rc = 1.12 skin = 0.3 # skin for Verlet lists nvt = True timestep = 0.01 spline = 2 # spline interpolation type (1, 2, 3) conffile = 'polymer_melt.start' # file with inital configuration tabfileLJ = "pot-lj.txt" tabfileFENE = "pot-fene.txt" tabfileCosine = "pot-cosine.txt" ###################################################################### ## IT SHOULD BE UNNECESSARY TO MAKE MODIFICATIONS BELOW THIS LINE ## ###################################################################### bonds, angles, x, y, z, Lx, Ly, Lz = lammps.read(conffile) num_particles = len(x) density = num_particles / (Lx * Ly * Lz) size = (Lx, Ly, Lz) print '\n-- Tabulated Potentials Test --\n' print 'Steps: %3s' % steps print 'Particles: %3s' % num_particles print 'Cutoff: %3s' % rc print 'Density = %.4f' % (density) print 'dt =', timestep print 'Skin =', skin print 'nvt =', nvt # writes the tabulated file
from espressopp.tools import timers
# logging.getLogger("Storage").setLevel(logging.INFO)
# simulation parameters (nvt = False implies NVE)
steps = 10
rc = 2.5
skin = 0.3
nvt = False
timestep = 0.005
######################################################################
### IT SHOULD BE UNNECESSARY TO MAKE MODIFICATIONS BELOW THIS LINE ###
######################################################################
sys.stdout.write('Setting up simulation ...\n')
x, y, z, Lx, Ly, Lz, vx, vy, vz = lammps.read('espressopp_lennard_jones.start')
num_particles = len(x)
density = num_particles / (Lx * Ly * Lz)
size = (Lx, Ly, Lz)
system = espressopp.System()
system.rng = espressopp.esutil.RNG()
system.bc = espressopp.bc.OrthorhombicBC(system.rng, size)
system.skin = skin
comm = MPI.COMM_WORLD
nodeGrid = decomp.nodeGrid(comm.size, size, rc, skin)
cellGrid = decomp.cellGrid(size, nodeGrid, rc, skin)
system.storage = espressopp.storage.DomainDecomposition(
system, nodeGrid, cellGrid)
# add particles to the system and then decompose
props = ['id', 'type', 'mass', 'pos', 'v']
skin = 0.3
nvt = True
timestep = 0.01
# run with "tlj tfene tcos" to activate tabulated potentials
tabfileLJ = "pot-lj.txt"
tabfileFENE = "pot-fene.txt"
tabfileCosine = "pot-cosine.txt"
spline = 2 # spline interpolation type (1, 2, 3)
######################################################################
## 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 = espressopp.System()
system.rng = espressopp.esutil.RNG(54321)
system.bc = espressopp.bc.OrthorhombicBC(system.rng, size)
system.skin = skin
comm = MPI.COMM_WORLD
nodeGrid = decomp.nodeGrid(comm.size,size,rc,skin)
cellGrid = decomp.cellGrid(size, nodeGrid, rc, skin)
system.storage = espressopp.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]))
# logging.getLogger("Storage").setLevel(logging.INFO)
# simulation parameters (nvt = False implies NVE)
steps = 10
rc = 2.5
skin = 0.3
nvt = False
timestep = 0.005
######################################################################
### IT SHOULD BE UNNECESSARY TO MAKE MODIFICATIONS BELOW THIS LINE ###
######################################################################
sys.stdout.write('Setting up simulation ...\n')
x, y, z, Lx, Ly, Lz, vx, vy, vz = lammps.read('espressopp_lennard_jones.start')
num_particles = len(x)
density = num_particles / (Lx * Ly * Lz)
size = (Lx, Ly, Lz)
system = espressopp.System()
system.rng = espressopp.esutil.RNG()
system.bc = espressopp.bc.OrthorhombicBC(system.rng, size)
system.skin = skin
comm = MPI.COMM_WORLD
nodeGrid = decomp.nodeGrid(comm.size,size,rc,skin)
cellGrid = decomp.cellGrid(size, nodeGrid, rc, skin)
system.storage = espressopp.storage.DomainDecomposition(system, nodeGrid, cellGrid)
# add particles to the system and then decompose
props = ['id', 'type', 'mass', 'pos', 'v']
new_particles = []
equi_nloops = 200
equi_isteps = 50
# number of prod loops
prod_nloops = 50 #200
# number of integration steps performed in each production loop
prod_isteps = 10
Nx=1 # number of duplication
Ny=1 # number of duplication
Nz=1 # number of duplication
######################################################################
### 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('polymer_melt.lammps')
bonds, angles, x, y, z, Lx, Ly, Lz = replicate(bonds, angles, x, y, z, Lx, Ly, Lz, xdim=Nx, ydim=Ny, zdim=Nz)
num_particles = len(x)
density = num_particles / (Lx * Ly * Lz)
size = (Lx, Ly, Lz)
system = espressopp.System()
system.rng = espressopp.esutil.RNG()
system.bc = espressopp.bc.OrthorhombicBC(system.rng, size)
system.skin = skin
comm = MPI.COMM_WORLD
nodeGrid = espressopp.tools.decomp.nodeGrid(comm.size,size,rc,skin)
cellGrid = espressopp.tools.decomp.cellGrid(size,nodeGrid,rc,skin)
system.storage = espressopp.storage.DomainDecomposition(system, nodeGrid, cellGrid)
print("NCPUs = ", comm.size)