import shutil
import tempfile
import h5py as h5
from quickff.io import read_abinitio
from quickff.context import context
from quickff.io import read_abinitio
from quickff.reference import SecondOrderTaylor
from quickff.valence import ValenceFF
from yaff import System
from quickff.log import log
log.set_level('silent')
__all__ = ['log', 'read_system', 'tmpdir']
def read_system(name):
# Load system data.
fn = context.get_fn(os.path.join('systems', name))
numbers, coords, energy, grad, hess, masses, rvecs, pbc = read_abinitio(fn)
# Try to load charges.
charges = None
fns_wpart = glob(os.path.join(os.path.dirname(fn), 'gaussian_mbis.h5'))
if len(fns_wpart) > 0:
with h5.File(fns_wpart[0], 'r') as f:
charges = f['charges'][:]
# Create system object.
system = System(numbers, coords, charges=charges)
import shutil
import tempfile
import h5py as h5
from quickff.io import read_abinitio
from quickff.context import context
from quickff.io import read_abinitio
from quickff.reference import SecondOrderTaylor
from quickff.valence import ValenceFF
from yaff import System
from quickff.log import log
log.set_level('silent')
__all__ = ['log', 'read_system', 'tmpdir']
def read_system(name):
# Load system data.
fn = context.get_fn(os.path.join('systems', name))
numbers, coords, energy, grad, hess, masses, rvecs, pbc = read_abinitio(fn)
# Try to load charges.
charges = None
fns_wpart = glob(os.path.join(os.path.dirname(fn), 'gaussian_mbis.h5'))
if len(fns_wpart) > 0:
with h5.File(fns_wpart[0], 'r') as f:
charges = f['charges'][:]
# Create system object.
system = System(numbers, coords, charges=charges)
def main():
options, fns = parse()
#define logger
if options.silent:
log.set_level('silent')
else:
if options.very_verbose:
log.set_level('highest')
elif options.verbose:
log.set_level('high')
if options.logfile is not None and isinstance(options.logfile, str):
log.write_to_file(options.logfile)
with log.section('QFF', 1, timer='Initializing'):
log.dump('Initializing system')
#read system and ab initio reference
system = None
energy = 0.0
grad = None
hess = None
rvecs = None
for fn in fns:
if fn.endswith('.fchk') or fn.endswith('.xml'):
numbers, coords, energy, grad, hess, masses, rvecs, pbc = read_abinitio(
fn)
if system is None:
system = System(numbers,
coords,
rvecs=rvecs,
charges=None,
radii=None,
masses=masses)
else:
system.pos = coords.copy()
system.cell = Cell(rvecs)
system.numbers = numbers.copy()
if masses is not None: system.masses = masses.copy()
system._init_derived()
elif fn.endswith('.chk'):
sample = load_chk(fn)
if 'energy' in sample.keys(): energy = sample['energy']
if 'grad' in sample.keys(): grad = sample['grad']
elif 'gradient' in sample.keys(): grad = sample['gradient']
if 'hess' in sample.keys(): hess = sample['hess']
elif 'hessian' in sample.keys(): hess = sample['hessian']
if system is None:
system = System.from_file(fn)
else:
if 'pos' in sample.keys(): system.pos = sample['pos']
elif 'coords' in sample.keys():
system.pos = sample['coords']
if 'rvecs' in sample.keys():
system.cell = Cell(sample['rvecs'])
elif 'cell' in sample.keys():
system.cell = Cell(sample['cell'])
if 'bonds' in sample.keys(): system.bonds = sample['bonds']
if 'ffatypes' in sample.keys():
system.ffatypes = sample['ffatypes']
if 'ffatype_ids' in sample.keys():
system.ffatype_ids = sample['ffatype_ids']
system._init_derived()
else:
raise NotImplementedError('File format for %s not supported' %
fn)
assert system is not None, 'No system could be defined from input'
assert grad is not None, 'No ab initio gradient found in input'
assert hess is not None, 'No ab initio hessian found in input'
#complete the system information
if system.bonds is None: system.detect_bonds()
if system.masses is None: system.set_standard_masses()
if system.ffatypes is None:
if options.ffatypes in ['low', 'medium', 'high', 'highest']:
guess_ffatypes(system, options.ffatypes)
elif options.ffatypes is not None:
raise NotImplementedError(
'Guessing atom types from %s not implemented' %
options.ffatypes)
else:
raise AssertionError('No atom types defined')
#construct ab initio reference
ai = SecondOrderTaylor('ai',
coords=system.pos.copy(),
energy=energy,
grad=grad,
hess=hess,
pbc=pbc)
#detect a priori defined contributions to the force field
refs = []
if options.ei is not None:
if rvecs is None:
ff = ForceField.generate(system,
options.ei,
rcut=50 * angstrom)
else:
ff = ForceField.generate(system,
options.ei,
rcut=20 * angstrom,
alpha_scale=3.2,
gcut_scale=1.5,
smooth_ei=True)
refs.append(YaffForceField('EI', ff))
if options.vdw is not None:
ff = ForceField.generate(system, options.vdw, rcut=20 * angstrom)
refs.append(YaffForceField('vdW', ff))
if options.covres is not None:
ff = ForceField.generate(system, options.covres)
refs.append(YaffForceField('Cov res', ff))
#define quickff program
assert options.program_mode in allowed_programs, \
'Given program mode %s not allowed. Choose one of %s' %(
options.program_mode,
', '.join([prog for prog in allowed_programs if not prog=='BaseProgram'])
)
mode = program_modes[options.program_mode]
only_traj = 'PT_ALL'
if options.only_traj is not None: only_traj = options.only_traj.split(',')
program = mode(system,
ai,
ffrefs=refs,
fn_traj=options.fn_traj,
only_traj=only_traj,
plot_traj=options.ener_traj,
xyz_traj=options.xyz_traj,
suffix=options.suffix)
#run program
program.run()
def _set_log(self):
log.set_level(self.log_level)
f = self.log_file
if f is not None and (isinstance(f, str) or isinstance(f, IOBase)):
log.write_to_file(f)
def _set_log(self):
log.set_level(self.log_level)
f = self.log_file
if f is not None and (isinstance(f, str) or isinstance(f, IOBase)):
log.write_to_file(f)