- flood_counterThe FeatureFloodCount UserObject to get values from.
C++ Type:UserObjectName
Controllable:No
Description:The FeatureFloodCount UserObject to get values from.
- variableThe name of the variable that this object applies to
C++ Type:AuxVariableName
Unit:(no unit assumed)
Controllable:No
Description:The name of the variable that this object applies to
FeatureFloodCountAux
buildconstruction:Undocumented Class
The FeatureFloodCountAux has not been documented. The content listed below should be used as a starting point for documenting the class, which includes the typical automatic documentation associated with a MooseObject; however, what is contained is ultimately determined by what is necessary to make the documentation clear for users.
Feature detection by connectivity analysis
Overview
Example Input File Syntax
Input Parameters
- blockThe list of blocks (ids or names) that this object will be applied
C++ Type:std::vector<SubdomainName>
Controllable:No
Description:The list of blocks (ids or names) that this object will be applied
- boundaryThe list of boundaries (ids or names) from the mesh where this object applies
C++ Type:std::vector<BoundaryName>
Controllable:No
Description:The list of boundaries (ids or names) from the mesh where this object 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
Controllable:No
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_onINITIAL TIMESTEP_ENDThe list of flag(s) indicating when this object should be executed. For a description of each flag, see https://mooseframework.inl.gov/source/interfaces/SetupInterface.html.
Default:INITIAL TIMESTEP_END
C++ Type:ExecFlagEnum
Options:XFEM_MARK, FORWARD, ADJOINT, HOMOGENEOUS_FORWARD, ADJOINT_TIMESTEP_BEGIN, ADJOINT_TIMESTEP_END, NONE, INITIAL, LINEAR, LINEAR_CONVERGENCE, NONLINEAR, NONLINEAR_CONVERGENCE, POSTCHECK, TIMESTEP_END, TIMESTEP_BEGIN, MULTIAPP_FIXED_POINT_END, MULTIAPP_FIXED_POINT_BEGIN, MULTIAPP_FIXED_POINT_CONVERGENCE, FINAL, CUSTOM, PRE_DISPLACE
Controllable:No
Description:The list of flag(s) indicating when this object should be executed. For a description of each flag, see https://mooseframework.inl.gov/source/interfaces/SetupInterface.html.
- field_displayUNIQUE_REGIONDetermines how the auxilary field should be colored. (UNIQUE_REGION and VARIABLE_COLORING are nodal, CENTROID is elemental, default: UNIQUE_REGION)
Default:UNIQUE_REGION
C++ Type:MooseEnum
Options:UNIQUE_REGION, VARIABLE_COLORING, GHOSTED_ENTITIES, HALOS, CENTROID, ACTIVE_BOUNDS, INTERSECTS_SPECIFIED_BOUNDARY
Controllable:No
Description:Determines how the auxilary field should be colored. (UNIQUE_REGION and VARIABLE_COLORING are nodal, CENTROID is elemental, default: UNIQUE_REGION)
- map_indexThe index of which map to retrieve values from when using FeatureFloodCount with multiple maps.
C++ Type:unsigned int
Controllable:No
Description:The index of which map to retrieve values from when using FeatureFloodCount with multiple maps.
Optional Parameters
- control_tagsAdds user-defined labels for accessing object parameters via control logic.
C++ Type:std::vector<std::string>
Controllable:No
Description:Adds user-defined labels for accessing object parameters via control logic.
- enableTrueSet the enabled status of the MooseObject.
Default:True
C++ Type:bool
Controllable:Yes
Description:Set the enabled status of the MooseObject.
- search_methodnearest_node_connected_sidesChoice of search algorithm. All options begin by finding the nearest node in the primary boundary to a query point in the secondary boundary. In the default nearest_node_connected_sides algorithm, primary boundary elements are searched iff that nearest node is one of their nodes. This is fast to determine via a pregenerated node-to-elem map and is robust on conforming meshes. In the optional all_proximate_sides algorithm, primary boundary elements are searched iff they touch that nearest node, even if they are not topologically connected to it. This is more CPU-intensive but is necessary for robustness on any boundary surfaces which has disconnections (such as Flex IGA meshes) or non-conformity (such as hanging nodes in adaptively h-refined meshes).
Default:nearest_node_connected_sides
C++ Type:MooseEnum
Options:nearest_node_connected_sides, all_proximate_sides
Controllable:No
Description:Choice of search algorithm. All options begin by finding the nearest node in the primary boundary to a query point in the secondary boundary. In the default nearest_node_connected_sides algorithm, primary boundary elements are searched iff that nearest node is one of their nodes. This is fast to determine via a pregenerated node-to-elem map and is robust on conforming meshes. In the optional all_proximate_sides algorithm, primary boundary elements are searched iff they touch that nearest node, even if they are not topologically connected to it. This is more CPU-intensive but is necessary for robustness on any boundary surfaces which has disconnections (such as Flex IGA meshes) or non-conformity (such as hanging nodes in adaptively h-refined meshes).
- seed0The seed for the master random number generator
Default:0
C++ Type:unsigned int
Controllable:No
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
Controllable:No
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
- prop_getter_suffixAn optional suffix parameter that can be appended to any attempt to retrieve/get material properties. The suffix will be prepended with a '_' character.
C++ Type:MaterialPropertyName
Unit:(no unit assumed)
Controllable:No
Description:An optional suffix parameter that can be appended to any attempt to retrieve/get material properties. The suffix will be prepended with a '_' character.
- use_interpolated_stateFalseFor the old and older state use projected material properties interpolated at the quadrature points. To set up projection use the ProjectedStatefulMaterialStorageAction.
Default:False
C++ Type:bool
Controllable:No
Description:For the old and older state use projected material properties interpolated at the quadrature points. To set up projection use the ProjectedStatefulMaterialStorageAction.
Material Property Retrieval Parameters
Input Files
- (modules/phase_field/test/tests/flood_counter_aux_test/flood_aux.i)
- (modules/phase_field/test/tests/reconstruction/2phase_reconstruction4.i)
- (modules/phase_field/test/tests/flood_counter_aux_test/simple.i)
- (modules/combined/examples/phase_field-mechanics/poly_grain_growth_2D_eldrforce.i)
- (modules/phase_field/test/tests/initial_conditions/polycrystalcircles_clipped.i)
- (modules/combined/examples/phase_field-mechanics/grain_texture.i)
- (modules/combined/examples/phase_field-mechanics/EBSD_reconstruction_grain_growth_mech.i)
- (modules/phase_field/test/tests/feature_volume_vpp_test/boundary_area_2D_single.i)
- (modules/phase_field/test/tests/GBType/GB_Type_Phase1.i)
- (modules/phase_field/examples/grain_growth/grain_growth_3D.i)
- (modules/combined/test/tests/grain_texture/EulerAngleProvider2RGBAux_bicrystal.i)
- (modules/phase_field/test/tests/flood_counter_aux_test/boundary_intersection.i)
- (modules/phase_field/test/tests/grain_tracker_test/grain_tracker_volume_changing.i)
- (modules/phase_field/test/tests/grain_tracker_test/one_grain.i)
- (modules/phase_field/examples/grain_growth/grain_growth_linearized_interface.i)
- (modules/phase_field/test/tests/flood_counter_aux_test/flood_aux_elemental.i)
- (modules/phase_field/test/tests/grain_tracker_test/grain_halo_over_bc.i)
- (modules/phase_field/test/tests/MultiSmoothCircleIC/test_problem.i)
- (modules/combined/examples/phase_field-mechanics/hex_grain_growth_2D_eldrforce.i)
- (modules/phase_field/test/tests/grain_tracker_test/grain_tracker_nodal.i)
- (modules/combined/test/tests/grain_texture/EulerAngle2RGBAction.i)
- (modules/phase_field/test/tests/rigidbodymotion/update_orientation.i)
- (modules/phase_field/examples/ebsd_reconstruction/IN100-111grn.i)
- (modules/phase_field/test/tests/rigidbodymotion/grain_motion_fauxGT.i)
- (modules/combined/test/tests/grain_texture/random_grain_orientation.i)
- (modules/phase_field/test/tests/rigidbodymotion/grain_motion2.i)
- (modules/combined/test/tests/grain_texture/grain_texture_test_2.i)
- (modules/phase_field/examples/rigidbodymotion/grain_motion_GT.i)
- (modules/phase_field/test/tests/feature_volume_vpp_test/percolation_test.i)
- (modules/phase_field/test/tests/rigidbodymotion/grain_forcedensity.i)
- (modules/phase_field/test/tests/flood_counter_aux_test/nodal_flood_periodic_2var.i)
- (modules/phase_field/test/tests/feature_volume_vpp_test/boundary_area_2D.i)
- (modules/phase_field/test/tests/reconstruction/euler2rgb_no_grain_region.i)
- (modules/phase_field/test/tests/grain_tracker_test/grain_tracker_ebsd.i)
- (modules/phase_field/test/tests/rigidbodymotion/polycrystal_action.i)
- (modules/phase_field/test/tests/feature_flood_test/parallel_feature_count.i)
- (modules/combined/test/tests/grain_texture/grain_texture_test_1.i)
- (modules/phase_field/test/tests/rigidbodymotion/update_orientation_verify.i)
- (modules/phase_field/test/tests/boundary_intersecting_features/boundary_intersecting_features.i)
- (modules/phase_field/examples/grain_growth/grain_growth_2D_graintracker.i)
- (modules/phase_field/examples/grain_growth/3D_6000_gr.i)
- (modules/phase_field/test/tests/grain_tracker_test/distributed_poly_ic.i)
- (modules/phase_field/test/tests/reconstruction/1phase_reconstruction.i)
- (modules/phase_field/test/tests/grain_tracker_test/split_grain.i)
- (modules/phase_field/test/tests/grain_tracker_test/grain_tracker_remapping_test.i)
- (modules/phase_field/examples/grain_growth/grain_growth_2D_random.i)
- (modules/phase_field/test/tests/grain_tracker_test/grain_tracker_test_elemental.i)
- (modules/phase_field/test/tests/flood_counter_aux_test/flood_counter_boundary_restrictable.i)
- (modules/phase_field/test/tests/grain_tracker_test/grain_tracker_advanced_op.i)
- (modules/combined/test/tests/ACGrGrElasticDrivingForce/bicrystal.i)
(modules/phase_field/test/tests/flood_counter_aux_test/flood_aux.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 50
ny = 50
nz = 0
xmax = 40
ymax = 40
zmax = 0
elem_type = QUAD4
[]
[Variables]
[./u]
order = FIRST
family = LAGRANGE
[../]
[]
[AuxVariables]
[./bubble_map]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
active = 'diff forcing_1 forcing_2 forcing_3 forcing_4 dot'
[./diff]
type = Diffusion
variable = u
[../]
[./forcing_1]
type = GaussContForcing
variable = u
x_center = 1.0
y_center = 1.0
x_spread = 0.5
y_spread = 0.5
[../]
[./forcing_2]
type = GaussContForcing
variable = u
x_center = 20.0
y_center = 39.0
x_spread = 0.5
y_spread = 0.5
[../]
[./forcing_3]
type = GaussContForcing
variable = u
x_center = 39.0
y_center = 20.0
x_spread = 0.5
y_spread = 0.5
[../]
[./forcing_4]
type = GaussContForcing
variable = u
x_center = 15.0
y_center = 15.0
x_spread = 0.5
y_spread = 0.5
[../]
[./dot]
type = TimeDerivative
variable = u
[../]
[]
[AuxKernels]
[./mapper]
type = FeatureFloodCountAux
variable = bubble_map
execute_on = timestep_end
flood_counter = bubbles
[../]
[]
[BCs]
[./Periodic]
[./x]
variable = u
auto_direction = 'x y'
[../]
[../]
[]
[UserObjects]
[./bubbles]
type = FeatureFloodCount
variable = u
threshold = 0.3
execute_on = timestep_end
outputs = none
flood_entity_type = NODAL
[../]
[]
[Executioner]
active = ''
type = Transient
dt = 4.0
num_steps = 5
[./Adaptivity]
refine_fraction = .40
coarsen_fraction = .02
max_h_level = 3
error_estimator = KellyErrorEstimator
[../]
[]
[Outputs]
execute_on = 'timestep_end'
file_base = out
exodus = true
[]
(modules/phase_field/test/tests/reconstruction/2phase_reconstruction4.i)
#
# In this test we set the initial condition of a set of order parameters
# by pulling out the only grains from given EBSD data file that belong to a specified phase
#
[Problem]
type = FEProblem
solve = false
kernel_coverage_check = false
[]
[Mesh]
[ebsd_mesh]
type = EBSDMeshGenerator
filename = ebsd_40x40_2_phase.txt
[]
[]
[GlobalParams]
op_num = 6
var_name_base = gr
[]
[UserObjects]
[ebsd_reader]
type = EBSDReader
[]
[ebsd]
type = PolycrystalEBSD
coloring_algorithm = bt
ebsd_reader = ebsd_reader
phase = 2
output_adjacency_matrix = true
[]
[grain_tracker]
type = GrainTracker
polycrystal_ic_uo = ebsd
remap_grains = false
[]
[]
[AuxVariables]
[var_indices]
family = MONOMIAL
order = CONSTANT
[]
[]
[AuxKernels]
[var_indices]
type = FeatureFloodCountAux
variable = var_indices
flood_counter = grain_tracker
field_display = VARIABLE_COLORING
[]
[]
[ICs]
[PolycrystalICs]
[PolycrystalColoringIC]
polycrystal_ic_uo = ebsd
[]
[]
[]
[Variables]
[PolycrystalVariables]
[]
[]
[Executioner]
type = Transient
num_steps = 0
[]
[Outputs]
exodus = true
[]
(modules/phase_field/test/tests/flood_counter_aux_test/simple.i)
[Mesh]
file = square_nodes.e
uniform_refine = 0
[]
[Variables]
[./u]
order = FIRST
family = LAGRANGE
[../]
[./v]
order = FIRST
family = LAGRANGE
[../]
[]
[AuxVariables]
[./bubble_map0]
order = FIRST
family = LAGRANGE
[../]
[./bubble_map1]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
[./diff]
type = Diffusion
variable = u
[../]
[./diffv]
type = Diffusion
variable = v
[../]
[]
[AuxKernels]
[./mapper0]
type = FeatureFloodCountAux
variable = bubble_map0
execute_on = timestep_end
flood_counter = bubbles
map_index = 0
[../]
[./mapper1]
type = FeatureFloodCountAux
variable = bubble_map1
execute_on = timestep_end
flood_counter = bubbles
map_index = 1
[../]
[]
[BCs]
[./bott_left]
type = DirichletBC
variable = u
boundary = 1
value = 1
[../]
[./bott_right]
type = DirichletBC
variable = v
boundary = 2
value = 1
[../]
[./up_right]
type = DirichletBC
variable = u
boundary = 3
value = 1
[../]
[./up_left]
type = DirichletBC
variable = v
boundary = 4
value = 1
[../]
[./the_rest_u]
type = DirichletBC
variable = u
boundary = '5 6 7 8'
value = 0
[../]
[./the_rest_v]
type = DirichletBC
variable = v
boundary = '5 6 7 8'
value = 0
[../]
[]
[UserObjects]
[./bubbles]
use_single_map = false
type = FeatureFloodCount
variable = 'u v'
threshold = 0.3
execute_on = timestep_end
outputs = none
flood_entity_type = NODAL
[../]
[]
[Executioner]
type = Steady
[]
[Outputs]
execute_on = 'timestep_end'
exodus = true
[]
(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/test/tests/initial_conditions/polycrystalcircles_clipped.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 100
ny = 56
nz = 0
xmin = 80
xmax = 200
ymin = 0
ymax = 112
zmin = 0
zmax = 0
[]
[GlobalParams]
op_num = 6
var_name_base = gr
[]
[Variables]
[PolycrystalVariables]
[]
[]
[AuxVariables]
[unique_grains]
order = CONSTANT
family = MONOMIAL
[]
[var_indices]
order = CONSTANT
family = MONOMIAL
[]
[]
[AuxKernels]
[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'
[]
[]
[UserObjects]
[circle_IC]
type = PolycrystalCircles
file_name = 'circles.txt'
read_from_file = true
execute_on = 'initial'
int_width = 2
[]
[grain_tracker]
type = GrainTracker
remap_grains = true
compute_halo_maps = false
polycrystal_ic_uo = circle_IC
[]
[]
[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
[]
[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = PJFNK
num_steps = 0
[]
[Outputs]
exodus = true
csv = false
[]
(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/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 = NumElements
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/feature_volume_vpp_test/boundary_area_2D_single.i)
[Mesh]
[gen]
type = GeneratedMeshGenerator
dim = 2
nx = 50
ny = 50
xmin = 0
xmax = 50
ymin = 0
ymax = 50
elem_type = QUAD4
[]
[./left_side]
input = gen
type = SubdomainBoundingBoxGenerator
block_id = 1
bottom_left = '0 0 0'
top_right = '24.9 50 0'
[../]
[./right_side]
input = left_side
type = SubdomainBoundingBoxGenerator
block_id = 2
bottom_left = '25.1 0 0'
top_right = '50 50 0'
[../]
[./iface_u]
type = SideSetsBetweenSubdomainsGenerator
primary_block = 1
paired_block = 2
new_boundary = 10
input = right_side
[../]
[]
[Variables]
[./c]
order = FIRST
family = LAGRANGE
[]
[]
[AuxVariables]
[./unique_regions]
family = MONOMIAL
order = CONSTANT
[../]
[]
[ICs]
[./c]
type = SpecifiedSmoothCircleIC
variable = c
invalue = 1.0
outvalue = 0.0
radii = '4 5 10'
x_positions = '25 25 25'
y_positions = '37.5 25 0'
z_positions = '0 0 0'
int_width = 2.0
[]
[]
[Postprocessors]
[./flood_count]
type = FeatureFloodCount
variable = c
# Must be turned on to build data structures necessary for FeatureVolumeVPP
compute_var_to_feature_map = true
threshold = 0.5
execute_on = INITIAL
[../]
[]
[VectorPostprocessors]
[./features]
type = FeatureVolumeVectorPostprocessor
flood_counter = flood_count
# Turn on centroid output
output_centroids = true
execute_on = INITIAL
boundary = 10
single_feature_per_element = true
[../]
[]
[Kernels]
[diff]
type = Diffusion
variable = c
[]
[]
[AuxKernels]
[./unique_regions]
type = FeatureFloodCountAux
variable = unique_regions
flood_counter = flood_count
field_display = UNIQUE_REGION
[../]
[]
[Problem]
solve = false
[]
[Executioner]
type = Steady
[]
[Outputs]
csv = true
execute_on = INITIAL
[]
(modules/phase_field/test/tests/GBType/GB_Type_Phase1.i)
# MOOSE input file
# Written by Pierre-Clement Simon - Idaho National Laboratory
#
# Project:
# TRISO fuel fission gas transport: Silver diffusion in silicon carbide
#
# Published with:
# ---
#
# Phase Field Model: Isotropic diffusion equation
# type: Transient
# Grain structure: Single grain
# BCs: Fixed value on the right, flux on the left
#
#
# Info:
# - Input file used to generate polycrystals for SiC
#
# Updates from previous file:
# -
#
# Units
# length: --
# time: --
# energy: --
# quantity: --
# 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]
[ebsd_mesh]
type = EBSDMeshGenerator
# Two Parallel Grains
filename = 'EBSD_ThreeGrains.txt'
[]
[]
[GlobalParams]
# Parameters used by several kernels that are defined globally to simplify input file
op_num = 6 # Number of grains
var_name_base = gr # Base name of grains
[]
[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
threshold = 0.001
connecting_threshold = 0.008
compute_var_to_feature_map = true
compute_halo_maps = true # For displaying HALO fields
remap_grains = true
polycrystal_ic_uo = ebsd
[]
[]
[ICs]
[PolycrystalICs]
[PolycrystalColoringIC]
polycrystal_ic_uo = ebsd
[]
[]
[]
[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
[../]
[./unique_grains]
order = CONSTANT
family = MONOMIAL
[../]
[./aphi1]
order = CONSTANT
family = MONOMIAL
[../]
[./bPhi]
order = CONSTANT
family = MONOMIAL
[../]
[./cphi2]
order = CONSTANT
family = MONOMIAL
[../]
[./ebsd_numbers]
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'
[../]
# generate the unique ID from grain_tracker
[./unique_grains]
type = FeatureFloodCountAux
variable = unique_grains
execute_on = 'initial timestep_end'
flood_counter = grain_tracker
field_display = UNIQUE_REGION
[../]
# The phi will output the Euler angle from EBSD data, and the data structure
# will change with the guide from grain_tracker
[./aphi1]
type = OutputEulerAngles
variable = aphi1
euler_angle_provider = ebsd_reader
grain_tracker = grain_tracker
output_euler_angle = 'phi1'
execute_on = 'INITIAL TIMESTEP_END'
[../]
[./bPhi]
type = OutputEulerAngles
variable = bPhi
euler_angle_provider = ebsd_reader
grain_tracker = grain_tracker
output_euler_angle = 'Phi'
execute_on = 'INITIAL TIMESTEP_END'
[../]
[./cphi2]
type = OutputEulerAngles
variable = cphi2
euler_angle_provider = ebsd_reader
grain_tracker = grain_tracker
output_euler_angle = 'phi2'
execute_on = 'INITIAL TIMESTEP_END'
[../]
# Import the unique grain ID from ebsd data, and the data structure
# will change with the guide from grain_tracker
[ebsd_numbers]
type = EBSDReaderAvgDataAux
data_name = feature_id
ebsd_reader = ebsd_reader
grain_tracker = grain_tracker
variable = ebsd_numbers
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 # Quantitative material properties for copper grain growth. Dimensions are nm and ns
GBmob0 = 2.5e-6 # Mobility prefactor for Cu from schonfelder1997molecular bibtex entry
GBenergy = 0.708 # GB energy for Cu from schonfelder1997molecular bibtex entry
Q = 0.23 # Activation energy for grain growth from Schonfelder 1997
T = 450 # Constant temperature of the simulation (for mobility calculation)
wGB = 6 # Width of the diffuse GB
[../]
[./GB_type]
# The new developed Miso Bnds Aux Kernel
type = ComputeGBMisorientationType
ebsd_reader = ebsd_reader
grain_tracker = grain_tracker
output_properties = 'gb_type'
outputs = exodus
[../]
[]
[Postprocessors]
# Scalar postprocessors
[./dt]
# Outputs the current time step
type = TimestepSize
[../]
[n_elements]
type = NumElements
execute_on = 'initial timestep_end'
[]
[n_nodes]
type = NumNodes
execute_on = 'initial timestep_end'
[]
[DOFs]
type = NumDOFs
[]
[]
[Adaptivity]
initial_steps = 1
max_h_level = 1
marker = combined
[./Indicators]
[./error]
type = GradientJumpIndicator
variable = bnds
[../]
[../]
[./Markers]
[./bound_adapt]
type = ValueThresholdMarker
third_state = DO_NOTHING
coarsen = 0.999 #1.0
refine = 0.95 #0.95
variable = bnds
invert = true
[../]
[./errorfrac]
type = ErrorFractionMarker
coarsen = 0.1
indicator = error
refine = 0.7
[../]
[./combined]
type = ComboMarker
markers = 'bound_adapt errorfrac'
[../]
[../]
[]
[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 -pc_hypre_boomeramg_strong_threshold'
petsc_options_value = ' hypre boomeramg 0.7'
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 = IterationAdaptiveDT
cutback_factor = 0.9
dt = 1
growth_factor = 1.1
optimal_iterations = 7
[]
start_time = 0.0
num_steps = 2
[]
[Outputs]
perf_graph = true
exodus = true
[./console]
type = Console
max_rows = 10
[../]
[]
(modules/phase_field/examples/grain_growth/grain_growth_3D.i)
# This simulation predicts GB migration of a 3D copper polycrystal with 25 grains represented with 15 order parameters
# 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
xmax = 1000 # maximum x-coordinate of the mesh
ymax = 1000 # maximum y-coordinate of the mesh
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
[]
[Modules]
[PhaseField]
[GrainGrowth]
family = LAGRANGE
order = FIRST
[]
[]
[]
[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
[unique_grains]
[]
[var_indices]
[]
[ghost_regions]
[]
[halos]
[]
[halo0]
[]
[halo1]
[]
[halo2]
[]
[halo3]
[]
[halo4]
[]
[halo5]
[]
[halo6]
[]
[halo7]
[]
[halo8]
[]
[halo9]
[]
[halo10]
[]
[halo11]
[]
[halo12]
[]
[halo13]
[]
[halo14]
[]
[proc]
[]
[]
[AuxKernels]
# AuxKernel block, defining the equations used to calculate the auxvars
[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 schonfelder1997molecular bibtex entry
Q = 0.23 #eV for copper from schonfelder1997molecular bibtex entry
GBenergy = 0.708 #J/m^2 from schonfelder1997molecular bibtex entry
[]
[]
[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 = 20 # Max number of nonlinear iterations
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
[]
[]
[Outputs]
exodus = true
csv = true
[pg]
type = PerfGraphOutput
execute_on = 'initial final' # Default is "final"
level = 2 # Default is 1
[]
[]
(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/flood_counter_aux_test/boundary_intersection.i)
[Mesh]
[gen]
type = GeneratedMeshGenerator
dim = 2
nx = 10
ny = 50
xmax = 10
ymax = 50
[]
[]
[Variables]
[u]
[]
[]
[AuxVariables]
[v]
order = CONSTANT
family = MONOMIAL
[]
[pid]
[]
[]
[Kernels]
[diff]
type = Diffusion
variable = u
[]
[dot]
type = TimeDerivative
variable = u
[]
[]
[AuxKernels]
[intersect]
type = FeatureFloodCountAux
variable = v
flood_counter = intersection
field_display = INTERSECTS_SPECIFIED_BOUNDARY
execute_on = 'initial timestep_end'
[]
[pid]
type = ProcessorIDAux
variable = pid
[]
[]
[ICs]
[v]
type = BoundingBoxIC
variable = u
inside = 1
outside = 0
x1 = 3
x2 = 7
y1 = 0
y2 = 45
[]
[]
[Postprocessors]
[intersection]
type = FeatureFloodCount
variable = u
threshold = 0.3
specified_boundaries = bottom
compute_var_to_feature_map = true
execute_on = 'initial timestep_end'
[]
[vint]
type = ElementIntegralVariablePostprocessor
variable = v
[]
[]
[Executioner]
type = Transient
dt = 0.01
num_steps = 2
[]
[Outputs]
execute_on = 'timestep_end'
csv = 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 schonfelder1997molecular bibtex entry
Q = 0.23 # eV for copper from schonfelder1997molecular bibtex entry
GBenergy = 0.708 # J/m^2 from schonfelder1997molecular bibtex entry
[../]
[]
[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/test/tests/grain_tracker_test/one_grain.i)
[Mesh]
type = GeneratedMesh
dim = 2 # Problem dimension
nx = 4
ny = 4
[]
[Variables]
[u]
order = FIRST
family = LAGRANGE
initial_condition = 1.0
[]
[]
[AuxVariables]
[halos]
order = CONSTANT
family = MONOMIAL
[]
[]
[AuxKernels]
[halos]
type = FeatureFloodCountAux
variable = halos
flood_counter = grain_tracker
field_display = HALOS
execute_on = 'initial timestep_end'
[]
[]
[UserObjects]
[grain_tracker]
type = GrainTracker
variable = 'u'
compute_halo_maps = true # For displaying HALO fields
execute_on = 'initial timestep_end'
verbosity_level = 3
[]
[]
[Executioner]
type = Transient
num_steps = 2
[]
[Outputs]
csv = true
[]
[Problem]
solve = false
[]
(modules/phase_field/examples/grain_growth/grain_growth_linearized_interface.i)
[GlobalParams]
bound_value = 5.0
op_num = 8
var_name_base = phi
[]
[Mesh]
type = GeneratedMesh
dim = 2
xmax = 1000
ymax = 1000
nx = 100
ny = 100
uniform_refine = 1
[]
[Modules]
[PhaseField]
[GrainGrowthLinearizedInterface]
op_name_base = gr
mobility = L
kappa = kappa_op
[]
[]
[]
[ICs]
[PolycrystalICs]
[PolycrystalColoringIC]
polycrystal_ic_uo = RandomVoronoi
nonlinear_preconditioning = true
[]
[]
[]
[UserObjects]
[RandomVoronoi]
type = PolycrystalVoronoi
grain_num = 60
int_width = 10
rand_seed = 103838
[]
[grain_tracker]
type = GrainTracker
threshold = -4.0
compute_halo_maps = true # Only necessary for displaying HALOS
[]
[]
[AuxVariables]
[unique_grains]
order = CONSTANT
family = MONOMIAL
[]
[var_indices]
order = CONSTANT
family = MONOMIAL
[]
[halos]
order = CONSTANT
family = MONOMIAL
[]
[]
[AuxKernels]
[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'
[]
[halos]
type = FeatureFloodCountAux
variable = halos
flood_counter = grain_tracker
field_display = HALOS
execute_on = 'initial timestep_end'
[]
[]
[Materials]
[properties]
type = GenericConstantMaterial
prop_names = 'gbmob gbenergy gbwidth gamma_asymm'
prop_values = '100 6 10 1.5'
[]
[kappa_op]
type = ParsedMaterial
material_property_names = 'gbenergy gbwidth'
property_name = kappa_op
expression = '3/4*gbenergy*gbwidth'
[]
[L]
type = ParsedMaterial
material_property_names = 'gbmob gbwidth'
property_name = L
expression = '4/3*gbmob/gbwidth'
[]
[mu]
type = ParsedMaterial
material_property_names = 'gbenergy gbwidth'
property_name = mu
expression = '6*gbenergy/gbwidth'
[]
[]
[Postprocessors]
[dt]
type = TimestepSize
execute_on = 'initial TIMESTEP_END'
[]
[]
[BCs]
[Periodic]
[All]
auto_direction = 'x y'
[]
[]
[]
[Executioner]
type = Transient
scheme = bdf2
solve_type = PJFNK
petsc_options_iname = '-pc_type -pc_hypre_type -snes_type'
petsc_options_value = 'hypre boomeramg vinewtonrsls'
l_tol = 1e-4
nl_max_its = 10
l_max_its = 45
[TimeStepper]
type = IterationAdaptiveDT
dt = 0.02
optimal_iterations = 6
[]
end_time = 30
[]
[Outputs]
exodus = true
perf_graph = true
[]
(modules/phase_field/test/tests/flood_counter_aux_test/flood_aux_elemental.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 50
ny = 50
nz = 0
xmax = 40
ymax = 40
zmax = 0
elem_type = QUAD4
[]
[Variables]
[./u]
order = FIRST
family = LAGRANGE
[../]
[]
[AuxVariables]
[./bubble_map]
order = CONSTANT
family = MONOMIAL
[../]
[]
[Kernels]
active = 'diff forcing_1 forcing_2 forcing_3 forcing_4 dot'
[./diff]
type = Diffusion
variable = u
[../]
[./forcing_1]
type = GaussContForcing
variable = u
x_center = 1.0
y_center = 1.0
x_spread = 0.5
y_spread = 0.5
amplitude = 2.0
[../]
[./forcing_2]
type = GaussContForcing
variable = u
x_center = 20.0
y_center = 39.0
x_spread = 0.5
y_spread = 0.5
amplitude = 2.0
[../]
[./forcing_3]
type = GaussContForcing
variable = u
x_center = 39.0
y_center = 20.0
x_spread = 0.5
y_spread = 0.5
amplitude = 2.0
[../]
[./forcing_4]
type = GaussContForcing
variable = u
x_center = 15.0
y_center = 15.0
x_spread = 0.5
y_spread = 0.5
amplitude = 2.0
[../]
[./dot]
type = TimeDerivative
variable = u
[../]
[]
[AuxKernels]
[./mapper]
type = FeatureFloodCountAux
variable = bubble_map
execute_on = timestep_end
flood_counter = bubbles
[../]
[]
[BCs]
[./Periodic]
[./x]
variable = u
auto_direction = 'x y'
[../]
[../]
[]
[Postprocessors]
[./bubbles]
type = FeatureFloodCount
variable = u
threshold = 0.3
execute_on = timestep_end
[../]
[]
[Executioner]
active = ''
type = Transient
dt = 4.0
num_steps = 5
# [./Adaptivity]
# refine_fraction = .40
# coarsen_fraction = .02
# max_h_level = 3
# error_estimator = KellyErrorEstimator
# [../]
[]
[Outputs]
execute_on = 'timestep_end'
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-11
dt = 25
num_steps = 1
[]
[Outputs]
exodus = true # Exodus file will be outputted
[]
(modules/phase_field/test/tests/MultiSmoothCircleIC/test_problem.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 20
ny = 20
xmin = 0
xmax = 50
ymin = 0
ymax = 50
elem_type = QUAD4
[]
[Variables]
[./c]
order = FIRST
family = LAGRANGE
[../]
[]
[AuxVariables]
[./features]
order = CONSTANT
family = MONOMIAL
[../]
[./ghosts]
order = CONSTANT
family = MONOMIAL
[../]
[./halos]
order = CONSTANT
family = MONOMIAL
[../]
[./proc_id]
order = CONSTANT
family = MONOMIAL
[../]
[]
[ICs]
[./c]
type = LatticeSmoothCircleIC
variable = c
invalue = 1.0
outvalue = 0.0001
circles_per_side = '2 2'
pos_variation = 10.0
radius = 8.0
int_width = 5.0
radius_variation_type = uniform
avoid_bounds = false
[../]
[]
[BCs]
[./Periodic]
[./c]
variable = c
auto_direction = 'x y'
[../]
[../]
[]
[Kernels]
[./diff]
type = Diffusion
variable = c
[../]
[]
[AuxKernels]
[./features]
type = FeatureFloodCountAux
variable = features
execute_on = 'initial timestep_end'
flood_counter = features
[../]
[./ghosts]
type = FeatureFloodCountAux
variable = ghosts
field_display = GHOSTED_ENTITIES
execute_on = 'initial timestep_end'
flood_counter = features
[../]
[./halos]
type = FeatureFloodCountAux
variable = halos
field_display = HALOS
execute_on = 'initial timestep_end'
flood_counter = features
[../]
[./proc_id]
type = ProcessorIDAux
variable = proc_id
execute_on = 'initial timestep_end'
[../]
[]
[Postprocessors]
[./features]
type = FeatureFloodCount
variable = c
flood_entity_type = ELEMENTAL
execute_on = 'initial timestep_end'
[../]
[]
[Problem]
type = FEProblem
solve = false
[]
[Executioner]
type = Steady
[]
[Outputs]
exodus = 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/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/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/rigidbodymotion/update_orientation.i)
# test file for applyting advection term and observing rigid body motion of grains
[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
[../]
[./w]
order = FIRST
family = LAGRANGE
[../]
[./eta]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
[./c_res]
type = SplitCHParsed
variable = c
f_name = F
kappa_name = kappa_c
w = w
coupled_variables = eta
[../]
[./w_res]
type = SplitCHWRes
variable = w
mob_name = M
[../]
[./time]
type = CoupledTimeDerivative
variable = w
v = c
[../]
[./motion]
type = MultiGrainRigidBodyMotion
variable = w
c = c
v = eta
grain_tracker_object = grain_center
grain_force = grain_force
grain_volumes = grain_volumes
[../]
[./eta_dot]
type = TimeDerivative
variable = eta
[../]
[./vadv_eta]
type = SingleGrainRigidBodyMotion
variable = eta
c = c
v = eta
grain_tracker_object = grain_center
grain_force = grain_force
grain_volumes = grain_volumes
[../]
[./acint_eta]
type = ACInterface
variable = eta
mob_name = M
coupled_variables = c
kappa_name = kappa_eta
[../]
[./acbulk_eta]
type = AllenCahn
variable = eta
mob_name = M
f_name = F
coupled_variables = c
[../]
[]
[Materials]
[./pfmobility]
type = GenericConstantMaterial
prop_names = 'M kappa_c kappa_eta'
prop_values = '5.0 2.0 0.1'
[../]
[./free_energy]
type = DerivativeParsedMaterial
coupled_variables = 'c eta'
constant_names = 'barr_height cv_eq'
constant_expressions = '0.1 1.0e-2'
expression = 16*barr_height*(c-cv_eq)^2*(1-cv_eq-c)^2+(c-eta)^2
derivative_order = 2
[../]
[]
[AuxVariables]
[./unique_grains]
order = CONSTANT
family = MONOMIAL
[../]
[./var_indices]
order = CONSTANT
family = MONOMIAL
[../]
[./centroids]
order = CONSTANT
family = MONOMIAL
[../]
[./vadv_x]
order = CONSTANT
family = MONOMIAL
[../]
[./vadv_y]
order = CONSTANT
family = MONOMIAL
[../]
[./angle_initial]
order = CONSTANT
family = MONOMIAL
[../]
[./euler_angle]
order = CONSTANT
family = MONOMIAL
[../]
[]
[AuxKernels]
[./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
[../]
[./vadv_x]
type = GrainAdvectionAux
grain_force = grain_force
grain_volumes = grain_volumes
grain_tracker_object = grain_center
execute_on = timestep_begin
component = x
variable = vadv_x
[../]
[./vadv_y]
type = GrainAdvectionAux
grain_force = grain_force
grain_volumes = grain_volumes
grain_tracker_object = grain_center
execute_on = timestep_begin
component = y
variable = vadv_y
[../]
[./angle_initial]
type = OutputEulerAngles
variable = angle_initial
euler_angle_provider = euler_angle_initial
grain_tracker = grain_center
output_euler_angle = phi2
execute_on = timestep_begin
[../]
[./angle]
type = OutputEulerAngles
variable = euler_angle
euler_angle_provider = euler_angle
grain_tracker = grain_center
output_euler_angle = phi2
execute_on = timestep_begin
[../]
[]
[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
variable = eta
outputs = none
compute_var_to_feature_map = true
execute_on = 'initial timestep_begin'
[../]
[./grain_force]
type = ConstantGrainForceAndTorque
execute_on = 'initial timestep_begin linear nonlinear'
force = '0.5 0.0 0.0 '
torque = '0.0 0.0 10.0'
[../]
[./euler_angle_initial]
type = RandomEulerAngleProvider
grain_tracker_object = grain_center
execute_on = 'initial timestep_begin'
[../]
[./euler_angle]
type = EulerAngleUpdater
grain_tracker_object = grain_center
euler_angle_provider = euler_angle_initial
grain_torques_object = grain_force
grain_volumes = grain_volumes
execute_on = timestep_begin
[../]
[]
[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'
nl_max_its = 30
l_max_its = 30
l_tol = 1.0e-4
nl_rel_tol = 1.0e-10
start_time = 0.0
dt = 0.2
num_steps = 5
[]
[Outputs]
exodus = true
[]
[ICs]
[./rect_c]
y2 = 20.0
y1 = 5.0
inside = 1.0
x2 = 30.0
variable = c
x1 = 10.0
type = BoundingBoxIC
[../]
[./rect_eta]
y2 = 20.0
y1 = 5.0
inside = 1.0
x2 = 30.0
variable = eta
x1 = 10.0
type = BoundingBoxIC
[../]
[]
(modules/phase_field/examples/ebsd_reconstruction/IN100-111grn.i)
[Mesh]
[ebsd_mesh]
type = EBSDMeshGenerator
filename = IN100_120x120.txt
pre_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 = NumElements
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/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
coupled_variables = '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
#coupled_variables = c
kappa_name = kappa_eta
[../]
[./acbulk_eta0]
type = AllenCahn
variable = eta0
mob_name = M
f_name = F
coupled_variables = '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
#coupled_variables = c
kappa_name = kappa_eta
[../]
[./acbulk_eta1]
type = AllenCahn
variable = eta1
mob_name = M
f_name = F
coupled_variables = '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
property_name = F
coupled_variables = 'c eta0 eta1'
constant_names = 'barr_height cv_eq'
constant_expressions = '0.1 1.0e-2'
expression = 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/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/phase_field/test/tests/rigidbodymotion/grain_motion2.i)
# test file for applyting advection term and observing rigid body motion of grains
[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
[../]
[./w]
order = FIRST
family = LAGRANGE
[../]
[./eta]
order = FIRST
family = LAGRANGE
[../]
[]
[AuxVariables]
[./vadvx]
order = CONSTANT
family = MONOMIAL
[../]
[./vadvy]
order = CONSTANT
family = MONOMIAL
[../]
[./unique_grains]
order = CONSTANT
family = MONOMIAL
[../]
[./centroids]
order = CONSTANT
family = MONOMIAL
[../]
[]
[Kernels]
[./c_res]
type = SplitCHParsed
variable = c
f_name = F
kappa_name = kappa_c
w = w
coupled_variables = eta
[../]
[./w_res]
type = SplitCHWRes
variable = w
mob_name = M
[../]
[./time]
type = CoupledTimeDerivative
variable = w
v = c
[../]
[./motion]
type = MultiGrainRigidBodyMotion
variable = w
c = c
v = eta
grain_tracker_object = grain_center
grain_force = grain_force
grain_volumes = grain_volumes
[../]
[./eta_dot]
type = TimeDerivative
variable = eta
[../]
[./vadv_eta]
type = SingleGrainRigidBodyMotion
variable = eta
c = c
v = eta
grain_tracker_object = grain_center
grain_force = grain_force
grain_volumes = grain_volumes
[../]
[./acint_eta]
type = ACInterface
variable = eta
mob_name = M
coupled_variables = c
kappa_name = kappa_eta
[../]
[./acbulk_eta]
type = AllenCahn
variable = eta
mob_name = M
f_name = F
coupled_variables = c
[../]
[]
[AuxKernels]
[./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 = 'initial timestep_begin'
[../]
[./centroids]
type = FeatureFloodCountAux
variable = centroids
execute_on = 'initial timestep_begin'
field_display = CENTROID
flood_counter = grain_center
[../]
[]
[Materials]
[./pfmobility]
type = GenericConstantMaterial
prop_names = 'M kappa_c kappa_eta'
prop_values = '5.0 2.0 0.1'
[../]
[./free_energy]
type = DerivativeParsedMaterial
coupled_variables = 'c eta'
constant_names = 'barr_height cv_eq'
constant_expressions = '0.1 1.0e-2'
expression = 16*barr_height*(c-cv_eq)^2*(1-cv_eq-c)^2+(c-eta)^2
derivative_order = 2
[../]
[]
[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
variable = eta
outputs = none
compute_var_to_feature_map = true
execute_on = 'initial timestep_begin'
[../]
[./grain_force]
type = ConstantGrainForceAndTorque
execute_on = 'initial linear nonlinear'
force = '0.5 0.0 0.0 '
torque = '0.0 0.0 10.0 '
[../]
[]
[Preconditioning]
[./SMP]
type = SMP
full = true
[../]
[]
[Executioner]
type = Transient
nl_max_its = 30
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
dt = 0.5
num_steps = 1
[]
[Outputs]
exodus = true
[]
[ICs]
[./rect_c]
y2 = 20.0
y1 = 5.0
inside = 1.0
x2 = 30.0
variable = c
x1 = 10.0
type = BoundingBoxIC
[../]
[./rect_eta]
y2 = 20.0
y1 = 5.0
inside = 1.0
x2 = 30.0
variable = eta
x1 = 10.0
type = BoundingBoxIC
[../]
[]
(modules/combined/test/tests/grain_texture/grain_texture_test_2.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
[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 = 2 # Number of elements in the z-direction
xmin = 0 # minimum x-coordinate of the mesh
xmax = 100 # maximum x-coordinate of the mesh
ymin = 0 # minimum y-coordinate of the mesh
ymax = 100 # maximum y-coordinate of the mesh
zmin = 0 # minimum z-coordinate of the mesh
zmax = 20 # maximum z-coordinate of the mesh
elem_type = HEX8 # Type of elements used in the mesh
[]
[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
grain_num = 3 #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 = FauxGrainTracker # Note: FauxGrainTracker only used for testing purposes. Use GrainTracker when using GrainTextureVectorPostprocessor.
flood_entity_type = ELEMENTAL
outputs = none
[../]
[./euler_angle_file]
type = EulerAngleFileReader
file_name = grn_3_rand_2D.tex
[../]
[]
[ICs]
[./PolycrystalICs]
[./PolycrystalColoringIC]
polycrystal_ic_uo = voronoi
[../]
[../]
[]
[AuxVariables]
# Dependent variables
[./unique_grains]
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
[./unique_grains]
type = FeatureFloodCountAux
variable = unique_grains
execute_on = timestep_end
flood_counter = grain_tracker
field_display = UNIQUE_REGION
[../]
[]
[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
[../]
[]
[VectorPostprocessors]
[./textureInfo]
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'
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 = 1
[]
[Outputs]
execute_on = 'TIMESTEP_END'
csv = 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
coupled_variables = '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
expression = 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
property_name = F
#coupled_variables = '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'
coupled_variables = 'c eta0 eta1 eta2 eta3' #Must be changed as op_num changes. Copy/paste from line 4
expression = '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/phase_field/test/tests/feature_volume_vpp_test/percolation_test.i)
# This tests the percolation detection capability in FeatureFloodCount. One feature
# exists that intersects both left and right boundaries, so the FeatureVolumeVPP
# will return true for that feature based on the specified values of parameters
# primary_percolation_boundaries and secondary_percolation_boundaries.
# It also tests the capabilility of FeatureFloodCount to detect whether each feature
# is in contact with the boundaries set by the specified_boundaries parameter.
[Mesh]
type = GeneratedMesh
dim = 2
nx = 60
ny = 60
xmin = 0
xmax = 50
ymin = 0
ymax = 50
elem_type = QUAD4
[]
[Variables]
[./c]
order = FIRST
family = LAGRANGE
[]
[]
[AuxVariables]
[./unique_regions]
family = MONOMIAL
order = CONSTANT
[../]
[]
[ICs]
[./c]
type = MultiSmoothCircleIC
variable = c
invalue = 1.0
outvalue = 0.0001
radius = 4.0
int_width = 2.0
numbub = 35
bubspac = 2
[]
[]
[Postprocessors]
[./flood_count]
type = FeatureFloodCount
variable = c
# Must be turned out to build data structures necessary for FeatureVolumeVPP
compute_var_to_feature_map = true
threshold = 0.5
outputs = none
execute_on = INITIAL
primary_percolation_boundaries = 'left'
secondary_percolation_boundaries = 'right'
specified_boundaries = 'left right'
[../]
[]
[VectorPostprocessors]
[./features]
type = FeatureVolumeVectorPostprocessor
flood_counter = flood_count
# Turn on centroid output
output_centroids = true
execute_on = INITIAL
[../]
[]
[Kernels]
[diff]
type = Diffusion
variable = c
[]
[]
[AuxKernels]
[./unique_regions]
type = FeatureFloodCountAux
variable = unique_regions
flood_counter = flood_count
field_display = UNIQUE_REGION
[../]
[]
[Problem]
solve = false
[]
[Executioner]
type = Steady
[]
[Outputs]
csv = true
execute_on = INITIAL
[]
(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
coupled_variables = '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
#coupled_variables = c
kappa_name = kappa_eta
[../]
[./acbulk_eta0]
type = AllenCahn
variable = eta0
mob_name = M
f_name = F
coupled_variables = '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
#coupled_variables = c
kappa_name = kappa_eta
[../]
[./acbulk_eta1]
type = AllenCahn
variable = eta1
mob_name = M
f_name = F
coupled_variables = '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
property_name = F
coupled_variables = 'c eta0 eta1'
constant_names = 'barr_height cv_eq'
constant_expressions = '0.1 1.0e-2'
expression = 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/flood_counter_aux_test/nodal_flood_periodic_2var.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 30
ny = 30
nz = 0
xmax = 40
ymax = 40
zmax = 0
elem_type = QUAD4
[]
[Variables]
[./u]
order = FIRST
family = LAGRANGE
[../]
[./v]
order = FIRST
family = LAGRANGE
[../]
[]
[AuxVariables]
[./bubble_map0]
order = FIRST
family = LAGRANGE
[../]
[./bubble_map1]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
[./diff]
type = Diffusion
variable = u
[../]
[./diffv]
type = Diffusion
variable = v
[../]
[./forcing_1]
type = GaussContForcing
variable = u
x_center = 1.0
y_center = 1.0
x_spread = 0.5
y_spread = 0.5
[../]
[./forcing_2]
type = GaussContForcing
variable = u
x_center = 20.0
y_center = 39.0
x_spread = 0.5
y_spread = 0.5
[../]
[./forcing_3]
type = GaussContForcing
variable = u
x_center = 39.0
y_center = 20.0
x_spread = 0.5
y_spread = 0.5
[../]
[./forcing_4]
type = GaussContForcing
variable = u
x_center = 15.0
y_center = 15.0
x_spread = 0.5
y_spread = 0.5
[../]
[./forcing_1v]
type = GaussContForcing
variable = v
x_center = 8.0
y_center = 8.0
x_spread = 0.5
y_spread = 0.5
[../]
[./forcing_2v]
type = GaussContForcing
variable = v
x_center = 18.0
y_center = 22.0
x_spread = 0.5
y_spread = 0.5
[../]
[./forcing_3v]
type = GaussContForcing
variable = v
x_center = 39.0
y_center = 20.0
x_spread = 0.5
y_spread = 0.5
[../]
[./forcing_4v]
type = GaussContForcing
variable = v
x_center = 32.0
y_center = 8.0
x_spread = 0.5
y_spread = 0.5
[../]
[./dot]
type = TimeDerivative
variable = u
[../]
[./dotv]
type = TimeDerivative
variable = v
[../]
[]
[AuxKernels]
[./mapper0]
type = FeatureFloodCountAux
variable = bubble_map0
execute_on = timestep_end
flood_counter = bubbles
map_index = 0
[../]
[./mapper1]
type = FeatureFloodCountAux
variable = bubble_map1
execute_on = timestep_end
flood_counter = bubbles
map_index = 1
[../]
[]
[BCs]
[./Periodic]
[./all]
variable = 'u v'
auto_direction = 'x y'
[../]
[../]
[]
[UserObjects]
[./bubbles]
type = FeatureFloodCount
variable = 'u v'
threshold = 0.3
execute_on = timestep_end
use_single_map = false
use_global_numbering = true
outputs = none
flood_entity_type = NODAL
[../]
[]
[Executioner]
type = Transient
dt = 4.0
num_steps = 5
[]
[Outputs]
execute_on = 'timestep_end'
file_base = out_2var
exodus = true
[]
(modules/phase_field/test/tests/feature_volume_vpp_test/boundary_area_2D.i)
[Mesh]
[gen]
type = GeneratedMeshGenerator
dim = 2
nx = 50
ny = 50
xmin = 0
xmax = 50
ymin = 0
ymax = 50
elem_type = QUAD4
[]
[./left_side]
type = SubdomainBoundingBoxGenerator
block_id = 1
bottom_left = '0 0 0'
top_right = '24.9 50 0'
input = gen
[../]
[./right_side]
type = SubdomainBoundingBoxGenerator
block_id = 2
bottom_left = '25.1 0 0'
top_right = '50 50 0'
input = left_side
[../]
[./iface_u]
type = SideSetsBetweenSubdomainsGenerator
primary_block = 1
paired_block = 2
new_boundary = 10
input = right_side
[../]
[]
[Variables]
[./c]
order = FIRST
family = LAGRANGE
[]
[]
[AuxVariables]
[./unique_regions]
family = MONOMIAL
order = CONSTANT
[../]
[]
[ICs]
[./c]
type = SpecifiedSmoothCircleIC
variable = c
invalue = 1.0
outvalue = 0.0
radii = '4 5 10'
x_positions = '25 25 25'
y_positions = '37.5 25 0'
z_positions = '0 0 0'
int_width = 2.0
[]
[]
[Postprocessors]
[./flood_count]
type = FeatureFloodCount
variable = c
# Must be turned on to build data structures necessary for FeatureVolumeVPP
compute_var_to_feature_map = true
threshold = 0.001
execute_on = INITIAL
[../]
[]
[VectorPostprocessors]
[./features]
type = FeatureVolumeVectorPostprocessor
flood_counter = flood_count
# Turn on centroid output
output_centroids = true
execute_on = INITIAL
boundary = 10
single_feature_per_element = false
[../]
[]
[Kernels]
[diff]
type = Diffusion
variable = c
[]
[]
[AuxKernels]
[./unique_regions]
type = FeatureFloodCountAux
variable = unique_regions
flood_counter = flood_count
field_display = UNIQUE_REGION
[../]
[]
[Problem]
solve = false
[]
[Executioner]
type = Steady
[]
[Outputs]
csv = true
execute_on = INITIAL
[]
(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/grain_tracker_test/grain_tracker_ebsd.i)
[Mesh]
[ebsd_mesh]
type = EBSDMeshGenerator
filename = 'ebsd_9.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/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
coupled_variables = '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
property_name = F
coupled_variables = 'c eta0 eta1'
constant_names = 'barr_height cv_eq'
constant_expressions = '0.1 1.0e-2'
expression = 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/phase_field/test/tests/feature_flood_test/parallel_feature_count.i)
[Mesh]
type = ImageMesh
dim = 2
file = spiral_16x16.png
scale_to_one = false
[]
[Variables]
[./u]
order = CONSTANT
family = MONOMIAL
[../]
[]
[AuxVariables]
[./feature]
order = CONSTANT
family = MONOMIAL
[../]
[./proc_id]
order = CONSTANT
family = MONOMIAL
[../]
[./feature_ghost]
order = CONSTANT
family = MONOMIAL
[../]
[]
[AuxKernels]
[./nodal_flood_aux]
type = FeatureFloodCountAux
variable = feature
flood_counter = flood_count_pp
execute_on = 'initial timestep_end'
[../]
[./proc_id]
type = ProcessorIDAux
variable = proc_id
execute_on = 'initial timestep_end'
[../]
[./ghost]
type = FeatureFloodCountAux
variable = feature_ghost
field_display = GHOSTED_ENTITIES
flood_counter = flood_count_pp
execute_on = 'initial timestep_end'
[../]
[]
[Functions]
[./tif]
type = ImageFunction
component = 0
[../]
[]
[ICs]
[./u_ic]
type = FunctionIC
function = tif
variable = u
[../]
[]
[Postprocessors]
[./flood_count_pp]
type = FeatureFloodCount
variable = u
threshold = 1.0
execute_on = 'initial timestep_end'
[../]
[]
[Problem]
type = FEProblem
solve = false
[]
[Executioner]
type = Steady
[]
[Outputs]
csv = true
[]
(modules/combined/test/tests/grain_texture/grain_texture_test_1.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
[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
xmin = 0 # minimum x-coordinate of the mesh
xmax = 100 # maximum x-coordinate of the mesh
ymin = 0 # minimum y-coordinate of the mesh
ymax = 100 # 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 = 3 # Number of order parameters used
var_name_base = gr # Base name of grains
grain_num = 3 #Number of grains
[]
[Variables]
# Variable block, where all variables in the simulation are declared
[./PolycrystalVariables]
[../]
[]
[UserObjects]
[./euler_angle_file]
type = EulerAngleFileReader
file_name = grn_3_rand_2D.tex
[../]
[./grain_tracker]
type = FauxGrainTracker
outputs = none
[../]
[./voronoi]
type = PolycrystalVoronoi
coloring_algorithm = bt
[../]
[]
[ICs]
[./PolycrystalICs]
[./PolycrystalColoringIC]
polycrystal_ic_uo = voronoi
[../]
[../]
[]
[AuxVariables]
# Dependent variables
[./unique_grains]
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
[./unique_grains]
type = FeatureFloodCountAux
variable = unique_grains
execute_on = timestep_end
flood_counter = grain_tracker
field_display = UNIQUE_REGION
[../]
[]
[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 Schonfelder 1997
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
[../]
[]
[VectorPostprocessors]
[./textureInfo]
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'
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 = 1
[]
[Outputs]
execute_on = 'TIMESTEP_END'
csv = true
[]
(modules/phase_field/test/tests/rigidbodymotion/update_orientation_verify.i)
# test file for applyting advection term and observing rigid body motion of grains
[Mesh]
type = GeneratedMesh
dim = 3
nx = 14
ny = 7
nz = 7
xmax = 40
ymax = 25
zmax = 25
elem_type = HEX8
[]
[Variables]
[./c]
order = FIRST
family = LAGRANGE
[../]
[./w]
order = FIRST
family = LAGRANGE
[../]
[./eta]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
[./c_res]
type = SplitCHParsed
variable = c
f_name = F
kappa_name = kappa_c
w = w
coupled_variables = eta
[../]
[./w_res]
type = SplitCHWRes
variable = w
mob_name = M
[../]
[./time]
type = CoupledTimeDerivative
variable = w
v = c
[../]
[./motion]
type = MultiGrainRigidBodyMotion
variable = w
c = c
v = eta
grain_tracker_object = grain_center
grain_force = grain_force
grain_volumes = grain_volumes
[../]
[./eta_dot]
type = TimeDerivative
variable = eta
[../]
[./vadv_eta]
type = SingleGrainRigidBodyMotion
variable = eta
c = c
v = eta
grain_tracker_object = grain_center
grain_force = grain_force
grain_volumes = grain_volumes
[../]
[./acint_eta]
type = ACInterface
variable = eta
mob_name = M
coupled_variables = c
kappa_name = kappa_eta
[../]
[./acbulk_eta]
type = AllenCahn
variable = eta
mob_name = M
f_name = F
coupled_variables = c
[../]
[]
[Materials]
[./pfmobility]
type = GenericConstantMaterial
prop_names = 'M kappa_c kappa_eta'
prop_values = '5.0 2.0 0.1'
[../]
[./free_energy]
type = DerivativeParsedMaterial
coupled_variables = 'c eta'
constant_names = 'barr_height cv_eq'
constant_expressions = '0.1 1.0e-2'
expression = 16*barr_height*(c-cv_eq)^2*(1-cv_eq-c)^2+(c-eta)^2
derivative_order = 2
[../]
[]
[AuxVariables]
[./unique_grains]
order = CONSTANT
family = MONOMIAL
[../]
[./var_indices]
order = CONSTANT
family = MONOMIAL
[../]
[./centroids]
order = CONSTANT
family = MONOMIAL
[../]
[./vadv_x]
order = CONSTANT
family = MONOMIAL
[../]
[./vadv_y]
order = CONSTANT
family = MONOMIAL
[../]
[./angle_initial]
order = CONSTANT
family = MONOMIAL
[../]
[./euler_angle]
order = CONSTANT
family = MONOMIAL
[../]
[]
[AuxKernels]
[./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
[../]
[./vadv_x]
type = GrainAdvectionAux
grain_force = grain_force
grain_volumes = grain_volumes
grain_tracker_object = grain_center
execute_on = timestep_begin
component = x
variable = vadv_x
[../]
[./vadv_y]
type = GrainAdvectionAux
grain_force = grain_force
grain_volumes = grain_volumes
grain_tracker_object = grain_center
execute_on = timestep_begin
component = y
variable = vadv_y
[../]
[./angle_initial]
type = OutputEulerAngles
variable = angle_initial
euler_angle_provider = euler_angle_initial
grain_tracker = grain_center
output_euler_angle = phi2
execute_on = timestep_begin
[../]
[./angle]
type = OutputEulerAngles
variable = euler_angle
euler_angle_provider = euler_angle
grain_tracker = grain_center
output_euler_angle = phi2
execute_on = timestep_begin
[../]
[]
[VectorPostprocessors]
[./forces]
type = GrainForcesPostprocessor
grain_force = grain_force
[../]
[./grain_volumes]
type = FeatureVolumeVectorPostprocessor
flood_counter = grain_center
execute_on = 'initial timestep_begin'
[../]
[./angle_check]
type = EulerAngleUpdaterCheck
grain_tracker_object = grain_center
euler_angle_updater = euler_angle
grain_torques_object = grain_force
grain_volumes = grain_volumes
execute_on = timestep_begin
[../]
[]
[UserObjects]
[./grain_center]
type = GrainTracker
variable = eta
outputs = none
compute_var_to_feature_map = true
execute_on = 'initial timestep_begin'
[../]
[./grain_force]
type = ConstantGrainForceAndTorque
execute_on = 'initial timestep_begin linear nonlinear'
force = '0.5 0.0 0.0 '
torque = '-200.0 -120.0 1000.0'
[../]
[./euler_angle_initial]
type = RandomEulerAngleProvider
grain_tracker_object = grain_center
seed = 12356
execute_on = 'initial timestep_begin'
[../]
[./euler_angle]
type = EulerAngleUpdater
grain_tracker_object = grain_center
euler_angle_provider = euler_angle_initial
grain_torques_object = grain_force
grain_volumes = grain_volumes
execute_on = timestep_begin
[../]
[]
[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'
nl_max_its = 30
l_max_its = 30
l_tol = 1.0e-4
nl_rel_tol = 1.0e-10
start_time = 0.0
dt = 0.2
num_steps = 2
[]
[Outputs]
csv = true
exodus = true
[]
[ICs]
[./rect_c]
y2 = 20.0
y1 = 5.0
z1 = 5.0
z2 = 20.0
inside = 1.0
x2 = 30.0
variable = c
x1 = 10.0
type = BoundingBoxIC
[../]
[./rect_eta]
y2 = 20.0
y1 = 5.0
inside = 1.0
x2 = 30.0
variable = eta
x1 = 10.0
z1 = 5.0
z2 = 20.0
type = BoundingBoxIC
[../]
[]
(modules/phase_field/test/tests/boundary_intersecting_features/boundary_intersecting_features.i)
[Mesh]
# ImageMesh ignores nx, xmin, xmax (and similarly for y and z) and
# tries to read them from the image file...
type = ImageMesh
dim = 2
# Be sure to choose a corresponding image name below!
# file = image001_cropped3_closing_298.png # full size, 157 Mb Exodus file!
# file = eighth_image001_cropped3_closing_298.png # 1/8
file = sixteenth_image001_cropped3_closing_298.png # 1/16
# Uncomment to maintain 1:1 ratio between number of pixels and mesh size.
# scale_to_one = false
# Uncomment to set cells_per_pixel to something other than the default value of 1.0.
# Must be <= 1.
# cells_per_pixel = .75
# To crop an image to e.g. 1/8th size, install ImageMagick and run:
# convert image001_cropped3_closing_298.png -crop 230x198+100+100 eighth_image001_cropped3_closing_298.png
# Note: Do not use 'sips' on OSX to crop! It actually interpolates
# the colors in the image instead of just cropping.
[]
[Variables]
[./u]
order = CONSTANT
family = MONOMIAL
[../]
[]
[AuxVariables]
[./grain_auxvar]
order = CONSTANT
family = MONOMIAL
[../]
[./centroids]
order = CONSTANT
family = MONOMIAL
[../]
[]
[AuxKernels]
[./nodal_flood_aux]
variable = grain_auxvar
type = FeatureFloodCountAux
flood_counter = flood_count_pp
execute_on = 'initial timestep_end'
[../]
[./centroids]
type = FeatureFloodCountAux
variable = centroids
flood_counter = flood_count_pp
field_display = CENTROID
execute_on = 'initial timestep_end'
[../]
[]
[Functions]
[./tif]
# ImageFunction gets its file range parameters from ImageMesh,
# when it is present. This prevents duplicating information in
# input files.
type = ImageFunction
# In these sample images the features we want to analyze are RED (or close to pure red). The
# background is BLUE so we can easily distinguish between the two by selecting only the red channel.
component = 0
[../]
[]
[ICs]
[./u_ic]
type = FunctionIC
function = tif
variable = u
[../]
[]
[Postprocessors]
[./flood_count_pp]
type = FeatureFloodCount
variable = u
threshold = 1.0
compute_var_to_feature_map = true
execute_on = 'initial timestep_end'
[../]
[]
[VectorPostprocessors]
[./grain_volumes]
type = FeatureVolumeVectorPostprocessor
flood_counter = flood_count_pp
execute_on = 'initial timestep_end'
[../]
[]
[Problem]
type = FEProblem
solve = false
[../]
[Executioner]
type = Steady
[]
[Outputs]
csv = 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 8 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 = 44 # Number of elements in the x-direction
ny = 44 # 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 = 2 # 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
[]
[Modules]
[PhaseField]
[GrainGrowth]
[]
[]
[]
[UserObjects]
[voronoi]
type = PolycrystalVoronoi
grain_num = 100 # Number of grains
rand_seed = 10
int_width = 7
[]
[grain_tracker]
type = GrainTracker
[]
[]
[ICs]
[PolycrystalICs]
[PolycrystalColoringIC]
polycrystal_ic_uo = voronoi
[]
[]
[]
[AuxVariables]
# Dependent variables
[unique_grains]
order = CONSTANT
family = MONOMIAL
[]
[var_indices]
order = CONSTANT
family = MONOMIAL
[]
[]
[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'
[]
[]
[BCs]
# Boundary Condition block
[Periodic]
[All]
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 schonfelder1997molecular bibtex entry
Q = 0.23 #eV for copper from schonfelder1997molecular bibtex entry
GBenergy = 0.708 #J/m^2 from schonfelder1997molecular bibtex entry
[]
[]
[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'
petsc_options_value = 'hypre boomeramg'
l_max_its = 50 # Max number of linear iterations
l_tol = 1e-4 # Relative tolerance for linear solves
nl_max_its = 10 # Max number of nonlinear iterations
end_time = 4000
[TimeStepper]
type = IterationAdaptiveDT
dt = 20 # 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 = 0.8 # Fraction of high error that will be refined
coarsen_fraction = 0.05 # Fraction of low error that will coarsened
max_h_level = 2 # Max number of refinements used, starting from initial mesh (before uniform refinement)
[]
[]
[Outputs]
exodus = true # Exodus file will be outputted
csv = 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 = NumElements
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/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 schonfelder1997molecular bibtex entry
Q = 0.23 # eV for copper from schonfelder1997molecular bibtex entry
GBenergy = 0.708 # J/m^2 from schonfelder1997molecular bibtex entry
[]
[]
[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/phase_field/test/tests/reconstruction/1phase_reconstruction.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.
#
[Problem]
type = FEProblem
solve = false
kernel_coverage_check = false
[]
# The following sections are extracted in the documentation in
# moose/docs/content/modules/phase_field/ICs/EBSD.md
[Mesh]
# Create a mesh representing the EBSD data
[ebsd_mesh]
type = EBSDMeshGenerator
filename = IN100_001_28x28_Marmot.txt
[]
[]
[GlobalParams]
# Define the number and names of the order parameters used to represent the grains
op_num = 4
var_name_base = gr
[]
[UserObjects]
[ebsd_reader]
# Read in the EBSD data. Uses the filename given in the mesh block.
type = EBSDReader
[]
[ebsd]
type = PolycrystalEBSD
coloring_algorithm = bt
ebsd_reader = ebsd_reader
output_adjacency_matrix = true
[]
[grain_tracker]
type = GrainTracker
# For displaying HALO fields
compute_halo_maps = true
# Link in the ebsd userobject here so that grain tracker can extract info from it
polycrystal_ic_uo = ebsd
[]
[]
[Variables]
[PolycrystalVariables]
# Create all the order parameters
order = FIRST
family = LAGRANGE
[]
[]
[ICs]
[PolycrystalICs]
[PolycrystalColoringIC]
# Uses the data from the user object 'ebsd' to initialize the variables for all the order parameters.
polycrystal_ic_uo = ebsd
[]
[]
[]
#ENDDOC - End of the file section that is included in the documentation. Do not change this line!
[GlobalParams]
execute_on = 'initial'
family = MONOMIAL
order = CONSTANT
[]
[AuxVariables]
[PHI1]
[]
[PHI]
[]
[PHI2]
[]
[GRAIN]
[]
[unique_grains]
[]
[var_indices]
[]
[halo0]
[]
[halo1]
[]
[halo2]
[]
[halo3]
[]
[]
[AuxKernels]
[phi1_aux]
type = EBSDReaderPointDataAux
variable = PHI1
ebsd_reader = ebsd_reader
data_name = 'phi1'
[]
[phi_aux]
type = EBSDReaderPointDataAux
variable = PHI
ebsd_reader = ebsd_reader
data_name = 'phi'
[]
[phi2_aux]
type = EBSDReaderPointDataAux
variable = PHI2
ebsd_reader = ebsd_reader
data_name = 'phi2'
[]
[grain_aux]
type = EBSDReaderPointDataAux
variable = GRAIN
ebsd_reader = ebsd_reader
data_name = 'feature_id'
[]
[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
[]
[]
[Executioner]
type = Steady
[]
[Outputs]
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 = NumElements
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_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 schonfelder1997molecular bibtex entry
Q = 0.23 # eV for copper from schonfelder1997molecular bibtex entry
GBenergy = 0.708 # J/m^2 from schonfelder1997molecular bibtex entry
[../]
[]
[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
[./pg]
type = PerfGraphOutput
level = 2 # Default is 1
[../]
[]
(modules/phase_field/examples/grain_growth/grain_growth_2D_random.i)
# This initializes a polycrystal from random seeds at each node
# Mesh adaptivity and time step adaptivity are used
# Grain tracker is started once the grain structure is established
[Mesh]
# Mesh block. Meshes can be read in or automatically generated
type = GeneratedMesh
dim = 2 # Problem dimension
nx = 40 # Number of elements in the x-direction
ny = 40 # 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 = 2 # 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
[]
[Modules]
[PhaseField]
[GrainGrowth]
[]
[]
[]
[ICs]
[PolycrystalICs]
[PolycrystalRandomIC]
random_type = discrete
[]
[]
[]
[AuxVariables]
# Dependent variables
[unique_grains]
order = CONSTANT
family = MONOMIAL
[]
[var_indices]
order = CONSTANT
family = MONOMIAL
[]
[]
[AuxKernels]
# AuxKernel block, defining the equations used to calculate the auxvars
[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'
[]
[]
[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 schonfelder1997molecular bibtex entry
GBenergy = 0.708 # GB energy for Cu from schonfelder1997molecular bibtex entry
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
[]
[]
[UserObjects]
[grain_tracker]
type = GrainTracker
tracking_step = 20 #Tracking is delayed until the polycrystalline structure is established
[]
[]
[Postprocessors]
# Scalar postprocessors
[dt]
# Outputs the current time step
type = TimestepSize
[]
[num_nodes]
type = NumNodes
[]
[]
[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'
petsc_options_value = 'hypre boomeramg'
l_max_its = 20 # Max number of linear iterations
l_tol = 1e-4 # Relative tolerance for linear solves
start_time = 0.0
end_time = 4000
[TimeStepper]
type = IterationAdaptiveDT
dt = 1 # 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)
refine_fraction = 0.8 # Fraction of high error that will be refined
coarsen_fraction = 0.05 # Fraction of low error that will coarsened
max_h_level = 2 # Max number of refinements used, starting from initial mesh (before uniform refinement)
[]
[]
[Outputs]
exodus = true
csv = 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/test/tests/flood_counter_aux_test/flood_counter_boundary_restrictable.i)
[Mesh]
type = GeneratedMesh
dim = 2
nx = 20
ny = 20
nz = 0
xmax = 40
ymax = 40
zmax = 0
elem_type = QUAD4
[]
[Variables]
[./u]
order = FIRST
family = LAGRANGE
[../]
[]
[AuxVariables]
[./bubble_map]
order = CONSTANT
family = MONOMIAL
[../]
[]
[Kernels]
active = 'diff forcing_1 forcing_2 forcing_3 forcing_4 dot'
[./diff]
type = Diffusion
variable = u
[../]
[./forcing_1]
type = GaussContForcing
variable = u
x_center = 1.0
y_center = 1.0
x_spread = 0.5
y_spread = 0.5
amplitude = 2.0
[../]
[./forcing_2]
type = GaussContForcing
variable = u
x_center = 20.0
y_center = 39.0
x_spread = 0.5
y_spread = 0.5
amplitude = 2.0
[../]
[./forcing_3]
type = GaussContForcing
variable = u
x_center = 39.0
y_center = 20.0
x_spread = 0.5
y_spread = 0.5
amplitude = 2.0
[../]
[./forcing_4]
type = GaussContForcing
variable = u
x_center = 15.0
y_center = 15.0
x_spread = 0.5
y_spread = 0.5
amplitude = 2.0
[../]
[./dot]
type = TimeDerivative
variable = u
[../]
[]
[AuxKernels]
[./mapper]
type = FeatureFloodCountAux
variable = bubble_map
execute_on = 'initial timestep_end'
flood_counter = bubbles
[../]
[]
[Postprocessors]
[./bubbles]
type = FeatureFloodCount
variable = u
threshold = 0.1
execute_on = 'initial timestep_end'
boundary = 'top right left bottom'
[../]
[]
[Executioner]
type = Transient
dt = 4.0
num_steps = 2
[]
[Outputs]
execute_on = 'timestep_end'
csv = 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/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
[]