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["--xyz"]:
fname = args["--xyz"]
xyz = np.hstack((np.matrix(atom_ids_n).T, xyz))
ll.save_xyzfile(fname, xyz)
print("xyz file saved in", fname)
# ===== 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) + \
ll.mass2str(masses) + \
ll.pair_dpd_coeffs2str(a_ij) + \
ll.bond_coeffs2str(k_ij) + \
"Atoms\n\n" + xyz_str + \
"Bonds\n\n" + bonds_str
if args["--save"]:
fname = args["--save"]
open(fname, "w").write(final_string)
print "Data file saved in", fname
else:
print final_string
if args["--xyz"]:
fname = args["--xyz"]
ll.save_xyzfile(fname, final_xyz[:, 1:])
print "xyz file saved in", fname
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) + \
"Atoms\n\n" + xyz_str + \
"Bonds\n\n" + bonds_str
fname = args["--save"]
open(fname, "w").write(final_string)
print("Data file saved in", fname)
if args["--xyz"]:
fname = args["--xyz"]
ll.save_xyzfile(fname, xyz[:, 1:])
print("xyz file saved in", fname)
