def __init__(self,
system,
term,
other_terms,
cart_penalty=1e-3 * angstrom):
'''
A class deriving from the Yaff ForceField class to implement the
strain of a molecular geometry associated with the term defined by
term_index.
**Arguments**
system
A Yaff System instance containing all system information.
term
a Term instance representing the term of the perturbation
trajectory of the current strain
other_terms
a list of Term instances representing all other terms for ICs
for which a strain contribution should be added
**Keyword Arguments**
cart_penalty
Magnitude of an extra term added to the strain that penalises
a deviation of the cartesian coordinates of each atom with
respect to the equilibrium coordinates. This penalty is equal
to norm(R-R_eq)**2/(2.0*3*Natoms*cart_penalty**2) and prevents
global translations, global rotations as well as rotations of
molecular fragments far from the IC under consideration.
'''
self.coords0 = system.pos.copy()
self.ndof = np.prod(self.coords0.shape)
self.cart_penalty = cart_penalty
self.cons_ic_atindexes = term.get_atoms()
#construct main strain
strain = ForcePartValence(system)
for other in other_terms:
if other.kind == 3: continue #no cross terms
strain.add_term(Harmonic(1.0, None, other.ics[0]))
#set the rest values to the equilibrium values
strain.dlist.forward()
strain.iclist.forward()
for iterm in range(strain.vlist.nv):
vterm = strain.vlist.vtab[iterm]
ic = strain.iclist.ictab[vterm['ic0']]
vterm['par1'] = ic['value']
ForceField.__init__(self, system, [strain])
#Abuse the Chebychev1 polynomial to simply get the value of q-1 and
#implement the contraint
constraint = ForcePartValence(system)
constraint.add_term(Chebychev1(-2.0, term.ics[0]))
self.constraint = ForceField(system, [constraint])
self.constrain_target = None
self.constrain_value = None
self.value = None
def get_ei_ff(name, system, charges, scales, radii=None, average=True, pbc=[0,0,0]):
'''
A routine to construct a Yaff force field for the electrostatics
**Arguments**
name
A string for the name of the force field. This name will show in
possible plots visualizing contributions along perturbation
trajectories
system
A Yaff System instance representing the system
charges
A numpy array containing the charge of each separate atom
scales
A list of 4 floats, representing scale1, scale2, scale3, scale4,
i.e. the electrostatic scaling factors
**Optional Arguments**
radii
A numpy array containing the gaussian radii of each separate atom.
If this argument is omitted, point charges are used.
average
If set to True, the charges and radii will first be averaged over
atom types. This is True by default.
'''
if not (np.array(pbc)==0).all():
raise NotImplementedError('Periodic system not implemented in get_ei_ff')
if average:
qs = {}
rs = {}
ffatypes = [system.ffatypes[i] for i in system.ffatype_ids]
for i, atype in enumerate(ffatypes):
if atype in qs: qs[atype].append(charges[i])
else: qs[atype] = [charges[i]]
if radii is not None:
if atype in rs: rs[atype].append(radii[i])
else: rs[atype] = [radii[i]]
for i, atype in enumerate(ffatypes):
charges[i] = np.array(qs[atype]).mean()
if radii is not None:
radii[i] = np.array(rs[atype]).mean()
if radii is None: radii = np.zeros(len(system.ffatype_ids), float)
pair_pot = PairPotEI(charges.astype(np.float), 0.0, 50*angstrom, None, 1.0, radii.astype(np.float))
nlist = NeighborList(system, 0)
scalings = Scalings(system, scale1=scales[0], scale2=scales[1], scale3=scales[2], scale4=scales[3])
part = ForcePartPair(system, nlist, scalings, pair_pot)
ff = ForceField(system, [part], nlist=nlist)
return YaffForceField(name, ff)
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 __init__(self,
system,
cons_ic,
cons_ic_atindexes,
ics,
cart_penalty=1e-3 * angstrom):
'''
A class deriving from the Yaff ForceField class to implement the
strain of a molecular geometry associated with the term defined by
term_index.
**Arguments**
system
A Yaff System instance containing all system information.
cons_ic
An instance of Yaff Internal Coordinate representing the
constrained term in the strain.
cons_ic_atindexes
A list of the atoms involved in the constrained IC. This is
required for the implementation of the cartesian penalty. In
principle this could be extracted from the information stored
in cons_ic, but this is the lazy solution.
ics
A list of Yaff Internal Coordinate instances for which the
strain needs to be minimized.
cart_penalty
Magnitude of an extra term added to the strain that penalises
a deviation of the cartesian coordinates of each atom with
respect to the equilibrium coordinates. This penalty is equal
to norm(R-R_eq)**2/(2.0*3*Natoms*cart_penalty**2) and prevents
global translations, global rotations as well as rotations of
molecular fragments far from the IC under consideration.
'''
self.coords0 = system.pos.copy()
self.ndof = np.prod(self.coords0.shape)
self.cart_penalty = cart_penalty
self.cons_ic_atindexes = cons_ic_atindexes
part = ForcePartValence(system)
for ic in ics:
part.add_term(Harmonic(1.0, None, ic))
#set the rest values to the equilibrium values
part.dlist.forward()
part.iclist.forward()
for iterm in xrange(part.vlist.nv):
term = part.vlist.vtab[iterm]
ic = part.iclist.ictab[term['ic0']]
term['par1'] = ic['value']
ForceField.__init__(self, system, [part])
#Abuse the Chebychev1 polynomial to simply get the value of q-1 and
#implement the contraint
part = ForcePartValence(system)
part.add_term(Chebychev1(-2.0, cons_ic))
self.constraint = ForceField(system, [part])
self.constrain_target = None
self.constrain_value = None
self.value = None