コード例 #1
0
ファイル: gen_yamam3.py プロジェクト: petervanya/PhDcode
            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["--xyz"]:
        fname = "nafion.xyz"
        ll.save_xyzfile(fname, np.c_[atom_ids_n, xyz])
        print("xyz file saved in", fname)
 
コード例 #2
0
    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)
コード例 #3
0
    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)


コード例 #4
0
    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) + \
                   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"]