# cube_uniform
subsection Vascularization
  set Length scale = local mesh size
  subsection Discretization
    set Exterior target length = 0
    set Lower length factor    = 0.5
    set Numerical cell budget  = 1000000
    set Target length factor   = 1
    set Upper length factor    = 2
  end
  subsection Domain
    set Cube origin          = 0,0,0
    set Cube side length     = 1
    set Edge axis            = 2
    set Edge sides           = 0,0
    set Refinement focus     = none
    set Refinement fractions = .5,.25,.125
    set Shape                = cube
    set Sphere center        = .5,.5,.5
    set Sphere radius        = .5
    set Uniform refinements  = 1
  end
  subsection Growth
    set Candidate vessels          = 12
    set Clearance                  = 0
    set Dissipation weight         = 0
    set Geometry patch budget      = 100000
    set Geometry subdivision depth = 18
    set Local optimization steps   = 10
    set Minimum junction angle     = 15
    set Minimum vessel length      = .1
    set Seed length                = 1
  end
  subsection Input and ports
    set Evaluate reference      = true
    set Input archive           =
    set Mode                    = generate
    set Seed direction          = 1,0,0
    set Seed inward port normal = 0, 0, 0
    set Seed position           = .05,.25,.25
    set Seed radius             = .003
    set Selected terminal ids   =
  end
  subsection Objectives
    set Calibration attempt budget = 12
    set Coverage quadrature order  = 2
    set Maximum new terminals      = 0
    set Maximum service distance   = 1
    set Minimum new terminals      = 1
    set Minimum tissue coverage    = 0
    set Target volume fraction     = 0
    set Volume relative tolerance  = 0.05
  end
  subsection Output
    set Directory             = <run>/cube_uniform
    set Save physical archive = true
    set Write meshes          = true
    set Write tables          = true
  end
  subsection Physiology
    set Arterial Murray exponent              = 3
    set Demand integration point budget       = 4000000
    set Demand integration refinement budget  = 8
    set Demand quadrature order               = 2
    set Demand samples per requested terminal = 64
    set Dynamic viscosity                     = .004
    set Loaded tissue reference flow          = 0
    set Minimum radius                        = 0
    set Reference absolute flow tolerance     = 0
    set Reference conservation tolerance      = 1e-09
    set Reference iteration budget            = 10000
    set Reference linear tolerance            = 1e-12
    set Reference pressures                   = 0:12000
    set Tissue demand                         = 1
    set Total new-tissue reference flow       = 2e-9
    set Unpaired reference inflows            =
  end
  subsection Sampling
    set Density mesh exponent            = 3
    set Random seed                      = 23
    set Sample budget per insertion      = 2000
    set Spatial weight                   = 1
    set Spatial weight bound             = 1
    set Terminal count                   = 1
    set Terminal count multiplier factor = background cell count
  end
  subsection Venous network
    set Enabled                  = false
    set Microvascular resistance = 0
    set Murray exponent          = 3
    set Seed inward port normal  = 0, 0, 0
    set Seed position            = 0, 0, 0
    set Seed radius              = 0
    set Selected terminal ids    =
    set Terminal separation      = 0.25
  end
end

# cube_edge
subsection Vascularization
  set Length scale = local mesh size
  subsection Discretization
    set Exterior target length = 0
    set Lower length factor    = 0.5
    set Numerical cell budget  = 1000000
    set Target length factor   = 1
    set Upper length factor    = 2
  end
  subsection Domain
    set Cube origin          = 0,0,0
    set Cube side length     = 1
    set Edge axis            = 0
    set Edge sides           = 1,1
    set Refinement focus     = edge
    set Refinement fractions = .45,.225,.1125
    set Shape                = cube
    set Sphere center        = .5,.5,.5
    set Sphere radius        = .5
    set Uniform refinements  = 1
  end
  subsection Growth
    set Candidate vessels          = 12
    set Clearance                  = 0
    set Dissipation weight         = 0
    set Geometry patch budget      = 100000
    set Geometry subdivision depth = 18
    set Local optimization steps   = 10
    set Minimum junction angle     = 15
    set Minimum vessel length      = .1
    set Seed length                = 1
  end
  subsection Input and ports
    set Evaluate reference      = true
    set Input archive           =
    set Mode                    = generate
    set Seed direction          = 1,0,0
    set Seed inward port normal = 0, 0, 0
    set Seed position           = .05,.25,.25
    set Seed radius             = .003
    set Selected terminal ids   =
  end
  subsection Objectives
    set Calibration attempt budget = 12
    set Coverage quadrature order  = 2
    set Maximum new terminals      = 0
    set Maximum service distance   = 1
    set Minimum new terminals      = 1
    set Minimum tissue coverage    = 0
    set Target volume fraction     = 0
    set Volume relative tolerance  = 0.05
  end
  subsection Output
    set Directory             = <run>/cube_edge
    set Save physical archive = true
    set Write meshes          = true
    set Write tables          = true
  end
  subsection Physiology
    set Arterial Murray exponent              = 3
    set Demand integration point budget       = 4000000
    set Demand integration refinement budget  = 8
    set Demand quadrature order               = 2
    set Demand samples per requested terminal = 64
    set Dynamic viscosity                     = .004
    set Loaded tissue reference flow          = 0
    set Minimum radius                        = 0
    set Reference absolute flow tolerance     = 0
    set Reference conservation tolerance      = 1e-09
    set Reference iteration budget            = 10000
    set Reference linear tolerance            = 1e-12
    set Reference pressures                   = 0:12000
    set Tissue demand                         = 1
    set Total new-tissue reference flow       = 2e-9
    set Unpaired reference inflows            =
  end
  subsection Sampling
    set Density mesh exponent            = 3
    set Random seed                      = 23
    set Sample budget per insertion      = 2000
    set Spatial weight                   = 1
    set Spatial weight bound             = 1
    set Terminal count                   = 1
    set Terminal count multiplier factor = background cell count
  end
  subsection Venous network
    set Enabled                  = false
    set Microvascular resistance = 0
    set Murray exponent          = 3
    set Seed inward port normal  = 0, 0, 0
    set Seed position            = 0, 0, 0
    set Seed radius              = 0
    set Selected terminal ids    =
    set Terminal separation      = 0.25
  end
end

# sphere_uniform
subsection Vascularization
  set Length scale = local mesh size
  subsection Discretization
    set Exterior target length = 0
    set Lower length factor    = 0.5
    set Numerical cell budget  = 1000000
    set Target length factor   = 1
    set Upper length factor    = 2
  end
  subsection Domain
    set Cube origin          = 0,0,0
    set Cube side length     = 1
    set Edge axis            = 2
    set Edge sides           = 0,0
    set Refinement focus     = none
    set Refinement fractions = .5,.25,.125
    set Shape                = sphere
    set Sphere center        = .5,.5,.5
    set Sphere radius        = .5
    set Uniform refinements  = 1
  end
  subsection Growth
    set Candidate vessels          = 12
    set Clearance                  = 0
    set Dissipation weight         = 0
    set Geometry patch budget      = 100000
    set Geometry subdivision depth = 18
    set Local optimization steps   = 10
    set Minimum junction angle     = 15
    set Minimum vessel length      = .1
    set Seed length                = 1
  end
  subsection Input and ports
    set Evaluate reference      = true
    set Input archive           =
    set Mode                    = generate
    set Seed direction          = 1,0,0
    set Seed inward port normal = 0, 0, 0
    set Seed position           = .2,.5,.5
    set Seed radius             = .003
    set Selected terminal ids   =
  end
  subsection Objectives
    set Calibration attempt budget = 12
    set Coverage quadrature order  = 2
    set Maximum new terminals      = 0
    set Maximum service distance   = 1
    set Minimum new terminals      = 1
    set Minimum tissue coverage    = 0
    set Target volume fraction     = 0
    set Volume relative tolerance  = 0.05
  end
  subsection Output
    set Directory             = <run>/sphere_uniform
    set Save physical archive = true
    set Write meshes          = true
    set Write tables          = true
  end
  subsection Physiology
    set Arterial Murray exponent              = 3
    set Demand integration point budget       = 4000000
    set Demand integration refinement budget  = 8
    set Demand quadrature order               = 2
    set Demand samples per requested terminal = 64
    set Dynamic viscosity                     = .004
    set Loaded tissue reference flow          = 0
    set Minimum radius                        = 0
    set Reference absolute flow tolerance     = 0
    set Reference conservation tolerance      = 1e-09
    set Reference iteration budget            = 10000
    set Reference linear tolerance            = 1e-12
    set Reference pressures                   = 0:12000
    set Tissue demand                         = 1
    set Total new-tissue reference flow       = 2e-9
    set Unpaired reference inflows            =
  end
  subsection Sampling
    set Density mesh exponent            = 3
    set Random seed                      = 23
    set Sample budget per insertion      = 2000
    set Spatial weight                   = 1
    set Spatial weight bound             = 1
    set Terminal count                   = 1
    set Terminal count multiplier factor = background cell count
  end
  subsection Venous network
    set Enabled                  = false
    set Microvascular resistance = 0
    set Murray exponent          = 3
    set Seed inward port normal  = 0, 0, 0
    set Seed position            = 0, 0, 0
    set Seed radius              = 0
    set Selected terminal ids    =
    set Terminal separation      = 0.25
  end
end

# sphere_center
subsection Vascularization
  set Length scale = local mesh size
  subsection Discretization
    set Exterior target length = 0
    set Lower length factor    = 0.5
    set Numerical cell budget  = 1000000
    set Target length factor   = 1
    set Upper length factor    = 2
  end
  subsection Domain
    set Cube origin          = 0,0,0
    set Cube side length     = 1
    set Edge axis            = 2
    set Edge sides           = 0,0
    set Refinement focus     = center
    set Refinement fractions = .5,.25,.125
    set Shape                = sphere
    set Sphere center        = .5,.5,.5
    set Sphere radius        = .5
    set Uniform refinements  = 1
  end
  subsection Growth
    set Candidate vessels          = 12
    set Clearance                  = 0
    set Dissipation weight         = 0
    set Geometry patch budget      = 100000
    set Geometry subdivision depth = 18
    set Local optimization steps   = 10
    set Minimum junction angle     = 15
    set Minimum vessel length      = .1
    set Seed length                = 1
  end
  subsection Input and ports
    set Evaluate reference      = true
    set Input archive           =
    set Mode                    = generate
    set Seed direction          = 1,0,0
    set Seed inward port normal = 0, 0, 0
    set Seed position           = .2,.5,.5
    set Seed radius             = .003
    set Selected terminal ids   =
  end
  subsection Objectives
    set Calibration attempt budget = 12
    set Coverage quadrature order  = 2
    set Maximum new terminals      = 0
    set Maximum service distance   = 1
    set Minimum new terminals      = 1
    set Minimum tissue coverage    = 0
    set Target volume fraction     = 0
    set Volume relative tolerance  = 0.05
  end
  subsection Output
    set Directory             = <run>/sphere_center
    set Save physical archive = true
    set Write meshes          = true
    set Write tables          = true
  end
  subsection Physiology
    set Arterial Murray exponent              = 3
    set Demand integration point budget       = 4000000
    set Demand integration refinement budget  = 8
    set Demand quadrature order               = 2
    set Demand samples per requested terminal = 64
    set Dynamic viscosity                     = .004
    set Loaded tissue reference flow          = 0
    set Minimum radius                        = 0
    set Reference absolute flow tolerance     = 0
    set Reference conservation tolerance      = 1e-09
    set Reference iteration budget            = 10000
    set Reference linear tolerance            = 1e-12
    set Reference pressures                   = 0:12000
    set Tissue demand                         = 1
    set Total new-tissue reference flow       = 2e-9
    set Unpaired reference inflows            =
  end
  subsection Sampling
    set Density mesh exponent            = 3
    set Random seed                      = 23
    set Sample budget per insertion      = 2000
    set Spatial weight                   = 1
    set Spatial weight bound             = 1
    set Terminal count                   = 1
    set Terminal count multiplier factor = background cell count
  end
  subsection Venous network
    set Enabled                  = false
    set Microvascular resistance = 0
    set Murray exponent          = 3
    set Seed inward port normal  = 0, 0, 0
    set Seed position            = 0, 0, 0
    set Seed radius              = 0
    set Selected terminal ids    =
    set Terminal separation      = 0.25
  end
end

# arteriovenous
subsection Vascularization
  set Length scale = local mesh size
  subsection Discretization
    set Exterior target length = 0
    set Lower length factor    = 0.5
    set Numerical cell budget  = 1000000
    set Target length factor   = 1
    set Upper length factor    = 2
  end
  subsection Domain
    set Cube origin          = 0,0,0
    set Cube side length     = 1
    set Edge axis            = 2
    set Edge sides           = 0,0
    set Refinement focus     = none
    set Refinement fractions = .5,.25,.125
    set Shape                = cube
    set Sphere center        = .5,.5,.5
    set Sphere radius        = .5
    set Uniform refinements  = 2
  end
  subsection Growth
    set Candidate vessels          = 12
    set Clearance                  = 0
    set Dissipation weight         = 0
    set Geometry patch budget      = 100000
    set Geometry subdivision depth = 18
    set Local optimization steps   = 10
    set Minimum junction angle     = 15
    set Minimum vessel length      = .1
    set Seed length                = 1
  end
  subsection Input and ports
    set Evaluate reference      = true
    set Input archive           =
    set Mode                    = generate
    set Seed direction          = 1,0,0
    set Seed inward port normal = 0, 0, 0
    set Seed position           = .05,.25,.25
    set Seed radius             = .003
    set Selected terminal ids   =
  end
  subsection Objectives
    set Calibration attempt budget = 12
    set Coverage quadrature order  = 2
    set Maximum new terminals      = 0
    set Maximum service distance   = 1
    set Minimum new terminals      = 1
    set Minimum tissue coverage    = 0
    set Target volume fraction     = 0
    set Volume relative tolerance  = 0.05
  end
  subsection Output
    set Directory             = <run>/arteriovenous
    set Save physical archive = true
    set Write meshes          = true
    set Write tables          = true
  end
  subsection Physiology
    set Arterial Murray exponent              = 3
    set Demand integration point budget       = 4000000
    set Demand integration refinement budget  = 8
    set Demand quadrature order               = 2
    set Demand samples per requested terminal = 64
    set Dynamic viscosity                     = .004
    set Loaded tissue reference flow          = 0
    set Minimum radius                        = 0
    set Reference absolute flow tolerance     = 0
    set Reference conservation tolerance      = 1e-09
    set Reference iteration budget            = 10000
    set Reference linear tolerance            = 1e-12
    set Reference pressures                   = 0:12000,2:4000
    set Tissue demand                         = 1
    set Total new-tissue reference flow       = 2e-9
    set Unpaired reference inflows            =
  end
  subsection Sampling
    set Density mesh exponent            = 3
    set Random seed                      = 23
    set Sample budget per insertion      = 2000
    set Spatial weight                   = 1
    set Spatial weight bound             = 1
    set Terminal count                   = 1
    set Terminal count multiplier factor = background cell count
  end
  subsection Venous network
    set Enabled                  = true
    set Microvascular resistance = 0
    set Murray exponent          = 3
    set Seed inward port normal  = 0, 0, 0
    set Seed position            = .95,.75,.75
    set Seed radius              = .004
    set Selected terminal ids    =
    set Terminal separation      = 0.25
  end
end

# rediscretized
subsection Vascularization
  set Length scale = local mesh size
  subsection Discretization
    set Exterior target length = 0
    set Lower length factor    = .5
    set Numerical cell budget  = 1000000
    set Target length factor   = 1
    set Upper length factor    = 2
  end
  subsection Domain
    set Cube origin          = 0, 0, 0
    set Cube side length     = 1
    set Edge axis            = 2
    set Edge sides           = 0, 0
    set Refinement focus     = none
    set Refinement fractions = 0.5, 0.25, 0.125
    set Shape                = cube
    set Sphere center        = 0.5, 0.5, 0.5
    set Sphere radius        = 0.5
    set Uniform refinements  = 4
  end
  subsection Growth
    set Candidate vessels          = 12
    set Clearance                  = 0
    set Dissipation weight         = 0
    set Geometry patch budget      = 100000
    set Geometry subdivision depth = 18
    set Local optimization steps   = 10
    set Minimum junction angle     = 15
    set Minimum vessel length      = 0.1
    set Seed length                = 1
  end
  subsection Input and ports
    set Evaluate reference      = true
    set Input archive           = <run>/cube_uniform/network
    set Mode                    = load
    set Seed direction          = 0, 0, 0
    set Seed inward port normal = 0, 0, 0
    set Seed position           = 0, 0, 0
    set Seed radius             = 0
    set Selected terminal ids   =
  end
  subsection Objectives
    set Calibration attempt budget = 12
    set Coverage quadrature order  = 2
    set Maximum new terminals      = 0
    set Maximum service distance   = 1
    set Minimum new terminals      = 1
    set Minimum tissue coverage    = 0
    set Target volume fraction     = 0
    set Volume relative tolerance  = 0.05
  end
  subsection Output
    set Directory             = <run>/rediscretized
    set Save physical archive = true
    set Write meshes          = true
    set Write tables          = true
  end
  subsection Physiology
    set Arterial Murray exponent              = 3
    set Demand integration point budget       = 4000000
    set Demand integration refinement budget  = 8
    set Demand quadrature order               = 2
    set Demand samples per requested terminal = 64
    set Dynamic viscosity                     = 0
    set Loaded tissue reference flow          = 2e-9
    set Minimum radius                        = 0
    set Reference absolute flow tolerance     = 0
    set Reference conservation tolerance      = 1e-09
    set Reference iteration budget            = 10000
    set Reference linear tolerance            = 1e-12
    set Reference pressures                   = 0:12000
    set Tissue demand                         = 1
    set Total new-tissue reference flow       = 0
    set Unpaired reference inflows            =
  end
  subsection Sampling
    set Density mesh exponent            = 3
    set Random seed                      = 1
    set Sample budget per insertion      = 2000
    set Spatial weight                   = 1
    set Spatial weight bound             = 1
    set Terminal count                   = 1
    set Terminal count multiplier factor = background cell count
  end
  subsection Venous network
    set Enabled                  = false
    set Microvascular resistance = 0
    set Murray exponent          = 3
    set Seed inward port normal  = 0, 0, 0
    set Seed position            = 0, 0, 0
    set Seed radius              = 0
    set Selected terminal ids    =
    set Terminal separation      = 0.25
  end
end