def __init__(self,
universe,
alpha=2.0,
tau=1.5,
group=None,
radii_dict=None,
max_layers=1,
normal='guess',
molecular=True,
info=True,
mesh=None,
centered=False,
warnings=False,
**kargs):
self.symmetry = 'planar'
self.do_center = centered
sanity = pytim.SanityCheck(self)
sanity.assign_universe(universe,
radii_dict=radii_dict,
warnings=warnings)
self.target_mesh = mesh
if mesh is not None:
raise Exception("FFT-based version not implemented")
self.info = info
self.alpha = alpha
self.tau = tau
if (max_layers != 1):
raise Exception("max_layers !=1 not implemented yet!")
self.max_layers = max_layers
self._layers = np.empty([2, max_layers], dtype=type(universe.atoms))
self._surfaces = np.empty(max_layers, dtype=type(Surface))
self.normal = None
self.PDB = {}
self.molecular = molecular
# TODO implement cluster group
sanity.assign_groups(group, None, None)
sanity.assign_normal(normal)
sanity.assign_radii()
self.old_box = np.array([-1, -1, -1])
self.sorted_indices = None
self.surf = None
self.modes = [None, None]
pytim.PatchTrajectory(universe.trajectory, self)
self._assign_layers()
self._atoms = self.LayerAtomGroupFactory(self._layers[:].sum().indices,
self.universe)
def __init__(self,
universe,
mesh=0.4,
alpha=2.0,
normal='guess',
group=None,
radii_dict=None,
max_layers=1,
cluster_cut=None,
cluster_threshold_density=None,
molecular=True,
extra_cluster_groups=None,
info=False,
multiproc=True,
centered=False,
warnings=False,
**kargs):
self.symmetry = 'planar'
self.do_center = centered
sanity = pytim.SanityCheck(self)
sanity.assign_universe(universe,
radii_dict=radii_dict,
warnings=warnings)
sanity.assign_alpha(alpha)
sanity.assign_mesh(mesh)
self.cluster_threshold_density = cluster_threshold_density
self.max_layers = max_layers
self._layers = np.empty([2, max_layers], dtype=type(universe.atoms))
self._surfaces = np.empty(max_layers, dtype=type(Surface))
self.info = info
self.normal = None
self.PDB = {}
self.molecular = molecular
sanity.assign_groups(group, cluster_cut, extra_cluster_groups)
sanity.assign_normal(normal)
sanity.assign_radii()
self.grid = None
self.use_threads = False
self.use_kdtree = True
self.use_multiproc = multiproc
pytim.PatchTrajectory(universe.trajectory, self)
self._assign_layers()
self._atoms = self.LayerAtomGroupFactory(self._layers[:].sum().indices,
self.universe)
def __init__(self,
universe,
group=None,
alpha=2.0,
normal='guess',
molecular=True,
max_layers=1,
radii_dict=None,
cluster_cut=None,
cluster_threshold_density=None,
extra_cluster_groups=None,
biggest_cluster_only=False,
symmetry='spherical',
centered=False,
info=False,
warnings=False,
_noextrapoints=False,
**kargs):
# this is just for debugging/testing
self._noextrapoints = _noextrapoints
self.do_center = centered
self.biggest_cluster_only = biggest_cluster_only
sanity = SanityCheck(self)
sanity.assign_universe(universe,
radii_dict=radii_dict,
warnings=warnings)
sanity.assign_alpha(alpha)
self.cluster_threshold_density = cluster_threshold_density
self.max_layers = max_layers
self._layers = np.empty([max_layers], dtype=type(universe.atoms))
self.info = info
self.normal = None
self.PDB = {}
self.molecular = molecular
sanity.assign_groups(group, cluster_cut, extra_cluster_groups)
sanity.check_multiple_layers_options()
sanity.assign_radii()
self._assign_symmetry(symmetry)
if (self.symmetry == 'planar'):
sanity.assign_normal(normal)
pytim.PatchTrajectory(self.universe.trajectory, self)
self._assign_layers()
def __init__(self,
universe,
alpha=2.0,
mesh=2.0,
symmetry='spherical',
group=None,
radii_dict=None,
cluster_cut=None,
cluster_threshold_density=None,
extra_cluster_groups=None,
centered=False,
warnings=False,
fast=True,
**kargs):
self.do_center = centered
sanity = pytim.SanityCheck(self)
sanity.assign_universe(universe,
radii_dict=radii_dict,
warnings=warnings)
sanity.assign_alpha(alpha)
if mesh <= 0:
raise ValueError(self.MESH_NEGATIVE)
self.mesh = mesh
self.spacing = None
self.ngrid = None
self.PDB = {}
sanity.assign_radii()
sanity.assign_groups(group, cluster_cut, extra_cluster_groups)
self._assign_symmetry(symmetry)
if (self.symmetry == 'planar'):
sanity.assign_normal(normal)
self.fast = fast
pytim.PatchTrajectory(universe.trajectory, self)
self._assign_layers()
self._atoms = self._layers[:] # this is an empty AtomGroup
self.writevtk = WillardChandler.Writevtk(self)