def calcDistanceMatrix(coords, cutoff=None):
"""Calculate matrix of distances between coordinates within *cutoff*.
Other matrix entries are set to maximum of calculated distances.
:arg coords: a coordinate set or an object with :meth:`getCoords` method.
:type coords: :class:`~numpy.ndarray`, :class:`.Atomic`
:arg cutoff: cutoff distance for searching the KDTree.
Default (**None**) is to use the length of the longest coordinate axis.
:type cutoff: None, float
"""
try:
coords = (coords._getCoords()
if hasattr(coords, '_getCoords') else coords.getCoords())
except AttributeError:
try:
checkCoords(coords)
except TypeError:
raise TypeError('coords must be a Numpy array or an object '
'with `getCoords` method')
n_atoms = coords.shape[0]
dist_mat = zeros((n_atoms, n_atoms))
if cutoff is None:
cutoff = max(coords.max(axis=0) - coords.min(axis=0))
kdtree = KDTree(coords)
kdtree.search(cutoff)
dists = kdtree.getDistances()
r = 0
for i, j in kdtree.getIndices():
dist_mat[i, j] = dist_mat[j, i] = dists[r]
r += 1
for i in range(n_atoms):
for j in range(i + 1, n_atoms):
if dist_mat[i, j] == 0.:
dist_mat[i, j] = dist_mat[j, i] = max(dists)
return dist_mat
def buildKirchhoff(self, coords, cutoff=10., gamma=1., **kwargs):
"""Build Kirchhoff matrix for given coordinate set.
:arg coords: a coordinate set or an object with ``getCoords`` method
:type coords: :class:`numpy.ndarray` or :class:`.Atomic`
:arg cutoff: cutoff distance (Å) for pairwise interactions
default is 10.0 Å, , minimum is 4.0 Å
:type cutoff: float
:arg gamma: spring constant, default is 1.0
:type gamma: float
:arg sparse: elect to use sparse matrices, default is **False**. If
Scipy is not found, :class:`ImportError` is raised.
:type sparse: bool
:arg kdtree: elect to use KDTree for building Kirchhoff matrix faster,
default is **True**
:type kdtree: bool
Instances of :class:`Gamma` classes and custom functions are
accepted as *gamma* argument.
When Scipy is available, user can select to use sparse matrices for
efficient usage of memory at the cost of computation speed."""
try:
coords = (coords._getCoords() if hasattr(coords, '_getCoords') else
coords.getCoords())
except AttributeError:
try:
checkCoords(coords)
except TypeError:
raise TypeError('coords must be a Numpy array or an object '
'with `getCoords` method')
cutoff, g, gamma = checkENMParameters(cutoff, gamma)
self._reset()
self._cutoff = cutoff
self._gamma = g
n_atoms = coords.shape[0]
start = time.time()
if kwargs.get('sparse', False):
try:
from scipy import sparse as scipy_sparse
except ImportError:
raise ImportError('failed to import scipy.sparse, which is '
'required for sparse matrix calculations')
kirchhoff = scipy_sparse.lil_matrix((n_atoms, n_atoms))
else:
kirchhoff = np.zeros((n_atoms, n_atoms), 'd')
if kwargs.get('kdtree', True):
kdtree = KDTree(coords)
kdtree.search(cutoff)
dist2 = kdtree.getDistances() ** 2
r = 0
for i, j in kdtree.getIndices():
g = gamma(dist2[r], i, j)
kirchhoff[i, j] = -g
kirchhoff[j, i] = -g
kirchhoff[i, i] = kirchhoff[i, i] + g
kirchhoff[j, j] = kirchhoff[j, j] + g
r += 1
else:
LOGGER.info('Using slower method for building the Kirchhoff.')
cutoff2 = cutoff * cutoff
mul = np.multiply
for i in range(n_atoms):
xyz_i = coords[i, :]
i_p1 = i+1
i2j = coords[i_p1:, :] - xyz_i
mul(i2j, i2j, i2j)
for j, dist2 in enumerate(i2j.sum(1)):
if dist2 > cutoff2:
continue
j += i_p1
g = gamma(dist2, i, j)
kirchhoff[i, j] = -g
kirchhoff[j, i] = -g
kirchhoff[i, i] = kirchhoff[i, i] + g
kirchhoff[j, j] = kirchhoff[j, j] + g
LOGGER.debug('Kirchhoff was built in {0:.2f}s.'
.format(time.time()-start))
self._kirchhoff = kirchhoff
self._n_atoms = n_atoms
self._dof = n_atoms
def buildKirchhoff(self, coords, cutoff=10., gamma=1., **kwargs):
"""Build Kirchhoff matrix for given coordinate set.
:arg coords: a coordinate set or an object with ``getCoords`` method
:type coords: :class:`numpy.ndarray` or :class:`.Atomic`
:arg cutoff: cutoff distance (Å) for pairwise interactions
default is 10.0 Å, , minimum is 4.0 Å
:type cutoff: float
:arg gamma: spring constant, default is 1.0
:type gamma: float
:arg sparse: elect to use sparse matrices, default is **False**. If
Scipy is not found, :class:`ImportError` is raised.
:type sparse: bool
:arg kdtree: elect to use KDTree for building Kirchhoff matrix faster,
default is **True**
:type kdtree: bool
Instances of :class:`Gamma` classes and custom functions are
accepted as *gamma* argument.
When Scipy is available, user can select to use sparse matrices for
efficient usage of memory at the cost of computation speed."""
try:
coords = (coords._getCoords()
if hasattr(coords, '_getCoords') else coords.getCoords())
except AttributeError:
try:
checkCoords(coords)
except TypeError:
raise TypeError('coords must be a Numpy array or an object '
'with `getCoords` method')
cutoff, g, gamma = checkENMParameters(cutoff, gamma)
self._reset()
self._cutoff = cutoff
self._gamma = g
n_atoms = coords.shape[0]
start = time.time()
if kwargs.get('sparse', False):
try:
from scipy import sparse as scipy_sparse
except ImportError:
raise ImportError('failed to import scipy.sparse, which is '
'required for sparse matrix calculations')
kirchhoff = scipy_sparse.lil_matrix((n_atoms, n_atoms))
else:
kirchhoff = np.zeros((n_atoms, n_atoms), 'd')
if kwargs.get('kdtree', True):
kdtree = KDTree(coords)
kdtree.search(cutoff)
dist2 = kdtree.getDistances()**2
r = 0
for i, j in kdtree.getIndices():
g = gamma(dist2[r], i, j)
kirchhoff[i, j] = -g
kirchhoff[j, i] = -g
kirchhoff[i, i] = kirchhoff[i, i] + g
kirchhoff[j, j] = kirchhoff[j, j] + g
r += 1
else:
LOGGER.info('Using slower method for building the Kirchhoff.')
cutoff2 = cutoff * cutoff
mul = np.multiply
for i in range(n_atoms):
xyz_i = coords[i, :]
i_p1 = i + 1
i2j = coords[i_p1:, :] - xyz_i
mul(i2j, i2j, i2j)
for j, dist2 in enumerate(i2j.sum(1)):
if dist2 > cutoff2:
continue
j += i_p1
g = gamma(dist2, i, j)
kirchhoff[i, j] = -g
kirchhoff[j, i] = -g
kirchhoff[i, i] = kirchhoff[i, i] + g
kirchhoff[j, j] = kirchhoff[j, j] + g
LOGGER.debug('Kirchhoff was built in {0:.2f}s.'.format(time.time() -
start))
self._kirchhoff = kirchhoff
self._n_atoms = n_atoms
self._dof = n_atoms
