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
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