Source code for ase.atoms

# Copyright 2008, 2009 CAMd
# (see accompanying license files for details).

"""Definition of the Atoms class.

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

import copy
import numbers
import warnings
from math import cos, sin, pi

import numpy as np

import ase.units as units
from ase.atom import Atom
from ase.cell import Cell
from ase.constraints import FixConstraint, FixBondLengths, FixLinearTriatomic
from ase.data import atomic_masses, atomic_masses_common
from ase.utils import basestring
from ase.geometry import wrap_positions, find_mic, get_angles, get_distances
from ase.symbols import Symbols, symbols2numbers


[docs]class Atoms(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 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. 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 >>> h = Atoms('H', positions=[(0, 0, 0)], ... cell=(d, 0, 0), ... pbc=(1, 0, 0)) """ ase_objtype = 'atoms' # For JSONability def __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): self._cellobj = Cell.new() atoms = None if hasattr(symbols, 'get_positions'): atoms = symbols symbols = None elif (isinstance(symbols, (list, tuple)) and len(symbols) > 0 and isinstance(symbols[0], Atom)): # Get data from a list or tuple of Atom objects: data = [[atom.get_raw(name) for atom in symbols] for name in ['position', 'number', 'tag', 'momentum', 'mass', 'magmom', 'charge']] atoms = self.__class__(None, *data) symbols = None if atoms is not None: # Get data from another Atoms object: if scaled_positions is not None: raise NotImplementedError if symbols is None and numbers is None: numbers = atoms.get_atomic_numbers() if positions is None: positions = atoms.get_positions() if tags is None and atoms.has('tags'): tags = atoms.get_tags() if momenta is None and atoms.has('momenta'): momenta = atoms.get_momenta() if magmoms is None and atoms.has('initial_magmoms'): magmoms = atoms.get_initial_magnetic_moments() if masses is None and atoms.has('masses'): masses = atoms.get_masses() if charges is None and atoms.has('initial_charges'): charges = atoms.get_initial_charges() if cell is None: cell = atoms.get_cell() if celldisp is None: celldisp = atoms.get_celldisp() if pbc is None: pbc = atoms.get_pbc() if constraint is None: constraint = [c.copy() for c in atoms.constraints] if calculator is None: calculator = atoms.get_calculator() if info is None: info = copy.deepcopy(atoms.info) self.arrays = {} if symbols is None: if numbers is None: if positions is not None: natoms = len(positions) elif scaled_positions is not None: natoms = len(scaled_positions) else: natoms = 0 numbers = np.zeros(natoms, int) self.new_array('numbers', numbers, int) else: if numbers is not None: raise ValueError( 'Use only one of "symbols" and "numbers".') else: self.new_array('numbers', symbols2numbers(symbols), int) if cell is None: cell = np.zeros((3, 3)) self.set_cell(cell) if celldisp is None: celldisp = np.zeros(shape=(3, 1)) self.set_celldisp(celldisp) if positions is None: if scaled_positions is None: positions = np.zeros((len(self.arrays['numbers']), 3)) else: assert self.number_of_lattice_vectors == 3 positions = np.dot(scaled_positions, self.cell) else: if scaled_positions is not None: raise RuntimeError('Both scaled and cartesian positions set!') self.new_array('positions', positions, float, (3,)) self.set_constraint(constraint) self.set_tags(default(tags, 0)) self.set_masses(default(masses, None)) self.set_initial_magnetic_moments(default(magmoms, 0.0)) self.set_initial_charges(default(charges, 0.0)) if pbc is None: pbc = False self.set_pbc(pbc) self.set_momenta(default(momenta, (0.0, 0.0, 0.0)), apply_constraint=False) if info is None: self.info = {} else: self.info = dict(info) self.set_calculator(calculator) @property def symbols(self): """Get chemical symbols as a :class:`ase.symbols.Symbols` object. The object works like ``atoms.numbers`` except its values are strings. It supports in-place editing.""" return Symbols(self.numbers) @symbols.setter def symbols(self, obj): new_symbols = Symbols.fromsymbols(obj) self.numbers[:] = new_symbols.numbers
[docs] def set_calculator(self, calc=None): """Attach calculator object.""" self._calc = calc if hasattr(calc, 'set_atoms'): calc.set_atoms(self)
[docs] def get_calculator(self): """Get currently attached calculator object.""" return self._calc
def _del_calculator(self): self._calc = None calc = property(get_calculator, set_calculator, _del_calculator, doc='Calculator object.') @property def number_of_lattice_vectors(self): """Number of (non-zero) lattice vectors.""" return self.cell.rank
[docs] def set_constraint(self, constraint=None): """Apply one or more constrains. The *constraint* argument must be one constraint object or a list of constraint objects.""" if constraint is None: self._constraints = [] else: if isinstance(constraint, list): self._constraints = constraint elif isinstance(constraint, tuple): self._constraints = list(constraint) else: self._constraints = [constraint]
def _get_constraints(self): return self._constraints def _del_constraints(self): self._constraints = [] constraints = property(_get_constraints, set_constraint, _del_constraints, 'Constraints of the atoms.')
[docs] def set_cell(self, cell, scale_atoms=False, apply_constraint=True): """Set unit cell vectors. Parameters: 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). Examples: 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]) """ # Override pbcs if and only if given a Cell object: cell = Cell.new(cell) # XXX not working well during initialize due to missing _constraints if apply_constraint and hasattr(self, '_constraints'): for constraint in self.constraints: if hasattr(constraint, 'adjust_cell'): constraint.adjust_cell(self, cell) if scale_atoms: M = np.linalg.solve(self.cell.complete(), cell.complete()) self.positions[:] = np.dot(self.positions, M) self.cell[:] = cell
[docs] def set_celldisp(self, celldisp): """Set the unit cell displacement vectors.""" celldisp = np.array(celldisp, float) self._celldisp = celldisp
[docs] def get_celldisp(self): """Get the unit cell displacement vectors.""" return self._celldisp.copy()
[docs] def get_cell(self, complete=False): """Get the three unit cell vectors as a `class`:ase.cell.Cell` object. The Cell object resembles a 3x3 ndarray, and cell[i, j] is the jth Cartesian coordinate of the ith cell vector.""" if complete: cell = self.cell.complete() else: cell = self.cell.copy() return cell
[docs] def get_cell_lengths_and_angles(self): """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)] in degrees. """ return self.cell.cellpar()
[docs] def 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.""" return self.cell.reciprocal()
[docs] def set_pbc(self, pbc): """Set periodic boundary condition flags.""" self.cell._pbc[:] = pbc
[docs] def get_pbc(self): """Get periodic boundary condition flags.""" return self.pbc.copy()
[docs] def new_array(self, name, a, dtype=None, shape=None): """Add new array. If *shape* is not *None*, the shape of *a* will be checked.""" if dtype is not None: a = np.array(a, dtype, order='C') if len(a) == 0 and shape is not None: a.shape = (-1,) + shape else: if not a.flags['C_CONTIGUOUS']: a = np.ascontiguousarray(a) else: a = a.copy() if name in self.arrays: raise RuntimeError('Array {} already present'.format(name)) for b in self.arrays.values(): if len(a) != len(b): raise ValueError('Array "%s" has wrong length: %d != %d.' % (name, len(a), len(b))) break if shape is not None and a.shape[1:] != shape: raise ValueError('Array "%s" has wrong shape %s != %s.' % (a.name, a.shape, (a.shape[0:1] + shape))) self.arrays[name] = a
[docs] def get_array(self, name, copy=True): """Get an array. Returns a copy unless the optional argument copy is false. """ if copy: return self.arrays[name].copy() else: return self.arrays[name]
[docs] def 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.""" b = self.arrays.get(name) if b is None: if a is not None: self.new_array(name, a, dtype, shape) else: if a is None: del self.arrays[name] else: a = np.asarray(a) if a.shape != b.shape: raise ValueError('Array "%s" has wrong shape %s != %s.' % (name, a.shape, b.shape)) b[:] = a
[docs] def has(self, name): """Check for existence of array. name must be one of: 'tags', 'momenta', 'masses', 'initial_magmoms', 'initial_charges'.""" # XXX extend has to calculator properties return name in self.arrays
[docs] def set_atomic_numbers(self, numbers): """Set atomic numbers.""" self.set_array('numbers', numbers, int, ())
[docs] def get_atomic_numbers(self): """Get integer array of atomic numbers.""" return self.arrays['numbers'].copy()
[docs] def get_chemical_symbols(self): """Get list of chemical symbol strings. Equivalent to ``list(atoms.symbols)``.""" return list(self.symbols)
[docs] def set_chemical_symbols(self, symbols): """Set chemical symbols.""" self.set_array('numbers', symbols2numbers(symbols), int, ())
[docs] def get_chemical_formula(self, mode='hill', empirical=False): """Get the chemical formula as a string based on the chemical symbols. Parameters: mode: str There are four different modes available: 'all': The list of chemical symbols are contracted to a 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 chemical symbols (alphabetical metals, and alphabetical non-metals) empirical, bool (optional, default=False) Divide the symbol counts by their greatest common divisor to yield an empirical formula. Only for mode `metal` and `hill`. """ return self.symbols.get_chemical_formula(mode, empirical)
[docs] def set_tags(self, tags): """Set tags for all atoms. If only one tag is supplied, it is applied to all atoms.""" if isinstance(tags, int): tags = [tags] * len(self) self.set_array('tags', tags, int, ())
[docs] def get_tags(self): """Get integer array of tags.""" if 'tags' in self.arrays: return self.arrays['tags'].copy() else: return np.zeros(len(self), int)
[docs] def set_momenta(self, momenta, apply_constraint=True): """Set momenta.""" if (apply_constraint and len(self.constraints) > 0 and momenta is not None): momenta = np.array(momenta) # modify a copy for constraint in self.constraints: if hasattr(constraint, 'adjust_momenta'): constraint.adjust_momenta(self, momenta) self.set_array('momenta', momenta, float, (3,))
[docs] def set_velocities(self, velocities): """Set the momenta by specifying the velocities.""" self.set_momenta(self.get_masses()[:, np.newaxis] * velocities)
[docs] def get_momenta(self): """Get array of momenta.""" if 'momenta' in self.arrays: return self.arrays['momenta'].copy() else: return np.zeros((len(self), 3))
[docs] def set_masses(self, masses='defaults'): """Set atomic masses in atomic mass units. 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.""" if isinstance(masses, basestring): if masses == 'defaults': masses = atomic_masses[self.arrays['numbers']] elif masses == 'most_common': masses = atomic_masses_common[self.arrays['numbers']] elif isinstance(masses, (list, tuple)): newmasses = [] for m, Z in zip(masses, self.arrays['numbers']): if m is None: newmasses.append(atomic_masses[Z]) else: newmasses.append(m) masses = newmasses self.set_array('masses', masses, float, ())
[docs] def get_masses(self): """Get array of masses in atomic mass units.""" if 'masses' in self.arrays: return self.arrays['masses'].copy() else: return atomic_masses[self.arrays['numbers']]
[docs] def 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).""" if magmoms is None: self.set_array('initial_magmoms', None) else: magmoms = np.asarray(magmoms) self.set_array('initial_magmoms', magmoms, float, magmoms.shape[1:])
[docs] def get_initial_magnetic_moments(self): """Get array of initial magnetic moments.""" if 'initial_magmoms' in self.arrays: return self.arrays['initial_magmoms'].copy() else: return np.zeros(len(self))
[docs] def get_magnetic_moments(self): """Get calculated local magnetic moments.""" if self._calc is None: raise RuntimeError('Atoms object has no calculator.') return self._calc.get_magnetic_moments(self)
[docs] def get_magnetic_moment(self): """Get calculated total magnetic moment.""" if self._calc is None: raise RuntimeError('Atoms object has no calculator.') return self._calc.get_magnetic_moment(self)
[docs] def set_initial_charges(self, charges=None): """Set the initial charges.""" if charges is None: self.set_array('initial_charges', None) else: self.set_array('initial_charges', charges, float, ())
[docs] def get_initial_charges(self): """Get array of initial charges.""" if 'initial_charges' in self.arrays: return self.arrays['initial_charges'].copy() else: return np.zeros(len(self))
[docs] def get_charges(self): """Get calculated charges.""" if self._calc is None: raise RuntimeError('Atoms object has no calculator.') try: return self._calc.get_charges(self) except AttributeError: from ase.calculators.calculator import PropertyNotImplementedError raise PropertyNotImplementedError
[docs] def set_positions(self, newpositions, apply_constraint=True): """Set positions, honoring any constraints. To ignore constraints, use *apply_constraint=False*.""" if self.constraints and apply_constraint: newpositions = np.array(newpositions, float) for constraint in self.constraints: constraint.adjust_positions(self, newpositions) self.set_array('positions', newpositions, shape=(3,))
[docs] def get_positions(self, wrap=False): """Get array of positions. If wrap==True, wraps atoms back into unit cell. """ if wrap: scaled = self.get_scaled_positions() return np.dot(scaled, self.cell) else: return self.arrays['positions'].copy()
[docs] def get_potential_energy(self, force_consistent=False, apply_constraint=True): """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. """ if self._calc is None: raise RuntimeError('Atoms object has no calculator.') if force_consistent: energy = self._calc.get_potential_energy( self, force_consistent=force_consistent) else: energy = self._calc.get_potential_energy(self) if apply_constraint: for constraint in self.constraints: if hasattr(constraint, 'adjust_potential_energy'): energy += constraint.adjust_potential_energy(self) return energy
[docs] def get_potential_energies(self): """Calculate the potential energies of all the atoms. Only available with calculators supporting per-atom energies (e.g. classical potentials). """ if self._calc is None: raise RuntimeError('Atoms object has no calculator.') return self._calc.get_potential_energies(self)
[docs] def get_kinetic_energy(self): """Get the kinetic energy.""" momenta = self.arrays.get('momenta') if momenta is None: return 0.0 return 0.5 * np.vdot(momenta, self.get_velocities())
[docs] def get_velocities(self): """Get array of velocities.""" momenta = self.arrays.get('momenta') if momenta is None: return None m = self.arrays.get('masses') if m is None: m = atomic_masses[self.arrays['numbers']] return momenta / m.reshape(-1, 1)
[docs] def get_total_energy(self): """Get the total energy - potential plus kinetic energy.""" return self.get_potential_energy() + self.get_kinetic_energy()
[docs] def get_forces(self, apply_constraint=True, md=False): """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. When holonomic constraints for rigid linear triatomic molecules are present, ask the constraints to redistribute the forces within each triple defined in the constraints (required for molecular dynamics with this type of constraints).""" if self._calc is None: raise RuntimeError('Atoms object has no calculator.') forces = self._calc.get_forces(self) if apply_constraint: # We need a special md flag here because for MD we want # to skip real constraints but include special "constraints" # Like Hookean. for constraint in self.constraints: if md and hasattr(constraint, 'redistribute_forces_md'): constraint.redistribute_forces_md(self, forces) if not md or hasattr(constraint, 'adjust_potential_energy'): constraint.adjust_forces(self, forces) return forces
[docs] def get_stress(self, voigt=True, apply_constraint=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. """ if self._calc is None: raise RuntimeError('Atoms object has no calculator.') stress = self._calc.get_stress(self) shape = stress.shape if shape == (3, 3): # if Voigt form is not wanted, return rightaway if apply_constraint is False # If the user wants to apply constraints to the stress transform the Voigt form and # apply the constraint if not voigt and (not apply_constraint or not self.constraints): return stress warnings.warn('Converting 3x3 stress tensor from %s ' % self._calc.__class__.__name__ + 'calculator to the required Voigt form.') stress = np.array([stress[0, 0], stress[1, 1], stress[2, 2], stress[1, 2], stress[0, 2], stress[0, 1]]) else: assert shape == (6,) if apply_constraint: for constraint in self.constraints: if hasattr(constraint, 'adjust_stress'): constraint.adjust_stress(self, stress) if voigt: return stress else: xx, yy, zz, yz, xz, xy = stress return np.array([(xx, xy, xz), (xy, yy, yz), (xz, yz, zz)])
[docs] def 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. """ if self._calc is None: raise RuntimeError('Atoms object has no calculator.') return self._calc.get_stresses(self)
[docs] def get_dipole_moment(self): """Calculate the electric dipole moment for the atoms object. Only available for calculators which has a get_dipole_moment() method.""" if self._calc is None: raise RuntimeError('Atoms object has no calculator.') return self._calc.get_dipole_moment(self)
[docs] def copy(self): """Return a copy.""" atoms = self.__class__(cell=self.cell, pbc=self.pbc, info=self.info, celldisp=self._celldisp.copy()) atoms.arrays = {} for name, a in self.arrays.items(): atoms.arrays[name] = a.copy() atoms.constraints = copy.deepcopy(self.constraints) return atoms
[docs] def todict(self): """For basic JSON (non-database) support.""" d = dict(self.arrays) d['cell'] = np.asarray(self.cell) d['pbc'] = self.pbc if self._celldisp.any(): d['celldisp'] = self._celldisp if self.constraints: d['constraints'] = self.constraints if self.info: d['info'] = self.info # Calculator... trouble. return d
[docs] @classmethod def fromdict(cls, dct): """Rebuild atoms object from dictionary representation (todict).""" dct = dct.copy() kw = {} for name in ['numbers', 'positions', 'cell', 'pbc']: kw[name] = dct.pop(name) constraints = dct.pop('constraints', None) if constraints: from ase.constraints import dict2constraint constraints = [dict2constraint(d) for d in constraints] atoms = cls(constraint=constraints, celldisp=dct.pop('celldisp', None), info=dct.pop('info', None), **kw) natoms = len(atoms) # Some arrays are named differently from the atoms __init__ keywords. # Also, there may be custom arrays. Hence we set them directly: for name, arr in dct.items(): assert len(arr) == natoms, name assert isinstance(arr, np.ndarray) atoms.arrays[name] = arr return atoms
def __len__(self): return len(self.arrays['positions'])
[docs] def get_number_of_atoms(self): """Deprecated, please do not use. You probably want len(atoms). Or if your atoms are distributed, use (and see) get_global_number_of_atoms().""" import warnings warnings.warn('Use get_global_number_of_atoms() instead', np.VisibleDeprecationWarning) return len(self)
[docs] def get_global_number_of_atoms(self): """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. """ return len(self)
def __repr__(self): tokens = [] N = len(self) if N <= 60: symbols = self.get_chemical_formula('reduce') else: symbols = self.get_chemical_formula('hill') tokens.append("symbols='{0}'".format(symbols)) if self.pbc.any() and not self.pbc.all(): tokens.append('pbc={0}'.format(self.pbc.tolist())) else: tokens.append('pbc={0}'.format(self.pbc[0])) cell = self.cell if cell: if cell.orthorhombic: cell = cell.lengths().tolist() else: cell = cell.tolist() tokens.append('cell={0}'.format(cell)) for name in sorted(self.arrays): if name in ['numbers', 'positions']: continue tokens.append('{0}=...'.format(name)) if self.constraints: if len(self.constraints) == 1: constraint = self.constraints[0] else: constraint = self.constraints tokens.append('constraint={0}'.format(repr(constraint))) if self._calc is not None: tokens.append('calculator={0}(...)' .format(self._calc.__class__.__name__)) return '{0}({1})'.format(self.__class__.__name__, ', '.join(tokens)) def __add__(self, other): atoms = self.copy() atoms += other return atoms
[docs] def extend(self, other): """Extend atoms object by appending atoms from *other*.""" if isinstance(other, Atom): other = self.__class__([other]) n1 = len(self) n2 = len(other) for name, a1 in self.arrays.items(): a = np.zeros((n1 + n2,) + a1.shape[1:], a1.dtype) a[:n1] = a1 if name == 'masses': a2 = other.get_masses() else: a2 = other.arrays.get(name) if a2 is not None: a[n1:] = a2 self.arrays[name] = a for name, a2 in other.arrays.items(): if name in self.arrays: continue a = np.empty((n1 + n2,) + a2.shape[1:], a2.dtype) a[n1:] = a2 if name == 'masses': a[:n1] = self.get_masses()[:n1] else: a[:n1] = 0 self.set_array(name, a) return self
__iadd__ = extend
[docs] def append(self, atom): """Append atom to end.""" self.extend(self.__class__([atom]))
def __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. """ if isinstance(i, numbers.Integral): natoms = len(self) if i < -natoms or i >= natoms: raise IndexError('Index out of range.') return Atom(atoms=self, index=i) elif not isinstance(i, slice): i = np.array(i) # if i is a mask if i.dtype == bool: try: i = np.arange(len(self))[i] except IndexError: raise IndexError('length of item mask ' 'mismatches that of {0} ' 'object'.format(self.__class__.__name__)) import copy conadd = [] # Constraints need to be deepcopied, but only the relevant ones. for con in copy.deepcopy(self.constraints): if isinstance(con, (FixConstraint, FixBondLengths, FixLinearTriatomic)): try: con.index_shuffle(self, i) conadd.append(con) except IndexError: pass atoms = self.__class__(cell=self.cell, pbc=self.pbc, info=self.info, # should be communicated to the slice as well celldisp=self._celldisp) # TODO: Do we need to shuffle indices in adsorbate_info too? atoms.arrays = {} for name, a in self.arrays.items(): atoms.arrays[name] = a[i].copy() atoms.constraints = conadd return atoms def __delitem__(self, i): from ase.constraints import FixAtoms for c in self._constraints: if not isinstance(c, FixAtoms): raise RuntimeError('Remove constraint using set_constraint() ' 'before deleting atoms.') if isinstance(i, list) and len(i) > 0: # Make sure a list of booleans will work correctly and not be # interpreted at 0 and 1 indices. i = np.array(i) if len(self._constraints) > 0: n = len(self) i = np.arange(n)[i] if isinstance(i, int): i = [i] constraints = [] for c in self._constraints: c = c.delete_atoms(i, n) if c is not None: constraints.append(c) self.constraints = constraints mask = np.ones(len(self), bool) mask[i] = False for name, a in self.arrays.items(): self.arrays[name] = a[mask]
[docs] def pop(self, i=-1): """Remove and return atom at index *i* (default last).""" atom = self[i] atom.cut_reference_to_atoms() del self[i] return atom
def __imul__(self, m): """In-place repeat of atoms.""" if isinstance(m, int): m = (m, m, m) for x, vec in zip(m, self.cell): if x != 1 and not vec.any(): raise ValueError('Cannot repeat along undefined lattice ' 'vector') M = np.product(m) n = len(self) for name, a in self.arrays.items(): self.arrays[name] = np.tile(a, (M,) + (1,) * (len(a.shape) - 1)) positions = self.arrays['positions'] i0 = 0 for m0 in range(m[0]): for m1 in range(m[1]): for m2 in range(m[2]): i1 = i0 + n positions[i0:i1] += np.dot((m0, m1, m2), self.cell) i0 = i1 if self.constraints is not None: self.constraints = [c.repeat(m, n) for c in self.constraints] self.cell = np.array([m[c] * self.cell[c] for c in range(3)]) return self
[docs] def 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)*.""" atoms = self.copy() atoms *= rep return atoms
__mul__ = repeat
[docs] def 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).""" self.arrays['positions'] += np.array(displacement)
[docs] def center(self, 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. """ # Find the orientations of the faces of the unit cell cell = self.cell.complete() dirs = np.zeros_like(cell) for i in range(3): dirs[i] = np.cross(cell[i - 1], cell[i - 2]) dirs[i] /= np.sqrt(np.dot(dirs[i], dirs[i])) # normalize if np.dot(dirs[i], cell[i]) < 0.0: dirs[i] *= -1 if isinstance(axis, int): axes = (axis,) else: axes = axis # if vacuum and any(self.pbc[x] for x in axes): # warnings.warn( # 'You are adding vacuum along a periodic direction!') # Now, decide how much each basis vector should be made longer p = self.arrays['positions'] longer = np.zeros(3) shift = np.zeros(3) for i in axes: p0 = np.dot(p, dirs[i]).min() if len(p) else 0 p1 = np.dot(p, dirs[i]).max() if len(p) else 0 height = np.dot(cell[i], dirs[i]) if vacuum is not None: lng = (p1 - p0 + 2 * vacuum) - height else: lng = 0.0 # Do not change unit cell size! top = lng + height - p1 shf = 0.5 * (top - p0) cosphi = np.dot(cell[i], dirs[i]) / np.sqrt(np.dot(cell[i], cell[i])) longer[i] = lng / cosphi shift[i] = shf / cosphi # Now, do it! translation = np.zeros(3) for i in axes: nowlen = np.sqrt(np.dot(cell[i], cell[i])) if vacuum is not None or self.cell[i].any(): self.cell[i] = cell[i] * (1 + longer[i] / nowlen) translation += shift[i] * cell[i] / nowlen self.arrays['positions'] += translation # Optionally, translate to center about a point in space. if about is not None: for vector in self.cell: self.positions -= vector / 2.0 self.positions += about
[docs] def get_center_of_mass(self, scaled=False): """Get the center of mass. If scaled=True the center of mass in scaled coordinates is returned.""" m = self.get_masses() com = np.dot(m, self.arrays['positions']) / m.sum() if scaled: return np.linalg.solve(self.cell.T, com) else: return com
[docs] def 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. """ com = self.get_center_of_mass() positions = self.get_positions() positions -= com # translate center of mass to origin masses = self.get_masses() # Initialize elements of the inertial tensor I11 = I22 = I33 = I12 = I13 = I23 = 0.0 for i in range(len(self)): x, y, z = positions[i] m = masses[i] I11 += m * (y ** 2 + z ** 2) I22 += m * (x ** 2 + z ** 2) I33 += m * (x ** 2 + y ** 2) I12 += -m * x * y I13 += -m * x * z I23 += -m * y * z I = np.array([[I11, I12, I13], [I12, I22, I23], [I13, I23, I33]]) evals, evecs = np.linalg.eigh(I) if vectors: return evals, evecs.transpose() else: return evals
[docs] def get_angular_momentum(self): """Get total angular momentum with respect to the center of mass.""" com = self.get_center_of_mass() positions = self.get_positions() positions -= com # translate center of mass to origin return np.cross(positions, self.get_momenta()).sum(0)
[docs] def rotate(self, a, v=None, center=(0, 0, 0), rotate_cell=False): """Rotate atoms based on a vector and an angle, or two vectors. Parameters: 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'. 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. Examples: Rotate 90 degrees around the z-axis, so that the x-axis is rotated into the y-axis: >>> atoms = Atoms() >>> atoms.rotate(90, 'z') >>> atoms.rotate(90, (0, 0, 1)) >>> atoms.rotate(-90, '-z') >>> atoms.rotate('x', 'y') >>> atoms.rotate((1, 0, 0), (0, 1, 0)) """ if not isinstance(a, (float, int)): # old API maybe? warning = ('Please use new API: ' 'atoms_obj.rotate(a, v) ' 'where v is a vector to rotate around and ' 'a is the angle in degrees.') if isinstance(v, (float, int)): warnings.warn(warning, FutureWarning) a, v = v * 180 / pi, a elif v is None: warnings.warn(warning, FutureWarning) v = a a = None else: assert a is not None a, v = v, a else: assert a is not None norm = np.linalg.norm v = string2vector(v) if a is None: a = norm(v) * 180 / pi # old API normv = norm(v) if normv == 0.0: raise ZeroDivisionError('Cannot rotate: norm(v) == 0') if isinstance(a, (float, int)): a *= pi / 180 v /= normv c = cos(a) s = sin(a) else: v2 = string2vector(a) v /= normv normv2 = np.linalg.norm(v2) if normv2 == 0: raise ZeroDivisionError('Cannot rotate: norm(a) == 0') v2 /= norm(v2) c = np.dot(v, v2) v = np.cross(v, v2) s = norm(v) # In case *v* and *a* are parallel, np.cross(v, v2) vanish # and can't be used as a rotation axis. However, in this # case any rotation axis perpendicular to v2 will do. eps = 1e-7 if s < eps: v = np.cross((0, 0, 1), v2) if norm(v) < eps: v = np.cross((1, 0, 0), v2) assert norm(v) >= eps elif s > 0: v /= s if isinstance(center, basestring): if center.lower() == 'com': center = self.get_center_of_mass() elif center.lower() == 'cop': center = self.get_positions().mean(axis=0) elif center.lower() == 'cou': center = self.get_cell().sum(axis=0) / 2 else: raise ValueError('Cannot interpret center') else: center = np.array(center) p = self.arrays['positions'] - center self.arrays['positions'][:] = (c * p - np.cross(p, s * v) + np.outer(np.dot(p, v), (1.0 - c) * v) + center) if rotate_cell: rotcell = self.get_cell() rotcell[:] = (c * rotcell - np.cross(rotcell, s * v) + np.outer(np.dot(rotcell, v), (1.0 - c) * v)) self.set_cell(rotcell)
def rotate_euler(self, center=(0, 0, 0), phi=0.0, theta=0.0, psi=0.0): warnings.warn( 'Please use this method instead: ' 'euler_rotate(phi=0, theta=0, psi=0, center=(0, 0, 0)) ' 'where the angles are given in degrees', FutureWarning) self.euler_rotate(phi * 180 / pi, theta * 180 / pi, psi * 180 / pi, center)
[docs] def euler_rotate(self, 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. 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. """ if isinstance(center, basestring): if center.lower() == 'com': center = self.get_center_of_mass() elif center.lower() == 'cop': center = self.get_positions().mean(axis=0) elif center.lower() == 'cou': center = self.get_cell().sum(axis=0) / 2 else: raise ValueError('Cannot interpret center') else: center = np.array(center) phi *= pi / 180 theta *= pi / 180 psi *= pi / 180 # First move the molecule to the origin In contrast to MATLAB, # numpy broadcasts the smaller array to the larger row-wise, # so there is no need to play with the Kronecker product. rcoords = self.positions - center # First Euler rotation about z in matrix form D = np.array(((cos(phi), sin(phi), 0.), (-sin(phi), cos(phi), 0.), (0., 0., 1.))) # Second Euler rotation about x: C = np.array(((1., 0., 0.), (0., cos(theta), sin(theta)), (0., -sin(theta), cos(theta)))) # Third Euler rotation, 2nd rotation about z: B = np.array(((cos(psi), sin(psi), 0.), (-sin(psi), cos(psi), 0.), (0., 0., 1.))) # Total Euler rotation A = np.dot(B, np.dot(C, D)) # Do the rotation rcoords = np.dot(A, np.transpose(rcoords)) # Move back to the rotation point self.positions = np.transpose(rcoords) + center
[docs] def get_dihedral(self, 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. """ if a2 is None: # Old way - use radians warnings.warn( 'Please use new API (which will return the angle in degrees): ' 'atoms_obj.get_dihedral(a1,a2,a3,a4)*pi/180 instead of ' 'atoms_obj.get_dihedral([a1,a2,a3,a4])', FutureWarning) assert a3 is None and a4 is None a1, a2, a3, a4 = a1 f = pi / 180 else: f = 1 if any(a is None for a in [a2, a3, a4]): raise ValueError('a2, a3 and a4 must not be None') # vector 1->2, 2->3, 3->4 and their normalized cross products: a = self.positions[a2] - self.positions[a1] b = self.positions[a3] - self.positions[a2] c = self.positions[a4] - self.positions[a3] if mic: a, b, c = find_mic([a, b, c], self.cell, self.pbc)[0] bxa = np.cross(b, a) cxb = np.cross(c, b) bxanorm = np.linalg.norm(bxa) cxbnorm = np.linalg.norm(cxb) if bxanorm == 0 or cxbnorm == 0: raise ZeroDivisionError('Undefined dihedral angle') bxa /= bxanorm cxb /= cxbnorm angle = np.vdot(bxa, cxb) # check for numerical trouble due to finite precision: if angle < -1: angle = -1 if angle > 1: angle = 1 angle = np.arccos(angle) * 180 / pi if np.vdot(bxa, c) > 0: angle = 360 - angle return angle * f
def _masked_rotate(self, center, axis, diff, mask): # do rotation of subgroup by copying it to temporary atoms object # and then rotating that # # recursive object definition might not be the most elegant thing, # more generally useful might be a rotation function with a mask? group = self.__class__() for i in range(len(self)): if mask[i]: group += self[i] group.translate(-center) group.rotate(diff * 180 / pi, axis) group.translate(center) # set positions in original atoms object j = 0 for i in range(len(self)): if mask[i]: self.positions[i] = group[j].position j += 1
[docs] def set_dihedral(self, 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. If both *mask* and *indices* are given, *indices* overwrites *mask*. **Important**: If *mask* or *indices* is given and does not contain *a4*, *a4* will NOT be moved. In most cases you therefore want to include *a4* in *mask*/*indices*. 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]]) >>> atoms.set_dihedral(1, 2, 3, 4, 210, mask=[0, 0, 0, 1, 1, 1]) """ if isinstance(a1, int): if any(a is None for a in [a2, a3, a4, angle]): raise ValueError('a2, a3, a4, and angle must not be None') angle *= pi / 180 else: warnings.warn( 'Please use new API: ' 'atoms_obj.set_dihedral(a1,a2,a3,a4,angle) ' 'where angle is given in degrees', FutureWarning) if angle is None: angle = a2 if mask is None: mask = a3 if indices is None: indices = a4 else: assert a2 is None and a3 is None and a4 is None a1, a2, a3, a4 = a1 # if not provided, set mask to the last atom in the # dihedral description if mask is None and indices is None: mask = np.zeros(len(self)) mask[a4] = 1 elif indices is not None: mask = [index in indices for index in range(len(self))] # compute necessary in dihedral change, from current value current = self.get_dihedral(a1, a2, a3, a4) * pi / 180 diff = angle - current axis = self.positions[a3] - self.positions[a2] center = self.positions[a3] self._masked_rotate(center, axis, diff, mask)
[docs] def rotate_dihedral(self, a1, a2=None, a3=None, a4=None, angle=None, mask=None, indices=None): """Rotate dihedral angle. Same usage as in :meth:`ase.Atoms.set_dihedral`: Rotate a group by a predefined dihedral angle, starting from its current configuration. """ if not isinstance(a1, int): warnings.warn( 'Please use new API: ' 'atoms_obj.rotate_dihedral(a1,a2,a3,a4,angle) ' 'where angle is given in degrees', FutureWarning) if angle is None: angle = a2 if mask is None and indices is None: mask = a3 else: assert a2 is None and a3 is None and a4 is None a1, a2, a3, a4 = a1 if any(a is None for a in [a2, a3, a4, angle]): raise ValueError('a2, a3, a4, and angle must not be None') start = self.get_dihedral(a1, a2, a3, a4) self.set_dihedral(a1, a2, a3, a4, angle + start, mask, indices)
[docs] def get_angle(self, a1, a2, a3, 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. """ return self.get_angles([[a1, a2, a3]], mic=mic)[0]
[docs] def get_angles(self, indices, mic=False): """Get angle formed by three atoms for multiple groupings. calculate angle in degrees between vectors between atoms a2->a1 and a2->a3, where a1, a2, and a3 are in each row of indices. Use mic=True to use the Minimum Image Convention and calculate the angle across periodic boundaries. """ indices = np.array(indices) a1s = self.positions[indices[:, 0]] a2s = self.positions[indices[:, 1]] a3s = self.positions[indices[:, 2]] v12 = a1s - a2s v32 = a3s - a2s cell = None pbc = None if mic: cell = self.cell pbc = self.pbc return get_angles(v12, v32, cell=cell, pbc=pbc)
[docs] def set_angle(self, a1, a2=None, a3=None, angle=None, mask=None, indices=None, add=False): """Set angle (in degrees) formed by three atoms. Sets the angle between vectors *a2*->*a1* and *a2*->*a3*. If *add* is `True`, the angle will be changed by the value given. Same usage as in :meth:`ase.Atoms.set_dihedral`. If *mask* and *indices* are given, *indices* overwrites *mask*. If *mask* and *indices* are not set, only *a3* is moved.""" if not isinstance(a1, int): # old API (uses radians) warnings.warn( 'Please use new API: ' 'atoms_obj.set_angle(a1,a2,a3,angle) ' 'where angle is given in degrees', FutureWarning) if angle is None: angle = a2 if mask is None: mask = a3 a1, a2, a3 = a1 else: assert a2 is None and a3 is None angle *= 180 / pi if any(a is None for a in [a2, a3, angle]): raise ValueError('a2, a3, and angle must not be None') # If not provided, set mask to the last atom in the angle description if mask is None and indices is None: mask = np.zeros(len(self)) mask[a3] = 1 elif indices is not None: mask = [index in indices for index in range(len(self))] if add: diff = angle else: # Compute necessary in angle change, from current value diff = angle - self.get_angle(a1, a2, a3) diff *= pi / 180 # Do rotation of subgroup by copying it to temporary atoms object and # then rotating that v10 = self.positions[a1] - self.positions[a2] v12 = self.positions[a3] - self.positions[a2] v10 /= np.linalg.norm(v10) v12 /= np.linalg.norm(v12) axis = np.cross(v10, v12) center = self.positions[a2] self._masked_rotate(center, axis, diff, mask)
[docs] def rattle(self, stdev=0.001, seed=None, rng=None): """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! """ if seed is not None and rng is not None: raise ValueError('Please do not provide both seed and rng.') if rng is None: if seed is None: seed = 42 rng = np.random.RandomState(seed) positions = self.arrays['positions'] self.set_positions(positions + rng.normal(scale=stdev, size=positions.shape))
[docs] def get_distance(self, 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). """ return self.get_distances(a0, [a1], mic=mic, vector=vector)[0]
[docs] def get_distances(self, 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]). """ R = self.arrays['positions'] p1 = [R[a]] p2 = R[indices] cell = None pbc = None if mic: cell = self.cell pbc = self.pbc D, D_len = get_distances(p1, p2, cell=cell, pbc=pbc) if vector: D.shape = (-1, 3) return D else: D_len.shape = (-1,) return D_len
[docs] def get_all_distances(self, mic=False, vector=False): """Return distances of all of the atoms with all of the atoms. Use mic=True to use the Minimum Image Convention. """ R = self.arrays['positions'] cell = None pbc = None if mic: cell = self.cell pbc = self.pbc D, D_len = get_distances(R, cell=cell, pbc=pbc) if vector: return D else: return D_len
[docs] def set_distance(self, a0, a1, distance, fix=0.5, mic=False, mask=None, indices=None, add=False, factor=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. If *mask* or *indices* are set (*mask* overwrites *indices*), only the atoms defined there are moved (see :meth:`ase.Atoms.set_dihedral`). When *add* is true, the distance is changed by the value given. In combination with *factor* True, the value given is a factor scaling the distance. It is assumed that the atoms in *mask*/*indices* move together with *a1*. If *fix=1*, only *a0* will therefore be moved.""" if a0 % len(self) == a1 % len(self): raise ValueError('a0 and a1 must not be the same') if add: oldDist = self.get_distance(a0, a1, mic=mic) if factor: newDist = oldDist * distance else: newDist = oldDist + distance self.set_distance(a0, a1, newDist, fix=fix, mic=mic, mask=mask, indices=indices, add=False, factor=False) return R = self.arrays['positions'] D = np.array([R[a1] - R[a0]]) if mic: D, D_len = find_mic(D, self.cell, self.pbc) else: D_len = np.array([np.sqrt((D**2).sum())]) x = 1.0 - distance / D_len[0] if mask is None and indices is None: indices = [a0, a1] elif mask: indices = [i for i in range(len(self)) if mask[i]] for i in indices: if i == a0: R[a0] += (x * fix) * D[0] else: R[i] -= (x * (1.0 - fix)) * D[0]
[docs] def get_scaled_positions(self, wrap=True): """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.""" fractional = self.cell.scaled_positions(self.positions) if wrap: for i, periodic in enumerate(self.pbc): if periodic: # Yes, we need to do it twice. # See the scaled_positions.py test. fractional[:, i] %= 1.0 fractional[:, i] %= 1.0 return fractional
[docs] def set_scaled_positions(self, scaled): """Set positions relative to unit cell.""" self.positions[:] = self.cell.cartesian_positions(scaled)
[docs] def wrap(self, center=(0.5, 0.5, 0.5), pbc=None, pretty_translation=False, eps=1e-7): """Wrap positions to unit cell. Parameters: 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. pretty_translation: bool Translates atoms such that fractional coordinates are minimized. eps: float Small number to prevent slightly negative coordinates from being wrapped. See also the :func:`ase.geometry.wrap_positions` function. Example: >>> 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 ]]) """ if pbc is None: pbc = self.pbc self.positions[:] = wrap_positions(self.positions, self.cell, pbc, center, pretty_translation, eps)
[docs] def get_temperature(self): """Get the temperature in Kelvin.""" dof = len(self) * 3 for constraint in self._constraints: dof -= constraint.removed_dof ekin = self.get_kinetic_energy() return 2 * ekin / (dof * units.kB)
def __eq__(self, other): """Check for identity of two atoms objects. Identity means: same positions, atomic numbers, unit cell and periodic boundary conditions.""" if not isinstance(other, Atoms): return False a = self.arrays b = other.arrays return (len(self) == len(other) and (a['positions'] == b['positions']).all() and (a['numbers'] == b['numbers']).all() and (self.cell == other.cell).all() and (self.pbc == other.pbc).all()) def __ne__(self, other): """Check if two atoms objects are not equal. Any differences in positions, atomic numbers, unit cell or periodic boundary condtions make atoms objects not equal. """ eq = self.__eq__(other) if eq is NotImplemented: return eq else: return not eq __hash__ = None
[docs] def get_volume(self): """Get volume of unit cell.""" if self.cell.rank != 3: raise ValueError( 'You have {0} lattice vectors: volume not defined' .format(self.cell.rank)) return self.cell.volume
def _get_positions(self): """Return reference to positions-array for in-place manipulations.""" return self.arrays['positions'] def _set_positions(self, pos): """Set positions directly, bypassing constraints.""" self.arrays['positions'][:] = pos positions = property(_get_positions, _set_positions, doc='Attribute for direct ' + 'manipulation of the positions.') @property def adsorbate_info(self): """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'].""" warnings.warn("The adsorbate_info dictionary has been moved" + " inside the info dictionary, i.e. atoms." + "info['adsorbate_info']", FutureWarning) return self.info['adsorbate_info'] @adsorbate_info.setter def adsorbate_info(self, dct): warnings.warn("The adsorbate_info dictionary has been moved" + " inside the info dictionary, i.e. atoms." + "info['adsorbate_info']", FutureWarning) self.info['adsorbate_info'] = dct def _get_atomic_numbers(self): """Return reference to atomic numbers for in-place manipulations.""" return self.arrays['numbers'] numbers = property(_get_atomic_numbers, set_atomic_numbers, doc='Attribute for direct ' + 'manipulation of the atomic numbers.') def _get_cell(self): """Return reference to unit cell for in-place manipulations.""" return self._cellobj cell = property(_get_cell, set_cell, doc='Attribute for direct ' + 'manipulation of the unit :class:`ase.cell.Cell`.') def _get_pbc(self): """Return reference to pbc-flags for in-place manipulations.""" # XXX deprecating cell.pbc return self.cell._pbc pbc = property(_get_pbc, set_pbc, doc='Attribute for direct manipulation ' + 'of the periodic boundary condition flags.')
[docs] def write(self, filename, format=None, **kwargs): """Write atoms object to a file. see ase.io.write for formats. kwargs are passed to ase.io.write. """ from ase.io import write write(filename, self, format, **kwargs)
def iterimages(self): yield self
[docs] def edit(self): """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. """ from ase.gui.images import Images from ase.gui.gui import GUI images = Images([self]) gui = GUI(images) gui.run()
def string2vector(v): if isinstance(v, basestring): if v[0] == '-': return -string2vector(v[1:]) w = np.zeros(3) w['xyz'.index(v)] = 1.0 return w return np.array(v, float) def default(data, dflt): """Helper function for setting default values.""" if data is None: return None elif isinstance(data, (list, tuple)): newdata = [] allnone = True for x in data: if x is None: newdata.append(dflt) else: newdata.append(x) allnone = False if allnone: return None return newdata else: return data