def gatherStates(self):
r"""
Writes gathered solution to file.
"""
if (self.peano == None or self.libpeano == None):
raise Exception(
"self.peano and self.libpeano have to be initialized with the reference to the Peano grid by peanoclaw.Solver.setup(...)"
)
#Gather patches and states
self.gathered_patches = []
self.gathered_states = []
self.libpeano.pyclaw_peano_gatherSolution.argtypes = [c_void_p]
self.libpeano.pyclaw_peano_gatherSolution(self.peano)
if (len(self.gathered_patches) > 0):
#Assemble solution and write file
self.domain = pyclaw.Domain(self.gathered_patches)
self.solution = pyclaw.Solution(self.gathered_states, self.domain)
else:
self.domain = pyclaw.Domain(self.patch)
self.solution = pyclaw.Solution(self.state, self.domain)
self.t = self.solution.t
def burgers():
"""
Example from Chapter 11 of LeVeque, Figure 11.8.
Shows decay of an initial wave packet to an N-wave with Burgers' equation.
"""
import numpy as np
from clawpack import pyclaw
from clawpack import riemann
solver = pyclaw.ClawSolver1D(riemann.burgers_1D)
solver.limiters = pyclaw.limiters.tvd.MC
solver.bc_lower[0] = pyclaw.BC.periodic
solver.bc_upper[0] = pyclaw.BC.periodic
x = pyclaw.Dimension(-8.0,8.0,1000,name='x')
domain = pyclaw.Domain(x)
num_eqn = 1
state = pyclaw.State(domain,num_eqn)
xc = domain.grid.x.centers
state.q[0,:] = (xc>-np.pi)*(xc<np.pi)*(2.*np.sin(3.*xc)+np.cos(2.*xc)+0.2)
state.q[0,:] = state.q[0,:]*(np.cos(xc)+1.)
state.problem_data['efix']=True
claw = pyclaw.Controller()
claw.tfinal = 6.0
claw.num_output_times = 30
claw.solution = pyclaw.Solution(state,domain)
claw.solver = solver
return claw
def triplestate_pyclaw(ql, qm, qr, numframes):
# Set pyclaw for burgers equation 1D
meshpts = 600
claw = pyclaw.Controller()
claw.tfinal = 2.0 # Set final time
claw.keep_copy = True # Keep solution data in memory for plotting
claw.output_format = None # Don't write solution data to file
claw.num_output_times = numframes # Number of output frames
claw.solver = pyclaw.ClawSolver1D(
riemann.burgers_1D) # Choose burgers 1D Riemann solver
claw.solver.all_bcs = pyclaw.BC.extrap # Choose periodic BCs
claw.verbosity = False # Don't print pyclaw output
domain = pyclaw.Domain((-3., ), (3., ),
(meshpts, )) # Choose domain and mesh resolution
claw.solution = pyclaw.Solution(claw.solver.num_eqn, domain)
# Set initial condition
x = domain.grid.x.centers
q0 = 0.0 * x
xtick1 = int(meshpts / 3)
xtick2 = int(2 * meshpts / 3)
q0[0:xtick1] = ql
q0[xtick1:xtick2] = qm
q0[xtick2:meshpts] = qr
claw.solution.q[0, :] = q0
claw.solver.dt_initial = 1.e99
# Run pyclaw
status = claw.run()
return x, claw.frames
def bump_pyclaw(numframes):
"""Returns pyclaw solution of bump initial condition."""
# Set pyclaw for burgers equation 1D
claw = pyclaw.Controller()
claw.tfinal = 5.0 # Set final time
claw.keep_copy = True # Keep solution data in memory for plotting
claw.output_format = None # Don't write solution data to file
claw.num_output_times = numframes # Number of output frames
claw.solver = pyclaw.ClawSolver1D(
riemann.acoustics_1D) # Choose acoustics 1D Riemann solver
claw.solver.all_bcs = pyclaw.BC.wall # Choose periodic BCs
claw.verbosity = False # Don't print pyclaw output
domain = pyclaw.Domain((-2., ), (2., ),
(800, )) # Choose domain and mesh resolution
claw.solution = pyclaw.Solution(claw.solver.num_eqn, domain)
# Set initial condition
x = domain.grid.x.centers
claw.solution.q[0, :] = 4.0 * np.exp(-10 * (x - 1.0)**2)
claw.solution.q[1, :] = 0.0
claw.solver.dt_initial = 1.e99
# Set parameters
rho = 1.0
bulk = 1.0
claw.solution.problem_data['rho'] = rho
claw.solution.problem_data['bulk'] = bulk
claw.solution.problem_data['zz'] = np.sqrt(rho * bulk)
claw.solution.problem_data['cc'] = np.sqrt(bulk / rho)
# Run pyclaw
status = claw.run()
return x, claw.frames
def __init__(self, domain_config):
solver = pyclaw.ClawSolver2D(riemann.euler_4wave_2D)
solver.all_bcs = pyclaw.BC.periodic
xmin, xmax = domain_config.x_range
ymin, ymax = domain_config.y_range
nx, ny = domain_config.num_cells
domain = pyclaw.Domain([xmin, ymin], [xmax, ymax], [nx, ny])
solution = pyclaw.Solution(num_eqn, domain)
solution.problem_data["gamma"] = 2.0
solver.dimensional_split = False
solver.transverse_waves = 2
solver.step_source = q_src
claw = pyclaw.Controller()
claw.solution = solution
claw.solver = solver
claw.output_format = "ascii"
claw.outdir = "./_output"
self._solver = solver
self._domain = domain
self._solution = solution
self._claw = claw
def fig_61_62_63(kernel_language='Python',
iplot=False,
htmlplot=False,
solver_type='classic',
outdir='./_output'):
"""
Compare several methods for advecting a Gaussian and square wave.
The settings coded here are for Figure 6.1(a).
For Figure 6.1(b), set solver.order=2.
For Figure 6.2(a), set solver.order=2 and solver.limiters = pyclaw.limiters.tvd.minmod
For Figure 6.2(b), set solver.order=2 and solver.limiters = pyclaw.limiters.tvd.superbee
For Figure 6.2(c), set solver.order=2 and solver.limiters = pyclaw.limiters.tvd.MC
For Figure 6.3, set IC='wavepacket' and other options as appropriate.
"""
import numpy as np
from clawpack import pyclaw
if solver_type == 'sharpclaw':
solver = pyclaw.SharpClawSolver1D()
else:
solver = pyclaw.ClawSolver1D()
solver.kernel_language = kernel_language
from clawpack.riemann import rp_advection
solver.num_waves = rp_advection.num_waves
if solver.kernel_language == 'Python':
solver.rp = rp_advection.rp_advection_1d
solver.bc_lower[0] = 2
solver.bc_upper[0] = 2
solver.limiters = 0
solver.order = 1
solver.cfl_desired = 0.8
x = pyclaw.Dimension('x', 0.0, 1.0, mx)
grid = pyclaw.Grid(x)
num_eqn = 1
state = pyclaw.State(grid, num_eqn)
state.problem_data['u'] = 1.
xc = grid.x.center
if IC == 'gauss_square':
state.q[0, :] = np.exp(-beta * (xc - x0)**2) + (xc > 0.6) * (xc < 0.8)
elif IC == 'wavepacket':
state.q[0, :] = np.exp(-beta * (xc - x0)**2) * np.sin(80. * xc)
else:
raise Exception('Unrecognized initial condition specification.')
claw = pyclaw.Controller()
claw.solution = pyclaw.Solution(state)
claw.solver = solver
claw.outdir = outdir
claw.tfinal = 10.0
status = claw.run()
if htmlplot: pyclaw.plot.html_plot(outdir=outdir)
if iplot: pyclaw.plot.interactive_plot(outdir=outdir)
def advect_1d(u, qfunc, qkws={},
nx=200, dx=500.,
t_out=np.arange(0, 3601, 5*60),
sharp=True):
""" Run a 1D advection calculation via clawpack. CONSTANT U ONLY.
"""
rp = riemann.advection_1D
if sharp:
solver = pyclaw.SharpClawSolver1D(rp)
solver.weno_order = 5
else:
solver = pyclaw.ClawSolver1D(rp)
solver.bc_lower[0] = pyclaw.BC.periodic
solver.bc_upper[0] = pyclaw.BC.periodic
x = pyclaw.Dimension(0, dx*nx, nx, name='x')
domain = pyclaw.Domain(x)
state = pyclaw.State(domain, solver.num_eqn)
state.problem_data['u'] = u
x1d = domain.grid.x.centers
q = qfunc(x1d, t=0)
state.q[0, ...] = q
claw = pyclaw.Controller()
claw.keep_copy = True
claw.solution = pyclaw.Solution(state, domain)
claw.solver = solver
claw.tfinal = t_out[-1]
claw.out_times = t_out
claw.num_output_times = len(t_out) - 1
claw.run()
times = claw.out_times
tracers = [f.q.squeeze() for f in claw.frames]
tracers = np.asarray(tracers)
uarr = u*np.ones_like(x1d)
ds = xr.Dataset(
{'q': (('time', 'x'), tracers),
'u': (('x', ), uarr)},
{'time': times, 'x': x1d}
)
ds['time'].attrs.update({'long_name': 'time', 'units': 'seconds since 2000-01-01 0:0:0'})
ds['x'].attrs.update({'long_name': 'x-coordinate', 'units': 'm'})
ds['u'].attrs.update({'long_name': 'zonal wind', 'units': 'm/s'})
ds.attrs.update({
'Conventions': 'CF-1.7'
})
return ds
def setup(outdir='./_output'):
solver = pyclaw.ClawSolver1D(reactive_euler)
solver.step_source = step_reaction
solver.bc_lower[0]=pyclaw.BC.extrap
solver.bc_upper[0]=pyclaw.BC.extrap
# Initialize domain
mx=200;
x = pyclaw.Dimension('x',0.0,2.0,mx)
domain = pyclaw.Domain([x])
num_eqn = 4
state = pyclaw.State(domain,num_eqn)
state.problem_data['gamma']= gamma
state.problem_data['gamma1']= gamma1
state.problem_data['qheat']= qheat
state.problem_data['Ea'] = Ea
state.problem_data['k'] = k
state.problem_data['T_ign'] = T_ign
state.problem_data['fspeed'] = fspeed
rhol = 1.
rhor = 0.125
ul = 0.
ur = 0.
pl = 1.
pr = 0.1
Yl = 1.
Yr = 1.
xs1 = 0.75
xs2 = 1.25
x =state.grid.x.centers
state.q[0,:] = (x>xs1)*(x<xs2)*rhol + ~((x>xs1)*(x<xs2))*rhor
state.q[1,:] = (x>xs1)*(x<xs2)*rhol*ul + ~((x>xs1)*(x<xs2))*rhor*ur
state.q[2,:] = ((x>xs1)*(x<xs2)*(pl/gamma1 + rhol*ul**2/2) +
~((x>xs1)*(x<xs2))*(pr/gamma1 + rhor*ur**2/2) )
state.q[3,:] = (x>xs1)*(x<xs2)*(rhol*Yl) + ~((x>xs1)*(x<xs2))*(rhor*Yr)
claw = pyclaw.Controller()
claw.tfinal = 0.3
claw.solution = pyclaw.Solution(state,domain)
claw.solver = solver
claw.num_output_times = 10
claw.outdir = outdir
claw.setplot = setplot
claw.keep_copy = True
#state.mp = 1
#claw.compute_p = pressure
#claw.write_aux_always = 'True'
return claw
def create_volume_datafile(casepath):
"""Create a volume.csv for a case."""
import numpy
casepath = os.path.abspath(casepath)
out_path = os.path.join(casepath, "_output")
repo_path = os.path.dirname(os.path.abspath(__file__))
claw_path = os.path.join(repo_path, "src", "clawpack-v5.5.0")
logger.info("Creating total volume datafile for case %s", casepath)
if os.path.isfile(os.path.join(casepath, "volume.csv")):
logger.warning("%s exists. Skip.", os.path.join(casepath, "volume.csv"))
logger.handlers[0].flush()
logger.handlers[1].flush()
return
# add environment variables
os.environ["CLAW"] = claw_path
# add clawpack python package search path
if claw_path != sys.path[0]:
sys.path.insert(0, claw_path)
# import utilities
from clawpack import pyclaw
# get # of frames from setrun.py
if casepath != sys.path[0]:
sys.path.insert(0, casepath)
import setrun # import the setrun.py
rundata = setrun.setrun() # get ClawRunData object
nframes = rundata.clawdata.num_output_times + 1
nlevels = rundata.amrdata.amr_levels_max
del rundata
del sys.modules["setrun"]
del sys.path[0]
data = numpy.zeros((nframes, 1+nlevels), dtype=numpy.float64)
for fno in range(0, nframes):
# empty solution object
soln = pyclaw.Solution()
# read
soln.read(fno, out_path, file_format="binary", read_aux=False)
# calculate total volume at each grid level
data[fno, 0] = soln.state.t
data[fno, 1:] = get_volumes_single_frame(nlevels, soln)
numpy.savetxt(os.path.join(casepath, "volume.csv"), data, delimiter=",")
logger.info("Done creating total volume datafile.")
logger.handlers[0].flush()
logger.handlers[1].flush()
def advection_setup(nx=100,
solver_type='classic',
lim_type=2,
weno_order=5,
CFL=0.9,
time_integrator='SSP104',
outdir='./_output'):
riemann_solver = riemann.advection_1D
if solver_type == 'classic':
solver = pyclaw.ClawSolver1D(riemann_solver)
elif solver_type == 'sharpclaw':
solver = pyclaw.SharpClawSolver1D(riemann_solver)
solver.lim_type = lim_type
solver.weno_order = weno_order
solver.time_integrator = time_integrator
else:
raise Exception('Unrecognized value of solver_type.')
solver.kernel_language = 'Fortran'
solver.cfl_desired = CFL
solver.cfl_max = CFL * 1.1
solver.bc_lower[0] = pyclaw.BC.periodic
solver.bc_upper[0] = pyclaw.BC.periodic
x = pyclaw.Dimension(0.0, 1.0, nx, name='x')
domain = pyclaw.Domain(x)
state = pyclaw.State(domain, solver.num_eqn)
state.problem_data['u'] = 1. # Advection velocity
# Initial data
xc = state.grid.x.centers
beta = 100
gamma = 0
x0 = 0.75
state.q[0, :] = np.exp(-beta * (xc - x0)**2) * np.cos(gamma * (xc - x0))
claw = pyclaw.Controller()
claw.keep_copy = True
claw.solution = pyclaw.Solution(state, domain)
claw.solver = solver
if outdir is not None:
claw.outdir = outdir
else:
claw.output_format = None
claw.tfinal = 1.0
return claw
def read_write_and_compare(file_formats,
regression_dir,
regression_format,
frame_num,
aux=False):
r"""Test IO file formats:
- Reading in an HDF file
- Writing files in all formats (for now just ASCII, HDF5)
- Reading those files back in
- Checking that all the resulting Solution objects are identical
"""
ref_sol = pyclaw.Solution()
ref_sol.read(frame_num,
path=regression_dir,
file_format=regression_format,
read_aux=aux)
if aux:
assert (ref_sol.state.aux is not None)
# Write solution file in each format
io_test_dir = os.path.join(thisdir, './io_test')
for fmt in file_formats:
ref_sol.write(frame_num,
path=io_test_dir,
file_format=fmt,
write_aux=aux)
# Read solutions back in
s = {}
for fmt in file_formats:
s[fmt] = pyclaw.Solution()
s[fmt].read(frame_num,
path=io_test_dir,
file_format=fmt,
write_aux=aux)
# Compare solutions
# Probably better to do this by defining __eq__ for each class
for fmt, sol in s.iteritems():
check_solutions_are_same(sol, ref_sol)
def acoustics(problem='figure 9.4'):
"""
This example solves the 1-dimensional variable-coefficient acoustics
equations in a medium with a single interface.
"""
from numpy import sqrt, abs
from clawpack import pyclaw
from clawpack import riemann
solver = pyclaw.ClawSolver1D(riemann.acoustics_variable_1D)
solver.limiters = pyclaw.limiters.tvd.MC
solver.bc_lower[0] = pyclaw.BC.extrap
solver.bc_upper[0] = pyclaw.BC.extrap
solver.aux_bc_lower[0] = pyclaw.BC.extrap
solver.aux_bc_upper[0] = pyclaw.BC.extrap
x = pyclaw.Dimension(-5.0, 5.0, 500, name='x')
domain = pyclaw.Domain(x)
num_eqn = 2
num_aux = 2
state = pyclaw.State(domain, num_eqn, num_aux)
if problem == 'figure 9.4':
rhol = 1.0
cl = 1.0
rhor = 2.0
cr = 0.5
elif problem == 'figure 9.5':
rhol = 1.0
cl = 1.0
rhor = 4.0
cr = 0.5
zl = rhol * cl
zr = rhor * cr
xc = domain.grid.x.centers
state.aux[0, :] = (xc <= 0) * zl + (xc > 0) * zr # Impedance
state.aux[1, :] = (xc <= 0) * cl + (xc > 0) * cr # Sound speed
# initial condition: half-ellipse
state.q[0, :] = sqrt(abs(1. - (xc + 3.)**2)) * (xc > -4.) * (xc < -2.)
state.q[1, :] = state.q[0, :] + 0.
claw = pyclaw.Controller()
claw.solution = pyclaw.Solution(state, domain)
claw.solver = solver
claw.tfinal = 5.0
claw.num_output_times = 10
# Solve
return claw
def iniSourceVolume():
xMin = -0.5
xMax = 10.0
Nx = 5000
Gamma = 1.
f0 = 1.
Glob = Globals()
Glob.domain = pyclaw.Domain([xMin], [xMax], [Nx])
Glob.solver = pyclaw.ClawSolver1D(riemann.acoustics_variable_1D)
Glob.state = pyclaw.State(Glob.domain, 2, 2)
Glob.solution = pyclaw.Solution(Glob.state, Glob.domain)
Glob.x = Glob.domain.grid.p_centers[0]
Glob.dx = Glob.domain.grid.delta[0]
Glob.inRange = lambda (a, b): np.logical_and(Glob.x <= b, Glob.x >= a)
Glob.solver.bc_lower[0] = pyclaw.BC.extrap
Glob.solver.bc_upper[0] = pyclaw.BC.extrap
Glob.solver.aux_bc_lower[0] = pyclaw.BC.extrap
Glob.solver.aux_bc_upper[0] = pyclaw.BC.extrap
layers = {
0: ((-0.50, 10.00), (0.343, 0.01, 0.000)), # surrounding "air"
1: ((0.000, 5.500), (2.77, 1.7, 0.000)), # PMMA layer
2: ((4.980, 5.020), (2.50, 1.00, 0.000)), # Glue layer
3: ((4.995, 5.005), (2.25, 1.78, 0.000)), # PVDF
4: ((5.500, 5.550), (1.80, 1.00, 100.0)), # Ink
5: ((5.550, 9.550), (5.60, 2.63, 0.000)) # Glass
}
Glob.mua = np.zeros(Glob.x.size)
for no, (zR, (c, rho, mu)) in sorted(layers.iteritems()):
Glob.solution.state.aux[0, Glob.inRange(zR)] = rho
Glob.solution.state.aux[1, Glob.inRange(zR)] = c
Glob.mua[Glob.inRange(zR)] = mu
Glob.solver.dt_initial = Glob.dx * 0.3 / max(Glob.solution.state.aux[1, :])
Glob.state.q[
0, :] = Gamma * f0 * Glob.mua * np.exp(-np.cumsum(Glob.mua * Glob.dx))
#p0 = Gamma*f0*Glob.mua*np.exp(-np.cumsum(Glob.mua*Glob.dx))
#Glob.state.q[0,:] = convolveIniStressGauss(Glob.x,p0,0.03)
Glob.state.q[1, :] = 0.
xDMin, xDMax = 4.995, 5.005
Det = Detector(Glob.inRange((xDMin, xDMax)), xDMax - xDMin)
return Glob, Det
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)
"""
# these parameters will be used later, so assert their existence
assert 'nvars' in cparams
# add parameters as attributes for further reference
for k, v in cparams.items():
setattr(self, k, v)
# invoke super init, passing number of dofs, dtype_u and dtype_f
super(advection_2d_explicit, self).__init__(self.nvars, dtype_u,
dtype_f)
riemann_solver = riemann.advection_2D # NOTE: This uses the FORTRAN kernels of clawpack
self.solver = pyclaw.SharpClawSolver2D(riemann.advection_2D)
self.solver.weno_order = 5
self.solver.time_integrator = 'Euler' # Remove later
self.solver.kernel_language = 'Fortran'
self.solver.bc_lower[0] = pyclaw.BC.periodic
self.solver.bc_upper[0] = pyclaw.BC.periodic
self.solver.bc_lower[1] = pyclaw.BC.periodic
self.solver.bc_upper[1] = pyclaw.BC.periodic
self.solver.cfl_max = 1.0
assert self.solver.is_valid()
x = pyclaw.Dimension(-1.0, 1.0, self.nvars[1], name='x')
y = pyclaw.Dimension(0.0, 1.0, self.nvars[2], name='y')
self.domain = pyclaw.Domain([x, y])
self.state = pyclaw.State(self.domain, self.solver.num_eqn)
# self.dx = self.state.grid.x.centers[1] - self.state.grid.x.centers[0]
self.state.problem_data['u'] = 1.0
self.state.problem_data['v'] = 0.0
solution = pyclaw.Solution(self.state, self.domain)
self.solver.setup(solution)
self.xc, self.yc = self.state.grid.p_centers
def setup():
from clawpack import pyclaw
from clawpack.pyclaw.examples.advection_reaction_2d import advection_2d
solver = pyclaw.ClawSolver2D(advection_2d)
# Use dimensional splitting since no transverse solver is defined
solver.dimensional_split = 1
solver.all_bcs = pyclaw.BC.extrap
solver.aux_bc_lower[0] = pyclaw.BC.extrap
solver.aux_bc_upper[0] = pyclaw.BC.extrap
solver.aux_bc_lower[1] = pyclaw.BC.extrap
solver.aux_bc_upper[1] = pyclaw.BC.extrap
domain = pyclaw.Domain((0., 0.), (1., 1.), (100, 100))
solver.num_eqn = 2
solver.num_waves = 1
num_aux = 2
state = pyclaw.State(domain, solver.num_eqn, num_aux)
Xe, Ye = domain.grid.p_nodes
Xc, Yc = domain.grid.p_centers
dx, dy = domain.grid.delta
# Edge velocities
# u(x_(i-1/2),y_j)
state.aux[0, :, :] = -(psi(Xe[:-1, 1:], Ye[:-1, 1:]) -
psi(Xe[:-1, :-1], Ye[:-1, :-1])) / dy
# v(x_i,y_(j-1/2))
state.aux[1, :, :] = (psi(Xe[1:, :-1], Ye[1:, :-1]) -
psi(Xe[:-1, :-1], Ye[:-1, :-1])) / dx
solver.before_step = set_velocities
solver.step_source = source_step
solver.source_split = 1
state.q[0, :, :] = (Xc <= 0.5)
state.q[1, :, :] = (Yc <= 0.5)
claw = pyclaw.Controller()
claw.tfinal = t_period
claw.solution = pyclaw.Solution(state, domain)
claw.solver = solver
claw.keep_copy = True
claw.setplot = setplot
return claw
def setup(kernel_language='Fortran',
solver_type='classic',
use_petsc=False,
outdir='./_output'):
solver = pyclaw.ClawSolver2D(riemann.shallow_bathymetry_fwave_2D)
solver.dimensional_split = 1 # No transverse solver available
solver.bc_lower[0] = pyclaw.BC.custom
solver.user_bc_lower = wave_maker_bc
solver.bc_upper[0] = pyclaw.BC.extrap
solver.bc_lower[1] = pyclaw.BC.wall
solver.bc_upper[1] = pyclaw.BC.wall
solver.aux_bc_lower[0] = pyclaw.BC.extrap
solver.aux_bc_upper[0] = pyclaw.BC.extrap
solver.aux_bc_lower[1] = pyclaw.BC.extrap
solver.aux_bc_upper[1] = pyclaw.BC.extrap
my = 20
mx = 4 * my
x = pyclaw.Dimension(0., 4., mx, name='x')
y = pyclaw.Dimension(0, 1, my, name='y')
domain = pyclaw.Domain([x, y])
state = pyclaw.State(domain, num_eqn, num_aux=1)
X, Y = state.p_centers
state.aux[0, :, :] = bathymetry(X, Y)
state.q[depth, :, :] = 1. - state.aux[0, :, :]
state.q[x_momentum, :, :] = 0.
state.q[y_momentum, :, :] = 0.
state.problem_data['grav'] = 1.0
state.problem_data['dry_tolerance'] = 1.e-3
state.problem_data['sea_level'] = 0.
claw = pyclaw.Controller()
claw.tfinal = 10
claw.solution = pyclaw.Solution(state, domain)
claw.solver = solver
claw.num_output_times = 40
claw.setplot = setplot
claw.keep_copy = True
return claw
def burgers(params):
times = np.linspace(0, time_final, num_out + 1)
outputs = np.zeros((params.shape[0], num_out + 1))
for k in range(params.shape[0]):
# Define domain and mesh
x = pyclaw.Dimension(0.0, 10.0, 500, name='x')
domain = pyclaw.Domain(x)
num_eqn = 1
state = pyclaw.State(domain, num_eqn)
xc = state.grid.x.centers
state.problem_data['efix'] = True
a = params[k, 0]
for i in range(state.q.shape[1]):
if xc[i] <= (3.25 - a):
state.q[0, i] = fl
elif xc[i] > (3.25 + a):
state.q[0, i] = fr
else:
state.q[0, i] = 0.5 * \
((fl + fr) - (fl - fr) * (xc[i] - 3.25) / a)
# Set gauge
grid = state.grid
grid.add_gauges([[7.0]])
state.keep_gauges = True
# Setup and run
claw = pyclaw.Controller()
claw.tfinal = time_final
claw.num_output_times = num_out
claw.solution = pyclaw.Solution(state, domain)
claw.solver = solver
claw.outdir = './_output'
claw.run()
# Process output
A = np.loadtxt('./_output/_gauges/gauge7.0.txt')
idx = 0
vals = []
for j in range(A.shape[0]):
if A[j, 0] == times[idx]:
vals.append(A[j, 1])
idx += 1
outputs[k, :] = vals
return (times, outputs)
def __init__(self, solver, global_state, q, qbc, aux, position, size,
subdivision_factor, unknowns_per_cell, aux_fields_per_cell,
current_time):
r"""
Initializes this subgrid solver. It get's all information to prepare a domain and state for a
single subgrid.
:Input:
- *solver* - (:class:`pyclaw.Solver`) The PyClaw-solver used for advancing this subgrid in time.
- *global_state* - (:class:`pyclaw.State`) The global state. This is not the state used for
for the actual solving of the timestep on the subgrid.
- *q* - The array storing the current solution.
- *qbc* - The array storing the solution of the last timestep including the ghostlayer.
- *position* - A d-dimensional tuple holding the position of the grid in the computational domain.
This measures the continuous real-world position in floats, not the integer position
in terms of cells.
- *size* - A d-dimensional tuple holding the size of the grid in the computational domain. This
measures the continuous real-world size in floats, not the size in terms of cells.
- *subdivision_factor* - The number of cells in one dimension of this subgrid. At the moment only
square subgrids are allowed, so the total number of cells in the subgrid
(excluding the ghostlayer) is subdivision_factor x subdivision_factor.
- *unknowns_per_cell* - The number of equations or unknowns that are stored per cell of the subgrid.
"""
self.solver = solver
number_of_dimensions = get_number_of_dimensions(q)
self.domain = create_domain(number_of_dimensions, position, size,
subdivision_factor)
subgrid_state = create_subgrid_state(global_state, self.domain, q, qbc,
aux, unknowns_per_cell,
aux_fields_per_cell)
subgrid_state.problem_data = global_state.problem_data
self.solution = pyclaw.Solution(subgrid_state, self.domain)
self.solution.t = current_time
self.solver.bc_lower[:] = [pyclaw.BC.custom] * len(
self.solver.bc_lower)
self.solver.bc_upper[:] = [pyclaw.BC.custom] * len(
self.solver.bc_upper)
self.qbc = qbc
self.solver.user_bc_lower = self.user_bc_lower
self.solver.user_bc_upper = self.user_bc_upper
self.recover_ghostlayers = False
def plot_depth(data, transform, res, solndir, fno, border=False, level=1,
shaded=True, dry_tol=1e-5, vmin=None, vmax=None):
"""Plot depth on topography."""
from matplotlib import pyplot
# a new figure and topo ax
fig, ax = plot_topo(data, transform, res, shaded=shaded)
# empty solution object
soln = pyclaw.Solution()
# aux path
auxpath = os.path.join(solndir, "fort.a"+"{}".format(fno).zfill(4))
# read
soln.read(fno, solndir, file_format="binary", read_aux=os.path.isfile(auxpath))
print("Plotting frame No. {}, T={} secs ({} mins)".format(
fno, soln.state.t, int(soln.state.t/60.)))
# plot
im = plot_at_axes(soln, ax, field=0, border=border,
min_level=level, max_level=level,
vmin=vmin, vmax=vmax,
threshold=dry_tol)
# plot colorbar in a new axes for depth
cbarax = fig.add_axes([0.875, 0.125, 0.03, 0.75])
if im is None:
im = ax.pcolormesh([0, data.shape[1]], [0, data.shape[0]], [[0]])
im.remove()
cbar = pyplot.colorbar(im, cax=cbarax, ax=ax)
cbar.ax.set_yticklabels([0]*len(cbar.ax.get_yticks()))
else:
cbar = pyplot.colorbar(im, cax=cbarax, ax=ax)
cbar.set_label("Depth (m)")
# figure title
fig.suptitle("Topography and depth near rupture point, "
"T = {} (mins)".format(int(soln.state.t/60.)),
x=0.5, y=0.9, fontsize=16,
horizontalalignment="center",
verticalalignment="bottom")
return fig, ax
def acoustics(iplot=False, htmlplot=False, outdir='./_output'):
"""
This example solves the 1-dimensional acoustics equations in a homogeneous
medium.
"""
import numpy as np
from clawpack import riemann
from clawpack import pyclaw
solver = pyclaw.ClawSolver1D(riemann.acoustics_1D)
solver.bc_lower[0] = pyclaw.BC.wall
solver.bc_upper[0] = pyclaw.BC.wall
solver.cfl_desired = 1.0
solver.cfl_max = 1.0
x = pyclaw.Dimension(0.0, 1.0, 200, name='x')
domain = pyclaw.Domain(x)
num_eqn = 2
state = pyclaw.State(domain, num_eqn)
# Set problem-specific variables
rho = 1.0
bulk = 1.0
state.problem_data['rho'] = rho
state.problem_data['bulk'] = bulk
state.problem_data['zz'] = np.sqrt(rho * bulk)
state.problem_data['cc'] = np.sqrt(bulk / rho)
# Set the initial condition
xc = domain.grid.x.centers
state.q[0, :] = np.cos(2 * np.pi * xc)
state.q[1, :] = 0.
# Set up the controller
claw = pyclaw.Controller()
claw.solution = pyclaw.Solution(state, domain)
claw.solver = solver
claw.outdir = outdir
claw.num_output_times = 40
claw.tfinal = 2.0
return claw
def fig_61_62_63(solver_order=2, limiters=0):
"""
Compare several methods for advecting a Gaussian and square wave.
The settings coded here are for Figure 6.1(a).
For Figure 6.1(b), set solver.order=2.
For Figure 6.2(a), set solver.order=2 and solver.limiters = pyclaw.limiters.tvd.minmod (1)
For Figure 6.2(b), set solver.order=2 and solver.limiters = pyclaw.limiters.tvd.superbee (2)
For Figure 6.2(c), set solver.order=2 and solver.limiters = pyclaw.limiters.tvd.MC (4)
For Figure 6.3, set IC='wavepacket' and other options as appropriate.
"""
import numpy as np
from clawpack import pyclaw
from clawpack import riemann
solver = pyclaw.ClawSolver1D(riemann.advection_1D)
solver.bc_lower[0] = 2
solver.bc_upper[0] = 2
solver.limiters = limiters
solver.order = solver_order
solver.cfl_desired = 0.8
x = pyclaw.Dimension(0.0, 1.0, mx, name='x')
domain = pyclaw.Domain(x)
num_eqn = 1
state = pyclaw.State(domain, num_eqn)
state.problem_data['u'] = 1.
xc = domain.grid.x.centers
if IC == 'gauss_square':
state.q[0, :] = np.exp(-beta * (xc - x0)**2) + (xc > 0.6) * (xc < 0.8)
elif IC == 'wavepacket':
state.q[0, :] = np.exp(-beta * (xc - x0)**2) * np.sin(80. * xc)
else:
raise Exception('Unrecognized initial condition specification.')
claw = pyclaw.Controller()
claw.solution = pyclaw.Solution(state, domain)
claw.solver = solver
claw.tfinal = 10.0
return claw
def burgers(iplot=1, htmlplot=0, outdir='./_output'):
"""
Example from Chapter 11 of LeVeque, Figure 11.8.
Shows decay of an initial wave packet to an N-wave with Burgers' equation.
"""
import numpy as np
from clawpack import pyclaw
solver = pyclaw.ClawSolver1D()
solver.num_waves = 1
solver.limiters = pyclaw.limiters.tvd.MC
solver.bc_lower[0] = pyclaw.BC.periodic
solver.bc_upper[0] = pyclaw.BC.periodic
#===========================================================================
# Initialize grids and then initialize the solution associated to the grid
#===========================================================================
x = pyclaw.Dimension('x', -8.0, 8.0, 1000)
grid = pyclaw.Grid(x)
num_eqn = 1
state = pyclaw.State(grid, num_eqn)
xc = grid.x.center
state.q[0, :] = (xc > -np.pi) * (xc < np.pi) * (2. * np.sin(3. * xc) +
np.cos(2. * xc) + 0.2)
state.q[0, :] = state.q[0, :] * (np.cos(xc) + 1.)
state.problem_data['efix'] = True
#===========================================================================
# Setup controller and controller parameters. Then solve the problem
#===========================================================================
claw = pyclaw.Controller()
claw.tfinal = 6.0
claw.num_output_times = 30
claw.solution = pyclaw.Solution(state)
claw.solver = solver
claw.outdir = outdir
status = claw.run()
if htmlplot: pyclaw.plot.html_plot(outdir=outdir)
if iplot: pyclaw.plot.interactive_plot(outdir=outdir)
def fig_31_38(iplot=False, htmlplot=False, outdir='./_output'):
r"""Produces the output shown in Figures 3.1 and 3.8 of the FVM book.
These involve simple waves in the acoustics system."""
from clawpack import pyclaw
from clawpack import riemann
import numpy as np
solver = pyclaw.ClawSolver1D(riemann.acoustics_1D)
solver.limiters = pyclaw.limiters.tvd.MC
solver.bc_lower[0] = pyclaw.BC.wall
solver.bc_upper[0] = pyclaw.BC.extrap
x = pyclaw.Dimension(-1.0, 1.0, 800, name='x')
domain = pyclaw.Domain(x)
num_eqn = 2
state = pyclaw.State(domain, num_eqn)
# Set problem-specific variables
rho = 1.0
bulk = 0.25
state.problem_data['rho'] = rho
state.problem_data['bulk'] = bulk
state.problem_data['zz'] = np.sqrt(rho * bulk)
state.problem_data['cc'] = np.sqrt(bulk / rho)
# Set the initial condition
xc = domain.grid.x.centers
beta = 100
gamma = 0
x0 = 0.75
state.q[0, :] = 0.5 * np.exp(-80 * xc**2) + 0.5 * (np.abs(xc + 0.2) < 0.1)
state.q[1, :] = 0.
# Set up the controller
claw = pyclaw.Controller()
claw.solution = pyclaw.Solution(state, domain)
claw.solver = solver
claw.outdir = outdir
claw.tfinal = 3.0
claw.num_output_times = 30
return claw
def get_bounding_box(solndir, bg, ed, level):
"""
Get the bounding box of the result at a specific level.
Return:
[xleft, xright, ybottom, ytop]
"""
xleft = None
xright = None
ybottom = None
ytop = None
for fno in range(bg, ed):
# aux path
auxpath = os.path.join(solndir, "fort.a"+"{}".format(fno).zfill(4))
# solution
soln = pyclaw.Solution()
soln.read(fno, solndir, file_format="binary", read_aux=os.path.isfile(auxpath))
# search through AMR grid patched in this solution
for state in soln.states:
p = state.patch
if p.level != level:
continue
if xleft is None or xleft > p.lower_global[0]:
xleft = p.lower_global[0]
if ybottom is None or ybottom > p.lower_global[1]:
ybottom = p.lower_global[1]
if xright is None or xright < p.upper_global[0]:
xright = p.upper_global[0]
if ytop is None or ytop < p.upper_global[1]:
ytop = p.upper_global[1]
# finally, return
return [xleft, xright, ybottom, ytop]
def __init__(self,
domain_config,
solver_type="sharpclaw",
kernel_language="Python"):
tau = domain_config["tau"]
if kernel_language == "Python":
rs = riemann.euler_1D_py.euler_hllc_1D
elif kernel_language == "Fortran":
rs = riemann.euler_with_efix_1D
if solver_type == "sharpclaw":
solver = pyclaw.SharpClawSolver1D(rs)
solver.dq_src = lambda x, y, z: dq_src(x, y, z, tau)
elif solver_type == "classic":
solver = pyclaw.ClawSolver1D(rs)
solver.step_source = lambda x, y, z: q_src(x, y, z, tau)
solver.kernel_language = kernel_language
solver.bc_lower[0] = pyclaw.BC.periodic
solver.bc_upper[0] = pyclaw.BC.periodic
nx = domain_config["nx"]
xmin, xmax = domain_config["xmin"], domain_config["xmax"]
x = pyclaw.Dimension(xmin, xmax, nx, name="x")
domain = pyclaw.Domain([x])
state = pyclaw.State(domain, num_eqn)
state.problem_data["gamma"] = gamma
state.problem_data["gamma1"] = gamma - 1.0
solution = pyclaw.Solution(state, domain)
claw = pyclaw.Controller()
claw.solution = solution
claw.solver = solver
self._solver = solver
self._domain = domain
self._solution = solution
self._claw = claw
def main():
# (1) Define the Finite Voluem solver to be used with a Riemann Solver from
# the library
solver = pyclaw.ClawSolver1D(riemann.advection_1D)
solver.bc_lower[0] = pyclaw.BC.periodic
solver.bc_upper[0] = pyclaw.BC.periodic
# (2) Define the mesh
x_dimension = pyclaw.Dimension(0.0, 1.0, 100)
domain = pyclaw.Domain(x_dimension)
# (3) Instantiate a solution field on the Mesh
solution = pyclaw.Solution(
solver.num_eqn,
domain,
)
# (4) Prescribe an initial state
state = solution.state
cell_center_coordinates = state.grid.p_centers[0]
state.q[0, :] = np.where(
(cell_center_coordinates > 0.2)
& (cell_center_coordinates < 0.4),
1.0,
0.0,
)
# (5) Assign problem-specific parameters ("u" refers to the advection speed)
state.problem_data["u"] = 1.0
# (6) The controller takes care of the time integration
controller = pyclaw.Controller()
controller.solution = solution
controller.solver = solver
controller.tfinal = 1.0
# (7) Run and visualize
controller.run()
pyclaw.plot.interactive_plot()
def bump_pyclaw(numframes):
# Set pyclaw for burgers equation 1D
claw = pyclaw.Controller()
claw.tfinal = 1.5 # Set final time
claw.keep_copy = True # Keep solution data in memory for plotting
claw.output_format = None # Don't write solution data to file
claw.num_output_times = numframes # Number of output frames
claw.solver = pyclaw.ClawSolver1D(
riemann.burgers_1D) # Choose burgers 1D Riemann solver
claw.solver.all_bcs = pyclaw.BC.periodic # Choose periodic BCs
claw.verbosity = False # Don't print pyclaw output
domain = pyclaw.Domain((-1., ), (1., ),
(500, )) # Choose domain and mesh resolution
claw.solution = pyclaw.Solution(claw.solver.num_eqn, domain)
# Set initial condition
x = domain.grid.x.centers
claw.solution.q[0, :] = np.exp(-10 * (x)**2)
claw.solver.dt_initial = 1.e99
# Run pyclaw
status = claw.run()
return x, claw.frames
def triplestate_pyclaw(ql, qm, qr, numframes):
"""Returns pyclaw solution of triple-state initial condition."""
# Set pyclaw for burgers equation 1D
meshpts = 2400 #600
claw = pyclaw.Controller()
claw.tfinal = 2.0 # Set final time
claw.keep_copy = True # Keep solution data in memory for plotting
claw.output_format = None # Don't write solution data to file
claw.num_output_times = numframes # Number of output frames
claw.solver = pyclaw.ClawSolver1D(
riemann.burgers_1D) # Choose burgers 1D Riemann solver
claw.solver.all_bcs = pyclaw.BC.extrap # Choose periodic BCs
claw.verbosity = False # Don't print pyclaw output
domain = pyclaw.Domain((-12., ), (12., ),
(meshpts, )) # Choose domain and mesh resolution
claw.solution = pyclaw.Solution(claw.solver.num_eqn, domain)
# Set initial condition
x = domain.grid.x.centers
q0 = 0.0 * x
xtick1 = 900 + int(meshpts / 12)
xtick2 = xtick1 + int(meshpts / 12)
for i in range(xtick1):
q0[i] = ql + i * 0.0001
#q0[0:xtick1] = ql
for i in np.arange(xtick1, xtick2):
q0[i] = qm + i * 0.0001
#q0[xtick1:xtick2] = qm
for i in np.arange(xtick2, meshpts):
q0[i] = qr + i * 0.0001
#q0[xtick2:meshpts] = qr
claw.solution.q[0, :] = q0
claw.solver.dt_initial = 1.e99
# Run pyclaw
status = claw.run()
return x, claw.frames
def setup(use_petsc=False,
solver_type='classic',
outdir='./_output',
disable_output=False):
if use_petsc:
raise Exception(
"petclaw does not currently support mapped grids (go bug Lisandro who promised to implement them)"
)
if solver_type != 'classic':
raise Exception(
"Only Classic-style solvers (solver_type='classic') are supported on mapped grids"
)
solver = pyclaw.ClawSolver2D(riemann.shallow_sphere_2D)
solver.fmod = classic2
# Set boundary conditions
# =======================
solver.bc_lower[0] = pyclaw.BC.periodic
solver.bc_upper[0] = pyclaw.BC.periodic
solver.bc_lower[1] = pyclaw.BC.custom # Custom BC for sphere
solver.bc_upper[1] = pyclaw.BC.custom # Custom BC for sphere
solver.user_bc_lower = qbc_lower_y
solver.user_bc_upper = qbc_upper_y
# Auxiliary array
solver.aux_bc_lower[0] = pyclaw.BC.periodic
solver.aux_bc_upper[0] = pyclaw.BC.periodic
solver.aux_bc_lower[1] = pyclaw.BC.custom # Custom BC for sphere
solver.aux_bc_upper[1] = pyclaw.BC.custom # Custom BC for sphere
solver.user_aux_bc_lower = auxbc_lower_y
solver.user_aux_bc_upper = auxbc_upper_y
# Dimensional splitting ?
# =======================
solver.dimensional_split = 0
# Transverse increment waves and transverse correction waves are computed
# and propagated.
# =======================================================================
solver.transverse_waves = 2
# Use source splitting method
# ===========================
solver.source_split = 2
# Set source function
# ===================
solver.step_source = fortran_src_wrapper
# Set the limiter for the waves
# =============================
solver.limiters = pyclaw.limiters.tvd.MC
#===========================================================================
# Initialize domain and state, then initialize the solution associated to the
# state and finally initialize aux array
#===========================================================================
# Domain:
xlower = -3.0
xupper = 1.0
mx = 40
ylower = -1.0
yupper = 1.0
my = 20
# Check whether or not the even number of cells are used in in both
# directions. If odd numbers are used a message is print at screen and the
# simulation is interrupted.
if (mx % 2 != 0 or my % 2 != 0):
message = 'Please, use even numbers of cells in both direction. ' \
'Only even numbers allow to impose correctly the boundary ' \
'conditions!'
raise ValueError(message)
x = pyclaw.Dimension(xlower, xupper, mx, name='x')
y = pyclaw.Dimension(ylower, yupper, my, name='y')
domain = pyclaw.Domain([x, y])
dx = domain.grid.delta[0]
dy = domain.grid.delta[1]
# Define some parameters used in Fortran common blocks
solver.fmod.comxyt.dxcom = dx
solver.fmod.comxyt.dycom = dy
solver.fmod.sw.g = 11489.57219
solver.rp.comxyt.dxcom = dx
solver.rp.comxyt.dycom = dy
solver.rp.sw.g = 11489.57219
# Define state object
# ===================
num_aux = 16 # Number of auxiliary variables
state = pyclaw.State(domain, solver.num_eqn, num_aux)
# Override default mapc2p function
# ================================
state.grid.mapc2p = mapc2p_sphere_vectorized
# Set auxiliary variables
# =======================
# Get lower left corner coordinates
xlower, ylower = state.grid.lower[0], state.grid.lower[1]
num_ghost = 2
auxtmp = np.ndarray(shape=(num_aux, mx + 2 * num_ghost,
my + 2 * num_ghost),
dtype=float,
order='F')
auxtmp = problem.setaux(mx, my, num_ghost, mx, my, xlower, ylower, dx, dy,
auxtmp, Rsphere)
state.aux[:, :, :] = auxtmp[:, num_ghost:-num_ghost, num_ghost:-num_ghost]
# Set index for capa
state.index_capa = 0
# Set initial conditions
# ======================
# 1) Call fortran function
qtmp = np.ndarray(shape=(solver.num_eqn, mx + 2 * num_ghost,
my + 2 * num_ghost),
dtype=float,
order='F')
qtmp = problem.qinit(mx, my, num_ghost, mx, my, xlower, ylower, dx, dy,
qtmp, auxtmp, Rsphere)
state.q[:, :, :] = qtmp[:, num_ghost:-num_ghost, num_ghost:-num_ghost]
# 2) call python function define above
#qinit(state,mx,my)
#===========================================================================
# Set up controller and controller parameters
#===========================================================================
claw = pyclaw.Controller()
claw.keep_copy = True
if disable_output:
claw.output_format = None
claw.output_style = 1
claw.num_output_times = 10
claw.tfinal = 10
claw.solution = pyclaw.Solution(state, domain)
claw.solver = solver
claw.outdir = outdir
return claw
#!/usr/bin/env python
# encoding: utf-8
"""
Solve the Euler equations of compressible fluid dynamics.
"""
from clawpack import pyclaw
from clawpack import riemann
solver = pyclaw.ClawSolver2D(riemann.rp2_euler_4wave)
solver.all_bcs = pyclaw.BC.extrap
domain = pyclaw.Domain([0., 0.], [1., 1.], [100, 100])
solution = pyclaw.Solution(solver.num_eqn, domain)
gamma = 1.4
solution.problem_data['gamma'] = gamma
# Set initial data
xx, yy = domain.grid.p_centers
l = xx < 0.5
r = xx >= 0.5
b = yy < 0.5
t = yy >= 0.5
solution.q[0, ...] = 2. * l * t + 1. * l * b + 1. * r * t + 3. * r * b
solution.q[1, ...] = 0.75 * t - 0.75 * b
solution.q[2, ...] = 0.5 * l - 0.5 * r
solution.q[3, ...] = 0.5 * solution.q[0, ...] * (
solution.q[1, ...]**2 + solution.q[2, ...]**2) + 1. / (gamma - 1.)
#solver.evolve_to_time(solution,tend=0.3)
claw = pyclaw.Controller()
claw.tfinal = 0.3