new figures: paper
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37
kalman/graphics/figure_func.py
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37
kalman/graphics/figure_func.py
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import matplotlib.pyplot as plt
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import numpy as np
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from itertools import cycle
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import argparse
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import pickle
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import yaml
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from matplotlib import rc
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rc('font',**{'family':'sans-serif','sans-serif':['Helvetica']})
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rc('text', usetex=True)
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u = np.linspace(-2,2,100)
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utrue = 1
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venc1 = 0.9*utrue
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venc2 = 0.6*utrue
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fig1, ax1 = plt.subplots(1,1,figsize=(8, 5))
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J1 = 1 - np.cos((utrue-u)/venc1*np.pi)
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J2 = 1 - np.cos((utrue-u)/venc2*np.pi)
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lwidth = 2
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font_size = 28
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ax1.plot(u, J1, color = 'orangered', label = '$venc = 0.9 u_{true}$', linestyle='-',linewidth=lwidth)
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ax1.plot(u, J2, color = 'dodgerblue', label = '$venc = 0.6 u_{true}$', linestyle='-',linewidth=lwidth)
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ax1.axvline(x=1,color = 'black',linewidth = lwidth , label = '$u_{true}$')
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ax1.legend(fontsize=20, loc= 'upper right')
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ax1.tick_params(axis='both', which='major', labelsize=22)
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ax1.set_yticks([])
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ax1.set_xlabel('$u$',fontsize=font_size)
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plt.show()
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fig1.savefig('functionals.png', dpi=500, bbox_inches='tight')
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170
kalman/graphics/figure_func2.py
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kalman/graphics/figure_func2.py
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import matplotlib.pyplot as plt
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import numpy as np
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from itertools import cycle
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import argparse
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import pickle
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import yaml
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from matplotlib import rc
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rc('font',**{'family':'sans-serif','sans-serif':['Helvetica']})
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rc('text', usetex=True)
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fig1, ax1 = plt.subplots(1,1,figsize=(8, 5))
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lwidth = 2
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font_size = 28
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################ Flow Parameters
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Rd = 2.5
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Rt = 0.5
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GradP = 4
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mu = 0.5
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fac = 1
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nr = 50
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VENC = 0.6
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gamma = 267.513e6 # rad/Tesla/sec Gyromagnetic ratio for H nuclei
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Bo = 1.5 # Tesla Magnetic Field Strenght
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TE = 5e-3 # Echo-time
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M = np.ones(nr) # Magnetization
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phi0 = gamma*Bo*TE # Reference phase
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phi02 = phi0%3.14
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M1 = np.pi/(gamma*VENC)
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ff = np.pi/(1000*gamma*M1)
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uv = np.arange(-4*VENC,4*VENC,ff)
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r = np.linspace(-Rd, Rd, nr)
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dr = r[2]-r[1]
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vmax = 1
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v = vmax/Rt**2*( Rt**2 - r**2 )*(np.abs(r)<Rt); # Poiseuille Formula
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ai = v/vmax
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theta = np.linspace(-4,5,2000)
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vtest = np.linspace(-5,5,2000)
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JF = 0*theta
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jv = 0*theta
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JV = 0*theta
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Mjv = np.zeros([len(theta),len(ai)])
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jv0 = 0*theta
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JV0 = 0*theta
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Mjv0 = np.zeros([len(theta),len(ai)])
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#################################### MAGNETIZACION FROM V
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phiv = phi02 + v*np.pi/VENC
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modv = np.ones(phiv.shape)
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M1 = modv*np.cos(phi02) + 1j*modv*np.sin(phi02)
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M2 = modv*np.cos(phiv) + 1j*modv*np.sin(phiv)
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################################### FFT to COMPLEX M
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S1 = np.fft.fft(M1)
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S2 = np.fft.fft(M2)
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################################### SubSampling
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a1 = 0
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a2 = 1
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##### FILLED WITH ZEROS
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US1 = S1
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US2 = 0*S2
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US2[a1::a2] = S2[a1::a2]
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MR1 = np.fft.ifft(US1)
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MR2 = np.fft.ifft(US2)
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vrec1 = (np.angle(MR2)-phi02)*VENC/(np.pi)
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for k in range(len(ai)):
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jv0 = 1-np.cos(np.pi*(vrec1[k]-vtest)/VENC)
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Mjv0[:,k] = jv0[:]
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JV0 = JV0 + jv0
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for k in range(len(ai)):
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jv = 1-np.cos(np.pi*(vrec1[k]-theta*ai[k])/VENC)
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Mjv[:,k] = jv[:]
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JV = JV + jv
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NJV1 = JV*100/np.max(JV)
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MV = Mjv0
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V =NJV1
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left, bottom, width, height = [0.2, 0.2, 0.1, 0.1]
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fig = plt.figure(figsize=(12, 6), dpi=100)
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ax1 = plt.subplot(1,2,1)
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ch1 = 20
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ch2 = 23
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ax0 = fig.add_axes([left, bottom, width, height])
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ax0.plot(r,v,'b-')
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ax0.plot([r[ch1]],[v[ch1]],color='xkcd:coral',marker='o')
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ax0.plot([r[ch2]],[v[ch2]],color='xkcd:azure',marker='o')
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ax0.set_xlim((-1.5,1.5))
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#for k in range(22,39):
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# if k!=ch1 and k!=ch2 and np.sum(MV[:,k])!=0:
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# ax1.plot(vtest, MV[:,k],color='xkcd:beige',alpha=0.8)
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ax1.plot(vtest, MV[:,ch1],color='xkcd:coral',label='$v_1$')
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ax1.plot(vtest, MV[:,ch2],color='xkcd:azure',label='$v_2$')
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m1x = vtest[np.where( np.abs(MV[:,ch1] - np.min(MV[:,ch1]))<0.001 )]
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m1y = np.min(MV[:,ch1])
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m2x = vtest[np.where( np.abs(MV[:,ch2] - np.min(MV[:,ch2]))<0.001 )]
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#m2x = vtest[np.where(MV[:,ch2]==np.min(MV[:,ch2]))]
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m2y = np.min(MV[:,ch2])
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ax1.plot([m1x],[m1y],color='xkcd:coral',marker='o')
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ax1.plot([m2x],[m2y],color='xkcd:azure',marker='o')
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ax1.axvline(x=v[ch1], color='xkcd:coral', linestyle='--',label='$v_{1,true}$')
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ax1.axvline(x=v[ch2], color='xkcd:azure', linestyle='--',label='$v_{2,true}$')
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ax1.set_xlabel(r'$u$',fontsize=20)
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ax1.set_ylabel(r'$J_i(u)$',fontsize=20)
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#ax1.legend(loc='upper right', bbox_to_anchor=(0.5, 1.05),ncol=2, fancybox=True, shadow=True,fontsize=15)
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ax1.set_yticks([])
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ax1.set_xticks([])
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ax1.set_xlim((-3.5,3.5))
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ax1.set_ylim((-1.0,2.4))
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ax2 = plt.subplot(1,2,2)
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ax2.plot(theta,V,'b-')
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ax2.axvline(x=1, color='k', linestyle='--')
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ax2.set_xlabel(r'$\theta$',fontsize=20)
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ax2.set_ylabel(r'$J_T(\theta)$',fontsize=20)
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plt.yticks([])
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ax2.set_xticks([])
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plt.title(r'$\theta_{true}=1$' + '\n' +'$venc < v_{max}$',fontsize=15)
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plt.xlim((-2,3))
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plt.show()
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#ax1.plot(u, J1, color = 'orangered', label = '$venc = 0.9 u_{true}$', linestyle='-',linewidth=lwidth)
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#ax1.plot(u, J2, color = 'dodgerblue', label = '$venc = 0.6 u_{true}$', linestyle='-',linewidth=lwidth)
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#ax1.axvline(x=1,color = 'black',linewidth = lwidth , label = '$u_{true}$')
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ax1.legend(fontsize=20, loc= 'upper right')
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ax1.tick_params(axis='both', which='major', labelsize=22)
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ax1.set_yticks([])
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ax1.set_xlabel('$u$',fontsize=font_size)
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plt.show()
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#fig1.savefig('functionals.png', dpi=500, bbox_inches='tight')
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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: False
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stokes: False
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implicit_windkessel: False
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implicit_windkessel: True
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state_velocity: 'update'
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io:
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io:
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write_path: 'results/expl_1ms'
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write_path: 'results/updRz_Pb_wp0.5wm16.84'
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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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@ -27,8 +28,8 @@ boundary_conditions:
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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 #REFERENCE
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#U: 75 #REFERENCE
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U: 120
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#U: 120
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#U: 150 #Pa/Pb
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U: 150 #Pa/Pb
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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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@ -56,9 +57,9 @@ boundary_conditions:
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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 # REFERENCE
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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: 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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#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: 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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@ -87,9 +88,9 @@ boundary_conditions:
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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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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: 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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@ -118,7 +119,7 @@ timemarching:
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flux_report_normalize_boundary: 1
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flux_report_normalize_boundary: 1
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T: 0.8 # end time
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T: 0.8 # end time
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dt: 0.002
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dt: 0.001
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write_dt: 0.03
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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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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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@ -132,7 +133,7 @@ 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: [3,4,5,6]
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boundaries: [3,4,5,6]
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gamma: 20
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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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@ -159,27 +160,28 @@ estimation:
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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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# mode: 'Rd'
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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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mode: 'RdC'
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mode: 'Rd'
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initial_stddev: 1
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initial_stddev: 0.5
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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: 'RdC'
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mode: 'Rd'
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initial_stddev: 1
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initial_stddev: 0.5
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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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mode: 'RdC'
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mode: 'Rd'
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initial_stddev: 1
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initial_stddev: 0.5
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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: 0.5
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measurements:
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measurements:
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@ -187,13 +189,13 @@ estimation:
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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_dt1ms/Perturbation/Mg15V70/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_dt1ms/Perturbation/Mg15V70/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_exp_dt1ms/u_all.xdmf'
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#xdmf_file: 'measurements/aorta_exp_dt1ms/u_all.xdmf'
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||||||
file_root: 'measurements/aorta_exp_dt1ms/u{i}.h5'
|
#file_root: 'measurements/aorta_exp_dt1ms/u{i}.h5'
|
||||||
indices: 0 # indices of checkpoints to be processed. 0 == all
|
indices: 0 # indices of checkpoints to be processed. 0 == all
|
||||||
velocity_direction: [0,0,1]
|
velocity_direction: [0,0,1]
|
||||||
noise_stddev: 45 # standard deviation of Gaussian noise
|
noise_stddev: 16.84 # standard deviation of Gaussian noise
|
||||||
|
|
||||||
roukf:
|
roukf:
|
||||||
particles: 'simplex' # unique or simplex
|
particles: 'simplex' # unique or simplex
|
||||||
|
|||||||
@ -1,209 +0,0 @@
|
|||||||
|
|
||||||
mesh: './meshes/coaortaH1.h5'
|
|
||||||
# Physical parameters of the fluid
|
|
||||||
fluid:
|
|
||||||
density: 1.2
|
|
||||||
dynamic_viscosity: 0.035
|
|
||||||
stokes: False
|
|
||||||
implicit_windkessel: False
|
|
||||||
|
|
||||||
io:
|
|
||||||
write_path: 'results/exp_0.1ms'
|
|
||||||
restart:
|
|
||||||
path: '' # './projects/nse_coa3d/results/test_restart2/'
|
|
||||||
time: 0
|
|
||||||
write_xdmf: True
|
|
||||||
write_checkpoints: True
|
|
||||||
write_hdf5_timeseries: False
|
|
||||||
write_velocity: 'update' # update or tentative
|
|
||||||
|
|
||||||
boundary_conditions:
|
|
||||||
-
|
|
||||||
id: 2
|
|
||||||
type: 'dirichlet'
|
|
||||||
#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)) +
|
|
||||||
# -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)) +
|
|
||||||
# -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))' ]
|
|
||||||
value: ['0','0','-U*sin(DOLFIN_PI*t/Th)*(t<=Th) + (Th<t)*(U*DOLFIN_PI/Th*(t-Th)*exp(-(t-Th)*beta))']
|
|
||||||
parameters:
|
|
||||||
#U: 75 #REFERENCE 120
|
|
||||||
U: 100
|
|
||||||
#U: 150 #Pa/Pb
|
|
||||||
#U: 40 #Pc
|
|
||||||
Th: 0.36
|
|
||||||
beta: 70
|
|
||||||
t: 0
|
|
||||||
-
|
|
||||||
id: 1
|
|
||||||
type: 'dirichlet'
|
|
||||||
value: ['0','0','0']
|
|
||||||
-
|
|
||||||
id: 3
|
|
||||||
type: 'windkessel'
|
|
||||||
parameters:
|
|
||||||
R_p: 200
|
|
||||||
C: 0.0004
|
|
||||||
R_d: 4800
|
|
||||||
p0: 85
|
|
||||||
conv: 1333.223874
|
|
||||||
-
|
|
||||||
id: 4
|
|
||||||
type: 'windkessel'
|
|
||||||
parameters:
|
|
||||||
#R_p: 480
|
|
||||||
R_p: 480
|
|
||||||
#C: 0.0004 # REFERENCE
|
|
||||||
C: 0.001 # REFERENCE
|
|
||||||
#C: 0.0005 # Pa
|
|
||||||
#C: 0.0010 # Pb
|
|
||||||
#C: 0.0001 # Pc
|
|
||||||
#C: 0.0008 # Pg
|
|
||||||
#R_d: 7200 # REFERENCE
|
|
||||||
R_d: 15000 # REFERENCE
|
|
||||||
#R_d: 8760 #Pa
|
|
||||||
#R_d: 17520 #Pb x2
|
|
||||||
#R_d: 4000 #Pc
|
|
||||||
p0: 85
|
|
||||||
conv: 1333.223874
|
|
||||||
-
|
|
||||||
id: 5
|
|
||||||
type: 'windkessel'
|
|
||||||
parameters:
|
|
||||||
R_p: 520
|
|
||||||
C: 0.0003 # REFERENCE
|
|
||||||
#C: 0.0005 # Pa
|
|
||||||
#C: 0.0010 # Pb
|
|
||||||
#C: 0.0001 # Pc
|
|
||||||
#C: 0.0008 # Pg
|
|
||||||
#R_d: 11520 # REFERENCE
|
|
||||||
R_d: 40000
|
|
||||||
#R_d: 8760 #Pa
|
|
||||||
#R_d: 17520 #Pb x2
|
|
||||||
#R_d: 4000 #Pc
|
|
||||||
p0: 85
|
|
||||||
conv: 1333.223874
|
|
||||||
-
|
|
||||||
id: 6
|
|
||||||
type: 'windkessel'
|
|
||||||
parameters:
|
|
||||||
R_p: 520
|
|
||||||
C: 0.0003 # REFERENCE
|
|
||||||
#C: 0.0005 #Pa
|
|
||||||
#C: 0.0010 #Pb
|
|
||||||
#C: 0.0001 #Pc
|
|
||||||
R_d: 11520 # REFERENCE
|
|
||||||
#R_d: 35000
|
|
||||||
#R_d: 8760 #Pa
|
|
||||||
#R_d: 17520 #Pb x2
|
|
||||||
#R_d: 4000 #Pc
|
|
||||||
p0: 85
|
|
||||||
conv: 1333.223874
|
|
||||||
|
|
||||||
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: 0.0001
|
|
||||||
write_dt: 0.001
|
|
||||||
checkpoint_dt: 0.001 # <= 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: False
|
|
||||||
boundaries: [3,4,5,6]
|
|
||||||
gamma: 20
|
|
||||||
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: 3
|
|
||||||
# type: 'windkessel'
|
|
||||||
# initial_stddev: 1
|
|
||||||
-
|
|
||||||
id: 4
|
|
||||||
type: 'windkessel'
|
|
||||||
mode: 'RdC'
|
|
||||||
initial_stddev: 1
|
|
||||||
-
|
|
||||||
id: 5
|
|
||||||
type: 'windkessel'
|
|
||||||
mode: 'RdC'
|
|
||||||
initial_stddev: 1
|
|
||||||
-
|
|
||||||
id: 6
|
|
||||||
type: 'windkessel'
|
|
||||||
mode: 'RdC'
|
|
||||||
initial_stddev: 1
|
|
||||||
-
|
|
||||||
id: 2
|
|
||||||
type: 'dirichlet'
|
|
||||||
parameters: 'U'
|
|
||||||
initial_stddev: 1
|
|
||||||
|
|
||||||
|
|
||||||
measurements:
|
|
||||||
-
|
|
||||||
mesh: '/home/yeye/NuMRI/kalman/meshes/coaortaH3_leo2.0.h5'
|
|
||||||
#mesh: './meshes/coaortaH1.h5'
|
|
||||||
fe_degree: 1
|
|
||||||
#xdmf_file: 'measurements/aorta_dt1ms/Perturbation/Mg15V70/u_all.xdmf'
|
|
||||||
#file_root: 'measurements/aorta_dt1ms/Perturbation/Mg15V70/u{i}.h5'
|
|
||||||
xdmf_file: 'measurements/aorta_exp_dt1ms/u_all.xdmf'
|
|
||||||
file_root: 'measurements/aorta_exp_dt1ms/u{i}.h5'
|
|
||||||
indices: 0 # indices of checkpoints to be processed. 0 == all
|
|
||||||
velocity_direction: [0,0,1]
|
|
||||||
noise_stddev: 45 # standard deviation of Gaussian noise
|
|
||||||
|
|
||||||
roukf:
|
|
||||||
particles: 'simplex' # unique or simplex
|
|
||||||
observation_operator: 'postprocessing' #state or postprocessing
|
|
||||||
reparameterize: True
|
|
||||||
ODV_functional:
|
|
||||||
enable: False
|
|
||||||
VENC: 138
|
|
||||||
@ -1,209 +0,0 @@
|
|||||||
|
|
||||||
mesh: './meshes/coaortaH1.h5'
|
|
||||||
# Physical parameters of the fluid
|
|
||||||
fluid:
|
|
||||||
density: 1.2
|
|
||||||
dynamic_viscosity: 0.035
|
|
||||||
stokes: False
|
|
||||||
implicit_windkessel: True
|
|
||||||
|
|
||||||
io:
|
|
||||||
write_path: 'results/impl_0.1ms'
|
|
||||||
restart:
|
|
||||||
path: '' # './projects/nse_coa3d/results/test_restart2/'
|
|
||||||
time: 0
|
|
||||||
write_xdmf: True
|
|
||||||
write_checkpoints: True
|
|
||||||
write_hdf5_timeseries: False
|
|
||||||
write_velocity: 'update' # update or tentative
|
|
||||||
|
|
||||||
boundary_conditions:
|
|
||||||
-
|
|
||||||
id: 2
|
|
||||||
type: 'dirichlet'
|
|
||||||
#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)) +
|
|
||||||
# -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)) +
|
|
||||||
# -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))' ]
|
|
||||||
value: ['0','0','-U*sin(DOLFIN_PI*t/Th)*(t<=Th) + (Th<t)*(U*DOLFIN_PI/Th*(t-Th)*exp(-(t-Th)*beta))']
|
|
||||||
parameters:
|
|
||||||
#U: 75 #REFERENCE 120
|
|
||||||
U: 100
|
|
||||||
#U: 150 #Pa/Pb
|
|
||||||
#U: 40 #Pc
|
|
||||||
Th: 0.36
|
|
||||||
beta: 70
|
|
||||||
t: 0
|
|
||||||
-
|
|
||||||
id: 1
|
|
||||||
type: 'dirichlet'
|
|
||||||
value: ['0','0','0']
|
|
||||||
-
|
|
||||||
id: 3
|
|
||||||
type: 'windkessel'
|
|
||||||
parameters:
|
|
||||||
R_p: 200
|
|
||||||
C: 0.0004
|
|
||||||
R_d: 4800
|
|
||||||
p0: 85
|
|
||||||
conv: 1333.223874
|
|
||||||
-
|
|
||||||
id: 4
|
|
||||||
type: 'windkessel'
|
|
||||||
parameters:
|
|
||||||
#R_p: 480
|
|
||||||
R_p: 480
|
|
||||||
#C: 0.0004 # REFERENCE
|
|
||||||
C: 0.001 # REFERENCE
|
|
||||||
#C: 0.0005 # Pa
|
|
||||||
#C: 0.0010 # Pb
|
|
||||||
#C: 0.0001 # Pc
|
|
||||||
#C: 0.0008 # Pg
|
|
||||||
#R_d: 7200 # REFERENCE
|
|
||||||
R_d: 15000 # REFERENCE
|
|
||||||
#R_d: 8760 #Pa
|
|
||||||
#R_d: 17520 #Pb x2
|
|
||||||
#R_d: 4000 #Pc
|
|
||||||
p0: 85
|
|
||||||
conv: 1333.223874
|
|
||||||
-
|
|
||||||
id: 5
|
|
||||||
type: 'windkessel'
|
|
||||||
parameters:
|
|
||||||
R_p: 520
|
|
||||||
C: 0.0003 # REFERENCE
|
|
||||||
#C: 0.0005 # Pa
|
|
||||||
#C: 0.0010 # Pb
|
|
||||||
#C: 0.0001 # Pc
|
|
||||||
#C: 0.0008 # Pg
|
|
||||||
#R_d: 11520 # REFERENCE
|
|
||||||
R_d: 40000
|
|
||||||
#R_d: 8760 #Pa
|
|
||||||
#R_d: 17520 #Pb x2
|
|
||||||
#R_d: 4000 #Pc
|
|
||||||
p0: 85
|
|
||||||
conv: 1333.223874
|
|
||||||
-
|
|
||||||
id: 6
|
|
||||||
type: 'windkessel'
|
|
||||||
parameters:
|
|
||||||
R_p: 520
|
|
||||||
C: 0.0003 # REFERENCE
|
|
||||||
#C: 0.0005 #Pa
|
|
||||||
#C: 0.0010 #Pb
|
|
||||||
#C: 0.0001 #Pc
|
|
||||||
R_d: 11520 # REFERENCE
|
|
||||||
#R_d: 35000
|
|
||||||
#R_d: 8760 #Pa
|
|
||||||
#R_d: 17520 #Pb x2
|
|
||||||
#R_d: 4000 #Pc
|
|
||||||
p0: 85
|
|
||||||
conv: 1333.223874
|
|
||||||
|
|
||||||
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: 0.0001
|
|
||||||
write_dt: 0.001
|
|
||||||
checkpoint_dt: 0.001 # <= 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: False
|
|
||||||
boundaries: [3,4,5,6]
|
|
||||||
gamma: 20
|
|
||||||
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: 3
|
|
||||||
# type: 'windkessel'
|
|
||||||
# initial_stddev: 1
|
|
||||||
-
|
|
||||||
id: 4
|
|
||||||
type: 'windkessel'
|
|
||||||
mode: 'RdC'
|
|
||||||
initial_stddev: 1
|
|
||||||
-
|
|
||||||
id: 5
|
|
||||||
type: 'windkessel'
|
|
||||||
mode: 'RdC'
|
|
||||||
initial_stddev: 1
|
|
||||||
-
|
|
||||||
id: 6
|
|
||||||
type: 'windkessel'
|
|
||||||
mode: 'RdC'
|
|
||||||
initial_stddev: 1
|
|
||||||
-
|
|
||||||
id: 2
|
|
||||||
type: 'dirichlet'
|
|
||||||
parameters: 'U'
|
|
||||||
initial_stddev: 1
|
|
||||||
|
|
||||||
|
|
||||||
measurements:
|
|
||||||
-
|
|
||||||
mesh: '/home/yeye/NuMRI/kalman/meshes/coaortaH3_leo2.0.h5'
|
|
||||||
#mesh: './meshes/coaortaH1.h5'
|
|
||||||
fe_degree: 1
|
|
||||||
#xdmf_file: 'measurements/aorta_dt1ms/Perturbation/Mg15V70/u_all.xdmf'
|
|
||||||
#file_root: 'measurements/aorta_dt1ms/Perturbation/Mg15V70/u{i}.h5'
|
|
||||||
xdmf_file: 'measurements/aorta_exp_dt1ms/u_all.xdmf'
|
|
||||||
file_root: 'measurements/aorta_exp_dt1ms/u{i}.h5'
|
|
||||||
indices: 0 # indices of checkpoints to be processed. 0 == all
|
|
||||||
velocity_direction: [0,0,1]
|
|
||||||
noise_stddev: 45 # standard deviation of Gaussian noise
|
|
||||||
|
|
||||||
roukf:
|
|
||||||
particles: 'simplex' # unique or simplex
|
|
||||||
observation_operator: 'postprocessing' #state or postprocessing
|
|
||||||
reparameterize: True
|
|
||||||
ODV_functional:
|
|
||||||
enable: False
|
|
||||||
VENC: 138
|
|
||||||
Loading…
Reference in New Issue
Block a user