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This commit is contained in:
jeremias 2021-02-19 18:35:14 -03:00
parent c966a477fc
commit 7cc7f0ccbd
119 changed files with 87 additions and 1399 deletions
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6
kalman/graphics/figure2.py
View File

@ -43,11 +43,13 @@ def plot_parameters(dat, deparameterize=False, ref=None):
plt.ion() plt.ion()
inputfile_path = 'results/aorta/input.yaml' inputfile_path = 'results/aorta_C/input.yaml'
with open(inputfile_path) as file: with open(inputfile_path) as file:
inputfile = yaml.full_load(file) inputfile = yaml.full_load(file)
true_val = [10,250,250,250,30] #true_val = [10,250,250,250,30]
true_val = [94,250,683,615,30]
current_val = [] current_val = []
current_val.append(inputfile['boundary_conditions'][2]['value'][0]) current_val.append(inputfile['boundary_conditions'][2]['value'][0])
current_val.append(inputfile['boundary_conditions'][3]['value'][0]) current_val.append(inputfile['boundary_conditions'][3]['value'][0])

67
kalman/input_files/aorta.yaml
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@ -6,7 +6,7 @@ fluid:
dynamic_viscosity: 0.035 dynamic_viscosity: 0.035
io: io:
write_path: 'results/aorta' write_path: 'results/aorta_C'
restart: restart:
path: '' # './projects/nse_coa3d/results/test_restart2/' path: '' # './projects/nse_coa3d/results/test_restart2/'
time: 0 time: 0
@ -25,29 +25,38 @@ boundary_conditions:
type: 'dirichlet' type: 'dirichlet'
value: ['0','0','-U*sin(DOLFIN_PI*t/Th)*(t<=Th) + (Th<t)*(-3.67949466208*U*sin(9*DOLFIN_PI*t/Th)*exp(-t*10))'] value: ['0','0','-U*sin(DOLFIN_PI*t/Th)*(t<=Th) + (Th<t)*(-3.67949466208*U*sin(9*DOLFIN_PI*t/Th)*exp(-t*10))']
parameters: parameters:
U: 1 U: 30
Th: 0.35 Th: 0.35
t: 0 t: 0
- -
id: 3 id: 3
type: 'windkessel' type: 'windkessel'
value: [10,0,0] #value: [10,0,0]
p0: [0,1333.223874] #p0: [0,1333.223874]
value: [10,1000,0.01]
p0: [47,1333.223874]
- -
id: 4 id: 4
type: 'windkessel' type: 'windkessel'
value: [250,0,0] #value: [250,0,0]
p0: [0,1333.223874] #p0: [0,1333.223874]
value: [250,8000,0.0001]
p0: [47,1333.223874]
- -
id: 5 id: 5
type: 'windkessel' type: 'windkessel'
value: [250,0,0] #value: [250,0,0]
p0: [0,1333.223874] #p0: [0,1333.223874]
value: [250,8000,0.0001]
p0: [47,1333.223874]
- -
id: 6 id: 6
type: 'windkessel' type: 'windkessel'
value: [250,0,0] #value: [250,0,0]
p0: [0,1333.223874] #p0: [0,1333.223874]
value: [250,8000,0.0001]
p0: [47,1333.223874]
timemarching: timemarching:
velocity_pressure_coupling: 'fractionalstep' # monolithic, fractionalstep velocity_pressure_coupling: 'fractionalstep' # monolithic, fractionalstep
@ -111,22 +120,22 @@ linear_solver:
estimation: estimation:
boundary_conditions: boundary_conditions:
- #-
id: 3 # id: 3
type: 'windkessel' # type: 'windkessel'
initial_stddev: 1 # initial_stddev: 1
- #-
id: 4 # id: 4
type: 'windkessel' # type: 'windkessel'
initial_stddev: 1 # initial_stddev: 1
- #-
id: 5 # id: 5
type: 'windkessel' # type: 'windkessel'
initial_stddev: 1 # initial_stddev: 1
- #-
id: 6 # id: 6
type: 'windkessel' # type: 'windkessel'
initial_stddev: 1 # initial_stddev: 1
- -
id: 2 id: 2
type: 'dirichlet' type: 'dirichlet'
@ -138,8 +147,10 @@ estimation:
- -
mesh: '/home/yeye/NuMRI/kalman/meshes/coaortaH3_leo2.0.h5' mesh: '/home/yeye/NuMRI/kalman/meshes/coaortaH3_leo2.0.h5'
fe_degree: 1 fe_degree: 1
xdmf_file: 'measurements/aorta/Perturbation/Ks12V120/u.xdmf' #xdmf_file: 'measurements/aorta_C/Perturbation/Ks12V120/u.xdmf'
file_root: 'measurements/aorta/Perturbation/Ks12V120/u{i}.h5' #file_root: 'measurements/aorta_C/Perturbation/Ks12V120/u{i}.h5'
xdmf_file: 'measurements/aorta_C/u_all.xdmf'
file_root: 'measurements/aorta_C/u{i}.h5'
indices: 0 # indices of checkpoints to be processed. 0 == all indices: 0 # indices of checkpoints to be processed. 0 == all
velocity_direction: ~ velocity_direction: ~
noise_stddev: 15 # standard deviation of Gaussian noise noise_stddev: 15 # standard deviation of Gaussian noise

58
kalman/input_files/aorta_C.yaml
View File

@ -6,14 +6,14 @@ fluid:
dynamic_viscosity: 0.035 dynamic_viscosity: 0.035
io: io:
write_path: 'results/aorta/' write_path: 'results/aorta_corr'
restart: restart:
path: '' # './projects/nse_coa3d/results/test_restart2/' path: '' # './projects/nse_coa3d/results/test_restart2/'
time: 0 time: 0
write_xdmf: True write_xdmf: True
write_checkpoints: True write_checkpoints: True
write_hdf5_timeseries: False write_hdf5_timeseries: False
write_velocity: 'update' # tentative write_velocity: 'update' # tentative or update
boundary_conditions: boundary_conditions:
- -
@ -23,31 +23,42 @@ boundary_conditions:
- -
id: 2 id: 2
type: 'dirichlet' type: 'dirichlet'
value: ['0','0','-U*sin(DOLFIN_PI*t/Th)*(t<=Th) + (Th<t)*(-3.67949466208*U*sin(9*DOLFIN_PI*t/Th)*exp(-t*10))'] value: ['0','0','-U*sin(DOLFIN_PI*t/Th)*(t<=Th) + (t<=Tc)*(t>Th)*(-3.67949466208*U*sin(9*DOLFIN_PI*t/Th)*exp(-t*10))
- U*sin(DOLFIN_PI*(t-Tc)/Th)*(t>Tc)*(t<= Tc + Th) + (t>Tc+Th)*(-3.67949466208*U*sin(9*DOLFIN_PI*(t-Tc)/Th)*exp(-(t-Tc)*10))']
parameters: parameters:
U: 30 U: 30
Th: 0.35 Th: 0.35
Tc: 0.8
t: 0 t: 0
- -
id: 3 id: 3
type: 'windkessel' type: 'windkessel'
value: [10,1000,0.01] value: [10,1000,0.01] #paper corr
#value: [94,1794,0.0014] #paper windk
#value: [94,0,0]
p0: [47,1333.223874] p0: [47,1333.223874]
- -
id: 4 id: 4
type: 'windkessel' type: 'windkessel'
value: [250,8000,0.0001] value: [250,8000,0.0001] #paper corr
#value: [250,10000,0.0004] #paper windk
#value: [250,0,0] #paper
p0: [47,1333.223874] p0: [47,1333.223874]
- -
id: 5 id: 5
type: 'windkessel' type: 'windkessel'
value: [250,8000,0.0001] value: [250,8000,0.0001] #paper corr
#value: [683,12960,0.0002] #paper windk
#value: [683,0,0]
p0: [47,1333.223874] p0: [47,1333.223874]
- -
id: 6 id: 6
type: 'windkessel' type: 'windkessel'
value: [250,8000,0.0001] value: [250,8000,0.0001] #paper corr
#value: [615,11664,0.0002] #paper windk
#value: [615,0,0]
p0: [47,1333.223874] p0: [47,1333.223874]
timemarching: timemarching:
velocity_pressure_coupling: 'fractionalstep' # monolithic, fractionalstep velocity_pressure_coupling: 'fractionalstep' # monolithic, fractionalstep
@ -72,8 +83,8 @@ timemarching:
transpiration_bc_projection: 'robin' # robin, dirichlet transpiration_bc_projection: 'robin' # robin, dirichlet
flux_report_normalize_boundary: 1 flux_report_normalize_boundary: 1
T: 0.8 # end time T: 1.6 # end time
dt: 0.01 dt: 0.001
write_dt: 0.04 write_dt: 0.04
checkpoint_dt: 0.04 # <= 0: only last; else value + last checkpoint_dt: 0.04 # <= 0: only last; else value + last
report: 1 # 0: print nothing, 1: print time step and writeout, 2: 1 + flux report: 1 # 0: print nothing, 1: print time step and writeout, 2: 1 + flux
@ -87,7 +98,7 @@ fem:
convection_skew_symmetric: True # aka Temam term convection_skew_symmetric: True # aka Temam term
stabilization: stabilization:
forced_normal: forced_normal:
enabled: True enabled: False
boundaries: [6] boundaries: [6]
gamma: 10 gamma: 10
backflow_boundaries: [3,4,5,6] backflow_boundaries: [3,4,5,6]
@ -111,6 +122,22 @@ linear_solver:
estimation: estimation:
boundary_conditions: boundary_conditions:
-
id: 3
type: 'windkessel'
initial_stddev: 1
#-
# id: 4
# type: 'windkessel'
# initial_stddev: 1
#-
# id: 5
# type: 'windkessel'
# initial_stddev: 1
#-
# id: 6
# type: 'windkessel'
# initial_stddev: 1
- -
id: 2 id: 2
type: 'dirichlet' type: 'dirichlet'
@ -119,15 +146,18 @@ estimation:
measurements: measurements:
- -
mesh: './meshes/coaortaH1.h5' mesh: './meshes/coaortaH3_leo2.0.h5'
fe_degree: 1 fe_degree: 1
xdmf_file: 'results/aorta/measurements/u_all.xdmf' xdmf_file: 'measurements/aorta_C/u_all.xdmf'
file_root: 'results/aorta/measurements/u{i}.h5' file_root: 'measurements/aorta_C/u{i}.h5'
indices: 0 # indices of checkpoints to be processed. 0 == all indices: 0 # indices of checkpoints to be processed. 0 == all
velocity_direction: ~ velocity_direction: ~
noise_stddev: 12.5 # standard deviation of Gaussian noise noise_stddev: 15 # standard deviation of Gaussian noise
roukf: roukf:
particles: 'simplex' # unique or simplex particles: 'simplex' # unique or simplex
observation_operator: 'postprocessing' #state or postprocessing observation_operator: 'postprocessing' #state or postprocessing
reparameterize: True reparameterize: True
ODV_functional:
enable: False
VENC: 102 # 102,120% 59,70% 42 50%, 21,25%

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kalman/measurements/aorta/Perturbation/Ks12V120/u.h5
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Binary file not shown.

260
kalman/measurements/aorta/Perturbation/Ks12V120/u.xdmf
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@ -1,260 +0,0 @@
<?xml version="1.0"?>
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
<Xdmf Version="3.0" xmlns:xi="http://www.w3.org/2001/XInclude">
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@ -1,155 +0,0 @@
mesh: './meshes/coaortaH1.h5'
# Physical parameters of the fluid
fluid:
density: 1.2
dynamic_viscosity: 0.035
io:
write_path: 'results/aorta'
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: 1
type: 'dirichlet'
value: ['0','0','0']
-
id: 2
type: 'dirichlet'
value: ['0','0','-U*sin(DOLFIN_PI*t/Th)*(t<=Th) + (Th<t)*(-3.67949466208*U*sin(9*DOLFIN_PI*t/Th)*exp(-t*10))']
parameters:
U: 60
Th: 0.35
t: 0
-
id: 3
type: 'windkessel'
value: [20,0,0]
p0: [0,1333.223874]
-
id: 4
type: 'windkessel'
value: [500,0,0]
p0: [0,1333.223874]
-
id: 5
type: 'windkessel'
value: [500,0,0]
p0: [0,1333.223874]
-
id: 6
type: 'windkessel'
value: [500,0,0]
p0: [0,1333.223874]
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: 0.01
write_dt: 0.04
checkpoint_dt: 0.04 # <= 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: True
boundaries: [6]
gamma: 10
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'
initial_stddev: 1
-
id: 5
type: 'windkessel'
initial_stddev: 1
-
id: 6
type: 'windkessel'
initial_stddev: 1
-
id: 2
type: 'dirichlet'
parameters: 'U'
initial_stddev: 1
measurements:
-
mesh: './meshes/coaortaH3_leo2.0.h5'
fe_degree: 1
#xdmf_file: 'results/aorta/measurements/Perturbation/SNRinfV70/u_all.xdmf'
#file_root: 'results/aorta/measurements/Perturbation/SNRinfV70/u{i}.h5'
xdmf_file: 'results/aorta/measurements/u_all.xdmf'
file_root: 'results/aorta/measurements/u{i}.h5'
indices: 0 # indices of checkpoints to be processed. 0 == all
velocity_direction: ~
noise_stddev: 0 # standard deviation of Gaussian noise
roukf:
particles: 'simplex' # unique or simplex
observation_operator: 'postprocessing' #state or postprocessing
reparameterize: True
ODV_functional:
enable: True
VENC: 61 # cm/s ref: 61 for 70% and 44 for 50%

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