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Copy pathdelta_real_parameters_sub.i
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delta_real_parameters_sub.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]
[./potential] order = FIRST family = LAGRANGE [../]
[]
[AuxVariables]
[./gate_m] order = CONSTANT family = MONOMIAL [../]
[./gate_v] order = CONSTANT family = MONOMIAL [../]
[./gate_f] order = CONSTANT family = MONOMIAL [../]
[./gate_to] order = CONSTANT family = MONOMIAL [../]
[./gate_x] order = CONSTANT family = MONOMIAL [../]
[./dispx] order = FIRST family = LAGRANGE [../]
[./dispy] order = FIRST family = LAGRANGE [../]
[./dispz] order = FIRST family = LAGRANGE [../]
#
[./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 [../]
[]
[AuxKernels]
[./auxgate_m] type = MaterialStdVectorAux property = 'gates' variable = gate_m block = all index = 0 [../]
[./auxgate_v] type = MaterialStdVectorAux property = 'gates' variable = gate_v block = all index = 1 [../]
[./auxgate_f] type = MaterialStdVectorAux property = 'gates' variable = gate_f block = all index = 2 [../]
[./auxgate_to] type = MaterialStdVectorAux property = 'gates' variable = gate_to block = all index = 3 [../]
[./auxgate_x] type = MaterialStdVectorAux property = 'gates' variable = gate_x block = all index = 4 [../]
#
[./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
[../]
[]
[Kernels]
[./diff]
type = ElectrocardioDiffusion
variable = potential
surface_to_volume = 1000.0
capacitance = 1.0
use_displaced_mesh = true
conductivity = conductivity # this property does not exist in reality but enforces creation of an appropriately helpful arrow in the graphviz output
[../]
[./ecforcing]
type = ElectrocardioForcing
variable = potential
forcing_function = ElectrocardioForcing_function
#ion_coeff = 0.0
use_displaced_mesh = true
[../]
[./euler]
type = ElectrocardioTimeDerivative
variable = potential
use_displaced_mesh = true
[../]
[]
[Functions]
[./ElectrocardioForcing_function]
type = PiecewiseFunction
default_function = '0'
functions = 'PurkinjePacing'
left = ' 0.0'
right = ' 5.0'
[../]
[./PurkinjePacing]
# we are pacing at the following "early activation sites" which were hand-picked in Paraview
# to closely match [Potse2006, Figure 1]:
# 0.8 6.4 -3.1
# -1.4 6.4 -2.9
# 2.2 8.9 -4.2
type = ParsedFunction
value = 'A*( exp(-0.5*(pow(x-0.8,2)+pow(y-6.4,2)+pow(z+3.1,2))/pow(w,2))
+exp(-0.5*(pow(x+1.4,2)+pow(y-6.4,2)+pow(z+2.9,2))/pow(w,2))
+exp(-0.5*(pow(x-2.2,2)+pow(y-8.9,2)+pow(z+4.2,2))/pow(w,2)))'
vars = ' A w' # amplitude and spatial width of the Gaussians
vals = '-30 1.5'
[../]
[]
[BCs]
[./bc]
type = NeumannBC
variable = potential
boundary = 'ss_LV_inner ss_RV_inner ss_outer'
value = 0
[../]
[]
[Materials]
[./cardiac_properties]
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
[../]
[./electrocardio]
type = Electrocardio
vmem = 'potential'
block = all
outputs = all
#use_displaced_mesh = true # TODO: if activated I am getting a segfault
[../]
[./conductivity]
type = ElectrocardioConductivity
conductivities = '0.0012 0.003 0.003'
fibre_directions = cardiac_properties # this property does not exist in reality but enforces creation of an appropriately helpful arrow in the graphviz output
block = all
#use_displaced_mesh = true # TODO: if activated I am getting a segfault
[../]
[]
[Executioner]
type = Transient # Here we use the Transient Executioner
#Preconditioned JFNK (default)
solve_type = 'PJFNK'
#l_tol = 1e-6
# l_max_its = 10
nl_rel_tol = 1e-3
nl_abs_tol = 1e-6
nl_rel_step_tol = 1e-6
nl_max_its = 2
start_time = 0
end_time = 500.0
dtmin = 0.05
dtmax = 0.5
scheme = 'implicit-euler'
[]
[ICs]
[./ec]
type = ElectrocardioIC
variable = potential
block = all
[../]
[]
[Outputs]
#exodus = true
[./console]
type = Console
perf_log = false
linear_residuals = false
[../]
[]