def setup_logging(level, logfile=None, logfile_level=None, verbatim_filename=False):
# log level and format configuration
log_format = "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
logging.basicConfig(level=level, format=log_format)
# FEniCS logging
dolfin.set_log_active(True)
dolfin.set_log_level(logging.WARNING)
fenics_logger = logging.getLogger("FFC")
fenics_logger.setLevel(logging.WARNING)
fenics_logger = logging.getLogger("UFL")
fenics_logger.setLevel(logging.WARNING)
# explicitly set levels for certain loggers
logging.getLogger("spuq").setLevel(level)
logging.getLogger("spuq.application.egsz.multi_operator").setLevel(logging.WARNING)
#logging.getLogger("spuq.application.egsz.marking").setLevel(logging.INFO)
# output to logfile, if set
if logfile:
# replace .py or .conf with .log, if not prohibited
if not verbatim_filename:
logfile = basename(logfile, ".conf")
logfile = basename(logfile, ".py")
logfile = logfile + ".log"
# create a new file handler (obsolete: specify mode "w" for overwriting, instead of the default "a")
ch = logging.FileHandler(logfile, mode="a")
ch.setLevel(logfile_level if logfile_level else level)
ch.setFormatter(logging.Formatter(log_format))
# add to root logger
root = logging.getLogger()
root.addHandler(ch)
def make_logger(name, level=parameters["log_level"]):
def log_if_process0(record):
if dolfin.MPI.rank(mpi_comm_world()) == 0:
return 1
else:
return 0
mpi_filt = Object()
mpi_filt.filter = log_if_process0
logger = logging.getLogger(name)
logger.setLevel(level)
ch = logging.StreamHandler()
ch.setLevel(0)
# formatter = logging.Formatter('%(message)s')
formatter = logging.Formatter(
("%(asctime)s - " "%(name)s - " "%(levelname)s - " "%(message)s")
)
ch.setFormatter(formatter)
logger.addHandler(ch)
logger.addFilter(mpi_filt)
dolfin.set_log_level(logging.WARNING)
ffc_logger = logging.getLogger("FFC")
ffc_logger.setLevel(logging.WARNING)
ffc_logger.addFilter(mpi_filt)
ufl_logger = logging.getLogger("UFL")
ufl_logger.setLevel(logging.WARNING)
ufl_logger.addFilter(mpi_filt)
return logger
def make_logger(name, level=logging.INFO):
import logging
import dolfin
mpi_filt = lambda: None
def log_if_proc0(record):
if dolfin.mpi_comm_world().rank == 0:
return 1
else:
return 0
mpi_filt.filter = log_if_proc0
logger = logging.getLogger(name)
logger.setLevel(log_level)
ch = logging.StreamHandler()
ch.setLevel(0)
formatter = logging.Formatter("%(message)s")
ch.setFormatter(formatter)
logger.addHandler(ch)
logger.addFilter(mpi_filt)
dolfin.set_log_active(False)
dolfin.set_log_level(dolfin.WARNING)
return logger
def setup_logging(level):
# log level and format configuration
log_format = "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
logging.basicConfig(filename=__file__[:-2] + 'log', level=level,
format=log_format)
# FEniCS logging
from dolfin import (set_log_level, set_log_active, INFO, DEBUG, WARNING)
set_log_active(True)
set_log_level(WARNING)
fenics_logger = logging.getLogger("FFC")
fenics_logger.setLevel(logging.WARNING)
fenics_logger = logging.getLogger("UFL")
fenics_logger.setLevel(logging.WARNING)
# module logger
logger = logging.getLogger(__name__)
logging.getLogger("spuq.application.egsz.multi_operator").disabled = True
#logging.getLogger("spuq.application.egsz.marking").setLevel(logging.INFO)
# add console logging output
ch = logging.StreamHandler()
ch.setLevel(level)
ch.setFormatter(logging.Formatter(log_format))
logger.addHandler(ch)
logging.getLogger("spuq").addHandler(ch)
return logger
def main():
"Generates the mesh"
import mshr as m
import dolfin as d
import matplotlib.pyplot as plt
d.set_log_level(13) # PROGRESS
r_1 = 0.5 # inner
r_2 = 2.0 # outer
res = 10 # resolution
circle_inner = m.Circle(d.Point(0.0, 0.0), r_1)
circle_outer = m.Circle(d.Point(0.0, 0.0), r_2)
domain = circle_outer - circle_inner
domain.set_subdomain(1, circle_inner)
domain.set_subdomain(2, circle_outer)
mesh = m.generate_mesh(domain, res)
print("max edge length:", mesh.hmax())
mesh_file_pvd = d.File("mesh.pvd")
mesh_file_pvd.write(mesh)
plt.figure()
d.plot(mesh, title="Mesh")
plt.show()
def __init__(self, cparams, dtype_u, dtype_f):
"""
Initialization routine
Args:
cparams: custom parameters for the example
dtype_u: particle data type (will be passed parent class)
dtype_f: acceleration data type (will be passed parent class)
"""
# define the Dirichlet boundary
def Boundary(x, on_boundary):
return on_boundary
# these parameters will be used later, so assert their existence
assert 'c_nvars' in cparams
assert 'nu' in cparams
assert 't0' in cparams
assert 'family' in cparams
assert 'order' in cparams
assert 'refinements' in cparams
# add parameters as attributes for further reference
for k,v in cparams.items():
setattr(self,k,v)
df.set_log_level(df.WARNING)
df.parameters["form_compiler"]["optimize"] = True
df.parameters["form_compiler"]["cpp_optimize"] = True
# set mesh and refinement (for multilevel)
mesh = df.UnitIntervalMesh(self.c_nvars)
# mesh = df.UnitSquareMesh(self.c_nvars[0],self.c_nvars[1])
for i in range(self.refinements):
mesh = df.refine(mesh)
# self.mesh = mesh
# define function space for future reference
self.V = df.FunctionSpace(mesh, self.family, self.order)
tmp = df.Function(self.V)
print('DoFs on this level:',len(tmp.vector().array()))
# invoke super init, passing number of dofs, dtype_u and dtype_f
super(fenics_heat,self).__init__(self.V,dtype_u,dtype_f)
self.g = df.Expression('-sin(a*x[0]) * (sin(t) - b*a*a*cos(t))',a=np.pi,b=self.nu,t=self.t0,degree=self.order)
# rhs in weak form
self.w = df.Function(self.V)
v = df.TestFunction(self.V)
self.a_K = -self.nu*df.inner(df.nabla_grad(self.w), df.nabla_grad(v))*df.dx + self.g*v*df.dx
# mass matrix
u = df.TrialFunction(self.V)
a_M = u*v*df.dx
self.M = df.assemble(a_M)
self.bc = df.DirichletBC(self.V, df.Constant(0.0), Boundary)
def setup(self):
"""
Setup logging to file if requested in the simulation input
"""
# Ensure that the output directory exist
tmp = self.simulation.input.get_output_file_path('BOGUS', 'xxxxx')
output_dir = os.path.split(tmp)[0]
if output_dir and not os.path.exists(output_dir):
os.makedirs(output_dir)
log_name = self.simulation.input.get_output_file_path('output/log_name', '.log')
log_on_all_ranks = self.simulation.input.get_value(
'output/log_on_all_ranks', False, 'bool'
)
log_enabled = self.simulation.input.get_value(
'output/log_enabled', True, 'bool'
)
log_append_existing = self.simulation.input.get_value(
'output/log_append_to_existing_file', True, 'bool'
)
stdout_on_all_ranks = self.simulation.input.get_value(
'output/stdout_on_all_ranks', False, 'bool'
)
stdout_enabled = self.simulation.input.get_value(
'output/stdout_enabled', True, 'bool'
)
self.show_memory_usage = self.simulation.input.get_value(
'output/show_memory_usage', False, 'bool'
)
rank = self.simulation.rank
self.write_stdout = (rank == 0 or stdout_on_all_ranks) and stdout_enabled
self.write_log = False
if log_enabled:
if log_on_all_ranks and rank > 0:
log_name = '%s.%d' % (log_name, self.simulation.rank)
if rank == 0 or log_on_all_ranks:
self.write_log = True
self.log_file_name = log_name
if log_append_existing:
self.log_file = open(self.log_file_name, 'at')
self.log_file.write('\n\n')
else:
self.log_file = open(self.log_file_name, 'wt')
# Set the Ocellaris log level
log_level = self.simulation.input.get_value(
'output/ocellaris_log_level', 'info'
)
self.simulation.log.set_log_level(self.AVAILABLE_LOG_LEVELS[log_level])
# Set the Dolfin log level
df_log_level = self.simulation.input.get_value(
'output/dolfin_log_level', 'warning'
)
dolfin.set_log_level(self.AVAILABLE_LOG_LEVELS[df_log_level])
def init_ffc():
import dolfin as _dolfin
flags = ["-O3", "-ffast-math"] # , "-march=native"]
_dolfin.parameters["form_compiler"]["quadrature_degree"] = 4
_dolfin.parameters["form_compiler"]["representation"] = "uflacs"
_dolfin.parameters["form_compiler"]["cpp_optimize"] = True
_dolfin.parameters["form_compiler"]["cpp_optimize_flags"] = " ".join(flags)
_dolfin.set_log_level(_logging.WARNING)
def __init__(self, domain, **kwargs):
dolf.set_log_level(LOG_LEVEL)
self.domain = domain
self._visualization_files = None
experiment_id = kwargs.get("experiment_id", "")
if experiment_id:
experiment_id = "_" + experiment_id
self.vis_dir = "Visualization" + experiment_id + "/"
if not os.path.exists(self.vis_dir):
os.makedirs(self.vis_dir)
def setUp(self):
d.set_log_level(d.LogLevel.WARNING)
N = 50
order = 2
tF = 0.10
# Dirichlet boundary characteristic time
tau = tF / 10.0
# time step
h = 0.001
self.num_steps = round(tF / h)
# Mesh and Function space
mesh = d.UnitIntervalMesh(N)
V = d.FunctionSpace(mesh, "P", order)
w = d.TestFunction(V)
v = d.TrialFunction(V)
# Initial conditions chosen such that the wave travels to the right
uInit = d.Expression(
"((1./3 < x[0]) && (x[0] < 2./3)) ? 0.5*(1-cos(2*pi*3*(x[0]-1./3))) : 0.",
degree=2,
)
u = d.interpolate(uInit, V) # values
# Dirichlet boundary on the right with its derivatives
g = d.Expression(
"(t < total) ? 0.4*(1.-cos(2*pi*t/total))/2. : 0.",
degree=2,
t=0.0,
total=tau,
)
dg = d.Expression(
"(t < total) ? 0.4*(pi/total) * sin(2*pi*t/total) : 0.",
degree=2,
t=0.0,
total=tau,
)
def updateBC(t):
g.t = t
dg.t = t
def right(x, on_boundary):
return on_boundary and d.near(x[0], 1.0)
bc0 = d.DirichletBC(V, g, right)
bc1 = d.DirichletBC(V, dg, right)
self.bc = [bc0, bc1]
L1 = -d.inner(d.grad(w), d.grad(u)) * d.dx
L2 = w * v * d.dx
self.parameters = (L1, L2, u, h, updateBC)
def set_log_level(level):
"""Sets the log level.
Parameters
----------
level : int
Log level that should be set.
"""
df.set_log_level(level)
m3h3.parameters.update({"log_level": df.get_log_level()})
log(LogLevel.INFO, "Log level updated to {}".format(level))
def set_solver():
# "hypre_amg") #"hypre_euclid") # "hypre_amg") # "petsc_amg" "petsc_amg"
solver = d.KrylovSolver("cg", "hypre_amg")
solver.parameters["maximum_iterations"] = 1000
solver.parameters["absolute_tolerance"] = 1E-8
solver.parameters["error_on_nonconvergence"] = True
solver.parameters["monitor_convergence"] = True
# solver.parameters["divergence_limit"] = 1E+6
# solver.parameters["nonzero_initial_guess"] = True
d.info(solver.parameters, verbose=True)
d.set_log_level(d.PROGRESS)
return solver
def test_save_load():
"""Solve a problem, save the data, load it back and compare."""
df.set_log_level(100) # supress dolfin logger
# Setup solver
solver = SubdomainSolver(N=32)
with tempfile.TemporaryDirectory() as tmpdirname:
tmpdirname = "foo"
casedir = Path(tmpdirname) / "test_pp_casedir"
# Setup saver
field_spec = FieldSpec(stride_timestep=1, save_as=("checkpoint", "hdf5"))
saver_spec = SaverSpec(casedir=str(casedir))
saver = Saver(saver_spec)
saver.store_mesh(
solver.mesh,
cell_domains=solver.cell_function,
facet_domains=solver.facet_function
)
saver.add_field(Field("u", field_spec))
# Solver loop
time_func_dict = {}
for timestep, (t, u) in enumerate(solver.solve(0, 100, 1.0)):
saver.update(t, timestep, {"u": u})
time_func_dict[timestep] = u.copy(True)
saver.close()
# Define loader
loader_spec = LoaderSpec(casedir=str(casedir))
loader = Loader(loader_spec)
loaded_mesh = loader.load_mesh()
loaded_cell_function = loader.load_mesh_function("cell_function")
loaded_facet_function = loader.load_mesh_function("facet_function")
# Compare mesh and meshfunctions
assert np.sum(solver.mesh.coordinates() - loaded_mesh.coordinates()) == 0
assert np.sum(solver.mesh.cells() - loaded_mesh.cells()) == 0
assert np.sum(solver.cell_function.array() - loaded_cell_function.array()) == 0
assert np.sum(solver.facet_function.array() - loaded_facet_function.array()) == 0
# Compare functions and time checkpoint
for timestep, (loaded_t, loaded_u) in enumerate(loader.load_checkpoint("u")):
diff = np.sum(time_func_dict[timestep].vector().get_local() - loaded_u.vector().get_local())
assert diff == 0, diff
# Compare functions and time hdf5
for timestep, (loaded_t, loaded_u) in enumerate(loader.load_field("u")):
diff = np.sum(time_func_dict[timestep].vector().get_local() - loaded_u.vector().get_local())
assert diff == 0, diff
def test_mpset():
#set_log_level(DEBUG)
# Print parameters and their values
#mpset.show()
# Check that assignment out of range raises
# FIXME: dolfin/parameter/Parameter.cpp is broken.
# It doesn't raise when assigning a value out of range;
# see 921c56cee4f50f016a07f49a5e90f6627c7317a6
# with pytest.raises(RuntimeError):
# mpset["discretization"]["N"] = 1
# with pytest.raises(RuntimeError):
# mpset["model"]["mobility"]["beta"] = 2.0
with pytest.raises(RuntimeError):
mpset["model"]["mobility"]["m"] = 0.0
# Try to add parameter
mpset.add("foo", "bar")
assert mpset["foo"] == "bar"
# Try direct access to a parameter
mpset["foo"] = "bar_"
assert mpset["foo"] == "bar_"
# Try to write parameters to a file
comm = mpi_comm_world()
tempdir = "/tmp/pytest-of-fenics"
fname = tempdir + "/foo.xml"
mpset.write(comm, fname)
if MPI.rank(comm) == 0:
assert os.path.isfile(fname)
MPI.barrier(comm) # wait until the file is written
# Change back value of parameter 'foo'
mpset["foo"] = "bar"
assert mpset["foo"] == "bar"
# Try to read parameters back
mpset.read(fname)
assert mpset["foo"] == "bar_"
MPI.barrier(comm) # wait until each process finishes reading
if MPI.rank(comm) == 0:
os.remove(fname)
del fname
# Check that every other call points to the same object
assert id(MuflonParameterSet()) == id(mpset)
# Cleanup
set_log_level(INFO)
mpset.refresh()
def setup_general_parameters():
"""
Parameters to speed up the compiler
"""
# Parameter for the compiler
flags = ["-O3", "-ffast-math", "-march=native"]
dolfin.parameters["form_compiler"]["quadrature_degree"] = 4
dolfin.parameters["form_compiler"]["representation"] = "uflacs"
dolfin.parameters["form_compiler"]["cpp_optimize"] = True
dolfin.parameters["form_compiler"]["cpp_optimize_flags"] = " ".join(flags)
# dolfin.set_log_active(False)
dolfin.set_log_level(logging.INFO)
def run_mms0():
df.set_log_level(20)
N = [2, 4, 8, 16, 32, 40, 50, 60, 70, 80]
errors = []
dxs = []
rho = 0.7
# load mms
p_code, m_code, q_code = manufactured_solution(rho)
for nx in N:
mesh = df.UnitCubeMesh(nx, nx, nx)
p_D = df.Expression(p_code, degree=2)
m_D = df.Expression(m_code, degree=2)
q_D = df.Expression(q_code, degree=2)
# load perspect solution
m = run_perspect(mesh, q_D, p_D, m_D, rho)
e = df.errornorm(m_D, m, degree_rise=0)
F = df.FunctionSpace(mesh, 'P', 2)
n = df.interpolate(m_D, F)
f = df.File("test.pvd")
f << m
errors.append(e)
dxs.append(mesh.hmin())
errors = np.array(errors)
dxs = np.array(dxs)
conv_rates = np.log(errors[1:] / errors[0:-1]) / np.log(
dxs[1:] / dxs[0:-1])
print(errors)
print(dxs)
print(conv_rates)
import matplotlib.pyplot as plt
plt.loglog(dxs, errors)
plt.loglog(dxs, errors, marker='o')
plt.xlabel("dx")
plt.ylabel("L2 errornorm")
plt.grid(True, which="both")
plt.savefig("mms0_convergence.png")
def make_logger(name, level=logging.INFO):
import logging
mpi_filt = lambda: None
def log_if_proc0(record):
if dolfin.MPI.rank(dolfin.mpi_comm_world()) == 0:
return 1
else:
return 0
mpi_filt.filter = log_if_proc0
logger = logging.getLogger(name)
logger.setLevel(level)
ch = logging.StreamHandler()
ch.setLevel(0)
formatter = logging.Formatter(
"%(message)s") #'\n%(name)s - %(levelname)s - %(message)s\n'
ch.setFormatter(formatter)
logger.addHandler(ch)
logger.addFilter(mpi_filt)
dolfin.set_log_active(False)
dolfin.set_log_level(dolfin.WARNING)
# ffc_logger = logging.getLogger('FFC')
# ffc_logger.setLevel(DEBUG)
# ffc_logger.addFilter(mpi_filt)
# ufl_logger = logging.getLogger('UFL')
# ufl_logger.setLevel(DEBUG)
# ufl_logger.addFilter(mpi_filt)
# from haosolver import logger as hao_logger
# hao_logger.setLevel(DEBUG)
return logger
def make_logger(name, level=logging.INFO):
def log_if_process0(record):
if dolfin.MPI.rank(dolfin.mpi_comm_world()) == 0:
return 1
else:
return 0
mpi_filt = Object()
mpi_filt.filter = log_if_process0
logger = logging.getLogger(name)
logger.setLevel(level)
ch = logging.StreamHandler()
ch.setLevel(0)
# formatter = logging.Formatter('%(message)s')
formatter = logging.Formatter(('%(asctime)s - '
'%(name)s - '
'%(levelname)s - '
'%(message)s'))
ch.setFormatter(formatter)
logger.addHandler(ch)
logger.addFilter(mpi_filt)
dolfin.set_log_active(False)
dolfin.set_log_level(dolfin.WARNING)
ffc_logger = logging.getLogger('FFC')
ffc_logger.setLevel(dolfin.WARNING)
ffc_logger.addFilter(mpi_filt)
ufl_logger = logging.getLogger('UFL')
ufl_logger.setLevel(dolfin.WARNING)
ufl_logger.addFilter(mpi_filt)
return logger
from dolfin import set_log_level, WARNING, Expression, FunctionSpace, \
DirichletBC, Function, errornorm, project, plot, interactive, triangle, \
norm, UnitIntervalMesh, pi, inner, grad, dx, ds, dot, UnitSquareMesh, \
FacetNormal, interval, RectangleMesh, TrialFunction, TestFunction, \
assemble, lhs, rhs, MPI
import maelstrom.time_steppers as ts
import sympy as smp
import numpy
import itertools
import helpers
# Turn down the log level to only error messages.
set_log_level(WARNING)
#set_log_level(ERROR)
#set_log_level(0)
def test_generator():
'''Test order of time discretization.
'''
# TODO add test for spatial order
problems = [
#problem_sinsin1d,
#problem_sinsin,
problem_coscos_cartesian,
#problem_coscos_cylindrical,
#problem_stefanboltzmann
]
def custom_apply(self_, *args, **kwargs):
set_log_level(ERROR)
original_apply(*args, **kwargs)
set_log_level(PROGRESS)
def project(*args, **kwargs):
set_log_level(ERROR)
output = dolfin_project(*args, **kwargs)
set_log_level(PROGRESS)
return output
def wrapped_f(*args, **kwargs):
old_level = get_log_level()
set_log_level(log_level)
f(*args, **kwargs)
set_log_level(old_level)
def test_stokes_noflow(gamma, Re, nu_interp, postprocessor):
#set_log_level(WARNING)
basename = postprocessor.basename
label = "{}_{}_gamma_{}_Re_{:.0e}".format(basename, nu_interp, gamma, Re)
c = postprocessor.get_coefficients()
c[r"\nu_1"] = c[r"\rho_1"] / Re
c[r"\nu_2"] = c[r"r_visc"] * c[r"\nu_1"]
c[r"\nu_1"] /= c[r"\rho_0"] * c[r"V_0"] * c[r"L_0"]
c[r"\nu_2"] /= c[r"\rho_0"] * c[r"V_0"] * c[r"L_0"]
cc = wrap_coeffs_as_constants(c)
nu = eval("nu_" + nu_interp) # choose viscosity interpolation
for level in range(1, 4):
mesh, boundary_markers, pinpoint, periodic_bnd = create_domain(level)
periodic_bnd = None
W = create_mixed_space(mesh, periodic_boundary=periodic_bnd)
bcs = create_bcs(W,
boundary_markers,
periodic_boundary=periodic_bnd,
pinpoint=pinpoint)
phi = create_fixed_vfract(mesh, c)
# Create forms
a, L = create_forms(W, rho(phi, cc), nu(phi, cc), c[r"g_a"],
boundary_markers, gamma)
# Solve problem
w = df.Function(W)
A, b = df.assemble_system(a, L, bcs)
solver = df.LUSolver("mumps")
df.PETScOptions.set("fieldsplit_u_mat_mumps_icntl_14", 500)
solver.set_operator(A)
try:
solver.solve(w.vector(), b)
except:
df.warning("Ooops! Something went wrong: {}".format(
sys.exc_info()[0]))
continue
# Pre-process results
v, p = w.split(True)
v.rename("v", "velocity")
p.rename("p", "pressure")
V_dv = df.FunctionSpace(mesh, "DG",
W.sub(0).ufl_element().degree() - 1)
div_v = df.project(df.div(v), V_dv)
div_v.rename("div_v", "velocity-divergence")
D_22 = df.project(v.sub(1).dx(1), V_dv)
p_h = create_hydrostatic_pressure(mesh, cc)
#p_ref = df.project(p_h, W.sub(1).ufl_element())
p_ref = df.project(
p_h,
df.FunctionSpace(mesh, df.FiniteElement("CG", mesh.ufl_cell(), 4)))
v_errL2, v_errH10, div_errL2, p_errL2 = compute_errornorms(
v, div_v, p, p_ref)
if nu_interp[:2] == "PW":
V_nu = df.FunctionSpace(mesh, "DG", phi.ufl_element().degree())
else:
V_nu = phi.function_space()
nu_0 = df.project(nu(phi, cc), V_nu)
T_22 = df.project(2.0 * nu(phi, cc) * v.sub(1).dx(1), V_nu)
# Save results
make_cut = postprocessor._make_cut
rs = dict(ndofs=W.dim(),
level=level,
h=mesh.hmin(),
r_dens=c[r"r_dens"],
r_visc=c[r"r_visc"],
gamma=gamma,
Re=Re,
nu_interp=nu_interp)
rs[r"$v_2$"] = make_cut(v.sub(1))
rs[r"$p$"] = make_cut(p)
rs[r"$\phi$"] = make_cut(phi)
rs[r"$D_{22}$"] = make_cut(D_22)
rs[r"$T_{22}$"] = make_cut(T_22)
rs[r"$\nu$"] = make_cut(nu_0)
rs[r"$||\mathbf{v} - \mathbf{v}_h||_{L^2}$"] = v_errL2
rs[r"$||\nabla (\mathbf{v} - \mathbf{v}_h)||_{L^2}$"] = v_errH10
rs[r"$||\mathrm{div} \mathbf{v}_h||_{L^2}$"] = div_errL2
rs[r"$||\mathbf{p} - \mathbf{p}_h||_{L^2}$"] = p_errL2
print(label, level)
# Send to posprocessor
comm = mesh.mpi_comm()
rank = df.MPI.rank(comm)
postprocessor.add_result(rank, rs)
# Plot results obtained in the last round
outdir = os.path.join(postprocessor.outdir, "XDMFoutput")
with df.XDMFFile(os.path.join(outdir, "v.xdmf")) as file:
file.write(v, 0.0)
with df.XDMFFile(os.path.join(outdir, "p.xdmf")) as file:
file.write(p, 0.0)
with df.XDMFFile(os.path.join(outdir, "phi.xdmf")) as file:
file.write(phi, 0.0)
with df.XDMFFile(os.path.join(outdir, "div_v.xdmf")) as file:
file.write(div_v, 0.0)
# Save results into a binary file
filename = "results_{}.pickle".format(label)
postprocessor.save_results(filename)
# Flush plots as we now have data for all level values
postprocessor.pop_items(["level", "h"])
postprocessor.flush_plots()
# Cleanup
df.set_log_level(df.INFO)
gc.collect()
import dolfin as df
import numpy as np
import perspect
import pulse
import sys
import time
from geometry import Geometry, MarkerFunctions, Microstructure
comm = df.MPI.comm_world
df.set_log_level(40)
mesh = df.BoxMesh(comm, df.Point(0, 0, 0), df.Point(3, 1, 0.1), 30, 10, 1)
class Base(df.SubDomain):
def inside(self, x, on_boundary):
return on_boundary and df.near(x[1], 0)
class Endo(df.SubDomain):
def inside(self, x, on_boundary):
return on_boundary and df.near(x[0], 0)
class Epi(df.SubDomain):
def inside(self, x, on_boundary):
return on_boundary and df.near(x[0], 1.0)
markers = {'BASE': (10, 1), 'ENDO': (30, 1), 'EPI': (40, 1), 'NONE': (0, 2)}
ffun = df.MeshFunction("size_t", mesh, mesh.topology().dim() - 1)
import sys; sys.path.append('../')
import numpy as np
import matplotlib; matplotlib.use('agg')
import matplotlib.pyplot as plt
import os
import warnings
warnings.filterwarnings('ignore',category=FutureWarning)
from dolfin import set_log_level; set_log_level(40)
from tensorflow.keras import Sequential, Model, Input
from tensorflow.keras.optimizers import Adam
from tensorflow.keras.layers import *
from tensorflow.keras.regularizers import l1_l2, l2, l1
from tensorflow.keras.callbacks import LearningRateScheduler
from deep_learning.generate_fin_dataset import gen_affine_avg_rom_dataset
def load_dataset_avg_rom(load_prev=True, tr_size=6000, v_size=500, genrand=False):
'''
Load dataset where the conductivity is parametrized as a FEniCS function
and the QoI is the averaged temperature per subfin
'''
if os.path.isfile('../data/z_aff_avg_tr.npy') and load_prev:
z_train = np.load('../data/z_aff_avg_tr.npy')
errors_train = np.load('../data/errors_aff_avg_tr.npy')
else:
(z_train, errors_train) = gen_affine_avg_rom_dataset(tr_size, genrand=genrand)
if os.path.isfile('../data/z_aff_avg_eval.npy') and load_prev:
z_val = np.load('../data/z_aff_avg_eval.npy')
args, remaining = parser.parse_known_args()
# additional output
PETScOptions.set('ksp_view') # shows info about used PETSc Solver and preconditioner
# if args.solver == 'ipcs1':
# PETScOptions.set('log_summary')
# Paralell run initialization
comm = mpi_comm_world()
rank = MPI.rank(comm)
# parameters["std_out_all_processes"] = False # print only rank==0 process output
# parameters["ghost_mode"] = "shared_facet" # may be needed for operating DG elements in parallel
# allows output using info() for the main process only
if rank == 0 or args.out == 'all':
set_log_level(INFO)
else:
set_log_level(INFO + 1)
info('Running on %d processor(s).' % MPI.size(comm))
if MPI.size(comm) > 1 and args.problem == 'womersley_cylinder':
info('Womersley cylinder problem is not runnable in parallel due to method of construction of analytic solution,'
' which is used to describe boundary conditions.') # the change of mesh format would be also needed
exit()
# dynamically import selected solver and problem files
exec('from solvers.%s import Solver' % args.solver)
exec('from problems.%s import Problem' % args.problem)
# setup and parse problem- and solver-specific command-line arguments
import dolfin
import numpy as np
import scipy.sparse.linalg as spsla
from time_int_schemes import expand_vp_dolfunc, get_dtstr
import dolfin_navier_scipy.problem_setups as dnsps
import dolfin_navier_scipy.stokes_navier_utils as snu
from prob_defs import FempToProbParams
import matlibplots.conv_plot_utils as cpu
dolfin.set_log_level(60)
samplerate = 1
N, Re, scheme, tE = 3, 60, 'CR', .2
# Ntslist = [2**x for x in range(6, 11)]
Ntslist = [2**x for x in range(8, 10)]
Ntsref = 2048
tol = 2**(-16)
tolcor = True
method = 1
svdatapathref = 'data/'
svdatapath = 'data/'
# svdatapath = 'edithadata/'
# svdatapath = 'edithadata_scm/' # with the scaled momentum eqn
femp, stokesmatsc, rhsd_vfrc, rhsd_stbc \
= dnsps.get_sysmats(problem='cylinderwake', N=N, Re=Re,
def __init__(self, cparams, dtype_u, dtype_f):
"""
Initialization routine
Args:
cparams: custom parameters for the example
dtype_u: particle data type (will be passed parent class)
dtype_f: acceleration data type (will be passed parent class)
"""
# define the Dirichlet boundary
def Boundary(x, on_boundary):
return on_boundary
# these parameters will be used later, so assert their existence
assert 'c_nvars' in cparams
assert 't0' in cparams
assert 'family' in cparams
assert 'order' in cparams
assert 'refinements' in cparams
# add parameters as attributes for further reference
for k,v in cparams.items():
setattr(self,k,v)
df.set_log_level(df.WARNING)
df.parameters["form_compiler"]["optimize"] = True
df.parameters["form_compiler"]["cpp_optimize"] = True
# set mesh and refinement (for multilevel)
# mesh = df.UnitIntervalMesh(self.c_nvars)
# mesh = df.UnitSquareMesh(self.c_nvars[0],self.c_nvars[1])
mesh = df.IntervalMesh(self.c_nvars,0,100)
# mesh = df.RectangleMesh(0.0,0.0,2.0,2.0,self.c_nvars[0],self.c_nvars[1])
for i in range(self.refinements):
mesh = df.refine(mesh)
# self.mesh = mesh
# define function space for future reference
V = df.FunctionSpace(mesh, self.family, self.order)
self.V = V*V
# invoke super init, passing number of dofs, dtype_u and dtype_f
super(fenics_grayscott,self).__init__(self.V,dtype_u,dtype_f)
# rhs in weak form
self.w = df.Function(self.V)
q1,q2 = df.TestFunctions(self.V)
self.w1,self.w2 = df.split(self.w)
self.F1 = (-self.Du*df.inner(df.nabla_grad(self.w1), df.nabla_grad(q1)) - self.w1*(self.w2**2)*q1 + self.A*(1-self.w1)*q1)*df.dx
self.F2 = (-self.Dv*df.inner(df.nabla_grad(self.w2), df.nabla_grad(q2)) + self.w1*(self.w2**2)*q2 - self.B* self.w2*q2)*df.dx
self.F = self.F1+self.F2
# mass matrix
u1,u2 = df.TrialFunctions(self.V)
a_M = u1*q1*df.dx
M1 = df.assemble(a_M)
a_M = u2*q2*df.dx
M2 = df.assemble(a_M)
self.M = M1+M2
def __init__(self, cparams, dtype_u, dtype_f):
"""
Initialization routine
Args:
cparams: custom parameters for the example
dtype_u: particle data type (will be passed parent class)
dtype_f: acceleration data type (will be passed parent class)
"""
# define the Dirichlet boundary
# def Boundary(x, on_boundary):
# return on_boundary
# Sub domain for Periodic boundary condition
class PeriodicBoundary(df.SubDomain):
# Left boundary is "target domain" G
def inside(self, x, on_boundary):
return bool(x[0] < df.DOLFIN_EPS and x[0] > -df.DOLFIN_EPS and on_boundary)
# Map right boundary (H) to left boundary (G)
def map(self, x, y):
y[0] = x[0] - 1.0
# these parameters will be used later, so assert their existence
assert 'c_nvars' in cparams
assert 'nu' in cparams
assert 't0' in cparams
assert 'family' in cparams
assert 'order' in cparams
assert 'refinements' in cparams
# add parameters as attributes for further reference
for k,v in cparams.items():
setattr(self,k,v)
df.set_log_level(df.WARNING)
# set mesh and refinement (for multilevel)
mesh = df.UnitIntervalMesh(self.c_nvars)
# mesh = df.UnitSquareMesh(self.c_nvars[0],self.c_nvars[1])
for i in range(self.refinements):
mesh = df.refine(mesh)
# define function space for future reference
self.V = df.FunctionSpace(mesh, self.family, self.order, constrained_domain=PeriodicBoundary())
tmp = df.Function(self.V)
print('DoFs on this level:',len(tmp.vector().array()))
# invoke super init, passing number of dofs, dtype_u and dtype_f
super(fenics_adv_diff_1d,self).__init__(self.V,dtype_u,dtype_f)
u = df.TrialFunction(self.V)
v = df.TestFunction(self.V)
# Stiffness term (diffusion)
a_K = -1.0*df.inner(df.nabla_grad(u), self.nu*df.nabla_grad(v))*df.dx
# Stiffness term (advection)
a_G = df.inner(self.mu*df.nabla_grad(u)[0], v)*df.dx
# Mass term
a_M = u*v*df.dx
self.M = df.assemble(a_M)
self.K = df.assemble(a_K)
self.G = df.assemble(a_G)
def wrapped(*args, **kwargs):
old_level = get_log_level()
set_log_level(log_level)
function(*args, **kwargs)
set_log_level(old_level)
__author__ = "Jan Blechta"
__version__ = "2017.1.0.dev0"
__license__ = 'LGPL v3'
# Avoid PETSc being initialized by DOLFIN, which sets some performance
# degrading parameters since e91b4100. This assumes that this module
# is imported before DOLFIN; otherwise the assertion may fail.
# TODO: Test whether it works!
from petsc4py import PETSc
from dolfin import SubSystemsManager
assert not SubSystemsManager.responsible_petsc()
del PETSc, SubSystemsManager
# Reduce DOLFIN logging bloat in parallel
from dolfin import set_log_level, get_log_level, MPI, mpi_comm_world
set_log_level(get_log_level()+(0 if MPI.rank(mpi_comm_world())==0 else 1))
del set_log_level, get_log_level
# Parse command-line options
# FIXME: Automatic parsing temporarily commented out as it disallows parsing
# our own application specific parameters. Do we need it somewhere?
#from dolfin import parameters
#parameters.parse()
# Enable info_{green,red,blue} on rank 0
import ufl
ufl.set_level(ufl.INFO if MPI.rank(mpi_comm_world())==0 else ufl.INFO+1)
del ufl, MPI, mpi_comm_world
from dolfintape.flux_reconstructor import FluxReconstructor
def __init__(self, cparams, dtype_u, dtype_f):
"""
Initialization routine
Args:
cparams: custom parameters for the example
dtype_u: particle data type (will be passed parent class)
dtype_f: acceleration data type (will be passed parent class)
"""
# define the Dirichlet boundary
# def Boundary(x, on_boundary):
# return on_boundary
# Sub domain for Periodic boundary condition
class PeriodicBoundary(df.SubDomain):
# Left boundary is "target domain" G
def inside(self, x, on_boundary):
# return True if on left or bottom boundary AND NOT on one of the two corners (0, 1) and (1, 0)
return bool((df.near(x[0], 0) or df.near(x[1], 0)) and
(not ((df.near(x[0], 0) and df.near(x[1], 1)) or
(df.near(x[0], 1) and df.near(x[1], 0)))) and on_boundary)
def map(self, x, y):
if df.near(x[0], 1) and df.near(x[1], 1):
y[0] = x[0] - 1.
y[1] = x[1] - 1.
elif df.near(x[0], 1):
y[0] = x[0] - 1.
y[1] = x[1]
else: # near(x[1], 1)
y[0] = x[0]
y[1] = x[1] - 1.
# these parameters will be used later, so assert their existence
assert 'c_nvars' in cparams
assert 'nu' in cparams
assert 't0' in cparams
assert 'family' in cparams
assert 'order' in cparams
assert 'refinements' in cparams
# add parameters as attributes for further reference
for k,v in cparams.items():
setattr(self,k,v)
df.set_log_level(df.WARNING)
# set mesh and refinement (for multilevel)
# mesh = df.UnitIntervalMesh(self.c_nvars)
mesh = df.UnitSquareMesh(self.c_nvars[0],self.c_nvars[1])
for i in range(self.refinements):
mesh = df.refine(mesh)
self.mesh = df.Mesh(mesh)
self.bc = PeriodicBoundary()
# define function space for future reference
self.V = df.FunctionSpace(mesh, self.family, self.order, constrained_domain=self.bc)
tmp = df.Function(self.V)
print('DoFs on this level:',len(tmp.vector().array()))
# invoke super init, passing number of dofs, dtype_u and dtype_f
super(fenics_vortex_2d,self).__init__(self.V,dtype_u,dtype_f)
w = df.TrialFunction(self.V)
v = df.TestFunction(self.V)
# Stiffness term (diffusion)
a_K = df.inner(df.nabla_grad(w), df.nabla_grad(v))*df.dx
# Mass term
a_M = w*v*df.dx
self.M = df.assemble(a_M)
self.K = df.assemble(a_K)
def test_shear(scheme, nu_interp, postprocessor):
#set_log_level(WARNING)
assert scheme == "SemiDecoupled"
dt = 0.0 # solve as the stationary problem
# Read parameters
scriptdir = os.path.dirname(os.path.realpath(__file__))
prm_file = os.path.join(scriptdir, "interface-parameters.xml")
mpset.read(prm_file)
# Adjust parameters
c = postprocessor.get_coefficients()
mpset["model"]["eps"] = c[r"\eps"]
mpset["model"]["rho"]["1"] = c[r"\rho_1"]
mpset["model"]["rho"]["2"] = c[r"\rho_2"]
mpset["model"]["nu"]["1"] = c[r"\nu_1"]
mpset["model"]["nu"]["2"] = c[r"\nu_2"]
mpset["model"]["chq"]["L"] = c[r"L_0"]
mpset["model"]["chq"]["V"] = c[r"V_0"]
mpset["model"]["chq"]["rho"] = c[r"\rho_0"]
mpset["model"]["mobility"]["M0"] = 1.0e+0
mpset["model"]["sigma"]["12"] = 1.0e-0
#mpset.show()
cc = wrap_coeffs_as_constants(c)
# Names and directories
basename = postprocessor.basename
label = "{}_{}".format(basename, nu_interp)
outdir = postprocessor.outdir
for level in range(2, 3):
# Prepare domain and discretization
mesh, boundary_markers, pinpoint, periodic_bnd = create_domain(
level, "crossed")
del periodic_bnd
DS, div_v = create_discretization(scheme, mesh, div_projection=True)
DS.parameters["PTL"] = 1
DS.setup()
# Prepare initial and boundary conditions
load_initial_conditions(DS, c)
bcs = create_bcs(DS, boundary_markers, pinpoint) # for Dirichlet
p_h = create_hydrostatic_pressure(mesh, cc) # for Neumann
# Force applied on the top plate
B = 0.0 if dt == 0.0 else 1.0
applied_force = df.Expression(
("A*(1.0 - B*exp(-alpha*t))", "0.0"),
degree=DS.subspace("v", 0).ufl_element().degree(),
t=0.0,
alpha=1.0,
A=1.0,
B=B)
# Prepare model
model = ModelFactory.create("Incompressible", DS, bcs)
model.parameters["THETA2"] = 0.0
#model.parameters["rho"]["itype"] = "lin"
#model.parameters["rho"]["trunc"] = "minmax"
model.parameters["nu"]["itype"] = nu_interp
model.parameters["nu"]["trunc"] = "minmax"
#model.parameters["nu"]["trunc"] = "clamp_hard"
#model.parameters["mobility"]["cut"] = True
# Prepare external source term
g_a = c[r"g_a"]
g_a /= mpset["model"]["chq"]["V"]**2.0 * mpset["model"]["chq"]["L"]
f_src = df.Constant((0.0, -g_a), cell=mesh.ufl_cell(), name="f_src")
model.load_sources(f_src)
# Create forms
forms = model.create_forms()
# Add boundary integrals
n = DS.facet_normal()
ds = df.Measure("ds", subdomain_data=boundary_markers)
test = DS.test_functions()
forms["lin"]["rhs"] +=\
df.inner(applied_force, test["v"]) * ds(3) # driving force
forms["lin"]["rhs"] -=\
p_h * df.inner(n, test["v"]) * (ds(2) + ds(4)) # hydrostatic balance
# Prepare solver
solver = SolverFactory.create(model, forms, fix_p=False)
# Prepare time-stepping algorithm
comm = mesh.mpi_comm()
pv = DS.primitive_vars_ctl()
modulo_factor = 1
xfields = list(zip(pv["phi"].split(), ("phi", )))
xfields.append((pv["p"].dolfin_repr(), "p"))
if scheme == "FullyDecoupled":
xfields += list(zip(pv["v"].split(), ("v1", "v2")))
else:
xfields.append((pv["v"].dolfin_repr(), "v"))
if div_v is not None:
xfields.append((div_v, "div_v"))
functionals = {"t": [], "E_kin": [], "Psi": [], "mean_p": []}
hook = prepare_hook(model, applied_force, functionals, modulo_factor,
div_v)
logfile = "log_{}.dat".format(label)
TS = TimeSteppingFactory.create("ConstantTimeStep",
comm,
solver,
hook=hook,
logfile=logfile,
xfields=xfields,
outdir=outdir)
TS.parameters["xdmf"]["folder"] = "XDMF_{}".format(label)
TS.parameters["xdmf"]["modulo"] = modulo_factor
TS.parameters["xdmf"]["flush"] = True
TS.parameters["xdmf"]["iconds"] = True
# Time-stepping
with Timer("Time stepping") as tmr_tstepping:
result = TS.run(0.0, 2.0, dt, OTD=1)
# Pre-process results
v = pv["v"].dolfin_repr()
p = pv["p"].dolfin_repr()
phi = pv["phi"].split()[0]
w_diff = DS.solution_ctl()[0].copy(True)
w0 = DS.solution_ptl(0)[0]
w_diff.vector().axpy(-1.0, w0.vector())
phi_diff = w_diff.split(True)[0]
phi_diff.rename("phi_diff", "phi_tstep_difference")
xdmfdir = \
os.path.join(outdir, TS.parameters["xdmf"]["folder"], "phi_diff.xdmf")
with df.XDMFFile(xdmfdir) as file:
file.write(phi_diff, 0.0)
D_12 = df.project(0.5 * v.sub(0).dx(1), div_v.function_space())
if nu_interp in [
"har",
]:
deg = DS.subspace("phi", 0).ufl_element().degree()
V_nu = df.FunctionSpace(mesh, "DG", deg)
else:
V_nu = DS.subspace("phi", 0, deepcopy=True)
nu_0 = df.project(model.coeffs["nu"], V_nu)
T_12 = df.project(model.coeffs["nu"] * v.sub(0).dx(1), V_nu)
#p_ref = df.project(p_h, df.FunctionSpace(mesh, W.sub(1).ufl_element()))
# Save results
make_cut = postprocessor._make_cut
rs = dict(level=level,
r_dens=c[r"r_dens"],
r_visc=c[r"r_visc"],
nu_interp=nu_interp)
rs[r"$v_1$"] = make_cut(v.sub(0))
rs[r"$p$"] = make_cut(p)
rs[r"$\phi$"] = make_cut(phi)
rs[r"$D_{12}$"] = make_cut(D_12)
rs[r"$T_{12}$"] = make_cut(T_12)
rs[r"$\nu$"] = make_cut(nu_0)
print(label, level)
# Send to posprocessor
comm = mesh.mpi_comm()
rank = df.MPI.rank(comm)
postprocessor.add_result(rank, rs)
# Save results into a binary file
filename = "results_{}.pickle".format(label)
postprocessor.save_results(filename)
# Flush plots as we now have data for all level values
postprocessor.flush_plots()
# Cleanup
df.set_log_level(df.INFO)
gc.collect()
def write_file(f, u, label, t):
df.set_log_level(40)
f.write_checkpoint(u, label, t)
df.set_log_level(30)
# mshr is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with mshr. If not, see <http://www.gnu.org/licenses/>.
#
import dolfin
import pygmsh
# from mshr import Sphere, Cylinder, CSGCGALDomain3D, generate_mesh
# dolfin.set_log_level(dolfin.TRACE)
dolfin.set_log_active(True)
dolfin.set_log_level(4)
# Define 3D geometry
# sphere = Sphere(dolfin.Point(0, 0, 0), 0.5)
# cone = Cylinder(dolfin.Point(0, 0, 0), dolfin.Point(0, 0, -1), .35, .1)
# geometry = cone + sphere
geom = pygmsh.opencascade.Geometry(characteristic_length_min=0.1,
characteristic_length_max=0.1)
sphere_a = geom.add_ball([0., 0., 0.], 0.5)
cone = geom.add_cylinder([0., 0., 0.], [0., 0., 1.], .1)
figure = geom.boolean_union([sphere_a, cone])
mesh = pygmsh.generate_mesh(geom, verbose=True)
# Geometry surfaces can be saved to off files
else:
dx = Measure("dx", domain=mesh)
# Optimization options for the form compiler
parameters["krylov_solver"]["maximum_iterations"] = 300
parameters["krylov_solver"]["relative_tolerance"] = 1.0e-10
parameters["krylov_solver"]["absolute_tolerance"] = 1.0e-10
# ================= MPI PARAMETERS ================= #
# MPI Parameters
comm = MPI.comm_world
rank = MPI.rank(comm)
# Set log level for parallel
set_log_level(LogLevel.ERROR)
if rank == 0:
set_log_level(LogLevel.PROGRESS)
ff = MeshFunction("size_t", mesh, mesh.geometry().dim() - 1)
Dirichlet(Lx, Ly, Lpml).mark(ff, 1)
# Create function spaces
VE = VectorElement("CG", mesh.ufl_cell(), 1, dim=2)
TE = TensorElement("DG", mesh.ufl_cell(), 0, shape=(2, 2), symmetry=True)
W = FunctionSpace(mesh, MixedElement([VE, TE]))
F = FunctionSpace(mesh, "CG", 2)
V = W.sub(0).collapse()
M = W.sub(1).collapse()
import dolfin as df
import numpy as np
import scipy as sp
import scipy.sparse as sps
# self defined modules
import sys
sys.path.append( "../" )
from util.dolfin_gadget import get_dof_coords,vec2fun
from util.sparse_geeklet import *
from util.Eigen import *
# set to warn only once for the same warnings
import warnings
warnings.simplefilter('once')
df.set_log_level(df.ERROR)
def _get_sqrtm(A,m_name='K',output_petsc=True,SAVE=True):
"""
Get the root of matrix A.
"""
if output_petsc and df.has_petsc4py():
from petsc4py import PETSc
rtA_f=os.path.join(os.getcwd(),'rt'+m_name+'_petsc.dat')
try:
viewer = PETSc.Viewer().createBinary(rtA_f, 'r')
rtA_petsc=df.PETScMatrix(PETSc.Mat().load(viewer))
print('Read the root of '+{'K':'kernel','C':'covariance'}[m_name]+' successfully!')
except:
import scipy.linalg as spla
rtA_sps = sps.csr_matrix(spla.sqrtm(A.array()).real)
import math
# from dolfin import *
from dolfin import ERROR, set_log_level, exp, near, File, Expression, tanh, \
Constant, SubDomain, VectorFunctionSpace, FunctionSpace, \
DirichletBC, Function, split, \
MixedFunctionSpace, TestFunctions, inner, sym, grad, div, dx, \
RectangleMesh, Point, solve, project, assign, interpolate
'''
This version of the code runs a swarm of simulations of various viscosities
and temperatures per viscosity. Since 5-29, it also includes an adiabatic
temperature variance at the LAB.
'''
set_log_level(ERROR)
rho_0 = 3300.
rhomelt = 2900.
darcy = 1e-13 # k over (mu*phi) in darcy
alpha = 2.5e-5
g = 9.81
# not actually used.. (in cian's notes he is using the non dimensional
# kappa in the equations, which here i have defined as 1 (as
# kappa/kappa_0) so i think i can get away with this)
kappa = 1.E-6
b = 12.7
cc = math.log(128)
#Ep = 0.014057
theta = 0.5
import sys
sys.path.append('../')
import matplotlib
matplotlib.use('macosx')
import time
import numpy as np
import matplotlib.pyplot as plt
import dolfin as dl
dl.set_log_level(40)
from utils import nb
# Tensorflow related imports
from tensorflow.keras.optimizers import Adam
# Scipy imports
from scipy.optimize import minimize, Bounds
# ROMML imports
from fom.forward_solve_exp import Fin
from fom.thermal_fin import get_space
from rom.averaged_affine_ROM import AffineROMFin
from deep_learning.dl_model import load_parametric_model_avg, load_bn_model
from gaussian_field import make_cov_chol
randobs = True
resolution = 40
V = get_space(resolution)
chol = make_cov_chol(V, length=1.2)
#
import numbers
import types
import pytest
from numpy import allclose as float_array_equal, array_equal as integer_array_equal, bmat, hstack as bvec, sort, unique, vstack
from dolfin import assemble, Constant, DOLFIN_EPS, dx, Expression, FiniteElement, Function, FunctionSpace, has_pybind11, inner, MixedElement, project as dolfin_project, set_log_level, SubDomain, TensorElement, TensorFunctionSpace, VectorElement, VectorFunctionSpace
if has_pybind11():
from dolfin.cpp.la import GenericMatrix, GenericVector
from dolfin.cpp.log import LogLevel
ERROR = LogLevel.ERROR
PROGRESS = LogLevel.PROGRESS
else:
from dolfin import ERROR, GenericMatrix, GenericVector, PROGRESS
from multiphenics import assign, block_assemble, block_assign, BlockDirichletBC, BlockFunction, block_split, BlockTestFunction, BlockTrialFunction, DirichletBC
set_log_level(PROGRESS)
# ================ PYTEST HELPER ================ #
def pytest_mark_slow_for_cartesian_product(generator_1, generator_2):
for i in generator_1():
for j in generator_2():
slow = False
if hasattr(i, "mark"):
assert i.name == "slow"
assert len(i.args) is 1
i = i.args[0]
slow = True
if hasattr(j, "mark"):
assert j.name == "slow"
assert len(j.args) is 1
j = j.args[0]
def read_file(f, u, label, i):
df.set_log_level(40)
f.read_checkpoint(u, label, i)
df.set_log_level(30)
return u
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# mshr is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with mshr. If not, see <http://www.gnu.org/licenses/>.
from __future__ import print_function
import dolfin
from mshr import *
dolfin.set_log_level(dolfin.TRACE)
# Define 2D geometry
domain = Rectangle(dolfin.Point(0., 0.), dolfin.Point(5., 5.)) \
- Rectangle(dolfin.Point(2., 1.25), dolfin.Point(3., 1.75)) \
- Circle(dolfin.Point(1, 4), .25) \
- Circle(dolfin.Point(4, 4), .25)
domain.set_subdomain(1, Rectangle(dolfin.Point(1., 1.), dolfin.Point(4., 3.)))
domain.set_subdomain(2, Rectangle(dolfin.Point(2., 2.), dolfin.Point(3., 4.)))
dolfin.info("\nVerbose output of 2D geometry:")
dolfin.info(domain, True)
# Generate and plot mesh
mesh2d = generate_mesh(domain, 45)
print(mesh2d)
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# mshr is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with mshr. If not, see <http://www.gnu.org/licenses/>.
from __future__ import print_function
import dolfin
from mshr import *
dolfin.set_log_level(dolfin.TRACE)
# Define 2D geometry
domain = Rectangle(dolfin.Point(0., 0.), dolfin.Point(5., 5.)) \
- Rectangle(dolfin.Point(2., 1.25), dolfin.Point(3., 1.75)) \
- Circle(dolfin.Point(1, 4), .25) \
- Circle(dolfin.Point(4, 4), .25)
domain.set_subdomain(1, Rectangle(dolfin.Point(1., 1.), dolfin.Point(4., 3.)))
domain.set_subdomain(2, Rectangle(dolfin.Point(2., 2.), dolfin.Point(3., 4.)))
dolfin.info("\nVerbose output of 2D geometry:")
dolfin.info(domain, True)
# Generate and plot mesh
mesh2d = generate_mesh(domain, 45)
print(mesh2d)
from time import clock
from os import makedirs
import math
# from dolfin import *
from dolfin import ERROR, set_log_level, exp, near, File, Expression, tanh, \
Constant, SubDomain, VectorFunctionSpace, FunctionSpace, \
DirichletBC, Function, split, \
MixedFunctionSpace, TestFunctions, inner, sym, grad, div, dx, \
RectangleMesh, Point, solve, project, assign, interpolate
'''
This version of the code runs a swarm of simulations of various viscosities
and temperatures per viscosity. Since 5-29, it also includes an adiabatic
temperature variance at the LAB.
'''
set_log_level(ERROR)
rho_0 = 3300.
rhomelt = 2900.
darcy = 1e-13 # k over (mu*phi) in darcy
alpha = 2.5e-5
g = 9.81
# not actually used.. (in cian's notes he is using the non dimensional
# kappa in the equations, which here i have defined as 1 (as
# kappa/kappa_0) so i think i can get away with this)
kappa = 1.E-6
b = 12.7
cc = math.log(128)
#Ep = 0.014057
theta = 0.5