clean up
This commit is contained in:
jeremias
parent
3e67cec21d
commit
ec76080839
@ -52,15 +52,41 @@ def plot_parameters(dat, input_file, deparameterize=False, ref=None):
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inputfile = yaml.full_load(file)
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inputfile = yaml.full_load(file)
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true_values = {
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#true_values = {
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3: 2400,
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# 3: 3400,
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4: 4200,
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# 4: 4200,
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5: 11000,
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# 5: 11000,
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6: 7800,
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# 6: 7800,
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2: 100
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# 2: 100
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}
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# }
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true_values = {
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3: 4800,
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4: 7020,
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5: 11520,
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6: 11520,
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2: 75
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}
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true_values_c = {
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3: 0.0008,
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4: 0.00034,
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5: 0.00034,
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6: 0.00034,
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2: 100
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}
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true_values_rp = {
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3: 10,
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4: 60,
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5: 220,
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6: 160,
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2: 100
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}
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current_val = []
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current_val = []
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labels = []
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labels = []
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ids = []
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ids = []
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@ -75,10 +101,9 @@ def plot_parameters(dat, input_file, deparameterize=False, ref=None):
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labels.append('$R_' + str(bnd_c['id']))
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labels.append('$R_' + str(bnd_c['id']))
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elif 'dirichlet' in bnd_c['type']:
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elif 'dirichlet' in bnd_c['type']:
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current_val.append(inputfile['boundary_conditions'][1]['parameters']['U'])
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current_val.append(inputfile['boundary_conditions'][0]['parameters']['U'])
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ids.append(bnd_c['id'])
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ids.append(bnd_c['id'])
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labels.append('U')
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labels.append('$U')
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dim = dat['theta'].shape[-1]
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dim = dat['theta'].shape[-1]
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fig1, axes = plt.subplots(1,1,figsize=(8,6))
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fig1, axes = plt.subplots(1,1,figsize=(8,6))
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@ -107,10 +132,10 @@ def plot_parameters(dat, input_file, deparameterize=False, ref=None):
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for i in range(dim):
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for i in range(dim):
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true_level = np.log(true_values[ids[i]]/current_val[i])/np.log(2)
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true_level = np.log(true_values[ids[i]]/current_val[i])/np.log(2)
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rec_value = np.round(2**theta[-1, i]*current_val[i],1)
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rec_value = np.round(2**theta[-1, i]*current_val[i],2)
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cur_key = ids[i]
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cur_key = ids[i]
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axes.plot(t, theta[:, i] + 1.5*i, '-', color=col_,label=legends_ + '= ' + str(rec_value) + '/' + str(true_values[cur_key]) + '$')
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axes.plot(t, theta[:, i] + 1.5*i, '-', color=col_,label= legends_ + '= ' + str(rec_value) + '/' + str(true_values[cur_key]) + '$')
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axes.fill_between(t, theta[:, i] + 1.5*i - np.sqrt(P[:, i, i]),
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axes.fill_between(t, theta[:, i] + 1.5*i - np.sqrt(P[:, i, i]),
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theta[:, i] + 1.5*i + np.sqrt(P[:, i, i]), alpha=0.3,
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theta[:, i] + 1.5*i + np.sqrt(P[:, i, i]), alpha=0.3,
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color=col_)
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color=col_)
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@ -4,10 +4,11 @@ mesh: './meshes/coaortaH1.h5'
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fluid:
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fluid:
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density: 1.2
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density: 1.2
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dynamic_viscosity: 0.035
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dynamic_viscosity: 0.035
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stokes: True
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stokes: False
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implicit_windkessel: True
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io:
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io:
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write_path: 'results/aorta_1ms'
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write_path: 'results/aorta25_zPb_3R'
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restart:
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restart:
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path: '' # './projects/nse_coa3d/results/test_restart2/'
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path: '' # './projects/nse_coa3d/results/test_restart2/'
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time: 0
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time: 0
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@ -17,53 +18,67 @@ io:
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write_velocity: 'update' # update or tentative
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write_velocity: 'update' # update or tentative
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boundary_conditions:
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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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#value: ['0','0','-U*sin(DOLFIN_PI*t/Th)*(t<=Th) + (t<0.8)*(Th<t)*(U*DOLFIN_PI/Th*(t-Th)*exp(-(t-Th)*beta)) +
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# -U*sin(DOLFIN_PI*(t-0.8)/Th)*(t<= 0.8+Th )*(t>0.8) + (t<1.6)*(0.8+Th<t)*(U*DOLFIN_PI/Th*(t-0.8-Th)*exp(-(t-0.8-Th)*beta)) +
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# -U*sin(DOLFIN_PI*(t-1.6)/Th)*(t<= 1.6+Th )*(t>1.6) + (t<2.4)*(1.6+Th<t)*(U*DOLFIN_PI/Th*(t-1.6-Th)*exp(-(t-1.6-Th)*beta))' ]
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value: ['0','0','-U*sin(DOLFIN_PI*t/Th)*(t<=Th) + (Th<t)*(U*DOLFIN_PI/Th*(t-Th)*exp(-(t-Th)*beta))']
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parameters:
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#U: 75
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#U: 150 #Pa
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U: 40 #Pb
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Th: 0.36
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beta: 70
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t: 0
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-
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-
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id: 1
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id: 1
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type: 'dirichlet'
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type: 'dirichlet'
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value: ['0','0','0']
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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: 100
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Th: 0.35
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t: 0
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-
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-
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id: 3
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id: 3
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type: 'windkessel'
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type: 'windkessel'
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parameters:
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parameters:
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R_p: 10
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R_p: 200
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C: 0.0008
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C: 0.0005
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R_d: 2400
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#R_d: 4800
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p0: 80
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#R_d: 9000 #Pa
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R_d: 2000 #Pb
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p0: 85
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conv: 1333.223874
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conv: 1333.223874
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-
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-
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id: 4
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id: 4
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type: 'windkessel'
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type: 'windkessel'
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parameters:
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parameters:
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R_p: 60
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R_p: 480
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C: 0.00034
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C: 0.00045
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R_d: 4200
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#R_d: 7200
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p0: 80
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#R_d: 12000 #Pa
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R_d: 4000 #Pb
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p0: 85
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conv: 1333.223874
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conv: 1333.223874
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-
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-
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id: 5
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id: 5
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type: 'windkessel'
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type: 'windkessel'
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parameters:
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parameters:
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R_p: 220
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R_p: 520
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C: 0.00034
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C: 0.00045
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R_d: 11000
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#R_d: 11520
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p0: 80
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#R_d: 23000 #Pa
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R_d: 6000 #Pb
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p0: 85
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conv: 1333.223874
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conv: 1333.223874
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-
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-
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id: 6
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id: 6
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type: 'windkessel'
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type: 'windkessel'
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parameters:
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parameters:
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R_p: 160
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R_p: 520
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C: 0.00034
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C: 0.00045
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R_d: 7800
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R_d: 11520
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p0: 80
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#R_d: 23000 #Pa
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#R_d: 6000 #Pb
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p0: 85
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conv: 1333.223874
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conv: 1333.223874
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timemarching:
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timemarching:
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@ -91,8 +106,8 @@ timemarching:
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T: 0.8 # end time
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T: 0.8 # end time
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dt: 0.001
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dt: 0.001
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write_dt: 0.04
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write_dt: 0.03
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checkpoint_dt: 0.04 # <= 0: only last; else value + last
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checkpoint_dt: 0.03 # <= 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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report: 1 # 0: print nothing, 1: print time step and writeout, 2: 1 + flux
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# solver setup
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# solver setup
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@ -104,9 +119,9 @@ fem:
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convection_skew_symmetric: True # aka Temam term
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convection_skew_symmetric: True # aka Temam term
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stabilization:
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stabilization:
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forced_normal:
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forced_normal:
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enabled: False
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enabled: True
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boundaries: [6]
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boundaries: [3,4,5,6]
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gamma: 10
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gamma: 20
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backflow_boundaries: [3,4,5,6]
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backflow_boundaries: [3,4,5,6]
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streamline_diffusion:
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streamline_diffusion:
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enabled: False
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enabled: False
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@ -128,39 +143,41 @@ linear_solver:
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estimation:
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estimation:
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boundary_conditions:
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boundary_conditions:
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#-
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-
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# id: 3
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id: 3
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# type: 'windkessel'
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type: 'windkessel'
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# initial_stddev: 1
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initial_stddev: 1
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-
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-
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id: 4
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id: 4
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type: 'windkessel'
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type: 'windkessel'
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initial_stddev: 1
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initial_stddev: 1
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#-
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-
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# id: 5
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id: 5
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# type: 'windkessel'
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type: 'windkessel'
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# initial_stddev: 1
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initial_stddev: 1
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#-
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#-
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# id: 6
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# id: 6
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# type: 'windkessel'
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# type: 'windkessel'
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# initial_stddev: 1
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# initial_stddev: 1
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#-
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-
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# id: 2
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id: 2
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# type: 'dirichlet'
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type: 'dirichlet'
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# parameters: 'U'
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parameters: 'U'
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# initial_stddev: 1
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initial_stddev: 1
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measurements:
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measurements:
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-
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-
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#mesh: '/home/yeye/NuMRI/kalman/meshes/coaortaH3_leo2.0.h5'
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mesh: '/home/yeye/NuMRI/kalman/meshes/coaortaH3_leo2.0.h5'
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mesh: './meshes/coaortaH1.h5'
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#mesh: './meshes/coaortaH1.h5'
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fe_degree: 1
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fe_degree: 1
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xdmf_file: 'measurements/aorta/u_all.xdmf'
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xdmf_file: 'measurements/aorta25_z/Perturbation/Mg15V120/u_all.xdmf'
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file_root: 'measurements/aorta/u{i}.h5'
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file_root: 'measurements/aorta25_z/Perturbation/Mg15V120/u{i}.h5'
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#xdmf_file: 'measurements/aorta25_z/u_all.xdmf'
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#file_root: 'measurements/aorta25_z/u{i}.h5'
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indices: 0 # indices of checkpoints to be processed. 0 == all
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indices: 0 # indices of checkpoints to be processed. 0 == all
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velocity_direction: ~
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velocity_direction: [0,0,1]
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noise_stddev: 0 # standard deviation of Gaussian noise
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noise_stddev: 55 # standard deviation of Gaussian noise
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roukf:
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roukf:
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particles: 'simplex' # unique or simplex
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particles: 'simplex' # unique or simplex
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@ -1,150 +0,0 @@
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mesh: './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_leo'
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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','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: [10,0,0]
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p0: [0,1333.223874]
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-
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id: 4
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type: 'windkessel'
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value: [250,0,0]
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p0: [0,1333.223874]
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-
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id: 5
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type: 'windkessel'
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value: [250,0,0]
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p0: [0,1333.223874]
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-
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id: 6
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type: 'windkessel'
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value: [250,0,0]
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p0: [0,1333.223874]
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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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-
|
|
||||||
id: 3
|
|
||||||
type: 'windkessel'
|
|
||||||
initial_stddev: 1
|
|
||||||
-
|
|
||||||
id: 4
|
|
||||||
type: 'windkessel'
|
|
||||||
initial_stddev: 1
|
|
||||||
-
|
|
||||||
id: 5
|
|
||||||
type: 'windkessel'
|
|
||||||
initial_stddev: 1
|
|
||||||
-
|
|
||||||
id: 6
|
|
||||||
type: 'windkessel'
|
|
||||||
initial_stddev: 1
|
|
||||||
-
|
|
||||||
id: 2
|
|
||||||
type: 'dirichlet'
|
|
||||||
parameters: 'U'
|
|
||||||
initial_stddev: 1
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
measurements:
|
|
||||||
-
|
|
||||||
mesh: './meshes/coaortaH3_leo2.0.h5'
|
|
||||||
fe_degree: 1
|
|
||||||
xdmf_file: 'results/aorta_leo/measurements/u_all.xdmf'
|
|
||||||
file_root: 'results/aorta_leo/measurements/u{i}.h5'
|
|
||||||
indices: 0 # indices of checkpoints to be processed. 0 == all
|
|
||||||
velocity_direction: ~
|
|
||||||
noise_stddev: 5 # standard deviation of Gaussian noise
|
|
||||||
|
|
||||||
roukf:
|
|
||||||
particles: 'simplex' # unique or simplex
|
|
||||||
observation_operator: 'postprocessing' #state or postprocessing
|
|
||||||
reparameterize: True
|
|
||||||
@ -1,129 +0,0 @@
|
|||||||
|
|
||||||
mesh: './meshes/coaortaH1.h5'
|
|
||||||
# Physical parameters of the fluid
|
|
||||||
fluid:
|
|
||||||
density: 1.2
|
|
||||||
dynamic_viscosity: 0.035
|
|
||||||
|
|
||||||
io:
|
|
||||||
write_path: 'results/aorta/'
|
|
||||||
restart:
|
|
||||||
path: '' # './projects/nse_coa3d/results/test_restart2/'
|
|
||||||
time: 0
|
|
||||||
write_xdmf: True
|
|
||||||
write_checkpoints: True
|
|
||||||
write_hdf5_timeseries: False
|
|
||||||
write_velocity: 'update' # tentative
|
|
||||||
|
|
||||||
boundary_conditions:
|
|
||||||
-
|
|
||||||
id: 1
|
|
||||||
type: 'dirichlet'
|
|
||||||
value: ['0','0','0']
|
|
||||||
-
|
|
||||||
id: 2
|
|
||||||
type: 'dirichlet'
|
|
||||||
value: ['0','0','-U*sin(DOLFIN_PI*t/Th)*(t<=Th) + (Th<t)*(-3.67949466208*U*sin(9*DOLFIN_PI*t/Th)*exp(-t*10))']
|
|
||||||
parameters:
|
|
||||||
U: 30
|
|
||||||
Th: 0.35
|
|
||||||
t: 0
|
|
||||||
-
|
|
||||||
id: 3
|
|
||||||
type: 'neumann'
|
|
||||||
value: 0
|
|
||||||
-
|
|
||||||
id: 4
|
|
||||||
type: 'neumann'
|
|
||||||
value: 0
|
|
||||||
-
|
|
||||||
id: 5
|
|
||||||
type: 'neumann'
|
|
||||||
value: 0
|
|
||||||
-
|
|
||||||
id: 6
|
|
||||||
type: 'neumann'
|
|
||||||
value: 0
|
|
||||||
|
|
||||||
timemarching:
|
|
||||||
velocity_pressure_coupling: 'fractionalstep' # monolithic, fractionalstep
|
|
||||||
|
|
||||||
monolithic:
|
|
||||||
timescheme: 'gmp' # generalized midpoint, steady FIXME TODO
|
|
||||||
theta: 1 # 1: Euler, 0.5: implicit midpoint rule (one-legged)
|
|
||||||
nonlinear:
|
|
||||||
method: 'constant_extrapolation' # constant_extrapolation, linear_extrapolation, newton, picard, snes
|
|
||||||
maxit: 20
|
|
||||||
init_steps: 30
|
|
||||||
use_aitken: 1 # 0: False, 1: Picard only, 2: all
|
|
||||||
report: 1 # 0: None, 1: residuals, 2: residuals and energy (inflow/driving/forcing via ESSENTIAL Dbcs!)
|
|
||||||
atol: 1.e-6 # note: dot required!!
|
|
||||||
rtol: 1.e-16
|
|
||||||
stol: 0.0
|
|
||||||
|
|
||||||
fractionalstep:
|
|
||||||
scheme: 'CT' # CT, IPCS
|
|
||||||
coupled_velocity: False # False faster, True needed if robin_bc implicit
|
|
||||||
robin_bc_velocity_scheme: 'implicit' # explicit, semi-implicit, implicit
|
|
||||||
transpiration_bc_projection: 'robin' # robin, dirichlet
|
|
||||||
flux_report_normalize_boundary: 1
|
|
||||||
|
|
||||||
T: 0.8 # end time
|
|
||||||
dt: 0.01
|
|
||||||
write_dt: 0.04
|
|
||||||
checkpoint_dt: 0.04 # <= 0: only last; else value + last
|
|
||||||
report: 1 # 0: print nothing, 1: print time step and writeout, 2: 1 + flux
|
|
||||||
|
|
||||||
# solver setup
|
|
||||||
fem:
|
|
||||||
velocity_space: p1 # p1 p1b/p1+ p2
|
|
||||||
pressure_space: p1 # p1 p0/dg0 dg1
|
|
||||||
|
|
||||||
strain_symmetric: False
|
|
||||||
convection_skew_symmetric: True # aka Temam term
|
|
||||||
stabilization:
|
|
||||||
forced_normal:
|
|
||||||
enabled: True
|
|
||||||
boundaries: [6]
|
|
||||||
gamma: 10
|
|
||||||
backflow_boundaries: [3,4,5,6]
|
|
||||||
streamline_diffusion:
|
|
||||||
enabled: False
|
|
||||||
parameter: 'standard' # standard, shakib, codina, klr
|
|
||||||
length_scale: 'metric' # average, max, metric
|
|
||||||
parameter_element_constant: True
|
|
||||||
Cinv: ~
|
|
||||||
monolithic:
|
|
||||||
infsup: 'pspg' # pspg, pressure-stabilization
|
|
||||||
graddiv: False
|
|
||||||
consistent: False
|
|
||||||
pressure_stab_constant: 1.
|
|
||||||
|
|
||||||
fix_pressure: False
|
|
||||||
fix_pressure_point: [0., 0. , 0.]
|
|
||||||
|
|
||||||
linear_solver:
|
|
||||||
method: 'lu'
|
|
||||||
|
|
||||||
estimation:
|
|
||||||
boundary_conditions:
|
|
||||||
-
|
|
||||||
id: 2
|
|
||||||
type: 'dirichlet'
|
|
||||||
parameters: 'U'
|
|
||||||
initial_stddev: 1
|
|
||||||
|
|
||||||
measurements:
|
|
||||||
-
|
|
||||||
mesh: './meshes/coaortaH1.h5'
|
|
||||||
fe_degree: 1
|
|
||||||
xdmf_file: 'results/aorta/measurements/u_all.xdmf'
|
|
||||||
file_root: 'results/aorta/measurements/u{i}.h5'
|
|
||||||
indices: 0 # indices of checkpoints to be processed. 0 == all
|
|
||||||
velocity_direction: ~
|
|
||||||
noise_stddev: 1.5 # standard deviation of Gaussian noise
|
|
||||||
|
|
||||||
roukf:
|
|
||||||
particles: 'simplex' # unique or simplex
|
|
||||||
observation_operator: 'postprocessing' #state or postprocessing
|
|
||||||
reparameterize: True
|
|
||||||
Loading…
Reference in New Issue
Block a user