def get_hessian_contrib(self, index, fc=None):
'''
Get the contribution to the covalent hessian of term with given
index (and its slaves). If fc is given, set the fc of the master
and its slave to the given fc.
'''
val = ForcePartValence(self.system)
kind = self.vlist.vtab[index]['kind']
masterslaves = [index] + self.terms[index].slaves
if kind == 4: #Cosine
m, k, rv = self.get_params(index)
if fc is not None: k = fc
for jterm in masterslaves:
ics = self.terms[jterm].ics
args = (m, k, rv) + tuple(ics)
val.add_term(Cosine(*args))
elif kind == 3: #cross
k, rv0, rv1 = self.get_params(index)
if fc is not None: k = fc
for jterm in masterslaves:
ics = self.terms[jterm].ics
args = (k, rv0, rv1) + tuple(ics)
val.add_term(Cross(*args))
elif kind == 1: #Polyfour
a0, a1, a2, a3 = list(self.get_params(index))
if fc is not None:
a3 = 2.0 * fc
a1 = -4.0 * fc * np.cos(a0)**2
for jterm in masterslaves:
ics = self.terms[jterm].ics
args = ([0.0, a1, 0.0, a3], ) + tuple(ics)
val.add_term(PolyFour(*args))
elif kind == 0: #Harmonic:
k, rv = self.get_params(index)
if fc is not None: k = fc
for jterm in masterslaves:
ics = self.terms[jterm].ics
args = (k, rv) + tuple(ics)
val.add_term(Harmonic(*args))
else:
raise ValueError('Term kind %i not supported' % kind)
ff = ForceField(self.system, [val])
hcov = estimate_cart_hessian(ff)
return hcov
def run(self, ff):
result = GeoOptSimulation.run(self, ff)
result['hessian'] = estimate_cart_hessian(ff)
return result
def hessian(self, coords):
self.ff.update_pos(coords.copy())
hess = estimate_cart_hessian(self.ff)
natoms = len(coords)
return hess.reshape([natoms, 3, natoms, 3])