def __call__(self, iterative):
r'''When this point is reached, a complete time integration step was
finished and PLUMED should be notified about this.
'''
if not self.hooked:
if log.do_high:
log.hline()
log("Reinitializing PLUMED")
log.hline()
if log.do_warning:
log.warn("You are using PLUMED as a hook for your integrator. "
"If PLUMED adds time-dependent forces (for instance "
"when performing metadynamics) there is no energy "
"conservation. The conserved quantity reported by "
"YAFF is irrelevant in this case.")
self.setup_plumed(timestep=iterative.timestep,
restart=iterative.counter > 0)
self.hooked = True
# PLUMED provides a setEnergy command, which should pass the
# current potential energy. It seems that this is never used, so we
# don't pass anything for the moment.
# current_energy = sum([part.energy for part in iterative.ff.parts[:-1] if not isinstance(part, ForcePartPlumed)])
# self.plumed.cmd("setEnergy", current_energy)
self.plumedstep = iterative.counter
self._internal_compute(None, None)
self.plumed.cmd("update")
def apply_generators(system, parameters, ff_args):
'''Populate the attributes of ff_args, prepares arguments for ForceField
**Arguments:**
system
A System instance for which the force field object is being made
ff_args
An instance of the FFArgs class.
parameters
An instance of the Parameters, typically made by
``Parmaeters.from_file('parameters.txt')``.
'''
# Collect all the generators that have a prefix.
generators = {}
for x in globals().values():
if isinstance(x, type) and issubclass(x, Generator) and x.prefix is not None:
generators[x.prefix] = x()
# Go through all the sections of the parameter file and apply the
# corresponding generator.
for prefix, section in parameters.sections.iteritems():
generator = generators.get(prefix)
if generator is None:
if log.do_warning:
log.warn('There is no generator named %s.' % prefix)
else:
generator(system, section, ff_args)
def apply(self, par_table, system, ff_args):
'''Generate terms for the system based on the par_table
**Arguments:**
par_table
A dictionary with tuples of ffatypes is keys and lists of
parameters as values.
system
The system for which the force field is generated.
ff_args
An instance of the FFArgs class.
'''
if system.bonds is None:
raise ValueError('The system must have bonds in order to define valence cross terms.')
part_valence = ff_args.get_part_valence(system)
for indexes in self.iter_indexes(system):
key = tuple(system.get_ffatype(i) for i in indexes)
par_list = par_table.get(key, [])
if len(par_list) == 0 is None and log.do_warning:
log.warn('No valence %s parameters found for atoms %s with key %s' % (self.prefix, indexes, key))
continue
for pars in par_list:
indexes0 = self.get_indexes0(indexes)
indexes1 = self.get_indexes1(indexes)
indexes2 = self.get_indexes2(indexes)
args_01 = (pars[0], pars[3], pars[4]) + (self.ICClass0(*indexes0), self.ICClass1(*indexes1))
args_02 = (pars[1], pars[3], pars[5]) + (self.ICClass0(*indexes0), self.ICClass2(*indexes2))
args_12 = (pars[2], pars[4], pars[5]) + (self.ICClass1(*indexes1), self.ICClass2(*indexes2))
part_valence.add_term(self.VClass01(*args_01))
part_valence.add_term(self.VClass02(*args_02))
part_valence.add_term(self.VClass12(*args_12))
def apply(self, par_table, system, ff_args):
'''Generate terms for the system based on the par_table
**Arguments:**
par_table
A dictionary with tuples of ffatypes is keys and lists of
parameters as values.
system
The system for which the force field is generated.
ff_args
An instance of the FFArgs class.
'''
if system.bonds is None:
raise ValueError('The system must have bonds in order to define valence terms.')
part_valence = ff_args.get_part_valence(system)
for indexes in self.iter_indexes(system):
key = tuple(system.get_ffatype(i) for i in indexes)
par_list = par_table.get(key, [])
if len(par_list) == 0 and log.do_warning:
log.warn('No valence %s parameters found for atoms %s with key %s' % (self.prefix, indexes, key))
continue
for pars in par_list:
vterm = self.get_vterm(pars, indexes)
part_valence.add_term(vterm)
def apply(self, par_table, scale_table, system, ff_args):
# Prepare the atomic parameters
sigmas = np.zeros(system.natom)
epsilons = np.zeros(system.natom)
onlypaulis = np.zeros(system.natom, np.int32)
for i in xrange(system.natom):
key = (system.get_ffatype(i),)
par_list = par_table.get(key, [])
if len(par_list) == 0:
if log.do_warning:
log.warn('No MM3 parameters found for atom %i with fftype %s.' % (i, system.get_ffatype(i)))
else:
sigmas[i], epsilons[i], onlypaulis[i] = par_list[0]
# Prepare the global parameters
scalings = Scalings(system, scale_table[1], scale_table[2], scale_table[3])
# Get the part. It should not exist yet.
part_pair = ff_args.get_part_pair(PairPotMM3)
if part_pair is not None:
raise RuntimeError('Internal inconsistency: the MM3 part should not be present yet.')
pair_pot = PairPotMM3(sigmas, epsilons, onlypaulis, ff_args.rcut, ff_args.tr)
nlist = ff_args.get_nlist(system)
part_pair = ForcePartPair(system, nlist, scalings, pair_pot)
ff_args.parts.append(part_pair)
def apply_lammps_generators(system, parameters):
'''Populate the attributes of ff_args, prepares arguments for ForceField
**Arguments:**
system
A System instance for which the force field object is being made
parameters
An instance of the Parameters, typically made by
``Parmaeters.from_file('parameters.txt')``.
'''
# Collect all the generators that have a prefix.
generators = {}
for x in globals().values():
if isinstance(x, type) and issubclass(
x, Generator) and x.prefix is not None:
generators[x.prefix] = x()
output = {}
# Go through all the sections of the parameter file and apply the
# corresponding generator.
for prefix, section in parameters.sections.items():
generator = generators.get(prefix)
if generator is None:
if log.do_warning:
log.warn(
'There is no generator named %s. It will be ignored.' %
prefix)
else:
output[prefix] = generator(system, section)
return output
def propagate(self):
success = self.minimizer.propagate()
self.x = self.minimizer.x
if success == False:
if log.do_warning:
log.warn('Line search failed in optimizer. Aborting optimization. This is probably due to a dicontinuity in the energy or the forces. Check the truncation of the non-bonding interactions and the Ewald summation parameters.')
return True
return BaseOptimizer.propagate(self)
def set_standard_masses(self):
"""Initialize the ``masses`` attribute based on the atomic numbers."""
with log.section('SYS'):
from molmod.periodic import periodic
if self.masses is not None:
if log.do_warning:
log.warn('Overwriting existing masses with default masses.')
self.masses = np.array([periodic[n].mass for n in self.numbers])
def propagate(self):
success = self.minimizer.propagate()
self.x = self.minimizer.x
if success == False:
if log.do_warning:
log.warn('Line search failed in optimizer. Aborting optimization. This is probably due to a dicontinuity in the energy or the forces. Check the truncation of the non-bonding interactions and the Ewald summation parameters.')
return True
return BaseOptimizer.propagate(self)
def set_standard_masses(self):
"""Initialize the ``masses`` attribute based on the atomic numbers."""
with log.section('SYS'):
from molmod.periodic import periodic
if self.masses is not None:
if log.do_warning:
log.warn('Overwriting existing masses with default masses.')
self.masses = np.array([periodic[n].mass for n in self.numbers])
def g09log_to_hdf5(f, fn_log):
"""Convert Gaussian09 BOMD log file to Yaff HDF5 format.
**Arguments:**
f
An open and writable HDF5 file.
fn_log
The name of the Gaussian log file.
"""
with log.section('G09H5'):
if log.do_medium:
log('Loading Gaussian 09 file \'%s\' into \'trajectory\' of HDF5 file \'%s\'' % (
fn_log, f.filename
))
# First make sure the HDF5 file has a system description that is consistent
# with the XYZ file.
if 'system' not in f:
raise ValueError('The HDF5 file must contain a system group.')
if 'numbers' not in f['system']:
raise ValueError('The HDF5 file must have a system group with atomic numbers.')
natom = f['system/numbers'].shape[0]
# Take care of the trajectory group
tgrp = get_trajectory_group(f)
# Take care of the pos and vel datasets
dss = get_trajectory_datasets(tgrp,
('pos', (natom, 3)),
('vel', (natom, 3)),
('frc', (natom, 3)),
('time', (1,)),
('step', (1,)),
('epot', (1,)),
('ekin', (1,)),
('etot', (1,)),
)
ds_pos, ds_vel, ds_frc, ds_time, ds_step, ds_epot, ds_ekin, ds_etot = dss
# Load frame by frame
row = get_last_trajectory_row(dss)
for numbers, pos, vel, frc, time, step, epot, ekin, etot in _iter_frames_g09(fn_log):
if (numbers != f['system/numbers']).any():
log.warn('The element numbers of the HDF5 and LOG file do not match.')
write_to_dataset(ds_pos, pos, row)
write_to_dataset(ds_vel, vel, row)
write_to_dataset(ds_frc, frc, row)
write_to_dataset(ds_time, time, row)
write_to_dataset(ds_step, step, row)
write_to_dataset(ds_epot, epot, row)
write_to_dataset(ds_ekin, ekin, row)
write_to_dataset(ds_etot, etot, row)
row += 1
# Check number of rows
check_trajectory_rows(tgrp, dss, row)
def apply(self, par_table, cpar_table, scale_table, mixing_rules, system, ff_args):
# Prepare the atomic parameters
amps = np.zeros(system.nffatype, float)
bs = np.zeros(system.nffatype, float)
for i in xrange(system.nffatype):
key = (system.ffatypes[i],)
par_list = par_table.get(key, [])
if len(par_list) == 0:
if log.do_warning:
log.warn('No EXPREP parameters found for ffatype %s.' % system.ffatypes[i])
else:
amps[i], bs[i] = par_list[0]
# Prepare the cross parameters
amp_cross = np.zeros((system.nffatype, system.nffatype), float)
b_cross = np.zeros((system.nffatype, system.nffatype), float)
for i0 in xrange(system.nffatype):
for i1 in xrange(i0+1):
cpar_list = cpar_table.get((system.ffatypes[i0], system.ffatypes[i1]), [])
if len(cpar_list) == 0:
if log.do_high:
log('No EXPREP cross parameters found for ffatypes %s,%s. Mixing rule will be used' % (system.ffatypes[i0], system.ffatypes[i1]))
else:
amp_cross[i0,i1], b_cross[i0,i1] = cpar_list[0]
if i0 != i1:
amp_cross[i1,i0], b_cross[i1,i0] = cpar_list[0]
# Prepare the global parameters
scalings = Scalings(system, scale_table[1], scale_table[2], scale_table[3])
amp_mix, amp_mix_coeff = mixing_rules['A']
if amp_mix == 0:
amp_mix_coeff = 0.0
elif amp_mix == 1:
amp_mix_coeff = amp_mix_coeff[0]
b_mix, b_mix_coeff = mixing_rules['B']
if b_mix == 0:
b_mix_coeff = 0.0
elif b_mix == 1:
b_mix_coeff = b_mix_coeff[0]
# Get the part. It should not exist yet.
part_pair = ff_args.get_part_pair(PairPotExpRep)
if part_pair is not None:
raise RuntimeError('Internal inconsistency: the EXPREP part should not be present yet.')
pair_pot = PairPotExpRep(
system.ffatype_ids, amp_cross, b_cross, ff_args.rcut, ff_args.tr,
amps, amp_mix, amp_mix_coeff, bs, b_mix, b_mix_coeff,
)
nlist = ff_args.get_nlist(system)
part_pair = ForcePartPair(system, nlist, scalings, pair_pot)
ff_args.parts.append(part_pair)
def _verify_hooks(self):
with log.section('ENSEM'):
thermo = None
index_thermo = 0
baro = None
index_baro = 0
# Look for the presence of a thermostat and/or barostat
if hasattr(self.hooks, '__len__'):
for index, hook in enumerate(self.hooks):
if hook.method == 'thermostat':
thermo = hook
index_thermo = index
elif hook.method == 'barostat':
baro = hook
index_baro = index
elif self.hooks is not None:
if self.hooks.method == 'thermostat':
thermo = self.hooks
elif self.hooks.method == 'barostat':
baro = self.hooks
# If both are present, delete them and generate TBCombination element
if thermo is not None and baro is not None:
from yaff.sampling.npt import TBCombination
if log.do_warning:
log.warn(
'Both thermostat and barostat are present separately and will be merged'
)
del self.hooks[max(index_thermo, index_thermo)]
del self.hooks[min(index_thermo, index_baro)]
self.hooks.append(TBCombination(thermo, baro))
if hasattr(self.hooks, '__len__'):
for hook in self.hooks:
if hook.name == 'TBCombination':
thermo = hook.thermostat
baro = hook.barostat
elif self.hooks is not None:
if self.hooks.name == 'TBCombination':
thermo = self.hooks.thermostat
baro = self.hooks.barostat
if log.do_warning:
if thermo is not None:
log('Temperature coupling achieved through ' +
str(thermo.name) + ' thermostat')
if baro is not None:
log('Pressure coupling achieved through ' +
str(baro.name) + ' barostat')
def _verify_hooks(self):
with log.section('ENSEM'):
thermo = None
index_thermo = 0
baro = None
index_baro = 0
# Look for the presence of a thermostat and/or barostat
if hasattr(self.hooks, '__len__'):
for index, hook in enumerate(self.hooks):
if hook.method == 'thermostat':
thermo = hook
index_thermo = index
elif hook.method == 'barostat':
baro = hook
index_baro = index
elif self.hooks is not None:
if self.hooks.method == 'thermostat':
thermo = self.hooks
elif self.hooks.method == 'barostat':
baro = self.hooks
# If both are present, delete them and generate TBCombination element
if thermo is not None and baro is not None:
from yaff.sampling.npt import TBCombination
if log.do_warning:
log.warn('Both thermostat and barostat are present separately and will be merged')
del self.hooks[max(index_thermo, index_thermo)]
del self.hooks[min(index_thermo, index_baro)]
self.hooks.append(TBCombination(thermo, baro))
if hasattr(self.hooks, '__len__'):
for hook in self.hooks:
if hook.name == 'TBCombination':
thermo = hook.thermostat
baro = hook.barostat
elif self.hooks is not None:
if self.hooks.name == 'TBCombination':
thermo = self.hooks.thermostat
baro = self.hooks.barostat
if log.do_warning:
if thermo is not None:
log('Temperature coupling achieved through ' + str(thermo.name) + ' thermostat')
if baro is not None:
log('Pressure coupling achieved through ' + str(baro.name) + ' barostat')
def detect_ffatypes(self, rules):
"""Initialize the ``ffatypes`` attribute based on ATSELECT rules.
**Argument:**
rules
A list of (ffatype, rule) pairs that will be used to initialize
the attributes ``self.ffatypes`` and ``self.ffatype_ids``.
If the system already has FF atom types, they will be overwritten.
"""
with log.section('SYS'):
# Give warning if needed
if self.ffatypes is not None:
if log.do_warning:
log.warn('Overwriting existing FF atom types.')
# Compile all the rules
my_rules = []
for ffatype, rule in rules:
check_name(ffatype)
if isinstance(rule, str):
rule = atsel_compile(rule)
my_rules.append((ffatype, rule))
# Use the rules to detect the atom types
lookup = {}
self.ffatypes = []
self.ffatype_ids = np.zeros(self.natom, int)
for i in range(self.natom):
my_ffatype = None
for ffatype, rule in my_rules:
if rule(self, i):
my_ffatype = ffatype
break
if my_ffatype is None:
raise ValueError(
'Could not detect FF atom type of atom %i.' % i)
ffatype_id = lookup.get(my_ffatype)
if ffatype_id is None:
ffatype_id = len(lookup)
self.ffatypes.append(my_ffatype)
lookup[my_ffatype] = ffatype_id
self.ffatype_ids[i] = ffatype_id
# Make sure all is done well ...
self._init_derived_ffatypes()
def detect_ffatypes(self, rules):
"""Initialize the ``ffatypes`` attribute based on ATSELECT rules.
**Argument:**
rules
A list of (ffatype, rule) pairs that will be used to initialize
the attributes ``self.ffatypes`` and ``self.ffatype_ids``.
If the system already has FF atom types, they will be overwritten.
"""
with log.section('SYS'):
# Give warning if needed
if self.ffatypes is not None:
if log.do_warning:
log.warn('Overwriting existing FF atom types.')
# Compile all the rules
my_rules = []
for ffatype, rule in rules:
check_name(ffatype)
if isinstance(rule, basestring):
rule = atsel_compile(rule)
my_rules.append((ffatype, rule))
# Use the rules to detect the atom types
lookup = {}
self.ffatypes = []
self.ffatype_ids = np.zeros(self.natom, int)
for i in xrange(self.natom):
my_ffatype = None
for ffatype, rule in my_rules:
if rule(self, i):
my_ffatype = ffatype
break
if my_ffatype is None:
raise ValueError('Could not detect FF atom type of atom %i.' % i)
ffatype_id = lookup.get(my_ffatype)
if ffatype_id is None:
ffatype_id = len(lookup)
self.ffatypes.append(my_ffatype)
lookup[my_ffatype] = ffatype_id
self.ffatype_ids[i] = ffatype_id
# Make sure all is done well ...
self._init_derived_ffatypes()
def apply(self, atom_table, bond_table, scale_table, dielectric, system, ff_args):
if system.charges is None:
system.charges = np.zeros(system.natom)
elif log.do_warning and abs(system.charges).max() != 0:
log.warn('Overwriting charges in system.')
system.charges[:] = 0.0
system.radii = np.zeros(system.natom)
# compute the charges
for i in xrange(system.natom):
pars = atom_table.get(system.get_ffatype(i))
if pars is not None:
charge, radius = pars
system.charges[i] += charge
system.radii[i] = radius
elif log.do_warning:
log.warn('No charge defined for atom %i with fftype %s.' % (i, system.get_ffatype(i)))
for i0, i1 in system.iter_bonds():
ffatype0 = system.get_ffatype(i0)
ffatype1 = system.get_ffatype(i1)
if ffatype0 == ffatype1:
continue
charge_transfer = bond_table.get((ffatype0, ffatype1))
if charge_transfer is None:
if log.do_warning:
log.warn('No charge transfer parameter for atom pair (%i,%i) with fftype (%s,%s).' % (i0, i1, system.get_ffatype(i0), system.get_ffatype(i1)))
else:
system.charges[i0] += charge_transfer
system.charges[i1] -= charge_transfer
# prepare other parameters
scalings = Scalings(system, scale_table[1], scale_table[2], scale_table[3])
# Setup the electrostatic pars
ff_args.add_electrostatic_parts(system, scalings, dielectric)
def apply(self, par_table, cpar_table, scale_table, system, ff_args):
# Prepare the atomic parameters
c6s = np.zeros(system.nffatype, float)
bs = np.zeros(system.nffatype, float)
vols = np.zeros(system.nffatype, float)
for i in xrange(system.nffatype):
key = (system.ffatypes[i],)
par_list = par_table.get(key, [])
if len(par_list) == 0:
if log.do_warning:
log.warn('No DAMPDISP parameters found for atom %i with fftype %s.' % (i, system.get_ffatype(i)))
else:
c6s[i], bs[i], vols[i] = par_list[0]
# Prepare the cross parameters
c6_cross = np.zeros((system.nffatype, system.nffatype), float)
b_cross = np.zeros((system.nffatype, system.nffatype), float)
for i0 in xrange(system.nffatype):
for i1 in xrange(i0+1):
cpar_list = cpar_table.get((system.ffatypes[i0], system.ffatypes[i1]), [])
if len(cpar_list) == 0:
if log.do_high:
log('No DAMPDISP cross parameters found for ffatypes %s,%s. Mixing rule will be used' % (system.ffatypes[i0], system.ffatypes[i1]))
else:
c6_cross[i0,i1], b_cross[i0,i1] = cpar_list[0]
if i0 != i1:
c6_cross[i1,i0], b_cross[i1,i0] = cpar_list[0]
# Prepare the global parameters
scalings = Scalings(system, scale_table[1], scale_table[2], scale_table[3])
# Get the part. It should not exist yet.
part_pair = ff_args.get_part_pair(PairPotDampDisp)
if part_pair is not None:
raise RuntimeError('Internal inconsistency: the DAMPDISP part should not be present yet.')
pair_pot = PairPotDampDisp(system.ffatype_ids, c6_cross, b_cross, ff_args.rcut, ff_args.tr, c6s, bs, vols)
nlist = ff_args.get_nlist(system)
part_pair = ForcePartPair(system, nlist, scalings, pair_pot)
ff_args.parts.append(part_pair)
def apply(self, atom_table, bond_table, scale_table, dielectric, system):
if system.charges is None:
system.charges = np.zeros(system.natom)
elif log.do_warning and abs(system.charges).max() != 0:
log.warn('Overwriting charges in system.')
system.charges[:] = 0.0
system.radii = np.zeros(system.natom)
# compute the charges
for i in range(system.natom):
pars = atom_table.get(system.get_ffatype(i))
if pars is not None:
charge, radius = pars
system.charges[i] += charge
system.radii[i] = radius
elif log.do_warning:
log.warn('No charge defined for atom %i with fftype %s.' %
(i, system.get_ffatype(i)))
for i0, i1 in system.iter_bonds():
ffatype0 = system.get_ffatype(i0)
ffatype1 = system.get_ffatype(i1)
if ffatype0 == ffatype1:
continue
charge_transfer = bond_table.get((ffatype0, ffatype1))
if charge_transfer is None:
if log.do_warning:
log.warn(
'No charge transfer parameter for atom pair (%i,%i) with fftype (%s,%s).'
% (i0, i1, system.get_ffatype(i0),
system.get_ffatype(i1)))
else:
system.charges[i0] += charge_transfer
system.charges[i1] -= charge_transfer
def detect_bonds(self, exceptions=None):
"""Initialize the ``bonds`` attribute based on inter-atomic distances
**Optional argument:**
exceptions:
Specify custom threshold for certain pairs of elements. This
must be a dictionary with ((num0, num1), threshold) as items.
For each pair of elements, a distance threshold is used to detect
bonded atoms. The distance threshold is based on a database of known
bond lengths. If the database does not contain a record for the given
element pair, the threshold is based on the sum of covalent radii.
"""
with log.section('SYS'):
from molmod.bonds import bonds
if self.bonds is not None:
if log.do_warning:
log.warn('Overwriting existing bonds.')
work = np.zeros((self.natom*(self.natom-1))/2, float)
self.cell.compute_distances(work, self.pos)
ishort = (work < bonds.max_length*1.01).nonzero()[0]
new_bonds = []
for i in ishort:
i0, i1 = _unravel_triangular(i)
n0 = self.numbers[i0]
n1 = self.numbers[i1]
if exceptions is not None:
threshold = exceptions.get((n0, n1))
if threshold is None and n0!=n1:
threshold = exceptions.get((n1, n0))
if threshold is not None:
if work[i] < threshold:
new_bonds.append([i0, i1])
continue
if bonds.bonded(n0, n1, work[i]):
new_bonds.append([i0, i1])
self.bonds = np.array(new_bonds)
self._init_derived_bonds()
def detect_bonds(self, exceptions=None):
"""Initialize the ``bonds`` attribute based on inter-atomic distances
**Optional argument:**
exceptions:
Specify custom threshold for certain pairs of elements. This
must be a dictionary with ((num0, num1), threshold) as items.
For each pair of elements, a distance threshold is used to detect
bonded atoms. The distance threshold is based on a database of known
bond lengths. If the database does not contain a record for the given
element pair, the threshold is based on the sum of covalent radii.
"""
with log.section('SYS'):
from molmod.bonds import bonds
if self.bonds is not None:
if log.do_warning:
log.warn('Overwriting existing bonds.')
work = np.zeros((self.natom * (self.natom - 1)) // 2, float)
self.cell.compute_distances(work, self.pos)
ishort = (work < bonds.max_length * 1.01).nonzero()[0]
new_bonds = []
for i in ishort:
i0, i1 = _unravel_triangular(i)
n0 = self.numbers[i0]
n1 = self.numbers[i1]
if exceptions is not None:
threshold = exceptions.get((n0, n1))
if threshold is None and n0 != n1:
threshold = exceptions.get((n1, n0))
if threshold is not None:
if work[i] < threshold:
new_bonds.append([i0, i1])
continue
if bonds.bonded(n0, n1, work[i]):
new_bonds.append([i0, i1])
self.bonds = np.array(new_bonds)
self._init_derived_bonds()
def write_pseudo_atoms(ff, workdir):
"""
Write pseudo_atoms.def file
"""
system = ff.system
if system.masses is None: system.set_standard_masses()
# If no charges are present, we write q=0
if system.charges is None:
charges = np.zeros(system.natom)
else:
charges = system.charges
# RASPA cannot handle Gaussian charges
if system.radii is not None and np.any(system.radii != 0.0):
if log.do_warning:
log.warn("Atomic radii were specified, but RASPA will not take "
"this into account for electrostatic interactions")
raise ValueError("Gaussian electrostatics not supported by RASPA")
# We need to write an entry for each atomtype, specifying the charge. If
# atoms of the same atomtype show different charges, this means the
# atomtypes need to be fine grained
ffatypes, ffatype_ids = get_lammps_ffatypes(ff)
# Write the file
with open(os.path.join(workdir, 'pseudo_atoms.def'), 'w') as f:
f.write("#number of pseudo atoms\n%d\n" % (len(ffatypes)))
f.write("#type print as chem oxidation mass "
"charge polarization B-factor radii connectivity "
"anisotropic anisotropic-type tinker-type\n")
for iffa, ffa in enumerate(ffatypes):
iatom = np.where(ffatype_ids == iffa)[0][0]
symbol = periodic[system.numbers[iatom]].symbol
f.write(
"%-12s yes %6s %6s %10d %12.8f %+32.20f %6.3f "
"%6.3f %6.3f %5d %5d %10s %5d\n" %
(ffa, symbol, symbol, 0, system.masses[iatom] / amu,
charges[iatom], 0.0, 1.0, 1.0, 0, 0, "absolute", 0))
return ffatypes, ffatype_ids
def __init__(self,
ff,
fn_system,
fn_log="none",
suffix='',
do_table=True,
fn_table='lammps.table',
scalings_table=[0.0, 0.0, 1.0],
do_ei=True,
kspace='ewald',
kspace_accuracy=1e-7,
scalings_ei=[0.0, 0.0, 1.0],
triclinic=True,
comm=None,
move_central_cell=False):
r'''Initalize LAMMPS ForcePart
**Arguments:**
system
An instance of the ``System`` class.
fn_system
The file containing the system data in LAMMPS format, can be
generated using external.lammpsio.write_lammps_system_data
**Optional Arguments:**
fn_log
Filename where LAMMPS output is stored. This is probably only
necessary for debugging. Default: None, which means no output
is stored
suffix
The suffix of the liblammps_*.so library file
do_table
Boolean, compute a potentual using tabulated values
fn_table
Filename of file containing tabulated non-bonded potential
without point-charge electrostatics.
Can be written using the ```write_lammps_table``` method.
Default: lammps.table
scalings_vdw
List containing vdW scaling factors for 1-2, 1-3 and 1-4
neighbors
do_ei
Boolean, compute a point-charge electrostatic contribution
kspace
Method to treat long-range electrostatics, should be one of
ewald or pppm
kspace_accuracy
Desired relative error in electrostatic forces
Default: 1e-6
scalings_ei
List containing electrostatic scaling factors for 1-2, 1-3 and
1-4 neighbors
triclinic
Boolean, specify whether a triclinic cell will be used during
the simulation. If the cell is orthogonal, set it to False
as LAMMPS should run slightly faster.
Default: True
comm
MPI communicator, required if LAMMPS should run in parallel
move_central_cell
Boolean, if True, every atom is moved to the central cell
(centered at the origin) before passing positions to LAMMPS.
Change this if LAMMPS gives a Atoms Lost ERROR.
'''
self.system = ff.system
# Try to load the lammps package, quit if not possible
try:
from lammps import lammps
except:
log("Could not import the lammps python package which is required to use LAMMPS as a library"
)
raise ImportError
# Some safety checks...
if self.system.cell.nvec != 3:
raise ValueError(
'The system must be 3D periodic for LAMMPS calculations.')
if not os.path.isfile(fn_system):
raise ValueError('Could not read file %s' % fn_system)
if do_table:
if not os.path.isfile(fn_table):
raise ValueError('Could not read file %s' % fn_table)
tables = read_lammps_table(fn_table)
table_names = [table[0] for table in tables]
npoints, _, rcut = tables[0][1]
elif do_ei:
rcut = 0
for part in ff.parts:
if part.name == 'pair_ei':
rcut = part.pair_pot.rcut
if rcut == 0:
log("ERROR, do_ei set to True, but pair_ei was not found in the ff"
)
else:
raise NotImplementedError
if not kspace in ['ewald', 'pppm']:
raise ValueError('kspace should be one of ewald or pppm')
if self.system.natom > 2000 and kspace == 'ewald' and log.do_warning:
log.warn("You are simulating a more or less large system."
"It might be more efficient to use kspace=pppm")
if self.system.natom < 1000 and kspace == 'pppm' and log.do_warning:
log.warn("You are simulating a more or less small system."
"It might be better to use kspace=ewald")
# Initialize a class instance and some attributes
ForcePart.__init__(self, 'lammps', self.system)
self.comm = comm
self.triclinic = triclinic
self.move_central_cell = move_central_cell
ffatypes, ffatype_ids = get_lammps_ffatypes(ff)
nffa = len(ffatypes)
# Pass all commands that would normally appear in the LAMMPS input file
# to our instance of LAMMPS.
self.lammps = lammps(name=suffix,
comm=self.comm,
cmdargs=["-screen", fn_log, "-log", "none"])
self.lammps.command("units electron")
self.lammps.command("atom_style full")
self.lammps.command("atom_modify map array")
self.lammps.command("box tilt large")
self.lammps.command("read_data %s" % fn_system)
self.lammps.command("mass * 1.0")
self.lammps.command("bond_style none")
# Hybrid style combining electrostatics and table
if do_ei and do_table:
self.lammps.command(
"pair_style hybrid/overlay coul/long %13.8f table spline %d" %
(rcut, npoints))
self.lammps.command("pair_coeff * * coul/long")
self.lammps.command("kspace_style %s %10.5e" %
(kspace, kspace_accuracy))
# Only electrostatics
elif do_ei:
self.lammps.command("pair_style coul/long %13.8f" % rcut)
self.lammps.command("pair_coeff * *")
self.lammps.command("kspace_style %s %10.5e" %
(kspace, kspace_accuracy))
# Only table
elif do_table:
self.lammps.command("pair_style table spline %d" % (npoints))
else:
raise NotImplementedError
for i in range(nffa):
ffai = ffatypes[i]
for j in range(i, nffa):
ffaj = ffatypes[j]
if ffai > ffaj:
name = '%s---%s' % (str(ffai), str(ffaj))
else:
name = '%s---%s' % (str(ffaj), str(ffai))
if do_ei and do_table:
self.lammps.command("pair_coeff %d %d table %s %s" %
(i + 1, j + 1, fn_table, name))
elif do_table:
self.lammps.command("pair_coeff %d %d %s %s" %
(i + 1, j + 1, fn_table, name))
if do_ei is not None:
self.lammps.command(
"special_bonds lj %f %f %f coul %f %f %f" %
(scalings_table[0], scalings_table[1], scalings_table[2],
scalings_ei[0], scalings_ei[1], scalings_ei[2]))
else:
self.lammps.command(
"special_bonds lj %f %f %f" %
(scalings_table[0], scalings_table[1], scalings_table[2]))
self.lammps.command("neighbor 0.0 bin")
self.lammps.command("neigh_modify delay 0 every 1 check no")
self.lammps.command("compute virial all pressure NULL virial")
self.lammps.command("variable eng equal pe")
self.lammps.command("variable Wxx equal c_virial[1]")
self.lammps.command("variable Wyy equal c_virial[2]")
self.lammps.command("variable Wzz equal c_virial[3]")
self.lammps.command("variable Wxy equal c_virial[4]")
self.lammps.command("variable Wxz equal c_virial[5]")
self.lammps.command("variable Wyz equal c_virial[6]")
thermo_style = "step time etotal evdwl ecoul elong etail "
thermo_style += " ".join(["c_virial[%d]" % i for i in range(1, 7)])
self.lammps.command("thermo_style custom %s" % thermo_style)
self.lammps.command("fix 1 all nve")
# LAMMPS needs cell vectors (ax,0,0), (bx,by,0) and (cx,cy,cz)
# This means we need to perform a rotation to switch between Yaff and
# LAMMPS coordinates. All information about this rotation is stored
# in the variables defined below
self.rvecs = np.eye(3)
self.cell = Cell(self.rvecs)
self.rot = np.zeros((3, 3))
self.vtens_lammps = np.zeros((6, ))
def __init__(self,
system,
timestep=0.0,
restart=0,
fn='plumed.dat',
kernel=None,
fn_log='plumed.log'):
r'''Initialize a PLUMED ForcePart. More information on the interface
between PLUMED and MD codes can be found on
http://tcb.ucas.ac.cn/plumed2/developer-doc/html/_how_to_plumed_your_m_d.html
Unfortunately, PLUMED partially breaks the orthogonality of the pes
and the sampling modules in Yaff: PLUMED sometimes requires
information from the integrator. For example, in metadynamics
PLUMED needs to know when a time integration step has been
completed (which is not necessarily after each force calculation).
ForcePartPlumed therefore also inherits from Hook and
by attaching this hook to the integrator, it is possible to obtain
the necessary information from the integrator. Problems within
PLUMED for this approach to work, particularly in the VES module,
have been resolved; see the discussion at
https://groups.google.com/forum/?fromgroups=#!topic/plumed-users/kPZu_tNZtgk
**Arguments:**
system
An instance of the System class
**Optional Arguments:**
timestep
The timestep (in au) of the integrator
restart
Set to a value different from 0 to let PLUMED know that this
is a restarted run
fn
A filename from which the PLUMED instructions are read, default
is plumed.dat
kernel
Path to the PLUMED library (something like
/path/to/libplumedKernel.so). If None is provided, the
environment variable $PLUMED_KERNEL should point to the library
file.
fn_log
Path to the file where PLUMED logs output, default is
plumed.log
'''
self.system = system
self.fn = fn
self.kernel = kernel
self.fn_log = fn_log
self.plumedstep = 0
# TODO In the LAMMPS-PLUMED interface (src/USER-PLUMED/fix_plumed.cpp)
# it is mentioned that biasing is not possible when tailcorrections are
# included. Maybe this should be checked...
# Check cell dimensions, only 0D and 3D systems supported
if not self.system.cell.nvec in [0, 3]:
raise NotImplementedError
# Setup PLUMED by sending commands to the PLUMED API
self.setup_plumed(timestep, restart)
# PLUMED requires masses to be set...
if self.system.masses is None:
self.system.set_standard_masses()
# Initialize the ForcePart
ForcePart.__init__(self, 'plumed', self.system)
# Initialize the Hook, can't see a reason why start and step could
# differ from default values
Hook.__init__(self, start=0, step=1)
self.hooked = False
if log.do_warning:
log.warn("When using PLUMED as a hook for your integrator "
"and PLUMED adds time-dependent forces (for instance "
"when performing metadynamics), there is no energy "
"conservation. The conserved quantity reported by "
"YAFF is irrelevant in this case.")
def _init_derived_ffatypes(self):
if self.ffatype_ids is None:
if len(self.ffatypes) != self.natom:
raise TypeError('When the ffatype_ids are derived automatically, the length of the ffatypes list must match the number of atoms.')
lookup = {}
ffatypes = []
self.ffatype_ids = np.zeros(self.natom, int)
for i in xrange(self.natom):
if self.scope_ids is None:
ffatype = self.ffatypes[i]
key = ffatype, None
else:
scope_id = self.scope_ids[i]
ffatype = self.ffatypes[i]
key = ffatype, scope_id
ffatype_id = lookup.get(key)
if ffatype_id is None:
ffatype_id = len(ffatypes)
ffatypes.append(ffatype)
lookup[key] = ffatype_id
self.ffatype_ids[i] = ffatype_id
self.ffatypes = ffatypes
for ffatype in self.ffatypes:
check_name(ffatype)
# check the range of the ids
if self.ffatype_ids.min() != 0 or self.ffatype_ids.max() != len(self.ffatypes)-1:
raise ValueError('The ffatype_ids have incorrect bounds.')
# differentiate ffatype_ids if the same ffatype_id is used in different
# scopes
if self.scopes is not None:
self.ffatype_id_to_scope_id = {}
fixed_fids = {}
for i in xrange(self.natom):
fid = self.ffatype_ids[i]
sid = self.ffatype_id_to_scope_id.get(fid)
if sid is None:
self.ffatype_id_to_scope_id[fid] = self.scope_ids[i]
elif sid != self.scope_ids[i]:
# We found the same ffatype_id in a different scope_id. This
# must be fixed. First check if we have already a new
# scope_id ready
sid = self.scope_ids[i]
new_fid = fixed_fids.get((sid, fid))
if new_fid is None:
# No previous new fid create, do it now.
new_fid = len(self.ffatypes)
# Copy the ffatype label
self.ffatypes.append(self.ffatypes[fid])
# Keep track of the new fid
fixed_fids[(sid, fid)] = new_fid
if log.do_warning:
log.warn('Atoms with type ID %i in scope %s were changed to type ID %i.' % (fid, self.scopes[sid], new_fid))
# Apply the new fid
self.ffatype_ids[i] = new_fid
self.ffatype_id_to_scope_id[new_fid] = sid
# Turn the ffatypes in the scopes into array
if self.ffatypes is not None:
self.ffatypes = np.array(self.ffatypes, copy=False)
if self.scopes is not None:
self.scopes = np.array(self.scopes, copy=False)
# check the range of the ids
if self.ffatype_ids.min() != 0 or self.ffatype_ids.max() != len(self.ffatypes)-1:
raise ValueError('The ffatype_ids have incorrect bounds.')
if log.do_medium:
log('The following atom types are present in the system:')
log.hline()
if self.scopes is None:
log(' Atom type ID Number of atoms')
log.hline()
for ffatype_id, ffatype in enumerate(self.ffatypes):
log('%22s %3i %3i' % (ffatype, ffatype_id, (self.ffatype_ids==ffatype_id).sum()))
else:
log(' Scope Atom type ID Number of atoms')
log.hline()
for ffatype_id, ffatype in enumerate(self.ffatypes):
scope = self.scopes[self.ffatype_id_to_scope_id[ffatype_id]]
log('%22s %22s %3i %3i' % (scope, ffatype, ffatype_id, (self.ffatype_ids==ffatype_id).sum()))
log.hline()
log.blank()
def run(self, nsteps, mc_moves=None, initial=None, einit=0,
translation_stepsize=1.0*angstrom,
volumechange_stepsize=10.0*angstrom**3,
close_contact=0.4*angstrom):
"""
Perform Monte-Carlo steps
**Arguments:**
nsteps
Number of Monte-Carlo steps
**Optional Arguments:**
mc_moves
Dictionary containing relative probabilities of the different
Monte-Carlo moves. It is not required that the probabilities
sum to 1, they are normalized automatically. Example
initial
System instance describing the initial configuration of guest
molecules
einit
The energy of the initial state
translation_stepsize
The maximal magnitude of a TrialTranslation
volumechange_stepsize
The maximal magnitude of a TrialVolumechange
close_contact
Automatically reject TrialMove if atoms are placed shorter
than this distance apart
"""
if log.do_warning:
log.warn("Currently, Yaff does not consider interactions of a guest molecule "
"with its periodic images in MC simulations. Make sure that you choose a system size "
"that is large compared to the guest dimensions, so it is indeed "
"acceptable to neglect these interactions.")
with log.section(self.log_name), timer.section(self.log_name):
# Initialization
self.translation_stepsize = translation_stepsize
self.volumechange_stepsize = volumechange_stepsize
self.close_contact = close_contact
if initial is not None:
self.N = initial.natom//self.guest.natom
assert self.guest.natom*self.N==initial.natom, ("Initial configuration does not contain correct number of atoms")
self.current_configuration = initial
self.get_ff(self.N).system.pos[:] = initial.pos
if self.ewald_reci is not None:
self.ewald_reci.compute_structurefactors(
initial.pos,
initial.charges,
self.ewald_reci.cosfacs, self.ewald_reci.sinfacs)
else:
self.current_configuration = self.get_ff(self.N).system
self.energy = einit
if not self.conditions_set:
raise ValueError("External conditions have not been set!")
# Normalized probabilities and accompanying methods specifying the trial MC moves
# Trial moves are sorted alphabetically
if mc_moves is None: mc_moves = self.default_trials
trials, probabilities = [], []
for t in sorted(mc_moves.keys()):
if not t in self.allowed_trials:
raise ValueError("Trial move %s not allowed!"%t)
trial = getattr(mctrials,"Trial"+t.capitalize(),None)
if trial is None:
raise NotImplementedError("The requested trial move %s is not implemented"%(t))
# Trials is a list containing instances of Trial classes from the mctrials module
trials.append(trial(self))
probabilities.append(mc_moves[t])
probabilities = np.asarray(probabilities)
probabilities /= np.sum(probabilities)
assert np.all(probabilities>=0.0), "Negative probabilities are not allowed!"
# Take the cumulative sum, makes it a bit easier to determine which MC move is selected
probabilities = np.cumsum(probabilities)
# Array to keep track of accepted (1st column) and tried (2nd column)
# moves, with rows corresponding to different possible moves
acceptance = np.zeros((len(trials),2), dtype=int)
# Start performing MC moves
self.Nmean = self.N
self.emean = self.energy
self.Vmean = self.current_configuration.cell.volume
self.counter = 0
self.call_hooks()
for istep in range(nsteps):
switch = np.random.rand()
# Select one of the possible MC moves
imove = np.where(switch<probabilities)[0][0]
# Call the corresponding method
accepted = trials[imove]()
# Update records with accepted and tried MC moves
acceptance[imove,1] += 1
if accepted: acceptance[imove,0] += 1
self.counter += 1
self.Nmean += (self.N-self.Nmean)/self.counter
self.emean += (self.energy-self.emean)/self.counter
self.Vmean += (self.current_configuration.cell.volume-self.Vmean)/self.counter
self.call_hooks()
return acceptance
def write_lammps_system_data(system,
ff=None,
fn='lammps.data',
triclinic=True):
'''
Write information about a Yaff system to a LAMMPS data file
Following information is written: cell vectors, atom type ids
and topology (as defined by the bonds)
**Arguments**
system
Yaff system
fn
Filename to write the LAMMPS data to
triclinic
Boolean, specify whether a triclinic cell will be used during
the simulation. If the cell is orthogonal, set it to False
as LAMMPS should run slightly faster.
Default: True
'''
if system.cell.nvec != 3:
raise ValueError(
'The system must be 3D periodic for Lammps calculations.')
if system.ffatypes is None:
raise ValueError('Atom types need to be defined.')
if system.bonds is None:
raise ValueError('Bonds need to be defined')
if system.charges is None:
if log.do_warning:
log.warn(
"System has no charges, writing zero charges to LAMMPS file")
charges = np.zeros((system.natom, ))
else:
charges = system.charges
if ff is None:
ffatypes, ffatype_ids = system.ffatypes, system.ffatype_ids
else:
ffatypes, ffatype_ids = get_lammps_ffatypes(ff)
fdat = open(fn, 'w')
fdat.write(
"Generated by Yaff\n\n%20d atoms\n%20d bonds\n%20d angles \n%20d dihedrals\n%20d impropers\n\n"
% (system.natom, system.nbond, 0, 0, 0))
fdat.write(
"%20d atom types\n%20d bond types\n%20d angle types\n%20d dihedral types\n%20d improper types\n\n"
% (np.amax(ffatype_ids) + 1, 1, 0, 0, 0))
rvecs, R = cell_lower(system.cell.rvecs)
pos = np.einsum('ij,kj', system.pos, R)
fdat.write(
"%30.24f %30.24f xlo xhi\n%30.24f %30.24f ylo yhi\n%30.24f %30.24f zlo zhi\n"
% (0.0, rvecs[0, 0], 0.0, rvecs[1, 1], 0.0, rvecs[2, 2]))
if triclinic:
fdat.write("%30.24f %30.24f %30.24f xy xz yz\n" %
(rvecs[1, 0], rvecs[2, 0], rvecs[2, 1]))
fdat.write("Atoms\n\n")
for i in range(system.natom):
fdat.write("%5d %3d %3d %30.24f %30.24f %30.24f %30.24f\n" %
(i + 1, 1, ffatype_ids[i] + 1, charges[i], pos[i, 0],
pos[i, 1], pos[i, 2]))
fdat.write("\nBonds\n\n")
for i in range(system.nbond):
fdat.write("%5d %3d %5d %5d\n" %
(i + 1, 1, system.bonds[i, 0] + 1, system.bonds[i, 1] + 1))
fdat.close()
def write_lammps_table(ff,
fn='lammps.table',
rmin=0.50 * angstrom,
nrows=2500,
unit_style='electron'):
'''
Write tables containing noncovalent interactions for LAMMPS.
For every pair of ffatypes, a separate table is generated.
Because electrostatic interactions require a specific treatment, point-
charge electrostatics are NOT included in the tables.
When distributed charge distributions (e.g. Gaussian) are used, this
complicates matters. LAMMPS will still only treat point-charge
electrostatics using a dedicated method (e.g. Ewald or PPPM), so the
table has to contain the difference between the distributed charges and
the point charge electrostatic interactions. This also means that every
ffatype need a unique charge distribution, i.e. all atoms of the same
atom type need to have the same charge and Gaussian radius.
All pair potentials contributing to the table need to have the same
scalings for near-neighbor interactions; this is however independent
of the generation of the table and is dealt with elsewhere
**Arguments:**
ff
Yaff ForceField instance
**Optional arguments:**
fn
Filename where tables will be stored
'''
# Find out if we are dealing with electrostatics from distributed charges
corrections = []
for part in ff.parts:
if part.name == 'pair_ei':
if np.any(part.pair_pot.radii != 0.0):
# Create a ForcePart with electrostatics from distributed
# charges, completely in real space.
pair_pot_dist = PairPotEI(part.pair_pot.charges,
0.0,
part.pair_pot.rcut,
tr=part.pair_pot.get_truncation(),
dielectric=part.pair_pot.dielectric,
radii=part.pair_pot.radii)
fp_dist = ForcePartPair(ff.system, ff.nlist, part.scalings,
pair_pot_dist)
corrections.append((fp_dist, 1.0))
# Create a ForcePart with electrostatics from point
# charges, completely in real space.
pair_pot_point = PairPotEI(part.pair_pot.charges,
0.0,
part.pair_pot.rcut,
tr=part.pair_pot.get_truncation(),
dielectric=part.pair_pot.dielectric)
fp_point = ForcePartPair(ff.system, ff.nlist, part.scalings,
pair_pot_point)
corrections.append((fp_point, -1.0))
# Find the largest cut-off
rmax = 0.0
for part in ff.parts:
if part.name.startswith('pair_'):
if part.name == 'pair_ei' and len(corrections) == 0: continue
rmax = np.amax([rmax, part.pair_pot.rcut])
# Get LAMMPS ffatypes
ffatypes, ffatype_ids = get_lammps_ffatypes(ff)
# Select atom pairs for each pair of atom types
ffa_pairs = []
for i in range(len(ffatypes)):
index0 = np.where(ffatype_ids == i)[0][0]
for j in range(i, len(ffatypes)):
index1 = -1
candidates = np.where(ffatype_ids == j)[0]
for cand in candidates:
if cand==index0 or cand in ff.system.neighs1[index0] or\
cand in ff.system.neighs2[index0] or cand in ff.system.neighs3[index0] or\
cand in ff.system.neighs4[index0]:
continue
else:
index1 = cand
break
if index1 == -1:
log("ERROR constructing LAMMPS tables: there is no pair of atom types %s-%s which are not near neighbors"
% (ffatypes[i], ffatypes[j]))
log("Consider using a supercell to fix this problem")
raise ValueError
ffa_pairs.append([index0, index1])
if log.do_medium:
with log.section('LAMMPS'):
log("Generating LAMMPS table with covalent interactions")
log.hline()
log("rmin = %s | rmax = %s" % (log.length(rmin), log.length(rmax)))
# We only consider one neighbor interaction
ff.compute()
ff.nlist.nneigh = 1
# Construct array of evenly spaced values
distances = np.linspace(rmin, rmax, nrows)
ftab = open(fn, 'w')
ftab.write("# LAMMPS tabulated potential generated by Yaff\n")
ftab.write("# All quantities in atomic units\n")
ftab.write(
"# The names of the tables refer to the ffatype_ids that have to be used in the Yaff system\n"
)
ftab.write("#%4s %13s %21s %21s\n" % ("i", "d", "V", "F"))
# Loop over all atom pairs
for index0, index1 in ffa_pairs:
energies = []
for d in distances:
gposnn = np.zeros(ff.system.pos.shape, float)
ff.nlist.neighs[0] = (index0, index1, d, 0.0, 0.0, d, 0, 0, 0)
energy = 0.0
for part in ff.parts:
if not part.name.startswith('pair'): continue
if part.name == 'pair_ei': continue
energy += part.compute(gpos=gposnn)
for part, sign in corrections:
gposcorr = np.zeros(ff.system.pos.shape, float)
energy += sign * part.compute(gpos=gposcorr)
gposnn[:] += sign * gposcorr
row = [d, energy, gposnn[index0, 2]]
energies.append(row)
energies = np.asarray(energies)
ffai = ffatypes[ffatype_ids[index0]]
ffaj = ffatypes[ffatype_ids[index1]]
if np.all(energies[:, 1] == 0.0):
log.warn("Noncovalent energies between atoms %d (%s) and %d (%s) are zero"\
% (index0,ffai,index1,ffaj))
if np.all(energies[:, 2] == 0.0):
log.warn("Noncovalent forces between atoms %d (%s) and %d (%s) are zero"\
% (index0,ffai,index1,ffaj))
if ffai > ffaj:
name = '%s---%s' % (str(ffai), str(ffaj))
else:
name = '%s---%s' % (str(ffaj), str(ffai))
ftab.write("%s\nN %d R %13.8f %13.8f\n\n" %
(name, nrows, rmin / lammps_units[unit_style]['distance'],
rmax / lammps_units[unit_style]['distance']))
for irow, row in enumerate(energies):
ftab.write(
"%05d %+13.8f %+21.12f %+21.12f\n" %
(irow + 1, row[0] / lammps_units[unit_style]['distance'],
row[1] / lammps_units[unit_style]['energy'],
row[2] / lammps_units[unit_style]['energy'] *
lammps_units[unit_style]['distance']))
if log.do_medium:
log("%s done" % name)
def _init_derived_ffatypes(self):
if self.ffatype_ids is None:
if len(self.ffatypes) != self.natom:
raise TypeError(
'When the ffatype_ids are derived automatically, the length of the ffatypes list must match the number of atoms.'
)
lookup = {}
ffatypes = []
self.ffatype_ids = np.zeros(self.natom, int)
for i in range(self.natom):
if self.scope_ids is None:
ffatype = self.ffatypes[i]
key = ffatype, None
else:
scope_id = self.scope_ids[i]
ffatype = self.ffatypes[i]
key = ffatype, scope_id
ffatype_id = lookup.get(key)
if ffatype_id is None:
ffatype_id = len(ffatypes)
ffatypes.append(ffatype)
lookup[key] = ffatype_id
self.ffatype_ids[i] = ffatype_id
self.ffatypes = ffatypes
for ffatype in self.ffatypes:
check_name(ffatype)
# check the range of the ids
if self.ffatype_ids.min() != 0 or self.ffatype_ids.max() != len(
self.ffatypes) - 1:
raise ValueError('The ffatype_ids have incorrect bounds.')
# differentiate ffatype_ids if the same ffatype_id is used in different
# scopes
if self.scopes is not None:
self.ffatype_id_to_scope_id = {}
fixed_fids = {}
for i in range(self.natom):
fid = self.ffatype_ids[i]
sid = self.ffatype_id_to_scope_id.get(fid)
if sid is None:
self.ffatype_id_to_scope_id[fid] = self.scope_ids[i]
elif sid != self.scope_ids[i]:
# We found the same ffatype_id in a different scope_id. This
# must be fixed. First check if we have already a new
# scope_id ready
sid = self.scope_ids[i]
new_fid = fixed_fids.get((sid, fid))
if new_fid is None:
# No previous new fid create, do it now.
new_fid = len(self.ffatypes)
# Copy the ffatype label
self.ffatypes.append(self.ffatypes[fid])
# Keep track of the new fid
fixed_fids[(sid, fid)] = new_fid
if log.do_warning:
log.warn(
'Atoms with type ID %i in scope %s were changed to type ID %i.'
% (fid, self.scopes[sid], new_fid))
# Apply the new fid
self.ffatype_ids[i] = new_fid
self.ffatype_id_to_scope_id[new_fid] = sid
# Turn the ffatypes in the scopes into array
if self.ffatypes is not None:
self.ffatypes = np.array(self.ffatypes, copy=False)
if self.scopes is not None:
self.scopes = np.array(self.scopes, copy=False)
# check the range of the ids
if self.ffatype_ids.min() != 0 or self.ffatype_ids.max() != len(
self.ffatypes) - 1:
raise ValueError('The ffatype_ids have incorrect bounds.')
if log.do_medium:
log('The following atom types are present in the system:')
log.hline()
if self.scopes is None:
log(' Atom type ID Number of atoms')
log.hline()
for ffatype_id, ffatype in enumerate(self.ffatypes):
log('%22s %3i %3i' %
(ffatype, ffatype_id,
(self.ffatype_ids == ffatype_id).sum()))
else:
log(' Scope Atom type ID Number of atoms'
)
log.hline()
for ffatype_id, ffatype in enumerate(self.ffatypes):
scope = self.scopes[
self.ffatype_id_to_scope_id[ffatype_id]]
log('%22s %22s %3i %3i' %
(scope, ffatype, ffatype_id,
(self.ffatype_ids == ffatype_id).sum()))
log.hline()
log.blank()
def check_mic(self, system):
'''Check if each scale2 and scale3 are uniquely defined.
**Arguments:**
system
An instance of the system class, i.e. the one that is used to
create this scaling object.
This check is done by constructing for each scaled pair, all possible
bond paths between the two atoms. For each path, the bond vectors
(after applying the minimum image convention) are added. If for a
given pair, these sums of bond vectors differ between all possible
paths, the differences are expanded in cell vectors which can be used
to construct a proper supercell in which scale2 and scale3 pairs are
all uniquely defined.
'''
if system.cell.nvec == 0:
return
troubles = False
with log.section('SCALING'):
for i0, i1, scale, nbond in self.stab:
if nbond == 1:
continue
all_deltas = []
paths = []
for path in iter_paths(system, i0, i1, nbond):
delta_total = 0
for j0 in xrange(nbond):
j1 = j0 + 1
delta = system.pos[path[j0]] - system.pos[path[j1]]
system.cell.mic(delta)
delta_total += delta
all_deltas.append(delta_total)
paths.append(path)
all_deltas = np.array(all_deltas)
if abs(all_deltas.mean(axis=0) - all_deltas).max() > 1e-10:
troubles = True
if log.do_warning:
log.warn('Troublesome pair scaling detected.')
log('The following bond paths connect the same pair of '
'atoms, yet the relative vectors are different.')
for ipath in xrange(len(paths)):
log('%2i %27s %10s %10s %10s' % (
ipath,
','.join(str(index) for index in paths[ipath]),
log.length(all_deltas[ipath,0]),
log.length(all_deltas[ipath,1]),
log.length(all_deltas[ipath,2]),
))
log('Differences between relative vectors in fractional '
'coordinates:')
for ipath0 in xrange(1, len(paths)):
for ipath1 in xrange(ipath0):
diff = all_deltas[ipath0] - all_deltas[ipath1]
diff_frac = np.dot(system.cell.gvecs, diff)
log('%2i %2i %10.4f %10.4f %10.4f' % (
ipath0, ipath1,
diff_frac[0], diff_frac[1], diff_frac[2]
))
log.blank()
if troubles:
raise AssertionError('Due to the small spacing between some crystal planes, the scaling of non-bonding interactions will not work properly. Use a supercell to avoid this problem.')
def xyz_to_hdf5(f, fn_xyz, sub=slice(None), file_unit=angstrom, name='pos'):
"""Convert XYZ trajectory file to Yaff HDF5 format.
**Arguments:**
f
An open and writable HDF5 file.
fn_xyz
The filename of the XYZ trajectory file.
**Optional arguments:**
sub
The sub argument for the XYZReader. This must be a slice object that
defines the subsampling of the XYZ file reader. By default all
frames are read.
file_unit
The unit of the data in the XYZ file. [default=angstrom]
name
The name of the HDF5 dataset where the trajectory is stored. This
array is stored in the 'trajectory' group.
This routine will also test the consistency of the row attribute of the
trajectory group. If some trajectory data is already present, it will be
replaced by the new data. It is highly recommended to first initialize
the HDF5 file with the ``to_hdf5`` method of the System class.
"""
with log.section('XYZH5'):
if log.do_medium:
log('Loading XYZ file \'%s\' into \'trajectory/%s\' of HDF5 file \'%s\''
% (fn_xyz, name, f.filename))
# First make sure the HDF5 file has a system description that is consistent
# with the XYZ file.
if 'system' not in f:
raise ValueError('The HDF5 file must contain a system group.')
if 'numbers' not in f['system']:
raise ValueError(
'The HDF5 file must have a system group with atomic numbers.')
xyz_reader = XYZReader(fn_xyz, sub=sub, file_unit=file_unit)
if len(xyz_reader.numbers) != len(f['system/numbers']):
raise ValueError(
'The number of atoms in the HDF5 and the XYZ files does not match.'
)
if (xyz_reader.numbers != f['system/numbers']).any():
log.warn(
'The atomic numbers of the HDF5 and XYZ file do not match.')
# Take care of the trajectory group
tgrp = get_trajectory_group(f)
# Take care of the dataset
ds, = get_trajectory_datasets(tgrp,
(name, (len(xyz_reader.numbers), 3)))
# Fill the dataset with data.
row = get_last_trajectory_row([ds])
for title, coordinates in xyz_reader:
write_to_dataset(ds, coordinates, row)
row += 1
# Check number of rows
check_trajectory_rows(tgrp, [ds], row)
def xyz_to_hdf5(f, fn_xyz, sub=slice(None), file_unit=angstrom, name='pos'):
"""Convert XYZ trajectory file to Yaff HDF5 format.
**Arguments:**
f
An open and writable HDF5 file.
fn_xyz
The filename of the XYZ trajectory file.
**Optional arguments:**
sub
The sub argument for the XYZReader. This must be a slice object that
defines the subsampling of the XYZ file reader. By default all
frames are read.
file_unit
The unit of the data in the XYZ file. [default=angstrom]
name
The name of the HDF5 dataset where the trajectory is stored. This
array is stored in the 'trajectory' group.
This routine will also test the consistency of the row attribute of the
trajectory group. If some trajectory data is already present, it will be
replaced by the new data. It is highly recommended to first initialize
the HDF5 file with the ``to_hdf5`` method of the System class.
"""
with log.section('XYZH5'):
if log.do_medium:
log('Loading XYZ file \'%s\' into \'trajectory/%s\' of HDF5 file \'%s\'' % (
fn_xyz, name, f.filename
))
# First make sure the HDF5 file has a system description that is consistent
# with the XYZ file.
if 'system' not in f:
raise ValueError('The HDF5 file must contain a system group.')
if 'numbers' not in f['system']:
raise ValueError('The HDF5 file must have a system group with atomic numbers.')
xyz_reader = XYZReader(fn_xyz, sub=sub, file_unit=file_unit)
if len(xyz_reader.numbers) != len(f['system/numbers']):
raise ValueError('The number of atoms in the HDF5 and the XYZ files does not match.')
if (xyz_reader.numbers != f['system/numbers']).any():
log.warn('The atomic numbers of the HDF5 and XYZ file do not match.')
# Take care of the trajectory group
tgrp = get_trajectory_group(f)
# Take care of the dataset
ds, = get_trajectory_datasets(tgrp, (name, (len(xyz_reader.numbers), 3)))
# Fill the dataset with data.
row = get_last_trajectory_row([ds])
for title, coordinates in xyz_reader:
write_to_dataset(ds, coordinates, row)
row += 1
# Check number of rows
check_trajectory_rows(tgrp, [ds], row)
def g09log_to_hdf5(f, fn_log):
"""Convert Gaussian09 BOMD log file to Yaff HDF5 format.
**Arguments:**
f
An open and writable HDF5 file.
fn_log
The name of the Gaussian log file.
"""
with log.section('G09H5'):
if log.do_medium:
log('Loading Gaussian 09 file \'%s\' into \'trajectory\' of HDF5 file \'%s\''
% (fn_log, f.filename))
# First make sure the HDF5 file has a system description that is consistent
# with the XYZ file.
if 'system' not in f:
raise ValueError('The HDF5 file must contain a system group.')
if 'numbers' not in f['system']:
raise ValueError(
'The HDF5 file must have a system group with atomic numbers.')
natom = f['system/numbers'].shape[0]
# Take care of the trajectory group
tgrp = get_trajectory_group(f)
# Take care of the pos and vel datasets
dss = get_trajectory_datasets(
tgrp,
('pos', (natom, 3)),
('vel', (natom, 3)),
('frc', (natom, 3)),
('time', (1, )),
('step', (1, )),
('epot', (1, )),
('ekin', (1, )),
('etot', (1, )),
)
ds_pos, ds_vel, ds_frc, ds_time, ds_step, ds_epot, ds_ekin, ds_etot = dss
# Load frame by frame
row = get_last_trajectory_row(dss)
for numbers, pos, vel, frc, time, step, epot, ekin, etot in _iter_frames_g09(
fn_log):
if (numbers != f['system/numbers']).any():
log.warn(
'The element numbers of the HDF5 and LOG file do not match.'
)
write_to_dataset(ds_pos, pos, row)
write_to_dataset(ds_vel, vel, row)
write_to_dataset(ds_frc, frc, row)
write_to_dataset(ds_time, time, row)
write_to_dataset(ds_step, step, row)
write_to_dataset(ds_epot, epot, row)
write_to_dataset(ds_ekin, ekin, row)
write_to_dataset(ds_etot, etot, row)
row += 1
# Check number of rows
check_trajectory_rows(tgrp, dss, row)
def check_mic(self, system):
'''Check if each scale2 and scale3 are uniquely defined.
**Arguments:**
system
An instance of the system class, i.e. the one that is used to
create this scaling object.
This check is done by constructing for each scaled pair, all possible
bond paths between the two atoms. For each path, the bond vectors
(after applying the minimum image convention) are added. If for a
given pair, these sums of bond vectors differ between all possible
paths, the differences are expanded in cell vectors which can be used
to construct a proper supercell in which scale2 and scale3 pairs are
all uniquely defined.
'''
if system.cell.nvec == 0:
return
troubles = False
with log.section('SCALING'):
for i0, i1, scale, nbond in self.stab:
if nbond == 1:
continue
all_deltas = []
paths = []
for path in iter_paths(system, i0, i1, nbond):
delta_total = 0
for j0 in range(nbond):
j1 = j0 + 1
delta = system.pos[path[j0]] - system.pos[path[j1]]
system.cell.mic(delta)
delta_total += delta
all_deltas.append(delta_total)
paths.append(path)
all_deltas = np.array(all_deltas)
if abs(all_deltas.mean(axis=0) - all_deltas).max() > 1e-10:
troubles = True
if log.do_warning:
log.warn('Troublesome pair scaling detected.')
log('The following bond paths connect the same pair of '
'atoms, yet the relative vectors are different.')
for ipath in range(len(paths)):
log('%2i %27s %10s %10s %10s' % (
ipath,
','.join(str(index) for index in paths[ipath]),
log.length(all_deltas[ipath, 0]),
log.length(all_deltas[ipath, 1]),
log.length(all_deltas[ipath, 2]),
))
log('Differences between relative vectors in fractional '
'coordinates:')
for ipath0 in range(1, len(paths)):
for ipath1 in range(ipath0):
diff = all_deltas[ipath0] - all_deltas[ipath1]
diff_frac = np.dot(system.cell.gvecs, diff)
log('%2i %2i %10.4f %10.4f %10.4f' %
(ipath0, ipath1, diff_frac[0], diff_frac[1],
diff_frac[2]))
log.blank()
if troubles:
raise AssertionError(
'Due to the small spacing between some crystal planes, the scaling of non-bonding interactions will not work properly. Use a supercell to avoid this problem.'
)