# @surface

## Contents

### Keep Out

seminar:atoms_object

ase.atoms	index
/usr/local/lib/python2.7/dist-packages/ase/atoms.py
Definition of the Atoms class.

This module defines the central object in the ASE package: the Atoms
object.

Modules

numpy
ase.units
warnings

Classes

__builtin__.object
Atoms

class Atoms(__builtin__.object)
Atoms object.

The Atoms object can represent an isolated molecule, or a
periodically repeated structure.  It has a unit cell and
there may be periodic boundary conditions along any of the three
unit cell axes.

Information about the atoms (atomic numbers and position) is
stored in ndarrays.  Optionally, there can be information about
tags, momenta, masses, magnetic moments and charges.

In order to calculate energies, forces and stresses, a calculator
object has to attached to the atoms object.

Parameters:

symbols: str (formula) or list of str
Can be a string formula, a list of symbols or a list of
Atom objects.  Examples: 'H2O', 'COPt12', ['H', 'H', 'O'],
[Atom('Ne', (x, y, z)), ...].
positions: list of xyz-positions
Atomic positions.  Anything that can be converted to an
ndarray of shape (n, 3) will do: [(x1,y1,z1), (x2,y2,z2),
...].
scaled_positions: list of scaled-positions
Like positions, but given in units of the unit cell.
Can not be set at the same time as positions.
numbers: list of int
Atomic numbers (use only one of symbols/numbers).
tags: list of int
Special purpose tags.
momenta: list of xyz-momenta
Momenta for all atoms.
masses: list of float
Atomic masses in atomic units.
magmoms: list of float or list of xyz-values
Magnetic moments.  Can be either a single value for each atom
for collinear calculations or three numbers for each atom for
non-collinear calculations.
charges: list of float
Atomic charges.
cell: 3x3 matrix
Unit cell vectors.  Can also be given as just three
numbers for orthorhombic cells.  Default value: [1, 1, 1].
celldisp: Vector
Unit cell displacement vector. To visualize a displaced cell
around the center of mass of a Systems of atoms. Default value
= (0,0,0)
pbc: one or three bool
Periodic boundary conditions flags.  Examples: True,
False, 0, 1, (1, 1, 0), (True, False, False).  Default
value: False.
constraint: constraint object(s)
Used for applying one or more constraints during structure
optimization.
calculator: calculator object
Used to attach a calculator for calculating energies and atomic
forces.
info: dict of key-value pairs
Dictionary of key-value pairs with additional information
about the system.  The following keys may be used by ase:

- spacegroup: Spacegroup instance
- unit_cell: 'conventional' | 'primitive' | int | 3 ints

Items in the info attribute survives copy and slicing and can
key is a string, the value is picklable and, if the value is a
user-defined object, its base class is importable.  One should
not make any assumptions about the existence of keys.

Examples:

These three are equivalent:

>>> d = 1.104  # N2 bondlength
>>> a = Atoms('N2', [(0, 0, 0), (0, 0, d)])
>>> a = Atoms(numbers=[7, 7], positions=[(0, 0, 0), (0, 0, d)])
>>> a = Atoms([Atom('N', (0, 0, 0)), Atom('N', (0, 0, d)])

FCC gold:

>>> a = 4.05  # Gold lattice constant
>>> b = a / 2
>>> fcc = Atoms('Au',
...             cell=[(0, b, b), (b, 0, b), (b, b, 0)],
...             pbc=True)

Hydrogen wire:

>>> d = 0.9  # H-H distance
>>> L = 7.0
>>> h = Atoms('H', positions=[(0, L / 2, L / 2)],
...           cell=(d, L, L),
...           pbc=(1, 0, 0))

Methods defined here:
__delitem__(self, i)
__eq__(self, other)
Check for identity of two atoms objects.

Identity means: same positions, atomic numbers, unit cell and
periodic boundary conditions.
__getitem__(self, i)
Return a subset of the atoms.

i -- scalar integer, list of integers, or slice object
describing which atoms to return.

If i is a scalar, return an Atom object. If i is a list or a
slice, return an Atoms object with the same cell, pbc, and
other associated info as the original Atoms object. The
indices of the constraints will be shuffled so that they match
the indexing in the subset returned.
__imul__(self, m)
In-place repeat of atoms.
__init__(self, symbols=None, positions=None, numbers=None, tags=None, momenta=None, masses=None, magmoms=None, charges=None, scaled_positions=None, cell=None, pbc=None, celldisp=None, constraint=None, calculator=None, info=None)
__len__(self)
__mul__ = repeat(self, rep)
__ne__(self, other)
__repr__(self)
append(self, atom)
Append atom to end.
center(self, vacuum=None, axis=None)
Center atoms in unit cell.

Centers the atoms in the unit cell, so there is the same
amount of vacuum on all sides.

Parameters:

vacuum (default: None): If specified adjust the amount of
vacuum when centering.  If vacuum=10.0 there will thus be 10
Angstrom of vacuum on each side.

axis (default: None): If specified, only act on the specified
axis.  Default: Act on all axes.
copy(self)
Return a copy.
edit(self)
Modify atoms interactively through ag viewer.

Conflicts leading to undesirable behaviour might arise
when matplotlib has been pre-imported with certain
incompatible backends and while trying to use the
plot feature inside the interactive ag. To circumvent,
please set matplotlib.use('gtk') before calling this
method.
extend(self, other)
Extend atoms object by appending atoms from *other*.
get_angle(self, list)
Get angle formed by three atoms.

calculate angle between the vectors list[1]->list[0] and
list[1]->list[2], where list contains the atomic indexes in
question.
get_angular_momentum(self)
Get total angular momentum with respect to the center of mass.
get_array(self, name, copy=True)
Get an array.

Returns a copy unless the optional argument copy is false.
get_atomic_numbers(self)
Get integer array of atomic numbers.
get_calculation_done(self)
Let the calculator calculate its thing,
using the current input.
get_calculator(self)
Get currently attached calculator object.
get_cell(self)
Get the three unit cell vectors as a 3x3 ndarray.
get_celldisp(self)
Get the unit cell displacement vectors .
get_center_of_mass(self, scaled=False)
Get the center of mass.

If scaled=True the center of mass in scaled coordinates
is returned.
get_charges(self)
Get calculated charges.
get_chemical_formula(self, mode='hill')
Get the chemial formula as a string based on the chemical symbols.

Parameters:

mode:
There are three different modes available:

'all': The list of chemical symbols are contracted to at string,
e.g. ['C', 'H', 'H', 'H', 'O', 'H'] becomes 'CHHHOH'.

'reduce': The same as 'all' where repeated elements are contracted
to a single symbol and a number, e.g. 'CHHHOCHHH' is reduced to
'CH3OCH3'.

'hill': The list of chemical symbols are contracted to a string
following the Hill notation (alphabetical order with C and H
first), e.g. 'CHHHOCHHH' is reduced to 'C2H6O' and 'SOOHOHO' to
'H2O4S'. This is default.
get_chemical_symbols(self, reduce=False)
Get list of chemical symbol strings.
get_dihedral(self, list)
Calculate dihedral angle.

Calculate dihedral angle between the vectors list[0]->list[1]
and list[2]->list[3], where list contains the atomic indexes
in question.
get_dipole_moment(self)
Calculate the electric dipole moment for the atoms object.

Only available for calculators which has a get_dipole_moment()
method.
get_distance(self, a0, a1, mic=False)
Return distance between two atoms.

Use mic=True to use the Minimum Image Convention.
get_forces(self, apply_constraint=True)
Calculate atomic forces.

Ask the attached calculator to calculate the forces and apply
constraints.  Use *apply_constraint=False* to get the raw
forces.
get_initial_charges(self)
Get array of initial charges.
get_initial_magnetic_moments(self)
Get array of initial magnetic moments.
get_isotropic_pressure(self, stress)
Get the current calculated pressure, assume isotropic medium.
in Bar
get_kinetic_energy(self)
Get the kinetic energy.
get_magnetic_moment(self)
Get calculated total magnetic moment.
get_magnetic_moments(self)
Get calculated local magnetic moments.
get_masses(self)
Get array of masses.
get_momenta(self)
Get array of momenta.
get_moments_of_inertia(self, vectors=False)
Get the moments of inertia along the principal axes.

The three principal moments of inertia are computed from the
eigenvalues of the symmetric inertial tensor. Periodic boundary
conditions are ignored. Units of the moments of inertia are
amu*angstrom**2.
get_name(self)
get_number_of_atoms(self)
Returns the number of atoms.

Equivalent to len(atoms) in the standard ASE Atoms class.
get_pbc(self)
Get periodic boundary condition flags.
get_positions(self, wrap=False)
Get array of positions. If wrap==True, wraps atoms back
into unit cell.
get_potential_energies(self)
Calculate the potential energies of all the atoms.

Only available with calculators supporting per-atom energies
(e.g. classical potentials).
get_potential_energy(self)
Calculate potential energy.
get_reciprocal_cell(self)
Get the three reciprocal lattice vectors as a 3x3 ndarray.

Note that the commonly used factor of 2 pi for Fourier
transforms is not included here.
get_scaled_positions(self)
Get positions relative to unit cell.

Atoms outside the unit cell will be wrapped into the cell in
those directions with periodic boundary conditions so that the
scaled coordinates are between zero and one.
get_stress(self, voigt=True)
Calculate stress tensor.

Returns an array of the six independent components of the
symmetric stress tensor, in the traditional Voigt order
(xx, yy, zz, yz, xz, xy) or as a 3x3 matrix.  Default is Voigt
order.
get_stresses(self)
Calculate the stress-tensor of all the atoms.

Only available with calculators supporting per-atom energies and
stresses (e.g. classical potentials).  Even for such calculators
there is a certain arbitrariness in defining per-atom stresses.
get_tags(self)
Get integer array of tags.
get_temperature(self)
Get the temperature. in Kelvin
get_total_energy(self)
Get the total energy - potential plus kinetic energy.
get_velocities(self)
Get array of velocities.
get_volume(self)
Get volume of unit cell.
has(self, name)
Check for existence of array.

name must be one of: 'tags', 'momenta', 'masses', 'magmoms',
'charges'.
new_array(self, name, a, dtype=None, shape=None)

If *shape* is not *None*, the shape of *a* will be checked.
pop(self, i=-1)
Remove and return atom at index *i* (default last).
rattle(self, stdev=0.001, seed=42)
Randomly displace atoms.

This method adds random displacements to the atomic positions,
taking a possible constraint into account.  The random numbers are
drawn from a normal distribution of standard deviation stdev.

For a parallel calculation, it is important to use the same
seed on all processors!
repeat(self, rep)
Create new repeated atoms object.

The *rep* argument should be a sequence of three positive
integers like *(2,3,1)* or a single integer (*r*) equivalent
to *(r,r,r)*.
rotate(self, v, a=None, center=(0, 0, 0), rotate_cell=False)
Rotate atoms based on a vector and an angle, or two vectors.

Parameters:

v:
Vector to rotate the atoms around. Vectors can be given as
strings: 'x', '-x', 'y', ... .

a = None:
Angle that the atoms is rotated around the vecor 'v'. If an angle
is not specified, the length of 'v' is used as the angle
(default). The angle can also be a vector and then 'v' is rotated
into 'a'.

center = (0, 0, 0):
The center is kept fixed under the rotation. Use 'COM' to fix
the center of mass, 'COP' to fix the center of positions or
'COU' to fix the center of cell.

rotate_cell = False:
If true the cell is also rotated.

Examples:

Rotate 90 degrees around the z-axis, so that the x-axis is
rotated into the y-axis:

>>> a = pi / 2
>>> atoms.rotate('z', a)
>>> atoms.rotate((0, 0, 1), a)
>>> atoms.rotate('-z', -a)
>>> atoms.rotate((0, 0, a))
>>> atoms.rotate('x', 'y')
Rotate dihedral angle.

Complementing the two routines above: rotate a group by a
predefined dihedral angle, starting from its current
configuration
rotate_euler(self, center=(0, 0, 0), phi=0.0, theta=0.0, psi=0.0)
Rotate atoms via Euler angles.

See e.g http://mathworld.wolfram.com/EulerAngles.html for explanation.

Parameters:

center :
The point to rotate about. A sequence of length 3 with the
coordinates, or 'COM' to select the center of mass, 'COP' to
select center of positions or 'COU' to select center of cell.
phi :
The 1st rotation angle around the z axis.
theta :
Rotation around the x axis.
psi :
2nd rotation around the z axis.
Set angle formed by three atoms.

Sets the angle between vectors list[1]->list[0] and
list[1]->list[2].

Same usage as in set_dihedral.
set_array(self, name, a, dtype=None, shape=None)
Update array.

If *shape* is not *None*, the shape of *a* will be checked.
If *a* is *None*, then the array is deleted.
set_atomic_numbers(self, numbers)
Set atomic numbers.
set_calculator(self, calc=None)
Attach calculator object.
set_cell(self, cell, scale_atoms=False, fix=None)
Set unit cell vectors.

Parameters:

cell :
Unit cell.  A 3x3 matrix (the three unit cell vectors) or
just three numbers for an orthorhombic cell.
scale_atoms : bool
Fix atomic positions or move atoms with the unit cell?
Default behavior is to *not* move the atoms (scale_atoms=False).

Examples:

Two equivalent ways to define an orthorhombic cell:

>>> a.set_cell([a, b, c])
>>> a.set_cell([(a, 0, 0), (0, b, 0), (0, 0, c)])

FCC unit cell:

>>> a.set_cell([(0, b, b), (b, 0, b), (b, b, 0)])
set_celldisp(self, celldisp)
set_charges(self, charges=None)
Deprecated method. Use set_initial_charges.
set_chemical_symbols(self, symbols)
Set chemical symbols.
set_constraint(self, constraint=None)
Apply one or more constrains.

The *constraint* argument must be one constraint object or a
list of constraint objects.
set the dihedral angle between vectors list[0]->list[1] and
list[2]->list[3] by changing the atom indexed by list[3]
(read: the entire subgroup) are moved

example: the following defines a very crude
ethane-like molecule and twists one half of it by 30 degrees.

>>> atoms = Atoms('HHCCHH', [[-1, 1, 0], [-1, -1, 0], [0, 0, 0],
[1, 0, 0], [2, 1, 0], [2, -1, 0]])
set_distance(self, a0, a1, distance, fix=0.5)
Set the distance between two atoms.

Set the distance between atoms *a0* and *a1* to *distance*.
By default, the center of the two atoms will be fixed.  Use
*fix=0* to fix the first atom, *fix=1* to fix the second
atom and *fix=0.5* (default) to fix the center of the bond.
set_initial_charges(self, charges=None)
Set the initial charges.
set_initial_magnetic_moments(self, magmoms=None)
Set the initial magnetic moments.

Use either one or three numbers for every atom (collinear
or non-collinear spins).
set_masses(self, masses='defaults')
Set atomic masses.

The array masses should contain a list of masses.  In case
the masses argument is not given or for those elements of the
masses list that are None, standard values are set.
set_momenta(self, momenta)
Set momenta.
set_pbc(self, pbc)
Set periodic boundary condition flags.
set_positions(self, newpositions)
Set positions, honoring any constraints.
set_scaled_positions(self, scaled)
Set positions relative to unit cell.
set_tags(self, tags)
Set tags for all atoms. If only one tag is supplied, it is
applied to all atoms.
set_velocities(self, velocities)
Set the momenta by specifying the velocities.
translate(self, displacement)
Translate atomic positions.

The displacement argument can be a float an xyz vector or an
nx3 array (where n is the number of atoms).
write(self, filename, format=None, **kwargs)
Write yourself to a file.
Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)
calc
Calculator object.
cell
Attribute for direct manipulation of the unit cell.
constraints
Constraints of the atoms.
numbers
Attribute for direct manipulation of the atomic numbers.
pbc
Attribute for direct manipulation of the periodic boundary condition flags.
positions
Attribute for direct manipulation of the positions.
Data and other attributes defined here:
__hash__ = None

Functions

cos(...)
cos(x)

Return the cosine of x (measured in radians).
default(data, dflt)
Helper function for setting default values.
sin(...)
sin(x)

Return the sine of x (measured in radians).
string2symbols(s)
Convert string to list of chemical symbols.
string2vector(v)
symbols2numbers(symbols)

Data
atomic_masses = array([ 0. , 1.00794, 4.0026 , 6.... nan, nan, nan, nan])
atomic_numbers = {'Ac': 89, 'Ag': 47, 'Al': 13, 'Am': 95, 'Ar': 18, 'As': 33, 'At': 85, 'Au': 79, 'B': 5, 'Ba': 56, ...}
chemical_symbols = ['X', 'H', 'He', 'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Na', 'Mg', 'Al', 'Si', 'P', 'S', 'Cl', 'Ar', 'K', ...]

seminar/atoms_object.txt · 最終更新: 2020/08/18 13:39 by kimi