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delta_real_parameters.i
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delta_real_parameters.i
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[Mesh]
file=07-heart_geometry_new.e
block_id='1'
block_name='all'
displacements='dispx dispy dispz'
# uniform_refine=1
[]
[Variables]
[./dispx] order=FIRST family=LAGRANGE [../]
[./dispy] order=FIRST family=LAGRANGE [../]
[./dispz] order=FIRST family=LAGRANGE [../]
[./hydrostatic_pressure] order=FIRST family=SCALAR [../]
[]
[Kernels]
[./stressdiv_dispx] type=CardiacKirchhoffStressDivergence variable=dispx component=0 displacements='dispx dispy dispz' [../]
[./stressdiv_dispy] type=CardiacKirchhoffStressDivergence variable=dispy component=1 displacements='dispx dispy dispz' [../]
[./stressdiv_dispz] type=CardiacKirchhoffStressDivergence variable=dispz component=2 displacements='dispx dispy dispz' [../]
#[./inertia_x] type=SecondOrderImplicitEulerWithDensity variable=dispx density=0.0 lumping=false [../]
#[./inertia_y] type=SecondOrderImplicitEulerWithDensity variable=dispy density=0.0 lumping=false [../]
#[./inertia_z] type=SecondOrderImplicitEulerWithDensity variable=dispz density=0.0 lumping=false [../]
[]
[ScalarKernels]
[./incompressibility] type=CardiacIncompressibilityLagrangeMultiplier variable=hydrostatic_pressure volume_ratio_postprocessor=volume_ratio [../]
[]
[AuxVariables]
[./distance_outer] order=FIRST family=LAGRANGE [../]
[./distance_RV_inner] order=FIRST family=LAGRANGE [../]
[./distance_LV_inner] order=FIRST family=LAGRANGE [../]
[./thickness_parameter] order=FIRST family=LAGRANGE [../]
[./potential_from_sub] order=FIRST family=LAGRANGE [../]
[./active_tension] order=CONSTANT family=MONOMIAL [../]
[]
[AuxKernels]
[./auxdistance_outer] type=VolumeNearestNodeDistanceAux variable=distance_outer block=all paired_boundary=ss_outer [../]
[./auxdistance_RV_inner] type=VolumeNearestNodeDistanceAux variable=distance_RV_inner block=all paired_boundary=ss_RV_inner [../]
[./auxdistance_LV_inner] type=VolumeNearestNodeDistanceAux variable=distance_LV_inner block=all paired_boundary=ss_LV_inner [../]
[./auxthickness]
type=CardiacThicknessParameterAux variable=thickness_parameter
distance_RV_inner=distance_RV_inner
distance_LV_inner=distance_LV_inner
distance_outer =distance_outer
[../]
[./aux_active_tension] type=MaterialRealAux
material=active_tension_material # this property does not exist in reality but enforces creation of an appropriately helpful arrow in the graphviz output
variable=active_tension
[../]
[]
[Materials]
[./fibres]
type=CardiacFibresMaterial
block=all
thickness_parameter=thickness_parameter
#fixed_R='0.36 0.48 -0.8 -0.8 0.6 0.0 0.48 0.64 0.60'
#fixed_R='0 0 1 1 0 0 0 1 0'
outputs=all
[../]
[./cardiac_material]
type=CardiacHolzapfel2009Material
block=all
use_displaced_mesh=false
fibre_directions = fibres # this property does not exist in reality but enforces creation of an appropriately helpful arrow in the graphviz output
# material parameters as given in Table 1 of [Holzapfel 2009]
#in following order: a, b, a_f, b_f, a_s, b_s, a_fs, b_fs
material_parameters='0.059 8.023 18.472 16.026 2.481 11.120 0.216 11.436'
displacements ='dispx dispy dispz'
outputs=all
output_properties='Kirchhoff_stress'
Ta=active_tension
p=hydrostatic_pressure
[../]
[./active_tension_material]
type=ActiveTensionODE
Vmem=potential_from_sub
block=all
# these are the default parameter values, including them here to make sure they are not forgotten as tunable options
epsilon_recovery=0.01
epsilon_development=0.04
kTa=47.9
Vrest=-90.272
Vmax=0.
[../]
[]
[BCs]
[./dispx_fixed] type=DirichletBC variable=dispx boundary='ss_apex' value=0 [../]
[./dispy_fixed] type=DirichletBC variable=dispy boundary='ss_apex' value=0 [../]
[./dispz_fixed] type=DirichletBC variable=dispz boundary='ss_apex' value=0 [../]
# [./ns_lower_polar_point_x] type=DirichletBC variable=dispx boundary=ns_lower_polar_point value=0 [../]
# [./ns_lower_polar_point_y] type=DirichletBC variable=dispy boundary=ns_lower_polar_point value=0 [../]
# [./ns_lower_polar_point_z] type=DirichletBC variable=dispz boundary=ns_lower_polar_point value=0 [../]
# [./ns_lower_polar_neighbour_x] type=DirichletBC variable=dispx boundary=ns_lower_polar_neighbour value=0 [../]
# [./ns_lower_polar_neighbour_y] type=DirichletBC variable=dispy boundary=ns_lower_polar_neighbour value=0 [../]
# [./ns_lower_polar_neighbour_z] type=DirichletBC variable=dispz boundary=ns_lower_polar_neighbour value=0 [../]
# [./ring_x] type=DirichletBC variable=dispx value=0 boundary=ns_LV_opening [../]
# [./ring_y] type=DirichletBC variable=dispy value=0 boundary=ns_LV_opening [../]
# [./ring_z] type=DirichletBC variable=dispz value=0 boundary=ns_LV_opening [../]
[]
[Postprocessors]
#[./elastic_energy] type=ElementIntegralMaterialProperty execute_on=timestep mat_prop=elastic_energy_density [../]
[./volume_ratio] type=CardiacMaterialVolumeRatioPostprocessor execute_on=residual
material=cardiac_material # this property does not exist in reality but enforces creation of an appropriately helpful arrow in the graphviz output
[../]
[]
[Executioner]
type=Transient
solve_type=PJFNK
splitting = 'saddlepoint_fieldsplit'
petsc_options='-fp_trap -info -snes_monitor -snes_converged_reason -ksp_monitor -ksp_converged_reason -ksp_monitor_true_residual -pc_svd_monitor'
nl_rel_tol=1e-5
nl_abs_tol=1e-5
nl_rel_step_tol=1e-6
nl_abs_step_tol=1e-6
l_tol=1.e-8
l_max_its=30
#l_abs_step_tol=1.e-12
#l_max_its=20
#line_search=default # TODO: what else?
start_time=0
end_time =500.0
dtmin =0.025
dtmax =0.5
[]
[Splits]
[./saddlepoint_fieldsplit]
splitting = 'disp pressure'
splitting_type = schur
schur_type = full
schur_pre = S
petsc_options = '-dm_view'
[../]
[./disp]
vars = 'dispx dispy dispz'
petsc_options = '-dm_view'
petsc_options_iname = '-pc_type -pc_hypre_type -pc_hypre_boomeramg_max_iter'
petsc_options_value = ' hypre boomeramg 8 '
[../]
[./pressure]
vars = 'hydrostatic_pressure'
petsc_options = '-dm_view'
petsc_options_iname = '-pc_type'
petsc_options_value = ' none'
[../]
[]
[Outputs]
[./console]
type=Console
perf_log=true
linear_residuals=true
[../]
[./exodus_displaced]
type=Exodus
[../]
[]
[MultiApps]
[./electrocardio]
type=TransientMultiApp
app_type=EweApp
execute_on=timestep_begin
input_files=delta_real_parameters_sub.i
positions='0.0 0.0 0.0'
[../]
[]
[Transfers]
[./dispx_to_sub]
type=MultiAppNearestNodeTransfer
direction=to_multiapp
execute_on=timestep_begin
multi_app=electrocardio
source_variable=dispx
variable=dispx
fixed_meshes=true # independent of any deformation we want to make sure that transfer always happens between the same node pairs
[../]
[./dispy_to_sub]
type=MultiAppNearestNodeTransfer
direction=to_multiapp
execute_on=timestep_begin
multi_app=electrocardio
source_variable=dispy
variable=dispy
fixed_meshes=true # independent of any deformation we want to make sure that transfer always happens between the same node pairs
[../]
[./dispz_to_sub]
type=MultiAppNearestNodeTransfer
direction=to_multiapp
execute_on=timestep_begin
multi_app=electrocardio
source_variable=dispz
variable=dispz
fixed_meshes=true # independent of any deformation we want to make sure that transfer always happens between the same node pairs
[../]
[./from_sub]
type=MultiAppNearestNodeTransfer
direction=from_multiapp
execute_on=timestep_begin
multi_app=electrocardio
source_variable=potential
variable=potential_from_sub
fixed_meshes=true # independent of any deformation we want to make sure that transfer always happens between the same node pairs
[../]
[]