mlb_amgx.sif

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!! Elmer Solver input file
!!
!! Vectorized Stokes solution for Midre Lovenbreen.
!! Including Semi-Lagrangian dating solver.
!!
!! All units are in m-MPa-year
!! Temperatures are in Kelvin
!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! switch that on for debugging only
! ---------------------------------
! check keywords warn
! echo on
!!!!!!!!!!!!!!!!!!!!!!!!!
! DEFINITIONS used in run
!!!!!!!!!!!!!!!!!!!!!!!!!!
$name="S_1995_DEMs_ser_amgx"

! Note that the Mesh2MeshSolver requires solver specific
! mesh and hence this must be different than primary mesh,
! even symlink is ok.
$restartdir="outline62_lc25"
$restartfile="s_1995_dems_init_2d.result"

$directmethod="mumps" !cPardiso"

$yearinsec = 365.25*24*60*60
$rhoi = 910.0/(1.0e6*yearinsec^2)   
$gravity = -9.81*yearinsec^2

$n = 3.0
$m = 1.0/n

! rate factors and molar activiation energies
! after Paterson 2010
$A1 = 2.89165e-13*yearinsec*1.0e18 
$A2 = 2.42736e-02*yearinsec*1.0e18 
$Q1 = 60.0e3
$Q2 = 115.0e3

! Temperature of the simulation in Celsius
! with the formula for A works only if T > -10
$Tc = -1.0

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! HEADER
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! Partitioned mesh
Header
  Mesh DB "." "outline62_lc25"
End

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! CONSTANTS
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Constants
End


!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! SIMULATION
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Simulation
  Coordinate System  = "Cartesian 3D"
  Simulation Type = "Steady State"             

  ! Internal extrusion parameters, may be altered.
  Extruded Mesh Levels = Integer 9 
  Extruded Max Coordinate = Real 2000		

  ! Coupled iterations between different solvers
  !---------------------------------------------
  Steady State Max Iterations = 1 
  Steady State Min Iterations = 1

  ! usually, Dirichlet BC's are initialized before everything else. Sometimes those 
  ! conditions are dependent on solutions of earlier solvers; next line ensures that
  ! this is not an issue.
  !-----------------------------------------
  Initialize Dirichlet Conditions = Logical False
  
  ! Output files
  ! ------------
  Post File = $name$.vtu
  vtu: Save Bulk Only = Logical True

  Scalars File = $name$.dat
  scalars: Parallel Reduce = Logical True

  Output File = $name$.result

  ! Restart happens in Solver 1
  Restart Before Initial Conditions = Logical True
  Interpolation Passive Coordinate = Integer 3 

  ! how verbose the solver should be
  !  3 = Only warnings
  ! 32 = Maximum verbosity
  !-------------------------------------------------------
  Max Output Level = 3
End

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! SOLVER
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!


Solver 1
  Exec Solver = before all
  Equation = "InterpSolver"

! Perform the interpolation solver before all other solvers, only once.
  Exec Solver = Before all
  Procedure = "Mesh2MeshSolver" "Mesh2MeshSolver"

  ! Restart is always in a serial mesh
  Mesh = -single $restartdir
  Restart File = $restartfile

  ! We use the primary mesh an single process and unextruded
  ! We want to have unique copy of it.   
  Mesh Enforce Local Copy = Logical True

  ! These are the variables for restart 
  Restart Position = Integer 0
  Restart Time = Real 2000.0
  Restart Variable 1 = String "bedrockDEM"
  Restart Variable 2 = String "surfaceDEM1995"

! Continue even if some node is not found, deal with problems!
  Restart Error Continue = Logical True  

! These are the variables to be mapped from 2D ThisMesh to 3D TargetMesh'
! All existing variables are automatically mapped. 
!  Variable 1 = "bedrockDEM"
!  Variable 2 = "surfaceDEM1995"

! Ensures that we perform interpolation on plane 
  Interpolation Passive Coordinate = Integer 3 
End 


! Maps the constant-thickness mesh between given bedrock and surface topology
Solver 2 
  Exec Solver = "before simulation"
  Equation = "MapCoordinate"
  Procedure = "StructuredMeshMapper" "StructuredMeshMapper"

  Active Coordinate = Integer 3

  Displacement Mode = Logical False
  Correct Surface = Logical True
  Minimum Height = Real 5.0

  Correct Surface Mask = String "Glaciated"
  Dot Product Tolerance = 1.0e-3

  ! These are needed to host the variables that are read in
  Variable = MeshUpdate

  Exported Variable 1 = "bedrockDEM"
  Exported Variable 1 Mask = String "BedRock"

  Exported Variable 2 = "surfaceDEM1995"
  Exported Variable 2 Mask = String "Surface"
End


! Computes height and depth assuming an extruded mesh.
Solver 3 
  Exec Solver = "before simulation" 
  Equation = "HeightDepth"
  Procedure = "StructuredProjectToPlane" "StructuredProjectToPlane"
  Active Coordinate = Integer 3
  Operator 1 = depth
  Operator 2 = height
End 


! vectorized & threaded version of the Navier-Stokes solver.
Solver 4
  Equation = "Stokes-Vec"
  Procedure = "IncompressibleNSVec" "IncompressibleNSSolver"
  Div-Curl Discretization = Logical False

  Optimize Bandwidth = Logical True
  Flow Model = Stokes
  Stabilization Method = String Stabilized

  Linear System Abort Not Converged = Logical False

  Block Gauss-Seidel = Logical True
  Block Matrix Reuse = Logical False
  Block Scaling = Logical False
  Block Preconditioner = Logical True

! Block Structure(4) = Integer 1 1 1 2
  Block Order(4) = Integer 1 2 3 4

! Linear System Scaling = False

! Linear system solver for outer loop
!-----------------------------------------
  Linear System Residual Output = 25

! Linear System Solver = iterative
! Linear System Iterative Method = GCR !BiCGStab
! Linear System Convergence Tolerance = 1.0e-08
! Linear System Preconditioning = ILU1
! Linear System Max Iterations = 1000
! Linear System Abort Not Converged = Logical False

  Linear System Solver = "Block"

  Outer: Linear System Solver = "Iterative"
  Outer: Linear System Iterative Method = GCR
  Outer: Linear System GCR Restart =  250
  Outer: Linear System Residual Output =  25
  Outer: Linear System Max Iterations =  200
  Outer: Linear System Abort Not Converged = False
  Outer: Linear System Convergence Tolerance = 1e-8

  $blocktol = 0.001

  block 11: Linear System Scaling = false
  block 11: Linear System Solver = amgx

  block 22: Linear System Solver = amgx
  block 22: Linear System Scaling = false

  block 33: Linear System Scaling = false
  block 33: Linear System Solver = amgx

  block 44: Linear System Solver = amgx
  block 44: Linear System Scaling = true

  AMGX config = string "config.json"
  Block AMGX M-V = Logical True
  
  Nonlinear System Max Iterations = 1
  Nonlinear System Convergence Tolerance  = 1.0e-5
  Nonlinear System Newton After Iterations = 10
  Nonlinear System Newton After Tolerance = 1.0e-01
  Nonlinear System Relaxation Factor = 1.00
  Nonlinear System Reset Newton = Logical True
  Steady State Convergence Tolerance = Real 1.0e-3


  ! Convergence on timelevel (not required here)
  !---------------------------------------------
  Steady State Convergence Tolerance = Real 1.0e-3

  !Relative Integration Order = -1
  Number of Integration Points = Integer 44 ! 21, 28, 44, 64, ...

  ! 1st iteration viscosity is constant
  Constant-Viscosity Start = Logical True

! Some timing info
  Boundary Assembly Timing = Logical True
  Bulk Assembly Timing = Logical True
  Solver Timing = Logical True
  Linear System Timing = Logical True
End


! Semilagrangian solver for advection dominated flow
Solver 5
  Equation = ParticleAdvector
  Procedure = "ParticleAdvector" "ParticleAdvector"

! Initialize particles at center of elements (as opposed to nodes)
  Advect Elemental = Logical True

!  Reinitialize Particles = Logical True
!  Particle Accurate At Face = Logical False

! Timestepping strategy
  Simulation Timestep Sizes = Logical False
  Particle Dt Constant = Logical False
  Max Timestep Intervals = Integer 1000

! Time in average 4 steps in each element 
! Timestep Unisotropic Courant Number = Real 0.25
  Max Timestep Size = Real 1.0e3

! Give up integration if particles are tool old
  Max Integration Time = Real 1.0e4

! Integration forward in time
  Runge Kutta = Logical False
  Velocity Gradient Correction = Logical True
  Velocity Variable Name = String "Flow Solution" 

! Show some info in the end
  Particle Info = Logical True
  Particle Time = Logical True

! The internal variables for this solver
  Variable 1 = String "Particle Distance"
  Variable 2 = String "Particle Time"
  Operator 2 = "cumulative"

! The field variables being advected
  Variable 3 = String "Coordinate 1"
  Result Variable 3 = String "Advected X"
  Variable 4 = String "Coordinate 2"
  Result Variable 4 = String "Advected Y"
  Variable 5 = String "Coordinate 3"
  Result Variable 5 = String "Advected Z"

  Solver Timing = True
  exec solver = never
End 



!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! BODIES (i.e., domains to compute on)
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Body 1
  Name = "glacier"
  Equation = 1
  Material = 1
  Body Force = 1
  Initial Condition = 1
End

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! EQUATION
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Equation 1
  Active Solvers(4) = 2 3 4 5 
  Convection = Computed 
End


!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! INITIAL CONDITIONS
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Initial Condition 1
  ! Initial velocity is not really needed when using newtonian start
  Velocity 1 = 0.0
  Velocity 2 = 0.0
  Velocity 3 = 0.0
End


!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! BODY FORCE
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Body Force 1
  Flow BodyForce 1 = 0.0
  Flow BodyForce 2 = 0.0 
  Flow BodyForce 3 = $gravity
End

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! MATERIAL
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Material 1
  Name = "Ice"
  Density = Real $rhoi

  ! First viscosity with newtonian fluid
  ! happens to give velocities of proper size
  Viscosity = Real 1.0 

  ! Nonnewtonian viscosity
  Viscosity Model = String Glen
  Glen Exponent = Real 3.0
  Critical Shear Rate =  Real 1.0E-10
  ! Paterson value in MPa^-3a^-1
  Limit Temperature = Real -10.0
  Rate Factor 1 = Real $A1 
  Rate Factor 2 = Real $A2 
  Activation Energy 1 = Real $Q1    
  Activation Energy 2 = Real $Q2 
  Glen Enhancement Factor = Real 1.0
  Relative Temperature = Real $Tc
End

Boundary Condition 1
  ComputeNormal = Logical False
  Name = "sides1"
  Target Boundaries(1) = 1
  ! no slip
  !-------------------------
  Velocity 1 = 0
  Velocity 2 = 0
  Velocity 3 = 0
End

Boundary Condition 2
  ComputeNormal = Logical False
  Name = "sides2"
  Target Boundaries(1)  = 2
  ! no slip
  !-------------------------
  Velocity 1 = 0
  Velocity 2 = 0
  Velocity 3 = 0
End

!! DON'T CHANGE ORDER OF NEXT 2 BC's!
!! They are automaticaly created in internal extrusion
!! bedrock:
Boundary Condition 3
  ComputeNormal = Logical True
  Name = "bedrock"

  ! No-slip velocity conditions
  Velocity 1 = Real 0.0
  Velocity 2 = Real 0.0
  Velocity 3 = Real 0.0
  Bottom Surface = Equals "bedrockDEM"

! Mask for creating the restart fields only where needed
! Refererred by: Exported Variable 1 Mask = ...
  Bedrock = Logical True
End

Boundary Condition 4
  ComputeNormal = Logical False
  Name = "surface"
  Top Surface = Equals "surfaceDEM1995"

! Referred by: Exported Variable 2 Mask = ...
  Surface = Logical True  
End