def satisfy(self, vterm, pars, part, system):
if self.pars == pars:
part_valence = ForcePartValence(system)
part_valence.add_term(vterm)
energy = part_valence.compute()
ic_index = part_valence.vlist.vtab[0]['ic0']
ic = part_valence.vlist.iclist.ictab[ic_index]['value']
return np.abs(ic - self.rv) < self.eps
else:
return True
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_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, specs=None):
'''
**Arguments**
system
an instance of the Yaff System class containing all system
properties
**Keyword Arguments**
specs
Not yet implemented
'''
with log.section('VAL', 2, timer='Initializing'):
log.dump('Initializing valence force field')
self.system = system
self.terms = []
ForcePartValence.__init__(self, system)
self.init_bond_terms()
self.init_bend_terms()
self.init_dihedral_terms()
self.init_oop_terms()
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 __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
def add_term(self, pot, ics, atypes, tasks, units):
'''
Adds new term both to the Yaff vlist object and a new QuickFF
list (self.terms) which holds all information about the term
for easy access later in QuickFF.
**Arguments**
pot
an instance of ValenceTerm from `yaff.pes.vlist.py` representing
the potential chosen for the term
ics
list of InternalCoordinate instances from `yaff.pes.iclist.py`
atypes
ordered string of atom types (required to assign name to the
term)
tasks
List of strings defining all tasks that have to be performed for
this term. Possible tasks are: PT_ALL, HC_FC_DIAG, HC_FC_CROSS,
EQ_RV.
units
Units for all parameters in this term (ordered in the same
way as parameters are stored in `yaff.vlist.vtab`)
'''
index = len(self.terms)
#define the name
if len(ics) == 1:
tmp = {
(0, 0): 'BondHarm/',
(2, 0): 'BendAHarm/',
(4, 4): 'Torsion/',
(3, 1): 'TorsC2Harm/',
(10, 0): 'Oopdist/',
(11, 0): 'SqOopdist/',
}
prefix = tmp[(ics[0].kind, pot.kind)]
suffix = ''
else:
assert len(ics) == 2 and pot.kind == 3
prefix = 'Cross/'
if ics[0].kind == 0 and ics[1].kind == 0:
suffix = '/bb' #first bond and second bond
elif ics[0].kind == 0 and ics[1].kind == 2:
if set(ics[0].index_pairs[0]) == set(ics[1].index_pairs[0]):
suffix = '/b0a' #first bond and angle
elif set(ics[0].index_pairs[0]) == set(ics[1].index_pairs[1]):
suffix = '/b1a' #second bond and angle
else:
raise ValueError(
'Incompatible bond/angle given in cross term')
else:
raise ValueError('Incompatible ICs given in cross term')
basename = prefix + '.'.join(atypes) + suffix
#search for possible master and update slaves
master = None
slaves = None
for i, term in enumerate(self.terms):
if term.basename == basename:
if term.is_master():
master = term.index
term.slaves.append(index)
else:
assert master == term.master
if master is None:
master = index
slaves = []
#add term to self.terms and self.vlist.vtab
term = Term(index,
basename,
pot.kind,
ics,
tasks,
units,
master=master,
slaves=slaves)
self.terms.append(term)
if pot.kind == 1: #all 4 parameters of PolyFour are given as 1 tuple
args = [(None, ) * len(units)] + ics
else:
args = [
None,
] * len(units) + ics
ForcePartValence.add_term(self, pot(*args))
return term