Source code for ase.db.row

from random import randint
from typing import Dict, Tuple, Any

import numpy as np

from ase import Atoms
from ase.constraints import dict2constraint
from ase.calculators.calculator import (get_calculator_class, all_properties,
from ase.calculators.singlepoint import SinglePointCalculator
from import chemical_symbols, atomic_masses
from ase.formula import Formula
from ase.geometry import cell_to_cellpar
from import decode

class FancyDict(dict):
    """Dictionary with keys available as attributes also."""
    def __getattr__(self, key):
        if key not in self:
            return dict.__getattribute__(self, key)
        value = self[key]
        if isinstance(value, dict):
            return FancyDict(value)
        return value

    def __dir__(self):
        return self.keys()  # for tab-completion

def atoms2dict(atoms):
    dct = {
        'numbers': atoms.numbers,
        'positions': atoms.positions,
        'unique_id': '%x' % randint(16**31, 16**32 - 1)}
    if atoms.pbc.any():
        dct['pbc'] = atoms.pbc
    if atoms.cell.any():
        dct['cell'] = atoms.cell
    if atoms.has('initial_magmoms'):
        dct['initial_magmoms'] = atoms.get_initial_magnetic_moments()
    if atoms.has('initial_charges'):
        dct['initial_charges'] = atoms.get_initial_charges()
    if atoms.has('masses'):
        dct['masses'] = atoms.get_masses()
    if atoms.has('tags'):
        dct['tags'] = atoms.get_tags()
    if atoms.has('momenta'):
        dct['momenta'] = atoms.get_momenta()
    if atoms.constraints:
        dct['constraints'] = [c.todict() for c in atoms.constraints]
    if atoms.calc is not None:
        dct['calculator'] =
        dct['calculator_parameters'] = atoms.calc.todict()
        if len(atoms.calc.check_state(atoms)) == 0:
            for prop in all_properties:
                    x = atoms.calc.get_property(prop, atoms, False)
                except PropertyNotImplementedError:
                    if x is not None:
                        dct[prop] = x
    return dct

[docs]class AtomsRow: def __init__(self, dct): if isinstance(dct, dict): dct = dct.copy() if 'calculator_parameters' in dct: # Earlier version of ASE would encode the calculator # parameter dict again and again and again ... while isinstance(dct['calculator_parameters'], str): dct['calculator_parameters'] = decode( dct['calculator_parameters']) else: dct = atoms2dict(dct) assert 'numbers' in dct self._constraints = dct.pop('constraints', []) self._constrained_forces = None self._data = dct.pop('data', {}) kvp = dct.pop('key_value_pairs', {}) self._keys = list(kvp.keys()) self.__dict__.update(kvp) self.__dict__.update(dct) if 'cell' not in dct: self.cell = np.zeros((3, 3)) if 'pbc' not in dct: self.pbc = np.zeros(3, bool) def __contains__(self, key): return key in self.__dict__ def __iter__(self): return (key for key in self.__dict__ if key[0] != '_')
[docs] def get(self, key, default=None): """Return value of key if present or default if not.""" return getattr(self, key, default)
@property def key_value_pairs(self): """Return dict of key-value pairs.""" return dict((key, self.get(key)) for key in self._keys)
[docs] def count_atoms(self): """Count atoms. Return dict mapping chemical symbol strings to number of atoms. """ count = {} for symbol in self.symbols: count[symbol] = count.get(symbol, 0) + 1 return count
def __getitem__(self, key): return getattr(self, key) def __setitem__(self, key, value): setattr(self, key, value) def __str__(self): return '<AtomsRow: formula={0}, keys={1}>'.format( self.formula, ','.join(self._keys)) @property def constraints(self): """List of constraints.""" if not isinstance(self._constraints, list): # Lazy decoding: cs = decode(self._constraints) self._constraints = [] for c in cs: # Convert to new format: name = c.pop('__name__', None) if name: c = {'name': name, 'kwargs': c} if c['name'].startswith('ase'): c['name'] = c['name'].rsplit('.', 1)[1] self._constraints.append(c) return [dict2constraint(d) for d in self._constraints] @property def data(self): """Data dict.""" if isinstance(self._data, str): self._data = decode(self._data) # lazy decoding elif isinstance(self._data, bytes): from ase.db.core import bytes_to_object self._data = bytes_to_object(self._data) # lazy decoding return FancyDict(self._data) @property def natoms(self): """Number of atoms.""" return len(self.numbers) @property def formula(self): """Chemical formula string.""" return Formula('', _tree=[(self.symbols, 1)]).format('metal') @property def symbols(self): """List of chemical symbols.""" return [chemical_symbols[Z] for Z in self.numbers] @property def fmax(self): """Maximum atomic force.""" forces = self.constrained_forces return (forces**2).sum(1).max()**0.5 @property def constrained_forces(self): """Forces after applying constraints.""" if self._constrained_forces is not None: return self._constrained_forces forces = self.forces constraints = self.constraints if constraints: forces = forces.copy() atoms = self.toatoms() for constraint in constraints: constraint.adjust_forces(atoms, forces) self._constrained_forces = forces return forces @property def smax(self): """Maximum stress tensor component.""" return (self.stress**2).max()**0.5 @property def mass(self): """Total mass.""" if 'masses' in self: return self.masses.sum() return atomic_masses[self.numbers].sum() @property def volume(self): """Volume of unit cell.""" if self.cell is None: return None vol = abs(np.linalg.det(self.cell)) if vol == 0.0: raise AttributeError return vol @property def charge(self): """Total charge.""" charges = self.get('inital_charges') if charges is None: return 0.0 return charges.sum()
[docs] def toatoms(self, attach_calculator=False, add_additional_information=False): """Create Atoms object.""" atoms = Atoms(self.numbers, self.positions, cell=self.cell, pbc=self.pbc, magmoms=self.get('initial_magmoms'), charges=self.get('initial_charges'), tags=self.get('tags'), masses=self.get('masses'), momenta=self.get('momenta'), constraint=self.constraints) if attach_calculator: params = self.get('calculator_parameters', {}) atoms.calc = get_calculator_class(self.calculator)(**params) else: results = {} for prop in all_properties: if prop in self: results[prop] = self[prop] if results: atoms.calc = SinglePointCalculator(atoms, **results) = self.get('calculator', 'unknown') if add_additional_information: = {}['unique_id'] = self.unique_id if self._keys:['key_value_pairs'] = self.key_value_pairs data = self.get('data') if data:['data'] = data return atoms
def row2dct(row, key_descriptions: Dict[str, Tuple[str, str, str]] = {} ) -> Dict[str, Any]: """Convert row to dict of things for printing or a web-page.""" from ase.db.core import float_to_time_string, now dct = {} atoms = Atoms(cell=row.cell, pbc=row.pbc) dct['size'] = kptdensity2monkhorstpack(atoms, kptdensity=1.8, even=False) dct['cell'] = [['{:.3f}'.format(a) for a in axis] for axis in row.cell] par = ['{:.3f}'.format(x) for x in cell_to_cellpar(row.cell)] dct['lengths'] = par[:3] dct['angles'] = par[3:] stress = row.get('stress') if stress is not None: dct['stress'] = ', '.join('{0:.3f}'.format(s) for s in stress) dct['formula'] = Formula(row.formula).format('abc') dipole = row.get('dipole') if dipole is not None: dct['dipole'] = ', '.join('{0:.3f}'.format(d) for d in dipole) data = row.get('data') if data: dct['data'] = ', '.join(data.keys()) constraints = row.get('constraints') if constraints: dct['constraints'] = ', '.join(c.__class__.__name__ for c in constraints) keys = ({'id', 'energy', 'fmax', 'smax', 'mass', 'age'} | set(key_descriptions) | set(row.key_value_pairs)) dct['table'] = [] for key in keys: if key == 'age': age = float_to_time_string(now() - row.ctime, True) dct['table'].append(('ctime', 'Age', age)) continue value = row.get(key) if value is not None: if isinstance(value, float): value = '{:.3f}'.format(value) elif not isinstance(value, str): value = str(value) desc, unit = key_descriptions.get(key, ['', '', ''])[1:] if unit: value += ' ' + unit dct['table'].append((key, desc, value)) return dct