The Atoms object¶
Atoms object is a collection of atoms. Here
is how to define a CO molecule:
from ase import Atoms d = 1.1 co = Atoms('CO', positions=[(0, 0, 0), (0, 0, d)])
Here, the first argument specifies the type of the atoms and we used
positions keywords to specify their positions. Other
possible keywords are:
Here is how you could make an infinite gold wire with a bond length of 2.9 Å:
from ase import Atoms d = 2.9 L = 10.0 wire = Atoms('Au', positions=[[0, L / 2, L / 2]], cell=[d, L, L], pbc=[1, 0, 0])
Here, two more optional keyword arguments were used:
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) or six numbers (three legths and three angles in degrees). The default value is [0,0,0] which is the same as [[0,0,0],[0,0,0],[0,0,0]] or [0,0,0,90,90,90] meaning that none of the three lattice vectors are defined.
pbc: 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.
Working with the array methods of Atoms objects¶
Like with a single
Atom the properties of a collection of atoms
can be accessed and changed with get- and set-methods. For example
the positions of the atoms can be addressed as
>>> from ase import Atoms >>> a = Atoms('N3', [(0, 0, 0), (1, 0, 0), (0, 0, 1)]) >>> a.get_positions() array([[ 0., 0., 0.], [ 1., 0., 0.], [ 0., 0., 1.]]) >>> a.set_positions([(2, 0, 0), (0, 2, 2), (2, 2, 0)]) >>> a.get_positions() array([[ 2., 0., 0.], [ 0., 2., 2.], [ 2., 2., 0.]])
Here is the full list of the get/set methods operating on all the
atoms at once. The get methods return an array of quantities, one for
each atom; the set methods take similar arrays.
get_positions() return N * 3 numbers,
get_atomic_numbers() return N integers.
These methods return copies of the internal arrays, it is thus safe to modify the returned arrays.
There are also a number of get/set methods that operate on quantities common to all the atoms or defined for the collection of atoms:
Unit cell and boundary conditions¶
Atoms object holds a unit cell which is a 3x3 matrix as can be
>>> a.get_cell() array([[ 0., 0., 0.], [ 0., 0., 0.], [ 0., 0., 0.]])
The cell can be defined or changed using the
set_cell() method. Changing the unit cell
does per default not move the atoms:
>>> import numpy as np >>> a.set_cell(2 * np.identity(3)) >>> a.get_cell() array([[ 2., 0., 0.], [ 0., 2., 0.], [ 0., 0., 2.]]) >>> a.set_positions([(2, 0, 0), (1, 1, 0), (2, 2, 0)]) >>> a.get_positions() array([[ 2., 0., 0.], [ 1., 1., 0.], [ 2., 2., 0.]])
However if we set
scale_atoms=True the atomic positions are scaled with
the unit cell:
>>> a.set_cell(np.identity(3), scale_atoms=True) >>> a.get_positions() array([[ 1. , 0. , 0. ], [ 0.5, 0.5, 0. ], [ 1. , 1. , 0. ]])
set_pbc() method specifies whether
periodic boundary conditions are to be used in the directions of the
three vectors of the unit cell. A slab calculation with periodic
boundary conditions in x and y directions and free boundary
conditions in the z direction is obtained through
>>> a.set_pbc((True, True, False))
>>> a.pbc = (True, True, False)
It is also possible to work directly with the attributes
we change the position of the 2nd atom (which has count number 1
because Python starts counting at zero) and the type of the first
>>> a.positions *= 2 >>> a.positions = (1, 1, 0) >>> a.get_positions() array([[ 2., 0., 0.], [ 1., 1., 0.], [ 2., 2., 0.]]) >>> a.positions array([[ 2., 0., 0.], [ 1., 1., 0.], [ 2., 2., 0.]]) >>> a.numbers array([7, 7, 7]) >>> a.numbers = 13 >>> a.get_chemical_symbols() ['Al', 'N', 'N']
Check for periodic boundary conditions:
>>> a.pbc # equivalent to a.get_pbc() array([ True, True, False], dtype=bool) >>> a.pbc.any() True >>> a.pbc = 1 >>> a.pbc array([ True, True, True], dtype=bool)
Hexagonal unit cell:
>>> a.cell = [2.5, 2.5, 15, 90, 90, 120]
Adding a calculator¶
A calculator can be attached to the atoms with the purpose
of calculating energies and forces on the atoms. ASE works with many
A calculator object calc is attached to the atoms like this:
After the calculator has been appropriately setup the energy of the atoms can be obtained through
The term “potential energy” here means for example the total energy of a DFT calculation, which includes both kinetic, electrostatic, and exchange-correlation energy for the electrons. The reason it is called potential energy is that the atoms might also have a kinetic energy (from the moving nuclei) and that is obtained with
In case of a DFT calculator, it is up to the user to check exactly what
get_potential_energy() method returns. For
example it may be the result of a calculation with a finite
temperature smearing of the occupation numbers extrapolated to zero
temperature. More about this can be found for the different
The following methods can only be called if a calculator is present:
Not all of these methods are supported by all calculators.
Note that the
del method can be used with the more powerful numpy-style indexing, as in the second example above. This can be combined with python list comprehension in order to selectively delete atoms within an ASE Atoms object. For example, the below code creates an ethanol molecule and subsequently strips all the hydrogen atoms from it:
from ase.build import molecule atoms = molecule('CH3CH2OH') del atoms[[atom.index for atom in atoms if atom.symbol=='H']]
List of all Methods¶
Atoms(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)¶
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.
- 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
- Initial atomic charges.
- cell: 3x3 matrix or length 3 or 6 vector
- Unit cell vectors. Can also be given as just three numbers for orthorhombic cells, or 6 numbers, where first three are lengths of unit cell vectors, and the other three are angles between them (in degrees), in following order: [len(a), len(b), len(c), angle(b,c), angle(a,c), angle(a,b)]. First vector will lie in x-direction, second in xy-plane, and the third one in z-positive subspace. Default value: [0, 0, 0].
- 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
- adsorbate_info: Information about special adsorption sites
Items in the info attribute survives copy and slicing and can be stored in and retrieved from trajectory files given that the key is a string, the value is JSON-compatible 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.
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))])
>>> a = 4.05 # Gold lattice constant >>> b = a / 2 >>> fcc = Atoms('Au', ... cell=[(0, b, b), (b, 0, b), (b, b, 0)], ... pbc=True)
>>> d = 0.9 # H-H distance >>> h = Atoms('H', positions=[(0, 0, 0)], ... cell=(d, 0, 0), ... pbc=(1, 0, 0))
Return the adsorbate information set by one of the surface builder functions. This function is only supplied in order to give a warning if this attribute (atoms.adsorbate_info) is asked for. The dictionary with adsorbate information has been moved to the info dictionary, i.e. atoms.info[‘adsorbate_info’].
Append atom to end.
Attribute for direct manipulation of the unit cell.
center(vacuum=None, axis=(0, 1, 2), about=None)¶
Center atoms in unit cell.
Centers the atoms in the unit cell, so there is the same amount of vacuum on all sides.
- vacuum: float (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: int or sequence of ints
- Axis or axes to act on. Default: Act on all axes.
- about: float or array (default: None)
- If specified, center the atoms about <about>. I.e., about=(0., 0., 0.) (or just “about=0.”, interpreted identically), to center about the origin.
Constraints of the atoms.
Return a copy.
Modify atoms interactively through ASE’s GUI 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 GUI. To circumvent, please set matplotlib.use(‘gtk’) before calling this method.
euler_rotate(phi=0.0, theta=0.0, psi=0.0, center=(0, 0, 0))¶
Rotate atoms via Euler angles (in degrees).
See e.g http://mathworld.wolfram.com/EulerAngles.html for explanation.
- 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.
Extend atoms object by appending atoms from other.
Return distances of all of the atoms with all of the atoms.
Use mic=True to use the Minimum Image Convention.
get_angle(a1, a2=None, a3=None, mic=False)¶
Get angle formed by three atoms.
calculate angle in degrees between the vectors a2->a1 and a2->a3.
Use mic=True to use the Minimum Image Convention and calculate the angle across periodic boundaries.
Get total angular momentum with respect to the center of mass.
Get an array.
Returns a copy unless the optional argument copy is false.
Get integer array of atomic numbers.
Get currently attached calculator object.
Get the three unit cell vectors as a 3x3 ndarray.
Get unit cell parameters. Sequence of 6 numbers.
First three are unit cell vector lengths and second three are angles between them:
[len(a), len(b), len(c), angle(b,c), angle(a,c), angle(a,b)]
Get the unit cell displacement vectors.
Get the center of mass.
If scaled=True the center of mass in scaled coordinates is returned.
Get calculated charges.
Get the chemial formula as a string based on the chemical symbols.
- mode: str
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.
‘metal’: The list of checmical symbols (alphabetical metals, and alphabetical non-metals)
Get list of chemical symbol strings.
get_dihedral(a1, a2=None, a3=None, a4=None, mic=False)¶
Calculate dihedral angle.
Calculate dihedral angle (in degrees) between the vectors a1->a2 and a3->a4.
Use mic=True to use the Minimum Image Convention and calculate the angle across periodic boundaries.
Calculate the electric dipole moment for the atoms object.
Only available for calculators which has a get_dipole_moment() method.
get_distance(a0, a1, mic=False, vector=False)¶
Return distance between two atoms.
Use mic=True to use the Minimum Image Convention. vector=True gives the distance vector (from a0 to a1).
get_distances(a, indices, mic=False, vector=False)¶
Return distances of atom No.i with a list of atoms.
Use mic=True to use the Minimum Image Convention. vector=True gives the distance vector (from a to self[indices]).
Calculate atomic forces.
Ask the attached calculator to calculate the forces and apply constraints. Use apply_constraint=False to get the raw forces.
For molecular dynamics (md=True) we don’t apply the constraint to the forces but to the momenta.
Get array of initial charges.
Get array of initial magnetic moments.
Get the kinetic energy.
Get calculated total magnetic moment.
Get calculated local magnetic moments.
Get array of masses.
Get array of momenta.
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.
Returns the global number of atoms in a distributed-atoms parallel simulation.
DO NOT USE UNLESS YOU KNOW WHAT YOU ARE DOING!
Equivalent to len(atoms) in the standard ASE Atoms class. You should normally use len(atoms) instead. This function’s only purpose is to make compatibility between ASE and Asap easier to maintain by having a few places in ASE use this function instead. It is typically only when counting the global number of degrees of freedom or in similar situations.
Get periodic boundary condition flags.
Get array of positions. If wrap==True, wraps atoms back into unit cell.
Calculate the potential energies of all the atoms.
Only available with calculators supporting per-atom energies (e.g. classical potentials).
Calculate potential energy.
Ask the attached calculator to calculate the potential energy and apply constraints. Use apply_constraint=False to get the raw forces.
When supported by the calculator, either the energy extrapolated to zero Kelvin or the energy consistent with the forces (the free energy) can be returned.
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 positions relative to unit cell.
If wrap is True, 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.
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.
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 integer array of tags.
Get the temperature in Kelvin.
Get the total energy - potential plus kinetic energy.
Get array of velocities.
Get volume of unit cell.
Check for existence of array.
name must be one of: ‘tags’, ‘momenta’, ‘masses’, ‘initial_magmoms’, ‘initial_charges’.
new_array(name, a, dtype=None, shape=None)¶
Add new array.
If shape is not None, the shape of a will be checked.
Number of (non-zero) lattice vectors.
Attribute for direct manipulation of the atomic numbers.
Attribute for direct manipulation of the periodic boundary condition flags.
Remove and return atom at index i (default last).
Attribute for direct manipulation of the positions.
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!
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(a, v=None, center=(0, 0, 0), rotate_cell=False)¶
Rotate atoms based on a vector and an angle, or two vectors.
- a = None:
- Angle that the atoms is rotated around the vecor ‘v’. ‘a’ can also be a vector and then ‘a’ is rotated into ‘v’.
- Vector to rotate the atoms around. Vectors can be given as strings: ‘x’, ‘-x’, ‘y’, … .
- 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.
Rotate 90 degrees around the z-axis, so that the x-axis is rotated into the y-axis:
>>> from math import pi >>> atoms = Atoms() >>> atoms.rotate(90, 'z') >>> atoms.rotate(90, (0, 0, 1)) >>> atoms.rotate(-90, '-z') >>> atoms.rotate('x', 'y')
rotate_dihedral(a1, a2=None, a3=None, a4=None, angle=None, mask=None)¶
Rotate dihedral angle.
Complementing the two routines above: rotate a group by a predefined dihedral angle, starting from its current configuration
set_angle(a1, a2=None, a3=None, angle=None, mask=None)¶
Set angle (in degrees) formed by three atoms.
Sets the angle between vectors a2->a1 and a2->a3.
Same usage as in set_dihedral().
set_array(name, a, dtype=None, shape=None)¶
If shape is not None, the shape of a will be checked. If a is None, then the array is deleted.
Set atomic numbers.
Attach calculator object.
Set unit cell vectors.
- cell: 3x3 matrix or length 3 or 6 vector
- Unit cell. A 3x3 matrix (the three unit cell vectors) or just three numbers for an orthorhombic cell. Another option is 6 numbers, which describes unit cell with lengths of unit cell vectors and with angles between them (in degrees), in following order: [len(a), len(b), len(c), angle(b,c), angle(a,c), angle(a,b)]. First vector will lie in x-direction, second in xy-plane, and the third one in z-positive subspace.
- scale_atoms: bool
- Fix atomic positions or move atoms with the unit cell? Default behavior is to not move the atoms (scale_atoms=False).
Two equivalent ways to define an orthorhombic cell:
>>> atoms = Atoms('He') >>> a, b, c = 7, 7.5, 8 >>> atoms.set_cell([a, b, c]) >>> atoms.set_cell([(a, 0, 0), (0, b, 0), (0, 0, c)])
FCC unit cell:
>>> atoms.set_cell([(0, b, b), (b, 0, b), (b, b, 0)])
Hexagonal unit cell:
>>> atoms.set_cell([a, a, c, 90, 90, 120])
Rhombohedral unit cell:
>>> alpha = 77 >>> atoms.set_cell([a, a, a, alpha, alpha, alpha])
Set the unit cell displacement vectors.
Set chemical symbols.
Apply one or more constrains.
The constraint argument must be one constraint object or a list of constraint objects.
set_dihedral(a1, a2=None, a3=None, a4=None, angle=None, mask=None, indices=None)¶
Set the dihedral angle (degrees) between vectors a1->a2 and a3->a4 by changing the atom indexed by a4 if mask is not None, all the atoms described in mask (read: the entire subgroup) are moved. Alternatively to the mask, the indices of the atoms to be rotated can be supplied.
example: the following defines a very crude ethane-like molecule and twists one half of it by 30 degrees.
>>> from math import pi >>> atoms = Atoms('HHCCHH', [[-1, 1, 0], [-1, -1, 0], [0, 0, 0], ... [1, 0, 0], [2, 1, 0], [2, -1, 0]]) >>> atoms.set_dihedral(1, 2, 3, 4, 210, mask=[0, 0, 0, 1, 1, 1])
set_distance(a0, a1, distance, fix=0.5, mic=False)¶
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 the initial charges.
Set the initial magnetic moments.
Use either one or three numbers for every atom (collinear or non-collinear spins).
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 periodic boundary condition flags.
Set positions, honoring any constraints. To ignore constraints, use apply_constraint=False.
Set positions relative to unit cell.
Set tags for all atoms. If only one tag is supplied, it is applied to all atoms.
Set the momenta by specifying the velocities.
Translate atomic positions.
The displacement argument can be a float an xyz vector or an nx3 array (where n is the number of atoms).
wrap(center=(0.5, 0.5, 0.5), pbc=None, eps=1e-07)¶
Wrap positions to unit cell.
- center: three float
- The positons in fractional coordinates that the new positions will be nearest possible to.
- pbc: one or 3 bool
- For each axis in the unit cell decides whether the positions will be moved along this axis. By default, the boundary conditions of the Atoms object will be used.
- eps: float
- Small number to prevent slightly negative coordinates from being wrapped.
See also the
>>> a = Atoms('H', ... [[-0.1, 1.01, -0.5]], ... cell=[[1, 0, 0], [0, 1, 0], [0, 0, 4]], ... pbc=[1, 1, 0]) >>> a.wrap() >>> a.positions array([[ 0.9 , 0.01, -0.5 ]])
write(filename, format=None, **kwargs)¶
Write atoms object to a file.
see ase.io.write for formats. kwargs are passed to ase.io.write.