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clean up

master
jeremias 1 year ago
parent
3e67cec21d
commit
ec76080839
4 changed files with 104 additions and 341 deletions
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  1. 49
      kalman/graphics/figure2.py
  2. 117
      kalman/input_files/aorta.yaml
  3. 150
      kalman/input_files/aorta_leo.yaml
  4. 129
      kalman/input_files/aorta_neumann.yaml

49
kalman/graphics/figure2.py
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@ -52,15 +52,41 @@ def plot_parameters(dat, input_file, deparameterize=False, ref=None): @@ -52,15 +52,41 @@ def plot_parameters(dat, input_file, deparameterize=False, ref=None):
inputfile = yaml.full_load(file)
#true_values = {
# 3: 3400,
# 4: 4200,
# 5: 11000,
# 6: 7800,
# 2: 100
# }
true_values = {
3: 2400,
4: 4200,
5: 11000,
6: 7800,
2: 100
3: 4800,
4: 7020,
5: 11520,
6: 11520,
2: 75
}
true_values_c = {
3: 0.0008,
4: 0.00034,
5: 0.00034,
6: 0.00034,
2: 100
}
true_values_rp = {
3: 10,
4: 60,
5: 220,
6: 160,
2: 100
}
current_val = []
labels = []
ids = []
@ -75,10 +101,9 @@ def plot_parameters(dat, input_file, deparameterize=False, ref=None): @@ -75,10 +101,9 @@ def plot_parameters(dat, input_file, deparameterize=False, ref=None):
labels.append('$R_' + str(bnd_c['id']))
elif 'dirichlet' in bnd_c['type']:
current_val.append(inputfile['boundary_conditions'][1]['parameters']['U'])
current_val.append(inputfile['boundary_conditions'][0]['parameters']['U'])
ids.append(bnd_c['id'])
labels.append('U')
labels.append('$U')
dim = dat['theta'].shape[-1]
fig1, axes = plt.subplots(1,1,figsize=(8,6))
@ -107,10 +132,10 @@ def plot_parameters(dat, input_file, deparameterize=False, ref=None): @@ -107,10 +132,10 @@ def plot_parameters(dat, input_file, deparameterize=False, ref=None):
for i in range(dim):
true_level = np.log(true_values[ids[i]]/current_val[i])/np.log(2)
rec_value = np.round(2**theta[-1, i]*current_val[i],1)
rec_value = np.round(2**theta[-1, i]*current_val[i],2)
cur_key = ids[i]
axes.plot(t, theta[:, i] + 1.5*i, '-', color=col_,label=legends_ + '= ' + str(rec_value) + '/' + str(true_values[cur_key]) + '$')
axes.plot(t, theta[:, i] + 1.5*i, '-', color=col_,label= legends_ + '= ' + str(rec_value) + '/' + str(true_values[cur_key]) + '$')
axes.fill_between(t, theta[:, i] + 1.5*i - np.sqrt(P[:, i, i]),
theta[:, i] + 1.5*i + np.sqrt(P[:, i, i]), alpha=0.3,
color=col_)

117
kalman/input_files/aorta.yaml
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@ -4,10 +4,11 @@ mesh: './meshes/coaortaH1.h5' @@ -4,10 +4,11 @@ mesh: './meshes/coaortaH1.h5'
fluid:
density: 1.2
dynamic_viscosity: 0.035
stokes: True
stokes: False
implicit_windkessel: True
io:
write_path: 'results/aorta_1ms'
write_path: 'results/aorta25_zPb_3R'
restart:
path: '' # './projects/nse_coa3d/results/test_restart2/'
time: 0
@ -17,53 +18,67 @@ io: @@ -17,53 +18,67 @@ io:
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))']
#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: 100
Th: 0.35
t: 0
#U: 75
#U: 150 #Pa
U: 40 #Pb
Th: 0.36
beta: 70
t: 0
-
id: 1
type: 'dirichlet'
value: ['0','0','0']
-
id: 3
type: 'windkessel'
parameters:
R_p: 10
C: 0.0008
R_d: 2400
p0: 80
R_p: 200
C: 0.0005
#R_d: 4800
#R_d: 9000 #Pa
R_d: 2000 #Pb
p0: 85
conv: 1333.223874
-
id: 4
type: 'windkessel'
parameters:
R_p: 60
C: 0.00034
R_d: 4200
p0: 80
R_p: 480
C: 0.00045
#R_d: 7200
#R_d: 12000 #Pa
R_d: 4000 #Pb
p0: 85
conv: 1333.223874
-
id: 5
type: 'windkessel'
parameters:
R_p: 220
C: 0.00034
R_d: 11000
p0: 80
R_p: 520
C: 0.00045
#R_d: 11520
#R_d: 23000 #Pa
R_d: 6000 #Pb
p0: 85
conv: 1333.223874
-
id: 6
type: 'windkessel'
parameters:
R_p: 160
C: 0.00034
R_d: 7800
p0: 80
R_p: 520
C: 0.00045
R_d: 11520
#R_d: 23000 #Pa
#R_d: 6000 #Pb
p0: 85
conv: 1333.223874
timemarching:
@ -91,8 +106,8 @@ timemarching: @@ -91,8 +106,8 @@ timemarching:
T: 0.8 # end time
dt: 0.001
write_dt: 0.04
checkpoint_dt: 0.04 # <= 0: only last; else value + last
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
# solver setup
@ -104,9 +119,9 @@ fem: @@ -104,9 +119,9 @@ fem:
convection_skew_symmetric: True # aka Temam term
stabilization:
forced_normal:
enabled: False
boundaries: [6]
gamma: 10
enabled: True
boundaries: [3,4,5,6]
gamma: 20
backflow_boundaries: [3,4,5,6]
streamline_diffusion:
enabled: False
@ -128,39 +143,41 @@ linear_solver: @@ -128,39 +143,41 @@ linear_solver:
estimation:
boundary_conditions:
#-
# id: 3
# type: 'windkessel'
# initial_stddev: 1
-
id: 3
type: 'windkessel'
initial_stddev: 1
-
id: 4
type: 'windkessel'
initial_stddev: 1
#-
# id: 5
# 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
-
id: 2
type: 'dirichlet'
parameters: 'U'
initial_stddev: 1
measurements:
-
#mesh: '/home/yeye/NuMRI/kalman/meshes/coaortaH3_leo2.0.h5'
mesh: './meshes/coaortaH1.h5'
mesh: '/home/yeye/NuMRI/kalman/meshes/coaortaH3_leo2.0.h5'
#mesh: './meshes/coaortaH1.h5'
fe_degree: 1
xdmf_file: 'measurements/aorta/u_all.xdmf'
file_root: 'measurements/aorta/u{i}.h5'
xdmf_file: 'measurements/aorta25_z/Perturbation/Mg15V120/u_all.xdmf'
file_root: 'measurements/aorta25_z/Perturbation/Mg15V120/u{i}.h5'
#xdmf_file: 'measurements/aorta25_z/u_all.xdmf'
#file_root: 'measurements/aorta25_z/u{i}.h5'
indices: 0 # indices of checkpoints to be processed. 0 == all
velocity_direction: ~
noise_stddev: 0 # standard deviation of Gaussian noise
velocity_direction: [0,0,1]
noise_stddev: 55 # standard deviation of Gaussian noise
roukf:
particles: 'simplex' # unique or simplex

150
kalman/input_files/aorta_leo.yaml
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@ -1,150 +0,0 @@ @@ -1,150 +0,0 @@
mesh: './meshes/coaortaH1.h5'
# Physical parameters of the fluid
fluid:
density: 1.2
dynamic_viscosity: 0.035
io:
write_path: 'results/aorta_leo'
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: 30
Th: 0.35
t: 0
-
id: 3
type: 'windkessel'
value: [10,0,0]
p0: [0,1333.223874]
-
id: 4
type: 'windkessel'
value: [250,0,0]
p0: [0,1333.223874]
-
id: 5
type: 'windkessel'
value: [250,0,0]
p0: [0,1333.223874]
-
id: 6
type: 'windkessel'
value: [250,0,0]
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_leo/measurements/u_all.xdmf'
file_root: 'results/aorta_leo/measurements/u{i}.h5'
indices: 0 # indices of checkpoints to be processed. 0 == all
velocity_direction: ~
noise_stddev: 5 # standard deviation of Gaussian noise
roukf:
particles: 'simplex' # unique or simplex
observation_operator: 'postprocessing' #state or postprocessing
reparameterize: True

129
kalman/input_files/aorta_neumann.yaml
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@ -1,129 +0,0 @@ @@ -1,129 +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' # 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: 30
Th: 0.35
t: 0
-
id: 3
type: 'neumann'
value: 0
-
id: 4
type: 'neumann'
value: 0
-
id: 5
type: 'neumann'
value: 0
-
id: 6
type: 'neumann'
value: 0
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: 2
type: 'dirichlet'
parameters: 'U'
initial_stddev: 1
measurements:
-
mesh: './meshes/coaortaH1.h5'
fe_degree: 1
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: 1.5 # standard deviation of Gaussian noise
roukf:
particles: 'simplex' # unique or simplex
observation_operator: 'postprocessing' #state or postprocessing
reparameterize: True
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