def test_tribend(self):
self.system.actors.clear()
# two triangles with bending interaction
# move nodes, should relax back
system = self.system
system.virtual_sites = VirtualSitesInertialessTracers()
system.part.clear()
# Add four particles
system.part.add(id=0, pos=[5, 5, 5], virtual=1)
system.part.add(id=1, pos=[5, 5, 6], virtual=1)
system.part.add(id=2, pos=[5, 6, 6], virtual=1)
system.part.add(id=3, pos=[5, 6, 5], virtual=1)
# Add first triel, weak modulus
from espressomd.interactions import IBM_Triel
tri1 = IBM_Triel(
ind1=0, ind2=1, ind3=2, elasticLaw="Skalak", k1=0.1, k2=0, maxDist=2.4)
system.bonded_inter.add(tri1)
system.part[0].add_bond((tri1, 1, 2))
# Add second triel
tri2 = IBM_Triel(
ind1=0, ind2=2, ind3=3, elasticLaw="Skalak", k1=10, k2=0, maxDist=2.4)
system.bonded_inter.add(tri2)
system.part[0].add_bond((tri2, 2, 3))
# Add bending
from espressomd.interactions import IBM_Tribend
tribend = IBM_Tribend(
ind1=0, ind2=1, ind3=2, ind4=3, kb=1, refShape="Initial")
system.bonded_inter.add(tribend)
system.part[0].add_bond((tribend, 1, 2, 3))
# twist
system.part[1].pos = [5.2, 5, 6]
self.reset_lb()
# Perform integration
last_angle = self.compute_angle()
for i in range(6):
system.integrator.run(430)
angle = self.compute_angle()
self.assertLess(angle, last_angle)
last_angle = angle
self.assertLess(angle, 0.03)
def AddSoft(system, comX, comY, comZ, k1, k2):
# currently only works for ONE SINGLE soft object
# open file and add nodes
with open("tables/softPositions", "r") as fp:
numPoints = int(fp.readline())
print("Found {} nodes".format(numPoints))
# actual add
for i in range(0, numPoints):
line = str.split(fp.readline())
X = float(line[0]) + comX
Y = float(line[1]) + comY
Z = float(line[2]) + comZ
# print X, Y, Z
system.part.add(id=i, pos=[X, Y, Z], virtual=1)
# triangles
from espressomd.interactions import IBM_Triel
with open("tables/softTriangles", "r") as fp:
numTri = int(fp.readline())
print("Found {} triangles".format(numTri))
# actual add
for i in range(0, numTri):
line = str.split(fp.readline())
id1 = int(line[0])
id2 = int(line[1])
id3 = int(line[2])
tri = IBM_Triel(ind1=id1, ind2=id2, ind3=id3,
elasticLaw="Skalak", k1=k1, k2=k2, maxDist=5)
system.bonded_inter.add(tri)
system.part[id1].add_bond((tri, id2, id3))
def test_triel(self):
self.system.actors.clear()
system = self.system
system.virtual_sites = VirtualSitesInertialessTracers()
system.virtual_sites = VirtualSitesInertialessTracers()
system.part.clear()
# Add particles: 0-2 are non-bonded, 3-5 are weakly bonded, 6-8 are
# strongly bonded
system.part.add(id=0, pos=[5, 5, 5], virtual=True)
system.part.add(id=1, pos=[5, 5, 6], virtual=True)
system.part.add(id=2, pos=[5, 6, 6], virtual=True)
system.part.add(id=3, pos=[2, 5, 5], virtual=True)
system.part.add(id=4, pos=[2, 5, 6], virtual=True)
system.part.add(id=5, pos=[2, 6, 6], virtual=True)
system.part.add(id=6, pos=[4, 7, 7], virtual=True)
system.part.add(id=7, pos=[4, 7, 8], virtual=True)
system.part.add(id=8, pos=[4, 8, 8], virtual=True)
# Add triel, weak modulus for 3-5
from espressomd.interactions import IBM_Triel
triWeak = IBM_Triel(ind1=3,
ind2=4,
ind3=5,
elasticLaw="Skalak",
k1=5,
k2=0,
maxDist=2.4)
system.bonded_inter.add(triWeak)
system.part[3].add_bond((triWeak, 4, 5))
# Add triel, strong modulus for 6-8
triStrong = IBM_Triel(ind1=6,
ind2=7,
ind3=8,
elasticLaw="Skalak",
k1=15,
k2=0,
maxDist=2.4)
system.bonded_inter.add(triStrong)
system.part[6].add_bond((triStrong, 7, 8))
self.reset_lb(ext_force_density=[0.1, 0, 0])
# Perform integration
system.integrator.run(4500)
# For the cpu variant, check particle velocities
if isinstance(self.lbf, lb.LBFluid): # as opposed to LBFluidGPU
for p in system.part:
np.testing.assert_allclose(
np.copy(p.v),
np.copy(self.lbf.get_interpolated_velocity(p.pos)),
atol=2E-2)
# get new shapes
dist1non = np.linalg.norm(
np.array(system.part[1].pos - system.part[0].pos))
dist2non = np.linalg.norm(
np.array(system.part[2].pos - system.part[0].pos))
dist1weak = np.linalg.norm(
np.array(system.part[3].pos - system.part[4].pos))
dist2weak = np.linalg.norm(
np.array(system.part[3].pos - system.part[5].pos))
dist1strong = np.linalg.norm(
np.array(system.part[6].pos - system.part[7].pos))
dist2strong = np.linalg.norm(
np.array(system.part[6].pos - system.part[8].pos))
print("** Distances: non-bonded, weak, strong, expected")
print(
str(dist1non) + " " + str(dist1weak) + " " +
str(dist1strong) + " 1")
print(
str(dist2non) + " " + str(dist2weak) + " " +
str(dist2strong) + " 1.414")
# test:
# non-bonded should move apart by the flow (control group)
# weakly-bonded should stretch somewhat
# strongly-bonded should basically not stretch
self.assertGreater(dist1non, 1.5)
self.assertAlmostEqual(dist1weak, 1, delta=0.2)
self.assertAlmostEqual(dist1strong, 1, delta=0.04)
self.assertGreater(dist2non, 2)
self.assertAlmostEqual(dist2weak, np.sqrt(2), delta=0.3)
self.assertAlmostEqual(dist2strong, np.sqrt(2), delta=0.1)
def test_tribend(self):
# two triangles with bending interaction
# move nodes, should relax back
system = self.system
system.virtual_sites = VirtualSitesInertialessTracers()
self.lbf.set_params(ext_force_density=(0.0, 0., 0.))
self.stop_fluid()
system.part.clear()
## Add four particles
system.part.add(id=0, pos=[5, 5, 5], virtual=1)
system.part.add(id=1, pos=[5, 5, 6], virtual=1)
system.part.add(id=2, pos=[5, 6, 6], virtual=1)
system.part.add(id=3, pos=[5, 6, 5], virtual=1)
## Add first triel, weak modulus
from espressomd.interactions import IBM_Triel
tri1 = IBM_Triel(ind1=0,
ind2=1,
ind3=2,
elasticLaw="Skalak",
k1=0.1,
k2=0,
maxDist=2.4)
system.bonded_inter.add(tri1)
system.part[0].add_bond((tri1, 1, 2))
## Add second triel
tri2 = IBM_Triel(ind1=0,
ind2=2,
ind3=3,
elasticLaw="Skalak",
k1=10,
k2=0,
maxDist=2.4)
system.bonded_inter.add(tri2)
system.part[0].add_bond((tri2, 2, 3))
## Add bending
from espressomd.interactions import IBM_Tribend
tribend = IBM_Tribend(ind1=0,
ind2=1,
ind3=2,
ind4=3,
kb=1,
refShape="Initial")
system.bonded_inter.add(tribend)
system.part[0].add_bond((tribend, 1, 2, 3))
## output before
print("Angle before twisting: " + str(self.compute_angle()))
## twist
system.part[1].pos = [5.2, 5, 6]
## output after
print("Angle after twisting: " + str(self.compute_angle()))
## Perform integrat[ion
last_angle = self.compute_angle()
for i in range(8):
system.integrator.run(500)
angle = self.compute_angle()
print("Angle after relaxation: ", angle)
self.assertLess(angle, last_angle)
last_angle = angle
self.assertLess(angle, 0.03)