def getClosest(a, B):
D = []
for b in B:
d = getDistance(a._getCoords(), b._getCoords())
D.append(d)
i = argmin(D)
return B[i]
def getClosest(a, B):
D = []
for b in B:
d = getDistance(a._getCoords(), b._getCoords())
D.append(d)
i = argmin(D)
return B[i]
def calcDistance(atoms1, atoms2, unitcell=None):
"""Returns the Euclidean distance between *atoms1* and *atoms2*. Arguments
may be :class:`~.Atomic` instances or NumPy arrays. Shape of numpy arrays
must be ``([M,]N,3)``, where *M* is number of coordinate sets and *N* is
the number of atoms. If *unitcell* array is provided, periodic boundary
conditions will be taken into account.
:arg atoms1: atom or coordinate data
:type atoms1: :class:`.Atomic`, :class:`numpy.ndarray`
:arg atoms2: atom or coordinate data
:type atoms2: :class:`.Atomic`, :class:`numpy.ndarray`
:arg unitcell: orthorhombic unitcell dimension array with shape ``(3,)``
:type unitcell: :class:`numpy.ndarray`"""
if not isinstance(atoms1, ndarray):
try:
atoms1 = atoms1._getCoords()
except AttributeError:
raise TypeError('atoms1 must be Atomic instance or an array')
if not isinstance(atoms2, ndarray):
try:
atoms2 = atoms2._getCoords()
except AttributeError:
raise TypeError('atoms2 must be Atomic instance or an array')
if atoms1.shape[-1] != 3 or atoms2.shape[-1] != 3:
raise ValueError('atoms1 and atoms2 must have shape ([M,]N,3)')
if unitcell is not None:
if not isinstance(unitcell, ndarray):
raise TypeError('unitcell must be an array')
elif unitcell.shape != (3, ):
raise ValueError('unitcell.shape must be (3,)')
return getDistance(atoms1, atoms2, unitcell)
def calcDistance(atoms1, atoms2, unitcell=None):
"""Returns the Euclidean distance between *atoms1* and *atoms2*. Arguments
may be :class:`~.Atomic` instances or NumPy arrays. Shape of numpy arrays
must be ``([M,]N,3)``, where *M* is number of coordinate sets and *N* is
the number of atoms. If *unitcell* array is provided, periodic boundary
conditions will be taken into account.
:arg atoms1: atom or coordinate data
:type atoms1: :class:`.Atomic`, :class:`numpy.ndarray`
:arg atoms2: atom or coordinate data
:type atoms2: :class:`.Atomic`, :class:`numpy.ndarray`
:arg unitcell: orthorhombic unitcell dimension array with shape ``(3,)``
:type unitcell: :class:`numpy.ndarray`"""
if not isinstance(atoms1, ndarray):
try:
atoms1 = atoms1._getCoords()
except AttributeError:
raise TypeError('atoms1 must be Atomic instance or an array')
if not isinstance(atoms2, ndarray):
try:
atoms2 = atoms2._getCoords()
except AttributeError:
raise TypeError('atoms2 must be Atomic instance or an array')
if atoms1.shape[-1] != 3 or atoms2.shape[-1] != 3:
raise ValueError('atoms1 and atoms2 must have shape ([M,]N,3)')
if unitcell is not None:
if not isinstance(unitcell, ndarray):
raise TypeError('unitcell must be an array')
elif unitcell.shape != (3,):
raise ValueError('unitcell.shape must be (3,)')
return getDistance(atoms1, atoms2, unitcell)
def buildDistMatrix(atoms1, atoms2=None, unitcell=None, format='mat'):
"""Returns distance matrix. When *atoms2* is given, a distance matrix
with shape ``(len(atoms1), len(atoms2))`` is built. When *atoms2* is
**None**, a symmetric matrix with shape ``(len(atoms1), len(atoms1))``
is built. If *unitcell* array is provided, periodic boundary conditions
will be taken into account.
:arg atoms1: atom or coordinate data
:type atoms1: :class:`.Atomic`, :class:`numpy.ndarray`
:arg atoms2: atom or coordinate data
:type atoms2: :class:`.Atomic`, :class:`numpy.ndarray`
:arg unitcell: orthorhombic unitcell dimension array with shape ``(3,)``
:type unitcell: :class:`numpy.ndarray`
:arg format: format of the resulting array, one of ``'mat'`` (matrix,
default), ``'rcd'`` (arrays of row indices, column indices, and
distances), or ``'arr'`` (only array of distances)
:type format: bool"""
if not isinstance(atoms1, ndarray):
try:
atoms1 = atoms1._getCoords()
except AttributeError:
raise TypeError('atoms1 must be Atomic instance or an array')
if atoms2 is None:
symmetric = True
atoms2 = atoms1
else:
symmetric = False
if not isinstance(atoms2, ndarray):
try:
atoms2 = atoms2._getCoords()
except AttributeError:
raise TypeError('atoms2 must be Atomic instance or an array')
if atoms2.ndim == 1:
atoms2 = atoms2.reshape((1, 3))
if atoms1.shape[-1] != 3 or atoms2.shape[-1] != 3:
raise ValueError('one and two must have shape ([M,]N,3)')
if unitcell is not None:
if not isinstance(unitcell, ndarray):
raise TypeError('unitcell must be an array')
elif unitcell.shape != (3, ):
raise ValueError('unitcell.shape must be (3,)')
dist = zeros((len(atoms1), len(atoms2)))
if symmetric:
if format not in DISTMAT_FORMATS:
raise ValueError('format must be one of mat, rcd, or arr')
if format == 'mat':
for i, xyz in enumerate(atoms1[:-1]):
dist[i,
i + 1:] = dist[i + 1:,
i] = getDistance(xyz, atoms2[i + 1:],
unitcell)
else:
dist = concatenate([
getDistance(xyz, atoms2[i + 1:], unitcell)
for i, xyz in enumerate(atoms1)
])
if format == 'rcd':
n_atoms = len(atoms1)
rc = array([(i, j) for i in range(n_atoms)
for j in range(i + 1, n_atoms)])
row, col = rc.T
dist = (row, col, dist)
else:
for i, xyz in enumerate(atoms1):
dist[i] = getDistance(xyz, atoms2, unitcell)
return dist
def buildDistMatrix(atoms1, atoms2=None, unitcell=None, format='mat'):
"""Returns distance matrix. When *atoms2* is given, a distance matrix
with shape ``(len(atoms1), len(atoms2))`` is built. When *atoms2* is
**None**, a symmetric matrix with shape ``(len(atoms1), len(atoms1))``
is built. If *unitcell* array is provided, periodic boundary conditions
will be taken into account.
:arg atoms1: atom or coordinate data
:type atoms1: :class:`.Atomic`, :class:`numpy.ndarray`
:arg atoms2: atom or coordinate data
:type atoms2: :class:`.Atomic`, :class:`numpy.ndarray`
:arg unitcell: orthorhombic unitcell dimension array with shape ``(3,)``
:type unitcell: :class:`numpy.ndarray`
:arg format: format of the resulting array, one of ``'mat'`` (matrix,
default), ``'rcd'`` (arrays of row indices, column indices, and
distances), or ``'arr'`` (only array of distances)
:type format: bool"""
if not isinstance(atoms1, ndarray):
try:
atoms1 = atoms1._getCoords()
except AttributeError:
raise TypeError('atoms1 must be Atomic instance or an array')
if atoms2 is None:
symmetric = True
atoms2 = atoms1
else:
symmetric = False
if not isinstance(atoms2, ndarray):
try:
atoms2 = atoms2._getCoords()
except AttributeError:
raise TypeError('atoms2 must be Atomic instance or an array')
if atoms2.ndim == 1:
atoms2 = atoms2.reshape((1,3))
if atoms1.shape[-1] != 3 or atoms2.shape[-1] != 3:
raise ValueError('one and two must have shape ([M,]N,3)')
if unitcell is not None:
if not isinstance(unitcell, ndarray):
raise TypeError('unitcell must be an array')
elif unitcell.shape != (3,):
raise ValueError('unitcell.shape must be (3,)')
dist = zeros((len(atoms1), len(atoms2)))
if symmetric:
if format not in DISTMAT_FORMATS:
raise ValueError('format must be one of mat, rcd, or arr')
if format == 'mat':
for i, xyz in enumerate(atoms1[:-1]):
dist[i, i+1:] = dist[i+1:, i] = getDistance(xyz, atoms2[i+1:],
unitcell)
else:
dist = concatenate([getDistance(xyz, atoms2[i+1:], unitcell)
for i, xyz in enumerate(atoms1)])
if format == 'rcd':
n_atoms = len(atoms1)
rc = array([(i, j) for i in range(n_atoms)
for j in range(i + 1, n_atoms)])
row, col = rc.T
dist = (row, col, dist)
else:
for i, xyz in enumerate(atoms1):
dist[i] = getDistance(xyz, atoms2, unitcell)
return dist
