mod

kalman/graphics/figure2.py

@@ -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])

kalman/input_files/aorta.yaml

@@ -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:
         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:
 
 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:
         -
             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

kalman/input_files/aorta_C.yaml

@@ -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:
     - 
         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:
         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:
     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:
 
 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:
 
     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%

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

@@ -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">
-          <DataItem Dimensions="5946 3" Format="HDF">u.h5:/Mesh/3/mesh/geometry</DataItem>
-        </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>
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-        </Geometry>
-        <Time Value="1.600000000000000e-01" />
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-        </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/5/mesh/topology</DataItem>
-        </Topology>
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-        </Geometry>
-        <Time Value="2.000000000000000e-01" />
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-        </Attribute>
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-        <Topology NumberOfElements="28742" TopologyType="Tetrahedron" NodesPerElement="4">
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kalman/measurements/aorta/Perturbation/Ks12V25/u.xdmf

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kalman/measurements/aorta/Perturbation/Ks12V50/u.xdmf

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kalman/measurements/aorta/Perturbation/Ks12V70/u.xdmf

@@ -1,260 +0,0 @@
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-<Xdmf Version="3.0" xmlns:xi="http://www.w3.org/2001/XInclude">
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kalman/measurements/aorta/input.yaml

@@ -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: