def open_stream(self, mode):
"""Opens the output stream(s)."""
# prepare format string for zero-padded number of beads,
# including underscpre
fmt_bead = "{0:0" + str(int(1 + np.floor(np.log(self.system.beads.nbeads) / np.log(10)))) + "d}"
if getkey(self.what) in ["positions", "velocities", "forces", "extras", "forces_sc", "momenta"]:
# must write out trajectories for each bead, so must create b streams
# prepare format string for file name
if getkey(self.what) == "extras":
fmt_fn = self.filename + "_" + fmt_bead
else:
fmt_fn = self.filename + "_" + fmt_bead + "." + self.format
# open all files
self.out = []
for b in range(self.system.beads.nbeads):
if (self.ibead < 0 and (b % (-self.ibead) == 0)) or (self.ibead == b):
self.out.append(open_backup(fmt_fn.format(b), mode))
else:
# Create null outputs if a single bead output is chosen.
self.out.append(None)
else:
# open one file
filename = self.filename + "." + self.format
self.out = open_backup(filename, mode)
def open_stream(self):
"""Opens the output stream."""
# Is this the start of the simulation?
is_start = self.system.simul.step == 0
# Only open a new file if this is a new run, otherwise append.
if is_start:
mode = "w"
else:
mode = "a"
self.out = open_backup(self.filename, mode)
# print nice header if information is available on the properties
if is_start:
icol = 1
for what in self.outlist:
ohead = "# "
key = getkey(what)
prop = self.system.properties.property_dict[key]
if "size" in prop and prop["size"] > 1:
ohead += "cols. %3d-%-3d" % (icol,
icol + prop["size"] - 1)
icol += prop["size"]
else:
ohead += "column %3d " % (icol)
icol += 1
ohead += " --> %s " % (what)
if "help" in prop:
ohead += ": " + prop["help"]
self.out.write(ohead + "\n")
def open_stream(self):
"""Opens the output stream."""
# Is this the start of the simulation?
is_start = self.system.simul.step == 0
# Only open a new file if this is a new run, otherwise append.
if is_start:
mode = "w"
else:
mode = "a"
self.out = open_backup(self.filename, mode)
# print nice header if information is available on the properties
if is_start:
icol = 1
for what in self.outlist:
ohead = "# "
key = getkey(what)
prop = self.system.properties.property_dict[key]
if "size" in prop and prop["size"] > 1:
ohead += "cols. %3d-%-3d" % (icol, icol + prop["size"] - 1)
icol += prop["size"]
else:
ohead += "column %3d " % (icol)
icol += 1
ohead += " --> %s " % (what)
if "help" in prop:
ohead += ": " + prop["help"]
self.out.write(ohead + "\n")
def open_stream(self):
"""Opens the output stream(s)."""
# Is this the start of the simulation?
is_start = self.system.simul.step == 0
# Only open a new file if this is a new run, otherwise append.
if is_start:
mode = "w"
else:
mode = "a"
# prepare format string for zero-padded number of beads,
# including underscpre
fmt_bead = "{0:0" + str(
int(1 + np.floor(np.log(self.system.beads.nbeads) /
np.log(10)))) + "d}"
if getkey(self.what) in [
"positions", "velocities", "forces", "extras", "forces_sc",
"momenta"
]:
# must write out trajectories for each bead, so must create b streams
# prepare format string for file name
if getkey(self.what) == "extras":
fmt_fn = self.filename + "_" + fmt_bead
else:
fmt_fn = self.filename + "_" + fmt_bead + "." + self.format
# open all files
self.out = []
for b in range(self.system.beads.nbeads):
if (self.ibead < 0 and
(b % (-self.ibead) == 0)) or (self.ibead == b):
self.out.append(open_backup(fmt_fn.format(b), mode))
else:
# Create null outputs if a single bead output is chosen.
self.out.append(None)
else:
# open one file
filename = self.filename + "." + self.format
self.out = open_backup(filename, mode)
def main(fns_in, fn_out, begin, end, stride):
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(fn) for fn in fns_in]
# 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
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 trj in trjs_in:
frame = trj.next()
# ... and possibly save them in the output trajectory.
if do_output:
print_file(mode_out, frame['atoms'], frame['cell'], f_out)
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 open_stream(self, mode):
"""Opens the output stream(s)."""
# prepare format string for zero-padded number of beads,
# including underscore
fmt_bead = ("{0:0" + str(
int(1 + np.floor(np.log(self.system.beads.nbeads) / np.log(10)))) +
"d}")
if getkey(self.what) in [
"positions",
"velocities",
"forces",
"extras",
"extras_component",
"forces_sc",
"momenta",
]:
# must write out trajectories for each bead, so must create b streams
# prepare format string for file name
if getkey(self.what) == "extras" or getkey(
self.what) == "extras_component":
fmt_fn = self.filename + "_" + fmt_bead
else:
fmt_fn = self.filename + "_" + fmt_bead + "." + self.format
# open all files
self.out = []
for b in range(self.system.beads.nbeads):
if (self.ibead < 0 and
(b % (-self.ibead) == 0)) or (self.ibead == b):
self.out.append(open_backup(fmt_fn.format(b), mode))
else:
# Create null outputs if a single bead output is chosen.
self.out.append(None)
else:
# open one file
filename = self.filename + "." + self.format
self.out = open_backup(filename, mode)
def contract_trajectory(fns_in, fn_out_template, n_new):
n = len(fns_in)
# Generate output file names.
if n_new == 1:
fns_out = [fn_out_template]
else:
fns_out = [fn_out_template.format(i) for i in range(n_new)]
print "Contracting {:d} beads to {:d} beads.".format(n, n_new)
print
print "input file names:"
for fn in fns_in:
print fn
print
print "output file names:"
for fn in fns_out:
print fn
print
# Open input trajectory iterators.
trjs_in = [iter_file_name(fn) for fn in fns_in]
# Open output files.
fs_out = [open_backup(fn, "w") for fn in fns_out]
mode_out = os.path.splitext(fn_out_template)[1]
# prepare ring polymer rescaler
rescale = nm_rescale(n, n_new)
# Loop over all frames.
i_frame = 0
while True:
try:
# Get the frames for all beads.
frames = [trj.next() for trj in trjs_in]
except StopIteration:
# Stop when any of the trajectories runs out of frames.
break
# Consistency check.
h = frames[0]["cell"].h
natoms = frames[0]["atoms"].natoms
for i in range(n):
# Check that all the cells are the same.
if (frames[i]["cell"].h != h).any():
msg = "Cell for beads {:d} and {:d} differ in frame {:d}."
raise ValueError(msg.format(0, i, i_frame))
# Check that the numbers of atoms are the same.
if frames[i]["atoms"].natoms != natoms:
msg = "Different numbers fo atoms for beads {:d} and {:d} in frame {:d}."
raise ValueError(msg.format(0, i, i_frame))
# Reuse the first frame for output.
cell = frames[0]["cell"]
atoms = frames[0]["atoms"]
# Compose the ring polymer.
q = np.vstack([frame["atoms"].q for frame in frames])
# Contract the coordinates to `n_new` beads.
q_c = rescale.b1tob2(q)
# Save the output data.
for i, f_out in enumerate(fs_out):
atoms.q = q_c[i, :]
print_file(mode_out, atoms, cell, f_out)
# Count frames and print information on progress.
i_frame += 1
if i_frame % 100 == 0:
print "\rframe {:d}".format(i_frame),
sys.stdout.flush()
for f_out in fs_out:
f_out.close()
print
print
print "Processed {:d} frames.".format(i_frame)
def open_stream(self, mode="w"):
"""Opens the output stream"""
# Only open a new file if this is a new run, otherwise append.
self.mode = mode
self.out = open_backup(self.filename, self.mode)
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 contract_trajectory(fns_in, fn_out_template, n_new, cell_units_in, cell_units_out):
verbosity.level = "low"
n = len(fns_in)
# Generate output file names.
if n_new == 1:
fns_out = [fn_out_template]
else:
fns_out = [fn_out_template.format(i) for i in range(n_new)]
print("Contracting {:d} beads to {:d} beads.".format(n, n_new))
print()
print("input file names:")
for fn in fns_in:
print(fn)
print()
print("output file names:")
for fn in fns_out:
print(fn)
print()
# Open input trajectory iterators.
trjs_in = [iter_file_name_raw(fn) for fn in fns_in]
mode = os.path.splitext(fn)[-1]
# Open output files.
fs_out = [open_backup(fn, "w") for fn in fns_out]
mode_out = os.path.splitext(fn_out_template)[-1]
# prepare ring polymer rescaler
rescale = nm_rescale(n, n_new)
# Loop over all frames.
i_frame = 0
while True:
try:
# Get the frames for all beads.
frames = [trj.next() for trj in trjs_in]
except StopIteration:
# Stop when any of the trajectories runs out of frames.
break
# gets units from first frame
dimension, units, cell_units = auto_units(comment=frames[0]["comment"], cell_units=cell_units_in)
if cell_units_out == "automatic": cell_units_out = cell_units # re-use units unless otherwise specified
# Consistency check.
h = frames[0]["cell"]
natoms = len(frames[0]["data"]) / 3
for i in range(n):
# Check that all the cells are the same.
if (frames[i]["cell"] != h).any():
msg = "Cell for beads {:d} and {:d} differ in frame {:d}."
raise ValueError(msg.format(0, i, i_frame))
# Check that the numbers of atoms are the same.
if len(frames[i]["data"]) != 3 * natoms:
msg = "Different numbers of atoms for beads {:d} and {:d} in frame {:d}."
raise ValueError(msg.format(0, i, i_frame))
cell = Cell()
cell.h = frames[0]["cell"]
atoms = Atoms(natoms)
atoms.names = frames[0]["names"]
# Compose the ring polymer.
q = np.vstack([frame["data"] for frame in frames]) * unit_to_internal(dimension, units, 1) # units transformation
# Contract the coordinates to `n_new` beads.
q_c = rescale.b1tob2(q)
# Save the output data.
for i, f_out in enumerate(fs_out):
atoms.q = q_c[i, :]
print_file(mode_out, atoms, cell, f_out, dimension=dimension, units=units, cell_units=cell_units_out)
# 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()
for f_out in fs_out:
f_out.close()
print()
print()
print("Processed {:d} frames.".format(i_frame))
def contract_trajectory(fns_in, fn_out_template, n_new, cell_units_in,
cell_units_out):
verbosity.level = "low"
n = len(fns_in)
# Generate output file names.
if n_new == 1:
fns_out = [fn_out_template]
else:
fns_out = [fn_out_template.format(i) for i in range(n_new)]
print("Contracting {:d} beads to {:d} beads.".format(n, n_new))
print()
print("input file names:")
for fn in fns_in:
print(fn)
print()
print("output file names:")
for fn in fns_out:
print(fn)
print()
# Open input trajectory iterators.
trjs_in = [iter_file_name_raw(fn) for fn in fns_in]
mode = os.path.splitext(fn)[-1]
# Open output files.
fs_out = [open_backup(fn, "w") for fn in fns_out]
mode_out = os.path.splitext(fn_out_template)[-1]
# prepare ring polymer rescaler
rescale = nm_rescale(n, n_new)
# Loop over all frames.
i_frame = 0
while True:
try:
# Get the frames for all beads.
frames = [trj.next() for trj in trjs_in]
except StopIteration:
# Stop when any of the trajectories runs out of frames.
break
# gets units from first frame
dimension, units, cell_units = auto_units(comment=frames[0]["comment"],
cell_units=cell_units_in)
if cell_units_out == "automatic":
cell_units_out = cell_units # re-use units unless otherwise specified
# Consistency check.
h = frames[0]["cell"]
natoms = len(frames[0]["data"]) / 3
for i in range(n):
# Check that all the cells are the same.
if (frames[i]["cell"] != h).any():
msg = "Cell for beads {:d} and {:d} differ in frame {:d}."
raise ValueError(msg.format(0, i, i_frame))
# Check that the numbers of atoms are the same.
if len(frames[i]["data"]) != 3 * natoms:
msg = "Different numbers of atoms for beads {:d} and {:d} in frame {:d}."
raise ValueError(msg.format(0, i, i_frame))
cell = Cell()
cell.h = frames[0]["cell"]
atoms = Atoms(natoms)
atoms.names = frames[0]["names"]
# Compose the ring polymer.
q = np.vstack([frame["data"] for frame in frames]) * unit_to_internal(
dimension, units, 1) # units transformation
# Contract the coordinates to `n_new` beads.
q_c = rescale.b1tob2(q)
# Save the output data.
for i, f_out in enumerate(fs_out):
atoms.q = q_c[i, :]
print_file(mode_out,
atoms,
cell,
f_out,
dimension=dimension,
units=units,
cell_units=cell_units_out)
# 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()
for f_out in fs_out:
f_out.close()
print()
print()
print("Processed {:d} frames.".format(i_frame))
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))
def open_stream(self, mode="w"):
"""Opens the output stream."""
# Only open a new file if this is a new run, otherwise append.
self.mode = mode
self.out = open_backup(self.filename, self.mode)
