def _compile_acceleration_eval(self, arrays):
names = [x.name for x in self.particle_arrays]
if self.equations is None:
if self.method == 'shepard':
equations = [
InterpolateFunction(dest='interpolate', sources=names)
]
elif self.method == 'sph':
equations = [InterpolateSPH(dest='interpolate', sources=names)]
else:
equations = [
Group(equations=[
SummationDensity(dest=name, sources=names)
for name in names
],
real=False),
Group(equations=[
SPHFirstOrderApproximationPreStep(dest='interpolate',
sources=names,
dim=self.dim)
],
real=True),
Group(equations=[
SPHFirstOrderApproximation(dest='interpolate',
sources=names,
dim=self.dim)
],
real=True)
]
else:
equations = self.equations
self.func_eval = AccelerationEval(arrays, equations, self.kernel)
compiler = SPHCompiler(self.func_eval, None)
compiler.compile()
def __init__(self,
arrays,
equations,
dim,
kernel=None,
domain_manager=None):
"""Constructor.
Parameters
----------
arrays: list(ParticleArray)
equations: list
dim: int
kernel: kernel instance.
domain_manager: DomainManager
"""
self.arrays = arrays
self.equations = equations
self.domain_manager = domain_manager
self.dim = dim
if kernel is None:
self.kernel = Gaussian(dim=dim)
else:
self.kernel = kernel
self.func_eval = AccelerationEval(arrays, equations, self.kernel)
compiler = SPHCompiler(self.func_eval, None)
compiler.compile()
self._create_nnps(arrays)
def _setup_integrator(self, equations, integrator):
kernel = CubicSpline(dim=1)
arrays = [self.pa]
a_eval = AccelerationEval(particle_arrays=arrays,
equations=equations,
kernel=kernel)
comp = SPHCompiler(a_eval, integrator=integrator)
comp.compile()
nnps = LinkedListNNPS(dim=kernel.dim, particles=arrays)
a_eval.set_nnps(nnps)
integrator.set_nnps(nnps)
def _compile_acceleration_eval(self, arrays):
names = [x.name for x in self.particle_arrays]
if self.equations is None:
equations = [
InterpolateFunction(dest='interpolate', sources=names)
]
else:
equations = self.equations
self.func_eval = AccelerationEval(arrays, equations, self.kernel)
compiler = SPHCompiler(self.func_eval, None)
compiler.compile()
def _make_accel_eval(self, equations, cache_nnps=False):
arrays = [self.pa]
kernel = CubicSpline(dim=self.dim)
a_eval = AccelerationEval(
particle_arrays=arrays, equations=equations, kernel=kernel
)
comp = SPHCompiler(a_eval, integrator=None)
comp.compile()
nnps = NNPS(dim=kernel.dim, particles=arrays, cache=cache_nnps)
nnps.update()
a_eval.set_nnps(nnps)
return a_eval
def _make_accel_eval(self, equations):
arrays = [self.pa]
kernel = CubicSpline(dim=self.dim)
a_eval = AccelerationEval(
particle_arrays=arrays, equations=equations, kernel=kernel
)
comp = SPHCompiler(a_eval, integrator=None)
comp.compile()
nnps = NNPS(dim=kernel.dim, particles=arrays)
nnps.update()
a_eval.set_nnps(nnps)
return a_eval
def _setup_integrator(self, equations, integrator):
pytest.importorskip('pysph.base.gpu_nnps')
kernel = CubicSpline(dim=1)
arrays = [self.pa]
from pysph.base.gpu_nnps import BruteForceNNPS as GPUNNPS
a_eval = AccelerationEval(
particle_arrays=arrays, equations=equations, kernel=kernel,
backend='opencl'
)
comp = SPHCompiler(a_eval, integrator=integrator)
comp.compile()
nnps = GPUNNPS(dim=kernel.dim, particles=arrays, cache=True)
nnps.update()
a_eval.set_nnps(nnps)
integrator.set_nnps(nnps)
def _make_accel_eval(self, equations, cache_nnps=True):
pytest.importorskip('pysph.base.gpu_nnps')
from pysph.base.gpu_nnps import ZOrderGPUNNPS as GPUNNPS
arrays = [self.pa]
kernel = CubicSpline(dim=self.dim)
a_eval = AccelerationEval(
particle_arrays=arrays, equations=equations, kernel=kernel,
backend='opencl'
)
comp = SPHCompiler(a_eval, integrator=None)
comp.compile()
self.sph_compiler = comp
nnps = GPUNNPS(dim=kernel.dim, particles=arrays, cache=cache_nnps)
nnps.update()
a_eval.set_nnps(nnps)
return a_eval
def setup(self, particles, equations, nnps, kernel=None, fixed_h=False):
""" Setup the solver.
The solver's processor id is set if the in_parallel flag is set
to true.
The order of the integrating calcs is determined by the solver's
order attribute.
This is usually called at the start of a PySPH simulation.
"""
self.particles = particles
if kernel is not None:
self.kernel = kernel
mode = 'mpi' if self.in_parallel else 'serial'
self.acceleration_evals = make_acceleration_evals(
particles, equations, self.kernel, mode)
sep = '-' * 70
eqn_info = '[\n' + ',\n'.join([str(e) for e in equations]) + '\n]'
logger.info('Using equations:\n%s\n%s\n%s' % (sep, eqn_info, sep))
logger.info('Using integrator:\n%s\n %s\n%s' %
(sep, self.integrator, sep))
sph_compiler = SPHCompiler(self.acceleration_evals, self.integrator)
sph_compiler.compile()
# Set the nnps for all concerned objects.
for ae in self.acceleration_evals:
ae.set_nnps(nnps)
self.integrator.set_nnps(nnps)
# set the parallel manager for the integrator
self.integrator.set_parallel_manager(self.pm)
# Set the post_stage_callback.
self.integrator.set_post_stage_callback(self._post_stage_callback)
# set integrator option for constant smoothing length
self.fixed_h = fixed_h
self.integrator.set_fixed_h(fixed_h)
logger.debug("Solver setup complete.")
def _make_integrator(self):
arrays = [self.pa]
kernel = CubicSpline(dim=self.dim)
eqs = [[Eq1(dest='fluid', sources=['fluid'])],
[Eq2(dest='fluid', sources=['fluid'])]]
meqs = MultiStageEquations(eqs)
a_evals = make_acceleration_evals(arrays,
meqs,
kernel,
backend=self.backend)
integrator = MyIntegrator(fluid=MyStepper())
comp = SPHCompiler(a_evals, integrator=integrator)
comp.compile()
nnps = self.NNPS_cls(dim=kernel.dim, particles=arrays)
nnps.update()
for ae in a_evals:
ae.set_nnps(nnps)
return integrator
def __init__(self,
arrays,
equations,
dim,
kernel=None,
domain_manager=None,
backend=None,
nnps_factory=NNPS):
"""Constructor.
Parameters
----------
arrays: list(ParticleArray)
equations: list
dim: int
kernel: kernel instance.
domain_manager: DomainManager
backend: str: indicates the backend to use.
one of ('opencl', 'cython', '', None)
nnps_factory: A factory that creates an NNPSBase instance.
"""
self.arrays = arrays
self.equations = equations
self.domain_manager = domain_manager
self.dim = dim
if kernel is None:
self.kernel = Gaussian(dim=dim)
else:
self.kernel = kernel
self.nnps_factory = nnps_factory
self.backend = backend
self.func_eval = AccelerationEval(arrays,
equations,
self.kernel,
backend=backend)
compiler = SPHCompiler(self.func_eval, None)
compiler.compile()
self._create_nnps(arrays)
def test_detection_of_missing_arrays_for_integrator(self):
# Given.
x = np.asarray([1.0])
u = np.asarray([0.0])
h = np.ones_like(x)
pa = get_particle_array(name='fluid', x=x, u=u, h=h, m=h)
arrays = [pa]
# When
integrator = LeapFrogIntegrator(fluid=LeapFrogStep())
equations = [SHM(dest="fluid", sources=None)]
kernel = CubicSpline(dim=1)
a_eval = AccelerationEval(particle_arrays=arrays,
equations=equations,
kernel=kernel)
comp = SPHCompiler(a_eval, integrator=integrator)
# Then
self.assertRaises(RuntimeError, comp.compile)
def test_detect_missing_arrays_for_many_particle_arrays(self):
# Given.
x = np.asarray([1.0])
u = np.asarray([0.0])
h = np.ones_like(x)
fluid = get_particle_array_wcsph(name='fluid', x=x, u=u, h=h, m=h)
solid = get_particle_array(name='solid', x=x, u=u, h=h, m=h)
arrays = [fluid, solid]
# When
integrator = PECIntegrator(fluid=TwoStageRigidBodyStep(),
solid=TwoStageRigidBodyStep())
equations = [SHM(dest="fluid", sources=None)]
kernel = CubicSpline(dim=1)
a_eval = AccelerationEval(particle_arrays=arrays,
equations=equations,
kernel=kernel)
comp = SPHCompiler(a_eval, integrator=integrator)
# Then
self.assertRaises(RuntimeError, comp.compile)
], update_nnps=False
)
]
from pysph.sph.acceleration_eval import AccelerationEval
from pysph.sph.sph_compiler import SPHCompiler
kernel = CubicSpline(dim=2)
integrator = SWEIntegrator(fluid=SWEStep())
tf = 2
solver = Solver(
kernel=kernel,
dim=2,
integrator=integrator,
cfl=0.1,
adaptive_timestep=True,
output_at_times=[0.1, 0.2, 0.3, 0.4, 0.5, 0.6],
tf=tf
)
part_arr = app.create_particles
eqns = app.create_equations()
app.setup(solver=solver, equations=eqns,
particle_factory=part_arr)
a_eval = AccelerationEval(
solver.particles, equations=one_time_equations, kernel=CubicSpline(dim=2))
compiler = SPHCompiler(a_eval, None)
compiler.compile()
a_eval.set_nnps(app.nnps)
a_eval.compute(0.0, 1e-4)
app.run()
def __init__(self,
all_particles,
scheme,
domain=None,
innerloop=True,
updates=True,
parallel=False,
steps=None,
D=0):
"""The second integrator is a simple Euler-Integrator (accurate
enough due to very small time steps; very fast) using EBGSteps.
EBGSteps are basically the same as EulerSteps, exept for the fact
that they work with an intermediate ebg velocity [eu, ev, ew].
This velocity does not interfere with the actual velocity, which
is neseccery to not disturb the real velocity through artificial
damping in this step. The ebg velocity is initialized for each
inner loop again and reset in the outer loop."""
from math import ceil
from pysph.base.kernels import CubicSpline
from pysph.sph.integrator_step import EBGStep
from compyle.config import get_config
from pysph.sph.integrator import EulerIntegrator
from pysph.sph.scheme import BeadChainScheme
from pysph.sph.equation import Group
from pysph.sph.fiber.utils import (HoldPoints, Contact,
ComputeDistance)
from pysph.sph.fiber.beadchain import (Tension, Bending,
ArtificialDamping)
from pysph.base.nnps import DomainManager, LinkedListNNPS
from pysph.sph.acceleration_eval import AccelerationEval
from pysph.sph.sph_compiler import SPHCompiler
if not isinstance(scheme, BeadChainScheme):
raise TypeError("Scheme must be BeadChainScheme")
self.innerloop = innerloop
self.dt = scheme.dt
self.fiber_dt = scheme.fiber_dt
self.domain_updates = updates
self.steps = steps
self.D = D
self.eta0 = scheme.rho0 * scheme.nu
# if there are more than 1 particles involved, elastic equations are
# iterated in an inner loop.
if self.innerloop:
# second integrator
# self.fiber_integrator = EulerIntegrator(fiber=EBGStep())
steppers = {}
for f in scheme.fibers:
steppers[f] = EBGStep()
self.fiber_integrator = EulerIntegrator(**steppers)
# The type of spline has no influence here. It must be large enough
# to contain the next particle though.
kernel = CubicSpline(dim=scheme.dim)
equations = []
g1 = []
for fiber in scheme.fibers:
g1.append(ComputeDistance(dest=fiber, sources=[fiber]))
equations.append(Group(equations=g1))
g2 = []
for fiber in scheme.fibers:
g2.append(
Tension(dest=fiber, sources=None, ea=scheme.E * scheme.A))
g2.append(
Bending(dest=fiber, sources=None, ei=scheme.E * scheme.Ip))
g2.append(
Contact(dest=fiber,
sources=scheme.fibers,
E=scheme.E,
d=scheme.dx,
dim=scheme.dim,
k=scheme.k,
lim=scheme.lim,
eta0=self.eta0))
g2.append(ArtificialDamping(dest=fiber, sources=None,
d=self.D))
equations.append(Group(equations=g2))
g3 = []
for fiber in scheme.fibers:
g3.append(HoldPoints(dest=fiber, sources=None, tag=100))
equations.append(Group(equations=g3))
# These equations are applied to fiber particles only - that's the
# reason for computational speed up.
particles = [p for p in all_particles if p.name in scheme.fibers]
# A seperate DomainManager is needed to ensure that particles don't
# leave the domain.
if domain:
xmin = domain.manager.xmin
ymin = domain.manager.ymin
zmin = domain.manager.zmin
xmax = domain.manager.xmax
ymax = domain.manager.ymax
zmax = domain.manager.zmax
periodic_in_x = domain.manager.periodic_in_x
periodic_in_y = domain.manager.periodic_in_y
periodic_in_z = domain.manager.periodic_in_z
gamma_yx = domain.manager.gamma_yx
gamma_zx = domain.manager.gamma_zx
gamma_zy = domain.manager.gamma_zy
n_layers = domain.manager.n_layers
N = self.steps or int(ceil(self.dt / self.fiber_dt))
# dt = self.dt/N
self.domain = DomainManager(xmin=xmin,
xmax=xmax,
ymin=ymin,
ymax=ymax,
zmin=zmin,
zmax=zmax,
periodic_in_x=periodic_in_x,
periodic_in_y=periodic_in_y,
periodic_in_z=periodic_in_z,
gamma_yx=gamma_yx,
gamma_zx=gamma_zx,
gamma_zy=gamma_zy,
n_layers=n_layers,
dt=self.dt,
calls_per_step=N)
else:
self.domain = None
# A seperate list for the nearest neighbourhood search is
# benefitial since it is much smaller than the original one.
nnps = LinkedListNNPS(dim=scheme.dim,
particles=particles,
radius_scale=kernel.radius_scale,
domain=self.domain,
fixed_h=False,
cache=False,
sort_gids=False)
# The acceleration evaluator needs to be set up in order to compile
# it together with the integrator.
if parallel:
self.acceleration_eval = AccelerationEval(
particle_arrays=particles,
equations=equations,
kernel=kernel)
else:
self.acceleration_eval = AccelerationEval(
particle_arrays=particles,
equations=equations,
kernel=kernel,
mode='serial')
# Compilation of the integrator not using openmp, because the
# overhead is too large for those few fiber particles.
comp = SPHCompiler(self.acceleration_eval, self.fiber_integrator)
if parallel:
comp.compile()
else:
config = get_config()
config.use_openmp = False
comp.compile()
config.use_openmp = True
self.acceleration_eval.set_nnps(nnps)
# Connecting neighbourhood list to integrator.
self.fiber_integrator.set_nnps(nnps)
def _compile_acceleration_eval(self, arrays):
names = [x.name for x in self.particle_arrays]
equations = [InterpolateFunction(dest='interpolate', sources=names)]
self.func_eval = AccelerationEval(arrays, equations, self.kernel)
compiler = SPHCompiler(self.func_eval, None)
compiler.compile()
