def __init__(self, problem, scheme):
ng = self.number_guard_zones()
domain = cowpy.DistributedDomain(problem.resolution, guard=ng)
descr = problem.fluid_descriptor
self.shape = tuple([n + 2*ng for n in domain.local_shape])
self.fluid = FluidStateVector(self.shape, descr)
self.scheme = scheme
self.driving = getattr(problem, 'driving', None)
self.poisson_solver = getattr(problem, 'poisson_solver', None)
self.domain = domain
self.problem = problem
def pad_out(x, v):
return x + (v,) * (3 - len(self.shape))
x0 = np.array(problem.lower_bounds)
x1 = np.array(problem.upper_bounds)
dX = (x1 - x0) / pad_out(domain.global_shape, 1)
X0 = x0 + dX * pad_out(domain.global_start, 0)
X1 = X0 + dX * pad_out(domain.local_shape, 1)
Nx, Ny, Nz = pad_out(self.fluid.shape, 1)
dx = (X1[0] - X0[0])/(Nx - (2*ng if Nx > 1 else 0))
dy = (X1[1] - X0[1])/(Ny - (2*ng if Ny > 1 else 0))
dz = (X1[2] - X0[2])/(Nz - (2*ng if Nz > 1 else 0))
self.Nx, self.Ny, self.Nz = Nx, Ny, Nz
self.dx, self.dy, self.dz = dx, dy, dz
self.X0, self.X1 = X0, X1
class ParallelSynchronization(object):
"""
Currently restricted to periodic BC's
"""
def __init__(self, mara):
members = ['rho', 'pre', 'vx', 'vy', 'vz']
self.domain = mara.domain
self.fluid = mara.fluid
self.field = cowpy.DataField(self.domain, members=members)
def set_boundary(self, X, ng, field='cons'):
self.field.set_buffer(X)
self.field.sync_guard()
self.boundary = ParallelSynchronization(self)
def __init__(self, problem, scheme):
descr = problem.fluid_descriptor
X0 = problem.lower_bounds
X1 = problem.upper_bounds
ng = self.number_guard_zones()
self.shape = tuple([n + 2*ng for n in problem.resolution])
self.fluid = FluidStateVector(self.shape, descr)
self.scheme = scheme
self.boundary = problem.build_boundary(self)
self.driving = getattr(problem, 'driving', None)
self.poisson_solver = getattr(problem, 'poisson_solver', None)
self.problem = problem
Nx, Ny, Nz = self.fluid.shape + (1,) * (3 - len(self.shape))
dx = (X1[0] - X0[0])/(Nx - (2*ng if Nx > 1 else 0))
dy = (X1[1] - X0[1])/(Ny - (2*ng if Ny > 1 else 0))
dz = (X1[2] - X0[2])/(Nz - (2*ng if Nz > 1 else 0))
self.Nx, self.Ny, self.Nz = Nx, Ny, Nz
self.dx, self.dy, self.dz = dx, dy, dz
self.X0, self.X1 = X0, X1
class MaraEvolutionOperator(object):
def __init__(self, problem, scheme):
descr = problem.fluid_descriptor
X0 = problem.lower_bounds
X1 = problem.upper_bounds
ng = self.number_guard_zones()
self.shape = tuple([n + 2*ng for n in problem.resolution])
self.fluid = FluidStateVector(self.shape, descr)
self.scheme = scheme
self.boundary = problem.build_boundary(self)
self.driving = getattr(problem, 'driving', None)
self.poisson_solver = getattr(problem, 'poisson_solver', None)
self.problem = problem
Nx, Ny, Nz = self.fluid.shape + (1,) * (3 - len(self.shape))
dx = (X1[0] - X0[0])/(Nx - (2*ng if Nx > 1 else 0))
dy = (X1[1] - X0[1])/(Ny - (2*ng if Ny > 1 else 0))
dz = (X1[2] - X0[2])/(Nz - (2*ng if Nz > 1 else 0))
self.Nx, self.Ny, self.Nz = Nx, Ny, Nz
self.dx, self.dy, self.dz = dx, dy, dz
self.X0, self.X1 = X0, X1
@property
def fields(self):
P = self.fluid.primitive
G = self.fluid.gravity
return {'rho': P[...,0],
'pre': P[...,1],
'vx' : P[...,2],
'vy' : P[...,3],
'vz' : P[...,4],
'phi': G[...,0] if self.fluid.descriptor.ngravity else None,
'gph': G[...,1] if self.fluid.descriptor.ngravity else None}
def write_checkpoint(self, status, dir=".", **extras):
try:
os.makedirs(dir)
print "creating data directory", dir
except OSError: # Directory exists
pass
chkpt = { "prim": self.fluid.primitive,
"problem": self.problem,
"status": status.__dict__ }
chkpt.update(extras)
chkpt_name = "%s/chkpt.%04d.pk" % (dir, status.chkpt_number)
chkpt_file = open(chkpt_name, 'w')
print "Writing checkpoint", chkpt_name
cPickle.dump(chkpt, chkpt_file)
def measure(self):
meas = { }
P = self.fluid.primitive
U = self.fluid.conserved()
rho = P[...,0]
vx = P[...,2]
vy = P[...,3]
vz = P[...,4]
meas["kinetic"] = (rho * (vx*vx + vy*vy + vz*vz)).mean()
meas["density_max"] = rho.max()
meas["density_min"] = rho.min()
meas["conserved_avg"] = [U[...,i].mean() for i in range(5)]
meas["primitive_avg"] = [P[...,i].mean() for i in range(5)]
return meas
def min_grid_spacing(self):
return min([self.dx, self.dy, self.dz][:len(self.shape)])
def number_guard_zones(self):
return 3
def number_nonzero(self, X):
"""
Return the number of nonzero entries of the array X
"""
return (X != 0).sum()
def coordinate_grid(self):
ng = self.number_guard_zones()
Nx, Ny, Nz = self.Nx, self.Ny, self.Nz
dx, dy, dz = self.dx, self.dy, self.dz
x0, y0, z0 = self.X0
x1, y1, z1 = self.X1
if self.Nx > 1: x0 -= ng * dx
if self.Ny > 1: y0 -= ng * dy
if self.Nz > 1: z0 -= ng * dz
if self.Nx > 1: x1 += ng * dx
if self.Ny > 1: y1 += ng * dy
if self.Nz > 1: z1 += ng * dz
return np.mgrid[x0+dx/2 : x1+dx/2 : dx,
y0+dy/2 : y1+dy/2 : dy,
z0+dz/2 : z1+dz/2 : dz]
def initial_model(self, pinit, ginit=None):
npr = self.fluid.descriptor.nprimitive
ngr = self.fluid.descriptor.ngravity
if ginit is None: ginit = lambda x,y,z: np.zeros(ngr)
shape = self.shape
X, Y, Z = self.coordinate_grid()
P = np.ndarray(
shape=shape + (npr,), buffer=np.array(
[pinit(x, y, z) for x, y, z in zip(X.flat, Y.flat, Z.flat)]))
G = np.ndarray(
shape=shape + (ngr,), buffer=np.array(
[ginit(x, y, z) for x, y, z in zip(X.flat, Y.flat, Z.flat)]))
self.fluid.primitive = P
self.fluid.gravity = G
def set_boundary(self):
"""
This function does not call BC's on gravitational field right now.
"""
ng = self.number_guard_zones()
self.boundary.set_boundary(self.fluid.primitive, ng, field='prim')
def advance(self, dt, rk=3):
start = time.clock()
U0 = self.fluid.conserved()
# RungeKuttaSingleStep
if rk == 1:
U1 = U0 + dt * self.dUdt(U0)
# RungeKuttaRk2Tvd
if rk == 2:
U1 = U0 + dt*self.dUdt(U0)
U1 = 0.5*(U0 + U1 + dt*self.dUdt(U1))
# RungeKuttaShuOsherRk3
if rk == 3:
U1 = U0 + dt * self.dUdt(U0)
U1 = 3./4*U0 + 1./4*U1 + 1./4 * dt * self.dUdt(U1)
U1 = 1./3*U0 + 2./3*U1 + 2./3 * dt * self.dUdt(U1)
# RungeKuttaClassicRk4
if rk == 4:
L1 = self.dUdt(U0)
L2 = self.dUdt(U0 + (0.5*dt) * L1)
L3 = self.dUdt(U0 + (0.5*dt) * L2)
L4 = self.dUdt(U0 + (1.0*dt) * L3)
U1 = U0 + dt * (L1 + 2.0*L2 + 2.0*L3 + L4) / 6.0
ng = self.number_guard_zones()
self.boundary.set_boundary(U1, ng)
self.from_conserved(U1)
try:
self.driving.advance(dt)
self.driving.drive(self, dt)
except AttributeError:
# no driving module
pass
return time.clock() - start
def update_gravity(self):
"""
Notes:
------
(1) Only works in 1d for now.
(2) To see the bug introduced by not accounting for the background
density, do
self.fluid.descriptor.rhobar = 0.0 #rhobar
"""
if self.poisson_solver is None:
return
if len(self.shape) > 1:
raise NotImplementedError
try:
ng = self.number_guard_zones()
G, rhobar = self.poisson_solver.solve(self.fields['rho'][ng:-ng],
retrhobar=True)
self.fluid.descriptor.rhobar = rhobar
self.fluid.gravity[ng:-ng] = G
self.boundary.set_boundary(self.fluid.gravity, ng, field='grav')
except AttributeError: # no poisson_solver
pass
except ValueError: # no gravity array
pass
def from_conserved(self, U, safe=True, context=""):
"""
A safe version of the fluid's from_conserved method.
"""
if not safe:
self.fluid.from_conserved(U)
return
self.fluid.userflag = 0
self.fluid.from_conserved(U)
numerr = self.number_nonzero(self.fluid.userflag)
if numerr != 0:
raise RuntimeError("conserved inversion failed on %d zones %s" % (
numerr, context))
def validate_gravity(self):
if len(self.shape) > 1:
raise NotImplementedError
import matplotlib.pyplot as plt
ng = self.number_guard_zones()
phi0 = self.fields['phi']
gph0 = self.fields['gph']
gph1 = np.gradient(phi0, self.dx)
plt.semilogy(abs(((gph1 - gph0))[ng:-ng]))
plt.show()
def dUdt(self, U):
ng = self.number_guard_zones()
dx = [self.dx, self.dy, self.dz]
self.boundary.set_boundary(U, ng)
self.from_conserved(U)
self.update_gravity()
L = self.scheme.time_derivative(self.fluid, dx)
if self.fluid.descriptor.fluid in ['gravp', 'gravs']:
S = self.fluid.source_terms()
return L + S
else:
return L
def diffusion(self, r):
"""
Applies diffusion across troubled zones, larger r => more diffusion.
"""
start = time.clock()
orig = self.scheme.solver_type
ng = self.number_guard_zones()
dx = [self.dx, self.dy, self.dz]
U = self.fluid.conserved()
self.boundary.set_boundary(U, ng)
self.scheme.solver_type = 'diffusion'
L = self.scheme.time_derivative(self.fluid, dx)
U += L * r
self.boundary.set_boundary(U, ng)
self.from_conserved(U, context="after a diffusion step")
self.scheme.solver_type = orig
return time.clock() - start
def timestep(self, CFL):
ml = abs(self.fluid.eigenvalues()).max()
return CFL * self.min_grid_spacing() / ml
class ParallelSimulation(MaraEvolutionOperator):
def __init__(self, problem, scheme):
ng = self.number_guard_zones()
domain = cowpy.DistributedDomain(problem.resolution, guard=ng)
descr = problem.fluid_descriptor
self.shape = tuple([n + 2*ng for n in domain.local_shape])
self.fluid = FluidStateVector(self.shape, descr)
self.scheme = scheme
self.driving = getattr(problem, 'driving', None)
self.poisson_solver = getattr(problem, 'poisson_solver', None)
self.domain = domain
self.problem = problem
def pad_out(x, v):
return x + (v,) * (3 - len(self.shape))
x0 = np.array(problem.lower_bounds)
x1 = np.array(problem.upper_bounds)
dX = (x1 - x0) / pad_out(domain.global_shape, 1)
X0 = x0 + dX * pad_out(domain.global_start, 0)
X1 = X0 + dX * pad_out(domain.local_shape, 1)
Nx, Ny, Nz = pad_out(self.fluid.shape, 1)
dx = (X1[0] - X0[0])/(Nx - (2*ng if Nx > 1 else 0))
dy = (X1[1] - X0[1])/(Ny - (2*ng if Ny > 1 else 0))
dz = (X1[2] - X0[2])/(Nz - (2*ng if Nz > 1 else 0))
self.Nx, self.Ny, self.Nz = Nx, Ny, Nz
self.dx, self.dy, self.dz = dx, dy, dz
self.X0, self.X1 = X0, X1
class ParallelSynchronization(object):
"""
Currently restricted to periodic BC's
"""
def __init__(self, mara):
members = ['rho', 'pre', 'vx', 'vy', 'vz']
self.domain = mara.domain
self.fluid = mara.fluid
self.field = cowpy.DataField(self.domain, members=members)
def set_boundary(self, X, ng, field='cons'):
self.field.set_buffer(X)
self.field.sync_guard()
self.boundary = ParallelSynchronization(self)
def number_nonzero(self, X):
"""
Return the number of nonzero entries of the array X, over all subgrids.
"""
return self.domain.reduce((X != 0).sum(), type=int, op='sum')
def write_checkpoint(self, status, dir=".", **extras):
chkpt_name = "%s/chkpt.%04d.h5" % (dir, status.chkpt_number)
if self.domain.cart_rank == 0:
try:
os.makedirs(dir)
print "creating data directory", dir
except OSError: # Directory exists
pass
h5f = h5py.File(chkpt_name, 'w')
chkpt = { "problem": self.problem,
"status": status.__dict__ }
for k,v in chkpt.items():
if type(v) is dict:
grp = h5f.create_group(k)
for k1,v1 in v.items():
grp[k1] = v1
else:
h5f[k] = cPickle.dumps(v)
h5f.close()
field = cowpy.DataField(self.domain, buffer=self.fluid.primitive,
members=['rho', 'pre', 'vx', 'vy', 'vz'],
name='prim')
print "Writing checkpoint", chkpt_name
field.dump(chkpt_name)
def timestep(self, CFL):
ml = self.domain.reduce(abs(self.fluid.eigenvalues()).max(), op='max')
return CFL * self.min_grid_spacing() / ml