def get_box_from_system(item, structure_indices='all', check=True):
if check:
_digest_item(item, _form)
structure_indices = _digest_structure_indices(structure_indices)
from molsysmt._private.math import serie_to_chunks
if structure_indices is 'all':
n_structures = get_n_structures_from_system(item)
structure_indices = np.arange(n_structures)
starts_serie_frames, size_serie_frames = serie_to_chunks(structure_indices)
box_list = []
for start, size in zip(starts_serie_frames, size_serie_frames):
item.seek(start)
_, _, _, box = item.read(n_frames=size)
box_list.append(box)
box = np.concatenate(box_list)
del (box_list)
box = box.astype('float64')
box = box * _puw.unit(item.distance_unit)
box = _puw.standardize(box)
return box
def get_step_from_system(item, structure_indices='all', check=True):
if check:
_digest_item(item, _form)
structure_indices = _digest_structure_indices(structure_indices)
from molsysmt._private.math import serie_to_chunks
if structure_indices is 'all':
n_structures = get_n_structures_from_system(item)
structure_indices = _np.arange(n_structures)
starts_serie_frames, size_serie_frames = serie_to_chunks(structure_indices)
step_list = []
for start, size in zip(starts_serie_frames, size_serie_frames):
item.seek(start)
_, _, step, _ = item.read(n_frames=size)
step_list.append(step)
step = _np.concatenate(step_list)
del (step_list)
step = step.astype('int64')
return step
def get_time_from_system(item, structure_indices='all', check=True):
if check:
_digest_item(item, _form)
structure_indices = _digest_structure_indices(structure_indices)
from molsysmt._private.math import serie_to_chunks
if structure_indices is 'all':
n_structures = get_n_structures_from_system(item)
structure_indices = np.arange(n_structures)
starts_serie_frames, size_serie_frames = serie_to_chunks(structure_indices)
time_list = []
for start, size in zip(starts_serie_frames, size_serie_frames):
item.seek(start)
_, time, _, _ = item.read(n_frames=size)
time_list.append(time)
time = _np.concatenate(time_list)
del (time_list)
time = time.astype('float64')
time = time * _puw.unit('ps')
time = _puw.standardize(time)
return time
def get_box_from_system(item, structure_indices='all', check=True):
if check:
_digest_item(item, _form)
structure_indices = _digest_structure_indices(structure_indices)
from molsysmt._private.math import serie_to_chunks
from molsysmt.pbc import box_vectors_from_box_lengths_and_angles
if structure_indices is 'all':
structure_indices = _np.arange(get_n_structures_from_system(item))
starts_serie_frames, size_serie_frames = serie_to_chunks(structure_indices)
box_list = []
for start, size in zip(starts_serie_frames, size_serie_frames):
item.seek(start)
frame_hdf5 = item.read(n_frames=size)
cell_lengths = frame_hdf5.cell_lengths
cell_angles = frame_hdf5.cell_angles
box = box_vectors_from_box_lengths_and_angles(
cell_lengths * _puw.unit('nm'), cell_angles * _puw.unit('degrees'))
box_list.append(_puw.get_value(box))
box = _np.concatenate(box_list)
del (box_list)
box = box.astype('float64')
box = box * _puw.unit('nm')
box = _puw.standardize(box)
return box
def load_frame(item, atom_indices='all', structure_indices='all'):
# It doesn't really work. seek doesn't work. Once the file is read can not be rewinded.
step = None
if structure_indices is 'all':
coordinates, time, box = item.read()
if atom_indices is not 'all':
coordinates = coordinates[:, atom_indices, :]
else:
from molsysmt._private.math import serie_to_chunks
starts_serie_frames, size_serie_frames = serie_to_chunks(
structure_indices)
coordinates_list = []
time_list = []
step_list = []
box_list = []
for start, size in zip(starts_serie_frames, size_serie_frames):
item.seek(start)
coordinates, time, box = item.read(n_structures=size,
atom_indices=atom_indices)
coordinates_list.append(coordinates)
time_list.append(time)
step_list.append(step)
box_list.append(box)
coordinates = np.concatenate(coordinates_list)
time = np.concatenate(time_list)
box = np.concatenate(box_list)
del (coordinates_list, time_list, box_list)
if len(box) == 0:
box = None
else:
box = box * unit.nanometer
if len(time) == 0:
time = None
else:
time = time * unit.picoseconds
coordinates = coordinates * unit.nanometer
return step, time, coordinates, box
def get_coordinates_from_atom(item,
indices='all',
structure_indices='all',
check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
structure_indices = _digest_structure_indices(structure_indices)
from molsysmt._private.math import serie_to_chunks
if structure_indices is 'all':
n_structures = get_n_structures_from_system(item)
structure_indices = _np.arange(n_structures)
starts_serie_frames, size_serie_frames = serie_to_chunks(structure_indices)
xyz_list = []
for start, size in zip(starts_serie_frames, size_serie_frames):
item.seek(start)
if indices is 'all':
xyz, _, _, _ = item.read(n_structures=size)
else:
xyz, _, _, _ = item.read(n_structures=size, atom_indices=indices)
xyz_list.append(xyz)
xyz = _np.concatenate(xyz_list)
del (xyz_list)
xyz = xyz.astype('float64')
xyz = xyz * _puw.unit(item.distance_unit)
xyz = _puw.standardize(xyz)
return xyz