def do_bendcharm(self, thresshold=2 * deg):
'''
No Harmonic bend can have a rest value equal to are large than
180 deg - thresshold. If a master (or its slaves) has such a rest
value, convert master and all slaves to BendCharm with
cos(phis0)=-1.
'''
for master in self.valence.iter_masters(label='BendAHarm'):
indices = [master.index]
for slave in master.slaves:
indices.append(slave)
found = False
for index in indices:
rv = self.valence.get_params(index, only='rv')
if rv >= 180.0 * deg - thresshold:
found = True
break
if found:
log.dump(
'%s has rest value > 180-%.0f deg, converted to BendCHarm with cos(phi0)=-1'
% (master.basename, thresshold / deg))
for index in indices:
term = self.valence.terms[index]
self.valence.modify_term(
index, Harmonic, [BendCos(*term.get_atoms())],
term.basename.replace('BendAHarm', 'BendCHarm'),
['HC_FC_DIAG'], ['kjmol', 'au'])
self.valence.set_params(index, fc=0.0, rv0=-1.0)
for traj in self.trajectories:
if traj.term.index == index:
traj.rv = None
traj.fc = None
traj.active = False
def do_squarebend(self, thresshold=20 * deg):
'''
Identify bend patterns in which 4 atoms of type A surround a central
atom of type B with A-B-A angles of 90/180 degrees. A simple
harmonic pattern will not be adequate since a rest value of 90 and
180 degrees is possible for the same A-B-A term. Therefore, a
cosine term with multiplicity of 4 is used (which corresponds to a
chebychev4 potential with sign=-1):
V = K/2*[1-cos(4*theta)]
To identify the patterns, it is assumed that the rest values have
already been estimated from the perturbation trajectories. For each
master and slave of a BENDAHARM term, its rest value is computed and
checked if it lies either the interval [90-thresshold,90+thresshold]
or [180-thresshold,180]. If this is the case, the new cosine term
is used.
**Optional arguments**
thresshold
the (half) the width of the interval around 180 deg (90 degrees)
to check if a square BA4
'''
for master in self.valence.iter_masters(label='BendAHarm'):
rvs = np.zeros([len(master.slaves) + 1], float)
rvs[0] = self.valence.get_params(master.index, only='rv')
for i, islave in enumerate(master.slaves):
rvs[1 + i] = self.valence.get_params(islave, only='rv')
n90 = 0
n180 = 0
nother = 0
for i, rv in enumerate(rvs):
if 90 * deg - thresshold <= rv and rv <= 90 * deg + thresshold:
n90 += 1
elif 180 * deg - thresshold <= rv and rv <= 180 * deg + thresshold:
n180 += 1
else:
nother += 1
if n90 > 0 and n180 > 0:
log.dump(
'%s has rest values around 90 deg and 180 deg, converted to BendCheby4'
% master.basename)
#modify master and slaves
indices = [master.index]
for slave in master.slaves:
indices.append(slave)
for index in indices:
term = self.valence.terms[index]
self.valence.modify_term(
index, Chebychev4, [BendCos(*term.get_atoms())],
term.basename.replace('BendAHarm', 'BendCheby4'),
['HC_FC_DIAG'], ['kjmol', 'au'])
self.valence.set_params(index, sign=-1)
for traj in self.trajectories:
if traj.term.index == index:
traj.active = False
traj.fc = None
traj.rv = None