def monomer_system(num_particles, density=0.8, seed=None):
num_particles = num_particles
L = pow(num_particles/density, 1./3.)
box = (L, L, L)
# Initialize the espresso system
system = espresso.System()
if seed is not None:
system.rng = espresso.esutil.RNG(seed)
else:
system.rng = espresso.esutil.RNG()
system.bc = espresso.bc.OrthorhombicBC(system.rng, box)
system.skin = skin
nodeGrid = espresso.tools.decomp.nodeGrid(MPI.COMM_WORLD.size)
cellGrid = espresso.tools.decomp.cellGrid(box, nodeGrid, rc, skin)
system.storage = espresso.storage.DomainDecomposition(system, nodeGrid, cellGrid)
def normal_v():
return espresso.Real3D(system.rng.normal()*0.5, system.rng.normal()*0.5, system.rng.normal()*0.5)
# Add the individual particles
Xs = []
pid = 0
for i in range(num_particles):
pos = system.bc.getRandomPos()
v = espresso.Real3D(system.rng.normal(),system.rng.normal(),system.rng.normal())
Xs.append([pid, pos, v])
pid += 1
system.storage.addParticles(Xs, 'id', 'pos', 'v')
# Define capped LJ potential
verletList = espresso.VerletList(system, cutoff=rc)
LJCapped = espresso.interaction.VerletListLennardJonesCapped(verletList)
LJCapped.setPotential(type1=0, type2=0, potential=espresso.interaction.LennardJonesCapped(epsilon=epsilon, sigma=sigma, cutoff=rc, caprad=caprad_LJ))
system.addInteraction(LJCapped)
# Define integrator and StochasticVelocityRescaling thermostat
integrator = espresso.integrator.VelocityVerlet(system)
thermostat = espresso.integrator.StochasticVelocityRescaling(system)
thermostat.temperature = 1.0
integrator.addExtension(thermostat)
system.storage.decompose()
return system, integrator, LJCapped, verletList, thermostat, num_particles
system.rng = espresso.esutil.RNG(54321)
system.bc = espresso.bc.OrthorhombicBC(system.rng, size)
system.skin = skin
comm = MPI.COMM_WORLD
nodeGrid = decomp.nodeGrid(comm.size)
cellGrid = decomp.cellGrid(size, nodeGrid, rc, skin)
system.storage = espresso.storage.DomainDecomposition(system, nodeGrid,
cellGrid)
# add particles to the system and then decompose
for pid in range(num_particles):
system.storage.addParticle(pid + 1, Real3D(x[pid], y[pid], z[pid]))
system.storage.decompose()
# Lennard-Jones with Verlet list
vl = espresso.VerletList(system, cutoff=rc + system.skin)
potTabLJ = espresso.interaction.Tabulated(itype=spline,
filename=tabfileLJ,
cutoff=rc)
potLJ = espresso.interaction.LennardJones(sigma=1.0,
epsilon=1.0,
cutoff=rc,
shift=False)
if sys.argv.count("tlj") > 0:
print('tabulated potential from file %s' % potTabLJ.filename)
interLJ = espresso.interaction.VerletListTabulated(vl)
interLJ.setPotential(type1=0, type2=0, potential=potTabLJ)
else:
interLJ = espresso.interaction.VerletListLennardJones(vl)
interLJ.setPotential(type1=0, type2=0, potential=potLJ)
system.addInteraction(interLJ)
new_particles = []
mass = 1.0
type = 0
for pid in range(num_particles):
pos = espresso.Real3D(x[pid], y[pid], z[pid])
vel = espresso.Real3D(0, 0, 0)
part = [pid, type, pos, vel, mass]
new_particles.append(part)
system.storage.addParticles(new_particles, *props)
system.storage.decompose()
##########################################################################################
# interaction
vl = espresso.VerletList(system, cutoff=rc)
tabP = espresso.interaction.Tabulated(itype=1, filename='CG_CG.tab', cutoff=rc)
tabI = espresso.interaction.VerletListTabulated(vl)
tabI.setPotential(type1=0, type2=0, potential=tabP)
system.addInteraction(tabI)
##########################################################################################
# integrator
integrator = espresso.integrator.VelocityVerlet(system)
integrator.dt = timestep
# thermostat
lT = espresso.integrator.LangevinThermostat(system)
lT.gamma = 5.0
lT.temperature = 2.5
def chains_x_system(num_chains,
monomers_per_chain,
num_X,
density=0.8,
seed=None):
num_particles = num_chains * monomers_per_chain + num_X
L = pow(num_particles / density, 1. / 3.)
box = (L, L, L)
# Initialize the espresso system
system = espresso.System()
if seed is not None:
system.rng = espresso.esutil.RNG(seed)
else:
system.rng = espresso.esutil.RNG()
system.bc = espresso.bc.OrthorhombicBC(system.rng, box)
system.skin = skin
nodeGrid = espresso.tools.decomp.nodeGrid(MPI.COMM_WORLD.size)
cellGrid = espresso.tools.decomp.cellGrid(box, nodeGrid, rc, skin)
system.storage = espresso.storage.DomainDecomposition(
system, nodeGrid, cellGrid)
def normal_v():
return espresso.Real3D(system.rng.normal() * 0.5,
system.rng.normal() * 0.5,
system.rng.normal() * 0.5)
# Add the chains
chainFPL = espresso.FixedPairList(system.storage)
pid = 0
for i in range(num_chains):
chain = []
startpos = system.bc.getRandomPos()
positions, bonds = espresso.tools.topology.polymerRW(
pid, startpos, monomers_per_chain, bondlen)
for k in range(monomers_per_chain):
part = [pid + k, positions[k], normal_v()]
chain.append(part)
pid += monomers_per_chain
system.storage.addParticles(chain, 'id', 'pos', 'v')
chainFPL.addBonds(bonds)
# Add the individual particles
Xs = []
for i in range(num_X):
pos = system.bc.getRandomPos()
v = espresso.Real3D(system.rng.normal(), system.rng.normal(),
system.rng.normal())
Xs.append([pid, pos, v])
pid += 1
system.storage.addParticles(Xs, 'id', 'pos', 'v')
# Define capped LJ potential
verletList = espresso.VerletList(system, cutoff=rc)
LJCapped = espresso.interaction.VerletListLennardJonesCapped(verletList)
LJCapped.setPotential(type1=0,
type2=0,
potential=espresso.interaction.LennardJonesCapped(
epsilon=epsilon,
sigma=sigma,
cutoff=rc,
caprad=caprad_LJ))
system.addInteraction(LJCapped)
# Define capped FENE potential
potFENE = espresso.interaction.FENECapped(K=K,
r0=0.0,
rMax=rMax,
caprad=caprad_FENE)
FENECapped = espresso.interaction.FixedPairListFENECapped(
system, chainFPL, potFENE)
system.addInteraction(FENECapped)
# Define integrator and StochasticVelocityRescaling thermostat
integrator = espresso.integrator.VelocityVerlet(system)
thermostat = espresso.integrator.StochasticVelocityRescaling(system)
thermostat.temperature = 1.0
integrator.addExtension(thermostat)
system.storage.decompose()
return system, integrator, LJCapped, verletList, FENECapped, chainFPL, thermostat, num_particles