def test1():
print('generating graphene structure')
graphene = GrapheneGenerator(armchair_edge_length=5,
zigzag_edge_length=5)
lattice = graphene.lattice
print('graphene.bounds:\n{}'.format(graphene.bounds))
print('graphene.centroid:\n{}'.format(graphene.centroid))
print('graphene.lattice:\n{}'.format(lattice))
print('graphene.lattice.a1:\n{}'.format(lattice.a1))
print('graphene.lattice.a2:\n{}'.format(lattice.a2))
print('graphene.lattice.a3:\n{}'.format(lattice.a3))
print('graphene.lattice.orientation_matrix:\n{}'.format(
lattice.orientation_matrix))
print('rotating graphene')
graphene.rotate(angle=-np.pi/2, axis='x')
print('graphene.bounds:\n{}'.format(graphene.bounds))
print('graphene.centroid:\n{}'.format(graphene.centroid))
print('graphene.lattice:\n{}'.format(lattice))
print('graphene.lattice.a1:\n{}'.format(lattice.a1))
print('graphene.lattice.a2:\n{}'.format(lattice.a2))
print('graphene.lattice.a3:\n{}'.format(lattice.a3))
print('graphene.lattice.orientation_matrix:\n{}'.format(
lattice.orientation_matrix))
assert_true(np.allclose(lattice.angles, 3 * [90.0]))
lattice_region = Cuboid(pmax=lattice.lengths)
# lattice_region = Parallelepiped(u=lattice.a * xhat,
# v=lattice.b * yhat,
# w=lattice.c * zhat)
assert_equal(lattice_region.a, lattice.a)
assert_equal(lattice_region.b, lattice.b)
assert_equal(lattice_region.c, lattice.c)
print('lattice_region:\n{}'.format(lattice_region))
print('lattice_region.centroid:\n{}'.format(lattice_region.centroid))
print('\nrotating lattice_region')
lattice_region.rotate(transform_matrix=lattice.orientation_matrix)
# assert_equal(lattice_region.a, lattice.a)
# assert_equal(lattice_region.b, lattice.b)
# assert_equal(lattice_region.c, lattice.c)
print('lattice_region:\n{}'.format(lattice_region))
print('lattice_region.centroid:\n{}'.format(lattice_region.centroid))
print('\ncentering lattice_region on graphene centroid')
tvec = Vector(Point(graphene.centroid) - lattice_region.centroid)
lattice_region.translate(tvec)
# assert_equal(lattice_region.a, lattice.a)
# assert_equal(lattice_region.b, lattice.b)
# assert_equal(lattice_region.c, lattice.c)
print('lattice_region:\n{}'.format(lattice_region))
print('lattice_region.centroid:\n{}'.format(lattice_region.centroid))
bounding_box = generate_bounding_box(from_lattice=lattice,
center=graphene.centroid,
verbose=True)
print('bounding_box:\n{}'.format(bounding_box))
assert_equal(bounding_box, lattice_region)
print('lattice_region.lengths: {}, {}, {}'.format(
lattice_region.a, lattice_region.b, lattice_region.c))
def test1():
print('generating graphene structure')
graphene = GrapheneGenerator(armchair_edge_length=5, zigzag_edge_length=5)
lattice = graphene.lattice
print('graphene.bounds:\n{}'.format(graphene.bounds))
print('graphene.centroid:\n{}'.format(graphene.centroid))
print('graphene.lattice:\n{}'.format(lattice))
print('graphene.lattice.a1:\n{}'.format(lattice.a1))
print('graphene.lattice.a2:\n{}'.format(lattice.a2))
print('graphene.lattice.a3:\n{}'.format(lattice.a3))
print('graphene.lattice.orientation_matrix:\n{}'.format(
lattice.orientation_matrix))
print('rotating graphene')
graphene.rotate(angle=-np.pi / 2, axis='x')
print('graphene.bounds:\n{}'.format(graphene.bounds))
print('graphene.centroid:\n{}'.format(graphene.centroid))
print('graphene.lattice:\n{}'.format(lattice))
print('graphene.lattice.a1:\n{}'.format(lattice.a1))
print('graphene.lattice.a2:\n{}'.format(lattice.a2))
print('graphene.lattice.a3:\n{}'.format(lattice.a3))
print('graphene.lattice.orientation_matrix:\n{}'.format(
lattice.orientation_matrix))
assert_true(np.allclose(lattice.angles, 3 * [90.0]))
lattice_region = Cuboid(pmax=lattice.lengths)
# lattice_region = Parallelepiped(u=lattice.a * xhat,
# v=lattice.b * yhat,
# w=lattice.c * zhat)
assert_equal(lattice_region.a, lattice.a)
assert_equal(lattice_region.b, lattice.b)
assert_equal(lattice_region.c, lattice.c)
print('lattice_region:\n{}'.format(lattice_region))
print('lattice_region.centroid:\n{}'.format(lattice_region.centroid))
print('\nrotating lattice_region')
lattice_region.rotate(transform_matrix=lattice.orientation_matrix)
# assert_equal(lattice_region.a, lattice.a)
# assert_equal(lattice_region.b, lattice.b)
# assert_equal(lattice_region.c, lattice.c)
print('lattice_region:\n{}'.format(lattice_region))
print('lattice_region.centroid:\n{}'.format(lattice_region.centroid))
print('\ncentering lattice_region on graphene centroid')
tvec = Vector(Point(graphene.centroid) - lattice_region.centroid)
lattice_region.translate(tvec)
# assert_equal(lattice_region.a, lattice.a)
# assert_equal(lattice_region.b, lattice.b)
# assert_equal(lattice_region.c, lattice.c)
print('lattice_region:\n{}'.format(lattice_region))
print('lattice_region.centroid:\n{}'.format(lattice_region.centroid))
bounding_box = generate_bounding_box(from_lattice=lattice,
center=graphene.centroid,
verbose=True)
print('bounding_box:\n{}'.format(bounding_box))
assert_equal(bounding_box, lattice_region)
print('lattice_region.lengths: {}, {}, {}'.format(lattice_region.a,
lattice_region.b,
lattice_region.c))
def write(cls, fname=None, outpath=None, fpath=None, structure=None,
atoms=None, atom_style='full', bounding_box=None,
comment_line=None, assert_unique_ids=False,
enforce_consecutive_ids=True, pad_box=False,
xpad=10., ypad=10., zpad=10., pad_tol=0.01,
verbose=False, **kwargs):
"""Write structure data to file.
Parameters
----------
fname : str, optional
Output file name.
outpath : str, optional
Output file path.
fpath : str, optional
Full path (directory path + file name) to output data file.
atoms : :class:`~sknano.core.atoms.Atoms`
An :class:`~sknano.core.atoms.Atoms` instance.
bounding_box : dict, optional
If `None`, determined automatically from the `atoms` coordinates.
comment_line : str, optional
A string written to the first line of `data` file. If `None`,
then it is set to the full path of the output `data` file.
assert_unique_ids : bool, optional
Check that each :class:`~sknano.core.atoms.Atom` in `atoms`
has a unique :attr:`~sknano.core.atoms.Atom.id`.
If the check fails, then assign a unique
:attr:`~sknano.core.atoms.Atom.id`.
to each :class:`~sknano.core.atoms.Atom`.
If `assert_unique_ids` is True, but the id's are not unique,
LAMMPS will not be able to read the data file.
enforce_consecutive_ids : bool, optional
pad_box : bool, optional
xpad, ypad, zpad : float, optional
pad_tol : float, optional
verbose : bool, optional
verbose output
"""
if structure is None and atoms is None:
raise ValueError('Expected either `structure` or `atoms` object.')
if structure is not None and atoms is None:
atoms = structure.atoms
if fpath is None:
fpath = get_fpath(fname=fname, ext='data', outpath=outpath,
overwrite=True, add_fnum=False)
if comment_line is None:
comment_line = default_comment_line
atoms.rezero()
atoms.assign_unique_types()
typemap = atoms.typemap
Natoms = atoms.Natoms
Natoms_width = \
8 if len(str(Natoms)) <= 12 else len(str(Natoms)) + 4
Ntypes = atoms.Ntypes
Ntypes_width = Natoms_width
id_width = len(str(Natoms)) + 1
type_width = len(str(Ntypes)) + 1
if (enforce_consecutive_ids and
atoms.ids.max() != atoms.Natoms) or \
(not assert_unique_ids and
len(set(atoms.ids)) != atoms.Natoms):
atoms.assign_unique_ids()
if bounding_box is None:
if structure is not None and structure.lattice is not None:
bounding_box = \
generate_bounding_box(from_lattice=structure.lattice,
center=atoms.centroid)
else:
bounding_box = \
generate_bounding_box(from_array=atoms.coords)
if pad_box:
boxpad = {'x': xpad, 'y': ypad, 'z': zpad}
# for dim, pad in boxpad.items():
for i, dim in enumerate(('x', 'y', 'z')):
pad = boxpad[dim]
dmin = dim + 'min'
dmax = dim + 'max'
if abs(getattr(bounding_box, dmin) -
atoms.coords[:, i].min()) < pad - pad_tol:
setattr(bounding_box, dmin,
getattr(bounding_box, dmin) - pad)
if abs(getattr(bounding_box, dmax) -
atoms.coords[:, i].max()) < pad - pad_tol:
setattr(bounding_box, dmax,
getattr(bounding_box, dmax) + pad)
if verbose:
print('bounding_box: {}'.format(bounding_box))
lohi_width = 0
for dim in ('x', 'y', 'z'):
lohi_width = \
max(lohi_width, len('{:.6f} {:.6f}'.format(
getattr(bounding_box, dim + 'min'),
getattr(bounding_box, dim + 'max'))) + 4)
with zopen(fpath, 'wt') as f:
f.write('# {}\n\n'.format(comment_line.lstrip('#').strip()))
f.write('{}atoms\n'.format(
'{:d}'.format(Natoms).ljust(Natoms_width)))
f.write('{}atom types\n\n'.format(
'{:d}'.format(Ntypes).ljust(Ntypes_width)))
for dim in ('x', 'y', 'z'):
f.write('{}{dim}lo {dim}hi\n'.format(
'{:.6f} {:.6f}'.format(
getattr(bounding_box, dim + 'min'),
getattr(bounding_box, dim + 'max')).ljust(lohi_width),
dim=dim))
f.write('\nMasses\n\n')
for atomtype, properties in list(typemap.items()):
f.write('{}{:.4f}\n'.format(
'{:d}'.format(atomtype).ljust(Natoms_width),
properties['mass']))
f.write('\nAtoms\n\n')
for atom in atoms:
line = ''
line += "{:>{}}".format(atom.id, id_width)
line += "{:>{}}".format(atom.mol, 3)
line += "{:>{}}".format(atom.type, type_width)
line += "{:>{}}".format('{:.1f}'.format(atom.q), 4)
line += "{:>{}}".format('{:f}'.format(atom.x), 14)
line += "{:>{}}".format('{:f}'.format(atom.y), 14)
line += "{:>{}}".format('{:f}'.format(atom.z), 14)
line += "{:>{}}".format('{:d}'.format(atom.ix), 3)
line += "{:>{}}".format('{:d}'.format(atom.iy), 3)
line += "{:>{}}".format('{:d}'.format(atom.iz), 3)
line += '\n'
f.write(line)
f.write('\nVelocities\n\n')
for atom in atoms:
line = ''
line += "{:>{}}".format(atom.id, id_width)
line += "{:>{}}".format('{:f}'.format(atom.vx), 14)
line += "{:>{}}".format('{:f}'.format(atom.vy), 14)
line += "{:>{}}".format('{:f}'.format(atom.vz), 14)
line += '\n'
f.write(line)
def write(cls,
fname=None,
outpath=None,
fpath=None,
structure=None,
atoms=None,
atom_style='full',
bounding_box=None,
comment_line=None,
assert_unique_ids=False,
enforce_consecutive_ids=True,
pad_box=False,
xpad=10.,
ypad=10.,
zpad=10.,
pad_tol=0.01,
verbose=False,
**kwargs):
"""Write structure data to file.
Parameters
----------
fname : str, optional
Output file name.
outpath : str, optional
Output file path.
fpath : str, optional
Full path (directory path + file name) to output data file.
atoms : :class:`~sknano.core.atoms.Atoms`
An :class:`~sknano.core.atoms.Atoms` instance.
bounding_box : dict, optional
If `None`, determined automatically from the `atoms` coordinates.
comment_line : str, optional
A string written to the first line of `data` file. If `None`,
then it is set to the full path of the output `data` file.
assert_unique_ids : bool, optional
Check that each :class:`~sknano.core.atoms.Atom` in `atoms`
has a unique :attr:`~sknano.core.atoms.Atom.id`.
If the check fails, then assign a unique
:attr:`~sknano.core.atoms.Atom.id`.
to each :class:`~sknano.core.atoms.Atom`.
If `assert_unique_ids` is True, but the id's are not unique,
LAMMPS will not be able to read the data file.
enforce_consecutive_ids : bool, optional
pad_box : bool, optional
xpad, ypad, zpad : float, optional
pad_tol : float, optional
verbose : bool, optional
verbose output
"""
if structure is None and atoms is None:
raise ValueError('Expected either `structure` or `atoms` object.')
if structure is not None and atoms is None:
atoms = structure.atoms
if fpath is None:
fpath = get_fpath(fname=fname,
ext='data',
outpath=outpath,
overwrite=True,
add_fnum=False)
if comment_line is None:
comment_line = default_comment_line
atoms.rezero()
atoms.assign_unique_types()
typemap = atoms.typemap
Natoms = atoms.Natoms
Natoms_width = \
8 if len(str(Natoms)) <= 12 else len(str(Natoms)) + 4
Ntypes = atoms.Ntypes
Ntypes_width = Natoms_width
id_width = len(str(Natoms)) + 1
type_width = len(str(Ntypes)) + 1
if (enforce_consecutive_ids and
atoms.ids.max() != atoms.Natoms) or \
(not assert_unique_ids and
len(set(atoms.ids)) != atoms.Natoms):
atoms.assign_unique_ids()
if bounding_box is None:
if structure is not None and structure.lattice is not None:
bounding_box = \
generate_bounding_box(from_lattice=structure.lattice,
center=atoms.centroid)
else:
bounding_box = \
generate_bounding_box(from_array=atoms.coords)
if pad_box:
boxpad = {'x': xpad, 'y': ypad, 'z': zpad}
# for dim, pad in boxpad.items():
for i, dim in enumerate(('x', 'y', 'z')):
pad = boxpad[dim]
dmin = dim + 'min'
dmax = dim + 'max'
if abs(getattr(bounding_box, dmin) -
atoms.coords[:, i].min()) < pad - pad_tol:
setattr(bounding_box, dmin,
getattr(bounding_box, dmin) - pad)
if abs(getattr(bounding_box, dmax) -
atoms.coords[:, i].max()) < pad - pad_tol:
setattr(bounding_box, dmax,
getattr(bounding_box, dmax) + pad)
if verbose:
print('bounding_box: {}'.format(bounding_box))
lohi_width = 0
for dim in ('x', 'y', 'z'):
lohi_width = \
max(lohi_width, len('{:.6f} {:.6f}'.format(
getattr(bounding_box, dim + 'min'),
getattr(bounding_box, dim + 'max'))) + 4)
with zopen(fpath, 'wt') as f:
f.write('# {}\n\n'.format(comment_line.lstrip('#').strip()))
f.write('{}atoms\n'.format(
'{:d}'.format(Natoms).ljust(Natoms_width)))
f.write('{}atom types\n\n'.format(
'{:d}'.format(Ntypes).ljust(Ntypes_width)))
for dim in ('x', 'y', 'z'):
f.write('{}{dim}lo {dim}hi\n'.format('{:.6f} {:.6f}'.format(
getattr(bounding_box, dim + 'min'),
getattr(bounding_box, dim + 'max')).ljust(lohi_width),
dim=dim))
f.write('\nMasses\n\n')
for atomtype, properties in list(typemap.items()):
f.write('{}{:.4f}\n'.format(
'{:d}'.format(atomtype).ljust(Natoms_width),
properties['mass']))
f.write('\nAtoms\n\n')
for atom in atoms:
line = ''
line += "{:>{}}".format(atom.id, id_width)
line += "{:>{}}".format(atom.mol, 3)
line += "{:>{}}".format(atom.type, type_width)
line += "{:>{}}".format('{:.1f}'.format(atom.q), 4)
line += "{:>{}}".format('{:f}'.format(atom.x), 14)
line += "{:>{}}".format('{:f}'.format(atom.y), 14)
line += "{:>{}}".format('{:f}'.format(atom.z), 14)
line += "{:>{}}".format('{:d}'.format(atom.ix), 3)
line += "{:>{}}".format('{:d}'.format(atom.iy), 3)
line += "{:>{}}".format('{:d}'.format(atom.iz), 3)
line += '\n'
f.write(line)
f.write('\nVelocities\n\n')
for atom in atoms:
line = ''
line += "{:>{}}".format(atom.id, id_width)
line += "{:>{}}".format('{:f}'.format(atom.vx), 14)
line += "{:>{}}".format('{:f}'.format(atom.vy), 14)
line += "{:>{}}".format('{:f}'.format(atom.vz), 14)
line += '\n'
f.write(line)
