def continuous_coordinates(coords, volume, resolution):
cachedir = os.path.expanduser(config.Path.cache_dir)
cachepath = os.path.join(cachedir, 'discretization_cache.hdf5')
dcache = DiscretizationCache(cachepath)
disc = dcache.get_discretization(volume, resolution)
return np.array(map(disc.discrete_to_continuous, coords))
def continuous_coordinates(coords, volume, resolution):
cachedir = os.path.expanduser(config.Path.cache_dir)
cachepath = os.path.join(cachedir, 'discretization_cache.hdf5')
dcache = DiscretizationCache(cachepath)
disc = dcache.get_discretization(volume, resolution)
return np.array(map(disc.discrete_to_continuous, coords))
def __init__(self, *args):
"""
Create a sample from atom and cavity positions and smooth them to
get the PDFs
The constructor can be called in two ways:
- ``PDF(results)`` :
retrieve the data from :class:`core.data.Results`
- ``PDF(positions, elements, cavitycenters, volume)`` :
use the given arrays and the volume object
"""
if len(args) == 1:
results = args[0]
positions = results.atoms.positions
elements = results.atoms.elements
volume = results.atoms.volume
if results.domains is not None:
centers = results.domains.centers
cachedir = os.path.expanduser(config.Path.cache_dir)
cachepath = os.path.join(cachedir, 'discretization_cache.hdf5')
dcache = DiscretizationCache(cachepath)
disc = dcache.get_discretization(volume, results.resolution)
centers = map(disc.discrete_to_continuous, centers)
else:
centers = []
elif len(args) == 4:
positions, elements, centers, volume = args
else:
raise TypeError("PDF expects 1 or 4 parameters")
self.positions = np.array(positions, copy=False)
self.elements = np.array(elements, dtype="|S4", copy=False)
self.centers = np.array(centers, copy=False)
self.volume = volume
self.num_atoms = np.where(self.elements != "cav")[0].size
self.numberdensity = float(self.num_atoms) / self.volume.volume
self.stats = self._genstats(self.positions,
self.elements,
self.centers,
self.volume)
def __init__(self, *args):
"""
Create a sample from atom and cavity positions and smooth them to
get the PDFs
The constructor can be called in two ways:
- ``PDF(results)`` :
retrieve the data from :class:`core.data.Results`
- ``PDF(positions, elements, cavitycenters, volume)`` :
use the given arrays and the volume object
"""
if len(args) == 1:
results = args[0]
positions = results.atoms.positions
elements = results.atoms.elements
volume = results.atoms.volume
if results.domains is not None:
centers = results.domains.centers
cachedir = os.path.expanduser(config.Path.cache_dir)
cachepath = os.path.join(cachedir, 'discretization_cache.hdf5')
dcache = DiscretizationCache(cachepath)
disc = dcache.get_discretization(volume, results.resolution)
centers = map(disc.discrete_to_continuous, centers)
else:
centers = []
elif len(args) == 4:
positions, elements, centers, volume = args
else:
raise TypeError("PDF expects 1 or 4 parameters")
self.positions = np.array(positions, copy=False)
self.elements = np.array(elements, dtype="|S4", copy=False)
self.centers = np.array(centers, copy=False)
self.volume = volume
self.num_atoms = np.where(self.elements != "cav")[0].size
self.numberdensity = float(self.num_atoms) / self.volume.volume
self.stats = self._genstats(self.positions, self.elements,
self.centers, self.volume)
