adding kalman
This commit is contained in:
parent
8196e39547
commit
ccf35cea16
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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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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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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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timemarching:
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velocity_pressure_coupling: 'fractionalstep' # monolithic, fractionalstep
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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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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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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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# 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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fix_pressure: False
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fix_pressure_point: [0., 0. , 0.]
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linear_solver:
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method: 'lu'
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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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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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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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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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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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# 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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timemarching:
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velocity_pressure_coupling: 'fractionalstep' # monolithic, fractionalstep
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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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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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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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# 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: 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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fix_pressure: False
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fix_pressure_point: [0., 0.]
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linear_solver:
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method: 'lu'
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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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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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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 @@
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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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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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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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# 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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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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timemarching:
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velocity_pressure_coupling: 'fractionalstep' # monolithic, fractionalstep
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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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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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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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# 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: 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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fix_pressure: False
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fix_pressure_point: [0., 0. , 0.]
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linear_solver:
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method: 'lu'
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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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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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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 @@
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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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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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def find_checkpoints(options, path_checkpoint):
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indices = options['estimation']['measurements'][0]['indices']
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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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# 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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else:
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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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# 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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# 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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dt = options['timemarching']['dt']
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times = dt*np.array(indices)
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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)
|
||||
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 get_h5_fun_name(file):
|
||||
if 'X0.h5' in file:
|
||||
fun = '/X'
|
||||
else:
|
||||
fun = '/u'
|
||||
|
||||
return fun
|
||||
|
||||
|
||||
def filter_indices(ind1, ind2, files1, files2):
|
||||
''' Filter indices and files such that only maching files and indicies
|
||||
remain.
|
||||
|
||||
Args:
|
||||
ind1 (list): list of indices of dataset 1
|
||||
ind2 (list): list of indices of dataset 2
|
||||
files1 (list): list of files of dataset 1
|
||||
files2 (list): list of files of dataset 2
|
||||
'''
|
||||
ind = []
|
||||
files_filt1 = []
|
||||
files_filt2 = []
|
||||
for i in ind1:
|
||||
if i in ind2:
|
||||
ind.append(i)
|
||||
files_filt1.append(files1[list(ind1).index(i)])
|
||||
files_filt2.append(files2[list(ind2).index(i)])
|
||||
|
||||
return ind, files_filt1, files_filt2
|
||||
|
||||
|
||||
def compute_errors(inputfile, path_checkpoint_1,
|
||||
path_checkpoint_2, relative=False):
|
||||
|
||||
options = inout.read_parameters(inputfile)
|
||||
|
||||
indices1, times1, files1 = find_checkpoints(options, path_checkpoint_1)
|
||||
indices2, times2, files2 = find_checkpoints(options, path_checkpoint_2)
|
||||
|
||||
indices, files1, files2 = filter_indices(indices1, indices2, files1,
|
||||
files2)
|
||||
|
||||
fun1 = get_h5_fun_name(files1[0])
|
||||
fun2 = get_h5_fun_name(files2[0])
|
||||
|
||||
# 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 @@
|
|||
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)
|
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
|
@ -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 @@
|
|||
# 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
|
||||
# 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_stddev: 21 # standard deviation of Gaussian noise
|
||||
# noise level 48 ==> 15% of max(u) = 320
|
||||
-
|
||||
mesh: './meshes/coa3d_bend_slice_inclined3_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_inclined3_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_inclined3_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: [0.98426389, 0., -0.17670481]
|
||||
noise_stddev: 21 # standard deviation of Gaussian noise
|
||||
# noise level 48 ==> 15% of max(u) = 320
|
||||
roukf:
|
||||
particles: 'simplex'
|
||||
observation_operator: 'postprocessing'
|
||||
reparameterize: True
|
||||
|
||||
# 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:
|
||||
backflow_boundaries: [2]
|
||||
streamline_diffusion:
|
||||
enabled: True
|
||||
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.]
|
||||
|
||||
linear_solver:
|
||||
method: 'default'
|
||||
# inputfile: './projects/nse_coa3d/input/pc/MUMPS_default.yaml'
|
||||
# inputfile: './input/pc/fgmres_gamg_rtol1e-6.yaml'
|
|
@ -0,0 +1,376 @@
|
|||
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
|
||||
|
||||
from mpi4py import MPI
|
||||
comm = MPI.COMM_WORLD
|
||||
size = comm.Get_size()
|
||||
rank = comm.Get_rank()
|
||||
|
||||
|
||||
def solution_function_space(options):
|
||||
mesh, _, _ = inout.read_mesh(options['mesh'])
|
||||
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()))
|
||||
|
||||
V = FunctionSpace(mesh, Evel)
|
||||
|
||||
return V
|
||||
|
||||
|
||||
def measurement_function_spaces(options):
|
||||
|
||||
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']
|
||||