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()
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()
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()
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')#
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)
# 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()
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')
