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, 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 __call__(self, parameters):
# prepare force field
ff = ForceField.generate(self.system, parameters, **self.kwargs)
# run actual simulation
return self.run(ff)
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
class Strain(ForceField):
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 gradient(self, X):
'''
Compute the gradient of the strain wrt Cartesian coordinates of the
system. For every ic that needs to be constrained, a Lagrange multiplier
is included.
'''
#small check
#assert X.shape[0] == self.ndof + 1
#initialize return value
grad = np.zeros((len(X), ))
#compute strain gradient
gstrain = np.zeros(self.coords0.shape)
self.update_pos(self.coords0 + X[:self.ndof].reshape((-1, 3)))
self.value = self.compute(gpos=gstrain)
#compute constraint gradient
gconstraint = np.zeros(self.coords0.shape)
self.constraint.update_pos(self.coords0 +
X[:self.ndof].reshape((-1, 3)))
self.constrain_value = self.constraint.compute(gpos=gconstraint) + 1.0
#construct gradient
grad[:self.ndof] = gstrain.reshape(
(-1, )) + X[self.ndof] * gconstraint.reshape((-1, ))
grad[self.ndof] = self.constrain_value - self.constrain_target
#cartesian penalty, i.e. extra penalty for deviation w.r.t. cartesian equilibrium coords
indices = np.array([[3 * i, 3 * i + 1, 3 * i + 2]
for i in xrange(self.ndof / 3)
if i not in self.cons_ic_atindexes]).ravel()
if len(indices) > 0:
grad[indices] += X[indices] / (self.ndof * self.cart_penalty**2)
with log.section('PTGEN', 4, timer='PT Generate'):
log.dump(' Gradient: rms = %.3e max = %.3e cnstr = %.3e' %
(np.sqrt(
(grad[:self.ndof]**2).mean()), max(
grad[:self.ndof]), grad[self.ndof]))
return grad
class Strain(ForceField):
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 gradient(self, X):
'''
Compute the gradient of the strain w.r.t. Cartesian coordinates of
the system. For the ic that needs to be constrained, a Lagrange
multiplier is included.
'''
#initialize return value
grad = np.zeros((len(X),))
#compute strain gradient
gstrain = np.zeros(self.coords0.shape)
self.update_pos(self.coords0 + X[:self.ndof].reshape((-1,3)))
self.value = self.compute(gpos=gstrain)
#compute constraint gradient
gconstraint = np.zeros(self.coords0.shape)
self.constraint.update_pos(self.coords0 + X[:self.ndof].reshape((-1,3)))
self.constrain_value = self.constraint.compute(gpos=gconstraint) + 1.0
#construct gradient
grad[:self.ndof] = gstrain.reshape((-1,)) + X[self.ndof]*gconstraint.reshape((-1,))
grad[self.ndof] = self.constrain_value - self.constrain_target
#cartesian penalty, i.e. extra penalty for deviation w.r.t. cartesian equilibrium coords
indices = np.array([[3*i,3*i+1,3*i+2] for i in range(self.ndof//3) if i not in self.cons_ic_atindexes]).ravel()
if len(indices)>0:
grad[indices] += X[indices]/(self.ndof*self.cart_penalty**2)
with log.section('PTGEN', 4, timer='PT Generate'):
log.dump(' Gradient: rms = %.3e max = %.3e cnstr = %.3e' %(np.sqrt((grad[:self.ndof]**2).mean()), max(grad[:self.ndof]), grad[self.ndof]))
return grad
class Strain(ForceField):
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 gradient(self, X):
'''
Compute the gradient of the strain w.r.t. Cartesian coordinates of
the system. For the ic that needs to be constrained, a Lagrange
multiplier is included.
'''
#initialize return value
grad = np.zeros((len(X),))
#compute strain gradient
gstrain = np.zeros(self.coords0.shape)
self.update_pos(self.coords0 + X[:self.ndof].reshape((-1,3)))
self.value = self.compute(gpos=gstrain)
#compute constraint gradient
gconstraint = np.zeros(self.coords0.shape)
self.constraint.update_pos(self.coords0 + X[:self.ndof].reshape((-1,3)))
self.constrain_value = self.constraint.compute(gpos=gconstraint) + 1.0
#construct gradient
grad[:self.ndof] = gstrain.reshape((-1,)) + X[self.ndof]*gconstraint.reshape((-1,))
grad[self.ndof] = self.constrain_value - self.constrain_target
#cartesian penalty, i.e. extra penalty for deviation w.r.t. cartesian equilibrium coords
indices = np.array([[3*i,3*i+1,3*i+2] for i in range(self.ndof//3) if i not in self.cons_ic_atindexes]).ravel()
if len(indices)>0:
grad[indices] += X[indices]/(self.ndof*self.cart_penalty**2)
with log.section('PTGEN', 4, timer='PT Generate'):
log.dump(' Gradient: rms = %.3e max = %.3e cnstr = %.3e' %(np.sqrt((grad[:self.ndof]**2).mean()), max(grad[:self.ndof]), grad[self.ndof]))
return grad
def write_raspa_input(guests,
parameters,
host=None,
workdir='.',
guestdata=None,
hostname='host'):
"""
Prepare input files that can be used to run RASPA simulations. Only a
small subset of the full capabilities of RASPA can be explored.
**Arguments:**
guests
A list specifying the guest molecules. Each entry can be one of
two types: (i) the filename of a system file
describing one guest molecule, (ii) a System instance of
one guest molecule
parameters
Force-field parameters describing guest-guest and optionally
host-guest interaction.
Three types are accepted: (i) the filename of the parameter
file, which is a text file that adheres to YAFF parameter
format, (ii) a list of such filenames, or (iii) an instance of
the Parameters class.
**Optional arguments:**
host
Two types are accepted: (i) the filename of a system file
describing the host system, (ii) a System instance of the host
workdir
The directory where output files will be placed.
guestdata
List with the same length as guests. Each entry contains a tuple
either looking as (name, Tc, Pc, omega) or (name). In the latter
case, the parameters Tc, Pc, and omega will be loaded from a data
file based on the name. Otherwise, these will be left blank in the
input file.
"""
# Load the guest Systems
guests = [
System.from_file(guest) if isinstance(guest, str) else guest
for guest in guests
]
for guest in guests:
assert isinstance(guest, System)
if guestdata is None:
guestdata = [("guest%03d" % iguest, ) for iguest in range(len(guests))]
assert len(guests) == len(guestdata)
# Load the host System
if host is not None:
if isinstance(host, str):
host = System.from_file(host)
assert isinstance(host, System)
complex = host
# Merge all systems
for guest in guests:
complex = complex.merge(guest)
# Generate the ForceField, we don't really care about settings such as
# cutoffs etc. We only need the parameters in the end
ff = ForceField.generate(complex, parameters)
# Write the force-field parameters
write_raspa_forcefield(ff, workdir)
# Write masses and charges of all atoms
ffatypes, ffatype_ids = write_pseudo_atoms(ff, workdir)
# Write the guest information
if host == None: counter = 0
else: counter = host.natom
for iguest, (guest, data) in enumerate(zip(guests, guestdata)):
write_guest(guest, data, workdir, [
ffatypes[iffa]
for iffa in ffatype_ids[counter:counter + guest.natom]
])
counter += guest.natom
# Write the host coordinates to a cif file
if host is not None:
dump_cif(
host,
os.path.join(workdir, '%s.cif' % hostname),
ffatypes=[ffatypes[iffa] for iffa in ffatype_ids[:host.natom]])
# A fairly standard input file for GCMC simulations
dump_input(workdir, hostname, [data[0] for data in guestdata])
def ff_generator(system, guest):
return ForceField.generate(system, parameters, nlow=max(0,system.natom-guest.natom), nhigh=max(0,system.natom-guest.natom), **kwargs)
def from_files(cls, guest, parameters, **kwargs):
"""Automated setup of GCMC simulation
**Arguments:**
guest
Two types are accepted: (i) the filename of a system file
describing one guest molecule, (ii) a System instance of
one guest molecule
parameters
Force-field parameters describing guest-guest and optionally
host-guest interaction.
Three types are accepted: (i) the filename of the parameter
file, which is a text file that adheres to YAFF parameter
format, (ii) a list of such filenames, or (iii) an instance of
the Parameters class.
**Optional arguments:**
hooks
A list of MCHooks
host
Two types are accepted: (i) the filename of a system file
describing the host system, (ii) a System instance of the host
All other keyword arguments are passed to the ForceField constructor
See the constructor of the :class:`yaff.pes.generator.FFArgs` class
for the available optional arguments.
"""
# Load the guest System
if isinstance(guest, str):
guest = System.from_file(guest)
assert isinstance(guest, System)
# We want to control nlow and nhigh here ourselves, so remove it from the
# optional arguments if the user provided it.
kwargs.pop('nlow', None)
kwargs.pop('nhigh', None)
# Rough guess for number of adsorbed guests
nguests = kwargs.pop('nguests', 10)
# Load the host if it is present as a keyword
host = kwargs.pop('host', None)
# Extract the hooks
hooks = kwargs.pop('hooks', [])
# Efficient treatment of reciprocal ewald contribution
if not 'reci_ei' in kwargs.keys():
kwargs['reci_ei'] = 'ewald_interaction'
if host is not None:
if isinstance(host, str):
host = System.from_file(host)
assert isinstance(host, System)
# If the guest molecule is currently an isolated molecule, than put
# it in the same periodic box as the host
if guest.cell is None or guest.cell.nvec==0:
guest.cell = Cell(host.cell.rvecs)
# Construct a complex of host and one guest and the corresponding
# force field excluding host-host interactions
hostguest = host.merge(guest)
external_potential = ForceField.generate(hostguest, parameters,
nlow=host.natom, nhigh=host.natom, **kwargs)
else:
external_potential = None
# # Compare the energy of the guest, once isolated, once in a periodic box
# guest_isolated = guest.subsystem(np.arange(guest.natom))
# guest_isolated.cell = Cell(np.zeros((0,3)))
# optional_arguments = {}
# for key in kwargs.keys():
# if key=='reci_ei': continue
# optional_arguments[key] = kwargs[key]
# ff_guest_isolated = ForceField.generate(guest_isolated, parameters, **optional_arguments)
# e_isolated = ff_guest_isolated.compute()
# guest_periodic = guest.subsystem(np.arange(guest.natom))
# ff_guest_periodic = ForceField.generate(guest_periodic, parameters, **optional_arguments)
# e_periodic = ff_guest_periodic.compute()
# if np.abs(e_isolated-e_periodic)>1e-4:
# if log.do_warning:
# log.warn("An interaction energy of %s of the guest with its periodic "
# "images was detected. The interaction of a guest with its periodic "
# "images will however NOT be taken into account in this simulation. "
# "If the energy difference is large compared to k_bT, you should "
# "consider using a supercell." % (log.energy(e_isolated-e_periodic)))
# By making use of nlow=nhigh, we automatically discard intramolecular energies
eguest = 0.0
# Generator of guest-guest force fields, excluding interactions
# between the first N-1 guests
def ff_generator(system, guest):
return ForceField.generate(system, parameters, nlow=max(0,system.natom-guest.natom), nhigh=max(0,system.natom-guest.natom), **kwargs)
return cls(guest, ff_generator, external_potential=external_potential,
eguest=eguest, hooks=hooks, nguests=nguests)