# natoms, frames, comment, expected_cell, precision
tests_read_xyz = [
(1, 1, 'just a string plus few numbers: 1.10 2 .1',
default_cell_mat, 5),
(2, 1, 'another random comment',
default_cell_mat, 5),
(1, 2, 'random comment', default_cell_mat, 5),
(2, 2, 'random comment', default_cell_mat, 5),
(10, 2, 'random comment', default_cell_mat, 5),
(10, 10, 'random comment', default_cell_mat, 5),
(2, 3, '# CELL(abcABC): 5.1 5.2 5.0 91.0 89 90',
mt.abc2h(5.1, 5.2, 5.0, 91 * deg2rad, 89 * deg2rad, 90 * deg2rad), 5),
(2, 3, '# CELL[GENH]: ' + cell_string,
mt.abc2h(5.1, 5.2, 5.0, 91 * deg2rad, 89 * deg2rad, 90 * deg2rad), 5),
(2, 3, '# CELL{H}: ' + cell_string,
mt.abc2h(*mt.genh2abc(mt.abc2h(5.1, 5.2, 5.0, 91 * deg2rad, 89 * deg2rad, 90 * deg2rad))), 5),
(2, 3, '100 aaa # CELL(abcABC): 5.1 5.2 5.0 91.0 89 90 100 aaa',
mt.abc2h(5.1, 5.2, 5.0, 91 * deg2rad, 89 * deg2rad, 90 * deg2rad), 5),
(2, 3, '100 aaa # CELL[GENH]: ' + cell_string + ' 100 aaa',
mt.abc2h(5.1, 5.2, 5.0, 91 * deg2rad, 89 * deg2rad, 90 * deg2rad), 5),
(2, 3, '# CELL{H}: ' + cell_string + ' 100 aaa',
mt.abc2h(*mt.genh2abc(mt.abc2h(5.1, 5.2, 5.0, 91 * deg2rad, 89 * deg2rad, 90 * deg2rad))), 5),
]
@pytest.fixture(params=tests_read_xyz)
def create_random_xyz_traj_to_read(request):
natoms, frames, comment, expected_cell, precision = request.param
filedesc, xyz, atom_names = xyz_gen.xyz_traj_filedesc(natoms,
def read_xyz(filedesc):
"""Reads an XYZ-style file with i-PI style comments and returns data in raw format for further units transformation
and other post processing.
Args:
filedesc: An open readable file object from a xyz formatted file with i-PI header comments.
Returns:
i-Pi comment line, cell array, data (positions, forces, etc.), atoms names and masses
"""
try:
natoms = int(filedesc.next())
except (StopIteration, ValueError):
raise EOFError
comment = filedesc.next()
# Extracting cell
cell = [key.search(comment) for key in cell_re]
usegenh = False
if cell[0] is not None: # abcABC
a, b, c = [float(x) for x in cell[0].group(1).split()[:3]]
alpha, beta, gamma = [float(x) * deg2rad
for x in cell[0].group(1).split()[3:6]]
h = mt.abc2h(a, b, c, alpha, beta, gamma)
elif cell[1] is not None: # H
h = np.array(cell[1].group(1).split()[:9], float)
h.resize((3, 3))
elif cell[2] is not None: # GENH
genh = np.array(cell[2].group(1).split()[:9], float)
genh.resize((3, 3))
invgenh = np.linalg.inv(genh)
# convert back & forth from abcABC representation to get an upper triangular h
h = mt.abc2h(*mt.genh2abc(genh))
usegenh = True
else: # defaults to unit box
h = np.array([[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, -1.0]])
cell = h
qatoms = np.zeros(3 * natoms)
names = np.zeros(natoms, dtype='|S4')
masses = np.zeros(natoms)
# Extracting a time-frame information
atom_counter = 0
for iat, line in enumerate(filedesc):
body = line.split()
names[iat], masses[iat] = body[0], Elements.mass(body[0])
x, y, z = float(body[1]), float(body[2]), float(body[3])
if usegenh:
# must convert from the input cell parameters to the internal convention
u = np.array([x, y, z])
us = np.dot(u, invgenh)
u = np.dot(h, us)
x, y, z = u
qatoms[3 * iat], qatoms[3 * iat + 1], qatoms[3 * iat + 2] = x, y, z
atom_counter += 1
if atom_counter == natoms:
break
if natoms != len(names):
raise ValueError("The number of atom records does not match the header of the xyz file.")
return comment, cell, qatoms, names, masses
def read_xyz(filedesc):
"""Reads an XYZ-style file with i-PI style comments and returns data in raw format for further units transformation
and other post processing.
Args:
filedesc: An open readable file object from a xyz formatted file with i-PI header comments.
Returns:
i-Pi comment line, cell array, data (positions, forces, etc.), atoms names and masses
"""
try:
natoms = int(filedesc.next())
except (StopIteration, ValueError):
raise EOFError
comment = filedesc.next()
# Extracting cell
cell = [key.search(comment) for key in cell_re]
usegenh = False
if cell[0] is not None: # abcABC
a, b, c = [float(x) for x in cell[0].group(1).split()[:3]]
alpha, beta, gamma = [float(x) * deg2rad
for x in cell[0].group(1).split()[3:6]]
h = mt.abc2h(a, b, c, alpha, beta, gamma)
elif cell[1] is not None: # GENH
h = np.array(cell[1].group(1).split()[:9], float)
h.resize((3, 3))
elif cell[2] is not None: # H
genh = np.array(cell[2].group(1).split()[:9], float)
genh.resize((3, 3))
invgenh = np.linalg.inv(genh)
# convert back & forth from abcABC representation to get an upper triangular h
h = mt.abc2h(*mt.genh2abc(genh))
usegenh = True
else: # defaults to unit box
h = np.array([[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, -1.0]])
cell = h
qatoms = np.zeros(3 * natoms)
names = np.zeros(natoms, dtype='|S4')
masses = np.zeros(natoms)
# Extracting a time-frame information
atom_counter = 0
for iat, line in enumerate(filedesc):
body = line.split()
names[iat], masses[iat] = body[0], Elements.mass(body[0])
x, y, z = float(body[1]), float(body[2]), float(body[3])
# TODO: The following in matrices would use vectorial computaiton
if usegenh:
# must convert from the input cell parameters to the internal convention
u = np.array([x, y, z])
us = np.dot(u, invgenh)
u = np.dot(h, us)
x, y, z = u
qatoms[3 * iat], qatoms[3 * iat + 1], qatoms[3 * iat + 2] = x, y, z
atom_counter += 1
if atom_counter == natoms:
break
if natoms != len(names):
raise ValueError("The number of atom records does not match the header of the xyz file.")
return comment, cell, qatoms, names, masses
5,
),
(
2,
3,
"# CELL[GENH]: " + cell_string,
mt.abc2h(5.1, 5.2, 5.0, 91 * deg2rad, 89 * deg2rad, 90 * deg2rad),
5,
),
(
2,
3,
"# CELL{H}: " + cell_string,
mt.abc2h(
*mt.genh2abc(
mt.abc2h(5.1, 5.2, 5.0, 91 * deg2rad, 89 * deg2rad, 90 * deg2rad)
)
),
5,
),
(
2,
3,
"100 aaa # CELL(abcABC): 5.1 5.2 5.0 91.0 89 90 100 aaa",
mt.abc2h(5.1, 5.2, 5.0, 91 * deg2rad, 89 * deg2rad, 90 * deg2rad),
5,
),
(
2,
3,
"100 aaa # CELL[GENH]: " + cell_string + " 100 aaa",
