def create_mons(self):
# """creates monomers along an axis"""
curr_id = self.nnodes # the last position of atoms (nodes)
# its also the first position of mons
mons_list = [None]*(self.npoly - 1)
for neigh in self.neighs:
a1 = self.nodes[neigh.i]
a2 = self.nodes[neigh.j]
xyz_, bond_length = distances.mons_alng_line(a1.position, a2.position, self.npoly, self.box)
for i, xyz in enumerate(xyz_):
curr_id += 1
mons_list[i] = Atom("O", m=1.0)
mons_list[i].q = -1.
mons_list[i].position = xyz
mons_list[i].idx = curr_id
mons_list[i].ityp = 2
if i < (self.npoly - 2):
self.bonds.append(Bond(curr_id, curr_id + 1, bond_length))
self.bonds.append(Bond(a1.idx, mons_list[0].idx, bond_length))
self.bonds.append(Bond(a2.idx, mons_list[-1].idx, bond_length))
self.mons.extend(mons_list)
# now connecting the atoms with pbc
# if a1.nneighs < 4:
# for node in self.nodes:
# if node.nneighs < 4:
# d_pbc = distances.dist_w_pbc(a1.position, node.position, self.box)
# if np.allclose(d_pbc, self.rcut) < self.eps and a1.idx != node.idx:
# self.bonds.append(Bond(a1.idx, node.idx, d_pbc))
# a1.neighbors.append(node.idx - 1)
# node.neighbors.append(a1.idx - 1)
return None
def create_mons(self):
"""creates monomers along an axis"""
shift_idx = self.nparticles
_curr_id = shift_idx # the last position of atoms (nodes)
chaincount = 0
_m_mons = 1.
for neigh in self.neighs:
chaincount += 1
a1 = self.nodes[neigh.i]
a2 = self.nodes[neigh.j]
npolychain = self.npoly
mons_list = [None] * (npolychain - 1)
if self.rand_walk_chain:
xyz_vec, bond_length = distances.chain_alng_line(
a1.position, a2.position, npolychain, self.box)
else:
xyz_vec, bond_length = distances.mons_alng_line(
a1.position, a2.position, npolychain, self.box)
self.ionization_count += 1
for i, xyz in enumerate(xyz_vec):
_curr_id += 1
mons_list[i] = Atom("O", m=_m_mons)
self.ionization_count += 1
if (self.ionization_count % self.ionization_every == 0):
mons_list[i].q = -1 * (abs(self.valency))
mons_list[i].position = xyz
mons_list[i].idx = _curr_id
mons_list[i].ityp = 2
mons_list[i].chainnum = chaincount
if i < (npolychain - 2):
self.bonds.append(Bond(_curr_id, _curr_id + 1,
bond_length))
if (self.ionization_count % self.ionization_every == 0):
mons_list[i].q = -1 * (abs(self.valency))
self.ionization_count += 1
self.bonds.append(Bond(a1.idx, mons_list[0].idx, bond_length))
self.bonds.append(Bond(a2.idx, mons_list[-1].idx, bond_length))
self.mons.extend(mons_list)
self.nmons = len(list(self.mons))
self.number_of_chains = chaincount
self.name_species.append('mons')
self.species.append(self.mons)
self.nspecies.append(self.nmons)
self.mspecies.append(float(_m_mons))
return None
def create_mons(self):
"""creates monomers along an axis"""
shift_idx = self.nparticles
_curr_id = shift_idx # the last position of atoms (nodes)
chaincount = 0
_m_mons = 1.
print("nnodes", len(self.nodes))
print("nnodes", (self.nnodes))
all_nodes = self.nodes + self.termnodes
for neigh in self.neighs:
chaincount += 1
if self.verbose:
print("i-j", neigh.i - 1, neigh.j - 1)
a1 = all_nodes[neigh.i - 1]
a2 = all_nodes[neigh.j - 1]
# for _n in self.nodes:
# if _n.idx == neigh.i:
# a1 = _n
# continue
# elif _n.idx == neigh.j:
# a2 = _n
# continue
# if (a1.ityp == 2) or (a2.ityp == 2):
# print( "here is the tether")
# print( a1.idx)
# print( a2.idx)
# a1 = self.nodes[neigh.i]
# a2 = self.nodes[neigh.j]
npolychain = self.npoly
mons_list = [None] * (npolychain - 1)
if a1.position[0] < self.box[0] / 2.:
self.ionization_every = self.ionization_every_left
elif a1.position[0] >= self.box[0] / 2.:
self.ionization_every = self.ionization_every_right
if self.rand_walk_chain:
xyz_vec, bond_length = distances.chain_alng_line(
a1.position, a2.position, npolychain, self.box)
else:
xyz_vec, bond_length = distances.mons_alng_line(
a1.position, a2.position, npolychain, self.box)
self.ionization_count += 1
for i, xyz in enumerate(xyz_vec):
_curr_id += 1
mons_list[i] = Atom("O", m=_m_mons)
self.ionization_count += 1
if (self.ionization_count % self.ionization_every == 0):
mons_list[i].q = -1 * (abs(self.valency))
mons_list[i].position = xyz
mons_list[i].idx = _curr_id
mons_list[i].ityp = 3
mons_list[i].chainnum = chaincount
if i < (npolychain - 2):
self.bonds.append(Bond(_curr_id, _curr_id + 1,
bond_length))
if (self.ionization_count % self.ionization_every == 0):
mons_list[i].q = -1 * (abs(self.valency))
self.ionization_count += 1
self.bonds.append(Bond(a1.idx, mons_list[0].idx, bond_length))
self.bonds.append(Bond(a2.idx, mons_list[-1].idx, bond_length))
self.mons.extend(mons_list)
# self.nmons = len(list(self.mons))
self.number_of_chains = chaincount
self.name_species.append('mons')
self.species.append(self.mons)
self.nspecies.append(self.nmons)
self.mspecies.append(float(_m_mons))
return None