def test_convex_polyhedron(self):
context.initialize()
self.system = hoomd.init.read_gsd(filename='init.gsd')
with self.assertRaises(RuntimeError):
self.mc = hpmc.integrate.convex_polyhedron(seed=2234, d=0.3, a=0.4, restore_state=True);
def setUp(self):
self._name = None;
hexuc = hoomd.lattice.hex(a=2.0);
system = init.read_snapshot(hexuc.get_snapshot());
system.replicate(nx=8, ny=8, nz=1);
self.snapshot2d = system.take_snapshot(particles=True);
context.initialize();
bccuc = hoomd.lattice.bcc(a=4.0);
system = init.read_snapshot(bccuc.get_snapshot());
system.replicate(nx=4, ny=4, nz=4);
self.snapshot3d = system.take_snapshot(particles=True);
# self.snapshot3d = data.make_snapshot(N=20, box=system.box, particle_types=['A']);
context.initialize();
v2d = 0.33*np.array([(-1,-1), (1,-1), (1,1), (-1,1)]);
v2dup = v2d+0.1*np.array([(1,-1), (-1,-1), (1,-1), (1,1)]);
r = 0.1234;
rup = 0.3;
v3d = 0.33*np.array([(1,1,1), (1,-1,1), (-1,-1,1), (-1,1,1),(1,1,-1), (1,-1,-1), (-1,-1,-1), (-1,1,-1)]);
v3dup = v3d + 0.1*np.array([(-1,1,-1), (1,1,1), (1,-1,-1), (-1,1,-1),(-1,-1,-1), (1,1,1), (-1,1,-1), (-1,1,1)]);
self.a = 0.5;
self.d = 0.5;
self.params = dict(
sphere=dict(first=dict(diameter=1.5), second=dict(diameter=3.0)),
ellipsoid=dict(first=dict(a=0.5, b=0.54, c=0.35), second=dict(a=0.98*0.5, b=1.05*0.54, c=1.1*0.35)),
convex_polygon=dict(first=dict(vertices=v2d), second=dict(vertices=v2dup)),
convex_spheropolygon=dict(first=dict(vertices=v2d, sweep_radius=r), second=dict(vertices=v2dup, sweep_radius=rup)),
simple_polygon=dict(first=dict(vertices=v2d), second=dict(vertices=v2dup)),
convex_polyhedron=dict(first=dict(vertices=v3d), second=dict(vertices=v3dup)),
convex_spheropolyhedron=dict(first=dict(vertices=v3d, sweep_radius=r), second=dict(vertices=v3dup, sweep_radius=rup))
)
def test_convex_polyhedron(self):
context.initialize()
self.system = hoomd.init.read_gsd(filename='init.gsd')
with self.assertRaises(RuntimeError):
self.mc = hpmc.integrate.convex_polyhedron(seed=2234, d=0.3, a=0.4, restore_state=True);
def tearDown(self):
del self.mc
del self.patch
del self.snapshot
del self.log
context.initialize()
context.current.device.gpu_error_checking = True
def setUp(self):
self._name = None;
hexuc = hoomd.lattice.hex(a=2.0);
system = init.read_snapshot(hexuc.get_snapshot());
system.replicate(nx=8, ny=8, nz=1);
self.snapshot2d = system.take_snapshot(particles=True);
context.initialize();
bccuc = hoomd.lattice.bcc(a=4.0);
system = init.read_snapshot(bccuc.get_snapshot());
system.replicate(nx=4, ny=4, nz=4);
self.snapshot3d = system.take_snapshot(particles=True);
# self.snapshot3d = data.make_snapshot(N=20, box=system.box, particle_types=['A']);
context.initialize();
v2d = 0.33*np.array([(-1,-1), (1,-1), (1,1), (-1,1)]);
v2dup = v2d+0.1*np.array([(1,-1), (-1,-1), (1,-1), (1,1)]);
r = 0.1234;
rup = 0.3;
v3d = 0.33*np.array([(1,1,1), (1,-1,1), (-1,-1,1), (-1,1,1),(1,1,-1), (1,-1,-1), (-1,-1,-1), (-1,1,-1)]);
v3dup = v3d + 0.1*np.array([(-1,1,-1), (1,1,1), (1,-1,-1), (-1,1,-1),(-1,-1,-1), (1,1,1), (-1,1,-1), (-1,1,1)]);
self.a = 0.5;
self.d = 0.5;
self.params = dict(
sphere=dict(first=dict(diameter=1.5,orientable=False), second=dict(diameter=3.0,orientable=True)),
ellipsoid=dict(first=dict(a=0.5, b=0.54, c=0.35), second=dict(a=0.98*0.5, b=1.05*0.54, c=1.1*0.35)),
convex_polygon=dict(first=dict(vertices=v2d), second=dict(vertices=v2dup)),
convex_spheropolygon=dict(first=dict(vertices=v2d, sweep_radius=r), second=dict(vertices=v2dup, sweep_radius=rup)),
simple_polygon=dict(first=dict(vertices=v2d), second=dict(vertices=v2dup)),
convex_polyhedron=dict(first=dict(vertices=v3d), second=dict(vertices=v3dup)),
convex_spheropolyhedron=dict(first=dict(vertices=v3d, sweep_radius=r), second=dict(vertices=v3dup, sweep_radius=rup))
)
def tearDown(self):
del self.lattice
del self.gsd
del self.system
filename = "init.gsd"
if hoomd.comm.get_rank() == 0 and os.path.exists(filename):
os.remove(filename);
context.initialize()
def setUp(self):
context.initialize()
self.lattice = hoomd.lattice.sc(a=1.5, type_name='A');
self.system = hoomd.init.create_lattice(self.lattice, n=3);
self.gsd = hoomd.dump.gsd('init.gsd', period=100, group=hoomd.group.all(), overwrite=True);
self.gsd.write_restart();
def setUp(self):
context.initialize()
self.lattice = hoomd.lattice.sc(a=1.5, type_name='A');
self.system = hoomd.init.create_lattice(self.lattice, n=3);
self.gsd = hoomd.dump.gsd('init.gsd', period=100, group=hoomd.group.all(), overwrite=True);
self.gsd.write_restart();
def tearDown(self):
del self.lattice
del self.gsd
del self.system
filename = "init.gsd"
if hoomd.context.current.device.comm.rank == 0 and os.path.exists(filename):
os.remove(filename);
context.initialize()
def tearDown(self):
del self.lattice
del self.gsd
del self.system
filename = "init.gsd"
if hoomd.comm.get_rank() == 0 and os.path.exists(filename):
os.remove(filename)
context.initialize()
def tearDown(self):
del self.mc
del self.patch
del self.snapshot
del self.log
context.initialize()
def test_access(self):
N = 2
L = 10
context.initialize()
self.snapshot = data.make_snapshot(N=N,
box=data.boxdim(L=L, dimensions=2),
particle_types=['A'])
# sphere
diam = 1.125
self.system = init.read_snapshot(self.snapshot)
self.mc = hpmc.integrate.sphere(seed=2398, d=0.0)
self.mc.shape_param.set('A', diameter=diam)
self.assertAlmostEqual(self.mc.shape_param['A'].diameter, diam)
del self.mc
del self.system
context.initialize()
# ellipsoid
a = 1.125
b = 0.238
c = 2.25
self.system = init.read_snapshot(self.snapshot)
self.mc = hpmc.integrate.ellipsoid(seed=2398, d=0.0)
self.mc.shape_param.set('A', a=a, b=b, c=c)
self.assertAlmostEqual(self.mc.shape_param['A'].a, a)
self.assertAlmostEqual(self.mc.shape_param['A'].b, b)
self.assertAlmostEqual(self.mc.shape_param['A'].c, c)
del self.mc
del self.system
context.initialize()
# convex_polygon
v = [(-1, -1), (1, -1), (1, 1), (-1, 1)]
self.system = init.read_snapshot(self.snapshot)
self.mc = hpmc.integrate.convex_polygon(seed=2398, d=0.1, a=0.1)
self.mc.shape_param.set('A', vertices=v)
diff = (np.array(v) -
np.array(self.mc.shape_param['A'].vertices)).flatten()
self.assertAlmostEqual(diff.dot(diff), 0)
del self.mc
del self.system
context.initialize()
# convex_spheropolygon
v = [(-1, -1), (1, -1), (1, 1), (-1, 1)]
r = 0.1234
self.system = init.read_snapshot(self.snapshot)
self.mc = hpmc.integrate.convex_spheropolygon(seed=2398, d=0.1, a=0.1)
self.mc.shape_param.set('A', vertices=v, sweep_radius=r)
diff = (np.array(v) -
np.array(self.mc.shape_param['A'].vertices)).flatten()
self.assertAlmostEqual(diff.dot(diff), 0)
self.assertAlmostEqual(self.mc.shape_param['A'].sweep_radius, r)
del self.mc
del self.system
context.initialize()
#simple_polygon
v = [(-1, -1), (1, -1), (1, 1), (-1, 1)]
self.system = init.read_snapshot(self.snapshot)
self.mc = hpmc.integrate.simple_polygon(seed=2398, d=0.1, a=0.1)
self.mc.shape_param.set('A', vertices=v)
diff = (np.array(v) -
np.array(self.mc.shape_param['A'].vertices)).flatten()
self.assertAlmostEqual(diff.dot(diff), 0)
del self.mc
del self.system
context.initialize()
# polyhedron
import math
v = [(-0.5, -0.5, 0), (-0.5, 0.5, 0), (0.5, -0.5, 0), (0.5, 0.5, 0),
(0, 0, 1.0 / math.sqrt(2)), (0, 0, -1.0 / math.sqrt(2))]
f = [(0, 4, 1), (1, 4, 2), (2, 4, 3), (3, 4, 0), (0, 5, 1), (1, 5, 2),
(2, 5, 3), (3, 5, 0)]
r = 0.0
self.system = init.read_snapshot(self.snapshot)
self.mc = hpmc.integrate.polyhedron(seed=10)
self.mc.shape_param.set('A', vertices=v, faces=f, sweep_radius=r)
diff = (np.array(v) -
np.array(self.mc.shape_param['A'].vertices)).flatten()
self.assertAlmostEqual(diff.dot(diff), 0)
diff = (np.array(f) -
np.array(self.mc.shape_param['A'].faces)).flatten()
self.assertAlmostEqual(diff.dot(diff), 0)
self.assertAlmostEqual(self.mc.shape_param['A'].sweep_radius, r)
del self.mc
del self.system
context.initialize()
# convex_polyhedron
v = [(1, 1, 1), (1, -1, 1), (-1, -1, 1), (-1, 1, 1), (1, 1, -1),
(1, -1, -1), (-1, -1, -1), (-1, 1, -1)]
self.system = init.read_snapshot(self.snapshot)
self.mc = hpmc.integrate.convex_polyhedron(seed=2398, d=0.1, a=0.1)
self.mc.shape_param.set('A', vertices=v)
diff = (np.array(v) -
np.array(self.mc.shape_param['A'].vertices)).flatten()
self.assertAlmostEqual(diff.dot(diff), 0)
del self.mc
del self.system
context.initialize()
# convex_spheropolyhedron
v = [(1, 1, 1), (1, -1, 1), (-1, -1, 1), (-1, 1, 1), (1, 1, -1),
(1, -1, -1), (-1, -1, -1), (-1, 1, -1)]
r = 0.1234
self.system = init.read_snapshot(self.snapshot)
self.mc = hpmc.integrate.convex_spheropolyhedron(seed=2398,
d=0.1,
a=0.1)
self.mc.shape_param.set('A', vertices=v, sweep_radius=r)
diff = (np.array(v) -
np.array(self.mc.shape_param['A'].vertices)).flatten()
self.assertAlmostEqual(diff.dot(diff), 0)
self.assertAlmostEqual(self.mc.shape_param['A'].sweep_radius, r)
del self.mc
del self.system
context.initialize()
# faceted_sphere
v = [(-1, -1, -1), (-1, -1, 1), (-1, 1, -1), (-1, 1, 1), (1, -1, -1),
(1, -1, 1), (1, 1, -1), (1, 1, 1)]
offs = [-1] * 6
norms = [(-1, 0, 0), (1, 0, 0), (
0,
1,
0,
), (0, -1, 0), (0, 0, 1), (0, 0, -1)]
diam = 2
orig = (0, 0, 0)
self.system = init.read_snapshot(self.snapshot)
self.mc = hpmc.integrate.faceted_sphere(seed=10)
self.mc.shape_param.set('A',
normals=norms,
offsets=offs,
vertices=v,
diameter=diam,
origin=orig)
diff = (np.array(v) -
np.array(self.mc.shape_param['A'].vertices)).flatten()
self.assertAlmostEqual(diff.dot(diff), 0)
diff = (np.array(offs) -
np.array(self.mc.shape_param['A'].offsets)).flatten()
self.assertAlmostEqual(diff.dot(diff), 0)
diff = (np.array(norms) -
np.array(self.mc.shape_param['A'].normals)).flatten()
self.assertAlmostEqual(diff.dot(diff), 0)
diff = (np.array(orig) -
np.array(self.mc.shape_param['A'].origin)).flatten()
self.assertAlmostEqual(diff.dot(diff), 0)
self.assertAlmostEqual(self.mc.shape_param['A'].diameter, diam)
del self.mc
del self.system
context.initialize()
# sphinx
# GPU Sphinx is not built on most the time
if not hoomd.context.current.device.cpp_exec_conf.isCUDAEnabled():
cent = [(0, 0, 0), (0, 0, 1.15), (0, 0, -1.15)]
diams = [2, -2.2, -2.2]
self.system = init.read_snapshot(self.snapshot)
self.mc = hpmc.integrate.sphinx(seed=10)
self.mc.shape_param.set('A', diameters=diams, centers=cent)
diff = (np.array(cent) -
np.array(self.mc.shape_param['A'].centers)).flatten()
self.assertAlmostEqual(diff.dot(diff), 0)
diff = (np.array(diams) -
np.array(self.mc.shape_param['A'].diameters)).flatten()
self.assertAlmostEqual(diff.dot(diff), 0)
del self.mc
del self.system
context.initialize()
# sphere_union
cent = [(0, 0, 0), (0, 0, 1.15), (0, 0, -1.15)]
diams = [2, 2.2, 1.75]
self.system = init.read_snapshot(self.snapshot)
self.mc = hpmc.integrate.sphere_union(seed=10)
self.mc.shape_param.set('A', diameters=diams, centers=cent)
diff = (np.array(cent) -
np.array(self.mc.shape_param['A'].centers)).flatten()
self.assertAlmostEqual(diff.dot(diff), 0)
for i, m in enumerate(self.mc.shape_param['A'].members):
self.assertAlmostEqual(m.diameter, diams[i])
del self.mc
del self.system
del self.snapshot
context.initialize()
try:
from hoomd import context
import hoomd
except ImportError:
from hoomd_script import context
HOOMD_v1 = True
else:
HOOMD_v1 = False
hoomd.util.quiet_status()
except ImportError:
HOOMD = False
else:
HOOMD = True
if HOOMD:
context.initialize('--mode=cpu')
if not HOOMD_v1:
hoomd.option.set_notice_level(0)
try:
if HOOMD_v1:
from hoomd_plugins import hpmc
else:
from hoomd import hpmc
except ImportError:
HPMC = False
else:
HPMC = True
else:
HPMC = False
def tearDown(self):
context.initialize()
from __future__ import division
from __future__ import print_function
import hoomd
from hoomd import context, data, init
from hoomd import hpmc
import unittest
import numpy as np
import math
context.initialize()
class map_overlaps_test(unittest.TestCase):
def setUp(self):
snap = data.make_snapshot(N=0,box=data.boxdim(Lx = 10, Ly = 10, Lz = 10))
self.system = init.read_snapshot(snap)
self.mc = hpmc.integrate.convex_polyhedron(seed=123)
def tearDown(self):
context.initialize()
def test_single_overlap(self):
# two cubes, with one rotated by 45 degrees around two axes
qi = [1,0,0,0]
#alpha = math.pi/4.0;
#q1 = (math.cos(alpha/2),math.sin(alpha/2),0,0)
#q2 = (math.cos(alpha/2),0,0,math.sin(alpha/2))
def test_lattice(self):
N = 128
latticeq = [[1, 0, 0, 0] for i in range(N)]
k = 10.0
kalt = np.exp(15)
dx2d = np.array([0.1, 0.1, 0.0])
theta = np.pi / 6
eng_check2d = round(N * k * dx2d.dot(dx2d), 3)
dx3d = np.array([0.1, 0.1, 0.1])
eng_check3d = round(N * k * dx3d.dot(dx3d), 3)
dq = np.array([np.cos(theta / 2.0), 0., 0., np.sin(theta / 2)])
ddq = np.array([1., 0., 0., 0.]) - dq
eng_checkq = round(10.0 * k * N * ddq.dot(ddq), 3)
hexuc = hoomd.lattice.hex(a=2.0)
self.system = init.read_snapshot(hexuc.get_snapshot())
self.system.replicate(nx=8, ny=8, nz=1)
self.snapshot2d = self.system.take_snapshot(particles=True)
#data.make_snapshot(N=N, box=data.boxdim(L=L, dimensions=3), particle_types=['A'])
lattice2d = []
if hoomd.comm.get_rank() == 0:
lattice2d = self.snapshot2d.particles.position[:]
self.snapshot2d_s = data.make_snapshot(N=N,
box=self.system.box,
particle_types=['A'])
if hoomd.comm.get_rank() == 0:
self.snapshot2d_s.particles.position[:] = self.snapshot2d.particles.position[:] + dx2d
self.snapshot2d_s.particles.orientation[:] = np.array(
[dq for _ in range(N)])
del self.system
context.initialize()
bccuc = hoomd.lattice.bcc(a=2.0)
self.system = init.read_snapshot(bccuc.get_snapshot())
self.system.replicate(nx=4, ny=4, nz=4)
self.snapshot3d = self.system.take_snapshot(particles=True)
#data.make_snapshot(N=N, box=data.boxdim(L=L, dimensions=3), particle_types=['A'])
lattice3d = []
if hoomd.comm.get_rank() == 0:
lattice3d = self.snapshot3d.particles.position[:]
self.snapshot3d_s = data.make_snapshot(N=N,
box=self.system.box,
particle_types=['A'])
if hoomd.comm.get_rank() == 0:
self.snapshot3d_s.particles.position[:] = self.snapshot3d.particles.position[:] + dx3d
self.snapshot3d_s.particles.orientation[:] = np.array(
[dq for _ in range(N)])
del self.system
context.initialize()
# sphere
print("****************************************")
print("* sphere *")
print("****************************************")
# d = 0.0014284726343172743, p = 0.20123046875
uein = 1.5 # kT
diam = 1.0
self.system = init.read_snapshot(self.snapshot3d)
self.mc = hpmc.integrate.sphere(seed=2398, d=0.0)
self.mc.shape_param.set('A', diameter=diam)
self.run_test(latticep=lattice3d,
latticeq=[],
k=k,
kalt=kalt,
q=0,
qalt=0,
uein=1.5,
snapshot_s=self.snapshot3d_s,
eng_check=eng_check3d,
d=0.001428)
self.tear_down()
# ellipsoid
print("****************************************")
print("* ellipsoid *")
print("****************************************")
# a = 0.00038920117896296716, p = 0.2035860456051452
# d = 0.0014225507698958867, p = 0.19295361127422195
a = 0.5
b = 0.54
c = 0.35
uein = 3.0 # kT
self.system = init.read_snapshot(self.snapshot3d)
self.mc = hpmc.integrate.ellipsoid(seed=2398, d=0.0, a=0.0)
self.mc.shape_param.set('A', a=a, b=b, c=c)
self.run_test(latticep=lattice3d,
latticeq=latticeq,
k=k,
kalt=kalt,
q=k * 10.0,
qalt=kalt * 10.0,
uein=3.0,
snapshot_s=self.snapshot3d_s,
eng_check=(eng_check3d + eng_checkq),
a=0.000389,
d=0.001423)
self.tear_down()
# convex_polygon
print("****************************************")
print("* convex_polygon *")
print("****************************************")
# a = 0.001957745443687172, p = 0.19863574351978172
# d = 0.0017185407622231329, p = 0.2004306126443531
self.system = init.read_snapshot(self.snapshot2d)
v = 0.33 * np.array([(-1, -1), (1, -1), (1, 1), (-1, 1)])
self.mc = hpmc.integrate.convex_polygon(seed=2398, d=0.0, a=0.0)
self.mc.shape_param.set('A', vertices=v)
self.run_test(latticep=lattice2d,
latticeq=latticeq,
k=k,
kalt=kalt,
q=k * 10.0,
qalt=kalt * 10.0,
uein=1.5,
snapshot_s=self.snapshot2d_s,
eng_check=(eng_check2d + eng_checkq),
a=0.001958,
d=0.001719)
self.tear_down()
# convex_spheropolygon
print("****************************************")
print("* convex_spheropolygon *")
print("****************************************")
self.system = init.read_snapshot(self.snapshot2d)
v = 0.33 * np.array([(-1, -1), (1, -1), (1, 1), (-1, 1)])
r = 0.1234
self.mc = hpmc.integrate.convex_spheropolygon(seed=2398, d=0.0, a=0.0)
self.mc.shape_param.set('A', vertices=v, sweep_radius=r)
diff = (np.array(v) -
np.array(self.mc.shape_param['A'].vertices)).flatten()
self.run_test(latticep=lattice2d,
latticeq=latticeq,
k=k,
kalt=kalt,
q=k * 10.0,
qalt=kalt * 10.0,
uein=None,
snapshot_s=self.snapshot2d_s,
eng_check=(eng_check2d + eng_checkq))
self.tear_down()
#simple_polygon
print("****************************************")
print("* simple_polygon *")
print("****************************************")
self.system = init.read_snapshot(self.snapshot2d)
v = 0.33 * np.array([(-1, -1), (1, -1), (1, 1), (-1, 1)])
self.mc = hpmc.integrate.simple_polygon(seed=2398, d=0.0, a=0.0)
self.mc.shape_param.set('A', vertices=v)
self.run_test(latticep=lattice2d,
latticeq=latticeq,
k=k,
kalt=kalt,
q=k * 10.0,
qalt=kalt * 10.0,
uein=None,
snapshot_s=self.snapshot2d_s,
eng_check=(eng_check2d + eng_checkq))
self.tear_down()
# polyhedron
print("****************************************")
print("* polyhedron *")
print("****************************************")
self.system = init.read_snapshot(self.snapshot3d)
v = 0.33 * np.array([(-0.5, -0.5, -0.5), (-0.5, -0.5, 0.5),
(-0.5, 0.5, -0.5), (-0.5, 0.5, 0.5),
(0.5, -0.5, -0.5), (0.5, -0.5, 0.5),
(0.5, 0.5, -0.5), (0.5, 0.5, 0.5)])
f = [(7, 3, 1, 5), (7, 5, 4, 6), (7, 6, 2, 3), (3, 2, 0, 1),
(0, 2, 6, 4), (1, 0, 4, 5)]
r = 0.0
self.mc = hpmc.integrate.polyhedron(seed=10)
self.mc.shape_param.set('A', vertices=v, faces=f, sweep_radius=r)
diff = (np.array(v) -
np.array(self.mc.shape_param['A'].vertices)).flatten()
self.assertAlmostEqual(diff.dot(diff), 0)
diff = (np.array(f) -
np.array(self.mc.shape_param['A'].faces)).flatten()
self.assertAlmostEqual(diff.dot(diff), 0)
self.assertAlmostEqual(self.mc.shape_param['A'].sweep_radius, r)
del self.mc
del self.system
context.initialize()
# convex_polyhedron
print("****************************************")
print("* convex_polyhedron *")
print("****************************************")
#a = 0.00038920117896296716, p = 0.2035860456051452
#d = 0.0014225507698958867, p = 0.19295361127422195
self.system = init.read_snapshot(self.snapshot3d)
v = 0.33 * np.array([(1, 1, 1), (1, -1, 1), (-1, -1, 1), (-1, 1, 1),
(1, 1, -1), (1, -1, -1), (-1, -1, -1),
(-1, 1, -1)])
self.mc = hpmc.integrate.convex_polyhedron(seed=2398, d=0.0, a=0.0)
self.mc.shape_param.set('A', vertices=v)
self.run_test(latticep=lattice3d,
latticeq=latticeq,
k=k,
kalt=kalt,
q=k * 10.0,
qalt=kalt * 10.0,
uein=3.0,
snapshot_s=self.snapshot3d_s,
eng_check=(eng_check3d + eng_checkq),
a=0.0003892,
d=0.00142255)
self.tear_down()
# convex_spheropolyhedron
print("****************************************")
print("* convex_spheropolyhedron *")
print("****************************************")
self.system = init.read_snapshot(self.snapshot3d)
v = 0.33 * np.array([(1, 1, 1), (1, -1, 1), (-1, -1, 1), (-1, 1, 1),
(1, 1, -1), (1, -1, -1), (-1, -1, -1),
(-1, 1, -1)])
r = 0.1234
self.mc = hpmc.integrate.convex_spheropolyhedron(seed=2398,
d=0.0,
a=0.0)
self.mc.shape_param.set('A', vertices=v, sweep_radius=r)
self.run_test(latticep=lattice3d,
latticeq=latticeq,
k=k,
kalt=kalt,
q=k * 10.0,
qalt=kalt * 10.0,
uein=None,
snapshot_s=self.snapshot3d_s,
eng_check=(eng_check3d + eng_checkq))
self.tear_down()
# faceted_sphere
print("****************************************")
print("* faceted_sphere *")
print("****************************************")
self.system = init.read_snapshot(self.snapshot3d)
v = 0.33 * np.array([(-1, -1, -1), (-1, -1, 1), (-1, 1, -1),
(-1, 1, 1), (1, -1, -1), (1, -1, 1), (1, 1, -1),
(1, 1, 1)])
offs = [-1] * 6
norms = [(-1, 0, 0), (1, 0, 0), (
0,
1,
0,
), (0, -1, 0), (0, 0, 1), (0, 0, -1)]
diam = 1.0
orig = (0, 0, 0)
self.mc = hpmc.integrate.faceted_sphere(seed=10, d=0.0, a=0.0)
self.mc.shape_param.set('A',
normals=norms,
offsets=offs,
vertices=v,
diameter=diam,
origin=orig)
self.run_test(latticep=lattice3d,
latticeq=latticeq,
k=k,
kalt=kalt,
q=k * 10.0,
qalt=kalt * 10.0,
uein=None,
snapshot_s=self.snapshot3d_s,
eng_check=(eng_check3d + eng_checkq))
self.tear_down()
# sphinx
print("****************************************")
print("* sphinx *")
print("****************************************")
self.system = init.read_snapshot(self.snapshot3d)
cent = [(0, 0, 0), (0, 0, 1.15), (0, 0, -1.15)]
diams = [1, -1.2, -1.2]
self.mc = hpmc.integrate.sphinx(seed=10, d=0.0, a=0.0)
self.mc.shape_param.set('A', diameters=diams, centers=cent)
self.run_test(latticep=lattice3d,
latticeq=latticeq,
k=k,
kalt=kalt,
q=k * 10.0,
qalt=kalt * 10.0,
uein=None,
snapshot_s=self.snapshot3d_s,
eng_check=(eng_check3d + eng_checkq))
self.tear_down()
# sphere_union
print("****************************************")
print("* sphere_union *")
print("****************************************")
self.system = init.read_snapshot(self.snapshot3d)
cent = [(0, 0, 0), (0, 0, 0.15), (0, 0, -0.15)]
diams = [1, 1, 1]
self.mc = hpmc.integrate.sphere_union(seed=10, d=0.0, a=0.0)
self.mc.shape_param.set('A', diameters=diams, centers=cent)
self.run_test(latticep=lattice3d,
latticeq=latticeq,
k=k,
kalt=kalt,
q=k * 10.0,
qalt=kalt * 10.0,
uein=None,
snapshot_s=self.snapshot3d_s,
eng_check=(eng_check3d + eng_checkq))
self.tear_down()
def tear_down(self):
del self.gsd
del self.mc
del self.system
context.initialize()
def tearDown(self):
context.initialize()
from __future__ import division
from __future__ import print_function
import hoomd
from hoomd import context, data, init
from hoomd import hpmc
import unittest
import os
import numpy as np
import itertools
import sys
context.initialize()
def create_empty(**kwargs):
snap = data.make_snapshot(**kwargs)
return init.read_snapshot(snap)
class hpmc_gsd_state(unittest.TestCase):
def setUp(self):
self._name = None
hexuc = hoomd.lattice.hex(a=2.0)
system = init.read_snapshot(hexuc.get_snapshot())
system.replicate(nx=8, ny=8, nz=1)
self.snapshot2d = system.take_snapshot(particles=True)
context.initialize()
bccuc = hoomd.lattice.bcc(a=4.0)
system = init.read_snapshot(bccuc.get_snapshot())
def tearDown(self):
del self.logger
del self.patch
context.initialize()
context.current.device.gpu_error_checking = True
def tear_down(self):
del self.mc
del self.system
del self.lattice
del self.remove_drift
context.initialize()
def tearDown(self):
del self.logger
del self.patch
context.initialize()
def tear_down(self):
del self.mc
del self.system
del self.lattice
del self.remove_drift
context.initialize()
def test_access(self):
N=2
L=10
context.initialize()
self.snapshot = data.make_snapshot(N=N, box=data.boxdim(L=L, dimensions=2), particle_types=['A'])
# sphere
diam = 1.125;
self.system = init.read_snapshot(self.snapshot)
self.mc = hpmc.integrate.sphere(seed=2398, d=0.0)
self.mc.shape_param.set('A', diameter=diam)
self.assertAlmostEqual(self.mc.shape_param['A'].diameter, diam);
del self.mc
del self.system
context.initialize()
# ellipsoid
a = 1.125;
b = 0.238;
c = 2.25;
self.system = init.read_snapshot(self.snapshot)
self.mc = hpmc.integrate.ellipsoid(seed=2398, d=0.0)
self.mc.shape_param.set('A', a=a, b=b, c=c)
self.assertAlmostEqual(self.mc.shape_param['A'].a, a);
self.assertAlmostEqual(self.mc.shape_param['A'].b, b);
self.assertAlmostEqual(self.mc.shape_param['A'].c, c);
del self.mc
del self.system
context.initialize()
# convex_polygon
v = [(-1,-1), (1,-1), (1,1), (-1,1)];
self.system = init.read_snapshot(self.snapshot)
self.mc = hpmc.integrate.convex_polygon(seed=2398, d=0.1, a=0.1)
self.mc.shape_param.set('A', vertices=v)
diff = (np.array(v) - np.array(self.mc.shape_param['A'].vertices)).flatten();
self.assertAlmostEqual(diff.dot(diff), 0);
del self.mc
del self.system
context.initialize()
# convex_spheropolygon
v = [(-1,-1), (1,-1), (1,1), (-1,1)];
r = 0.1234;
self.system = init.read_snapshot(self.snapshot)
self.mc = hpmc.integrate.convex_spheropolygon(seed=2398, d=0.1, a=0.1)
self.mc.shape_param.set('A', vertices=v, sweep_radius=r)
diff = (np.array(v) - np.array(self.mc.shape_param['A'].vertices)).flatten();
self.assertAlmostEqual(diff.dot(diff), 0);
self.assertAlmostEqual(self.mc.shape_param['A'].sweep_radius, r);
del self.mc
del self.system
context.initialize()
#simple_polygon
v = [(-1,-1), (1,-1), (1,1), (-1,1)];
self.system = init.read_snapshot(self.snapshot)
self.mc = hpmc.integrate.simple_polygon(seed=2398, d=0.1, a=0.1)
self.mc.shape_param.set('A', vertices=v)
diff = (np.array(v) - np.array(self.mc.shape_param['A'].vertices)).flatten();
self.assertAlmostEqual(diff.dot(diff), 0);
del self.mc
del self.system
context.initialize()
# polyhedron
import math
v = [(-0.5, -0.5, 0), (-0.5, 0.5, 0), (0.5, -0.5, 0), (0.5, 0.5, 0), (0,0, 1.0/math.sqrt(2)),(0,0,-1.0/math.sqrt(2))];
f = [(0,4,1),(1,4,2),(2,4,3),(3,4,0),(0,5,1),(1,5,2),(2,5,3),(3,5,0)]
r = 0.0;
self.system = init.read_snapshot(self.snapshot)
self.mc = hpmc.integrate.polyhedron(seed=10);
self.mc.shape_param.set('A', vertices=v, faces =f, sweep_radius=r);
diff = (np.array(v) - np.array(self.mc.shape_param['A'].vertices)).flatten();
self.assertAlmostEqual(diff.dot(diff), 0);
diff = (np.array(f) - np.array(self.mc.shape_param['A'].faces)).flatten();
self.assertAlmostEqual(diff.dot(diff), 0);
self.assertAlmostEqual(self.mc.shape_param['A'].sweep_radius, r);
del self.mc
del self.system
context.initialize()
# convex_polyhedron
v = [(1,1,1), (1,-1,1), (-1,-1,1), (-1,1,1),(1,1,-1), (1,-1,-1), (-1,-1,-1), (-1,1,-1)];
self.system = init.read_snapshot(self.snapshot)
self.mc = hpmc.integrate.convex_polyhedron(seed=2398, d=0.1, a=0.1)
self.mc.shape_param.set('A', vertices=v)
diff = (np.array(v) - np.array(self.mc.shape_param['A'].vertices)).flatten();
self.assertAlmostEqual(diff.dot(diff), 0);
del self.mc
del self.system
context.initialize()
# convex_spheropolyhedron
v = [(1,1,1), (1,-1,1), (-1,-1,1), (-1,1,1),(1,1,-1), (1,-1,-1), (-1,-1,-1), (-1,1,-1)];
r = 0.1234;
self.system = init.read_snapshot(self.snapshot)
self.mc = hpmc.integrate.convex_spheropolyhedron(seed=2398, d=0.1, a=0.1)
self.mc.shape_param.set('A', vertices=v, sweep_radius=r)
diff = (np.array(v) - np.array(self.mc.shape_param['A'].vertices)).flatten();
self.assertAlmostEqual(diff.dot(diff), 0);
self.assertAlmostEqual(self.mc.shape_param['A'].sweep_radius, r);
del self.mc
del self.system
context.initialize()
# faceted_sphere
v = [(-1,-1,-1),(-1,-1,1),(-1,1,-1),(-1,1,1),(1,-1,-1),(1,-1,1),(1,1,-1),(1,1,1)];
offs = [-1]*6;
norms =[(-1,0,0), (1,0,0), (0,1,0,), (0,-1,0), (0,0,1), (0,0,-1)];
diam = 2;
orig = (0,0,0);
self.system = init.read_snapshot(self.snapshot)
self.mc = hpmc.integrate.faceted_sphere(seed=10);
self.mc.shape_param.set('A', normals=norms,
offsets=offs,
vertices=v,
diameter=diam,
origin=orig);
diff = (np.array(v) - np.array(self.mc.shape_param['A'].vertices)).flatten();
self.assertAlmostEqual(diff.dot(diff), 0);
diff = (np.array(offs) - np.array(self.mc.shape_param['A'].offsets)).flatten();
self.assertAlmostEqual(diff.dot(diff), 0);
diff = (np.array(norms) - np.array(self.mc.shape_param['A'].normals)).flatten();
self.assertAlmostEqual(diff.dot(diff), 0);
diff = (np.array(orig) - np.array(self.mc.shape_param['A'].origin)).flatten();
self.assertAlmostEqual(diff.dot(diff), 0);
self.assertAlmostEqual(self.mc.shape_param['A'].diameter, diam);
del self.mc
del self.system
context.initialize()
# sphinx
# GPU Sphinx is not built on most the time
if not hoomd.context.exec_conf.isCUDAEnabled():
cent = [(0,0,0), (0,0,1.15), (0,0,-1.15)]
diams = [2,-2.2,-2.2];
self.system = init.read_snapshot(self.snapshot)
self.mc = hpmc.integrate.sphinx(seed=10);
self.mc.shape_param.set('A', diameters=diams, centers=cent);
diff = (np.array(cent) - np.array(self.mc.shape_param['A'].centers)).flatten();
self.assertAlmostEqual(diff.dot(diff), 0);
diff = (np.array(diams) - np.array(self.mc.shape_param['A'].diameters)).flatten();
self.assertAlmostEqual(diff.dot(diff), 0);
del self.mc
del self.system
context.initialize()
# sphere_union
cent = [(0,0,0), (0,0,1.15), (0,0,-1.15)]
diams = [2,2.2,1.75];
self.system = init.read_snapshot(self.snapshot)
self.mc = hpmc.integrate.sphere_union(seed=10);
self.mc.shape_param.set('A', diameters=diams, centers=cent);
diff = (np.array(cent) - np.array(self.mc.shape_param['A'].centers)).flatten();
self.assertAlmostEqual(diff.dot(diff), 0);
for i,m in enumerate(self.mc.shape_param['A'].members):
self.assertAlmostEqual(m.diameter, diams[i]);
del self.mc
del self.system
del self.snapshot
context.initialize()
def test_lattice(self):
N=128;
latticeq = [[1,0,0,0] for i in range(N)];
k = 10.0;
kalt = np.exp(15);
dx2d = np.array([0.1, 0.1, 0.0]);
theta = np.pi/6;
eng_check2d = round(N*k*dx2d.dot(dx2d), 3);
dx3d = np.array([0.1, 0.1, 0.1]);
eng_check3d = round(N*k*dx3d.dot(dx3d), 3);
dq = np.array([np.cos(theta/2.0),0.,0.,np.sin(theta/2)])
ddq = np.array([1.,0.,0.,0.]) - dq;
eng_checkq = round(10.0*k*N*ddq.dot(ddq), 3);
hexuc = hoomd.lattice.hex(a=2.0);
self.system = init.read_snapshot(hexuc.get_snapshot());
self.system.replicate(nx=8, ny=8, nz=1);
self.snapshot2d = self.system.take_snapshot(particles=True); #data.make_snapshot(N=N, box=data.boxdim(L=L, dimensions=3), particle_types=['A'])
lattice2d = [];
if hoomd.comm.get_rank() == 0:
lattice2d = self.snapshot2d.particles.position[:];
self.snapshot2d_s = data.make_snapshot(N=N, box=self.system.box, particle_types=['A']);
if hoomd.comm.get_rank() == 0:
self.snapshot2d_s.particles.position[:] = self.snapshot2d.particles.position[:]+dx2d;
self.snapshot2d_s.particles.orientation[:] = np.array([dq for _ in range(N)]);
del self.system
context.initialize();
bccuc = hoomd.lattice.bcc(a=2.0);
self.system = init.read_snapshot(bccuc.get_snapshot());
self.system.replicate(nx=4, ny=4, nz=4);
self.snapshot3d = self.system.take_snapshot(particles=True); #data.make_snapshot(N=N, box=data.boxdim(L=L, dimensions=3), particle_types=['A'])
lattice3d = [];
if hoomd.comm.get_rank() == 0:
lattice3d = self.snapshot3d.particles.position[:];
self.snapshot3d_s = data.make_snapshot(N=N, box=self.system.box, particle_types=['A']);
if hoomd.comm.get_rank() == 0:
self.snapshot3d_s.particles.position[:] = self.snapshot3d.particles.position[:]+dx3d;
self.snapshot3d_s.particles.orientation[:] = np.array([dq for _ in range(N)]);
del self.system
context.initialize();
# sphere
print("****************************************")
print("* sphere *")
print("****************************************")
# d = 0.0014284726343172743, p = 0.20123046875
uein = 1.5 # kT
diam = 1.0;
self.system = init.read_snapshot(self.snapshot3d)
self.mc = hpmc.integrate.sphere(seed=2398, d=0.0)
self.mc.shape_param.set('A', diameter=diam)
self.run_test(latticep=lattice3d, latticeq=[], k=k, kalt=kalt, q=0, qalt=0, uein=1.5, snapshot_s=self.snapshot3d_s, eng_check=eng_check3d, d=0.001428 );
self.tear_down()
# ellipsoid
print("****************************************")
print("* ellipsoid *")
print("****************************************")
# a = 0.00038920117896296716, p = 0.2035860456051452
# d = 0.0014225507698958867, p = 0.19295361127422195
a = 0.5;
b = 0.54;
c = 0.35;
uein = 3.0 # kT
self.system = init.read_snapshot(self.snapshot3d)
self.mc = hpmc.integrate.ellipsoid(seed=2398, d=0.0, a=0.0)
self.mc.shape_param.set('A', a=a, b=b, c=c)
self.run_test(latticep=lattice3d, latticeq=latticeq, k=k, kalt=kalt, q=k*10.0, qalt=kalt*10.0, uein=3.0, snapshot_s=self.snapshot3d_s, eng_check=(eng_check3d+eng_checkq), a = 0.000389, d = 0.001423);
self.tear_down()
# convex_polygon
print("****************************************")
print("* convex_polygon *")
print("****************************************")
# a = 0.001957745443687172, p = 0.19863574351978172
# d = 0.0017185407622231329, p = 0.2004306126443531
self.system = init.read_snapshot(self.snapshot2d)
v = 0.33*np.array([(-1,-1), (1,-1), (1,1), (-1,1)]);
self.mc = hpmc.integrate.convex_polygon(seed=2398, d=0.0, a=0.0)
self.mc.shape_param.set('A', vertices=v)
self.run_test(latticep=lattice2d, latticeq=latticeq, k=k, kalt=kalt, q=k*10.0, qalt=kalt*10.0, uein=1.5, snapshot_s=self.snapshot2d_s, eng_check=(eng_check2d+eng_checkq), a = 0.001958, d = 0.001719);
self.tear_down()
# convex_spheropolygon
print("****************************************")
print("* convex_spheropolygon *")
print("****************************************")
self.system = init.read_snapshot(self.snapshot2d)
v = 0.33*np.array([(-1,-1), (1,-1), (1,1), (-1,1)]);
r = 0.1234;
self.mc = hpmc.integrate.convex_spheropolygon(seed=2398, d=0.0, a=0.0)
self.mc.shape_param.set('A', vertices=v, sweep_radius=r)
diff = (np.array(v) - np.array(self.mc.shape_param['A'].vertices)).flatten();
self.run_test(latticep=lattice2d, latticeq=latticeq, k=k, kalt=kalt, q=k*10.0, qalt=kalt*10.0, uein=None, snapshot_s=self.snapshot2d_s, eng_check=(eng_check2d+eng_checkq));
self.tear_down()
#simple_polygon
print("****************************************")
print("* simple_polygon *")
print("****************************************")
self.system = init.read_snapshot(self.snapshot2d)
v = 0.33*np.array([(-1,-1), (1,-1), (1,1), (-1,1)]);
self.mc = hpmc.integrate.simple_polygon(seed=2398, d=0.0, a=0.0)
self.mc.shape_param.set('A', vertices=v)
self.run_test(latticep=lattice2d, latticeq=latticeq, k=k, kalt=kalt, q=k*10.0, qalt=kalt*10.0, uein=None, snapshot_s=self.snapshot2d_s, eng_check=(eng_check2d+eng_checkq));
self.tear_down()
# polyhedron
print("****************************************")
print("* polyhedron *")
print("****************************************")
self.system = init.read_snapshot(self.snapshot3d)
v = 0.33*np.array([(-0.5, -0.5, -0.5), (-0.5, -0.5, 0.5), (-0.5, 0.5, -0.5), (-0.5, 0.5, 0.5), (0.5, -0.5, -0.5), (0.5, -0.5, 0.5), (0.5, 0.5, -0.5), (0.5, 0.5, 0.5)]);
f = [(7, 3, 1, 5), (7, 5, 4, 6), (7, 6, 2, 3), (3, 2, 0, 1), (0, 2, 6, 4), (1, 0, 4, 5)];
r = 0.0;
self.mc = hpmc.integrate.polyhedron(seed=10);
self.mc.shape_param.set('A', vertices=v, faces =f, sweep_radius=r);
diff = (np.array(v) - np.array(self.mc.shape_param['A'].vertices)).flatten();
self.assertAlmostEqual(diff.dot(diff), 0);
diff = (np.array(f) - np.array(self.mc.shape_param['A'].faces)).flatten();
self.assertAlmostEqual(diff.dot(diff), 0);
self.assertAlmostEqual(self.mc.shape_param['A'].sweep_radius, r);
del self.mc
del self.system
context.initialize()
# convex_polyhedron
print("****************************************")
print("* convex_polyhedron *")
print("****************************************")
#a = 0.00038920117896296716, p = 0.2035860456051452
#d = 0.0014225507698958867, p = 0.19295361127422195
self.system = init.read_snapshot(self.snapshot3d)
v = 0.33*np.array([(1,1,1), (1,-1,1), (-1,-1,1), (-1,1,1),(1,1,-1), (1,-1,-1), (-1,-1,-1), (-1,1,-1)]);
self.mc = hpmc.integrate.convex_polyhedron(seed=2398, d=0.0, a=0.0)
self.mc.shape_param.set('A', vertices=v)
self.run_test(latticep=lattice3d, latticeq=latticeq, k=k, kalt=kalt, q=k*10.0, qalt=kalt*10.0, uein=3.0, snapshot_s=self.snapshot3d_s, eng_check=(eng_check3d+eng_checkq), a = 0.0003892, d = 0.00142255);
self.tear_down()
# convex_spheropolyhedron
print("****************************************")
print("* convex_spheropolyhedron *")
print("****************************************")
self.system = init.read_snapshot(self.snapshot3d)
v = 0.33*np.array([(1,1,1), (1,-1,1), (-1,-1,1), (-1,1,1),(1,1,-1), (1,-1,-1), (-1,-1,-1), (-1,1,-1)]);
r = 0.1234;
self.mc = hpmc.integrate.convex_spheropolyhedron(seed=2398, d=0.0, a=0.0)
self.mc.shape_param.set('A', vertices=v, sweep_radius=r)
self.run_test(latticep=lattice3d, latticeq=latticeq, k=k, kalt=kalt, q=k*10.0, qalt=kalt*10.0, uein=None, snapshot_s=self.snapshot3d_s, eng_check=(eng_check3d+eng_checkq));
self.tear_down()
# faceted_sphere
print("****************************************")
print("* faceted_sphere *")
print("****************************************")
self.system = init.read_snapshot(self.snapshot3d)
v = 0.33*np.array([(-1,-1,-1),(-1,-1,1),(-1,1,-1),(-1,1,1),(1,-1,-1),(1,-1,1),(1,1,-1),(1,1,1)]);
offs = [-1]*6;
norms =[(-1,0,0), (1,0,0), (0,1,0,), (0,-1,0), (0,0,1), (0,0,-1)];
diam = 1.0;
orig = (0,0,0);
self.mc = hpmc.integrate.faceted_sphere(seed=10, d=0.0, a=0.0);
self.mc.shape_param.set('A', normals=norms,
offsets=offs,
vertices=v,
diameter=diam,
origin=orig);
self.run_test(latticep=lattice3d, latticeq=latticeq, k=k, kalt=kalt, q=k*10.0, qalt=kalt*10.0, uein=None, snapshot_s=self.snapshot3d_s, eng_check=(eng_check3d+eng_checkq));
self.tear_down()
# sphinx
print("****************************************")
print("* sphinx *")
print("****************************************")
self.system = init.read_snapshot(self.snapshot3d)
cent = [(0,0,0), (0,0,1.15), (0,0,-1.15)]
diams = [1,-1.2,-1.2];
self.mc = hpmc.integrate.sphinx(seed=10, d=0.0, a=0.0);
self.mc.shape_param.set('A', diameters=diams, centers=cent);
self.run_test(latticep=lattice3d, latticeq=latticeq, k=k, kalt=kalt, q=k*10.0, qalt=kalt*10.0, uein=None, snapshot_s=self.snapshot3d_s, eng_check=(eng_check3d+eng_checkq));
self.tear_down()
# sphere_union
print("****************************************")
print("* sphere_union *")
print("****************************************")
self.system = init.read_snapshot(self.snapshot3d)
cent = [(0,0,0), (0,0,0.15), (0,0,-0.15)]
diams = [1,1,1];
self.mc = hpmc.integrate.sphere_union(seed=10, d=0.0, a=0.0);
self.mc.shape_param.set('A', diameters=diams, centers=cent);
self.run_test(latticep=lattice3d, latticeq=latticeq, k=k, kalt=kalt, q=k*10.0, qalt=kalt*10.0, uein=None, snapshot_s=self.snapshot3d_s, eng_check=(eng_check3d+eng_checkq));
self.tear_down()
def tear_down(self):
del self.gsd
del self.mc
del self.system
context.initialize()
for name, shapedef in frame.shapedef.items():
shapedef.color = None
self.assertEqual(frame0, frame1)
def test_hpmc_dialect(self):
self.read_write_injavis(garnett.samples.POS_HPMC)
def test_incsim_dialect(self):
self.read_write_injavis(garnett.samples.POS_INCSIM)
def test_monotype_dialect(self):
self.read_write_injavis(garnett.samples.POS_MONOTYPE)
def test_injavis_dialect(self):
self.read_write_injavis(garnett.samples.POS_INJAVIS)
def test_hpmc_dialect_2d(self):
self.read_write_injavis(garnett.samples.POS_HPMC_2D)
def test_incsim_dialect_2d(self):
self.read_write_injavis(garnett.samples.POS_INCSIM_2D)
def test_monotype_dialect_2d(self):
self.read_write_injavis(garnett.samples.POS_MONOTYPE_2D)
if __name__ == '__main__':
context.initialize("--mode=cpu")
hoomd.option.set_notice_level(0)
unittest.main()
