Class Com
object --+
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GeomAnalyzerBase --+
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CenterOf --+
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Com
- Known Subclasses:
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Class for computing averaged position weighted by atomic mass, under the
periodic boundary condition.
Basic usage:
ana = Com(msys_model, cms_model, gids=[1, 23, 34, 5, 6])
results = analyze(tr, ana)
where C{tr} is a trajectory, and C{results} will contain a list of 2-tuples:
(unwrapped-center-of-mass, [unwrapped-positions-of-involved-atoms]), and
each 2-tuple in the list corresponds to a trajectory frame.
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__init__(self,
msys_model,
cms_model,
asl=None,
gids=None)
x.__init__(...) initializes x; see help(type(x)) for signature |
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Inherited from GeomAnalyzerBase:
__call__
Inherited from object:
__delattr__,
__format__,
__getattribute__,
__hash__,
__new__,
__reduce__,
__reduce_ex__,
__repr__,
__setattr__,
__sizeof__,
__str__,
__subclasshook__
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__init__(self,
msys_model,
cms_model,
asl=None,
gids=None)
(Constructor)
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x.__init__(...) initializes x; see help(type(x)) for signature
- Parameters:
asl (str) - ASL expression to specify the atom selectiongids (list of ints) - GIDs of atoms
Both msys_model and cms_model must be previously obtained through
the read_cms function. They both should
have the same atom coordinates and the same simulation box
matrix. cms_model is used to obtain
atom GIDs from ASL selection. msys_model is used to retrieve atom attribute
from GIDs.
Either asl or gids must be specified, but not both. msys_model (msys.System)cms_model (schrodinger.structure.Structure) - Overrides:
object.__init__
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