From bccae559501702ecd49cdb6bdf01b7d31cf19a4a Mon Sep 17 00:00:00 2001
From: "J.E. Garay Labra" <p283370@fwn-bborg-5-166.fwn.rug.nl>
Date: Mon, 13 Jan 2020 14:47:16 +0100
Subject: [PATCH] asd

---
 test.yaml | 141 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 141 insertions(+)
 create mode 100755 test.yaml

diff --git a/test.yaml b/test.yaml
new file mode 100755
index 0000000..3a0d205
--- /dev/null
+++ b/test.yaml
@@ -0,0 +1,141 @@
+# Set of default parameters for steady Navier-Stokes
+mesh:       '/home/p283370/Desktop/PhD/AORTA/MESH/aorta_coarse/aorta_coarse_marked.h5'
+density: 1.2
+dynamic_viscosity: 0.035
+stokes: False
+
+io:
+    write_hdf5: False
+    write_hdf5_timeseries: False
+    write_xdmf: False
+    write_path: '/home/p283370/Desktop/kalman/results/coarse/dt0.0005'
+    restart:
+        path: ''  # './projects/nse_coa3d/results/test_restart2/' 
+        time: 0
+    write_checkpoints: True
+    write_velocity: 'update'     # tentative
+    log: False
+    write_outlets: False
+    out_mode     :  'u'
+    outlets_path: '/home/p283370/Desktop/kalman/outlets/'
+    theta_path: '/home/p283370/Desktop/kalman/results/'
+    theta_name: 'theta_unique_fine2'
+
+
+boundary_conditions: 
+    - id: 2
+      type: 'dirichlet'
+      value: ['0','0','U*sin(DOLFIN_PI*t/Th)*(t<=ts) + (ts<t)*(afac*U*sin(Delta*DOLFIN_PI*t/Th)*exp(-t*beta))']
+      degree: 3
+      parameters: 
+              U: -60   # 60 original
+              Th: 0.37 
+              t: 0
+              afac: 5613.816803204635
+              beta: 29.466876946384286
+              Delta: 5
+              ts:  0.33
+    - id: 1
+      type: 'dirichlet'
+      value: ['0','0','0']
+      degree: 2
+    - id: 3
+      type: 'windkessel'
+      value: [100,0.01,1000]
+    - id: 4
+      type: 'windkessel'
+      value: [250,0.0001,8000]    # [R,C,R_d]
+    - id: 5
+      type: 'windkessel'
+      value: [250,0.00001,8000]    # [R,C,R_d]
+    - id: 6
+      type: 'windkessel'
+      value: [250,0.0001,8000]    # [R,C,R_d]
+
+
+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: 0.9       # end time
+    dt: 0.0005
+    write_dt: 0.01
+    checkpoint_dt:  0.01 # <= 0: only last; else value + last
+    report: 1   # 0: print nothing, 1: print time step and writeout, 2: 1 + flux
+
+estimation:
+    boundary_conditions:
+        - id: 2
+          type: 'dirichlet'
+          initial_stddev: [10]
+          parameters: [U]
+
+    measurements:
+        -
+            mesh: '/home/p283370/Desktop/PhD/AORTA/MESH/aorta_coarse/aorta_coarse_marked.h5'
+            fe_degree: 1
+            xdmf_file: '/home/p283370/Desktop/PhD/AORTA/DATA/ct/aorta_coarse/dt0.0005/measurements/meas.h5'
+            file_root: '/home/p283370/Desktop/PhD/AORTA/DATA/ct/aorta_coarse/dt0.0005/measurements/u{i}.h5'
+            indices: 0
+            noise_stddev: 20     # standard deviation of Gaussian noise
+    
+    roukf:
+        particles: 'unique' # unique or simplex
+        observation_operator: 'state'         #state or postprocessing
+        reparameterize: False
+        
+    #observations:
+    #    mesh: '/home/yeye/Desktop/PhD/AORTA/MESH/aorta_coarse/aorta_coarse_marked.h5'
+    #    timeseries: '/home/yeye/Desktop/PhD/AORTA/DATA/ct/aorta_coarse2/measurements'
+    #    stddev: 10.   # noiselevel x VENC
+
+# solver setup
+fem:
+    velocity_space: p1  # p1 p1b/p1+ p2
+    pressure_space: p1  # p1 p0/dg0 dg1
+
+    strain_symmetric: 0
+    convection_skew_symmetric: 1    # aka Temam term
+    stabilization:
+        forced_normal:
+            boundaries:
+            gamma: 10
+        backflow_boundaries: [3,4,5,6]
+        streamline_diffusion:
+            enabled: False
+            parameter: 'shakib'   # standard, shakib, codina, klr
+            length_scale: 'metric' # average, max, metric
+            consistent: False   # deprecated
+            Cinv: ~
+        monolithic:
+            infsup: False    # pspg, pressure-stabilization
+            graddiv: False
+            consistent: False
+            pressure_stab_constant: 1.
+
+    fix_pressure: False
+    fix_pressure_point: [0., 0. , 0.]
+
+linear_solver:
+    method: 'lu'
+    # inputfile: './projects/nse_coa3d/input/pc/MUMPS_default.yaml'
+    # inputfile: './input/pc/fgmres_gamg_rtol1e-6.yaml'