def detect_ffatypes(self, ffatypes=None, ffatype_rules=None, ffatype_level=None):
'''
Define atom types by explicitely giving them through the
ffatypes keyword, defining atype rules using the ATSELECT
language implemented in Yaff (see the Yaff documentation at
http://molmod.github.io/yaff/ug_atselect.html) or by specifying
the ffatype_level employing the built-in routine in QuickFF.
'''
numbers = np.array([pt[symbol].number for symbol in self.structure.get_chemical_symbols()])
if self.structure.cell is None:
system = System(numbers, self.structure.positions.copy()*angstrom)
else:
system = System(numbers, self.structure.positions.copy()*angstrom, rvecs=self.structure.cell*angstrom)
system.detect_bonds()
if not sum([ffatypes is None, ffatype_rules is None, ffatype_level is None]) == 2:
raise IOError('Exactly one of ffatypes, ffatype_rules and ffatype_level should be defined')
if ffatypes is not None:
assert ffatype_rules is None, 'ffatypes and ffatype_rules cannot be defined both'
system.ffatypes = ffatypes
system.ffatype_ids = None
system._init_derived_ffatypes()
if ffatype_rules is not None:
system.detect_ffatypes(ffatype_rules)
if ffatype_level is not None:
set_ffatypes(system, ffatype_level)
self.ffatypes = system.ffatypes.copy()
self.ffatype_ids = system.ffatype_ids.copy()
coords = fchk.fields.get('Current cartesian coordinates').reshape([len(numbers), 3])
grad = fchk.fields.get('Cartesian Gradient').reshape([len(numbers), 3])
hess = fchk.get_hessian().reshape([len(numbers), 3, len(numbers), 3])
#Construct Yaff System file
system = System(numbers, coords)
system.detect_bonds()
system.set_standard_masses()
#Construct a QuickFF SecondOrderTaylor object containing the AI reference
with log.section('INIT', 2, timer='Initialization'):
ai = SecondOrderTaylor('ai', coords=coords, energy=energy, grad=grad, hess=hess)
#define atom types
rules = [
('H', '1 & =1%8'), #hydrogen atom with one oxygen neighbor
('O', '8 & =2%1'), #oxygen atom with two hydrogen neighbors
]
system.detect_ffatypes(rules)
#construct electrostatic force field from HE charges in gaussian_wpart.h5
with h5.File('gaussian_mbis.h5') as f:
charges = f['charges'][:]
scales = [1.0, 1.0, 1.0, 1.0]
with log.section('INIT', 2, timer='Initialization'):
ff_ei = get_ei_ff('EI', system, charges, scales, radii=None, average=True, pbc=[0,0,0])
#initialize and run program
program = Program(system, ai, settings, ffrefs=[ff_ei] )
program.run()