Ejemplo n.º 1
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def read(fn, **kwargs):
    """
    Convenience function: Detect file extension and read via Atomistica or ASE.
    If reading a NetCDF files, frame numbers can be appended via '@'.
    e.g., a = read('traj.nc@5')
    """
    ext = fn[fn.rfind('.'):].split('@')
    if len(ext) == 1:
        if ext[0] == '.out' or ext[0] == '.dat':
            dirname = os.path.dirname(fn)
            if len(dirname) == 0:
                dirname = '.'
            cycfn = dirname + '/cyc.dat'
            if os.path.exists(cycfn):
                return read_atoms(fn, cycfn=cycfn)
            return read_atoms(fn)
        elif ext[0] == '.nc':
            traj = NetCDFTrajectory(fn, **kwargs)
            return traj[-1]
        else:
            return ase.io.read(fn, **kwargs)
    elif len(ext) == 2:
        if ext[0] == '.nc':
            frame = int(ext[1])
            fn = fn[:fn.rfind('@')]
            traj = NetCDFTrajectory(fn)
            return traj[frame]
        else:
            return ase.io.read(fn, **kwargs)
    else:
        return ase.io.read(fn, **kwargs)
Ejemplo n.º 2
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def test_netcdf_with_nonconsecutive_index(netCDF4):
    nc = netCDF4.Dataset('7.nc', 'w')
    nc.createDimension('frame', None)
    nc.createDimension('atom', 3)
    nc.createDimension('spatial', 3)
    nc.createDimension('cell_spatial', 3)
    nc.createDimension('cell_angular', 3)

    nc.createVariable('atom_types', 'i', ('atom', ))
    nc.createVariable('coordinates', 'f4', (
        'frame',
        'atom',
        'spatial',
    ))
    nc.createVariable('cell_lengths', 'f4', (
        'frame',
        'cell_spatial',
    ))
    nc.createVariable('cell_angles', 'f4', (
        'frame',
        'cell_angular',
    ))
    nc.createVariable('id', 'i', (
        'frame',
        'atom',
    ))

    r0 = np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9]], dtype=float)
    r1 = 2 * r0

    nc.variables['atom_types'][:] = [1, 2, 3]
    nc.variables['coordinates'][0] = r0
    nc.variables['coordinates'][1] = r1
    nc.variables['cell_lengths'][:] = 0
    nc.variables['cell_angles'][:] = 90
    nc.variables['id'][0] = [13, 3, 5]
    nc.variables['id'][1] = [-1, 0, -5]

    nc.close()

    traj = NetCDFTrajectory('7.nc', 'r')
    assert (traj[0].numbers == [2, 3, 1]).all()
    assert (traj[1].numbers == [3, 1, 2]).all()
    traj.close()
Ejemplo n.º 3
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def test_netcdf_with_variable_atomic_numbers(netCDF4):
    # Create a NetCDF file with a per-file definition of atomic numbers. ASE
    # NetCDFTrajectory can read but not write these types of files.
    nc = netCDF4.Dataset('6.nc', 'w')
    nc.createDimension('frame', None)
    nc.createDimension('atom', 2)
    nc.createDimension('spatial', 3)
    nc.createDimension('cell_spatial', 3)
    nc.createDimension('cell_angular', 3)

    nc.createVariable('atom_types', 'i', ('atom', ))
    nc.createVariable('coordinates', 'f4', (
        'frame',
        'atom',
        'spatial',
    ))
    nc.createVariable('cell_lengths', 'f4', (
        'frame',
        'cell_spatial',
    ))
    nc.createVariable('cell_angles', 'f4', (
        'frame',
        'cell_angular',
    ))

    r0 = np.array([[1, 2, 3], [4, 5, 6]], dtype=float)
    r1 = 2 * r0

    nc.variables['atom_types'][:] = [1, 2]
    nc.variables['coordinates'][0] = r0
    nc.variables['coordinates'][1] = r1
    nc.variables['cell_lengths'][:] = 0
    nc.variables['cell_angles'][:] = 90

    nc.close()

    traj = NetCDFTrajectory('6.nc', 'r')
    assert np.allclose(traj[0].positions, r0)
    assert np.allclose(traj[1].positions, r1)
    traj.close()
Ejemplo n.º 4
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def write(fn, a, **kwargs):
    """
    Convenience function: Detect file extension and write via Atomistica or ASE.
    Has support for writing LAMMPS data files.
    """
    ext = fn[fn.rfind('.'):].split('@')
    if ext[0] == '.out' or ext[0] == '.dat':
        return write_atoms(fn, a)
    elif ext[0] == '.lammps':
        return write_lammps_data(fn, a, velocities=True, **kwargs)
    elif ext[0] == '.nc':
        return NetCDFTrajectory(fn, 'w').write(a)
    else:
        return ase.io.write(fn, a, **kwargs)
Ejemplo n.º 5
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import os
import warnings

import numpy as np

from ase import Atom, Atoms
from ase.io import read
from ase.io import NetCDFTrajectory

co = Atoms([Atom('C', (0, 0, 0)),
            Atom('O', (0, 0, 1.2))],
            cell=[3, 3, 3],
            pbc=True)
traj = NetCDFTrajectory('1.nc', 'w', co)
for i in range(5):
    co.positions[:, 2] += 0.1
    traj.write()
del traj
traj = NetCDFTrajectory('1.nc', 'a')
co = traj[-1]
print(co.positions)
co.positions[:] += 1
traj.write(co)
del traj
t = NetCDFTrajectory('1.nc', 'a')

print(t[-1].positions)
print('.--------')
for i, a in enumerate(t):
    if i < 4:
        print(1, a.positions[-1, 2], 1.3 + i * 0.1)
Ejemplo n.º 6
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from ase.test import NotAvailable

import numpy as np
import ase.io.netcdftrajectory as netcdftrajectory

if not netcdftrajectory.have_nc:
    raise NotAvailable('No NetCDF module available (netCDF4-python, '
                       'scipy.io.netcdf)')

import os
from ase import Atom, Atoms
from ase.io import NetCDFTrajectory

co = Atoms([Atom('C', (0, 0, 0)),
            Atom('O', (0, 0, 1.2))], pbc=True)
traj = NetCDFTrajectory('1.nc', 'w', co)
for i in range(5):
    co.positions[:, 2] += 0.1
    traj.write()
del traj
if netcdftrajectory.have_nc == netcdftrajectory.NC_IS_NETCDF4:
    traj = NetCDFTrajectory('1.nc', 'a')
    co = traj[-1]
    print(co.positions)
    co.positions[:] += 1
    traj.write(co)
    del traj
    t = NetCDFTrajectory('1.nc', 'a')
else:
    t = NetCDFTrajectory('1.nc', 'r')
Ejemplo n.º 7
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from ase.test import NotAvailable

import ase.io.netcdftrajectory as netcdftrajectory

if not netcdftrajectory.have_nc:
    raise NotAvailable('No NetCDF module available (netCDF4-python, '
                       'scipy.io.netcdf)')

import os
from ase import Atom, Atoms
from ase.io import NetCDFTrajectory

co = Atoms([Atom('C', (0, 0, 0)), Atom('O', (0, 0, 1.2))], pbc=True)
traj = NetCDFTrajectory('1.nc', 'w', co)
for i in range(5):
    co.positions[:, 2] += 0.1
    traj.write()
del traj
if netcdftrajectory.have_nc == netcdftrajectory.NC_IS_NETCDF4:
    traj = NetCDFTrajectory('1.nc', 'a')
    co = traj[-1]
    print(co.positions)
    co.positions[:] += 1
    traj.write(co)
    del traj
    t = NetCDFTrajectory('1.nc', 'a')
else:
    t = NetCDFTrajectory('1.nc', 'r')

print(t[-1].positions)
print('.--------')
Ejemplo n.º 8
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import numpy as np
from scipy.sparse import csr_matrix
from ase.io import NetCDFTrajectory
from ase.io import read
import matscipy.calculators.pair_potential as calculator


# Load atomic configuration
MinStructure = NetCDFTrajectory(
    "structure/PBC.KA.N256.Min.nc", "r", keep_open=True)

# Paramters for a binary Kob-Anderson glass.
# Kob, Walter, and Hans C. Andersen. Phys. Rev. E 51.5 (1995): 4626.
# The interaction is modeled via a quadratic shifted Lennard-Jones potential.
parameters = {(1, 1): calculator.LennardJonesQuadratic(1, 1, 3), (1, 2): calculator.LennardJonesQuadratic(
    1.5, 0.8, 2.4), (2, 2): calculator.LennardJonesQuadratic(0.5, 0.88, 2.64)}
a = calculator.PairPotential(parameters)

# Exemplary code for the calculation of the full hessian matrix.
# Sparse
H_sparse = a.calculate_hessian_matrix(
    MinStructure[len(MinStructure)-1], "sparse")

# Dense
H_dense = a.calculate_hessian_matrix(
    MinStructure[len(MinStructure)-1], "dense")

# Compute the only rows of the Hessian matrix which correspong to atom Ids = 5,6
H_sparse1 = a.calculate_hessian_matrix(
    MinStructure[len(MinStructure)-1], "sparse", limits=(5, 7))
Ejemplo n.º 9
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def test_netcdftrajectory(co):
    rng = np.random.RandomState(17)
    traj = NetCDFTrajectory('1.nc', 'w', co)
    for i in range(5):
        co.positions[:, 2] += 0.1
        traj.write()
    del traj
    traj = NetCDFTrajectory('1.nc', 'a')
    co = traj[-1]
    print(co.positions)
    co.positions[:] += 1
    traj.write(co)
    del traj
    t = NetCDFTrajectory('1.nc', 'a')

    print(t[-1].positions)
    print('.--------')
    for i, a in enumerate(t):
        if i < 4:
            print(1, a.positions[-1, 2], 1.3 + i * 0.1)
            assert abs(a.positions[-1, 2] - 1.3 - i * 0.1) < 1e-6
        else:
            print(1, a.positions[-1, 2], 1.7 + i - 4)
            assert abs(a.positions[-1, 2] - 1.7 - i + 4) < 1e-6
        assert a.pbc.all()
    co.positions[:] += 1
    t.write(co)
    for i, a in enumerate(t):
        if i < 4:
            print(2, a.positions[-1, 2], 1.3 + i * 0.1)
            assert abs(a.positions[-1, 2] - 1.3 - i * 0.1) < 1e-6
        else:
            print(2, a.positions[-1, 2], 1.7 + i - 4)
            assert abs(a.positions[-1, 2] - 1.7 - i + 4) < 1e-6
    assert len(t) == 7

    # Change atom type and append
    co[0].number = 1
    t.write(co)
    t2 = NetCDFTrajectory('1.nc', 'r')
    co2 = t2[-1]
    assert (co2.numbers == co.numbers).all()
    del t2

    co[0].number = 6
    t.write(co)

    co.pbc = False
    o = co.pop(1)
    try:
        t.write(co)
    except ValueError:
        pass
    else:
        assert False

    co.append(o)
    co.pbc = True
    t.write(co)
    del t

    # append to a nonexisting file
    fname = '2.nc'
    t = NetCDFTrajectory(fname, 'a', co)
    del t

    fname = '3.nc'
    t = NetCDFTrajectory(fname, 'w', co)
    # File is not created before first write
    co.set_pbc([True, False, False])
    d = co.get_distance(0, 1)
    with pytest.warns(None):
        t.write(co)
    del t
    # Check pbc
    for c in [1, 1000]:
        t = NetCDFTrajectory(fname, chunk_size=c)
        a = t[-1]
        assert a.pbc[0] and not a.pbc[1] and not a.pbc[2]
        assert abs(a.get_distance(0, 1) - d) < 1e-6
        del t
    # Append something in Voigt notation
    t = NetCDFTrajectory(fname, 'a')
    for frame, a in enumerate(t):
        test = rng.random([len(a), 6])
        a.set_array('test', test)
        t.write_arrays(a, frame, ['test'])
    del t

    # Check cell origin
    co.set_pbc(True)
    co.set_celldisp([1, 2, 3])
    traj = NetCDFTrajectory('4.nc', 'w', co)
    traj.write(co)
    traj.close()

    traj = NetCDFTrajectory('4.nc', 'r')
    a = traj[0]
    assert np.all(abs(a.get_celldisp() - np.array([1, 2, 3])) < 1e-12)
    traj.close()

    # Add 'id' field and check if it is read correctly
    co.set_array('id', np.array([2, 1]))
    traj = NetCDFTrajectory('5.nc', 'w', co)
    traj.write(co, arrays=['id'])
    traj.close()

    traj = NetCDFTrajectory('5.nc', 'r')
    assert np.all(traj[0].numbers == [8, 6])
    assert np.all(
        np.abs(traj[0].positions -
               np.array([[2, 2, 3.7], [2., 2., 2.5]])) < 1e-6)
    traj.close()

    a = read('5.nc')
    assert (len(a) == 2)
Ejemplo n.º 10
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def test_types_to_numbers_argument(co):
    traj = NetCDFTrajectory('8.nc', 'w', co)
    traj.write()
    traj.close()
    d = {6: 15, 8: 15}
    traj = NetCDFTrajectory('8.nc', mode="r", types_to_numbers=d)
    assert np.allclose(traj[-1].get_masses(), 30.974)
    assert (traj[-1].numbers == [15, 15]).all()
    d = {3: 14}
    traj = NetCDFTrajectory('8.nc', mode="r", types_to_numbers=d)
    assert (traj[-1].numbers == [6, 8]).all()
    traj = NetCDFTrajectory('8.nc',
                            'r',
                            types_to_numbers=[0, 0, 0, 0, 0, 0, 15])
    assert (traj[-1].numbers == [15, 8]).all()

    traj.close()
Ejemplo n.º 11
0
#! /usr/bin/env python

from __future__ import print_function

import sys

import numpy as np

from ase.data import chemical_symbols
from ase.io import NetCDFTrajectory
from matscipy.neighbours import mic

###

traj = NetCDFTrajectory(sys.argv[1])

ref_frame = traj[0]

individual_elements = set(ref_frame.numbers)
s = '#{:>9s}'.format('frame')
if 'time' in ref_frame.info:
    s = '{} {:>10s}'.format(s, 'time')
s = '{} {:>10s}'.format(s, 'tot. rms')
for element in individual_elements:
    s = '{} {:>10s}'.format(s, 'rms ({})'.format(chemical_symbols[element]))
print(s)

last_frame = traj[0]
displacements = np.zeros_like(ref_frame.positions)
for i, frame in enumerate(traj[1:]):
    last_frame.set_cell(frame.cell, scale_atoms=True)
Ejemplo n.º 12
0
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>.
# ======================================================================

"""
Run Voronoi analysis of a trajectory, and store the results into that
trajectory.
"""

import os
import sys

from ase.io import NetCDFTrajectory

from atomistica.analysis import voropp

###

traj = NetCDFTrajectory(sys.argv[1], 'a')

for i, a in enumerate(traj):
    sys.stdout.write('=== {0}/{1} ===\r'.format(i+1, len(traj)))

    vol, area = voropp(a, q='%v %F', fast=True)

    a.set_array('voronoi_volume', vol)
    a.set_array('voronoi_surface_area', area)

    traj.write_arrays(a, i, ['voronoi_volume', 'voronoi_surface_area'])
traj.close()
Ejemplo n.º 13
0
#
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>.
# ======================================================================
"""
Run Voronoi analysis of a trajectory, and store the results into that
trajectory.
"""

import os
import sys

from ase.io import NetCDFTrajectory

from atomistica.analysis import voropp

###

traj = NetCDFTrajectory(sys.argv[1], 'a')

for i, a in enumerate(traj):
    sys.stdout.write('=== {0}/{1} ===\r'.format(i + 1, len(traj)))

    vol, area = voropp(a, q='%v %F', fast=True)

    a.set_array('voronoi_volume', vol)
    a.set_array('voronoi_surface_area', area)

    traj.write_arrays(a, i, ['voronoi_volume', 'voronoi_surface_area'])
traj.close()
Ejemplo n.º 14
0
from ase.test import NotAvailable

import ase.io.netcdftrajectory as netcdftrajectory

if not netcdftrajectory.have_nc:
    raise NotAvailable('No NetCDF module available (netCDF4-python, '
                       'scipy.io.netcdf)')

import os
from ase import Atom, Atoms
from ase.io import NetCDFTrajectory

co = Atoms([Atom('C', (0, 0, 0)),
            Atom('O', (0, 0, 1.2))], pbc=True)
traj = NetCDFTrajectory('1.nc', 'w', co)
for i in range(5):
    co.positions[:, 2] += 0.1
    traj.write()
del traj
if netcdftrajectory.have_nc == netcdftrajectory.NC_IS_NETCDF4:
    traj = NetCDFTrajectory('1.nc', 'a')
    co = traj[-1]
    print(co.positions)
    co.positions[:] += 1
    traj.write(co)
    del traj
    t = NetCDFTrajectory('1.nc', 'a')
else:
    t = NetCDFTrajectory('1.nc', 'r')

print(t[-1].positions)
def test_netcdftrajectory():
    import os
    import warnings

    import numpy as np

    from pytest import importorskip
    importorskip('netCDF4')

    from ase import Atom, Atoms
    from ase.io import read
    from ase.io import NetCDFTrajectory

    co = Atoms([Atom('C',
                     (0, 0, 0)), Atom('O', (0, 0, 1.2))],
               cell=[3, 3, 3],
               pbc=True)
    traj = NetCDFTrajectory('1.nc', 'w', co)
    for i in range(5):
        co.positions[:, 2] += 0.1
        traj.write()
    del traj
    traj = NetCDFTrajectory('1.nc', 'a')
    co = traj[-1]
    print(co.positions)
    co.positions[:] += 1
    traj.write(co)
    del traj
    t = NetCDFTrajectory('1.nc', 'a')

    print(t[-1].positions)
    print('.--------')
    for i, a in enumerate(t):
        if i < 4:
            print(1, a.positions[-1, 2], 1.3 + i * 0.1)
            assert abs(a.positions[-1, 2] - 1.3 - i * 0.1) < 1e-6
            assert a.pbc.all()
        else:
            print(1, a.positions[-1, 2], 1.7 + i - 4)
            assert abs(a.positions[-1, 2] - 1.7 - i + 4) < 1e-6
            assert a.pbc.all()
    co.positions[:] += 1
    t.write(co)
    for i, a in enumerate(t):
        if i < 4:
            print(2, a.positions[-1, 2], 1.3 + i * 0.1)
            assert abs(a.positions[-1, 2] - 1.3 - i * 0.1) < 1e-6
        else:
            print(2, a.positions[-1, 2], 1.7 + i - 4)
            assert abs(a.positions[-1, 2] - 1.7 - i + 4) < 1e-6
    assert len(t) == 7

    # Change atom type and append
    co[0].number = 1
    t.write(co)
    t2 = NetCDFTrajectory('1.nc', 'r')
    co2 = t2[-1]
    assert (co2.numbers == co.numbers).all()
    del t2

    os.remove('1.nc')

    co[0].number = 6
    co.pbc = True
    t.write(co)

    co.pbc = False
    o = co.pop(1)
    try:
        t.write(co)
    except ValueError:
        pass
    else:
        assert False

    co.append(o)
    co.pbc = True
    t.write(co)
    del t

    # append to a nonexisting file
    fname = '2.nc'
    if os.path.isfile(fname):
        os.remove(fname)
    t = NetCDFTrajectory(fname, 'a', co)
    del t

    fname = '3.nc'
    t = NetCDFTrajectory(fname, 'w', co)
    # File is not created before first write
    co.set_pbc([True, False, False])
    d = co.get_distance(0, 1)
    with warnings.catch_warnings():
        warnings.simplefilter('ignore', UserWarning)
        t.write(co)
    del t
    # Check pbc
    for c in [1, 1000]:
        t = NetCDFTrajectory(fname, chunk_size=c)
        a = t[-1]
        assert a.pbc[0] and not a.pbc[1] and not a.pbc[2]
        assert abs(a.get_distance(0, 1) - d) < 1e-6
        del t
    # Append something in Voigt notation
    t = NetCDFTrajectory(fname, 'a')
    for frame, a in enumerate(t):
        test = np.random.random([len(a), 6])
        a.set_array('test', test)
        t.write_arrays(a, frame, ['test'])
    del t
    os.remove(fname)

    # Check cell origin
    co.set_pbc(True)
    co.set_celldisp([1, 2, 3])
    traj = NetCDFTrajectory('4.nc', 'w', co)
    traj.write(co)
    traj.close()

    traj = NetCDFTrajectory('4.nc', 'r')
    a = traj[0]
    assert np.all(abs(a.get_celldisp() - np.array([1, 2, 3])) < 1e-12)
    traj.close()

    os.remove('4.nc')

    # Add 'id' field and check if it is read correctly
    co.set_array('id', np.array([2, 1]))
    traj = NetCDFTrajectory('5.nc', 'w', co)
    traj.write(co, arrays=['id'])
    traj.close()

    traj = NetCDFTrajectory('5.nc', 'r')  #
    assert np.all(traj[0].numbers == [8, 6])
    assert np.all(
        np.abs(traj[0].positions -
               np.array([[2, 2, 3.7], [2., 2., 2.5]])) < 1e-6)
    traj.close()

    a = read('5.nc')
    assert (len(a) == 2)

    os.remove('5.nc')

    # Create a NetCDF file with a per-file definition of atomic numbers. ASE
    # NetCDFTrajectory can read but not write these types of files.
    import netCDF4
    nc = netCDF4.Dataset('6.nc', 'w')
    nc.createDimension('frame', None)
    nc.createDimension('atom', 2)
    nc.createDimension('spatial', 3)
    nc.createDimension('cell_spatial', 3)
    nc.createDimension('cell_angular', 3)

    nc.createVariable('atom_types', 'i', ('atom', ))
    nc.createVariable('coordinates', 'f4', (
        'frame',
        'atom',
        'spatial',
    ))
    nc.createVariable('cell_lengths', 'f4', (
        'frame',
        'cell_spatial',
    ))
    nc.createVariable('cell_angles', 'f4', (
        'frame',
        'cell_angular',
    ))

    r0 = np.array([[1, 2, 3], [4, 5, 6]], dtype=np.float)
    r1 = 2 * r0

    nc.variables['atom_types'][:] = [1, 2]
    nc.variables['coordinates'][0] = r0
    nc.variables['coordinates'][1] = r1
    nc.variables['cell_lengths'][:] = 0
    nc.variables['cell_angles'][:] = 90

    nc.close()

    traj = NetCDFTrajectory('6.nc', 'r')
    assert np.allclose(traj[0].positions, r0)
    assert np.allclose(traj[1].positions, r1)
    traj.close()

    os.remove('6.nc')

    # Create a NetCDF file with a non-consecutive index.
    import netCDF4
    nc = netCDF4.Dataset('7.nc', 'w')
    nc.createDimension('frame', None)
    nc.createDimension('atom', 3)
    nc.createDimension('spatial', 3)
    nc.createDimension('cell_spatial', 3)
    nc.createDimension('cell_angular', 3)

    nc.createVariable('atom_types', 'i', ('atom', ))
    nc.createVariable('coordinates', 'f4', (
        'frame',
        'atom',
        'spatial',
    ))
    nc.createVariable('cell_lengths', 'f4', (
        'frame',
        'cell_spatial',
    ))
    nc.createVariable('cell_angles', 'f4', (
        'frame',
        'cell_angular',
    ))
    nc.createVariable('id', 'i', (
        'frame',
        'atom',
    ))

    r0 = np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9]], dtype=np.float)
    r1 = 2 * r0

    nc.variables['atom_types'][:] = [1, 2, 3]
    nc.variables['coordinates'][0] = r0
    nc.variables['coordinates'][1] = r1
    nc.variables['cell_lengths'][:] = 0
    nc.variables['cell_angles'][:] = 90
    nc.variables['id'][0] = [13, 3, 5]
    nc.variables['id'][1] = [-1, 0, -5]

    nc.close()

    traj = NetCDFTrajectory('7.nc', 'r')
    assert (traj[0].numbers == [2, 3, 1]).all()
    assert (traj[1].numbers == [3, 1, 2]).all()
    traj.close()

    os.remove('7.nc')
Ejemplo n.º 16
0
import numpy as np
import ase.io.netcdftrajectory as netcdftrajectory

if not netcdftrajectory.have_nc:
    raise NotAvailable('No NetCDF module available (netCDF4-python, '
                       'scipy.io.netcdf)')

import os
from ase import Atom, Atoms
from ase.io import NetCDFTrajectory

co = Atoms([Atom('C', (0, 0, 0)), Atom('O', (0, 0, 1.2))],
           cell=[3, 3, 3],
           pbc=True)
traj = NetCDFTrajectory('1.nc', 'w', co)
for i in range(5):
    co.positions[:, 2] += 0.1
    traj.write()
del traj
if netcdftrajectory.have_nc == netcdftrajectory.NC_IS_NETCDF4:
    traj = NetCDFTrajectory('1.nc', 'a')
    co = traj[-1]
    print(co.positions)
    co.positions[:] += 1
    traj.write(co)
    del traj
    t = NetCDFTrajectory('1.nc', 'a')
else:
    t = NetCDFTrajectory('1.nc', 'r')