def __init__(self,
trajectory,
kgrid=None,
tgrid=None,
nk=8,
tsamples=60,
dk=0.1,
kmin=1.0,
kmax=10.0,
ksamples=10,
norigins=-1):
FourierSpaceCorrelation.__init__(self, trajectory, [kgrid, tgrid], ('k', 't'), \
'fkt.self', 'self intermediate scattering function F_s(k,t)',
'pos-unf', nk, dk, kmin, kmax, ksamples)
# Setup time grid
# Before setting up the time grid, we need to check periodicity over blocks
check_block_size(self.trajectory.steps, self.trajectory.block_size)
if tgrid is None:
self.grid[1] = [0.0] + logx_grid(
trajectory.timestep, trajectory.total_time * 0.75, tsamples)
self._discrete_tgrid = setup_t_grid(trajectory, self.grid[1])
self.skip = adjust_skip(trajectory, norigins)
# TODO: Can this be moved up?
self.k_sorted, self.k_selected = self._decimate_k()
def __init__(self,
trajectory,
kgrid=None,
tgrid=None,
nk=1,
tsamples=1,
dk=0.1,
kmin=1.0,
kmax=10.0,
ksamples=10,
norigins=-1,
fix_cm=False,
normalize=True):
FourierSpaceCorrelation.__init__(self, trajectory, [kgrid, tgrid],
norigins, nk, dk, kmin, kmax,
ksamples, fix_cm, normalize)
# Before setting up the time grid, we need to check periodicity over blocks
try:
check_block_size(self.trajectory.steps, self.trajectory.block_size)
except IndexError as e:
_log.warn(
'issue with trajectory blocks, the time grid may not correspond to the requested one (%s)',
e.message)
# Setup time grid
if self.grid[1] is None:
self.grid[1] = logx_grid(0.0, self.trajectory.total_time * 0.75,
tsamples)
else:
# If the values are normalized, we make sure the
# user-provided time grid includes t=0. It is removed
# after normalization
if self.normalize:
if self.grid[1][0] > 0:
_log.info(
'adding t=0 to the time grid to normalize F_s(k,t)')
self.grid[1] = [0.0] + self.grid[1]
# When a single time origin is requested,
# make sure no additional time origins except the first frame is used
self._discrete_tgrid = setup_t_grid(self.trajectory,
self.grid[1],
offset=norigins != '1'
and norigins != 1)
def __init__(self,
trajectory,
kgrid=None,
tgrid=None,
nk=100,
dk=0.1,
tsamples=60,
kmin=1.0,
kmax=10.0,
ksamples=10):
FourierSpaceCorrelation.__init__(
self, trajectory, [kgrid, tgrid], ('k', 't'), 'fkt.total',
'intermediate scattering function F(k,t)', 'pos', nk, dk, kmin,
kmax, ksamples)
# Setup time grid
check_block_size(self.trajectory.steps, self.trajectory.block_size)
if tgrid is None:
self.grid[1] = logx_grid(0.0, trajectory.total_time * 0.75,
tsamples)
self._discrete_tgrid = setup_t_grid(trajectory, self.grid[1])
def test_block_size(self):
from atooms.trajectory.utils import check_block_size, get_block_size
steps = [2**i for i in range(5)]
block = get_block_size(steps)
check_block_size(steps, block)
def main(args):
"""Convert trajectory `file_inp` to `file_out`."""
args.file_inp = args.file_inp[0]
if args.fields is not None:
args.fields = args.fields.split(',')
if args.out is not None and not args.out in trajectory.Trajectory.formats:
# available_formats()
__import__('pdb').set_trace()
raise ValueError('Unknown output format %s' % args.out)
if args.file_out == '-':
args.file_out = '/dev/stdout'
if args.verbose:
setup_logging('atooms', 20)
import atooms.core.progress
if args.file_out != '/dev/stdout':
atooms.core.progress.active = True
if args.folder:
t = trajectory.folder.Foldered(args.file_inp, cls=args.inp)
else:
t = trajectory.Trajectory(args.file_inp, fmt=args.inp)
# If no output format is provided we use the input one
if args.out is None:
out_class = t.__class__
else:
out_class = args.out
if args.precision is not None:
t.precision = args.precision
if args.flatten_steps:
t.steps = range(1, len(t) + 1)
# Reset random number generator
if args.seed:
random.seed(args.seed)
# Trick to allow some trajectory formats to set the box side.
# This way the cell is defined as we read the sample (callbacks
# will not do that).
if args.side is not None:
def fix_cell(system, side):
from atooms.system import Cell
system.cell = Cell(side)
return system
L = args.side.split(',')
if len(L) == 1:
t.add_callback(fix_cell, [L, L, L])
else:
t.add_callback(fix_cell, [float(_) for _ in L])
# Define slice.
# We interpret --first N --last N as a request of step N
if args.last == args.first and args.last is not None:
args.last += 1
sl = fractional_slice(args.first, args.last, args.skip, len(t))
# Unfold if requested
if args.unfold:
tu = trajectory.Unfolded(t) #, fix_cm=True)
else:
tu = t
# Fix CM and fold back
if args.fix_cm:
tu.add_callback(trajectory.fix_cm)
tu.add_callback(trajectory.fold)
# Here we could you a trajectory slice t[sl] but this will load
# everything in ram (getitem doesnt provide a generator). This
# will be fixed with python 3.
ts = trajectory.Sliced(tu, sl)
# Change number of particles
if args.N > 0:
def decimate_system(system, N):
from atooms.system.particle import decimate
system.particle = decimate(system.particle, N)
return system
ts.register_callback(decimate_system, args.N)
# Change density and temperature
if args.rho is not None:
ts.register_callback(trajectory.decorators.set_density, args.rho)
if args.temperature is not None:
ts.register_callback(trajectory.decorators.set_temperature,
args.temperature)
# Change species layout if requested
if args.species_layout is not None:
ts.register_callback(trajectory.decorators.change_species,
args.species_layout)
# Sort by species id
if args.species_sort:
ts.register_callback(trajectory.decorators.sort)
# We enforce regular periodicity; steps is None is trajectory is not periodic
try:
steps = check_block_size(ts.steps, ts.block_size, prune=True)
except IndexError:
print('# Warning: something wrong with periodicity check.')
print(
'# We will proceed, but you should check the converted trajectory.'
)
steps = ts.steps
#
# ---------------------
# Trajectory conversion
# ---------------------
#
include_list, exclude_list = [], []
if len(args.fields_include) > 0:
include_list = args.fields_include.split(',')
if len(args.fields_exclude) > 0:
exclude_list = args.fields_exclude.split(',')
fout = trajectory.convert(ts,
out_class,
args.file_out,
fields=args.fields,
include=include_list,
exclude=exclude_list,
steps=steps)
if args.ff:
from atooms.trajectory.hdf5 import add_interaction_hdf5
add_interaction_hdf5(fout, args.ff)
if args.verbose and args.file_out != '/dev/stdout':
print('# converted %s to %s' % (args.file_inp, fout))
t.close()
def test_block_size_5(self):
more = [0, 1, 2, 4, 8, 16, 24, 32]
more += [40 + i for i in more]
self.assertEqual(utils.get_block_size(more), 8)
self.assertEqual(
utils.check_block_size(more, utils.get_block_size(more)), more)
def test_block_size_4(self):
more = [0, 1, 2, 4, 8, 16]
more += [32 + i for i in more]
self.assertEqual(utils.get_block_size(more), 6)
self.assertEqual(
utils.check_block_size(more, utils.get_block_size(more)), more)
def test_block_size_3(self):
more = [0, 1, 2, 4, 8, 16]
more += [32, 33, 34, 36, 40, 48]
self.assertEqual(utils.get_block_size(more), 6)
self.assertEqual(
utils.check_block_size(more, utils.get_block_size(more)), more)
def test_block_size_2(self):
more = [0, 1, 10, 11, 20, 21]
self.assertEqual(utils.get_block_size(more), 2)
self.assertEqual(
utils.check_block_size(more, utils.get_block_size(more)), more)
def test_block_size_1(self):
more = [0, 1, 2, 3, 4]
self.assertEqual(utils.get_block_size(more), 1)
self.assertEqual(
utils.check_block_size(more, utils.get_block_size(more)), None)