def read_json(filedesc, **kwargs):
"""Reads a JSON-style file with i-pi style comments and creates an Atoms and Cell object.
Args:
filedesc: An open readable file object from a json formatted file with i-PI header comments.
Returns:
An Atoms object with the appropriate atom labels, masses and positions.
A Cell object.
"""
try:
line = json.loads(filedesc.readline())
except ValueError:
raise EOFError("The file descriptor hit EOF.")
atoms = Atoms(line[0])
atoms.q = np.asarray(line[8])
atoms.names = np.asarray(line[9], dtype='|S4')
atoms.m = np.asarray(map(Elements.mass, atoms.names))
a = float(line[1])
b = float(line[2])
c = float(line[3])
alpha = float(line[4]) * np.pi / 180
beta = float(line[5]) * np.pi / 180
gamma = float(line[6]) * np.pi / 180
h = mt.abc2h(a, b, c, alpha, beta, gamma)
cell = Cell(h)
return {"atoms": atoms, "cell": cell}
def create_random_xyz_traj_to_write(request):
natoms, frames, comment, expected_cell, precision = request.param
a, b, c, alpha, beta, gamma = mt.h2abc_deg(expected_cell)
fmt_header = "# CELL(abcABC): %10.5f %10.5f %10.5f %10.5f %10.5f %10.5f %s"
comment = fmt_header % (a, b, c, alpha, beta, gamma, comment)
filedesc, xyz, atom_names = xyz_gen.xyz_traj_filedesc(natoms, frames, comment)
filedesc.seek(0)
masses = [Elements.mass(_am) for _am in atom_names]
cell_list = []
atoms_list = []
for _fr in xrange(frames):
cell = Cell(expected_cell)
atoms = Atoms(natoms)
atoms.q[:] = xyz[_fr * natoms * 3:(_fr + 1) * natoms * 3]
atoms.names = atom_names[_fr * natoms:(_fr + 1) * natoms]
atoms.m[:] = masses[_fr * natoms:(_fr + 1) * natoms]
atoms_list.append(atoms)
cell_list.append(cell)
return (filedesc, atoms_list, cell_list, comment, precision)
def main(prefix, suffix="pos", outprefix="fixcom"):
ipos = []
imode = []
for filename in sorted(glob.glob(prefix + "." + suffix + "*")):
imode.append(filename.split(".")[-1])
ipos.append(open(filename, "r"))
nbeads = len(ipos)
natoms = 0
ifr = 0
lout = []
for b in range(nbeads):
# zero-padded bead number
padb = ("%0" + str(int(1 + np.floor(np.log(nbeads) / np.log(10)))) + "d") % (b)
lout.append(
open(
prefix + "." + outprefix + "." + suffix + "_" + padb + "." + imode[b],
"a",
)
)
while True:
allbeads = []
for i in range(nbeads):
try:
poscell = read_file(imode[i], ipos[i])
cell = poscell["cell"]
pos = poscell["atoms"]
allbeads.append(pos)
if natoms == 0:
natoms = pos.natoms
atoms = Atoms(natoms)
atoms.q += pos.q
atoms.names = pos.names
atoms.m += pos.m
except EOFError: # finished reading files
for ib in range(nbeads):
lout[ib].close()
sys.exit(0)
atoms.q /= nbeads
atoms.m /= nbeads
com = np.zeros(3)
tm = 0
for i in range(atoms.natoms):
com += atoms.m[i] * atoms.q[3 * i : 3 * (i + 1)]
tm += atoms.m[i]
com /= tm
for ib in range(nbeads):
for i in range(allbeads[ib].natoms):
allbeads[ib].q[3 * i : 3 * (i + 1)] -= com
print_file(imode[ib], allbeads[ib], cell, filedesc=lout[ib])
atoms.q[:] = 0.0
atoms.m[:] = 0.0
ifr += 1
def read_pdb(filedesc):
"""Takes a pdb-style file and creates an Atoms and Cell object.
Args:
filedesc: An open readable file object from a pdb formatted file.
Returns:
An Atoms object with the appropriate atom labels, masses and positions,
and a Cell object with the appropriate cell dimensions and an estimate
of a reasonable cell mass.
"""
header = filedesc.readline()
if "TITLE" in header:
header = filedesc.readline() # skip the comment field
if header == "":
raise EOFError("End of file or empty header in PDB file")
a = float(header[6:15])
b = float(header[15:24])
c = float(header[24:33])
alpha = float(header[33:40])
beta = float(header[40:47])
gamma = float(header[47:54])
alpha *= np.pi / 180.0
beta *= np.pi / 180.0
gamma *= np.pi / 180.0
h = mt.abc2h(a, b, c, alpha, beta, gamma)
cell = Cell(h)
natoms = 0
body = filedesc.readline()
qatoms = []
names = []
masses = []
while (body.strip() != "" and body.strip() != "END"):
natoms += 1
name = body[12:16].strip()
names.append(name)
masses.append(Elements.mass(name))
x = float(body[31:39])
y = float(body[39:47])
z = float(body[47:55])
qatoms.append(x)
qatoms.append(y)
qatoms.append(z)
body = filedesc.readline()
atoms = Atoms(natoms)
atoms.q = np.asarray(qatoms)
atoms.names = np.asarray(names, dtype='|S4')
atoms.m = np.asarray(masses)
return atoms, cell
def read_pdb(filedesc):
"""Takes a pdb-style file and creates an Atoms and Cell object.
Args:
filedesc: An open readable file object from a pdb formatted file.
Returns:
An Atoms object with the appropriate atom labels, masses and positions,
and a Cell object with the appropriate cell dimensions and an estimate
of a reasonable cell mass.
"""
header = filedesc.readline()
if "TITLE" in header: header = filedesc.readline() # skip the comment field
if header == "":
raise EOFError("End of file or empty header in PDB file")
a = float(header[6:15])
b = float(header[15:24])
c = float(header[24:33])
alpha = float(header[33:40])
beta = float(header[40:47])
gamma = float(header[47:54])
alpha *= np.pi/180.0
beta *= np.pi/180.0
gamma *= np.pi/180.0
h = mt.abc2h(a, b, c, alpha, beta, gamma)
cell = Cell(h)
natoms = 0
body = filedesc.readline()
qatoms = []
names = []
masses = []
while (body.strip() != "" and body.strip() != "END"):
natoms += 1
name = body[12:16].strip()
names.append(name)
masses.append(Elements.mass(name))
x = float(body[31:39])
y = float(body[39:47])
z = float(body[47:55])
qatoms.append(x)
qatoms.append(y)
qatoms.append(z)
body = filedesc.readline()
atoms = Atoms(natoms)
atoms.q = np.asarray(qatoms)
atoms.names = np.asarray(names,dtype='|S4')
atoms.m = np.asarray(masses)
return atoms, cell
def read_xyz(filedesc):
"""Takes a xyz-style file and creates an Atoms object.
Args:
filedesc: An open readable file object from a xyz formatted file.
Returns:
An Atoms object with the appropriate atom labels, masses and positions.
"""
natoms = filedesc.readline()
if natoms == "":
raise EOFError("The file descriptor hit EOF.")
natoms = int(natoms)
comment = filedesc.readline()
qatoms = []
names = []
masses = []
iat = 0
while (iat < natoms):
body = filedesc.readline()
if body.strip() == "":
break
body = body.split()
name = body[0]
names.append(name)
masses.append(Elements.mass(name))
x = float(body[1])
y = float(body[2])
z = float(body[3])
qatoms.append(x)
qatoms.append(y)
qatoms.append(z)
iat += 1
if natoms != len(names):
raise ValueError(
"The number of atom records does not match the header of the xyz file."
)
atoms = Atoms(natoms)
# for i in range(natoms):
# nat = atoms[i]
# nat.q = qatoms[i]
# nat.name = names[i]
# nat.m = Elements.mass(names[i])
atoms.q = np.asarray(qatoms)
atoms.names = np.asarray(names, dtype='|S4')
atoms.m = np.asarray(masses)
return atoms
def read_xyz(filedesc):
"""Takes a xyz-style file and creates an Atoms object.
Args:
filedesc: An open readable file object from a xyz formatted file.
Returns:
An Atoms object with the appropriate atom labels, masses and positions.
"""
natoms = filedesc.readline()
if natoms == "":
raise EOFError("The file descriptor hit EOF.")
natoms = int(natoms)
comment = filedesc.readline()
qatoms = []
names = []
masses = []
iat = 0
while iat < natoms:
body = filedesc.readline()
if body.strip() == "":
break
body = body.split()
name = body[0]
names.append(name)
masses.append(Elements.mass(name))
x = float(body[1])
y = float(body[2])
z = float(body[3])
qatoms.append(x)
qatoms.append(y)
qatoms.append(z)
iat += 1
if natoms != len(names):
raise ValueError("The number of atom records does not match the header of the xyz file.")
atoms = Atoms(natoms)
# for i in range(natoms):
# nat = atoms[i]
# nat.q = qatoms[i]
# nat.name = names[i]
# nat.m = Elements.mass(names[i])
atoms.q = np.asarray(qatoms)
atoms.names = np.asarray(names, dtype="|S4")
atoms.m = np.asarray(masses)
return atoms
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))
