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.. module:: ase.filters
=======
Filters
=======
The Filter class
================
Constraints can also be applied via filters, which acts as a wrapper
around an atoms object. A typical use case will look like this::
------- -------- ----------
| | | | | |
| Atoms |<----| Filter |<----| Dynamics |
| | | | | |
------- -------- ----------
and in Python this would be::
>>> atoms = Atoms(...)
>>> filter = Filter(atoms, ...)
>>> dyn = Dynamics(filter, ...)
This class hides some of the atoms in an Atoms object.
.. class:: Filter(atoms, indices=None, mask=None)
You must supply either the indices of the atoms that should be kept
visible or a mask. The mask is a list of booleans, one for each atom,
being true if the atom should be kept visible.
Example of use::
>>> from ase import Atoms
>>> from ase.filters import Filter
>>> atoms=Atoms(positions=[[ 0 , 0 , 0],
... [ 0.773, 0.600, 0],
... [-0.773, 0.600, 0]],
... symbols='OH2')
>>> f1 = Filter(atoms, indices=[1, 2])
>>> f2 = Filter(atoms, mask=[0, 1, 1])
>>> f3 = Filter(atoms, mask=[a.z == 1 for a in atoms])
>>> f1.get_positions()
[[ 0.773 0.6 0. ]
[-0.773 0.6 0. ]]
In all three filters only the hydrogen atoms are made
visible. When asking for the positions only the positions of the
hydrogen atoms are returned.
The UnitCellFilter class
========================
The unit cell filter is for optimizing positions and unit cell
simultaneously. Note that :class:`ExpCellFilter` will probably
perform better.
.. autoclass:: UnitCellFilter
The StrainFilter class
======================
The strain filter is for optimizing the unit cell while keeping
scaled positions fixed.
.. autoclass:: StrainFilter
The ExpCellFilter class
=======================
The exponential cell filter is an improved :class:`UnitCellFilter`
which is parameter free.
.. autoclass:: ExpCellFilter
The FrechetCellFilter class
===========================
.. autoclass:: FrechetCellFilter
|
