# number of AT particles
num_particles = len(x)
# set up the system
sys.stdout.write('Setting up simulation ...\n')
density = num_particles / (Lx * Ly * Lz)
size = (Lx, Ly, Lz)
system = espresso.System()
system.rng = espresso.esutil.RNG()
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)
# (H-)AdResS domain decomposition
system.storage = espresso.storage.DomainDecompositionAdress(system, nodeGrid, cellGrid)
# prepare AT particles
allParticlesAT = []
allParticles = []
tuples = []
for pidAT in range(num_particles):#logging.getLogger("StorageAdress").setLevel(logging.DEBUG)
allParticlesAT.append([pidAT, # add here these particles just temporarily
Real3D(x[pidAT], y[pidAT], z[pidAT]), # position
Real3D(vx[pidAT], vy[pidAT], vz[pidAT]), # velocity
Real3D(0, 0, 0), # force
1, 1.0, 1]) # type, mass, is AT particle
print 'number of particles: ', num_particles
######################################################################
# system
sys.stdout.write('Setting up simulation ...\n')
density = num_particles / (Lx * Ly * Lz)
box = (Lx, Ly, Lz)
system = espresso.System()
system.rng = espresso.esutil.RNG()
system.bc = espresso.bc.OrthorhombicBC(system.rng, box)
system.skin = skin
comm = MPI.COMM_WORLD
nodeGrid = decomp.nodeGrid(comm.size)
cellGrid = decomp.cellGrid(box, nodeGrid, rc, skin)
system.storage = espresso.storage.DomainDecomposition(system, nodeGrid,
cellGrid)
######################################################################
# adding particles
props = ['id', 'type', 'pos', 'v', 'mass']
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]
######################################################################
## IT SHOULD BE UNNECESSARY TO MAKE MODIFICATIONS BELOW THIS LINE ##
######################################################################
sys.stdout.write('Setting up simulation ...\n')
bonds, angles, x, y, z, Lx, Ly, Lz = lammps.read(
'espressopp_polymer_melt.start')
num_particles = len(x)
density = num_particles / (Lx * Ly * Lz)
size = (Lx, Ly, Lz)
system = espresso.System()
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,
print 'number of particles: ', num_particles
######################################################################
# system
sys.stdout.write('Setting up simulation ...\n')
density = num_particles / (Lx * Ly * Lz)
box = (Lx, Ly, Lz)
system = espresso.System()
system.rng = espresso.esutil.RNG()
system.bc = espresso.bc.OrthorhombicBC(system.rng, box)
system.skin = skin
comm = MPI.COMM_WORLD
nodeGrid = decomp.nodeGrid(comm.size)
cellGrid = decomp.cellGrid(box, nodeGrid, rc, skin)
system.storage = espresso.storage.DomainDecomposition(system, nodeGrid, cellGrid)
######################################################################
# adding particles
props = ['id', 'type', 'pos', 'v', 'mass']
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)
