# ===== 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["--xyz"]:
fname = "nafion.xyz"
ll.save_xyzfile(fname, np.c_[atom_ids_n, xyz])
print("xyz file saved in", fname)
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["--xyz"]:
fname = args["--xyz"]
ll.save_xyzfile(fname, poly_xyz[:, 1:])
print("xyz file saved in", fname)
N = int(rho * L**3)
if f < 0.0 or f > 1.0:
print("Fraction f of A beads must be between 0 and 1.")
sys.exit()
print("=== LAMMPS data file for binary mixture ====")
print("L: %.1f | rho: %.1f | f: %.2f" % (L, rho, f))
xyz = np.random.rand(N, 3) * L
names = [1] * int(f * N) + [2] * int((1 - f) * N)
header = header2str(N, L)
final_string = header + \
mass2str(1.0, 1.0) + \
atoms2str(names, xyz)
if args["--vel"]:
T = float(args["--vel"])
print("Initialising velocities, temperature: %.1f" % T)
vel = np.random.randn(N, 3) * T
final_string += vel2str(vel)
fname = "binmixt.data"
open(fname, "w").write(final_string)
print("Data file written in", fname)
if args["--xyz"]:
fname = "binmixt.xyz"
ll.save_xyzfile(fname, np.hstack((np.matrix(names).T, xyz)))
print("xyz file written in", fname)
print("L: %.2f | Beadtype: %i | Beads: %i" % (L, bead, len(xyz)))
print("Nx: %i | Total cells %i | Cell size: %.2f" % (Nx, Nx**3, Lx))
print("Smearing sigma: %.2f | Cutoff: %.2f" % (sigma, rc))
print("Density grid size: %.2f | Total points: %i" % (dx, Ngrid**2))
if args["test"]:
n = 10
print("Atoms in link cell %i\n" % n, lc[n].atoms)
print("Number of atoms in link cells:")
natoms = np.array([len(lc[i].atoms) for i in range(Nx**3)])
print(natoms)
print("Total: %i" % sum(natoms))
temp_xyz = xyz[lc[n].atoms]
temp_A = np.vstack((bead*np.ones(len(temp_xyz)), temp_xyz.T)).T
ll.save_xyzfile("test_cell.xyz", temp_A)
print("===========")
test_neighbour_cells()
print("===========")
if args["2d"]:
planes = {"xy": (0, 1), "yz": (1, 2), "xz": (0, 2)}
try:
plane = planes[args["<plane>"]]
except KeyError:
sys.exit("Choose plane from 'xy', 'yz', 'xz'.")
ax = set([0, 1, 2]).difference(plane)
ax = list(ax)[0]
d = float(args["--depth"])
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)
if args["--xyz"]:
fname = args["--xyz"]
ll.save_xyzfile(fname, poly_xyz[:, 1:])
print("xyz file saved in", fname)
NA = int(f * N)
NB = N - NA
names = [1] * NA + [2] * NB
xyz = np.random.rand(N, 3) * L
if args["--loc"]:
xyz[:NA, 0] = np.random.rand(NA) * f * L[0]
xyz[NA:, 0] = np.random.rand(NB) * (1 - f) * L[0] + f * L[0]
header = header2str(N, L)
final_string = header + \
mass2str(1.0, 1.0) + \
atoms2str(names, xyz)
if args["--vel"]:
T = float(args["--vel"])
print("Initialising velocities, temperature: %.1f" % T)
vel = np.random.randn(N, 3) * T
vel -= np.sum(vel, 0) / N
final_string += vel2str(vel)
fname = "binmixt.data"
open(fname, "w").write(final_string)
print("Data file written in", fname)
if args["--xyz"]:
fname = "binmixt.xyz"
save_xyzfile(fname, np.c_[names, xyz])
print("xyz file written in", fname)
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)
#!/usr/bin/env python
"""Usage:
si2dpd.py <infile> [--rc <rc>]
[AD HOC] Modify xyz files by converting metres to DPD units
to conform with VMD standards.
Options:
--rc <rc> DPD units [default: 8.14e-10]
[email protected], 11/01/16
"""
import numpy as np
from docopt import docopt
import lmp_lib as ll
args = docopt(__doc__)
rc = float(args["--rc"])
print("rc = %.2e" % rc)
A = ll.read_xyzfile(args["<infile>"])
A[:, 1:] /= rc
outfile = "converted.xyz"
ll.save_xyzfile(outfile, A)
print("xyz frame in DPD units saved in", outfile)
print("Fraction f of A beads must be between 0 and 1.")
sys.exit()
print("=== LAMMPS data file for binary mixture ====")
print("L: %.1f | rho: %.1f | f: %.2f" % (L, rho, f))
xyz = np.random.rand(N, 3)*L
names = [1]*int(f*N) + [2]*int((1-f)*N)
header = header2str(N, L)
final_string = header + \
mass2str(1.0, 1.0) + \
atoms2str(names, xyz)
if args["--vel"]:
T = float(args["--vel"])
print("Initialising velocities, temperature: %.1f" % T)
vel = np.random.randn(N, 3)*T
final_string += vel2str(vel)
fname = "binmixt.data"
open(fname, "w").write(final_string)
print("Data file written in", fname)
if args["--xyz"]:
fname = "binmixt.xyz"
ll.save_xyzfile(fname, np.hstack((np.matrix(names).T, xyz)) )
print("xyz file written 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
