def test_process_units_object(units_preparation):
natoms, frames, comment, conver_xyz, conver_cell = units_preparation
output = "objects"
filedesc, xyz, atom_names = xyz_gen.xyz_traj_filedesc(
natoms, frames, comment)
cell = mt.abc2h(1.0, 1.0, 1.0, np.pi / 2.0, np.pi / 2.0, np.pi / 2.0)
masses = []
_count = 0
for _at in atom_names:
print(Elements.mass(_at), _count, _at)
masses.append(Elements.mass(_at))
_count += 1
masses = np.array(masses)
res = testing.process_units(
comment,
cell.copy(),
xyz.copy(),
np.array(atom_names).copy(),
np.array(masses).copy(),
output=output,
)
npt.assert_array_almost_equal(res["atoms"].q, xyz * conver_xyz, 5)
npt.assert_array_almost_equal(res["atoms"].m, masses, 5)
npt.assert_array_almost_equal(res["cell"].h, cell * conver_cell, 5)
npt.assert_array_equal(res["atoms"].names, atom_names, 5)
def test_process_units_noobj(units_preparation):
natoms, frames, comment, conver_xyz, conver_cell = units_preparation
output = "noobj"
filedesc, xyz, atom_names = xyz_gen.xyz_traj_filedesc(
natoms, frames, comment)
cell = mt.abc2h(1.0, 1.0, 1.0, np.pi / 2.0, np.pi / 2.0, np.pi / 2.0)
masses = []
_count = 0
print("atom_names", atom_names)
for _at in atom_names:
print(Elements.mass(_at), _count, _at)
masses.append(Elements.mass(_at))
_count += 1
masses = np.array(masses)
type(masses)
res = testing.process_units(
comment,
cell.copy(),
xyz.copy(),
np.array(atom_names).copy(),
np.array(masses).copy(),
output=output,
)
print(xyz, res["data"])
npt.assert_array_almost_equal(res["data"], xyz * conver_xyz, 5)
npt.assert_array_almost_equal(res["masses"], masses, 5)
npt.assert_array_almost_equal(res["cell"], cell * conver_cell, 5)
npt.assert_array_equal(res["names"], atom_names, 5)
assert res["natoms"] == natoms
def test_process_units_object(units_preparation):
natoms, frames, comment, conver_xyz, conver_cell = units_preparation
output = 'objects'
filedesc, xyz, atom_names = xyz_gen.xyz_traj_filedesc(natoms,
frames, comment)
cell = mt.abc2h(1.0, 1.0, 1.0, np.pi / 2.0, np.pi / 2.0, np.pi / 2.0)
masses = []
_count = 0
for _at in atom_names:
print Elements.mass(_at), _count, _at
masses.append(Elements.mass(_at))
_count += 1
masses = np.array(masses)
res = testing.process_units(comment, cell.copy(), xyz.copy(), np.array(atom_names).copy(), np.array(masses).copy(), output=output)
npt.assert_array_almost_equal(res['atoms'].q, xyz * conver_xyz, 5)
npt.assert_array_almost_equal(res['atoms'].m, masses, 5)
npt.assert_array_almost_equal(res['cell'].h, cell * conver_cell, 5)
npt.assert_array_equal(res['atoms'].names, atom_names, 5)
def test_process_units_noobj(units_preparation):
natoms, frames, comment, conver_xyz, conver_cell = units_preparation
output = 'noobj'
filedesc, xyz, atom_names = xyz_gen.xyz_traj_filedesc(natoms,
frames, comment)
cell = mt.abc2h(1.0, 1.0, 1.0, np.pi / 2.0, np.pi / 2.0, np.pi / 2.0)
masses = []
_count = 0
print 'atom_names', atom_names
for _at in atom_names:
print Elements.mass(_at), _count, _at
masses.append(Elements.mass(_at))
_count += 1
masses = np.array(masses)
type(masses)
res = testing.process_units(comment, cell.copy(), xyz.copy(), np.array(atom_names).copy(), np.array(masses).copy(), output=output)
print xyz, res['data']
npt.assert_array_almost_equal(res['data'], xyz * conver_xyz, 5)
npt.assert_array_almost_equal(res['masses'], masses, 5)
npt.assert_array_almost_equal(res['cell'], cell * conver_cell, 5)
npt.assert_array_equal(res['names'], atom_names, 5)
assert res['natoms'] == natoms
def main(fns_in, fn_out, begin, end, stride, wrap, unwrap):
verbosity.level = "low"
print('Multiplexing {:d} beads into one trajectory.'.format(len(fns_in)))
print()
print('input file names:')
for fn in fns_in:
print(fn)
print()
print('output file name:', fn_out)
print()
# Open input trajectory iterators.
trjs_in = [iter_file_name_raw(fn) for fn in fns_in]
mode = os.path.splitext(fns_in[0])[-1]
# Open output file.
f_out = open_backup(fn_out, 'w')
mode_out = os.path.splitext(fn_out)[-1]
# Loop over all frames.
i_frame = 0
i_frame_saved = 0
# There can be multiple trajectories, so we store a frame_last for each trajectory
frame_last = [None] * len(fns_in)
while True:
# Check the endpoint index, exit if we're done.
if (end > -1) and (i_frame >= end):
break
# Should we save output from this frame?
do_output = (i_frame >= begin) and ((i_frame % stride) == 0)
try:
# Get the frames from all trajectories...
for idx, trj in enumerate(trjs_in):
frame = next(trj)
# gets units from first frame
dimension, units, cell_units = auto_units(
comment=frame["comment"])
frame = process_units(dimension=dimension,
units=units,
cell_units=cell_units,
mode=mode,
**frame)
if wrap:
frame = wrap_positions(frame)
if unwrap:
frame = unwrap_positions(frame, frame_last[idx])
frame_last[idx] = frame.copy()
# ... and possibly save them in the output trajectory.
if do_output:
print_file(mode_out,
frame['atoms'],
frame['cell'],
f_out,
dimension=dimension,
units=units,
cell_units=cell_units)
if do_output:
i_frame_saved += 1
except StopIteration:
# Stop when any of the trajectories runs out of frames.
break
# Count frames and print information on progress.
i_frame += 1
if i_frame % 100 == 0:
print('\rframe {:d}'.format(i_frame), end='')
sys.stdout.flush()
f_out.close()
print()
print()
print('Loaded {:d} frames.'.format(i_frame))
print('Saved {:d} frames.'.format(i_frame_saved))
def main(fns_in, fn_out, begin, end, stride, wrap, unwrap):
verbosity.level = "low"
print('Multiplexing {:d} beads into one trajectory.'.format(len(fns_in)))
print()
print('input file names:')
for fn in fns_in:
print(fn)
print()
print('output file name:', fn_out)
print()
# Open input trajectory iterators.
trjs_in = [iter_file_name_raw(fn) for fn in fns_in]
mode = os.path.splitext(fns_in[0])[-1]
# Open output file.
f_out = open_backup(fn_out, 'w')
mode_out = os.path.splitext(fn_out)[-1]
# Loop over all frames.
i_frame = 0
i_frame_saved = 0
# There can be multiple trajectories, so we store a frame_last for each trajectory
frame_last = [None] * len(fns_in)
while True:
# Check the endpoint index, exit if we're done.
if (end > -1) and (i_frame >= end):
break
# Should we save output from this frame?
do_output = (i_frame >= begin) and ((i_frame % stride) == 0)
try:
# Get the frames from all trajectories...
for idx,trj in enumerate(trjs_in):
frame = trj.next()
# gets units from first frame
dimension, units, cell_units = auto_units(comment=frame["comment"])
frame = process_units(dimension=dimension, units=units, cell_units=cell_units, mode=mode, **frame)
if wrap:
frame = wrap_positions(frame)
if unwrap:
frame = unwrap_positions(frame,frame_last[idx])
frame_last[idx] = frame.copy()
# ... and possibly save them in the output trajectory.
if do_output:
print_file(mode_out, frame['atoms'], frame['cell'], f_out, dimension=dimension, units=units, cell_units=cell_units)
if do_output:
i_frame_saved += 1
except StopIteration:
# Stop when any of the trajectories runs out of frames.
break
# Count frames and print information on progress.
i_frame += 1
if i_frame % 100 == 0:
print('\rframe {:d}'.format(i_frame), end='')
sys.stdout.flush()
f_out.close()
print()
print()
print('Loaded {:d} frames.'.format(i_frame))
print('Saved {:d} frames.'.format(i_frame_saved))
