def test_constrain_rg(self):
# set up normal domain decomposition
nodeGrid = espressopp.tools.decomp.nodeGrid(
espressopp.MPI.COMM_WORLD.size, self.box, rc=1.5, skin=0.3)
cellGrid = espressopp.tools.decomp.cellGrid(self.box,
nodeGrid,
rc=1.5,
skin=0.3)
self.system.storage = espressopp.storage.DomainDecomposition(
self.system, nodeGrid, cellGrid)
# add some particles (normal, coarse-grained particles only)
particle_list = [
(1, 1, 0, espressopp.Real3D(4.0, 5.0, 5.0), 1.0, 0, 1.),
(2, 1, 0, espressopp.Real3D(4.5, 5.866, 5.0), 1.0, 0, 1.),
(3, 1, 0, espressopp.Real3D(5.0, 5.0, 5.0), 1.0, 0, 1.),
(4, 1, 0, espressopp.Real3D(5.5, 4.134, 5.0), 1.0, 0, 1.),
(5, 1, 0, espressopp.Real3D(6.0, 5.0, 5.0), 1.0, 0, 1.),
]
self.system.storage.addParticles(particle_list, 'id', 'type', 'q',
'pos', 'mass', 'adrat', 'radius')
self.system.storage.decompose()
# integrator
integrator = espressopp.integrator.VelocityVerlet(self.system)
integrator.dt = 0.005
# Langevin Thermostat
langevin = espressopp.integrator.LangevinThermostat(self.system)
langevin.gamma = 1.0
langevin.temperature = 1.0
integrator.addExtension(langevin)
# Harmonic bonds
bondlist = espressopp.FixedPairList(self.system.storage)
for i in range(1, 5):
bondlist.add(i, i + 1)
potBond = espressopp.interaction.Harmonic(K=100., r0=1.0)
interBond = espressopp.interaction.FixedPairListHarmonic(
self.system, bondlist, potBond)
self.system.addInteraction(interBond)
# constrain center of mass
tuplelist = espressopp.FixedLocalTupleList(self.system.storage)
tuple = []
for i in range(1, 6):
tuple.append(i)
tuplelist.addTuple(tuple)
potRG = espressopp.interaction.ConstrainRG(2000.)
interRG = espressopp.interaction.FixedLocalTupleListConstrainRG(
self.system, tuplelist, potRG)
self.system.addInteraction(interRG, 'Constrain_RG')
# radius of gyration of particles before integration
before = [0., 0., 0.]
particle = self.system.storage.getParticle(1)
dmy_p = []
dmy_ele = []
for i in xrange(3):
dmy_ele.append(particle.pos[i])
dmy_p.append(dmy_ele)
for i in xrange(2, 6):
particle = self.system.storage.getParticle(i)
diff = []
for j in xrange(3):
x_i = particle.pos[j] - dmy_p[i - 2][j]
x_i = x_i - round(x_i / self.L) * self.L
diff.append(x_i + dmy_p[i - 2][j])
dmy_p.append(diff)
for i in xrange(5):
for j in xrange(3):
before[j] += dmy_p[i][j]
for i in xrange(3):
before[i] /= 5.
print "before COM =", before
before_rg = 0.
for i in xrange(5):
for j in xrange(3):
before_rg += (dmy_p[i][j] - before[j])**2
before_rg = before_rg**0.5
print "before Rg =", before_rg
# run twenty thousand steps
integrator.run(20000)
# center of mass of particles after integration
after = [0., 0., 0.]
particle = self.system.storage.getParticle(1)
dmy_p = []
dmy_ele = []
for i in xrange(3):
dmy_ele.append(particle.pos[i])
dmy_p.append(dmy_ele)
for i in xrange(2, 6):
particle = self.system.storage.getParticle(i)
diff = []
for j in xrange(3):
x_i = particle.pos[j] - dmy_p[i - 2][j]
x_i = x_i - round(x_i / self.L) * self.L
diff.append(x_i + dmy_p[i - 2][j])
dmy_p.append(diff)
for i in xrange(5):
for j in xrange(3):
after[j] += dmy_p[i][j]
for i in xrange(3):
after[i] /= 5.
print "after COM =", after
after_rg = 0.
for i in xrange(5):
for j in xrange(3):
after_rg += (dmy_p[i][j] - after[j])**2
after_rg = after_rg**0.5
print "after Rg =", after_rg
# run checks
self.assertTrue(fabs((before_rg - after_rg) / before_rg) < 0.03)
def setUp(self) :
system = espressopp.System()
rng = espressopp.esutil.RNG()
N = 4
SIZE = float(N)
box = Real3D(SIZE)
bc = espressopp.bc.OrthorhombicBC(None, box)
system.bc = bc
# a small skin avoids rounding problems
system.skin = 0.001
cutoff = SIZE/2. - system.skin
comm = espressopp.MPI.COMM_WORLD
nodeGrid = espressopp.tools.decomp.nodeGrid(espressopp.MPI.COMM_WORLD.size,box,cutoff,system.skin)
cellGrid = espressopp.tools.decomp.cellGrid(box, nodeGrid, cutoff, system.skin)
print 'NodeGrid = %s'%(nodeGrid,)
print 'CellGrid = %s'%cellGrid
system.storage = espressopp.storage.DomainDecomposition(system, nodeGrid, cellGrid)
pid = 0
for i in xrange(N):
for j in xrange(N):
for k in xrange(N):
r = 0.5
x = (i + r) / N * SIZE
y = (j + r) / N * SIZE
z = (k + r) / N * SIZE
system.storage.addParticle(pid, Real3D(x, y, z))
pid = pid + 1
for i in xrange(N):
for j in xrange(N):
for k in xrange(N):
r = 0.25
x = (i + r) / N * SIZE
y = (j + r) / N * SIZE
z = (k + r) / N * SIZE
system.storage.addParticle(pid, Real3D(x, y, z))
pid = pid + 1
system.storage.decompose()
# now build Fixed Local Tuple List
tuplelist = espressopp.FixedLocalTupleList(system.storage)
self.system = system
self.N = N
self.tuplelist = tuplelist
def test_constrain_com(self):
# set up normal domain decomposition
nodeGrid = espressopp.tools.decomp.nodeGrid(espressopp.MPI.COMM_WORLD.size,self.box,rc=1.5, skin=self.skin)
cellGrid = espressopp.tools.decomp.cellGrid(self.box, nodeGrid, rc=1.5, skin=self.skin)
self.system.storage = espressopp.storage.DomainDecomposition(self.system, nodeGrid, cellGrid)
# add some particles (normal, coarse-grained particles only)
particle_list = [
(1, 1, 0, espressopp.Real3D(3.0, 5.0, 5.0), 1.0, 0, 1.),
(2, 1, 0, espressopp.Real3D(4.0, 5.0, 5.0), 2.0, 0, 1.),
(3, 1, 0, espressopp.Real3D(5.0, 5.0, 5.0), 3.0, 0, 1.),
(4, 1, 0, espressopp.Real3D(6.0, 5.0, 5.0), 2.0, 0, 1.),
(5, 1, 0, espressopp.Real3D(7.0, 5.0, 5.0), 1.0, 0, 1.),
]
self.system.storage.addParticles(particle_list, 'id', 'type', 'q', 'pos', 'mass','adrat', 'radius')
self.system.storage.decompose()
# integrator
integrator = espressopp.integrator.VelocityVerlet(self.system)
integrator.dt = 0.005
# Langevin Thermostat
langevin = espressopp.integrator.LangevinThermostat(self.system)
langevin.gamma = 1.0
langevin.temperature = 1.0
integrator.addExtension(langevin)
# Harmonic bonds
bondlist = espressopp.FixedPairList(self.system.storage)
for i in range(1, 5):
bondlist.add(i, i + 1)
potBond = espressopp.interaction.Harmonic(K=100., r0 = 1.0)
interBond = espressopp.interaction.FixedPairListHarmonic(self.system, bondlist, potBond)
self.system.addInteraction(interBond)
# constrain center of mass
tuplelist = espressopp.FixedLocalTupleList(self.system.storage)
tuple = []
for i in range(1, 6):
tuple.append(i)
tuplelist.addTuple(tuple)
potCOM = espressopp.interaction.ConstrainCOM(1000.)
interCOM = espressopp.interaction.FixedLocalTupleListConstrainCOM(self.system, tuplelist, potCOM)
self.system.addInteraction(interCOM, 'Constrain_COM')
# center of mass of particles before integration
before = [0., 0., 0.]
particle = self.system.storage.getParticle(1)
dmy_p = []
dmy_ele = []
mass = []
for i in range(3):
dmy_ele.append(particle.pos[i])
dmy_p.append(dmy_ele)
mass.append(particle.mass)
for i in range(2, 6):
particle = self.system.storage.getParticle(i)
mass.append(particle.mass)
diff = []
for j in range(3):
x_i = particle.pos[j] - dmy_p[i - 2][j]
x_i = x_i - round(x_i/self.L)*self.L
diff.append(x_i + dmy_p[i - 2][j])
dmy_p.append(diff)
total_mass = 0.
for i in range(5):
total_mass += mass[i]
for j in range(3):
before[j] += mass[i]*dmy_p[i][j]
for i in range(3):
before[i] /= total_mass
print("before", before)
# run twenty thousand steps
integrator.run(20000)
# center of mass of particles after integration
after= [0., 0., 0.]
particle = self.system.storage.getParticle(1)
dmy_p = []
dmy_ele = []
mass = []
for i in range(3):
dmy_ele.append(particle.pos[i])
dmy_p.append(dmy_ele)
mass.append(particle.mass)
for i in range(2, 6):
particle = self.system.storage.getParticle(i)
mass.append(particle.mass)
diff = []
for j in range(3):
x_i = particle.pos[j] - dmy_p[i - 2][j]
x_i = x_i - round(x_i/self.L)*self.L
diff.append(x_i + dmy_p[i - 2][j])
dmy_p.append(diff)
total_mass = 0.
for i in range(5):
total_mass += mass[i]
for j in range(3):
after[j] += mass[i]*dmy_p[i][j]
for i in range(3):
after[i] /= total_mass
print("after", after)
# run checks
self.assertTrue(fabs(before[0] - after[0]) < 0.04)
self.assertTrue(fabs(before[1] - after[1]) < 0.04)
self.assertTrue(fabs(before[2] - after[2]) < 0.04)
(float(parameters[8 - i_diff]) + 2.*L)%L)
print i*monomers_per_chain + j, " ", res_positions
radius = float(parameters[10 - i_diff])
part = [res_positions, radius]
cg_chain.append(part)
j +=1
# Init fine-grained polymer configuration
N_blob = N_blob/2
monomers_per_chain *= 2
props = ['id', 'type', 'mass', 'pos', 'v', 'radius', 'vradius']
bondlist = espressopp.FixedPairList(system.storage)
anglelist = espressopp.FixedTripleList(system.storage)
tuplelist = espressopp.FixedLocalTupleList(system.storage)
pid = 1
type = 0
mass = 1.0*N_blob
integrator.dt = timestep*(mass*B_cg**2/temperature)**0.5 #0.005*sqrt(Nb*m*l^2/kbT)=unit_time/200
#integrator.dt = timestep*(mass/temperature)**0.5 #0.005*sqrt(Nb*m*l^2/kbT)=unit_time/200/B_cg
chain = []
for i in range(num_chains):
startpos = system.bc.getRandomPos()
positions, bonds, angles = espressopp.tools.topology.polymerRW(pid, startpos, monomers_per_chain, bondlen, True)
for j in range(monomers_per_chain/2):
id = i*(monomers_per_chain/2) + j
vector = []
if j == 0: