jeremias 1 year ago
parent
commit
7cc7f0ccbd
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  101. Some files were not shown because too many files have changed in this diff Show More

6
kalman/graphics/figure2.py

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

67
kalman/input_files/aorta.yaml

@ -6,7 +6,7 @@ fluid: @@ -6,7 +6,7 @@ fluid:
dynamic_viscosity: 0.035
io:
write_path: 'results/aorta'
write_path: 'results/aorta_C'
restart:
path: '' # './projects/nse_coa3d/results/test_restart2/'
time: 0
@ -25,29 +25,38 @@ boundary_conditions: @@ -25,29 +25,38 @@ boundary_conditions:
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: 1
U: 30
Th: 0.35
t: 0
-
id: 3
type: 'windkessel'
value: [10,0,0]
p0: [0,1333.223874]
#value: [10,0,0]
#p0: [0,1333.223874]
value: [10,1000,0.01]
p0: [47,1333.223874]
-
id: 4
type: 'windkessel'
value: [250,0,0]
p0: [0,1333.223874]
#value: [250,0,0]
#p0: [0,1333.223874]
value: [250,8000,0.0001]
p0: [47,1333.223874]
-
id: 5
type: 'windkessel'
value: [250,0,0]
p0: [0,1333.223874]
#value: [250,0,0]
#p0: [0,1333.223874]
value: [250,8000,0.0001]
p0: [47,1333.223874]
-
id: 6
type: 'windkessel'
value: [250,0,0]
p0: [0,1333.223874]
#value: [250,0,0]
#p0: [0,1333.223874]
value: [250,8000,0.0001]
p0: [47,1333.223874]
timemarching:
velocity_pressure_coupling: 'fractionalstep' # monolithic, fractionalstep
@ -111,22 +120,22 @@ linear_solver: @@ -111,22 +120,22 @@ linear_solver:
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: 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'
@ -138,8 +147,10 @@ estimation: @@ -138,8 +147,10 @@ estimation:
-
mesh: '/home/yeye/NuMRI/kalman/meshes/coaortaH3_leo2.0.h5'
fe_degree: 1
xdmf_file: 'measurements/aorta/Perturbation/Ks12V120/u.xdmf'
file_root: 'measurements/aorta/Perturbation/Ks12V120/u{i}.h5'
#xdmf_file: 'measurements/aorta_C/Perturbation/Ks12V120/u.xdmf'
#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
velocity_direction: ~
noise_stddev: 15 # standard deviation of Gaussian noise

58
kalman/input_files/aorta_C.yaml

@ -6,14 +6,14 @@ fluid: @@ -6,14 +6,14 @@ fluid:
dynamic_viscosity: 0.035
io:
write_path: 'results/aorta/'
write_path: 'results/aorta_corr'
restart:
path: '' # './projects/nse_coa3d/results/test_restart2/'
time: 0
write_xdmf: True
write_checkpoints: True
write_hdf5_timeseries: False
write_velocity: 'update' # tentative
write_velocity: 'update' # tentative or update
boundary_conditions:
-
@ -23,31 +23,42 @@ boundary_conditions: @@ -23,31 +23,42 @@ boundary_conditions:
-
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<=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:
U: 30
Th: 0.35
Tc: 0.8
t: 0
-
id: 3
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]
-
id: 4
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]
-
id: 5
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]
-
id: 6
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]
timemarching:
velocity_pressure_coupling: 'fractionalstep' # monolithic, fractionalstep
@ -72,8 +83,8 @@ timemarching: @@ -72,8 +83,8 @@ timemarching:
transpiration_bc_projection: 'robin' # robin, dirichlet
flux_report_normalize_boundary: 1
T: 0.8 # end time
dt: 0.01
T: 1.6 # end time
dt: 0.001
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
@ -87,7 +98,7 @@ fem: @@ -87,7 +98,7 @@ fem:
convection_skew_symmetric: True # aka Temam term
stabilization:
forced_normal:
enabled: True
enabled: False
boundaries: [6]
gamma: 10
backflow_boundaries: [3,4,5,6]
@ -111,6 +122,22 @@ linear_solver: @@ -111,6 +122,22 @@ linear_solver:
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'
@ -119,15 +146,18 @@ estimation: @@ -119,15 +146,18 @@ estimation:
measurements:
-
mesh: './meshes/coaortaH1.h5'
mesh: './meshes/coaortaH3_leo2.0.h5'
fe_degree: 1
xdmf_file: 'results/aorta/measurements/u_all.xdmf'
file_root: 'results/aorta/measurements/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
velocity_direction: ~
noise_stddev: 12.5 # standard deviation of Gaussian noise
noise_stddev: 15 # standard deviation of Gaussian noise
roukf:
particles: 'simplex' # unique or simplex
observation_operator: 'postprocessing' #state or postprocessing
reparameterize: True
ODV_functional:
enable: False
VENC: 102 # 102,120% 59,70% 42 50%, 21,25%

BIN
kalman/measurements/aorta/Perturbation/Ks12V120/u.h5

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260
kalman/measurements/aorta/Perturbation/Ks12V120/u.xdmf

@ -1,260 +0,0 @@ @@ -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">
<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">
<DataItem Dimensions="5946 3" Format="HDF">u.h5:/Mesh/1/mesh/geometry</DataItem>
</Geometry>
<Time Value="4.000000000000000e-02" />
<Attribute Name="velocity" AttributeType="Vector" Center="Node">
<DataItem Dimensions="5946 3" Format="HDF">u.h5:/VisualisationVector/1</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/2/mesh/topology</DataItem>
</Topology>
<Geometry GeometryType="XYZ">
<DataItem Dimensions="5946 3" Format="HDF">u.h5:/Mesh/2/mesh/geometry</DataItem>
</Geometry>
<Time Value="8.000000000000000e-02" />
<Attribute Name="velocity" AttributeType="Vector" Center="Node">
<DataItem Dimensions="5946 3" Format="HDF">u.h5:/VisualisationVector/2</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/3/mesh/topology</DataItem>
</Topology>
<Geometry GeometryType="XYZ">
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</Geometry>
<Time Value="1.200000000000000e-01" />
<Attribute Name="velocity" AttributeType="Vector" Center="Node">
<DataItem Dimensions="5946 3" Format="HDF">u.h5:/VisualisationVector/3</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/4/mesh/topology</DataItem>
</Topology>
<Geometry GeometryType="XYZ">
<DataItem Dimensions="5946 3" Format="HDF">u.h5:/Mesh/4/mesh/geometry</DataItem>
</Geometry>
<Time Value="1.600000000000000e-01" />
<Attribute Name="velocity" AttributeType="Vector" Center="Node">
<DataItem Dimensions="5946 3" Format="HDF">u.h5:/VisualisationVector/4</DataItem>
</Attribute>
</Grid>
<Grid Name="mesh" GridType="Uniform">
<Topology NumberOfElements="28742" TopologyType="Tetrahedron" NodesPerElement="4">
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<Time Value="2.000000000000000e-01" />
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<Attribute Name="velocity" AttributeType="Vector" Center="Node">
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