def data_assimilation(opal_options):
global Model_updated, iter_count
# functions used within data_assimilation: J() and gradJ()
def J(v):
global Model_updated, iter_count
iter_count = iter_count + 1
vT = np.transpose(v)
vTv = np.dot(vT,v)
Vv = np.dot(V,v)
HVv = np.dot(H,Vv)
# we need the model results - check if these are already available, if not, run the forward model with Vv as the input
if Model_updated:
print "in J(): using pre-exiting forward model model solution"
Model_updated = False
else:
print "in J(): updating the forward model solution"
# prepare directory and input files for forward model
input_file_name = prepare_inputs_for_forward_model(k)
# modify initial condition of tracer
field = modify_initial_conditions_at_tk(k,Vv)
# run forward model
run_forward_model_tk(k,opal_options.executable,input_file_name)
Model_updated = True
# retrieve the forward model results, MVv
path_to_vtu_file = str(k) + '/2d_canyon_1.vtu'
vtu_data = vtktools.vtu(path_to_vtu_file)
MVv = vtu_data.GetScalarField(field)
# print "J(): MVv[0:10]", MVv[0:10]
##MVv = np.dot(M,Vv)
HMVv = np.dot(H,MVv)
Jmis = np.subtract(HVv,d)
JmisM = np.subtract(HMVv,d)
invR = np.linalg.inv(R)
JmisT = np.transpose(Jmis)
JmisMT = np.transpose(JmisM)
RJmis = np.dot(invR,JmisT)
RJmisM = np.dot(invR,JmisMT)
J1 = np.dot(Jmis,RJmis)
JM1 = np.dot(JmisM,RJmisM)
Jv = (vTv + J1 + JM1) / 2
return Jv
###############################################
####### GRADIENT OF J ########
###############################################
def gradJ(v):
global Model_updated
Vv = np.dot(V,v)
HVv = np.dot(H,Vv)
# CODE COPIED FROM J() ###########################################
# we need the model results - check if these are already available,
# if not, run the forward model with Vv as the input
if Model_updated:
print "in gradJ(): using pre-exiting forward model model solution"
Model_updated = False
else:
print "in gradJ(): updating the forward model solution"
# prepare directory and input files for forward model
input_file_name = prepare_inputs_for_forward_model(k)
# modify initial condition of tracer
field = modify_initial_conditions_at_tk(k,Vv)
# run forward model
run_forward_model_tk(k,opal_options.executable,input_file_name)
Model_updated = True
# END OF CODE COPIED FROM J() ###########################################
# MVv = np.dot(M,Vv)
# retrieve the forward model results, MVv
path_to_vtu_file = str(k) + '/2d_canyon_1.vtu'
vtu_data = vtktools.vtu(path_to_vtu_file)
MVv = vtu_data.GetScalarField('Tracer') #vtu_data.GetScalarField(field)
# print "gradJ: MVv[0:10]", MVv[0:10]
HMVv = np.dot(H,MVv)
Jmis = np.subtract(HVv,d)
JmisM = np.subtract(HMVv,d)
invR = np.linalg.inv(R)
RJmis = np.dot(invR,Jmis)
RJmisM = np.dot(invR,JmisM)
HT = np.transpose(H)
g1 = np.dot(HT,RJmis)
g1M = np.dot(HT,RJmisM)
##MT = ... MT(g1M) = from importance map t_k+1 , map at t_k
VT = np.transpose(V)
##VTMT = np.dot(VT,MT)
g2 = np.dot(VT,g1)
ggJ = v + g2 ##+ VTMT
return ggJ
#print "exectuable which has been selected:", opal_options.executable
# ......... read the input .........
###############################################
## TRUNCATION AND REGULARIZATION PARAMETERS ###
###############################################
# inputs
n = 852
lam = 1 #REGULARIZATION PARAMETER
m = 45 #TRUNCATION PARAMETER FROM buildV.py
xB = np.ones(n)
y = np.ones(n)
k = 8 # time at which observation is known
###############################################
######## INTIAL RUN OF FLUIDITY #############
###############################################
# put checkpointing on for file k
print "name of fwd_input_file", opal_options.data_assimilation.fwd_input_file
libspud.load_options('2d_canyon.flml')#(opal_options.data_assimilation.fwd_input_file)
# don't need these currently
if libspud.have_option('io/checkpointing/checkpoint_at_start'):
libspud.delete_option('io/checkpointing/checkpoint_at_start')
if libspud.have_option('io/checkpointing/checkpoint_at_end'):
libspud.delete_option('io/checkpointing/checkpoint_at_end')
if libspud.have_option('io/checkpointing/checkpoint_period_in_dumps'):
libspud.set_option('io/checkpointing/checkpoint_period_in_dumps',k)
else:
print "checkpoint_period_in_dumps option missing from xml file"
sys.exit(0)
libspud.write_options(opal_options.data_assimilation.fwd_input_file)
libspud.clear_options()
string = opal_options.executable + " " + opal_options.data_assimilation.fwd_input_file
# run code which will checkpoint every "k" dumps at the moment....
print string
os.system(string)
###############################################
######## COVARIANCE MATRICES #############
###############################################
V = np.loadtxt('matrixVprec'+str(m)+'.txt', usecols=range(m))
R = lam * 0.5 * np.identity(n)
H = np.identity(n)
###############################################
####### FROM PHYSICAL TO CONTROL SPACE ########
###############################################
x0 = np.ones(n)
Vin = np.linalg.pinv(V)
v0 = np.dot(Vin,x0)
###############################################
####### COMPUTE THE MISFIT ########
###############################################
VT = np.transpose(V)
HxB = np.dot(H,xB)
# consider multiple observations later - just one for now
d = np.subtract(y,HxB)
###############################################
####### COMPUTE THE MINIMUM OF J ########
###############################################
t = time.time()
iter_count = 0
Model_updated = False
res = minimize(J, v0, method='L-BFGS-B', jac=gradJ,
options={'disp': True})
###############################################
####### FROM CONTROL TO PHYSICAL SPACE ########
###############################################
vDA = np.array([])
vDA = res.x
deltaxDA = np.dot(V,vDA)
xDA = xB + deltaxDA
elapsed = time.time() - t
print " iter_count", iter_count
#return
###############################################
####### PRECONDITIONED COST FUNCTION J ########
###############################################
return
try:
libspud.add_option('/foo')
except libspud.SpudNewKeyWarning, e:
print "caught libspud.SpudNewKeyWarning: " + e.message
print libspud.option_count('/foo')
libspud.set_option('/problem_type', 'helloworld')
print libspud.get_option('/problem_type')
try:
libspud.set_option_attribute('/foo/bar', 'foobar')
except libspud.SpudNewKeyWarning, e:
print "caught libspud.SpudNewKeyWarning: " + e.message
print libspud.get_option('/foo/bar')
libspud.delete_option('/foo')
print libspud.option_count('/foo')
try:
libspud.get_option('/foo')
except libspud.SpudKeyError, e:
print "caught libspud.SpudKeyError: " + e.message
try:
libspud.get_option('/geometry')
except libspud.SpudTypeError, e:
print "caught libspud.SpudTypeError: " + e.message
libspud.write_options('test_out.flml')
pass
assert libspud.option_count('/foo') == 1
libspud.set_option('/problem_type', 'helloworld')
assert libspud.get_option('/problem_type') == "helloworld"
try:
libspud.set_option_attribute('/foo/bar', 'foobar')
assert False
except libspud.SpudNewKeyWarning, e:
pass
assert libspud.get_option('/foo/bar') == "foobar"
libspud.delete_option('/foo')
assert libspud.option_count('/foo') == 0
try:
libspud.get_option('/foo')
assert False
except libspud.SpudKeyError, e:
pass
try:
libspud.get_option('/geometry')
assert False
except libspud.SpudTypeError, e:
pass
libspud.write_options('test_out.flml')