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Merge branch 'TBendall/update_ref_profile' of github.com:firedrakepro…
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tommbendall committed Sep 21, 2024
2 parents 6418788 + f4b43fe commit 028fae6
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1 change: 1 addition & 0 deletions .github/workflows/build.yml
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Expand Up @@ -38,6 +38,7 @@ jobs:
. /home/firedrake/firedrake/bin/activate
firedrake-clean
export GUSTO_PARALLEL_LOG=FILE
export PYOP2_CFLAGS=-O0
python -m pytest \
-n 12 --dist worksteal \
--durations=100 \
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6 changes: 5 additions & 1 deletion Makefile
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Expand Up @@ -32,4 +32,8 @@ integration_test:

example:
@echo " Running all examples"
@python3 -m pytest examples $(PYTEST_ARGS)
@python3 -m pytest examples -v -m "not parallel" $(PYTEST_ARGS)

parallel_example:
@echo " Running all parallel examples"
@python3 -m pytest examples -v -m "parallel" $(PYTEST_ARGS)
2 changes: 1 addition & 1 deletion docs/Gemfile.lock
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Expand Up @@ -222,7 +222,7 @@ GEM
rb-fsevent (0.11.2)
rb-inotify (0.10.1)
ffi (~> 1.0)
rexml (3.3.3)
rexml (3.3.6)
strscan
rouge (3.26.0)
ruby2_keywords (0.0.5)
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288 changes: 184 additions & 104 deletions examples/boussinesq/skamarock_klemp_compressible.py
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@@ -1,114 +1,194 @@
"""
The gravity wave test case of Skamarock and Klemp (1994), solved using the
incompressible Boussinesq equations.
This example uses the compressible Boussinesq equations to solve the vertical
slice gravity wave test case of Skamarock and Klemp, 1994:
``Efficiency and Accuracy of the Klemp-Wilhelmson Time-Splitting Technique'',
MWR.
Buoyancy is transported using SUPG.
Buoyancy is transported using SUPG, and the degree 1 elements are used.
"""

from gusto import *
from firedrake import (as_vector, PeriodicIntervalMesh, ExtrudedMesh,
sin, SpatialCoordinate, Function, pi)
import sys

# ---------------------------------------------------------------------------- #
# Test case parameters
# ---------------------------------------------------------------------------- #

dt = 6.
L = 3.0e5 # Domain length
H = 1.0e4 # Height position of the model top

if '--running-tests' in sys.argv:
tmax = dt
dumpfreq = 1
columns = 30 # number of columns
nlayers = 5 # horizontal layers

else:
tmax = 3600.
dumpfreq = int(tmax / (2*dt))
columns = 300 # number of columns
nlayers = 10 # horizontal layers

# ---------------------------------------------------------------------------- #
# Set up model objects
# ---------------------------------------------------------------------------- #

# Domain
m = PeriodicIntervalMesh(columns, L)
mesh = ExtrudedMesh(m, layers=nlayers, layer_height=H/nlayers)
domain = Domain(mesh, dt, 'CG', 1)

# Equation
parameters = BoussinesqParameters(cs=300)
eqns = BoussinesqEquations(domain, parameters)

# I/O
output = OutputParameters(
dirname='skamarock_klemp_compressible',
dumpfreq=dumpfreq,
dumplist=['u'],
from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter
from firedrake import (
as_vector, PeriodicIntervalMesh, ExtrudedMesh, sin, SpatialCoordinate,
Function, pi
)
# list of diagnostic fields, each defined in a class in diagnostics.py
diagnostic_fields = [CourantNumber(), Divergence(), Perturbation('b')]
io = IO(domain, output, diagnostic_fields=diagnostic_fields)

# Transport schemes
b_opts = SUPGOptions()
transported_fields = [TrapeziumRule(domain, "u"),
SSPRK3(domain, "p"),
SSPRK3(domain, "b", options=b_opts)]
transport_methods = [DGUpwind(eqns, "u"),
DGUpwind(eqns, "p"),
DGUpwind(eqns, "b", ibp=b_opts.ibp)]

# Linear solver
linear_solver = BoussinesqSolver(eqns)

# Time stepper
stepper = SemiImplicitQuasiNewton(eqns, io, transported_fields,
transport_methods,
linear_solver=linear_solver)
from gusto import (
Domain, IO, OutputParameters, SemiImplicitQuasiNewton, SSPRK3, DGUpwind,
TrapeziumRule, SUPGOptions, Divergence, Perturbation, CourantNumber,
BoussinesqParameters, BoussinesqEquations, BoussinesqSolver,
boussinesq_hydrostatic_balance
)

skamarock_klemp_compressible_bouss_defaults = {
'ncolumns': 300,
'nlayers': 10,
'dt': 6.0,
'tmax': 3600.,
'dumpfreq': 300,
'dirname': 'skamarock_klemp_compressible_bouss'
}


def skamarock_klemp_compressible_bouss(
ncolumns=skamarock_klemp_compressible_bouss_defaults['ncolumns'],
nlayers=skamarock_klemp_compressible_bouss_defaults['nlayers'],
dt=skamarock_klemp_compressible_bouss_defaults['dt'],
tmax=skamarock_klemp_compressible_bouss_defaults['tmax'],
dumpfreq=skamarock_klemp_compressible_bouss_defaults['dumpfreq'],
dirname=skamarock_klemp_compressible_bouss_defaults['dirname']
):

# ------------------------------------------------------------------------ #
# Test case parameters
# ------------------------------------------------------------------------ #

domain_width = 3.0e5 # Width of domain (m)
domain_height = 1.0e4 # Height of domain (m)
wind_initial = 20. # Initial wind in x direction (m/s)
pert_width = 5.0e3 # Width parameter of perturbation (m)
deltab = 1.0e-2 # Magnitude of buoyancy perturbation (m/s^2)
N = 0.01 # Brunt-Vaisala frequency (1/s)
cs = 300. # Speed of sound (m/s)

# ------------------------------------------------------------------------ #
# Our settings for this set up
# ------------------------------------------------------------------------ #

element_order = 1

# ------------------------------------------------------------------------ #
# Set up model objects
# ------------------------------------------------------------------------ #

# Domain
base_mesh = PeriodicIntervalMesh(ncolumns, domain_width)
mesh = ExtrudedMesh(base_mesh, nlayers, layer_height=domain_height/nlayers)
domain = Domain(mesh, dt, 'CG', element_order)

# Equation
parameters = BoussinesqParameters(cs=cs)
eqns = BoussinesqEquations(domain, parameters)

# I/O
output = OutputParameters(
dirname=dirname, dumpfreq=dumpfreq, dump_vtus=True, dump_nc=False,
)
# list of diagnostic fields, each defined in a class in diagnostics.py
diagnostic_fields = [CourantNumber(), Divergence(), Perturbation('b')]
io = IO(domain, output, diagnostic_fields=diagnostic_fields)

# Transport schemes
b_opts = SUPGOptions()
transported_fields = [
TrapeziumRule(domain, "u"),
SSPRK3(domain, "p"),
SSPRK3(domain, "b", options=b_opts)
]
transport_methods = [
DGUpwind(eqns, "u"),
DGUpwind(eqns, "p"),
DGUpwind(eqns, "b", ibp=b_opts.ibp)
]

# Linear solver
linear_solver = BoussinesqSolver(eqns)

# Time stepper
stepper = SemiImplicitQuasiNewton(
eqns, io, transported_fields, transport_methods,
linear_solver=linear_solver
)

# ------------------------------------------------------------------------ #
# Initial conditions
# ------------------------------------------------------------------------ #

u0 = stepper.fields("u")
b0 = stepper.fields("b")
p0 = stepper.fields("p")

# spaces
Vb = b0.function_space()
Vp = p0.function_space()

x, z = SpatialCoordinate(mesh)

# first setup the background buoyancy profile
# z.grad(bref) = N**2
bref = z*(N**2)
# interpolate the expression to the function
b_b = Function(Vb).interpolate(bref)

# setup constants
b_pert = (
deltab * sin(pi*z/domain_height)
/ (1 + (x - domain_width/2)**2 / pert_width**2)
)
# interpolate the expression to the function
b0.interpolate(b_b + b_pert)

p_b = Function(Vp)
boussinesq_hydrostatic_balance(eqns, b_b, p_b)
p0.assign(p_b)

uinit = (as_vector([wind_initial, 0.0]))
u0.project(uinit)

# set the background buoyancy
stepper.set_reference_profiles([('p', p_b), ('b', b_b)])

# ------------------------------------------------------------------------ #
# Run
# ------------------------------------------------------------------------ #
stepper.run(t=0, tmax=tmax)

# ---------------------------------------------------------------------------- #
# Initial conditions
# MAIN
# ---------------------------------------------------------------------------- #

u0 = stepper.fields("u")
b0 = stepper.fields("b")
p0 = stepper.fields("p")

# spaces
Vb = b0.function_space()
Vp = p0.function_space()

x, z = SpatialCoordinate(mesh)

# first setup the background buoyancy profile
# z.grad(bref) = N**2
N = parameters.N
bref = z*(N**2)
# interpolate the expression to the function
b_b = Function(Vb).interpolate(bref)

# setup constants
a = 5.0e3
deltab = 1.0e-2
b_pert = deltab*sin(pi*z/H)/(1 + (x - L/2)**2/a**2)
# interpolate the expression to the function
b0.interpolate(b_b + b_pert)

p_b = Function(Vp)
boussinesq_hydrostatic_balance(eqns, b_b, p_b)
p0.assign(p_b)

uinit = (as_vector([20.0, 0.0]))
u0.project(uinit)

# set the background buoyancy
stepper.set_reference_profiles([('p', p_b), ('b', b_b)])

# ---------------------------------------------------------------------------- #
# Run
# ---------------------------------------------------------------------------- #
stepper.run(t=0, tmax=tmax)
if __name__ == "__main__":

parser = ArgumentParser(
description=__doc__,
formatter_class=ArgumentDefaultsHelpFormatter
)
parser.add_argument(
'--ncolumns',
help="The number of columns in the vertical slice mesh.",
type=int,
default=skamarock_klemp_compressible_bouss_defaults['ncolumns']
)
parser.add_argument(
'--nlayers',
help="The number of layers for the mesh.",
type=int,
default=skamarock_klemp_compressible_bouss_defaults['nlayers']
)
parser.add_argument(
'--dt',
help="The time step in seconds.",
type=float,
default=skamarock_klemp_compressible_bouss_defaults['dt']
)
parser.add_argument(
"--tmax",
help="The end time for the simulation in seconds.",
type=float,
default=skamarock_klemp_compressible_bouss_defaults['tmax']
)
parser.add_argument(
'--dumpfreq',
help="The frequency at which to dump field output.",
type=int,
default=skamarock_klemp_compressible_bouss_defaults['dumpfreq']
)
parser.add_argument(
'--dirname',
help="The name of the directory to write to.",
type=str,
default=skamarock_klemp_compressible_bouss_defaults['dirname']
)
args, unknown = parser.parse_known_args()

skamarock_klemp_compressible_bouss(**vars(args))
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