elif args["lammps"]:
# ===== pair coeffs
a_ij_lmp = {}
for k in a_ij.keys():
k_new = " ".join([str(bt2num[i]) for i in k.split()])
a_ij_lmp[k_new] = a_ij[k]
for v in a_ij.values():
v[1], v[2] = v[2], v[1] # swap gamma/rc
# ===== molecular ids
Nmol = Nw + Nelb + Nc # total num of molecules
mol_ids = list(range(1, Nw+Nelb+1))
for i in range(Nw+Nelb+1, Nmol+1): #(1, Nc+1): # chains
mol_ids += [i]*Nbc
xyz_str = ll.atoms2str(np.hstack((np.matrix(mol_ids).T,\
np.matrix(atom_ids_n).T, xyz)))
# ===== bonds
bond_mat = gen_bonds(Nmc, Nc, mono_beads, start=Nw+Nelb)
bonds_str = ll.bonds2str2(bond_mat)
print("%i bonds created." % len(bond_mat))
data_string = ll.header2str(len(xyz), len(bond_mat), Nbt, len(k_ij), L) + \
ll.mass2str(masses) + \
ll.pair_dpd_coeffs2str(a_ij_lmp) + \
ll.bond_coeffs2str(k_ij) + \
"Atoms\n\n" + xyz_str + \
"Bonds\n\n" + bonds_str
fname = "nafion.data"
open(fname, "w").write(data_string)
print("Data file saved in", fname)
L = float(args["--L"])
rho = float(args["--rho"])
np.random.seed(1234)
Nb = int(rho * L**3)
Nc = int(Nb / N)
rc = 1.0
mu = rc / 2.0
print("=== Creating LAMMPS data file for diblock copolymer melt ===")
print("Set interaction params in the input file")
print("Box: %.1f | Rho: %.1f | Chain length: %i | A beads/chain: %i" % \
(L, rho, N, int(N*f) ))
poly_xyz = grow_polymer(L, f, N, Nc, mu)
xyz_str = ll.atoms2str(poly_xyz)
print(len(poly_xyz), "beads created, density:", len(poly_xyz) / L**3)
bonds = gen_bonds(N, Nc)
bonds_str = ll.bonds2str(bonds)
print(len(bonds), "bonds created")
final_string = ll.header2str(len(poly_xyz), len(bonds), 2, 1, L) + \
ll.mass2str({1: 1.0, 2: 1.0}) + \
"\nAtoms\n\n" + xyz_str + \
"\nBonds\n\n" + bonds_str
fname = "diblock.data"
open(fname, "w").write(final_string)
print("Data file written in", fname)
else:
sys.exit("<L> should have size 1 or 3.")
if f < 0.0 or f > 1.0:
sys.exit("f should be between 0 and 1.")
Nb = int(rho * np.prod(L))
Nc = int(Nb / N)
rc = 1.0
print("=== Creating LAMMPS data file for diblock copolymer melt ===")
print("Set interaction params in the input file")
print("Box: %s | Rho: %.1f | Chain length: %i | A beads/chain: %i" % \
(L, rho, N, int(N*f) ))
poly_xyz = grow_polymer(L, f, N, Nc, mu=1.0)
xyz_str = ll.atoms2str(poly_xyz)
print(len(poly_xyz), "beads created, density:", len(poly_xyz) / L**3)
bonds = gen_bonds(N, Nc)
bonds_str = ll.bonds2str(bonds)
print(len(bonds), "bonds created")
final_string = ll.header2str(len(poly_xyz), len(bonds), 2, 1, L[0]) + \
ll.mass2str({1: 1.0, 2: 1.0}) + \
"\nAtoms\n\n" + xyz_str + \
"\nBonds\n\n" + bonds_str
fname = "diblock.data"
open(fname, "w").write(final_string)
print("Data file written in", fname)
if args["--density"] == "real":
print "Using real density, rho_PMMA = 1180, rho_water = 1000"
Vw = pw * L**3
Nc = int(num_chains(rho_PMMA, L, n)) # number of PMMA chains
if args["water"]:
nw = int(rho_water * vw/(m_sol*mau))
elif args["meth"]:
nw = int(rho_meth * vw/(m_sol*mau))
else:
print "Using DPD bead density = 3"
Nw = int(pw * rho_DPD/rc**3 * L**3)
Nc = int((1-pw) * rho_DPD/rc**3 * L**3/n)
poly_xyz = grow_polymer(L, n, Nc, mu=rc, sigma=rc/10)
water_xyz = gen_water_beads(L, Nw, count=Nc+1)
final_xyz = np.vstack((poly_xyz, water_xyz))
xyz_str = ll.atoms2str(final_xyz)
print len(final_xyz), "beads created, density:", len(final_xyz) / (L/rc)**3
# ===== bonds
bonds = create_bonds(n, Nc)
bonds_str = ll.bonds2str(bonds)
print len(bonds), "bonds created"
# ===== pair and bond parameters
Nbt = len(bead_types)
r0 = 0.85 * rc # from Dorenbos, JCP, 2015
a_ij = gen_pair_coeffs(bead_types, data["ksi-params"], gamma, rc, a_ii)
k_ij = gen_bond_coeffs(bead_types, data["bond-coeffs"], r0)
masses = {1: m_PMMA*MAU, 2: m_sol*MAU}
final_string = ll.header2str(len(final_xyz), len(bonds), Nbt, len(k_ij), L) + \