# Pop results that we do not want to report at the moment
postprocessor.pop_items(
["ndofs", "tmr_prepare", "tmr_solve", "tmr_tstepping", "it", "h_min"])
# Flush plots as we now have data for all level values
postprocessor.flush_plots()
# Store timings
#datafile = os.path.join(outdir, "timings.xml")
#dump_timings_to_xml(datafile, TimingClear_clear)
# Cleanup
set_log_level(INFO)
#mpset.write(comm, prm_file) # uncomment to save parameters
mpset.refresh()
gc.collect()
@pytest.fixture(scope='module')
def postprocessor(request):
t_end = 0.5 # CHANGE #3: Set to "t_end = 3.0"
OTD = 2 # Order of Time Discretization
rank = MPI.rank(mpi_comm_world())
scriptdir = os.path.dirname(os.path.realpath(__file__))
outdir = os.path.join(scriptdir, __name__)
proc = Postprocessor(t_end, OTD, outdir)
# Decide what should be plotted
proc.register_fixed_variables((("t_end", t_end), ("OTD", OTD)))
#proc.register_fixed_variables(
def test_scaling_time(scheme, matching_p, postprocessor):
"""
Compute convergence rates for fixed element order, fixed mesh and
gradually decreasing time step.
"""
# Additional test configuration w.r.t. chosen scheme
if scheme == "SemiDecoupled":
OTD = 1
method = "it"
elif scheme == "FullyDecoupled":
OTD = 2
method = "lu" # iterative solvers not yet supported
else:
assert False
# Run test
set_log_level(WARNING)
degrise = 3 # degree rise for computation of errornorm
# Read parameters
scriptdir = os.path.dirname(os.path.realpath(__file__))
prm_file = os.path.join(scriptdir, "mms-parameters.xml")
mpset.read(prm_file)
# Fixed parameters
level = postprocessor.level
k = postprocessor.OPA
t_end = postprocessor.t_end
# Names and directories
basename = postprocessor.basename
outdir = postprocessor.outdir
# Mesh independent predefined quantities
msol = create_manufactured_solution()
ic = create_initial_conditions(msol)
# Prepare space discretization, exact solution and bcs
mesh, boundary_markers = create_domain(level)
DS = create_discretization(scheme, mesh, k)
DS.parameters["PTL"] = OTD
DS.setup()
esol = create_exact_solution(msol, DS.finite_elements(), degrise)
bcs = create_bcs(DS, boundary_markers, esol, method)
# Iterate over time step
for m in range(6): # CHANGE #1: set "m in range(7)"
dt = 0.1*0.5**m
label = "{}_dt_{}_{}".format(scheme, dt, basename)
with Timer("Prepare") as tmr_prepare:
# Reset sol_ptl[0] back to initial conditions
DS.load_ic_from_simple_cpp(ic)
# Prepare model
model = ModelFactory.create("Incompressible", DS, bcs)
cell = DS.mesh().ufl_cell()
t_src_ctl = Constant(0.0, cell=cell, name="t_src_ctl")
t_src_ptl = Constant(0.0, cell=cell, name="t_src_ptl")
f_src_ctl, g_src_ctl = \
create_source_terms(t_src_ctl, mesh, model, msol, matching_p)
f_src_ptl, g_src_ptl = \
create_source_terms(t_src_ptl, mesh, model, msol, matching_p)
t_src = [t_src_ctl,]
f_src = [f_src_ctl,]
g_src = [g_src_ctl,]
if OTD == 2 and scheme in ["Monolithic", "SemiDecoupled"]:
t_src.append(t_src_ptl)
g_src.append(g_src_ptl)
if scheme == "Monolithic":
f_src.append(f_src_ptl)
model.load_sources(f_src, g_src)
forms = model.create_forms(matching_p)
# Prepare solver
comm = mesh.mpi_comm()
solver = SolverFactory.create(model, forms, fix_p=(method == "it"))
if method == "it":
solver.data["solver"]["CH"]["lin"] = \
create_ch_solver(comm, "bjacobi")
solver.data["solver"]["NS"] = \
create_pcd_solver(comm, "BRM1", "iterative")
# prefix_ch = solver.data["solver"]["CH"]["lin"].get_options_prefix()
# PETScOptions.set(prefix_ch+"ksp_monitor_true_residual")
# solver.data["solver"]["CH"]["lin"].set_from_options()
# prefix_ns = solver.data["solver"]["NS"].get_options_prefix()
# PETScOptions.set(prefix_ns+"ksp_monitor")
# solver.data["solver"]["NS"].set_from_options()
# Prepare time-stepping algorithm
xfields = None
# NOTE: Uncomment the following block of code to get XDMF output
# pv = DS.primitive_vars_ctl()
# phi, chi, v, p = pv["phi"], pv["chi"], pv["v"], pv["p"]
# phi_, chi_, v_ = phi.split(), chi.split(), v.split()
# xfields = list(zip(phi_, len(phi_)*[None,])) \
# + list(zip(v_, len(v_)*[None,])) \
# + [(p.dolfin_repr(), None),]
hook = prepare_hook(t_src, model, esol, degrise, {})
logfile = "log_{}.dat".format(label)
TS = TimeSteppingFactory.create("ConstantTimeStep", comm, solver,
hook=hook, logfile=logfile, xfields=xfields, outdir=outdir)
# Time-stepping
t_beg = 0.0
with Timer("Time stepping") as tmr_tstepping:
it = 0
if OTD == 2:
if scheme == "FullyDecoupled":
dt0 = dt
result = TS.run(t_beg, dt0, dt0, OTD=1, it=it)
t_beg = dt
elif scheme == "Monolithic":
dt0 = 1.0e-4*dt
result = TS.run(t_beg, dt0, dt0, OTD=1, it=it)
if dt - dt0 > 0.0:
it = 0.5
result = TS.run(dt0, dt, dt - dt0, OTD=2, it=it)
t_beg = dt
it = 1
result = TS.run(t_beg, t_end, dt, OTD, it)
# Prepare results
name = logfile[4:-4]
result.update(
method=method,
ndofs=DS.num_dofs(),
scheme=scheme,
dt=dt,
t_end=t_end,
OTD=OTD,
err=hook.err,
level=level,
k=k,
tmr_prepare=tmr_prepare.elapsed()[0],
tmr_tstepping=tmr_tstepping.elapsed()[0]
)
print(name, result["ndofs"], result["tmr_prepare"],
result["tmr_solve"], result["it"], result["tmr_tstepping"])
# Send to posprocessor
rank = MPI.rank(comm)
postprocessor.add_result(rank, result)
# Save results into a binary file
filename = "results_{}.pickle".format(label)
postprocessor.save_results(filename)
# Pop results that we do not want to report at the moment
postprocessor.pop_items(["ndofs", "tmr_prepare", "tmr_solve", "it", "OTD"])
# Flush plots as we now have data for all level values
postprocessor.flush_plots()
# Store timings
#datafile = os.path.join(outdir, "timings.xml")
#dump_timings_to_xml(datafile, TimingClear_clear)
# Cleanup
set_log_level(INFO)
#mpset.write(comm, prm_file) # uncomment to save parameters
mpset.refresh()
gc.collect()
def test_scaling_mesh(pcd_variant, ls, matching_p, postprocessor):
"""
Compute convergence rates for fixed time step and gradually refined mesh or
increasing element order.
"""
set_log_level(WARNING)
degrise = 3 # degree rise for computation of errornorm
# Read parameters
scriptdir = os.path.dirname(os.path.realpath(__file__))
prm_file = os.path.join(scriptdir, "mms-parameters.xml")
mpset.read(prm_file)
# Fixed parameters
OTD = postprocessor.OTD
dt = postprocessor.dt
t_end = postprocessor.t_end
test_type = postprocessor.test
# Discretization
scheme = "SemiDecoupled"
# Names and directories
basename = postprocessor.basename
outdir = postprocessor.outdir
# Mesh independent predefined quantities
msol = create_manufactured_solution()
ic = create_initial_conditions(msol)
# Iterate over refinement level
for it in range(1, 6): # CHANGE #1: set "it in range(1, 8)"
# Decide which test to perform
if test_type == "ref":
level = it
k = 1
elif test_type == "ord":
level = 1
k = it
label = "{}_{}_level_{}_k_{}_{}".format(pcd_variant, ls, level, k,
basename)
with Timer("Prepare") as tmr_prepare:
# Prepare discretization
mesh, boundary_markers = create_domain(level)
DS = create_discretization(scheme, mesh, k)
DS.parameters["PTL"] = OTD
DS.setup()
DS.load_ic_from_simple_cpp(ic)
esol = create_exact_solution(msol, DS.finite_elements(), degrise)
bcs = create_bcs(DS, boundary_markers, esol)
# Prepare model
model = ModelFactory.create("Incompressible", DS, bcs)
cell = DS.mesh().ufl_cell()
t_src_ctl = Constant(0.0, cell=cell, name="t_src_ctl")
t_src_ptl = Constant(0.0, cell=cell, name="t_src_ptl")
f_src_ctl, g_src_ctl = \
create_source_terms(t_src_ctl, mesh, model, msol, matching_p)
f_src_ptl, g_src_ptl = \
create_source_terms(t_src_ptl, mesh, model, msol, matching_p)
# NOTE: Source terms are time-dependent. Updates to these terms
# are possible via 't_src.assign(Constant(t))', where 't'
# denotes the actual time value.
t_src = [
t_src_ctl,
]
f_src = [
f_src_ctl,
]
g_src = [
g_src_ctl,
]
if OTD == 2:
t_src.append(t_src_ptl)
g_src.append(g_src_ptl)
model.load_sources(f_src, g_src)
forms = model.create_forms(matching_p)
# NOTE: Here is the possibility to modify forms, e.g. by adding
# boundary integrals.
# Prepare solver
comm = mesh.mpi_comm()
solver = SolverFactory.create(model, forms, fix_p=True)
solver.data["solver"]["NS"] = \
create_pcd_solver(comm, pcd_variant, ls, mumps_debug=False)
# PETScOptions.set("ksp_monitor")
# solver.data["solver"]["NS"].set_from_options()
# Prepare time-stepping algorithm
xfields = None
# NOTE: Uncomment the following block of code to get XDMF output
# pv = DS.primitive_vars_ctl()
# phi, chi, v, p = pv["phi"], pv["chi"], pv["v"], pv["p"]
# phi_, chi_, v_ = phi.split(), chi.split(), v.split()
# xfields = list(zip(phi_, len(phi_)*[None,])) \
# + list(zip(v_, len(v_)*[None,])) \
# + [(p.dolfin_repr(), None),]
hook = prepare_hook(t_src, model, esol, degrise, {})
logfile = "log_{}.dat".format(label)
#info("BREAK POINT %ia" % level)
TS = TimeSteppingFactory.create("ConstantTimeStep",
comm,
solver,
hook=hook,
logfile=logfile,
xfields=xfields,
outdir=outdir)
#info("BREAK POINT %ib" % level) <-- not reached for level == 2
# when running in parallel
# Time-stepping
t_beg = 0.0
with Timer("Time stepping") as tmr_tstepping:
result = TS.run(t_beg, t_end, dt, OTD)
# Get number of Krylov iterations if relevant
try:
krylov_it = solver.iters["NS"][0]
except AttributeError:
krylov_it = 0
# Prepare results
name = logfile[4:-4]
x_var = k if test_type == "ord" else mesh.hmin()
result.update(scheme=scheme,
pcd_variant=pcd_variant,
ls=ls,
krylov_it=krylov_it,
ndofs=DS.num_dofs(),
dt=dt,
t_end=t_end,
OTD=OTD,
err=hook.err,
x_var=x_var,
tmr_prepare=tmr_prepare.elapsed()[0],
tmr_tstepping=tmr_tstepping.elapsed()[0])
print(name, result["ndofs"], result["it"], result["krylov_it"],
result["tmr_tstepping"])
# Send to posprocessor
rank = MPI.rank(comm)
postprocessor.add_result(rank, result)
# Save results into a binary file
filename = "results_{}.pickle".format(label)
postprocessor.save_results(filename)
# Pop results that we do not want to report at the moment
postprocessor.pop_items(["ndofs", "scheme", "tmr_prepare"])
# Flush plots as we now have data for all level values
postprocessor.flush_plots()
# Store timings
#datafile = os.path.join(outdir, "timings.xml")
#dump_timings_to_xml(datafile, TimingClear_clear)
# Cleanup
set_log_level(INFO)
#mpset.write(comm, prm_file) # uncomment to save parameters
mpset.refresh()
gc.collect()
def test_scaling_mesh(nu, pcd_variant, ls, postprocessor):
#set_log_level(WARNING)
# Read parameters
scriptdir = os.path.dirname(os.path.realpath(__file__))
prm_file = os.path.join(scriptdir, "step-parameters.xml")
mpset.read(prm_file)
# Adjust parameters
mpset["model"]["nu"]["1"] = nu
mpset["model"]["nu"]["2"] = nu
# Parameters for setting up MUFLON components
dt = postprocessor.dt
t_end = postprocessor.t_end # final time of the simulation
scheme = "SemiDecoupled"
OTD = 1
k = 1
modulo_factor = 2
# Names and directories
outdir = postprocessor.outdir
# Mesh independent predefined quantities
ic = SimpleCppIC()
ic.add("phi", "1.0")
# Prepare figure for plotting the vorticity
fig_curl = pyplot.figure()
gs = gridspec.GridSpec(2, 2, height_ratios=[3, 1], width_ratios=[0.01, 1], hspace=0.05)
ax_curl = fig_curl.add_subplot(gs[0, 1])
ax_curl.set_xlabel(r"time $t$")
ax_curl.set_ylabel(r"$\omega_\Omega = \int_\Omega \nabla \times \mathbf{v}$")
del gs
for level in range(4):
with Timer("Prepare") as tmr_prepare:
# Prepare space discretization
mesh, boundary_markers = create_domain(level)
#pyplot.figure(); plot(mesh)
#pyplot.savefig(os.path.join(outdir, "mesh.pdf"))
if dt is None:
hh = mesh.hmin()/(2.0**0.5) # mesh size in the direction of inflow
umax = 1.0 # max velocity at the inlet
dt = 0.8*hh/umax # automatically computed time step
del hh, umax
label = "level_{}_nu_{}_{}_{}_dt_{}_{}".format(
level, nu, pcd_variant, ls, dt, postprocessor.basename)
DS = create_discretization(scheme, mesh, k)
DS.setup()
DS.load_ic_from_simple_cpp(ic)
# Prepare boundary conditions
bcs, inflow = create_bcs(DS, boundary_markers, pcd_variant) #, t0=10*dt
# Prepare model
model = ModelFactory.create("Incompressible", DS, bcs)
#model.parameters["THETA2"] = 0.0
# Create forms
forms = model.create_forms()
if ls == "direct":
forms["pcd"]["a_pc"] = None
# Add boundary integrals
n = DS.facet_normal()
ds_marked = Measure("ds", subdomain_data=boundary_markers)
test = DS.test_functions()
trial = DS.trial_functions()
pv = DS.primitive_vars_ctl(indexed=True)
pv0 = DS.primitive_vars_ptl(0, indexed=True)
cc = model.coeffs
w = cc["rho"]*pv0["v"] + cc["THETA2"]*cc["J"]
a_surf = (
0.5*inner(w, n)*inner(trial["v"], test["v"])
- cc["nu"]*inner(dot(grad(trial["v"]).T, n), test["v"])
)*ds_marked(2)
forms["lin"]["lhs"] += a_surf
if forms["pcd"]["a_pc"] is not None:
forms["pcd"]["a_pc"] += a_surf
if pcd_variant == "BRM2":
forms["pcd"]["kp"] -= \
(1.0/cc["nu"])*inner(w, n)*test["p"]*trial["p"]*ds_marked(1)
# TODO: Is this beneficial?
# forms["pcd"]["kp"] -= \
# (1.0/cc["nu"])*inner(w, n)*test["p"]*trial["p"]*ds_marked(0)
# TODO: Alternatively try:
# forms["pcd"]["kp"] -= \
# (1.0/cc["nu"])*inner(w, n)*test["p"]*trial["p"]*ds
# Prepare solver
comm = mesh.mpi_comm()
solver = SolverFactory.create(model, forms)
prefix = "LU"
solver.data["solver"]["NS"] = \
create_pcd_solver(comm, pcd_variant, ls, mumps_debug=False)
prefix = solver.data["solver"]["NS"].get_options_prefix()
#PETScOptions.set(prefix+"ksp_monitor")
#solver.data["solver"]["NS"].set_from_options()
# Prepare time-stepping algorithm
pv = DS.primitive_vars_ctl()
xfields = list(zip(pv["phi"].split(), ("phi",)))
xfields.append((pv["p"].dolfin_repr(), "p"))
xfields.append((pv["v"].dolfin_repr(), "v"))
functionals = {"t": [], "vorticity": []}
hook = prepare_hook(DS, functionals, modulo_factor, inflow)
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
t_beg = 0.0
with Timer("Time stepping") as tmr_tstepping:
result = TS.run(t_beg, t_end, dt, OTD)
# Get number of Krylov iterations if relevant
try:
krylov_it = solver.iters["NS"][0]
except AttributeError:
krylov_it = 0
# Prepare results (already contains dt, it, t_end, tmr_solve)
result.update(
nu=nu,
pcd_variant=pcd_variant,
ls=ls,
krylov_it=krylov_it,
ndofs=DS.num_dofs(),
level=level,
h_min=mesh.hmin(),
tmr_prepare=tmr_prepare.elapsed()[0],
tmr_tstepping=tmr_tstepping.elapsed()[0],
scheme=scheme,
OTD=OTD,
k=k,
t=functionals["t"],
vorticity=functionals["vorticity"]
)
print(label, prefix, result["ndofs"], result["it"],
result["tmr_tstepping"], result["krylov_it"])
# Send to posprocessor
rank = MPI.rank(comm)
postprocessor.add_result(rank, result)
# Add vorticity plot
ax_curl.plot(functionals["t"], functionals["vorticity"], label=label)
ax_curl.legend(bbox_to_anchor=(0, -0.2), loc=2, borderaxespad=0,
fontsize='x-small', ncol=1)
# Save results into a binary file
filename = "results_{}.pickle".format(label)
postprocessor.save_results(filename)
# Pop results that we do not want to report at the moment
postprocessor.pop_items([
"level", "h_min", "tmr_prepare", "tmr_tstepping",
"scheme", "OTD", "k", "t", "vorticity"])
# Flush plots as we now have data for all level values
postprocessor.flush_plots()
fig_curl.savefig(os.path.join(outdir, "fig_vorticity_{}.pdf".format(label)))
# # Plot last obtained solution
# pv = DS.primitive_vars_ctl()
# v = as_vector(pv["v"].split())
# p = pv["p"].dolfin_repr()
# #phi = pv["phi"].split()
# size = MPI.size(mesh.mpi_comm())
# rank = MPI.rank(mesh.mpi_comm())
# pyplot.figure()
# pyplot.subplot(2, 1, 1)
# plot(v, title="velocity")
# pyplot.subplot(2, 1, 2)
# plot(p, title="pressure")
# pyplot.savefig(os.path.join(outdir, "fig_v_p_size{}_rank{}.pdf".format(size, rank)))
# pyplot.figure()
# plot(p, title="pressure", mode="warp")
# pyplot.savefig(os.path.join(outdir, "fig_warp_size{}_rank{}.pdf".format(size, rank)))
# Store timings
#datafile = os.path.join(outdir, "timings.xml")
#dump_timings_to_xml(datafile, TimingClear_clear)
# Cleanup
set_log_level(INFO)
#mpset.write(comm, prm_file) # uncomment to save parameters
mpset.refresh()
gc.collect()