19 changed files with 2177 additions and 6 deletions
@ -0,0 +1,133 @@
@@ -0,0 +1,133 @@
|
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|
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mesh: '/home/yeye/Desktop/kalman/meshes/coaortaH1.h5' |
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# Physical parameters of the fluid |
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fluid: |
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density: 1.2 |
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dynamic_viscosity: 0.035 |
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|
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io: |
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write_path: 'results/aorta/' |
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restart: |
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path: '' # './projects/nse_coa3d/results/test_restart2/' |
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time: 0 |
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write_xdmf: True |
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write_checkpoints: True |
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write_hdf5_timeseries: False |
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write_velocity: 'update' # tentative |
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|
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boundary_conditions: |
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- |
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id: 1 |
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type: 'dirichlet' |
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value: ['0','0','0'] |
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- |
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id: 2 |
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type: 'dirichlet' |
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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))'] |
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parameters: |
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U: 30 |
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Th: 0.35 |
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t: 0 |
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- |
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id: 3 |
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type: 'windkessel' |
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value: [10,0.01,1000] |
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p0: [47,1333.223874] |
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- |
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id: 4 |
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type: 'windkessel' |
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value: [250,0.0001,8000] |
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p0: [47,1333.223874] |
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- |
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id: 5 |
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type: 'windkessel' |
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value: [250,0.0001,8000] |
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p0: [47,1333.223874] |
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- |
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id: 6 |
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type: 'windkessel' |
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value: [250,0.0001,8000] |
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p0: [47,1333.223874] |
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|
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timemarching: |
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velocity_pressure_coupling: 'fractionalstep' # monolithic, fractionalstep |
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|
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monolithic: |
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timescheme: 'gmp' # generalized midpoint, steady FIXME TODO |
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theta: 1 # 1: Euler, 0.5: implicit midpoint rule (one-legged) |
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nonlinear: |
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method: 'constant_extrapolation' # constant_extrapolation, linear_extrapolation, newton, picard, snes |
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maxit: 20 |
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init_steps: 30 |
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use_aitken: 1 # 0: False, 1: Picard only, 2: all |
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report: 1 # 0: None, 1: residuals, 2: residuals and energy (inflow/driving/forcing via ESSENTIAL Dbcs!) |
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atol: 1.e-6 # note: dot required!! |
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rtol: 1.e-16 |
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stol: 0.0 |
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|
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fractionalstep: |
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scheme: 'CT' # CT, IPCS |
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coupled_velocity: False # False faster, True needed if robin_bc implicit |
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robin_bc_velocity_scheme: 'implicit' # explicit, semi-implicit, implicit |
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transpiration_bc_projection: 'robin' # robin, dirichlet |
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flux_report_normalize_boundary: 1 |
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|
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T: 0.8 # end time |
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dt: 0.01 |
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write_dt: 0.04 |
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checkpoint_dt: 0.04 # <= 0: only last; else value + last |
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report: 1 # 0: print nothing, 1: print time step and writeout, 2: 1 + flux |
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|
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# solver setup |
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fem: |
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velocity_space: p1 # p1 p1b/p1+ p2 |
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pressure_space: p1 # p1 p0/dg0 dg1 |
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strain_symmetric: False |
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convection_skew_symmetric: True # aka Temam term |
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stabilization: |
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forced_normal: |
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enabled: True |
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boundaries: [6] |
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gamma: 10 |
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backflow_boundaries: [3,4,5,6] |
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streamline_diffusion: |
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enabled: False |
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parameter: 'standard' # standard, shakib, codina, klr |
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length_scale: 'metric' # average, max, metric |
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parameter_element_constant: True |
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Cinv: ~ |
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monolithic: |
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infsup: 'pspg' # pspg, pressure-stabilization |
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graddiv: False |
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consistent: False |
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pressure_stab_constant: 1. |
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|
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fix_pressure: False |
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fix_pressure_point: [0., 0. , 0.] |
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|
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linear_solver: |
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method: 'lu' |
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|
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estimation: |
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boundary_conditions: |
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- |
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id: 2 |
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type: 'dirichlet' |
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parameters: 'U' |
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initial_stddev: 1 |
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|
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measurements: |
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- |
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mesh: '/home/yeye/Desktop/kalman/meshes/coaortaH1.h5' |
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fe_degree: 1 |
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xdmf_file: 'results/aorta/measurements/u_all.xdmf' |
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file_root: 'results/aorta/measurements/u{i}.h5' |
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indices: 0 # indices of checkpoints to be processed. 0 == all |
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velocity_direction: ~ |
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noise_stddev: 3.5 # standard deviation of Gaussian noise |
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roukf: |
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particles: 'simplex' # unique or simplex |
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observation_operator: 'postprocessing' #state or postprocessing |
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reparameterize: True |
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@ -0,0 +1,153 @@
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mesh: '/home/yeye/Desktop/kalman/meshes/channel2d.h5' |
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# Physical parameters of the fluid |
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fluid: |
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density: 1.2 |
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dynamic_viscosity: 0.035 |
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|
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io: |
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write_path: 'results/channel2d/' |
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restart: |
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path: '' # './projects/nse_coa3d/results/test_restart2/' |
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time: 0 |
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write_xdmf: True |
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write_checkpoints: True |
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write_hdf5_timeseries: False |
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write_velocity: 'update' # update or tentative |
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|
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boundary_conditions: |
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- |
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id: 1 |
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type: 'dirichlet' |
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value: ['0','0'] |
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- |
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id: 2 |
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type: 'dirichlet' |
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value: ['U*(1- (x[1]-1)*(x[1]-1) )*sin(DOLFIN_PI*t/T)','0'] |
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parameters: |
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U: 30 |
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T: 0.9 |
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t: 0 |
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- |
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id: 3 |
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type: 'neumann' |
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value: '0' |
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|
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|
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ale: |
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type: 'manual' |
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io: |
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# read XDMF files from external solver |
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read_checkpoints: False # True, False |
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# path where displacement files are stored |
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# |
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read_path: |
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# origin mesh path |
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mesh_path: |
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# fem space of solution files |
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fem_type: p1 |
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|
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# Settings of the time integration method |
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timemarching: |
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# Time step for reading the input file |
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read_dt: # 0.05 |
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fem: |
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# function spaces for the displacement |
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# options available: p1 p2 |
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displacement_space: p1 |
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lifting: |
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type: 'elastic_element' # 'harmonic', 'elastic', 'elastic_element' |
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# when chosing 'harmonic', no parameters required (ignored) |
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# otherwise, they must be specified below. |
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parameters: |
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mu: 0.0 # float value e.g. 1., 0.1, 0.01 |
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# deformations will be read whenever chosen 'manual' |
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# if chosen 'external' then deformations list will be OMITTED!. |
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deformations: |
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# The dashes separate the list entries |
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- |
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id : 1 |
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type: 'dirichlet' |
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value: ['0.', '0.'] |
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|
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timemarching: |
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velocity_pressure_coupling: 'fractionalstep' # monolithic, fractionalstep |
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|
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monolithic: |
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timescheme: 'gmp' # generalized midpoint, steady FIXME TODO |
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theta: 1 # 1: Euler, 0.5: implicit midpoint rule (one-legged) |
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nonlinear: |
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method: 'constant_extrapolation' # constant_extrapolation, linear_extrapolation, newton, picard, snes |
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maxit: 20 |
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init_steps: 30 |
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use_aitken: 1 # 0: False, 1: Picard only, 2: all |
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report: 1 # 0: None, 1: residuals, 2: residuals and energy (inflow/driving/forcing via ESSENTIAL Dbcs!) |
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atol: 1.e-6 # note: dot required!! |
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rtol: 1.e-16 |
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stol: 0.0 |
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|
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fractionalstep: |
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scheme: 'CT' # CT, IPCS |
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coupled_velocity: False # False faster, True needed if robin_bc implicit |
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robin_bc_velocity_scheme: 'implicit' # explicit, semi-implicit, implicit |
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transpiration_bc_projection: 'robin' # robin, dirichlet |
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flux_report_normalize_boundary: 1 |
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|
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T: 0.8 # end time |
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dt: 0.01 |
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write_dt: 0.04 |
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checkpoint_dt: 0.04 # <= 0: only last; else value + last |
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report: 1 # 0: print nothing, 1: print time step and writeout, 2: 1 + flux |
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|
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# solver setup |
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fem: |
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velocity_space: p1 # p1 p1b/p1+ p2 |
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pressure_space: p1 # p1 p0/dg0 dg1 |
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|
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strain_symmetric: False |
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convection_skew_symmetric: True # aka Temam term |
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stabilization: |
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forced_normal: |
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enabled: False |
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boundaries: [6] |
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gamma: 10 |
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backflow_boundaries: [] |
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streamline_diffusion: |
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enabled: False |
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parameter: 'standard' # standard, shakib, codina, klr |
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length_scale: 'metric' # average, max, metric |
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parameter_element_constant: True |
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Cinv: ~ |
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monolithic: |
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infsup: 'pspg' # pspg, pressure-stabilization |
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graddiv: False |
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consistent: False |
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pressure_stab_constant: 1. |
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|
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fix_pressure: False |
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fix_pressure_point: [0., 0.] |
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|
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linear_solver: |
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method: 'lu' |
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|
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estimation: |
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boundary_conditions: |
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- |
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id: 2 |
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type: 'dirichlet' |
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parameters: 'U' |
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initial_stddev: 1 |
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|
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measurements: |
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- |
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mesh: '/home/yeye/Desktop/kalman/meshes/channel2d.h5' |
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fe_degree: 0 |
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xdmf_file: 'results/channel2d/measurements/u_all.xdmf' |
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file_root: 'results/channel2d/measurements/u{i}.h5' |
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indices: 0 # indices of checkpoints to be processed. 0 == all |
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velocity_direction: ~ |
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noise_stddev: 1.0 # standard deviation of Gaussian noise |
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|
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roukf: |
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particles: 'simplex' # unique or simplex |
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observation_operator: 'postprocessing' #state or postprocessing |
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reparameterize: True |
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@ -0,0 +1,155 @@
@@ -0,0 +1,155 @@
|
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mesh: '/home/yeye/Desktop/kalman/meshes/channel3d.h5' |
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# Physical parameters of the fluid |
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fluid: |
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density: 1.2 |
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dynamic_viscosity: 0.035 |
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|
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io: |
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write_path: 'results/channel3d/' |
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restart: |
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path: '' # './projects/nse_coa3d/results/test_restart2/' |
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time: 0 |
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write_xdmf: True |
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write_checkpoints: True |
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write_hdf5_timeseries: False |
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write_velocity: 'update' # update or tentative |
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|
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ale: |
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type: 'manual' |
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io: |
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# read XDMF files from external solver |
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read_checkpoints: False # True, False |
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# path where displacement files are stored |
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# |
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read_path: |
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# origin mesh path |
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mesh_path: |
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# fem space of solution files |
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fem_type: p1 |
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|
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# Settings of the time integration method |
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timemarching: |
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# Time step for reading the input file |
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read_dt: # 0.05 |
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fem: |
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# function spaces for the displacement |
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# options available: p1 p2 |
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displacement_space: p1 |
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lifting: |
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type: 'elastic_element' # 'harmonic', 'elastic', 'elastic_element' |
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# when chosing 'harmonic', no parameters required (ignored) |
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# otherwise, they must be specified below. |
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parameters: |
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mu: 0.0 # float value e.g. 1., 0.1, 0.01 |
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# deformations will be read whenever chosen 'manual' |
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# if chosen 'external' then deformations list will be OMITTED!. |
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deformations: |
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# The dashes separate the list entries |
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- |
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id : 1 |
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type: 'dirichlet' |
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value: ['0.', '0.', '0.'] |
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|
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|
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boundary_conditions: |
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- |
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id: 1 |
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type: 'dirichlet' |
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value: ['0','0','0'] |
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- |
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id: 2 |
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type: 'dirichlet' |
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value: ['0','0','U*(1-x[0]*x[0] - x[1]*x[1])*sin(DOLFIN_PI*t/T)'] |
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parameters: |
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U: 30 |
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T: 0.9 |
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t: 0 |
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- |
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id: 3 |
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type: 'neumann' |
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value: '0' |
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|
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|
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|
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timemarching: |
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velocity_pressure_coupling: 'fractionalstep' # monolithic, fractionalstep |
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|
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monolithic: |
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timescheme: 'gmp' # generalized midpoint, steady FIXME TODO |
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theta: 1 # 1: Euler, 0.5: implicit midpoint rule (one-legged) |
||||
nonlinear: |
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method: 'constant_extrapolation' # constant_extrapolation, linear_extrapolation, newton, picard, snes |
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maxit: 20 |
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init_steps: 30 |
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use_aitken: 1 # 0: False, 1: Picard only, 2: all |
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report: 1 # 0: None, 1: residuals, 2: residuals and energy (inflow/driving/forcing via ESSENTIAL Dbcs!) |
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atol: 1.e-6 # note: dot required!! |
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rtol: 1.e-16 |
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stol: 0.0 |
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|
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fractionalstep: |
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scheme: 'CT' # CT, IPCS |
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coupled_velocity: False # False faster, True needed if robin_bc implicit |
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robin_bc_velocity_scheme: 'implicit' # explicit, semi-implicit, implicit |
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transpiration_bc_projection: 'robin' # robin, dirichlet |
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flux_report_normalize_boundary: 1 |
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|
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T: 0.8 # end time |
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dt: 0.01 |
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write_dt: 0.04 |
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checkpoint_dt: 0.04 # <= 0: only last; else value + last |
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report: 1 # 0: print nothing, 1: print time step and writeout, 2: 1 + flux |
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|
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# solver setup |
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fem: |
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velocity_space: p1 # p1 p1b/p1+ p2 |
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pressure_space: p1 # p1 p0/dg0 dg1 |
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|
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strain_symmetric: False |
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convection_skew_symmetric: True # aka Temam term |
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stabilization: |
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forced_normal: |
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enabled: False |
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boundaries: [6] |
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gamma: 10 |
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backflow_boundaries: [] |
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streamline_diffusion: |
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enabled: False |
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parameter: 'standard' # standard, shakib, codina, klr |
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length_scale: 'metric' # average, max, metric |
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parameter_element_constant: True |
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Cinv: ~ |
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monolithic: |
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infsup: 'pspg' # pspg, pressure-stabilization |
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graddiv: False |
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consistent: False |
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pressure_stab_constant: 1. |
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|
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fix_pressure: False |
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fix_pressure_point: [0., 0. , 0.] |
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|
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linear_solver: |
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method: 'lu' |
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|
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estimation: |
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boundary_conditions: |
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- |
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id: 2 |
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type: 'dirichlet' |
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parameters: 'U' |
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initial_stddev: 1 |
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|
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measurements: |
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- |
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mesh: '/home/yeye/Desktop/kalman/meshes/channel3d.h5' |
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fe_degree: 0 |
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xdmf_file: 'results/channel3d/measurements/u_all.xdmf' |
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file_root: 'results/channel3d/measurements/u{i}.h5' |
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indices: 0 # indices of checkpoints to be processed. 0 == all |
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velocity_direction: ~ |
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noise_stddev: 1.0 # standard deviation of Gaussian noise |
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|
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roukf: |
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particles: 'simplex' # unique or simplex |
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observation_operator: 'postprocessing' #state or postprocessing |
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reparameterize: True |
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@ -0,0 +1,185 @@
@@ -0,0 +1,185 @@
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from dolfin import * |
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import numpy as np |
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from common import inout |
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from pathlib import Path |
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import argparse |
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|
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|
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def get_indices_glob(path): |
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path_all = list(Path().glob(path.format(i='*'))) |
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indices = sorted(int(str(s).split('/')[-2]) for s in path_all) |
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return indices |
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|
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|
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def find_checkpoints(options, path_checkpoint): |
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|
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indices = options['estimation']['measurements'][0]['indices'] |
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|
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# look for u.h5 checkpoints |
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chkpt_root = str(Path(path_checkpoint).joinpath('{i}/u.h5')) |
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|
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# if indices were given in input file, check if u.h5 checkpoints or X0.h5 |
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if indices: |
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if not Path(chkpt_root.format(indices[0])).is_file(): |
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chkpt_root = str(Path(path_checkpoint).joinpath('{i}/X0.h5')) |
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if not Path(chkpt_root.format(indices[0])).is_file(): |
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raise Exception('No checkpoints found in folder ' + chkpt_root) |
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|
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else: |
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|
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# get indices from folder names of u.h5 checkpoints |
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indices = get_indices_glob(chkpt_root) |
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|
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# if no indices were found, look for X0.h5 files |
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if not indices: |
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chkpt_root = str(Path(path_checkpoint).joinpath('{i}/X0.h5')) |
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indices = get_indices_glob(chkpt_root) |
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|
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# still no indices? raise Exception |
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if not indices: |
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print(chkpt_root) |
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raise Exception('No checkpoint indices found') |
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|
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dt = options['timemarching']['dt'] |
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times = dt*np.array(indices) |
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|
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if MPI.rank(MPI.comm_world) == 0: |
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print('indices: \n') |
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print('\t', indices) |
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print('times: \n') |
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print('\t', times) |
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|
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files = [chkpt_root.format(i=i) for i in indices] |
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|
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# check if all files are found |
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for f in files: |
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if not Path(f).is_file(): |
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raise FileNotFoundError(f) |
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|
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return indices, times, files |
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|
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|
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def get_h5_fun_name(file): |
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if 'X0.h5' in file: |
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fun = '/X' |
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else: |
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fun = '/u' |
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|
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return fun |
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|
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|
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def filter_indices(ind1, ind2, files1, files2): |
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''' Filter indices and files such that only maching files and indicies |
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remain. |
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|
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Args: |
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ind1 (list): list of indices of dataset 1 |
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ind2 (list): list of indices of dataset 2 |
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files1 (list): list of files of dataset 1 |
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files2 (list): list of files of dataset 2 |
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''' |
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ind = [] |
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files_filt1 = [] |
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files_filt2 = [] |
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for i in ind1: |
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if i in ind2: |
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ind.append(i) |
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files_filt1.append(files1[list(ind1).index(i)]) |
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files_filt2.append(files2[list(ind2).index(i)]) |
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|
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return ind, files_filt1, files_filt2 |
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|
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|
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def compute_errors(inputfile, path_checkpoint_1, |
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path_checkpoint_2, relative=False): |
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|
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options = inout.read_parameters(inputfile) |
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|
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indices1, times1, files1 = find_checkpoints(options, path_checkpoint_1) |
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indices2, times2, files2 = find_checkpoints(options, path_checkpoint_2) |
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|
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indices, files1, files2 = filter_indices(indices1, indices2, files1, |
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files2) |
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|
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fun1 = get_h5_fun_name(files1[0]) |
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fun2 = get_h5_fun_name(files2[0]) |
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|
||||
# assert np.allclose(indices1, indices2), 'Indices do not match!' |
||||
# assert np.allclose(times1, times2), 'Time stamps do not match!' |
||||
|
||||
mesh, _, _ = inout.read_mesh(options['mesh']) |
||||
|
||||
if 'fluid' in options: |
||||
assert options['fem']['velocity_space'] in ('p1', 'p2'), ( |
||||
'velocity space not supported, use p1 or p2') |
||||
deg = int(options['fem']['velocity_space'][-1]) |
||||
|
||||
elif 'material' in options: |
||||
deg = options['solver']['fe_degree'] |
||||
|
||||
V = VectorFunctionSpace(mesh, 'P', deg) |
||||
|
||||
u1 = Function(V) |
||||
u2 = Function(V) |
||||
|
||||
err_l2 = [] |
||||
err_linf = [] |
||||
|
||||
for i, (f1, f2) in enumerate(zip(files1, files2)): |
||||
# file_ref = str(Path(path_fwd_tentative_checkpoint).joinpath( |
||||
# '{i}/u.h5'.format(i=i))) |
||||
# file_roukf = str(Path(path_roukf_state_checkpoint).joinpath( |
||||
# '{i}/X0.h5'.format(i=i))) |
||||
|
||||
t0 = inout.read_HDF5_data(V.mesh().mpi_comm(), f1, u1, fun1) |
||||
t1 = inout.read_HDF5_data(V.mesh().mpi_comm(), f2, u2, fun2) |
||||
|
||||
assert np.allclose(t0, t1), ('Timestamps do not match! {} vs {} ' |
||||
'(HDF5 files)'.format(t0, t1)) |
||||
|
||||
if relative: |
||||
u_l2 = norm(u1, 'l2') |
||||
u_linf = norm(u1.vector(), 'linf') |
||||
if u_l2 == 0: |
||||
u_l2 = 1 |
||||
print('i = {} \t norm(u1) == 0, do not normalize!'.format(i)) |
||||
if u_linf == 0: |
||||
u_linf = 1 |
||||
print('i = {} \t max(u1) == 0, do not normalize!'.format(i)) |
||||
else: |
||||
u_l2 = u_linf = 1 |
||||
|
||||
err_l2.append(errornorm(u1, u2, 'l2', degree_rise=0)/u_l2) |
||||
err_linf.append(norm(u1.vector() - u2.vector(), 'linf')/u_linf) |
||||
|
||||
print('i = {} \t L2 error: {} \t Linf error: {}'.format(i, err_l2[-1], |
||||
err_linf[-1])) |
||||
|
||||
print('max L2 error: {}'.format(max(err_l2))) |
||||
print('max Linf error: {}'.format(max(err_linf))) |
||||
|
||||
|
||||
def get_parser(): |
||||
parser = argparse.ArgumentParser( |
||||
description=''' |
||||
Compute errors between vector function checkpoints of two simulations. |
||||
|
||||
Can be ROUKF checkpoints, but if forward and ROUKF |
||||
files are found in the same checkpoint folder (0/u.h5 and 0/X.5), |
||||
the forward file will be preferred.''', |
||||
formatter_class=argparse.RawDescriptionHelpFormatter) |
||||
parser.add_argument('inputfile', type=str, help='path to yaml input file') |
||||
parser.add_argument('path_checkpoint_1', type=str, |
||||
help='Path to checkpoints of simulation 1') |
||||
parser.add_argument('path_checkpoint_2', type=str, |
||||
help='Path to checkpoints of simulation 2') |
||||
parser.add_argument('-r', '--relative', action='store_true', |
||||
help='compute relative errors') |
||||
return parser |
||||
|
||||
|
||||
if __name__ == '__main__': |
||||
args = get_parser().parse_args() |
||||
|
||||
compute_errors(args.inputfile, args.path_checkpoint_1, |
||||
args.path_checkpoint_2, relative=args.relative) |
||||
@ -0,0 +1,505 @@
@@ -0,0 +1,505 @@
|
||||
from dolfin import * |
||||
import dolfin |
||||
import argparse |
||||
from common import inout |
||||
import numpy as np |
||||
import sys |
||||
# import ruamel.yaml as yaml |
||||
from pathlib import Path |
||||
import csv |
||||
import shutil |
||||
|
||||
# parameters['allow_extrapolation'] = True |
||||
# careful with this option... can give nonsensical results outside |
||||
|
||||
|
||||
if '2017' in dolfin.__version__: |
||||
class MPI(MPI): |
||||
comm_world = MPI.comm_world |
||||
|
||||
|
||||
def solution_function_space(options): |
||||
''' Create function space to read in solution checkpoints, as specified in |
||||
options. |
||||
|
||||
Args: |
||||
options (dict): Options dictionary (from input file) |
||||
|
||||
Returns: |
||||
FunctionSpace: Solution checkpoint function space |
||||
''' |
||||
mesh, _, _ = inout.read_mesh(options['mesh']) |
||||
|
||||
if 'fluid' in options: |
||||
if options['fem']['velocity_space'].lower() == 'p2': |
||||
Evel = VectorElement('P', mesh.ufl_cell(), 2) |
||||
|
||||
elif options['fem']['velocity_space'].lower() == 'p1': |
||||
Evel = VectorElement('P', mesh.ufl_cell(), 1) |
||||
|
||||
else: |
||||
raise Exception('Velocity space {} not yet implemented!'.format( |
||||
options['fem']['velocity_space'].lower())) |
||||
|
||||
elif 'material' in options: |
||||
if options['incompressibility']['mixed_formulation']: |
||||
raise Exception('Only compressible hyperelasticity data is ' |
||||
'supported here, for simplicity') |
||||
|
||||
deg = options['solver']['fe_degree'] |
||||
Evel = VectorElement('P', mesh.ufl_cell(), deg) |
||||
|
||||
V = FunctionSpace(mesh, Evel) |
||||
|
||||
return V |
||||
|
||||
|
||||
def measurement_function_spaces(options): |
||||
''' Create function space for measurements, as specified in |
||||
options. |
||||
|
||||
Args: |
||||
options (dict): Options dictionary (from input file) |
||||
|
||||
Returns: |
||||
list((Vector)FunctionSpace): list of function spaces on measurement |
||||
mesh, scalar if measurements are scalar, else VectorFunctionSpace |
||||
list(VectorFunctionSpace): if scalar measurements, a list of |
||||
corresponding VectorFunctionSpace for interpolation, else empty |
||||
list |
||||
''' |
||||
|
||||
measurement_lst = options['estimation']['measurements'] |
||||
if not isinstance(measurement_lst, list): |
||||
measurement_lst = [measurement_lst] |
||||
|
||||
meshes = [meas['mesh'] for meas in measurement_lst] |
||||
|
||||
if 'fe_degree' in options['estimation']['measurements'][0]: |
||||
degree = options['estimation']['measurements'][0]['fe_degree'] |
||||
else: |
||||
degree = 1 |
||||
|
||||
for measurement in measurement_lst[1:]: |
||||
if not degree == measurement['fe_degree']: |
||||
raise Exception('fe_degree must the the same for all ' |
||||
'measurements!') |
||||
|
||||
if degree in (1, 2): |
||||
element_family = 'P' |
||||
elif degree == 0: |
||||
element_family = 'DG' |
||||
else: |
||||
raise Exception('Unsupported measurement FE degree: {}' |
||||
.format(degree)) |
||||
|
||||
scalar = [False]*len(measurement_lst) |
||||
for i, measurement in enumerate(measurement_lst): |
||||
if 'velocity_direction' in measurement: |
||||
direction = measurement['velocity_direction'] |
||||
if direction and None not in direction and sum(direction) > 0: |
||||
scalar[i] = True |
||||
|
||||
V = [] |
||||
V_aux = [] |
||||
for scal, file in zip(scalar, meshes): |
||||
mesh, _, _ = inout.read_mesh(file) |
||||
if scal: |
||||
V.append(FunctionSpace(mesh, element_family, degree)) |
||||
# 1. interpolate velocity vector onto measurement grid (V_aux) |
||||
# 2. perform component projection in the measurement space |
||||
# ---> need to store both scalar and vector spaces |
||||
V_aux.append(VectorFunctionSpace(mesh, element_family, degree)) |
||||
else: |
||||
V.append(VectorFunctionSpace(mesh, element_family, degree)) |
||||
|
||||
return V, V_aux |
||||
|
||||
|
||||
def find_checkpoints(options): |
||||
''' Find all checkpoints of a simulation from configuration in options |
||||
dictionary. |
||||
|
||||
Args: |
||||
options (dict): Options dictionary (from YAML input file) |
||||
|
||||
Returns: |
||||
list: List of found checkpoint indices |
||||
list: List of found checkpoint times |
||||
list: List of found checkpoint files |
||||
''' |
||||
if MPI.rank(MPI.comm_world) > 0: |
||||
return |
||||
|
||||
chkpt_root = options['io']['write_path'] + '/checkpoint/{i}/u.h5' |
||||
|
||||
indices = options['estimation']['measurements'][0]['indices'] |
||||
if not indices: |
||||
path_all = list(Path().glob(chkpt_root.format(i='*'))) |
||||
indices = sorted(int(str(s).split('/')[-2]) for s in path_all) |
||||
|
||||
# dt_meas = options['timemarching']['checkpoint_dt'] |
||||
# times = np.concatenate(([options['timemarching']['dt']], |
||||
# dt_meas*np.array(indices[1:]))) |
||||
dt = options['timemarching']['dt'] |
||||
times = dt*np.array(indices) |
||||
|
||||
print('indices: \n') |
||||
print('\t', indices) |
||||
print('times: \n') |
||||
print('\t', times) |
||||
|
||||
files = [chkpt_root.format(i=i) for i in indices] |
||||
|
||||
# check if all files are found |
||||
for f in files: |
||||
if not Path(f).is_file(): |
||||
raise FileNotFoundError(f) |
||||
|
||||
return indices, times, files |
||||
|
||||
|
||||
def generate(options, seed_lst, print_norms=False): |
||||
''' Generate measurements. |
||||
|
||||
Args: |
||||
options (dict): Options dictionary (from input file) |
||||
seed_lst (list): list of random seeds |
||||
print_norms (bool): switch for printing norms of measurements |
||||
''' |
||||
|
||||
V = solution_function_space(options) |
||||
ndim = V.mesh().topology().dim() |
||||
u = Function(V) |
||||
|
||||
V_meas_lst, V_aux_lst = measurement_function_spaces(options) |
||||
u_meas_lst = [Function(V_meas, name='measurement') for V_meas in |
||||
V_meas_lst] |
||||
u_meas_cpy = [Function(V_meas, name='measurement') for V_meas in |
||||
V_meas_lst] |
||||
LI = LagrangeInterpolator |
||||
if V_aux_lst: |
||||
u_aux_lst = [Function(V_aux) for V_aux in V_aux_lst] |
||||
comp_assigner = [FunctionAssigner([V]*ndim, V_aux) for V, V_aux in |
||||
zip(V_meas_lst, V_aux_lst)] |
||||
|
||||
measurement_lst = options['estimation']['measurements'] |
||||
noise_sd = [meas['noise_stddev'] for meas in measurement_lst] |
||||
|
||||
# if 'project' in options['estimation']['measurements']: |
||||
# project_switch = bool(options['estimation']['measurements'] |
||||
# ['project']) |
||||
# else: |
||||
# project_switch = False |
||||
project_switch = False |
||||
|
||||
indices, times, files = find_checkpoints(options) |
||||
|
||||
outfile_root_lst = [meas['file_root'] for meas in measurement_lst] |
||||
xdmf_paths = [meas['xdmf_file'] for meas in measurement_lst] |
||||
|
||||
# don't automatically append seed{s} do path anymore! |
||||
# suppose seed{s} is included |
||||
# if seed_lst[0] > 0: |
||||
# for i, (out, xdmf) in enumerate(zip(outfile_root_lst, xdmf_paths)): |
||||
# # if isinstance(out, str) and 'seed{s}' not in out: |
||||
# # out_ = out.split('/') |
||||
# # outfile_root_lst[i] = '/'.join(out_[:-1] + ['seed{s}', |
||||
# # out_[-1]]) |
||||
# if isinstance(xdmf, str) and 'seed{s}' not in xdmf: |
||||
# xdmf_ = xdmf.split('/') |
||||
# xdmf_paths[i] = '/'.join(xdmf_[:-1] + ['seed{s}', xdmf_[-1]]) |
||||
|
||||
# check if a list of seeds is given that {s} is included in path |
||||
if len(seed_lst) > 1: |
||||
for out in outfile_root_lst: |
||||
assert '{s}' in out, ('For a list of seeds, the string \'{s}\' ' |
||||
'must be included in the file_root and will ' |
||||
'be replaced by the seed number') |
||||
|
||||
if any(xdmf_paths): |
||||
xdmf_lst = [] |
||||
for pth in xdmf_paths: |
||||
if not isinstance(pth, str): |
||||
raise TypeError('xdmf_file setting must be None or a string ' |
||||
'indicating the target XDMF file. Got type {}'. |
||||
format(type(pth))) |
||||
|
||||
seed_dict = {} |
||||
for seed in seed_lst: |
||||
file = XDMFFile(pth.format(s=seed)) |
||||
file.parameters['rewrite_function_mesh'] = False |
||||
seed_dict[seed] = file |
||||
xdmf_lst.append(seed_dict) |
||||
else: |
||||
xdmf_lst = [None]*len(u_meas_lst) |
||||
|
||||
for count, (index, time, infile) in enumerate(zip(indices, times, files)): |
||||
if MPI.rank(MPI.comm_world) == 0: |
||||
print('Processing {} at t = {}'.format(infile, time)) |
||||
|
||||
t_ = inout.read_HDF5_data(u.function_space().mesh().mpi_comm(), infile, |
||||
u, '/u') |
||||
|
||||
assert np.allclose(time, t_), ('Timestamps do not match! {} vs {} ' |
||||
'(HDF5 file)'.format(time, t_)) |
||||
|
||||
# interpolate u to measurement meshes |
||||
for k, (u_meas, outfile_root, xdmf, sd) in enumerate(zip( |
||||
u_meas_lst, outfile_root_lst, xdmf_lst, noise_sd)): |
||||
|
||||
if project_switch: |
||||
u_meas.assign(project(u, u_meas.function_space())) |
||||
|
||||
else: |
||||
if V_aux_lst: |
||||
if MPI.rank(MPI.comm_world) == 0: |
||||
print('- Scalar velocity component') |
||||
direction = (options['estimation']['measurements'][k] |
||||
['velocity_direction']) |
||||
if direction.count(0) == 2 and direction.count(1) == 1: |
||||
LI.interpolate(u_meas, u.sub(direction.index(1))) |
||||
|
||||
else: |
||||
assert u_meas.value_shape() == [] |
||||
# normalize projection direction |
||||
direction = np.array(direction, dtype=np.float64) |
||||
direction /= np.sqrt(np.dot(direction, direction)) |
||||
if MPI.rank(MPI.comm_world) == 0: |
||||
print('- direction: {}'.format(direction)) |
||||
|
||||
LagrangeInterpolator.interpolate(u_aux_lst[k], u) |
||||
|
||||
# This is faster than simply Xobs_aux.split(True) ! |
||||
u_i = [u_meas] + [u_meas.copy(True) for j in |
||||
range(ndim - 1)] |
||||
|
||||
comp_assigner[k].assign(u_i, u_aux_lst[k]) |
||||
u_meas.vector()[:] *= direction[0] |
||||
for ui, d in zip(u_i[1:], direction[1:]): |
||||
if d: |
||||
u_meas.vector().axpy(d, ui.vector()) |
||||
|
||||
else: |
||||
if MPI.rank(MPI.comm_world) == 0: |
||||
print('- Full velocity vector') |
||||
LI.interpolate(u_meas, u) |
||||
if sd: |
||||
u_meas_cpy[k].assign(u_meas) |
||||
|
||||
# add noise |
||||
for seed in seed_lst: |
||||
if sd: |
||||
if seed > 0: |
||||
np.random.seed(seed + count) |
||||
|
||||
if MPI.rank(MPI.comm_world) == 0: |
||||
print('- Add noise with stddev = {}, seed = {}' |
||||
.format(sd, seed + count)) |
||||
|
||||
noise = np.random.normal(0., sd, |
||||
u_meas.vector().local_size()) |
||||
u_meas.assign(u_meas_cpy[k]) |
||||
u_meas.vector()[:] += noise |
||||
|
||||
if MPI.rank(MPI.comm_world) == 0: |
||||
if print_norms: |
||||
print('Writing file at t = {}\t |u_m| = {}'.format( |
||||
time, norm(u_meas))) |
||||
else: |
||||
print('Writing file at t = {}\t'.format(time)) |
||||
|
||||
outfile = outfile_root.format(i=index, s=seed) |
||||
inout.write_HDF5_data( |
||||
u_meas.function_space().mesh().mpi_comm(), outfile, u_meas, |
||||
'/u', time) |
||||
|
||||
if xdmf: |
||||
xdmf[seed].write(u_meas, time) |
||||
|
||||
# THIS IS OBSOLETE NOW |
||||
# write indices and timesteps |
||||
# write_timestamps(options, indices, times, seed_lst) |
||||
|
||||
|
||||
def write_timestamps(options, indices, times, seed_lst): |
||||
''' Write time stamps of measurements to csv file. |
||||
|
||||
Args: |
||||
options (dict): Options dictionary (from YAML input file) |
||||
indices (list): List of checkpoint indices |
||||
times (list): List of checpoint times |
||||
seed_lst (list): List of random seeds |
||||
''' |
||||
if MPI.rank(MPI.comm_world) > 0: |
||||
return |
||||
|
||||
warning('timestamps.csv is OBSOLETE!') |
||||
|
||||
file_root_lst = [meas['file_root'] for meas in options['estimation'] |
||||
['measurements']] |
||||
|
||||
# if seed_lst[0]: |
||||
# for i, out in enumerate(file_root_lst): |
||||
# if isinstance(out, str) and 'seed{s}' not in out: |
||||
# out_ = out.split('/') |
||||
# file_root_lst[i] = '/'.join(out_[:-1] |
||||
# + ['seed{s}', out_[-1]]) |
||||
|
||||
for file_root in file_root_lst: |
||||
for seed in seed_lst: |
||||
path = Path(file_root.format(s=seed, i=-1)).parent |
||||
if seed > 0 and 'seed{s}'.format(s=seed) not in str(path): |
||||
path = path.joinpath('seed{s}'.format(s=seed)) |
||||
path = path.joinpath('timestamps.csv') |
||||
print('Writing timestamps to file: {}'.format(path)) |
||||
with path.open('w') as file: |
||||
writer = csv.writer(file, delimiter=' ') |
||||
for i, t in zip(indices, times): |
||||
writer.writerow((i, t)) |
||||
|
||||
|
||||
def copy_inputfile(options, inputfile, seed_lst): |
||||
''' Copy input file of reference solution to measurements directory. |
||||
|
||||
Args: |
||||
options (dict): Options dictionary (from YAML input file) |
||||
inputfile (str): Path of input file to be copied |
||||
seed_lst (list): List of random seeds |
||||
''' |
||||
if MPI.rank(MPI.comm_world) > 0: |
||||
return |
||||
|
||||
file_root_lst = [meas['file_root'] for meas in options['estimation'] |
||||
['measurements']] |
||||
for file_root in file_root_lst: |
||||
for seed in seed_lst: |
||||
path = Path(file_root.format(s=seed, i=-1)).parent |
||||
# if seed > 0 and 'seed{s}'.format(s=seed) not in str(path): |
||||
# path = path.joinpath('seed{s}'.format(s=seed)) |
||||
path = path.joinpath('input.yaml') |
||||
# path.parent.mkdir(parents=True, exist_ok=True) |
||||
shutil.copy2(str(inputfile), str(path)) |
||||
print('Copied input file to {}'.format(path)) |
||||
|
||||
|
||||
def dump_example_options(path): |
||||
''' Dump example options to given path and exit. |
||||
|
||||
Args: |
||||
path (str): Path to input file |
||||
''' |
||||
example = '''\ |
||||
# example fractional step inputfile for gen_measurements_from_checkpoints.py |
||||
mesh: './meshes/mesh.h5' |
||||
|
||||
io: |
||||
# Path containing checkpoints in a checkpoints/ folder |
||||
write_path: './results/test/' |
||||
|
||||
timemarching: |
||||
# final time of simulation to be processed |
||||
T: 0.4 |
||||
# simulation time step size (not dt_checkpoint) |
||||
dt: 0.001 |
||||
|
||||
fem: |
||||
# Velocity and presse (for monolithic) function spaces of checkpoints |
||||
velocity_space: 'p1' |
||||
pressure_space: 'p1' |
||||
|
||||
estimation: |
||||
measurements: |
||||
# List of measurements |
||||
- |
||||
# Mesh of 1. measurement set |
||||
mesh: './measurements/mesh_meas.h5' |
||||
|
||||
# degree of finite element function space |
||||
# (1 for linear, 0 for discontinuous piece-wise constant) |
||||
fe_degree: 0 |
||||
|
||||
# velocity measurement files to be written by this tool |
||||
# {i} will be replaced by the corresponding index of the checkpoint |
||||
# if given, {s} may be replaced by the seed number, for instance |
||||
# path/seed{s}/u{i}.h5 |
||||
file_root: './measurements/u{i}.h5' |
||||
|
||||
# XDMF file where measurements are optionally stored for |
||||
# visualization (one file for all time steps) |
||||
xdmf_file: './measurements/meas.xdmf' |
||||
|
||||
# Select a velocity component: |
||||
# * None (~) means "use complete vector" |
||||
# * else, use a scalar velocity by projecting onto the given |
||||
# direction vector, [x, y, (z)] |
||||
velocity_direction: ~ |
||||
|
||||
# (absolute) standard deviation of Gaussian noise |
||||
noise_stddev: 10. |
||||
|
||||
# indices of checkpoints to be processed: |
||||
# * 0 == all |
||||
# * a list of integes |
||||
indices: 0 |
||||
|
||||
- |
||||
# second measurement ... |
||||
- |
||||
# further measurements ... |
||||
''' |
||||
|
||||
with open(path, 'w') as f: |
||||
f.write(example) |
||||
print('Example options:\n\n') |
||||
print(example) |
||||
print('\ndumped example options to file: {}'.format(path)) |
||||
sys.exit(0) |
||||
|
||||
|
||||
def get_parser(): |
||||
parser = argparse.ArgumentParser(description='''\ |
||||
Generate measurements from HDF5 checkpoints, generated by the Fractional-Step |
||||
or the monolithic Navier-Stokes solvers. |
||||
|
||||
Reads options from the given input file. |
||||
|
||||
See the example options for further explanations:: |
||||
(`gen_measurements_from_checkpoints.py -d example.yaml`). |
||||
''', formatter_class=argparse.RawDescriptionHelpFormatter) |
||||
parser.add_argument('inputfile', type=str, help='path to yaml input file') |
||||
# parser.add_argument('-s', '--seed', type=int, default=-1, |
||||
# help='seed for random generator') |
||||
parser.add_argument('-s', '--seed', nargs='+', help='seed or list of seeds' |
||||
' for noise random number generator. ' |
||||
'Will take the given seed for the first time step ' |
||||
'and increment by +1 for all subsequent time steps, ' |
||||
'so that noise is different for all times ' |
||||
'but reproducible', default=[-1], type=int) |
||||
parser.add_argument('-n', '--print_norms', action='store_true', |
||||
help='print norms') |
||||
parser.add_argument('-d', '--dump', action='store_true', |
||||
help='dump minimal example parameters to inputfile') |
||||
|
||||
return parser |
||||
|
||||
|
||||
if __name__ == '__main__': |
||||
args = get_parser().parse_args() |
||||
|
||||
if args.dump: |
||||
dump_example_options(args.inputfile) |
||||
|
||||
seed = args.seed |
||||
|
||||
if seed[0] <= 0: |
||||
assert len(seed) == 1, 'if multiple seeds are given, all should be > 0' |
||||
|
||||
try: |
||||
options = inout.read_parameters(args.inputfile) |
||||
except IOError: |
||||
raise IOError('File could not be read: {}'.format(args.inputfile)) |
||||
|
||||
generate(options, seed, args.print_norms) |
||||
|
||||
copy_inputfile(options, args.inputfile, seed) |
||||
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@ -0,0 +1,137 @@
@@ -0,0 +1,137 @@
|
||||
from common import inout |
||||
from gen_measurements_from_checkpoints import generate, copy_inputfile |
||||
|
||||
path_chan2d = './projects/DA_testbench/input/channel2d/measurements/' |
||||
inputfiles_chan2d = [ |
||||
# 'chan2d_CT_Rtop0.9_slip0.332_no-pen_h0.05_noise0.yaml', |
||||
# 'chan2d_CT_Rtop0.9_slip0.332_no-pen_h0.05_noise6.5.yaml', |
||||
# # # 'chan2d_CT_Rtop0.9_slip0.332_no-pen_dt0.001_h0.05_noise0.yaml', |
||||
# # # 'chan2d_CT_Rtop0.9_slip0.332_no-pen_dt0.001_h0.05_noise6.5.yaml', |
||||
# 'chan2d_CT_Rtop0.9_slip0.332_trans3600_h0.05_noise0.yaml', |
||||
'chan2d_CT_Rtop0.9_slip0.332_trans3600_h0.05_noise6.5.yaml', |
||||
# 'chan2d_CT_R1_no-slip_h0.05_noise0.yaml', |
||||
# 'chan2d_CT_R1_no-slip_h0.05_noise6.5.yaml', |
||||
# # 'chan2d_CT_R1_no-slip_steady_h0.05_noise0.yaml', |
||||
# # 'chan2d_CT_R1_no-slip_steady_h0.05_noise6.5.yaml', |
||||
# 'chan2d_mono_Rtop0.9_slip0.332_no-pen_h0.05_noise0.yaml', |
||||
# 'chan2d_mono_Rtop0.9_slip0.332_no-pen_h0.05_noise6.5.yaml', |
||||
# # 'chan2d_mono_Rtop0.9_slip0.332_no-pen_dt0.001_h0.05_noise0.yaml', |
||||
# # 'chan2d_mono_Rtop0.9_slip0.332_no-pen_dt0.001_h0.05_noise6.5.yaml', |
||||
# 'chan2d_mono_Rtop0.9_slip0.332_trans3600_h0.05_noise0.yaml', |
||||
# 'chan2d_mono_Rtop0.9_slip0.332_trans3600_h0.05_noise6.5.yaml', |
||||
# 'chan2d_mono_R1_no-slip_h0.05_noise0.yaml', |
||||
# 'chan2d_mono_R1_no-slip_h0.05_noise6.5.yaml', |
||||
# # 'chan2d_mono_R1_no-slip_steady_h0.05_noise0.yaml', |
||||
# # 'chan2d_mono_R1_no-slip_steady_h0.05_noise6.5.yaml', |
||||
# # |
||||
# # 'chan2d_CT_Rtop0.9_slip0.332_no-pen_h0.05_state_noise0.yaml', |
||||
] |
||||
|
||||
path_coa2d = './projects/DA_testbench/input/coa2d/measurements/' |
||||
inputfiles_coa2d = [ |
||||
# CT H=h, DT=dt |
||||
# 'coa2d_CT_d0.1_slip0.001_trans1000_h0.025_supg_noise0.yaml', |
||||
# 'coa2d_CT_d0.1_slip0.332_trans3600_h0.025_supg_noise0.yaml', |
||||
# 'coa2d_CT_d0.1_slip0.001_trans1000_h0.025_supg_noise10.yaml', |
||||
# 'coa2d_CT_d0.1_slip0.332_trans3600_h0.025_supg_noise10.yaml', |
||||
# 'coa2d_CT_d0_noslip_h0.025_supg_noise10.yaml', |
||||
# 'coa2d_CT_d0_noslip_h0.025_supg_noise0.yaml', |
||||
# MONO |
||||
# 'coa2d/coa2d_mono_d0.1_slip0.001_trans1000_h0.025_supg.yaml', |
||||
# 'coa2d/coa2d_mono_d0.1_slip0.332_trans3600_h0.025_supg.yaml', |
||||
# 'coa2d/coa2d_mono_d0_noslip_h0.025_supg.yaml', |
||||
# H, DT var |
||||
# 'coa2d_CT_d0_noslip_h0.025_supg_d0.1_H0.1.yaml', |
||||
# 'coa2d_CT_d0_noslip_h0.025_supg_DT0.01_H0.025.yaml', |
||||
# 'coa2d_CT_d0_noslip_h0.025_supg_DT0.02_H0.025.yaml', |
||||
# 'coa2d_CT_d0_noslip_h0.025_supg_DT0.02_H0.1.yaml', |
||||
# PLUG FLOW |
||||
# 'coa2d_CT_d0_noslip_h0.025_supg_plug_d0_H0.1.yaml', |
||||
'coa2d_CT_d0_noslip_h0.025_supg_plug_d0.1_H0.1.yaml', |
||||
# 'coa2d_CT_d0_noslip_h0.025_supg_plug_d0.2_H0.2.yaml', |
||||
] |
||||
|
||||
path_pipe3d = './projects/DA_testbench/input/pipe3d/measurements/' |
||||
inputfiles_pipe3d = [ |
||||
'pipe3d_CT_R0.9_slip0.332_trans3600_h0.05_noise0.yaml', |
||||
'pipe3d_CT_R0.9_slip0.332_trans3600_h0.05_noise10.yaml', |
||||
'pipe3d_CT_R0.9_slip0.332_trans3600_h0.1_noise0.yaml', |
||||
'pipe3d_CT_R0.9_slip0.332_trans3600_h0.1_noise10.yaml', |
||||
'pipe3d_CT_R1_noslip_h0.1_noise10.yaml', |
||||
'pipe3d_CT_R1_noslip_h0.05_noise10.yaml', |
||||
] |
||||
|
||||
path_coa3d = './projects/DA_testbench/input/coa3d/measurements/' |
||||
inputfiles_coa3d = [ |
||||
# 'coa3d_CT_R0.9_slip0.001_trans1000_h0.025_noise0.yaml', |
||||
# 'coa3d_CT_R0.9_slip0.001_trans1000_h0.025_noise10.yaml', |
||||
# 'coa3d_CT_R1_noslip_h0.025_noise0.yaml', |
||||
# 'coa3d_CT_R1_noslip_h0.025_noise10.yaml', |
||||
# 'coa3d_CT_R1_noslip_h0.025_H0.1_DT0.001_noise10.yaml', |
||||
# 'coa3d_CT_R1_noslip_h0.025_H0.1_DT0.01_noise10.yaml', |
||||
# 'coa3d_CT_R1_noslip_h0.025_H0.1_DT0.02_noise10.yaml', |
||||
# 'coa3d_CT_R1_noslip_h0.025_H0.025_DT0.01_noise10.yaml', |
||||
# 'coa3d_CT_R1_noslip_h0.025_H0.025_DT0.02_noise10.yaml', |
||||
# 'coa3d_CT_R1_noslip_h0.025_H0.025_DT0.02_noise10.yaml', |
||||
# 'coa3d_asym_CT_R1_noslip_h0.025_H0.1_DT0.02_noise10.yaml', |
||||
# 'coa3d_asym_CT_R1_noslip_h0.025_H0.2_DT0.02_noise10.yaml', |
||||
# 'coa3d_bend_CT_R1_noslip_h0.025_H0.1_DT0.02_noise10.yaml', |
||||
# 'coa3d_bend_CT_R1_noslip_h0.025_H0.2_DT0.02_noise10.yaml', |
||||
# PLUG FLOW |
||||
# 'coa3d_bend_CT_R1_noslip_plug_h0.025_d0_H0.1_DT0.02_noise10.yaml', |
||||
# 'coa3d_bend_CT_R1_noslip_plug_h0.025_H0.1_DT0.02_noise10.yaml', |
||||
# 'coa3d_bend_CT_R1_noslip_plug_h0.025_H0.2_DT0.02_noise10.yaml', |
||||
# slices |
||||
# 'coa3d_CT_R1_noslip_plug_h0.025_H0.1_DT0.02_noise10.yaml', |
||||
# 'coa3d_CT_R1_noslip_plug_h0.025_H0.2_DT0.02_noise10.yaml', |
||||
# 'coa3d_CT_R1_noslip_plug_h0.025_slices_isZY_H0.1_DT0.02_noise10.yaml', |
||||
# 'coa3d_CT_R1_noslip_plug_h0.025_slices_Z_P0_H0.1_DT0.02_noise10.yaml', |
||||
# 'coa3d_CT_R1_noslip_plug_h0.025_slices_Z_P0_H0.2_DT0.02_noise10.yaml', |
||||
# 'coa3d_CT_R1_noslip_plug_h0.025_slices_isZY_P0_H0.1_DT0.02_noise10.yaml', |
||||
# 'coa3d_CT_R1_noslip_plug_h0.025_slices_isZY_H0.2_DT0.02_noise10.yaml' |
||||
# 'coa3d_bend_f0.3_CT_R1_noslip_plug_h0.025_slices_P0_H0.1-0.2_DT0.02_noise48.yaml', |
||||
# 'coa3d_bend_f0.3_CT_R1_noslip_plug_h0.025_slices_P0_H0.1-0.2_DT0.02_noise0.yaml', |
||||
# 'coa3d_bend_CT_R1_noslip_plug_h0.025_slices_P0_H0.1-0.2_DT0.02_noise48.yaml', |
||||
# 'coa3d_bend_CT_R1_noslip_plug_h0.025_slices_P0_H0.1-0.2_DT0.02_noise0.yaml', |
||||
# 'coa3d_bend_f0.0_CT_R1_noslip_plug_h0.025_slices_P0_H0.1-0.2_DT0.02_noise0.yaml', # <------ compute these! |
||||
# 'coa3d_bend_f0.0_CT_R1_noslip_plug_h0.025_slices_P0_H0.1-0.2_DT0.02_noise48.yaml', |
||||
# 'coa3d_bend_f0.5_CT_R1_noslip_plug_h0.025_slices_P0_H0.1-0.2_DT0.02_noise0.yaml', |
||||
# 'coa3d_bend_f0.5_CT_R1_noslip_plug_h0.025_slices_P0_H0.1-0.2_DT0.02_noise48.yaml', |
||||
# 'coa3d_bend_f0.5_CT_R1_noslip_plug_h0.025_slices_P0_H0.1-0.2_DT0.02_noise10.yaml', |
||||
|
||||
# 'coa3d_bend_f0.4_CT_R1_noslip_plug_h0.025_slices_P0_H0.1-0.2_DT0.02_noise0.yaml', |
||||
# 'coa3d_bend_f0.4_CT_R1_noslip_plug_h0.025_slices_P0_H0.1-0.2_DT0.02_noiseVENC.yaml', |
||||
# 'coa3d_bend_f0.5_CT_R1_noslip_plug_h0.025_slices_P0_H0.1-0.2_DT0.02_noiseVENC.yaml', |
||||
# 'coa3d_bend_f0.6_CT_R1_noslip_plug_h0.025_slices_P0_H0.1-0.2_DT0.02_noiseVENC.yaml', |
||||
|
||||
'coa3d_bend_f0.4_CT_R1_noslip_plug_h0.025_slices_par_P0_H0.1-0.2_DT0.02_noiseVENC.yaml', |
||||
'coa3d_bend_f0.5_CT_R1_noslip_plug_h0.025_slices_par_P0_H0.1-0.2_DT0.02_noiseVENC.yaml', |
||||
'coa3d_bend_f0.6_CT_R1_noslip_plug_h0.025_slices_par_P0_H0.1-0.2_DT0.02_noiseVENC.yaml', |
||||
|
||||
|
||||
] |
||||
|
||||
seed = range(11, 51) |
||||
# seed = 2 |
||||
|
||||
path = path_coa3d |
||||
inputfiles = inputfiles_coa3d |
||||
|
||||
# |
||||
if isinstance(seed, range): |
||||
seed = list(seed) |
||||
elif isinstance(seed, int): |
||||
seed = [seed] |
||||
|
||||
assert isinstance(seed, list), ('type(seed) must be list, but is {}'. |
||||
format(type(seed))) |
||||
|
||||
for inpfile in inputfiles: |
||||
try: |
||||
options = inout.read_parameters(path + inpfile) |
||||
except IOError: |
||||
raise IOError('File could not be read: {}'.format(path + inpfile)) |
||||
|
||||
generate(options, seed, False) |
||||
|
||||
copy_inputfile(options, path + inpfile, seed) |
||||
@ -0,0 +1,173 @@
@@ -0,0 +1,173 @@
|
||||
# Set of default parameters for steady Navier-Stokes |
||||
mesh: './meshes/coa3d_bend_Lc2_L6.3_f0.4_d0_ns1_h0.025.h5' |
||||
density: 1.0 |
||||
dynamic_viscosity: 0.035 |
||||
stokes: False |
||||
|
||||
io: |
||||
write_hdf5: False |
||||
write_hdf5_timeseries: False |
||||
write_xdmf: True |
||||
write_path: './projects/DA_testbench/results/coa3d/coa3d_bend_f0.4_CT_R1_noslip_plug_h0.025/' |
||||
restart: |
||||
path: '' # './projects/nse_coa3d/results/test_restart2/' |
||||
time: 0 |
||||
write_checkpoints: True |
||||
write_velocity: 'update' |
||||
log: True |
||||
|
||||
boundary_conditions: |
||||
- id: 1 |
||||
preset: 'sine_parabola_inlet' |
||||
value: |
||||
R: 1.0 |
||||
U: 43.75 |
||||
a: 2.5 |
||||
flow_direction: 0 # (0, 1, 2) |
||||
symmetric: False |
||||
- id: 2 |
||||
preset: 'outlet' |
||||
value: 0. |
||||
- id: 3 |
||||
type: 'dirichlet' |
||||
value: [0, 0, 0] |
||||
|
||||
timemarching: |
||||
velocity_pressure_coupling: 'fractionalstep' # monolithic, fractionalstep |
||||
|
||||
monolithic: |
||||
timescheme: 'gmp' # generalized midpoint, steady FIXME TODO |
||||
theta: 1 # 1: Euler, 2: 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 |
||||
robin_bc_velocity_scheme: 'implicit' # explicit, semi-implicit, implicit |
||||
transpiration_bc_projection: 'robin' # robin, dirichlet |
||||
flux_report_normalize_boundary: 1 |
||||
|
||||
T: 0.4 |
||||
dt: 0.001 |
||||
write_dt: 0.001 |
||||
checkpoint_dt: 0.02 # <= 0: only last; else value + last |
||||
report: 1 # 0: print nothing, 1: print time step and writeout, 2: 1 + flux |
||||
|
||||
estimation: |
||||
boundary_conditions: |
||||
- id: 3 |
||||
type: 'navierslip' |
||||
initial_stddev: 1 |
||||
- id: 3 |
||||
type: 'transpiration' |
||||
initial_stddev: 1 |
||||
measurements: |
||||
# - |
||||
# mesh: './meshes/coa3d_bend_slice_XZ_H0.1.h5' |
||||
# fe_degree: 0 |
||||
# xdmf_file: './projects/DA_testbench/results/coa3d/coa3d_bend_f0.4_CT_R1_noslip_plug_h0.025/measurements/slice_XZ_par_P0_H0.1_DT0.02_noise0/u_meas.xdmf' |
||||
# file_root: './projects/DA_testbench/results/coa3d/coa3d_bend_f0.4_CT_R1_noslip_plug_h0.025/measurements/slice_XZ_par_P0_H0.1_DT0.02_noise0/u{i}.h5' |
||||
# indices: [1, 20, 40, 60, 80, 100, 120, 140, 160, 180, 200, 220, 240, 260, 280, 300, 320, 340, 360, 380, 400] |
||||
# noise_stddev: 0 # standard deviation of Gaussian noise |
||||
# # noise level 48 ==> 15% of max(u) = 320 |
||||
# - |
||||
# mesh: './meshes/coa3d_bend_slice_XZ_H0.2.h5' |
||||
# fe_degree: 0 |
||||
# xdmf_file: './projects/DA_testbench/results/coa3d/coa3d_bend_f0.4_CT_R1_noslip_plug_h0.025/measurements/slice_XZ_par_P0_H0.2_DT0.02_noise0/u_meas.xdmf' |
||||
# file_root: './projects/DA_testbench/results/coa3d/coa3d_bend_f0.4_CT_R1_noslip_plug_h0.025/measurements/slice_XZ_par_P0_H0.2_DT0.02_noise0/u{i}.h5' |
||||
# indices: [1, 20, 40, 60, 80, 100, 120, 140, 160, 180, 200, 220, 240, 260, 280, 300, 320, 340, 360, 380, 400] |
||||
# noise_stddev: 0 # standard deviation of Gaussian noise |
||||
# # noise level 48 ==> 15% of max(u) = 320 |
||||
- |
||||
mesh: './meshes/coa3d_bend_slice_inlet_H0.1.h5' |
||||
fe_degree: 0 |
||||
xdmf_file: './projects/DA_testbench/results/coa3d/coa3d_bend_f0.4_CT_R1_noslip_plug_h0.025/measurements/slice_inlet_par_P0_H0.1_DT0.02_noiseVENC/u_meas.xdmf' |
||||
file_root: './projects/DA_testbench/results/coa3d/coa3d_bend_f0.4_CT_R1_noslip_plug_h0.025/measurements/slice_inlet_par_P0_H0.1_DT0.02_noiseVENC/u{i}.h5' |
||||
indices: [1, 20, 40, 60, 80, 100, 120, 140, 160, 180, 200, 220, 240, 260, 280, 300, 320, 340, 360, 380, 400] |
||||
velocity_direction: [1, 0, 0] |
||||
noise_stddev: 6.5625 # standard deviation of Gaussian noise |
||||
# noise level 48 ==> 15% of max(u) = 320 |
||||
- |
||||
mesh: './meshes/coa3d_bend_slice_inlet_H0.2.h5' |
||||
fe_degree: 0 |
||||
xdmf_file: './projects/DA_testbench/results/coa3d/coa3d_bend_f0.4_CT_R1_noslip_plug_h0.025/measurements/slice_inlet_par_P0_H0.2_DT0.02_noiseVENC/u_meas.xdmf' |
||||
file_root: './projects/DA_testbench/results/coa3d/coa3d_bend_f0.4_CT_R1_noslip_plug_h0.025/measurements/slice_inlet_par_P0_H0.2_DT0.02_noiseVENC/u{i}.h5' |
||||
indices: [1, 20, 40, 60, 80, 100, 120, 140, 160, 180, 200, 220, 240, 260, 280, 300, 320, 340, 360, 380, 400] |
||||
velocity_direction: [1, 0, 0] |
||||
noise_stddev: 6.5625 # standard deviation of Gaussian noise |
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# noise level 48 ==> 15% of max(u) = 320 |
||||
# - |
||||
# mesh: './meshes/coa3d_bend_slice_inclined2_H0.1.h5' |
||||
# fe_degree: 0 |
||||
# xdmf_file: './projects/DA_testbench/results/coa3d/coa3d_bend_f0.4_CT_R1_noslip_plug_h0.025/measurements/slice_inclined2_par_P0_H0.1_DT0.02_noise0/u_meas.xdmf' |
||||
# file_root: './projects/DA_testbench/results/coa3d/coa3d_bend_f0.4_CT_R1_noslip_plug_h0.025/measurements/slice_inclined2_par_P0_H0.1_DT0.02_noise0/u{i}.h5' |
||||
# indices: [1, 20, 40, 60, 80, 100, 120, 140, 160, 180, 200, 220, 240, 260, 280, 300, 320, 340, 360, 380, 400] |
||||
# noise_stddev: 0 # standard deviation of Gaussian noise |
||||
# # noise level 48 ==> 15% of max(u) = 320 |
||||
# - |
||||
# mesh: './meshes/coa3d_bend_slice_inclined2_H0.2.h5' |
||||
# fe_degree: 0 |
||||
# xdmf_file: './projects/DA_testbench/results/coa3d/coa3d_bend_f0.4_CT_R1_noslip_plug_h0.025/measurements/slice_inclined2_par_P0_H0.2_DT0.02_noise0/u_meas.xdmf' |
||||
# file_root: './projects/DA_testbench/results/coa3d/coa3d_bend_f0.4_CT_R1_noslip_plug_h0.025/measurements/slice_inclined2_par_P0_H0.2_DT0.02_noise0/u{i}.h5' |
||||
# indices: [1, 20, 40, 60, 80, 100, 120, 140, 160, 180, 200, 220, 240, 260, 280, 300, 320, 340, 360, 380, 400] |
||||
# noise_stddev: 0 # standard deviation of Gaussian noise |
||||
# # noise level 48 ==> 15% of max(u) = 320 |
||||
- |
||||
mesh: './meshes/coa3d_bend_slice_inclined3_H0.1.h5' |
||||
fe_degree: 0 |
||||
xdmf_file: './projects/DA_testbench/results/coa3d/coa3d_bend_f0.4_CT_R1_noslip_plug_h0.025/measurements/slice_inclined3_par_P0_H0.1_DT0.02_noiseVENC/u_meas.xdmf' |
||||
file_root: './projects/DA_testbench/results/coa3d/coa3d_bend_f0.4_CT_R1_noslip_plug_h0.025/measurements/slice_inclined3_par_P0_H0.1_DT0.02_noiseVENC/u{i}.h5' |
||||
indices: [1, 20, 40, 60, 80, 100, 120, 140, 160, 180, 200, 220, 240, 260, 280, 300, 320, 340, 360, 380, 400] |
||||
velocity_direction: [0.98426389, 0., -0.17670481] |
||||
noise_ | ||||