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J.E. Garay Labra 11 months ago
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3 changed files with 422 additions and 4 deletions
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  1. 8
      kalman/input_files/aorta.yaml
  2. 209
      kalman/input_files/aorta_old.yaml
  3. 209
      kalman/input_files/aorta_old2.yaml

8
kalman/input_files/aorta.yaml
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@ -5,10 +5,10 @@ fluid: @@ -5,10 +5,10 @@ fluid:
density: 1.2
dynamic_viscosity: 0.035
stokes: False
implicit_windkessel: True
implicit_windkessel: False
io:
write_path: 'results/impl_1ms'
write_path: 'results/expl_1ms'
restart:
path: '' # './projects/nse_coa3d/results/test_restart2/'
time: 0
@ -27,7 +27,7 @@ boundary_conditions: @@ -27,7 +27,7 @@ boundary_conditions:
value: ['0','0','-U*sin(DOLFIN_PI*t/Th)*(t<=Th) + (Th<t)*(U*DOLFIN_PI/Th*(t-Th)*exp(-(t-Th)*beta))']
parameters:
#U: 75 #REFERENCE
U: 80
U: 120
#U: 150 #Pa/Pb
#U: 40 #Pc
Th: 0.36
@ -118,7 +118,7 @@ timemarching: @@ -118,7 +118,7 @@ timemarching:
flux_report_normalize_boundary: 1
T: 0.8 # end time
dt: 0.001
dt: 0.002
write_dt: 0.03
checkpoint_dt: 0.03 # <= 0: only last; else value + last
report: 1 # 0: print nothing, 1: print time step and writeout, 2: 1 + flux

209
kalman/input_files/aorta_old.yaml
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@ -0,0 +1,209 @@ @@ -0,0 +1,209 @@
mesh: './meshes/coaortaH1.h5'
# Physical parameters of the fluid
fluid:
density: 1.2
dynamic_viscosity: 0.035
stokes: False
implicit_windkessel: False
io:
write_path: 'results/exp_0.1ms'
restart:
path: '' # './projects/nse_coa3d/results/test_restart2/'
time: 0
write_xdmf: True
write_checkpoints: True
write_hdf5_timeseries: False
write_velocity: 'update' # update or tentative
boundary_conditions:
-
id: 2
type: 'dirichlet'
#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)) +
# -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)) +
# -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))' ]
value: ['0','0','-U*sin(DOLFIN_PI*t/Th)*(t<=Th) + (Th<t)*(U*DOLFIN_PI/Th*(t-Th)*exp(-(t-Th)*beta))']
parameters:
#U: 75 #REFERENCE 120
U: 100
#U: 150 #Pa/Pb
#U: 40 #Pc
Th: 0.36
beta: 70
t: 0
-
id: 1
type: 'dirichlet'
value: ['0','0','0']
-
id: 3
type: 'windkessel'
parameters:
R_p: 200
C: 0.0004
R_d: 4800
p0: 85
conv: 1333.223874
-
id: 4
type: 'windkessel'
parameters:
#R_p: 480
R_p: 480
#C: 0.0004 # REFERENCE
C: 0.001 # REFERENCE
#C: 0.0005 # Pa
#C: 0.0010 # Pb
#C: 0.0001 # Pc
#C: 0.0008 # Pg
#R_d: 7200 # REFERENCE
R_d: 15000 # REFERENCE
#R_d: 8760 #Pa
#R_d: 17520 #Pb x2
#R_d: 4000 #Pc
p0: 85
conv: 1333.223874
-
id: 5
type: 'windkessel'
parameters:
R_p: 520
C: 0.0003 # REFERENCE
#C: 0.0005 # Pa
#C: 0.0010 # Pb
#C: 0.0001 # Pc
#C: 0.0008 # Pg
#R_d: 11520 # REFERENCE
R_d: 40000
#R_d: 8760 #Pa
#R_d: 17520 #Pb x2
#R_d: 4000 #Pc
p0: 85
conv: 1333.223874
-
id: 6
type: 'windkessel'
parameters:
R_p: 520
C: 0.0003 # REFERENCE
#C: 0.0005 #Pa
#C: 0.0010 #Pb
#C: 0.0001 #Pc
R_d: 11520 # REFERENCE
#R_d: 35000
#R_d: 8760 #Pa
#R_d: 17520 #Pb x2
#R_d: 4000 #Pc
p0: 85
conv: 1333.223874
timemarching:
velocity_pressure_coupling: 'fractionalstep' # monolithic, fractionalstep
monolithic:
timescheme: 'gmp' # generalized midpoint, steady FIXME TODO
theta: 1 # 1: Euler, 0.5: implicit midpoint rule (one-legged)
nonlinear:
method: 'constant_extrapolation' # constant_extrapolation, linear_extrapolation, newton, picard, snes
maxit: 20
init_steps: 30
use_aitken: 1 # 0: False, 1: Picard only, 2: all
report: 1 # 0: None, 1: residuals, 2: residuals and energy (inflow/driving/forcing via ESSENTIAL Dbcs!)
atol: 1.e-6 # note: dot required!!
rtol: 1.e-16
stol: 0.0
fractionalstep:
scheme: 'CT' # CT, IPCS
coupled_velocity: False # False faster, True needed if robin_bc implicit
robin_bc_velocity_scheme: 'implicit' # explicit, semi-implicit, implicit
transpiration_bc_projection: 'robin' # robin, dirichlet
flux_report_normalize_boundary: 1
T: 0.8 # end time
dt: 0.0001
write_dt: 0.001
checkpoint_dt: 0.001 # <= 0: only last; else value + last
report: 1 # 0: print nothing, 1: print time step and writeout, 2: 1 + flux
# solver setup
fem:
velocity_space: p1 # p1 p1b/p1+ p2
pressure_space: p1 # p1 p0/dg0 dg1
strain_symmetric: False
convection_skew_symmetric: True # aka Temam term
stabilization:
forced_normal:
enabled: False
boundaries: [3,4,5,6]
gamma: 20
backflow_boundaries: [3,4,5,6]
streamline_diffusion:
enabled: False
parameter: 'standard' # standard, shakib, codina, klr
length_scale: 'metric' # average, max, metric
parameter_element_constant: True
Cinv: ~
monolithic:
infsup: 'pspg' # pspg, pressure-stabilization
graddiv: False
consistent: False
pressure_stab_constant: 1.
fix_pressure: False
fix_pressure_point: [0., 0. , 0.]
linear_solver:
method: 'lu'
estimation:
boundary_conditions:
#-
# id: 3
# type: 'windkessel'
# initial_stddev: 1
-
id: 4
type: 'windkessel'
mode: 'RdC'
initial_stddev: 1
-
id: 5
type: 'windkessel'
mode: 'RdC'
initial_stddev: 1
-
id: 6
type: 'windkessel'
mode: 'RdC'
initial_stddev: 1
-
id: 2
type: 'dirichlet'
parameters: 'U'
initial_stddev: 1
measurements:
-
mesh: '/home/yeye/NuMRI/kalman/meshes/coaortaH3_leo2.0.h5'
#mesh: './meshes/coaortaH1.h5'
fe_degree: 1
#xdmf_file: 'measurements/aorta_dt1ms/Perturbation/Mg15V70/u_all.xdmf'
#file_root: 'measurements/aorta_dt1ms/Perturbation/Mg15V70/u{i}.h5'
xdmf_file: 'measurements/aorta_exp_dt1ms/u_all.xdmf'
file_root: 'measurements/aorta_exp_dt1ms/u{i}.h5'
indices: 0 # indices of checkpoints to be processed. 0 == all
velocity_direction: [0,0,1]
noise_stddev: 45 # standard deviation of Gaussian noise
roukf:
particles: 'simplex' # unique or simplex
observation_operator: 'postprocessing' #state or postprocessing
reparameterize: True
ODV_functional:
enable: False
VENC: 138

209
kalman/input_files/aorta_old2.yaml
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@ -0,0 +1,209 @@ @@ -0,0 +1,209 @@
mesh: './meshes/coaortaH1.h5'
# Physical parameters of the fluid
fluid:
density: 1.2
dynamic_viscosity: 0.035
stokes: False
implicit_windkessel: True
io:
write_path: 'results/impl_0.1ms'
restart:
path: '' # './projects/nse_coa3d/results/test_restart2/'
time: 0
write_xdmf: True
write_checkpoints: True
write_hdf5_timeseries: False
write_velocity: 'update' # update or tentative
boundary_conditions:
-
id: 2
type: 'dirichlet'
#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)) +
# -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)) +
# -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))' ]
value: ['0','0','-U*sin(DOLFIN_PI*t/Th)*(t<=Th) + (Th<t)*(U*DOLFIN_PI/Th*(t-Th)*exp(-(t-Th)*beta))']
parameters:
#U: 75 #REFERENCE 120
U: 100
#U: 150 #Pa/Pb
#U: 40 #Pc
Th: 0.36
beta: 70
t: 0
-
id: 1
type: 'dirichlet'
value: ['0','0','0']
-
id: 3
type: 'windkessel'
parameters:
R_p: 200
C: 0.0004
R_d: 4800
p0: 85
conv: 1333.223874
-
id: 4
type: 'windkessel'
parameters:
#R_p: 480
R_p: 480
#C: 0.0004 # REFERENCE
C: 0.001 # REFERENCE
#C: 0.0005 # Pa
#C: 0.0010 # Pb
#C: 0.0001 # Pc
#C: 0.0008 # Pg
#R_d: 7200 # REFERENCE
R_d: 15000 # REFERENCE
#R_d: 8760 #Pa
#R_d: 17520 #Pb x2
#R_d: 4000 #Pc
p0: 85
conv: 1333.223874
-
id: 5
type: 'windkessel'
parameters:
R_p: 520
C: 0.0003 # REFERENCE
#C: 0.0005 # Pa
#C: 0.0010 # Pb
#C: 0.0001 # Pc
#C: 0.0008 # Pg
#R_d: 11520 # REFERENCE
R_d: 40000
#R_d: 8760 #Pa
#R_d: 17520 #Pb x2
#R_d: 4000 #Pc
p0: 85
conv: 1333.223874
-
id: 6
type: 'windkessel'
parameters:
R_p: 520
C: 0.0003 # REFERENCE
#C: 0.0005 #Pa
#C: 0.0010 #Pb
#C: 0.0001 #Pc
R_d: 11520 # REFERENCE
#R_d: 35000
#R_d: 8760 #Pa
#R_d: 17520 #Pb x2
#R_d: 4000 #Pc
p0: 85
conv: 1333.223874
timemarching:
velocity_pressure_coupling: 'fractionalstep' # monolithic, fractionalstep
monolithic:
timescheme: 'gmp' # generalized midpoint, steady FIXME TODO
theta: 1 # 1: Euler, 0.5: implicit midpoint rule (one-legged)
nonlinear:
method: 'constant_extrapolation' # constant_extrapolation, linear_extrapolation, newton, picard, snes
maxit: 20
init_steps: 30
use_aitken: 1 # 0: False, 1: Picard only, 2: all
report: 1 # 0: None, 1: residuals, 2: residuals and energy (inflow/driving/forcing via ESSENTIAL Dbcs!)
atol: 1.e-6 # note: dot required!!
rtol: 1.e-16
stol: 0.0
fractionalstep:
scheme: 'CT' # CT, IPCS
coupled_velocity: False # False faster, True needed if robin_bc implicit
robin_bc_velocity_scheme: 'implicit' # explicit, semi-implicit, implicit
transpiration_bc_projection: 'robin' # robin, dirichlet
flux_report_normalize_boundary: 1
T: 0.8 # end time
dt: 0.0001
write_dt: 0.001
checkpoint_dt: 0.001 # <= 0: only last; else value + last
report: 1 # 0: print nothing, 1: print time step and writeout, 2: 1 + flux
# solver setup
fem:
velocity_space: p1 # p1 p1b/p1+ p2
pressure_space: p1 # p1 p0/dg0 dg1
strain_symmetric: False
convection_skew_symmetric: True # aka Temam term
stabilization:
forced_normal:
enabled: False
boundaries: [3,4,5,6]
gamma: 20
backflow_boundaries: [3,4,5,6]
streamline_diffusion:
enabled: False
parameter: 'standard' # standard, shakib, codina, klr
length_scale: 'metric' # average, max, metric
parameter_element_constant: True
Cinv: ~
monolithic:
infsup: 'pspg' # pspg, pressure-stabilization
graddiv: False
consistent: False
pressure_stab_constant: 1.
fix_pressure: False
fix_pressure_point: [0., 0. , 0.]
linear_solver:
method: 'lu'
estimation:
boundary_conditions:
#-
# id: 3
# type: 'windkessel'
# initial_stddev: 1
-
id: 4
type: 'windkessel'
mode: 'RdC'
initial_stddev: 1
-
id: 5
type: 'windkessel'
mode: 'RdC'
initial_stddev: 1
-
id: 6
type: 'windkessel'
mode: 'RdC'
initial_stddev: 1
-
id: 2
type: 'dirichlet'
parameters: 'U'
initial_stddev: 1
measurements:
-
mesh: '/home/yeye/NuMRI/kalman/meshes/coaortaH3_leo2.0.h5'
#mesh: './meshes/coaortaH1.h5'
fe_degree: 1
#xdmf_file: 'measurements/aorta_dt1ms/Perturbation/Mg15V70/u_all.xdmf'
#file_root: 'measurements/aorta_dt1ms/Perturbation/Mg15V70/u{i}.h5'
xdmf_file: 'measurements/aorta_exp_dt1ms/u_all.xdmf'
file_root: 'measurements/aorta_exp_dt1ms/u{i}.h5'
indices: 0 # indices of checkpoints to be processed. 0 == all
velocity_direction: [0,0,1]
noise_stddev: 45 # standard deviation of Gaussian noise
roukf:
particles: 'simplex' # unique or simplex
observation_operator: 'postprocessing' #state or postprocessing
reparameterize: True
ODV_functional:
enable: False
VENC: 138
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