def NEBForce(self, isclimbing, image, left, right, greal, icenter):
"""
Calculate NEB force for 1 image. That contains projected real force and spring force.
The current implementation is the DNEB (doubly nudged elastic band) as described in
"A doubly nudged elastic band method for finding transition states"
S***n A. Trygubenko and David J. Wales
J. Chem. Phys. 120, 2082 (2004); doi: 10.1063/1.1636455
"""
# construct tangent vector
d_left, g_left = self.distance(image[1], left[1], distance=True)#self.with_springenergy)
d_right, g_right = self.distance(image[1], right[1], distance=True)#self.with_springenergy)
self.distances[icenter-1] = np.sqrt(d_left)
self.distances[icenter] = np.sqrt(d_right)
#print g_left, g_right
t = self.tangent(image[0],left[0],right[0], g_left, g_right)
if(isclimbing):
return greal - 2.*np.dot(greal, t) * t
if self.dneb:
g_spring = self.k*(g_left + g_right)
else:
g_spring = self.k*(norm(g_left) - norm(g_right))*t
#print "spring", np.dot(g_spring, t)
if True:
import _NEB_utils
E, g_tot = _NEB_utils.neb_force(t,greal, g_spring, self.k, self.dneb)
if self.with_springenergy:
return E, g_tot
else:
return 0., g_tot
else:
# project out parallel part
gperp = greal - np.dot(greal, t) * t
# calculate parallel spring force and energy
#gspring = -self.k * (np.linalg.norm(d2) - np.linalg.norm(d1)) * t
# this is the spring
# the parallel part
gs_par = np.dot(g_spring,t)*t
g_tot = gperp + gs_par
if(self.dneb):
# perpendicular part of spring
gs_perp = g_spring - gs_par
# double nudging
g_tot += gs_perp - np.dot(gs_perp,gperp)*gperp/np.dot(gperp,gperp)
if(self.with_springenergy):
E = 0.5 / self.k * (d_left **2 + d_right**2)
else:
E = 0.
#print np.linalg.norm(gperp), np.linalg.norm(gs_par)
return E, g_tot
def NEBForce(self, isclimbing, image, left, right, greal, icenter):
"""
Calculate NEB force for 1 image. That contains projected real force and spring force.
The current implementation is the DNEB (doubly nudged elastic band) as described in
"A doubly nudged elastic band method for finding transition states"
S***n A. Trygubenko and David J. Wales
J. Chem. Phys. 120, 2082 (2004); doi: 10.1063/1.1636455
"""
# construct tangent vector
d_left, g_left = self.distance(image[1], left[1],
distance=True) #self.with_springenergy)
d_right, g_right = self.distance(
image[1], right[1], distance=True) #self.with_springenergy)
self.distances[icenter - 1] = np.sqrt(d_left)
self.distances[icenter] = np.sqrt(d_right)
#print g_left, g_right
t = self.tangent(image[0], left[0], right[0], g_left, g_right)
if (isclimbing):
return greal - 2. * np.dot(greal, t) * t
#print "spring", np.dot(g_spring, t)
if True:
import _NEB_utils
E, g_tot = _NEB_utils.neb_force(t, greal, d_left, g_left, d_right,
g_right, self.k, self.dneb)
if self.with_springenergy:
return E, g_tot
else:
return 0., g_tot
else:
# project out parallel part
gperp = greal - np.dot(greal, t) * t
# parallel part of spring force
gs_par = self.k * (d_left - d_right) * t
g_tot = gperp + gs_par
if (self.dneb):
g_spring = self.k * (g_left + g_right)
# perpendicular part of spring
gs_perp = g_spring - np.dot(g_spring, t) * t
# double nudging
g_tot += gs_perp - np.dot(gs_perp, gperp) * gperp / np.dot(
gperp, gperp)
if (self.with_springenergy):
E = 0.5 / self.k * (d_left**2 + d_right**2)
else:
E = 0.
#print np.linalg.norm(gperp), np.linalg.norm(gs_par)
return E, g_tot
