def create_table(
row, # AtomsRow
header, # List[str]
keys, # List[str]
key_descriptions, # Dict[str, Tuple[str, str, str]]
digits=3 # int
): # -> Dict[str, Any]
"""Create table-dict from row."""
table = []
for key in keys:
if key == 'age':
age = float_to_time_string(now() - row.ctime, True)
table.append(('Age', age))
continue
value = row.get(key)
if value is not None:
if isinstance(value, float):
value = '{:.{}f}'.format(value, digits)
elif not isinstance(value, str):
value = str(value)
desc, unit = key_descriptions.get(key, ['', key, ''])[1:]
if unit:
value += ' ' + unit
table.append((desc, value))
return {'type': 'table', 'header': header, 'rows': table}
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
def set_columns(self, columns):
self.values = []
for c in columns:
if c == 'age':
value = float_to_time_string(now() - self.dct.ctime)
elif c == 'pbc':
value = ''.join('FT'[int(p)] for p in self.dct.pbc)
else:
value = getattr(self.dct, c, None)
self.values.append(value)
def set_columns(self, columns):
self.values = []
for c in columns:
if c == 'age':
value = float_to_time_string(now() - self.dct.ctime)
elif c == 'pbc':
value = ''.join('FT'[p] for p in self.dct.pbc)
else:
value = getattr(self.dct, c, None)
self.values.append(value)
def age(self, d):
return float_to_time_string(now() - d.ctime)
def age(self, d):
return float_to_time_string(now() - d.ctime)
def __init__(self, dct, subscript=None):
self.dct = dct
self.cell = [['{0:.3f}'.format(a) for a in axis] for axis in dct.cell]
forces = dict2forces(dct)
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[dct.numbers[n]]
self.forces.append((n, symbol) + f)
elif n == 5:
self.forces.append((' ...', '',
' ...',
' ...',
' ...'))
self.stress = dct.get('stress')
if self.stress is not None:
self.stress = ', '.join('{0:.3f}'.format(s) for s in self.stress)
if 'masses' in dct:
mass = dct.masses.sum()
else:
mass = atomic_masses[dct.numbers].sum()
formula = hill(dct.numbers)
if subscript:
formula = subscript.sub(r'<sub>\1</sub>', formula)
table = [
('id', dct.id),
('age', float_to_time_string(now() - dct.ctime, True)),
('formula', formula),
('user', dct.user),
('calculator', dct.get('calculator')),
('energy [eV]', dct.get('energy')),
('fmax [eV/Ang]', fmax),
('charge [|e|]', dct.get('charge')),
('mass [au]', mass),
('unique id', dct.unique_id),
('volume [Ang^3]', abs(np.linalg.det(dct.cell)))]
self.table = [(name, value) for name, value in table
if value is not None]
if 'key_value_pairs' in dct:
self.key_value_pairs = sorted(dct.key_value_pairs.items())
else:
self.key_value_pairs = None
if 'keywords' in dct:
self.keywords = ', '.join(sorted(dct.keywords))
else:
self.keywords = None
self.dipole = dct.get('dipole')
if self.dipole is not None:
self.dipole = ', '.join('{0:.3f}'.format(d) for d in self.dipole)
self.data = dct.get('data')
if self.data:
self.data = ', '.join(self.data.keys())
self.constraints = dct.get('constraints')
if self.constraints:
self.constraints = ', '.join(d['name'] for d in self.constraints)
def age(self, d):
return float_to_time_string((time() - T0) / YEAR - d.timestamp)
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 __init__(self, dct, subscript=None):
self.dct = dct
self.cell = [['{0:.3f}'.format(a) for a in axis] for axis in dct.cell]
forces = dict2forces(dct)
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[dct.numbers[n]]
self.forces.append((n, symbol) + f)
elif n == 5:
self.forces.append(
(' ...', '', ' ...', ' ...', ' ...'))
self.stress = dct.get('stress')
if self.stress is not None:
self.stress = ', '.join('{0:.3f}'.format(s) for s in self.stress)
if 'masses' in dct:
mass = dct.masses.sum()
else:
mass = atomic_masses[dct.numbers].sum()
formula = hill(dct.numbers)
if subscript:
formula = subscript.sub(r'<sub>\1</sub>', formula)
table = [('id', dct.id),
('age', float_to_time_string(now() - dct.ctime, True)),
('formula', formula), ('user', dct.user),
('calculator', dct.get('calculator')),
('energy [eV]', dct.get('energy')), ('fmax [eV/Ang]', fmax),
('charge [|e|]', dct.get('charge')), ('mass [au]', mass),
('unique id', dct.unique_id),
('volume [Ang^3]', abs(np.linalg.det(dct.cell)))]
self.table = [(name, value) for name, value in table
if value is not None]
if 'key_value_pairs' in dct:
self.key_value_pairs = sorted(dct.key_value_pairs.items())
else:
self.key_value_pairs = None
if 'keywords' in dct:
self.keywords = ', '.join(sorted(dct.keywords))
else:
self.keywords = None
self.dipole = dct.get('dipole')
if self.dipole is not None:
self.dipole = ', '.join('{0:.3f}'.format(d) for d in self.dipole)
self.data = dct.get('data')
if self.data:
self.data = ', '.join(self.data.keys())
self.constraints = dct.get('constraints')
if self.constraints:
self.constraints = ', '.join(d['name'] for d in self.constraints)
def __init__(self, row, subscript=None):
self.row = row
self.cell = [["{0:.3f}".format(a) for a in axis] for axis in row.cell]
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()
formula = hill(row.numbers)
if subscript:
formula = subscript.sub(r"<sub>\1</sub>", formula)
table = [
("id", "", row.id),
("age", "", float_to_time_string(now() - row.ctime, True)),
("formula", "", formula),
("user", "", row.user),
("calculator", "", row.get("calculator")),
("energy", "eV", row.get("energy")),
("fmax", "eV/Ang", fmax),
("charge", "|e|", row.get("charge")),
("mass", "au", mass),
("magnetic moment", "au", row.get("magmom")),
("unique id", "", row.unique_id),
("volume", "Ang^3", row.get("volume")),
]
self.table = [(name, unit, value) for name, unit, value in table if value is not None]
self.key_value_pairs = sorted(row.key_value_pairs.items()) or None
self.dipole = row.get("dipole")
if self.dipole is not None:
self.dipole = ", ".join("{0:.3f}".format(d) for d in self.dipole)
self.plots = []
self.data = row.get("data")
if self.data:
plots = []
for name, value in self.data.items():
if isinstance(value, dict) and "xlabel" in value:
plots.append((value.get("number"), name))
self.plots = [name for number, name in sorted(plots)]
self.data = ", ".join(self.data.keys())
self.constraints = row.get("constraints")
if self.constraints:
self.constraints = ", ".join(d["name"] for d in self.constraints)
