m

kalman/input_files/aorta.yaml

@@ -5,10 +5,10 @@ fluid:
     density: 1.2
     dynamic_viscosity: 0.035
     stokes: False
-    implicit_windkessel: True
+    implicit_windkessel: False
 
 io:
-    write_path: 'results/impl_1ms'
+    write_path: 'results/expl_1ms'
     restart:
         path: ''  # './projects/nse_coa3d/results/test_restart2/' 
         time: 0
@@ -27,7 +27,7 @@ boundary_conditions:
         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: 75  #REFERENCE
-            U: 80  
+            U: 120  
             #U: 150 #Pa/Pb
             #U: 40 #Pc
             Th: 0.36
@@ -118,7 +118,7 @@ timemarching:
         flux_report_normalize_boundary: 1
 
     T: 0.8       # end time
-    dt: 0.001
+    dt: 0.002
     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

kalman/input_files/aorta_old.yaml

@@ -0,0 +1,209 @@
+
+mesh: './meshes/coaortaH1.h5'
+# Physical parameters of the fluid  
+fluid:
+    density: 1.2
+    dynamic_viscosity: 0.035
+    stokes: False
+    implicit_windkessel: False
+
+io:
+    write_path: 'results/exp_0.1ms'
+    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: 2
+        type: 'dirichlet'
+        #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: 75  #REFERENCE 120
+            U: 100 
+            #U: 150 #Pa/Pb
+            #U: 40 #Pc
+            Th: 0.36
+            beta: 70
+            t: 0
+    - 
+        id: 1
+        type: 'dirichlet'
+        value: ['0','0','0']
+    - 
+        id: 3
+        type: 'windkessel'
+        parameters:
+            R_p: 200
+            C: 0.0004
+            R_d: 4800
+            p0: 85
+            conv: 1333.223874   
+    - 
+        id: 4
+        type: 'windkessel'
+        parameters:
+            #R_p: 480
+            R_p: 480
+            #C: 0.0004  #  REFERENCE
+            C: 0.001  #  REFERENCE
+            #C: 0.0005   # Pa
+            #C: 0.0010   # Pb
+            #C: 0.0001   # Pc
+            #C: 0.0008   # Pg
+            #R_d: 7200  # REFERENCE
+            R_d: 15000  # REFERENCE
+            #R_d:  8760  #Pa
+            #R_d: 17520 #Pb x2
+            #R_d: 4000  #Pc
+            p0: 85
+            conv: 1333.223874   
+    - 
+        id: 5
+        type: 'windkessel'
+        parameters:
+            R_p: 520
+            C: 0.0003 # REFERENCE
+            #C: 0.0005 # Pa
+            #C: 0.0010 # Pb
+            #C: 0.0001 # Pc
+            #C: 0.0008 # Pg
+            #R_d: 11520 # REFERENCE
+            R_d: 40000 
+            #R_d:  8760  #Pa
+            #R_d: 17520 #Pb x2
+            #R_d: 4000 #Pc
+            p0: 85
+            conv: 1333.223874   
+    - 
+        id: 6
+        type: 'windkessel'
+        parameters:
+            R_p: 520
+            C: 0.0003 # REFERENCE
+            #C: 0.0005 #Pa
+            #C: 0.0010 #Pb
+            #C: 0.0001 #Pc
+            R_d: 11520 # REFERENCE
+            #R_d: 35000
+            #R_d:  8760 #Pa
+            #R_d: 17520 #Pb x2
+            #R_d: 4000 #Pc
+            p0: 85
+            conv: 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: 0.0001
+    write_dt: 0.001
+    checkpoint_dt:  0.001 # <= 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: False
+            boundaries: [3,4,5,6]
+            gamma: 20
+        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'
+            mode: 'RdC'
+            initial_stddev: 1
+        - 
+            id: 5
+            type: 'windkessel'
+            mode: 'RdC'
+            initial_stddev: 1
+        - 
+            id: 6
+            type: 'windkessel'
+            mode: 'RdC'
+            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'
+            fe_degree: 1
+            #xdmf_file: 'measurements/aorta_dt1ms/Perturbation/Mg15V70/u_all.xdmf'
+            #file_root: 'measurements/aorta_dt1ms/Perturbation/Mg15V70/u{i}.h5'
+            xdmf_file: 'measurements/aorta_exp_dt1ms/u_all.xdmf'
+            file_root: 'measurements/aorta_exp_dt1ms/u{i}.h5'
+            indices: 0 # indices of checkpoints to be processed. 0 == all
+            velocity_direction: [0,0,1]
+            noise_stddev: 45     # standard deviation of Gaussian noise
+    
+    roukf:
+        particles: 'simplex' # unique or simplex
+        observation_operator: 'postprocessing'         #state or postprocessing
+        reparameterize: True
+        ODV_functional:
+            enable: False
+            VENC: 138

kalman/input_files/aorta_old2.yaml

@@ -0,0 +1,209 @@
+
+mesh: './meshes/coaortaH1.h5'
+# Physical parameters of the fluid  
+fluid:
+    density: 1.2
+    dynamic_viscosity: 0.035
+    stokes: False
+    implicit_windkessel: True
+
+io:
+    write_path: 'results/impl_0.1ms'
+    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: 2
+        type: 'dirichlet'
+        #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: 75  #REFERENCE 120
+            U: 100
+            #U: 150 #Pa/Pb
+            #U: 40 #Pc
+            Th: 0.36
+            beta: 70
+            t: 0
+    - 
+        id: 1
+        type: 'dirichlet'
+        value: ['0','0','0']
+    - 
+        id: 3
+        type: 'windkessel'
+        parameters:
+            R_p: 200
+            C: 0.0004
+            R_d: 4800
+            p0: 85
+            conv: 1333.223874   
+    - 
+        id: 4
+        type: 'windkessel'
+        parameters:
+            #R_p: 480
+            R_p: 480
+            #C: 0.0004  #  REFERENCE
+            C: 0.001  #  REFERENCE
+            #C: 0.0005   # Pa
+            #C: 0.0010   # Pb
+            #C: 0.0001   # Pc
+            #C: 0.0008   # Pg
+            #R_d: 7200  # REFERENCE
+            R_d: 15000  # REFERENCE
+            #R_d:  8760  #Pa
+            #R_d: 17520 #Pb x2
+            #R_d: 4000  #Pc
+            p0: 85
+            conv: 1333.223874   
+    - 
+        id: 5
+        type: 'windkessel'
+        parameters:
+            R_p: 520
+            C: 0.0003 # REFERENCE
+            #C: 0.0005 # Pa
+            #C: 0.0010 # Pb
+            #C: 0.0001 # Pc
+            #C: 0.0008 # Pg
+            #R_d: 11520 # REFERENCE
+            R_d: 40000 
+            #R_d:  8760  #Pa
+            #R_d: 17520 #Pb x2
+            #R_d: 4000 #Pc
+            p0: 85
+            conv: 1333.223874   
+    - 
+        id: 6
+        type: 'windkessel'
+        parameters:
+            R_p: 520
+            C: 0.0003 # REFERENCE
+            #C: 0.0005 #Pa
+            #C: 0.0010 #Pb
+            #C: 0.0001 #Pc
+            R_d: 11520 # REFERENCE
+            #R_d: 35000
+            #R_d:  8760 #Pa
+            #R_d: 17520 #Pb x2
+            #R_d: 4000 #Pc
+            p0: 85
+            conv: 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: 0.0001
+    write_dt: 0.001
+    checkpoint_dt:  0.001 # <= 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: False
+            boundaries: [3,4,5,6]
+            gamma: 20
+        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'
+            mode: 'RdC'
+            initial_stddev: 1
+        - 
+            id: 5
+            type: 'windkessel'
+            mode: 'RdC'
+            initial_stddev: 1
+        - 
+            id: 6
+            type: 'windkessel'
+            mode: 'RdC'
+            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'
+            fe_degree: 1
+            #xdmf_file: 'measurements/aorta_dt1ms/Perturbation/Mg15V70/u_all.xdmf'
+            #file_root: 'measurements/aorta_dt1ms/Perturbation/Mg15V70/u{i}.h5'
+            xdmf_file: 'measurements/aorta_exp_dt1ms/u_all.xdmf'
+            file_root: 'measurements/aorta_exp_dt1ms/u{i}.h5'
+            indices: 0 # indices of checkpoints to be processed. 0 == all
+            velocity_direction: [0,0,1]
+            noise_stddev: 45     # standard deviation of Gaussian noise
+    
+    roukf:
+        particles: 'simplex' # unique or simplex
+        observation_operator: 'postprocessing'         #state or postprocessing
+        reparameterize: True
+        ODV_functional:
+            enable: False
+            VENC: 138