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)
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) + \
el_xyz = gen_electrodes(Nelb, L, Lcl, count=Nc+Nw+1)
pt_xyz = gen_platinum(NPt, L, Lcl, count=Nc+Nw+Nelb+1)
xyz = np.vstack((poly_xyz, wb_xyz, el_xyz, pt_xyz))
bead_types += "EP"
Nbt = len(bead_types)
else:
xyz = np.vstack((poly_xyz, wb_xyz))
print(len(xyz), "beads created, density:", float(len(xyz)) / L**3)
masses = dict( (i, 1.0) for i in range(1, Nbt+1) ) # all beads weigh the same
if units == "SI":
masses = dict( (i, m0) for i in range(1, Nbt+1) )
xyz *= rc
L *= rc
xyz_str = ll.atoms2str(xyz)
# ===== bonds
bonds = bonds_mat2(data["topology"], Nc)
bonds_str = ll.bonds2str(bonds)
print(len(bonds), "bonds created")
# ===== pair and bond parameters
a_ij = gen_pair_coeffs(bead_types, data["chi-params"], gamma, units)
k_ij = gen_bond_coeffs(bead_types, data["bond-coeffs"], r0, units)
# ===== putting it together
final_string = ll.header2str(len(xyz), len(bonds), Nbt, len(k_ij), L) + \
ll.mass2str(masses) + \
ll.pair_dpd_coeffs2str(a_ij) + \
ll.bond_coeffs2str(k_ij) + \