Browse Source

adding poi temp

master
jeremias 1 year ago
parent
commit
4764bb4bb8
  1. 12
      kalman/graphics/figure2.py
  2. 52
      kalman/input_files/aorta.yaml
  3. BIN
      poi/checkpoint/0/p.h5
  4. BIN
      poi/checkpoint/0/u.h5
  5. BIN
      poi/checkpoint/19/p.h5
  6. BIN
      poi/checkpoint/19/u.h5
  7. BIN
      poi/checkpoint/29/p.h5
  8. BIN
      poi/checkpoint/29/u.h5
  9. BIN
      poi/checkpoint/39/p.h5
  10. BIN
      poi/checkpoint/39/u.h5
  11. BIN
      poi/checkpoint/49/p.h5
  12. BIN
      poi/checkpoint/49/u.h5
  13. BIN
      poi/checkpoint/59/p.h5
  14. BIN
      poi/checkpoint/59/u.h5
  15. BIN
      poi/checkpoint/69/p.h5
  16. BIN
      poi/checkpoint/69/u.h5
  17. BIN
      poi/checkpoint/79/p.h5
  18. BIN
      poi/checkpoint/79/u.h5
  19. BIN
      poi/checkpoint/89/p.h5
  20. BIN
      poi/checkpoint/89/u.h5
  21. BIN
      poi/checkpoint/9/p.h5
  22. BIN
      poi/checkpoint/9/u.h5
  23. BIN
      poi/checkpoint/99/p.h5
  24. BIN
      poi/checkpoint/99/u.h5
  25. BIN
      poi/p.h5
  26. 140
      poi/p.xdmf
  27. BIN
      poi/poiseuille.h5
  28. BIN
      poi/seq.npz
  29. BIN
      poi/seq_new.npz
  30. BIN
      poi/u.h5
  31. 140
      poi/u.xdmf

12
kalman/graphics/figure2.py

@ -51,12 +51,12 @@ def plot_parameters(dat, input_file, deparameterize=False, ref=None): @@ -51,12 +51,12 @@ def plot_parameters(dat, input_file, deparameterize=False, ref=None):
with open(inputfile_path) as file:
inputfile = yaml.full_load(file)
#true_val = [10,250,250,250,30]
true_values = {
3: 10,
4: 60,
5: 220,
6: 160,
3: 2400,
4: 4200,
5: 11000,
6: 7800,
2: 100
}
@ -71,7 +71,7 @@ def plot_parameters(dat, input_file, deparameterize=False, ref=None): @@ -71,7 +71,7 @@ def plot_parameters(dat, input_file, deparameterize=False, ref=None):
for bnd_set in inputfile['boundary_conditions']:
if bnd_c['id'] == bnd_set['id']:
ids.append(bnd_c['id'])
current_val.append(bnd_set['value'][0])
current_val.append(bnd_set['parameters']['R_d'])
labels.append('$R_' + str(bnd_c['id']))
elif 'dirichlet' in bnd_c['type']:

52
kalman/input_files/aorta.yaml

@ -4,10 +4,10 @@ mesh: './meshes/coaortaH1.h5' @@ -4,10 +4,10 @@ mesh: './meshes/coaortaH1.h5'
fluid:
density: 1.2
dynamic_viscosity: 0.035
stokes: False
stokes: True
io:
write_path: 'results/aorta'
write_path: 'results/aorta_1ms'
restart:
path: '' # './projects/nse_coa3d/results/test_restart2/'
time: 0
@ -32,34 +32,39 @@ boundary_conditions: @@ -32,34 +32,39 @@ boundary_conditions:
-
id: 3
type: 'windkessel'
#value: [10,0,0]
value: [10,0.0008,2400]
p0: [80,1333.223874]
#p0: [0,1333.223874]
parameters:
R_p: 10
C: 0.0008
R_d: 2400
p0: 80
conv: 1333.223874
-
id: 4
type: 'windkessel'
#value: [60,0,0]
#value: [250,0,0]
value: [60,0.00034,4200]
p0: [80,1333.223874]
#p0: [0,1333.223874]
parameters:
R_p: 60
C: 0.00034
R_d: 4200
p0: 80
conv: 1333.223874
-
id: 5
type: 'windkessel'
#value: [220,0,0]
#value: [250,0,0]
value: [220,0.00034,11000]
p0: [80,1333.223874]
#p0: [0,1333.223874]
parameters:
R_p: 220
C: 0.00034
R_d: 11000
p0: 80
conv: 1333.223874
-
id: 6
type: 'windkessel'
#value: [160,0,0]
#value: [250,0,0]
value: [160,0.00034,7800]
p0: [80,1333.223874]
#p0: [0,1333.223874]
parameters:
R_p: 160
C: 0.00034
R_d: 7800
p0: 80
conv: 1333.223874
timemarching:
velocity_pressure_coupling: 'fractionalstep' # monolithic, fractionalstep
@ -148,13 +153,14 @@ estimation: @@ -148,13 +153,14 @@ estimation:
measurements:
-
mesh: '/home/yeye/NuMRI/kalman/meshes/coaortaH3_leo2.0.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'
indices: 0 # indices of checkpoints to be processed. 0 == all
velocity_direction: ~
noise_stddev: 500 # standard deviation of Gaussian noise
noise_stddev: 0 # standard deviation of Gaussian noise
roukf:
particles: 'simplex' # unique or simplex

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poi/checkpoint/0/u.h5

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poi/checkpoint/9/p.h5

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poi/p.h5

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140
poi/p.xdmf

@ -0,0 +1,140 @@ @@ -0,0 +1,140 @@
<?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_pressure" GridType="Collection" CollectionType="Temporal">
<Grid Name="mesh" GridType="Uniform">
<Topology NumberOfElements="12332" TopologyType="Tetrahedron" NodesPerElement="4">
<DataItem Dimensions="12332 4" NumberType="UInt" Format="HDF">p.h5:/Mesh/0/mesh/topology</DataItem>
</Topology>
<Geometry GeometryType="XYZ">
<DataItem Dimensions="2466 3" Format="HDF">p.h5:/Mesh/0/mesh/geometry</DataItem>
</Geometry>
<Time Value="0.000000000000000e+00" />
<Attribute Name="pressure" AttributeType="Scalar" Center="Node">
<DataItem Dimensions="2466 1" Format="HDF">p.h5:/VisualisationVector/0</DataItem>
</Attribute>
</Grid>
<Grid Name="mesh" GridType="Uniform">
<Topology NumberOfElements="12332" TopologyType="Tetrahedron" NodesPerElement="4">
<DataItem Dimensions="12332 4" NumberType="UInt" Format="HDF">p.h5:/Mesh/1/mesh/topology</DataItem>
</Topology>
<Geometry GeometryType="XYZ">
<DataItem Dimensions="2466 3" Format="HDF">p.h5:/Mesh/1/mesh/geometry</DataItem>
</Geometry>
<Time Value="9.000000000000000e+00" />
<Attribute Name="pressure" AttributeType="Scalar" Center="Node">
<DataItem Dimensions="2466 1" Format="HDF">p.h5:/VisualisationVector/1</DataItem>
</Attribute>
</Grid>
<Grid Name="mesh" GridType="Uniform">
<Topology NumberOfElements="12332" TopologyType="Tetrahedron" NodesPerElement="4">
<DataItem Dimensions="12332 4" NumberType="UInt" Format="HDF">p.h5:/Mesh/2/mesh/topology</DataItem>
</Topology>
<Geometry GeometryType="XYZ">
<DataItem Dimensions="2466 3" Format="HDF">p.h5:/Mesh/2/mesh/geometry</DataItem>
</Geometry>
<Time Value="1.900000000000000e+01" />
<Attribute Name="pressure" AttributeType="Scalar" Center="Node">
<DataItem Dimensions="2466 1" Format="HDF">p.h5:/VisualisationVector/2</DataItem>
</Attribute>
</Grid>
<Grid Name="mesh" GridType="Uniform">
<Topology NumberOfElements="12332" TopologyType="Tetrahedron" NodesPerElement="4">
<DataItem Dimensions="12332 4" NumberType="UInt" Format="HDF">p.h5:/Mesh/3/mesh/topology</DataItem>
</Topology>
<Geometry GeometryType="XYZ">
<DataItem Dimensions="2466 3" Format="HDF">p.h5:/Mesh/3/mesh/geometry</DataItem>
</Geometry>
<Time Value="2.900000000000000e+01" />
<Attribute Name="pressure" AttributeType="Scalar" Center="Node">
<DataItem Dimensions="2466 1" Format="HDF">p.h5:/VisualisationVector/3</DataItem>
</Attribute>
</Grid>
<Grid Name="mesh" GridType="Uniform">
<Topology NumberOfElements="12332" TopologyType="Tetrahedron" NodesPerElement="4">
<DataItem Dimensions="12332 4" NumberType="UInt" Format="HDF">p.h5:/Mesh/4/mesh/topology</DataItem>
</Topology>
<Geometry GeometryType="XYZ">
<DataItem Dimensions="2466 3" Format="HDF">p.h5:/Mesh/4/mesh/geometry</DataItem>
</Geometry>
<Time Value="3.900000000000000e+01" />
<Attribute Name="pressure" AttributeType="Scalar" Center="Node">
<DataItem Dimensions="2466 1" Format="HDF">p.h5:/VisualisationVector/4</DataItem>
</Attribute>
</Grid>
<Grid Name="mesh" GridType="Uniform">
<Topology NumberOfElements="12332" TopologyType="Tetrahedron" NodesPerElement="4">
<DataItem Dimensions="12332 4" NumberType="UInt" Format="HDF">p.h5:/Mesh/5/mesh/topology</DataItem>
</Topology>
<Geometry GeometryType="XYZ">
<DataItem Dimensions="2466 3" Format="HDF">p.h5:/Mesh/5/mesh/geometry</DataItem>
</Geometry>
<Time Value="4.900000000000000e+01" />
<Attribute Name="pressure" AttributeType="Scalar" Center="Node">
<DataItem Dimensions="2466 1" Format="HDF">p.h5:/VisualisationVector/5</DataItem>
</Attribute>
</Grid>
<Grid Name="mesh" GridType="Uniform">
<Topology NumberOfElements="12332" TopologyType="Tetrahedron" NodesPerElement="4">
<DataItem Dimensions="12332 4" NumberType="UInt" Format="HDF">p.h5:/Mesh/6/mesh/topology</DataItem>
</Topology>
<Geometry GeometryType="XYZ">
<DataItem Dimensions="2466 3" Format="HDF">p.h5:/Mesh/6/mesh/geometry</DataItem>
</Geometry>
<Time Value="5.900000000000000e+01" />
<Attribute Name="pressure" AttributeType="Scalar" Center="Node">
<DataItem Dimensions="2466 1" Format="HDF">p.h5:/VisualisationVector/6</DataItem>
</Attribute>
</Grid>
<Grid Name="mesh" GridType="Uniform">
<Topology NumberOfElements="12332" TopologyType="Tetrahedron" NodesPerElement="4">
<DataItem Dimensions="12332 4" NumberType="UInt" Format="HDF">p.h5:/Mesh/7/mesh/topology</DataItem>
</Topology>
<Geometry GeometryType="XYZ">
<DataItem Dimensions="2466 3" Format="HDF">p.h5:/Mesh/7/mesh/geometry</DataItem>
</Geometry>
<Time Value="6.900000000000000e+01" />
<Attribute Name="pressure" AttributeType="Scalar" Center="Node">
<DataItem Dimensions="2466 1" Format="HDF">p.h5:/VisualisationVector/7</DataItem>
</Attribute>
</Grid>
<Grid Name="mesh" GridType="Uniform">
<Topology NumberOfElements="12332" TopologyType="Tetrahedron" NodesPerElement="4">
<DataItem Dimensions="12332 4" NumberType="UInt" Format="HDF">p.h5:/Mesh/8/mesh/topology</DataItem>
</Topology>
<Geometry GeometryType="XYZ">
<DataItem Dimensions="2466 3" Format="HDF">p.h5:/Mesh/8/mesh/geometry</DataItem>
</Geometry>
<Time Value="7.900000000000000e+01" />
<Attribute Name="pressure" AttributeType="Scalar" Center="Node">
<DataItem Dimensions="2466 1" Format="HDF">p.h5:/VisualisationVector/8</DataItem>
</Attribute>
</Grid>
<Grid Name="mesh" GridType="Uniform">
<Topology NumberOfElements="12332" TopologyType="Tetrahedron" NodesPerElement="4">
<DataItem Dimensions="12332 4" NumberType="UInt" Format="HDF">p.h5:/Mesh/9/mesh/topology</DataItem>
</Topology>
<Geometry GeometryType="XYZ">
<DataItem Dimensions="2466 3" Format="HDF">p.h5:/Mesh/9/mesh/geometry</DataItem>
</Geometry>
<Time Value="8.900000000000000e+01" />
<Attribute Name="pressure" AttributeType="Scalar" Center="Node">
<DataItem Dimensions="2466 1" Format="HDF">p.h5:/VisualisationVector/9</DataItem>
</Attribute>
</Grid>
<Grid Name="mesh" GridType="Uniform">
<Topology NumberOfElements="12332" TopologyType="Tetrahedron" NodesPerElement="4">
<DataItem Dimensions="12332 4" NumberType="UInt" Format="HDF">p.h5:/Mesh/10/mesh/topology</DataItem>
</Topology>
<Geometry GeometryType="XYZ">
<DataItem Dimensions="2466 3" Format="HDF">p.h5:/Mesh/10/mesh/geometry</DataItem>
</Geometry>
<Time Value="9.900000000000000e+01" />
<Attribute Name="pressure" AttributeType="Scalar" Center="Node">
<DataItem Dimensions="2466 1" Format="HDF">p.h5:/VisualisationVector/10</DataItem>
</Attribute>
</Grid>
</Grid>
</Domain>
</Xdmf>

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poi/poiseuille.h5

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poi/seq.npz

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poi/seq_new.npz

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poi/u.h5

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140
poi/u.xdmf

@ -0,0 +1,140 @@ @@ -0,0 +1,140 @@
<?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="12332" TopologyType="Tetrahedron" NodesPerElement="4">
<DataItem Dimensions="12332 4" NumberType="UInt" Format="HDF">u.h5:/Mesh/0/mesh/topology</DataItem>
</Topology>
<Geometry GeometryType="XYZ">
<DataItem Dimensions="2466 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="2466 3" Format="HDF">u.h5:/VisualisationVector/0</DataItem>
</Attribute>
</Grid>
<Grid Name="mesh" GridType="Uniform">
<Topology NumberOfElements="12332" TopologyType="Tetrahedron" NodesPerElement="4">
<DataItem Dimensions="12332 4" NumberType="UInt" Format="HDF">u.h5:/Mesh/1/mesh/topology</DataItem>
</Topology>
<Geometry GeometryType="XYZ">
<DataItem Dimensions="2466 3" Format="HDF">u.h5:/Mesh/1/mesh/geometry</DataItem>
</Geometry>
<Time Value="9.000000000000000e+00" />
<Attribute Name="velocity" AttributeType="Vector" Center="Node">
<DataItem Dimensions="2466 3" Format="HDF">u.h5:/VisualisationVector/1</DataItem>
</Attribute>
</Grid>
<Grid Name="mesh" GridType="Uniform">
<Topology NumberOfElements="12332" TopologyType="Tetrahedron" NodesPerElement="4">
<DataItem Dimensions="12332 4" NumberType="UInt" Format="HDF">u.h5:/Mesh/2/mesh/topology</DataItem>
</Topology>
<Geometry GeometryType="XYZ">
<DataItem Dimensions="2466 3" Format="HDF">u.h5:/Mesh/2/mesh/geometry</DataItem>
</Geometry>
<Time Value="1.900000000000000e+01" />
<Attribute Name="velocity" AttributeType="Vector" Center="Node">
<DataItem Dimensions="2466 3" Format="HDF">u.h5:/VisualisationVector/2</DataItem>
</Attribute>
</Grid>
<Grid Name="mesh" GridType="Uniform">
<Topology NumberOfElements="12332" TopologyType="Tetrahedron" NodesPerElement="4">
<DataItem Dimensions="12332 4" NumberType="UInt" Format="HDF">u.h5:/Mesh/3/mesh/topology</DataItem>
</Topology>
<Geometry GeometryType="XYZ">
<DataItem Dimensions="2466 3" Format="HDF">u.h5:/Mesh/3/mesh/geometry</DataItem>
</Geometry>
<Time Value="2.900000000000000e+01" />
<Attribute Name="velocity" AttributeType="Vector" Center="Node">
<DataItem Dimensions="2466 3" Format="HDF">u.h5:/VisualisationVector/3</DataItem>
</Attribute>
</Grid>
<Grid Name="mesh" GridType="Uniform">
<Topology NumberOfElements="12332" TopologyType="Tetrahedron" NodesPerElement="4">
<DataItem Dimensions="12332 4" NumberType="UInt" Format="HDF">u.h5:/Mesh/4/mesh/topology</DataItem>
</Topology>
<Geometry GeometryType="XYZ">
<DataItem Dimensions="2466 3" Format="HDF">u.h5:/Mesh/4/mesh/geometry</DataItem>
</Geometry>
<Time Value="3.900000000000000e+01" />
<Attribute Name="velocity" AttributeType="Vector" Center="Node">
<DataItem Dimensions="2466 3" Format="HDF">u.h5:/VisualisationVector/4</DataItem>
</Attribute>
</Grid>
<Grid Name="mesh" GridType="Uniform">
<Topology NumberOfElements="12332" TopologyType="Tetrahedron" NodesPerElement="4">
<DataItem Dimensions="12332 4" NumberType="UInt" Format="HDF">u.h5:/Mesh/5/mesh/topology</DataItem>
</Topology>
<Geometry GeometryType="XYZ">
<DataItem Dimensions="2466 3" Format="HDF">u.h5:/Mesh/5/mesh/geometry</DataItem>
</Geometry>
<Time Value="4.900000000000000e+01" />
<Attribute Name="velocity" AttributeType="Vector" Center="Node">
<DataItem Dimensions="2466 3" Format="HDF">u.h5:/VisualisationVector/5</DataItem>
</Attribute>
</Grid>
<Grid Name="mesh" GridType="Uniform">
<Topology NumberOfElements="12332" TopologyType="Tetrahedron" NodesPerElement="4">
<DataItem Dimensions="12332 4" NumberType="UInt" Format="HDF">u.h5:/Mesh/6/mesh/topology</DataItem>
</Topology>
<Geometry GeometryType="XYZ">
<DataItem Dimensions="2466 3" Format="HDF">u.h5:/Mesh/6/mesh/geometry</DataItem>
</Geometry>
<Time Value="5.900000000000000e+01" />
<Attribute Name="velocity" AttributeType="Vector" Center="Node">
<DataItem Dimensions="2466 3" Format="HDF">u.h5:/VisualisationVector/6</DataItem>
</Attribute>
</Grid>
<Grid Name="mesh" GridType="Uniform">
<Topology NumberOfElements="12332" TopologyType="Tetrahedron" NodesPerElement="4">
<DataItem Dimensions="12332 4" NumberType="UInt" Format="HDF">u.h5:/Mesh/7/mesh/topology</DataItem>
</Topology>
<Geometry GeometryType="XYZ">
<DataItem Dimensions="2466 3" Format="HDF">u.h5:/Mesh/7/mesh/geometry</DataItem>
</Geometry>
<Time Value="6.900000000000000e+01" />
<Attribute Name="velocity" AttributeType="Vector" Center="Node">
<DataItem Dimensions="2466 3" Format="HDF">u.h5:/VisualisationVector/7</DataItem>
</Attribute>
</Grid>
<Grid Name="mesh" GridType="Uniform">
<Topology NumberOfElements="12332" TopologyType="Tetrahedron" NodesPerElement="4">
<DataItem Dimensions="12332 4" NumberType="UInt" Format="HDF">u.h5:/Mesh/8/mesh/topology</DataItem>
</Topology>
<Geometry GeometryType="XYZ">
<DataItem Dimensions="2466 3" Format="HDF">u.h5:/Mesh/8/mesh/geometry</DataItem>
</Geometry>
<Time Value="7.900000000000000e+01" />
<Attribute Name="velocity" AttributeType="Vector" Center="Node">
<DataItem Dimensions="2466 3" Format="HDF">u.h5:/VisualisationVector/8</DataItem>
</Attribute>
</Grid>
<Grid Name="mesh" GridType="Uniform">
<Topology NumberOfElements="12332" TopologyType="Tetrahedron" NodesPerElement="4">
<DataItem Dimensions="12332 4" NumberType="UInt" Format="HDF">u.h5:/Mesh/9/mesh/topology</DataItem>
</Topology>
<Geometry GeometryType="XYZ">
<DataItem Dimensions="2466 3" Format="HDF">u.h5:/Mesh/9/mesh/geometry</DataItem>
</Geometry>
<Time Value="8.900000000000000e+01" />
<Attribute Name="velocity" AttributeType="Vector" Center="Node">
<DataItem Dimensions="2466 3" Format="HDF">u.h5:/VisualisationVector/9</DataItem>
</Attribute>
</Grid>
<Grid Name="mesh" GridType="Uniform">
<Topology NumberOfElements="12332" TopologyType="Tetrahedron" NodesPerElement="4">
<DataItem Dimensions="12332 4" NumberType="UInt" Format="HDF">u.h5:/Mesh/10/mesh/topology</DataItem>
</Topology>
<Geometry GeometryType="XYZ">
<DataItem Dimensions="2466 3" Format="HDF">u.h5:/Mesh/10/mesh/geometry</DataItem>
</Geometry>
<Time Value="9.900000000000000e+01" />
<Attribute Name="velocity" AttributeType="Vector" Center="Node">
<DataItem Dimensions="2466 3" Format="HDF">u.h5:/VisualisationVector/10</DataItem>
</Attribute>
</Grid>
</Grid>
</Domain>
</Xdmf>
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