class PeriodicBox3DTestCase(PeriodicBox2DTestCase):
"""Test the periodicity algorithms in the Domain Manager.
We create a 3D box with periodicity along x, y and z. We check if this
produces a constant density with summation density.
"""
def setUp(self):
# create the particle arrays
L = 1.0
n = 5
dx = L / n
hdx = 1.5
self.L = L
self.vol = vol = dx * dx * dx
# fluid particles
xx, yy, zz = np.mgrid[dx / 2:L:dx, dx / 2:L:dx, dx / 2:L:dx]
x = xx.ravel()
y = yy.ravel()
z = zz.ravel() # particle positions
p = self._get_pressure(x, y, z)
h = np.ones_like(x) * hdx * dx # smoothing lengths
m = np.ones_like(x) * vol # mass
V = np.zeros_like(x) # volumes
fluid = get_particle_array(name='fluid', x=x, y=y, z=z,
h=h, m=m, V=V, p=p
)
# particles and domain
self.fluid = fluid
self.domain = DomainManager(
xmin=0, xmax=L, ymin=0, ymax=L, zmin=0, zmax=L,
periodic_in_x=True, periodic_in_y=True, periodic_in_z=True
)
self.kernel = get_compiled_kernel(Gaussian(dim=3))
self.orig_n = self.fluid.get_number_of_particles()
self.nnps = LinkedListNNPS(
dim=3, particles=[self.fluid],
domain=self.domain,
radius_scale=self.kernel.radius_scale)
def test_summation_density(self):
self._check_summation_density()
def test_box_wrapping(self):
# Given
fluid = self.fluid
fluid.x += 0.35
fluid.y += 0.35
fluid.z += 0.35
self._check_summation_density()
def test_periodicity(self):
# Given.
fluid = self.fluid
# When
self.domain.update()
# Then.
x, y, z, p = fluid.get('x', 'y', 'z', 'p', only_real_particles=False)
xmin, xmax, ymin, ymax = x.min(), x.max(), y.min(), y.max()
zmin, zmax = z.min(), z.max()
new_n = fluid.get_number_of_particles()
self.assertTrue(new_n > self.orig_n)
self.assertTrue(xmin < 0.0)
self.assertTrue(xmax > self.L)
self.assertTrue(ymin < 0.0)
self.assertTrue(ymax > self.L)
self.assertTrue(zmin < 0.0)
self.assertTrue(zmax > self.L)
p_expect = self._get_pressure(x, y, z)
diff = np.abs(p - p_expect).max()
message = "Pressure not equal, max diff: %s" % diff
self.assertTrue(np.allclose(p, p_expect, atol=1e-14), message)
class FiberIntegrator(Tool):
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 post_stage(self, current_time, dt, stage):
"""This post stage function gets called after each outer loop and
starts an inner loop for the fiber iteration."""
from math import ceil
if self.innerloop:
# 1) predictor
# 2) post stage 1:
if stage == 1:
N = self.steps or int(ceil(self.dt / self.fiber_dt))
for n in range(0, N):
self.fiber_integrator.step(current_time, dt / N)
current_time += dt / N
if self.domain_updates and self.domain:
self.domain.update()