Example #1
0
def bonds_mat2(raw_topo, Nc):
    """Create bond matrix from topology string and number of chains"""
    bead_list, Nmc = pt.parse_beads(raw_topo)
    Nbm = len(bead_list)
    bonds = pt.construct_bonds(bead_list, Nmc, 0)
    for i in range(1, Nc):
        bonds = np.vstack( (bonds, pt.construct_bonds(bead_list, Nmc, i*Nmc*Nbm)) ) 
    return bonds
Example #2
0
            Natoms = NA * rho_el[elmat] * Vcl/(elem_wts["C"]*1e-3)
        elif elmat == "quartz":
            Natoms = NA * rho_el[elmat] * Vcl/((elem_wts["Si"] + 2*elem_wts["O"])*1e-3)
        elif elmat == "silica":
            Natoms = NA * rho_el[elmat] * Vcl/((elem_wts["Si"] + 2*elem_wts["O"])*1e-3)
        print("CL:", int(Natoms/Nelb*rc**3), "electrode atoms per bead at density", rho_el[elmat])
        print("Electrode beads: %i | Platinum beads: %i" % (Nelb, NPt))
    else:
        Lcl, Vcl = 0.0, 0.0
        print("Electrodes off.")

    # ===== set polymer parameters
    if args["--parsetopo"]:
        raw_topo = data["topology"]
        print("Topology:", raw_topo)
        bead_list, Nmc = pt.parse_beads(raw_topo)   # information about connectivity
        Nbm = len(bead_list)
        bead_dict = pt.gen_bead_dict(raw_topo)      # dict of beads in one monomer
        bead_types = sorted("".join(bead_dict.keys()) + "W")
        Nbt = len(bead_types)
        coeff2num = dict((coeff, num) for num, coeff in zip(range(1, Nbt+1), bead_types))
        beads = []
        [[beads.append(coeff2num[k]) for i in range(v)] for k, v in sorted(bead_dict.items())]
    else:
        Nbm, Nmc = 5, data["mono-per-chain"]
        bead_types = "ABCW"
        beads = [1, 1, 1, 2, 3]
        Nbt = len(bead_types)
    print("Nmc: %i, Nbm: %i" % (Nmc, Nbm))

    # ===== setting numbers