def __init__(self, row, meta={}, subscript=None, prefix=''):
self.row = row
self.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)]
self.lengths = par[:3]
self.angles = par[3:]
self.stress = row.get('stress')
if self.stress is not None:
self.stress = ', '.join('{0:.3f}'.format(s) for s in self.stress)
self.formula = formula_metal(row.numbers)
if subscript:
self.formula = subscript.sub(r'<sub>\1</sub>', self.formula)
kd = meta.get('key_descriptions', {})
create_layout = meta.get('layout') or default_layout
self.layout = create_layout(row, kd, prefix)
self.dipole = row.get('dipole')
if self.dipole is not None:
self.dipole = ', '.join('{0:.3f}'.format(d) for d in self.dipole)
self.data = row.get('data')
if self.data:
self.data = ', '.join(self.data.keys())
self.constraints = row.get('constraints')
if self.constraints:
self.constraints = ', '.join(c.__class__.__name__
for c in self.constraints)
def get_reduced_chemical_formula(atoms):
numbers = atoms.numbers
unique_numbers, counts = np.unique(numbers, return_counts=True)
denominator = reduce(gcd, counts)
reduced_numbers = []
for i, atomic_number in enumerate(unique_numbers):
reduced_count = int(counts[i] / denominator)
reduced_numbers += [atomic_number] * reduced_count
return formula_metal(reduced_numbers)
def get_chemical_formula(self, mode='hill', empirical=False):
"""Get chemical formula.
See documentation of ase.atoms.Atoms.get_chemical_formula()."""
if mode in ('reduce', 'all') and empirical:
warnings.warn("Empirical chemical formula not available "
"for mode '{}'".format(mode))
if len(self) == 0:
return ''
numbers = self.numbers
if mode == 'reduce':
n = len(numbers)
changes = np.concatenate(
([0], np.arange(1, n)[numbers[1:] != numbers[:-1]]))
symbols = [chemical_symbols[e] for e in numbers[changes]]
counts = np.append(changes[1:], n) - changes
tokens = []
for s, c in zip(symbols, counts):
tokens.append(s)
if c > 1:
tokens.append(str(c))
formula = ''.join(tokens)
elif mode == 'hill':
formula = formula_hill(numbers, empirical=empirical)
elif mode == 'all':
formula = ''.join([chemical_symbols[n] for n in numbers])
elif mode == 'metal':
formula = formula_metal(numbers, empirical=empirical)
else:
raise ValueError("Use mode = 'all', 'reduce', 'hill' or 'metal'.")
return formula
def formula(self):
"""Chemical formula string."""
return formula_metal(self.numbers)
def _formula(self):
return formula_metal(self.numbers)
def __init__(self, row, meta={}, subscript=None, prefix='', tmpdir='.'):
self.row = row
self.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)]
self.lengths = par[:3]
self.angles = par[3:]
forces = row.get('constrained_forces')
if forces is None:
fmax = None
self.forces = None
else:
fmax = (forces**2).sum(1).max()**0.5
N = len(forces)
self.forces = []
for n, f in enumerate(forces):
if n < 5 or n >= N - 5:
f = tuple('{0:10.3f}'.format(x) for x in f)
symbol = chemical_symbols[row.numbers[n]]
self.forces.append((n, symbol) + f)
elif n == 5:
self.forces.append(
(' ...', '', ' ...', ' ...', ' ...'))
self.stress = row.get('stress')
if self.stress is not None:
self.stress = ', '.join('{0:.3f}'.format(s) for s in self.stress)
if 'masses' in row:
mass = row.masses.sum()
else:
mass = atomic_masses[row.numbers].sum()
self.formula = formula_metal(row.numbers)
if subscript:
self.formula = subscript.sub(r'<sub>\1</sub>', self.formula)
age = float_to_time_string(now() - row.ctime, True)
table = dict(
(key, value) for key, value in
[('id', row.id), ('age', age), ('formula',
self.formula), ('user', row.user),
('calculator',
row.get('calculator')), (
'energy',
row.get('energy')), ('fmax',
fmax), ('charge', row.get('charge')),
('mass',
mass), ('magmom',
row.get('magmom')), (
'unique id',
row.unique_id), ('volume', row.get('volume'))]
if value is not None)
table.update(row.key_value_pairs)
for key, value in table.items():
if isinstance(value, float):
table[key] = '{:.3f}'.format(value)
kd = meta.get('key_descriptions', {})
misc = set(table.keys())
self.layout = []
for headline, columns in meta['layout']:
empty = True
newcolumns = []
for column in columns:
newcolumn = []
for block in column:
if block is None:
pass
elif isinstance(block, tuple):
title, keys = block
rows = []
for key in keys:
value = table.get(key, None)
if value is not None:
if key in misc:
misc.remove(key)
desc, unit = kd.get(key, [0, key, ''])[1:]
rows.append((desc, value, unit))
if rows:
block = (title, rows)
else:
continue
elif any(block.endswith(ext) for ext in ['.png', '.csv']):
name = op.join(tmpdir, prefix + block)
if not op.isfile(name):
self.create_figures(row, prefix, tmpdir,
meta['functions'])
if op.getsize(name) == 0:
# Skip empty files:
block = None
elif block.endswith('.csv'):
block = read_csv_table(name)
else:
assert block in ['ATOMS', 'CELL', 'FORCES'], block
newcolumn.append(block)
if block is not None:
empty = False
newcolumns.append(newcolumn)
if not empty:
self.layout.append((headline, newcolumns))
if misc:
rows = []
for key in sorted(misc):
value = table[key]
desc, unit = kd.get(key, [0, key, ''])[1:]
rows.append((desc, value, unit))
self.layout.append(('Miscellaneous', [[('Items', rows)]]))
self.dipole = row.get('dipole')
if self.dipole is not None:
self.dipole = ', '.join('{0:.3f}'.format(d) for d in self.dipole)
self.data = row.get('data')
if self.data:
self.data = ', '.join(self.data.keys())
self.constraints = row.get('constraints')
if self.constraints:
self.constraints = ', '.join(d['name'] for d in self.constraints)
def get_reduced_chemical_formula(atoms):
numbers = atoms.numbers
reduced_numbers, den = get_reduced_numbers(numbers)
return formula_metal(reduced_numbers)
def formula(self):
"""Chemical formula string."""
return formula_metal(self.numbers)
