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new figures: paper

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J.E. Garay Labra 2021-07-09 15:22:23 +02:00
parent 056b2e8a14
commit 8817ed4b4c
5 changed files with 233 additions and 442 deletions
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37
kalman/graphics/figure_func.py Normal file
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@ -0,0 +1,37 @@
import matplotlib.pyplot as plt
import numpy as np
from itertools import cycle
import argparse
import pickle
import yaml
from matplotlib import rc
rc('font',**{'family':'sans-serif','sans-serif':['Helvetica']})
rc('text', usetex=True)
u = np.linspace(-2,2,100)
utrue = 1
venc1 = 0.9*utrue
venc2 = 0.6*utrue
fig1, ax1 = plt.subplots(1,1,figsize=(8, 5))
J1 = 1 - np.cos((utrue-u)/venc1*np.pi)
J2 = 1 - np.cos((utrue-u)/venc2*np.pi)
lwidth = 2
font_size = 28
ax1.plot(u, J1, color = 'orangered', label = '$venc = 0.9 u_{true}$', linestyle='-',linewidth=lwidth)
ax1.plot(u, J2, color = 'dodgerblue', label = '$venc = 0.6 u_{true}$', linestyle='-',linewidth=lwidth)
ax1.axvline(x=1,color = 'black',linewidth = lwidth , label = '$u_{true}$')
ax1.legend(fontsize=20, loc= 'upper right')
ax1.tick_params(axis='both', which='major', labelsize=22)
ax1.set_yticks([])
ax1.set_xlabel('$u$',fontsize=font_size)
plt.show()
fig1.savefig('functionals.png', dpi=500, bbox_inches='tight')

170
kalman/graphics/figure_func2.py Normal file
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@ -0,0 +1,170 @@
import matplotlib.pyplot as plt
import numpy as np
from itertools import cycle
import argparse
import pickle
import yaml
from matplotlib import rc
rc('font',**{'family':'sans-serif','sans-serif':['Helvetica']})
rc('text', usetex=True)
fig1, ax1 = plt.subplots(1,1,figsize=(8, 5))
lwidth = 2
font_size = 28
################ Flow Parameters
Rd = 2.5
Rt = 0.5
GradP = 4
mu = 0.5
fac = 1
nr = 50
VENC = 0.6
gamma = 267.513e6 # rad/Tesla/sec Gyromagnetic ratio for H nuclei
Bo = 1.5 # Tesla Magnetic Field Strenght
TE = 5e-3 # Echo-time
M = np.ones(nr) # Magnetization
phi0 = gamma*Bo*TE # Reference phase
phi02 = phi0%3.14
M1 = np.pi/(gamma*VENC)
ff = np.pi/(1000*gamma*M1)
uv = np.arange(-4*VENC,4*VENC,ff)
r = np.linspace(-Rd, Rd, nr)
dr = r[2]-r[1]
vmax = 1
v = vmax/Rt**2*( Rt**2 - r**2 )*(np.abs(r)<Rt); # Poiseuille Formula
ai = v/vmax
theta = np.linspace(-4,5,2000)
vtest = np.linspace(-5,5,2000)
JF = 0*theta
jv = 0*theta
JV = 0*theta
Mjv = np.zeros([len(theta),len(ai)])
jv0 = 0*theta
JV0 = 0*theta
Mjv0 = np.zeros([len(theta),len(ai)])
#################################### MAGNETIZACION FROM V
phiv = phi02 + v*np.pi/VENC
modv = np.ones(phiv.shape)
M1 = modv*np.cos(phi02) + 1j*modv*np.sin(phi02)
M2 = modv*np.cos(phiv) + 1j*modv*np.sin(phiv)
################################### FFT to COMPLEX M
S1 = np.fft.fft(M1)
S2 = np.fft.fft(M2)
################################### SubSampling
a1 = 0
a2 = 1
##### FILLED WITH ZEROS
US1 = S1
US2 = 0*S2
US2[a1::a2] = S2[a1::a2]
MR1 = np.fft.ifft(US1)
MR2 = np.fft.ifft(US2)
vrec1 = (np.angle(MR2)-phi02)*VENC/(np.pi)
for k in range(len(ai)):
jv0 = 1-np.cos(np.pi*(vrec1[k]-vtest)/VENC)
Mjv0[:,k] = jv0[:]
JV0 = JV0 + jv0
for k in range(len(ai)):
jv = 1-np.cos(np.pi*(vrec1[k]-theta*ai[k])/VENC)
Mjv[:,k] = jv[:]
JV = JV + jv
NJV1 = JV*100/np.max(JV)
MV = Mjv0
V =NJV1
left, bottom, width, height = [0.2, 0.2, 0.1, 0.1]
fig = plt.figure(figsize=(12, 6), dpi=100)
ax1 = plt.subplot(1,2,1)
ch1 = 20
ch2 = 23
ax0 = fig.add_axes([left, bottom, width, height])
ax0.plot(r,v,'b-')
ax0.plot([r[ch1]],[v[ch1]],color='xkcd:coral',marker='o')
ax0.plot([r[ch2]],[v[ch2]],color='xkcd:azure',marker='o')
ax0.set_xlim((-1.5,1.5))
#for k in range(22,39):
# if k!=ch1 and k!=ch2 and np.sum(MV[:,k])!=0:
# ax1.plot(vtest, MV[:,k],color='xkcd:beige',alpha=0.8)
ax1.plot(vtest, MV[:,ch1],color='xkcd:coral',label='$v_1$')
ax1.plot(vtest, MV[:,ch2],color='xkcd:azure',label='$v_2$')
m1x = vtest[np.where( np.abs(MV[:,ch1] - np.min(MV[:,ch1]))<0.001 )]
m1y = np.min(MV[:,ch1])
m2x = vtest[np.where( np.abs(MV[:,ch2] - np.min(MV[:,ch2]))<0.001 )]
#m2x = vtest[np.where(MV[:,ch2]==np.min(MV[:,ch2]))]
m2y = np.min(MV[:,ch2])
ax1.plot([m1x],[m1y],color='xkcd:coral',marker='o')
ax1.plot([m2x],[m2y],color='xkcd:azure',marker='o')
ax1.axvline(x=v[ch1], color='xkcd:coral', linestyle='--',label='$v_{1,true}$')
ax1.axvline(x=v[ch2], color='xkcd:azure', linestyle='--',label='$v_{2,true}$')
ax1.set_xlabel(r'$u$',fontsize=20)
ax1.set_ylabel(r'$J_i(u)$',fontsize=20)
#ax1.legend(loc='upper right', bbox_to_anchor=(0.5, 1.05),ncol=2, fancybox=True, shadow=True,fontsize=15)
ax1.set_yticks([])
ax1.set_xticks([])
ax1.set_xlim((-3.5,3.5))
ax1.set_ylim((-1.0,2.4))
ax2 = plt.subplot(1,2,2)
ax2.plot(theta,V,'b-')
ax2.axvline(x=1, color='k', linestyle='--')
ax2.set_xlabel(r'$\theta$',fontsize=20)
ax2.set_ylabel(r'$J_T(\theta)$',fontsize=20)
plt.yticks([])
ax2.set_xticks([])
plt.title(r'$\theta_{true}=1$' + '\n' +'$venc < v_{max}$',fontsize=15)
plt.xlim((-2,3))
plt.show()
#ax1.plot(u, J1, color = 'orangered', label = '$venc = 0.9 u_{true}$', linestyle='-',linewidth=lwidth)
#ax1.plot(u, J2, color = 'dodgerblue', label = '$venc = 0.6 u_{true}$', linestyle='-',linewidth=lwidth)
#ax1.axvline(x=1,color = 'black',linewidth = lwidth , label = '$u_{true}$')
ax1.legend(fontsize=20, loc= 'upper right')
ax1.tick_params(axis='both', which='major', labelsize=22)
ax1.set_yticks([])
ax1.set_xlabel('$u$',fontsize=font_size)
plt.show()
#fig1.savefig('functionals.png', dpi=500, bbox_inches='tight')

50
kalman/input_files/aorta.yaml
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@ -5,10 +5,11 @@ fluid:
density: 1.2
dynamic_viscosity: 0.035
stokes: False
implicit_windkessel: False
implicit_windkessel: True
state_velocity: 'update'
io:
write_path: 'results/expl_1ms'
write_path: 'results/updRz_Pb_wp0.5wm16.84'
restart:
path: '' # './projects/nse_coa3d/results/test_restart2/'
time: 0
@ -27,8 +28,8 @@ boundary_conditions:
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
U: 120
#U: 150 #Pa/Pb
#U: 120
U: 150 #Pa/Pb
#U: 40 #Pc
Th: 0.36
beta: 70
@ -56,9 +57,9 @@ boundary_conditions:
#C: 0.0010 # Pb
#C: 0.0001 # Pc
#C: 0.0008 # Pg
R_d: 7200 # REFERENCE
#R_d: 7200 # REFERENCE
#R_d: 8760 #Pa
#R_d: 17520 #Pb x2
R_d: 17520 #Pb x2
#R_d: 4000 #Pc
p0: 85
conv: 1333.223874
@ -72,9 +73,9 @@ boundary_conditions:
#C: 0.0010 # Pb
#C: 0.0001 # Pc
#C: 0.0008 # Pg
R_d: 11520 # REFERENCE
#R_d: 11520 # REFERENCE
#R_d: 8760 #Pa
#R_d: 17520 #Pb x2
R_d: 17520 #Pb x2
#R_d: 4000 #Pc
p0: 85
conv: 1333.223874
@ -87,9 +88,9 @@ boundary_conditions:
#C: 0.0005 #Pa
#C: 0.0010 #Pb
#C: 0.0001 #Pc
R_d: 11520 # REFERENCE
#R_d: 11520 # REFERENCE
#R_d: 8760 #Pa
#R_d: 17520 #Pb x2
R_d: 17520 #Pb x2
#R_d: 4000 #Pc
p0: 85
conv: 1333.223874
@ -118,7 +119,7 @@ timemarching:
flux_report_normalize_boundary: 1
T: 0.8 # end time
dt: 0.002
dt: 0.001
write_dt: 0.03
checkpoint_dt: 0.03 # <= 0: only last; else value + last
report: 1 # 0: print nothing, 1: print time step and writeout, 2: 1 + flux
@ -132,7 +133,7 @@ fem:
convection_skew_symmetric: True # aka Temam term
stabilization:
forced_normal:
enabled: False
enabled: True
boundaries: [3,4,5,6]
gamma: 20
backflow_boundaries: [3,4,5,6]
@ -159,27 +160,28 @@ estimation:
#-
# id: 3
# type: 'windkessel'
# mode: 'Rd'
# initial_stddev: 1
-
id: 4
type: 'windkessel'
mode: 'RdC'
initial_stddev: 1
mode: 'Rd'
initial_stddev: 0.5
-
id: 5
type: 'windkessel'
mode: 'RdC'
initial_stddev: 1
mode: 'Rd'
initial_stddev: 0.5
-
id: 6
type: 'windkessel'
mode: 'RdC'
initial_stddev: 1
mode: 'Rd'
initial_stddev: 0.5
-
id: 2
type: 'dirichlet'
parameters: 'U'
initial_stddev: 1
initial_stddev: 0.5
measurements:
@ -187,13 +189,13 @@ estimation:
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'
xdmf_file: 'measurements/aorta_zdir/Perturbation/Mg15V120/u_all.xdmf'
file_root: 'measurements/aorta_zdir/Perturbation/Mg15V120/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
noise_stddev: 16.84 # standard deviation of Gaussian noise
roukf:
particles: 'simplex' # unique or simplex

209
kalman/input_files/aorta_old.yaml
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@ -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

209
kalman/input_files/aorta_old2.yaml
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@ -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