- bottom_leftThe bottom left point (in x,y,z with spaces in-between).
C++ Type:libMesh::VectorValue
Description:The bottom left point (in x,y,z with spaces in-between).
- insideHow to mark elements inside the box.
C++ Type:MooseEnum
Description:How to mark elements inside the box.
- outsideHow to mark elements outside the box.
C++ Type:MooseEnum
Description:How to mark elements outside the box.
- top_rightThe bottom left point (in x,y,z with spaces in-between).
C++ Type:libMesh::VectorValue
Description:The bottom left point (in x,y,z with spaces in-between).
BoxMarker
Marks the region inside and outside of a 'box' domain for refinement or coarsening.
Description
The BoxMarker is a stand-alone marker that marks all elements inside and outside for coarsening or refinement. The marker operates using a bounding box that is specified by lower and upper extents of the bounding box, in 3 dimensions regardless of the dimensions of the problem.
Example Input Syntax
[Adaptivity]
[./Markers]
[./box]
type = BoxMarker
bottom_left = '0.3 0.3 0'
top_right = '0.6 0.6 0'
inside = refine
outside = do_nothing
[../]
[../]
[]
/opt/civet/build_0/moose/test/tests/markers/box_marker/box_marker_test.i
[Mesh]
type = GeneratedMesh
dim = 2
nx = 10
ny = 10
nz = 0
zmax = 0
elem_type = QUAD4
[]
[Variables]
[./u]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
[./diff]
type = Diffusion
variable = u
[../]
[]
[BCs]
[./left]
type = DirichletBC
variable = u
boundary = 1
value = 0
[../]
[./right]
type = DirichletBC
variable = u
boundary = 2
value = 1
[../]
[]
[Executioner]
type = Steady
solve_type = 'PJFNK'
[]
[Adaptivity]
[./Markers]
[./box]
type = BoxMarker
bottom_left = '0.3 0.3 0'
top_right = '0.6 0.6 0'
inside = refine
outside = do_nothing
[../]
[../]
[]
[Outputs]
exodus = true
[]
Input Parameters
- blockThe list of block ids (SubdomainID) that this object will be applied
C++ Type:std::vector
Options:
Description:The list of block ids (SubdomainID) that this object will be applied
Optional Parameters
- control_tagsAdds user-defined labels for accessing object parameters via control logic.
C++ Type:std::vector
Options:
Description:Adds user-defined labels for accessing object parameters via control logic.
- enableTrueSet the enabled status of the MooseObject.
Default:True
C++ Type:bool
Options:
Description:Set the enabled status of the MooseObject.
- outputsVector of output names were you would like to restrict the output of variables(s) associated with this object
C++ Type:std::vector
Options:
Description:Vector of output names were you would like to restrict the output of variables(s) associated with this object
Advanced Parameters
Input Files
- test/tests/markers/dont_mark/dont_mark_test.i
- test/tests/outputs/output_interface/marker.i
- test/tests/misc/serialized_solution/adapt.i
- test/tests/postprocessors/num_dofs/num_dofs.i
- test/tests/dirackernels/point_caching/point_caching_adaptive_refinement.i
- test/tests/postprocessors/num_adaptivity_cycles/num_adaptivity_cycles_toggle_adaptivity_wait.i
- modules/level_set/test/tests/transfers/markers/single_level/master.i
- test/tests/outputs/exodus/variable_output_test.i
- test/tests/userobjects/toggle_mesh_adaptivity/toggle_mesh_adaptivity.i
- test/tests/postprocessors/memory_usage/vector_memory_usage.i
- test/tests/adaptivity/initial_adapt/initial_adapt.i
- test/tests/adaptivity/interval/adapt_interval.i
- test/tests/markers/box_marker/box_marker_test.i
- modules/combined/test/tests/contact_adaptivity/sm/contact_initial_adaptivity_sm.i
- test/tests/postprocessors/num_elems/num_elems.i
- test/tests/postprocessors/num_adaptivity_cycles/num_adaptivity_cycles_toggle_adaptivity.i
- test/tests/postprocessors/num_nodes/num_nodes.i
- test/tests/time_integrators/explicit-euler/ee-2d-linear-adapt.i
- test/tests/markers/box_marker/box_marker_adapt_test.i
- modules/porous_flow/examples/lava_lamp/2phase_convection.i
- test/tests/adaptivity/initial_marker/initial_marker.i
- modules/porous_flow/examples/lava_lamp/1phase_convection.i
- test/tests/materials/stateful_prop/spatial_adaptivity_test.i
- test/tests/postprocessors/num_adaptivity_cycles/num_adaptivity_cycles.i
- test/tests/interfacekernels/adaptivity/adaptivity.i
- test/tests/adaptivity/max_h_level/max_h_level.i
- modules/combined/test/tests/contact_adaptivity/contact_initial_adaptivity.i
- modules/level_set/test/tests/functions/olsson_bubble/olsson_bubble.i
- test/tests/userobjects/toggle_mesh_adaptivity/toggle_mesh_adaptivity_wait.i
- test/tests/markers/combo_marker/combo_marker_test.i
- test/tests/misc/selective_reinit/selective_reinit_test.i
- test/tests/kernels/diffusion_with_hanging_node/simple_diffusion.i
- test/tests/time_integrators/actually_explicit_euler_verification/ee-2d-linear-adapt.i
- test/tests/outputs/oversample/adapt.i
- test/tests/materials/stateful_prop/stateful_prop_adaptivity_test.i
test/tests/markers/dont_mark/dont_mark_test.i
[Mesh]
type = GeneratedMesh
dim = 2
nx = 10
ny = 10
nz = 0
zmax = 0
elem_type = QUAD4
[]
[Variables]
[./u]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
[./diff]
type = Diffusion
variable = u
[../]
[]
[BCs]
[./left]
type = DirichletBC
variable = u
boundary = 1
value = 0
[../]
[./right]
type = DirichletBC
variable = u
boundary = 2
value = 1
[../]
[]
[Executioner]
type = Steady
solve_type = 'PJFNK'
[]
[Adaptivity]
[./Markers]
[./box]
type = BoxMarker
bottom_left = '0.3 0.3 0'
top_right = '0.6 0.6 0'
inside = refine
outside = coarsen
[../]
[./combo]
type = ComboMarker
markers = 'box box2'
[../]
[./box2]
type = BoxMarker
bottom_left = '0.5 0.5 0'
top_right = '0.8 0.8 0'
inside = dont_mark
outside = refine
[../]
[../]
[]
[Outputs]
exodus = true
[]
test/tests/outputs/output_interface/marker.i
[Mesh]
type = GeneratedMesh
dim = 2
nx = 10
ny = 10
[]
[Variables]
[./u]
[../]
[]
[Kernels]
[./diff]
type = Diffusion
variable = u
[../]
[]
[BCs]
[./left]
type = DirichletBC
variable = u
boundary = left
value = 0
[../]
[./right]
type = DirichletBC
variable = u
boundary = right
value = 1
[../]
[]
[Executioner]
type = Steady
solve_type = PJFNK
petsc_options_iname = '-pc_type -pc_hypre_type'
petsc_options_value = 'hypre boomeramg'
[]
[Adaptivity]
[./Indicators]
[./indicator_0]
type = GradientJumpIndicator
variable = u
outputs = none
[../]
[./indicator_1]
type = GradientJumpIndicator
variable = u
outputs = none
[../]
[../]
[./Markers]
[./marker_0]
type = ValueThresholdMarker
outputs = markers
refine = 0.5
variable = u
[../]
[./marker_1]
type = BoxMarker
bottom_left = '0.25 0.25 0'
top_right = '0.75 0.75 0'
inside = REFINE
outside = DONT_MARK
outputs = markers
[../]
[../]
[]
[Outputs]
[./markers]
type = Exodus
[../]
[./no_markers]
type = Exodus
[../]
[]
test/tests/misc/serialized_solution/adapt.i
[Mesh]
type = GeneratedMesh
dim = 2
nx = 10
ny = 10
[]
[Variables]
[./u]
[../]
[]
[Kernels]
[./diff]
type = CoefDiffusion
variable = u
coef = 0.1
[../]
[./time]
type = TimeDerivative
variable = u
[../]
[]
[BCs]
[./left]
type = DirichletBC
variable = u
boundary = left
value = 0
[../]
[./right]
type = DirichletBC
variable = u
boundary = right
value = 1
[../]
[]
[Postprocessors]
[./aux_serialized]
type = TestSerializedSolution
system = aux
[../]
[./nl_serialized]
type = TestSerializedSolution
system = nl
[../]
[]
[Executioner]
type = Transient
num_steps = 3
dt = 0.1
solve_type = PJFNK
petsc_options_iname = '-pc_type -pc_hypre_type'
petsc_options_value = 'hypre boomeramg'
[]
[Adaptivity]
marker = box_refine
[./Markers]
[./box_refine]
type = BoxMarker
bottom_left = '0.2 0.2 0'
top_right = '0.8 0.8 0'
inside = REFINE
outside = DONT_MARK
[../]
[../]
[]
[Outputs]
execute_on = 'timestep_end'
exodus = true
[]
test/tests/postprocessors/num_dofs/num_dofs.i
[Mesh]
type = GeneratedMesh
dim = 2
nx = 4
ny = 4
nz = 0
zmax = 0
elem_type = QUAD4
[]
[Variables]
[./u]
order = FIRST
family = LAGRANGE
[../]
[]
[AuxVariables]
[./u_aux]
order = FIRST
family = LAGRANGE
[../]
[./v_aux]
order = FIRST
family = LAGRANGE
[../]
[]
[Functions]
[./force]
type = ParsedFunction
value = t
[../]
[]
[Kernels]
[./diff]
type = Diffusion
variable = u
[../]
[./force]
type = BodyForce
variable = u
function = force
[../]
[]
[BCs]
[./right]
type = DirichletBC
variable = u
boundary = right
value = 1
[../]
[./left]
type = DirichletBC
variable = u
boundary = left
value = 0
[../]
[]
[Executioner]
type = Transient
num_steps = 4
dt = 1
solve_type = PJFNK
[]
[Adaptivity]
steps = 1
marker = box
max_h_level = 2
[./Markers]
[./box]
bottom_left = '0.3 0.3 0'
inside = refine
top_right = '0.6 0.6 0'
outside = do_nothing
type = BoxMarker
[../]
[../]
[]
[Postprocessors]
[./num_dofs_nl]
type = NumDOFs
system = NL
[../]
[./num_dofs_aux]
type = NumDOFs
system = AUX
[../]
# default
[./num_dofs_all]
type = NumDOFs
system = ALL
[../]
[]
[Outputs]
csv = true
[]
test/tests/dirackernels/point_caching/point_caching_adaptive_refinement.i
[Mesh]
type = GeneratedMesh
dim = 2
xmin = 0
xmax = 1
ymin = 0
ymax = 1
nx = 2
ny = 2
elem_type = QUAD4
uniform_refine = 2
[]
[Variables]
[./u]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
active = 'diff'
[./diff]
type = Diffusion
variable = u
[../]
[]
[DiracKernels]
active = 'point_source'
[./point_source]
type = CachingPointSource
variable = u
[../]
[]
[BCs]
[./left]
type = DirichletBC
variable = u
boundary = 3
value = 0
[../]
[./right]
type = DirichletBC
variable = u
boundary = 1
value = 1
[../]
[]
[Executioner]
type = Steady
solve_type = 'PJFNK'
[]
[Adaptivity]
steps = 3
marker = 'combo'
[./Markers]
[./combo]
# In a real problem you would want to mark based on an error
# indicator, but we want this test to run consistently in
# parallel, so we just mark elements within a box for
# refinement. The boxes here are based on the 8x8
# uniformly-refined initial grid.
type = ComboMarker
markers = 'box1 box2 box3'
[../]
[./box1]
type = BoxMarker
bottom_left = '0.125 0.625 0'
top_right = '0.375 0.875 0'
inside = refine
outside = dont_mark
[../]
[./box2]
type = BoxMarker
bottom_left = '0.625 0.625 0'
top_right = '0.875 0.875 0'
inside = refine
outside = dont_mark
[../]
[./box3]
type = BoxMarker
bottom_left = '0.625 0.125 0'
top_right = '0.875 0.375 0'
inside = refine
outside = dont_mark
[../]
[../]
[]
[Outputs]
execute_on = 'timestep_end'
exodus = true
[]
test/tests/postprocessors/num_adaptivity_cycles/num_adaptivity_cycles_toggle_adaptivity_wait.i
[Mesh]
type = GeneratedMesh
dim = 2
nx = 10
ny = 10
nz = 0
zmax = 0
elem_type = QUAD4
[]
[Variables]
[./u]
order = FIRST
family = LAGRANGE
[../]
[]
[Functions]
[./force]
type = ParsedFunction
value = t
[../]
[]
[Kernels]
[./diff]
type = Diffusion
variable = u
[../]
[./force]
type = BodyForce
variable = u
function = force
[../]
[]
[BCs]
[./right]
type = DirichletBC
variable = u
boundary = right
value = 1
[../]
[./left]
type = DirichletBC
variable = u
boundary = left
value = 0
[../]
[]
[Executioner]
type = Transient
num_steps = 4
dt = 1
solve_type = 'PJFNK'
[]
[Adaptivity]
cycles_per_step = 1
marker = box
max_h_level = 2
initial_steps = 4
initial_marker = initial_box
[./Markers]
[./box]
bottom_left = '0.3 0.3 0'
inside = refine
top_right = '0.6 0.6 0'
outside = dont_mark
type = BoxMarker
[../]
[./initial_box]
type = BoxMarker
bottom_left = '0.8 0.1 0'
top_right = '0.9 0.2 0'
inside = refine
outside = dont_mark
[../]
[../]
[]
[UserObjects]
[./toggle_adaptivity]
type = ToggleMeshAdaptivity
mesh_adaptivity = 'off'
apply_after_timestep = 1
[../]
[]
[Postprocessors]
[./adaptivity_cycles]
type = NumAdaptivityCycles
execute_on = 'initial timestep_end'
[../]
[]
[Outputs]
csv = true
[]
modules/level_set/test/tests/transfers/markers/single_level/master.i
[Mesh]
type = GeneratedMesh
dim = 2
nx = 10
ny = 10
[]
[Adaptivity]
marker = marker
max_h_level = 1
[./Markers]
[./marker]
type = BoxMarker
bottom_left = '0.25 0.25 0'
top_right = '0.75 0.75 0'
outside = DO_NOTHING
inside = REFINE
[../]
[../]
[]
[Variables]
[./u]
[../]
[]
[Kernels]
[./time]
type = TimeDerivative
variable = u
[../]
[./diff]
type = Diffusion
variable = u
[../]
[]
[BCs]
[./left]
type = DirichletBC
variable = u
boundary = left
value = 0
[../]
[./right]
type = DirichletBC
variable = u
boundary = right
value = 1
[../]
[]
[Problem]
type = LevelSetProblem
[]
[Executioner]
type = Transient
num_steps = 2
solve_type = 'PJFNK'
petsc_options_iname = '-pc_type -pc_hypre_type'
petsc_options_value = 'hypre boomeramg'
[]
[MultiApps]
[./sub]
type = LevelSetReinitializationMultiApp
input_files = 'sub.i'
execute_on = TIMESTEP_BEGIN
[../]
[]
[Transfers]
[./marker_to_sub]
type = LevelSetMeshRefinementTransfer
multi_app = sub
source_variable = marker
variable = marker
[../]
[]
[Outputs]
exodus = true
[]
test/tests/outputs/exodus/variable_output_test.i
[Mesh]
type = GeneratedMesh
dim = 2
nx = 10
ny = 10
nz = 0
zmax = 0
elem_type = QUAD4
[]
[Variables]
[./u]
order = FIRST
family = LAGRANGE
[../]
[]
[AuxVariables]
[./aux]
family = SCALAR
[../]
[]
[Functions]
[./force]
type = ParsedFunction
value = t
[../]
[]
[Kernels]
[./diff]
type = Diffusion
variable = u
[../]
[./force]
type = BodyForce
variable = u
function = force
[../]
[]
[BCs]
[./right]
type = DirichletBC
variable = u
boundary = right
value = 1
[../]
[./left]
type = DirichletBC
variable = u
boundary = left
value = 0
[../]
[]
[Executioner]
type = Transient
num_steps = 4
dt = 1
solve_type = PJFNK
[]
[Adaptivity]
steps = 1
marker = box
max_h_level = 2
[./Markers]
[./box]
bottom_left = '0.3 0.3 0'
inside = refine
top_right = '0.6 0.6 0'
outside = do_nothing
type = BoxMarker
[../]
[../]
[]
[Postprocessors]
[./aux_pp]
type = ScalarVariable
variable = aux
outputs = none
[../]
[]
[Outputs]
execute_on = 'timestep_end'
[./exodus]
type = Exodus
file_base = new_out
hide_variables = 'u box aux_pp'
scalar_as_nodal = true
execute_scalars_on = none
[../]
[./console]
Type = Console
[../]
[]
test/tests/userobjects/toggle_mesh_adaptivity/toggle_mesh_adaptivity.i
[Mesh]
type = GeneratedMesh
dim = 2
nx = 20
ny = 20
[]
[Variables]
[./u]
[../]
[]
[Kernels]
[./diff]
type = Diffusion
variable = u
[../]
[]
[Problem]
solve = false
[]
[Executioner]
type = Transient
num_steps = 4
dt = 0.1
[]
[Adaptivity]
cycles_per_step = 1
marker = marker
max_h_level = 2
[./Markers]
[./marker]
type = BoxMarker
bottom_left = '0.35 0.25 0'
top_right = '0.5 0.5 0'
inside = refine
outside = coarsen
[../]
[../]
[]
[UserObjects]
[./mesh_adaptivity_off]
type = ToggleMeshAdaptivity
mesh_adaptivity = 'off'
[../]
[]
[Outputs]
exodus = true
[./console]
type = Console
print_mesh_changed_info = true
[../]
[]
test/tests/postprocessors/memory_usage/vector_memory_usage.i
[Mesh]
type = GeneratedMesh
dim = 2
nx = 20
ny = 20
[]
[GlobalParams]
order = CONSTANT
family = MONOMIAL
[]
[Variables]
[./u]
[../]
[]
[Adaptivity]
[./Markers]
[./box]
type = BoxMarker
bottom_left = '0.6 0.7 0'
top_right = '0.9 0.9 0'
inside = refine
outside = do_nothing
[../]
[../]
marker = box
[]
[Problem]
kernel_coverage_check = false
solve = false
[]
[VectorPostprocessors]
[./mem]
type = VectorMemoryUsage
execute_on = 'INITIAL TIMESTEP_END NONLINEAR LINEAR'
report_peak_value = true
mem_units = kilobytes # or bytes, megabytes, gigabytes
[../]
[]
[Executioner]
type = Transient
num_steps = 2
[]
[Outputs]
csv = true
[]
test/tests/adaptivity/initial_adapt/initial_adapt.i
[Mesh]
type = GeneratedMesh
dim = 2
nx = 10
ny = 10
nz = 0
zmax = 0
elem_type = QUAD4
[]
[Variables]
[./u]
order = FIRST
family = LAGRANGE
[../]
[]
[Functions]
[./force]
type = ParsedFunction
value = t
[../]
[]
[Kernels]
[./diff]
type = Diffusion
variable = u
[../]
[./force]
type = BodyForce
variable = u
function = force
[../]
[]
[BCs]
[./right]
type = DirichletBC
variable = u
boundary = right
value = 1
[../]
[./left]
type = DirichletBC
variable = u
boundary = left
value = 0
[../]
[]
[Executioner]
type = Transient
num_steps = 4
dt = 1
solve_type = 'PJFNK'
[]
[Adaptivity]
steps = 1
marker = box
max_h_level = 2
initial_steps = 2
[./Markers]
[./box]
bottom_left = '0.3 0.3 0'
inside = refine
top_right = '0.6 0.6 0'
outside = do_nothing
type = BoxMarker
[../]
[../]
[]
[Outputs]
exodus = true
[]
test/tests/adaptivity/interval/adapt_interval.i
[Mesh]
type = GeneratedMesh
dim = 2
nx = 10
ny = 10
nz = 0
zmax = 0
elem_type = QUAD4
[]
[Variables]
[./u]
order = FIRST
family = LAGRANGE
[../]
[]
[Functions]
[./force]
type = ParsedFunction
value = t
[../]
[]
[Kernels]
[./diff]
type = Diffusion
variable = u
[../]
[./force]
type = BodyForce
variable = u
function = force
[../]
[]
[BCs]
[./right]
type = DirichletBC
variable = u
boundary = right
value = 1
[../]
[./left]
type = DirichletBC
variable = u
boundary = left
value = 0
[../]
[]
[Executioner]
type = Transient
num_steps = 6
dt = 1
solve_type = 'PJFNK'
[]
[Adaptivity]
steps = 1
marker = box
max_h_level = 2
interval = 2
[./Markers]
[./box]
bottom_left = '0.3 0.3 0'
inside = refine
top_right = '0.6 0.6 0'
outside = do_nothing
type = BoxMarker
[../]
[../]
[]
[Outputs]
exodus = true
[]
test/tests/markers/box_marker/box_marker_test.i
[Mesh]
type = GeneratedMesh
dim = 2
nx = 10
ny = 10
nz = 0
zmax = 0
elem_type = QUAD4
[]
[Variables]
[./u]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
[./diff]
type = Diffusion
variable = u
[../]
[]
[BCs]
[./left]
type = DirichletBC
variable = u
boundary = 1
value = 0
[../]
[./right]
type = DirichletBC
variable = u
boundary = 2
value = 1
[../]
[]
[Executioner]
type = Steady
solve_type = 'PJFNK'
[]
[Adaptivity]
[./Markers]
[./box]
type = BoxMarker
bottom_left = '0.3 0.3 0'
top_right = '0.6 0.6 0'
inside = refine
outside = do_nothing
[../]
[../]
[]
[Outputs]
exodus = true
[]
modules/combined/test/tests/contact_adaptivity/sm/contact_initial_adaptivity_sm.i
# This is a test of the usage of initial adaptivity with contact.
# It ensures that contact is enforced on the new nodes that are
# created due to refinement on the slave side of the interface.
[GlobalParams]
volumetric_locking_correction = false
[]
[Mesh]
file = 2blocks.e
displacements = 'disp_x disp_y'
patch_size = 80
parallel_type = replicated
[]
[Variables]
[./disp_x]
[../]
[./disp_y]
[../]
[]
[AuxVariables]
[./penetration]
order = FIRST
family = LAGRANGE
[../]
[]
[Functions]
[./negramp]
type = ParsedFunction
value = -t/10
[../]
[]
[SolidMechanics]
[./solid]
disp_x = disp_x
disp_y = disp_y
[../]
[]
[AuxKernels]
[./penetration]
type = PenetrationAux
variable = penetration
boundary = 3
paired_boundary = 2
[../]
[]
[Postprocessors]
[./nonlinear_its]
type = NumNonlinearIterations
execute_on = timestep_end
[../]
[]
[BCs]
[./left_x]
type = DirichletBC
variable = disp_x
boundary = 1
value = 0.0
[../]
[./left_y]
type = DirichletBC
variable = disp_y
boundary = 1
value = 0.0
[../]
[./right_x]
type = FunctionDirichletBC
variable = disp_x
boundary = 4
function = negramp
[../]
[./right_y]
type = DirichletBC
variable = disp_y
boundary = 4
value = 0.0
[../]
[]
[Materials]
[./left]
type = Elastic
formulation = NonlinearPlaneStrain
block = '1 2'
disp_y = disp_y
disp_x = disp_x
poissons_ratio = 0.3
youngs_modulus = 1e6
[../]
[]
[Contact]
[./leftright]
slave = 3
displacements = 'disp_x disp_y'
master = 2
model = frictionless
penalty = 1e+6
system = constraint
normal_smoothing_distance = 0.1
[../]
[]
[Adaptivity]
steps = 0
marker = box
max_h_level = 2
initial_steps = 2
[./Markers]
[./box]
type = BoxMarker
bottom_left = '0.5 -2.0 0.0'
top_right = '0.75 2.0 0.0'
inside = refine
outside = do_nothing
[../]
[../]
[]
[Executioner]
type = Transient
solve_type = 'PJFNK'
petsc_options_iname = '-pc_type -pc_factor_mat_solver_package'
petsc_options_value = 'lu superlu_dist'
line_search = 'none'
l_max_its = 100
nl_max_its = 1000
dt = 0.2
end_time = 1.0
l_tol = 1e-6
nl_rel_tol = 1e-12
nl_abs_tol = 1e-9
[]
[Outputs]
exodus = true
console = true
[]
test/tests/postprocessors/num_elems/num_elems.i
[Mesh]
type = GeneratedMesh
dim = 2
nx = 4
ny = 4
nz = 0
zmax = 0
elem_type = QUAD4
uniform_refine = 1
[]
[Variables]
[./u]
order = FIRST
family = LAGRANGE
[../]
[]
[AuxVariables]
[./u_aux]
order = FIRST
family = LAGRANGE
[../]
[./v_aux]
order = FIRST
family = LAGRANGE
[../]
[]
[Functions]
[./force]
type = ParsedFunction
value = t
[../]
[]
[Kernels]
[./diff]
type = Diffusion
variable = u
[../]
[./force]
type = BodyForce
variable = u
function = force
[../]
[]
[BCs]
[./right]
type = DirichletBC
variable = u
boundary = right
value = 1
[../]
[./left]
type = DirichletBC
variable = u
boundary = left
value = 0
[../]
[]
[Executioner]
type = Transient
num_steps = 3
dt = 1
solve_type = PJFNK
[]
[Adaptivity]
steps = 1
marker = box
max_h_level = 3
[./Markers]
[./box]
bottom_left = '0.3 0.3 0'
inside = refine
top_right = '0.6 0.6 0'
outside = do_nothing
type = BoxMarker
[../]
[../]
[]
[Postprocessors]
[./num_elems_active]
type = NumElems
elem_filter = 'ACTIVE'
execute_on = 'initial timestep_end'
[../]
[./num_elems_total]
type = NumElems
elem_filter = 'TOTAL'
execute_on = 'initial timestep_end'
[../]
[]
[Outputs]
csv = true
[]
test/tests/postprocessors/num_adaptivity_cycles/num_adaptivity_cycles_toggle_adaptivity.i
[Mesh]
type = GeneratedMesh
dim = 2
nx = 10
ny = 10
nz = 0
zmax = 0
elem_type = QUAD4
[]
[Variables]
[./u]
order = FIRST
family = LAGRANGE
[../]
[]
[Functions]
[./force]
type = ParsedFunction
value = t
[../]
[]
[Kernels]
[./diff]
type = Diffusion
variable = u
[../]
[./force]
type = BodyForce
variable = u
function = force
[../]
[]
[BCs]
[./right]
type = DirichletBC
variable = u
boundary = right
value = 1
[../]
[./left]
type = DirichletBC
variable = u
boundary = left
value = 0
[../]
[]
[Executioner]
type = Transient
num_steps = 4
dt = 1
solve_type = 'PJFNK'
[]
[Adaptivity]
cycles_per_step = 1
marker = box
max_h_level = 2
initial_steps = 4
initial_marker = initial_box
[./Markers]
[./box]
bottom_left = '0.3 0.3 0'
inside = refine
top_right = '0.6 0.6 0'
outside = dont_mark
type = BoxMarker
[../]
[./initial_box]
type = BoxMarker
bottom_left = '0.8 0.1 0'
top_right = '0.9 0.2 0'
inside = refine
outside = dont_mark
[../]
[../]
[]
[UserObjects]
[./toggle_adaptivity]
type = ToggleMeshAdaptivity
mesh_adaptivity = 'off'
[../]
[]
[Postprocessors]
[./adaptivity_cycles]
type = NumAdaptivityCycles
execute_on = 'initial timestep_end'
[../]
[]
[Outputs]
csv = true
[]
test/tests/postprocessors/num_nodes/num_nodes.i
[Mesh]
type = GeneratedMesh
dim = 2
nx = 4
ny = 4
nz = 0
zmax = 0
elem_type = QUAD4
uniform_refine = 1
[]
[Variables]
[./u]
order = FIRST
family = LAGRANGE
[../]
[]
[AuxVariables]
[./u_aux]
order = FIRST
family = LAGRANGE
[../]
[./v_aux]
order = FIRST
family = LAGRANGE
[../]
[]
[Functions]
[./force]
type = ParsedFunction
value = t
[../]
[]
[Kernels]
[./diff]
type = Diffusion
variable = u
[../]
[./force]
type = BodyForce
variable = u
function = force
[../]
[]
[BCs]
[./right]
type = DirichletBC
variable = u
boundary = right
value = 1
[../]
[./left]
type = DirichletBC
variable = u
boundary = left
value = 0
[../]
[]
[Executioner]
type = Transient
num_steps = 3
dt = 1
solve_type = PJFNK
[]
[Adaptivity]
steps = 1
marker = box
max_h_level = 3
[./Markers]
[./box]
bottom_left = '0.3 0.3 0'
inside = refine
top_right = '0.6 0.6 0'
outside = do_nothing
type = BoxMarker
[../]
[../]
[]
[Postprocessors]
[./num_nodes]
type = NumNodes
execute_on = 'initial timestep_end'
[../]
[]
[Outputs]
csv = true
[]
test/tests/time_integrators/explicit-euler/ee-2d-linear-adapt.i
[Mesh]
type = GeneratedMesh
dim = 2
xmin = -1
xmax = 1
ymin = -1
ymax = 1
nx = 10
ny = 10
elem_type = QUAD4
[]
[Functions]
[./ic]
type = ParsedFunction
value = 0
[../]
[./forcing_fn]
type = ParsedFunction
value = (x+y)
[../]
[./exact_fn]
type = ParsedFunction
value = t*(x+y)
[../]
[]
[Variables]
[./u]
order = FIRST
family = LAGRANGE
[./InitialCondition]
type = FunctionIC
function = ic
[../]
[../]
[]
[Kernels]
[./ie]
type = TimeDerivative
variable = u
lumping = true
implicit = true
[../]
[./diff]
type = Diffusion
variable = u
implicit = false
[../]
[./ffn]
type = BodyForce
variable = u
function = forcing_fn
implicit = false
[../]
[]
[BCs]
active = 'all'
[./all]
type = FunctionDirichletBC
variable = u
boundary = '0 1 2 3'
function = exact_fn
implicit = true
[../]
[]
[Adaptivity]
steps = 1
marker = box
max_h_level = 2
[./Markers]
[./box]
bottom_left = '-0.4 -0.4 0'
inside = refine
top_right = '0.4 0.4 0'
outside = do_nothing
type = BoxMarker
[../]
[../]
[]
[Postprocessors]
[./l2_err]
type = ElementL2Error
variable = u
function = exact_fn
[../]
[]
[Executioner]
type = Transient
scheme = 'explicit-euler'
start_time = 0.0
num_steps = 4
dt = 0.005
[]
[Outputs]
exodus = true
[./console]
type = Console
max_rows = 10
[../]
[]
test/tests/markers/box_marker/box_marker_adapt_test.i
[Mesh]
type = GeneratedMesh
dim = 2
nx = 10
ny = 10
nz = 0
zmax = 0
elem_type = QUAD4
[]
[Variables]
[./u]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
[./diff]
type = Diffusion
variable = u
[../]
[]
[BCs]
[./right]
type = DirichletBC
variable = u
boundary = right
value = 1
[../]
[./top]
type = DirichletBC
variable = u
boundary = top
value = 0
[../]
[]
[Executioner]
type = Steady
solve_type = 'PJFNK'
[]
[Adaptivity]
steps = 1
marker = box
[./Markers]
[./box]
bottom_left = '0.3 0.3 0'
inside = refine
top_right = '0.6 0.6 0'
outside = do_nothing
type = BoxMarker
[../]
[../]
[]
[Outputs]
exodus = true
[]
modules/porous_flow/examples/lava_lamp/2phase_convection.i
# Two phase density-driven convection of dissolved CO2 in brine
#
# Initially, the model has a gas phase at the top with a saturation of 0.29
# (which corresponds to an initial value of zi = 0.2).
# Diffusion of the dissolved CO2
# component from the saturated liquid to the unsaturated liquid below reduces the
# amount of CO2 in the gas phase. As the density of the CO2-saturated brine is greater
# than the unsaturated brine, a gravitational instability arises and density-driven
# convection of CO2-rich fingers descend into the unsaturated brine.
#
# The instability is seeded by a random perturbation to the porosity field.
# Mesh adaptivity is used to refine the mesh as the fingers form.
[GlobalParams]
PorousFlowDictator = 'dictator'
gravity = '0 -9.81 0'
[]
[Adaptivity]
max_h_level = 2
marker = marker
initial_marker = initial
initial_steps = 2
[./Indicators]
[./indicator]
type = GradientJumpIndicator
variable = zi
[../]
[../]
[./Markers]
[./marker]
type = ErrorFractionMarker
indicator = indicator
refine = 0.8
[../]
[./initial]
type = BoxMarker
bottom_left = '0 1.95 0'
top_right = '2 2 0'
inside = REFINE
outside = DO_NOTHING
[../]
[../]
[]
[Mesh]
type = GeneratedMesh
dim = 2
ymax = 2
xmax = 2
ny = 40
nx = 40
bias_y = 0.95
[]
[AuxVariables]
[./xnacl]
initial_condition = 0.01
[../]
[./saturation_gas]
order = FIRST
family = MONOMIAL
[../]
[./xco2l]
order = FIRST
family = MONOMIAL
[../]
[./density_liquid]
order = FIRST
family = MONOMIAL
[../]
[./porosity]
order = CONSTANT
family = MONOMIAL
[../]
[]
[AuxKernels]
[./saturation_gas]
type = PorousFlowPropertyAux
variable = saturation_gas
property = saturation
phase = 1
execute_on = 'timestep_end'
[../]
[./xco2l]
type = PorousFlowPropertyAux
variable = xco2l
property = mass_fraction
phase = 0
fluid_component = 1
execute_on = 'timestep_end'
[../]
[./density_liquid]
type = PorousFlowPropertyAux
variable = density_liquid
property = density
phase = 0
execute_on = 'timestep_end'
[../]
[]
[Variables]
[./pgas]
[../]
[./zi]
scaling = 1e4
[../]
[]
[ICs]
[./pressure]
type = FunctionIC
function = 10e6-9.81*1000*y
variable = pgas
[../]
[./zi]
type = BoundingBoxIC
variable = zi
x1 = 0
x2 = 2
y1 = 1.95
y2 = 2
inside = 0.2
outside = 0
[../]
[./porosity]
type = RandomIC
variable = porosity
min = 0.25
max = 0.275
[../]
[]
[Kernels]
[./mass0]
type = PorousFlowMassTimeDerivative
fluid_component = 0
variable = pgas
[../]
[./flux0]
type = PorousFlowAdvectiveFlux
fluid_component = 0
variable = pgas
[../]
[./diff0]
type = PorousFlowDispersiveFlux
fluid_component = 0
variable = pgas
disp_long = '0 0'
disp_trans = '0 0'
[../]
[./mass1]
type = PorousFlowMassTimeDerivative
fluid_component = 1
variable = zi
[../]
[./flux1]
type = PorousFlowAdvectiveFlux
fluid_component = 1
variable = zi
[../]
[./diff1]
type = PorousFlowDispersiveFlux
fluid_component = 1
variable = zi
disp_long = '0 0'
disp_trans = '0 0'
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = 'pgas zi'
number_fluid_phases = 2
number_fluid_components = 2
[../]
[./pc]
type = PorousFlowCapillaryPressureConst
pc = 0
[../]
[./fs]
type = PorousFlowBrineCO2
brine_fp = brine
co2_fp = co2
capillary_pressure = pc
[../]
[]
[Modules]
[./FluidProperties]
[./co2sw]
type = CO2FluidProperties
[../]
[./co2]
type = TabulatedFluidProperties
fp = co2sw
[../]
[./brine]
type = BrineFluidProperties
[../]
[../]
[]
[Materials]
[./temperature]
type = PorousFlowTemperature
temperature = '45'
[../]
[./brineco2]
type = PorousFlowFluidState
gas_porepressure = 'pgas'
z = 'zi'
temperature_unit = Celsius
xnacl = 'xnacl'
capillary_pressure = pc
fluid_state = fs
[../]
[./porosity]
type = PorousFlowPorosityConst
porosity = porosity
[../]
[./permeability]
type = PorousFlowPermeabilityConst
permeability = '1e-11 0 0 0 1e-11 0 0 0 1e-11'
[../]
[./relperm_water]
type = PorousFlowRelativePermeabilityCorey
phase = 0
n = 2
s_res = 0.1
sum_s_res = 0.2
[../]
[./relperm_gas]
type = PorousFlowRelativePermeabilityCorey
phase = 1
n = 2
s_res = 0.1
sum_s_res = 0.2
[../]
[./diffusivity]
type = PorousFlowDiffusivityConst
diffusion_coeff = '2e-9 2e-9 2e-9 2e-9'
tortuosity = '1 1'
[../]
[]
[Preconditioning]
active = basic
[./mumps_is_best_for_parallel_jobs]
type = SMP
full = true
petsc_options_iname = '-pc_type -pc_factor_mat_solver_package'
petsc_options_value = ' lu mumps'
[../]
[./basic]
type = SMP
full = true
petsc_options_iname = '-ksp_type -pc_type -sub_pc_type -sub_pc_factor_shift_type -pc_asm_overlap'
petsc_options_value = 'gmres asm lu NONZERO 2 '
[../]
[]
[Executioner]
type = Transient
solve_type = NEWTON
end_time = 1e6
nl_max_its = 25
l_max_its = 100
dtmax = 1e4
nl_abs_tol = 1e-6
[./TimeStepper]
type = IterationAdaptiveDT
dt = 10
growth_factor = 2
cutback_factor = 0.5
[../]
[]
[Functions]
[./flux]
type = ParsedFunction
vals = 'delta_xco2 dt'
vars = 'dx dt'
value = 'dx/dt'
[../]
[]
[Postprocessors]
[./total_co2_in_gas]
type = PorousFlowFluidMass
phase = 1
fluid_component = 1
[../]
[./total_co2_in_liquid]
type = PorousFlowFluidMass
phase = 0
fluid_component = 1
[../]
[./numdofs]
type = NumDOFs
[../]
[./delta_xco2]
type = ChangeOverTimePostprocessor
postprocessor = total_co2_in_liquid
[../]
[./dt]
type = TimestepSize
[../]
[./flux]
type = FunctionValuePostprocessor
function = flux
[../]
[]
[Outputs]
print_linear_residuals = false
perf_graph = true
exodus = true
csv = true
[]
test/tests/adaptivity/initial_marker/initial_marker.i
[Mesh]
type = GeneratedMesh
dim = 2
nx = 10
ny = 10
nz = 0
zmax = 0
elem_type = QUAD4
[]
[Variables]
[./u]
order = FIRST
family = LAGRANGE
[../]
[]
[Functions]
[./force]
type = ParsedFunction
value = t
[../]
[]
[Kernels]
[./diff]
type = Diffusion
variable = u
[../]
[./force]
type = BodyForce
variable = u
function = force
[../]
[]
[BCs]
[./right]
type = DirichletBC
variable = u
boundary = right
value = 1
[../]
[./left]
type = DirichletBC
variable = u
boundary = left
value = 0
[../]
[]
[Executioner]
type = Transient
num_steps = 4
dt = 1
solve_type = 'PJFNK'
[]
[Adaptivity]
steps = 1
marker = box
max_h_level = 2
initial_steps = 4
initial_marker = initial_box
[./Markers]
[./box]
bottom_left = '0.3 0.3 0'
inside = refine
top_right = '0.6 0.6 0'
outside = dont_mark
type = BoxMarker
[../]
[./initial_box]
type = BoxMarker
bottom_left = '0.8 0.1 0'
top_right = '0.9 0.2 0'
inside = refine
outside = dont_mark
[../]
[../]
[]
[Outputs]
execute_on = 'timestep_end'
exodus = true
[]
modules/porous_flow/examples/lava_lamp/1phase_convection.i
# Two phase density-driven convection of dissolved CO2 in brine
#
# The model starts with CO2 in the liquid phase only. The CO2 diffuses into the brine.
# As the density of the CO2-saturated brine is greater
# than the unsaturated brine, a gravitational instability arises and density-driven
# convection of CO2-rich fingers descend into the unsaturated brine.
#
# The instability is seeded by a random perturbation to the porosity field.
# Mesh adaptivity is used to refine the mesh as the fingers form.
[GlobalParams]
PorousFlowDictator = 'dictator'
gravity = '0 -9.81 0'
[]
[Adaptivity]
max_h_level = 2
marker = marker
initial_marker = initial
initial_steps = 2
[./Indicators]
[./indicator]
type = GradientJumpIndicator
variable = zi
[../]
[../]
[./Markers]
[./marker]
type = ErrorFractionMarker
indicator = indicator
refine = 0.8
[../]
[./initial]
type = BoxMarker
bottom_left = '0 1.95 0'
top_right = '2 2 0'
inside = REFINE
outside = DO_NOTHING
[../]
[../]
[]
[Mesh]
type = GeneratedMesh
dim = 2
ymin = 1.5
ymax = 2
xmax = 2
ny = 20
nx = 40
bias_y = 0.95
[]
[AuxVariables]
[./xnacl]
initial_condition = 0.01
[../]
[./saturation_gas]
order = FIRST
family = MONOMIAL
[../]
[./xco2l]
order = FIRST
family = MONOMIAL
[../]
[./density_liquid]
order = FIRST
family = MONOMIAL
[../]
[./porosity]
order = CONSTANT
family = MONOMIAL
[../]
[]
[AuxKernels]
[./saturation_gas]
type = PorousFlowPropertyAux
variable = saturation_gas
property = saturation
phase = 1
execute_on = 'timestep_end'
[../]
[./xco2l]
type = PorousFlowPropertyAux
variable = xco2l
property = mass_fraction
phase = 0
fluid_component = 1
execute_on = 'timestep_end'
[../]
[./density_liquid]
type = PorousFlowPropertyAux
variable = density_liquid
property = density
phase = 0
execute_on = 'timestep_end'
[../]
[]
[Variables]
[./pgas]
[../]
[./zi]
scaling = 1e4
[../]
[]
[ICs]
[./pressure]
type = FunctionIC
function = 10e6-9.81*1000*y
variable = pgas
[../]
[./zi]
type = ConstantIC
value = 0
variable = zi
[../]
# [./zi]
# type = BoundingBoxIC
# variable = zi
# x1 = 0
# x2 = 2
# y1 = 1.95
# y2 = 2
# inside = 0.1
# outside = 0
# [../]
[./porosity]
type = RandomIC
variable = porosity
min = 0.25
max = 0.275
[../]
[]
[BCs]
[./top]
type = DirichletBC
value = 0.04
variable = zi
boundary = top
[../]
[]
[Kernels]
[./mass0]
type = PorousFlowMassTimeDerivative
fluid_component = 0
variable = pgas
[../]
[./flux0]
type = PorousFlowAdvectiveFlux
fluid_component = 0
variable = pgas
[../]
[./diff0]
type = PorousFlowDispersiveFlux
fluid_component = 0
variable = pgas
disp_long = '0 0'
disp_trans = '0 0'
[../]
[./mass1]
type = PorousFlowMassTimeDerivative
fluid_component = 1
variable = zi
[../]
[./flux1]
type = PorousFlowAdvectiveFlux
fluid_component = 1
variable = zi
[../]
[./diff1]
type = PorousFlowDispersiveFlux
fluid_component = 1
variable = zi
disp_long = '0 0'
disp_trans = '0 0'
[../]
[]
[UserObjects]
[./dictator]
type = PorousFlowDictator
porous_flow_vars = 'pgas zi'
number_fluid_phases = 2
number_fluid_components = 2
[../]
[./pc]
type = PorousFlowCapillaryPressureConst
pc = 0
[../]
[./fs]
type = PorousFlowBrineCO2
brine_fp = brine
co2_fp = co2
capillary_pressure = pc
[../]
[]
[Modules]
[./FluidProperties]
[./co2sw]
type = CO2FluidProperties
[../]
[./co2]
type = TabulatedFluidProperties
fp = co2sw
[../]
[./brine]
type = BrineFluidProperties
[../]
[../]
[]
[Materials]
[./temperature]
type = PorousFlowTemperature
temperature = '45'
[../]
[./brineco2]
type = PorousFlowFluidState
gas_porepressure = 'pgas'
z = 'zi'
temperature_unit = Celsius
xnacl = 'xnacl'
capillary_pressure = pc
fluid_state = fs
[../]
[./porosity]
type = PorousFlowPorosityConst
porosity = porosity
[../]
[./permeability]
type = PorousFlowPermeabilityConst
permeability = '1e-11 0 0 0 1e-11 0 0 0 1e-11'
[../]
[./relperm_water]
type = PorousFlowRelativePermeabilityCorey
phase = 0
n = 2
s_res = 0.1
sum_s_res = 0.2
[../]
[./relperm_gas]
type = PorousFlowRelativePermeabilityCorey
phase = 1
n = 2
s_res = 0.1
sum_s_res = 0.2
[../]
[./diffusivity]
type = PorousFlowDiffusivityConst
diffusion_coeff = '2e-9 2e-9 2e-9 2e-9'
tortuosity = '1 1'
[../]
[]
[Preconditioning]
active = basic
[./mumps_is_best_for_parallel_jobs]
type = SMP
full = true
petsc_options_iname = '-pc_type -pc_factor_mat_solver_package'
petsc_options_value = ' lu mumps'
[../]
[./basic]
type = SMP
full = true
petsc_options_iname = '-ksp_type -pc_type -sub_pc_type -sub_pc_factor_shift_type -pc_asm_overlap'
petsc_options_value = 'gmres asm lu NONZERO 2 '
[../]
[]
[Executioner]
type = Transient
solve_type = NEWTON
end_time = 1e6
nl_max_its = 25
l_max_its = 100
dtmax = 1e4
nl_abs_tol = 1e-6
[./TimeStepper]
type = IterationAdaptiveDT
dt = 100
growth_factor = 2
cutback_factor = 0.5
[../]
[]
[Functions]
[./flux]
type = ParsedFunction
vals = 'delta_xco2 dt'
vars = 'dx dt'
value = 'dx/dt'
[../]
[]
[Postprocessors]
[./total_co2_in_gas]
type = PorousFlowFluidMass
phase = 1
fluid_component = 1
[../]
[./total_co2_in_liquid]
type = PorousFlowFluidMass
phase = 0
fluid_component = 1
[../]
[./numdofs]
type = NumDOFs
[../]
[./delta_xco2]
type = ChangeOverTimePostprocessor
postprocessor = total_co2_in_liquid
[../]
[./dt]
type = TimestepSize
[../]
[./flux]
type = FunctionValuePostprocessor
function = flux
[../]
[]
[Outputs]
print_linear_residuals = false
perf_graph = true
exodus = true
csv = true
[]
test/tests/materials/stateful_prop/spatial_adaptivity_test.i
[Mesh]
type = GeneratedMesh
dim = 2
nx = 2
ny = 2
uniform_refine = 3
# This option is necessary if you have uniform refinement + stateful material properties + adaptivity
skip_partitioning = true
# stateful material properties + adaptivity are not yet compatible
# with distributed meshes
parallel_type = replicated
[]
[Variables]
[./u]
[../]
[]
[AuxVariables]
[./ssm]
order = CONSTANT
family = MONOMIAL
[../]
[]
[Kernels]
[./diff]
type = Diffusion
variable = u
[../]
[./conv]
type = Convection
variable = u
velocity = '1 0 0'
[../]
[]
[AuxKernels]
[./ssm]
type = MaterialRealAux
variable = ssm
property = diffusivity
[../]
[]
[BCs]
[./left]
type = DirichletBC
variable = u
boundary = left
value = 0
[../]
[./right]
type = DirichletBC
variable = u
boundary = right
value = 1
[../]
[]
[Materials]
[./ssm]
type = SpatialStatefulMaterial
block = 0
[../]
[]
[Executioner]
type = Transient
solve_type = 'PJFNK'
num_steps = 4
dt = 1
petsc_options_iname = '-pc_type -pc_hypre_type'
petsc_options_value = 'hypre boomeramg'
[]
[Adaptivity]
marker = box
[./Markers]
[./box]
type = BoxMarker
bottom_left = '0.2 0.2 0'
top_right = '0.4 0.4 0'
inside = refine
outside = coarsen
[../]
[../]
[]
[Outputs]
execute_on = 'timestep_end'
exodus = true
[]
test/tests/postprocessors/num_adaptivity_cycles/num_adaptivity_cycles.i
[Mesh]
type = GeneratedMesh
dim = 2
nx = 10
ny = 10
nz = 0
zmax = 0
elem_type = QUAD4
[]
[Variables]
[./u]
order = FIRST
family = LAGRANGE
[../]
[]
[Functions]
[./force]
type = ParsedFunction
value = t
[../]
[]
[Kernels]
[./diff]
type = Diffusion
variable = u
[../]
[./force]
type = BodyForce
variable = u
function = force
[../]
[]
[BCs]
[./right]
type = DirichletBC
variable = u
boundary = right
value = 1
[../]
[./left]
type = DirichletBC
variable = u
boundary = left
value = 0
[../]
[]
[Executioner]
type = Transient
num_steps = 4
dt = 1
solve_type = 'PJFNK'
[]
[Adaptivity]
cycles_per_step = 1
marker = box
max_h_level = 2
initial_steps = 4
initial_marker = initial_box
[./Markers]
[./box]
bottom_left = '0.3 0.3 0'
inside = refine
top_right = '0.6 0.6 0'
outside = dont_mark
type = BoxMarker
[../]
[./initial_box]
type = BoxMarker
bottom_left = '0.8 0.1 0'
top_right = '0.9 0.2 0'
inside = refine
outside = dont_mark
[../]
[../]
[]
[Postprocessors]
[./adaptivity_cycles]
type = NumAdaptivityCycles
execute_on = 'initial timestep_end'
[../]
[]
[Outputs]
csv = true
[]
test/tests/interfacekernels/adaptivity/adaptivity.i
# This input file is used for two tests:
# 1) Check that InterfaceKernels work with mesh adaptivity
# 2) Error out when InterfaceKernels are used with adaptivity
# and stateful material prpoerties
[Mesh]
parallel_type = 'replicated'
[gen]
type = GeneratedMeshGenerator
dim = 2
nx = 2
ny = 2
[]
[./subdomain1]
input = gen
type = SubdomainBoundingBoxGenerator
bottom_left = '0.5 0 0'
top_right = '1 1 0'
block_id = 1
[../]
[./interface]
type = SideSetsBetweenSubdomainsGenerator
input = subdomain1
master_block = '0'
paired_block = '1'
new_boundary = 'master0_interface'
[../]
[./break_boundary]
input = interface
type = BreakBoundaryOnSubdomainGenerator
[../]
[]
[Variables]
[./u]
[./InitialCondition]
type = ConstantIC
value = 1
[../]
block = 0
[../]
[./u_neighbor]
[./InitialCondition]
type = ConstantIC
value = 1
[../]
block = 1
[../]
[]
[Functions]
[./forcing_fn]
type = ParsedFunction
value = (x*x*x)-6.0*x
[../]
[./bc_fn]
type = ParsedFunction
value = (x*x*x)
[../]
[]
[Kernels]
[./diff]
type = MatDiffusionTest
variable = u
prop_name = diffusivity
block = 0
[../]
[./abs]
type = Reaction
variable = u
block = 0
[../]
[./forcing]
type = BodyForce
variable = u
function = forcing_fn
block = 0
[../]
[./diffn]
type = MatDiffusionTest
variable = u_neighbor
prop_name = diffusivity
block = 1
[../]
[./absn]
type = Reaction
variable = u_neighbor
block = 1
[../]
[./forcingn]
type = BodyForce
variable = u_neighbor
function = forcing_fn
block = 1
[../]
[]
[InterfaceKernels]
[./flux_match]
type = PenaltyInterfaceDiffusion
variable = u
neighbor_var = u_neighbor
boundary = master0_interface
penalty = 1e6
[../]
[]
[BCs]
[./u]
type = FunctionDirichletBC
variable = u
boundary = 'left'
function = bc_fn
[../]
[./u_neighbor]
type = FunctionDirichletBC
variable = u_neighbor
boundary = 'right'
function = bc_fn
[../]
[]
[Materials]
active = 'constant'
[./stateful]
type = StatefulTest
prop_names = 'diffusivity'
prop_values = '1'
block = '0 1'
[../]
[./constant]
type = GenericConstantMaterial
prop_names = 'diffusivity'
prop_values = '1'
block = '0 1'
[../]
[]
[Preconditioning]
[./smp]
type = SMP
full = true
[../]
[]
[Executioner]
type = Steady
solve_type = 'NEWTON'
[]
[Adaptivity]
marker = 'marker'
steps = 1
[./Markers]
[./marker]
type = BoxMarker
bottom_left = '0 0 0'
top_right = '1 1 0'
inside = refine
outside = coarsen
[../]
[../]
[]
[Outputs]
exodus = true
[]
test/tests/adaptivity/max_h_level/max_h_level.i
[Mesh]
type = GeneratedMesh
dim = 2
nx = 10
ny = 10
nz = 0
zmax = 0
elem_type = QUAD4
[]
[Variables]
[./u]
order = FIRST
family = LAGRANGE
[../]
[]
[Functions]
[./force]
type = ParsedFunction
value = t
[../]
[]
[Kernels]
[./diff]
type = Diffusion
variable = u
[../]
[./force]
type = BodyForce
variable = u
function = force
[../]
[]
[BCs]
[./right]
type = DirichletBC
variable = u
boundary = right
value = 1
[../]
[./left]
type = DirichletBC
variable = u
boundary = left
value = 0
[../]
[]
[Executioner]
type = Transient
num_steps = 4
dt = 1
solve_type = PJFNK
[]
[Adaptivity]
steps = 1
marker = box
max_h_level = 2
[./Markers]
[./box]
bottom_left = '0.3 0.3 0'
inside = refine
top_right = '0.6 0.6 0'
outside = do_nothing
type = BoxMarker
[../]
[../]
[]
[Outputs]
execute_on = 'timestep_end'
[./out]
type = Exodus
execute_scalars_on = none
[../]
[]
modules/combined/test/tests/contact_adaptivity/contact_initial_adaptivity.i
# This is a test of the usage of initial adaptivity with contact.
# It ensures that contact is enforced on the new nodes that are
# created due to refinement on the slave side of the interface.
[GlobalParams]
volumetric_locking_correction = false
displacements = 'disp_x disp_y'
[]
[Mesh]
file = 2blocks.e
patch_size = 80
parallel_type = replicated
[]
[AuxVariables]
[./penetration]
order = FIRST
family = LAGRANGE
[../]
[]
[Functions]
[./negramp]
type = ParsedFunction
value = -t/10
[../]
[]
[Modules/TensorMechanics/Master]
[./all]
add_variables = true
strain = FINITE
[]
[]
[AuxKernels]
[./penetration]
type = PenetrationAux
variable = penetration
boundary = 3
paired_boundary = 2
[../]
[]
[Postprocessors]
[./nonlinear_its]
type = NumNonlinearIterations
execute_on = timestep_end
[../]
[]
[BCs]
[./left_x]
type = DirichletBC
variable = disp_x
boundary = 1
value = 0.0
[../]
[./left_y]
type = DirichletBC
variable = disp_y
boundary = 1
value = 0.0
[../]
[./right_x]
type = FunctionDirichletBC
variable = disp_x
boundary = 4
function = negramp
[../]
[./right_y]
type = DirichletBC
variable = disp_y
boundary = 4
value = 0.0
[../]
[]
[Materials]
[./stiffStuff1]
type = ComputeIsotropicElasticityTensor
block = '1 2'
youngs_modulus = 1e6
poissons_ratio = 0.3
[../]
[./stiffStuff1_stress]
type = ComputeFiniteStrainElasticStress
block = '1 2'
[../]
[]
[Contact]
[./leftright]
slave = 3
master = 2
model = frictionless
penalty = 1e+6
system = constraint
normal_smoothing_distance = 0.1
[../]
[]
[Adaptivity]
steps = 0
marker = box
max_h_level = 2
initial_steps = 2
[./Markers]
[./box]
type = BoxMarker
bottom_left = '0.5 -2.0 0.0'
top_right = '0.75 2.0 0.0'
inside = refine
outside = do_nothing
[../]
[../]
[]
[Executioner]
type = Transient
solve_type = 'PJFNK'
petsc_options_iname = '-pc_type -pc_factor_mat_solver_package'
petsc_options_value = 'lu superlu_dist'
line_search = 'none'
l_max_its = 100
nl_max_its = 1000
dt = 0.2
end_time = 1.0
l_tol = 1e-6
nl_rel_tol = 1e-12
nl_abs_tol = 1e-9
[]
[Outputs]
exodus = true
console = true
[]
modules/level_set/test/tests/functions/olsson_bubble/olsson_bubble.i
[Mesh]
type = GeneratedMesh
dim = 2
nx = 20
ny = 20
[]
[Adaptivity]
initial_marker = marker
initial_steps = 2
max_h_level = 2
[./Markers]
[./marker]
type = BoxMarker
bottom_left = '0 0 0'
top_right = '0.5 0.5 0'
inside = REFINE
outside = DO_NOTHING
[../]
[../]
[]
[AuxVariables]
[./bubble]
[../]
[]
[AuxKernels]
[./bubble_aux]
type = FunctionAux
variable = bubble
function = bubble_func
execute_on = initial
[../]
[]
[Functions]
[./bubble_func]
type = LevelSetOlssonBubble
center = '0.25 0.25 0'
radius = 0.15
[../]
[]
[Problem]
solve = false
[]
[Executioner]
type = Steady
[]
[Outputs]
execute_on = 'TIMESTEP_END'
exodus = true
[]
test/tests/userobjects/toggle_mesh_adaptivity/toggle_mesh_adaptivity_wait.i
[Mesh]
type = GeneratedMesh
dim = 2
nx = 20
ny = 20
[]
[Variables]
[./u]
[../]
[]
[Kernels]
[./diff]
type = Diffusion
variable = u
[../]
[]
[Problem]
solve = false
[]
[Executioner]
type = Transient
num_steps = 4
dt = 0.1
[]
[Adaptivity]
cycles_per_step = 1
marker = marker
max_h_level = 4
[./Markers]
[./marker]
type = BoxMarker
bottom_left = '0.35 0.25 0'
top_right = '0.5 0.5 0'
inside = refine
outside = coarsen
[../]
[../]
[]
[UserObjects]
[./mesh_adaptivity_off]
type = ToggleMeshAdaptivity
mesh_adaptivity = 'off'
apply_after_timestep = 1
[../]
[]
[Outputs]
exodus = true
[./console]
type = Console
print_mesh_changed_info = true
[../]
[]
test/tests/markers/combo_marker/combo_marker_test.i
[Mesh]
type = GeneratedMesh
dim = 2
nx = 10
ny = 10
nz = 0
zmax = 0
elem_type = QUAD4
[]
[Variables]
[./u]
order = FIRST
family = LAGRANGE
[../]
[]
[Kernels]
[./diff]
type = Diffusion
variable = u
[../]
[]
[BCs]
[./left]
type = DirichletBC
variable = u
boundary = 1
value = 0
[../]
[./right]
type = DirichletBC
variable = u
boundary = 2
value = 1
[../]
[]
[Executioner]
type = Steady
solve_type = 'PJFNK'
[]
[Adaptivity]
[./Markers]
[./box]
type = BoxMarker
bottom_left = '0.3 0.3 0'
top_right = '0.6 0.6 0'
inside = refine
outside = do_nothing
[../]
[./combo]
type = ComboMarker
markers = 'box box2'
[../]
[./box2]
type = BoxMarker
bottom_left = '0.5 0.5 0'
top_right = '0.8 0.8 0'
inside = refine
outside = coarsen
[../]
[../]
[]
[Outputs]
exodus = true
[]
test/tests/misc/selective_reinit/selective_reinit_test.i
[Mesh]
type = GeneratedMesh
dim = 2
nx = 10
ny = 10
[]
[Variables]
[./u]
[../]
[]
[AuxVariables]
[./dummy]
order = CONSTANT
family = MONOMIAL
[../]
[]
[Kernels]
[./diff]
type = Diffusion
variable = u
[../]
[]
[AuxKernels]
[./constant_dummy]
type = ConstantAux
variable = dummy
execute_on = 'initial timestep_end'
value = 4
[../]
[]
[BCs]
[./left]
type = DirichletBC
variable = u
boundary = left
value = 0
[../]
[./right]
type = DirichletBC
variable = u
boundary = right
value = 1
[../]
[]
[Postprocessors]
[./u_integral]
type = ElementIntegralVariablePostprocessor
variable = u
execute_on = linear
[../]
[]
[Executioner]
type = Steady
solve_type = 'PJFNK'
petsc_options_iname = '-pc_type -pc_hypre_type'
petsc_options_value = 'hypre boomeramg'
[]
[Adaptivity]
[./Indicators]
[./indicator]
type = GradientJumpIndicator
variable = u
[../]
[../]
[./Markers]
[./box]
type = BoxMarker
bottom_left = '0.2 0.2 0'
top_right = '0.8 0.8 0'
inside = refine
outside = coarsen
[../]
[../]
[]
[Outputs]
exodus = true
show = u
[]
[LotsOfAuxVariables]
[./avar]
number = 2000
[../]
[]
test/tests/kernels/diffusion_with_hanging_node/simple_diffusion.i
[Mesh]
type = GeneratedMesh
dim = 2
nx = 2
ny = 1
[]
[Variables]
[./u]
[../]
[]
[Kernels]
[./diff]
type = Diffusion
variable = u
[../]
[]
[BCs]
# BCs cannot be preset due to Jacobian test
[./left]
type = DirichletBC
preset = false
variable = u
boundary = left
value = 0
[../]
[./right]
type = DirichletBC
preset = false
variable = u
boundary = right
value = 1
[../]
[]
[Preconditioning]
[./pre]
type = SMP
full = true
[../]
[]
[Executioner]
type = Steady
solve_type = 'NEWTON'
petsc_options = '-pc_svd_monitor -ksp_view_pmat'
petsc_options_iname = '-pc_type'
petsc_options_value = 'svd'
[]
[Outputs]
exodus = true
[]
[Adaptivity]
marker = box
max_h_level = 1
initial_steps = 1
[./Markers]
[./box]
type = BoxMarker
bottom_left = '0.5 0 0'
top_right = '1 1 0'
inside = 'refine'
outside = 'do_nothing'
[../]
[../]
[]
test/tests/time_integrators/actually_explicit_euler_verification/ee-2d-linear-adapt.i
[Mesh]
type = GeneratedMesh
dim = 2
xmin = -1
xmax = 1
ymin = -1
ymax = 1
nx = 10
ny = 10
elem_type = QUAD4
[]
[Functions]
[./ic]
type = ParsedFunction
value = 0
[../]
[./forcing_fn]
type = ParsedFunction
value = (x+y)
[../]
[./exact_fn]
type = ParsedFunction
value = t*(x+y)
[../]
[]
[Variables]
[./u]
order = FIRST
family = LAGRANGE
[./InitialCondition]
type = FunctionIC
function = ic
[../]
[../]
[]
[Kernels]
[./ie]
type = TimeDerivative
variable = u
[../]
[./diff]
type = Diffusion
variable = u
[../]
[./ffn]
type = BodyForce
variable = u
function = forcing_fn
[../]
[]
[BCs]
[./all]
type = FunctionDirichletBC
variable = u
preset = false
boundary = '0 1 2 3'
function = exact_fn
[../]
[]
[Adaptivity]
steps = 1
marker = box
max_h_level = 2
[./Markers]
[./box]
bottom_left = '-0.4 -0.4 0'
inside = refine
top_right = '0.4 0.4 0'
outside = do_nothing
type = BoxMarker
[../]
[../]
[]
[Postprocessors]
[./l2_err]
type = ElementL2Error
variable = u
function = exact_fn
[../]
[]
[Executioner]
type = Transient
start_time = 0.0
num_steps = 4
dt = 0.005
l_tol = 1e-12
[./TimeIntegrator]
type = ActuallyExplicitEuler
[../]
[]
[Outputs]
exodus = true
[./console]
type = Console
max_rows = 10
[../]
[]
test/tests/outputs/oversample/adapt.i
[Mesh]
type = GeneratedMesh
dim = 2
nx = 10
ny = 10
nz = 0
zmax = 0
elem_type = QUAD4
[]
[Variables]
[./u]
order = FIRST
family = LAGRANGE
[../]
[]
[Functions]
[./force]
type = ParsedFunction
value = t*t
[../]
[]
[Kernels]
[./diff]
type = Diffusion
variable = u
[../]
[./force]
type = BodyForce
variable = u
function = force
[../]
[]
[BCs]
[./right]
type = DirichletBC
variable = u
boundary = right
value = 1
[../]
[./left]
type = DirichletBC
variable = u
boundary = left
value = 0
[../]
[]
[Executioner]
type = Transient
num_steps = 4
dt = 1
solve_type = PJFNK
[]
[Adaptivity]
steps = 1
marker = box
max_h_level = 2
[./Markers]
[./box]
bottom_left = '0.3 0.3 0'
inside = refine
top_right = '0.6 0.6 0'
outside = do_nothing
type = BoxMarker
[../]
[../]
[]
[Outputs]
execute_on = 'timestep_end'
exodus = true
[./oversample]
type = Exodus
refinements = 2
file_base = adapt_out_oversample
execute_on = 'initial timestep_end'
[../]
[]
test/tests/materials/stateful_prop/stateful_prop_adaptivity_test.i
[Mesh]
type = GeneratedMesh
dim = 3
nx = 2
ny = 2
nz = 2
uniform_refine = 2
# This option is necessary if you have uniform refinement + stateful material properties + adaptivity
skip_partitioning = true
# stateful material properties + adaptivity are not yet compatible
# with distributed meshes
parallel_type = replicated
[]
[Variables]
[./u]
order = FIRST
family = LAGRANGE
[../]
[]
[AuxVariables]
[./prop1]
order = CONSTANT
family = MONOMIAL
[../]
[]
[Kernels]
[./heat]
type = MatDiffusionTest
variable = u
prop_name = thermal_conductivity
prop_state = old # Use the "Old" value to compute conductivity
[../]
[./ie]
type = TimeDerivative
variable = u
[../]
[]
[AuxKernels]
[./prop1_output]
type = MaterialRealAux
variable = prop1
property = thermal_conductivity
[../]
[]
[BCs]
[./bottom]
type = DirichletBC
variable = u
boundary = 1
value = 0.0
[../]
[./top]
type = DirichletBC
variable = u
boundary = 2
value = 1.0
[../]
[]
[Materials]
[./stateful]
type = StatefulTest
prop_names = thermal_conductivity
prop_values = 1.0
[../]
[]
[Postprocessors]
[./integral]
type = ElementAverageValue
variable = prop1
[../]
[]
[Executioner]
type = Transient
solve_type = 'PJFNK'
l_max_its = 10
start_time = 0.0
num_steps = 4
dt = .1
petsc_options_iname = '-pc_type -pc_hypre_type'
petsc_options_value = 'hypre boomeramg'
[]
[Adaptivity]
marker = box
[./Markers]
[./box]
type = BoxMarker
bottom_left = '0.2 0.2 0.2'
top_right = '0.4 0.4 0.4'
inside = refine
outside = coarsen
[../]
[../]
[]
[Outputs]
exodus = true
csv = true
[]