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 callback_initialization(
q, qbc, aux, subdivision_factor_x0, subdivision_factor_x1,
subdivision_factor_x2, unknowns_per_subcell,
aux_fields_per_subcell, size_x, size_y, size_z, position_x,
position_y, position_z, skip_q_initialization):
import clawpack.pyclaw as pyclaw
dim = get_number_of_dimensions(q)
if dim is 2:
self.dim_x = pyclaw.Dimension('x', position_x,
position_x + size_x,
subdivision_factor_x0)
self.dim_y = pyclaw.Dimension('y', position_y,
position_y + size_y,
subdivision_factor_x1)
domain = pyclaw.Domain([self.dim_x, self.dim_y])
elif dim is 3:
self.dim_x = pyclaw.Dimension('x', position_x,
position_x + size_x,
subdivision_factor_x0)
self.dim_y = pyclaw.Dimension('y', position_y,
position_y + size_y,
subdivision_factor_x1)
self.dim_z = pyclaw.Dimension('z', position_z,
position_z + size_z,
subdivision_factor_x2)
domain = pyclaw.Domain([self.dim_x, self.dim_y, self.dim_z])
subgrid_state = pyclaw.State(domain, unknowns_per_subcell,
aux_fields_per_subcell)
subgrid_state.q = q
if (aux_fields_per_subcell > 0):
subgrid_state.aux = aux
subgrid_state.problem_data = self.solver.solution.state.problem_data
if not skip_q_initialization:
self.q_initialization(subgrid_state)
if (self.aux_initialization != None
and aux_fields_per_subcell > 0):
self.aux_initialization(subgrid_state)
#Steer refinement
if self.refinement_criterion != None:
return self.refinement_criterion(subgrid_state)
else:
return self.initial_minimal_mesh_width
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 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 __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 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 momentum2(current_data):
x = pyclaw.Dimension(xlower, xupper, cells_number, name='x')
domain = pyclaw.Domain(x)
state = pyclaw.State(domain, 2, 2)
xc = state.grid.x.centers
x_wall = nw_edge_p
axis = plt.gca()
axis.plot(xc, hu1[current_data.frameno, :], 'r:')
axis.plot([x_wall, x_wall],
[-1.1 * current_data.q[1, nw], 1.1 * current_data.q[1, nw]],
":")
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 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 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 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 height2(current_data):
x = pyclaw.Dimension(xlower, xupper, cells_number, name='x')
domain = pyclaw.Domain(x)
state = pyclaw.State(domain, 2, 2)
xc = state.grid.x.centers
print(len(xc))
print(len(h1[current_data.frameno, :]))
axis = plt.gca()
jump = numpy.zeros(len(xc))
jump[nw] = 0.1 #wall height
axis.plot(xc, h1[current_data.frameno, :] + bathy(current_data) + jump,
'r:')
x_wall = nw_edge_p
y1 = current_data.aux[0, nw - 1]
y2 = y1 + wall_height
axis.plot([x_wall, x_wall], [y1, y2], 'g', linewidth=2.5)
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 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_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 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
from clawpack import riemann
solver = pyclaw.ClawSolver1D(riemann.burgers_1D)
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)
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
#===========================================================================
# 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, domain)
claw.solver = solver
claw.outdir = outdir
return claw
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
def macro_riemann_plot(which, context='notebook', figsize=(10, 3)):
"""
Some simulations to show that the Riemann solution describes macroscopic behavior
in the Cauchy problem.
"""
from IPython.display import HTML
from clawpack import pyclaw
from matplotlib import animation
from clawpack.riemann import shallow_roe_tracer_1D
depth = 0
momentum = 1
tracer = 2
solver = pyclaw.ClawSolver1D(shallow_roe_tracer_1D)
solver.num_eqn = 3
solver.num_waves = 3
solver.bc_lower[0] = pyclaw.BC.wall
solver.bc_upper[0] = pyclaw.BC.wall
x = pyclaw.Dimension(-1.0, 1.0, 2000, name='x')
domain = pyclaw.Domain(x)
state = pyclaw.State(domain, solver.num_eqn)
state.problem_data['grav'] = 1.0
grid = state.grid
xc = grid.p_centers[0]
hl = 3.
hr = 1.
ul = 0.
ur = 0.
xs = 0.1
alpha = (xs - xc) / (2. * xs)
if which == 'linear':
state.q[depth, :] = hl * (xc <= -xs) + hr * (xc > xs) + (
alpha * hl + (1 - alpha) * hr) * (xc > -xs) * (xc <= xs)
state.q[momentum, :] = hl * ul * (xc <= -xs) + hr * ur * (xc > xs) + (
alpha * hl * ul + (1 - alpha) * hr * ur) * (xc > -xs) * (xc <= xs)
elif which == 'oscillatory':
state.q[depth, :] = hl * (xc <= -xs) + hr * (xc > xs) + (
alpha * hl + (1 - alpha) * hr +
0.2 * np.sin(8 * np.pi * xc / xs)) * (xc > -xs) * (xc <= xs)
state.q[momentum, :] = hl * ul * (xc <= -xs) + hr * ur * (xc > xs) + (
alpha * hl * ul + (1 - alpha) * hr * ur +
0.2 * np.cos(8 * np.pi * xc / xs)) * (xc > -xs) * (xc <= xs)
state.q[tracer, :] = xc
claw = pyclaw.Controller()
claw.tfinal = 0.5
claw.solution = pyclaw.Solution(state, domain)
claw.solver = solver
claw.keep_copy = True
claw.num_output_times = 5
claw.verbosity = 0
claw.run()
fig = plt.figure(figsize=figsize)
ax_h = fig.add_subplot(121)
ax_u = fig.add_subplot(122)
fills = []
frame = claw.frames[0]
h = frame.q[0, :]
u = frame.q[1, :] / h
b = 0 * h
surface = h + b
tracer = frame.q[2, :]
x, = frame.state.grid.p_centers
line, = ax_h.plot(x, surface, '-k', linewidth=3)
line_u, = ax_u.plot(x, u, '-k', linewidth=3)
fills = {
'navy': None,
'blue': None,
'cornflowerblue': None,
'deepskyblue': None
}
colors = fills.keys()
def set_stripe_regions(tracer):
widthl = 0.3 / hl
widthr = 0.3 / hr
# Designate areas for each color of stripe
stripes = {}
stripes['navy'] = (tracer >= 0)
stripes['blue'] = (tracer % widthr >= widthr / 2.) * (tracer >= 0)
stripes['cornflowerblue'] = (tracer <= 0)
stripes['deepskyblue'] = (tracer % widthl >= widthl / 2.) * (tracer <=
0)
return stripes
stripes = set_stripe_regions(tracer)
for color in colors:
fills[color] = ax_h.fill_between(x,
b,
surface,
facecolor=color,
where=stripes[color],
alpha=0.5)
ax_h.set_xlabel('$x$')
ax_u.set_xlabel('$x$')
ax_h.set_xlim(-1, 1)
ax_h.set_ylim(0, 3.5)
ax_u.set_xlim(-1, 1)
ax_u.set_ylim(-1, 1)
ax_u.set_title('Velocity')
ax_h.set_title('Depth')
def fplot(frame_number):
fig.suptitle('Solution at time $t=' + str(frame_number / 10.) + '$',
fontsize=12)
# Remove old fill_between plots
for color in colors:
fills[color].remove()
frame = claw.frames[frame_number]
h = frame.q[0, :]
u = frame.q[1, :] / h
b = 0 * h
tracer = frame.q[2, :]
surface = h + b
line.set_data(x, surface)
line_u.set_data(x, u)
stripes = set_stripe_regions(tracer)
for color in colors:
fills[color] = ax_h.fill_between(x,
b,
surface,
facecolor=color,
where=stripes[color],
alpha=0.5)
return line,
if context in ['notebook', 'html']:
anim = animation.FuncAnimation(fig,
fplot,
frames=len(claw.frames),
interval=200,
repeat=False)
plt.close()
return HTML(anim.to_jshtml())
else: # PDF output
fplot(0)
plt.show()
fplot(2)
return fig
def acoustics(problem='Brahmananda'):
"""
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
import numpy as np
import math
import press_ran as pran
solver = pyclaw.ClawSolver1D(riemann.acoustics_variable_1D)
solver.bc_lower[0] = pyclaw.BC.periodic
solver.bc_upper[0] = pyclaw.BC.periodic
solver.aux_bc_lower[0] = pyclaw.BC.periodic
solver.aux_bc_upper[0] = pyclaw.BC.periodic
tFinal = 100
tFrames = 100
Nx = 1024
xmin = 0
xmax = 10 * math.pi
sigma = sigma
mu = mu
epsilon = epsilon
k = k
x = pyclaw.Dimension(xmin, xmax, Nx, name='x')
domain = pyclaw.Domain(x)
num_eqn = 2
num_aux = 2
state = pyclaw.State(domain, num_eqn, num_aux)
if problem == 'Brahmananda':
rho = 1.0
bulk = epsilon
xc = domain.grid.x.centers
for i in range(len(xc)):
U1 = np.random.rand()
U2 = np.random.rand()
GRn = sigma * sqrt(-2 * math.log(U1)) * math.cos(2 * math.pi * U2) + mu
z = 1 + bulk * GRn
state.aux[0, i] = rho * z # Impedance
state.aux[1, i] = z # Sound speed
state.q[0, :] = np.sin(k * xc)
state.q[1, :] = state.q[0, :] + 0.
claw = pyclaw.Controller()
claw.solution = pyclaw.Solution(state, domain)
claw.solver = solver
claw.tfinal = tFinal
claw.num_output_times = tFrames
# Solve
return claw
import matplotlib.pyplot as plt
q = frame.q
x, y = frame.state.grid.c_centers
plt.pcolormesh(x, y, q[density, ...])
def plot_results():
from clawpack.visclaw import iplot
ip = iplot.Iplot(load_frame, plot_frame)
ip.plotloop()
solver = pyclaw.ClawSolver2D(riemann.euler_4wave_2D)
solver.all_bcs = pyclaw.BC.extrap
domain = pyclaw.Domain([0., 0.], [1., 1.], [200, 200])
solution = pyclaw.Solution(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[density, ...] = 2. * l * t + 1. * l * b + 1. * r * t + 3. * r * b
solution.q[x_momentum, ...] = 0.75 * t - 0.75 * b
solution.q[y_momentum, ...] = 0.5 * l - 0.5 * r
solution.q[energy, ...] = 0.5 * solution.q[density, ...] * (solution.q[
x_momentum, ...]**2 + solution.q[y_momentum, ...]**2) + 1. / (gamma - 1.)
