def test_write():
gro = Trajectory.open(cwd + '/files/100-SPCE.gro')
tmp = os.path.join(tempdir, 'gro-out.xtc')
xtc = Trajectory.open(tmp, 'w')
for i in range(gro.n_frame):
frame = gro.read_frame(i)
xtc.write_frame(frame)
xtc.close()
assert filecmp.cmp(tmp, cwd + '/files/baselines/gro-out.xtc')
def test_write():
top = Topology.open(cwd + '/files/100-SPCE.psf')
xtc = Trajectory.open(cwd + '/files/100-SPCE.xtc')
tmp = os.path.join(tempdir, 'xtc-out.xyz')
xyz = Trajectory.open(tmp, 'w')
for i in range(xtc.n_frame):
frame = xtc.read_frame(i)
xyz.write_frame(frame, top, subset=list(range(150, 300)))
xyz.close()
filecmp.cmp(tmp, cwd + '/files/baselines/xtc-out.xyz')
def test_write():
gro = Trajectory.open(cwd + '/files/100-SPCE.gro')
tmp = os.path.join(tempdir, 'gro-out.dcd')
dcd = Trajectory.open(tmp, 'w')
for i in range(gro.n_frame):
frame = gro.read_frame(i)
dcd.write_frame(frame)
dcd.close()
# It's annoying that DCD files generated are different every time. Compare the size instead of the content.
assert os.path.getsize(tmp) == os.path.getsize(
cwd + '/files/baselines/gro-out.dcd')
def test_read():
trj = Trajectory.open(
[cwd + '/files/100-SPCE.gro', cwd + '/files/100-SPCE.lammpstrj'])
assert trj.n_atom == 300
assert trj.n_frame == 6
frame = trj.read_frame(0)
assert frame.has_velocity == True
assert pytest.approx(frame.positions[0], abs=1E-6) == [1.283, 1.791, 1.658]
assert frame.has_charge == False
frame = trj.read_frame(1)
assert frame.cell.is_rectangular
assert pytest.approx(frame.cell.size,
abs=1E-6) == [3.00906, 3.00906, 3.00906]
assert pytest.approx(frame.velocities[-1],
abs=1E-6) == [-1.0323, 0.5604, -0.3797]
frame = trj.read_frame(2)
assert frame.has_velocity == False
assert pytest.approx(frame.positions[0],
abs=1E-6) == [2.2545, 1.45688, 1.98961]
assert frame.has_charge == True
assert pytest.approx(frame.charges[:4],
abs=1E-6) == [0.4238, -0.8476, 0.4238, 0.4238]
frame = trj.read_frame(3)
assert frame.cell.is_rectangular
assert pytest.approx(frame.cell.size, abs=1E-6) == [3.0004316] * 3
assert pytest.approx(frame.positions[-1],
abs=1E-6) == [2.11148, 0.241373, 0.664092]
def test_read():
xyz = Trajectory.open(cwd + '/files/100-SPCE.xyz')
assert xyz.n_frame == 4
assert xyz.n_atom == 300
frame1 = xyz.read_frame(1)
assert pytest.approx(frame1.positions[150],
abs=1E-6) == [1.227000, 1.109000, 2.458000]
frame2, frame0 = xyz.read_frames([2, 0])
assert pytest.approx(frame0.positions[150],
abs=1E-6) == [1.410000, 1.315000, 2.851000]
assert pytest.approx(frame2.positions[-1],
abs=1E-6) == [2.529000, 0.136000, 1.780000]
def test_read():
gro = Trajectory.open(cwd + '/files/100-SPCE.gro')
assert gro.n_atom == 300
assert gro.n_frame == 2
frame = gro.read_frame(0)
assert frame.has_velocity == True
assert pytest.approx(frame.positions[0], abs=1E-6) == [1.283, 1.791, 1.658]
frame = gro.read_frame(1)
assert frame.cell.is_rectangular
assert pytest.approx(frame.cell.size,
abs=1E-6) == [3.00906, 3.00906, 3.00906]
assert pytest.approx(frame.velocities[-1],
abs=1E-6) == [-1.0323, 0.5604, -0.3797]
def test_read():
xtc = Trajectory.open(cwd + '/files/100-SPCE.xtc')
assert xtc.n_atom == 300
assert xtc.n_frame == 4
frame = xtc.read_frame(0)
assert frame.has_velocity == False
assert frame.has_charge == False
assert pytest.approx(frame.positions[0], abs=1E-4) == [1.283, 1.791, 1.658]
assert pytest.approx(frame.positions[-1],
abs=1E-4) == [2.726, 2.750, 1.876]
frame2, frame1 = xtc.read_frames([2, 1])
assert pytest.approx(frame1.positions[0],
abs=1E-4) == [1.335, 1.775, 1.818]
assert pytest.approx(frame2.positions[-1],
abs=1E-4) == [2.529, 0.136, 1.780]
def test_read():
dcd = Trajectory.open(cwd + '/files/100-SPCE.dcd')
assert dcd.n_atom == 300
assert dcd.n_frame == 3
frame = dcd.read_frame(0)
assert frame.has_velocity == False
assert frame.has_charge == False
assert pytest.approx(frame.positions[0],
abs=1E-6) == [1.180277, 1.421659, 1.885429]
frame2, frame1 = dcd.read_frames([2, 1])
assert pytest.approx(frame1.positions[0],
abs=1E-6) == [1.645082, 1.233684, 2.165311]
assert pytest.approx(frame2.positions[-1],
abs=1E-6) == [2.545774, 2.661569, 1.707037]
assert pytest.approx(frame2.cell.lengths,
abs=1E-6) == [2.983427, 2.983427, 2.983427]
def test_read():
trj = Trajectory.open(cwd + '/files/100-SPCE.lammpstrj')
assert trj.n_atom == 300
assert trj.n_frame == 4
frame = trj.read_frame(0)
assert frame.has_velocity == False
assert pytest.approx(frame.positions[0],
abs=1E-6) == [2.2545, 1.45688, 1.98961]
assert frame.has_charge == True
assert pytest.approx(frame.charges[:4],
abs=1E-6) == [0.4238, -0.8476, 0.4238, 0.4238]
frame = trj.read_frame(1)
assert frame.cell.is_rectangular
assert pytest.approx(frame.cell.size, abs=1E-6) == [3.0004316] * 3
assert pytest.approx(frame.positions[-1],
abs=1E-6) == [2.11148, 0.241373, 0.664092]
],
"EAN-N": [
atom.id for atom in top.atoms
if atom.symbol == 'N' and atom.molecule.name == 'N0002'
],
"EAN-O": [
atom.id for atom in top.atoms
if atom.symbol == 'O' and atom.molecule.name == 'NO3'
],
}
idx_dict = {k: v for k, v in idx_dict.items() if v}
print(len(idx_zn1), len(idx_zn2))
print({k: len(l) for k, l in idx_dict.items()})
trj = Trajectory.open(args.input)
if args.end > trj.n_frame or args.end == -1:
args.end = trj.n_frame
def wrap_pbc(positions, origin, cell):
displace_array = positions - origin
delta_array = np.floor(displace_array / cell.lengths + 0.5)
return positions - delta_array * cell.lengths
def cartesian2cylindrical(positions, origin, vec_unit):
vec_relative = positions - origin
z_array = vec_relative.dot(vec_unit)
rsq_array = np.sum(vec_relative * vec_relative, axis=1) - z_array**2
else:
typer = None
molecules = []
for inp, n in zip(args.input, args.number):
if inp.startswith(':'):
if typer is None:
raise Exception('--typer is required for SMILES input')
top = Topology.open(inp)
molecules += top.molecules * n
top = Topology(molecules)
top.remove_drude_particles()
top.remove_virtual_sites()
if args.trj is not None:
frame = Trajectory.read_frame_from_file(args.trj, -1)
if frame.cell.volume != 0:
top.cell.set_box(frame.cell.vectors)
if args.box is not None:
top.cell.set_box(args.box)
ff = ForceField.open(*args.forcefield)
if args.nodrude:
ff.polarizable_terms.clear()
ff.virtual_site_terms.clear()
if args.ljscale is not None:
scaler = PaduaLJScaler(args.ljscale)
scaler.scale(ff)
if args.scaleeps != 1.0 or args.scalesig != 1.0:
required=True,
type=str,
help='output dcd file')
parser.add_argument('--anode',
required=True,
type=float,
help='z coordinate (in nm) of anode (right electrode)')
parser.add_argument('--ignore',
nargs='+',
default=[],
type=str,
help='ignore these atom types')
args = parser.parse_args()
top = Topology.open(args.topology)
trj = Trajectory.open(args.input)
frame = trj.read_frame(0)
atoms_non_img = [atom for atom in top.atoms if atom.type != 'IMG']
ids_gen = [atom.id for atom in atoms_non_img if atom.type not in args.ignore]
print('Topology info: ', top.n_atom, 'atoms;', top.n_molecule, 'molecules')
print('Trajectory info: ', trj.n_atom, 'atoms;', trj.n_frame, 'frames')
print('Image info: ', len(atoms_non_img), 'non-image atoms;', len(ids_gen),
'images to gen')
assert len(atoms_non_img) == trj.n_atom
assert trj.n_atom + len(ids_gen) == top.n_atom
trj_out = Trajectory.open(args.output, 'w')