ListOfAtomsクラスオブジェクト

A ListOfAtoms object is a collection of atoms. The ASE implementation of a ListOfAtoms can be used like this:

>>> from ASE import Atom, ListOfAtoms
>>> m = ListOfAtoms([Atom('C', (0, 0, 0)),
...                  Atom('O', (0, 0, 1.0))])

The first argument to the ListOfAtoms constructor must be a python list of atoms. There are two optional keyword arguments:

cell: Unit cell size

This can be a sequence of three numbers for
an orthorhombic unit cell or three by three numbers for a general
unit cell (a sequence of three sequences of three numbers).  The
default value is ''(1, 1, 1)''.

periodic: Boundary conditions

The default value is ``False`` - a value of ``True`` would give
periodic boundary conditions along all three axes.  It is possible
to give a sequence of three booleans to specify periodicity along
specific axes.

Here is how you could make an infinite gold wire with a bond length of 2.9

>>> from ASE import Atom, ListOfAtoms
>>> d = 2.9
>>> L = 10.0
>>> wire = ListOfAtoms([Atom('Au', (L / 2, L / 2, 0))],
...                    cell=(L, L, d), periodic=(0, 0, 1))

You can also use the following methods to work with the unit cell and the boundary conditions:

GetUnitCell():

Returns a three by three array.

SetUnitCell(cell, fix=False):

Change the size of the unit cell.  If the optional argument ''fix''
is ''True'' (defaults to ''False''), then the positons of the atoms
are fixed, otherwise the atoms are moved so that their positions
relative to the unit cell are kept.

GetBoundaryConditions():

Returns a tuple of three booleans.

Here is how you would do bulk ruthenium (hcp):

>>> from math import sqrt
>>> a = 2.70
>>> c = 1.59 * a
>>> bulk = ListOfAtoms([Atom('Ru', (0, 0, 0)),
...                     Atom('Ru', (1 / 3., 1 / 3., 1 / 2.))],
...                    periodic=True)
>>> bulk.SetUnitCell([(a, 0, 0),
...                   (a / 2, a * sqrt(3) / 2, 0),
...                   (0, 0, c)])

In addition, an ListOfAtoms instance has the following methods:

GetKineticEnergy():

 Returns the total kinetic energy.

Copy():

 Return a fresh copy.  Everything but a possibly attached
 calculator is copied (next section will explain how to attach a
 calculator).

Repeat(repeat):

 The argument ''repeat'' is a sequence of three
 positive integers (''n1'', ''n2'', ''n3'' - one for each axis), and
 a copy of the ''ListOfAtoms'' object repeated ''n1 * n2 * n3''
 times is returned.

Using the same atom object in several ListOfAtoms objects is not allowed! Use a copy instead:

>>> loa1.append(loa2[7])
RuntimeError: Atom belongs to another ListOfAtoms!
>>> loa1.append(loa2[7].Copy())

Array methods

It is possible to work with the properties of atoms in a ListOfAtoms by using the methods defined for the individual atoms like this:

>>> m = ListOfAtoms([Atom('O', (0, 0, 0)),
...                  Atom('H', (0.773, 0.600, 0)),
...                  Atom('H', (-0.773, 0.600, 0))])
>>> m[1].GetCartesianPosition()
array([ 0.773,  0.6  ,  0.   ])
>>> m[0].SetCartesianPosition((0, -0.1, 0))

However, a ListOfAtoms that conforms to the ASE specification must have a set of array methods to do the same for all atoms in one step:

>>> m.GetCartesianPositions()
array([[ 0.   ,  0.   ,  0.   ],
       [ 0.773,  0.6  ,  0.   ],
       [-0.773,  0.6  ,  0.   ]])
>>> m.SetCartesianPositions([(0, -0.1, 0),
...                          (0.773, 0.600, 0),
...                          (-0.773, 0.600, 0)])

The following methods must be defined:

Get methods Set methods type shape
GetCartesianPositions SetCartesianPositions Float (n, 3)
GetCartesianMomenta SetCartesianMomenta Float (n, 3)
GetCartesianVelocities SetCartesianVelocities Float (n, 3)
GetCartesianForces SetCartesianForces Float (n, 3)
GetTags SetTags Int (n,)
GetAtomicNumbers SetAtomicNumbers Int (n,)
GetMasses SetMasses Float (n,)
GetKineticEnergies Float (n,)
GetGeneralizedPositions SetGeneralizedPositions Float (n*3,)
GetGeneralizedForces SetGeneralizedForces Float (n*3,)

The Get methods will return Numeric arrays of the given shape (n is the number of atoms) and type, and the Set methods will take anything with the correct shape.

from ASE import ListOfAtoms
a = ListOfAtoms([])
a = ListOfAtoms([p1])
a = ListOfAtoms([Atom('H', (0, 0, 0), tag = 1, magmom = 1.0)])
a = ListOfAtoms([p1], cell = (4, 4, 4))
a = ListOfAtoms([p1], cell = [(4, 0, 0), (0, 4, 0), (0, 0, 4)])
ab_initio/listofatomsオブジェクト.txt · 最終更新: 2009/02/02 21:53 by kimi
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