def create_nodes(self):
"""creates nodes atoms"""
Lat = Lattice(self.topol, self.scale, self.n_)
self.box, self.rcut = Lat.gen_lattice()
print "generated lattice with bounds", self.box
# self._cell_dims, self.rcut = Lat.gen_lattice()
self.nnodes = Lat.nsites
print self.nnodes
self.nodes = [None] * self.nnodes
for i, site in enumerate(Lat.site):
# self.nodes[i] = Atom("C" + str(i+1), m=1.0)
self.nodes[i] = Atom("C", m=1.0)
# self.nodes[i].q = -1.
self.nodes[i].position = np.array(site)
self.nodes[i].idx = i + 1
for i1 in xrange(0, self.nnodes):
for i2 in xrange(i1 + 1, self.nnodes):
d_pbc = distances.dist_w_pbc(self.nodes[i1].position,
self.nodes[i2].position,
bounds=self.box)
# d_pbc = distances.dist_wo_pbc(self.nodes[i1].position, self.nodes[i2].position, bounds=self.box)
free_spots_flag = (self.nodes[i1].nneighs <= 4)
if np.allclose(d_pbc,
self.rcut) and i1 != i2 and free_spots_flag:
self.nodes[i1].neighbors.append(i2) #iden-fy neigh nodes
self.nodes[i2].neighbors.append(i1)
self.neighs.append(Bond(i1, i2, d_pbc))
print "----------done node------------"
print "node ", self.nodes[i1]
# print
return None
def create_nodes(self):
"""creates nodes atoms"""
shift_idx = self.nparticles
Lat = Lattice(self.topol, self.scale, self.n_)
self.box, self.rcut = Lat.gen_lattice()
if self.verbose:
print("generated lattice with bounds", self.box)
self.nnodes = Lat.nsites
self.system_box = self.box
if self.verbose:
print(self.nnodes)
self.nodes = [None] * self.nnodes
_m_nodes = 1.
node_ionization_every = 1
# if we have nx ny nz lattice
# first ny*nz sites are so from 0 to ny*nz - 1 - are bottom
# the last ny*nz sites are top
ninterface_nodes = int(self.n_[1] * self.n_[2])
print("ninterface_nodes", ninterface_nodes)
for i, site in enumerate(Lat.site):
# self.nodes[i] = Atom("C" + str(i+1), m=1.0)
self.nodes[i] = Atom("C", m=_m_nodes)
self.nodes[i].position = np.array(site)
self.nodes[i].idx = shift_idx + i + 1
if i <= (ninterface_nodes - 1):
self.nodes[i].boundary_type = 'bottom'
elif i >= (self.nnodes - ninterface_nodes):
self.nodes[i].boundary_type = 'top'
else:
self.nodes[i].boundary_type = 'no'
if (self.ionization_count % node_ionization_every == 0):
self.nodes[i].q = -1 * (abs(self.valency))
self.ionization_count += 1
if self.static_mid_boundary_flag:
if self.nodes[i].position[0] == 25. + int(self.n_[0] / 2 -
1) * self.scale:
self.nodes[i].ityp = 2
for i1 in range(0, self.nnodes):
for i2 in range(i1 + 1, self.nnodes):
d_w_pbc = distances.dist_w_pbc(self.nodes[i1].position,
self.nodes[i2].position,
bounds=self.box)
d_wo_pbc = distances.dist_wo_pbc(self.nodes[i1].position,
self.nodes[i2].position,
bounds=self.box)
i2_pos_pbc = distances.get_pbc(
self.nodes[i1].position,
self.nodes[i2].position,
bounds=self.box) # returns position of i2 with pbc
free_spots_flag = (self.nodes[i1].nneighs <=
self.max_connections)
close_neigh_flag = np.allclose(d_wo_pbc, self.rcut)
pbc_neigh_flag = np.allclose(d_w_pbc, self.rcut)
# close_neigh_flag = d_wo_pbc < self.rcut
# pbc_neigh_flag = d_w_pbc < self.rcut
print("n1 = {0}, n2={1}".format(i1, i2))
print('rcut, d_w_pbc, d_wo_pbc')
print(self.rcut, d_w_pbc, d_wo_pbc)
print('flags ', close_neigh_flag, pbc_neigh_flag)
connect_flag = False
xlo = 0
xhi = self.box[0]
ylo = 0
yhi = self.box[1]
zlo = 0
zhi = self.box[2]
# print( self.nodes[i2].position)
if close_neigh_flag and i1 != i2 and free_spots_flag:
connect_flag = True
if pbc_neigh_flag and i1 != i2 and free_spots_flag and self.pbc_x:
if ((i2_pos_pbc[0] < xlo) or (i2_pos_pbc[0] > xhi)):
connect_flag = True
if pbc_neigh_flag and i1 != i2 and free_spots_flag and self.pbc_y:
if ((i2_pos_pbc[1] < ylo) or (i2_pos_pbc[1] > yhi)):
connect_flag = True
if pbc_neigh_flag and i1 != i2 and free_spots_flag and self.pbc_z:
if ((i2_pos_pbc[2] < zlo) or (i2_pos_pbc[2] > zhi)):
connect_flag = True
if connect_flag:
self.nodes[i1].neighbors.append(i2) #iden-fy neigh nodes
self.nodes[i2].neighbors.append(i1)
self.neighs.append(
Bond(self.nodes[i1].idx, self.nodes[i2].idx,
d_w_pbc[0]))
if self.verbose:
print("----------done node------------")
print("node ", self.nodes[i1])
self.name_species.append('nodes')
self.species.append(self.nodes)
self.nspecies.append(self.nnodes)
self.mspecies.append(float(_m_nodes))
return None