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mesh: './meshes/coaortaH1.h5'
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# Physical parameters of the fluid
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fluid:
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density: 1.2
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dynamic_viscosity: 0.035
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stokes: False
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implicit_windkessel: True
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io:
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write_path: 'results/aortaRR_Pa'
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restart:
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path: '' # './projects/nse_coa3d/results/test_restart2/'
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time: 0
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write_xdmf: True
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write_checkpoints: True
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write_hdf5_timeseries: False
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write_velocity: 'update' # update or tentative
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boundary_conditions:
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-
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id: 2
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type: 'dirichlet'
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#value: ['0','0','-U*sin(DOLFIN_PI*t/Th)*(t<=Th) + (t<0.8)*(Th<t)*(U*DOLFIN_PI/Th*(t-Th)*exp(-(t-Th)*beta)) +
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# -U*sin(DOLFIN_PI*(t-0.8)/Th)*(t<= 0.8+Th )*(t>0.8) + (t<1.6)*(0.8+Th<t)*(U*DOLFIN_PI/Th*(t-0.8-Th)*exp(-(t-0.8-Th)*beta)) +
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# -U*sin(DOLFIN_PI*(t-1.6)/Th)*(t<= 1.6+Th )*(t>1.6) + (t<2.4)*(1.6+Th<t)*(U*DOLFIN_PI/Th*(t-1.6-Th)*exp(-(t-1.6-Th)*beta))' ]
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value: ['0','0','-U*sin(DOLFIN_PI*t/Th)*(t<=Th) + (Th<t)*(U*DOLFIN_PI/Th*(t-Th)*exp(-(t-Th)*beta))']
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parameters:
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U: 75
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Th: 0.36
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beta: 70
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t: 0
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-
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id: 1
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type: 'dirichlet'
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value: ['0','0','0']
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-
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id: 3
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type: 'windkessel'
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parameters:
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R_p: 200
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C: 0.0005
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R_d: 4800
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p0: 85
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conv: 1333.223874
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-
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id: 4
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type: 'windkessel'
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parameters:
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R_p: 480
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C: 0.00045
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R_d: 7200
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p0: 85
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conv: 1333.223874
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-
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id: 5
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type: 'windkessel'
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parameters:
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R_p: 520
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C: 0.00045
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R_d: 11520
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p0: 85
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conv: 1333.223874
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-
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id: 6
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type: 'windkessel'
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parameters:
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R_p: 520
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C: 0.00045
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R_d: 11520
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p0: 85
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conv: 1333.223874
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timemarching:
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velocity_pressure_coupling: 'fractionalstep' # monolithic, fractionalstep
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monolithic:
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timescheme: 'gmp' # generalized midpoint, steady FIXME TODO
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theta: 1 # 1: Euler, 0.5: implicit midpoint rule (one-legged)
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nonlinear:
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method: 'constant_extrapolation' # constant_extrapolation, linear_extrapolation, newton, picard, snes
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maxit: 20
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init_steps: 30
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use_aitken: 1 # 0: False, 1: Picard only, 2: all
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report: 1 # 0: None, 1: residuals, 2: residuals and energy (inflow/driving/forcing via ESSENTIAL Dbcs!)
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atol: 1.e-6 # note: dot required!!
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rtol: 1.e-16
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stol: 0.0
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fractionalstep:
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scheme: 'CT' # CT, IPCS
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coupled_velocity: False # False faster, True needed if robin_bc implicit
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robin_bc_velocity_scheme: 'implicit' # explicit, semi-implicit, implicit
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transpiration_bc_projection: 'robin' # robin, dirichlet
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flux_report_normalize_boundary: 1
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T: 0.8 # end time
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dt: 0.001
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write_dt: 0.03
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checkpoint_dt: 0.03 # <= 0: only last; else value + last
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report: 1 # 0: print nothing, 1: print time step and writeout, 2: 1 + flux
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# solver setup
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fem:
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velocity_space: p1 # p1 p1b/p1+ p2
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pressure_space: p1 # p1 p0/dg0 dg1
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strain_symmetric: False
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convection_skew_symmetric: True # aka Temam term
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stabilization:
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forced_normal:
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enabled: True
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boundaries: [3,4,5,6]
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gamma: 20
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backflow_boundaries: [3,4,5,6]
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streamline_diffusion:
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enabled: False
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parameter: 'standard' # standard, shakib, codina, klr
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length_scale: 'metric' # average, max, metric
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parameter_element_constant: True
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Cinv: ~
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monolithic:
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infsup: 'pspg' # pspg, pressure-stabilization
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graddiv: False
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consistent: False
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pressure_stab_constant: 1.
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fix_pressure: False
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fix_pressure_point: [0., 0. , 0.]
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linear_solver:
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method: 'lu'
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estimation:
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boundary_conditions:
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#-
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# id: 3
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# type: 'windkessel'
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# initial_stddev: 1
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-
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id: 4
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type: 'windkessel'
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initial_stddev: 1
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-
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id: 5
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type: 'windkessel'
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initial_stddev: 1
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-
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id: 6
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type: 'windkessel'
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initial_stddev: 1
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-
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id: 2
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type: 'dirichlet'
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parameters: 'U'
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initial_stddev: 1
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measurements:
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-
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mesh: '/home/yeye/NuMRI/kalman/meshes/coaortaH3_leo2.0.h5'
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#mesh: './meshes/coaortaH1.h5'
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fe_degree: 1
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xdmf_file: 'measurements/aortaRR/Perturbation/Mg15V120/u_all.xdmf'
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file_root: 'measurements/aortaRR/Perturbation/Mg15V120/u{i}.h5'
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#xdmf_file: 'measurements/aortaRR/u_all.xdmf'
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#file_root: 'measurements/aortaRR/u{i}.h5'
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indices: 0 # indices of checkpoints to be processed. 0 == all
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velocity_direction: ~
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noise_stddev: 55 # standard deviation of Gaussian noise
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roukf:
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particles: 'simplex' # unique or simplex
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observation_operator: 'postprocessing' #state or postprocessing
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reparameterize: True
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ODV_functional:
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enable: False
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VENC: 102 # 102,120% 59,70% 42 50%, 21,25%
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@ -0,0 +1,62 @@
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config_name: test
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petsc_options:
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# - u_ten_ksp_view
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- u_ten_ksp_converged_reason
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- u_ten_ksp_monitor_true_residual
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- u_ten_ksp_type bcgs
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- u_ten_ksp_rtol 1.0e-6
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- u_ten_ksp_initial_guess_nonzero
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- u_ten_pc_type jacobi
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- d_ksp_type cg
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- d_ksp_rtol 1.0e-6
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# - p_ksp_view
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- p_ksp_converged_reason
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- p_ksp_monitor_true_residual
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- p_ksp_type fgmres
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- p_ksp_rtol 1.0e-6
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- p_ksp_initial_guess_nonzero
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#- p_pc_type gamg
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#- p_pc_gamg_type agg
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#- p_pc_gamg_threshold 0.03
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#- p_pc_gamg_square_graph 10 # no effect ??
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#- p_pc_gamg_sym_graph
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- p_mg_levels_ksp_type richardson
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- p_mg_levels_pc_type sor
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- p_mass_ksp_type cg
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- p_mass_ksp_converged_reason
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- p_mass_ksp_monitor_true_residual
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- p_mass_ksp_rtol 1.0e-8
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- p_mass_ksp_initial_guess_nonzero
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- p_mass_pc_type jacobi
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- u_upd_ksp_type cg
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- u_upd_ksp_rtol 1.0e-8
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- u_upd_ksp_initial_guess_nonzero
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- u_upd_pc_type jacobi
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- p_pc_type hypre
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- p_pc_hypre_type boomeramg
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- p_pc_hypre_boomeramg_strong_threshold 0.75
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- p_pc_hypre_boomeramg_max_levels 25
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- p_pc_hypre_boomeramg_smooth_type Euclid
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- p_pc_hypre_boomeramg_eu_bj
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# - p_pc_type hypre
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# - p_pc_hypre_type boomeramg
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# - p_pc_hypre_boomeramg_agg_nl 4
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# - p_pc_hypre_boomeramg_agg_num_paths 2
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# # Truncation factor for interpolation (note: increasing towrds 1
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# # appears to reduce memory useage
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# - p_pc_hypre_boomeramg_truncfactor 0.9
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# # Max elements per row for interpolation operator
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# - p_pc_hypre_boomeramg_P_max 5
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# # - p_pc_hypre_boomeramg_max_levels 10
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# # Strong threshold (BoomerAMG docs recommend 0.5-0.6 for 3D
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# # Poisson
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# - p_pc_hypre_boomeramg_strong_threshold 0.5
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@ -0,0 +1,82 @@
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config_name: test
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petsc_options:
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# - u_ten_ksp_view
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# - u_ten_ksp_converged_reason
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# - u_ten_ksp_monitor_true_residual
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- u_ten_ksp_type preonly
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# - u_ten_ksp_rtol 1.0e-6
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# - u_ten_ksp_initial_guess_nonzero
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# - u_ten_pc_type jacobi
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# - u_ten_pc_side right
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- u_ten_pc_type lu
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# - u_ten_pc_gamg_type agg
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# - u_ten_pc_gamg_threshold 0.03
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# - u_ten_pc_gamg_square_graph 10 # no effect ??
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# - u_ten_pc_gamg_sym_graph
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# - u_ten_mg_levels_ksp_type richardson
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# - u_ten_mg_levels_pc_type sor
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# # - u_ten_pc_gamg_coarse_eq_limit 50 # ignored !?!?!
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# - p_ksp_view
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- p_ksp_converged_reason
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- p_ksp_monitor_true_residual
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# - p_ksp_type gmres
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# - p_ksp_norm_type unpreconditioned
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- p_ksp_type fgmres
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- p_ksp_rtol 1.0e-8
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- p_ksp_initial_guess_nonzero
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- p_pc_type gamg
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- p_pc_gamg_type agg
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- p_pc_gamg_threshold 0.03
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- p_pc_gamg_square_graph 10 # no effect ??
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- p_pc_gamg_sym_graph
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- p_mg_levels_ksp_type richardson
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- p_mg_levels_pc_type sor
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- p_mass_ksp_type preonly
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# - p_mass_ksp_rtol 1.0e-8
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# - p_mass_ksp_initial_guess_nonzero
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- p_mass_pc_type lu
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# - p_pc_type hypre
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# - p_pc_hypre_type boomeramg
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# - p_pc_hypre_boomeramg_strong_threshold 0.75
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# - p_pc_hypre_boomeramg_max_levels 25
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# - p_pc_hypre_boomeramg_smooth_type Euclid
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# - p_pc_hypre_boomeramg_eu_bj
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# - p_ksp_type preonly
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# - p_pc_type lu
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# - p_pc_factor_mat_solver_package mumps
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# - p_mat_mumps_icntl_14 80
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# - p_ksp_type cg
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# - p_ksp_converged_reason
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# - p_ksp_monitor_true_residual
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# - p_ksp_rtol 1.0e-8
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# - p_pc_type hypre
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# - p_pc_hypre_type boomeramg
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# - p_pc_hypre_boomeramg_agg_nl 4
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# - p_pc_hypre_boomeramg_agg_num_paths 2
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# # Truncation factor for interpolation (note: increasing towrds 1
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# # appears to reduce memory useage
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# - p_pc_hypre_boomeramg_truncfactor 0.9
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# # Max elements per row for interpolation operator
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# - p_pc_hypre_boomeramg_P_max 5
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# # - p_pc_hypre_boomeramg_max_levels 10
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# # Strong threshold (BoomerAMG docs recommend 0.5-0.6 for 3D
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# # Poisson
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# - p_pc_hypre_boomeramg_strong_threshold 0.5
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# - u_upd_ksp_converged_reason
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# - u_upd_ksp_monitor_true_residual
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# - u_upd_ksp_view
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- u_upd_ksp_type preonly
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# - u_upd_ksp_rtol 1.0e-8
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# - u_upd_ksp_initial_guess_nonzero
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- u_upd_pc_type lu
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