def _get_system_copy(self):
'Routine to get a copy of the equilibrium system'
numbers = self.system0.numbers.copy()
coords = self.system0.pos.copy()
rvecs = self.system_rvecs.copy()
masses = self.system0.masses.copy()
bonds = self.system0.bonds.copy()
ffatypes = self.system0.ffatypes.copy()
ffatype_ids = self.system0.ffatype_ids.copy()
return System(
numbers, coords, rvecs=rvecs,
ffatypes=ffatypes, ffatype_ids=ffatype_ids,
masses=masses, bonds=bonds
)
def _generate_ffs(self, nguests):
for iguest in range(len(self._ffs),nguests):
if len(self._ffs)==0:
# The very first force field, no guests
system = System.create_empty()
system.cell = Cell(self.guest.cell.rvecs)
elif len(self._ffs)==1:
# The first real force field, a single guest
system = self.guest
else:
# Take the system of the lastly generated force field (N-1) guests
# and add an additional guest
system = self._ffs[-1].system.merge(self.guest)
self._ffs.append(self.ff_generator(system, self.guest))
def simulate():
T = 298.0*kelvin
# Input files
fn_guest = 'CO2.chk'
fn_host = 'MIL53.chk'
fn_pars = ['pars.txt']
host = System.from_file(fn_host).supercell(1,1,1)
# Description of allowed MC moves and their corresponding probabilities
mc_moves = {'insertion':1.0, 'deletion':1.0,
'translation':1.0, 'rotation':1.0}
# Construct equation of state to link pressure, fugacity and chemical potential
eos = PREOS.from_name('carbondioxide')
# Loop over pressures to construct isotherm
pressures = np.array([0.1,0.5,1.0,3.0,5.0,10.0])*bar
uptake = np.zeros(pressures.shape)
for iP, P in enumerate(pressures):
fugacity = eos.calculate_fugacity(T,P)
mu = eos.calculate_mu(T,P)
# Screen logger
screenlog = MCScreenLog(step=10000)
# HDF5 logger
fh5 = h5.File('trajectory_%d.h5'%iP,'w')
hdf5writer = MCHDF5Writer(fh5, step=10000)
# Setup the GCMC calculation, this generates a lot of output so when
# force fields are generated, so we silence the logging for a while.
log.set_level(log.silent)
gcmc = GCMC.from_files(fn_guest, fn_pars, host=host,
rcut=12.0*angstrom, tr=None, tailcorrections=True, hooks=[screenlog, hdf5writer],
reci_ei='ewald_interaction', nguests=30)
log.set_level(log.medium)
# Set the external conditions
gcmc.set_external_conditions(T, fugacity)
# Run MC simulation
gcmc.run(1000000, mc_moves=mc_moves)
uptake[iP] = gcmc.Nmean
fh5.close()
np.save('results.npy', np.array([pressures,uptake]).T)
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 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)