def calculate_image_eigenmode(self, i):
img = self.images[i]
if self.decouple_modes:
img.set_basis(None)
else:
nm = normalize(img.get_eigenmode())
nt = normalize(self.tangents[i])
img.set_basis(nt)
img.set_eigenmode(normalize(perpendicular_vector(nm, nt)))
img.get_forces()
def invert_eigenmode_forces(self):
for i in range(1, self.nimages - 1):
f_r = self.forces['real'][i]
t = self.tangents[i]
nt = normalize(t)
nm = self.images[i].get_eigenmode()
self.forces['dimer'][i] = f_r - 2 * np.vdot(f_r, nm) * nm
hydrogen_index = pairs[0]
else:
new_constraints.append(c)
# remove all FixBondLengths
atoms.set_constraint(new_constraints)
# start DIMER
initial_mode_method = "displacement"
displacement_method = 'vector'
# set up initial guess for DIMER
natoms = atoms.get_number_of_atoms()
displacement_vector = np.zeros(shape=(natoms, 3))
pos = atoms.get_positions()
_delta_x = normalize(pos[carbon_index] - pos[hydrogen_index]) * 0.01
displacement_vector[hydrogen_index] = _delta_x
mask = [False] * natoms
mask[hydrogen_index] = True
calc = Vasp2(encut=400,
ispin=2,
ediff=1.0e-7,
nelm=120,
nelmin=5,
xc='pbe',
kpts=(1, 1, 1),
gamma=True,
prec="N",
algo="N",
ismear=0,
def plot_pseudo_3d_pes(self):
import pylab as plt
from pylab import subplot, subplot2grid
fig = plt.figure(figsize = (8,8))
if self.plot_subplot:
plt.axes()
ax1 = subplot2grid((4, 4), (0, 0), rowspan = 3, colspan = 3)
ax2 = subplot2grid((4, 4), (3, 0), colspan = 3)
ax3 = subplot2grid((4, 4), (0, 3), rowspan = 3)
ax2_base_scale = 0.00000002
else:
plt.axes()
ax1 = subplot(111)
ax2 = None
ax3 = None
def make_line(pos, orient, c, size=0.2, width=1, dim=[0, 1], ax=plt):
p = pos[-1]
o = orient[-1]
d1 = dim[0]
d2 = dim[1]
ax.plot((p[d1] - o[d1] * size, p[d1] + o[d1] * size), (p[d2] - o[d2] * size, p[d2] + o[d2] * size), c, lw = width)
def make_arrow(pos, end, c, scale=1.0, width=1, dim=[0,1], ax=plt, head_scale=0.9, base_scale=0.6):
x = head_scale
if ax == ax2:
y = ax2_base_scale
else:
y = base_scale
p = pos[-1]
e = end[-1]
d1 = dim[0]
d2 = dim[1]
p1 = p[d1]
p2 = p[d2]
e1 = e[d1] * scale + p1
e2 = e[d2] * scale + p2
a1 = p1 * (1 - x) + x * e1
a2 = p2 * (1 - x) + x * e2
b1 = a1 + (a2 - e2)
b2 = a2 - (a1 - e1)
c1 = a1 - (a2 - e2)
c2 = a2 + (a1 - e1)
b1 = a1 * (1 - y) + y * b1
b2 = a2 * (1 - y) + y * b2
c1 = a1 * (1 - y) + y * c1
c2 = a2 * (1 - y) + y * c2
ax.plot((p1, e1), (p2, e2), 'k', lw = width + 1)
ax.plot((b1, e1, c1), (b2, e2, c2), 'k', lw = width + 1)
ax.plot((p1, e1), (p2, e2), c, lw = width)
ax.plot((b1, e1, c1), (b2, e2, c2), c, lw = width)
def make_circle(pos, r, c, dim=[0, 1], ax=plt):
p = pos[-1]
d1 = dim[0]
d2 = dim[1]
ax.plot((p[d1]), (p[d2]), 'k.', markersize = r + 1)
ax.plot((p[d1]), (p[d2]), '%s.' % c, markersize = r)
n = self.nimages
ts = self.tangents
ms = []
ps = []
for i in range(n):
ms.append(self.images[i].get_eigenmode())
ps.append(self.images[i].get_positions())
f_rs = self.forces['real']
f_ds = self.forces['dimer']
f_ss = self.forces['spring']
f_ns = self.forces['neb']
# ax1.text(0.6, 0.6, self.phase, color = 'k')
for i in range(n):
p = ps[i]
t = normalize(ts[i]) * 0.25
m = normalize(ms[i]) * 0.25
f_r = f_rs[i]
f_d = f_ds[i]
f_s = f_ss[i]
f_n = f_ns[i]
if i in [0, n - 1]:
make_circle(p, 20.0, 'y', ax = ax1)
else:
if self.climb and i == self.imax:
make_circle(p, 35.0, 'c', ax = ax1)
else:
make_circle(p, 35.0, 'y', ax = ax1)
make_arrow(p, f_s, 'g', ax = ax1)
make_arrow(p, f_r, 'w', ax = ax1)
make_arrow(p, f_d, 'b', ax = ax1)
make_arrow(p, f_n, 'k', ax = ax1)
make_line(p, t, 'r', ax = ax1)
make_line(p, m, 'b', ax = ax1)
if self.plot_subplot:
if i in [0, n - 1]:
make_circle(p, 20.0, 'y', dim = [0, 2], ax = ax2)
else:
if self.climb and i == self.imax:
make_circle(p, 35.0, 'c', dim = [0, 2], ax = ax2)
else:
make_circle(p, 35.0, 'y', dim = [0, 2], ax = ax2)
make_arrow(p, f_s, 'g', dim = [0, 2], ax = ax2)
make_arrow(p, f_r, 'w', dim = [0, 2], ax = ax2)
make_arrow(p, f_d, 'b', dim = [0, 2], ax = ax2)
make_arrow(p, f_n, 'k', dim = [0, 2], ax = ax2)
make_line(p, t, 'r', dim = [0, 2], ax = ax2)
make_line(p, m, 'b', dim = [0, 2], ax = ax2)
if i in [0, n - 1]:
make_circle(p, 20.0, 'y', dim = [2, 1], ax = ax3)
else:
if self.climb and i == self.imax:
make_circle(p, 35.0, 'c', dim = [2, 1], ax = ax3)
else:
make_circle(p, 35.0, 'y', dim = [2, 1], ax = ax3)
make_arrow(p, f_s, 'g', dim = [2, 1], ax = ax3)
make_arrow(p, f_r, 'w', dim = [2, 1], ax = ax3)
make_arrow(p, f_d, 'b', dim = [2, 1], ax = ax3)
make_arrow(p, f_n, 'k', dim = [2, 1], ax = ax3)
make_line(p, t, 'r', dim = [2, 1], ax = ax3)
make_line(p, m, 'b', dim = [2, 1], ax = ax3)
if self.plot_e is not None:
ax1.contourf(self.plot_x, self.plot_y, self.plot_e, 30)
if self.plot_animate < 10:
animate = '000' + str(self.plot_animate)
elif self.plot_animate < 100:
animate = '00' + str(self.plot_animate)
elif self.plot_animate < 1000:
animate = '0' + str(self.plot_animate)
else:
animate = str(self.plot_animate)
axis1 = ax1.get_axes()
if self.plot_e is not None:
axis1.set_xlim(xmin = min(self.plot_x), xmax = max(self.plot_x))
axis1.set_ylim(ymin = min(self.plot_y), ymax = max(self.plot_y))
else:
if self.xrange is not None:
axis1.set_xlim(xmin = self.xrange[0], xmax = self.xrange[1])
else:
axis1.set_xlim(xmin = 0.0, xmax = 5.0)
if self.yrange is not None:
axis1.set_ylim(ymin = self.yrange[0], ymax = self.yrange[1])
else:
axis1.set_ylim(ymin = 0.0, ymax = 5.0)
if self.plot_subplot:
axis2 = ax2.get_axes()
axis3 = ax3.get_axes()
if self.plot_e is not None:
axis2.set_xlim(xmin = min(self.plot_x), xmax = max(self.plot_x))
axis3.set_ylim(ymin = min(self.plot_y), ymax = max(self.plot_y))
else:
if self.xrange is not None:
axis2.set_xlim(xmin = self.xrange[0], xmax = self.xrange[1])
axis3.set_ylim(ymin = self.yrange[0], ymax = self.yrange[1])
else:
axis2.set_xlim(xmin = 0.0, xmax = 5.0)
axis3.set_ylim(ymin = 0.0, ymax = 5.0)
# axis2.set_ylim(ymin = -3.0e-9, ymax = 3.0e-9)
plt.savefig('_fig-' + animate + '.png')
# plt.savefig('_fig-' + animate + '.svg')
plt.draw()
plt.close()
# plt.show()
self.plot_animate += 1