mod2

kalman/aorta.yaml

@@ -1,5 +1,5 @@
 
-mesh: '/home/yeye/Desktop/kalman/meshes/coaortaH1.h5'
+mesh: './meshes/coaortaH1.h5'
 # Physical parameters of the fluid
 fluid:
     density: 1.2
@@ -112,20 +112,20 @@ linear_solver:
 estimation:
     boundary_conditions:
         - 
-            id: 2
+            id: 4
-            type: 'dirichlet'
+            type: 'windkessel'
             parameters: 'U'
             initial_stddev: 1
 
     measurements:
         -
-            mesh: '/home/yeye/Desktop/kalman/meshes/coaortaH1.h5'
+            mesh: './meshes/coaortaH1.h5'
             fe_degree: 1
             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: 3.5     # standard deviation of Gaussian noise
+            noise_stddev: 1.5     # standard deviation of Gaussian noise
     
     roukf:
         particles: 'simplex' # unique or simplex

kalman/aorta_neumann.yaml

@@ -0,0 +1,129 @@
+
+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'     # 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: 30
+            Th: 0.35
+            t: 0   
+    - 
+        id: 3
+        type: 'neumann'
+        value: 0
+    - 
+        id: 4
+        type: 'neumann'
+        value: 0
+    - 
+        id: 5
+        type: 'neumann'
+        value: 0
+    - 
+        id: 6
+        type: 'neumann'
+        value: 0
+
+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: 2
+            type: 'dirichlet'
+            parameters: 'U'
+            initial_stddev: 1
+
+    measurements:
+        -
+            mesh: './meshes/coaortaH1.h5'
+            fe_degree: 1
+            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: 1.5     # standard deviation of Gaussian noise
+    
+    roukf:
+        particles: 'simplex' # unique or simplex
+        observation_operator: 'postprocessing'         #state or postprocessing
+        reparameterize: True

kalman/channel2d.yaml

@@ -1,4 +1,4 @@
-mesh: '/home/yeye/Desktop/kalman/meshes/channel2d.h5'
+mesh: './meshes/channel2d.h5'
 # Physical parameters of the fluid
 fluid:
     density: 1.2
@@ -139,7 +139,7 @@ estimation:
 
     measurements:
         -
-            mesh: '/home/yeye/Desktop/kalman/meshes/channel2d.h5'
+            mesh: './meshes/channel2d.h5'
             fe_degree: 0
             xdmf_file: 'results/channel2d/measurements/u_all.xdmf'
             file_root: 'results/channel2d/measurements/u{i}.h5'

kalman/channel3d.yaml

@@ -1,4 +1,4 @@
-mesh: '/home/yeye/Desktop/kalman/meshes/channel3d.h5'
+mesh: './meshes/channel3d.h5'
 # Physical parameters of the fluid
 fluid:
     density: 1.2
@@ -14,41 +14,6 @@ io:
     write_hdf5_timeseries: False
     write_velocity: 'update'     # update or tentative
 
-ale:
-  type: 'manual' 
-  io:
-      # read XDMF files from external solver
-      read_checkpoints: False # True, False
-      # path where displacement files are stored
-      #
-      read_path:
-      # origin mesh path
-      mesh_path:
-      # fem space of solution files
-      fem_type: p1
-
-  # Settings of the time integration method
-  timemarching:
-      # Time step for reading the input file
-      read_dt: # 0.05
-  fem:
-      # function spaces for the displacement
-      # options available: p1 p2
-      displacement_space: p1
-  lifting: 
-      type: 'elastic_element' # 'harmonic', 'elastic', 'elastic_element'
-      # when chosing 'harmonic', no parameters required (ignored)
-      # otherwise, they must be specified below.
-      parameters:
-          mu: 0.0 # float value e.g. 1., 0.1, 0.01
-  # deformations will be read whenever chosen 'manual'
-  # if chosen 'external' then deformations list will be OMITTED!.
-  deformations:
-      # The dashes separate the list entries
-      -
-          id : 1
-          type: 'dirichlet'
-          value: ['0.', '0.', '0.']
 
 
 boundary_conditions:
@@ -70,7 +35,6 @@ boundary_conditions:
         value: '0'
  
 
-
 timemarching:
     velocity_pressure_coupling: 'fractionalstep'    # monolithic, fractionalstep
 
@@ -141,7 +105,7 @@ estimation:
 
     measurements:
         -
-            mesh: '/home/yeye/Desktop/kalman/meshes/channel3d.h5'
+            mesh: './meshes/channel3d.h5'
             fe_degree: 0
             xdmf_file: 'results/channel3d/measurements/u_all.xdmf'
             file_root: 'results/channel3d/measurements/u{i}.h5'