s
This commit is contained in:
jeremias
parent
b75e5995e0
commit
6e8598b897
@ -76,10 +76,13 @@ def plot_parameters(dat, input_file, deparameterize=False, ref=None):
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}
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}
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dim = dat['theta'].shape[-1]
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meas_flag = False
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meas_flag = False
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RC_flag = False
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if dim==7:
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RC_flag = True
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else:
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RC_flag = False
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line_split = 1.5
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line_split = 1.5
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current_val = []
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current_val = []
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current_val_C = []
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current_val_C = []
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@ -110,7 +113,6 @@ def plot_parameters(dat, input_file, deparameterize=False, ref=None):
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dim = dat['theta'].shape[-1]
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fig1, axes1 = plt.subplots(1,1,figsize=(12,6))
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fig1, axes1 = plt.subplots(1,1,figsize=(12,6))
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if RC_flag:
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if RC_flag:
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fig2, axes2 = plt.subplots(1,1,figsize=(12,6))
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fig2, axes2 = plt.subplots(1,1,figsize=(12,6))
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@ -200,6 +202,7 @@ def plot_parameters(dat, input_file, deparameterize=False, ref=None):
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axes1.set_ylabel(r'$R_d$',fontsize=22)
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axes1.set_ylabel(r'$R_d$',fontsize=22)
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axes1.legend(fontsize=18,loc='upper right')
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axes1.legend(fontsize=18,loc='upper right')
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axes1.set_xlim([-0.01,0.81])
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axes1.set_xlim([-0.01,0.81])
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axes1.set_ylim([1700,35000])
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axes1.set_xlabel(r'$t (s)$',fontsize=22)
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axes1.set_xlabel(r'$t (s)$',fontsize=22)
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plt.savefig('C.png')
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plt.savefig('C.png')
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@ -8,7 +8,7 @@ fluid:
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implicit_windkessel: True
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implicit_windkessel: True
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io:
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io:
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write_path: 'results/Rz_Pa_vnoise'
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write_path: 'results/Rz_Pc7'
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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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@ -26,10 +26,9 @@ boundary_conditions:
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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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# -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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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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parameters:
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#U: 75 #P0
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#U: 75 #REFERENCE
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U: 150 #Pa
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#U: 150 #Pa
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#U: 100 #Pg
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U: 40 #Pc
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#U: 40 #Pc
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Th: 0.36
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Th: 0.36
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beta: 70
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beta: 70
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t: 0
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t: 0
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@ -51,16 +50,15 @@ boundary_conditions:
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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: 480
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R_p: 480
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#C: 0.0004 # P0
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C: 0.0004 # REFERENCE
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C: 0.0005 # Pa
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#C: 0.0005 # Pa
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#C: 0.0010 # Pb
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#C: 0.0010 # Pb
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#C: 0.0001 # Pc
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#C: 0.0001 # Pc
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#C: 0.0008 # Pg
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#C: 0.0008 # Pg
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#R_d: 7200 #P0
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#R_d: 7200 # REFERENCE
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R_d: 8760 #Pa
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#R_d: 8760 #Pa
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#R_d: 17520 #Pb x2
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#R_d: 17520 #Pb x2
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#R_d: 10000 #Pg
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R_d: 4000 #Pc
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#R_d: 4000 #Pc
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p0: 85
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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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@ -68,17 +66,15 @@ boundary_conditions:
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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: 520
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R_p: 520
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#C: 0.0003 # REFERENCE
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C: 0.0003 # REFERENCE
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C: 0.0005 # Pa
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#C: 0.0005 # Pa
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#C: 0.0010 # Pb
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#C: 0.0010 # Pb
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#C: 0.0001 # Pc
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#C: 0.0001 # Pc
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#C: 0.0008 # Pg
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#C: 0.0008 # Pg
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#R_d: 11520 # REFERENCE
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#R_d: 11520 # REFERENCE
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R_d: 8760 #Pa
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#R_d: 8760 #Pa
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#R_d: 17520 #Pb x2
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#R_d: 17520 #Pb x2
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#R_d: 26280 #Pc x3
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R_d: 4000 #Pc
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#R_d: 10000 #Pg
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#R_d: 4000 #Pc
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p0: 85
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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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@ -86,17 +82,14 @@ boundary_conditions:
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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: 520
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R_p: 520
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#C: 0.0003 # REFERENCE
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C: 0.0003 # REFERENCE
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C: 0.0005 #Pa
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#C: 0.0005 #Pa
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#C: 0.0010 #Pb
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#C: 0.0010 #Pb
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#C: 0.0001 #Pc
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#C: 0.0001 #Pc
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#C: 0.0008 #Pg
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#R_d: 11520 # REFERENCE
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#R_d: 11520 # REFERENCE
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R_d: 8760 #Pa
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#R_d: 8760 #Pa
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#R_d: 17520 #Pb x2
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#R_d: 17520 #Pb x2
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#R_d: 26280 #Pc x3
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R_d: 4000 #Pc
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#R_d: 10000 #Pg
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#R_d: 4000 #Pc
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p0: 85
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p0: 85
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conv: 1333.223874
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conv: 1333.223874
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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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mode: 'Rd'
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mode: 'Rd'
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initial_stddev: 1
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initial_stddev: 2
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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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mode: 'Rd'
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mode: 'Rd'
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initial_stddev: 1
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initial_stddev: 2
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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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mode: 'Rd'
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mode: 'Rd'
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initial_stddev: 1
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initial_stddev: 2
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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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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_zdir/Perturbation/Mg15V120/u_all.xdmf'
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xdmf_file: 'measurements/aorta_zdir/Perturbation/Mg15V120/u_all.xdmf'
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#file_root: 'measurements/aorta_zdir/Perturbation/Mg15V120/u{i}.h5'
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file_root: 'measurements/aorta_zdir/Perturbation/Mg15V120/u{i}.h5'
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xdmf_file: 'measurements/aorta_zdir_vnoise/u_all.xdmf'
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#xdmf_file: 'measurements/aorta_zdir_NV/u_all.xdmf'
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file_root: 'measurements/aorta_zdir_vnoise/u{i}.h5'
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#file_root: 'measurements/aorta_zdir_NV/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: [0,0,1]
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velocity_direction: [0,0,1]
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noise_stddev: 45 # standard deviation of Gaussian noise
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noise_stddev: 25 # 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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178
kalman/input_files/aorta_reference.yaml
Executable file
178
kalman/input_files/aorta_reference.yaml
Executable file
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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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stokes: False
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implicit_windkessel: True
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io:
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write_path: 'results/aortaRR_Pa'
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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: 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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Th: 0.36
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beta: 70
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t: 0
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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: 3
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type: 'windkessel'
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parameters:
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R_p: 200
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C: 0.0005
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R_d: 4800
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p0: 85
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conv: 1333.223874
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-
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id: 4
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type: 'windkessel'
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parameters:
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R_p: 480
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C: 0.00045
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R_d: 7200
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p0: 85
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conv: 1333.223874
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-
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id: 5
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type: 'windkessel'
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parameters:
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R_p: 520
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C: 0.00045
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R_d: 11520
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p0: 85
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conv: 1333.223874
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-
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id: 6
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type: 'windkessel'
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parameters:
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R_p: 520
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C: 0.00045
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R_d: 11520
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p0: 85
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conv: 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: 0.001
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write_dt: 0.03
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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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# 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: [3,4,5,6]
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gamma: 20
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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: 3
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# type: 'windkessel'
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# initial_stddev: 1
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-
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id: 4
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type: 'windkessel'
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initial_stddev: 1
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-
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id: 5
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type: 'windkessel'
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initial_stddev: 1
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-
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id: 6
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type: 'windkessel'
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initial_stddev: 1
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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/NuMRI/kalman/meshes/coaortaH3_leo2.0.h5'
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#mesh: './meshes/coaortaH1.h5'
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fe_degree: 1
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xdmf_file: 'measurements/aortaRR/Perturbation/Mg15V120/u_all.xdmf'
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file_root: 'measurements/aortaRR/Perturbation/Mg15V120/u{i}.h5'
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#xdmf_file: 'measurements/aortaRR/u_all.xdmf'
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#file_root: 'measurements/aortaRR/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: 55 # 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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ODV_functional:
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enable: False
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VENC: 102 # 102,120% 59,70% 42 50%, 21,25%
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