w_res]
type = SplitCHWRes
variable = w
mob_name = M
[../]
[./time]
type = CoupledTimeDerivative
variable = w
v = c
[../]
[./motion]
type = MultiGrainRigidBodyMotion
variable = w
c = c
v = 'eta0 eta1 eta2 eta3'
grain_tracker_object = grain_center
grain_force = grain_force
grain_volumes = grain_volumes
[../]
[./RigidBodyMultiKernel]
# Creates all of the necessary Allen Cahn kernels automatically
c = c
f_name = F
mob_name = L
kappa_name = kappa_eta
grain_force = grain_force
grain_volumes = grain_volumes
grain_tracker_object = grain_center
[../]
[]
[Functions]
[./load_x]
# Defines the force on the grains in the x-direction
type = ParsedFunction
value = 0.005*cos(x*pi/600)
[../]
[./load_y]
# Defines the force on the grains in the y-direction
type = ConstantFunction
value = 0.002
[../]
[]
[Materials]
[./pfmobility]
type = GenericConstantMaterial
prop_names = 'M L kappa_c kappa_eta'
prop_values = '4.5 60 250 4000'
[../]
[./free_energy]
type = DerivativeParsedMaterial
f_name = F
#args = 'c eta0 eta1 eta2 eta3'
#constant_names = 'barr_height cv_eq'
#constant_expressions = '0.1 1.0e-2'
#function = '16*barr_height*(c-cv_eq)^2*(1-cv_eq-c)^2
# +eta0*(1-eta0)*c+eta1*(1-eta1)*c
# +eta2*(1-eta2)*c+eta3*(1-eta3)*c'
constant_names = 'A B'
constant_expressions = '450 1.5'
args = 'c eta0 eta1 eta2 eta3' #Must be changed as op_num changes. Copy/paste from line 4
function = 'A*c^2*(1-c)^2+B*(c^2+6*(1-c)*(eta0^2+eta1^2+eta2^2+eta3^2)
-4*(2-c)*(eta0^3+eta1^3+eta2^3+eta3^3)
+3*(eta0^2+eta1^2+eta2^2+eta3^2)^2)'
derivative_order = 2
[../]
#[./force_density]
# type = ForceDensityMaterial
# c = c
# etas = 'eta0 eta1 eta2 eta3'
#[../]
[./force_density]
type = ExternalForceDensityMaterial
c = c
k = 10.0
etas = 'eta0 eta1 eta2 eta3'
force_x = load_x
force_y = load_y
[../]
[]
[AuxVariables]
[./bnds]
[../]
[./unique_grains]
order = CONSTANT
family = MONOMIAL
[../]
[./var_indices]
order = CONSTANT
family = MONOMIAL
[../]
[./centroids]
order = CONSTANT
family = MONOMIAL
[../]
[]
[AuxKernels]
[./bnds]
type = BndsCalcAux
variable = bnds
#var_name_base = eta
#op_num = 4.0
v = 'eta0 eta1 eta2 eta3'
[../]
[./unique_grains]
type = FeatureFloodCountAux
variable = unique_grains
flood_counter = grain_center
field_display = UNIQUE_REGION
execute_on = timestep_begin
[../]
[./var_indices]
type = FeatureFloodCountAux
variable = var_indices
flood_counter = grain_center
field_display = VARIABLE_COLORING
execute_on = timestep_begin
[../]
[./centroids]
type = FeatureFloodCountAux
variable = centroids
execute_on = timestep_begin
field_display = CENTROID
flood_counter = grain_center
[../]
[]
[ICs]
[./ic_eta1]
x_positions = '32.5 24.0'
int_width = 1.0
z_positions = '0 0'
y_positions = '6.0 14.0'
radii = '4.0 4.0'
3D_spheres = false
outvalue = 0
variable = eta1
invalue = 1
type = SpecifiedSmoothCircleIC
block = 0
[../]
[./multip]
x_positions = '5.5 15.5 24.0 32.5 7.0 15.5 24.0 32.5'
int_width = 1.0
z_positions = '0 0'
y_positions = '6.0 6.0 6.0 6.0 14.5 14.5 14.0 14.5'
radii = '4.0 4.0 4.0 4.0 4.0 4.0 4.0 4.0'
3D_spheres = false
outvalue = 0.001
variable = c
invalue = 0.999
type = SpecifiedSmoothCircleIC
block = 0
[../]
[./ic_eta0]
x_positions = '5.5 15.5'
int_width = 1.0
z_positions = '0 0'
y_positions = '6.0 6.0'
radii = '4.0 4.0'
3D_spheres = false
outvalue = 0.0
variable = eta0
invalue = 1.0
type = SpecifiedSmoothCircleIC
block = 0
[../]
[./ic_eta2]
x_positions = '24.0 7.0'
int_width = 1.0
z_positions = '0 0'
y_positions = '6.0 14.5 '
radii = '4.0 4.0 '
3D_spheres = false
outvalue = 0.0
variable = eta2
invalue = 1.0
type = SpecifiedSmoothCircleIC
block = 0
[../]
[./ic_eta3]
x_positions = '15.5 32.5'
int_width = 1.0
z_positions = '0 0'
y_positions = '14.5 14.5'
radii = '4.0 4.0'
3D_spheres = false
outvalue = 0.0
variable = eta3
invalue = 1.0
type = SpecifiedSmoothCircleIC
block = 0
[../]
[]
[VectorPostprocessors]
[./forces]
type = GrainForcesPostprocessor
grain_force = grain_force
[../]
[./grain_volumes]
type = FeatureVolumeVectorPostprocessor
flood_counter = grain_center
execute_on = 'initial timestep_begin'
[../]
[]
[UserObjects]
[./grain_center]
type = GrainTracker
outputs = none
compute_var_to_feature_map = true
execute_on = 'initial timestep_begin'
[../]
[./grain_force]
type = ComputeExternalGrainForceAndTorque
c = c
grain_data = grain_center
force_density = force_density_ext
etas = 'eta0 eta1 eta2 eta3'
execute_on = 'initial linear nonlinear'
[../]
[]
[Preconditioning]
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = NEWTON
petsc_options_iname = '-pc_type -ksp_gmres_restart -sub_ksp_type -sub_pc_type -pc_asm_overlap'
petsc_options_value = 'asm 31 preonly lu 1'
l_max_its = 30
l_tol = 1.0e-4
nl_rel_tol = 1.0e-10
start_time = 0.0
num_steps = 20
dt = 0.01
[]
[Outputs]
exodus = true
[]
(modules/combined/test/tests/grain_texture/EulerAngleProvider2RGBAux_bicrystal.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 40
ny = 12
xmax = 1000
ymax = 300
elem_type = QUAD4
[]
[GlobalParams]
op_num = 2
var_name_base = gr
[]
[Variables]
[./PolycrystalVariables]
[../]
[]
[ICs]
[./PolycrystalICs]
[./BicrystalBoundingBoxIC]
x1 = 0
y1 = 0
x2 = 500
y2 = 1000
[../]
[../]
[]
[AuxVariables]
[./bnds]
order = FIRST
family = LAGRANGE
[../]
[./unique_grains]
order = CONSTANT
family = MONOMIAL
[../]
[./var_indices]
order = CONSTANT
family = MONOMIAL
[../]
[./active_bounds_elemental]
order = CONSTANT
family = MONOMIAL
[../]
[./rgb]
order = CONSTANT
family = MONOMIAL
[../]
[]
[Kernels]
[./PolycrystalKernel]
[../]
[]
[AuxKernels]
[./bnds_aux]
type = BndsCalcAux
variable = bnds
execute_on = timestep_end
[../]
[./unique_grains]
type = FeatureFloodCountAux
variable = unique_grains
flood_counter = grain_tracker
execute_on = 'initial timestep_begin'
field_display = UNIQUE_REGION
[../]
[./var_indices]
type = FeatureFloodCountAux
variable = var_indices
flood_counter = grain_tracker
execute_on = 'initial timestep_begin'
field_display = VARIABLE_COLORING
[../]
[./active_bounds_elemental]
type = FeatureFloodCountAux
variable = active_bounds_elemental
field_display = ACTIVE_BOUNDS
execute_on = 'initial timestep_begin'
flood_counter = grain_tracker
[../]
[./rgb]
type = EulerAngleProvider2RGBAux
variable = rgb
euler_angle_provider = euler_angle_file
grain_tracker = grain_tracker
crystal_structure = cubic
execute_on = 'initial timestep_end'
[../]
[]
[Materials]
[./Copper]
type = GBEvolution
block = 0
T = 500 # K
wGB = 75 # nm
GBmob0 = 2.5e-6 #m^4/(Js) from Schoenfelder 1997
Q = 0.23 #Migration energy in eV
GBenergy = 0.708 #GB energy in J/m^2
time_scale = 1.0e-6
[../]
[]
[UserObjects]
[./grain_tracker]
type = FauxGrainTracker
connecting_threshold = 0.05
compute_var_to_feature_map = true
flood_entity_type = elemental
execute_on = 'initial timestep_begin'
outputs = none
[../]
[./euler_angle_file]
type = EulerAngleFileReader
file_name = test.tex
[../]
[]
[Postprocessors]
[./gr0_area]
type = ElementIntegralVariablePostprocessor
variable = gr0
[../]
[]
[Preconditioning]
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
solve_type = 'NEWTON'
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart -pc_hypre_boomeramg_strong_threshold'
petsc_options_value = 'hypre boomeramg 31 0.7'
l_max_its = 30
l_tol = 1e-4
nl_max_its = 30
nl_rel_tol = 1e-9
start_time = 0.0
num_steps = 3
dt = 0.2
[]
[Outputs]
execute_on = 'initial timestep_end'
exodus = true
perf_graph = true
[]
(modules/phase_field/test/tests/grain_growth/voronoi_columnar_3D.i)
[Mesh]
type = GeneratedMesh
dim = 3
nx = 40
ny = 40
nz = 1
xmin = 0
xmax = 1000
ymin = 0
ymax = 1000
zmin = 0
zmax = 25
elem_type = HEX8
[]
[GlobalParams]
op_num = 4
var_name_base = gr
[]
[Variables]
[./PolycrystalVariables]
[../]
[]
[UserObjects]
[./voronoi]
type = PolycrystalVoronoi
rand_seed = 47
grain_num = 4
columnar_3D = true
coloring_algorithm = bt
[../]
[]
[ICs]
[./PolycrystalICs]
[./PolycrystalColoringIC]
polycrystal_ic_uo = voronoi
[../]
[../]
[]
[AuxVariables]
[./bnds]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
[./PolycrystalKernel]
[../]
[]
[AuxKernels]
[./BndsCalc]
type = BndsCalcAux
variable = bnds
execute_on = timestep_end
[../]
[]
[BCs]
[./Periodic]
[./All]
auto_direction = 'x y'
[../]
[../]
[]
[Materials]
[./Copper]
type = GBEvolution
T = 500 # K
wGB = 60 # nm
GBmob0 = 2.5e-6 #m^4/(Js) from Schoenfelder 1997
Q = 0.23 #Migration energy in eV
GBenergy = 0.708 #GB energy in J/m^2
[../]
[]
[Postprocessors]
active = ''
[./ngrains]
type = FeatureFloodCount
variable = bnds
threshold = 0.7
[../]
[]
[Executioner]
type = Transient
scheme = 'bdf2'
solve_type = 'PJFNK'
petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart'
petsc_options_value = 'hypre boomeramg 31'
l_tol = 1.0e-5
l_max_its = 15
nl_max_its = 20
nl_rel_tol = 1.0e-10
start_time = 0.0
num_steps = 1
dt = 40.0
[]
[Outputs]
exodus = true
[]