def plot_posits(atoms, edge, bond, vecs=None):
positions = atoms.positions
pos_used = []
n_set = make_neighSet(15, edge, bond)
for i, r in enumerate(positions):
if atoms[i].number == 6:
norms = [np.linalg.norm(x) for x in positions[pos_used] - r]
if len(norms) != 0:
if 12 < np.min([np.linalg.norm(x) for x in positions[pos_used] - r]):
neigh_set = get_setOrig(r, edge, bond) + n_set
pos_used.append(i)
plt.scatter(neigh_set[:,0], neigh_set[:,1], color = 'red', alpha = .5)
else:
neigh_set = get_setOrig(r, edge, bond) + n_set
pos_used.append(i)
plt.scatter(neigh_set[:,0], neigh_set[:,1], color = 'red', alpha = .5)
plt.scatter(positions[:,0], positions[:,1], color = 'black')
if vecs != None:
for vec in vecs:
plot_vec = np.array([positions[0],
positions[0] + vec])
plt.plot(plot_vec[:,0], plot_vec[:,1])
plt.axis('equal')
plt.show()
def plot_posits(atoms, edge, bond, vecs=None):
positions = atoms.positions
pos_used = []
n_set = make_neighSet(15, edge, bond)
for i, r in enumerate(positions):
if atoms[i].number == 6:
norms = [np.linalg.norm(x) for x in positions[pos_used] - r]
if len(norms) != 0:
if 12 < np.min(
[np.linalg.norm(x) for x in positions[pos_used] - r]):
neigh_set = get_setOrig(r, edge, bond) + n_set
pos_used.append(i)
plt.scatter(neigh_set[:, 0],
neigh_set[:, 1],
color='red',
alpha=.5)
else:
neigh_set = get_setOrig(r, edge, bond) + n_set
pos_used.append(i)
plt.scatter(neigh_set[:, 0],
neigh_set[:, 1],
color='red',
alpha=.5)
plt.scatter(positions[:, 0], positions[:, 1], color='black')
if vecs != None:
for vec in vecs:
plot_vec = np.array([positions[0], positions[0] + vec])
plt.plot(plot_vec[:, 0], plot_vec[:, 1])
plt.axis('equal')
plt.show()
[bond/2, y2], [bond/2 + bond, y2], [bond/2 + 2*bond, y2],
[0, y1], [bond, y1], [2*bond, y1], [3*bond, y1]])
traj = PickleTrajectory(pathf + 'w=%i/r=%i/' %(width, ratio) + filen)
xmin, xmax = np.min(traj[0].positions[:,0]), np.max(traj[0].positions[:,0])
ymin, ymax = np.min(traj[0].positions[:,1]), np.max(traj[0].positions[:,1])
for j in range(len(traj)):
if j%10 == 0:
atoms = traj[j]
coll_ids= []
r_ids = []
for i, r in enumerate(atoms.positions):
if atoms[i].number == 6:
ro = get_setOrig(r, edge, bond)[:2] + asum_dev
alset = np.array(ro) + nset
for dev in alset - r[:2]:
if np.linalg.norm(dev) < rlim:
coll_ids.append(i)
r_ids.append(np.linalg.norm(dev))
'''
if np.abs(ro[1] - r[1]) < rlim or \
np.abs(ro[1] + np.sqrt(3)/2*bond - r[1]) < rlim:
if np.abs(ro[0] - r[0]) < rlim or \
np.abs(ro[0] + bond - r[0]) < rlim or \
traj = PickleTrajectory(pathf + 'w=%i/r=%i/' % (width, ratio) +
filen)
xmin, xmax = np.min(traj[0].positions[:, 0]), np.max(
traj[0].positions[:, 0])
ymin, ymax = np.min(traj[0].positions[:, 1]), np.max(
traj[0].positions[:, 1])
for j in range(len(traj)):
if j % 10 == 0:
atoms = traj[j]
coll_ids = []
r_ids = []
for i, r in enumerate(atoms.positions):
if atoms[i].number == 6:
ro = get_setOrig(r, edge, bond)[:2] + asum_dev
alset = np.array(ro) + nset
for dev in alset - r[:2]:
if np.linalg.norm(dev) < rlim:
coll_ids.append(i)
r_ids.append(np.linalg.norm(dev))
'''
if np.abs(ro[1] - r[1]) < rlim or \
np.abs(ro[1] + np.sqrt(3)/2*bond - r[1]) < rlim:
if np.abs(ro[0] - r[0]) < rlim or \
np.abs(ro[0] + bond - r[0]) < rlim or \
np.abs(ro[0] + 2*bond - r[0]) < rlim or \
np.abs(ro[0] + bond/2 - r[0]) < rlim or \
np.abs(ro[0] + (1./2 + np.sqrt(3))*bond - r[0]) < rlim:
