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)
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()
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)
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)
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')
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('.--------')
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))
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)
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()
#! /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)
# 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()
#
# 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()
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')
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')