def Parameters(file_name):
try:
libspud.load_options(file_name)
except:
print "This file doesn't exist or is the wrong file type. It should be a .osml file. Use -h for help"
sys.exit()
try:
start = float(libspud.get_option('/diffusion_model/timestepping/start_time',))
end = float(libspud.get_option('/diffusion_model/timestepping/end_time'))
time_step = float(libspud.get_option('/diffusion_model/timestepping/timestep'))
mesh_int = int(libspud.get_option('/diffusion_model/mesh/initial_mesh_size'))
alpha = float(libspud.get_option('/diffusion_model/model_parameters/diffusion_coefficient'))
initial_conditions = str(libspud.get_option('/diffusion_model/model_parameters/topography_conditions'))
sediment_conditions =str(libspud.get_option('/diffusion_model/model_parameters/sediment_conditions'))
except:
print 'The information provided was incomplete, please recreate the file'
sys.exit()
if ((start-end) >= 0):
print 'The start time is after the end time'
sys.exit()
elif (time_step == 0):
print 'The time step cannot be 0'
sys.exit()
elif (mesh_int == 0):
print 'The mesh has to have a size greater than 0'
sys.exit()
elif ((end - start) < time_step):
print 'The time step is too large for the total time'
sys.exit()
return start, end, time_step, mesh_int, alpha, initial_conditions, sediment_conditions
def get_parameters_from_options(options_file=None,**kwargs):
if options_file:
libspud.load_options(options_file)
parameters = []
options_base = '/embedded_models/particle_model/particle_classes'
def get_option(pclass,key,default=None):
result = default
if libspud.have_option('/'.join((options_base,pclass,key))):
result = libspud.get_option('/'.join((options_base,pclass,key)))
return result
for i in range(libspud.get_number_of_children(options_base)):
key = libspud.get_child_name(options_base,i)
name = get_option(key,'name')
diameter = get_option(key,'diameter')
distribution = get_option(key,'distribution')
density = get_option(key,'density',default=2.5e3)
parameters.append(PhysicalParticle(diameter=diameter,
rho=density,
distribution=distribution,
material_name=name,
**kwargs))
return parameters
def test8(self):
#should be an osml file
libspud.load_options('test8.osml')
start = float(libspud.get_option('/diffusion_model/timestepping/start_time',))
end = float(libspud.get_option('/diffusion_model/timestepping/end_time'))
time_step = float(libspud.get_option('/diffusion_model/timestepping/timestep'))
mesh_int = int(libspud.get_option('/diffusion_model/mesh/initial_mesh_size'))
alpha = float(libspud.get_option('/diffusion_model/model_parameters/diffusion_coefficient'))
initial_conditions = str(libspud.get_option('/diffusion_model/model_parameters/initial_conditions'))
#create a simple testcase
model = SedimentModel()
mesh = UnitSquareMesh(mesh_int,mesh_int)
model.set_mesh(mesh)
init_cond = Expression(initial_conditions) # simple slope
init_sed = Expression('x[0]') # this gives
# total of above gives a slope of 0 to 2 (over the unit square)
model.set_initial_conditions(init_cond,init_sed)
model.set_end_time(end)
model.set_diffusion_coeff(alpha)
model.init()
model.solve()
# answer should be 1 everywhere
plot(model.get_total_height(),interactive=True)
answer = model.get_total_height_array()
for i in answer:
self.assert_(-1e-8 < i - 1 < 1e-8)
def test14(self):
with self.assertRaises(SystemExit):
#should be an osml file
libspud.load_options('test14.osml')
start = float(libspud.get_option('/diffusion_model/timestepping/start_time',))
end = float(libspud.get_option('/diffusion_model/timestepping/end_time'))
time_step = float(libspud.get_option('/diffusion_model/timestepping/timestep'))
mesh_int = int(libspud.get_option('/diffusion_model/mesh/initial_mesh_size'))
alpha = float(libspud.get_option('/diffusion_model/model_parameters/diffusion_coefficient'))
initial_conditions = str(libspud.get_option('/diffusion_model/model_parameters/initial_conditions'))
if ((start-end) >= 0):
print 'The start time is after the end time'
sys.exit()
elif (time_step == 0):
print 'The time step cannot be 0'
sys.exit()
#create a simple testcase
model = SedimentModel()
mesh = UnitSquareMesh(mesh_int,mesh_int)
model.set_mesh(mesh)
init_cond = Expression(initial_conditions) # simple slope
init_sed = Expression('x[0]') # this gives
# total of above gives a slope of 0 to 2 (over the unit square)
model.set_initial_conditions(init_cond,init_sed)
model.set_end_time(end)
model.set_diffusion_coeff(alpha)
model.init()
model.solve()
# answer should be 1 everywhere
plot(model.get_total_height(),interactive=True)
answer = model.get_total_height_array()
def __init__(self, options_file=None):
if options_file:
libspud.load_options(options_file)
self.simulation_name = libspud.get_option('/simulation_name')
self.dimension = libspud.get_option('/geometry/dimension')
def get_parameters_from_options(options_file=None, **kwargs):
"""Read particle data from Fluidity options file."""
if options_file:
libspud.load_options(options_file)
parameters = []
options_base = '/embedded_models/particle_model/particle_classes'
def get_option(pclass, key, default=None):
"""Get option from key."""
result = default
if libspud.have_option('/'.join((options_base, pclass, key))):
result = libspud.get_option('/'.join((options_base, pclass, key)))
return result
for i in range(libspud.get_number_of_children(options_base)):
key = libspud.get_child_name(options_base, i)
name = get_option(key, 'name')
diameter = get_option(key, 'diameter')
distribution = get_option(key, 'distribution')
density = get_option(key, 'density', default=2.5e3)
parameters.append(
PhysicalParticle(diameter=diameter,
rho=density,
distribution=distribution,
material_name=name,
**kwargs))
return parameters
def test11(self):
#should be an osml file
libspud.load_options('test11.osml')
start = float(
libspud.get_option('/diffusion_model/timestepping/start_time', ))
end = float(
libspud.get_option('/diffusion_model/timestepping/end_time'))
time_step = float(
libspud.get_option('/diffusion_model/timestepping/timestep'))
mesh_int = int(
libspud.get_option('/diffusion_model/mesh/initial_mesh_size'))
alpha = float(
libspud.get_option(
'/diffusion_model/model_parameters/diffusion_coefficient'))
initial_conditions = str(
libspud.get_option(
'/diffusion_model/model_parameters/initial_conditions'))
#create a simple testcase
model = SedimentModel()
mesh = UnitSquareMesh(mesh_int, mesh_int)
model.set_mesh(mesh)
init_cond = Expression(initial_conditions) # simple slope
init_sed = Expression('x[0]') # this gives
# total of above gives a slope of 0 to 2 (over the unit square)
model.set_initial_conditions(init_cond, init_sed)
model.set_end_time(end)
model.set_diffusion_coeff(alpha)
model.init()
model.solve()
# answer should be 1 everywhere
plot(model.get_total_height(), interactive=True)
answer = model.get_total_height_array()
def pre_init(model, xml_path):
# load options file
libspud.load_options(xml_path)
# model name
model.project_name = libspud.get_option('project_name')
# mesh options
model.ele_count = get_optional('mesh/element_count', default=20)
# time options
option_path = 'time_options/time_discretisation::'
if libspud.have_option(option_path + 'runge_kutta'):
model.time_discretise = time_discretisation.runge_kutta
elif libspud.have_option(option_path + 'crank_nicholson'):
model.time_discretise = time_discretisation.crank_nicholson
elif libspud.have_option(option_path + 'explicit'):
model.time_discretise = time_discretisation.explicit
elif libspud.have_option(option_path + 'implicit'):
model.time_discretise = time_discretisation.implicit
else:
raise Exception('unrecognised time discretisation in options file')
if libspud.have_option('time_options/finish_time'):
model.finish_time = libspud.get_option('time_options/finish_time')
model.tol = None
elif libspud.have_option('time_options/steady_state_tolerance'):
model.tol = libspud.get_option('time_options/steady_state_tolerance')
model.finish_time = None
else:
raise Exception('unrecognised finishing criteria')
# spatial_discretisation
if libspud.have_option('spatial_discretiation/discretisation::continuous'):
model.disc = 'CG'
elif libspud.have_option(
'spatial_discretisation/discretisation::discontinuous'):
model.disc = 'DG'
model.slope_limit = libspud.have_option(
'spatial_discretisation/discretisation/slope_limit')
else:
raise Exception('unrecognised spatial discretisation in options file')
model.degree = get_optional('spatial_discretisation/polynomial_degree',
default=1)
# tests
if libspud.have_option('testing/test::mms'):
option_path = 'testing/test::mms/source_terms/'
model.mms = True
model.S_e = (read_ic(option_path + 'momentum_source', default=None),
read_ic(option_path + 'height_source', default=None),
read_ic(option_path + 'volume_fraction_source',
default=None),
read_ic(option_path + 'deposit_depth_source',
default=None))
else:
model.mms = False
def superspud(filename, cmd):
libspud.load_options(filename)
r = None
if hasattr(cmd, '__iter__'):
for c in cmd:
exec("try: r = " + c + "\nexcept libspud.SpudNewKeyWarning: pass")
else:
exec("try: r = " + cmd + "\nexcept libspud.SpudNewKeyWarning: pass")
libspud.clear_options()
return r
def superspud(filename, cmd):
libspud.load_options(filename)
r = None
if hasattr(cmd, '__iter__'):
for c in cmd:
exec "try: r = " + c + "\nexcept libspud.SpudNewKeyWarning: pass"
else:
exec "try: r = " + cmd + "\nexcept libspud.SpudNewKeyWarning: pass"
libspud.clear_options()
return r
def test17(self):
with self.assertRaises(SystemExit):
#should be an osml file
libspud.clear_options()
try:
libspud.load_options('test17.osml')
except:
print "This file doesn't exist or is the wrong file type. It should be a .osml file"
sys.exit()
try:
start = float(libspud.get_option('/diffusion_model/timestepping/start_time',))
end = float(libspud.get_option('/diffusion_model/timestepping/end_time'))
time_step = float(libspud.get_option('/diffusion_model/timestepping/timestep'))
mesh_int = int(libspud.get_option('/diffusion_model/mesh/initial_mesh_size'))
alpha = float(libspud.get_option('/diffusion_model/model_parameters/diffusion_coefficient'))
initial_conditions = str(libspud.get_option('/diffusion_model/model_parameters/initial_conditions'))
except:
print 'The information provided was incomplete, please recreate the file'
sys.exit()
print start
print end
print time_step
print mesh_int
print alpha
print initial_conditions
#create a simple testcase
model = SedimentModel()
mesh = UnitSquareMesh(mesh_int,mesh_int)
model.set_mesh(mesh)
init_cond = Expression(initial_conditions) # simple slope
init_sed = Expression('x[0]') # this gives
# total of above gives a slope of 0 to 2 (over the unit square)
model.set_initial_conditions(init_cond,init_sed)
model.set_end_time(end)
model.set_diffusion_coeff(alpha)
model.init()
model.solve()
# answer should be 1 everywhere
plot(model.get_total_height(),interactive=True)
answer = model.get_total_height_array()
def test15(self):
with self.assertRaises(SystemExit):
#should be an osml file
libspud.load_options('test15.osml')
start = float(
libspud.get_option(
'/diffusion_model/timestepping/start_time', ))
end = float(
libspud.get_option('/diffusion_model/timestepping/end_time'))
time_step = float(
libspud.get_option('/diffusion_model/timestepping/timestep'))
mesh_int = int(
libspud.get_option('/diffusion_model/mesh/initial_mesh_size'))
alpha = float(
libspud.get_option(
'/diffusion_model/model_parameters/diffusion_coefficient'))
initial_conditions = str(
libspud.get_option(
'/diffusion_model/model_parameters/initial_conditions'))
if ((start - end) >= 0):
print 'The start time is after the end time'
sys.exit()
elif (time_step == 0):
print 'The time step cannot be 0'
sys.exit()
elif ((end - start) <= time_step):
print 'The time step is too large for the total time'
sys.exit()
#create a simple testcase
model = SedimentModel()
mesh = UnitSquareMesh(mesh_int, mesh_int)
model.set_mesh(mesh)
init_cond = Expression(initial_conditions) # simple slope
init_sed = Expression('x[0]') # this gives
# total of above gives a slope of 0 to 2 (over the unit square)
model.set_initial_conditions(init_cond, init_sed)
model.set_end_time(end)
model.set_diffusion_coeff(alpha)
model.init()
model.solve()
# answer should be 1 everywhere
plot(model.get_total_height(), interactive=True)
answer = model.get_total_height_array()
def geterrors(self,checkpoint_file):
"""
reads checkpoint file and accompanying .xml solution file and
extracts the time, and calculates shape and phase errors for the solitary waves
"""
# this seems to be a dangerous thing but I'm going to clear
# the option then load the new ones from the checkpoint file
libspud.clear_options()
libspud.load_options(checkpoint_file)
time = libspud.get_option("/timestepping/current_time")
dt = libspud.get_option("/timestepping/timestep/coefficient/type/rank/value/constant")
print "t=",time," dt=", dt
#load xml file
xml_file = checkpoint_file.replace("checkpoint",self.system_name)
xml_file = xml_file.replace("tfml","xml")
# load function and extract porosity
u = df.Function(self.functionspace,xml_file)
fields = u.split(deepcopy = True)
f = fields[self.f_index]
#initialize Error Object
err = WaveError(f,self.swave,self.x0,self.h)
#minimize error using fsolve
#out = err.min_grad(delta_0)
delta_0=np.zeros(self.dim)
out = err.min_grad_z(delta_0[-1])
delta = out[0]
err_min = out[1]
elapsed_time = out[2]
L2_f= err.L2_f
rel_error = err_min/L2_f
c_rel_error = np.sign(delta)*np.sqrt(np.dot(delta,delta))/(self.swave.c*time)
#print "delta=",delta, " err =",err_min, " elapsed_time=",elapsed_time
#print "L2_f=",L2_f, "rel_err =",rel_error, " c_rel_error=",c_rel_error
#print "L2_error=",err_min," delta=",delta," rel_error=",rel_error," c_rel_error=",c_rel_error
return [time,dt,err_min,delta,rel_error,c_rel_error,elapsed_time]
def geterrors(self, checkpoint_file):
"""
reads checkpoint file and accompanying .xml solution file and
extracts the time, and calculates shape and phase errors for the solitary waves
"""
# this seems to be a dangerous thing but I'm going to clear
# the option then load the new ones from the checkpoint file
libspud.clear_options()
libspud.load_options(checkpoint_file)
time = libspud.get_option("/timestepping/current_time")
dt = libspud.get_option(
"/timestepping/timestep/coefficient/type/rank/value/constant")
print "t=", time, " dt=", dt
#load xml file
xml_file = checkpoint_file.replace("checkpoint", self.system_name)
xml_file = xml_file.replace("tfml", "xml")
# load function and extract porosity
u = df.Function(self.functionspace, xml_file)
fields = u.split(deepcopy=True)
f = fields[self.f_index]
#initialize Error Object
err = WaveError(f, self.swave, self.x0, self.h)
#minimize error using fsolve
#out = err.min_grad(delta_0)
delta_0 = np.zeros(self.dim)
out = err.min_grad_z(delta_0[-1])
delta = out[0]
err_min = out[1]
elapsed_time = out[2]
L2_f = err.L2_f
rel_error = err_min / L2_f
c_rel_error = np.sign(delta) * np.sqrt(np.dot(
delta, delta)) / (self.swave.c * time)
#print "delta=",delta, " err =",err_min, " elapsed_time=",elapsed_time
#print "L2_f=",L2_f, "rel_err =",rel_error, " c_rel_error=",c_rel_error
#print "L2_error=",err_min," delta=",delta," rel_error=",rel_error," c_rel_error=",c_rel_error
return [time, dt, err_min, delta, rel_error, c_rel_error, elapsed_time]
def prepare_inputs_for_forward_model(k):
''' make directory to run the fowrard model in, copy across the input files and
modify the time step in flml so the forward model will run just for one time step'''
# make a directory to run the code in and copy across input files
cwd = os.getcwd()
input_file_name = "fwd_model.flml"
# print "files in cwd"
# for files in os.listdir(cwd):
# print files
if not os.path.isdir( str(k) ):
print "attempting to mkdir"
os.mkdir(str(k))
os.system('cp *.msh ' + str(k))
os.system('cp *_' +str(k)+ '_checkpoint* ' + str(k))
os.chdir(str(k))
# modify the checkpoint file times
for files in os.listdir('./'):
# get the name of the checkpoint flml
if files.endswith(str(k)+"_checkpoint.flml"):
# pos = files.rfind('.')
checkpoint_file_name = files
# print "checkpoint fname", checkpoint_file_name
# load options from checkpoint file
libspud.load_options(checkpoint_file_name)
# change the name of the output
libspud.set_option('/simulation_name','2d_canyon')
# change the final time so it runs from t_k to t_k+1 only
t0 = libspud.get_option('/timestepping/current_time')
dt = libspud.get_option('/timestepping/timestep')
libspud.set_option('/timestepping/finish_time',t0+dt)
# could check with vtu's that these are the correct times
# rename input file
libspud.write_options(input_file_name)
libspud.clear_options()
os.chdir(cwd)
return input_file_name
def Parameters(file_name):
try:
libspud.load_options(file_name)
except:
print "This file doesn't exist or is the wrong file type. It should be a .osml file. Use -h for help"
sys.exit()
try:
start = float(
libspud.get_option('/diffusion_model/timestepping/start_time', ))
end = float(
libspud.get_option('/diffusion_model/timestepping/end_time'))
time_step = float(
libspud.get_option('/diffusion_model/timestepping/timestep'))
mesh_int = int(
libspud.get_option('/diffusion_model/mesh/initial_mesh_size'))
alpha = float(
libspud.get_option(
'/diffusion_model/model_parameters/diffusion_coefficient'))
initial_conditions = str(
libspud.get_option(
'/diffusion_model/model_parameters/initial_conditions'))
except:
print 'The information provided was incomplete, please recreate the file'
sys.exit()
if ((start - end) >= 0):
print 'The start time is after the end time'
sys.exit()
elif (time_step == 0):
print 'The time step cannot be 0'
sys.exit()
elif (mesh_int == 0):
print 'The mesh has to have a size greater than 0'
sys.exit()
elif ((end - start) < time_step):
print 'The time step is too large for the total time'
sys.exit()
return start, end, time_step, mesh_int, alpha, initial_conditions
import libspud
import shutil
class flml_things:
"list of things to change in an flml file"
def __init__(self,name='',mesh='',dt=0.2):
self.name = name
self.dt = dt
self.mesh = mesh
parent_file = 'diffusion_dg1'
diffusion_dg_A = flml_things(name='diffusion_dg_A',mesh='MMS_A',dt=0.2)
diffusion_dg_B = flml_things(name='diffusion_dg_B',mesh='MMS_B',dt=0.2)
diffusion_dg_C = flml_things(name='diffusion_dg_C',mesh='MMS_C',dt=0.2)
diffusion_dg_D = flml_things(name='diffusion_dg_D',mesh='MMS_D',dt=0.2)
diffusion_dg_E = flml_things(name='diffusion_dg_E',mesh='MMS_E',dt=0.2)
filelist = [diffusion_dg_A,diffusion_dg_B,diffusion_dg_C,diffusion_dg_D,diffusion_dg_E]
for file in filelist:
shutil.copy(parent_file+'.flml',file.name+'.flml')
libspud.load_options(file.name+'.flml')
libspud.set_option('/simulation_name', file.name)
libspud.set_option('/geometry/mesh[@name="CoordinateMesh"]/from_file/file_name', file.mesh)
libspud.set_option('/timestepping/timestep', file.dt)
libspud.write_options(file.name+'.flml')
def __init__(self, path):
""" Initialise a new shallow water simulation, using an options file.
:param str path: The path to the simulation's configuration/options file.
:returns: None
"""
LOG.info("Initialising simulation...")
# Remove any stored options.
libspud.clear_options()
# Load the options from the options tree.
libspud.load_options(path)
# Populate the options dictionary
self.populate_options()
# Read in the input mesh (or construct one)
self.mesh = self.get_mesh(path)
# Create a dictionary containing all the function spaces
LOG.info("Creating function spaces...")
self.function_spaces = {}
# The Velocity field's function space
name = "VelocityFunctionSpace"
path = "/function_spaces/function_space::%s" % name
family = libspud.get_option(path+"/family")
degree = libspud.get_option(path+"/degree")
try:
if(family == "Continuous Lagrange"):
self.function_spaces[name] = VectorFunctionSpace(self.mesh, "CG", degree)
elif(family == "Discontinuous Lagrange"):
self.function_spaces[name] = VectorFunctionSpace(self.mesh, "DG", degree)
else:
raise ValueError("Unknown element family: %s." % family)
except ValueError as e:
LOG.exception(e)
sys.exit()
LOG.debug("Created a new %s function space of degree %d for Velocity" % (family, degree))
# The FreeSurfacePerturbation field's function space
name = "FreeSurfaceFunctionSpace"
path = "/function_spaces/function_space::%s" % name
family = libspud.get_option(path+"/family")
degree = libspud.get_option(path+"/degree")
try:
if(family == "Continuous Lagrange"):
self.function_spaces[name] = FunctionSpace(self.mesh, "CG", degree)
elif(family == "Discontinuous Lagrange"):
self.function_spaces[name] = FunctionSpace(self.mesh, "DG", degree)
else:
raise ValueError("Unknown element family: %s." % family)
except ValueError as e:
LOG.exception(e)
sys.exit()
LOG.debug("Created a new %s function space of degree %d for FreeSurfacePerturbation" % (family, degree))
# Define the mixed function space
U = self.function_spaces["VelocityFunctionSpace"]
H = self.function_spaces["FreeSurfaceFunctionSpace"]
self.W = MixedFunctionSpace([U, H])
# Set up the output streams
self.create_output_streams()
return
def get_opal_options():
"Initialises the structure for the options."
opal_options = Opal_input()
nirom_options = Nirom_input()
fwd_options = Forward_model_options()
#Read the input data from the user
opal_input_file = str(sys.argv[1])
#Load the .opal file
libspud.load_options(opal_input_file)
##Create Opal Variable
# opal_options = Opal_input()
##Start reading options
print "reading opal input file", opal_input_file
if libspud.have_option('/avoid_perturbing_near_wells'):
opal_options.avoid_perturbing_near_wells = True
if (libspud.have_option('/opal_operation/importance_map')):
opal_options.opal_operation = 'importance_map'
im_path = '/opal_operation/importance_map/'
opal_options = read_in_importance_map_options(im_path, opal_options)
elif (libspud.have_option('/opal_operation/data_assimilation')):
opal_options.opal_operation = 'da'
opal_options.data_assimilation.fwd_input_file = libspud.get_option(
'/opal_operation/data_assimilation/fwd_input_file')
#print "opal_options.data_assimilation.fwd_input_file", opal_options.data_assimilation.fwd_input_file
elif (libspud.have_option('/opal_operation/nirom')):
opal_options.opal_operation = 'nirom'
nirom_path = 'opal_operation/nirom/'
opal_options, nirom_options, fwd_options = read_in_nirom_options(
nirom_path, opal_options, nirom_options, fwd_options)
elif (libspud.have_option('/opal_operation/second_order_da')):
opal_options.opal_operation = 'second_order_da'
da_path = '/opal_operation/second_order_da/'
opal_options = read_in_soda_options(da_path, opal_options)
elif (libspud.have_option('/opal_operation/ga_optimisation')):
opal_options.opal_operation = 'ga_optimisation'
path = '/opal_operation/ga_optimisation'
# previously these three options were at the top level
opal_options.output_filename = libspud.get_option(path +
'/Output_filename')
opal_options.executable = libspud.get_option(path + '/Executable')
opal_options.input_file = libspud.get_option(path + '/Input_file')
opal_options.ga_max_generations = libspud.get_option(
path + '/convergence_settings/Maximum_generations')
opal_options.ga_locations_to_study = libspud.get_option(
path + '/Locations_to_study/value')
if libspud.have_option(path + '/Locations_to_study/Initial_guess'):
opal_options.ga_initial_guess = libspud.get_option(
path + '/Locations_to_study/Initial_guess')
if libspud.have_option(path + '/Locations_to_study/Mind_the_gap'):
opal_options.mind_the_gap = libspud.get_option(
path + '/Locations_to_study/Mind_the_gap')
if libspud.have_option(path + '/Trelis_integration'):
opal_options.trelis_path = libspud.get_option(
path + '/Trelis_integration/trelis_path')
opal_options.trelis_input_file = libspud.get_option(
path + '/Trelis_integration/trelis_input_file')
opal_options.optimise_input = libspud.have_option(path +
'/optimise_input')
if libspud.have_option(path +
'/convergence_settings/Gradient_convergence'):
opal_options.ga_gradient_convergence = libspud.get_option(
path + '/convergence_settings/Gradient_convergence')
if libspud.have_option(path +
'/convergence_settings/Absolute_convergence'):
opal_options.ga_absolute_convergence = libspud.get_option(
path + '/convergence_settings/Absolute_convergence')
if libspud.have_option(path + '/Number_processors'):
opal_options.number_processors = libspud.get_option(
path + '/Number_processors')
if libspud.have_option(path + '/Number_processors/MPI_runs'):
opal_options.MPI_runs = libspud.get_option(
path + '/Number_processors/MPI_runs')
opal_options.number_processors /= opal_options.MPI_runs
opal_options.ga_population_generation = libspud.get_option(
path + '/Population_generation')
opal_options.ga_breeding_prob = libspud.get_option(
path + '/Breeding_probability/value')
if libspud.have_option(path +
'/Breeding_probability/Generation_method'):
opal_options.generation_method = libspud.get_option(
path + '/Breeding_probability/Generation_method')
opal_options.ga_mutation_prob = libspud.get_option(
path + '/Mutation_probability/value')
if libspud.have_option(path + '/Mutation_probability/Mutation_method'):
opal_options.mutation_method = libspud.get_option(
path + '/Mutation_probability/Mutation_method')
opal_options.precision = libspud.get_option(path + '/Precision')
if libspud.have_option(path + '/Fitness/python_function'):
opal_options.ga_fitness_functional = libspud.get_option(
path + '/Fitness/python_function')
opal_options.ga_Minimise = libspud.have_option(
path + '/Fitness/Optimisation/Minimise')
opal_options.producer_ids = libspud.get_option(path +
'/Fitness/producer_ids')
opal_options.injector_ids = libspud.get_option(path +
'/Fitness/injector_ids')
if libspud.have_option(path +
'/GA_methods/Evolutionary_algorithm/eaSimple'):
opal_options.ga_evol_algorithm = 1
elif libspud.have_option(
path + '/GA_methods/Evolutionary_algorithm/eaMuCommaLambda'):
opal_options.ga_evol_algorithm = 2
opal_options.ga_mu = libspud.get_option(
path + '/GA_methods/Evolutionary_algorithm/eaMuCommaLambda/Mu')
opal_options.ga_lambda = libspud.get_option(
path +
'/GA_methods/Evolutionary_algorithm/eaMuCommaLambda/Lambda')
elif libspud.have_option(
path + '/GA_methods/Evolutionary_algorithm/eaMuPlusLambda'):
opal_options.ga_evol_algorithm = 3
opal_options.ga_mu = libspud.get_option(
path + '/GA_methods/Evolutionary_algorithm/eaMuPlusLambda/Mu')
opal_options.ga_lambda = libspud.get_option(
path +
'/GA_methods/Evolutionary_algorithm/eaMuPlusLambda/Lambda')
if libspud.have_option(path + '/GA_methods/Selection_method/selBest'):
opal_options.ga_selection_method = 1
elif libspud.have_option(path +
'/GA_methods/Selection_method/selNSGA2'):
opal_options.ga_selection_method = 2
elif libspud.have_option(path +
'/GA_methods/Selection_method/selSPEA2'):
opal_options.ga_selection_method = 3
opal_options.ga_CMA = False
if libspud.have_option(path + '/GA_methods/Use_CMA'):
opal_options.ga_CMA = True
opal_options.ga_centroid = libspud.get_option(
path + '/GA_methods/Use_CMA/centroid')
opal_options.ga_sigma = libspud.get_option(
path + '/GA_methods/Use_CMA/sigma')
if libspud.have_option(path + 'Hall_of_fame'):
opal_options.ga_hall_of_fame = libspud.get_option(path +
'Hall_of_fame')
nfields = libspud.option_count(path + '/Variables')
for i in range(nfields):
temp_field = ga_variable()
fieldpath = path + '/Variables[' + str(i) + ']'
temp_field.name = libspud.get_option(fieldpath + '/name')
temp_field.min_limit = libspud.get_option(fieldpath + '/Min_limit')
temp_field.max_limit = libspud.get_option(fieldpath + '/Max_limit')
temp_field.variable_pattern = libspud.get_option(
fieldpath + '/Variable_pattern')
temp_field.normaliser = 1.0
if libspud.have_option(fieldpath + '/normaliser'):
temp_field.normaliser = libspud.get_option(fieldpath +
'/normaliser')
##Now append to the variables list
opal_options.ga_variables.append(temp_field)
libspud.clear_options()
return opal_options, fwd_options, nirom_options
#Authors: P. Salinas
import operator
from opal_classes import *
from deap import tools, base, creator, cma
from importance_map_tools import *
import libspud
from exodus2gmsh import convertExodusII2MSH
#Read Opal options, for the time being just so we can call the same subroutines
# read in the opal options
opal_options, fwd_options, nirom_options = get_opal_options()
# get xml extension (mpml or flml)
xml_extension = get_xml_extension(opal_options.input_file)
# load the options for the forward model from xml file
libspud.load_options(opal_options.input_file)
# Production file
prod_file = libspud.get_option('/simulation_name') + "_outfluxes.csv"
# Final time to extract from the csv file
final_time = libspud.get_option('/timestepping/finish_time')
#Retrieve extra variables required to run the optimisation
MIN = opal_options.ga_variables[0].min_limit
MAX = opal_options.ga_variables[0].max_limit
spatial_precision = int((abs(MIN) + abs(MAX)) * opal_options.precision)
##Global variable to be used for gradient convergence
previous_convergence = [0.0, 0.0]
##Geothermal if we have temperature field
geothermal = libspud.have_option('material_phase[' + str(0) +
']/scalar_field::Temperature')
##Already visited studied
explored_locations = []
def tfmlgeterrors(name):
# get arguments from .tfml file
tfmlfile = name+'.tfml'
libspud.load_options(tfmlfile)
# get the mesh parameters and reconstruct the mesh
meshtype = libspud.get_option("/geometry/mesh/source[0]/name")
if meshtype == 'UnitSquare':
number_cells = libspud.get_option("/geometry/mesh[0]/source[0]/number_cells")
diagonal = libspud.get_option("/geometry/mesh[0]/source[0]/diagonal")
mesh = UnitSquare(number_cells[0],number_cells[1],diagonal)
elif meshtype == 'UnitCube':
number_cells = libspud.get_option("/geometry/mesh[0]/source[0]/number_cells")
mesh = UnitCube(number_cells[0],number_cells[1],number_cells[2])
else:
error("Error: unknown mesh type "+meshtype)
# get the mesh dimension
dim = mesh.topology().dim()
# get and set the mixed function space
p_family = libspud.get_option("/system[0]/field[0]/type/rank/element/family")
p_degree = libspud.get_option("/system[0]/field[0]/type/rank/element/degree")
f_family = libspud.get_option("/system[0]/field[1]/type/rank/element/family")
f_degree = libspud.get_option("/system[0]/field[1]/type/rank/element/degree")
Vp = FunctionSpace(mesh,p_family,p_degree)
Vf = FunctionSpace(mesh,f_family,f_degree)
ME = Vp*Vf
# get the solitarywave profile
solwave_code = libspud.get_option("/system::magma/field::Porosity/type::Function/rank::Scalar/initial_condition/python")
exec(solwave_code)
# print wave parameters
print 'Solitary Wave parameters: c =',swave.c,', n = ',swave.n,', m = ',swave.m,', d = ',swave.d
print 'h_on_delta =', h_on_delta
# calculate dh_nodes_per_compaction length
dh = mesh.hmin() # cell diameter (circum-circle)
dh_node = dh/sqrt(dim)/2.
dh_node_delta = dh_node*h_on_delta
# cd to build directory to loop over checkpoint files
# os.chdir('build')
# get and sort xml files by time
tfml_files = glob(name+'*checkpoint*.tfml')
xml_files = glob(name+'*.xml')
dtype = [ ('time', float), ('name','S28')]
values = []
for i in range(len(tfml_files)):
libspud.load_options(tfml_files[i])
time = libspud.get_option("/timestepping/current_time")
dt = libspud.get_option("/timestepping/timestep/coefficient/type/rank/value/constant")
values = values + [(time, xml_files[i])]
a = array(values,dtype)
t_file=sort(a,order='time')
set_log_active(False) # turn off dolfin messages
# initialize output arrays
t = []
delta = []
err_min = []
L2_f = []
rel_error = []
c_rel_error = []
elapsed_time = []
# loop over files and check errors for each one
delta_0 = zeros(dim)
for i in range(len(t_file)):
# get time and filename
t.append(t_file[i][0])
name = t_file[i][1]
# load function and extract porosity
u = Function(ME,name)
p, f = u.split(deepcopy = True)
#initialize Error Object
err = WaveError(f,swave,x0,h_on_delta)
#minimize error using fsolve
#out = err.min_grad(delta_0)
out = err.min_grad_z(delta_0[-1])
# collect output variables
delta_i = out[0]
delta.append(delta_i)
err_min.append(out[1])
elapsed_time = out[2]
#print "delta= ", delta_i
L2_f.append(err.L2_f)
rel_error.append(err_min[-1]/L2_f[-1])
c_rel_error.append(sign(delta_i[-1])*sqrt(dot(delta_i,delta_i))/(c*t[-1]))
#create string and dump to screen and file
if dim == 2:
str = "%g\t [ %g %g ] \t %g\t %g\t %g\t %g\t%g" % (t[-1],delta_i[0],delta_i[1],err_min[-1],L2_f[-1],rel_error[-1],c_rel_error[-1],elapsed_time)
elif dim == 3:
str = "%g\t [ %g %g %g ] \t %g\t %g\t %g\t %g\t%g" % (t[-1],delta_i[0],delta_i[1],delta_i[2],err_min[-1],L2_f[-1],rel_error[-1],c_rel_error[-1],elapsed_time)
disp(str)
delta_0 = delta_i
# set up dictionary and pickle
list = [['c', swave.c],['d', swave.d],['n',swave.n],['m',swave.m],
['h_on_delta',h_on_delta],['dh_on_delta', dh_node_delta],['dt',dt],
[ 'time', t], ['delta', delta], ['min_err', err_min], ['L2_f', L2_f], ['rel_error', rel_error], ['c_rel_error',c_rel_error]]
d = dict(list)
f = file('ErrorFile.pkl','w+')
dump(d,f)
def convert(fluidity_options_file_path, ff_options_file_path):
# Read in Fluidity simulation options
libspud.clear_options()
libspud.load_options(fluidity_options_file_path)
# Simulation name
simulation_name = libspud.get_option("/simulation_name")
# Geometry
base = "/geometry"
dimension = libspud.get_option(base + "/dimension")
mesh_path = libspud.get_option(
base + "/mesh::CoordinateMesh/from_file/file_name"
) + ".msh" # FIXME: Always assumes gmsh format.
# Function spaces
velocity_function_space = FunctionSpace("/geometry", 1)
freesurface_function_space = FunctionSpace("/geometry", 2)
# Timestepping
base = "/timestepping"
current_time = libspud.get_option(base + "/current_time")
timestep = libspud.get_option(base + "/timestep")
finish_time = libspud.get_option(base + "/finish_time")
## Steady-state
if (libspud.have_option(base + "/steady_state")):
if (libspud.have_option(base + "/steady_state/tolerance")):
steady_state = libspud.get_option(base + "/steady_state/tolerance")
else:
steady_state = 1e-7
else:
steady_state = None
# I/O
base = "/io"
dump_format = libspud.get_option(base + "/dump_format")
if (libspud.have_option(base + "/dump_period")):
dump_period = libspud.get_option(base + "/dump_period/constant")
elif (libspud.have_option(base + "/dump_period_in_timesteps")):
dump_period = libspud.get_option(
base + "/dump_period_in_timesteps/constant") * timestep
else:
print "Unable to obtain dump_period."
sys.exit()
# Gravity
g_magnitude = libspud.get_option("/physical_parameters/gravity/magnitude")
# Velocity field (momentum equation)
base = "/material_phase[0]/vector_field::Velocity"
## Depth (free surface mean height)
c = libspud.get_child_name(
base +
"/prognostic/equation::ShallowWater/scalar_field::BottomDepth/prescribed/value::WholeMesh/",
1)
depth = libspud.get_option(
base +
"/prognostic/equation::ShallowWater/scalar_field::BottomDepth/prescribed/value::WholeMesh/%s"
% c)
## Bottom drag coefficient
if (libspud.have_option(base +
"/prognostic/equation::ShallowWater/bottom_drag")):
c = libspud.get_child_name(
base +
"/prognostic/equation::ShallowWater/bottom_drag/scalar_field::BottomDragCoefficient/prescribed/value::WholeMesh/",
1)
bottom_drag = libspud.get_option(
base +
"/prognostic/equation::ShallowWater/bottom_drag/scalar_field::BottomDragCoefficient/prescribed/value::WholeMesh/%s"
% c)
else:
bottom_drag = None
## Viscosity
if (libspud.have_option(base + "/prognostic/tensor_field::Viscosity")):
viscosity = libspud.get_option(
base +
"/prognostic/tensor_field::Viscosity/prescribed/value::WholeMesh/anisotropic_symmetric/constant"
)[0][0]
else:
viscosity = None
## Momentum source
if (libspud.have_option(base + "/prognostic/vector_field::Source")):
c = libspud.get_child_name(
base +
"/prognostic/vector_field::Source/prescribed/value::WholeMesh/", 1)
momentum_source = libspud.get_option(
base +
"/prognostic/vector_field::Source/prescribed/value::WholeMesh/%s" %
c)
else:
momentum_source = None
## Initial condition
if (libspud.have_option(base +
"/prognostic/initial_condition::WholeMesh")):
c = libspud.get_child_name(
base + "/prognostic/initial_condition::WholeMesh/", 1)
velocity_initial_condition = libspud.get_option(
base + "/prognostic/initial_condition::WholeMesh/%s" % c)
else:
velocity_initial_condition = 0.0
## Boundary conditions
number_of_bcs = libspud.option_count(base +
"/prognostic/boundary_conditions")
velocity_bcs = []
for i in range(number_of_bcs):
velocity_bcs.append(
VelocityBoundaryCondition(base +
"/prognostic/boundary_conditions[%d]" %
i))
# Pressure field (continuity equation)
base = "/material_phase[0]/scalar_field::Pressure"
integrate_by_parts = libspud.have_option(
base +
"/prognostic/spatial_discretisation/continuous_galerkin/integrate_continuity_by_parts"
)
## Initial condition
if (libspud.have_option(base +
"/prognostic/initial_condition::WholeMesh")):
c = libspud.get_child_name(
base + "/prognostic/initial_condition::WholeMesh/", 1)
pressure_initial_condition = libspud.get_option(
base + "/prognostic/initial_condition::WholeMesh/%s" % c)
else:
pressure_initial_condition = 0.0
## Boundary conditions
number_of_bcs = libspud.option_count(base +
"/prognostic/boundary_conditions")
pressure_bcs = []
for i in range(number_of_bcs):
pressure_bcs.append(
PressureBoundaryCondition(base +
"/prognostic/boundary_conditions[%d]" %
i))
## Continuity source
if (libspud.have_option(base + "/prognostic/scalar_field::Source")):
c = libspud.get_child_name(
base +
"/prognostic/scalar_field::Source/prescribed/value::WholeMesh/", 1)
continuity_source = libspud.get_option(
base +
"/prognostic/scalar_field::Source/prescribed/value::WholeMesh/%s" %
c)
else:
continuity_source = None
# Write out to a Firedrake-Fluids simulation configuration file
libspud.clear_options()
# Create a bare-bones .swml file to add to.
f = open(ff_options_file_path, "w")
f.write("<?xml version='1.0' encoding='utf-8'?>\n")
f.write("<shallow_water_options>\n")
f.write("</shallow_water_options>\n")
f.close()
libspud.load_options(ff_options_file_path)
# Simulation name
libspud.set_option("/simulation_name", simulation_name)
# Geometry
base = "/geometry"
libspud.set_option(base + "/dimension", dimension)
libspud.set_option(base + "/mesh/from_file/relative_path", mesh_path)
# Function spaces
base = "/function_spaces"
libspud.set_option(base + "/function_space::VelocityFunctionSpace/degree",
velocity_function_space.degree)
libspud.set_option(base + "/function_space::VelocityFunctionSpace/family",
velocity_function_space.family)
libspud.set_option(
base + "/function_space::FreeSurfaceFunctionSpace/degree",
freesurface_function_space.degree)
libspud.set_option(
base + "/function_space::FreeSurfaceFunctionSpace/family",
freesurface_function_space.family)
# I/O
base = "/io"
libspud.set_option(base + "/dump_format", dump_format)
libspud.set_option(base + "/dump_period", dump_period)
# Timestepping
base = "/timestepping"
print timestep
libspud.set_option(base + "/current_time", current_time)
try:
libspud.set_option(base + "/timestep", timestep)
except:
pass
libspud.set_option(base + "/finish_time", finish_time)
## Steady-state
if (steady_state):
libspud.set_option(base + "/steady_state/tolerance", steady_state)
# Gravity
libspud.set_option("/physical_parameters/gravity/magnitude", g_magnitude)
# System/Core Fields: Velocity
base = "/system/core_fields/vector_field::Velocity"
## Initial condition
if (isinstance(velocity_initial_condition, str)):
libspud.set_option(base + "/initial_condition/python",
velocity_initial_condition)
else:
libspud.set_option(base + "/initial_condition/constant",
velocity_initial_condition)
## Boundary conditions
try:
for i in range(len(velocity_bcs)):
libspud.set_option(
base +
"/boundary_condition::%s/surface_ids" % velocity_bcs[i].name,
velocity_bcs[i].surface_ids)
libspud.set_option_attribute(
base +
"/boundary_condition::%s/type/name" % velocity_bcs[i].name,
velocity_bcs[i].type)
if (velocity_bcs[i].type == "dirichlet"):
if (isinstance(velocity_bcs[i].value, str)):
libspud.set_option(
base +
"/boundary_condition::%s/type::dirichlet/value/python"
% velocity_bcs[i].name, velocity_bcs[i].value)
else:
libspud.set_option(
base +
"/boundary_condition::%s/type::dirichlet/value/constant"
% velocity_bcs[i].name, velocity_bcs[i].value)
except:
pass
# System/Core Fields: FreeSurfacePerturbation
base = "/system/core_fields/scalar_field::FreeSurfacePerturbation"
#FIXME: Pressure initial and boundary conditions are multiplied by 'g' in Fluidity, but not in Firedrake-Fluids.
## Initial condition
if (isinstance(pressure_initial_condition, str)):
libspud.set_option(base + "/initial_condition/python",
pressure_initial_condition)
else:
libspud.set_option(base + "/initial_condition/constant",
pressure_initial_condition)
## Boundary conditions
try:
for i in range(len(pressure_bcs)):
libspud.set_option(
base +
"/boundary_condition::%s/surface_ids" % pressure_bcs[i].name,
pressure_bcs[i].surface_ids)
libspud.set_option(
base +
"/boundary_condition::%s/type/name" % pressure_bcs[i].name,
pressure_bcs[i].type)
if (pressure_bcs[i].type == "dirichlet"):
if (isinstance(pressure_bcs[i].value, str)):
libspud.set_option(
base +
"/boundary_condition::%s/type::dirichlet/value/python"
% pressure_bcs[i].name, pressure_bcs[i].value)
else:
libspud.set_option(
base +
"/boundary_condition::%s/type::dirichlet/value/constant"
% pressure_bcs[i].name, pressure_bcs[i].value)
except:
pass
# System/Core Fields: FreeSurfaceMean
base = "/system/core_fields/scalar_field::FreeSurfaceMean"
if (isinstance(depth, str)):
libspud.set_option(base + "/value/python", depth)
else:
libspud.set_option(base + "/value/constant", depth)
# Equations: Continuity equation
base = "/system/equations/continuity_equation"
libspud.set_option(base + "/integrate_by_parts", integrate_by_parts)
## Source term
if (continuity_source is not None):
if (isinstance(continuity_source, str)):
libspud.set_option(
base + "/source_term/scalar_field::Source/value/python",
continuity_source)
else:
libspud.set_option(
base + "/source_term/scalar_field::Source/value/constant",
continuity_source)
# Equations: Momentum equation
base = "/system/equations/momentum_equation"
## Viscosity
if (viscosity is not None):
if (isinstance(viscosity, str)):
libspud.set_option(
base + "/stress_term/scalar_field::Viscosity/value/python",
viscosity)
else:
libspud.set_option(
base + "/stress_term/scalar_field::Viscosity/value/constant",
viscosity)
## Bottom drag
if (bottom_drag is not None):
if (isinstance(bottom_drag, str)):
libspud.set_option(
base +
"/drag_term/scalar_field::BottomDragCoefficient/value/python",
bottom_drag)
else:
libspud.set_option(
base +
"/drag_term/scalar_field::BottomDragCoefficient/value/constant",
bottom_drag)
## Source term
if (momentum_source is not None):
if (isinstance(momentum_source, str)):
libspud.set_option(
base + "/source_term/vector_field::Source/value/python",
momentum_source)
else:
libspud.set_option(
base + "/source_term/vector_field::Source/value/constant",
momentum_source)
# Write all the applied options to file.
libspud.write_options(ff_options_file_path)
return
def extract():
table0 = []
table0.append("\\begin{tabular}{c|ccccccc}\n")
table0.append(
" & $\Nu$ & $v_{rms}$ & $\max(u|_{z=1})$ & $<u|_{z=1}>$ & $<T + \\bar{T}>$ & $<\phi>$ & $<W>$ \\\\\n"
)
table0.append("\hline\n")
libspud.load_options(name + ".tfml")
ioname = libspud.get_option("/io/output_base_name")
Ra = libspud.get_option(
"/system::Stokes/coefficient::RayleighNumber/type::Constant/rank::Scalar/value::WholeMesh/constant"
)
Di = libspud.get_option(
"/system::Stokes/coefficient::DissipationNumber/type::Constant/rank::Scalar/value::WholeMesh/constant"
)
for n in ncells:
dir_name = "run_" + ` n `
chdir(dir_name)
try:
stat = parser(ioname + ".stat")
except IOError:
os.chdir("../")
continue
try:
det = parser(ioname + ".det")
except IOError:
os.chdir("../")
continue
nu = -1.0 * (
stat["Stokes"]["Temperature"]["FullTopSurfaceIntegral"][-1])
v_rms = sqrt(stat["Stokes"]["Velocity"]["L2NormSquared"][-1]) * Ra
v_surf_max = abs(det["Stokes"]["Velocity_0"]["Array"][:,
-1]).max() * Ra
v_surf_int = stat["Stokes"]["Velocity"]["TopSurfaceIntegral"][-1] * Ra
T_int = stat["Stokes"]["Temperature"]["FullIntegral"][-1]
phi_int = stat["ViscousDissipation"]["ViscousDissipation"]["Integral"][
-1] * Ra * Di
W_int = stat["WorkDone"]["WorkDone"]["Integral"][-1] * Ra
table0.append(
"{0:2d}$\\times${0:2d} & {1:.3f} & {2:.3f} & {3:.3f} & {4:.3f} & {5:.3f} & {6:.3f} & {7:.3f} \\\\\n"
.format(n, nu, v_rms, v_surf_max, v_surf_int, T_int, phi_int,
W_int))
os.chdir("../")
libspud.clear_options()
Raind = int(round(Ra))
Diind = '%d' % Di if Di == int(Di) else '%s' % Di
f = file("../../../tables.dict", 'r')
tables = pickle.load(f)
f.close()
table0.append("\hline\n")
for code, values in tables[approx][Raind][Diind].iteritems():
if len(values) > 0 and code in comparisoncodes:
line = "Benchmark (" + code + ") & "
for v in range(len(values) - 1):
line += '%.3f' % values[v] + " & "
line += '%.3f' % values[-1] + " \\\\\n"
table0.append(line)
table0.append("\\end{tabular}\n")
for line in table0:
print line[0:-1]
filename = "table0.tex"
filehandle = file(filename, 'w')
filehandle.writelines(table0)
filehandle.close()
def convert(fluidity_options_file_path, ff_options_file_path):
# Read in Fluidity simulation options
libspud.clear_options()
libspud.load_options(fluidity_options_file_path)
# Simulation name
simulation_name = libspud.get_option("/simulation_name")
# Geometry
base = "/geometry"
dimension = libspud.get_option(base + "/dimension")
mesh_path = libspud.get_option(base + "/mesh::CoordinateMesh/from_file/file_name") + ".msh" # FIXME: Always assumes gmsh format.
# Function spaces
velocity_function_space = FunctionSpace("/geometry", 1)
freesurface_function_space = FunctionSpace("/geometry", 2)
# Timestepping
base = "/timestepping"
current_time = libspud.get_option(base + "/current_time")
timestep = libspud.get_option(base + "/timestep")
finish_time = libspud.get_option(base + "/finish_time")
## Steady-state
if(libspud.have_option(base + "/steady_state")):
if(libspud.have_option(base + "/steady_state/tolerance")):
steady_state = libspud.get_option(base + "/steady_state/tolerance")
else:
steady_state = 1e-7
else:
steady_state = None
# I/O
base = "/io"
dump_format = libspud.get_option(base + "/dump_format")
if(libspud.have_option(base + "/dump_period")):
dump_period = libspud.get_option(base + "/dump_period/constant")
elif(libspud.have_option(base + "/dump_period_in_timesteps")):
dump_period = libspud.get_option(base + "/dump_period_in_timesteps/constant")*timestep
else:
print "Unable to obtain dump_period."
sys.exit()
# Gravity
g_magnitude = libspud.get_option("/physical_parameters/gravity/magnitude")
# Velocity field (momentum equation)
base = "/material_phase[0]/vector_field::Velocity"
## Depth (free surface mean height)
c = libspud.get_child_name(base + "/prognostic/equation::ShallowWater/scalar_field::BottomDepth/prescribed/value::WholeMesh/", 1)
depth = libspud.get_option(base + "/prognostic/equation::ShallowWater/scalar_field::BottomDepth/prescribed/value::WholeMesh/%s" % c)
## Bottom drag coefficient
if(libspud.have_option(base + "/prognostic/equation::ShallowWater/bottom_drag")):
c = libspud.get_child_name(base + "/prognostic/equation::ShallowWater/bottom_drag/scalar_field::BottomDragCoefficient/prescribed/value::WholeMesh/", 1)
bottom_drag = libspud.get_option(base + "/prognostic/equation::ShallowWater/bottom_drag/scalar_field::BottomDragCoefficient/prescribed/value::WholeMesh/%s" % c)
else:
bottom_drag = None
## Viscosity
if(libspud.have_option(base + "/prognostic/tensor_field::Viscosity")):
viscosity = libspud.get_option(base + "/prognostic/tensor_field::Viscosity/prescribed/value::WholeMesh/anisotropic_symmetric/constant")[0][0]
else:
viscosity = None
## Momentum source
if(libspud.have_option(base + "/prognostic/vector_field::Source")):
c = libspud.get_child_name(base + "/prognostic/vector_field::Source/prescribed/value::WholeMesh/", 1)
momentum_source = libspud.get_option(base + "/prognostic/vector_field::Source/prescribed/value::WholeMesh/%s" % c)
else:
momentum_source = None
## Initial condition
if(libspud.have_option(base + "/prognostic/initial_condition::WholeMesh")):
c = libspud.get_child_name(base + "/prognostic/initial_condition::WholeMesh/", 1)
velocity_initial_condition = libspud.get_option(base + "/prognostic/initial_condition::WholeMesh/%s" % c)
else:
velocity_initial_condition = 0.0
## Boundary conditions
number_of_bcs = libspud.option_count(base + "/prognostic/boundary_conditions")
velocity_bcs = []
for i in range(number_of_bcs):
velocity_bcs.append(VelocityBoundaryCondition(base + "/prognostic/boundary_conditions[%d]" % i))
# Pressure field (continuity equation)
base = "/material_phase[0]/scalar_field::Pressure"
integrate_by_parts = libspud.have_option(base + "/prognostic/spatial_discretisation/continuous_galerkin/integrate_continuity_by_parts")
## Initial condition
if(libspud.have_option(base + "/prognostic/initial_condition::WholeMesh")):
c = libspud.get_child_name(base + "/prognostic/initial_condition::WholeMesh/", 1)
pressure_initial_condition = libspud.get_option(base + "/prognostic/initial_condition::WholeMesh/%s" % c)
else:
pressure_initial_condition = 0.0
## Boundary conditions
number_of_bcs = libspud.option_count(base + "/prognostic/boundary_conditions")
pressure_bcs = []
for i in range(number_of_bcs):
pressure_bcs.append(PressureBoundaryCondition(base + "/prognostic/boundary_conditions[%d]" % i))
## Continuity source
if(libspud.have_option(base + "/prognostic/scalar_field::Source")):
c = libspud.get_child_name(base + "/prognostic/scalar_field::Source/prescribed/value::WholeMesh/", 1)
continuity_source = libspud.get_option(base + "/prognostic/scalar_field::Source/prescribed/value::WholeMesh/%s" % c)
else:
continuity_source = None
# Write out to a Firedrake-Fluids simulation configuration file
libspud.clear_options()
# Create a bare-bones .swml file to add to.
f = open(ff_options_file_path, "w")
f.write("<?xml version='1.0' encoding='utf-8'?>\n")
f.write("<shallow_water_options>\n")
f.write("</shallow_water_options>\n")
f.close()
libspud.load_options(ff_options_file_path)
# Simulation name
libspud.set_option("/simulation_name", simulation_name)
# Geometry
base = "/geometry"
libspud.set_option(base + "/dimension", dimension)
libspud.set_option(base + "/mesh/from_file/relative_path", mesh_path)
# Function spaces
base = "/function_spaces"
libspud.set_option(base + "/function_space::VelocityFunctionSpace/degree", velocity_function_space.degree)
libspud.set_option(base + "/function_space::VelocityFunctionSpace/family", velocity_function_space.family)
libspud.set_option(base + "/function_space::FreeSurfaceFunctionSpace/degree", freesurface_function_space.degree)
libspud.set_option(base + "/function_space::FreeSurfaceFunctionSpace/family", freesurface_function_space.family)
# I/O
base = "/io"
libspud.set_option(base + "/dump_format", dump_format)
libspud.set_option(base + "/dump_period", dump_period)
# Timestepping
base = "/timestepping"
print timestep
libspud.set_option(base + "/current_time", current_time)
try:
libspud.set_option(base + "/timestep", timestep)
except:
pass
libspud.set_option(base + "/finish_time", finish_time)
## Steady-state
if(steady_state):
libspud.set_option(base + "/steady_state/tolerance", steady_state)
# Gravity
libspud.set_option("/physical_parameters/gravity/magnitude", g_magnitude)
# System/Core Fields: Velocity
base = "/system/core_fields/vector_field::Velocity"
## Initial condition
if(isinstance(velocity_initial_condition, str)):
libspud.set_option(base + "/initial_condition/python", velocity_initial_condition)
else:
libspud.set_option(base + "/initial_condition/constant", velocity_initial_condition)
## Boundary conditions
try:
for i in range(len(velocity_bcs)):
libspud.set_option(base + "/boundary_condition::%s/surface_ids" % velocity_bcs[i].name, velocity_bcs[i].surface_ids)
libspud.set_option_attribute(base + "/boundary_condition::%s/type/name" % velocity_bcs[i].name, velocity_bcs[i].type)
if(velocity_bcs[i].type == "dirichlet"):
if(isinstance(velocity_bcs[i].value, str)):
libspud.set_option(base + "/boundary_condition::%s/type::dirichlet/value/python" % velocity_bcs[i].name, velocity_bcs[i].value)
else:
libspud.set_option(base + "/boundary_condition::%s/type::dirichlet/value/constant" % velocity_bcs[i].name, velocity_bcs[i].value)
except:
pass
# System/Core Fields: FreeSurfacePerturbation
base = "/system/core_fields/scalar_field::FreeSurfacePerturbation"
#FIXME: Pressure initial and boundary conditions are multiplied by 'g' in Fluidity, but not in Firedrake-Fluids.
## Initial condition
if(isinstance(pressure_initial_condition, str)):
libspud.set_option(base + "/initial_condition/python", pressure_initial_condition)
else:
libspud.set_option(base + "/initial_condition/constant", pressure_initial_condition)
## Boundary conditions
try:
for i in range(len(pressure_bcs)):
libspud.set_option(base + "/boundary_condition::%s/surface_ids" % pressure_bcs[i].name, pressure_bcs[i].surface_ids)
libspud.set_option(base + "/boundary_condition::%s/type/name" % pressure_bcs[i].name, pressure_bcs[i].type)
if(pressure_bcs[i].type == "dirichlet"):
if(isinstance(pressure_bcs[i].value, str)):
libspud.set_option(base + "/boundary_condition::%s/type::dirichlet/value/python" % pressure_bcs[i].name, pressure_bcs[i].value)
else:
libspud.set_option(base + "/boundary_condition::%s/type::dirichlet/value/constant" % pressure_bcs[i].name, pressure_bcs[i].value)
except:
pass
# System/Core Fields: FreeSurfaceMean
base = "/system/core_fields/scalar_field::FreeSurfaceMean"
if(isinstance(depth, str)):
libspud.set_option(base + "/value/python", depth)
else:
libspud.set_option(base + "/value/constant", depth)
# Equations: Continuity equation
base = "/system/equations/continuity_equation"
libspud.set_option(base + "/integrate_by_parts", integrate_by_parts)
## Source term
if(continuity_source is not None):
if(isinstance(continuity_source, str)):
libspud.set_option(base + "/source_term/scalar_field::Source/value/python", continuity_source)
else:
libspud.set_option(base + "/source_term/scalar_field::Source/value/constant", continuity_source)
# Equations: Momentum equation
base = "/system/equations/momentum_equation"
## Viscosity
if(viscosity is not None):
if(isinstance(viscosity, str)):
libspud.set_option(base + "/stress_term/scalar_field::Viscosity/value/python", viscosity)
else:
libspud.set_option(base + "/stress_term/scalar_field::Viscosity/value/constant", viscosity)
## Bottom drag
if(bottom_drag is not None):
if(isinstance(bottom_drag, str)):
libspud.set_option(base + "/drag_term/scalar_field::BottomDragCoefficient/value/python", bottom_drag)
else:
libspud.set_option(base + "/drag_term/scalar_field::BottomDragCoefficient/value/constant", bottom_drag)
## Source term
if(momentum_source is not None):
if(isinstance(momentum_source, str)):
libspud.set_option(base + "/source_term/vector_field::Source/value/python", momentum_source)
else:
libspud.set_option(base + "/source_term/vector_field::Source/value/constant", momentum_source)
# Write all the applied options to file.
libspud.write_options(ff_options_file_path)
return
def __init__(self, path, checkpoint=None):
""" Initialise a new shallow water simulation, using an options file.
:param str path: The path to the simulation's configuration/options file.
:param str checkpoint: The path to a checkpoint file.
:returns: None
"""
LOG.info("Initialising simulation...")
# Remove any stored options.
libspud.clear_options()
# Load the options from the options tree.
libspud.load_options(path)
# Populate the options dictionary
self.populate_options()
# Read in the input mesh (or construct one)
self.mesh = self.get_mesh(path)
# Create a dictionary containing all the function spaces
LOG.info("Creating function spaces...")
self.function_spaces = {}
# The Velocity field's function space
name = "VelocityFunctionSpace"
path = "/function_spaces/function_space::%s" % name
family = libspud.get_option(path+"/family")
degree = libspud.get_option(path+"/degree")
try:
if(family == "Continuous Lagrange"):
self.function_spaces[name] = VectorFunctionSpace(self.mesh, "CG", degree)
elif(family == "Discontinuous Lagrange"):
self.function_spaces[name] = VectorFunctionSpace(self.mesh, "DG", degree)
else:
raise ValueError("Unknown element family: %s." % family)
except ValueError as e:
LOG.exception(e)
sys.exit()
LOG.debug("Created a new %s function space of degree %d for Velocity" % (family, degree))
# The FreeSurfacePerturbation field's function space
name = "FreeSurfaceFunctionSpace"
path = "/function_spaces/function_space::%s" % name
family = libspud.get_option(path+"/family")
degree = libspud.get_option(path+"/degree")
try:
if(family == "Continuous Lagrange"):
self.function_spaces[name] = FunctionSpace(self.mesh, "CG", degree)
elif(family == "Discontinuous Lagrange"):
self.function_spaces[name] = FunctionSpace(self.mesh, "DG", degree)
else:
raise ValueError("Unknown element family: %s." % family)
except ValueError as e:
LOG.exception(e)
sys.exit()
LOG.debug("Created a new %s function space of degree %d for FreeSurfacePerturbation" % (family, degree))
# Get the function spaces
U = self.function_spaces["VelocityFunctionSpace"]
H = self.function_spaces["FreeSurfaceFunctionSpace"]
# Test functions
self.w = TestFunction(U)
self.v = TestFunction(H)
LOG.info("Test functions created.")
# Trial functions (i.e. the solutions for time n+1)
self.u = TrialFunction(U)
self.h = TrialFunction(H)
LOG.info("Trial functions created.")
# Normal vector to each element facet
self.n = FacetNormal(self.mesh)
# Set up initial conditions
LOG.info("Setting initial conditions...")
h_initial = ExpressionFromOptions(path = "/system/core_fields/scalar_field::FreeSurfacePerturbation/initial_condition").get_expression()
u_initial = ExpressionFromOptions(path = "/system/core_fields/vector_field::Velocity/initial_condition").get_expression()
# The solution at time n.
self.u0 = Function(U).interpolate(u_initial)
self.h0 = Function(H).interpolate(h_initial)
# The solution at time n-1.
self.u00 = Function(U)
self.u00.assign(self.u0)
# Load initial conditions from the specified checkpoint file if desired.
if(checkpoint is not None):
self.solution_old.dat.load(checkpoint)
LOG.debug("Loaded initial condition from checkpoint file.")
# Mean free surface height
self.h_mean = Function(H)
self.h_mean.interpolate(ExpressionFromOptions(path = "/system/core_fields/scalar_field::FreeSurfaceMean/value").get_expression())
# Set up the functions used to write fields to file.
self.output_functions = {}
self.output_functions["Velocity"] = Function(U, name="Velocity")
self.output_functions["FreeSurfacePerturbation"] = Function(H, name="FreeSurfacePerturbation")
# Set up the output stream
LOG.info("Initialising output file streams...")
self.output_files = {}
for field in self.output_functions.keys():
self.output_files[field] = File("%s_%s.pvd" % (self.options["simulation_name"], field))
# Write initial conditions to file
LOG.info("Writing initial conditions to file...")
self.output_functions["Velocity"].assign(self.u0)
self.output_files["Velocity"] << self.output_functions["Velocity"]
self.output_functions["FreeSurfacePerturbation"].assign(self.h0)
self.output_files["FreeSurfacePerturbation"] << self.output_functions["FreeSurfacePerturbation"]
return
def exception_test(test_str, exception):
"""Test should throw exception."""
try:
suite.test_cases.append(TestCase("%s fails" % test_str))
eval(test_str)
suite.test_cases[-1].add_failure_info('No exception')
except exception as e:
return
# reach here on test failure
suite.test_cases[-1].add_failure_info('Exception', str(e))
try:
suite.test_cases.append(TestCase('libspud for python.load_options'))
libspud.load_options(dirpath + '/test.flml')
except:
suite.test_cases[-1].add_failure_info('Exception')
with open('test_results.xml', 'w') as handle:
suite.to_file(handle, [suite])
raise ValueError
test("libspud.get_option('/timestepping/timestep') == 0.025")
test("libspud.get_number_of_children('/geometry') == 5")
test("libspud.get_child_name('geometry', 0) == 'dimension'")
test("libspud.option_count('/problem_type') == 1")
test("libspud.have_option('/problem_type')")
test("libspud.get_option_type('/geometry/dimension') is int")
test("libspud.get_option_type('/problem_type') is str")
def __init__(self, filename):
libspud.load_options(filename)
def load_options(self, filename):
self.lock.acquire()
try:
libspud.load_options(filename)
except:
self.lock.release()
def gen_flmls(params, template_dir, output_dir, paths, names, verbose):
import types
# get flml file from template_dir - first one we come across
# If you have more in there, tough.
full_flml = glob.glob(os.path.join(template_dir, '*.flml'))[0]
# strip to the filename only
flml = os.path.basename(full_flml)
f = open(os.path.join(output_dir, 'runs', "directory_listing.csv"), "w")
# append data to directory listing file
line = "Directory number"
for n in names:
line = line + "," + n
line = line + "\n"
f.write(line)
# loop over paramas
# create a new directory, with a unqiue number, starting from 1
# This makes it easier to use in an array job on CX1
dir_num = 1
for p_set in params:
if (verbose):
print "Processing " + str(dir_num)
# copy contents from template folder to directory number
dirname = os.path.join(output_dir, 'runs', str(dir_num))
if (os.path.exists(os.path.join(dirname))):
shutil.rmtree(dirname)
shutil.copytree(template_dir, dirname)
# open FLML file
output_file = os.path.join(dirname, flml)
# This load the data into the memory of the libspud library
libspud.load_options(output_file)
i = 0
for path in paths:
path = path.strip()
# get type
path_type = libspud.get_option_type(path)
path_rank = libspud.get_option_rank(path)
path_shape = libspud.get_option_shape(path)
if (path_type is float and path_rank == 0):
libspud.set_option(path, float(p_set[i]))
elif (path_rank == 1 and path_type is float):
value = eval(p_set[i])
val = list(map(float, value))
libspud.set_option(path, val)
elif (path_rank == 2 and path_type is float):
value = eval(p_set[i])
val = []
for row in value:
val.append(list(map(float, row)))
libspud.set_option(path, val)
i = i + 1
# save file
libspud.write_options(output_file)
# append data to directory listing file
line = str(dir_num)
for p in p_set:
# quoting the params so csv parsers can get the columns right
line = line + "," + '"' + str(p) + '"'
line = line + "\n"
f.write(line)
dir_num += 1
f.close()
def test17(self):
with self.assertRaises(SystemExit):
#should be an osml file
libspud.clear_options()
try:
libspud.load_options('test17.osml')
except:
print "This file doesn't exist or is the wrong file type. It should be a .osml file"
sys.exit()
try:
start = float(
libspud.get_option(
'/diffusion_model/timestepping/start_time', ))
end = float(
libspud.get_option(
'/diffusion_model/timestepping/end_time'))
time_step = float(
libspud.get_option(
'/diffusion_model/timestepping/timestep'))
mesh_int = int(
libspud.get_option(
'/diffusion_model/mesh/initial_mesh_size'))
alpha = float(
libspud.get_option(
'/diffusion_model/model_parameters/diffusion_coefficient'
))
initial_conditions = str(
libspud.get_option(
'/diffusion_model/model_parameters/initial_conditions')
)
except:
print 'The information provided was incomplete, please recreate the file'
sys.exit()
print start
print end
print time_step
print mesh_int
print alpha
print initial_conditions
#create a simple testcase
model = SedimentModel()
mesh = UnitSquareMesh(mesh_int, mesh_int)
model.set_mesh(mesh)
init_cond = Expression(initial_conditions) # simple slope
init_sed = Expression('x[0]') # this gives
# total of above gives a slope of 0 to 2 (over the unit square)
model.set_initial_conditions(init_cond, init_sed)
model.set_end_time(end)
model.set_diffusion_coeff(alpha)
model.init()
model.solve()
# answer should be 1 everywhere
plot(model.get_total_height(), interactive=True)
answer = model.get_total_height_array()
def generate():
libspud.load_options(name + ".tfml")
meshbasename = libspud.get_option("/geometry/mesh::Mesh/source::File/file")
libspud.clear_options()
for n in ncells:
dir_name = "run_" + ` n `
try:
os.mkdir(dir_name)
except OSError:
pass
chdir(dir_name)
tempgeo = file("../../../../../src/transfinite_square_template.geo",
'r')
templines = tempgeo.readlines()
tempgeo.close()
lines = []
for templine in templines:
line = template(templine).substitute({'ncells': n, 'factor': 0.01})
lines.append(line)
geo = file(meshbasename + "_temp.geo", 'w')
geo.writelines(lines)
geo.close()
try:
checksum = hashlib.md5(open(meshbasename +
".geo").read()).hexdigest()
except:
checksum = None
if checksum != hashlib.md5(
open(meshbasename + "_temp.geo").read()).hexdigest():
# file has changed
shutil.copy(meshbasename + "_temp.geo", meshbasename + ".geo")
try:
subprocess.check_call(
["gmsh", "-2", "-algo", "del2d", meshbasename + ".geo"])
except:
print "ERROR while calling gmsh in directory ", dir_name
os.chdir("../")
sys.exit(1)
try:
subprocess.check_call([
"dolfin-convert", meshbasename + ".msh",
meshbasename + ".xml"
])
except:
print "ERROR while calling dolfin-convert in directory ", dir_name
os.chdir("../")
sys.exit(1)
extensions = [".xml", "_facet_region.xml"]
for ext in extensions:
try:
subprocess.check_call(["gzip", "-f", meshbasename + ext])
except:
print "ERROR while calling gzip in directory ", dir_name, " on extension ", ext
os.chdir("../")
sys.exit(1)
os.chdir("../")
def __init__(self, tfml_file,system_name='magma',p_name='Pressure',f_name='Porosity',c_name='c',n_name='n',m_name='m',d_name='d',N_name='N',h_squared_name='h_squared',x0_name='x0'):
"""read the tfml_file and use libspud to populate the internal parameters
c: wavespeed
n: permeability exponent
m: bulk viscosity exponent
d: wave dimension
N: number of collocation points
x0: coordinate wave peak
h_squared: the size of the system in compaction lengths
squared (h/delta)**2
"""
# initialize libspud and extract parameters
libspud.clear_options()
libspud.load_options(tfml_file)
# get model dimension
self.dim = libspud.get_option("/geometry/dimension")
self.system_name = system_name
# get solitary wave parameters
path="/system::"+system_name+"/coefficient::"
scalar_value="/type::Constant/rank::Scalar/value::WholeMesh/constant"
vector_value="/type::Constant/rank::Vector/value::WholeMesh/constant::dim"
c = libspud.get_option(path+c_name+scalar_value)
n = int(libspud.get_option(path+n_name+scalar_value))
m = int(libspud.get_option(path+m_name+scalar_value))
d = float(libspud.get_option(path+d_name+scalar_value))
N = int(libspud.get_option(path+N_name+scalar_value))
self.h = np.sqrt(libspud.get_option(path+h_squared_name+scalar_value))
self.x0 = np.array(libspud.get_option(path+x0_name+vector_value))
self.swave = SolitaryWave(c,n,m,d,N)
self.rmax = self.swave.r[-1]
self.tfml_file = tfml_file
# check that d <= dim
assert (d <= self.dim)
# sort out appropriate index for calculating distance r
if d == 1:
self.index = [self.dim - 1]
else:
self.index = range(0,int(d))
# check that the origin point is the correct dimension
assert (len(self.x0) == self.dim)
#read in information for constructing Function space and dolfin objects
# get the mesh parameters and reconstruct the mesh
meshtype = libspud.get_option("/geometry/mesh/source[0]/name")
if meshtype == 'UnitSquare':
number_cells = libspud.get_option("/geometry/mesh[0]/source[0]/number_cells")
diagonal = libspud.get_option("/geometry/mesh[0]/source[0]/diagonal")
mesh = df.UnitSquareMesh(number_cells[0],number_cells[1],diagonal)
elif meshtype == 'Rectangle':
x0 = libspud.get_option("/geometry/mesh::Mesh/source::Rectangle/lower_left")
x1 = libspud.get_option("/geometry/mesh::Mesh/source::Rectangle/upper_right")
number_cells = libspud.get_option("/geometry/mesh::Mesh/source::Rectangle/number_cells")
diagonal = libspud.get_option("/geometry/mesh[0]/source[0]/diagonal")
mesh = df.RectangleMesh(x0[0],x0[1],x1[0],x1[1],number_cells[0],number_cells[1],diagonal)
elif meshtype == 'UnitCube':
number_cells = libspud.get_option("/geometry/mesh[0]/source[0]/number_cells")
mesh = df.UnitCubeMesh(number_cells[0],number_cells[1],number_cells[2])
elif meshtype == 'Box':
x0 = libspud.get_option("/geometry/mesh::Mesh/source::Box/lower_back_left")
x1 = libspud.get_option("/geometry/mesh::Mesh/source::Box/upper_front_right")
number_cells = libspud.get_option("/geometry/mesh::Mesh/source::Box/number_cells")
mesh = df.BoxMesh(x0[0],x0[1],x0[2],x1[0],x1[1],x1[2],number_cells[0],number_cells[1],number_cells[2])
elif meshtype == 'UnitInterval':
number_cells = libspud.get_option("/geometry/mesh::Mesh/source::UnitInterval/number_cells")
mesh = df.UnitIntervalMesh(number_cells)
elif meshtype == 'Interval':
number_cells = libspud.get_option("/geometry/mesh::Mesh/source::Interval/number_cells")
left = libspud.get_option("/geometry/mesh::Mesh/source::Interval/left")
right = libspud.get_option("/geometry/mesh::Mesh/source::Interval/right")
mesh = df.IntervalMesh(number_cells,left,right)
elif meshtype == 'File':
mesh_filename = libspud.get_option("/geometry/mesh::Mesh/source::File/file")
print "tfml_file = ",self.tfml_file, "mesh_filename=",mesh_filename
mesh = df.Mesh(mesh_filename)
else:
df.error("Error: unknown mesh type "+meshtype)
#set the functionspace for n-d solitary waves
path="/system::"+system_name+"/field::"
p_family = libspud.get_option(path+p_name+"/type/rank/element/family")
p_degree = libspud.get_option(path+p_name+"/type/rank/element/degree")
f_family = libspud.get_option(path+f_name+"/type/rank/element/family")
f_degree = libspud.get_option(path+f_name+"/type/rank/element/degree")
pe = df.FiniteElement(p_family, mesh.ufl_cell(), p_degree)
ve = df.FiniteElement(f_family, mesh.ufl_cell(), f_degree)
e = pe*ve
self.functionspace = df.FunctionSpace(mesh, e)
#work out the order of the fields
for i in xrange(libspud.option_count("/system::"+system_name+"/field")):
name = libspud.get_option("/system::"+system_name+"/field["+`i`+"]/name")
if name == f_name:
self.f_index = i
if name == p_name:
self.p_index = i
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
from importance_map_tools import *
from importance_map import *
import time
import random
#sys.path.insert(1, '/home/zdt16/MultiFluids_Dev/libspud/')
import libspud
#To load the vtu files and read the coordinates of the nodes
#vtu_data = vtktools.vtu("Input_Importance_map_1.vtu") ###Hardcoded
#coordinates = vtu_data.GetLocations()
#To get the mpml file
path = os.getcwd()
mpmlfile = get_mpml_filename(path)
libspud.load_options(mpmlfile + '.mpml')
meshname_base = libspud.get_option('/geometry[0]/mesh[0]/from_file/file_name')
NDIM = libspud.get_option('/geometry/dimension')
Dt_n = libspud.get_option('/timestepping/timestep') #timestep
tlevel_begin = libspud.get_option('/timestepping/current_time') #start time
tlevel_end = libspud.get_option('/timestepping/finish_time') #end time
NSCALAR = libspud.option_count('/Field_to_study')
DELTA_T = libspud.get_option(
'/io/dump_period_in_timesteps/constant'
) ###change to point to checkpint file in unperturbed
libspud.clear_options()
DT = tlevel_end - tlevel_begin #total simulation period
NTIME = int(DT / Dt_n) + 1 # number of timelevels
def __init__(self,
tfml_file,
system_name='magma',
p_name='Pressure',
f_name='Porosity',
c_name='c',
n_name='n',
m_name='m',
d_name='d',
N_name='N',
h_squared_name='h_squared',
x0_name='x0'):
"""read the tfml_file and use libspud to populate the internal parameters
c: wavespeed
n: permeability exponent
m: bulk viscosity exponent
d: wave dimension
N: number of collocation points
x0: coordinate wave peak
h_squared: the size of the system in compaction lengths
squared (h/delta)**2
"""
# initialize libspud and extract parameters
libspud.clear_options()
libspud.load_options(tfml_file)
# get model dimension
self.dim = libspud.get_option("/geometry/dimension")
self.system_name = system_name
# get solitary wave parameters
path = "/system::" + system_name + "/coefficient::"
scalar_value = "/type::Constant/rank::Scalar/value::WholeMesh/constant"
vector_value = "/type::Constant/rank::Vector/value::WholeMesh/constant::dim"
c = libspud.get_option(path + c_name + scalar_value)
n = int(libspud.get_option(path + n_name + scalar_value))
m = int(libspud.get_option(path + m_name + scalar_value))
d = float(libspud.get_option(path + d_name + scalar_value))
N = int(libspud.get_option(path + N_name + scalar_value))
self.h = np.sqrt(
libspud.get_option(path + h_squared_name + scalar_value))
self.x0 = np.array(libspud.get_option(path + x0_name + vector_value))
self.swave = SolitaryWave(c, n, m, d, N)
self.rmax = self.swave.r[-1]
self.tfml_file = tfml_file
# check that d <= dim
assert (d <= self.dim)
# sort out appropriate index for calculating distance r
if d == 1:
self.index = [self.dim - 1]
else:
self.index = range(0, int(d))
# check that the origin point is the correct dimension
assert (len(self.x0) == self.dim)
#read in information for constructing Function space and dolfin objects
# get the mesh parameters and reconstruct the mesh
meshtype = libspud.get_option("/geometry/mesh/source[0]/name")
if meshtype == 'UnitSquare':
number_cells = libspud.get_option(
"/geometry/mesh[0]/source[0]/number_cells")
diagonal = libspud.get_option(
"/geometry/mesh[0]/source[0]/diagonal")
mesh = df.UnitSquareMesh(number_cells[0], number_cells[1],
diagonal)
elif meshtype == 'Rectangle':
x0 = libspud.get_option(
"/geometry/mesh::Mesh/source::Rectangle/lower_left")
x1 = libspud.get_option(
"/geometry/mesh::Mesh/source::Rectangle/upper_right")
number_cells = libspud.get_option(
"/geometry/mesh::Mesh/source::Rectangle/number_cells")
diagonal = libspud.get_option(
"/geometry/mesh[0]/source[0]/diagonal")
mesh = df.RectangleMesh(x0[0], x0[1], x1[0], x1[1],
number_cells[0], number_cells[1], diagonal)
elif meshtype == 'UnitCube':
number_cells = libspud.get_option(
"/geometry/mesh[0]/source[0]/number_cells")
mesh = df.UnitCubeMesh(number_cells[0], number_cells[1],
number_cells[2])
elif meshtype == 'Box':
x0 = libspud.get_option(
"/geometry/mesh::Mesh/source::Box/lower_back_left")
x1 = libspud.get_option(
"/geometry/mesh::Mesh/source::Box/upper_front_right")
number_cells = libspud.get_option(
"/geometry/mesh::Mesh/source::Box/number_cells")
mesh = df.BoxMesh(x0[0], x0[1], x0[2], x1[0], x1[1], x1[2],
number_cells[0], number_cells[1],
number_cells[2])
elif meshtype == 'UnitInterval':
number_cells = libspud.get_option(
"/geometry/mesh::Mesh/source::UnitInterval/number_cells")
mesh = df.UnitIntervalMesh(number_cells)
elif meshtype == 'Interval':
number_cells = libspud.get_option(
"/geometry/mesh::Mesh/source::Interval/number_cells")
left = libspud.get_option(
"/geometry/mesh::Mesh/source::Interval/left")
right = libspud.get_option(
"/geometry/mesh::Mesh/source::Interval/right")
mesh = df.IntervalMesh(number_cells, left, right)
elif meshtype == 'File':
mesh_filename = libspud.get_option(
"/geometry/mesh::Mesh/source::File/file")
print "tfml_file = ", self.tfml_file, "mesh_filename=", mesh_filename
mesh = df.Mesh(mesh_filename)
else:
df.error("Error: unknown mesh type " + meshtype)
#set the functionspace for n-d solitary waves
path = "/system::" + system_name + "/field::"
p_family = libspud.get_option(path + p_name +
"/type/rank/element/family")
p_degree = libspud.get_option(path + p_name +
"/type/rank/element/degree")
f_family = libspud.get_option(path + f_name +
"/type/rank/element/family")
f_degree = libspud.get_option(path + f_name +
"/type/rank/element/degree")
pe = df.FiniteElement(p_family, mesh.ufl_cell(), p_degree)
ve = df.FiniteElement(f_family, mesh.ufl_cell(), f_degree)
e = pe * ve
self.functionspace = df.FunctionSpace(mesh, e)
#work out the order of the fields
for i in xrange(
libspud.option_count("/system::" + system_name + "/field")):
name = libspud.get_option("/system::" + system_name + "/field[" +
` i ` + "]/name")
if name == f_name:
self.f_index = i
if name == p_name:
self.p_index = i
def gen_flmls(params, template_dir, output_dir, paths, names, verbose):
import types
# get flml file from template_dir - first one we come across
# If you have more in there, tough.
full_flml = glob.glob(os.path.join(template_dir,'*.flml'))[0]
# strip to the filename only
flml = os.path.basename(full_flml)
f = open(os.path.join(output_dir,'runs',"directory_listing.csv"),"w")
# append data to directory listing file
line = "Directory number"
for n in names:
line = line+","+n
line = line + "\n"
f.write(line)
# loop over paramas
# create a new directory, with a unqiue number, starting from 1
# This makes it easier to use in an array job on CX1
dir_num = 1
for p_set in params:
if (verbose):
print "Processing "+str(dir_num)
# copy contents from template folder to directory number
dirname = os.path.join(output_dir,'runs',str(dir_num))
if (os.path.exists(os.path.join(dirname))):
shutil.rmtree(dirname)
shutil.copytree(template_dir,dirname)
# open FLML file
output_file = os.path.join(dirname,flml)
# This load the data into the memory of the libspud library
libspud.load_options(output_file)
i = 0
for path in paths:
path = path.strip()
# get type
path_type = libspud.get_option_type(path)
path_rank = libspud.get_option_rank(path)
path_shape = libspud.get_option_shape(path)
if (path_type is float and path_rank == 0):
libspud.set_option(path,float(p_set[i]))
elif (path_rank == 1 and path_type is float):
value = eval(p_set[i])
val = list(map(float, value))
libspud.set_option(path,val)
elif (path_rank == 2 and path_type is float):
value = eval(p_set[i])
val = []
for row in value:
val.append(list(map(float, row)))
libspud.set_option(path,val)
i = i+1
# save file
libspud.write_options(output_file)
# append data to directory listing file
line = str(dir_num)
for p in p_set:
# quoting the params so csv parsers can get the columns right
line = line+","+'"'+str(p)+'"'
line = line +"\n"
f.write(line)
dir_num += 1
f.close()
import libspud
print libspud.__file__
libspud.load_options('test.flml')
libspud.print_options()
print libspud.number_of_children('/geometry')
print libspud.get_child_name('geometry', 0)
print libspud.option_count('/problem_type')
print libspud.have_option('/problem_type')
print libspud.get_option_type('/geometry/dimension')
print libspud.get_option_type('/problem_type')
print libspud.get_option_rank('/geometry/dimension')
print libspud.get_option_rank(
'/physical_parameters/gravity/vector_field::GravityDirection/prescribed/value/constant'
)
print libspud.get_option_shape('/geometry/dimension')
print libspud.get_option_shape('/problem_type')
print libspud.get_option('/problem_type')
print libspud.get_option('/geometry/dimension')
libspud.set_option('/geometry/dimension', 3)
print libspud.get_option('/geometry/dimension')
list_path = '/material_phase::Material1/scalar_field::MaterialVolumeFraction/prognostic/boundary_conditions::LetNoOneLeave/surface_ids'
print libspud.get_option_shape(list_path)
import libspud
libspud.load_options('test.flml')
#libspud.print_options()
assert libspud.get_option('/timestepping/timestep') == 0.025
assert libspud.get_number_of_children('/geometry') == 5
assert libspud.get_child_name('geometry', 0) == "dimension"
assert libspud.option_count('/problem_type') == 1
assert libspud.have_option('/problem_type')
assert libspud.get_option_type('/geometry/dimension') is int
assert libspud.get_option_type('/problem_type') is str
assert libspud.get_option_rank('/geometry/dimension') == 0
assert libspud.get_option_rank('/physical_parameters/gravity/vector_field::GravityDirection/prescribed/value/constant') == 1
assert libspud.get_option_shape('/geometry/dimension') == (-1, -1)
assert libspud.get_option_shape('/problem_type')[0] > 1
assert libspud.get_option_shape('/problem_type')[1] == -1
assert libspud.get_option('/problem_type') == "multimaterial"
assert libspud.get_option('/geometry/dimension') == 2
libspud.set_option('/geometry/dimension', 3)
assert libspud.get_option('/geometry/dimension') == 3
def main():
parser = argparse.ArgumentParser(
prog="plot 2D",
description="""Plot a 2D (time vs depth) of a variable"""
)
parser.add_argument(
'-v',
'--verbose',
action='store_true',
help="Verbose output: mainly progress reports.",
default=False
)
parser.add_argument(
'-s',
'--station',
choices=['papa', 'india', 'bermuda'],
help="Choose a station: india, papa or bermuda",
required=True
)
parser.add_argument(
'--var',
choices=['dz', 'chlor', 'det', 'nit', 'zoo', 'phyto', 'pp', 'temp', 'sal', 'rho', 'tke','vertdiff'],
help="Choose a variable to plot",
required=True
)
parser.add_argument(
'-m',
'--no_mld',
help="Do not plot the MLD",
required=False,
action="store_true",
default=False
)
parser.add_argument(
'--tke',
help="Plot MLD based on TKE, not density",
action='store_true',
default=False
)
parser.add_argument(
'-z',
type=float,
help="Maximum depth to plot",
default=500,
required=False,
)
parser.add_argument(
'-n',
'--nyears',
type=int,
default=None,
help="Number of years to plot. Default is longest time from Fluidity data",
required=False,
)
parser.add_argument(
'--minvalue',
default=None,
type=float,
help="Set a minimum value to use in the plot",
required=False,
)
parser.add_argument(
'--maxvalue',
default=None,
type=float,
help="Set a maximum value to use in the plot",
required=False,
)
parser.add_argument(
'--logscale',
help="Use a log colour scale",
action='store_true',
default=False
)
parser.add_argument(
'input',
metavar='input',
help="Fluidity results directory",
)
parser.add_argument(
'output_file',
metavar='output_file',
help='The output filename'
)
args = parser.parse_args()
verbose = args.verbose
adaptive = False
output_file = args.output_file
max_depth = args.z
plot_tke = args.tke
var = args.var
minvalue = args.minvalue
maxvalue = args.maxvalue
logscale = args.logscale
if (args.nyears == None):
nDays = None
else:
nDays = args.nyears*365
# actually irrelavent as we do it by day of year...
start = datetime.strptime("1970-01-01 00:00:00", "%Y-%m-%d %H:%M:%S")
variable = None
long_name = None
# work out which variable to pull out
# 'dz', 'chlor', 'det', 'nit', 'zoo', 'phyto', 'pp', 'temp', 'sal', 'rho', 'tke'
if (var == 'dz'):
variable = None # don't need one - special case
long_name = r'$\delta z$'
elif (var == 'chlor'):
variable = 'Chlorophyll'
long_name = 'Chlorophyll-a ($mmol/m^3$)'
elif (var == 'det'):
variable = 'Detritus'
long_name = 'Detritus ($mmol/m^3$)'
elif (var == 'nit'):
variable = 'Nutrient'
long_name = 'Nitrate ($mmol/m^3$)'
elif (var == 'zoo'):
variable = 'Zooplankton'
long_name = 'Zooplankton ($mmol/m^3$)'
elif (var == 'phyto'):
variable = 'Phytoplankton'
long_name = 'Phytoplankton ($mmol/m^3$)'
elif (var == 'pp'):
variable = 'DailyAveragedPrimaryProduction'
long_name = 'Primary Production ($mmol/m^3$)'
elif (var == 'temp'):
variable = 'Temperature'
long_name = 'Temperature ($^/circ C$)'
elif (var == 'sal'):
variable = 'Salinity'
long_name = 'Salinity ($PSU$)'
elif (var == 'rho'):
variable = 'Density'
long_name = 'Density ($kg/m^3$)'
elif (var == 'tke'):
variable = 'GLSTurbulentKineticEnergy'
long_name = 'Turbulent Kinetic Energy ($m^2s^{-2}$)'
elif (var == 'vertdiff'):
variable = 'GLSVerticalDiffusivity'
long_name = 'Vertical Diffusivity ($m^2s^{-1}$)'
else:
print "Unknown variable"
sys.exit(-1)
if (verbose):
print "Plot 2D plot of : "
files = get_vtus(args.input)
if (not verbose):
# print progress bar
total_vtus = len(files)
percentPerVtu = 100.0/float(total_vtus)
if (args.station == 'bermuda'):
pp_averaged = True
else:
pp_averaged = False
# Are we adaptive - if so, set up some variables
# We need maxdepth, min edge length, max edge length, etc
# I think the easiest is to parse the flml...glob flml files
# that don't have checkpoint in their name...
flmls = (glob.glob(os.path.join(args.input, "*.flml")))
flmls.sort()
# grab bits of the flml we want
if flmls == None or len(flmls) == 0:
print "No flml files available: can't check for adaptivity, this might fail..."
elif len(flmls) > 1:
print "Found multiple FLMLs, using the first one"
else:
flml = flmls[0]
# grab min_edge_length, max_edge_length, bottom depth and starting resolution
libspud.load_options(flml)
if (libspud.have_option('mesh_adaptivity/')):
adaptive = True
minEdgeLength = libspud.get_option('/mesh_adaptivity/hr_adaptivity/tensor_field::MinimumEdgeLengths/anisotropic_symmetric/constant')[-1][-1]
maxEdgeLength = libspud.get_option('/mesh_adaptivity/hr_adaptivity/tensor_field::MaximumEdgeLengths/anisotropic_symmetric/constant')[-1][-1]
maxDepth = libspud.get_option('/geometry/mesh::CoordinateMesh/from_mesh/extrude/regions::WholeMesh/bottom_depth/constant')
initial_spacing = min(minEdgeLength,libspud.get_option('/geometry/mesh::CoordinateMesh/from_mesh/extrude/regions::WholeMesh/sizing_function/constant'))
nPoints = int(maxDepth/max(initial_spacing,minEdgeLength))+1 # maximum number of points will be at start with uniform resolution
if (verbose):
print minEdgeLength, maxEdgeLength, maxDepth, nPoints, initial_spacing
else:
# If not found, it's not adaptive...
adaptive = False
if (verbose):
print "Adaptive run: ", adaptive
current_file = 1
# set up our master variables
mld = []
data = []
dates = []
depths = []
for vtu in files:
if (not verbose):
progress(50,current_file*percentPerVtu)
# obtain surface values from each dataset
try:
#if (verbose):
# print vtu
os.stat(vtu)
except:
print "No such file: %s" % file
sys.exit(1)
# open vtu and derive the field indices of the edge at (x=0,y=0) ordered by depth
u=vtktools.vtu(vtu)
pos = u.GetLocations()
ind = get_1d_indices(pos)
# deal with depths
depth = [-pos[i,2] for i in ind]
if (adaptive):
depth.extend([maxDepth+1 for i in range(len(ind),nPoints)])
depths.append(depth)
# handle time and convert to calendar time
time = u.GetScalarField('Time')
tt = [time[i] for i in ind]
cur_dt = start + timedelta(seconds=time[0])
days = (cur_dt - start).days
tt = [days for i in ind]
if (adaptive):
tt.extend([days for i in range(len(ind),nPoints)])
dates.append( tt )
if plot_tke:
d = u.GetScalarField('GLSTurbulentKineticEnergy')
den = [d[i] for i in ind]
if (adaptive):
den.extend([1e-10 for i in range(len(ind),nPoints)])
mld.append(calc_mld_tke(den, depth))
else:
# grab density profile and calculate MLD_den
d = u.GetScalarField('Density')
den = [d[i] * 1000 for i in ind]
if (adaptive):
den.extend([d[-1]*1000. for i in range(len(ind),nPoints)])
mld.append(calc_mld_den(den, depth, den0=0.125) )
if (var == 'dz'):
z = []
for i in range(1,len(depth)):
if (depth[i] - depth[i-1] < minEdgeLength): # we're in the region where we've made up the edges...
z.append(minEdgeLength)
else:
z.append(depth[i] - depth[i-1])
z.append(100) # to make sure shape(dz) == shape(depths)
data.append(vtktools.arr(z))
else:
# primprod is depth integrated or averaged, so we need the whole field
t = u.GetScalarField(variable)
if (var == 'pp'):
temp = [6.7*12*8.64e4*t[i] for i in ind]
elif (var == 'density'):
temp = [1024.0*t[i] for i in ind]
else:
temp = [t[i] for i in ind]
if (adaptive):
temp.extend([t[-1] for i in range(len(ind),nPoints)])
data.append(temp)
current_file = current_file + 1
if (not nDays):
nDays = dates[-1][0]
filename = output_file
data = numpy.array(data)
if (var == 'dz'):
# Add or subtract a bit more than edgelength as DZ might be a bit more or less than this
min_data = minEdgeLength - (0.1*minEdgeLength)
max_data = maxEdgeLength + (0.1*maxEdgeLength)
else:
if (minvalue == None):
min_data = data.min()
else:
min_data = minvalue
if (maxvalue == None):
max_data = data.max()
else:
max_data = maxvalue
plot_2d_data(data, depths, dates, filename, long_name, finish_day=nDays,mld_data=mld,max_depth=max_depth,minimum=min_data,maximum=max_data,logscale=logscale)
def __init__(self, path, checkpoint=None):
""" Initialise a new shallow water simulation, using an options file.
:param str path: The path to the simulation's configuration/options file.
:param str checkpoint: The path to a checkpoint file.
:returns: None
"""
LOG.info("Initialising simulation...")
# Remove any stored options.
libspud.clear_options()
# Load the options from the options tree.
libspud.load_options(path)
# Populate the options dictionary
self.populate_options()
# Read in the input mesh (or construct one)
self.mesh = self.get_mesh(path)
# Create a dictionary containing all the function spaces
LOG.info("Creating function spaces...")
self.function_spaces = {}
# The Velocity field's function space
name = "VelocityFunctionSpace"
path = "/function_spaces/function_space::%s" % name
family = libspud.get_option(path + "/family")
degree = libspud.get_option(path + "/degree")
try:
if (family == "Continuous Lagrange"):
self.function_spaces[name] = VectorFunctionSpace(
self.mesh, "CG", degree)
elif (family == "Discontinuous Lagrange"):
self.function_spaces[name] = VectorFunctionSpace(
self.mesh, "DG", degree)
else:
raise ValueError("Unknown element family: %s." % family)
except ValueError as e:
LOG.exception(e)
sys.exit()
LOG.debug("Created a new %s function space of degree %d for Velocity" %
(family, degree))
# The FreeSurfacePerturbation field's function space
name = "FreeSurfaceFunctionSpace"
path = "/function_spaces/function_space::%s" % name
family = libspud.get_option(path + "/family")
degree = libspud.get_option(path + "/degree")
try:
if (family == "Continuous Lagrange"):
self.function_spaces[name] = FunctionSpace(
self.mesh, "CG", degree)
elif (family == "Discontinuous Lagrange"):
self.function_spaces[name] = FunctionSpace(
self.mesh, "DG", degree)
else:
raise ValueError("Unknown element family: %s." % family)
except ValueError as e:
LOG.exception(e)
sys.exit()
LOG.debug(
"Created a new %s function space of degree %d for FreeSurfacePerturbation"
% (family, degree))
# Get the function spaces
U = self.function_spaces["VelocityFunctionSpace"]
H = self.function_spaces["FreeSurfaceFunctionSpace"]
# Test functions
self.w = TestFunction(U)
self.v = TestFunction(H)
LOG.info("Test functions created.")
# Trial functions (i.e. the solutions for time n+1)
self.u = TrialFunction(U)
self.h = TrialFunction(H)
LOG.info("Trial functions created.")
# Normal vector to each element facet
self.n = FacetNormal(self.mesh)
# Set up initial conditions
LOG.info("Setting initial conditions...")
h_initial = ExpressionFromOptions(
path=
"/system/core_fields/scalar_field::FreeSurfacePerturbation/initial_condition"
).get_expression()
u_initial = ExpressionFromOptions(
path="/system/core_fields/vector_field::Velocity/initial_condition"
).get_expression()
# The solution at time n.
self.u0 = Function(U).interpolate(u_initial)
self.h0 = Function(H).interpolate(h_initial)
# The solution at time n-1.
self.u00 = Function(U)
self.u00.assign(self.u0)
# Load initial conditions from the specified checkpoint file if desired.
if (checkpoint is not None):
self.solution_old.dat.load(checkpoint)
LOG.debug("Loaded initial condition from checkpoint file.")
# Mean free surface height
self.h_mean = Function(H)
self.h_mean.interpolate(
ExpressionFromOptions(
path="/system/core_fields/scalar_field::FreeSurfaceMean/value"
).get_expression())
# Set up the functions used to write fields to file.
self.output_functions = {}
self.output_functions["Velocity"] = Function(U, name="Velocity")
self.output_functions["FreeSurfacePerturbation"] = Function(
H, name="FreeSurfacePerturbation")
# Set up the output stream
LOG.info("Initialising output file streams...")
self.output_files = {}
for field in self.output_functions.keys():
self.output_files[field] = File(
"%s_%s.pvd" % (self.options["simulation_name"], field))
# Write initial conditions to file
LOG.info("Writing initial conditions to file...")
self.output_functions["Velocity"].assign(self.u0)
self.output_files["Velocity"] << self.output_functions["Velocity"]
self.output_functions["FreeSurfacePerturbation"].assign(self.h0)
self.output_files["FreeSurfacePerturbation"] << self.output_functions[
"FreeSurfacePerturbation"]
return
