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J.E. Garay Labra 2021-02-12 15:24:03 -03:00
parent ffdc03c62e
commit c966a477fc
118 changed files with 1443 additions and 31 deletions
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95
kalman/compute_errors_kalman.py
View File

@ -6,8 +6,7 @@ def compute_relative_error(vcur,vref):
for i in range(len(vref)): for i in range(len(vref)):
eps += ((vcur[i] - vref[i])/vref[i])**2 eps += ((vcur[i] - vref[i])/vref[i])**2
return np.sqrt(eps) return np.sqrt(eps)/len(vcur)
@ -15,57 +14,117 @@ def compute_relative_error(vcur,vref):
vref = [10, 250, 250, 250, 30] vref = [10, 250, 250, 250, 30]
#case 1 #case 1
v_no_case1 = [ 10.05 , 248.34, 250.52 , 254.43 , 29.82] v_120_case1 = [ 10.22 , 249.1 , 254.37 , 259.15 , 29.81 ]
v_70_case1 = [20.38, 211.19, 189.01, 207.09, 28.78] v_70_case1 = [20.38, 211.19, 189.01, 207.09, 28.78]
v_50_case1 = [90.45, 240.98, 241.03, 316.89, 21.27] v_50_case1 = [90.45, 240.98, 241.03, 316.89, 21.27]
v_25_case1 = [2012.53, 1004.3, 1172.01, 1755.02, 12.69]
vnew_120_case1 = [ 10.26 , 249.84, 254.6, 259.69 , 29.81]
vnew_70_case1 = [ 10.26 , 250.73, 252.78, 256.62 , 29.77] vnew_70_case1 = [ 10.26 , 250.73, 252.78, 256.62 , 29.77]
vnew_50_case1 = [ 10.27 , 248.41 ,254.71 ,253.01 , 29.82] vnew_50_case1 = [ 10.27 , 248.41 ,254.71 ,253.01 , 29.82]
vnew_25_case1 = [ 10.18 , 251.13 ,253.78 ,257.4 , 29.82]
#case 2 #case 2
v_no_case2 = [ 9.77, 249.7 , 251.94, 254.91 , 29.82] v_120_case2 = [ 9.95, 248.5, 254.4, 253.4, 29.80]
v_70_case2 = [ 20.7 , 214.77 , 196.47 , 209.31 , 28.76] v_70_case2 = [ 20.7 , 214.77 , 196.47 , 209.31 , 28.76]
v_50_case2 = [ 88.4, 236.73 ,240.39 ,312.85, 21.22] v_50_case2 = [ 88.40, 236.7, 240.4, 312.9, 21.22]
v_25_case2 = [ 880.4, 747.2, 822.7, 1380, 9.37]
vnew_70_case2 = [ 10 , 250.24 ,252.05 ,254.98 , 29.76] vnew_120_case2 = [ 10, 246.6, 250.5, 254.5, 29.80]
vnew_50_case2 = [ 9.92 ,247.61 ,253.35 ,250.64 ,29.81] vnew_70_case2 = [ 10.00, 250.2, 252.1, 255.0, 29.76]
vnew_50_case2 = [ 9.92, 247.6, 253.4, 250.6, 29.81]
vnew_25_case2 = [ 10.04 , 247.95 , 250.51 , 253.49 , 29.8 ]
eps_ref_case1 = compute_relative_error(v_no_case1,vref)
#case 3
v_120_case3 = [ 9.91 , 236.69 , 236.44 , 224.36 ,30.15]
v_70_case3 = [ 16.48 , 192.8 , 155.69 , 148.34 , 29.01]
v_50_case3 = [231.07 , 369.12 , 521.28 , 458.69 , 23.66]
v_25_case3 = [ 0, 0, 0, 0, 0]
vnew_120_case3 = [ 10.17 , 247.95, 249.76 , 248.29 ,29.91]
vnew_70_case3 = [ 9.98 , 249.29 , 248.97 , 251.16 ,29.8 ]
vnew_50_case3 = [ 9.98 , 246.89 , 251.51 , 245.14 , 29.89]
vnew_25_case3 = [ 9.6 , 244.93 , 244.42 , 245.22 ,29.84]
#######################################################################
eps_120_case1 = compute_relative_error(v_120_case1,vref)
eps_70_case1 = compute_relative_error(v_70_case1,vref) eps_70_case1 = compute_relative_error(v_70_case1,vref)
eps_new70_case1 = compute_relative_error(vnew_70_case1,vref)
eps_50_case1 = compute_relative_error(v_50_case1,vref) eps_50_case1 = compute_relative_error(v_50_case1,vref)
eps_25_case1 = compute_relative_error(v_25_case1,vref)
eps_new120_case1 = compute_relative_error(vnew_120_case1,vref)
eps_new70_case1 = compute_relative_error(vnew_70_case1,vref)
eps_new50_case1 = compute_relative_error(vnew_50_case1,vref) eps_new50_case1 = compute_relative_error(vnew_50_case1,vref)
eps_new25_case1 = compute_relative_error(vnew_25_case1,vref)
eps_ref_case2 = compute_relative_error(v_no_case2,vref) eps_120_case2 = compute_relative_error(v_120_case2,vref)
eps_70_case2 = compute_relative_error(v_70_case2,vref) eps_70_case2 = compute_relative_error(v_70_case2,vref)
eps_new70_case2 = compute_relative_error(vnew_70_case2,vref)
eps_50_case2 = compute_relative_error(v_50_case2,vref) eps_50_case2 = compute_relative_error(v_50_case2,vref)
eps_25_case2 = compute_relative_error(v_25_case2,vref)
eps_new120_case2 = compute_relative_error(vnew_120_case2,vref)
eps_new70_case2 = compute_relative_error(vnew_70_case2,vref)
eps_new50_case2 = compute_relative_error(vnew_50_case2,vref) eps_new50_case2 = compute_relative_error(vnew_50_case2,vref)
eps_new25_case2 = compute_relative_error(vnew_25_case2,vref)
eps_120_case3 = compute_relative_error(v_120_case3,vref)
eps_70_case3 = compute_relative_error(v_70_case3,vref)
eps_50_case3 = compute_relative_error(v_50_case3,vref)
eps_25_case3 = compute_relative_error(v_25_case3,vref)
eps_new120_case3 = compute_relative_error(vnew_120_case3,vref)
eps_new70_case3 = compute_relative_error(vnew_70_case3,vref)
eps_new50_case3 = compute_relative_error(vnew_50_case3,vref)
eps_new25_case3 = compute_relative_error(vnew_25_case3,vref)
print('--------- CASE 1 ---------') print('--------- CASE 1 ---------')
print('reference error = {e}'.format(e=np.round(100*eps_ref_case1,2))) print('venc 120% error = {e}'.format(e=np.round(100*eps_120_case1,2)))
print('venc 70% error = {e}'.format(e=np.round(100*eps_70_case1,2))) print('venc 70% error = {e}'.format(e=np.round(100*eps_70_case1,2)))
print('odv venc 70% error = {e}'.format(e=np.round(100*eps_new70_case1,2)))
print('venc 50% error = {e}'.format(e=np.round(100*eps_50_case1,2))) print('venc 50% error = {e}'.format(e=np.round(100*eps_50_case1,2)))
print('venc 25% error = {e}'.format(e=np.round(100*eps_25_case1,2)))
print('odv venc 120% error = {e}'.format(e=np.round(100*eps_new120_case1,2)))
print('odv venc 70% error = {e}'.format(e=np.round(100*eps_new70_case1,2)))
print('odv venc 50% error = {e}'.format(e=np.round(100*eps_new50_case1,2))) print('odv venc 50% error = {e}'.format(e=np.round(100*eps_new50_case1,2)))
print('odv venc 25% error = {e}'.format(e=np.round(100*eps_new25_case1,2)))
print('--------- CASE 2 ---------') print('--------- CASE 2 ---------')
print('reference error = {e}'.format(e=np.round(100*eps_ref_case2,2)))
print('venc 70% error = {e}'.format(e=np.round(100*eps_70_case2,2)))
print('odv venc 70% error = {e}'.format(e=np.round(100*eps_new70_case2,2)))
print('venc 50% error = {e}'.format(e=np.round(100*eps_50_case2,2)))
print('odv venc 50% error = {e}'.format(e=np.round(100*eps_new50_case2,2)))
print('venc 120% error = {e}'.format(e=np.round(100*eps_120_case2,2)))
print('venc 70% error = {e}'.format(e=np.round(100*eps_70_case2,2)))
print('venc 50% error = {e}'.format(e=np.round(100*eps_50_case2,2)))
print('venc 25% error = {e}'.format(e=np.round(100*eps_25_case2,2)))
print('odv venc 120% error = {e}'.format(e=np.round(100*eps_new120_case2,2)))
print('odv venc 70% error = {e}'.format(e=np.round(100*eps_new70_case2,2)))
print('odv venc 50% error = {e}'.format(e=np.round(100*eps_new50_case2,2)))
print('odv venc 25% error = {e}'.format(e=np.round(100*eps_new25_case2,2)))
print('--------- CASE 3 ---------')
print('venc 120% error = {e}'.format(e=np.round(100*eps_120_case3,2)))
print('venc 70% error = {e}'.format(e=np.round(100*eps_70_case3,2)))
print('venc 50% error = {e}'.format(e=np.round(100*eps_50_case3,2)))
print('venc 25% error = {e}'.format(e=np.round(100*eps_25_case3,2)))
print('odv venc 120% error = {e}'.format(e=np.round(100*eps_new120_case3,2)))
print('odv venc 70% error = {e}'.format(e=np.round(100*eps_new70_case3,2)))
print('odv venc 50% error = {e}'.format(e=np.round(100*eps_new50_case3,2)))
print('odv venc 25% error = {e}'.format(e=np.round(100*eps_new25_case3,2)))

22
kalman/input_files/aorta.yaml
View File

@ -25,28 +25,28 @@ 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: 60 U: 1
Th: 0.35 Th: 0.35
t: 0 t: 0
- -
id: 3 id: 3
type: 'windkessel' type: 'windkessel'
value: [20,0,0] value: [10,0,0]
p0: [0,1333.223874] p0: [0,1333.223874]
- -
id: 4 id: 4
type: 'windkessel' type: 'windkessel'
value: [500,0,0] value: [250,0,0]
p0: [0,1333.223874] p0: [0,1333.223874]
- -
id: 5 id: 5
type: 'windkessel' type: 'windkessel'
value: [500,0,0] value: [250,0,0]
p0: [0,1333.223874] p0: [0,1333.223874]
- -
id: 6 id: 6
type: 'windkessel' type: 'windkessel'
value: [500,0,0] value: [250,0,0]
p0: [0,1333.223874] p0: [0,1333.223874]
timemarching: timemarching:
@ -136,12 +136,10 @@ estimation:
measurements: measurements:
- -
mesh: './meshes/coaortaH3_leo2.0.h5' mesh: '/home/yeye/NuMRI/kalman/meshes/coaortaH3_leo2.0.h5'
fe_degree: 1 fe_degree: 1
xdmf_file: 'results/aorta/measurements/Perturbation/Ks12V50/u_all.xdmf' xdmf_file: 'measurements/aorta/Perturbation/Ks12V120/u.xdmf'
file_root: 'results/aorta/measurements/Perturbation/Ks12V50/u{i}.h5' file_root: 'measurements/aorta/Perturbation/Ks12V120/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 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
@ -151,5 +149,5 @@ estimation:
observation_operator: 'postprocessing' #state or postprocessing observation_operator: 'postprocessing' #state or postprocessing
reparameterize: True reparameterize: True
ODV_functional: ODV_functional:
enable: True enable: False
VENC: 42 # cm/s ref: 59 for 70% and 42 for 50% VENC: 102 # 102,120% 59,70% 42 50%, 21,25%

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

260
kalman/measurements/aorta/Perturbation/Ks12V120/u.xdmf Normal file
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@ -0,0 +1,260 @@
<?xml version="1.0"?>
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
<Xdmf Version="3.0" xmlns:xi="http://www.w3.org/2001/XInclude">
<Domain>
<Grid Name="TimeSeries_velocity" GridType="Collection" CollectionType="Temporal">
<Grid Name="mesh" GridType="Uniform">
<Topology NumberOfElements="28742" TopologyType="Tetrahedron" NodesPerElement="4">
<DataItem Dimensions="28742 4" NumberType="UInt" Format="HDF">u.h5:/Mesh/0/mesh/topology</DataItem>
</Topology>
<Geometry GeometryType="XYZ">
<DataItem Dimensions="5946 3" Format="HDF">u.h5:/Mesh/0/mesh/geometry</DataItem>
</Geometry>
<Time Value="0.000000000000000e+00" />
<Attribute Name="velocity" AttributeType="Vector" Center="Node">
<DataItem Dimensions="5946 3" Format="HDF">u.h5:/VisualisationVector/0</DataItem>
</Attribute>
</Grid>
<Grid Name="mesh" GridType="Uniform">
<Topology NumberOfElements="28742" TopologyType="Tetrahedron" NodesPerElement="4">
<DataItem Dimensions="28742 4" NumberType="UInt" Format="HDF">u.h5:/Mesh/1/mesh/topology</DataItem>
</Topology>
<Geometry GeometryType="XYZ">
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<Time Value="4.000000000000000e-02" />
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<Time Value="8.000000000000000e-02" />
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</Attribute>
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kalman/measurements/aorta/input.yaml Executable file
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@ -0,0 +1,155 @@
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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